Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 62 of 147
Found at i:11717912 original size:22 final size:22
Alignment explanation
Indices: 11717879--11717978 Score: 155
Period size: 22 Copynumber: 4.5 Consensus size: 22
11717869 CTAAATGTTG
* *
11717879 GATGTGAATCTTATGATTTACA
1 GATGCGAATCTTATGATTTGCA
* *
11717901 GATACGAATCTTATGATTTGTA
1 GATGCGAATCTTATGATTTGCA
11717923 GATGCGAATCTTATGATTTGCA
1 GATGCGAATCTTATGATTTGCA
11717945 GATGCGAATCTTATGATTTGCA
1 GATGCGAATCTTATGATTTGCA
*
11717967 AATGCGAATCTT
1 GATGCGAATCTT
11717979 GAAATTTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (22 bp):
GATGCGAATCTTATGATTTGCA
Found at i:11718062 original size:19 final size:19
Alignment explanation
Indices: 11718038--11718110 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
11718028 TTTTAGTAAA
11718038 TTCTTGCGAAGCTGAAAGG
1 TTCTTGCGAAGCTGAAAGG
11718057 TTCTTGCGAAGCTGAAAGG
1 TTCTTGCGAAGCTGAAAGG
11718076 TTCTTGCGAAGCTGAAAGG
1 TTCTTGCGAAGCTGAAAGG
* *
11718095 TTATTGCGAATCTGAA
1 TTCTTGCGAAGCTGAA
11718111 CCTTTGATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (19 bp):
TTCTTGCGAAGCTGAAAGG
Found at i:11718496 original size:7 final size:7
Alignment explanation
Indices: 11718479--11718507 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
11718469 ATGTTTGTTA
11718479 TTTTA-T
1 TTTTATT
11718485 TTTTATT
1 TTTTATT
11718492 TTTTATT
1 TTTTATT
11718499 TTTTATT
1 TTTTATT
11718506 TT
1 TT
11718508 ATTTTAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTATT
Found at i:11718497 original size:13 final size:12
Alignment explanation
Indices: 11718476--11718512 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
11718466 TACATGTTTG
11718476 TTATTTTATTTT
1 TTATTTTATTTT
*
11718488 TATTTTTTATTTT
1 T-TATTTTATTTT
11718501 TTATTTTATTTT
1 TTATTTTATTTT
11718513 AGGATAATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:11719749 original size:178 final size:177
Alignment explanation
Indices: 11719424--11719752 Score: 420
Period size: 178 Copynumber: 1.8 Consensus size: 177
11719414 TAAAAAATAA
** * *
11719424 AAAAAAAATAAAATTTTGAGAATAAATATTAATTATCCAATGATGGAATTTATAGAAATTTCAAA
1 AAAAAAAATAAAATTTTGAGAATAAATACAAATGATCCAAGGATGGAATTTATAGAAATTTCAAA
** * *
11719489 TGGTAAATTTTTTTATAAAATTCTTAGGTGAGAAATTTGTCTAAATTTATCCCAAATGGTAGAAT
66 TGGTAAA-TTTCCTATAAAATTCTTAAGTGAGAAATTTATCTAAATTTATCCCAAATGGTAGAAT
11719554 AATTTAGATAAAGTTTCAATATCAATAATTAATATTTATTTCAAACAT
130 AATTTAGATAAAGTTTCAATATCAATAATTAATATTTATTTCAAACAT
*
11719602 AAAAAATATAAAAATTTTGA-AATTAAATACAAATGATCCAAGGAT-GAGATTCT-TAGAAATTT
1 AAAAAAAAT-AAAATTTTGAGAA-TAAATACAAATGATCCAAGGATGGA-ATT-TATAGAAATTT
* *
11719664 CAAATGGTAAA-TTCCTA-AGAAA-TCTCTAAGTGAGAAATTTTATCTAAATTTATCTCAAATTG
62 CAAATGGTAAATTTCCTATA-AAATTCT-TAAGTGAGAAA-TTTATCTAAATTTATCCCAAATGG
*
11719726 T-GAAATAATTTAGATGAAGTTTCAATA
124 TAG-AATAATTTAGATAAAGTTTCAATA
11719753 AAAGTAATTG
Statistics
Matches: 131, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
176 4 0.03
177 18 0.14
178 57 0.44
179 51 0.39
180 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (177 bp):
AAAAAAAATAAAATTTTGAGAATAAATACAAATGATCCAAGGATGGAATTTATAGAAATTTCAAA
TGGTAAATTTCCTATAAAATTCTTAAGTGAGAAATTTATCTAAATTTATCCCAAATGGTAGAATA
ATTTAGATAAAGTTTCAATATCAATAATTAATATTTATTTCAAACAT
Found at i:11720787 original size:109 final size:109
Alignment explanation
Indices: 11720649--11720869 Score: 442
Period size: 109 Copynumber: 2.0 Consensus size: 109
11720639 AGGGTTTATA
11720649 AATCTTATGACTAAATTTATTTACTTTACTATTTTTAAATTTAATATTTTTTTATCAAAATAATA
1 AATCTTATGACTAAATTTATTTACTTTACTATTTTTAAATTTAATATTTTTTTATCAAAATAATA
11720714 ACTTAACTTGACTAATAAAAATGGATATATTTGTTTTCTTGTAC
66 ACTTAACTTGACTAATAAAAATGGATATATTTGTTTTCTTGTAC
11720758 AATCTTATGACTAAATTTATTTACTTTACTATTTTTAAATTTAATATTTTTTTATCAAAATAATA
1 AATCTTATGACTAAATTTATTTACTTTACTATTTTTAAATTTAATATTTTTTTATCAAAATAATA
11720823 ACTTAACTTGACTAATAAAAATGGATATATTTGTTTTCTTGTAC
66 ACTTAACTTGACTAATAAAAATGGATATATTTGTTTTCTTGTAC
11720867 AAT
1 AAT
11720870 AACTATTTAA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 112 1.00
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.48
Consensus pattern (109 bp):
AATCTTATGACTAAATTTATTTACTTTACTATTTTTAAATTTAATATTTTTTTATCAAAATAATA
ACTTAACTTGACTAATAAAAATGGATATATTTGTTTTCTTGTAC
Found at i:11721233 original size:2 final size:2
Alignment explanation
Indices: 11721221--11721255 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
11721211 GGATAATGTT
*
11721221 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11721256 AACTCGATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11724321 original size:17 final size:18
Alignment explanation
Indices: 11724288--11724322 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
11724278 TCATGTTCAT
*
11724288 ATTTAAGTTATTTATGTC
1 ATTTAAGTTATTCATGTC
11724306 ATTTAAG-TATTCATGTC
1 ATTTAAGTTATTCATGTC
11724323 GTGTTCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
ATTTAAGTTATTCATGTC
Found at i:11730589 original size:8 final size:8
Alignment explanation
Indices: 11730562--11730595 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
11730552 TTTTATGGTA
11730562 TTTTTTAT
1 TTTTTTAT
11730570 TTTTTATAAT
1 TTTTT-T-AT
11730580 TTTTTTAT
1 TTTTTTAT
11730588 TTTTTTAT
1 TTTTTTAT
11730596 GATAACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.62
9 2 0.08
10 7 0.29
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:11731433 original size:14 final size:14
Alignment explanation
Indices: 11731414--11731442 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
11731404 GATTTCATTA
11731414 TTTTTTTCTTT-AT
1 TTTTTTTCTTTGAT
11731427 TTTTTTTCTTTGAT
1 TTTTTTTCTTTGAT
11731441 TT
1 TT
11731443 GTTCCTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTTTTCTTTGAT
Found at i:11732329 original size:18 final size:19
Alignment explanation
Indices: 11732295--11732330 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11732285 TTGATTTGGT
*
11732295 CTTTTGTGTTTTTATTTTA
1 CTTTTGTGTTGTTATTTTA
11732314 CTTTTGT-TTGTTATTTT
1 CTTTTGTGTTGTTATTTT
11732331 GTTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.08, C:0.06, G:0.11, T:0.75
Consensus pattern (19 bp):
CTTTTGTGTTGTTATTTTA
Found at i:11732336 original size:18 final size:17
Alignment explanation
Indices: 11732296--11732350 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
11732286 TGATTTGGTC
11732296 TTTTGTGTTTTTATTTTA
1 TTTT-TGTTTTTATTTTA
* *
11732314 CTTTTGTTTGTTATTTTG
1 TTTTTGTTT-TTATTTTA
11732332 TTTTT-TTTTT-TTATTA
1 TTTTTGTTTTTATT-TTA
11732348 TTT
1 TTT
11732351 GTTTCTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 2 0.06
16 7 0.23
17 8 0.26
18 14 0.45
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (17 bp):
TTTTTGTTTTTATTTTA
Found at i:11732339 original size:21 final size:20
Alignment explanation
Indices: 11732315--11732354 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11732305 TTTATTTTAC
*
11732315 TTTTGTTTGTTATTTTGTTTT
1 TTTTGTTTATTA-TTTGTTTT
*
11732336 TTTTTTTTATTATTTGTTT
1 TTTTGTTTATTATTTGTTT
11732355 CTTCTTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.82
Consensus pattern (20 bp):
TTTTGTTTATTATTTGTTTT
Found at i:11735606 original size:21 final size:21
Alignment explanation
Indices: 11735577--11735626 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
11735567 GGATTTAAGG
* **
11735577 TTTAAGGTTTAGGGTTTTGAT
1 TTTAGGGTTTAGGGTTTCAAT
*
11735598 TTTAGGGTTTATGGTTTCAAT
1 TTTAGGGTTTAGGGTTTCAAT
11735619 TTTAGGGT
1 TTTAGGGT
11735627 CTAAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.02, G:0.28, T:0.52
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTCAAT
Found at i:11735689 original size:14 final size:15
Alignment explanation
Indices: 11735672--11735804 Score: 75
Period size: 14 Copynumber: 9.3 Consensus size: 15
11735662 AAGTTTAGGG
11735672 TTTAGGGTTTTAG-T
1 TTTAGGGTTTTAGAT
* **
11735686 TTTAGTGTTTTAAGGG
1 TTTAGGGTTTT-AGAT
*
11735702 TTTAGGGTTAT-GAT
1 TTTAGGGTTTTAGAT
* *
11735716 TTTAGGGTTTGAG-G
1 TTTAGGGTTTTAGAT
*
11735730 TTT-GGG-TTTCGAT
1 TTTAGGGTTTTAGAT
* **
11735743 TTTAAGGTGTGGAGAT
1 TTTAGGGT-TTTAGAT
11735759 TTTAGGGTTTT-GAT
1 TTTAGGGTTTTAGAT
* * *
11735773 TTTAAGGTTTAAG-G
1 TTTAGGGTTTTAGAT
11735787 TTTAGGGTTTT-GAT
1 TTTAGGGTTTTAGAT
11735801 TTTA
1 TTTA
11735805 AGATATATAT
Statistics
Matches: 85, Mismatches: 25, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
12 3 0.04
13 7 0.08
14 50 0.59
15 5 0.06
16 20 0.24
ACGTcount: A:0.18, C:0.01, G:0.31, T:0.50
Consensus pattern (15 bp):
TTTAGGGTTTTAGAT
Found at i:11735783 original size:21 final size:21
Alignment explanation
Indices: 11735780--11735897 Score: 94
Period size: 21 Copynumber: 5.4 Consensus size: 21
11735770 GATTTTAAGG
11735780 TTTAAGGTTTAGGGTTTTGAT
1 TTTAAGGTTTAGGGTTTTGAT
* * *
11735801 TTTAAGATATATATGGTTTAGGAT
1 TTTAAGGT-T-TAGGGTTT-TGAT
* *
11735825 TTTGA-TTTTAGGGTTTTGAAAT
1 TTTAAGGTTTAGGGTTTTG--AT
** *
11735847 TTTTGGGTTTAGGGCTTTGAT
1 TTTAAGGTTTAGGGTTTTGAT
* *
11735868 TTTAGGGTTTAGGGTTTGGAT
1 TTTAAGGTTTAGGGTTTTGAT
11735889 TTTAAGGTT
1 TTTAAGGTT
11735898 CAAAGAAAGC
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 42 0.55
22 7 0.09
23 19 0.25
24 7 0.09
ACGTcount: A:0.20, C:0.01, G:0.28, T:0.51
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTTGAT
Found at i:11735821 original size:30 final size:28
Alignment explanation
Indices: 11735665--11735834 Score: 128
Period size: 30 Copynumber: 5.9 Consensus size: 28
11735655 GTTTGGAAAG
* * *
11735665 TTTAGGGTTTAGGGTTTT-AGTTTTAGTGT
1 TTTAAGGTTTAGGGTTTTGA-TTTTA-AGA
* * *
11735694 TTTAAGGGTTTAGGGTTATGATTTTAGGG
1 TTTAA-GGTTTAGGGTTTTGATTTTAAGA
* * *
11735723 TTTGAGGTTT-GGGTTTCGATTTTAAGG
1 TTTAAGGTTTAGGGTTTTGATTTTAAGA
** * *
11735750 TGTGGAGATTTTAGGGTTTTGATTTTAAGG
1 T-TTAAG-GTTTAGGGTTTTGATTTTAAGA
11735780 TTTAAGGTTTAGGGTTTTGATTTTAAGA
