Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 52 of 444
Found at i:12531691 original size:46 final size:46
Alignment explanation
Indices: 12531641--12531816 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
12531631 TGGTTGAGCA
12531641 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
12531687 TCCGAACTCGTTGAGTTGAGTACGAATTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
12531732 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
12531780 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12531817 GCAGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.57
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:12531797 original size:93 final size:93
Alignment explanation
Indices: 12531638--12531809 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
12531628 GGATGGTTGA
* *
12531638 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12531703 TGAGTACGAATTCGTGAGATGTAACTAG
66 TGAGTACGAATTCGTGAGATGTAACTAG
*
12531731 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
* *
12531796 TGAGTCCGAGTTCG
66 TGAGTACGAATTCG
12531810 CTTATGGGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTACGAATTCGTGAGATGTAACTAG
Found at i:12541489 original size:52 final size:53
Alignment explanation
Indices: 12541365--12541524 Score: 157
Period size: 52 Copynumber: 3.1 Consensus size: 53
12541355 CAGATCACAT
* * * *
12541365 ATCATACCGATGCCATATCCCAGATATGGTCTTATATAGAATCACATTATCAC
1 ATCACACCGATGCCATAGCCCAGATATGGTCTTATAGAGAATCACAGTATCAC
* * * *
12541418 ATCACACTGAAGCCATAGCCCAGCTATGGTCTTATACGGGAA-CAC-GTATCAC
1 ATCACACCGATGCCATAGCCCAGATATGGTCTTATA-GAGAATCACAGTATCAC
** * * *
12541470 ATTGCACCGATGCCATAGCCCAGTTATGGTCTTACACGA-AAGCACA-TATCAC
1 ATCACACCGATGCCATAGCCCAGATATGGTCTTATA-GAGAATCACAGTATCAC
12541522 ATC
1 ATC
12541525 TTTTCCGTCA
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
51 2 0.02
52 49 0.56
53 34 0.39
54 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (53 bp):
ATCACACCGATGCCATAGCCCAGATATGGTCTTATAGAGAATCACAGTATCAC
Found at i:12544589 original size:26 final size:26
Alignment explanation
Indices: 12544560--12544612 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
12544550 AATATTAAAT
12544560 TATTTGTATAATTT-TATTATATATTA
1 TATTTGTA-AATTTGTATTATATATTA
* * *
12544586 TATTTTTAAATTTGTATTTTCTATTA
1 TATTTGTAAATTTGTATTATATATTA
12544612 T
1 T
12544613 TTTTTAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (26 bp):
TATTTGTAAATTTGTATTATATATTA
Found at i:12550240 original size:74 final size:72
Alignment explanation
Indices: 12550113--12550260 Score: 172
Period size: 74 Copynumber: 2.0 Consensus size: 72
12550103 AAATATTGGA
** * * *
12550113 GGGGCCTACTTATATTTTTAGGAAGGCTTTAATATATTTACAAATGAAAAAATT-ATAAAAATTT
1 GGGGCCTACTTATATTTTTAGGAAGGCCATAATAAATTTACAAAGGAAAAAATTGA-AAAAAATT
12550177 TAAACTTT
65 TAAACTTT
* * * **
12550185 GGGGGCTACTTATATTTTTGGGAGGGCCATAGTATAAATTTACAAAGGATTAAATTGAAAAAAAT
1 GGGGCCTACTTATATTTTTAGGAAGGCCATA--ATAAATTTACAAAGGAAAAAATTGAAAAAAAT
12550250 TTAAACTTT
64 TTAAACTTT
12550259 GG
1 GG
12550261 AGAGTCCATG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
72 26 0.41
74 36 0.57
75 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.36
Consensus pattern (72 bp):
GGGGCCTACTTATATTTTTAGGAAGGCCATAATAAATTTACAAAGGAAAAAATTGAAAAAAATTT
AAACTTT
Found at i:12556187 original size:11 final size:11
Alignment explanation
Indices: 12556171--12556200 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12556161 TAACATTAAG
12556171 AATATATATAT
1 AATATATATAT
*
12556182 AATATAAATAT
1 AATATATATAT
12556193 AATATATA
1 AATATATA
12556201 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:12556993 original size:22 final size:20
Alignment explanation
Indices: 12556965--12557004 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12556955 GTTAGGTGGC
12556965 TAGGTTTTTTTATCTTTTTTGT
1 TAGG-TTTTTT-TCTTTTTTGT
12556987 TAGGTTTTTTTCTTTTTT
1 TAGGTTTTTTTCTTTTTT
12557005 CTTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.07, C:0.05, G:0.12, T:0.75
Consensus pattern (20 bp):
TAGGTTTTTTTCTTTTTTGT
Found at i:12557062 original size:14 final size:14
Alignment explanation
Indices: 12557045--12557077 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12557035 TTGGGGTAAG
12557045 TTTTTCTTT-TTCTT
1 TTTTTCTTTGTT-TT
12557059 TTTTTCTTTGTTTT
1 TTTTTCTTTGTTTT
12557073 TTTTT
1 TTTTT
12557078 GGGTTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (14 bp):
TTTTTCTTTGTTTT
Found at i:12558110 original size:74 final size:74
Alignment explanation
Indices: 12558010--12558288 Score: 377
Period size: 74 Copynumber: 3.8 Consensus size: 74
12558000 AAGATAGAAT
* * * *
12558010 TTGAAAATACCTTAGCGTGCCGCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGATT
1 TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATT
12558075 TAATGGGAA
66 TAATGGGAA
* *
12558084 TTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTAGATT
1 TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATT
12558149 TAATGGGAA
66 TAATGGGAA
* * *
12558158 TTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA--
1 TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATT
*
12558221 AACAT--GAA
66 TA-ATGGGAA
* * * ***
12558229 TTGAAATTACCCCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
12558289 CTTGGAAACA
Statistics
Matches: 188, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
71 55 0.29
72 1 0.01
73 2 0.01
74 130 0.69
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (74 bp):
TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATT
TAATGGGAA
Found at i:12558200 original size:148 final size:145
Alignment explanation
Indices: 12558010--12558765 Score: 528
Period size: 158 Copynumber: 4.9 Consensus size: 145
12558000 AAGATAGAAT
* *
12558010 TTGAAAATACCTTAGCGTGCCGCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGATT
1 TTGAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGA--
* * * * *
12558075 TA-ATGGGAATTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTG
64 AACAT--GAATTGAAATTACCCCAACGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
12558139 ATTTTAGATTTAATGGGAA
127 ATTTTAGATTTAATGGGAA
* * * * *
12558158 TTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
1 TTGAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGAAA
* ***
12558223 CATGAATTGAAATTACCCCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
66 CATGAATTGAAATTACCCCAACGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
** * *
12558288 TCTTGGAAACATGAACTAAAAAGCAGAAA
129 T-TT------A-G-A-TTTAATG--GGAA
** * * *
12558317 TTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
1 TTGAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGAAA
* * ***
12558382 CATAAATTGAAATTA-CCCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
66 CATGAATTGAAATTACCCCAACGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
** * *
12558446 TCTTGGAAACATGAACTAAAAAGCAGAAA
129 T-TT------A-G-A-TTTAATG--GGAA
** * * *
12558475 TTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
1 TTGAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGAAA
* * * *** *
12558540 CATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
66 CATGAATTGAAATTACCCCAACGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
* * *
12558605 TCTTGGAAAACATGAATTAAAAAGTAGAAA
129 T-TT-------A-G-ATT--TAA-TGGGAA
* * *
12558635 TTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG-CTGCTTTTTGAA
1 TTGAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTC-GATTTTAGAA
* * * *** *
12558699 ACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATT
65 ACATGAATTGAAATTACCCCAACGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
12558764 TT
130 TT
12558766 CTTGGAAAAC
Statistics
Matches: 552, Mismatches: 35, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
145 51 0.09
146 1 0.00
147 4 0.01
148 58 0.11
154 1 0.00
155 1 0.00
156 1 0.00
157 6 0.01
158 160 0.29
159 130 0.24
160 136 0.25
161 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (145 bp):
TTGAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGAAA
CATGAATTGAAATTACCCCAACGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TAGATTTAATGGGAA
Found at i:12558271 original size:71 final size:72
Alignment explanation
Indices: 12557965--12558288 Score: 354
Period size: 74 Copynumber: 4.5 Consensus size: 72
12557955 AATTAAAAGA
* * * *
12557965 CTCAACTCACCTCTCGTAATATGAATTGACTCTTTAAGAT--A--GAATTTGAAAATACCTTAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGA-T-TTT-AGATAAATGGAA-TTGAAATTACCTCAGC
*
12558026 GTGCCGCAAGG
62 GTGCCCCAAGG
* *
12558037 CTCAACTCACCTCTCGCAATATGAGTCGATTTTAGATTTAATGGGAATTGAAATTACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGA-TAAAT-GGAATTGAAATTACCTCAGCGT
12558102 GCCCCAAGG
64 GCCCCAAGG
* * *
12558111 TTCAACTCACTTCTCGCAATATGAGTTGATTTTAGATTTAATGGGAATTGAAATTACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGA-TAAAT-GGAATTGAAATTACCTCAGCGT
12558176 GCCCCAAGG
64 GCCCCAAGG
* * * * *
