Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009574.1 Hibiscus syriacus cultivar Beakdansim tig00116939_pilon, 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: 2686660
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2453312 original size:20 final size:19
Alignment explanation
Indices: 2453277--2453343 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2453267 GAAACTTAAA
2453277 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
2453296 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
2453316 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2453335 ATCGCAACG
1 ATCGCAACG
2453344 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2453351 original size:14 final size:14
Alignment explanation
Indices: 2453332--2453389 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2453322 ATGCGAAATG
2453332 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2453346 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2453362 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2453378 AAAATCGCAACG
1 AAAATCGCAACG
2453390 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2453374 original size:32 final size:33
Alignment explanation
Indices: 2453316--2453394 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2453306 GGAAATGGCT
*
2453316 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2453349 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2453381 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2453395 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2453442 original size:14 final size:14
Alignment explanation
Indices: 2453423--2453480 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2453413 TTTCATTTCG
2453423 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2453437 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
2453453 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
2453469 CGTTGCGATTTT
1 CGTTGCGATTTT
2453481 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2453492 original size:33 final size:33
Alignment explanation
Indices: 2453406--2453496 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
2453396 ACAAATCGCA
*
2453406 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
2453439 TTGCGA-TTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2453471 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2453497 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2453532 original size:20 final size:20
Alignment explanation
Indices: 2453481--2453524 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2453471 TTGCGATTTT
*
2453481 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
2453500 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
2453520 CATTT
1 CATTT
2453525 TCGTGTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:2454034 original size:18 final size:18
Alignment explanation
Indices: 2454008--2454052 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2453998 GTCGATCAGA
*
2454008 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2454026 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2454044 TGATGGCTC
1 TGATGGCTC
2454053 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2455387 original size:20 final size:20
Alignment explanation
Indices: 2455362--2455399 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2455352 AATAGTTTCT
2455362 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2455382 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2455400 GAGAGAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2455688 original size:22 final size:22
Alignment explanation
Indices: 2455663--2455706 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2455653 GATTTAGATA
2455663 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2455685 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2455707 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2455919 original size:20 final size:20
Alignment explanation
Indices: 2455894--2455946 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2455884 GATTATGTAT
2455894 TATCGCGTTGCGAAAG-ACAG
1 TATCGCGTTGCGAAAGTA-AG
2455914 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
2455934 TATCTCGTTGCGA
1 TATCGCGTTGCGA
2455947 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:2455986 original size:21 final size:21
Alignment explanation
Indices: 2455957--2456032 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2455947 TTTTTTATTA
*
2455957 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
2455978 TCGTGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
2455998 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
2456019 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
2456033 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:2456002 original size:41 final size:41
Alignment explanation
Indices: 2455939--2456049 Score: 179
Period size: 41 Copynumber: 2.7 Consensus size: 41
2455929 GTAAGTATCT
*
2455939 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGATTTTCCCAATTCG
*
2455981 TGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
2456022 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTACTTATTCGCATTGCGA
2456050 ATTGGGAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
41 51 0.78
42 11 0.17
43 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
Found at i:2456006 original size:20 final size:20
Alignment explanation
Indices: 2455983--2456049 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
2455973 CCAATTCGTG
2455983 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
2456003 TTGCGATTTTCCCAATTCGCG
1 TTGCGA-TTTACTTATTCGCA
2456024 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
2456044 TTGCGA
1 TTGCGA
2456050 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:2457033 original size:20 final size:21
Alignment explanation
Indices: 2457008--2457059 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2456998 TTTTCCTAAT
*
2457008 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
2457028 TCGCAATGCAAATTTGAAAAA
1 TCGCAATGCGAATAAGAAAAA
2457049 TCGCAATGCGA
1 TCGCAATGCGA
2457060 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:2457073 original size:20 final size:20
Alignment explanation
Indices: 2457048--2457202 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
2457038 AATTTGAAAA
*
2457048 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2457068 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
2457089 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2457109 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2457129 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
2457149 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
2457169 TTCGCAACGGGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
2457189 ATCGCAACGAGATA
1 ATCGCAACGCGATA
2457203 ATACAGAATC
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
19 2 0.02
20 101 0.85
21 14 0.12
22 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2457971 original size:24 final size:24
Alignment explanation
Indices: 2457944--2457997 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2457934 GTATTCGAAA
*
2457944 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
2457968 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2457992 TTTGAT
1 TTTGAT
2457998 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2458189 original size:12 final size:12
Alignment explanation
Indices: 2458172--2458196 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2458162 ATATAATCCT
2458172 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2458184 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2458196 G
1 G
2458197 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2459668 original size:24 final size:24
Alignment explanation
Indices: 2459647--2459693 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2459637 TATTTTACTA
2459647 AGTATTATTTATTTAAATTTACAC
1 AGTATTATTTATTTAAATTTACAC
*
2459671 GGTATTATTTATTTAAATTTACA
1 AGTATTATTTATTTAAATTTACA
2459694 GGAACATTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (24 bp):
AGTATTATTTATTTAAATTTACAC
Found at i:2460570 original size:19 final size:19
Alignment explanation
Indices: 2460548--2460678 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
2460538 GGAAATGACT
*
2460548 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
2460567 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
* *
2460581 ACCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
2460600 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2460614 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2460633 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
2460647 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2460666 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2460679 TTTAGTTTCG
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 26 0.31
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.47
