Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold86
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1697160
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 169504 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:1403 original size:24 final size:24
Alignment explanation
Indices: 1356--1403 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1346 TTATTCTGCA
* *
1356 CATGTCGGTTTCAGGAGCAATATT
1 CATGTCGATTTCAGGAACAATATT
*
1380 CATGTCGATTTCAGGAACAGTATT
1 CATGTCGATTTCAGGAACAATATT
1404 TATATAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (24 bp):
CATGTCGATTTCAGGAACAATATT
Found at i:1586 original size:2 final size:2
Alignment explanation
Indices: 1579--1616 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1569 ACTGGCAATA
1579 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1617 CACAGCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2375 original size:17 final size:17
Alignment explanation
Indices: 2353--2387 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2343 GCTATGTTGC
2353 AACCACTATTGAAATAA
1 AACCACTATTGAAATAA
2370 AACCACTATTGAAATAA
1 AACCACTATTGAAATAA
2387 A
1 A
2388 TTATTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (17 bp):
AACCACTATTGAAATAA
Found at i:7886 original size:14 final size:14
Alignment explanation
Indices: 7864--7895 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
7854 TTCGAATCTC
7864 GAATTTCGTATTTT
1 GAATTTCGTATTTT
7878 GAATTTCGTATTTT
1 GAATTTCGTATTTT
7892 GAAT
1 GAAT
7896 CTCGAATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (14 bp):
GAATTTCGTATTTT
Found at i:10155 original size:179 final size:179
Alignment explanation
Indices: 9715--10496 Score: 1193
Period size: 179 Copynumber: 4.4 Consensus size: 179
9705 GACATAATAA
* *
9715 ACACGACCAGTAAGAGGCTTAGCTAGCCTGGCG--AA----A-ATTTCCAATATTACAGTTAAAA
1 ACACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAA
** * * *
9773 TGGGATAGCTTTTAAGGGGCTGGCTAAAACCCTGTATCCCATATTTGGGCCTTCATATTTAGTGG
66 TGGGATTTCTTTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGG
* *
9838 GGATGGGGCCCCATGACAGCCCAGTCAACCCTCAAAAGG-ATTGGGTTA
131 GGATGGGGCCCCAGGACAGCCCAGTCAACCCTCAAAAGGAATTGGGTTT
* *
9886 ACACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACATTTATAG
1 ACACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAA
9951 TGGGATTTCTTTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGG
66 TGGGATTTCTTTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGG
* *
10016 GGATGGGGCCCCGGGACAGCCCAGTCAACCCTCAAAAGGAATTAGGTTT
131 GGATGGGGCCCCAGGACAGCCCAGTCAACCCTCAAAAGGAATTGGGTTT
** * *
10065 ACAAAACAAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAG
1 ACACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAA
10130 TGGGATTTCTTTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGG
66 TGGGATTTCTTTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGG
* *
10195 GGATGGGGCCCCGGGACAGCCAAGTCAACCCTCAAAAGGAATTGGGTTT
131 GGATGGGGCCCCAGGACAGCCCAGTCAACCCTCAAAAGGAATTGGGTTT
* * * * *
10244 ACACGACCAGTAAGAGGCTAAGCTAGCCTGACAAAAAATGCAACATTTCCAATATTACAGTTATA
1 ACACGACCAGTAAGAGGCTTAGCTAGCCTGGC-GAAAATGCGACATTTCCAATAATACAGTTATA
* *
10309 ATGGGATATCATTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTG
65 ATGGGATTTCTTTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTG
** * * * *
10374 AAGATGGCGCTCCATGACAGCCCAGTCGACCCTCAAAAGGAATTGGGTTT
130 GGGATGGGGCCCCAGGACAGCCCAGTCAACCCTCAAAAGGAATTGGGTTT
*
10424 ACACGACCAGTAAGAGGCTTAGCTAGCCTGGTGAAAATGCGACATTTCCAATAATACAGTTATAA
1 ACACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAA
*
10489 TAGGATTT
66 TGGGATTT
10497 TGAATAGCGG
Statistics
Matches: 556, Mismatches: 46, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
171 33 0.06
173 2 0.00
177 1 0.00
178 115 0.21
179 243 0.44
180 162 0.29
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (179 bp):
ACACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAA
TGGGATTTCTTTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGG
GGATGGGGCCCCAGGACAGCCCAGTCAACCCTCAAAAGGAATTGGGTTT
Found at i:10425 original size:359 final size:357
Alignment explanation
Indices: 9723--10496 Score: 1175
Period size: 359 Copynumber: 2.2 Consensus size: 357
9713 AAACACGACC
* * **
9723 AGTAAGAGGCTTAGCTAGCCTGGCG--AA----A-ATTTCCAATATTACAGTTAAAATGGGATAG
1 AGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAATGGGATTT
*
9781 CTTTTAAGGGGCTGGCTAAAACCCTGTATCCCATATTTGGGCCTTCATATTTAGTGGGGATGGGG
66 CTTTCAAGGGGCTGGCTAAAACCCTGTATCCCATATTTGGGCCTTCATATTTAGTGGGGATGGGG
* * *
9846 CCCCATGACAGCCCAGTCAACCCTCAAAAGGATTGGGTTAACACGACCAGTAAGAGGCTTAGCTA
131 CCCCAGGACAGCCAAGTCAACCCTCAAAAGGATTGGGTTAACACGACCAGTAAGAGGCTAAGCTA
* * * * * * *
9911 GCCTGGCGAAAATGCGACATTTCCAATAATACATTTATAGTGGGATTTCTTTCAAGGGGCTGGCT
196 GCCTGACAAAAATGCAACATTTCCAATAATACAGTTATAATGGGATATCATTCAAGGGGCTGGCT
** * *
9976 AACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGGGGATGGGGCCCCGGGACAGCCCAGT
261 AACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGAAGATGGCGCCCCAGGACAGCCCAGT
10041 CAACCCTCAAAAGGAATTAGGTTTACAAAACA
326 CAACCCTCAAAAGGAATTAGGTTTACAAAACA
*
10073 AGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAGTGGGATTT
1 AGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAATGGGATTT
* *
10138 CTTTCAAGGGGCTGGCTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGGGGATGGGG
66 CTTTCAAGGGGCTGGCTAAAACCCTGTATCCCATATTTGGGCCTTCATATTTAGTGGGGATGGGG
* *
10203 CCCCGGGACAGCCAAGTCAACCCTCAAAAGGAATTGGGTTTACACGACCAGTAAGAGGCTAAGCT
131 CCCCAGGACAGCCAAGTCAACCCTCAAAAGG-ATTGGGTTAACACGACCAGTAAGAGGCTAAGCT
*
10268 AGCCTGACAAAAAATGCAACATTTCCAATATTACAGTTATAATGGGATATCATTCAAGGGGCTGG
195 AGCCTGAC-AAAAATGCAACATTTCCAATAATACAGTTATAATGGGATATCATTCAAGGGGCTGG
* *
10333 CTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGAAGATGGCGCTCCATGACAGCCCA
259 CTAACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGAAGATGGCGCCCCAGGACAGCCCA
* * ** *
10398 GTCGACCCTCAAAAGGAATTGGGTTTACACGACC
324 GTCAACCCTCAAAAGGAATTAGGTTTACAAAACA
* *
10432 AGTAAGAGGCTTAGCTAGCCTGGTGAAAATGCGACATTTCCAATAATACAGTTATAATAGGATTT
1 AGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAATGGGATTT
10497 TGAATAGCGG
Statistics
Matches: 380, Mismatches: 35, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
350 25 0.07
352 2 0.01
356 1 0.00
357 115 0.30
358 38 0.10
359 199 0.52
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (357 bp):
AGTAAGAGGCTTAGCTAGCCTGGCGAAAATGCGACATTTCCAATAATACAGTTATAATGGGATTT
CTTTCAAGGGGCTGGCTAAAACCCTGTATCCCATATTTGGGCCTTCATATTTAGTGGGGATGGGG
CCCCAGGACAGCCAAGTCAACCCTCAAAAGGATTGGGTTAACACGACCAGTAAGAGGCTAAGCTA
GCCTGACAAAAATGCAACATTTCCAATAATACAGTTATAATGGGATATCATTCAAGGGGCTGGCT
AACACCCTGTATCCCATATTTGGGCCTTCATATTTGGTGAAGATGGCGCCCCAGGACAGCCCAGT
CAACCCTCAAAAGGAATTAGGTTTACAAAACA
Found at i:13995 original size:170 final size:168
Alignment explanation
Indices: 13814--14320 Score: 570
Period size: 168 Copynumber: 3.0 Consensus size: 168
13804 AATACATGAA
* *
13814 GATGCTTCCACACAAATTTCAGCTTTCCTGGCTGATTATTTCTGAGAAGATTTTTAAAGATTTAC
1 GATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTGTTT-TGAGAAGATTTTTAAAGATTTAC
*
13879 TATATATATTCCAATGTAAAACTTCAACCTCCCCCTCCCCCATTGTTGCCCCACCTTATCCCCGG
65 TATATATATTCCAATGTAAAACTTCAACC-CCCCCTCCCCCATTGTTGCCCCACCTTACCCCCGG
13944 GGACCATGATTTTAACAAACTTGAATCTACACTATCTGAG
129 GGACCATGATTTTAACAAACTTGAATCTACACTATCTGAG
* * ** * * *
13984 GATGCTTCCACACAAGTTTCAGCTTTTCTGACCAAATGGTTTTTGAGAAGAAAATTATAAAAGAT
1 GATGCTTCCACACAAGTTTCAGCTTTCCTG-GCTGATTG-TTTTGAGAAG---ATTTTTAAAGAT
* * * * *
14049 ATA-TACTATATATTCCAATGTAAAAGTAT-GACCCCCCCT------TT-TATGCCCCCCCCCTA
61 TTACTA-TATATATTCCAATGTAAAACT-TCAACCCCCCCTCCCCCATTGT-TG-CCCCACCTTA
* *
14105 CCCCCGGGGATCATGATTTTAACAAACTTGAATCTACACTACCTGAG
122 CCCCCGGGGACCATGATTTTAACAAACTTGAATCTACACTATCTGAG
14152 GATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTGGTTGTTGAGAAGAGGATTTTTAAAGAT
1 GATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATT-GTT-TTGAG-A-A-GATTTTTAAAGAT
* * * * *
14217 TTACTCTATATATT-CTATATAAAACTTCAA-CCCCCC-CCCCCATTGTTACCCCACCTAACCCC
61 TTACTATATATATTCCAATGTAAAACTTCAACCCCCCCTCCCCCATTGTTGCCCCACCTTACCCC
* *
14279 CGGGGACAATGATTTAAACAAACTTGAATCTACACTATCTGA
126 CGGGGACCATGATTTTAACAAACTTGAATCTACACTATCTGA
14321 AAATGCTGGT
Statistics
Matches: 276, Mismatches: 38, Indels: 46
0.77 0.11 0.13
Matches are distributed among these distances:
166 8 0.03
167 19 0.07
168 107 0.39
169 2 0.01
170 78 0.28
171 14 0.05
172 4 0.01
173 8 0.03
174 35 0.13
175 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (168 bp):
GATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTGTTTTGAGAAGATTTTTAAAGATTTACT
ATATATATTCCAATGTAAAACTTCAACCCCCCCTCCCCCATTGTTGCCCCACCTTACCCCCGGGG
ACCATGATTTTAACAAACTTGAATCTACACTATCTGAG
Found at i:14131 original size:168 final size:165
Alignment explanation
Indices: 13618--14315 Score: 540
Period size: 168 Copynumber: 4.1 Consensus size: 165
13608 TACATTATCA
13618 TTAACAAACTTGAATCTACACTACATGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGTCCAAA
1 TTAACAAACTTGAATCTACACTACATGAGGATGCTTCCACACAAGTTTCAGCTTTTCTG-CCAAA
* * * ** * ** *
13683 TGGATTTTGAGAAGAAAATTTTAAAAGATATACACTATATATTTTCTTTGTAAAAGTACGATACT
65 TGGTTTTTGAGAAGAAAATTTTAAAAGATATATACTATATA-TTCCAATGTAAAAGTATGACCCC
* * * * * * * *
13748 CCATTGTGGCCCCTCCATTCCTCTGGGGGTCATTG-TT
129 CCCTTTTTGCCCCACCATACCCCCGGGGATCA-TGATT
* * * * * * * * **
13785 TTCAC-AACTTTCAATTTACAATACATGAAGATGCTTCCACACAAATTTCAGCTTTCCTGGCTGA
1 TTAACAAAC-TTGAATCTACACTACATGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGCCAAA
** * * * * *
13849 TTATTTCTGAGAAG---ATTTTTAAAGATTTACTA-TATATATTCCAATGTAAAACT-TCAACCT
65 TGGTTTTTGAGAAGAAAATTTTAAAAGATATA-TACTATATATTCCAATGTAAAAGTAT-GACC-
* * *
13909 CCCCCTCCCCCATTGTTGCCCCACCTTATCCCCGGGGACCATGATT
127 CCCCCT------TT-TTGCCCCACCATACCCCCGGGGATCATGATT
13955 TTAACAAACTTGAATCTACACTATC-TGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGACCAA
1 TTAACAAACTTGAATCTACACTA-CATGAGGATGCTTCCACACAAGTTTCAGCTTTTCTG-CCAA
*
14019 ATGGTTTTTGAGAAGAAAATTATAAAAGATATATACTATATATTCCAATGTAAAAGTATGACCCC
64 ATGGTTTTTGAGAAGAAAATTTTAAAAGATATATACTATATATTCCAATGTAAAAGTATGACCCC
* *
14084 CCCTTTTATGCCCCCCCCCTACCCCCGGGGATCATGATT
129 CCCTTTT-TG-CCCCACCATACCCCCGGGGATCATGATT
* * ** *
14123 TTAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGAT
1 TTAACAAACTTGAATCTACACTACATGAGGATGCTTCCACACAAGTTTCAGCTTTTCT-GCCAAA
* ** * * * * * *
14188 TGGTTGTTGAGAAGAGGATTTTTAAAGATTTACT-CTATATATT-CTATATAAAACT-TCAACCC
65 TGGTTTTTGAGAAGAAAATTTTAAAAGATATA-TACTATATATTCCAATGTAAAAGTAT-GA---
* *
14250 CCCCCCCCATTGTTACCCCACC-TAACCCCCGGGGA-CAATGATT
125 -CCCCCCC-TTTTTGCCCCACCAT-ACCCCCGGGGATC-ATGATT
*
14293 TAAACAAACTTGAATCTACACTA
1 TTAACAAACTTGAATCTACACTA
14316 TCTGAAAATG
Statistics
Matches: 421, Mismatches: 77, Indels: 63
0.75 0.14 0.11
Matches are distributed among these distances:
162 12 0.03
163 23 0.05
164 1 0.00
166 17 0.04
167 63 0.15
168 116 0.28
169 7 0.02
170 110 0.26
171 25 0.06
172 3 0.01
173 8 0.02
174 35 0.08
175 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.32
Consensus pattern (165 bp):
TTAACAAACTTGAATCTACACTACATGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGCCAAAT
GGTTTTTGAGAAGAAAATTTTAAAAGATATATACTATATATTCCAATGTAAAAGTATGACCCCCC
CTTTTTGCCCCACCATACCCCCGGGGATCATGATT
Found at i:14314 original size:338 final size:337
Alignment explanation
Indices: 13620--14320 Score: 925
Period size: 338 Copynumber: 2.1 Consensus size: 337
13610 CATTATCATT
*
13620 AACAAACTTGAATCTACACTA-CATGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGTCCAAAT
1 AACAAACTTGAATCTACACTATC-TGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGACCAAAT
* * ** * *
13684 GGATTTTGAGAAGAAAATTTTAAAAGATATACACTATATATTTTCTTTGTAAAAGTACGATACTC
65 GGATTTTGAGAAGAAAATTATAAAAGATATACACTATATATTTCCAATGTAAAAGTACGACACCC
* * * * * * * * *
13749 CATTGTGGCCCCTCCATTCCTCTGGGGGTCATTGTTTTCACAACTTTCAATTTACAATACATGAA
130 CATTATGCCCCCCCCATACCCCCGGGGATCATTGTTTTAACAACTTTCAATCTACAATACATGAA
13814 GATGCTTCCACACAAATTTCAGCTTTCCTGGCTGATTATTTCTGAGAAGATTTTTAAAGATTTAC
195 GATGCTTCCACACAAATTTCAGCTTTCCTGGCTGATTATTTCTGAGAAGATTTTTAAAGATTTAC
* * * *
13879 TATATATATTCCAATGTAAAACTTCAACCTCCCCCTCCCCCATTGTTGCCCCACCTTATCCCCGG
260 TATATATATTCCAATATAAAACTTCAACCTCCCCCTCCCCCATTGTTACCCCACCTAACCCCCGG
* *
13944 GGACCATGATTTT
325 GGACAATGATTTA
13957 AACAAACTTGAATCTACACTATCTGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGACCAAATG
1 AACAAACTTGAATCTACACTATCTGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGACCAAATG
* * * *
14022 GTTTTTGAGAAGAAAATTATAAAAGATATATACTATATA-TTCCAATGTAAAAGTATGACCCCCC
66 GATTTTGAGAAGAAAATTATAAAAGATATACACTATATATTTCCAATGTAAAAGTACGA-CACCC
* * * * *
14086 CTTTTATGCCCCCCCCCTACCCCCGGGGATCA-TGATTTTAACAAAC-TTGAATCTACACTACCT
130 C-ATTATGCCCCCCCCATACCCCCGGGGATCATTG-TTTTAAC-AACTTTCAATCTACAATACAT
* * *
14149 GAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTGGTTGT-TGAGAAGAGGATTTTTAA
192 GAAGATGCTTCCACACAAATTTCAGCTTTCCTGGCTGATT-ATT-TCTGAG-A-A-GATTTTTAA
* *
14213 AGATTTACTCTATATATT-CTATATAAAACTTCAA-C-CCCCC-CCCCCATTGTTACCCCACCTA
252 AGATTTACTATATATATTCCAATATAAAACTTCAACCTCCCCCTCCCCCATTGTTACCCCACCTA
14274 ACCCCCGGGGACAATGATTTA
317 ACCCCCGGGGACAATGATTTA
14295 AACAAACTTGAATCTACACTATCTGA
1 AACAAACTTGAATCTACACTATCTGA
14321 AAATGCTGGT
Statistics
Matches: 318, Mismatches: 36, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
336 15 0.05
337 103 0.32
338 142 0.45
339 14 0.04
340 3 0.01
341 15 0.05
342 26 0.08
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (337 bp):
AACAAACTTGAATCTACACTATCTGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGACCAAATG
GATTTTGAGAAGAAAATTATAAAAGATATACACTATATATTTCCAATGTAAAAGTACGACACCCC
ATTATGCCCCCCCCATACCCCCGGGGATCATTGTTTTAACAACTTTCAATCTACAATACATGAAG
ATGCTTCCACACAAATTTCAGCTTTCCTGGCTGATTATTTCTGAGAAGATTTTTAAAGATTTACT
ATATATATTCCAATATAAAACTTCAACCTCCCCCTCCCCCATTGTTACCCCACCTAACCCCCGGG
GACAATGATTTA
Found at i:19083 original size:14 final size:14
Alignment explanation
Indices: 19064--19094 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19054 TTAGCTTAGC
19064 TACTAGTAACTGGT
1 TACTAGTAACTGGT
19078 TACTAGTAACTGGT
1 TACTAGTAACTGGT
19092 TAC
1 TAC
19095 GAGAAGTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (14 bp):
TACTAGTAACTGGT
Found at i:19096 original size:93 final size:88
Alignment explanation
Indices: 18897--19145 Score: 313
Period size: 93 Copynumber: 2.8 Consensus size: 88
18887 GGTAAAGTAA
* * * *
18897 GTTACTAGTAAATGGCTACGAGAAGTAAGAAAACCTAGCTTCTAG--AGTGGCTACGAGATTAAA
1 GTTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAAGTGGCTACGAGATGAAA
18960 TAAAAGTGAGCAACTAGTAACTG
