Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 27 of 133
Found at i:6493042 original size:65 final size:65
Alignment explanation
Indices: 6492891--6493042 Score: 162
Period size: 65 Copynumber: 2.3 Consensus size: 65
6492881 CTCTTGGTTT
* * * * *
6492891 AATCCTGATCACCTGTTTTGATTTTAGCTTAGTCTAGATCATTTCATGTTTTTTACTCGTAGTTA
1 AATCCCGATCACCTGTTTTGATTTTAGCTTAATCTAGATCATTTCATATTTCTTACTCGTAATTA
* * * *
6492956 AATCCCGATCACCTATGTTGATTTT-GATTTAATCTAGATCATTTTATATTTCTTACTCGTAATT
1 AATCCCGATCACCTGTTTTGATTTTAG-CTTAATCTAGATCATTTCATATTTCTTACTCGTAATT
*
6493020 C
65 A
** * *
6493021 AATCTTGGTCACATGTTTTGAT
1 AATCCCGATCACCTGTTTTGAT
6493043 ATCGACTCAA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
64 1 0.01
65 69 0.99
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (65 bp):
AATCCCGATCACCTGTTTTGATTTTAGCTTAATCTAGATCATTTCATATTTCTTACTCGTAATTA
Found at i:6493065 original size:65 final size:65
Alignment explanation
Indices: 6492991--6493157 Score: 156
Period size: 65 Copynumber: 2.6 Consensus size: 65
6492981 GATTTAATCT
* * * *
6492991 AGATCATTTTATATTTCTTACTCGTAATTCAATCTTGGTCACATGTTTTGATATCGACTCAATTC
1 AGATTATTTTATATTTCTTACTCGTAATTCAATCTTGGTCACATATTTTAATATCGACTCAATAC
* * * * * * * * * * *
6493056 AGATTATTTTATGTTTCTGACTTGCAATTCTATCTCGGTCACTTATTTTAATTTTGGCTCAGTAC
1 AGATTATTTTATATTTCTTACTCGTAATTCAATCTTGGTCACATATTTTAATATCGACTCAATAC
** *
6493121 AGATTATTTTA-ATTTCTTGTTTCGTAGTTCAATCTTG
1 AGATTATTTTATATTTCTT-ACTCGTAATTCAATCTTG
6493158 ATGATACCTT
Statistics
Matches: 77, Mismatches: 24, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
64 5 0.06
65 72 0.94
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (65 bp):
AGATTATTTTATATTTCTTACTCGTAATTCAATCTTGGTCACATATTTTAATATCGACTCAATAC
Found at i:6493445 original size:3 final size:3
Alignment explanation
Indices: 6493437--6493511 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
6493427 ACCCATATTG
6493437 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6493485 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
6493512 CTAGTTTATT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6493911 original size:33 final size:32
Alignment explanation
Indices: 6493836--6493914 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 32
6493826 AGGCTTTGGG
*
6493836 TTTTTTGTTATTTTTAGTTAGGTTTTGGGTTT
1 TTTTTTGTTGTTTTTAGTTAGGTTTTGGGTTT
* *
6493868 TGTTTATGTTGTTTTTAAGTT-GGATTTTTGGTTT
1 T-TTTTTGTTGTTTTT-AGTTAGG-TTTTGGGTTT
6493902 TTTTTTGTTGTTT
1 TTTTTTGTTGTTT
6493915 GGAATACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.03
33 25 0.62
34 14 0.35
ACGTcount: A:0.09, C:0.00, G:0.22, T:0.70
Consensus pattern (32 bp):
TTTTTTGTTGTTTTTAGTTAGGTTTTGGGTTT
Found at i:6493968 original size:27 final size:28
Alignment explanation
Indices: 6493926--6493979 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
6493916 GAATACCTAA
*
6493926 AAAAAATTTTTGAAAAA-GTGGGTTTTG
1 AAAAAATTTTTGAAAAATCTGGGTTTTG
6493953 AAAAAA-TTTTGAAAAAATCTGGGTTTT
1 AAAAAATTTTTG-AAAAATCTGGGTTTT
6493980 AAGTTGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 11 0.46
28 8 0.33
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.37
Consensus pattern (28 bp):
AAAAAATTTTTGAAAAATCTGGGTTTTG
Found at i:6494334 original size:27 final size:26
Alignment explanation
Indices: 6494290--6494381 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 26
6494280 CGCTGGTTTT
*
6494290 TTTTA-TTATTTTGTTTTTCAATTACA
1 TTTTACTTATTTT-ATTTTCAATTACA
* *
6494316 TTTTTATTTATTTTATTTT-AA-TATA
1 -TTTTACTTATTTTATTTTCAATTACA
* *
6494341 TTTT-CTTA-TTTATTTTCTATTTCA
1 TTTTACTTATTTTATTTTCAATTACA
6494365 TTTTACTTATTTTATTT
1 TTTTACTTATTTTATTT
6494382 GTTTAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
22 8 0.15
23 4 0.07
24 10 0.19
25 7 0.13
26 9 0.17
27 9 0.17
28 7 0.13
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.71
Consensus pattern (26 bp):
TTTTACTTATTTTATTTTCAATTACA
Found at i:6494356 original size:12 final size:12
Alignment explanation
Indices: 6494339--6494381 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
6494329 TATTTTAATA
6494339 TATTTTCTTATT
1 TATTTTCTTATT
6494351 TATTTTC-TATT
1 TATTTTCTTATT
6494362 TCATTTTACTTATTT
1 T-ATTTT-CTTA-TT
6494377 TATTT
1 TATTT
6494382 GTTTAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.19
12 12 0.44
13 1 0.04
14 6 0.22
15 3 0.11
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTTCTTATT
Found at i:6499652 original size:15 final size:14
Alignment explanation
Indices: 6499627--6499661 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
6499617 GACTTGGGGC
*
6499627 TTTTGTTTTGTTTT
1 TTTTTTTTTGTTTT
6499641 TATTTTTTTTGTTTT
1 T-TTTTTTTTGTTTT
6499656 TTTTTT
1 TTTTTT
6499662 AAAGAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTGTTTT
Found at i:6500150 original size:30 final size:32
Alignment explanation
Indices: 6500116--6500182 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
6500106 AATAAAAGAT
6500116 AAATATCTA-TATAT-AAAATTAATAAAAAGG
1 AAATATCTATTATATGAAAATTAATAAAAAGG
* *
6500146 AAATATTTATTTATATGAAAATTAGTAAAAAGG
1 AAATATCTA-TTATATGAAAATTAATAAAAAGG
6500179 AAAT
1 AAAT
6500183 TAAAATCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 8 0.25
32 5 0.16
33 19 0.59
ACGTcount: A:0.57, C:0.01, G:0.09, T:0.33
Consensus pattern (32 bp):
AAATATCTATTATATGAAAATTAATAAAAAGG
Found at i:6500325 original size:27 final size:28
Alignment explanation
Indices: 6500295--6500347 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
6500285 TAATCATTTT
6500295 TATTAACATTTTT-TAATTAATTTTATA
1 TATTAACATTTTTATAATTAATTTTATA
** *
6500322 TATTATTATTTTTATAATTATTTTTA
1 TATTAACATTTTTATAATTAATTTTA
6500348 ATTATAGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (28 bp):
TATTAACATTTTTATAATTAATTTTATA
Found at i:6500341 original size:15 final size:16
Alignment explanation
Indices: 6500310--6500343 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6500300 ACATTTTTTA
6500310 ATTAATTTTATATATT
1 ATTAATTTTATATATT
*
6500326 ATTATTTTTATA-ATT
1 ATTAATTTTATATATT
6500341 ATT
1 ATT
6500344 TTTAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTAATTTTATATATT
Found at i:6500717 original size:17 final size:18
Alignment explanation
Indices: 6500695--6500733 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
6500685 GATTTAAAAC
6500695 GATTTAATTATAAAATT-
1 GATTTAATTATAAAATTA
6500712 GATTTAATTATAAAATTA
1 GATTTAATTATAAAATTA
6500730 GATT
1 GATT
6500734 GATTTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (18 bp):
GATTTAATTATAAAATTA
Found at i:6501397 original size:2 final size:2
Alignment explanation
Indices: 6501390--6501420 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6501380 ATGCTTCCTT
6501390 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6501421 CAAACTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6504494 original size:11 final size:11
Alignment explanation
Indices: 6504480--6504510 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
6504470 TTAAATAAAG
*
6504480 TTGAAATAACT
1 TTGACATAACT
6504491 TTGACATAACT
1 TTGACATAACT
6504502 TTGACATAA
1 TTGACATAA
6504511 AGTAGATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (11 bp):
TTGACATAACT
Found at i:6511126 original size:18 final size:19
Alignment explanation
Indices: 6511090--6511127 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6511080 ACTGACCAAA
* *
6511090 TTTGGAAGCTTGAATTTTT
1 TTTGGAAGCTTCAAATTTT
6511109 TTTGG-AGCTTCAAATTTT
1 TTTGGAAGCTTCAAATTTT
6511127 T
1 T
6511128 GTTTGAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.21, C:0.08, G:0.18, T:0.53
Consensus pattern (19 bp):
TTTGGAAGCTTCAAATTTT
Found at i:6517005 original size:156 final size:156
Alignment explanation
Indices: 6516739--6517034 Score: 565
Period size: 156 Copynumber: 1.9 Consensus size: 156
6516729 GTTAGTTGTT
*
6516739 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAAAAAATTCCCTCACCTCAAG
*
6516804 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTATTTAAAGAAAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
6516869 CAAGATCAACCAATTAATTAATTATC
131 CAAGATCAACCAATTAATTAATTATC
*
