Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000250.1 Hibiscus syriacus cultivar Beakdansim tig00000452_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: 2850692
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1254700 original size:19 final size:19
Alignment explanation
Indices: 1254678--1254714 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1254668 ATAACCCCAT
*
1254678 GGGGGTATCGATTCCCCTA
1 GGGGGAATCGATTCCCCTA
*
1254697 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
1254715 TCAAAGGGGG
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:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTA
Found at i:1254738 original size:21 final size:22
Alignment explanation
Indices: 1254696--1254738 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1254686 CGATTCCCCT
1254696 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTT-CCCTTCAA
1254719 AGGGGGAATCGGTT-CCTTCA
1 AGGGGGAATCGGTTCCCTTCA
1254739 TGAGGGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
23 14 0.70
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCTTCAA
Found at i:1258606 original size:22 final size:21
Alignment explanation
Indices: 1258564--1258603 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1258554 GAGTTTATTT
*
1258564 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1258585 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1258604 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1264562 original size:26 final size:25
Alignment explanation
Indices: 1264532--1264588 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
1264522 TCTTCACAGT
*
1264532 TATTTAAAATTTTATTTCTTTTAAAAC
1 TATTTAAAATTTTA--ACTTTTAAAAC
**
1264559 -ATTTCTAATTTTAACTTTTAAAAC
1 TATTTAAAATTTTAACTTTTAAAAC
1264583 TATTTA
1 TATTTA
1264589 TTTATTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 10 0.40
25 4 0.16
26 11 0.44
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTTAAAATTTTAACTTTTAAAAC
Found at i:1267624 original size:29 final size:30
Alignment explanation
Indices: 1267577--1267639 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
1267567 TTTTGGTCCT
**
1267577 TAAACTTTTCAAAGTTTATAATTTAGCCAC
1 TAAACTTTTCAAAACTTATAATTTAGCCAC
* *
1267607 TAAAC-TTTCAAAACTTATATTTTAGTCAC
1 TAAACTTTTCAAAACTTATAATTTAGCCAC
1267636 TAAA
1 TAAA
1267640 TAAAATTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATAATTTAGCCAC
Found at i:1268163 original size:232 final size:232
Alignment explanation
Indices: 1267757--1268222 Score: 851
Period size: 232 Copynumber: 2.0 Consensus size: 232
1267747 AGCAAACAAA
* * *
1267757 TATTTTGTTAATAAGAATTTCCTAGCCTTTAAGATAGATAGGGGATGTTCAAATACGTAGAAATA
1 TATTTTGTTAAAAAGAATTTCCTAGCCTTTAAGATAGATAGAGGATGTTCAAATACATAGAAATA
1267822 TCGAGACTAGACCATCGGATAGGGTCGAGTGAATTATCCTCGTTAAATCTAAGTATAGGAACATT
66 TCGAGACTAGACCATCGGATAGGGTCGAGTGAATTATCCTCGTTAAATCTAAGTATAGGAACATT
*
1267887 TATCTATCATCCTGATTAATTTTGAGGTGTTATCATTTTAATTGGTTTCACTAGAGGATATTTAT
131 TATCTATCACCCTGATTAATTTTGAGGTGTTATCATTTTAATTGGTTTCACTAGAGGATATTTAT
*
1267952 TTATTTTAAATTAACAGAATATGATTATCAAATAGAT
196 TTATTTTAAATTAACAGAATATGATTATCAAAGAGAT
1267989 TATTTTGTTAAAAAGAATTTCCTAGCCTTTAAGATAGATAGAGGATGTTCAAATACATAGAAATA
1 TATTTTGTTAAAAAGAATTTCCTAGCCTTTAAGATAGATAGAGGATGTTCAAATACATAGAAATA
* *
1268054 TTGAGACTAGACCATCGGATAGGGTCGAGTGAATTATCCTCGTTAAATCTAAGTATATGAACATT
66 TCGAGACTAGACCATCGGATAGGGTCGAGTGAATTATCCTCGTTAAATCTAAGTATAGGAACATT
* *
1268119 TATCTATCACCCTGATTAATTTTGAGGTGTTATCATTTTAATTGGTTTCAGTGGAGGATATTTAT
131 TATCTATCACCCTGATTAATTTTGAGGTGTTATCATTTTAATTGGTTTCACTAGAGGATATTTAT
1268184 TTATTTTAAATTAACAGAATATGATTATCAAAGAGAT
196 TTATTTTAAATTAACAGAATATGATTATCAAAGAGAT
1268221 TA
1 TA
1268223 AGACAACCCT
Statistics
Matches: 225, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
232 225 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (232 bp):
TATTTTGTTAAAAAGAATTTCCTAGCCTTTAAGATAGATAGAGGATGTTCAAATACATAGAAATA
TCGAGACTAGACCATCGGATAGGGTCGAGTGAATTATCCTCGTTAAATCTAAGTATAGGAACATT
TATCTATCACCCTGATTAATTTTGAGGTGTTATCATTTTAATTGGTTTCACTAGAGGATATTTAT
TTATTTTAAATTAACAGAATATGATTATCAAAGAGAT
Found at i:1268812 original size:22 final size:20
Alignment explanation
Indices: 1268756--1268808 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 20
1268746 TAATATTATT
1268756 TTTATTAA-ATTAATAAATAA
1 TTTATTAATATT-ATAAATAA
*
1268776 --TATTAATTTTATAAATAA
1 TTTATTAATATTATAAATAA
1268794 TTTATTATATATTAT
1 TTTATTA-ATATTAT
1268809 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 14 0.52
19 2 0.07
20 5 0.19
21 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATTAATATTATAAATAA
Found at i:1269497 original size:10 final size:10
Alignment explanation
Indices: 1269484--1269509 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1269474 TGAAAAGGTT
1269484 AAAAAAAGAG
1 AAAAAAAGAG
1269494 AAAAAAAGAG
1 AAAAAAAGAG
1269504 AAAAAA
1 AAAAAA
1269510 TAAACAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:1270591 original size:21 final size:21
Alignment explanation
Indices: 1270567--1270606 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1270557 CAGATTGCTC
1270567 AGAGGGAACCGATTCCCCCCG
1 AGAGGGAACCGATTCCCCCCG
* *
1270588 AGAGGGTATCGATTCCCCC
1 AGAGGGAACCGATTCCCCC
1270607 TGAATGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.28, T:0.15
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCCG
Found at i:1274518 original size:9 final size:9
Alignment explanation
Indices: 1274504--1274546 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
1274494 ATTTTTTTTT
1274504 CAAAAAAAA
1 CAAAAAAAA
1274513 CAAAAAAAA
1 CAAAAAAAA
1274522 C--AAAAAA
1 CAAAAAAAA
**
1274529 CAAAAAAGG
1 CAAAAAAAA
1274538 CAAAAAAAA
1 CAAAAAAAA
1274547 AAAGGCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 7 0.25
9 21 0.75
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:1274528 original size:16 final size:15
Alignment explanation
Indices: 1274507--1274566 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1274497 TTTTTTTCAA
1274507 AAAAAACAAAAAAAAC
1 AAAAAA-AAAAAAAAC
**
1274523 AAAAAACAAAAAAGGC
1 AAAAAA-AAAAAAAAC
**
1274539 -AAAAAAAAAAAGGC
1 AAAAAAAAAAAAAAC
1274553 AAAAAAAAAAAAAA
1 AAAAAAAAAAAAAA
1274567 GAGCCAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
14 9 0.23
15 16 0.41
16 14 0.36
ACGTcount: A:0.85, C:0.08, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:1274533 original size:14 final size:13
Alignment explanation
Indices: 1274505--1274564 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
1274495 TTTTTTTTTC
1274505 AAAAAAAACAAAA
1 AAAAAAAACAAAA
* *
1274518 AAAACAAA-AAAC
1 AAAAAAAACAAAA
**
1274530 AAAAAAGGCAAAA
1 AAAAAAAACAAAA
*
1274543 AAAAAAAGGCAAAA
1 AAAAAAA-ACAAAA
1274557 AAAAAAAA
1 AAAAAAAA
1274565 AAGAGCCAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 8 0.22
13 16 0.43
14 13 0.35
ACGTcount: A:0.85, C:0.08, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:1274546 original size:13 final size:14
Alignment explanation
Indices: 1274524--1274563 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
1274514 AAAAAAAACA
1274524 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGGC
1274539 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
1274553 AAAAAAAAAAA
1 AAAAAAAAAAA
1274564 AAAGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:1274575 original size:19 final size:17
Alignment explanation
Indices: 1274504--1274567 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
1274494 ATTTTTTTTT
**
1274504 CAAAAAAAACAAAAAAAA
1 CAAAAAAAA-AAAAAAGG
*
1274522 C-AAAAAACAAAAAAGG
1 CAAAAAAAAAAAAAAGG
1274538 C---AAAAAAAAAAAGG
1 CAAAAAAAAAAAAAAGG
1274552 CAAAAAAAAAAAAAAG
1 CAAAAAAAAAAAAAAG
1274568 AGCCAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 13 0.33
16 7 0.18
17 18 0.46
18 1 0.03
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAAAAAAGG
Found at i:1279566 original size:22 final size:22
Alignment explanation
Indices: 1279538--1279585 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1279528 TGGTAGATGA
* *
1279538 CTATTCTAGATATATTTGGGTT
1 CTATTCTAGATATACTTGGATT
1279560 CTATTCTAGATATACTTGGATT
1 CTATTCTAGATATACTTGGATT
1279582 CTAT
1 CTAT
1279586 AACTAGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (22 bp):
CTATTCTAGATATACTTGGATT
Found at i:1282188 original size:21 final size:21
Alignment explanation
Indices: 1282144--1282204 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
1282134 TTGGTATAAA
1282144 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCC-TGAAG
*
1282166 GGGAATCGATTCCCCCT-ACAG
1 GGGAATCGATACCCCCTGA-AG
*
1282187 GGGAATTGATACCCCCTG
1 GGGAATCGATACCCCCTG
1282205 GGGGTTCTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 18 0.53
22 15 0.44
ACGTcount: A:0.25, C:0.30, G:0.26, T:0.20
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGAAG
Found at i:1283750 original size:18 final size:18
Alignment explanation
Indices: 1283737--1283783 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1283727 TGACGATGAG
1283737 CAAGAACAACACGAGGAA
1 CAAGAACAACACGAGGAA
*
1283755 CAAGCACAAC-CAGAGGAA
1 CAAGAACAACAC-GAGGAA
*
1283773 CAAGTACAACA
1 CAAGAACAACA
1283784 AGAAGATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.53, C:0.26, G:0.19, T:0.02
Consensus pattern (18 bp):
CAAGAACAACACGAGGAA
Found at i:1284758 original size:22 final size:22
Alignment explanation
Indices: 1284732--1284776 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1284722 CAGATTGCTC
1284732 AGAGGGAACCGATTCCCCCCTA
1 AGAGGGAACCGATTCCCCCCTA
* *
1284754 AGAGGGTACCGATTTCCCCCTA
1 AGAGGGAACCGATTCCCCCCTA
1284776 A
1 A
1284777 ATGGTTTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (22 bp):
AGAGGGAACCGATTCCCCCCTA
Found at i:1289813 original size:8 final size:8
Alignment explanation
Indices: 1289800--1289830 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1289790 TGAGTTCATT
1289800 CTTTCTAG
1 CTTTCTAG
1289808 CTTTCTAG
1 CTTTCTAG
*
1289816 CTTGCTAG
1 CTTTCTAG
1289824 CTTTCTA
1 CTTTCTA
1289831 TCCTTGTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (8 bp):
CTTTCTAG
Found at i:1292914 original size:17 final size:17
Alignment explanation
Indices: 1292892--1292932 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1292882 GTGTTGGTGT
1292892 GTGGAGTGCCAGACTTC
1 GTGGAGTGCCAGACTTC
*
1292909 GTGGAGTGCTAGACTTC
1 GTGGAGTGCCAGACTTC
1292926 GTGGAGT
1 GTGGAGT
1292933 AAGAAGGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.27
Consensus pattern (17 bp):
GTGGAGTGCCAGACTTC
Found at i:1293997 original size:8 final size:8
Alignment explanation
Indices: 1293984--1294024 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
1293974 TGAGTTTATT
1293984 CTTTCTAG
1 CTTTCTAG
1293992 CTTTCTAG
1 CTTTCTAG
*
1294000 CTTGCTAG
1 CTTTCTAG
*
1294008 CTTGCTAG
1 CTTTCTAG
1294016 CTTTCTAG
1 CTTTCTAG
1294024 C
1 C
1294025 CTTGTCGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.44
Consensus pattern (8 bp):
CTTTCTAG
Found at i:1297051 original size:21 final size:21
Alignment explanation
Indices: 1297027--1297072 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1297017 TAAGCATGAG
*
1297027 TATTGTTACCATAAGAACGAT
1 TATTGGTACCATAAGAACGAT
* *
1297048 TATTGGTACCATATGGACGAT
1 TATTGGTACCATAAGAACGAT