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2460592 original size:33 final size:33
Alignment explanation
Indices: 2460548--2460674 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
2460538 GGAAATGACT
2460548 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
*
2460581 ACCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
* *
2460614 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
* *
2460647 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATAAAAATCGCAACG
2460675 CGAATTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
Found at i:2460726 original size:33 final size:33
Alignment explanation
Indices: 2460684--2460788 Score: 183
Period size: 33 Copynumber: 3.2 Consensus size: 33
2460674 GCGAATTTAG
* *
2460684 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
2460717 TTTCGCGTTGCAATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
2460750 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
2460783 TTTCGC
1 TTTCGC
2460789 ATTACGATAG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:2460774 original size:14 final size:14
Alignment explanation
Indices: 2460722--2460778 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2460712 TTTCATTTCG
*
2460722 CGTTGCAATTCTCT
1 CGTTGCGATTCTCT
*
2460736 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2460755 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2460769 CGTTGCGATT
1 CGTTGCGATT
2460779 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2460922 original size:14 final size:14
Alignment explanation
Indices: 2460903--2460939 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2460893 CATCAATTAA
2460903 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2460917 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2460931 ACAAATCAA
1 ACAAATCAA
2460940 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2462375 original size:42 final size:42
Alignment explanation
Indices: 2462329--2462408 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
2462319 CGATGGCAGT
* * *
2462329 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
2462371 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
2462409 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:2462848 original size:19 final size:19
Alignment explanation
Indices: 2462832--2462897 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
2462822 AAAAATGACT
2462832 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2462851 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
2462865 ATCGCAACGCAAAATGAAA
1 ATCGCAACGCGAAATGAAA
2462884 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2462898 CCAAAAGACA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 1 0.03
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2462903 original size:19 final size:19
Alignment explanation
Indices: 2462864--2462903 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2462854 GCAACGAGAG
**
2462864 AATCGCAACGCAAAATGAA
1 AATCGCAACGCAAAACCAA
*
2462883 AATCGCAACGCGAAACCAA
1 AATCGCAACGCAAAACCAA
2462902 AA
1 AA
2462904 GACAAAACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.25, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCAAAACCAA
Found at i:2463093 original size:94 final size:94
Alignment explanation
Indices: 2462984--2463359 Score: 593
Period size: 94 Copynumber: 4.1 Consensus size: 94
2462974 ATGGATTGTA
* * *
2462984 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATATACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2463048 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
2463077 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2463142 TTAGCAGAATTGGTAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2463171 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
2463236 TTACCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2463265 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
2463325 TTTATCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
2463355 TTACT
1 TTACT
2463360 AAGCAATCTA
Statistics
Matches: 267, Mismatches: 13, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
90 40 0.15
93 22 0.08
94 205 0.77
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2465111 original size:14 final size:14
Alignment explanation
Indices: 2465092--2465180 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
2465082 GAAATAGACT
2465092 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2465106 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
2465123 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
* *
2465139 ATCACAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
*
2465158 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
2465172 ATCGCAACG
1 ATCGCAACG
2465181 CGAAATGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
14 24 0.42
15 1 0.02
16 8 0.14
17 7 0.12
18 1 0.02
19 16 0.28
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2465199 original size:33 final size:33
Alignment explanation
Indices: 2465071--2465197 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
2465061 AGATAATGAA
**
2465071 AATCGCAACGCGAAATAGACTATCGCAACGAGAG
1 AATCGCAACGCGAAAT-GAAAATCGCAACGAGAG
**
2465105 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
2465138 AATCACAACGCGAAATGAAAATCGCAATGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
2465171 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2465198 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 72 0.82
34 16 0.18
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2465252 original size:19 final size:20
Alignment explanation
Indices: 2465228--2465282 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2465218 GCGATTATCT
*
2465228 CGTTGCAATTTTCATTT-CG
1 CGTTGCGATTTTCATTTCCG
**
2465247 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
2465267 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
2465283 CTCGAAACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:2465850 original size:20 final size:20
Alignment explanation
Indices: 2465827--2465920 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
2465817 CGATAGTCAG
2465827 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
2465847 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* * *
2465867 AATTCACATTGCGACTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
2465888 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2465908 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2465921 ATTATGAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 44 0.73
21 16 0.27
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2465933 original size:41 final size:41
Alignment explanation
Indices: 2465827--2466058 Score: 127
Period size: 41 Copynumber: 5.7 Consensus size: 41
2465817 CGATAGTCAG
* * * * * *
2465827 ATTCGCATTGCGATTTACG-TATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGAATTATGAAAATCGCATTGCGATTTACGT
* * * *
2465867 AATTCACATTGCGACTTACT--TAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGAATTA-TGAAAATCGCATTGCGATTTACGT
** *
2465908 ATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGT
1 ATTCGCATTGCGAATTATGAAAATCGCATTGCGATTTACGT
* * * * * * *
2465948 AAATCACAATACGAATTAGGAAAATTGCATTGCGATAGT-CAGT
1 -ATTCGCATTGCGAATTATGAAAATCGCATTGCGAT-TTAC-GT
* * * *
2465991 A-TCGCATTGCG-ATTTTCCAAATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGAATTAT-GAAAATCGCATTGCGATTTACGT
* *
2466031 ATTCGCATTGCGAATTGTGAAAAACGCA
1 ATTCGCATTGCGAATTATGAAAATCGCA
2466059 ACGCGAAATT
Statistics
Matches: 143, Mismatches: 37, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
39 1 0.01
40 26 0.18
41 107 0.75
42 6 0.04
43 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (41 bp):
ATTCGCATTGCGAATTATGAAAATCGCATTGCGATTTACGT
Found at i:2466036 original size:20 final size:21
Alignment explanation
Indices: 2465992--2466043 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2465982 ATAGTCAGTA
*
2465992 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
2466013 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2466033 TCGCATTGCGA
1 TCGCATTGCGA
2466044 ATTGTGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2466085 original size:21 final size:22
Alignment explanation
Indices: 2466033--2466085 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2466023 ATTTACTTAT
2466033 TCGCATTGCG-AATTGTGAAAA
1 TCGCATTGCGAAATTGTGAAAA
* **
2466054 ACGCAACGCGAAATTG-GAAAA
1 TCGCATTGCGAAATTGTGAAAA
2466075 TCGCATTGCGA
1 TCGCATTGCGA
2466086 TAGTTATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGTGAAAA
Found at i:2469016 original size:35 final size:35
Alignment explanation
Indices: 2468977--2469051 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
2468967 TTTATGTTCA
*
2468977 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
1 AAATTCAAAAACACTTCAATTACATTCTAAACCCT
* * *
2469012 AAATTCAAAAATACTTTAATTACATTTTAAACCCT
1 AAATTCAAAAACACTTCAATTACATTCTAAACCCT
2469047 AAATT
1 AAATT
2469052 AAAGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATTCAAAAACACTTCAATTACATTCTAAACCCT
