Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold867
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: 1160077
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29
Warning! 150854 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:2738 original size:13 final size:13
Alignment explanation
Indices: 2720--2749 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2710 TTTTAAGGAG
2720 ACATTTAAGTGTT
1 ACATTTAAGTGTT
2733 ACATTTAAGTGTT
1 ACATTTAAGTGTT
2746 -CATT
1 ACATT
2750 GATTTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (13 bp):
ACATTTAAGTGTT
Found at i:6789 original size:167 final size:166
Alignment explanation
Indices: 6485--6791 Score: 386
Period size: 167 Copynumber: 1.8 Consensus size: 166
6475 GGCGTGTGTC
*
6485 TTTAAAAATCTTCTCAAGAACCACTGCACCAGAAATGCCAAAATTTACACAAAAGCTTGGACATG
1 TTTAAAAATCTTCTCAAGAACAACTGCACCAGAAATGCCAAAATTTACACAAAA----GGACATG
* * * * *
6550 TATATAAAGTGAAGATTCTAAATTGTAAAAATCGTGACTCTCGGACCAAAACTGGGGTCCCAGGC
62 TATATAAAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACAAAAACTGGAGCCCCAGGC
6615 AGGGTTCAAAGTTTAACATAGAAATGCATATGAAACATTA
127 AGGGTTCAAAGTTTAACATAGAAATGCATATGAAACATTA
* * * *
6655 TTTAAAAATCTTCTTTCCAAGAACAACTGCACCAGAAATGCCAATATTTATATAAAA-GA-TTGT
1 TTTAAAAATCTTC--T-CAAGAACAACTGCACCAGAAATGCCAAAATTTACACAAAAGGACATGT
* * * * *
6718 ATATATAGTGAAGATTCTAAATTGTTAAAATTGTGACCCCCGGACAAAAAGTGTAGCCCCAGG-A
63 ATATAAAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACAAAAACTGGAGCCCCAGGCA
6782 GGGGTTCAAA
128 -GGGTTCAAA
6792 AATTAACACA
Statistics
Matches: 118, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
166 1 0.01
167 65 0.55
168 2 0.02
170 13 0.11
172 1 0.01
173 36 0.31
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (166 bp):
TTTAAAAATCTTCTCAAGAACAACTGCACCAGAAATGCCAAAATTTACACAAAAGGACATGTATA
TAAAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACAAAAACTGGAGCCCCAGGCAGGG
TTCAAAGTTTAACATAGAAATGCATATGAAACATTA
Found at i:12174 original size:63 final size:63
Alignment explanation
Indices: 12098--12221 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 63
12088 CCAACAATGG
*
12098 TTCAAATGTTATTCCTCCACGCA-TCGTTCCAAAGAAACAGCATACTTTTGAT-TCAAAGGTTTT
1 TTCAAATGTTATTCCTCCACGCATTC-TTCCAAAGAAACAACATACTTTTGATAT-AAAGGTTTT
*
12161 TTCAAATGTTATTCCTCCACGCATTCTTCCAAAGAAGCAACATACTTTTGATATAAAGGTT
1 TTCAAATGTTATTCCTCCACGCATTCTTCCAAAGAAACAACATACTTTTGATATAAAGGTT
12222 GCTAACAGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
63 54 0.95
64 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (63 bp):
TTCAAATGTTATTCCTCCACGCATTCTTCCAAAGAAACAACATACTTTTGATATAAAGGTTTT
Found at i:19501 original size:2 final size:2
Alignment explanation
Indices: 19473--19537 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
19463 CAGGTCATAT
*
19473 GA GA GA AA GA GA -A GA GA -A GA G- GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19512 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
19538 ATATGAAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19627 original size:15 final size:16
Alignment explanation
Indices: 19599--19679 Score: 87
Period size: 15 Copynumber: 5.1 Consensus size: 16
19589 AGGTCAAATG
19599 AGAGAAAGAGAAGAGA
1 AGAGAAAGAGAAGAGA
19615 AGAGAAA-AGAAGAGA
1 AGAGAAAGAGAAGAGA
*
19630 AGAGAGAGAG-AGAG-
1 AGAGAAAGAGAAGAGA
*
19644 AGAGAGAGAGAGAGAGA
1 AGAGAAAGAGA-AGAGA
*
19661 GAGAGAGAGAGAGAGAGA
1 -AGAGAAAGAGA-AGAGA
19679 A
1 A
19680 TATGAAATTC
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
14 10 0.17
15 18 0.31
16 13 0.22
17 1 0.02
18 17 0.29
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAGAAGAGA
Found at i:19637 original size:2 final size:2
Alignment explanation
Indices: 19598--19678 Score: 109
Period size: 2 Copynumber: 43.0 Consensus size: 2
19588 CAGGTCAAAT
* *
19598 GA GA GA AA GA GA -A GA GA -A GA GA -A AA GA -A GA GA -A GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19635 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19677 GA
1 GA
19679 ATATGAAATT
Statistics
Matches: 71, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
1 5 0.07
2 66 0.93
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:22393 original size:18 final size:18
Alignment explanation
Indices: 22370--22424 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 18
22360 ACCCCCCCCC
22370 CCCAAAAAAAAAAAACAA
1 CCCAAAAAAAAAAAACAA
*
22388 CCC--AAAAAACAAACAA
1 CCCAAAAAAAAAAAACAA
* *
22404 ACCAAAAAAAACAAAAAAA
1 CCCAAAAAAAA-AAAACAA
22423 CC
1 CC
22425 TCAAGAGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 14 0.48
18 9 0.31
19 6 0.21
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (18 bp):
CCCAAAAAAAAAAAACAA
Found at i:22396 original size:16 final size:16
Alignment explanation
Indices: 22375--22414 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
22365 CCCCCCCCAA
*
22375 AAAAAAAAAACAACCC
1 AAAAAAAAAACAAACC
*
22391 AAAAAACAAACAAACC
1 AAAAAAAAAACAAACC
22407 AAAAAAAA
1 AAAAAAAA
22415 CAAAAAAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAACC
Found at i:23395 original size:16 final size:15
Alignment explanation
Indices: 23370--23404 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
23360 CCCCCCCCCC
23370 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
*
23385 CAAAAACAAAAACAAA
1 CAAAAA-AAAAAAAAA
23401 CAAA
1 CAAA
23405 CCAAGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:23788 original size:162 final size:157
Alignment explanation
Indices: 23450--23864 Score: 543
Period size: 162 Copynumber: 2.6 Consensus size: 157
23440 CTTGAAAACA
* * * *
23450 TCTGCAAAGAAAATGAACGGAAACTACAAATAATAGAAAATTTTCTAAGTCCAAGGGGCATAAGT
1 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGAAATTTTTCTACGTCCAAGGGGCATAAGT
* * * * *
23515 CGAAAATTGCTCGAACGTACCCAAAATCAACTTTAACCTAGATATTATTATGATTAAGCTGTATA
66 CGAAAATTGCTAGAACGTACCCAAAATCAAATTTAACCTAGATATTATTATAATAAACCTGTATA
*
23580 CCAAATTTCATTTCAATATGCACATCC
131 CCAAATTTCAATTCAATATGCACATCC
*
23607 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGGAATTTTTCTACGTCCAAGGGGCATAAGT
1 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGAAATTTTTCTACGTCCAAGGGGCATAA--
* * *
23672 CTGTCGAAAATTGCTAGATCGTACCCAGAATCAAATTTGACCTAGATATTATTATAATAAAACCT
64 --GTCGAAAATTGCTAGAACGTACCCAAAATCAAATTTAACCTAGATATTATTATAAT-AAACCT
*
23737 GTATACCAAATTTCAATTCAATATGCGCATCC
126 GTATACCAAATTTCAATTCAATATGCACATCC
** * * *
23769 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTTTAATTTTTCTACCTCTAA--GTC-T--GT
1 TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGAAATTTTTCTACGTCCAAGGGGCATAAGT
* * *
23829 CGAAAATTGCTCGAACGTACCCAAACTCAAACTTAA
66 CGAAAATTGCTAGAACGTACCCAAAATCAAATTTAA
23865 GGTAGTCCTA
Statistics
Matches: 227, Mismatches: 26, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
153 32 0.14
157 58 0.26
159 1 0.00
160 2 0.01
161 50 0.22
162 84 0.37
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (157 bp):
TCTGCAAAGAAAATGAACGGAAACTGCAAATAATTGAAATTTTTCTACGTCCAAGGGGCATAAGT
CGAAAATTGCTAGAACGTACCCAAAATCAAATTTAACCTAGATATTATTATAATAAACCTGTATA
CCAAATTTCAATTCAATATGCACATCC
Found at i:25095 original size:16 final size:16
Alignment explanation
Indices: 25074--25105 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25064 GTTGGTGAAA
25074 CGACCGACCGACAGAC
1 CGACCGACCGACAGAC
25090 CGACCGACCGACAGAC
1 CGACCGACCGACAGAC
25106 AGCAGCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.44, G:0.25, T:0.00
Consensus pattern (16 bp):
CGACCGACCGACAGAC
Found at i:33399 original size:18 final size:18
Alignment explanation
Indices: 33376--33417 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
33366 CCAACTGATG
*
33376 TATTATTACTATCACTAT
1 TATTATTAATATCACTAT
*
33394 TATTATTAATATTACTAT
1 TATTATTAATATCACTAT
33412 TATTAT
1 TATTAT
33418 CATTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTAATATCACTAT
Found at i:33400 original size:6 final size:6
Alignment explanation
Indices: 33376--33435 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
33366 CCAACTGATG
* * * * * *
33376 TATTAT TACTAT CACTAT TATTAT TAATAT TACTAT TATTAT CATTAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
*
33424 TATCAT TATTAT
1 TATTAT TATTAT
33436 AATCATTTGA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (6 bp):
TATTAT
Found at i:44738 original size:14 final size:14
Alignment explanation
Indices: 44719--44747 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44709 TTTATGCAAT
44719 GTGCACAAAGAACA
1 GTGCACAAAGAACA
44733 GTGCACAAAGAACA
1 GTGCACAAAGAACA
44747 G
1 G
44748 AACAATCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.21, G:0.24, T:0.07
Consensus pattern (14 bp):
GTGCACAAAGAACA
Found at i:55105 original size:396 final size:398
Alignment explanation
Indices: 54415--55204 Score: 1110
Period size: 396 Copynumber: 2.0 Consensus size: 398
54405 GTCTAAACTC
* * *
54415 TTTTATTTTGTAGATCTTTGCTGAGGGGTATTTTGTAATAGGTTATAGAAGCGGAAATGTTTATC
1 TTTTATTTTGTAGATCATTACTGAGGGGTATTTTGTAATAGGTTATAGAAGCGAAAATGTTTATC
* * * *
54480 TAATAGTTATGTACCCATACAATATAACGACTCTCTCATGTGTGGCGTATTTCGGGGTTTTAAGG
66 TAATAGTTATGTACCCATACAATATAAAGACTCTCTCATGTGTGACGTATTTAGAGGTTTTAAGG
* ** *
54545 GGCCAGAAGTTCAAAACTTTAATCATATATATCTAGTAAAGGAAAAATATTTTGATGAGCATTTA
131 GGCCAGAAATTCAAAACTTTAATCATATATATCTAGTAAAGGAAAAATATTTTGACAAGCATATA
*
54610 AGAAAAAAAAAGATGCTCAAAATGATGTACTCAACAATATTCAACCCTAAAATTTCATTAAAGGG
196 AGAAAAAAAAAGATGCTCAAAATGATGTACTCAACAATATTCAACCCTAAAATTTCATTAAACGG
* * * * **
54675 TCCCGATAAGGAGATAAGGTGGCGGCCCCTAAAATCTTCTTTCTTGGATATCTTAAAAACGATTA
261 CCCCAATAAGGAGATAAGGTGGCGGCCCCTAAAATCGTCTTTCTTGGATATCTCAAAAACGAAAA
54740 CAAATTTGTAAACACTTGTTGTAA-AAAATGTGTGTAGTTCAAAGTCACCTTTCATTTAATACCA
326 CAAATTTGTAAACACTTGTTG-AACAAAATGTGTGTAGTTCAAAGTCACCTTTCATTTAATACCA
54804 AGAAAAGTA
390 AGAAAAGTA
*
54813 TTTTA-TTTGTAGCTCATTACTGAGGGGTATTTTGTAATAGGTTATAGAAGC-AAAATGTTTATC
1 TTTTATTTTGTAGATCATTACTGAGGGGTATTTTGTAATAGGTTATAGAAGCGAAAATGTTTATC
* * * *
54876 TAATAGTTATGTACCCATATAATTTAAAGACTTTCTCATGTGTGACGTATTTAGAGGTTTTTAGG
66 TAATAGTTATGTACCCATACAATATAAAGACTCTCTCATGTGTGACGTATTTAGAGGTTTTAAGG
* * * * *
54941 GGGCAGAAAATAT-AAAATTTTAATCATCTTTATCTAGTAAAGGAAAACTATTTTGACAAGCAGT
131 GGCCAG-AAAT-TCAAAACTTTAATCATATATATCTAGTAAAGGAAAAATATTTTGACAAGCA-T
* * * * *
55005 AT-AG-AAGAAAAA-ATGCTCTAAATGATGTACTCAACAATATTTATCCCTCAAAATTTCATTGA
193 ATAAGAAAAAAAAAGATGCTCAAAATGATGTACTCAACAATATTCAACCCT-AAAATTTCATTAA
* *
55067 ACGGCCCCAATAAGGAGATAAGG-GGTTGGCCGCTAAAATCGTCTTTCTTGGATATCTCAAAAAC
257 ACGGCCCCAATAAGGAGATAAGGTGG-CGGCCCCTAAAATCGTCTTTCTTGGATATCTCAAAAAC
* ** * *
55131 GAAAACAAATTTTTAAACACTTGTTGAACAAAATGTGTGTAGTTTTAGGTCACCTTTCATTTTAT
321 GAAAACAAATTTGTAAACACTTGTTGAACAAAATGTGTGTAGTTCAAAGTCACCTTTCATTTAAT
55196 ACCAAGAAA
386 ACCAAGAAA
55205 TAGGGAATGG
