Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:3163469 original size:12 final size:10
Alignment explanation
Indices: 3163441--3163474 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
3163431 GGAGACCTGG
3163441 AAAAAGAAAA
1 AAAAAGAAAA
3163451 AAAAAGAAAA
1 AAAAAGAAAA
3163461 AAATGAAGAAAA
1 AAA--AAGAAAA
3163473 AA
1 AA
3163475 GCTCACCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
12 9 0.41
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:3181772 original size:4 final size:4
Alignment explanation
Indices: 3181763--3181821 Score: 57
Period size: 4 Copynumber: 13.8 Consensus size: 4
3181753 AAACATGCAA
*
3181763 AAAG AAAG AAAG TAAAAG AAAAG ACA- AAAG AAAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG --AAAG -AAAG AAAG AAAG -AAAG AAAG AAAG AAAG
3181810 AAAG AAAAG AAA
1 AAAG -AAAG AAA
3181822 AGCAAAGTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
3 2 0.04
4 29 0.60
5 13 0.27
6 4 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:3181786 original size:5 final size:5
Alignment explanation
Indices: 3181762--3181828 Score: 56
Period size: 4 Copynumber: 14.0 Consensus size: 5
3181752 GAAACATGCA
3181762 AAAAG -AAAG -AAAG TAAAAG AAAAG ACAAAAG AAAAG -AAAG -AAAG
1 AAAAG AAAAG AAAAG -AAAAG AAAAG --AAAAG AAAAG AAAAG AAAAG
*
3181806 -AAAG -AAAG AAAAG AAAAG CAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
3181829 TTAAAACCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
4 24 0.43
5 23 0.41
6 4 0.07
7 5 0.09
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:3181793 original size:12 final size:12
Alignment explanation
Indices: 3181776--3181827 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
3181766 GAAAGAAAGT
3181776 AAAAGAAAAGAC
1 AAAAGAAAAGAC
*
3181788 AAAAGAAAAGAA
1 AAAAGAAAAGAC
* *
3181800 AGAAAGAAAGAAAG
1 A-AAAGAAA-AGAC
3181814 AAAAGAAAAG-C
1 AAAAGAAAAGAC
3181825 AAA
1 AAA
3181828 GTTAAAACCA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
11 3 0.09
12 13 0.39
13 14 0.42
14 3 0.09
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAC
Found at i:3181798 original size:17 final size:18
Alignment explanation
Indices: 3181762--3181821 Score: 81
Period size: 17 Copynumber: 3.4 Consensus size: 18
3181752 GAAACATGCA
3181762 AAAAGAAAGAAAGTAAAAG
1 AAAAGAAAGAAAG-AAAAG
*
3181781 AAAAGACA-AAAGAAAAG
1 AAAAGAAAGAAAGAAAAG
3181798 -AAAGAAAGAAAG-AAAG
1 AAAAGAAAGAAAGAAAAG
3181814 AAAAGAAA
1 AAAAGAAA
3181822 AGCAAAGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 10 0.27
17 16 0.43
18 4 0.11
19 7 0.19
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAAGAAAGAAAAG
Found at i:3181800 original size:31 final size:26
Alignment explanation
Indices: 3181763--3181821 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
3181753 AAACATGCAA
*
3181763 AAAGAAAGAAAGTAAAAGAAAAGACA-
1 AAAGAAAGAAAG-AAAAGAAAAGAAAG
3181789 AAAGAAAAGAAAG-AAAG-AAAGAAAG
1 AAAG-AAAGAAAGAAAAGAAAAGAAAG
3181814 AAAAGAAA
1 -AAAGAAA
3181822 AGCAAAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 6 0.21
25 7 0.24
26 8 0.28
27 8 0.28
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAGAAAGAAAGAAAAGAAAAGAAAG
Found at i:3181803 original size:21 final size:21
Alignment explanation
Indices: 3181763--3181828 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
3181753 AAACATGCAA
3181763 AAAGAAAGAAAGTAAAAGAAAAG
1 AAAGAAAGAAAG-AAAAG-AAAG
*
3181786 ACA-AAAGAAA-AGAAAGAAAG
1 AAAGAAAGAAAGA-AAAGAAAG
3181806 AAAGAAAGAAAAGAAAAGCAAAG
1 AAAGAAAG-AAAGAAAAG-AAAG
3181829 TTAAAACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
20 7 0.19
21 8 0.22
22 14 0.39
23 7 0.19
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAGAAAAGAAAG
Found at i:3188490 original size:14 final size:14
Alignment explanation
Indices: 3188471--3188510 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
3188461 GATTGGGTTC
3188471 ACATAAATGAACGA
1 ACATAAATGAACGA
* *
3188485 ACATAACTGAATGA
1 ACATAAATGAACGA
3188499 ACATAAATGAAC
1 ACATAAATGAAC
3188511 ATAACCGAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.17
Consensus pattern (14 bp):
ACATAAATGAACGA
Found at i:3189627 original size:23 final size:23
Alignment explanation
Indices: 3189601--3189645 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3189591 CACCACAGCT
* *
3189601 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
3189624 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
3189646 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:3191495 original size:21 final size:21
Alignment explanation
Indices: 3191471--3191515 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3191461 TTTTGTTCGT
* *
3191471 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3191492 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3191513 TTG
1 TTG
3191516 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3194823 original size:23 final size:23
Alignment explanation
Indices: 3194797--3194841 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3194787 CACCACAGCT
* *
3194797 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
3194820 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
3194842 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:3196697 original size:21 final size:21
Alignment explanation
Indices: 3196655--3196699 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3196645 TTTTGTTGGT
* *
