Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1452063 original size:19 final size:18
Alignment explanation
Indices: 1452014--1452063 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 18
1452004 ATCTAAAAAT
*
1452014 TATTAAATTTTTTATTTTA
1 TATTAAA-TTTATATTTTA
1452033 TATTAATATTTATATTTTA
1 TATTAA-ATTTATATTTTA
1452052 TAATTAAATTTA
1 T-ATTAAATTTA
1452064 AATAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTAAATTTATATTTTA
Found at i:1454322 original size:2 final size:2
Alignment explanation
Indices: 1454317--1454347 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1454307 TGTGTGTGTG
*
1454317 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1454348 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1456798 original size:22 final size:22
Alignment explanation
Indices: 1456755--1456800 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1456745 TTCTCTCTAT
* *
1456755 TTTTTTTATTTAAGAATCTAAA
1 TTTTTTTAATAAAGAATCTAAA
* *
1456777 TTTTTTTAATAAATAATTTAAA
1 TTTTTTTAATAAAGAATCTAAA
1456799 TT
1 TT
1456801 ATTACTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTTTTAATAAAGAATCTAAA
Found at i:1457037 original size:13 final size:13
Alignment explanation
Indices: 1457028--1457068 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1457018 ATATTTATAT
*
1457028 TATTTTTTTATTTA
1 TATTATTTT-TTTA
*
1457042 TATTATATTTTTA
1 TATTATTTTTTTA
1457055 TATTATTTTTTTA
1 TATTATTTTTTTA
1457068 T
1 T
1457069 GTCATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTATTTTTTTA
Found at i:1457039 original size:17 final size:17
Alignment explanation
Indices: 1457019--1457060 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
1457009 ATATATATCA
*
1457019 TATTTATATTATTTTTT
1 TATTTATATTATATTTT
1457036 TATTTATATTATATTTT
1 TATTTATATTATATTTT
1457053 TATATTAT
1 TAT-TTAT
1457061 TTTTTTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTATATTATATTTT
Found at i:1457052 original size:19 final size:17
Alignment explanation
Indices: 1457018--1457058 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
1457008 TATATATATC
1457018 ATATTTATATTATTTTT
1 ATATTTATATTATTTTT
*
1457035 TTATTTATATTATATTTTT
1 ATATTTATA-T-TATTTTT
1457054 ATATT
1 ATATT
1457059 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATATTTATATTATTTTT
Found at i:1457055 original size:30 final size:32
Alignment explanation
Indices: 1457006--1457068 Score: 103
Period size: 30 Copynumber: 2.0 Consensus size: 32
1456996 TTTACAAATT
1457006 TTTATATATATCATATTTATATTATTTTTTTA
1 TTTATATATATCATATTTATATTATTTTTTTA
*
1457038 TTTATAT-TAT-ATTTTTATATTATTTTTTTA
1 TTTATATATATCATATTTATATTATTTTTTTA
1457068 T
1 T
1457069 GTCATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 20 0.67
31 3 0.10
32 7 0.23
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (32 bp):
TTTATATATATCATATTTATATTATTTTTTTA
Found at i:1457076 original size:28 final size:27
Alignment explanation
Indices: 1457004--1457082 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 27
1456994 TTTTTACAAA
*
1457004 TTTTTATATATATCATATTTATATTATT
1 TTTTTATATATAT-ATTTTTATATTATT
1457032 TTTTTATTTATATTATATTTTTATATTATT
1 TTTTTA--TATA-TATATTTTTATATTATT
* *
1457062 TTTTTATGTCATATAATTTTA
1 TTTTTATAT-ATATATTTTTA
1457083 AGATATACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 17 0.39
29 1 0.02
30 23 0.52
31 3 0.07
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (27 bp):
TTTTTATATATATATTTTTATATTATT
Found at i:1457212 original size:10 final size:10
Alignment explanation
Indices: 1457155--1457210 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 10
1457145 TTATTAATCT
*
1457155 ATTTAAATTG
1 ATTTAATTTG
1457165 ATTTAA-TTG
1 ATTTAATTTG
*
1457174 ATTAAATTTG
1 ATTTAATTTG
* *
1457184 A-TTAATATA
1 ATTTAATTTG
1457193 ATTTAATTT-
1 ATTTAATTTG
1457202 ATTTAATTT
1 ATTTAATTT
1457211 TAAAATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
9 23 0.59
10 16 0.41
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (10 bp):
ATTTAATTTG
Found at i:1457378 original size:21 final size:20
Alignment explanation
Indices: 1457313--1457378 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
1457303 TGAATTCTTA
*
1457313 ATTATATTATACATATTTATAT
1 ATTAT-TTATA-ATATATATAT
* *
1457335 AATAATTTAAAAT-TATATAAT
1 -ATTATTTATAATATATAT-AT
1457356 ATTATTTATAATATATATGAT
1 ATTATTTATAATATATAT-AT
1457377 AT
1 AT
1457379 AAATATTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 14 0.40
21 13 0.37
22 4 0.11
23 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTATTTATAATATATATAT
Found at i:1457406 original size:26 final size:27
Alignment explanation
Indices: 1457348--1457409 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1457338 AATTTAAAAT
1457348 TATATAATATTATTTATAATATATATGA
1 TATA-AATATTATTTATAATATATATGA
* *
1457376 TATAAATATTTTTATATAATA-ATATTA
1 TATAAATATTATT-TATAATATATATGA
1457403 -ATAAATA
1 TATAAATA
1457410 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 7 0.23
27 13 0.42
28 11 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TATAAATATTATTTATAATATATATGA
Found at i:1463304 original size:85 final size:88
Alignment explanation
Indices: 1463183--1463344 Score: 258
Period size: 85 Copynumber: 1.9 Consensus size: 88
1463173 GATGAACATC
* *
1463183 AAGCTGATAGTAGAAATGCAAAGAAAACTGAGAAAGAGATGGAAGCAGACCT-AAAAATGGC-AC
1 AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTGAAAAATGGCAAA
1463246 AAAAATCTGAAATCAAGAAAATG
66 AAAAATCTGAAATCAAGAAAATG
* * *
1463269 AAGCTGATCGTAGAAAT-CAAAGAAAACAGAGAAAGAGATGGAAGCCGACCTGTAAAATGGCAAA
1 AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTGAAAAATGGCAAA
1463333 AAAAATCTGAAA
66 AAAAATCTGAAA
1463345 AAAAAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
85 32 0.46
86 24 0.35
87 13 0.19
ACGTcount: A:0.52, C:0.12, G:0.22, T:0.14
Consensus pattern (88 bp):
AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTGAAAAATGGCAAA
AAAAATCTGAAATCAAGAAAATG
Found at i:1468529 original size:28 final size:28
Alignment explanation
Indices: 1468482--1468547 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1468472 GCTAATCAAC
1468482 TTTTATTAATATATTATTTTAATTTAT-T
1 TTTTATTAATATATTATTTT-ATTTATAT
1468510 TTTTATCTAATAATATT-TTTT-TTTATAT
1 TTTTAT-TAAT-ATATTATTTTATTTATAT
*
1468538 TTTTAATAAT
1 TTTTATTAAT
1468548 TAAAAAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 9 0.26
28 12 0.35
29 8 0.24
30 5 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTATTAATATATTATTTTATTTATAT
Found at i:1469140 original size:25 final size:24
Alignment explanation
Indices: 1469084--1469130 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1469074 ATTTTTTTTT
* *
1469084 ATATTTTTAAATTTAATATAAAAA
1 ATATTTTTAAACTTAAAATAAAAA
1469108 ATTATTTTTAAACTTAAAATAAA
1 A-TATTTTTAAACTTAAAATAAA
1469131 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATTTTTAAACTTAAAATAAAAA
Found at i:1469487 original size:18 final size:18
Alignment explanation
Indices: 1469456--1469501 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1469446 TATCTAAAAT
*
1469456 ATAAATTTTTTATTTTATA
1 ATAAA-TTTATATTTTATA
*
1469475 TTAAATTTATATTTTATA
1 ATAAATTTATATTTTATA
1469493 ATAAATTTA
1 ATAAATTTA
1469502 ATAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAAATTTATATTTTATA
Found at i:1469667 original size:19 final size:18
Alignment explanation
Indices: 1469645--1469707 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
