Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold354
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: 1097647
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.30
Warning! 124483 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:842063 original size:42 final size:41
Alignment explanation
Indices: 842001--842134 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 41
841991 TACACCATAG
*
842001 CATAGCATAGCATTGAAATCTCATAGCATAGCATTGA-AATCT
1 CATAGCATAGCATTGAAATCTCATACCATAGCA-T-ACAATCT
*
842043 CATAGCATAGCATTGGAATCTCATACCATAGCATACAATCT
1 CATAGCATAGCATTGAAATCTCATACCATAGCATACAATCT
* * ** * * **
842084 CATAGAATCGCATTCGTCATATCATACCATAGCATACCATAG
1 CATAGCATAGCATT-GAAATCTCATACCATAGCATACAATCT
842126 CATAGCATA
1 CATAGCATA
842135 CAACAGTATT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 18 0.23
42 59 0.76
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (41 bp):
CATAGCATAGCATTGAAATCTCATACCATAGCATACAATCT
Found at i:842119 original size:10 final size:10
Alignment explanation
Indices: 842101--842134 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
842091 TCGCATTCGT
*
842101 CATATCATAC
1 CATAGCATAC
842111 CATAGCATAC
1 CATAGCATAC
*
842121 CATAGCATAG
1 CATAGCATAC
842131 CATA
1 CATA
842135 CAACAGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (10 bp):
CATAGCATAC
Found at i:842124 original size:15 final size:15
Alignment explanation
Indices: 842101--842135 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
842091 TCGCATTCGT
*
842101 CATATCATACCATAG
1 CATACCATACCATAG
*
842116 CATACCATAGCATAG
1 CATACCATACCATAG
842131 CATAC
1 CATAC
842136 AACAGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.23
Consensus pattern (15 bp):
CATACCATACCATAG
Found at i:842297 original size:10 final size:10
Alignment explanation
Indices: 842282--842311 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
842272 GTTCAAATCT
842282 CATAGCATAC
1 CATAGCATAC
*
842292 CATAGCATAG
1 CATAGCATAC
842302 CATAGCATAC
1 CATAGCATAC
842312 AACATCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (10 bp):
CATAGCATAC
Found at i:842365 original size:21 final size:21
Alignment explanation
Indices: 842339--842418 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
842329 CACTTCAATT
842339 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
842360 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
*
842381 TCTCATAGCATATCATTA-AAA
1 TCTCATAGCATAGCA-TACAAA
* *
842402 TCGCATACCATAGCATA
1 TCTCATAGCATAGCATA
842419 GCATTAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 2 0.04
21 50 0.93
22 2 0.04
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:845698 original size:4 final size:4
Alignment explanation
Indices: 845689--845819 Score: 226
Period size: 4 Copynumber: 32.8 Consensus size: 4
845679 TAACAAAAAA
* *
845689 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AGAG AGAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* *
845737 AGAG AGAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
845785 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
845820 TGAATCTATC
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 125 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.22
Consensus pattern (4 bp):
ATAG
Found at i:846970 original size:4 final size:4
Alignment explanation
Indices: 846963--846997 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
846953 TCATTGATTA
* *
846963 TATT TATT TATT TATC TGTT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
846998 CTATATGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:847057 original size:2 final size:2
Alignment explanation
Indices: 847050--847079 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
847040 TCATTTACTG
847050 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
847080 TTAGATAGAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:847258 original size:11 final size:11
Alignment explanation
Indices: 847230--847270 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
847220 ACTAAACCCC
847230 GGGTTTACTCTAT
1 GGGTTTACT-T-T
847243 GGGTTTACTTT
1 GGGTTTACTTT
*
847254 GGGTTTACTTC
1 GGGTTTACTTT
847265 GGGTTT
1 GGGTTT
847271 CCTAGTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 17 0.63
12 1 0.04
13 9 0.33
ACGTcount: A:0.10, C:0.12, G:0.29, T:0.49
Consensus pattern (11 bp):
GGGTTTACTTT
Found at i:851696 original size:2 final size:2
Alignment explanation
Indices: 851678--851725 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
851668 TTTACAGTGT
* *
851678 TC TC TC CC TC TC CC 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
851720 TC TC TC
1 TC TC TC
851726 AAACATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:851793 original size:20 final size:20
Alignment explanation
Indices: 851768--851807 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
851758 TATCTAAAGA
851768 ATATATATATCTATATATCT
1 ATATATATATCTATATATCT
* *
851788 ATATATTTATCTATCTATCT
1 ATATATATATCTATATATCT
851808 TCCTTTCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATATATCTATATATCT
Found at i:851807 original size:8 final size:8
Alignment explanation
Indices: 851771--851805 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
851761 CTAAAGAATA
851771 TATATATC
1 TATATATC
851779 TATATATC
1 TATATATC
*
851787 TATATATT
1 TATATATC
*
851795 TATCTATC
1 TATATATC
851803 TAT
1 TAT
851806 CTTCCTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (8 bp):
TATATATC
Found at i:854410 original size:65 final size:65
Alignment explanation
Indices: 854331--854639 Score: 318
Period size: 65 Copynumber: 4.8 Consensus size: 65
854321 GTGAAGAGAA
* * * *
854331 AAGTATGCATAACAATAAAGTATTATACACTGTTTGTGATGTTTAATTTTAACTAAAGATAAAAG
1 AAGTATGCATAACAATGAAGTATTATACACTGTTTGTGATGTTTGATTTCAACTAAAGAGAAAAG
* * *
854396 AAG-ATTGCATAACAATGAAGTATTATCCACTGTTTGTTATGTTTGATTTCAAGTAAAGAGAAAA
1 AAGTA-TGCATAACAATGAAGTATTATACACTGTTTGTGATGTTTGATTTCAACTAAAGAGAAAA
854460 G
65 G
* * *
854461 AAGTATGCCTTACAATGAAGTATT-TCACACTGTTTGTGATGTTTGATTTCATGC-AAAGAGAAA
1 AAGTATGCATAACAATGAAGTATTAT-ACACTGTTTGTGATGTTTGATTTCA-ACTAAAGAGAAA
*
854524 GG
64 AG
* * * * * * * **
854526 AAATATGCCTAACACTGAAGTATTCTACATTGTTGGTGATGTTTGGTTTCAAGGAAAGAGAAAAG
1 AAGTATGCATAACAATGAAGTATTATACACTGTTTGTGATGTTTGATTTCAACTAAAGAGAAAAG
* * * * * * * *
854591 GAGTATACCTAACAATAAAGTATTCTTCAGTGTTTGTAATGTTTGATTT
