Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008160.1 Hibiscus syriacus cultivar Beakdansim tig00110729_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: 1466564
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1424530 original size:52 final size:52
Alignment explanation
Indices: 1424474--1424643 Score: 279
Period size: 52 Copynumber: 3.2 Consensus size: 52
1424464 AACGGGAGAA
* *
1424474 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1424526 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
1424578 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
1424631 TCGCATTGCGATT
1 TCGCATTGCGATT
1424644 CTCTCGTTGC
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
52 70 0.62
53 41 0.37
54 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1424665 original size:33 final size:33
Alignment explanation
Indices: 1424480--1424657 Score: 157
Period size: 33 Copynumber: 5.2 Consensus size: 33
1424470 AGAATCGCAA
*
1424480 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1424513 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
1424551 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
*
1424584 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
1424618 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1424651 TGCGATT
1 TGCGATT
1424658 GTAATTTCCG
Statistics
Matches: 115, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
31 4 0.03
32 7 0.06
33 57 0.50
34 16 0.14
35 5 0.04
36 4 0.03
37 2 0.02
38 8 0.07
39 3 0.03
40 9 0.08
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1427826 original size:20 final size:20
Alignment explanation
Indices: 1427798--1428047 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
1427788 AAATTTCAGT
* * *
1427798 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1427818 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1427838 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1427858 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1427878 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
1427898 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1427918 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1427938 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
1427958 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1427978 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1427998 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1428018 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1428038 GTTGCGATTT
1 GTTGCGATTT
1428048 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1428064 original size:21 final size:21
Alignment explanation
Indices: 1428034--1428116 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1428024 ATTTTCATAT
*
1428034 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1428055 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1428076 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1428097 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1428117 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1428107 original size:42 final size:43
Alignment explanation
Indices: 1428014--1428112 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1428004 ATTTATGTGT
* *
1428014 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1428055 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1428097 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1428113 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1428619 original size:22 final size:22
Alignment explanation
Indices: 1428592--1428633 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1428582 AAATAGTTGA
*
1428592 ATTTATAAATAATCGAATTTAT
1 ATTTATAAATAATCAAATTTAT
*
1428614 ATTTATAAATAGTCAAATTT
1 ATTTATAAATAATCAAATTT
1428634 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTTATAAATAATCAAATTTAT
Found at i:1428760 original size:21 final size:22
Alignment explanation
Indices: 1428734--1428778 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1428724 TGATTACTGA
