Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 41 of 210
Found at i:12882135 original size:31 final size:31
Alignment explanation
Indices: 12882061--12882157 Score: 131
Period size: 31 Copynumber: 3.0 Consensus size: 31
12882051 TTATGTAAGT
**
12882061 TGTAAGTTATGTAAGGTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
12882092 TTAATTAAGTTATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
12882126 TGTAAGTTATGCAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
12882157 T
1 T
12882158 TAATTAAGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
31 29 0.50
32 1 0.02
33 1 0.02
34 27 0.47
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.46
Consensus pattern (31 bp):
TGTAAGTTATGTAATTTATGTATAATATTAA
Found at i:12885736 original size:21 final size:21
Alignment explanation
Indices: 12885712--12885751 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12885702 CTATACCCTT
*
12885712 AACCCTAAACCTCAAACCCCA
1 AACCCTAAAACTCAAACCCCA
* *
12885733 AACCGTAAAACTTAAACCC
1 AACCCTAAAACTCAAACCC
12885752 TAACACGTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.40, G:0.03, T:0.12
Consensus pattern (21 bp):
AACCCTAAAACTCAAACCCCA
Found at i:12885799 original size:26 final size:26
Alignment explanation
Indices: 12885761--12885810 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
12885751 CTAACACGTC
*
12885761 AATTAACCGTAAAACACCAAACCACCA
1 AATTAACCATAAAA-ACCAAACCACCA
*
12885788 AATT-ACCATAAAATCCAAACCAC
1 AATTAACCATAAAAACCAAACCAC
12885811 AATATATCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 8 0.38
27 4 0.19
ACGTcount: A:0.52, C:0.32, G:0.02, T:0.14
Consensus pattern (26 bp):
AATTAACCATAAAAACCAAACCACCA
Found at i:12885854 original size:25 final size:26
Alignment explanation
Indices: 12885825--12885876 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
12885815 TATCGTAGAC
*
12885825 ATTAACCATAGATC-TTAAACCC-TAA
1 ATTAACCATA-AACATTAAACCCGTAA
12885850 ATTAACCATAAACATTAAACCCGTAA
1 ATTAACCATAAACATTAAACCCGTAA
12885876 A
1 A
12885877 CCACAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 2 0.08
25 18 0.75
26 4 0.17
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (26 bp):
ATTAACCATAAACATTAAACCCGTAA
Found at i:12885970 original size:13 final size:14
Alignment explanation
Indices: 12885935--12885975 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
12885925 CAAACCCCTA
*
12885935 AAGT-CTAAACCGT
1 AAGTCCTAAACCAT
*
12885948 AAGTCATAAACCAT
1 AAGTCCTAAACCAT
12885962 AA-TCCTAAACCAT
1 AAGTCCTAAACCAT
12885975 A
1 A
12885976 TCTTTGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (14 bp):
AAGTCCTAAACCAT
Found at i:12887592 original size:16 final size:16
Alignment explanation
Indices: 12887571--12887601 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12887561 AATTCAATCC
12887571 ATTTCAATCCACTATA
1 ATTTCAATCCACTATA
*
12887587 ATTTCAATTCACTAT
1 ATTTCAATCCACTAT
12887602 CAAAGTGCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTCAATCCACTATA
Found at i:12888223 original size:13 final size:13
Alignment explanation
Indices: 12888194--12888231 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
12888184 ATTCTCCAAC
12888194 TTTTCTTTCCTTATT
1 TTTTCTTT-CTT-TT
12888209 TTTT-TTTCTTTT
1 TTTTCTTTCTTTT
12888221 TTTTCTTTCTT
1 TTTTCTTTCTT
12888232 CTCTTTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
13 9 0.41
14 3 0.14
15 4 0.18
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:12890659 original size:22 final size:23
Alignment explanation
Indices: 12890623--12890665 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12890613 AACCCTTCCA
12890623 AAAAAATCCTAAACCCTAAAATT
1 AAAAAATCCTAAACCCTAAAATT
* *
12890646 AAAAAA-CCTTAACCTTAAAA
1 AAAAAATCCTAAACCCTAAAA
12890666 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (23 bp):
AAAAAATCCTAAACCCTAAAATT
Found at i:12893640 original size:228 final size:228
Alignment explanation
Indices: 12893221--12893640 Score: 493
Period size: 228 Copynumber: 1.8 Consensus size: 228
12893211 AATCTAAAAT
* * * * * * *
12893221 CAAATTTAATCCCATAATAGTTTACTAATATTCACTTCAAGAAGGTATGGAAAAGAAACGAAATC
1 CAAATTTAACCCCATAATAGATTACTAATAGTCAATTCAAAAAAGTAAGGAAAAGAAACGAAATC
* * * **
12893286 AAACTATCAATCCTAAGTGTTTTGATGCTAAACAATATAACAATCCAAGCCTACTTAATCCCTGG
66 AAACTAGCAATCCTAAGTGTTCTGATACTAAACAATATAACAATCCAAGCCTACTTAATCCCCAG
* * ** **
12893351 CAAAAACTTCGTTCATTAGGTGCAAATTTTCGGGTTTGTTTGAGTTCCAAAATCACATAAAACAT
131 CAAAAACTTCGTTCATTAGGGGCAAATTTTCAGGTTCCTTCAAGTTCCAAAATCACATAAAACAT
12893416 TCACATTCCGGAATACATATCTTTACCACAAAC
196 TCACATTCCGGAATACATATCTTTACCACAAAC
* * * *
12893449 CAAATTTAACCCCATGATAGATTACTAATAGTCAATTTAAAAAAGTAAGGAAAAGAAATGAGATC
1 CAAATTTAACCCCATAATAGATTACTAATAGTCAATTCAAAAAAGTAAGGAAAAGAAACGAAATC
* * * * * ***
12893514 GAGCTAGGAATCTTAAGTGTTCTGATACTGAAA-AATATACCAATTTGAGCCTAC-TAAGTCCCC
66 AAACTAGCAATCCTAAGTGTTCTGATACT-AAACAATATAACAATCCAAGCCTACTTAA-TCCCC
* * * * *
12893577 AGCAAAGACTTGGTTCATTCGGGGCAAGTTTTCAGGTTCCTTCAAGTTCCAAAATCTCATAAAA
129 AGCAAAAACTTCGTTCATTAGGGGCAAATTTTCAGGTTCCTTCAAGTTCCAAAATCACATAAAA
12893641 GCAAACCAAT
Statistics
Matches: 155, Mismatches: 35, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
227 3 0.02
228 149 0.96
229 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (228 bp):
CAAATTTAACCCCATAATAGATTACTAATAGTCAATTCAAAAAAGTAAGGAAAAGAAACGAAATC
AAACTAGCAATCCTAAGTGTTCTGATACTAAACAATATAACAATCCAAGCCTACTTAATCCCCAG
CAAAAACTTCGTTCATTAGGGGCAAATTTTCAGGTTCCTTCAAGTTCCAAAATCACATAAAACAT
TCACATTCCGGAATACATATCTTTACCACAAAC
Found at i:12895339 original size:19 final size:19
Alignment explanation
Indices: 12895317--12895386 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
12895307 AGGTTTAAGG
12895317 TTTAGGGTTTTATTTATTT
1 TTTAGGGTTTTATTTATTT
* *
12895336 TTTAGTG-TTTATTAATTAT
1 TTTAGGGTTTTATTTATT-T
*
12895355 GGATTTAGGGTTTTATTTAATT
1 ---TTTAGGGTTTTATTTATTT
12895377 TTTAGGGTTT
1 TTTAGGGTTT
12895387 AGGGATTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 9 0.22
19 17 0.41
22 7 0.17
23 8 0.20
ACGTcount: A:0.20, C:0.00, G:0.19, T:0.61
Consensus pattern (19 bp):
TTTAGGGTTTTATTTATTT
Found at i:12895371 original size:41 final size:40
Alignment explanation
Indices: 12895275--12895389 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 40
12895265 AATTAAGGTT
* * *
12895275 AGGATTTAAGGTTTT-TTAATTTTTAAGTGTTTAGGTTTA
1 AGGATTTAGGGTTTTATTTATTTTTTAGTGTTTAGGTTTA
*
12895314 AGG-TTTAGGGTTTTATTTATTTTTTAGTGTTTA-TTAATTA
1 AGGATTTAGGGTTTTATTTATTTTTTAGTGTTTAGGT--TTA
* * *
12895354 TGGATTTAGGGTTTTATTTAATTTTTAGGGTTTAGG
1 AGGATTTAGGGTTTTATTTATTTTTTAGTGTTTAGG
12895390 GATTCTAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
38 11 0.17
39 19 0.30
40 5 0.08
41 28 0.44
ACGTcount: A:0.23, C:0.00, G:0.22, T:0.56
Consensus pattern (40 bp):
AGGATTTAGGGTTTTATTTATTTTTTAGTGTTTAGGTTTA
Found at i:12895447 original size:29 final size:29
Alignment explanation
Indices: 12895392--12895475 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
12895382 GGTTTAGGGA
*
12895392 TTCTAAAAAAATAAATTTT-ACAAGATAGG
1 TTCTAAAAAAAT-AATTTTGACAAGATAAG
***
12895421 TTCTAAAAAAATAATTTTGAGGGGATAAG
1 TTCTAAAAAAATAATTTTGACAAGATAAG
* *
12895450 TTCTGAAGAAATAATTTTGACAAGAT
1 TTCTAAAAAAATAATTTTGACAAGAT
12895476 GGGTTGAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 6 0.13
29 39 0.87
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.32
Consensus pattern (29 bp):
TTCTAAAAAAATAATTTTGACAAGATAAG
Found at i:12898584 original size:23 final size:23
Alignment explanation
Indices: 12898554--12898598 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
12898544 TCATTTGCCA
12898554 ATAACCTCAGTTGTGAAAGAGAC
1 ATAACCTCAGTTGTGAAAGAGAC
12898577 ATAACCTCAGTTGTGAAAGAGA
1 ATAACCTCAGTTGTGAAAGAGA
12898599 TATACTTCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (23 bp):
ATAACCTCAGTTGTGAAAGAGAC
Found at i:12903247 original size:17 final size:17
Alignment explanation
Indices: 12903225--12903276 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
12903215 AGCAAATGCT
12903225 TATTTTTGTAATTAATA
1 TATTTTTGTAATTAATA
*
12903242 TA-TTTT-TCA-T-ATA
1 TATTTTTGTAATTAATA
12903255 T-TTTTTGTAATTAAT-
1 TATTTTTGTAATTAATA
12903270 TATTTTT
1 TATTTTT
12903277 TACATTAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
15 4 0.14
16 11 0.39
17 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (17 bp):
TATTTTTGTAATTAATA
Found at i:12908139 original size:50 final size:50
Alignment explanation
Indices: 12908014--12908254 Score: 234
Period size: 50 Copynumber: 4.7 Consensus size: 50
12908004 GATAATAACA
* ** * * *
12908014 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
12908063 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** * *
12908113 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
12908163 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAGTCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA---TC---GG
12908219 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
12908255 GTCTCTTTAC
Statistics
Matches: 155, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.25
50 79 0.51
53 2 0.01
56 35 0.23
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:12908630 original size:30 final size:30
Alignment explanation
Indices: 12908596--12908653 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
12908586 CCTTGACTCG
12908596 AACTTTGGAAAAATTACGA-TTTTGCCCCTA
1 AACTTTGGAAAAATTAC-ACTTTTGCCCCTA
* * *
12908626 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTGGAAAAATTACACTTTTGCCCC
12908654 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.36
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:12908945 original size:19 final size:22
Alignment explanation
Indices: 12908921--12908983 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
12908911 ACCCTAGGGT
12908921 TCACTTAC-AAGG-G-TTGGAA
1 TCACTTACTAAGGAGCTTGGAA
*
12908940 TCACTTACTATGGAGCTTGGAA
1 TCACTTACTAAGGAGCTTGGAA
**
12908962 TCACTTACTATCGAGCTTGGAA
1 TCACTTACTAAGGAGCTTGGAA
12908984 GCTTGAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 8 0.21
