Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 10 of 145
Found at i:3403769 original size:15 final size:14
Alignment explanation
Indices: 3403738--3403767 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3403728 TCATATAAAA
3403738 TTATTAAAGATGAT
1 TTATTAAAGATGAT
*
3403752 TTATTTAAGATGAT
1 TTATTAAAGATGAT
3403766 TT
1 TT
3403768 TAAATTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TTATTAAAGATGAT
Found at i:3414429 original size:23 final size:24
Alignment explanation
Indices: 3414385--3414431 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3414375 TTTTTTTGAA
* * *
3414385 TTTCGAATTTAAATCGAGTTAAAT
1 TTTCGAATTCAAATCAACTTAAAT
3414409 TTTCGAATTCAAAT-AACTTAAAT
1 TTTCGAATTCAAATCAACTTAAAT
3414432 AAATCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTCGAATTCAAATCAACTTAAAT
Found at i:3420176 original size:22 final size:22
Alignment explanation
Indices: 3420145--3420188 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3420135 TACACCAAAA
* *
3420145 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCAGCGCTTTTT
3420167 TAGGCCTTTAGCAGCGCTTTTT
1 TAGGCCTTTAGCAGCGCTTTTT
3420189 AGCGCCACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.43
Consensus pattern (22 bp):
TAGGCCTTTAGCAGCGCTTTTT
Found at i:3420338 original size:43 final size:43
Alignment explanation
Indices: 3420282--3420515 Score: 283
Period size: 43 Copynumber: 5.3 Consensus size: 43
3420272 TTACAGAAAT
* ** * * *
3420282 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTTACCCAT
1 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTA-TCAC
3420325 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
* * *
3420368 AAACG-CTACTAAAGAACATGATCTTTAACAGCGCTTTTATCAC
1 AAACGCCGA-TAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
3420411 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
*
3420454 AAACGCCGCTAACGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAT
1 AAACGCCG---A---TAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
*
3420503 AAACGCCGCTAAA
1 AAACGCCGATAAA
3420516 AATACGATTT
Statistics
Matches: 168, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.01
43 118 0.70
44 6 0.04
46 1 0.01
49 41 0.24
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
Found at i:3420487 original size:49 final size:49
Alignment explanation
Indices: 3420420--3420514 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
3420410 CAAACGCCGA
3420420 TAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAACGC
1 TAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAACGC
*
3420469 TAAAGAACATGATCTTTAGCGGCGCTTTTATCATAAACGCCGCTAA
1 TAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
3420515 AAATACGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (49 bp):
TAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAACGC
Found at i:3427841 original size:73 final size:72
Alignment explanation
Indices: 3427758--3427937 Score: 297
Period size: 73 Copynumber: 2.5 Consensus size: 72
3427748 AGATAAAATA
*
3427758 TTTTTAGCGGCGCTTTTCAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGG
1 TTTTTTGCGGCGCTTTTC-AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGG
3427823 GCTTAGGT
65 GCTTAGGT
* * *
3427831 TTTTTTGCGGCGCTTTACCAAAAACGCCGCTAAATCCCTGAAAGTTCAGAAAACGGCGTCGTTGG
1 TTTTTTGCGGCGCTTT-TCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGG
3427896 GCTTAGGT
65 GCTTAGGT
3427904 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAA
1 TTTTTTGCGGCGCTTT-TCAAAAACGCCGCTAAA
3427938 GCCCTAGGCA
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
73 100 0.99
74 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (72 bp):
TTTTTTGCGGCGCTTTTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
CTTAGGT
Found at i:3428039 original size:113 final size:113
Alignment explanation
Indices: 3427850--3428162 Score: 488
Period size: 113 Copynumber: 2.8 Consensus size: 113
3427840 GCGCTTTACC
*
3427850 AAAAACGCCGCTAAATCC-CTGAAAG-TTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCG
1 AAAAACGCCGCTAAATCCTC-AAAAGATT-A-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCG
* *
3427913 GCGCTTTATCAAAAACGCCGCTAAAGCCCTAG-GCATTAGCGGCGCTTCCTT
63 GCGCTTTCTCAAAAACGCCGCTAAAACCC-AGAGCATTAGCGGCGCTTCCTT
*
3427964 AAAAAGGCCGCTAAATCCTCAAAAGATTAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
1 AAAAACGCCGCTAAATCCTCAAAAGATTAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
* * * *
3428029 CTTTCCCAAAAATGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTCTT
66 CTTTCTCAAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCCTT
3428077 AAAAACGCCGCTAAATCCTCAAAAGATTAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
1 AAAAACGCCGCTAAATCCTCAAAAGATTAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
*
3428142 CTTTCTCAAAAACGCCACTAA
66 CTTTCTCAAAAACGCCGCTAA
3428163 TGCTTATTTT
Statistics
Matches: 184, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
112 1 0.01
113 158 0.86
114 22 0.12
115 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (113 bp):
AAAAACGCCGCTAAATCCTCAAAAGATTAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
CTTTCTCAAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCCTT
Found at i:3428464 original size:2 final size:2
Alignment explanation
Indices: 3428457--3428482 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3428447 TTGAAAATGA
3428457 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
3428483 TATCAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3435847 original size:19 final size:19
Alignment explanation
Indices: 3435798--3435849 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
3435788 TTCTCATAAA
3435798 AAATATTAAAAA-ATTATG
1 AAATATTAAAAATATTATG
* * * *
3435816 AAAAATCATAAATATTATT
1 AAATATTAAAAATATTATG
3435835 AAATATTAAAAATAT
1 AAATATTAAAAATAT
3435850 ACAATCACAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATATTAAAAATATTATG
Found at i:3445990 original size:27 final size:27
Alignment explanation
Indices: 3445960--3446062 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
3445950 TCATCTCCTA
3445960 GGGGTATTTC-GATCATTTTACCATATG
1 GGGGTATTTCAG-TCATTTTACCATATG
* *
3445987 GGGGTATTTCAGCCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCATATG
* *
3446014 GGGGTATTTCAGTCATTTAACCTTATG
1 GGGGTATTTCAGTCATTTTACCATATG
**
3446041 GGGGTATTTTGGTCATTTTACC
1 GGGGTATTTCAGTCATTTTACC
3446063 CTATAAGGCT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 66 0.99
28 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCATATG
Found at i:3446030 original size:54 final size:54
Alignment explanation
Indices: 3445960--3446066 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
3445950 TCATCTCCTA
*
3445960 GGGGTATTTCGATCATTTTACCATATGGGGGTATTTCAGCCATTTTACCCTATG
1 GGGGTATTTCGATCATTTAACCATATGGGGGTATTTCAGCCATTTTACCCTATG
* ** *
3446014 GGGGTATTTC-AGTCATTTAACCTTATGGGGGTATTTTGGTCATTTTACCCTAT
1 GGGGTATTTCGA-TCATTTAACCATATGGGGGTATTTCAGCCATTTTACCCTAT
3446067 AAGGCTATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 1 0.02
54 46 0.98
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (54 bp):
GGGGTATTTCGATCATTTAACCATATGGGGGTATTTCAGCCATTTTACCCTATG
Found at i:3446075 original size:27 final size:27
Alignment explanation
Indices: 3445960--3446089 Score: 134
Period size: 27 Copynumber: 4.8 Consensus size: 27
3445950 TCATCTCCTA
* * *
3445960 GGGGTATTTCGATCATTTTACCATATG
1 GGGGTATTTTGGTCATTTTACCCTATG
** *
3445987 GGGGTATTTCAGCCATTTTACCCTATG
1 GGGGTATTTTGGTCATTTTACCCTATG
** * *
3446014 GGGGTATTTCAGTCATTTAACCTTATG
1 GGGGTATTTTGGTCATTTTACCCTATG
*
3446041 GGGGTATTTTGGTCATTTTACCCTATA
1 GGGGTATTTTGGTCATTTTACCCTATG
* * *
3446068 AGGCTATTTTGGTTATTTTACC
1 GGGGTATTTTGGTCATTTTACC
3446090 TATTTTTGGG
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (27 bp):
GGGGTATTTTGGTCATTTTACCCTATG
Found at i:3456855 original size:37 final size:39
Alignment explanation
Indices: 3456811--3456891 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 39
3456801 TTCGAAATAA
* * *
3456811 TAAATTGACAACC-GGTGTCTTATC-AGTTAAA-TCGAAG
1 TAAATTGAC-ACCTAGTGTCTCATCGACTTAAAGTCGAAG
3456848 TAAATTGACACCTAGTGTCTCATCGACTTAAAGTCGAAG
1 TAAATTGACACCTAGTGTCTCATCGACTTAAAGTCGAAG
3456887 -AAATT
1 TAAATT
3456892 CCTGAACTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
36 3 0.08
37 18 0.47
38 11 0.29
39 6 0.16
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (39 bp):
TAAATTGACACCTAGTGTCTCATCGACTTAAAGTCGAAG
Found at i:3457775 original size:16 final size:17
Alignment explanation
Indices: 3457751--3457794 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3457741 TTTCTCTTTA
*
3457751 TTTCTTTCTCTTTTTC-
1 TTTCTTTCTCTGTTTCG
*
3457767 TTTCCTTCTCTGTTTCG
1 TTTCTTTCTCTGTTTCG
3457784 TTTCTTTCTCT
1 TTTCTTTCTCT
3457795 CCTTCTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTCTTTCTCTGTTTCG
Found at i:3457844 original size:5 final size:5
Alignment explanation
Indices: 3457834--3457920 Score: 149
Period size: 5 Copynumber: 17.6 Consensus size: 5
3457824 TTAATTATTT
*
3457834 TAATA TAATA TAATA TAATA TAATA TAATA TAATA CAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
*
3457884 TAATA TAATA TAATA TAATA TAAAA TAATA T-ATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
3457921 AACATAAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
4 4 0.05
5 73 0.95
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:3460638 original size:35 final size:35
Alignment explanation
Indices: 3460598--3460716 Score: 84
