Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 107 of 136
Found at i:36231619 original size:101 final size:101
Alignment explanation
Indices: 36231350--36231781 Score: 489
Period size: 102 Copynumber: 4.2 Consensus size: 101
36231340 TTGGGCTAAT
* * * * *
36231350 ATTTTTTATGAATGTAATTTTTTTTATAATTATTTTAAAATTATTTTTTTAGTAA--TATGATTA
1 ATTTTTTATGAATGTAA-TTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTA
* * *
36231413 TGTTATAATTTGTTTGTGTTTTAGTTTAGTGTTTTGTG
65 GGTTATAAATTGATTGTG-TTTAGTTTAGTGTTTTGTG
* * * * * * * *
36231451 A-ATTTCATGTAAATTTTTTTTATTTTTT-TAAATTATTTTATAGTTATTTTGTTAATAACTTAA
1 ATTTTTTATG--AA----TGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTAT
* *
36231514 GATTAGGTCATAAATTG-TTGTGCTTAGTTTAGTGTTTTGTG
60 GATTAGGTTATAAATTGATTGTGTTTAGTTTAGTGTTTTGTG
* *
36231555 ATTTTTTATTAATGTAATTTTTTAAAAGATTATTTTATAGTTATTTTGCTAGTAATTTATGATTA
1 ATTTTTTATGAATGTAATTTTTTAAAA-ATTATTTTATAGTTATTTTGTTAGTAATTTATGATTA
* * *
36231620 GGTTATAAATTGATAGTGTTTAGTTTAGCGTTTTGTA
65 GGTTATAAATTGATTGTGTTTAGTTTAGTGTTTTGTG
* *
36231657 ATTTTTTATGAATGTAAATTTTTTAAAATTTATTTTATAGTTATTTTGTTATTAATTTATGATTA
1 ATTTTTTATGAATGT-AATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTA
36231722 GGTTATAAATTG-TTAGTGTTTAGTTTAGTGTTTTGTG
65 GGTTATAAATTGATT-GTGTTTAGTTTAGTGTTTTGTG
*
36231759 ATTTTTTATGAAAGTAATTTTTT
1 ATTTTTTATGAATGTAATTTTTT
36231782 TATAATGTAA
Statistics
Matches: 279, Mismatches: 38, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
99 9 0.03
100 8 0.03
101 54 0.19
102 116 0.42
103 14 0.05
104 43 0.15
105 16 0.06
106 19 0.07
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (101 bp):
ATTTTTTATGAATGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAG
GTTATAAATTGATTGTGTTTAGTTTAGTGTTTTGTG
Found at i:36231782 original size:17 final size:16
Alignment explanation
Indices: 36231760--36231795 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
36231750 TGTTTTGTGA
36231760 TTTTTTATGAAAGTAAT
1 TTTTTTAT-AAAGTAAT
*
36231777 TTTTTTATAATGTAAT
1 TTTTTTATAAAGTAAT
36231793 TTT
1 TTT
36231796 ATTTGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
TTTTTTATAAAGTAAT
Found at i:36238120 original size:24 final size:26
Alignment explanation
Indices: 36238093--36238141 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
36238083 ATAAACATTA
*
36238093 AACTAAC-AAATAA-TTTATAATAAT
1 AACTAACAAAATAACTTTAAAATAAT
36238117 AACTAACAAAATAACTTTAAAATAA
1 AACTAACAAAATAACTTTAAAATAA
36238142 ATTAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AACTAACAAAATAACTTTAAAATAAT
Found at i:36238278 original size:4 final size:4
Alignment explanation
Indices: 36238254--36238291 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
36238244 TACATTATTC
36238254 TTCT TT-T TTCT TCTCCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT T-T-CT TTCT TTCT TTCT TTCT TTCT T
36238292 CTTCCTTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 3 0.10
4 23 0.74
5 2 0.06
6 3 0.10
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:36241447 original size:6 final size:6
Alignment explanation
Indices: 36241438--36241465 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
36241428 TCCAACTCAA
36241438 CAAAAT CAAAAT CAAAAT CAAAAT CAAA
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAA
36241466 CTGAAACCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.14
Consensus pattern (6 bp):
CAAAAT
Found at i:36241525 original size:6 final size:6
Alignment explanation
Indices: 36241514--36241547 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
36241504 AGAGCAATTT
*
36241514 AAAAGA AAAAGA AAAGGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
36241548 AGAACTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:36243648 original size:124 final size:124
Alignment explanation
Indices: 36243341--36243734 Score: 610
Period size: 124 Copynumber: 3.2 Consensus size: 124
36243331 TTATTTCGAG
* *
36243341 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGTTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * * * *
36243406 AAATCGCGCCCTTGTGGACGCGATTTTACTACAGTAGGTCATGTAAGAAGTAA-TTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATTTTTT
* * * * *
36243464 TTAATGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTCAGAAGAAATCGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
36243529 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATTTTTT
* *
36243588 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTATACCAGGATGCTATATGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * * *
36243653 AAATCGTGCCTTCGTGGATGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATT-TTTT
36243713 TTGACGTTTCTGAGCAAATAGT
1 TTGACGTTTCTGAGCAAATAGT
36243735 GTCAAATTGC
Statistics
Matches: 246, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
123 106 0.43
124 114 0.46
125 26 0.11
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATTTTTT
Found at i:36245467 original size:30 final size:29
Alignment explanation
Indices: 36245429--36245549 Score: 139
Period size: 30 Copynumber: 4.3 Consensus size: 29
36245419 CAGTGGTGTC
36245429 AGGTTAGGGCAATGGGTTTTTAATTAAATT
1 AGGTTAGGGCAA-GGGTTTTTAATTAAATT
* *
36245459 ATGTTAGGGTTAA-GGTTTTTAATTAAATT
1 AGGTTAGGG-CAAGGGTTTTTAATTAAATT
36245488 AGGTT------AGGGTTTTTAATTAAATT
1 AGGTTAGGGCAAGGGTTTTTAATTAAATT
*
36245511 AGGTTAGGGCAGTGGGTTTTTAATTAAATT
1 AGGTTAGGGCA-AGGGTTTTTAATTAAATT
36245541 AGGTTAGGG
1 AGGTTAGGG
36245550 TTATTAATTA
Statistics
Matches: 78, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
22 1 0.01
23 21 0.27
29 20 0.26
30 34 0.44
31 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.42
Consensus pattern (29 bp):
AGGTTAGGGCAAGGGTTTTTAATTAAATT
Found at i:36245498 original size:23 final size:23
Alignment explanation
Indices: 36245466--36245566 Score: 121
Period size: 23 Copynumber: 4.1 Consensus size: 23
36245456 ATTATGTTAG
*
36245466 GGTTAAGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
36245489 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
36245512 GGTTAGGGCAGTGGGTTTTTAATTAAATTA
1 GGTT-----A--GGGTTTTTAATTAAATTA
*
36245542 GGTTAGGGTTATTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
36245565 GG
1 GG
36245567 GTTTTTATTA
Statistics
Matches: 69, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
23 45 0.65
25 1 0.01
28 1 0.01
30 22 0.32
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.44
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:36245549 original size:53 final size:52
Alignment explanation
Indices: 36245442--36245566 Score: 189
Period size: 53 Copynumber: 2.4 Consensus size: 52
36245432 TTAGGGCAAT
* *
36245442 GGGTTTTTAATTAAATTATGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGGGTAAGGTTTTTAATTAAATTAGGTTA
*
36245494 GGGTTTTTAATTAAATTAGGTTAGGGCAGT-GGGTTTTTAATTAAATTAGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGG--GTAAGGTTTTTAATTAAATTAGGTTA
*
36245547 GGGTTATTAATTAAATTAGG
1 GGGTTTTTAATTAAATTAGG
36245567 GTTTTTATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
52 25 0.37
53 41 0.61
54 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.24, T:0.45
Consensus pattern (52 bp):
GGGTTTTTAATTAAATTAGGTTAGGGGTAAGGTTTTTAATTAAATTAGGTTA
Found at i:36245676 original size:71 final size:71
Alignment explanation
Indices: 36245572--36245756 Score: 307
Period size: 71 Copynumber: 2.6 Consensus size: 71
36245562 TTAGGGTTTT
* * *
36245572 TATTACATCAAATAGAACTTATATTTTATTATATCAAATAATATCAAGATAACTCGAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAACTT
36245637 CTATGCC
65 CTATGCC
*
36245644 TATTATATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAACTTC
1 TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAACTTC
*
36245709 TATGCG
66 TATGCC
*
36245715 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATA
36245757 AATTTAAATA
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 93 0.88
72 13 0.12
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAACTTC
TATGCC
Found at i:36245749 original size:25 final size:25
Alignment explanation
Indices: 36245644--36245754 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
36245634 TTTCTATGCC
*
36245644 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
* *
36245669 TATTATATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * **
36245690 AATAAC-TCGAAA-AAACTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
36245715 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
36245740 TATTACATCAAATAA
1 TATTACATCAAATAA
36245755 TAAATTTAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
20 2 0.03
21 10 0.15
22 2 0.03
23 2 0.03
24 4 0.06
25 35 0.52
26 12 0.18
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:36245895 original size:24 final size:24
Alignment explanation
Indices: 36245868--36245920 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
36245858 GGCGGTTGTT
*
36245868 CTTCCTCTGGTGGTGATTGTGGTC
1 CTTCCTCCGGTGGTGATTGTGGTC
* *
36245892 CTTCCTCCGGTGGTGGTTGTGGTT
1 CTTCCTCCGGTGGTGATTGTGGTC
36245916 CTTCC
1 CTTCC
36245921 GGTTCCGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.02, C:0.25, G:0.32, T:0.42
Consensus pattern (24 bp):
CTTCCTCCGGTGGTGATTGTGGTC
Found at i:36246179 original size:18 final size:18
Alignment explanation
Indices: 36246152--36246186 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36246142 CGGAAAAGGA
* *
36246152 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
