Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 1 of 203
Found at i:14087 original size:25 final size:28
Alignment explanation
Indices: 14053--14114 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
14043 TATTAAAATT
14053 AAATTAAATTAT-ATTTTTT-TAATATA
1 AAATTAAATTATAATTTTTTATAATATA
* *
14079 AAATT-AATTTTAATTTTTTATGATATA
1 AAATTAAATTATAATTTTTTATAATATA
*
14106 AAAATAAAT
1 AAATTAAAT
14115 ATTTTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 12 0.40
27 10 0.33
28 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
AAATTAAATTATAATTTTTTATAATATA
Found at i:15801 original size:29 final size:32
Alignment explanation
Indices: 15769--15828 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
15759 TTTTTGCTTC
15769 TTTCTTCAATCTAG-CCC-AATTGT-TTCCTT
1 TTTCTTCAATCTAGCCCCGAATTGTATTCCTT
* *
15798 TTTCTTCTATTTAGCCCCGAATTGTATTCCT
1 TTTCTTCAATCTAGCCCCGAATTGTATTCCT
15829 GCACAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 12 0.46
30 3 0.12
31 6 0.23
32 5 0.19
ACGTcount: A:0.17, C:0.27, G:0.08, T:0.48
Consensus pattern (32 bp):
TTTCTTCAATCTAGCCCCGAATTGTATTCCTT
Found at i:16894 original size:19 final size:19
Alignment explanation
Indices: 16870--16922 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
16860 GTTTTCCTAC
*
16870 AAAAATAAAATAAAATAGT
1 AAAAATAAAATAAAATAGG
16889 AAAAAT-AAATAATAATAGG
1 AAAAATAAAATAA-AATAGG
*
16908 AAAATTAAAA-AAAAT
1 AAAAATAAAATAAAAT
16923 TTCTTTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 9 0.30
19 18 0.60
20 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAAATAAAATAAAATAGG
Found at i:18904 original size:19 final size:19
Alignment explanation
Indices: 18882--18919 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18872 GAGGCTCTTT
*
18882 CCCTATTCTTTGGCTAAGA
1 CCCTATTCTTTGGCCAAGA
18901 CCCTATTCTTTGGCCAAGA
1 CCCTATTCTTTGGCCAAGA
18920 ACAGCTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (19 bp):
CCCTATTCTTTGGCCAAGA
Found at i:26769 original size:12 final size:12
Alignment explanation
Indices: 26752--26779 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
26742 GTTTTTATTT
26752 TATAATATAATA
1 TATAATATAATA
26764 TATAATATAATA
1 TATAATATAATA
26776 TATA
1 TATA
26780 TTCTTAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAATATAATA
Found at i:27734 original size:45 final size:44
Alignment explanation
Indices: 27670--27754 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
27660 GGTCAATACA
* *
27670 AAAATATATATTTTTAATTTTAATTTATTTTTTAATTATTTTTACC
1 AAAATATATA-TTTTAAATTTAATTT-TTTATTAATTATTTTTACC
*
27716 AAAA-ATATATTTTAAATTTAATTTTTTATTATTTATTTT
1 AAAATATATATTTTAAATTTAATTTTTTATTAATTATTTT
27755 AGATTTGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 13 0.36
44 14 0.39
45 5 0.14
46 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (44 bp):
AAAATATATATTTTAAATTTAATTTTTTATTAATTATTTTTACC
Found at i:34729 original size:20 final size:21
Alignment explanation
Indices: 34682--34729 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
34672 AATATTAGTT
*
34682 TTAAT-TAAAATAATATATTT
1 TTAATATAAAATAATATATTA
*
34702 TTTA-ATAAAATAATA-ATTA
1 TTAATATAAAATAATATATTA
34721 TTAATATAA
1 TTAATATAA
34730 TGACATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATATAAAATAATATATTA
Found at i:38094 original size:16 final size:18
Alignment explanation
Indices: 38055--38096 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
38045 TAAGTTTATA
38055 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
38072 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
38089 A-ATTTATA
1 ATATTTATA
38097 ACACATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:42059 original size:9 final size:9
Alignment explanation
Indices: 42045--42099 Score: 85
Period size: 9 Copynumber: 6.2 Consensus size: 9
42035 TTTGGTTAAA
*
42045 AATTACCCG
1 AATTAACCG
*
42054 AATTACCCG
1 AATTAACCG
42063 AATTAACCG
1 AATTAACCG
42072 AATTAACCG
1 AATTAACCG
42081 AATTAACCG
1 AATTAACCG
42090 AATT-ACCG
1 AATTAACCG
42098 AA
1 AA
42100 AAATGCCCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
8 6 0.13
9 39 0.87
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTAACCG
Found at i:42828 original size:13 final size:14
Alignment explanation
Indices: 42795--42833 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
42785 ATTGATACAA
42795 AATTTTAATATTTT
1 AATTTTAATATTTT
*
42809 AAATTTAAT-TTTT
1 AATTTTAATATTTT
*
42822 ATTTTTAATATT
1 AATTTTAATATT
42834 CAAACTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTTAATATTTT
Found at i:44547 original size:16 final size:17
Alignment explanation
Indices: 44526--44559 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
44516 TCTTTAGATA
*
44526 TTTAAA-TATTTTAATT
1 TTTAAATTATTATAATT
44542 TTTAAATTATTATAATT
1 TTTAAATTATTATAATT
44559 T
1 T
44560 GATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATTATTATAATT
Found at i:45400 original size:9 final size:9
Alignment explanation
Indices: 45388--45425 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
45378 ATTTAATATT
45388 ATTATAAAA
1 ATTATAAAA
*
45397 ATTATAACA
1 ATTATAAAA
45406 ATTATAAAA
1 ATTATAAAA
45415 ATTATAAAA
1 ATTATAAAA
45424 AT
1 AT
45426 ATTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
ATTATAAAA
Found at i:45760 original size:17 final size:17
Alignment explanation
Indices: 45738--45776 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
45728 GTAATAAAAG
45738 TAAAACCCTTTGACTTT
1 TAAAACCCTTTGACTTT
45755 TAAAACCCTTTGACTTT
1 TAAAACCCTTTGACTTT
45772 TAAAA
1 TAAAA
45777 GGTACCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (17 bp):
TAAAACCCTTTGACTTT
Found at i:46124 original size:29 final size:30
Alignment explanation
Indices: 46068--46133 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
46058 ATTTATAAAA
* * *
46068 AATTAAATTAAATAAAAAATTTACATATA-
1 AATTACATAAAATAAAAAATTGACATATAT
*
46097 AAGTTACATAAAAT-AAAAATTGATATATAT
1 AA-TTACATAAAATAAAAAATTGACATATAT
46127 AATTACA
1 AATTACA
46134 AAACTCGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (30 bp):
AATTACATAAAATAAAAAATTGACATATAT
Found at i:50169 original size:22 final size:23
Alignment explanation
Indices: 50150--50192 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
50140 CTTTTTTTAG
*
50150 GCTTTAATTTGGTAA-CTTTTGT
1 GCTTTAATTTGATAACCTTTTGT
50172 GCTTTAATTTGATAACCTTTT
1 GCTTTAATTTGATAACCTTTT
50193 TTTACAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (23 bp):
GCTTTAATTTGATAACCTTTTGT
Found at i:51175 original size:114 final size:114
Alignment explanation
Indices: 51013--51237 Score: 389
Period size: 114 Copynumber: 2.0 Consensus size: 114
51003 CTAATTTTTA
*
51013 ACTTAACTGTCTTATAAACATGACCGAAGTTTATTAATCATAAATGAAAATACAAATATGTATTT
1 ACTTAACTGTCTTATAAACATGACCGAAGTTTATTAATCATAAATGAAAATACAAACATGTATTT
*
51078 GAATTTAGGAATTTAAATAATTATAAAATGATATTTTAGATAGAATATG
66 GAATTTAGGAATTTAAATAATTATAAAATGATATTTTAAATAGAATATG
* * *
51127 ACTTAACTGTCTTATAAGCATGACC-AGAGTTTATTAATCATAAATGAAACTGCAAACATGTATT
1 ACTTAACTGTCTTATAAACATGACCGA-AGTTTATTAATCATAAATGAAAATACAAACATGTATT
51191 TGAATTTAGGAATTTAAATAATTATAAAATGATATTTTAAATAGAAT
65 TGAATTTAGGAATTTAAATAATTATAAAATGATATTTTAAATAGAAT
51238 TTTGTTACTT
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
113 1 0.01
114 104 0.99
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (114 bp):
ACTTAACTGTCTTATAAACATGACCGAAGTTTATTAATCATAAATGAAAATACAAACATGTATTT
GAATTTAGGAATTTAAATAATTATAAAATGATATTTTAAATAGAATATG
Found at i:56806 original size:25 final size:25
Alignment explanation
Indices: 56778--56858 Score: 92
Period size: 25 Copynumber: 3.3 Consensus size: 25
56768 AGCGCTCTCT
*
56778 TGAGCCATATAATGGGAAGCTCATG
1 TGAGCCATATAATAGGAAGCTCATG
* * *
56803 TGAGCCATATAACAGAAAGCTCATA
1 TGAGCCATATAATAGGAAGCTCATG
* *
56828 AGAGCCATA-ATTAGGAAGCTCATG
1 TGAGCCATATAATAGGAAGCTCATG
*
56852 CGAGCCA
1 TGAGCCA
56859 ATACTTGGTA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
24 17 0.37
25 29 0.63
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (25 bp):
TGAGCCATATAATAGGAAGCTCATG
Found at i:56977 original size:26 final size:25
Alignment explanation
Indices: 56948--57006 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
56938 GAAGCTCCGG
56948 AGAGCCATTAATCAGGAAACTCACAA
1 AGAGCCATTAATCAGGAAACTC-CAA
* * * *
56974 AGAGCCTTTAATCGGGAAGCTCCGA
1 AGAGCCATTAATCAGGAAACTCCAA
56999 AGAGCCAT
1 AGAGCCAT
57007 ATATCGGGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (25 bp):
AGAGCCATTAATCAGGAAACTCCAA
Found at i:57012 original size:25 final size:25
Alignment explanation
Indices: 56868--57020 Score: 95
Period size: 25 Copynumber: 6.2 Consensus size: 25
56858 AATACTTGGT
* *
56868 AGCTCCGATGAGCCAT-TAACGGGA
1 AGCTCCGAAGAGCCATATATCGGGA
* * *
56892 AGCTCCGGATAGCCATATATCTGGA
1 AGCTCCGAAGAGCCATATATCGGGA
* *
56917 AG-TTC-AAGTG--AGTCATATCGGGA
1 AGCTCCGAAGAGCCA-T-ATATCGGGA
* *
56940 AGCTCCGGAGAGCCAT-TAATCAGGA
1 AGCTCCGAAGAGCCATAT-ATCGGGA
* * *
56965 AACTCACAAAGAGCC-TTTAATCGGGA
1 AGCTC-CGAAGAGCCATAT-ATCGGGA
56991 AGCTCCGAAGAGCCATATATCGGGA
1 AGCTCCGAAGAGCCATATATCGGGA
*
57016 CGCTC
1 AGCTC
57021 ATAAGAACTG
Statistics
Matches: 96, Mismatches: 22, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 12 0.12
24 18 0.19
25 41 0.43
26 22 0.23
27 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.20
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATATATCGGGA
Found at i:61526 original size:30 final size:28
Alignment explanation