Period size: 33 Copynumber: 3.4 Consensus size: 35
3460588 AATAATGATG
3460598 ACAATATAAATAAAATAATACAAGCAAAATAATAA
1 ACAATATAAATAAAATAATACAAGCAAAATAATAA
* * ** * *
3460633 ACAATA-AAA-ACAATCATACGGGCAAAACAACAA
1 ACAATATAAATAAAATAATACAAGCAAAATAATAA
* * *
3460666 ATAATATGAAACTAAAGTAATA-AAACGAACAATAATAA
1 ACAATAT-AAA-TAAAATAATACAAGC-AA-AATAATAA
*
3460704 AC-ATGTAAATAAA
1 ACAATATAAATAAA
3460717 TGTGTGAACA
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
33 23 0.38
34 3 0.05
35 13 0.21
36 4 0.07
37 11 0.18
38 7 0.11
ACGTcount: A:0.64, C:0.12, G:0.07, T:0.18
Consensus pattern (35 bp):
ACAATATAAATAAAATAATACAAGCAAAATAATAA
Found at i:3464253 original size:15 final size:15
Alignment explanation
Indices: 3464229--3464288 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
3464219 ATCAATACCG
3464229 CCCAACTAGCCTAAA
1 CCCAACTAGCCTAAA
* *
3464244 CCCAATTAGCCTAAG
1 CCCAACTAGCCTAAA
* *
3464259 CCCAA-TACCCT-AG
1 CCCAACTAGCCTAAA
3464272 CCCAACTAGCCTAAA
1 CCCAACTAGCCTAAA
3464287 CC
1 CC
3464289 AGAAGTCAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 7 0.18
14 10 0.26
15 21 0.55
ACGTcount: A:0.35, C:0.42, G:0.08, T:0.15
Consensus pattern (15 bp):
CCCAACTAGCCTAAA
Found at i:3464498 original size:16 final size:16
Alignment explanation
Indices: 3464476--3464518 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
3464466 AAACCAATGG
*
3464476 GATTTTTATTTTATTT
1 GATTTTTATTTCATTT
*
3464492 TATTTTTATTTCATTT
1 GATTTTTATTTCATTT
3464508 GATTTTT-TTTC
1 GATTTTTATTTC
3464519 GGGTTCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (16 bp):
GATTTTTATTTCATTT
Found at i:3467197 original size:16 final size:15
Alignment explanation
Indices: 3467176--3467206 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
3467166 CTAATAAAAG
3467176 TATTTTTAATTAATAT
1 TATTTTT-ATTAATAT
3467192 TATTTTTATTAATAT
1 TATTTTTATTAATAT
3467207 ACTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTATTAATAT
Found at i:3467357 original size:20 final size:20
Alignment explanation
Indices: 3467319--3467357 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3467309 AGTTGTTATA
**
3467319 TAATAAAAAAATATTTATTT
1 TAATAAAAAAATAAATATTT
*
3467339 TAATAAAGAAATAAATATT
1 TAATAAAAAAATAAATATT
3467358 AATTCAAGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TAATAAAAAAATAAATATTT
Found at i:3470910 original size:59 final size:58
Alignment explanation
Indices: 3470800--3470958 Score: 160
Period size: 59 Copynumber: 2.7 Consensus size: 58
3470790 ATTTGGCATT
* * * ** *
3470800 TGAATTTGACATTTTTTCTTAATTTGGTA-TCTAAGAGTTTTTGGGTTCAATTTGATACC
1 TGAACTTGACACTTTTTCTTAATTTGATACT-TAA-TCTTTTTGGGTCCAATTTGATACC
* *
3470859 T-AAGCTTGACACTTTTTCTTAATTTGATACTTAATCTTTTTGGGGTCCAATTTGGTATC
1 TGAA-CTTGACACTTTTTCTTAATTTGATACTTAATCTTTTT-GGGTCCAATTTGATACC
** * *
3470918 TGAACTTGATTCTTTTTCCTAATTTGATACCTAATCTTTTT
1 TGAACTTGACACTTTTTCTTAATTTGATACTTAATCTTTTT
3470959 TTTGTTCGAT
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
58 7 0.08
59 74 0.88
60 3 0.04
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (58 bp):
TGAACTTGACACTTTTTCTTAATTTGATACTTAATCTTTTTGGGTCCAATTTGATACC
Found at i:3471417 original size:32 final size:32
Alignment explanation
Indices: 3471380--3471449 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
3471370 AGCTTAGGTG
*
3471380 CCAAATTAGGAAAAAAATGCTAAGTTCAAGTA
1 CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
** * * *
3471412 CCAAATTAGGCCAAAAATATTAAGTTTAAGTG
1 CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
3471444 CCAAAT
1 CCAAAT
3471450 ATTATATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (32 bp):
CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
Found at i:3473712 original size:70 final size:71
Alignment explanation
Indices: 3473618--3473762 Score: 283
Period size: 70 Copynumber: 2.1 Consensus size: 71
3473608 ATATGAAAAA
3473618 TTATGAATTTATATACATATATATTAAATAAAATTAATACGAATATAAAAAAAATACTAAGTTTA
1 TTATGAATTTATATACATATATATTAAATAAAATTAATACGAATATAAAAAAAATACTAAGTTTA
3473683 ACACAT
66 ACACAT
3473689 TTATGAATTTA-ATACATATATATTAAATAAAATTAATACGAATATAAAAAAAATACTAAGTTTA
1 TTATGAATTTATATACATATATATTAAATAAAATTAATACGAATATAAAAAAAATACTAAGTTTA
3473753 ACACAT
66 ACACAT
3473759 TTAT
1 TTAT
3473763 TTTGTTTTTG
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 63 0.85
71 11 0.15
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (71 bp):
TTATGAATTTATATACATATATATTAAATAAAATTAATACGAATATAAAAAAAATACTAAGTTTA
ACACAT
Found at i:3474452 original size:30 final size:29
Alignment explanation
Indices: 3474416--3474477 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
3474406 ACTTAACAAG
3474416 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAA-AAAATTAA
* *
3474446 CAAATGTCTTTAAAATAATAATAAATTAA
1 CAAATGTCTCTAAAATAATAAAAAATTAA
3474475 CAA
1 CAA
3474478 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.29
Consensus pattern (29 bp):
CAAATGTCTCTAAAATAATAAAAAATTAA
Found at i:3483868 original size:73 final size:73
Alignment explanation
Indices: 3483749--3483892 Score: 209
Period size: 73 Copynumber: 2.0 Consensus size: 73
3483739 ATTGTCTCAG
* * * *
3483749 GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCATGCAATTGTTATCAATACCTTGTCATA
1 GGTAGGTCACTTTATAACCTTACCCTCAACTGGGAGCATGAAATTGTTATCAATACATTGCCATA
3483814 ACACACAT
66 ACACACAT
** *
3483822 GGTAGGTCACTTTATAACCTTACCCTTGACTGGGGGC-TAGAAATTGTTATCAATACATTGCCAT
1 GGTAGGTCACTTTATAACCTTACCCTCAACTGGGAGCAT-GAAATTGTTATCAATACATTGCCAT
3483886 AACACAC
65 AACACAC
3483893 CTTGCCACCC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
72 1 0.02
73 62 0.98
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (73 bp):
GGTAGGTCACTTTATAACCTTACCCTCAACTGGGAGCATGAAATTGTTATCAATACATTGCCATA
ACACACAT
Found at i:3485088 original size:17 final size:17
Alignment explanation
Indices: 3485066--3485100 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3485056 TAAAATATAT
3485066 ATTTTATAAAACATCAA
1 ATTTTATAAAACATCAA
*
3485083 ATTTTATAAAATATCAA
1 ATTTTATAAAACATCAA
3485100 A
1 A
3485101 GATTTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTTATAAAACATCAA
Found at i:3497685 original size:3 final size:3
Alignment explanation
Indices: 3497677--3497771 Score: 83
Period size: 3 Copynumber: 32.7 Consensus size: 3
3497667 CCTTTTTAGC
* * *
3497677 ATT ATT ATT ATT -TT -TT CTT CATT ATT -TT AAT GTT ATT ATCT -TT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT AT-T ATT
***
3497720 -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GCC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3497767 ATT AT
1 ATT AT
3497772 AATTGCTCTT
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
2 9 0.12
3 64 0.84
4 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3497783 original size:18 final size:18
Alignment explanation
Indices: 3497743--3497777 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3497733 TATTATTATT
*
3497743 ATTATTATTATTATTGCC
1 ATTATTATTATAATTGCC
3497761 ATTATTATTATAATTGC
1 ATTATTATTATAATTGC
3497778 TCTTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTATTATTATAATTGCC
Found at i:3498536 original size:107 final size:107
Alignment explanation
Indices: 3498296--3498615 Score: 446
Period size: 107 Copynumber: 3.0 Consensus size: 107
3498286 TTCAAAAAAG
* ** * * *
3498296 AAAAATTTTCAAAATAAGGCAATATTAAGCATTTGGAAATTCGAGAAAACGTGCTCTAATGTGCT
1 AAAAA-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTG-T
* * * * * *
3498361 GGGGTTT-GATTTTTCTCGTTCAACCAAATAACTAAGTATCCTTTT
64 TGGGTTTCGA--TTTCTCGTTTAACCAAATAGCCAAATATCCTTTC
*
3498406 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGTAATTCGAGGAAACGTGCCCTAATGTGTTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGTTG
3498471 GGTTTCGATTTCTCGTTTAACCAAATAGCCAAATATCCTTTC
66 GGTTTCGATTTCTCGTTTAACCAAATAGCCAAATATCCTTTC
* *
3498513 AAGAATTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGG-AACGTGCCCTAATGTGTTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGTTG
*
3498577 GGTTTCGATTTCTCGTTTAACCAAATAGCCAAACATCCT
66 GGTTTCGATTTCTCGTTTAACCAAATAGCCAAATATCCT
3498616 CTTGAATTTT
Statistics
Matches: 192, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
106 57 0.30
107 71 0.37
108 7 0.04
109 52 0.27
110 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (107 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGTTG
GGTTTCGATTTCTCGTTTAACCAAATAGCCAAATATCCTTTC
Found at i:3506954 original size:51 final size:50
Alignment explanation
Indices: 3506789--3506972 Score: 190
Period size: 51 Copynumber: 3.6 Consensus size: 50
3506779 AGTGGAAGTG
** * *
3506789 ATGGTCAGGTGTGTAGTACTATGTGCAGGCTGCTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGT
* * * * * *
3506840 A-GGTCGCATGTGTAGTACTATGTGCAGGGTACTATGCGTACCGAATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* * * * *
3506889 TTCGATCCCGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
*
3506940 AATGGTCACATGTGTAGTACTATGTGCAAGCTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTA
3506973 TTATGTGAAA
Statistics
Matches: 105, Mismatches: 25, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
49 3 0.03
50 35 0.33
51 66 0.63
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
Found at i:3507035 original size:45 final size:45
Alignment explanation
Indices: 3506986--3507073 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
3506976 TGTGAAACGA
* *
3506986 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
3507031 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