6516895 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAAAAAATTCCCTCACCTCAGG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAAAAAATTCCCTCACCTCAAG
6516960 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
6517025 CAAGATCAAC
131 CAAGATCAAC
6517035 ATCAAAGTCA
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 137 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (156 bp):
GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAAAAAATTCCCTCACCTCAAG
AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
CAAGATCAACCAATTAATTAATTATC
Found at i:6517067 original size:16 final size:16
Alignment explanation
Indices: 6517042--6517072 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6517032 AACATCAAAG
*
6517042 TCAAATAAAAAAAAAT
1 TCAAAAAAAAAAAAAT
6517058 TCAAAAAAAAAAAAA
1 TCAAAAAAAAAAAAA
6517073 AAAACAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (16 bp):
TCAAAAAAAAAAAAAT
Found at i:6517080 original size:18 final size:18
Alignment explanation
Indices: 6517048--6517082 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6517038 AAAGTCAAAT
**
6517048 AAAAAAAAATTCAAAAAA
1 AAAAAAAAAAACAAAAAA
6517066 AAAAAAAAAAACAAAAA
1 AAAAAAAAAAACAAAAA
6517083 CCTGGAGCGG
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:0.89, C:0.06, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAAAAAACAAAAAA
Found at i:6517121 original size:15 final size:16
Alignment explanation
Indices: 6517090--6517139 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
6517080 AAACCTGGAG
*
6517090 CGGCTCGGATCGCGGCT
1 CGGCTCGGCT-GCGGCT
*
6517107 CGGCTTGG-TGCGGCT
1 CGGCTCGGCTGCGGCT
6517122 CGGCTCGGCT-CGGCT
1 CGGCTCGGCTGCGGCT
6517137 CGG
1 CGG
6517140 AGGGGCTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 21 0.70
16 2 0.07
17 7 0.23
ACGTcount: A:0.02, C:0.34, G:0.44, T:0.20
Consensus pattern (16 bp):
CGGCTCGGCTGCGGCT
Found at i:6517125 original size:5 final size:5
Alignment explanation
Indices: 6517102--6517139 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
6517092 GCTCGGATCG
*
6517102 CGGCT CGGCT TGG-T GCGGCT CGGCT CGGCT CGGCT CGG
1 CGGCT CGGCT CGGCT -CGGCT CGGCT CGGCT CGGCT CGG
6517140 AGGGGCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 27 0.93
6 1 0.03
ACGTcount: A:0.00, C:0.34, G:0.45, T:0.21
Consensus pattern (5 bp):
CGGCT
Found at i:6517383 original size:19 final size:19
Alignment explanation
Indices: 6517359--6517403 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
6517349 GAACGCCGGT
6517359 GCCGGATTCTGGAAAATTC
1 GCCGGATTCTGGAAAATTC
* * *
6517378 GCCGGAATCTGGGAATTTC
1 GCCGGATTCTGGAAAATTC
6517397 GCCGGAT
1 GCCGGAT
6517404 ATTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.24
Consensus pattern (19 bp):
GCCGGATTCTGGAAAATTC
Found at i:6517503 original size:31 final size:31
Alignment explanation
Indices: 6517465--6517537 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
6517455 AAACTGGGTC
*
6517465 TGTCGCCGGAAACTTC-AAAGTTCGCCGGAAT
1 TGTCGCCGGAAAATTCAAAAG-TCGCCGGAAT
6517496 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
1 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
*
6517527 TTTCGCCGGAA
1 TGTCGCCGGAA
6517538 TCTGGAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 35 0.90
32 4 0.10
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (31 bp):
TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
Found at i:6517912 original size:43 final size:45
Alignment explanation
Indices: 6517863--6517973 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 45
6517853 AAATCAAAAA
* * *
6517863 TAAAAAAAATACTAGATAATAATCA-GATAAATCA-AA-AGATATT
1 TAAAAAAAATAATA-ATAATAATCAGGAAAAATCAGAACAGATAAT
* * *
6517906 TAAAAAAAAAAATATCTGATAATCAGGAAAAATCAGAACAGATAAT
1 TAAAAAAAATAATA-ATAATAATCAGGAAAAATCAGAACAGATAAT
*
6517952 TAAAAATAATAATAATAATAAT
1 TAAAAAAAATAATAATAATAAT
6517974 AATAATAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
43 20 0.37
44 8 0.15
45 8 0.15
46 18 0.33
ACGTcount: A:0.62, C:0.06, G:0.07, T:0.24
Consensus pattern (45 bp):
TAAAAAAAATAATAATAATAATCAGGAAAAATCAGAACAGATAAT
Found at i:6517964 original size:3 final size:3
Alignment explanation
Indices: 6517956--6518136 Score: 62
Period size: 3 Copynumber: 59.3 Consensus size: 3
6517946 GATAATTAAA
* **
6517956 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- GAT AA- ACCC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
6517999 AAGT ATAT ATT ACA- AA- AAA AAT AAT AAT AAT AAT AAT AA- AAT ATAT
1 AA-T A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * *
6518045 AACT ATAT ACAT -AT AA- ATCT AAT -CT AAT AA- AAA AAT AAAT AAAT
1 AA-T A-AT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT -AAT
*
6518089 ATAT ACAT AAT AAT AAT AAT AAT AA- AAT ACAT AA- AAT ACAA AAT AAT
1 A-AT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT
6518136 A
1 A
6518137 TAGGACAAAT
Statistics
Matches: 138, Mismatches: 17, Indels: 46
0.69 0.08 0.23
Matches are distributed among these distances:
2 19 0.14
3 85 0.62
4 32 0.23
5 2 0.01
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:6518310 original size:8 final size:8
Alignment explanation
Indices: 6518300--6518358 Score: 70
Period size: 7 Copynumber: 7.5 Consensus size: 8
6518290 CATTTTTTGG
6518300 TTTTGTTGT
1 TTTTGTT-T
6518309 TTTT-TTT
1 TTTTGTTT
*
6518316 TGTT-TTT
1 TTTTGTTT
6518323 TTTTGTTTT
1 TTTTG-TTT
6518332 TTTTGTTT
1 TTTTGTTT
6518340 TTTTGTTT
1 TTTTGTTT
6518348 TTTT-TTT
1 TTTTGTTT
6518355 TTTT
1 TTTT
6518359 TACCAAAGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
7 17 0.37
8 17 0.37
9 12 0.26
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (8 bp):
TTTTGTTT
Found at i:6518312 original size:1 final size:1
Alignment explanation
Indices: 6518308--6518359 Score: 68
Period size: 1 Copynumber: 52.0 Consensus size: 1
6518298 GGTTTTGTTG
* * * *
6518308 TTTTTTTTTGTTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6518360 ACCAAAGCTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (1 bp):
T
Found at i:6518316 original size:19 final size:17
Alignment explanation
Indices: 6518292--6518359 Score: 79
Period size: 17 Copynumber: 3.9 Consensus size: 17
6518282 CAACTCAACA
6518292 TTTTTTGGTTTTGTTGTTT-
1 TTTTTT-GTTTT-TT-TTTG
6518311 TTTTTTGTTTTTTTTTG
1 TTTTTTGTTTTTTTTTG
6518328 TTTTTT-TTGTTTTTTTG
1 TTTTTTGTT-TTTTTTTG
6518345 TTTTTT-TTTTTTTTT
1 TTTTTTGTTTTTTTTT
6518360 ACCAAAGCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
16 12 0.26
17 24 0.51
18 5 0.11
19 6 0.13
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (17 bp):
TTTTTTGTTTTTTTTTG
Found at i:6518318 original size:10 final size:10
Alignment explanation
Indices: 6518300--6518359 Score: 83
Period size: 10 Copynumber: 6.4 Consensus size: 10
6518290 CATTTTTTGG
*
6518300 TTTTGTTGTT
1 TTTTTTTGTT
6518310 TTTTTTTGTT
1 TTTTTTTGTT
6518320 TTTTTTTG-T
1 TTTTTTTGTT
6518329 TTTTTTTG--
1 TTTTTTTGTT
6518337 TTTTTTTGTT
1 TTTTTTTGTT
6518347 TTTTTTT-TT
1 TTTTTTTGTT
6518356 TTTT
1 TTTT
6518360 ACCAAAGCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
8 8 0.17
9 15 0.32
10 24 0.51
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:6518321 original size:9 final size:9
Alignment explanation
Indices: 6518292--6518359 Score: 86
Period size: 9 Copynumber: 7.6 Consensus size: 9
6518282 CAACTCAACA
*
6518292 TTTTTTGGT
1 TTTTTTGTT
*
6518301 TTTGTTGTTT
1 TTTTTTG-TT
6518311 TTTTTTGTTT
1 TTTTTTG-TT
6518321 TTTTTTGTT
1 TTTTTTGTT
6518330 TTTTTTG-T
1 TTTTTTGTT
6518338 TTTTTTGTT
1 TTTTTTGTT
6518347 TTTTTT-TT
1 TTTTTTGTT
6518355 TTTTT
1 TTTTT
6518360 ACCAAAGCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
8 15 0.28
9 22 0.41
10 17 0.31
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:6518455 original size:41 final size:42
Alignment explanation
Indices: 6518366--6518919 Score: 790
Period size: 42 Copynumber: 13.4 Consensus size: 42
6518356 TTTTACCAAA
* *
6518366 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
* *
6518408 GCTCCTCTAAGCAGAGGTACCACGACTTTAG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
* * *
6518449 GCTCCTCTAAACAGAGG--CAACGAACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGTACCACG-ACTTTGGAAAAGTAAATT