Indices: 61471--61528 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
61461 TAATGGTAAG
* *
61471 ATATATATATTACATTCTCAAATAATAT
1 ATATATATATTAAATTCTAAAATAATAT
*
61499 ATATATATATTTAAATTTTAAAGATAATAT
1 ATATATATA-TTAAATTCTAAA-ATAATAT
61529 TATTGAGAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.36
29 9 0.36
30 7 0.28
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (28 bp):
ATATATATATTAAATTCTAAAATAATAT
Found at i:61888 original size:2 final size:2
Alignment explanation
Indices: 61869--61907 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
61859 AAGATACTTT
*
61869 TA TA TA -A TCA TA TT TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61908 TGTGTAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62543 original size:14 final size:13
Alignment explanation
Indices: 62515--62539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62505 TGTCTATTCT
62515 TTTTTAATATTTA
1 TTTTTAATATTTA
62528 TTTTTAATATTT
1 TTTTTAATATTT
62540 TATTATACCT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATATTTA
Found at i:63495 original size:37 final size:37
Alignment explanation
Indices: 63451--63542 Score: 175
Period size: 37 Copynumber: 2.5 Consensus size: 37
63441 CACTTGTCCC
63451 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
*
63488 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
63525 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
63543 TAAAGCTATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
Found at i:63585 original size:52 final size:52
Alignment explanation
Indices: 63523--63974 Score: 754
Period size: 52 Copynumber: 8.8 Consensus size: 52
63513 CACTTTGTTT
* ** * *
63523 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
* *
63575 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC--T----TTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
63621 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
63673 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
63725 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
63777 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
63829 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
63881 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
* ** **
63933 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTT
63975 GTCACTTGAT
Statistics
Matches: 385, Mismatches: 9, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
46 43 0.11
48 1 0.00
50 1 0.00
52 340 0.88
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
Found at i:70725 original size:18 final size:18
Alignment explanation
Indices: 70704--70813 Score: 91
Period size: 18 Copynumber: 6.1 Consensus size: 18
70694 AATAAAAGAA
70704 TTTTAGAAACACGAAATT
1 TTTTAGAAACACGAAATT
* *
70722 TTTTAAAAACACGAAA-A
1 TTTTAGAAACACGAAATT
*
70739 TTTT-GAAACACGAGATTT
1 TTTTAGAAACACGA-AATT
* *
70757 TTTTTGAAAACACGAATTTT
1 TTTTAG-AAACACGAA-ATT
* *
70777 CTTTTTGAAACACGAAAAT
1 -TTTTAGAAACACGAAATT
*
70796 TTTTA-AAACACAAAATT
1 TTTTAGAAACACGAAATT
70813 T
1 T
70814 GTTTTTGAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.11
17 16 0.21
18 23 0.30
19 3 0.04
20 20 0.26
21 6 0.08
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (18 bp):
TTTTAGAAACACGAAATT
Found at i:70758 original size:16 final size:16
Alignment explanation
Indices: 70702--70813 Score: 62
Period size: 17 Copynumber: 6.3 Consensus size: 16
70692 AAAATAAAAG
*
70702 AATTTTAGAAACACGA
1 AATTTTTGAAACACGA
*
70718 AATTTTTTAAAAACACGA
1 AA-TTTTT-GAAACACGA
*
70736 AAATTTTGAAACACGA
1 AATTTTTGAAACACGA
*
70752 GATTTTTTTTGAAAACACGA
1 -A--ATTTTTG-AAACACGA
*
70772 ATTTTCTTTTTGAAACACGAA
1 A----ATTTTTGAAACACG-A
* *
70793 AATTTTTAAAACACAA
1 AATTTTTGAAACACGA
70809 AATTT
1 AATTT
70814 GTTTTTGAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
16 16 0.21
17 20 0.26
18 10 0.13
19 6 0.08
20 15 0.19
21 10 0.13
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (16 bp):
AATTTTTGAAACACGA
Found at i:70760 original size:36 final size:36
Alignment explanation
Indices: 70666--70772 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 36
70656 CTTTTTCTTT
* *
70666 TTTTGAAAACACGAATTTTTTTTTTAAAAATA-AAAGAA
1 TTTTG-AAACACGAA--TTTTTTTTAAAAACACGAAGAA
*
70704 TTTTAGAAACACGAA-ATTTTTTAAAAACACGAA-AA
1 TTTT-GAAACACGAATTTTTTTTAAAAACACGAAGAA
*
70739 TTTTGAAACACGAGATTTTTTTTGAAAACACGAA
1 TTTTGAAACACGA-ATTTTTTTTAAAAACACGAA
70773 TTTTCTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
34 9 0.15
35 19 0.32
36 18 0.30
38 13 0.22
39 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (36 bp):
TTTTGAAACACGAATTTTTTTTAAAAACACGAAGAA
Found at i:70826 original size:38 final size:37
Alignment explanation
Indices: 70757--71148 Score: 150
Period size: 38 Copynumber: 10.3 Consensus size: 37
70747 CACGAGATTT
* *
70757 TTTTTGAAAACACGAATTTTCTTTTTG-AAACACGAAAA
1 TTTTT-AAAACACAAAATTT-TTTTTGAAAACACGAAAA
**
70795 TTTTTAAAACACAAAATTTGTTTTTGAAAACATAAAAA
1 TTTTTAAAACACAAAATTT-TTTTTGAAAACACGAAAA
*
70833 TTTGGATAAAATACGAAACACAAGGATTTTTTTTG-AAACACGAAAA
1 TTT---T----TA--AAACACAA-AATTTTTTTTGAAAACACGAAAA
* * * *
70879 TTTTTGAAAGACGAGAATTTTTTTTGAAAACACGGAAA
1 TTTTTAAAACAC-AAAATTTTTTTTGAAAACACGAAAA
* * *
70917 TTTATGAAACACGGAAAATTTTTTTTGAAAACAAGAAAA
1 TTTTTAAAACAC--AAAATTTTTTTTGAAAACACGAAAA
** * ** *
70956 TTTTCGAAATACGGGAA---TTTTTGAAAACACGGGAAAT
1 TTTTTAAAACAC-AAAATTTTTTTTGAAAACAC--GAAAA
*
70993 TTTTTGAAAATACGAAAA---TTTTTG-AAACACTG-AAA
1 TTTTT-AAAACAC-AAAATTTTTTTTGAAAACAC-GAAAA
* * * *
71028 TTTTGAAAACACGAAGA---TTTTTG-AAACATGAGAA
1 TTTTTAAAACAC-AAAATTTTTTTTGAAAACACGAAAA
* * * *
71062 TTTTTGAAAACAC--GATTTTTTTTAAAAAACCCGGAAA
1 TTTTT-AAAACACAAAATTTTTTTT-GAAAACACGAAAA
* * * *
71099 TTTTTGAAACACAAGAAATTTTTCTGAAAACATGAAAA
1 TTTTTAAAACACAA-AATTTTTTTTGAAAACACGAAAA
*
71137 TTTTTGAAACAC
1 TTTTTAAAACAC
71149 GATTTTTTTT
Statistics
Matches: 277, Mismatches: 50, Indels: 54
0.73 0.13 0.14
Matches are distributed among these distances:
32 2 0.01
33 1 0.00
34 27 0.10
35 30 0.11
36 7 0.03
37 59 0.21
38 77 0.28
39 40 0.14
41 1 0.00
43 1 0.00
45 2 0.01
46 12 0.04
47 14 0.05
48 4 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (37 bp):
TTTTTAAAACACAAAATTTTTTTTGAAAACACGAAAA
Found at i:70835 original size:22 final size:20
Alignment explanation
Indices: 70795--70836 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
70785 AACACGAAAA
*
70795 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACAAAAAATTTG
70815 TTTTTGAAAACATAAAAATTTG
1 TTTTT-AAAACA-AAAAATTTG
70837 GATAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
TTTTTAAAACAAAAAATTTG
Found at i:70899 original size:16 final size:17
Alignment explanation
Indices: 70862--71150 Score: 168
Period size: 17 Copynumber: 15.8 Consensus size: 17
70852 ACAAGGATTT
70862 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* *
70879 TTTTTGAAAGACGAGAATTT
1 TTTTTGAAACACGA-AA--A
*
70899 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
*
70917 TTTATGAAACACGGAAAA
1 TTTTTGAAACAC-GAAAA
*
70935 TTTTTTTTGAAAACAAGAAAA
1 ---TTTTTG-AAACACGAAAA
* * **
70956 TTTTCGAAATACGGGAA
1 TTTTTGAAACACGAAAA
*
70973 TTTTTGAAAACACGGGAAAT
1 TTTTTG-AAACAC--GAAAA
*
70993 TTTTTGAAAATACGAAAA
1 TTTTTG-AAACACGAAAA
71011 TTTTTGAAACACTG-AAA
1 TTTTTGAAACAC-GAAAA
*
71028 -TTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
* *
71045 TTTTTGAAACATGAGAA
1 TTTTTGAAACACGAAAA
***
71062 TTTTTGAAAACACGATTT
1 TTTTTG-AAACACGAAAA
* * *
71080 TTTTTAAAAAACCCGGAAA
1 TTTTT--GAAACACGAAAA
*
71099 TTTTTGAAACACAAGAAAT
1 TTTTTGAAACAC--GAAAA
*
71118 TTTTCTGAAAACATGAAAA
1 TTTT-TG-AAACACGAAAA
71137 TTTTTGAAACACGA
1 TTTTTGAAACACGA
71151 TTTTTTTTAA
Statistics
Matches: 206, Mismatches: 43, Indels: 46
0.70 0.15 0.16
Matches are distributed among these distances:
16 6 0.03
17 73 0.35
18 51 0.25
19 26 0.13
20 24 0.12
21 21 0.10
22 5 0.02
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:70937 original size:39 final size:38
Alignment explanation
Indices: 70858--70977 Score: 147
Period size: 39 Copynumber: 3.2 Consensus size: 38
70848 AAACACAAGG
*
70858 ATTTTTTTTG-AAACACGAAAATTTTTGAAAGAC-GAGA
1 ATTTTTTTTGAAAACACGAAAA-TTTTGAAACACGGAGA
* *
70895 ATTTTTTTTGAAAACACGGAAATTTATGAAACACGGAAA
1 ATTTTTTTTGAAAACACGAAAATTT-TGAAACACGGAGA
* *
70934 ATTTTTTTTGAAAACAAGAAAATTTTCGAAATACGG-GA
1 ATTTTTTTTGAAAACACGAAAATTTT-GAAACACGGAGA
70972 ATTTTT
1 ATTTTT
70978 GAAAACACGG
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
37 13 0.18
38 25 0.35
39 34 0.47
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (38 bp):
ATTTTTTTTGAAAACACGAAAATTTTGAAACACGGAGA
Found at i:71329 original size:18 final size:18
Alignment explanation
Indices: 71268--71334 Score: 100
Period size: 17 Copynumber: 3.7 Consensus size: 18
71258 TGATTCTATT
*
71268 AAAACATGAGAATTTAAAA
1 AAAACACGAGAATTT-AAA
71287 AAAACACGAGAATTT-AA
1 AAAACACGAGAATTTAAA
*
71304 ATAACACGAGAATTTAAA
1 AAAACACGAGAATTTAAA
71322 AAAACACGAGAAT
1 AAAACACGAGAAT
71335 CGTGTTTAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
17 16 0.36
18 14 0.32
19 14 0.32
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.18
Consensus pattern (18 bp):
AAAACACGAGAATTTAAA
Found at i:71449 original size:27 final size:29
Alignment explanation
Indices: 71419--71476 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
71409 TGCCTTATTT
* *
71419 ATTGAAATT-ATTTAAATTTAAAATA-AA
1 ATTGAAATTAAATTAAATTAAAAATATAA
71446 ATTGAAATTAAATTAAATTAAAAATATAA
1 ATTGAAATTAAATTAAATTAAAAATATAA
71475 AT
1 AT
