Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 37 of 117
Found at i:6532518 original size:31 final size:31
Alignment explanation
Indices: 6532480--6532538 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
6532470 AAATGAGCAA
** *
6532480 AACCCATGACTATTAACATCAAACTAAGCCC
1 AACCCATGAAGATGAACATCAAACTAAGCCC
*
6532511 AACCCATGAAGATGAACATTAAACTAAG
1 AACCCATGAAGATGAACATCAAACTAAG
6532539 TATAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19
Consensus pattern (31 bp):
AACCCATGAAGATGAACATCAAACTAAGCCC
Found at i:6543603 original size:31 final size:31
Alignment explanation
Indices: 6543560--6543628 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
6543550 AGCTGAAATG
* * * *
6543560 AGCAAAACCCATGGATATTAACATCAAACTA
1 AGCACAACCCATGAAGATGAACATCAAACTA
6543591 AGCACAACCCATGAAGATGAACATCAAACTA
1 AGCACAACCCATGAAGATGAACATCAAACTA
*
6543622 AGTACAA
1 AGCACAA
6543629 AAATACAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.23, G:0.12, T:0.16
Consensus pattern (31 bp):
AGCACAACCCATGAAGATGAACATCAAACTA
Found at i:6543703 original size:95 final size:95
Alignment explanation
Indices: 6543589--6543778 Score: 310
Period size: 95 Copynumber: 2.0 Consensus size: 95
6543579 AACATCAAAC
* * *
6543589 TAAGCACAACCCATGAAGATGAACATCAAACTAAGTACAAAAATACAAAGAAAACGGCA-AAAGA
1 TAAGCACAACCCATAAAGATGAACATCAAACTAAGCACAAAAATACAAAGAAAACAG-AGAAAGA
* *
6543653 GAGGGAAGCAGACCTGCAAAAATTCAGGGAA
65 GAAGGAAGCAGACCAGCAAAAATTCAGGGAA
*
6543684 TAAGCACAACCCATAAAGATGAATATCAAACTAAGCACAAAAATACAAAGAAAACAGAGAAAGAG
1 TAAGCACAACCCATAAAGATGAACATCAAACTAAGCACAAAAATACAAAGAAAACAGAGAAAGAG
6543749 AAGGAAGCAGACCAGCAAAAATTCAGGGAA
66 AAGGAAGCAGACCAGCAAAAATTCAGGGAA
6543779 AAAGTGTGGA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 1 0.01
95 87 0.99
ACGTcount: A:0.54, C:0.17, G:0.19, T:0.10
Consensus pattern (95 bp):
TAAGCACAACCCATAAAGATGAACATCAAACTAAGCACAAAAATACAAAGAAAACAGAGAAAGAG
AAGGAAGCAGACCAGCAAAAATTCAGGGAA
Found at i:6545412 original size:147 final size:147
Alignment explanation
Indices: 6545221--6545486 Score: 446
Period size: 147 Copynumber: 1.8 Consensus size: 147
6545211 ACCAAACCTA
*
6545221 GCACAACACTCTAAATTGCAATCTGAAGTGAGCAAAACCTATGAAGACGAATATCAAACTAAGCA
1 GCACAACACTCTAAATTGCAATCTGAAGTGAGCAAAACCTATGAAGACGAACATCAAACTAAGCA
*
6545286 TAAAAACGTAAAGAAAACAGAGAAAGAGATGGAAACTGA-CATACAAAAATTCAGGTAAGGGCAA
66 TAAAAACGCAAAGAAAACAGAGAAAGAGATGGAAACTGATC-TACAAAAATTCAGGTAAGGGCAA
6545350 AGGTTGAAACAAATTTTG
130 AGGTTGAAACAAATTTTG
*
6545368 GCACAACACTCTAAATTGCAATCTGAAGTGAGCAAAA-CTCATGAAGATGAACATCAAACTAAGC
1 GCACAACACTCTAAATTGCAATCTGAAGTGAGCAAAACCT-ATGAAGACGAACATCAAACTAAGC
* * *
6545432 ATAAAAATGCAAATAAAACAGAGAAAGAGATGGAAACTGATCTGCAAAAATTCAG
65 ATAAAAACGCAAAGAAAACAGAGAAAGAGATGGAAACTGATCTACAAAAATTCAG
6545487 AAGAAAACAG
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
146 2 0.02
147 108 0.97
148 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (147 bp):
GCACAACACTCTAAATTGCAATCTGAAGTGAGCAAAACCTATGAAGACGAACATCAAACTAAGCA
TAAAAACGCAAAGAAAACAGAGAAAGAGATGGAAACTGATCTACAAAAATTCAGGTAAGGGCAAA
GGTTGAAACAAATTTTG
Found at i:6545495 original size:44 final size:44
Alignment explanation
Indices: 6545446--6545530 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
6545436 AAATGCAAAT
*
6545446 AAAACAGAGAAAGAGATGGAAACTGATCTGCAAAAATTCAGAAG
1 AAAACAGAGAAAGAAATGGAAACTGATCTGCAAAAATTCAGAAG
6545490 AAAACAGAGAAAGAAATGGAAACTGATCTGCAAAAATTCAG
1 AAAACAGAGAAAGAAATGGAAACTGATCTGCAAAAATTCAG
6545531 GTCAGGGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.14
Consensus pattern (44 bp):
AAAACAGAGAAAGAAATGGAAACTGATCTGCAAAAATTCAGAAG
Found at i:6550362 original size:2 final size:2
Alignment explanation
Indices: 6550355--6550401 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
6550345 GTTGCAATGG
* *
6550355 TA TA TA TA TG TT 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
6550397 TA TA T
1 TA TA T
6550402 TCACATTTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6550864 original size:231 final size:232
Alignment explanation
Indices: 6550597--6551075 Score: 687
Period size: 232 Copynumber: 2.1 Consensus size: 232
6550587 AAGAGAAGCT
* * *
6550597 TGATGTACAAGAGAAACTTTTTTGAAGTTGTTTTGGTATTTATATATTTTTTAACAT-TTTT-TT
1 TGATGTATAAGAGAAACTTTTATAAAGTTGTTTTGGTATTTATA-ATTTTTTAACATATTTTCTT
* * *
6550660 TGTGAAATATATTTAAAAGCTAAAAACAATGTAAATATTATTTATAAAAAATATTAAATATATTA
65 TGTGAAATATATTTAAAAGCTAAAAACAATATAAAAATTATTTATAAAAAATATTAAAGATATTA
* * * * * *
6550725 AATAATA-TTTTTAAAAGTTGTGATAAATTTAAATATTTATGTTAACTGTAGATAAA-TTTAAAA
130 AATAATATTTTTTAAAA-TTATGATAAATTTAAATACTCATATTAACTCTAAATAAATTTTAAAA
* * *
6550788 AGATAAATCACTTTAAAATTGATTTTATATTGAGATGAGG
194 A-ATAAATCACTTTAAAATTAATTTTAAATTGAGATAAGG
* **
6550828 TGATGTATATGAGAAACTTTTATAAAGTTGTTTTGGTATTTATAATTTTTTTTCATATTTTCTTT
1 TGATGTATAAGAGAAACTTTTATAAAGTTGTTTTGGTATTTATAATTTTTTAACATATTTTCTTT
* *
6550893 GTGAAATATATTTAAAAGCTAAAGATAATATAAAAATTATTTATAAAAAATATTAAAGATATTAA
66 GTGAAATATATTTAAAAGCTAAAAACAATATAAAAATTATTTATAAAAAATATTAAAGATATTAA
6550958 ATAATATTTTTTAAAATTATGATAAATTTAAATACTCATATTAACTCTAAATAAATTTTAAAAAA
131 ATAATATTTTTTAAAATTATGATAAATTTAAATACTCATATTAACTCTAAATAAATTTTAAAAAA
* *
6551023 TAAATTATTTTAAAATTAATTTTAAATTGAGATAAGG
196 TAAATCACTTTAAAATTAATTTTAAATTGAGATAAGG
* *
6551060 TGATATATAACAGAAA
1 TGATGTATAAGAGAAA
6551076 AAAATTTCAT
Statistics
Matches: 219, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
230 10 0.05
231 44 0.20
232 148 0.68
233 17 0.08
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (232 bp):
TGATGTATAAGAGAAACTTTTATAAAGTTGTTTTGGTATTTATAATTTTTTAACATATTTTCTTT
GTGAAATATATTTAAAAGCTAAAAACAATATAAAAATTATTTATAAAAAATATTAAAGATATTAA
ATAATATTTTTTAAAATTATGATAAATTTAAATACTCATATTAACTCTAAATAAATTTTAAAAAA
TAAATCACTTTAAAATTAATTTTAAATTGAGATAAGG
Found at i:6551113 original size:18 final size:19
Alignment explanation
Indices: 6551090--6551125 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6551080 TTTCATTCAA
6551090 ATTTAA-ATTAAATTTTTT
1 ATTTAATATTAAATTTTTT
*
6551108 ATTTAATTTTAAATTTTT
1 ATTTAATATTAAATTTTT
6551126 AAATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTAATATTAAATTTTTT
Found at i:6551140 original size:20 final size:21
Alignment explanation
Indices: 6551117--6551155 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
6551107 TATTTAATTT
6551117 TAAATTTTTAAATA-ATTTAA
1 TAAATTTTTAAATATATTTAA
6551137 TAAATTTTTAAATATATTT
1 TAAATTTTTAAATATATTT
6551156 TTTATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAAATTTTTAAATATATTTAA
Found at i:6551175 original size:33 final size:34
Alignment explanation
Indices: 6551121--6551187 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
6551111 TAATTTTAAA
**
6551121 TTTTTAAATAATTTAATAAATTTTTAAATATATT
1 TTTTTAAATAATTTAATAAATTAATAAATATATT
6551155 TTTTATAAATAATTT-A-AAATTAATAAATATATT
1 TTTT-TAAATAATTTAATAAATTAATAAATATATT
6551188 ATGTGCCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 15 0.50
34 5 0.17
35 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TTTTTAAATAATTTAATAAATTAATAAATATATT
Found at i:6554878 original size:95 final size:95
Alignment explanation
Indices: 6554695--6554879 Score: 273
Period size: 95 Copynumber: 1.9 Consensus size: 95
6554685 CAAACTAACA
* ** * * *
6554695 ACAACCCATGAAGATGAACATCAAACTAAGTATAAAAATACAAAGAAAACAGCGAAAGAGAGGGA
1 ACAACCCATAAAGATGAACATCAAACTAAACACAAAAATACAAAGAAAACAGAGAAAGAGAAGGA
*
6554760 AGCAGACCTCCAACAATTCAGGGAATAAGC
66 AGCAGACCTCCAAAAATTCAGGGAATAAGC
*
6554790 ACAACCCATAAAGATGAATATCAAACTAAACACAAAAATACAAAGAAAACAGAGAAAGAGAAGGA
1 ACAACCCATAAAGATGAACATCAAACTAAACACAAAAATACAAAGAAAACAGAGAAAGAGAAGGA
*
6554855 AGCAGACCTGCAAAAAGTT-AGGGAA
66 AGCAGACCTCCAAAAA-TTCAGGGAA
6554880 AAAGTTTGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 78 0.98
96 2 0.03
ACGTcount: A:0.54, C:0.17, G:0.18, T:0.11
Consensus pattern (95 bp):
ACAACCCATAAAGATGAACATCAAACTAAACACAAAAATACAAAGAAAACAGAGAAAGAGAAGGA
AGCAGACCTCCAAAAATTCAGGGAATAAGC
Found at i:6554909 original size:28 final size:28
Alignment explanation
Indices: 6554864--6554919 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
6554854 AAGCAGACCT
*
6554864 GCAAAAAGTTAGGGAAAAAGTTTGAAAA
1 GCAAAAAGTTAGGAAAAAAGTTTGAAAA
*
6554892 GCAAAAA-TTCAGGAAAAAGGTTTGAAAA
1 GCAAAAAGTT-AGGAAAAAAGTTTGAAAA
6554920 CAGATCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.54, C:0.05, G:0.23, T:0.18
Consensus pattern (28 bp):
GCAAAAAGTTAGGAAAAAAGTTTGAAAA
Found at i:6555665 original size:31 final size:31
Alignment explanation
Indices: 6555630--6555700 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
6555620 AGCTAAAATG
* *
6555630 AGCAAAAACCATGAATATTAATATCAAACTA
1 AGCAAAAACCATGAAGATGAATATCAAACTA
* *
6555661 AGCAAAACCCATGAAGATGAATATCAAATTA
1 AGCAAAAACCATGAAGATGAATATCAAACTA
6555692 AGCATAAAA
1 AGCA-AAAA
6555701 ATACAAAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (31 bp):
AGCAAAAACCATGAAGATGAATATCAAACTA
Found at i:6557180 original size:113 final size:114
Alignment explanation
Indices: 6556981--6557200 Score: 345
Period size: 113 Copynumber: 1.9 Consensus size: 114
6556971 TCGAGGTTTT
* * *
