Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 104 of 125
Found at i:31485934 original size:35 final size:33
Alignment explanation
Indices: 31485828--31485967 Score: 147
Period size: 34 Copynumber: 4.1 Consensus size: 33
31485818 GTTTTAATGC
* * *
31485828 TTTTTTACTGTTTTAATTGTTA-TTTTAGTGCTA
1 TTTTTTACTGTTTT-GTTGTTATTTTTACTGTTA
* *
31485861 TTTTTTACTGTTTTGATGTTATTTTTGCTGTTA
1 TTTTTTACTGTTTTGTTGTTATTTTTACTGTTA
*
31485894 TTTTTATTACTGTTTTTGTTGTTATTTTTACTATTA
1 -TTTT-TTACTG-TTTTGTTGTTATTTTTACTGTTA
** *
31485930 TTTTATTGTTGTTTTGTTGTTATTTTTACTGTTG
1 TTTT-TTACTGTTTTGTTGTTATTTTTACTGTTA
31485964 TTTT
1 TTTT
31485968 GGTTGTTATT
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
32 5 0.05
33 22 0.24
34 29 0.32
35 15 0.16
36 20 0.22
ACGTcount: A:0.14, C:0.05, G:0.13, T:0.69
Consensus pattern (33 bp):
TTTTTTACTGTTTTGTTGTTATTTTTACTGTTA
Found at i:31485956 original size:23 final size:24
Alignment explanation
Indices: 31485930--31485979 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
31485920 TTTACTATTA
*
31485930 TTTTATTGTTGTTTT-GTTGTTAT
1 TTTTACTGTTGTTTTGGTTGTTAT
31485953 TTTTACTGTTGTTTTGGTTGTTAT
1 TTTTACTGTTGTTTTGGTTGTTAT
31485977 TTT
1 TTT
31485980 GGTTGTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.08, C:0.02, G:0.18, T:0.72
Consensus pattern (24 bp):
TTTTACTGTTGTTTTGGTTGTTAT
Found at i:31497583 original size:23 final size:23
Alignment explanation
Indices: 31497557--31497680 Score: 160
Period size: 23 Copynumber: 5.4 Consensus size: 23
31497547 GAACACTAGC
* * *
31497557 GTGCTCTTTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
31497580 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
31497603 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
31497626 GTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
31497649 GTGCTATCTGATTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
31497671 GTACTCTCTG
1 GTGCTCTCTG
31497681 TTTGTTCCGT
Statistics
Matches: 88, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
22 8 0.09
23 80 0.91
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:31497633 original size:46 final size:46
Alignment explanation
Indices: 31497557--31497680 Score: 178
Period size: 46 Copynumber: 2.7 Consensus size: 46
31497547 GAACACTAGC
* * * * *
31497557 GTGCTCTTTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTTTGT
*
31497603 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTTTGT
*
31497649 GTGCTATCTGATTAGTACTTTG-GTACTCTCTG
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTG
31497681 TTTGTTCCGT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 10 0.14
46 61 0.86
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (46 bp):
GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTTTGT
Found at i:31500586 original size:2 final size:2
Alignment explanation
Indices: 31500579--31500612 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31500569 CTCCATTTTC
31500579 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
31500613 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31500617 original size:2 final size:2
Alignment explanation
Indices: 31500612--31500652 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
31500602 TCTCTCTCTC
31500612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31500653 TGGAGGATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31502515 original size:16 final size:16
Alignment explanation
Indices: 31502491--31502522 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31502481 TTATATTACC
*
31502491 AAAAGAAAGAAAGAAA
1 AAAAAAAAGAAAGAAA
31502507 AAAAAAAAGAAAGAAA
1 AAAAAAAAGAAAGAAA
31502523 GTAAACATTT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAGAAA
Found at i:31508610 original size:20 final size:22
Alignment explanation
Indices: 31508585--31508624 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31508575 AAGAGAATAG
31508585 AAAATA-AAAA-AAAAATTACA
1 AAAATATAAAAGAAAAATTACA
31508605 AAAATATAAAAGAAAAATTA
1 AAAATATAAAAGAAAAATTA
31508625 AAGTGCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAATATAAAAGAAAAATTACA
Found at i:31510183 original size:29 final size:29
Alignment explanation
Indices: 31510123--31510184 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
31510113 AATTTTCATC
* **
31510123 AAATAAAGAAAGTGAGAATTATGTTCAAA
1 AAATAAAGAAAGTGAGAATCATAATCAAA
31510152 AAATAAAGAAAGTGAGAATCA-AATCAACA
1 AAATAAAGAAAGTGAGAATCATAATCAA-A
31510181 AAAT
1 AAAT
31510185 TAAAAGGCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (29 bp):
AAATAAAGAAAGTGAGAATCATAATCAAA
Found at i:31513255 original size:79 final size:79
Alignment explanation
Indices: 31513124--31513281 Score: 262
Period size: 79 Copynumber: 2.0 Consensus size: 79
31513114 AGAATAGCAC
* ** * * *
31513124 CGGCCCTAAACGTTTCTAATGTTAATACCTTTCGAATTATCTTGTTGTATGTTATTTTGCAAAAA
1 CGGCCCTAAACGTTTCGAATGTTAATACCTTAAGAACTATCTTATTGTATGTTATTTTACAAAAA
31513189 AAGCGAATTTGTGT
66 AAGCGAATTTGTGT
31513203 CGGCCCTAAACGTTTCGAATGTTAATACCTTAAGAACTATCTTATTGTATGTTATTTTACAAAAA
1 CGGCCCTAAACGTTTCGAATGTTAATACCTTAAGAACTATCTTATTGTATGTTATTTTACAAAAA
31513268 AAGCGAATTTGTGT
66 AAGCGAATTTGTGT
31513282 AGGGCGATGG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (79 bp):
CGGCCCTAAACGTTTCGAATGTTAATACCTTAAGAACTATCTTATTGTATGTTATTTTACAAAAA
AAGCGAATTTGTGT
Found at i:31513493 original size:13 final size:13
Alignment explanation
Indices: 31513475--31513503 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31513465 AAGCGAAAAC
31513475 AAATCAAAGAAGG
1 AAATCAAAGAAGG
31513488 AAATCAAAGAAGG
1 AAATCAAAGAAGG
31513501 AAA
1 AAA
31513504 AAGAAGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (13 bp):
AAATCAAAGAAGG
Found at i:31523299 original size:135 final size:135
Alignment explanation
Indices: 31523057--31523337 Score: 553
Period size: 135 Copynumber: 2.1 Consensus size: 135
31523047 AGTAAATCTT
31523057 GGCGACCTTCTAAGATTCTTACCCTCTACAGTTGTACTTTCCTTAATTTTCCTTTTATAACCTTC
1 GGCGACCTTCTAAGATTCTTACCCTCTACAGTTGTACTTTCCTTAATTTTCCTTTTATAACCTTC
*
31523122 AGTTTCTAAACTCACAATGGCCTTGGGCCTCACATTTGCGCTCTCCCCCACGACCAACGCTGAAT
66 AGTTTCTAAACTCACAATGGCCTTGAGCCTCACATTTGCGCTCTCCCCCACGACCAACGCTGAAT
31523187 TTCTG
131 TTCTG
31523192 GGCGACCTTCTAAGATTCTTACCCTCTACAGTTGTACTTTCCTTAATTTTCCTTTTATAACCTTC
1 GGCGACCTTCTAAGATTCTTACCCTCTACAGTTGTACTTTCCTTAATTTTCCTTTTATAACCTTC
31523257 AGTTTCTAAACTCACAATGGCCTTGAGCCTCACATTTGCGCTCTCCCCCACGACCAACGCTGAAT
66 AGTTTCTAAACTCACAATGGCCTTGAGCCTCACATTTGCGCTCTCCCCCACGACCAACGCTGAAT
31523322 TTCTG
131 TTCTG
31523327 GGCGACCTTCT
1 GGCGACCTTCT
31523338 CAGGCATCTC
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 145 1.00
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.35
Consensus pattern (135 bp):
GGCGACCTTCTAAGATTCTTACCCTCTACAGTTGTACTTTCCTTAATTTTCCTTTTATAACCTTC
AGTTTCTAAACTCACAATGGCCTTGAGCCTCACATTTGCGCTCTCCCCCACGACCAACGCTGAAT
TTCTG
Found at i:31525408 original size:15 final size:16
Alignment explanation
Indices: 31525378--31525411 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
31525368 AAAATGTAAT
31525378 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
31525394 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
31525409 TTT
1 TTT
31525412 TTAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:31525622 original size:55 final size:55
Alignment explanation
Indices: 31525538--31525683 Score: 213
Period size: 54 Copynumber: 2.7 Consensus size: 55
31525528 TTGAAATTCA
* *
31525538 TATTTAAAACTAAGTTTAAAAAATCATTTTAATTTCAATTTTGATTGTAAACGAG
1 TATTTAGAACTAAGTTTAAAAAATCATTTTAATTTCAATTTTAATTGTAAACGAG
* * *
31525593 TATTTCGAACTAAGTTTAAAGAACCATTTTAA-TTCAATTTTAATTGTAAACGAG
1 TATTTAGAACTAAGTTTAAAAAATCATTTTAATTTCAATTTTAATTGTAAACGAG
* * *
31525647 TCTTTAGAATTAAGTTTAAAAAATTATTTTAATTTCA
1 TATTTAGAACTAAGTTTAAAAAATCATTTTAATTTCA
31525684 GTAAACGAGT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 47 0.59
55 32 0.41
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (55 bp):
TATTTAGAACTAAGTTTAAAAAATCATTTTAATTTCAATTTTAATTGTAAACGAG
Found at i:31528695 original size:16 final size:17
Alignment explanation
Indices: 31528674--31528715 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
31528664 CTATGATGTG
31528674 AGTAAAAAAT-TAATTA
1 AGTAAAAAATATAATTA
*
31528690 AGT-AAAAATATATTTA
1 AGTAAAAAATATAATTA
31528706 A-TAAAAAATA
1 AGTAAAAAATA
31528716 ACGTAAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AGTAAAAAATATAATTA
Found at i:31536580 original size:2 final size:2
Alignment explanation
Indices: 31536575--31536601 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31536565 CATTTTTTTA
31536575 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31536602 ATAACTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31540733 original size:26 final size:26
Alignment explanation
Indices: 31540704--31540780 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
31540694 ATACATTAAC
31540704 AAAGAATATCCTAAAGATATTATGAA
1 AAAGAATATCCTAAAGATATTATGAA
* * *
31540730 AAAGGATATCC-AGAGGATATCATTGAA
1 AAAGAATATCCTA-AAGATATTA-TGAA
* * *
31540757 AAGGATTATCCGTAATGATATTAT
1 AAAGAATATCC-TAAAGATATTAT
31540781 AGAGAGAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
25 1 0.03
26 17 0.44
27 13 0.33
28 7 0.18
29 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (26 bp):
AAAGAATATCCTAAAGATATTATGAA
Found at i:31548443 original size:8 final size:8
Alignment explanation
Indices: 31548430--31548467 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
31548420 TTACGATGAT
31548430 CCATATCA
1 CCATATCA
31548438 CCATATCA
1 CCATATCA
*
31548446 CCATATCC
1 CCATATCA
31548454 CCATATCA
1 CCATATCA
31548462 CCATAT
1 CCATAT
31548468 TGCCTCTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.26
Consensus pattern (8 bp):