* *
1428734 TAATGATTTATTATTAAT-ATC
1 TAATGATTTAATACTAATAATC
1428755 TAATGATTTAATACTAATAATC
1 TAATGATTTAATACTAATAATC
1428777 TA
1 TA
1428779 GTAATGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (22 bp):
TAATGATTTAATACTAATAATC
Found at i:1428858 original size:15 final size:15
Alignment explanation
Indices: 1428835--1428873 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1428825 AATCTTTTAA
1428835 TAATGATTTTATATT
1 TAATGATTTTATATT
*
1428850 TAATTATTTTATATT
1 TAATGATTTTATATT
1428865 TAATGATTT
1 TAATGATTT
1428874 AGTAATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
TAATGATTTTATATT
Found at i:1428888 original size:16 final size:16
Alignment explanation
Indices: 1428867--1428898 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1428857 TTTATATTTA
*
1428867 ATGATTTAGTAATGAT
1 ATGATTTACTAATGAT
1428883 ATGATTTACTAATGAT
1 ATGATTTACTAATGAT
1428899 TACTAATAAT
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:0.38, C:0.03, G:0.16, T:0.44
Consensus pattern (16 bp):
ATGATTTACTAATGAT
Found at i:1428989 original size:11 final size:11
Alignment explanation
Indices: 1428883--1429039 Score: 86
Period size: 11 Copynumber: 13.0 Consensus size: 11
1428873 TAGTAATGAT
*
1428883 ATGATTTACTA
1 ATGATTTAATA
1428894 ATGATTACTAATA
1 ATGATT--TAATA
1428907 ATGATTTATTATTA
1 ATGATTTA--A-TA
1428921 AT-ATTTAATA
1 ATGATTTAATA
*
1428931 AT--TTGATACTA
1 ATGATT--TAATA
*
1428942 ATGATTTAGTA
1 ATGATTTAATA
1428953 ATGATTAGTAATA
1 ATGATT--TAATA
*
1428966 ATAAAATTATAATA
1 AT--GATT-TAATA
1428980 ATGATTTAATA
1 ATGATTTAATA
1428991 CTATTGATTTAATA
1 --A-TGATTTAATA
1429005 ATGATTACTAATA
1 ATGATT--TAATA
*
1429018 ATAATTTAATA
1 ATGATTTAATA
*
1429029 ATGATTAAATA
1 ATGATTTAATA
1429040 TTTAAATAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 36
0.72 0.06 0.22
Matches are distributed among these distances:
9 2 0.02
10 4 0.03
11 49 0.42
12 4 0.03
13 35 0.30
14 21 0.18
15 3 0.03
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:1428999 original size:52 final size:49
Alignment explanation
Indices: 1428926--1429039 Score: 147
Period size: 52 Copynumber: 2.3 Consensus size: 49
1428916 TATTAATATT
* * * *
1428926 TAATAATTTGATACTAATGATTTAGTAATGATTAGTAATAATAAAATTATAA
1 TAATGATTTAATACTAATGATTTAATAATGATTACTAATAAT--AATT-TAA
*
1428978 TAATGATTTAATACTATTGATTTAATAATGATTACTAATAATAATTTAA
1 TAATGATTTAATACTAATGATTTAATAATGATTACTAATAATAATTTAA
*
1429027 TAATGATTAAATA
1 TAATGATTTAATA
1429040 TTTAAATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 15 0.27
50 4 0.07
52 37 0.66
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (49 bp):
TAATGATTTAATACTAATGATTTAATAATGATTACTAATAATAATTTAA
Found at i:1429191 original size:17 final size:15
Alignment explanation
Indices: 1429157--1429196 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
1429147 AGGGACATGC
1429157 ATATTTAATATTATA
1 ATATTTAATATTATA
*
1429172 ATATTTAAGTTTTAATA
1 ATATTTAA-TATT-ATA
1429189 ATATTTAA
1 ATATTTAA
1429197 CATATGCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTATA
Found at i:1431886 original size:4 final size:4
Alignment explanation
Indices: 1431877--1431901 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1431867 AACTATTCCC
1431877 ACTA ACTA ACTA ACTA ACTA ACTA A
1 ACTA ACTA ACTA ACTA ACTA ACTA A
1431902 TAATTTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACTA
Found at i:1433394 original size:24 final size:24
Alignment explanation
Indices: 1433367--1433429 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 24
1433357 TTACTTTTTG
1433367 AAATTTAGTTTTTATATTAATTAT
1 AAATTTAGTTTTTATATTAATTAT
1433391 AAATTTA-----TATA-T-ATTAT
1 AAATTTAGTTTTTATATTAATTAT
*
1433408 AAATTTGGTTTTTATATTAATT
1 AAATTTAGTTTTTATATTAATT
1433430 CCAATTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 14
0.67 0.02 0.30
Matches are distributed among these distances:
17 11 0.35
18 1 0.03
19 4 0.13
22 4 0.13
23 1 0.03
24 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