*
6518490 GCTCCTCTAAACAGAGG--CAACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACG-ACTTTGGAAAAGTAAATT
*
6518530 GCTCCTCTAAATAGAGGTACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
*
6518572 GCTCCTCTAAATAGAGGTACCACGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
* *
6518613 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
*
6518655 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
*
6518696 GCTCCTCTAAACAGAGGTACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
* *
6518738 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
* *
6518780 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
*
6518821 GCTCCTCTAAACAGAGG--CAACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACG-ACTTTGGAAAAGTAAATT
* ** *
6518861 GCTCCTCTCAACAGAGACACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
6518903 GCTCCTCTAAACAGAGG
1 GCTCCTCTAAACAGAGG
6518920 CAACGGAACT
Statistics
Matches: 471, Mismatches: 30, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
39 8 0.02
40 63 0.13
41 180 0.38
42 220 0.47
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
Found at i:6518619 original size:83 final size:83
Alignment explanation
Indices: 6518366--6518942 Score: 814
Period size: 83 Copynumber: 7.0 Consensus size: 83
6518356 TTTTACCAAA
* *
6518366 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAGCAGAGGTACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
6518431 GACTTT-AGAAAGTAAATT
66 GACTTTGA-AAAGTAAATT
* * *
6518449 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGG--CAA
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCA
6518510 CGAACTTTGAAAAGTAAATT
65 CG-ACTTTGAAAAGTAAATT
* * *
6518530 GCTCCTCTAAATAGAGGTACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGTACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
*
6518595 GACTTTGGAAAGTAAATT
66 GACTTTGAAAAGTAAATT
* * *
6518613 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGTACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
*
6518678 GACTTTGAAAAATAAATT
66 GACTTTGAAAAGTAAATT
* * *
6518696 GCTCCTCTAAACAGAGGTACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
*
6518761 GACTTTGGAAAAATAAATT
66 GACTTT-GAAAAGTAAATT
* *
6518780 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGG--CAAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
6518842 GAACTTTGAAAAGTAAATT
66 G-ACTTTGAAAAGTAAATT
* * * *
6518861 GCTCCTCTCAACAGAGACACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGG--CAAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
6518924 GGAACTTTGAAAAGTAAAT
66 -G-ACTTTGAAAAGTAAAT
6518943 ACTCCTAGAC
Statistics
Matches: 455, Mismatches: 28, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
80 4 0.01
81 78 0.17
82 101 0.22
83 229 0.50
84 43 0.09
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (83 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
GACTTTGAAAAGTAAATT
Found at i:6520141 original size:8 final size:8
Alignment explanation
Indices: 6520128--6520184 Score: 62
Period size: 8 Copynumber: 7.1 Consensus size: 8
6520118 TTTGGATCTC
6520128 TTTTTTCA
1 TTTTTTCA
*
6520136 TTTTTTAA
1 TTTTTTCA
6520144 TTTTTTCA
1 TTTTTTCA
*
6520152 TTTTCTCA
1 TTTTTTCA
6520160 TTTTTTC-
1 TTTTTTCA
**
6520167 TTCTTTTTT
1 TT-TTTTCA
6520176 TTTTTTCA
1 TTTTTTCA
6520184 T
1 T
6520185 CATTTTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
7 2 0.05
8 36 0.90
9 2 0.05
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:6520178 original size:15 final size:15
Alignment explanation
Indices: 6520160--6520203 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
6520150 CATTTTCTCA
6520160 TTTTTTCTTCTTTTTT
1 TTTTTTCTTC-TTTTT
* *
6520176 TTTTTTCATCATTTT
1 TTTTTTCTTCTTTTT
6520191 TTTTTTCATTCTT
1 TTTTTTC-TTCTT
6520204 CACCTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTCTTTTT
Found at i:6520190 original size:16 final size:16
Alignment explanation
Indices: 6520160--6520196 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6520150 CATTTTCTCA
* *
6520160 TTTTTTCTTCTTTTTT
1 TTTTTTCATCATTTTT
6520176 TTTTTTCATCATTTTT
1 TTTTTTCATCATTTTT
6520192 TTTTT
1 TTTTT
6520197 CATTCTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCATCATTTTT
Found at i:6524103 original size:156 final size:156
Alignment explanation
Indices: 6523837--6524132 Score: 574
Period size: 156 Copynumber: 1.9 Consensus size: 156
6523827 GTTAGTTGTT
6523837 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
*
6523902 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTATTTAAAGAAAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
6523967 CAAGATCAACCAATTAATTAATTATC
131 CAAGATCAACCAATTAATTAATTATC
*
6523993 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
6524058 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
6524123 CAAGATCAAC
131 CAAGATCAAC
6524133 ATCAAAGTCA
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 138 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (156 bp):
GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
CAAGATCAACCAATTAATTAATTATC
Found at i:6524163 original size:9 final size:10
Alignment explanation
Indices: 6524148--6524174 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6524138 AGTCAAATAA
6524148 AAAAAAATTC
1 AAAAAAATTC
6524158 AAAAAAATTC
1 AAAAAAATTC
6524168 AAAAAAA
1 AAAAAAA
6524175 AAAAAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:6524220 original size:15 final size:16
Alignment explanation
Indices: 6524189--6524238 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
6524179 AAACCTGGAG
*
6524189 CGGCTCGGATCGCGGCT
1 CGGCTCGGCT-GCGGCT
*
6524206 CGGCTTGG-TGCGGCT
1 CGGCTCGGCTGCGGCT
6524221 CGGCTCGGCT-CGGCT
1 CGGCTCGGCTGCGGCT
6524236 CGG
1 CGG
6524239 AGGGGCTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 21 0.70
16 2 0.07
17 7 0.23
ACGTcount: A:0.02, C:0.34, G:0.44, T:0.20
Consensus pattern (16 bp):
CGGCTCGGCTGCGGCT
Found at i:6524224 original size:5 final size:5
Alignment explanation
Indices: 6524201--6524238 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
6524191 GCTCGGATCG
*
6524201 CGGCT CGGCT TGG-T GCGGCT CGGCT CGGCT CGGCT CGG
1 CGGCT CGGCT CGGCT -CGGCT CGGCT CGGCT CGGCT CGG
6524239 AGGGGCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 27 0.93
6 1 0.03
ACGTcount: A:0.00, C:0.34, G:0.45, T:0.21
Consensus pattern (5 bp):
CGGCT
Found at i:6524997 original size:42 final size:44
Alignment explanation
Indices: 6524949--6525057 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 44
6524939 AAATCAAAAA
* * *
6524949 TAAAAAAATACTAGATAATAATCA-GATAAATCA-AA-AGATATT
1 TAAAAAAATAATA-ATAATAATCAGGAAAAATCAGAACAGATAAT
* * *
6524991 TAAAAAAAAAATATCTGATAATCAGGAAAAATCAGAACAGATAAT
1 TAAAAAAATAATA-ATAATAATCAGGAAAAATCAGAACAGATAAT
6525036 TAAAAATAATAATAATAATAAT
1 TAAAAA-AATAATAATAATAAT
6525058 AATAATAATA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
42 19 0.36
43 8 0.15
44 2 0.04
45 18 0.34
46 6 0.11
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.25
Consensus pattern (44 bp):
TAAAAAAATAATAATAATAATCAGGAAAAATCAGAACAGATAAT
Found at i:6525048 original size:3 final size:3
Alignment explanation
Indices: 6525040--6525221 Score: 76
Period size: 3 Copynumber: 58.3 Consensus size: 3
6525030 GATAATTAAA
* **
6525040 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- GAT AA- ACCC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
6525083 AAGT ATAT ATT ACAA AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATAT
1 AA-T A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT
* * *
6525130 AACT ATAT ACAT -AT AA- ATCT AAT -CT AAT AA- AAA AAT AAAT AAAT
1 AA-T A-AT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT -AAT
*
6525174 ATAT ACAT AAT AAT AAT AAT AAT AA- AAT ACAT AA- AAT ACAA AAT AAT
1 A-AT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT
6525221 A
1 A
6525222 TAGGACAAAT
Statistics
Matches: 139, Mismatches: 18, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
2 14 0.10
3 87 0.63
4 36 0.26
5 2 0.01
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6525619 original size:24 final size:24
Alignment explanation
