Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_pilon, 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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 37
Found at i:1128838 original size:71 final size:72
Alignment explanation
Indices: 1128714--1128879 Score: 271
Period size: 71 Copynumber: 2.3 Consensus size: 72
1128704 CGAAACCAAA
* **
1128714 ATCGCATTGCGATTTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGA
1 ATCGCGTTGCGA-TTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGA
*
1128779 TTTTCATT
65 TTCTCATT
1128787 -TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGAT
1 ATCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGAT
1128851 TCTCATT
66 TCTCATT
*
1128858 ATCTCGTTGCGATTTTCATTTC
1 ATCGCGTTGCGATTTTCATTTC
1128880 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 57 0.66
72 30 0.34
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (72 bp):
ATCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGAT
TCTCATT
Found at i:1131320 original size:24 final size:24
Alignment explanation
Indices: 1131286--1131339 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1131276 CTGAAACATC
* *
1131286 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1131310 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1131334 ATCAAA
1 ATCAAA
1131340 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1132405 original size:20 final size:20
Alignment explanation
Indices: 1132377--1132434 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1132367 ATTCATTTGA
1132377 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1132397 CTATTGCAACGCAAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1132417 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1132435 CGCAATGCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1132482 original size:19 final size:19
Alignment explanation
Indices: 1132460--1132508 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1132450 GATTTTCTCG
1132460 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1132479 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1132498 TTGCGATTTTC
1 TTGCGATTTTC
1132509 TCGTTACGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1132644 original size:14 final size:14
Alignment explanation
Indices: 1132625--1132661 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1132615 CATCAATTAA
1132625 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1132639 ACAAATCATCTTTT
1 ACAAATCAACATTT
1132653 ACAAATCAA
1 ACAAATCAA
1132662 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1134564 original size:20 final size:19
Alignment explanation
Indices: 1134529--1134584 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
1134519 GAAACTTAAA
1134529 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1134548 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
1134568 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
1134585 AAATCGTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1134590 original size:19 final size:19
Alignment explanation
Indices: 1134512--1134595 Score: 69
Period size: 20 Copynumber: 4.3 Consensus size: 19
1134502 GTTTACTTTT
* *
1134512 GCAACACGAAACTTAAAATC
1 GCAACGCGAAA-TGAAAATC
**
1134532 GCAACGCGAAATGACTATC
1 GCAACGCGAAATGAAAATC
***
1134551 GCAACGCGGAAATGGCTATC
1 GCAACGC-GAAATGAAAATC
*
1134571 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
1134590 GTAACG
1 GCAACG
1134596 ACAAAATCAC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
19 25 0.48
20 27 0.52
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.15
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:1134626 original size:18 final size:19
Alignment explanation
Indices: 1134599--1134634 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1134589 CGTAACGACA
1134599 AAATCACAACG-CAAAATG
1 AAATCACAACGACAAAATG
*
1134617 AAATCGCAACGACAAAAT
1 AAATCACAACGACAAAAT
1134635 CGTAACGCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.22, G:0.11, T:0.11
Consensus pattern (19 bp):
AAATCACAACGACAAAATG
Found at i:1134675 original size:19 final size:17
Alignment explanation
Indices: 1134653--1134748 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
1134643 GAAACACAAA
1134653 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
1134672 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
1134688 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
1134704 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
1134720 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
1134737 TCGCATTGCGAT
1 TCGC-TTGCGAT
1134749 AGCTATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:1134694 original size:14 final size:14
Alignment explanation
Indices: 1134675--1134732 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1134665 TTTCATTTCG
1134675 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1134689 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1134705 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1134721 CGTTGCGATTTT
1 CGTTGCGATTTT
1134733 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1134739 original size:33 final size:33
Alignment explanation
Indices: 1134658--1134748 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1134648 ACAAATCGCA
1134658 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1134691 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
1134723 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
1134749 AGCTATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1134776 original size:20 final size:19
Alignment explanation
Indices: 1134721--1134787 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
1134711 GCGATTTTGT
**
1134721 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1134740 CATTGCGATAG-CTATTTCCG
1 CGTTGCGATAGTC-ATTT-CG
1134760 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
1134780 TGTTGCGA
1 CGTTGCGA
1134788 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.03
19 12 0.31
20 22 0.56
21 4 0.10
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1135297 original size:18 final size:18
Alignment explanation
Indices: 1135274--1135313 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1135264 TCAGATAATG
*
1135274 GCTCTGGGTGAGGTGATA
1 GCTCTGGGCGAGGTGATA
*
1135292 GCTCTGGGCGAGGTGATG
1 GCTCTGGGCGAGGTGATA
1135310 GCTC
1 GCTC
1135314 CCGAAGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.17, G:0.45, T:0.25
Consensus pattern (18 bp):
GCTCTGGGCGAGGTGATA
Found at i:1136680 original size:20 final size:20
Alignment explanation
Indices: 1136632--1136690 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1136622 AATAGTTTCT
** *
1136632 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1136652 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1136672 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1136691 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1136980 original size:22 final size:22
Alignment explanation
Indices: 1136953--1136996 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1136943 GATGGAGATA
1136953 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1136975 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1136997 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1137214 original size:20 final size:20
Alignment explanation
Indices: 1137185--1137256 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1137175 ATTATGTATT
*
1137185 ATCGCATTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
1137205 ATCGCGTTGCGAAAGTCA-A
1 ATCGCGTTGCGAAAGTCAGA
* *
1137224 TATCGCGTTGCGAAAGTAAGT
1 -ATCGCGTTGCGAAAGTCAGA
*
1137245 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1137257 TTTTGTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.98
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1137291 original size:21 final size:20
Alignment explanation