3507074 GAGTATCTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:3509435 original size:27 final size:27
Alignment explanation
Indices: 3509391--3509442 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3509381 GTATATATAT
3509391 ATTTAAGTCCATAATCTAACATTTTCC
1 ATTTAAGTCCATAATCTAACATTTTCC
* *
3509418 ATTTAAGTCCTTAGTCTAACATTTT
1 ATTTAAGTCCATAATCTAACATTTT
3509443 TCCTGTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (27 bp):
ATTTAAGTCCATAATCTAACATTTTCC
Found at i:3511296 original size:21 final size:21
Alignment explanation
Indices: 3511270--3511317 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3511260 ATCTCTAAAT
3511270 AAATTGAATAAATTCTGAAGA
1 AAATTGAATAAATTCTGAAGA
* * *
3511291 ACATTGCATCAATTCTGAAGA
1 AAATTGAATAAATTCTGAAGA
3511312 AAATTG
1 AAATTG
3511318 TTCTTCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (21 bp):
AAATTGAATAAATTCTGAAGA
Found at i:3515666 original size:7 final size:7
Alignment explanation
Indices: 3515654--3515683 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3515644 TTGGCAAAGT
3515654 TTGCAGA
1 TTGCAGA
3515661 TTGCAGA
1 TTGCAGA
3515668 TTGCAGA
1 TTGCAGA
3515675 TTGCAGA
1 TTGCAGA
3515682 TT
1 TT
3515684 ACTGAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (7 bp):
TTGCAGA
Found at i:3518272 original size:18 final size:17
Alignment explanation
Indices: 3518253--3518304 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
3518243 GCAACCCAAT
3518253 TTTATTTTATTTTTTTA
1 TTTATTTTATTTTTTTA
**
3518270 TTTATTTTAATAATTTTA
1 TTTATTTT-ATTTTTTTA
3518288 TTTATCTTTATTTTTTT
1 TTTAT-TTTATTTTTTT
3518305 TTGTTCTAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 8 0.28
18 18 0.62
19 3 0.10
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTTTTTTA
Found at i:3518273 original size:12 final size:13
Alignment explanation
Indices: 3518252--3518338 Score: 52
Period size: 13 Copynumber: 6.2 Consensus size: 13
3518242 GGCAACCCAA
3518252 TTTTATTTTATTT
1 TTTTATTTTATTT
3518265 TTTTA-TTTATTT
1 TTTTATTTTATTT
* *
3518277 TAATAATTTTATTT
1 T-TTTATTTTATTT
3518291 ATCTTTATTTT-TTT
1 -T-TTTATTTTATTT
* *
3518305 TTGTTCTAGTTATTT
1 TT-TTAT-TTTATTT
3518320 CTAGTTTATTTTATTT
1 -T--TTTATTTTATTT
3518336 TTT
1 TTT
3518339 AATAGGATTG
Statistics
Matches: 56, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
12 9 0.16
13 13 0.23
14 12 0.21
15 11 0.20
16 7 0.12
17 3 0.05
18 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:3518302 original size:35 final size:36
Alignment explanation
Indices: 3518253--3518339 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 36
3518243 GCAACCCAAT
*
3518253 TTTATTTTATTTTTTTATTTATTTTAATAATTT-TA-
1 TTTATTTTA-TTTTTTATTTATTCTAATAATTTCTAG
* * *
3518288 TTTATCTTTATTTTTT-TTTGTTCTAGTTATTTCTAG
1 TTTAT-TTTATTTTTTATTTATTCTAATAATTTCTAG
3518324 TTTATTTTATTTTTTA
1 TTTATTTTATTTTTTA
3518340 ATAGGATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
34 12 0.27
35 23 0.52
36 9 0.20
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (36 bp):
TTTATTTTATTTTTTATTTATTCTAATAATTTCTAG
Found at i:3532961 original size:4 final size:4
Alignment explanation
Indices: 3532952--3532976 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3532942 TAATGGACAT
3532952 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
3532977 CATCAAGTAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:3533104 original size:3 final size:3
Alignment explanation
Indices: 3533096--3533120 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3533086 TAAATGAGTA
3533096 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3533121 TAAGATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3536114 original size:14 final size:14
Alignment explanation
Indices: 3536097--3536125 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3536087 TATATTATTA
3536097 TATTACCATTAAAG
1 TATTACCATTAAAG
3536111 TATTACCATTAAAG
1 TATTACCATTAAAG
3536125 T
1 T
3536126 TTAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
TATTACCATTAAAG
Found at i:3536170 original size:17 final size:16
Alignment explanation
Indices: 3536138--3536185 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
3536128 AATTTTATAG
*
3536138 ATTTTA-ATACTTATT
1 ATTTTATATAATTATT
3536153 AATTTTATATAATTATT
1 -ATTTTATATAATTATT
3536170 ATTCTTATATAATTAT
1 ATT-TTATATAATTAT
3536186 AGTGTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATATAATTATT
Found at i:3536888 original size:17 final size:17
Alignment explanation
Indices: 3536837--3536889 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
3536827 TACGATTTAG
3536837 CTTGTAAGAGATTATCC
1 CTTGTAAGAGATTATCC
*
3536854 CTTG-AATTATCTGATTATCC
1 CTTGTAA-GA---GATTATCC
3536874 CTTGTAAGAGATTATC
1 CTTGTAAGAGATTATC
3536890 ATCATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
16 2 0.07
17 12 0.41
20 13 0.45
21 2 0.07
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (17 bp):
CTTGTAAGAGATTATCC
Found at i:3538476 original size:9 final size:9
Alignment explanation
Indices: 3538462--3538519 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
3538452 TAATTTTTTT
3538462 TAAAAATTA
1 TAAAAATTA
3538471 TAAAAATTA
1 TAAAAATTA
*
3538480 TTAAAAGTTA
1 -TAAAAATTA
3538490 CTAAAAAGTATA
1 -TAAAAA-T-TA
* *
3538502 AAAAAAGTA
1 TAAAAATTA
3538511 TAAAAATTA
1 TAAAAATTA
3538520 AATATGTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 18 0.46
10 13 0.33
11 6 0.15
12 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:3538506 original size:11 final size:11
Alignment explanation
Indices: 3538492--3538516 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3538482 AAAAGTTACT
3538492 AAAAAGTATAA
1 AAAAAGTATAA
3538503 AAAAAGTATAA
1 AAAAAGTATAA
3538514 AAA
1 AAA
3538517 TTAAATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAAGTATAA
Found at i:3538569 original size:17 final size:18
Alignment explanation
Indices: 3538536--3538576 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3538526 TAATTTTTCA
*
3538536 ATAAAATTTTACCATATT
1 ATAAAATTTTACAATATT
*
3538554 -TAAAATTTTATAATATT
1 ATAAAATTTTACAATATT
3538571 ATAAAA
1 ATAAAA
3538577 AAATTAACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAAATTTTACAATATT
Found at i:3541140 original size:12 final size:12
Alignment explanation
Indices: 3541123--3541149 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3541113 CAACAGTTAG
3541123 CTAACTAGCTAA
1 CTAACTAGCTAA
3541135 CTAACTAGCTAA
1 CTAACTAGCTAA
3541147 CTA
1 CTA
3541150 TTAACTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (12 bp):
CTAACTAGCTAA
Found at i:3544299 original size:62 final size:62
Alignment explanation
Indices: 3544165--3544309 Score: 211
Period size: 62 Copynumber: 2.3 Consensus size: 62
3544155 TTATTAGTTG
* * *
3544165 ACTCTGAAAAAATGGATGAAAAGGCACCGCCTAGGGGAGAAATATAGGTAGGACCTTTTCAA
1 ACTCTGAAAAAATGGATGAAAAGGCACCGCCTAGGGGAAAAATACAAGTAGGACCTTTTCAA
* ** *
3544227 ACTCTAAAAAAAAAGATGAAAAGGCACCGCCTGAGGGGAAAAATACAAGTAGGACCTTTTCAG
1 ACTCTGAAAAAATGGATGAAAAGGCACCGCCT-AGGGGAAAAATACAAGTAGGACCTTTTCAA
3544290 AC-CTGAAAAAATGGATGAAA
1 ACTCTGAAAAAATGGATGAAA
3544310 TGCACACCTA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
62 44 0.61
63 28 0.39
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.17
Consensus pattern (62 bp):
ACTCTGAAAAAATGGATGAAAAGGCACCGCCTAGGGGAAAAATACAAGTAGGACCTTTTCAA
Found at i:3544881 original size:16 final size:16
Alignment explanation
Indices: 3544855--3544913 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
3544845 TAATTTTCAT
3544855 AATTCTTTACATCTTTA
1 AATT-TTTACATCTTTA
*
3544872 AATTTTTACAATTTTTAA
1 AATTTTTAC-ATCTTT-A
* *
3544890 TAATTTTTATAGCTTTA
1 -AATTTTTACATCTTTA
3544907 AATTTTT
1 AATTTTT
3544914 TTTATAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.34
17 10 0.29
18 5 0.14
19 8 0.23
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (16 bp):
AATTTTTACATCTTTA
Found at i:3545355 original size:27 final size:27
Alignment explanation
Indices: 3545325--3545381 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3545315 CTGGAATTTC
3545325 AATACTGAAACCGAGCCGACAACATCA
1 AATACTGAAACCGAGCCGACAACATCA
* * *
3545352 AATATTGAAACTGAGCCGACACCATCA
1 AATACTGAAACCGAGCCGACAACATCA
3545379 AAT
1 AAT
3545382 CATCCGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (27 bp):
AATACTGAAACCGAGCCGACAACATCA
Found at i:3545850 original size:16 final size:15
Alignment explanation
Indices: 3545831--3545860 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3545821 TATTGCAGCT
3545831 TTTATTTATTGTTGTA
1 TTTATTTATT-TTGTA
3545847 TTTATTTATTTTGT
1 TTTATTTATTTTGT
3545861 CATTATATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (15 bp):
TTTATTTATTTTGTA
Found at i:3546616 original size:35 final size:31
Alignment explanation
Indices: 3546576--3546647 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
3546566 CCTCAGAATT
*
3546576 TTTATTTACAGTTCAAATTAGCTTTTTTTATTTTC
1 TTTATTTACAATT--AATTAG-TTTTTTTA-TTTC
**
3546611 TTTATTTTTAATTAATTAGTTTTTTTATTTC
1 TTTATTTACAATTAATTAGTTTTTTTATTTC
3546642 TTTATT
1 TTTATT
3546648 ATTTCTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 10 0.29
32 8 0.24
33 6 0.18
35 10 0.29
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (31 bp):
TTTATTTACAATTAATTAGTTTTTTTATTTC
Found at i:3558674 original size:44 final size:45
Alignment explanation
Indices: 3558626--3558734 Score: 127
Period size: 45 Copynumber: 2.4 Consensus size: 45
3558616 CTTATTTCCC
*