1 TTTAAGGTTTAGGGTTTTGATTTTAAGA
* *
11735808 TATATATGGTTTAGGATTTTGATTTTA
1 T-T-TAAGGTTTAGGGTTTTGATTTTA
11735835 GGGTTTTGAA
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
27 15 0.13
28 30 0.26
29 16 0.14
30 55 0.47
31 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.50
Consensus pattern (28 bp):
TTTAAGGTTTAGGGTTTTGATTTTAAGA
Found at i:11735828 original size:58 final size:58
Alignment explanation
Indices: 11735700--11735840 Score: 171
Period size: 58 Copynumber: 2.4 Consensus size: 58
11735690 GTGTTTTAAG
* * * *
11735700 GGTTTAGGGTTATGATTTTAGGGTTTGAGGTTTGGGTTTCGATTTTAAGGTGTGGAGAT
1 GGTTTAGGGTTTTGATTTTAGGGTTTAAGGTTTGGGTTTCGATTTTAAGATAT-GAGAT
* * *
11735759 --TTTAGGGTTTTGATTTTAAGGTTTAAGGTTTAGGGTTTTGATTTTAAGATAT-ATAT
1 GGTTTAGGGTTTTGATTTTAGGGTTTAAGGTTT-GGGTTTCGATTTTAAGATATGAGAT
*
11735815 GGTTTAGGATTTTGATTTTAGGGTTT
1 GGTTTAGGGTTTTGATTTTAGGGTTT
11735841 TGAAATTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
56 3 0.04
57 28 0.40
58 39 0.56
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (58 bp):
GGTTTAGGGTTTTGATTTTAGGGTTTAAGGTTTGGGTTTCGATTTTAAGATATGAGAT
Found at i:11736382 original size:11 final size:11
Alignment explanation
Indices: 11736368--11736410 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
11736358 CCAAAACAAT
11736368 ATAAAAAATAA
1 ATAAAAAATAA
11736379 ATAAAAAATAA
1 ATAAAAAATAA
11736390 ATAAAATAA-AA
1 ATAAAA-AATAA
11736401 ATAAAAAATA
1 ATAAAAAATA
11736411 CTTGAACCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.07
11 26 0.87
12 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:11736393 original size:15 final size:16
Alignment explanation
Indices: 11736373--11736410 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
11736363 ACAATATAAA
11736373 AAATAAATA-AAAAAT
1 AAATAAATATAAAAAT
11736388 AAATAAA-ATAAAAAT
1 AAATAAATATAAAAAT
11736403 AAA-AAATA
1 AAATAAATA
11736411 CTTGAACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAATATAAAAAT
Found at i:11736553 original size:21 final size:21
Alignment explanation
Indices: 11736528--11736582 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
11736518 GGGCAGTTTA
**
11736528 ATCAACGATTTGAGTGGTTC-
1 ATCAACGATTTGAGTGACTCG
* *
11736548 AGTCAACGGTTTGGGTGACTCG
1 A-TCAACGATTTGAGTGACTCG
11736570 ATCAACGATTTGA
1 ATCAACGATTTGA
11736583 TGAACGATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (21 bp):
ATCAACGATTTGAGTGACTCG
Found at i:11737774 original size:26 final size:26
Alignment explanation
Indices: 11737731--11737785 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
11737721 AACCTCCCTC
* * *
11737731 TTTTTGTTTTCTTCTTTTTTTTAATTT
1 TTTTTGTTTTATTATTTTTTGT-ATTT
11737758 TTTTTG-TTTATTATTTTTTGTATTT
1 TTTTTGTTTTATTATTTTTTGTATTT
11737783 TTT
1 TTT
11737786 AATATTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 12 0.48
27 6 0.24
ACGTcount: A:0.09, C:0.04, G:0.05, T:0.82
Consensus pattern (26 bp):
TTTTTGTTTTATTATTTTTTGTATTT
Found at i:11737961 original size:12 final size:12
Alignment explanation
Indices: 11737944--11737968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11737934 TGTCTACACA
11737944 ATACCTTTTTTT
1 ATACCTTTTTTT
11737956 ATACCTTTTTTT
1 ATACCTTTTTTT
11737968 A
1 A
11737969 GTGAAGATAG
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:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (12 bp):
ATACCTTTTTTT
Found at i:11746062 original size:2 final size:2
Alignment explanation
Indices: 11746055--11746079 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11746045 TATGTGCAAG
11746055 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 T
11746080 TTAACCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11747845 original size:34 final size:35
Alignment explanation
Indices: 11747765--11747861 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 35
11747755 AATAGCAGCG
* * *
11747765 TTTTTAAGAACAAATGTCGCTAAATTTAATGGTGTT
1 TTTTTAA-TACAAATGTCACTAAATTTAATGGTGAT
* *
11747801 TTTTTTATACAAATGCCACTAAATTTAACT-GT-AT
1 TTTTTAATACAAATGTCACTAAATTTAA-TGGTGAT
**
11747835 TTTTTAATACAAACATCACTAAATTTA
1 TTTTTAATACAAATGTCACTAAATTTA
11747862 GTATTTAACG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
34 24 0.47
35 20 0.39
36 7 0.14
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.42
Consensus pattern (35 bp):
TTTTTAATACAAATGTCACTAAATTTAATGGTGAT
Found at i:11750228 original size:66 final size:64
Alignment explanation
Indices: 11750050--11750305 Score: 181
Period size: 64 Copynumber: 4.0 Consensus size: 64
11750040 TATTTTTTGA
* * * *
11750050 AAAAAAAAAACTCCTTCAATAATCTCTCTCAATTTTTTTA-AAGGGACTATTAAAGACATTTT-T
1 AAAAAAAAAA-T-CTTCAATAATCCCTCTCAA-TTTTTTAGAAGGAATTATTAAAGTCATTTTCT
11750113 -T
63 AT
* ** * *
11750114 -GACCAAAAATGCTTTCAATAATCCC-CTTC-ATTTTAAATGAGAA-G-ATTATTGAAAG-CGTT
1 AAAAAAAAAAT-C-TTCAATAATCCCTC-TCAATTTT---TTAGAAGGAATTATT-AAAGTCATT
*
11750173 TTTTAT
59 TTCTAT
*
11750179 AAAAAAAAAATACATTCAATAAT-CCTCTCTAATTTTTTGGAAGGAATTATTAAAGTCATTTTCT
1 AAAAAAAAAAT-C-TTCAATAATCCCTCTC-AATTTTTTAGAAGGAATTATTAAAGTCATTTTCT
11750243 AT
63 AT
* * * * *
11750245 AAAAAAAATATCTTTAATAATCCCTTTCAATTTTTTATAAGGAATTATTAAAGACATTTTC
1 AAAAAAAAAATCTTCAATAATCCCTCTCAATTTTTTAGAAGGAATTATTAAAGTCATTTTC
11750306 AGGCAAAACA
Statistics
Matches: 152, Mismatches: 23, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
61 4 0.03
62 4 0.03
63 29 0.19
64 50 0.33
65 18 0.12
66 42 0.28
67 5 0.03
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (64 bp):
AAAAAAAAAATCTTCAATAATCCCTCTCAATTTTTTAGAAGGAATTATTAAAGTCATTTTCTAT
Found at i:11756912 original size:31 final size:32
Alignment explanation
Indices: 11756874--11756953 Score: 110
Period size: 31 Copynumber: 2.5 Consensus size: 32
11756864 GAAGGCTATT
11756874 TTATTCATGGAACAACTCTTTTATCA-AACAG-
1 TTATTCATGGAACAACTCTTTTA-CATAACAGC
11756905 TTATTCATGGAACAACTCTTTTACATAACAGC
1 TTATTCATGGAACAACTCTTTTACATAACAGC
** *
11756937 ACATTTATGGAACAACT
1 TTATTCATGGAACAACT
11756954 ATTGTCAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.05
31 28 0.64
32 14 0.32
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (32 bp):
TTATTCATGGAACAACTCTTTTACATAACAGC
Found at i:11758478 original size:20 final size:20
Alignment explanation
Indices: 11758435--11758479 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11758425 ATAATAGCCT
* *
11758435 AAATTACGTCTATAATATTG
1 AAATTACGTCTATAATACTA
* *
11758455 AAATTCCGTTTATAATACTA
1 AAATTACGTCTATAATACTA
11758475 AAATT
1 AAATT
11758480 TTATCTGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (20 bp):
AAATTACGTCTATAATACTA
Found at i:11764049 original size:36 final size:37
Alignment explanation
Indices: 11763966--11764126 Score: 116
Period size: 37 Copynumber: 4.4 Consensus size: 37
11763956 AAAAACGTTC
* **
11763966 TCATTACTTA-TTTT-TATATTTTTAAAAAAAG-CATT
1 TCATTACTTATTTTTCTATTTTTTTAGGAAAAGAC-TT
* *
11764001 TCTATTAATTATTTTTCTA-TTTTTTAGGAAAAGATTT
1 TC-ATTACTTATTTTTCTATTTTTTTAGGAAAAGACTT
* * *
11764038 TCATTACTTATTCTAT-TAGTTTTTTTGGGAAAAAACTT
1 TCATTACTTATT-TTTCTA-TTTTTTTAGGAAAAGACTT
* ** * * *
11764076 CCATTACTTGCTTTACAATTTTTTTAGGAAAATACTT
1 TCATTACTTATTTTTCTATTTTTTTAGGAAAAGACTT
*
11764113 ACATTACTTATTTT
1 TCATTACTTATTTT
11764127 CATATTTATT
Statistics
Matches: 97, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
35 2 0.02
36 18 0.19
37 50 0.52
38 27 0.28
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.52
Consensus pattern (37 bp):
TCATTACTTATTTTTCTATTTTTTTAGGAAAAGACTT
Found at i:11764061 original size:37 final size:37
Alignment explanation
Indices: 11764020--11764125 Score: 106
Period size: 38 Copynumber: 2.8 Consensus size: 37
11764010 TATTTTTCTA
* * * **
11764020 TTTTTTAGGAAAAGATTTTCATTACTTATTCTATTAGT
1 TTTTTTAGGAAAAAACTTACATTACTTATT-TACAAGT
* * *
11764058 TTTTTTGGGAAAAAACTTCCATTACTTGCTTTACAA-T
1 TTTTTTAGGAAAAAACTTACATTACTT-ATTTACAAGT
*
11764095 TTTTTTAGGAAAATACTTACATTACTTATTT
1 TTTTTTAGGAAAAAACTTACATTACTTATTT
11764126 TCATATTTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
36 3 0.05
37 25 0.45
38 26 0.46
39 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (37 bp):
TTTTTTAGGAAAAAACTTACATTACTTATTTACAAGT
Found at i:11765150 original size:2 final size:2
Alignment explanation
Indices: 11765143--11765182 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
11765133 AAATATTTCT
11765143 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11765183 AGAAACACAA
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):
TA
Found at i:11765974 original size:28 final size:28
Alignment explanation
Indices: 11765934--11766015 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 28
11765924 ACATTTGATG
**
11765934 ATATAATACAAAAAAATATATAAAATTT
1 ATATAATTTAAAAAAATATATAAAATTT
*** *
11765962 ATATAATTTAAAATTTTA-ATAAAAATT
1 ATATAATTTAAAAAAATATATAAAATTT
*
11765989 ATATATATTTAATAAAAAT-TAAAAAAT
1 ATATA-ATTTAA-AAAAATATATAAAAT
11766016 AAATTTCATG
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
27 13 0.32
28 19 0.47
29 8 0.20
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATAATTTAAAAAAATATATAAAATTT
Found at i:11767425 original size:19 final size:19
Alignment explanation
Indices: 11767401--11767439 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11767391 TCAAACCAAA
11767401 TTATATATTTTATTAATTT
1 TTATATATTTTATTAATTT
*
11767420 TTATATATTTTTTTAATTT
1 TTATATATTTTATTAATTT
11767439 T
1 T
11767440 ATAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATATATTTTATTAATTT
Found at i:11771747 original size:10 final size:11
Alignment explanation
Indices: 11771727--11771751 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11771717 TAAAAGATGG
11771727 TTTTTCTTTTT
1 TTTTTCTTTTT
11771738 TTTTTCTTTTT
1 TTTTTCTTTTT
11771749 TTT
1 TTT
11771752 GCTTGAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:11772130 original size:34 final size:32
Alignment explanation