1469635 ATTTATTATC
1469645 TTTTTTATAATAAATAATA
1 TTTTTTA-AATAAATAATA
*
1469664 -TTTTTAATTAAATTAA-A
1 TTTTTTAAATAAA-TAATA
1469681 TTTTTTAAAATAAA-AATA
1 TTTTTT-AAATAAATAATA
1469699 TTTATTTAA
1 TTT-TTTAA
1469708 CTTGACTCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
17 8 0.22
18 20 0.54
19 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTTTAAATAAATAATA
Found at i:1469946 original size:28 final size:30
Alignment explanation
Indices: 1469908--1469967 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1469898 AATTATATTA
* * *
1469908 TATATATATATTTAA-AAAATATAAATAATC
1 TATACATAT-TTTAATAAAATAAAAAAAATC
1469938 TATACATATTTTAATAAAATAAAAAAAATC
1 TATACATATTTTAATAAAATAAAAAAAATC
1469968 CTGACTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (30 bp):
TATACATATTTTAATAAAATAAAAAAAATC
Found at i:1474357 original size:17 final size:18
Alignment explanation
Indices: 1474334--1474373 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1474324 TTTATATATC
1474334 ATATTTATA-TTATTTTT
1 ATATTTATATTTATTTTT
*
1474351 TTATTTATATTTATTTTT
1 ATATTTATATTTATTTTT
1474369 ATATT
1 ATATT
1474374 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATATTTATATTTATTTTT
Found at i:1474369 original size:12 final size:11
Alignment explanation
Indices: 1474322--1474379 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
1474312 TTTTTTACAC
*
1474322 ATTTTATATATC
1 ATTTT-TATATT
*
1474334 ATATTTATATT
1 ATTTTTATATT
1474345 A-TTTT-T-TT
1 ATTTTTATATT
*
1474353 ATTTATAT-TT
1 ATTTTTATATT
1474363 ATTTTTATATT
1 ATTTTTATATT
1474374 ATTTTT
1 ATTTTT
1474380 TTATGTCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 3 0.08
9 4 0.11
10 13 0.34
11 14 0.37
12 4 0.11
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:1474495 original size:10 final size:9
Alignment explanation
Indices: 1474486--1474530 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
1474476 TAATTGATTA
1474486 AATTTAATT
1 AATTTAATT
1474495 AATATTAATT
1 AAT-TTAATT
*
1474505 AATTTATTT
1 AATTTAATT
1474514 AATTTTAAATT
1 AA-TTT-AATT
1474525 AATTTA
1 AATTTA
1474531 TTATGAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 11 0.35
10 15 0.48
11 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTAATT
Found at i:1474524 original size:20 final size:19
Alignment explanation
Indices: 1474486--1474532 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
1474476 TAATTGATTA
*
1474486 AATTTAATTAATATTAATT
1 AATTTATTTAATATTAATT
*
1474505 AATTTATTTAATTTTAAATT
1 AATTTATTTAATATT-AATT
1474525 AATTTATT
1 AATTTATT
1474533 ATGAAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTATTTAATATTAATT
Found at i:1480724 original size:89 final size:89
Alignment explanation
Indices: 1480597--1480763 Score: 291
Period size: 89 Copynumber: 1.9 Consensus size: 89
1480587 GATGAACATC
* *
1480597 AAGCTGATAGTAGAAATGCAAAGAAAACTGAGAAAGAGATGGAAGCAGACCTGTAAAAATGGCAC
1 AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTGT-AAAATGGCAA
1480662 AAAAAATCTGAAAATCAAGAAAATG
65 AAAAAATCTGAAAATCAAGAAAATG
*
1480687 AAGCTGATCGTAGAAAT-CAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTGTAAAATGGCAAA
1 AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTGTAAAATGGCAAA
1480751 AAAAATCTGAAAA
66 AAAAATCTGAAAA
1480764 AAATTTGGAC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
88 23 0.31
89 35 0.47
90 16 0.22
ACGTcount: A:0.53, C:0.11, G:0.22, T:0.14
Consensus pattern (89 bp):
AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTGTAAAATGGCAAA
AAAAATCTGAAAATCAAGAAAATG
Found at i:1485687 original size:15 final size:16
Alignment explanation
Indices: 1485667--1485699 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1485657 ATTAAATTTG
1485667 ATTTAG-TAATTTTAA
1 ATTTAGATAATTTTAA
1485682 ATTTAGATTAATTTTAA
1 ATTTAGA-TAATTTTAA
1485699 A
1 A
1485700 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATTTAGATAATTTTAA
Found at i:1485753 original size:27 final size:28
Alignment explanation
Indices: 1485718--1485782 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
1485708 ATTTTTATTC
*
1485718 ATTTATATTTAAAATAAGTTTTAG-TTAA
1 ATTT-TATTTAAAACAAGTTTTAGATTAA
* * *
1485746 ATTTTATTTCAAACAATTTTTAGATTCA
1 ATTTTATTTAAAACAAGTTTTAGATTAA
*
1485774 ACTTTATTT
1 ATTTTATTT
1485783 TCTTGTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTTTATTTAAAACAAGTTTTAGATTAA
Found at i:1486003 original size:22 final size:21
Alignment explanation
Indices: 1485964--1486004 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1485954 ATATTAAATA
1485964 TAAAAATTTTAAAATAATAAT
1 TAAAAATTTTAAAATAATAAT
* *
1485985 TAAATAATTTTTAATTAATA
1 TAAA-AATTTTAAAATAATA
1486005 TTACGTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAATTTTAAAATAATAAT
Found at i:1487082 original size:19 final size:18
Alignment explanation
Indices: 1487033--1487082 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 18
1487023 ATCTAAAAAT
*
1487033 TATTAAATTTTTTATTTTA
1 TATTAAA-TTTATATTTTA
1487052 TATTAATATTTATATTTTA
1 TATTAA-ATTTATATTTTA
1487071 TAATTAAATTTA
1 T-ATTAAATTTA
1487083 AATAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTAAATTTATATTTTA
Found at i:1487554 original size:32 final size:35
Alignment explanation
Indices: 1487481--1487556 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 35
1487471 AGTTTTTTAT
1487481 ATATAAAAATTATATTATATATATATATTTAAAAA
1 ATATAAAAATTATATTATATATATATATTTAAAAA
*
1487516 ATATAAATATTA-ATTATA-A-ATAT-TTTAATAAA
1 ATATAAAAATTATATTATATATATATATTTAA-AAA
1487548 ATATAAAAA
1 ATATAAAAA
1487557 AATCCTGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
31 5 0.13
32 15 0.39
33 1 0.03
34 6 0.16
35 11 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
ATATAAAAATTATATTATATATATATATTTAAAAA
Found at i:1492038 original size:13 final size:13
Alignment explanation
Indices: 1492029--1492069 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1492019 ATATTTATAT
*
1492029 TATTTTTTTATTTA
1 TATTATTTT-TTTA
*
1492043 TATTATATTTTTA
1 TATTATTTTTTTA
1492056 TATTATTTTTTTA
1 TATTATTTTTTTA
1492069 T
1 T
1492070 GTCATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTATTTTTTTA
Found at i:1492040 original size:17 final size:17
Alignment explanation
Indices: 1492020--1492061 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
1492010 ATATATATCA
*
1492020 TATTTATATTATTTTTT
1 TATTTATATTATATTTT
1492037 TATTTATATTATATTTT
1 TATTTATATTATATTTT
1492054 TATATTAT
1 TAT-TTAT
1492062 TTTTTTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTATATTATATTTT
Found at i:1492053 original size:19 final size:17
Alignment explanation
Indices: 1492019--1492059 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
1492009 TATATATATC
1492019 ATATTTATATTATTTTT
1 ATATTTATATTATTTTT
*
1492036 TTATTTATATTATATTTTT
1 ATATTTATA-T-TATTTTT
1492055 ATATT
1 ATATT
1492060 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATATTTATATTATTTTT
Found at i:1492056 original size:30 final size:32
Alignment explanation
Indices: 1492007--1492069 Score: 103
Period size: 30 Copynumber: 2.0 Consensus size: 32
1491997 TTTACAAATT
1492007 TTTATATATATCATATTTATATTATTTTTTTA
1 TTTATATATATCATATTTATATTATTTTTTTA
*
1492039 TTTATAT-TAT-ATTTTTATATTATTTTTTTA
1 TTTATATATATCATATTTATATTATTTTTTTA
1492069 T
1 T
1492070 GTCATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 20 0.67
31 3 0.10
32 7 0.23