1297069 TATT
1 TATT
1297073 AATACTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (21 bp):
TATTGGTACCATAAGAACGAT
Found at i:1297120 original size:20 final size:21
Alignment explanation
Indices: 1297069--1297122 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1297059 TATGGACGAT
*
1297069 TATTAATACTCATACATTAAG
1 TATTAATACTCATACATGAAG
* *
1297090 TATTTAGACTCA-ACATGAAG
1 TATTAATACTCATACATGAAG
*
1297110 TATTGATACTCAT
1 TATTAATACTCAT
1297123 TTGTGGACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (21 bp):
TATTAATACTCATACATGAAG
Found at i:1302237 original size:2 final size:2
Alignment explanation
Indices: 1302230--1302254 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1302220 ATTATATCAT
1302230 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 T
1302255 TAATGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1302446 original size:32 final size:32
Alignment explanation
Indices: 1302401--1302472 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1302391 AAGTAAAAAC
1302401 ATTA-TTTTTTATTGTATTTAAAGCATTTAAA
1 ATTATTTTTTTATTGTATTTAAAGCATTTAAA
1302432 ATTATTTTTTTATTGTATTTAAAGCATTTAAA
1 ATTATTTTTTTATTGTATTTAAAGCATTTAAA
1302464 ATTATTTTT
1 ATTATTTTT
1302473 ATTCAACAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 4 0.10
32 36 0.90
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (32 bp):
ATTATTTTTTTATTGTATTTAAAGCATTTAAA
Found at i:1306550 original size:24 final size:24
Alignment explanation
Indices: 1306520--1306575 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
1306510 AATTGAGTAT
1306520 GTTATTAAAGTGCTGGA-AATTTTG
1 GTTATTAAAGTGCT-GACAATTTTG
1306544 GTTATTAAAGTGCTGACAATTTTG
1 GTTATTAAAGTGCTGACAATTTTG
*
1306568 GTAATTAA
1 GTTATTAA
1306576 TGTGAGATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.41
Consensus pattern (24 bp):
GTTATTAAAGTGCTGACAATTTTG
Found at i:1308533 original size:147 final size:148
Alignment explanation
Indices: 1308329--1308613 Score: 376
Period size: 147 Copynumber: 1.9 Consensus size: 148
1308319 CTTAAAACAA
* * *** * *
1308329 TCATTTATTACTCCAATCGAAATGAAAATATATCATTATTTTGTCTTAAAATTCAATATCGATTC
1 TCATTTATTACTCCAATCAAAATGAAAAGATATCATTATTCCATCTTAAAAATCAATATCAATTC
** * *
1308394 GATTGAAAAC-GATAATATCTAATAATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGA
66 GAGAGAAAACTG-TAATATCAAATAATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGA
1308458 AATCATTTATTATGAGAGG
130 AATCATTTATTATGAGAGG
* * * *
1308477 TCATTTATTGCTCTAAT-AAAATGAAGAGATATCATTATTCCATCTTAAAAATCAATATTAATTC
1 TCATTTATTACTCCAATCAAAATGAAAAGATATCATTATTCCATCTTAAAAATCAATATCAATTC
* * * *
1308541 GAGAGAAAACTGTAATATCAAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGCA
66 GAGAGAAAACTGTAATATCAAATAATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGAA
1308606 ATCATTTA
131 ATCATTTA
1308614 ATACTCCAAC
Statistics
Matches: 117, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
147 101 0.86
148 16 0.14
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (148 bp):
TCATTTATTACTCCAATCAAAATGAAAAGATATCATTATTCCATCTTAAAAATCAATATCAATTC
GAGAGAAAACTGTAATATCAAATAATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGAA
ATCATTTATTATGAGAGG
Found at i:1309525 original size:33 final size:31
Alignment explanation
Indices: 1309487--1309554 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
1309477 AAAAGTGGGT
*
1309487 AAATTAAA-AAACAGTTAAGGGGGACCTAAACAA
1 AAATTAAACAAA-AATTAA-GGGGA-CTAAACAA
1309520 AAATTAAACCAAAAATTAAGGGGACTAAACAA
1 AAATTAAA-CAAAAATTAAGGGGACTAAACAA
1309552 AAA
1 AAA
1309555 CACACTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
32 11 0.34
33 13 0.41
34 5 0.16
35 3 0.09
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (31 bp):
AAATTAAACAAAAATTAAGGGGACTAAACAA
Found at i:1309576 original size:117 final size:117
Alignment explanation
Indices: 1309444--1309712 Score: 520
Period size: 117 Copynumber: 2.3 Consensus size: 117
1309434 ATGGATTAAA
*
1309444 AAACAAATAATCCTAAAAATACATAACATGCATAAAAGTGGGTAAATTAAAAAACAGTTAAGGGG
1 AAACAAATAACCCTAAAAATACATAACATGCATAAAAGTGGGTAAATTAAAAAACAGTTAAGGGG
1309509 GACCTAAACAAAAATTAAACCAAAAATTAAGGGGACTAAACAAAAACACACT
66 GACCTAAACAAAAATTAAACCAAAAATTAAGGGGACTAAACAAAAACACACT
1309561 AAACAAATAACCCTAAAAATACATAACATGCATAAAAGTGGGTAAATTAAAAAACAGTTAAGGGG
1 AAACAAATAACCCTAAAAATACATAACATGCATAAAAGTGGGTAAATTAAAAAACAGTTAAGGGG
*
1309626 GACCTAAACAAAAATTAAACCAAAAATTACGGGGACTAAACAAAAACACACT
66 GACCTAAACAAAAATTAAACCAAAAATTAAGGGGACTAAACAAAAACACACT
1309678 AAACAAATAACCCTAAAAATACATAACATGCATAA
1 AAACAAATAACCCTAAAAATACATAACATGCATAA
1309713 GTATTTTAAC
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 150 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.17
Consensus pattern (117 bp):
AAACAAATAACCCTAAAAATACATAACATGCATAAAAGTGGGTAAATTAAAAAACAGTTAAGGGG
GACCTAAACAAAAATTAAACCAAAAATTAAGGGGACTAAACAAAAACACACT
Found at i:1311429 original size:20 final size:20
Alignment explanation
Indices: 1311385--1311432 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1311375 TGATGCAATC
*
1311385 AGTATCGATACCGAAGTGGA
1 AGTATCGATACCGAAGTAGA
*
1311405 AGTATTGATACCGAAG-AGA
1 AGTATCGATACCGAAGTAGA
1311424 AGGTATCGA
1 A-GTATCGA
1311433 GACCATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (20 bp):
AGTATCGATACCGAAGTAGA
Found at i:1311484 original size:19 final size:21
Alignment explanation
Indices: 1311460--1311510 Score: 79
Period size: 19 Copynumber: 2.5 Consensus size: 21
1311450 TGCAAAAATG
1311460 GTATCGATACCATA-ATAG-A
1 GTATCGATACCATAGATAGTA
1311479 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
1311501 GTATCGATAC
1 GTATCGATAC
1311511 AATGGTAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.48
21 4 0.14
22 11 0.38
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:1311966 original size:55 final size:55
Alignment explanation
Indices: 1311891--1312241 Score: 526
Period size: 55 Copynumber: 6.4 Consensus size: 55
1311881 TCCATACTAA
* * *
1311891 GTATGGGCACTTTATGTGTAAATTTAAGAAATTCATACTAAGTGGATGAATTTTC
1 GTATGGGCACCTTGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
* *
1311946 ATATGGGCACCTTGTATGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
1 GTATGGGCACCTTGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
1312001 GTATGGGCACCTTGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAA-TTTC
1 GTATGGGCACCTTGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
* * * *
1312055 TGTATGGGTACTTTATGTGTAAATTTAAGAAATTCATACTAAGTGGATGAATTTTC
1 -GTATGGGCACCTTGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
*
1312111 GTATGGGCACCTAGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAA-TTTC
1 GTATGGGCACCTTGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
* * * * *
1312165 TGTATAGGCACTTTATGTGTAAATTTAAGAAATTCATACTAAGTGGATGAATTTCC
1 -GTATGGGCACCTTGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
*
1312221 GTATAGGCACCTTGTGTGTAA
1 GTATGGGCACCTTGTGTGTAA
1312242 CACCTCCAAC
Statistics
Matches: 268, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
54 8 0.03
55 253 0.94
56 7 0.03
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (55 bp):
GTATGGGCACCTTGTGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
Found at i:1313009 original size:23 final size:23
Alignment explanation
Indices: 1312966--1313009 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1312956 GAAGTGCCAC
*
1312966 GTAGAATTACACCGTAGTGCCGT
1 GTAGAATTACACCGCAGTGCCGT
* *
1312989 GTAGAATTGCACCGCATTGCC
1 GTAGAATTACACCGCAGTGCC
1313010 ATATAATAAT
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:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
GTAGAATTACACCGCAGTGCCGT
Found at i:1315662 original size:16 final size:16
Alignment explanation
Indices: 1315623--1315665 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1315613 ATCATCAGTT
*
1315623 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
1315639 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
1315656 CTTATCAATC
1 CTTATCAATC
1315666 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:1318024 original size:23 final size:23
Alignment explanation
Indices: 1317990--1318050 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1317980 CTCATATAAA
*
1317990 TGCACCGGAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
1318013 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
1318036 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1318051 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:1319750 original size:21 final size:21
Alignment explanation
Indices: 1319726--1319770 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1319716 ATTTGTTCAT
* *
1319726 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1319747 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1319768 TTG
1 TTG
1319771 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1320541 original size:55 final size:55
Alignment explanation
Indices: 1320480--1320634 Score: 206
Period size: 55 Copynumber: 2.8 Consensus size: 55
1320470 TGTTACATTG
1320480 TGTGTAAACTTAAGAAATTCATAC-ATAGTGGATGAATTTCTGTATGGACACTTTA
1 TGTGTAAACTTAAGAAATTCATACTA-AGTGGATGAATTTCTGTATGGACACTTTA
* *
1320535 TGTGTAAACTTAAGGAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTA
1 TGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGACACTTTA
* * * * * *
1320590 TGTGCAAAAC-TAGGAAATTAATACTAAGTGTATAAATTTCCGTAT
1 TGTG-TAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTAT
1320635 TGGAAATGGT
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
55 84 0.94
56 5 0.06
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (55 bp):
TGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGACACTTTA
Found at i:1328495 original size:35 final size:35
Alignment explanation
Indices: 1328452--1328519 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1328442 ACGAGGGAGT
1328452 AGTTTCTCATTCGAACTAAATAGGATAAGAGCGGG
1 AGTTTCTCATTCGAACTAAATAGGATAAGAGCGGG
1328487 AGTTTCTCATTCGAACTAAATAGGATAAGAGCG
1 AGTTTCTCATTCGAACTAAATAGGATAAGAGCG
1328520 TGGTTTTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (35 bp):
AGTTTCTCATTCGAACTAAATAGGATAAGAGCGGG
Found at i:1330638 original size:18 final size:18
Alignment explanation
Indices: 1330617--1330651 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1330607 ATAATTAATT
1330617 ATAATATAATAATAATAC
1 ATAATATAATAATAATAC
* *
1330635 ATAATATTATTATAATA
1 ATAATATAATAATAATA
1330652 TTTATAACGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATATAATAATAATAC
Found at i:1341034 original size:81 final size:81
Alignment explanation
Indices: 1340936--1341146 Score: 268
Period size: 81 Copynumber: 2.6 Consensus size: 81
1340926 CCCAAAGGAA
* * *
1340936 TTTAACCTTTCATCTAACTTGAATGATTGAC-CCTTGT-TTGCCAAATGCACATCT-ATGCCATT
1 TTTAACCATTCATCTAACTTGAATAATTGACACCTT-TCTT-CCAAATGCACAACTAAT-CCATT
*
1340998 TATCTTTTACTCCACGATC
63 TATCTTTTACTCAACGATC
** *
1341017 TTTAACCGGTCATCTAAC-TGACATAATTGACACCTTTCTTCCAAATCCACAACTAATCCATTTA
1 TTTAACCATTCATCTAACTTGA-ATAATTGACACCTTTCTTCCAAATGCACAACTAATCCATTTA
*
1341081 TCTTTTACTCAACGGTC
65 TCTTTTACTCAACGATC
* *
1341098 TTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCA
1 TTTAACCATTCATCTAACTTGAATAATTGACACCTTTCTTCCAAATGCA
1341147 AAGCCAGGCC
