Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 26 of 168
Found at i:6757597 original size:81 final size:83
Alignment explanation
Indices: 6757440--6757588 Score: 234
Period size: 81 Copynumber: 1.8 Consensus size: 83
6757430 TGGGCTTAGG
* *
6757440 TTTTTAGCGGCGGTTTTTTAAAAAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTTAGAA
1 TTTTTAGCGGCGGTTTTTTAAAAAAGTGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTCTAGAA
*
6757505 AGTGCCACTAATACTCTA
66 AATGCCACTAATACTCTA
*
6757523 TTTTTAGCGGC-G-TTTTTAAAAAAGTGCCACTAATGCTCGGGGCTTTAGCGGCG-TTTCT-GAA
1 TTTTTAGCGGCGGTTTTTTAAAAAAGTGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTCTAGAA
6757584 AATGC
66 AATGC
6757589 GCTGCTAATG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
79 7 0.11
80 4 0.06
81 39 0.63
82 1 0.02
83 11 0.18
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (83 bp):
TTTTTAGCGGCGGTTTTTTAAAAAAGTGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTCTAGAA
AATGCCACTAATACTCTA
Found at i:6757637 original size:41 final size:40
Alignment explanation
Indices: 6757442--6757665 Score: 141
Period size: 41 Copynumber: 5.5 Consensus size: 40
6757432 GGCTTAGGTT
* * * *
6757442 TTTAGCGGCGGTTTTTTAAAAAAGTGCCGCTAATGCTCAGGGC
1 TTTAGCGGC-G-TTTTT-GAAAAGCGGCGCTAATGCTCAAGGC
* * * * * * **
6757485 TTTAGCGGCGTTTTTTAGAAAGTGCCACTAATACTCTA-TT
1 TTTAGCGGCGTTTTTGA-AAAGCGGCGCTAATGCTCAAGGC
* * * * **
6757525 TTTAGCGGCGTTTTTAAAAAAGTGCCACTAATGCTCGGGGC
1 TTTAGCGGCGTTTTT-GAAAAGCGGCGCTAATGCTCAAGGC
* *
6757566 TTTAGCGGCGTTTCTGAAAATGC-GCTGCTAATGCTTAAGGC
1 TTTAGCGGCGTTTTTGAAAA-GCGGC-GCTAATGCTCAAGGC
* *
6757607 TTTAGCGGCGTTTTTGAAGAAGCGGCGCTAATGCTCTA--T
1 TTTAGCGGCGTTTTTGAA-AAGCGGCGCTAATGCTCAAGGC
*
6757646 TTTAGCAGCGTTTTTGAAAA
1 TTTAGCGGCGTTTTTGAAAA
6757666 AGCGCCGCAA
Statistics
Matches: 148, Mismatches: 26, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
38 2 0.01
39 17 0.11
40 38 0.26
41 77 0.52
42 5 0.03
43 9 0.06
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGAAAAGCGGCGCTAATGCTCAAGGC
Found at i:6763099 original size:21 final size:21
Alignment explanation
Indices: 6763075--6763120 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
6763065 ATATATATAT
6763075 GTTTAGCTTAGTATTGATCTG
1 GTTTAGCTTAGTATTGATCTG
*
6763096 GTTTAGCTTAGTATTGGTCTG
1 GTTTAGCTTAGTATTGATCTG
6763117 GTTT
1 GTTT
6763121 TTTTACATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (21 bp):
GTTTAGCTTAGTATTGATCTG
Found at i:6765395 original size:24 final size:23
Alignment explanation
Indices: 6765367--6765414 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
6765357 AATTTAAAAA
6765367 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
6765391 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
6765414 A
1 A
6765415 AAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:6766063 original size:18 final size:16
Alignment explanation
Indices: 6766040--6766077 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
6766030 GTTTCATTTA
6766040 ATTTTTTAATATTCCATT
1 ATTTTTTAATA--CCATT
6766058 A-TTTTTAATACCATT
1 ATTTTTTAATACCATT
6766073 ATTTT
1 ATTTT
6766078 AAATCTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.32
16 3 0.16
17 9 0.47
18 1 0.05
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTTAATACCATT
Found at i:6766073 original size:15 final size:16
Alignment explanation
Indices: 6766042--6766077 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
6766032 TTCATTTAAT
6766042 TTTTTAATATTCCATTA
1 TTTTTAATA-TCCATTA
6766059 TTTTTAATA-CCATTA
1 TTTTTAATATCCATTA
6766074 TTTT
1 TTTT
6766078 AAATCTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.53
17 9 0.47
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTAATATCCATTA
Found at i:6766357 original size:27 final size:27
Alignment explanation
Indices: 6766303--6766371 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
6766293 TAAATTTATT
*
6766303 ACTTTA-TATATA-TTT-TTTAATCCT
1 ACTTTATTATATATTTTATTTAATCCA
* *
6766327 ACTTTATTATATATTTTATTTATTTCA
1 ACTTTATTATATATTTTATTTAATCCA
6766354 AC-TTATTA-ATATTATTAT
1 ACTTTATTATATATT-TTAT
6766372 ATATATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.16
25 11 0.29
26 13 0.34
27 8 0.21
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (27 bp):
ACTTTATTATATATTTTATTTAATCCA
Found at i:6771429 original size:43 final size:43
Alignment explanation
Indices: 6771368--6771454 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
6771358 CTGGTTCTAT
*
6771368 AATAGTAGGTTGTCTATTTAAAACTTACTTAAACCAGTCTTGA
1 AATAGTAGGTTGTCTATTTAAAACTTACTTAAACCAATCTTGA
6771411 AATAGTAGGTTGTCTATTTAAAACTTACTTAAACCAATCTTGA
1 AATAGTAGGTTGTCTATTTAAAACTTACTTAAACCAATCTTGA
6771454 A
1 A
6771455 TTTTAGCAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (43 bp):
AATAGTAGGTTGTCTATTTAAAACTTACTTAAACCAATCTTGA
Found at i:6772381 original size:49 final size:52
Alignment explanation
Indices: 6772289--6772403 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 52
6772279 AAATGATTCT
* **
6772289 GGCGTGTTTTTGGGGGTAGATGTAAAGCATACGGGCTTGGCACTTGGTCCT-A
1 GGCGTGTTTTTGGAGG-AGATGTAAAGCATACGGGCTAAGCACTTGGTCCTCA
* * *
6772341 GGCGTGTTTTTGGAGG-GATGT-TAGCCTACGGGCTAAGCACTTGGTGCTCA
1 GGCGTGTTTTTGGAGGAGATGTAAAGCATACGGGCTAAGCACTTGGTCCTCA
* *
6772391 GGCATGTTCTTGG
1 GGCGTGTTTTTGG
6772404 TTCGATTGGC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
49 22 0.41
50 17 0.31
52 15 0.28
ACGTcount: A:0.16, C:0.17, G:0.37, T:0.31
Consensus pattern (52 bp):
GGCGTGTTTTTGGAGGAGATGTAAAGCATACGGGCTAAGCACTTGGTCCTCA
Found at i:6776511 original size:2 final size:2
Alignment explanation
Indices: 6776506--6776542 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6776496 GACAGAGAGC
*
6776506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6776543 TTTGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6779683 original size:2 final size:2
Alignment explanation
Indices: 6779676--6779723 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6779666 ATGTCTCATT
6779676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6779718 TA TA TA
1 TA TA TA
6779724 AATTATTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6781615 original size:21 final size:22
Alignment explanation
Indices: 6781565--6781627 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
6781555 TATGTGATTT
*
6781565 TATACATTTT-TAATTTATTAAA
1 TATATATTTTGTAA-TTATTAAA
6781587 TAATATATTTTGTAATT-TTAAA
1 T-ATATATTTTGTAATTATTAAA
6781609 TATATATTTGTGCTAATTA
1 TATATATTT-TG-TAATTA
6781628 AATGATGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 8 0.23
22 9 0.26
23 15 0.43
24 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (22 bp):
TATATATTTTGTAATTATTAAA
Found at i:6781625 original size:23 final size:22
Alignment explanation
Indices: 6781582--6781626 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
6781572 TTTTAATTTA
6781582 TTAAATAATATATTTTGTAATT
1 TTAAATAATATATTTTGTAATT
6781604 TTAAAT-ATATATTTGTGCTAATT
1 TTAAATAATATATTT-TG-TAATT
6781627 AAATGATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (22 bp):
TTAAATAATATATTTTGTAATT
Found at i:6792425 original size:80 final size:80
Alignment explanation
Indices: 6792292--6792451 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
6792282 TACATAAACT
6792292 CACATCCGTTTGTCTGTTCTGTTCAGGTAATCCACAGACATAGGCGGGTCGGTGCGACGGAGGCT
1 CACATCCGTTTGTCTGTTCTGTTCAGGTAATCCACAGACATAGGCGGGTCGGTGCGACGGAGGCT
6792357 CAGCGGTAACCACTC
66 CAGCGGTAACCACTC
6792372 CACATCCGTTTGTCTGTTCTGTTCAGGTAATCCACAGACATAGGCGGGTCGGTGCGACGGAGGCT
1 CACATCCGTTTGTCTGTTCTGTTCAGGTAATCCACAGACATAGGCGGGTCGGTGCGACGGAGGCT
6792437 CAGCGGTAACCACTC
66 CAGCGGTAACCACTC
6792452 GACGGGAAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.20, C:0.28, G:0.29, T:0.24
Consensus pattern (80 bp):