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (32 bp):
TTTATATATATCATATTTATATTATTTTTTTA
Found at i:1492077 original size:28 final size:27
Alignment explanation
Indices: 1492005--1492083 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 27
1491995 TTTTTACAAA
*
1492005 TTTTTATATATATCATATTTATATTATT
1 TTTTTATATATAT-ATTTTTATATTATT
1492033 TTTTTATTTATATTATATTTTTATATTATT
1 TTTTTA--TATA-TATATTTTTATATTATT
* *
1492063 TTTTTATGTCATATAATTTTA
1 TTTTTATAT-ATATATTTTTA
1492084 AGATATACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 17 0.39
29 1 0.02
30 23 0.52
31 3 0.07
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (27 bp):
TTTTTATATATATATTTTTATATTATT
Found at i:1492211 original size:9 final size:9
Alignment explanation
Indices: 1492149--1492211 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
1492139 ATCGAAATTA
*
1492149 TTAATCTAT
1 TTAATTTAT
*
1492158 TTAAATTGAT
1 TT-AATTTAT
*
1492168 TTAATTGAT
1 TTAATTTAT
* *
1492177 TAAATTTAA
1 TTAATTTAT
*
1492186 TTAATATAAT
1 TTAAT-TTAT
1492196 TTAATTTAT
1 TTAATTTAT
1492205 TTAATTT
1 TTAATTT
1492212 TAAAATTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 29 0.67
10 14 0.33
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (9 bp):
TTAATTTAT
Found at i:1492379 original size:21 final size:20
Alignment explanation
Indices: 1492330--1492379 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
1492320 TTATACGTAG
1492330 TTATATAATA--ATTTAAAA
1 TTATATAATATTATTTAAAA
*
1492348 TTATATAATATTATTTATAA
1 TTATATAATATTATTTAAAA
*
1492368 TATATATGATAT
1 T-TATATAATAT
1492380 AAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 10 0.37
20 8 0.30
21 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTATATAATATTATTTAAAA
Found at i:1492406 original size:25 final size:27
Alignment explanation
Indices: 1492349--1492415 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
1492339 AATTTAAAAT
1492349 TATATAATATTATT-TATAATATATATGA
1 TATA-AATATT-TTATATAATATATATGA
*
1492377 TATAAATATTTTATATAATA-ATATTA
1 TATAAATATTTTATATAATATATATGA
*
1492403 -ATAAATAATTTAT
1 TATAAATATTTTAT
1492416 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 12 0.33
26 7 0.19
27 13 0.36
28 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TATAAATATTTTATATAATATATATGA
Found at i:1495947 original size:29 final size:30
Alignment explanation
Indices: 1495891--1495949 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1495881 AAAAAATATT
**
1495891 AAAAAATATTTTATTATTAAATTTTAATAA
1 AAAAAATATTTTATTATTAAATAATAATAA
1495921 AAAAAATATTTT-TTATT-AATAAATAATAA
1 AAAAAATATTTTATTATTAAAT-AATAATAA
1495950 TTTAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 11 0.42
30 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAAAATATTTTATTATTAAATAATAATAA
Found at i:1496687 original size:12 final size:11
Alignment explanation
Indices: 1496669--1496724 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 11
1496659 TATTTATATC
*
1496669 TAATATATATT
1 TAATATAAATT
1496680 TAAATATAAATT
1 T-AATATAAATT
*
1496692 TTATA-AAATT
1 TAATATAAATT
*
1496702 TAATATATATT
1 TAATATAAATT
1496713 TAAATATAAATT
1 T-AATATAAATT
1496725 ATATAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
10 9 0.24
11 9 0.24
12 19 0.51
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATATAAATT
Found at i:1496696 original size:19 final size:19
Alignment explanation
Indices: 1496672--1496729 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 19
1496662 TTATATCTAA
1496672 TATATATTTAAATATAAAT
1 TATATATTTAAATATAAAT
* *
1496691 T-T-TA-TAAAAT-TTAA-
1 TATATATTTAAATATAAAT
1496705 TATATATTTAAATATAAAT
1 TATATATTTAAATATAAAT
1496724 TATATA
1 TATATA
1496730 AAATAATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 1 0.03
15 4 0.13
16 7 0.23
17 7 0.23
18 4 0.13
19 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATATTTAAATATAAAT
Found at i:1496711 original size:33 final size:33
Alignment explanation
Indices: 1496669--1496733 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1496659 TATTTATATC
*
1496669 TAATATATATTTAAATATAAATTTTATAAAATT
1 TAATATATATTTAAATATAAATTATATAAAATT
1496702 TAATATATATTTAAATATAAATTATATAAAAT
1 TAATATATATTTAAATATAAATTATATAAAAT
1496734 AATCTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TAATATATATTTAAATATAAATTATATAAAATT
Found at i:1503039 original size:12 final size:12
Alignment explanation
Indices: 1503022--1503144 Score: 99
Period size: 12 Copynumber: 10.2 Consensus size: 12
1503012 CGACTTCCTC
*
1503022 TCCCTTTCTTTT
1 TCCCTTTCTCTT
*
1503034 TCCCTTTCCCTT
1 TCCCTTTCTCTT
1503046 TCCCTTTCTCTT
1 TCCCTTTCTCTT
* *
1503058 TCTCTCTCTCTT
1 TCCCTTTCTCTT
*
1503070 TCTCTTTCTCTT
1 TCCCTTTCTCTT
*
1503082 TCCC--TCT-TC
1 TCCCTTTCTCTT
* *
1503091 TCCCGTTCTCGT
1 TCCCTTTCTCTT
* *
1503103 TCTCTTTCCCTT
1 TCCCTTTCTCTT
1503115 TCCCGCTTCTCTCTT
1 T-CC-CTT-TCTCTT
*
1503130 TCCCTATCTCTT
1 TCCCTTTCTCTT
1503142 TCC
1 TCC
1503145 TTCTCCCTAG
Statistics
Matches: 88, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
9 5 0.06
10 3 0.03
11 3 0.03
12 63 0.72
13 3 0.03
14 5 0.06
15 6 0.07
ACGTcount: A:0.01, C:0.43, G:0.02, T:0.54
Consensus pattern (12 bp):
TCCCTTTCTCTT
Found at i:1503041 original size:6 final size:6
Alignment explanation
Indices: 1503022--1503118 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
1503012 CGACTTCCTC
** * * * *
1503022 TCCCTT TCTTTT TCCCTT TCCCTT TCCCTT TCTCTT TCTCTC TCTCTT
1 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT
* * * * * *
1503070 TCTCTT TCTCTT TCCCTCTT CTCCCGT TCTCGT TCTCTT TCCCTT TCCC
1 TCCCTT TCCCTT T-CC-CTT -TCCCTT TCCCTT TCCCTT TCCCTT TCCC
1503119 GCTTCTCTCT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
6 67 0.88
7 3 0.04
8 5 0.07
9 1 0.01
ACGTcount: A:0.00, C:0.43, G:0.02, T:0.55
Consensus pattern (6 bp):
TCCCTT
Found at i:1503053 original size:18 final size:18
Alignment explanation
Indices: 1503022--1503152 Score: 84
Period size: 18 Copynumber: 6.9 Consensus size: 18
1503012 CGACTTCCTC
*
1503022 TCCCTTTCTTTTTCCCTT
1 TCCCTTTCTCTTTCCCTT
* *
1503040 TCCCTTTCCCTTTCTCTT
1 TCCCTTTCTCTTTCCCTT
* * *
1503058 TCTCTCTCTCTTTCTCTT
1 TCCCTTTCTCTTTCCCTT
* *
1503076 TCTCTTTCCCTCTTCTCCCGT
1 TCCCTTT--CTCTT-TCCCTT
* *
1503097 TCTCGTTCTCTTTCCCTT
1 TCCCTTTCTCTTTCCCTT
*
1503115 TCCCGCTTCTCTCTTTCCCTA
1 T-CC-CTT-TCTCTTTCCCTT
*
1503136 TCTCTTTC-CTTCTCCCT
1 TCCCTTTCTCTT-TCCCT
1503153 AGTTCTTTCC
Statistics
Matches: 91, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.03
18 49 0.54
19 9 0.10
20 8 0.09
21 22 0.24
ACGTcount: A:0.01, C:0.44, G:0.02, T:0.53
Consensus pattern (18 bp):
TCCCTTTCTCTTTCCCTT
Found at i:1503107 original size:19 final size:19
Alignment explanation
Indices: 1503085--1503126 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1503075 TTCTCTTTCC
*
1503085 CTCTTCTCCCGTTCTCG-TT
1 CTCTT-TCCCGTTCCCGCTT
*
1503104 CTCTTTCCCTTTCCCGCTT
1 CTCTTTCCCGTTCCCGCTT
1503123 CTCT
1 CTCT
1503127 CTTTCCCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.48
Consensus pattern (19 bp):
CTCTTTCCCGTTCCCGCTT
Found at i:1503140 original size:33 final size:33
Alignment explanation
Indices: 1503032--1503152 Score: 115
Period size: 33 Copynumber: 3.8 Consensus size: 33
1503022 TCCCTTTCTT
*
1503032 TTTCCCTTTCCCTTTCCCTTT--CTCTT-TCTC
1 TTTCCCTTTCTCTTTCCCTTTCCCTCTTCTCTC
* * * *
1503062 TCTCTCTTTCTCTTTCTCTTTCCCTCTTCTCCC
1 TTTCCCTTTCTCTTTCCCTTTCCCTCTTCTCTC
* * * *