66 TAAAAGTGAGCAACTAGTAACTG
* * * * *
18983 GCTATTGGAAACTGGCTACGAGAAGTAAGAAAAGCTAGATACTAGTAAGTGGCTACGAGATGAAA
1 GTTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAAGTGGCTACGAGATGAAA
* *
19048 TCAAAGTTAGCTTAGCTACTAGTAACTG
66 T-AAA---AG-TGAGCAACTAGTAACTG
* *
19076 GTTACTAGTAACTGGTTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGCTACGAGATGAAA
1 GTTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAAGTGGCTACGAGATGAAA
*
19141 GAAAA
66 TAAAA
19146 CTTGGCTACT
Statistics
Matches: 137, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
86 37 0.27
88 18 0.13
89 4 0.03
92 5 0.04
93 73 0.53
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (88 bp):
GTTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAAGTGGCTACGAGATGAAA
TAAAAGTGAGCAACTAGTAACTG
Found at i:19133 original size:37 final size:37
Alignment explanation
Indices: 19078--19159 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
19068 AGTAACTGGT
* *
19078 TACTAGTAACTGGTTACGAGAAGTAAGAAAAGC-TAGC
1 TACTAGTAACTGGCTACGAGAAGAAAGAAAA-CTTAGC
* *
19115 TACTAGTAACTGGCTACGAGATGAAAGAAAACTTGGC
1 TACTAGTAACTGGCTACGAGAAGAAAGAAAACTTAGC
19152 TACTAGTA
1 TACTAGTA
19160 CTAGTAACTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 1 0.03
37 39 0.98
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (37 bp):
TACTAGTAACTGGCTACGAGAAGAAAGAAAACTTAGC
Found at i:28093 original size:15 final size:14
Alignment explanation
Indices: 28065--28135 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 14
28055 GTTATATAAA
*
28065 ATGAAATTGTATAT
1 ATGATATTGTATAT
28079 ATGATATTGTAATATT
1 ATGATATTGT-ATA-T
*
28095 ATGAAATATCGTATTAT
1 ATG--ATATTGTA-TAT
*
28112 ACGATATTGTATAAT
1 ATGATATTGTAT-AT
*
28127 ATAATATTG
1 ATGATATTG
28136 GTTTATAGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
14 10 0.22
15 19 0.42
16 4 0.09
17 4 0.09
18 8 0.18
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (14 bp):
ATGATATTGTATAT
Found at i:29179 original size:22 final size:22
Alignment explanation
Indices: 29151--29201 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
29141 ATCAAAAAAG
29151 GCGAAGGCGAA-AGTGCGAAGAT
1 GCGAAGGC-AAGAGTGCGAAGAT
*
29173 GCGAAGGCAAGAGTGCGAAGTT
1 GCGAAGGCAAGAGTGCGAAGAT
*
29195 GGGAAGG
1 GCGAAGG
29202 AGCGATAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.33, C:0.12, G:0.45, T:0.10
Consensus pattern (22 bp):
GCGAAGGCAAGAGTGCGAAGAT
Found at i:30202 original size:32 final size:32
Alignment explanation
Indices: 30161--30254 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
30151 TTCAGGCAAA
30161 GGGGTCATTTTTCTACGTAGAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCGG
*
30193 GGGGTCATTTTTCTGCGTAGAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCGG
* * *
30225 GGGGTCATTATTCTACGTCGAAAAATGACC
1 GGGGTCATTTTTCTACGTAGAATAATGACC
30255 CCCGGTCATT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (32 bp):
GGGGTCATTTTTCTACGTAGAATAATGACCGG
Found at i:32890 original size:168 final size:169
Alignment explanation
Indices: 32497--32879 Score: 563
Period size: 168 Copynumber: 2.3 Consensus size: 169
32487 ATGACAAATG
* * * *
32497 AATTTCATAATTTTGATAGAGGGCCTCATGGACATCATAATCATGCATTTAG-TCTTTAACAAAT
1 AATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTTAACAAAT
* ** * *
32561 ATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGG
66 ATATATGGGAGTAAAGAAGAAGATTTTCTAAGATTTAATACAGCTTTACTATATGACCATATTGG
* * *
32626 CCCCACCCTAGATCCTGAACCCCTGACCCAGGGGTCATA
131 CCCCACCCTAGAGCCAGAACCCCTGACCCAGGGGCCATA
* * * * *
32665 ATTTTTACAATGTAGGTAGAGGGCTTCATGGACATCATAATTATGCATTTAGTTTTTTAA-AAAT
1 AATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTTAACAAAT
*
32729 ATATATGGTAGTAAAGAAGAAGATTTTCTAAGATTTAATACAGCTTTACTATATGACCATATTGG
66 ATATATGGGAGTAAAGAAGAAGATTTTCTAAGATTTAATACAGCTTTACTATATGACCATATTGG
* *
32794 CCCCATCCTAGAGCCAGAACCCCTGACCCTGGGGCCATA
131 CCCCACCCTAGAGCCAGAACCCCTGACCCAGGGGCCATA
*
32833 AATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAACCATGCA
1 AATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCA
32880 ACTGGTTTTT
Statistics
Matches: 188, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
168 182 0.97
169 6 0.03
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (169 bp):
AATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTTAACAAAT
ATATATGGGAGTAAAGAAGAAGATTTTCTAAGATTTAATACAGCTTTACTATATGACCATATTGG
CCCCACCCTAGAGCCAGAACCCCTGACCCAGGGGCCATA
Found at i:36761 original size:437 final size:437
Alignment explanation
Indices: 36152--37584 Score: 2302
Period size: 438 Copynumber: 3.3 Consensus size: 437
36142 TATAAAGTCA
* * * * *
36152 AGAGCTTTTATGTGACATCAAGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTA
1 AGAGCTTTCATTTGAAATCAAGAAAAAGGGACTGGCCCTTCAAATAAGGGGCTGAGGGGCCTCTA
* * * *
36217 AAGTCTTTTAATGATAACTTTTCACTGTGAAATATTTTGTGATACATTATAGAAGCAACTGTGTT
66 AAGTCTTTTAATGATAACTTTTTACCGTGAAATATTTTGTGATACATTATAGAAGCAATTATGTT
* * *
36282 CATTCTAACGTTATCCACCTACACATGGCAATCATTTACTCCTATGTTACGTAATTAAGGATTTT
131 CATTCTAAAGTTATTCACCTACACATGGCAATCATTTACTCCTATGTTACGTAATTAGGGATTTT
36347 AAGGGGCCAGAAGTCCAAAAATTTGATGCTCAATATCTCAAAATGGAGGAAACTTTTGAAAAGCA
196 AAGGGGCCAGAAGTCCAAAAATTTGATGCTCAATATCTCAAAATGGAGGAAACTTTTGAAAAGCA
*
36412 ATATTGAACAAAAGATGCTCAAAATATTGAGCTTAACAATTTGCAACCATAATTTCTTTGTTATG
261 ATATTGAACAAAAGATGCTCAAAATATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTATG
* * *
36477 CTGTCCCTAAAAGGAGTTACAGGGTCGGTCCCTAAAACGACCCTTTCAAGATATCTCGAGAACGG
326 CAGTCCCTAAAAGGAGTTACAGGGTCGG-CCCTGAAACGACCCTCTCAAGATATCTCGAGAACGG
* * *
36542 TAGAAAATTTGTAAACACTTGTTG-AACAAAATGTGTTTGAATTGATT
390 TACAAAATTTGTAAACACTTGTTGAAAAAAAAAGTGTTTGAATTGATT
36589 AGAGCTTTCATTTGAAATCAAGAAAAAGGGACTGGCCCTTCAAATAAGGGGCTGAGGGAGCCT-T
1 AGAGCTTTCATTTGAAATCAAGAAAAAGGGACTGGCCCTTCAAATAAGGGGCTGAGGG-GCCTCT
*
36653 AAAGTTTTTTAATGATAACTTTTTACCGTGAAATATTTTGTGATACATTATAGAAGCAATTATGT
65 AAAGTCTTTTAATGATAACTTTTTACCGTGAAATATTTTGTGATACATTATAGAAGCAATTATGT
* * * * * *
36718 TCATTCTAATGTCATTCACCTACACATGACAATCATTTACTCCTATATTACATTATTAGGGGA-T
130 TCATTCTAAAGTTATTCACCTACACATGGCAATCATTTACTCCTATGTTACGTAATTA-GGGATT
36782 TTAAGGGGCCAGAAGTCCAAAAATTTGATGCTCAATATCTCAAAATGGAGGAAACTTTTGAAAAG
194 TTAAGGGGCCAGAAGTCCAAAAATTTGATGCTCAATATCTCAAAATGGAGGAAACTTTTGAAAAG
36847 CAATATTGAACAAAAGATGCTCAAAATATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTA
259 CAATATTGAACAAAAGATGCTCAAAATATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTA
*
36912 TGCAGTCCCTAAAAGGAGTTACAGGGTCGGCCCCTGAAACGACCCTCTCAAGATTTCTCGAGAAC
324 TGCAGTCCCTAAAAGGAGTTACAGGGTCGG-CCCTGAAACGACCCTCTCAAGATATCTCGAGAAC
36977 GGTACAAAATTTGTAAACACTTGTTGAAAAAAAAAGTGTTTGAATTGATT
388 GGTACAAAATTTGTAAACACTTGTTGAAAAAAAAAGTGTTTGAATTGATT
* * * * * *
37027 AGATCTTTCATCTGAAATCATGTAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAAGGGG-CACT
1 AGAGCTTTCATTTGAAATCAAGAAAAAGGGACTGGCCCTTCAAATAAGGGGCTG-AGGGGCCTCT
37091 AAAGTCTTTTAATGATAACTTTTTACCGTGAAATATTTTGTGATACATTATAGAAGCAATTATGT
65 AAAGTCTTTTAATGATAACTTTTTACCGTGAAATATTTTGTGATACATTATAGAAGCAATTATGT
* *
37156 TCATTCTAAAGTTATTTACCTATACATGGCAATCATTTACTCCTATGTTACGTAATTAGGGATTT
130 TCATTCTAAAGTTATTCACCTACACATGGCAATCATTTACTCCTATGTTACGTAATTAGGGATTT
* * *
37221 TAAGGGGCCAGAATTCCAAAAATTTGATGCTCAATATTTCAAAATAGAGGACAA-TTTTGAAAAG
195 TAAGGGGCCAGAAGTCCAAAAATTTGATGCTCAATATCTCAAAATGGAGGA-AACTTTTGAAAAG
*
37285 CAATTTTGAACAAAAGATGCTCAAAATATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTA
259 CAATATTGAACAAAAGATGCTCAAAATATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTA
* *
37350 TGCGGTCCCTAAAAGGAGTTACAGGGTCTGGCCCTGAAATGACCCTCTCAAGATATCTCGAGAAC
324 TGCAGTCCCTAAAAGGAGTTACAGGGTC-GGCCCTGAAACGACCCTCTCAAGATATCTCGAGAAC
**
37415 GGTACAAAATTTGTAAACACTTGTTGAAAAAAAAAGTGTTTGAATTGACA
388 GGTACAAAATTTGTAAACACTTGTTGAAAAAAAAAGTGTTTGAATTGATT
* * *
37465 AGAACATTC-TTATGAAATCAAGAAAAAAGGGACTGGCCCTTCAAATAAGGGGCTGAGGGGGCTC
1 AGAGCTTTCATT-TGAAATCAAG-AAAAAGGGACTGGCCCTTCAAATAAGGGGCTGAGGGGCCTC
* * *
37529 TAAAGTATTTAAATGATAACTTTTTACCGTGAAATATTTTGCGATACATTATAGAA
64 TAAAGTCTTTTAATGATAACTTTTTACCGTGAAATATTTTGTGATACATTATAGAA
37585 CAAATTTAAC
Statistics
Matches: 924, Mismatches: 61, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
437 387 0.42
438 444 0.48
439 93 0.10
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (437 bp):
AGAGCTTTCATTTGAAATCAAGAAAAAGGGACTGGCCCTTCAAATAAGGGGCTGAGGGGCCTCTA
AAGTCTTTTAATGATAACTTTTTACCGTGAAATATTTTGTGATACATTATAGAAGCAATTATGTT
CATTCTAAAGTTATTCACCTACACATGGCAATCATTTACTCCTATGTTACGTAATTAGGGATTTT
AAGGGGCCAGAAGTCCAAAAATTTGATGCTCAATATCTCAAAATGGAGGAAACTTTTGAAAAGCA
ATATTGAACAAAAGATGCTCAAAATATTGAGCTTAACAATCTGCAACCATAATTTCTTTGTTATG
CAGTCCCTAAAAGGAGTTACAGGGTCGGCCCTGAAACGACCCTCTCAAGATATCTCGAGAACGGT
ACAAAATTTGTAAACACTTGTTGAAAAAAAAAGTGTTTGAATTGATT
Found at i:39421 original size:180 final size:179
Alignment explanation
Indices: 39132--39623 Score: 813
Period size: 180 Copynumber: 2.7 Consensus size: 179
39122 GACTAAACTC
* * * *
39132 AAAAGCTGGTATTTTTTTTCATAAATATTCAGAAATTAAAATCCTAGCAATATGCACACCTCTGT
1 AAAAGCTGGTA-TTTTTTTCTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGT
* *
39197 TATATGCACAATTGATCTGCAAAAGAACAACTTCCTAACTTGAAAACTGTAGGAGGAGTTATCCG
65 TATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCG
*
39262 TACAATGAGGGTACCCCATAAGTAATATTTCTCCAAAAAATGACTATGTTT
130 TACAATGAGGGTACCCCATAAGCAATATTTCTCC-AAAAATGACTATGTTT
39313 AAAAGCTGGTATTTTTTTCTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGTT
1 AAAAGCTGGTATTTTTTTCTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGTT
*
39378 ATATGTACAATTGATCTGCAAAAGAACAATTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGT
66 ATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGT
* * *
39443 ACAATGAGGGTACCCTATTAGCAATATTTCTCCAAAAATGACTTTGTTT
131 ACAATGAGGGTACCCCATAAGCAATATTTCTCCAAAAATGACTATGTTT
* *
39492 AAAAGCTGGTATTTTTTTTTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGAT
1 AAAAGCTGGTATTTTTTTCTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGTT
* * * *
39557 ATATGTACAATTTATCTGCAAAAGAACAACTTCCTATCTTGAAAACTATACGAGGGGTTATCCGT
66 ATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGT
39622 AC
131 AC
39624 CCTTTTGGCA
Statistics
Matches: 293, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
179 140 0.48
180 142 0.48
181 11 0.04
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (179 bp):
AAAAGCTGGTATTTTTTTCTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGTT
ATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGT
ACAATGAGGGTACCCCATAAGCAATATTTCTCCAAAAATGACTATGTTT
Found at i:39567 original size:179 final size:180
Alignment explanation
Indices: 39132--39623 Score: 815
Period size: 179 Copynumber: 2.7 Consensus size: 180
39122 GACTAAACTC
* * * *
39132 AAAAGCTGGTATTTTTTTTCATAAATATTCAGAAATTAAAATCCTAGCAATATGCACACCTCTGT
1 AAAAGCTGGTATTTTTTTT-TTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGT
* *
39197 TATATGCACAATTGATCTGCAAAAGAACAACTTCCTAACTTGAAAACTGTAGGAGGAGTTATCCG
65 TATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCG
*
39262 TACAATGAGGGTACCCCATAAGTAATATTTCTCCAAAAAATGACTATGTTT
130 TACAATGAGGGTACCCCATAAGCAATATTTCTCCAAAAAATGACTATGTTT
*
39313 AAAAGCTGGTATTTTTTTCTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGTT
1 AAAAGCTGGTATTTTTTTTTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGTT
*
39378 ATATGTACAATTGATCTGCAAAAGAACAATTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGT
66 ATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGT
* * *
39443 ACAATGAGGGTACCCTATTAGCAATATTTCTCC-AAAAATGACTTTGTTT
131 ACAATGAGGGTACCCCATAAGCAATATTTCTCCAAAAAATGACTATGTTT
*
39492 AAAAGCTGGTATTTTTTTTTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGAT
1 AAAAGCTGGTATTTTTTTTTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGTT
* * * *
39557 ATATGTACAATTTATCTGCAAAAGAACAACTTCCTATCTTGAAAACTATACGAGGGGTTATCCGT
66 ATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGT
39622 AC
131 AC
39624 CCTTTTGGCA
Statistics
Matches: 292, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
179 140 0.48
180 134 0.46
181 18 0.06
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (180 bp):
AAAAGCTGGTATTTTTTTTTTAAATAATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGTT
ATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGT
ACAATGAGGGTACCCCATAAGCAATATTTCTCCAAAAAATGACTATGTTT
Found at i:40924 original size:164 final size:163
Alignment explanation
Indices: 40690--41116 Score: 533
Period size: 170 Copynumber: 2.6 Consensus size: 163
40680 AAAGCTGGCA
* * *
40690 TCCGATTGGTACAGAAATATATCCCACAATATGGCATGCCCAAACAAATAGTGTGTTCAAATTTC
1 TCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTC
*
40755 AAGCATCTGCGATAAATAGCTGCTGAGAAATC-TTGA-GGAAAATTTGTTTGAAAATTTTGGCT-
66 AAGCATCTGCGATAAATAG-TGCTGAGAAATCTTTGACGG-AAATTTGTTCGAAAATTTTGGCTA
*
40817 AAAATAAACGAAGT-ACTCATTTA-ACAGGAAGTTGACG
129 AAAATAAAC--AGTCA-TCATTTACA-AAGAAGTTGACG
* * ** * *
40854 TTCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACAAACACTGTG-TAAAATTTT
1 TCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGTGTTAAAA-TTT
40918 CAAGCATCTCATTCTGCGATAAATAGTGGCTGAGAAATCTTTGACGGAAATTTGTTCGAAAATTT
65 CAAG-----CA-TCTGCGATAAATAGT-GCTGAGAAATCTTTGACGGAAATTTGTTCGAAAATTT
*
40983 TGGCTAAAAATAAACAGTCATTATTTACAAAGAAGTTGACG
123 TGGCTAAAAATAAACAGTCATCATTTACAAAGAAGTTGACG
* * * *
41024 TCCAATTGATACAAAAATATATCCAACAATATGGCATGCCAAAACAAATAGTGTGTTTAAATTTC
1 TCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTC
41089 AAGCATCTGCGATAAATAGTTGCTGAGA
66 AAGCATCTGCGATAAATAG-TGCTGAGA
41117 TAAATGCGAC
Statistics
Matches: 227, Mismatches: 21, Indels: 30
0.82 0.08 0.11
Matches are distributed among these distances:
163 4 0.02
164 76 0.33
165 3 0.01
169 3 0.01
170 98 0.43
171 32 0.14
172 11 0.05
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (163 bp):
TCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTC
AAGCATCTGCGATAAATAGTGCTGAGAAATCTTTGACGGAAATTTGTTCGAAAATTTTGGCTAAA
AATAAACAGTCATCATTTACAAAGAAGTTGACG
Found at i:41167 original size:16 final size:16
Alignment explanation
Indices: 41148--41178 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41138 TTACAGGCGG
41148 ACGGACAGACAGACAC
1 ACGGACAGACAGACAC
41164 ACGGACAGACAGACA
1 ACGGACAGACAGACA
41179 GCCACACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.29, G:0.26, T:0.00
Consensus pattern (16 bp):
ACGGACAGACAGACAC
Found at i:41174 original size:20 final size:20
Alignment explanation
Indices: 41145--41185 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41135 TTGTTACAGG
*
41145 CGGACGGACAGACAGACACA
1 CGGACAGACAGACAGACACA
*
41165 CGGACAGACAGACAGCCACA