AAATTTAGTTTTTATATTAATTAT
Found at i:1434226 original size:22 final size:22
Alignment explanation
Indices: 1434200--1434244 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1434190 AAACCCTTAC
**
1434200 AAATATCAAGTAGAAGCAAACA
1 AAATATCAAACAGAAGCAAACA
1434222 AAATATCAAACAGAAGCAAACA
1 AAATATCAAACAGAAGCAAACA
1434244 A
1 A
1434245 TATAAAATAG
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:0.62, C:0.16, G:0.11, T:0.11
Consensus pattern (22 bp):
AAATATCAAACAGAAGCAAACA
Found at i:1434256 original size:20 final size:21
Alignment explanation
Indices: 1434198--1434256 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1434188 CCAAACCCTT
* *
1434198 ACAAATATCAAGTAGAAGCAA
1 ACAAATATAAAATAGAAGCAA
* *
1434219 ACAAAATATCAAACAGAAGCAA
1 AC-AAATATAAAATAGAAGCAA
1434241 AC-AATATAAAATAGAA
1 ACAAATATAAAATAGAA
1434257 TAATGCAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 12 0.36
21 2 0.06
22 19 0.58
ACGTcount: A:0.63, C:0.14, G:0.10, T:0.14
Consensus pattern (21 bp):
ACAAATATAAAATAGAAGCAA
Found at i:1435636 original size:31 final size:31
Alignment explanation
Indices: 1435598--1435661 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1435588 CTATTTGTTT
* *
1435598 ATTGCTCATATCAAACAAGGACATAATGACA
1 ATTGCTCATACCAAACAAGGAAATAATGACA
*
1435629 ATTGCTCATACCAAACAGGGAAATAATGACA
1 ATTGCTCATACCAAACAAGGAAATAATGACA
1435660 AT
1 AT
1435662 CTTTTAGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (31 bp):
ATTGCTCATACCAAACAAGGAAATAATGACA
Found at i:1437224 original size:61 final size:61
Alignment explanation
Indices: 1437134--1437280 Score: 179
Period size: 61 Copynumber: 2.4 Consensus size: 61
1437124 TTGTCTCTTA
* * * * * *
1437134 ATTTTAAATTTATTTAATTTAGTCTAAATTTAATGATT-TAATATATTAATTTAAGGTTTAT
1 ATTTAAAATTTATTCAATTTAATCCAAATTTAAAG-TTATAATATATTAATTTAAGGTTCAT
* * * *
1437195 ATTTCAACTTTTTTCAATTTAATCCAAATTTAAAGTTATAATTTATTAATTTAAGGTTCAT
1 ATTTAAAATTTATTCAATTTAATCCAAATTTAAAGTTATAATATATTAATTTAAGGTTCAT
*
1437256 ATTTAAAATTTATTCAATTTGATCC
1 ATTTAAAATTTATTCAATTTAATCC
1437281 TTATATATTT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 2 0.03
61 70 0.97
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (61 bp):
ATTTAAAATTTATTCAATTTAATCCAAATTTAAAGTTATAATATATTAATTTAAGGTTCAT
Found at i:1437358 original size:18 final size:18
Alignment explanation
Indices: 1437335--1437532 Score: 169
Period size: 18 Copynumber: 10.9 Consensus size: 18
1437325 AATAAATTAA
1437335 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
1437353 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
1437371 TA-AT-GAATTATATA-A-
1 TATATAG-TTTATATATAC
1437386 TATATAGTTTGTATATACCATATAC
1 TATATAG--T-T-TAT---ATATAC
*
1437411 TATATAGGTTATATATAC
1 TATATAGTTTATATATAC
* *
1437429 TA-AT-GAATTGTATA-A-
1 TATATAG-TTTATATATAC
1437444 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
1437462 TATATAGTTTATATATAA
1 TATATAGTTTATATATAC
*
1437480 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* * *
1437498 CATATAGTATATATATAT
1 TATATAGTTTATATATAC
1437516 TATATAGTTTATATATA
1 TATATAGTTTATATATA
1437533 ATAATAAACT
Statistics
Matches: 145, Mismatches: 19, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
15 4 0.03
16 14 0.10
17 20 0.14
18 88 0.61
19 1 0.01
20 3 0.02
21 3 0.02
22 1 0.01
23 3 0.02
24 1 0.01
25 7 0.05
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:1437366 original size:51 final size:52
Alignment explanation
Indices: 1437311--1437529 Score: 151
Period size: 51 Copynumber: 4.1 Consensus size: 52
1437301 TCAATAAATA
*
1437311 TATATGTTTATATTAATAAAT-TAATATATAGTTTATATATACTGTATAGTT
1 TATATGTTTATATTAATAAATATAATATATAGTTTATATATACTATATAGTT
* * * * * * * *
1437362 TATATATACTA-ATGAAT-TATATAATATATAGTTTGTATATACCATATACTA
1 TATATGT-TTATATTAATAAATATAATATATAGTTTATATATACTATATAGTT
* *
1437413 TATAGGTTATATATACTAATGAATTGTATAATATATAGTTTATATATACTATATAGTT
1 TATATGTT-TATAT--TAAT-AA--ATATAATATATAGTTTATATATACTATATAGTT
* * ** * *
1437471 TATATATAATGTATAGTT--TATATATACCATATAGTATATATATATTATATAGTT