12558185 TTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA-AACAT-GAATTGAAATTACCCCAACGTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATAA-ATGGAATTGAAATTACCTCAGCGTG
* ***
12558248 TCTTGAGG
65 CCCCAAGG
12558256 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
12558289 CTTGGAAACA
Statistics
Matches: 226, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
69 3 0.01
70 4 0.02
71 56 0.25
72 28 0.12
73 2 0.01
74 130 0.58
75 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (72 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATAAATGGAATTGAAATTACCTCAGCGTGC
CCCAAGG
Found at i:12558429 original size:70 final size:71
Alignment explanation
Indices: 12558314--12558446 Score: 214
Period size: 70 Copynumber: 1.9 Consensus size: 71
12558304 TAAAAAGCAG
* *
12558314 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
12558379 AAACAT
66 AAACAT
* * *
12558385 AAATTGAAATTACC-CAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
12558447 CTTGGAAACA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
70 44 0.77
71 13 0.23
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (71 bp):
AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
AAACAT
Found at i:12558473 original size:158 final size:160
Alignment explanation
Indices: 12558156--12558856 Score: 1237
Period size: 160 Copynumber: 4.4 Consensus size: 160
12558146 ATTTAATGGG
* ** *
12558156 AATTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
* * *
12558221 AACATGAATTGAAATTACCCCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
12558286 TTTCTTGG-AAACATGAACTAAAAAGCAGA
131 TTTCTTGGAAAACATGAACTAAAAAGCAGA
12558315 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
*
12558380 AACATAAATTGAAATTACC-CAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
12558444 TTTCTTGG-AAACATGAACTAAAAAGCAGA
131 TTTCTTGGAAAACATGAACTAAAAAGCAGA
12558473 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
12558538 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
* *
12558603 TTTCTTGGAAAACATGAATTAAAAAGTAGA
131 TTTCTTGGAAAACATGAACTAAAAAGCAGA
* * * *
12558633 AATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGCTTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
12558698 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
*
12558763 TTTCTTGGAAAACATGAATTAAAAAGCAGA
131 TTTCTTGGAAAACATGAACTAAAAAGCAGA
*
12558793 AATTGGAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG
12558857 GAAAAAAACA
Statistics
Matches: 522, Mismatches: 18, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
158 158 0.30
159 131 0.25
160 233 0.45
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (160 bp):
AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
TTTCTTGGAAAACATGAACTAAAAAGCAGA
Found at i:12558588 original size:71 final size:71
Alignment explanation
Indices: 12558472--12558765 Score: 237
Period size: 71 Copynumber: 3.9 Consensus size: 71
12558462 TAAAAAGCAG
* * * * *
12558472 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
12558537 AAACAT
66 AAACAT
*
12558543 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTCT
1 AAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-TTT-T
12558608 TGGAAAACAT
64 T-G-AAACAT
* * * ** * ** * * * * *
12558618 GAATTAAAAAGTAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
1 AAATT-GAAA-T--TACCTCAACGTGCCT-TGAG-G-CTC-A-ACT-----CACCTCTCGCAATA
*
12558683 TGAGCTGCTTTTTGAAACAT
52 TGAGCTGATTTTTGAAACAT
*
12558703 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 AAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
12558766 CTTGGAAAAC
Statistics
Matches: 169, Mismatches: 36, Indels: 36
0.70 0.15 0.15
Matches are distributed among these distances:
71 78 0.46
72 3 0.02
73 2 0.01
74 1 0.01
75 10 0.06
76 5 0.03
77 2 0.01
78 2 0.01
79 8 0.05
80 4 0.02
81 8 0.05
82 2 0.01
83 2 0.01
84 5 0.03
85 10 0.06
86 1 0.01
87 2 0.01
88 3 0.02
89 21 0.12
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (71 bp):
AAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
AAACAT
Found at i:12574744 original size:52 final size:55
Alignment explanation
Indices: 12574655--12574769 Score: 155
Period size: 54 Copynumber: 2.1 Consensus size: 55
12574645 TATAAATCGG
*
12574655 TTAATTTTCAACTTTAGTCCTTTTAATATGCTTAAATTTGA-A-ATAATTCTTATACT
1 TTAA-TTTCAACTTTAGTCC--TTAATATGCTTAAATTAGATATATAATTCTTATACT
* *
12574711 TTAATTTCAATTTTAGTCC-TAATATGCTTAAATTAGATATTTAATTCTTATACT
1 TTAATTTCAACTTTAGTCCTTAATATGCTTAAATTAGATATATAATTCTTATACT
12574765 TTAAT
1 TTAAT
12574770 CTCTAACACC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
52 17 0.31
53 1 0.02
54 18 0.33
55 14 0.26
56 4 0.07
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.50
Consensus pattern (55 bp):
TTAATTTCAACTTTAGTCCTTAATATGCTTAAATTAGATATATAATTCTTATACT
Found at i:12583362 original size:27 final size:27
Alignment explanation
Indices: 12583331--12583385 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
12583321 AGAAGAGACA
*
12583331 TACTCTCTTGTGGTGGATGCAACTACT
1 TACTCTCTTGTGGTGGATGCAACCACT
12583358 TACTCTCTTGTGGTGGATGCAACCACT
1 TACTCTCTTGTGGTGGATGCAACCACT
12583385 T
1 T
12583386 TTAGGTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TACTCTCTTGTGGTGGATGCAACCACT
Found at i:12588973 original size:29 final size:28
Alignment explanation
Indices: 12588926--12588985 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
12588916 GTCTCGAAAT
*
12588926 ATTCTATTTAATTGAGTGACTTTTATAAG
1 ATTCTATTTAATTGAGTGACTTGTAT-AG
**
12588955 ATTCTATTTAATTTTGTGACTTGTATAG
1 ATTCTATTTAATTGAGTGACTTGTATAG
12588983 ATT
1 ATT
12588986 ATTGTACTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (28 bp):
ATTCTATTTAATTGAGTGACTTGTATAG
Found at i:12592235 original size:26 final size:26
Alignment explanation
Indices: 12592195--12592247 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
12592185 TTAGTAACTA
* * *
12592195 ATTGCATAAAGATGGGAAAAAGAAAG
1 ATTGCATAAAAATGGCAAAAAAAAAG
12592221 ATTGCATAAAAATGGCAAAAAAAAAG
1 ATTGCATAAAAATGGCAAAAAAAAAG
12592247 A
1 A
12592248 AATAAAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (26 bp):
ATTGCATAAAAATGGCAAAAAAAAAG
Found at i:12592594 original size:21 final size:21
Alignment explanation
Indices: 12592568--12592607 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12592558 TATTACACAT
*
12592568 GAATAAATTTTATTAGGATGA
1 GAATAAATTATATTAGGATGA
12592589 GAATAAATTATATTAGGAT
1 GAATAAATTATATTAGGAT
12592608 CATCCTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (21 bp):
GAATAAATTATATTAGGATGA
Found at i:12592631 original size:124 final size:123
Alignment explanation
Indices: 12592464--12592686 Score: 374
Period size: 124 Copynumber: 1.8 Consensus size: 123
12592454 ATTAATTAAA
* *
12592464 GAGAATAAATTATATTAAGATCATCTAAAAAGTATAGCTTTTAGGCACTAATAAAATAGTGTCAC
1 GAGAATAAATTATATTAAGATCATCTAAAAAGTATAGCTTTTAGGCACCAATAAAATAGTATCAC
*
12592529 ATCATTAAATTTTAAAGATAACAAAATATTATTACACATGAATAAATTTTATTAGGAT
66 ATCATTAAATTTTAAAAATAACAAAATATTATTACACATGAATAAATTTTATTAGGAT
* *
12592587 GAGAATAAATTATATTAGGATCATCCTAAAAAGTATAGTTTTTAGGCACCAATAAAATAGTATCA
1 GAGAATAAATTATATTAAGATCAT-CTAAAAAGTATAGCTTTTAGGCACCAATAAAATAGTATCA
* *
12592652 CGTCATTAAATTTTAAAAATAACAAAGTATTATTA
65 CATCATTAAATTTTAAAAATAACAAAATATTATTA
12592687 TACACTCATC
Statistics
Matches: 92, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
123 23 0.25
124 69 0.75
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (123 bp):
GAGAATAAATTATATTAAGATCATCTAAAAAGTATAGCTTTTAGGCACCAATAAAATAGTATCAC
ATCATTAAATTTTAAAAATAACAAAATATTATTACACATGAATAAATTTTATTAGGAT
Found at i:12592754 original size:18 final size:16
Alignment explanation
Indices: 12592731--12592765 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12592721 AATTTAACTT
12592731 TAATTAAATTATTTAAAA
1 TAATT-AATT-TTTAAAA
12592749 TAATTAATTTTTAAAA
1 TAATTAATTTTTAAAA
12592765 T
1 T
12592766 TATAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTAATTTTTAAAA
Found at i:12592968 original size:19 final size:20
Alignment explanation
Indices: 12592930--12592970 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12592920 GGGTTTGAGA
*
12592930 TTTAAGGTTCAAGGTTTGGG
1 TTTAAGGTTCAAGATTTGGG
*
12592950 TTTAA-GTTTAAGATTTGGG
1 TTTAAGGTTCAAGATTTGGG
12592969 TT
1 TT
12592971 CGAGATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.46
Consensus pattern (20 bp):
TTTAAGGTTCAAGATTTGGG
Found at i:12594968 original size:12 final size:12
Alignment explanation
Indices: 12594951--12594976 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12594941 CTCCAACCTT
12594951 GCTTTGCTAATA
1 GCTTTGCTAATA
12594963 GCTTTGCTAATA
1 GCTTTGCTAATA
12594975 GC
1 GC
12594977 ACAATATTAA
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:0.19, G:0.19, T:0.38
Consensus pattern (12 bp):
GCTTTGCTAATA
Found at i:12599254 original size:2 final size:2
Alignment explanation
Indices: 12599247--12599275 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12599237 GAAGGTATTA