20 3 0.08
21 1 0.03
22 27 0.69
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (22 bp):
TCACTTACTAAGGAGCTTGGAA
Found at i:12908962 original size:22 final size:22
Alignment explanation
Indices: 12908934--12908983 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
12908924 CTTACAAGGG
*
12908934 TTGGAATCACTTACTATGGAGC
1 TTGGAATCACTTACTATCGAGC
12908956 TTGGAATCACTTACTATCGAGC
1 TTGGAATCACTTACTATCGAGC
12908978 TTGGAA
1 TTGGAA
12908984 GCTTGAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (22 bp):
TTGGAATCACTTACTATCGAGC
Found at i:12911235 original size:21 final size:20
Alignment explanation
Indices: 12911185--12911238 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
12911175 ATTTCGAAAT
* *
12911185 AAAACTTTGA-TTTTTAAGA
1 AAAATTTTGATTTTTTAAAA
**
12911204 AAAATAGTGATTTTTTAAAA
1 AAAATTTTGATTTTTTAAAA
12911224 GAAAATTTTGATTTT
1 -AAAATTTTGATTTT
12911239 GCAAAAAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 7 0.26
20 8 0.30
21 12 0.44
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (20 bp):
AAAATTTTGATTTTTTAAAA
Found at i:12919835 original size:15 final size:15
Alignment explanation
Indices: 12919815--12919843 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12919805 TTTAAAAATA
12919815 TTTATATAATTTTAT
1 TTTATATAATTTTAT
12919830 TTTATATAATTTTA
1 TTTATATAATTTTA
12919844 AATTTATTAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATATAATTTTAT
Found at i:12920120 original size:31 final size:30
Alignment explanation
Indices: 12920082--12920185 Score: 113
Period size: 31 Copynumber: 3.5 Consensus size: 30
12920072 TAAAAAGTTT
12920082 ATAGTTGGGTGACCAAAAAAGAAACAAATCC
1 ATAGTTGGGTGACCAAAAAAGAAA-AAATCC
*** * *
12920113 ATAGTT-GGTGACCAATTTA-AATAAATTC
1 ATAGTTGGGTGACCAAAAAAGAAAAAATCC
* *
12920141 ATAGTTGAGTGACCAAAAAAGAAAATGATCC
1 ATAGTTGGGTGACCAAAAAAGAAAA-AATCC
12920172 ATAGTTGGGTGACC
1 ATAGTTGGGTGACC
12920186 TATGGTGTAC
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 11 0.19
29 11 0.19
30 13 0.23
31 22 0.39
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.24
Consensus pattern (30 bp):
ATAGTTGGGTGACCAAAAAAGAAAAAATCC
Found at i:12920126 original size:59 final size:60
Alignment explanation
Indices: 12920054--12920185 Score: 180
Period size: 59 Copynumber: 2.2 Consensus size: 60
12920044 CAATCTCAAT
* * * *
12920054 TAGTAGGGTGACCAATTTTAAA-AAGTTTATAGTTGGGTGACCAAAAAAGAAACA-AATCCA
1 TAGTTGGGTGACCAA-TTTAAATAAATTCATAGTTGAGTGACCAAAAAAGAAA-ATAATCCA
*
12920114 TAGTT-GGTGACCAATTTAAATAAATTCATAGTTGAGTGACCAAAAAAGAAAATGATCCA
1 TAGTTGGGTGACCAATTTAAATAAATTCATAGTTGAGTGACCAAAAAAGAAAATAATCCA
12920173 TAGTTGGGTGACC
1 TAGTTGGGTGACC
12920186 TATGGTGTAC
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
58 7 0.11
59 46 0.72
60 11 0.17
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (60 bp):
TAGTTGGGTGACCAATTTAAATAAATTCATAGTTGAGTGACCAAAAAAGAAAATAATCCA
Found at i:12921530 original size:15 final size:16
Alignment explanation
Indices: 12921510--12921542 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12921500 AATTTATATT
12921510 AAAAA-TTTAAAACCC
1 AAAAATTTTAAAACCC
*
12921525 AAAAATTTTTAAACCC
1 AAAAATTTTAAAACCC
12921541 AA
1 AA
12921543 TAACTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATTTTAAAACCC
Found at i:12929106 original size:44 final size:44
Alignment explanation
Indices: 12928628--12929105 Score: 652
Period size: 44 Copynumber: 10.9 Consensus size: 44
12928618 ATCACAAAGC
* *
12928628 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAAT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * * * *
12928672 TCTAGCTCCCTGAACAGTAGTGGATTAGGTTGAAGATTGCAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
12928716 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* *
12928760 CTTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGC
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * * *
12928804 CCGATCTCCCTAACAAGCATTGGAATAGGTTGAAGATTGCAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* *
12928848 CCTATCTCCTTGACCAGCAGTGGGATAGGTTGAAGATTGCAAG-
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * **
12928891 CCTTATCTCCCTAACCAGCAGTGGAATAGGTTAAAGATTGTGAGT
1 CC-TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
12928936 TCTATCTCCCTGACCAGCATTAGAATAGGTTGAAGATTGCAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
12928980 CCTATCTCCCTGACCAACATTGGAATAGGCTGAAGATTGCAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
12929024 CCTATCTCCCTAACCAGTAGTGGAATAGGTTGAAGATTACAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * * *
12929068 CCTATCTCCCTAACCAACAGTGGAAAAGGTGGAAGATT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
12929106 AGTTTCTATG
Statistics
Matches: 379, Mismatches: 53, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
43 2 0.01
44 376 0.99
45 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
Found at i:12947631 original size:19 final size:19
Alignment explanation
Indices: 12947607--12947647 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
12947597 TATTTTAAAG
*
12947607 TTATTTAGGTAGATAAATC
1 TTATTTAAGTAGATAAATC
12947626 TTATTTAAGTAGATAAATC
1 TTATTTAAGTAGATAAATC
12947645 TTA
1 TTA
12947648 GAATACATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (19 bp):
TTATTTAAGTAGATAAATC
Found at i:12951473 original size:19 final size:19
Alignment explanation
Indices: 12951449--12951487 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12951439 TATTTTAAAA
*
12951449 TTATTTAGGTAGATAAATC
1 TTATTTAAGTAGATAAATC
12951468 TTATTTAAGTAGATAAATC
1 TTATTTAAGTAGATAAATC
12951487 T
1 T
12951488 AAGAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (19 bp):
TTATTTAAGTAGATAAATC
Found at i:12951575 original size:41 final size:41
Alignment explanation
Indices: 12951527--12951608 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
12951517 ATATTTTATT
12951527 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
12951568 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
12951609 CAATTAGATT
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:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
Found at i:12959822 original size:14 final size:14
Alignment explanation
Indices: 12959803--12959833 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12959793 AAAACATAGA
12959803 AAACAAGGGGTTTT
1 AAACAAGGGGTTTT
12959817 AAACAAGGGGTTTT
1 AAACAAGGGGTTTT
12959831 AAA
1 AAA
12959834 TTTTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (14 bp):
AAACAAGGGGTTTT
Found at i:12961166 original size:21 final size:22
Alignment explanation
Indices: 12961123--12961169 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
12961113 AATTTTAAAT
12961123 AAATTTTACTATTTTAAATATA
1 AAATTTTACTATTTTAAATATA
*
12961145 AAATTTTA-T-TTTTATATCATA
1 AAATTTTACTATTTTAAAT-ATA
12961166 AAAT
1 AAAT
12961170 ATTAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 8 0.35
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTTACTATTTTAAATATA
Found at i:12964280 original size:17 final size:18
Alignment explanation
Indices: 12964258--12964291 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12964248 GTATTGGTCG
12964258 ATATTTAA-TTTATTTTA
1 ATATTTAATTTTATTTTA
12964275 ATATTTAATTTTATTTT
1 ATATTTAATTTTATTTT
12964292 CACTAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATTTAATTTTATTTTA
Found at i:12964987 original size:29 final size:25
Alignment explanation
Indices: 12964937--12964988 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
12964927 AGATTACTTG
12964937 TTTGAATTTAATTACAAACAATTAA
1 TTTGAATTTAATTACAAACAATTAA
*
12964962 TTTGAATTTAATTACAAACAATCAA
1 TTTGAATTTAATTACAAACAATTAA
12964987 TT
1 TT
12964989 CTTAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (25 bp):
TTTGAATTTAATTACAAACAATTAA
Found at i:12966417 original size:14 final size:14
Alignment explanation
Indices: 12966400--12966436 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12966390 GTGCAGGACC
12966400 GGAGGTGGACCGGT
1 GGAGGTGGACCGGT
**
12966414 GGAGGTGGATTGGT
1 GGAGGTGGACCGGT
12966428 GGAGGTGGA
1 GGAGGTGGA
12966437 GGTAGCTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.16, C:0.05, G:0.59, T:0.19
Consensus pattern (14 bp):
GGAGGTGGACCGGT
Found at i:12967892 original size:29 final size:30
Alignment explanation
Indices: 12967838--12967897 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
12967828 CCGAAATTCA
12967838 TGTGTATCTCTAAAAAAAAAAACAATATTG
1 TGTGTATCTCTAAAAAAAAAAACAATATTG
12967868 TGTGTATCTCT-AAAAAAAAAACAATATTG
1 TGTGTATCTCTAAAAAAAAAAACAATATTG
12967897 T
1 T
12967898 AACTTCTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (30 bp):
TGTGTATCTCTAAAAAAAAAAACAATATTG
Found at i:12968916 original size:113 final size:114
Alignment explanation
Indices: 12968577--12969019 Score: 604
Period size: 114 Copynumber: 3.9 Consensus size: 114
12968567 AAAATAAGCA
** * *
12968577 TTAGCGGCGTTTTCCAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGATGCCATTTTCTGAGCAT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
*
12968641 TCTGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
12968690 TTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCAT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
* *
12968755 TCTGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTTAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
12968804 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTT-TGAGTAA
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
* ***
12968868 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCG-GGAGGGATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCG-CTAATGCTCAGGGCT
* ***** * *
12968917 TTAGCGGGGGAGGGGGGAGAAAGCGTCGCAAAAAAACCTTAAGCCCAACTACGCCGTTTTCTGAG
1 TTAGC-GGCG-TTTTTGAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACGCCGTTTTCTGAG
* *
12968982 CTTTCGGGGATTTAGCGGCGTTTTTGAGAAAGCGCCGC
63 CATTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
12969020 AAAAAAACCT
Statistics
Matches: 294, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
112 1 0.00
