Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 196 of 259
Found at i:62695513 original size:22 final size:22
Alignment explanation
Indices: 62695481--62695528 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
62695471 AATTGAGAAT
*
62695481 ATATAATTATTAACT-AAAAATA
1 ATATAAATATT-ACTAAAAAATA
*
62695503 ATATAAATATTATTAAAAAATA
1 ATATAAATATTACTAAAAAATA
62695525 ATAT
1 ATAT
62695529 GAGTGATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATAAATATTACTAAAAAATA
Found at i:62695527 original size:25 final size:24
Alignment explanation
Indices: 62695478--62695527 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
62695468 AATAATTGAG
* *
62695478 AATATATAATTATTAACTAAAAAT
1 AATATAAAATTATTAACAAAAAAT
62695502 AATATAAATATTATTAA-AAAATAAT
1 AATATAAA-ATTATTAACAAAA-AAT
62695527 A
1 A
62695528 TGAGTGATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AATATAAAATTATTAACAAAAAAT
Found at i:62696223 original size:6 final size:6
Alignment explanation
Indices: 62696214--62696242 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
62696204 GTTCTCTTGT
62696214 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
62696243 TTTCCCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCC
Found at i:62699846 original size:17 final size:17
Alignment explanation
Indices: 62699824--62699857 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
62699814 TATTTGTTTC
62699824 TTTAAGGAGCAATTGTG
1 TTTAAGGAGCAATTGTG
62699841 TTTAAGGAGCAATTGTG
1 TTTAAGGAGCAATTGTG
62699858 GTTAGTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (17 bp):
TTTAAGGAGCAATTGTG
Found at i:62700155 original size:20 final size:20
Alignment explanation
Indices: 62700113--62700155 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
62700103 TATTTGTTAA
**
62700113 TTTTATTTGACTTGAAATTT
1 TTTTATTTGACTTGAAAAAT
*
62700133 TTTTATTTGATTTGAAAAAT
1 TTTTATTTGACTTGAAAAAT
62700153 TTT
1 TTT
62700156 AAATGAGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.60
Consensus pattern (20 bp):
TTTTATTTGACTTGAAAAAT
Found at i:62701593 original size:239 final size:239
Alignment explanation
Indices: 62701169--62701646 Score: 559
Period size: 239 Copynumber: 2.0 Consensus size: 239
62701159 ATGAACAAAT
* * * *
62701169 CAAATGCTCTTGTATCAACAAAAGCACTTATTCTTCAGCCTGCTAAGTTGATGTCTACGAATATC
1 CAAATGCCCATGTATCAACAAAAGCACTTATTCTTCAGCCTGCTAAGTTAATGTCTACGAACATC
* * * *
62701234 AATCATTTTTGCTTGTAATCCCTCTTCACTCTAATAGAATTGAATATCATTGGACCAATCTTTAA
66 AACCATTTCTGCTTGTAATCCCTCTTCACTCTAACAGAATTGAATATCATTGGACCAAGCTTTAA
* ** * *
62701299 AGCCTCTGTAACACCCCTTGCTTGACCCGTTCGTCAAGTCTGAGCTACAGAATGCTATATTCATT
131 AGCCTCTATAACACCCCTTGCTCAACCCGTTCATCAAGTCTGAGCTACAGAATGCTACATTCATT
* * * * *
62701364 GCCGGAGCAATTACAGCCAATTAGACATCATATAATCATTTATA
196 GCCAGAACAACTACAACCAATTAGACATCATACAATCATTTATA
* * *
62701408 CAAATGCCCATGTATCAACAAAAGCACTTATTCTT-TGACCTG-TGATGTTAATGTCTATGAACA
1 CAAATGCCCATGTATCAACAAAAGCACTTATTCTTCAG-CCTGCT-AAGTTAATGTCTACGAACA
* * ** * * *
62701471 TCAACCATTTCTGCTTGTGATCCCTTTTTGCTTTAGCAGAATTGAGTATCATTGGACCAAGCTTT
64 TCAACCATTTCTGCTTGTAATCCCTCTTCACTCTAACAGAATTGAATATCATTGGACCAAGCTTT
* * * * **
62701536 AAAGCTTCTATAACATCCCTT-ATCCAACCCCG-TCATCAGGTCTGAGCTATGGAATGCTACATT
129 AAAGCCTCTATAACACCCCTTGCT-CAA-CCCGTTCATCAAGTCTGAGCTACAGAATGCTACATT
* * *
62701599 CGTTGTCAGAACAACTACAACCAATTAGACATCATACAATTATTTATA
192 CATTGCCAGAACAACTACAACCAATTAGACATCATACAATCATTTATA
62701647 TATATAATTT
Statistics
Matches: 198, Mismatches: 37, Indels: 8
0.81 0.15 0.03
Matches are distributed among these distances:
238 3 0.02
239 191 0.96
240 4 0.02
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (239 bp):
CAAATGCCCATGTATCAACAAAAGCACTTATTCTTCAGCCTGCTAAGTTAATGTCTACGAACATC
AACCATTTCTGCTTGTAATCCCTCTTCACTCTAACAGAATTGAATATCATTGGACCAAGCTTTAA
AGCCTCTATAACACCCCTTGCTCAACCCGTTCATCAAGTCTGAGCTACAGAATGCTACATTCATT
GCCAGAACAACTACAACCAATTAGACATCATACAATCATTTATA
Found at i:62705426 original size:16 final size:16
Alignment explanation
Indices: 62705404--62705472 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
62705394 TTTGGTTCGC
62705404 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
62705420 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62705436 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
62705453 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62705469 TGTA
1 TGTA
62705473 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:62705450 original size:33 final size:32
Alignment explanation
Indices: 62705404--62705472 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
62705394 TTTGGTTCGC
62705404 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
62705436 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
62705469 TGTA
1 TGTA
62705473 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:62705537 original size:44 final size:45
Alignment explanation
Indices: 62705453--62705543 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
62705443 GGATTAGAGG
* * *
62705453 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
62705498 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
62705542 TG
1 TG
62705544 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:62705729 original size:18 final size:17
Alignment explanation
Indices: 62705708--62705742 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62705698 TTATTATTAA
*
62705708 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
62705726 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
62705743 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:62705963 original size:30 final size:30
Alignment explanation
Indices: 62705928--62706084 Score: 78
Period size: 30 Copynumber: 5.2 Consensus size: 30
62705918 GTAAAATATA
62705928 AATTAACATAATTATTATTAAATATATTTT
1 AATTAACATAATTATTATTAAATATATTTT
* * * *
62705958 AATTAAAAT-A-TATAATTTAATGAAATTCTT
1 AATTAACATAATTATTATTAAAT-ATATT-TT
* * * *
62705988 AATTGA-ATAA-TATTCTTATAT-TAATTT
1 AATTAACATAATTATTATTAAATATATTTT
* * *
62706015 ACTGAAATCATAATATATGATACTGTAAA-ATA--TA
1 AAT-TAA-CATAAT-TAT--TA-T-TAAATATATTTT
62706049 AATTAACATAATTATTATTAAATATATTTT
1 AATTAACATAATTATTATTAAATATATTTT
62706079 AATTAA
1 AATTAA
62706085 ACTATATAAT
Statistics
Matches: 91, Mismatches: 20, Indels: 32
0.64 0.14 0.22
Matches are distributed among these distances:
27 8 0.09
28 16 0.18
29 9 0.10
30 34 0.37
31 3 0.03
32 9 0.10
33 2 0.02
34 4 0.04
35 1 0.01
36 5 0.05
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (30 bp):
AATTAACATAATTATTATTAAATATATTTT
Found at i:62706206 original size:120 final size:120
Alignment explanation
Indices: 62705691--62706555 Score: 1554
Period size: 120 Copynumber: 7.2 Consensus size: 120
62705681 ATCATATTTA
*
62705691 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
62705756 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * *
62705811 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGA-T
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAA-T-AATT
*
62705875 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
64 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
62705932 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGAA-T
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAA-T-AATT
*
62705996 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
64 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
62706053 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
62706118 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
62706173 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
62706238 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
62706293 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
62706358 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
62706413 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
62706478 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
62706533 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
62706556 AACTTGAAAA
Statistics
Matches: 730, Mismatches: 12, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
119 2 0.00
120 493 0.68
121 234 0.32
122 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:62709616 original size:33 final size:33
Alignment explanation
Indices: 62709577--62709652 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
62709567 ATTATAAAGC
*
62709577 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
62709610 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
62709643 ATGTATAATT
1 ATGTATAATT
62709653 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:62709750 original size:37 final size:37
Alignment explanation
Indices: 62709695--62709776 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
62709685 GTATAAATAT
* * *
62709695 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAGC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
62709732 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
62709769 ATTGATTA
1 ATTGATTA
62709777 ATAAATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:62725372 original size:18 final size:16
Alignment explanation
Indices: 62725336--62725367 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
62725326 TAGATATTAA
62725336 TATATATTTAAATAAT
1 TATATATTTAAATAAT
*
62725352 TATATATTTGAATAAT
1 TATATATTTAAATAAT
62725368 CTTATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:62745651 original size:30 final size:30
Alignment explanation
Indices: 62745617--62745676 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