71477 ACAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 9 0.33
28 14 0.52
29 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTGAAATTAAATTAAATTAAAAATATAA
Found at i:74642 original size:20 final size:19
Alignment explanation
Indices: 74600--74645 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
74590 TGTGCTTATT
74600 TTATATA-TATATACATAC
1 TTATATATTATATACATAC
* *
74618 TTATATATTATTTATATAC
1 TTATATATTATATACATAC
74637 TCTATATAT
1 T-TATATAT
74646 ATACACGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 10 0.42
20 7 0.29
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATATATTATATACATAC
Found at i:83265 original size:10 final size:11
Alignment explanation
Indices: 83233--83266 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
83223 CTAACAATTC
83233 TAAAATATATT
1 TAAAATATATT
83244 TAAAA-ATATT
1 TAAAATATATT
83254 TAAAATAT-TT
1 TAAAATATATT
83264 TAA
1 TAA
83267 TATTTACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAAATATATT
Found at i:88659 original size:23 final size:23
Alignment explanation
Indices: 88563--88662 Score: 121
Period size: 23 Copynumber: 4.3 Consensus size: 23
88553 TAGTGTTATT
*
88563 TATCAGTGGTAGCTTTGGCTACA
1 TATCAGTGGTAGCTTCGGCTACA
* * *
88586 TTTCAGTGGTAGCTACGGGTACA
1 TATCAGTGGTAGCTTCGGCTACA
*
88609 T-TACAGTGGTAGCTTCGACTACA
1 TAT-CAGTGGTAGCTTCGGCTACA
*
88632 TATCAGTGGTAGCTTTGGCTACA
1 TATCAGTGGTAGCTTCGGCTACA
*
88655 CATCAGTG
1 TATCAGTG
88663 TGACACTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
22 1 0.02
23 63 0.97
24 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (23 bp):
TATCAGTGGTAGCTTCGGCTACA
Found at i:91410 original size:103 final size:103
Alignment explanation
Indices: 91224--91432 Score: 382
Period size: 103 Copynumber: 2.0 Consensus size: 103
91214 TGTGATCGGC
* *
91224 CCACCTTAAAAATAATTTTGGTCTGCGAAATTTGAGAACACAGGCTCGGAAGTCAGTTACGCACG
1 CCACCTTAAAAATAATTTTGGTCTGCGAAATTTGAGAAAACAAGCTCGGAAGTCAGTTACGCACG
* *
91289 AGGAAGGATTAGCGCCCTCGTAACGCCCAAAATTGGTA
66 AGGAAGGATTAACACCCTCGTAACGCCCAAAATTGGTA
91327 CCACCTTAAAAATAATTTTGGTCTGCGAAATTTGAGAAAACAAGCTCGGAAGTCAGTTACGCACG
1 CCACCTTAAAAATAATTTTGGTCTGCGAAATTTGAGAAAACAAGCTCGGAAGTCAGTTACGCACG
91392 AGGAAGGATTAACACCCTCGTAACGCCCAAAATTGGTA
66 AGGAAGGATTAACACCCTCGTAACGCCCAAAATTGGTA
91430 CCA
1 CCA
91433 AATTGAATTT
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (103 bp):
CCACCTTAAAAATAATTTTGGTCTGCGAAATTTGAGAAAACAAGCTCGGAAGTCAGTTACGCACG
AGGAAGGATTAACACCCTCGTAACGCCCAAAATTGGTA
Found at i:95366 original size:100 final size:100
Alignment explanation
Indices: 94755--95340 Score: 949
Period size: 100 Copynumber: 5.9 Consensus size: 100
94745 TTGAAAAGTA
* * *
94755 AAAAGGTTGAAGCCACAACGGCAGATCTTACTTCCTTAGTAGTACAGTGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
94820 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
* * *
94855 AAAATATTGAAGCCACAACGGCGGATCTTATTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
* *
94920 TGACAGCGGATCTGGTTTCCCTGATATTGCGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
94955 AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
95020 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
*
95055 AAAGGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
95120 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
* *
95155 AAAGGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGTAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
* *
95220 TGACGGCGGATCTGGTTTCCCTGATCTTGCGATTT
66 CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
* * * * * * * * *
95255 AAAAGATTGAAGCCACGACGACGGATCTTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCT
1 AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAG-CAGTACAGCGGAGCAGATTGAAGCT
*
95319 ACGACGGCGAATCTGGTTTCCC
65 ACGACGGCGGATCTGGTTTCCC
95341 CAACATTGCA
Statistics
Matches: 455, Mismatches: 30, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
99 1 0.00
100 454 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTACAGCGGAGCAGATTGAAGCTA
CGACGGCGGATCTGGTTTCCCTGATATTGCGATTT
Found at i:96622 original size:8 final size:8
Alignment explanation
Indices: 96609--96638 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
96599 ACCTGTTGAG
96609 TTTTTTTA
1 TTTTTTTA
96617 TTTTTTTA
1 TTTTTTTA
96625 -TTTTTTA
1 TTTTTTTA
96632 TTTTTTT
1 TTTTTTT
96639 CTCATTCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:96630 original size:15 final size:15
Alignment explanation
Indices: 96610--96638 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
96600 CCTGTTGAGT
96610 TTTTTTATTTTTTTA
1 TTTTTTATTTTTTTA
96625 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
96639 CTCATTCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTATTTTTTTA
Found at i:97111 original size:15 final size:17
Alignment explanation
Indices: 97070--97115 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
97060 ATTATCATTG
*
97070 TATCCTCATTATTATAT
1 TATCCTTATTATTATAT
*
97087 TATGCATTATT-TT-TAT
1 TAT-CCTTATTATTATAT
97103 TATCCTTATTATT
1 TATCCTTATTATT
97116 TTCAGGCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 6 0.25
16 8 0.33
17 5 0.21
18 5 0.21
ACGTcount: A:0.26, C:0.13, G:0.02, T:0.59
Consensus pattern (17 bp):
TATCCTTATTATTATAT
Found at i:97244 original size:22 final size:22
Alignment explanation
Indices: 97218--97259 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
97208 TTTATTTTCA
97218 TATTTT-TTTAATATATTATACT
1 TATTTTATTT-ATATATTATACT
*
97240 TATTTTATTTATATTTTATA
1 TATTTTATTTATATATTATA
97260 AAGTACATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTATTTATATATTATACT
Found at i:99406 original size:38 final size:39
Alignment explanation
Indices: 99364--99442 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 39
99354 GTTTTTTTTT
* * *
99364 ATATTTTTAATGATTTTAATGA-TTTTTAATTTTTAAAA
1 ATATTTTTAATAATTTTAATGATTTTTTAAATTTAAAAA
* **
99402 ATATTTTTTATAATTTTTTTGATTTTTTAAATTTAAAAA
1 ATATTTTTAATAATTTTAATGATTTTTTAAATTTAAAAA
99441 AT
1 AT
99443 TAATTAAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 18 0.53
39 16 0.47
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (39 bp):
ATATTTTTAATAATTTTAATGATTTTTTAAATTTAAAAA
Found at i:102143 original size:100 final size:98
Alignment explanation
Indices: 102027--102256 Score: 424
Period size: 100 Copynumber: 2.3 Consensus size: 98
102017 TGTCTAACAA
*
102027 ATACTGCTAACAAATGTGTTATAAATTTAATGTATGTATGTATATAAAACATTAAAGTCCTATAA
1 ATACTGCTAACAAATGTGTTATAAATTTAATGTATGTATGTAAATAAAACATTAAAGTCCTATAA
*
102092 GTCACATAAGTCCACATGTATGTATATAATGTCAG
66 GTCACATAAGT-C-CATGTATGTATATAATGACAG
102127 ATACTGCTAACAAATGTGTTATAAATTTAATGTATGTATGTAAATAAAACATTAAAGTCCTATAA
1 ATACTGCTAACAAATGTGTTATAAATTTAATGTATGTATGTAAATAAAACATTAAAGTCCTATAA
102192 GTCACATAAGTCCATGTATGTATATAATGACAG
66 GTCACATAAGTCCATGTATGTATATAATGACAG
102225 ATACTGCTAACAAATGTGTTATAAATTTAATG
1 ATACTGCTAACAAATGTGTTATAAATTTAATG
102257 CTTCATTTAG
Statistics
Matches: 128, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 52 0.41
99 1 0.01
100 75 0.59
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (98 bp):
ATACTGCTAACAAATGTGTTATAAATTTAATGTATGTATGTAAATAAAACATTAAAGTCCTATAA
GTCACATAAGTCCATGTATGTATATAATGACAG
Found at i:105062 original size:26 final size:28
Alignment explanation
Indices: 105027--105082 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
105017 TTTGTTCAAA
105027 TTTAAGATTT-AATTTATATACT-TAAT
1 TTTAAGATTTAAATTTATATACTATAAT
* * *
105053 TTTAATATTTAAATTTTTATTCTATAAT
1 TTTAAGATTTAAATTTATATACTATAAT
105081 TT
1 TT
105083 AATCAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 10 0.40
28 6 0.24
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTAAGATTTAAATTTATATACTATAAT
Found at i:106346 original size:26 final size:27
Alignment explanation
Indices: 106306--106371 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 27
106296 TCAATAGTGG
106306 TCACACGAG-CTGTGAAATGGGTCTGC
1 TCACACGAGTCTGTGAAATGGGTCTGC
106332 TCACACGAGTC-GTGAAATGGGTCTGC
1 TCACACGAGTCTGTGAAATGGGTCTGC
* *
106358 TTACATGAGT-TGTG
1 TCACACGAGTCTGTG
106372 GGTTGGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 35 0.97
27 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (27 bp):
TCACACGAGTCTGTGAAATGGGTCTGC
Found at i:108185 original size:18 final size:18
Alignment explanation
Indices: 108162--108198 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
108152 AAAAATGTTG
108162 ATAAATATATAA-ACTAAT
1 ATAAATA-ATAATACTAAT
108180 ATAAATAATAATACTAAT
1 ATAAATAATAATACTAAT
108198 A
1 A
108199 ATAATGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATACTAAT
Found at i:108515 original size:17 final size:17
Alignment explanation
Indices: 108493--108533 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
108483 GGACTGGGGT
108493 TATAAATAACCCAATTG
1 TATAAATAACCCAATTG
108510 TATAAAT-ACCCAATTG
1 TATAAATAACCCAATTG
108526 TATAAATA
1 TATAAATA
108534 TCATGCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.32
Consensus pattern (17 bp):
TATAAATAACCCAATTG
Found at i:108691 original size:26 final size:26
Alignment explanation
Indices: 108651--108716 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 26
108641 TCAATAGTGT
108651 TCACACGAGCTGTGAAATGGGTCTGC
1 TCACACGAGCTGTGAAATGGGTCTGC
108677 TCACACGAG-TCGTGAAATGGGTCTGC
1 TCACACGAGCT-GTGAAATGGGTCTGC
* *
108703 TTACATGAGCTGTG
1 TCACACGAGCTGTG
108717 GGTTGGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
25 1 0.03
26 34 0.94
27 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (26 bp):