1 AAGTATGCATAACAATGAAGTATTATACACTGTTTGTGATGTTTGATTT
854640 AAAAATTGAT
Statistics
Matches: 205, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
64 2 0.01
65 201 0.98
66 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (65 bp):
AAGTATGCATAACAATGAAGTATTATACACTGTTTGTGATGTTTGATTTCAACTAAAGAGAAAAG
Found at i:854545 original size:130 final size:130
Alignment explanation
Indices: 854314--854639 Score: 360
Period size: 130 Copynumber: 2.5 Consensus size: 130
854304 AAAAGTCTTT
* *
854314 ATTTCAAGTGAAGAG--AA-AAGTATGCATAACAATAAAGTATTAT-ACACTGTTTGTGATGTTT
1 ATTTCAAGTAAAGAGAAAAGAAGTATGCCTAACAATAAAGTATT-TCACACTGTTTGTGATGTTT
* * * * * *
854375 AATTTTAACTAAAGATAAAAGAAGATTGCATAACAATGAAGTATTATCCACTGTTTGTTATGTTT
65 GATTTCAACTAAAGAGAAAAGAAGATTGCATAACAATGAAGTATTATACACTGTTGGTGATGTTT
854440 G
130 G
* *
854441 ATTTCAAGTAAAGAGAAAAGAAGTATGCCTTACAATGAAGTATTTCACACTGTTTGTGATGTTTG
1 ATTTCAAGTAAAGAGAAAAGAAGTATGCCTAACAATAAAGTATTTCACACTGTTTGTGATGTTTG
* * * * * *
854506 ATTTCATGC-AAAGAGAAAGGAA-ATATGCCTAACACTGAAGTATTCTACATTGTTGGTGATGTT
66 ATTTCA-ACTAAAGAGAAAAGAAGAT-TGCATAACAATGAAGTATTATACACTGTTGGTGATGTT
854569 TG
129 TG
* * * * * * *
854571 GTTTCAAGGAAAGAGAAAAGGAGTATACCTAACAATAAAGTA-TTCTTCAGTGTTTGTAATGTTT
1 ATTTCAAGTAAAGAGAAAAGAAGTATGCCTAACAATAAAGTATTTC-ACACTGTTTGTGATGTTT
854635 GATTT
65 GATTT
854640 AAAAATTGAT
Statistics
Matches: 167, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
127 14 0.08
129 8 0.05
130 144 0.86
131 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (130 bp):
ATTTCAAGTAAAGAGAAAAGAAGTATGCCTAACAATAAAGTATTTCACACTGTTTGTGATGTTTG
ATTTCAACTAAAGAGAAAAGAAGATTGCATAACAATGAAGTATTATACACTGTTGGTGATGTTTG
Found at i:856777 original size:16 final size:15
Alignment explanation
Indices: 856742--856777 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
856732 AATAAGTATT
* *
856742 TAAAAACAAATAGGG
1 TAAAAAAAAATAAGG
856757 TAAAAAAAAATAAGG
1 TAAAAAAAAATAAGG
856772 TAAAAA
1 TAAAAA
856778 GAACCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (15 bp):
TAAAAAAAAATAAGG
Found at i:873209 original size:11 final size:11
Alignment explanation
Indices: 873193--873257 Score: 76
Period size: 11 Copynumber: 5.9 Consensus size: 11
873183 GTCTAAACTT
*
873193 CTTTAATCCAC
1 CTTTAAGCCAC
*
873204 CTTTAAGCTAC
1 CTTTAAGCCAC
*
873215 CTTTAAGCTAC
1 CTTTAAGCCAC
873226 CTTTAAGCCAC
1 CTTTAAGCCAC
* * *
873237 ATTAAAGCCGC
1 CTTTAAGCCAC
873248 CTTTAAGCCA
1 CTTTAAGCCA
873258 TTAAAAAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 45 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:874463 original size:112 final size:112
Alignment explanation
Indices: 874266--874488 Score: 410
Period size: 112 Copynumber: 2.0 Consensus size: 112
874256 AACCCTGACG
*
874266 TGCACCTGGGCACACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTG
1 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTG
* *
874331 TTCTTAAGTTGGATAAACAATAGACTTTAATTAGATATACACAAACA
66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA
*
874378 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTG
874443 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAAC
66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAAC
874489 TATGTCTAGA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (112 bp):
TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTG
TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA
Found at i:874705 original size:2 final size:2
Alignment explanation
Indices: 874694--874764 Score: 99
Period size: 2 Copynumber: 36.0 Consensus size: 2
874684 CGGATGAACT
*
874694 GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA TA 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
* * *
874735 GA GA AA AA GA GA GA GA AA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
874765 TTTCACCGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.55, C:0.00, G:0.44, T:0.01
Consensus pattern (2 bp):
GA
Found at i:875155 original size:11 final size:11
Alignment explanation
Indices: 875141--875182 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
875131 CACTTAAAGA
875141 TGCTTAAAGGT
1 TGCTTAAAGGT
*
875152 TGCTTAAAGAT
1 TGCTTAAAGGT
*
875163 GGCTTAAAGG-
1 TGCTTAAAGGT
875173 TGACTTAAAG
1 TG-CTTAAAG
875183 AGGTTTGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 1 0.04
11 25 0.96
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (11 bp):
TGCTTAAAGGT
Found at i:875157 original size:21 final size:22
Alignment explanation
Indices: 875132--875183 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
875122 CGTAAATGCC
875132 ACTTAAAGAT-GCTTAAAGGTTG
1 ACTTAAAGATGGCTTAAAGG-TG
875154 -CTTAAAGATGGCTTAAAGGTG
1 ACTTAAAGATGGCTTAAAGGTG
875175 ACTTAAAGA
1 ACTTAAAGA
875184 GGTTTGGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (22 bp):
ACTTAAAGATGGCTTAAAGGTG
Found at i:875419 original size:11 final size:11
Alignment explanation
Indices: 875402--875452 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
875392 GAGCAGNATG
875402 CTTAAAGGTAGA
1 CTTAAAGGT-GA
* *
875414 -TTAAAGATGG
1 CTTAAAGGTGA
875424 CTTAAAGGTGA
1 CTTAAAGGTGA
875435 CTTAAAGGTGA
1 CTTAAAGGTGA
875446 CTTAAAG
1 CTTAAAG
875453 AAGTTTGGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 1 0.03
11 33 0.97
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.27
Consensus pattern (11 bp):
CTTAAAGGTGA
Found at i:902313 original size:18 final size:18
Alignment explanation
Indices: 902292--902370 Score: 55
Period size: 18 Copynumber: 4.7 Consensus size: 18
902282 ATAGCACCAA
902292 CACATAAAAAAGCACATT
1 CACATAAAAAAGCACATT
* * *
902310 CACATTAAACAGCACCTGT
1 CACATAAAAAAGCACAT-T
*
902329 -ACAT-AAAAA-CACAAT
1 CACATAAAAAAGCACATT
*
902344 CATATAAAAAA--A-A-T
1 CACATAAAAAAGCACATT
902358 CACATAAAAAAGC
1 CACATAAAAAAGC
902371 CCCATCATCA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
14 11 0.23
15 2 0.04
16 7 0.15
17 9 0.19
18 18 0.38
19 1 0.02
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (18 bp):
CACATAAAAAAGCACATT
Found at i:902358 original size:14 final size:15
Alignment explanation
Indices: 902329--902368 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
902319 CAGCACCTGT
902329 ACATAAAAACACAATC
1 ACATAAAAA-ACAATC
*
902345 ATATAAAAAA-AATC
1 ACATAAAAAACAATC
902359 ACATAAAAAA
1 ACATAAAAAA
902369 GCCCCATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 1 0.05
16 8 0.36
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (15 bp):