CCATATCA
Found at i:31552939 original size:6 final size:6
Alignment explanation
Indices: 31552910--31552940 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
31552900 TCTCACATTC
*
31552910 ACATGC ACATGG ACATGG ACATGG ACATGG A
1 ACATGG ACATGG ACATGG ACATGG ACATGG A
31552941 AGCTTTTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.16
Consensus pattern (6 bp):
ACATGG
Found at i:31558454 original size:27 final size:27
Alignment explanation
Indices: 31558424--31558490 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
31558414 GAGGGACACA
* *
31558424 AAGTGGCGGCATTGAAGGAGGATATTC
1 AAGTGGCGGCACTGAAGAAGGATATTC
*
31558451 AAGTGGCGGCACTGAAGAAGGATCTTC
1 AAGTGGCGGCACTGAAGAAGGATATTC
*
31558478 AAGTGACGGCACT
1 AAGTGGCGGCACT
31558491 AAGGGGTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.34, T:0.19
Consensus pattern (27 bp):
AAGTGGCGGCACTGAAGAAGGATATTC
Found at i:31558887 original size:18 final size:18
Alignment explanation
Indices: 31558864--31558898 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31558854 GAAAGAAATG
31558864 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
31558882 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
31558899 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:31558992 original size:23 final size:23
Alignment explanation
Indices: 31558918--31558995 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
31558908 TTTAAAATAT
*
31558918 TTTAATTTGTTAGTTAATTTGATTA
1 TTTAATTT-TTA-TTGATTTGATTA
* * *
31558943 TTTTAAGTTTT-TTGTTTTGTTTAA
1 -TTTAATTTTTATTGATTTGATT-A
31558967 TTTAATTTTTAATTGATTTG-TTA
1 TTTAATTTTT-ATTGATTTGATTA
31558990 TTTAAT
1 TTTAAT
31558996 GTTGTTATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
23 24 0.56
24 3 0.07
25 9 0.21
26 7 0.16
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.65
Consensus pattern (23 bp):
TTTAATTTTTATTGATTTGATTA
Found at i:31559637 original size:21 final size:23
Alignment explanation
Indices: 31559602--31559644 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
31559592 AGGTAAAATT
31559602 AATTATATAATAAAATTATAAAA
1 AATTATATAATAAAATTATAAAA
*
31559625 AATTA-AT-ATAAAATTTTAAA
1 AATTATATAATAAAATTATAAA
31559645 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATTATATAATAAAATTATAAAA
Found at i:31561588 original size:45 final size:45
Alignment explanation
Indices: 31561462--31561595 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 45
31561452 CTAACTCATC
* **
31561462 AAGCCAAGGATATCAACCTCAGTTTGACGAGCCACTACAATACTT
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTT
*
31561507 AAGCCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTT
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTT
** * * *
31561552 AAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCGTAATACT
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACT
31561596 CTACTCTTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (45 bp):
AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTT
Found at i:31561857 original size:14 final size:14
Alignment explanation
Indices: 31561840--31561901 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
31561830 CCTTAAATCA
*
31561840 TAAATCGTAAACTC
1 TAAATCCTAAACTC
*
31561854 TAAACCCTAAACT-
1 TAAATCCTAAACTC
*
31561867 TAGAATCGTAAA-TC
1 TA-AATCCTAAACTC
*
31561881 TTAAATCCTAAACCC
1 -TAAATCCTAAACTC
31561896 TAAATC
1 TAAATC
31561902 TTATACATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
13 3 0.08
14 32 0.84
15 3 0.08
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (14 bp):
TAAATCCTAAACTC
Found at i:31563314 original size:91 final size:91
Alignment explanation
Indices: 31563159--31563344 Score: 372
Period size: 91 Copynumber: 2.0 Consensus size: 91
31563149 AGGAGCAATG
31563159 TGTCGGCTGCAGTAAACCGATTTTCATGGTACACTAGTACGCCTAATGGTCGCAATAATACCCTT
1 TGTCGGCTGCAGTAAACCGATTTTCATGGTACACTAGTACGCCTAATGGTCGCAATAATACCCTT
31563224 CCCTCTATCGGAGATTATGCAAATAT
66 CCCTCTATCGGAGATTATGCAAATAT
31563250 TGTCGGCTGCAGTAAACCGATTTTCATGGTACACTAGTACGCCTAATGGTCGCAATAATACCCTT
1 TGTCGGCTGCAGTAAACCGATTTTCATGGTACACTAGTACGCCTAATGGTCGCAATAATACCCTT
31563315 CCCTCTATCGGAGATTATGCAAATAT
66 CCCTCTATCGGAGATTATGCAAATAT
31563341 TGTC
1 TGTC
31563345 ATTATGAATC
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 95 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (91 bp):
TGTCGGCTGCAGTAAACCGATTTTCATGGTACACTAGTACGCCTAATGGTCGCAATAATACCCTT
CCCTCTATCGGAGATTATGCAAATAT
Found at i:31565028 original size:4 final size:4
Alignment explanation
Indices: 31565019--31565051 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
31565009 TCATTCTTCT
31565019 TTTC TTTC TTTC TTTC TTTC TTTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
31565052 CCGTTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:31565364 original size:6 final size:7
Alignment explanation
Indices: 31565351--31565380 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
31565341 AATATATAAC
31565351 AATAAAA
1 AATAAAA
31565358 AATAAAA
1 AATAAAA
31565365 AATAAAA
1 AATAAAA
31565372 AATAAAA
1 AATAAAA
31565379 AA
1 AA
31565381 AATTCGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:31574609 original size:29 final size:29
Alignment explanation
Indices: 31574577--31574659 Score: 105
Period size: 31 Copynumber: 2.8 Consensus size: 29
31574567 TAAAAAATTT
31574577 AAATTTTTTTATCAACTTTTAAGGGTCTC
1 AAATTTTTTTATCAACTTTTAAGGGTCTC
*
31574606 AAATTTTTTT-TCTTTAATTTTTAAGGGTCTC
1 AAATTTTTTTATC---AACTTTTAAGGGTCTC
* *
31574637 AATTTTTTTTACCAACTTTTAAG
1 AAATTTTTTTATCAACTTTTAAG
31574660 AGATTTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 2 0.04
29 19 0.41
31 24 0.52
32 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (29 bp):
AAATTTTTTTATCAACTTTTAAGGGTCTC
Found at i:31574615 original size:31 final size:29
Alignment explanation
Indices: 31574580--31574659 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
31574570 AAAATTTAAA
31574580 TTTTTTTATCAACTTTTAAGGGTCTCAAAT
1 TTTTTTTATCAACTTTTAAGGGTCTC-AAT
* * *
31574610 TTTTTTTCTTTAATTTTTAAGGGTCTCAAT
1 TTTTTTT-ATCAACTTTTAAGGGTCTCAAT
*
31574640 TTTTTTTACCAACTTTTAAG
1 TTTTTTTATCAACTTTTAAG
31574660 AGATTTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 9 0.21
30 17 0.40
31 16 0.38
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (29 bp):
TTTTTTTATCAACTTTTAAGGGTCTCAAT
Found at i:31574992 original size:2 final size:2
Alignment explanation
Indices: 31574987--31575013 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31574977 ATACACACAC
31574987 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31575014 AAAGAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31576868 original size:16 final size:16
Alignment explanation
Indices: 31576849--31576882 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
31576839 AGGTAAGGAA
31576849 AAGAAAA-AGAAAAAAG
1 AAGAAAACA-AAAAAAG
31576865 AAGAAAACAAAAAAAG
1 AAGAAAACAAAAAAAG
31576881 AA
1 AA
31576883 AGAGATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAAAACAAAAAAAG
Found at i:31578586 original size:23 final size:25
Alignment explanation
Indices: 31578560--31578605 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31578550 CCAATTAAGG
31578560 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
31578583 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
31578606 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:31585233 original size:12 final size:12
Alignment explanation
Indices: 31585216--31585257 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
31585206 TCATGTTCTT
31585216 AAAAAAATTGAA
1 AAAAAAATTGAA
31585228 AAAAAAATT-AA
1 AAAAAAATTGAA
*
31585239 AAAAAAGTTTGAA
1 AAAAAA-ATTGAA
31585252 AAAAAA
1 AAAAAA
31585258 TAAAGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.30
12 11 0.41
13 8 0.30
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:31585268 original size:15 final size:17
Alignment explanation
Indices: 31585237--31585273 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
31585227 AAAAAAAATT
31585237 AAAAA-AAAGTTTGAAA
1 AAAAATAAAGTTTGAAA
31585253 AAAAATAAAG-TT-AAA
1 AAAAATAAAGTTTGAAA
31585268 AAAAAT
1 AAAAAT
31585274 TAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 7 0.35
17 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (17 bp):
AAAAATAAAGTTTGAAA
Found at i:31585315 original size:28 final size:26
Alignment explanation
Indices: 31585273--31585328 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 26
31585263 TTAAAAAAAA
*
31585273 TTAGTTTATTTATTTCATTTTTAGTT
1 TTAGTTTATTTATTTCATTTTTAATT
*
31585299 TTAGTTTTATTTTATTTTATTTTTAATT
1 TTAG-TTTA-TTTATTTCATTTTTAATT
31585327 TT
1 TT
31585329 TTTAATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 4 0.15
27 4 0.15
28 18 0.69
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (26 bp):
TTAGTTTATTTATTTCATTTTTAATT
Found at i:31586269 original size:10 final size:10
Alignment explanation
Indices: 31586254--31586280 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31586244 ATTATTTAGA
31586254 AAAAAAATTG
1 AAAAAAATTG
31586264 AAAAAAATTG
1 AAAAAAATTG
31586274 AAAAAAA
1 AAAAAAA
31586281 GGAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:31587350 original size:23 final size:25
Alignment explanation
Indices: 31587324--31587369 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31587314 CCAATTAAGG
31587324 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
31587347 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
31587370 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:31588880 original size:58 final size:58
Alignment explanation
Indices: 31588809--31589059 Score: 210
Period size: 58 Copynumber: 4.3 Consensus size: 58
31588799 ACCCGAGGGC
*