Indices: 11772071--11772185 Score: 86
Period size: 34 Copynumber: 3.4 Consensus size: 32
11772061 CATCTCTTAT
* *
11772071 ATTTTTAAATTTTTAGATTTGTAAATTCAAAAA
1 ATTTTAAAATTTTTA-ATTTATAAATTCAAAAA
*
11772104 ATTTTAAAAGTTTTTGAATTTATAAATTCGAAAA
1 ATTTTAAAA-TTTTT-AATTTATAAATTCAAAAA
* * * ** * *
11772138 CTCTTAAAAAATTTTTTATTTGCATATTTAAAAA
1 AT-TT-TAAAATTTTTAATTTATAAATTCAAAAA
*
11772172 CTTTTAAAATTTTT
1 ATTTTAAAATTTTT
11772186 TGAATTTACA
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
32 9 0.14
33 10 0.15
34 35 0.53
35 8 0.12
36 4 0.06
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (32 bp):
ATTTTAAAATTTTTAATTTATAAATTCAAAAA
Found at i:11772198 original size:34 final size:34
Alignment explanation
Indices: 11772095--11772204 Score: 107
Period size: 34 Copynumber: 3.2 Consensus size: 34
11772085 AGATTTGTAA
* * * *
11772095 ATTCAAAAAATTTTAAAAGTTTTTGAATTTATAA
1 ATTCAAAAACTTTTAAAATTTTTTGAATTTACAT
* * *
11772129 ATTCGAAAACTCTTAAAAAATTTTTT--ATTTGCAT
1 ATTCAAAAACT-TT-TAAAATTTTTTGAATTTACAT
*
11772163 ATTTAAAAACTTTTAAAATTTTTTGAATTTACAT
1 ATTCAAAAACTTTTAAAATTTTTTGAATTTACAT
*
11772197 ATCCAAAA
1 ATTCAAAA
11772205 CCTTACAAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
32 10 0.17
33 2 0.03
34 36 0.61
35 2 0.03
36 9 0.15
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (34 bp):
ATTCAAAAACTTTTAAAATTTTTTGAATTTACAT
Found at i:11772861 original size:23 final size:23
Alignment explanation
Indices: 11772835--11772882 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
11772825 ATTATATTAA
11772835 TTTTAAATAATTTTAATAAAACT
1 TTTTAAATAATTTTAATAAAACT
* ** *
11772858 TTTTATATTTTTTTTATAAAACT
1 TTTTAAATAATTTTAATAAAACT
11772881 TT
1 TT
11772883 ACTTTTCACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAAATAATTTTAATAAAACT
Found at i:11785175 original size:20 final size:21
Alignment explanation
Indices: 11785141--11785181 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11785131 TAAAAGTGTG
11785141 GATCCCATATAAATT-TTAAT
1 GATCCCATATAAATTATTAAT
11785161 GATCTCCATAT-AATTATTAAT
1 GATC-CCATATAAATTATTAAT
11785182 TATAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (21 bp):
GATCCCATATAAATTATTAAT
Found at i:11788337 original size:3 final size:3
Alignment explanation
Indices: 11788329--11788392 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
11788319 AAGAGAAAAG
11788329 AAT AAT AAT AAT 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
11788377 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
11788393 TTCTTTTATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11788597 original size:2 final size:2
Alignment explanation
Indices: 11788590--11788618 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11788580 ATCTTATAAT
11788590 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11788619 ACGTTGTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11790671 original size:21 final size:22
Alignment explanation
Indices: 11790633--11790674 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
11790623 ACTTATATAA
*
11790633 ATTAAAATTTTGATAAAAATAT
1 ATTAAAATTTTGAAAAAAATAT
11790655 ATTAAAA-TTTGAAAAAAATA
1 ATTAAAATTTTGAAAAAAATA
11790675 AAAAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
ATTAAAATTTTGAAAAAAATAT
Found at i:11798057 original size:17 final size:15
Alignment explanation
Indices: 11798022--11798051 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11798012 GAAATTGAAA
*
11798022 TTGAAATTTTTTTAG
1 TTGAAATTGTTTTAG
11798037 TTGAAATTGTTTTAG
1 TTGAAATTGTTTTAG
11798052 ATTTGAGTAA
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:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
TTGAAATTGTTTTAG
Found at i:11799106 original size:26 final size:26
Alignment explanation
Indices: 11799077--11799128 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
11799067 ATCAGGGGTT
11799077 TATCTTTAGTCTTCAATGAATCCAAG
1 TATCTTTAGTCTTCAATGAATCCAAG
11799103 TATCTTTAGTCTTCAATGAATCCAAG
1 TATCTTTAGTCTTCAATGAATCCAAG
11799129 GCTGGGGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (26 bp):
TATCTTTAGTCTTCAATGAATCCAAG
Found at i:11805277 original size:2 final size:2
Alignment explanation
Indices: 11805270--11805297 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11805260 TATCACATGA
11805270 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
11805298 TACAAAAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11805733 original size:193 final size:193
Alignment explanation
Indices: 11805401--11805778 Score: 537
Period size: 193 Copynumber: 2.0 Consensus size: 193
11805391 TATTATTTAT
* * *
11805401 CAAATAACTTTATTTAACAAATTATTTAAATTTAATATTTTTGGATAATTATTTAAATTCAAATT
1 CAAATAACTTTATTTAACAAATTATCTAAATTTAATATTTTTGGATAACTATTTAAATTCAAATC
*
11805466 AAAATCTATAAAAGATTAAAAATTTTACATAAATTTTTAATTCAAATATATTAAATCATAATTTA
66 AAAATCTATAAAAGATTAAAAATTTTACATAAATTTTGAATTCAAATATATTAAATCATAATTTA
* *
11805531 TCCTTTCTTTTCAAATTTAGTCATAGTTCCAAATATATATGCTTAATAGATTTTTAGCTGCTGC
131 TCCTTTCTTTTCAAATTTAATCATAGTTCCAAATATATATGCTTAA-AAATTTTTAGCTGCTGC
* * *
11805595 CAAATAA-TTCTATTTAATAAATTATCTAAATTTAATATTTTTGGTTAACTA-TTAACTTCAAAT
1 CAAATAACTT-TATTTAACAAATTATCTAAATTTAATATTTTTGGATAACTATTTAAATTCAAAT
* * ** * *
11805658 CAAACTCTATTAGCGTTTAAAAATTTTACATAAATTTTGAATTTAAATATATTAAA-CTATAATT
65 CAAAATCTATAAAAGATTAAAAATTTTACATAAATTTTGAATTCAAATATATTAAATC-ATAATT
* * * *
11805722 TATCTTTTCTTTTTAAATTTAATCTTAGTTTCAAATATATATGCTTAAAAATTTTTA
129 TATCCTTTCTTTTCAAATTTAATCATAGTTCCAAATATATATGCTTAAAAATTTTTA
11805779 TCTGATGAAA
Statistics
Matches: 163, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
192 9 0.06
193 110 0.67
194 44 0.27
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (193 bp):
CAAATAACTTTATTTAACAAATTATCTAAATTTAATATTTTTGGATAACTATTTAAATTCAAATC
AAAATCTATAAAAGATTAAAAATTTTACATAAATTTTGAATTCAAATATATTAAATCATAATTTA
TCCTTTCTTTTCAAATTTAATCATAGTTCCAAATATATATGCTTAAAAATTTTTAGCTGCTGC
Found at i:11808692 original size:5 final size:6
Alignment explanation
Indices: 11808677--11808702 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11808667 TATATGGGAA
11808677 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
11808703 TTTTATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:11808786 original size:15 final size:15
Alignment explanation
Indices: 11808766--11808800 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
11808756 AATAATTTTA
11808766 CTTTTCCTTTTC-TTT
1 CTTTT-CTTTTCATTT
11808781 CTTTTCTTTTCATTT
1 CTTTTCTTTTCATTT
11808796 CTTTT
1 CTTTT
11808801 TTCCTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTCTTTTCATTT
Found at i:11809963 original size:14 final size:15
Alignment explanation
Indices: 11809944--11809976 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11809934 CAAAGGTAAT
*
11809944 AATAATA-ATTATTG
1 AATAATATATTATTA
11809958 AATAATATATTATTA
1 AATAATATATTATTA
11809973 AATA
1 AATA
11809977 GAGAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
AATAATATATTATTA
Found at i:11810957 original size:14 final size:15
Alignment explanation
Indices: 11810938--11810971 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11810928 CAAAGGTAAT
*
11810938 AATAATA-ATTATTG
1 AATAATATATTATTA
11810952 AATAATATATTATTA
1 AATAATATATTATTA
11810967 AATAA
1 AATAA
11810972 AGAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATAATATATTATTA
Found at i:11811572 original size:15 final size:17
Alignment explanation
Indices: 11811537--11811573 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
11811527 ATACAAAGGT
*
11811537 AATAATAATAGTTATTG
1 AATAATAATAGTTATTA
11811554 AATAAT-ATA-TTATTA
1 AATAATAATAGTTATTA
11811569 AATAA
1 AATAA
11811574 AGAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AATAATAATAGTTATTA
Found at i:11816802 original size:459 final size:460
Alignment explanation
Indices: 11815933--11816842 Score: 1431
Period size: 459 Copynumber: 2.0 Consensus size: 460
11815923 TTTTTAGTAA
* * * **
11815933 TTTTTTTATAATTTTTAATTTAATTTAATTTTTTATTATTATATTTTTTTTATAATTAGACTAAA
1 TTTTGTTATAATTTTTAATTTAAATGAATTTTTTATTATTATACCTTTTTTATAATTAGACTAAA
*
11815998 AAATTACTAAAAGTGATTGAGACTGTTAATAGTGATCAACCTAAATATCCTTATAATAAAAATTT
66 AAATTACTAAAAGTGATTGAGACTGTTAATAGTGATCAACCTAAATACCCTTATAATAAAAATTT
11816063 ATCCTTAAATATATAACTTTTATTAATTTATTTAAATTTAATTTAAATAAACTAAAATTAAAAAT
131 ATCCTTAAATATATAACTTTTATTAATTTATTTAAATTTAATTTAAATAAACTAAAATTAAAAAT
*
11816128 AAAGTTTATGAGAAATTAAACTAAAAATCTTAAAATTTTAATTTTAAGTGTTAATAGTGATTGAA
196 AAAATTTATGAGAAATTAAACTAAAAATCTTAAAATTTTAATTTTAAGTGTTAATAGTGATTGAA
*
11816193 TAAAATTTCTTTAGTAAATTTTTAAAAATTTTTAATTTAAATAAATTTTTTGTTATTAGACTTTT
261 TAAAATATCTTTAGTAAATTTTTAAAAATTTTTAATTTAAATAAATTTTTTGTTATTAGACTTTT
*
11816258 TTTATAATTAGACTAAAAATATACTAAAAATGATTCAGTAAACCCTTAATAAAATTTTAATTTAA
326 TTTATAATTAGACTAAAAAAATACTAAAAATGATTCAGTAAACCCTT-ATAAAATTTTAATTTAA
* * *
11816323 AAAAATTAAGAGTAATTGATTAAAATACCATTAGTAA-TTTTTTATAAATTTTATTTTTAATATT
390 AAAAATTAAGAGTAATTGATTAAAAAACCATTAGAAATTTTTTTATAAATTTTAATTTTAATATT
11816387 AAACTC
455 AAACTC
11816393 TTTTGTTATAA-TTTTAATTTAAATGAATTTTTTATTATTAGT-CCTTTTTTATAATTAGACTAA
1 TTTTGTTATAATTTTTAATTTAAATGAATTTTTTATTATTA-TACCTTTTTTATAATTAGACTAA
* * ** *
11816456 AAAATTACTAAAAGTGATTGATATTGTTAATAGTGATTGACTTAAATACCCTTATAATAACAAAT
65 AAAATTACTAAAAGTGATTGAGACTGTTAATAGTGATCAACCTAAATACCCTTATAATAA-AAAT
* *
11816521 TTATCCTTAAATATATAATTTTTATTAATTTATTTAAATTTAATTTAAATCAACTAAAATTAAAA
129 TTATCCTTAAATATATAACTTTTATTAATTTATTTAAATTTAATTTAAATAAACTAAAATTAAAA
*
11816586 ATAAAATTTATGAGAAATTAAACTACTTAAAATCTTAAAATTTTAATTTTAATTGTTAATAGTGA
194 ATAAAATTTATGAGAAATTAAACTA---AAAATCTTAAAATTTTAATTTTAAGTGTTAATAGTGA
* * *
11816651 TTGAATACAATATCTTTAGTAAATTTTTTATAA-TTTTAATTTAAATAAATTTTTTGTTATTAGA
256 TTGAATAAAATATCTTTAGTAAATTTTTAAAAATTTTTAATTTAAATAAATTTTTTGTTATTAGA
** * *
11816715 CTTTTTTTATAATTAGACTAAAAAAATACTGAAAGCT-ATTGAGTAAACTC-T-T-AAATTTTAA