TCACACGAGCTGTGAAATGGGTCTGC
Found at i:109137 original size:35 final size:35
Alignment explanation
Indices: 109093--109161 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
109083 GATACTTTTA
109093 TTCAATTAAGTACTTCAAATAACTTCAAGTATTCT
1 TTCAATTAAGTACTTCAAATAACTTCAAGTATTCT
109128 TTCAATTAAGTACTTCAAATAACTTCAAGTATTC
1 TTCAATTAAGTACTTCAAATAACTTCAAGTATTC
109162 AACTCAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (35 bp):
TTCAATTAAGTACTTCAAATAACTTCAAGTATTCT
Found at i:110635 original size:3 final size:3
Alignment explanation
Indices: 110627--110652 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
110617 TATTTTCTCC
110627 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
110653 TTCATGTACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:110936 original size:19 final size:20
Alignment explanation
Indices: 110900--110942 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
110890 TACCCTTTTT
* *
110900 ATATTTTTATTTTGTTATAA
1 ATATTTTTATATTATTATAA
*
110920 ATATTTTT-TATTATTATAT
1 ATATTTTTATATTATTATAA
110939 ATAT
1 ATAT
110943 ATTCCATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
ATATTTTTATATTATTATAA
Found at i:112648 original size:30 final size:30
Alignment explanation
Indices: 112613--112773 Score: 204
Period size: 30 Copynumber: 5.4 Consensus size: 30
112603 TCATGTTTAA
112613 AAAATTACATTTTGACCCCTAAAATTTTCT
1 AAAATTACATTTTGACCCCTAAAATTTTCT
*
112643 AAAATTACATTTTGACCCCTAAACTTTT-T
1 AAAATTACATTTTGACCCCTAAAATTTTCT
**
112672 CAAAATTACATTTCAACCCCTAAAATTTTCT
1 -AAAATTACATTTTGACCCCTAAAATTTTCT
*
112703 -AAATTACATTTTGACCCTTAAAA-TTTCTT
1 AAAATTACATTTTGACCCCTAAAATTTTC-T
* * *
112732 GAAATTACATTTTGACCCTTAAACTTTATC-
1 AAAATTACATTTTGACCCCTAAAATTT-TCT
112762 AAAATTACATTT
1 AAAATTACATTT
112774 CGGCCCTAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
28 4 0.03
29 22 0.19
30 85 0.73
31 3 0.03
32 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAAATTTTCT
Found at i:113327 original size:27 final size:26
Alignment explanation
Indices: 113287--113337 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
113277 TGAACGAAGG
113287 AGAAGAAAAAAAAAAGAAGAAAAAAGA
1 AGAAGAAAAAAAAAA-AAGAAAAAAGA
** *
113314 AGAAGAAAGGAAAAAAATAAAAAA
1 AGAAGAAAAAAAAAAAAGAAAAAA
113338 ATAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (26 bp):
AGAAGAAAAAAAAAAAAGAAAAAAGA
Found at i:114189 original size:18 final size:16
Alignment explanation
Indices: 114141--114187 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
114131 AAAAAACTAA
114141 TCGTGTTTCAAAATTT
1 TCGTGTTTCAAAATTT
*
114157 TCATGTTTTCAAAATTT
1 TCGTG-TTTCAAAATTT
114174 CTCGTGTTTCAAAA
1 -TCGTGTTTCAAAA
114188 ATAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (16 bp):
TCGTGTTTCAAAATTT
Found at i:114311 original size:18 final size:18
Alignment explanation
Indices: 114283--114682 Score: 230
Period size: 17 Copynumber: 22.3 Consensus size: 18
114273 AAATAAAATT
114283 GTGTTTT-AAAAATTTTC
1 GTGTTTTCAAAAATTTTC
114300 GTGTTTTCAAAAAAATTTCTC
1 GTGTTTTC--AAAAATTT-TC
**
114321 GTGTTTTCAAAAATTCCC
1 GTGTTTTCAAAAATTTTC
*
114339 GT-ATTTC-AAAATTTTC
1 GTGTTTTCAAAAATTTTC
*
114355 -TCGTTTTCAGAAAAAAATTTCC
1 GT-GTTTTC----AAAAATTTTC
* *
114377 GTGTTTT-ATAAATTTCC
1 GTGTTTTCAAAAATTTTC
*
114394 GTGTTTTCAAAAA-TTCC
1 GTGTTTTCAAAAATTTTC
*
114411 GAT-ATTTCAAAAATTTTC
1 G-TGTTTTCAAAAATTTTC
*
114429 GTGTTTTC-AAAATTTCTG
1 GTGTTTTCAAAAATTT-TC
* ** *
114447 GTG-ATAAAAAAAATTT-
1 GTGTTTTCAAAAATTTTC
114463 GTGTTTTCAAGGAAAATTTT-
1 GTGTTTTC-A--AAAATTTTC
**
114483 GTG-TTTCAAAAATCCTC
1 GTGTTTTCAAAAATTTTC
*
114500 GTGTTTTCAAAAA-TTCC
1 GTGTTTTCAAAAATTTTC
114517 GGTGTTTT-AAAAATTTTC
1 -GTGTTTTCAAAAATTTTC
**
114535 GTGTTTTCAAAAAAAAATT-
1 GTGTTTTC--AAAAATTTTC
114554 -TG-TTTCAAAAATTTTC
1 GTGTTTTCAAAAATTTTC
* **
114570 ATGTTTTCAAAAAATTCCC
1 GTGTTTTC-AAAAATTTTC
114589 GTGTTTT-AAAAA-TTTC
1 GTGTTTTCAAAAATTTTC
114605 AGTGTTTTCAAAAATTTTC
1 -GTGTTTTCAAAAATTTTC
* * *
114624 GTATTTTTAAGAATTTTC
1 GTGTTTTCAAAAATTTTC
* * *
114642 GTG-TCTCTAAAATTCTC
1 GTGTTTTCAAAAATTTTC
*
114659 ATGTTTT-AAAAATTTTTC
1 GTGTTTTCAAAAA-TTTTC
114677 GTGTTT
1 GTGTTT
114683 AAAAAAAAAT
Statistics
Matches: 295, Mismatches: 50, Indels: 75
0.70 0.12 0.18
Matches are distributed among these distances:
15 8 0.03
16 18 0.06
17 105 0.36
18 86 0.29
19 29 0.10
20 25 0.08
21 10 0.03
22 13 0.04
23 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (18 bp):
GTGTTTTCAAAAATTTTC
Found at i:114402 original size:56 final size:56
Alignment explanation
Indices: 114283--114693 Score: 215
Period size: 53 Copynumber: 7.6 Consensus size: 56
114273 AAATAAAATT
*
114283 GTGTTTTAAAAATTTTCGTGTTTTCAAAAAAATTTCTCGTGTTTTCAAAAATTCCC
1 GTGTTTTCAAAATTTTCGTGTTTTCAAAAAAATTTCTCGTGTTTTCAAAAATTCCC
* * *
114339 GT-ATTTCAAAATTTTC-TCGTTTTCAGAAAAAAATTTC-CGTGTTTT-ATAAATTTCC
1 GTGTTTTCAAAATTTTCGT-GTTTTC--AAAAAAATTTCTCGTGTTTTCAAAAATTCCC
* * * * **
114394 GTGTTTTCAAAAATTCCGAT-ATTTC--AAAAATTT-TCGTGTTTTCAAAATTTCTG
1 GTGTTTTCAAAATTTTCG-TGTTTTCAAAAAAATTTCTCGTGTTTTCAAAAATTCCC
* *** * *
114447 GTGATAAAAAAAATTT-GTGTTTTCAAGGAAAATTT-T-GTG-TTTCAAAAA-TCCTC
1 GTGTTTTCAAAATTTTCGTGTTTTCAA-AAAAATTTCTCGTGTTTTCAAAAATTCC-C
* * *****
114500 GTGTTTTCAAAAATTCCGGTGTTTT---AAAAATTT-TCGTGTTTTCAAAAAAAAAT
1 GTGTTTTCAAAATTTTC-GTGTTTTCAAAAAAATTTCTCGTGTTTTCAAAAATTCCC
* * * * *
114553 TTG-TTTCAAAAATTTTCATGTTTTC-AAAAAA-TTCCCGTGTTTT-AAAAATTTCA
1 GTGTTTTC-AAAATTTTCGTGTTTTCAAAAAAATTTCTCGTGTTTTCAAAAATTCCC
* * * * * *
114606 GTGTTTTCAAAAATTTTCGTATTTT--TAAGAATTT-TCGTG-TCTCTAAAATTCTC
1 GTGTTTTC-AAAATTTTCGTGTTTTCAAAAAAATTTCTCGTGTTTTCAAAAATTCCC
* * **
114659 ATGTTTTAAAAATTTTTCGTGTTTAAAAAAAAATT
1 GTGTTTTCAAAA-TTTTCGTGTTTTCAAAAAAATT
114694 GTTTCAAAAA
Statistics
Matches: 267, Mismatches: 60, Indels: 57
0.70 0.16 0.15
Matches are distributed among these distances:
51 9 0.03
52 42 0.16
53 92 0.34
54 38 0.14
55 49 0.18
56 25 0.09
57 11 0.04
58 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (56 bp):
GTGTTTTCAAAATTTTCGTGTTTTCAAAAAAATTTCTCGTGTTTTCAAAAATTCCC
Found at i:114425 original size:35 final size:34
Alignment explanation
Indices: 114283--114620 Score: 193
Period size: 35 Copynumber: 9.4 Consensus size: 34
114273 AAATAAAATT
*
114283 GTGTTTT-AAAAATTTTCGTGTTTTCAAAAAAATTTCTC
1 GTGTTTTCAAAAA-TTCCGTG-TTTC--AAAAATTTC-C
* *
114321 GTGTTTTCAAAAATTCCCGTATTTC-AAAATTTTC
1 GTGTTTTCAAAAATT-CCGTGTTTCAAAAATTTCC
* *
114355 -TCGTTTTCAGAAAAAAATTTCCGTGTTTTATAAATTTCC
1 GT-GTTTTC----AAAAA-TTCCGTGTTTCAAAAATTTCC
* *
114394 GTGTTTTCAAAAATTCCGATATTTCAAAAATTTTC
1 GTGTTTTCAAAAATTCCG-TGTTTCAAAAATTTCC
* * ***
114429 GTGTTTTCAAAATTTCTGGTGATAAAAAAAATTT--
1 GTGTTTTCAAAAATTC-CGTG-TTTCAAAAATTTCC
** *
114463 GTGTTTTCAAGGAAAATTTTGTGTTTCAAAAA-TCCTC
1 GTGTTTTC-A--AAAATTCCGTGTTTCAAAAATTTC-C
* *
114500 GTGTTTTCAAAAATTCCGGTGTTTTAAAAATTTTC
1 GTGTTTTCAAAAATTCC-GTGTTTCAAAAATTTCC
***** *
114535 GTGTTTTCAAAAAAAAATTTGTTTCAAAAATTTTC
1 GTGTTTTC-AAAAATTCCGTGTTTCAAAAATTTCC
* * *
114570 ATGTTTTCAAAAAATTCCCGTGTTTTAAAAATTTCA
1 GTGTTTTC-AAAAATT-CCGTGTTTCAAAAATTTCC
114606 GTGTTTTCAAAAATT
1 GTGTTTTCAAAAATT
114621 TTCGTATTTT
Statistics
Matches: 232, Mismatches: 45, Indels: 49
0.71 0.14 0.15
Matches are distributed among these distances:
33 1 0.00
34 27 0.12
35 102 0.44
36 40 0.17
37 13 0.06
38 25 0.11
39 23 0.10
40 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (34 bp):
GTGTTTTCAAAAATTCCGTGTTTCAAAAATTTCC
Found at i:114564 original size:106 final size:105
Alignment explanation
Indices: 114366--114620 Score: 246
Period size: 106 Copynumber: 2.4 Consensus size: 105
114356 CGTTTTCAGA
* * * *
114366 AAAAAATTTCCGTGTTTTATAAATTTCCGTGTTTTCAAAAATTCCGATATTTCAAAAATTTTCGT
1 AAAAAATTCCCGTGTTTCAAAAATCT-CGTGTTTTCAAAAATTCCGATATTTCAAAAATTTTCGT
**** *
114431 GTTTTCAAAATTTCTGGTGATAAAAAAAATTT-GTGTTTTC
65 GTTTTCAAAAAAAATGGTGATAAAAAAAATTTCATGTTTTC
** * * *
114471 AAGGAAAATT-TTGTGTTTCAAAAATCCTCGTGTTTTCAAAAATTCCGGTGTTTTAAAAATTTTC
1 AA--AAAATTCCCGTGTTTCAAAAAT-CTCGTGTTTTCAAAAATTCCGATATTTCAAAAATTTTC
* * ** *
114535 GTGTTTTCAAAAAAAAAT-TTGTTTCAAAAATTTTCATGTTTTC
63 GTGTTTTC-AAAAAAAATGGTGATAAAAAAAATTTCATGTTTTC
* *
114578 AAAAAATTCCCGTGTTTTAAAAATTTCAGTGTTTTCAAAAATT
1 AAAAAATTCCCGTGTTTCAAAAATCTC-GTGTTTTCAAAAATT
114621 TTCGTATTTT
Statistics
Matches: 121, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
105 10 0.08
106 90 0.74
107 21 0.17
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (105 bp):
AAAAAATTCCCGTGTTTCAAAAATCTCGTGTTTTCAAAAATTCCGATATTTCAAAAATTTTCGTG
TTTTCAAAAAAAATGGTGATAAAAAAAATTTCATGTTTTC
Found at i:118732 original size:9 final size:9
Alignment explanation
Indices: 118718--118754 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
118708 TAATAAATAA
118718 AAAATATAT
1 AAAATATAT
118727 AAAATATAT
1 AAAATATAT
118736 AAAAT-TAT
1 AAAATATAT
*
118744 TAAATAT-T
1 AAAATATAT
118752 AAA
1 AAA
118755 TAAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 10 0.40
9 15 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATATAT
Found at i:125101 original size:36 final size:36
Alignment explanation
Indices: 125059--125130 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
125049 ATGTAATATA
*
125059 TATAAATACCTTTTTATATGTGTATCTATTTAACCC
1 TATAAATACCTTTTTATATGTGTATCTATATAACCC
125095 TATAAATACCTTTTTATATGTGTATCTATATAACCC
1 TATAAATACCTTTTTATATGTGTATCTATATAACCC
125131 CTCTTTTACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.46
Consensus pattern (36 bp):
TATAAATACCTTTTTATATGTGTATCTATATAACCC