1 TATATGT--T-TATA-TTAATAAATATAATATATAGTTTATATATACTATATAGTT
1437525 TATAT
1 TATAT
1437530 ATAATAATAA
Statistics
Matches: 127, Mismatches: 28, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
50 2 0.02
51 43 0.34
52 4 0.03
54 36 0.28
56 1 0.01
57 1 0.01
58 33 0.26
59 1 0.01
60 5 0.04
61 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (52 bp):
TATATGTTTATATTAATAAATATAATATATAGTTTATATATACTATATAGTT
Found at i:1437414 original size:25 final size:25
Alignment explanation
Indices: 1437380--1437428 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1437370 CTAATGAATT
* *
1437380 ATATAATATATAGTTTGTATATACC
1 ATATAATATATAGGTTATATATACC
*
1437405 ATATACTATATAGGTTATATATAC
1 ATATAATATATAGGTTATATATAC
1437429 TAATGAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (25 bp):
ATATAATATATAGGTTATATATACC
Found at i:1437423 original size:58 final size:58
Alignment explanation
Indices: 1437347--1437467 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 58
1437337 TATAGTTTAT
* * *
1437347 ATATACTGTATAGTTTATATATACTAATGAATTATATAATATATAGTTTGTATATACC
1 ATATACTATATAGGTTATATATACTAATGAATTATATAATATATAGTTTATATATACC
* *
1437405 ATATACTATATAGGTTATATATACTAATGAATTGTATAATATATAGTTTATATATACT
1 ATATACTATATAGGTTATATATACTAATGAATTATATAATATATAGTTTATATATACC
1437463 ATATA
1 ATATA
1437468 GTTTATATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (58 bp):
ATATACTATATAGGTTATATATACTAATGAATTATATAATATATAGTTTATATATACC
Found at i:1437458 original size:9 final size:9
Alignment explanation
Indices: 1437444--1437530 Score: 56
Period size: 9 Copynumber: 9.7 Consensus size: 9
1437434 AATTGTATAA
1437444 TATATAGTT
1 TATATAGTT
*
1437453 TATATA-TAC
1 TATATAGT-T
1437462 TATATAGTT
1 TATATAGTT
*
1437471 TATATA-TAA
1 TATATAGT-T
*
1437480 TGTATAGTT
1 TATATAGTT
*
1437489 TATATA-TAC
1 TATATAGT-T
* *
1437498 CATATAGTA
1 TATATAGTT
1437507 TATATA-TAT
1 TATATAGT-T
1437516 TATATAGTT
1 TATATAGTT
1437525 TATATA
1 TATATA
1437531 TAATAATAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 16
0.69 0.13 0.19
Matches are distributed among these distances:
8 4 0.07
9 51 0.86
10 4 0.07
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.49
Consensus pattern (9 bp):
TATATAGTT
Found at i:1439394 original size:2 final size:2
Alignment explanation
Indices: 1439382--1439416 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
1439372 AAATATCAAC
1439382 TA TA GTA 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
1439417 GGTCATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1439449 original size:33 final size:32
Alignment explanation
Indices: 1439399--1439467 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
1439389 TATATATATA
1439399 TATATATATATATATATAGGTCATATGTAAAC
1 TATATATATATATATATAGGTCATATGTAAAC
* *
1439431 TATATAGTTTATATATATAGTTCATATGTAAAC
1 TATATA-TATATATATATAGGTCATATGTAAAC
1439464 TATA
1 TATA
1439468 GTTCATATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (32 bp):
TATATATATATATATATAGGTCATATGTAAAC
Found at i:1439468 original size:31 final size:32
Alignment explanation
Indices: 1439407--1439475 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
1439397 TATATATATA
1439407 TATATATATAGGTCATATGTAAACTATATAGTT
1 TATATATATAGGTCATATGTAAAC-ATATAGTT
*
1439440 TATATATATAGTTCATATGTAAAC-TATAGTT
1 TATATATATAGGTCATATGTAAACATATAGTT
*
1439471 CATAT
1 TATAT
1439476 GTAAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 11 0.32
33 23 0.68
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (32 bp):
TATATATATAGGTCATATGTAAACATATAGTT
Found at i:1439469 original size:18 final size:18
Alignment explanation
Indices: 1439446--1439480 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1439436 AGTTTATATA
1439446 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
1439464 TATAGTTCATATGTAAA
1 TATAGTTCATATGTAAA
1439481 TATTAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:1439538 original size:33 final size:32
Alignment explanation