321 CTTTTTTTATAATTAGACTAAAAAAATACT-AAAAATGATTCAGTAAACCCTTATAAAATTTTAA
* *
11816776 TTTCAAAAATATTAAGAGTGATTGATTAAAAAACCATTAGAAATTTTTTTATAAATTTTAATTTT
385 TTT-AAAAAAATTAAGAGTAATTGATTAAAAAACCATTAGAAATTTTTTTATAAATTTTAATTTT
11816841 AA
449 AA
11816843 ATGATTTTAT
Statistics
Matches: 413, Mismatches: 29, Indels: 16
0.90 0.06 0.03
Matches are distributed among these distances:
458 12 0.03
459 136 0.33
460 124 0.30
461 1 0.00
462 71 0.17
463 69 0.17
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (460 bp):
TTTTGTTATAATTTTTAATTTAAATGAATTTTTTATTATTATACCTTTTTTATAATTAGACTAAA
AAATTACTAAAAGTGATTGAGACTGTTAATAGTGATCAACCTAAATACCCTTATAATAAAAATTT
ATCCTTAAATATATAACTTTTATTAATTTATTTAAATTTAATTTAAATAAACTAAAATTAAAAAT
AAAATTTATGAGAAATTAAACTAAAAATCTTAAAATTTTAATTTTAAGTGTTAATAGTGATTGAA
TAAAATATCTTTAGTAAATTTTTAAAAATTTTTAATTTAAATAAATTTTTTGTTATTAGACTTTT
TTTATAATTAGACTAAAAAAATACTAAAAATGATTCAGTAAACCCTTATAAAATTTTAATTTAAA
AAAATTAAGAGTAATTGATTAAAAAACCATTAGAAATTTTTTTATAAATTTTAATTTTAATATTA
AACTC
Found at i:11817955 original size:15 final size:15
Alignment explanation
Indices: 11817935--11817967 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
11817925 TTTTAATATT
11817935 TTTATATAATAA-AAA
1 TTTATAT-ATAATAAA
11817950 TTTATATATAATAAA
1 TTTATATATAATAAA
11817965 TTT
1 TTT
11817968 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTATATATAATAAA
Found at i:11817957 original size:17 final size:17
Alignment explanation
Indices: 11817932--11817964 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11817922 GTATTTTAAT
*
11817932 ATTTTTATATAATAAAA
1 ATTTATATATAATAAAA
11817949 ATTTATATATAATAAA
1 ATTTATATATAATAAA
11817965 TTTTTTAAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTATATATAATAAAA
Found at i:11817976 original size:18 final size:18
Alignment explanation
Indices: 11817950--11817984 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11817940 ATAATAAAAA
* *
11817950 TTTATATATAATAAATTT
1 TTTAAATATAAAAAATTT
11817968 TTTAAATATAAAAAATT
1 TTTAAATATAAAAAATT
11817985 AAACTTTCAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAATATAAAAAATTT
Found at i:11819478 original size:60 final size:60
Alignment explanation
Indices: 11819401--11819516 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
11819391 TATTTAATTT
11819401 TCAGTGTTCATGCGCATATATATTAAGAATATATGATACATGTGCTAGAGTAAAGGTATA
1 TCAGTGTTCATGCGCATATATATTAAGAATATATGATACATGTGCTAGAGTAAAGGTATA
* *
11819461 TCAGTGTTCATGTGCATATATATTAAGAATATATGATACATGTGTTAGAGTAAAGG
1 TCAGTGTTCATGCGCATATATATTAAGAATATATGATACATGTGCTAGAGTAAAGG
11819517 CATAGTATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (60 bp):
TCAGTGTTCATGCGCATATATATTAAGAATATATGATACATGTGCTAGAGTAAAGGTATA
Found at i:11819503 original size:30 final size:30
Alignment explanation
Indices: 11819409--11819504 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
11819399 TTTCAGTGTT
*
11819409 CATGCGCATATATATTAAGAATATATGATA
1 CATGTGCATATATATTAAGAATATATGATA
* * *
11819439 CATGTGC-TAGAGTA--AAGGTATATCAGTG-TT
1 CATGTGCATATA-TATTAA-GAATAT-A-TGATA
11819469 CATGTGCATATATATTAAGAATATATGATA
1 CATGTGCATATATATTAAGAATATATGATA
11819499 CATGTG
1 CATGTG
11819505 TTAGAGTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
28 2 0.04
29 10 0.20
30 27 0.53
31 10 0.20
32 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (30 bp):
CATGTGCATATATATTAAGAATATATGATA
Found at i:11820655 original size:22 final size:21
Alignment explanation
Indices: 11820602--11820655 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
11820592 TTTTAATTTT
11820602 TAAATATAAATTTAATTTGAGA
1 TAAA-ATAAATTTAATTTGAGA
*
11820624 TAAAATTAAATTTATTTATTGA-A
1 TAAAA-TAAATTTA-AT-TTGAGA
11820647 TAAAATAAA
1 TAAAATAAA
11820656 ATAAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 16 0.57
23 7 0.25
24 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (21 bp):
TAAAATAAATTTAATTTGAGA
Found at i:11820663 original size:23 final size:26
Alignment explanation
Indices: 11820602--11820663 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 26
11820592 TTTTAATTTT
11820602 TAAATATAAATTTAATTTGAGATAAAA
1 TAAA-ATAAATTTAATTTGAGATAAAA
* **
11820629 TTAAATTTATTT-A-TTGA-ATAAAA
1 TAAAATAAATTTAATTTGAGATAAAA
11820652 TAAAATAAATTT
1 TAAAATAAATTT
11820664 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 15 0.52
24 4 0.14
25 1 0.03
26 6 0.21
27 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (26 bp):
TAAAATAAATTTAATTTGAGATAAAA
Found at i:11823810 original size:35 final size:37
Alignment explanation
Indices: 11823759--11823828 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
11823749 TTAGGTAAAT
*
11823759 TTGTTTTTTTTAATTTT-CTAATTTTTTTATATACTA
1 TTGTTTTTGTTAATTTTACTAATTTTTTTATATACTA
* *
11823795 TTGTTTTTGTT-ATTTTAAGTATTTTTTTTATATA
1 TTGTTTTTGTTAATTTT-ACTAATTTTTTTATATA
11823829 TTTATGCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 5 0.17
36 10 0.34
37 14 0.48
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (37 bp):
TTGTTTTTGTTAATTTTACTAATTTTTTTATATACTA
Found at i:11824314 original size:15 final size:16
Alignment explanation
Indices: 11824297--11824362 Score: 64
Period size: 15 Copynumber: 4.2 Consensus size: 16
11824287 CTAGGTTTTT
11824297 AAACCCTAAAAATCTA
1 AAACCCTAAAAATCTA
* *
11824313 AAATCC-AAAAATCTT
1 AAACCCTAAAAATCTA
* *
11824328 AAATCCT-AAAATCTG
1 AAACCCTAAAAATCTA
*
11824343 AAACTCCTAAAAATCCA
1 AAAC-CCTAAAAATCTA
11824360 AAA
1 AAA
11824363 TCTCAAACCT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
15 24 0.59
16 8 0.20
17 9 0.22
ACGTcount: A:0.55, C:0.23, G:0.02, T:0.21
Consensus pattern (16 bp):
AAACCCTAAAAATCTA
Found at i:11824377 original size:24 final size:25
Alignment explanation
Indices: 11824297--11824370 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 25
11824287 CTAGGTTTTT
11824297 AAAC-CCTAAAAAT-CTAAAATC-C
1 AAACTCCTAAAAATCCTAAAATCTC
* * *
11824319 AAAAAT-CT-TAAATCCTAAAATCTG
1 -AAACTCCTAAAAATCCTAAAATCTC
11824343 AAACTCCTAAAAATCC-AAAATCTC
1 AAACTCCTAAAAATCCTAAAATCTC
11824367 AAAC
1 AAAC
11824371 CTTTAAACTC
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
22 4 0.10
23 17 0.43
24 13 0.32
25 6 0.15
ACGTcount: A:0.53, C:0.24, G:0.01, T:0.22
Consensus pattern (25 bp):
AAACTCCTAAAAATCCTAAAATCTC
Found at i:11824471 original size:30 final size:30
Alignment explanation
Indices: 11824436--11824573 Score: 92
Period size: 30 Copynumber: 4.6 Consensus size: 30
11824426 AACCTGAAAT
11824436 TTTAAAATCGAAACCCTAAAATCTTCAAAC
1 TTTAAAATCGAAACCCTAAAATCTTCAAAC
** *
11824466 TTTAAAATAAAAACCCT-AAACCTTCCAAAC
1 TTTAAAATCGAAACCCTAAAATCTT-CAAAC
* * *
11824496 TTTAAAA-CCAAAACCTAAAA-CACTCAAAAC
1 TTTAAAATCGAAACCCTAAAATC-TTC-AAAC
* *
11824526 -TT-AAATC-AAACCCTTAAAATC-TGAATC
1 TTTAAAATCGAAACCC-TAAAATCTTCAAAC
*
11824553 TTCAAAATCTTGAAACCCTAA
1 TTTAAAATC--GAAACCCTAA
11824574 TCTTGAAAAC
Statistics
Matches: 85, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
27 3 0.04
28 10 0.12
29 27 0.32
30 36 0.42
31 3 0.04
32 6 0.07
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.25
Consensus pattern (30 bp):
TTTAAAATCGAAACCCTAAAATCTTCAAAC
Found at i:11824523 original size:29 final size:29
Alignment explanation
Indices: 11824367--11824514 Score: 90
Period size: 30 Copynumber: 5.1 Consensus size: 29
11824357 CCAAAATCTC
* * * *
11824367 AAACCTTTAAACTCTTAAATCCAAACCCCT
1 AAACCTTCAAACT-TTAAAACAAAAACCCT
* * * *
11824397 AAA-ATTCAAACCCTT-AAATAAAAACCCC
1 AAACCTTCAAA-CTTTAAAACAAAAACCCT
* * *
11824425 AAACC-TGAAATTTTAAAATC-GAAACCCT
1 AAACCTTCAAACTTTAAAA-CAAAAACCCT
* *
11824453 AAAATCTTCAAACTTTAAAATAAAAACCCT
1 -AAACCTTCAAACTTTAAAACAAAAACCCT
*
11824483 AAACCTTCCAAACTTTAAAACCAAAA-CCT
1 AAACCTT-CAAACTTTAAAACAAAAACCCT
11824512 AAA
1 AAA
11824515 ACACTCAAAA
Statistics
Matches: 87, Mismatches: 23, Indels: 17
0.69 0.18 0.13
Matches are distributed among these distances:
27 2 0.02
28 24 0.28
29 23 0.26
30 38 0.44
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.23
Consensus pattern (29 bp):
AAACCTTCAAACTTTAAAACAAAAACCCT
Found at i:11826135 original size:13 final size:13
Alignment explanation
Indices: 11826072--11826106 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11826062 TAAAAATTAC
*
11826072 CACAATATTCTGT
1 CACAATATTCTAT
*
11826085 CATAATATTCTAT
1 CACAATATTCTAT
11826098 CACAATATT
1 CACAATATT
11826107 AAAAAATCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (13 bp):
CACAATATTCTAT
Found at i:11827013 original size:20 final size:20
Alignment explanation
Indices: 11826984--11827032 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
11826974 TAAATGATAA
11826984 TAATAATATTAATT-ATTAAT
1 TAATAATATT-ATTAATTAAT
*
11827004 TAATACTATTATTAATTAAT
1 TAATAATATTATTAATTAAT
*
11827024 TAATTATAT
1 TAATAATAT
11827033 ATAATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATAATATTATTAATTAAT
Found at i:11827406 original size:52 final size:51
Alignment explanation
Indices: 11827348--11827446 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 51
11827338 ATTAAATTTG
* *
11827348 TTTTGAA-AATATAAAAAAAAGCTGAAATATATAATTTTTTTCTTAAATAAAA
1 TTTTGAATAAT-TAAAAAAAAGCTGAAATAT-CAATTTTTTTCTAAAATAAAA
* *
11827400 TTTTGAATAATTAAAAAAAAGTTGAGATATCAATTTTTTTCTAAAAT
1 TTTTGAATAATTAAAAAAAAGCTGAAATATCAATTTTTTTCTAAAAT
11827447 TTTGAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 15 0.36
52 24 0.57
53 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.40
Consensus pattern (51 bp):
TTTTGAATAATTAAAAAAAAGCTGAAATATCAATTTTTTTCTAAAATAAAA
Found at i:11829387 original size:2 final size:2
Alignment explanation
Indices: 11829382--11829408 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11829372 AATGTGTGTG
11829382 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11829409 GTTTAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11829974 original size:18 final size:19