1 CGGACAGACAGACAGACACA
41185 C
1 C
41186 AAGGGTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.34, G:0.27, T:0.00
Consensus pattern (20 bp):
CGGACAGACAGACAGACACA
Found at i:42427 original size:194 final size:195
Alignment explanation
Indices: 42088--42462 Score: 603
Period size: 194 Copynumber: 1.9 Consensus size: 195
42078 ATATATATAT
*
42088 AGACGACATTCAATTAATAACGATAAATACGCCTCCGGAAGGAAAGTATTCCCGAGAAAAGGGTT
1 AGACGACATTCAATTAATAACGATAAATACGCCTCCGGAAGGAAAGTATTCCCGAGAAAAGGATT
* *
42153 TTCTTTGGGGGAAAAACATCAGAAAATGGGGTTTAGAATCTTTTTGGGGAACATTCAAAAGGTGA
66 TTCTTTGGGGGAAAAACATCAGAAAATGGGGTTTAGAATCTCTTGGGGGAACATTCAAAAGGTGA
* * *
42218 AATCAGCAACATCTGAAATACGTTC-AATTAATCTGCACCGCGGTGCAGATAACAGGAGTAAGAG
131 AATCAGAAACATCTGAAATACGCTCAAACTAATCTGCACCGCGGTGCAGATAACAGGAGTAAGAG
* * *
42282 AGACGACATTCAATTAATCACGATAAATACG-CTCCCGTAAGGGAAGTATTCCCGAGAAAAGGAT
1 AGACGACATTCAATTAATAACGATAAATACGCCT-CCGGAAGGAAAGTATTCCCGAGAAAAGGAT
* *
42346 TTTCTTTGGGGGATAAACATCAGAAAATGGGGTTTAGAGTCTCTTGGGGGAACATTCAAAAGGTG
65 TTTCTTTGGGGGAAAAACATCAGAAAATGGGGTTTAGAATCTCTTGGGGGAACATTCAAAAGGTG
*
42411 AAATCA-AAAGCATCTGATATACGCTCAAACTAATCTGCACCGCGGTGCAGAT
130 AAATCAGAAA-CATCTGAAATACGCTCAAACTAATCTGCACCGCGGTGCAGAT
42463 GACAAAAGTG
Statistics
Matches: 166, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
193 4 0.02
194 138 0.83
195 24 0.14
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (195 bp):
AGACGACATTCAATTAATAACGATAAATACGCCTCCGGAAGGAAAGTATTCCCGAGAAAAGGATT
TTCTTTGGGGGAAAAACATCAGAAAATGGGGTTTAGAATCTCTTGGGGGAACATTCAAAAGGTGA
AATCAGAAACATCTGAAATACGCTCAAACTAATCTGCACCGCGGTGCAGATAACAGGAGTAAGAG
Found at i:42553 original size:2 final size:2
Alignment explanation
Indices: 42546--42571 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42536 ACAATGTCAC
42546 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
42572 GGGTTGTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48001 original size:41 final size:41
Alignment explanation
Indices: 47944--48026 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
47934 ATTTCCAAAC
*
47944 ACCATCTAATTGTATGGCAAGCCTTTTACTGTATCTTGAAA
1 ACCATCTAATTGTATGGCAAGCCTTTTACTGTATCTTAAAA
47985 ACCATCTAATTGTATGGCAAGCCTTTTACTGTATCTTAAAA
1 ACCATCTAATTGTATGGCAAGCCTTTTACTGTATCTTAAAA
48026 A
1 A
48027 GAATTGTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (41 bp):
ACCATCTAATTGTATGGCAAGCCTTTTACTGTATCTTAAAA
Found at i:54283 original size:17 final size:18
Alignment explanation
Indices: 54263--54301 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
54253 AAATGCCATG
54263 TTGA-TAAAAATAAGACA
1 TTGATTAAAAATAAGACA
*
54280 TTGATTGAAAATAAGACA
1 TTGATTAAAAATAAGACA
54298 TTGA
1 TTGA
54302 CTTTGGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.28
Consensus pattern (18 bp):
TTGATTAAAAATAAGACA
Found at i:56444 original size:36 final size:35
Alignment explanation
Indices: 56335--56530 Score: 183
Period size: 30 Copynumber: 6.0 Consensus size: 35
56325 ATTTAGGGTC
56335 AGTAGTTATTTACCTGAGGAGTTTTGGGTCAG--T
1 AGTAGTTATTTACCTGAGGAGTTTTGGGTCAGTAT
*
56368 AG--G-TATTTACCTGAGGAGTTTTTGGTC---AT
1 AGTAGTTATTTACCTGAGGAGTTTTGGGTCAGTAT
*
56397 --TAGTTATTTACCTGAGGAGTTATGGGTCAGTAT
1 AGTAGTTATTTACCTGAGGAGTTTTGGGTCAGTAT
56430 ACGTAGTTATTTACCTGAGGAGTTTTGGGTCA-T-T
1 A-GTAGTTATTTACCTGAGGAGTTTTGGGTCAGTAT
* *
56464 AGTTATTTTAAATTACCTGAGGAGTTTTGGGTCAG--T
1 AG-TA-GTT-ATTTACCTGAGGAGTTTTGGGTCAGTAT
* *
56500 A--A-TCACTTACCTGAGGAGTTTTGGGTCAGTA
1 AGTAGTTATTTACCTGAGGAGTTTTGGGTCAGTA
56531 ATCACTTACC
Statistics
Matches: 139, Mismatches: 8, Indels: 33
0.77 0.04 0.18
Matches are distributed among these distances:
29 2 0.01
30 69 0.50
31 2 0.01
33 6 0.04
34 4 0.03
35 3 0.02
36 53 0.38
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (35 bp):
AGTAGTTATTTACCTGAGGAGTTTTGGGTCAGTAT
Found at i:56469 original size:30 final size:30
Alignment explanation
Indices: 56432--56556 Score: 124
Period size: 30 Copynumber: 4.0 Consensus size: 30
56422 GTCAGTATAC
56432 GTAGTTATTTACCTGAGGAGTTTTGGGTCA
1 GTAGTTATTTACCTGAGGAGTTTTGGGTCA
*
56462 TTAGTTATTTTAAATTACCTGAGGAGTTTTGGGTCA
1 GTAGTTA---T---TTACCTGAGGAGTTTTGGGTCA
* * *
56498 GTAATCACTTACCTGAGGAGTTTTGGGTCA
1 GTAGTTATTTACCTGAGGAGTTTTGGGTCA
* * * *
56528 GTAATCACTTACCTGAGGAGTTTTTGGTC
1 GTAGTTATTTACCTGAGGAGTTTTGGGTC
56557 GCTGCATGGC
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
30 56 0.67
33 1 0.01
36 26 0.31
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (30 bp):
GTAGTTATTTACCTGAGGAGTTTTGGGTCA
Found at i:56510 original size:66 final size:60
Alignment explanation
Indices: 56330--56556 Score: 240
Period size: 66 Copynumber: 3.6 Consensus size: 60
56320 CTGGTATTTA
* *
56330 GGGTCAGTAGTTATTTACCTGAGGAGTTTTGGGTCAGTAGGTATTTACCTGAGGAGTTTT
1 GGGTCATTAGTTATTTACCTGAGGAGTTTTGGGTCAGTAGATATTTACCTGAGGAGTTTT
* *
56390 TGGTCATTAGTTATTTACCTGAGGAGTTATGGGTCAGTATACGTAGTTATTTACCTGAGGAGTTT
1 GGGTCATTAGTTATTTACCTGAGGAGTTTTGGGTCAG--TA-G-A--TATTTACCTGAGGAGTTT
56455 T
60 T
*
56456 GGGTCATTAGTTATTTTAAATTACCTGAGGAGTTTTGGGTCAGTA-ATCACTTACCTGAGGAGTT
1 GGGTCATTAGTTA---T---TTACCTGAGGAGTTTTGGGTCAGTAGAT-ATTTACCTGAGGAGTT
56520 TT
59 TT
* * * * *
56522 GGGTCAGTAATCACTTACCTGAGGAGTTTTTGGTC
1 GGGTCATTAGTTATTTACCTGAGGAGTTTTGGGTC
56557 GCTGCATGGC
Statistics
Matches: 142, Mismatches: 12, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
60 54 0.38
62 2 0.01
63 1 0.01
65 1 0.01
66 58 0.41
67 1 0.01
69 1 0.01
70 2 0.01
72 22 0.15
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (60 bp):
GGGTCATTAGTTATTTACCTGAGGAGTTTTGGGTCAGTAGATATTTACCTGAGGAGTTTT
Found at i:61242 original size:146 final size:146
Alignment explanation
Indices: 60680--61233 Score: 991
Period size: 146 Copynumber: 3.8 Consensus size: 146
60670 TTTGAAACAA
* * *
60680 TGACCTTGAACTTTCTCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * *
60745 CTTTGTGTGAAGTAAAAACTCCCAATGTTTCCCCATAAGAAAGATATGGACCGGACACAAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACAAATTTT
60810 GCACTTTTTCTGCCAG
131 GCACTTTTTCTGCCAG
*
60826 TGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
60891 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACAAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACAAATTTT
60956 GCACTTTTTCTGCCAG
131 GCACTTTTTCTGCCAG
*
60972 TAACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * **
61037 CTTTGTGTGAAGTAAGAATTTCCAATGTTTCTCCATAAGAAAGATATGGACGGGACATGAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACAAATTTT
61102 GCACTTTTTCTGCCAG
131 GCACTTTTTCTGCCAG
*
61118 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCGTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
61183 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGAC
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGAC
61234 AAGACATGAT
Statistics
Matches: 392, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
146 392 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (146 bp):
TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACAAATTTT
GCACTTTTTCTGCCAG
Found at i:61256 original size:4 final size:4
Alignment explanation
Indices: 61247--61292 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
61237 ACATGATTGC
61247 ACAG ACAG AC-G CACAG ACAG AC-G TACAG ACAG ACAG ACAG ACAG AC
1 ACAG ACAG ACAG -ACAG ACAG ACAG -ACAG ACAG ACAG ACAG ACAG AC
61293 GGACGGACGG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.05
4 34 0.89
5 2 0.05
ACGTcount: A:0.46, C:0.28, G:0.24, T:0.02
Consensus pattern (4 bp):
ACAG
Found at i:61262 original size:12 final size:12
Alignment explanation
Indices: 61245--61293 Score: 73
Period size: 12 Copynumber: 4.1 Consensus size: 12
61235 AGACATGATT
61245 GCACAGACAGAC
1 GCACAGACAGAC
61257 GCACAGACAGAC
1 GCACAGACAGAC
*
61269 GTACAGACAGAC
1 GCACAGACAGAC
61281 AG-ACAGACAGAC
1 -GCACAGACAGAC
61293 G
1 G
61294 GACGGACGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
11 1 0.03
12 33 0.94
13 1 0.03
ACGTcount: A:0.43, C:0.29, G:0.27, T:0.02
Consensus pattern (12 bp):
GCACAGACAGAC
Found at i:66839 original size:13 final size:13
Alignment explanation
Indices: 66818--66848 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
66808 TATCAGTAAA
66818 CCAAAGACCCCAC
1 CCAAAGACCCCAC
*
66831 CCAAGGACCCCAC
1 CCAAAGACCCCAC
66844 CCAAA
1 CCAAA
66849 TACCAGAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.39, C:0.52, G:0.10, T:0.00
Consensus pattern (13 bp):
CCAAAGACCCCAC
Found at i:70230 original size:14 final size:14
Alignment explanation
Indices: 70213--70246 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
70203 AGTTGATTTT
70213 AACAGTTCCAATCC
1 AACAGTTCCAATCC
*
70227 AACAGTTCCAGTCC
1 AACAGTTCCAATCC
70241 AACAGT
1 AACAGT
70247 CAAAATACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.12, T:0.21
Consensus pattern (14 bp):
AACAGTTCCAATCC
Found at i:70550 original size:45 final size:45
Alignment explanation
Indices: 70499--70590 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
70489 GAGTTCATAA
70499 AATATGTAGAACAGTCTAGTTTAAGGTAACCCTACCTGAATCAGC
1 AATATGTAGAACAGTCTAGTTTAAGGTAACCCTACCTGAATCAGC
**
70544 AATATGTAGAACAGTCTAGTTTAAGGTATTCCTACCTGAATCAGC
1 AATATGTAGAACAGTCTAGTTTAAGGTAACCCTACCTGAATCAGC
70589 AA
1 AA
70591 ACCTAGTCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (45 bp):
AATATGTAGAACAGTCTAGTTTAAGGTAACCCTACCTGAATCAGC
Found at i:70783 original size:26 final size:26
Alignment explanation
Indices: 70754--70803 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
70744 GGAACAATGC
*
70754 TGATCAATTTTTCTCATAATTATGAT
1 TGATCAATTTTTCCCATAATTATGAT
70780 TGATCAATTTTTCCCATAATTATG
1 TGATCAATTTTTCCCATAATTATG
70804 TATGGTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (26 bp):
TGATCAATTTTTCCCATAATTATGAT
Found at i:73602 original size:2 final size:2
Alignment explanation
Indices: 73595--73632 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
73585 ACCATATACA
73595 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
73633 TATCACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:75052 original size:20 final size:20
Alignment explanation
Indices: 75002--75281 Score: 109
Period size: 20 Copynumber: 14.7 Consensus size: 20
74992 AGGCATCATC
*
75002 ACATGTAACTTATTGTACAG
1 ACATGTAACTTGTTGTACAG
** * *
75022 ATTTGTTACTTGCTGTACAG
1 ACATGTAACTTGTTGTACAG
*
75042 ACATGTAACTTGTTGAACAG
1 ACATGTAACTTGTTGTACAG
* * *
75062 ATATGTAACTTATTGTATAG
1 ACATGTAACTTGTTGTACAG
* * * *
75082 ACCTATAACTTATTCT--A-
1 ACATGTAACTTGTTGTACAG
* * *
75099 ACTTGTAGC---TTGTACAT
1 ACATGTAACTTGTTGTACAG
* * * *
75116 ACTTATAACTTGGTGTACAC
1 ACATGTAACTTGTTGTACAG
*
75136 ACATGTAACTTGTTGAACAG
1 ACATGTAACTTGTTGTACAG
* * * *
75156 ATAGGTAACTTATTGTATAG
1 ACATGTAACTTGTTGTACAG
* * * **
75176 ACCTATAACTTATCCT--A-
1 ACATGTAACTTGTTGTACAG
* * *
75193 ACTTGTAGC---TTGTACAT
1 ACATGTAACTTGTTGTACAG
* *
75210 ACTTGTAACTTGGTGTACAG
1 ACATGTAACTTGTTGTACAG
* *
75230 ACATGTAACTTGTTGTAGAA
1 ACATGTAACTTGTTGTACAG
* *
75250 ACATGT-ACATGTTGGACAG
1 ACATGTAACTTGTTGTACAG
*
75269 ACATGTACCTTGT
1 ACATGTAACTTGT
75282 ATCGATATAT
Statistics
Matches: 187, Mismatches: 60, Indels: 26
0.68 0.22 0.10
Matches are distributed among these distances:
14 5 0.03
16 2 0.01
17 27 0.14
18 2 0.01
19 15 0.08
20 136 0.73
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (20 bp):
ACATGTAACTTGTTGTACAG
Found at i:75133 original size:94 final size:94
Alignment explanation
Indices: 75029--75244 Score: 387
Period size: 94 Copynumber: 2.3 Consensus size: 94
75019 CAGATTTGTT
* *
75029 ACTTGCTGTACAGACATGTAACTTGTTGAACAGATATGTAACTTATTGTATAGACCTATAACTTA
1 ACTTGGTGTACAGACATGTAACTTGTTGAACAGATAGGTAACTTATTGTATAGACCTATAACTTA
*
75094 TTCTAACTTGTAGCTTGTACATACTTATA
66 TCCTAACTTGTAGCTTGTACATACTTATA
*
75123 ACTTGGTGTACACACATGTAACTTGTTGAACAGATAGGTAACTTATTGTATAGACCTATAACTTA
1 ACTTGGTGTACAGACATGTAACTTGTTGAACAGATAGGTAACTTATTGTATAGACCTATAACTTA
*
75188 TCCTAACTTGTAGCTTGTACATACTTGTA
66 TCCTAACTTGTAGCTTGTACATACTTATA
75217 ACTTGGTGTACAGACATGTAACTTGTTG
1 ACTTGGTGTACAGACATGTAACTTGTTG
75245 TAGAAACATG
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 116 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (94 bp):
ACTTGGTGTACAGACATGTAACTTGTTGAACAGATAGGTAACTTATTGTATAGACCTATAACTTA
TCCTAACTTGTAGCTTGTACATACTTATA
Found at i:75272 original size:19 final size:19
Alignment explanation
Indices: 75226--75276 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
75216 AACTTGGTGT
* *
75226 ACAGACATGTAACTTGTTGT
1 ACAGACATGT-ACATGTTGG
* *
75246 AGAAACATGTACATGTTGG
1 ACAGACATGTACATGTTGG
75265 ACAGACATGTAC
1 ACAGACATGTAC
75277 CTTGTATCGA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (19 bp):
ACAGACATGTACATGTTGG
Found at i:76562 original size:2 final size:2
Alignment explanation
Indices: 76555--76622 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
76545 TGAGAGTGAT
76555 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
76597 TC TC TC TC TC AC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
76623 ATTATTCTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.01, C:0.50, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:81066 original size:22 final size:22
Alignment explanation
Indices: 81020--81068 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
81010 TCGACGCGTG
*
81020 TATTTATTGATCTTTTATCTGT
1 TATTTATTGATCTTTTATCCGT
81042 TATTTA-TGAT-TTTTATACCGCT
1 TATTTATTGATCTTTTAT-CCG-T
81064 TATTT
1 TATTT
81069 TGTCTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 6 0.25
22 12 0.50
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (22 bp):
TATTTATTGATCTTTTATCCGT
Found at i:81853 original size:18 final size:18
Alignment explanation
Indices: 81830--81898 Score: 129
Period size: 18 Copynumber: 3.8 Consensus size: 18
81820 TTATCTTTAC
81830 ATAGATTACAAATGTTAA
1 ATAGATTACAAATGTTAA
81848 ATAGATTACAAATGTTAA
1 ATAGATTACAAATGTTAA
*
81866 ATAGATTACAAATGTTAC
1 ATAGATTACAAATGTTAA
81884 ATAGATTACAAATGT
1 ATAGATTACAAATGT
81899 GAACCAAGAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (18 bp):
ATAGATTACAAATGTTAA
Found at i:93976 original size:30 final size:30
Alignment explanation
Indices: 93942--94106 Score: 204
Period size: 30 Copynumber: 5.2 Consensus size: 30
93932 TTGATTCAGA
*
93942 AGACACTATCTCACACACACGTGTTACAAGAG
1 AGACACTATCTCACACACACGAGTTAC-A-AG
93974 ACAAGACACTATCTCACACACACGAGTTACAAGAG
1 ---AGACACTATCTCACACACACGAGTTAC-A-AG
94009 ACAAGACACTATCTCACACACACGAGTTACAAG
1 ---AGACACTATCTCACACACACGAGTTACAAG
* *
94042 AGACACTATCACACACACACGTGTTACAAG
1 AGACACTATCTCACACACACGAGTTACAAG
*
94072 AGACACTATCACACACACACGAGTTACAAG
1 AGACACTATCTCACACACACGAGTTACAAG
94102 AGACA
1 AGACA
94107 NTACATGTAT
Statistics