113 75 0.26
114 142 0.48
115 21 0.07
116 20 0.07
117 34 0.12
118 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:12969054 original size:73 final size:74
Alignment explanation
Indices: 12968933--12969092 Score: 252
Period size: 73 Copynumber: 2.2 Consensus size: 74
12968923 GGGGAGGGGG
*
12968933 GAGAAAGCGTCGCAAAAAAACCTTAAGCCCAACTACGCCGTTTTCTGAGCTTTCGGGGATTTAGC
1 GAGAAAGCGCCGCAAAAAAACCTTAAGCCCAACTACGCCGTTTTCTGAGCTTTCGGGGATTTAGC
12968998 GGCGTTTTT
66 GGCGTTTTT
* *
12969007 GAGAAAGCGCCGCAAAAAAACC-TAAGCTCAA-TGACGTCGTTTTCTGAGCTTTCGGGGATTTAG
1 GAGAAAGCGCCGCAAAAAAACCTTAAGCCCAACT-ACGCCGTTTTCTGAGCTTTCGGGGATTTAG
12969070 CGGCGTTTTT
65 CGGCGTTTTT
* *
12969080 AAGAAAGCACCGC
1 GAGAAAGCGCCGC
12969093 TAATGCTCAA
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
72 1 0.01
73 58 0.73
74 21 0.26
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (74 bp):
GAGAAAGCGCCGCAAAAAAACCTTAAGCCCAACTACGCCGTTTTCTGAGCTTTCGGGGATTTAGC
GGCGTTTTT
Found at i:12969192 original size:114 final size:114
Alignment explanation
Indices: 12968992--12969362 Score: 589
Period size: 114 Copynumber: 3.2 Consensus size: 114
12968982 CTTTCGGGGA
* * * *
12968992 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCTCAATGACGTCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
12969057 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGC
* * * *
12969106 TTTAGCGTCATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCA
1 TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
12969171 GTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGC
* * *
12969220 TTTTAGCGGCGTTTTTGAGAAAGCACCGTAAAAAAACCTAATCCGAACGACGCCGTTTTCTGAGC
1 -TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
*
12969285 TTTCGGGGATTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAAGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGC
12969335 TTTAGCGGCGTTTTTGAGAAAGCACCGC
1 TTTAGCGGCGTTTTTGAGAAAGCACCGC
12969363 TAATGCTCAG
Statistics
Matches: 233, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
114 131 0.56
115 102 0.44
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGC
Found at i:12969201 original size:187 final size:188
Alignment explanation
Indices: 12968803--12969206 Score: 537
Period size: 187 Copynumber: 2.1 Consensus size: 188
12968793 TGCTTAGGGC
12968803 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTGAGTAA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTGAGTAA
** * * * *
12968868 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGGGAGGGATGCTCAGGGCTTTAGCGGGGGAGGGGG
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCCCGACGAATGCTCAAGGCTTTAGC-GGGCAGGGGG
* * **
12968933 GAGAAAGCGTCGCAAAAAAACCTTAAGCCCAACTACGCCGTTTTCTGAGCTTTCGGGGA
130 GAGAAAGCGCCGCAAAAAAACCTTAAGCCCAACGACGCCGTTTTCTGAGCAGTCGGGGA
* * *
12968992 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCTCAATGACGTCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTT-TGAG-T
* * * ***
12969057 -TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCG-CTAATGCTCAAGGCTTTAGC-GTCATTT
64 AATCGGGGATTTAGCGGCGTTTTTAAGAAAGC-CCGACGAATGCTCAAGGCTTTAGCGGGCAGGG
**
12969119 TTGAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACGCCGTTTTCTGAGCAGTCGGGGA
128 GGGAGAAAGCGCCGCAAAAAAACCTTAAGCCCAACGACGCCGTTTTCTGAGCAGTCGGGGA
* *
12969179 TTTAGCGGTGTTTTTAAGAAAGCGCCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
12969207 TAATGCTCAG
Statistics
Matches: 189, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
187 59 0.31
188 23 0.12
189 55 0.29
190 50 0.26
191 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (188 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTGAGTAA
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCCCGACGAATGCTCAAGGCTTTAGCGGGCAGGGGGG
AGAAAGCGCCGCAAAAAAACCTTAAGCCCAACGACGCCGTTTTCTGAGCAGTCGGGGA
Found at i:12969242 original size:303 final size:302
Alignment explanation
Indices: 12968689--12969321 Score: 912
Period size: 303 Copynumber: 2.1 Consensus size: 302
12968679 TGCTCAGGGC
*
12968689 TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCA
1 TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCA
* * * * *
12968754 TTCTGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGCTTTAGCGGCATTTTTG
*
12968819 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTGAGTAATCGGGGATTTAGCGGC
131 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTGAGCAATCGGGGATTTAGCGGC
* * * * **
12968884 GTTTTTAAGAAAGCGGGAGGGATGCTCAGGGCTTTAGCGGGGGAGGGGGGAGAAAGCGTCGCAAA
196 GTTTTTAAGAAAGCGCGACGAATGCTCAGGGCTTTAGCGGGCGAGGGGGGAGAAAGCACCGCAAA
*
12968949 AAAACCTTAAGCCCAACTACGCCGTTTTCTGAGCTTTCGGGGA
261 AAAACC-TAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* * * * *
12968992 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCTCAATGACGTCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCA
*
12969057 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGCTTTAGCGTCATTTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGCTTTAGCGGCATTTTTG
*
12969122 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAGTCGGGGATTTAGCGG
131 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTT-TGAGCAATCGGGGATTTAGCGG
* * ***** *
12969187 TGTTTTTAAGAAAGCGCCG-CTAATGCTCAGGGCTTTTAGC-GGCG-TTTTTGAGAAAGCACCGT
195 CGTTTTTAAGAAAGCG-CGACGAATGCTCAGGGC-TTTAGCGGGCGAGGGGGGAGAAAGCACCGC
* *
12969249 AAAAAAACCTAATCCGAACGACGCCGTTTTCTGAGCTTTCGGGGA
258 AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* *
12969294 TTTAGCGGCATTTTTAAGAAAGCACCGC
1 TTTAGCGGCGTTTTTGAGAAAGCACCGC
12969322 TAATGCTCAA
Statistics
Matches: 293, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
302 58 0.20
303 179 0.61
304 49 0.17
305 7 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (302 bp):
TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCA
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAAGGCTTTAGCGGCATTTTTG
AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTGAGCAATCGGGGATTTAGCGGC
GTTTTTAAGAAAGCGCGACGAATGCTCAGGGCTTTAGCGGGCGAGGGGGGAGAAAGCACCGCAAA
AAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
Found at i:12969355 original size:41 final size:41
Alignment explanation
Indices: 12969294--12969371 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
12969284 CTTTCGGGGA
12969294 TTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAAGGC
1 TTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAAGGC
* *
12969335 TTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTCA
1 TTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCA
12969372 GGAATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAAGGC
Found at i:12972620 original size:16 final size:15
Alignment explanation
Indices: 12972595--12972626 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
12972585 TTTTAATTTT
12972595 TTTAATATAGATATA
1 TTTAATATAGATATA
12972610 TTTAGATATAGATATA
1 TTTA-ATATAGATATA
12972626 T
1 T
12972627 ATATGTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTAATATAGATATA
Found at i:12973403 original size:43 final size:43
Alignment explanation
Indices: 12973342--12973529 Score: 331
Period size: 43 Copynumber: 4.4 Consensus size: 43
12973332 AAAAGTCATA
*
12973342 TTCTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCTTG
1 TTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
*
12973385 TTCTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTG
1 TTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
* *
12973428 TTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAATGTCTTG
1 TTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
*
12973471 TTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
1 TTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
12973514 TTCTTTAGCGGCGTTT
1 TTCTTTAGCGGCGTTT
12973530 ATTTCTAAAA
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 136 1.00
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.33
Consensus pattern (43 bp):
TTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
Found at i:12980259 original size:20 final size:20
Alignment explanation
Indices: 12980230--12980270 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12980220 AAATATTACT
12980230 TGGATATCAATATCGATACC
1 TGGATATCAATATCGATACC
*
12980250 TGGATGTCAATATCGATACC
1 TGGATATCAATATCGATACC
12980270 T
1 T
12980271 ACGGACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (20 bp):
TGGATATCAATATCGATACC
Found at i:12981843 original size:15 final size:15
Alignment explanation
Indices: 12981823--12981854 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12981813 GGTTTATTTT
12981823 TGATTGATAACATGG
1 TGATTGATAACATGG
*
12981838 TGATTGATAACGTGG
1 TGATTGATAACATGG
12981853 TG
1 TG
12981855 TGTGAGGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.31, T:0.34
Consensus pattern (15 bp):
TGATTGATAACATGG
Found at i:13010085 original size:21 final size:21
Alignment explanation
Indices: 13010036--13010087 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 21
13010026 TTGCTACTGT
*
13010036 AGAAGAGAAA-ATTGTTGCTGA
1 AGAAGAGAAAGA-AGTTGCTGA
13010057 AG-A-A-AAAGAAGTTGCTGA
1 AGAAGAGAAAGAAGTTGCTGA
13010075 AGAAGAGAAAGAA
1 AGAAGAGAAAGAA
13010088 AGAAAAGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 13 0.50
19 3 0.12
20 2 0.08
21 8 0.31
ACGTcount: A:0.52, C:0.04, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAAGAGAAAGAAGTTGCTGA
Found at i:13017094 original size:19 final size:20
Alignment explanation
Indices: 13017070--13017108 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
13017060 AGGTAAATTG
13017070 AAAATGAT-TATTTGAGTTT
1 AAAATGATATATTTGAGTTT
* *
13017089 AAAATGCTATGTTTGAGTTT
1 AAAATGATATATTTGAGTTT
13017109 GATTATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (20 bp):
AAAATGATATATTTGAGTTT
Found at i:13020568 original size:44 final size:43
Alignment explanation
Indices: 13020505--13020662 Score: 137
Period size: 42 Copynumber: 3.7 Consensus size: 43
13020495 TATGTGTTAT
**
13020505 TGTGTAAGACCGCGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTGTAAGACCATGTCTGGGACGTTGGCATCGATATT--GATTTA