Alignment explanation
Indices: 11829943--11829978 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11829933 TCACTACTTT
11829943 TTTTTTCATATTTTATTTA
1 TTTTTTCATATTTTATTTA
*
11829962 TTTTTT-ATTTTTTATTT
1 TTTTTTCATATTTTATTT
11829979 CCACCATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTCATATTTTATTTA
Found at i:11830387 original size:14 final size:14
Alignment explanation
Indices: 11830368--11830396 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11830358 ATAAGATTAA
11830368 TAGTTTATGAATAT
1 TAGTTTATGAATAT
11830382 TAGTTTATGAATAT
1 TAGTTTATGAATAT
11830396 T
1 T
11830397 CTACTAATAT
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:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TAGTTTATGAATAT
Found at i:11830926 original size:82 final size:82
Alignment explanation
Indices: 11830840--11831006 Score: 316
Period size: 82 Copynumber: 2.0 Consensus size: 82
11830830 CAAGGTTTAA
11830840 TTCTAAAGTACAAATTAAATATGTTTAATAGATTTTCAAATTCTATTTATTTTATAAGCAAGTGA
1 TTCTAAAGTACAAATTAAATATGTTTAATAGATTTTCAAATTCTATTTATTTTATAAGCAAGTGA
11830905 AATGTCATTTAAATGTT
66 AATGTCATTTAAATGTT
* *
11830922 TTCTAAAGTACAAATTAAATATGTTTAATTGATTTTCAAATTCTATTTATTTTGTAAGCAAGTGA
1 TTCTAAAGTACAAATTAAATATGTTTAATAGATTTTCAAATTCTATTTATTTTATAAGCAAGTGA
11830987 AATGTCATTTAAATGTT
66 AATGTCATTTAAATGTT
11831004 TTC
1 TTC
11831007 CATGAGTGTC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (82 bp):
TTCTAAAGTACAAATTAAATATGTTTAATAGATTTTCAAATTCTATTTATTTTATAAGCAAGTGA
AATGTCATTTAAATGTT
Found at i:11832991 original size:31 final size:30
Alignment explanation
Indices: 11832956--11833035 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
11832946 TTAAATAATT
11832956 TCATTTTTCCTTTCTTTCTTTTCTTTTCTTC
1 TCATTTTTCCTTTCTTTCTTTT-TTTTCTTC
**
11832987 TCATTTTTTCC-TTCTTT-TGCTTTTTCTTC
1 TCA-TTTTTCCTTTCTTTCTTTTTTTTCTTC
*
11833016 TACA-TTTT-CTTTTTTTCTTT
1 T-CATTTTTCCTTTCTTTCTTT
11833036 CTTCCTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.03
28 9 0.22
29 10 0.25
30 4 0.10
31 9 0.22
32 7 0.17
ACGTcount: A:0.05, C:0.23, G:0.01, T:0.71
Consensus pattern (30 bp):
TCATTTTTCCTTTCTTTCTTTTTTTTCTTC
Found at i:11832996 original size:27 final size:27
Alignment explanation
Indices: 11832966--11833049 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 27
11832956 TCATTTTTCC
11832966 TTTCTTTCTTTTCTTTTCTTCTCATTT
1 TTTCTTTCTTTTCTTTTCTTCTCATTT
*
11832993 TTTCCTTCTTTTGCTTTTTCTTCTACA--T
1 TTTCTTTCTTTT-C-TTTTCTTCT-CATTT
11833021 TTTCTTT-TTTTC-TTTCTTC-C-TTT
1 TTTCTTTCTTTTCTTTTCTTCTCATTT
11833044 TTTCTT
1 TTTCTT
11833050 CCTCTCGCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
22 1 0.02
23 7 0.14
24 7 0.14
26 1 0.02
27 15 0.30
28 8 0.16
29 9 0.18
30 2 0.04
ACGTcount: A:0.04, C:0.23, G:0.01, T:0.73
Consensus pattern (27 bp):
TTTCTTTCTTTTCTTTTCTTCTCATTT
Found at i:11833081 original size:15 final size:15
Alignment explanation
Indices: 11833021--11833083 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
11833011 TCTTCTACAT
11833021 TTTCTTTTTTTCTTTC
1 TTTCTTTTTTT-TTTC
* *
11833037 TTCCTTTTTTCTTCCTC
1 TTTCTTTTTT-TT-TTC
** *
11833054 TCGCTTCTTTTTTTC
1 TTTCTTTTTTTTTTC
11833069 TTTCTTTTTTTTTTC
1 TTTCTTTTTTTTTTC
11833084 CTTTTTCCCT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
15 14 0.39
16 12 0.33
17 10 0.28
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTTTTTTC
Found at i:11835168 original size:17 final size:16
Alignment explanation
Indices: 11835138--11835171 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11835128 TTATCTAATT
11835138 AAAAAAATAAAAAACA
1 AAAAAAATAAAAAACA
*
11835154 AAAAAAATGACAAAACA
1 AAAAAAAT-AAAAAACA
11835171 A
1 A
11835172 TGAGCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAAATAAAAAACA
Found at i:11835400 original size:13 final size:13
Alignment explanation
Indices: 11835382--11835426 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
11835372 ATATAAAAAG
11835382 AAAAATAAATATA
1 AAAAATAAATATA
11835395 AAAAATATTTAAT-TA
1 AAAAATA---AATATA
11835410 AAAAATAAATATA
1 AAAAATAAATATA
11835423 AAAA
1 AAAA
11835427 GAAAGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
15 9 0.32
16 3 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAATAAATATA
Found at i:11835400 original size:27 final size:27
Alignment explanation
Indices: 11835370--11835426 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
11835360 AATATTTATT
* *
11835370 AAATATAAAAAGAAAAATAAATATAAA
1 AAATATTAAAAAAAAAATAAATATAAA
**
11835397 AAATATTTAATTAAAAAATAAATATAAA
1 AAATA-TTAAAAAAAAAATAAATATAAA
11835425 AA
1 AA
11835427 GAAAGTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (27 bp):
AAATATTAAAAAAAAAATAAATATAAA
Found at i:11837053 original size:15 final size:17
Alignment explanation
Indices: 11837018--11837054 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
11837008 ATACAAAGGT
*
11837018 AATAATAATAGTTATTG
1 AATAATAATAGTTATTA
11837035 AATAAT-ATA-TTATTA
1 AATAATAATAGTTATTA
11837050 AATAA
1 AATAA
11837055 AGAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AATAATAATAGTTATTA
Found at i:11841133 original size:2 final size:2
Alignment explanation
Indices: 11841126--11841150 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11841116 ATAAACACAA
11841126 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11841151 CACGCCTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11842736 original size:18 final size:18
Alignment explanation
Indices: 11842709--11842743 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11842699 TTGAATTTTA
* *
11842709 ATTTTTAAATATAAATTT
1 ATTTTGAAATAAAAATTT
11842727 ATTTTGAAATAAAAATT
1 ATTTTGAAATAAAAATT
11842744 AATTATTTAA
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTTTGAAATAAAAATTT
Found at i:11842769 original size:14 final size:14
Alignment explanation
Indices: 11842739--11842776 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11842729 TTTGAAATAA
*
11842739 AAATTAA-TTATTT
1 AAATTAATTTAATT
11842752 AAATTAATTTAATT
1 AAATTAATTTAATT
*
11842766 AAATTTATTTA
1 AAATTAATTTA
11842777 TTGAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATTAATTTAATT
Found at i:11842791 original size:23 final size:23
Alignment explanation
Indices: 11842714--11842795 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
11842704 TTTTAATTTT
*
11842714 TAAATATAAATTTA-TT-TTGAAA
1 TAAAAATAAATTTATTTATTG-AA
*
11842736 TAAAAATTAA-TTATTTAAATT-AA
1 TAAAAATAAATTTATTT--ATTGAA
** *
11842759 TTTAATTAAATTTATTTATTGAA
1 TAAAAATAAATTTATTTATTGAA
11842782 TAAAAATAAATTTA
1 TAAAAATAAATTTA
11842796 ATTTTTTAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
21 3 0.07
22 13 0.29
23 21 0.47
24 6 0.13
25 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAAAATAAATTTATTTATTGAA
Found at i:11842813 original size:20 final size:19
Alignment explanation
Indices: 11842788--11842827 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
11842778 TGAATAAAAA
* *
11842788 TAAATTTAATTTTTTAATTT
1 TAAATTCAATTATTT-ATTT
11842808 TAAATTCAATTATTTATTT
1 TAAATTCAATTATTTATTT
11842827 T
1 T
11842828 CAAACATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TAAATTCAATTATTTATTT
Found at i:11845315 original size:22 final size:22
Alignment explanation
Indices: 11845288--11845345 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
11845278 AGTAATCATC
* *
11845288 AATAACTTAATAGTAAATTAGT
1 AATAACTTAATAGTAAATGAAT
*
11845310 AATAACTTAATAATAAATGAAT
1 AATAACTTAATAGTAAATGAAT
* *
11845332 GATAATTTAATAGT
1 AATAACTTAATAGT
11845346 TAATAGTTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (22 bp):
AATAACTTAATAGTAAATGAAT
Found at i:11845850 original size:22 final size:22
Alignment explanation
Indices: 11845825--11845877 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 22
11845815 TATAAAAATA
11845825 TAGTTGTAAATCATTGATAATT
1 TAGTTGTAAATCATTGATAATT
11845847 TAGTAT-T-AA--ATTGATAATT
1 TAGT-TGTAAATCATTGATAATT
*
11845866 TAGTAGTAAATC
1 TAGTTGTAAATC
11845878 CCTAATAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 10
0.69 0.03 0.28
Matches are distributed among these distances:
19 15 0.60
20 2 0.08
21 2 0.08
22 5 0.20
23 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (22 bp):
TAGTTGTAAATCATTGATAATT
Found at i:11845861 original size:19 final size:19
Alignment explanation
Indices: 11845837--11845876 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
11845827 GTTGTAAATC
*
11845837 ATTGATAATTTAGTATTAA
1 ATTGATAATTTAGTAGTAA
11845856 ATTGATAATTTAGTAGTAA
1 ATTGATAATTTAGTAGTAA
11845875 AT
1 AT
11845877 CCCTAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (19 bp):
ATTGATAATTTAGTAGTAA
Found at i:11845883 original size:19 final size:19
Alignment explanation
Indices: 11845841--11845883 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
11845831 TAAATCATTG
* **
11845841 ATAATTTAGTATTAAATTG
1 ATAATTTAGTAGTAAATCC
11845860 ATAATTTAGTAGTAAATCC
1 ATAATTTAGTAGTAAATCC
*
11845879 CTAAT
1 ATAAT
11845884 AACATAATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (19 bp):
ATAATTTAGTAGTAAATCC
Found at i:11845940 original size:11 final size:11
Alignment explanation
Indices: 11845895--11846016 Score: 72
Period size: 11 Copynumber: 11.4 Consensus size: 11
11845885 ACATAATAGC
*
11845895 AAATTACTAAT
1 AAATTAGTAAT
* *
11845906 AACTTAGTTAT
1 AAATTAGTAAT
* *
11845917 AAATCAGTGAT
1 AAATTAGTAAT
*
11845928 AATTTAGTAAT
1 AAATTAGTAAT
11845939 AAATTAGT--T
1 AAATTAGTAAT
* *
11845948 -AATTATTGAT
1 AAATTAGTAAT
* ** *
11845958 AACTTTTTAGT
1 AAATTAGTAAT
**
11845969 AAATTACCAAT
1 AAATTAGTAAT
11845980 AAATTAGTAAT
1 AAATTAGTAAT
*
11845991 AAATTAGTTAT
1 AAATTAGTAAT
11846002 AAATTTA-TAAT
1 AAA-TTAGTAAT
11846013 AAAT
1 AAAT
11846017 CATCAATAAC
Statistics
Matches: 83, Mismatches: 24, Indels: 9
0.72 0.21 0.08
Matches are distributed among these distances:
8 6 0.07
9 1 0.01