Matches: 126, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
30 62 0.49
33 2 0.02
34 1 0.01
35 61 0.48
ACGTcount: A:0.42, C:0.29, G:0.14, T:0.15
Consensus pattern (30 bp):
AGACACTATCTCACACACACGAGTTACAAG
Found at i:93987 original size:35 final size:35
Alignment explanation
Indices: 93941--94106 Score: 226
Period size: 35 Copynumber: 5.0 Consensus size: 35
93931 CTTGATTCAG
*
93941 AAGACACTATCTCACACACACGTGTTACAAGAGAC
1 AAGACACTATCTCACACACACGAGTTACAAGAGAC
93976 AAGACACTATCTCACACACACGAGTTACAAGAGAC
1 AAGACACTATCTCACACACACGAGTTACAAGAGAC
94011 AAGACACTATCTCACACACACGAGTTAC-A-AG--
1 AAGACACTATCTCACACACACGAGTTACAAGAGAC
* *
94042 -AGACACTATCACACACACACGTGTTAC-A-AG--
1 AAGACACTATCTCACACACACGAGTTACAAGAGAC
*
94072 -AGACACTATCACACACACACGAGTTACAAGAGAC
1 AAGACACTATCTCACACACACGAGTTACAAGAGAC
94106 A
1 A
94107 NTACATGTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
30 54 0.44
31 1 0.01
32 2 0.02
33 2 0.02
34 1 0.01
35 62 0.51
ACGTcount: A:0.42, C:0.29, G:0.14, T:0.15
Consensus pattern (35 bp):
AAGACACTATCTCACACACACGAGTTACAAGAGAC
Found at i:94282 original size:37 final size:37
Alignment explanation
Indices: 94229--94496 Score: 430
Period size: 37 Copynumber: 7.1 Consensus size: 37
94219 CTTGATTCAG
*
94229 AAGACACTATCTCACACACAC-ACGTGTTACAAGAGAC
1 AAGACACTATCACACACACACTA-GTGTTACAAGAGAC
94266 AAGACACTATCACACACACACTTATGTGTTACAAGAGAC
1 AAGACACTATCACACACACAC-TA-GTGTTACAAGAGAC
94305 AAGACACTATCACACACACACTAGTGTTACAAGAGAC
1 AAGACACTATCACACACACACTAGTGTTACAAGAGAC
94342 AAGACACTATCACACACACACTAGTGTTACAAGAGAC
1 AAGACACTATCACACACACACTAGTGTTACAAGAGAC
94379 AAGACACTATCACACACACACTAGTGTTACAAGAGAC
1 AAGACACTATCACACACACACTAGTGTTACAAGAGAC
*
94416 AAGACATTATCACACACACACTAGTGTTACAAGAGAC
1 AAGACACTATCACACACACACTAGTGTTACAAGAGAC
* *
94453 AGGACACTATCACACACACACACACATGTGTTACAAGAGAC
1 AAGACACTAT--CACACACACAC-TA-GTGTTACAAGAGAC
94494 AAG
1 AAG
94497 TGCTTGCTAG
Statistics
Matches: 218, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
37 152 0.70
38 2 0.01
39 47 0.22
40 1 0.00
41 16 0.07
ACGTcount: A:0.43, C:0.27, G:0.14, T:0.17
Consensus pattern (37 bp):
AAGACACTATCACACACACACTAGTGTTACAAGAGAC
Found at i:94434 original size:111 final size:113
Alignment explanation
Indices: 94229--94496 Score: 443
Period size: 113 Copynumber: 2.4 Consensus size: 113
94219 CTTGATTCAG
*
94229 AAGACACTATCTCACACACACACGTGTTACAAGAGACAAGACACTATCACACACACACTTATGTG
1 AAGACACTATCACACACACACACGTGTTACAAGAGACAAGACACTATCACACACACACTTATGTG
94294 TTACAAGAGACAAGACACTATCACACACACACTAGTGTTACAAGAGAC
66 TTACAAGAGACAAGACACTATCACACACACACTAGTGTTACAAGAGAC
94342 AAGACACTATCACACACACACTA-GTGTTACAAGAGACAAGACACTATCACACACACAC-TA-GT
1 AAGACACTATCACACACACAC-ACGTGTTACAAGAGACAAGACACTATCACACACACACTTATGT
*
94404 GTTACAAGAGACAAGACATTATCACACACACACTAGTGTTACAAGAGAC
65 GTTACAAGAGACAAGACACTATCACACACACACTAGTGTTACAAGAGAC
*
94453 AGGACACTATCACACACACACACACATGTGTTACAAGAGACAAG
1 AAGACACTAT--CACACACACACAC--GTGTTACAAGAGACAAG
94497 TGCTTGCTAG
Statistics
Matches: 146, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
111 59 0.40
112 3 0.02
113 66 0.45
114 1 0.01
115 17 0.12
ACGTcount: A:0.43, C:0.27, G:0.14, T:0.17
Consensus pattern (113 bp):
AAGACACTATCACACACACACACGTGTTACAAGAGACAAGACACTATCACACACACACTTATGTG
TTACAAGAGACAAGACACTATCACACACACACTAGTGTTACAAGAGAC
Found at i:95448 original size:55 final size:53
Alignment explanation
Indices: 95339--95501 Score: 211
Period size: 55 Copynumber: 3.0 Consensus size: 53
95329 TCTTGGAAGT
* * * *
95339 GCCCCACCACAGGACTATAGACATTCTATCTATATGTACGGTATGTTACCTGGAGAC
1 GCCCCACCCCAGGACTATAGAGATTCTAT-T-TA-CTA-TGTATGTTACCTGGAGAC
95396 GCCCCACCCCAGGAACTATAGAGATTCTATTTACCTATGTATGTTACCTGGAGAC
1 GCCCCACCCCAGG-ACTATAGAGATTCTATTTA-CTATGTATGTTACCTGGAGAC
*
95451 GCCCCACCCCAGGGACTATAGAGATTCTATTTAC-ATATATGTTACCTGGAG
1 GCCCCACCCCA-GGACTATAGAGATTCTATTTACTATGTATGTTACCTGGAG
95502 GTTTCATGCC
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
53 16 0.16
54 1 0.01
55 47 0.48
56 6 0.06
57 13 0.13
58 15 0.15
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (53 bp):
GCCCCACCCCAGGACTATAGAGATTCTATTTACTATGTATGTTACCTGGAGAC
Found at i:112613 original size:2 final size:2
Alignment explanation
Indices: 112606--112642 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
112596 ATTGGTATAC
112606 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
112643 TTAGTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:116724 original size:9 final size:9
Alignment explanation
Indices: 116710--116766 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
116700 GGACTCTTCA
116710 TTCATCATC
1 TTCATCATC
116719 TTCATCA--
1 TTCATCATC
116726 -TCATCATC
1 TTCATCATC
* *
116734 TTCCTCCTC
1 TTCATCATC
*
116743 TTCTTCATC
1 TTCATCATC
*
116752 TTCCTCATC
1 TTCATCATC
116761 TTCATC
1 TTCATC
116767 GCCATTCTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 6 0.15
9 33 0.85
ACGTcount: A:0.16, C:0.39, G:0.00, T:0.46
Consensus pattern (9 bp):
TTCATCATC
Found at i:116731 original size:15 final size:14
Alignment explanation
Indices: 116704--116766 Score: 60
Period size: 15 Copynumber: 4.6 Consensus size: 14
116694 TCACTGGGAC
116704 TCTTCAT-TCATCA
1 TCTTCATCTCATCA
116717 TCTTCATCATCATCA
1 TCTTCATC-TCATCA
* *
116732 TCTTC--CTCCTCT
1 TCTTCATCTCATCA
*
116744 TCTTCATCTTCCTCA
1 TCTTCATC-TCATCA
116759 TCTTCATC
1 TCTTCATC
116767 GCCATTCTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.21
13 8 0.19
14 1 0.02
15 24 0.57
ACGTcount: A:0.16, C:0.38, G:0.00, T:0.46
Consensus pattern (14 bp):
TCTTCATCTCATCA
Found at i:116750 original size:18 final size:18
Alignment explanation
Indices: 116704--116763 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
116694 TCACTGGGAC
* *
116704 TCTTCATTCATCATCTTCA
1 TCTTC-TTCATCTTCCTCA
* * *
116723 TCATCATCATCTTCCTCC
1 TCTTCTTCATCTTCCTCA
116741 TCTTCTTCATCTTCCTCA
1 TCTTCTTCATCTTCCTCA
116759 TCTTC
1 TCTTC
116764 ATCGCCATTC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 29 0.88
19 4 0.12
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.47
Consensus pattern (18 bp):
TCTTCTTCATCTTCCTCA
Found at i:122617 original size:17 final size:17
Alignment explanation
Indices: 122568--122676 Score: 59
Period size: 17 Copynumber: 7.3 Consensus size: 17
122558 TTTGTATAAT
122568 TACATGTAATATGTACG
1 TACATGTAATATGTACG
**
122585 TACA--T-ATA--TAAT
1 TACATGTAATATGTACG
122597 TACATGTAATATGTACG
1 TACATGTAATATGTACG
**
122614 TACA--T-ATA--TAAT
1 TACATGTAATATGTACG
122626 TACATGTAATATGTACG
1 TACATGTAATATGTACG
**
122643 TACA--T-ATA--TAAT
1 TACATGTAATATGTACG
122655 TACATGTAATATGTACG
1 TACATGTAATATGTACG
122672 TACAT
1 TACAT
122677 ATTTTAAATC
Statistics
Matches: 65, Mismatches: 12, Indels: 30
0.61 0.11 0.28
Matches are distributed among these distances:
12 18 0.28
14 12 0.18
15 12 0.18
17 23 0.35
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (17 bp):
TACATGTAATATGTACG
Found at i:122692 original size:29 final size:29
Alignment explanation
Indices: 122562--122678 Score: 234
Period size: 29 Copynumber: 4.0 Consensus size: 29
122552 AATACATTTG
122562 TATAATTACATGTAATATGTACGTACATA
1 TATAATTACATGTAATATGTACGTACATA
122591 TATAATTACATGTAATATGTACGTACATA
1 TATAATTACATGTAATATGTACGTACATA
122620 TATAATTACATGTAATATGTACGTACATA
1 TATAATTACATGTAATATGTACGTACATA
122649 TATAATTACATGTAATATGTACGTACATA
1 TATAATTACATGTAATATGTACGTACATA
122678 T
1 T
122679 TTTAAATCCT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 88 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (29 bp):
TATAATTACATGTAATATGTACGTACATA
Found at i:140828 original size:32 final size:32
Alignment explanation
Indices: 140791--141189 Score: 452
Period size: 32 Copynumber: 12.5 Consensus size: 32
140781 ACAATGCAGA
* * * *
140791 CTATTACCTCCGTGATAAATCACAATGATAGC
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
* *
140823 CTATTACTTCTGAGAGAAATCTCAATGATAGA
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
*
140855 CTATTACCTCAGAGAGAAATCTCAATGATAGC
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
* *
140887 CTAATACCTCGGAGAGAAATCTCAATGATACATTGC
1 CTATTACCTCTGAGAGAAATCTCAATGAT--A--GC
* *
140923 AGACTAATACCTCTGAGAGAAACCTCAATG--A--
1 ---CTATTACCTCTGAGAGAAATCTCAATGATAGC
*
140954 -TA--ACCTATGAGAGAAATCTCAATGATAGC
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
*
140983 CTAATACCTCTGAGAGAAATCTCAATGATAGC
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
*
141015 CTATTACCTCTGAGAGAAATCTCAATGACAGC
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
* * * * *
141047 CTATTACTTTTTAGAGAAATCTCAATGTTAGA
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
** *
141079 CTATTACCTCTGAGTTAAATCTCAATGACAGC
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
*
141111 CTATTACCTCTGAGAGAAATCTCAATGACAGC
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
* * *
141143 CTATTACTTTTTAGAGAAATCTCAATGATAGC
1 CTATTACCTCTGAGAGAAATCTCAATGATAGC
141175 CTATTACCTCTGAGA
1 CTATTACCTCTGAGA
141190 AATAAAAAAA
Statistics
Matches: 312, Mismatches: 41, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
25 20 0.06
27 3 0.01
30 2 0.01
32 258 0.83
34 1 0.00
35 1 0.00
36 2 0.01
39 25 0.08
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (32 bp):
CTATTACCTCTGAGAGAAATCTCAATGATAGC
Found at i:140965 original size:25 final size:25
Alignment explanation
Indices: 140931--140985 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
140921 GCAGACTAAT
*
140931 ACCTCTGAGAGAAACCTCAATGATA
1 ACCTATGAGAGAAACCTCAATGATA
*
140956 ACCTATGAGAGAAATCTCAATGATA
1 ACCTATGAGAGAAACCTCAATGATA
*
140981 GCCTA
1 ACCTA
140986 ATACCTCTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (25 bp):
ACCTATGAGAGAAACCTCAATGATA
Found at i:143944 original size:38 final size:37
Alignment explanation
Indices: 143854--143976 Score: 153
Period size: 38 Copynumber: 3.4 Consensus size: 37
143844 CCTAATTGTT
* *
143854 TCATTGTCATATGAAAAATGAATTCATA-C--CTATG
1 TCATGGTCACATGAAAAATGAATTCATACCTACTATG
* * *
143888 TCATGGTCGCATGTAAAATAAATTCATACCATACTATG
1 TCATGGTCACATGAAAAATGAATTCATACC-TACTATG
*
143926 TCATTGTCACATGAAAAATGAATTCATACCTAACTATG
1 TCATGGTCACATGAAAAATGAATTCATACCT-ACTATG
143964 TCATGGTCACATG
1 TCATGGTCACATG
143977 TTAAGCTAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
34 23 0.31
35 1 0.01
37 1 0.01
38 49 0.66
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (37 bp):
TCATGGTCACATGAAAAATGAATTCATACCTACTATG
Found at i:154012 original size:13 final size:13
Alignment explanation
Indices: 153994--154022 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
153984 TTTACTGTGT
153994 AAAAAAAAAACAA
1 AAAAAAAAAACAA
154007 AAAAAAAAAACAA
1 AAAAAAAAAACAA
154020 AAA
1 AAA
154023 CAATATGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:158197 original size:2 final size:2
Alignment explanation
Indices: 158192--158230 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
158182 ACTGAAAAAA
158192 TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
158231 ATGCTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:159836 original size:38 final size:39
Alignment explanation
Indices: 159785--159973 Score: 193
Period size: 38 Copynumber: 4.6 Consensus size: 39
159775 GAAAGGGGTT
159785 CAAATGCTCAGTACAGAATAATGTTAT-ATATTATGATA
1 CAAATGCTCAGTACAGAATAATGTTATAATATTATGATA
159823 CAAATGCTCAGTACAGAATAATGTTATACATGTATATCATGATA
1 CAAATGCTCAGTACAGAATAATGTTATA-A--TAT-T-ATGATA
159867 CAAATGCTCAGTTAGTACAGAATAATGTTATTTATAATATTATGATA
1 CAAATGCTC----AGTACAGAATAATG----TTATAATATTATGATA
* * * * *
159914 CAAATGCACATTACTGAATAATGTTAT-ATAATATGATG
1 CAAATGCTCAGTACAGAATAATGTTATAATATTATGATA
*
159952 CAAGTGCTCAGTACAGAATAAT
1 CAAATGCTCAGTACAGAATAAT
159974 ACATGCATTA
Statistics
Matches: 128, Mismatches: 9, Indels: 28
0.78 0.05 0.17
Matches are distributed among these distances:
38 54 0.42
39 4 0.03
40 1 0.01
42 3 0.02
43 13 0.10
44 15 0.12
47 14 0.11
48 15 0.12
49 3 0.02
51 1 0.01
52 5 0.04
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (39 bp):
CAAATGCTCAGTACAGAATAATGTTATAATATTATGATA
Found at i:167111 original size:20 final size:19
Alignment explanation
Indices: 167077--167114 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
167067 GTACAGAGGT
*
167077 TGTTGTGTCTTTGTACAGC
1 TGTTGTGTATTTGTACAGC
167096 TGTTGATGTATTTGTACAG
1 TGTTG-TGTATTTGTACAG
167115 ATATGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.16, C:0.11, G:0.26, T:0.47
Consensus pattern (19 bp):
TGTTGTGTATTTGTACAGC
Found at i:167191 original size:18 final size:17
Alignment explanation
Indices: 167161--167194 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
167151 GTACACAGAT
*
167161 TGTTATATTTGTACAAA
1 TGTTATATCTGTACAAA
167178 TGTTGATATCTGTACAA
1 TGTT-ATATCTGTACAA
167195 TACATTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (17 bp):
TGTTATATCTGTACAAA
Found at i:167239 original size:25 final size:26
Alignment explanation
Indices: 167210--167258 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
167200 TGTATCTTTG
167210 TACAGATGTCGCTA-TTTTGTACATT
1 TACAGATGTCGCTATTTTTGTACATT
* * *
167235 TACAGTTGTTGGTATTTTTGTACA
1 TACAGATGTCGCTATTTTTGTACA
167259 GGTGTTGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (26 bp):
TACAGATGTCGCTATTTTTGTACATT
Found at i:167264 original size:20 final size:20
Alignment explanation
Indices: 167235--167335 Score: 64
Period size: 20 Copynumber: 5.2 Consensus size: 20
167225 TTTGTACATT
* * *
167235 TACAGTTGTTGGTATTTTTG
1 TACAGGTGTTGCTATATTTG
167255 TACAGGTGTTGCTATATTTG
1 TACAGGTGTTGCTATATTTG
* ** *
167275 TGCAATTGTTG---TGTTTG
1 TACAGGTGTTGCTATATTTG
* * *
167292 AACAGGTGTTGCTGTCTTTG
1 TACAGGTGTTGCTATATTTG
* * *
167312 TAAAGTTGTTGCTATTTTTG
1 TACAGGTGTTGCTATATTTG
167332 TACA
1 TACA
167336 AATATTTTGA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
17 12 0.20
20 48 0.80
ACGTcount: A:0.18, C:0.09, G:0.25, T:0.49
Consensus pattern (20 bp):
TACAGGTGTTGCTATATTTG
Found at i:167321 original size:37 final size:37
Alignment explanation
Indices: 167251--167322 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
167241 TGTTGGTATT
* *
167251 TTTGTACAGGTGTTGCTATATTTGTGCAATTGTTGTG
1 TTTGAACAGGTGTTGCTATATTTGTGAAATTGTTGTG
* *
167288 TTTGAACAGGTGTTGCTGTCTTTGT-AAAGTTGTTG
1 TTTGAACAGGTGTTGCTATATTTGTGAAA-TTGTTG
167323 CTATTTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 2 0.07
37 28 0.93
ACGTcount: A:0.17, C:0.08, G:0.28, T:0.47
Consensus pattern (37 bp):
TTTGAACAGGTGTTGCTATATTTGTGAAATTGTTGTG
Found at i:167433 original size:20 final size:20
Alignment explanation
Indices: 167408--167831 Score: 200
Period size: 20 Copynumber: 20.9 Consensus size: 20
167398 TGTTGCTAAC
167408 TTGCTATCTTTGTACAGATG