6556981 CACTGTTTAAGAGAGTAAAACAGACCAAGCCCAGGGAAAAAACTTAGAATGGCAATCTGAAGTGA
1 CACTGTCTAAGAGAGTAAAACAGACCAAACCCAGGCAAAAAACTTAGAATGGCAATCTGAAGTGA
*
6557046 GCAAAACCCATGAAGATGAATATCAAACTAAGCATAAAAATGCAAAATC
66 GCAAAACCCATGAAGACGAATATCAAACTAAGCATAAAAATGCAAAATC
* * * *
6557095 CACTGTCTAAGAGAGTAAAACAGACCAAACCTA-GCACAACACTCTA-AATTGCAATCTGAAGTG
1 CACTGTCTAAGAGAGTAAAACAGACCAAACCCAGGCAAAAAACT-TAGAATGGCAATCTGAAGTG
6557158 AGCAAAACCCATGAAGACGAATATCAAACTAAGCATAAAAATG
65 AGCAAAACCCATGAAGACGAATATCAAACTAAGCATAAAAATG
6557201 TAAAGAAAAC
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
113 65 0.67
114 32 0.33
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.17
Consensus pattern (114 bp):
CACTGTCTAAGAGAGTAAAACAGACCAAACCCAGGCAAAAAACTTAGAATGGCAATCTGAAGTGA
GCAAAACCCATGAAGACGAATATCAAACTAAGCATAAAAATGCAAAATC
Found at i:6560124 original size:14 final size:14
Alignment explanation
Indices: 6560086--6560115 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6560076 ACATACCACC
6560086 AACTACAACATAGT
1 AACTACAACATAGT
6560100 AACTACAACATAGT
1 AACTACAACATAGT
6560114 AA
1 AA
6560116 TTATTACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (14 bp):
AACTACAACATAGT
Found at i:6562931 original size:22 final size:21
Alignment explanation
Indices: 6562906--6563022 Score: 94
Period size: 22 Copynumber: 5.3 Consensus size: 21
6562896 AATTTAGACA
*
6562906 AAATCAATAATAACTTTATACT
1 AAAT-AATAATAACTTTATAGT
*
6562928 AAATTAATGATAA-TTGTATAGT
1 AAA-TAATAATAACTT-TATAGT
** * *
6562950 AAATTGTGGATAACTTAATAGT
1 AAATAAT-AATAACTTTATAGT
*
6562972 AAAATAATAATAACTTAATAGT
1 -AAATAATAATAACTTTATAGT
6562994 AAATAAATAATAA-TTTAGTAGT
1 AAAT-AATAATAACTTTA-TAGT
6563016 AAATAAT
1 AAATAAT
6563023 TGATAAAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 15
0.77 0.09 0.15
Matches are distributed among these distances:
21 14 0.18
22 57 0.72
23 8 0.10
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (21 bp):
AAATAATAATAACTTTATAGT
Found at i:6563028 original size:22 final size:22
Alignment explanation
Indices: 6562828--6563028 Score: 67
Period size: 22 Copynumber: 9.2 Consensus size: 22
6562818 TGGCAAATCA
* * *
6562828 ATAACTTAGTAGTAAAT-GTATA
1 ATAATTTAGTAGTAAATAAT-TG
* * *
6562850 ATAATATAGTAGCAAATTATTG
1 ATAATTTAGTAGTAAATAATTG
* * * *
6562872 ATAATTTTGTTA-TACATGAGTG
1 ATAATTTAG-TAGTAAATAATTG
** *
6562894 ATAATTTAG-ACAAAATCAA-TA
1 ATAATTTAGTAGTAAAT-AATTG
*
6562915 ATAACTTTA-TACTAAATTAA-TG
1 ATAA-TTTAGTAGTAAA-TAATTG
** *
6562937 ATAATTGTA-TAGTAAATTGTGG
1 ATAATT-TAGTAGTAAATAATTG
* * *
6562959 ATAACTTAATAGTAAAATAA-TA
1 ATAATTTAGTAGT-AAATAATTG
* * * *
6562981 ATAACTTAATAGTAAATAAATA
1 ATAATTTAGTAGTAAATAATTG
6563003 ATAATTTAGTAGTAAATAATTG
1 ATAATTTAGTAGTAAATAATTG
6563025 ATAA
1 ATAA
6563029 AATTGTGTAT
Statistics
Matches: 136, Mismatches: 31, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.01
21 19 0.14
22 108 0.79
23 8 0.06
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (22 bp):
ATAATTTAGTAGTAAATAATTG
Found at i:6563087 original size:22 final size:22
Alignment explanation
Indices: 6563040--6563088 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
6563030 ATTGTGTATG
*
6563040 ATAACATAATAATAAATATATT
1 ATAACATAATAATAAATATATA
*
6563062 ATAACATAGTAATAAATA-ATAA
1 ATAACATAATAATAAATATAT-A
6563084 ATAAC
1 ATAAC
6563089 TTAACAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAACATAATAATAAATATATA
Found at i:6563201 original size:44 final size:44
Alignment explanation
Indices: 6563135--6563251 Score: 137
Period size: 44 Copynumber: 2.7 Consensus size: 44
6563125 TAACACATAT
* *
6563135 TAGTAAATTAAAGATAAATTAATAA-AAAATAAATGATAACTTAG
1 TAGTAAATTAATGATAAATTAATAATAAAA-AAATGATAACTTAA
* ** * *
6563179 TAGTTAATTTTTGATAATTTAATAATAAAACAATGATAACTTAA
1 TAGTAAATTAATGATAAATTAATAATAAAAAAATGATAACTTAA
* *
6563223 TAGTAAATTAATGATAACTTAATAGTAAA
1 TAGTAAATTAATGATAAATTAATAATAAA
6563252 TAAGATTTAG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 56 0.93
45 4 0.07
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (44 bp):
TAGTAAATTAATGATAAATTAATAATAAAAAAATGATAACTTAA
Found at i:6563252 original size:22 final size:22
Alignment explanation
Indices: 6563135--6563252 Score: 119
Period size: 22 Copynumber: 5.4 Consensus size: 22
6563125 TAACACATAT
* *
6563135 TAGTAAATTAAAGATAAATTAA
1 TAGTAAATTAATGATAACTTAA
** * *
6563157 TAAAAAATAAATGATAACTTAG
1 TAGTAAATTAATGATAACTTAA
* ** *
6563179 TAGTTAATTTTTGATAATTTAA
1 TAGTAAATTAATGATAACTTAA
* **
6563201 TAATAAAACAATGATAACTTAA
1 TAGTAAATTAATGATAACTTAA
6563223 TAGTAAATTAATGATAACTTAA
1 TAGTAAATTAATGATAACTTAA
6563245 TAGTAAAT
1 TAGTAAAT
6563253 AAGATTTAGT
Statistics
Matches: 72, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (22 bp):
TAGTAAATTAATGATAACTTAA
Found at i:6563692 original size:22 final size:21
Alignment explanation
Indices: 6563628--6563700 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
6563618 TAATAATTAA
* *
6563628 AAATTAAAAGTAAATCA-ATAT
1 AAATTAATAGTTAATCATA-AT
* *
6563649 AACTTAATA-ATAATCATCAAT
1 AAATTAATAGTTAATCAT-AAT
6563670 AAATTAATAGTTAATCAGTAAT
1 AAATTAATAGTTAATCA-TAAT
*
6563692 AATTTAATA
1 AAATTAATA
6563701 TAGTAAATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
20 5 0.12
21 17 0.41
22 18 0.44
23 1 0.02
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (21 bp):
AAATTAATAGTTAATCATAAT
Found at i:6563819 original size:22 final size:22
Alignment explanation
Indices: 6563794--6563852 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
6563784 AACTTAATAA
*
6563794 TAAATCAATTATAACATAGCTG
1 TAAATCAATAATAACATAGCTG
*
6563816 TAAATGCAA-AATAACATAGTTG
1 TAAAT-CAATAATAACATAGCTG
* *
6563838 TAAATTAATGATAAC
1 TAAATCAATAATAAC
6563853 TTAATAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 26 0.84
23 3 0.10
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (22 bp):
TAAATCAATAATAACATAGCTG
Found at i:6564115 original size:22 final size:22
Alignment explanation
Indices: 6564077--6564216 Score: 104
Period size: 22 Copynumber: 6.4 Consensus size: 22
6564067 AATAGTATAA
* *
6564077 TAGTAAATCATTAATAATTTAG
1 TAGTAAATCATTGATAACTTAG
*
6564099 TAGTAAATTATTGATAACTTAG
1 TAGTAAATCATTGATAACTTAG
* * ** *
6564121 T-GATAAATCACTAATAACGCAA
1 TAG-TAAATCATTGATAACTTAG
*
6564143 TAGTAAAACATTGATAACTTAG
1 TAGTAAATCATTGATAACTTAG
* * * *
6564165 TTGTAAATTAGTGATAATTTAG
1 TAGTAAATCATTGATAACTTAG
* *
6564187 TTA-TAAATCAATGATAATTTAG
1 -TAGTAAATCATTGATAACTTAG
*
6564209 TTGTAAAT
1 TAGTAAAT
6564217 TAGTTAATTA
Statistics
Matches: 90, Mismatches: 24, Indels: 8
0.74 0.20 0.07
Matches are distributed among these distances:
21 2 0.02
22 86 0.96
23 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (22 bp):
TAGTAAATCATTGATAACTTAG
Found at i:6564128 original size:44 final size:44
Alignment explanation
Indices: 6564080--6564385 Score: 181
Period size: 44 Copynumber: 6.8 Consensus size: 44
6564070 AGTATAATAG
* *
6564080 TAAATCATTAATAATTTAGTAGTAAATTATTGATAACTTAGTGA
1 TAAATCATTAATAATTTAGTAGTAAATCATTGATAACTTAGTAA
* *** * * **
6564124 TAAATCACTAATAACGCAATAGTAAAACATTGATAACTTAGTTG
1 TAAATCATTAATAATTTAGTAGTAAATCATTGATAACTTAGTAA
* * * * *
6564168 TAAATTAGTGATAATTTAGTTA-TAAATCAATGATAATTTAGTTGTAAA
1 TAAATCATTAATAATTTAG-TAGTAAATCATTGATAACTTA---GT-AA
* ** *
6564216 TTAGTTAATTATTAATAATTTTA-TAGTAAATCATAAATAATATTA-TAA
1 -TA---AATCATTAATAA-TTTAGTAGTAAATCATTGATAA-CTTAGTAA
* * * * **
6564264 TAAATTATTAATAACTTAATAGTAAATTATCAATAACTTAGTAA
1 TAAATCATTAATAATTTAGTAGTAAATCATTGATAACTTAGTAA
* * * * *
6564308 TAAATCGTTTATAACTTAGCAATAAATCATT-ATAACTTAGTAA
1 TAAATCATTAATAATTTAGTAGTAAATCATTGATAACTTAGTAA
* * *
6564351 TAAATCA-TGATAATTTAGTAATAAATCAGTGATAA
1 TAAATCATTAATAATTTAGTAGTAAATCATTGATAA
6564386 TATAATAGTA
Statistics
Matches: 203, Mismatches: 44, Indels: 31
0.73 0.16 0.11
Matches are distributed among these distances:
42 19 0.09
43 28 0.14
44 115 0.57
45 2 0.01
47 4 0.02
48 2 0.01
49 3 0.01
51 2 0.01
52 21 0.10
53 7 0.03
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (44 bp):
TAAATCATTAATAATTTAGTAGTAAATCATTGATAACTTAGTAA
Found at i:6564215 original size:66 final size:66
Alignment explanation
Indices: 6564075--6564203 Score: 177
Period size: 66 Copynumber: 2.0 Consensus size: 66
6564065 ATAATAGTAT
* * * *
6564075 AATAGTAAATCATTAATAATTTAGTAGTAAATTATTGATAACTTAGTGATAAATCACTAATAACG
1 AATAGTAAAACATTAATAACTTAGTAGTAAATTAGTGATAACTTAGTGATAAATCAATAATAACG
6564140 C
66 C
* * * * *
6564141 AATAGTAAAACATTGATAACTTAGTTGTAAATTAGTGATAATTTAGTTATAAATCAATGATAA
1 AATAGTAAAACATTAATAACTTAGTAGTAAATTAGTGATAACTTAGTGATAAATCAATAATAA
6564204 TTTAGTTGTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.36
Consensus pattern (66 bp):
AATAGTAAAACATTAATAACTTAGTAGTAAATTAGTGATAACTTAGTGATAAATCAATAATAACG
C
Found at i:6564275 original size:11 final size:11
Alignment explanation
Indices: 6564222--6564312 Score: 62
Period size: 11 Copynumber: 8.3 Consensus size: 11
6564212 TAAATTAGTT
6564222 AATTATTAAT-
1 AATTATTAATA
6564232 AATT-TTATAGTA
1 AATTATTA-A-TA
* *
6564244 AATCATAAATA
1 AATTATTAATA
6564255 ATATTA-TAATA
1 A-ATTATTAATA
6564266 AATTATTAATA
1 AATTATTAATA
* * *
6564277 ACTTAATAGTA