CACATCCGTTTGTCTGTTCTGTTCAGGTAATCCACAGACATAGGCGGGTCGGTGCGACGGAGGCT
CAGCGGTAACCACTC
Found at i:6794698 original size:29 final size:28
Alignment explanation
Indices: 6794665--6794725 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
6794655 AAAAAGCTGT
6794665 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
6794694 TTTTTTGATTATTTATCGGAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
6794722 TTTT
1 TTTT
6794726 CTGGGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:6802670 original size:21 final size:21
Alignment explanation
Indices: 6802625--6802694 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
6802615 TTTTGAACCC
* * *
6802625 TAAACGTCGAACCCTGACT-T
1 TAAACCTCGAATCTTGACTCT
* *
6802645 TAAACTTTGAATCTTGAAC-CT
1 TAAACCTCGAATCTTG-ACTCT
6802666 TAAACCTCGAATCTTGACTCT
1 TAAACCTCGAATCTTGACTCT
6802687 TAAACCTC
1 TAAACCTC
6802695 AAACTCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (21 bp):
TAAACCTCGAATCTTGACTCT
Found at i:6805985 original size:17 final size:18
Alignment explanation
Indices: 6805963--6806004 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
6805953 GCAAATACAT
* *
6805963 AATAAAAG-AAATCATCA
1 AATAAAAGTAAATAAACA
6805980 AATAAAAGTAAATAAACA
1 AATAAAAGTAAATAAACA
6805998 AATAAAA
1 AATAAAA
6806005 ATTAAAGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (18 bp):
AATAAAAGTAAATAAACA
Found at i:6806232 original size:3 final size:3
Alignment explanation
Indices: 6806224--6806252 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6806214 NNNNNNNAAC
6806224 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6806253 AATTGCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6820572 original size:17 final size:18
Alignment explanation
Indices: 6820550--6820591 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
6820540 GCAAATACAT
* *
6820550 AATAAAAG-AAATCATCA
1 AATAAAAGTAAATAAACA
6820567 AATAAAAGTAAATAAACA
1 AATAAAAGTAAATAAACA
6820585 AATAAAA
1 AATAAAA
6820592 ATTAAAGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (18 bp):
AATAAAAGTAAATAAACA
Found at i:6820839 original size:2 final size:2
Alignment explanation
Indices: 6820832--6820887 Score: 96
Period size: 2 Copynumber: 28.0 Consensus size: 2
6820822 AAACATGTAA
6820832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6820874 AT AT A- AGT AT AT AT
1 AT AT AT A-T AT AT AT
6820888 GAGTTCTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6820993 original size:3 final size:3
Alignment explanation
Indices: 6820985--6821035 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
6820975 AATAAATAGG
6820985 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6821033 TAA
1 TAA
6821036 AGATACTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6825409 original size:13 final size:14
Alignment explanation
Indices: 6825391--6825419 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6825381 GAGTAATTGA
6825391 TTAAAAAA-TATTT
1 TTAAAAAACTATTT
6825404 TTAAAAAACTATTT
1 TTAAAAAACTATTT
6825418 TT
1 TT
6825420 TATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAAAAACTATTT
Found at i:6826797 original size:21 final size:22
Alignment explanation
Indices: 6826771--6826815 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
6826761 ATTAGTCAGC
* *
6826771 AAGAAATGAATAA-AAATGAGG
1 AAGAAATGAAGAAGAAAAGAGG
6826792 AAGAAATGAAGAAGAAAAGAGG
1 AAGAAATGAAGAAGAAAAGAGG
6826814 AA
1 AA
6826816 ATTTCAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (22 bp):
AAGAAATGAAGAAGAAAAGAGG
Found at i:6826800 original size:11 final size:11
Alignment explanation
Indices: 6826771--6826808 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6826761 ATTAGTCAGC
*
6826771 AAGAAATGAAT
1 AAGAAATGAAG
*
6826782 AA-AAATGAGG
1 AAGAAATGAAG
6826792 AAGAAATGAAG
1 AAGAAATGAAG
6826803 AAGAAA
1 AAGAAA
6826809 AGAGGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.11
Consensus pattern (11 bp):
AAGAAATGAAG
Found at i:6826929 original size:3 final size:3
Alignment explanation
Indices: 6826923--6826961 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
6826913 AGTGGTGGTT
6826923 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
6826962 AACATTGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6829544 original size:154 final size:154
Alignment explanation
Indices: 6829111--6829583 Score: 652
Period size: 155 Copynumber: 3.0 Consensus size: 154
6829101 TTTAGTGTGT
* * *
6829111 TTTTTATTGAAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGACCGAAATAAGGAGTTTTT
1 TTTTTATTGAAAGTAATAAAATCCGG-GAAAAAATACGAACAAAGG-GCGAAATAA-GAG-TTTT
* * *
6829176 TTTAAAAAAAATTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTATTAAAGTAA
62 TTT--AAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAA
* *
6829241 TGTAAAATTAGAAAATTAGAAAATAGTATA
125 TGTAAAATAATAAAATTAGAAAATAGTATA
* * *
6829271 -TTTT-TTAAAAGTAATAAAATCCAGGGAAAAAAATAGGAACAAAGGGTCAAAATAAGAGTTTTT
1 TTTTTATTGAAAGTAATAAAATCC-GGG-AAAAAATACGAACAAAGGG-CGAAATAAGAGTTTTT
* * *
6829334 ATT-TAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATG
63 -TTAAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATG
*
6829398 TAAAATAATAAAA-TACGAAAATAATATA
127 TAAAATAATAAAATTA-GAAAATAGTATA
6829426 TTTTTATTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGGGCGGAAATAAG-GTTTTTTT
1 TTTTTATTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGGGC-GAAATAAGAGTTTTTTT
*
6829490 AAAAATTTATTAAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
65 AAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
6829555 AATAATAAAATTAGAAAATAGTA-A
130 AATAATAAAATTAGAAAATAGTATA
6829579 TTTTT
1 TTTTT
6829584 TTAAAGAAAA
Statistics
Matches: 280, Mismatches: 23, Indels: 27
0.85 0.07 0.08
Matches are distributed among these distances:
153 8 0.03
154 88 0.31
155 104 0.37
156 7 0.03
157 22 0.08
158 21 0.08
159 30 0.11
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (154 bp):
TTTTTATTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGGGCGAAATAAGAGTTTTTTTA
AAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
ATAATAAAATTAGAAAATAGTATA
Found at i:6839486 original size:22 final size:20
Alignment explanation
Indices: 6839448--6839488 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
6839438 AAACTTTAAC
*
6839448 TTTTTTATGAATAAGTATAT
1 TTTTTTATAAATAAGTATAT
6839468 TTTTTTATAATATATAGTATA
1 TTTTTTATAA-ATA-AGTATA
6839489 GACACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTTTTATAAATAAGTATAT
Found at i:6842417 original size:30 final size:30
Alignment explanation
Indices: 6842372--6842430 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
6842362 GAAGAGCATC
6842372 AAGGCATTGGAAGCACGAAGAAGAAGAAAT
1 AAGGCATTGGAAGCACGAAGAAGAAGAAAT
* * *
6842402 AAGGCTTTGGGAGCACGTAGAAGAAGAAA
1 AAGGCATTGGAAGCACGAAGAAGAAGAAA
6842431 CATTGCGAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.32, T:0.12
Consensus pattern (30 bp):
AAGGCATTGGAAGCACGAAGAAGAAGAAAT
Found at i:6843217 original size:6 final size:6
Alignment explanation
Indices: 6843206--6843231 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6843196 ACTAAAGTTG
6843206 AAGATA AAGATA AAGATA AAGATA AA
1 AAGATA AAGATA AAGATA AAGATA AA
6843232 AGTTTTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAGATA
Found at i:6846222 original size:17 final size:17
Alignment explanation
Indices: 6846200--6846234 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6846190 AGAAACCGAT
6846200 AGTATTGTTATTCCTAG
1 AGTATTGTTATTCCTAG
6846217 AGTATTGTTATTCCTAG
1 AGTATTGTTATTCCTAG
6846234 A
1 A
6846235 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (17 bp):
AGTATTGTTATTCCTAG
Found at i:6848441 original size:45 final size:46
Alignment explanation
Indices: 6848384--6848569 Score: 286
Period size: 47 Copynumber: 4.0 Consensus size: 46
6848374 TTTTTTTCAC