Statistics
Matches: 113, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
80 3 0.03
81 101 0.89
82 9 0.08
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (81 bp):
TTTAACCATTCATCTAACTTGAATAATTGACACCTTTCTTCCAAATGCACAACTAATCCATTTAT
CTTTTACTCAACGATC
Found at i:1341510 original size:68 final size:68
Alignment explanation
Indices: 1341106--1341497 Score: 579
Period size: 68 Copynumber: 5.8 Consensus size: 68
1341096 TCTTTAACCA
* **
1341106 TTCATCTAACTGGCATAATTGACACCTTTCT-TCCAAATGCAAAGCCAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGT-CAAATGCACAGTTAGGCCTCAAAGGCACTTA
1341170 GCCT
65 GCCT
* *
1341174 TTCATCTAATTGGCATACTTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1341239 CCT
66 CCT
*
1341242 TTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1341307 CCT
66 CCT
* * *
1341310 TTCATCTGACTAGTATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1341375 CCT
66 CCT
** * * * * * * *
1341378 TTCATCTAGTTGGCATAATTGGCACTTTTCTATCAAATGCATAGTTAGGCCTCAAAGACATTTAT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1341443 CCT
66 CCT
* * *
1341446 TTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGCATAGTTAGGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
1341498 ATTAATCTTT
Statistics
Matches: 293, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
68 292 1.00
69 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1344404 original size:21 final size:20
Alignment explanation
Indices: 1344380--1344421 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1344370 AAGAATATAT
1344380 TTTTTCAATTTTAATAACTAA
1 TTTTTCAA-TTTAATAACTAA
*
1344401 TTTTTTAATTTAATAACTAA
1 TTTTTCAATTTAATAACTAA
1344421 T
1 T
1344422 GGATTATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTCAATTTAATAACTAA
Found at i:1344904 original size:2 final size:2
Alignment explanation
Indices: 1344899--1344936 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1344889 TTTTTTGATG
1344899 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
1344937 TCAAATTTTA
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:1351634 original size:18 final size:19
Alignment explanation
Indices: 1351599--1351635 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1351589 CACGGAATGT
1351599 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1351619 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1351636 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1356034 original size:68 final size:67
Alignment explanation
Indices: 1355909--1356045 Score: 179
Period size: 68 Copynumber: 2.0 Consensus size: 67
1355899 AAGGAGATAC
* * * *
1355909 ATTTCATTAAAGGATGAACATTCATTCATCCAATTTCTCCTTGTAGACACTTAAGGTCGTGAATT
1 ATTTCATTAAAGGATGAACATTCATTCATCCAAATTCTCCATGTACACACTTAAGGTCATGAATT
1355974 GT
66 GT
* *
1355976 ATTTCATTAAAGGAATGAACATTCATTTCAT-CAAATTCATTCATGTACACACTT-AGGTCATGC
1 ATTTCATTAAAGG-ATGAACATTCA-TTCATCCAAATTC-TCCATGTACACACTTAAGGTCATGA
1356039 ATTGT
63 ATTGT
1356044 AT
1 AT
1356046 CTTAGAATCC
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
67 13 0.21
68 31 0.51
69 17 0.28
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (67 bp):
ATTTCATTAAAGGATGAACATTCATTCATCCAAATTCTCCATGTACACACTTAAGGTCATGAATT
GT
Found at i:1357442 original size:51 final size:50
Alignment explanation
Indices: 1357366--1357478 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 50
1357356 GTGCAGCCGT
*
1357366 AGGTCGCCATGACTTCCGGGCGAGCTATTGAAGGTCGCCATGCACGGCCAA
1 AGGTCGCCATGCCTTCCGGGCGAGCTATTGAAGGTCGCCA-GCACGGCCAA
* * * * * *
1357417 AGGTCGTCATGCCTTCCGGGCGAGCTGTTGAAGGTTGCCAGCATGGTCAG
1 AGGTCGCCATGCCTTCCGGGCGAGCTATTGAAGGTCGCCAGCACGGCCAA
1357467 AGGTCGCCATGC
1 AGGTCGCCATGC
1357479 ACTCCCATGC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
50 18 0.33
51 36 0.67
ACGTcount: A:0.19, C:0.27, G:0.34, T:0.20
Consensus pattern (50 bp):
AGGTCGCCATGCCTTCCGGGCGAGCTATTGAAGGTCGCCAGCACGGCCAA
Found at i:1357791 original size:19 final size:20
Alignment explanation
Indices: 1357753--1357792 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1357743 ACAACAAAGC
1357753 AAGAACAGGAGAAGAGAGAA
1 AAGAACAGGAGAAGAGAGAA
1357773 AAGAA-AGGAAGAAGA-AGAA
1 AAGAACAGG-AGAAGAGAGAA
1357792 A
1 A
1357793 GGGAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.65, C:0.03, G:0.33, T:0.00
Consensus pattern (20 bp):
AAGAACAGGAGAAGAGAGAA
Found at i:1357792 original size:14 final size:13
Alignment explanation
Indices: 1357769--1357802 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1357759 AGGAGAAGAG
1357769 AGAAAAGAAAGGA
1 AGAAAAGAAAGGA
*
1357782 AGAAGAAGAAAGGG
1 AGAA-AAGAAAGGA
1357796 AGAAAAG
1 AGAAAAG
1357803 TTCGAAGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGGA
Found at i:1359007 original size:17 final size:17
Alignment explanation
Indices: 1358985--1359043 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
1358975 ATTTATTTCC
1358985 GTTTAAAAAAATATTTT
1 GTTTAAAAAAATATTTT
1359002 GTTTAAAAATATATATTGTT
1 GTTTAAAAA-A-ATATT-TT
1359022 GTTT-AAAAAATATTTT
1 GTTTAAAAAAATATTTT
*
1359038 ATTTAA
1 GTTTAA
1359044 TTTATATTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 5 0.14
17 15 0.41
18 2 0.05
19 9 0.24
20 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
GTTTAAAAAAATATTTT
Found at i:1359032 original size:21 final size:19
Alignment explanation
Indices: 1358985--1359034 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1358975 ATTTATTTCC
1358985 GTTTAAAAA-A-ATATTTT
1 GTTTAAAAATATATATTTT
1359002 GTTTAAAAATATATATTGTT
1 GTTTAAAAATATATATT-TT
1359022 GTTTAAAAA-ATAT
1 GTTTAAAAATATAT
1359035 TTTATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.30
18 1 0.03
19 9 0.30
20 11 0.37
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
GTTTAAAAATATATATTTT
Found at i:1362252 original size:21 final size:22
Alignment explanation
Indices: 1362207--1362274 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 22
1362197 ATTGAAGTTG
1362207 AATTATAATAATGATTTCATACTAAT
1 AATTATAATAATGA--T--TACTAAT
* *
1362233 GATT-TAGTAATGATTACTAA-
1 AATTATAATAATGATTACTAAT
1362253 AATTATAATAATGATTA-TAAT
1 AATTATAATAATGATTACTAAT
1362274 A
1 A
1362275 GTCGAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
20 6 0.17
21 18 0.50
23 1 0.03
25 8 0.22
26 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (22 bp):
AATTATAATAATGATTACTAAT
Found at i:1362293 original size:21 final size:23
Alignment explanation
Indices: 1362267--1362308 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1362257 ATAATAATGA
1362267 TTAT-AATA-GTCGAATTTATCT
1 TTATAAATATGTCGAATTTATCT
1362288 TTATAAATATGTCGAATTTAT
1 TTATAAATATGTCGAATTTAT
1362309 TTTTTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (23 bp):
TTATAAATATGTCGAATTTATCT
Found at i:1374873 original size:139 final size:139
Alignment explanation
Indices: 1374623--1374901 Score: 540
Period size: 139 Copynumber: 2.0 Consensus size: 139
1374613 TTCACTAAAT
1374623 TAACAACCTAACCATTTGTAACACCCTATTCCTGTCCGACCTGAAGATCCATGGATTACGACGCC
1 TAACAACCTAACCATTTGTAACACCCTATTCCTGTCCGACCTGAAGATCCATGGATTACGACGCC
1374688 ACACGGGACCACCGAAATGGCCAACATTAAAATTTGTTTTCAAAAAGATTTATGCTTATCAAAAT
66 ACACGGGACCACCGAAATGGCCAACATTAAAATTTGTTTTCAAAAAGATTTATGCTTATCAAAAT
1374753 CATTCATCA
131 CATTCATCA
*
1374762 TAACAACCTAACCATTTGTAACACCCTATTCTTGTCCGACCTGAAGATCCATGGATTACGACGCC
1 TAACAACCTAACCATTTGTAACACCCTATTCCTGTCCGACCTGAAGATCCATGGATTACGACGCC
*
1374827 ACACGGGACCACCGAAATGGTCAACATTAAAATTTGTTTTCAAAAAGATTTATGCTTATCAAAAT
66 ACACGGGACCACCGAAATGGCCAACATTAAAATTTGTTTTCAAAAAGATTTATGCTTATCAAAAT
1374892 CATTCATCA
131 CATTCATCA
1374901 T
1 T
1374902 CTCATAAGCA
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (139 bp):
TAACAACCTAACCATTTGTAACACCCTATTCCTGTCCGACCTGAAGATCCATGGATTACGACGCC
ACACGGGACCACCGAAATGGCCAACATTAAAATTTGTTTTCAAAAAGATTTATGCTTATCAAAAT
CATTCATCA
Found at i:1379184 original size:20 final size:20
Alignment explanation
Indices: 1379155--1379206 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1379145 CCTATGGGGA
1379155 GTATCGATACTCTACCCTGG
1 GTATCGATACTCTACCCTGG
*
1379175 GTATCAATACTCTACCCTGG
1 GTATCGATACTCTACCCTGG
1379195 GTATCGATACTC
1 GTATCGATACTC
1379207 GTATGAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (20 bp):
GTATCGATACTCTACCCTGG
Found at i:1379758 original size:25 final size:25
Alignment explanation
Indices: 1379724--1379771 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
1379714 TAGAGCTCTC
1379724 ACCCTTCTCTTGAACTAGTTAGATT
1 ACCCTTCTCTTGAACTAGTTAGATT
1379749 ACCCTTCTCTTGAACTAGTTAGA
1 ACCCTTCTCTTGAACTAGTTAGA
1379772 ATAAATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (25 bp):
ACCCTTCTCTTGAACTAGTTAGATT
Found at i:1379938 original size:17 final size:19
Alignment explanation
Indices: 1379902--1379938 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1379892 CAAAGACCAA
1379902 TCATATGATGATTGTATTG
1 TCATATGATGATTGTATTG
*
1379921 TCATAT-ATTATT-TATTG
1 TCATATGATGATTGTATTG
1379938 T
1 T
1379939 ATTTATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (19 bp):
TCATATGATGATTGTATTG
Found at i:1385045 original size:24 final size:24
Alignment explanation
Indices: 1385018--1385105 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
1385008 ATTTCCGACT
*
1385018 TGAATTCTATTCTGATATATGA-C
1 TGAATTCTGTTCTGATATATGATC
* *
1385041 ATGAATTCTGTTCTGATTTCTGATC
1 -TGAATTCTGTTCTGATATATGATC
* *
1385066 TGGATTCTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATATATGATC
*
1385090 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
1385106 TTCTGATATC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGATC
Found at i:1385067 original size:12 final size:12
Alignment explanation
Indices: 1385046--1385110 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
1385036 ATGACATGAA
1385046 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
1385058 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
1385070 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* * *
1385082 ATATGTTCTGAA
1 TTCTGTTCTGAT
*
1385094 TTCTGTTTTGAT
1 TTCTGTTCTGAT
1385106 TTCTG
1 TTCTG
1385111 ATATCTCCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:1385109 original size:48 final size:48
Alignment explanation
Indices: 1385004--1385112 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
1384994 AAATATTTTA
* *
1385004 TCTGATTTCCGA-CTTGAATTCTATTCTGATATATGACATGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTATTCTGATATATGACATGAATTCTGT
* *
1385052 TCTGATTTCTGATCTGGATTCTGTTCTGATATATGTTC-TGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTATTCTGATATATG-ACATGAATTCTGT
*
1385100 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1385113 ATCTCCGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTATTCTGATATATGACATGAATTCTGT
Found at i:1387984 original size:21 final size:22
Alignment explanation
Indices: 1387957--1388012 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
1387947 GATCAAATAG
* *
1387957 AGAAAATCAAGAAGAAAGGAGT
1 AGAAAATCAAGAACAAAGGAAT
*
1387979 -GAAAATCAATAACAAAGGAAT
1 AGAAAATCAAGAACAAAGGAAT
*
1388000 AGAAAATGAAGAA
1 AGAAAATCAAGAA
1388013 TAAGAGTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.62, C:0.05, G:0.21, T:0.11
Consensus pattern (22 bp):
AGAAAATCAAGAACAAAGGAAT