* * *
13020549 TGTGTAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTC
1 TGTGTAAGACCATGTCTGGGACGTTGGCATCGATA-TTGATTTA
* * *
13020592 T-TGTAAGACCCTGTTTGGGACAG-TGGCATTGATATTGA-TTA
1 TGTGTAAGACCATGTCTGGGAC-GTTGGCATCGATATTGATTTA
** * *
13020633 CATGTAAGACCATGCCTGAGACGTTGGCAT
1 TGTGTAAGACCATGTCTGGGACGTTGGCAT
13020663 TGTACGAGTT
Statistics
Matches: 92, Mismatches: 16, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
41 3 0.03
42 49 0.53
43 11 0.12
44 27 0.29
45 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTGTAAGACCATGTCTGGGACGTTGGCATCGATATTGATTTA
Found at i:13021005 original size:17 final size:18
Alignment explanation
Indices: 13020961--13021005 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
13020951 TATGAAATTT
13020961 TGATATGAAATGTGAGTA
1 TGATATGAAATGTGAGTA
*
13020979 TGAT-TAAAATGATGA-TA
1 TGATATGAAATG-TGAGTA
13020996 T-ATATGAAAT
1 TGATATGAAAT
13021006 ATATGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (18 bp):
TGATATGAAATGTGAGTA
Found at i:13027649 original size:26 final size:26
Alignment explanation
Indices: 13027616--13027668 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
13027606 ATTCGTTATC
13027616 TAATTTATATGTAAATAAATGAGATG
1 TAATTTATATGTAAATAAATGAGATG
13027642 TAATTTATATGTAAATAAATGAGATG
1 TAATTTATATGTAAATAAATGAGATG
13027668 T
1 T
13027669 TAATGATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (26 bp):
TAATTTATATGTAAATAAATGAGATG
Found at i:13027677 original size:26 final size:26
Alignment explanation
Indices: 13027616--13027678 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
13027606 ATTCGTTATC
*
13027616 TAATTTATATGTAAATAAATGAGATG
1 TAATTGATATGTAAATAAATGAGATG
*
13027642 TAATTTATATGTAAATAAATGAGATG
1 TAATTGATATGTAAATAAATGAGATG
13027668 TTAA-TGATATG
1 -TAATTGATATG
13027679 GGTTGGAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 32 0.91
27 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (26 bp):
TAATTGATATGTAAATAAATGAGATG
Found at i:13034956 original size:9 final size:9
Alignment explanation
Indices: 13034917--13034976 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
13034907 GCCCAGAGCT
13034917 ACTTCTTTC
1 ACTTCTTTC
**
13034926 TTTTCTTTC
1 ACTTCTTTC
* *
13034935 TCTTGTTTC
1 ACTTCTTTC
*
13034944 ACTTCTTTT
1 ACTTCTTTC
*
13034953 ACTTCCTTC
1 ACTTCTTTC
13034962 ACTTCTTTC
1 ACTTCTTTC
*
13034971 TCTTCT
1 ACTTCT
13034977 GCTGGAATTG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.07, C:0.30, G:0.02, T:0.62
Consensus pattern (9 bp):
ACTTCTTTC
Found at i:13035427 original size:48 final size:48
Alignment explanation
Indices: 13035368--13035556 Score: 272
Period size: 48 Copynumber: 3.9 Consensus size: 48
13035358 CTAACGCTTC
* * * *
13035368 CTTCCTCTGCAGATTTCGGAACAGAACTTACTGCTCTCGGTTTATTGG
1 CTTCTTCTACAGATTTCGGAACAGAACTTACTGCTTTCGGTTCATTGG
* *
13035416 CTTCTTCTGCAGATTTCGGAACAGAACTTACTGCTTTCGGTTCATTGA
1 CTTCTTCTACAGATTTCGGAACAGAACTTACTGCTTTCGGTTCATTGG
*
13035464 CTTCTTCTACAGATTTCGGAACAGAACTTACTGCTTTCGGTTCATCGG
1 CTTCTTCTACAGATTTCGGAACAGAACTTACTGCTTTCGGTTCATTGG
* * *
13035512 CTT-TCTCTACAGATTTTGGAACAGAACTTATTGCTTTCGATTCAT
1 CTTCT-TCTACAGATTTCGGAACAGAACTTACTGCTTTCGGTTCAT
13035557 CAGCCATGGC
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
47 1 0.01
48 129 0.99
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (48 bp):
CTTCTTCTACAGATTTCGGAACAGAACTTACTGCTTTCGGTTCATTGG
Found at i:13037946 original size:29 final size:29
Alignment explanation
Indices: 13037901--13037957 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
13037891 GTAAAGTAAG
* **
13037901 GCCTATAGGTTGTTTTTTTAATTAATTAA
1 GCCTATAGGTTGGTTTTAAAATTAATTAA
*
13037930 GCCTTTAGGTTGGTTTTAAAATTAATTA
1 GCCTATAGGTTGGTTTTAAAATTAATTA
13037958 GGGAAATAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (29 bp):
GCCTATAGGTTGGTTTTAAAATTAATTAA
Found at i:13041021 original size:18 final size:19
Alignment explanation
Indices: 13040979--13041027 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
13040969 GTTTCACATC
13040979 TCATTTCTCCATTTCATATT
1 TCATTTCT-CATTTCATATT
*
13040999 TCATTTCTCATTTCGTA-T
1 TCATTTCTCATTTCATATT
*
13041017 TCATTTATCAT
1 TCATTTCTCAT
13041028 CTTTGCCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 11 0.41
19 8 0.30
20 8 0.30
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.55
Consensus pattern (19 bp):
TCATTTCTCATTTCATATT
Found at i:13042672 original size:2 final size:2
Alignment explanation
Indices: 13042665--13042711 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
13042655 TATAAAAGTT
13042665 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13042707 T- TA TA
1 TA TA TA
13042712 AGAATGCATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13044600 original size:18 final size:19
Alignment explanation
Indices: 13044565--13044601 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
13044555 TTTATTATGT
13044565 TTATATTATAATATCATTA
1 TTATATTATAATATCATTA
13044584 TTAT-TTAT-ATATACATTA
1 TTATATTATAATAT-CATTA
13044602 AAGTTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATTATAATATCATTA
Found at i:13044615 original size:2 final size:2
Alignment explanation
Indices: 13044610--13044654 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
13044600 TAAAGTTAAC
* * *
13044610 AT AT AT AT A- AT AT AC AC AT GT 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
13044651 AT AT
1 AT AT
13044655 CTTTAAACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:13045933 original size:198 final size:199
Alignment explanation
Indices: 13045589--13045970 Score: 640
Period size: 198 Copynumber: 1.9 Consensus size: 199
13045579 ATGCCAAACT
* * * *
13045589 CATGCCAGGACAGACGCCAAGGTATGCACCTTCACCGATGGCGATACCGCTGCAGATGCTTGTGC
1 CATGCCAAGACAGACACCAAGGTATGCACCGTCACCGATGGCGATACCGATGCAGATGCTTGTGC
*
13045654 AACAATTGATGATGATGATGATGCCCAACAGCGTTCTGATGTACCCAAGATTTGGGGCACCTTAT
66 AACAATTGATGATGATGACGATGCCCAACAGCGTTCTGATGTACCCAAGATTTGGGGCACCTTAT
*
13045719 GGTTACACGACTATAGTGACCTAAACACCGCACACATCACTTTTTCATG-GGTTTCTAATGCCGA
131 GGTTACACGACTATAGTGACCCAAACACCGCACACATCACTTTTTCATGAGGTTTCTAATGCCGA
13045783 ACCC
196 ACCC
* *
13045787 CATGCCAAGACAGACACCAAGGTATGCACCGTCACCGATGGCGATACCGATGTAGATGCTTGTGT
1 CATGCCAAGACAGACACCAAGGTATGCACCGTCACCGATGGCGATACCGATGCAGATGCTTGTGC
* * * *
13045852 AGCAATTGATGATGATGACGATGCCCGACAGCGTTTTGATGTACCCAATATTTGGGGCACCTTAT
66 AACAATTGATGATGATGACGATGCCCAACAGCGTTCTGATGTACCCAAGATTTGGGGCACCTTAT
*
13045917 GGTTACACGCCTATAGTGACCCAAACACCGCACACATCACTTTTTCATGAGGTT
131 GGTTACACGACTATAGTGACCCAAACACCGCACACATCACTTTTTCATGAGGTT
13045971 GGCTCATCAT
Statistics
Matches: 170, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
198 166 0.98
199 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.25
Consensus pattern (199 bp):
CATGCCAAGACAGACACCAAGGTATGCACCGTCACCGATGGCGATACCGATGCAGATGCTTGTGC
AACAATTGATGATGATGACGATGCCCAACAGCGTTCTGATGTACCCAAGATTTGGGGCACCTTAT
GGTTACACGACTATAGTGACCCAAACACCGCACACATCACTTTTTCATGAGGTTTCTAATGCCGA
ACCC
Found at i:13048843 original size:12 final size:12
Alignment explanation
Indices: 13048826--13048863 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
13048816 GTTGATAAAG
13048826 AAAATAAAATAA
1 AAAATAAAATAA
13048838 AAAAT-AAATAA
1 AAAATAAAATAA
13048849 GAAAATAAAATAA
1 -AAAATAAAATAA
13048862 AA
1 AA
13048864 TTAGAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.25
12 12 0.50
13 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:13052908 original size:25 final size:25
Alignment explanation
Indices: 13052856--13052908 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
13052846 TTAGTGTAGA
* * *
13052856 TTAAAACATTTGAAGAAATACTTTC
1 TTAAAACATTTAAAGAAAAAATTTC
13052881 TTAAAA-ATTTAAAGAAAAAATTTAC
1 TTAAAACATTTAAAGAAAAAATTT-C
13052906 TTA
1 TTA
13052909 TTTAGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.36
Consensus pattern (25 bp):
TTAAAACATTTAAAGAAAAAATTTC
Found at i:13053481 original size:27 final size:28
Alignment explanation
Indices: 13053449--13053501 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
13053439 ATACGGGTTC
*
13053449 AATACGAGTAGTTGGGTGGTA-GGGTAA
1 AATACGAGTAGTTGGATGGTATGGGTAA
* *
13053476 AATACGGGTATTTGGATGGTATGGGT
1 AATACGAGTAGTTGGATGGTATGGGT
13053502 GGTGCCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.26, C:0.04, G:0.40, T:0.30
Consensus pattern (28 bp):
AATACGAGTAGTTGGATGGTATGGGTAA
Found at i:13068471 original size:36 final size:36
Alignment explanation
Indices: 13068411--13068529 Score: 125
Period size: 36 Copynumber: 3.3 Consensus size: 36
13068401 ACTATCTGTT
* ** * ** *
13068411 TTGGTGTGTTTAGGTTGGACTAGCTCTTCGGAGCCA
1 TTGGTGTGTTTCGAATGGATTAGCTCTTATGAGCTA
*
13068447 TTGGTGTGTTTCGAATGGATTAGCTCTGATGAG-TA
1 TTGGTGTGTTTCGAATGGATTAGCTCTTATGAGCTA
*
13068482 TTTGGTGTGTTTC-AGATGGATTAGCTCTTATGAGCTT
1 -TTGGTGTGTTTCGA-ATGGATTAGCTCTTATGAGCTA
13068519 TTGGTGTGTTT
1 TTGGTGTGTTT
13068530 TGGTTGCATT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
35 2 0.03
36 67 0.96
37 1 0.01
ACGTcount: A:0.15, C:0.11, G:0.31, T:0.43
Consensus pattern (36 bp):
TTGGTGTGTTTCGAATGGATTAGCTCTTATGAGCTA
Found at i:13069697 original size:4 final size:4
Alignment explanation
Indices: 13069688--13069717 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
13069678 ATAGGGACGT
13069688 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
13069718 AATGGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:13072075 original size:13 final size:13
Alignment explanation
Indices: 13072059--13072511 Score: 207
Period size: 13 Copynumber: 34.5 Consensus size: 13
13072049 CATCTCTTTC
13072059 CATATAACCATTT
1 CATATAACCATTT
* *
13072072 CATATATCAATTT
1 CATATAACCATTT
* *
13072085 CCATGT-ACTTGAT-T
1 -CATATAAC--CATTT
13072099 CATATAACCATTT
1 CATATAACCATTT
* *
13072112 CATATATCTATTT
1 CATATAACCATTT
13072125 CCATATAACCGA-TT
1 -CATATAACC-ATTT
*
13072139 CATATATCCATTT
1 CATATAACCATTT
* * *
13072152 CATATATCTACTTC
1 CATATAACCA-TTT
13072166 CATATAACCGATTT
1 CATATAACC-ATTT
13072180 -ATATAACCATTT
1 CATATAACCATTT
* *
13072192 CATCT-A--TTTT