36246170 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
36246187 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:36247711 original size:40 final size:40
Alignment explanation
Indices: 36247667--36247753 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 40
36247657 GAAATTGAGG
*
36247667 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTAGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAAATTTAGAA
* *
36247707 GGAAATTGAAATTAAATATGGGTTTGAGAGAAATTTGGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAAATTTAGAA
36247747 GGAAATT
1 GGAAATT
36247754 TGGAAGGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (40 bp):
GGAAATTGAAATTAAATATGGATTTGAGAGAAATTTAGAA
Found at i:36247753 original size:12 final size:12
Alignment explanation
Indices: 36247736--36247761 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36247726 GGGTTTGAGA
36247736 GAAATTTGGAAG
1 GAAATTTGGAAG
36247748 GAAATTTGGAAG
1 GAAATTTGGAAG
36247760 GA
1 GA
36247762 TTAGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (12 bp):
GAAATTTGGAAG
Found at i:36248669 original size:13 final size:13
Alignment explanation
Indices: 36248651--36248682 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
36248641 ATGTACCTGG
36248651 ATTTAATAGAGAA
1 ATTTAATAGAGAA
36248664 ATTTAATAGAGAA
1 ATTTAATAGAGAA
*
36248677 TTTTAA
1 ATTTAA
36248683 CAGTGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (13 bp):
ATTTAATAGAGAA
Found at i:36268314 original size:27 final size:27
Alignment explanation
Indices: 36268278--36268329 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
36268268 CGTTTTACAA
* * * *
36268278 TTCATTATTAGGGTTCGTGGTTACCCT
1 TTCATGATTAAGGTTCATGGCTACCCT
36268305 TTCATGATTAAGGTTCATGGCTACC
1 TTCATGATTAAGGTTCATGGCTACC
36268330 ATTCCTAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (27 bp):
TTCATGATTAAGGTTCATGGCTACCCT
Found at i:36271533 original size:46 final size:46
Alignment explanation
Indices: 36271457--36271573 Score: 193
Period size: 46 Copynumber: 2.6 Consensus size: 46
36271447 TACGTATGAT
* * *
36271457 CACTTATCAC-TTGTC-CCTAATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
36271501 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
36271547 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
36271574 AGTACTCAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 10 0.15
45 5 0.07
46 53 0.78
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:36272420 original size:28 final size:28
Alignment explanation
Indices: 36272385--36272443 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
36272375 CAGAATTTGG
*
36272385 ATAATATTCTCGTTTATTTATTTTGAAA
1 ATAATATTCTCATTTATTTATTTTGAAA
36272413 ATAATATTCTCATTTATTTATTTTGAAA
1 ATAATATTCTCATTTATTTATTTTGAAA
36272441 ATA
1 ATA
36272444 GACTCATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.53
Consensus pattern (28 bp):
ATAATATTCTCATTTATTTATTTTGAAA
Found at i:36272449 original size:25 final size:27
Alignment explanation
Indices: 36272392--36272451 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
36272382 TGGATAATAT
* *
36272392 TCTCGTTTATTTATTTTGAAAATAATA
1 TCTCATTTATTTATTTTGAAAATAAGA
36272419 TTCTCATTTATTTATTTTGAAAAT-AGA
1 -TCTCATTTATTTATTTTGAAAATAAGA
36272446 -CTCATT
1 TCTCATT
36272452 CAAGATTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 6 0.20
27 2 0.07
28 22 0.73
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.52
Consensus pattern (27 bp):
TCTCATTTATTTATTTTGAAAATAAGA
Found at i:36277690 original size:20 final size:20
Alignment explanation
Indices: 36277662--36277705 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
36277652 TAAGGTAATA
*
36277662 AAATTGTAAGTTCATACTTG
1 AAATAGTAAGTTCATACTTG
36277682 AAATAGTAAGTTCATACTTG
1 AAATAGTAAGTTCATACTTG
36277702 AAAT
1 AAAT
36277706 GGAAAGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (20 bp):
AAATAGTAAGTTCATACTTG
Found at i:36277712 original size:20 final size:20
Alignment explanation
Indices: 36277669--36277712 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
36277659 ATAAAATTGT
*
36277669 AAGTTCATACTTGAAATAGT
1 AAGTTCATACTTGAAATAGA
*
36277689 AAGTTCATACTTGAAATGGA
1 AAGTTCATACTTGAAATAGA
36277709 AAGT
1 AAGT
36277713 GATGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (20 bp):
AAGTTCATACTTGAAATAGA
Found at i:36284685 original size:15 final size:16
Alignment explanation
Indices: 36284659--36284688 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
36284649 TTTCTTAATA
36284659 TATTACTTTATTTTAT
1 TATTACTTTATTTTAT
36284675 TATTA-TTTATTTTA
1 TATTACTTTATTTTA
36284689 ACATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTACTTTATTTTAT
Found at i:36293365 original size:17 final size:17
Alignment explanation
Indices: 36293343--36293384 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
36293333 ATGTTGAATG
36293343 TGGAAATAAATATGTTT
1 TGGAAATAAATATGTTT
*
36293360 TGGAAAGAAATATGTTT
1 TGGAAATAAATATGTTT
36293377 TGGAAATA
1 TGGAAATA
36293385 CTACTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (17 bp):
TGGAAATAAATATGTTT
Found at i:36293560 original size:24 final size:24
Alignment explanation
Indices: 36293528--36293576 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
36293518 TTATGATGCA
*
36293528 AAAAATAATTGAGAATTCAATTGG
1 AAAAATAATTGAAAATTCAATTGG
36293552 AAAAATAATTGAAAATTCAATTGG
1 AAAAATAATTGAAAATTCAATTGG
36293576 A
1 A
36293577 CACCCATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (24 bp):
AAAAATAATTGAAAATTCAATTGG
Found at i:36294601 original size:21 final size:21
Alignment explanation
Indices: 36294577--36294625 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
36294567 AGCATAGAAG
36294577 ACTGTTATCCCAATAGGGCAA
1 ACTGTTATCCCAATAGGGCAA
*
36294598 ACTGATATCCCAATAGGGCAA
1 ACTGTTATCCCAATAGGGCAA
36294619 ACTGTTA
1 ACTGTTA
36294626 GTGCAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (21 bp):
ACTGTTATCCCAATAGGGCAA
Found at i:36295355 original size:18 final size:18
Alignment explanation
Indices: 36295341--36295383 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
36295331 GAAAATCCTT
36295341 GAAGGATTTAAAATCCCA
1 GAAGGATTTAAAATCCCA
36295359 GAAGGATTTAAAATCCCA
1 GAAGGATTTAAAATCCCA
36295377 GAAGGAT
1 GAAGGAT
36295384 ATAGAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (18 bp):
GAAGGATTTAAAATCCCA
Found at i:36296627 original size:145 final size:145
Alignment explanation
Indices: 36296364--36296655 Score: 487
Period size: 145 Copynumber: 2.0 Consensus size: 145
36296354 ATCAAAGGTG
* * *
36296364 ACAGAACGAAATGTATTTTACCAAAATTATTCTTTACCCATGATCTTGAGAAAAGAGGTGATATA
1 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATA
* *
36296429 AATGTTCAAAAAATTCGTTTTAGTGAGAATTTAGTAGATTTTTTTACTAAGGCATTGCCAACTTC
66 AATGTTCAAAAAATTCGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTTC
*
36296494 AACCTTTGAAAGACT
131 AACATTTGAAAGACT
*
36296509 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCTATGATCTTGCA-AAAAGAGGTGATAT
1 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTG-AGAAAAGAGGTGATAT
* *
36296573 AAATGTTCAACAAATTTGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTT
65 AAATGTTCAAAAAATTCGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTT
36296638 CAACATTTGAAAGACT
130 CAACATTTGAAAGACT
36296654 AC
1 AC
36296656 TACACAAGAT
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
145 136 0.99
146 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (145 bp):
ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATA
AATGTTCAAAAAATTCGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTTC
AACATTTGAAAGACT
Found at i:36297438 original size:17 final size:17
Alignment explanation
Indices: 36297416--36297468 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
36297406 TTGTTGAAGA
36297416 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
*
36297433 ATCTGTTT-G--TTT-A
1 ATCTGTTTGGATTTTGC
36297446 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
36297463 ATCTGT
1 ATCTGT
36297469 CTGTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.27
14 4 0.13
16 4 0.13
17 14 0.47
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.55
Consensus pattern (17 bp):
ATCTGTTTGGATTTTGC
Found at i:36297450 original size:30 final size:30
Alignment explanation
Indices: 36297415--36297473 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
36297405 TTTGTTGAAG
*
36297415 AATCTGTTTGGATTTTGCATCTGTTTGTTT
1 AATCTGTTTGGATTTTGCATCTGTCTGTTT
36297445 AATCTGTTTGGATTTTGCATCTGTCTGTT
1 AATCTGTTTGGATTTTGCATCTGTCTGTT
36297474 GAAGAATCTT
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:0.14, C:0.12, G:0.20, T:0.54
Consensus pattern (30 bp):
AATCTGTTTGGATTTTGCATCTGTCTGTTT
Found at i:36300646 original size:18 final size:19
Alignment explanation
Indices: 36300609--36300660 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
36300599 AATATGGGAA
*
36300609 ATGTATGTGTATTCTAAAAT
1 ATGTATGTATATT-TAAAAT
36300629 ATGTATGTATATTT-AAAT
1 ATGTATGTATATTTAAAAT
* *
36300647 ATATATGTACATTT
1 ATGTATGTATATTT
36300661 GTAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 16 0.55
19 1 0.03
20 12 0.41
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (19 bp):
ATGTATGTATATTTAAAAT
Found at i:36300791 original size:3 final size:3
Alignment explanation
Indices: 36300783--36300880 Score: 144
Period size: 3 Copynumber: 32.7 Consensus size: 3