Indices: 1137267--1137318 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1137257 TTTTGTATTA
*
1137267 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
1137288 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
1137308 TCGCATTGCGA
1 TCGCATTGCGA
1137319 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:1138148 original size:24 final size:24
Alignment explanation
Indices: 1138116--1138166 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1138106 TCAACTTTCT
*
1138116 ATCAAATGAGTGAGAGTGAATTCC
1 ATCAAATGAGTGAAAGTGAATTCC
1138140 ATCAAATGAGTGAAAGTGAATTCC
1 ATCAAATGAGTGAAAGTGAATTCC
1138164 ATC
1 ATC
1138167 CAAGAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (24 bp):
ATCAAATGAGTGAAAGTGAATTCC
Found at i:1138391 original size:37 final size:37
Alignment explanation
Indices: 1138347--1138429 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
1138337 TATTTTGGTT
*
1138347 GAGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTC
1 GAGTCGGGTCGATTTTTTAAAGTGTGATATTCGGGTC
*
1138384 GAGTCGGGTCGGTTTTTTAAAGTGTGATATTCGGGTC
1 GAGTCGGGTCGATTTTTTAAAGTGTGATATTCGGGTC
*
1138421 GGGTCGGGT
1 GAGTCGGGT
1138430 TTAGGGTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.37
Consensus pattern (37 bp):
GAGTCGGGTCGATTTTTTAAAGTGTGATATTCGGGTC
Found at i:1139059 original size:17 final size:17
Alignment explanation
Indices: 1139037--1139099 Score: 99
Period size: 17 Copynumber: 3.6 Consensus size: 17
1139027 TATAGAATTG
1139037 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
1139054 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
1139071 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
*
1139089 GATTTCAATTC
1 GATTCCAATTC
1139100 TCTCAGAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
17 29 0.67
18 14 0.33
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:1141996 original size:26 final size:26
Alignment explanation
Indices: 1141942--1141996 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
1141932 TTTATTTGGT
* *
1141942 TTGAAAATGAGTCCTTTTTTTTATTAA
1 TTGAAAATGAGTCCTTTTGTTCA-TAA
1141969 TTGAAAATGAGTCCTTTTAGTTCA-AA
1 TTGAAAATGAGTCCTTTT-GTTCATAA
1141995 TT
1 TT
1141997 ATCGAGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 18 0.72
28 3 0.12
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (26 bp):
TTGAAAATGAGTCCTTTTGTTCATAA
Found at i:1143484 original size:18 final size:18
Alignment explanation
Indices: 1143461--1143503 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1143451 ACGATAAAAA
1143461 TAATTTTATATCA-ATTTT
1 TAATTTT-TATCACATTTT
*
1143479 TAATTTTTTTCACATTTT
1 TAATTTTTATCACATTTT
1143497 T-ATTTTT
1 TAATTTTT
1143504 CATAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATTTTTATCACATTTT
Found at i:1149749 original size:21 final size:21
Alignment explanation
Indices: 1149698--1149750 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1149688 ATTATGACTA
1149698 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
1149719 TTGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1149740 TCGCAATGCGA
1 TCGCAATGCGA
1149751 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1149765 original size:20 final size:20
Alignment explanation
Indices: 1149740--1149792 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1149730 TTTTCCCAAT
1149740 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
1149760 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
1149780 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1149793 TTGGAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1149824 original size:41 final size:41
Alignment explanation
Indices: 1149797--1149934 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
1149787 GCGAATTTGG
*
1149797 AAAATCGCAACGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
1149838 AAAATCGCAATGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
1149878 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
1149919 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1149935 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
40 31 0.41
41 44 0.59
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1149867 original size:20 final size:20
Alignment explanation
Indices: 1149850--1149908 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
1149840 AATCGCAATG
1149850 CGATACTGACTTTCGCAACT
1 CGATACTGACTTTCGCAACT
* *
1149870 CGATACTTAATTTCGCAACT
1 CGATACTGACTTTCGCAACT
*
1149890 CAATACTGACTTTCGCAAC
1 CGATACTGACTTTCGCAAC
1149909 GAGATAATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (20 bp):
CGATACTGACTTTCGCAACT
Found at i:1150129 original size:22 final size:22
Alignment explanation
Indices: 1150101--1150144 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1150091 CACTCTCTCA
*
1150101 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
1150123 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
1150145 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:1150445 original size:20 final size:20
Alignment explanation
Indices: 1150406--1150464 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1150396 TTTATTCTCT
* **
1150406 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1150426 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* * *
1150446 TGTTGCAATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1150465 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1151805 original size:18 final size:18
Alignment explanation
Indices: 1151784--1151831 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1151774 TCCACTTCGG
1151784 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1151802 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1151820 GAGCCATCACCT
1 GAGCCATCACCT
1151832 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1152387 original size:20 final size:20
Alignment explanation
Indices: 1152370--1152434 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
1152360 TTTCGCAACA
1152370 CGAAAATGACTATCGCAAAG
1 CGAAAATGACTATCGCAAAG
1152390 CGAAAATGACTATCGCAAAG
1 CGAAAATGACTATCGCAAAG
* *
1152410 CGAAAATGGCTATCGCAATG
1 CGAAAATGACTATCGCAAAG
1152430 CGAAA
1 CGAAA
1152435 TGAAAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (20 bp):
CGAAAATGACTATCGCAAAG
Found at i:1152443 original size:19 final size:19
Alignment explanation
Indices: 1152421--1152503 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
1152411 GAAAATGGCT
1152421 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1152440 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1152454 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1152473 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1152492 ATCGCAATGCGA
1 ATCGCAATGCGA
1152504 TTTGTGTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.71
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1152568 original size:20 final size:20
Alignment explanation
Indices: 1152543--1152635 Score: 132
Period size: 20 Copynumber: 4.7 Consensus size: 20
1152533 GCGATTTTCA
*
1152543 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
1152563 TTTCGCGTTACGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
* *
1152583 TTCCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
* *
1152603 TTCCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
1152623 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
1152636 AAGTAAGTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:1152646 original size:20 final size:19
Alignment explanation
Indices: 1152581--1152661 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 19
1152571 TACGATAGCC
* *
1152581 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
*
1152601 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
1152622 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
1152641 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
1152661 A
1 A
1152662 ACTATTCTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.02