Statistics
Matches: 346, Mismatches: 40, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
395 37 0.11
396 210 0.61
397 91 0.26
398 8 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (398 bp):
TTTTATTTTGTAGATCATTACTGAGGGGTATTTTGTAATAGGTTATAGAAGCGAAAATGTTTATC
TAATAGTTATGTACCCATACAATATAAAGACTCTCTCATGTGTGACGTATTTAGAGGTTTTAAGG
GGCCAGAAATTCAAAACTTTAATCATATATATCTAGTAAAGGAAAAATATTTTGACAAGCATATA
AGAAAAAAAAAGATGCTCAAAATGATGTACTCAACAATATTCAACCCTAAAATTTCATTAAACGG
CCCCAATAAGGAGATAAGGTGGCGGCCCCTAAAATCGTCTTTCTTGGATATCTCAAAAACGAAAA
CAAATTTGTAAACACTTGTTGAACAAAATGTGTGTAGTTCAAAGTCACCTTTCATTTAATACCAA
GAAAAGTA
Found at i:55859 original size:38 final size:38
Alignment explanation
Indices: 55817--55895 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
55807 GGAGATTTTT
*
55817 TTTGTTGCATGCATTTGTAACTAATAATAGGTACAGTA
1 TTTGTTGCATGCATTTGTAACTAATAATAGGCACAGTA
55855 TTTGTTGCATGCATTTGTAACTAATAATAGGCACAGTA
1 TTTGTTGCATGCATTTGTAACTAATAATAGGCACAGTA
55893 TTT
1 TTT
55896 AACAATAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (38 bp):
TTTGTTGCATGCATTTGTAACTAATAATAGGCACAGTA
Found at i:58069 original size:17 final size:18
Alignment explanation
Indices: 58020--58063 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
58010 GATTTTACGT
*
58020 CAACAATTTTGAG-CAGGC
1 CAAC-ATTTGGAGCCAGGC
58038 CAACATTTGGAGCCAGGC
1 CAACATTTGGAGCCAGGC
58056 CAA-ATTTG
1 CAACATTTG
58064 AGGCCAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (18 bp):
CAACATTTGGAGCCAGGC
Found at i:61738 original size:8 final size:8
Alignment explanation
Indices: 61725--61774 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
61715 TGAAAAGTGT
61725 ACAGACGG
1 ACAGACGG
*
61733 ACAGACAG
1 ACAGACGG
* *
61741 ACGGACAG
1 ACAGACGG
*
61749 ACGGACGG
1 ACAGACGG
61757 ACAGACGG
1 ACAGACGG
61765 AC-GACGG
1 ACAGACGG
61772 ACA
1 ACA
61775 AAATGTGATC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
7 7 0.19
8 30 0.81
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:61742 original size:12 final size:12
Alignment explanation
Indices: 61725--61767 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
61715 TGAAAAGTGT
61725 ACAGACGGACAG
1 ACAGACGGACAG
61737 ACAGACGGACAG
1 ACAGACGGACAG
*
61749 ACGGACGGACAG
1 ACAGACGGACAG
*
61761 ACGGACG
1 ACAGACG
61768 ACGGACAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:64274 original size:2 final size:2
Alignment explanation
Indices: 64267--64293 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64257 TGTTAAATAG
64267 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
64294 TAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64300 original size:2 final size:2
Alignment explanation
Indices: 64295--64334 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
64285 TATATATATT
64295 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG
64335 TCGGATTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:66123 original size:2 final size:2
Alignment explanation
Indices: 66098--66162 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
66088 TTACTTATTT
* * * *
66098 TC TC TC TT TC TC CC TG TC TG 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
*
66140 TC TC TC TC TC TA TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
66163 TGTATATTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.02, C:0.45, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:76726 original size:31 final size:32
Alignment explanation
Indices: 76666--76726 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
76656 ATCAGGAAGG
* *
76666 TTTTGGTTAAGTCGTACTAAAAATCATTCGGA
1 TTTTGGTTAAGTCGTACCAAAAATAATTCGGA
**
76698 TTTT-GTTAAGTCGTACCAGGAATAATTCG
1 TTTTGGTTAAGTCGTACCAAAAATAATTCG
76727 ATTATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (32 bp):
TTTTGGTTAAGTCGTACCAAAAATAATTCGGA
Found at i:76855 original size:17 final size:17
Alignment explanation
Indices: 76833--76873 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
76823 GACCCACTCG
76833 TTGCTCTGCAACGAGCT
1 TTGCTCTGCAACGAGCT
76850 TTGCTCTGCAACGAGCT
1 TTGCTCTGCAACGAGCT
76867 TTGCTCT
1 TTGCTCT
76874 AGTTTCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.15, C:0.29, G:0.22, T:0.34
Consensus pattern (17 bp):
TTGCTCTGCAACGAGCT
Found at i:78952 original size:2 final size:2
Alignment explanation
Indices: 78945--79013 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
78935 ATCCCAATAT
* *
78945 GA GA GA GA GA GA GA GA GA GA GA AA GA AA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
78987 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
79014 CACCTTGCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:80523 original size:2 final size:2
Alignment explanation
Indices: 80516--80553 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
80506 GTTAAAACAA
80516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80554 NNNNNNNNNN
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80742 original size:2 final size:2
Alignment explanation
Indices: 80735--80768 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
80725 NNNNNNNNNN
80735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80769 CACACAATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84017 original size:207 final size:209
Alignment explanation
Indices: 83675--84196 Score: 832
Period size: 207 Copynumber: 2.5 Consensus size: 209
83665 AAAATGATTT
* * *
83675 TGATTCCATTACTTAGTAATAAAAGAACCATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC
1 TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC
83740 TTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT
66 TTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT
* *
83805 GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTATAGAAAATTCAGT-GG-TTTTTTTTCGATT
131 GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTAAAGAAAATTCAATGGGTTTTTTTTTCGATT
83868 TTGAAAAATA-ACTA
196 TTGAAAAA-AGACTA
83882 TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC
1 TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC
*
83947 TTATTTATATCGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT
66 TTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT
84012 GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTAAAGAAAATTCAATGGGTTTTTTTTTTCGAT
131 GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTAAAGAAAATTCAATGGG-TTTTTTTTTCGAT
*
84077 TTTGAAAAAAGACTT
195 TTTGAAAAAAGACTA
* * * *
84092 TGATTCCATTTCTTATTAAT-AAAAAAACATCACTTGGAAATAATACAAAGG-------ATCTTC
1 TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAAC-AAGGAACTTTTATCTTC
*
84149 CTTATTTATATAGTAATATATCATACAACTATTGTAAGGTCGCCTGAG
65 CTTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAG
84197 ATCGATTAAA
Statistics
Matches: 297, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
203 52 0.18
207 172 0.58
208 2 0.01
209 24 0.08
210 47 0.16
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (209 bp):
TGATTCCATTTCTTAGTAATAAAAAAAACATTACTTGGGAATAAAACAAGGAACTTTTATCTTCC
TTATTTATATAGTATTATATCATACAACTATTGTAAGGTCGCCTGAGGTTTAATGATAGTAAAAT
GTATTTTCTTGTACATTTGTAGTTTGTTAAACTTAAAGAAAATTCAATGGGTTTTTTTTTCGATT
TTGAAAAAAGACTA
Found at i:87467 original size:35 final size:35
Alignment explanation
Indices: 87421--87687 Score: 369
Period size: 35 Copynumber: 7.6 Consensus size: 35
87411 ACTGTCCATA
* * *
87421 AAATTAAACTGTATTTATACTATAAATTATACATG
1 AAATTCAACTGTATATATACTATAAATTCTACATG
*
87456 AAATTCAACTGTATATATAC-AGTAAATTCTGCATG
1 AAATTCAACTGTATATATACTA-TAAATTCTACATG
87491 AAATTCAACTGTATATATAC-AGTAAATTCTACATG
1 AAATTCAACTGTATATATACTA-TAAATTCTACATG
87526 AAATTCAACTGTATATATACTATAAATTCTACATG
1 AAATTCAACTGTATATATACTATAAATTCTACATG
* * *
87561 AAATTCAATTGTATACATACAATAAACTT-TACATG
1 AAATTCAACTGTATATATACTATAAA-TTCTACATG
*
87596 AAATTCAACTGTATATATACTATAAATTCTATATG
1 AAATTCAACTGTATATATACTATAAATTCTACATG
* * * *
87631 AAATTCAATTGTATACATACAATAAATTTTACATG
1 AAATTCAACTGTATATATACTATAAATTCTACATG
*
87666 AAATTCAACTGTATTTATACTA
1 AAATTCAACTGTATATATACTA
87688 AAACTTTAAT
Statistics
Matches: 207, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
34 3 0.01
35 201 0.97
36 3 0.01
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
AAATTCAACTGTATATATACTATAAATTCTACATG
Found at i:90532 original size:11 final size:11
Alignment explanation
Indices: 90502--90533 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
90492 TAAAGACGAT
*
90502 CTTTAAGCCAC
1 CTTTAAGCTAC
90513 CTTTAAGCTAC
1 CTTTAAGCTAC
90524 CTTTAAGCTA
1 CTTTAAGCTA
90534 TAAGTATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:90592 original size:22 final size:22
Alignment explanation
Indices: 90542--90594 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
90532 TATAAGTATT
*
90542 GCTTAAAGGTGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
90564 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
90586 GCTTAAAGA
1 GCTTAAAGA
90595 CTATCTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:90615 original size:11 final size:11
Alignment explanation
Indices: 90599--90627 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
90589 TAAAGACTAT
90599 CTTTAAGCCAC
1 CTTTAAGCCAC
90610 CTTTAAGCCAC
1 CTTTAAGCCAC
90621 CTTTAAG
1 CTTTAAG
90628 GACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:90707 original size:10 final size:11
Alignment explanation
Indices: 90659--90708 Score: 84
Period size: 11 Copynumber: 4.6 Consensus size: 11
90649 GTCCAAACTT
90659 CTTTAAGCCAC
1 CTTTAAGCCAC
90670 CTTTAAGCCAC
1 CTTTAAGCCAC
90681 CTTTAAGCCAC
1 CTTTAAGCCAC
*
90692 CTTTAAG-CAT
1 CTTTAAGCCAC
90702 CTTTAAG
1 CTTTAAG
90709 TGGCATTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:90758 original size:22 final size:22
Alignment explanation
Indices: 90701--90761 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
90691 CCTTTAAGCA
* *
90701 TCTTTAAGTGGCATTTACGCTC
1 TCTTTAAGTGGCCTTTACACTC
* *
90723 TCTTTACACT-GCCTTTACACTG
1 TCTTTA-AGTGGCCTTTACACTC
90745 TCTTTAAGTGGCCTTTA
1 TCTTTAAGTGGCCTTTA
90762 AGTCAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43
Consensus pattern (22 bp):
TCTTTAAGTGGCCTTTACACTC
Found at i:91093 original size:2 final size:2
Alignment explanation
Indices: 91088--91117 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
91078 GTGAAAAAAA
91088 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
91118 AGTTCATCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:91529 original size:112 final size:112
Alignment explanation
Indices: 91332--91554 Score: 419
Period size: 112 Copynumber: 2.0 Consensus size: 112
91322 AGTTTTGTTC
*
91332 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA
*
91397 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
*
91444 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA
91509 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
91555 CGTCAGGGTT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 108 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (112 bp):
GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA
GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
Found at i:98533 original size:30 final size:30
Alignment explanation
Indices: 98499--99053 Score: 770
Period size: 30 Copynumber: 18.8 Consensus size: 30
98489 TTTTTCAAGT
** *
98499 GAACCTCTGAACATTTACAATTATCAAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
* **
98529 GAACCTCTGAACACTTACCATTATTTAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98559 GAACCTCTGAACACCTACCATTATCTAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98589 GAACCTCTGAGCACCTACCATTATCAAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
* *
98619 GAACCTCTGAGCACCTACCATTATCTAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98649 GAACCTCTGAACACCTACCATTATCTAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98679 GAACTTCTGAACACCTACCATTATCAAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
98709 GAACCTCTGAACACCTACCATTATCAAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
* * *
98739 GAACCTCTGAACACTTATCATTATCAGAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98769 GAACCTCTGAACACTTACCATTATCAAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98799 GAACCTCTGAACACTTACCATTAT------
1 GAACCTCTGAACACCTACCATTATCAAAGA
* *
98823 ----CTCTGAGCACCTACCATTATCTAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98849 GAACCTCTGAACACCTACCATTATCTAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98879 GAACTTCTGAACACCTACCATTATCAAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
98909 GAACCTCTGAACACCTACCATTATCAAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
* * *
98939 GAACCTCTGAACACTTATCATTATCAGAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
*
98969 GAACCTCTGAACACTTACCATTATCAAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
* **
98999 GAACCTCTGAACACTTACCATTATTTAAGA
1 GAACCTCTGAACACCTACCATTATCAAAGA
* *
99029 GAACCTCTGAACACTTACCTTTATC
1 GAACCTCTGAACACCTACCATTATC
99054 TATGTGAACT
Statistics
Matches: 482, Mismatches: 33, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
20 18 0.04
30 464 0.96
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (30 bp):
GAACCTCTGAACACCTACCATTATCAAAGA
Found at i:98828 original size:20 final size:20
Alignment explanation
Indices: 98803--98844 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
98793 CAAAGAGAAC
*
98803 CTCTGAACACTTACCATTAT
1 CTCTGAACACCTACCATTAT
*
98823 CTCTGAGCACCTACCATTAT
1 CTCTGAACACCTACCATTAT
98843 CT
1 CT
98845 AAGAGAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.07, T:0.33
Consensus pattern (20 bp):
CTCTGAACACCTACCATTAT
Found at i:98854 original size:20 final size:20
Alignment explanation
Indices: 98814--98854 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
98804 TCTGAACACT
** *
98814 TACCATTATCTCTGAGCACC
1 TACCATTATCTAAGAGAACC
98834 TACCATTATCTAAGAGAACC
1 TACCATTATCTAAGAGAACC
98854 T
1 T
98855 CTGAACACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (20 bp):
TACCATTATCTAAGAGAACC
Found at i:98942 original size:170 final size:170
Alignment explanation
Indices: 98653--98993 Score: 601
Period size: 170 Copynumber: 2.0 Consensus size: 170
98643 CTAAGAGAAC
*
98653 CTCTGAACACCTACCATTATCTAAGAGAACTTCTGAACACCTACCATTATCAAAGAGAACCTCTG
1 CTCTGAACACCTACCATTATCTAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTG
* * *
98718 AACACCTACCATTATCAAAGAGAACCTCTGAACACTTATCATTATCAGAGAGAACCTCTGAACAC
66 AACACCTACCATTATCAAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTGAACAC
98783 TTACCATTATCAAAGAGAACCTCTGAACACTTACCATTAT
131 TTACCATTATCAAAGAGAACCTCTGAACACTTACCATTAT
* * *
98823 CTCTGAGCACCTACCATTATCTAAGAGAACCTCTGAACACCTACCATTATCTAAGAGAACTTCTG
1 CTCTGAACACCTACCATTATCTAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTG
98888 AACACCTACCATTATCAAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTGAACAC
66 AACACCTACCATTATCAAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTGAACAC
* *
98953 TTATCATTATCAGAGAGAACCTCTGAACACTTACCATTAT
131 TTACCATTATCAAAGAGAACCTCTGAACACTTACCATTAT
98993 C
1 C
98994 AAAGAGAACC
Statistics
Matches: 162, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
170 162 1.00
ACGTcount: A:0.37, C:0.28, G:0.10, T:0.25
Consensus pattern (170 bp):
CTCTGAACACCTACCATTATCTAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTG
AACACCTACCATTATCAAAGAGAACCTCTGAACACCTACCATTATCAAAGAGAACCTCTGAACAC
TTACCATTATCAAAGAGAACCTCTGAACACTTACCATTAT
Found at i:102505 original size:22 final size:23
Alignment explanation
Indices: 102480--102524 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
102470 TGAAAGCTAA
*
102480 TTTTTGG-TGGGATCGAGATTTT
1 TTTTTGGTTGGGATCAAGATTTT
102502 TTTTTGGTTTGGGATCAAGATTT
1 TTTTTGG-TTGGGATCAAGATTT
102525 CATCGGGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.16, C:0.04, G:0.29, T:0.51
Consensus pattern (23 bp):
TTTTTGGTTGGGATCAAGATTTT
Found at i:102940 original size:30 final size:30
Alignment explanation
Indices: 102906--102967 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
102896 CATATGAAAC
102906 TTTGTTTCCTTGGTATTAACTAAGATTAAA
1 TTTGTTTCCTTGGTATTAACTAAGATTAAA
102936 TTTGTTTCCTTGGTATTAACTAAGATTAAA
1 TTTGTTTCCTTGGTATTAACTAAGATTAAA
102966 TT
1 TT
102968 ATAAAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (30 bp):
TTTGTTTCCTTGGTATTAACTAAGATTAAA
Found at i:104151 original size:208 final size:207
Alignment explanation
Indices: 103793--104208 Score: 814
Period size: 208 Copynumber: 2.0 Consensus size: 207
103783 GGTTGACTAT
103793 TGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACAG
1 TGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACAG
*
103858 AAACGCGGAAGAAAAAATCTTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGATG
66 AAACGCGGAAGAAAAAATCGTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGATG
103923 TGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGGC
131 TGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGGC
103988 TTAAATTTTAGA
196 TTAAATTTTAGA
104000 NTGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACA
1 -TGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACA
104065 GAAACGCGGAAGAAAAAATCGTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGAT
65 GAAACGCGGAAGAAAAAATCGTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGAT
104130 GTGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGG
130 GTGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGG
104195 CTTAAATTTTAGA
195 CTTAAATTTTAGA
104208 T
1 T
104209 AAAAGCCTTC
Statistics
Matches: 207, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
207 1 0.00
208 206 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (207 bp):
TGGACCTTCGATTTAATGAACCTTCTGGTTACTGGGCAGACCCCTTGTTCATCATTACGAAACAG
AAACGCGGAAGAAAAAATCGTGGATTTCTTGACCATAGTTGTTTTGCAGATATAATGTACTGATG
TGTGTGAATCTAGACATCATGGAAAGTGAACCCCCAATAAACATGATAAACCTTTTATGCTCGGC
TTAAATTTTAGA
Found at i:107344 original size:32 final size:31
Alignment explanation
Indices: 107273--107383 Score: 141
Period size: 31 Copynumber: 3.5 Consensus size: 31
107263 TTCAGGCAAA
*
107273 GGGGTCATTTTTCTACGAAGAATAATGACCG
1 GGGGTCATTTTTCTACGTAGAATAATGACCG
*
107304 GGGGTCATTTTTCTGCGTAGAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACC-G
* * *
107336 GGGGTCATTATTCTACGTAGAAAAATGACCC
1 GGGGTCATTTTTCTACGTAGAATAATGACCG
** *
107367 CCGGTCATTATTCTACG
1 GGGGTCATTTTTCTACG
107384 GGGGTCATTA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 43 0.61
32 28 0.39
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (31 bp):
GGGGTCATTTTTCTACGTAGAATAATGACCG
Found at i:108189 original size:2 final size:2
Alignment explanation
Indices: 108182--108210 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
108172 GCTAGGTGAT
108182 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
108211 CCGATGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:108406 original size:4 final size:4
Alignment explanation
Indices: 108399--108435 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
108389 ACTCTCTCTG
* *
108399 TGTC TGTC TGGC TGTC TGTC TGTC TGTC TCTC TGTC T
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC T
108436 CTCTCTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.27, G:0.24, T:0.49
Consensus pattern (4 bp):
TGTC
Found at i:108433 original size:12 final size:12
Alignment explanation
Indices: 108391--108457 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
108381 ACTACAAAAC
108391 TCTCTCTG--TG
1 TCTCTCTGTCTG
* *
108401 TCTGTCTGGCTG
1 TCTCTCTGTCTG
*
108413 TCTGTCTGTCTG
1 TCTCTCTGTCTG
*
108425 TCTCTCTGTCTCTC
1 TCTCTCTG--TCTG
*
108439 TCTCTCTCTCTG
1 TCTCTCTGTCTG
108451 TCTCTCT
1 TCTCTCT
108458 CTCTCTCTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 7 0.15
12 30 0.64
14 10 0.21
ACGTcount: A:0.00, C:0.34, G:0.16, T:0.49
Consensus pattern (12 bp):
TCTCTCTGTCTG
Found at i:108436 original size:8 final size:8
Alignment explanation
Indices: 108393--108465 Score: 65
Period size: 8 Copynumber: 8.9 Consensus size: 8
108383 TACAAAACTC
*
108393 TCTCTGTG
1 TCTCTCTG
*
108401 TCTGTCTG
1 TCTCTCTG
* *
108409 GCTGTCTG
1 TCTCTCTG
*
108417 TCTGTCTG
1 TCTCTCTG
108425 TCTCTCTG
1 TCTCTCTG
*
108433 TCTCTCTCTC
1 --TCTCTCTG
108443 TCTCTCTG
1 TCTCTCTG
*
108451 TCTCTCTC
1 TCTCTCTG
108459 TCTCTCT
1 TCTCTCT
108466 CATATCGACA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
8 48 0.87
10 7 0.13
ACGTcount: A:0.00, C:0.36, G:0.15, T:0.49
Consensus pattern (8 bp):
TCTCTCTG
Found at i:108438 original size:2 final size:2
Alignment explanation
Indices: 108425--108466 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
108415 TGTCTGTCTG
* *
108425 TC TC TC TG TC TC TC TC TC TC TC TC TG 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
108467 ATATCGACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (2 bp):
TC
Found at i:108976 original size:7 final size:7
Alignment explanation
Indices: 108961--109027 Score: 64
Period size: 7 Copynumber: 9.6 Consensus size: 7
108951 TTTAGATATG
108961 GAATCTC
1 GAATCTC
*
108968 GAATTTC
1 GAATCTC
108975 GAATCTC
1 GAATCTC
108982 GAATCTC
1 GAATCTC
*
108989 -ATATTTC
1 GA-ATCTC
108996 GAATCTC
1 GAATCTC
* * *
109003 GTATTTT
1 GAATCTC
109010 GAATCTC
1 GAATCTC
*
109017 GAATCTT
1 GAATCTC
109024 GAAT
1 GAAT
109028 GATCCTTCTC
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
6 1 0.02
7 45 0.96
8 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (7 bp):
GAATCTC
Found at i:108986 original size:21 final size:21
Alignment explanation