1 AATTATTAATA
*
6564288 AATTATCAATA
1 AATTATTAATA
* *
6564299 ACTTAGTAATA
1 AATTATTAATA
6564310 AAT
1 AAT
6564313 CGTTTATAAC
Statistics
Matches: 60, Mismatches: 15, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
9 3 0.05
10 9 0.15
11 39 0.65
12 7 0.12
13 2 0.03
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (11 bp):
AATTATTAATA
Found at i:6564300 original size:22 final size:22
Alignment explanation
Indices: 6564217--6564312 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 22
6564207 AGTTGTAAAT
* * *
6564217 TAGTTAATTATTAATAATTTTA
1 TAGTAAATTATTAATAACTTAA
* * *
6564239 TAGTAAATCATAAATAA-TATTA
1 TAGTAAATTATTAATAACT-TAA
*
6564261 TAATAAATTATTAATAACTTAA
1 TAGTAAATTATTAATAACTTAA
* *
6564283 TAGTAAATTATCAATAACTTAG
1 TAGTAAATTATTAATAACTTAA
*
6564305 TAATAAAT
1 TAGTAAAT
6564313 CGTTTATAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
21 1 0.02
22 59 0.97
23 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
TAGTAAATTATTAATAACTTAA
Found at i:6564342 original size:21 final size:21
Alignment explanation
Indices: 6564261--6564378 Score: 128
Period size: 22 Copynumber: 5.5 Consensus size: 21
6564251 AATAATATTA
* *
6564261 TAATAAATTATTAATAACTTAA
1 TAATAAATCATT-ATAACTTAG
* * *
6564283 TAGTAAATTATCAATAACTTAG
1 TAATAAATCAT-TATAACTTAG
*
6564305 TAATAAATCGTTTATAACTTAG
1 TAATAAATC-ATTATAACTTAG
*
6564327 CAATAAATCATTATAACTTAG
1 TAATAAATCATTATAACTTAG
* *
6564348 TAATAAATCATGATAATTTAG
1 TAATAAATCATTATAACTTAG
6564369 TAATAAATCA
1 TAATAAATCA
6564379 GTGATAATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
21 39 0.48
22 42 0.51
23 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.37
Consensus pattern (21 bp):
TAATAAATCATTATAACTTAG
Found at i:6564386 original size:22 final size:21
Alignment explanation
Indices: 6564296--6564385 Score: 117
Period size: 21 Copynumber: 4.2 Consensus size: 21
6564286 TAAATTATCA
* *
6564296 ATAACTTAGTAATAAATCGTTT
1 ATAACTTAGTAATAAATC-ATG
* *
6564318 ATAACTTAGCAATAAATCATT
1 ATAACTTAGTAATAAATCATG
6564339 ATAACTTAGTAATAAATCATG
1 ATAACTTAGTAATAAATCATG
*
6564360 ATAATTTAGTAATAAATCAGTG
1 ATAACTTAGTAATAAATCA-TG
6564382 ATAA
1 ATAA
6564386 TATAATAGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 39 0.63
22 23 0.37
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
ATAACTTAGTAATAAATCATG
Found at i:6564795 original size:22 final size:22
Alignment explanation
Indices: 6564629--6564987 Score: 137
Period size: 22 Copynumber: 16.5 Consensus size: 22
6564619 TTAATAGAAT
* *
6564629 ATCATAAATAACTTAGTAGTAA
1 ATCATTAATAACTTAGTAATAA
* * * * *
6564651 TTCAATGATAATTTAGTAGTAA
1 ATCATTAATAACTTAGTAATAA
* * * *
6564673 ATAATTGATAACTTAATAGCTAA
1 ATCATTAATAACTTAGTA-ATAA
6564696 AT-ATTGAA-AACTTAGTAAT--
1 ATCATT-AATAACTTAGTAATAA
* * * *
6564715 AT-ATTAATGA-TAATTAGTAA
1 ATCATTAATAACTTAGTAATAA
* *
6564735 ATGCA-TAATAA-TATAATAGTAA
1 AT-CATTAATAACT-TAGTAATAA
* *
6564757 ATCACTAATAACGTAGTAATAA
1 ATCATTAATAACTTAGTAATAA
* * ** *
6564779 GTCATTTATAACTTAGTTGTAT
1 ATCATTAATAACTTAGTAATAA
* * *
6564801 ATCAATAATAATTTTGTAATAA
1 ATCATTAATAACTTAGTAATAA
* *
6564823 ATCATTGATAACTTCA-TAGTAA
1 ATCATTAATAACTT-AGTAATAA
* *
6564845 ATTAGCT-ATAACTTTA-TAATAA
1 ATCA-TTAATAAC-TTAGTAATAA
* * *
6564867 ATTATCAATAACTTAGTACTAA
1 ATCATTAATAACTTAGTAATAA
* * *
6564889 ATCATCAATAACTTAATAGTAA
1 ATCATTAATAACTTAGTAATAA
* * *
6564911 ATCATTTATAACTTAATAGTAA
1 ATCATTAATAACTTAGTAATAA
* *
6564933 ATCATTAATAATTTAATAATAA
1 ATCATTAATAACTTAGTAATAA
* * * * * *
6564955 ACCACTGATAACATAATAATGA
1 ATCATTAATAACTTAGTAATAA
*
6564977 ATCAGTAATAA
1 ATCATTAATAA
6564988 GTTAATTGTC
Statistics
Matches: 255, Mismatches: 67, Indels: 30
0.72 0.19 0.09
Matches are distributed among these distances:
18 7 0.03
19 6 0.02
20 2 0.01
21 12 0.05
22 219 0.86
23 9 0.04
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (22 bp):
ATCATTAATAACTTAGTAATAA
Found at i:6564877 original size:66 final size:66
Alignment explanation
Indices: 6564807--6564981 Score: 179
Period size: 66 Copynumber: 2.7 Consensus size: 66
6564797 GTATATCAAT
* * * * *
6564807 AATAATTTTGTAATAAATCATTGATAACTTCATAGTAAATTAGCTATAACTTTATAATAAATTAT
1 AATAATTTAGTAATAAATCATTGATAACTTAATAGTAAATCAGCTATAACTTAATAATAAATCAT
6564872 C
66 C
* * ** ** *
6564873 AATAACTTAGTACTAAATCATCAATAACTTAATAGTAAATCATTTATAACTTAATAGTAAATCAT
1 AATAATTTAGTAATAAATCATTGATAACTTAATAGTAAATCAGCTATAACTTAATAATAAATCAT
*
6564938 T
66 C
* * * * * *
6564939 AATAATTTAATAATAAACCACTGATAACATAATAATGAATCAG
1 AATAATTTAGTAATAAATCATTGATAACTTAATAGTAAATCAG
6564982 TAATAAGTTA
Statistics
Matches: 85, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
66 85 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (66 bp):
AATAATTTAGTAATAAATCATTGATAACTTAATAGTAAATCAGCTATAACTTAATAATAAATCAT
C
Found at i:6564966 original size:44 final size:44
Alignment explanation
Indices: 6564748--6564993 Score: 183
Period size: 44 Copynumber: 5.6 Consensus size: 44
6564738 CATAATAATA
** * * *
6564748 TAATAGTAAATCACTAATAACGTAGTAATAAGTCATTTATAACT
1 TAATAGTAAATCACTAATAATTTAATAATAAATCATTGATAACT
* * * * **
6564792 TAGTTGTATATCAATAATAATTTTGTAATAAATCATTGATAACT
1 TAATAGTAAATCACTAATAATTTAATAATAAATCATTGATAACT
* * * **
6564836 TCATAGTAAATTAGCT-ATAACTTT-ATAATAAATTATCAATAACT
1 TAATAGTAAATCA-CTAATAA-TTTAATAATAAATCATTGATAACT
* * * * *
6564880 TAGTACTAAATCA-TCAATAACTTAATAGTAAATCATTTATAACT
1 TAATAGTAAATCACT-AATAATTTAATAATAAATCATTGATAACT
* * * *
6564924 TAATAGTAAATCATTAATAATTTAATAATAAACCACTGATAACA
1 TAATAGTAAATCACTAATAATTTAATAATAAATCATTGATAACT
* * * *
6564968 TAATAATGAATCAGTAATAAGTTAAT
1 TAATAGTAAATCACTAATAATTTAAT
6564994 TGTCAATTGA
Statistics
Matches: 156, Mismatches: 40, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 148 0.95
45 5 0.03
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (44 bp):
TAATAGTAAATCACTAATAATTTAATAATAAATCATTGATAACT
Found at i:6564993 original size:22 final size:22
Alignment explanation
Indices: 6564732--6564993 Score: 152
Period size: 22 Copynumber: 11.9 Consensus size: 22
6564722 TGATAATTAG
*
6564732 TAAATGCA-TAATAA-TATAATAG
1 TAAAT-CATTAATAACT-TAATAA
* * *
6564754 TAAATCACTAATAACGTAGTAA
1 TAAATCATTAATAACTTAATAA
* * * **
6564776 TAAGTCATTTATAACTTAGTTG
1 TAAATCATTAATAACTTAATAA
* * * **
6564798 TATATCAATAATAATTTTGTAA
1 TAAATCATTAATAACTTAATAA
* * *
6564820 TAAATCATTGATAACTTCATAG
1 TAAATCATTAATAACTTAATAA
* * *
6564842 TAAATTAGCT-ATAACTTTATAA
1 TAAATCA-TTAATAACTTAATAA
* * * *
6564864 TAAATTATCAATAACTTAGTAC
1 TAAATCATTAATAACTTAATAA
* *
6564886 TAAATCATCAATAACTTAATAG
1 TAAATCATTAATAACTTAATAA
* *
6564908 TAAATCATTTATAACTTAATAG
1 TAAATCATTAATAACTTAATAA
*
6564930 TAAATCATTAATAATTTAATAA
1 TAAATCATTAATAACTTAATAA
* * * *
6564952 TAAACCACTGATAACATAATAA
1 TAAATCATTAATAACTTAATAA
* * *
6564974 TGAATCAGTAATAAGTTAAT
1 TAAATCATTAATAACTTAAT
6564994 TGTCAATTGA
Statistics
Matches: 184, Mismatches: 52, Indels: 8
0.75 0.21 0.03
Matches are distributed among these distances:
21 2 0.01
22 181 0.98
23 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (22 bp):
TAAATCATTAATAACTTAATAA
Found at i:6565189 original size:22 final size:22
Alignment explanation
Indices: 6565158--6565234 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
6565148 AAATCAATGA
*
6565158 TAATAATAAATCAATAATAACT
1 TAATAGTAAATCAATAATAACT
* ** *
6565180 TATTAGTAAATCAATTTTAGCT
1 TAATAGTAAATCAATAATAACT
*
6565202 TAGTAGTAAAGTC--TGAATAACT
1 TAATAGTAAA-TCAAT-AATAACT
6565224 TAATAGTAAAT
1 TAATAGTAAAT
6565235 TATTCATATT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 2 0.05
22 39 0.91
23 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATAGTAAATCAATAATAACT
Found at i:6565265 original size:22 final size:22
Alignment explanation
Indices: 6565223--6565265 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6565213 TCTGAATAAC
* * *
6565223 TTAATAGTAAATTATTCATATT
1 TTAATAATAAATTAGTAATATT
6565245 TTAATAATAAATTAGTAATAT
1 TTAATAATAAATTAGTAATAT
6565266 AATTTAGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TTAATAATAAATTAGTAATATT
Found at i:6570529 original size:94 final size:95
Alignment explanation
Indices: 6570408--6570594 Score: 272
Period size: 94 Copynumber: 2.0 Consensus size: 95
6570398 AGCTGAAATG
* * * *
6570408 AGCAAAACCCATGAATATTAACATCAAACTAAGTATAAAAATACAAAGAAAACAGCA-AAACAGA
1 AGCAAAACCCATGAAGATGAACATCAAACTAAGCACAAAAATACAAAGAAAACAG-AGAAACAGA
*
6570472 GGGAAGCAGACCTGC-AAAATTCAGGGAATA
65 AGGAAGCAGACCTGCAAAAATTCAGGGAATA
*
6570502 AGCACAAA-CCATGAAGATGAATATCAAACTAAGCACAAAAATACAAAGAAAACAGAGAAACAGA
1 AGCA-AAACCCATGAAGATGAACATCAAACTAAGCACAAAAATACAAAGAAAACAGAGAAACAGA
*
6570566 AGGAAGCAGACCTGCAAAAATTGAGGGAA
65 AGGAAGCAGACCTGCAAAAATTCAGGGAA
6570595 AAAGTTTAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
93 1 0.01
94 67 0.81
95 15 0.18
ACGTcount: A:0.54, C:0.17, G:0.18, T:0.12
Consensus pattern (95 bp):
AGCAAAACCCATGAAGATGAACATCAAACTAAGCACAAAAATACAAAGAAAACAGAGAAACAGAA
GGAAGCAGACCTGCAAAAATTCAGGGAATA
Found at i:6570624 original size:28 final size:28
Alignment explanation
Indices: 6570579--6570634 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
6570569 AAGCAGACCT