31588809 AAAATGGTAATTTTGGAC-TCTCGGGGGTAAAATGGTAATTTTAGAAAATTTTGAGGGTT-
1 AAAATGG-AATTTTGGACATC-CGAGGGTAAAATGGTAATTTTAGAAAATTTTGA-GGTTA
* * * *** * * *
31588868 AAAATGGGATTTTAGACATCCGAAGGTAAAACAATAATTTTTAGAAAA-ATCGA-GATA
1 AAAATGGAATTTTGGACATCCGAGGGTAAAATGGTAA-TTTTAGAAAATTTTGAGGTTA
* *
31588925 AAAATGGAATTTTTGGACATCCGAGGGTAAAATGGTAATTTT-GAAAGTTTTGGGGTTA
1 AAAATGGAA-TTTTGGACATCCGAGGGTAAAATGGTAATTTTAGAAAATTTTGAGGTTA
* * * *
31588983 AAAAT-GAAGTTTTTTTGACAT-CTAGGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTTA
1 AAAATGGAA---TTTTGGACATCCGA-GGGTAAAATGGTAATTTTAGAAAATTTTGAGGTTA
*
31589043 AAAATGAGATTTTTGGA
1 AAAATG-GAATTTTGGA
31589060 TGTTTAGGGG
Statistics
Matches: 154, Mismatches: 26, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
56 6 0.04
57 17 0.11
58 56 0.36
59 53 0.34
60 20 0.13
62 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTGGACATCCGAGGGTAAAATGGTAATTTTAGAAAATTTTGAGGTTA
Found at i:31588967 original size:28 final size:28
Alignment explanation
Indices: 31588801--31588967 Score: 83
Period size: 28 Copynumber: 5.8 Consensus size: 28
31588791 TTTTAAATAC
*
31588801 CCGAGGGCAAAATGGTAATTTTGGAC-T
1 CCGAGGGTAAAATGGTAATTTTGGACAT
* * *
31588828 CTCGGGGGTAAAATGGTAATTTTAGAAAATT
1 C-CGAGGGTAAAATGGTAATTTT-GGACA-T
** * *
31588859 TTGAGGGTTAAAATGG-GATTTTAGACAT
1 CCGAGGG-TAAAATGGTAATTTTGGACAT
* *** * *
31588887 CCGAAGGTAAAACAATAATTTTTAGAAAAAT
1 CCGAGGGTAAAATGGTAA-TTTT-G-GACAT
*
31588918 -CGA-GATAAAAATGG-AATTTTTGGACAT
1 CCGAGGGT-AAAATGGTAA-TTTTGGACAT
31588945 CCGAGGGTAAAATGGTAATTTTG
1 CCGAGGGTAAAATGGTAATTTTG
31588968 AAAGTTTTGG
Statistics
Matches: 99, Mismatches: 28, Indels: 25
0.65 0.18 0.16
Matches are distributed among these distances:
27 9 0.09
28 41 0.41
29 21 0.21
30 16 0.16
31 12 0.12
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (28 bp):
CCGAGGGTAAAATGGTAATTTTGGACAT
Found at i:31589035 original size:60 final size:59
Alignment explanation
Indices: 31588819--31589085 Score: 203
Period size: 59 Copynumber: 4.6 Consensus size: 59
31588809 AAAATGGTAA
* * * *
31588819 TTTTGGAC-TCTCGGGGGTAAAATGGTAATTTTAGAAAATTTTGAGGGTT-AAAATGGGA-
1 TTTTGGACATCT-AGGGGTAAAATGGTAATTTTTGAAAGTTTTGA-GGTTAAAAATGAGAT
* * * *** ** * *
31588877 TTTTAGACATC-CGAAGGTAAAACAATAATTTTTAGAAA-AATCGA-GATAAAAATG-GAAT
1 TTTTGGACATCTAG-GGGTAAAATGGTAATTTTT-GAAAGTTTTGAGGTTAAAAATGAG-AT
* * *
31588935 TTTTGGACATC-CGAGGGTAAAATGGTAA-TTTTGAAAGTTTTGGGGTTAAAAATGAAGTT
1 TTTTGGACATCTAG-GGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTTAAAAATG-AGAT
*
31588994 TTTTTGACATCTAGGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTTAAAAATGAGAT
1 TTTTGGACATCTAGGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTTAAAAATGAGAT
** *
31589053 TTTTGGATGTTTAGGGGTAAAAAT-GTAATTTTT
1 TTTTGGACATCTAGGGGT-AAAATGGTAATTTTT
31589086 TTGGAAAAGT
Statistics
Matches: 166, Mismatches: 30, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
56 7 0.04
57 14 0.08
58 56 0.34
59 57 0.34
60 32 0.19
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (59 bp):
TTTTGGACATCTAGGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTTAAAAATGAGAT
Found at i:31589086 original size:60 final size:59
Alignment explanation
Indices: 31588949--31589285 Score: 273
Period size: 60 Copynumber: 5.7 Consensus size: 59
31588939 GGACATCCGA
* * * *
31588949 GGGT-AAAATGGTAA-TTTTGAAAGTTTTGGGGTTAAAAATGAAGTTTTTTTGACA-TCTAG
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTTGAGGTTAAAAATG-AGATTTTTGGA-AGTTTAG
*
31589008 GGGT-AAAATGGTAATTTTTGAAAGTTTTGAGGTTAAAAATGAGATTTTTGGATGTTTAG
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTTGAGGTTAAAAATGAGATTTTTGGAAGTTTAG
* * * *** *
31589067 GGGTAAAAATGTAATTTTTTTGGAAAAG--TTG-GGGTAAAAATGAAAATTTAAAAAGTTCAG
1 GGGTAAAAATGTAA--TTTTT-G-AAAGTTTTGAGGTTAAAAATGAGATTTTTGGAAGTTTAG
* * * *
31589127 GGGTAAAAATATAATTTTTGGAGAA-ATTAG-GGTTAAAAATTGA-ATTTTTGAAAGTTTAG
1 GGGTAAAAATGTAATTTTT-GA-AAGTTTTGAGGTTAAAAA-TGAGATTTTTGGAAGTTTAG
* * * * *
31589186 GGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAAATGGGATTTTTGGAAGTTT-G
1 GGGTAAAAATGTAATTTTTGAAAGTTTTGAGGT-TAAAAATGAGATTTTTGGAAGTTTAG
**
31589245 GAGGTAAAAATGTAATTTTTGAAAGTTACGAGGTTAAAAAT
1 G-GGTAAAAATGTAATTTTTGAAAGTTTTGAGGTTAAAAAT
31589286 TTTTTGGTCA
Statistics
Matches: 232, Mismatches: 30, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
57 3 0.01
58 13 0.06
59 89 0.38
60 114 0.49
61 8 0.03
62 1 0.00
63 4 0.02
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (59 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTTGAGGTTAAAAATGAGATTTTTGGAAGTTTAG
Found at i:31589234 original size:31 final size:30
Alignment explanation
Indices: 31589161--31589285 Score: 121
Period size: 29 Copynumber: 4.2 Consensus size: 30
31589151 AATTAGGGTT
* * * *
31589161 AAAAATTGAATTTTTGAAAGTTTAGGGGTA
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTA
31589191 AAAATAT--AATTTTTGGAAGTTTCGAGGTAA
1 AAAA-ATGGAATTTTTGGAAGTTTCGAGGT-A
* *
31589221 AAAAATGGGATTTTTGGAAGTTTGGAGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTA
* * * *
31589250 AAAAATGTAATTTTTGAAAGTTACGAGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTA
31589280 AAAAAT
1 AAAAAT
31589286 TTTTTGGTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
29 44 0.55
30 15 0.19
31 21 0.26
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTA
Found at i:31589270 original size:29 final size:28
Alignment explanation
Indices: 31588949--31589271 Score: 185
Period size: 29 Copynumber: 10.9 Consensus size: 28
31588939 GGACATCCGA
31588949 GGGT-AAAATGGTAA-TTTTGAAAGTTTTG
1 GGGTAAAAAT-GTAATTTTTGAAAG-TTTG
* *
31588977 GGGTTAAAAATG-AAGTTTTTTTGACA-TCTAG
1 GGG-TAAAAATGTAA---TTTTTGAAAGT-TTG
31589008 GGGT-AAAATGGTAATTTTTGAAAGTTTTG
1 GGGTAAAAAT-GTAATTTTTGAAAG-TTTG
* * *
31589037 AGGTTAAAAATG-AGATTTTTGGATGTTTAG
1 -GGGTAAAAATGTA-ATTTTTGAAAGTTT-G
31589067 GGGTAAAAATGTAATTTTTTTGGAAAAG-TTG
1 GGGTAAAAATGTAA--TTTTT-G-AAAGTTTG
* * ** *
31589098 GGGTAAAAATGAAAATTTAAAAAGTTCAG
1 GGGTAAAAATGTAATTTTTGAAAGTT-TG
* * *
31589127 GGGTAAAAATATAATTTTTGGAGAAATTAG
1 GGGTAAAAATGTAATTTTT-GA-AAGTTTG
*
31589157 GGTTAAAAAT-TGAATTTTTGAAAGTTTAG
1 GGGTAAAAATGT-AATTTTTGAAAGTTT-G
* *
31589186 GGGTAAAAATATAATTTTTGGAAGTTTCG
1 GGGTAAAAATGTAATTTTTGAAAGTTT-G
* ** *
31589215 AGGTAAAAAAATGGGATTTTTGGAAGTTTG
1 GGGT--AAAAATGTAATTTTTGAAAGTTTG
31589245 GAGGTAAAAATGTAATTTTTGAAAGTT
1 G-GGTAAAAATGTAATTTTTGAAAGTT
31589272 ACGAGGTTAA
Statistics
Matches: 230, Mismatches: 35, Indels: 59
0.71 0.11 0.18
Matches are distributed among these distances:
27 4 0.02
28 18 0.08
29 93 0.40
30 45 0.20
31 58 0.25
32 10 0.04
33 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTG
Found at i:31590143 original size:32 final size:31
Alignment explanation
Indices: 31590073--31590149 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
31590063 TTTATTATTA
* * *
31590073 AATATTATTATCAAAAATATTTATTACTATT
1 AATATTATTATTAAAAATATTTATTAATAAT
* *
31590104 AATTATTATTATTAAAGATTTATTATTAATAAT
1 AA-TATTATTATTAAAAATAT-TTATTAATAAT
*
31590137 AATATTAGTATTA
1 AATATTATTATTA
31590150 TTTATTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 2 0.05
32 25 0.66
33 11 0.29
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
AATATTATTATTAAAAATATTTATTAATAAT
Found at i:31590143 original size:45 final size:45
Alignment explanation
Indices: 31590064--31590156 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
31590054 TTCACTTTCT
* *
31590064 TTATTATTAAATATTATTATCAAAAATATTTATTACTATTAATTA
1 TTATTATTAAAGATTATTATCAAAAATATATATTACTATTAATTA
* * * *
31590109 TTATTATTAAAGATTTATTATTAATAATA-ATATTAGTATTATTTA
1 TTATTATTAAAGA-TTATTATCAAAAATATATATTACTATTAATTA
31590154 TTA
1 TTA
31590157 AATACGTTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 28 0.68
46 13 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (45 bp):
TTATTATTAAAGATTATTATCAAAAATATATATTACTATTAATTA
Found at i:31591675 original size:206 final size:204
Alignment explanation
Indices: 31591235--31591730 Score: 591
Period size: 206 Copynumber: 2.4 Consensus size: 204
31591225 TCTGGTTTCA
* * * * *
31591235 TTGACTTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACTACATCACTTGTTTTGATCCAG-T
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGAC-GCATCACTTGTTTTAATCC-GCT
* * * * * ** * * *
31591299 TCTTTGTGTTTCATCATGAAGAAGGATTTGGTTTACTTCTCCGTATCATCAGGAAGCTAGCCACT
64 TCTCTGTATCTCATCAGGAAGAAGAATTTGGTCCACTTCTCAGTATCATCAGGAAACTAACCACT
* * * * * * *
31591364 TTATTGCTTCAACCTGCTTCTTAGTATCTCATCAGGAAGTTGGTGGTTCAAAGATTTGCTCACAT
129 TTATTACCTCAACCTACTTCTCAGTATCTCATCAGGAAGCTGGAGGTTCAAAGATTTACTCACAT
*
31591429 CGAGCGTGGGT
194 CGAGCGAGGGT
* * * *
31591440 TTGATTCGATCTTTTTCTCAGTATCTCATCAAGAAGATGATCGCATCACTTGTTTTAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGA-CGCATCACTTGTTTTAATCCGCTT
* * *
31591505 CTCTGTATCTCACCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAACTAACCAC
65 CTCTGTATCTCATCAGGAAGAAGAATTTGGTCCACTTCTCAGTA--TCATCAGGAAACTAACCAC
* * * *
31591570 TTTATTACCTCGACCTACTTCTCAGTATCTCATCAGGAAGCT-GAGGTTCGAAGATTTACTTATA
128 TTTATTACCTCAACCTACTTCTCAGTATCTCATCAGGAAGCTGGAGGTTCAAAGATTTACTCACA
31591634 TCGAGCGAGGGT
193 TCGAGCGAGGGT
* * *
31591646 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCGCTTGTTTCAATCCTCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGA-CGCATCACTTGTTTTAATCCGCTT
31591711 CTCTGTATCTCATCAGGAAG
65 CTCTGTATCTCATCAGGAAG
31591731 CTAGCCACTT
Statistics
Matches: 244, Mismatches: 43, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
204 1 0.00
205 86 0.35
206 105 0.43
207 52 0.21
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (204 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACGCATCACTTGTTTTAATCCGCTTC
TCTGTATCTCATCAGGAAGAAGAATTTGGTCCACTTCTCAGTATCATCAGGAAACTAACCACTTT
ATTACCTCAACCTACTTCTCAGTATCTCATCAGGAAGCTGGAGGTTCAAAGATTTACTCACATCG