3196655 TTGAAGGGGTATCGGTTACCC
1 TTGAAGGGGTACCGATTACCC
* *
3196676 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTACCC
3196697 TTG
1 TTG
3196700 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTACCC
Found at i:3198426 original size:17 final size:18
Alignment explanation
Indices: 3198398--3198435 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
3198388 AAAAATACTA
3198398 AGGTATTTTTGGGTTAAT
1 AGGTATTTTTGGGTTAAT
3198416 AGGTA-TTTTGGGTTAAT
1 AGGTATTTTTGGGTTAAT
3198433 AGG
1 AGG
3198436 CTTAATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.45
Consensus pattern (18 bp):
AGGTATTTTTGGGTTAAT
Found at i:3199428 original size:24 final size:25
Alignment explanation
Indices: 3199353--3199418 Score: 125
Period size: 24 Copynumber: 2.7 Consensus size: 25
3199343 GCACATGTTT
3199353 AAAAATTATATTTAAATTATTACCA
1 AAAAATTATATTTAAATTATTACCA
3199378 AAAAA-TATATTTAAATTATTACCA
1 AAAAATTATATTTAAATTATTACCA
3199402 AAAAATTATATTTAAAT
1 AAAAATTATATTTAAAT
3199419 AAATAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 24 0.60
25 16 0.40
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAAATTATATTTAAATTATTACCA
Found at i:3200140 original size:10 final size:10
Alignment explanation
Indices: 3200125--3200166 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
3200115 CATTTAATAA
3200125 ATAAACGAAC
1 ATAAACGAAC
3200135 ATAAACGAAC
1 ATAAACGAAC
3200145 ----ACGAAC
1 ATAAACGAAC
3200151 ATAAACGAAC
1 ATAAACGAAC
3200161 ATAAAC
1 ATAAAC
3200167 ATTGGAGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 22 0.79
ACGTcount: A:0.60, C:0.21, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3200150 original size:16 final size:16
Alignment explanation
Indices: 3200129--3200161 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3200119 TAATAAATAA
3200129 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3200145 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3200161 A
1 A
3200162 TAAACATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3200167 original size:16 final size:16
Alignment explanation
Indices: 3200132--3200168 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3200122 TAAATAAACG
*
3200132 AACATAAACGAACACG
1 AACATAAACGAACACA
*
3200148 AACATAAACGAACATA
1 AACATAAACGAACACA
3200164 AACAT
1 AACAT
3200169 TGGAGACCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.22, G:0.08, T:0.11
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:3200527 original size:14 final size:14
Alignment explanation
Indices: 3200510--3200550 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
3200500 GATTGGGTTA
*
3200510 AACATAAATAAACG
1 AACATAAACAAACG
*
3200524 AACATAAACGAACG
1 AACATAAACAAACG
3200538 AACATAAACAAAC
1 AACATAAACAAAC
3200551 ATAATCGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.63, C:0.20, G:0.07, T:0.10
Consensus pattern (14 bp):
AACATAAACAAACG
Found at i:3200544 original size:24 final size:24
Alignment explanation
Indices: 3200517--3200574 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
3200507 TTAAACATAA
3200517 ATAAACGAACATAAACGAACGAAC
1 ATAAACGAACATAAACGAACGAAC
* *
3200541 ATAAACAAACATAATCGAACGAAC
1 ATAAACGAACATAAACGAACGAAC
*
3200565 ATAACCGAAC
1 ATAAACGAAC
3200575 GTTCACGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.57, C:0.22, G:0.10, T:0.10
Consensus pattern (24 bp):
ATAAACGAACATAAACGAACGAAC
Found at i:3200565 original size:14 final size:13
Alignment explanation
Indices: 3200520--3200575 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
3200510 AACATAAATA
3200520 AACGAACATAAACG
1 AACGAACAT-AACG
3200534 AACGAACAT-A--
1 AACGAACATAACG
*
3200544 AACAAACATAATCG
1 AACGAACATAA-CG
3200558 AACGAACATAACCG
1 AACGAACATAA-CG
3200572 AACG
1 AACG
3200576 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
12 1 0.03
14 25 0.71
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.09
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:3201638 original size:17 final size:19
Alignment explanation
Indices: 3201603--3201640 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
3201593 AGTAAATGTA
3201603 TGATTTTTACAATGAATTT
1 TGATTTTTACAATGAATTT
3201622 TGATTTTT-CAA-GAATTT
1 TGATTTTTACAATGAATTT
3201639 TG
1 TG
3201641 GTCCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (19 bp):
TGATTTTTACAATGAATTT
Found at i:3202678 original size:41 final size:41
Alignment explanation
Indices: 3202621--3202703 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
3202611 TCCTTGGTGA
3202621 TTTTTGATCTCTAATTATACTTAACTTTGAGATTAACCATC
1 TTTTTGATCTCTAATTATACTTAACTTTGAGATTAACCATC
*
3202662 TTTTTGATCTCTAATTATACTTTACTTTGAGATTAACCATC
1 TTTTTGATCTCTAATTATACTTAACTTTGAGATTAACCATC
3202703 T
1 T
3202704 GGTGTATGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (41 bp):
TTTTTGATCTCTAATTATACTTAACTTTGAGATTAACCATC
Found at i:3202690 original size:23 final size:23
Alignment explanation
Indices: 3202623--3202691 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
3202613 CTTGGTGATT
*
3202623 TTTGATCTCTAATTATACTTAAC
1 TTTGATCTCTAATTATACTTTAC
** **
3202646 TTTGAGAT-TAACCAT-C-TT--
1 TTTGATCTCTAATTATACTTTAC
3202664 TTTGATCTCTAATTATACTTTAC
1 TTTGATCTCTAATTATACTTTAC
3202687 TTTGA
1 TTTGA
3202692 GATTAACCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
18 6 0.19
19 5 0.16
20 2 0.06
21 3 0.09
22 5 0.16
23 11 0.34