* *
6570579 GCAAAAATTGAGGGAAAAAGTTTAAAAA
1 GCAAAAATTCAGGAAAAAAGTTTAAAAA
*
6570607 GCAAAAATTCAGGAAAAAAGTTTGAAAA
1 GCAAAAATTCAGGAAAAAAGTTTAAAAA
6570635 CAGATCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (28 bp):
GCAAAAATTCAGGAAAAAAGTTTAAAAA
Found at i:6570830 original size:31 final size:31
Alignment explanation
Indices: 6570792--6570852 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
6570782 ATGAGCAAAG
*
6570792 CCATGAATATTAACATCAAACTAAGCATAAC
1 CCATGAATATGAACATCAAACTAAGCATAAC
*
6570823 CCATGAATATGAACATCAAATTAAGCATAA
1 CCATGAATATGAACATCAAACTAAGCATAA
6570853 AAATACAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.23
Consensus pattern (31 bp):
CCATGAATATGAACATCAAACTAAGCATAAC
Found at i:6570919 original size:95 final size:95
Alignment explanation
Indices: 6570811--6571002 Score: 260
Period size: 95 Copynumber: 2.0 Consensus size: 95
6570801 TTAACATCAA
* * * * * *
6570811 ACTAAGCATAACCCATGAATATGAACATCAAATTAAGCATAAAAATAC-AAAGAAAACATAGAAA
1 ACTAAGAACAACCCATGAAGATGAACATCAAACTAAGCATAAAAATACAAAAAAAAACAGAGAAA
6570875 GAGAGGGAAGCAGACCTGCAAAAATTCAGGG
66 GAGAGGG-AGCAGACCTGCAAAAATTCAGGG
*
6570906 ACTAAGAACAACCCATGAAGATGAACGTCAAACTAAGCATAAAAATACAAAAAAAAAAAAACAGA
1 ACTAAGAACAACCCATGAAGATGAACATCAAACTAAGCATAAAAATAC----AAAAAAAAACAGA
*
6570971 GAAAGAGAGGGAGCAGGCCTGCAAAAATTCAG
62 GAAAGAGAGGGAGCAGACCTGCAAAAATTCAG
6571003 AAAAAAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 43 0.51
99 20 0.24
100 21 0.25
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.12
Consensus pattern (95 bp):
ACTAAGAACAACCCATGAAGATGAACATCAAACTAAGCATAAAAATACAAAAAAAAACAGAGAAA
GAGAGGGAGCAGACCTGCAAAAATTCAGGG
Found at i:6571822 original size:104 final size:104
Alignment explanation
Indices: 6571642--6571855 Score: 410
Period size: 104 Copynumber: 2.1 Consensus size: 104
6571632 ACTGACATGC
**
6571642 AAAAATTCAGGTCAGGGCAAAAGTTGAAAAAATTTTTGGCACAACATTCTAAATTGCAATCTGAA
1 AAAAATTCAGGTCAGGGCAAAAGTTGAAAAAAAATTTGGCACAACATTCTAAATTGCAATCTGAA
6571707 GTGAGCAAAACTCATGAAGATGAACATCAAACTAAGCAT
66 GTGAGCAAAACTCATGAAGATGAACATCAAACTAAGCAT
6571746 AAAAATTCAGGTCAGGGCAAAAGTTGAAAAAAAATTTGGCACAACATTCTAAATTGCAATCTGAA
1 AAAAATTCAGGTCAGGGCAAAAGTTGAAAAAAAATTTGGCACAACATTCTAAATTGCAATCTGAA
6571811 GTGAGCAAAACTCATGAAGATGAACATCAAACTAAGCAT
66 GTGAGCAAAACTCATGAAGATGAACATCAAACTAAGCAT
6571850 AAAAAT
1 AAAAAT
6571856 GGAAAGAAAA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 108 1.00
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (104 bp):
AAAAATTCAGGTCAGGGCAAAAGTTGAAAAAAAATTTGGCACAACATTCTAAATTGCAATCTGAA
GTGAGCAAAACTCATGAAGATGAACATCAAACTAAGCAT
Found at i:6571908 original size:44 final size:44
Alignment explanation
Indices: 6571859--6571943 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
6571849 TAAAAATGGA
* *
6571859 AAGAAAACAGAGAAAGAGATGGAAACTGATCTGCAAAAATTAAG
1 AAGAAAACAGAAAAAGAGATGGAAACTGATCTCCAAAAATTAAG
6571903 AAGAAAACAGAAAAAGAGATGGAAACTGATCTCCAAAAATT
1 AAGAAAACAGAAAAAGAGATGGAAACTGATCTCCAAAAATT
6571944 CAGGTCAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.55, C:0.11, G:0.20, T:0.14
Consensus pattern (44 bp):
AAGAAAACAGAAAAAGAGATGGAAACTGATCTCCAAAAATTAAG
Found at i:6577353 original size:19 final size:19
Alignment explanation
Indices: 6577329--6577368 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
6577319 TAATAATTTG
*
6577329 ATTAAATAAATTTTATAAT
1 ATTAAATAAATTTTAAAAT
6577348 ATTAAATAAATTTTAAAAT
1 ATTAAATAAATTTTAAAAT
6577367 AT
1 AT
6577369 ATTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAAATAAATTTTAAAAT
Found at i:6577519 original size:2 final size:2
Alignment explanation
Indices: 6577496--6577535 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
6577486 AGTTAGTAAT
*
6577496 TA TA TA TG T- TA TA -A TA TA -A 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
6577535 T
1 T
6577536 GATTTACAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6579168 original size:4 final size:4
Alignment explanation
Indices: 6579127--6579181 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
6579117 CACTAGGAGA
* * * * *
6579127 ATAT ATAT AAAT ATAT ACAT ACAT AAAT ATAT AAAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
6579175 ATGT ATA
1 ATAT ATA
6579182 ACTAGCTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:6579176 original size:8 final size:8
Alignment explanation
Indices: 6579129--6579175 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
6579119 CTAGGAGAAT
6579129 ATATATAA
1 ATATATAA
*
6579137 ATATATAC
1 ATATATAA
*
6579145 ATACATAA
1 ATATATAA
6579153 ATATATAA
1 ATATATAA
*
6579161 ATATATAT
1 ATATATAA
6579169 ATATATA
1 ATATATA
6579176 TGTATAACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAA
Found at i:6581722 original size:118 final size:118
Alignment explanation
Indices: 6581568--6581795 Score: 314
Period size: 118 Copynumber: 1.9 Consensus size: 118
6581558 TAGTACCAAA
* * *
6581568 AAACACTTGAATATAAAACTTAAGGAGTGAAGAAGCAAAAGTGAAAATCAAGAACAAAGAACAGC
1 AAACACTTGAATATAAAACTTAAGGAGAGAAAAAGCAAAAGAGAAAATCAAGAACAAAGAACAGC
* * *
6581633 ACTTGTTCAATCTCCT-AGGCCGACATTTTTCTTTCACTATCATTCCTACCCAG
66 ACCTGTTCAAGCTCCTCA-GCCAACATTTTTCTTTCACTATCATTCCTACCCAG
* *** * *
6581686 AAACACTTGAATATAAAACTTAAGGGGAGAAAAAGCAAAAGAGAAAATCAAGATTGAAGCATAGC
1 AAACACTTGAATATAAAACTTAAGGAGAGAAAAAGCAAAAGAGAAAATCAAGAACAAAGAACAGC
* *
6581751 ACCTGTTCAAGCTCCTCAGCCAACTTTTTTCTTTCACTTTCATTC
66 ACCTGTTCAAGCTCCTCAGCCAACATTTTTCTTTCACTATCATTC
6581796 AGTGCCTCAC
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
118 94 0.99
119 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (118 bp):
AAACACTTGAATATAAAACTTAAGGAGAGAAAAAGCAAAAGAGAAAATCAAGAACAAAGAACAGC
ACCTGTTCAAGCTCCTCAGCCAACATTTTTCTTTCACTATCATTCCTACCCAG
Found at i:6585399 original size:16 final size:18
Alignment explanation
Indices: 6585374--6585406 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6585364 TTAAATAAAA
6585374 TAATATTCAAAT-TTTAG
1 TAATATTCAAATATTTAG
6585391 TAATA-TCAAATATTTA
1 TAATATTCAAATATTTA
6585407 ATTTTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (18 bp):
TAATATTCAAATATTTAG
Found at i:6586377 original size:12 final size:12
Alignment explanation
Indices: 6586341--6586379 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
6586331 TAAATGTTAT
6586341 AAATAATAT-TA
1 AAATAATATATA
*
6586352 AAATATACATATA
1 AAATA-ATATATA
6586365 AAATAATATATA
1 AAATAATATATA
6586377 AAA
1 AAA
6586380 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 12 0.50
13 7 0.29
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATAATATATA
Found at i:6587578 original size:30 final size:30
Alignment explanation
Indices: 6587533--6587593 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
6587523 TTTTAATTAA
* * * *
6587533 TTAATTATATATATTTATATAATGATATTT
1 TTAAATATATATATTTAAAAAATAATATTT
*
6587563 TTAAATATTTATATTTAAAAAATAATATTT
1 TTAAATATATATATTTAAAAAATAATATTT
6587593 T
1 T
6587594 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TTAAATATATATATTTAAAAAATAATATTT
Found at i:6587596 original size:21 final size:22
Alignment explanation
Indices: 6587566--6587617 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
6587556 GATATTTTTA
6587566 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
6587586 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
6587608 AATATTTTAT
1 AATATTTTAT
6587618 TAATTTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:6599008 original size:31 final size:30
Alignment explanation
Indices: 6598970--6599029 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
6598960 TTAATGAATT
** *
6598970 AAATAATATTATTTTATTAATAAAATAAATC
1 AAATAATAACATTTCATTAA-AAAATAAATC
6599001 AAATAATAACATTTCATTAAAAAATAAAT
1 AAATAATAACATTTCATTAAAAAATAAAT
6599030 GAATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (30 bp):
AAATAATAACATTTCATTAAAAAATAAATC
Found at i:6600332 original size:33 final size:34
Alignment explanation
Indices: 6600290--6600354 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
6600280 CAGCAACGAC
6600290 GGCGGTGCAAC-AGGGCAACTA-CGGCACAATGAT
1 GGCGGTGCAACGAGGGCAA-TACCGGCACAATGAT
*
6600323 GGCGGTGCAACGATGGCAATACCGGCACAATG
1 GGCGGTGCAACGAGGGCAATACCGGCACAATG
6600355 CGGCGGCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 13 0.45
34 16 0.55
ACGTcount: A:0.29, C:0.25, G:0.34, T:0.12
Consensus pattern (34 bp):
GGCGGTGCAACGAGGGCAATACCGGCACAATGAT
Found at i:6600360 original size:33 final size:33
Alignment explanation
Indices: 6600278--6600360 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
6600268 CGACGTGAAA
*
6600278 GGCAGCAACGACGGCGGTGCAACAGGGCAACTAC
1 GGCA-CAATGACGGCGGTGCAACAGGGCAACTAC
* *
6600312 GGCACAATGATGGCGGTGCAACGATGGCAA-TACC
1 GGCACAATGACGGCGGTGCAAC-AGGGCAACTA-C
6600346 GGCACAATG-CGGCGG
1 GGCACAATGACGGCGG
6600361 CAATGCTGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
33 23 0.53
34 20 0.47
ACGTcount: A:0.28, C:0.27, G:0.36, T:0.10
Consensus pattern (33 bp):
GGCACAATGACGGCGGTGCAACAGGGCAACTAC
Found at i:6600701 original size:36 final size:37
Alignment explanation
Indices: 6600643--6600724 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 37