AGCGAGGGT
Found at i:31591841 original size:170 final size:169
Alignment explanation
Indices: 31591539--31591900 Score: 499
Period size: 170 Copynumber: 2.1 Consensus size: 169
31591529 ATTTGGTCCA
* * * *
31591539 CTTCTCAGTATCTCATTAGGAAACTAACCACTTTATTACCTCGACCTACTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTACCTCAACCTACTTCTCAGTATCTCATC
* * * * * *
31591604 AGGAAGCTGAGGTTCGAAGATTTACTTATATCGAGCGAGGGTTTGATTTGGTCTTCTTCTCAGTA
66 AAGAAGCTGAGGTTCAAAGATTTACTCACATCGAGCGAGGGTTTGATTCGATCTTCTTCTCAGTA
* *
31591669 TCTCATCAAGAAGATGACCGCATCGCTTGTTTCAATCCT
131 TCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCG
* * * * *
31591708 CTTCTCTGTATCTCATCAGGAAGCTAGCCACTTTATTGCTTCAACCTGCTTCTTAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTACCTCAACCTACTTCTCAGTATCTCATC
* * * * * *
31591773 AAGAAGTTGGGGGTTCAAAGATTTGCTCACATTGAGCGTGGGTTTGATTCGATCTTCTTCTTAGT
66 AAGAAGCT-GAGGTTCAAAGATTTACTCACATCGAGCGAGGGTTTGATTCGATCTTCTTCTCAGT
*
31591838 ATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATTCG
130 ATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCG
31591878 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
31591901 ACGAATTTGG
Statistics
Matches: 168, Mismatches: 24, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
169 62 0.37
170 106 0.63
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (169 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTACCTCAACCTACTTCTCAGTATCTCATC
AAGAAGCTGAGGTTCAAAGATTTACTCACATCGAGCGAGGGTTTGATTCGATCTTCTTCTCAGTA
TCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCG
Found at i:31592037 original size:376 final size:376
Alignment explanation
Indices: 31591344--31592106 Score: 1375
Period size: 376 Copynumber: 2.0 Consensus size: 376
31591334 CTTCTCCGTA
* *
31591344 TCATCAGGAAGCTAGCCACTTTATTGCTTCAACCTGCTTCTTAGTATCTCATCAGGAAGTTGGTG
1 TCATCAGGAAGCTAGCCACTTTATTGCTTCAACCTGCTTCTTAGTATCTCATCAAGAAGTTGGGG
*
31591409 GTTCAAAGATTTGCTCACATCGAGCGTGGGTTTGATTCGATCTTTTTCTCAGTATCTCATCAAGA
66 GTTCAAAGATTTGCTCACATCGAGCGTGGGTTTGATTCGATCTTCTTCTCAGTATCTCATCAAGA
* *
31591474 AGATGATCGCATCACTTGTTTTAATTCGCTTCTCTGTATCTCACCAGGAAGACGAATTTGGTCCA
131 AGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGTATCTCACCAGGAAGACGAATTTGGTCCA
*
31591539 CTTCTCAGTATCTCATTAGGAAACTAACCACTTTATTACCTCGACCTACTTCTCAGTATCTCATC
196 CTTCTCAGTATCTCATTAAGAAACTAACCACTTTATTACCTCGACCTACTTCTCAGTATCTCATC
* *
31591604 AGGAAGCTGAGGTTCGAAGATTTACTTATATCGAGCGAGGGTTTGATTTGGTCTTCTTCTCAGTA
261 AGGAAGCTGAGGTTCGAAGATTTACTCACATCGAGCGAGGGTTTGATTTGGTCTTCTTCTCAGTA
* *
31591669 TCTCATCAAGAAGATGACCG-CATCGCTTGTTTCAATCCTCTTCTCTGTATC
326 TCTCATCAAGAAGATGACCGTC-TCACTTGTTTCAATCCGCTTCTCTGTATC
31591720 TCATCAGGAAGCTAGCCACTTTATTGCTTCAACCTGCTTCTTAGTATCTCATCAAGAAGTTGGGG
1 TCATCAGGAAGCTAGCCACTTTATTGCTTCAACCTGCTTCTTAGTATCTCATCAAGAAGTTGGGG
* *
31591785 GTTCAAAGATTTGCTCACATTGAGCGTGGGTTTGATTCGATCTTCTTCTTAGTATCTCATCAAGA
66 GTTCAAAGATTTGCTCACATCGAGCGTGGGTTTGATTCGATCTTCTTCTCAGTATCTCATCAAGA
*
31591850 AGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCA
131 AGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGTATCTCACCAGGAAGACGAATTTGGTCCA
* *
31591915 CTTCTCAGTATCTCATTAAGAAGCTAACCACTTTATTACCTCGACCTGCTTCTCAGTATCTCATC
196 CTTCTCAGTATCTCATTAAGAAACTAACCACTTTATTACCTCGACCTACTTCTCAGTATCTCATC
31591980 AGGAAGCTGAGGTTCGAAGATTTACTCACATCGAGCGAGGGTTTGATTTGGTCTTCTTCTCAGTA
261 AGGAAGCTGAGGTTCGAAGATTTACTCACATCGAGCGAGGGTTTGATTTGGTCTTCTTCTCAGTA
31592045 TCTCATCAAGAAGATGACCGTCTCACTTGTTTCAATCCGCTTCTCTGTATC
326 TCTCATCAAGAAGATGACCGTCTCACTTGTTTCAATCCGCTTCTCTGTATC
31592096 TCATCAGGAAG
1 TCATCAGGAAG
31592107 ACGAATTTGG
Statistics
Matches: 371, Mismatches: 15, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
376 370 1.00
377 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (376 bp):
TCATCAGGAAGCTAGCCACTTTATTGCTTCAACCTGCTTCTTAGTATCTCATCAAGAAGTTGGGG
GTTCAAAGATTTGCTCACATCGAGCGTGGGTTTGATTCGATCTTCTTCTCAGTATCTCATCAAGA
AGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGTATCTCACCAGGAAGACGAATTTGGTCCA
CTTCTCAGTATCTCATTAAGAAACTAACCACTTTATTACCTCGACCTACTTCTCAGTATCTCATC
AGGAAGCTGAGGTTCGAAGATTTACTCACATCGAGCGAGGGTTTGATTTGGTCTTCTTCTCAGTA
TCTCATCAAGAAGATGACCGTCTCACTTGTTTCAATCCGCTTCTCTGTATC
Found at i:31592073 original size:206 final size:206
Alignment explanation
Indices: 31591708--31592296 Score: 914
Period size: 206 Copynumber: 2.9 Consensus size: 206
31591698 TTTCAATCCT
* * * * *
31591708 CTTCTCTGTATCTCATCAGGAAGCTAGCCACTTTATTGCTTCAACCTGCTTCTTAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* * * * * *
31591773 AAGAAGTTGGGGGTTCAAAGATTTGCTCACATTGAGCGTGGGTTTGATTCGATCTTCTTCTTAGT
66 AAGAAGCT-GGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGT
*
31591838 ATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGAC
130 ATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC
31591903 GAATTTGGTCCA
195 GAATTTGGTCCA
* * *
31591915 CTTCTCAGTATCTCATTAAGAAGCTAACCACTTTATTACCTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* * * *
31591980 AGGAAGCTGAGGTTCGAAGATTTACTCACATCGAGCGAGGGTTTGATTTGGTCTTCTTCTCAGTA
66 AAGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
31592045 TCTCATCAAGAAGATGACCGTC-TCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC
131 TCTCATCAAGAAGATGACCG-CATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC
31592109 GAATTTGGTCCA
195 GAATTTGGTCCA
*
31592121 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* *
31592186 AAGAAGCTGGGGTTCGAAGACTTGCT--CATCGAGCGTGGGTTTGATTTTGTCTTCTTCTCAGTA
66 AAGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
* * *
31592249 TCTTATCAAGAAGATGACCGCATCATTTGTTTCAATCCGCCTCTCTGT
131 TCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGT
31592297 TTGTGGATAA
Statistics
Matches: 348, Mismatches: 32, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
203 1 0.00
204 78 0.22
206 205 0.59
207 64 0.18
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
AAGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
TCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACG
AATTTGGTCCA
Found at i:31594052 original size:14 final size:15
Alignment explanation
Indices: 31594029--31594074 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
31594019 TTCTTTTCTT
*
31594029 TTTTCCTTTTTTTGT-
1 TTTTGCTTTTTTT-TC
31594044 TTTTG-TTTTTTTTC
1 TTTTGCTTTTTTTTC
*
31594058 TTTTGCTTTTTCTTC
1 TTTTGCTTTTTTTTC
31594073 TT
1 TT
31594075 CTTTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 12 0.44
15 14 0.52
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTGCTTTTTTTTC
Found at i:31599426 original size:96 final size:96
Alignment explanation
Indices: 31599248--31599429 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 96
31599238 AAGGATGTTT
**
31599248 GATTATCTCAATTTGAAGAAAGGTTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
1 GATTATCTCAATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
**
31599313 TAAGGAAACATTACCTCGATTAAGGGTATTC
66 TAAAAAAACATTACCTCGATTAAGGGTATTC
* * * *
31599344 GATTATTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCAG-ACATTTTC-GAAACTTGA
1 GATTATCTCAATTTGAAGAAAAATTACACCTAGTAAGTTAAGGC-GCAAATTTTCAG-AA-TCGA
* *
31599407 A-ATAAAAAAATATTGCCTCGATT
63 AGATAAAAAAACATTACCTCGATT
31599430 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 1 0.01
96 67 0.92
97 5 0.07
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
GATTATCTCAATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
TAAAAAAACATTACCTCGATTAAGGGTATTC
Found at i:31599753 original size:59 final size:59
Alignment explanation
Indices: 31599682--31599896 Score: 187
Period size: 59 Copynumber: 3.7 Consensus size: 59
31599672 ATTGGATCGG
*
31599682 GGGTAAAATGGTAGTTTTAGGAAA-TTTTGAGGGTTAAAAATGGAA-TTTTAGACATTCAA
1 GGGTAAAATGGTAATTTT--GAAAGTTTTGAGGGTTAAAAATGGAATTTTTAGACATTCAA
** * * * * *
31599741 GGGTAAAATGGTAATTTTTAGAAA-AATCGA--GATAAAAATGGAATTTTTGGACATCCGA
1 GGGTAAAATGGTAA-TTTT-GAAAGTTTTGAGGGTTAAAAATGGAATTTTTAGACATTCAA
* * * **
31599799 GGGTAAAATGGTAATTTTGAAAGTTTTG-GTGTCAAAAAT-GAAGTTTTTTTGACA-TCCG
1 GGGTAAAATGGTAATTTTGAAAGTTTTGAGGGTTAAAAATGGAA--TTTTTAGACATTCAA
31599857 GGGTAAAATGGTAATTTTTGAAAGTTTT-AGGGTTAAAAAT
1 GGGTAAAATGGTAA-TTTTGAAAGTTTTGAGGGTTAAAAAT
31599897 AAAAAAATTA
Statistics
Matches: 127, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
56 4 0.03
57 21 0.17
58 47 0.37
59 51 0.40
60 4 0.03
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTGAAAGTTTTGAGGGTTAAAAATGGAATTTTTAGACATTCAA
Found at i:31599759 original size:29 final size:28
Alignment explanation
Indices: 31599682--31599816 Score: 94
Period size: 29 Copynumber: 4.6 Consensus size: 28
31599672 ATTGGATCGG
* * * *
31599682 GGGTAAAATGGTAGTTTTAGGAAATTTTGA
1 GGGTAAAATGGAATTTTTA-GACA-TTCGA
*
31599712 GGGTTAAAAATGGAA-TTTTAGACATTCAA
1 GGG-T-AAAATGGAATTTTTAGACATTCGA
* *
31599741 GGGTAAAATGGTAATTTTTAGAAAAATCGA
1 GGGTAAAATGG-AATTTTTAG-ACATTCGA
* * *
31599771 -GATAAAAATGGAATTTTTGGACATCCGA
1 GGGT-AAAATGGAATTTTTAGACATTCGA
31599799 GGGTAAAATGGTAATTTT
1 GGGTAAAATGG-AATTTT
31599817 GAAAGTTTTG
Statistics
Matches: 84, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
27 7 0.08
28 15 0.18
29 30 0.36
30 18 0.21
31 6 0.07
32 8 0.10
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (28 bp):
GGGTAAAATGGAATTTTTAGACATTCGA
Found at i:31599836 original size:58 final size:58
Alignment explanation
Indices: 31599682--31599884 Score: 188
Period size: 58 Copynumber: 3.5 Consensus size: 58
31599672 ATTGGATCGG
* * *
31599682 GGGTAAAATGGT-AGTTTTAGGAAATTTTGAGGGTTAAAAATGGAA-TTTTAGACATTCAA
1 GGGTAAAATGGTAATTTTTA-GAAATTTTGA-GG-TAAAAATGGAATTTTTAGACATCCGA
** * * *
31599741 GGGTAAAATGGTAATTTTTAGAAAAATCGAGATAAAAATGGAATTTTTGGACATCCGA
1 GGGTAAAATGGTAATTTTTAGAAATTTTGAGGTAAAAATGGAATTTTTAGACATCCGA