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (23 bp):
TTTGATCTCTAATTATACTTTAC
Found at i:3204297 original size:21 final size:21
Alignment explanation
Indices: 3204271--3204487 Score: 169
Period size: 21 Copynumber: 10.5 Consensus size: 21
3204261 GTTTCCAGGT
*
3204271 TCGCAACGCGAACATGGACTA
1 TCGCAATGCGAACATGGACTA
*
3204292 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACATGGACTA
* * *
3204313 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACATGGACTA
* *
3204333 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACATGGACTA
* * *
3204354 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACATGGACTA
* *
3204374 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACATGGACTA
* * *
3204395 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACATGGACTA
* *
3204415 TCGC-ATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACATGGACTA
*
3204435 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACATGGACTA
* *
3204456 TCGCAATGCGAACTTGGACCA
1 TCGCAATGCGAACATGGACTA
*
3204477 TCGCATTGCGA
1 TCGCAATGCGA
3204488 TTTACATATT
Statistics
Matches: 156, Mismatches: 30, Indels: 20
0.76 0.15 0.10
Matches are distributed among these distances:
19 8 0.05
20 42 0.27
21 106 0.68
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACATGGACTA
Found at i:3204336 original size:41 final size:41
Alignment explanation
Indices: 3204291--3204522 Score: 271
Period size: 41 Copynumber: 5.7 Consensus size: 41
3204281 AACATGGACT
* *
3204291 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAA
3204332 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
3204373 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
* *
3204414 ATCGC-ATGCGATAGTCGACTATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAA-TATGTA-A
* * * *
3204455 ATCGCAATGCGA-ACTTGGACCATCGCATTGCG-AT-T-TACA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTA-A
*
3204494 TATTCGCATTGCGATAGTCGACTATCGCA
1 -A-TCGCAATGCGATAGTCGACTATCGCA
3204523 TTGAGTCCAA
Statistics
Matches: 169, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
39 2 0.01
40 34 0.20
41 111 0.66
42 22 0.13
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (41 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
Found at i:3204337 original size:20 final size:20
Alignment explanation
Indices: 3204312--3204424 Score: 119
Period size: 20 Copynumber: 5.6 Consensus size: 20
3204302 AACTTGGACT
3204312 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
3204332 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
3204353 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
3204373 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
3204394 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
3204414 ATCGC-ATGCGA
1 ATCGCAATGCGA
3204425 TAGTCGACTA
Statistics
Matches: 79, Mismatches: 4, Indels: 21
0.76 0.04 0.20
Matches are distributed among these distances:
18 4 0.05
19 12 0.15
20 29 0.37
21 24 0.30
22 6 0.08
23 4 0.05
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:3204377 original size:82 final size:83
Alignment explanation
Indices: 3204271--3204522 Score: 320
Period size: 82 Copynumber: 3.1 Consensus size: 83
3204261 GTTTCCAGGT
* * *
3204271 TCGCAACGCGAACATGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTGGACAATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
3204336 CAATGCGATAGTCGACTA
66 CAATGCGATAGTCGACTA
* * *
3204354 TCGCAATGCGAA-TATGTA-AATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAAAT
1 TCGCAATGCGAACT-TGGACAATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAAAT
3204416 CGC-ATGCGATAGTCGACTA
64 CGCAATGCGATAGTCGACTA
* * *
3204435 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACCATCGCATTGCG-AT-T-TACATAT
1 TCGCAATGCGAACTTGGACAATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A-
*
3204497 TCGCATTGCGATAGTCGACTA
63 TCGCAATGCGATAGTCGACTA
3204518 TCGCA
1 TCGCA
3204523 TTGAGTCCAA
Statistics
Matches: 147, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
79 2 0.01
80 2 0.01
81 35 0.24
82 73 0.50
83 35 0.24
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (83 bp):
TCGCAATGCGAACTTGGACAATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
CAATGCGATAGTCGACTA
Found at i:3204438 original size:61 final size:61
Alignment explanation
Indices: 3204373--3204522 Score: 157
Period size: 61 Copynumber: 2.4 Consensus size: 61
3204363 GAATATGTAA
*
3204373 ATCGCAATGCGATAGTCGACTATCGCAATGCGAA-TATGTA-AATCGCA-TGCGATAGTCGAC-T
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACT-TGGACAATCGCATTGCGAT--T-GACAT
* * * *
3204434 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTGGACCATCGCATTGCGATTTACAT
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACAATCGCATTGCGATTGACAT
*
3204495 ATTCGCATTGCGATAGTCGACTATCGCA
1 A-TCGCAATGCGATAGTCGACTATCGCA
3204523 TTGAGTCCAA
Statistics
Matches: 74, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
60 3 0.04
61 36 0.49
62 28 0.38
63 7 0.09
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (61 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACAATCGCATTGCGATTGACAT
Found at i:3204525 original size:21 final size:21
Alignment explanation
Indices: 3204287--3204522 Score: 144
Period size: 21 Copynumber: 11.5 Consensus size: 21
3204277 CGCGAACATG
* *
3204287 GACTATCGCAATGCGA-ACTTG
1 GACTATCGCAATGCGATA-GTC
3204308 GACTATCGCAATGCGAATA-T-
1 GACTATCGCAATGCG-ATAGTC