20 50 0.93
21 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:1152653 original size:40 final size:39
Alignment explanation
Indices: 1152563--1152655 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
1152553 CGATAGCCAT
* * *
1152563 TTTCGCGTTACGATAGCCATTTCCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTAA
* *
1152602 TTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAA
1 TTT-CGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTAA
*
1152642 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
1152656 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.07
40 40 0.87
41 3 0.07
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (39 bp):
TTTCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTAA
Found at i:1152653 original size:60 final size:59
Alignment explanation
Indices: 1152529--1152655 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 59
1152519 GCGATTTTGT
** * *
1152529 CGTTGCGATTTTCATTTCGCATTGCGATAGCCATTTTCGCGTTACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCGCATTGCGATAGCCATTTTCGCGTTACGAAAGCAATTTCCG
* * * *
1152588 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAGTTT-CG
1 CGTTGCGATAGTCATTT-CGCATTGCGATAGCCATTTTCGCGTTACGAAAGCAA-TTTCCG
*
1152648 TGTTGCGA
1 CGTTGCGA
1152656 AAGTAAACTA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 15 0.26
60 39 0.68
61 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (59 bp):
CGTTGCGATAGTCATTTCGCATTGCGATAGCCATTTTCGCGTTACGAAAGCAATTTCCG
Found at i:1153091 original size:41 final size:42
Alignment explanation
Indices: 1153001--1153091 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
1152991 CCCGACTCAC
* * *
1153001 CTGTCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCT
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
1153043 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
1153084 CTGTCATC
1 CTGTCATC
1153092 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.23
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:1154687 original size:19 final size:17
Alignment explanation
Indices: 1154662--1154711 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
1154652 TATCGCATCG
1154662 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
1154680 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
1154695 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
1154712 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:1154706 original size:14 final size:14
Alignment explanation
Indices: 1154653--1154706 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1154643 GAAACTGACT
*
1154653 ATCGCATCGAGAAA
1 ATCGCAACGAGAAA
1154667 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1154686 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1154700 ATCGCAA
1 ATCGCAA
1154707 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1154755 original size:20 final size:20
Alignment explanation
Indices: 1154738--1154825 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
1154728 CGATTTTCTA
1154738 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
1154758 GTTGCGATTTTTC-TTTTCGA
1 GTTGCGA-TAGCCATTTTCGC
* *
1154778 ATTGCGATAACCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1154798 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1154818 GTTGCGAT
1 GTTGCGAT
1154826 TTCCCCGTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 2 0.04
20 51 0.93
21 2 0.04
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:1154763 original size:34 final size:36
Alignment explanation
Indices: 1154718--1154805 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
1154708 GCGATTTTCA
* * *
1154718 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAACCAT
1154752 TTTCGCGTTGCGATTTTTCTTTTCGAATTGCGATAACCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAACCAT
1154792 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1154806 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
34 12 0.27
35 5 0.11
38 1 0.02
39 1 0.02
40 26 0.58
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.43
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAACCAT
Found at i:1155064 original size:20 final size:20
Alignment explanation
Indices: 1155039--1155088 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1155029 TTGTAGATGA
1155039 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1155059 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
1155079 TTGCGATTTT
1 TTGCGATTTT
1155089 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1156011 original size:12 final size:12
Alignment explanation
Indices: 1155994--1156018 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1155984 ATATAATCCT
1155994 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1156006 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1156018 G
1 G
1156019 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1158331 original size:19 final size:19
Alignment explanation
Indices: 1158289--1158425 Score: 123
Period size: 19 Copynumber: 7.7 Consensus size: 19
1158279 CTTAATGTCT
* **
1158289 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
*
1158309 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1158328 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
1158342 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1158361 ATCGCAACGCG-AAT----
1 ATCGCAACGCGAAATGAAA
* *
1158375 TTCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1158394 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1158413 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1158426 TTGCGATTTT
Statistics
Matches: 96, Mismatches: 11, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.20
15 4 0.04
16 2 0.02
17 2 0.02
18 4 0.04
19 56 0.58
20 9 0.09
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1158373 original size:52 final size:52
Alignment explanation
Indices: 1158289--1158426 Score: 138
Period size: 52 Copynumber: 2.6 Consensus size: 52
1158279 CTTAATGTCT
* ** * *
1158289 ATCGCAACGCGGAAATTACTATCGCAATGCGAA-AT-GAAAAT-CGCAACGAGAGA
1 ATCGCAACGC-GAAATGAAAATCGCAACGCGAATATCG-AAATGCGAAACGA-A-A
* * * *
1158342 ATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAATATCGAAATGCGAAACGAAA
1158394 ATCGCAACGCGAAATGAAAATCGCAACGCGAAT
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAT
1158427 TGCGATTTTC
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
52 51 0.71
53 14 0.19
54 7 0.10
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (52 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAATATCGAAATGCGAAACGAAA
Found at i:1158403 original size:33 final size:32
Alignment explanation
Indices: 1158309--1158408 Score: 164
Period size: 33 Copynumber: 3.1 Consensus size: 32
1158299 GGAAATTACT
*
1158309 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1158342 ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAA
*
1158374 TTTCGCAATGCGAAATGAAAATCGCAACGCGAA
1 -ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1158407 AT
1 AT
1158409 GAAAATCGCA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 2 0.03
33 61 0.97
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAA
Found at i:1158449 original size:19 final size:19
Alignment explanation
Indices: 1158425--1158484 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1158415 CGCAACGCGA
1158425 ATTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
*
1158444 ATTGCGA--TTC-TCTCG-
1 ATTGCGATTTTCATTTCGC
*
1158459 -TTGTGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
1158477 ATTGCGAT
1 ATTGCGAT
1158485 AGTACTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.22
17 7 0.22
19 13 0.41
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
ATTGCGATTTTCATTTCGC
Found at i:1158610 original size:14 final size:14
Alignment explanation
Indices: 1158591--1158627 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1158581 CATCAATTAA