Indices: 108961--109027 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
108951 TTTAGATATG
108961 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
108982 GAATCTC-ATATTTCGAATCTC
1 GAATCTCGA-ATTTCGAATCTC
* * * * *
109003 GTATTTTGAATCTCGAATCTT
1 GAATCTCGAATTTCGAATCTC
109024 GAAT
1 GAAT
109028 GATCCTTCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:117510 original size:13 final size:13
Alignment explanation
Indices: 117492--117517 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
117482 GACAGTTTTA
117492 AATAAAGTACCCG
1 AATAAAGTACCCG
117505 AATAAAGTACCCG
1 AATAAAGTACCCG
117518 TCAATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (13 bp):
AATAAAGTACCCG
Found at i:119457 original size:12 final size:12
Alignment explanation
Indices: 119430--119489 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
119420 CCTCATCGGG
* *
119430 TGTTGTTTTTTG
1 TGTTGTTCTTTC
* *
119442 TGTTATTCTATC
1 TGTTGTTCTTTC
*
119454 TGTTGTTTTTTC
1 TGTTGTTCTTTC
119466 TGTTGTTCTTTC
1 TGTTGTTCTTTC
*
119478 TGTTGTTTTTTC
1 TGTTGTTCTTTC
119490 CGAAACTACA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.03, C:0.10, G:0.17, T:0.70
Consensus pattern (12 bp):
TGTTGTTCTTTC
Found at i:119462 original size:24 final size:24
Alignment explanation
Indices: 119430--119489 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
119420 CCTCATCGGG
*
119430 TGTTGTTTTTTGTGTTATTCTATC
1 TGTTGTTTTTTCTGTTATTCTATC
* *
119454 TGTTGTTTTTTCTGTTGTTCTTTC
1 TGTTGTTTTTTCTGTTATTCTATC
119478 TGTTGTTTTTTC
1 TGTTGTTTTTTC
119490 CGAAACTACA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.03, C:0.10, G:0.17, T:0.70
Consensus pattern (24 bp):
TGTTGTTTTTTCTGTTATTCTATC
Found at i:119584 original size:2 final size:2
Alignment explanation
Indices: 119579--119612 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
119569 AGAGAGAAAG
119579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
119613 GAGAGAGAGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119617 original size:2 final size:2
Alignment explanation
Indices: 119612--119691 Score: 115
Period size: 2 Copynumber: 40.0 Consensus size: 2
119602 ATATATATAT
119612 AG AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG AG
* * * * *
119654 AN AT AT AT AC AG 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 AG AG AG AG AG AG
119692 GGGATACATG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.01, G:0.44, T:0.04
Consensus pattern (2 bp):
AG
Found at i:123700 original size:15 final size:15
Alignment explanation
Indices: 123680--123710 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
123670 TGTTTGGATG
*
123680 TTATTTGGATGAAGA
1 TTATTTGAATGAAGA
123695 TTATTTGAATGAAGA
1 TTATTTGAATGAAGA
123710 T
1 T
123711 GATTAAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (15 bp):
TTATTTGAATGAAGA
Found at i:132766 original size:2 final size:2
Alignment explanation
Indices: 132759--132814 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
132749 GATGAGTTGG
132759 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
132801 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
132815 TTATCAAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:139300 original size:8 final size:8
Alignment explanation
Indices: 139272--139368 Score: 64
Period size: 8 Copynumber: 12.8 Consensus size: 8
139262 ACATATTGAC
139272 CCTTATAAT
1 CCTTAT-AT
139281 CC-T-TAT
1 CCTTATAT
139287 CCTTATAT
1 CCTTATAT
139295 -CTT-TAT
1 CCTTATAT
139301 CCTTATAT
1 CCTTATAT
*
139309 CCTTATAA
1 CCTTATAT
*
139317 CCTTATAA
1 CCTTATAT
* *
139325 ACAT-TAT
1 CCTTATAT
*
139332 CCTTATAA
1 CCTTATAT
*
139340 CCTTATAAA
1 CCTTAT-AT
139349 CC-T-TAT
1 CCTTATAT
*
139355 CCTTATAA
1 CCTTATAT
139363 CCTTAT
1 CCTTAT
139369 CCTTATAGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
6 10 0.14
7 14 0.20
8 41 0.58
9 6 0.08
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (8 bp):
CCTTATAT
Found at i:139302 original size:14 final size:14
Alignment explanation
Indices: 139272--139338 Score: 62
Period size: 15 Copynumber: 4.5 Consensus size: 14
139262 ACATATTGAC
*
139272 CCTTATAATCCTTAT
1 CCTTAT-ATCTTTAT
139287 CCTTATATCTTTAT
1 CCTTATATCTTTAT
*
139301 CCTTATATCCTTATAA
1 CCTTATAT-CTT-TAT
* *
139317 CCTTATAAACATTAT
1 CCTTAT-ATCTTTAT
139332 CCTTATA
1 CCTTATA
139339 ACCTTATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
14 16 0.36
15 17 0.39
16 10 0.23
17 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (14 bp):
CCTTATATCTTTAT
Found at i:139336 original size:23 final size:23
Alignment explanation
Indices: 139306--139368 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
139296 TTTATCCTTA
139306 TATCCTTATAACCTTATAAACAT
1 TATCCTTATAACCTTATAAACAT
*
139329 TATCCTTATAACCTTATAAACCT
1 TATCCTTATAACCTTATAAACAT
139352 TATCCTTATAACCTTAT
1 TATCCTTATAACCTTAT
139369 CCTTATAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (23 bp):
TATCCTTATAACCTTATAAACAT
Found at i:139364 original size:14 final size:14
Alignment explanation
Indices: 139272--139375 Score: 101
Period size: 14 Copynumber: 7.5 Consensus size: 14
139262 ACATATTGAC
139272 CCTTATAATCCTTAT
1 CCTTATAA-CCTTAT
* *
139287 CCTTATATCTTTAT
1 CCTTATAACCTTAT
*
139301 CCTTATATCCTTAT
1 CCTTATAACCTTAT
*
139315 AACCTTATAAACATTAT
1 --CCTTAT-AACCTTAT
139332 CCTTATAACCTTA-
1 CCTTATAACCTTAT
139345 ---TA-AACCTTAT
1 CCTTATAACCTTAT
139355 CCTTATAACCTTAT
1 CCTTATAACCTTAT
139369 CCTTATA
1 CCTTATA
139376 GATGTTTTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.09
10 2 0.03
13 2 0.03
14 39 0.52
15 13 0.17
16 6 0.08
17 6 0.08
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (14 bp):
CCTTATAACCTTAT
Found at i:151301 original size:3 final size:3
Alignment explanation
Indices: 151293--151348 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
151283 GTCAAAACCG
151293 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
151341 GAA GAA GA
1 GAA GAA GA
151349 CGACACATGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:151946 original size:11 final size:11
Alignment explanation
Indices: 151930--151957 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
151920 ATGGATAAAA
151930 AAAACTGTTTG
1 AAAACTGTTTG
151941 AAAACTGTTTG
1 AAAACTGTTTG
151952 AAAACT
1 AAAACT
151958 TATCTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (11 bp):
AAAACTGTTTG
Found at i:152662 original size:11 final size:11
Alignment explanation
Indices: 152632--152663 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
152622 TAAAGACGAT
*
152632 CTTTAAGCCAC
1 CTTTAAGCTAC
152643 CTTTAAGCTAC
1 CTTTAAGCTAC
152654 CTTTAAGCTA
1 CTTTAAGCTA
152664 TATGTATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:152722 original size:22 final size:22
Alignment explanation
Indices: 152672--152724 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
152662 TATATGTATT
*
152672 GCTTAAAGGTGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
152694 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
152716 GCTTAAAGA
1 GCTTAAAGA
152725 CTATCTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:152805 original size:11 final size:11
Alignment explanation
Indices: 152789--152842 Score: 90
Period size: 11 Copynumber: 4.9 Consensus size: 11
152779 GTCCAAACTT
152789 CTTTAAGCCAC
1 CTTTAAGCCAC
152800 CTTTAAGCCAC
1 CTTTAAGCCAC
* *
152811 ATTTAAGCTAC
1 CTTTAAGCCAC
152822 CTTTAAGCCAC
1 CTTTAAGCCAC
152833 CTTTAAGCCA
1 CTTTAAGCCA
152843 TTAAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:159679 original size:19 final size:17
Alignment explanation
Indices: 159655--159696 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
159645 CATAGTCTTA
159655 TTTAAAAGTTAATATAATG
1 TTTAAAAGTT--TATAATG
*
159674 TTTAAATGTTTATAATG
1 TTTAAAAGTTTATAATG
159691 TTTAAA
1 TTTAAA
159697 TTTTAGCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.59
19 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (17 bp):
TTTAAAAGTTTATAATG
Found at i:159689 original size:17 final size:16
Alignment explanation
Indices: 159667--159701 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
159657 TAAAAGTTAA
159667 TATAATGTTTAAATGTT
1 TATAATGTTTAAAT-TT
159684 TATAATGTTTAAATTT
1 TATAATGTTTAAATTT
159700 TA
1 TA
159702 GCAATGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (16 bp):
TATAATGTTTAAATTT
Found at i:159707 original size:17 final size:17
Alignment explanation
Indices: 159670--159709 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
159660 AAGTTAATAT
*
159670 AATGTTTAAATGTTTAT
1 AATGTTTAAATGTTTAC
159687 AATGTTTAAAT-TTTAGC
1 AATGTTTAAATGTTTA-C
159704 AATGTT
1 AATGTT
159710 CAATTATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
AATGTTTAAATGTTTAC
Found at i:163733 original size:4 final size:4
Alignment explanation
Indices: 163724--163770 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
163714 ACTGAAGTGG
* *
163724 GACA GACA GACA GACA GACA GACG GACG GACA GACA GA-A GGACA GAC
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA -GACA GAC
163771 GGACTGACGG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 1 0.03
4 37 0.95
5 1 0.03
ACGTcount: A:0.45, C:0.23, G:0.32, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:163774 original size:8 final size:8
Alignment explanation
Indices: 163723--163782 Score: 66
Period size: 8 Copynumber: 7.5 Consensus size: 8
163713 AACTGAAGTG
163723 GGACAGAC
1 GGACAGAC
*
163731 AGACAGAC
1 GGACAGAC
*
163739 AGACAGAC
1 GGACAGAC
*
163747 GGACGGAC
1 GGACAGAC
* *
163755 AGACAGAA
1 GGACAGAC
163763 GGACAGAC
1 GGACAGAC
*
163771 GGACTGAC
1 GGACAGAC
163779 GGAC
1 GGAC
163783 GCAGAGGAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.40, C:0.23, G:0.35, T:0.02
Consensus pattern (8 bp):
GGACAGAC
Found at i:170572 original size:140 final size:140
Alignment explanation
Indices: 170235--170630 Score: 621
Period size: 140 Copynumber: 2.8 Consensus size: 140
170225 ATCTTAGAAA
* * *
170235 GAAGTATTTGGCGCATTCTGATATTCGTCAGCACCAATGTTTTCATACGTTTCATGACCTGTATA
1 GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA
170300 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATGAAGATTGTTGATTATCTTTTT
66 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTG-T-TATAT----A-TGTTGATTATCTTTTT
*
170365 CTGTACGCTCTCTCATC
124 CTGTACACTCTCTCATC
* *
170382 GAAATGTTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA
1 GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA
170447 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATGTTGATTATCTTTTTCTGTACA
66 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATGTTGATTATCTTTTTCTGTACA
*
170512 CTCTCTCATT
131 CTCTCTCATC
* *
170522 GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGCTTTCATACGTTTCAAGACCTGTATA
1 GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA
* * *
170587 ACTAGTTCTCGAAGTATTACGGTGACTTTGGCTTGTTATATATG
66 ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATG
170631 AAGATTGTTG
Statistics
Matches: 235, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
140 133 0.57
141 1 0.00
145 5 0.02
146 1 0.00
147 95 0.40
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (140 bp):
GAAGTATTTGGCGCATTCTGGTATTCCTCAGCATCAATGTTTTCATACGTTTCATGACCTGTATA
ACTAGTTCTCGAAGTTTTACGGTCACTGTGGCTTGTTATATATGTTGATTATCTTTTTCTGTACA
CTCTCTCATC
Found at i:171129 original size:2 final size:2
Alignment explanation
Indices: 171122--171151 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
171112 NNNNNNNNNN
171122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
171152 CACACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:173005 original size:11 final size:12
Alignment explanation
Indices: 172979--173005 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
172969 GTTCATTGAC
172979 TTTTATCTTTAT
1 TTTTATCTTTAT
172991 TTTTATCTTTAT
1 TTTTATCTTTAT
173003 TTT
1 TTT
173006 GTTTGAGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATCTTTAT
Found at i:181982 original size:2 final size:2
Alignment explanation
Indices: 181975--182019 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
181965 AAACTGGTAA
181975 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
182017 TC T
1 TC T
182020 NNNNNNNNNN
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:185379 original size:2 final size:2
Alignment explanation
Indices: 185372--185410 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
185362 AAGGCATGAA
*
185372 AG AG AG AG AG AG AG AG AG AG AG TG 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 AG A
185411 TTAATTACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
AG
Found at i:193708 original size:24 final size:24
Alignment explanation
Indices: 193676--193754 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
193666 CCTCATCGGG
* *
193676 TGTTGTTTTTTCTATTTTTCTTTC
1 TGTTGTTTTTTCTGTTGTTCTTTC
*
193700 TGTTGTTTTTTCTGTCGTTCTTTC
1 TGTTGTTTTTTCTGTTGTTCTTTC
193724 TGTTGTTTTTTCTGTTGTTCTTTC
1 TGTTGTTTTTTCTGTTGTTCTTTC
193748 TGTTGTT
1 TGTTGTT
193755 CCTTCTGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.01, C:0.13, G:0.15, T:0.71
Consensus pattern (24 bp):
TGTTGTTTTTTCTGTTGTTCTTTC
Found at i:193755 original size:12 final size:12
Alignment explanation
Indices: 193676--193762 Score: 111
Period size: 12 Copynumber: 7.2 Consensus size: 12
193666 CCTCATCGGG
*
193676 TGTTGTTTTTTC
1 TGTTGTTCTTTC
* *
193688 TATTTTTCTTTC
1 TGTTGTTCTTTC
*
193700 TGTTGTTTTTTC
1 TGTTGTTCTTTC
*
193712 TGTCGTTCTTTC
1 TGTTGTTCTTTC
*
193724 TGTTGTTTTTTC
1 TGTTGTTCTTTC
193736 TGTTGTTCTTTC
1 TGTTGTTCTTTC
*
193748 TGTTGTTCCTTC
1 TGTTGTTCTTTC
193760 TGT
1 TGT
193763 AACGACATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.01, C:0.15, G:0.15, T:0.69
Consensus pattern (12 bp):
TGTTGTTCTTTC
Found at i:194666 original size:433 final size:432
Alignment explanation
Indices: 193927--194764 Score: 1324
Period size: 433 Copynumber: 1.9 Consensus size: 432
193917 TCAAAGGGTG
* * * *
193927 ATATTTTGAAATATCTTACGATGTCCTACTACATCCATGAAAAAGTTTTTCTCTACCATACTAAA
1 ATATTTTAAAATATCTTAAGATGCCCTACTACATCCATGAAAAAGTTTTTCTCTACCACACTAAA
* *
193992 CAAAAGAGATACAAAAACCAATTAATTAAGAGATTTCCAGATGACCTTGACCTTTGACCTTTATG
66 CAAAAGAGATACAAAAACCAATTAATTAAGAGATTTCCAGATGACCTTGACCTTTGAACTATATG
*
194057 TCATTTTGTGCGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTCTATGATAAGTAAT
131 TCATTTTGTGCGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTCTATGATAAATAAT
*
194122 AAAAAAGTTGGAAGTGGTTTTATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGG
196 AAAAAAGTTGGAAGTGATTTTATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGG
*
194187 GGCTCAGATCCTTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAA
261 GGCTCAGATCCTTTCGGTATGAATAAATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAA
* *
194252 AGTTTCAAGTTTCTATCTCTTATGGTTTCAGAGGAGTAGCCATAACAAGCTTTTCGTACAAAAGG
326 AGTTCCAAGTCTCTATCTCTTATGGTTTCAGAGGAGTAGCCATAACAAGCTTTTCGTACAAAA-G
194317 GGCAATAACTCTGTAACTATTTAAAAGAAGGAGCCAAGGGGAT
390 GGCAATAACTCTGTAACTATTTAAAAGAAGGAGCCAAGGGGAT
* * * * *
194360 ATATTTTAAAATGTCTTAAGATGCCCTATTGCATCCATGAAAAAGTTTTTCTTTACTACACTAAA
1 ATATTTTAAAATATCTTAAGATGCCCTACTACATCCATGAAAAAGTTTTTCTCTACCACACTAAA
**
194425 CAAAAGAGAT-CTAAAAACTC-ATTAATTAAGAGATTTTGAGATGACCTTGACCTTTGAACTATA
66 CAAAAGAGATAC-AAAAAC-CAATTAATTAAGAGATTTCCAGATGACCTTGACCTTTGAACTATA
** *
194488 TGTCATTTTGTTTGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTTTATGATAAATA
129 TGTCATTTTGTGCGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTCTATGATAAATA
*
194553 ATAAAAAAGTTGGAAGTGATTTTATGGAAAT-TCAAATACTTTCAGGGGCAATAACTGA-TAGAA
194 ATAAAAAAGTTGGAAGTGATTTTATAGAAATGT-AAATACTTTCAGGGGCAATAACT-ACTAGAA
* * * * *
194616 GGGGGTCTCGGATCCTTTCGGTATTAGTAAATTGAAGAACCCTCTAAGTGTACTGGAGACATTGG
257 GGGGGGCTCAGATCCTTTCGGTATGAATAAATTGAAGAACCCTCTAAGTGTACTGAAGACATTGG
* * *
194681 TAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCAGAGGAGTTGCGATAACAAGCTTTTCGTACAC
322 TAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCAGAGGAGTAGCCATAACAAGCTTTTCGTACAA
*
194746 AAGGGCAATAACTTTGTAA
387 AAGGGCAATAACTCTGTAA
194765 GTTCTGGGAG
Statistics
Matches: 370, Mismatches: 31, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
432 18 0.05
433 350 0.95
434 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (432 bp):
ATATTTTAAAATATCTTAAGATGCCCTACTACATCCATGAAAAAGTTTTTCTCTACCACACTAAA
CAAAAGAGATACAAAAACCAATTAATTAAGAGATTTCCAGATGACCTTGACCTTTGAACTATATG
TCATTTTGTGCGGCCAAGGTAGACGCTTCCATCCCAAGTGGTCCGAAGTCTCTATGATAAATAAT
AAAAAAGTTGGAAGTGATTTTATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGG
GGCTCAGATCCTTTCGGTATGAATAAATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAA
AGTTCCAAGTCTCTATCTCTTATGGTTTCAGAGGAGTAGCCATAACAAGCTTTTCGTACAAAAGG
GCAATAACTCTGTAACTATTTAAAAGAAGGAGCCAAGGGGAT
Found at i:195823 original size:433 final size:432
Alignment explanation
Indices: 195225--196216 Score: 1408
Period size: 433 Copynumber: 2.3 Consensus size: 432
195215 TTGGACCCTG
* * * * *
195225 TCGGTATGAATAGATTGAAGAAGCGTCTAAGTATACTGAATACATTAGTAAAAGTTTCAAGTCTC
1 TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAGTCTC
* * * *
195290 TATCTCTAACGG-TTAATGAGGAGTAGCGATAACAAGCATTTTGTACAATAGGGGCAATAACTCT
66 TATCTCTTATGGTTTCA-GAGGAGTAGCGATAACAAGC-TTTTGTACAAAAGGGGCAATAACTCT
* * *
195354 ATAATTGTAACATGGTAAGGGTCAAAGGGTTATATTTTGAAATGTCTTAAGATGTCCTACTACAT
129 ATAATTGTAACATAGTAAGGGTCAAAGGGATATATTTTAAAATGTCTTAAGATGTCCTACTACAT
* * *
195419 CCATGAAAAAGTTTTTCTCTACCATCCTAAACAAAAGAGATCTAAAAACTCATT-ATTTAACAGA
194 CCATGAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCCAAAAACCCATTAATTT-ACAGA
195483 TTTCCAAATGACCTTGACCTTTGACCTTTATGTCATTTTGTTCGGCAAA-AGTAAACGCTTCCAT
258 TTTCCAAATGACCTTGACCTTTGACCTTTATGTCATTTTGTTCGGCAAAGA-TAAACGCTTCCAT
* * * *
195547 CCCAAGTGGTCCGAAGTCTCTATGATAAGTAATAAAAAAGTTGGATGTGATTTTATAGAAATGTA
322 CCCAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTAAAGAAATGTA
* *
195612 AATAATTTCAGGAGCAATAACTACTAGAAGGGGGGCTCAGATCCTT
387 AATAAGTTCAGGAGCAATAACTACTAGAAGGAGGGCTCAGATCCTT
* * *
195658 TCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAATTTC
1 TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAGTCTC
* *
195723 TATCTCTTGTGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCAGT-CAAAAGGGGCAATTACTCT
66 TATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTT--GTACAAAAGGGGCAATAACTCT
* * * *
195787 GTAACTATTTAA-A-AG-AAGGAG-CCAAGGTGATATATTTTAAAATGTCTTAAGATGTCCTATT
129 ATAA-T-TGTAACATAGTAAGG-GTCAAAGG-GATATATTTTAAAATGTCTTAAGATGTCCTACT
*
195848 ACATCCATGAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCCAAAAACCCATTAATTTCC
190 ACATCCATGAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCCAAAAACCCATTAATTTAC
* * * * * *
195913 AGATTTTCAGATGACCTTGGCCTTTGACCTTTATGTCATTTTGTTCGGCCAAGATAGACGCTTCT
255 AGATTTCCAAATGACCTTGACCTTTGACCTTTATGTCATTTTGTTCGGCAAAGATAAACGCTTCC
* *
195978 ATCCCAAGTGGTCCGAAGTTTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTAAAGATATG
320 ATCCCAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTAAAGAAATG
* * * *
196043 TTAATACGTTCAGGGGCAATAACTACTTGAAGGAGGGCTCAGATCCTT
385 TAAATAAGTTCAGGAGCAATAACTACTAGAAGGAGGGCTCAGATCCTT
*
196091 TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTCCAAGTCTC
1 TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAGTCTC
* *
196156 TATCTCTTATGGTTTCAGAGGAGTAGTGATAACAAGCTTTTTGTACACAA-GGGCAATAACT
66 TATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGC-TTTTGTACAAAAGGGGCAATAACT
196217 TTGTAAGTTC
Statistics
Matches: 498, Mismatches: 50, Indels: 23
0.87 0.09 0.04
Matches are distributed among these distances:
432 25 0.05
433 453 0.91
434 16 0.03
435 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (432 bp):
TCGGTATGAATAGATTGAAGAACCATCTAAGTGTACTGAAGACATTGGTAAAAGTTTCAAGTCTC
TATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTGTACAAAAGGGGCAATAACTCTAT
AATTGTAACATAGTAAGGGTCAAAGGGATATATTTTAAAATGTCTTAAGATGTCCTACTACATCC
ATGAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCCAAAAACCCATTAATTTACAGATTT
CCAAATGACCTTGACCTTTGACCTTTATGTCATTTTGTTCGGCAAAGATAAACGCTTCCATCCCA
AGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTAAAGAAATGTAAATA
AGTTCAGGAGCAATAACTACTAGAAGGAGGGCTCAGATCCTT
Found at i:196418 original size:54 final size:54
Alignment explanation
Indices: 196354--196517 Score: 266
Period size: 54 Copynumber: 3.1 Consensus size: 54
196344 AGAAAAAAAA
196354 TAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
1 TAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
*
196408 TAATAAAAAACATAAGAAATACAATAGGTCTTTCACCTGAAAGGTGGAAAGACC
1 TAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
*
196462 ---T-AAAAACATAAAGAAA-ACAAGAGGTCTTTCACCTGAAAGGTGGAAAGACC
1 TAATAAAAAACAT-AAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
196512 TAATAA
1 TAATAA
196518 TGATTAAATC
Statistics
Matches: 103, Mismatches: 2, Indels: 10
0.90 0.02 0.09
Matches are distributed among these distances:
50 41 0.40
51 7 0.07
53 1 0.01
54 54 0.52
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (54 bp):
TAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
Found at i:199266 original size:2 final size:2
Alignment explanation
Indices: 199259--199292 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
199249 ATTAATATGC
*
199259 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
199293 AAATAAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:203767 original size:182 final size:179
Alignment explanation
Indices: 203547--203880 Score: 503
Period size: 182 Copynumber: 1.8 Consensus size: 179