*
3204328 GTA-AATCGCAATGCGATAGTC
1 G-ACTATCGCAATGCGATAGTC
3204349 GACTATCGCAATGCGAATA-T-
1 GACTATCGCAATGCG-ATAGTC
*
3204369 GTA-AATCGCAATGCGATAGTC
1 G-ACTATCGCAATGCGATAGTC
3204390 GACTATCGCAATGCGAATA-T-
1 GACTATCGCAATGCG-ATAGTC
*
3204410 GTA-AATCGC-ATGCGATAGTC
1 G-ACTATCGCAATGCGATAGTC
* *
3204430 GACTATCGCAATGCGA-ACTTG
1 GACTATCGCAATGCGATA-GTC
* *
3204451 GACTATCGCAATGCGA-ACTTG
1 GACTATCGCAATGCGATA-GTC
* *
3204472 GACCATCGCATTGCGAT--T-
1 GACTATCGCAATGCGATAGTC
* *
3204490 TACATATTCGCATTGCGATAGTC
1 GAC-TA-TCGCAATGCGATAGTC
3204513 GACTATCGCA
1 GACTATCGCA
3204523 TTGAGTCCAA
Statistics
Matches: 178, Mismatches: 13, Indels: 48
0.74 0.05 0.20
Matches are distributed among these distances:
18 5 0.03
19 15 0.08
20 53 0.30
21 92 0.52
22 10 0.06
23 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (21 bp):
GACTATCGCAATGCGATAGTC
Found at i:3205164 original size:6 final size:6
Alignment explanation
Indices: 3205134--3205186 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
3205124 GTCTCGTCTC
3205134 GTCG-G GTCG-G GTCG-G GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
3205178 GTCGTG GTC
1 GTCGTG GTC
3205187 ATTTTGGCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 19 0.40
6 28 0.60
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.28
Consensus pattern (6 bp):
GTCGTG
Found at i:3206561 original size:16 final size:17
Alignment explanation
Indices: 3206540--3206581 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
3206530 TCGTCCCGTT
3206540 TTATATTATTATTA-TA
1 TTATATTATTATTATTA
3206556 TTATATTATTATTATTA
1 TTATATTATTATTATTA
3206573 TTATTATTA
1 TTA-TATTA
3206582 AATAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 14 0.58
17 5 0.21
18 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATTATTATTATTA
Found at i:3206598 original size:3 final size:3
Alignment explanation
Indices: 3206543--3206581 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
3206533 TCCCGTTTTA
3206543 TAT TAT TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3206582 AATAATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3206802 original size:16 final size:16
Alignment explanation
Indices: 3206781--3206814 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3206771 TTCTTCCAGC
*
3206781 CGCCAGCCTTCTTAGT
1 CGCCAGCCTTCTCAGT
*
3206797 CGCCAGCTTTCTCAGT
1 CGCCAGCCTTCTCAGT
3206813 CG
1 CG
3206815 TTGGATCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.21, T:0.29
Consensus pattern (16 bp):
CGCCAGCCTTCTCAGT
Found at i:3213053 original size:100 final size:101
Alignment explanation
Indices: 3212935--3213136 Score: 289
Period size: 101 Copynumber: 2.0 Consensus size: 101
3212925 CCAAATTATA
* * * ** **
3212935 ATATTATATTTATACAATAAAGCTTGAACTGTCCC-CTAGAGAAATTGGTTAAACGCCTTGGCTT
1 ATATTATATATATACAATAAAGCTTGAACTGTCCCTATAGAGAAATTAGTTAAACGCCCCGAATT
3212999 TATGGATAAGATTCAGCTAGCCTGATAAAGGTGATT
66 TATGGATAAGATTCAGCTAGCCTGATAAAGGTGATT
* ** *
3213035 ATATTATATATATGCAATAAAGCTTGAGTTGTCCCTATAGAGCAATTAGTTAAACGCCCCGAATT
1 ATATTATATATATACAATAAAGCTTGAACTGTCCCTATAGAGAAATTAGTTAAACGCCCCGAATT
*
3213100 TATGGATCAGATTCAGCTAGCCTGATAAAGGTGATT
66 TATGGATAAGATTCAGCTAGCCTGATAAAGGTGATT
3213136 A
1 A
3213137 CAATAAAGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
100 31 0.35
101 58 0.65
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (101 bp):
ATATTATATATATACAATAAAGCTTGAACTGTCCCTATAGAGAAATTAGTTAAACGCCCCGAATT
TATGGATAAGATTCAGCTAGCCTGATAAAGGTGATT
Found at i:3216321 original size:258 final size:259
Alignment explanation
Indices: 3215545--3216571 Score: 1488
Period size: 258 Copynumber: 4.0 Consensus size: 259
3215535 CAAGTTGTTT
* ** *
3215545 TGAAAATGAAAAAATGATTACCAAAGTTTCTGATTTAATCTTTTCTA-AAAATGAAA-TCTTTGA
1 TGAAAATGAGAAAACAATTACCAAAGTTTCTCATTTAATC--TTC-AGAAAATGAAATTC-TTGA
*
3215608 AAAGTAAGAAAGCTATTACCAAAGATTCTTACCCAGTAAATTATTTTCCAAGTTTGTAAATCCTT
62 AAAGTAAGAAAGCTATTACCAAAGATTCTTACCCAGTAAATTATTTCCCAAGTTTGTAAATCCTT
* * * * *
3215673 CTGGTCATCATTAAGTCTTTTGAGCATTATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTTGA
127 CGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGA
** * ** * *
3215738 ATAAGATGATAAGTCCTTCGGGCCATCTATAATATCTTCGGGTAGGATGTTTACACATGATTTTC
192 GCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGGGTAGGATGTTTACACATGATTTTC
3215803 ACA
257 ACA
* *
3215806 TGAAAATGAGAAACCAATTACCAAAGTTTCTCATTTAATGTTCAGAAAATGAAATTCTTGAAAAG
1 TGAAAATGAGAAAACAATTACCAAAGTTTCTCATTTAATCTTCAGAAAATGAAATTCTTGAAAAG
*
3215871 TAAGAAAGCTATTACCAAAGATTCTTACCCAGTAAATTATTCCCCAAGTTTGTAAATCCTTCGGG
66 TAAGAAAGCTATTACCAAAGATTCTTACCCAGTAAATTATTTCCCAAGTTTGTAAATCCTTCGGG
* ** * * * *
3215936 TCATCAGTAAGTCTTTCGATCATGATGCTTAAATCCTTTGGGTTATATGTAAGTCTTTTGAGAAA
131 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAA
* * *
3216001 GATGATAAGTCATTCAAGCCATCCGTAAGACCTTCGAGTAGGATGTTTACACATGA-TTTCACA
196 GATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGGGTAGGATGTTTACACATGATTTTCACA
* *
3216064 TGAAAATGAGAAAACAATTACCAAAGTTTCTTATTCAATCTTCAGAAAATGAAATTCTTGAAAAG
1 TGAAAATGAGAAAACAATTACCAAAGTTTCTCATTTAATCTTCAGAAAATGAAATTCTTGAAAAG
*
3216129 TAAGAAAGCTATTACCAAAGATTCTTA-CCAGTAAATTATTTTCCAAGTTTGTAAATCCTTCGGG
66 TAAGAAAGCTATTACCAAAGATTCTTACCCAGTAAATTATTTCCCAAGTTTGTAAATCCTTCGGG
* *
3216193 TCATCAGTAAGTCTTTCGAGCATAATGCTTAAATTCTTCAGGTCATCTGTAAGTCTTTCGAGCAA