*
31599799 GGGTAAAATGGTAA-TTTT-GAAAGTTTTG-GTGTCAAAAAT-GAAGTTTTTTTGACATCCG-
1 GGGTAAAATGGTAATTTTTAGAAA-TTTTGAG-GT-AAAAATGGAA--TTTTTAGACATCCGA
31599857 GGGTAAAATGGTAATTTTT-GAAAGTTTT
1 GGGTAAAATGGTAATTTTTAGAAA-TTTT
31599885 AGGGTTAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
56 5 0.04
57 21 0.17
58 46 0.37
59 45 0.37
60 6 0.05
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTAGAAATTTTGAGGTAAAAATGGAATTTTTAGACATCCGA
Found at i:31599924 original size:59 final size:57
Alignment explanation
Indices: 31599856--31600059 Score: 216
Period size: 59 Copynumber: 3.5 Consensus size: 57
31599846 TTTGACATCC
* * ** *
31599856 GGGGT-AAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAAATAAAAAAATTAGATGTTT-
1 GGGGTAAAAAT-GTAATTTTTGAAAG--TTAGAGTTAAAAATAGAAATTTTAGAAGTTTG
* * *
31599914 GGGGTAAAAATGTAATTTTTTGGAGAAGTCAGAGTTAAAAAT-GGAATTTTGGAAAGTTTG
1 GGGGTAAAAATGTAA-TTTTT-GA-AAGTTAGAGTTAAAAATAGAAATTTTAG-AAGTTTG
* *
31599974 GGGGTAAAAATGTAATTTTTGGAAGTTACGAGTTCAAAAATAGAATTTTTAGAAGTTTG
1 GGGGTAAAAATGTAATTTTTGAAAGTTA-GAGTT-AAAAATAGAAATTTTAGAAGTTTG
31600033 GGGGTAAAAATGTAATTTTTGAAAGTT
1 GGGGTAAAAATGTAATTTTTGAAAGTT
31600060 TTAGGGTCAA
Statistics
Matches: 123, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
57 5 0.04
58 20 0.16
59 71 0.58
60 24 0.20
61 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.35
Consensus pattern (57 bp):
GGGGTAAAAATGTAATTTTTGAAAGTTAGAGTTAAAAATAGAAATTTTAGAAGTTTG
Found at i:31599996 original size:30 final size:30
Alignment explanation
Indices: 31599910--31600120 Score: 145
Period size: 29 Copynumber: 7.1 Consensus size: 30
31599900 AAAATTAGAT
31599910 GTTT-GGGGTAAAAATGTAATTTTTTGGAGAA
1 GTTTCGGGGTAAAAATGTAA-TTTTTGGA-AA
* * *
31599941 G--TCAGAGTTAAAAATGGAA-TTTTGGAAA
1 GTTTC-GGGGTAAAAATGTAATTTTTGGAAA
*
31599969 GTTTGGGGGTAAAAATGTAATTTTTGG-AA
1 GTTTCGGGGTAAAAATGTAATTTTTGGAAA
* * * *
31599998 GTTACGAGTTCAAAAATAG-AATTTTTAG-AA
1 GTTTCGGGGT-AAAAAT-GTAATTTTTGGAAA
*
31600028 GTTTGGGGGTAAAAATGTAATTTTT-GAAA
1 GTTTCGGGGTAAAAATGTAATTTTTGGAAA
** * *
31600057 GTTTTAGGGTCAAAAGTGAAATTTTTGG-AA
1 GTTTCGGGGT-AAAAATGTAATTTTTGGAAA
* * *
31600087 G-TCCGGGGTAAAAAATATAATTTTTGGATA
1 GTTTCGGGGT-AAAAATGTAATTTTTGGAAA
31600117 GTTT
1 GTTT
31600121 AGGGACCTCT
Statistics
Matches: 138, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
28 5 0.04
29 70 0.51
30 47 0.34
31 16 0.12
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
GTTTCGGGGTAAAAATGTAATTTTTGGAAA
Found at i:31600066 original size:29 final size:29
Alignment explanation
Indices: 31599857--31600088 Score: 104
Period size: 29 Copynumber: 7.9 Consensus size: 29
31599847 TTGACATCCG
31599857 GGGT-AAAATGGTAATTTTTGAAAGTTTTA
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTTA
** *** * *
31599886 GGGTTAAAAATAAAAAAATT-AGA-TGTTTG
1 GGG-TAAAAATGTAATTTTTGAAAGT-TTTA
*
31599915 GGGTAAAAATGTAATTTTTTGGAGAAG--TCA
1 GGGTAAAAATGTAA-TTTTT-GA-AAGTTTTA
* * * **
31599945 GAGTTAAAAATGGAATTTTGGAAAGTTTGG
1 G-GGTAAAAATGTAATTTTTGAAAGTTTTA
*
31599975 GGGTAAAAATGTAATTTTTGGAAG--TTA
1 GGGTAAAAATGTAATTTTTGAAAGTTTTA
* **
31600002 CGAGTTCAAAAATAG-AATTTTT-AGAAGTTTGG
1 -G-GGT-AAAAAT-GTAATTTTTGA-AAGTTTTA
31600034 GGGTAAAAATGTAATTTTTGAAAGTTTTA
1 GGGTAAAAATGTAATTTTTGAAAGTTTTA
* * *
31600063 GGGTCAAAAGTGAAATTTTTGGAAGT
1 GGGT-AAAAATGTAATTTTTGAAAGT
31600089 CCGGGGTAAA
Statistics
Matches: 146, Mismatches: 36, Indels: 41
0.65 0.16 0.18
Matches are distributed among these distances:
27 1 0.01
28 15 0.10
29 59 0.40
30 50 0.34
31 19 0.13
32 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTTA
Found at i:31600070 original size:59 final size:58
Alignment explanation
Indices: 31599799--31600112 Score: 204
Period size: 59 Copynumber: 5.3 Consensus size: 58
31599789 GGACATCCGA
* *
31599799 GGGT-AAAATGGTAA-TTTTGAAAGTTTT-GGTGTCAAAAATGAAGTTTTTTTGACA--TCCG
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTTAGG-GTCAAAAATGAA--TTTTTAGA-AGTTTCG
* * *** *
31599857 GGGT-AAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAAATAAAAAAATTAGATGTTT-G
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTTAGGGTCAAAAAT-GAATTTTTAGAAGTTTCG
* * * * *
31599915 GGGTAAAAATGTAATTTTTTGGAGAAG--TCAGAGTTAAAAATGGAA-TTTTGGAAAGTTTGG
1 GGGTAAAAATGTAA-TTTTT-GA-AAGTTTTAGGGTCAAAAAT-GAATTTTTAG-AAGTTTCG
* * *
31599975 GGGTAAAAATGTAATTTTTGGAAG--TTACGAGTTCAAAAATAGAATTTTTAGAAGTTTGG
1 GGGTAAAAATGTAATTTTTGAAAGTTTTA-G-GGTCAAAAAT-GAATTTTTAGAAGTTTCG
* * *
31600034 GGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAGTGAAATTTTTGGAAG-TCCG
1 GGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAATG-AATTTTTAGAAGTTTCG
*
31600092 GGGTAAAAAATATAATTTTTG
1 GGGT-AAAAATGTAATTTTTG
31600113 GATAGTTTAG
Statistics
Matches: 208, Mismatches: 30, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
57 5 0.02
58 39 0.19
59 131 0.63
60 27 0.13
61 6 0.03
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAATGAATTTTTAGAAGTTTCG
Found at i:31601243 original size:51 final size:51
Alignment explanation
Indices: 31601158--31601256 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
31601148 TTCACTTTCT
* *
31601158 TTATTATTAAATATTATTATCAAAAATATTTATTACTATTAATTATTATTA
1 TTATTATTAAAGATTATTATCAAAAATATATATTACTATTAATTATTATTA
* * * *
31601209 TTATTATTAAAGATTTATTATTAATAATA-ATATTAGTATTATTTATTA
1 TTATTATTAAAGA-TTATTATCAAAAATATATATTACTATTAATTATTA
31601257 AATACGTTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 28 0.68
52 13 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (51 bp):
TTATTATTAAAGATTATTATCAAAAATATATATTACTATTAATTATTATTA
Found at i:31602292 original size:21 final size:21
Alignment explanation
Indices: 31602222--31602298 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
31602212 AGAATACTAC
* *
31602222 TTCT-TTTGAATTAATTGTCT
1 TTCTGTTTGAATCAATTGTTT
* * **
31602242 TTATGTTTAAATTGATTG-TT
1 TTCTGTTTGAATCAATTGTTT
*
31602262 TT-TATTTGAATCAATTGTTT
1 TTCTGTTTGAATCAATTGTTT
31602282 TTCTGTTTGAATCAATT
1 TTCTGTTTGAATCAATT
31602299 CATTATTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
19 11 0.24
20 10 0.22
21 24 0.53
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.58
Consensus pattern (21 bp):
TTCTGTTTGAATCAATTGTTT
Found at i:31602314 original size:20 final size:20
Alignment explanation
Indices: 31602285--31602331 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31602275 ATTGTTTTTC
*
31602285 TGTTTGAATCAATTCATTAT
1 TGTTTAAATCAATTCATTAT
* * *
31602305 TGTTTAAATCGATTCTTTGT
1 TGTTTAAATCAATTCATTAT
31602325 TGTTTAA
1 TGTTTAA
31602332 CATGATTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.53
Consensus pattern (20 bp):
TGTTTAAATCAATTCATTAT
Found at i:31603354 original size:13 final size:14
Alignment explanation
Indices: 31603338--31603367 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
31603328 TGTTTAGGTG
31603338 TAATTTTT-AAAAA
1 TAATTTTTGAAAAA
31603351 TAATTTTTGAAAAA
1 TAATTTTTGAAAAA
31603365 TAA
1 TAA
31603368 AAATACGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
TAATTTTTGAAAAA
Found at i:31604155 original size:27 final size:26
Alignment explanation
Indices: 31604106--31604165 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
31604096 ACCAAACATG
* * *
31604106 TTTTCTTTATTAAAAATAATTTTTTA
1 TTTTATTTATCAAAAATAATTTTTAA
* *
31604132 TTTCTATTTATCAAATATATTTTTTAA
1 TTT-TATTTATCAAAAATAATTTTTAA
31604159 TTTTATT
1 TTTTATT
31604166 GAAAATGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTATTTATCAAAAATAATTTTTAA
Found at i:31604207 original size:26 final size:24
Alignment explanation
Indices: 31604165--31604215 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 24
31604155 TTAATTTTAT
*
31604165 TGAAAATGATAATTATTTTCTAAAAA
1 TGAAAATGATAAATA-TTTC-AAAAA
31604191 TGAAAATAGA-AAATATTTCAAAAA
1 TGAAAAT-GATAAATATTTCAAAAA
31604215 T
1 T
31604216 CAAAGGAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 6 0.26
25 4 0.17
26 11 0.48
27 2 0.09
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (24 bp):
TGAAAATGATAAATATTTCAAAAA
Found at i:31604371 original size:29 final size:31
Alignment explanation
Indices: 31604326--31604409 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 31
31604316 TGATTTAATA
* *
31604326 TGTAATTATATATAT-AAACTTTAATT-TGG
1 TGTAATTATACACATAAAACTTTAATTGTGG
*
31604355 TGTAATTATACACATAAAACTCTAATTGTGG
1 TGTAATTATACACATAAAACTTTAATTGTGG
* * * *
31604386 TTTAAATATACACTTGAAACTTTA
1 TGTAATTATACACATAAAACTTTA
31604410 CTTTTGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 13 0.29
30 10 0.22
31 22 0.49
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (31 bp):
TGTAATTATACACATAAAACTTTAATTGTGG
Found at i:31607849 original size:15 final size:15
Alignment explanation
Indices: 31607804--31607842 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
31607794 TGCTAAATTA
*
31607804 TTTAAATTAATTTAAT
1 TTTAAA-TAATTAAAT
*
31607820 ATTAAATAATTAAAT
1 TTTAAATAATTAAAT
31607835 TTTAAATA
1 TTTAAATA
31607843 TTGAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTAAATAATTAAAT
Found at i:31608650 original size:18 final size:20
Alignment explanation
Indices: 31608627--31608666 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
31608617 AAATTAAAAA
31608627 TAATAAA-AAAT-TAATTTT
1 TAATAAATAAATATAATTTT
31608645 TAATAAATAAATATAATTTT
1 TAATAAATAAATATAATTTT
31608665 TA
1 TA
31608667 TCTATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAAATAAATATAATTTT
Found at i:31608664 original size:19 final size:19
Alignment explanation
Indices: 31608627--31608684 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
31608617 AAATTAAAAA
31608627 TAATAAA-AAAT-TAATTTT
1 TAATAAATAAATATAA-TTT
31608645 TAATAAATAAATATAATTT
1 TAATAAATAAATATAATTT
* ** *
31608664 TTATCTATAAATATGATTT
1 TAATAAATAAATATAATTT
31608683 TA
1 TA