Found at i:1391778 original size:27 final size:27
Alignment explanation
Indices: 1391740--1391797 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1391730 ACAACTCTTA
1391740 CTCCATTTCCCACTTGTAGGTCTACCT
1 CTCCATTTCCCACTTGTAGGTCTACCT
1391767 CTCCATTTCCCACTTGTAGGTCTACCT
1 CTCCATTTCCCACTTGTAGGTCTACCT
1391794 CTCC
1 CTCC
1391798 TTTAGCCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.14, C:0.40, G:0.10, T:0.36
Consensus pattern (27 bp):
CTCCATTTCCCACTTGTAGGTCTACCT
Found at i:1395721 original size:20 final size:20
Alignment explanation
Indices: 1395696--1395759 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1395686 TGACCAAGTA
*
1395696 CATCGGTGCACTGGGGTATG
1 CATCGGTGCACTGGGGTGTG
1395716 CATCGGTGCACTGGGGTGTG
1 CATCGGTGCACTGGGGTGTG
* * *
1395736 CATCAGTACACTTGGGTGTG
1 CATCGGTGCACTGGGGTGTG
1395756 CATC
1 CATC
1395760 AATGCACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.22, G:0.36, T:0.27
Consensus pattern (20 bp):
CATCGGTGCACTGGGGTGTG
Found at i:1395824 original size:64 final size:64
Alignment explanation
Indices: 1395752--1395887 Score: 154
Period size: 65 Copynumber: 2.1 Consensus size: 64
1395742 TACACTTGGG
* * *
1395752 TGTGCATCAATGCA-CAAATCTACTTCGATGTTTTAA-AATAGCCA-GAGTGCATCGATGCATGG
1 TGTGCATCAATGCATAAAAT-AAATTCGATGTTTTAATAATA--CAGGAGTGCATCGATGCATGG
1395814 CT-
63 -TA
* *
1395816 TGTGCATCAGTGCATAAAATAAATTCGATGTTTTAATAATACATGGAGTGCCTCGATGCATGGTA
1 TGTGCATCAATGCATAAAATAAATTCGATGTTTTAATAATACA-GGAGTGCATCGATGCATGGTA
1395881 TGTGCAT
1 TGTGCAT
1395888 TGTACATAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
63 2 0.03
64 28 0.45
65 32 0.52
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (64 bp):
TGTGCATCAATGCATAAAATAAATTCGATGTTTTAATAATACAGGAGTGCATCGATGCATGGTA
Found at i:1395906 original size:64 final size:63
Alignment explanation
Indices: 1395775--1395911 Score: 156
Period size: 64 Copynumber: 2.1 Consensus size: 63
1395765 ACAAATCTAC
*
1395775 TTCGATGTTTTAAAATAGCCAGAGTGCATCGATGCATGGCTTGTGCATCAGTGCATAAAATAAA
1 TTCGATGTTTTAAAATA-CCAGAGTGCATCGATGCATGGCTTGTGCATCAGTACATAAAATAAA
* *
1395839 TTCGATGTTTTAATAATA-CATGGAGTGCCTCGATGCATGG-TATGTGCAT-TGTACATAAAAGT
1 TTCGATGTTTTAA-AATACCA--GAGTGCATCGATGCATGGCT-TGTGCATCAGTACATAAAA-T
*
1395901 -TA
61 AAA
1395903 TTCGATGTT
1 TTCGATGTT
1395912 CAATTAAAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
63 2 0.03
64 33 0.52
65 29 0.45
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (63 bp):
TTCGATGTTTTAAAATACCAGAGTGCATCGATGCATGGCTTGTGCATCAGTACATAAAATAAA
Found at i:1396293 original size:12 final size:13
Alignment explanation
Indices: 1396260--1396293 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1396250 TAAGATTTTC
1396260 TTTGAAAATAATT
1 TTTGAAAATAATT
*
1396273 TTTGTAAATAA-T
1 TTTGAAAATAATT
1396285 TTTGAAAAT
1 TTTGAAAAT
1396294 TTATTCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (13 bp):
TTTGAAAATAATT
Found at i:1398068 original size:11 final size:12
Alignment explanation
Indices: 1398052--1398084 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1398042 TGGGCAAGAT
1398052 TTTGAAAAT-TA
1 TTTGAAAATATA
1398063 TTTGAAAATAATA
1 TTTGAAAAT-ATA
1398076 TTTGAAAAT
1 TTTGAAAAT
1398085 CATAATACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
13 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (12 bp):
TTTGAAAATATA
Found at i:1398548 original size:21 final size:21
Alignment explanation
Indices: 1398524--1398587 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 21
1398514 TCAGTGCATC
1398524 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* *
1398545 TTCAAATGGATGGATCGATGCACC
1 TTC--AT-GATGTATCGATGCACA
1398569 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
1398588 TTATGCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.39
22 2 0.06
23 2 0.06
24 17 0.47
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:1404492 original size:65 final size:64
Alignment explanation
Indices: 1404362--1404566 Score: 188
Period size: 65 Copynumber: 3.2 Consensus size: 64
1404352 TGACCAAGTA
* * *
1404362 CATCGATGCACTGGTGTGTGCATCGGTG-A-ACAAATCTACTTCGATGTTTTAA-AATAGC-CGG
1 CATCGATGCA-TGGT-AGTGCATCGGTGCATA-AAATC-AATTCGATGTTTTAATAATA-CAAGG
1404423 AGTG
61 AGTG
*
1404427 CATCGATGCATGGCTAGTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTG
1 CATCGATGCATGG-TAGTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACAAGGAGTG
* * * * * * * *
1404492 CATCGATGCATGGTATATGCATCAGTACGTAAAATCTATTCGAAG-TTCAATTAAAACAAGG-GT
1 CATCGATGCATGGTA-GTGCATCGGTGCATAAAATCAATTCGATGTTTTAA-TAATACAAGGAGT
1404555 G
64 G
1404556 CATCGATGCAT
1 CATCGATGCAT
1404567 TGATTTATGC
Statistics
Matches: 121, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
64 49 0.40
65 71 0.59
66 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (64 bp):
CATCGATGCATGGTAGTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACAAGGAGTG
Found at i:1406429 original size:38 final size:38
Alignment explanation
Indices: 1406378--1406454 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1406368 AATCTATCCT
1406378 TCTTATCATAAGAGAGATATCTCAGGGGCCCTAGATGA
1 TCTTATCATAAGAGAGATATCTCAGGGGCCCTAGATGA
1406416 TCTTATCATAAGAGAGATATCTCAGGGGCCCTAGATGA
1 TCTTATCATAAGAGAGATATCTCAGGGGCCCTAGATGA
1406454 T
1 T
1406455 TGAGATTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (38 bp):
TCTTATCATAAGAGAGATATCTCAGGGGCCCTAGATGA
Found at i:1406948 original size:14 final size:14
Alignment explanation
Indices: 1406929--1406968 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1406919 ATTTGATTTT
1406929 TAAATAATATTAAA
1 TAAATAATATTAAA
**
1406943 TAAATAATA-TAGT
1 TAAATAATATTAAA
1406956 TAAATAATATTAA
1 TAAATAATATTAA
1406969 GATTTGGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TAAATAATATTAAA
Found at i:1408448 original size:978 final size:970
Alignment explanation
Indices: 1406427--1411045 Score: 6102
Period size: 978 Copynumber: 4.7 Consensus size: 970
1406417 CTTATCATAA
* *
1406427 GAGAGATATCTCAGGGGCCCTAGATGATTGAGATTGAAAAAATGCATGGTCGTGCTTAAATGAGT
1 GAGAGATATCTCAAGGGCCCTCGATGATTGAGATTGAAAAAATGCATGGTCGTGCTTAAATGAGT
* * * *
1406492 TAATAGAGATCAATATCATTTATTTAATCAGTTCAATTGGGTATCGAGAAATTAAAAATAAAGCG
66 TGATAGAGATCAATATCATTTATTTAATCAGTTCAATTGGGTATCGAGAAATTGAAGATAGAGCG
* * * * * *
1406557 ATATAAGATTGAAATTTTCCATGTCTTATATTTTATCAAGAAAACATGAGATAAAAGAATTATGA
131 ATATAAGGTTGACATTTTCCATGTCTTATATTCTATCAAGATATCGTGAGATAAAAGAATTATGA
* * * *
1406622 CATAAGATGTATTAAGGTTGTATCATATCATGAGTTTTTCATTTAACTTGGGTGGTCATAACGTC
196 CATAAGATGTATTAAGGTTGTCTCATATCATGAGCTTTTCATTTAACTTGGGTAGTCATAATGTC
* *
1406687 TTGCTAGAGATTTGTATGATCAAATGTGATTTTATCTACTACAAAAGTTAACTGAACCTATAGGG
261 TTGCTAGAGACTTGTATGATCAAATGTGATTTTATCTACTACCAAAGTTAACTGAACCTATAGGG
* * * ** * *
1406752 TCGCACACCTAGAATAAATTAGAATGGTCGTACTTATTATTATAAATGATAATTTAAGACAGTAA
326 TCGTACACTTAGAATGAATTAGAATGGTCGTGGTTATTATTATAAATGATAATTTAAGATAATAA
* * * *
1406817 GATTGTTTTAAATTATATTATAAGATAGTATTTATTATTCAAATTTTAATCAGTTAAATTTATAT
391 GATTGTTTTAAATTATATTATAAGATATTATTTATTATTCAAATTTAAATAAGTTAAATTTGTAT
1406882 TCTTTTGATAGAATATTTTGTTTATTATTATTTCTTAATTTGATTTTTAAATAATATTAAATAAA
456 TCTTTTGATAGAATATTTTGTTTATTATTATTTCTTAATTTGA--TTTAAATAATATT-AATAAA
* * *
1406947 TAATATAGTTAAATAATATTAAGATTTGGATGAATTTGAATTTCTTGTCAAATAAGAAATTTGTT
518 TAATATAGTTAAATAATATCAAGATTTGGATGAATTTGAATTTCTTATCAGATAAGAAATTTGTT
* * *
1407012 AATATTTATTTAAGTGAGTTTTAGATAAATAATAATTATGTTAGAATTTAATTTAAAAGAGTTTT
583 ATTATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTTATAATTTAATTTAAAAGAGTTTT
*
1407077 AAATTAAATATGATTAAAAA-GGTAGGATTAATTAACCCTAATAAAGTC---ATATATATATGTG
648 AAATTAAATATGATTAAAAACAG-AGGATTAATTAACCCTAATAAAGTCATAATATATATATGTG
* * * * *
1407138 ATATATTATTAGGTTTAAAGGTCAATCTTCTACAGATATCCATAACCAAAAACTCACAAAAATAG
712 ATATATGATTAGGTTTAAAAGTTAATCTTCTACAGCTATCCATAACCAAAAACTCACAAAAACAG
* *
1407203 TTTTTA-AGGAAAACATATTAGAACTAGCATTATATTACCATTCGTTGTTCATTCGCGTGT-GAA
777 -TTTTAGAGAAAAACATATTAGAACTAGCATTATATTACCATTCGTTGTTCGTTCGCGTGTAG-A
* **
1407266 TACTTGTAGAGGGTGGTCGTCTATCCGAAAGGAAACACTTTAAAGATCTAAAGAGAACCAAAGAT
840 TACTTGTAGAGGGTGGTCGTCTTTCCGAAAGGCGACACTTTAAAGATCTAAAGAGAACCAAAGAT
* ** *
1407331 TATGGTAATAGCACGACTTTAATTTACAACAACTAGTATGATATGCATGAGATCCTAGGATTGCT
905 TAAGGTAATCCCACGACTTTATTTTACAACAACTAGTATGATATGCATGAGATCCTAGGATTGCT
1407396 -
970 C
* * *
1407396 GAAGAGATATCTTAGGGGCCCTCGATGATTGAGACTGAAAAAATGCATGGTCGTGCTTAAATGAG
1 G-AGAGATATCTCAAGGGCCCTCGATGATTGAGATTGAAAAAATGCATGGTCGTGCTTAAATGAG
*
1407461 TTGATAGAGATCAATATCATTTATTTAATCAGTTCAATTGGGTATCAAGAAATTGAAGATAGAGC
65 TTGATAGAGATCAATATCATTTATTTAATCAGTTCAATTGGGTATCGAGAAATTGAAGATAGAGC
**
1407526 GATATAAGGTTGACATTTTCCATGTCTTATATTCTATCAAGATATCGTGAGATAAAA-AATTACA
130 GATATAAGGTTGACATTTTCCATGTCTTATATTCTATCAAGATATCGTGAGATAAAAGAATTATG
* * *
1407590 ACAT-AGTTGTATTAAGGTTGTCTCATATAATGAGCTTTTCATTTAACTTGGATAGTCATAATGT
195 ACATAAGATGTATTAAGGTTGTCTCATATCATGAGCTTTTCATTTAACTTGGGTAGTCATAATGT
* * * **
1407654 CTTGTTAAAGACTTGTATGACCAAATGTGATTTTATCTACTACCAAAGTTAACTGAACCTATACT
260 CTTGCTAGAGACTTGTATGATCAAATGTGATTTTATCTACTACCAAAGTTAACTGAACCTATAGG
*
1407719 GTCGTACACTTAGAATGAATTAGAATGGTTGTGGTTATTATTATAAATGATAATTTAAGATAATA
325 GTCGTACACTTAGAATGAATTAGAATGGTCGTGGTTATTATTATAAATGATAATTTAAGATAATA
* * *
1407784 AGATTGTTTTAAATTATATTATAAGATATTACTTATTATTCAAATTTAAATAAGTTTAATTTTTA
390 AGATTGTTTTAAATTATATTATAAGATATTATTTATTATTCAAATTTAAATAAGTTAAATTTGTA
*
1407849 TCCTTTTGATAGAATATTTTGTTTATTATTATTTCTTAATTTGATATATAAATAATATTAATAAA
455 TTCTTTTGATAGAATATTTTGTTTATTATTATTTCTTAATTTGAT-T-TAAATAATATTAATAAA
* ** * * * *
1407914 TAATATAGCTACGTAATATCAAGATTTGAATGAATTTGAATTTCTAATCAAATATGAAATTTGTT
518 TAATATAGTTAAATAATATCAAGATTTGGATGAATTTGAATTTCTTATCAGATAAGAAATTTGTT
*
1407979 ATTATTTATTTAGGTGT-TTTTAGATAAATAATAATTATGTTATAATTTAATTTAAAAGAGTTTT
583 ATTATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTTATAATTTAATTTAAAAGAGTTTT
*
1408043 AAATTAAATATGATTAAAAACAGAGGATTAATTAACCCAAATAAAGTCATAAATATATATATGTG
648 AAATTAAATATGATTAAAAACAGAGGATTAATTAACCCTAATAAAGTCAT-AATATATATA----
* * * *
1408108 TGTGTGTGATATATGATTATGTTTAAAAGTTAATCTTCTACAGCTGTCCATAACCGAAAACTTAC
708 ----TGTGATATATGATTAGGTTTAAAAGTTAATCTTCTACAGCTATCCATAACCAAAAACTCAC
* *
1408173 AAAAACAGTTTTAGAGAAAAACATATTAGAACTAGCATTATATTACCATTCTTTGTTCGTTCGCA
769 AAAAACAGTTTTAGAGAAAAACATATTAGAACTAGCATTATATTACCATTCGTTGTTCGTTCGCG
* * *
1408238 TGTAGATACTTGTAGAGGGTGGTCATCTTTCCGAAATGCGACACTTTAAAGATCTAATGAGAACC
834 TGTAGATACTTGTAGAGGGTGGTCGTCTTTCCGAAAGGCGACACTTTAAAGATCTAAAGAGAACC
* * *
1408303 AAATATTAAGGTAATCCCACGATTTTATTTTACAACAACTAGTATAATATGCATGAGATCCTAGG
899 AAAGATTAAGGTAATCCCACGACTTTATTTTACAACAACTAGTATGATATGCATGAGATCCTAGG
1408368 ATTGCTC
964 ATTGCTC
* * * * * * *
1408375 GAGAGATATCTCAAGTGCCGTCGATGATTTAGACTGAAAAAATTCATGGTCGTTCGTAAATGAGT
1 GAGAGATATCTCAAGGGCCCTCGATGATTGAGATTGAAAAAATGCATGGTCGTGCTTAAATGAGT
* * * *
1408440 TGATAGAGATCAATATCATTTATTTAATCAGTTTAAATGGGTATCGAGATATTGAAGATATAGCG
66 TGATAGAGATCAATATCATTTATTTAATCAGTTCAATTGGGTATCGAGAAATTGAAGATAGAGCG
* * *
1408505 ATATAAAGTTGACATTTTCCAAGTCTTATATTCTATCAATATATCGTGAGATAGAAA-AATTATG
131 ATATAAGGTTGACATTTTCCATGTCTTATATTCTATCAAGATATCGTGAGATA-AAAGAATTATG
*
1408569 ACATAAGATGTATTAAGGTTGTCTCATATCATGAGCTTTTTATTTAACTTGGGTAGTCATAATGT
195 ACATAAGATGTATTAAGGTTGTCTCATATCATGAGCTTTTCATTTAACTTGGGTAGTCATAATGT