Indices: 6525587--6525634 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
6525577 TCCCTTAGCA
*
6525587 TCATTTTCAGTAGATAGTTTTACC
1 TCATTTTCAATAGATAGTTTTACC
6525611 TCATTTTCAATAGATAGTTTTACC
1 TCATTTTCAATAGATAGTTTTACC
6525635 CCTTAGTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (24 bp):
TCATTTTCAATAGATAGTTTTACC
Found at i:6527662 original size:14 final size:14
Alignment explanation
Indices: 6527643--6527671 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6527633 CTGATTCTTT
6527643 CTTTATTAAAGTTA
1 CTTTATTAAAGTTA
6527657 CTTTATTAAAGTTA
1 CTTTATTAAAGTTA
6527671 C
1 C
6527672 CTTACTATTA
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:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (14 bp):
CTTTATTAAAGTTA
Found at i:6530878 original size:2 final size:2
Alignment explanation
Indices: 6530865--6530906 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
6530855 TGGCGGGGTC
* *
6530865 CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6530907 TCTGTTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6535071 original size:2 final size:2
Alignment explanation
Indices: 6535064--6535104 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6535054 ATGTAAACGC
6535064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6535105 CACACACTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6535599 original size:62 final size:65
Alignment explanation
Indices: 6535497--6535623 Score: 188
Period size: 62 Copynumber: 2.0 Consensus size: 65
6535487 TTTTAGTGAG
* *
6535497 AAAATAAAAAAGTTCAGGCGAGAAGAAGCTTATCTCATTTGAGGATCAGGGCATACTATAGGTTT
1 AAAATAAAAAAGTTCAGGCGAGAAAAAACTTATCTCATTTGAGGATCAGGGCATACTATAGGTTT
* * *
6535562 AAAAT-AAAAAGTTCA-GTGAGAAAAAAC-TATCTCATTTGAGGATCCGGGCATGCTATAGGTTT
1 AAAATAAAAAAGTTCAGGCGAGAAAAAACTTATCTCATTTGAGGATCAGGGCATACTATAGGTTT
6535624 TAGTGAGAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
62 33 0.58
63 9 0.16
64 10 0.18
65 5 0.09
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.27
Consensus pattern (65 bp):
AAAATAAAAAAGTTCAGGCGAGAAAAAACTTATCTCATTTGAGGATCAGGGCATACTATAGGTTT
Found at i:6535974 original size:43 final size:44
Alignment explanation
Indices: 6535913--6535999 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
6535903 ACCTCTGGTG
* * * *
6535913 ACTTTTATGGCAT-TTTTTTATTGAGGAGAATACGACAAGGATA
1 ACTTTTATAGCATCTTTTTAATTAAGGAGAATACAACAAGGATA
* *
6535956 ACTTTTATAGCATCTTTTTAATTAAGTAGAATATAACAAGGATA
1 ACTTTTATAGCATCTTTTTAATTAAGGAGAATACAACAAGGATA
6536000 GATAAAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 12 0.32
44 25 0.68
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (44 bp):
ACTTTTATAGCATCTTTTTAATTAAGGAGAATACAACAAGGATA
Found at i:6538819 original size:2 final size:2
Alignment explanation
Indices: 6538812--6538846 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6538802 TATACAAAGA
6538812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6538847 CTTTTCAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6544811 original size:21 final size:21
Alignment explanation
Indices: 6544786--6544826 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6544776 TATACAATTG
* *
6544786 AAAAAATACAAAAGATAAAAGC
1 AAAAAA-AAAAAAGAAAAAAGC
6544808 AAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAGAAAAAA
6544827 AGGTGTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.83, C:0.05, G:0.07, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAAAAGAAAAAAGC
Found at i:6547227 original size:61 final size:62
Alignment explanation
Indices: 6547145--6547273 Score: 181
Period size: 61 Copynumber: 2.1 Consensus size: 62
6547135 TTTTATCTAG
* *
6547145 TAAAATCTCACAAATTTTCACCATAAATAAT-GAAATTATAAAATACATAAAACTTAGTAAAT
1 TAAAATCTCACAAATTCTCACCATAAATAATAG-AATTATAAAATACATAAAACTTAGTAAAC
* * * *
6547207 TAAAA-CTCACAAATTCTCACCATAGATGATAGAATTATGAAATATATAAAACTTAGTAAAC
1 TAAAATCTCACAAATTCTCACCATAAATAATAGAATTATAAAATACATAAAACTTAGTAAAC
6547268 TAAAAT
1 TAAAAT
6547274 TTAAACATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
61 53 0.90
62 6 0.10
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.29
Consensus pattern (62 bp):
TAAAATCTCACAAATTCTCACCATAAATAATAGAATTATAAAATACATAAAACTTAGTAAAC
Found at i:6555653 original size:26 final size:26
Alignment explanation
Indices: 6555623--6555675 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
6555613 TAATTGAGTG
* *
6555623 AAAATTTAAATTTAAAATTTTAATTA
1 AAAATATAAATTTAAAAATTTAATTA
*
6555649 AAAATATATATTTAAAAATTTAATTA
1 AAAATATAAATTTAAAAATTTAATTA
6555675 A
1 A
6555676 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATATAAATTTAAAAATTTAATTA
Found at i:6555694 original size:14 final size:14
Alignment explanation
Indices: 6555675--6555726 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
6555665 AATTTAATTA
6555675 ATTTAAAATAAAAT
1 ATTTAAAATAAAAT
**
6555689 ATTTAAAATTTAAT
1 ATTTAAAATAAAAT
* *
6555703 TTATTGAAATAAAAT
1 AT-TTAAAATAAAAT
6555718 ATTTAAAAT
1 ATTTAAAAT
6555727 TTAAATAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATTTAAAATAAAAT
Found at i:6555698 original size:21 final size:21
Alignment explanation
Indices: 6555661--6555701 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
6555651 AATATATATT
6555661 TAAAAATTTAATTAATTTAAAA
1 TAAAAATTTAA-TAATTTAAAA
6555683 TAAAATATTTAA-AATTTAA
1 TAAAA-ATTTAATAATTTAA
6555702 TTTATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATTTAATAATTTAAAA
Found at i:6555719 original size:29 final size:30
Alignment explanation
Indices: 6555642--6555736 Score: 122
Period size: 29 Copynumber: 3.2 Consensus size: 30
6555632 ATTTAAAATT
* *
6555642 TTAATTAAAAAT-ATATATTTAAAAATTTAA
1 TTAATTTAAAATAAAATATTT-AAAATTTAA
6555672 TTAATTTAAAATAAAATATTTAAAATTTAA
1 TTAATTTAAAATAAAATATTTAAAATTTAA
* *
6555702 TTTA-TTGAAATAAAATATTTAAAATTTAA
1 TTAATTTAAAATAAAATATTTAAAATTTAA
*
6555731 ATAATT
1 TTAATT
6555737 ATTAAATTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 26 0.46
30 24 0.42
31 7 0.12
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (30 bp):
TTAATTTAAAATAAAATATTTAAAATTTAA
Found at i:6555999 original size:7 final size:7
Alignment explanation
Indices: 6555987--6556017 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
6555977 TTCCTTCTTT
6555987 AAAATGG
1 AAAATGG
6555994 AAAATGG
1 AAAATGG
6556001 AAAATGG
1 AAAATGG
6556008 AAAATGG
1 AAAATGG
6556015 AAA
1 AAA
6556018 TTCGATCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (7 bp):
AAAATGG
Found at i:6557255 original size:13 final size:13
Alignment explanation
Indices: 6557237--6557263 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6557227 GGACTTCAGT
6557237 TATCATCTAAGAG
1 TATCATCTAAGAG
6557250 TATCATCTAAGAG
1 TATCATCTAAGAG
6557263 T
1 T
6557264 TCTTTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TATCATCTAAGAG
Found at i:6565099 original size:83 final size:85
Alignment explanation
Indices: 6564998--6565163 Score: 196
Period size: 83 Copynumber: 2.0 Consensus size: 85
6564988 ATGTCAACAT
* * * *
6564998 AAAAAAATAAATAATTTATAATAA-TTTAAAATTTTCTAAAAACTTTTTTAAATATT-TAAAAGT
1 AAAAAAATAAATAATTTATAAAAATTTTAAAAATTT-T-AAAACTTTTTTAAAGATTATAAAAAT
6565061 TCAAAAAAATTATAAAAATTCA
64 TCAAAAAAATTATAAAAATTCA
* * *
6565083 AAAAAAAT-AAT-TTTTATAAAAATTTTAAAAATTTTAAAATTTTTTTAAAGCTTATAAAAATTC
1 AAAAAAATAAATAATTTATAAAAATTTTAAAAATTTTAAAACTTTTTTAAAGATTATAAAAATTC
* * *
6565146 TAACAAATTTTAAAAATT
66 AAAAAAATTATAAAAATT
6565164 TGTAAAGACT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
82 15 0.22
83 33 0.48
84 13 0.19
85 8 0.12
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (85 bp):
AAAAAAATAAATAATTTATAAAAATTTTAAAAATTTTAAAACTTTTTTAAAGATTATAAAAATTC
AAAAAAATTATAAAAATTCA
Found at i:6565164 original size:9 final size:9
Alignment explanation
Indices: 6565099--6565192 Score: 71
Period size: 9 Copynumber: 9.7 Consensus size: 9
6565089 ATAATTTTTA
6565099 TAAAAATTT
1 TAAAAATTT
6565108 TAAAAATTT
1 TAAAAATTT
*
6565117 TAAAATTTTTT
1 TAAAA--ATTT
** *
6565128 TAAAGCTTA
1 TAAAAATTT
*
6565137 TAAAAATTC
1 TAAAAATTT
6565146 TAACAAATTT
1 TAA-AAATTT
6565156 TAAAAATTT
1 TAAAAATTT
*
6565165 GTAAAGACTTTT
1 -TAAA-A-ATTT
6565177 TAAAAATTT