36300773 TGTACATGAA
* *
36300783 AAT AAT AAT TAC AAT -AT CAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
36300828 AAT AGT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36300876 AAT AA
1 AAT AA
36300881 GGAGAAAATA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.02
3 81 0.95
4 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36303227 original size:32 final size:32
Alignment explanation
Indices: 36303188--36303280 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
36303178 TTAGATATTG
36303188 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
* *
36303220 ATTATGTTTTAAGCTTGTTGGATATTCAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
36303252 ATTATGTTTTAAGCTTGTTAGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
36303281 ATGATTGACA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:36304688 original size:19 final size:19
Alignment explanation
Indices: 36304642--36304690 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
36304632 CATCCAAACA
36304642 CCAGAAAAGTAAATCATTTT
1 CCAGAAAA-TAAATCATTTT
** *
36304662 AAAAAAAATAAATCATTTT
1 CCAGAAAATAAATCATTTT
36304681 CCAGAAAATA
1 CCAGAAAATA
36304691 TTTCACTAGC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (19 bp):
CCAGAAAATAAATCATTTT
Found at i:36308706 original size:22 final size:22
Alignment explanation
Indices: 36308674--36308720 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
36308664 GTCTCTATCT
36308674 TGAGGTATTTCAATTTTTTGAC
1 TGAGGTATTTCAATTTTTTGAC
*
36308696 TGAGGTTTTTCAATTTTTTGAC
1 TGAGGTATTTCAATTTTTTGAC
36308718 TGA
1 TGA
36308721 ATGCTAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (22 bp):
TGAGGTATTTCAATTTTTTGAC
Found at i:36311877 original size:72 final size:72
Alignment explanation
Indices: 36311760--36311905 Score: 240
Period size: 72 Copynumber: 2.0 Consensus size: 72
36311750 TGGGGATTTG
* *
36311760 ATCTTTCAAATTAGTACACAAAATTTCAGAGAATATTTACTTTCTTTCCTAAGGAT-GGATATTA
1 ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTT-CTAAGGATGGGATATTA
36311824 GAAAAGAT
65 GAAAAGAT
* *
36311832 ATCTTCCAAATTAGCACACAAAATTTCAGAGAATGTTTGCTTTCTTTCTAAGGATGGGATATTAG
1 ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTTCTAAGGATGGGATATTAG
36311897 AAAAGAT
66 AAAAGAT
36311904 AT
1 AT
36311906 TTTGTGTGGG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 8 0.12
72 61 0.88
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (72 bp):
ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTTCTAAGGATGGGATATTAG
AAAAGAT
Found at i:36320263 original size:48 final size:48
Alignment explanation
Indices: 36320192--36320288 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
36320182 TACCTTCAAA
*
36320192 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCTATT
1 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
*
36320240 GCACACACCACCACTACTATTCAATTTAAATCTAGTTGCCTTTCCATT
1 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
36320288 G
1 G
36320289 TTCAATTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (48 bp):
GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
Found at i:36327341 original size:19 final size:19
Alignment explanation
Indices: 36327307--36327347 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
36327297 ATACATTTAT
*
36327307 AAACATGAAAACAAATATTA
1 AAACAAGAAAACAAATA-TA
36327327 AAACAAGAAAA-AAATATA
1 AAACAAGAAAACAAATATA
36327345 AAA
1 AAA
36327348 TGATACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (19 bp):
AAACAAGAAAACAAATATA
Found at i:36327609 original size:23 final size:24
Alignment explanation
Indices: 36327554--36327628 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 24
36327544 AAGTAGCACC
* *
36327554 AAAATAGCATAAAAACAACATAAA
1 AAAATAGCATACAAACAACACAAA
* *
36327578 AATACAGCA-ACAAACAACACAAA
1 AAAATAGCATACAAACAACACAAA
* *
36327601 AAAATAGCATCACTAACAACACCAA
1 AAAATAGCAT-ACAAACAACACAAA
36327626 AAA
1 AAA
36327629 CCTGCAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 19 0.46
24 7 0.17
25 15 0.37
ACGTcount: A:0.65, C:0.21, G:0.04, T:0.09
Consensus pattern (24 bp):
AAAATAGCATACAAACAACACAAA
Found at i:36327673 original size:24 final size:23
Alignment explanation
Indices: 36327637--36327683 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
36327627 AACCTGCAAA
36327637 ATATAATCAACCAACCAAAATAT
1 ATATAATCAACCAACCAAAATAT
* * *
36327660 ATATACATTAACCAATCAACATAT
1 ATATA-ATCAACCAACCAAAATAT
36327684 TTAATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (23 bp):
ATATAATCAACCAACCAAAATAT
Found at i:36332904 original size:29 final size:29
Alignment explanation
Indices: 36332872--36332941 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
36332862 GAACAAACCA
* *
36332872 AAACAAAATAGAGTACAACAACACATTTC
1 AAACAAAATAGAGCACAACAACACAATTC
* * *
36332901 AAACAGAACAGAGCAGAACAACACAATTC
1 AAACAAAATAGAGCACAACAACACAATTC
36332930 AAACAAAATAGA
1 AAACAAAATAGA
36332942 ACCGAATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.11
Consensus pattern (29 bp):
AAACAAAATAGAGCACAACAACACAATTC
Found at i:36336965 original size:29 final size:29
Alignment explanation
Indices: 36336907--36336998 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 29
36336897 TGTATAGCTG
* *
36336907 GCCCGTATGACTCCACACAGTCC-AACACAC
1 GCCCGTATGTC-CCACACAG-CCTGACACAC
* * *
36336937 GCCCGTATGTCCCACACTGCTTGAGACAC
1 GCCCGTATGTCCCACACAGCCTGACACAC
*
36336966 GCCCGTGTGTCCCACACAGCCTGACACAC
1 GCCCGTATGTCCCACACAGCCTGACACAC
36336995 GCCC
1 GCCC
36336999 ATGTCACCTG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.02
29 41 0.79
30 10 0.19
ACGTcount: A:0.23, C:0.43, G:0.18, T:0.15
Consensus pattern (29 bp):
GCCCGTATGTCCCACACAGCCTGACACAC
Found at i:36345056 original size:25 final size:25
Alignment explanation
Indices: 36345014--36345068 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
36345004 ACGAGCTGTT
* *
36345014 ATATACAGAAAACTCCACAAATGCA
1 ATATACAGAAAACGCCACAAAGGCA
**
36345039 ATATACAGAGTACGCCACAAAGGCA
1 ATATACAGAAAACGCCACAAAGGCA
36345064 ATATA
1 ATATA
36345069 ATGCCACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.22, G:0.13, T:0.16
Consensus pattern (25 bp):
ATATACAGAAAACGCCACAAAGGCA
Found at i:36345076 original size:19 final size:20
Alignment explanation
Indices: 36345052--36345137 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
36345042 TACAGAGTAC
* *
36345052 GCCACAAAGGC-AATATAAT
1 GCCACAAAGGCTAACAAAAT
*
36345071 GCCACAATGGCTAACAAAAT
1 GCCACAAAGGCTAACAAAAT
*
36345091 GTCACAAAGGCCTAATCAAAAT
1 GCCACAAAGG-CTAA-CAAAAT
* *
36345113 ACGCCATAAAGACTAACAAAAT
1 --GCCACAAAGGCTAACAAAAT
36345135 GCC
1 GCC
36345138 CCCAAGCACC
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
19 10 0.19
20 17 0.31
21 4 0.07
22 12 0.22
23 4 0.07
24 7 0.13
ACGTcount: A:0.47, C:0.24, G:0.14, T:0.15
Consensus pattern (20 bp):
GCCACAAAGGCTAACAAAAT
Found at i:36348971 original size:88 final size:88
Alignment explanation
Indices: 36348876--36349056 Score: 362
Period size: 88 Copynumber: 2.1 Consensus size: 88
36348866 CTCTCAATGA
36348876 GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
1 GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
36348941 CTAACTAGCAAAGCAAACCTACT
66 CTAACTAGCAAAGCAAACCTACT
36348964 GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
1 GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
36349029 CTAACTAGCAAAGCAAACCTACT
66 CTAACTAGCAAAGCAAACCTACT
36349052 GGTAA
1 GGTAA
36349057 AACTAATTCA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 93 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (88 bp):
GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
CTAACTAGCAAAGCAAACCTACT
Found at i:36355549 original size:17 final size:17
Alignment explanation
Indices: 36355509--36355549 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
36355499 TCAACCCACA
36355509 ATTTTTTTTAATTTTCT
1 ATTTTTTTTAATTTTCT
36355526 -TTCTTTTTT-ATATTTCT
1 ATT-TTTTTTAAT-TTTCT
36355543 ATTTTTT
1 ATTTTTT
36355550 ATTTTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.19
17 15 0.71
18 2 0.10
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTTTTTAATTTTCT
Found at i:36356336 original size:18 final size:18
Alignment explanation
Indices: 36356313--36356347 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
36356303 TAGGCTAACT
36356313 AAGTATATTGAAACTCTC
1 AAGTATATTGAAACTCTC
36356331 AAGTATATTGAAACTCT
1 AAGTATATTGAAACTCT
36356348 AATTAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (18 bp):
AAGTATATTGAAACTCTC
Found at i:36360405 original size:91 final size:89
Alignment explanation
Indices: 36360218--36360389 Score: 231
Period size: 91 Copynumber: 1.9 Consensus size: 89
36360208 ATTAAGCCCC
* * * * *
36360218 TTTTTTTTCACTCAATTGGATAGTTGAATTTTCAAAATGCATCAAAAAAGCTCTCAAACTTTTTC
1 TTTTTTTACACTCAATTGGATACTTGAACTGTCAAAATGCATAAAAAAAGCTCTCAAACTTTTTC
*
36360283 AAAAAAAAAACAATTAAGCCTTTATT
66 --AAAAAAAACAATTAAGCCTTTATG
* *
36360309 TTTTTTTACACTCAATTAGG-TACTTGAACTGTCAAAATGCATAAAAAAAGTTCTCAAAGTTTTT
1 TTTTTTTACACTCAATT-GGATACTTGAACTGTCAAAATGCATAAAAAAAGCTCTCAAACTTTTT
36360373 C-AAAAAAACAATTAAGC
65 CAAAAAAAACAATTAAGC
36360390 TCATGCTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
88 16 0.22
91 55 0.75
92 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (89 bp):
TTTTTTTACACTCAATTGGATACTTGAACTGTCAAAATGCATAAAAAAAGCTCTCAAACTTTTTC
AAAAAAAACAATTAAGCCTTTATG
Found at i:36360564 original size:10 final size:10