* * *
1408634 CTTGCT-GAAAGCTTGTATAATCAAATGTGATTTTATCTACTACCAAAGTCAACTGAACCTATAG
260 CTTGCTAGAGA-CTTGTATGATCAAATGTGATTTTATCTACTACCAAAGTTAACTGAACCTATAG
* * * * * *
1408698 GGTCGTACACTTAGAATGAATTAAAATGATCGTGGTTATTTTTACAAATAATAATTTAAAATAAT
324 GGTCGTACACTTAGAATGAATTAGAATGGTCGTGGTTATTATTATAAATGATAATTTAAGATAAT
* * *
1408763 AAGATT-TTTT-AATTATATTATAAGATATTGTTTATTCTTCAAATTTAAAAAAGTTAAATTTGT
389 AAGATTGTTTTAAATTATATTATAAGATATTATTTATTATTCAAATTTAAATAAGTTAAATTTGT
*
1408826 ATTCTTTTTTATAGAATATTTTGTTTATTATTATTTCTTAATTTGATTT--ATAA-ATTAATAAA
454 ATTC-TTTTGATAGAATATTTTGTTTATTATTATTTCTTAATTTGATTTAAATAATATTAATAAA
* * *
1408888 TAATATAGTTAATTAATATCAAGATTTGGATGAATTTGAATTTCATATCAGATATGAAATTTGTT
518 TAATATAGTTAAATAATATCAAGATTTGGATGAATTTGAATTTCTTATCAGATAAGAAATTTGTT
* * *
1408953 ATTATTTATTTTAGTGTGTTTTAGATAACTAATAATTATGTTATAATTTAATTGAAAAGAGTTTT
583 ATTATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTTATAATTTAATTTAAAAGAGTTTT
1409018 AAATTAAATATGATTAAAAACAGAGGATTAATTAACCCTAATACCCTAATAAAGTCATATATATA
648 AAATTAAATATGATTAAAAACAGAGGATTAA-T-----T-A-ACCCTAATAAAGTCATA-ATATA
* * ** * * * * * * *
1409083 TATATAT-ATATATATATATATATATTATATATGTGTGCATGTGTGTGATA--TAT-GATTAGGT
704 TATATGTGATATAT-GAT-TAGGT-TTA-A-AAGT-T-AATCT-TCT-ACAGCTATCCA-TA--A
** * ** * * * * *
1409144 TTAAAGGTTAATCTTCTACAGCTATCCA-TATCTAAAAACTCACAAAAACAGTTTTTGAAAAATC
757 CCAAA----AA-C-TC-ACA--AAAACAGT-T-T---TA--GAGAAAAACA--TATT--AGAA-C
* * * * * * *
1409208 GTATTAGAACTAGCATTA-TATTACCATTCGTTGTTCGTTCGCGTGTAGATACTTGCAGTGGGTG
801 ----TAGCATTA-TATTACCATT--CGTT-G---TTCGTTCGCGTGTAGATACTTGTAGAGGGTG
* *
1409272 GTCGTCTTTCCGAAAGGC-ATCACTTTAAATATGTAAAGAGAACCAAAGATTAAGGTAATCCCAC
855 GTCGTCTTTCCGAAAGGCGA-CACTTTAAAGATCTAAAGAGAACCAAAGATTAAGGTAATCCCAC
* *
1409336 GACTTTATTTTACTACAACTAGTATGATATGCATGAGATCCAAGGATTGCTC
919 GACTTTATTTTACAACAACTAGTATGATATGCATGAGATCCTAGGATTGCTC
* * *
1409388 GAGAGATATCTCAAGGGCCCTCGTTGATTGAGATTTAAAAAATGCATGGTCGTGCTTAAATGATT
1 GAGAGATATCTCAAGGGCCCTCGATGATTGAGATTGAAAAAATGCATGGTCGTGCTTAAATGAGT
* **
1409453 TGATAGAGATCAATATCATTTATTTAATAAGTTCAATTGGGTAT-GAGAAATTGAAGATAGAAAG
66 TGATAGAGATCAATATCATTTATTTAATCAGTTCAATTGGGTATCGAGAAATTGAAGATAGAGCG
*
1409517 ATATAAGGTTGACGTTTTCCATGTCTTATATTCTATCAAGATATCGTGAGATAAAAGAATTATGA
131 ATATAAGGTTGACATTTTCCATGTCTTATATTCTATCAAGATATCGTGAGATAAAAGAATTATGA
1409582 CATAAGATGTATTAAGGTTGTCTCA-ATCATGAGCTTTTCATTTAACTTGGGTAGTCATAATGTC
196 CATAAGATGTATTAAGGTTGTCTCATATCATGAGCTTTTCATTTAACTTGGGTAGTCATAATGTC
*
1409646 TTGCTAGAGACTTGTATGATCAAATGTGATTTTATTTACTACCAAAGTTAACTGAACCTATAGGG
261 TTGCTAGAGACTTGTATGATCAAATGTGATTTTATCTACTACCAAAGTTAACTGAACCTATAGGG
* *
1409711 TCGTACACTTAGAATGAATTAGAATGGTCGTGATTATTATTATAAATGATAACTTAAGATAATAA
326 TCGTACACTTAGAATGAATTAGAATGGTCGTGGTTATTATTATAAATGATAATTTAAGATAATAA
* * * * *
1409776 AATTGTTTTAAATTATATTATAAGTTATTATTTATTATTCTAGTTTAAATAAGTTAAATTTTTAT
391 GATTGTTTTAAATTATATTATAAGATATTATTTATTATTCAAATTTAAATAAGTTAAATTTGTAT
* * *
1409841 TCTTTTGATATAATATTTTGTTTATTAATATTTTTTAATTTGATTT---T--TA--AATAAATAA
456 TCTTTTGATAGAATATTTTGTTTATTATTATTTCTTAATTTGATTTAAATAATATTAATAAATAA
* * *
1409899 TATAGTTAAATAATATCAAGAATTGGATGAATTTGAATTTATTATCAGATAGGAAATTTGTTATT
521 TATAGTTAAATAATATCAAGATTTGGATGAATTTGAATTTCTTATCAGATAAGAAATTTGTTATT
*
1409964 ATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTTATAATTTAATTTAAAAGATTTTTAAA
586 ATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTTATAATTTAATTTAAAAGAGTTTTAAA
* *
1410029 TTAAATATGATTAAAAACCGAGGATTAATTAACTCTAATAAAGTC-----ATATATATGTGATAT
651 TTAAATATGATTAAAAACAGAGGATTAATTAACCCTAATAAAGTCATAATATATATATGTGATAT
* * *
1410089 ATGATTAGGTTT-AAAGGTATATCTTCTACAGCTATCCATAACCAAAAACTTACAAAAATAGTGT
716 ATGATTAGGTTTAAAAGTTA-ATCTTCTACAGCTATCCATAACCAAAAACTCACAAAAACAGT-T
* * ** *
1410153 TT-GAGAAAAACGA-ATTAGAACTAGCATTATATTAACATTCGTTGTTTGTTCGTTTGTGGATAC
779 TTAGAGAAAAAC-ATATTAGAACTAGCATTATATTACCATTCGTTGTTCGTTCGCGTGTAGATAC
* *
1410216 TTGTAGAGGGTGGTCGTCTTTCCGAAAGGTGGCACTTTAAAGATCTAAAGAGAACCAAAGATTAA
843 TTGTAGAGGGTGGTCGTCTTTCCGAAAGGCGACACTTTAAAGATCTAAAGAGAACCAAAGATTAA
* * * *
1410281 GGTACTCCCACGACTTTTTTTTTACAACAACTAGTATGATATACATGAGTTCCTAGGATTGCTC
908 GGTAATCCCACGAC-TTTATTTTACAACAACTAGTATGATATGCATGAGATCCTAGGATTGCTC
* * * *
1410345 AAGAGATATCTC-AGGGTCCCTCGATGATTGTGAATTAAAAAAATGCATGGTCGTGCTTAAATTA
1 GAGAGATATCTCAAGGG-CCCTCGATGATTGAG-ATTGAAAAAATGCATGGTCGTGCTTAAATGA
* * * * * *
1410409 GATGATAGAGATCAAAATCATTTAATTAAACATTTCAATTGTGTATCGAGAAATTGAAGATAGAG
64 GTTGATAGAGATCAATATCATTTATTTAATCAGTTCAATTGGGTATCGAGAAATTGAAGATAGAG
* * *
1410474 CGATATATGGTTGACATTTTTCATGTCTTATATTCTATCAAGATATCGCGAGATAAAAGAATTAT
129 CGATATAAGGTTGACATTTTCCATGTCTTATATTCTATCAAGATATCGTGAGATAAAAGAATTAT
* *
1410539 GACATAAGATGTATTAAGGTTGTCTCATATCATGATCTTTTCAATTAACTTGGGTAGTCATAATG
194 GACATAAGATGTATTAAGGTTGTCTCATATCATGAGCTTTTCATTTAACTTGGGTAGTCATAATG
* * *
1410604 TCTTGCTAGAGTCTTGTATGATCAAATGTGATTTTATCTACTACCAAAGTTATCTGAACCAATAG
259 TCTTGCTAGAGACTTGTATGATCAAATGTGATTTTATCTACTACCAAAGTTAACTGAACCTATAG
** * * * *
1410669 GGTTATACACTTAGAATGAATTACAATAGTCTTGGTTATTATTATAAATTATAATTTAAGATAAT
324 GGTCGTACACTTAGAATGAATTAGAATGGTCGTGGTTATTATTATAAATGATAATTTAAGATAAT
**
1410734 AAGATTGTTTTAAATTATATTATAAGATATTATTTATTATTTGAATTTAAATAAGTTAAATTTGT
389 AAGATTGTTTTAAATTATATTATAAGATATTATTTATTATTCAAATTTAAATAAGTTAAATTTGT
* * *
1410799 ATTCTTTTGACAGAATATTTTGTTTATCATTATTTCTTAATTTTATTTATAAATAATATTAAATA
454 ATTCTTTTGATAGAATATTTTGTTTATTATTATTTCTTAATTTGA-TT-TAAATAATATT-AATA
*
1410864 AATAATATAGTTAAATAATATCAAGATTTGGATGAATTTGAATTTCTTATTAGATAAGAAATTTG
516 AATAATATAGTTAAATAATATCAAGATTTGGATGAATTTGAATTTCTTATCAGATAAGAAATTTG
* ***
1410929 TTATTATTTATTTAAGTGTGTTTTAGGTAAATAATAATTATGTTATAATTTAATTTAAAATCTTT
581 TTATTATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTTATAATTTAATTTAAAAGAGTT
* **
1410994 TTAAATTAAATGTGATT-AAAATGGAGGATTAATTAACCCTAATAAAGTCATA
646 TTAAATTAAATATGATTAAAAACAGAGGATTAATTAACCCTAATAAAGTCATA
1411046 TATTGTTATT
Statistics
Matches: 3198, Mismatches: 342, Indels: 217
0.85 0.09 0.06
Matches are distributed among these distances:
956 90 0.03
957 68 0.02
958 67 0.02
959 105 0.03
960 254 0.08
961 6 0.00
962 10 0.00
965 1 0.00
966 92 0.03
967 84 0.03
968 281 0.09
969 41 0.01
970 323 0.10
971 7 0.00
972 1 0.00
974 88 0.03
975 84 0.03
976 5 0.00
977 12 0.00
978 448 0.14
979 67 0.02
980 176 0.06
981 9 0.00
982 6 0.00
983 28 0.01
986 5 0.00
987 4 0.00
988 10 0.00
989 4 0.00
990 4 0.00
991 1 0.00
992 6 0.00
993 4 0.00
994 11 0.00
995 6 0.00
996 1 0.00
998 8 0.00
1000 16 0.01
1001 1 0.00
1002 4 0.00
1003 1 0.00
1007 10 0.00
1008 161 0.05
1009 3 0.00
1010 2 0.00
1011 159 0.05
1012 146 0.05
1013 278 0.09
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (970 bp):
GAGAGATATCTCAAGGGCCCTCGATGATTGAGATTGAAAAAATGCATGGTCGTGCTTAAATGAGT
TGATAGAGATCAATATCATTTATTTAATCAGTTCAATTGGGTATCGAGAAATTGAAGATAGAGCG
ATATAAGGTTGACATTTTCCATGTCTTATATTCTATCAAGATATCGTGAGATAAAAGAATTATGA
CATAAGATGTATTAAGGTTGTCTCATATCATGAGCTTTTCATTTAACTTGGGTAGTCATAATGTC
TTGCTAGAGACTTGTATGATCAAATGTGATTTTATCTACTACCAAAGTTAACTGAACCTATAGGG
TCGTACACTTAGAATGAATTAGAATGGTCGTGGTTATTATTATAAATGATAATTTAAGATAATAA
GATTGTTTTAAATTATATTATAAGATATTATTTATTATTCAAATTTAAATAAGTTAAATTTGTAT
TCTTTTGATAGAATATTTTGTTTATTATTATTTCTTAATTTGATTTAAATAATATTAATAAATAA
TATAGTTAAATAATATCAAGATTTGGATGAATTTGAATTTCTTATCAGATAAGAAATTTGTTATT
ATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTTATAATTTAATTTAAAAGAGTTTTAAA
TTAAATATGATTAAAAACAGAGGATTAATTAACCCTAATAAAGTCATAATATATATATGTGATAT
ATGATTAGGTTTAAAAGTTAATCTTCTACAGCTATCCATAACCAAAAACTCACAAAAACAGTTTT
AGAGAAAAACATATTAGAACTAGCATTATATTACCATTCGTTGTTCGTTCGCGTGTAGATACTTG
TAGAGGGTGGTCGTCTTTCCGAAAGGCGACACTTTAAAGATCTAAAGAGAACCAAAGATTAAGGT
AATCCCACGACTTTATTTTACAACAACTAGTATGATATGCATGAGATCCTAGGATTGCTC
Found at i:1409081 original size:2 final size:2
Alignment explanation
Indices: 1409074--1409114 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1409064 TAATAAAGTC
1409074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
1409115 GTGTGCATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1410866 original size:14 final size:14
Alignment explanation
Indices: 1410847--1410884 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1410837 AATTTTATTT
1410847 ATAAATAATATTAA
1 ATAAATAATATTAA
*
1410861 ATAAATAATA-TAG
1 ATAAATAATATTAA
*
1410874 TTAAATAATAT
1 ATAAATAATAT
1410885 CAAGATTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
ATAAATAATATTAA
Found at i:1411054 original size:122 final size:122
Alignment explanation
Indices: 1410926--1411170 Score: 402
Period size: 122 Copynumber: 2.0 Consensus size: 122
1410916 GATAAGAAAT
* * *
1410926 TTGTTATTATTTATTTAAGTGTGTTTTAGGTAAATAATAATTATGTTATAATTTAATTTAAAATC
1 TTGTTATTATTTATTTAAGTGTGTTTTAGATAAATAATAATTATG-TATAAATTAATTTAAAAGC
* * * *
1410991 TTTTTAAATTAAATGTGATT-AAAATGGAGGATTAATTAACCCTAATAAAGTCATATA
65 GTTTTAAAATAAATATGATTAAAAATGGAGGATTAATGAACCCTAATAAAGTCATATA
1411048 TTGTTATTATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTATAAATTAATTTAAAAGCG
1 TTGTTATTATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTATAAATTAATTTAAAAGCG
*
1411113 TTTTAAAATAAATATGATTAAAAATGGAGTATTAATGAACCCTAATAAAGTCATATA
66 TTTTAAAATAAATATGATTAAAAATGGAGGATTAATGAACCCTAATAAAGTCATATA
1411170 T
1 T
1411171 ATATATGTGT
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
121 34 0.30
122 80 0.70
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (122 bp):
TTGTTATTATTTATTTAAGTGTGTTTTAGATAAATAATAATTATGTATAAATTAATTTAAAAGCG
TTTTAAAATAAATATGATTAAAAATGGAGGATTAATGAACCCTAATAAAGTCATATA
Found at i:1411953 original size:14 final size:14
Alignment explanation
Indices: 1411934--1411971 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1411924 AATTTGATTT
1411934 ATAAATAATATTAA
1 ATAAATAATATTAA
*
1411948 ATAAATAATA-TAG
1 ATAAATAATATTAA
*
1411961 TTAAATAATAT
1 ATAAATAATAT
1411972 CAAGATTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
ATAAATAATATTAA
Found at i:1412412 original size:13 final size:13
Alignment explanation
Indices: 1412394--1412424 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1412384 GCCATAAATC
*
1412394 TATGACGCACATT
1 TATGACACACATT
1412407 TATGACACACATT
1 TATGACACACATT
1412420 TATGA
1 TATGA
1412425 TGCTCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (13 bp):
TATGACACACATT
Found at i:1412485 original size:15 final size:15
Alignment explanation
Indices: 1412467--1412505 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1412457 AAGCCCCCGT
*
1412467 CATAAATTTGTTTGA
1 CATAAATTTGTGTGA
* *
1412482 CATACATTTGTGTGT
1 CATAAATTTGTGTGA
1412497 CATAAATTT
1 CATAAATTT
1412506 ATGACACGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (15 bp):
CATAAATTTGTGTGA
Found at i:1412612 original size:2 final size:2
Alignment explanation
Indices: 1412605--1412639 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1412595 CGTAAATTAT
* *
1412605 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1412640 TGAAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1414562 original size:16 final size:16
Alignment explanation
Indices: 1414541--1414601 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
1414531 TAATAAATAA