Found at i:134891 original size:12 final size:12
Alignment explanation
Indices: 134874--134898 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
134864 TTCGATGATT
134874 CAGGTGAATAGA
1 CAGGTGAATAGA
134886 CAGGTGAATAGA
1 CAGGTGAATAGA
134898 C
1 C
134899 TCGAGGCAAT
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:0.40, C:0.12, G:0.32, T:0.16
Consensus pattern (12 bp):
CAGGTGAATAGA
Found at i:137690 original size:44 final size:44
Alignment explanation
Indices: 137531--138023 Score: 189
Period size: 44 Copynumber: 11.0 Consensus size: 44
137521 TAGACCGAAG
* * *
137531 AATTTCAGATCTTATCTCCCTGAGGTTACAGTGAAGCAGATT-G
1 AATTTAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAA
*** * * * * *
137574 AAGCCAGAGATCTTATCTCCCTTAGATTACAGCGGAGTAGATCCAA
1 AATTTA-AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGAT-TAA
* * ** * * * *
137620 GA--CACTATCCTATCTCCCTAAAGTTACAGTGGAGCGGATTAA
1 AATTTAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAA
* * * **
137662 AATTTAAGATCTTATCTCTCTGAGGTTACAGTAGAGTAGA-TCG
1 AATTTAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAA
* * * * * **
137705 CATCT--GGTCTTATCTCCCTGAGGTTACAGTGTAGTAGACCGAAA
1 AATTTAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA--TTAA
* * * * **
137749 AAATTCAGATCTTATCTCCCTAAGATTACAGCAGAGCAGATTGAA
1 AATTTAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-AA
* * * **
137794 GATAGT-A-ATCCTATCTCCCTGAAATTACAGTGGAGCAGATTAA
1 AAT-TTAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAA
* ** * *
137837 AA-TAAAGGATCTTATCTCCCTGAAATTATAGTGGAGCGGATTAA
1 AATTTAA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAA
* * * * *
137881 AA-TAAAGGATCTTATCTCTCTG-GAGTTACAGTAGAGTAGATCACA
1 AATTTAA-GATCTTATCTCCCTGAG-GTTACAGTGGAGCAGATTA-A
* * * *
137926 TCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAA
1 --A-ATTTAA---G---ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAA
* * ** *
137979 AATTTAGGATCTTATCTCCCTGAGATTACAACGGAGTAGATTAA
1 AATTTAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAA
138023 A
1 A
138024 GACACTATCC
Statistics
Matches: 327, Mismatches: 96, Indels: 53
0.69 0.20 0.11
Matches are distributed among these distances:
41 29 0.09
42 4 0.01
43 35 0.11
44 186 0.57
45 5 0.02
46 28 0.09
47 2 0.01
48 1 0.00
49 3 0.01
50 4 0.01
51 2 0.01
53 1 0.00
54 27 0.08
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
AATTTAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAA
Found at i:137691 original size:87 final size:86
Alignment explanation
Indices: 137543--137864 Score: 251
Period size: 87 Copynumber: 3.7 Consensus size: 86
137533 TTTCAGATCT
* * * * *** * *
137543 TATCTCCCTGAGGTTACAGTGAAGCAGATTGAAGCCAGAGATCTTATCTCCCTTAGATTACAGCG
1 TATCTCCCTAAAGTTACAGTGGAGCAGATTAAAATTA-AGATCTTATCTCCCTGAGATTACAGCA
137608 GAGTAGATCCAAGACACT-ATCC
65 GAGTAGAT-CAAGACACTAATCC
* * * *
137630 TATCTCCCTAAAGTTACAGTGGAGCGGATTAAAATTTAAGATCTTATCTCTCTGAGGTTACAGTA
1 TATCTCCCTAAAGTTACAGTGGAGCAGATTAAAA-TTAAGATCTTATCTCCCTGAGATTACAGCA
** *
137695 GAGTAGATC--G-CATCTGGTCT
65 GAGTAGATCAAGACA-CTAATCC
* * * * * *
137715 TATCTCCCTGAGGTTACAGTGTAGTAGACCGA-AAAAATTCAGATCTTATCTCCCTAAGATTACA
1 TATCTCCCTAAAGTTACAGTG--G-AG-CAGATTAAAATTAAGATCTTATCTCCCTGAGATTACA
* * * *
137779 GCAGAGCAGATTGAAGATAGTAATCC
62 GCAGAGTAGA-TCAAGACACTAATCC
* *
137805 TATCTCCCTGAAA-TTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCCCTGAAATTA
1 TATCTCCCT-AAAGTTACAGTGGAGCAGATTAAAATTAA-GATCTTATCTCCCTGAGATTA
137865 TAGTGGAGCG
Statistics
Matches: 182, Mismatches: 39, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
83 2 0.01
84 3 0.02
85 21 0.12
86 4 0.02
87 98 0.54
88 28 0.15
89 3 0.02
90 21 0.12
91 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (86 bp):
TATCTCCCTAAAGTTACAGTGGAGCAGATTAAAATTAAGATCTTATCTCCCTGAGATTACAGCAG
AGTAGATCAAGACACTAATCC
Found at i:138100 original size:44 final size:44
Alignment explanation
Indices: 137947--138106 Score: 128
Period size: 44 Copynumber: 3.7 Consensus size: 44
137937 CCGATAATCC
** **
137947 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATTTAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATAAAGGATCT
** * * ** *
137991 TATCTCCCTG-AGATTACAACGGAGTAGATT-AAAGACACTATCC
1 TATCTCCCTGAAG-TTACAGTGGAGTAGATTAAAATAAAGGATCT
* * * *
138034 TATCCCCCTG-AGATTTCAGTAGAGTGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAG-TTACAGTGGAGTAGATTAAAATAAAGGATCT
* *
138078 TATCTCTCTGAAGTTACAGTAGAGTAGAT
1 TATCTCCCTGAAGTTACAGTGGAGTAGAT
138107 CGTGTCAGAT
Statistics
Matches: 88, Mismatches: 25, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
43 33 0.38
44 53 0.60
45 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATAAAGGATCT
Found at i:138103 original size:87 final size:87
Alignment explanation
Indices: 137943--138106 Score: 206
Period size: 87 Copynumber: 1.9 Consensus size: 87
137933 GAAGCCGATA
* * **
137943 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATTTAGGATCTTATCTCCCTGAGATTAC
1 ATCCTATCCCCCTGAAGTTACAGTAGAGCGGATTAAAATAAAGGATCTTATCTCCCTGAGATTAC
*
138008 AACGGAGTAGATTAAAGACACT
66 AACAGAGTAGATTAAAGACACT
* * *
138030 ATCCTATCCCCCTG-AGATTTCAGTAGAGTGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTT
1 ATCCTATCCCCCTGAAG-TTACAGTAGAGCGGATTAAAATAAAGGATCTTATCTCCCTGAGA-TT
**
138093 ACAGTAGAGTAGAT
64 ACAACAGAGTAGAT
138107 CGTGTCAGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 3 0.05
87 62 0.95
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (87 bp):
ATCCTATCCCCCTGAAGTTACAGTAGAGCGGATTAAAATAAAGGATCTTATCTCCCTGAGATTAC
AACAGAGTAGATTAAAGACACT
Found at i:143495 original size:22 final size:23
Alignment explanation
Indices: 143457--143504 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
143447 ATAGTTCATA
143457 AAGGAGTGAGATTAAA-TAAATG
1 AAGGAGTGAGATTAAATTAAATG
*
143479 AAGGATTGA-ATTGAAATTTAAATG
1 AAGGAGTGAGATT-AAA-TTAAATG
143503 AA
1 AA
143505 ATTAAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 3 0.14
22 11 0.50
24 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (23 bp):
AAGGAGTGAGATTAAATTAAATG
Found at i:147003 original size:72 final size:70
Alignment explanation
Indices: 146892--147023 Score: 201
Period size: 72 Copynumber: 1.9 Consensus size: 70
146882 TGTTTTTAGA
*
146892 AAAGTTAGGGCAAAATTAAAGAAAATTAAAGAAGAAAAGGGTAGCAAGAAAACTACGTTTATCAT
1 AAAGTTAGGGCAAAATAAAAGAAAATTAAAGAAGAAAAGGGTAGCAAGAAAACTACGTTTATCAT
146957 TTTTT
66 TTTTT
* * * *
146962 AAAGTTTGGGCAAAAATAAAAGGAAATTTAAAGAGGCAAAGGGTAGCAAGAAAACTACGTTT
1 AAAGTTAGGGC-AAAATAAAA-GAAAATTAAAGAAGAAAAGGGTAGCAAGAAAACTACGTTT
147024 TATTTTATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 10 0.18
71 8 0.15
72 37 0.67
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (70 bp):
AAAGTTAGGGCAAAATAAAAGAAAATTAAAGAAGAAAAGGGTAGCAAGAAAACTACGTTTATCAT
TTTTT
Found at i:148444 original size:31 final size:31
Alignment explanation
Indices: 148401--148502 Score: 147
Period size: 31 Copynumber: 3.4 Consensus size: 31
148391 ACATTTAAAC
*
148401 AAAAGTGCCTAAAATGTAATTTGATACAAAT
1 AAAAGTGACTAAAATGTAATTTGATACAAAT
* *
148432 AAAAGTGACTAAAATGTAACATT--T-CAAAC
1 AAAAGTGACTAAAATGTAA-TTTGATACAAAT
148461 AAAAGTGACTAAAATGTAATTTGATACAAAT
1 AAAAGTGACTAAAATGTAATTTGATACAAAT
148492 AAAAGTGACTA
1 AAAAGTGACTA
148503 TTTTTGTAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
28 2 0.03
29 23 0.37
30 2 0.03
31 33 0.53
32 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (31 bp):
AAAAGTGACTAAAATGTAATTTGATACAAAT
Found at i:148469 original size:29 final size:29
Alignment explanation
Indices: 148375--148479 Score: 142
Period size: 29 Copynumber: 3.6 Consensus size: 29
148365 ACAATAATGT
148375 AAGTGACTAAAATGTAACATTT-AAACAA
1 AAGTGACTAAAATGTAACATTTCAAACAA
* * *
148403 AAGTGCCTAAAATGTAA-TTTGATACAAATAA
1 AAGTGACTAAAATGTAACATT--T-CAAACAA
148434 AAGTGACTAAAATGTAACATTTCAAACAA
1 AAGTGACTAAAATGTAACATTTCAAACAA
148463 AAGTGACTAAAATGTAA
1 AAGTGACTAAAATGTAA
148480 TTTGATACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
27 2 0.03
28 16 0.24
29 24 0.36
30 1 0.02
31 21 0.32
32 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.26
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATTTCAAACAA
Found at i:148479 original size:60 final size:59
Alignment explanation
Indices: 148375--148502 Score: 238
Period size: 60 Copynumber: 2.2 Consensus size: 59
148365 ACAATAATGT
*
148375 AAGTGACTAAAATGTAACATTTAAACAAAAGTGCCTAAAATGTAATTTGATACAAATAA
1 AAGTGACTAAAATGTAACATTTAAACAAAAGTGACTAAAATGTAATTTGATACAAATAA
148434 AAGTGACTAAAATGTAACATTTCAAACAAAAGTGACTAAAATGTAATTTGATACAAATAA
1 AAGTGACTAAAATGTAACATTT-AAACAAAAGTGACTAAAATGTAATTTGATACAAATAA
148494 AAGTGACTA
1 AAGTGACTA
148503 TTTTTGTAGT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 22 0.33
60 45 0.67
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (59 bp):
AAGTGACTAAAATGTAACATTTAAACAAAAGTGACTAAAATGTAATTTGATACAAATAA
Found at i:149906 original size:20 final size:20
Alignment explanation
Indices: 149883--149920 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
149873 ATATTTTTAG
149883 ATTTGTAAAAATA-TATACAT
1 ATTTG-AAAAATATTATACAT
149903 ATTTGAAAAATATTATAC
1 ATTTGAAAAATATTATAC
149921 CCCTGAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTTGAAAAATATTATACAT
Found at i:150712 original size:22 final size:22
Alignment explanation
Indices: 150658--150713 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
150648 AATACCCTTA
*
150658 AAATATATATATATTTTTTGTTTT