Alignment explanation
Indices: 36360551--36360597 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
36360541 AGAAAATTTG
36360551 TAAAAATTAA
1 TAAAAATTAA
**
36360561 TAAATTTTAA
1 TAAAAATTAA
36360571 TAAAAATTAGA
1 TAAAAATTA-A
*
36360582 -AAAAATTTA
1 TAAAAATTAA
36360591 TAAAAAT
1 TAAAAAT
36360598 CATAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 1 0.03
10 28 0.93
11 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:36360602 original size:29 final size:29
Alignment explanation
Indices: 36360570--36360643 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
36360560 ATAAATTTTA
36360570 ATAAAAATTAGAAAAAATTTATAAAAATC
1 ATAAAAATTAGAAAAAATTTATAAAAATC
* ** *
36360599 ATAAAAAAATA-TTAAATTTTATAAAAATC
1 AT-AAAAATTAGAAAAAATTTATAAAAATC
36360628 ATAAAATATATAGAAA
1 ATAAAA-AT-TAGAAA
36360644 TGTATAGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
28 4 0.12
29 20 0.59
30 9 0.26
31 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
ATAAAAATTAGAAAAAATTTATAAAAATC
Found at i:36360604 original size:20 final size:20
Alignment explanation
Indices: 36360531--36360606 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
36360521 AATGATAAAA
*
36360531 ATAAAAATCA-AGAAAATTT
1 ATAAAAATCATAAAAAATTT
* *
36360550 GTAAAAAT--TAATAAATTTT
1 ATAAAAATCATAA-AAAATTT
* *
36360569 AATAAAAATTAGAAAAAATTT
1 -ATAAAAATCATAAAAAATTT
36360590 ATAAAAATCATAAAAAA
1 ATAAAAATCATAAAAAA
36360607 ATATTAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.02
19 13 0.30
20 22 0.50
21 6 0.14
22 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (20 bp):
ATAAAAATCATAAAAAATTT
Found at i:36360649 original size:28 final size:29
Alignment explanation
Indices: 36360583--36360683 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 29
36360573 AAAATTAGAA
36360583 AAAATTTATAAAAATCATAAAAAAATATT
1 AAAATTTATAAAAATCATAAAAAAATATT
* *
36360612 AAATTTTATAAAAATCAT-AAAATATA-T
1 AAAATTTATAAAAATCATAAAAAAATATT
* *
36360639 AGAAATGTATAGAAAT-ATAGAAAAGAATATAT
1 A-AAATTTATAAAAATCATA-AAAA-AATAT-T
36360671 AAAATTTTATAAA
1 AAAA-TTTATAAA
36360684 GTCGTAAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
27 4 0.07
28 18 0.32
29 21 0.37
30 3 0.05
31 3 0.05
32 8 0.14
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTTATAAAAATCATAAAAAAATATT
Found at i:36360708 original size:11 final size:11
Alignment explanation
Indices: 36360692--36360744 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 11
36360682 AAGTCGTAAG
36360692 AAAATGATAAA
1 AAAATGATAAA
36360703 AAAATG-TAAA
1 AAAATGATAAA
36360713 AAAAT-AT-AA
1 AAAATGATAAA
* *
36360722 AATACG-TAAA
1 AAAATGATAAA
*
36360732 AAAATTATAAA
1 AAAATGATAAA
36360743 AA
1 AA
36360745 TTATCATACC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
9 6 0.18
10 15 0.45
11 12 0.36
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.21
Consensus pattern (11 bp):
AAAATGATAAA
Found at i:36360712 original size:10 final size:10
Alignment explanation
Indices: 36360687--36360745 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
36360677 TTATAAAGTC
*
36360687 GTAAGAAAAT
1 GTAAAAAAAT
36360697 GATAAAAAAAT
1 G-TAAAAAAAT
36360708 GTAAAAAAAT
1 GTAAAAAAAT
* * *
36360718 AT-AAAATAC
1 GTAAAAAAAT
36360727 GTAAAAAAAT
1 GTAAAAAAAT
*
36360737 -TATAAAAAT
1 GTAAAAAAAT
36360746 TATCATACCA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 14 0.36
10 16 0.41
11 9 0.23
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
GTAAAAAAAT
Found at i:36360721 original size:20 final size:20
Alignment explanation
Indices: 36360686--36360744 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
36360676 TTTATAAAGT
*
36360686 CGTAAGAAAATGATAAAAAAA
1 CGTAAAAAAAT-ATAAAAAAA
* *
36360707 TGTAAAAAAATAT-AAAATA
1 CGTAAAAAAATATAAAAAAA
36360726 CGTAAAAAAATTATAAAAA
1 CGTAAAAAAA-TATAAAAA
36360745 TTATCATACC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 14 0.44
20 5 0.16
21 13 0.41
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.20
Consensus pattern (20 bp):
CGTAAAAAAATATAAAAAAA
Found at i:36360969 original size:20 final size:20
Alignment explanation
Indices: 36360946--36360984 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36360936 TTTTTTATGA
36360946 TTTTCATAAAATTTTACAAC
1 TTTTCATAAAATTTTACAAC
* * *
36360966 TTTTTATATATTTTTACAA
1 TTTTCATAAAATTTTACAA
36360985 TTGATATATA
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:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTCATAAAATTTTACAAC
Found at i:36362908 original size:96 final size:96
Alignment explanation
Indices: 36362438--36362888 Score: 735
Period size: 96 Copynumber: 4.7 Consensus size: 96
36362428 GCCTTATCCT
* * * *
36362438 ACAACGGAACCCCAATACTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
* *
36362503 CAGGCTTGACATGGGGCTTTCTGGTTGTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTCGTGAA
36362534 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
*
36362599 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTCGTGAA
*
36362630 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACATGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
36362695 CAGGCTTGACGTGGGGCTTTCTGG-CGCTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTCG-TGAA
* *
36362726 ACAAAGGAACGTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACATGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
36362791 CAGGCTTGACGTGGGGCTTTCTGG-CGCTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTCG-TGAA
* * * * *
36362822 ACAAAGGAACGTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATATAGGGAAAATTTTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
36362887 CA
66 CA
36362889 AGTTTGATGT
Statistics
Matches: 342, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
95 1 0.00
96 341 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (96 bp):
ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
CAGGCTTGACGTGGGGCTTTCTGGTCGTGAA
Found at i:36369453 original size:12 final size:12
Alignment explanation
Indices: 36369424--36369455 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
36369414 ATATATTTTT
36369424 AAATT-ATATAA
1 AAATTAATATAA
36369435 AAA-TAATATAA
1 AAATTAATATAA
36369446 AAATTAATAT
1 AAATTAATAT
36369456 GGGCAGGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 12 0.63
12 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:36371067 original size:27 final size:27
Alignment explanation
Indices: 36370999--36371068 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
36370989 GAATATATAA
36370999 TAAATATATATTTTTATTTTTTTAATTT
1 TAAA-ATATATTTTTATTTTTTTAATTT
* *
36371027 TAAAATACTTTTTTTATTTTTTTATTTT
1 TAAAATA-TATTTTTATTTTTTTAATTT
*
36371055 TAAAATAAATTTTT
1 TAAAATATATTTTT
36371069 GGTGTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 8 0.22
28 29 0.78
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (27 bp):
TAAAATATATTTTTATTTTTTTAATTT
Found at i:36376754 original size:43 final size:42
Alignment explanation
Indices: 36376704--36376802 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
36376694 TCCCAGACGT
* * *
36376704 GGTCTTACATGTAATCAAATAACGATGCCACTGTCCCAAACAG
1 GGTCTTACAAGTAATCAAAT-ACGACGCCAATGTCCCAAACAG
* * * * *
36376747 GGTCTTACACGTAATCATATACGGCGCCAATGTCCCAGACAT
1 GGTCTTACAAGTAATCAAATACGACGCCAATGTCCCAAACAG
36376789 GGTCTTACAAGTAA
1 GGTCTTACAAGTAA
36376803 ATCTCAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 30 0.62
43 18 0.38
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (42 bp):
GGTCTTACAAGTAATCAAATACGACGCCAATGTCCCAAACAG
Found at i:36376794 original size:42 final size:43
Alignment explanation
Indices: 36376688--36376841 Score: 134
Period size: 43 Copynumber: 3.6 Consensus size: 43
36376678 TCGTACAACA
* * * *
36376688 CCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACGATG
1 CCAATGTCCCAGACATGGTCTTACAAGTAATCAAATAACGACG
* * * * * *
36376731 CCACTGTCCCAAACAGGGTCTTACACGTAATCATAT-ACGGCG
1 CCAATGTCCCAGACATGGTCTTACAAGTAATCAAATAACGACG
* *
36376773 CCAATGTCCCAGACATGGTCTTACAAGTAAATCTCAAAT--TGATG
1 CCAATGTCCCAGACATGGTCTTACAAGT-AA--TCAAATAACGACG
* *
36376817 CCAACGTCCCAGACGTGGTCTTACA
1 CCAATGTCCCAGACATGGTCTTACA
36376842 CGATATCACA
Statistics
Matches: 89, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
42 28 0.31
43 31 0.35
44 25 0.28
45 5 0.06
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (43 bp):
CCAATGTCCCAGACATGGTCTTACAAGTAATCAAATAACGACG
Found at i:36379038 original size:2 final size:2
Alignment explanation
Indices: 36379033--36379072 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
36379023 ATTATACACA
36379033 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
36379073 TGAAAGTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36388338 original size:44 final size:44
Alignment explanation
Indices: 36388275--36388367 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
36388265 AGAAATATCC
*
36388275 AAGACCACAGAGAATGAAAGCTTTTCTTGGTTAGCCTTTAAGTA
1 AAGACCACAGAGAATGAAAGCTTTTCTTGGTAAGCCTTTAAGTA
36388319 AAGACCACAGAGAATGAAAGCTTTTCTTGGTAAGCCTTTAAGTA
1 AAGACCACAGAGAATGAAAGCTTTTCTTGGTAAGCCTTTAAGTA
36388363 AAGAC
1 AAGAC
36388368 TTCTTACAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (44 bp):
AAGACCACAGAGAATGAAAGCTTTTCTTGGTAAGCCTTTAAGTA
Found at i:36390543 original size:40 final size:41
Alignment explanation
Indices: 36390481--36390562 Score: 157
Period size: 40 Copynumber: 2.0 Consensus size: 41