1414541 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1414557 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1414573 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1414589 ACGAACATAAACG
1 ACGAACATAAACG
1414602 TTGGAGACCC
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:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1415364 original size:14 final size:14
Alignment explanation
Indices: 1415347--1415407 Score: 104
Period size: 14 Copynumber: 4.4 Consensus size: 14
1415337 GAATGAACAT
*
1415347 AAACGAACATAATC
1 AAACGAACATAACC
1415361 AAACGAACATAACC
1 AAACGAACATAACC
1415375 AAACGAACATAACC
1 AAACGAACATAACC
1415389 AAACGAACATAACC
1 AAACGAACATAACC
*
1415403 GAACG
1 AAACG
1415408 TTCATGAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 45 1.00
ACGTcount: A:0.56, C:0.26, G:0.10, T:0.08
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:1418471 original size:192 final size:192
Alignment explanation
Indices: 1418121--1418472 Score: 470
Period size: 192 Copynumber: 1.8 Consensus size: 192
1418111 TTGCTACAAT
** * *
1418121 ATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGACAATATAAATTATCAATAAC
1 ATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCAGTAACAATATAAATCATCAATAAC
** * *
1418186 GAAATCTTATTTAATTTAGTGACGTAATCAACTGTCATAGAATATAAATTATAAAGTGACATTAT
66 GAAATCTTACATAATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCGACATTAT
* ** *
1418251 CCATAAACGTCATTTATAATATTATTAGGTAACATTTATATTATGTCACTAAAAATATGACA
131 ACATAAACGTCATCCATAATAATATTAGGTAACATTTATATTATGTCACTAAAAATATGACA
* * *
1418313 ATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTATCAGTAACGATATAAATCATCAATAAC
1 ATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCAGTAACAATATAAATCATCAATAAC
* * ** * * * *
1418378 GAAATTTTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGCGACGTTAT
66 GAAATCTTACATAATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCGACATTAT
* * *
1418443 ATATAAATGTCATCCATGATAATATTAGGT
131 ACATAAACGTCATCCATAATAATATTAGGT
1418473 GACGATACAA
Statistics
Matches: 134, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
192 134 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (192 bp):
ATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCAGTAACAATATAAATCATCAATAAC
GAAATCTTACATAATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCGACATTAT
ACATAAACGTCATCCATAATAATATTAGGTAACATTTATATTATGTCACTAAAAATATGACA
Found at i:1418506 original size:192 final size:192
Alignment explanation
Indices: 1418121--1418525 Score: 461
Period size: 192 Copynumber: 2.1 Consensus size: 192
1418111 TTGCTACAAT
** * *
1418121 ATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGACAATATAAATTATCAATAAC
1 ATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCAGTAACAATATAAATCATCAATAAC
** * *
1418186 GAAATCTTATTTAATTTAGTGACGTAATCAACTGTCATAGAATATAAATTATAAAGTGACATTAT
66 GAAATCTTACATAATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCGACATTAT
* ** * ** * *
1418251 CCATAAACGTCATTTATAATATTATTAGGTAACATTTATATTATGTCACTAAAAATATGACA
131 ACATAAACGTCATCCATAATAATATTAGGTAACATACATACTACGTCACTAAAAATATGACA
* * *
1418313 ATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTATCAGTAACGATATAAATCATCAATAAC
1 ATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCAGTAACAATATAAATCATCAATAAC
* * ** * * * *
1418378 GAAATTTTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGCGACGTTAT
66 GAAATCTTACATAATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCGACATTAT
* * * * * * *
1418443 ATATAAATGTCATCCATGATAATATTAGGTGACGATACA-ACTACGTTACTAACAATGTGACA
131 ACATAAACGTCATCCATAATAATATTAGGTAAC-ATACATACTACGTCACTAAAAATATGACA
*
1418505 ATTTTCTTTTCGTCACATATA
1 A-TCTC-TTTCGTCACATATA
1418526 CAATGAAGTT
Statistics
Matches: 175, Mismatches: 35, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
192 155 0.89
193 6 0.03
194 14 0.08
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (192 bp):
ATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCAGTAACAATATAAATCATCAATAAC
GAAATCTTACATAATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCGACATTAT
ACATAAACGTCATCCATAATAATATTAGGTAACATACATACTACGTCACTAAAAATATGACA
Found at i:1419940 original size:15 final size:15
Alignment explanation
Indices: 1419922--1419955 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1419912 TATTTATGTT
*
1419922 ACTTATGCATCAATA
1 ACTTACGCATCAATA
1419937 ACTTACGCATCAATA
1 ACTTACGCATCAATA
1419952 ACTT
1 ACTT
1419956 GCTTCAACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (15 bp):
ACTTACGCATCAATA
Found at i:1420662 original size:39 final size:40
Alignment explanation
Indices: 1420603--1420687 Score: 145
Period size: 39 Copynumber: 2.1 Consensus size: 40
1420593 TTTCTTTCTT
1420603 TTTTCTCCTCTTCGGTGTCCCTTCTCCTTTCACCTCTTCC
1 TTTTCTCCTCTTCGGTGTCCCTTCTCCTTTCACCTCTTCC
* *
1420643 TTTT-TCCTTTTCGGTGTCCCTTCTCCTTTCCCCTCTTCC
1 TTTTCTCCTCTTCGGTGTCCCTTCTCCTTTCACCTCTTCC
1420682 TTTTCT
1 TTTTCT
1420688 TTCACTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 37 0.88
40 5 0.12
ACGTcount: A:0.01, C:0.40, G:0.07, T:0.52
Consensus pattern (40 bp):
TTTTCTCCTCTTCGGTGTCCCTTCTCCTTTCACCTCTTCC
Found at i:1420710 original size:51 final size:50
Alignment explanation
Indices: 1420642--1420737 Score: 156
Period size: 51 Copynumber: 1.9 Consensus size: 50
1420632 TCACCTCTTC
*
1420642 CTTTTTCCTTTTCGGTGTCCCTTCTCCTTTCCCCTCTTCCTTTTCTTTCA
1 CTTTTTCCTCTTCGGTGTCCCTTCTCCTTTCCCCTCTTCCTTTTCTTTCA
* *
1420692 CTTTTTCCATCTTCGGTGTCCCTTCTCCTTTCTCCTCTTCTTTTTC
1 CTTTTTCC-TCTTCGGTGTCCCTTCTCCTTTCCCCTCTTCCTTTTC
1420738 AACAAGTTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 8 0.19
51 34 0.81
ACGTcount: A:0.02, C:0.38, G:0.06, T:0.54
Consensus pattern (50 bp):
CTTTTTCCTCTTCGGTGTCCCTTCTCCTTTCCCCTCTTCCTTTTCTTTCA
Found at i:1420730 original size:26 final size:26
Alignment explanation
Indices: 1420640--1420731 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 26
1420630 TTTCACCTCT
* *
1420640 TCCTTTTTCCTTTTCGGTGTCCCTTC
1 TCCTTTCTCCTCTTCGGTGTCCCTTC
* * **
1420666 TCCTTTCCCCTCTTC-CT-TTTCTT-
1 TCCTTTCTCCTCTTCGGTGTCCCTTC
*
1420689 TCACTTTTTCCATCTTCGGTGTCCCTTC
1 TC-CTTTCTCC-TCTTCGGTGTCCCTTC
1420717 TCCTTTCTCCTCTTC
1 TCCTTTCTCCTCTTC
1420732 TTTTTCAACA
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
23 2 0.04
24 10 0.20
25 6 0.12
26 18 0.37
27 11 0.22
28 2 0.04
ACGTcount: A:0.02, C:0.39, G:0.07, T:0.52
Consensus pattern (26 bp):
TCCTTTCTCCTCTTCGGTGTCCCTTC
Found at i:1424539 original size:15 final size:15
Alignment explanation
Indices: 1424509--1424550 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1424499 GATGCTTTCT
*
1424509 TTTTCTTTCTTTGACG
1 TTTTC-TTCTTAGACG
1424525 TTTTCTTCTTAGACG
1 TTTTCTTCTTAGACG
*
1424540 TTGTCTTCTTA
1 TTTTCTTCTTA
1424551 CCCTATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.10, C:0.19, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTTCTTCTTAGACG
Found at i:1430254 original size:60 final size:60
Alignment explanation
Indices: 1430096--1430273 Score: 182
Period size: 60 Copynumber: 3.0 Consensus size: 60
1430086 ATGAATTTGG
* * * * * * * *
1430096 GGATAAAATTGAAAGA-TCTAAAAGTTTAGGGACCAATTTAAAATTAGATTCATAGTTT-G
1 GGATAAAATTCAAATATTC-AAAAATTTAAGGACTAATTTAAAATAAGAGTCATAGTTTAA
* * * *
1430155 GGATGAAATTCAAATGTTCAAAAGTTTAAGGACTGATTTAAAATAAGAGTCATAGTTTAA
1 GGATAAAATTCAAATATTCAAAAATTTAAGGACTAATTTAAAATAAGAGTCATAGTTTAA
* * *
1430215 GGATAAAATT-AGAATATTTAAAAATTTAAGGATTAATTTAAAATAAAAGTCATAGTTTA
1 GGATAAAATTCA-AATATTCAAAAATTTAAGGACTAATTTAAAATAAGAGTCATAGTTTA
1430274 CGGACATGTG
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
59 47 0.47
60 52 0.53
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (60 bp):
GGATAAAATTCAAATATTCAAAAATTTAAGGACTAATTTAAAATAAGAGTCATAGTTTAA
Found at i:1430358 original size:21 final size:22
Alignment explanation
Indices: 1430319--1430362 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1430309 TTTACTTTGG
1430319 AACTACTAAAATAACTTTACAA
1 AACTACTAAAATAACTTTACAA
* *
1430341 AACTATTAAATTAA-TTTACAA
1 AACTACTAAAATAACTTTACAA
1430362 A
1 A
1430363 TTATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
AACTACTAAAATAACTTTACAA
Found at i:1430892 original size:2 final size:2
Alignment explanation
Indices: 1430887--1430923 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1430877 TATCAATAAT
1430887 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
1430924 TTGACTTATG
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:1431035 original size:31 final size:31
Alignment explanation
Indices: 1430996--1431065 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
1430986 TATTTCATCG
1430996 GATATTGATCT-GACCCAAAAATCAATTAATCT
1 GATATTGAT-TAGACCC-AAAATCAATTAATCT
* * *
1431028 GAT-TTGATTAGATCCGAAATCAATTGATCT
1 GATATTGATTAGACCCAAAATCAATTAATCT
1431058 GATATTGA
1 GATATTGA
1431066 CTCGATCCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 17 0.52
31 13 0.39
32 3 0.09
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (31 bp):
GATATTGATTAGACCCAAAATCAATTAATCT
Found at i:1431205 original size:64 final size:64
Alignment explanation
Indices: 1431084--1431209 Score: 148
Period size: 64 Copynumber: 2.0 Consensus size: 64
1431074 TATACCTGAA
* *
1431084 CCGACCCAACTTACTATAGGCCCGAATAAAACCAAAACCTGAAATGACCCAATCCGACCCGATC
1 CCGACCCAACTTACTATAGACCCGAATAAAACCAAAACCTGAAATGACCCAACCCGACCCGATC
* ** * * *
1431148 CCGACCCGACTTACTATAGACTTGAATAAAATCGAAA-CTCGAAATGA-CTAGACCCGACCCGA
1 CCGACCCAACTTACTATAGACCCGAATAAAACCAAAACCT-GAAATGACCCA-ACCCGACCCGA
1431210 ACTTGACCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
63 4 0.08
64 48 0.92
ACGTcount: A:0.37, C:0.33, G:0.14, T:0.16
Consensus pattern (64 bp):
CCGACCCAACTTACTATAGACCCGAATAAAACCAAAACCTGAAATGACCCAACCCGACCCGATC
Found at i:1432435 original size:11 final size:11
Alignment explanation
Indices: 1432419--1432445 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1432409 GACATTTACA
1432419 TATTTATATTG
1 TATTTATATTG
1432430 TATTTATATTG
1 TATTTATATTG
1432441 TATTT
1 TATTT
1432446 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
TATTTATATTG
Found at i:1434214 original size:20 final size:20
Alignment explanation
Indices: 1434177--1434213 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1434167 TACTGAGTTT
1434177 GTATATAAATAATTTTTTGA
1 GTATATAAATAATTTTTTGA
*
1434197 GTATAT-AATTATTTTTT
1 GTATATAAATAATTTTTT
1434214 TACACTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (20 bp):
GTATATAAATAATTTTTTGA
Found at i:1436772 original size:25 final size:25
Alignment explanation
Indices: 1436691--1436774 Score: 62
Period size: 29 Copynumber: 3.2 Consensus size: 25
1436681 GAGATGTATA
*
1436691 TAATTTATTTAAATATA-TAATATTAT
1 TAATTT-TATAAATATATTAAT-TTAT
* ** *
1436717 TTATGATATAAATATATTATTTTAGGCAT
1 TAATTTTATAAATATATTAATTT----AT
1436746 TAATTTTATAAATATATTAATTTAT
1 TAATTTTATAAATATATTAATTTAT
1436771 TAAT
1 TAAT
1436775 GTCTTTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
25 17 0.39
26 6 0.14
29 21 0.48
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (25 bp):
TAATTTTATAAATATATTAATTTAT
Found at i:1437177 original size:2 final size:2
Alignment explanation
Indices: 1437170--1437203 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1437160 ATAATATCTA
1437170 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