Indices: 1439501--1439567 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
1439491 AGTTTATATG
*
1439501 TAAACTATAGTTCATACATATAGTATATAAATA
1 TAAACTATAGTTCATACAAATAGTATA-AAATA
* *
1439534 TAAACTATAGTTTATATAAATAGTATAAAATA
1 TAAACTATAGTTCATACAAATAGTATAAAATA
1439566 TA
1 TA
1439568 GTATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (32 bp):
TAAACTATAGTTCATACAAATAGTATAAAATA
Found at i:1439542 original size:20 final size:20
Alignment explanation
Indices: 1439518--1439591 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
1439508 TAGTTCATAC
1439518 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
1439538 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
1439563 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
1439583 TTATAGTAT
1 ATATAGTAT
1439592 GTAGTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:1439567 original size:25 final size:23
Alignment explanation
Indices: 1439518--1439578 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
1439508 TAGTTCATAC
1439518 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
1439538 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
1439563 ATATAGTATATAAATA
1 ATATAGTATATAAATA
1439579 TAAATTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:1439570 original size:12 final size:13
Alignment explanation
Indices: 1439531--1439580 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1439521 TAGTATATAA
1439531 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
1439545 TTATATAA-ATAGT
1 ATATA-AATATAGT
1439558 ATA-AAATATAGT
1 ATATAAATATAGT
1439570 ATATAAATATA
1 ATATAAATATA
1439581 AATTATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:1439637 original size:2 final size:2
Alignment explanation
Indices: 1439630--1439783 Score: 73
Period size: 2 Copynumber: 81.5 Consensus size: 2
1439620 CCTAGGCCCC
*
1439630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA ACT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
1439672 AT TT AT AT -T A- AT AA ACT AT AT A- AT TT AT AC A- AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1439711 -T AT TT AT A- AT -T AT AC AT A- AT AT AT AA AT AT AA AT -T GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1439748 AT AGT TT AT AT AT A- AT -T CAT AT AT A- AT TT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT A
1439784 AACTATGCAG
Statistics
Matches: 113, Mismatches: 22, Indels: 34
0.67 0.13 0.20
Matches are distributed among these distances:
1 13 0.12
2 96 0.85
3 4 0.04
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1439782 original size:13 final size:11
Alignment explanation
Indices: 1439631--1439784 Score: 70
Period size: 11 Copynumber: 13.8 Consensus size: 11
1439621 CTAGGCCCCA
*
1439631 TATATATATATA
1 TATATATA-ATT
*
1439643 TATATATATATA
1 TATATATA-ATT
1439655 TATATATAA--
1 TATATATAATT
1439664 -ACTATATAATT
1 TA-TATATAATT
*
1439675 TATAT-TAATA
1 TATATATAATT
*
1439685 AACTATATAATT
1 TA-TATATAATT
*
1439697 TATACAATATATAT
1 TATA-TATA-AT-T
*
1439711 TATTTATAA-T
1 TATATATAATT
*
1439721 TATACATAATAT
1 TATATATAAT-T
* *
1439733 ATAAATATAA-A
1 -TATATATAATT
* *
1439744 T-TGTATAGTT
1 TATATATAATT
1439754 TATATATAATT
1 TATATATAATT
*
1439765 CATATATAATT
1 TATATATAATT
1439776 TATATATAA
1 TATATATAA
1439785 ACTATGCAGT
Statistics
Matches: 108, Mismatches: 20, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
8 1 0.01
9 11 0.10
10 15 0.14
11 34 0.31
12 31 0.29
13 12 0.11
14 4 0.04
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (11 bp):
TATATATAATT
Found at i:1439872 original size:27 final size:28
Alignment explanation
Indices: 1439826--1439894 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
1439816 ATATATAAGC
* **
1439826 TATATAGTATTATATTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
*
1439854 TATATAGT-TTATGCTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
1439881 TATATA-TATATATA
1 TATATAGTAT-TATA
1439895 TATATATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.03
27 22 0.65
28 11 0.32