62745607 TATTTTATTA
62745617 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
62745647 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
62745677 CTTGTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:62745778 original size:18 final size:19
Alignment explanation
Indices: 62745752--62745799 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
62745742 TTGTTGGAAA
* *
62745752 ATATTTATTTTGATTTATT
1 ATATATATTTTGATGTATT
*
62745771 TTA-ATATTTTTGATGTATT
1 ATATATA-TTTTGATGTATT
62745790 ATATATATTT
1 ATATATATTT
62745800 AAAAATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.09
19 18 0.78
20 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
ATATATATTTTGATGTATT
Found at i:62745781 original size:19 final size:20
Alignment explanation
Indices: 62745759--62745799 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
62745749 AAAATATTTA
* *
62745759 TTTTGATTTATTTTA-ATAT
1 TTTTGATGTATTATATATAT
62745778 TTTTGATGTATTATATATAT
1 TTTTGATGTATTATATATAT
62745798 TT
1 TT
62745800 AAAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTGATGTATTATATATAT
Found at i:62748501 original size:19 final size:18
Alignment explanation
Indices: 62748470--62748507 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
62748460 TTCCTAAACA
62748470 TATTCTCCTCTCTTCTTC
1 TATTCTCCTCTCTTCTTC
*
62748488 TATTCTCTCTCTCTTTTTC
1 TATTCTC-CTCTCTTCTTC
62748507 T
1 T
62748508 CTTTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTCTCCTCTCTTCTTC
Found at i:62750907 original size:3 final size:3
Alignment explanation
Indices: 62750833--62750881 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
62750823 CAAAAATGGC
*
62750833 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62750881 A
1 A
62750882 TAACGTAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:62751067 original size:14 final size:14
Alignment explanation
Indices: 62751048--62751143 Score: 73
Period size: 14 Copynumber: 7.1 Consensus size: 14
62751038 TGGGATAATG
62751048 TATAAAAATATATA
1 TATAAAAATATATA
*
62751062 TATAAATAATGTGATA
1 TATAAA-AATAT-ATA
62751078 T-TAAAAATATATA
1 TATAAAAATATATA
*
62751091 CATAAAAATA-ATA
1 TATAAAAATATATA
62751104 TAT----ATATA-A
1 TATAAAAATATATA
*
62751113 TATACATAATATAGTA
1 TATA-AAAATATA-TA
62751129 T-TAAAAATATATA
1 TATAAAAATATATA
62751142 TA
1 TA
62751144 ATACATACAC
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
9 7 0.11
10 1 0.02
13 11 0.17
14 30 0.46
15 10 0.15
16 6 0.09
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.36
Consensus pattern (14 bp):
TATAAAAATATATA
Found at i:62751098 original size:15 final size:17
Alignment explanation
Indices: 62751083--62751150 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
62751073 TGATATTAAA
62751083 AATATATACATAAAAAT
1 AATATATACATAAAAAT
*
62751100 AATATATATATAATATACAT
1 AATATATACATAA-A-A-AT
*
62751120 AATATAGTA-TTAAAAAT
1 AATATA-TACATAAAAAT
62751137 ATATATAATACATA
1 A-ATAT-ATACATA
62751151 CACACTAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
17 15 0.37
18 8 0.20
19 5 0.12
20 11 0.27
21 2 0.05
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (17 bp):
AATATATACATAAAAAT
Found at i:62751408 original size:24 final size:24
Alignment explanation
Indices: 62751341--62751397 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
62751331 TAGTAATTAT
* * * *
62751341 AATACTAATACTAATAATAAATAC
1 AATAATAATAGTAAAAATAAACAC
*
62751365 AATAATAGTAGTAAAAATAAACAC
1 AATAATAATAGTAAAAATAAACAC
62751389 AATAATAAT
1 AATAATAAT
62751398 CATGAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (24 bp):
AATAATAATAGTAAAAATAAACAC
Found at i:62754376 original size:7 final size:7
Alignment explanation
Indices: 62754366--62754398 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
62754356 TATGAATTAT
62754366 GATATTG
1 GATATTG
62754373 GATATTG
1 GATATTG
62754380 GATATTG
1 GATATTG
62754387 GATATTG
1 GATATTG
62754394 GATAT
1 GATAT
62754399 GAATTGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.42
Consensus pattern (7 bp):
GATATTG
Found at i:62763445 original size:192 final size:193
Alignment explanation
Indices: 62763118--62763505 Score: 679
Period size: 192 Copynumber: 2.0 Consensus size: 193
62763108 CTTAGCTCAG
*
62763118 TTGGTAGAGCGGAGGACTGTAGTGGTAAAAGTCAGAGCAATCCTTAGGTCGCTGGTTCGAATCCG
1 TTGGTAGAGCGGAGGACTGTAGTGGTAAAAGTCAGAGCAATCCTTAGGTCGCTGGTTCGAATCCA
* ** *
62763183 GCAGGTCGGAATTTTTTTTAACTATACTTTTATAATTGGGTTAATATGCGCTTTGATATCTTAAT
66 GCAGGTCAGAACCTTTTTTAACTATACTTTTATAATTGGGTTAATATACGCTTTGATATCTTAAT
* *
62763248 TTTGCTTCAATGTTCAATTTAGCAACCGGGTCTTTTTT-TTTTTATCAATTTGGTACATATGT
131 TTTGCTTCAATGTTCAATTTAGCAACCAGGTCTTTTTTATTATTATCAATTTGGTACATATGT
* *
62763310 TTGGTAGAGCGGAGGACTGTAGTGGTAAATGTCAGAGCAATCGTTAGGTCGCTGGTTCGAATCCA
1 TTGGTAGAGCGGAGGACTGTAGTGGTAAAAGTCAGAGCAATCCTTAGGTCGCTGGTTCGAATCCA
*
62763375 GCAGGTCAGAACCTTTTTTAACTATACTTTTATAATTGGGTTAATATACTCTTTGATATCTTAAT
66 GCAGGTCAGAACCTTTTTTAACTATACTTTTATAATTGGGTTAATATACGCTTTGATATCTTAAT
62763440 TTTGCTTCAATGTTCAATTTAGCAACCAGGTCTTTTTTATTATTATCAATTTGGTACATATGT
131 TTTGCTTCAATGTTCAATTTAGCAACCAGGTCTTTTTTATTATTATCAATTTGGTACATATGT
62763503 TTG
1 TTG
62763506 ATTTCAATAT
Statistics
Matches: 185, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
192 159 0.86
193 26 0.14
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (193 bp):
TTGGTAGAGCGGAGGACTGTAGTGGTAAAAGTCAGAGCAATCCTTAGGTCGCTGGTTCGAATCCA
GCAGGTCAGAACCTTTTTTAACTATACTTTTATAATTGGGTTAATATACGCTTTGATATCTTAAT
TTTGCTTCAATGTTCAATTTAGCAACCAGGTCTTTTTTATTATTATCAATTTGGTACATATGT
Found at i:62765299 original size:103 final size:103
Alignment explanation
Indices: 62765154--62765360 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
62765144 AACATTGTCG
62765154 ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
1 ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
62765219 ATCATTATACTTGTAATAATAATTTAAAACTAATCTGT
66 ATCATTATACTTGTAATAATAATTTAAAACTAATCTGT
62765257 ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
1 ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
62765322 ATCATTATACTTGTAATAATAATTTAAAACTAATCTGT
66 ATCATTATACTTGTAATAATAATTTAAAACTAATCTGT
62765360 A
1 A
62765361 ACACTTCGTA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (103 bp):
ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
ATCATTATACTTGTAATAATAATTTAAAACTAATCTGT
Found at i:62768775 original size:132 final size:132
Alignment explanation
Indices: 62768430--62768820 Score: 434
Period size: 130 Copynumber: 3.0 Consensus size: 132
62768420 ATAATTATTC
** *
62768430 TTCTAAAAA-TCCTTTAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATTGTGCCCTA
1 TTCTAAAAACT-C-TTAAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTA
* * * *
62768494 ACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAAGGTCCATTTAGAATTTCACCCAT
64 ACGTGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAGGTCCCTTTAGAATTTCACTCAT
62768559 GTCT
129 GTCT
* * * * *
62768563 TT-TAAAATC-CTTTAAACGAAGGCGATGTTCGATATTTGACAATTCGCA-GAATCGTGCCCTAA
1 TTCTAAAAACTCTTAAAACGAAGGCAATGTTCGATATTTGGCAATTC-AAGGAATCGTGCCCTAA
* * * * *
62768625 CGTGCTGGGTTGTAATTTCTCGTTTGTTCAAAATAATCGAAGGTCCCTTTTGAAATTCACTTATG
65 CGTGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAGGTCCCTTTAGAATTTCACTCATG
62768690 T-T
130 TCT
* * * * *
62768692 TTCTAAAAACTCTTCAAAATGAAGGTAATATTCGATGTTTGGCAATTCAAGGAATCGTGCCCTAT
1 TTCTAAAAACTCTT-AAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAA
* * * * * * *
62768757 CGTGCTGGGTAGCGATTTCTTGCTTGGC-CAAAATGATCGAAGATTCCTTTAGAATTTCACTCAT
65 CGTGCTGGGTTGCAATTTCTCG-TTTGCTCAAAATAATCGAAGGTCCCTTTAGAATTTCACTCAT
62768821 ACTCTCTAAA
Statistics
Matches: 213, Mismatches: 38, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
129 3 0.01
130 108 0.51
131 5 0.02
132 92 0.43
133 5 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (132 bp):
TTCTAAAAACTCTTAAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAAC
GTGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAGGTCCCTTTAGAATTTCACTCATGT
CT
Found at i:62768829 original size:132 final size:128
Alignment explanation
Indices: 62768431--62768830 Score: 381
Period size: 132 Copynumber: 3.0 Consensus size: 128
62768421 TAATTATTCT
** *
62768431 TCTAAAAATCCTTTAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATTGTGCCCTAAC
1 TCTAAAAATCC-TTAAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAAC
* * * * * *
62768496 GTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAAGGTCCATTTAGAATTTCACCCATGT
65 GTGCTGGGTTGCAATTTCTCGTTGGC-CAAAATAATCGAAGTTCC-TTTAGAATTTCACTCATCT
62768561 C
128 C
* * * * * *
62768562 TTTTAAAATCCTTTAAACGAAGGCGATGTTCGATATTTGACAATTCGCA-GAATCGTGCCCTAAC
1 TCTAAAAATCCTTAAAACGAAGGCAATGTTCGATATTTGGCAATTC-AAGGAATCGTGCCCTAAC
* ** * * * * *
62768626 GTGCTGGGTTGTAATTTCTCGTTTGTTCAAAATAATCGAAGGTCCCTTTTGAAATTCACTTATGT
65 GTGCTGGGTTGCAATTTCTCG-TTGGCCAAAATAATCGAA-GTTCCTTTAGAATTTCACTCAT-C
*
62768691 TT
127 TC
* * * * *
62768693 TCTAAAAA-CTCTTCAAAATGAAGGTAATATTCGATGTTTGGCAATTCAAGGAATCGTGCCCTAT
1 TCTAAAAATC-CTT-AAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAA
* * * *
62768757 CGTGCTGGGTAGCGATTTCTTGCTTGGCCAAAATGATCGAAGATTCCTTTAGAATTTCACTCATA
64 CGTGCTGGGTTGCAATTTCTCG-TTGGCCAAAATAATCGAAG-TTCCTTTAGAATTTCACTCAT-
62768822 CTC
126 CTC
62768825 TCTAAA
1 TCTAAA
62768831 TTCTAAAATA
Statistics
Matches: 213, Mismatches: 48, Indels: 15
0.77 0.17 0.05
Matches are distributed among these distances:
130 91 0.43
131 26 0.12