1158591 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1158605 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1158619 ACAAATCAA
1 ACAAATCAA
1158628 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1162638 original size:33 final size:33
Alignment explanation
Indices: 1162582--1162710 Score: 195
Period size: 33 Copynumber: 3.9 Consensus size: 33
1162572 CGAGATAATA
*
1162582 AGAATCGCAACGCGGAAATGACTATCACAACGAG
1 AGAATCGCAACGC-GAAATGACTATCGCAACGAG
*
1162616 AGAATCACAACGCGAAATGACTATCGCAACGAG
1 AGAATCGCAACGCGAAATGACTATCGCAACGAG
**
1162649 AGAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AGAATCGCAACGCGAAATGACTATCGCAACGAG
**
1162682 AGAATCGCAACGCGAAATGAAAATCGCAA
1 AGAATCGCAACGCGAAATGACTATCGCAA
1162711 TGCGATTTTG
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 78 0.87
34 12 0.13
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AGAATCGCAACGCGAAATGACTATCGCAACGAG
Found at i:1162657 original size:14 final size:14
Alignment explanation
Indices: 1162638--1162693 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1162628 CGAAATGACT
1162638 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1162652 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1162671 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1162685 ATCGCAACG
1 ATCGCAACG
1162694 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1162733 original size:19 final size:19
Alignment explanation
Indices: 1162711--1162755 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1162701 AAAATCGCAA
** *
1162711 TGCGATTTTGGTTTCGTGT
1 TGCGATTTTCATTTCGCGT
1162730 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1162749 TGCGATT
1 TGCGATT
1162756 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1163335 original size:20 final size:20
Alignment explanation
Indices: 1163310--1163421 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
1163300 GCTATGTAAA
1163310 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
1163330 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
1163350 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* ** *
1163371 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
1163391 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
1163411 TCGCATTGCGA
1 TCGCATTGCGA
1163422 ATTATGAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:1163434 original size:41 final size:41
Alignment explanation
Indices: 1163302--1163559 Score: 145
Period size: 41 Copynumber: 6.3 Consensus size: 41
1163292 CGAATGGCGC
* * * *
1163302 TATGTAAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGAT-TTACGTATTCGCATTGCGAAT
* * * * * *
1163343 TACG-TATTCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT
* *
1163384 TACT--TAATCGCGTTGCGATTTACGTATTCGCATTGCGAAT
1 TA-TGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
** * * * *
1163424 TATGAAAATCGCAACGCGA-ATACGTAAATCACAATGCGAAT
1 TATGAAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT
* * * *
1163465 TAGGAAAATTGCATTGCGATAGT-CAGCA-TCGCATTGCG-AT
1 TATGAAAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAAT
* * * *
1163505 TTTCCAAATTCGCATTGCGATTTACTTATTCGCATTGCGAAT
1 TAT-GAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
**
1163547 TGGGAAAATCGCA
1 TATGAAAATCGCA
1163560 ACGCGAAATT
Statistics
Matches: 163, Mismatches: 41, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
39 2 0.01
40 39 0.24
41 115 0.71
42 5 0.03
43 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
TATGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
Found at i:1163442 original size:21 final size:21
Alignment explanation
Indices: 1163418--1163473 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
1163408 TATTCGCATT
* *
1163418 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCACAAC
* *
1163439 GCGAA-TACGTAAATCACAAT
1 GCGAATTACGAAAATCACAAC
*
1163459 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
1163474 TGCATTGCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCACAAC
Found at i:1163482 original size:21 final size:21
Alignment explanation
Indices: 1163411--1163483 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
1163401 ATTTACGTAT
* *
1163411 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
1163432 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
* *
1163452 TCACAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
1163473 TTGCATTGCGA
1 TCGCAATGCGA
1163484 TAGTCAGCAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:1163537 original size:20 final size:21
Alignment explanation
Indices: 1163493--1163544 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1163483 ATAGTCAGCA
*
1163493 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1163514 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1163534 TCGCATTGCGA
1 TCGCATTGCGA
1163545 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1163586 original size:21 final size:22
Alignment explanation
Indices: 1163534--1163586 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1163524 ATTTACTTAT
*
1163534 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGAAAAA
**
1163555 TCGCAACGCGAAATT-GAAAAA
1 TCGCATTGCGAAATTGGAAAAA
1163576 TCGCATTGCGA
1 TCGCATTGCGA
1163587 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:1163658 original size:19 final size:19
Alignment explanation
Indices: 1163634--1163670 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1163624 CGATAATGGA
*
1163634 GATCGCGTTGCGAATTTGC
1 GATCGCATTGCGAATTTGC
*
1163653 GATCGCATTGCGATTTTG
1 GATCGCATTGCGAATTTG
1163671 TTGGTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.30, T:0.35
Consensus pattern (19 bp):
GATCGCATTGCGAATTTGC
Found at i:1169019 original size:33 final size:32
Alignment explanation
Indices: 1168947--1169019 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
1168937 ATAAATATCA
* *
1168947 TATTTTTATAAATTATATTTAATTAATTATTT
1 TATTTTTAGAAATAATATTTAATTAATTATTT
* *
1168979 TATTTTTAGAAA-AATATTTTATTAATATTTATT
1 TATTTTTAGAAATAATATTTAATTAAT-TAT-TT
1169012 TATTTTTA
1 TATTTTTA
1169020 ATATTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.34
32 13 0.37
33 10 0.29
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (32 bp):
TATTTTTAGAAATAATATTTAATTAATTATTT
Found at i:1169107 original size:2 final size:2
Alignment explanation
Indices: 1169100--1169139 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1169090 ATAAAAATAA
1169100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1169140 TTCTTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1173730 original size:16 final size:16
Alignment explanation
Indices: 1173709--1173745 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1173699 CTCGTCCATC
1173709 AAAAAAAAAATAAAGG
1 AAAAAAAAAATAAAGG
**
1173725 AAAAAAGTAATAAAGG
1 AAAAAAAAAATAAAGG
1173741 AAAAA
1 AAAAA
1173746 TTAATCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAAAAAAAATAAAGG
Found at i:1176599 original size:113 final size:113
Alignment explanation
Indices: 1176401--1176978 Score: 659
Period size: 113 Copynumber: 4.9 Consensus size: 113
1176391 CATGGCTATT
1176401 GAATTCATCACTTA-ATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAA
1 GAATTCATCAC-TAGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
1176465 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* *
1176514 GAATTCATCACTCGATGGATCAACATTCCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCACTAGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
1176579 AAGGAAGAAGAAGTTTATAATGAGAATAACTTGTTCAA-ATTTGTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT-TGCTC
*
1176627 G-ATTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGATAAAGTTCATAATGAGAAGA
1 GAATTC-ATCAC---------TAGAT--GGATCAACATTTCCAGATAAAGTTCATAATGAGAAGA
* *
1176691 ACTCATCAGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
54 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * * * *
1176751 GAATTCATCACTCGATGCATCAACTTTTCCAGAGAAAGTTCTTAATGAGAAGAACAT-ATCTAAA
1 GAATTCATCACTAGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAAC-TCATCTGAA
*
1176815 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
** *
1176863 G-ATTCTATCACAGAATGAGATAGATCAGCATCAACATTTCCAGA-AGTGTTCATAACGAGAAGA
1 GAATTC-ATCAC----T-AGAT-G----G-ATCAACATTTCCAGATAAAGTTCATAATGAGAAGA
*
1176926 ACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTT
54 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
1176979 GCCTTAATTC
Statistics
Matches: 401, Mismatches: 33, Indels: 53
0.82 0.07 0.11
Matches are distributed among these distances:
111 4 0.01
112 59 0.15
113 147 0.37
114 1 0.00
115 4 0.01
116 1 0.00
117 3 0.01
118 1 0.00
121 1 0.00
122 64 0.16
123 17 0.04
124 92 0.23
125 7 0.02
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (113 bp):
GAATTCATCACTAGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:1176675 original size:124 final size:123
Alignment explanation
Indices: 1176532--1176978 Score: 593
Period size: 124 Copynumber: 3.7 Consensus size: 123
1176522 CACTCGATGG
* *
1176532 ATCAACATTCCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTAT
1 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
1176597 AATGAGAATAACTTGTTCAA-ATTTGTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTT-TGCTCGATTCTATCACAGAA-GAGATAGATCAGC
* *
1176656 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAAAAGAAGTTCAT
1 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
1176721 AATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTC-ATCAC--------TCGAT--GC
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCG-ATTCTATCACAGAAGAGATAGATCAGC
* * * *
1176769 ATCAACTTTTCCAGAGAAAGTTCTTAATGAGAAGAACAT-ATCTAAAG-AGGAAGAAGAAGTTCA
1 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAAC-TCATCTGAAGAAGGAAGAAGAAGTTCA
*
1176832 TAATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAATGAGATAGATCAGC
65 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCACAGAA-GAGATAGATCAGC
** *
1176892 ATCAACATTTCCAGA-AGTGTTCATAACGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAT
1 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
1176955 AATGAGAATAACTTGTTCAACCTT
66 AATGAGAAGAACTTGTTCAACCTT
1176979 GCCTTAATTC
Statistics
Matches: 284, Mismatches: 22, Indels: 36
0.83 0.06 0.11
Matches are distributed among these distances:
111 4 0.01
112 51 0.18
113 42 0.15
114 1 0.00
115 4 0.01
121 5 0.02
122 60 0.21
123 19 0.07
124 91 0.32
125 7 0.02
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGAGATAGATCAGC
Found at i:1176852 original size:112 final size:113
Alignment explanation
Indices: 1176654--1176978 Score: 374
Period size: 122 Copynumber: 2.8 Consensus size: 113
1176644 AGATAGATCA
*
1176654 GCATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAAAAGAAGTTC
1 GCATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAAAAGAAGTTC
1176719 ATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGAT
66 ATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGAT
* * *
1176767 GCATCAACTTTTCCAGAGAAAGTTCTTAATGAGAAGAACAT-ATCTA-AAG-AGGAAGAAGAAGT
1 GCATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC-TCATC-AGAAGAAGGAAAAAGAAGT
* *
1176829 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG-ATTCTATCACAGAATGAGATAGAT
64 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTC-ATCAC---------TCGAT
** * * *
1176888 CAGCATCAACATTTCCAGA-AGTGTTCATAACGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGT
1 --GCATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAAAAGAAGT
*
1176951 TCATAATGAGAATAACTTGTTCAACCTT
64 TCATAATGAGAAGAACTTGTTCAACCTT
1176979 GCCTTAATTC
Statistics
Matches: 182, Mismatches: 13, Indels: 25
0.83 0.06 0.11
Matches are distributed among these distances:
111 4 0.02
112 51 0.28
113 42 0.23
114 2 0.01
121 5 0.03
122 59 0.32
123 19 0.10
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (113 bp):
GCATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAAAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGAT
Found at i:1179240 original size:23 final size:23
Alignment explanation
Indices: 1179204--1179247 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1179194 GTTTTTCTGA
* *
1179204 TATTTCTAAGTAAATAAATATCT
1 TATTTATAAATAAATAAATATCT
*
1179227 TATTTATAAATAAATATATAT
1 TATTTATAAATAAATAAATAT
1179248 ATATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATCT
Found at i:1179240 original size:140 final size:142
Alignment explanation
Indices: 1178996--1179251 Score: 346
Period size: 140 Copynumber: 1.8 Consensus size: 142
1178986 TATATTATTT
*
1178996 AAATATTAATATTATTTATTTTTAATATAAGAAATGGGTTGTCTTAAAGCATCTAGAAGCTCTTT
1 AAATATTAATATTATTTATTTTTAATATAAGAAATGGGTTGTCTTAAAGCACCTAGAAGCTCTTT
* * *
1179061 TTTTATATTCTTAAATAAATAAATATTCTATTTTTATAAAT-TATAAATATTAATTTATTTTAAT
66 TCTGATATTCTTAAATAAATAAATATTCTATTTTAATAAATATATAAATATTAATTTATTTTAAT
1179125 TATTTTTAGAAA
131 TATTTTTAGAAA
* *
1179137 AAATTTTAATATT-TTTATTTTTAATATTAAG-AATGGGTTGTCTTAAAGCACCTATAAG-T-TT
1 AAATATTAATATTATTTATTTTTAATA-TAAGAAATGGGTTGTCTTAAAGCACCTAGAAGCTCTT
* *
1179198 TTCTGATATT-TCTAAGTAAATAAATA-TCTTATTTATAAATAAATATATATATAT
65 TTCTGATATTCT-TAAATAAATAAATATTC-TATTT-T-AATAAATATATAAATAT
1179252 ATATATTAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
137 3 0.03
138 28 0.28
139 2 0.02
140 44 0.44
141 24 0.24
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (142 bp):
AAATATTAATATTATTTATTTTTAATATAAGAAATGGGTTGTCTTAAAGCACCTAGAAGCTCTTT
TCTGATATTCTTAAATAAATAAATATTCTATTTTAATAAATATATAAATATTAATTTATTTTAAT
TATTTTTAGAAA
Found at i:1200636 original size:56 final size:56
Alignment explanation
Indices: 1200576--1200688 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
1200566 ACATAATTTT
1200576 AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
1 AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
1200632 AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
1 AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
1200688 A
1 A
1200689 GGGTAAAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (56 bp):
AAGATTCATAATTAATAAAAATATAATATAATTTTAATTCTAGTGTAAAAAGTAAA
Found at i:1202404 original size:2 final size:2
Alignment explanation
Indices: 1202389--1202443 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
1202379 ATGACACGTA
1202389 AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1202429 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1202444 AAAGAAAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1203878 original size:3 final size:3
Alignment explanation
Indices: 1203862--1203902 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1203852 ATACCAAAAA
*
1203862 TAT TAT TAA T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1203903 AACAATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1204679 original size:21 final size:21
Alignment explanation
Indices: 1204637--1204679 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1204627 TTTCTGGGCT
* *
1204637 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1204658 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1204679 A
1 A
1204680 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1205372 original size:23 final size:23
Alignment explanation
Indices: 1205339--1205401 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1205329 ATTATTATAT
*
1205339 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
**
1205362 GGCACTTCGGTGCAATTCTACTT
1 GGCACTTCGGTGCAATTCTACGC
*
1205385 GGCACTTCGGTGTAATT
1 GGCACTTCGGTGCAATT
1205402 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1222016 original size:31 final size:31
Alignment explanation
Indices: 1221993--1222071 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1221983 CATAGATTCT
* *
1221993 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
1222024 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