1 TAAAAATTT
6565186 ATAAAAA
1 -TAAAAA
6565193 AAATAAAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
9 34 0.50
10 19 0.28
11 12 0.18
12 3 0.04
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (9 bp):
TAAAAATTT
Found at i:6565274 original size:19 final size:18
Alignment explanation
Indices: 6565252--6565313 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
6565242 AAAAAAATTG
6565252 CAAAATTTAATAAAAAAT
1 CAAAATTTAATAAAAAAT
6565270 CCAAAATTT--TCAAAAAAT
1 -CAAAATTTAAT-AAAAAAT
*
6565288 GAAAATTTTAAT-AAAAAT
1 CAAAA-TTTAATAAAAAAT
*
6565306 TAAAATTT
1 CAAAATTT
6565314 TCTTATAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.22
18 20 0.54
19 8 0.22
20 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (18 bp):
CAAAATTTAATAAAAAAT
Found at i:6565284 original size:18 final size:17
Alignment explanation
Indices: 6565263--6565315 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
6565253 AAAATTTAAT
6565263 AAAAAATCCAAAATTTTC
1 AAAAAAT-CAAAATTTTC
* *
6565281 AAAAAATGAAAATTTTA
1 AAAAAATCAAAATTTTC
*
6565298 ATAAAAATTAAAATTTTC
1 A-AAAAATCAAAATTTTC
6565316 TTATAGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAAAATCAAAATTTTC
Found at i:6565292 original size:17 final size:18
Alignment explanation
Indices: 6565272--6565315 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
6565262 TAAAAAATCC
6565272 AAAATTTTCA-AAAAATG
1 AAAATTTTCATAAAAATG
* *
6565289 AAAATTTTAATAAAAATT
1 AAAATTTTCATAAAAATG
6565307 AAAATTTTC
1 AAAATTTTC
6565316 TTATAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATTTTCATAAAAATG
Found at i:6565382 original size:20 final size:21
Alignment explanation
Indices: 6565357--6565396 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
6565347 AAACTAAAAA
6565357 TTGAAAAAATCT-AAAATTTT
1 TTGAAAAAATCTGAAAATTTT
*
6565377 TTGAAAAAATTTGAAAATTT
1 TTGAAAAAATCTGAAAATTT
6565397 AAATATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (21 bp):
TTGAAAAAATCTGAAAATTTT
Found at i:6565509 original size:30 final size:29
Alignment explanation
Indices: 6565467--6565543 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
6565457 TATGAGTCAT
* * *
6565467 AAAAATTAAAAAAAAAACTTAAAA-TTTTG
1 AAAAATTTAAAAAAAAA-TGAAAATTTTTC
*
6565496 AAAAATATTAAAAAAATATGAAAATTTTTC
1 AAAAAT-TTAAAAAAAAATGAAAATTTTTC
6565526 AAAAATTTAAAAAAAAAT
1 AAAAATTTAAAAAAAAAT
6565544 TTTAATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAATTTAAAAAAAAATGAAAATTTTTC
Found at i:6565695 original size:22 final size:22
Alignment explanation
Indices: 6565666--6565720 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
6565656 TTAAAATCTT
6565666 AATTTTTAAAATTTTT-TTAAA
1 AATTTTTAAAATTTTTATTAAA
* * *
6565687 AGATTTTTAGAATTTTTATTTAG
1 A-ATTTTTAAAATTTTTATTAAA
6565710 AATTTTTAAAA
1 AATTTTTAAAA
6565721 AATTTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.04
22 23 0.82
23 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTTTTAAAATTTTTATTAAA
Found at i:6565708 original size:13 final size:13
Alignment explanation
Indices: 6565692--6565717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6565682 TTAAAAGATT
6565692 TTTAGAATTTTTA
1 TTTAGAATTTTTA
6565705 TTTAGAATTTTTA
1 TTTAGAATTTTTA
6565718 AAAAATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TTTAGAATTTTTA
Found at i:6566798 original size:17 final size:18
Alignment explanation
Indices: 6566776--6566812 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6566766 TTTTTTAATT
6566776 TAAAATT-TTTAAAAAAA
1 TAAAATTCTTTAAAAAAA
6566793 TAAAATTCTTTAAAAAAA
1 TAAAATTCTTTAAAAAAA
6566811 TA
1 TA
6566813 CTAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATTCTTTAAAAAAA
Found at i:6566914 original size:11 final size:10
Alignment explanation
Indices: 6566836--6566919 Score: 57
Period size: 11 Copynumber: 8.3 Consensus size: 10
6566826 AAATTTTGTT
6566836 AAAATTTTAA
1 AAAATTTTAA
6566846 AAAATTCTTAA
1 AAAATT-TTAA
*
6566857 AAAA-TTCAA
1 AAAATTTTAA
*
6566866 AACAATTTGAA
1 AA-AATTTTAA
*
6566877 AAATTTTTTAA
1 AAA-ATTTTAA
* *
6566888 AAAGTTTT-T
1 AAAATTTTAA
*
6566897 AATATTTATAA
1 AAAATTT-TAA
6566908 AAAA-TTTAA
1 AAAATTTTAA
6566917 AAA
1 AAA
6566920 TATTAATTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
9 16 0.28
10 17 0.29
11 25 0.43
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:6566921 original size:21 final size:21
Alignment explanation
Indices: 6566839--6566923 Score: 54
Period size: 21 Copynumber: 4.1 Consensus size: 21
6566829 TTTTGTTAAA
6566839 ATTT-TAAAAAATTCTTAAAAA-
1 ATTTATAAAAAA-T-TTAAAAAT
* *
6566860 ATTCA-AAACAATTTGAAAAAT
1 ATTTATAAAAAATTT-AAAAAT
* * **
6566881 -TTTTTAAAAAGTTT-TTAAT
1 ATTTATAAAAAATTTAAAAAT
6566900 ATTTATAAAAAATTTAAAAAT
1 ATTTATAAAAAATTTAAAAAT
6566921 ATT
1 ATT
6566924 AATTTTTTTA
Statistics
Matches: 46, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
19 5 0.11
20 20 0.43
21 21 0.46
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTATAAAAAATTTAAAAAT
Found at i:6566935 original size:27 final size:27
Alignment explanation
Indices: 6566894--6566954 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
6566884 TTAAAAAGTT
6566894 TTTAATATTTATAAAAAATT-TAAAAA
1 TTTAATATTTATAAAAAATTCTAAAAA
* *
6566920 TATTAATTTTTTTAAAAAATTCTAAAAA
1 T-TTAATATTTATAAAAAATTCTAAAAA
6566948 TTTAATA
1 TTTAATA
6566955 AAAAATCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 22 0.73
28 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTAATATTTATAAAAAATTCTAAAAA
Found at i:6567038 original size:9 final size:9
Alignment explanation
Indices: 6567026--6567101 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
6567016 AAAGAAATCA
6567026 TAAAAATTT
1 TAAAAATTT
6567035 TAAAAA--T
1 TAAAAATTT
**
6567042 TAAATTTTT
1 TAAAAATTT
6567051 TGAAAAATTT
1 T-AAAAATTT
*
6567061 TGAAAATTT
1 TAAAAATTT
*
6567070 TAAGAAA-AT
1 TAA-AAATTT
6567079 TAAAAATTT
1 TAAAAATTT
*
6567088 TTAAAATTT
1 TAAAAATTT
*
6567097 GAAAA
1 TAAAA
6567102 TAAAAGAAGA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
7 5 0.10
8 3 0.06
9 33 0.65
10 10 0.20
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (9 bp):
TAAAAATTT
Found at i:6567342 original size:26 final size:27
Alignment explanation
Indices: 6567276--6567342 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
6567266 TCATTTAGAC
6567276 TTTTAAGAAATTTTTATTTTTATTAAAAT
1 TTTTAA-AAA-TTTTATTTTTATTAAAAT
* * * *
6567305 CTTT-AAATTTTTATTTTT-TTGAATT
1 TTTTAAAAATTTTATTTTTATTAAAAT
6567330 TTTTAAAAATTTT
1 TTTTAAAAATTTT
6567343 GAAAATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
25 8 0.26
26 17 0.55
27 2 0.06
28 1 0.03
29 3 0.10
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (27 bp):
TTTTAAAAATTTTATTTTTATTAAAAT
Found at i:6567424 original size:10 final size:9
Alignment explanation
Indices: 6567398--6567423 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6567388 AATTTCCATA
6567398 ATTTTTTTG
1 ATTTTTTTG
6567407 ATTTTTTTG
1 ATTTTTTTG
6567416 ATTTTTTT
1 ATTTTTTT
6567424 TAAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.81
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:6567474 original size:21 final size:21
Alignment explanation
Indices: 6567421--6567473 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
6567411 TTTTGATTTT
* *
6567421 TTTTA-AAATTTTAGAATTTC
1 TTTTAGAATTTTTAGAATGTC
6567441 TTTTAGAATTTTTAGAA-GTC
1 TTTTAGAATTTTTAGAATGTC
*
6567461 TTTTAGATTTTTT
1 TTTTAGAATTTTT
6567474 TTTGAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTTAGAATTTTTAGAATGTC
Found at i:6568543 original size:12 final size:12
Alignment explanation
Indices: 6568526--6568550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6568516 CAAATAAACA
6568526 TTATCAATATAT
1 TTATCAATATAT
6568538 TTATCAATATAT
1 TTATCAATATAT
6568550 T
1 T
6568551 GAAAGGTTTA
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATCAATATAT
Found at i:6570441 original size:40 final size:40
Alignment explanation
Indices: 6570396--6570485 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 40
6570386 AAACAAGAAC
* *
6570396 ACAATCTCTTTAA-ATAATCAAAGCTACCCTTTTACAATTG
1 ACAATCTCTTTAATA-AATCAAAGATACCCTTTTACAAGTG
6570436 ACAATCTC-TTAATGAAATCAAAGATACCCTTTTACAAGTG