31608685 TTTAAATATG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 7 0.21
19 23 0.70
20 3 0.09
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TAATAAATAAATATAATTT
Found at i:31608692 original size:16 final size:18
Alignment explanation
Indices: 31608651--31608696 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
31608641 TTTTTAATAA
*
31608651 ATAAATATAATTTTTATCT
1 ATAAATATGA-TTTTATCT
31608670 ATAAATATGATTTTAT-T
1 ATAAATATGATTTTATCT
31608687 -TAAATATGAT
1 ATAAATATGAT
31608697 AATAATTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 6 0.23
19 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
ATAAATATGATTTTATCT
Found at i:31608748 original size:113 final size:118
Alignment explanation
Indices: 31608604--31608823 Score: 283
Period size: 113 Copynumber: 1.9 Consensus size: 118
31608594 AAAATAATTT
*
31608604 AATATAATTGGATAAATTAAAAATAAT-AAAAAATTAAT-TTTTAATA-AATAAATATAATTT-T
1 AATAAAATTGGATAAATTAAAAATAATAAAAAAATTAATGTTTTAATATAATAAATATAATTTAT
31608665 TATCTAT-AAATATGATTTTAT-TTAAATATGATAATAATTAGATCAATACTTA
66 T-TCTATCAAATATGATTTTATGTTAAATATGATAATAATTAGATCAATACTTA
* * * *
31608717 AATAAAATTGGATAAATTAAAAA-AATAAAAAAAATTTATGTTTTCATATAATTAATTTAATTTA
1 AATAAAATTGGATAAATTAAAAATAAT-AAAAAAATTAATGTTTTAATATAATAAATATAATTT-
* * * *
31608781 ATTTTTATCTAGTATGATTTTATGTTAACTATGATAATAATTA
64 ATTTCTATCAAATATGATTTTATGTTAAATATGATAATAATTA
31608824 AACCATGTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
112 3 0.03
113 22 0.24
114 10 0.11
115 7 0.08
116 12 0.13
117 4 0.04
118 14 0.16
119 18 0.20
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (118 bp):
AATAAAATTGGATAAATTAAAAATAATAAAAAAATTAATGTTTTAATATAATAAATATAATTTAT
TTCTATCAAATATGATTTTATGTTAAATATGATAATAATTAGATCAATACTTA
Found at i:31608915 original size:16 final size:18
Alignment explanation
Indices: 31608902--31608934 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31608892 GATAATATCA
31608902 AATAT-TGTTAATATAAT
1 AATATGTGTTAATATAAT
31608919 AATATGTGTT-ATATAA
1 AATATGTGTTAATATAA
31608935 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (18 bp):
AATATGTGTTAATATAAT
Found at i:31614798 original size:45 final size:45
Alignment explanation
Indices: 31614716--31615003 Score: 238
Period size: 45 Copynumber: 6.8 Consensus size: 45
31614706 ATAAATAAGA
** * *
31614716 AAGAGGAAGC-GCAGCCCGAGACCTTAACAGACAAGGAAGAGAAAA
1 AAGAGG-AGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAG
* * * *
31614761 AAAAGGAGCAGCAGACTGAGAGTTTACGAGACAAGGAAGAGAAAG
1 AAGAGGAGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAG
* * *
31614806 AGGAGGCGCAGCAGCCCAAGAGTTTACCAGACAAGGAAGAGAAAG
1 AAGAGGAGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAG
31614851 AAGAGGCA-CAGCAGCCCGAGAGTTTACCAGACAAGG-A-AG--AG
1 AAGAGG-AGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAG
* * *
31614892 AA-A-GA--TGC-GCCCAAAAGTTTACCAGACAAGG-A-AG--AG
1 AAGAGGAGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAG
* * *
31614928 AA-A-GA--TGC-GCCCAAGAGTTTACCAGACAAGGAAGAGAACG
1 AAGAGGAGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAG
* * *
31614968 AGGAGGCGCAGCATCCCGAGAGTTTACCAGACAAGG
1 AAGAGGAGCAGCAGCCCGAGAGTTTACCAGACAAGG
31615004 CTGCAAGTCC
Statistics
Matches: 204, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
36 56 0.27
37 3 0.01
38 3 0.01
39 1 0.00
40 3 0.01
41 5 0.02
42 1 0.00
43 2 0.01
44 6 0.03
45 124 0.61
ACGTcount: A:0.42, C:0.19, G:0.31, T:0.08
Consensus pattern (45 bp):
AAGAGGAGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAG
Found at i:31614911 original size:36 final size:36
Alignment explanation
Indices: 31614871--31614965 Score: 181
Period size: 36 Copynumber: 2.6 Consensus size: 36
31614861 GCAGCCCGAG
31614871 AGTTTACCAGACAAGGAAGAGAAAGATGCGCCCAAA
1 AGTTTACCAGACAAGGAAGAGAAAGATGCGCCCAAA
*
31614907 AGTTTACCAGACAAGGAAGAGAAAGATGCGCCCAAG
1 AGTTTACCAGACAAGGAAGAGAAAGATGCGCCCAAA
31614943 AGTTTACCAGACAAGGAAGAGAA
1 AGTTTACCAGACAAGGAAGAGAA
31614966 CGAGGAGGCG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.44, C:0.18, G:0.26, T:0.12
Consensus pattern (36 bp):
AGTTTACCAGACAAGGAAGAGAAAGATGCGCCCAAA
Found at i:31620057 original size:29 final size:29
Alignment explanation
Indices: 31620025--31620114 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
31620015 TTCAAATTTA
31620025 ATTAATTTTATTTATCTGGTTTCTGCTTC
1 ATTAATTTTATTTATCTGGTTTCTGCTTC
** * * ** *
31620054 ATT-ATTCAATTT-TTTTGTGTTCTATTTA
1 ATTAATTTTATTTATCTGGT-TTCTGCTTC
31620082 ATTAATTTTATTTATCTGGTTTCTGCTTC
1 ATTAATTTTATTTATCTGGTTTCTGCTTC
31620111 ATTA
1 ATTA
31620115 TTCAATTTTT
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
27 4 0.09
28 16 0.36
29 20 0.45
30 4 0.09
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (29 bp):
ATTAATTTTATTTATCTGGTTTCTGCTTC
Found at i:31620076 original size:28 final size:28
Alignment explanation
Indices: 31620045--31620133 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
31620035 TTTATCTGGT
31620045 TTCTGCTTCATTATTCAATTTTTTTGTG
1 TTCTGCTTCATTATTCAATTTTTTTGTG
** * ** * *
31620073 TTCTATTTAATTAATTTTATTTATCTG-G
1 TTCTGCTTCATT-ATTCAATTTTTTTGTG
31620101 TTTCTGCTTCATTATTCAATTTTTTTGTG
1 -TTCTGCTTCATTATTCAATTTTTTTGTG
31620130 TTCT
1 TTCT
31620134 ATTTAATTTT
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
28 24 0.55
29 20 0.45
ACGTcount: A:0.17, C:0.12, G:0.09, T:0.62
Consensus pattern (28 bp):
TTCTGCTTCATTATTCAATTTTTTTGTG
Found at i:31620108 original size:57 final size:57
Alignment explanation
Indices: 31620020--31620141 Score: 244
Period size: 57 Copynumber: 2.1 Consensus size: 57
31620010 TTAGTTTCAA
31620020 ATTTAATTAATTTTATTTATCTGGTTTCTGCTTCATTATTCAATTTTTTTGTGTTCT
1 ATTTAATTAATTTTATTTATCTGGTTTCTGCTTCATTATTCAATTTTTTTGTGTTCT
31620077 ATTTAATTAATTTTATTTATCTGGTTTCTGCTTCATTATTCAATTTTTTTGTGTTCT
1 ATTTAATTAATTTTATTTATCTGGTTTCTGCTTCATTATTCAATTTTTTTGTGTTCT
31620134 ATTTAATT
1 ATTTAATT
31620142 TTTTAATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (57 bp):
ATTTAATTAATTTTATTTATCTGGTTTCTGCTTCATTATTCAATTTTTTTGTGTTCT
Found at i:31620149 original size:28 final size:28
Alignment explanation
Indices: 31620061--31620150 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
31620051 TTCATTATTC
31620061 AATTTTTTTGTGTTCTATTTAATTAATTTT
1 AATTTTTTTGTGTTCTATTTAATT--TTTT
* * ** * * *
31620091 -ATTTATCTG-GTTTCTGCTTCATTATTC
1 AATTTTTTTGTG-TTCTATTTAATTTTTT
31620118 AATTTTTTTGTGTTCTATTTAATTTTTT
1 AATTTTTTTGTGTTCTATTTAATTTTTT
31620146 AATTT
1 AATTT
31620151 CATTCTTGGT
Statistics
Matches: 43, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
27 2 0.05
28 24 0.56
29 17 0.40
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (28 bp):
AATTTTTTTGTGTTCTATTTAATTTTTT
Found at i:31640315 original size:21 final size:21
Alignment explanation
Indices: 31640254--31640325 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
31640244 TGATGCAACC
* *
31640254 ACTGCTCCAGTTGAATCTTCC
1 ACTGCTCCAATTGAATCTTCA
31640275 A-TGGCTCCAATTGAATCTTCA
1 ACT-GCTCCAATTGAATCTTCA
* *
31640296 ACTTCTCCAATTG-ATCCTTCC
1 ACTGCTCCAATTGAAT-CTTCA
31640317 ACTGCTCCA
1 ACTGCTCCA
31640326 TCCCTTCCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.07
21 39 0.91
22 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (21 bp):
ACTGCTCCAATTGAATCTTCA
Found at i:31641733 original size:29 final size:30
Alignment explanation
Indices: 31641673--31641735 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
31641663 ACTTATTTTA
* * * * *
31641673 TTGTTAATTTTGTTATTATTTTATATGCAT
1 TTGTCAATTTGGTTACTATTTTAGATACAT
31641703 TTGTCAATTTGGTTACTATTTTAGA-ACAT
1 TTGTCAATTTGGTTACTATTTTAGATACAT
31641732 TTGT
1 TTGT
31641736 TTGTTAAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.24, C:0.06, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTCAATTTGGTTACTATTTTAGATACAT
Found at i:31641881 original size:13 final size:13
Alignment explanation
Indices: 31641852--31641888 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
31641842 TCATATATAT
31641852 TTAAAAATT-ATA
1 TTAAAAATTAATA
31641864 -T-AAAATTAATA
1 TTAAAAATTAATA
31641875 TTAAAAATTAATA
1 TTAAAAATTAATA
31641888 T
1 T
31641889 GGGCGGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.27
11 4 0.18
12 1 0.05
13 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAAAATTAATA
Found at i:31642295 original size:86 final size:87
Alignment explanation
Indices: 31642126--31642300 Score: 230
Period size: 86 Copynumber: 2.0 Consensus size: 87
31642116 TGAACATTCC
*
31642126 GTTTGAATTAAAAAAGGAAACTAGAGAAGAGGAATTTCTGAAAAAAAAAAAAAAGATAAATGATT
1 GTTTGAATTAAAAAAGGAAACTAGAGAAGAGGAATTTATG-AAAAAAAAAAAAAGATAAATGATT
*
31642191 CATCTTTCAAAGTGAGAGGGAGA
65 CATCTTTCAAAGTAAGAGGGAGA
* * * * * *
31642214 GTTTGAATTAAAAAATGAAACTAGATAAGATGATTTTATG-AAGAAAAGAAAAGATGAACA-G-T
1 GTTTGAATTAAAAAAGGAAACTAGAGAAGAGGAATTTATGAAAAAAAAAAAAAGAT-AA-ATGAT
31642276 TCATCTTTCAAAGTAAGAGGGAGA
64 TCATCTTTCAAAGTAAGAGGGAGA
31642300 G
1 G
31642301 AGCATTCGAG
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
86 38 0.49
87 3 0.04
88 36 0.47
ACGTcount: A:0.49, C:0.06, G:0.22, T:0.23
Consensus pattern (87 bp):
GTTTGAATTAAAAAAGGAAACTAGAGAAGAGGAATTTATGAAAAAAAAAAAAAGATAAATGATTC
ATCTTTCAAAGTAAGAGGGAGA
Found at i:31642647 original size:16 final size:16
Alignment explanation
Indices: 31642626--31642692 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
31642616 TGAATTAGTG
31642626 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* *
31642642 ATTACAATTCTATTTC
1 ATTACAACTCTATTCC
** * *
31642658 ATTATTACTTTATTTC
1 ATTACAACTCTATTCC
* *
31642674 ATTACGACTTTATTCC
1 ATTACAACTCTATTCC
31642690 ATT
1 ATT
31642693 CATCCTAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.01, T:0.49
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:31651457 original size:3 final size:3