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:1439885 original size:2 final size:2
Alignment explanation
Indices: 1439878--1439903 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1439868 TTTATACATA
1439878 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
1439904 TAGTTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1440293 original size:210 final size:212
Alignment explanation
Indices: 1439927--1440741 Score: 1275
Period size: 210 Copynumber: 3.8 Consensus size: 212
1439917 TTTTTTCTCA
* *
1439927 ACTTATTACTTTTTTATATTTATT-AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTA-T
1 ACTTATTACTTATTTATATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
*
1439990 ATTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTT-T-TGTGCTGT
65 -TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTATGTGTGTTGT
*
1440053 TTAATATATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTT
129 TTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTT
*
1440118 GCACCTGAAATTGACCCAT
194 GCATCTGAAATTGACCCAT
* *
1440137 ACTTATTACTTATTTATATTTTTAAATTGGCCCTTAACTTTTTAAATGGTTATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * *
1440202 TTTTTTATTAATTTCAACCTCAAAATTTTAAATTATTTTGATTTGATCCCTT-T-TGTGTTGTTT
66 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTATGTGTGTTGTTT
1440265 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
131 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
1440330 ATCTGAAATTGACCCAT
196 ATCTGAAATTGACCCAT
* *
1440347 ACTTATTACTTATTTCTATTTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * *
1440412 TTTTGTATTAATTTCAACATCACAATATAAAATTATTTCGATTTGATCCCTCATTAATGTGTGTT
66 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGAT-CC-C-TT-ATGTGTGTT
*
1440477 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
127 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
* *
1440542 TTGCATATGAAATTGATCCAT
192 TTGCATCTGAAATTGACCCAT
* * *
1440563 ACTTATTACTTAATTCT-TTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC-T
*
1440627 TTTTTGTATTAATTTCAACCTCATAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
65 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT--T--ATGTGTGT
*
1440692 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
126 TGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1440742 ATTCTTAAAT
Statistics
Matches: 564, Mismatches: 29, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
209 2 0.00
210 297 0.53
211 3 0.01
212 1 0.00
213 3 0.01
214 1 0.00
215 47 0.08
216 210 0.37
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (212 bp):
ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTATGTGTGTTGTTT
AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
ATCTGAAATTGACCCAT
Found at i:1441722 original size:19 final size:19
Alignment explanation
Indices: 1441698--1441736 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1441688 ATACTTAGAA
1441698 TGACATATATTTCCATTTG
1 TGACATATATTTCCATTTG
1441717 TGACATATATTTCCATTTG
1 TGACATATATTTCCATTTG
1441736 T
1 T
1441737 TTCTCAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (19 bp):
TGACATATATTTCCATTTG
Found at i:1448662 original size:13 final size:12
Alignment explanation
Indices: 1448644--1448687 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1448634 ACCCTGTACC
1448644 TATTTTTTATTTT
1 TATTTTTTA-TTT
*
1448657 TATTTTCTATTT
1 TATTTTTTATTT
* *
1448669 TACTTTTTATAT
1 TATTTTTTATTT
1448681 TATTTTT
1 TATTTTT
1448688 AACTACGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:1451824 original size:20 final size:20
Alignment explanation
Indices: 1451799--1451898 Score: 137
Period size: 21 Copynumber: 4.9 Consensus size: 20
1451789 CATTAGACAA
*
1451799 GGGGAATCGGTACCCCCTAG
1 GGGGAATCTGTACCCCCTAG
* *
1451819 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGTACCCCCT-AG
* *
1451840 GGGGAATCGGTACCCCCTGG
1 GGGGAATCTGTACCCCCTAG
1451860 GGGGAATCTGTACCCCCTAGG
1 GGGGAATCTGTACCCCCTA-G
1451881 GGGGAATCTGTACCCCCT
1 GGGGAATCTGTACCCCCT