36390471 ATAGACTCGC
36390481 TAAGATTTCATTTCATATCTTATTCACTCTCTAATTCTATT
1 TAAGATTTCATTTCATATCTTATTCACTCTCTAATTCTATT
36390522 TAAGATTTCA-TTCATATCTTATTCACTCTCTAATTCTATT
1 TAAGATTTCATTTCATATCTTATTCACTCTCTAATTCTATT
36390562 T
1 T
36390563 CCACTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 31 0.76
41 10 0.24
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.51
Consensus pattern (41 bp):
TAAGATTTCATTTCATATCTTATTCACTCTCTAATTCTATT
Found at i:36390557 original size:23 final size:23
Alignment explanation
Indices: 36390492--36390557 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
36390482 AAGATTTCAT
36390492 TTCATATCTTATTCACTCTCTAA
1 TTCATATCTTATTCACTCTCTAA
** *
36390515 TTC-TAT-TTA-AGA-T-T-TCA
1 TTCATATCTTATTCACTCTCTAA
36390532 TTCATATCTTATTCACTCTCTAA
1 TTCATATCTTATTCACTCTCTAA
36390555 TTC
1 TTC
36390558 TATTTCCACT
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
17 5 0.16
18 4 0.13
19 4 0.13
20 2 0.06
21 4 0.13
22 4 0.13
23 8 0.26
ACGTcount: A:0.26, C:0.23, G:0.02, T:0.50
Consensus pattern (23 bp):
TTCATATCTTATTCACTCTCTAA
Found at i:36404962 original size:63 final size:64
Alignment explanation
Indices: 36404873--36405001 Score: 251
Period size: 63 Copynumber: 2.0 Consensus size: 64
36404863 TATTTCATTC
36404873 ATATAGTTTGCATACTTAGGATAATTTGCATTAGGGATCCTTGCATTTAGTTTAATATATTTTA
1 ATATAGTTTGCATACTTAGGATAATTTGCATTAGGGATCCTTGCATTTAGTTTAATATATTTTA
36404937 ATATAGTTTGC-TACTTAGGATAATTTGCATTAGGGATCCTTGCATTTAGTTTAATATATTTTA
1 ATATAGTTTGCATACTTAGGATAATTTGCATTAGGGATCCTTGCATTTAGTTTAATATATTTTA
36405000 AT
1 AT
36405002 CACCACTTCT
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 54 0.83
64 11 0.17
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (64 bp):
ATATAGTTTGCATACTTAGGATAATTTGCATTAGGGATCCTTGCATTTAGTTTAATATATTTTA
Found at i:36410511 original size:70 final size:71
Alignment explanation
Indices: 36410403--36410556 Score: 204
Period size: 70 Copynumber: 2.2 Consensus size: 71
36410393 AGAGTATCCT
* * * * * * * *
36410403 GATATCAACACCTTGGAATTGCGATACCTTTAATAGTATTGAAGAATGGAGACA-TCTTTAGTGG
1 GATATCCACACTTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCTTCAATGG
36410467 TATCGC
66 TATCGC
* *
36410473 GATATCCACACTTTGGAATCGTGATACCTCTAACAGTATTGAAGAATGGGGACACCCTTCAATGG
1 GATATCCACACTTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCTTCAATGG
36410538 TATCGC
66 TATCGC
36410544 GATATCCAC-CTTT
1 GATATCCACACTTT
36410557 CCAAAAAGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
70 51 0.70
71 22 0.30
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (71 bp):
GATATCCACACTTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCTTCAATGG
TATCGC
Found at i:36410642 original size:22 final size:22
Alignment explanation
Indices: 36410589--36410643 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
36410579 CACTGCCTAA
*
36410589 GGTATCGTGATATCCTCTTATG
1 GGTATCGCGATATCCTCTTATG
*** * *
36410611 AAAATTGCGATATCTTCTTATG
1 GGTATCGCGATATCCTCTTATG
36410633 GGTATCGCGAT
1 GGTATCGCGAT
36410644 GTAACAACCC
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
GGTATCGCGATATCCTCTTATG
Found at i:36413280 original size:13 final size:13
Alignment explanation
Indices: 36413262--36413286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36413252 TAACTTATAT
36413262 GTGTGAAAATTTC
1 GTGTGAAAATTTC
36413275 GTGTGAAAATTT
1 GTGTGAAAATTT
36413287 TATCGTTTTT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:36414504 original size:43 final size:44
Alignment explanation
Indices: 36414402--36414518 Score: 118
Period size: 43 Copynumber: 2.7 Consensus size: 44
36414392 TGAGTTATCG
* *
36414402 TGTAAGACCACGTCT-GGG-ATGTTGGCATGGAATTGAGATTTACG
1 TGTAAGACCACGTCTGGGGCA-G-TGGCATTGAATTGAGATTTACA
*
36414446 TGTAAGACC-CTGTCTGGGGCAGTGGCATTGATATT-TGA-TTACA
1 TGTAAGACCAC-GTCTGGGGCAGTGGCATTGA-ATTGAGATTTACA
* *
36414489 TGTAAGACCACGTCTGGGACATTGGCATTG
1 TGTAAGACCACGTCTGGGGCAGTGGCATTG
36414519 TACGAGCTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
43 31 0.49
44 24 0.38
45 7 0.11
46 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGGCAGTGGCATTGAATTGAGATTTACA
Found at i:36429321 original size:26 final size:25
Alignment explanation
Indices: 36429292--36429363 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
36429282 AACACGTCAG
36429292 AAAAGGAAGCCATTGTGGCATAATAC
1 AAAAGGAAGCC-TTGTGGCATAATAC
*
36429318 AAAAGGAAGCCTTTGTGGCATAATAT
1 AAAAGGAAGCC-TTGTGGCATAATAC
*
36429344 AAAAGAAAGCCTCTGTGGCA
1 AAAAGGAAGCCT-TGTGGCA
36429364 AAACTCGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
25 1 0.02
26 41 0.98
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (25 bp):
AAAAGGAAGCCTTGTGGCATAATAC
Found at i:36437319 original size:43 final size:43
Alignment explanation
Indices: 36437250--36437391 Score: 144
Period size: 43 Copynumber: 3.3 Consensus size: 43
36437240 TTTTTCACAT
* *
36437250 AAACGCCGCTATAGATCAT-TACCTTTAGCAGCGCTTTTATATC
1 AAACACCGCTAAAGATCATGT-CCTTTAGCAGCGCTTTTATATC
* * * * *
36437293 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAAC
1 AAACACCGCTAAAGATCATGTCCTTTAGCAGCGCTTTTATATC
* * * * *
36437336 AAACACCACTAAAGAACATGACCTTTAGCAGCACTTTTTTCAT-
1 AAACACCGCTAAAGATCATGTCCTTTAGCAGCGCTTTTAT-ATC
36437379 AAACACCGCTAAA
1 AAACACCGCTAAA
36437392 AGTACTGTTC
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
43 79 0.98
44 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
AAACACCGCTAAAGATCATGTCCTTTAGCAGCGCTTTTATATC
Found at i:36437405 original size:43 final size:43
Alignment explanation
Indices: 36437272--36437405 Score: 130
Period size: 43 Copynumber: 3.1 Consensus size: 43
36437262 AGATCATTAC
* *
36437272 CTTTAGCAGCGCTTTTATATCAAACGCCGCTAAAGGT-CATGTT
1 CTTTAGCAGCGCTTTTATAT-AAACACCGCTAAAAGTACATGTT
* * * * **
36437315 CTTTAGCGGCGCTTTTATAACAAACACCACT-AAAGAACATGAC
1 CTTTAGCAGCGCTTTTAT-ATAAACACCGCTAAAAGTACATGTT
* *
36437358 CTTTAGCAGCACTTTTTTCATAAACACCGCTAAAAGTAC-TGTT
1 CTTTAGCAGCGCTTTTAT-ATAAACACCGCTAAAAGTACATGTT
36437401 CTTTA
1 CTTTA
36437406 ACGGCGTTTT
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
42 3 0.04
43 61 0.86
44 7 0.10
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (43 bp):
CTTTAGCAGCGCTTTTATATAAACACCGCTAAAAGTACATGTT
Found at i:36442227 original size:9 final size:9
Alignment explanation
Indices: 36442213--36442703 Score: 180
Period size: 9 Copynumber: 53.9 Consensus size: 9
36442203 TAAGTATAAT
36442213 TAAGTTATG
1 TAAGTTATG
36442222 TAAGTTATG
1 TAAGTTATG
36442231 TAAGTTATG
1 TAAGTTATG
*
36442240 -ATA-TTATA
1 TA-AGTTATG
*
36442248 TATATTTATG
1 TA-AGTTATG
36442258 TAAGTTA--
1 TAAGTTATG
36442265 TAAG-TATG
1 TAAGTTATG
36442273 ATTAAGTTATG
1 --TAAGTTATG
*
36442284 TAAGCTATG
1 TAAGTTATG
* * *
36442293 ATATGATATA
1 -TAAGTTATG
*
36442303 T-ATTTATG
1 TAAGTTATG
36442311 T-A-TTATG
1 TAAGTTATG
36442318 TAAGTTATG
1 TAAGTTATG
36442327 TAAGTTATG
1 TAAGTTATG
*
36442336 TGAGTT-TCG
1 TAAGTTAT-G
36442345 TAAGTTATG
1 TAAGTTATG
* * *
36442354 ATATGATATA
1 -TAAGTTATG
*
36442364 TATG-TA--
1 TAAGTTATG
36442370 TAAGTTAT-
1 TAAGTTATG
36442378 TAAGTTATG
1 TAAGTTATG
36442387 TAAGTTATG
1 TAAGTTATG
* *
36442396 TGAGTTATCA
1 TAAGTTAT-G
* *
36442406 TATGATATATA
1 TAAG-T-TATG
* *
36442417 TAAGTAATT
1 TAAGTTATG
36442426 TAAGAATTTTATG
1 TAAG----TTATG
*
36442439 TATG-TATG
1 TAAGTTATG
*
36442447 TGAGTTATG
1 TAAGTTATG
36442456 TAAGTTATG
1 TAAGTTATG
36442465 TAAGTTATG
1 TAAGTTATG
* *
36442474 TATTTGTTTTG
1 TA--AGTTATG
36442485 TAAGTTATGG
1 TAAGTTAT-G
* *
36442495 TATGATATATA
1 TAAG-T-TATG
36442506 TAAGTTAT-
1 TAAGTTATG
36442514 TAAGTTATG
1 TAAGTTATG
*
36442523 TGAGTTATG
1 TAAGTTATG
* *
36442532 AAATGATATATA
1 TAA-G-T-TATG
36442544 TAAGTTAT-
1 TAAGTTATG
36442552 TAAGTTATG
1 TAAGTTATG
*
36442561 TATG-TATG
1 TAAGTTATG
*
36442569 TGAGTTATG
1 TAAGTTATG
36442578 TAAGTTATG
1 TAAGTTATG
* * *
36442587 ATATGATATA
1 -TAAGTTATG
*
36442597 T-ATTTATG
1 TAAGTTATG
* *
36442605 -CA-TTTTG
1 TAAGTTATG
36442612 TAAGTTATG
1 TAAGTTATG
36442621 TAAGTTATGTG
1 TAAGTTA--TG
** *
36442632 TTCGTTTTG
1 TAAGTTATG
36442641 TAAGTTATGG
1 TAAGTTAT-G
* *
36442651 TATGATATATA
1 TAAG-T-TATG
*
36442662 TAAGTTA-A
1 TAAGTTATG
36442670 TAAGTTATG
1 TAAGTTATG
*
36442679 TATG-TATG
1 TAAGTTATG
* *
36442687 TGAGTTATT
1 TAAGTTATG
36442696 TAAGTTAT
1 TAAGTTAT
36442704 TATCTGATAT
Statistics
Matches: 364, Mismatches: 71, Indels: 94
0.69 0.13 0.18
Matches are distributed among these distances:
6 5 0.01
7 16 0.04
8 69 0.19
9 178 0.49
10 44 0.12
11 32 0.09
12 14 0.04
13 6 0.02
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:36442322 original size:53 final size:52
Alignment explanation
Indices: 36442213--36442417 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 52
36442203 TAAGTATAAT
* *
36442213 TAAGTTATGTAAGTTATGTAAGTTATGATATTATATATATTTATGTAAGTTA
1 TAAGTTATGTAAGTTATGTAAGCTATGATATGATATATATTTATGTAAGTTA
36442265 TAAG-TATGATTAAGTTATGTAAGCTATGATATGATATATATTTATGT-A-TTA
1 TAAGTTATG--TAAGTTATGTAAGCTATGATATGATATATATTTATGTAAGTTA
* * * *
36442316 TGTAAGTTATGTAAGTTATGTGAGTTTCGTAAGTTATGATATGATATATATGTATAAGTTA
1 --TAAGTTATGTAAGTTATGTAAG---C-TATGATATGATAT-ATATTTATG--TAAGTTA
* * *
36442377 TTAAGTTATGTAAGTTATGTGAGTTATCATATGATATATAT
1 -TAAGTTATGTAAGTTATGTAAGCTATGATATGATATATAT
36442418 AAGTAATTTA
Statistics
Matches: 128, Mismatches: 11, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
51 7 0.05
52 17 0.13
53 39 0.30
54 4 0.03
55 5 0.04