1 AAATA-ATA-ATATTTGTTGTTTT
*
150682 --ATAAAAATATTTGTTGTTTT
1 AAATAATAATATTTGTTGTTTT
150702 AAATAATAATAT
1 AAATAATAATAT
150714 AAATTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 13 0.48
21 2 0.07
22 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
AAATAATAATATTTGTTGTTTT
Found at i:151167 original size:41 final size:41
Alignment explanation
Indices: 151117--151202 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
151107 ATTAAGAAAC
*
151117 AAATGAACTTTCTCAATTCTTTGAGAA-AAACAAAATTAAAA
1 AAATGAACTTTCTCAATTCTTCGAGAACAAA-AAAATTAAAA
*
151158 AAATGAACTTTCTCAATTCTTCGAGAACAAAAAGATTAAAA
1 AAATGAACTTTCTCAATTCTTCGAGAACAAAAAAATTAAAA
151199 AAAT
1 AAAT
151203 TTAATGCTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 39 0.93
42 3 0.07
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (41 bp):
AAATGAACTTTCTCAATTCTTCGAGAACAAAAAAATTAAAA
Found at i:160520 original size:20 final size:20
Alignment explanation
Indices: 160497--160540 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
160487 ACAATGTTCC
160497 TATTGGGAATACAAATCCTT
1 TATTGGGAATACAAATCCTT
160517 TATTGGGAATACAAATCCTT
1 TATTGGGAATACAAATCCTT
160537 TATT
1 TATT
160541 ATTGATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
TATTGGGAATACAAATCCTT
Found at i:163697 original size:45 final size:45
Alignment explanation
Indices: 163633--163721 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
163623 TTTACTACGA
* *
163633 ACATCACTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCACTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
*
163678 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCACTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
163722 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (45 bp):
ACATCACTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:167696 original size:27 final size:27
Alignment explanation
Indices: 167658--167712 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
167648 CTAAAAACTC
167658 TATCGTCAGTGTACCAAATATCATATA
1 TATCGTCAGTGTACCAAATATCATATA
167685 TATCGTCAGTGTACCAAATATCATATA
1 TATCGTCAGTGTACCAAATATCATATA
167712 T
1 T
167713 TTATACGATT
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:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (27 bp):
TATCGTCAGTGTACCAAATATCATATA
Found at i:168202 original size:21 final size:21
Alignment explanation
Indices: 168178--168233 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
168168 GGTAAAACTT
168178 TTTTGGTGTTGTAATATGCTA
1 TTTTGGTGTTGTAATATGCTA
** * **
168199 TTTTCTTTTTAAAATATGCTA
1 TTTTGGTGTTGTAATATGCTA
168220 TTTTGGTGTTGTAA
1 TTTTGGTGTTGTAA
168234 AATTTAATAT
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.55
Consensus pattern (21 bp):
TTTTGGTGTTGTAATATGCTA
Found at i:170620 original size:41 final size:41
Alignment explanation
Indices: 170563--170644 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
170553 TTGATGATCA
170563 GCTTCATCACATCTCACATCCAATATCCAAAAGACATAAAT
1 GCTTCATCACATCTCACATCCAATATCCAAAAGACATAAAT
170604 GCTTCATCACATCTCACATCCAATATCCAAAAGACATAAAT
1 GCTTCATCACATCTCACATCCAATATCCAAAAGACATAAAT
170645 CTCTTCATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.29, G:0.05, T:0.24
Consensus pattern (41 bp):
GCTTCATCACATCTCACATCCAATATCCAAAAGACATAAAT
Found at i:173461 original size:29 final size:28
Alignment explanation
Indices: 173394--173467 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
173384 TTAGCCTTAA
**
173394 TTAATTTTTTAAAATATATTTATATTTT
1 TTAATTTTTTAAAATATATTTATAAATT
*
173422 TTAATAATTTTAAAATATATTTTTATAAATT
1 TTAAT-TTTTTAAAATATA--TTTATAAATT
*
173453 TTGATTTTTTAAAAT
1 TTAATTTTTTAAAAT
173468 TTTAAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 5 0.13
29 12 0.32
30 9 0.24
31 12 0.32
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
TTAATTTTTTAAAATATATTTATAAATT
Found at i:176653 original size:22 final size:22
Alignment explanation
Indices: 176627--176671 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
176617 ATCTCAACAA
176627 CATCAATCCTTCAATCAACTAT
1 CATCAATCCTTCAATCAACTAT
176649 CATCAATCCTTCAATCAACTAT
1 CATCAATCCTTCAATCAACTAT
176671 C
1 C
176672 TTTTCATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (22 bp):
CATCAATCCTTCAATCAACTAT
Found at i:182470 original size:25 final size:25
Alignment explanation
Indices: 182442--182520 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
182432 AACACACCAC
* **
182442 AGCTCGTATGAGCTTACTGATTTGT
1 AGCTCGTATGAGCTTACCGATTCAT
182467 AGCTCGTGA-GAGCTTACCGATTCAT
1 AGCTCGT-ATGAGCTTACCGATTCAT
182492 AGCTCGTATGAGCTTACCGATTCAT
1 AGCTCGTATGAGCTTACCGATTCAT
182517 AGCT
1 AGCT
182521 TGTGAAAGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTCAT
Found at i:182520 original size:50 final size:50
Alignment explanation
Indices: 182442--182552 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 50
182432 AACACACCAC
* ** * *
182442 AGCTCGTATGAGCTTACTGATTTGTAGCTCGTGAGAGCTTACCGATTCAT
1 AGCTCGTATGAGCTTACCGATTCATAGCTCGTGAAAGCATACCGATTCAT
* * *
182492 AGCTCGTATGAGCTTACCGATTCATAGCTTGTGAAAGCATATCGATTTAT
1 AGCTCGTATGAGCTTACCGATTCATAGCTCGTGAAAGCATACCGATTCAT
*
182542 AGCTCGAATGA
1 AGCTCGTATGA
182553 CCATACATGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (50 bp):
AGCTCGTATGAGCTTACCGATTCATAGCTCGTGAAAGCATACCGATTCAT
Found at i:185084 original size:18 final size:18
Alignment explanation
Indices: 185061--185109 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
185051 CTTTTTTATT
*
185061 TTCCCCCAAAACTTTTAC
1 TTCCCCCAAAAATTTTAC
185079 TTCCCCCTAAAAAATTTTAC
1 TTCCCCC--AAAAATTTTAC
185099 TTCCTCCCAAA
1 TTCC-CCCAAA
185110 CCCCCAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.26
19 3 0.11
20 14 0.52
21 3 0.11
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.33
Consensus pattern (18 bp):
TTCCCCCAAAAATTTTAC
Found at i:185144 original size:74 final size:72
Alignment explanation
Indices: 185001--185160 Score: 207
Period size: 75 Copynumber: 2.2 Consensus size: 72
184991 AAAAAAAACC
* * * *
185001 CTTTTACTTTCCCCAAAAATTTTACTTCCCCCAAACCCCAAAATATTTTTCTTTTTTATTTTCCC
1 CTTTTACTTCCCCCAAAAATTTTACTTCCCCCAAACCCCAAAACATTTTTCTCTTCTATTTTCCC
185066 CC-AAAA
66 CCAAAAA
*
185072 CTTTTACTTCCCCCTAAAAAATTTTACTTCCTCCCAAACCCCCAAAACGTTTTTC-CTTCTATTT
1 CTTTTACTTCCCCC--AAAAATTTTACTTCC-CCCAAA-CCCCAAAACATTTTTCTCTTCTATTT
**
185136 TCTTCCAAAAA
62 TCCCCCAAAAA
185147 CTTTTACTTCCCCC
1 CTTTTACTTCCCCC
185161 CCAACCCCAA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
71 13 0.17
73 15 0.19
74 17 0.22
75 32 0.42
ACGTcount: A:0.26, C:0.34, G:0.01, T:0.39
Consensus pattern (72 bp):
CTTTTACTTCCCCCAAAAATTTTACTTCCCCCAAACCCCAAAACATTTTTCTCTTCTATTTTCCC
CCAAAAA
Found at i:186757 original size:20 final size:22
Alignment explanation
Indices: 186723--186781 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
186713 TTTGCCCCAA
* *
186723 AGTGCCACTAACACTT-A-TGT
1 AGTGCCACTATCACTTCACCGT
*
186743 AGTGCCACTTTCACTTGCACCGT
1 AGTGCCACTATCACTT-CACCGT
186766 AGTGCCACTATCACTT
1 AGTGCCACTATCACTT
186782 GCGAGCATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 14 0.44
22 1 0.03
23 17 0.53
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (22 bp):
AGTGCCACTATCACTTCACCGT
Found at i:200693 original size:17 final size:17
Alignment explanation
Indices: 200667--200714 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
200657 GAATAATCCC
*
200667 GTTGAAAACAACTTGAT
1 GTTGAGAACAACTTGAT
200684 GTTGAGAACAACTT--T
1 GTTGAGAACAACTTGAT
200699 GTTG-GAACAACATTGA
1 GTTGAGAACAAC-TTGA
200715 AAGGCTAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 7 0.26
17 13 0.48
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (17 bp):
GTTGAGAACAACTTGAT
Found at i:207435 original size:18 final size:18
Alignment explanation
Indices: 207414--207448 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
207404 CTTTTTAAAC
207414 TCAATTCAAATT-TTTAAT
1 TCAATT-AAATTATTTAAT
207432 TCAATTAAATTATTTAA
1 TCAATTAAATTATTTAA
207449 AAAACCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
TCAATTAAATTATTTAAT
Found at i:208276 original size:17 final size:19
Alignment explanation
Indices: 208256--208302 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
208246 TTTTTATACC
208256 TTTTAAATAATTTTT-A-T
1 TTTTAAATAATTTTTGATT
*
208273 TTTTAAAT-TTTTTTGATT
1 TTTTAAATAATTTTTGATT
208291 TTTTAAATAATT
1 TTTTAAATAATT
208303 AAAAGTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.20
17 9 0.36
18 9 0.36
19 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTAAATAATTTTTGATT
Found at i:220335 original size:12 final size:12
Alignment explanation
Indices: 220290--220342 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
220280 AGATACGAAC
* *
220290 AAGAACAAGAAC
1 AAGAACAAAAAG
220302 AAGAACAAAAAG
1 AAGAACAAAAAG
* *
220314 AATAAAAAAAAG
1 AAGAACAAAAAG
*
220326 AAGAACAAAATG
1 AAGAACAAAAAG
220338 AAGAA
1 AAGAA
220343 GGTACATTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.04
Consensus pattern (12 bp):
AAGAACAAAAAG
Found at i:224238 original size:73 final size:70
Alignment explanation
Indices: 224109--224249 Score: 203
Period size: 69 Copynumber: 2.0 Consensus size: 70
224099 TTTTTTGTAG
* * *
224109 GGGTGAGTAAAATACGATTTGATTTGAAAAAAAATAAAAAAATCGAATTTTAAGTTATT-TAATT
1 GGGTGAGTAAAATACGATTCGATTTGAAAAAAAATAAAAAAATCAAATTTTAAGTTATTCAAATT
224173 TTTAA
66 TTTAA
*
224178 GGGTGAGTAAAATACGATTCGATTTGAAAAAAATATAAAAAAAAAATCAAATTTTGAGTTATTCA
1 GGGTGAGTAAAATACGATTCGATTTGAAAAAAA-AT---AAAAAAATCAAATTTTAAGTTATTCA