1437204 TGTCACGGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1439685 original size:117 final size:117
Alignment explanation
Indices: 1439440--1439688 Score: 390
Period size: 117 Copynumber: 2.1 Consensus size: 117
1439430 TGCCCAAACA
**
1439440 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGAAAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
* * * *
1439505 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGATTGCACCAATG
66 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
** *
1439557 AAGCAGGGCTCGGTGAAAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGAAAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
* *
1439622 TTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
66 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
*
1439674 AAGTAAAGCTCGGTG
1 AAGCAAAGCTCGGTG
1439689 CGAAAGCCAA
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.16
Consensus pattern (117 bp):
AAGCAAAGCTCGGTGAAAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
Found at i:1439717 original size:117 final size:116
Alignment explanation
Indices: 1439440--1439751 Score: 351
Period size: 117 Copynumber: 2.7 Consensus size: 116
1439430 TGCCCAAACA
** * * *
1439440 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGAAAATGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* * * *
1439505 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGATTGCACCAATG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
** * *
1439557 AAGCAGGGCTCGGTGAAAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGAAAATGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* *
1439622 TTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
* * * *
1439674 AAGTAAAGCTCGGTGCGAAA-GCCAAG-GGCCAAGCTGAA-GAGCCGAGGGTAAATAAGCGAGAG
1 AAGCAAAGCTCGGTG-AAAATG-CAAGTGGCCAAGC--AACAAGCCGAGGGTAAAGAAGCGAGAG
* * *
1439736 CAACTGGAGTGTTTCC
62 CCATTGAAGTGTTTCC
1439752 GGTGCAAAGG
Statistics
Matches: 169, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
117 161 0.95
118 6 0.04
119 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.15
Consensus pattern (116 bp):
AAGCAAAGCTCGGTGAAAATGCAAGTGGCCAAGCAACAAGCCGAGGGTAAAGAAGCGAGAGCCAT
TGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
Found at i:1443864 original size:17 final size:17
Alignment explanation
Indices: 1443832--1443879 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
1443822 CTTCATTGCA
* *
1443832 TTTAATAAACGAACTAG
1 TTTAATGAATGAACTAG
*
1443849 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
1443866 TTTAATGAAT-AACT
1 TTTAATGAATGAACT
1443880 TCCCTAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:1448601 original size:16 final size:16
Alignment explanation
Indices: 1448577--1448608 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1448567 AATTAGTAAT
1448577 AAAAAAAAAACCTCAC
1 AAAAAAAAAACCTCAC
*
1448593 AAAAGAAAAACCTCAC
1 AAAAAAAAAACCTCAC
1448609 CCAACACTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.25, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAACCTCAC
Found at i:1449789 original size:2 final size:2
Alignment explanation
Indices: 1449782--1449874 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
1449772 CAAAACTTAG
1449782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1449824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1449866 TA TA TA TA T
1 TA TA TA TA T
1449875 CCCCCTATTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1450315 original size:20 final size:20
Alignment explanation
Indices: 1450273--1450315 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1450263 AAATAAAAAT
* *
1450273 AAAAATAAAATACACAGTTA
1 AAAAATAAAATACAAAGTAA
1450293 AAAAATAAAA-ACAAATGTAA
1 AAAAATAAAATACAAA-GTAA
1450313 AAA
1 AAA
1450316 TAACCTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAAATAAAATACAAAGTAA
Found at i:1450523 original size:11 final size:11
Alignment explanation
Indices: 1450503--1450536 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1450493 ACTGGTTTAG
1450503 TGGA-AGCTGC
1 TGGAGAGCTGC
1450513 TGGAGAGCTGC
1 TGGAGAGCTGC
*
1450524 TGGAGTGCTGC
1 TGGAGAGCTGC
1450535 TG
1 TG
1450537 AAACGTGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.15, C:0.18, G:0.44, T:0.24
Consensus pattern (11 bp):
TGGAGAGCTGC
Found at i:1451191 original size:123 final size:123
Alignment explanation
Indices: 1450988--1453901 Score: 3865
Period size: 123 Copynumber: 23.7 Consensus size: 123
1450978 GAATCTAGCT
*
1450988 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTTTTCCTCTTCAGATGAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
** * * * * *
1451053 CGAACTCCTTCTGGAAATGTTGATAATACTCTATCTTCTTCTGTGATAGAGTCAAGAA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * *
1451111 AAAGGTTGAGTAAGTTCTTTAGATTATGAACTTCTTCTTCCTCTTCAGATTAGTTATTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * *
1451176 CGAACTCCTTTTGGAAATATTGATACTTCTCTATCTCCTTCTGCGATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * * *
1451234 AAAGGTTGAATAAATTATTCAGAATATGAATTTCTT-TCTCCTCTTCAGATGAGTTCTTTTTATT
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT-TCCTCTTCAGATGAGTTCTTCTTATT
* * *
1451298 ACGAACTCCTTCTAGAAATGTTGATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCA
65 ACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * *
1451357 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTTAGATGAGTTTTTCTTCTTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * ** * * *
1451422 CGAACTCATTCTGGAAATGTTCATTTTGCTTTATCTCCTTCTGCGATAAAGTCTAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * * * * *
1451480 AAAGGTTCAATAAGTTCTTAAGATTATTAACTTCTTTTTCCTCTTCAGATTAGCTATTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
*
1451545 CGAACTCCTTCTGGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * *
1451603 AAAGGTTGAATACGTTCTTCAGATTATGAACTTCTTATTCCTCTTCATATAAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* ** * *
1451668 CTAACTCCTTCAAGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* *
1451726 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTT-CTTTTCCAGATGAGCTCTTCTTATT
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTT-CAGATGAGTTCTTCTTATT
* * * **
1451790 ACGAACTCCTTTTGGAAATGTTGATGTTGCTTTATCTCCTTCCACGATAGAGTCGAGCA
65 ACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * *
1451849 AAAGGTTGAATAAGTTCTTCAGATTATGAACTT-TTGTTTTCTCTTCAGATGAGTTATTCTTATT
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTT-CTTCCTCTTCAGATGAGTTCTTCTTATT
* * * * * ** * *
1451913 ACAAACTCCTTCTGGAAATATTGATACTGGTTTATCTCCTTCTATGAGAGAGTCGAGGA
65 ACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * *
1451972 AAA-ATTAAATAAGTTCTTCAGATTATGAACATCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * * * * * *
1452036 CAAACTCCTTCTGGAAATATTGATACTGGTTTATCTCCTTCTGTGAGAGAGTCGAGGA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * * *
1452094 AAA-ATTAAATAAGTTATTCAGATTATGAACATCTTCTTTCTCTTCAGATGAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * * *
1452158 TGAACACCTCCAGGAAATTTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * * *
1452216 AAAAGTTGAATAATTTCTTCAGATTATGAACTTCTTTTTCCTTTTTAGATGAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * *
1452281 CCAACTCCTTCTGGAAATGTTGATACTACTCTATCTCCTTCTGCGATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
1452339 AAAGGTT-AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * *
1452403 GGAACTCCTTCTGGAAATGTTGATGCTTCTATATATCCTTCTGCGATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* *
1452461 AAAGGTTGAATAAGTTCTAT-AGATTATGAGCTTCTTTTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAATAAGTTCT-TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * * * * * **
1452525 ACGAACTCCTTTTAGAAATATTGATGTTTCTCTATATCCTTCTGAAATAGAGTCGAGCA
65 ACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* *
1452584 AAAGATTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTTTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * *
1452649 TGAACTCGTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCAAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * *
1452707 AAAGGTTGAATAAGTTCTTTAAATTATGAACATCTTCTTCCTCTTCAGAAGA-TCTCTTCTTATT
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGT-TCTTCTTATT
* * * *
1452771 ACGAACTCCTT-TCGAAAATATTGATGCTGCTCTATCTCCTTCTGTGATAAAGTCGAGCA
65 ACGAACTCCTTCT-GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * * *
1452830 AAATGTTGAATAAGTTCTCCAGATTATGAACTTCTTCTTCCTCTTAATATGAGTTCTTCTTATCA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * *
1452895 CGAACTCCTTCTTGAAATATTGATGCTGCTCTATCTCATTCTACGATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* ** * *
1452953 AAAAGTTGAATAAGTTCTTCAGATTACAAACTTCTT-TTCCTCTTCAAATAAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * * * * * *
1453017 CAAACTCCTTCTAGAAATATTGATACTGGTATATCTCCTTCTGTGATAGAGCCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
** * *
1453075 AAAAATTGAATAAGTTCTTCAGATTATGAACATCTTCTTCCTTTTCAGATGAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * *
1453140 CGAAC-ACATCTAGGAAATGTTGATGCTGCTCTATATCCTTCTGTGATAGAGTCGAGCA
66 CGAACTCCTTCT-GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * *
1453198 AAAGGTTGAATAATTTCTACAGATTATGAACTTCTTTTTCCTCTTCAGATGAATTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * * * *
1453263 CGAACTTCTTCTGAAAATGTTGATGCTTCTTTATATCCTTCTGCAATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * *
1453321 AAAGATTGAATAAGTTCTTTAGATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* * * * * * *
1453386 TGAACTCATTATGGAAATGTTGATGCAGCTCTATCTCCTTCTACGATAAAGTCGGGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * **
1453444 AAAGGTTGAATAAGTTCTTTAGATTATGAACTTATTCTTCCTCTTCAGATGACCTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
*
1453509 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGGA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * * *
1453567 AAATGTTGAATAAGTTCTTTAGATTATGAACTTATTCTTCCTCTTCATATGAGTTCTTCTTATTA
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
* *
1453632 CGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
66 CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* * *
1453690 AAAGGTTGAATAAGTTCTTCAAATTATGAACTTTTTCTTCCTCTTCAGAT-ATGTTCATCTTATT
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGA-GTTCTTCTTATT
* * * *
1453754 ACAAACTCCTTCTGGAAATGTTGATGCCGCTCTATCTCCTTATTCGATAGAGTCGAGCA
65 ACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
* *
1453813 AAAGGTTGAATAAGTTCTTTAGATTATGAA-TATCTTCTTCCTCTTCAGATGAGTTCTTATTATT
1 AAAGGTTGAATAAGTTCTTCAGATTATGAACT-TCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* *
1453877 ACAAACTCCTTCTTGAAATGTTGAT
65 ACGAACTCCTTCTGGAAATGTTGAT
1453902 CCATCGAGTG
Statistics
Matches: 2462, Mismatches: 309, Indels: 40
0.88 0.11 0.01
Matches are distributed among these distances:
122 453 0.18
123 1996 0.81
124 13 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (123 bp):
AAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA
CGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA
Found at i:1456920 original size:20 final size:19
Alignment explanation
Indices: 1456891--1456938 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