1 CATATAACCATTT
*
13072202 CATATAACTGA-TT
1 CATATAAC-CATTT
*
13072215 CATATAATCATTT
1 CATATAACCATTT
* * *
13072228 CATATATCTACTTC
1 CATATAACCA-TTT
* *
13072242 CATATAACTGA-AT
1 CATATAAC-CATTT
13072255 CATATAACCATTT
1 CATATAACCATTT
* * *
13072268 CATTTATCTATTT
1 CATATAACCATTT
*
13072281 CCATATAAACGA-TT
1 -CATAT-AACCATTT
13072295 CATATAACCATTT
1 CATATAACCATTT
* * * *
13072308 TATATATCTACTTC
1 CATATAACCA-TTT
13072322 CATATAACC-TATT
1 CATATAACCAT-TT
13072335 CATATAACCATTT
1 CATATAACCATTT
* * *
13072348 CATTTATCTATTT
1 CATATAACCATTT
**
13072361 CCATATAATTGA-TT
1 -CATATAA-CCATTT
13072375 CATATAACCATTT
1 CATATAACCATTT
* * *
13072388 CATTTATCTATTT
1 CATATAACCATTT
*
13072401 CCATATAATCGA-TT
1 -CATATAA-CCATTT
13072415 CATATAACCATTT
1 CATATAACCATTT
* ***
13072428 CTTATATTTA-TT
1 CATATAACCATTT
*
13072440 CATATAATCGA-TT
1 CATATAA-CCATTT
13072453 CATATAACCATTT
1 CATATAACCATTT
* * *
13072466 CATTTATCTATTT
1 CATATAACCATTT
* *
13072479 CCATATAATCAATT
1 -CATATAACCATTT
13072493 CATATAACCATTT
1 CATATAACCATTT
13072506 CATATA
1 CATATA
13072512 CTACTCTTCA
Statistics
Matches: 323, Mismatches: 83, Indels: 68
0.68 0.18 0.14
Matches are distributed among these distances:
10 7 0.02
11 1 0.00
12 27 0.08
13 204 0.63
14 73 0.23
15 11 0.03
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.43
Consensus pattern (13 bp):
CATATAACCATTT
Found at i:13072103 original size:40 final size:40
Alignment explanation
Indices: 13072059--13072511 Score: 541
Period size: 40 Copynumber: 11.5 Consensus size: 40
13072049 CATCTCTTTC
* * *
13072059 CATATAACCATTTCATATATCAATTTCCATGTACTTGATT
1 CATATAACCATTTCATATATCTATTTCCATATACTCGATT
13072099 CATATAACCATTTCATATATCTATTTCCATATAAC-CGATT
1 CATATAACCATTTCATATATCTATTTCCATAT-ACTCGATT
* *
13072139 CATATATCCATTTCATATATCTACTTCCATATAAC-CGATT
1 CATATAACCATTTCATATATCTATTTCCATAT-ACTCGATT
* *
13072179 TATATAACCATTTC----ATCTATTTTCATATAACT-GATT
1 CATATAACCATTTCATATATCTATTTCCATAT-ACTCGATT
* * *
13072215 CATATAATCATTTCATATATCTACTTCCATATAACT-GAAT
1 CATATAACCATTTCATATATCTATTTCCATAT-ACTCGATT
* **
13072255 CATATAACCATTTCATTTATCTATTTCCATATAAACGATT
1 CATATAACCATTTCATATATCTATTTCCATATACTCGATT
* * *
13072295 CATATAACCATTTTATATATCTACTTCCATATAAC-CTATT
1 CATATAACCATTTCATATATCTATTTCCATAT-ACTCGATT
* * *
13072335 CATATAACCATTTCATTTATCTATTTCCATATAATTGATT
1 CATATAACCATTTCATATATCTATTTCCATATACTCGATT
* *
13072375 CATATAACCATTTCATTTATCTATTTCCATATAATCGATT
1 CATATAACCATTTCATATATCTATTTCCATATACTCGATT
* * *
13072415 CATATAACCATTTCTTATATTTA-TT-CATATAATCGATT
1 CATATAACCATTTCATATATCTATTTCCATATACTCGATT
* * *
13072453 CATATAACCATTTCATTTATCTATTTCCATATAATCAATT
1 CATATAACCATTTCATATATCTATTTCCATATACTCGATT
13072493 CATATAACCATTTCATATA
1 CATATAACCATTTCATATA
13072512 CTACTCTTCA
Statistics
Matches: 362, Mismatches: 40, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
36 31 0.09
38 33 0.09
39 6 0.02
40 289 0.80
41 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.43
Consensus pattern (40 bp):
CATATAACCATTTCATATATCTATTTCCATATACTCGATT
Found at i:13072150 original size:80 final size:81
Alignment explanation
Indices: 13072059--13072511 Score: 597
Period size: 80 Copynumber: 5.7 Consensus size: 81
13072049 CATCTCTTTC
* * * *
13072059 CATATAACCATTTCATATATCAATTTCCATGT-ACTTGATTCATATAACCATTTCATATATCTAT
1 CATATAACCATTTCATATATCTACTTCCATATAACTCGATTCATATAACCATTTCATATATCTAT
13072123 TTCCATATAACCGATT
66 TTCCATATAACCGATT
* *
13072139 CATATATCCATTTCATATATCTACTTCCATATAAC-CGATTTATATAACCATTTC----ATCTAT
1 CATATAACCATTTCATATATCTACTTCCATATAACTCGATTCATATAACCATTTCATATATCTAT
* *
13072199 TTTCATATAACTGATT
66 TTCCATATAACCGATT
* * *
13072215 CATATAATCATTTCATATATCTACTTCCATATAACT-GAATCATATAACCATTTCATTTATCTAT
1 CATATAACCATTTCATATATCTACTTCCATATAACTCGATTCATATAACCATTTCATATATCTAT
*
13072279 TTCCATATAAACGATT
66 TTCCATATAACCGATT
* * *
13072295 CATATAACCATTTTATATATCTACTTCCATATAAC-CTATTCATATAACCATTTCATTTATCTAT
1 CATATAACCATTTCATATATCTACTTCCATATAACTCGATTCATATAACCATTTCATATATCTAT
**
13072359 TTCCATATAATTGATT
66 TTCCATATAACCGATT
* * * *
13072375 CATATAACCATTTCATTTATCTATTTCCATATAA-TCGATTCATATAACCATTTCTTATATTTA-
1 CATATAACCATTTCATATATCTACTTCCATATAACTCGATTCATATAACCATTTCATATATCTAT
*
13072438 TT-CATATAATCGATT
66 TTCCATATAACCGATT
* * *
13072453 CATATAACCATTTCATTTATCTATTTCCATATAA-TCAATTCATATAACCATTTCATATA
1 CATATAACCATTTCATATATCTACTTCCATATAACTCGATTCATATAACCATTTCATATA
13072512 CTACTCTTCA
Statistics
Matches: 334, Mismatches: 31, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
76 69 0.21
78 69 0.21
79 2 0.01
80 192 0.57
81 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.43
Consensus pattern (81 bp):
CATATAACCATTTCATATATCTACTTCCATATAACTCGATTCATATAACCATTTCATATATCTAT
TTCCATATAACCGATT
Found at i:13072998 original size:27 final size:28
Alignment explanation
Indices: 13072955--13073014 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
13072945 AAACAAACTC
*
13072955 AATCACAACCTACATAAATAATT-ATTA
1 AATCACAACATACATAAATAATTAATTA
* *
13072982 AATCACAA-ATACAATAACTAATTAATTT
1 AATCACAACATAC-ATAAATAATTAATTA
13073010 AATCA
1 AATCA
13073015 ATTTACAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.11
27 17 0.61
28 8 0.29
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (28 bp):
AATCACAACATACATAAATAATTAATTA
Found at i:13081630 original size:19 final size:20
Alignment explanation
Indices: 13081606--13081646 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
13081596 TGCTTGTGAA
13081606 AGAAAA-AGAAAAAAAAAAG
1 AGAAAAGAGAAAAAAAAAAG
*
13081625 AGAAAAGTGAAAAAAAAAAG
1 AGAAAAGAGAAAAAAAAAAG
13081645 AG
1 AG
13081647 CATATGTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AGAAAAGAGAAAAAAAAAAG
Found at i:13083722 original size:17 final size:17
Alignment explanation
Indices: 13083700--13083733 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13083690 ATTCTAAGTT
13083700 AAGAAATGTAATTAATC
1 AAGAAATGTAATTAATC
13083717 AAGAAATGTAATTAATC
1 AAGAAATGTAATTAATC
13083734 TAACACAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
AAGAAATGTAATTAATC
Found at i:13091285 original size:27 final size:28
Alignment explanation
Indices: 13091255--13091318 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
13091245 TATTTCTGAG
**
13091255 ACTGTATCTG-AATGGGCTGAGGCCCAA
1 ACTGTATCTGTAATGGGCACAGGCCCAA
*
13091282 ACTG-ATTCTGTGATGGGCACAGGCCCAA
1 ACTGTA-TCTGTAATGGGCACAGGCCCAA
*
13091310 ACTATATCT
1 ACTGTATCT
13091319 AACTAAATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 1 0.03
27 8 0.27
28 20 0.67
29 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (28 bp):
ACTGTATCTGTAATGGGCACAGGCCCAA
Found at i:13092891 original size:34 final size:31
Alignment explanation
Indices: 13092840--13092913 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 31
13092830 TCAAGTCCGA
13092840 GCCCAACCCATAATTCAAAGGGCCTAA-ATTTTT
1 GCCCAACCCATAATTC-AA--GCCTAATATTTTT
**
13092873 GCCCAAGCCCATTCTTCAAGCCTAATATTTTT
1 GCCCAA-CCCATAATTCAAGCCTAATATTTTT
13092905 GCCCAACCC
1 GCCCAACCC
13092914 TCCCACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
31 9 0.24
32 12 0.32
33 8 0.22
34 8 0.22
ACGTcount: A:0.28, C:0.34, G:0.11, T:0.27
Consensus pattern (31 bp):
GCCCAACCCATAATTCAAGCCTAATATTTTT
Found at i:13095708 original size:61 final size:61
Alignment explanation
Indices: 13095635--13095752 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 61
13095625 ATTAGTTTAA
* *
13095635 TAAATTTAATTTAATATTTATCTTCATAGTATTTTATTAATATAGTATTAATGTGAGATAT
1 TAAATTTAATTTAATATTTATCTTCATAGTATTTTATTAATATAATATTAATATGAGATAT
* * * *
13095696 TAAATTTGATTTAATATTTATCTTGATAGTGTTTTATTAATTTAATATTAATATGAG
1 TAAATTTAATTTAATATTTATCTTCATAGTATTTTATTAATATAATATTAATATGAG
13095753 TAATTTCAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (61 bp):
TAAATTTAATTTAATATTTATCTTCATAGTATTTTATTAATATAATATTAATATGAGATAT
Found at i:13095741 original size:31 final size:31
Alignment explanation
Indices: 13095640--13095744 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
13095630 TTTAATAAAT
*
13095640 TTAATTTAATATTTATCTTCATAGTATTTTA
1 TTAATTTAATATTTATCTTGATAGTATTTTA
* * * * * **
13095671 TTAATATAGTATTAAT-GTGAGA-TATTAAA
1 TTAATTTAATATTTATCTTGATAGTATTTTA
* *
13095700 TTTGATTTAATATTTATCTTGATAGTGTTTTA
1 -TTAATTTAATATTTATCTTGATAGTATTTTA
13095732 TTAATTTAATATT
1 TTAATTTAATATT
13095745 AATATGAGTA
Statistics
Matches: 53, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
29 5 0.09
30 15 0.28
31 29 0.55
32 4 0.08
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (31 bp):
TTAATTTAATATTTATCTTGATAGTATTTTA
Found at i:13103587 original size:23 final size:23
Alignment explanation
Indices: 13103557--13103611 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
13103547 CTACATCCCT
13103557 AATCCCTTAAAACCAAATCGTGA
1 AATCCCTTAAAACCAAATCGTGA
*
13103580 AATCCCTTAAAACCCAATCGTGA
1 AATCCCTTAAAACCAAATCGTGA
13103603 AAT-CCTTAA
1 AATCCCTTAA
13103612 TCTTTTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (23 bp):
AATCCCTTAAAACCAAATCGTGA
Found at i:13104833 original size:16 final size:16
Alignment explanation
Indices: 13104812--13104849 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
13104802 TATGATTAGT
*
13104812 CTATACACCATTCACC
1 CTATACACCATCCACC
*
13104828 CTATACACCATCCACG
1 CTATACACCATCCACC
13104844 CTATAC
1 CTATAC
13104850 CAGCCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.42, G:0.03, T:0.24
Consensus pattern (16 bp):
CTATACACCATCCACC
Found at i:13105448 original size:12 final size:12
Alignment explanation
Indices: 13105428--13105457 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13105418 GAGAGGAGCC
*
13105428 TTTCGCTTGTTA
1 TTTCACTTGTTA
13105440 TTTCACTTGTTA
1 TTTCACTTGTTA
13105452 TTTCAC
1 TTTCAC
13105458 GACTTGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.20, G:0.10, T:0.57
Consensus pattern (12 bp):
TTTCACTTGTTA
Found at i:13114473 original size:36 final size:37
Alignment explanation
Indices: 13114405--13114488 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 37
13114395 ACAATTGAAC
* * ** * *
13114405 TTATAAGTGATTCGGCCTATTGATGTATTTGTAATA-