131 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAA
* * * * *
3216258 GATGATAAGTCTTTTAGGCTACCCGTAAGACCTTCGGGTAGAATGTTTACACATGATTTTCACA
196 GATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGGGTAGGATGTTTACACATGATTTTCACA
*** * * * * *
3216322 TGAAAATGAGAAAGTGATTACCAAAGTTTATCATTTAATGTTTAGAAAATAAAATTCTTAAAAAG
1 TGAAAATGAGAAAACAATTACCAAAGTTTCTCATTTAATCTTCAGAAAATGAAATTCTTGAAAAG
*
3216387 TAAGAAAGCTATTACCAAAGATTCTTA-CCAGTAAATTATTTCCCAAGTTTGTAAATCCTTCGAG
66 TAAGAAAGCTATTACCAAAGATTCTTACCCAGTAAATTATTTCCCAAGTTTGTAAATCCTTCGGG
* * *
3216451 TCATCATTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAA
131 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAA
* * *
3216516 GATGTTAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGA
196 GATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGGGTAGGATGTTTACACATGA
3216572 AAATGAGAAA
Statistics
Matches: 689, Mismatches: 74, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
257 140 0.20
258 328 0.48
259 185 0.27
260 2 0.00
261 34 0.05
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (259 bp):
TGAAAATGAGAAAACAATTACCAAAGTTTCTCATTTAATCTTCAGAAAATGAAATTCTTGAAAAG
TAAGAAAGCTATTACCAAAGATTCTTACCCAGTAAATTATTTCCCAAGTTTGTAAATCCTTCGGG
TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAA
GATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGGGTAGGATGTTTACACATGATTTTCACA
Found at i:3216497 original size:42 final size:41
Alignment explanation
Indices: 3216438--3216544 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 41
3216428 CCCAAGTTTG
* * *
3216438 TAAATCCTTCGAGTCATCAT-TAAGTCTTTTGAGCATGATGCT
1 TAAATCCTTCGGGTCATC-TGTAAGTCTTTCGAGCAAGATG-T
3216480 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGT
1 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGT
* * *
3216521 TAAGTCCTTCGGGCCATCCGTAAG
1 TAAATCCTTCGGGTCATCTGTAAG
3216545 ACCTTCGGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 23 0.40
42 35 0.60
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGT
Found at i:3216562 original size:41 final size:41
Alignment explanation
Indices: 3216468--3216551 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
3216458 TAAGTCTTTT
* * * * *
3216468 GAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTC
1 GAGCAAGATG-TTAAATCCTTCGGGCCATCCGTAAGACCTTC
*
3216510 GAGCAAGATGTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
1 GAGCAAGATGTTAAATCCTTCGGGCCATCCGTAAGACCTTC
3216551 G
1 G
3216552 GGTAGGATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 27 0.75
42 9 0.25
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (41 bp):
GAGCAAGATGTTAAATCCTTCGGGCCATCCGTAAGACCTTC
Found at i:3216708 original size:189 final size:188
Alignment explanation
Indices: 3216389--3216752 Score: 505
Period size: 189 Copynumber: 1.9 Consensus size: 188
3216379 TTAAAAAGTA
* * * *
3216389 AGAAAGCTATTACCAAAGATTCTTACCAGTAAATTATTTCCCAAGTTTGTAAATCCTTCGAGTCA
1 AGAAAGCGATTACCAAAGATTCTTACCAGTAAACTATTTCCCAAATTTGTAAATCCTTCGAGCCA
* * * *
3216454 TCATTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGAT
66 TCATTAAGTCTTTCGAGCATGATGATAAAATCCTTCGGGTCATCTGTAACTCTTTCGAGCAAGAT
* *
3216519 GTTAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAAAATG
131 GATAAGTCCTTCGAGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAAAATG
* * * *
3216577 AGAAAGCGATTACCAAAGTTTCTTACGCATTAAACTATTTCTCAAATTTGTAAGTCCTTCG-GAC
1 AGAAAGCGATTACCAAAGATTCTTAC-CAGTAAACTATTTCCCAAATTTGTAAATCCTTCGAG-C
* * * * *
3216641 CATCATTAATTCTTTCGAGCATGATGATAAAATTCTTTGGGTCATCTGTCACTCTTTTGAGCAAG
64 CATCATTAAGTCTTTCGAGCATGATGATAAAATCCTTCGGGTCATCTGTAACTCTTTCGAGCAAG
* * *
3216706 ATGATAAGTCCTTTGAGCTATCCGTAAGACCTTTGGGTAGGATGTTT
129 ATGATAAGTCCTTCGAGCCATCCGTAAGACCTTCGGGTAGGATGTTT
3216753 GCACTATTTT
Statistics
Matches: 152, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
188 25 0.16
189 127 0.84
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (188 bp):
AGAAAGCGATTACCAAAGATTCTTACCAGTAAACTATTTCCCAAATTTGTAAATCCTTCGAGCCA
TCATTAAGTCTTTCGAGCATGATGATAAAATCCTTCGGGTCATCTGTAACTCTTTCGAGCAAGAT
GATAAGTCCTTCGAGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAAAATG
Found at i:3216813 original size:37 final size:37
Alignment explanation
Indices: 3216760--3216948 Score: 193
Period size: 37 Copynumber: 4.9 Consensus size: 37
3216750 TTTGCACTAT
* *
3216760 TTTTTATTTTTAACTTCATAGTAAAGAGAAGTCAATA
1 TTTTTATTTTTGACTTCCTAGTAAAGAGAAGTCAATA
* * *
3216797 TTTTTATTATTGACTTCGTAGTAAAGAGAAGT-AATTTTT
1 TTTTTATTTTTGACTTCCTAGTAAAGAGAAGTCAA---TA
3216836 TTTTTATTTTTGACTTCCTAGTAAA-AGAATGTCAATA
1 TTTTTATTTTTGACTTCCTAGTAAAGAGAA-GTCAATA
* * * *
3216873 TTTGTTATTATTGACTTCCTTGTGAAGAAAGAAGTCAATC
1 TTT-TTATTTTTGACTTCCTAGT-AA-AGAGAAGTCAATA
* *
3216913 TTTGTTATTTTTGACTTCCTCGTGAAGAGAAGTCAA
1 TTT-TTATTTTTGACTTCCTAGTAAAGAGAAGTCAA
3216949 CCTTTATTAT
Statistics
Matches: 129, Mismatches: 14, Indels: 17
0.81 0.09 0.11
Matches are distributed among these distances:
36 2 0.02
37 33 0.26
38 31 0.24
39 29 0.22
40 30 0.23
41 4 0.03
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (37 bp):
TTTTTATTTTTGACTTCCTAGTAAAGAGAAGTCAATA
Found at i:3216959 original size:38 final size:38
Alignment explanation
Indices: 3216757--3216948 Score: 201
Period size: 38 Copynumber: 5.0 Consensus size: 38
3216747 ATGTTTGCAC
* * *
3216757 TATTTTTTATTTTTAACTTCATAGTAAAGAGAAGTCAA
1 TATTTGTTATTTTTGACTTCCTAGTAAAGAGAAGTCAA
* *