56 21 0.16
57 8 0.06
59 1 0.01
60 23 0.18
61 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (52 bp):
TAAGTTATGTAAGTTATGTAAGCTATGATATGATATATATTTATGTAAGTTA
Found at i:36442357 original size:61 final size:60
Alignment explanation
Indices: 36442283--36442401 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 60
36442273 ATTAAGTTAT
* *
36442283 GTAAGCTATGATATGATATATATTTATGTA-TTATGTAAGTTATGTAAGTTATGTGAGTTTC
1 GTAAGCTATGATATGATATATATGTAT-AAGTTAT-TAAGTTATGTAAGTTATGTGAGTTTC
*
36442344 GTAAGTTATGATATGATATATATGTATAAGTTATTAAGTTATGTAAGTTATGTGAGTT
1 GTAAGCTATGATATGATATATATGTATAAGTTATTAAGTTATGTAAGTTATGTGAGTT
36442402 ATCATATGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
60 25 0.46
61 29 0.54
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (60 bp):
GTAAGCTATGATATGATATATATGTATAAGTTATTAAGTTATGTAAGTTATGTGAGTTTC
Found at i:36442402 original size:51 final size:52
Alignment explanation
Indices: 36442211--36442417 Score: 215
Period size: 51 Copynumber: 3.8 Consensus size: 52
36442201 GATAAGTATA
* *
36442211 ATTAAGTTATGTAAGTTATGTAAGTTATGATATTATATATATTTATGTAAGTT
1 ATTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATATGTA-GTAAGTT
*
36442264 A-TAAG-TATGATTAAGTTATGTAAGCTATGATATGATATATATTTATGTATTATGTAAGTT
1 ATTAAGTTATG--TAAGTTATGTAAGTTATGATATG--ATATA--TATG---TA-GTAAGTT
*
36442324 ATGTAAGTTATGTGAGTT-TCGTAAGTTATGATATGATATATATGTA-TAAGTT
1 AT-TAAGTTATGTAAGTTAT-GTAAGTTATGATATGATATATATGTAGTAAGTT
* *
36442376 ATTAAGTTATGTAAGTTATGTGAGTTATCATATGATATATAT
1 ATTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
36442418 AAGTAATTTA
Statistics
Matches: 132, Mismatches: 8, Indels: 30
0.78 0.05 0.18
Matches are distributed among these distances:
51 39 0.30
52 13 0.10
53 22 0.17
54 2 0.02
55 5 0.04
57 7 0.05
59 5 0.04
60 12 0.09
61 19 0.14
62 4 0.03
63 4 0.03
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATATGTAGTAAGTT
Found at i:36442418 original size:114 final size:112
Alignment explanation
Indices: 36442213--36442417 Score: 290
Period size: 114 Copynumber: 1.8 Consensus size: 112
36442203 TAAGTATAAT
* *
36442213 TAAGTTATGTAAGTTATGTAAGTTATGATATTATATATATTTATGTAAGTTATAAGTATGATTAA
1 TAAGTTATGTAAGTTATGTAAGTTATGATATGATATATATGTA-GTAAGTTATAAGTATGA-TAA
*
36442278 GTTATGTAAGCTATGATATGATATATATTTATGTATTATGTAAGTTATG
64 GTTATGTAAGCTATCATATGATATATATTTATGTATTATGTAAGTTATG
*
36442327 TAAGTTATGTGAGTT-TCGTAAGTTATGATATGATATATATGTA-TAAGTTATTAAGTTATG-TA
1 TAAGTTATGTAAGTTAT-GTAAGTTATGATATGATATATATGTAGTAAGTTA-TAAG-TATGATA
* *
36442389 AGTTATGTGAGTTATCATATGATATATAT
63 AGTTATGTAAGCTATCATATGATATATAT
36442418 AAGTAATTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
112 35 0.43
113 5 0.06
114 42 0.51
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (112 bp):
TAAGTTATGTAAGTTATGTAAGTTATGATATGATATATATGTAGTAAGTTATAAGTATGATAAGT
TATGTAAGCTATCATATGATATATATTTATGTATTATGTAAGTTATG
Found at i:36442489 original size:29 final size:29
Alignment explanation
Indices: 36442301--36442591 Score: 125
Period size: 30 Copynumber: 10.2 Consensus size: 29
36442291 TGATATGATA
36442301 TATAT-TTATGT-A-TTATGTAAGTTATG
1 TATATGTTATGTAAGTTATGTAAGTTATG
*
36442327 TA-A-GTTATGTGAGTT-TCGTAAGTTATG
1 TATATGTTATGTAAGTTAT-GTAAGTTATG
*
36442354 ATATGATATATATGTATAAGTTAT-TAAGTTATG
1 -TAT-ATGT-TATG--TAAGTTATGTAAGTTATG
* * * * *
36442387 TA-A-GTTATGTGAGTTATCATATGATATA
1 TATATGTTATGTAAGTTAT-GTAAGTTATG
* * * *
36442415 TATAAGTAATTTAAGAATT-T-TATG-TATG
1 TATATGTTATGTAAG--TTATGTAAGTTATG
*
36442443 TATGTGAGTTATGTAAGTTATGTAAGTTATG
1 TATAT--GTTATGTAAGTTATGTAAGTTATG
* * * * *
36442474 TATTTGTTTTGTAAGTTATGGTATGATATA
1 TATATGTTATGTAAGTTAT-GTAAGTTATG
* *
36442504 TATAAGTTAT-TAAGTTATGTGAGTTATG
1 TATATGTTATGTAAGTTATGTAAGTTATG
* *
36442532 -AAATGATATATATAAGTTAT-TAAGTTATG
1 TATATG-T-TATGTAAGTTATGTAAGTTATG
*
36442561 --TATG-TATGTGAGTTATGTAAGTTATG
1 TATATGTTATGTAAGTTATGTAAGTTATG
36442587 -ATATG
1 TATATG
36442592 ATATATATTT
Statistics
Matches: 202, Mismatches: 34, Indels: 57
0.69 0.12 0.19
Matches are distributed among these distances:
25 17 0.08
26 20 0.10
27 19 0.09
28 32 0.16
29 39 0.19
30 42 0.21
31 10 0.05
32 8 0.04
33 9 0.04
34 5 0.02
35 1 0.00
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (29 bp):
TATATGTTATGTAAGTTATGTAAGTTATG
Found at i:36442509 original size:21 final size:20
Alignment explanation
Indices: 36442485--36442551 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
36442475 ATTTGTTTTG
36442485 TAAGTTATGGTATGATATATA
1 TAAGTTAT-GTATGATATATA
* *
36442506 TAAGTTAT-TAAG-T-TATG
1 TAAGTTATGTATGATATATA
* *
36442523 TGAGTTATGAAATGATATATA
1 TAAGTTATG-TATGATATATA
36442544 TAAGTTAT
1 TAAGTTAT
36442552 TAAGTTATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
17 10 0.29
18 1 0.03
19 5 0.14
20 1 0.03
21 18 0.51
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (20 bp):
TAAGTTATGTATGATATATA
Found at i:36442529 original size:38 final size:38
Alignment explanation
Indices: 36442487--36442561 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
36442477 TTGTTTTGTA
**
36442487 AGTTATGGTATGATATATATAAGTTATTAAGTTATGTG
1 AGTTATGAAATGATATATATAAGTTATTAAGTTATGTG
36442525 AGTTATGAAATGATATATATAAGTTATTAAGTTATGT
1 AGTTATGAAATGATATATATAAGTTATTAAGTTATGT
36442562 ATGTATGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (38 bp):
AGTTATGAAATGATATATATAAGTTATTAAGTTATGTG
Found at i:36443656 original size:29 final size:29
Alignment explanation
Indices: 36443612--36443725 Score: 103
Period size: 29 Copynumber: 4.1 Consensus size: 29
36443602 TCAATTAATC
*
36443612 AAATATAAAATCGATAATTTATTAAATTA
1 AAATAAAAAATCGATAATTTATTAAATTA
* * *
36443641 AAATAAAAAATTGATAATTTATTCACTTA
1 AAATAAAAAATCGATAATTTATTAAATTA
* *
36443670 AAAT--CAAA-C-ATAATTTATTCAATT-
1 AAATAAAAAATCGATAATTTATTAAATTA
* * *
36443694 AAATCAAAAATTGATAATTTATTCACATTA
1 AAATAAAAAATCGATAATTTATT-AAATTA
36443724 AA
1 AA
36443726 CCGAATAAAC
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
24 4 0.06
25 14 0.21
26 3 0.04
27 3 0.04
28 10 0.15
29 32 0.47
30 2 0.03
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (29 bp):
AAATAAAAAATCGATAATTTATTAAATTA
Found at i:36443683 original size:25 final size:24
Alignment explanation
Indices: 36443654--36443701 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
36443644 TAAAAAATTG
*
36443654 ATAATTTATTCACTTAAAATCAAAC
1 ATAATTTATTCAATT-AAATCAAAC
36443679 ATAATTTATTCAATTAAATCAAA
1 ATAATTTATTCAATTAAATCAAA
36443702 AATTGATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAATTTATTCAATTAAATCAAAC
Found at i:36445748 original size:30 final size:30
Alignment explanation
Indices: 36445714--36445773 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
36445704 TAAATTTGTT
36445714 TCTATATTTGAAAGGTTTAATTATTTCTTA
1 TCTATATTTGAAAGGTTTAATTATTTCTTA
36445744 TCTATATTTGAAAGGTTTAATTATTTCTTA
1 TCTATATTTGAAAGGTTTAATTATTTCTTA
36445774 AATTCCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (30 bp):
TCTATATTTGAAAGGTTTAATTATTTCTTA
Found at i:36446244 original size:8 final size:7
Alignment explanation
Indices: 36446157--36446368 Score: 83
Period size: 7 Copynumber: 29.7 Consensus size: 7
36446147 ACTAATTAAT
36446157 CTAAACC
1 CTAAACC
36446164 CTAAACCC
1 CTAAA-CC
*
36446172 CTAACCC
1 CTAAACC
*
36446179 CT-ATCC
1 CTAAACC
*
36446185 CTTAAATC
1 C-TAAACC
* * *
36446193 TTGAATC
1 CTAAACC
36446200 CTAAACTC
1 CTAAAC-C
36446208 CTAAACC
1 CTAAACC
36446215 CTAAACC
1 CTAAACC
*
36446222 TTAAA-C
1 CTAAACC
36446228 C-ACAACC
1 CTA-AACC
36446235 CTTAAACC
1 C-TAAACC
*
36446243 CTAAACT
1 CTAAACC
* *
36446250 ATAATCC
1 CTAAACC
36446257 CTAAACC
1 CTAAACC
*
36446264 CATAATCC
1 C-TAAACC
*
36446272 ATAAACC
1 CTAAACC
*
36446279 TTAAA--
1 CTAAACC
*
36446284 ATAGTAACTC
1 CTA--AAC-C
36446294 CTAAACC
1 CTAAACC
*
36446301 TTAAACC
1 CTAAACC
*
36446308 ATAAACC
1 CTAAACC
* *
36446315 ATAATCC
1 CTAAACC
36446322 CTAAACC
1 CTAAACC
*
36446329 TTAAACC
1 CTAAACC
* *
36446336 TTAAAAC
1 CTAAACC
36446343 CTAAACC
1 CTAAACC
* *
36446350 ATATACC
1 CTAAACC
*
36446357 ATAAACC
1 CTAAACC
*
36446364 ATAAA
1 CTAAA
36446369 TTCTAAACTA
Statistics
Matches: 156, Mismatches: 35, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
5 3 0.02
6 7 0.04
7 115 0.74
8 28 0.18
9 1 0.01
10 2 0.01
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:36446270 original size:15 final size:15
Alignment explanation
Indices: 36446231--36446278 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
36446221 CTTAAACCAC
* *
36446231 AACCCTTAAACCCTA
1 AACCCATAATCCCTA
*
36446246 AA-CTATAATCCCTA
1 AACCCATAATCCCTA
*
36446260 AACCCATAATCCATA
1 AACCCATAATCCCTA
36446275 AACC
1 AACC
36446279 TTAAAATAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCATAATCCCTA
Found at i:36446328 original size:21 final size:21
Alignment explanation
Indices: 36446209--36446368 Score: 119
Period size: 21 Copynumber: 7.5 Consensus size: 21
36446199 CCTAAACTCC
*
36446209 TAAACCCTAAACCTTAAACCA
1 TAAACCCTAAACCATAAACCA
* * *
36446230 -CAACCCTTAAACCCTAAACTA
1 TAAACCC-TAAACCATAAACCA
* *
36446251 TAATCCCTAAACCCATAATCCA
1 TAAACCCTAAA-CCATAAACCA
* *
36446273 TAAACCTTAAA--ATAGTAACTCC
1 TAAACCCTAAACCATA--AAC-CA
*
36446295 TAAACCTTAAACCATAAACCA
1 TAAACCCTAAACCATAAACCA
* * *
36446316 TAATCCCTAAACCTTAAACCT
1 TAAACCCTAAACCATAAACCA
* *
36446337 TAAAACCTAAACCATATACCA
1 TAAACCCTAAACCATAAACCA
*
36446358 TAAACCATAAA
1 TAAACCCTAAA
36446369 TTCTAAACTA
Statistics