224243 AATTTTT
62 AATTTTT
224250 CGAGTCAACT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
69 32 0.51
70 2 0.03
73 22 0.35
74 7 0.11
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (70 bp):
GGGTGAGTAAAATACGATTCGATTTGAAAAAAAATAAAAAAATCAAATTTTAAGTTATTCAAATT
TTTAA
Found at i:224542 original size:15 final size:15
Alignment explanation
Indices: 224522--224551 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
224512 TTTGAAAAAG
224522 TTTTCAAATCTATAT
1 TTTTCAAATCTATAT
*
224537 TTTTCAAATTTATAT
1 TTTTCAAATCTATAT
224552 GCTATAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTCAAATCTATAT
Found at i:236851 original size:22 final size:19
Alignment explanation
Indices: 236812--236853 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
236802 TGTAAAGTTG
236812 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
236831 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
236853 A
1 A
236854 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:254009 original size:40 final size:40
Alignment explanation
Indices: 253953--254164 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
253943 ACTAACCGAA
**
253953 GTATGTGTTTTCAGGGGTACCGAAGTACAAACAGGGGCAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
* * * *
253993 GTGTGTGCATTTAGGGGTACCGAAGTACAAACAGAGGCAT
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
** * *
254033 GTAAATGCATTCAGGGGTACCAAAGTACAAAACA-GGGCAT
1 GTATGTGCATTCAGGGGTACCGAAGTAC-AAACAGGGGCAC
* * * * *
254073 GTATGTGCATTCAAGGATATCAAAGTACAAACAGGGGAAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
* *
254113 GTAAGTGCATTCAGGGGTATCGAAGTACAAACA-GGGCAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
*
254152 ATATGTGCATTCA
1 GTATGTGCATTCA
254165 ACAATAATTA
Statistics
Matches: 144, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 21 0.15
40 118 0.82
41 5 0.03
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (40 bp):
GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
Found at i:254099 original size:80 final size:79
Alignment explanation
Indices: 253962--254165 Score: 264
Period size: 80 Copynumber: 2.6 Consensus size: 79
253952 AGTATGTGTT
* * * * *
253962 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTGTGTGCATTTAGGGGTACCGAAGTACAAACAG
1 TTCAGGGGTACCGAAGTACAAACA-GGGCACGTATGTGCATTCAAGGATACCAAAGTACAAACAG
* *
254027 AGGCATGTAAATGCA
65 AGGAACGTAAATGCA
* * *
254042 TTCAGGGGTACCAAAGTACAAAACAGGGCATGTATGTGCATTCAAGGATATCAAAGTACAAACAG
1 TTCAGGGGTACCGAAGTAC-AAACAGGGCACGTATGTGCATTCAAGGATACCAAAGTACAAACAG
* *
254107 GGGAACGTAAGTGCA
65 AGGAACGTAAATGCA
* *
254122 TTCAGGGGTATCGAAGTACAAACAGGGCACATATGTGCATTCAA
1 TTCAGGGGTACCGAAGTACAAACAGGGCACGTATGTGCATTCAA
254166 CAATAATTAT
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
79 23 0.21
80 79 0.74
81 5 0.05
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (79 bp):
TTCAGGGGTACCGAAGTACAAACAGGGCACGTATGTGCATTCAAGGATACCAAAGTACAAACAGA
GGAACGTAAATGCA
Found at i:254147 original size:20 final size:20
Alignment explanation
Indices: 254090--254148 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
254080 CATTCAAGGA
*
254090 TATCAAAGTACAAACAGGGG
1 TATCGAAGTACAAACAGGGG
* * **
254110 -AACGTAAGTGCATTCAGGGG
1 TATCG-AAGTACAAACAGGGG
254130 TATCGAAGTACAAACAGGG
1 TATCGAAGTACAAACAGGG
254149 CACATATGTG
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (20 bp):
TATCGAAGTACAAACAGGGG
Found at i:257328 original size:25 final size:25
Alignment explanation
Indices: 257300--257348 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
257290 AGTTAATAAT
257300 AATT-CTCATTGAGTTT-TTCTTAAAG
1 AATTGCTC-TTGAGTTTCTT-TTAAAG
257325 AATTGCTCTTGAGTTTCTTTTAAA
1 AATTGCTCTTGAGTTTCTTTTAAA
257349 AGCTGTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (25 bp):
AATTGCTCTTGAGTTTCTTTTAAAG
Found at i:258587 original size:96 final size:96
Alignment explanation
Indices: 258402--258580 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 96
258392 ATAGGAGTAT
* * * * **
258402 GATTGATCTCTCACCTGTTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATGAGGTTTTCCGGT
1 GATTGAGCTATCACCTGTTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATAAGGGTTTCCAAT
258467 GTCCAATTAAATATCCAAATAGAGACAATAA
66 GTCCAATTAAATATCCAAATAGAGACAATAA
* * *
258498 GATTGAGCTATCACCTTTTGTGAAATTTTATTTGTGTAGTTCAAAAGATCATAAGGGTTTCCAAT
1 GATTGAGCTATCACCTGTTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATAAGGGTTTCCAAT
258563 GTCCAATTAAATATCCAA
66 GTCCAATTAAATATCCAA
258581 CAAGAGAAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (96 bp):
GATTGAGCTATCACCTGTTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATAAGGGTTTCCAAT
GTCCAATTAAATATCCAAATAGAGACAATAA
Found at i:259633 original size:28 final size:28
Alignment explanation
Indices: 259570--259633 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
259560 CTTGTGCTAA
** *
259570 GCCGTGTGGTAGCTGTGTGTGACACATG
1 GCCGTGTGGTAGCCATGTGTGACACACG
* *
259598 ACCATGTGGTAGCCATGTGTGACACACG
1 GCCGTGTGGTAGCCATGTGTGACACACG
259626 GCCGTGTG
1 GCCGTGTG
259634 ACAAGTCGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (28 bp):
GCCGTGTGGTAGCCATGTGTGACACACG
Found at i:266118 original size:21 final size:23
Alignment explanation
Indices: 266078--266119 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
266068 TATACAATAT
*
266078 TAAAAATGCTAACTAAAATGTTC
1 TAAAAAAGCTAACTAAAATGTTC
266101 TAAAAAAGC-AAC-AAAATGT
1 TAAAAAAGCTAACTAAAATGT
266120 ACTTAAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (23 bp):
TAAAAAAGCTAACTAAAATGTTC
Found at i:271099 original size:165 final size:165
Alignment explanation
Indices: 270827--271150 Score: 567
Period size: 165 Copynumber: 2.0 Consensus size: 165
270817 AAGTGATCAA
*
270827 TATCATTCCCACGAGTATCGAGTTGAGGCAAAAAATTGGTCAAGTTATTATAATAAAATGTGATT
1 TATCATTCCCACGAGTATCGAATTGAGGCAAAAAATTGGTCAAGTTATTATAATAAAATGTGATT
** *
270892 AATGCTATGGAAAAATTTGTGATAAATATGCAGTGGCAATTAGTGGAGTAGTGATGTAAGCAATA
66 AATGCTATGGAAAAATCAGTGATAAATATGCAGTGGCAATTAGTGGAGTAATGATGTAAGCAATA
* *
270957 CGTGGAATTATTGAGTAACTGAAAATGCTGATGAG
131 CGTGGAATTAATGAGTAACTAAAAATGCTGATGAG
*
270992 TATCATTCCCACGAGTATCGAATTGAGGCACAAAATTGGTCAAGTTATTATAATAAAATGTGATT
1 TATCATTCCCACGAGTATCGAATTGAGGCAAAAAATTGGTCAAGTTATTATAATAAAATGTGATT
* *
271057 AATGCTATGGTAAAATCAGTGATAAATATGTAGTGGCAATTAGTGGAGTAATGATGTAAGCAATA
66 AATGCTATGGAAAAATCAGTGATAAATATGCAGTGGCAATTAGTGGAGTAATGATGTAAGCAATA
271122 CGTGGAATTAATGAGTAACTAAAAATGCT
131 CGTGGAATTAATGAGTAACTAAAAATGCT
271151 ACGGAAAAAG
Statistics
Matches: 150, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
165 150 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (165 bp):
TATCATTCCCACGAGTATCGAATTGAGGCAAAAAATTGGTCAAGTTATTATAATAAAATGTGATT
AATGCTATGGAAAAATCAGTGATAAATATGCAGTGGCAATTAGTGGAGTAATGATGTAAGCAATA
CGTGGAATTAATGAGTAACTAAAAATGCTGATGAG
Found at i:274109 original size:29 final size:29
Alignment explanation
Indices: 274048--274232 Score: 108
Period size: 29 Copynumber: 6.3 Consensus size: 29
274038 CAACGAATGG
* *
274048 AAAGGGATAGCTTCGACTATCGAATA-CA
1 AAAGGGATAGCTTCGACTATCGATTATGA
274076 GAAAGGGATAGCTTCGACTATCGATTATGA
1 -AAAGGGATAGCTTCGACTATCGATTATGA
* * * * **
274106 AAAGGGAT-GGTGACGACCATCAACAATGA
1 AAAGGGATAGCT-TCGACTATCGATTATGA
* * * *
274135 AAAGAGAT-GGTGAT-GACCATCGAACTATGA
1 AAAGGGATAGCT--TCGACTATCG-ATTATGA
* * * *
274165 AAAAGGATGGCTTCGGCTATTGATCTATGA
1 AAAGGGATAGCTTCGACTATCGAT-TATGA
* * *
274195 AAAAGGATAGCTTCGGCTATCAAATTATGA
1 AAAGGGATAGCTTCGACTATC-GATTATGA
274225 AAAGGGAT
1 AAAGGGAT
274233 GTGATGACCA
Statistics
Matches: 124, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
28 2 0.02
29 64 0.52
30 54 0.44
31 4 0.03
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
AAAGGGATAGCTTCGACTATCGATTATGA
Found at i:274224 original size:30 final size:30
Alignment explanation
Indices: 274159--274232 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
274149 GACCATCGAA
* **
274159 CTATGAAAAAGGATGGCTTCGGCTATTGAT
1 CTATGAAAAAGGATAGCTTCGGCTATAAAT
274189 CTATGAAAAAGGATAGCTTCGGCTATCAAAT
1 CTATGAAAAAGGATAGCTTCGGCTAT-AAAT
*
274220 -TATGAAAAGGGAT
1 CTATGAAAAAGGAT
274233 GTGATGACCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (30 bp):
CTATGAAAAAGGATAGCTTCGGCTATAAAT
Found at i:274252 original size:119 final size:119
Alignment explanation
Indices: 274052--274351 Score: 347
Period size: 119 Copynumber: 2.5 Consensus size: 119
274042 GAATGGAAAG
* * * *
274052 GGATAGCTTCGACTATCGAA-TA-CAGAAAGGGATAGCTTCGACTATC-GATTATGAAAAGGGAT
1 GGATAGCTTCGACTATCGAACTATGA-AAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGAT
* * ** *
274114 GGTGACGACCATCAACAATGAAAAGAGATGGTGATGACCATCGAACTATGAAAAA
65 GGTGACGACCATCAACAATGAAAAGAAATCGTGACAACCATCAAACTATGAAAAA
* * * *
274169 GGATGGCTTCGGCTATTGATCTATGAAAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGAT-
1 GGATAGCTTCGACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGATG
* * *
274233 GTGATGACCATCGAACAATGAAAAGAAATCGTGACAACCATCAAATTATGAAAAG
66 GTGACGACCATC-AACAATGAAAAGAAATCGTGACAACCATCAAACTATGAAAAA
* * * * * **
274288 GGATAGCTTTGACTGTCGAACTATGAAAAGGGATAACTTCGGTTATCAAATTACAAAAAGGGAT
1 GGATAGCTTCGACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGAT
274352 ACGTCAAGCA
Statistics
Matches: 152, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
117 16 0.11
118 32 0.21
119 104 0.68
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (119 bp):
GGATAGCTTCGACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGATG
GTGACGACCATCAACAATGAAAAGAAATCGTGACAACCATCAAACTATGAAAAA
Found at i:274284 original size:30 final size:29
Alignment explanation
Indices: 274213--274287 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 29
274203 AGCTTCGGCT
** **
274213 ATCAAATTATGAAAAGGGATGTGATGACC
1 ATCAAATTATGAAAAGAAATGTGACAACC
* **
274242 ATCGAACAATGAAAAGAAATCGTGACAACC
1 ATCAAATTATGAAAAGAAAT-GTGACAACC
274272 ATCAAATTATGAAAAG
1 ATCAAATTATGAAAAG
274288 GGATAGCTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (29 bp):
ATCAAATTATGAAAAGAAATGTGACAACC
Found at i:275372 original size:12 final size:12
Alignment explanation
Indices: 275355--275380 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
275345 GCGGTTACAT
275355 GGCCTAGCACAC
1 GGCCTAGCACAC
275367 GGCCTAGCACAC
1 GGCCTAGCACAC
275379 GG
1 GG
275381 ACGTGTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:278387 original size:155 final size:155
Alignment explanation
Indices: 278105--278415 Score: 586
Period size: 155 Copynumber: 2.0 Consensus size: 155
278095 TTTGTGTGCC
* *
278105 TATATAAGGCTTTGTAATAGGACATTTTGAGGTTAATGAACTTTTATCTAAGTGAGATTATTAAA
1 TATATAAGACTTTGTAATAGGACATTTTGAGGTTAATGAAATTTTATCTAAGTGAGATTATTAAA
278170 GAGTTTTCACTCTTCTTTCTTTTACAAATTCGAGTTGACTTATCAACATTGTTTGTGGCGTCAAT
66 GAGTTTTCACTCTTCTTTCTTTTACAAATTCGAGTTGACTTATCAACATTGTTTGTGGCGTCAAT
278235 CCGATTGTCTACAATCCTTTGATAT
131 CCGATTGTCTACAATCCTTTGATAT
278260 TATATAAGACTTTGTAATAGGACATTTTGAGGTTAATGAAATTTTATCTAAGTGAGATTATTAAA
1 TATATAAGACTTTGTAATAGGACATTTTGAGGTTAATGAAATTTTATCTAAGTGAGATTATTAAA
*
278325 GAGTTTTCACTCTTCTTTCTTTTACAAATTCGAGTTGACTTATCAATATTGTTTGTGGCGTCAAT
66 GAGTTTTCACTCTTCTTTCTTTTACAAATTCGAGTTGACTTATCAACATTGTTTGTGGCGTCAAT
*
278390 CCGGTTGTCTACAATCCTTTGATAT
131 CCGATTGTCTACAATCCTTTGATAT
278415 T
1 T
278416 GTCGGTTCCT
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 152 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (155 bp):
TATATAAGACTTTGTAATAGGACATTTTGAGGTTAATGAAATTTTATCTAAGTGAGATTATTAAA
GAGTTTTCACTCTTCTTTCTTTTACAAATTCGAGTTGACTTATCAACATTGTTTGTGGCGTCAAT
CCGATTGTCTACAATCCTTTGATAT
Found at i:278687 original size:23 final size:23
Alignment explanation
Indices: 278656--278707 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
278646 TTGTTTTTGT
278656 AAAAAAAATTC-AAAAAAAAAGA
1 AAAAAAAATTCGAAAAAAAAAGA
*
278678 AAAATAAAATTCGAAAAGAAAAGA
1 AAAA-AAAATTCGAAAAAAAAAGA
278702 AAAAAA
1 AAAAAA
278708 TTGTATACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 9 0.33
24 14 0.52
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.10
Consensus pattern (23 bp):
AAAAAAAATTCGAAAAAAAAAGA
Found at i:278776 original size:15 final size:15
Alignment explanation
Indices: 278756--278804 Score: 98
Period size: 15 Copynumber: 3.3 Consensus size: 15
278746 AGTATCCGCA
278756 AAAAAAATTTGACCC
1 AAAAAAATTTGACCC
278771 AAAAAAATTTGACCC
1 AAAAAAATTTGACCC
278786 AAAAAAATTTGACCC
1 AAAAAAATTTGACCC
278801 AAAA
1 AAAA
278805 GTCTGGAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.57, C:0.18, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAAAAATTTGACCC
Found at i:282234 original size:50 final size:50
Alignment explanation
Indices: 282159--282259 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
282149 GTGATGCTTC
*
282159 AGGTATTGGAATTGGCACGGTACTATCTCAAGAAGGAAAACCGATTGCCT
1 AGGTATTGGAATTGGCACGGTACTATCTCAAAAAGGAAAACCGATTGCCT
*
282209 AGGTATTGGAATTGGCGCGGTACTATCTCAAAAAGGAAAACCGATTGCCT
1 AGGTATTGGAATTGGCACGGTACTATCTCAAAAAGGAAAACCGATTGCCT
282259 A
1 A
282260 CTTTAGTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.24
Consensus pattern (50 bp):
AGGTATTGGAATTGGCACGGTACTATCTCAAAAAGGAAAACCGATTGCCT
Found at i:283988 original size:22 final size:23
Alignment explanation
Indices: 283940--283988 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
283930 TATAAGTATG
283940 ATTAATGTGTCCTAATAAGTCGT
1 ATTAATGTGTCCTAATAAGTCGT
* *
283963 -TTAATGTGTCTTAATAGGT-GT
1 ATTAATGTGTCCTAATAAGTCGT
283984 ATTAA
1 ATTAA
283989 AGAAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGTGTCCTAATAAGTCGT
Found at i:286475 original size:49 final size:51
Alignment explanation
Indices: 286419--286545 Score: 168
Period size: 49 Copynumber: 2.5 Consensus size: 51
286409 TTGCATCTTT
*
286419 TAATTATGACATGCATTATGTAACTCTCATGTTGGTT-AAGTTTACAT-AA
1 TAATTATGACATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCAA
* * *
286468 TAATTATGACATGCTTTATGTAACTCTCATGTTAGTTAAAGTTTGCATCAT
1 TAATTATGACATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCAA
* * *
286519 TAAATTAAGTCATGCATTAAGTAACTC
1 T-AATTATGACATGCATTATGTAACTC
286546 ATTTGTTCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 35 0.52
50 9 0.13
51 2 0.03
52 21 0.31
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (51 bp):
TAATTATGACATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCAA
Found at i:288707 original size:17 final size:19
Alignment explanation
Indices: 288687--288728 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
288677 AAATGAGAGA
*
288687 AAAAGAAATTG-AA-AAAG
1 AAAAGAAAGTGAAAGAAAG
*
288704 AAAAGAGAGTGAAAGAAAG
1 AAAAGAAAGTGAAAGAAAG
288723 AAAAGA
1 AAAAGA
288729 GTGATTGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 2 0.10
19 10 0.48
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (19 bp):
AAAAGAAAGTGAAAGAAAG
Found at i:292052 original size:50 final size:52
Alignment explanation
Indices: 291985--292116 Score: 169
Period size: 50 Copynumber: 2.6 Consensus size: 52
291975 ACGTGTTTTG
* * *
291985 CATTAAATAAAGCCATGCATTATGTAACTCCCATGTTAGTT-AAGTTTACAT
1 CATTAAATTAAGACATGCATTAAGTAACTCCCATGTTAGTTAAAGTTTACAT
* * * * *
292036 CA-TAAATTATGACATGCTTTACGTAACTCTCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGACATGCATTAAGTAACTCCCATGTTAGTTAAAGTTTACAT
*
292087 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGACATGCATTAAGTAACTC
292117 ATTTCATTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 32 0.47
51 13 0.19
52 23 0.34
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (52 bp):
CATTAAATTAAGACATGCATTAAGTAACTCCCATGTTAGTTAAAGTTTACAT
Found at i:295117 original size:19 final size:18
Alignment explanation
Indices: 295093--295128 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
295083 ACGTATTAAA
295093 CCGAGTTACAAAATTTCAT
1 CCGAGTTA-AAAATTTCAT
*
295112 CCGAGTTAAAACTTTCA
1 CCGAGTTAAAAATTTCA
295129 ACTTTTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (18 bp):
CCGAGTTAAAAATTTCAT
Found at i:298892 original size:50 final size:52
Alignment explanation
Indices: 298792--298979 Score: 204
Period size: 50 Copynumber: 3.6 Consensus size: 52
298782 TTTTCTGTAC
* * * * * *
298792 TGCCAATGCCATATCCTAGATACGGTCTTACATGGGA-GT-TCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTCATCTCGG
* * *
298842 TGCCCATGTCATGTCCCAGACATGGTCTTACA-GGGGCC-CTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTCATCTCGG
* * *
298892 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-TCATCTC---GG
298948 TGCCAATGCCATGTCCCAGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
298980 CTGGCTCACA
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
49 3 0.03
50 65 0.57
51 5 0.04
52 3 0.03
53 6 0.05
56 32 0.28
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTCATCTCGG
Found at i:298924 original size:100 final size:103
Alignment explanation
Indices: 298792--298979 Score: 238
Period size: 100 Copynumber: 1.8 Consensus size: 103
298782 TTTTCTGTAC
* * * ** * * *
298792 TGCCAATGCCATATCCTAGATACGGTCTTACATGGGAGTTCTCAT-A-TC-GGTGCCCATGTCAT
1 TGCCAACGCCATATCCCAGACACGGTCTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
298854 GTCCCAGACATGGTCTTACAGGGGCCCTCTCATCTCGG
66 GTCCCAGACATGGTCTTACAGGGGCCCTCTCATCTCGG
* *
298892 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGC
1 TGCCAACGCCATATCCCAGACACGGTCTTACATGGGACCTCTCATAA-CTC-A-GATGCCAATGC
298957 CATGTCCCAGACATGGTCTTACA
63 CATGTCCCAGACATGGTCTTACA
298980 CTGGCTCACA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 38 0.53
101 1 0.01
103 2 0.03
106 31 0.43
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (103 bp):
TGCCAACGCCATATCCCAGACACGGTCTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
GTCCCAGACATGGTCTTACAGGGGCCCTCTCATCTCGG
Found at i:299691 original size:19 final size:18
Alignment explanation
Indices: 299667--299702 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
299657 ACGTATTAAA
299667 CCGAGTTACAAAATTTCAT
1 CCGAGTTA-AAAATTTCAT
*
299686 CCGAGTTAAAACTTTCA
1 CCGAGTTAAAAATTTCA
299703 AATTTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (18 bp):
CCGAGTTAAAAATTTCAT
Found at i:301320 original size:12 final size:12
Alignment explanation
Indices: 301303--301333 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
301293 TTTCTTATAT
301303 ATACTAAATAAA
1 ATACTAAATAAA
301315 ATACT-AATAAA
1 ATACTAAATAAA
301326 ATACTAAA
1 ATACTAAA
301334 ATATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (12 bp):
ATACTAAATAAA
Found at i:307220 original size:25 final size:25
Alignment explanation
Indices: 307164--307223 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
307154 TAAACATACA
*
307164 TGTTCTGTTCTGCTATGCTTCGTTC
1 TGTTCTGTTCTGCTATGCTCCGTTC
** * * *
307189 TAATCTGTTCTTCTTTGCTCCGTTT
1 TGTTCTGTTCTGCTATGCTCCGTTC
307214 TGTTCTGTTC
1 TGTTCTGTTC
307224 AGTATTACTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.05, C:0.23, G:0.17, T:0.55
Consensus pattern (25 bp):
TGTTCTGTTCTGCTATGCTCCGTTC
Done.