1 TTATAAGTGATTCAGCATAACGATATAGTTGTAATAT
13114441 TTATAAGTGATTCAGCATAACGATATAGTTGTAATAT
1 TTATAAGTGATTCAGCATAACGATATAGTTGTAATAT
*
13114478 TTAAAAGTGAT
1 TTATAAGTGAT
13114489 AATTATATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 30 0.75
37 10 0.25
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (37 bp):
TTATAAGTGATTCAGCATAACGATATAGTTGTAATAT
Found at i:13119673 original size:24 final size:24
Alignment explanation
Indices: 13119641--13119686 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
13119631 CACAGTAGCT
13119641 GAAAAACTTGAAAGATTACAAGCA
1 GAAAAACTTGAAAGATTACAAGCA
13119665 GAAAAACTTGAAAGATTACAAG
1 GAAAAACTTGAAAGATTACAAG
13119687 TAGACTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (24 bp):
GAAAAACTTGAAAGATTACAAGCA
Found at i:13124662 original size:126 final size:123
Alignment explanation
Indices: 13124437--13124714 Score: 457
Period size: 126 Copynumber: 2.2 Consensus size: 123
13124427 NNNNNNCGCG
* *
13124437 GCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTGACTTTTCTGAGC
1 GCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTGACTTCTCTGACC
* *
13124502 AAATAGTATAAAATCGCTTTTAGCATGATGCTATTTGAGAAGAATTTGTGAAATCGCA
66 AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCA
*
13124560 GCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTTTTTGACTTCTCTG
1 GCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATA---ATTTTTTTGACTTCTCTG
* *
13124625 ACCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTTAGAAGAATTTGTGAAATCGCG
63 ACCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCA
*
13124686 GCCTCGTGGGCGCGCTTTTGCTACAGTAG
1 GCCTCGTGGACGCGCTTTTGCTACAGTAG
13124715 CATGTTTGGG
Statistics
Matches: 144, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
123 44 0.31
126 100 0.69
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (123 bp):
GCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTGACTTCTCTGACC
AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCA
Found at i:13127931 original size:22 final size:22
Alignment explanation
Indices: 13127900--13128028 Score: 116
Period size: 22 Copynumber: 5.5 Consensus size: 22
13127890 AAATATGGAT
13127900 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
13127922 TTAAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* * **
13127944 TTGAGAGGAA-ATTGAAATTAAA
1 TTGAGA-GAATTTTGGAAGGAAA
13127966 TATGGATTTAAGAGAATTTTGGAAGGAAA
1 T-T-G-----AGAGAATTTTGGAAGGAAA
*
13127995 TTGAGAGAATTTTGGAAAGAAA
1 TTGAGAGAATTTTGGAAGGAAA
13128017 TTGAGAGGAATT
1 TTGAGA-GAATT
13128029 GAGAGGAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
22 59 0.69
23 9 0.10
24 1 0.01
27 1 0.01
28 4 0.05
29 12 0.14
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:13127941 original size:73 final size:73
Alignment explanation
Indices: 13127864--13128030 Score: 291
Period size: 73 Copynumber: 2.3 Consensus size: 73
13127854 TATTTTAAAA
*
13127864 AAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATTAAGAG
1 AAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTAAGAGAATTTTGGAAGGAAATTAAGAG
13127929 AATTTTGG
66 AATTTTGG
* *
13127937 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAAGGAAATTGAGAG
1 AAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTAAGAGAATTTTGGAAGGAAATTAAGAG
13128002 AATTTTGG
66 AATTTTGG
*
13128010 AAAGAAATTGAGAGG-AATTGA
1 AAGGAAATTGAGAGGAAATTGA
13128031 GAGGAAATAT
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 6 0.07
73 84 0.93
ACGTcount: A:0.45, C:0.01, G:0.28, T:0.27
Consensus pattern (73 bp):
AAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTAAGAGAATTTTGGAAGGAAATTAAGAG
AATTTTGG
Found at i:13128045 original size:12 final size:11
Alignment explanation
Indices: 13128013--13128045 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
13128003 ATTTTGGAAA
13128013 GAAATTGAGAG
1 GAAATTGAGAG
13128024 G-AATTGAGAG
1 GAAATTGAGAG
13128034 GAAATATGAGAG
1 GAAAT-TGAGAG
13128046 AGGATTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:13129216 original size:32 final size:32
Alignment explanation
Indices: 13129175--13129239 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 32
13129165 GACACCTATG
13129175 TTTCCTATTTTGTTTCAAT-TCCTTACCATATA
1 TTTCCTATTTTGTTTCAATAT-CTTACCATATA
13129207 TTTCCTATTTTGTTTCAATATCTTACCATATA
1 TTTCCTATTTTGTTTCAATATCTTACCATATA
13129239 T
1 T
13129240 GTATGTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.54
Consensus pattern (32 bp):
TTTCCTATTTTGTTTCAATATCTTACCATATA
Found at i:13131322 original size:34 final size:35
Alignment explanation
Indices: 13131262--13131331 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
13131252 AAGGAAGGAA
* *
13131262 TTGATATATCTGTTTGCAGTTTTTGTATTTCATGT
1 TTGATATATCTGTTTGCAGTTGTTGTATTGCATGT
*
13131297 TTGAT-TATCTGTTTGTA-TTAGTTGTATTGCATGT
1 TTGATATATCTGTTTGCAGTT-GTTGTATTGCATGT
13131331 T
1 T
13131332 AGAAGGGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.06
34 24 0.77
35 5 0.16
ACGTcount: A:0.17, C:0.07, G:0.19, T:0.57
Consensus pattern (35 bp):
TTGATATATCTGTTTGCAGTTGTTGTATTGCATGT
Found at i:13134307 original size:174 final size:175
Alignment explanation
Indices: 13133936--13134419 Score: 733
Period size: 174 Copynumber: 2.8 Consensus size: 175
13133926 TACAAGACAG
*
13133936 CTAAAACAAAGTAATAAATCAACAAAGAAACTGAATTTGAACAAATTTTGTTGCTCAGGTAACCG
1 CTAAAACAAAGTAATAAATCAACAAAGAAATTGAATTTGAACAAATTTTGTTGCTCAGGTAACCG
* *
13134001 CTCAGATCGACATGGTTGTCGATGTTTCATTAAATTTTCATAAATTCTAATATAATCATCACAGC
66 CTCAGATCGACATAGTTGTCGATGTTTCACTAAATTTTCATAAATTCTAATATAATCATCACAGC
13134066 AACAAAACCACAGATTCACATACAATAAAATGTATCATAAGACGA
131 AACAAAACCACAGATTCACATACAATAAAATGTATCATAAGACGA
* *
13134111 CTAAAGA-AACGTAATAAATCAACAAGGAAATTGAATTTGAACAAATTTTGTTGCTCAGGTAACC
1 CTAAA-ACAAAGTAATAAATCAACAAAGAAATTGAATTTGAACAAATTTTGTTGCTCAGGTAACC
*
13134175 GCTCAGATCGACATAGTTGTCGATGTTTCA-TAAATCTTCATAAATTCTAATATAATCATCACAG
65 GCTCAGATCGACATAGTTGTCGATGTTTCACTAAATTTTCATAAATTCTAATATAATCATCACAG
** * **
13134239 CAACAAAACTGCAGATTCACATACAATAAGAT-TAATTGTAAGACGA
130 CAACAAAACCACAGATTCACATACAATAAAATGT-ATCATAAGACGA
* * ** *
13134285 CTAAAACAATGTGATAAATCAACAAAGCGATAGAATTTGAACAAATTTTGTTGCTCAGGTAACCG
1 CTAAAACAAAGTAATAAATCAACAAAGAAATTGAATTTGAACAAATTTTGTTGCTCAGGTAACCG
* * * * *
13134350 CTC-GACCGACATAGTTGCCGATGATTCACAAAATTTTCATAAATTTTAATATAATCATCACAGC
66 CTCAGATCGACATAGTTGTCGATGTTTCACTAAATTTTCATAAATTCTAATATAATCATCACAGC
13134414 AACAAA
131 AACAAA
13134420 TATGCAAATT
Statistics
Matches: 283, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
173 24 0.08
174 170 0.60
175 88 0.31
176 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.28
Consensus pattern (175 bp):
CTAAAACAAAGTAATAAATCAACAAAGAAATTGAATTTGAACAAATTTTGTTGCTCAGGTAACCG
CTCAGATCGACATAGTTGTCGATGTTTCACTAAATTTTCATAAATTCTAATATAATCATCACAGC
AACAAAACCACAGATTCACATACAATAAAATGTATCATAAGACGA
Found at i:13140972 original size:6 final size:6
Alignment explanation
Indices: 13140961--13141006 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
13140951 CATATTTAAT
*
13140961 TATTTA TATTTA CATTTA TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATT
13141007 AATAAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (6 bp):
TATTTA
Found at i:13141380 original size:17 final size:18
Alignment explanation
Indices: 13141358--13141397 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
13141348 AGCAAGTTTA
13141358 TATAAGATATTA-ATTAT
1 TATAAGATATTACATTAT
*
13141375 TATAAGATTTTACATTAT
1 TATAAGATATTACATTAT
13141393 TATAA
1 TATAA
13141398 AATAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (18 bp):
TATAAGATATTACATTAT
Found at i:13145515 original size:17 final size:18
Alignment explanation
Indices: 13145478--13145521 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
13145468 CGATTTCTGC
*
13145478 TTCTTTTATTCTCGTACGT
1 TTCTTTTCTTCTCG-ACGT
13145497 TTCTTTTCTTCTC-ACGT
1 TTCTTTTCTTCTCGACGT
13145514 TT-TTTTCT
1 TTCTTTTCT
13145522 GTTCTCCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 6 0.25
19 12 0.50
ACGTcount: A:0.07, C:0.23, G:0.07, T:0.64
Consensus pattern (18 bp):
TTCTTTTCTTCTCGACGT
Found at i:13149161 original size:28 final size:27
Alignment explanation
Indices: 13149112--13149205 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 27
13149102 TTCATATAAG
* *
13149112 AATAATTA-TATTGAATTTTATTAAAT
1 AATAATTATTATTAAATTATATTAAAT
** * *
13149138 TCTATATTTTTATTAAATTATATTTAAT
1 AATA-ATTATTATTAAATTATATTAAAT
**
13149166 AATAATTATT-TTAAATTATATTTTAT
1 AATAATTATTATTAAATTATATTAAAT
13149192 AAT-ATTATATATTA
1 AATAATTAT-TATTA
13149206 TGATTTTAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
25 5 0.09
26 21 0.39
27 11 0.20
28 17 0.31
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
AATAATTATTATTAAATTATATTAAAT
Found at i:13149179 original size:26 final size:25
Alignment explanation
Indices: 13149141--13149199 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
13149131 ATTAAATTCT
*
13149141 ATATTTTTATTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
13149167 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
13149193 ATATTAT
1 ATATTAT
13149200 ATATTATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.67
27 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:13149205 original size:22 final size:24
Alignment explanation
Indices: 13149180--13149226 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
13149170 ATTATTTTAA
13149180 ATTAT-ATTTTA-TAATATT-ATAT
1 ATTATGATTTTAGTAA-ATTCATAT
13149202 ATTATGATTTTAGTAAATTCATAT
1 ATTATGATTTTAGTAAATTCATAT
13149226 A
1 A
13149227 AAATAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTATGATTTTAGTAAATTCATAT
Found at i:13149380 original size:44 final size:46
Alignment explanation
Indices: 13149317--13149405 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
13149307 GTCTCTATTC
*
13149317 CATTCAACCAAACACAAGAA-TACC-ATCACG-CCTCTATTCCATTT
1 CATTCAACCAAACAAAAGAATTACCTATCA-GACCTCTATTCCATTT
*
13149361 CATTCAACCAAACAAAAGAATTACCTATTAGACCTCTATTCCATT
1 CATTCAACCAAACAAAAGAATTACCTATCAGACCTCTATTCCATT