1 TTGCTATCTTTGTACAGATG
167428 TTGCTATCTTTGTACAGATG
1 TTGCTATCTTTGTACAGATG
* *
167448 TTTTGGTATATTTGTACAGATG
1 --TTGCTATCTTTGTACAGATG
* *
167470 TTG-T-TTTTTGTACATATG
1 TTGCTATCTTTGTACAGATG
* * *
167488 TTGCTAACTGTGTACAGCTG
1 TTGCTATCTTTGTACAGATG
* *
167508 TTGCTATCTTTGTACATATAT
1 TTGCTATCTTTGTACAGAT-G
*
167529 TTGGAATATCTTT-TACAGATG
1 TT-G-CTATCTTTGTACAGATG
* *
167550 ATGCTATCTTTGTACA-ATT
1 TTGCTATCTTTGTACAGATG
* *
167569 TTGATAT-TGTTGTACAGATATT
1 TTGCTATCT-TTGTACAG--ATG
*
167591 TTG-AATACTTTGTACAGATG
1 TTGCTAT-CTTTGTACAGATG
* * *
167611 ATGCTATCTTTGTACAGTTC
1 TTGCTATCTTTGTACAGATG
* *
167631 TTGGT-TTTGTTGTACAGATG
1 TTGCTATCT-TTGTACAGATG
* * * * *
167651 ATGCTTTCTTTGTTCAGTTC
1 TTGCTATCTTTGTACAGATG
* *
167671 TTGGT-TTTGTTGTACAGATG
1 TTGCTATCT-TTGTACAGATG
* * * *
167691 ATGCTTTCTTTGTACAGTTC
1 TTGCTATCTTTGTACAGATG
* *
167711 TTGGT-TTTGTTGTACAGATG
1 TTGCTATCT-TTGTACAGATG
* * *
167731 ATGCTCTCGTTGTACAGATATG
1 TTGCTATCTTTGTACAG--ATG
* ** * *
167753 TTGATATCTGAGCACAGATA
1 TTGCTATCTTTGTACAGATG
* * *
167773 TTGATATCTTTGCACAGATC
1 TTGCTATCTTTGTACAGATG
* * * *
167793 TAGATATCTTTGCACAGATC
1 TTGCTATCTTTGTACAGATG
* * *
167813 TAGATATCTTTGCACAGAT
1 TTGCTATCTTTGTACAGAT
167832 CTACATGTAG
Statistics
Matches: 310, Mismatches: 71, Indels: 46
0.73 0.17 0.11
Matches are distributed among these distances:
18 16 0.05
19 29 0.09
20 193 0.62
21 12 0.04
22 52 0.17
23 8 0.03
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.45
Consensus pattern (20 bp):
TTGCTATCTTTGTACAGATG
Found at i:167556 original size:42 final size:40
Alignment explanation
Indices: 167412--167587 Score: 157
Period size: 42 Copynumber: 4.3 Consensus size: 40
167402 GCTAACTTGC
*
167412 TATCTTTGTACAGATGTTGCTATCTTTGTACAGATGTTTTGGTA
1 TATC-TTGTACAGATGTTGCTATCTTTGTAC--ATATTTTGG-A
* * *
167456 TAT-TTGTACAGATGTTG-T-TTTTTGTACATATGTT-GC
1 TATCTTGTACAGATGTTGCTATCTTTGTACATATTTTGGA
* *
167492 TAACTGTGTACAGCTGTTGCTATCTTTGTACATATATTTGGAA
1 TATCT-TGTACAGATGTTGCTATCTTTGTACATAT-TTTGG-A
* *
167535 TATCTTTTACAGATGATGCTATCTTTGTACA-ATTTT-GA
1 TATCTTGTACAGATGTTGCTATCTTTGTACATATTTTGGA
*
167573 TATTGTTGTACAGAT
1 TA-TCTTGTACAGAT
167588 ATTTTGAATA
Statistics
Matches: 109, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
36 2 0.02
37 2 0.02
38 20 0.18
39 12 0.11
40 23 0.21
41 5 0.05
42 38 0.35
43 4 0.04
44 3 0.03
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.47
Consensus pattern (40 bp):
TATCTTGTACAGATGTTGCTATCTTTGTACATATTTTGGA
Found at i:167590 original size:61 final size:62
Alignment explanation
Indices: 167517--167649 Score: 198
Period size: 61 Copynumber: 2.2 Consensus size: 62
167507 GTTGCTATCT
*
167517 TTGTACATATATTTGGAATATCTTT-TACAGATGATGCTATCTTTGTACAATT-TTGATATTG
1 TTGTACAGATATTTGGAATA-CTTTGTACAGATGATGCTATCTTTGTACAATTCTTGATATTG
* * * *
167578 TTGTACAGATATTTTGAATACTTTGTACAGATGATGCTATCTTTGTACAGTTCTTGGTTTTG
1 TTGTACAGATATTTGGAATACTTTGTACAGATGATGCTATCTTTGTACAATTCTTGATATTG
167640 TTGTACAGAT
1 TTGTACAGAT
167650 GATGCTTTCT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 4 0.06
61 44 0.68
62 17 0.26
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.47
Consensus pattern (62 bp):
TTGTACAGATATTTGGAATACTTTGTACAGATGATGCTATCTTTGTACAATTCTTGATATTG
Found at i:167647 original size:40 final size:40
Alignment explanation
Indices: 167600--167747 Score: 260
Period size: 40 Copynumber: 3.7 Consensus size: 40
167590 TTTGAATACT
*
167600 TTGTACAGATGATGCTATCTTTGTACAGTTCTTGGTTTTG
1 TTGTACAGATGATGCTTTCTTTGTACAGTTCTTGGTTTTG
*
167640 TTGTACAGATGATGCTTTCTTTGTTCAGTTCTTGGTTTTG
1 TTGTACAGATGATGCTTTCTTTGTACAGTTCTTGGTTTTG
167680 TTGTACAGATGATGCTTTCTTTGTACAGTTCTTGGTTTTG
1 TTGTACAGATGATGCTTTCTTTGTACAGTTCTTGGTTTTG
* *
167720 TTGTACAGATGATGCTCTCGTTGTACAG
1 TTGTACAGATGATGCTTTCTTTGTACAG
167748 ATATGTTGAT
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.47
Consensus pattern (40 bp):
TTGTACAGATGATGCTTTCTTTGTACAGTTCTTGGTTTTG
Found at i:167903 original size:33 final size:33
Alignment explanation
Indices: 167863--167940 Score: 138
Period size: 33 Copynumber: 2.3 Consensus size: 33
167853 TGTTGTTGTC
167863 CTTGTACAGATTTCAGTATATGTGTGGTGATAT
1 CTTGTACAGATTTCAGTATATGTGTGGTGATAT
167896 CTTGTACAGATTTCAGTATATGTGTGGTGATAT
1 CTTGTACAGATTTCAGTATATGTGTGGTGATAT
*
167929 ATTCGTACAGAT
1 CTT-GTACAGAT
167941 ATTTGTATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 35 0.81
34 8 0.19
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (33 bp):
CTTGTACAGATTTCAGTATATGTGTGGTGATAT
Found at i:168360 original size:68 final size:68
Alignment explanation
Indices: 168122--168448 Score: 308
Period size: 68 Copynumber: 4.7 Consensus size: 68
168112 AAACAAGCTG
* * * *
168122 TATGTCATTGGAGGTATGTTATACA-ATGTATGTTTCTATGTCATTGGAGGTATGTCAGACTATG
1 TATGTCATTGGAGGTATGTCAGA-ATTTGTATGTATCTATGTCATTGGAGGTATGTCAGACTA--
168186 TCTGTTTC
63 --TGTTTC
* * * *
168194 TATGTCATTGGAGATATGTCAG-A--T-TATGT-TTTATATCATTAGAGGTATGTCAGACTATGT
1 TATGTCATTGGAGGTATGTCAGAATTTGTATGTATCTATGTCATTGGAGGTATGTCAGACTATG-
*
168254 ATGTTT
65 -T-TTC
* * * *
168260 TATATCATTGGAGGTATATCAGACTTTGTATGTATCTATGTCAATGGAGGTATGTCAGACTATGT
1 TATGTCATTGGAGGTATGTCAGAATTTGTATGTATCTATGTCATTGGAGGTATGTCAGACTATGT
168325 TTC
66 TTC
* * *
168328 TATGTCATTTGAGGGATGTCAGAATTTGTATGTATATATGTCATTGGAGGTATGTCAGACTATGT
1 TATGTCATTGGAGGTATGTCAGAATTTGTATGTATCTATGTCATTGGAGGTATGTCAGACTATG-
*
168393 CTAGTTT
65 -T--TTC
* * *
168400 TATATCATTGGAGGTATGTCAG-ATTATGTTTGTTTCTATGTCATTGGAG
1 TATGTCATTGGAGGTATGTCAGAATT-TGTATGTATCTATGTCATTGGAG
168449 ACATGTCTAA
Statistics
Matches: 212, Mismatches: 30, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
63 2 0.01
65 1 0.00
66 21 0.10
67 25 0.12
68 64 0.30
69 3 0.01
70 7 0.03
71 29 0.14
72 60 0.28
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (68 bp):
TATGTCATTGGAGGTATGTCAGAATTTGTATGTATCTATGTCATTGGAGGTATGTCAGACTATGT
TTC
Found at i:168455 original size:36 final size:36
Alignment explanation
Indices: 168122--168448 Score: 370
Period size: 36 Copynumber: 9.4 Consensus size: 36
168112 AAACAAGCTG
* * *
168122 TATGTCATTGGAGGTATGTTATACAATGTATGTTTC
1 TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
*
168158 TATGTCATTGGAGGTATGTCAGACTATGTCTGTTTC
1 TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
*
168194 TATGTCATTGGAGATATGTCAG---AT-TATGTTT-
1 TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
* *
168225 TATATCATTAGAGGTATGTCAGACTATGTATGTTT-
1 TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
* * * *
168260 TATATCATTGGAGGTATATCAGACTTTGTATGTATC
1 TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
*
168296 TATGTCAATGGAGGTATGTCAGAC----TATGTTTC
1 TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
* * * * * *
168328 TATGTCATTTGAGGGATGTCAGAATTTGTATGTATA
1 TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
*
168364 TATGTCATTGGAGGTATGTCAGACTATGTCTAGTTT-
1 TATGTCATTGGAGGTATGTCAGACTATGTAT-GTTTC
* * *
168400 TATATCATTGGAGGTATGTCAGATTATGTTTGTTTC
1 TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
168436 TATGTCATTGGAG
1 TATGTCATTGGAG
168449 ACATGTCTAA
Statistics
Matches: 247, Mismatches: 33, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
31 19 0.08
32 33 0.13
33 2 0.01
34 2 0.01
35 42 0.17
36 146 0.59
37 3 0.01
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (36 bp):
TATGTCATTGGAGGTATGTCAGACTATGTATGTTTC
Found at i:170026 original size:55 final size:55
Alignment explanation
Indices: 169935--170099 Score: 294
Period size: 55 Copynumber: 3.0 Consensus size: 55
169925 CATCGTGCAC
* *
169935 TGTCGTGTTAGGAGATCGTGCAGTTGACCTTTTCCCGTATAGCGGCGTTGTTCTT
1 TGTCGTGTTAGGAGATCGTGCAGTTGGCCTTGTCCCGTATAGCGGCGTTGTTCTT
169990 TGTCGTGTTAGGAGATCGTGCAGTTGGCCTTGTCCCGTATAGCGGCGTTGTTCTT
1 TGTCGTGTTAGGAGATCGTGCAGTTGGCCTTGTCCCGTATAGCGGCGTTGTTCTT
* *
170045 TGTCATGCTAGGAGATCGTGCAGTTGGCCTTGTCCCGTATAGCGGCGTTGTTCTT
1 TGTCGTGTTAGGAGATCGTGCAGTTGGCCTTGTCCCGTATAGCGGCGTTGTTCTT
170100 GCGTTTGTCA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 106 1.00
ACGTcount: A:0.12, C:0.21, G:0.31, T:0.36
Consensus pattern (55 bp):
TGTCGTGTTAGGAGATCGTGCAGTTGGCCTTGTCCCGTATAGCGGCGTTGTTCTT
Found at i:170311 original size:50 final size:52
Alignment explanation
Indices: 170221--170323 Score: 156
Period size: 50 Copynumber: 2.0 Consensus size: 52
170211 GATAGAATGG
*
170221 AATTTAAAAAGAAAGAAATGAAGGAATCGTTATCGGAAAGTTACAAATGTGA
1 AATTTAAAAAGAAAGAAATGAAGGAATCGTTATCGAAAAGTTACAAATGTGA
* **
170273 AATTTAAAAAGAAAGATA-G-AGGAATCGTTATCGAAAAGTTATTAATGTGA
1 AATTTAAAAAGAAAGAAATGAAGGAATCGTTATCGAAAAGTTACAAATGTGA
170323 A
1 A
170324 TTCATGCTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
50 29 0.62
51 1 0.02
52 17 0.36
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (52 bp):
AATTTAAAAAGAAAGAAATGAAGGAATCGTTATCGAAAAGTTACAAATGTGA
Found at i:174740 original size:200 final size:200
Alignment explanation
Indices: 174397--174793 Score: 794
Period size: 200 Copynumber: 2.0 Consensus size: 200
174387 GGCGTGGTTT
174397 CTTCCTGTCCAATTAAAAGCAGAACATTCATTGGTATATTGTCGCTCTTAACATGCTATCTAATA
1 CTTCCTGTCCAATTAAAAGCAGAACATTCATTGGTATATTGTCGCTCTTAACATGCTATCTAATA
174462 AATTTTCTGGGTGTTTCAATTAAAATGATTTCAATACTTAGCTTTGATATGAAGAAATGGACACA
66 AATTTTCTGGGTGTTTCAATTAAAATGATTTCAATACTTAGCTTTGATATGAAGAAATGGACACA
174527 TACCCTAAGTAAGAGCTTTCCCTGCATTCTCTGAAATACACATATATTCATTCGAAAACCCTGAT
131 TACCCTAAGTAAGAGCTTTCCCTGCATTCTCTGAAATACACATATATTCATTCGAAAACCCTGAT
174592 TCTTC
196 TCTTC
174597 CTTCCTGTCCAATTAAAAGCAGAACATTCATTGGTATATTGTCGCTCTTAACATGCTATCTAATA
1 CTTCCTGTCCAATTAAAAGCAGAACATTCATTGGTATATTGTCGCTCTTAACATGCTATCTAATA
174662 AATTTTCTGGGTGTTTCAATTAAAATGATTTCAATACTTAGCTTTGATATGAAGAAATGGACACA
66 AATTTTCTGGGTGTTTCAATTAAAATGATTTCAATACTTAGCTTTGATATGAAGAAATGGACACA
174727 TACCCTAAGTAAGAGCTTTCCCTGCATTCTCTGAAATACACATATATTCATTCGAAAACCCTGAT
131 TACCCTAAGTAAGAGCTTTCCCTGCATTCTCTGAAATACACATATATTCATTCGAAAACCCTGAT
174792 TC
196 TC
174794 CTTATTCAAC
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 197 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (200 bp):
CTTCCTGTCCAATTAAAAGCAGAACATTCATTGGTATATTGTCGCTCTTAACATGCTATCTAATA
AATTTTCTGGGTGTTTCAATTAAAATGATTTCAATACTTAGCTTTGATATGAAGAAATGGACACA
TACCCTAAGTAAGAGCTTTCCCTGCATTCTCTGAAATACACATATATTCATTCGAAAACCCTGAT
TCTTC
Found at i:189319 original size:17 final size:17
Alignment explanation
Indices: 189297--189686 Score: 512
Period size: 17 Copynumber: 23.0 Consensus size: 17
189287 TGACATACCT
*
189297 TGTACATACCCCGTATA
1 TGTACATACCCCATATA
189314 TGTACATACCCCATATA
1 TGTACATACCCCATATA
*
189331 TGTACATACCCAATATA
1 TGTACATACCCCATATA
*
189348 CGTACATACCCCATATA
1 TGTACATACCCCATATA
*
189365 TGTACATACCCAATATA
1 TGTACATACCCCATATA
*
189382 CGTACATACCCCATATA
1 TGTACATACCCCATATA
*
189399 TGTACATACCCAATATA
1 TGTACATACCCCATATA
*
189416 CGTACATACCCCATATA
1 TGTACATACCCCATATA
*
189433 TGTACATACCCAATATA
1 TGTACATACCCCATATA
*
189450 CGTACATACCCCATATA
1 TGTACATACCCCATATA
* *
189467 TGTACATACCACGTATA
1 TGTACATACCCCATATA
* *
189484 TGTACATATCCCGTATA
1 TGTACATACCCCATATA
*
189501 TGTACATACCCCATACA
1 TGTACATACCCCATATA
189518 TGTACATACCCCATATA
1 TGTACATACCCCATATA
* *
189535 TTTACATACCCC-TAGA
1 TGTACATACCCCATATA
* *
189551 TGTACAAACCCCATCTA
1 TGTACATACCCCATATA
*
189568 CGTACATACCCCATATA
1 TGTACATACCCCATATA
* *
189585 TATACATACCCCATACA
1 TGTACATACCCCATATA
*
189602 TGTACATACCCCATAGA
1 TGTACATACCCCATATA
*
189619 TATACATACCCCATATA
1 TGTACATACCCCATATA
* *
189636 CGTACATACCCCGTATA
1 TGTACATACCCCATATA
* * *
189653 TATACATACCACATACA
1 TGTACATACCCCATATA
*
189670 TGTACATACCCCGTATA
1 TGTACATACCCCATATA
189687 ACTCCCCGAT
Statistics
Matches: 319, Mismatches: 53, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
16 13 0.04
17 306 0.96
ACGTcount: A:0.36, C:0.30, G:0.07, T:0.27
Consensus pattern (17 bp):
TGTACATACCCCATATA
Found at i:190266 original size:49 final size:48
Alignment explanation
Indices: 190112--190431 Score: 385
Period size: 49 Copynumber: 6.6 Consensus size: 48
190102 TAGTCATTTA
* * *
190112 ACCCTTACCCTGTCTCTGATATCAAGG-CATAGATTTT-GAGGTTTTGTT
1 ACCCTTACCCTGTTTCTGATGTCGAGGTC-TAG-TTTTAGAGGTTTTGTT
* * * *
190160 ACCCTTATCTTGTTTCTGATATCGAGGCCTA-TTTTAGAGGTTTTGTT
1 ACCCTTACCCTGTTTCTGATGTCGAGGTCTAGTTTTAGAGGTTTTGTT
*
190207 ACCCTTACCCTGTTTCTGATGTCGAGGGTCTAGTTTTAGAGGCTTTGTT
1 ACCCTTACCCTGTTTCTGATGTCGA-GGTCTAGTTTTAGAGGTTTTGTT
* * * * * *
190256 ACTCTAACCCTGTTTCTGATATCGAGGCCTAGTTTTCGAGGTTTTTTTT
1 ACCCTTACCCTGTTTCTGATGTCGAGGTCTAGTTTTAGAGG-TTTTGTT
* * * *
190305 ACCCTTACCCTGTTTCCGATGTCGAGGGTCTGGTTTAAGAAGTTTTGTT
1 ACCCTTACCCTGTTTCTGATGTCGA-GGTCTAGTTTTAGAGGTTTTGTT
*
190354 ACCCTTACCCTGTCTCTGATGTCGAAGGTCTAGTTTTAGAGGTTTTGTT
1 ACCCTTACCCTGTTTCTGATGTCG-AGGTCTAGTTTTAGAGGTTTTGTT
*
190403 ACCCTTACCCTGTTTCTGATGTCAAGGTC
1 ACCCTTACCCTGTTTCTGATGTCGAGGTC
190432 CGGATTGTGC
Statistics
Matches: 232, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
46 4 0.02
47 33 0.14
48 49 0.21
49 134 0.58
50 12 0.05
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (48 bp):
ACCCTTACCCTGTTTCTGATGTCGAGGTCTAGTTTTAGAGGTTTTGTT
Found at i:213376 original size:127 final size:127
Alignment explanation
Indices: 213214--213471 Score: 493
Period size: 127 Copynumber: 2.0 Consensus size: 127
213204 TATTGGTATT
213214 TAAA-AAAAAAAAAATGAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGGA
1 TAAATAAAAAAAAAATGAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGGA
213278 ATCTATCGCATTTGTACAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCA
66 ATCTATCGCATTTGTACAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCA
213340 TAAATNAAAAAAAAAA-GAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGG
1 TAAAT-AAAAAAAAAATGAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGG
213404 AATCTATCGCATTTGTACAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCA
65 AATCTATCGCATTTGTACAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCA
213467 TAAAT
1 TAAAT
213472 CATTTTAAAT
Statistics
Matches: 130, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
126 4 0.03
127 116 0.89
128 10 0.08
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (127 bp):
TAAATAAAAAAAAAATGAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGGA
ATCTATCGCATTTGTACAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCA
Found at i:213638 original size:155 final size:155
Alignment explanation
Indices: 213356--213661 Score: 612
Period size: 155 Copynumber: 2.0 Consensus size: 155
213346 AAAAAAAAAA
213356 GAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGGAATCTATCGCATTTGTA
1 GAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGGAATCTATCGCATTTGTA
213421 CAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCATAAATCATTTTAAATAAAA
66 CAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCATAAATCATTTTAAATAAAA
213486 GTGCACATTCAATCTCAATATAAAT
131 GTGCACATTCAATCTCAATATAAAT
213511 GAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGGAATCTATCGCATTTGTA
1 GAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGGAATCTATCGCATTTGTA
213576 CAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCATAAATCATTTTAAATAAAA
66 CAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCATAAATCATTTTAAATAAAA
213641 GTGCACATTCAATCTCAATAT
131 GTGCACATTCAATCTCAATAT
213662 TGTTGATAAA
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 151 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (155 bp):
GAATAATTGGGTGGTCATGCATATATCTATTGTTTATAAAATCCATGGAATCTATCGCATTTGTA
CAAATTATTTAGGTCAAGGAACTCTGAGCATACTCGACTAAGATCATAAATCATTTTAAATAAAA
GTGCACATTCAATCTCAATATAAAT
Found at i:218484 original size:2 final size:2
Alignment explanation
Indices: 218477--218510 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
218467 TTAGTTTTCA
218477 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
218511 AGTGTTAGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:221863 original size:12 final size:12
Alignment explanation
Indices: 221816--221854 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
221806 AAGTGGGACA
*
221816 GACAGACGGACG
1 GACAGACAGACG
* *
221828 GGCGGACAGACG
1 GACAGACAGACG
221840 GACAGACAGACG
1 GACAGACAGACG
221852 GAC
1 GAC
221855 TGACGGACGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.26, G:0.41, T:0.00
Consensus pattern (12 bp):
GACAGACAGACG
Found at i:226525 original size:17 final size:15
Alignment explanation
Indices: 226478--226523 Score: 92
Period size: 15 Copynumber: 3.1 Consensus size: 15
226468 TTTATGTACT
226478 TGAACTATATATATA
1 TGAACTATATATATA
226493 TGAACTATATATATA
1 TGAACTATATATATA
226508 TGAACTATATATATA
1 TGAACTATATATATA
226523 T
1 T
226524 ATATATACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
TGAACTATATATATA
Found at i:233366 original size:2 final size:2
Alignment explanation
Indices: 233359--233446 Score: 155
Period size: 2 Copynumber: 45.5 Consensus size: 2
233349 ACCTACTAAA
233359 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT -T CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
233399 C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
233440 CT CT CT C
1 CT CT CT C
233447 CTAAGATATA
Statistics
Matches: 83, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 80 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:236937 original size:166 final size:166
Alignment explanation
Indices: 236663--237621 Score: 1386
Period size: 166 Copynumber: 5.8 Consensus size: 166
236653 GTGAATATGC
* * * * * * * *
236663 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATAAATCCCATA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * * *
236728 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATTAATAGTTGCTGAGA
66 ATATGGCATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
236793 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
131 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
* * * * * *
236829 AAAATAAACAAAGTCTTAATTTAACACGAAGTTGACGTCCGATTGGTACAAAAATATTTCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
*
236894 ATATGGCATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCCGAGA
66 ATATGGCATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
236959 AATCTTTGACGGAAATTTGTTTGAAAAATTTGGCTA
131 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
* * * * *
236995 AAAATAAGCAAAGTCTTCATTTAACAGGAAGTTAACTTCCGATTGATACAACAATATATCCCACA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* *
237060 ATATGGGATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGTGATAAATAGTTGCTGAGA
66 ATATGGCATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
** *
237125 AATCTTTGACAAAAATTTGTTTGAAAACTTTGGCTA
131 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
* * *
237161 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACTTCCGATTGATACAAAAATATATCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * * *
237226 ATATGGCATGCCAAAACAAATATTGTGTTAAAATTTTAAGCATCTGCGATAAATAGTTGCTGAGA
66 ATATGGCATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
237291 AATCTTTGACGGAAATTTGTTTCAAAATTTTGGCTA
131 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
* * * *
237327 AAAATAAGCAAAG-CACTCATTAAACAGGAAGTTGACGTCTGATTGGTACAAAAATATCTCCCAC
1 AAAATAAGCAAAGTC-GTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* * * *
237391 GATATGACATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGTGATAAATACTTGCTGAG
65 AATATGGCATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* *
237456 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
130 AAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCT-A
* *
237494 AAAAAAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCATA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * *
237559 ATATGGCATGCCT-TAACAAACA--CTGTAAAAATTTCAAGTATCTGCGATAAATAGTTGCTGAG
66 ATATGGCATGCCTAT-ACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
237621 A
130 A
237622 TAAATGCGAC
Statistics
Matches: 711, Mismatches: 78, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
165 38 0.05
166 597 0.84
167 75 0.11
168 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (166 bp):
AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
ATATGGCATGCCTATACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
Found at i:237654 original size:4 final size:4
Alignment explanation
Indices: 237652--237690 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
237642 GTTACGGACG
* * *
237652 GACA GACA GACA GACA GACA GACG GACG GACG GACA GAC
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GAC
237691 TGTCACACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.41, C:0.26, G:0.33, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:243894 original size:101 final size:100
Alignment explanation
Indices: 243773--243981 Score: 337
Period size: 101 Copynumber: 2.1 Consensus size: 100
243763 AAATGATAAC
* *
243773 AATGTTTAGAAAATGTAAACATTTCTTCGAAATGTTTTTAGAAAATGTTATTATAACGTAACAAA
1 AATGTTTTGAAAATGTAAACATTTCTTCGAAACGTTTTTAGAAAATGTTATTATAACGTAA-AAA
* *
243838 AACCACACAGATTTACGTTGTAATAACGTTTTTAAA
65 AACCACACAGATTCACGTTGTAATAACGTTTCTAAA
* * *
243874 AATGTTTTGAACATGTAAACATTTCTTGGAAACGTTTTTAGAAAATGTTATTCTAACGTAAAAAA
1 AATGTTTTGAAAATGTAAACATTTCTTCGAAACGTTTTTAGAAAATGTTATTATAACGTAAAAAA
*
243939 CCCACACAGATTCACGTTGTAATAACGTTTCTAAA
66 ACCACACAGATTCACGTTGTAATAACGTTTCTAAA
243974 AATGTTTT
1 AATGTTTT
243982 AGTAACATTT
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
100 44 0.44
101 56 0.56
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (100 bp):
AATGTTTTGAAAATGTAAACATTTCTTCGAAACGTTTTTAGAAAATGTTATTATAACGTAAAAAA
ACCACACAGATTCACGTTGTAATAACGTTTCTAAA
Found at i:245412 original size:14 final size:14
Alignment explanation
Indices: 245395--245422 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
245385 AAAATGCCCC
245395 GAGAATCAGAAAAA
1 GAGAATCAGAAAAA
245409 GAGAATCAGAAAAA
1 GAGAATCAGAAAAA
245423 CTACATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.21, T:0.07
Consensus pattern (14 bp):
GAGAATCAGAAAAA
Found at i:245492 original size:2 final size:2
Alignment explanation
Indices: 245487--245531 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
245477 TCCCTCTCTA
245487 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
245529 AC A
1 AC A
245532 TAAAACATCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:248277 original size:2 final size:2
Alignment explanation
Indices: 248270--248300 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
248260 ACATTGCACA
*
248270 TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
248301 NATCTATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:248319 original size:179 final size:178
Alignment explanation
Indices: 248122--248479 Score: 698
Period size: 179 Copynumber: 2.0 Consensus size: 178
248112 ATGTATTTCT
248122 TATCTATATCTAAGTTATATCTATAAAAAAAAACTACAATTTAACAATTTATATACACATCAAAT
1 TATCTATATCTAAGTTATATCTATAAAAAAAAACTACAATTTAACAATTTATATACACATCAAAT
248187 CAAAATTAACATTTGATTTTATGAAAGCAAAAATTGCAGCATGTATTATACAGATACATGTAAAA
66 CAAAATTAACATTTGATTTTATGAAAGCAAAAATTGCAGCATGTATTATACAGATACATGTAAAA
248252 GTCAACATACATTGCACATCTCTCTCCCTCTCTCTCTCTCTCTCTCTC
131 GTCAACATACATTGCACATCTCTCTCCCTCTCTCTCTCTCTCTCTCTC
248300 TNATCTATATCTAAGTTATATCTATAAAAAAAAACTACAATTTAACAATTTATATACACATCAAA
1 T-ATCTATATCTAAGTTATATCTATAAAAAAAAACTACAATTTAACAATTTATATACACATCAAA
248365 TCAAAATTAACATTTGATTTTATGAAAGCAAAAATTGCAGCATGTATTATACAGATACATGTAAA
65 TCAAAATTAACATTTGATTTTATGAAAGCAAAAATTGCAGCATGTATTATACAGATACATGTAAA
*
248430 AGTCAACATACATTGCACATCTCTCTCCTTCTCTCTCTCTCTCTCTCTC
130 AGTCAACATACATTGCACATCTCTCTCCCTCTCTCTCTCTCTCTCTCTC
248479 T
1 T
248480 CTCTCTCTCT
Statistics
Matches: 178, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
178 1 0.01
179 177 0.99
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (178 bp):
TATCTATATCTAAGTTATATCTATAAAAAAAAACTACAATTTAACAATTTATATACACATCAAAT
CAAAATTAACATTTGATTTTATGAAAGCAAAAATTGCAGCATGTATTATACAGATACATGTAAAA
GTCAACATACATTGCACATCTCTCTCCCTCTCTCTCTCTCTCTCTCTC
Found at i:248456 original size:2 final size:2
Alignment explanation
Indices: 248449--248496 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
248439 ACATTGCACA
248449 TC TC TC TC -C T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
248489 TC TC TC TC
1 TC TC TC TC
248497 AGTAAAACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:255837 original size:28 final size:28
Alignment explanation
Indices: 255791--255865 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
255781 GAAACAAATG
**
255791 TAGCAATCAATGATGTGTAAACTAAAGA
1 TAGCAATCAATGACATGTAAACTAAAGA
* * * *
255819 TAGCAATCAATGACATGTAAATTGATGG
1 TAGCAATCAATGACATGTAAACTAAAGA
*
255847 TAGCAATCACTGACATGTA
1 TAGCAATCAATGACATGTA
255866 TGACGAAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (28 bp):
TAGCAATCAATGACATGTAAACTAAAGA
Found at i:256821 original size:12 final size:13
Alignment explanation
Indices: 256798--256827 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
256788 TTAGAAAACA
256798 TTTGTGTTTTTTT
1 TTTGTGTTTTTTT
*
256811 TTTGTTTTTTTTT
1 TTTGTGTTTTTTT
256824 TTTG
1 TTTG
256828 GGGGGGGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (13 bp):
TTTGTGTTTTTTT
Found at i:257166 original size:28 final size:28
Alignment explanation
Indices: 257128--257236 Score: 96
Period size: 28 Copynumber: 3.9 Consensus size: 28
257118 TGACGGGTTG
* *
257128 AACAAAGGTAGCAATCAATGACGTGTAAA
1 AACAAAAGTAGCAATCAATGACATG-AAA
*
257157 AA-AAAAGTAGCAATCCATGACATGAAA
1 AACAAAAGTAGCAATCAATGACATGAAA
* * *
257184 AACGAAGGTAGCAATCAATGTCAT-AAA
1 AACAAAAGTAGCAATCAATGACATGAAA
** * *
257211 TAATGAAAGTAGCAAACAATGGCATG
1 -AACAAAAGTAGCAATCAATGACATG
257237 TTAAACGAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
27 8 0.12
28 56 0.85
29 2 0.03
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17
Consensus pattern (28 bp):
AACAAAAGTAGCAATCAATGACATGAAA
Found at i:257528 original size:28 final size:28
Alignment explanation
Indices: 257491--257557 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
257481 CAGAACATGT
*
257491 AAATGAAGGTGGCAA-CTAATGACAGGTA
1 AAATGAAGGTAGCAATC-AATGACAGGTA
** *
257519 ATTTGAAGGTAGCAATCAATGACATGTA
1 AAATGAAGGTAGCAATCAATGACAGGTA
257547 AAATGAAGGTA
1 AAATGAAGGTA
257558 AAGATGAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.22
Consensus pattern (28 bp):
AAATGAAGGTAGCAATCAATGACAGGTA
Found at i:257626 original size:28 final size:28
Alignment explanation
Indices: 257576--257629 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
257566 GGACTCAAAG
* * * *
257576 CATATTAAATGAAGGTGGGAATCAATAA
1 CATATAAAATGAAAGTAGCAATCAATAA
257604 CATATAAAATGAAAGTAGCAATCAAT
1 CATATAAAATGAAAGTAGCAATCAAT
257630 GACAATTGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (28 bp):
CATATAAAATGAAAGTAGCAATCAATAA
Found at i:257911 original size:84 final size:83
Alignment explanation
Indices: 257739--258037 Score: 413
Period size: 84 Copynumber: 3.6 Consensus size: 83
257729 TTAAAAGTAT
* * * * * *
257739 CAATAAATGACACGTCAAATGAAGGTAGCAATCAATGACTTGTTACAAAAGAAAGCGATAAATCA
1 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCTA-AAAA-AAAACGATAAATCA
* *
257804 TTGACCACATGTTAAACTAA
64 TTGACCACATGTTCACCTAA
257824 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCTAAAAAAAGAACGATAAATCAT
1 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCTAAAAAAA-AACGATAAATCAT
*
257889 TGACCATATGTTCACCTAA
65 TGACCACATGTTCACCTAA
*
257908 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCT--AAAACAACGATAAATCATT
1 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCTAAAAAAAAACGATAAATCATT
257971 GACCACATGTTCACCTAA
66 GACCACATGTTCACCTAA
* ** * * *
257989 CAATCAAAGACATGTAAAATGAAGAAAACAATTAATGACATGTTAAAAA
1 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCTAAAAA
258038 GGGTAGCAAT
Statistics
Matches: 194, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
81 69 0.36
82 4 0.02
83 5 0.03
84 76 0.39
85 40 0.21
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.22
Consensus pattern (83 bp):
CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCTAAAAAAAAACGATAAATCATT
GACCACATGTTCACCTAA
Found at i:258049 original size:81 final size:80
Alignment explanation
Indices: 257739--258049 Score: 331
Period size: 81 Copynumber: 3.8 Consensus size: 80
257729 TTAAAAGTAT
* * * *
257739 CAATAAATGACACGTCAAATGAAGGTAGCAATCAATGACTTGTTACAAAAGAAAGCGATA-AATC
1 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGTT---AAA-AAAG-G-TAGAATC
* *
257803 ATTGACCACATGTTAAACTAA
60 ATTGACCACATGTTCACCTAA
*
257824 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCTAAAAAAAGAACGATA-AATCA
1 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATG-TTAAAAAAG---G-TAGAATCA
*
257888 TTGACCATATGTTCACCTAA
61 TTGACCACATGTTCACCTAA
* *
257908 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGCTAAAACAACGATA-AATCATTG
1 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGTTAAAA-AA-GGTAGAATCATTG
257972 ACCACATGTTCACCTAA
64 ACCACATGTTCACCTAA
* ** * * *
257989 CAATCAAAGACATGTAAAATGAAGAAAACAATTAATGACATGTTAAAAAGGGTAGCAATCA
1 CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGTTAAAAAAGGTAG-AATCA
258050 ATGCATGTAA
Statistics
Matches: 199, Mismatches: 20, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.02
80 1 0.01
81 73 0.37
82 4 0.02
83 7 0.04
84 71 0.36
85 39 0.20
86 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (80 bp):