132 96 0.45
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (128 bp):
TCTAAAAATCCTTAAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAACG
TGCTGGGTTGCAATTTCTCGTTGGCCAAAATAATCGAAGTTCCTTTAGAATTTCACTCATCTC
Found at i:62770961 original size:20 final size:20
Alignment explanation
Indices: 62770924--62770980 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
62770914 ATTTATCATT
*
62770924 ATTATTATTCTATCAAATTATA
1 ATTATTA-T-TATTAAATTATA
*
62770946 ATT-TATATTATTAAATTATG
1 ATTAT-TATTATTAAATTATA
62770966 ATTATTATTATTAAA
1 ATTATTATTATTAAA
62770981 AATAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 23 0.74
21 3 0.10
22 5 0.16
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTATTATTATTAAATTATA
Found at i:62771109 original size:18 final size:17
Alignment explanation
Indices: 62771086--62771126 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
62771076 TATTTAAGTA
**
62771086 AAAATATTTTATTATATT
1 AAAATATTAAATTATA-T
62771104 AAAATATTAAATTATAT
1 AAAATATTAAATTATAT
62771121 AAAATA
1 AAAATA
62771127 AATAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATATTAAATTATAT
Found at i:62772116 original size:21 final size:21
Alignment explanation
Indices: 62772091--62772156 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
62772081 TTGTTTGGAA
62772091 TACTGCATTGAATTGTGAAGT
1 TACTGCATTGAATTGTGAAGT
* * *
62772112 TACTG-AAT--ATTGTTATGT
1 TACTGCATTGAATTGTGAAGT
* *
62772130 GTACTGCATTGAACTGTGAAAT
1 -TACTGCATTGAATTGTGAAGT
62772152 TACTG
1 TACTG
62772157 AAGTAATGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
18 8 0.24
19 5 0.15
20 4 0.12
21 10 0.30
22 6 0.18
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (21 bp):
TACTGCATTGAATTGTGAAGT
Found at i:62772123 original size:40 final size:40
Alignment explanation
Indices: 62772072--62772158 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
62772062 AATTATGGAA
* *
62772072 TACTGAATATTGTT-TG-GAATACTGCATTGAATTGTGAAGT
1 TACTGAATATTGTTATGTG--TACTGCATTGAACTGTGAAAT
62772112 TACTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
62772152 TACTGAA
1 TACTGAA
62772159 GTAATGAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 40 0.93
41 2 0.05
42 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (40 bp):
TACTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
Found at i:62772430 original size:45 final size:45
Alignment explanation
Indices: 62772362--62772462 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 45
62772352 GCCGACTACT
* *
62772362 GTTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCGACACTTTGTGAGTCGAATACTGTTACC
* *
62772407 GTTACTGTTACAGATTC-AGCACTTTGTGAGTTGAATACTGTTACT
1 GTTACTGTTACAGATTCGA-CACTTTGTGAGTCGAATACTGTTACC
*
62772452 GTTGCTGTTAC
1 GTTACTGTTAC
62772463 TGCTACCGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (45 bp):
GTTACTGTTACAGATTCGACACTTTGTGAGTCGAATACTGTTACC
Found at i:62772453 original size:6 final size:6
Alignment explanation
Indices: 62772442--62772485 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
62772432 GTGAGTTGAA
* * *
62772442 TACTGT TACTGT TGCTGT TACTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
62772486 TAGGTACTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:62773233 original size:16 final size:17
Alignment explanation
Indices: 62773202--62773234 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62773192 TTCATAAGTA
62773202 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
62773219 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
62773235 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:62773673 original size:46 final size:46
Alignment explanation
Indices: 62773519--62773658 Score: 201
Period size: 46 Copynumber: 3.0 Consensus size: 46
62773509 TTTGACATGA
* * * * *
62773519 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATAGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
* *
62773565 TGCCATGGTATCTTTCAACCATTGTCTTATTCTTTTCATGTCACGT
1 TGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
62773611 TGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
62773657 TG
1 TG
62773659 GTCTTATTCA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
45 5 0.06
46 79 0.94
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.45
Consensus pattern (46 bp):
TGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
Found at i:62773680 original size:117 final size:117
Alignment explanation
Indices: 62773540--62773756 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 117
62773530 CTTTCAACTA
* * * * ** * *
62773540 TGGTCTTACTCATTTTCTATCATGTTGCCATGGTATCTTTCAACCATTGTCTTATTCTTTTCATG
1 TGGTCTTACTCATTTTCTATCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCATA
*
62773605 TCACGTTGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
66 TCACGTAGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
* *
62773657 TGGTCTTATTCA-TTTCATGTCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCAT
1 TGGTCTTACTCATTTTC-TATCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCAT
* *
62773721 ATCATGTAGCCATGGTATCTTTCAACCATGGTCTTA
65 ATCACGTAGCCATAGTATCTTTCAACCATGGTCTTA
62773757 CACATTTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
116 4 0.05
117 82 0.95
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (117 bp):
TGGTCTTACTCATTTTCTATCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCATA
TCACGTAGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
Found at i:62773719 original size:71 final size:71
Alignment explanation
Indices: 62773588--62773720 Score: 185
Period size: 71 Copynumber: 1.9 Consensus size: 71
62773578 TTCAACCATT
* * * * ** *
62773588 GTCTTATTCTTTTCATGTCACGTTGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTC
1 GTCTTATTCATTTCATGTCACGCTACCATAGCATCTTTCAACCATGGTCTTACACATTTCATGTC
62773653 ACGTTG
66 ACGTTG
* *
62773659 GTCTTATTCATTTCATGTCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCAT
1 GTCTTATTCATTTCATGTCACGCTACCATAGCATCTTTCAACCATGGTCTTACACATTTCAT
62773721 ATCATGTAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (71 bp):
GTCTTATTCATTTCATGTCACGCTACCATAGCATCTTTCAACCATGGTCTTACACATTTCATGTC
ACGTTG
Found at i:62773815 original size:46 final size:46
Alignment explanation
Indices: 62773657--62773816 Score: 239
Period size: 46 Copynumber: 3.5 Consensus size: 46
62773647 CATGTCACGT
** * * * *
62773657 TGGTCTTATTCATTTCATGTCATGCTACCATGGCATCTTTCAACCA
1 TGGTCTTACACATTTCATTTCATGTTGCCATGGTATCTTTCAACCA
* *
62773703 TGGTCTTACACATTTCATATCATGTAGCCATGGTATCTTTCAACCA
1 TGGTCTTACACATTTCATTTCATGTTGCCATGGTATCTTTCAACCA
*
62773749 TGGTCTTACACATTTTATTTCATGTTGCCATGGTATCTTTCAACCA
1 TGGTCTTACACATTTCATTTCATGTTGCCATGGTATCTTTCAACCA
62773795 TGGTCTTACACATTTCATTTCA
1 TGGTCTTACACATTTCATTTCA
62773817 GAAAGCACAT
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 103 1.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (46 bp):
TGGTCTTACACATTTCATTTCATGTTGCCATGGTATCTTTCAACCA
Found at i:62775648 original size:11 final size:11
Alignment explanation
Indices: 62775632--62775679 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
62775622 CTTTATATAC
62775632 TAATAAAATAA
1 TAATAAAATAA
*
62775643 TAATAAAATATCT
1 TAATAAAATA--A
* *
62775656 TATTAAAATAT
1 TAATAAAATAA
62775667 TAATAAAATAA
1 TAATAAAATAA
62775678 TA
1 TA
62775680 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:62778803 original size:17 final size:17
Alignment explanation
Indices: 62778781--62778825 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
62778771 ATTGTTAAAT
*
62778781 AGAGTTATTCTTGAACA
1 AGAGTTATTCTTAAACA
* *
62778798 AGAGTTGTTCTTAAATA
1 AGAGTTATTCTTAAACA
*
62778815 AGGGTTATTCT
1 AGAGTTATTCT
62778826 GACATGTTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (17 bp):
AGAGTTATTCTTAAACA
Found at i:62793574 original size:19 final size:19
Alignment explanation
Indices: 62793549--62793591 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
62793539 ATAATATAAT
*
62793549 AAAAGAAATAATA-AAAGA
1 AAAAGAAATAAAATAAAGA
62793567 ATAAAGAAATAAAATAAAGA
1 A-AAAGAAATAAAATAAAGA
62793587 AAAAG
1 AAAAG
62793592 GAAAGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAGAAATAAAATAAAGA
Found at i:62798784 original size:40 final size:39
Alignment explanation
Indices: 62798722--62798801 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
62798712 TAACGACTTA
* *
62798722 TCGGCTAAAATGGCACTCAGTGTGTAGTTTGAAATAGCT
1 TCGGCTAAAATGGCACTCAGTGTGCAATTTGAAATAGCT
* *
62798761 TCGGCTAAAAGTGGCACTTAGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTCAGTGTGCAATTTGAAATAGCT
62798801 T
1 T
62798802 TGACTATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 10 0.28
40 26 0.72
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTCAGTGTGCAATTTGAAATAGCT
Found at i:62798881 original size:28 final size:28
Alignment explanation
Indices: 62798822--62798890 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 28
62798812 TATATAAATG
** ** * *
62798822 GCACTTAGTGTGCAAAGTATTGAGGATG
1 GCACTTAGTGTGCAAAACATCCAGAATA
62798850 GCACTTAGTGTGCAAAACATCCAGAATA
1 GCACTTAGTGTGCAAAACATCCAGAATA
*
62798878 GCACTTAGGGTGC
1 GCACTTAGTGTGC
62798891 GAGGTATCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (28 bp):
GCACTTAGTGTGCAAAACATCCAGAATA
Found at i:62800472 original size:18 final size:18
Alignment explanation
Indices: 62800449--62800485 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
62800439 TGACACAGCC
62800449 ATATGTCTCAGCTGTGTG
1 ATATGTCTCAGCTGTGTG
62800467 ATATGTCTCAGCTGTGTG