ACATAAAAAACAATC
Found at i:902462 original size:42 final size:42
Alignment explanation
Indices: 902416--902557 Score: 142
Period size: 42 Copynumber: 3.4 Consensus size: 42
902406 AAGCATAATA
* *
902416 TTCATACAATAAAGCAATATCTTCACATAATAAATCTTCATC
1 TTCATACAATAAAGCACTATCTTCAAATAATAAATCTTCATC
* * * * *
902458 TTCATAGAATAAAGCACTATCTTCAAATACTGAAGCATCATC
1 TTCATACAATAAAGCACTATCTTCAAATAATAAATCTTCATC
* * * * *
902500 TTCATACTACAAAGCACCATCTTCATATTATAAATCATT-ATC
1 TTCATACAATAAAGCACTATCTTCAAATAATAAATC-TTCATC
* *
902542 TTTATATAATAAAGCA
1 TTCATACAATAAAGCA
902558 GCATCTGCAC
Statistics
Matches: 78, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 77 0.99
43 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (42 bp):
TTCATACAATAAAGCACTATCTTCAAATAATAAATCTTCATC
Found at i:902563 original size:21 final size:21
Alignment explanation
Indices: 902361--902563 Score: 108
Period size: 21 Copynumber: 9.8 Consensus size: 21
902351 AAAAAATCAC
* * *
902361 ATAAAAAAGCCCCATCATCAT
1 ATAATAAAGCACCATCTTCAT
** *
902382 ATAATAAA-CAGAATCCTCAT
1 ATAATAAAGCACCATCTTCAT
** *
902402 A-AA-AAAGCATAATATTCAT
1 ATAATAAAGCACCATCTTCAT
* ** *
902421 ACAATAAAGCAATATCTTCAC
1 ATAATAAAGCACCATCTTCAT
* **
902442 ATAATAAATCTTCATCTTCAT
1 ATAATAAAGCACCATCTTCAT
* * *
902463 AGAATAAAGCACTATCTTCAA
1 ATAATAAAGCACCATCTTCAT
* * *
902484 ATACTGAAGCATCATCTTCAT
1 ATAATAAAGCACCATCTTCAT
*
902505 ACT-ACAAAGCACCATCTTCAT
1 A-TAATAAAGCACCATCTTCAT
* * ** *
902526 ATTATAAATCATTATCTTTAT
1 ATAATAAAGCACCATCTTCAT
*
902547 ATAATAAAGCAGCATCT
1 ATAATAAAGCACCATCT
902564 GCACATGAAG
Statistics
Matches: 134, Mismatches: 43, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
18 3 0.02
19 12 0.09
20 12 0.09
21 106 0.79
22 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAATAAAGCACCATCTTCAT
Found at i:909252 original size:21 final size:21
Alignment explanation
Indices: 909234--909295 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
909224 ATGGTATGCA
909234 ATTTTAATGATATGCTATGAG
1 ATTTTAATGATATGCTATGAG
*
909255 ATTTTAAATCA-ATGCTATGAG
1 ATTTT-AATGATATGCTATGAG
*
909276 ATTTGT-ATGCTATGCTATGA
1 ATTT-TAATGATATGCTATGA
909296 AAAATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 28 0.80
22 5 0.14
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (21 bp):
ATTTTAATGATATGCTATGAG
Found at i:909520 original size:10 final size:10
Alignment explanation
Indices: 909494--909530 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
909484 TTGTATGCTG
*
909494 TGCTATAGTA
1 TGCTATGGTA
*
909504 TGTTATGGTA
1 TGCTATGGTA
909514 TGCTATGGTA
1 TGCTATGGTA
909524 TGCTATG
1 TGCTATG
909531 ACGAATGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (10 bp):
TGCTATGGTA
Found at i:910291 original size:14 final size:14
Alignment explanation
Indices: 910272--910298 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
910262 CAGGCTCATT
910272 CGAGATTCAAAATA
1 CGAGATTCAAAATA
910286 CGAGATTCAAAAT
1 CGAGATTCAAAAT
910299 GATTCAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (14 bp):
CGAGATTCAAAATA
Found at i:919197 original size:45 final size:45
Alignment explanation
Indices: 919142--919231 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
919132 TTTTTTCAAA
*
919142 ATGTTAGACAATGTTTT-CCTCTCTTTAATCTAATACTTTTTGTGT
1 ATGTCAGACAATGTTTTCCCT-TCTTTAATCTAATACTTTTTGTGT
919187 ATGTCAGACAATGTTTTCCCTTCTTTAATCTAATACTTTTTGTGT
1 ATGTCAGACAATGTTTTCCCTTCTTTAATCTAATACTTTTTGTGT
919232 CAAGTTTAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 40 0.93
46 3 0.07
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (45 bp):
ATGTCAGACAATGTTTTCCCTTCTTTAATCTAATACTTTTTGTGT
Found at i:922106 original size:21 final size:21
Alignment explanation
Indices: 922080--922171 Score: 157
Period size: 21 Copynumber: 4.4 Consensus size: 21
922070 TTAGATGATT
922080 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
922101 TTATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
* *
922122 TAATTATATGCTGTGGATCTA
1 TTATTATATGCTGTGGGTCTA
922143 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
922164 TTATTATA
1 TTATTATA
922172 CATGTATGCT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.49
Consensus pattern (21 bp):
TTATTATATGCTGTGGGTCTA
Found at i:932980 original size:21 final size:21
Alignment explanation
Indices: 932950--933115 Score: 138
Period size: 21 Copynumber: 7.8 Consensus size: 21
932940 ATAAAATAAC
* *
932950 ATAAAAAAGCACCATATTCAT
1 ATAATAAAGCACCATCTTCAT
* *
932971 ACAATAAAGCACCATCTTCAC
1 ATAATAAAGCACCATCTTCAT
* **
932992 ATGATAAAGCTTCATCTTCAT
1 ATAATAAAGCACCATCTTCAT
* *
933013 AGAAAAAAGAACACCATCTTCAT
1 ATAATAAAG--CACCATCTTCAT
* *
933036 ATACA-AAAGCATCATCATT-AC
1 ATA-ATAAAGCACCATC-TTCAT
* **
933057 ACAAGGAAGCACCATCTTCAT
1 ATAATAAAGCACCATCTTCAT
* *
933078 ATTATAAAGCACCATTTTCAT
1 ATAATAAAGCACCATCTTCAT
933099 ATAATAAAGCACCATCT
1 ATAATAAAGCACCATCT
933116 GCACATGAAA
Statistics
Matches: 111, Mismatches: 28, Indels: 12
0.74 0.19 0.08
Matches are distributed among these distances:
20 3 0.03
21 89 0.80
22 2 0.02
23 16 0.14
24 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.25
Consensus pattern (21 bp):
ATAATAAAGCACCATCTTCAT
Found at i:936307 original size:11 final size:11
Alignment explanation
Indices: 936300--936330 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
936290 ACTAGAGTGG
936300 ACCCAGAGTAA
1 ACCCAGAGTAA
*
936311 ACCCAAAGTAA
1 ACCCAGAGTAA
936322 ACCCAGAGT
1 ACCCAGAGT
936331 GGACACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.16, T:0.10
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:936516 original size:11 final size:11
Alignment explanation
Indices: 936500--936601 Score: 73
Period size: 11 Copynumber: 9.5 Consensus size: 11
936490 ATCCTCTAGA
936500 AAACCCAAAGT
1 AAACCCAAAGT
**
936511 AAACCCCGAGT
1 AAACCCAAAGT
936522 AAACCCAAAGT
1 AAACCCAAAGT
*
936533 AAACCC-GAGT
1 AAACCCAAAGT
**
936543 GGACCCAAA-T
1 AAACCCAAAGT
*** **
936553 TTTCATAAAGT
1 AAACCCAAAGT
*
936564 AAACCCAGAGT
1 AAACCCAAAGT
*
936575 AAACCCATAGT
1 AAACCCAAAGT
*
936586 AAACCCATAGT
1 AAACCCAAAGT
936597 AAACC
1 AAACC
936602 AAGAAAGTAA
Statistics
Matches: 69, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
10 12 0.17
11 57 0.83
ACGTcount: A:0.45, C:0.27, G:0.13, T:0.15
Consensus pattern (11 bp):
AAACCCAAAGT
Found at i:936541 original size:21 final size:22
Alignment explanation