Found at i:2469122 original size:35 final size:34
Alignment explanation
Indices: 2469046--2469123 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
2469036 TTTTAAACCC
*
2469046 TAAATTAAAGTATTTTAGAATTTGGGGTTTAAAA
1 TAAATTGAAGTATTTTAGAATTTGGGGTTTAAAA
* * *
2469080 TATAATTGAATTATTTTGGAATTTGGGGTTTAGAA
1 TA-AATTGAAGTATTTTAGAATTTGGGGTTTAAAA
2469115 TGAAATTGA
1 T-AAATTGA
2469124 GGACTATGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.05
35 35 0.92
36 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (34 bp):
TAAATTGAAGTATTTTAGAATTTGGGGTTTAAAA
Found at i:2469573 original size:52 final size:52
Alignment explanation
Indices: 2469514--2469632 Score: 204
Period size: 51 Copynumber: 2.3 Consensus size: 52
2469504 TATCTTAAAT
2469514 ATATGTAAAATTAATTTTTTTTACGTAATATAAATGGATCCTAACTATATAC
1 ATATGTAAAATTAATTTTTTTTACGTAATATAAATGGATCCTAACTATATAC
2469566 ATATGTAAAATTAA-TTTTTTTACGTAATATAAATGGATCCTAACTATATAC
1 ATATGTAAAATTAATTTTTTTTACGTAATATAAATGGATCCTAACTATATAC
* * *
2469617 GTATATAAAGTTAATT
1 ATATGTAAAATTAATT
2469633 GATGTCAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
51 48 0.76
52 15 0.24
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (52 bp):
ATATGTAAAATTAATTTTTTTTACGTAATATAAATGGATCCTAACTATATAC
Found at i:2477630 original size:26 final size:26
Alignment explanation
Indices: 2477601--2477665 Score: 107
Period size: 24 Copynumber: 2.6 Consensus size: 26
2477591 GTATACTATT
2477601 GACTTACTACAAGTTTTTTTTTAACC
1 GACTTACTACAAGTTTTTTTTTAACC
*
2477627 GACTTACTACAAG--TTTTTTTAACT
1 GACTTACTACAAGTTTTTTTTTAACC
2477651 GACTTACTACAAGTT
1 GACTTACTACAAGTT
2477666 GAGTATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 23 0.64
26 13 0.36
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.43
Consensus pattern (26 bp):
GACTTACTACAAGTTTTTTTTTAACC
Found at i:2489580 original size:226 final size:227
Alignment explanation
Indices: 2489265--2489686 Score: 617
Period size: 226 Copynumber: 1.9 Consensus size: 227
2489255 GATATTCGAG
* * * *
2489265 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACTCGACCCGGAAATATATATAATTTTACCTTAT
1 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAAGACCCGACCCGAAAAAATATATAATTTTACCTTAT
* *
2489330 ATATTTAGGAATAATTACAATAATA-CCC-CTCTATATATATATTTTTTTCAATTAAGTCACTGT
66 ATATTTAGGAATAATTACAATAATACCCCTCTCTATATATATATATTTTT-AATTAAGTCAATGT
*
2489393 TTTTATTGAATAAAAATAATTT-TT-TTA-TT-ATTTCG-GTCGGGTCG-GATTTCTAATTCATA
130 TTTTATTGAAT-AAAATAATTTATTATTATTTCATGTCGTGTCGGGTCGAG-TTTCTAATTCATA
2489452 TATTCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
193 TATTCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
* *
2489487 TCGGGTCGGGTTCTGGTTTAGGGTGAAAAACCCAGACCCGACCCGAAAAAATATATAATTTTACC
1 TCGGGTCGAGTTCGGGTTTAGGGTG-AAAA---AGACCCGACCCGAAAAAATATATAATTTTACC
2489552 TTATATATTTAGGAATAATTACAATAATACCCCTCTCTATATATATATATTTTTAATTAAGTCAA
62 TTATATATTTAGGAATAATTACAATAATACCCCTCTCTATATATATATATTTTTAATTAAGTCAA
* **
2489617 TGTTTTTATTGAATAAATTTTTTTATTATTATTTCATGTCGTGTCGGGTCGAGTTTCTAATTCAT
127 TGTTTTTATTGAATAAAATAATTTATTATTATTTCATGTCGTGTCGGGTCGAGTTTCTAATTCAT
2489682 ATATT
192 ATATT
2489687 GAATAAAAAT
Statistics
Matches: 176, Mismatches: 12, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
222 23 0.13
223 4 0.02
226 64 0.36
227 29 0.16
228 22 0.12
229 2 0.01
230 5 0.03
231 26 0.15
232 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (227 bp):
TCGGGTCGAGTTCGGGTTTAGGGTGAAAAAGACCCGACCCGAAAAAATATATAATTTTACCTTAT
ATATTTAGGAATAATTACAATAATACCCCTCTCTATATATATATATTTTTAATTAAGTCAATGTT
TTTATTGAATAAAATAATTTATTATTATTTCATGTCGTGTCGGGTCGAGTTTCTAATTCATATAT
TCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:2490045 original size:44 final size:44
Alignment explanation
Indices: 2489982--2490065 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
2489972 TTTACACATG
* * *
2489982 TCTGCGAACCACACAGAATATGGAATTGGATTCTAATTCCATAT
1 TCTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATAT
*
2490026 TCTGCCAACCAAATAGAATATGGAATTGGATTCCAATTCC
1 TCTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCC
2490066 TGACAGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (44 bp):
TCTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATAT
Found at i:2490099 original size:18 final size:17
Alignment explanation
Indices: 2490054--2490100 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
2490044 TATGGAATTG
*
2490054 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
2490071 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
2490089 TATTCCAATTCC
1 GATTCCAATTCC
2490101 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:2492512 original size:21 final size:20
Alignment explanation
Indices: 2492426--2492583 Score: 88
Period size: 21 Copynumber: 7.8 Consensus size: 20
2492416 AAATGACCAA
* **
2492426 CAAAATCGCAATGCGAAATT
1 CAAAATCGCAACGCGATTTT
**
2492446 -AAAATCGCAACGCGA-TCC
1 CAAAATCGCAACGCGATTTT
** *
2492464 CAAGAATCGCAAATC-AGTTTC
1 CAA-AATCGCAACGCGA-TTTT
2492485 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2492506 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2492527 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2492547 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2492568 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2492584 ACACATAAAT
Statistics
Matches: 105, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
19 17 0.16
20 36 0.34
21 52 0.50
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2492612 original size:20 final size:20
Alignment explanation
Indices: 2492550--2492700 Score: 173
Period size: 20 Copynumber: 7.7 Consensus size: 20
2492540 CGATTTTCCA
* ** *
2492550 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2492570 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2492590 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2492610 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2492630 ATATCGCAACG-GTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
2492649 AAATCGCAACG-ATATACAT
1 AAATCGCAACGCGTATCCGT
2492668 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
2492688 AAATCGCAACGCG
1 AAATCGCAACGCG
2492701 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 35 0.31
20 75 0.67
21 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2492656 original size:39 final size:39
Alignment explanation
Indices: 2492550--2492698 Score: 176
Period size: 39 Copynumber: 3.8 Consensus size: 39
2492540 CGATTTTCCA
* ** * *
2492550 AAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAA--CGATATACAT
* * *
2492590 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-ATATACAT
*
2492630 ATATCGCAACG-GTATCCGTAAATCGCAACGATATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGATATACAT
2492668 AAATCGCAACGCGTATCCGTAAATCGCAACG
1 AAATCGCAACGCGTATCCGTAAATCGCAACG
2492699 CGATATTTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
38 17 0.18
39 38 0.41
40 38 0.41
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGATATACAT
Found at i:2493113 original size:33 final size:33
Alignment explanation
Indices: 2493074--2493141 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
2493064 TTCACTTAGA
*
2493074 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2493107 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2493140 TT
1 TT
2493142 CAAGTTAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2493266 original size:20 final size:20
Alignment explanation
Indices: 2493222--2493296 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
2493212 TGCAGAAGAG
*
2493222 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
2493243 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
2493263 TCGCAACGAGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
2493282 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
2493297 CGCAACGCGA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.35
20 19 0.41
21 11 0.24
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:2493284 original size:39 final size:36
Alignment explanation
Indices: 2493215--2493329 Score: 137
Period size: 33 Copynumber: 3.1 Consensus size: 36
2493205 TTCAATTTGC
*
2493215 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAG--AAATGAAAATCGCAACGAG
2493253 AGAATGACTGTCGCAACGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAAATGAAAATCGCAACGAG
* *
2493292 AG-A-A-TCGCAACGCGAAATGAAAATCGCAACTAG
1 AGAATAGTCGCAACGAGAAATGAAAATCGCAACGAG
2493325 AGAAT
1 AGAAT
2493330 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
33 29 0.42
34 1 0.01
36 1 0.01
38 5 0.07
39 22 0.32
41 11 0.16
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.12
Consensus pattern (36 bp):
AGAATAGTCGCAACGAGAAATGAAAATCGCAACGAG
Found at i:2493285 original size:19 final size:19
Alignment explanation
Indices: 2493222--2493321 Score: 102
Period size: 19 Copynumber: 5.4 Consensus size: 19
2493212 TGCAGAAGAG
2493222 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AAATGAAAA
***
2493243 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGA-AATGAAAA