1 ATATGTCTCAGCTGTGTG
62800485 A
1 A
62800486 GGGACACGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.38
Consensus pattern (18 bp):
ATATGTCTCAGCTGTGTG
Found at i:62803038 original size:13 final size:13
Alignment explanation
Indices: 62803020--62803044 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62803010 TAATTGCTTA
62803020 ATTTTTTTATTTT
1 ATTTTTTTATTTT
62803033 ATTTTTTTATTT
1 ATTTTTTTATTT
62803045 CATATCTAAT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTTTATTTT
Found at i:62805954 original size:12 final size:12
Alignment explanation
Indices: 62805937--62805972 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
62805927 AACATTTTGA
62805937 CATTCATGCATT
1 CATTCATGCATT
62805949 CATTCATGCATT
1 CATTCATGCATT
*
62805961 CATTCATACATT
1 CATTCATGCATT
62805973 GCATATCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:62814477 original size:120 final size:121
Alignment explanation
Indices: 62814272--62814496 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 121
62814262 TTTTTTTAAA
** *
62814272 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAGTTTAT
***** ** **
62814337 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTGTTTTTC
66 AAAAAAAATCAACTCATATTGCGAGAAATGAGTTAAGCCTTTTAATTTTGTTTTTC
* *
62814393 AAAATCAACTCATATTGCGAGAA-TGAGTTGAGCCTCAAGACACG-TGAGGTATTTTTAAATTT-
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT-AGTTTA
*
62814455 TAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
65 T-AAAAAAAATCAACTCATATTGCGAGAAATGAGTTAAGCCT
62814497 CGGGGCACGC
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
119 12 0.14
120 52 0.60
121 23 0.26
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (121 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAGTTTAT
AAAAAAAATCAACTCATATTGCGAGAAATGAGTTAAGCCTTTTAATTTTGTTTTTC
Found at i:62814524 original size:189 final size:193
Alignment explanation
Indices: 62814201--62814620 Score: 749
Period size: 189 Copynumber: 2.2 Consensus size: 193
62814191 CTTTCCAAGG
62814201 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
** *
62814266 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
65 TAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
62814331 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAA-TTTTG-TTTTTC
130 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTTC
62814393 AAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACG-TGAGGTATTTTTAAA-TTTT
1 AAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTT
62814456 AAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 AAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
62814521 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTTC
* *
62814584 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 AAAATCAACTCATATTGCGAGA-ATGAGTTGAGCCTC
62814621 GGCTCACATG
Statistics
Matches: 220, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
189 116 0.53
190 20 0.09
191 50 0.23
192 34 0.15
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.35
Consensus pattern (193 bp):
AAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTT
AAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTTC
Found at i:62814785 original size:85 final size:84
Alignment explanation
Indices: 62814579--62814820 Score: 294
Period size: 88 Copynumber: 2.8 Consensus size: 84
62814569 AATTTTTGTT
62814579 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTTT
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CAC--GCTGAGGTATTTT
**
62814643 CAATTTATGTTTTTTCAATCTA
63 CAATTTATGTTTACTCAATCTA
* *
62814665 TGCTTTCAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CACGCTGAGGTATTTT
1 T--TTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACGCTGAGGTATTTT
*
62814729 CAATTTCTGCTTTACT-AATTCTA
63 CAATTTATG-TTTACTCAA-TCTA
* *
62814752 CTTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTT
1 -TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG-C-CACGCTGAGGTATTTT
62814816 CAATT
63 CAATT
62814821 CTGTTTTTAA
Statistics
Matches: 137, Mismatches: 9, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
86 28 0.20
87 28 0.20
88 43 0.31
90 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (84 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACGCTGAGGTATTTTCAA
TTTATGTTTACTCAATCTA
Found at i:62814999 original size:54 final size:55
Alignment explanation
Indices: 62814927--62815143 Score: 315
Period size: 54 Copynumber: 4.1 Consensus size: 55
62814917 TCAATTTCTA
*
62814927 CTTTTCAA-TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
62814981 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
62815035 C--TT---TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
62815086 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
62815141 CTT
1 CTT
62815144 GGCTCACGTG
Statistics
Matches: 149, Mismatches: 6, Indels: 15
0.88 0.04 0.09
Matches are distributed among these distances:
50 12 0.08
51 35 0.23
52 2 0.01
53 4 0.03
54 50 0.34
55 37 0.25
56 5 0.03
57 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (55 bp):
CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:62815439 original size:29 final size:29
Alignment explanation
Indices: 62815406--62815504 Score: 146
Period size: 29 Copynumber: 3.4 Consensus size: 29
62815396 TTAAAAATAA
* *
62815406 AAATTGCATTTTGACCCCTAAACTTTCCT
1 AAATTTCATTTTGACCCCTAAACTTTCTT
*
62815435 AAATTTCATTTTGACCCTTAAACTTTCTT
1 AAATTTCATTTTGACCCCTAAACTTTCTT
*
62815464 AAATTTCA-TTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTC-TT
62815493 AAATTTCATTTT
1 AAATTTCATTTT
62815505 AATCATAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
28 16 0.26
29 44 0.71
30 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (29 bp):
AAATTTCATTTTGACCCCTAAACTTTCTT
Found at i:62815513 original size:29 final size:28
Alignment explanation
Indices: 62815406--62815519 Score: 111
Period size: 29 Copynumber: 4.0 Consensus size: 28
62815396 TTAAAAATAA
* * *
62815406 AAATTGCATTTTGACCCCTAAACTTTCCT
1 AAATTTCATTTT-ACCCATAAACTTTCTT
*
62815435 AAATTTCATTTTGACCCTTAAACTTTCTT
1 AAATTTCATTTT-ACCCATAAACTTTCTT
** *
62815464 AAATTTCATTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTACCCATAAACTTTC-TT
** *
62815493 AAATTTCATTTTAATCATAAATTTTCT
1 AAATTTCATTTTACCCATAAACTTTCT
62815520 AAAAATTACA
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
28 14 0.19
29 58 0.81
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (28 bp):
AAATTTCATTTTACCCATAAACTTTCTT
Found at i:62815526 original size:58 final size:58
Alignment explanation
Indices: 62815403--62815531 Score: 145
Period size: 58 Copynumber: 2.2 Consensus size: 58
62815393 AAATTAAAAA
* * * *
62815403 TAAAAATTGCATTTTGACCCCTAAACTTTCCTAAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTACA-TTAGACCCCTAAACTTTCCTAAATTTCATTTTGAACCATAAACTTTC
* * * * *
62815462 T-TAAATTTCATTAGACCCCTAAACTTTCATTAAATTTCATTTT-AATCATAAATTTTC
1 TAAAAATTACATTAGACCCCTAAACTTTC-CTAAATTTCATTTTGAACCATAAACTTTC
62815519 TAAAAATTACATT
1 TAAAAATTACATT
62815532 TAGCCCCAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
57 28 0.48
58 29 0.50
59 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (58 bp):
TAAAAATTACATTAGACCCCTAAACTTTCCTAAATTTCATTTTGAACCATAAACTTTC
Found at i:62815752 original size:18 final size:17
Alignment explanation
Indices: 62815729--62815770 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
62815719 CATGAATCCC
62815729 AAAAAAAAG-TTCAAAGA
1 AAAAAAAAGCTTCAAA-A
*
62815746 GAAAAAAAGCTTCAAAA
1 AAAAAAAAGCTTCAAAA
62815763 AAAAAAAA
1 AAAAAAAA
62815771 ATGGGAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAAAAGCTTCAAAA
Found at i:62815771 original size:18 final size:17
Alignment explanation
Indices: 62815729--62815771 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
62815719 CATGAATCCC
*
62815729 AAAAAAAAGTTCAAAGA
1 AAAAAAAAGTTCAAAAA
*
62815746 GAAAAAAAGCTTCAAAAA
1 AAAAAAAAG-TTCAAAAA
62815764 AAAAAAAA
1 AAAAAAAA
62815772 TGGGAGAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAAAAAAGTTCAAAAA
Found at i:62815871 original size:3 final size:3
Alignment explanation
Indices: 62815863--62815918 Score: 67
Period size: 3 Copynumber: 17.0 Consensus size: 3
62815853 GGGCTCAGTT
62815863 GAA GAA GAA GAA GAA GGAA GAA GAA GAA GAAA GAAA GAGA GAA GAA GAAA
1 GAA GAA GAA GAA GAA -GAA GAA GAA GAA G-AA G-AA GA-A GAA GAA G-AA
62815913 GAA GAA
1 GAA GAA
62815919 AAAAAGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 33 0.67
4 16 0.33
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:62815884 original size:10 final size:9
Alignment explanation
Indices: 62815863--62815918 Score: 67
Period size: 10 Copynumber: 5.7 Consensus size: 9
62815853 GGGCTCAGTT
62815863 GAAGAAGAA
1 GAAGAAGAA
62815872 GAAGAAGGAA
1 GAAGAA-GAA
62815882 GAAGAAGAA
1 GAAGAAGAA
62815891 GAAAGAAAGAGA
1 G-AAG-AAGA-A
62815903 GAAGAAGAAA
1 GAAGAAG-AA
62815913 GAAGAA
1 GAAGAA
62815919 AAAAAGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 10 0.24
10 22 0.52
11 8 0.19
12 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (9 bp):
GAAGAAGAA
Found at i:62815884 original size:13 final size:14
Alignment explanation
Indices: 62815866--62815918 Score: 67
Period size: 13 Copynumber: 3.9 Consensus size: 14
62815856 CTCAGTTGAA
62815866 GAAG-AAGAAGAAG
1 GAAGAAAGAAGAAG
62815879 GAAG-AAGAAGAAG
1 GAAGAAAGAAGAAG
*
62815892 AAAGAAAGAGAGAA-
1 GAAGAAAGA-AGAAG
62815906 GAAGAAAGAAGAA
1 GAAGAAAGAAGAA
62815919 AAAAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