Indices: 936500--936551 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
936490 ATCCTCTAGA
936500 AAACCCAAAGTAAACCCCGAGT
1 AAACCCAAAGTAAACCCCGAGT
936522 AAACCCAAAGTAAA-CCCGAGT
1 AAACCCAAAGTAAACCCCGAGT
**
936543 GGACCCAAA
1 AAACCCAAA
936552 TTTTCATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (22 bp):
AAACCCAAAGTAAACCCCGAGT
Found at i:948044 original size:53 final size:52
Alignment explanation
Indices: 947964--948117 Score: 215
Period size: 49 Copynumber: 3.0 Consensus size: 52
947954 TCTTTCATTT
* *
947964 TTAAGGTCTTCCATTTCCTACGGAAGACCTTATAGTTTTCGTACAGTTTCTTA
1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTAT-GTTTTCGTACAGTTTCTTA
* * *
948017 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTTTTTCG-A-ACTGT-TTA
1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATGTTTTCGTACAGTTTCTTA
*
948066 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTCGTACTGTTTCTT
1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTA-TGTTTTCGTACAGTTTCTT
948118 GTTATTATTT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
49 35 0.40
50 10 0.11
51 2 0.02
52 8 0.09
53 33 0.38
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (52 bp):
TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATGTTTTCGTACAGTTTCTTA
Found at i:949711 original size:14 final size:14
Alignment explanation
Indices: 949692--949733 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
949682 TAGTATAGAA
949692 GTTTGTATCTATAT
1 GTTTGTATCTATAT
949706 GTTTGTATCTATAT
1 GTTTGTATCTATAT
949720 GTTTGTATCTATAT
1 GTTTGTATCTATAT
949734 CGGTTGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTTGTATCTATAT
Found at i:955541 original size:165 final size:165
Alignment explanation
Indices: 955124--955633 Score: 623
Period size: 165 Copynumber: 3.1 Consensus size: 165
955114 TGGTATTTTC
* * * *
955124 AAAAATCTTCTTCTCAAAAACTATTCGGCCTGAAAATCTTAAACTTGTGTGGAGGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTTAAACTTGTGTAGAGGCATCCTCAGG
* * * *
955189 TAGTGTAGATTGAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATAGT-CCCTGGGGTAGGGTGGGGCCACAATGGGGGGA
* * *
955254 TCAAGTTTTACATAGGGATATATAGAGAAAATCTTTT
130 TGAATTTTTACATAGGAATATATAGAGAAAATC-TTT
* * *
955291 AAAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGC-TCAATTTGT-TATGGAAGCATCCT
1 --AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTTAAACTTGTGTA--GAGGCATCCT
* *
955354 CATGTAGTTTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGTAGGGTGGGGCCACAATGGGG
62 CAGGTAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGTAGGGTGGGGCCACAATGGGG
*
955419 GGGTGAATTTTTACATAGGAATATATAGAGAAAATCTTT
127 GGATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * * *
955458 AAAAATCTTCTTTTTAAAGACTATTAGGCCAGAAAAGCTTAAACTTGTGTAGAGGCATCCTCGGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTTAAACTTGTGTAGAGGCATCCTCAGG
* * * *** * *
955523 TAGTGTAAATTCAAGTTTG--CAAAATCACAGTCCCTAGTGGTAGGGTGGGGCCGTGATGGCGGT
66 TAGTGTAGATTCAAGTTTGTTC-AAATCATAGTCCCT-GGGGTAGGGTGGGGCCACAATGGGGGG
* *
955586 TTGAATTTTTACATAGGAATATACAGAGAAAATCTTT
129 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
* *
955623 TAAAATATTCT
1 AAAAATCTTCT
955634 GGGGAAGTTC
Statistics
Matches: 297, Mismatches: 38, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
163 1 0.00
164 13 0.04
165 128 0.43
166 7 0.02
167 6 0.02
168 66 0.22
169 76 0.26
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTTAAACTTGTGTAGAGGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGTAGGGTGGGGCCACAATGGGGGGAT
GAATTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:956488 original size:17 final size:17
Alignment explanation
Indices: 956466--956498 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
956456 TCTTGTTTTG
956466 TAAACAAAATCAAAGTA
1 TAAACAAAATCAAAGTA
956483 TAAACAAAATCAAAGT
1 TAAACAAAATCAAAGT
956499 GTCAATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAACAAAATCAAAGTA
Found at i:959215 original size:36 final size:36
Alignment explanation
Indices: 959107--959216 Score: 211
Period size: 36 Copynumber: 3.1 Consensus size: 36
959097 AAAGTAACGG
959107 TAGTGTCTACAGTTAGTAACCACACATTTGTTTAGT
1 TAGTGTCTACAGTTAGTAACCACACATTTGTTTAGT
*
959143 AAGTGTCTACAGTTAGTAACCACACATTTGTTTAGT
1 TAGTGTCTACAGTTAGTAACCACACATTTGTTTAGT
959179 TAGTGTCTACAGTTAGTAACCACACATTTGTTTAGT
1 TAGTGTCTACAGTTAGTAACCACACATTTGTTTAGT
959215 TA
1 TA
959217 AAAAGTTATA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (36 bp):
TAGTGTCTACAGTTAGTAACCACACATTTGTTTAGT
Found at i:961488 original size:18 final size:18
Alignment explanation
Indices: 961467--961510 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
961457 AGATGATGAT
*
961467 GTTGTTGTTAATAATTCA
1 GTTGTTGTCAATAATTCA
*
961485 GTTGTTGTCAATGATTCA
1 GTTGTTGTCAATAATTCA
961503 GTTGTTGT
1 GTTGTTGT
961511 ACTATGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (18 bp):
GTTGTTGTCAATAATTCA
Found at i:963468 original size:2 final size:2
Alignment explanation
Indices: 963461--963535 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
963451 AGATTTAGTC
963461 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
*
963503 AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
963536 CTGAGTTTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:966937 original size:134 final size:134
Alignment explanation
Indices: 966500--967836 Score: 1489
Period size: 134 Copynumber: 10.0 Consensus size: 134
966490 AATAAAGACT
* **
966500 AGAAAGATGTCATCAGAAGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTGGAA-TACGTCT
1 AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTA-GTCT
* * * ** *
966564 GAGCTCATT-TAAACACAATTAAAATGAGTTTAAAA-TTTAAAAAAAATTAAATTTCATCCAATC
65 GAGGTCATTCT-AACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATC
*
966627 AATTCG
129 AATTCC
* * *
966633 AGAAAGATGTCATCAGACGCCA-ACTTGCAAGCGCAACTTTA-ATATCATGTTTTAAAATTAGCC
1 AGAAAGATGTCATCAGACG-CAGAATTGCAAGTGCAAC-TTAGATATCATGTTTTAAAATTAGTC
* * * * * * *
966696 CGAGGTCCTTTTAACACGATTTAAATGAGTTGAAATTTTTTTAAAAAAATTTAAATTTCATACAA
64 TGAGGTCATTCTAACACGATTTAAATGAGTTTAAA-ATTTTT-GAAAAATTTAAATTTCATCCAA
*
966761 TCAATTCT
127 TCAATTCC
* ** * * *
966769 AAAAAGATG-CAATCAGAATCAGAACTGCAGGTGCAACTTAGATATCATGTTTGAAAA-TATGTC
1 AGAAAGATGTC-ATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTA-GTC
** ** * * * ** * **
966832 AAAGGTCATTCTAACGTGATTTGAATGAGTTAAAAAATTTTGAAATTTTTTAATTTCATTTAATC
64 TGAGGTCATTCTAACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATC
966897 AATTCC
129 AATTCC
* * * * * * *
966903 AGAAAGATGTAATCAGACGCAGAATTGAAAGTGCAACTTATAAATCATGTTTTTAAACTAGTCTA
1 AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTAGTCTG
* * *
966968 AGGTCATTCTTACACGATTTAAATGAG-TTAAACAATTTTGAAAAATTTAAATTTCATCTAATCA
66 AGGTCATTCTAACACGATTTAAATGAGTTTAAA-ATTTTTGAAAAATTTAAATTTCATCCAATCA
*
967032 ATTCGA
130 ATTC-C
* * * * * *
967038 AAAAAGATGTCATCATACGCAGAATTGCAAGTGCAACTTAAATATCATGTTTTCAAATTAATCTT
1 AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTAGTCTG
* * * *
967103 AGGTCATTCGAACACGATTTAAATGAGTTTAAATTTTTTGAAAAATTAAAATTTCATCTAATCAA
66 AGGTCATTCTAACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATCAA
967168 TT-C
131 TTCC
* * * * *
967171 -G--AGATTGTCATCATACGCAGAATTGCAAGCGCAACTTAAATATTATGTTTTCAAATTAGTCT
1 AGAAAGA-TGTCATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTAGTCT
* * *
967233 GAGGTCATTTTAACACGATTTAAATGAGTTTAAATTTTTTGAAAAATTTTAATTTCATCCAATCA
65 GAGGTCATTCTAACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATCA
*
967298 ATTCG
130 ATTCC
* * * * * * *
967303 AGAAATATGTCCTCAGACGCAGAATTGCAATTGCAACTAAGAAATCGTG-TTTAAAAATATGTCT
1 AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTA-GTCT
** * * * *
967367 GAGGTCATTCAATTAATGCAATTTAAATGAGTATAAAAATTTTGAAAAATTTAAATTTCATCAAA
65 GAGGTCATTC---TAACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAA
967432 TCAATTCC
127 TCAATTCC
* *
967440 AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGAAATCATGTTTTTAAATTAGTCTG
1 AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTAGTCTG
* * * *
967505 AGGTCATTCGAACATGATTTAAATGAGTTTAAATTTTTTGAAAAATTTAAATTTCATCCAATCGA
66 AGGTCATTCTAACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATCAA
*
967570 TTCT
131 TTCC
* * * * *
967574 AGAAAGATGTCATCAGATGCAGAATTGCAAGCGCAACTTAAATATCATGTTCTAAAATTAGACTG
1 AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTAGTCTG
* * *
967639 -GGTCATTTTAACACAATATAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATCAA
66 AGGTCATTCTAACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATCAA
**
967703 TTTG
131 TTCC
* * *
967707 AGAAAGATGTCATCAGACGCAGAGTTCCAAGTGCAACTTATGA-ATCATGTTTTTAAATTAGTCT
1 AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTA-GATATCATGTTTTAAAATTAGTCT
* *
967771 GAGGTCATTCTAACACGATTTGAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCTAATCA
65 GAGGTCATTCTAACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATCA
967836 A
130 A
967837 GCGCAAGTTA
Statistics
Matches: 1015, Mismatches: 161, Indels: 55
0.82 0.13 0.04
Matches are distributed among these distances:
130 3 0.00
131 116 0.11
133 201 0.20
134 347 0.34
135 130 0.13
136 101 0.10
137 109 0.11
138 8 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (134 bp):
AGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTAAAATTAGTCTG
AGGTCATTCTAACACGATTTAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATCAA
TTCC
Found at i:967757 original size:267 final size:266
Alignment explanation
Indices: 966498--967836 Score: 1523
Period size: 269 Copynumber: 5.0 Consensus size: 266
966488 CTAATAAAGA
* * ** *
966498 CTAGAAAGATGTCATCAGAAGCAGAATTGCAAGTGCAACTTAGATATCATGTTTTGGAATACGTC
1 CTAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAAATATCATG-TTTAAAATATGTC
* * * ** *
966563 TGAGCTCATTTAAACACAATTAAAATGAGTTT-AAAATTTAAAAAAAATTAAATTTCATCCAATC
65 TG-GGTCATTTTAACACAATTTAAATGAGTTTAAAAATTTTGAAAAATTTAAATTTCATCCAATC
* * *
966627 AATTCGAGAAAGATGTCATCAGACGCCA-ACTTGCAAGCGCAACTT-TAATATCATGTTTTAAAA
129 AATTCGAGAAAGATGTCATCAGACG-CAGAATTGCAAGTGCAACTTATAA-ATCATGTTTTTAAA
* * * * * *
966690 TTAGCCCGAGGTCCTTTTAACACGATTTAAATGAGTTGAAATTTTTTTAAAAAAATTTAAATTTC
192 TTAGTCTGAGGTCATTCTAACACGATTTAAATGAGTTTAAA-TTTTTT-GAAAAATTTAAATTTC
*
966755 ATACAATCAATT
255 ATCCAATCAATT
* ** * * *
966767 CTAAAAAGATG-CAATCAGAATCAGAACTGCAGGTGCAACTTAGATATCATGTTTGAAAATATGT
1 CTAGAAAGATGTC-ATCAGACGCAGAATTGCAAGTGCAACTTAAATATCATGTTT-AAAATATGT
** * *** * * ** * **
966831 CAAAGGTCATTCTAACGTGATTTGAATGAGTTAAAAAATTTTGAAATTTTTTAATTTCATTTAAT
64 C-TGGGTCATTTTAACACAATTTAAATGAGTTTAAAAATTTTGAAAAATTTAAATTTCATCCAAT
* * * *
966896 CAATTCCAGAAAGATGTAATCAGACGCAGAATTGAAAGTGCAACTTATAAATCATGTTTTTAAAC
128 CAATTCGAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTATAAATCATGTTTTTAAAT
* * **
966961 TAGTCTAAGGTCATTCTTACACGATTTAAATGAG-TTAAACAATTTTGAAAAATTTAAATTTCAT
193 TAGTCTGAGGTCATTCTAACACGATTTAAATGAGTTTAAA-TTTTTTGAAAAATTTAAATTTCAT
*
967025 CTAATCAATT
257 CCAATCAATT
* * * * *
967035 CGAAAAAAGATGTCATCATACGCAGAATTGCAAGTGCAACTTAAATATCATGTTTTCAAAT-TAA
1 C-TAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAAATATCATG-TTTAAAATAT-G
* ** * ** * *
967099 TCTTAGGTCATTCGAACACGATTTAAATGAGTTTAAATTTTTTGAAAAATTAAAATTTCATCTAA
63 TC-TGGGTCATTTTAACACAATTTAAATGAGTTTAAAAATTTTGAAAAATTTAAATTTCATCCAA
* * * * *
967164 TCAATTCGAG--A-TTGTCATCATACGCAGAATTGCAAGCGCAACTTA-AATATTATGTTTTCAA
127 TCAATTCGAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTATAA-ATCATGTTTTTAA
* *
967225 ATTAGTCTGAGGTCATTTTAACACGATTTAAATGAGTTTAAATTTTTTGAAAAATTTTAATTTCA
191 ATTAGTCTGAGGTCATTCTAACACGATTTAAATGAGTTTAAATTTTTTGAAAAATTTAAATTTCA
967290 TCCAATCAATT
256 TCCAATCAATT
* * * * * *
967301 CGAGAAATATGTCCTCAGACGCAGAATTGCAATTGCAAC-TAAGAAATCGTGTTTAAAAATATGT
1 CTAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAA-ATATCATGTTT-AAAATATGT
** * *
967365 CTGAGGTCATTCAATTAATGCAATTTAAATGAGTATAAAAATTTTGAAAAATTTAAATTTCATCA
64 CTG-GGTCATT---TTAACACAATTTAAATGAGTTTAAAAATTTTGAAAAATTTAAATTTCATCC
* *
967430 AATCAATTCCAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAGAAATCATGTTTTTA
125 AATCAATTCGAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTATAAATCATGTTTTTA
* *
967495 AATTAGTCTGAGGTCATTCGAACATGATTTAAATGAGTTTAAATTTTTTGAAAAATTTAAATTTC
190 AATTAGTCTGAGGTCATTCTAACACGATTTAAATGAGTTTAAATTTTTTGAAAAATTTAAATTTC
*
967560 ATCCAATCGATT
255 ATCCAATCAATT
* * *
967572 CTAGAAAGATGTCATCAGATGCAGAATTGCAAGCGCAACTTAAATATCATGTTCTAAAAT-TAGA
1 CTAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAAATATCATGTT-TAAAATAT-GT
* *
967636 CTGGGTCATTTTAACACAATATAAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCCAATC
64 CTGGGTCATTTTAACACAATTTAAATGAGTTTAAAAATTTTGAAAAATTTAAATTTCATCCAATC
* * * *
967701 AATTTGAGAAAGATGTCATCAGACGCAGAGTTCCAAGTGCAACTTATGAATCATGTTTTTAAATT