1 ACAATCTCTTTAAT-AAATCAAAGATACCCTTTTACAAGTG
*
6570476 ATAATCTCTT
1 ACAATCTCTT
6570486 AATGAAGGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 4 0.09
40 38 0.86
41 2 0.05
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (40 bp):
ACAATCTCTTTAATAAATCAAAGATACCCTTTTACAAGTG
Found at i:6570486 original size:40 final size:40
Alignment explanation
Indices: 6570411--6570491 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
6570401 CTCTTTAAAT
* *
6570411 AATCAAAGCTACCCTTTTACAATTGACAATCTCTTAATGA
1 AATCAAAGATACCCTTTTACAAGTGACAATCTCTTAATGA
*
6570451 AATCAAAGATACCCTTTTACAAGTGATAATCTCTTAATGA
1 AATCAAAGATACCCTTTTACAAGTGACAATCTCTTAATGA
6570491 A
1 A
6570492 GGATCATGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (40 bp):
AATCAAAGATACCCTTTTACAAGTGACAATCTCTTAATGA
Found at i:6573518 original size:64 final size:65
Alignment explanation
Indices: 6573450--6573572 Score: 221
Period size: 65 Copynumber: 1.9 Consensus size: 65
6573440 AAAAAAACTA
*
6573450 TCCACTGATTTGAA-ATTTTTAAATATAATTTTTATTTTCTTTTCACCCACTATGGTTGCTTTAT
1 TCCACTCATTTGAATATTTTTAAATATAATTTTTATTTTCTTTTCACCCACTATGGTTGCTTTAT
*
6573514 TCCACTCATTTGAATTTTTTTAAATATAATTTTTATTTTCTTTTCACCCACTATGGTTG
1 TCCACTCATTTGAATATTTTTAAATATAATTTTTATTTTCTTTTCACCCACTATGGTTG
6573573 TGTCAAATCT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 13 0.23
65 43 0.77
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.52
Consensus pattern (65 bp):
TCCACTCATTTGAATATTTTTAAATATAATTTTTATTTTCTTTTCACCCACTATGGTTGCTTTAT
Found at i:6574301 original size:23 final size:23
Alignment explanation
Indices: 6574274--6574337 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 23
6574264 CCGGTTTTGT
6574274 TTTATCTTTATTTTGATTAAGTC
1 TTTATCTTTATTTTGATTAAGTC
* * *
6574297 TTTA---TT-TTTGGCTT-TGT-
1 TTTATCTTTATTTTGATTAAGTC
6574314 TTTATCTTTATTTTGATTAAGTC
1 TTTATCTTTATTTTGATTAAGTC
6574337 T
1 T
6574338 AAAATAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
17 4 0.14
18 2 0.07
19 6 0.21
20 4 0.14
21 6 0.21
22 2 0.07
23 5 0.17
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (23 bp):
TTTATCTTTATTTTGATTAAGTC
Found at i:6575026 original size:39 final size:39
Alignment explanation
Indices: 6574982--6575063 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
6574972 GCCAAGTATT
6574982 TGGTTGTGATTATTTTGCTTAATAAAGAGTCTCTGCCTC
1 TGGTTGTGATTATTTTGCTTAATAAAGAGTCTCTGCCTC
* *
6575021 TGGTTGTGGTTATTTTGCTTAATAAAGAGTCTTTGCCTC
1 TGGTTGTGATTATTTTGCTTAATAAAGAGTCTCTGCCTC
6575060 TGGT
1 TGGT
6575064 GGTTCAACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.45
Consensus pattern (39 bp):
TGGTTGTGATTATTTTGCTTAATAAAGAGTCTCTGCCTC
Found at i:6594269 original size:2 final size:2
Alignment explanation
Indices: 6594258--6594307 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
6594248 AGGTGTCTTT
* *
6594258 TA TA -A TA TA TA TA TA TA TA TA TA TG TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6594299 TA TA T- TA TA
1 TA TA TA TA TA
6594308 CCTGTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6594486 original size:2 final size:2
Alignment explanation
Indices: 6594479--6594504 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6594469 TTAATTCAGC
6594479 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6594505 GGGTTTCTTT
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):
TA
Found at i:6594793 original size:15 final size:15
Alignment explanation
Indices: 6594773--6594802 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6594763 AATATATCCA
*
6594773 TTTATCTATAAAACC
1 TTTATCAATAAAACC
6594788 TTTATCAATAAAACC
1 TTTATCAATAAAACC
6594803 CTATAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTATCAATAAAACC
Found at i:6600411 original size:2 final size:2
Alignment explanation
Indices: 6600406--6600432 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6600396 AAATTTTGAA
6600406 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6600433 GAGCAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6601046 original size:17 final size:16
Alignment explanation
Indices: 6601015--6601053 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
6601005 GTTGGCAACA
6601015 ATATTTTAATTTAAAT
1 ATATTTTAATTTAAAT
*
6601031 ATATTATTATTTTAAAT
1 ATATT-TTAATTTAAAT
*
6601048 AAATTT
1 ATATTT
6601054 CTTAATAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTTAATTTAAAT
Found at i:6601727 original size:22 final size:23
Alignment explanation
Indices: 6601710--6601755 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
6601700 TGAATATATT
6601710 TTGTTTTT-TTAAATAATATACA
1 TTGTTTTTCTTAAATAATATACA
*
6601732 TTGTTTTTCTTAAA-AAAATACA
1 TTGTTTTTCTTAAATAATATACA
6601754 TT
1 TT
6601756 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (23 bp):
TTGTTTTTCTTAAATAATATACA
Found at i:6601761 original size:22 final size:23
Alignment explanation
Indices: 6601713--6601766 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
6601703 ATATATTTTG
* *
6601713 TTTTTTTAAATAATATACATT-G
1 TTTTTTTAAATAAAATACATTAA
6601735 TTTTTCTTAAA-AAAATACATTAA
1 TTTTT-TTAAATAAAATACATTAA
6601758 TTTTTTTAA
1 TTTTTTTAA
6601767 TACATCTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTTTTAAATAAAATACATTAA
Found at i:6622620 original size:12 final size:12
Alignment explanation
Indices: 6622600--6622636 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
6622590 AAATTTGTTA
6622600 TTTTT-ATATAT
1 TTTTTAATATAT
*
6622611 TTTTTAATATAA
1 TTTTTAATATAT
6622623 TTTTTAATATAT
1 TTTTTAATATAT
6622635 TT
1 TT
6622637 AAATAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAATATAT
Found at i:6622632 original size:22 final size:22
Alignment explanation
Indices: 6622599--6622646 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
6622589 TAAATTTGTT
* *
6622599 ATTTTTATATATTTTTTAATATA
1 ATTTTTATATATATTTAAATA-A
6622622 ATTTTTA-ATATATTTAAATAA
1 ATTTTTATATATATTTAAATAA
6622643 ATTT
1 ATTT
6622647 AAATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 11 0.48
23 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTTATATATATTTAAATAA
Found at i:6622651 original size:20 final size:21
Alignment explanation
Indices: 6622613--6622653 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6622603 TTATATATTT
* *
6622613 TTTAATATAATTTTTAATATA
1 TTTAATATAAATTTAAATATA
6622634 TTTAA-ATAAATTTAAATATA
1 TTTAATATAAATTTAAATATA
6622654 AAATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATATAAATTTAAATATA
Found at i:6622660 original size:37 final size:38
Alignment explanation
Indices: 6622619--6622696 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 38
6622609 ATTTTTTAAT
6622619 ATAATT-TTTAATATATTTA-AATAAATTT-AAATATA-AA
1 ATAATTATTT-ATAT-TTTATAA-AAATTTGAAATATACAA
*
6622656 ATAATTATTTTTATTTTATAAAAATTTGAAATATACAA
1 ATAATTATTTATATTTTATAAAAATTTGAAATATACAA
6622694 ATA
1 ATA
6622697 TTAATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
36 10 0.28
37 18 0.50
38 8 0.22
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (38 bp):
ATAATTATTTATATTTTATAAAAATTTGAAATATACAA
Found at i:6622741 original size:15 final size:17
Alignment explanation
Indices: 6622722--6622763 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
6622712 AATTTAATTC
6622722 AATTTAATTTTTAA-CT
1 AATTTAATTTTTAATCT
6622738 -ATTT-ATTTTTAATCT
1 AATTTAATTTTTAATCT
6622753 AAATTTAATTT
1 -AATTTAATTT
6622764 ATATTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.36
15 6 0.27
17 4 0.18
18 4 0.18
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTAATTTTTAATCT
Found at i:6622787 original size:11 final size:11
Alignment explanation
Indices: 6622745--6622792 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
6622735 ACTATTTATT
*
6622745 TTTAATCTAAA
1 TTTAATTTAAA
*
6622756 TTTAATTTATA
1 TTTAATTTAAA
6622767 TTTAATATTTAAA
1 TTT-A-ATTTAAA
*
6622780 TTTAATTTGAA
1 TTTAATTTAAA
6622791 TT
1 TT
6622793 AAATAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 20 0.65
12 2 0.06
13 9 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:6622797 original size:24 final size:24
Alignment explanation
Indices: 6622752--6622797 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6622742 ATTTTTAATC