1456881 TTCTTCTTAT
* *
1456891 TTTTTCTCTTTTTTTTTTC
1 TTTTTCTCTTTTTTTCTCC
1456910 TTTTTCATCTTTTTTTCTCC
1 TTTTTC-TCTTTTTTTCTCC
1456930 TTTTTCTCT
1 TTTTTCTCT
1456939 ATTGAATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTCTCTTTTTTTCTCC
Found at i:1456924 original size:11 final size:10
Alignment explanation
Indices: 1456890--1456938 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 10
1456880 TTTCTTCTTA
1456890 TTTTTTCTCT
1 TTTTTTCTCT
1456900 TTTTTT-T-T
1 TTTTTTCTCT
1456908 TCTTTTTCATCT
1 T-TTTTTC-TCT
1456920 TTTTTTCTC-
1 TTTTTTCTCT
*
1456929 CTTTTTCTCT
1 TTTTTTCTCT
1456939 ATTGAATGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
8 2 0.06
9 14 0.42
10 8 0.24
11 7 0.21
12 2 0.06
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:1462836 original size:6 final size:6
Alignment explanation
Indices: 1462825--1462878 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
1462815 TATTTCGAAG
* *
1462825 ATAAAA ATAAAA AT-AAA ATAAAA AGCTGAAAA ATAAAA ATAAAT GTAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA A--T-AAAA ATAAAA ATAAAA ATAAAA
1462875 ATAA
1 ATAA
1462879 CCTTTGTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 5 0.12
6 28 0.70
7 1 0.03
8 1 0.03
9 5 0.12
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:1463481 original size:5 final size:5
Alignment explanation
Indices: 1463467--1463496 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1463457 TTTAAACTTG
1463467 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1463497 GATTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:1464754 original size:17 final size:17
Alignment explanation
Indices: 1464722--1464764 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1464712 TAAGAGTTAA
* *
1464722 TTTAATAAACGAACTAG
1 TTTAATGAATGAACTAG
*
1464739 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
1464756 TTTAATGAA
1 TTTAATGAA
1464765 CTACTTCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:1467674 original size:18 final size:16
Alignment explanation
Indices: 1467653--1467687 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1467643 GCTCTAATCG
1467653 TTAATAAATTAATAATTT
1 TTAATAAA-TAAT-ATTT
1467671 TTAATAAATAATATTT
1 TTAATAAATAATATTT
1467687 T
1 T
1467688 GACTAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATAAATAATATTT
Found at i:1467911 original size:31 final size:31
Alignment explanation
Indices: 1467873--1467952 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
1467863 TGTTTCGATT
*
1467873 TGTTCGATTTTAATGCATAACATTATTGATA
1 TGTTCGATTTTAATCCATAACATTATTGATA
* * *
1467904 TGTTCGATTTTAGTCCCTAATATTATTGATA
1 TGTTCGATTTTAATCCATAACATTATTGATA
* *
1467935 TATTCGATTTTAGTCCAT
1 TGTTCGATTTTAATCCAT
1467953 CGGTCATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (31 bp):
TGTTCGATTTTAATCCATAACATTATTGATA
Found at i:1473262 original size:20 final size:20
Alignment explanation
Indices: 1473218--1473262 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1473208 AATATTTAAA
1473218 TATAACAAATAAATTAAAAC
1 TATAACAAATAAATTAAAAC
* *
1473238 AATAA-AAATACAATTAGAAC
1 TATAACAAATA-AATTAAAAC
1473258 TATAA
1 TATAA
1473263 GAAAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.24
Consensus pattern (20 bp):
TATAACAAATAAATTAAAAC
Found at i:1474369 original size:3 final size:3
Alignment explanation
Indices: 1474361--1474411 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1474351 AATTATTTTT
* * *
1474361 TAA TAA TAA TAA TTA TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1474409 TAA
1 TAA
1474412 AATGAGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1474381 original size:15 final size:15
Alignment explanation
Indices: 1474361--1474411 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
1474351 AATTATTTTT
1474361 TAATAATAATAATTA
1 TAATAATAATAATTA
1474376 TAATAATAATAATTA
1 TAATAATAATAATTA
* *
1474391 TTATAATAATAATAA
1 TAATAATAATAATTA
1474406 TAATAA
1 TAATAA
1474412 AATGAGTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:1474847 original size:117 final size:111
Alignment explanation
Indices: 1474641--1475284 Score: 539
Period size: 113 Copynumber: 5.6 Consensus size: 111
1474631 GAGTCATTCC
* * * * * *
1474641 AAAGGTTGAATAAGCTCTTCTTATTATGAACTTCTTATTTCTTTTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT-CTTCCTCTTCAGATAAGTTCTTCTCATT
*
1474706 ATGAACTTTCTCTGGAAAGGTTGATGCTAACAT-ATATGTGATAAAATTATG-TA
65 ATGAACTTTCTCTGGAAAGATTGAT-C---CATCA-A-GTGAT-AAATT-TGATA
* * *
1474759 AAAGGTTGAACAGGCTCTTCTCATTGTGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
* *
1474824 TGAACTTTCTCTGGAAATATTGATCCATCAAGTGATGAATTTGAATA
66 TGAACTTTCTCTGGAAAGATTGATCCATCAAGTGATAAATTTG-ATA
* * * *
1474871 AAAGGTTAAACAAGTTATTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAA-TTCTTCTCAT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGAT-AAGTTCTTCTCAT
**** * * *
1474935 TATGAACTCGAACTGGAAA-AGCTGATCCATCAAGTGATGAATTTGAGCA
64 TATGAACTTTCTCTGGAAAGA-TTGATCCATCAAGTGATAAATTTGA-TA
* ** *
1474984 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTCAT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGAT-AAGTTCTTCTCAT
**** * * * *
1475048 TATGAACTCGAACTGGAAAAACTGATCCATCAAGTGATGAATTTGAACA
64 TATGAACTTTCTCTGGAAAGATTGATCCATCAAGTGATAAATTTG-ATA
** *
1475097 AAAGGTT-AACCAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTCA
1 AAAGGTTGAA-CAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGAT-AAGTTCTTCTCA
**** * ** *
1475160 TTATGAACTCGAACTGGAAA-AGCTGATCCATCAAGTGATGGATTTGAGCA
63 TTATGAACTTTCTCTGGAAAGA-TTGATCCATCAAGTGATAAATTTGA-TA
* ** * *
1475210 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCTTCTC
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTC--A-GATAAGTTCTTCTC
1475275 ATTATGAACT
62 ATTATGAACT
1475285 CGAATTGGAA
Statistics
Matches: 478, Mismatches: 31, Indels: 36
0.88 0.06 0.07
Matches are distributed among these distances:
110 2 0.00
111 4 0.01
112 48 0.10
113 315 0.66
114 7 0.01
115 2 0.00
116 22 0.05
117 46 0.10
118 32 0.07
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (111 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAGATTGATCCATCAAGTGATAAATTTGATA
Found at i:1474961 original size:113 final size:113
Alignment explanation
Indices: 1474774--1475324 Score: 822
Period size: 113 Copynumber: 4.8 Consensus size: 113
1474764 TTGAACAGGC
* * * ****
1474774 TCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAGAT-AAGTTCTTCTTATTATGAACTTTCTCTG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTCATTATGAACTCGAACTG
* * *
1474837 GAAATA-TTGATCCATCAAGTGATGAATTTGAATAAAAGGTTAAACAAGT
65 GAAA-AGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAAT
*
1474886 TATTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTG
1 TCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTG
*
1474950 GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
65 GAAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAAT
1474999 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
* *
1475064 AAAAACTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAACCAAAT
66 AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAAT
1475112 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
* *
1475177 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAAT
66 AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAAT
* *
1475225 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCTTCTCATTATGAACTCGAAT
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTC--A-GATGAATTCTTCTCATTATGAACTCGAAC
* * *
1475290 TGGAAAATGCTAATCCATCAAATGATGGATTTGAA
63 TGGAAAA-GCTGATCCATCAAGTGATGAATTTGAA
1475325 TCTTTGCTAA
Statistics
Matches: 405, Mismatches: 25, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
112 24 0.06
113 320 0.79
114 2 0.00
115 1 0.00
116 34 0.08
117 24 0.06
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (113 bp):
TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAAT
Found at i:1476141 original size:92 final size:92
Alignment explanation
Indices: 1476013--1476731 Score: 1240
Period size: 92 Copynumber: 7.8 Consensus size: 92
1476003 TTCATCTTTT
* * * *
1476013 AATTCCAATGATTGGTTCTGTGGTTCCTATCGAACCAGATCAGATAATTCAAAGAACACTTCCAG
1 AATT-CAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
* *
1476078 AAGATGCTATTAGCACATTCCTCTTCCA
65 AAGATGCTATGAGCACATTCATCTTCCA
* *
1476106 AATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
* * *
1476171 AGATACTATGAGAACATTTATCTTCCA
66 AGATGCTATGAGCACATTCATCTTCCA
1476198 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
*
1476263 AGATGCTATGAGCACATTTATCTTCCA
66 AGATGCTATGAGCACATTCATCTTCCA
* *
1476290 AATTCAATGATTGGTTATGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCTAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1476355 AGATGCTATGAGCACATTCATCTTCCA
66 AGATGCTATGAGCACATTCATCTTCCA
1476382 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
*
1476447 AGATGCTATGAGCACATTCATCTTCTA
66 AGATGCTATGAGCACATTCATCTTCCA
*
1476474 AATTCAATGATTGGTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1476539 AGATGCTATGAGCACATTCATCTTCCA
66 AGATGCTATGAGCACATTCATCTTCCA
* *
1476566 AATTCAATGATTGGTTATGTGGTTCATACCAAACCAGATCAGATAAATCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1476631 AGATGCTATGAGCACATTCATCTTCCA
66 AGATGCTATGAGCACATTCATCTTCCA
* *
1476658 AATTCAATGATTGATTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
*
1476723 AAATGCTAT
66 AGATGCTAT
1476732 TGGGTCTTCT
Statistics
Matches: 597, Mismatches: 29, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
92 593 0.99
93 4 0.01
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (92 bp):
AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
AGATGCTATGAGCACATTCATCTTCCA
Found at i:1477802 original size:16 final size:17
Alignment explanation
Indices: 1477749--1477803 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
1477739 TTCATAGAAG
*
1477749 AATAAATTGAATTTTCGAA
1 AATAAATTGAATCTT--AA
1477768 AATAAATTGAATCTT-A
1 AATAAATTGAATCTTAA
1477784 AATAAATTGAA-CTTAA
1 AATAAATTGAATCTTAA
1477800 AATA
1 AATA
1477804 GATAGAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 3 0.09
16 17 0.50
19 14 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (17 bp):
AATAAATTGAATCTTAA
Found at i:1478144 original size:16 final size:15
Alignment explanation
Indices: 1478123--1478171 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1478113 CTTGACCCCC
1478123 CTTTTTTTTCTTTTTT
1 CTTTTTTTT-TTTTTT
*
1478139 CTTTTTCCTTTTTTTT
1 CTTTTT-TTTTTTTTT
* *
1478155 CTGTTCTTTTTTTTT
1 CTTTTTTTTTTTTTT
1478170 CT
1 CT
1478172 GTTCTTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 10 0.36
16 16 0.57
17 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (15 bp):
CTTTTTTTTTTTTTT
Found at i:1478145 original size:13 final size:12
Alignment explanation
Indices: 1478124--1478169 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 12
1478114 TTGACCCCCC
1478124 TTTTTTTTCTTT
1 TTTTTTTTCTTT
1478136 TTTCTTTTTCCTTT
1 TTT-TTTTT-CTTT
1478150 TTTTTCTGTTCTTT
1 TTTTT-T-TTCTTT
1478164 TTTTTT
1 TTTTTT
1478170 CTGTTCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.10
13 8 0.27
14 17 0.57
15 2 0.07
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (12 bp):
TTTTTTTTCTTT
Done.