203537 AAGGTGTACC
*
203547 CTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATT-
1 CTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCAAAAATT-TTC
*
203611 GGAAATCAAAATCCTACCAATTATG-CACACCTCTGATATATGTACAATTGA-TCTGCAAAAGAA
65 GGAAATCAAAATCCTACCAA-TATGACACACCTCTGATATATGTACAA-TAATTCTGCAAAAGAA
* *
203674 CAACTTCCTATCTTGAAAAATGTAGACGGAGTTATCCGTACAATGAGGGTATA
128 CAAATTCCTAACTT-AAAAATGTAGACGGAGTTATCCGTACAATGAGGGTATA
* * *
203727 CTATATGCAATATTTTGCCCAAAAAATGACTTAGTTCAAAAGCTTGTGTTTTTTTCAAAAATTTT
1 CTATATGCAATATTTTG-CC-AAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCAAAAATTTT
*
203792 CGGAAATCAAAATCCTAGCAATATGCACACACCTCTGATATATGTACAATAATTCTGCAAAAGAA
64 CGGAAATCAAAATCCTACCAATATG-ACACACCTCTGATATATGTACAATAATTCTGCAAAAGAA
*
203857 CAAATTCCTAACTTAAAATTGTAG
128 CAAATTCCTAACTTAAAAATGTAG
203881 GAGGTACCCT
Statistics
Matches: 139, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
180 17 0.12
181 8 0.06
182 68 0.49
183 46 0.33
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (179 bp):
CTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCAAAAATTTTCG
GAAATCAAAATCCTACCAATATGACACACCTCTGATATATGTACAATAATTCTGCAAAAGAACAA
ATTCCTAACTTAAAAATGTAGACGGAGTTATCCGTACAATGAGGGTATA
Found at i:206841 original size:24 final size:24
Alignment explanation
Indices: 206809--206856 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
206799 TTAATGAAAT
*
206809 TAATAATTTGTTATAGTATTAATG
1 TAATAATTTGTAATAGTATTAATG
*
206833 TAATAATTTGTAATGGTATTAATG
1 TAATAATTTGTAATAGTATTAATG
206857 GTTTGGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (24 bp):
TAATAATTTGTAATAGTATTAATG
Found at i:207168 original size:16 final size:16
Alignment explanation
Indices: 207132--207170 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
207122 AAATGGAGTG
207132 CACACACATACATACA
1 CACACACATACATACA
*
207148 TACACACATACGA-ACA
1 CACACACATAC-ATACA
207164 CACACAC
1 CACACAC
207171 GCACGGTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.49, C:0.38, G:0.03, T:0.10
Consensus pattern (16 bp):
CACACACATACATACA
Found at i:217826 original size:17 final size:17
Alignment explanation
Indices: 217804--217839 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
217794 GTTCTGTTAA
217804 TGGTTTTTGGTCTAAGT
1 TGGTTTTTGGTCTAAGT
217821 TGGTTTTTGGTCTAAGT
1 TGGTTTTTGGTCTAAGT
217838 TG
1 TG
217840 CTTCTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.06, G:0.31, T:0.53
Consensus pattern (17 bp):
TGGTTTTTGGTCTAAGT
Found at i:217847 original size:17 final size:17
Alignment explanation
Indices: 217810--217848 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
217800 TTAATGGTTT
* *
217810 TTGGTCTAAGTTGGTTT
1 TTGGTCTAAGTTGCTTC
217827 TTGGTCTAAGTTGCTTC
1 TTGGTCTAAGTTGCTTC
217844 TTGGT
1 TTGGT
217849 TACTGGTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.28, T:0.51
Consensus pattern (17 bp):
TTGGTCTAAGTTGCTTC
Found at i:232207 original size:261 final size:261
Alignment explanation
Indices: 231743--232265 Score: 965
Period size: 261 Copynumber: 2.0 Consensus size: 261
231733 TTAAAAAGTG
231743 AATAAAGTGAAGCTGCATATTCATGATAATGACAAGCACTGTTTTTATTACGCAAATGTATCAAA
1 AATAAAGTGAAGCTGCATATTCATGATAATGACAAGCACTGTTTTTATTACGCAAATGTATCAAA
*
231808 AATGATTCAAAATAGTTTTATATGTTTAAAGACCTTATCTTCATTCTTGCAAAGGGGTTTGGAGA
66 AATGATTCAAAATAGTTTTATATGTTTAAAGACCTTATCTTCATTCTTGCAAAGGGATTTGGAGA
231873 GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG
131 GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG
* *
231938 ATTAAACTAGACAGGATCTCGTTGCAAGCAACGAAGAGGTCTTCCGTCTGATTTAGAATTTGAGA
196 ATTAAACTAGACACGATCTCGTTGCAAGCAACGAAGAGGCCTTCCGTCTGATTTAGAATTTGAGA
232003 T
261 T
* * *
232004 AATAAAGTGAAGCTGCATATTCATGTTAATGACAAGCACTGTTTTTTTTACGCAAATGTGTCAAA
1 AATAAAGTGAAGCTGCATATTCATGATAATGACAAGCACTGTTTTTATTACGCAAATGTATCAAA
*
232069 AATGATTCAAAATAGTTTTATATGTTTAAAGACTTTATCTTCATTCTTGCAAAGGGATTTGGAGA
66 AATGATTCAAAATAGTTTTATATGTTTAAAGACCTTATCTTCATTCTTGCAAAGGGATTTGGAGA
232134 GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG
131 GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG
* *
232199 ATTAAACTAGACACGATCTCGTTGCGAGCAACGAGGAGGCCTTCCGTCTGATTTAGAATTTGAGA
196 ATTAAACTAGACACGATCTCGTTGCAAGCAACGAAGAGGCCTTCCGTCTGATTTAGAATTTGAGA
232264 T
261 T
232265 A
1 A
232266 TATGTTCGAT
Statistics
Matches: 253, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
261 253 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (261 bp):
AATAAAGTGAAGCTGCATATTCATGATAATGACAAGCACTGTTTTTATTACGCAAATGTATCAAA
AATGATTCAAAATAGTTTTATATGTTTAAAGACCTTATCTTCATTCTTGCAAAGGGATTTGGAGA
GTTGCAGAGTGGGTTTACAAATATGAAGGGTAACAGACAAGTTAGTTTAACAAACGGATAATAAG
ATTAAACTAGACACGATCTCGTTGCAAGCAACGAAGAGGCCTTCCGTCTGATTTAGAATTTGAGA
T
Found at i:250139 original size:18 final size:18
Alignment explanation
Indices: 250087--250139 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
250077 TATTATGGTT
* *
250087 AGAGCTATTCATTTTCTT
1 AGAGCTATTCATTTGCTG
* *
250105 AAAGCTATTCATATGCTG
1 AGAGCTATTCATTTGCTG
*
250123 AGAGCTATTCGTTTGCT
1 AGAGCTATTCATTTGCT
250140 TAAAAGTTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (18 bp):
AGAGCTATTCATTTGCTG
Found at i:252795 original size:8 final size:8
Alignment explanation
Indices: 252784--252841 Score: 73
Period size: 8 Copynumber: 7.4 Consensus size: 8
252774 TAAAAAGTTT
252784 ACAGACGG
1 ACAGACGG
*
252792 ACAGACAG
1 ACAGACGG
* *
252800 ACGGACAG
1 ACAGACGG
252808 ACAGACGG
1 ACAGACGG
*
252816 ACGGACGG
1 ACAGACGG
252824 ACAGACGG
1 ACAGACGG
252832 AC-GACGG
1 ACAGACGG
252839 ACA
1 ACA
252842 AAATGTGATC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
7 7 0.16
8 36 0.84
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:252801 original size:12 final size:12
Alignment explanation
Indices: 252784--252841 Score: 73
Period size: 12 Copynumber: 4.9 Consensus size: 12
252774 TAAAAAGTTT
252784 ACAGACGGACAG
1 ACAGACGGACAG
252796 ACAGACGGACAG
1 ACAGACGGACAG
*
252808 ACAGACGGACGG
1 ACAGACGGACAG
* * *
252820 ACGGACAGACGG
1 ACAGACGGACAG
252832 AC-GACGGACA
1 ACAGACGGACA
252842 AAATGTGATC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 6 0.15
12 35 0.85
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:252834 original size:4 final size:4
Alignment explanation
Indices: 252787--252840 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
252777 AAAGTTTACA
* * * * *
252787 GACG GACA GACA GACG GACA GACA GACG GACG GACG GACA GACG GAC-
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
252834 GACG GAC
1 GACG GAC
252841 AAAATGTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 3 0.07
4 40 0.93
ACGTcount: A:0.35, C:0.26, G:0.39, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:260043 original size:20 final size:20
Alignment explanation
Indices: 260020--260069 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
260010 TATATGAAAT
260020 AATACTGTATCATATGC-TAC
1 AATACTGTATCATAT-CATAC
*
260040 AATAGTGTATCATATCATAC
1 AATACTGTATCATATCATAC
*
260060 AATACCGTAT
1 AATACTGTAT
260070 TATAAAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (20 bp):
AATACTGTATCATATCATAC
Found at i:261402 original size:165 final size:165
Alignment explanation
Indices: 260940--261967 Score: 977
Period size: 166 Copynumber: 6.1 Consensus size: 165
260930 ATTTGAAAGA
**
260940 TATATATTCCTATGTAAAAAGTT-GACCCCCCATTGTGGCCCCATCGAACCCCCAAGGGTCATGA
1 TATATATTCCTATGTAAAAA-TTGGACCCCCCATTGTGGCCCCATCCTA-CCCCAAGGGTCATGA
* * * * * * *
261004 TTTTCACAACTTTGAATTCTCACTACCTGAGGATGCTTCTATACAAGTTTCCGA-TTTCCTGG-C
64 TTTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTT-CAACTTTCCTGGCC
* * *
261067 ATAATGGTT-TCTGAGAAGAAGATCTTTAAAAATATACTC
128 A-AATGGTTCT-TGAGAAGAAGATTTTTAAAGATTTACTC
* * * * * ** * *
261106 TGTATATTTCTATGTAAAAATTCGTCCCACTTTTATGGACCCATCCTACCCCTAAGGGTCATGAT
1 TATATATTCCTATGTAAAAATTGGACCCCCCATTGTGGCCCCATCCTACCCC-AAGGGTCATGAT
* * * * *
261171 TTTCACAACTTTGAA-TCTACACTACCTGAGGATGTTTCCACACAAGTTTCCGA-TTTCCTGGCC
65 TTTCACAACCTTGAATTC-ACACTACCTAAGGATGCTTCCACATAAGTTT-CAACTTTCCTGGCC
*
261234 AAATGGTTCTTGAGAAGATGATTTTTAAAGATTTACTC
128 AAATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC
* ** *
261272 GATATATTTATATGTAAAAATTGGA-CCCCCATTGTGGCCCCAACCTACCCTCAAGGGTCAT-AG
1 TATATATTCCTATGTAAAAATTGGACCCCCCATTGTGGCCCCATCCTACCC-CAAGGGTCATGA-
* * * *
261335 TTTTCACAACCTTGAATTCACGCCAGCTAAGGATGCTTCCACATAAGTTTCAACTTTCCTTGCCA
64 TTTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTTCAACTTTCCTGGCCA
261400 AATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC
129 AATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC
* * * ***
261437 TATATTTTCCTATGTAAAAA-TGAAACCCCCCATTGTGGCCTCATCCTACCCTTGGGGTTCATGA
1 TATATATTCCTATGTAAAAATTG-GACCCCCCATTGTGGCCCCATCCTACCCCAAGGG-TCATGA
* ** * ** * * *
261501 TTTTCACAACTTTGAATTTTCACTACCCAAGGATGCTTTAACAAAAGTTTCAGCCTTT-CTGGCT
64 TTTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTTCA-ACTTTCCTGGCC
* * *
261565 GATTGCTT-TCTGAGAAGAA-ATTTTTTTTTTAAAGATTTACTC
128 AAATGGTTCT-TGAGAAGAAGA-----TTTTTAAAGATTTACTC
* * * * * *
261607 TATATATTCCTATGTAAAAAGTCGACCCCCAAATGTGGCCCCACCCTACCCCCAAGGGTCTTGAT
1 TATATATTCCTATGTAAAAATTGGACCCCCCATTGTGGCCCCATCCTA-CCCCAAGGGTCATGAT
* * * * * * *
261672 TTTCACAACCTTAAATTAACACTACCTGAGGGTGCTTCCATACT-AGTTTCAGCTTTCCTGGCCT
65 TTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACA-TAAGTTTCAACTTTCCTGGCCA
* * *
261736 CATGGTTCTTGAGAAGAAGATTTTTTAAAAATTTATTC
129 AATGGTTCTTGAGAAGAAGA-TTTTTAAAGATTTACTC
* * * *
261774 TATATATTCCTCTGTAAAAATTTGACCATCCCCCCCCCATTGTGGCCTCA-CCGTAACCCCGAGG
1 TATATATTCCTATGTAAAAA-TTG--GA----CCCCCCATTGTGGCCCCATCC-T-ACCCCAAGG
* * * *
261838 GTCATAATTTTCACAACCTTGAAATCACACCAACTAAGGATGCTTCCACATAAGTTTCAACTTTC
57 GTCATGATTTTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTTCAACTTTC
*
261903 CAGGCCAAATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC
122 CTGGCCAAATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC
261947 TATATATTCCTATGTAAAAAT
1 TATATATTCCTATGTAAAAAT
261968 NAAAAGGTGT
Statistics
Matches: 706, Mismatches: 120, Indels: 66
0.79 0.13 0.07
Matches are distributed among these distances:
164 5 0.01
165 144 0.20
166 242 0.34
167 43 0.06
168 1 0.00
169 4 0.01
170 120 0.17
171 9 0.01
172 1 0.00
173 37 0.05
174 99 0.14
175 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (165 bp):
TATATATTCCTATGTAAAAATTGGACCCCCCATTGTGGCCCCATCCTACCCCAAGGGTCATGATT
TTCACAACCTTGAATTCACACTACCTAAGGATGCTTCCACATAAGTTTCAACTTTCCTGGCCAAA
TGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTC
Found at i:261581 original size:331 final size:332
Alignment explanation
Indices: 260941--261967 Score: 951
Period size: 331 Copynumber: 3.1 Consensus size: 332
260931 TTTGAAAGAT
* * **