12599247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12599276 GCTTCTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12607876 original size:2 final size:2
Alignment explanation
Indices: 12607869--12607895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12607859 GAAGGTATTA
12607869 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12607896 GCTAGATAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12612360 original size:45 final size:46
Alignment explanation
Indices: 12612271--12612371 Score: 177
Period size: 45 Copynumber: 2.2 Consensus size: 46
12612261 GTACTTATGT
12612271 TTTAATATTATTTTATGTTCGTATTTTTTTTAATAACTGACGTTTAA
1 TTTAATATTATTTTATGTTCGTA-TTTTTTTAATAACTGACGTTTAA
*
12612318 TTTAATATTATTTTATGTTCGTA-TTTTTTAGTAACTGACGTTTAA
1 TTTAATATTATTTTATGTTCGTATTTTTTTAATAACTGACGTTTAA
12612363 TTTAATATT
1 TTTAATATT
12612372 TTTATCTATC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
45 30 0.57
47 23 0.43
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (46 bp):
TTTAATATTATTTTATGTTCGTATTTTTTTAATAACTGACGTTTAA
Found at i:12613310 original size:27 final size:27
Alignment explanation
Indices: 12613272--12613327 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
12613262 AATGGAAAAC
*
12613272 GATATGGATCAACTTTCAATAAATTAA
1 GATATGGATCAACTTTCAATAAATGAA
12613299 GATATGGATCAACTTTCAATAAATGAA
1 GATATGGATCAACTTTCAATAAATGAA
12613326 GA
1 GA
12613328 AGAAGACGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (27 bp):
GATATGGATCAACTTTCAATAAATGAA
Found at i:12618363 original size:16 final size:17
Alignment explanation
Indices: 12618342--12618374 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12618332 CACATTGAAG
12618342 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
12618358 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
12618375 CTTCTTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:12619254 original size:27 final size:28
Alignment explanation
Indices: 12619224--12619336 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 28
12619214 CTATTCAGAA
* *
12619224 ATCAGTGTTAA-CTGGGCCTTAGCCCAT
1 ATCAGTATTAATCTGGGCCATAGCCCAT
12619251 ATCAGTATTAATCTGGGCCATAGCCCCTTACAGT
1 ATCAGTATTAATCTGGGCCATAG--CC---CA-T
*
12619285 ATCAG-AGTATAT-TGGGCC-TAGCCCAT
1 ATCAGTATTA-ATCTGGGCCATAGCCCAT
*
12619311 ATCAGTATTAATCTGGGCCGTAGCCC
1 ATCAGTATTAATCTGGGCCATAGCCC
12619337 TATTACAAGT
Statistics
Matches: 71, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
26 8 0.11
27 21 0.30
28 16 0.23
30 4 0.06
32 3 0.04
33 11 0.15
34 8 0.11
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (28 bp):
ATCAGTATTAATCTGGGCCATAGCCCAT
Found at i:12619356 original size:60 final size:59
Alignment explanation
Indices: 12619236--12619372 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 59
12619226 CAGTGTTAAC
*
12619236 TGGGCCTTAGCCCATATCAGTATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATAT
1 TGGGCC-TAGCCCATATCAGTATTAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATAT
*
12619297 TGGGCCTAGCCCATATCAGTATTAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATAT
1 TGGGCCTAGCCCATATCAGTATTAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TATAT
* *
12619357 TGGGTCTTGCCCATAT
1 TGGGCCTAGCCCATAT
12619373 TAACACAGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
59 4 0.06
60 54 0.78
61 11 0.16
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAGTATTAATCTGGGCCATAGCCCATTACAGATCAGAGTATAT
Found at i:12619390 original size:20 final size:20
Alignment explanation
Indices: 12619365--12619410 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12619355 ATTGGGTCTT
12619365 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
12619385 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
12619404 GCCCATA
1 GCCCATA
12619411 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:12619419 original size:19 final size:20
Alignment explanation
Indices: 12619377--12619420 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
12619367 CCATATTAAC
** *
12619377 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
12619397 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
12619416 ACAGT
1 ACAGT
12619421 CTAATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:12622159 original size:29 final size:29
Alignment explanation
Indices: 12622125--12622182 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
12622115 ATTTTCTAAC
*
12622125 ATTTCCATAAAATTGATTTTAGTGTTTTT
1 ATTTCCATAAAATCGATTTTAGTGTTTTT
12622154 ATTTCCATAAAATCGATTTTAGTGTTTTT
1 ATTTCCATAAAATCGATTTTAGTGTTTTT
12622183 CCGTAGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (29 bp):
ATTTCCATAAAATCGATTTTAGTGTTTTT
Found at i:12623292 original size:28 final size:27
Alignment explanation
Indices: 12623180--12623292 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
12623170 CTATTCAGAA
* *
12623180 ATCAGTGTTAA-CTGGGCCTTAGCCTAT
1 ATCAGTATTAATCTGGGCC-TAGCCCAT
*
12623207 ATCAATATTAATCTGGGCCATAGCCCCTTACAGT
1 ATCAGTATTAATCTGGGCC-TAG--CC---CA-T
* *
12623241 ATCAG-AGTATAT-TAGGCCTAGCCCAT
1 ATCAGTATTA-ATCTGGGCCTAGCCCAT
12623267 ATCAGTATTAATCTGGGCCGTAGCCC
1 ATCAGTATTAATCTGGGCC-TAGCCC
12623293 TATTACAAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
26 8 0.12
27 19 0.29
28 16 0.24
30 4 0.06
32 3 0.05
33 9 0.14
34 7 0.11
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (27 bp):
ATCAGTATTAATCTGGGCCTAGCCCAT
Found at i:12623319 original size:60 final size:59
Alignment explanation
Indices: 12623192--12623328 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
12623182 CAGTGTTAAC
* *
12623192 TGGGCCTTAGCCTATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATAT
1 TGGGCC-TAGCCCATATCAATATTAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATAT
* * *
12623253 TAGGCCTAGCCCATATCAGTATTAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATAT
1 TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TATAT
**
12623313 TGGGCCTTTCCCATAT
1 TGGGCCTAGCCCATAT
12623329 TAACACAGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 4 0.06
60 51 0.78
61 10 0.15
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCATTACAGATCAGAGTATAT
Found at i:12626185 original size:6 final size:7
Alignment explanation
Indices: 12626168--12626192 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12626158 TTATTTTCAA
12626168 AAAAAAG
1 AAAAAAG
12626175 AAAAAAG
1 AAAAAAG
12626182 AAAAAAG
1 AAAAAAG
12626189 AAAA
1 AAAA
12626193 TGGAAATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:12629131 original size:14 final size:14
Alignment explanation
Indices: 12629112--12629142 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12629102 GAGCATGTAC
12629112 AAGCTTATTGAAAA
1 AAGCTTATTGAAAA
12629126 AAGCTTATTGAAAA
1 AAGCTTATTGAAAA
12629140 AAG
1 AAG
12629143 AAAGAAAGTA
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:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (14 bp):
AAGCTTATTGAAAA
Found at i:12642825 original size:5 final size:5
Alignment explanation
Indices: 12642815--12642863 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
12642805 TTATCTTAAA
* * *
12642815 TCAAG TCAAG TCAAG TCAAG TCAAG TCAAG TCAAA TCAAA TCAAA TCAA
1 TCAAG TCAAG TCAAG TCAAG TCAAG TCAAG TCAAG TCAAG TCAAG TCAA
12642864 TTGTTTTACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (5 bp):
TCAAG
Found at i:12648914 original size:12 final size:13
Alignment explanation
Indices: 12648889--12648973 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 13
12648879 TTTATCACGA
*
12648889 TAAATATT-AGAT
1 TAAATATTAATAT
12648901 TAAAT-TTAATAT
1 TAAATATTAATAT
* *
12648913 TAAATCTT-ATCAA
1 TAAATATTAAT-AT
* *
12648926 AATAATATTAAGA-
1 TA-AATATTAATAT
12648939 TAAATATTAA-AT
1 TAAATATTAATAT
12648951 TAAAT-TTAATAT
1 TAAATATTAATAT
12648963 TAAACTATTAA
1 TAAA-TATTAA
12648974 AATAATATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
11 7 0.12
12 34 0.59
13 6 0.10
14 10 0.17
15 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (13 bp):
TAAATATTAATAT
Found at i:12648933 original size:38 final size:39
Alignment explanation
Indices: 12648857--12648958 Score: 108
Period size: 38 Copynumber: 2.7 Consensus size: 39
12648847 CTTAATCACT
* **
12648857 TTAATATTAAA-TTAATA-TAATATTTATCACGATAAATA
1 TTAAGATTAAATTTAATATTAA-ATTTATCAAAATAAATA
12648895 TT-AGATTAAATTTAATATTAAATCTTATCAAAAT-AATA
1 TTAAGATTAAATTTAATATTAAAT-TTATCAAAATAAATA
12648933 TTAAGA-TAAATATTAA-ATTAAATTTA
1 TTAAGATTAAAT-TTAATATTAAATTTA
12648959 ATATTAAACT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
37 10 0.18
38 28 0.50
39 18 0.32
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (39 bp):
TTAAGATTAAATTTAATATTAAATTTATCAAAATAAATA
Found at i:12648953 original size:50 final size:48
Alignment explanation
Indices: 12648887--12648982 Score: 156
Period size: 50 Copynumber: 2.0 Consensus size: 48
12648877 TATTTATCAC
*
12648887 GATAAATATTAGATTAAATTTAATATTAAATCTTATCAAAATAATATTAA
1 GATAAATATTAAATTAAATTTAATATTAAA-C-TATCAAAATAATATTAA
*
12648937 GATAAATATTAAATTAAATTTAATATTAAACTATTAAAATAATATT
1 GATAAATATTAAATTAAATTTAATATTAAACTATCAAAATAATATT