* *
6848384 CAAAATTGGACAGCATAT-ATACAAAATTGGACTGCATTTATACGT
1 CAAAATTTGACAGCATATAATACAAAATTGGACTGCATTTATACAT
* *
6848429 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAATTTGACAGCATATA-ATACAAAATTGGACTGCATTTATACAT
6848476 CAAAATTTGACAGCATAT-ATACAAAATTGGACTGCATTTATACAT
1 CAAAATTTGACAGCATATAATACAAAATTGGACTGCATTTATACAT
* *
6848521 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAATTTGACAGCATATA-ATACAAAATTGGACTGCATTTATACAT
6848568 CA
1 CA
6848570 CAATATAATT
Statistics
Matches: 129, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
45 60 0.47
47 69 0.53
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (46 bp):
CAAAATTTGACAGCATATAATACAAAATTGGACTGCATTTATACAT
Found at i:6848497 original size:92 final size:92
Alignment explanation
Indices: 6848384--6848569 Score: 354
Period size: 92 Copynumber: 2.0 Consensus size: 92
6848374 TTTTTTTCAC
*
6848384 CAAAATTGGACAGCATATATACAAAATTGGACTGCATTTATACGTCAAAATTTGACAGCATATAC
1 CAAAATTGGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAGCATATAC
6848449 ATATATAATTGGACTGCATTTATACAT
66 ATATATAATTGGACTGCATTTATACAT
*
6848476 CAAAATTTGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAGCATATAC
1 CAAAATTGGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAGCATATAC
6848541 ATATATAATTGGACTGCATTTATACAT
66 ATATATAATTGGACTGCATTTATACAT
6848568 CA
1 CA
6848570 CAATATAATT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (92 bp):
CAAAATTGGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAGCATATAC
ATATATAATTGGACTGCATTTATACAT
Found at i:6848585 original size:29 final size:29
Alignment explanation
Indices: 6848543--6848598 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
6848533 GCATATACAT
*
6848543 ATATAATTGGACTGCATTTATACATCACA
1 ATATAATTGGACTGCAATTATACATCACA
6848572 ATATAATTGGACTGCAATTATACATCA
1 ATATAATTGGACTGCAATTATACATCA
6848599 AAATTTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (29 bp):
ATATAATTGGACTGCAATTATACATCACA
Found at i:6848624 original size:21 final size:21
Alignment explanation
Indices: 6848598--6848682 Score: 66
Period size: 21 Copynumber: 3.9 Consensus size: 21
6848588 ATTATACATC
6848598 AAAATTTG-ACAGCATATATAT
1 AAAA-TTGAACAGCATATATAT
* *
6848619 AAAATTGAACTGCATTTATACAT
1 AAAATTGAACAGCA--TATATAT
* *
6848642 CAAAATTTG-ACAGCATATGTAC
1 -AAAA-TTGAACAGCATATATAT
*
6848664 AAAATTGAACAGCACATAT
1 AAAATTGAACAGCATATAT
6848683 TCAATTTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
20 6 0.12
21 22 0.44
22 4 0.08
23 6 0.12
24 9 0.18
25 3 0.06
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAATTGAACAGCATATATAT
Found at i:6848632 original size:45 final size:45
Alignment explanation
Indices: 6848576--6848673 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 45
6848566 ATCACAATAT
* *
6848576 AATTGGACTGCAATTATACATCAAAATTTGACAGCATATATATAA
1 AATTGAACTGCAATTATACATCAAAATTTGACAGCATATATACAA
* *
6848621 AATTGAACTGCATTTATACATCAAAATTTGACAGCATATGTACAA
1 AATTGAACTGCAATTATACATCAAAATTTGACAGCATATATACAA
6848666 AATTGAAC
1 AATTGAAC
6848674 AGCACATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (45 bp):
AATTGAACTGCAATTATACATCAAAATTTGACAGCATATATACAA
Found at i:6849047 original size:14 final size:15
Alignment explanation
Indices: 6849023--6849057 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6849013 TATATACATT
6849023 ACCATATAAATACTA
1 ACCATATAAATACTA
6849038 ACCATA-AAATACTA
1 ACCATATAAATACTA
6849052 ATCCAT
1 A-CCAT
6849058 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:6849770 original size:43 final size:43
Alignment explanation
Indices: 6849700--6849823 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 43
6849690 AACTCGTACA
* *
6849700 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
* *
6849743 ATGCC-ACTGTCCCAGACAG-GGTTTTACACGTAAACACAAGTTG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
* *
6849786 ATGCCAACGTCCCAGACGTTGTATTACACG-ATAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTA-AACACA
6849824 TATCGGAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
42 5 0.07
43 61 0.88
44 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:6850986 original size:15 final size:16
Alignment explanation
Indices: 6850968--6851001 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6850958 TTAAAACACG
6850968 AAAATTC-CACACAAT
1 AAAATTCTCACACAAT
*
6850983 AAAATTCTCACATAAT
1 AAAATTCTCACACAAT
6850999 AAA
1 AAA
6851002 CACACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATTCTCACACAAT
Found at i:6852202 original size:50 final size:52
Alignment explanation
Indices: 6852139--6852262 Score: 135
Period size: 56 Copynumber: 2.3 Consensus size: 52
6852129 TTGCTGAAAT
** * *
6852139 GTCTTACGGGGGACCTCTCAT-CT-TGGTGCCAACGCCATGTCCCAAATATG
1 GTCTTACATGGGACCTCTCATACTATGATGCCAACGCCATGTCCCAAACATG
* *
6852189 GTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATGCCATGTCCCAGACATG
1 GTCTTACATGGGACCTCTCAT-A-CT--ATGATGCCAACGCCATGTCCCAAACATG
*
6852245 GTCTTACATGGGATCTCT
1 GTCTTACATGGGACCTCT
6852263 TTACCCAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
50 19 0.31
53 2 0.03
56 40 0.66
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (52 bp):
GTCTTACATGGGACCTCTCATACTATGATGCCAACGCCATGTCCCAAACATG
Found at i:6857253 original size:30 final size:31
Alignment explanation
Indices: 6857199--6857256 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
6857189 AGGTGAGTCG
*
6857199 GGAAGGGAATAAAAGTTTTAGGGGAAAAGTA
1 GGAAGGGAATAAAAATTTTAGGGGAAAAGTA
* *
6857230 GGAA-GGAGTAAAAATTTTGGGGGAAAA
1 GGAAGGGAATAAAAATTTTAGGGGAAAA
6857257 TAAAAGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (31 bp):
GGAAGGGAATAAAAATTTTAGGGGAAAAGTA
Found at i:6857561 original size:9 final size:9
Alignment explanation
Indices: 6857544--6857574 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6857534 TCGATTTGAT
6857544 TCGAATAAC
1 TCGAATAAC
*
6857553 TCGATTAAC
1 TCGAATAAC
6857562 TCGAATAAC
1 TCGAATAAC
6857571 TCGA
1 TCGA
6857575 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:6859083 original size:3 final size:3
Alignment explanation
Indices: 6859075--6859119 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
6859065 TAGTTCACCC
6859075 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6859120 AGGAAATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6859581 original size:19 final size:19
Alignment explanation
Indices: 6859543--6859581 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6859533 TAGTGAGAAA
* *
6859543 ACAACAAGAAAATAACAGC
1 ACAACAACAAAAAAACAGC
*
6859562 ACAACAACAAAAAAAGAGC
1 ACAACAACAAAAAAACAGC
6859581 A
1 A
6859582 AAAAGTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.67, C:0.21, G:0.10, T:0.03
Consensus pattern (19 bp):
ACAACAACAAAAAAACAGC
Found at i:6865245 original size:27 final size:25
Alignment explanation
Indices: 6865185--6865249 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
6865175 CTATACATGT
* *
6865185 ATGCTCACACGAGCTTTGAATCAGA
1 ATGCTCACACAAGCTGTGAATCAGA
6865210 ATGCTCACACAAGCTGTGAATCAGA
1 ATGCTCACACAAGCTGTGAATCAGA
6865235 ATGCTCACACAAGCT
1 ATGCTCACACAAGCT
6865250 ATAAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (25 bp):
ATGCTCACACAAGCTGTGAATCAGA
Found at i:6869538 original size:13 final size:13
Alignment explanation
Indices: 6869520--6869544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6869510 CTGTTCACAT
6869520 AGAGCTCGCATAG
1 AGAGCTCGCATAG
6869533 AGAGCTCGCATA
1 AGAGCTCGCATA
6869545 TTATTGTTCA
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:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (13 bp):
AGAGCTCGCATAG
Found at i:6870135 original size:27 final size:27
Alignment explanation
Indices: 6870105--6870162 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
6870095 ACTTACCAGC
*
6870105 GAACCACAGCTTGCCAAACCTGCTAAT