1503095 GTTCTCGTTCTCTTTCCCTTTCCCGCTTCTCTC
1 TTTCCCTTTCTCTTTCCCTTTCCCTCTTCTCTC
*
1503128 TTTCCCTATCTCTTT-CCTTCTCCCT
1 TTTCCCTTTCTCTTTCCCTT-TCCCT
1503153 AGTTCTTTCC
Statistics
Matches: 71, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
30 17 0.24
32 9 0.13
33 45 0.63
ACGTcount: A:0.01, C:0.44, G:0.02, T:0.53
Consensus pattern (33 bp):
TTTCCCTTTCTCTTTCCCTTTCCCTCTTCTCTC
Found at i:1503752 original size:3 final size:3
Alignment explanation
Indices: 1503744--1503784 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
1503734 GTAAACTATA
*
1503744 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAATT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AA-T AAT AAT AAT
1503785 TTTTACTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.85
4 4 0.12
5 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1505808 original size:19 final size:18
Alignment explanation
Indices: 1505784--1505828 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
1505774 TATGTAAAAA
1505784 TAAATATAAT-ATAAATTAT
1 TAAATATAATCA-AAATT-T
1505803 TAAATAT-ATCAAAATTT
1 TAAATATAATCAAAATTT
1505820 TAAATATAA
1 TAAATATAA
1505829 ATATGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATAATCAAAATTT
Found at i:1506457 original size:2 final size:2
Alignment explanation
Indices: 1506450--1506474 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1506440 TTATGCGAAC
1506450 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1506475 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1506479 original size:2 final size:2
Alignment explanation
Indices: 1506474--1506506 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1506464 ATATATATAT
1506474 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1506507 ATCATGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1507155 original size:16 final size:16
Alignment explanation
Indices: 1507134--1507166 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1507124 TGGATGTTAC
1507134 CTCCTACAAATAATTA
1 CTCCTACAAATAATTA
1507150 CTCCTACAAATAATTA
1 CTCCTACAAATAATTA
1507166 C
1 C
1507167 ATGAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (16 bp):
CTCCTACAAATAATTA
Found at i:1511676 original size:14 final size:14
Alignment explanation
Indices: 1511650--1511687 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1511640 TATTTAAATT
1511650 TAATTAA-AATATA
1 TAATTAATAATATA
1511663 TAATTAATAATATA
1 TAATTAATAATATA
* *
1511677 AAAATAATAAT
1 TAATTAATAAT
1511688 TACAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTAATAATATA
Found at i:1511678 original size:21 final size:20
Alignment explanation
Indices: 1511650--1511689 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1511640 TATTTAAATT
1511650 TAATT-AAAATATATAATTAA
1 TAATTAAAAATA-ATAATTAA
1511670 TAATATAAAAATAATAATTA
1 TAAT-TAAAAATAATAATTA
1511690 CAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATTAAAAATAATAATTAA
Found at i:1513158 original size:27 final size:27
Alignment explanation
Indices: 1513128--1513196 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
1513118 ATATATCACC
*
1513128 TTAATCAATATTTAT-TATCATTATATA
1 TTAATCAATATTT-TCTATCATTACATA
1513155 TTAATCAATATTTTCTATCATTACATA
1 TTAATCAATATTTTCTATCATTACATA
*
1513182 TTAATTAATATTTTC
1 TTAATCAATATTTTC
1513197 ATATATATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAATCAATATTTTCTATCATTACATA
Found at i:1513338 original size:25 final size:25
Alignment explanation
Indices: 1513284--1513339 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1513274 TAAAAATATC
* **
1513284 GAATAAAAACTTTTAAATAATTTAT
1 GAATAAAAACTTATAAATAAGCTAT
*
1513309 TAATAAAAACTTATAAATAAAGCT-T
1 GAATAAAAACTTATAAAT-AAGCTAT
1513334 GAATAA
1 GAATAA
1513340 TAAATAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (25 bp):
GAATAAAAACTTATAAATAAGCTAT
Found at i:1513971 original size:15 final size:15
Alignment explanation
Indices: 1513953--1514002 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 15
1513943 TATATTTTTA
1513953 AAATATAATTTAAAT
1 AAATATAATTTAAAT
1513968 AAATATAATTTTAATTAAT
1 AAATATAA-TTT-A--AAT
1513987 AAATAATAATTTAAAT
1 AAAT-ATAATTTAAAT
1514003 TAGCTTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 8 0.27
16 6 0.20
17 1 0.03
18 1 0.03
19 10 0.33
20 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATAATTTAAAT
Found at i:1513989 original size:19 final size:20
Alignment explanation
Indices: 1513965--1514004 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1513955 ATATAATTTA
*
1513965 AATAAAT-ATAATTTTAATT
1 AATAAATAATAATTTAAATT
1513984 AATAAATAATAATTTAAATT
1 AATAAATAATAATTTAAATT
1514004 A
1 A
1514005 GCTTAGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAAATAATAATTTAAATT
Found at i:1515307 original size:91 final size:90
Alignment explanation
Indices: 1515178--1515345 Score: 198
Period size: 91 Copynumber: 1.9 Consensus size: 90
1515168 CATTTTTGTT
* * * *
1515178 ATTGGGTTAACTTGATGCTGTTCAAGCAGTGTGCTTAGCAGCAGCATTAGTAATTTTTCATGGTT
1 ATTGGGTTAACTTGATGCTGTTCAAACAGTGTGCTTAGCAACAGCATTAGT-ATTATTCACGGTT
*
1515243 CGTATATTTTTTTTTGAATATTTTAA
65 CGTATAGTTTTTTTTGAATATTTTAA
* * *
1515269 ATTGGGTTAA-TTCGATGCTGTTCAAACTA-T-TGATTTAGCAATAGCTTTAGTATTATTCACGG
1 ATTGGGTTAACTT-GATGCTGTTCAAAC-AGTGTG-CTTAGCAACAGCATTAGTATTATTCACGG
*
1515331 TTCGTTTAGTTTTTT
63 TTCGTATAGTTTTTT
1515346 GAATAAATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
90 26 0.40
91 38 0.58
92 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (90 bp):
ATTGGGTTAACTTGATGCTGTTCAAACAGTGTGCTTAGCAACAGCATTAGTATTATTCACGGTTC
GTATAGTTTTTTTTGAATATTTTAA
Found at i:1520320 original size:15 final size:15
Alignment explanation
Indices: 1520300--1520328 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1520290 AAAGAAGCAC
1520300 TCTATAATCTAAGAG
1 TCTATAATCTAAGAG
1520315 TCTATAATCTAAGA
1 TCTATAATCTAAGA
1520329 ATAGTCTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (15 bp):
TCTATAATCTAAGAG
Found at i:1521515 original size:22 final size:23
Alignment explanation
Indices: 1521478--1521520 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1521468 AATATATTAA
*
1521478 AATTTAATTTAATTTAAATAATT
1 AATTTAATTAAATTTAAATAATT
*
1521501 AATTT-ATTAAATTTATATAA
1 AATTTAATTAAATTTAAATAA
1521521 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTAATTAAATTTAAATAATT
Found at i:1521529 original size:26 final size:27
Alignment explanation
Indices: 1521464--1521538 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 27
1521454 ATAACTAAAG
*
1521464 TATAAATATATTAA-AATTT-AATTTAA
1 TATAAATA-ATTAATATTTTAAATTTAA
*
1521490 TTTAAATAATTAAT-TTATTAAATTT-A
1 TATAAATAATTAATATT-TTAAATTTAA
1521516 TATAAAT-ATATAATATTTTAAAT
1 TATAAATAAT-TAATATTTTAAAT
1521539 ATTGTTATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
25 8 0.20
26 26 0.63
27 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TATAAATAATTAATATTTTAAATTTAA
Found at i:1524981 original size:17 final size:17
Alignment explanation
Indices: 1524959--1525007 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
1524949 TCAAGTGTGA
1524959 GTGTTGGATATGGGTGT
1 GTGTTGGATATGGGTGT
*
1524976 GTGTTGGATATGGATGT
1 GTGTTGGATATGGGTGT
**
1524993 GTGTCCGATATGGGT
1 GTGTTGGATATGGGT
1525008 ATTTTTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.14, C:0.04, G:0.43, T:0.39
Consensus pattern (17 bp):
GTGTTGGATATGGGTGT
Found at i:1524994 original size:19 final size:18