2493263 TCGCAACGAGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
2493282 TCGCAACGAG--A-G--AA
1 TCGCAACGAGAAATGAAAA
*
2493296 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
2493315 TCGCAAC
1 TCGCAAC
2493322 TAGAGAATCG
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.17
16 2 0.03
17 2 0.03
19 25 0.38
20 16 0.24
21 10 0.15
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
TCGCAACGAGAAATGAAAA
Found at i:2493299 original size:14 final size:14
Alignment explanation
Indices: 2493280--2493336 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2493270 GAGAAATGAA
2493280 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2493294 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2493313 AATCGCAACTAGAG
1 AATCGCAACGAGAG
2493327 AATCGCAACG
1 AATCGCAACG
2493337 CGAAAACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2493309 original size:33 final size:33
Alignment explanation
Indices: 2493234--2493341 Score: 144
Period size: 33 Copynumber: 3.1 Consensus size: 33
2493224 GCAACGAGAT
*
2493234 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
2493273 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
*
2493306 AAATGAAAATCGCAACTAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
2493339 AAA
1 AAA
2493342 ACCAAAATCG
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
33 44 0.66
36 1 0.01
38 1 0.01
39 21 0.31
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:2493376 original size:19 final size:18
Alignment explanation
Indices: 2493349--2493411 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
2493339 AAAACCAAAA
*
2493349 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
2493368 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
2493382 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
2493400 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2493412 CTCTAGTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.27
15 3 0.08
17 3 0.08
18 11 0.30
19 10 0.27
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:2493390 original size:14 final size:14
Alignment explanation
Indices: 2493371--2493455 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 14
2493361 TTTCATTTCG
2493371 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2493385 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
2493403 CGTTGCGA-TCTCT
1 CGTTGCGATTCTCT
* * *
2493416 AGTTGC-TTTCATTTCG
1 CGTTGCGATTC---TCT
2493432 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2493446 CGTTGCGATT
1 CGTTGCGATT
2493456 TCATTTCAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
13 9 0.17
14 20 0.37
15 3 0.06
16 9 0.17
17 3 0.06
18 10 0.19
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2493401 original size:32 final size:32
Alignment explanation
Indices: 2493354--2493462 Score: 179
Period size: 32 Copynumber: 3.5 Consensus size: 32
2493344 CAAAATCGCA
2493354 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
*
2493387 TTGCGATTTCATTTCGCGTTGCGA-TCTCTAG
1 TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
2493418 TTGC--TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
2493448 TTGCGATTTCATTTC
1 TTGCGATTTCATTTC
2493463 AACCAAAAGA
Statistics
Matches: 71, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
29 18 0.25
30 10 0.14
31 10 0.14
32 27 0.38
33 6 0.08
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2494603 original size:208 final size:204
Alignment explanation
Indices: 2494206--2494611 Score: 760
Period size: 208 Copynumber: 2.0 Consensus size: 204
2494196 ACCGCAAAAG
2494206 TTTGCGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGAATTTC
1 TTTGCGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGAATTTC
2494271 TATAATGTTCTAAAATATAATTAATTATTTAACAATTACTAATTTGTTATTATATTGTTTGTAGA
66 TATAATGTTCTAAAATATAATTAATTATTTAACAATTACTAATTTGTTATTATATTGTTTGTAGA
2494336 TTTGGATATTCGAGGTTTCCCCAACATGCGTACATATGCAATAAAAACGTCAAATGATATTCCCA
131 TTTGGATATTCGAGGTTTCCCCAACATGCGTACATATGCAATAAAAACGTCAAATGATATTCCCA
2494401 GGGATTCCT
196 GGGATTCCT
2494410 TTTGCGGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTG-TTGGGCCTTTAAGGTAAGAATTT
1 TTTGC-GGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGAATTT
2494474 CTATATAATGTTCTAAAATATAATTAATTATTTAACAATTACTAATTTTGTTATTATATTGTTTG
65 C--TATAATGTTCTAAAATATAATTAATTATTTAACAATTACTAA-TTTGTTATTATATTGTTTG
2494539 TAGATTTGGATATTCGAGGCTTTCCCCAACATGCGTACATATGCAATAAAAACGTCAAATGATAT
127 TAGATTTGGATATTCGAGG-TTTCCCCAACATGCGTACATATGCAATAAAAACGTCAAATGATAT
2494604 TCCCAGGG
191 TCCCAGGG
2494612 CTATTCCTGG
Statistics
Matches: 197, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
204 29 0.15
205 35 0.18
206 42 0.21
207 38 0.19
208 53 0.27
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (204 bp):
TTTGCGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGAATTTC
TATAATGTTCTAAAATATAATTAATTATTTAACAATTACTAATTTGTTATTATATTGTTTGTAGA
TTTGGATATTCGAGGTTTCCCCAACATGCGTACATATGCAATAAAAACGTCAAATGATATTCCCA
GGGATTCCT
Found at i:2495586 original size:93 final size:93
Alignment explanation
Indices: 2495318--2495968 Score: 1217
Period size: 93 Copynumber: 7.1 Consensus size: 93
2495308 TAGATTGCTT
*
2495318 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2495383 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2495411 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
2495476 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2495505 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2495570 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2495598 AGTAAATTTG-TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2495662 TTTGTCTTGTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTT-TGTTTTGTCTTTTGGTTGAA
2495691 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2495756 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2495784 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2495849 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2495876 GGTAAATTTGTT--GTTGCTGCCAATTCTGCTAAACTGTGTATTC--TAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2495937 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2495964 AGTAA
1 AGTAA
2495969 TGCAATCCAT
Statistics
Matches: 551, Mismatches: 3, Indels: 13
0.97 0.01 0.02
Matches are distributed among these distances:
88 23 0.04
89 25 0.05
90 31 0.06
92 100 0.18
93 217 0.39
94 155 0.28
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2496111 original size:19 final size:19
Alignment explanation
Indices: 2496040--2496152 Score: 92
Period size: 19 Copynumber: 5.8 Consensus size: 19
2496030 GCGATTTTCA
2496040 TCATTTCGCGTTGCGA--T
1 TCATTTCGCGTTGCGATTT
2496057 TC-TTT--CGTTGCGATTT
1 TCATTTCGCGTTGCGATTT
2496073 TCGCATTGTTCTGTCGTTGCGATTT
1 T--CA-T-TTC-G-CGTTGCGATTT
2496098 TCATTTCGCGTTGCGATTT
1 TCATTTCGCGTTGCGATTT
**
2496117 TGGTTTCGCGTTGCGATTT
1 TCATTTCGCGTTGCGATTT
* *
2496136 TAAGTTTCGTGTTGCGA
1 TCA-TTTCGCGTTGCGA
2496153 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
14 8 0.10
16 5 0.06
17 2 0.03
18 1 0.01
19 29 0.37
20 14 0.18
21 5 0.06
22 1 0.01
23 2 0.03
25 12 0.15
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.47
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATTT
Found at i:2499417 original size:20 final size:20
Alignment explanation
Indices: 2499389--2499658 Score: 281
Period size: 20 Copynumber: 13.5 Consensus size: 20
2499379 AAATTTCAGT
* * *
2499389 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2499409 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2499429 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2499449 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* * *
2499469 GTTGCAATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2499489 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2499509 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2499529 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2499549 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
2499569 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
2499589 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2499609 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2499629 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2499649 GTTGCGATTT
1 GTTGCGATTT
2499659 TGGAAAATCG
Statistics
Matches: 218, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
20 217 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2499675 original size:21 final size:21
Alignment explanation
Indices: 2499645--2499727 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2499635 ATTTTCATAT
*
2499645 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2499666 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2499687 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2499708 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2499728 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2499718 original size:42 final size:43
Alignment explanation
Indices: 2499625--2499723 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2499615 ATTTATGTGT