12648983 TTTTTGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 14 0.32
49 1 0.02
50 29 0.66
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (48 bp):
GATAAATATTAAATTAAATTTAATATTAAACTATCAAAATAATATTAA
Found at i:12655690 original size:15 final size:15
Alignment explanation
Indices: 12655672--12655703 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12655662 AGATGATTAA
12655672 CTTTGAAATGAAAGT
1 CTTTGAAATGAAAGT
12655687 CTTTGAAATGAAAGT
1 CTTTGAAATGAAAGT
12655702 CT
1 CT
12655704 GTTCAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (15 bp):
CTTTGAAATGAAAGT
Found at i:12660164 original size:46 final size:45
Alignment explanation
Indices: 12660101--12660196 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 45
12660091 GGTAGGAACA
* * * * *
12660101 TTTGTATCTGAATCTGATTTGTTCTGCATATGAAACTGAAATTGCT
1 TTTGTATATGAATCTGATCTATCCTGAATATG-AACTGAAATTGCT
*
12660147 TTTGTATATGTAA-CTGATCTATCCTGAATCTGAACTGAAATTGCT
1 TTTGTATATG-AATCTGATCTATCCTGAATATGAACTGAAATTGCT
12660192 TTTGT
1 TTTGT
12660197 TACCAAACCG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
45 18 0.42
46 23 0.53
47 2 0.05
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.44
Consensus pattern (45 bp):
TTTGTATATGAATCTGATCTATCCTGAATATGAACTGAAATTGCT
Found at i:12660959 original size:28 final size:30
Alignment explanation
Indices: 12660900--12660959 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
12660890 AATTATTACC
*
12660900 TTTTTTATATATTTTAAAAATAATATTTAT
1 TTTTTTATATATTTTAAAAATAATATTAAT
*
12660930 TTTTATTA-ATATTTTAAATATAA-A-TAAT
1 TTTT-TTATATATTTTAAAAATAATATTAAT
12660958 TT
1 TT
12660960 AACATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 1 0.04
30 18 0.67
31 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTTTATATATTTTAAAAATAATATTAAT
Found at i:12667763 original size:23 final size:23
Alignment explanation
Indices: 12667723--12667789 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
12667713 GCATTGAATC
* * *
12667723 AAATATAACATACGTAAAGTGAT
1 AAATATAACACACATAAAGCGAT
* * * *
12667746 GATTATAACACGCATAAAGCGCT
1 AAATATAACACACATAAAGCGAT
12667769 AAATATAACACACATAAAGCG
1 AAATATAACACACATAAAGCG
12667790 TTGAATCTCC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.21
Consensus pattern (23 bp):
AAATATAACACACATAAAGCGAT
Found at i:12670041 original size:46 final size:46
Alignment explanation
Indices: 12669986--12670166 Score: 224
Period size: 46 Copynumber: 3.9 Consensus size: 46
12669976 TAGGATGGTT
12669986 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
12670032 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
12670078 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** * *
12670125 GAACGCCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12670167 GCGGGTTACA
Statistics
Matches: 115, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 70 0.61
47 33 0.29
48 2 0.02
50 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:12670147 original size:93 final size:93
Alignment explanation
Indices: 12669988--12670158 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
12669978 GGATGGTTGA
* * *
12669988 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
12670053 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
12670081 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
12670146 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
12670159 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:12673506 original size:16 final size:15
Alignment explanation
Indices: 12673464--12673515 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 15
12673454 GTAGAGAGAG
12673464 AAGAGGAAAAAAAATCA
1 AAGAGGAAAAAAAA--A
*
12673481 ACAGAAGAAAAAAAGAA
1 A-AGAGGAAAAAAA-AA
*
12673498 AAGAGGAAAGAAAAA
1 AAGAGGAAAAAAAAA
12673513 AAG
1 AAG
12673516 TGAAGAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.17
16 10 0.33
17 3 0.10
18 11 0.37
19 1 0.03
ACGTcount: A:0.73, C:0.04, G:0.21, T:0.02
Consensus pattern (15 bp):
AAGAGGAAAAAAAAA
Found at i:12674723 original size:14 final size:13
Alignment explanation
Indices: 12674701--12674752 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
12674691 AAATTATTAT
*
12674701 TTAATTAATTATAA
1 TTAAATAATTA-AA
12674715 TTAAATAATTGAAA
1 TTAAATAATT-AAA
*
12674729 TTAAA-AATGAAA
1 TTAAATAATTAAA
12674741 TTAAATTAATTA
1 TTAAA-TAATTA
12674753 GTCATCATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 8 0.25
13 3 0.09
14 20 0.62
15 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TTAAATAATTAAA
Found at i:12674741 original size:12 final size:14
Alignment explanation
Indices: 12674713--12674751 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
12674703 AATTAATTAT
12674713 AATTAAATAATTGA
1 AATTAAATAATTGA
12674727 AATTAAA-AA-TGA
1 AATTAAATAATTGA
12674739 AATTAAATTAATT
1 AATTAAA-TAATT
12674752 AGTCATCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.45
13 2 0.09
14 9 0.41
15 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (14 bp):
AATTAAATAATTGA
Found at i:12679031 original size:27 final size:25
Alignment explanation
Indices: 12678961--12679032 Score: 65
Period size: 27 Copynumber: 2.8 Consensus size: 25
12678951 ATACAAAGAT
* *
12678961 ATATATAAAA-ATTTCAAAATAAATA
1 ATATGTAAAATATTT-AAAAGAAATA
* *
12678986 ATACGTATAATAGTTTAAAAGAAATAA
1 ATATGTAAAATA-TTTAAAAGAAAT-A
12679013 CATATGTAAAATATTTAAAA
1 -ATATGTAAAATATTTAAAA
12679033 TTGATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 7 0.19
26 9 0.24
27 11 0.30
28 10 0.27
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (25 bp):
ATATGTAAAATATTTAAAAGAAATA
Found at i:12679075 original size:3 final size:3
Alignment explanation
Indices: 12679067--12679419 Score: 148
Period size: 3 Copynumber: 119.3 Consensus size: 3
12679057 TATGTTCAAA
12679067 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * *
12679115 AAT AAT AAT AGT AAT AGC AAT AAT AAT -GT AAAT AAAT ACA- AA- AAG
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT A-AT AAT AAT
* * * * *
12679160 AA- AAT ATAT AAT -GT GAC AA- AAT CAAT -AT AA- AATT AATT AGT -TT
1 AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AA-T AA-T AAT AAT
* * ** * *
12679203 AAT AAT AA- GAT GAT AGC AAT AAT AAT AAT -AT AAT AAT AA- AGT AGAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * *
12679249 AAT AAT AAC AAT AAT AGAA AAT AAT GAT GA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
12679294 AA- ACT AAGG AAT ACT AAT AAT ACT AAC AAT AAT -AT AAAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * ** * * *
12679339 AAA AAC AAT AAG AGA- AAT AGC AAC AAT AAT AGT AAT AA- AAG AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
12679383 AA- AAGT AAT AAT AAT AAT AAT AAT ACC AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12679420 GAATTAACAA
Statistics
Matches: 266, Mismatches: 56, Indels: 56
0.70 0.15 0.15
Matches are distributed among these distances:
2 27 0.10
3 212 0.80
4 27 0.10
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:12679430 original size:18 final size:18
Alignment explanation
Indices: 12679409--12679448 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
12679399 ATAATAATAC
*
12679409 CAATAATAATAGAATTAA-
1 CAATAA-AATAAAATTAAT
12679427 CAATAAAATAAAATTAAT
1 CAATAAAATAAAATTAAT
12679445 CAAT
1 CAAT
12679449 TTTAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (18 bp):
CAATAAAATAAAATTAAT
Found at i:12680721 original size:20 final size:20
Alignment explanation
Indices: 12680696--12680734 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12680686 AACGAGACAA
*
12680696 CTGATGTGGCAAGTTAACTG
1 CTGATGTGACAAGTTAACTG
*
12680716 CTGATGTGACCAGTTAACT
1 CTGATGTGACAAGTTAACT
12680735 TGCCACATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
CTGATGTGACAAGTTAACTG
Found at i:12681466 original size:15 final size:15
Alignment explanation
Indices: 12681436--12681468 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12681426 ACTAGAGGTA
12681436 TCTCCATTTTTCTCT
1 TCTCCATTTTTCTCT
12681451 TCTCC-TTTTTCTTCT
1 TCTCCATTTTTC-TCT
12681466 TCT
1 TCT
12681469 TTTTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (15 bp):
TCTCCATTTTTCTCT
Found at i:12681485 original size:12 final size:12
Alignment explanation
Indices: 12681465--12681504 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
12681455 CTTTTTCTTC
*
12681465 TTCTT-TTTTTT
1 TTCTTATTTTCT
12681476 TTCTTATTTTCT
1 TTCTTATTTTCT
12681488 TTCTTATTTTCT
1 TTCTTATTTTCT
12681500 TTCTT
1 TTCTT
12681505 TTCTCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (12 bp):
TTCTTATTTTCT
Found at i:12681497 original size:22 final size:22
Alignment explanation
Indices: 12681474--12681515 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
12681464 CTTCTTTTTT
12681474 TTTTC-TTATTTTCT-TTCTTA
1 TTTTCTTTATTTTCTCTTCTTA
*
12681494 TTTTCTTTCTTTTCTCTTCTTA
1 TTTTCTTTATTTTCTCTTCTTA
12681516 AACACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTCTTTATTTTCTCTTCTTA
Found at i:12681789 original size:3 final size:3