13 20 0.56
14 12 0.33
15 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
GAAGAAAGAAGAAG
Found at i:62816221 original size:23 final size:22
Alignment explanation
Indices: 62816192--62816247 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
62816182 GCAGCCCAGC
**
62816192 AGAAAAAAAAAAGGAAGAAAAAGG
1 AGAAAAAAAAAA--AAGAAAAACA
62816216 AGAAAAAAGAAAAAAGAAAAACA
1 AGAAAAAA-AAAAAAGAAAAACA
62816239 AGAAAAAAA
1 AGAAAAAAA
62816248 GGGGTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.03
23 16 0.55
24 8 0.28
25 4 0.14
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (22 bp):
AGAAAAAAAAAAAAGAAAAACA
Found at i:62816225 original size:16 final size:16
Alignment explanation
Indices: 62816192--62816246 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
62816182 GCAGCCCAGC
**
62816192 AGAAAAAA-AAAAGGA
1 AGAAAAAAGAAAAACA
*
62816207 AGAAAAAGGAGAAAA-A
1 AGAAAAAAGA-AAAACA
62816223 AGAAAAAAGAAAAACA
1 AGAAAAAAGAAAAACA
62816239 AGAAAAAA
1 AGAAAAAA
62816247 AGGGGTTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 11 0.32
16 20 0.59
17 3 0.09
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAAAAACA
Found at i:62816241 original size:9 final size:8
Alignment explanation
Indices: 62816197--62816248 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 8
62816187 CCAGCAGAAA
62816197 AAAAAAAGG
1 AAAAAAA-G
62816206 AAGAAAAAGG
1 AA-AAAAA-G
62816216 AGAAAAAAG
1 A-AAAAAAG
62816225 -AAAAAAG
1 AAAAAAAG
62816232 AAAAACAAG
1 AAAAA-AAG
62816241 AAAAAAAG
1 AAAAAAAG
62816249 GGGTTCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.18
8 7 0.18
9 11 0.28
10 13 0.33
11 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:62816406 original size:5 final size:5
Alignment explanation
Indices: 62816396--62816423 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
62816386 GCATTTATAT
62816396 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
62816424 TTATTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:62816423 original size:26 final size:25
Alignment explanation
Indices: 62816388--62816451 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
62816378 ATATTTTGGC
62816388 ATTTATATTTTAATTTAATTTAATTT
1 ATTTA-ATTTTAATTTAATTTAATTT
* ** *
62816414 AATTTAATTTTTATTTTCTTTTATTT
1 -ATTTAATTTTAATTTAATTTAATTT
*
62816440 ATTTTATTTTAA
1 ATTTAATTTTAA
62816452 ATACTTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 10 0.32
26 16 0.52
27 5 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTTAATTTTAATTTAATTTAATTT
Found at i:62816648 original size:21 final size:20
Alignment explanation
Indices: 62816616--62816657 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
62816606 TCGCGTTTCG
62816616 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
62816636 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
62816657 A
1 A
62816658 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:62816658 original size:19 final size:19
Alignment explanation
Indices: 62816616--62816657 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
62816606 TCGCGTTTCG
62816616 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
62816636 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
62816656 AA
1 AA
62816658 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:62816791 original size:18 final size:18
Alignment explanation
Indices: 62816770--62817251 Score: 186
Period size: 17 Copynumber: 26.8 Consensus size: 18
62816760 AGAAAATTTT
62816770 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
62816788 TCGTGTTTTCAAAAAATT-
1 TCGTGTTTTC-AAAAATTC
** * *
62816806 TTAT-TTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTC
62816823 TCGTGTTTTCTAAAAATT-
1 TCGTGTTTTC-AAAAATTC
* * * *
62816841 TCCAT-ATTTCTAAAATTT
1 T-CGTGTTTTCAAAAATTC
*
62816859 TCGTG-TTTAAAAAATT-
1 TCGTGTTTTCAAAAATTC
* * *
62816875 TCGTATTTTCAAAATTTTT
1 TCGTGTTTTCAAAA-ATTC
** * *
62816894 TATTTTTTTCAACAATTC
1 TCGTGTTTTCAAAAATTC
* *
62816912 TCGAG-TTTCACAAATTC
1 TCGTGTTTTCAAAAATTC
* *
62816929 TCGTGTTTT-AAAATTTT
1 TCGTGTTTTCAAAAATTC
** *
62816946 TTATGTTTTAAAAAATAAATTTC
1 TCGTGTTTT---CAA-AAA-TTC
*
62816969 TCGTG-TTTCAAAAAAATTG
1 TCGTGTTTTC--AAAAATTC
* *
62816988 TCATGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
62817005 TCATG-TTTCTAAAATGT-
1 TCGTGTTTTCAAAAAT-TC
*
62817022 T--TGTATTTCAAAAAATCC
1 TCGTGT-TTTC-AAAAATTC
62817040 TCGTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTC
* *
62817057 TCATG-TTT-AAAAAATC
1 TCGTGTTTTCAAAAATTC
62817073 TTCGTGTTTTC-AAAATTC
1 -TCGTGTTTTCAAAAATTC
* *
62817091 TAGTG-TTT-AAAAATTT
1 TCGTGTTTTCAAAAATTC
*
62817107 TCATGTTTTCAAAAATTTC
1 TCGTGTTTTCAAAAA-TTC
* *
62817126 CCCTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
62817144 TCGTATTTT-GAAAATTT
1 TCGTGTTTTCAAAAATTC
*
62817161 TCTTGTTTTCAAAAAAAAAACTT-
1 TCGTGTTTTC-----AAAAA-TTC
*
62817184 TCGTGTTTT-ATAAA-TC
1 TCGTGTTTTCAAAAATTC
62817200 TCCGTGTTTTCAAAAAATTC
1 T-CGTGTTTTC-AAAAATTC
* *
62817220 TCGT-CTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
62817237 TCGTGTTTTCAAAAA
1 TCGTGTTTTCAAAAA
62817252 ATTGACCTTG
Statistics
Matches: 346, Mismatches: 70, Indels: 96
0.68 0.14 0.19
Matches are distributed among these distances:
15 3 0.01
16 36 0.10
17 137 0.40
18 74 0.21
19 56 0.16
20 12 0.03
21 4 0.01
22 5 0.01
23 17 0.05
24 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:62816817 original size:35 final size:36
Alignment explanation
Indices: 62816775--62817175 Score: 148
Period size: 35 Copynumber: 11.3 Consensus size: 36
62816765 ATTTTTCGTG
*
62816775 TTTTCAAAAATTCTCGTGTTTTCAAAAAATTT-TAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
* * *
62816810 TTTTCAAAATTTTTCGTGTTTTCTAAAAATTTCCAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
* *
62816846 ATTTCTAAAATTTTCGTG-TTT-AAAAAATTTCGTA-
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTC-TAT
* ** * * *
62816880 TTTTCAAAATTTTTTATTTTTTTC-AACAATTCTCGA-
1 TTTTCAAAA-ATTTTCGTGTTTTCAAAAAATT-TCTAT
* * * * *
62816916 GTTTCACAAATTCTCGTGTTTT--AAAATTTTTTAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
*
62816950 GTTTTAAAAAATAAATTTC-TCGTGTTTCAAAAAAATTGTC-AT
1 -TTTTCAAAAAT---TTTCGT-GT-TTTC-AAAAAATT-TCTAT
* * *
62816992 GTTTT-AAAAATTTTCATG-TTTC-TAAAATGTT-TGT
1 -TTTTCAAAAATTTTCGTGTTTTCAAAAAAT-TTCTAT
* **
62817026 ATTTCAAAAAATCCTCGTGTTTT--AAAAA-TTCTCAT
1 TTTTC-AAAAATTTTCGTGTTTTCAAAAAATTTCT-AT
* * *
62817061 GTTTAAAAAATCTTCGTGTTTTC--AAAA-TTCTAGT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTA-T
* * **
62817095 GTTT-AAAAATTTTCATGTTTTC-AAAAATTTCCCCT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTT-CTAT
* * * *
62817130 GTTTTCAAAAATTCTCGTATTTT-GAAAATTTTCT-T
1 -TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
62817165 GTTTTCAAAAA
1 -TTTTCAAAAA
62817176 AAAAACTTTC
Statistics
Matches: 278, Mismatches: 55, Indels: 66
0.70 0.14 0.17
Matches are distributed among these distances:
33 24 0.09
34 62 0.22
35 88 0.32
36 46 0.17
37 24 0.09
38 10 0.04
39 4 0.01
41 6 0.02
42 13 0.05
43 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (36 bp):
TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCTAT
Found at i:62817047 original size:52 final size:50
Alignment explanation
Indices: 62816991--62817168 Score: 146
Period size: 52 Copynumber: 3.4 Consensus size: 50
62816981 AAAATTGTCA
** * *
62816991 TGTTTTAAAAATTTTCATGTTTCTAAAATGTT-TGTATTTCAAAAAATCCTCG
1 TGTTTTAAAAATTTTCATGTTTAAAAAATCTTCTGT-TTTC--AAAATCCTAG
* *
62817043 TGTTTTAAAAATTCTCATGTTTAAAAAATCTTCGTGTTTTCAAAATTCTAG
1 TGTTTTAAAAATTTTCATGTTTAAAAAATCTTC-TGTTTTCAAAATCCTAG
* * *
62817094 TG-TTTAAAAATTTTCATGTTTTCAAAAAT-TTCCCCTGTTTTCAAAAATTCTCG
1 TGTTTTAAAAATTTTCATG-TTTAAAAAATCTT---CTGTTTTC-AAAATCCTAG
* * *
62817147 TATTTTGAAAATTTTCTTGTTT
1 TGTTTTAAAAATTTTCATGTTT
62817169 TCAAAAAAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
50 17 0.16
51 19 0.18
52 35 0.33
53 18 0.17
54 17 0.16
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (50 bp):
TGTTTTAAAAATTTTCATGTTTAAAAAATCTTCTGTTTTCAAAATCCTAG
Found at i:62817105 original size:16 final size:17
Alignment explanation
Indices: 62817032--62817123 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 17
62817022 TTGTATTTCA
* *
62817032 AAAAATCCTCGTGTTTT
1 AAAAATTCTAGTGTTTT
62817049 AAAAATTCTCA-TG-TTT
1 AAAAATTCT-AGTGTTTT
* *
62817065 AAAAAATCTTCGTGTTTT
1 AAAAATTC-TAGTGTTTT
*
62817083 CAAAATTCTAGTG-TTT
1 AAAAATTCTAGTGTTTT
*
62817099 AAAAATTTTCA-TGTTTT
1 AAAAATTCT-AGTGTTTT
62817116 CAAAAATT
1 -AAAAATT
62817124 TCCCCTGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
16 22 0.37
17 21 0.36
18 16 0.27
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (17 bp):
AAAAATTCTAGTGTTTT
Found at i:62817300 original size:36 final size:36
Alignment explanation
Indices: 62817185--62817305 Score: 127
Period size: 36 Copynumber: 3.3 Consensus size: 36
62817175 AAAAAACTTT
* * *
62817185 CGTGTTTTATAAATCTCCGTGTTTTCAAAAAATTCT
1 CGTGTTTCATAAATTTCCGTGTTTTCAAAAAATTCC
* * * *
62817221 CGTCTTTCAAAAATTTTCGTGTTTTCAAAAAATTGAC
1 CGTGTTTCATAAATTTCCGTGTTTTCAAAAAATT-CC
* * *
62817258 CTTGTTTCATAAATTTCCGCG-TTTCAAAAAAAATCC
1 CGTGTTTCATAAATTTCCGTGTTTTC-AAAAAATTCC
62817294 CGTGTTTCATAA
1 CGTGTTTCATAA
62817306 TTTATCAAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
36 45 0.66
37 23 0.34
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (36 bp):
CGTGTTTCATAAATTTCCGTGTTTTCAAAAAATTCC
Found at i:62817354 original size:22 final size:22
Alignment explanation