3558626 TGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAGTCTTAT-CCTCT
1 TGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCAAATCTTATACC-CT
*
3558670 TGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCTTATACCCT
1 TGAAGTTGCAGTGGA-GCAGACTGAAGATAGCAAATCTTATACCCT
* *
3558715 TGAAGTTGTAGTGGAACAGA
1 TGAAGTTGCAGTGGAGCAGA
3558735 TTAAAGCCGA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
43 2 0.04
44 19 0.34
45 30 0.54
46 5 0.09
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (45 bp):
TGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATACCCT
Found at i:3559083 original size:128 final size:130
Alignment explanation
Indices: 3558851--3559124 Score: 419
Period size: 128 Copynumber: 2.1 Consensus size: 130
3558841 CTTAAAGTTG
**
3558851 CAGTGGAGCAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
1 CAGTGGAATAGATTGAAGATTTCAGATCTTA-CT-CCTAAGCAGTAGTGGAGCAGATCGAAGATG
* * *
3558916 GCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGG
64 GCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATCCTATC-TCCCTAGG
3558980 CAA
128 CAA
* *
3558983 CAGTGGAATAGATTGAAGATTTCAGATCTTA-T-CTAAGCAGTAGTGGAGTAGATCGAAGATGGT
1 CAGTGGAATAGATTGAAGATTTCAGATCTTACTCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
* *
3559046 GGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATCCTATCTCCCTAGTCAG
66 GGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATCCTATCTCCCTAGGCAA
3559111 CAGTGGAATAGATT
1 CAGTGGAATAGATT
3559125 ATCTTCCTGA
Statistics
Matches: 132, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
128 101 0.77
129 1 0.01
130 1 0.01
132 29 0.22
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (130 bp):
CAGTGGAATAGATTGAAGATTTCAGATCTTACTCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
GGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATCCTATCTCCCTAGGCAA
Found at i:3560622 original size:35 final size:31
Alignment explanation
Indices: 3560582--3560653 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
3560572 CCTCAGAATT
*
3560582 TTTATTTACAGTTCAAATTAGCTTTTTTTATTTTC
1 TTTATTTACAATT--AATTAG-TTTTTTTA-TTTC
**
3560617 TTTATTTTTAATTAATTAGTTTTTTTATTTC
1 TTTATTTACAATTAATTAGTTTTTTTATTTC
3560648 TTTATT
1 TTTATT
3560654 ATTTCTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 10 0.29
32 8 0.24
33 6 0.18
35 10 0.29
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (31 bp):
TTTATTTACAATTAATTAGTTTTTTTATTTC
Found at i:3560800 original size:24 final size:25
Alignment explanation
Indices: 3560751--3560819 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
3560741 TTATTTTTAT
* *
3560751 TTTATTTTTATTTATATGTA-ATTA
1 TTTATTTTAATATATATGTATATTA
*
3560775 TTT-TTTATAATCTATATGTATA-TA
1 TTTATTT-TAATATATATGTATATTA
*
3560799 TTTATTTTAGTATATATGTAT
1 TTTATTTTAATATATATGTAT
3560820 GTATACATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 3 0.08
24 31 0.82
25 4 0.11
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.62
Consensus pattern (25 bp):
TTTATTTTAATATATATGTATATTA
Found at i:3571846 original size:26 final size:25
Alignment explanation
Indices: 3571792--3571846 Score: 58
Period size: 26 Copynumber: 2.1 Consensus size: 25
3571782 AGTTTTTTCC
* *
3571792 TTTTGAAATAGGGAAAATGTCATCCT
1 TTTTGAAATAAGGAAAATATCAT-CT
3571818 TTTTGAAACTAAGGAATAATATCAT-T
1 TTTTGAAA-TAAGGAA-AATATCATCT
3571844 TTT
1 TTT
3571847 GTTATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 12 0.48
27 6 0.24
28 7 0.28
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (25 bp):
TTTTGAAATAAGGAAAATATCATCT
Found at i:3577821 original size:21 final size:21
Alignment explanation
Indices: 3577795--3577838 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3577785 TTTTACCAAA
3577795 AATGTGTA-TTGGACTAAATTG
1 AATGTG-AGTTGGACTAAATTG
* *
3577816 AATGTGAGTTGTATTAAATTG
1 AATGTGAGTTGGACTAAATTG
3577837 AA
1 AA
3577839 CTAAATTCAT
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:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (21 bp):
AATGTGAGTTGGACTAAATTG
Found at i:3578198 original size:25 final size:25
Alignment explanation
Indices: 3578173--3578422 Score: 169
Period size: 25 Copynumber: 10.1 Consensus size: 25
3578163 CGCAAGGGCA
* *
3578173 TCCCGTTAATTAGCTCTCATGAGCAT
1 TCCCGATAATTGGCTCTCATGAGC-T
* * *
3578199 T--CTATTATTTGGCTCTCTTGAGCT
1 TCCCGATAAT-TGGCTCTCATGAGCT
* *
3578223 TCCCGTTTA-TGGCTCGT-ATGAGCT
1 TCCCGATAATTGGCTC-TCATGAGCT
3578247 TCCCGATAATTGGCTCTC-TGGAGCT
1 TCCCGATAATTGGCTCTCAT-GAGCT
**
3578272 TCTTGATAATTGGCTCTCATGAGCT
1 TCCCGATAATTGGCTCTCATGAGCT
* *
3578297 TTCTGATAATTGGCTCTCATGAGCT
1 TCCCGATAATTGGCTCTCATGAGCT
** * *
3578322 TCCTTATTAA-TAGCTCTC-CGAAGCT
1 TCCCGA-TAATTGGCTCTCATG-AGCT
*
3578347 TCCCGAT-ATTGGCTCGCATGAGCT
1 TCCCGATAATTGGCTCTCATGAGCT
* * *
3578371 TCTCGATTA-TGGCTCTTATGAGCT
1 TCCCGATAATTGGCTCTCATGAGCT
* * *
3578395 TCTCGTTACA-TGGCTCACATGAGCT
1 TCCCGATA-ATTGGCTCTCATGAGCT
3578420 TCC
1 TCC
3578423 TGTTATAAGG
Statistics
Matches: 179, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
23 1 0.01
24 64 0.36
25 105 0.59
26 9 0.05
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (25 bp):
TCCCGATAATTGGCTCTCATGAGCT
Found at i:3578358 original size:99 final size:97
Alignment explanation
Indices: 3578179--3578429 Score: 244
Period size: 99 Copynumber: 2.5 Consensus size: 97
3578169 GGCATCCCGT
* * * * * *
3578179 TAATTAGCTCTCATGAGCATTCT-ATTATTTGGCTCTCTTGAGCTTCCCGTTTATGGCTCGTATG
1 TAATTGGCTCTCATGAGC-TTCTGA-TAATTGGCTCTCATGAGCTT-CCTTTTATAGCTCGTACG
* *
3578243 AGCTTCCCGATAATTGGCTCTC-TGGAGCTTCTTGA
63 AGCTTCCCGATAATTGGCTCGCAT-GAGCTTCTCGA
*
3578278 TAATTGGCTCTCATGAGCTTTCTGATAATTGGCTCTCATGAGCTTCCTTATTAATAGCTC-TCCG
1 TAATTGGCTCTCATGAGC-TTCTGATAATTGGCTCTCATGAGCTTCCTT-TT-ATAGCTCGTACG
3578342 AAGCTTCCCGAT-ATTGGCTCGCATGAGCTTCTCGA
63 -AGCTTCCCGATAATTGGCTCGCATGAGCTTCTCGA
* * * * *
3578377 TTA-TGGCTCTTATGAGCTTCTCGTTACA-TGGCTCACATGAGCTTCCTGTTATA
1 TAATTGGCTCTCATGAGCTTCT-GATA-ATTGGCTCTCATGAGCTTCCTTTTATA
3578430 AGGCTCGAAA
Statistics
Matches: 130, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
96 3 0.02
97 6 0.05
98 37 0.28
99 65 0.50
100 19 0.15
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.38
Consensus pattern (97 bp):
TAATTGGCTCTCATGAGCTTCTGATAATTGGCTCTCATGAGCTTCCTTTTATAGCTCGTACGAGC
TTCCCGATAATTGGCTCGCATGAGCTTCTCGA
Found at i:3578427 original size:25 final size:25
Alignment explanation
Indices: 3578356--3578421 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
3578346 TTCCCGATAT
*
3578356 TGGCTCGCATGAGCTTCTCGATT--A
1 TGGCTCACATGAGCTTCTCG-TTACA
**
3578380 TGGCTCTTATGAGCTTCTCGTTACA
1 TGGCTCACATGAGCTTCTCGTTACA
3578405 TGGCTCACATGAGCTTC
1 TGGCTCACATGAGCTTC
3578422 CTGTTATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 2 0.06
24 18 0.50
25 16 0.44
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.35
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCTCGTTACA
Found at i:3578434 original size:25 final size:25
Alignment explanation
Indices: 3578357--3578435 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
3578347 TCCCGATATT
* *
3578357 GGCTCGCATGAGCTTCTCGATT--AT
1 GGCTCACATGAGCTTCTCG-TTACAA
** *
3578381 GGCTCTTATGAGCTTCTCGTTACAT
1 GGCTCACATGAGCTTCTCGTTACAA
*
3578406 GGCTCACATGAGCTTC-CTGTTATAA
1 GGCTCACATGAGCTTCTC-GTTACAA
3578431 GGCTC
1 GGCTC
3578436 GAAAGAGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
23 2 0.04
24 18 0.39
25 26 0.57
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (25 bp):
GGCTCACATGAGCTTCTCGTTACAA
Found at i:3580227 original size:21 final size:21
Alignment explanation
Indices: 3580201--3580244 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3580191 TTTTACCAAA
3580201 AATGTGTA-TTGGACTAAATTG
1 AATGTG-AGTTGGACTAAATTG
* *
3580222 AATGTGAGTTGTATTAAATTG
1 AATGTGAGTTGGACTAAATTG
3580243 AA
1 AA
3580245 CTAAATTCAT
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:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (21 bp):
AATGTGAGTTGGACTAAATTG
Found at i:3580727 original size:25 final size:24
Alignment explanation
Indices: 3580585--3580728 Score: 96
Period size: 25 Copynumber: 5.8 Consensus size: 24
3580575 GGCATCCCGT
* *
3580585 TAATTAGCTCTCATGAGCATTCT-A
1 TAATTGGCTCTC-TGAGCTTTCTGA
* * * *
3580609 TTATTTGGCTCTCTTGAGCTTCCCGT
1 -TAATTGGCTCTC-TGAGCTTTCTGA
* * * *
3580635 TTA-TGGCTCGTATGAGCTTCCCGA
1 TAATTGGCTC-TCTGAGCTTTCTGA
*
3580659 TAATTGGCTCTCTGGAGC-TTCTTAA
1 TAATTGGCTCTCT-GAGCTTTC-TGA
3580684 TAATTGGCTCTCATGAGCTTTCTGA
1 TAATTGGCTCTC-TGAGCTTTCTGA
3580709 TAATTGGCTCTCGTGAGCTT
1 TAATTGGCTCTC-TGAGCTT
3580729 CCTTATTAAT
Statistics
Matches: 94, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
24 23 0.24
25 67 0.71
26 4 0.04
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (24 bp):
TAATTGGCTCTCTGAGCTTTCTGA
Found at i:3580744 original size:50 final size:50
Alignment explanation
Indices: 3580584--3580745 Score: 149
Period size: 50 Copynumber: 3.3 Consensus size: 50
3580574 GGGCATCCCG
* * *
3580584 TTAATTAGCTCTCATGAGCATTCT-ATTATTTGGCTCTCTTGAGCTTCCCGT-
1 TTAATTAGCTCTCATGAGCTTTCTGA-TAATTGGCTCTC-TGAGCTT-CCTTA
* * *
3580635 TT-A-TGGCTCGT-ATGAGCTTCCCGATAATTGGCTCTCTGGAGCTT-CTTA
1 TTAATTAGCTC-TCATGAGCTTTCTGATAATTGGCTCTCT-GAGCTTCCTTA
* *
3580683 ATAATTGGCTCTCATGAGCTTTCTGATAATTGGCTCTCGTGAGCTTCCTTA
1 TTAATTAGCTCTCATGAGCTTTCTGATAATTGGCTCTC-TGAGCTTCCTTA
3580734 TTAA-TAGCTCTC
1 TTAATTAGCTCTC
3580746 CGAAGCTTCC
Statistics
Matches: 91, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
47 2 0.02
48 2 0.02
49 32 0.35