1222055 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
1222072 CCTCGACCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:1222696 original size:36 final size:36
Alignment explanation
Indices: 1222637--1222706 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
1222627 TCATTTAGGG
1222637 GGAATCGATACTCCCCCCAGGGGGAATATGTTCCTGA
1 GGAATCGATAC-CCCCCCAGGGGGAATATGTTCCTGA
*
1222674 GGAATCGATA-CCCCCCAGGGGGGAATCTGTTCC
1 GGAATCGATACCCCCCCA-GGGGGAATATGTTCC
1222707 CCCTGCACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 7 0.23
36 14 0.45
37 10 0.32
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.20
Consensus pattern (36 bp):
GGAATCGATACCCCCCCAGGGGGAATATGTTCCTGA
Found at i:1224036 original size:2 final size:2
Alignment explanation
Indices: 1224029--1224066 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1224019 CAAACTATCC
1224029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1224067 TCTTTCAGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1225340 original size:14 final size:14
Alignment explanation
Indices: 1225317--1225348 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1225307 TAAACAGTAA
*
1225317 AATATGGTATGAAC
1 AATATCGTATGAAC
1225331 AATATCGTATGAAC
1 AATATCGTATGAAC
1225345 AATA
1 AATA
1225349 CCCAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (14 bp):
AATATCGTATGAAC
Found at i:1225999 original size:31 final size:31
Alignment explanation
Indices: 1225961--1226085 Score: 162
Period size: 31 Copynumber: 4.0 Consensus size: 31
1225951 CCCGAAGGAC
* * *
1225961 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1225992 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
** * *
1226023 CAGTCCATATGTCAAGAATAACATAGATAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1226054 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1226085 C
1 C
1226086 CCTCGACCCT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
31 79 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1233276 original size:15 final size:16
Alignment explanation
Indices: 1233248--1233278 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1233238 AAAGTCATTT
1233248 TAATAAAGAAAATATA
1 TAATAAAGAAAATATA
1233264 TAATAAA-AAAATATA
1 TAATAAAGAAAATATA
1233279 AGACTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAATAAAGAAAATATA
Found at i:1238388 original size:34 final size:34
Alignment explanation
Indices: 1238349--1238415 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1238339 ATGCACGTCT
* *
1238349 CCAACACTCCCATGCATAGGTCGCCATGCCTTCC
1 CCAACACTCCCATACATAGGTCGACATGCCTTCC
1238383 CCAACACTCCCATACATAGGTCGACATGCCTTC
1 CCAACACTCCCATACATAGGTCGACATGCCTTC
1238416 GCCATGCACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.21
Consensus pattern (34 bp):
CCAACACTCCCATACATAGGTCGACATGCCTTCC
Found at i:1238434 original size:27 final size:28
Alignment explanation
Indices: 1238404--1238457 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
1238394 ATACATAGGT
1238404 CGACATGCCT-TCGCCATGCACGCCCAG
1 CGACATGCCTGTCGCCATGCACGCCCAG
*
1238431 CGACATGCTTGGTCGCCATGCACGCCC
1 CGACATGCCT-GTCGCCATGCACGCCC
1238458 GGCAACCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
29 15 0.62
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.17
Consensus pattern (28 bp):
CGACATGCCTGTCGCCATGCACGCCCAG
Found at i:1238912 original size:21 final size:21
Alignment explanation
Indices: 1238887--1238930 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1238877 AATTTAGTTA
1238887 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1238908 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1238929 AT
1 AT
1238931 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1238940 original size:28 final size:28
Alignment explanation
Indices: 1238907--1238960 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1238897 TAGTATAAAT
1238907 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
1238935 TATTAGTTTGTTAGTTTAAGTTATAT
1 TATTAGTTTGTTAGTTTAAGTTATAT
1238961 ATTAGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTTAAGTTATATTA
Found at i:1239032 original size:44 final size:49
Alignment explanation
Indices: 1238936--1239043 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 49
1238926 GTTATATTAT
1238936 ATTAGTTTGTTAGTTTAAGTTATATATTAGATTATATAAAAAATTAGTTA
1 ATTAGTTTGTTAGTTTAAGTTATATA-TAGATTATATAAAAAATTAGTTA
* *
1238986 ATTAGTTTCTTAGTTTAAGTTAT-TA-A-ATGTA-A-AAAAAA-TATTTA
1 ATTAGTTTGTTAGTTTAAGTTATATATAGAT-TATATAAAAAATTAGTTA
*
1239030 ATTAATTTGTTAGT
1 ATTAGTTTGTTAGT
1239044 GTGTTAAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
44 17 0.32
45 6 0.11
46 3 0.06
47 3 0.06
49 2 0.04
50 22 0.42
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (49 bp):
ATTAGTTTGTTAGTTTAAGTTATATATAGATTATATAAAAAATTAGTTA
Found at i:1241214 original size:30 final size:30
Alignment explanation
Indices: 1241180--1241285 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
1241170 TTCTCTTAAA
1241180 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
1241210 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * * *
1241240 AAACTAATAAACAATTTTTTAATTATAATTT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
* *
1241271 ACTACTAAAAAACTA
1 -CAACTAATAAACTA
1241286 ATTAACTAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
30 49 0.74
31 7 0.11
32 10 0.15
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:1241232 original size:15 final size:16
Alignment explanation
Indices: 1241184--1241238 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1241174 CTTAAACAAC
1241184 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
1241199 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
1241214 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
1241229 TAATATAACT
1 TAATATAACT
1241239 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:1241491 original size:21 final size:21
Alignment explanation
Indices: 1241467--1241506 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1241457 TTTCTATATG
1241467 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1241488 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1241507 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1242145 original size:21 final size:21
Alignment explanation
Indices: 1242102--1242164 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1242092 TGTATGATAG
*
1242102 AACTTAAACTAACAATAAT-AT
1 AACTTAAACTAACAA-ACTAAT
1242123 AACTTAAACTAACAAACTAAT
1 AACTTAAACTAACAAACTAAT
* *
1242144 AATTTAAAAC-AATAAACTAAT
1 AACTT-AAACTAACAAACTAAT
1242165 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.05
21 31 0.84
22 4 0.11
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (21 bp):
AACTTAAACTAACAAACTAAT
Found at i:1243524 original size:20 final size:18
Alignment explanation
Indices: 1243501--1243540 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1243491 AATGCCATAG
1243501 TTTAAATACTTATTTTTTAA
1 TTTAAA-ACTTA-TTTTTAA
*
1243521 TTTAAACCTTATTTTTAA
1 TTTAAAACTTATTTTTAA
1243539 TT
1 TT
1243541 AATTATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAAACTTATTTTTAA
Found at i:1244904 original size:9 final size:9
Alignment explanation
Indices: 1244876--1244914 Score: 60
Period size: 9 Copynumber: 4.1 Consensus size: 9
1244866 TAATATTCTC
1244876 AAAAAATTT
1 AAAAAATTT
1244885 CAAAGAAATTT
1 -AAA-AAATTT
1244896 AAAAAATTT
1 AAAAAATTT
1244905 AAAAAATTT
1 AAAAAATTT
1244914 A
1 A
1244915 TGGGTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 16 0.57
10 6 0.21
11 6 0.21
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAAATTT
Found at i:1246252 original size:20 final size:21
Alignment explanation
Indices: 1246207--1246252 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
1246197 GTCATTTTGA
* *
1246207 TATTTTTTAAACATTTGTGTT
1 TATTTTTTAAACAATTATGTT
*
1246228 T-TTTTTTAAATAATTAT-TT
1 TATTTTTTAAACAATTATGTT