Alignment explanation
Indices: 1524953--1524996 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
1524943 ACGGACTCAA
*
1524953 GTGTGAGTGTTGGATATG
1 GTGTGTGTGTTGGATATG
1524971 G-GTGTGTGTTGGATATG
1 GTGTGTGTGTTGGATATG
1524988 GATGTGTGT
1 G-TGTGTGT
1524997 CCGATATGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 16 0.70
18 1 0.04
19 6 0.26
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (18 bp):
GTGTGTGTGTTGGATATG
Found at i:1525126 original size:13 final size:13
Alignment explanation
Indices: 1525110--1525139 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1525100 AGAGTTGGAG
1525110 TATAGGTTTGGTA
1 TATAGGTTTGGTA
1525123 TATAGGTTTGGTA
1 TATAGGTTTGGTA
1525136 TATA
1 TATA
1525140 AAATAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (13 bp):
TATAGGTTTGGTA
Found at i:1527342 original size:2 final size:2
Alignment explanation
Indices: 1527335--1527361 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1527325 TAAGTGCTGT
1527335 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1527362 GAGCATTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1535234 original size:41 final size:40
Alignment explanation
Indices: 1535179--1535275 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 40
1535169 AATTATTATT
* *
1535179 TATGATAATATTTTTA-TATTAAATATAATAATTGATAGTTCA
1 TATGATAAT-TTTTTATTATTAAAAATAATAATT--TAGTTAA
* * *
1535221 TTTGATAATTTTTTATTTATTAAAAATTATAATTTATTTAA
1 TATGATAATTTTTTA-TTATTAAAAATAATAATTTAGTTAA
1535262 TATGATAATTTTTT
1 TATGATAATTTTTT
1535276 TCAAAATGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
41 24 0.51
42 8 0.17
43 15 0.32
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (40 bp):
TATGATAATTTTTTATTATTAAAAATAATAATTTAGTTAA
Found at i:1539247 original size:2 final size:2
Alignment explanation
Indices: 1539236--1539270 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1539226 TATAGTTGAA
1539236 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1539271 GTTTTCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1540325 original size:2 final size:2
Alignment explanation
Indices: 1540318--1540372 Score: 67
Period size: 2 Copynumber: 27.0 Consensus size: 2
1540308 TTGAATTTCA
*
1540318 AT AT AT AT AT AT AT AT AT AT AT AT TT AGT -T AT CAT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT
*
1540361 AT AT GT AT AT AT
1 AT AT AT AT AT AT
1540373 TCTTGCTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 1 0.02
2 42 0.91
3 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1542548 original size:14 final size:15
Alignment explanation
Indices: 1542501--1542538 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1542491 TTTTATATAT
1542501 ATTAAAATTTTAAAA
1 ATTAAAATTTTAAAA
* *
1542516 ATT-AAATTTTGAAC
1 ATTAAAATTTTAAAA
1542530 ATTAAAATT
1 ATTAAAATT
1542539 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (15 bp):
ATTAAAATTTTAAAA
Found at i:1542620 original size:4 final size:4
Alignment explanation
Indices: 1542611--1542635 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1542601 GTAATTTTAG
1542611 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1542636 TTGTTTATGT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1542844 original size:20 final size:21
Alignment explanation
Indices: 1542822--1542861 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1542812 TTAATTTTTT
1542822 AAAAATTTGATTTATTTTATA
1 AAAAATTTGATTTATTTTATA
*
1542843 AAAAATTTGATAT-TTTTAT
1 AAAAATTTGATTTATTTTAT
1542862 TGTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
AAAAATTTGATTTATTTTATA
Found at i:1544936 original size:24 final size:25
Alignment explanation
Indices: 1544904--1544962 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
1544894 ATACGTATCT
*
1544904 TATTTTATTTACTATATTAT-TTTA
1 TATTTTATTTAATATATTATATTTA
*
1544928 -ATATTTATTAAATATATTATATTTA
1 TAT-TTTATTTAATATATTATATTTA
1544953 TATTTTATTT
1 TATTTTATTT
1544963 TCATAACACC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.07
24 15 0.52
25 10 0.34
26 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTTTATTTAATATATTATATTTA
Found at i:1546869 original size:27 final size:28
Alignment explanation
Indices: 1546825--1546878 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
1546815 AATTTTGAAT
*
1546825 TTTGTTGTTATTTGTTTT-TTAATTTTG
1 TTTGTTGTTATTTATTTTATTAATTTTG
*
1546852 TTTGTATGTT-TTTATTTTATTATTTTT
1 TTTGT-TGTTATTTATTTTATTAATTTT
1546879 TAATAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (28 bp):
TTTGTTGTTATTTATTTTATTAATTTTG
Found at i:1547641 original size:16 final size:15
Alignment explanation
Indices: 1547605--1547646 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
1547595 TGCTATGTTA
1547605 ATAAAATTAA-AATT
1 ATAAAATTAATAATT
1547619 ATAAAATTAATAATTT
1 ATAAAATTAATAA-TT
*
1547635 TTAAAATTAATA
1 ATAAAATTAATA
1547647 TTTAAAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATTAATAATT
Found at i:1548307 original size:16 final size:16
Alignment explanation
Indices: 1548278--1548317 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1548268 AATTATATGT
* *
1548278 TAAATATAATATTTAA
1 TAAATTTAAAATTTAA
1548294 TAAATTTAAAATTTAA
1 TAAATTTAAAATTTAA
*
1548310 TATATTTA
1 TAAATTTA
1548318 TAATATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATTTAAAATTTAA
Found at i:1550097 original size:12 final size:12
Alignment explanation
Indices: 1550076--1550155 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
1550066 AATTTATGAG
1550076 TATAATAAATAT
1 TATAATAAATAT
*
1550088 TATTATAAATATT
1 TATAATAAATA-T
1550101 TATAATAAATAT
1 TATAATAAATAT
*
1550113 AAATAATAAA-A-
1 -TATAATAAATAT
*
1550124 TATATTAAA-AT
1 TATAATAAATAT
1550135 TATTAA-ATAATAAT
1 TA-TAATA-AAT-AT
1550149 TATAATA
1 TATAATA
1550156 TGATTAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 8 0.15
11 3 0.06
12 16 0.30
13 22 0.41
14 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATAATAAATAT
Found at i:1550645 original size:24 final size:21
Alignment explanation
Indices: 1550596--1550646 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
1550586 GTTTTATTTT
1550596 AATTT-TTTTATTTATATTAA
1 AATTTATTTTATTTATATTAA
*
1550616 ATTTTATTTTATTTGATATTATTA
1 AATTTATTTTATTT-ATATTA--A
1550640 AATTTAT
1 AATTTAT
1550647 ATAAAATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.16
21 8 0.32
22 6 0.24
24 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
AATTTATTTTATTTATATTAA
Found at i:1551216 original size:17 final size:19
Alignment explanation
Indices: 1551168--1551246 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 19
1551158 ATATCATTAA
*
1551168 TATAATACATTTAATATATT
1 TATAATATATTTAAT-TATT
*
1551188 CTCATATTTATATTTAA-TATT
1 -T-ATA-ATATATTTAATTATT
1551209 T-TAATATA-TTAATTATT
1 TATAATATATTTAATTATT
*
1551226 TATATTATATTT--TTATT
1 TATAATATATTTAATTATT
1551243 TATA
1 TATA
1551247 TGATTAATAG
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
16 4 0.08
17 18 0.37
18 8 0.16
19 2 0.04
20 1 0.02
21 5 0.10
22 3 0.06
23 8 0.16
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TATAATATATTTAATTATT
Found at i:1551217 original size:23 final size:23
Alignment explanation
Indices: 1551129--1551236 Score: 69
Period size: 23 Copynumber: 4.5 Consensus size: 23
1551119 AATATGATAA
* *
1551129 ATTTAATAAATATAATAT-TATAT
1 ATTTAATATAT-TAATATATTTAT
* *
1551152 ATTTATATATCATTAATATA-ATAC
1 ATTTA-ATAT-ATTAATATATTTAT