Indices: 62817312--62817353 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
62817302 ATAATTTATC
*
62817312 AAAATTTTTGTGTTTTCAAAAT
1 AAAATTTTTGTGTTTTAAAAAT
62817334 AAAA-TTTTGTGTTTTAAAAA
1 AAAATTTTTGTGTTTTAAAAA
62817354 AATTCTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
AAAATTTTTGTGTTTTAAAAAT
Found at i:62817371 original size:17 final size:18
Alignment explanation
Indices: 62817351--62817393 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
62817341 TGTGTTTTAA
62817351 AAAAATTCTCATG-TTTC
1 AAAAATTCTCATGTTTTC
* * *
62817368 AAAAACTGTCGTGTTTTC
1 AAAAATTCTCATGTTTTC
62817386 AAAAATTC
1 AAAAATTC
62817394 CCGTGTTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (18 bp):
AAAAATTCTCATGTTTTC
Found at i:62817444 original size:18 final size:19
Alignment explanation
Indices: 62817418--62817467 Score: 77
Period size: 17 Copynumber: 2.7 Consensus size: 19
62817408 TTTGTGTTTT
62817418 CGTGTTTTCAAAAAATTTC
1 CGTGTTTTCAAAAAATTTC
*
62817437 CGTG-TTTC-AAAAATTTT
1 CGTGTTTTCAAAAAATTTC
62817454 CGTGTTTTCAAAAA
1 CGTGTTTTCAAAAA
62817468 TTATTATTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 12 0.43
18 8 0.29
19 8 0.29
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (19 bp):
CGTGTTTTCAAAAAATTTC
Found at i:62817468 original size:18 final size:18
Alignment explanation
Indices: 62817414--62817469 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
62817404 AAATTTTGTG
62817414 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
62817433 TTTCCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
62817450 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
62817468 TT
1 TT
62817470 ATTATTCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 12 0.35
18 15 0.44
19 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:62818065 original size:6 final size:6
Alignment explanation
Indices: 62818054--62818092 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
62818044 ACGTTAGTTC
*
62818054 TTTCTT TTTCTT TTTCCT TTTCTT TTTCTT TTT-TT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
62818093 GAATTTTCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:62818778 original size:62 final size:62
Alignment explanation
Indices: 62818699--62818923 Score: 283
Period size: 62 Copynumber: 3.6 Consensus size: 62
62818689 GTGTAGGTTT
62818699 CACACGGCCAAGGACACGGGCGTGTGCCCAGGCCGTGTAACTCACTGTTTGGGGTATAAAAC
1 CACACGGCCAAGGACACGGGCGTGTGCCCAGGCCGTGTAACTCACTGTTTGGGGTATAAAAC
* * * * * *
62818761 CACACGGCC-AGGAACACGGGCTTTTGTCTAGGCCTTATAACTCACTGTTTGGGGTATAAAAC
1 CACACGGCCAAGG-ACACGGGCGTGTGCCCAGGCCGTGTAACTCACTGTTTGGGGTATAAAAC
* * * * * *
62818823 CACACAGCCAAGGACACGGGCGTGTGCCCAAGACC-TGTAACTTATTTTTTGGGGTATAAGAC
1 CACACGGCCAAGGACACGGGCGTGTGCCC-AGGCCGTGTAACTCACTGTTTGGGGTATAAAAC
* *
62818885 CACACGGCCAAGGCACGCGGGTGTGTGCCCAGGCCGTGT
1 CACACGGCCAAGG-ACACGGGCGTGTGCCCAGGCCGTGT
62818924 GGTAAAATAT
Statistics
Matches: 137, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
61 3 0.02
62 110 0.80
63 24 0.18
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (62 bp):
CACACGGCCAAGGACACGGGCGTGTGCCCAGGCCGTGTAACTCACTGTTTGGGGTATAAAAC
Found at i:62819717 original size:26 final size:26
Alignment explanation
Indices: 62819688--62819737 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
62819678 ATTTGTTTTA
62819688 GAATGTTATGGATTTATGAAGATTAT
1 GAATGTTATGGATTTATGAAGATTAT
62819714 GAATGTTATGGATTTATGAAGATT
1 GAATGTTATGGATTTATGAAGATT
62819738 TTGTCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (26 bp):
GAATGTTATGGATTTATGAAGATTAT
Found at i:62820558 original size:22 final size:22
Alignment explanation
Indices: 62820533--62820578 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
62820523 AACTTTCCAA
62820533 TAATCATAGAAATAACATACTT
1 TAATCATAGAAATAACATACTT
* *
62820555 TAATCATAGAAATAATATATTT
1 TAATCATAGAAATAACATACTT
62820577 TA
1 TA
62820579 CATGCTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (22 bp):
TAATCATAGAAATAACATACTT
Found at i:62821343 original size:14 final size:14
Alignment explanation
Indices: 62821324--62821350 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62821314 TGTTTAGATT
62821324 ATTTTAAAATTAAC
1 ATTTTAAAATTAAC
62821338 ATTTTAAAATTAA
1 ATTTTAAAATTAA
62821351 GACATTACAA
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:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAAAATTAAC
Found at i:62823337 original size:20 final size:20
Alignment explanation
Indices: 62823299--62823335 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62823289 AGTTCACTAC
62823299 TTTTATTTCTTAGAATTTAG
1 TTTTATTTCTTAGAATTTAG
*
62823319 TTTTATTTTTTA-AATTT
1 TTTTATTTCTTAGAATTT
62823336 TAAAAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTATTTCTTAGAATTTAG
Found at i:62844313 original size:26 final size:27
Alignment explanation
Indices: 62844283--62844345 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
62844273 CTTTGTTAAA
*
62844283 TTTCTTGAAAGTTAACAAATCAGAAGC
1 TTTCTTCAAAGTTAACAAATCAGAAGC
* *
62844310 TTCTCTTTCAAATTTAACTAATCAGAAGC
1 TT-TC-TTCAAAGTTAACAAATCAGAAGC
62844339 TTCTCTT
1 TT-TCTT
62844346 TCAACTCCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 4 0.13
29 25 0.81
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (27 bp):
TTTCTTCAAAGTTAACAAATCAGAAGC
Found at i:62844326 original size:29 final size:29
Alignment explanation
Indices: 62844294--62844349 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
62844284 TTCTTGAAAG
62844294 TTAACAAATCAGAAGCTTCTCTTTCAAAT
1 TTAACAAATCAGAAGCTTCTCTTTCAAAT
*
62844323 TTAACTAATCAGAAGCTTCTCTTTCAA
1 TTAACAAATCAGAAGCTTCTCTTTCAA
62844350 CTCCTCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (29 bp):
TTAACAAATCAGAAGCTTCTCTTTCAAAT
Found at i:62866181 original size:23 final size:22
Alignment explanation
Indices: 62866156--62866198 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
62866146 ATAAAAGTAA
*
62866156 AAAAATTA-AATATATATTTTAG
1 AAAAATTACAATAAAT-TTTTAG
62866178 AAAAATTACAATAAATTTTTA
1 AAAAATTACAATAAATTTTTA
62866199 ATTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAATTACAATAAATTTTTAG
Found at i:62866516 original size:15 final size:14
Alignment explanation
Indices: 62866496--62866527 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
62866486 GTTTAACTTT
62866496 TTTTTATATTTTATA
1 TTTTTATATTTTA-A
62866511 TTTTTATATTTTAA
1 TTTTTATATTTTAA
62866525 TTT
1 TTT
62866528 AAATAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTATATTTTAA
Found at i:62868323 original size:22 final size:22
Alignment explanation
Indices: 62868295--62868339 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
62868285 AATTTACAGA
62868295 AGAAGAAGATAGAAAGAAAGAAAGG
1 AGAAGAAGA-A-AAA-AAAGAAAGG
62868320 AGAAGAAGAAAAAAAAGAAA
1 AGAAGAAGAAAAAAAAGAAA
62868340 AGGTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 1 0.05
25 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (22 bp):
AGAAGAAGAAAAAAAAGAAAGG
Found at i:62871140 original size:86 final size:86
Alignment explanation
Indices: 62870995--62871165 Score: 333
Period size: 86 Copynumber: 2.0 Consensus size: 86
62870985 TGTTTTAATA
62870995 ATTTAGGCCAATACTATAACTTATCTTTCCTTAATACATATACAGCGCACGAGCTGGAGCCACAT
1 ATTTAGGCCAATACTATAACTTATCTTTCCTTAATACATATACAGCGCACGAGCTGGAGCCACAT
62871060 ATTTTTCGCCAAAGAATGGCG
66 ATTTTTCGCCAAAGAATGGCG
*
62871081 ATTTAGGCCAATACTATAACTTATCTTTCCTTAATACATATACAGCGCACGAGTTGGAGCCACAT
1 ATTTAGGCCAATACTATAACTTATCTTTCCTTAATACATATACAGCGCACGAGCTGGAGCCACAT
62871146 ATTTTTCGCCAAAGAATGGC
66 ATTTTTCGCCAAAGAATGGC
62871166 TCGACTTGAG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (86 bp):
ATTTAGGCCAATACTATAACTTATCTTTCCTTAATACATATACAGCGCACGAGCTGGAGCCACAT
ATTTTTCGCCAAAGAATGGCG
Found at i:62874787 original size:30 final size:29
Alignment explanation
Indices: 62874747--62874803 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
62874737 GGCTTTTTTT
*
62874747 ATTTTTATTTTCGGATTTTATTTTTTAAA
1 ATTTTTATTTTCAGATTTTATTTTTTAAA
*
62874776 ATTTATTATTTTCATATTTTATTTTTTA
1 ATTT-TTATTTTCAGATTTTATTTTTTA
62874804 TATTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (29 bp):
ATTTTTATTTTCAGATTTTATTTTTTAAA
Found at i:62874806 original size:14 final size:14
Alignment explanation
Indices: 62874761--62874807 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
62874751 TTATTTTCGG
*
62874761 ATTTTATTTTTTAA
1 ATTTTATTTTTTAT
*
62874775 AATTTATTATTTTCAT
1 ATTTTATT-TTTT-AT
62874791 ATTTTATTTTTTAT
1 ATTTTATTTTTTAT
62874805 ATT
1 ATT
62874808 ATTTTAGTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 12 0.43
15 8 0.29
16 8 0.29
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTATTTTTTAT
Found at i:62874828 original size:142 final size:143
Alignment explanation
Indices: 62874600--62875333 Score: 906
Period size: 142 Copynumber: 5.2 Consensus size: 143
62874590 TATTTTGGTA
* ** *
62874600 TTTA-TTTTATTTTTCAGATTTTAAAATTTTAAAATATACTATTTTCGTATTTTATTGTTTTATA
1 TTTATTTTTA-TTTTCGGATTTT-ATTTTTTAAAATATATTATTTTCGTATTTTATT-TTTTATA
62874664 TTATTTTAGTACATAATGTTTCAAATGTATTATTTTAG-TTTTTTATATTAATTTAGAAAAAAAC
63 TTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGAAAAAAAC
62874728 TCTGATTTTGGCTTTT
128 TCTGATTTTGGCTTTT
* *
62874744 TTTATTTTTATTTTCGGATTTTATTTTTTAAAATTTATTATTTTCATATTTTATTTTTTATATTA
1 TTTATTTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTA
*
62874809 TTTTAGTACATAATGTTTC--ATGTATTATTTTAGTTTTTTTATATTAATTTAGAAAAAAAACCC
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAG-AAAAAAACTC