* *
2499625 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
2499666 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
2499708 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2499724 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:2507899 original size:2 final size:2
Alignment explanation
Indices: 2507892--2507927 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2507882 ATAGTTTTGA
*
2507892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2507928 TTGTAATTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2509521 original size:25 final size:25
Alignment explanation
Indices: 2509487--2509546 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
2509477 TTTGTCCCAC
2509487 AAAATTTTATAAGTTAACTCATCTT
1 AAAATTTTATAAGTTAACTCATCTT
* ** *
2509512 AAAATCTTATAAGTTTGCTCCTCTT
1 AAAATTTTATAAGTTAACTCATCTT
2509537 AAAATTTTAT
1 AAAATTTTAT
2509547 GAATTCGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (25 bp):
AAAATTTTATAAGTTAACTCATCTT
Found at i:2512763 original size:13 final size:13
Alignment explanation
Indices: 2512745--2512770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2512735 TCTTAAGGCC
2512745 TTAAAACTTAAAT
1 TTAAAACTTAAAT
2512758 TTAAAACTTAAAT
1 TTAAAACTTAAAT
2512771 ATTTATCAAA
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:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAACTTAAAT
Found at i:2514320 original size:13 final size:13
Alignment explanation
Indices: 2514302--2514327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2514292 TCTTAAGGCC
2514302 TTAAAACTTAAAT
1 TTAAAACTTAAAT
2514315 TTAAAACTTAAAT
1 TTAAAACTTAAAT
2514328 ATTTATCAAA
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:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAACTTAAAT
Found at i:2515183 original size:21 final size:21
Alignment explanation
Indices: 2515158--2515225 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
2515148 ATCTCTTGAG
2515158 TAGTATTGTTATGATCGCAGT
1 TAGTATTGTTATGATCGCAGT
* *
2515179 TAGTA--G-GAGTGATCTCTTGAG-
1 TAGTATTGTTA-TGATCGC---AGT
2515200 TAGTATTGTTATGATCGCAGT
1 TAGTATTGTTATGATCGCAGT
2515221 TAGTA
1 TAGTA
2515226 GGAGTGACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 1 0.03
19 7 0.20
20 2 0.06
21 15 0.43
22 2 0.06
23 7 0.20
24 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (21 bp):
TAGTATTGTTATGATCGCAGT
Found at i:2515249 original size:42 final size:42
Alignment explanation
Indices: 2515140--2515237 Score: 187
Period size: 42 Copynumber: 2.3 Consensus size: 42
2515130 ATAGTGCAAT
2515140 TAGGAGTGATCTCTTGAGTAGTATTGTTATGATCGCAGTTAG
1 TAGGAGTGATCTCTTGAGTAGTATTGTTATGATCGCAGTTAG
2515182 TAGGAGTGATCTCTTGAGTAGTATTGTTATGATCGCAGTTAG
1 TAGGAGTGATCTCTTGAGTAGTATTGTTATGATCGCAGTTAG
*
2515224 TAGGAGTGACCTCT
1 TAGGAGTGATCTCT
2515238 CCAGGAGTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (42 bp):
TAGGAGTGATCTCTTGAGTAGTATTGTTATGATCGCAGTTAG
Found at i:2520426 original size:29 final size:30
Alignment explanation
Indices: 2520367--2520426 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
2520357 TAAAATATGT
* **
2520367 GTTAAATTAGTTTTTTTTTTAAATTTGAGA
1 GTTAAATTAGTTTTATTTTTAAATTCAAGA
2520397 GTTAAATTAG-TTTATTTTTAAATTCAAGA
1 GTTAAATTAGTTTTATTTTTAAATTCAAGA
2520426 G
1 G
2520427 CTTGTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (30 bp):
GTTAAATTAGTTTTATTTTTAAATTCAAGA
Found at i:2520489 original size:24 final size:24
Alignment explanation
Indices: 2520444--2520489 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2520434 ATTTTATTAG
* *
2520444 AAAAATAAAAATTATTTTAAATTT
1 AAAAATAAAAATTATCTAAAATTT
2520468 AAAATATAAAAA-TATCTAAAAT
1 AAAA-ATAAAAATTATCTAAAAT
2520490 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAAATAAAAATTATCTAAAATTT
Found at i:2521585 original size:54 final size:54
Alignment explanation
Indices: 2521521--2521635 Score: 203
Period size: 54 Copynumber: 2.1 Consensus size: 54
2521511 CGGAGTGCAC
2521521 ACTTGTTTGAATTTATTATGATTTGAAATGTTATGTGGTGGTTTTGTAACTACT
1 ACTTGTTTGAATTTATTATGATTTGAAATGTTATGTGGTGGTTTTGTAACTACT
* *
2521575 ACTTGTTTGAATTTATTATGATTTGAATTGTTATGTGGTGGTTTTGTAACTGCT
1 ACTTGTTTGAATTTATTATGATTTGAAATGTTATGTGGTGGTTTTGTAACTACT
*
2521629 ATTTGTT
1 ACTTGTT
2521636 AGTTTTCGTC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.22, C:0.05, G:0.21, T:0.52
Consensus pattern (54 bp):
ACTTGTTTGAATTTATTATGATTTGAAATGTTATGTGGTGGTTTTGTAACTACT
Found at i:2524508 original size:46 final size:45
Alignment explanation
Indices: 2524416--2524540 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
2524406 AATTAAATTG
* * ** **
2524416 AACATCGAATGTATTTCATGCATCGATATACTAAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACTTTGGATTTTATG-A
*
2524462 AACATCGAATGCATTTGATGCATCGATGCACTTTGG-TTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTTTGGATT-TTATGA
* *
2524507 AACATCGAATGCACTTGATACATCGATGCACTTT
1 AACATCGAATGCATTTGATGCATCGATGCACTTT
2524541 TAGTGCACCG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 35 0.51
46 34 0.49
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (45 bp):
AACATCGAATGCATTTGATGCATCGATGCACTTTGGATTTTATGA
Found at i:2524537 original size:17 final size:18
Alignment explanation
Indices: 2524503--2524539 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2524493 TTTGGTTATT
2524503 TTGAAACATCGAATGCAC
1 TTGAAACATCGAATGCAC
*
2524521 TTGATACATCG-ATGCAC
1 TTGAAACATCGAATGCAC
2524538 TT
1 TT
2524540 TTAGTGCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (18 bp):
TTGAAACATCGAATGCAC
Found at i:2530392 original size:21 final size:21
Alignment explanation
Indices: 2530327--2530421 Score: 77
Period size: 23 Copynumber: 4.4 Consensus size: 21
2530317 TTGTGCTTAA
*
2530327 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
* *
2530347 TGCACCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
2530369 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
2530390 TGCACCGATGAACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
2530413 TGCATCGAT
1 TGCATCGAT
2530422 GCACAAGGCC
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.17
21 17 0.29
22 12 0.21
23 19 0.33
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:2530417 original size:44 final size:42
Alignment explanation
Indices: 2530327--2530421 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
2530317 TTGTGCTTAA
* *
2530327 TGCATCGATACACCTAACAGTGCACCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGAAGCCTTGAATG
*
2530369 TGCATCGATACACCATGAA-GGTGCACCGATGAACGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGAA-GCCTTGAATG
2530413 TGCATCGAT
1 TGCATCGAT
2530422 GCACAAGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 20 0.43
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGAAGCCTTGAATG
Found at i:2532372 original size:14 final size:15
Alignment explanation
Indices: 2532347--2532375 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2532337 TTATTTTTTA
2532347 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
2532362 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
2532376 AAATGCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:2532684 original size:23 final size:23
Alignment explanation
Indices: 2532655--2532698 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2532645 TAACAAAAAG
2532655 GGGGAGAAATATTAAGTGTTAAA
1 GGGGAGAAATATTAAGTGTTAAA
* *
2532678 GGGGAGAAGTGTTAAGTGTTA
1 GGGGAGAAATATTAAGTGTTA
2532699 TAGTAAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.27
Consensus pattern (23 bp):
GGGGAGAAATATTAAGTGTTAAA
Found at i:2533175 original size:66 final size:62
Alignment explanation
Indices: 2533038--2533248 Score: 187
Period size: 66 Copynumber: 3.3 Consensus size: 62
2533028 TTTATCAAAG
* * * *
2533038 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGA
1 TGATGCATCGATGCA-CAA-CCATGCATCGATACACTCAGGATATT---TTGAAACATCGAATGC
2533100 ATT
61 A-T
* *
2533103 TCATGCATCGATGCACATACCATGCATCGATACACTGAGGAT-TTTATGAAAAACATCGAATGCA
1 TGATGCATCGATGCACA-ACCATGCATCGATACACTCAGGATATTT-TG--AAACATCGAATGCA
2533167 T
62 T
* * * *
2533168 ATGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 -TGATGCATCGATGCA-CAACCATGCATCGATACACTCAGGATATTTTGAAACATCGAATGCA-T
2533233 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
2533249 TCTTAGTGAA
Statistics
Matches: 123, Mismatches: 12, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 46 0.37
65 21 0.17
66 47 0.38
67 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (62 bp):
TGATGCATCGATGCACAACCATGCATCGATACACTCAGGATATTTTGAAACATCGAATGCAT
Found at i:2536228 original size:54 final size:55
Alignment explanation
Indices: 2536163--2536274 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 55
2536153 TAGTGCGGAG
2536163 TGCACACTTGTTTGAATTTATTATGATTTGAACTGTTATGTGGTGGTTTTGTAAC
1 TGCACACTTGTTTGAATTTATTATGATTTGAACTGTTATGTGGTGGTTTTGTAAC
*
2536218 TGCA-ACTTGTTTGAATTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAAC
1 TGCACACTTGTTTGAATTTATTATGATTTGAACTGTTATGTGGTGGTTTTGTAAC