6600633 AATTATGATG
*
6600643 TTTTTATATTAAAAAATAATGTAATATTTGA-TTTAAT
1 TTTTTATATTAAAAAATAATGTAATAATT-ATTTTAAT
** *
6600680 TTTTTATATT-AATTATGATGTAATAATTATTTTAAT
1 TTTTTATATTAAAAAATAATGTAATAATTATTTTAAT
6600716 TTTTTATAT
1 TTTTTATAT
6600725 CAAATACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.73
37 10 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (37 bp):
TTTTTATATTAAAAAATAATGTAATAATTATTTTAAT
Found at i:6602488 original size:17 final size:17
Alignment explanation
Indices: 6602466--6602500 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6602456 CATTATTTGG
6602466 AGTGAATTATCTTTTAA
1 AGTGAATTATCTTTTAA
6602483 AGTGAATTATCTTTTAA
1 AGTGAATTATCTTTTAA
6602500 A
1 A
6602501 CTTCATTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (17 bp):
AGTGAATTATCTTTTAA
Found at i:6602528 original size:72 final size:72
Alignment explanation
Indices: 6602406--6602555 Score: 266
Period size: 72 Copynumber: 2.1 Consensus size: 72
6602396 ACTTACATTA
*
6602406 TTTAGAGTGAATTATCTTTTAAAATCGATTGCTGTTCCCATATGAACTTACATTATTTGGAGTGA
1 TTTAAAGTGAATTATCTTTTAAAATCGATTGCTGTTCCCATATGAACTTACATTATTTGGAGTGA
6602471 ATTATCT
66 ATTATCT
*
6602478 TTTAAAGTGAATTATCTTTTAAACTTC-ATTGCTGTTCCCATATGAACTTACATTATTTGGAGTG
1 TTTAAAGTGAATTATCTTTTAAA-ATCGATTGCTGTTCCCATATGAACTTACATTATTTGGAGTG
6602542 AATTATCT
65 AATTATCT
6602550 TTTAAA
1 TTTAAA
6602556 ATTAATTTCT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 73 0.97
73 2 0.03
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (72 bp):
TTTAAAGTGAATTATCTTTTAAAATCGATTGCTGTTCCCATATGAACTTACATTATTTGGAGTGA
ATTATCT
Found at i:6615293 original size:3 final size:3
Alignment explanation
Indices: 6615285--6615313 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6615275 TGTGAGAGAC
6615285 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6615314 TTGAAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6619036 original size:22 final size:22
Alignment explanation
Indices: 6619010--6619063 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
6619000 TCCGAAATTA
6619010 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
* *
6619032 ATAAATTTTTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
6619054 ATAAATATAT
1 ATAAA-ATAT
6619064 ATAAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:6619089 original size:22 final size:25
Alignment explanation
Indices: 6619049--6619097 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
6619039 TTTATTTTTT
6619049 AAAATATAAATATATATAAATAAAA
1 AAAATATAAATATATATAAATAAAA
*
6619074 AAAAT-TAAATA-A-ATAATTAAAA
1 AAAATATAAATATATATAAATAAAA
6619096 AA
1 AA
6619098 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 1 0.04
24 6 0.26
25 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAATATAAATATATATAAATAAAA
Found at i:6619568 original size:23 final size:23
Alignment explanation
Indices: 6619542--6619596 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
6619532 ATGATTTATA
6619542 TAATTTTTTTAAAAAATAAATTT
1 TAATTTTTTTAAAAAATAAATTT
** ***
6619565 TAATAATTTTAAATTTTAAATTT
1 TAATTTTTTTAAAAAATAAATTT
*
6619588 AAATTTTTT
1 TAATTTTTT
6619597 GTAATTTTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAATTTTTTTAAAAAATAAATTT
Found at i:6619590 original size:13 final size:16
Alignment explanation
Indices: 6619558--6619594 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 16
6619548 TTTTAAAAAA
6619558 TAAATTTTAATAATTT
1 TAAATTTTAATAATTT
6619574 TAAATTTT-A-AA-TT
1 TAAATTTTAATAATTT
6619587 TAAATTTT
1 TAAATTTT
6619595 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 1 0.05
16 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAAATTTTAATAATTT
Found at i:6619611 original size:13 final size:13
Alignment explanation
Indices: 6619591--6619621 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6619581 TAAATTTAAA
6619591 TTTT-TTGTAATT
1 TTTTATTGTAATT
6619603 TTTTATTGTAATT
1 TTTTATTGTAATT
6619616 TTTTAT
1 TTTTAT
6619622 ATAAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTATTGTAATT
Found at i:6620184 original size:14 final size:13
Alignment explanation
Indices: 6620130--6620184 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
6620120 TTATTACATA
*
6620130 TAATATGATATAAT
1 TAATAT-ATTTAAT
6620144 TAATATATTTAA-
1 TAATATATTTAAT
* *
6620156 -AATTTATTTATT
1 TAATATATTTAAT
6620168 TAATATAATTTAAT
1 TAATAT-ATTTAAT
6620182 TAA
1 TAA
6620185 CACAACATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 9 0.27
13 9 0.27
14 15 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TAATATATTTAAT
Found at i:6622291 original size:2 final size:2
Alignment explanation
Indices: 6622286--6622315 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6622276 TGTGTGTAAC
6622286 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6622316 TACCTTAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6624729 original size:12 final size:12
Alignment explanation
Indices: 6624712--6624736 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6624702 AATAAAATTC
6624712 TCTTTTTTTTTT
1 TCTTTTTTTTTT
6624724 TCTTTTTTTTTT
1 TCTTTTTTTTTT
6624736 T
1 T
6624737 TTTCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:6624734 original size:15 final size:16
Alignment explanation
Indices: 6624714--6624746 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
6624704 TAAAATTCTC
6624714 TTTTTTTTTTTCT-TT
1 TTTTTTTTTTTCTATT
6624729 TTTTTTTTTTTCTATT
1 TTTTTTTTTTTCTATT
6624745 TT
1 TT
6624747 GCATATTTCG
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:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTTTTTTTTCTATT
Found at i:6624738 original size:14 final size:14
Alignment explanation
Indices: 6624709--6624737 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6624699 CGCAATAAAA
6624709 TTCTCTTTTTTTTT
1 TTCTCTTTTTTTTT
6624723 TTCT-TTTTTTTTT
1 TTCTCTTTTTTTTT
6624736 TT
1 TT
6624738 TTCTATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTCTCTTTTTTTTT
Found at i:6628811 original size:21 final size:22
Alignment explanation
Indices: 6628763--6628813 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
6628753 AAGTTCATGA
*
6628763 AAAATTTT-ATTATTAAATATT
1 AAAATTTTAATTATAAAATATT
*
6628784 -TAATTTTAATT-TAAAATATT
1 AAAATTTTAATTATAAAATATT
6628804 AAAATTTTAA
1 AAAATTTTAA
6628814 CACAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATTTTAATTATAAAATATT
Found at i:6633155 original size:18 final size:18
Alignment explanation
Indices: 6633131--6633167 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6633121 AGAAAAGCAA
*
6633131 AAAAAAAAAAAACAGAGAG
1 AAAAAAAAGAAA-AGAGAG
6633150 AAAAAAAAGAAAAGAGAG
1 AAAAAAAAGAAAAGAGAG
6633168 TTAGTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAGAGAG
Found at i:6633155 original size:20 final size:20
Alignment explanation
Indices: 6633130--6633167 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6633120 AAGAAAAGCA
6633130 AAAAAAAAAAAAACAGAGAG
1 AAAAAAAAAAAAACAGAGAG
* *
6633150 AAAAAAAAGAAAAGAGAG
1 AAAAAAAAAAAAACAGAG
6633168 TTAGTTGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAACAGAGAG
Found at i:6635775 original size:20 final size:21
Alignment explanation
Indices: 6635738--6635776 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6635728 ATCTTTCATG
* *
6635738 AAAAAAACTATAGCAGACTTT
1 AAAAAAAATATAGAAGACTTT
6635759 AAAAAAAATA-AGAAGACT
1 AAAAAAAATATAGAAGACT
6635777 AACACGGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (21 bp):
AAAAAAAATATAGAAGACTTT
Found at i:6636737 original size:226 final size:227
Alignment explanation
Indices: 6636342--6636798 Score: 756
Period size: 226 Copynumber: 2.0 Consensus size: 227
6636332 TCTTTGCTCC
* *
6636342 AGTTATAAAGATAAGTTCTATTCGAGTGGTACTAGGATTAGCAGCTAGTTTGAATCTTGAGCTTG
1 AGTTATAAAGATAAGTTCTATTCGAGTGATACTAGGATTAGCAGCTAGTTTAAATCTTGAGCTTG
*
6636407 AGCAACTTGATGTTAAAACTGTATTTTTGCATAGTGATTTATAGGAGGACATTTATATGAATCAG
66 AGCAACTTGATGTTAAAACTGTATTTTTGCATAGTGATTTACAGGAGGACATTTATATGAATCAG
* *
6636472 CTTGAGGGTTTTGAAGTGAAAGGAAAAGAGCACTTAGTTTACAAATTGAAGAAAAACTTGTATGG
131 CTTAAGGGTTTTGAAGTGAAAGAAAAAGAGCACTTAGTTTACAAATTGAAGAAAAACTTGTATGG
*
6636537 CTTGAAACAAGCTTTGCAATAGTGGTACAAAA
196 CTTGAAACAAGCTCTGCAATAGTGGTACAAAA
*
6636569 AGTTATAAAGATGAGTTCTATTCGAGTGATACT-GAGATTAGCAGCTAGTTTAAATCTTGAGCTT
1 AGTTATAAAGATAAGTTCTATTCGAGTGATACTAG-GATTAGCAGCTAGTTTAAATCTTGAGCTT
* * * * *
6636633 GAGTAACTTGATGTT-AAACTGTATTTTTGCATGGTGATTTGCATGAGGATATTTATATGAATCA
65 GAGCAACTTGATGTTAAAACTGTATTTTTGCATAGTGATTTACAGGAGGACATTTATATGAATCA
*
6636697 GCTTAAGGGTTTTGAAGTGAAAGAAAAAGAGCACTTAGTTTATAAATTGAAGAAAAACTTGTATG
130 GCTTAAGGGTTTTGAAGTGAAAGAAAAAGAGCACTTAGTTTACAAATTGAAGAAAAACTTGTATG
* *
6636762 GCTTGAAACAAGCTCTGCGATAGTGGTACAAGA
195 GCTTGAAACAAGCTCTGCAATAGTGGTACAAAA
6636795 AGTT
1 AGTT
6636799 TGATTCTTTT
Statistics
Matches: 214, Mismatches: 15, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
226 141 0.66
227 73 0.34
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (227 bp):
AGTTATAAAGATAAGTTCTATTCGAGTGATACTAGGATTAGCAGCTAGTTTAAATCTTGAGCTTG
AGCAACTTGATGTTAAAACTGTATTTTTGCATAGTGATTTACAGGAGGACATTTATATGAATCAG