Matches: 107, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.03
20 5 0.05
21 61 0.57
22 35 0.33
24 3 0.03
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.22
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACCA
Found at i:36446393 original size:23 final size:23
Alignment explanation
Indices: 36446367--36446436 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
36446357 ATAAACCATA
36446367 AATTCTAAACTATAATGATAATT
1 AATTCTAAACTATAATGATAATT
**
36446390 AATTC-AATA-TATAA--ACCA-T
1 AATTCTAA-ACTATAATGATAATT
36446409 AATTCTAAACTATAATGATAATT
1 AATTCTAAACTATAATGATAATT
36446432 AATTC
1 AATTC
36446437 AATATTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
19 7 0.19
20 9 0.24
22 9 0.24
23 12 0.32
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (23 bp):
AATTCTAAACTATAATGATAATT
Found at i:36446414 original size:42 final size:43
Alignment explanation
Indices: 36446357--36446441 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 43
36446347 ACCATATACC
36446357 ATAAACCATAAATTCTAAACTATAATGATAATTAATTCAATAT
1 ATAAACCATAAATTCTAAACTATAATGATAATTAATTCAATAT
36446400 ATAAACCAT-AATTCTAAACTATAATGATAATTAATTCAATAT
1 ATAAACCATAAATTCTAAACTATAATGATAATTAATTCAATAT
36446442 TTTAAAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 33 0.79
43 9 0.21
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (43 bp):
ATAAACCATAAATTCTAAACTATAATGATAATTAATTCAATAT
Found at i:36446429 original size:19 final size:19
Alignment explanation
Indices: 36446367--36446431 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
36446357 ATAAACCATA
36446367 AATTCTAAACTATAATGAT
1 AATTCTAAACTATAATGAT
* **
36446386 AATTAATTCAATA-TATAAACCAT
1 AATT--CT-AA-ACTAT-AATGAT
36446409 AATTCTAAACTATAATGAT
1 AATTCTAAACTATAATGAT
36446428 AATT
1 AATT
36446432 AATTCAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
19 13 0.38
20 5 0.15
21 2 0.06
22 5 0.15
23 9 0.26
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (19 bp):
AATTCTAAACTATAATGAT
Found at i:36448797 original size:43 final size:43
Alignment explanation
Indices: 36448744--36448964 Score: 293
Period size: 43 Copynumber: 5.1 Consensus size: 43
36448734 ACAAATGCTA
36448744 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
* * *
36448787 CTAAATACCAAGACCTTTAGCGGTGCTTTTCCTACAAACGCCG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
*
36448830 CTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
* ** *
36448873 CTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCTGAAGCGCCG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
* * * * *
36448916 CTAAAAAACAAGACCATTT-GCGACGC-TTTCTCCAAAAACGCCA
1 CTAAAGACCAAGACC-TTTAGCGGCGCTTTTC-CCACAAACGCCG
36448959 CTAAAG
1 CTAAAG
36448965 GTCACAAAAA
Statistics
Matches: 155, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
42 4 0.03
43 148 0.95
44 3 0.02
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
CTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
Found at i:36449563 original size:7 final size:7
Alignment explanation
Indices: 36449553--36449583 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
36449543 CCCTAACTAT
36449553 TAACCCC
1 TAACCCC
36449560 TAACCCC
1 TAACCCC
*
36449567 TAACTCC
1 TAACCCC
36449574 TAACCCC
1 TAACCCC
36449581 TAA
1 TAA
36449584 ACCTTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (7 bp):
TAACCCC
Found at i:36449577 original size:21 final size:21
Alignment explanation
Indices: 36449519--36449583 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
36449509 CCCTAACCCG
* * *
36449519 ACCCTTAAATCCTAAACCCTAA
1 ACCCCTAACTCCTAACCCCT-A
* **
36449541 ATCCCTAACTATTAACCCCTA
1 ACCCCTAACTCCTAACCCCTA
36449562 ACCCCTAACTCCTAACCCCTA
1 ACCCCTAACTCCTAACCCCTA
36449583 A
1 A
36449584 ACCTTAAATC
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (21 bp):
ACCCCTAACTCCTAACCCCTA
Found at i:36449599 original size:21 final size:21
Alignment explanation
Indices: 36449554--36449607 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
36449544 CCTAACTATT
* * *
36449554 AACCCCTAACCCCTAACTCCT
1 AACCCCTAAACCCTAAATCCC
*
36449575 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCCTAAATCCC
*
36449596 AACCCTTAAACC
1 AACCCCTAAACC
36449608 ATATTCCCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCCTAAACCCTAAATCCC
Found at i:36449623 original size:14 final size:15
Alignment explanation
Indices: 36449602--36449640 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
36449592 TCCCAACCCT
36449602 TAAA-CCATATTCCC
1 TAAATCCATATTCCC
*
36449616 T-AATCCATAATCCC
1 TAAATCCATATTCCC
36449630 TAAATCCATAT
1 TAAATCCATAT
36449641 GTAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATCCATATTCCC
Found at i:36449956 original size:7 final size:7
Alignment explanation
Indices: 36449946--36450127 Score: 59
Period size: 7 Copynumber: 25.6 Consensus size: 7
36449936 ATATAAATAA
36449946 TAAACCC
1 TAAACCC
36449953 TAAACCCC
1 TAAA-CCC
*
36449961 T-AACACT
1 TAAAC-CC
*
36449968 TAACCCC
1 TAAACCC
36449975 T-AACTCC
1 TAAAC-CC
*
36449982 TAACCCC
1 TAAACCC
36449989 T-AACCC
1 TAAACCC
*
36449995 TTAAACCA
1 -TAAACCC
* *
36450003 TAAATCA
1 TAAACCC
*
36450010 TAATCCC
1 TAAACCC
36450017 TAAACCC
1 TAAACCC
* *
36450024 ATAATCCA
1 -TAAACCC
*
36450032 TAAACCT
1 TAAACCC
*
36450039 TAAA--A
1 TAAACCC
36450044 TAGTAACTCC
1 TA--AAC-CC
*
36450054 TAAACCT
1 TAAACCC
*
36450061 TAAACCA
1 TAAACCC
*
36450068 TAAACCA
1 TAAACCC
*
36450075 TAATCCC
1 TAAACCC
*
36450082 TAAACCT
1 TAAACCC
*
36450089 TAAACCT
1 TAAACCC
*
36450096 TAAAACC
1 TAAACCC
*
36450103 TAAACCA
1 TAAACCC
* *
36450110 TATACCA
1 TAAACCC
*
36450117 TAAACCA
1 TAAACCC
36450124 TAAA
1 TAAA
36450128 TTCTAAACTA
Statistics
Matches: 132, Mismatches: 30, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
5 2 0.02
6 7 0.05
7 101 0.77
8 20 0.15
10 2 0.02
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:36450025 original size:22 final size:21
Alignment explanation
Indices: 36449990--36450127 Score: 89
Period size: 21 Copynumber: 6.4 Consensus size: 21
36449980 CCTAACCCCT
36449990 AACCCTTAAACCATAAATCATA
1 AACCC-TAAACCATAAATCATA
*
36450012 ATCCCTAAACCCAT-AATCCATA
1 AACCCTAAA-CCATAAAT-CATA
* ** * *
36450034 AACCTTAAAATAGTAACTCCTA
1 AACCCTAAACCA-TAAATCATA
* *
36450056 AACCTTAAACCATAAACCATA
1 AACCCTAAACCATAAATCATA
* * * *
36450077 ATCCCTAAACCTTAAACCTTA
1 AACCCTAAACCATAAATCATA
* * *
36450098 AAACCTAAACCATATACCATA
1 AACCCTAAACCATAAATCATA
*
36450119 AACCATAAA
1 AACCCTAAA
36450128 TTCTAAACTA
Statistics
Matches: 89, Mismatches: 23, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
21 54 0.61
22 33 0.37
23 2 0.02
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (21 bp):
AACCCTAAACCATAAATCATA
Found at i:36450028 original size:15 final size:15
Alignment explanation
Indices: 36449990--36450037 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
36449980 CCTAACCCCT
* *
36449990 AACCCTTAAACCATA
1 AACCCATAATCCATA
* *
36450005 AA-TCATAATCCCTA
1 AACCCATAATCCATA
36450019 AACCCATAATCCATA
1 AACCCATAATCCATA
36450034 AACC
1 AACC
36450038 TTAAAATAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:36450073 original size:14 final size:14
Alignment explanation
Indices: 36449996--36450127 Score: 90
Period size: 14 Copynumber: 9.3 Consensus size: 14
36449986 CCCTAACCCT
*
36449996 TAAACCATAAATCA
1 TAAACCATAAACCA
* *
36450010 TAATCCCTAAACCCA
1 TAAACCATAAA-CCA
* *
36450025 TAATCCATAAACCT
1 TAAACCATAAACCA
*
36450039 TAAA--ATAGTAACTCC
1 TAAACCATA--AAC-CA
*
36450054 TAAACCTTAAACCA
1 TAAACCATAAACCA
* *
36450068 TAAACCATAATCCC
1 TAAACCATAAACCA
* *
36450082 TAAACCTTAAACCT
1 TAAACCATAAACCA
36450096 TAAAACC-TAAACCA
1 T-AAACCATAAACCA
*
36450110 TATACCATAAACCA
1 TAAACCATAAACCA
36450124 TAAA
1 TAAA
36450128 TTCTAAACTA
Statistics
Matches: 92, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
12 3 0.03
13 4 0.04
14 58 0.63
15 25 0.27
17 2 0.02
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.23
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:36450103 original size:8 final size:7
Alignment explanation
Indices: 36450054--36450127 Score: 60
Period size: 7 Copynumber: 10.6 Consensus size: 7
36450044 TAGTAACTCC
36450054 TAAACCT
1 TAAACCT
*
36450061 TAAACCA
1 TAAACCT
*
36450068 TAAACCA
1 TAAACCT
* *
36450075 TAATCCC
1 TAAACCT
36450082 TAAACCT
1 TAAACCT
36450089 TAAACCT
1 TAAACCT
36450096 TAAAACC-
1 T-AAACCT
*
36450103 TAAACCA
1 TAAACCT
* *
36450110 TATACCA
1 TAAACCT
*
36450117 TAAACCA
1 TAAACCT
36450124 TAAA
1 TAAA
36450128 TTCTAAACTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 5 0.09
7 48 0.83
8 5 0.09
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCT
Found at i:36450624 original size:107 final size:109
Alignment explanation
Indices: 36450428--36450729 Score: 421
Period size: 114 Copynumber: 2.7 Consensus size: 109
36450418 ACAGATGTTT
* *
36450428 TTAATTTTTTTGCGGCGTTTTTCAAA-AGCGCCGCTAATGCTCGACATATAGCGACATTTTTCAA
1 TTAA-TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTC-A
* *
36450492 AAAAGCGCCGCTAATGCCACTAAAGCTCAACAT-A-GGCGTTGTGC
64 ACAAGCGCCGCTAATGCCACTAAAGCTCAACATAAGGGCATTGTGC
* * *
36450536 TTAATTTTTTGTGGCGTGTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAAC
1 TTAATTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAAC
*
36450601 AAGCGCCGCTAATTCCACTAAAGCTCAACATAAAACGAGGGCATTGTGC
66 AAGCGCCGCTAATGCCACTAAAGCTCAACAT---A--AGGGCATTGTGC
* * *