2536272 TGC
1 TGC
2536275 TATTTGTTAG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 52 0.93
55 4 0.07
ACGTcount: A:0.21, C:0.10, G:0.22, T:0.47
Consensus pattern (55 bp):
TGCACACTTGTTTGAATTTATTATGATTTGAACTGTTATGTGGTGGTTTTGTAAC
Found at i:2541060 original size:15 final size:15
Alignment explanation
Indices: 2541040--2541069 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2541030 ATCAAAAAAC
2541040 GAATTAACGTCGCAT
1 GAATTAACGTCGCAT
*
2541055 GAATTAACGTTGCAT
1 GAATTAACGTCGCAT
2541070 CGCATGAATT
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:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (15 bp):
GAATTAACGTCGCAT
Found at i:2541074 original size:20 final size:20
Alignment explanation
Indices: 2541049--2541089 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2541039 CGAATTAACG
2541049 TCGCATGAATTAACGTTGCA
1 TCGCATGAATTAACGTTGCA
2541069 TCGCATGAATTAACGTTGCA
1 TCGCATGAATTAACGTTGCA
2541089 T
1 T
2541090 GGGACATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (20 bp):
TCGCATGAATTAACGTTGCA
Found at i:2541227 original size:22 final size:22
Alignment explanation
Indices: 2541195--2541243 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2541185 TTTGGCCCTA
*
2541195 CTCCCCGCTGCATGCTCGCCTG
1 CTCCCCACTGCATGCTCGCCTG
2541217 CTCCCCACTGCATGCTCGCCTG
1 CTCCCCACTGCATGCTCGCCTG
*
2541239 TTCCC
1 CTCCC
2541244 GCTGCTCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.06, C:0.51, G:0.18, T:0.24
Consensus pattern (22 bp):
CTCCCCACTGCATGCTCGCCTG
Found at i:2541873 original size:15 final size:16
Alignment explanation
Indices: 2541845--2541878 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2541835 GTTTGTTACT
2541845 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
2541861 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
2541876 TTA
1 TTA
2541879 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:2544065 original size:10 final size:10
Alignment explanation
Indices: 2544050--2544076 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2544040 TAATTTCATT
2544050 ATTACTAATC
1 ATTACTAATC
2544060 ATTACTAATC
1 ATTACTAATC
2544070 ATTACTA
1 ATTACTA
2544077 TCAAATCATT
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:2544129 original size:59 final size:60
Alignment explanation
Indices: 2543986--2544192 Score: 314
Period size: 59 Copynumber: 3.5 Consensus size: 60
2543976 ATAATAATTT
* *
2543986 CATTATTACTAAAT-ATTACTAAATCATTAATATCAAATCATTAAATATTAATAA-TAATTT
1 CATTATTACT-AATCAGTACTAAATCATTACTATCAAATCATTAAATATTAATAATTAA-TT
*
2544046 CATTATTACTAATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAA-TAATT
1 CATTATTACTAATCAGTACTAAATCATTACTATCAAATCATTAAATATTAATAATTAATT
*
2544104 CATTATTACTAATCAGTACTAAATCATTACTATCAAATCATTAAATATTAATAATTATTT
1 CATTATTACTAATCAGTACTAAATCATTACTATCAAATCATTAAATATTAATAATTAATT
* *
2544164 TATTATTACTAATCATTACTAAATCATTA
1 CATTATTACTAATCAGTACTAAATCATTA
2544193 TTATAATTTC
Statistics
Matches: 139, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
58 21 0.15
59 71 0.51
60 47 0.34
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (60 bp):
CATTATTACTAATCAGTACTAAATCATTACTATCAAATCATTAAATATTAATAATTAATT
Found at i:2544192 original size:21 final size:21
Alignment explanation
Indices: 2544050--2544192 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
2544040 TAATTTCATT
2544050 ATTACTAATCATTACT-AATC
1 ATTACTAATCATTACTAAATC
* *
2544070 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * *
2544091 ATTAATAATAATT-C---ATT
1 ATTACTAATCATTACTAAATC
*
2544108 ATTACTAATCAGTACTAAATC
1 ATTACTAATCATTACTAAATC
* *
2544129 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
2544150 ATTAATAATTATT--T-TATT
1 ATTACTAATCATTACTAAATC
2544168 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
2544189 ATTA
1 ATTA
2544193 TTATAATTTC
Statistics
Matches: 86, Mismatches: 21, Indels: 31
0.62 0.15 0.22
Matches are distributed among these distances:
16 2 0.02
17 12 0.14
18 13 0.15
19 3 0.03
20 14 0.16
21 28 0.33
22 14 0.16
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:2544285 original size:13 final size:13
Alignment explanation
Indices: 2544267--2544311 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
2544257 TCAAGTCGTA
2544267 AATCATTACTATC
1 AATCATTACTATC
2544280 AATCATTACTA--
1 AATCATTACTATC
*
2544291 AATCATTAATATC
1 AATCATTACTATC
2544304 AATCATTA
1 AATCATTA
2544312 AATATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 10 0.34
13 19 0.66
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (13 bp):
AATCATTACTATC
Found at i:2544344 original size:46 final size:45
Alignment explanation
Indices: 2544282--2544389 Score: 180
Period size: 46 Copynumber: 2.4 Consensus size: 45
2544272 TTACTATCAA
2544282 TCATTACTAAATCATTAATATCAATCATTAAATATTAATAATAATT
1 TCATTACT-AATCATTAATATCAATCATTAAATATTAATAATAATT
* *
2544328 ATTATTACTAATCATTACTATCAATCATTAAATATTAATAATAATT
1 -TCATTACTAATCATTAATATCAATCATTAAATATTAATAATAATT
2544374 TCATTACTAATCATTA
1 TCATTACTAATCATTA
2544390 TTAAATCATT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 15 0.26
46 36 0.62
47 7 0.12
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (45 bp):
TCATTACTAATCATTAATATCAATCATTAAATATTAATAATAATT
Found at i:2544396 original size:102 final size:99
Alignment explanation
Indices: 2544280--2544626 Score: 376
Period size: 102 Copynumber: 3.3 Consensus size: 99
2544270 CATTACTATC
*
2544280 AATCATTACTAAATCATTAATATCAATCATTAAATATTAATAATAATTATTATTACTAATCATTA
1 AATCATTATTAAATCATTAATATCAATCATTAAATATTAATAATAATTATTATTACTAATCATTA
* *
2544345 CTATCAATCATTAAAT-ATT-AATAATAATTTCATTA
66 CTATCAATCATTAAATCATTAAATATTAA--T-AATA
*
2544380 CTAATCATTATTAAATCATTAGTATCAATCATTAAATATTAATAATAATTATTATTACTAATCAT
1 --AATCATTATTAAATCATTAATATCAATCATTAAATATTAATAATAATTATTATTACTAATCAT
* *
2544445 TACTAATCATTACTATCAAATCATTAAATATTAATAATA
64 TACT-ATCAAT-C-ATTAAATCATTAAATATTAATAATA
* *
2544484 AATTATTATTACTAATCATTACTATCAAATCATTAAA-ATTAATAATAATTTCATTATTACTAAT
1 AATCATTATTA--AATCATTAATATC-AATCATTAAATATTAATAATAA-TT-ATTATTACTAAT
* *
2544548 CATTACTAAATCATTAATATCAAATCATTAAATATTAATAATA
61 CATTACT--ATCAATCAT-T-AAATCATTAAATATTAATAATA
* *
2544591 ATTTCATTATTACTAATCATTACTATCAAATCATTA
1 A-ATCATTATTA--AATCATTAATATC-AATCATTA
2544627 TTATTAAATT
Statistics
Matches: 219, Mismatches: 12, Indels: 22
0.87 0.05 0.09
Matches are distributed among these distances:
102 75 0.34
103 5 0.02
104 27 0.12
105 21 0.10
106 22 0.10
107 37 0.17
108 32 0.15
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (99 bp):
AATCATTATTAAATCATTAATATCAATCATTAAATATTAATAATAATTATTATTACTAATCATTA
CTATCAATCATTAAATCATTAAATATTAATAATA
Found at i:2544446 original size:10 final size:10
Alignment explanation
Indices: 2544433--2544459 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2544423 AATAATTATT
2544433 ATTACTAATC
1 ATTACTAATC
2544443 ATTACTAATC
1 ATTACTAATC
2544453 ATTACTA
1 ATTACTA
2544460 TCAAATCATT
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:2544498 original size:48 final size:48
Alignment explanation
Indices: 2544443--2544555 Score: 201
Period size: 48 Copynumber: 2.4 Consensus size: 48
2544433 ATTACTAATC
2544443 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACTAATCATTACTATCAAATCATTAAA-ATTAATAATAAATTCATT
*
2544491 ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAAATTCATT
2544539 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
2544556 AATCATTAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
47 13 0.21
48 50 0.79
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAAATTCATT
Found at i:2544504 original size:27 final size:27
Alignment explanation
Indices: 2544474--2544552 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 27
2544464 ATCATTAAAT
2544474 ATTAATAATAAATTATTATTACTAATC
1 ATTAATAATAAATTATTATTACTAATC
* * *
2544501 ATTACT-ATCAA--ATCATTA--AA--
1 ATTAATAATAAATTATTATTACTAATC
*
2544521 ATTAATAATAATTTCATTATTACTAATC
1 ATTAATAATAAATT-ATTATTACTAATC
2544549 ATTA
1 ATTA
2544553 CTAAATCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 15
0.63 0.12 0.25
Matches are distributed among these distances:
20 5 0.14
21 3 0.08
22 2 0.05
24 12 0.32
26 6 0.16
27 5 0.14
28 4 0.11
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (27 bp):
ATTAATAATAAATTATTATTACTAATC
Found at i:2544603 original size:60 final size:59
Alignment explanation
Indices: 2544491--2544615 Score: 225
Period size: 60 Copynumber: 2.1 Consensus size: 59
2544481 ATAAATTATT
*
2544491 ATTACT-AATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
2544549 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAA-ATTAATAATAATTTCATTATTACTAATC
2544609 ATTACTA
1 ATTACTA
2544616 TCAAATCATT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
58 6 0.09
59 23 0.36
60 35 0.55
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.42
Consensus pattern (59 bp):
ATTACTAAATCATTAATATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
Found at i:2544624 original size:14 final size:13
Alignment explanation
Indices: 2544594--2544832 Score: 131