260941 ATATATTCCTATGTAAAAAGTTGACCCCCCATTGTGGCCCCATCGAACCCCCAAGGGTCATGATT
1 ATATATTCATATGTAAAAA-TTGA-CCCCCATTGTGGCCCCAACCTACCCCCAAGGGTCATGATT
* * * * * *
261006 TTCACAACTTTGAATTCTCACTACCTGAGGATGCTTCTATACAAGTTTCCGA-TTTCC-TGGCAT
64 TTCACAACCTTGAATTCACACTACCTGAGGATGCTTCCATATAAGTTT-CAACTTTCCTTGCCA-
* * * ****
261069 AATGGTT-TCTGAGAAGAAGATCTTTAAAAATATACTCTGTATATTT-CTATGTAAAAATTCGTC
127 AATGGTTCT-TGAGAAGAAGATTTTTAAAAATTTACTCTATAT-TTTCCTATGTAAAAATGAAAC
**
261132 CCACTTTTATGGACCCATCCTACCCCTAAGGGTCATGATTTTCACAACTTTGAATCTACACTACC
190 CCACCATTATGGACCCATCCTACCCCTAAGGGTCATGATTTTCACAACTTTGAATCTACACTACC
** * * *
261197 TGAGGATGTTTCCACACAAGTTTCCGATTTCCTGGCCAAATGGTTCTTGAGAAG-A-TGATTTTT
255 CAAGGATGTTTCAACAAAAGTTTCAGATTTCCTGGCCAAATGGTTCTTGAGAAGAATTGATTTTT
261260 AAAGATTTACTCG
320 AAAGATTTACTCG
* *
261273 ATATATTTATATGTAAAAATTGGACCCCCATTGTGGCCCCAACCTACCCTCAAGGGTCAT-AGTT
1 ATATATTCATATGTAAAAATT-GACCCCCATTGTGGCCCCAACCTACCCCCAAGGGTCATGA-TT
* * * * *
261337 TTCACAACCTTGAATTCACGCCAGCTAAGGATGCTTCCACATAAGTTTCAACTTTCCTTGCCAAA
64 TTCACAACCTTGAATTCACACTACCTGAGGATGCTTCCATATAAGTTTCAACTTTCCTTGCCAAA
* *
261402 TGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTCTATATTTTCCTATGTAAAAATGAAACCCCC
129 TGGTTCTTGAGAAGAAGATTTTTAAAAATTTACTCTATATTTTCCTATGTAAAAATGAAACCCAC
* ** * *
261467 CATTGTGG-CCTCATCCTA-CCCTTGGGGTTCATGATTTTCACAACTTTGAATTTTCACTACCCA
194 CATTATGGACC-CATCCTACCCCTAAGGG-TCATGATTTTCACAACTTTGAATCTACACTACCCA
* ** * * **
261530 AGGATGCTTT-AACAAAAGTTTCAGCCTTT-CTGGCTGATTGCTT-TCTGAGAAGAAATTTTTTT
257 AGGATG-TTTCAACAAAAGTTTCAG-ATTTCCTGGCCAAATGGTTCT-TGAGAAG-AA-TTGATT
*
261592 TTTAAAGATTTACTCT
317 TTTAAAGATTTACTCG
* * * * *
261608 ATATATTCCTATGTAAAAAGTCGACCCCCAAATGTGGCCCCACCCTACCCCCAAGGGTCTTGATT
1 ATATATTCATATGTAAAAA-TTGACCCCC-ATTGTGGCCCCAACCTACCCCCAAGGGTCATGATT
* * * * * **
261673 TTCACAACCTTAAATTAACACTACCTGAGGGTGCTTCCATACT-AGTTTCAGCTTTCCTGGCCTC
64 TTCACAACCTTGAATTCACACTACCTGAGGATGCTTCCATA-TAAGTTTCAACTTTCCTTGCCAA
* * *
261737 ATGGTTCTTGAGAAGAAGATTTTTTAAAAATTTATTCTATATATTCCTCTGTAAAAATTTGACCA
128 ATGGTTCTTGAGAAGAAGA-TTTTTAAAAATTTACTCTATATTTTCCTATGTAAAAA--TGA--A
* * * * * *
261802 TCCCCCCCCCATTGTGG-CCTCA-CCGTAACCCC-GAGGGTCATAATTTTCACAACCTTGAAATC
188 ---ACCCACCATTATGGACC-CATCC-T-ACCCCTAAGGGTCATGATTTTCACAACTTTG-AATC
* * * * * * *
261864 -ACACCAACTAAGGATGCTTCCACATAAGTTTCA-ACTTTCCAGGCCAAATGGTTCTTGAGAAGA
246 TACACTACCCAAGGATGTTTCAACAAAAGTTTCAGA-TTTCCTGGCCAAATGGTTCTTGAGAAGA
*
261927 A--GATTTTTAAAGATTTACTCT
310 ATTGATTTTTAAAGATTTACTCG
*
261948 ATATATTCCTATGTAAAAAT
1 ATATATTCATATGTAAAAAT
261968 NAAAAGGTGT
Statistics
Matches: 570, Mismatches: 90, Indels: 63
0.79 0.12 0.09
Matches are distributed among these distances:
330 16 0.03
331 209 0.37
332 30 0.05
333 1 0.00
335 42 0.07
336 99 0.17
337 35 0.06
339 4 0.01
340 37 0.06
341 1 0.00
343 9 0.02
344 76 0.13
345 8 0.01
346 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (332 bp):
ATATATTCATATGTAAAAATTGACCCCCATTGTGGCCCCAACCTACCCCCAAGGGTCATGATTTT
CACAACCTTGAATTCACACTACCTGAGGATGCTTCCATATAAGTTTCAACTTTCCTTGCCAAATG
GTTCTTGAGAAGAAGATTTTTAAAAATTTACTCTATATTTTCCTATGTAAAAATGAAACCCACCA
TTATGGACCCATCCTACCCCTAAGGGTCATGATTTTCACAACTTTGAATCTACACTACCCAAGGA
TGTTTCAACAAAAGTTTCAGATTTCCTGGCCAAATGGTTCTTGAGAAGAATTGATTTTTAAAGAT
TTACTCG
Found at i:262632 original size:153 final size:152
Alignment explanation
Indices: 262318--262632 Score: 374
Period size: 153 Copynumber: 2.1 Consensus size: 152
262308 TTAGCCAGCT
** * *
262318 CAAAAACCTTAAGTTCATCCAGCATCTGAAACCTACGGCTCAGATTCAACATTTAAGCCTGTCAA
1 CAAAAACCTTAACCTCATCCAGCATCTGAAACCTACGGCTCAGATTCAACATTCAAACCTGTCAA
* * *
262383 GTGCATCAGTATCATTATGCGCACCATCCATGCACGTTTTGTGAAGTTAGGACCAGTATAAGATA
66 GTGCATCAGTATCATTAAGCGCACCATCAATGCACGTTTGGTGAAGTTAGGACCAG-ATAAGATA
* **
262448 TAATTATCAGAGGGCATCTGCTC
130 TAATTATCAAAGGGCATCTGAAC
* * * *
262471 CAAAAACCTTAACCTCATCCATCATCTTAAACCTATGGCTCAGATTCAGCATTCAAACCTGTCAA
1 CAAAAACCTTAACCTCATCCAGCATCTGAAACCTACGGCTCAGATTCAACATTCAAACCTGTCAA
* * *
262536 GTTCATCAGTATTA-TAAGACGCACCATCAATGCAGGTTTGGTGAAGTTAGGACCAG-T-AG-TA
66 GTGCATCAGTATCATTAAG-CGCACCATCAATGCACGTTTGGTGAAGTTAGGACCAGATAAGATA
* *
262597 -ACTTA-GAAAGGGCA-CATGAAC
130 TAATTATCAAAGGGCATC-TGAAC
*
262618 CAAAAACTTTAACCT
1 CAAAAACCTTAACCT
262633 GCTCCAAAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
146 1 0.01
147 24 0.17
148 4 0.03
149 2 0.01
150 2 0.01
151 1 0.01
152 3 0.02
153 103 0.74
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (152 bp):
CAAAAACCTTAACCTCATCCAGCATCTGAAACCTACGGCTCAGATTCAACATTCAAACCTGTCAA
GTGCATCAGTATCATTAAGCGCACCATCAATGCACGTTTGGTGAAGTTAGGACCAGATAAGATAT
AATTATCAAAGGGCATCTGAAC
Found at i:267048 original size:23 final size:22
Alignment explanation
Indices: 267022--267065 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
267012 TCTAATTAAA
267022 TGATTAATAATAATTTAAAAAAT
1 TGATTAATAA-AATTTAAAAAAT
**
267045 TGATTTTTAAAATTTAAAAAA
1 TGATTAATAAAATTTAAAAAA
267066 AAAAAGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
TGATTAATAAAATTTAAAAAAT
Found at i:270865 original size:2 final size:2
Alignment explanation
Indices: 270853--270912 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
270843 TCTCAAGGGA
270853 AG AG A- AG AG AG AG AG 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 AG AG AG AG AG AG AG AG
*
270894 AG AG AA AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
270913 ACTAGAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:271360 original size:20 final size:20
Alignment explanation
Indices: 271317--271364 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
271307 CACTCCCCCC
* *
271317 AACGAAACGAAATCTACATG
1 AACGAAACGAAACCTACACG
271337 AACGAAACGAAACCTAC-CG
1 AACGAAACGAAACCTACACG
271356 AAACGAAAC
1 -AACGAAAC
271365 TATCATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.52, C:0.25, G:0.15, T:0.08
Consensus pattern (20 bp):
AACGAAACGAAACCTACACG
Found at i:271816 original size:21 final size:21
Alignment explanation
Indices: 271809--271962 Score: 175
Period size: 21 Copynumber: 7.3 Consensus size: 21
271799 CAATAGTAGT
271809 ATCATTATATGCAGTGGTAAC
1 ATCATTATATGCAGTGGTAAC
271830 ATCATTATATGCAGTGGTAAC
1 ATCATTATATGCAGTGGTAAC
*
271851 ATCATTACATGCAGTGGTAAC
1 ATCATTATATGCAGTGGTAAC
*
271872 ATCATTATATGCAGTGCTAAC
1 ATCATTATATGCAGTGGTAAC
* ** *
271893 ATCATTATATACTA-TTATATC
1 ATCATTATATGC-AGTGGTAAC
* * * *
271914 ACCATTATATTCAGGGGTAAA
1 ATCATTATATGCAGTGGTAAC
* *
271935 ATCTTTATATGAAGTGGTAAC
1 ATCATTATATGCAGTGGTAAC
*
271956 ATTATTA
1 ATCATTA
271963 CGTTATGTCG
Statistics
Matches: 109, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
20 1 0.01
21 107 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (21 bp):
ATCATTATATGCAGTGGTAAC
Found at i:271838 original size:42 final size:42
Alignment explanation
Indices: 271792--271899 Score: 146
Period size: 42 Copynumber: 2.6 Consensus size: 42
271782 GGTATCTTAT
** *
271792 TTATATGCAATAGTAGTATCATTATATGCAGTGGTAACATCA
1 TTATATGCAATAGTAACATCATTACATGCAGTGGTAACATCA
* *
271834 TTATATGCAGTGGTAACATCATTACATGCAGTGGTAACATCA
1 TTATATGCAATAGTAACATCATTACATGCAGTGGTAACATCA
*
271876 TTATATGCAGT-GCTAACATCATTA
1 TTATATGCAATAG-TAACATCATTA
271900 TATACTATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.02
42 59 0.98
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (42 bp):
TTATATGCAATAGTAACATCATTACATGCAGTGGTAACATCA
Found at i:271848 original size:63 final size:63
Alignment explanation
Indices: 271770--271902 Score: 160
Period size: 63 Copynumber: 2.1 Consensus size: 63
271760 TCAATTTCAT
* * * ** *
271770 ATTATATGAACTGGTATC-TTATTTATATGCAATAGTAGTATCATTATATGCAGTGGTAACATC
1 ATTATATGAACTGGTAACATCA-TTACATGCAATAGTAACATCATTATATGCAGTGCTAACATC
* * * *
271833 ATTATATGCAGTGGTAACATCATTACATGCAGTGGTAACATCATTATATGCAGTGCTAACATC
1 ATTATATGAACTGGTAACATCATTACATGCAATAGTAACATCATTATATGCAGTGCTAACATC
271896 ATTATAT
1 ATTATAT
271903 ACTATTATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 57 0.97
64 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (63 bp):
ATTATATGAACTGGTAACATCATTACATGCAATAGTAACATCATTATATGCAGTGCTAACATC
Found at i:272229 original size:21 final size:21
Alignment explanation
Indices: 272203--272245 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
272193 TATGGTGTAT
272203 TAAAACCATT-ATGTATGGTGG
1 TAAAACC-TTAATGTATGGTGG
*
272224 TAAAACCTTAATGTATTGTGG
1 TAAAACCTTAATGTATGGTGG
272245 T
1 T
272246 GAAAGCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (21 bp):
TAAAACCTTAATGTATGGTGG
Found at i:281280 original size:165 final size:165
Alignment explanation
Indices: 281001--281335 Score: 570
Period size: 165 Copynumber: 2.0 Consensus size: 165
280991 NNNNNNNNNN
281001 ATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGGA
1 ATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGGA
281066 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAG-TTCAGCTTTC
66 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
281130 CTGGCTGATTAGT-TTC-TGAGAAGAAGATTTTT-AAA
131 CTGGCT--TT-GTGTTCTTGAGAAGAAGATTTTTGAAA
*
281165 GATTTACTCTTTATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGG
1 -ATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGG
* *
281230 TGTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGTTTCCACACAAGTTTCAGCTTT
65 AGTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT
281295 CCTGGCTTTGTGGTTCTTGAGAAGAAGATTTTTGAAA
130 CCTGGCTTTGT-GTTCTTGAGAAGAAGATTTTTGAAA
281332 ATTT
1 ATTT
281336 CTCGAAATTT
Statistics
Matches: 162, Mismatches: 3, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
163 2 0.01
164 2 0.01
165 119 0.73
166 36 0.22
167 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (165 bp):
ATTTACTCTATATATTCCTATGTAAAACTTCGAGCCCCCATTGTGGCCCCACCCTACCCCCGGGA
GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
CTGGCTTTGTGTTCTTGAGAAGAAGATTTTTGAAA
Found at i:281794 original size:31 final size:31
Alignment explanation
Indices: 281741--281889 Score: 120
Period size: 31 Copynumber: 4.7 Consensus size: 31
281731 GACACTCCTT
* * *
281741 ATAAAGCCAGTCATCCGGGGGAAAGTTTCCCC
1 ATAAAGTCAGTCCT-CGGGGGAAAGTTTCCCA
* *
281773 ATAAATTCAGTCCTCGGGGGAAAGCTTCCCA
1 ATAAAGTCAGTCCTCGGGGGAAAGTTTCCCA
* * * * *
281804 ATAAAGTCAGTCCTTGGGGGTAAGTCTCACT
1 ATAAAGTCAGTCCTCGGGGGAAAGTTTCCCA
* * * *
281835 ATATAGCCAGTTCTCTGGGGGAAAGTTTCACA
1 ATAAAGTCAGTCCTC-GGGGGAAAGTTTCCCA
* *
281867 ATATAA-CCAGTCTTCGGGGGAAA
1 ATA-AAGTCAGTCCTCGGGGGAAA
281890 TTAAGTCTCA
Statistics
Matches: 93, Mismatches: 22, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
31 58 0.62
32 34 0.37
33 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (31 bp):
ATAAAGTCAGTCCTCGGGGGAAAGTTTCCCA
Found at i:286334 original size:48 final size:46
Alignment explanation
Indices: 286202--286334 Score: 167