1 GAACCACAGCTTGCCAAACCTGATAAT
* *
6870132 GAACCCCAGCTTGCCAAACTTGATAAT
1 GAACCACAGCTTGCCAAACCTGATAAT
6870159 GAAC
1 GAAC
6870163 ACTAGCTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (27 bp):
GAACCACAGCTTGCCAAACCTGATAAT
Found at i:6870169 original size:27 final size:27
Alignment explanation
Indices: 6870111--6870169 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
6870101 CAGCGAACCA
* *
6870111 CAGCTTGCCAAACCTGCTAATGAACCC
1 CAGCTTGCCAAACCTGATAATGAACAC
*
6870138 CAGCTTGCCAAACTTGATAATGAACAC
1 CAGCTTGCCAAACCTGATAATGAACAC
*
6870165 TAGCT
1 CAGCT
6870170 CATTGAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (27 bp):
CAGCTTGCCAAACCTGATAATGAACAC
Found at i:6878935 original size:18 final size:18
Alignment explanation
Indices: 6878875--6878931 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
6878865 TAAGCGATTT
* * *
6878875 ACATAGAATAAACAATTC
1 ACATAAAATAAGCAGTTC
6878893 ACATAAAATAAGCAGTTC
1 ACATAAAATAAGCAGTTC
*
6878911 A-AGTAAAAT-ATCAGTTC
1 ACA-TAAAATAAGCAGTTC
6878928 ACAT
1 ACAT
6878932 TAAACAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 10 0.30
18 23 0.70
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.25
Consensus pattern (18 bp):
ACATAAAATAAGCAGTTC
Found at i:6879704 original size:17 final size:18
Alignment explanation
Indices: 6879674--6879708 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6879664 CGCGTACCAT
6879674 GGTTCGCATAATAACATG
1 GGTTCGCATAATAACATG
*
6879692 GGTTCGCA-CATAACATG
1 GGTTCGCATAATAACATG
6879709 TATAGAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (18 bp):
GGTTCGCATAATAACATG
Found at i:6879794 original size:34 final size:34
Alignment explanation
Indices: 6879754--6879826 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
6879744 TATATAGTAG
* *
6879754 GGGTTCACACATATGGAA-G-GTTCGCGCATATGGA
1 GGGTTCACACATAT--AACGAGTTCACACATATGGA
*
6879788 GGGTTCACATATATAACGAGTTCACACATATGGA
1 GGGTTCACACATATAACGAGTTCACACATATGGA
6879822 GGGTT
1 GGGTT
6879827 TGCACAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 2 0.06
33 1 0.03
34 31 0.91
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (34 bp):
GGGTTCACACATATAACGAGTTCACACATATGGA
Found at i:6879801 original size:17 final size:17
Alignment explanation
Indices: 6879754--6879826 Score: 76
Period size: 17 Copynumber: 4.3 Consensus size: 17
6879744 TATATAGTAG
6879754 GGGTTCACACATATGGA
1 GGGTTCACACATATGGA
* * *
6879771 AGGTTCGCGCATATGGA
1 GGGTTCACACATATGGA
* *
6879788 GGGTTCACATATAT-AA
1 GGGTTCACACATATGGA
*
6879804 CGAGTTCACACATATGGA
1 -GGGTTCACACATATGGA
6879822 GGGTT
1 GGGTT
6879827 TGCACAAATG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
16 1 0.02
17 40 0.95
18 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (17 bp):
GGGTTCACACATATGGA
Found at i:6894443 original size:15 final size:15
Alignment explanation
Indices: 6894423--6894452 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6894413 AATTAAAAAT
6894423 AATTTTTAAATTAAA
1 AATTTTTAAATTAAA
*
6894438 AATTTTTAATTTAAA
1 AATTTTTAAATTAAA
6894453 TCTCTTTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTTTAAATTAAA
Found at i:6904765 original size:6 final size:6
Alignment explanation
Indices: 6904754--6904789 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
6904744 AGAGGATCGC
6904754 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
6904790 AAGAAGATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:6908046 original size:16 final size:16
Alignment explanation
Indices: 6908025--6908057 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6908015 TTGGTTTGTT
6908025 CAGTTGCTGCAAAAGA
1 CAGTTGCTGCAAAAGA
6908041 CAGTTGCTGCAAAAGA
1 CAGTTGCTGCAAAAGA
6908057 C
1 C
6908058 TAAGCTTTTC
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:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (16 bp):
CAGTTGCTGCAAAAGA
Found at i:6912581 original size:12 final size:12
Alignment explanation
Indices: 6912546--6912581 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
6912536 AGACTCGTGG
6912546 AAGGTTCTTTTT
1 AAGGTTCTTTTT
*
6912558 AAGAGTTGTTTTT
1 AAG-GTTCTTTTT
6912571 AAGGTTCTTTT
1 AAGGTTCTTTT
6912582 ATCATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (12 bp):
AAGGTTCTTTTT
Found at i:6928359 original size:27 final size:26
Alignment explanation
Indices: 6928329--6928379 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6928319 GTCGACGTCA
* *
6928329 TGAACTTGAATTGAGTCAAAACCAATT
1 TGAA-TTGAAATGACTCAAAACCAATT
*
6928356 TGAATTTAAATGACTCAAAACCAA
1 TGAATTGAAATGACTCAAAACCAA
6928380 ATTATCTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (26 bp):
TGAATTGAAATGACTCAAAACCAATT
Found at i:6937477 original size:2 final size:2
Alignment explanation
Indices: 6937470--6937500 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6937460 GTATGTGATC
*
6937470 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6937501 GTTAAATAGA
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:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6938753 original size:158 final size:158
Alignment explanation
Indices: 6938465--6938776 Score: 570
Period size: 158 Copynumber: 2.0 Consensus size: 158
6938455 ATTTTGGTTG
*
6938465 GTTTGGTCTTCGATCTCATAGGCATGTTGAAATCCTTAATGCATAATTGGATTGTTGAAATGGTA
1 GTTTGGTCTTCGATCTCATAGGCATGTTGAAATCCTTAACGCATAATTGGATTGTTGAAATGGTA
* *
6938530 TTTATATGATAGGCTAATTGGTGAACTTCAATTGATGAATTTTGCATTTGGTATTTGTTGTTGAT
66 TTTATATGATAGGCTAATTGGTGAACTACAATTGATGAATTTGGCATTTGGTATTTGTTGTTGAT
6938595 TTGGTGAATGTATAAGCTTGGAAAGTTC
131 TTGGTGAATGTATAAGCTTGGAAAGTTC
* * *
6938623 GTTTGGTCTTTGATGTCATAGGCATGTTGAAATCCTTAACGCATACTTGGATTGTTGAAATGGTA
1 GTTTGGTCTTCGATCTCATAGGCATGTTGAAATCCTTAACGCATAATTGGATTGTTGAAATGGTA
6938688 TTTATATGATAGGCTAATTGGTGAACTACAATTGATGAATTTGGCATTTGGTATTTGTTGTTGAT
66 TTTATATGATAGGCTAATTGGTGAACTACAATTGATGAATTTGGCATTTGGTATTTGTTGTTGAT
6938753 TTGGTGAATGTATAAGCTTGGAAA
131 TTGGTGAATGTATAAGCTTGGAAA
6938777 TTTAGTTTTG
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
158 148 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (158 bp):
GTTTGGTCTTCGATCTCATAGGCATGTTGAAATCCTTAACGCATAATTGGATTGTTGAAATGGTA
TTTATATGATAGGCTAATTGGTGAACTACAATTGATGAATTTGGCATTTGGTATTTGTTGTTGAT
TTGGTGAATGTATAAGCTTGGAAAGTTC
Found at i:6938887 original size:22 final size:19
Alignment explanation
Indices: 6938858--6938900 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
6938848 GACACTTAGG
6938858 TTGAATGTTATTTGGTATATT
1 TTGAATG-T-TTTGGTATATT
*
6938879 TTGACATGTTTTGGTGTATT
1 TTGA-ATGTTTTGGTATATT
6938899 TT
1 TT
6938901 AGATAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 5 0.25
22 3 0.15
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (19 bp):
TTGAATGTTTTGGTATATT
Found at i:6949988 original size:5 final size:5
Alignment explanation
Indices: 6949978--6950002 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6949968 AAGTCTCATG
6949978 TATGC TATGC TATGC TATGC TATGC
1 TATGC TATGC TATGC TATGC TATGC
6950003 ACACACCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TATGC
Found at i:6952602 original size:54 final size:54
Alignment explanation
Indices: 6952488--6952611 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
6952478 CATGTGTGAA
** *
6952488 AACTCAGAGAGTTACACGGCCTAGCACACAGGCGGGCACACGGGCATTTGTGAC
1 AACTCAGAGAGTTACACGGCCTAGCACACAGGCGGGCACACAAGCATTTGGGAC
* * * *
6952542 AACTCAGAGAGTTACACTGCCTAGCACAC-GGTCTGGCACACAAGCGTTTGGGGC
1 AACTCAGAGAGTTACACGGCCTAGCACACAGG-CGGGCACACAAGCATTTGGGAC
* **
6952596 ATCTCAGTTAGTTACA
1 AACTCAGAGAGTTACA
6952612 AGGGTGATGA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 2 0.03
54 57 0.97
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (54 bp):
AACTCAGAGAGTTACACGGCCTAGCACACAGGCGGGCACACAAGCATTTGGGAC