Period size: 12 Copynumber: 19.3 Consensus size: 13
2544584 AATAATAATT
2544594 TCATTATTACT-AA
1 TCATTATTA-TAAA
*
2544607 TCATTACTATCAAA
1 TCATTATTAT-AAA
2544621 TCATTATTATTAAA
1 TCATTATTA-TAAA
*
2544635 TTATTATTAT-AA
1 TCATTATTATAAA
*
2544647 TGATTATTATTAAA
1 TCATTATTA-TAAA
2544661 TCATTATTAT-AA
1 TCATTATTATAAA
*
2544673 TGATTATTATCAAA
1 TCATTATTAT-AAA
2544687 TCATTA-T-TAAA
1 TCATTATTATAAA
* * * *
2544698 TCATCA-AATCAT
1 TCATTATTATAAA
* *
2544710 TAAATATT-TAAA
1 TCATTATTATAAA
2544722 TCATTA-T-TAAA
1 TCATTATTATAAA
*
2544733 TTATTATTAT-AA
1 TCATTATTATAAA
*
2544745 TGATTATTACTAAA
1 TCATTATTA-TAAA
2544759 TC---ATTAT--A
1 TCATTATTATAAA
2544767 TCATTATTAT-AA
1 TCATTATTATAAA
*
2544779 TGATTATTATCAAA
1 TCATTATTAT-AAA
2544793 TCATTATTAT-AA
1 TCATTATTATAAA
* *
2544805 TGA-TATTAT-CA
1 TCATTATTATAAA
2544816 T-ATTATTACTAAA
1 TCATTATTA-TAAA
2544829 TCAT
1 TCAT
2544833 CAAATCATTA
Statistics
Matches: 176, Mismatches: 27, Indels: 45
0.71 0.11 0.18
Matches are distributed among these distances:
8 3 0.02
10 2 0.01
11 40 0.23
12 60 0.34
13 16 0.09
14 54 0.31
15 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (13 bp):
TCATTATTATAAA
Found at i:2544658 original size:29 final size:26
Alignment explanation
Indices: 2544596--2544908 Score: 144
Period size: 26 Copynumber: 12.8 Consensus size: 26
2544586 TAATAATTTC
* * *
2544596 ATTATTACT-AATCATTACTATCAAATC
1 ATTATTATTAAATCATTATTAT--AATG
*
2544623 ATTATTATTAAATTATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
2544649 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
2544675 ATTATTATCAAATCATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATG
* *
2544700 ATCAAATCATT-AA--A-TATT-TAA--
1 AT--TATTATTAAATCATTATTATAATG
* *
2544721 ATCATTATTAAATTATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
2544747 ATTATTACTAAATC---ATTAT-ATC
1 ATTATTATTAAATCATTATTATAATG
*
2544769 ATTATTA-T-AATGATTATTATCAA--
1 ATTATTATTAAATCATTATTAT-AATG
* * *
2544792 ATCATTATTATAATGA-TATTATCAT-
1 ATTATTATTA-AATCATTATTATAATG
* * *
2544817 ATTATTACTAAATC---ATCA-AATC
1 ATTATTATTAAATCATTATTATAATG
*
2544839 ATTAAATATTAAATTCATTATTA-AAT-
1 ATT-ATTATTAAA-TCATTATTATAATG
*
2544865 -TCATTATTAAATC---ATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
2544887 ATTATTATCAAATCATTTTTAT
1 ATTATTATTAAATCATTATTAT
2544909 GGTATGTATG
Statistics
Matches: 222, Mismatches: 32, Indels: 65
0.70 0.10 0.20
Matches are distributed among these distances:
19 5 0.02
20 9 0.04
21 8 0.04
22 16 0.07
23 46 0.21
24 19 0.09
25 21 0.09
26 70 0.32
27 18 0.08
28 10 0.05
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATG
Found at i:2544859 original size:131 final size:132
Alignment explanation
Indices: 2544637--2544882 Score: 408
Period size: 131 Copynumber: 1.9 Consensus size: 132
2544627 TTATTAAATT
* *
2544637 ATTATTATAATGATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTATTAAATCAT
1 ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
*
2544702 CAAATCATTAAATATTTAAATCATTATTAAATT-ATTATTATAATGATTATTACTAAATCATTAT
66 CAAATCATTAAATATTTAAATCATTATTAAATTCATTATTA-AATCATTATTACTAAATCATTAT
2544766 ATC
130 ATC
* *
2544769 ATTATTATAATGATTATTATCAAATCATTATTATAATGA-TATTATCATATTATTACTAAATCAT
1 ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
2544833 CAAATCATTAAATA-TTAAATTCATTATTAAATTCATTATTAAATCATTAT
66 CAAATCATTAAATATTTAAA-TCATTATTAAATTCATTATTAAATCATTAT
2544883 AATGATTATT
Statistics
Matches: 107, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
130 5 0.05
131 57 0.53
132 45 0.42
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (132 bp):
ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
CAAATCATTAAATATTTAAATCATTATTAAATTCATTATTAAATCATTATTACTAAATCATTATA
TC
Found at i:2544862 original size:12 final size:12
Alignment explanation
Indices: 2544845--2544882 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2544835 AATCATTAAA
2544845 TATTAAATTCAT
1 TATTAAATTCAT
2544857 TATTAAATTCAT
1 TATTAAATTCAT
2544869 TATTAAA-TCAT
1 TATTAAATTCAT
2544880 TAT
1 TAT
2544883 AATGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:2544869 original size:106 final size:105
Alignment explanation
Indices: 2544615--2544908 Score: 298
Period size: 106 Copynumber: 2.7 Consensus size: 105
2544605 AATCATTACT
*
2544615 ATCAAATCATTATTATTAAATTATTATTATAATGATTATTATTAAATCATTATTATAATGATTAT
1 ATCAAATCATTATTATTAAATTATTATTATAAT--TCATTA-T--ATCATTATTATAATGATTAT
2544680 TATCAAATCATTATTA-AATCATCAAATCATTAAATATTTAAATC
61 TATCAAATCATTATTATAATCATCAAATCATTAAATATTTAAATC
* * *
2544724 ATTATTAA--ATTATTATTATAATGATTATTACTAAATCATTATATCATTATTATAATGATTATT
1 ATCA--AATCATTATTATTA-AATTATTATTA-TAATTCATTATATCATTATTATAATGATTATT
* * *
2544787 ATCAAATCATTATTATAATGAT-ATTATCA-T-ATTATTACTAAATC
62 ATCAAATCATTATTATAATCATCA-AATCATTAAATATT--TAAATC
* * *
2544831 ATCAAATCATTAAATATTAAATTCATTATTA-AATTCATTAT-TAAATCATTATAATGATTATTA
1 ATCAAATCATT-ATTATTAAATT-ATTATTATAATTCATTATAT-CATTATTATAATGATTATTA
*
2544894 TCAAATCATTTTTAT
63 TCAAATCATTATTAT
2544909 GGTATGTATG
Statistics
Matches: 158, Mismatches: 14, Indels: 29
0.79 0.07 0.14
Matches are distributed among these distances:
105 8 0.05
106 79 0.50
107 24 0.15
108 14 0.09
109 18 0.11
110 10 0.06
111 5 0.03
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (105 bp):
ATCAAATCATTATTATTAAATTATTATTATAATTCATTATATCATTATTATAATGATTATTATCA
AATCATTATTATAATCATCAAATCATTAAATATTTAAATC
Found at i:2548238 original size:28 final size:28
Alignment explanation
Indices: 2548204--2548257 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
2548194 ATAATCTAAT
*
2548204 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
2548232 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
2548258 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:2548264 original size:28 final size:28
Alignment explanation
Indices: 2548200--2548264 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
2548190 TTATATAATC
*
2548200 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
2548228 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
2548256 TAATTTATA
1 TAATATATA
2548265 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:2548267 original size:21 final size:21
Alignment explanation
Indices: 2548234--2548282 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2548224 TTAATATAAT
2548234 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2548255 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2548276 ATTAACT
1 A-TAACT
2548283 AAATTTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2549011 original size:29 final size:29
Alignment explanation
Indices: 2548956--2549033 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
2548946 GTTGGACGCC
*
2548956 GGGCATGCATGGCGACCTATAAGGTCGCT
1 GGGCATGCATGGCGACCTACAAGGTCGCT
* * *
2548985 GGGCGTGCATGGCGACCTACCATGTCGCT
1 GGGCATGCATGGCGACCTACAAGGTCGCT
*
2549014 GGG-ATGCCCTGGCGACCTAC
1 GGGCATG-CATGGCGACCTAC
2549034 GCCAACACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 2 0.05
29 40 0.95
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (29 bp):
GGGCATGCATGGCGACCTACAAGGTCGCT
Found at i:2572008 original size:64 final size:65
Alignment explanation
Indices: 2571938--2572117 Score: 247
Period size: 65 Copynumber: 2.8 Consensus size: 65
2571928 TGGAACACTT
* * * *
2571938 AGTGCATCGGTGCACT-AAGTGTGCATCGATGTATAAAATGCATTCGATGTTTAGAAT-AAACCT
1 AGTGCATCGATGCA-TGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTACAATAAAACCT
2572001 A
65 A
* * * *
2572002 AGTGCATCGATGCATGGTGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTACAATAAAACCTA
* *
2572067 AGTGCATCGATGCATGGAGAGTGCATCGATGCATAAACTGCATTCGATGTT
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTT
2572118 CAATTTATTC
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
63 1 0.01
64 48 0.47
65 54 0.52
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTACAATAAAACCTA
Found at i:2572165 original size:65 final size:64
Alignment explanation
Indices: 2571938--2572158 Score: 223
Period size: 64 Copynumber: 3.4 Consensus size: 64
2571928 TGGAACACTT
* * * ** *
2571938 AGTGCATCGGTGCACT-AAGTGTGCATCGATGTATAAAATGCATTCGATGTTT-AGAATAAACCT
1 AGTGCATCGATGCA-TGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTCATTA-AAACAT
*
2572001 A
64 G
* *
2572002 AGTGCATCGATGCATGGTGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATG-TTTCATTAAAACATG
* * * ** *
2572067 AGTGCATCGATGCATGGAGAGTGCATCGATGCATAAACTGCATTCGATG-TTCAATTTATTCATT
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTC-ATTAAAACATG
* *
2572131 TGTGCATCGGTGCATGGAGTGGTGCATC
1 AGTGCATCGATGCATGGAGT-GTGCATC
2572159 AGTGCATTCC
Statistics
Matches: 134, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
63 4 0.03
64 66 0.49
65 62 0.46
66 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTCATTAAAACATG
Found at i:2572267 original size:21 final size:21
Alignment explanation
Indices: 2572238--2572277 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2572228 TCAATTAATG
2572238 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