10 2 0.02
11 71 0.86
12 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (11 bp):
AAATTAGTAAT
Found at i:11846057 original size:21 final size:22
Alignment explanation
Indices: 11846012--11846059 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11846002 AAATTTATAA
* *
11846012 TAAATCATCAATAACTTAATGG
1 TAAATCACCAATAACTGAATGG
*
11846034 TAAATCACCAATAA-TGATTGG
1 TAAATCACCAATAACTGAATGG
11846055 TAAAT
1 TAAAT
11846060 TGTTCATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (22 bp):
TAAATCACCAATAACTGAATGG
Found at i:11846098 original size:21 final size:22
Alignment explanation
Indices: 11846062--11846119 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
11846052 TGGTAAATTG
* *
11846062 TTCATAACTTAATAGCAAATC-
1 TTCATAAATTAGTAGCAAATCA
**
11846083 TTTTTAAATTAGTAGCAAATCA
1 TTCATAAATTAGTAGCAAATCA
11846105 TTCATAAATTAGTAG
1 TTCATAAATTAGTAG
11846120 TACATTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (22 bp):
TTCATAAATTAGTAGCAAATCA
Found at i:11846133 original size:22 final size:22
Alignment explanation
Indices: 11846087--11846145 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
11846077 CAAATCTTTT
*
11846087 TAAATTAGTAGCAAATCATTCA
1 TAAATTAGTAGTAAATCATTCA
* * *
11846109 TAAATTAGTAGTACATTATTTA
1 TAAATTAGTAGTAAATCATTCA
*
11846131 TAACTTAGTAGTAAA
1 TAAATTAGTAGTAAA
11846146 CAACTACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (22 bp):
TAAATTAGTAGTAAATCATTCA
Found at i:11846500 original size:45 final size:45
Alignment explanation
Indices: 11846436--11846530 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 45
11846426 CAATGATTGG
* **
11846436 TTAAT-AAAAAATAAGTGATAACTTATTAGTTAA-TAATTGATAAC
1 TTAATAAAAAAATAAGTGATAACTTAATAGAAAATTAA-TGATAAC
*
11846480 TTAATAAAAAAATCAA-TGATAATTTAATAGAAAATTAATGATAAC
1 TTAATAAAAAAAT-AAGTGATAACTTAATAGAAAATTAATGATAAC
11846525 TTAATA
1 TTAATA
11846531 GTAAATTAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
44 5 0.11
45 34 0.77
46 5 0.11
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (45 bp):
TTAATAAAAAAATAAGTGATAACTTAATAGAAAATTAATGATAAC
Found at i:11846506 original size:23 final size:23
Alignment explanation
Indices: 11846473--11846530 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
11846463 AGTTAATAAT
11846473 TGATAACTTAATAAAAAAATCAA
1 TGATAACTTAATAAAAAAATCAA
* * *
11846496 TGATAATTTAAT-AGAAAATTAA
1 TGATAACTTAATAAAAAAATCAA
11846518 TGATAACTTAATA
1 TGATAACTTAATA
11846531 GTAAATTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (23 bp):
TGATAACTTAATAAAAAAATCAA
Found at i:11846519 original size:22 final size:22
Alignment explanation
Indices: 11846489--11846748 Score: 140
Period size: 22 Copynumber: 11.7 Consensus size: 22
11846479 CTTAATAAAA
* *
11846489 AAATCAATGATAATTTAATAGA
1 AAATTAATGATAATTTAATAGT
*
11846511 AAATTAATGATAACTTAATAGT
1 AAATTAATGATAATTTAATAGT
* *
11846533 AAATTAGT-TTCAATTTAATAGT
1 AAATTAATGAT-AATTTAATAGT
*
11846555 -AATTAATTGATAAATTTAGTAGT
1 AAATTAA-TGAT-AATTTAATAGT
*
11846578 GAATCATAA--ATAATTTAATAGT
1 AAAT--TAATGATAATTTAATAGT
* *
11846600 AAATCAATGATAATTTAGTAGT
1 AAATTAATGATAATTTAATAGT
* * * ** *
11846622 TAATTATTGAAAACCTAAAAGT
1 AAATTAATGATAATTTAATAGT
* *
11846644 AAATCAATG-TAATTTAGTAGT
1 AAATTAATGATAATTTAATAGT
* * *
11846665 -AGTTAATCATCAATAACATAATAGT
1 AAATTAATGAT-AAT---TTAATAGT
* * *
11846690 TAATTAATGATAACTTGATAGT
1 AAATTAATGATAATTTAATAGT
* *
11846712 AAA-TCATGAACAATTTAATA-T
1 AAATTAATG-ATAATTTAATAGT
*
11846733 AAAATAATGATAATTT
1 AAATTAATGATAATTT
11846749 GATAATGAAT
Statistics
Matches: 175, Mismatches: 47, Indels: 33
0.69 0.18 0.13
Matches are distributed among these distances:
20 7 0.04
21 28 0.16
22 105 0.60
23 13 0.07
24 3 0.02
25 8 0.05
26 11 0.06
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (22 bp):
AAATTAATGATAATTTAATAGT
Found at i:11846731 original size:44 final size:45
Alignment explanation
Indices: 11846500--11846750 Score: 158
Period size: 44 Copynumber: 5.6 Consensus size: 45
11846490 AATCAATGAT
* * * **
11846500 AATTTAATAGAAAATTAATGATAACTT-AATAGTAAATTA-GTTTC
1 AATTTAATAGTAAATTAATGATAACTTGAGTAGTAAATCATG-AAC
* * * * *
11846544 AATTTAATAGT-AATTAATTGATAAATTTAGTAGTGAATCATAAAT
1 AATTTAATAGTAAATTAA-TGATAACTTGAGTAGTAAATCATGAAC
* * * *
11846589 AATTTAATAGTAAATCAATGATAA-TTTAGTAGTTAATTATTGAA-
1 AATTTAATAGTAAATTAATGATAACTTGAGTAGTAAATCA-TGAAC
** * * * * * *
11846633 AACCTAAAAGTAAATCAATG-TAATTTAGTAGTAGTTAATCATCAAT
1 AATTTAATAGTAAATTAATGATAACTT-G-AGTAGTAAATCATGAAC
** *
11846679 AACATAATAGTTAATTAATGATAACTTGA-TAGTAAATCATGAAC
1 AATTTAATAGTAAATTAATGATAACTTGAGTAGTAAATCATGAAC
* *
11846723 AATTTAATA-TAAAATAATGATAATTTGA
1 AATTTAATAGTAAATTAATGATAACTTGA
11846751 TAATGAATCA
Statistics
Matches: 165, Mismatches: 32, Indels: 21
0.76 0.15 0.10
Matches are distributed among these distances:
43 25 0.15
44 69 0.42
45 33 0.20
46 33 0.20
47 5 0.03
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.37
Consensus pattern (45 bp):
AATTTAATAGTAAATTAATGATAACTTGAGTAGTAAATCATGAAC
Found at i:11846747 original size:90 final size:87
Alignment explanation
Indices: 11846504--11846761 Score: 229
Period size: 90 Copynumber: 2.9 Consensus size: 87
11846494 AATGATAATT
* ** *
11846504 TAATAGAAAATTAATGATAACTTAATAGTAAATTA-GTTTCAATTTAATAGTAATTAATTGATAA
1 TAATAGTAAATTAATGATAACTTAATAGTAAATTATG-AACAATTTAATAGTAAATAA-TGAT-A
**
11846568 ATTTAGTAGTGAATCATAAATAATT
63 ATTTAGTAGTGAATCATAAATAACA
* * * * ** *
11846593 TAATAGTAAATCAATGATAATTTAGTAGTTAATTATTGAA-AACCTAAAAGTAAATCAATG-TAA
1 TAATAGTAAATTAATGATAACTTAATAGTAAATTA-TGAACAATTTAATAGTAAAT-AATGATAA
*
11846656 TTTAGTAGTAGTTAATCATCAATAACA
64 TTTAGTAGT-G--AATCATAAATAACA
* * *
11846683 TAATAGTTAATTAATGATAACTTGATAGTAAATCATGAACAATTTAATA-TAAAATAATGATAAT
1 TAATAGTAAATTAATGATAACTTAATAGTAAATTATGAACAATTTAATAGT-AAATAATGATAAT
*
11846747 TT-GATAATGAATCAT
65 TTAG-TAGTGAATCAT
11846762 GGTTAATTTT
Statistics
Matches: 134, Mismatches: 25, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
87 17 0.13
88 2 0.01
89 54 0.40
90 60 0.45
91 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.37
Consensus pattern (87 bp):
TAATAGTAAATTAATGATAACTTAATAGTAAATTATGAACAATTTAATAGTAAATAATGATAATT
TAGTAGTGAATCATAAATAACA
Found at i:11846891 original size:22 final size:22
Alignment explanation
Indices: 11846815--11846892 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
11846805 TCCAAAAGTA
* * *
11846815 AGTAGTAAATCAATGATAACAT
1 AGTAGTAAATTATTGATAACTT
* *
11846837 AATAGTAAA-TAGTTGATAATTT
1 AGTAGTAAATTA-TTGATAACTT
11846859 AG-ATGTAAATTATTGATAACTT
1 AGTA-GTAAATTATTGATAACTT
11846881 AGTAGTAAATTA
1 AGTAGTAAATTA
11846893 CTAATAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
21 2 0.04
22 40 0.89
23 3 0.07
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (22 bp):
AGTAGTAAATTATTGATAACTT
Found at i:11846970 original size:22 final size:22
Alignment explanation
Indices: 11846944--11847007 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
11846934 AGTTAATCAC
*
11846944 TATAACTTTGTAGTAAA-CCAT
1 TATAACTTTGTAGTAAATCAAT
* **
11846965 TGATAAATTCATAGTAAATCAAT
1 T-ATAACTTTGTAGTAAATCAAT
*
11846988 TATAACTTTGTAATAAATCA
1 TATAACTTTGTAGTAAATCA
11847008 TCAGTTAGTA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.03
22 28 0.85
23 4 0.12
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.38
Consensus pattern (22 bp):
TATAACTTTGTAGTAAATCAAT
Found at i:11847037 original size:22 final size:22
Alignment explanation
Indices: 11847012--11847091 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
11847002 AAATCATCAG
*
11847012 TTAGTAGTAAATCATTAATAAT
1 TTAGTAGTAAATCAATAATAAT
* * * *
11847034 TTAGTATTAAATTAATCATAAC
1 TTAGTAGTAAATCAATAATAAT
* *
11847056 TTAGTAGTAAATAAATACTAAT
1 TTAGTAGTAAATCAATAATAAT
* *
11847078 TTAATGGTAAATCA
1 TTAGTAGTAAATCA
11847092 TTGATAGTTT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (22 bp):
TTAGTAGTAAATCAATAATAAT
Found at i:11847089 original size:44 final size:44
Alignment explanation
Indices: 11847003--11847089 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
11846993 CTTTGTAATA
* * * * * *
11847003 AATCATCAGTTAGTAGTAAATCATTAATAATTTAGTATTAAATT
1 AATCATAACTTAGTAGTAAATAAATAATAATTTAATAGTAAATT
* *
11847047 AATCATAACTTAGTAGTAAATAAATACTAATTTAATGGTAAAT
1 AATCATAACTTAGTAGTAAATAAATAATAATTTAATAGTAAAT
11847090 CATTGATAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (44 bp):
AATCATAACTTAGTAGTAAATAAATAATAATTTAATAGTAAATT
Found at i:11847487 original size:20 final size:21
Alignment explanation
Indices: 11847464--11847508 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
11847454 ATATCATAAG
11847464 TTATCAAAAGATTACTAAAAT
1 TTATCAAAAGATTACTAAAAT
* *
11847485 TATATCAAGAGGTTACTAAAAT
1 T-TATCAAAAGATTACTAAAAT
11847507 TT
1 TT
11847509 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
TTATCAAAAGATTACTAAAAT
Found at i:11847490 original size:22 final size:22
Alignment explanation
Indices: 11847465--11847574 Score: 77
Period size: 21 Copynumber: 5.1 Consensus size: 22
11847455 TATCATAAGT
11847465 TATCAAAAGATTACTAAAATTA
1 TATCAAAAGATTACTAAAATTA
* * *
11847487 TATCAAGAGGTTACTAAAATTT
1 TATCAAAAGATTACTAAAATTA
*
11847509 TAT-AAAAAATTAGC-AAAATTA
1 TATCAAAAGATTA-CTAAAATTA
* * * *
11847530 TGT-TAATGGTTA-TCAAAATTA
1 TATCAAAAGATTACT-AAAATTA
* *
11847551 TATCATAAG-TTACCAAAATTA
1 TATCAAAAGATTACTAAAATTA
11847572 TAT
1 TAT
11847575 TGAAAGTTAT
Statistics
Matches: 66, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
21 41 0.62
22 25 0.38
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (22 bp):
TATCAAAAGATTACTAAAATTA
Found at i:11847548 original size:42 final size:42
Alignment explanation
Indices: 11847502--11847592 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
11847492 AGAGGTTACT
* * * *
11847502 AAAATTTTATAAAAAATTAGCAAAATTATGTT-AATGGTTATC
1 AAAATTATATAAAAAATTACCAAAATTATATTGAA-AGTTATC
* * *