Alignment explanation
Indices: 31651449--31651475 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31651439 AGTAGAAAGG
31651449 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
31651476 AACCATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:31652204 original size:3 final size:3
Alignment explanation
Indices: 31652192--31652225 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
31652182 ACATCTCCAT
31652192 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
31652226 TAACTACCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:31654539 original size:30 final size:30
Alignment explanation
Indices: 31654498--31654582 Score: 163
Period size: 30 Copynumber: 2.9 Consensus size: 30
31654488 AAGTAACCTA
31654498 ATATAA-GTCAACTTGTGTGAGCAACCTTG
1 ATATAATGTCAACTTGTGTGAGCAACCTTG
31654527 ATATAATGTCAACTTGTGTGAGCAACCTTG
1 ATATAATGTCAACTTGTGTGAGCAACCTTG
31654557 ATATAATGTCAACTTGTGTGAGCAAC
1 ATATAATGTCAACTTGTGTGAGCAAC
31654583 TTAATCACCT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 6 0.11
30 49 0.89
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (30 bp):
ATATAATGTCAACTTGTGTGAGCAACCTTG
Found at i:31659707 original size:110 final size:110
Alignment explanation
Indices: 31659514--31659736 Score: 385
Period size: 110 Copynumber: 2.0 Consensus size: 110
31659504 AACCTGCCTA
31659514 CTGATCAGATTAATTTCTTTTATCTGTTACATGGGAAACAAAGTTTAATGGGCCTTCTGTATGTC
1 CTGATCAGATTAATTTCTTTTATCTGTTACATGGGAAACAAAGTTTAATGGGCCTTCTGTATGTC
* *
31659579 CTAAGAACAAAATTTTGGAGTGGGGTTATTGAAGAAATGCTAAAG
66 CTAAGAACAAAATTTTGGAGTGAGGTTATTGAAGAAAGGCTAAAG
*
31659624 CTGATCAGATTAATTTCTTTTATCTGTTACATTGGAAACAAAGTTTAATGGGCCTTCTGTATGTC
1 CTGATCAGATTAATTTCTTTTATCTGTTACATGGGAAACAAAGTTTAATGGGCCTTCTGTATGTC
* *
31659689 CTAAGGGA-AACATTTTGGAGTGAGGTTATTGAAGAAAGGCTAAAG
66 CTAA-GAACAAAATTTTGGAGTGAGGTTATTGAAGAAAGGCTAAAG
31659734 CTG
1 CTG
31659737 TATTCTATAA
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 105 0.98
111 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (110 bp):
CTGATCAGATTAATTTCTTTTATCTGTTACATGGGAAACAAAGTTTAATGGGCCTTCTGTATGTC
CTAAGAACAAAATTTTGGAGTGAGGTTATTGAAGAAAGGCTAAAG
Found at i:31662920 original size:16 final size:16
Alignment explanation
Indices: 31662899--31662931 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31662889 AATCATATTT
31662899 TAAATAGAACAATATA
1 TAAATAGAACAATATA
31662915 TAAATAGAACAATATA
1 TAAATAGAACAATATA
31662931 T
1 T
31662932 TTAAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAATAGAACAATATA
Found at i:31662958 original size:24 final size:24
Alignment explanation
Indices: 31662931--31663002 Score: 58
Period size: 25 Copynumber: 3.0 Consensus size: 24
31662921 GAACAATATA
31662931 TTTA-AAAAATGAAAGAATTAAAAG
1 TTTATAAAAATGAAA-AATTAAAAG
* *
31662955 TTTATTAAAATTAAAAATTAAATCA-
1 TTTATAAAAATGAAAAATTAAA--AG
* * *
31662980 TTTTTAAATATAAAAAATTAAAA
1 TTTATAAAAATGAAAAATTAAAA
31663003 TTCAATGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
23 1 0.03
24 11 0.28
25 26 0.67
26 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (24 bp):
TTTATAAAAATGAAAAATTAAAAG
Found at i:31669643 original size:15 final size:15
Alignment explanation
Indices: 31669609--31669649 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
31669599 GTTTTTTACT
31669609 AAAATAATATA-AAA
1 AAAATAATATATAAA
**
31669623 AAAATAATATATATC
1 AAAATAATATATAAA
31669638 AAAATAATATAT
1 AAAATAATATAT
31669650 TCCTCCCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATAATATATAAA
Found at i:31669879 original size:27 final size:27
Alignment explanation
Indices: 31669848--31669900 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
31669838 GTATTTTTGG
*
31669848 GTGGTGTCTGTCTGGTAGGCGGCACCA
1 GTGGTGCCTGTCTGGTAGGCGGCACCA
31669875 GTGGTGCCTGTCTGGTAGGCGGCACC
1 GTGGTGCCTGTCTGGTAGGCGGCACC
31669901 TCATTCCTCG
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:0.25, G:0.42, T:0.25
Consensus pattern (27 bp):
GTGGTGCCTGTCTGGTAGGCGGCACCA
Found at i:31670831 original size:17 final size:17
Alignment explanation
Indices: 31670798--31670830 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
31670788 AATTCAATTG
31670798 ATATATTTAAATATTTT
1 ATATATTTAAATATTTT
31670815 ATATA-TTAAATATTTT
1 ATATATTTAAATATTTT
31670831 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTTAAATATTTT
Found at i:31672809 original size:6 final size:6
Alignment explanation
Indices: 31672798--31672840 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
31672788 TTTCAGCCGG
*
31672798 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC TTGAGC C
1 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC C
31672841 GCAGTCGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.19
Consensus pattern (6 bp):
CTGAGC
Found at i:31673284 original size:6 final size:6
Alignment explanation
Indices: 31673273--31673325 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
31673263 GGCCATTAAA
*
31673273 TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT
1 TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT
31673321 TATGT
1 TATGT
31673326 ATGCAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 1 0.02
6 41 0.95
7 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:31676318 original size:25 final size:25
Alignment explanation
Indices: 31676284--31676333 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
31676274 TTTGTTTCCT
31676284 TTCCTTCTTCAAAAATTTACTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
*
31676309 TTCCTTCTTCAAAAATTTGCTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
31676334 AACAGATCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (25 bp):
TTCCTTCTTCAAAAATTTACTGTTA
Found at i:31676625 original size:20 final size:23
Alignment explanation
Indices: 31676602--31676642 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
31676592 ATTTAATTTA
31676602 ATTTTTT-TA-AATT-TTATAAT
1 ATTTTTTCTACAATTCTTATAAT
31676622 ATTTTTTCTACAATTCTTATA
1 ATTTTTTCTACAATTCTTATA
31676643 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 4 0.22
23 5 0.28
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTTCTACAATTCTTATAAT
Found at i:31676831 original size:27 final size:27
Alignment explanation
Indices: 31676751--31676831 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
31676741 AAATAGGAGT
* * ** *
31676751 TGGTGCCACCTGATAGAAAGGCACCAT
1 TGGTGCCGCCTGACAGGTAGGCACCAC
31676778 TGGTGCCGCCTGACAGGTAGGCACCAC
1 TGGTGCCGCCTGACAGGTAGGCACCAC
*
31676805 TGGTGCCGCCTGTCAGGTAGGCACCAC
1 TGGTGCCGCCTGACAGGTAGGCACCAC
31676832 CCATTTATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (27 bp):
TGGTGCCGCCTGACAGGTAGGCACCAC
Found at i:31677884 original size:21 final size:21
Alignment explanation
Indices: 31677859--31677909 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
31677849 ATAATAGCAT
*
31677859 AATCCAAATATAAAGTTTAGA
1 AATCCAAATATAAAATTTAGA
* *
31677880 AATCCAAACATAAAATTTATA
1 AATCCAAATATAAAATTTAGA
31677901 AATCCAAAT
1 AATCCAAAT
31677910 TACAGAATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAGA
Found at i:31679285 original size:16 final size:18
Alignment explanation
Indices: 31679259--31679292 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31679249 GATACAAGTA
31679259 CTTGTAATAAA-TTTTTG
1 CTTGTAATAAACTTTTTG
31679276 CTTG-AATAAACTTTTTG
1 CTTGTAATAAACTTTTTG
31679293 AGTGGAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (18 bp):
CTTGTAATAAACTTTTTG
Found at i:31680019 original size:5 final size:5
Alignment explanation
Indices: 31680009--31680033 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31679999 ATTTGTAACT
31680009 CATTC CATTC CATTC CATTC CATTC
1 CATTC CATTC CATTC CATTC CATTC
31680034 ATTGTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
CATTC
Found at i:31682718 original size:12 final size:12
Alignment explanation
Indices: 31682703--31682727 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31682693 GTGAGAACTA
31682703 ATCCTAGAAGAT
1 ATCCTAGAAGAT
31682715 ATCCTAGAAGAT
1 ATCCTAGAAGAT
31682727 A
1 A
31682728 AGAAAGAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
ATCCTAGAAGAT
Found at i:31684374 original size:6 final size:6
Alignment explanation
Indices: 31684363--31684391 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31684353 CATTTCCTTT
31684363 CCCATG CCCATG CCCATG CCCATG CCCAT
1 CCCATG CCCATG CCCATG CCCATG CCCAT
31684392 CATCCTCATT
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:0.17, C:0.52, G:0.14, T:0.17
Consensus pattern (6 bp):
CCCATG
Found at i:31685107 original size:29 final size:30
Alignment explanation
Indices: 31685075--31685131 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
31685065 TAGTTTAATA
31685075 TGCAATTGTATACATG-AACTTTGATTTTG
1 TGCAATTGTATACATGAAACTTTGATTTTG
* * *
31685104 TGCAATTTTATCCATGAAATTTTGATTT
1 TGCAATTGTATACATGAAACTTTGATTT
31685132 GATCTAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (30 bp):
TGCAATTGTATACATGAAACTTTGATTTTG
Found at i:31686583 original size:17 final size:19
Alignment explanation
Indices: 31686556--31686594 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
31686546 GATATGGGAC
*
31686556 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
31686574 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
31686592 AAA
1 AAA
31686595 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:31688621 original size:29 final size:31
Alignment explanation
Indices: 31688548--31688628 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
31688538 AATCAAAATC
* *
31688548 AAAGTTTCAAGTATACATTTGA-ACCATAATT
1 AAAGTTTCACGTATACAATT-ACACCATAATT
* *
31688579 AGAGTTTCACGTATATAATTACACCA-AATT
1 AAAGTTTCACGTATACAATTACACCATAATT
*
31688609 AAAG-TTCATGTATACAATTA
1 AAAGTTTCACGTATACAATTA