Alignment explanation
Indices: 12681783--12681817 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12681773 AACTACTACT
12681783 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12681818 TACACATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12682922 original size:6 final size:7
Alignment explanation
Indices: 12682905--12682946 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
12682895 TTAATGATTT
12682905 TTTTTAA
1 TTTTTAA
12682912 TTTTTAA
1 TTTTTAA
12682919 TTTTTAA
1 TTTTTAA
*
12682926 TTTTAAA
1 TTTTTAA
12682933 TATTTTATA
1 T-TTTTA-A
12682942 TTTTT
1 TTTTT
12682947 TAAAATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 21 0.68
8 8 0.26
9 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTAA
Found at i:12683907 original size:14 final size:14
Alignment explanation
Indices: 12683888--12683917 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12683878 CGTGGGATGC
*
12683888 CAAAATGGAAATGA
1 CAAAATAGAAATGA
12683902 CAAAATAGAAATGA
1 CAAAATAGAAATGA
12683916 CA
1 CA
12683918 CGTGGACCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.13
Consensus pattern (14 bp):
CAAAATAGAAATGA
Found at i:12684390 original size:31 final size:31
Alignment explanation
Indices: 12684312--12684394 Score: 107
Period size: 29 Copynumber: 2.7 Consensus size: 31
12684302 CAAGAATTGG
*
12684312 ATTAAATTAAAATTTCATGTATAAAATTACAC
1 ATTAAATTAAAA-TTCATGTATAAAATCACAC
* *
12684344 A--AAATCAAAATTCATGTATACAATCACAC
1 ATTAAATTAAAATTCATGTATAAAATCACAC
*
12684373 ATTAAATTATAATTCATGTATA
1 ATTAAATTAAAATTCATGTATA
12684395 TTTTTAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.41
30 8 0.18
31 17 0.39
32 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (31 bp):
ATTAAATTAAAATTCATGTATAAAATCACAC
Found at i:12687209 original size:15 final size:16
Alignment explanation
Indices: 12687189--12687221 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
12687179 AAATATATTA
12687189 AAATATTAAAAAA-AT
1 AAATATTAAAAAACAT
12687204 AAATATTAAAAAACAT
1 AAATATTAAAAAACAT
12687220 AA
1 AA
12687222 TTCAACTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATATTAAAAAACAT
Found at i:12687528 original size:13 final size:13
Alignment explanation
Indices: 12687510--12687583 Score: 69
Period size: 13 Copynumber: 5.7 Consensus size: 13
12687500 TTTTCGTTAT
12687510 TTTTGAAAAGTAC
1 TTTTGAAAAGTAC
*
12687523 TTTTGAAAAGT-G
1 TTTTGAAAAGTAC
* *
12687535 TTGTAGAAAAGTAT
1 TT-TTGAAAAGTAC
*
12687549 TTTTGAGAAGTAC
1 TTTTGAAAAGTAC
* *
12687562 TTTTGAGAAGTGC
1 TTTTGAAAAGTAC
*
12687575 TTTAGAAAA
1 TTTTGAAAA
12687584 ATTTAAGTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
12 2 0.04
13 46 0.92
14 2 0.04
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTAC
Found at i:12687560 original size:39 final size:39
Alignment explanation
Indices: 12687507--12687583 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
12687497 AGTTTTTCGT
12687507 TATTTTTGAAAAGTACTTTTGAAAAGTG-TTGTAGAAAAG
1 TATTTTTGAAAAGTACTTTTGAAAAGTGCTT-TAGAAAAG
* *
12687546 TATTTTTGAGAAGTACTTTTGAGAAGTGCTTTAGAAAA
1 TATTTTTGAAAAGTACTTTTGAAAAGTGCTTTAGAAAA
12687584 ATTTAAGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (39 bp):
TATTTTTGAAAAGTACTTTTGAAAAGTGCTTTAGAAAAG
Found at i:12691337 original size:12 final size:12
Alignment explanation
Indices: 12691320--12691346 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12691310 GAAAATAGGG
12691320 TTTTAGCGGCGT
1 TTTTAGCGGCGT
12691332 TTTTAGCGGCGT
1 TTTTAGCGGCGT
12691344 TTT
1 TTT
12691347 ATCAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:12691621 original size:41 final size:41
Alignment explanation
Indices: 12691382--12691622 Score: 315
Period size: 41 Copynumber: 5.9 Consensus size: 41
12691372 AAACACAGAT
* * * *
12691382 CAATAGCGGCGTTTTTGGTAAAACGCCACTAAAA-ACAGAG
1 CAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAG
* * * *
12691422 CAATAGCGGCACTTTTTGTTAAAACGCCGCTAAAA-ACAGAG
1 CAATAGCGGCGC-TTTTGGTAAAACGCCGCTAAAAGTCGGAG
* *
12691463 CAATAGCGGCGCTTTTGGTCAAACGCCGCCAAAAGTCGGAG
1 CAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAG
* ** *
12691504 CAATAGCTGCGCTTCCGGTAAAACGCCGCTAAAATTCGGAG
1 CAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAG
*
12691545 CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCGGAG
1 CAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAG
*
12691586 CAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGTC
1 CAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
12691623 ATATAACCCC
Statistics
Matches: 178, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
40 29 0.16
41 149 0.84
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (41 bp):
CAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAG
Found at i:12691857 original size:7 final size:7
Alignment explanation
Indices: 12691845--12691908 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
12691835 TTTATTTTTT
*
12691845 GGTTTAC
1 GGTTTAA
12691852 GGTTTAA
1 GGTTTAA
**
12691859 TATTTAA
1 GGTTTAA
12691866 GGTTTAA
1 GGTTTAA
* *
12691873 GGTCTAT
1 GGTTTAA
*
12691880 GGTTTAG
1 GGTTTAA
*
12691887 GGTTTTAT
1 GG-TTTAA
12691895 GGTTTAA
1 GGTTTAA
12691902 GGTTTAA
1 GGTTTAA
12691909 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:12691897 original size:15 final size:15
Alignment explanation
Indices: 12691861--12691911 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
12691851 CGGTTTAATA
*
12691861 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
12691875 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
12691890 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
12691905 TTAATGG
1 TTTATGG
12691912 CCATGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:12692528 original size:8 final size:8
Alignment explanation
Indices: 12692517--12692579 Score: 83
Period size: 8 Copynumber: 8.0 Consensus size: 8
12692507 ACTCAAAAAA
12692517 TAAAAATT
1 TAAAAATT
12692525 TAAAAATT
1 TAAAAATT
12692533 TAAAAATT
1 TAAAAATT
12692541 TAAAAA-T
1 TAAAAATT
*
12692548 AAAAAATT
1 TAAAAATT
* *
12692556 AAAAAACT
1 TAAAAATT
*
12692564 TAAAAACT
1 TAAAAATT
12692572 TAAAAATT
1 TAAAAATT
12692580 AATATTTTAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
7 6 0.12
8 44 0.88
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (8 bp):
TAAAAATT
Found at i:12692553 original size:31 final size:30
Alignment explanation
Indices: 12692512--12692578 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
12692502 AATAAACTCA
* * *
12692512 AAAAATAAAAATTTAAAAATTTAAAAATTT
1 AAAAATAAAAATTAAAAAACTTAAAAACTT
12692542 AAAAATAAAAAATTAAAAAACTTAAAAACTT
1 AAAAAT-AAAAATTAAAAAACTTAAAAACTT
12692573 AAAAAT
1 AAAAAT
12692579 TAATATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (30 bp):
AAAAATAAAAATTAAAAAACTTAAAAACTT
Found at i:12693834 original size:17 final size:17
Alignment explanation
Indices: 12693812--12693844 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12693802 TGGAAGAAGA
*
12693812 AATGGGTTTTCTGAAAC
1 AATGGGTTTTCAGAAAC
12693829 AATGGGTTTTCAGAAA
1 AATGGGTTTTCAGAAA
12693845 GAAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (17 bp):
AATGGGTTTTCAGAAAC
Found at i:12695331 original size:19 final size:21
Alignment explanation
Indices: 12695303--12695350 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
12695293 TTATTATTTA
12695303 TTTTAGTTTTGATTCTAA-AT
1 TTTTAGTTTTGATTCTAATAT
* *
12695323 TTTTA-TTTTTATTTTAATAT
1 TTTTAGTTTTGATTCTAATAT
12695343 TTTTAGTT
1 TTTTAGTT
12695351 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTGATTCTAATAT
Found at i:12695449 original size:27 final size:28
Alignment explanation
Indices: 12695414--12695467 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
12695404 TATTTTGATA
*
12695414 ATGAATTTTA-AATTTTTTATATTTTTC
1 ATGAATTTTATAATATTTTATATTTTTC
* *
12695441 ATGACTTTTATAATATTTTATTTTTTT
1 ATGAATTTTATAATATTTTATATTTTT
12695468 TAAAATTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (28 bp):
ATGAATTTTATAATATTTTATATTTTTC
Found at i:12696079 original size:17 final size:18
Alignment explanation
Indices: 12696059--12696096 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12696049 CATTGATATC
12696059 TTTA-TATTTAATTTAAT
1 TTTATTATTTAATTTAAT
* *
12696076 TTTATTATTTATTTTAGT
1 TTTATTATTTAATTTAAT
12696094 TTT
1 TTT
12696097 GATTCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATTATTTAATTTAAT
Found at i:12696115 original size:19 final size:21
Alignment explanation
Indices: 12696087--12696134 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
12696077 TTATTATTTA
12696087 TTTTAGTTTTGATTCTAA-AT
1 TTTTAGTTTTGATTCTAATAT
* *
12696107 TTTTA-TTTTTATTTTAATAT
1 TTTTAGTTTTGATTCTAATAT
12696127 TTTTAGTT
1 TTTTAGTT
12696135 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTGATTCTAATAT
Found at i:12696233 original size:27 final size:28
Alignment explanation
Indices: 12696198--12696251 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
12696188 TATTTTGATA
*
12696198 ATGAATTTTA-AATTTTTTATATTTTTC