CAATCAATGACATGTAAAATGAAGGTAGCAATCAATGACATGTTAAAAAAGGTAGAATCATTGAC
CACATGTTCACCTAA
Found at i:258127 original size:31 final size:31
Alignment explanation
Indices: 258092--258201 Score: 139
Period size: 31 Copynumber: 3.5 Consensus size: 31
258082 ATGTAAAGAT
* * * *
258092 GAAGGTATTTATCAATGAAATGATGTTGAAC
1 GAAGGTAGTAATCAATGTAATGATGTAGAAC
* *
258123 GAAGGTAGTAATCAATGTAATTATGAAGAAC
1 GAAGGTAGTAATCAATGTAATGATGTAGAAC
* *
258154 GTAGGTAGCAATCAATGTAATGATGTAGAAC
1 GAAGGTAGTAATCAATGTAATGATGTAGAAC
*
258185 GAAGGTAGCAATCAATG
1 GAAGGTAGTAATCAATG
258202 AAAAGTGCAA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.26
Consensus pattern (31 bp):
GAAGGTAGTAATCAATGTAATGATGTAGAAC
Found at i:259903 original size:13 final size:13
Alignment explanation
Indices: 259885--259912 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
259875 TTGGCTGCAC
259885 CAAAGGTCAAGGT
1 CAAAGGTCAAGGT
259898 CAAAGGTCAAGGT
1 CAAAGGTCAAGGT
259911 CA
1 CA
259913 TCTGAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (13 bp):
CAAAGGTCAAGGT
Found at i:260294 original size:7 final size:6
Alignment explanation
Indices: 260275--260345 Score: 81
Period size: 7 Copynumber: 11.2 Consensus size: 6
260265 TTTTTTAGGT
260275 TTGACC TTGACC TCTGACC TTGACC TCTGACC TTGACC TTTGACC TTTGACC
1 TTGACC TTGACC T-TGACC TTGACC T-TGACC TTGACC -TTGACC -TTGACC
*
260327 -TGACA TTGACC TTTGACC T
1 TTGACC TTGACC -TTGACC T
260346 CTTAGAACTA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
5 4 0.07
6 23 0.40
7 31 0.53
ACGTcount: A:0.17, C:0.32, G:0.15, T:0.35
Consensus pattern (6 bp):
TTGACC
Found at i:260294 original size:13 final size:13
Alignment explanation
Indices: 260276--260345 Score: 90
Period size: 13 Copynumber: 5.5 Consensus size: 13
260266 TTTTTAGGTT
260276 TGACCTTGACCTC
1 TGACCTTGACCTC
260289 TGACCTTGACCTC
1 TGACCTTGACCTC
*
260302 TGACCTTGACCTT
1 TGACCTTGACCTC
260315 TGACCTTTGA-C-C
1 TGACC-TTGACCTC
* *
260327 TGACATTGACCTT
1 TGACCTTGACCTC
260340 TGACCT
1 TGACCT
260346 CTTAGAACTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
11 4 0.08
12 5 0.10
13 36 0.73
14 4 0.08
ACGTcount: A:0.17, C:0.33, G:0.16, T:0.34
Consensus pattern (13 bp):
TGACCTTGACCTC
Found at i:262321 original size:8 final size:8
Alignment explanation
Indices: 262305--262413 Score: 110
Period size: 8 Copynumber: 13.6 Consensus size: 8
262295 AAAAAAGTGT
*
262305 GACGGACG
1 GACGCACG
262313 GACGCACG
1 GACGCACG
*
262321 GACCCACG
1 GACGCACG
*
262329 GATGCACG
1 GACGCACG
*
262337 GACCCACG
1 GACGCACG
262345 GACGCACG
1 GACGCACG
*
262353 GACCCACG
1 GACGCACG
*
262361 GACACACG
1 GACGCACG
* *
262369 GACCCATG
1 GACGCACG
*
262377 GACACACG
1 GACGCACG
*
262385 GACCCACG
1 GACGCACG
*
262393 GACACACG
1 GACGCACG
*
262401 GACGGACG
1 GACGCACG
262409 GACGC
1 GACGC
262414 CCATCATTTC
Statistics
Matches: 83, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 83 1.00
ACGTcount: A:0.28, C:0.39, G:0.32, T:0.02
Consensus pattern (8 bp):
GACGCACG
Found at i:262335 original size:16 final size:16
Alignment explanation
Indices: 262310--262413 Score: 145
Period size: 16 Copynumber: 6.5 Consensus size: 16
262300 AGTGTGACGG
262310 ACGGACGCACGGACCC
1 ACGGACGCACGGACCC
*
262326 ACGGATGCACGGACCC
1 ACGGACGCACGGACCC
262342 ACGGACGCACGGACCC
1 ACGGACGCACGGACCC
*
262358 ACGGACACACGGACCC
1 ACGGACGCACGGACCC
* *
262374 ATGGACACACGGACCC
1 ACGGACGCACGGACCC
* **
262390 ACGGACACACGGACGG
1 ACGGACGCACGGACCC
262406 ACGGACGC
1 ACGGACGC
262414 CCATCATTTC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 80 1.00
ACGTcount: A:0.28, C:0.39, G:0.31, T:0.02
Consensus pattern (16 bp):
ACGGACGCACGGACCC
Found at i:264391 original size:67 final size:67
Alignment explanation
Indices: 264283--264411 Score: 197
Period size: 67 Copynumber: 1.9 Consensus size: 67
264273 AGGATGCTTT
* *
264283 TACACAAGTTTCAGCTTTCCTGACTGATTAGTTTCCGAGAAGAAGATTTTTAAAGATTTACTCTA
1 TACACAAGTGTCAGCTTGCCTGACTGATTAGTTTCCGAGAAGAAGATTTTTAAAGATTTACTCTA
264348 TA
66 TA
* * *
264350 TACACAAGTGTCAGCTCTGCC-GGCTGATTTGTTTCTGAGAAGAAGATTTTTAAAGATTTACT
1 TACACAAGTGTCAGCT-TGCCTGACTGATTAGTTTCCGAGAAGAAGATTTTTAAAGATTTACT
264412 ATTTATATTC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 53 0.95
68 3 0.05
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (67 bp):
TACACAAGTGTCAGCTTGCCTGACTGATTAGTTTCCGAGAAGAAGATTTTTAAAGATTTACTCTA
TA
Found at i:264724 original size:166 final size:164
Alignment explanation
Indices: 264351--265402 Score: 1272
Period size: 166 Copynumber: 6.4 Consensus size: 164
264341 TACTCTATAT
* * *
264351 ACACAAGTGTCAGCTCTGCC-GGCTGATTTGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATT
1 ACACAAGTTTCAGCT-TTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATT
* **
264415 TATATTCCTATGTAAAACTTCGACCCCACATTGTGGCCCTACCCTACCCCCAGGGG-C-TAGTAT
65 TATATTCCTATGT-AAACTTCGACCCC-CATTGTGGCCCCACCCTACCCCTGGGGGTCAT-G-AT
* *
264478 TTTCACAA-TTTGAATTTACACTACCTGAGGATGCTTCC
126 TTTCACAACTTTGAATCTACACTACCGGAGGATGCTTCC
* * * * * *
264516 ACAAAAGTTTCAGCTTTGCC-GGCTGATTAGTTTTTAAGAAGAAGATTTTTAGAGATTTACTCTA
1 ACACAAGTTTCAGCTTT-CCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATT
* * *
264580 TATATTCCTATGATAAACTTTGACACCCCATTGTGGCCCCACCATACCCCTGGGGGCCATGATTT
65 TATATTCCTATG-TAAACTTCGAC-CCCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTT
* *
264645 TCACAATTTTGAATCTACACTACCGGTGGATGCTTCC
128 TCACAACTTTGAATCTACACTACCGGAGGATGCTTCC
*
264682 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAGAGATTTACTATTT
1 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATTT
* *
264747 ATATTCCTACAT-TAAACTTTGATCCCCCATTGTGGCCCCACCCTA-CACTGAGGGGTCATGATT
66 ATATTCCT--ATGTAAACTTCGA-CCCCCATTGTGGCCCCACCCTACCCCTG-GGGGTCATGATT
* * *
264810 TTCACAACTTTGAATCTACACTACCTGATGATGCTTTC
127 TTCACAACTTTGAATCTACACTACCGGAGGATGCTTCC
* * * *
264848 ATACAAGTTTCAGCTTTCCTGGCTGAGTAGTTTCTGAGAAGAAGATTTTTAGAGATTAACTATTT
1 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATTT
* * * *
264913 ATATTCCTATGTTAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGATAACGATTTT
66 ATATTCCTATG-TAAACTTCGA-CCCCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTT
* * * * *
264978 CACAATTTTGAATTTACACTACCTGATGATGCTTTC
129 CACAACTTTGAATCTACACTACCGGAGGATGCTTCC
*
265014 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACTATAT
1 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATTT
* * * *
265076 ATATTCCTATGTACAACTTCGACCCCCCATTGTGGCCCTATCCTGCCCC-CGGGGTCATGATTTT
66 ATATTCCTATGTA-AACTTCGA-CCCCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTT
* * *
265140 CACAACTTTGAATCTACATTACCTTTCCTGAGGATTCTTCC
129 CACAACTTTGAATCTAC---A-C-TACCGGAGGATGCTTCC
* * *
265181 ACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAGATATAC--TCT
1 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATTT
*
265244 ATATTCATATGTTAAACTTCGACACCCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTT
66 ATATTCCTATG-TAAACTTCGAC-CCCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTT
* *
265309 CACAACTTTGTATCTACACTACCTGAGGATGCTTCC
129 CACAACTTTGAATCTACACTACCGGAGGATGCTTCC
* *
265345 ACACAAGTTTCAGCTTTCCT-GCT-CTTATGGTTCATGAGAAGAAGATTTTTGAAA-ATTT
1 ACACAAGTTTCAGCTTTCCTGGCTGATTA-GTTTC-TGAGAAGAAGATTTTT-AAAGATTT
265403 CTCAATATTT
Statistics
Matches: 783, Mismatches: 75, Indels: 59
0.85 0.08 0.06
Matches are distributed among these distances:
162 31 0.04
163 72 0.09
164 58 0.07
165 119 0.15
166 353 0.45
167 53 0.07
168 44 0.06
169 33 0.04
170 20 0.03
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (164 bp):
ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATTT
ATATTCCTATGTAAACTTCGACCCCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTTCA
CAACTTTGAATCTACACTACCGGAGGATGCTTCC
Found at i:265314 original size:497 final size:495
Alignment explanation
Indices: 264351--265365 Score: 1442
Period size: 497 Copynumber: 2.0 Consensus size: 495
264341 TACTCTATAT
* * * * *
264351 ACACAAGTGTCAGCTCTGCC-GGCTGATTTGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATT
1 ACACAAGTTTCAGCT-TTCCTGGCTGAGTAGTTTCTGAGAAGAAGATTTTTAAAGATTAACTATT
* *
264415 TATATTCCTATGTAAAACTTCGACCCCACATTGTGGCCCTACCCTACCCCCAGGGGCTAGTATTT
65 TATATTCCTATGTAAAACTTCGACCCCACATTGTGGCCCCACCCTACCCCCAGGGGATAGTATTT
264480 TCACAATTTGAATTTACACTACCTGAGGATGCTTCCACAAAAGTTTCAGCTTTGCCGGCTGATTA
130 TCACAATTTGAATTTACACTACCTGAGGATGCTTCCACAAAAGTTTCAGCTTTGCCGGCTGATTA
* * * *
264545 GTTTTTAAGAAGAAGATTTTTAGAGATTTACTCTATATATTCCTATGATAAACTTTGACACCCCA
195 GTTTCT-AGAAGAAGATTTTTAAAGATTTACTATATATATTCCTATGATAAACTTCGACACCCCA
* * *
264610 TTGTGGCCCCACCATACCCCTGGGGGCCATGATTTTCACAATTTTGAATCTACACTACCGGTGGA
259 TTGTGGCCCCACCATACCCCTCGGGGCCATGATTTTCACAACTTTGAATCTACACTACCGGAGGA
* * *
264675 TGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAGAGATTT
324 TGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAGATAT
* * *
264740 ACTATTTATATTCCTACATTAAACTTTGATCCCCCATTGTGGCCCCACCCTACACTGAGGGGTCA
389 AC-ATCTATATTCATACATTAAACTTCGATCCCCCATTGTGGCCCCACCCTACACTGAGGGGTCA
* *
264805 TGATTTTCACAACTTTGAATCTACACTACCTGATGATGCTTTC
453 TGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCC
* *
264848 ATACAAGTTTCAGCTTTCCTGGCTGAGTAGTTTCTGAGAAGAAGATTTTTAGAGATTAACTATTT
1 ACACAAGTTTCAGCTTTCCTGGCTGAGTAGTTTCTGAGAAGAAGATTTTTAAAGATTAACTATTT
* *
264913 ATATTCCTATGTTAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCC-GGGGATAACG-ATT
66 ATATTCCTATGTAAAACTTCGACCCCACATTGTGGCCCCACCCTACCCCCAGGGGAT-A-GTATT
* * *
264976 TTCACAATTTTGAATTTACACTACCTGATGATGCTTTCACACAAGTTTCAGCTTT-CCTGGCTGA
129 TTCACAA-TTTGAATTTACACTACCTGAGGATGCTTCCACAAAAGTTTCAGCTTTGCC-GGCTGA
*
265040 TTAGTTTCT-G-AGAAGATTTTTAAAGATTTACTATATATATTCCTATG-TACAACTTCGACCCC
192 TTAGTTTCTAGAAGAAGATTTTTAAAGATTTACTATATATATTCCTATGATA-AACTTCGACACC
* * *
265102 CCATTGTGGCCCTATCC-TGCCCC-CGGGGTCATGATTTTCACAACTTTGAATCTACATTACCTT
256 CCATTGTGGCCCCA-CCATACCCCTCGGGGCCATGATTTTCACAACTTTGAATCTAC---A-C-T
* * *
265165 TCCTGAGGATTCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATTTT
315 ACCGGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATTTT
** *
265230 TAAAGATATAC-TCTATATTCATATGTTAAACTTCGA-CACCCCATTGTGGCCCCACCCTACCCC
380 TAAAGATATACATCTATATTCATACATTAAACTTCGATC-CCCCATTGTGGCCCCACCCTA-CAC
*
265293 TG-GGGGTCATGATTTTCACAACTTTGTATCTACACTACCTGAGGATGCTTCC
443 TGAGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCC
265345 ACACAAGTTTCAGCTTTCCTG
1 ACACAAGTTTCAGCTTTCCTG
265366 CTCTTATGGT
Statistics
Matches: 463, Mismatches: 41, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
494 31 0.07
495 63 0.14
496 12 0.03
497 223 0.48
498 64 0.14
499 70 0.15
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (495 bp):
ACACAAGTTTCAGCTTTCCTGGCTGAGTAGTTTCTGAGAAGAAGATTTTTAAAGATTAACTATTT
ATATTCCTATGTAAAACTTCGACCCCACATTGTGGCCCCACCCTACCCCCAGGGGATAGTATTTT
CACAATTTGAATTTACACTACCTGAGGATGCTTCCACAAAAGTTTCAGCTTTGCCGGCTGATTAG
TTTCTAGAAGAAGATTTTTAAAGATTTACTATATATATTCCTATGATAAACTTCGACACCCCATT
GTGGCCCCACCATACCCCTCGGGGCCATGATTTTCACAACTTTGAATCTACACTACCGGAGGATG
CTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAGATATAC
ATCTATATTCATACATTAAACTTCGATCCCCCATTGTGGCCCCACCCTACACTGAGGGGTCATGA
TTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCC
Found at i:265329 original size:331 final size:326
Alignment explanation
Indices: 264351--265365 Score: 1355
Period size: 331 Copynumber: 3.1 Consensus size: 326
264341 TACTCTATAT
* * *
264351 ACACAAGTGTCAGCTCTGCC-GGCTGATTTGTTTCTGAGAAGAAGATTTTTAAAGATTTACTATT
1 ACACAAGTTTCAGCT-TTCCTGGCTGATTAGTTTCT-AGAAGAAGATTTTTAAAGATTTACTATT
*
264415 TATATTCCTATGTAAAACTTCGACCCCACATTGTGGCCCTACCCTACCCCCAGGGG-C-TAGTAT
64 TATATTCCTATGT-AAACTTCGACCCCCCATTGTGGCCCTACCCTACCCCC-GGGGTCAT-G-AT
* *
264478 TTTCACAA-TTTGAATTTACACTACCTGAGGATGCTTCCACAAAAGTTTCAGCTTTGCC-GGCTG
125 TTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT-CCTGGCTG
* * * *
264541 ATTAGTTTTTAAGAAGAAGATTTTTAGAGATTTACTCTATATATTCCTATGATAAACTTTGACAC
189 ATTAGTTTCTGAGAAGAAGATTTTTAGAGA-TTACTC--TATATTCCTATGTTAAACTTCGACAC
* *
264606 CCCATTGTGGCCCCACCATACCCCTGGGGGCCATGATTTTCACAATTTTGAATCTACACTACC-G
251 CCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTTCACAATTTTGAATCTACACTACCTG
*
264670 GTGGATGCTTCC
316 AT-GATGCTTCC
*
264682 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAGAGATTTACTATTT
1 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCT-AGAAGAAGATTTTTAAAGATTTACTATTT
* * * ***
264747 ATATTCCTACAT-TAAACTTTGATCCCCCATTGTGGCCCCACCCTACACTGAGGGGTCATGATTT
65 ATATTCCT--ATGTAAACTTCGACCCCCCATTGTGGCCCTACCCTAC-CCCCGGGGTCATGATTT
* * * *
264811 TCACAACTTTGAATCTACACTACCTGATGATGCTTTCATACAAGTTTCAGCTTTCCTGGCTGAGT
127 TCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATT
* *
264876 AGTTTCTGAGAAGAAGATTTTTAGAGATTAACTATTTATATTCCTATGTTAAACTTCGACCCCCC
192 AGTTTCTGAGAAGAAGATTTTTAGAGATT-AC--TCTATATTCCTATGTTAAACTTCGACACCCC
* * * * *
264941 ATTGTGGCCCCACCCTACCCCCGGGGATAACGATTTTCACAATTTTGAATTTACACTACCTGATG
254 ATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTTCACAATTTTGAATCTACACTACCTGATG
*
265006 ATGCTTTC
319 ATGCTTCC
*
265014 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCT-G-AGAAGATTTTTAAAGATTTACTATATA
1 ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTAGAAGAAGATTTTTAAAGATTTACTATTTA
* *
265077 TATTCCTATGTACAACTTCGACCCCCCATTGTGGCCCTATCCTGCCCCCGGGGTCATGATTTTCA
66 TATTCCTATGTA-AACTTCGACCCCCCATTGTGGCCCTACCCTACCCCCGGGGTCATGATTTTCA
* * *
265142 CAACTTTGAATCTACATTACCTTTCCTGAGGATTCTTCCACACAAGTTTCAGCTTTCCTGGCCGA
130 CAACTTTGAATCTAC---A-C-TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGA
* *
265207 TTAGTTTCTGAGAAGAAGATTTTTAAAGATATACTCTATATTCATATGTTAAACTTCGACACCCC
190 TTAGTTTCTGAGAAGAAGATTTTTAGAGAT-TACTCTATATTCCTATGTTAAACTTCGACACCCC
* * *
265272 ATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTTCACAACTTTGTATCTACACTACCTGAGG
254 ATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTTCACAATTTTGAATCTACACTACCTGATG
265337 ATGCTTCC
319 ATGCTTCC
265345 ACACAAGTTTCAGCTTTCCTG
1 ACACAAGTTTCAGCTTTCCTG
265366 CTCTTATGGT
Statistics
Matches: 602, Mismatches: 62, Indels: 40
0.86 0.09 0.06
Matches are distributed among these distances:
327 2 0.00
328 34 0.06
329 59 0.10
330 4 0.01
331 226 0.38
332 203 0.34
333 72 0.12
334 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (326 bp):
ACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTAGAAGAAGATTTTTAAAGATTTACTATTTA
TATTCCTATGTAAACTTCGACCCCCCATTGTGGCCCTACCCTACCCCCGGGGTCATGATTTTCAC
AACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTT
TCTGAGAAGAAGATTTTTAGAGATTACTCTATATTCCTATGTTAAACTTCGACACCCCATTGTGG
CCCCACCCTACCCCTGGGGGTCATGATTTTCACAATTTTGAATCTACACTACCTGATGATGCTTC
C
Found at i:265578 original size:12 final size:12