*
1551176 ATTTAATATATT-CTCATATTTAT
1 ATTTAATATATTAAT-ATATTTAT
* *
1551199 ATTTAATATTTTAATATATTAATT
1 ATTTAATATATTAATATATTTA-T
1551223 ATTTATATTATATT
1 ATTTA-A-TATATT
1551237 TTTATTTATA
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
21 1 0.01
22 6 0.09
23 28 0.42
24 24 0.36
25 3 0.04
26 5 0.07
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTAATATATTAATATATTTAT
Found at i:1551513 original size:10 final size:10
Alignment explanation
Indices: 1551495--1551584 Score: 54
Period size: 12 Copynumber: 8.1 Consensus size: 10
1551485 AATTTATGAT
*
1551495 TTAAGTTAAA
1 TTAATTTAAA
1551505 TTAATTTAAAA
1 TTAATTT-AAA
*
1551516 TTATATATTATA
1 TTA-AT-TTAAA
*
1551528 TTATTTTAAA
1 TTAATTTAAA
*
1551538 TAATATTTAAAA
1 TTA-ATTT-AAA
*
1551550 TTAATTTTAA
1 TTAATTTAAA
1551560 TTAATATTTAAAA
1 TT-A-ATTT-AAA
1551573 TTAAATTTAAA
1 TT-AATTTAAA
1551584 T
1 T
1551585 ATAAAAATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
10 16 0.25
11 19 0.30
12 20 0.32
13 8 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:1551556 original size:23 final size:23
Alignment explanation
Indices: 1551502--1551585 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
1551492 GATTTAAGTT
* *
1551502 AAATTAATTTAAAATTATATATT-
1 AAATTAATTTTAAATAATAT-TTA
*
1551525 ATATT-ATTTTAAATAATATTTA
1 AAATTAATTTTAAATAATATTTA
*
1551547 AAATTAATTTTAATTAATATTTA
1 AAATTAATTTTAAATAATATTTA
*
1551570 AAATTAAATTTAAATA
1 AAATTAATTTTAAATA
1551586 TAAAAATATT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.04
22 16 0.31
23 34 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATTAATTTTAAATAATATTTA
Found at i:1556636 original size:20 final size:20
Alignment explanation
Indices: 1556594--1556639 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1556584 ATTGAGTATT
*
1556594 TTAAA-AATTAATTTAAATG
1 TTAAATAATTAATTTAAATA
* *
1556613 TTAAATAATTAATTTTAGTA
1 TTAAATAATTAATTTAAATA
1556633 TTAAATA
1 TTAAATA
1556640 TTATAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TTAAATAATTAATTTAAATA
Found at i:1559187 original size:30 final size:29
Alignment explanation
Indices: 1559130--1559191 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
1559120 TTTACTTTTG
1559130 TTTGATTGAATTTTTTAATAAATTTTAACT
1 TTTGATTGAATTTTTTAATAAATTTTAA-T
* *
1559160 TTTGATTGAATTTTATTACTTAA-TTTAAT
1 TTTGATTGAATTTT-TTAATAAATTTTAAT
1559189 TTT
1 TTT
1559192 AAACATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.14
30 19 0.66
31 6 0.21
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (29 bp):
TTTGATTGAATTTTTTAATAAATTTTAAT
Found at i:1563217 original size:18 final size:19
Alignment explanation
Indices: 1563185--1563221 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1563175 ATTAACACAT
*
1563185 TTTTATTTATTTATTTTAA
1 TTTTATTTATATATTTTAA
1563204 TTTT-TTTATATATTTTAA
1 TTTTATTTATATATTTTAA
1563222 AAGATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATTTATATATTTTAA
Found at i:1566582 original size:26 final size:26
Alignment explanation
Indices: 1566534--1566644 Score: 104
Period size: 26 Copynumber: 4.2 Consensus size: 26
1566524 AAAAATAATT
1566534 TATTTAT-ATTATATTATGTATTTTTATA
1 TATTTATAATTATA-TA--TATTTTTATA
*
1566562 TATTTA-AATTAT-TATCAATTTTATTA
1 TATTTATAATTATATAT-ATTTTTA-TA
*
1566588 TATTAATAATTATATATATTTTTATA
1 TATTTATAATTATATATATTTTTATA
* *
1566614 TATTTATATTTATAATATATTTTAAT-
1 TATTTATAATTAT-ATATATTTTTATA
1566640 TATTT
1 TATTT
1566645 TTATATCATA
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
24 1 0.01
25 6 0.08
26 27 0.38
27 23 0.32
28 14 0.20
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (26 bp):
TATTTATAATTATATATATTTTTATA
Found at i:1567220 original size:21 final size:20
Alignment explanation
Indices: 1567180--1567217 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1567170 GCAAATAGAT
1567180 TAAAATTATTATTTAATTAA
1 TAAAATTATTATTTAATTAA
1567200 TAAAATTTATT-TTTAATT
1 TAAAA-TTATTATTTAATT
1567218 TAAATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAATTATTATTTAATTAA
Found at i:1567224 original size:17 final size:18
Alignment explanation
Indices: 1567179--1567225 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
1567169 TGCAAATAGA
*
1567179 TTAAAATTATTATTTAAT
1 TTAAATTTATTATTTAAT
1567197 TAATAAAATTTATT-TTTAAT
1 T--T-AAATTTATTATTTAAT
1567217 TTAAATTTA
1 TTAAATTTA
1567226 ATAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
20 8 0.32
21 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATTTATTATTTAAT
Found at i:1567225 original size:31 final size:32
Alignment explanation
Indices: 1567190--1567270 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
1567180 TAAAATTATT
** *
1567190 ATTTAATTAATAAAATTTATTTTTA-ATTTAA
1 ATTTAATTAATAAAATAAATTTTAATATTTAA
* *
1567221 ATTTAATAATATAAAATAAATTTTAATATTTAT
1 ATTTAATTA-ATAAAATAAATTTTAATATTTAA
* *
1567254 ATATAAATAATAAAATA
1 ATTTAATTAATAAAATA
1567271 TGTTTTTCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
31 8 0.20
32 21 0.52
33 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTTAATTAATAAAATAAATTTTAATATTTAA
Found at i:1567453 original size:29 final size:31
Alignment explanation
Indices: 1567415--1567478 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1567405 TTTAAAATAA
1567415 TATAAATAAA-TTAAA-AAAAATATAATAT-T
1 TATAAATAAATTTAAATAAAAATAT-ATATGT
* *
1567444 TATAATTAAATTTAAATAACAATATATATGT
1 TATAAATAAATTTAAATAAAAATATATATGT
1567475 TATA
1 TATA
1567479 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.30
30 9 0.30
31 12 0.40
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
TATAAATAAATTTAAATAAAAATATATATGT
Found at i:1571293 original size:17 final size:16
Alignment explanation
Indices: 1571253--1571294 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1571243 TAATGTAAAT
*
1571253 TATTTATTGTAATTTA
1 TATTTATTTTAATTTA
*
1571269 TCTTTATTTTAATTTA
1 TATTTATTTTAATTTA
1571285 TGATTTATTT
1 T-ATTTATTT
1571295 AACTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (16 bp):
TATTTATTTTAATTTA
Found at i:1571683 original size:15 final size:14
Alignment explanation
Indices: 1571663--1571697 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1571653 TGTTATACAA
1571663 TATATTTAATATATG
1 TATATTTAATA-ATG
*
1571678 TATATTTAATAATT
1 TATATTTAATAATG
1571692 TATATT
1 TATATT
1571698 ATATTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TATATTTAATAATG
Found at i:1572273 original size:13 final size:13
Alignment explanation
Indices: 1572255--1572279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1572245 AATGTACATA
1572255 AAATATAAATATC
1 AAATATAAATATC
1572268 AAATATAAATAT
1 AAATATAAATAT
1572280 ATTTTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAAATATC
Found at i:1577768 original size:15 final size:15
Alignment explanation
Indices: 1577702--1577769 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 15
1577692 AATATATTTT
1577702 AAAA-TTAAA-TAAA
1 AAAATTTAAATTAAA
*
1577715 ATAATATTTAATTTATAA
1 A-AA-ATTTAAATTA-AA
* * *
1577733 ATATTTTCAATTAAA
1 AAAATTTAAATTAAA
1577748 ATAAATTTAAATTAAA
1 A-AAATTTAAATTAAA
1577764 AAAATT
1 AAAATT
1577770 ATATTCACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
13 1 0.02
14 2 0.05
15 9 0.22
16 23 0.56
17 3 0.07
18 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTAAATTAAA
Found at i:1578948 original size:23 final size:23
Alignment explanation