Found at i:6954725 original size:26 final size:26
Alignment explanation
Indices: 6954683--6954741 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
6954673 TATTTTCTCG
* * *
6954683 AAATTTTACCAGAGGTAGAGTCGTCA
1 AAATTTTACAAGAGGTAAAATCGTCA
*
6954709 AAATTTTACAAGGGGTAAAATCGTCA
1 AAATTTTACAAGAGGTAAAATCGTCA
6954735 AAATTTT
1 AAATTTT
6954742 GTTGGGAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (26 bp):
AAATTTTACAAGAGGTAAAATCGTCA
Found at i:6959843 original size:40 final size:38
Alignment explanation
Indices: 6959799--6959887 Score: 88
Period size: 40 Copynumber: 2.2 Consensus size: 38
6959789 ATAAAGAATA
* * *
6959799 ATATTTTTATATTAAATTACATTAAAATATTCTTATTTTT
1 ATATTTTTATATTAAA-AACATTAAAACATT-TTATTTAT
* **
6959839 ATATTAAATTATATTAAAAATTTTAAAACATTTTATTTAT
1 ATATT--TTTATATTAAAAACATTAAAACATTTTATTTAT
6959879 ATATTTTTA
1 ATATTTTTA
6959888 AATTTAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
38 3 0.08
40 17 0.43
41 10 0.25
42 10 0.25
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (38 bp):
ATATTTTTATATTAAAAACATTAAAACATTTTATTTAT
Found at i:6961547 original size:21 final size:21
Alignment explanation
Indices: 6961515--6961561 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
6961505 TATTGAGACA
*
6961515 AGAAATCCCATATAA-TAAAT
1 AGAAATCCCATAAAACTAAAT
*
6961535 AGAAATGCCCATAAAACTTAAT
1 AGAAAT-CCCATAAAACTAAAT
6961557 AGAAA
1 AGAAA
6961562 AACAAGCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 8 0.35
22 9 0.39
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (21 bp):
AGAAATCCCATAAAACTAAAT
Found at i:6962019 original size:19 final size:19
Alignment explanation
Indices: 6961995--6962031 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6961985 GACATCTTTA
* *
6961995 AATTTTGTTTTTTTTTTCC
1 AATTTTCTTTTTCTTTTCC
6962014 AATTTTCTTTTTCTTTTC
1 AATTTTCTTTTTCTTTTC
6962032 TTGTTTTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.73
Consensus pattern (19 bp):
AATTTTCTTTTTCTTTTCC
Found at i:6972073 original size:14 final size:13
Alignment explanation
Indices: 6972045--6972071 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6972035 CTTAATAGGT
6972045 AGAAATAAAAAAA
1 AGAAATAAAAAAA
6972058 AGAAATAAAAAAA
1 AGAAATAAAAAAA
6972071 A
1 A
6972072 AGCCTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AGAAATAAAAAAA
Found at i:6975624 original size:27 final size:27
Alignment explanation
Indices: 6975592--6975644 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
6975582 GTTAATATGG
*
6975592 TCGGTTAACCGAATTAATTGAAATATT
1 TCGGTTAACCGAATTAATCGAAATATT
*
6975619 TCGGTTAACTGAATTAATCGAAATAT
1 TCGGTTAACCGAATTAATCGAAATAT
6975645 ATATGTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (27 bp):
TCGGTTAACCGAATTAATCGAAATATT
Found at i:6978016 original size:21 final size:21
Alignment explanation
Indices: 6977973--6978016 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6977963 TTTCTCTTAT
* *
6977973 AACAAAACATTTGTAATATCA
1 AACAAAAAATTTGTAATAACA
6977994 AACAAAAAATTTG-AGATAACA
1 AACAAAAAATTTGTA-ATAACA
6978015 AA
1 AA
6978017 ACATTTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.23
Consensus pattern (21 bp):
AACAAAAAATTTGTAATAACA
Found at i:6978260 original size:30 final size:30
Alignment explanation
Indices: 6978153--6978294 Score: 123
Period size: 30 Copynumber: 4.8 Consensus size: 30
6978143 AGGACCAAAA
* * **
6978153 TTTTCAAAA-TGGTCATATAAGGTTTAACC
1 TTTTCAAAAGTGCTCAAATAAGGTCAAACC
*
6978182 TTTAT-AAAATTGCTCAAATGAAGGTCAAACC
1 TTT-TCAAAAGTGCTCAAAT-AAGGTCAAACC
* * *
6978213 -TTTCAAAA-TGGTTAAATATGAGTCAAACC
1 TTTTCAAAAGTGCTCAAATAAG-GTCAAACC
* *
6978242 TTTTTAAAA-TGCTCAAATAAGGGTCAAACA
1 TTTTCAAAAGTGCTCAAATAA-GGTCAAACC
6978272 TTTTCAAAAGTGCTCAAATAAGG
1 TTTTCAAAAGTGCTCAAATAAGG
6978295 GATTCTCAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.02
29 23 0.25
30 46 0.50
31 21 0.23
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (30 bp):
TTTTCAAAAGTGCTCAAATAAGGTCAAACC
Found at i:6979406 original size:29 final size:30
Alignment explanation
Indices: 6979348--6979424 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
6979338 ATCCCAAAAC
* * *
6979348 TATACATGAACTATGGTTTAATATGCAATTA
1 TATACATGAACTTTGATTT-ATATACAATTA
*
6979379 TATACATGAACTTTGATTT-TATACAATTT
1 TATACATGAACTTTGATTTATATACAATTA
*
6979408 TATACATGAAATTTGAT
1 TATACATGAACTTTGAT
6979425 CTGATCCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 24 0.59
31 17 0.41
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATATACAATTA
Found at i:6979434 original size:29 final size:29
Alignment explanation
Indices: 6979373--6979435 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
6979363 GTTTAATATG
* * *
6979373 CAATTATATACATGAACTTTGATTTTATA
1 CAATTATATACATGAAATTTGATCTGATA
* *
6979402 CAATTTTATACATGAAATTTGATCTGATC
1 CAATTATATACATGAAATTTGATCTGATA
6979431 CAATT
1 CAATT
6979436 CTTTTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.43
Consensus pattern (29 bp):
CAATTATATACATGAAATTTGATCTGATA
Found at i:6990198 original size:18 final size:18
Alignment explanation
Indices: 6990149--6990198 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
6990139 TAAAAAAATA
*
6990149 TTTTGAAATTGAATAACG
1 TTTTGAAAATGAATAACG
* * *
6990167 ATTTGTAAATGAATAATG
1 TTTTGAAAATGAATAACG
*
6990185 TTTTGAAAACGAAT
1 TTTTGAAAATGAAT
6990199 GACACGATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTTGAAAATGAATAACG
Found at i:6996875 original size:18 final size:18
Alignment explanation
Indices: 6996835--6996878 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6996825 AAAAAAATTA
6996835 TTTTGAAATTGAATAACG
1 TTTTGAAATTGAATAACG
* *
6996853 ATTTGTAAA-TGAATAATG
1 TTTTG-AAATTGAATAACG
6996871 TTTTGAAA
1 TTTTGAAA
6996879 ACGAACGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 16 0.73
19 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (18 bp):
TTTTGAAATTGAATAACG
Found at i:7004836 original size:18 final size:16
Alignment explanation
Indices: 7004802--7004832 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7004792 TCTTAATTCT
7004802 TTGTCTTTTCTCTCTA
1 TTGTCTTTTCTCTCTA
*
7004818 TTGTCTCTTCTCTCT
1 TTGTCTTTTCTCTCT
7004833 CTATCAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.29, G:0.06, T:0.61
Consensus pattern (16 bp):
TTGTCTTTTCTCTCTA
Found at i:7011302 original size:6 final size:6
Alignment explanation
Indices: 7011293--7011341 Score: 71
Period size: 6 Copynumber: 7.8 Consensus size: 6
7011283 TACAAGTACG
*
7011293 TTTCTC TTTCTC TTTCTC TTTCTTTT TTTCTC TTTCTC TTTCTC TTTCT
1 TTTCTC TTTCTC TTTCTC TTTC--TC TTTCTC TTTCTC TTTCTC TTTCT
7011342 TAGCTTAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 34 0.87
8 5 0.13
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTCTC
Found at i:7011322 original size:26 final size:26
Alignment explanation
Indices: 7011293--7011342 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
7011283 TACAAGTACG
7011293 TTTCTCTTTCTCTTTCTCTTTCTTTT
1 TTTCTCTTTCTCTTTCTCTTTCTTTT
7011319 TTTCTCTTTCTCTTTCTCTTTCTT
1 TTTCTCTTTCTCTTTCTCTTTCTT
7011343 AGCTTAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTCTCTTTCTCTTTCTCTTTCTTTT
Found at i:7012417 original size:18 final size:18
Alignment explanation
Indices: 7012384--7012436 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
7012374 ATTCACCTAA
*
7012384 ACCCAATCCAAACCCAAAT
1 ACCCAA-CCCAACCCAAAT
** *
7012403 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAAT
7012421 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
7012437 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.43, C:0.45, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAAT
Found at i:7012546 original size:9 final size:9
Alignment explanation
Indices: 7012528--7012594 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
7012518 GTAGTGATTC