50 45 0.49
51 10 0.11
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (50 bp):
TTAATTAGCTCTCATGAGCTTTCTGATAATTGGCTCTCTGAGCTTCCTTA
Found at i:3580753 original size:50 final size:50
Alignment explanation
Indices: 3580648--3580778 Score: 144
Period size: 50 Copynumber: 2.6 Consensus size: 50
3580638 TGGCTCGTAT
* *
3580648 GAGCTTCCCGATAATTGGCTCTCTGGAGCTT-CTTAATAATTGGCTCTCAT
1 GAGCTTCCCGATAATTGGCTCTCT-GAGCTTCCTTAATAATTAGCTCTCAC
* * *
3580698 GAGCTTTCTGATAATTGGCTCTCGTGAGCTTCCTTATTAA-TAGCTCTC-C
1 GAGCTTCCCGATAATTGGCTCTC-TGAGCTTCCTTAATAATTAGCTCTCAC
*
3580747 GAAGCTTCCCGAT-ATTGGCTCGCATGAGCTTC
1 G-AGCTTCCCGATAATTGGCTCTC-TGAGCTTC
3580779 TCGATTATGG
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
49 18 0.26
50 43 0.62
51 8 0.12
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (50 bp):
GAGCTTCCCGATAATTGGCTCTCTGAGCTTCCTTAATAATTAGCTCTCAC
Found at i:3580764 original size:99 final size:99
Alignment explanation
Indices: 3580585--3580801 Score: 230
Period size: 99 Copynumber: 2.2 Consensus size: 99
3580575 GGCATCCCGT
* * * * * *
3580585 TAATTAGCTCTCATGAGCATTCTATTATTTGGCTCTCTTGAGCTTCCCGTTTATGGCTCGTATGA
1 TAATTGGCTCTCATGAGCTTTCTATTAATTGGCTCTCGTGAGCTTCCCGTTTATAGCTCGTACGA
* *
3580650 GCTTCCCGATAATTGGCTCTC-TGGAGCTTCTTAA
66 GCTTCCCGATAATTGGCTCGCAT-GAGCTTCTCAA
* *
3580684 TAATTGGCTCTCATGAGCTTTCTGA-TAATTGGCTCTCGTGAGCTT-CCTTATTAATAGCTC-TC
1 TAATTGGCTCTCATGAGCTTTCT-ATTAATTGGCTCTCGTGAGCTTCCCGT-TT-ATAGCTCGTA
*
3580746 CGAAGCTTCCCGAT-ATTGGCTCGCATGAGCTTCTCGA
63 CG-AGCTTCCCGATAATTGGCTCGCATGAGCTTCTCAA
* *
3580783 TTA-TGGCTCTTATGAGCTT
1 TAATTGGCTCTCATGAGCTT
3580802 CTCGTTACAT
Statistics
Matches: 100, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
98 18 0.18
99 63 0.63
100 19 0.19
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (99 bp):
TAATTGGCTCTCATGAGCTTTCTATTAATTGGCTCTCGTGAGCTTCCCGTTTATAGCTCGTACGA
GCTTCCCGATAATTGGCTCGCATGAGCTTCTCAA
Found at i:3580822 original size:25 final size:24
Alignment explanation
Indices: 3580749--3580827 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
3580739 AGCTCTCCGA
* *
3580749 AGCTTCCCGA-TATTGGCTCGCATG
1 AGCTTCTCGATTA-TGGCTCACATG
**
3580773 AGCTTCTCGATTATGGCTCTTATG
1 AGCTTCTCGATTATGGCTCACATG
3580797 AGCTTCTCG-TTACATGGCTCACATG
1 AGCTTCTCGATT--ATGGCTCACATG
3580822 AGCTTC
1 AGCTTC
3580828 CTGTTATAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.04
24 27 0.57
25 18 0.38
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.34
Consensus pattern (24 bp):
AGCTTCTCGATTATGGCTCACATG
Found at i:3580833 original size:25 final size:25
Alignment explanation
Indices: 3580762--3580827 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
3580752 TTCCCGATAT
*
3580762 TGGCTCGCATGAGCTTCTCGATT--A
1 TGGCTCACATGAGCTTCTCG-TTACA
**
3580786 TGGCTCTTATGAGCTTCTCGTTACA
1 TGGCTCACATGAGCTTCTCGTTACA
3580811 TGGCTCACATGAGCTTC
1 TGGCTCACATGAGCTTC
3580828 CTGTTATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 2 0.06
24 18 0.50
25 16 0.44
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.35
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCTCGTTACA
Found at i:3580840 original size:25 final size:25
Alignment explanation
Indices: 3580763--3580841 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
3580753 TCCCGATATT
* *
3580763 GGCTCGCATGAGCTTCTCGATT--AT
1 GGCTCACATGAGCTTCTCG-TTACAA
** *
3580787 GGCTCTTATGAGCTTCTCGTTACAT
1 GGCTCACATGAGCTTCTCGTTACAA
*
3580812 GGCTCACATGAGCTTC-CTGTTATAA
1 GGCTCACATGAGCTTCTC-GTTACAA
3580837 GGCTC
1 GGCTC
3580842 GAAAGAGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
23 2 0.04
24 18 0.39
25 26 0.57
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (25 bp):
GGCTCACATGAGCTTCTCGTTACAA
Found at i:3595417 original size:3 final size:3
Alignment explanation
Indices: 3595409--3595445 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3595399 GGTTCAGGTC
3595409 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3595446 CAATAACTGT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3595752 original size:42 final size:42
Alignment explanation
Indices: 3595637--3595758 Score: 172
Period size: 42 Copynumber: 2.9 Consensus size: 42
3595627 TGAAGAAAAA
* **
3595637 CGCCGCTAAAGAATATGATCTTTAGCGGCGCATTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
**
3595679 CGTTGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* *
3595721 CGCCGCTAAAGAACATGACCTTTAGCAGCGTTTATTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTT
3595759 TGTAAACGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 66 0.94
43 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:3600964 original size:29 final size:28
Alignment explanation
Indices: 3600932--3600997 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
3600922 TTAAACCCAG
* *
3600932 ATTTTAAAATATGAAAATAGAAAAACTAA
1 ATTTTAAAA-ATAAAAATACAAAAACTAA
**
3600961 ATTTCTAAAAATAAAAATACAAGTACTAA
1 ATTT-TAAAAATAAAAATACAAAAACTAA
*
3600990 ATTCTAAA
1 ATTTTAAA
3600998 TTTTCGAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.13
29 22 0.71
30 5 0.16
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.29
Consensus pattern (28 bp):
ATTTTAAAAATAAAAATACAAAAACTAA
Found at i:3601753 original size:16 final size:15
Alignment explanation
Indices: 3601716--3601745 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3601706 GAAATAGTTT
3601716 CAAAA-AATAAACTC
1 CAAAACAATAAACTC
3601730 CAAAACAATAAACTC
1 CAAAACAATAAACTC
3601745 C
1 C
3601746 CTAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (15 bp):
CAAAACAATAAACTC
Found at i:3602365 original size:2 final size:2
Alignment explanation
Indices: 3602360--3602385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3602350 CGCGCGCGCG
3602360 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
3602386 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3604891 original size:30 final size:30
Alignment explanation
Indices: 3604855--3604913 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3604845 ATTTAAAGAG
*
3604855 ATTGCTTGCAAGTCAAGTTAAACAAAATAT
1 ATTGCTTACAAGTCAAGTTAAACAAAATAT
3604885 ATTGCTTACAAGTCAAGTTAAACAAAATA
1 ATTGCTTACAAGTCAAGTTAAACAAAATA
3604914 CATTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (30 bp):
ATTGCTTACAAGTCAAGTTAAACAAAATAT
Found at i:3609244 original size:166 final size:168
Alignment explanation
Indices: 3609045--3609382 Score: 662
Period size: 166 Copynumber: 2.0 Consensus size: 168
3609035 TATAATTTTT
3609045 AAAAGATTAAATCTAATGTAAAATACTAATTTAAAATTTTAAAAATTAAAAAAGTTACAATTTAA
1 AAAAGATTAAATCTAATGTAAAATACTAATTTAAAATTTTAAAAATTAAAAAAGTTACAATTTAA
3609110 GGAGCTGTTGCCCTGGCCAGCCCCTCGGTACGCCACAAGCCATAACCCGACTGGTTGAGAGTATT
66 GGAGCTGTTGCCCTGGCCAGCCCCTCGGTACGCCACAAGCCATAACCCGACTGGTTGAGAGTATT
3609175 TTGTCGCAATCCGCAACTGCAATATACGCATGAGAAA-
131 TTGTCGCAATCCGCAACTGCAATATACGCATGAGAAAG
3609212 AAAAGATT-AATCTAATGTAAAATACTAATTTAAAATTTTAAAAATTAAAAAAGTTACAATTTAA
1 AAAAGATTAAATCTAATGTAAAATACTAATTTAAAATTTTAAAAATTAAAAAAGTTACAATTTAA
3609276 GGAGCTGTTGCCCTGGCCAGCCCCTCGGTACGCCACAAGCCATAACCCGACTGGTTGAGAGTATT
66 GGAGCTGTTGCCCTGGCCAGCCCCTCGGTACGCCACAAGCCATAACCCGACTGGTTGAGAGTATT
3609341 TTGTCGCAATCCGCAACTGCAATATACGCATGAGAAAG
131 TTGTCGCAATCCGCAACTGCAATATACGCATGAGAAAG
3609379 AAAA
1 AAAA
3609383 TACATCCGTA
Statistics
Matches: 170, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
166 158 0.93
167 12 0.07
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (168 bp):
AAAAGATTAAATCTAATGTAAAATACTAATTTAAAATTTTAAAAATTAAAAAAGTTACAATTTAA
GGAGCTGTTGCCCTGGCCAGCCCCTCGGTACGCCACAAGCCATAACCCGACTGGTTGAGAGTATT
TTGTCGCAATCCGCAACTGCAATATACGCATGAGAAAG
Found at i:3611263 original size:1 final size:1
Alignment explanation
Indices: 3611257--3611290 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
3611247 ACTGCTTCGG
3611257 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3611291 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3614587 original size:17 final size:17
Alignment explanation
Indices: 3614565--3614601 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3614555 GATTCTATTG
3614565 ATTTACATGTTATACGC
1 ATTTACATGTTATACGC
3614582 ATTTACATGTTATACGC
1 ATTTACATGTTATACGC
3614599 ATT
1 ATT
3614602 AAGCCAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (17 bp):
ATTTACATGTTATACGC
Found at i:3615789 original size:18 final size:18
Alignment explanation
Indices: 3615746--3615789 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3615736 AGTGAAATTT
* *
3615746 ATATGAAAATCCCTAAAGG
1 ATAT-AAAATCCCAAAAAG
*
3615765 ATTTAAAATCCCAAAAAG
1 ATATAAAATCCCAAAAAG
3615783 ATATAAA
1 ATATAAA
3615790 GTTTCTTGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (18 bp):
ATATAAAATCCCAAAAAG
Found at i:3623489 original size:2 final size:2
Alignment explanation
Indices: 3623482--3623733 Score: 504
Period size: 2 Copynumber: 126.0 Consensus size: 2
3623472 TCATGTCATC
3623482 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
3623524 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
3623566 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
3623608 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
3623650 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
3623692 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
3623734 CATGTTTTTC
Statistics
Matches: 250, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 250 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3624662 original size:12 final size:12
Alignment explanation