129 AATTCGAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTATAAATCATGTTTTTAAATT
* * *
967766 AGTCTGAGGTCATTCTAACACGATTTGAATGAGTTTAAAATTTTTGAAAAATTTAAATTTCATCT
194 AGTCTGAGGTCATTCTAACACGATTTAAATGAGTTTAAATTTTTTGAAAAATTTAAATTTCATCC
967831 AATCAA
259 AATCAA
967837 GCGCAAGTTA
Statistics
Matches: 900, Mismatches: 144, Indels: 54
0.82 0.13 0.05
Matches are distributed among these distances:
264 7 0.01
265 53 0.06
266 104 0.12
267 179 0.20
268 83 0.09
269 187 0.21
270 115 0.13
271 166 0.18
272 6 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (266 bp):
CTAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTAAATATCATGTTTAAAATATGTCT
GGGTCATTTTAACACAATTTAAATGAGTTTAAAAATTTTGAAAAATTTAAATTTCATCCAATCAA
TTCGAGAAAGATGTCATCAGACGCAGAATTGCAAGTGCAACTTATAAATCATGTTTTTAAATTAG
TCTGAGGTCATTCTAACACGATTTAAATGAGTTTAAATTTTTTGAAAAATTTAAATTTCATCCAA
TCAATT
Found at i:969895 original size:212 final size:218
Alignment explanation
Indices: 969498--969902 Score: 651
Period size: 212 Copynumber: 1.9 Consensus size: 218
969488 TAATATGTCA
* * *
969498 CCAGGCAAAACATAGGAATGGTTAATCAGAAGTCAATATTGTACTGACAATCTAACATTGTAAAA
1 CCAGACAAAACATAGGAATGATTAATCAGAAGTCAATATTGTACTGACAATCTAACATTGAAAAA
969563 ATGCAATCAGAAATTACAGAGCTAGACTAAGTTCTTCATCTACGTCTAACGTCTAATGAAAGATA
66 ATGCAATCAGAAATTACAGAGCTAGACTAAGTTCTT-ATCTACG-CTAACGTCTAATGAAAGATA
* *
969628 AATGGTATCTACAAGGATCAATGCAAAATAAGATTTTGATCATCTTGAAAATTAAAGACAGGAGC
129 AATGGTATCCACAAGGATCAATGCAAAATAAGATGTTGATCATCTTGAAAATTAAAGACAGGAGC
969693 TCTTTGGCATAGTAATATGTCCTCG
194 TCTTTGGCATAGTAATATGTCCTCG
* * *
969718 CCAGACAAAACGTTGGAATGATTAATCAGAAGTCAATATTGTATTGACAATCTAACATT-AAAAA
1 CCAGACAAAACATAGGAATGATTAATCAGAAGTCAATATTGTACTGACAATCTAACATTGAAAAA
**
969782 ATGCAATCAGAAATTACAGAGCTAGACTAAGTTC-T-TC-AC-CT-ACGTCTAATGAAAGATGGA
66 ATGCAATCAGAAATTACAGAGCTAGACTAAGTTCTTATCTACGCTAACGTCTAATGAAAGATAAA
*
969842 TGGTATCCACAAGGATCAATGCAAAATAAGATGTTGATCATCTTGATAATTAAAGACAGGA
131 TGGTATCCACAAGGATCAATGCAAAATAAGATGTTGATCATCTTGAAAATTAAAGACAGGA
969903 AAAACCCTCT
Statistics
Matches: 174, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
212 75 0.43
213 2 0.01
215 2 0.01
216 2 0.01
218 1 0.01
219 38 0.22
220 54 0.31
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (218 bp):
CCAGACAAAACATAGGAATGATTAATCAGAAGTCAATATTGTACTGACAATCTAACATTGAAAAA
ATGCAATCAGAAATTACAGAGCTAGACTAAGTTCTTATCTACGCTAACGTCTAATGAAAGATAAA
TGGTATCCACAAGGATCAATGCAAAATAAGATGTTGATCATCTTGAAAATTAAAGACAGGAGCTC
TTTGGCATAGTAATATGTCCTCG
Found at i:974019 original size:27 final size:28
Alignment explanation
Indices: 973972--974024 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
973962 ACTGAAGTGG
*
973972 GACAGACGGACGAACGGACAGACAGAAA
1 GACAGACGGACAAACGGACAGACAGAAA
974000 GACAGACGG-CAAACGGACAGACAGA
1 GACAGACGGACAAACGGACAGACAGA
974025 CTGACTGACG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.45, C:0.23, G:0.32, T:0.00
Consensus pattern (28 bp):
GACAGACGGACAAACGGACAGACAGAAA
Found at i:974436 original size:24 final size:23
Alignment explanation
Indices: 974408--974456 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
974398 TAAAGACAAC
974408 AAAACAA-AAACAAAACGAAAAAAA
1 AAAACAACAAA-AAAA-GAAAAAAA
*
974432 AAAACAACAAAAAAAGAAAAGAA
1 AAAACAACAAAAAAAGAAAAAAA
974455 AA
1 AA
974457 GTAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 11 0.48
25 3 0.13
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (23 bp):
AAAACAACAAAAAAAGAAAAAAA
Found at i:974444 original size:16 final size:16
Alignment explanation
Indices: 974403--974451 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
974393 CAAAATAAAG
*
974403 ACAACAAAACAAAAACA
1 ACAACAAAA-AAAAAAA
*
974420 A-AACGAAAAAAAAAA
1 ACAACAAAAAAAAAAA
974435 ACAACAAAAAAAGAAAA
1 ACAACAAAAAAA-AAAA
974452 GAAAAGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.26
16 15 0.56
17 5 0.19
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (16 bp):
ACAACAAAAAAAAAAA
Found at i:978400 original size:4 final size:4
Alignment explanation
Indices: 978385--978414 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
978375 ATCACATTTT
978385 GTCC GT-C GTCC GTCC GTCC GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
978415 TGTCTATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.47, G:0.27, T:0.27
Consensus pattern (4 bp):
GTCC
Found at i:978703 original size:19 final size:19
Alignment explanation
Indices: 978679--978716 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
978669 TATGGAAAGG
978679 ATCTGAGTTATTACGAAAA
1 ATCTGAGTTATTACGAAAA
978698 ATCTGAGTTATTACGAAAA
1 ATCTGAGTTATTACGAAAA
978717 TAATAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
ATCTGAGTTATTACGAAAA
Found at i:988516 original size:39 final size:39
Alignment explanation
Indices: 988459--988536 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
988449 TATTTTATAA
* *
988459 GAACTTTTTTTGCATTTTTTTAGTGAAATATGAAAAACT
1 GAACTTTTTTTGCATTTTTTCAGTGAAATAGGAAAAACT
*
988498 GAAC-TTTTTTGTATTTTTTCAGTGAAATAGGAAAAACT
1 GAACTTTTTTTGCATTTTTTCAGTGAAATAGGAAAAACT
988536 G
1 G
988537 TTTTGAGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 32 0.89
39 4 0.11
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (39 bp):
GAACTTTTTTTGCATTTTTTCAGTGAAATAGGAAAAACT
Found at i:988722 original size:21 final size:21
Alignment explanation
Indices: 988698--988747 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
988688 TTAACTGTCA
* *
988698 ACTGCCAATTGCTTACTGCTT
1 ACTGCCAACTGCCTACTGCTT
988719 ACTGCCAACTGCCTACTGCTT
1 ACTGCCAACTGCCTACTGCTT
988740 ACTGCCAA
1 ACTGCCAA
988748 GTAAGCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.30
Consensus pattern (21 bp):
ACTGCCAACTGCCTACTGCTT
Found at i:988722 original size:28 final size:28
Alignment explanation
Indices: 988691--988744 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
988681 TAATTCTTTA
* *
988691 ACTGTCAACTGCCAATTGCTTACTGCTT
1 ACTGCCAACTGCCAACTGCTTACTGCTT
*
988719 ACTGCCAACTGCCTACTGCTTACTGC
1 ACTGCCAACTGCCAACTGCTTACTGC
988745 CAAGTAAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.31
Consensus pattern (28 bp):
ACTGCCAACTGCCAACTGCTTACTGCTT
Found at i:990966 original size:2 final size:2
Alignment explanation
Indices: 990959--991018 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
990949 GTTATTTGTT
990959 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
991001 GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