1246247 TATTTT
1 TATTTT
1246253 ATTTTTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 17 0.81
21 1 0.05
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TATTTTTTAAACAATTATGTT
Found at i:1251280 original size:2 final size:2
Alignment explanation
Indices: 1251273--1251299 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1251263 CGTAGTCAGG
1251273 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1251300 TTTGCTGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1252745 original size:133 final size:133
Alignment explanation
Indices: 1252507--1252776 Score: 522
Period size: 133 Copynumber: 2.0 Consensus size: 133
1252497 ATACAACACA
*
1252507 TACCATAGATTTATAGCATCACATGTAATGGGATTAACAGAGATTTAAGGGTAGGGATGAAGAAC
1 TACCATAGATTTATAGCATCACATGTAATGGGATTAACAGAGATTTAAGGGTAGCGATGAAGAAC
*
1252572 TGTTTTTCTTTCTTATTCCATTATTTGAAAGATCTCTTACTAGACGTTTTATCTTTGATCTTGAG
66 TGTTTTTCTTTCTTATTCCATTATTTGAAAGATCTCTTACTAGACGTTTTATCTTTGATCTTAAG
1252637 AAT
131 AAT
1252640 TACCATAGATTTATAGCATCACATGTAATGGGATTAACAGAGATTTAAGGGTAGCGATGAAGAAC
1 TACCATAGATTTATAGCATCACATGTAATGGGATTAACAGAGATTTAAGGGTAGCGATGAAGAAC
1252705 TGTTTTTCTTTCTTATTCCATTATTTGAAAGATCTCTTACTAGACGTTTTATCTTTGATCTTAAG
66 TGTTTTTCTTTCTTATTCCATTATTTGAAAGATCTCTTACTAGACGTTTTATCTTTGATCTTAAG
1252770 AAT
131 AAT
1252773 TACC
1 TACC
1252777 CTTTTGTGTT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 135 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (133 bp):
TACCATAGATTTATAGCATCACATGTAATGGGATTAACAGAGATTTAAGGGTAGCGATGAAGAAC
TGTTTTTCTTTCTTATTCCATTATTTGAAAGATCTCTTACTAGACGTTTTATCTTTGATCTTAAG
AAT
Found at i:1256926 original size:20 final size:20
Alignment explanation
Indices: 1256901--1256947 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1256891 TATTCTCTGA
1256901 TAATCTTTTATTCCCACTGG
1 TAATCTTTTATTCCCACTGG
1256921 TAATCTTTTATTCCCACTGG
1 TAATCTTTTATTCCCACTGG
1256941 TAATCTT
1 TAATCTT
1256948 ACATTCCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGG
Found at i:1256953 original size:20 final size:20
Alignment explanation
Indices: 1256910--1256954 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1256900 ATAATCTTTT
**
1256910 ATTCCCACTGGTAATCTTTT
1 ATTCCCACTGGTAATCTTAC
1256930 ATTCCCACTGGTAATCTTAC
1 ATTCCCACTGGTAATCTTAC
1256950 ATTCC
1 ATTCC
1256955 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.40
Consensus pattern (20 bp):
ATTCCCACTGGTAATCTTAC
Found at i:1266941 original size:14 final size:13
Alignment explanation
Indices: 1266907--1266938 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1266897 TAATTTTTTG
1266907 AAAA-ATTA-ATA
1 AAAATATTATATA
1266918 AAAATATTATATA
1 AAAATATTATATA
1266931 AAAATATT
1 AAAATATT
1266939 TATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.21
12 4 0.21
13 11 0.58
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAATATTATATA
Found at i:1274776 original size:22 final size:22
Alignment explanation
Indices: 1274751--1274823 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
1274741 TTATAATGTT
1274751 AAAATATATTATTTAATTATTA
1 AAAATATATTATTTAATTATTA
*
1274773 AAAATATATTA---AAATATTA
1 AAAATATATTATTTAATTATTA
* * *
1274792 TGAAATATATTATTTTAATAATTT
1 -AAAATATATTA-TTTAATTATTA
1274816 AAAATATA
1 AAAATATA
1274824 ACAAATGATT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
19 7 0.17
20 10 0.25
22 11 0.28
23 7 0.17
24 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (22 bp):
AAAATATATTATTTAATTATTA
Found at i:1274822 original size:43 final size:42
Alignment explanation
Indices: 1274745--1274852 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 42
1274735 TTTATTTTAT
*
1274745 AATG-TTA-AAATATATTA-TTTAATTATTAAAAATATATTA-A
1 AATGATTATAAATATATTATTTTAATAATTAAAAATATA--ACA
*
1274785 AAT-ATTATGAAATATATTATTTTAATAATTTAAAATATAACA
1 AATGATTAT-AAATATATTATTTTAATAATTAAAAATATAACA
1274827 AATGATTATAAATATATTATTATTAA
1 AATGATTATAAATATATTATT-TTAA
1274853 AATAATTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
40 6 0.10
41 1 0.02
42 26 0.44
43 26 0.44
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (42 bp):
AATGATTATAAATATATTATTTTAATAATTAAAAATATAACA
Found at i:1274864 original size:15 final size:17
Alignment explanation
Indices: 1274831--1274867 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1274821 ATAACAAATG
1274831 ATTATAAATATATTATT
1 ATTATAAATATATTATT
*
1274848 ATTA-AAATA-ATTTTT
1 ATTATAAATATATTATT
1274863 ATTAT
1 ATTAT
1274868 TTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATAAATATATTATT
Found at i:1281733 original size:21 final size:21
Alignment explanation
Indices: 1281708--1281749 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1281698 CCATGAACAG
1281708 TGCTACAGTGTACCGATGCAC
1 TGCTACAGTGTACCGATGCAC
*
1281729 TGCTACAGTGTACTGATGCAC
1 TGCTACAGTGTACCGATGCAC
1281750 AAAAACATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAC
Found at i:1282501 original size:37 final size:37
Alignment explanation
Indices: 1282449--1282549 Score: 157
Period size: 37 Copynumber: 2.7 Consensus size: 37
1282439 AGGTAATCAG
*
1282449 TCCATATGTCTCGAAGAACATAGGTAATCTATAACTC
1 TCCATATGTCCCGAAGAACATAGGTAATCTATAACTC
* * *
1282486 TCCATATGTCCCGAAGAACATAAGTAATCTGTAACTG
1 TCCATATGTCCCGAAGAACATAGGTAATCTATAACTC
*
1282523 TCCATATGTCCCAAAGAACATAGGTAA
1 TCCATATGTCCCGAAGAACATAGGTAA
1282550 CCCTCGACTC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (37 bp):
TCCATATGTCCCGAAGAACATAGGTAATCTATAACTC
Found at i:1282815 original size:26 final size:27
Alignment explanation
Indices: 1282773--1282824 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
1282763 TCGTATATTC
* *
1282773 TCATATCTCATTTTCACGTA-TTCATT
1 TCATATCTCATTGTCACATAGTTCATT
1282799 TCATAT-TCATATGTCACATAGTTCAT
1 TCATATCTCAT-TGTCACATAGTTCAT
1282825 ATCACTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 13 0.59
27 5 0.23
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (27 bp):
TCATATCTCATTGTCACATAGTTCATT
Found at i:1282857 original size:2 final size:2
Alignment explanation
Indices: 1282850--1282882 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1282840 AATCACATAA
1282850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1282883 CTTTTTCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1283053 original size:16 final size:16
Alignment explanation
Indices: 1283034--1283067 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1283024 AAGTCATGTC
1283034 ACATATAATAACATAT
1 ACATATAATAACATAT
1283050 ACATATAATAACATAT
1 ACATATAATAACATAT
1283066 AC
1 AC
1283068 TTATTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (16 bp):
ACATATAATAACATAT
Found at i:1284388 original size:20 final size:20
Alignment explanation
Indices: 1284327--1284379 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1284317 AGACCGAACC
*
1284327 GAGTCAACCCGAACCGATTT
1 GAGTCAACCTGAACCGATTT
1284347 GAGTCAACCTGAACCGATTT
1 GAGTCAACCTGAACCGATTT
1284367 GAGTCAACCTGAA
1 GAGTCAACCTGAA
1284380 TTGGTTTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
GAGTCAACCTGAACCGATTT
Found at i:1285240 original size:35 final size:35
Alignment explanation
Indices: 1285201--1285269 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
1285191 AAGTCTCTGC
* *
1285201 AGGTTCAG-CTCGGTCAAATTGGTAATTCCTTATAT
1 AGGTTCAGAC-CGATCAAACTGGTAATTCCTTATAT
* *
1285236 AGGTTCAGACCGATCGAGCTGGTAATTCCTTATA
1 AGGTTCAGACCGATCAAACTGGTAATTCCTTATA
1285270 GACCTAAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (35 bp):
AGGTTCAGACCGATCAAACTGGTAATTCCTTATAT
Found at i:1296414 original size:16 final size:17
Alignment explanation
Indices: 1296393--1296425 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1296383 TTACTATTCA
1296393 CATGAATAGT-AAATTT
1 CATGAATAGTGAAATTT
1296409 CATGAATAGTGAAATTT
1 CATGAATAGTGAAATTT
1296426 TGTCGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (17 bp):
CATGAATAGTGAAATTT
Found at i:1305819 original size:2 final size:2