CTTAAGGGTTTTGAAGTGAAAGAAAAAGAGCACTTAGTTTACAAATTGAAGAAAAACTTGTATGG
CTTGAAACAAGCTCTGCAATAGTGGTACAAAA
Found at i:6638944 original size:21 final size:22
Alignment explanation
Indices: 6638896--6638947 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
6638886 TATTTTTTTT
*
6638896 TATT-TTA-TAAAATTTATATA
1 TATTATTATTAAAATTTATAAA
6638916 TAATTATTATTAAAATTT-TAAA
1 T-ATTATTATTAAAATTTATAAA
6638938 TATTATTATT
1 TATTATTATT
6638948 TTTATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 12 0.43
22 7 0.25
23 8 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATTATTAAAATTTATAAA
Found at i:6638958 original size:24 final size:24
Alignment explanation
Indices: 6638903--6638947 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6638893 TTTTATTTTA
*
6638903 TAAAA-TTTATATATAATTATTAT
1 TAAAATTTTAAATATAATTATTAT
*
6638926 TAAAATTTTAAATATTATTATT
1 TAAAATTTTAAATATAATTATT
6638948 TTTATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAAATTTTAAATATAATTATTAT
Found at i:6641130 original size:18 final size:17
Alignment explanation
Indices: 6641107--6641155 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
6641097 AATAAATTCT
6641107 ATTTATTTAAATATTTGA
1 ATTTATTTAAATATTT-A
*
6641125 ATTTATTAAAATA-TTA
1 ATTTATTTAAATATTTA
6641141 ATTTATTTAAA-ATTT
1 ATTTATTTAAATATTT
6641156 TTATTGTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 13 0.46
17 2 0.07
18 12 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTATTTAAATATTTA
Found at i:6648333 original size:6 final size:6
Alignment explanation
Indices: 6648322--6648467 Score: 120
Period size: 6 Copynumber: 23.8 Consensus size: 6
6648312 CCTCCGCTTC
* * *
6648322 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTCGACT T-CCTC TCTCTC TCCCTT
1 TCCCTT TCCCTT TCCCTT TCCCTT TCCCT----T TCCCTT TCCCTT TCCCTT
* * *
6648373 TCCTTT TCCCTT TCTCTT TCCCTCTT CTCCCTT TCCCTT TCTCTT TCCCTT
1 TCCCTT TCCCTT TCCCTT T-CC-CTT -TCCCTT TCCCTT TCCCTT TCCCTT
* * *
6648424 T---TT TCCCTT TCCCTC TCCCTT TCCTTT TCCCTT GCCCTT TCCCT
1 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCT
6648468 CTCTTTTTCT
Statistics
Matches: 113, Mismatches: 16, Indels: 22
0.75 0.11 0.15
Matches are distributed among these distances:
3 3 0.03
5 1 0.01
6 94 0.83
7 4 0.04
8 5 0.04
9 4 0.04
10 2 0.02
ACGTcount: A:0.01, C:0.48, G:0.01, T:0.50
Consensus pattern (6 bp):
TCCCTT
Found at i:6648373 original size:39 final size:35
Alignment explanation
Indices: 6648328--6648455 Score: 120
Period size: 33 Copynumber: 3.7 Consensus size: 35
6648318 CTTCTCCCTT
6648328 TCCCTTTCCCTTTCCCTTTCCCTCGACTTCCTCTCTCTC
1 TCCCTTTCCCTTTCCCTTTCCCTC--CTTCC-CTCT-TC
* *
6648367 TCCCTTTCCTTTTCCCTTT--CTCTTTCCCTCTTC
1 TCCCTTTCCCTTTCCCTTTCCCTCCTTCCCTCTTC
* ** *
6648400 TCCCTTTCCCTTTCTCTTTCCCTTTTTTCC-CTT-
1 TCCCTTTCCCTTTCCCTTTCCCTCCTTCCCTCTTC
* *
6648433 TCCCTCTCCCTTTCCTTTTCCCT
1 TCCCTTTCCCTTTCCCTTTCCCT
6648456 TGCCCTTTCC
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
33 39 0.50
34 7 0.09
35 11 0.14
37 3 0.04
39 18 0.23
ACGTcount: A:0.01, C:0.48, G:0.01, T:0.51
Consensus pattern (35 bp):
TCCCTTTCCCTTTCCCTTTCCCTCCTTCCCTCTTC
Found at i:6648419 original size:72 final size:72
Alignment explanation
Indices: 6648328--6648469 Score: 196
Period size: 72 Copynumber: 2.0 Consensus size: 72
6648318 CTTCTCCCTT
* * *
6648328 TCCCTTTCCCTTTCCCTTTCCCTCGACTT-CCTCTCTCTCTCCCTTTCCTTTTCCCTTTCTCTTT
1 TCCCTTTCCCTTTCCCTTTCCCT-GACTTCCCTCTCCCTCTCCCTTTCCTTTTCCCTTGCCCTTT
6648392 CCCTCTTC
65 CCCTCTTC
* *** *
6648400 TCCCTTTCCCTTTCTCTTTCCCTTTTTTCCCTTTCCCTCTCCCTTTCCTTTTCCCTTGCCCTTTC
1 TCCCTTTCCCTTTCCCTTTCCCTGACTTCCCTCTCCCTCTCCCTTTCCTTTTCCCTTGCCCTTTC
6648465 CCTCT
66 CCTCT
6648470 CTTTTTCTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 2 0.03
72 59 0.97
ACGTcount: A:0.01, C:0.48, G:0.01, T:0.50
Consensus pattern (72 bp):
TCCCTTTCCCTTTCCCTTTCCCTGACTTCCCTCTCCCTCTCCCTTTCCTTTTCCCTTGCCCTTTC
CCTCTTC
Found at i:6648428 original size:21 final size:21
Alignment explanation
Indices: 6648404--6648445 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6648394 CTCTTCTCCC
* *
6648404 TTTCCCTTTCTCTTTCCCTTT
1 TTTCCCTTTCCCTCTCCCTTT
6648425 TTTCCCTTTCCCTCTCCCTTT
1 TTTCCCTTTCCCTCTCCCTTT
6648446 CCTTTTCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTCCCTTTCCCTCTCCCTTT
Found at i:6653368 original size:16 final size:16
Alignment explanation
Indices: 6653341--6653381 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
6653331 GACAAATTTT
*
6653341 TTTTTATATTTTA-TA
1 TTTTTATTTTTTATTA
6653356 TTTGTTATTTTTTATTA
1 TTT-TTATTTTTTATTA
6653373 TTTTTATTT
1 TTTTTATTT
6653382 GGCCATGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 3 0.13
16 15 0.65
17 5 0.22
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTATTTTTTATTA
Found at i:6655450 original size:21 final size:21
Alignment explanation
Indices: 6655386--6655457 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
6655376 TTGTAGCATA
* *
6655386 TTTATAATATTTGTAAT-ATT
1 TTTATAGTATTTTTAATCATT
6655406 TTTAT--TACTTTTATAA-C-TT
1 TTTATAGTA-TTTT-TAATCATT
*
6655425 GTTATAGTATTTTTAATCATT
1 TTTATAGTATTTTTAATCATT
*
6655446 TTTATAGCATTT
1 TTTATAGTATTT
6655458 GTAGCATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
18 2 0.05
19 12 0.29
20 13 0.32
21 14 0.34
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTATAGTATTTTTAATCATT
Found at i:6655846 original size:10 final size:9
Alignment explanation
Indices: 6655791--6655848 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 9
6655781 TAGTATTGAT
6655791 ATAATTTTG
1 ATAATTTTG
*
6655800 ATAATTTATA
1 ATAATTT-TG
*
6655810 ATAATTTTA
1 ATAATTTTG
6655819 ATAATATTTG
1 ATAAT-TTTG
6655829 ATATAATTTTG
1 --ATAATTTTG
6655840 ATAAATTTT
1 AT-AATTTT
6655849 ATAGTATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
9 16 0.38
10 17 0.40
11 4 0.10
12 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (9 bp):
ATAATTTTG
Found at i:6655859 original size:21 final size:20
Alignment explanation
Indices: 6655789--6655851 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
6655779 AATAGTATTG
6655789 ATATAATTTTGAT-AA-TTT
1 ATATAATTTTGATAAATTTT
* *
6655807 ATAATAATTTTAATAATATTTG
1 AT-ATAATTTTGATAA-ATTTT
6655829 ATATAATTTTGATAAATTTT
1 ATATAATTTTGATAAATTTT
6655849 ATA
1 ATA
6655852 GTATTTTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 2 0.05
19 10 0.27
20 8 0.22
21 13 0.35
22 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
ATATAATTTTGATAAATTTT
Found at i:6655926 original size:21 final size:20
Alignment explanation
Indices: 6655885--6655948 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 20
6655875 CTATTATAGT
*
6655885 ATTTT-TAA-TTTTATAATA
1 ATTTTATAATTTTTATAAAA
*
6655903 ATTTTGATAATTTTTGTAAAA
1 ATTTT-ATAATTTTTATAAAA
*
6655924 ATTTTATTA-TTTTAT-AAA
1 ATTTTATAATTTTTATAAAA
6655942 ATTTTAT
1 ATTTTAT
6655949 GTATGTAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 15 0.38
19 5 0.13
20 6 0.15
21 13 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTTTATAATTTTTATAAAA
Found at i:6655944 original size:18 final size:18
Alignment explanation
Indices: 6655810--6655948 Score: 68
Period size: 21 Copynumber: 7.1 Consensus size: 18
6655800 ATAATTTATA
*
6655810 ATAATTTTAATAATATTTGAT
1 ATAATTTT-ATAAAATTT--T
6655831 ATAATTTTGAT-AAATTTT
1 ATAATTTT-ATAAAATTTT
*
6655849 ATAGTATTTT-TAGCATATTTT
1 ATA--ATTTTATA--AAATTTT
* **
6655870 ATAACCTATTATAGTATTTT
1 ATAA--TTTTATAAAATTTT
6655890 -TAATTTTATAATAATTTT
1 ATAATTTTATAA-AATTTT
*
6655908 GATAATTTTTGTAAAAATTTT
1 -ATAA-TTTTAT-AAAATTTT
*
6655929 ATTATTTTATAAAATTTT
1 ATAATTTTATAAAATTTT
6655947 AT
1 AT
6655949 GTATGTAGAT
Statistics
Matches: 94, Mismatches: 11, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
17 6 0.06
18 20 0.21
19 9 0.10
20 22 0.23
21 33 0.35
22 4 0.04
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.55
Consensus pattern (18 bp):
ATAATTTTATAAAATTTT
Found at i:6658728 original size:21 final size:21
Alignment explanation
Indices: 6658686--6658728 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
6658676 TTATTTTTAA
**
6658686 TTTTTTATTGTATGTTTTTTT
1 TTTTTTATTGTATGTTGATTT
6658707 TTTTTTATTGGT-TGTTGATTT
1 TTTTTTATT-GTATGTTGATTT
6658728 T
1 T
6658729 GGACGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.09, C:0.00, G:0.14, T:0.77
Consensus pattern (21 bp):
TTTTTTATTGTATGTTGATTT
Found at i:6666963 original size:21 final size:20
Alignment explanation
Indices: 6666931--6666974 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6666921 TTATTATTTA
**
6666931 TTTGTTTGTTTTTGTTTATC
1 TTTGTTTGTTTTAATTTATC
*
6666951 TTTGATTTTTTTTAATTTATC
1 TTTG-TTTGTTTTAATTTATC
6666972 TTT
1 TTT
6666975 TAGGATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (20 bp):
TTTGTTTGTTTTAATTTATC
Found at i:6667567 original size:15 final size:16
Alignment explanation
Indices: 6667547--6667576 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6667537 AAGAGAAAGG
6667547 AGAGAAGAGG-GAAGA
1 AGAGAAGAGGAGAAGA
6667562 AGAGAAGAGGAGAAG
1 AGAGAAGAGGAGAAG
6667577 GAAAATCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (16 bp):