13149406 ACAGCGAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 19 0.47
45 5 0.12
46 16 0.40
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.27
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATCAGACCTCTATTCCATTT
Found at i:13149717 original size:21 final size:18
Alignment explanation
Indices: 13149691--13149740 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
13149681 CGTATTTCTC
13149691 AAATTCAATTGCAATACCTAA
1 AAATTCAATTG-AAT-CC-AA
13149712 AAATTCGAATTGAATCCAA
1 AAATTC-AATTGAATCCAA
*
13149731 CAATTCAATT
1 AAATTCAATT
13149741 AAAAACATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 2 0.07
21 9 0.33
22 5 0.19
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (18 bp):
AAATTCAATTGAATCCAA
Found at i:13154965 original size:22 final size:22
Alignment explanation
Indices: 13154935--13155011 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 22
13154925 AAAATCTTTT
*
13154935 AAATGAAATTGAAAATTCTAAAA
1 AAAT-AAATTGAAAATTATAAAA
*
13154958 GAATAAATTGAAAATTATAAAAA
1 AAATAAATTGAAAATTAT-AAAA
**
13154981 AATATAAATTTTAAATATATAAAA
1 AA-ATAAATTGAAAAT-TATAAAA
*
13155005 ACATAAA
1 AAATAAA
13155012 AAAAAAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
22 13 0.29
23 13 0.29
24 16 0.36
25 3 0.07
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (22 bp):
AAATAAATTGAAAATTATAAAA
Found at i:13154987 original size:24 final size:23
Alignment explanation
Indices: 13154935--13155005 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
13154925 AAAATCTTTT
*
13154935 AAATGAAATTGAAAATTCT-AAAA
1 AAAT-AAATTGAAAATTATAAAAA
*
13154958 GAATAAATTGAAAATTATAAAAA
1 AAATAAATTGAAAATTATAAAAA
**
13154981 AATATAAATTTTAAATATATAAAAA
1 AA-ATAAATTGAAAAT-TATAAAAA
13155006 CATAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 13 0.32
23 8 0.20
24 11 0.28
25 8 0.20
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (23 bp):
AAATAAATTGAAAATTATAAAAA
Found at i:13157348 original size:3 final size:3
Alignment explanation
Indices: 13157331--13157397 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
13157321 GTTAAATTGT
* **
13157331 TTA TTA CTA -TA TTA TTA TTA GCA TTTA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
13157374 TTA -TA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
13157398 ACATATATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
2 8 0.15
3 45 0.83
4 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:13157368 original size:27 final size:25
Alignment explanation
Indices: 13157331--13157408 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 25
13157321 GTTAAATTGT
*
13157331 TTATTACTATATTATTATTAGCATTTA
1 TTATTATTATATTATTATTA-CA-TTA
*
13157358 TTATTATTATATTA-TATTATATTA
1 TTATTATTATATTATTATTACATTA
13157382 TTATTA-T-TATTATTA-TACATATA
1 TTATTATTATATTATTATTACAT-TA
13157405 TTAT
1 TTAT
13157409 ATGCGCATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
22 9 0.20
23 9 0.20
24 9 0.20
25 1 0.02
26 5 0.11
27 13 0.28
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (25 bp):
TTATTATTATATTATTATTACATTA
Found at i:13157403 original size:24 final size:24
Alignment explanation
Indices: 13157331--13157408 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
13157321 GTTAAATTGT
*
13157331 TTATTACTATATTATTATTA-GCAT-
1 TTATTA-T-TATTATTATTATACATA
*
13157355 TTATTATTATTA-TATTATATTATA
1 TTATTATTATTATTATTATA-CATA
13157379 TTATTATTATTATTATTATACATA
1 TTATTATTATTATTATTATACATA
13157403 -TATTAT
1 TTATTAT
13157409 ATGCGCATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 5 0.11
22 5 0.11
23 9 0.19
24 21 0.45
25 7 0.15
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (24 bp):
TTATTATTATTATTATTATACATA
Found at i:13169233 original size:3 final size:3
Alignment explanation
Indices: 13169216--13169283 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
13169206 GTTAAATTGT
* ** *
13169216 TTA TTA CTA -TA TTA TTA TTA GCA TTTA TTA TTA CTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
13169260 TTA -TA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
13169284 ACATATATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 6 0.11
3 47 0.87
4 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:13169268 original size:25 final size:25
Alignment explanation
Indices: 13169216--13169294 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 25
13169206 GTTAAATTGT
*
13169216 TTATTACTA-TATTATTATTAGCATTTA
1 TTATTACTATTATTA-TATTA-TA-TTA
13169243 TTATTACTATTATTATATTATATTA
1 TTATTACTATTATTATATTATATTA
* *
13169268 TTATTATTATTATTATACATATATTA
1 TTATTACTATTATTATA-TTATATTA
13169294 T
1 T
13169295 ATGCGCATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
25 19 0.40
26 9 0.19
27 14 0.30
28 5 0.11
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.58
Consensus pattern (25 bp):
TTATTACTATTATTATATTATATTA
Found at i:13169280 original size:22 final size:21
Alignment explanation
Indices: 13169215--13169280 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
13169205 TGTTAAATTG
*
13169215 TTTATTACTATATTATTATTAGCA
1 TTTATTA-T-TATTATTATTA-TA
*
13169239 TTTATTATTACTATTATTATA
1 TTTATTATTATTATTATTATA
13169260 TTATATTATTATTATTATTAT
1 TT-TATTATTATTATTATTAT
13169281 TATACATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 3 0.08
22 27 0.71
23 1 0.03
24 7 0.18
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTATTATTATTATTATTATA
Found at i:13172337 original size:15 final size:14
Alignment explanation
Indices: 13172319--13172374 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
13172309 ATTAATTTAA
13172319 TATTATTATTACCGT
1 TATTATTATTACC-T
13172334 TATTATT-TTACCCT
1 TATTATTATTA-CCT
13172348 TATTATTTATATA-CT
1 TATTA-TTAT-TACCT
13172363 TATTATTATTAC
1 TATTATTATTAC
13172375 TATATTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.06
14 13 0.36
15 18 0.50
16 1 0.03
17 2 0.06
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (14 bp):
TATTATTATTACCT
Found at i:13173750 original size:21 final size:21
Alignment explanation
Indices: 13173726--13173818 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
13173716 TTTCTTTGAA
* * * *
13173726 CCTCAGCTTCTCTCGTTGTTG
1 CCTCTGCTTCCCTCGCTGCTG
* *
13173747 CCTCTGCTTCTCTCGATGCTG
1 CCTCTGCTTCCCTCGCTGCTG
*
13173768 CCTCTGCTTCCCTCACTGCTG
1 CCTCTGCTTCCCTCGCTGCTG
*
13173789 CCTCTGCTTCCCTCGCTGTTG
1 CCTCTGCTTCCCTCGCTGCTG
13173810 CCTCTGCTT
1 CCTCTGCTT
13173819 TAAGTTGTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.03, C:0.41, G:0.17, T:0.39
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCTG
Found at i:13179356 original size:9 final size:9
Alignment explanation
Indices: 13179339--13179588 Score: 165
Period size: 9 Copynumber: 28.8 Consensus size: 9
13179329 TATGTTTTAG
*
13179339 GTAAATTAT
1 GTAAGTTAT
13179348 GTAAGTTAT
1 GTAAGTTAT
13179357 GT-A-TTAT
1 GTAAGTTAT
*
13179364 ATAAGTTAT
1 GTAAGTTAT
13179373 GTAAGTTAT
1 GTAAGTTAT
13179382 GT-A-TTAT
1 GTAAGTTAT
*
13179389 GTGTA-TTAT
1 GT-AAGTTAT
13179398 GTAAGTTAT
1 GTAAGTTAT
13179407 GT-A-TTAT
1 GTAAGTTAT
*
13179414 GTATGTTAT
1 GTAAGTTAT
*
13179423 GTATAATATTAAT
1 G--TAA-GTT-AT
13179436 -TAAGTTAT
1 GTAAGTTAT
*
13179444 GTAAGTTGT
1 GTAAGTTAT
*
13179453 GT-A-TAAT
1 GTAAGTTAT
*
13179460 GTTAGTTAT
1 GTAAGTTAT
**
13179469 CAAAGTTAT
1 GTAAGTTAT
13179478 GT-A-TTAT
1 GTAAGTTAT
13179485 GTAAGTTAT
1 GTAAGTTAT
*
13179494 TTAAGTTAT
1 GTAAGTTAT
*
13179503 GTAAGTTGT
1 GTAAGTTAT
13179512 GT-A-TTAT
1 GTAAGTTAT
13179519 GTAAGTTAT
1 GTAAGTTAT
13179528 GTAAGTTAT
1 GTAAGTTAT
* *
13179537 GTAGGCTAT
1 GTAAGTTAT
13179546 GT-A-TTAT
1 GTAAGTTAT
13179553 GTAAGTTAT
1 GTAAGTTAT
*
13179562 -TATGTTATTAT
1 GTAAG---TTAT
13179573 GTAAGTTAT
1 GTAAGTTAT
*
13179582 GCAAGTT
1 GTAAGTT
13179589 TATATATAAG
Statistics
Matches: 189, Mismatches: 28, Indels: 48
0.71 0.11 0.18
Matches are distributed among these distances:
7 37 0.20
8 17 0.09
9 119 0.63
10 3 0.02
11 6 0.03
12 5 0.03
13 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.48
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:13179358 original size:25 final size:25
Alignment explanation
Indices: 13179328--13179539 Score: 159
Period size: 25 Copynumber: 8.6 Consensus size: 25
13179318 TGATATATAT
* *
13179328 TTATGTTTTAGGTAAATTATGTAAG
1 TTATGTATTATGTAAATTATGTAAG
* *
13179353 TTATGTATTATATAAGTTATGTAAG
1 TTATGTATTATGTAAATTATGTAAG
**
13179378 TTATGTATTATGTGTATTATGTAAG
1 TTATGTATTATGTAAATTATGTAAG
**
13179403 TTATGTATTATGTATGTTATGT-A-
1 TTATGTATTATGTAAATTATGTAAG
* *
13179426 -TA-ATATTAAT-TAAGTTATGTAAG
1 TTATGTATT-ATGTAAATTATGTAAG
* * * * **
13179449 TTGTGTATAATGTTAGTTATCAAAG
1 TTATGTATTATGTAAATTATGTAAG
* *
13179474 TTATGTATTATGTAAGTTATTTAAG
1 TTATGTATTATGTAAATTATGTAAG
*
13179499 TTATGTAAGTTGTGT--ATTATGTAAG
1 TTATGT-A-TTATGTAAATTATGTAAG
13179524 TTATGTAAGTTATGTA
1 TTATGT-A-TTATGTA
13179540 GGCTATGTAT
Statistics
Matches: 151, Mismatches: 27, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
21 13 0.09
22 5 0.03
24 4 0.03
25 123 0.81
26 1 0.01
27 5 0.03
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.49
Consensus pattern (25 bp):
TTATGTATTATGTAAATTATGTAAG
Found at i:13179382 original size:34 final size:32
Alignment explanation
Indices: 13179299--13179555 Score: 154
Period size: 34 Copynumber: 7.8 Consensus size: 32
13179289 ACTATAAATG
*
13179299 AGTTATGTAAGTTATG-A-TATGATATATATTTA
1 AGTTATGTAAGTTATGTATTATG-TAT-TATATA
* * *
13179331 TGTTTTAGGTAAATTATGTAAGTTATGTATTATATA
1 AG--TTATGTAAGTTATGT-A-TTATGTATTATATA
*
13179367 AGTTATGTAAGTTATGTATTATGTGTATTATGTA
1 AGTTATGTAAGTTATGTATTA--TGTATTATATA
13179401 AGTTATGT-A-TTATGTATGTTATGTA-TA-AT-
1 AGTTATGTAAGTTATGTA--TTATGTATTATATA
* * * *
13179430 A-TTAAT-TAAGTTATGTAAGTTGTGTATAATGTT
1 AGTT-ATGTAAGTTATGT-A-TTATGTATTATATA
** *
13179463 AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
1 AGTTATGTAAGTTATGTATTATGT-A-TTATATA
* *
13179497 AGTTATGTAAGTTGTGTATTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTATTATGT-A-TTATATA
* *
13179531 AGTTATGTAGGCTATGTATTATGTA
1 AGTTATGTAAGTTATGTATTATGTA
13179556 AGTTATTATG
Statistics