11847544 AAAATTATATCATAAGTTACCAAAATTATATTGAAAGTTATC
1 AAAATTATATAAAAAATTACCAAAATTATATTGAAAGTTATC
11847586 AAAATTA
1 AAAATTA
11847593 AAATTATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 39 0.95
43 2 0.05
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (42 bp):
AAAATTATATAAAAAATTACCAAAATTATATTGAAAGTTATC
Found at i:11847562 original size:21 final size:21
Alignment explanation
Indices: 11847538--11847592 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
11847528 TATGTTAATG
11847538 GTTATCAAAATTATA-TCATAA
1 GTTATCAAAATTATATTCA-AA
* *
11847559 GTTACCAAAATTATATTGAAA
1 GTTATCAAAATTATATTCAAA
11847580 GTTATCAAAATTA
1 GTTATCAAAATTA
11847593 AAATTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.36
Consensus pattern (21 bp):
GTTATCAAAATTATATTCAAA
Found at i:11847598 original size:48 final size:48
Alignment explanation
Indices: 11847544--11847646 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 48
11847534 AATGGTTATC
*
11847544 AAAATTATATCATAAGTTACCAAAATTATA-TTGA-AAGTTATCAAAATT
1 AAAATTATATCAAAAGTTACC-AAATTATACTT-ATAAGTTATCAAAATT
* * * **
11847592 AAAATTATATTAAAAGTTATCAAATTTTACTTATATTTTATCAAAATT
1 AAAATTATATCAAAAGTTACCAAATTATACTTATAAGTTATCAAAATT
11847640 AAAATTA
1 AAAATTA
11847647 AAATATTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 8 0.17
48 39 0.83
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.40
Consensus pattern (48 bp):
AAAATTATATCAAAAGTTACCAAATTATACTTATAAGTTATCAAAATT
Found at i:11848798 original size:60 final size:60
Alignment explanation
Indices: 11848705--11848820 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
11848695 TAGAAATTTT
11848705 TCAGTGTTCATGCGCATATATATTGAGAATATATGATACATGTGCTAGAGTAAAGGTATA
1 TCAGTGTTCATGCGCATATATATTGAGAATATATGATACATGTGCTAGAGTAAAGGTATA
* * *
11848765 TCAGTGTTCATGTGTATATATATT-AGGAATATATGATACATGTGTTAGAGTAAAGG
1 TCAGTGTTCATGCGCATATATATTGA-GAATATATGATACATGTGCTAGAGTAAAGG
11848821 CATAGTATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 1 0.02
60 51 0.98
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.35
Consensus pattern (60 bp):
TCAGTGTTCATGCGCATATATATTGAGAATATATGATACATGTGCTAGAGTAAAGGTATA
Found at i:11850063 original size:14 final size:14
Alignment explanation
Indices: 11850026--11850064 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11850016 TTTGAAATAA
* *
11850026 AAATTAAATTATTT
1 AAATTAATTTAATT
11850040 AAATTAATTTAATT
1 AAATTAATTTAATT
*
11850054 AAATTTATTTA
1 AAATTAATTTA
11850065 TTGAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATTAATTTAATT
Found at i:11850101 original size:20 final size:19
Alignment explanation
Indices: 11850076--11850115 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
11850066 TGAATAAAAA
* *
11850076 TAAATTTAATTTTTTAATTT
1 TAAATTCAATTATTT-ATTT
11850096 TAAATTCAATTATTTATTT
1 TAAATTCAATTATTTATTT
11850115 T
1 T
11850116 CAAACATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TAAATTCAATTATTTATTT
Found at i:11859046 original size:315 final size:315
Alignment explanation
Indices: 11858465--11859110 Score: 1204
Period size: 315 Copynumber: 2.1 Consensus size: 315
11858455 TCTTATATAG
* * *
11858465 ATGATTTAT-GATTTGATTTTAGTTTTGCTCGCTTGAATATCAAATATATTTGAATAATTATTTG
1 ATGATTGATGGATTTGATTTTAGTTTTGCTCGCTTGAATATCAAATATATTCGAATAATTATTTA
* *
11858529 ATTTTTTCTCTCATCCGTGAATGTAGGTTATTTTGGATTAAACTGAACTACATTAAATTATTGTC
66 ATTTTTTCTCTCATCCATGAATATAGGTTATTTTGGATTAAACTGAACTACATTAAATTATTGTC
*
11858594 TCTTATGTAAATAATTTATGGTTTGATTTTACTTCCGCTTGTTTGAATGTTAAACATGTTGAAAC
131 TCTTATATAAATAATTTATGGTTTGATTTTACTTCCGCTTGTTTGAATGTTAAACATGTTGAAAC
11858659 AATTAATGGATCTTTTTTTTTATTCGTGGATGTAGGCCACTTTCGATTGGATTGAACCATATTTA
196 AATTAATGGATCTTTTTTTTTATTCGTGGATGTAGGCCACTTTCGATTGGATTGAACCATATTTA
11858724 ATTGTTATCTTTTGTGTAGATGATTTATAATTTGATCATACCTCTACTTACTTAT
261 ATTGTTATCTTTTGTGTAGATGATTTATAATTTGATCATACCTCTACTTACTTAT
*
11858779 ATGATTGATGGATTTGATTTTAGTTTTGCTCGCTTGAATATCGAATATATTCGAATAATTATTTA
1 ATGATTGATGGATTTGATTTTAGTTTTGCTCGCTTGAATATCAAATATATTCGAATAATTATTTA
11858844 ATTTTTTCTCTCATCCATGAATATAGGTTATTTTGGATTAAACTGAACTACATTAAATTATTGTC
66 ATTTTTTCTCTCATCCATGAATATAGGTTATTTTGGATTAAACTGAACTACATTAAATTATTGTC
*
11858909 TCTTATATAGATAATTTATGGTTTGATTTTACTTCCGCTTGTTTGAATGTTAAACATGTTGAAAC
131 TCTTATATAAATAATTTATGGTTTGATTTTACTTCCGCTTGTTTGAATGTTAAACATGTTGAAAC
*
11858974 AATTAATTGATCTTTTTTTTTATTCGTGGATGTAGGCCACTTTCGATTGGATTGAACCATATTTA
196 AATTAATGGATCTTTTTTTTTATTCGTGGATGTAGGCCACTTTCGATTGGATTGAACCATATTTA
11859039 ATTGTTATCTTTTGTGTAGATGATTTATAATTTGATCATACCTCTACTTACTTAT
261 ATTGTTATCTTTTGTGTAGATGATTTATAATTTGATCATACCTCTACTTACTTAT
11859094 ATGATTGATGGATTTGA
1 ATGATTGATGGATTTGA
11859111 GGTTACTTTC
Statistics
Matches: 322, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
314 8 0.02
315 314 0.98
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (315 bp):
ATGATTGATGGATTTGATTTTAGTTTTGCTCGCTTGAATATCAAATATATTCGAATAATTATTTA
ATTTTTTCTCTCATCCATGAATATAGGTTATTTTGGATTAAACTGAACTACATTAAATTATTGTC
TCTTATATAAATAATTTATGGTTTGATTTTACTTCCGCTTGTTTGAATGTTAAACATGTTGAAAC
AATTAATGGATCTTTTTTTTTATTCGTGGATGTAGGCCACTTTCGATTGGATTGAACCATATTTA
ATTGTTATCTTTTGTGTAGATGATTTATAATTTGATCATACCTCTACTTACTTAT
Found at i:11862586 original size:18 final size:20
Alignment explanation
Indices: 11862563--11862607 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11862553 TATAAAATAG
*
11862563 TAATAAATT-AAAAT-TGAT
1 TAATAAATTAAAAATATAAT
11862581 TAATAAATTAAAAATATAAT
1 TAATAAATTAAAAATATAAT
11862601 TAATAAA
1 TAATAAA
11862608 AATGAGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TAATAAATTAAAAATATAAT
Found at i:11864028 original size:19 final size:19
Alignment explanation
Indices: 11864006--11864057 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
11863996 CAAAACAAAA
11864006 CAAAATAAACAAAAAATCT
1 CAAAATAAACAAAAAATCT
11864025 CAAAACATAAA-AAAAAA-CT
1 C-AAA-ATAAACAAAAAATCT
11864044 --AAA-AAACAAAAAAT
1 CAAAATAAACAAAAAAT
11864058 GTTTTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
14 3 0.10
15 7 0.24
16 2 0.07
19 3 0.10
20 9 0.31
21 5 0.17
ACGTcount: A:0.75, C:0.13, G:0.00, T:0.12
Consensus pattern (19 bp):
CAAAATAAACAAAAAATCT
Found at i:11874598 original size:48 final size:48
Alignment explanation
Indices: 11874546--11874881 Score: 308
Period size: 48 Copynumber: 7.0 Consensus size: 48
11874536 TGAAGAACAT
* * * *
11874546 ATGAGATTTTTAAAGTTGTTGAGCTTTTGTTGAGAGAAGCTTTTTTAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAG
* * * *
11874594 ATGAGATTTTTAAAGTTGTTGAGCCTTTACTAAGAGGAGC-TTTTT-C
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAG
* *
11874640 A--AGA-TTTTAAAGTTGTTGAGCCTCTGCT-AGAAGGAGCTTTTTCCAT
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAG-AGGAGCTTTTT-TAG
* * **
11874686 ATGAGATTTTTAAAGTTGTTGAGCCTCTGTTGAAAGGAGCTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAG
* * * * *
11874734 ATGAAATTTTTAAAGTCGTTAAGCCTCTGTTGAGAGAAGCTTTTTTAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAG
* * * * **
11874782 ATGAAATTTTTAAACTCGTTGAGCCTTTGCTGAGAGGAGCCTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTTAG
* * * * *
11874831 ATGA-ATTTTTTAAAGTTGTTAAACCTTTGGTAAGAGGAGTCTTTTTTAG
1 ATGAGA-TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTTAG
11874880 AT
1 AT
11874882 TTTAAATTTT
Statistics
Matches: 240, Mismatches: 38, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.01
43 28 0.12
44 7 0.03
46 2 0.01
47 5 0.02
48 115 0.48
49 80 0.33
50 1 0.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.40
Consensus pattern (48 bp):
ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAG
Found at i:11874775 original size:140 final size:144
Alignment explanation
Indices: 11874543--11874850 Score: 358
Period size: 140 Copynumber: 2.2 Consensus size: 144
11874533 ATTTGAAGAA
* * * ** *
11874543 CATATGAGATTTTTAAAGTTGTTGAGCTTTTGTTGAGAGAAGCTTTTTTAGATGAGATTTTTAAA
1 CATATGAGATTTTTAAAGTTGTTGAGCCTCTGTTGAAAGAAGCTTTTCAAGATGAAATTTTTAAA
* * * * * *
11874608 GTTGTTGAGCCTTTACTAAGAGGAGCTTTTTCA-A-G-A-TTTTAAAGTTGTTGAGCCTCTGCT-
66 GTCGTTAAGCCTCTACTAAGAGAAGCTTTTTCAGATGAATTTTTAAACTCGTTGAGCCTCTGCTG
*
11874668 AGAAGGAGCTTTTTC
131 AG-AGGAGCCTTTTC
*
11874683 CATATGAGATTTTTAAAGTTGTTGAGCCTCTGTTGAAAGGAGCTTTTCAAGATGAAATTTTTAAA
1 CATATGAGATTTTTAAAGTTGTTGAGCCTCTGTTGAAAGAAGCTTTTCAAGATGAAATTTTTAAA
** * * *
11874748 GTCGTTAAGCCTCTGTTGAGAGAAGCTTTTTTAGATGAAATTTTTAAACTCGTTGAGCCTTTGCT
66 GTCGTTAAGCCTCTACTAAGAGAAGCTTTTTCAGATG-AATTTTTAAACTCGTTGAGCCTCTGCT
11874813 GAGAGGAGCCTTTTC
130 GAGAGGAGCCTTTTC
* *
11874828 AAGATGA-ATTTTTTAAAGTTGTT
1 CATATGAGA-TTTTTAAAGTTGTT
11874851 AAACCTTTGG
Statistics
Matches: 140, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
140 83 0.59
141 1 0.01
142 1 0.01
144 2 0.01
145 51 0.36
146 2 0.01
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (144 bp):
CATATGAGATTTTTAAAGTTGTTGAGCCTCTGTTGAAAGAAGCTTTTCAAGATGAAATTTTTAAA
GTCGTTAAGCCTCTACTAAGAGAAGCTTTTTCAGATGAATTTTTAAACTCGTTGAGCCTCTGCTG
AGAGGAGCCTTTTC
Found at i:11875204 original size:19 final size:19
Alignment explanation
Indices: 11875188--11875234 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
11875178 ACATAATATA
11875188 AAAAAATACCAAAAATAAT
1 AAAAAATACCAAAAATAAT
* *
11875207 ACAAAATACCAAAAAAAAT
1 AAAAAATACCAAAAATAAT
11875226 AAACAAATA
1 AAA-AAATA
11875235 GAAAAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAAAATACCAAAAATAAT
Found at i:11875205 original size:17 final size:18
Alignment explanation
Indices: 11875172--11875228 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
11875162 AACATTAAAC
*
11875172 AAAAATA-CATAATATAA-
1 AAAAATACCA-AAAATAAT
11875189 AAAAATACCAAAAATAAT
1 AAAAATACCAAAAATAAT
*
11875207 ACAAAATACCAAAAAAAAT
1 A-AAAATACCAAAAATAAT
11875226 AAA
1 AAA
11875229 CAAATAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 13 0.37
18 5 0.14
19 17 0.49