Indices: 1578916--1578962 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1578906 ATAAAAATAA
*
1578916 AAAATAAAATTTAAAT-ATATTTT
1 AAAATAAAA-TAAAATAATATTTT
*
1578939 AAAATTAAATAAAATAATATTTT
1 AAAATAAAATAAAATAATATTTT
1578962 A
1 A
1578963 TTTATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATAAAATAAAATAATATTTT
Found at i:1579254 original size:33 final size:33
Alignment explanation
Indices: 1579211--1579299 Score: 94
Period size: 33 Copynumber: 2.6 Consensus size: 33
1579201 AAAATAAAAT
*
1579211 TAATAATAAAAAATATTTTTA-TTTTAATTTTAA
1 TAATATTAAAAAATATTTTTATTTTTAA-TTTAA
*
1579244 TAATATTAAAATAA-A-TATTATTTTTAATTTAA
1 TAATATTAAAA-AATATTTTTATTTTTAATTTAA
1579276 TAATAATTAAAATAAATATTTTTA
1 TAAT-ATT-AAA-AAATATTTTTA
1579300 AAATTTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
32 13 0.28
33 20 0.43
34 7 0.15
35 2 0.04
36 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
TAATATTAAAAAATATTTTTATTTTTAATTTAA
Found at i:1579275 original size:32 final size:34
Alignment explanation
Indices: 1579232--1579295 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
1579222 AATATTTTTA
1579232 TTTTAATTTTAATAAT-ATTAAAATAAATATTAT
1 TTTTAATTTTAATAATAATTAAAATAAATATTAT
1579265 TTTTAA-TTTAATAATAATTAAAATAAATATT
1 TTTTAATTTTAATAATAATTAAAATAAATATT
1579296 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 9 0.30
33 21 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TTTTAATTTTAATAATAATTAAAATAAATATTAT
Found at i:1579305 original size:32 final size:32
Alignment explanation
Indices: 1579205--1579305 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
1579195 TTTTTAAAAA
* * *
1579205 TAAAA-TTAATAATA-AAAAAT-ATTTTTATT
1 TAAAATTTAATAATATTAAAATAAATATTATT
* *
1579234 TTAATTTTAATAATATTAAAATAAATATTATT
1 TAAAATTTAATAATATTAAAATAAATATTATT
**
1579266 TTTAATTTAATAATAATTAAAATAAATATT-TT
1 TAAAATTTAATAAT-ATTAAAATAAATATTATT
1579298 TAAAATTT
1 TAAAATTT
1579306 TTTTTTAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 3 0.05
30 9 0.15
31 5 0.08
32 27 0.46
33 15 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TAAAATTTAATAATATTAAAATAAATATTATT
Found at i:1579936 original size:17 final size:18
Alignment explanation
Indices: 1579910--1579950 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1579900 ATCGAAATGA
1579910 AATAAATTAA-TT-ATAG
1 AATAAATTAAGTTAATAG
*
1579926 TAATAATTTAAGTTAATAG
1 -AATAAATTAAGTTAATAG
1579945 AATAAA
1 AATAAA
1579951 ATATTATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
18 7 0.35
19 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (18 bp):
AATAAATTAAGTTAATAG
Found at i:1580225 original size:35 final size:35
Alignment explanation
Indices: 1580148--1580321 Score: 167
Period size: 35 Copynumber: 5.0 Consensus size: 35
1580138 AAATTTATTG
*
1580148 TAAAAGCCTTGGAGTGTCGAAAGGGATTAGATGTAA
1 TAAAAGTCTTGGAGTGTCGAAAGGGA-TAGATGTAA
* *
1580184 TAAAAGTCTTGGGGTGTTGAAAGGGATAGATGTAA
1 TAAAAGTCTTGGAGTGTCGAAAGGGATAGATGTAA
** * *
1580219 CGAAAGTCTT-TAGGTGCCGAAAGGG-TAGATGTAA
1 TAAAAGTCTTGGA-GTGTCGAAAGGGATAGATGTAA
* *
1580253 TAAAAGTCTTGGAGTGTTG-ACGGGTATAGATGTAA
1 TAAAAGTCTTGGAGTGTCGAAAGGG-ATAGATGTAA
* * * * *
1580288 TAAAAATTTTGGA-TGCCGAAGGGGATGGATGTAA
1 TAAAAGTCTTGGAGTGTCGAAAGGGATAGATGTAA
1580322 AAGAAACTTG
Statistics
Matches: 112, Mismatches: 21, Indels: 12
0.77 0.14 0.08
Matches are distributed among these distances:
33 4 0.04
34 33 0.29
35 52 0.46
36 23 0.21
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (35 bp):
TAAAAGTCTTGGAGTGTCGAAAGGGATAGATGTAA
Found at i:1580319 original size:69 final size:69
Alignment explanation
Indices: 1580165--1580321 Score: 185
Period size: 69 Copynumber: 2.2 Consensus size: 69
1580155 CTTGGAGTGT
* * *
1580165 CGAAAGGGATTAGATGTAATAAAAGTCTTGGGGTGTTGAAAGGGATAGATGTAACGAAAGTCTTT
1 CGAAAGGG--TAGATGTAATAAAAGTCTTGGAGTGTTGAAAGGGATAGATGTAACAAAAATCTTT
1580230 AGGTGC
64 AGGTGC
* *
1580236 CGAAAGGGTAGATGTAATAAAAGTCTTGGAGTGTTG-ACGGGTATAGATGTAATAAAAAT-TTT-
1 CGAAAGGGTAGATGTAATAAAAGTCTTGGAGTGTTGAAAGGG-ATAGATGTAACAAAAATCTTTA
1580298 GGATGC
65 GG-TGC
* *
1580304 CGAAGGGGATGGATGTAA
1 CGAAAGGG-TAGATGTAA
1580322 AAGAAACTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
67 2 0.03
68 17 0.22
69 49 0.64
71 8 0.11
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.27
Consensus pattern (69 bp):
CGAAAGGGTAGATGTAATAAAAGTCTTGGAGTGTTGAAAGGGATAGATGTAACAAAAATCTTTAG
GTGC
Found at i:1581936 original size:19 final size:18
Alignment explanation
Indices: 1581888--1581938 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
1581878 AATATATGTA
1581888 TTATATTTATATTTAAAAT
1 TTATA-TTATATTTAAAAT
1581907 TT-TGA-TATATTTAATAAT
1 TTAT-ATTATATTTAA-AAT
1581925 TTATATTATATTTA
1 TTATATTATATTTA
1581939 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 12 0.43
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATATTATATTTAAAAT
Found at i:1581952 original size:18 final size:19
Alignment explanation
Indices: 1581911--1581952 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1581901 TAAAATTTTG
*
1581911 ATATATTTAATAATTTATA
1 ATATATTTAATAATTTAAA
* *
1581930 TTATATTT-ATATTTTAAA
1 ATATATTTAATAATTTAAA
1581948 ATATA
1 ATATA
1581953 AAAAGTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATTTAATAATTTAAA
Found at i:1582515 original size:6 final size:6
Alignment explanation
Indices: 1582491--1582529 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1582481 ATATATGTCC
*
1582491 ATAAAT ATATAT A-AAAT ATAAAT ATCAAAT ATAAAT ATA
1 ATAAAT ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATA
1582530 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.14
6 19 0.66
7 6 0.21
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:1582520 original size:13 final size:13
Alignment explanation
Indices: 1582499--1582529 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1582489 CCATAAATAT
1582499 ATATAAAATATAA
1 ATATAAAATATAA
*
1582512 ATATCAAATATAA
1 ATATAAAATATAA
1582525 ATATA
1 ATATA
1582530 TTTTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAAAATATAA
Found at i:1583675 original size:21 final size:21
Alignment explanation
Indices: 1583641--1583692 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1583631 TAAATTTAAA
*
1583641 TAAA-AATAATATTTATTAGT
1 TAAATAATTATATTTATTAGT
1583661 TAAATAATTATATTTATTAGT
1 TAAATAATTATATTTATTAGT
1583682 TAAATAATTAT
1 TAAATAATTAT
1583693 TTGAATCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
TAAATAATTATATTTATTAGT
Found at i:1584535 original size:37 final size:36
Alignment explanation
Indices: 1584494--1584575 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
1584484 ATTTTTTTAA
* *
1584494 AATAATTATATAAA-TTAATTAAATAAATTTTAAATTT
1 AATAAATAT-TAAATTTAATAAAATAAA-TTTAAATTT
*
1584531 AATAAATATTAAATTTTTATAAAATAAATTTAAATTT
1 AATAAATATTAAA-TTTAATAAAATAAATTTAAATTT
1584568 ATATAAAT
1 A-ATAAAT
1584576 TTATTTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 4 0.10
37 18 0.46
38 17 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
AATAAATATTAAATTTAATAAAATAAATTTAAATTT
Found at i:1584559 original size:22 final size:21
Alignment explanation
Indices: 1584531--1584574 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1584521 TTTTAAATTT
*
1584531 AATAAATATTAAATTTTTATAA
1 AATAAAT-TTAAATTTATATAA
1584553 AATAAATTTAAATTTATATAA
1 AATAAATTTAAATTTATATAA
1584574 A
1 A
1584575 TTTATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAAATTTAAATTTATATAA
Found at i:1584575 original size:16 final size:16
Alignment explanation
Indices: 1584499--1584578 Score: 60
Period size: 16 Copynumber: 4.8 Consensus size: 16
1584489 TTTAAAATAA
1584499 TTATATAAA-TT-AA-
1 TTATATAAATTTAAAT
*
1584512 TTAAATAAATTTTAAAT
1 TTATATAAA-TTTAAAT
1584529 TTA-ATAAATATTAAATTT
1 TTATATAAAT-TTAAA--T
1584547 TTATAAAATAAATTTAAAT
1 TTAT---ATAAATTTAAAT
1584566 TTATATAAATTTA
1 TTATATAAATTTA
1584579 TTTATTTTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 19
0.73 0.01 0.25
Matches are distributed among these distances:
13 8 0.15
15 3 0.05
16 21 0.38
17 3 0.05
18 4 0.07
19 5 0.09
21 5 0.09
22 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATATAAATTTAAAT
Found at i:1586036 original size:16 final size:17
Alignment explanation
Indices: 1586015--1586047 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1586005 TTTATATTTT
1586015 AATT-AATTTTAATAAA
1 AATTAAATTTTAATAAA
*
1586031 AATTAAATTTTATTAAA
1 AATTAAATTTTAATAAA
1586048 TAATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAAATTTTAATAAA
Found at i:1587008 original size:27 final size:27
Alignment explanation
Indices: 1586950--1587008 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
1586940 ATAATTAAAC
*
1586950 ATATAAAAAATAACACAAACATAATAT
1 ATATAAAAAATAACACAAACATAAAAT
1586977 ATATAAAAATATTAACA-AAAC-TAAAAT
1 ATATAAAAA-A-TAACACAAACATAAAAT
*
1587004 TTATA
1 ATATA
1587009 TGATTTCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 18 0.64
28 5 0.18
29 5 0.18
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.27
Consensus pattern (27 bp):
ATATAAAAAATAACACAAACATAAAAT
Found at i:1587008 original size:29 final size:27
Alignment explanation
Indices: 1586950--1587009 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 27
1586940 ATAATTAAAC
*
1586950 ATATAAAAAATAACACAAACATAATAT
1 ATATAAAAAATAACACAAACAAAATAT
*
1586977 ATATAAAAATATTAACA-AAACTAAAATTT
1 ATATAAAAA-A-TAACACAAAC-AAAATAT
1587006 ATAT
1 ATAT
1587010 GATTTCAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 9 0.32
28 5 0.18
29 14 0.50
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.28
Consensus pattern (27 bp):
ATATAAAAAATAACACAAACAAAATAT
Found at i:1587463 original size:22 final size:21
Alignment explanation
Indices: 1587430--1587505 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 21
1587420 TTATTTAAAT
1587430 ATATGAAAAATAACATAAACATA
1 ATAT-AAAAATAA-ATAAACATA
*
1587453 ATATAAAAATAATTAAAACATA
1 ATATAAAAATAAAT-AAACATA
*
1587475 ATA-AAAAATAAATATAACACGA
1 ATATAAAAATAAATA-AACA-TA
1587497 ATATAAAAA
1 ATATAAAAA
1587506 CATAAAATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 22 0.48
23 9 0.20
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.22
Consensus pattern (21 bp):
ATATAAAAATAAATAAACATA
Found at i:1587625 original size:14 final size:14
Alignment explanation
Indices: 1587587--1587626 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1587577 ATACATAAAA
*
1587587 TTTTTTTCCTCCTT
1 TTTTTTTCTTCCTT
*
1587601 TTTTTTCTCTTTCTT
1 TTTTTT-TCTTCCTT
1587616 TTTTTTTCTTC
1 TTTTTTTCTTC
1587627 TTCCTCTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTTCTTCCTT
Found at i:1587634 original size:19 final size:18
Alignment explanation
Indices: 1587592--1587634 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
1587582 TAAAATTTTT
*
1587592 TTCCTCCTTTTTTTTCTC
1 TTCCTCTTTTTTTTTCTC
1587610 TT--TCTTTTTTTTTCTTC
1 TTCCTCTTTTTTTTTC-TC
1587627 TTCCTCTT
1 TTCCTCTT
1587635 CCCATGACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 11 0.52
17 4 0.19
18 2 0.10
19 4 0.19
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTCCTCTTTTTTTTTCTC
Found at i:1587750 original size:20 final size:18
Alignment explanation
Indices: 1587727--1587770 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1587717 TTATAGATAG
1587727 ATATAAAAAATCAAAATATA
1 ATATAAAAAAT-AAAATA-A
*
1587747 ATATAAAAAATAATATAA
1 ATATAAAAAATAAAATAA
1587765 ATATAA
1 ATATAA
1587771 TATGAATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 5 0.22
20 11 0.48
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
ATATAAAAAATAAAATAA
Found at i:1587772 original size:11 final size:11
Alignment explanation
Indices: 1587740--1587778 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1587730 TAAAAAATCA
1587740 AAATATAATAT
1 AAATATAATAT
*
1587751 AAAAAATAATAT
1 -AAATATAATAT
1587763 AAATATAATAT
1 AAATATAATAT
*
1587774 GAATA
1 AAATA
1587779 CATAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1587945 original size:16 final size:16
Alignment explanation
Indices: 1587926--1587958 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1587916 ACATAATATG
*
1587926 AATATATATATATAAA
1 AATATATATAAATAAA
1587942 AATATATATAAATAAA
1 AATATATATAAATAAA
1587958 A
1 A
1587959 TAAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATATATAAATAAA
Found at i:1587986 original size:33 final size:31
Alignment explanation
Indices: 1587948--1588010 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
1587938 TAAAAATATA
*
1587948 TATAAATAAAATAA-ATTATTAATATGTAAAAAG
1 TATAAA-AAAATAATATT-TTAA-ATATAAAAAG
*
1587981 TATAAAAATATAATATTTTAAATATAAAAA
1 TATAAAAAAATAATATTTTAAATATAAAAA
1588011 ATAACATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 8 0.30
32 10 0.37
33 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (31 bp):
TATAAAAAAATAATATTTTAAATATAAAAAG
Found at i:1588047 original size:8 final size:8
Alignment explanation
Indices: 1588034--1588109 Score: 70
Period size: 8 Copynumber: 9.8 Consensus size: 8
1588024 AAAATATAAT
1588034 TTTTTTTC
1 TTTTTTTC
1588042 TTTTTTTC
1 TTTTTTTC
*
1588050 -CTTTTTC
1 TTTTTTTC
1588057 TTTTTTCTCC
1 TTTTTT-T-C
*
1588067 TTTCTTTC
1 TTTTTTTC
*
1588075 -TTTCTT-
1 TTTTTTTC
1588081 TTTTTTTC
1 TTTTTTTC
*
1588089 TTTTCTTC
1 TTTTTTTC
1588097 TTTTTTT-
1 TTTTTTTC
1588104 TTTTTT
1 TTTTTT
1588110 CAGCTGAACT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
7 21 0.38
8 26 0.47
9 2 0.04
10 6 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1588060 original size:22 final size:22
Alignment explanation
Indices: 1588033--1588110 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 22
1588023 CAAAATATAA
1588033 TTTTTTTTCTTTTTTTCCTTTT
1 TTTTTTTTCTTTTTTTCCTTTT
*
1588055 TCTTTTTTCTCCTTTCTTT-CTTTCT
1 T-TTTTTT-T-CTTTTTTTCCTTT-T
* *
1588080 TTTTTTTTCTTTTCTTCTTTTT
1 TTTTTTTTCTTTTTTTCCTTTT
1588102 TTTTTTTTC
1 TTTTTTTTC
1588111 AGCTGAACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
22 17 0.36
23 10 0.21
24 11 0.23
25 9 0.19
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTTTCTTTTTTTCCTTTT
Found at i:1588088 original size:18 final size:19
Alignment explanation
Indices: 1588067--1588110 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1588057 TTTTTTCTCC
1588067 TTTCTTTCT-TTCTTTTTT
1 TTTCTTTCTCTTCTTTTTT
1588085 TTTCTTT-TCTTCTTTTTT
1 TTTCTTTCTCTTCTTTTTT
*
1588103 TTTTTTTC
1 TTTCTTTC
1588111 AGCTGAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTCTTTCTCTTCTTTTTT
Found at i:1591330 original size:21 final size:22
Alignment explanation
Indices: 1591301--1591346 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1591291 TGTTCAGATA
**
1591301 AGTAGTACTCCGCAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1591323 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1591344 AGT
1 AGT
1591347 TTTAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Done.