7012528 AATTCGGTT
1 AATTCGGTT
*
7012537 AATTCAGTT
1 AATTCGGTT
*
7012546 AATTCGGGT
1 AATTCGGTT
* *
7012555 AATCCAGTT
1 AATTCGGTT
7012564 AATTCGGTT
1 AATTCGGTT
*
7012573 AATTCGGGT
1 AATTCGGTT
*
7012582 AATTCAGTT
1 AATTCGGTT
7012591 AATT
1 AATT
7012595 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:7012551 original size:18 final size:18
Alignment explanation
Indices: 7012528--7012594 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
7012518 GTAGTGATTC
7012528 AATTCGGTTAATTCAGTT
1 AATTCGGTTAATTCAGTT
* *
7012546 AATTCGGGTAATCCAGTT
1 AATTCGGTTAATTCAGTT
* *
7012564 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCAGTT
*
7012582 AATTCAGTTAATT
1 AATTCGGTTAATT
7012595 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (18 bp):
AATTCGGTTAATTCAGTT
Found at i:7012565 original size:27 final size:27
Alignment explanation
Indices: 7012534--7012594 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
7012524 ATTCAATTCG
7012534 GTTAATTCAGTTAATTCGGGTAATCCA
1 GTTAATTCAGTTAATTCGGGTAATCCA
* *
7012561 GTTAATTCGGTTAATTCGGGTAATTCA
1 GTTAATTCAGTTAATTCGGGTAATCCA
7012588 GTTAATT
1 GTTAATT
7012595 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (27 bp):
GTTAATTCAGTTAATTCGGGTAATCCA
Found at i:7012774 original size:12 final size:12
Alignment explanation
Indices: 7012754--7012790 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
7012744 TGTTATTTCG
7012754 GGTCGGTTAACC
1 GGTCGGTTAACC
*
7012766 GGTCAGTTAACC
1 GGTCGGTTAACC
7012778 GGTCGGTTAACC
1 GGTCGGTTAACC
7012790 G
1 G
7012791 AATGAACACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:7016083 original size:91 final size:91
Alignment explanation
Indices: 7015954--7016171 Score: 242
Period size: 91 Copynumber: 2.4 Consensus size: 91
7015944 TGTCTAATGG
* * * **
7015954 CCTAAACTATTAATCTGTGTATTATTTGGTACAAATACTTTCATAAAATG-TCTAATGTAGTACC
1 CCTAAACAATCAATTTGTGTATTATTTGGTACCTATACTTTCATAAAATGCTC-AATGTAGTACC
* *
7016018 TGTACTTTAAAAAT-ATCTATAATGGTA
65 TATACTTTAAAAATCATCAAT-ATGGTA
* * * * * *
7016045 CTTGAACAATCAATTTGTGTGTTATTTAGTACCTATACTTTCATAAAATGCTCAATGTGGTACTT
1 CCTAAACAATCAATTTGTGTATTATTTGGTACCTATACTTTCATAAAATGCTCAATGTAGTACCT
* *
7016110 ATACTTTGAAAATCTTCAATATGGTA
66 ATACTTTAAAAATCATCAATATGGTA
* *
7016136 CCTAAACTATCAATTTATGTATTATTATGGTACCTA
1 CCTAAACAATCAATTTGTGTATTATT-TGGTACCTA
7016172 AAGTTAACAC
Statistics
Matches: 103, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
91 89 0.86
92 14 0.14
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (91 bp):
CCTAAACAATCAATTTGTGTATTATTTGGTACCTATACTTTCATAAAATGCTCAATGTAGTACCT
ATACTTTAAAAATCATCAATATGGTA
Found at i:7018589 original size:15 final size:15
Alignment explanation
Indices: 7018569--7018600 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7018559 CATTTCACTA
*
7018569 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
7018584 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
7018599 TT
1 TT
7018601 TGCATCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:7019485 original size:35 final size:35
Alignment explanation
Indices: 7019439--7019509 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
7019429 GTTTTCAATC
7019439 ATAGTACTTCTTGTGGATTGACTCCATGATTAAGT
1 ATAGTACTTCTTGTGGATTGACTCCATGATTAAGT
7019474 ATAGTACTTCTTGTGGATTGACTCCATGATTAAGT
1 ATAGTACTTCTTGTGGATTGACTCCATGATTAAGT
7019509 A
1 A
7019510 GTTGCAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (35 bp):
ATAGTACTTCTTGTGGATTGACTCCATGATTAAGT
Found at i:7031409 original size:5 final size:6
Alignment explanation
Indices: 7031399--7031456 Score: 52
Period size: 5 Copynumber: 9.7 Consensus size: 6
7031389 AATAATATTT
7031399 TATTAA T-TTAA TATTAAA GTGATT-A TATTAA TATTAA TATTTAA T-TTAA
1 TATTAA TATTAA TATT-AA -T-ATTAA TATTAA TATTAA TA-TTAA TATTAA
7031448 T-TTAA TATT
1 TATTAA TATT
7031457 TATCTTGTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
5 18 0.40
6 15 0.33
7 8 0.18
8 1 0.02
9 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TATTAA
Found at i:7031454 original size:17 final size:17
Alignment explanation
Indices: 7031357--7031458 Score: 59
Period size: 17 Copynumber: 5.6 Consensus size: 17
7031347 ATTTTAATAG
* *
7031357 TTTAATATTAAATTTAG
1 TTTAATATTTAATTTAA
7031374 TTTAATATTT-ATCTTAA
1 TTTAATATTTAAT-TTAA
*
7031391 --TAATATTTTA-TTAA
1 TTTAATATTTAATTTAA
7031405 TTTAATATTAAAGTGATTATATTAA
1 TTTAATATT----T-A--AT-TTAA
7031430 TATTAATATTTAATTTAA
1 T-TTAATATTTAATTTAA
7031448 TTTAATATTTA
1 TTTAATATTTA
7031459 TCTTGTAGAT
Statistics
Matches: 68, Mismatches: 3, Indels: 28
0.69 0.03 0.28
Matches are distributed among these distances:
14 4 0.06
15 8 0.12
16 10 0.15
17 22 0.32
18 5 0.07
19 2 0.03
20 1 0.01
21 1 0.01
22 1 0.01
23 1 0.01
25 5 0.07
26 8 0.12
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAATATTTAATTTAA
Found at i:7038162 original size:12 final size:12
Alignment explanation
Indices: 7038145--7038175 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
7038135 CCAATGAGTT
7038145 ACACGGCCTAAC
1 ACACGGCCTAAC
*
7038157 ACACGGCCTCAC
1 ACACGGCCTAAC
7038169 ACACGGC
1 ACACGGC
7038176 GTGTGACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.45, G:0.19, T:0.06
Consensus pattern (12 bp):
ACACGGCCTAAC
Found at i:7039556 original size:5 final size:5
Alignment explanation
Indices: 7039548--7039584 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
7039538 AATAATTTAA
*
7039548 TTATT TTATT TTATT TTATT TTATT TTA-A TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTA
7039585 AGTTACCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:7039568 original size:15 final size:14
Alignment explanation
Indices: 7039543--7039584 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
7039533 TTTATAATAA
7039543 TTTAATTATTTTAT
1 TTTAATTATTTTAT
*
7039557 TTTATTTTATTTTAT
1 TTTA-ATTATTTTAT
7039572 TTTAATTATTTTA
1 TTTAATTATTTTA
7039585 AGTTACCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTAATTATTTTAT
Found at i:7041279 original size:20 final size:19
Alignment explanation
Indices: 7041248--7041344 Score: 76
Period size: 19 Copynumber: 5.2 Consensus size: 19
7041238 ATGGTTATTG
7041248 TTATTGTTATTAAAATATATA
1 TTATT-TTATTAAAATATA-A
*
7041269 TTATTTTATTAAATTATAA
1 TTATTTTATTAAAATATAA
* * *
7041288 TAATCTTATTAAAATTTAA
1 TTATTTTATTAAAATATAA
* * *
7041307 TAATATTCTT--AATATAA
1 TTATTTTATTAAAATATAA
7041324 TTA--TTATTAAAATATGAA
1 TTATTTTATTAAAATAT-AA
7041342 TTA
1 TTA
7041345 ATAAAATTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
15 4 0.06
17 13 0.21
18 5 0.08
19 24 0.38
20 12 0.19
21 5 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TTATTTTATTAAAATATAA
Found at i:7041296 original size:19 final size:19
Alignment explanation
Indices: 7041254--7041310 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
7041244 ATTGTTATTG
* * *
7041254 TTATTAAAATATATATTATT
1 TTATTAAATTATA-ATAATC
7041274 TTATTAAATTATAATAATC
1 TTATTAAATTATAATAATC
7041293 TTATTAAAATT-TAATAAT
1 TTATT-AAATTATAATAAT
7041311 ATTCTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTAAATTATAATAATC
Found at i:7041325 original size:22 final size:22
Alignment explanation
Indices: 7041284--7041325 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
7041274 TTATTAAATT
*
7041284 ATAATAATCTTATTAAAATTTA
1 ATAATAATCTTAATAAAATTTA
* *
7041306 ATAATATTCTTAATATAATT
1 ATAATAATCTTAATAAAATT
7041326 ATTATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATAATCTTAATAAAATTTA
Found at i:7044194 original size:46 final size:46
Alignment explanation
Indices: 7044127--7044311 Score: 325
Period size: 46 Copynumber: 4.0 Consensus size: 46
7044117 CATGGCAAAG
*
7044127 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
7044173 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
7044219 TATGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