**
62874872 TGATTTTGGCCCTT
130 TGATTTTGGCTTTT
* * *
62874886 TTTATTTTTATTTTTGGATTTTACTTTTTAAGATATATTATTTTCGTATTTTGA-TTTTTATATT
1 TTTATTTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTT-ATTTTTTATATT
* * *
62874950 ATTTTAGTACATAATG-TTC-AATGTATTATTTTTGTTTTTTTTATATTAATTTAGTAAAAATCT
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAG-TTTTTTTATATTAATTTAGAAAAAAACT
*
62875013 GTGATTTTGGCCTTTT
129 CTGATTTTGG-CTTTT
* *
62875029 TTT-TATTTTGTTTTCGGA--TT-TTTTTAAAAATATATTATTTTCGTATTTTATTTTTTATATT
1 TTTAT-TTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATT
* * * * ** *
62875090 ATTTTAGTATATAATGTTTCAAATG-AATAATTT-GTTTTTTTATATTAATTTAGTAAAAATTTT
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGAAAAAAACTC
*
62875153 TGATTTTAGCCGTTTGT
130 TGATTTT-GGC-TTT-T
* ** *
62875170 TTTTTATTTTATTTTCGGATTTTATTTTCCAAAATATACTATTTTCGTATTTTATTTTTT-TATT
1 TTTAT-TTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATT
* * * * *
62875234 ATTTTAGTACATAATGTTTCATATATATTATTTTAGTATATTTATATTAATTTAGTAAAAAACCT
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAG-AAAAAAACT
* *
62875299 CTAATTTT-GCCTTT
129 CTGATTTTGGCTTTT
62875313 TTTA-TTTTATTTTCGGATTTT
1 TTTATTTTTATTTTCGGATTTT
62875334 TTAAAATATA
Statistics
Matches: 518, Mismatches: 51, Indels: 45
0.84 0.08 0.07
Matches are distributed among these distances:
139 36 0.07
140 70 0.14
141 53 0.10
142 170 0.33
143 69 0.13
144 45 0.09
145 45 0.09
146 18 0.03
147 12 0.02
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (143 bp):
TTTATTTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTA
TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGAAAAAAACTCT
GATTTTGGCTTTT
Found at i:62875093 original size:12 final size:13
Alignment explanation
Indices: 62875059--62875101 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
62875049 TTTTTAAAAA
62875059 TATATTATTTTCG
1 TATATTATTTTCG
* *
62875072 TATTTTATTTT-T
1 TATATTATTTTCG
*
62875084 TATATTATTTTAG
1 TATATTATTTTCG
62875097 TATAT
1 TATAT
62875102 AATGTTTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (13 bp):
TATATTATTTTCG
Found at i:62875290 original size:285 final size:277
Alignment explanation
Indices: 62874600--62875349 Score: 935
Period size: 285 Copynumber: 2.6 Consensus size: 277
62874590 TATTTTGGTA
*
62874600 TTTATTTTATTTTTCAGATTTTAAAATTTTAAAATATACTATTTTCGTATTTTATTGTTTTATAT
1 TTTATTTTA-TTTTCGGATTTT---ATTTTAAAATATACTATTTTCGTATTTTATT-TTTT-TAT
*
62874665 TATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTATATTAATTTAGAAAAAAACTC
60 TATTTTAGTACATAATGTTTC-AATGTATTATTTTAGTTTTTTATATTAATTTAGTAAAAAACTC
*
62874730 TGATTTTGG-CTTTTTTTATTTTTATTTTCGGATTTTATTTTTTAAAATTTATTATTTTCATATT
124 TGATTTTGGCCTTTTTTTA-TTTTATTTTCGGA---T-TTTTTTAAAATATATTATTTTCATATT
* *
62874794 TTATTTTTTATATTATTTTAGTACATAATGTTTCATGTATTATTTTAGTTTTTTTATATTAATTT
184 TTATTTTTTATATTATTTTAGTACATAATGTTTCATGTAATAATTTAGTTTTTTTATATTAATTT
*
62874859 AGAAAAAAAACCCTGATTTTGGCCCTTTT
249 AGAAAAAAAACCCTGATTTTAGCCCTTTT
* * * * *
62874888 TAT-TTTTATTTTTGGATTTTACTTTTTAAGATATATTATTTTCGTATTTTGATTTTTATATTAT
1 TTTATTTTATTTTCGGATTTTA--TTTTAAAATATACTATTTTCGTATTTT-ATTTTTTTATTAT
* * *
62874952 TTTAGTACATAATG-TTCAATGTATTATTTTTGTTTTTTTTATATTAATTTAGTAAAAATCTGTG
63 TTTAGTACATAATGTTTCAATGTATTATTTTAG--TTTTTTATATTAATTTAGTAAAAAACTCTG
* *
62875016 ATTTTGGCCTTTTTTTTATTTTGTTTTCGGATTTTTTTAAAAATATATTATTTTCGTATTTTATT
126 ATTTTGGCC-TTTTTTTATTTTATTTTCGGATTTTTTT-AAAATATATTATTTTCATATTTTATT
*
62875081 TTTTATATTATTTTAGTATATAATGTTTCAAATG-AATAATTT-GTTTTTTTATATTAATTTAG-
189 TTTTATATTATTTTAGTACATAATGTTTC--ATGTAATAATTTAGTTTTTTTATATTAATTTAGA
* **** *
62875143 TAAAAATTTTTGATTTTAGCCGTTTGTTT
252 AAAAAAACCCTGATTTTAGCC--CT-TTT
62875172 TTTATTTTATTTTCGGATTTTATTTTCCAAAATATACTATTTTCGTATTTTATTTTTTTATTATT
1 TTTATTTTATTTTCGGATTTTATTTT--AAAATATACTATTTTCGTATTTTATTTTTTTATTATT
* * *
62875237 TTAGTACATAATGTTTCATATATATTATTTTAGTATATTTATATTAATTTAGTAAAAAACCTCTA
64 TTAGTACATAATGTTTCA-ATGTATTATTTTAGT-TTTTTATATTAATTTAGTAAAAAA-CTCTG
62875302 ATTTT-GCC-TTTTTTATTTTATTTTCGGA-TTTTTTAAAATATATT-TTTT
126 ATTTTGGCCTTTTTTTATTTTATTTTCGGATTTTTTTAAAATATATTATTTT
62875350 AAAATATACT
Statistics
Matches: 407, Mismatches: 35, Indels: 48
0.83 0.07 0.10
Matches are distributed among these distances:
280 4 0.01
281 31 0.08
282 93 0.23
283 34 0.08
284 89 0.22
285 108 0.27
286 41 0.10
287 5 0.01
288 2 0.00
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.59
Consensus pattern (277 bp):
TTTATTTTATTTTCGGATTTTATTTTAAAATATACTATTTTCGTATTTTATTTTTTTATTATTTT
AGTACATAATGTTTCAATGTATTATTTTAGTTTTTTATATTAATTTAGTAAAAAACTCTGATTTT
GGCCTTTTTTTATTTTATTTTCGGATTTTTTTAAAATATATTATTTTCATATTTTATTTTTTATA
TTATTTTAGTACATAATGTTTCATGTAATAATTTAGTTTTTTTATATTAATTTAGAAAAAAAACC
CTGATTTTAGCCCTTTT
Found at i:62875346 original size:14 final size:14
Alignment explanation
Indices: 62875329--62875357 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62875319 TTATTTTCGG
62875329 ATTTTTTAAAATAT
1 ATTTTTTAAAATAT
62875343 ATTTTTTAAAATAT
1 ATTTTTTAAAATAT
62875357 A
1 A
62875358 CTATTAAGCT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTTTAAAATAT
Found at i:62875806 original size:20 final size:20
Alignment explanation
Indices: 62875777--62875815 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62875767 TTTTTTTTCT
*
62875777 TTCTCTTTCTCTTCTTCTTC
1 TTCTCCTTCTCTTCTTCTTC
*
62875797 TTCTCCTTCTCTTTTTCTT
1 TTCTCCTTCTCTTCTTCTT
62875816 TCTCTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTCCTTCTCTTCTTCTTC
Found at i:62875822 original size:12 final size:12
Alignment explanation
Indices: 62875770--62875841 Score: 67
Period size: 12 Copynumber: 5.8 Consensus size: 12
62875760 ATTACCTTTT
62875770 TTTTTCTTTCTC
1 TTTTTCTTTCTC
*
62875782 TTTCTC-TTCTTC
1 TTTTTCTTTC-TC
*
62875794 TTCTTCTCCTTCTC
1 TT-TT-TCTTTCTC
62875808 TTTTTCTTTCTC
1 TTTTTCTTTCTC
*
62875820 TTTTT-TTTTTC
1 TTTTTCTTTCTC
62875831 TTTTTTCTTTC
1 -TTTTTCTTTC
62875842 CCTCACCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 8 0.16
12 26 0.53
13 6 0.12
14 6 0.12
15 3 0.06
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:62875884 original size:22 final size:22
Alignment explanation
Indices: 62875858--62875923 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
62875848 CAATGCCGCC
62875858 TCTTCCTCCTCCTTCTTCTTCT
1 TCTTCCTCCTCCTTCTTCTTCT
* *
62875880 TCTTCTTCTTCTCTTC-TCTTCT
1 TCTTCCTCCTC-CTTCTTCTTCT
* *
62875902 CCTTCC-CC-CTTTCTTCTTCT
1 TCTTCCTCCTCCTTCTTCTTCT
62875922 TC
1 TC
62875924 ACTCACGCAC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.09
20 8 0.23
21 1 0.03
22 19 0.54
23 4 0.11
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (22 bp):
TCTTCCTCCTCCTTCTTCTTCT
Found at i:62875923 original size:3 final size:3
Alignment explanation
Indices: 62875869--62875906 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
62875859 CTTCCTCCTC
*
62875869 CTT CTT CTT CTT CTT CTT CTT C-T CTT C-T CTT CTC CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
62875907 CCCCTTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:62876017 original size:22 final size:22
Alignment explanation
Indices: 62875989--62876030 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
62875979 ACAAAAGCAA
*
62875989 TGGCAGTGAGGAGTCTCGTCTG
1 TGGCAGTGAGGAGTCCCGTCTG
*
62876011 TGGCAGTGCGGAGTCCCGTC
1 TGGCAGTGAGGAGTCCCGTC
62876031 GGTGCAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
TGGCAGTGAGGAGTCCCGTCTG
Found at i:62876089 original size:27 final size:27
Alignment explanation
Indices: 62876048--62876100 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
62876038 AGGAGTGACC
*
62876048 GGTGCCGCCTGTGGGGTACCCTCCACT
1 GGTGCCGCCTATGGGGTACCCTCCACT
62876075 GGTGCCGCCTATGGGGTACCCTCCAC
1 GGTGCCGCCTATGGGGTACCCTCCAC
62876101 CCCTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.09, C:0.38, G:0.32, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCTATGGGGTACCCTCCACT
Found at i:62877013 original size:16 final size:16
Alignment explanation
Indices: 62876994--62877024 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62876984 ATATTAATTT
*
62876994 TATTTAATCTTAAAAA
1 TATTTAATATTAAAAA
62877010 TATTTAATATTAAAA
1 TATTTAATATTAAAA
62877025 CAATACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:62887362 original size:17 final size:16
Alignment explanation
Indices: 62887334--62887386 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
62887324 TTTGGTTCGC
62887334 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62887350 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
62887367 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62887383 TGTA
1 TGTA
62887387 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:62887643 original size:18 final size:17
Alignment explanation
Indices: 62887622--62887656 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62887612 TTATTATTAA
*
62887622 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
62887640 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
62887657 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:62887763 original size:18 final size:17
Alignment explanation
Indices: 62887742--62887776 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62887732 TTATTATTAA
*
62887742 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
62887760 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
62887777 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:62887818 original size:120 final size:120
Alignment explanation