Alignment explanation
Indices: 1305814--1305850 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1305804 ATCGTGTGTG
1305814 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1305851 GTGTGTGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1307898 original size:31 final size:31
Alignment explanation
Indices: 1307839--1307912 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
1307829 TAATATGTAG
* *
1307839 TTAAAAAAATTTGAATGTTAGAGTGATTAAA
1 TTAAAATAATTTGAAAGTTAGAGTGATTAAA
*
1307870 TTAAGAGTAATTTGAAAGTTA-AGTGATTAAA
1 TTAA-AATAATTTGAAAGTTAGAGTGATTAAA
1307901 TTAAAATAATTT
1 TTAAAATAATTT
1307913 AAACTTCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 7 0.18
31 18 0.47
32 13 0.34
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (31 bp):
TTAAAATAATTTGAAAGTTAGAGTGATTAAA
Found at i:1308360 original size:24 final size:24
Alignment explanation
Indices: 1308333--1308386 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1308323 CGTTCATTTA
1308333 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
1308357 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
1308381 CGTTCG
1 CGTTCG
1308387 ATTATGTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:1308362 original size:14 final size:14
Alignment explanation
Indices: 1308343--1308395 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
1308333 CGTTCGTGAA
1308343 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1308357 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1308371 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
1308381 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
1308395 C
1 C
1308396 TTTTATGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1308391 original size:24 final size:24
Alignment explanation
Indices: 1308344--1308418 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
1308334 GTTCGTGAAC
* *
1308344 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
1308368 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
* *
1308392 GTTCTTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
1308416 GTT
1 GTT
1308419 TAACCCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:1309160 original size:10 final size:10
Alignment explanation
Indices: 1309145--1309218 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1309135 AGGTCTCCAA
1309145 CGTTTATGTT
1 CGTTTATGTT
1309155 CGTTTATGTT
1 CGTTTATGTT
1309165 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1309176 ATGTTCGTGTT
1 -CGTTTATGTT
1309187 CGTTTATGTT
1 CGTTTATGTT
1309197 CG----TGTT
1 CGTTTATGTT
1309203 CGTTTATG-T
1 CGTTTATGTT
1309212 CGTTTAT
1 CGTTTAT
1309219 TTATTAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 17
0.68 0.08 0.23
Matches are distributed among these distances:
6 6 0.12
9 8 0.16
10 25 0.50
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1309176 original size:16 final size:16
Alignment explanation
Indices: 1309151--1309211 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
1309141 CCAACGTTTA
1309151 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1309167 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
1309183 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1309199 TGTTCGTTTATGT
1 TGTTCGTTTATGT
1309212 CGTTTATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1309303 original size:16 final size:16
Alignment explanation
Indices: 1309282--1309314 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1309272 AAAAAAATTT
1309282 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1309298 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1309314 T
1 T
1309315 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1310819 original size:5 final size:5
Alignment explanation
Indices: 1310809--1310846 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
1310799 TGACCGGTCT
*
1310809 GACCC GACCC GACCC GACCC GA-CT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
1310847 GTTGACCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.21, C:0.55, G:0.21, T:0.03
Consensus pattern (5 bp):
GACCC
Found at i:1310855 original size:7 final size:7
Alignment explanation
Indices: 1310843--1310886 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
1310833 GACCCGACCC
1310843 GACCGTT
1 GACCGTT
1310850 GACCGTT
1 GACCGTT
*
1310857 GATCGTT
1 GACCGTT
1310864 GACCG-T
1 GACCGTT
*
1310870 GGCCGTT
1 GACCGTT
1310877 GACCGTT
1 GACCGTT
1310884 GAC
1 GAC
1310887 TTCCTTTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.14, C:0.27, G:0.32, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:1310878 original size:13 final size:13
Alignment explanation
Indices: 1310843--1310882 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1310833 GACCCGACCC
1310843 GACCGTTGACCGTT
1 GACCGTTGACCG-T
*
1310857 GATCGTTGACCGT
1 GACCGTTGACCGT
*
1310870 GGCCGTTGACCGT
1 GACCGTTGACCGT
1310883 TGACTTCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.12, C:0.28, G:0.33, T:0.28
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:1323217 original size:19 final size:21
Alignment explanation
Indices: 1323193--1323243 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1323183 ATTTCCCAAT
1323193 TCGCAATGCGAA-TAGT-AAA
1 TCGCAATGCGAATTAGTAAAA
* *
1323212 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATTAGTAAAA
1323233 TCGCAATGCGA
1 TCGCAATGCGA
1323244 TACTGACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 13 0.48
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAATTAGTAAAA
Found at i:1323257 original size:20 final size:20
Alignment explanation
Indices: 1323232--1323339 Score: 119
Period size: 20 Copynumber: 5.3 Consensus size: 20
1323222 AATTGGTAAA
*
1323232 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1323252 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1323273 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1323293 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1323313 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1323333 TTCGCAA
1 ATCGCAA
1323340 GAGTAATACA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
19 2 0.03
20 60 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1323274 original size:41 final size:40
Alignment explanation
Indices: 1323229--1323364 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 40
1323219 GCGAATTGGT
* *
1323229 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAA-GCGATAATAC
*
1323270 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAA-GCGATAAT-AC
** * *
1323312 --TTTCGCAACGCGATTCTGACTTTCGCAAGAG-TAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAAGCGATAATAC
* *
1323349 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1323365 TTTTAAAGTT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
37 2 0.03
38 3 0.04
39 13 0.16
40 25 0.31
41 35 0.44
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (40 bp):
AAAATCGCAACGCGATACTGACTTTCGCAAGCGATAATAC
Found at i:1324102 original size:24 final size:24
Alignment explanation
Indices: 1324075--1324128 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1324065 GTATTCGAAA
*
1324075 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1324099 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1324123 TTTGAT
1 TTTGAT
1324129 GAGTTTCAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1326605 original size:18 final size:18
Alignment explanation
Indices: 1326582--1326644 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1326572 GGAAATTACT
1326582 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
1326600 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
1326614 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
* *
1326632 AACGCAACGCGAA
1 ATCGCAATGCGAA
1326645 TTTAATTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.22
15 1 0.03
16 8 0.22
17 1 0.03
18 19 0.51
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Done.