1 ATGAATTTTATAATATTTTATATTTTTC
* *
12696225 ATGACTTTTATAATATTTTATTTTTTT
1 ATGAATTTTATAATATTTTATATTTTT
12696252 TAAAATTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (28 bp):
ATGAATTTTATAATATTTTATATTTTTC
Found at i:12696258 original size:784 final size:780
Alignment explanation
Indices: 12694816--12696318 Score: 2875
Period size: 784 Copynumber: 1.9 Consensus size: 780
12694806 CACTTTTAAA
*
12694816 TCTATGAAGTATCTTGTGATCTTAATATTATCAGTTTCAAGAATCAGGACGTAATGAAATGTAAC
1 TCTATGAAGTATCTTGTGATCTTAATATTATCAGTTTCAAGAATCAGGACGTAAAGAAATGTAAC
12694881 TAGGTAGTTACCCCTTTTCTTTCAGGTATGCATACCCTTGGTGGAGAGAGAAAGAGATAATGTCT
66 TAGGTAGTTACCCCTTTTCTTTCAGGTATGCATACCCTTGGTGGAGAGAGAAAGAGATAATGTCT
*
12694946 GAAGAGAGGAGACAACAAGGGTTGTGTCCTCTGACACCCGAAGAAGCGACGCTAGTTTTGCAAGC
131 GAAGAGAGGAGACAACAAGGGTTGAGTCCTCTGACACCCGAAGAAGCGACGCTAGTTTTGCAAGC
12695011 ATTAGGTTTCGATAAGGAAACTCAGATTTACATAGCTTCTGGTGGAGATTTGTGGCAGTGAACGG
196 ATTAGGTTTCGATAAGGAAACTCAGATTTACATAGCTTCTGGTGGAGATTTGTGGCAGTGAACGG
12695076 AGATTGGCATCGCTAAGAGCTGCATTTCCACACATTGTGAGATTTTGACCCTGTAAATATTTTGC
261 AGATTGGCATCGCTAAGAGCTGCATTTCCACACATTGTGAGATTTTGACCCTGTAAATATTTTGC
12695141 TCTGGGCATTTGTAAGGTTGTTTAAAGCCTGGTGAGAGCACTGGGTTTCTATATTGACAACTTTT
326 TCTGGGCATTTGTAAGGTTGTTTAAAGCCTGGTGAGAGCACTGGGTTTCTATATTGACAACTTTT
*
12695206 TCGGATATCTTGATGATAATATCTTATATTTTACATGGTTATGATTTAAGTCCTTATTTCATTGA
391 TCGGATATCTTGATGATAATATCTTATATTTTACATAGTTATGATTTAAGTCCTTATTTCATTGA
12695271 TATCTTTATATTTAACTTAATTTTATTATTTATTTTAGTTTTGATTCTAAATTTTTATTTTTATT
456 TATCTTTATATTTAACTTAATTTTATTATTTATTTTAGTTTTGATTCTAAATTTTTATTTTTATT
12695336 TTAATATTTTTAGTTAAAAATTTAATAGAAAATTTTTATATTTATATCATGGATATTATTCTTCT
521 TTAATATTTTTAGTTAAAAATTTAATAGAAAATTTTTATATTTATATCATGGATATTATTCTTCT
12695401 CAATATTTTGATAATGAATTTTAAATTTTTTATATTTTTCATGACTTTTATAATATTTTATTTTT
586 CAATATTTTGATAATGAATTTTAAATTTTTTATATTTTTCATGACTTTTATAATATTTTATTTTT
*
12695466 TTTAAAATTTCATTACCTTTAGTGGCG-TTGTGGGAAAAGCGCCGCTAAAGGTCATGACCTTTAG
651 TTTAAAATTTCATTACCTTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCTGTAG
12695530 CGGCGTTTTTTTAAATAAACGCCACAAACTTTTGTGGCGCCGTCTATAGCGGCGTTTTTTGCGGC
716 CGGCGTTTTTTTAAATAAACGCCACAAACTTTTGTGGCGCCGTCTATAGCGGCGTTTTTTGCGGC
12695595 TCTATGAAGTATCTTGTGATCTTAATATTATCAGTTTCAAGAATCAGGACGCAATGATACAGAAA
1 TCTATGAAGTATCTTGTGATCTTAATATTATCAGTTTCAAGAATCAGGACG---T-A-A-AGAAA
12695660 TGTAACTAGGTAGTTACCCCTTTTCTTTCAGGTATGCATACCCTTGGTGGAGAGAGAAAGAGATA
60 TGTAACTAGGTAGTTACCCCTTTTCTTTCAGGTATGCATACCCTTGGTGGAGAGAGAAAGAGATA
12695725 ATGTCTGAAGAGAGGAGACAACAAGGGTTGAGTCCTCTGACACCCGAAGAAGCGACGCTAGTTTT
125 ATGTCTGAAGAGAGGAGACAACAAGGGTTGAGTCCTCTGACACCCGAAGAAGCGACGCTAGTTTT
*
12695790 GCAAGCATTAGGTTTCGATAAGGAAACTTAGATTTACATAGCTTCTGGT-GAGATTTGTGGCAGT
190 GCAAGCATTAGGTTTCGATAAGGAAACTCAGATTTACATAGCTTCTGGTGGAGATTTGTGGCAGT
*
12695854 GAACGGAGATTGGCATCGCTAAGAGCTGCATTTCCACACATTGTGAGATTTTGACCCTGTAAATG
255 GAACGGAGATTGGCATCGCTAAGAGCTGCATTTCCACACATTGTGAGATTTTGACCCTGTAAATA
12695919 TTTTGCTCTGGGCATTTGTAAGGTTGTTTAAAGCCTGGTGAGAGCACTGGGTTTCTATATTGACA
320 TTTTGCTCTGGGCATTTGTAAGGTTGTTTAAAGCCTGGTGAGAGCACTGGGTTTCTATATTGACA
12695984 ACTTTTTCGGATATCTTGATGATAATATCTTATATTTTACATAGTTATGATTTAAGTCCTTATTT
385 ACTTTTTCGGATATCTTGATGATAATATCTTATATTTTACATAGTTATGATTTAAGTCCTTATTT
*
12696049 CATTGATATCTTTATATTTAATTTAATTTTATTATTTATTTTAGTTTTGATTCTAAATTTTTATT
450 CATTGATATCTTTATATTTAACTTAATTTTATTATTTATTTTAGTTTTGATTCTAAATTTTTATT
12696114 TTTATTTTAATATTTTTAGTTAAAAATTTAATAGAAAATTTTTATATTTATATCATGGATATTAT
515 TTTATTTTAATATTTTTAGTTAAAAATTTAATAGAAAATTTTTATATTTATATCATGGATATTAT
12696179 TCTTCTCAATATTTTGATAATGAATTTTAAATTTTTTATATTTTTCATGACTTTTATAATATTTT
580 TCTTCTCAATATTTTGATAATGAATTTTAAATTTTTTATATTTTTCATGACTTTTATAATATTTT
12696244 ATTTTTTTTAAAATTTCATTACCTTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGAC
645 ATTTTTTTTAAAATTTCATTACCTTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGAC
12696309 CTGTAGCGGC
710 CTGTAGCGGC
12696319 ATTTGTGGGA
Statistics
Matches: 710, Mismatches: 7, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
779 51 0.07
782 1 0.00
783 1 0.00
784 436 0.61
785 221 0.31
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (780 bp):
TCTATGAAGTATCTTGTGATCTTAATATTATCAGTTTCAAGAATCAGGACGTAAAGAAATGTAAC
TAGGTAGTTACCCCTTTTCTTTCAGGTATGCATACCCTTGGTGGAGAGAGAAAGAGATAATGTCT
GAAGAGAGGAGACAACAAGGGTTGAGTCCTCTGACACCCGAAGAAGCGACGCTAGTTTTGCAAGC
ATTAGGTTTCGATAAGGAAACTCAGATTTACATAGCTTCTGGTGGAGATTTGTGGCAGTGAACGG
AGATTGGCATCGCTAAGAGCTGCATTTCCACACATTGTGAGATTTTGACCCTGTAAATATTTTGC
TCTGGGCATTTGTAAGGTTGTTTAAAGCCTGGTGAGAGCACTGGGTTTCTATATTGACAACTTTT
TCGGATATCTTGATGATAATATCTTATATTTTACATAGTTATGATTTAAGTCCTTATTTCATTGA
TATCTTTATATTTAACTTAATTTTATTATTTATTTTAGTTTTGATTCTAAATTTTTATTTTTATT
TTAATATTTTTAGTTAAAAATTTAATAGAAAATTTTTATATTTATATCATGGATATTATTCTTCT
CAATATTTTGATAATGAATTTTAAATTTTTTATATTTTTCATGACTTTTATAATATTTTATTTTT
TTTAAAATTTCATTACCTTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCTGTAG
CGGCGTTTTTTTAAATAAACGCCACAAACTTTTGTGGCGCCGTCTATAGCGGCGTTTTTTGCGGC
Found at i:12696338 original size:43 final size:43
Alignment explanation
Indices: 12696259--12696361 Score: 170
Period size: 43 Copynumber: 2.4 Consensus size: 43
12696249 TTTTAAAATT
* * *
12696259 TCATTACCTTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
1 TCATGACCTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGG
*
12696302 TCATGACCTGTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGG
1 TCATGACCTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGG
12696345 TCATGACCTTTAGCGGC
1 TCATGACCTTTAGCGGC
12696362 GTTTTTTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.25
Consensus pattern (43 bp):
TCATGACCTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGG
Found at i:12699096 original size:3 final size:3
Alignment explanation
Indices: 12699090--12699129 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12699080 CTTTTATCTC
12699090 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12699130 GATATTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12699573 original size:2 final size:2
Alignment explanation
Indices: 12699568--12699628 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
12699558 ATATATAGCC
* *
12699568 TA TA TA TA TA TA TA TA TA TC TT 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
12699610 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
12699629 CTTTAATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12703294 original size:24 final size:24
Alignment explanation
Indices: 12703266--12703314 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
12703256 AATAACTTAC
12703266 AATAGAATAATTCAAAAAATAAAA
1 AATAGAATAATTCAAAAAATAAAA
*
12703290 AATAGAATAATTCAAGAAATAAAA
1 AATAGAATAATTCAAAAAATAAAA
12703314 A
1 A
12703315 TCTTTAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (24 bp):
AATAGAATAATTCAAAAAATAAAA
Found at i:12703830 original size:24 final size:23
Alignment explanation
Indices: 12703803--12703854 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
12703793 AATGATTAAA
*
12703803 ATTTTTAAAAGGAAAAAAATATTT
1 ATTTTTAAAA-GAAAAAAATAATT
* * *
12703827 ATTTATAATATAAAAAAATAATT
1 ATTTTTAAAAGAAAAAAATAATT
12703850 ATTTT
1 ATTTT
12703855 AAGTAATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
ATTTTTAAAAGAAAAAAATAATT
Found at i:12711470 original size:21 final size:22
Alignment explanation
Indices: 12711426--12711478 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
12711416 TGGATCACCT
*
12711426 AATATTTTGATTGTTTTAATAA
1 AATATTTTGATTGTTTTAAAAA
12711448 AATATTTT-ATT-TTATTAAAAA
1 AATATTTTGATTGTT-TTAAAAA
12711469 AATGATTTTG
1 AAT-ATTTTG
12711479 GTCTACGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.53
Consensus pattern (22 bp):
AATATTTTGATTGTTTTAAAAA
Found at i:12712359 original size:3 final size:3
Alignment explanation
Indices: 12712353--12712382 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12712343 AACAATAATA
12712353 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
12712383 TAAAGATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:12715307 original size:20 final size:20
Alignment explanation
Indices: 12715271--12715313 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
12715261 CCAAACACCA
*
12715271 AAAAAGTAAATCATTTCTAG
1 AAAAAGTAAATCATTTCCAG
12715291 AAAAA-TAAATCATTTTCCAG
1 AAAAAGTAAATCA-TTTCCAG
12715311 AAA
1 AAA
12715314 TCATTTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAAAGTAAATCATTTCCAG
Found at i:12715650 original size:15 final size:15
Alignment explanation
Indices: 12715630--12715660 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12715620 AAATATTTAG
12715630 AGAGTAAGCATTAAA
1 AGAGTAAGCATTAAA
12715645 AGAGTAAGCATTAAA
1 AGAGTAAGCATTAAA
12715660 A
1 A
12715661 TCTTTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (15 bp):
AGAGTAAGCATTAAA
Found at i:12718172 original size:10 final size:10
Alignment explanation
Indices: 12718157--12718182 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12718147 CTTTGTAATT