36450650 TTAAATTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCAACCTATAGTGGCATTTTTCAAC
1 TTAATTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAAC
36450715 AAGCGCCGCTAATGC
66 AAGCGCCGCTAATGC
36450730 ACGACATATT
Statistics
Matches: 171, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
107 51 0.30
108 37 0.22
113 1 0.01
114 82 0.48
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (109 bp):
TTAATTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAAC
AAGCGCCGCTAATGCCACTAAAGCTCAACATAAGGGCATTGTGC
Found at i:36450750 original size:40 final size:40
Alignment explanation
Indices: 36450658--36450767 Score: 114
Period size: 40 Copynumber: 2.8 Consensus size: 40
36450648 GCTTAAATTT
* *
36450658 TTGCGGCGTTTTTCAA-AGAGCGCCGCTAATGCTCAACCTA
1 TTGCGGCGTTTTTCAACA-AGCGCCGCTAATGCACAACATA
* * * *
36450698 TAGTGGCATTTTTCAACAAGCGCCGCTAATGCACGACATA
1 TTGCGGCGTTTTTCAACAAGCGCCGCTAATGCACAACATA
* * * *
36450738 TTGCGACGTTTTTCGACTATCGCCGCTAAT
1 TTGCGGCGTTTTTCAACAAGCGCCGCTAAT
36450768 TCCCAATATA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 55 0.98
41 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (40 bp):
TTGCGGCGTTTTTCAACAAGCGCCGCTAATGCACAACATA
Found at i:36450899 original size:52 final size:52
Alignment explanation
Indices: 36450829--36450934 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
36450819 AAAATCTATT
36450829 TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
1 TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
36450881 TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
1 TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
36450933 TT
1 TT
36450935 AAACTTAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (52 bp):
TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
Found at i:36450933 original size:10 final size:10
Alignment explanation
Indices: 36450915--36450948 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
36450905 AAGTCATTAA
*
36450915 AATCCTAATT
1 AATCTTAATT
36450925 AATCTTAATT
1 AATCTTAATT
*
36450935 AAACTTAATT
1 AATCTTAATT
36450945 AATC
1 AATC
36450949 ATTTATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (10 bp):
AATCTTAATT
Found at i:36461930 original size:19 final size:19
Alignment explanation
Indices: 36461898--36461935 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
36461888 TATATACATT
36461898 TTTAGTTTTCAAA-TAAAA
1 TTTAGTTTTCAAATTAAAA
*
36461916 TTTAGTTTTTTAAATTAAAA
1 TTTAG-TTTTCAAATTAAAA
36461936 AATTAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTAGTTTTCAAATTAAAA
Found at i:36467400 original size:43 final size:43
Alignment explanation
Indices: 36467339--36467426 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
36467329 CAGTAACAAA
36467339 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
1 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
36467382 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
1 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
36467425 CA
1 CA
36467427 GCGAGTGAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
Found at i:36472522 original size:14 final size:15
Alignment explanation
Indices: 36472499--36472539 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
36472489 TCAACCTTTA
36472499 TTTTAATTTTAT-AT
1 TTTTAATTTTATCAT
*
36472513 TTTTAGTTTTATCA-
1 TTTTAATTTTATCAT
36472527 TTTTAATGTTTAT
1 TTTTAAT-TTTAT
36472540 GAAGATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTAATTTTATCAT
Found at i:36472711 original size:35 final size:35
Alignment explanation
Indices: 36472629--36472717 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 35
36472619 CCTTAAATAT
*
36472629 ATCTATCCCAACCTTTTT-GAGGTTGCCTTAGACT
1 ATCTATCCCAACCTTTTTAGAGGTTGCCTTAGACG
* * *
36472663 AGTATATCTCAACCTTTTTAG-GGTTGTCTTAGACGG
1 A-TCTATCCCAACCTTTTTAGAGGTTGCCTTAGAC-G
36472699 ATCTATCCCAACCTTTTTA
1 ATCTATCCCAACCTTTTTA
36472718 AAGTCGTCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
34 1 0.02
35 43 0.93
36 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (35 bp):
ATCTATCCCAACCTTTTTAGAGGTTGCCTTAGACG
Found at i:36472727 original size:35 final size:34
Alignment explanation
Indices: 36472629--36472727 Score: 108
Period size: 35 Copynumber: 2.9 Consensus size: 34
36472619 CCTTAAATAT
* * *
36472629 ATCTATCCCAACCTTTTTGAGGTTGCCTTAGACT
1 ATCTATCCCAACCTTTTTAAGGTTGTCTTAGACG
* * *
36472663 AGTATATCTCAACCTTTTTAGGGTTGTCTTAGACGG
1 A-TCTATCCCAACCTTTTTAAGGTTGTCTTAGAC-G
* *
36472699 ATCTATCCCAACCTTTTTAAAGTCGTCTT
1 ATCTATCCCAACCTTTTTAAGGTTGTCTT
36472728 TGACTTGGGC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
34 1 0.02
35 50 0.96
36 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (34 bp):
ATCTATCCCAACCTTTTTAAGGTTGTCTTAGACG
Found at i:36474773 original size:6 final size:6
Alignment explanation
Indices: 36474762--36474802 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
36474752 TAATAAAGCA
36474762 AATGGG AATGGG AATGGG AATGGG AATGGG AATGGG AATGG
1 AATGGG AATGGG AATGGG AATGGG AATGGG AATGGG AATGG
36474803 TTAAGGACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.49, T:0.17
Consensus pattern (6 bp):
AATGGG
Found at i:36475181 original size:23 final size:25
Alignment explanation
Indices: 36475145--36475192 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
36475135 CACACATCTC
36475145 CATTTTGTTTTTAAT-TTTT-TTTT
1 CATTTTGTTTTTAATCTTTTATTTT
36475168 CATTTT-TTTATTAATCTTTTATTTT
1 CATTTTGTTT-TTAATCTTTTATTTT
36475193 TTTAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.14
23 11 0.50
24 4 0.18
25 4 0.18
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (25 bp):
CATTTTGTTTTTAATCTTTTATTTT
Found at i:36477195 original size:9 final size:9
Alignment explanation
Indices: 36477172--36477209 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
36477162 TAAATCTAGC
36477172 GATATA-TA
1 GATATATTA
*
36477180 TATATATTA
1 GATATATTA
36477189 GATATATTA
1 GATATATTA
36477198 GATATATTA
1 GATATATTA
36477207 GAT
1 GAT
36477210 TAGCACACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (9 bp):
GATATATTA
Found at i:36477369 original size:28 final size:27
Alignment explanation
Indices: 36477329--36477383 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
36477319 ATAATTTTAT
*
36477329 ATTTTTATAATTTTTAAAGATTAAATTA
1 ATTTTTATAATTTTTAAAG-TCAAATTA
*
36477357 ATTTTTATCATTTTTAAAGTCAAATTA
1 ATTTTTATAATTTTTAAAGTCAAATTA
36477384 CAATTTTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTTTTATAATTTTTAAAGTCAAATTA
Found at i:36477390 original size:28 final size:28
Alignment explanation
Indices: 36477331--36477396 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
36477321 AATTTTATAT
* * *
36477331 TTTTATAATTTTTAAAGATTAAATTAAT
1 TTTTATCATTTTTAAAGATCAAATTAAA
36477359 TTTTATCATTTTTAAAG-TCAAATTACAA
1 TTTTATCATTTTTAAAGATCAAATTA-AA
*
36477387 TTTTAGCATT
1 TTTTATCATT
36477397 AATAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.21
28 26 0.79
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (28 bp):
TTTTATCATTTTTAAAGATCAAATTAAA
Found at i:36481987 original size:5 final size:5
Alignment explanation
Indices: 36481977--36482003 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
36481967 TAAATTTTAT
36481977 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
36482004 CAATGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:36483294 original size:34 final size:34
Alignment explanation
Indices: 36483256--36483333 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
36483246 CTACGGTGCC
*
36483256 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCAT
* * *
36483290 TTGGTGTGGTGTAGTTATCGCTTTATTGAGCCAT
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCAT
*
36483324 TTGATGTGGT
1 TTGGTGTGGT
36483334 CTATTGAGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.15, C:0.12, G:0.28, T:0.45
Consensus pattern (34 bp):
TTGGTGTGGTGTAATTATCGCTCTATTAAGCCAT
Found at i:36508085 original size:26 final size:26
Alignment explanation
Indices: 36508009--36508077 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
36507999 CCCAACAAAA
*
36508009 TTTTGACAATTTTACCCATGGTAAAG
1 TTTTGACGATTTTACCCATGGTAAAG
* * *
36508035 TTTTGATGATTTTACACGTGGTAAAG
1 TTTTGACGATTTTACCCATGGTAAAG
36508061 TTTTGACGATTTTACCC
1 TTTTGACGATTTTACCC
36508078 TTAGTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (26 bp):
TTTTGACGATTTTACCCATGGTAAAG
Found at i:36512343 original size:27 final size:27
Alignment explanation
Indices: 36512305--36512366 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
36512295 ATAAACTATT
36512305 GGCCCGATTCTTTCAGTGATCTCATAC
1 GGCCCGATTCTTTCAGTGATCTCATAC
36512332 GGCCCGATTCTTTCAGTGATCTCATAC
1 GGCCCGATTCTTTCAGTGATCTCATAC
36512359 GGCCCGAT
1 GGCCCGAT
36512367 AAAATGCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.18, C:0.31, G:0.21, T:0.31
Consensus pattern (27 bp):
GGCCCGATTCTTTCAGTGATCTCATAC
Found at i:36516600 original size:3 final size:3
Alignment explanation
Indices: 36516592--36516693 Score: 134
Period size: 3 Copynumber: 34.0 Consensus size: 3
36516582 ACTGTTTCTC
*
36516592 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
36516640 ATT ACT ATT ATT ATT ATT ATT ATT ATC ATC ATT TTT GTT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
36516686 -TT ATT ATT
1 ATT ATT ATT
36516694 TATTTCATTT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.02
3 83 0.94
4 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Done.