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATACCAAAAATAAT
Found at i:11875240 original size:20 final size:22
Alignment explanation
Indices: 11875198--11875241 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
11875188 AAAAAATACC
*
11875198 AAAAATAATACAAAATACCAAA
1 AAAAATAATACAAAATACAAAA
*
11875220 AAAAATAA-AC-AAATAGAAAA
1 AAAAATAATACAAAATACAAAA
11875240 AA
1 AA
11875242 TAGGGGATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.11
Consensus pattern (22 bp):
AAAAATAATACAAAATACAAAA
Found at i:11876037 original size:19 final size:19
Alignment explanation
Indices: 11876013--11876049 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11876003 TTGGTCTGAC
11876013 TGAACCGAAATCGAACCGT
1 TGAACCGAAATCGAACCGT
*
11876032 TGAACCTAAATCGAACCG
1 TGAACCGAAATCGAACCG
11876050 ATACCGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (19 bp):
TGAACCGAAATCGAACCGT
Found at i:11881853 original size:13 final size:13
Alignment explanation
Indices: 11881819--11881869 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
11881809 AACCACTCAA
11881819 AAACACCATTCAG
1 AAACACCATTCAG
* *
11881832 CAA-ACCATTTAG
1 AAACACCATTCAG
11881844 AAACACCATTCAG
1 AAACACCATTCAG
*
11881857 AGACACCATTCAG
1 AAACACCATTCAG
11881870 CATACTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 10 0.31
13 22 0.69
ACGTcount: A:0.43, C:0.29, G:0.10, T:0.18
Consensus pattern (13 bp):
AAACACCATTCAG
Found at i:11881856 original size:25 final size:25
Alignment explanation
Indices: 11881796--11881856 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
11881786 GTGCTCAGAC
* *
11881796 ACACCCTTCAACAAACCACTCAAAA
1 ACACCATTCAGCAAACCACTCAAAA
* * *
11881821 ACACCATTCAGCAAACCATTTAGAA
1 ACACCATTCAGCAAACCACTCAAAA
11881846 ACACCATTCAG
1 ACACCATTCAG
11881857 AGACACCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.44, C:0.34, G:0.05, T:0.16
Consensus pattern (25 bp):
ACACCATTCAGCAAACCACTCAAAA
Found at i:11883064 original size:185 final size:186
Alignment explanation
Indices: 11882515--11883782 Score: 1415
Period size: 185 Copynumber: 6.9 Consensus size: 186
11882505 TAGATAACCG
** * * ** *
11882515 CCTTCAATAATTATGTACAAAAATTAAGAA-GAATTACTAAAGGCATTTTTTTAGAATAAATGCC
1 CCTTCAATAATTATGTACGTAAATT-AGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCC
* * * * * * ** * * *
11882579 TTCACTAATCGTTTTAAAATTTGAGTAGTGGAATATTGAAAGTGTTTTTCATTGAAAGACGGCTT
65 TTCACTAACCATTTTAAAATTTAAGTAGTGAAAAATTGAAGGCATTTTTCACTGGAAGACGCCTT
** * ** *
11882644 TAATAATCTTAAAAATTTTAAGAGGTAATTATTGAAGGTGTTTGTTCTCAAAAAATA
130 TAATAATCCCAAAAATTTTAAGAGGAAATTATTGAAGGCATTTGTTCTAAAAAAATA
* * *
11882701 CTTTCAATAATTATGTACATAAATTAGAAGGAATTAGTG-A----CTTTTATAGAATAAATGCCT
1 CCTTCAATAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCT
* * * *
11882761 TCACTAACCATTTTAAAATTTGAGTAGT-AGAATATTGAAGGCATTTTTCATTGGCAGAC-CCTT
66 TCACTAACCATTTTAAAATTTAAGTAGTGA-AAAATTGAAGGCATTTTTCACTGGAAGACGCCTT
* * *
11882824 TAATAATCCCAAAAATTTTAAAAGGCAATTATTGAAGGCATTTGTTCCT-AAAAAACA
130 TAATAATCCCAAAAATTTTAAGAGGAAATTATTGAAGGCATTTGTT-CTAAAAAAATA
* *
11882881 CCTTCAATAATTATGTACATAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCAT
1 CCTTCAATAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCT
* * * *
11882946 TTACTAACTATTTTAAAATTTAAGTAGTGAAATATTGAAGGCATTTTTCATTGGCAA-ACGCCTT
66 TCACTAACCATTTTAAAATTTAAGTAGTGAAAAATTGAAGGCATTTTTCACTGG-AAGACGCCTT
* * *
11883010 TAATAATCCCAAAAATTTTAAGAGGCAATTATTGATGGCATTTGTTC-AAAAAAACA
130 TAATAATCCCAAAAATTTTAAGAGGAAATTATTGAAGGCATTTGTTCTAAAAAAATA
* * *
11883066 CCTTCAATAATTATGTATGTAAATTAGAAAGAATTAGTGAAGGTGTTTTTATAGAATAAACGCCT
1 CCTTCAATAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCT
* * *
11883131 TCACTAACCATTTTACAAA-TTAAGTAGTGAAAAATTAAAGGCATTTTTCAC-CG--GATGCCTT
66 TCACTAACCATTTTA-AAATTTAAGTAGTGAAAAATTGAAGGCATTTTTCACTGGAAGACGCCTT
** ** *
11883192 TAATAATCCCAAAAATTTTAAGAAAAAATTATTGAAGGTGTTTGTTCTCAAAAAATA
130 TAATAATCCCAAAAATTTTAAGAGGAAATTATTGAAGGCATTTGTTCTAAAAAAATA
* * *
11883249 CCTTCAATAATTATGTACGTAAGTTAGAAGGAATTAGTGAATGCGTTTTTATAGAATAAATGCCT
1 CCTTCAATAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCT
* * * * * *
11883314 TCACTAACCATCTTACAATTTGA-TAGTGAAAAATTGAAGGCATTTTTCACTGAAAGACACATTT
66 TCACTAACCATTTTAAAATTTAAGTAGTGAAAAATTGAAGGCATTTTTCACTGGAAGACGCCTTT
* * * *
11883378 AATAATCTCAAAAATTTTAAGAGGAAATTATTGAAGGTATTTATTCTAAAAAAATG
131 AATAATCCCAAAAATTTTAAGAGGAAATTATTGAAGGCATTTGTTCTAAAAAAATA
* * *
11883434 CCTTTAATAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAAAATAAATGCCG
1 CCTTCAATAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCT
* * * ****
11883499 TCACTAACCATCTTACAATTTAAGTTGTGAAAAATTGAAAATGTTTTTCACTGGAAGACGCCTTT
66 TCACTAACCATTTTAAAATTTAAGTAGTGAAAAATTGAAGGCATTTTTCACTGGAAGACGCCTTT
** * * *
11883564 AATAATCTAAAAAATTTTAAGAGAAAATTATTGAAGGCGTTTGTTCT-AAAAAATG
131 AATAATCCCAAAAATTTTAAGAGGAAATTATTGAAGGCATTTGTTCTAAAAAAATA
* * * * *
11883619 CCTTTAATAGTTATGTACGTAAATTAGAAAGAATTAGTGAAGATGTTTTTCTAGAATAAATGCCT
1 CCTTCAATAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCT
* * * * * * ** * ** *
11883684 TCACTAATCGTCTTACAATTTGAGT--TGCAGAAAATTAAAGGTGTTTCTCACT-GAATGATACT
66 TCACTAACCATTTTAAAATTTAAGTAGTG-A-AAAATTGAAGGCATTTTTCACTGGAA-GACGCC
* *
11883746 TTTAATAATCCTAAAAATTTTAAAAGGAAATTATTGA
128 TTTAATAATCCCAAAAATTTTAAGAGGAAATTATTGA
11883783 TGCGTTTGTT
Statistics
Matches: 946, Mismatches: 113, Indels: 47
0.86 0.10 0.04
Matches are distributed among these distances:
180 88 0.09
181 71 0.08
182 75 0.08
183 85 0.09
184 5 0.01
185 464 0.49
186 158 0.17
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (186 bp):
CCTTCAATAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCT
TCACTAACCATTTTAAAATTTAAGTAGTGAAAAATTGAAGGCATTTTTCACTGGAAGACGCCTTT
AATAATCCCAAAAATTTTAAGAGGAAATTATTGAAGGCATTTGTTCTAAAAAAATA
Found at i:11883302 original size:368 final size:368
Alignment explanation
Indices: 11882515--11883782 Score: 1433
Period size: 368 Copynumber: 3.4 Consensus size: 368
11882505 TAGATAACCG
* * * * *
11882515 CCTTCAATAATTATGTACAAAAATTAAGAA-GAATTACTAAAGGCATTTTTTTAGAATAAATGCC
1 CCTTCAATAATTATGTACATAAATT-AGAAGGAATTAGTGAAGGCGTTTTTATAGAATAAATGCC
* * * ** *
11882579 TTCACTAA-TCGTTTTAAAATTTGAGTAGTGGAATATTGAAAGTGTTTTTCATTGAAAGACGGCT
65 TTCACTAACT-ATTTTAAAATTTGAGTAGTGAAATATTGAAGGCATTTTTCATTGAAAGACGCCT
* * * * *
11882643 TTAATAATCTTAAAAATTTTAAGAGGTAATTATTGAAGGTGTTTGTTCTCAAAAAATACTTTCAA
129 TTAATAATCTCAAAAATTTTAAGAGGAAATTATTGAAGGTATTTGTTCTAAAAAAATACCTTCAA
* *
11882708 TAATTATGTACATAAATTAGAAGGAATTAGTG-A----CTTTTATAGAATAAATGCCTTCACTAA
194 TAATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCTTCACTAA
* * * **
11882768 CCATTTTA-AAATTTGAGTAGT-AGAATATTGAAGGCATTTTTCATTGGCAGACCCTTTAATAAT
259 CCATTTTACAAA-TTAAGTAGTGA-AAAATTAAAGGCATTTTTCACCGG-AG--CCTTTAATAAT
** * *
11882831 CCCAAAAATTTTAA-AAGGCAATTATTGAAGGCATTTGTTC-CTAAAAAACA
319 CCCAAAAATTTTAAGAA-AAAATTATTGAAGGCGTTTGTTCTC-AAAAAATA
* *
11882881 CCTTCAATAATTATGTACATAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCAT
1 CCTTCAATAATTATGTACATAAATTAGAAGGAATTAGTGAAGGCGTTTTTATAGAATAAATGCCT
* * *
11882946 TTACTAACTATTTTAAAATTTAAGTAGTGAAATATTGAAGGCATTTTTCATTGGCAA-ACGCCTT
66 TCACTAACTATTTTAAAATTTGAGTAGTGAAATATTGAAGGCATTTTTCATT-GAAAGACGCCTT
* * * * *
11883010 TAATAATCCCAAAAATTTTAAGAGGCAATTATTGATGGCATTTGTTC-AAAAAAACACCTTCAAT
130 TAATAATCTCAAAAATTTTAAGAGGAAATTATTGAAGGTATTTGTTCTAAAAAAATACCTTCAAT
* * *
11883074 AATTATGTATGTAAATTAGAAAGAATTAGTGAAGGTGTTTTTATAGAATAAACGCCTTCACTAAC
195 AATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCTTCACTAAC
11883139 CATTTTACAAATTAAGTAGTGAAAAATTAAAGGCATTTTTCACCGGATGCCTTTAATAATCCCAA
260 CATTTTACAAATTAAGTAGTGAAAAATTAAAGGCATTTTTCACCGGA-GCCTTTAATAATCCCAA
*
11883204 AAATTTTAAGAAAAAATTATTGAAGGTGTTTGTTCTCAAAAAATA
324 AAATTTTAAGAAAAAATTATTGAAGGCGTTTGTTCTCAAAAAATA
* * *
11883249 CCTTCAATAATTATGTACGTAAGTTAGAAGGAATTAGTGAATGCGTTTTTATAGAATAAATGCCT
1 CCTTCAATAATTATGTACATAAATTAGAAGGAATTAGTGAAGGCGTTTTTATAGAATAAATGCCT
* * * * * * *
11883314 TCACTAACCATCTTACAATTTGA-TAGTGAAAAATTGAAGGCATTTTTCACTGAAAGACACATTT
66 TCACTAACTATTTTAAAATTTGAGTAGTGAAATATTGAAGGCATTTTTCATTGAAAGACGCCTTT
* * *
11883378 AATAATCTCAAAAATTTTAAGAGGAAATTATTGAAGGTATTTATTCTAAAAAAATGCCTTTAATA
131 AATAATCTCAAAAATTTTAAGAGGAAATTATTGAAGGTATTTGTTCTAAAAAAATACCTTCAATA
* *
11883443 ATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAAAATAAATGCCGTCACTAACC
196 ATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCTTCACTAACC
* * * * *
11883508 ATCTTACAATTTAAGTTGTGAAAAATTGAAAATG--TTTTTCACTGGAAGACGCCTTTAATAATC
261 ATTTTACAAATTAAGTAGTGAAAAATT--AAAGGCATTTTTCAC-CG--GA-GCCTTTAATAATC
** * *
11883571 TAAAAAATTTTAAGAGAAAATTATTGAAGGCGTTTGTTCT-AAAAAATG
320 CCAAAAATTTTAAGAAAAAATTATTGAAGGCGTTTGTTCTCAAAAAATA
* * * * ** *
11883619 CCTTTAATAGTTATGTACGTAAATTAGAAAGAATTAGTGAAGATGTTTTTCTAGAATAAATGCCT
1 CCTTCAATAATTATGTACATAAATTAGAAGGAATTAGTGAAGGCGTTTTTATAGAATAAATGCCT
* * * * * * ** * * * ** *
11883684 TCACTAA-TCGTCTTACAATTTGAGTTGCAGAAA-ATTAAAGGTGTTTCTCACTGAATGATACTT
66 TCACTAACT-ATTTTAAAATTTGAGTAG-TGAAATATTGAAGGCATTTTTCATTGAAAGACGCCT
*
11883747 TTAATAATC-CTAAAAATTTTAAAAGGAAATTATTGA
129 TTAATAATCTC-AAAAATTTTAAGAGGAAATTATTGA
11883783 TGCGTTTGTT
Statistics
Matches: 779, Mismatches: 99, Indels: 43
0.85 0.11 0.05
Matches are distributed among these distances:
365 46 0.06
366 147 0.19
367 77 0.10
368 236 0.30
369 5 0.01
370 151 0.19
371 113 0.15
372 4 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (368 bp):
CCTTCAATAATTATGTACATAAATTAGAAGGAATTAGTGAAGGCGTTTTTATAGAATAAATGCCT
TCACTAACTATTTTAAAATTTGAGTAGTGAAATATTGAAGGCATTTTTCATTGAAAGACGCCTTT
AATAATCTCAAAAATTTTAAGAGGAAATTATTGAAGGTATTTGTTCTAAAAAAATACCTTCAATA
ATTATGTACGTAAATTAGAAGGAATTAGTGAAGGTGTTTTTATAGAATAAATGCCTTCACTAACC
ATTTTACAAATTAAGTAGTGAAAAATTAAAGGCATTTTTCACCGGAGCCTTTAATAATCCCAAAA
ATTTTAAGAAAAAATTATTGAAGGCGTTTGTTCTCAAAAAATA
Done.