*
6622752 TAAATTTAATTTATATTTAATATT
1 TAAATTTAATTTATATTAAATATT
6622776 TAAATTTAATTTGA-ATTAAATA
1 TAAATTTAATTT-ATATTAAATA
6622798 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TAAATTTAATTTATATTAAATATT
Found at i:6623007 original size:12 final size:13
Alignment explanation
Indices: 6622974--6623007 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
6622964 TATTAATTTT
6622974 AAATTATTTTAAA
1 AAATTATTTTAAA
6622987 AAATATATTTT-AA
1 AAAT-TATTTTAAA
6623000 AAATTATT
1 AAATTATT
6623008 AAATTATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 10 0.50
14 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTATTTTAAA
Found at i:6627914 original size:16 final size:16
Alignment explanation
Indices: 6627890--6627925 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6627880 AATATTTAAC
*
6627890 AAAACAAAACAAAAAG
1 AAAAAAAAACAAAAAG
*
6627906 AAAAAAAAACAAAACG
1 AAAAAAAAACAAAAAG
6627922 AAAA
1 AAAA
6627926 TCAGACAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAAAG
Found at i:6628101 original size:22 final size:22
Alignment explanation
Indices: 6628054--6628096 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6628044 CTCCTGCCAG
* *
6628054 CCACCCTACAGCTACCAACTAA
1 CCACCCTACAGCCACCAAATAA
6628076 CCACCCTACAGCCAGCCAAAT
1 CCACCCTACAGCCA-CCAAAT
6628097 CCCACTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.35, C:0.47, G:0.07, T:0.12
Consensus pattern (22 bp):
CCACCCTACAGCCACCAAATAA
Found at i:6628325 original size:12 final size:12
Alignment explanation
Indices: 6628308--6628344 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6628298 ATCTGCCGCA
*
6628308 CAAAAAAAATTT
1 CAAAAAAAATAT
6628320 CAAAAAAAATAT
1 CAAAAAAAATAT
6628332 -AAAAAAAA-AT
1 CAAAAAAAATAT
6628342 CAA
1 CAA
6628345 CACAGTCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 2 0.09
11 10 0.43
12 11 0.48
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
CAAAAAAAATAT
Found at i:6630907 original size:19 final size:20
Alignment explanation
Indices: 6630883--6630927 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
6630873 TTATTTAGAT
6630883 AATATCCTTTTAAATTTT-A
1 AATATCCTTTTAAATTTTAA
6630902 AATATCCTTTTAAATTTTAA
1 AATATCCTTTTAAATTTTAA
6630922 AATATC
1 AATATC
6630928 AATTGTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATCCTTTTAAATTTTAA
Found at i:6639939 original size:20 final size:20
Alignment explanation
Indices: 6639911--6639949 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6639901 TAAATCATTG
* *
6639911 TTTATAATTTAATACTATTA
1 TTTAAAATTTAAAACTATTA
6639931 TTTAAAATTTAAAACTATT
1 TTTAAAATTTAAAACTATT
6639950 TCATTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAATTTAAAACTATTA
Found at i:6642181 original size:23 final size:22
Alignment explanation
Indices: 6642155--6642197 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6642145 TGTAAAATGA
*
6642155 GATACACGGAAATTGAGAAATTG
1 GATACA-GGAAAATGAGAAATTG
*
6642178 GATAGAGGAAAATGAGAAAT
1 GATACAGGAAAATGAGAAAT
6642198 CAAAACCGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.28, T:0.19
Consensus pattern (22 bp):
GATACAGGAAAATGAGAAATTG
Found at i:6646815 original size:2 final size:2
Alignment explanation
Indices: 6646808--6646837 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6646798 TAAAATATGA
6646808 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
6646838 CTGCTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6657009 original size:1 final size:1
Alignment explanation
Indices: 6657003--6657029 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6656993 ATTTTCTTTC
6657003 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
6657030 GCAGAGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6657363 original size:32 final size:31
Alignment explanation
Indices: 6657297--6657364 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
6657287 TATTTTTTAT
* * *
6657297 ATTTTCACATCAATATAAATTATAATACATA
1 ATTTTCACATAAATATAAATAAAAATACATA
*
6657328 ATTTTCACATAAA-ATATAATAAAAATATATAA
1 ATTTTCACATAAATATA-AATAAAAATACAT-A
6657360 ATTTT
1 ATTTT
6657365 AATATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 3 0.10
31 22 0.71
32 6 0.19
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTTTCACATAAATATAAATAAAAATACATA
Found at i:6658499 original size:72 final size:71
Alignment explanation
Indices: 6658423--6658982 Score: 327
Period size: 71 Copynumber: 7.9 Consensus size: 71
6658413 ATATCCAATG
*
6658423 TATTTTTTATTTTAAAAACACGATCTTTATTAAATTTTCAAATTTTTAAAAATAAAGTTTCAACA
1 TATTTTTTATTTTAAAAACACGATCTTTGTTAAATTTTCAAA-TTTTAAAAATAAAGTTTCAACA
6658488 TCCACTA
65 TCCACTA
** ** * * *
6658495 TA-TTTTTATCTTTAAAATGAAAAT-TTTGTTAAAAATTTTAAAATTTTAAAAAGAAAATTTCAA
1 TATTTTTTAT-TTTAAAAACACGATCTTTGTT--AAATTTTCAAATTTTAAAAATAAAGTTTCAA
* * *
6658558 TATTCATTA
63 CATCCACTA
** * * * *
6658567 CGTTTTTTATCTTAAAAACACAAAT-TTTGTTAAA-TTCCATAATTTTGAAAATAAAGTTTCAAC
1 TATTTTTTATTTTAAAAACAC-GATCTTTGTTAAATTTTCA-AATTTTAAAAATAAAGTTTCAAC
*
6658630 ATCAACTA
64 ATCCACTA
* * ** * *
6658638 TGTTTTTTATCTTAAAAATGC-ATTCTTTGTTAAAATTTTAAAATTTTGAAAATGAAA-TTTCAA
1 TATTTTTTATTTTAAAAACACGA-TCTTTGTT-AAATTTTCAAATTTTAAAAAT-AAAGTTTCAA
6658701 CATCCACTA
63 CATCCACTA
* * * * * * *
6658710 CTTTTTTTTTAATCTAAAAACACTG-TCTATATTCAAA-TTTCATAATTTCAAAAATAATGTTTC
1 --TATTTTTTATTTTAAAAACAC-GATCTTTGTT-AAATTTTCA-AATTTTAAAAATAAAGTTTC
*
6658773 AA-A---A-TC
61 AACATCCACTA
* * * **
6658779 TA--TTTT-TTTTAAAATGCA--ATTTTTGTTAAA-ATTCAAGAATTTCGAAAATAAAGTTTCAA
1 TATTTTTTATTTTAAAA-ACACGATCTTTGTTAAATTTTC-A-AATTTTAAAAATAAAGTTTCAA
*
6658838 CATCCCCTA
63 CATCCACTA
* * ** * * * * *
6658847 TATTTCTTATCTTAAAAACTTGGTTTTTGTTAAATTTT-AAATTTTTGAAAATAAACTTTCAATA
1 TATTTTTTATTTTAAAAACACGATCTTTGTTAAATTTTCAAA-TTTTAAAAATAAAGTTTCAACA
6658911 TCCACTA
65 TCCACTA
* * * *
6658918 CA-TTCTTATTTTAAAAATGA-GATCTTTGTTAAAATTTCATAATTTTAAAAATAAAGTTTCAAC
1 TATTTTTTATTTTAAAAA-CACGATCTTTGTTAAATTTTCA-AATTTTAAAAATAAAGTTTCAAC
6658981 AT
64 AT
6658983 ACATTAGTTT
Statistics
Matches: 374, Mismatches: 79, Indels: 71
0.71 0.15 0.14
Matches are distributed among these distances:
62 6 0.02
63 26 0.07
64 7 0.02
65 6 0.02
67 1 0.00
68 3 0.01
69 2 0.01
70 39 0.10
71 118 0.32
72 85 0.23
73 41 0.11
74 40 0.11
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (71 bp):
TATTTTTTATTTTAAAAACACGATCTTTGTTAAATTTTCAAATTTTAAAAATAAAGTTTCAACAT
CCACTA
Found at i:6658696 original size:143 final size:144
Alignment explanation
Indices: 6658425--6658774 Score: 367
Period size: 143 Copynumber: 2.4 Consensus size: 144
6658415 ATCCAATGTA
* * *
6658425 TTTTTTATTTTAAAAACACGATCTTTATTAAATTTTCAAATTTTTAAAAATAAAGTTTCAACATC
1 TTTTTTATCTTAAAAACACAATCTTTATTAAATTTCCAAATTTTTAAAAATAAAGTTTCAACATC
* *
6658490 CACTATATTTTTATCTTTAAAATGAAAATTTTGTTAAAAATTTTAAAATTTTAAAAAGAAAATTT
66 AACTATATTTTTATCTTAAAAATGAAAATTTTGTTAAAAATTTTAAAATTTTAAAAAGAAAATTT
6658555 CAATATTCATTACG
131 CAATATTCATTACG
* *
6658569 TTTTTTATCTTAAAAACACAAAT-TTTGTTAAA-TTCCATAA-TTTTGAAAATAAAGTTTCAACA
1 TTTTTTATCTTAAAAACAC-AATCTTTATTAAATTTCCA-AATTTTTAAAAATAAAGTTTCAACA
* * * *
6658631 TCAACTATGTTTTTTATCTTAAAAATG-CATTCTTTGTT-AAAATTTTAAAATTTTGAAAATG-A
64 TCAACTAT-ATTTTTATCTTAAAAATGAAAAT-TTTGTTAAAAATTTTAAAATTTT-AAAAAGAA
* * * *
6658693 AATTTCAACATCCACTACTTT
126 AATTTCAATATTCATTAC--G
** * * *
6658714 TTTTTTAATC-TAAAAACACTGTCTATATTCAAATTT-CATAA-TTTCAAAAATAATGTTTCAA
1 TTTTTT-ATCTTAAAAACACAATCTTTATT-AAATTTCCA-AATTTTTAAAAATAAAGTTTCAA
6658775 AATCTATTTT
Statistics
Matches: 173, Mismatches: 22, Indels: 20
0.80 0.10 0.09
Matches are distributed among these distances:
143 66 0.38
144 56 0.32
145 21 0.12
146 28 0.16
147 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.44
Consensus pattern (144 bp):
TTTTTTATCTTAAAAACACAATCTTTATTAAATTTCCAAATTTTTAAAAATAAAGTTTCAACATC
AACTATATTTTTATCTTAAAAATGAAAATTTTGTTAAAAATTTTAAAATTTTAAAAAGAAAATTT
CAATATTCATTACG
Found at i:6659461 original size:17 final size:17
Alignment explanation
Indices: 6659439--6659471 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6659429 AGAAAAAGAC
6659439 TTTTTTACCTTTTTAAA
1 TTTTTTACCTTTTTAAA
*
6659456 TTTTTTACTTTTTTAA
1 TTTTTTACCTTTTTAA