Alignment explanation
Indices: 265561--265591 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
265551 TGAAAAGTTT
*
265561 ACAGACAGATGG
1 ACAGACAGACGG
265573 ACAGACAGACGG
1 ACAGACAGACGG
265585 ACAGACA
1 ACAGACA
265592 AAATGTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.23, G:0.29, T:0.03
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:278352 original size:10 final size:10
Alignment explanation
Indices: 278337--278366 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
278327 ATAGATCAGG
278337 GTATAATGAT
1 GTATAATGAT
278347 GTATAATGAT
1 GTATAATGAT
278357 GTATAATGAT
1 GTATAATGAT
278367 TTTATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (10 bp):
GTATAATGAT
Found at i:281370 original size:166 final size:165
Alignment explanation
Indices: 281086--282058 Score: 1455
Period size: 166 Copynumber: 5.9 Consensus size: 165
281076 GGTATTTTTC
* * * * * *** * *
281086 AAAAATCTTCTTCTCAAAAACTATTCGACCTGAGAAGCTTAAACTT-GTGTGTAGGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATGGAAGCATCCTCAG
* * * * *
281150 GTAGCGTAAATTCAAGTTTGTTCAAATCATGGACCCCGGGGGTAGGGAGGGGCCACAAGAGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGG-TCCCAGGGGTAGGGTGGGGCCACAAGAGGGGG
281215 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
129 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* *
281252 AAAAATCTTCTTCTCAAAAACTATTAGGCCCGAAAAGCTCAAATTAAAATGGAAGCATCCTTAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* ** *
281317 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCTCCAGGGGAAGGGTGGGGCCACAATTGGAGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTC-CCAGGGGTAGGGTGGGGCCACAAGAGGGGGA
*
281382 TCAAGTTTTACATAGAAATATATAGAGAAAATCTTT
130 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
** *
281418 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* ** *
281483 TAGTGTAGATTCAAGTTTGTTCAAATCATGATCCTTGTGGGTAGGGTGGGGCCACAATAGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCAG-GGGTAGGGTGGGGCCACAAGAGGGGGA
281548 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
130 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * *
281584 AAAAATCTTATTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTATAATGGAAGCTTCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
*
281649 TAGCGTAGATTCAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAAGA-GGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCA-GGGGTAGGGTGGGGCCACAAGAGGGGGA
* *
281713 TCAAGTTTTACATAGAAATATATAGACAAAATCTTT
130 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
*
281749 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCTTCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* * *
281814 TAGTGTAAATTCAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCGACAAGAGGGGAA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCA-GGGGTAGGGTGGGGCCACAAGAGGGGGA
* *
281879 TCAAGTTTGACAAAGGAATATATAGAGAAAATCTTT
130 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* *
281915 AAAAATCTTCTTCTTAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTAAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* *
281980 TAGTGTAGATTCAAGTTTGTTCAAATTATGGTCTCCAGGGGTAGGGTGGGGCCACAATAGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTC-CCAGGGGTAGGGTGGGGCCACAAGAGGGGGA
282045 TCAAGTTTTACATA
130 TCAAGTTTTACATA
282059 AATCTTTTAA
Statistics
Matches: 734, Mismatches: 67, Indels: 12
0.90 0.08 0.01
Matches are distributed among these distances:
165 162 0.22
166 568 0.77
167 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCAGGGGTAGGGTGGGGCCACAAGAGGGGGAT
CAAGTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:281861 original size:331 final size:331
Alignment explanation
Indices: 281086--282058 Score: 1518
Period size: 331 Copynumber: 2.9 Consensus size: 331
281076 GGTATTTTTC
* * * * * *** * *
281086 AAAAATCTTCTTCTCAAAAACTATTCGACCTGAGAAGCTTAAACTT-GTGTGTAGGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATGGAAGCATCCTCAG
* * * *
281150 GTAGCGTAAATTCAAGTTTGTTCAAATCATGGACCCCGGGGGTAGGGAGGGGCCACAAGAGGGGG
65 GTAGTGTAAATTCAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAAGAGGGGG
281215 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGG
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGG
* *
281280 CCCGAAAAGCTCAAATTAAAATGGAAGCATCCTTAGGTAGTGTAGATTCAAGTTTGTTCAAATCA
195 CCAGAAAAGCTCAAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATCA
* * *
281345 TGGTCTCCAGGGGAAGGGTGGGGCCACAATTGGAGGATCAAGTTTTACATAGAAATATATAGAGA
260 TGGTCTCCAGGGGTAGGGTGGGGCCACAATAGG-GGATCAAGTTTTACATAGAAATATATAGACA
281410 AAATCTTT
324 AAATCTTT
** *
281418 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* * ** * *
281483 TAGTGTAGATTCAAGTTTGTTCAAATCATGATCCTTGTGGGTAGGGTGGGGCCACAATAGGGGGA
66 TAGTGTAAATTCAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAAGAGGGGGA
*
281548 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTATTCTCAAAAACTATTAGGC
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGC
* * * * *
281613 CAGAAAAACTCAAATTATAATGGAAGCTTCCTCAGGTAGCGTAGATTCAAGTTTGTTCAAATCAT
196 CAGAAAAGCTCAAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATCAT
*
281678 GGTC-CCAGGGGGTAGGGTGGGGCCACAAGAGGGGATCAAGTTTTACATAGAAATATATAGACAA
261 GGTCTCCA-GGGGTAGGGTGGGGCCACAATAGGGGATCAAGTTTTACATAGAAATATATAGACAA
281742 AATCTTT
325 AATCTTT
*
281749 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCTTCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* *
281814 TAGTGTAAATTCAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCGACAAGAGGGGAA
66 TAGTGTAAATTCAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAAGAGGGGGA
* * *
281879 TCAAGTTTGACAAAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTTAAAAACTATTAGGC
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGC
*
281944 CAGAAAAGCTCAAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATTAT
196 CAGAAAAGCTCAAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATCAT
282009 GGTCTCCAGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATA
261 GGTCTCCAGGGGTAGGGTGGGGCCACAATA-GGGGATCAAGTTTTACATA
282059 AATCTTTTAA
Statistics
Matches: 586, Mismatches: 51, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
331 306 0.52
332 280 0.48
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (331 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
TAGTGTAAATTCAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAAGAGGGGGA
TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGC
CAGAAAAGCTCAAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATCAT
GGTCTCCAGGGGTAGGGTGGGGCCACAATAGGGGATCAAGTTTTACATAGAAATATATAGACAAA
ATCTTT
Found at i:282024 original size:497 final size:498
Alignment explanation
Indices: 281143--282058 Score: 1543
Period size: 497 Copynumber: 1.8 Consensus size: 498
281133 TGTGTAGGCA
*
281143 TCCTCAGGTAGCGTAAATTCAAGTTTGTTCAAATCATGGACCCCGGGGGTAGGGAGGGGCCACAA
1 TCCTCAGGTAGCGTAAATTCAAGTTTGTTCAAATCATGGACCCAGGGGGTAGGGAGGGGCCACAA
* *
281208 GAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAAC
66 GAGGGGGATCAAGTTTTACATAGAAATATATAGACAAAATCTTTAAAAATCTTCTTCTCAAAAAC
* * *
281273 TATTAGGCCCGAAAAGCTCAAATTAAAATGGAAGCATCCTTAGGTAGTGTAGATTCAAGTTTGTT
131 TATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGTAGTGTAAATTCAAGTTTGTT
** * *
281338 CAAATCATGGTCTCCAGGGGAAGGGTGGGGCCACAATTGGAGGATCAAGTTTTACATAGAAATAT
196 CAAATCATGGTCTCCAGGGGAAGGGTGGGGCCACAAGAGGAGGATCAAGTTTGACAAAGAAATAT
** *
281403 ATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGT
261 ATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAAT
* **
281468 GGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGATCCTTGTGGGTAGGGTGGG
326 GGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCAGTGGGTAGGGTGGG
281533 GCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTATTCT
391 GCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTATTCT
281598 CAAAAACTATTAGGCCAGAAAAACTCAAATTATAATGGAAGCT
456 CAAAAACTATTAGGCCAGAAAAACTCAAATTATAATGGAAGCT
* * *
281641 TCCTCAGGTAGCGTAGATTCAAGTTTGTTCAAATCATGGTCCCAGGGGGTAGGGTGGGGCCACAA
1 TCCTCAGGTAGCGTAAATTCAAGTTTGTTCAAATCATGGACCCAGGGGGTAGGGAGGGGCCACAA
281706 GA-GGGGATCAAGTTTTACATAGAAATATATAGACAAAATCTTTAAAAATCTTCTTCTCAAAAAC
66 GAGGGGGATCAAGTTTTACATAGAAATATATAGACAAAATCTTTAAAAATCTTCTTCTCAAAAAC
*
281770 TATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCTTCCTCAGGTAGTGTAAATTCAAGTTTGTT
131 TATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGTAGTGTAAATTCAAGTTTGTT
* * *
281835 CAAATCATGGTC-CCAGGGGGTAGGGTGGGGCGACAAGAGG-GGAATCAAGTTTGACAAAGGAAT
196 CAAATCATGGTCTCCA-GGGGAAGGGTGGGGCCACAAGAGGAGG-ATCAAGTTTGACAAAGAAAT
*
281898 ATATAGAGAAAATCTTTAAAAATCTTCTTCTTAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
259 ATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
* *
281963 ATGGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATTATGGTCTCCAG-GGGTAGGGT
324 ATGGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGATC-CCAGTGGGTAGGGT
282027 GGGGCCACAATAGGGGGATCAAGTTTTACATA
388 GGGGCCACAATAGGGGGATCAAGTTTTACATA
282059 AATCTTTTAA
Statistics
Matches: 389, Mismatches: 26, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
496 5 0.01
497 319 0.82
498 65 0.17
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (498 bp):
TCCTCAGGTAGCGTAAATTCAAGTTTGTTCAAATCATGGACCCAGGGGGTAGGGAGGGGCCACAA
GAGGGGGATCAAGTTTTACATAGAAATATATAGACAAAATCTTTAAAAATCTTCTTCTCAAAAAC
TATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGTAGTGTAAATTCAAGTTTGTT
CAAATCATGGTCTCCAGGGGAAGGGTGGGGCCACAAGAGGAGGATCAAGTTTGACAAAGAAATAT
ATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAAT
GGAAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCAGTGGGTAGGGTGGG
GCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTATTCT
CAAAAACTATTAGGCCAGAAAAACTCAAATTATAATGGAAGCT
Found at i:282264 original size:140 final size:141
Alignment explanation
Indices: 281902--282264 Score: 327
Period size: 150 Copynumber: 2.5 Consensus size: 141
281892 AGGAATATAT
* *
281902 AGAGAAAATCTTTAAAAATCTTCTTCTTAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGG
1 AGAGAAAATCTTTAAAAATCTTC-TC---AAAACTATTAGGCCAGGAAAGCTCAAATT-AGATGG
* * * * *
281967 AAGCATCCTAAGGTAGTGTAGATTCAAGTTTGTTCAAATTATGGTCTCCAGGGGTAGGGTGGGGC
61 AAGCATCCTAAGATAATGTAGATTCAAGTTTGTTCAAATCATGGTCTCCAGGGGTAGGGTCGGGA
*
282032 CACAATAGGGGGATCA
126 CACAATAGGGAGATCA
* * * * * *
282048 AGTTTTACATAAATCTTTTAAAAAATTCTTTTTAAAACTATTTGGCCAAGAAAGCTCAAATTGGC
1 AG----AGA-AAATC-TTT-AAAAA-TCTTCTCAAAACTATTAGGCCAGGAAAGCTCAAATTAG-
* * * *
282113 ATGTAACCATCCTCAGATAATGTAGATTCAAGTTTGTTCAAATCATGGTC-CCTGGGGGTAGGG-
57 ATGGAAGCATCCTAAGATAATGTAGATTCAAGTTTGTTCAAATCATGGTCTCC-AGGGGTAGGGT
* **** * *
282176 CGGGATA-AATTTTTATATGA
121 CGGGACACAATAGGGAGATCA
*
282196 AGAGAAAATCTTTAAAAATCTTCTCAAAACTATTAGGCCAGGAAAGCCCAAATTAGAGTGGAAGC
1 AGAGAAAATCTTTAAAAATCTTCTCAAAACTATTAGGCCAGGAAAGCTCAAATTAGA-TGGAAGC
282261 ATCC
65 ATCC
282265 CGGGGTCGAA
Statistics
Matches: 172, Mismatches: 34, Indels: 28
0.74 0.15 0.12
Matches are distributed among these distances:
139 1 0.01
140 41 0.24
141 5 0.03
142 3 0.02
143 5 0.03
144 2 0.01
146 2 0.01
148 8 0.05
149 6 0.03
150 81 0.47
151 5 0.03
152 3 0.02
153 6 0.03
154 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (141 bp):
AGAGAAAATCTTTAAAAATCTTCTCAAAACTATTAGGCCAGGAAAGCTCAAATTAGATGGAAGCA
TCCTAAGATAATGTAGATTCAAGTTTGTTCAAATCATGGTCTCCAGGGGTAGGGTCGGGACACAA
TAGGGAGATCA
Found at i:285714 original size:33 final size:33
Alignment explanation
Indices: 285667--285738 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
285657 TTTCTAATTT
* *
285667 GTTTTATAATTTCTTTATCATACCAAGTCATAG
1 GTTTTAGAAATTCTTTATCATACCAAGTCATAG
285700 GTTTTAGAAATTCTTTATCATACCAAGTCATAG
1 GTTTTAGAAATTCTTTATCATACCAAGTCATAG
285733 GTTTTA
1 GTTTTA
285739 CGAAGTTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (33 bp):
GTTTTAGAAATTCTTTATCATACCAAGTCATAG
Found at i:311959 original size:139 final size:138
Alignment explanation
Indices: 311709--311985 Score: 536
Period size: 139 Copynumber: 2.0 Consensus size: 138
311699 CACACTCTCG
311709 TCCTTGATCTGTGATTTCACCATTTCTGATTGCCGCGCAGTTTCGACTGCTTTCTCAAGTGTCAG
1 TCCTTGATCTGTGATTTCACCATTTCTGATTGCCGCGCAGTTTCGACTGCTTTCTCAAGTGTCAG
311774 ATCTTAGAAAGAATAAAGTGACTAAAAACATGCAGGTAATGAAGTGTATGTATGGTGCGATGTTC
66 ATCTTAGAAAGAATAAAGTGACTAAAAACATGCAGGTAATGAAGTGTATGTATGGTGCGATGTTC
311839 TTGTTCAA
131 TTGTTCAA
*
311847 NTCCTTGATCTGTGATTTCGCCATTTCTGATTGCCGCGCAGTTTCGACTGCTTTCTCAAGTGTCA
1 -TCCTTGATCTGTGATTTCACCATTTCTGATTGCCGCGCAGTTTCGACTGCTTTCTCAAGTGTCA
311912 GATCTTAGAAAGAATAAAGTGACTAAAAACATGCAGGTAATGAAGTGTATGTATGGTGCGATGTT
65 GATCTTAGAAAGAATAAAGTGACTAAAAACATGCAGGTAATGAAGTGTATGTATGGTGCGATGTT
311977 CTTGTTCAA
130 CTTGTTCAA
311986 GAAAATGTAC
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 137 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (138 bp):
TCCTTGATCTGTGATTTCACCATTTCTGATTGCCGCGCAGTTTCGACTGCTTTCTCAAGTGTCAG
ATCTTAGAAAGAATAAAGTGACTAAAAACATGCAGGTAATGAAGTGTATGTATGGTGCGATGTTC
TTGTTCAA
Found at i:312794 original size:20 final size:20
Alignment explanation
Indices: 312769--312836 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
312759 TAAAGAACAG
*
312769 TGTATCATATAAAACAATAT
1 TGTATCATATAATACAATAT
*
312789 TGTATCATACAATACAATAT
1 TGTATCATATAATACAATAT
*
312809 TGTATCATATTATACAATAT
1 TGTATCATATAATACAATAT
312829 TGTATCAT
1 TGTATCAT
312837 GTTACAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.40
Consensus pattern (20 bp):
TGTATCATATAATACAATAT
Found at i:316472 original size:20 final size:20
Alignment explanation
Indices: 316447--316487 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
316437 GTTTGGGAAG
*
316447 TACTGTGGAATCATTTAAAT
1 TACTGTGGAATCATTCAAAT
316467 TACTGTGGAATCATTCAAAT
1 TACTGTGGAATCATTCAAAT
316487 T
1 T
316488 CGTTGGGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (20 bp):
TACTGTGGAATCATTCAAAT
Found at i:319840 original size:2 final size:2
Alignment explanation
Indices: 319833--319862 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
319823 CATTGTGTTT
*
319833 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
319863 CAGACAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:320727 original size:14 final size:15
Alignment explanation
Indices: 320691--320730 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
320681 AGACGGGACA
*
320691 TCACCCTTATGAGAC
1 TCACCTTTATGAGAC
320706 TTCACCTTTATGAGAC
1 -TCACCTTTATGAGAC
320722 -CACCTTTAT
1 TCACCTTTAT
320731 CATATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.39
16 14 0.61
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (15 bp):
TCACCTTTATGAGAC
Done.