AGAGAAGAGGAGAAGA
Found at i:6673284 original size:21 final size:21
Alignment explanation
Indices: 6673242--6673362 Score: 138
Period size: 21 Copynumber: 5.7 Consensus size: 21
6673232 GAGTTTTTAG
*
6673242 ATGAGAATATTTAAGTTTTCAA
1 ATGAGAATATTTGAG-TTTCAA
6673264 ATGAGAATATTTGAGTTTCAA
1 ATGAGAATATTTGAGTTTCAA
*
6673285 ATGAGAATATTTGAGTTTCAG
1 ATGAGAATATTTGAGTTTCAA
* * *
6673306 ATAAAAATCTTT-ATGTTTTC-A
1 ATGAGAATATTTGA-G-TTTCAA
* *
6673327 ATGAGACTATTTGAGTTTTAA
1 ATGAGAATATTTGAGTTTCAA
6673348 ATGAGAATATTTGAG
1 ATGAGAATATTTGAG
6673363 ATGTAACATC
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
20 4 0.05
21 60 0.72
22 19 0.23
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
ATGAGAATATTTGAGTTTCAA
Found at i:6673775 original size:17 final size:17
Alignment explanation
Indices: 6673708--6673784 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 17
6673698 GAATCTGAAG
*
6673708 TGAAATTTTTGCGAATA
1 TGAAATTTTTGCAAATA
* **
6673725 T-AAATTCTTGCAAAGC
1 TGAAATTTTTGCAAATA
* * *
6673741 TGAAAAATCTTGCTAATA
1 TG-AAATTTTTGCAAATA
6673759 TGAAATTTTTGCAAATA
1 TGAAATTTTTGCAAATA
6673776 TGAAATTTT
1 TGAAATTTT
6673785 AAGAATCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
16 12 0.26
17 22 0.47
18 13 0.28
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (17 bp):
TGAAATTTTTGCAAATA
Found at i:6673827 original size:19 final size:19
Alignment explanation
Indices: 6673803--6673875 Score: 64
Period size: 18 Copynumber: 4.0 Consensus size: 19
6673793 AATTTTTGTG
6673803 AATTCTTGTGAAATTGAAA
1 AATTCTTGTGAAATTGAAA
* **
6673822 AATTCTTCTGAACCT-AAA
1 AATTCTTGTGAAATTGAAA
*
6673840 AATTTTTGTG-AATATG--A
1 AATTCTTGTGAAAT-TGAAA
*
6673857 AATTCTTGTGAAAATGAAA
1 AATTCTTGTGAAATTGAAA
6673876 TTTTGGTAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
17 13 0.32
18 14 0.35
19 13 0.32
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (19 bp):
AATTCTTGTGAAATTGAAA
Found at i:6673859 original size:17 final size:17
Alignment explanation
Indices: 6673839--6673879 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
6673829 CTGAACCTAA
*
6673839 AAATTTTTGTGAATATG
1 AAATTTTTGTGAAAATG
*
6673856 AAATTCTTGTGAAAATG
1 AAATTTTTGTGAAAATG
6673873 AAATTTT
1 AAATTTT
6673880 GGTAATCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (17 bp):
AAATTTTTGTGAAAATG
Found at i:6674187 original size:44 final size:43
Alignment explanation
Indices: 6674098--6674252 Score: 161
Period size: 44 Copynumber: 3.5 Consensus size: 43
6674088 GTGTGTACGT
* * *
6674098 CTTTATTTATTTTTCTAAAA-TTATTAAGCCTTTGTTTAAATGAG
1 CTTTATTTATTTTT-TAAAAGTTGTTGAGCCTTTGATTAAA-GAG
*
6674142 CTTTATTTATTTTTTAAAAGTTGTTGAGCTTTTGATTATAAGAG
1 CTTTATTTATTTTTTAAAAGTTGTTGAGCCTTTGATTA-AAGAG
* * * * *
6674186 CTTTATTTA-GTTTCAAAAGTCGTTGAGCCTCTGATTAGAGAAG
1 CTTTATTTATTTTTTAAAAGTTGTTGAGCCTTTGATTAAAG-AG
6674229 CTTTATTTAGTTTTTTCAAAAGTT
1 CTTTATTTA-TTTTTT-AAAAGTT
6674253 ATGAGTTTCT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
42 2 0.02
43 39 0.42
44 40 0.43
45 5 0.05
46 6 0.07
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (43 bp):
CTTTATTTATTTTTTAAAAGTTGTTGAGCCTTTGATTAAAGAG
Found at i:6674212 original size:43 final size:42
Alignment explanation
Indices: 6674124--6674241 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 42
6674114 AAAATTATTA
* * * * *
6674124 AGCCTTTGTTTAAATGAGCTTTATTTATTTTTTAAAAGTTGTTG
1 AGCCTCTGATTAAA-GAGCTTTATTTA-GTTTCAAAAGTCGTTG
* *
6674168 AGCTTTTGATTATAAGAGCTTTATTTAGTTTCAAAAGTCGTTG
1 AGCCTCTGATTA-AAGAGCTTTATTTAGTTTCAAAAGTCGTTG
*
6674211 AGCCTCTGATTAGAGAAGCTTTATTTAGTTT
1 AGCCTCTGATTAAAG-AGCTTTATTTAGTTT
6674242 TTTCAAAAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
42 2 0.03
43 38 0.59
44 22 0.34
45 2 0.03
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (42 bp):
AGCCTCTGATTAAAGAGCTTTATTTAGTTTCAAAAGTCGTTG
Found at i:6691613 original size:15 final size:15
Alignment explanation
Indices: 6691593--6691626 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6691583 ATCACATTAA
6691593 ACTTATAACGATAAC
1 ACTTATAACGATAAC
* *
6691608 ACTTATGAGGATAAC
1 ACTTATAACGATAAC
6691623 ACTT
1 ACTT
6691627 CTCTTCATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (15 bp):
ACTTATAACGATAAC
Found at i:6694457 original size:2 final size:2
Alignment explanation
Indices: 6694452--6694479 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6694442 GCACACACAG
6694452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6694480 GGACTAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6698042 original size:4 final size:4
Alignment explanation
Indices: 6698033--6698057 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6698023 TTGAATGTTT
6698033 GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
6698058 CCATGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:6698877 original size:12 final size:12
Alignment explanation
Indices: 6698860--6698887 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6698850 AAAAGTTGAT
6698860 AATCCTTTAATG
1 AATCCTTTAATG
6698872 AATCCTTTAATG
1 AATCCTTTAATG
6698884 AATC
1 AATC
6698888 AAGCTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (12 bp):
AATCCTTTAATG
Found at i:6701668 original size:16 final size:15
Alignment explanation
Indices: 6701649--6701683 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6701639 ATTACTAAAA
6701649 TTTTAAATTATATTAT
1 TTTTAAA-TATATTAT
*
6701665 TTTTATATATATTAT
1 TTTTAAATATATTAT
6701680 TTTT
1 TTTT
6701684 TTATTGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTAAATATATTAT
Found at i:6706188 original size:2 final size:2
Alignment explanation
Indices: 6706181--6706210 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6706171 AAATAAAAGG
*
6706181 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6706211 GTATGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6713239 original size:26 final size:26
Alignment explanation
Indices: 6713203--6713252 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
6713193 AAATATTAAA
6713203 ATTTATATTATATTTTATAAAAAAAT
1 ATTTATATTATATTTTATAAAAAAAT
6713229 ATTTATATTATATTTTATAAAAAA
1 ATTTATATTATATTTTATAAAAAA
6713253 TACATGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTATATTATATTTTATAAAAAAAT
Found at i:6719603 original size:19 final size:19
Alignment explanation
Indices: 6719581--6719620 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
6719571 TTGAATAATC
6719581 AATT-AATAAATTATAATAT
1 AATTAAATAAATT-TAATAT
6719600 AATTAAATAAATTTAATAT
1 AATTAAATAAATTTAATAT
6719619 AA
1 AA
6719621 AATTTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTAAATAAATTTAATAT
Found at i:6719963 original size:2 final size:2
Alignment explanation
Indices: 6719956--6719983 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6719946 AATAGCATCA
6719956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6719984 GAATGAGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6720391 original size:80 final size:80
Alignment explanation
Indices: 6720303--6720463 Score: 295
Period size: 80 Copynumber: 2.0 Consensus size: 80
6720293 CGCACGCACA
*
6720303 TATATATATATATATATAGTTTGTATCGCATTTTTATTTTTGTAACTGTCTGTTAGGCAGTTAAA
1 TATATATATATATATATAGTTTGTATCGCATTTGTATTTTTGTAACTGTCTGTTAGGCAGTTAAA
6720368 TAACTCAACTGTTTC
66 TAACTCAACTGTTTC
* *
6720383 TATATATATATATATATAGTTTGTATCGCATTTGTATTTTTGTAGCTGTCTGTTATGCAGTTAAA
1 TATATATATATATATATAGTTTGTATCGCATTTGTATTTTTGTAACTGTCTGTTAGGCAGTTAAA
6720448 TAACTCAACTGTTTC
66 TAACTCAACTGTTTC
6720463 T
1 T
6720464 GGGGTCCTCT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (80 bp):
TATATATATATATATATAGTTTGTATCGCATTTGTATTTTTGTAACTGTCTGTTAGGCAGTTAAA
TAACTCAACTGTTTC
Found at i:6723333 original size:2 final size:2
Alignment explanation
Indices: 6723326--6723351 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6723316 ACAATATTCA
6723326 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6723352 GGATTTGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6728685 original size:58 final size:57
Alignment explanation
Indices: 6728558--6728721 Score: 229
Period size: 58 Copynumber: 2.8 Consensus size: 57
6728548 TGTTTTTGTA
* * *
6728558 CAAAAAAAATTGATACTTTCAACTTTTTCTAAAAAAAAATCATTTTTTAGAAAATTATTTT
1 CAAAGAAAATTGATACTTTCAACTTTTCCT---CAAAAAT-ATTTTTTAGAAAATTATTTT
*
6728619 CAAAGAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAGAAAACTTATTTT
1 CAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAA-TTATTTT
*
6728677 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTT
1 CAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTT
6728722 TTGGAATTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
57 13 0.14
58 49 0.52
59 5 0.05
61 28 0.29
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (57 bp):
CAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAATTATTTT
Found at i:6728743 original size:58 final size:57
Alignment explanation
Indices: 6728563--6728744 Score: 197
Period size: 58 Copynumber: 3.1 Consensus size: 57
6728553 TTGTACAAAA
* * *
6728563 AAAATTGATACTTTCAACTTTTTCTAAAAAAAAATCATTTTTTAGAAAATTATT-TTCAAAG