Indices: 3624645--3624669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3624635 GGTGTTCATT
3624645 CGGTTAACCGAC
1 CGGTTAACCGAC
3624657 CGGTTAACCGAC
1 CGGTTAACCGAC
3624669 C
1 C
3624670 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:3624843 original size:9 final size:9
Alignment explanation
Indices: 3624829--3624921 Score: 116
Period size: 9 Copynumber: 10.2 Consensus size: 9
3624819 TTTGGTTAAA
3624829 AATTACCCG
1 AATTACCCG
3624838 AATTACCCG
1 AATTACCCG
* *
3624847 AATTATCTG
1 AATTACCCG
3624856 AATTACCCG
1 AATTACCCG
3624865 AATTACCCG
1 AATTACCCG
*
3624874 AATTAACCG
1 AATTACCCG
*
3624883 AATTAACCG
1 AATTACCCG
3624892 AATTA-CCG
1 AATTACCCG
*
3624900 AAAAATACCCG
1 --AATTACCCG
3624911 AATTACCCG
1 AATTACCCG
3624920 AA
1 AA
3624922 AATTTTTTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
8 3 0.04
9 64 0.86
10 4 0.05
11 3 0.04
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:3624913 original size:19 final size:19
Alignment explanation
Indices: 3624868--3624923 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
3624858 TTACCCGAAT
*
3624868 TACCCGAATTAACCG--AAT
1 TACCCGAATT-ACCGAAAAA
*
3624886 TAACCGAATTACCGAAAAA
1 TACCCGAATTACCGAAAAA
3624905 TACCCGAATTACCCGAAAA
1 TACCCGAATTA-CCGAAAA
3624924 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.12
18 9 0.28
19 12 0.38
20 7 0.22
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.18
Consensus pattern (19 bp):
TACCCGAATTACCGAAAAA
Found at i:3629967 original size:21 final size:21
Alignment explanation
Indices: 3629943--3629984 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3629933 ATCATGTATT
3629943 TTATCTTTTT-AATTTCTTTTA
1 TTAT-TTTTTAAATTTCTTTTA
3629964 TTATTTTTTAGAATTTCTTTT
1 TTATTTTTTA-AATTTCTTTT
3629985 TGTTAAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTTTTTAAATTTCTTTTA
Found at i:3634096 original size:30 final size:30
Alignment explanation
Indices: 3634060--3634127 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
3634050 TTACTTTCCT
3634060 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
3634090 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
*
3634120 TCTTTTTT
1 TTTTTTTT
3634128 GATTGTACGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.00, C:0.01, G:0.03, T:0.96
Consensus pattern (30 bp):
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
Found at i:3634127 original size:1 final size:1
Alignment explanation
Indices: 3634059--3634118 Score: 111
Period size: 1 Copynumber: 60.0 Consensus size: 1
3634049 ATTACTTTCC
*
3634059 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3634119 GTCTTTTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.00, C:0.00, G:0.02, T:0.98
Consensus pattern (1 bp):
T
Found at i:3637096 original size:3 final size:3
Alignment explanation
Indices: 3637088--3637123 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3637078 TCCTACCTTT
3637088 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
3637124 AGTAAACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3650897 original size:28 final size:28
Alignment explanation
Indices: 3650831--3650885 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
3650821 AATATATAGT
* *
3650831 ACTAATAATTATAAATTTTAGTGTTTTC
1 ACTAATATTTTTAAATTTTAGTGTTTTC
3650859 ACTAATATTTTTAAATTTTAGTGTTTT
1 ACTAATATTTTTAAATTTTAGTGTTTT
3650886 TATTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (28 bp):
ACTAATATTTTTAAATTTTAGTGTTTTC
Found at i:3652281 original size:716 final size:712
Alignment explanation
Indices: 3650870--3652321 Score: 2665
Period size: 716 Copynumber: 2.0 Consensus size: 712
3650860 CTAATATTTT
* *
3650870 TAAATTTTAGTGTTTTTATTTCTTTTTTATTTTTTTATTTTAATTTAATTCCATTTGTTAATTTG
1 TAAATTTTAGCGTTTTTATTTCATTTTTATTTTTTTATTTTAATTTAATTCCATTTGTTAATTTG
3650935 GTACTCTCCTAAAAACTCAAATGTTATATATTAATTTTTTTAACTTATTTATTAGTTTCATTTAA
66 GTACTCTCCTAAAAACTCAAATGTTATATATTAATTTTTTTAACTTATTTATTAGTTTCATTTAA
3651000 GTAATATTTATTATAAATAAATTAACAGTTTTAGTGTTTTAATTTCATTTTTATTTTTCTATTTT
131 GTAATATTTATTATAAATAAATTAACAGTTTTAGTGTTTTAATTTCATTTTTATTTTTCTATTTT
3651065 AATCTTATTTATTAATTAATTAGATTAAATTTTTTATTATTTGTATTTAAGGTAAATAAAAATTA
196 AATCTTATTTATTAATTAATTAGATTAAATTTTTTATTATTTGTATTTAAGGTAAATAAAAATTA
*
3651130 ATTGCGAGGGATTGAAAAACGACGGCGTATTAATTACAACAGATTCAAACTTTGCGGCGTTTTCA
261 ATTGCGAGGGATTAAAAAACGACGGCGTATTAATTACAACAGATTCAAACTTTGCGGCGTTTTCA
3651195 GCCTAGCGCCACGAATGCCCTAATAAAACGGTACGTTTTGTTTAAACCAAAGGCCAAAATTTGCG
326 GCCTAGCGCCACGAATGCCCTAATAAAACGGTACGTTTTGTTTAAACCAAAGGCCAAAATTTGCG
*
3651260 GCGTTTTTATCAACGCGCCGCTAATGCGCACCCACCTTTAGTGGCGTTTTCATCTAGCGCCGCTA
391 GCATTTTTATCAACGCGCCGCTAATGCGCACCCACCTTTAGTGGCGTTTTCATCTAGCGCCGCTA
3651325 AAGCCATTAAAATCGCACAAAGCTACGCCGTTTTGTAAAAAATTTAAAAATTTTTTCCGGCGTTC
456 AAGCCATTAAAATCGCACAAAGCTACGCCGTTTTGTAAAAAATTTAAAAATTTTTTCCGGCGTTC
3651390 GGAAAAAAAACGCCACCAATGACTCATTTATTGCGGCGTTTTTAGTGAAAACGCCACTATTACAT
521 GGAAAAAAAACGCCACCAATGACTCATTTATTGCGGCGTTTTTAGTGAAAACGCCACTATTACAT
*
3651455 CAAATTTTCTACTGAAACGGCTCCGTTTTTCTATTCCATGGTTTTGTTAAGTAATACTTATAATA
586 CAAATTTTCTACTGAAACGGCTCCGTTTTTCTATTCCATGGTTTCGTTAAGTAATACTTATAATA
3651520 TAGTACTAAAAATTATAATTTTTAGTGTTTTAACTAAAATTTATAAATTTTACATAAAATTA
651 TAGTACTAAAAATTATAATTTTTAGTGTTTTAACTAAAATTTATAAATTTTACATAAAATTA
*
3651582 TGAATTTTAGCG-TTTTATTTCATTTTTATTTTTTTATTTTAATTTAATTCCATTTGTTAATTTG
1 TAAATTTTAGCGTTTTTATTTCATTTTTATTTTTTTATTTTAATTTAATTCCATTTGTTAATTTG
3651646 GTACTCTCCTAAAAACTCAAATGTTATATATTAA-TTTTTTAACTTATTTATTAGTTTCATTTAA
66 GTACTCTCCTAAAAACTCAAATGTTATATATTAATTTTTTTAACTTATTTATTAGTTTCATTTAA
*
3651710 GTAATATTTATAATAAATTAGATAAAATTAACAGTTTTAGTGTTTTAATTTCATTTTTATTTTTC
131 GTAATATTTAT--T--A-TAAAT-AAATTAACAGTTTTAGTGTTTTAATTTCATTTTTATTTTTC
3651775 TATTTTAATCTTATTTATTAATTAATTAGATTAAATTTTTTATTATTTGTATTTAAGGTAAATAA
190 TATTTTAATCTTATTTATTAATTAATTAGATTAAATTTTTTATTATTTGTATTTAAGGTAAATAA
*
3651840 AAATTAATTGCGAGGGATTAAAAAATGACGGCGTATTAATTACAACAGATTCAAACTTTGCGGCG
255 AAATTAATTGCGAGGGATTAAAAAACGACGGCGTATTAATTACAACAGATTCAAACTTTGCGGCG
*
3651905 TTTTCAGCCTAGCGCCACGAATGCCCTGATAAAACGGTACGTTTTGTTTAAACCAAAGGCCAAAA
320 TTTTCAGCCTAGCGCCACGAATGCCCTAATAAAACGGTACGTTTTGTTTAAACCAAAGGCCAAAA
* * *
3651970 TTTGCGGCATTTTTATCAATGCGCTGCTAATGCGCACCCACCTTTAGTGGCGTTTTCATCTAGTG
385 TTTGCGGCATTTTTATCAACGCGCCGCTAATGCGCACCCACCTTTAGTGGCGTTTTCATCTAGCG
*
3652035 CCGCTAAAGCCATTAAAATCGCACAAAGCTACGCCGTTTTGTAAAAAATTTAAGAATTTTTTCCG
450 CCGCTAAAGCCATTAAAATCGCACAAAGCTACGCCGTTTTGTAAAAAATTTAAAAATTTTTTCCG
* * * *
3652100 GCGTTTGGAATAAAAACGCCGCCAATGACTCGTTTATTGCGGCGTTTTTAGTGAAAACGCCACTA
515 GCGTTCGGAAAAAAAACGCCACCAATGACTCATTTATTGCGGCGTTTTTAGTGAAAACGCCACTA
3652165 TTACATCAAATTTTCTACTGAAACGGCTCCGTTTTTCTATTCCATGGTTTCGTTAAGTAATACTT
580 TTACATCAAATTTTCTACTGAAACGGCTCCGTTTTTCTATTCCATGGTTTCGTTAAGTAATACTT
* *
3652230 ATAATATAGTACTAAAACTTATAATTTTTAGTGTTTTAACTATAATTTATAAATTTTACATAAAA
645 ATAATATAGTACTAAAAATTATAATTTTTAGTGTTTTAACTAAAATTTATAAATTTTACATAAAA
3652295 TTA
710 TTA
3652298 TAAATTTTAGCGTTTTTATTTCAT
1 TAAATTTTAGCGTTTTTATTTCAT
3652322 GAATTTTAGC
Statistics
Matches: 713, Mismatches: 20, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
710 41 0.06
711 85 0.12
712 11 0.02
714 1 0.00
715 4 0.01
716 560 0.79
717 11 0.02
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (712 bp):
TAAATTTTAGCGTTTTTATTTCATTTTTATTTTTTTATTTTAATTTAATTCCATTTGTTAATTTG
GTACTCTCCTAAAAACTCAAATGTTATATATTAATTTTTTTAACTTATTTATTAGTTTCATTTAA
GTAATATTTATTATAAATAAATTAACAGTTTTAGTGTTTTAATTTCATTTTTATTTTTCTATTTT
AATCTTATTTATTAATTAATTAGATTAAATTTTTTATTATTTGTATTTAAGGTAAATAAAAATTA
ATTGCGAGGGATTAAAAAACGACGGCGTATTAATTACAACAGATTCAAACTTTGCGGCGTTTTCA
GCCTAGCGCCACGAATGCCCTAATAAAACGGTACGTTTTGTTTAAACCAAAGGCCAAAATTTGCG
GCATTTTTATCAACGCGCCGCTAATGCGCACCCACCTTTAGTGGCGTTTTCATCTAGCGCCGCTA
AAGCCATTAAAATCGCACAAAGCTACGCCGTTTTGTAAAAAATTTAAAAATTTTTTCCGGCGTTC
GGAAAAAAAACGCCACCAATGACTCATTTATTGCGGCGTTTTTAGTGAAAACGCCACTATTACAT
CAAATTTTCTACTGAAACGGCTCCGTTTTTCTATTCCATGGTTTCGTTAAGTAATACTTATAATA
TAGTACTAAAAATTATAATTTTTAGTGTTTTAACTAAAATTTATAAATTTTACATAAAATTA
Found at i:3652339 original size:22 final size:23
Alignment explanation
Indices: 3652300--3652343 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
3652290 TAAAATTATA
3652300 AATTTTAGCGTTTTTATTTCATG
1 AATTTTAGCGTTTTTATTTCATG
3652323 AATTTTAGCG-TTTTATTTCAT
1 AATTTTAGCGTTTTTATTTCAT
3652344 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (23 bp):
AATTTTAGCGTTTTTATTTCATG
Found at i:3652735 original size:23 final size:23
Alignment explanation
Indices: 3652692--3652735 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3652682 CCTAAATTAT
* *
3652692 ACATATTTTACAATTACATAAGA
1 ACATATTTTAAAATTAAATAAGA
3652715 ACATA-TTTAAAATATAAATAA
1 ACATATTTTAAAAT-TAAATAA
3652736 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
ACATATTTTAAAATTAAATAAGA
Found at i:3653343 original size:114 final size:114
Alignment explanation
Indices: 3653143--3653557 Score: 767
Period size: 114 Copynumber: 3.6 Consensus size: 114
3653133 CGTTTTTTAA
* * *
3653143 AGACCATTAGCGGCGCTATACCAAAAACGCCACTAGGGCCACCTAAGGCCACTAAACGACGCCGT
1 AGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGT
3653208 TGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACTGCTAAAAACAC
66 TGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACTGCTAAAAACAC
3653257 AGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGT
1 AGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGT
3653322 TGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACTGCTAAAAACAC
66 TGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACTGCTAAAAACAC
*
3653371 AGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGACCACCGAAGGCCACTAAACGACGCCGT
1 AGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGT
3653436 TGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACTGCTAAAAACAC
66 TGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACTGCTAAAAACAC
* * *
3653485 AGACCATTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGTCGT
1 AGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGT
3653550 TGTATTTT
66 TGTATTTT
3653558 GCTAAAAACA
Statistics
Matches: 293, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 293 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (114 bp):
AGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGT
TGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACTGCTAAAAACAC
Found at i:3653565 original size:84 final size:84
Alignment explanation
Indices: 3653473--3653641 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 84
3653463 CTAAAAATAC
*
3653473 TGCTAAAAACACAGACCATTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACT
1 TGCTAAAAACACAGACCACTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACT
*
3653538 AAACGACGTCGTTGTATTT
66 AAACGACGCCGTTGTATTT
* * * *
3653557 TGCTAAAAACACAGAGCACTAGTGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACT
1 TGCTAAAAACACAGACCACTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACT
3653622 AAACGACGCCGTTGTATTT
66 AAACGACGCCGTTGTATTT
3653641 T
1 T
3653642 ATTTTTTGCG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (84 bp):
TGCTAAAAACACAGACCACTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACT
AAACGACGCCGTTGTATTT
Found at i:3653706 original size:198 final size:198
Alignment explanation
Indices: 3653359--3653839 Score: 809
Period size: 198 Copynumber: 2.4 Consensus size: 198
3653349 CTAAAAATAC
*
3653359 TGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGACCACCGAAGGCCACT
1 TGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACT
*
3653424 AAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACTGCTAAAAACACAGAC
66 AAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACCGCTAAAAACACAGAC
*
3653489 CATTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGTCGTTGTA
131 CATTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGTTGTA
3653554 TTT
196 TTT
* * *
3653557 TGCTAAAAACACAGAGCACTAGTGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACT
1 TGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACT
* ** * *
3653622 AAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTTTTTTTTAAAATGCCGCTAAAAACACAGAC
66 AAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACCGCTAAAAACACAGAC
* * *
3653687 CATTAGCGGTGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAATGACGCCGTTGTA
131 CATTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGTTGTA
3653752 TTT
196 TTT
* * *
3653755 TGCTAAAAACAGAGACCATTAGCGGCGTTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACT
1 TGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACT
3653820 AAACGACGCCGTTGTATTTT
66 AAACGACGCCGTTGTATTTT
3653840 GCTAAAAACA
Statistics
Matches: 263, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
198 263 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (198 bp):
TGCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGCCACT
AAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAATACCGCTAAAAACACAGAC
CATTAGCGGCGCAAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGACGCCGTTGTA
TTT
Found at i:3653772 original size:84 final size:84
Alignment explanation
Indices: 3653672--3653983 Score: 552
Period size: 84 Copynumber: 3.7 Consensus size: 84
3653662 TTAAAATGCC
*
3653672 GCTAAAAACACAGACCATTAGCGGTGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
1 GCTAAAAACACAGACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
*
3653737 AATGACGCCGTTGTATTTT
66 AACGACGCCGTTGTATTTT
* *
3653756 GCTAAAAACAGAGACCATTAGCGGCGTTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
1 GCTAAAAACACAGACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
3653821 AACGACGCCGTTGTATTTT
66 AACGACGCCGTTGTATTTT
* *
3653840 GCTAAAAACAGAGACCATTAGCGGCGTTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
1 GCTAAAAACACAGACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
*
3653905 AACGATGCCGTTGTATTTT
66 AACGACGCCGTTGTATTTT
*
3653924 GCTAAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAAGGC
1 GCTAAAAACACAGACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGC
3653984 GTTAGACAAA
Statistics
Matches: 220, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 220 1.00
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (84 bp):
GCTAAAAACACAGACCATTAGCGGCGCTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTA
AACGACGCCGTTGTATTTT
Found at i:3653995 original size:34 final size:35
Alignment explanation
Indices: 3653946--3654017 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 35
3653936 GACCATTAGC
3653946 GGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
1 GGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
*
3653981 GGCGTTAGA-CAAAAACGCCACTAAGGCCACCGAA
1 GGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
3654015 GGC
1 GGC
3654018 CACTAAACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 28 0.78
35 8 0.22
ACGTcount: A:0.36, C:0.32, G:0.25, T:0.07
Consensus pattern (35 bp):
GGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
Found at i:3654081 original size:118 final size:119
Alignment explanation
Indices: 3653862--3654101 Score: 473
Period size: 118 Copynumber: 2.0 Consensus size: 119
3653852 GACCATTAGC
3653862 GGCGTTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGATGCCGTTGTATTTTGCT
1 GGCGTTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGATGCCGTTGTATTTTGCT
3653927 AAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
66 AAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
3653981 GGCGTTAGAC-AAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGATGCCGTTGTATTTTGCT
1 GGCGTTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGATGCCGTTGTATTTTGCT
3654045 AAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
66 AAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
3654099 GGC
1 GGC
3654102 CACTAAACGA
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 111 0.92
119 10 0.08
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (119 bp):
GGCGTTAGACAAAAAACGCCACTAAGGCCACCGAAGGCCACTAAACGATGCCGTTGTATTTTGCT
AAAAACACAGACCATTAGCGGCGCTAGACCAAAAACGCCACTAAGGCCACCGAA
Found at i:3656250 original size:5 final size:5
Alignment explanation
Indices: 3656240--3656272 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
3656230 TAATTAAATA
3656240 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3656273 TCTTTTGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:3656676 original size:16 final size:14
Alignment explanation
Indices: 3656655--3656699 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3656645 TAACTTTTTT
3656655 ATTTATTATTATATAA
1 ATTTATT-TTA-ATAA
3656671 ATTTATTTTAATAA
1 ATTTATTTTAATAA
* *
3656685 AATTCTTTTAATAA
1 ATTTATTTTAATAA
3656699 A
1 A
3656700 ATCACAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 17 0.63
15 3 0.11
16 7 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATTTTAATAA
Found at i:3656788 original size:22 final size:21
Alignment explanation
Indices: 3656725--3656788 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
3656715 TTTTCTATTT
3656725 ATTTAACCAAATACTT-TAATAA
1 ATTTAA-CAAAT-CTTATAATAA
* *
3656747 A-TTAA-AATTCTTATTTATAA
1 ATTTAACAAATCTTA-TAATAA
3656767 ATTTAACAAATCTTATGAATAA
1 ATTTAACAAATCTTAT-AATAA
3656789 TAGAAATACG
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 6 0.18
21 9 0.27
22 12 0.36
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTAACAAATCTTATAATAA
Found at i:3662757 original size:6 final size:6
Alignment explanation
Indices: 3662742--3662781 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
3662732 GGGCTTCACT
*
3662742 TCTTCG TCTTCC TCTTCC TCTTCC TCTTTCC -CTTCC TCTT
1 TCTTCC TCTTCC TCTTCC TCTTCC TC-TTCC TCTTCC TCTT
3662782 GTTCTACTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 4 0.13
6 23 0.74
7 4 0.13
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (6 bp):
TCTTCC
Found at i:3674499 original size:25 final size:24
Alignment explanation
Indices: 3674465--3674522 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
3674455 AAATAAAATT
* * *
3674465 TTTTAATTTTCCTATTATTGTTATTA
1 TTTTATTTTTACTATT-TTATT-TTA
3674491 -TTTATTTTTACTATTTTATTTTA
1 TTTTATTTTTACTATTTTATTTTA
3674514 TTTTATTTT
1 TTTTATTTT
3674523 ATTTTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.11
24 12 0.43
25 13 0.46
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTATTTTTACTATTTTATTTTA
Found at i:3674500 original size:6 final size:6
Alignment explanation
Indices: 3674479--3674540 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
3674469 AATTTTCCTA
*
3674479 TTATTG TTATTAT TTATTT TTACTATT TTA-TT TTA-TT TTA-TT TTATTT
1 TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT TTATTT
*
3674527 TCATTT TTATTT TT
1 TTATTT TTATTT TT
3674541 GCAAGAAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 15 0.31
6 23 0.47
7 6 0.12
8 5 0.10
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:3674512 original size:5 final size:5
Alignment explanation