991019 TGTATTGTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1007797 original size:13 final size:13
Alignment explanation
Indices: 1007779--1007803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1007769 CTATGTAAAA
1007779 TAAATAAAATAAG
1 TAAATAAAATAAG
1007792 TAAATAAAATAA
1 TAAATAAAATAA
1007804 TTTTGGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
TAAATAAAATAAG
Found at i:1016745 original size:172 final size:172
Alignment explanation
Indices: 1016459--1016800 Score: 684
Period size: 172 Copynumber: 2.0 Consensus size: 172
1016449 ACTAACACTG
1016459 GCTTTTCTTCTTTTTACCCTTTTTTCTTCGCTTTCACTTCACCGAGTAATTACGTACTATTTCAT
1 GCTTTTCTTCTTTTTACCCTTTTTTCTTCGCTTTCACTTCACCGAGTAATTACGTACTATTTCAT
1016524 GTAATGATCATCTATTAAGTTTATTTGAAAATAATGAGAATGATGACGTTCTTATGTGTGTATGT
66 GTAATGATCATCTATTAAGTTTATTTGAAAATAATGAGAATGATGACGTTCTTATGTGTGTATGT
1016589 GGATTAAAAATGATAAGACATTTTAAAATAGCCAACAAAAGA
131 GGATTAAAAATGATAAGACATTTTAAAATAGCCAACAAAAGA
1016631 GCTTTTCTTCTTTTTACCCTTTTTTCTTCGCTTTCACTTCACCGAGTAATTACGTACTATTTCAT
1 GCTTTTCTTCTTTTTACCCTTTTTTCTTCGCTTTCACTTCACCGAGTAATTACGTACTATTTCAT
1016696 GTAATGATCATCTATTAAGTTTATTTGAAAATAATGAGAATGATGACGTTCTTATGTGTGTATGT
66 GTAATGATCATCTATTAAGTTTATTTGAAAATAATGAGAATGATGACGTTCTTATGTGTGTATGT
1016761 GGATTAAAAATGATAAGACATTTTAAAATAGCCAACAAAA
131 GGATTAAAAATGATAAGACATTTTAAAATAGCCAACAAAA
1016801 TTCATATCTA
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 170 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (172 bp):
GCTTTTCTTCTTTTTACCCTTTTTTCTTCGCTTTCACTTCACCGAGTAATTACGTACTATTTCAT
GTAATGATCATCTATTAAGTTTATTTGAAAATAATGAGAATGATGACGTTCTTATGTGTGTATGT
GGATTAAAAATGATAAGACATTTTAAAATAGCCAACAAAAGA
Found at i:1020147 original size:10 final size:10
Alignment explanation
Indices: 1020132--1020156 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1020122 GCCTTAAAAA
1020132 TAATTTGTAT
1 TAATTTGTAT
1020142 TAATTTGTAT
1 TAATTTGTAT
1020152 TAATT
1 TAATT
1020157 AAATGTCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (10 bp):
TAATTTGTAT
Found at i:1021483 original size:17 final size:15
Alignment explanation
Indices: 1021456--1021545 Score: 72
Period size: 18 Copynumber: 5.5 Consensus size: 15
1021446 AAGATAATGC
**
1021456 TGTTTTGTTTTTAGTT
1 TGTTTT-TTTTTTTTT
1021472 TGTTTTTTTTTTTTT
1 TGTTTTTTTTTTTTT
*
1021487 GGTTATTTTTTTTTGTT
1 TGTT-TTTTTTTTT-TT
*
1021504 TGTATATTTTTTATTTT
1 TGT-T-TTTTTTTTTTT
1021521 TGTTTTTTGGTTTTGTTT
1 TGTTTTTT--TTTT-TTT
1021539 TGTTTTT
1 TGTTTTT
1021546 AGGTTTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
15 14 0.23
16 16 0.26
17 12 0.19
18 20 0.32
ACGTcount: A:0.06, C:0.00, G:0.14, T:0.80
Consensus pattern (15 bp):
TGTTTTTTTTTTTTT
Found at i:1021526 original size:13 final size:12
Alignment explanation
Indices: 1021458--1021545 Score: 54
Period size: 13 Copynumber: 6.8 Consensus size: 12
1021448 GATAATGCTG
1021458 TTTTGTTTTTAGTT
1 TTTTGTTTTT--TT
1021472 TGTTT-TTTTTTT
1 T-TTTGTTTTTTT
*
1021484 TTTGGTTATTTTT
1 TTTTGTT-TTTTT
1021497 TTTTGTTTGTATATT
1 TTTTGTTT-T-T-TT
*
1021512 TTTTATTTTTGTT
1 TTTTGTTTTT-TT
* *
1021525 TTTTG-GTTTTG
1 TTTTGTTTTTTT
1021536 TTTTGTTTTT
1 TTTTGTTTTT
1021546 AGGTTTTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
11 8 0.14
12 12 0.20
13 19 0.32
14 8 0.14
15 12 0.20
ACGTcount: A:0.06, C:0.00, G:0.14, T:0.81
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:1021541 original size:18 final size:17
Alignment explanation
Indices: 1021517--1021556 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
1021507 ATATTTTTTA
*
1021517 TTTTTGTTTTTTGGTTT
1 TTTTTGTTTTTAGGTTT
1021534 TGTTTTGTTTTTAGGTTT
1 T-TTTTGTTTTTAGGTTT
1021552 TTTTT
1 TTTTT
1021557 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (17 bp):
TTTTTGTTTTTAGGTTT
Found at i:1021541 original size:35 final size:35
Alignment explanation
Indices: 1021458--1021538 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 35
1021448 GATAATGCTG
1021458 TTTTGTTTTTAGTTTGT-T-TTTTTT-TTTTTGGTTA
1 TTTTG-TTTT-GTTTGTATATTTTTTATTTTTGGTTA
*
1021492 TTTTTTTTTGTTTGTATATTTTTTATTTTT-GTT-
1 TTTTGTTTTGTTTGTATATTTTTTATTTTTGGTTA
1021525 TTTTGGTTTTGTTT
1 TTTT-GTTTTGTTT
1021539 TGTTTTTAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
32 6 0.15
33 9 0.22
34 21 0.51
35 5 0.12
ACGTcount: A:0.06, C:0.00, G:0.14, T:0.80
Consensus pattern (35 bp):
TTTTGTTTTGTTTGTATATTTTTTATTTTTGGTTA
Found at i:1029677 original size:2 final size:2
Alignment explanation
Indices: 1029670--1029735 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1029660 ATACGTCCAG
1029670 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
1029712 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
1029736 TATCTTTGGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1037538 original size:11 final size:12
Alignment explanation
Indices: 1037510--1037542 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1037500 TATGAAAATA
*
1037510 TATTTTTCAAAC
1 TATTTTTAAAAC
1037522 TATTTTTAAAAC
1 TATTTTTAAAAC
1037534 T-TTTTTAAA
1 TATTTTTAAA
1037543 CCTAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTTTTAAAAC
Found at i:1038992 original size:32 final size:32
Alignment explanation
Indices: 1038951--1039013 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1038941 AAAGTTAAAA
1038951 ACTATCACTGCACTAAAGGTCGACTTTTATCG
1 ACTATCACTGCACTAAAGGTCGACTTTTATCG
1038983 ACTATCACTGCACTAAAGGTCGACTTTTATC
1 ACTATCACTGCACTAAAGGTCGACTTTTATC
1039014 TATCTATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (32 bp):
ACTATCACTGCACTAAAGGTCGACTTTTATCG
Found at i:1055511 original size:69 final size:69
Alignment explanation
Indices: 1055400--1055540 Score: 282
Period size: 69 Copynumber: 2.0 Consensus size: 69
1055390 TTATTTAAGG
1055400 CTCTAGAATTTATACCAACAATAGGTTGGTGACACTCAAATCCTGCATATGCATGGGCTTATAGT
1 CTCTAGAATTTATACCAACAATAGGTTGGTGACACTCAAATCCTGCATATGCATGGGCTTATAGT
1055465 ACAT
66 ACAT
1055469 CTCTAGAATTTATACCAACAATAGGTTGGTGACACTCAAATCCTGCATATGCATGGGCTTATAGT
1 CTCTAGAATTTATACCAACAATAGGTTGGTGACACTCAAATCCTGCATATGCATGGGCTTATAGT
1055534 ACAT
66 ACAT
1055538 CTC
1 CTC
1055541 ACACATAGAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (69 bp):
CTCTAGAATTTATACCAACAATAGGTTGGTGACACTCAAATCCTGCATATGCATGGGCTTATAGT
ACAT
Found at i:1056767 original size:2 final size:2
Alignment explanation
Indices: 1056760--1056791 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1056750 TCGATTTGCA