Matches: 180, Mismatches: 24, Indels: 41
0.73 0.10 0.17
Matches are distributed among these distances:
28 3 0.02
29 4 0.02
30 14 0.08
31 4 0.02
32 21 0.12
33 8 0.04
34 112 0.62
36 7 0.04
37 3 0.02
38 4 0.02
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.48
Consensus pattern (32 bp):
AGTTATGTAAGTTATGTATTATGTATTATATA
Found at i:13179552 original size:25 final size:25
Alignment explanation
Indices: 13179495--13179561 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
13179485 GTAAGTTATT
* *
13179495 TAAGTTATGTAAGTTGTGTATTATG
1 TAAGTTATGTAAGTTATGTACTATG
13179520 TAAGTTATGTAAGTTATGTAGGCTATG
1 TAAGTTATGTAAGTTATGTA--CTATG
13179547 T-A-TTATGTAAGTTAT
1 TAAGTTATGTAAGTTAT
13179562 TATGTTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 32 0.84
26 1 0.03
27 5 0.13
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.46
Consensus pattern (25 bp):
TAAGTTATGTAAGTTATGTACTATG
Found at i:13179556 original size:34 final size:33
Alignment explanation
Indices: 13179475--13179569 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
13179465 TTATCAAAGT
*
13179475 TATGTATTATGTAAGTTATTTAAGTTATGTAAGT
1 TATGTATTATGTAAGTTA-TTAAGTTATGTAAGC
* *
13179509 TGTGTATTATGTAAGTTATGTAAGTTATGTAGGC
1 TATGTATTATGTAAGTTAT-TAAGTTATGTAAGC
*
13179543 TATGTATTATGTAAGTTATTATGTTAT
1 TATGTATTATGTAAGTTATTAAGTTAT
13179570 TATGTAAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 8 0.15
34 47 0.85
ACGTcount: A:0.29, C:0.01, G:0.20, T:0.49
Consensus pattern (33 bp):
TATGTATTATGTAAGTTATTAAGTTATGTAAGC
Found at i:13179599 original size:12 final size:12
Alignment explanation
Indices: 13179584--13179612 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
13179574 TAAGTTATGC
13179584 AAGTTTATATAT
1 AAGTTTATATAT
13179596 AAGTTTATATAT
1 AAGTTTATATAT
13179608 AAGTT
1 AAGTT
13179613 CTGTAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
AAGTTTATATAT
Found at i:13179890 original size:22 final size:18
Alignment explanation
Indices: 13179845--13180006 Score: 78
Period size: 18 Copynumber: 8.5 Consensus size: 18
13179835 GTATATAAAT
*
13179845 TTTAAATAATGTAATATA
1 TTTAAGTAATGTAATATA
13179863 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
* *
13179881 TTTTAGTAA-GTAATGTA
1 TTTAAGTAATGTAATATA
** * *
13179898 AGTAATGTAATATATACTTAAA
1 TTTAA-GTAATGTA-A--TATA
* * *
13179920 TTTTAGTAA-GTCATGTA
1 TTTAAGTAATGTAATATA
13179937 TTTAAGTCATGTATTTAAGTAATATA
1 TTTAAGT-A---A--T--GTAATATA
*
13179963 TTTAAGTAA-GTAATGTA
1 TTTAAGTAATGTAATATA
*
13179980 TTTAAGTTATGTAATATA
1 TTTAAGTAATGTAATATA
*
13179998 TTTCAGTAA
1 TTTAAGTAA
13180007 GTAGTGTAAG
Statistics
Matches: 105, Mismatches: 24, Indels: 30
0.66 0.15 0.19
Matches are distributed among these distances:
17 32 0.30
18 44 0.42
19 3 0.03
20 2 0.02
21 5 0.05
22 5 0.05
25 1 0.01
26 13 0.12
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:13179944 original size:13 final size:13
Alignment explanation
Indices: 13179926--13179969 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
13179916 TAAATTTTAG
13179926 TAAGTCATGTATT
1 TAAGTCATGTATT
13179939 TAAGTCATGTATT
1 TAAGTCATGTATT
* *
13179952 TAAGTAATATATT
1 TAAGTCATGTATT
13179965 TAAGT
1 TAAGT
13179970 AAGTAATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (13 bp):
TAAGTCATGTATT
Found at i:13179974 original size:17 final size:17
Alignment explanation
Indices: 13179952--13180009 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
13179942 GTCATGTATT
13179952 TAAGTAATATATTTAAG
1 TAAGTAATATATTTAAG
*
13179969 TAAGTAATGTATTTAAG
1 TAAGTAATATATTTAAG
* *
13179986 TTATGTAATATATTTCAG
1 -TAAGTAATATATTTAAG
13180004 TAAGTA
1 TAAGTA
13180010 GTGTAAGTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 21 0.60
18 14 0.40
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (17 bp):
TAAGTAATATATTTAAG
Found at i:13180017 original size:31 final size:34
Alignment explanation
Indices: 13179955--13180029 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 34
13179945 ATGTATTTAA
*
13179955 GTAATATATTTAAGTAAGTAATGTATTTAAGTTA-T
1 GTAATATATTTAAGTAAGTAATG-ATGTAAG-TAGT
*
13179990 GTAATATATTTCAGTAAGT-A-G-TGTAAGTAGT
1 GTAATATATTTAAGTAAGTAATGATGTAAGTAGT
13180021 GTAATATAT
1 GTAATATAT
13180030 ACTTAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 2 0.05
31 15 0.41
33 1 0.03
34 1 0.03
35 18 0.49
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.43
Consensus pattern (34 bp):
GTAATATATTTAAGTAAGTAATGATGTAAGTAGT
Found at i:13181615 original size:15 final size:15
Alignment explanation
Indices: 13181591--13181620 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13181581 TTTCTTTGTA
*
13181591 TTTTCTCTTTTGTTT
1 TTTTCCCTTTTGTTT
13181606 TTTTCCCTTTTGTTT
1 TTTTCCCTTTTGTTT
13181621 AGAACATGAC
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:0.00, C:0.17, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTTCCCTTTTGTTT
Found at i:13181740 original size:32 final size:31
Alignment explanation
Indices: 13181704--13181764 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
13181694 ATCGTGTACA
* *
13181704 GAAACGACGTCGTTTAATTAAAGTTTTAATCC
1 GAAACGACGCCGTTTAATT-AAGCTTTAATCC
*
13181736 GAAACGGCGCCGTTTAATTAAGCTTTAAT
1 GAAACGACGCCGTTTAATTAAGCTTTAAT
13181765 GCACAGTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (31 bp):
GAAACGACGCCGTTTAATTAAGCTTTAATCC
Found at i:13182376 original size:22 final size:23
Alignment explanation
Indices: 13182332--13182377 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13182322 TCAATACTTT
* * *
13182332 TTTAAACTTATTTATTAATTATA
1 TTTAAACTAATATATTAAATATA
13182355 TTTAAACTAATAT-TTAAATATA
1 TTTAAACTAATATATTAAATATA
13182377 T
1 T
13182378 CAAATGGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAACTAATATATTAAATATA
Found at i:13183658 original size:83 final size:84
Alignment explanation
Indices: 13183506--13183708 Score: 200
Period size: 83 Copynumber: 2.4 Consensus size: 84
13183496 GGCGCTTTTT
* * * * *
13183506 CAAAAACGCTGCT-AAAA-TCCGAACATTAGCGGCGTTAAATCAAAAATTGCCGCTAAAAACCAC
1 CAAAAACGCCGCTAAAAACCCCGAGCATTAGCGGCG-CAAATCAAAAATCGCCGCTAAAAACCAC
*
13183569 GAGCATTACCGATGC-TATAC
65 GAGCATTACCGACGCTTA-AC
* *
13183589 CAAAAACGCCGCTAAAAACCCCGAGCATTAGCGGCGCAACATCAAAAA-CGCCGCTAAAGACTAC
1 CAAAAACGCCGCTAAAAACCCCGAGCATTAGCGGCGCAA-ATCAAAAATCGCCGCTAAAAACCAC
* * *
13183653 G-GCATTAGCGGCGCTTAAT
65 GAGCATTACCGACGCTTAAC
* * * * *
13183672 CATAAACGCCGCTAAATACCCTGAGCAATAGCAGCGC
1 CAAAAACGCCGCTAAAAACCCCGAGCATTAGCGGCGC
13183709 TTGACCATAA
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
83 55 0.55
84 22 0.22
85 23 0.23
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16
Consensus pattern (84 bp):
CAAAAACGCCGCTAAAAACCCCGAGCATTAGCGGCGCAAATCAAAAATCGCCGCTAAAAACCACG
AGCATTACCGACGCTTAAC
Found at i:13183679 original size:41 final size:41
Alignment explanation
Indices: 13183494--13183789 Score: 181
Period size: 42 Copynumber: 7.1 Consensus size: 41
13183484 CAAGTCTTTT
** * * * *
13183494 GCGGCGCTTTTTCAAAAACGCTGCT-AAAATCCGAACATTA
1 GCGGCGCTTAATCATAAACGCCGCTAAAAACCCGAGCATTA
* *
13183534 GCGGCG-TTAAATCAAAAATTGCCGCTAAAAACCACGAGCATTA
1 GCGGCGCTT-AATCATAAA-CGCCGCTAAAAACC-CGAGCATTA
* ** * *
13183577 CCGATGC-TATACCAAAAACGCCGCTAAAAACCCCGAGCATTA
1 GCGGCGCTTA-ATCATAAACGCCGCTAAAAA-CCCGAGCATTA
* * * *
13183619 GCGGCGC-AACATCAAAAACGCCGCTAAAGACTACG-GCATTA
1 GCGGCGCTTA-ATCATAAACGCCGCTAAAAAC-CCGAGCATTA
* *
13183660 GCGGCGCTTAATCATAAACGCCGCTAAATACCCTGAGCAATA
1 GCGGCGCTTAATCATAAACGCCGCTAAAAACCC-GAGCATTA
* * * * **
13183702 GCAGCGCTTGACCATAAACGCCGCT-AAAACCCTAATTATTA
1 GCGGCGCTTAATCATAAACGCCGCTAAAAACCC-GAGCATTA
* * * * * *
13183743 GCGGCGCTTAATAAAAAATGCCGCCAAAACCCCGACCATTA
1 GCGGCGCTTAATCATAAACGCCGCTAAAAACCCGAGCATTA
*
13183784 GAGGCG
1 GCGGCG
13183790 ATATTCCAAA
Statistics
Matches: 200, Mismatches: 44, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
39 2 0.01
40 14 0.07
41 78 0.39
42 85 0.43
43 21 0.10
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTAATCATAAACGCCGCTAAAAACCCGAGCATTA
Found at i:13183720 original size:42 final size:41
Alignment explanation
Indices: 13183506--13183789 Score: 179
Period size: 41 Copynumber: 6.9 Consensus size: 41
13183496 GGCGCTTTTT
* * * *
13183506 CAAAAACGCTGCTAAAATCC-GAACATTAGCGGCG-TTAAAT
1 CAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCTT-AAC
* * **
13183546 CAAAAATTGCCGCTAAAAACCAC-GAGCATTACCGATGC-TATAC
1 CAAAAA-CGCCGCT-AAAACC-CTGAGCATTAGCGGCGCTTA-AC
*
13183589 CAAAAACGCCGCTAAAAACCCCGAGCATTAGCGGCGC--AAC
1 CAAAAACGCCGCT-AAAACCCTGAGCATTAGCGGCGCTTAAC
* *
13183629 ATCAAAAACGCCGCTAAAGACTAC-G-GCATTAGCGGCGCTTAAT
1 --CAAAAACGCCGCTAAA-AC-CCTGAGCATTAGCGGCGCTTAAC
* * * *
13183672 CATAAACGCCGCTAAATACCCTGAGCAATAGCAGCGCTTGAC
1 CAAAAACGCCGCTAAA-ACCCTGAGCATTAGCGGCGCTTAAC
* * ** *
13183714 CATAAACGCCGCTAAAACCCTAATTATTAGCGGCGCTTAAT
1 CAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCTTAAC
* * * * * *
13183755 AAAAAATGCCGCCAAAACCCCGACCATTAGAGGCG
1 CAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCG
13183790 ATATTCCAAA
Statistics
Matches: 193, Mismatches: 37, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
40 9 0.05
41 85 0.44
42 77 0.40
43 22 0.11
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.17
Consensus pattern (41 bp):
CAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCTTAAC
Found at i:13185196 original size:29 final size:29
Alignment explanation
Indices: 13185140--13185199 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
13185130 TTTAATAGAT
* *
13185140 TTAATATTATATTTAATTTATTTATTATC
1 TTAATATTAAATTTAATTTATGTATTATC
13185169 TTAATATTAAATTTAATTTAATGT-TTATC
1 TTAATATTAAATTTAATTT-ATGTATTATC
13185198 TT
1 TT
13185200 GTAGATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (29 bp):
TTAATATTAAATTTAATTTATGTATTATC
Found at i:13195107 original size:2 final size:2
Alignment explanation
Indices: 13195100--13195134 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13195090 TATTTTGCCT
13195100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13195135 CTCTTTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.