3216795 TATTT-TTATTATTGACTTCGTAGTAAAGAGAAGT-AA
1 TATTTGTTATTTTTGACTTCCTAGTAAAGAGAAGTCAA
* *
3216831 TTTTTTTTTTATTTTTGACTTCCTAGTAAA-AGAATGTCAA
1 --TATTTGTTATTTTTGACTTCCTAGTAAAGAGAA-GTCAA
* * *
3216871 TATTTGTTATTATTGACTTCCTTGTGAAGAAAGAAGTCAA
1 TATTTGTTATTTTTGACTTCCTAGT-AA-AGAGAAGTCAA
* * *
3216911 TCTTTGTTATTTTTGACTTCCTCGTGAAGAGAAGTCAA
1 TATTTGTTATTTTTGACTTCCTAGTAAAGAGAAGTCAA
3216949 CCTTTATTAT
Statistics
Matches: 131, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
36 2 0.02
37 26 0.20
38 44 0.34
39 25 0.19
40 30 0.23
41 4 0.03
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (38 bp):
TATTTGTTATTTTTGACTTCCTAGTAAAGAGAAGTCAA
Found at i:3216966 original size:38 final size:39
Alignment explanation
Indices: 3216884--3216966 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 39
3216874 TTGTTATTAT
* * * **
3216884 TGACTTCCTTGTGAAGAAAGAAGTCAATCTTTGTTATTTT
1 TGACTTCCTCGTGAAG-AAGAAGTCAACCTTTATTATTCC
3216924 TGACTTCCTCGTGAAG-AGAAGTCAACCTTTATTATTCC
1 TGACTTCCTCGTGAAGAAGAAGTCAACCTTTATTATTCC
3216962 TGACT
1 TGACT
3216967 CACAGTAGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 23 0.61
40 15 0.39
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (39 bp):
TGACTTCCTCGTGAAGAAGAAGTCAACCTTTATTATTCC
Found at i:3217018 original size:61 final size:62
Alignment explanation
Indices: 3216923--3217194 Score: 300
Period size: 61 Copynumber: 4.4 Consensus size: 62
3216913 TTTGTTATTT
* * * *
3216923 TTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTCCTGACT-CACAGTAGAGTTAATCG
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCCTGACTCCCCAGTAGAGTCAATCA
* * * *
3216984 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTATTA-TCTTTTACT-CCTAGTAGAGTCAATCT
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTC-CTGACTCCCCAGTAGAGTCAATCA
* * * ** * *
3217045 TTTACTTTCTCGTGAAGGGAAGTCAATCACTATTATTTCTGACTCCCCAGTAGAGTCAATCC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCCTGACTCCCCAGTAGAGTCAATCA
* * * ** *
3217107 TTGACTTCCTTGTGAAGAGAAGTTAA-CTTTTTTATTTTTGACTCCCCAATAGAGTCAATCA
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCCTGACTCCCCAGTAGAGTCAATCA
* *
3217168 TTGACTTCCTCGGGAAGAAAAGTCAAT
1 TTGACTTCCTCGTGAAGAGAAGTCAAT
3217195 ATTGCATATT
Statistics
Matches: 175, Mismatches: 32, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
60 2 0.01
61 136 0.78
62 37 0.21
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (62 bp):
TTGACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCCTGACTCCCCAGTAGAGTCAATCA
Found at i:3217160 original size:123 final size:122
Alignment explanation
Indices: 3216921--3217194 Score: 336
Period size: 123 Copynumber: 2.2 Consensus size: 122
3216911 TCTTTGTTAT
* ** * *
3216921 TTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTCCTGACTCACAGTAGAGTTAATCGTT
1 TTTT-ACTTCCTCGTGAAGAGAAGTCAATCACTATTATTCCTGACTCACAGTAGAGTCAATCCTT
* *
3216986 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATCTTTTACTCCTAGTAGAGTCAATC
65 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATCTTTTACTCCCAATAGAGTCAATC
* * * *
3217044 TTTTACTTTCTCGTGAAGGGAAGTCAATCACTATTATTTCTGACTCCCCAGTAGAGTCAATCCTT
1 TTTTACTTCCTCGTGAAGAGAAGTCAATCACTATTATTCCTGACT-CACAGTAGAGTCAATCCTT
* * *
3217109 GACTTCCTTGTGAAGAGAAGTTAA-CTTTTTTAT-TTTTGACTCCCCAATAGAGTCAATC
65 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATCTTTT-ACT-CCCAATAGAGTCAATC
* * * *
3217167 ATTGACTTCCTCGGGAAGAAAAGTCAAT
1 TTTTACTTCCTCGTGAAGAGAAGTCAAT
3217195 ATTGCATATT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
121 4 0.03
122 46 0.36
123 78 0.61
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (122 bp):
TTTTACTTCCTCGTGAAGAGAAGTCAATCACTATTATTCCTGACTCACAGTAGAGTCAATCCTTG
ACTTCCTCGTGAAGAGAAGTCAATCTTTATTATCTTTTACTCCCAATAGAGTCAATC
Found at i:3217320 original size:89 final size:89
Alignment explanation
Indices: 3217195--3217415 Score: 307
Period size: 89 Copynumber: 2.5 Consensus size: 89
3217185 AAAAGTCAAT
* * * *** * * *
3217195 ATTGCATATTTGGTCTTCCTGGAAAAGTAGTGAATCAAATCAACCTTGAGTCTGATCTCCATGGA
1 ATTGCAGATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAGTCTGATCTCCACGAA
*
3217260 AGAGTAGTGGAACATATTATTCTC
66 AGAGTAGTGGAACAGATTATTCTC
*
3217284 ATTGCAGATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAGTCTGATCTCTACGAA
1 ATTGCAGATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAGTCTGATCTCCACGAA
* *
3217349 AGAGTAGTGGAATAGATTCTTCTC
66 AGAGTAGTGGAACAGATTATTCTC
**
3217373 ATCCCAGATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAA
1 ATTGCAGATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAA
3217416 TTTCAATCTA
Statistics
Matches: 117, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 117 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (89 bp):
ATTGCAGATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAGTCTGATCTCCACGAA
AGAGTAGTGGAACAGATTATTCTC
Found at i:3217437 original size:89 final size:89
Alignment explanation
Indices: 3217202--3217445 Score: 258
Period size: 89 Copynumber: 2.7 Consensus size: 89
3217192 AATATTGCAT
* * *** * * * * * * *
3217202 ATTTGGTCTTCCTGGAAAAGTAGTGAATCAAATCAACCTTGAGTCTGATCTCCATGGAAGAGTAG
1 ATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAATCTAAGCTCTACGAAAGAGTAG
* **
3217267 TGGAACATATTATTCTCATTGCAG
66 TGGAACAGATTATTCTCATCCCAG
* * *
3217291 ATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAGTCTGATCTCTACGAAAGAGTAG