1056760 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
1056792 ATATTGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1062886 original size:443 final size:441
Alignment explanation
Indices: 1062055--1062941 Score: 1643
Period size: 443 Copynumber: 2.0 Consensus size: 441
1062045 TAACATTAAT
1062055 TAAGCAGAGAGGGGGATGTACAAGTCATAATAAGTCATTACATTAAACCTGTCCCATGTCTGCAA
1 TAAGCAGAGAGGGGGATGTACAAGTCATAATAAGTCATTACATTAAACCTGTCCCATGTCTGCAA
1062120 GCTTTACTTTATATGATGAGTAACATGAAGTGACTGTGATAGAATGAAGATCCTGATTCCATGTG
66 GCTTTACTTTATATGATGAGTAACATGAAGTGACTGTGATAGAATGAAGATCCTGATTCCATGTG
1062185 TAAATAGTCAATACTCTTGTAATCCTCTCTACAGGTAGACACATATGCATGTATGTGTTTGCTGT
131 TAAATAGTCAATACTCTTGTAATCCTCTCTACAGGTAGACACATATGCATGTATGTGTTTGC---
1062250 TTGTGTGTATATATACATGTGTATGGTACATACACAAATTGTTGTTGGGTGCTAAAACATTGTAA
193 TTGTGTGTATATATACATGTGTATGGTACATACACAAATTGTTGTTGGGTGCTAAAACATTGTAA
*
1062315 ATAAGTCTTTATATCTATAATCGTTAATATTAATAGAAATAATATATTTTTATCATGTGTGAAAG
258 ATAAGTCTTTATATCTATAATCATTAATATTAATAGAAATAATATATTTTTATCATGTGTGAAAG
* *
1062380 TATTTGCAGCTGCATTTAATAATATACTTCAGTTTGTGTGAATACAGTATGGAAGAGTTTGTCTG
323 TATCTGCAGCTGCATTTAATAATATACTTCAGTTTGTGTGAATACAGTATGGAAGAATTTGTCTG
1062445 GGTCATGAATATATAAAAGATCTGTGTTTTTCTGAATTTTCTTTCTGTAGAAAAAA
388 GGTCATGAATAT-T-AAAGATCTGTGTTTTTCTGAATTTTCTTTCTGTAGAAAAAA
1062501 NTAAGCAGAGAGGGGGATGTACAAGTCATAATAAGTCATTACATTAAACCTGTCCCATGTCTGCA
1 -TAAGCAGAGAGGGGGATGTACAAGTCATAATAAGTCATTACATTAAACCTGTCCCATGTCTGCA
*
1062566 AGCTTTACTTTATCTGATGAGTAACATGAAGTGACTGTGATAGAATGAAGATCCTGATTCCATGT
65 AGCTTTACTTTATATGATGAGTAACATGAAGTGACTGTGATAGAATGAAGATCCTGATTCCATGT
1062631 GTAAATAGTCAATACTCTTGTAATCCTCTCTACAGGTAGACACATATGCATGTATGTG-TTGAC-
130 GTAAATAGTCAATACTCTTGTAATCCTCTCTACAGGTAGACACATATGCATGTATGTGTTTG-CT
*
1062694 TGTGTGTATATATACATGTGTATGGTACATACACAATTTGTTGTTGGGTGCTAAAACATTGTAAA
194 TGTGTGTATATATACATGTGTATGGTACATACACAAATTGTTGTTGGGTGCTAAAACATTGTAAA
1062759 TAAGTCTTTATATCTATAATCATTAATATTAATAGAAATAATATATTTTTATCATGTGTGAAAGT
259 TAAGTCTTTATATCTATAATCATTAATATTAATAGAAATAATATATTTTTATCATGTGTGAAAGT
1062824 ATCTGCAGCTGCATTTAATAATATACTTCAGTTTGTGTGAATACAGTATGGAAGAATTTGTCTGG
324 ATCTGCAGCTGCATTTAATAATATACTTCAGTTTGTGTGAATACAGTATGGAAGAATTTGTCTGG
*
1062889 GTCATGAATATTAAAGATCTGTGTTTTTTTGAATTTTCTTTCTGTAGAAAAAA
389 GTCATGAATATTAAAGATCTGTGTTTTTCTGAATTTTCTTTCTGTAGAAAAAA
1062942 AAAAGATCAA
Statistics
Matches: 433, Mismatches: 6, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
441 40 0.09
442 1 0.00
443 202 0.47
446 3 0.01
447 187 0.43
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (441 bp):
TAAGCAGAGAGGGGGATGTACAAGTCATAATAAGTCATTACATTAAACCTGTCCCATGTCTGCAA
GCTTTACTTTATATGATGAGTAACATGAAGTGACTGTGATAGAATGAAGATCCTGATTCCATGTG
TAAATAGTCAATACTCTTGTAATCCTCTCTACAGGTAGACACATATGCATGTATGTGTTTGCTTG
TGTGTATATATACATGTGTATGGTACATACACAAATTGTTGTTGGGTGCTAAAACATTGTAAATA
AGTCTTTATATCTATAATCATTAATATTAATAGAAATAATATATTTTTATCATGTGTGAAAGTAT
CTGCAGCTGCATTTAATAATATACTTCAGTTTGTGTGAATACAGTATGGAAGAATTTGTCTGGGT
CATGAATATTAAAGATCTGTGTTTTTCTGAATTTTCTTTCTGTAGAAAAAA
Found at i:1065985 original size:14 final size:16
Alignment explanation
Indices: 1065966--1066002 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1065956 GGGATAAGGT
1065966 AAATAATGT-G-AATG
1 AAATAATGTAGTAATG
*
1065980 AAATAATGTAGTCATG
1 AAATAATGTAGTAATG
1065996 AAATAAT
1 AAATAAT
1066003 TTTCAAGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 10 0.50
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (16 bp):
AAATAATGTAGTAATG
Found at i:1076060 original size:2 final size:2
Alignment explanation
Indices: 1076053--1076104 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1076043 TTAGGTCATA
1076053 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1076095 CT CT CT CT CT
1 CT CT CT CT CT
1076105 GGCCCTTACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1083955 original size:31 final size:31
Alignment explanation
Indices: 1083920--1083979 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1083910 CCGCGTTAGC
*
1083920 GGGTTATGTAATTTTTTCCTGCAATGATCGG
1 GGGTTATATAATTTTTTCCTGCAATGATCGG
1083951 GGGTTATATAATTTTTTCCTGCAATGATC
1 GGGTTATATAATTTTTTCCTGCAATGATC
1083980 ACTACCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (31 bp):
GGGTTATATAATTTTTTCCTGCAATGATCGG
Found at i:1086071 original size:15 final size:15
Alignment explanation
Indices: 1086051--1086080 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1086041 TCCACTATAT
1086051 CCTACAGCTGTAACA
1 CCTACAGCTGTAACA
1086066 CCTACAGCTGTAACA
1 CCTACAGCTGTAACA
1086081 TGCGCGGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
CCTACAGCTGTAACA
Found at i:1096294 original size:167 final size:165
Alignment explanation
Indices: 1096095--1096541 Score: 465
Period size: 167 Copynumber: 2.7 Consensus size: 165
1096085 CCCTTTACGA
* * * * *
1096095 CCTGAACGCCTGACCCAGAGGCCATGAATTTCACAACTTAGGTAAAGGAATTTGTGGACATTATA
1 CCTGAACCCCAGACCCAGGGGCCATGAATTTCACAA-TTAGGTAGAGGAATTCGTGGACATTATA
* *
1096160 ACCATGCATTCAGTTTTTCCCCACATGTGTGGGAGTAAAGAAGAAGATTTTCTAAGATTTAATAC
65 ACCATGCATTCAGTTTTTCCACAAATGTGTGGGAGTAAAGAAGAAGATTTTCTAAGATTTAATAC
* *
1096225 ATTTTCACTATATGACTAAAGTGGCCCCACCCTAGAG
130 ATTTTCACTATATGACCAAAGTGG-CCCAACCTAGAG
* * *
1096262 CCTGAACCCCAGAGCCAGGGGCCATGAATTTCACAATTAAGGTAGA-GAAGTCCGTTGACATTAT
1 CCTGAACCCCAGACCCAGGGGCCATGAATTTCACAATT-AGGTAGAGGAA-TTCGTGGACATTAT
* * * * * * *
1096326 AACCATGTA-CCAGTTTTATTCAAAAATATATGGGAG--AA-CAGAAGATTTTCTAAGATTTAAT
64 AACCATGCATTCAGTTTT-TCCACAAATGTGTGGGAGTAAAGAAGAAGATTTTCTAAGATTTAAT
*
1096387 ACATTTTCACTATATGGCCAAAGTGGCCCAACCTAGAG
128 ACATTTTCACTATATGACCAAAGTGGCCCAACCTAGAG
* * ** ** * *
1096425 ACTGAACCCCTA-ACCCAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCACGGAGATCAT
1 CCTGAACCCC-AGACCCAGGGGCCATGAATTTCACAA-TTAGGTAGAGGAATTCGTGGACATTAT
* * * * * **
1096489 AACTATGCATTTAGTTTTTTCCTCATATGTGTTGGAGTAGGGAAGAAGATTTT
64 AACCATGCATTCAG-TTTTTCCACAAATGTGTGGGAGTAAAGAAGAAGATTTT
1096542 TTTTTAAATT
Statistics
Matches: 224, Mismatches: 45, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
163 64 0.29
164 63 0.28
165 6 0.03
166 12 0.05
167 79 0.35
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (165 bp):
CCTGAACCCCAGACCCAGGGGCCATGAATTTCACAATTAGGTAGAGGAATTCGTGGACATTATAA
CCATGCATTCAGTTTTTCCACAAATGTGTGGGAGTAAAGAAGAAGATTTTCTAAGATTTAATACA
TTTTCACTATATGACCAAAGTGGCCCAACCTAGAG
Done.