6659472 TAATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTACCTTTTTAAA
Found at i:6661479 original size:80 final size:80
Alignment explanation
Indices: 6661343--6661506 Score: 231
Period size: 80 Copynumber: 2.0 Consensus size: 80
6661333 GAGTGTGGTA
* **
6661343 TTTAGGACAATCGATTTAGAAAGTACAATCAATTAGGGGTTTTGTGTTTACGGCAATCGACTA-G
1 TTTAGGACAATCGATTTAGAAAGTACAATCAATAAGGGGTTTTGTGTTTAAAGCAATCGA-TAGG
*
6661407 TCTTTGAAATTGGGGG
65 CCTTTGAAATTGGGGG
* ** *
6661423 TTTAGGACAATCGATTTAGAAAGTGCAATTGATAAGGGGTTTTGTGTTTAAAGCAATTGATAGGC
1 TTTAGGACAATCGATTTAGAAAGTACAATCAATAAGGGGTTTTGTGTTTAAAGCAATCGATAGGC
*
6661488 CTTTGAAATTGGGGT
66 CTTTGAAATTGGGGG
6661503 TTTA
1 TTTA
6661507 TATTAGTGAC
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 2 0.03
80 72 0.97
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (80 bp):
TTTAGGACAATCGATTTAGAAAGTACAATCAATAAGGGGTTTTGTGTTTAAAGCAATCGATAGGC
CTTTGAAATTGGGGG
Found at i:6665807 original size:3 final size:3
Alignment explanation
Indices: 6665799--6665920 Score: 103
Period size: 3 Copynumber: 40.7 Consensus size: 3
6665789 AAAATAAATA
*
6665799 AAT AAT AAT -AT AAT AA- AAT AACT AAT GAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT
* **
6665844 AAAT AA- AAT AAAT AAT AA- ACAA AAT AAT AAT AAT AAT AAT GCT AAT
1 -AAT AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
*
6665890 AAT AAT AAT AAAT AAA AAT AA- AAT AA- AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
6665921 AAAAATGTGG
Statistics
Matches: 99, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
2 11 0.11
3 71 0.72
4 17 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:6665880 original size:50 final size:49
Alignment explanation
Indices: 6665790--6665920 Score: 157
Period size: 50 Copynumber: 2.7 Consensus size: 49
6665780 AAAAAAGATA
*
6665790 AAATAAATAAAT-AATAATATAATAAAATAACTAATGATAATAATAATAAT
1 AAATAAATAAATAAATAATA-AATAAAATAA-TAATAATAATAATAATAAT
* **
6665840 AAATAAATAAAATAAATAATAAACAAAATAATAATAATAATAATGCTAAT
1 AAATAAAT-AAATAAATAATAAATAAAATAATAATAATAATAATAATAAT
6665890 -AAT-AAT-AATAAATAA-AAATAAAATAA-AATAA
1 AAATAAATAAATAAATAATAAATAAAATAATAATAA
6665921 AAAAATGTGG
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
44 5 0.07
45 10 0.14
46 9 0.12
48 3 0.04
49 3 0.04
50 24 0.32
51 13 0.18
52 7 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (49 bp):
AAATAAATAAATAAATAATAAATAAAATAATAATAATAATAATAATAAT
Found at i:6665884 original size:59 final size:60
Alignment explanation
Indices: 6665787--6665921 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 60
6665777 AGAAAAAAAG
* *
6665787 ATAAAATAAATAAATAATAATATAATAAAATAACTAATGATAATAATAATAATAAAT-AA
1 ATAAAATAAATAAATAACAAAATAATAAAATAACTAATGATAATAATAATAATAAATAAA
*
6665846 ATAAAATAAAT-AATAAACAAAATAATAATAATAA-TAATGCTAATAATAATAATAAATAAAA
1 ATAAAATAAATAAAT-AACAAAATAATAA-AATAACTAATGATAATAATAATAATAAAT-AAA
6665907 ATAAAATAAAATAAA
1 ATAAAAT-AAATAAA
6665922 AAAATGTGGG
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
58 3 0.04
59 44 0.66
60 5 0.07
61 9 0.13
62 4 0.06
63 2 0.03
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.27
Consensus pattern (60 bp):
ATAAAATAAATAAATAACAAAATAATAAAATAACTAATGATAATAATAATAATAAATAAA
Found at i:6667028 original size:13 final size:12
Alignment explanation
Indices: 6667008--6667047 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
6666998 TTAAATTTTT
*
6667008 TTTAA-AAATAA
1 TTTAATAAAAAA
*
6667019 TTTAATAAAAAT
1 TTTAATAAAAAA
6667031 TTTAATAAAAAA
1 TTTAATAAAAAA
6667043 TTTAA
1 TTTAA
6667048 ATTGATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTTAATAAAAAA
Found at i:6677721 original size:15 final size:15
Alignment explanation
Indices: 6677701--6677731 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6677691 ATTCAGTTCG
6677701 ACTCTAAAATAATCA
1 ACTCTAAAATAATCA
6677716 ACTCTAAAATAATCA
1 ACTCTAAAATAATCA
6677731 A
1 A
6677732 AAGTTAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (15 bp):
ACTCTAAAATAATCA
Found at i:6678293 original size:12 final size:12
Alignment explanation
Indices: 6678276--6678300 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6678266 CATTATTTTT
6678276 ATTAAATTTTGA
1 ATTAAATTTTGA
6678288 ATTAAATTTTGA
1 ATTAAATTTTGA
6678300 A
1 A
6678301 AAATATATTT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATTAAATTTTGA
Found at i:6678358 original size:37 final size:37
Alignment explanation
Indices: 6678317--6678389 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
6678307 ATTTTTCATG
*
6678317 TTTTCAACAAAAATTATATTCTTATCTTAGAAACATC
1 TTTTCAACAAAAATAATATTCTTATCTTAGAAACATC
*
6678354 TTTTCAACAAAAATAATATTTTTATCTTAGAAACAT
1 TTTTCAACAAAAATAATATTCTTATCTTAGAAACAT
6678390 TGTCTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (37 bp):
TTTTCAACAAAAATAATATTCTTATCTTAGAAACATC
Found at i:6678685 original size:77 final size:77
Alignment explanation
Indices: 6678586--6678748 Score: 188
Period size: 77 Copynumber: 2.2 Consensus size: 77
6678576 AAATTTTGTC
* * * *
6678586 TTTTCAACAAAAATTACGTTTTTTATCTAAAAAATGTCATTTTTGTAAAATTTTGAAAGATAATT
1 TTTTCAACAAAAATCACGTTTTTTATCTAAAAAATGTCATTTTTGTAAAATTATGAAAAATAAAT
6678651 TTTTTTTTCATA
66 TTTTTTTTCATA
* * * * * * **
6678663 TTTTTAACAAAAATCATGTTTTTTGTTTTAAAAATGTTATTTTTGTTGAATTATGAAAAATAAA-
1 TTTTCAACAAAAATCACGTTTTTTATCTAAAAAATGTCATTTTTGTAAAATTATGAAAAATAAAT
*
6678727 --TTTTTTCATC
66 TTTTTTTTCATA
6678737 TTTTCAACAAAA
1 TTTTCAACAAAA
6678749 TTGTGTTTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
74 20 0.28
77 52 0.72
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (77 bp):
TTTTCAACAAAAATCACGTTTTTTATCTAAAAAATGTCATTTTTGTAAAATTATGAAAAATAAAT
TTTTTTTTCATA
Found at i:6686483 original size:3 final size:3
Alignment explanation
Indices: 6686475--6686500 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6686465 GCAGTACGAT
6686475 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
6686501 TAAAAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:6688219 original size:2 final size:2
Alignment explanation
Indices: 6688212--6688240 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6688202 TAGTTATAGT
6688212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6688241 TGATAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6688561 original size:26 final size:27
Alignment explanation
Indices: 6688532--6688597 Score: 71
Period size: 30 Copynumber: 2.4 Consensus size: 27
6688522 ATATAAAAAT
*
6688532 TTATTTTTAATTAAT-TAATTAATTAA
1 TTATTTTTAATTAATATAATTAAATAA
*
6688558 TTATTTATATATATTTATATAATTAAATAA
1 TTATTT-T-TA-ATTAATATAATTAAATAA
*
6688588 TTATATTTAA
1 TTATTTTTAA
6688598 AAAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 6 0.18
27 2 0.06
28 4 0.12
29 6 0.18
30 15 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATTTTTAATTAATATAATTAAATAA
Found at i:6688614 original size:21 final size:22
Alignment explanation
Indices: 6688588--6688634 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
6688578 AATTAAATAA
6688588 TTATA-TTTAAAAAATAATATT
1 TTATATTTTAAAAAATAATATT
6688609 TTATATTTTAAAAAATAATATT
1 TTATATTTTAAAAAATAATATT
6688631 TTAT
1 TTAT
6688635 TAATTTCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATATTTTAAAAAATAATATT
Found at i:6691436 original size:20 final size:21
Alignment explanation
Indices: 6691411--6691467 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
6691401 AATAAAAATA
6691411 TATAAAAATAAAATA-ATTTT
1 TATAAAAATAAAATATATTTT
*
6691431 TATAAAAATTATAATATATTTT
1 TATAAAAA-TAAAATATATTTT
6691453 T-T-AAAATAAAATATA
1 TATAAAAATAAAATATA
6691468 AATTTTAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 8 0.24
20 12 0.36
21 7 0.21
22 6 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TATAAAAATAAAATATATTTT
Found at i:6691910 original size:21 final size:22
Alignment explanation
Indices: 6691861--6691914 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
6691851 TCCAAAATTA
*
6691861 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAG
6691883 ATAAAATATTATTTTTTAAAAG
1 ATAAAATATTATTTTTTAAAAG
6691905 ATAAATATAT
1 ATAAA-ATAT
6691915 AAATATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAG
Done.