12718157 AATAATGTGA
1 AATAATGTGA
12718167 AATAATGTGA
1 AATAATGTGA
12718177 AATAAT
1 AATAAT
12718183 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (10 bp):
AATAATGTGA
Found at i:12719494 original size:10 final size:10
Alignment explanation
Indices: 12719462--12719511 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
12719452 TTAAATTCTA
12719462 AAAGATAAAT
1 AAAGATAAAT
*
12719472 ACAA-AGAAAT
1 A-AAGATAAAT
*
12719482 AAAGATAATT
1 AAAGATAAAT
12719492 AAAGATAAAT
1 AAAGATAAAT
*
12719502 AAAAATAAAT
1 AAAGATAAAT
12719512 CCAAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:12719832 original size:99 final size:101
Alignment explanation
Indices: 12719705--12719891 Score: 297
Period size: 99 Copynumber: 1.9 Consensus size: 101
12719695 TTTAATTTAA
* *
12719705 TTTATTTTTACTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
* *
12719770 CCTCGGTTACTCAAACCAACATACTCCTAATTTTTT
66 CCCCAGTTACTCAAACCAACATACTCCTAATTTTTT
* *
12719806 TTTA-TTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGATAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
*
12719869 CCCCAGTTACTCAACCCAACATA
66 CCCCAGTTACTCAAACCAACATA
12719892 TTCTTAAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 71 0.90
100 4 0.05
101 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (101 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
CCCCAGTTACTCAAACCAACATACTCCTAATTTTTT
Found at i:12722504 original size:7 final size:7
Alignment explanation
Indices: 12722462--12722513 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
12722452 TCCAAAATAA
12722462 AATAAAT
1 AATAAAT
*
12722469 AATTAAGT
1 AA-TAAAT
*
12722477 AATAAGT
1 AATAAAT
*
12722484 AATTAA-
1 AATAAAT
12722490 AATAAAAT
1 AAT-AAAT
12722498 AATAAAT
1 AATAAAT
12722505 AATAAAT
1 AATAAAT
12722512 AA
1 AA
12722514 AAGAAAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 3 0.08
7 26 0.68
8 9 0.24
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:12729516 original size:20 final size:20
Alignment explanation
Indices: 12729493--12729552 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
12729483 TTAAATTCTA
* *
12729493 AAAGATAAACACAAATAAAT
1 AAAGATAAATAAAAATAAAT
* *
12729513 AAAGATAATTAAAAATAATT
1 AAAGATAAATAAAAATAAAT
12729533 AAAGATAAATAAAAATAAAT
1 AAAGATAAATAAAAATAAAT
12729553 CTTAAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAGATAAATAAAAATAAAT
Found at i:12729520 original size:10 final size:10
Alignment explanation
Indices: 12729493--12729552 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
12729483 TTAAATTCTA
*
12729493 AAAGATAAAC
1 AAAGATAAAT
12729503 ACAA-ATAAAT
1 A-AAGATAAAT
*
12729513 AAAGATAATT
1 AAAGATAAAT
* *
12729523 AAAAATAATT
1 AAAGATAAAT
12729533 AAAGATAAAT
1 AAAGATAAAT
*
12729543 AAAAATAAAT
1 AAAGATAAAT
12729553 CTTAAATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
9 2 0.05
10 38 0.90
11 2 0.05
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:12729602 original size:14 final size:13
Alignment explanation
Indices: 12729566--12729603 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
12729556 AAATTTAAAT
12729566 CTAAATAATTATC
1 CTAAATAATTATC
*
12729579 CTTAATAATTATC
1 CTAAATAATTATC
12729592 CTAATATAATTA
1 CTAA-ATAATTA
12729604 AACATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (13 bp):
CTAAATAATTATC
Found at i:12730709 original size:16 final size:17
Alignment explanation
Indices: 12730688--12730759 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 17
12730678 ATTAAGGTTA
12730688 ATTGATTAAATTAGGG-
1 ATTGATTAAATTAGGGT
12730704 ATTGATTAAATTAGGGTT
1 ATTGATTAAATTAGGG-T
*
12730722 AATTGATTAAATTTAAGGCT
1 -ATTGATTAAA-TT-AGGGT
*
12730742 AATTGATTAATTTAGGGT
1 -ATTGATTAAATTAGGGT
12730760 TAATTGATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 16 0.33
18 4 0.08
19 12 0.25
20 13 0.27
21 3 0.06
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (17 bp):
ATTGATTAAATTAGGGT
Found at i:12730725 original size:35 final size:38
Alignment explanation
Indices: 12730678--12730767 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 38
12730668 AGTTTAGGGT
* *
12730678 ATTAAGGTTAATTGATTAAA-TT-AGG-GATTGATTAA
1 ATTAGGGTTAATTGATTAAATTTAAGGCAATTGATTAA
12730713 ATTAGGGTTAATTGATTAAATTTAAGGCTAATTGATTAA
1 ATTAGGGTTAATTGATTAAATTTAAGGC-AATTGATTAA
*
12730752 TTTAGGGTTAATTGAT
1 ATTAGGGTTAATTGAT
12730768 ACATAATGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
35 19 0.40
36 2 0.04
37 3 0.06
39 24 0.50
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (38 bp):
ATTAGGGTTAATTGATTAAATTTAAGGCAATTGATTAA
Found at i:12730728 original size:19 final size:19
Alignment explanation
Indices: 12730678--12730767 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
12730668 AGTTTAGGGT
*
12730678 ATTAAGGTTAATTGATTAA
1 ATTAGGGTTAATTGATTAA
12730697 ATTAGGG---ATTGATTAA
1 ATTAGGGTTAATTGATTAA
12730713 ATTAGGGTTAATTGATTAA
1 ATTAGGGTTAATTGATTAA
* *
12730732 ATTTAAGGCTAATTGATTAA
1 A-TTAGGGTTAATTGATTAA
*
12730752 TTTAGGGTTAATTGAT
1 ATTAGGGTTAATTGAT
12730768 ACATAATGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
16 16 0.26
19 29 0.48
20 16 0.26
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (19 bp):
ATTAGGGTTAATTGATTAA
Found at i:12731521 original size:126 final size:126
Alignment explanation
Indices: 12731311--12731676 Score: 606
Period size: 126 Copynumber: 2.9 Consensus size: 126
12731301 TTTTAAGTAG
* *
12731311 ACGTTTCTGAACAAATAGTGTCGAAAACGCTTGAAGCAGGATGCACCGTCAGCAAAATTTCTGAA
1 ACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTGAA
12731376 AAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAAAATAATTCTGAATAA
66 AAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAAAATAATTCTGAATAA
* **
12731437 ACGTTTCTGAACAAATATTGTCGAAAACGCTTCAAGCAGGATAAACTGTCAGCAAAATTTCTGAA
1 ACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTGAA
* * * * *
12731502 AAAAGCTCCCACATGGACGCTCTTTTGTTACAATAGTTCGTAGAAAAATAATTCTGAGTAG
66 AAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAAAATAATTCTGAATAA
* *
12731563 ACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGTAGGATGCACTGTCAGCAAAATTTTTGAA
1 ACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTGAA
* *
12731628 AAAAGCTCCCACGTGGACGCTCTTTTGCTACGGTAGTTCATAGAAAAAT
66 AAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAAAAT
12731677 GAGGCTATAA
Statistics
Matches: 220, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 220 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (126 bp):
ACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTGAA
AAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAAAATAATTCTGAATAA
Found at i:12735195 original size:18 final size:18
Alignment explanation
Indices: 12735169--12735211 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12735159 GACTAGGAAA
* * *
12735169 AGGAAACATATAAGGGTT
1 AGGATACATATAAAGGCT
12735187 AGGATACATATAAAGGCT
1 AGGATACATATAAAGGCT
12735205 AGGATAC
1 AGGATAC
12735212 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:12735838 original size:7 final size:7
Alignment explanation
Indices: 12735806--12735837 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
12735796 CATAATACAT
12735806 AATACTA
1 AATACTA
12735813 AATACTA
1 AATACTA
12735820 AATACTA
1 AATACTA
*
12735827 AATATTA
1 AATACTA
12735834 AATA
1 AATA
12735838 TGAAACGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (7 bp):
AATACTA
Found at i:12736847 original size:48 final size:48
Alignment explanation
Indices: 12736795--12736929 Score: 148
Period size: 48 Copynumber: 2.8 Consensus size: 48
12736785 ATGCAAACAT
*
12736795 CATAAATGAAAAAAAAATCAAGCAGTATTG-AAATTTTAATTATAA-TTG
1 CATAAATGAAAAAAAAATCAAACAGTATTGCAAA-TTTAATTA-AATTTG
* * *
12736843 CATAAATGAATAAAATATCAAATAGTATTGCAAATTTAATTAAATTTG
1 CATAAATGAAAAAAAAATCAAACAGTATTGCAAATTTAATTAAATTTG
* * * * * *
12736891 CATAAATTAAAAAAATATCGAATAATATTGAAAATTTAA
1 CATAAATGAAAAAAAAATCAAACAGTATTGCAAATTTAA
12736930 AATTATCACT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
47 2 0.03
48 71 0.93
49 3 0.04
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (48 bp):
CATAAATGAAAAAAAAATCAAACAGTATTGCAAATTTAATTAAATTTG
Found at i:12740788 original size:121 final size:121
Alignment explanation
Indices: 12740574--12740806 Score: 457
Period size: 121 Copynumber: 1.9 Consensus size: 121
12740564 AATTACAACA
*
12740574 AACAATGGCTATGATACACAGGAGATCAAGTTGATATAACCTTTGCTTATGAGCAAGCAATCTAT
1 AACAATGGCTATGATACACAGGAGACCAAGTTGATATAACCTTTGCTTATGAGCAAGCAATCTAT
12740639 ATGGAAGCAGTTAAATAGGCAGTGAAAGATCTCCCAAAAATTTGTCGGTATGGTAC
66 ATGGAAGCAGTTAAATAGGCAGTGAAAGATCTCCCAAAAATTTGTCGGTATGGTAC
12740695 AACAATGGCTATGATACACAGGAGACCAAGTTGATATAACCTTTGCTTATGAGCAAGCAATCTAT
1 AACAATGGCTATGATACACAGGAGACCAAGTTGATATAACCTTTGCTTATGAGCAAGCAATCTAT
12740760 ATGGAAGCAGTTAAATAGGCAGTGAAAGATCTCCCAAAAATTTGTCG
66 ATGGAAGCAGTTAAATAGGCAGTGAAAGATCTCCCAAAAATTTGTCG
12740807 TTATAGTAAA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (121 bp):
AACAATGGCTATGATACACAGGAGACCAAGTTGATATAACCTTTGCTTATGAGCAAGCAATCTAT