31688629 TACATTAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 14 0.33
30 8 0.19
31 20 0.48
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (31 bp):
AAAGTTTCACGTATACAATTACACCATAATT
Found at i:31700504 original size:50 final size:50
Alignment explanation
Indices: 31700424--31700518 Score: 111
Period size: 50 Copynumber: 1.9 Consensus size: 50
31700414 TTAATGAGTT
* * * * *
31700424 TTTTCAAAAACTTTGGTAGATTTAATTGAAACTTTCAGAAATTTTAGAGG
1 TTTTAAAAAACTTTGGAAGATCTAAGTGAAACTTTCAAAAATTTTAGAGG
* *
31700474 TTTTAAAAAACTTT-GAAGAGTCTAAGTGAAATTTTTAAAAATTTT
1 TTTTAAAAAACTTTGGAAGA-TCTAAGTGAAACTTTCAAAAATTTT
31700519 CAAAGGTGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
49 4 0.11
50 33 0.89
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTAAAAAACTTTGGAAGATCTAAGTGAAACTTTCAAAAATTTTAGAGG
Found at i:31700599 original size:31 final size:32
Alignment explanation
Indices: 31700474--31700601 Score: 95
Period size: 31 Copynumber: 4.1 Consensus size: 32
31700464 ATTTTAGAGG
* * * *
31700474 TTTTAAAAAACTTTGAAGAGTCTAAGTGAAAT
1 TTTTAAAAAACTTTCAAGGGTCTAATTAAAAT
* * *
31700506 TTTT-AAAAATTTTCAAAGGTGTAA-TAATAAT
1 TTTTAAAAAACTTTCAAGGGTCTAATTAA-AAT
* **
31700537 TTTTAAAAAAATTT-GGGTGGTCTAATT-AAAT
1 TTTTAAAAAACTTTCAAG-GGTCTAATTAAAAT
* *
31700568 TTTTAAAATACTTT-AAGGGTATAATTAAAAT
1 TTTTAAAAAACTTTCAAGGGTCTAATTAAAAT
31700599 TTT
1 TTT
31700602 AGAAACTTTG
Statistics
Matches: 75, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
30 10 0.13
31 45 0.60
32 19 0.25
33 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.41
Consensus pattern (32 bp):
TTTTAAAAAACTTTCAAGGGTCTAATTAAAAT
Found at i:31704202 original size:125 final size:125
Alignment explanation
Indices: 31703980--31704205 Score: 434
Period size: 125 Copynumber: 1.8 Consensus size: 125
31703970 CAAAGAATCT
*
31703980 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAATGGAAA
1 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAAGGGAAA
31704045 ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAATTCTTTTTATTTTCATTGGCATG
66 ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAATTCTTTTTATTTTCATTGGCATG
31704105 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAAGGGAAA
1 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAAGGGAAA
*
31704170 ATTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAA
66 ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAA
31704206 TACTTCTCTT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 99 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.25
Consensus pattern (125 bp):
CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAAGGGAAA
ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAATTCTTTTTATTTTCATTGGCATG
Found at i:31707347 original size:15 final size:15
Alignment explanation
Indices: 31707327--31707359 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
31707317 CCACCTACAA
31707327 AAATATGATATTATT
1 AAATATGATATTATT
31707342 AAATATGATATTATT
1 AAATATGATATTATT
31707357 AAA
1 AAA
31707360 AACACAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
AAATATGATATTATT
Found at i:31708503 original size:3 final size:3
Alignment explanation
Indices: 31708495--31708525 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31708485 GGAGGAAGGA
31708495 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
31708526 AACAACATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31712399 original size:143 final size:143
Alignment explanation
Indices: 31712100--31712392 Score: 534
Period size: 143 Copynumber: 2.0 Consensus size: 143
31712090 TTTTCCTTCA
31712100 TGAAAAATCAATTAAATTGTTTATTGTTTGGTTCGTGTTGCTCAAGCCTAAATTTGATGCAAATT
1 TGAAAAATCAATTAAATTGTTTATTGTTTGGTTCGTGTTGCTCAAGCCTAAATTTGATGCAAATT
* *
31712165 GAGGTACGAGGATAACTGAGAAAACTTGAAAGTTAGAAACAATACAAATCCGTCTCCAATGAAGC
66 GAGGTACGAGGATAACTGAGAAAACCTGAAAATTAGAAACAATACAAATCCGTCTCCAATGAAGC
31712230 ATAAATATATTTT
131 ATAAATATATTTT
*
31712243 TGAAAAATCAATTAAATTGTTTATTGTTTGGTTCGTGTTGCTTAAGCCTAAATTTGATGCAAATT
1 TGAAAAATCAATTAAATTGTTTATTGTTTGGTTCGTGTTGCTCAAGCCTAAATTTGATGCAAATT
*
31712308 GAGGTACGAGGATAACTGAGAAAACCTGAAAATTGGAAACAATACAAATCCGTCTCGC-ATGAAG
66 GAGGTACGAGGATAACTGAGAAAACCTGAAAATTAGAAACAATACAAATCCGTCTC-CAATGAAG
31712372 CATAAATATATTTT
130 CATAAATATATTTT
31712386 TGAAAAA
1 TGAAAAA
31712393 AAAATTATTA
Statistics
Matches: 145, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
143 144 0.99
144 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (143 bp):
TGAAAAATCAATTAAATTGTTTATTGTTTGGTTCGTGTTGCTCAAGCCTAAATTTGATGCAAATT
GAGGTACGAGGATAACTGAGAAAACCTGAAAATTAGAAACAATACAAATCCGTCTCCAATGAAGC
ATAAATATATTTT
Found at i:31712440 original size:143 final size:141
Alignment explanation
Indices: 31712143--31712422 Score: 323
Period size: 143 Copynumber: 2.0 Consensus size: 141
31712133 CGTGTTGCTC
* * *
31712143 AAGCCTAAATTTGATGCAAATTGAGGTACGAGGATAACTGAGAAAACTTGAAAGTTAGAAACAAT
1 AAGCCAAAATTTGATGCAAATTGAGGTACGAGGATAACTGAGAAAACCTGAAAATTAGAAACAAT
** * ** *** *
31712208 ACAAATCCGTCTCCAATGAAGCATAAATATATTTTTGAAAAATCAATTAAATTGTTTATTGTTTG
66 ACAAATCCGTCTCCAATGAAGCATAAATATATTTTTGAAAAAAAAATT-AATTCTACAAAATAT-
** *** *
31712273 GTTCGTGTTGCTT
129 GCACAAATTACTT
* *
31712286 AAGCCTAAATTTGATGCAAATTGAGGTACGAGGATAACTGAGAAAACCTGAAAATTGGAAACAAT
1 AAGCCAAAATTTGATGCAAATTGAGGTACGAGGATAACTGAGAAAACCTGAAAATTAGAAACAAT
31712351 ACAAATCCGTCTCGC-ATGAAGCATAAATATATTTTTGAAAAAAAAATT-ATTACTACAAAATAT
66 ACAAATCCGTCTC-CAATGAAGCATAAATATATTTTTGAAAAAAAAATTAATT-CTACAAAATAT
31712414 -CACAAATTA
129 GCACAAATTA
31712423 ACTTGATTTT
Statistics
Matches: 117, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
140 3 0.03
141 3 0.03
142 4 0.03
143 106 0.91
144 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (141 bp):
AAGCCAAAATTTGATGCAAATTGAGGTACGAGGATAACTGAGAAAACCTGAAAATTAGAAACAAT
ACAAATCCGTCTCCAATGAAGCATAAATATATTTTTGAAAAAAAAATTAATTCTACAAAATATGC
ACAAATTACTT
Found at i:31718756 original size:24 final size:24
Alignment explanation
Indices: 31718728--31718788 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
31718718 AGAAATAATC
*
31718728 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
* *
31718752 TTTCAATTAAACTGTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
* *
31718776 TTTGAATCAAACT
1 TTTCAATTAAACT
31718789 TTTATTAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:31721180 original size:2 final size:2
Alignment explanation
Indices: 31721113--31721161 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
31721103 GATAAGAATA
31721113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31721155 AT AT AT A
1 AT AT AT A
31721162 CGTGTTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31722350 original size:68 final size:65
Alignment explanation
Indices: 31722231--31722360 Score: 156
Period size: 68 Copynumber: 2.0 Consensus size: 65
31722221 ATTATTTTTT
* * * *
31722231 AATTTTTTTAAAAATATTTATTTTATTTTAATATTTAATAAATTTATATATTTTTTATTTATTGA
1 AATTTTTTTAAAAATATTTATATTATTTTAATATTTAATAAATATATATATTATATATTTATTGA
*
31722296 AATTTTTTTATATAATCATTTAATATTATTTTAATATTTATATTAAA-ATA-ATATTATATATTT
1 AATTTTTTTA-AAAAT-ATTT-ATATTATTTTAATATTTA-A-TAAATATATATATTATATATTT
31722359 AT
61 AT
31722361 ATATTTATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
65 10 0.18
66 4 0.07
67 4 0.07
68 30 0.55
69 3 0.05
70 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (65 bp):
AATTTTTTTAAAAATATTTATATTATTTTAATATTTAATAAATATATATATTATATATTTATTGA
Found at i:31722406 original size:17 final size:18
Alignment explanation
Indices: 31722384--31722430 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
31722374 TTTAATATGT
31722384 TATAAATTATATA-AATA
1 TATAAATTATATATAATA
31722401 TATAAA-TATAATATAATA
1 TATAAATTAT-ATATAATA
*
31722419 TAAAATATTATA
1 TATAA-ATTATA
31722431 AACTTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 9 0.36
18 8 0.32
19 2 0.08
20 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAAATTATATATAATA
Found at i:31724162 original size:15 final size:15
Alignment explanation
Indices: 31724144--31724192 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
31724134 CAATATTAAT
*
31724144 ATGTGCAACATCAAC
1 ATGTGCAACATGAAC
* *
31724159 ATGTACAACATGAAT
1 ATGTGCAACATGAAC
31724174 ATGTGCAACATGAAC
1 ATGTGCAACATGAAC
31724189 ATGT
1 ATGT
31724193 ACAGGATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (15 bp):
ATGTGCAACATGAAC
Found at i:31724175 original size:30 final size:30
Alignment explanation
Indices: 31724127--31724195 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
31724117 ATGAAGAGGG
* * *
31724127 ACATGTCCAATATTAATATGTGCAACATCA
1 ACATGTACAACATGAATATGTGCAACATCA
*
31724157 ACATGTACAACATGAATATGTGCAACATGA
1 ACATGTACAACATGAATATGTGCAACATCA
31724187 ACATGTACA
1 ACATGTACA
31724196 GGATTGACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (30 bp):
ACATGTACAACATGAATATGTGCAACATCA
Found at i:31731369 original size:4 final size:4
Alignment explanation
Indices: 31731362--31731387 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31731352 CAGGTTTTAC
31731362 TGCA TGCA TGCA TGCA TGCA TGCA TG
1 TGCA TGCA TGCA TGCA TGCA TGCA TG
31731388 AATGAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (4 bp):
TGCA
Found at i:31733353 original size:30 final size:31
Alignment explanation
Indices: 31733298--31733359 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 31
31733288 TAATATATGA
*
31733298 AATATTAATTTTAAATATTTCTAATTA-ATT
1 AATATTAATTTTAAATAATTCTAATTAGATT
31733328 AATATTAATTGTTTAAA-AATT-TAATTAGATT
1 AATATTAA-T-TTTAAATAATTCTAATTAGATT
31733359 A
1 A
31733360 TATAAACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 14 0.50
31 8 0.29
32 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (31 bp):
AATATTAATTTTAAATAATTCTAATTAGATT
Done.