1451899 GGGCAATCTG
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
20 35 0.49
21 36 0.51
ACGTcount: A:0.16, C:0.30, G:0.35, T:0.19
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTAG
Found at i:1451842 original size:21 final size:20
Alignment explanation
Indices: 1451799--1451901 Score: 152
Period size: 20 Copynumber: 5.0 Consensus size: 20
1451789 CATTAGACAA
* *
1451799 GGGGAATCGGTACCCCCTAG
1 GGGGAATCTGTACCCCCTGG
*
1451819 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGTACCCCCT-GG
*
1451840 GGGGAATCGGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
1451860 GGGGAATCTGTACCCCCTAGG
1 GGGGAATCTGTACCCCCT-GG
1451881 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
1451901 G
1 G
1451902 CAATCTGATT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 38 0.51
21 37 0.49
ACGTcount: A:0.16, C:0.29, G:0.37, T:0.18
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:1451899 original size:41 final size:41
Alignment explanation
Indices: 1451799--1451901 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
1451789 CATTAGACAA
* * *
1451799 GGGGAATCGGTACCCCCTAGGGGGAATCTGTTCCCCCTGGG
1 GGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTAGG
1451840 GGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTAGG
1 GGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTAGG
*
1451881 GGGGAATCTGTACCCCCTGGG
1 GGGGAATCGGTACCCCCTGGG
1451902 CAATCTGATT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.16, C:0.29, G:0.37, T:0.18
Consensus pattern (41 bp):
GGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTAGG
Found at i:1453054 original size:24 final size:24
Alignment explanation
Indices: 1453027--1453118 Score: 116
Period size: 24 Copynumber: 3.8 Consensus size: 24
1453017 CATAATTCAA
*
1453027 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCATATCAG-AATCCAT
* *
1453051 GTCAAGTAACAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
1453075 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
*
1453099 GTCAAGTATCATATAAGAAT
1 GTCAAGTATCATATCAGAAT
1453119 TCAAATCGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.08
24 52 0.88
25 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:1454699 original size:63 final size:63
Alignment explanation
Indices: 1454600--1454719 Score: 213
Period size: 63 Copynumber: 1.9 Consensus size: 63
1454590 TTGAACATTT
*
1454600 TCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTCCTAACACTC
1 TCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCATTCACAAACTCTCCTAACACTC
* *
1454663 TCTGATCTTGAAACTGTTCTCTTAATAGACTTCTAGTATCATTCACAAACTCTCCTA
1 TCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCATTCACAAACTCTCCTA
1454720 GGATTAAAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (63 bp):
TCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCATTCACAAACTCTCCTAACACTC
Found at i:1457417 original size:19 final size:20
Alignment explanation
Indices: 1457374--1457421 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1457364 TCTAAATCCT
*
1457374 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1457394 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1457413 TTTTCAAAA
1 TTTTCAAAA
1457422 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1458314 original size:32 final size:34
Alignment explanation
Indices: 1458278--1458347 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1458268 CCTTACAAAC
* *
1458278 TCCCTAGTTTTT-C-TGGGCTAAACTAGAACTTT
1 TCCCTAGTTTTTACACGGGCTAAACTAGAACATT
*
1458310 TCCCTAGTTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAGTTTTTACACGGGCTAAACTAGAACATT
1458344 TCCC
1 TCCC
1458348 CTTCACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.36
Consensus pattern (34 bp):
TCCCTAGTTTTTACACGGGCTAAACTAGAACATT
Found at i:1459094 original size:22 final size:22
Alignment explanation
Indices: 1459077--1459142 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
1459067 CTCGTATAAA