Period size: 46 Copynumber: 2.8 Consensus size: 46
286192 GGGGAAAGGA
* *
286202 TTATCTGAGGCTGAGGTGCTGGCTATACTATGAGGGACATGCATGC
1 TTATCTGAGGCTGAGGTGCTGGCTTTACTATGAGGGACATGCATAC
* * * * *
286248 TTATCTGGGGCTGAGGTGCTGCCTTTACTATAAAGGACATGCTTAC
1 TTATCTGAGGCTGAGGTGCTGGCTTTACTATGAGGGACATGCATAC
* *
286294 TAGTATCTGAGGCTGAGGTGCAGGCTTTACTCTGAGGGACA
1 T--TATCTGAGGCTGAGGTGCTGGCTTTACTATGAGGGACA
286335 GGATTATCTG
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
46 40 0.56
48 32 0.44
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (46 bp):
TTATCTGAGGCTGAGGTGCTGGCTTTACTATGAGGGACATGCATAC
Found at i:289958 original size:3 final size:3
Alignment explanation
Indices: 289950--289994 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
289940 CCATCAAAAA
289950 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
289995 AGATATTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:290775 original size:17 final size:17
Alignment explanation
Indices: 290724--290770 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
290714 TTTGAAGGTG
* *
290724 AATTTCAGGTCATTTGAA
1 AATTTCAGGTCAATT-CA
290742 AATTTCAGGTCAATTCA
1 AATTTCAGGTCAATTCA
290759 AATTCTCAGGTC
1 AATT-TCAGGTC
290771 TTTCACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (17 bp):
AATTTCAGGTCAATTCA
Found at i:290933 original size:16 final size:16
Alignment explanation
Indices: 290912--290944 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
290902 ATTTCAGGTC
290912 TTTCAGGTCATTAGTA
1 TTTCAGGTCATTAGTA
*
290928 TTTCAGGTCTTTAGTA
1 TTTCAGGTCATTAGTA
290944 T
1 T
290945 GTTCCAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (16 bp):
TTTCAGGTCATTAGTA
Found at i:293658 original size:29 final size:29
Alignment explanation
Indices: 293633--293919 Score: 249
Period size: 29 Copynumber: 9.9 Consensus size: 29
293623 GGCAAAACAC
* * *
293633 TCTCTTGTCATGATGTACCAGGAAAACTT
1 TCTCTAGTCAGGATGTACCAGCAAAACTT
* ** *
293662 TCTCTTGTCACAATGTATCTA-CAAAACTT
1 TCTCTAGTCAGGATGTA-CCAGCAAAACTT
*
293691 TCTCTAGTCAGGATATACCAGCAAAACTT
1 TCTCTAGTCAGGATGTACCAGCAAAACTT
*
293720 TCTCTAGTCAGGATATACCAGCAAAACTT
1 TCTCTAGTCAGGATGTACCAGCAAAACTT
*
293749 TCTCTAGTCAGGATATACCAGCAAAACTT
1 TCTCTAGTCAGGATGTACCAGCAAAACTT
* *
293778 TCTCTAGTCAGGATGTA-CGGCAAAACGT
1 TCTCTAGTCAGGATGTACCAGCAAAACTT
* * *
293806 TCTCTTGTCAGGATGT-CCAGCCATAACGT
1 TCTCTAGTCAGGATGTACCAG-CAAAACTT
* * ** ** * * *
293835 TCTCTTGTAACAATGTGTCTGCAAAGCAT
1 TCTCTAGTCAGGATGTACCAGCAAAACTT
* * *
293864 TCTCTAGTTAGGATGTCCCAGC-AAAGTGT
1 TCTCTAGTCAGGATGTACCAGCAAAACT-T
* **
293893 TCTCTTGTCAGGATGTACTGGCAAAAC
1 TCTCTAGTCAGGATGTACCAGCAAAAC
293920 GTTTTCTTGT
Statistics
Matches: 212, Mismatches: 39, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
28 30 0.14
29 175 0.83
30 7 0.03
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (29 bp):
TCTCTAGTCAGGATGTACCAGCAAAACTT
Found at i:293921 original size:87 final size:86
Alignment explanation
Indices: 293633--293931 Score: 289
Period size: 87 Copynumber: 3.5 Consensus size: 86
293623 GGCAAAACAC
* * *
293633 TCTCTTGTCATGATGTACCAGG-AAAACTTTCTCTTGTCACAATGTATCTACAAAACTTTCTCTA
1 TCTCTTGTCAGGATGTA-CAGGCAAAACGTTCTCTTGTCACAATGTATCTGCAAAACTTTCTCTA
*
293697 GTCAGGATATACCAGCAAAACT-T
65 GTCAGGATGT-CCAGCAAAA-TGT
* * * * ** * * *
293720 TCTCTAGTCAGGATATACCA-GCAAAACTTTCTCTAGTCAGGATATACCAGCAAAACTTTCTCTA
1 TCTCTTGTCAGGATGTA-CAGGCAAAACGTTCTCTTGTCACAATGTATCTGCAAAACTTTCTCTA
* * *
293784 GTCAGGATGTACGGCAAAACGT
65 GTCAGGATGTCCAGCAAAATGT
* * * * * * *
293806 TCTCTTGTCAGGATGTCCAGCCATAACGTTCTCTTGTAACAATGTGTCTGCAAAGCATTCTCTAG
1 TCTCTTGTCAGGATGTACAGGCAAAACGTTCTCTTGTCACAATGTATCTGCAAAACTTTCTCTAG
* *
293871 TTAGGATGTCCCAGCAAAGTGT
66 TCAGGATGT-CCAGCAAAATGT
* *
293893 TCTCTTGTCAGGATGTACTGGCAAAACGTTTTCTTGTCA
1 TCTCTTGTCAGGATGTACAGGCAAAACGTTCTCTTGTCA
293932 AGGTGTACTG
Statistics
Matches: 167, Mismatches: 41, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
85 2 0.01
86 63 0.38
87 102 0.61
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (86 bp):
TCTCTTGTCAGGATGTACAGGCAAAACGTTCTCTTGTCACAATGTATCTGCAAAACTTTCTCTAG
TCAGGATGTCCAGCAAAATGT
Found at i:305840 original size:2 final size:2
Alignment explanation
Indices: 305833--305893 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
305823 TAATCACCTA
305833 AG AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG AG
305875 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
305894 ATCTTTTTTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:312157 original size:21 final size:20
Alignment explanation
Indices: 312132--312531 Score: 363
Period size: 21 Copynumber: 19.0 Consensus size: 20
312122 TATTTTTTAT
**
312132 TAATTTGTTATAACGGATTA
1 TAATTTGTTATAACAAATTA
* *
312152 GTAATTTGTTTTAACAAATCA
1 -TAATTTGTTATAACAAATTA
* *
312173 TTAATTTGTTACAACAGATTA
1 -TAATTTGTTATAACAAATTA
312194 TCAATTTGTTATAACAAATTA
1 T-AATTTGTTATAACAAATTA
* *
312215 TTAATTTGTTATAACAGATAA
1 -TAATTTGTTATAACAAATTA
*
312236 GTAATTTGTTATAACAGATTA
1 -TAATTTGTTATAACAAATTA
*
312257 TCAATTTGTTATATCAAATTA
1 T-AATTTGTTATAACAAATTA
* *
312278 TTGATTTGTTATAACAGATTA
1 -TAATTTGTTATAACAAATTA
*
312299 GTAATTTGTTATAACAGATTA
1 -TAATTTGTTATAACAAATTA
*
312320 TCAATTTGGTATAACAAATTA
1 T-AATTTGTTATAACAAATTA
* * ** *
312341 GTAGTCTGTTATAACAGGTAA
1 -TAATTTGTTATAACAAATTA
312362 TCAATTT-TTATAACAAATTA
1 T-AATTTGTTATAACAAATTA
312382 TCAATTTGTTATAACAAATTA
1 T-AATTTGTTATAACAAATTA
* *
312403 CTAATCTGTTATAAAAAAAAATTA
1 -TAATTTGTTAT---AACAAATTA
*
312427 GTAATTTGTTATAACAAATAA
1 -TAATTTGTTATAACAAATTA
*
312448 TTAATTTGTTATAATAAATTA
1 -TAATTTGTTATAACAAATTA
*
312469 TTAATTTGTTATAACAAGTTA
1 -TAATTTGTTATAACAAATTA
*
312490 TCAATTTGTTATAACAGATTA
1 T-AATTTGTTATAACAAATTA
312511 TCAATTTGTT-TAAACAAATTA
1 T-AATTTGTTAT-AACAAATTA
312532 ATATTTACAA
Statistics
Matches: 316, Mismatches: 49, Indels: 28
0.80 0.12 0.07
Matches are distributed among these distances:
20 23 0.07
21 271 0.86
22 4 0.01
24 18 0.06
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (20 bp):
TAATTTGTTATAACAAATTA
Found at i:312177 original size:42 final size:41
Alignment explanation
Indices: 312128--312520 Score: 403
Period size: 42 Copynumber: 9.3 Consensus size: 41
312118 GCAGTATTTT
* *
312128 TTATTAATTTGTTATAACGGATTAGTAATTTGTTTTAACAAA
1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTATAACAAA
* *
312170 TCATTAATTTGTTACAACAGATTATCAATTTGTTATAACAAA
1 TTATTAATTTGTTATAACAGATTAT-AATTTGTTATAACAAA
* *
312212 TTATTAATTTGTTATAACAGATAAGTAATTTGTTATAACAGA
1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTATAACAAA
* * * * *
312254 TTATCAATTTGTTATATCAAATTATTGATTTGTTATAACAGA
1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTATAACAAA
* *
312296 TTAGTAATTTGTTATAACAGATTATCAATTTGGTATAACAAA
1 TTATTAATTTGTTATAACAGATTAT-AATTTGTTATAACAAA
* * * * *
312338 TTAGTAGTCTGTTATAACAGGTAATCAATTT-TTATAACAAA
1 TTATTAATTTGTTATAACAGATTAT-AATTTGTTATAACAAA
* * * *
312379 TTATCAATTTGTTATAACAAATTACTAATCTGTTATAAAAAAAAA
1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTAT---AACAAA
* * * *
312424 TTAGTAATTTGTTATAACAAATAATTAATTTGTTATAATAAA
1 TTATTAATTTGTTATAACAGATTA-TAATTTGTTATAACAAA
*
312466 TTATTAATTTGTTATAACA-AGTTATCAATTTGTTATAACAGA
1 TTATTAATTTGTTATAACAGA-TTAT-AATTTGTTATAACAAA
*
312508 TTATCAATTTGTT
1 TTATTAATTTGTT
312521 TAAACAAATT
Statistics
Matches: 295, Mismatches: 46, Indels: 20
0.82 0.13 0.06
Matches are distributed among these distances:
41 34 0.12
42 224 0.76
43 1 0.00
45 36 0.12
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (41 bp):
TTATTAATTTGTTATAACAGATTATAATTTGTTATAACAAA
Found at i:312241 original size:63 final size:63
Alignment explanation
Indices: 312128--312531 Score: 467
Period size: 63 Copynumber: 6.4 Consensus size: 63
312118 GCAGTATTTT
* ** * * * * * *
312128 TTATTAATTTGTTATAACGGATTAGTAATTTGTTTTAACAAATCATTAATTTGTTACAACAGA
1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGTAATTTGTTATAACAGA
*
312191 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATAAGTAATTTGTTATAACAGA
1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGTAATTTGTTATAACAGA
* *
312254 TTATCAATTTGTTATATCAAATTATTGATTTGTTATAACAGATTAGTAATTTGTTATAACAGA
1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGTAATTTGTTATAACAGA
* * * * * * *
312317 TTATCAATTTGGTATAACAAATTAGTAGTCTGTTATAACAG-GTAATCAATTT-TTATAACAAA
1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGT-AATTTGTTATAACAGA
* * * * *
312379 TTATCAATTTGTTATAACAAATTACTAATCTGTTATAAAAAAAAATTAGTAATTTGTTATAACAA
1 TTATCAATTTGTTATAACAAATTATTAATTTGTTAT---AACAGATTAGTAATTTGTTATAACAG
312444 A
63 A
* * *
312445 TAATTAATTTGTTATAATAAATTATTAATTTGTTATAACA-AGTTA-TCAATTTGTTATAACAGA
1 TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGA-TTAGT-AATTTGTTATAACAGA
312508 TTATCAATTTGTT-TAAACAAATTA
1 TTATCAATTTGTTAT-AACAAATTA
312532 ATATTTACAA
Statistics
Matches: 294, Mismatches: 38, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
62 48 0.16
63 194 0.66
65 8 0.03
66 44 0.15
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (63 bp):
TTATCAATTTGTTATAACAAATTATTAATTTGTTATAACAGATTAGTAATTTGTTATAACAGA
Found at i:312431 original size:24 final size:24
Alignment explanation
Indices: 312397--312450 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
312387 TTGTTATAAC
312397 AAATTACTAATCTGTTATAAAAAA
1 AAATTACTAATCTGTTATAAAAAA
* * *
312421 AAATTAGTAATTTGTTATAACAAA
1 AAATTACTAATCTGTTATAAAAAA
*
312445 TAATTA
1 AAATTA
312451 ATTTGTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATTACTAATCTGTTATAAAAAA
Found at i:312568 original size:21 final size:21
Alignment explanation
Indices: 312544--312589 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
312534 ATTTACAATA
*
312544 GCATAGAGATATCATAGCATT
1 GCATAGAAATATCATAGCATT
* *
312565 GCATAGAAATCTCATATCATT
1 GCATAGAAATATCATAGCATT
312586 GCAT
1 GCAT
312590 TTTTATACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
GCATAGAAATATCATAGCATT
Found at i:315126 original size:21 final size:21
Alignment explanation
Indices: 315102--315173 Score: 110
Period size: 21 Copynumber: 3.4 Consensus size: 21
315092 GATAATTGAT
*
315102 AATTGATAATCTGTTATAACA
1 AATTAATAATCTGTTATAACA
*
315123 AATTAATAATTTGTTATAACA
1 AATTAATAATCTGTTATAACA
315144 AA-TAACTAATCTGTTATAACA
1 AATTAA-TAATCTGTTATAACA
315165 AATTAATAA
1 AATTAATAA
315174 AAAAAAAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38
Consensus pattern (21 bp):
AATTAATAATCTGTTATAACA
Found at i:316218 original size:2 final size:2
Alignment explanation
Indices: 316213--316256 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
316203 ACGATTTCGT
316213 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
316255 TC
1 TC
316257 ACACACACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.