1 ATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAATCTAAGCTCTACGAAAGAGTAG
* *
3217356 TGGAATAGATTCTTCTCATCCCAG
66 TGGAACAGATTATTCTCATCCCAG
**
3217380 ATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAATTTC-AATCTAAGCT-TGCACGAAAGAGT
1 ATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAATCTAAGCTCT--ACGAAAGAGT
3217443 AGT
64 AGT
3217446 AAAGAAAATC
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
87 1 0.01
88 7 0.05
89 126 0.94
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (89 bp):
ATTTGGTCTTCCTGGCAAAGCAACAAATCAAATCAACCTCGAATCTAAGCTCTACGAAAGAGTAG
TGGAACAGATTATTCTCATCCCAG
Found at i:3217481 original size:36 final size:36
Alignment explanation
Indices: 3217418--3217568 Score: 178
Period size: 36 Copynumber: 4.2 Consensus size: 36
3217408 CAAATCAATT
* * *
3217418 TCAATCTAAGC-TTGCACGAAAGAGTAGTAAAGAAAA
1 TCAATCTAAGCATT-CACGGAAGAGTAGTGAAGCAAA
* * * * *
3217454 TCAATTTAAGCCTTCACGGACGGGTAGTGAAGCAAG
1 TCAATCTAAGCATTCACGGAAGAGTAGTGAAGCAAA
* *
3217490 TCAATCTAAGGATTCACGGAAGAGAAGTGAAGCAAA
1 TCAATCTAAGCATTCACGGAAGAGTAGTGAAGCAAA
* *
3217526 TCAATCTAAGCTTTCATGGAAGAGTAGTGAAGCAAA
1 TCAATCTAAGCATTCACGGAAGAGTAGTGAAGCAAA
3217562 TCAATCT
1 TCAATCT
3217569 CGATTCTTAT
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
36 94 0.98
37 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (36 bp):
TCAATCTAAGCATTCACGGAAGAGTAGTGAAGCAAA
Found at i:3217864 original size:3 final size:3
Alignment explanation
Indices: 3217856--3217889 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3217846 TCCTGTTTTA
*
3217856 TAT TAT TAT TA- TAC TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3217890 AATAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3219571 original size:17 final size:16
Alignment explanation
Indices: 3219542--3219583 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
3219532 AACGCATATC
3219542 AATT-TTTTATCTTTTAA
1 AATTATTTTATC--TTAA
3219559 AATTATTTT-TCTTAA
1 AATTATTTTATCTTAA
3219574 AATTATTTTA
1 AATTATTTTA
3219584 AAAGATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTATTTTATCTTAA
Found at i:3220407 original size:45 final size:45
Alignment explanation
Indices: 3220356--3220457 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
3220346 TCATTTTAAA
* * *
3220356 TCATAAATGAAATG-ATTAACGATGTATTAAAGGCATGAAAAGAT-
1 TCATAAATGAAATGCA-TAAAGATGCAGTAAAGGCATGAAAAGATG
* * *
3220400 TCCATAAATGAAATGCATAAAGGTGCAGTATAGGCATGAAAGGATG
1 T-CATAAATGAAATGCATAAAGATGCAGTAAAGGCATGAAAAGATG
3220446 TCATAAATGAAA
1 TCATAAATGAAA
3220458 ATAATGAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
44 1 0.02
45 46 0.94
46 2 0.04
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.25
Consensus pattern (45 bp):
TCATAAATGAAATGCATAAAGATGCAGTAAAGGCATGAAAAGATG
Found at i:3224457 original size:45 final size:45
Alignment explanation
Indices: 3224387--3224802 Score: 627
Period size: 45 Copynumber: 9.2 Consensus size: 45
3224377 GTTTTCATTA
* **
3224387 CATATATGAAATGCATAACAATGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
3224432 CATAAATGAAATGCATAACGTTGCATTAAAGGCATGAAAGGATAC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
3224477 CATAAATGAAATGCATAACGATGTATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*** *
3224522 CATAAATGAAATGCATAATACTGCATTAAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
3224567 CATAAAT-AAATTGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAA-TGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
3224612 CATAAATGAAATGCATAATGATGCATTAAAGGCATGAAAAGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
3224657 CATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * * *
3224702 CATAAATGAAATGCATAAAGGTGCATTATAGGCATGAAAGAATAC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
3224747 CATAAATGAAATGCATAACGGTGCATTAAAGGTATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
3224792 CCTAAATGAAA
1 CATAAATGAAA
3224803 ATAATGAATA
Statistics
Matches: 338, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
44 3 0.01
45 332 0.98
46 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:3227323 original size:17 final size:17
Alignment explanation
Indices: 3227301--3227496 Score: 108
Period size: 17 Copynumber: 11.3 Consensus size: 17
3227291 AATTAAGATT
*
3227301 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
* *
3227318 TAGTTTGATGAATGGAC
1 TAGTTTAATGAATGAAC
*
3227335 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* *
3227352 TAACTTT-ATCAAATGAAC
1 T-AGTTTAAT-GAATGAAC
* * **
3227370 TTGTAATCTTGAATGAAC
1 TAGT-TTAATGAATGAAC
* *
3227388 CAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
* *
3227405 TAGTTTAGTTAATGAAC
1 TAGTTTAATGAATGAAC
* *
3227422 TAACTTT-ATCAAATGAAC
1 T-AGTTTAAT-GAATGAAC
* * ** *
3227440 TTGTAATCTTGACTGAAC
1 TAGT-TTAATGAATGAAC
* *
3227458 CAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
3227475 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
3227492 TAGTT
1 TAGTT
3227497 AGTTAAATGA
Statistics
Matches: 131, Mismatches: 40, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
17 86 0.66
18 43 0.33
19 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:3227393 original size:70 final size:70
Alignment explanation
Indices: 3227311--3227493 Score: 330
Period size: 70 Copynumber: 2.6 Consensus size: 70
3227301 TAGTTTAATA
* *
3227311 AATGAACTAGTTTGATGAATGGACTAGTTTAATTAATGAACTAACTTTATCAAATGAACTTGTAA