Indices: 62887605--62888467 Score: 1690
Period size: 120 Copynumber: 7.2 Consensus size: 120
62887595 ATCATATTTA
*
62887605 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
62887670 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
62887725 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
62887790 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
62887845 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
62887910 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTGAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
62887965 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
62888030 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
62888085 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
62888150 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
62888205 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
62888270 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
62888325 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
62888390 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
62888445 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
62888468 AACTTGAAAA
Statistics
Matches: 739, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 739 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:62891755 original size:13 final size:13
Alignment explanation
Indices: 62891737--62891763 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62891727 TAATAACAAC
62891737 TATATTGTTTAAA
1 TATATTGTTTAAA
62891750 TATATTGTTTAAA
1 TATATTGTTTAAA
62891763 T
1 T
62891764 TAAACCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TATATTGTTTAAA
Found at i:62895079 original size:40 final size:38
Alignment explanation
Indices: 62894959--62895090 Score: 132
Period size: 35 Copynumber: 3.6 Consensus size: 38
62894949 TCCTCATTGA
* * *
62894959 AATACCATACCTACATTTTACAACTCGGTTTGG--GA-
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
* * ** *
62894994 AATGCCATACCTATATTTCTTAACTGAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGA--TGAT
62895034 AATACCATACCTACATTTCACAACTCAGTATGGATG--
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
62895070 -ATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
62895091 CTTTGCCATG
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
35 46 0.58
38 2 0.03
39 2 0.03
40 29 0.37
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (38 bp):
AATACCATACCTACATTTCACAACTCAGTATGGATGAT
Found at i:62900010 original size:34 final size:34
Alignment explanation
Indices: 62899961--62900027 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
62899951 CCCTGACGAT
* * *
62899961 GATCCTTAATTTATCATGGGCTAACTGGGTCCTC
1 GATCCTTAATCTATCATAGGCTAACTAGGTCCTC
*
62899995 GATCCTTGATCTATCATAGGCTAACTAGGTCCT
1 GATCCTTAATCTATCATAGGCTAACTAGGTCCT
62900028 TCTTCAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (34 bp):
GATCCTTAATCTATCATAGGCTAACTAGGTCCTC
Found at i:62903233 original size:13 final size:13
Alignment explanation
Indices: 62903215--62903240 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62903205 GCATCTAACA
62903215 TTTTTATTTTTAT
1 TTTTTATTTTTAT
62903228 TTTTTATTTTTAT
1 TTTTTATTTTTAT
62903241 CACTTTATTT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:62907880 original size:6 final size:6
Alignment explanation
Indices: 62907869--62907900 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
62907859 TTAAATAATA
62907869 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
62907901 CAAAACACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:62911699 original size:5 final size:6
Alignment explanation
Indices: 62911682--62911706 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
62911672 CATTTTACAG
62911682 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
62911707 CTATATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:62912801 original size:3 final size:3
Alignment explanation
Indices: 62912786--62912822 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
62912776 ATATTGTGCT
* *
62912786 TTA TTA ATA TTA TTA TTA TCA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
62912823 AACTTGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:62913021 original size:21 final size:20
Alignment explanation
Indices: 62912977--62913041 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 20
62912967 TTTATGATGT
62912977 TATA-ATTTTTATATTTA-A
1 TATATATTTTTATATTTATA
*
62912995 -ATAT-TTTTATAAATTTATA
1 TATATATTTT-TATATTTATA
62913014 T-TATATTTTTATATTTATA
1 TATATATTTTTATATTTATA
62913033 TATATATTT
1 TATATATTT
62913042 CAAAATAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 7 0.18
18 7 0.18
19 14 0.36
20 11 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATATTTTTATATTTATA
Found at i:62913679 original size:29 final size:31
Alignment explanation
Indices: 62913620--62913680 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
62913610 AAAACACCCC
* *
62913620 TTTAAGACAAAAAAAAAAGTCCATGTTAACA
1 TTTAAGACAAAAAAAAAAGTCCAAGTCAACA
62913651 TTTAAGACAAAAAAAAAA-T-CAAGTCAACA
1 TTTAAGACAAAAAAAAAAGTCCAAGTCAACA
62913680 T
1 T
62913681 AATAGGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
30 1 0.04
31 18 0.64
ACGTcount: A:0.57, C:0.13, G:0.08, T:0.21
Consensus pattern (31 bp):
TTTAAGACAAAAAAAAAAGTCCAAGTCAACA
Found at i:62921804 original size:27 final size:27
Alignment explanation
Indices: 62921774--62921828 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
62921764 TCAATTTTGT
62921774 ACTTGTATTTGAGCCTGAGGATAAATA
1 ACTTGTATTTGAGCCTGAGGATAAATA
62921801 ACTTGTATTTGAGCCTGAGGATAAATA
1 ACTTGTATTTGAGCCTGAGGATAAATA
62921828 A
1 A
62921829 TCGAGCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (27 bp):
ACTTGTATTTGAGCCTGAGGATAAATA
Found at i:62923097 original size:64 final size:65
Alignment explanation
Indices: 62922973--62923097 Score: 175
Period size: 64 Copynumber: 1.9 Consensus size: 65
62922963 CAAACATAAA
62922973 CATGCAATCATCTAAAAAATAAGAAGAGACATAACAGCGAAAACTTAAAAAGACCATAAAAATCA
1 CATGCAATCATCTAAAAAATAAGAAGAGA-ATAACAGCGAAAACTTAAAAAGACCATAAAAATCA
62923038 G
65 G
* * *
62923039 CATGCAATTATCTAAAAAAATAAGAAGAG-ATAGA-AGTG-AAGCTTAAAAAGACCATAAAA
1 CATGCAATCATCT-AAAAAATAAGAAGAGAATA-ACAGCGAAAACTTAAAAAGACCATAAAA
62923098 TTAACATCTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
64 20 0.37
65 6 0.11
66 13 0.24
67 15 0.28
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.17
Consensus pattern (65 bp):
CATGCAATCATCTAAAAAATAAGAAGAGAATAACAGCGAAAACTTAAAAAGACCATAAAAATCAG
Found at i:62923163 original size:79 final size:78
Alignment explanation
Indices: 62923055--62923204 Score: 212
Period size: 80 Copynumber: 1.9 Consensus size: 78
62923045 ATTATCTAAA
* ** *
62923055 AAAATAAGAAGAGATAGAAGTGAAGCTT-AAAAAGACCATAAAATTAACATCTTTCTCAAACACA
1 AAAATAAGAAGAGATAGAAGTGAAACTTAAAAAAGACCATAAAACCAACATCTTCCTCAAACACA
62923119 AACATGTAATCAG
66 AACATGTAATCAG
* *
62923132 AAAATAAGAAGAGACATAGAAGTGAAACTTAAAAAAGACCATAAAACCAGCATCTTCCTCGAACA
1 AAAATAAGAAGAG--ATAGAAGTGAAACTTAAAAAAGACCATAAAACCAACATCTTCCTCAAACA
*
62923197 CGAACATG
64 CAAACATG
62923205 CAATTATCTA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 13 0.21
79 14 0.22
80 36 0.57
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (78 bp):
AAAATAAGAAGAGATAGAAGTGAAACTTAAAAAAGACCATAAAACCAACATCTTCCTCAAACACA
AACATGTAATCAG
Found at i:62930590 original size:18 final size:18
Alignment explanation
Indices: 62930563--62930609 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
62930553 TGGGGTCGAT
62930563 AACAAAGAGGAAGCTGAG
1 AACAAAGAGGAAGCTGAG
* * *
62930581 AACGAAGAGGGAGTTGAG
1 AACAAAGAGGAAGCTGAG
62930599 AACAAAGAGGA
1 AACAAAGAGGA
62930610 TCTGAAAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.36, T:0.06
Consensus pattern (18 bp):
AACAAAGAGGAAGCTGAG
Found at i:62931259 original size:84 final size:85
Alignment explanation
Indices: 62931102--62931271 Score: 218
Period size: 84 Copynumber: 2.0 Consensus size: 85
62931092 AATGCTTCAC
* * *
62931102 ATACTTGTGTTGTTACAGGTATGTCACAAGATCATCCGAAATTGGATTCTAACCTGATTGCTGAC
1 ATACTTGTGTTGTTACAAGTATGTCACAAGATCATCCGAAACTAGATTCTAACCTGATTGCTGAC
* * *
62931167 GTTGTCTTACGTATGGTGAA
66 ATTATCTTACCTATGGTGAA
* * * * *
62931187 ATACTTGTGTTGTTGCAAGTATGTTAC-TGATCATCTGAAACTAGATTCTAACCTGATCT-TTGA
1 ATACTTGTGTTGTTACAAGTATGTCACAAGATCATCCGAAACTAGATTCTAACCTGAT-TGCTGA
62931250 CATTATCTTACCTATGGTGAA
65 CATTATCTTACCTATGGTGAA
62931271 A
1 A
62931272 ACAAGTCCTA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
84 48 0.66
85 25 0.34
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (85 bp):
ATACTTGTGTTGTTACAAGTATGTCACAAGATCATCCGAAACTAGATTCTAACCTGATTGCTGAC
ATTATCTTACCTATGGTGAA
Found at i:62932614 original size:17 final size:18
Alignment explanation
Indices: 62932576--62932615 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
62932566 ACAGGATTAG
*
62932576 AATTTAGTTGAGAAAATT
1 AATTTAATTGAGAAAATT
62932594 -ATTTAATT-AGAAAATT
1 AATTTAATTGAGAAAATT
62932610 AATTTA
1 AATTTA
62932616 TCTAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (18 bp):
AATTTAATTGAGAAAATT
Found at i:62934519 original size:9 final size:8
Alignment explanation
Indices: 62934505--62934538 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
62934495 CTTTTCTCAA
62934505 TTTTTTTC
1 TTTTTTTC
*
62934513 TTCTTTTC
1 TTTTTTTC
62934521 TTTATTTTC
1 TTT-TTTTC
62934530 TTTTTTTC
1 TTTTTTTC
62934538 T
1 T
62934539 GTCTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Done.