2572259 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
2572278 CCAGTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:2574830 original size:21 final size:21
Alignment explanation
Indices: 2574804--2574881 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
2574794 CTAGTGGCAA
* *
2574804 GTGCATGGTTGCACTGCAGAG
1 GTGCATGGATGCACTGCAGGG
*
2574825 GTGCATGGTTGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
2574846 GTGCATGGATACACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
2574867 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2574882 TTGACACCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:2578851 original size:22 final size:22
Alignment explanation
Indices: 2578826--2578869 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2578816 CATCAGGTAC
2578826 CGATACCTCAAGAGTAAAATTA
1 CGATACCTCAAGAGTAAAATTA
2578848 CGATACCTCAAGAGTAAAATTA
1 CGATACCTCAAGAGTAAAATTA
2578870 AGGAAGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (22 bp):
CGATACCTCAAGAGTAAAATTA
Found at i:2579574 original size:18 final size:18
Alignment explanation
Indices: 2579551--2579605 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
2579541 TCAAGGGATT
* *
2579551 ATAGTGGTCTTTTGGGAC
1 ATAGTGGTCCTTCGGGAC
2579569 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
* *
2579587 AGAGTGGTCCTTCAGGAC
1 ATAGTGGTCCTTCGGGAC
2579605 A
1 A
2579606 AATTTTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Found at i:2584722 original size:21 final size:21
Alignment explanation
Indices: 2584680--2584723 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2584670 TTATATTGAA
*
2584680 TTTTATTCACTTTTAATTCTT
1 TTTTATTCACTTTTAATACTT
*
2584701 TTTTATTGCA-TTTTTATACTT
1 TTTTATT-CACTTTTAATACTT
2584722 TT
1 TT
2584724 AATTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTATTCACTTTTAATACTT
Found at i:2584796 original size:20 final size:20
Alignment explanation
Indices: 2584773--2584810 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2584763 TTTAAAAACC
2584773 AATTAAAA-TGCAATAAAAAT
1 AATTAAAAGTG-AATAAAAAT
2584793 AATTAAAAGTGAATAAAA
1 AATTAAAAGTGAATAAAA
2584811 TTCAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (20 bp):
AATTAAAAGTGAATAAAAAT
Found at i:2585917 original size:64 final size:65
Alignment explanation
Indices: 2585845--2585969 Score: 225
Period size: 65 Copynumber: 1.9 Consensus size: 65
2585835 ATGCCTGATA
*
2585845 TATTATATTTTGAGTGATTGATGA-ATTGTTTTAACAAAAATAAACACTTAAAATAATAAAGATG
1 TATTATATTTTGAGTGATTGATAATATTGTTTTAACAAAAATAAACACTTAAAATAATAAAGATG
*
2585909 TATTATATTTTGAGTGATTGATAATATTTTTTTAACAAAAATAAACACTTAAAATAATAAA
1 TATTATATTTTGAGTGATTGATAATATTGTTTTAACAAAAATAAACACTTAAAATAATAAA
2585970 ATTAAAAACG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 23 0.40
65 35 0.60
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (65 bp):
TATTATATTTTGAGTGATTGATAATATTGTTTTAACAAAAATAAACACTTAAAATAATAAAGATG
Found at i:2592323 original size:16 final size:17
Alignment explanation
Indices: 2592293--2592324 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2592283 TATTTATACC
2592293 TTTTTAACATGTTTATT
1 TTTTTAACATGTTTATT
2592310 TTTTTAACAT-TTTAT
1 TTTTTAACATGTTTAT
2592325 ACCATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTAACATGTTTATT
Found at i:2599739 original size:2 final size:2
Alignment explanation
Indices: 2599732--2599763 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2599722 ACAGCTAAGA
2599732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2599764 GGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2601169 original size:42 final size:42
Alignment explanation
Indices: 2601123--2601210 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
2601113 GTTGAATATA
* * *
2601123 GTTTTTGGTAACTTATGCAATAGCTATTGAATTTTGAGGATG
1 GTTTTTGGTAACTTATGCAATAGATATTGAAGTTTAAGGATG
* * *
2601165 GTTTTTGGTAACTTTTGTAGTAGATATTGAAGTTTAAGGATG
1 GTTTTTGGTAACTTATGCAATAGATATTGAAGTTTAAGGATG
2601207 GTTT
1 GTTT
2601211 ATGCAATGGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (42 bp):
GTTTTTGGTAACTTATGCAATAGATATTGAAGTTTAAGGATG
Found at i:2602207 original size:81 final size:81
Alignment explanation
Indices: 2602099--2602286 Score: 238
Period size: 81 Copynumber: 2.3 Consensus size: 81
2602089 TGACTGATGG
*
2602099 AGCTCTGTTGAGAATTCATTATCCACCTTA-CTGTGGCGTC-TGATCCTTGTACTTGACTCCCTT
1 AGCTCTGTTGAGAATTCATCATCCACCTTATC-GTGGCG-CATGATCCTTGTACTTGACTCCCTT
2602162 GATGGCGCTGGCTAGTATA
64 GATGGCGCTGGCTAGTA-A
* * * * * *
2602181 A-CTCTATTGAGAATTTATCATTCACCTTATCGTGGTGCATGGTCCTTGTGCTTGACTCCCTTGA
1 AGCTCTGTTGAGAATTCATCATCCACCTTATCGTGGCGCATGATCCTTGTACTTGACTCCCTTGA
* *
2602245 TGGTGCTGGCTGGTAA
66 TGGCGCTGGCTAGTAA
*
2602261 AGCTCTGTTAAGAATTCATCATCCAC
1 AGCTCTGTTGAGAATTCATCATCCAC
2602287 GTGGTGCATG
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
80 3 0.03
81 85 0.94
82 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (81 bp):
AGCTCTGTTGAGAATTCATCATCCACCTTATCGTGGCGCATGATCCTTGTACTTGACTCCCTTGA
TGGCGCTGGCTAGTAA
Found at i:2602357 original size:75 final size:75
Alignment explanation
Indices: 2602211--2602361 Score: 191
Period size: 75 Copynumber: 2.0 Consensus size: 75
2602201 TTCACCTTAT
* *
2602211 CGTGGTGCATGGTCCTTGTGCTTGACTCCCTTGATGGTGCTGGCTGGTAAAGCTCTGTTAAGAAT
1 CGTGGTGCATGGTCCTTATGCTTGACTCCCTTGATGGTGCTGGCTGGTAAAGCTCTGTTAAGAAG
2602276 TCATCATCCA
66 TCATCATCCA
* ** * *
2602286 CGTGGTGCATGGTCCTTATGCTT-AGGTCTTTTGATGGTGTTGGCTGGTAGAGCTCTGTTGAA-A
1 CGTGGTGCATGGTCCTTATGCTTGA-CTCCCTTGATGGTGCTGGCTGGTAAAGCTCTGTT-AAGA
2602349 AGGT-ATCATCCA
64 A-GTCATCATCCA
2602361 C
1 C
2602362 CTTACTGTGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
74 1 0.02
75 62 0.94
76 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.34
Consensus pattern (75 bp):
CGTGGTGCATGGTCCTTATGCTTGACTCCCTTGATGGTGCTGGCTGGTAAAGCTCTGTTAAGAAG
TCATCATCCA
Found at i:2604982 original size:42 final size:40
Alignment explanation
Indices: 2604896--2605000 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 40
2604886 AAAATATAAA
*
2604896 CACAAACCCTAAATTGATTTCAAGCTCAAATAATTTTGATTT
1 CACAAACCCTAAATCGATTTCAA-C-CAAATAATTTTGATTT
2604938 CACAAACCCTAAGATCGATTTC-A-CAAATTAATTTTGATTATT
1 CACAAACCCTAA-ATCGATTTCAACCAAA-TAATTTTGA-T-TT
* * *
2604980 CACTAACCCTTAATTGATTTC
1 CACAAACCCTAAATCGATTTC
2605001 GATAAAGGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
39 4 0.07
40 9 0.16
41 9 0.16
42 25 0.45
43 8 0.15
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (40 bp):
CACAAACCCTAAATCGATTTCAACCAAATAATTTTGATTT
Found at i:2605309 original size:15 final size:15
Alignment explanation
Indices: 2605281--2605318 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2605271 TTATTCTTAA
2605281 TATTT-ATATATTTT
1 TATTTAATATATTTT
*
2605295 TATTTAATATTTTTT
1 TATTTAATATATTTT
*
2605310 TATCTAATA
1 TATTTAATA
2605319 AGATGATGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTAATATATTTT
Found at i:2605550 original size:12 final size:12
Alignment explanation
Indices: 2605533--2605557 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2605523 TCCTCTCTTC
2605533 ATATGCTTATTA
1 ATATGCTTATTA
2605545 ATATGCTTATTA
1 ATATGCTTATTA
2605557 A
1 A
2605558 CAGTTGGCGC
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:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATGCTTATTA
Found at i:2607886 original size:1 final size:1
Alignment explanation
Indices: 2607882--2607907 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2607872 TTTTTTTTTT
2607882 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
2607908 TGGGTTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2614628 original size:21 final size:21
Alignment explanation
Indices: 2614602--2614644 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2614592 TTTCTGGGTT
* *
2614602 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
2614623 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
2614644 A
1 A
2614645 CGAACATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:2614702 original size:64 final size:67
Alignment explanation
Indices: 2614624--2614772 Score: 196
Period size: 65 Copynumber: 2.3 Consensus size: 67
2614614 ACCCATTCAA
* *
2614624 GGGGAACCGATACCCCTTCAACGAACATG-ATTTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
2614687 -G
66 GG
* * * * *
2614688 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
2614753 GGG
66 -GG
*
2614756 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2614773 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 25 0.34
65 26 0.36
66 5 0.07
68 17 0.23
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:2615112 original size:34 final size:29
Alignment explanation
Indices: 2615073--2615144 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
2615063 CATATTATGA
*
2615073 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
2615102 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
2615131 TACATGACATGAAT
1 TACATGACATGAAT
2615145 ATGCAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Done.