1 AAAATTGATACTTTCAACTTTTCCT--CAAAAAAT-ATTTTTTAG-AAATT-TTATTTAAAG
* ** *
6728624 AAAATTGATACTTTCAACTTTTCCTC-GAAAATATTTTTTAGAAAACTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTAGAAATTTTA-TTT-AAAG
* *
6728682 AAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGGAATTTTATTTAAAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-ATATTTTTTAGAAATTTTATTTAAAG
6728740 AAAAT
1 AAAAT
6728745 CAAAAAATAA
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
55 2 0.02
56 3 0.03
57 11 0.11
58 42 0.41
59 6 0.06
60 15 0.15
61 24 0.23
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTAGAAATTTTATTTAAAG
Found at i:6728756 original size:6 final size:6
Alignment explanation
Indices: 6728747--6728801 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
6728737 AAGAAAATCA
*
6728747 AAAAAT -AAAAT -AAAAT AAAAAT AAAGAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
6728793 -AAAAT AAAA
1 AAAAAT AAAA
6728802 TACTAAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 15 0.33
6 30 0.67
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:6728758 original size:5 final size:5
Alignment explanation
Indices: 6728748--6728803 Score: 67
Period size: 5 Copynumber: 10.2 Consensus size: 5
6728738 AGAAAATCAA
6728748 AAAAT AAAAT AAAAT AAAAAT AAAGAT AAAAAT AAAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT AAA-AT -AAAAT -AAAAT -AAAAT AAAAT
6728798 AAAAT A
1 AAAAT A
6728804 CTAAATAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
5 24 0.50
6 21 0.44
7 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:6728767 original size:18 final size:18
Alignment explanation
Indices: 6728740--6728801 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
6728730 TTATTTAAAG
*
6728740 AAAATCAAAAAATAAAAT
1 AAAATAAAAAAATAAAAT
6728758 AAAAT--AAAAATAAAGAT
1 AAAATAAAAAAATAAA-AT
*
6728775 AAAA-ATAAAAATAAAAAT
1 AAAATAAAAAAAT-AAAAT
6728793 AAAATAAAA
1 AAAATAAAA
6728802 TACTAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 9 0.24
17 6 0.16
18 17 0.45
19 6 0.16
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAAAAAATAAAAT
Found at i:6728776 original size:12 final size:11
Alignment explanation
Indices: 6728748--6728801 Score: 83
Period size: 11 Copynumber: 4.8 Consensus size: 11
6728738 AGAAAATCAA
6728748 AAAAT-AAAAT
1 AAAATAAAAAT
6728758 AAAATAAAAAT
1 AAAATAAAAAT
6728769 AAAGATAAAAAT
1 AAA-ATAAAAAT
6728781 AAAAATAAAAAT
1 -AAAATAAAAAT
6728793 AAAATAAAA
1 AAAATAAAA
6728802 TACTAAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.12
11 17 0.41
12 16 0.39
13 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:6728833 original size:3 final size:3
Alignment explanation
Indices: 6728825--6728859 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
6728815 TAATCCAATC
6728825 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6728860 AAAATAAGAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6728840 original size:12 final size:12
Alignment explanation
Indices: 6728750--6728859 Score: 77
Period size: 12 Copynumber: 9.2 Consensus size: 12
6728740 AAAATCAAAA
6728750 AATAA-AATAA-
1 AATAATAATAAT
*
6728760 AATAAAAATAA-
1 AATAATAATAAT
* *
6728771 AGATAAAAATAAA
1 A-ATAATAATAAT
*
6728784 AATAAAAATAA-
1 AATAATAATAAT
*
6728795 AATAA-AATACT
1 AATAATAATAAT
**
6728806 AAATAATTCTAAT
1 -AATAATAATAAT
6728819 CCAATCAATAATAAT
1 --AAT-AATAATAAT
6728834 AATAATAATAAT
1 AATAATAATAAT
6728846 AATAATAATAAT
1 AATAATAATAAT
6728858 AA
1 AA
6728860 AAAATAAGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.11
11 11 0.13
12 48 0.56
13 7 0.08
14 3 0.04
15 7 0.08
ACGTcount: A:0.69, C:0.05, G:0.01, T:0.25
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:6728852 original size:18 final size:18
Alignment explanation
Indices: 6728750--6728859 Score: 77
Period size: 18 Copynumber: 6.1 Consensus size: 18
6728740 AAAATCAAAA
*
6728750 AATAA-AATAA-AATAAA
1 AATAATAATAATAATAAT
* *
6728766 AATAA-AGATAAAAATAAA
1 AATAATA-ATAATAATAAT
*
6728784 AATAAAAATAA-AATAA-
1 AATAATAATAATAATAAT
* **
6728800 AATACTAAATAATTCTAAT
1 AATAAT-AATAATAATAAT
6728819 CCAATCAATAATAATAATAAT
1 --AAT-AATAATAATAATAAT
6728840 AATAATAATAATAATAAT
1 AATAATAATAATAATAAT
6728858 AA
1 AA
6728860 AAAATAAGAA
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
16 10 0.13
17 14 0.18
18 35 0.45
19 4 0.05
21 13 0.17
22 2 0.03
ACGTcount: A:0.69, C:0.05, G:0.01, T:0.25
Consensus pattern (18 bp):
AATAATAATAATAATAAT
Found at i:6729675 original size:25 final size:25
Alignment explanation
Indices: 6729639--6729824 Score: 121
Period size: 25 Copynumber: 7.6 Consensus size: 25
6729629 AAAAAAAAAG
6729639 AGATAAATATAACAAAAAATATTAAT
1 AGATAAATATAA-AAAAAATATTAAT
6729665 AGATAAA-ATAAAAATAAA-A-TAAT
1 AGATAAATATAAAAA-AAATATTAAT
* * *
6729688 AGATAAATATAAAATATACATTAAT
1 AGATAAATATAAAAAAAATATTAAT
*
6729713 AGATAAATA-ATAAAAATATATTAAT
1 AGATAAATATA-AAAAAAATATTAAT
*
6729738 A-AT-AATA-AAAATGTATATATATTAAT
1 AGATAAATATAAAA---A-AAATATTAAT
*
6729764 AGAT-AA-AT--AAAAAAGATTAAT
1 AGATAAATATAAAAAAAATATTAAT
6729785 AGATAAATAATATTAAAAAAATA-T-AT
1 AGATAAAT-ATA--AAAAAAATATTAAT
*
6729811 ATATAAATA-AAAAA
1 AGATAAATATAAAAA
6729825 TAAAACTAAA
Statistics
Matches: 134, Mismatches: 8, Indels: 40
0.74 0.04 0.22
Matches are distributed among these distances:
21 12 0.09
22 10 0.07
23 18 0.13
24 17 0.13
25 37 0.28
26 28 0.21
27 5 0.04
28 7 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (25 bp):
AGATAAATATAAAAAAAATATTAAT
Found at i:6729699 original size:18 final size:18
Alignment explanation
Indices: 6729667--6729746 Score: 71
Period size: 17 Copynumber: 4.6 Consensus size: 18
6729657 ATATTAATAG
*
6729667 ATAA-AATAAAAATA-AA
1 ATAATAATAAATATATAA
6729683 ATAATAGATAAATATA-AA
1 ATAATA-ATAAATATATAA
* *
6729701 AT-ATACATTAATAGATAA
1 ATAATA-ATAAATATATAA
*
6729719 ATAATAA-AAATATATTA
1 ATAATAATAAATATATAA
6729736 ATAATAATAAA
1 ATAATAATAAA
6729747 AATGTATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
16 4 0.08
17 25 0.48
18 20 0.38
19 3 0.06
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAATAATAAATATATAA
Found at i:6729763 original size:26 final size:26
Alignment explanation
Indices: 6729728--6729829 Score: 89
Period size: 26 Copynumber: 3.8 Consensus size: 26
6729718 AATAATAAAA
* *
6729728 ATATATTAATAATAATAAAAATGTAT
1 ATATATAAATAATAATAAAAAAGTAT
*
6729754 ATATATTAATAGATAAATAAAAAAG-ATT
1 ATATATAAATA-AT-AATAAAAAAGTA-T
* * *
6729782 AATAGATAAATAATATTAAAAAAATAT
1 -ATATATAAATAATAATAAAAAAGTAT
*
6729809 ATATATAAATAAAAAATAAAA
1 ATATATAAAT-AATAATAAAA
6729830 CTAAAAATGC
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
26 20 0.32
27 20 0.32
28 13 0.21
29 9 0.15
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (26 bp):
ATATATAAATAATAATAAAAAAGTAT
Found at i:6729767 original size:51 final size:50
Alignment explanation
Indices: 6729639--6729777 Score: 144
Period size: 51 Copynumber: 2.8 Consensus size: 50
6729629 AAAAAAAAAG
* * *
6729639 AGATAAATATAACAAAAAATATTAATAGAT-AA-AATAAAAATAAAATAAT
1 AGATAAAAATAA-AATATATATTAATAGATAAATAATAAAAATAAAATAAT
* *
6729688 AGATAAATATAAAATATACATTAATAGATAAATAATAAAAATATATTAATAAT
1 AGATAAAAATAAAATATATATTAATAGATAAATAATAAAAATA-A--AATAAT
**
6729741 A-ATAAAAAT-GTATATATATTAATAGATAAATAA-AAAA
1 AGATAAAAATAAAATATATATTAATAGATAAATAATAAAA
6729778 GATTAATAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
48 14 0.18
49 14 0.18
50 14 0.18
51 22 0.28
52 7 0.09
53 7 0.09
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (50 bp):
AGATAAAAATAAAATATATATTAATAGATAAATAATAAAAATAAAATAAT
Found at i:6729799 original size:17 final size:17
Alignment explanation
Indices: 6729707--6729800 Score: 55
Period size: 17 Copynumber: 5.3 Consensus size: 17
6729697 TAAAATATAC
6729707 ATTAATAGATAAATAAT
1 ATTAATAGATAAATAAT
** * *
6729724 AAAAATATATTAATAAT
1 ATTAATAGATAAATAAT
* * **
6729741 AATAA-AAATGTATATAT
1 ATTAATAGATAAATA-AT
*
6729758 ATTAATAGATAAATAAAAAAG
1 ATTAATAGATAAAT----AAT
6729779 ATTAATAGATAAATAAT
1 ATTAATAGATAAATAAT
6729796 ATTAA
1 ATTAA
6729801 AAAAATATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
16 6 0.11
17 30 0.53
18 5 0.09
21 15 0.26
22 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
ATTAATAGATAAATAAT
Found at i:6729802 original size:55 final size:50
Alignment explanation
Indices: 6729657--6729829 Score: 151
Period size: 55 Copynumber: 3.4 Consensus size: 50
6729647 ATAACAAAAA
*
6729657 ATATTAATAGAT-AA-AATAAAA-ATA-AAATAATAGATAAATATAAA-ATAT
1 ATATTAATAGATAAATAAAAAAATATATAAATAATA-ATAAA-A-AAATATAT
* * **
6729705 ACATTAATAGATAAATAATAAAAATATATTAATAATAATAAAAATGTATAT
1 ATATTAATAGATAAATAA-AAAAATATATAAATAATAATAAAAAAATATAT
*
6729756 ATATTAATAGATAAATAAAAAAGATTAATAGATAAATAATATTAAAAAAATATAT
1 ATATTAATAGATAAATAAAAAA-A-T-AT--ATAAATAATAATAAAAAAATATAT
* *
6729811 ATATAAATA-AAAAATAAAA
1 ATATTAATAGATAAATAAAA
6729830 CTAAAAATGC
Statistics
Matches: 102, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
48 11 0.11
49 2 0.02
50 7 0.07
51 27 0.26
52 9 0.09
53 9 0.09
54 9 0.09
55 28 0.27
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (50 bp):
ATATTAATAGATAAATAAAAAAATATATAAATAATAATAAAAAAATATAT
Done.