7044265 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
7044311 T
1 T
7044312 ATAGCAATGT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
Found at i:7054776 original size:37 final size:37
Alignment explanation
Indices: 7054735--7054811 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
7054725 ACTTCACTGG
7054735 TTATGTCTCCTTGCTATGTGAAACCTTTTTCATCATT
1 TTATGTCTCCTTGCTATGTGAAACCTTTTTCATCATT
*
7054772 TTATGTCTCCTTGCTATGTGAAACCTTTTTCATCGTT
1 TTATGTCTCCTTGCTATGTGAAACCTTTTTCATCATT
7054809 TTA
1 TTA
7054812 ACTTTCGGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.49
Consensus pattern (37 bp):
TTATGTCTCCTTGCTATGTGAAACCTTTTTCATCATT
Found at i:7061188 original size:3 final size:3
Alignment explanation
Indices: 7061180--7061216 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
7061170 AAGTCTCTAA
7061180 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
7061217 TAGAAAGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7064651 original size:18 final size:19
Alignment explanation
Indices: 7064609--7064649 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
7064599 ATTAATATGA
7064609 TTTTAATCCAAAATTGATT
1 TTTTAATCCAAAATTGATT
*
7064628 TTTTAATCGAAAATTGATT
1 TTTTAATCCAAAATTGATT
7064647 TTT
1 TTT
7064650 AAGACTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTTAATCCAAAATTGATT
Found at i:7066161 original size:261 final size:263
Alignment explanation
Indices: 7065651--7066169 Score: 668
Period size: 261 Copynumber: 2.0 Consensus size: 263
7065641 AACAAAACAA
* * * * *
7065651 TGCAAATTAATACACAAATATCATGTCCACTGAATGATCCCAAAAGAGGAGAAAGACAAACCGAC
1 TGCAAATTAATAAACAAATACCATGTCCACTAAATAATCCCAAAAGAGGAGAAAGACAAACCAAC
*
7065716 TATAGCCATAACACTCGAAAAATTCAGAAACAAACTAAAAATGTATCACCTTGATCAAACCATTG
66 TATAGCCATAACACTCGAAAAATTCAGAAACAAACTAAAAATGCATCACCTTGATCAAACCATTG
* *
7065781 AAATTGCATCAAAACCCTATCATTATCAGACCAACCTAATGATGAACTCCAATTAACCAAAAAAC
131 AAATTGCATCAAAACCCTATCATTATCAGACCAACCTAACGATGAACTCAAATTAACCAAAAAAC
* * *
7065846 CACTGCCAAGACCCTAAAAGACCCACCACATCAGTGATGCACAAAATGTCAAATCTCATATAAGA
196 CACTACCAAGACCCTAAAAAACCCACCACATCAGTGATGCACAAAATGTCAAATCTCAAATAAGA
7065911 CAT
261 CAT
* * *
7065914 TGCAAATTAATAAACAAATGCCATGTCGACTAAATAATCCC-AAA-AGGAGAAAGACAAACTAAC
1 TGCAAATTAATAAACAAATACCATGTCCACTAAATAATCCCAAAAGAGGAGAAAGACAAACCAAC
* * *** ** * * * * *
7065977 TATAGTCATAACATTCGGGGAATTCAGAATTAAATTAAAGATGCCTCGCCTTGATCAAACTATTG
66 TATAGCCATAACACTCGAAAAATTCAGAAACAAACTAAAAATGCATCACCTTGATCAAACCATTG
* * * * * *
7066042 AAATTGCATCATAACCCTATCATTATCAGACCAACTTGACGATGATCTCAAATTAACCAAGAAAT
131 AAATTGCATCAAAACCCTATCATTATCAGACCAACCTAACGATGAACTCAAATTAACCAAAAAAC
* * * *
7066107 CACTATCGAGACCCTAAAAAACTCATCACATC-GATGATGCACAAAA-GATCAAATCTCAAATAA
196 CACTACCAAGACCCTAAAAAACCCACCACATCAG-TGATGCACAAAATG-TCAAATCTCAAATAA
7066170 TTTATCCTTC
Statistics
Matches: 218, Mismatches: 36, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
260 2 0.01
261 178 0.82
262 3 0.01
263 35 0.16
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.22
Consensus pattern (263 bp):
TGCAAATTAATAAACAAATACCATGTCCACTAAATAATCCCAAAAGAGGAGAAAGACAAACCAAC
TATAGCCATAACACTCGAAAAATTCAGAAACAAACTAAAAATGCATCACCTTGATCAAACCATTG
AAATTGCATCAAAACCCTATCATTATCAGACCAACCTAACGATGAACTCAAATTAACCAAAAAAC
CACTACCAAGACCCTAAAAAACCCACCACATCAGTGATGCACAAAATGTCAAATCTCAAATAAGA
CAT
Found at i:7066627 original size:19 final size:17
Alignment explanation
Indices: 7066596--7066638 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
7066586 GCTAATTAGG
*
7066596 TATTTTTTAT-T-TTTA
1 TATTTTTTATATATTTT
*
7066611 TAATTTTTATATATTTT
1 TATTTTTTATATATTTT
7066628 TATTTTTTATA
1 TATTTTTTATA
7066639 CAATATTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 9 0.39
16 1 0.04
17 13 0.57
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTTTATATATTTT
Found at i:7066634 original size:17 final size:16
Alignment explanation
Indices: 7066596--7066638 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
7066586 GCTAATTAGG
7066596 TATTTTTTAT-TTTTA
1 TATTTTTTATATTTTA
7066611 TAATTTTTATATATTTT-
1 T-ATTTTT-TATATTTTA
7066628 TATTTTTTATA
1 TATTTTTTATA
7066639 CAATATTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.20
16 12 0.48
17 4 0.16
18 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTTATATTTTA
Found at i:7067211 original size:28 final size:28
Alignment explanation
Indices: 7067154--7067211 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
7067144 TGACTCTTTT
* *
7067154 AAAAAGATTAAGGTTCAAATTTAATTAAA
1 AAAAAGAATAAGGGTCAAATTTAA-TAAA
* *
7067183 AAAAGGAATAAGGGTCAAA-TTGATAAA
1 AAAAAGAATAAGGGTCAAATTTAATAAA
7067210 AA
1 AA
7067212 TATTTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 6 0.24
28 3 0.12
29 16 0.64
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.24
Consensus pattern (28 bp):
AAAAAGAATAAGGGTCAAATTTAATAAA
Found at i:7067240 original size:18 final size:18
Alignment explanation
Indices: 7067219--7067284 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
7067209 AAATATTTAA
* *
7067219 ATTTGATATTATATATTT
1 ATTTAATATTATAAATTT
*
7067237 ATTTAATTTTATAAATTTT
1 ATTTAATATTATAAA-TTT
* *
7067256 AATATAATA-TAAAACATTT
1 -ATTTAATATTATAA-ATTT
7067275 ATTTAATATT
1 ATTTAATATT
7067285 TCAGGTGAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
18 19 0.51
19 11 0.30
20 7 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTAATATTATAAATTT
Found at i:7075805 original size:5 final size:5
Alignment explanation
Indices: 7075795--7075822 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
7075785 TGATACAAAA
7075795 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
7075823 GTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:7076727 original size:21 final size:20
Alignment explanation
Indices: 7076703--7076741 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
7076693 TCAAATTATG
7076703 TTAAAAATTAAAATATAAAGA
1 TTAAAAATTAAAAT-TAAAGA
**
7076724 TTAAATTTTAAAATTAAA
1 TTAAAAATTAAAATTAAA
7076742 TACATTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TTAAAAATTAAAATTAAAGA
Found at i:7078479 original size:3 final size:3
Alignment explanation
Indices: 7078447--7078515 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
7078437 TTATACTCAT
7078447 TTA TTCA TTA TTA -TA TT- TCTA -TA TTA -TA TTA TTA TT- TT- TGTA
1 TTA TT-A TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA
*
7078489 TTA TTA TTA -TA TTA TTA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
7078516 AGTTGCTCTT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
2 12 0.22
3 39 0.71
4 4 0.07
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:7078490 original size:11 final size:11
Alignment explanation
Indices: 7078448--7078515 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 11
7078438 TATACTCATT
7078448 TATTCATTATTA
1 TATT-ATTATTA
*
7078460 TATTTCTATATTA
1 TA-TTAT-TATTA
7078473 TATTATTATT-
1 TATTATTATTA
*
7078483 TTTGTATTATTA
1 TAT-TATTATTA
7078495 T-TATATTATTA
1 TAT-TATTATTA
7078506 TCATTATTAT
1 T-ATTATTAT
7078516 AGTTGCTCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
10 2 0.04
11 21 0.46
12 13 0.28
13 10 0.22
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (11 bp):
TATTATTATTA
Found at i:7078511 original size:17 final size:16
Alignment explanation
Indices: 7078468--7078516 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
7078458 TATATTTCTA
7078468 TATTATATTATTAT-T
1 TATTATATTATTATAT
*
7078483 TTTGTATTATTATTATAT
1 TAT-TA-TATTATTATAT
7078501 TATTATCATTATTATA
1 TATTAT-ATTATTATA
7078517 GTTGCTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 2 0.07
16 3 0.11
17 20 0.71
18 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTATATTATTATAT
Found at i:7078546 original size:21 final size:21