Indices: 3674502--3674539 Score: 58
Period size: 5 Copynumber: 7.2 Consensus size: 5
3674492 TTATTTTTAC
3674502 TATTT TATTT TATTT TATTT TATTT TCATTTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T-A-TTT TATTT T
3674540 TGCAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 25 0.81
6 2 0.06
7 4 0.13
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:3678387 original size:19 final size:19
Alignment explanation
Indices: 3678363--3678401 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3678353 AAAAAAAAAG
3678363 CCTTATCCTCGCTTTATAC
1 CCTTATCCTCGCTTTATAC
3678382 CCTTATCCTCGCTTTATAC
1 CCTTATCCTCGCTTTATAC
3678401 C
1 C
3678402 AGTCAAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.38, G:0.05, T:0.41
Consensus pattern (19 bp):
CCTTATCCTCGCTTTATAC
Found at i:3682595 original size:17 final size:18
Alignment explanation
Indices: 3682568--3682603 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3682558 TAATATTTTT
3682568 ATAAAATATATTAATTTA
1 ATAAAATATATTAATTTA
*
3682586 ATAAAA-ATATTTATTTA
1 ATAAAATATATTAATTTA
3682603 A
1 A
3682604 ATTAGTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAAATATATTAATTTA
Found at i:3688371 original size:26 final size:26
Alignment explanation
Indices: 3688342--3688393 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3688332 AAAAGATAAT
* *
3688342 AAAAAATGAACTTAAAGTCATGAGTG
1 AAAAAATAAACTCAAAGTCATGAGTG
3688368 AAAAAATAAACTCAAAGTCATGAGTG
1 AAAAAATAAACTCAAAGTCATGAGTG
3688394 TCATGGCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (26 bp):
AAAAAATAAACTCAAAGTCATGAGTG
Found at i:3693842 original size:12 final size:13
Alignment explanation
Indices: 3693820--3693849 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3693810 GGTCACTTCA
3693820 AAAATATAAAAAT
1 AAAATATAAAAAT
3693833 AAAA-ATAAAAAT
1 AAAATATAAAAAT
3693845 AAAAT
1 AAAAT
3693850 TGGAAACAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATATAAAAAT
Found at i:3700264 original size:16 final size:16
Alignment explanation
Indices: 3700235--3700268 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3700225 AACATAATTA
*
3700235 AATATAATATAATACC
1 AATATAATACAATACC
*
3700251 AATATGATACAATACC
1 AATATAATACAATACC
3700267 AA
1 AA
3700269 AATTTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (16 bp):
AATATAATACAATACC
Found at i:3706185 original size:19 final size:18
Alignment explanation
Indices: 3706149--3706186 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3706139 AAATAAAAAG
3706149 AGTAAAATTTTTTCAAAT
1 AGTAAAATTTTTTCAAAT
3706167 AGTATAAATTATTTT-AAAT
1 AGTA-AAATT-TTTTCAAAT
3706186 A
1 A
3706187 CGAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (18 bp):
AGTAAAATTTTTTCAAAT
Found at i:3710320 original size:24 final size:24
Alignment explanation
Indices: 3710281--3710330 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3710271 TTTTTCTTCA
3710281 TTGCATTTGGAGTTCTAGAAGTGT
1 TTGCATTTGGAGTTCTAGAAGTGT
3710305 TTGCATTTAGGA-TTCTAGAAGTGT
1 TTGCATTT-GGAGTTCTAGAAGTGT
3710329 TT
1 TT
3710331 TTTTCTTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.22, C:0.08, G:0.26, T:0.44
Consensus pattern (24 bp):
TTGCATTTGGAGTTCTAGAAGTGT
Found at i:3710354 original size:58 final size:58
Alignment explanation
Indices: 3710247--3710358 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
3710237 CAATATACCA
*
3710247 TTGCACTTCGGATTCTAAAAGTGTTTTTTCTTCATTGCATTTGGAGTTCTAGAAGTGT
1 TTGCACTTAGGATTCTAAAAGTGTTTTTTCTTCATTGCATTTGGAGTTCTAGAAGTGT
* * *
3710305 TTGCATTTAGGATTCTAGAAGTGTTTTTTTCTTCGTTGCATTTGG-GTTCTAGAA
1 TTGCACTTAGGATTCTAAAAGTG-TTTTTTCTTCATTGCATTTGGAGTTCTAGAA
3710359 AGTAAAAATG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 29 0.59
59 20 0.41
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.46
Consensus pattern (58 bp):
TTGCACTTAGGATTCTAAAAGTGTTTTTTCTTCATTGCATTTGGAGTTCTAGAAGTGT
Found at i:3710493 original size:23 final size:22
Alignment explanation
Indices: 3710428--3710495 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
3710418 TATAAAAATT
*
3710428 TAAATTA-ATTTATATTTTATGAA
1 TAAATTATATTTA-ATTTT-TAAA
*
3710451 T-AATTATATTAAATTATTTAAA
1 TAAATTATATTTAATT-TTTAAA
3710473 TAAATTATATTTAAGTTTTTAAA
1 TAAATTATATTTAA-TTTTTAAA
3710496 ATATGTTATG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 12 0.32
23 24 0.63
24 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
TAAATTATATTTAATTTTTAAA
Found at i:3710743 original size:15 final size:16
Alignment explanation
Indices: 3710720--3710752 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3710710 TCTACTACAA
3710720 TTTTCAATAACA-TTT
1 TTTTCAATAACACTTT
*
3710735 TTTTTAATAACACTTT
1 TTTTCAATAACACTTT
3710751 TT
1 TT
3710753 AATCGCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTCAATAACACTTT
Found at i:3711008 original size:139 final size:140
Alignment explanation
Indices: 3710743--3711018 Score: 457
Period size: 139 Copynumber: 2.0 Consensus size: 140
3710733 TTTTTTTAAT
* * *
3710743 AACACTTTTTAATCGCAACAACAATGGAGAATTAGCCCTAAAAACTAGTAAAGTCCAAACCAAAG
1 AACACTTTTCAATCGCAACAACAATGGAGAATTAACCCTAAAAACTAGTAAAGCCCAAACCAAAG
* * *
3710808 TCCACAAATGATAATCACACGTGATGTGACTAGAAGACCTATGTATATCATTGCCCATAATAAGT
66 TCCACAAATGATAATCACACATGATGTGACTAGAAGACCTACGCATATCATTGCCCATAATAAGT
3710873 TTCGAATTAG
131 TTCGAATTAG
3710883 AACACTTTTCAATC-CAACAACAATGGAGAATTAACCCTAAAAACTAGTAAAGCCCAAACCAAAG
1 AACACTTTTCAATCGCAACAACAATGGAGAATTAACCCTAAAAACTAGTAAAGCCCAAACCAAAG
* *
3710947 TCCACAAATGGTAATCACACATGATGTGACTA-AGAGACTTACGCATATCATTGCCCATAATAAG
66 TCCACAAATGATAATCACACATGATGTGACTAGA-AGACCTACGCATATCATTGCCCATAATAAG
3711011 TTTCGAAT
130 TTTCGAAT
3711019 CAAAGGTACT
Statistics
Matches: 127, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
138 1 0.01
139 113 0.89
140 13 0.10
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.24
Consensus pattern (140 bp):
AACACTTTTCAATCGCAACAACAATGGAGAATTAACCCTAAAAACTAGTAAAGCCCAAACCAAAG
TCCACAAATGATAATCACACATGATGTGACTAGAAGACCTACGCATATCATTGCCCATAATAAGT
TTCGAATTAG
Found at i:3716642 original size:6 final size:6
Alignment explanation
Indices: 3716627--3716659 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3716617 CACAAAAACG
*
3716627 GGGC-T GGGCTT GGGCTT GGGCTT GGTCTT GGGC
1 GGGCTT GGGCTT GGGCTT GGGCTT GGGCTT GGGC
3716660 CTGAGCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30
Consensus pattern (6 bp):
GGGCTT
Found at i:3717216 original size:20 final size:20
Alignment explanation
Indices: 3717192--3717230 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3717182 TATTTTTTAT
3717192 AAAAAGAATAAATTTATCGTG
1 AAAAA-AATAAATTTATCGTG
*
3717213 AAAAAAATCAATTTATCG
1 AAAAAAATAAATTTATCG
3717231 AACAGGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (20 bp):
AAAAAAATAAATTTATCGTG
Found at i:3722708 original size:185 final size:187
Alignment explanation
Indices: 3722337--3722733 Score: 576
Period size: 185 Copynumber: 2.2 Consensus size: 187
3722327 CATACTACTG
** *
3722337 CTGTAAAAGCTTTTAGTCTTTGAC---T--TTTAGAACTGGTAAACCTGTCTTTTATGTTCATCA
1 CTGTAAAAGCTTTTAGTCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATATTCATCA
* * * *
3722397 TCTCTTGATAATATCAGATTTAGATCATCCTAGCAGTGTCATTGAACACCGCAAAAATCCCTAAG
66 TCTCATGATAATACCAGATTTAGATCATCCTACCAGTGACATTGAACACCGCAAAAATCCCTAAG
* *
3722462 CCTGTTATGCCACATTATTCATGTGCTATTAGGTCATCCTACCAGTGTCATTGAACA
131 CCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAACA
* *
3722519 CTGTAAAAGCTTTTAGTCTTCGACTTTTAGTTTAGAACTGGTAGACCTACCTTTTATATTCATCA
1 CTGTAAAAGCTTTTAGTCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATATTCATCA
* *
3722584 TCTCATGATAATACCATATTTAGATCATCCTACCAGTGACATTG-A-A-CGCTAAAAATCCCTGA
66 TCTCATGATAATACCAGATTTAGATCATCCTACCAGTGACATTGAACACCGC-AAAAATCCCTAA
* * *
3722646 TCTTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAGCA
130 GCCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAACA
*
3722704 CTGTAAAAGCTTTTAGCCTTTGACTTTTAG
1 CTGTAAAAGCTTTTAGTCTTTGACTTTTAG
3722734 AAATGGTAAA
Statistics
Matches: 191, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
182 23 0.12
184 3 0.02
185 94 0.49
186 1 0.01
187 70 0.37
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (187 bp):
CTGTAAAAGCTTTTAGTCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATATTCATCA
TCTCATGATAATACCAGATTTAGATCATCCTACCAGTGACATTGAACACCGCAAAAATCCCTAAG
CCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAACA
Found at i:3738020 original size:39 final size:39
Alignment explanation
Indices: 3737965--3738071 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 39
3737955 TTTTAGGTGA
* *
3737965 TCAATTATTTTCTAGAAGTGAATTGTAAGGTTCA-TCAGT
1 TCAATCATTTTCTAGAATTGAATTGTAAGGTTCATTCA-T
* * * *
3738004 TCAATCATTTTTTAGAATTGAATTAGAAAGGTTGATTTAT
1 TCAATCATTTTCTAGAATTGAATT-GTAAGGTTCATTCAT
3738044 TCAATCATTTTCTAGAATTGAATTGTAA
1 TCAATCATTTTCTAGAATTGAATTGTAA
3738072 AGTTGATCTA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 24 0.41
40 32 0.55
41 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (39 bp):
TCAATCATTTTCTAGAATTGAATTGTAAGGTTCATTCAT
Found at i:3739653 original size:23 final size:23
Alignment explanation
Indices: 3739605--3739655 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3739595 TTCAATTAGC
* **
3739605 AAATATATTTTTAAAAACTACAA
1 AAATATATTATTAAAAAAAACAA
3739628 AAATATATTATTAAAAAAAACTAA
1 AAATATATTATTAAAAAAAAC-AA
3739652 AAAT
1 AAAT
3739656 CACATGCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (23 bp):
AAATATATTATTAAAAAAAACAA
Done.