1459077 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1459099 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1459121 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1459143 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1459403 original size:30 final size:31
Alignment explanation
Indices: 1459362--1459421 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1459352 TAGACATAGT
*
1459362 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
1459392 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
1459422 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:1459477 original size:28 final size:29
Alignment explanation
Indices: 1459437--1459504 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
1459427 TTCTGCATAA
**
1459437 TCATGTCATGTAATACA-TAAATATGAAT
1 TCATGTCATGTAATACATTAAATACAAAT
*
1459465 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATTAAATACAAAT
1459494 TCATGT-ATGTA
1 TCATGTCATGTA
1459505 TAATATGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 22 0.61
29 14 0.39
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (29 bp):
TCATGTCATGTAATACATTAAATACAAAT
Found at i:1459911 original size:64 final size:64
Alignment explanation
Indices: 1459800--1459944 Score: 177
Period size: 64 Copynumber: 2.2 Consensus size: 64
1459790 TTTTTCTCAT
* *
1459800 GGGGAATCGGTTCCCCCCCTGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATAACGATG-A
1 GGGGTATCGGTT-CCCCCCTGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATAACGATGAA
** * ** *
1459864 GGGGTATCGGTTCCCCCCTGGGGGTA-CGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTTGA
1 GGGGTATCGGTTCCCCCCT--GGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATAACGATGA
1459928 A
64 A
1459929 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
1459945 TTGAATGGGT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 7 0.10
64 41 0.59
65 22 0.31
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (64 bp):
GGGGTATCGGTTCCCCCCTGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATAACGATGAA
Found at i:1459954 original size:21 final size:21
Alignment explanation
Indices: 1459924--1459966 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1459914 ATTCATTTCG
* *
1459924 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1459945 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1459966 T
1 T
1459967 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1465856 original size:22 final size:22
Alignment explanation
Indices: 1465821--1465885 Score: 116
Period size: 21 Copynumber: 3.0 Consensus size: 22
1465811 GTCGTATAAA
1465821 TGCACCG-AGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1465842 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1465864 TGCA-CGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1465885 T
1 T
1465886 ATGTCCATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 25 0.58
22 18 0.42
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1466136 original size:29 final size:30
Alignment explanation
Indices: 1466096--1466153 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1466086 TAGACATAGT
1466096 ATTTCATACCTTTA-AACATAG-GCATATC
1 ATTTCATACCTTTATAACATAGTGCATATC
*
1466124 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTT-CATACCTTTATAACATAGTGCATAT
1466154 AACTTTTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 10 0.38
30 6 0.23
31 6 0.23
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (30 bp):
ATTTCATACCTTTATAACATAGTGCATATC
Found at i:1466206 original size:27 final size:28
Alignment explanation
Indices: 1466168--1466235 Score: 102
Period size: 27 Copynumber: 2.4 Consensus size: 28
1466158 TTTCTGCATA
*
1466168 TCATGTCATGTAATACATATAAT-GAAT
1 TCATGTCATGTAATACATATAATAAAAT
*
1466195 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATA-AAAT
1466224 TCATGTCATGTA
1 TCATGTCATGTA
1466236 TCATAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 22 0.59
29 15 0.41
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (28 bp):
TCATGTCATGTAATACATATAATAAAAT
Done.