Alignment explanation
Indices: 7078522--7078564 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7078512 TTATAGTTGC
*
7078522 TCTTACATATATACGTATATT
1 TCTTACATATATACATATATT
**
7078543 TCTTTTATATATACATATATT
1 TCTTACATATATACATATATT
7078564 T
1 T
7078565 TTCTAGATAT
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:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (21 bp):
TCTTACATATATACATATATT
Found at i:7080249 original size:16 final size:16
Alignment explanation
Indices: 7080228--7080268 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
7080218 TATGGTTATG
*
7080228 AAATAAATATTAAGAT
1 AAATAAATATAAAGAT
*
7080244 AAATAAAGATAAAGAT
1 AAATAAATATAAAGAT
*
7080260 AATTAAATA
1 AAATAAATA
7080269 ATATTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
AAATAAATATAAAGAT
Found at i:7080304 original size:21 final size:21
Alignment explanation
Indices: 7080265--7080313 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
7080255 AAGATAATTA
* *
7080265 AATAATATTTATTTTTATGAT
1 AATAATATTTATCTCTATGAT
*
7080286 AATAGTATTTATCTCTATGA-
1 AATAATATTTATCTCTATGAT
7080306 AA-AATATT
1 AATAATATT
7080314 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
21 17 0.71
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (21 bp):
AATAATATTTATCTCTATGAT
Found at i:7080814 original size:18 final size:18
Alignment explanation
Indices: 7080774--7080816 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
7080764 AAATTCAACT
7080774 TTTAAAATAAAATATTAA
1 TTTAAAATAAAATATTAA
*
7080792 ATTAAAATTAAAATATT-A
1 TTTAAAA-TAAAATATTAA
7080810 TTTAAAA
1 TTTAAAA
7080817 GTAATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAATAAAATATTAA
Found at i:7081852 original size:33 final size:37
Alignment explanation
Indices: 7081782--7081852 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
7081772 AATCTAAATA
7081782 TTAAAGTTAATAAATTAAGTAATGCAAAAATAGGATAG
1 TTAAAGTTAATAAATTAAGTAATGC-AAAATAGGATAG
*
7081820 TTAAA-TTAATAAATTAA-T-ATGC-AAATATGATAG
1 TTAAAGTTAATAAATTAAGTAATGCAAAATAGGATAG
7081853 GTTTTTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 10 0.31
35 4 0.12
36 1 0.03
37 12 0.38
38 5 0.16
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (37 bp):
TTAAAGTTAATAAATTAAGTAATGCAAAATAGGATAG
Found at i:7083095 original size:23 final size:23
Alignment explanation
Indices: 7083068--7083121 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
7083058 AGGTTAGGGT
*
7083068 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
7083091 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
7083114 TTAGGGTT
1 TTAGGGTT
7083122 AGGGTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAGG
Found at i:7083130 original size:29 final size:29
Alignment explanation
Indices: 7083049--7083259 Score: 263
Period size: 29 Copynumber: 7.3 Consensus size: 29
7083039 GTTTTAATTA
*
7083049 AATTAGATTAGGTTAGGGTTTAGGGTTTTT
1 AATTAAATTAGGTTAGGG-TTAGGGTTTTT
*
7083079 AA-T---TTA-ATTA-GGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTAGGGTTTTT
7083102 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AATTAAATTAGGTTAGGGTTAGGG--TTT--TT
*
7083135 AAATTAAATTAGGTTAGGGTTAGAGTTTTT
1 -AATTAAATTAGGTTAGGGTTAGGGTTTTT
*
7083165 AATTAAATTAGGTTAGGGTTTGGGTTTTT
1 AATTAAATTAGGTTAGGGTTAGGGTTTTT
7083194 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTAGGGTTTTT
* *
7083223 AATTAAATTAGGTTAGGGATAGGATTTTT
1 AATTAAATTAGGTTAGGGTTAGGGTTTTT
*
7083252 AATCAAAT
1 AATTAAAT
7083260 AATATCAAAA
Statistics
Matches: 161, Mismatches: 9, Indels: 23
0.83 0.05 0.12
Matches are distributed among these distances:
23 13 0.08
24 3 0.02
25 3 0.02
26 3 0.02
27 3 0.02
28 3 0.02
29 98 0.61
30 4 0.02
31 3 0.02
32 3 0.02
33 2 0.01
34 23 0.14
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (29 bp):
AATTAAATTAGGTTAGGGTTAGGGTTTTT
Found at i:7083239 original size:92 final size:87
Alignment explanation
Indices: 7083032--7083239 Score: 312
Period size: 92 Copynumber: 2.3 Consensus size: 87
7083022 TATCAAATTA
* *
7083032 GGTTAGGG-TTTTAATTAAATTAGATTAGGTTAGGGTTTAGGGTTTTTAATTTAATTAGGTTAGG
1 GGTTAGGGTTTTTAATTAAATTAGATTAGGTTAGGGTTTAGAGTTTTTAATTAAATTAGGTTAGG
7083096 GTTTTTAATTAAATTAGGTTAG
66 GTTTTTAATTAAATTAGGTTAG
*
7083118 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG-TTAGAGTTTTTAATTAAATTAGGTTAGG
1 GGTTAGGGTTTTTAATTAAATTAGATTAGGTTAGGGTTTAGAGTTTTTAATTAAATTAGGTTA--
7083182 GTTTGGGTTTTTAATTAAATTAGGTTAG
64 ----GGGTTTTTAATTAAATTAGGTTAG
*
7083210 GGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GGTTAGGGTTTTTAATTAAATTAGATTAGG
7083240 GATAGGATTT
Statistics
Matches: 110, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
86 32 0.29
87 26 0.24
92 52 0.47
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (87 bp):
GGTTAGGGTTTTTAATTAAATTAGATTAGGTTAGGGTTTAGAGTTTTTAATTAAATTAGGTTAGG
GTTTTTAATTAAATTAGGTTAG
Found at i:7085404 original size:14 final size:15
Alignment explanation
Indices: 7085387--7085420 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7085377 AATATTTATC
7085387 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
7085401 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
7085416 TAAAA
1 TAAAA
7085421 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:7085551 original size:28 final size:29
Alignment explanation
Indices: 7085518--7085575 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
7085508 TTGAAAATAT
7085518 TAAAAAT-TTTAAAATTATT-TTAAAAAAA
1 TAAAAATATTTAAAATT-TTCTTAAAAAAA
7085546 TAAAAATATTTAAAATTTTCTTAAAAAAA
1 TAAAAATATTTAAAATTTTCTTAAAAAAA
7085575 T
1 T
7085576 GAAATTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAATATTTAAAATTTTCTTAAAAAAA
Found at i:7085653 original size:21 final size:21
Alignment explanation
Indices: 7085609--7085657 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
7085599 TAATATGGAG
*
7085609 TTGAGAGATTTTTTGAAGGAAAT
1 TTGAG-GA-TTTTGGAAGGAAAT
7085632 TGTGAGGATTTTGGAAGG-AAT
1 T-TGAGGATTTTGGAAGGAAAT
7085653 TTGAG
1 TTGAG
7085658 AGTTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 9 0.38
23 3 0.12
24 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.37
Consensus pattern (21 bp):
TTGAGGATTTTGGAAGGAAAT
Found at i:7085684 original size:52 final size:52
Alignment explanation
Indices: 7085612--7085710 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
7085602 TATGGAGTTG
* * * *
7085612 AGAGATTTTTTGAAGGAAATTGTGAGGA-TTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAACTTTT-GAAGGAATTTGAGAGTTTA
7085664 AGAGAATTTTGGAAGGAAATTGAGAGAACTTTTGAAGGAATTTGAGA
1 AGAGAATTTTGGAAGGAAATTGAGAGAACTTTTGAAGGAATTTGAGA
7085711 TGGGATTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 38 0.90
53 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.30, T:0.32
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAACTTTTGAAGGAATTTGAGAGTTTA
Found at i:7085689 original size:22 final size:22
Alignment explanation
Indices: 7085664--7085710 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
7085654 TGAGAGTTTA
7085664 AGAGAA-TTTTGGAAGGAAATTG
1 AGAGAACTTTT-GAAGGAAATTG
*
7085686 AGAGAACTTTTGAAGGAATTTG
1 AGAGAACTTTTGAAGGAAATTG
7085708 AGA
1 AGA
7085711 TGGGATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.30, T:0.28
Consensus pattern (22 bp):
AGAGAACTTTTGAAGGAAATTG
Found at i:7085949 original size:29 final size:26
Alignment explanation
Indices: 7085899--7085957 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
7085889 GATTTCGGGG
*
7085899 AAAATGGCCCATTCCGGTAAATAATTAA
1 AAAATGGCCCATTCCGG-AAA-ATTTAA
* *
7085927 AAAATCGGCCTATTTCGGAAAATTTAA
1 AAAAT-GGCCCATTCCGGAAAATTTAA
7085954 AAAA
1 AAAA
7085958 AAGGGCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.33
28 8 0.30
29 10 0.37
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (26 bp):
AAAATGGCCCATTCCGGAAAATTTAA
Done.