ATGGAAGCAGTTAAATAGGCAGTGAAAGATCTCCCAAAAATTTGTCGGTATGGTAC
Found at i:12742666 original size:6 final size:7
Alignment explanation
Indices: 12742641--12742676 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
12742631 AAAGAGAAGA
*
12742641 CAAAAGG
1 CAAAAAG
12742648 CAAAAAG
1 CAAAAAG
12742655 CAAAAAG
1 CAAAAAG
12742662 CAAAAAG
1 CAAAAAG
12742669 CAAAAAG
1 CAAAAAG
12742676 C
1 C
12742677 GAAGGTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.67, C:0.17, G:0.17, T:0.00
Consensus pattern (7 bp):
CAAAAAG
Found at i:12743134 original size:3 final size:3
Alignment explanation
Indices: 12743126--12743169 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
12743116 CAAATTCTAA
12743126 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12743170 AATCAGGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12752205 original size:52 final size:52
Alignment explanation
Indices: 12752127--12752254 Score: 247
Period size: 52 Copynumber: 2.5 Consensus size: 52
12752117 TTTATCTATA
12752127 AATACAGAGCATGATGCTATCCCTCTTCTTTTAGAATATTCAAATATTAAGG
1 AATACAGAGCATGATGCTATCCCTCTTCTTTTAGAATATTCAAATATTAAGG
12752179 AATACAGAGCATGATGCTATCCCTCTTCTTTTAGAATATTCAAATATTAAGG
1 AATACAGAGCATGATGCTATCCCTCTTCTTTTAGAATATTCAAATATTAAGG
*
12752231 AATACAGAGCTTGATGCTATCCCT
1 AATACAGAGCATGATGCTATCCCT
12752255 TAGGGTACAG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (52 bp):
AATACAGAGCATGATGCTATCCCTCTTCTTTTAGAATATTCAAATATTAAGG
Found at i:12752508 original size:26 final size:26
Alignment explanation
Indices: 12752478--12752531 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
12752468 TGCTCAAAAG
12752478 TAAAAATGGCAGTATGGCAACTCAGC
1 TAAAAATGGCAGTATGGCAACTCAGC
12752504 TAAAAATGGCAGTATGGCAACTCAGC
1 TAAAAATGGCAGTATGGCAACTCAGC
12752530 TA
1 TA
12752532 TTAGATCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (26 bp):
TAAAAATGGCAGTATGGCAACTCAGC
Found at i:12754821 original size:6 final size:6
Alignment explanation
Indices: 12754807--12754836 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12754797 CCACATACTC
*
12754807 AATTAT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
12754837 TATCAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:12756875 original size:18 final size:18
Alignment explanation
Indices: 12756852--12756953 Score: 68
Period size: 18 Copynumber: 5.3 Consensus size: 18
12756842 TTATTGTAAT
12756852 ATCTTTTCTGACTCTCAA
1 ATCTTTTCTGACTCTCAA
*
12756870 ATCTTTGTATTTAGAGCT-TC-A
1 ATC-TT-T-TCT-GA-CTCTCAA
12756891 ATCTTTTCTGACTCTCAA
1 ATCTTTTCTGACTCTCAA
*
12756909 ATCTTTGTATTTAGAACT-TC-A
1 ATC-TT-T-TCT-G-ACTCTCAA
12756930 ATCTTTTCTGACTCTCAA
1 ATCTTTTCTGACTCTCAA
12756948 ATCTTT
1 ATCTTT
12756954 GTATTTAGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
16 5 0.08
17 7 0.11
18 18 0.27
19 6 0.09
20 6 0.09
21 12 0.18
22 7 0.11
23 5 0.08
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.47
Consensus pattern (18 bp):
ATCTTTTCTGACTCTCAA
Found at i:12756896 original size:39 final size:39
Alignment explanation
Indices: 12756852--12756970 Score: 229
Period size: 39 Copynumber: 3.1 Consensus size: 39
12756842 TTATTGTAAT
12756852 ATCTTTTCTGACTCTCAAATCTTTGTATTTAGAGCTTCA
1 ATCTTTTCTGACTCTCAAATCTTTGTATTTAGAGCTTCA
*
12756891 ATCTTTTCTGACTCTCAAATCTTTGTATTTAGAACTTCA
1 ATCTTTTCTGACTCTCAAATCTTTGTATTTAGAGCTTCA
12756930 ATCTTTTCTGACTCTCAAATCTTTGTATTTAGAGCTTCA
1 ATCTTTTCTGACTCTCAAATCTTTGTATTTAGAGCTTCA
12756969 AT
1 AT
12756971 TTGCAAGCAC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.46
Consensus pattern (39 bp):
ATCTTTTCTGACTCTCAAATCTTTGTATTTAGAGCTTCA
Found at i:12764179 original size:24 final size:22
Alignment explanation
Indices: 12764140--12764183 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
12764130 GGCACGTTAT
12764140 TTTTTGTTCTGTTTCTTCTTGG
1 TTTTTGTTCTGTTTCTTCTTGG
*
12764162 TTTTTGTTTTTGTGTTCTTCTT
1 TTTTTG-TTCTGT-TTCTTCTT
12764184 TTTGCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 8 0.42
ACGTcount: A:0.00, C:0.11, G:0.16, T:0.73
Consensus pattern (22 bp):
TTTTTGTTCTGTTTCTTCTTGG
Found at i:12764810 original size:21 final size:20
Alignment explanation
Indices: 12764785--12764834 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
12764775 ACGGCCTGAT
12764785 CACACGAC-TATGCCTCTATA
1 CACACGACGTATGCCTCTA-A
*
12764805 CAACACGAGCGTGTGCCTCTAA
1 C-ACACGA-CGTATGCCTCTAA
12764827 CACACGAC
1 CACACGAC
12764835 CGTGTGCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 12 0.46
22 3 0.12
23 9 0.35
ACGTcount: A:0.30, C:0.36, G:0.16, T:0.18
Consensus pattern (20 bp):
CACACGACGTATGCCTCTAA
Found at i:12764838 original size:21 final size:23
Alignment explanation
Indices: 12764795--12764841 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
12764785 CACACGACTA
*
12764795 TGCCTCTATACAACACGAGCGTG
1 TGCCTCTATACAACACGACCGTG
12764818 TGCCTCTA-AC-ACACGACCGTG
1 TGCCTCTATACAACACGACCGTG
12764839 TGC
1 TGC
12764842 TACCCTTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
22 2 0.09
23 8 0.35
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.21
Consensus pattern (23 bp):
TGCCTCTATACAACACGACCGTG
Found at i:12766771 original size:39 final size:40
Alignment explanation
Indices: 12766727--12766808 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
12766717 AATTTAATAC
*
12766727 TTATCTTGATAA-TATTTTATTACTTTAATATTAAAATGA
1 TTATCTTGATAAGTATTTTATTAATTTAATATTAAAATGA
* *
12766766 TTATCTTGATAAGTATTTTATTAATTTAATATTAGAGTGA
1 TTATCTTGATAAGTATTTTATTAATTTAATATTAAAATGA
12766806 TTA
1 TTA
12766809 AGTTTAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 12 0.31
40 27 0.69
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
TTATCTTGATAAGTATTTTATTAATTTAATATTAAAATGA
Found at i:12766824 original size:26 final size:26
Alignment explanation
Indices: 12766795--12766846 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12766785 ATTAATTTAA
12766795 TATTAGAGTGATTAAGTTTAATTATC
1 TATTAGAGTGATTAAGTTTAATTATC
12766821 TATTAGAGTGATTAAGTTTAATTATC
1 TATTAGAGTGATTAAGTTTAATTATC
12766847 GTTGAATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (26 bp):
TATTAGAGTGATTAAGTTTAATTATC
Found at i:12770144 original size:26 final size:26
Alignment explanation
Indices: 12770108--12770217 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
12770098 CATGAAATTC
*
12770108 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
12770134 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * * *
12770160 GTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
12770186 TTGTCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12770212 TTATCA
1 TTATCA
12770218 ATTTGTATCA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:12777901 original size:21 final size:20
Alignment explanation
Indices: 12777859--12777896 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
12777849 CTAGGTTTTG
*
12777859 AATTTTATTTGATTTAATCT
1 AATTTTATATGATTTAATCT
12777879 AATTTT-TATGATTTAATC
1 AATTTTATATGATTTAATC
12777897 CCTAACCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTTATATGATTTAATCT
Found at i:12789227 original size:19 final size:18
Alignment explanation
Indices: 12789203--12789238 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12789193 TGTTAATAAA
*
12789203 TTTATTTCTTTCTCTTTTT
1 TTTATTTATTTCT-TTTTT
12789222 TTTATTTATTTCTTTTT
1 TTTATTTATTTCTTTTT
12789239 ATCCTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTATTTATTTCTTTTTT
Found at i:12790655 original size:5 final size:5
Alignment explanation
Indices: 12790647--12790683 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
12790637 ATCTTGTGAA
12790647 AAAAT AAAAT AAAAT AAAAT AAAGA- AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AA
12790684 CACACAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:12795108 original size:5 final size:5
Alignment explanation
Indices: 12795098--12795127 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
12795088 CCAATTTGTG
12795098 AATAA AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
12795128 CACACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:12795968 original size:19 final size:19
Alignment explanation
Indices: 12795930--12795969 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12795920 TCTAAATAAT
*
12795930 ATTAATTTAAAGTTATTTG
1 ATTAATTTAAAGTTACTTG
**
12795949 ATTAATTTAATTTTACTTG
1 ATTAATTTAAAGTTACTTG
12795968 AT
1 AT
12795970 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAAGTTACTTG
Found at i:12798349 original size:26 final size:27
Alignment explanation
Indices: 12798292--12798347 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
12798282 TGAGATTTGA
* **
12798292 TTTTAATTATTATTATTTAAATCTTAG
1 TTTTAATTATTATTACTTAAATAATAG
12798319 TTTTAATT-TTA-TACTTAAATAATAG
1 TTTTAATTATTATTACTTAAATAATAG
12798344 TTTT
1 TTTT
12798348 TATTGATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 15 0.58
26 3 0.12
27 8 0.31
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (27 bp):
TTTTAATTATTATTACTTAAATAATAG
Done.