1 AATGAACCAGTTTGATGAATGAACTAGTTTAATTAATGAACTAACTTTATCAAATGAACTTGTAA
3227376 TCTTG
66 TCTTG
*
3227381 AATGAACCAGTTTGATGAATGAACTAGTTTAGTTAATGAACTAACTTTATCAAATGAACTTGTAA
1 AATGAACCAGTTTGATGAATGAACTAGTTTAATTAATGAACTAACTTTATCAAATGAACTTGTAA
3227446 TCTTG
66 TCTTG
*
3227451 ACTGAACCAGTTTGATGAATGAACTAGTTTAATTAATGAACTA
1 AATGAACCAGTTTGATGAATGAACTAGTTTAATTAATGAACTA
3227494 GTTAGTTAAA
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 108 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (70 bp):
AATGAACCAGTTTGATGAATGAACTAGTTTAATTAATGAACTAACTTTATCAAATGAACTTGTAA
TCTTG
Found at i:3227404 original size:35 final size:35
Alignment explanation
Indices: 3227363--3227475 Score: 115
Period size: 35 Copynumber: 3.2 Consensus size: 35
3227353 AACTTTATCA
3227363 AATGAACTTGTAATCTTGAATGAACCAGTTTGATG
1 AATGAACTTGTAATCTTGAATGAACCAGTTTGATG
* * * * * *
3227398 AATGAACTAGT-TTAGTT-AATGAACTAACTTT-ATCA
1 AATGAACTTGTAAT-CTTGAATGAAC-CAGTTTGAT-G
*
3227433 AATGAACTTGTAATCTTGACTGAACCAGTTTGATG
1 AATGAACTTGTAATCTTGAATGAACCAGTTTGATG
3227468 AATGAACT
1 AATGAACT
3227476 AGTTTAATTA
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
34 10 0.17
35 40 0.68
36 9 0.15
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (35 bp):
AATGAACTTGTAATCTTGAATGAACCAGTTTGATG
Found at i:3232438 original size:17 final size:17
Alignment explanation
Indices: 3232389--3232440 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
3232379 GAATAAAGTT
*
3232389 AGTTCATTAATTAAACT
1 AGTTCATTAATTAAACA
*** *
3232406 AGTTCAGCCATCAAACA
1 AGTTCATTAATTAAACA
*
3232423 AGTTCATTTATTAAACA
1 AGTTCATTAATTAAACA
3232440 A
1 A
3232441 ACTCTTAATT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (17 bp):
AGTTCATTAATTAAACA
Found at i:3243710 original size:17 final size:17
Alignment explanation
Indices: 3243688--3243721 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3243678 ACTTTGACCA
3243688 AAAAGTCAAATTTTATG
1 AAAAGTCAAATTTTATG
* *
3243705 AAAAGTTATATTTTATG
1 AAAAGTCAAATTTTATG
3243722 TTTTTCGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (17 bp):
AAAAGTCAAATTTTATG
Found at i:3246608 original size:2 final size:2
Alignment explanation
Indices: 3246601--3246625 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3246591 ACATTTGATT
3246601 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
3246626 TGAGTCTGAA
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:3250745 original size:19 final size:19
Alignment explanation
Indices: 3250721--3250758 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3250711 GTCCTATGGC
3250721 CTATTTTAGTGAGAAATTA
1 CTATTTTAGTGAGAAATTA
3250740 CTATTTTAGTGAGAAATTA
1 CTATTTTAGTGAGAAATTA
3250759 AGTCGAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
CTATTTTAGTGAGAAATTA
Found at i:3254658 original size:17 final size:17
Alignment explanation
Indices: 3254636--3254669 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3254626 ACCTTGACCA
3254636 AAAAGTCAAATTTTATG
1 AAAAGTCAAATTTTATG
*
3254653 AAAAGTCATATTTTATG
1 AAAAGTCAAATTTTATG
3254670 TTTTTCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAGTCAAATTTTATG
Found at i:3256157 original size:37 final size:37
Alignment explanation
Indices: 3256058--3256159 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 37
3256048 CCTTTTCGTC
*
3256058 CTACTAAGATTCAAACTCGTAAAAATAGGATAGAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* *
3256095 -T--TAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
3256129 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
3256160 TCACAAGCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
34 30 0.55
35 1 0.02
36 1 0.02
37 23 0.42
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:3256667 original size:20 final size:20
Alignment explanation
Indices: 3256642--3256679 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3256632 TTTATTATTA
3256642 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
3256662 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
3256680 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:3256708 original size:37 final size:40
Alignment explanation
Indices: 3256622--3256709 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 40
3256612 ATTACTTTTG
*
3256622 ATTTTCTTTTTTTATTATTATTTTACTTATATATATATGCT
1 ATTTTC-TTTTTTATTATTATTTTACTCATATATATATGCT
* * *
3256663 -TTTACTTTTTTA-TA-TATTTTACTCATTTATTTAT-CT
1 ATTTTCTTTTTTATTATTATTTTACTCATATATATATGCT
3256699 ATTTTCTTTTT
1 ATTTTCTTTTT
3256710 ATCTTTATCT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
36 2 0.05
37 26 0.63
38 2 0.05
39 7 0.17
40 4 0.10
ACGTcount: A:0.22, C:0.09, G:0.01, T:0.68
Consensus pattern (40 bp):
ATTTTCTTTTTTATTATTATTTTACTCATATATATATGCT
Found at i:3260193 original size:15 final size:15
Alignment explanation
Indices: 3260173--3260203 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3260163 GAACATTTCA
3260173 TGCATTCTTGCATTT
1 TGCATTCTTGCATTT
*
3260188 TGCATTTTTGCATTT
1 TGCATTCTTGCATTT
3260203 T
1 T
3260204 TTGCATCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (15 bp):
TGCATTCTTGCATTT
Found at i:3261386 original size:8 final size:8
Alignment explanation
Indices: 3261368--3261441 Score: 71
Period size: 8 Copynumber: 9.1 Consensus size: 8
3261358 AGATTCAATC
3261368 AGAACAAAA
1 AGAA-AAAA
3261377 AGAAAAAA
1 AGAAAAAA
3261385 AG-AAAAA
1 AGAAAAAA
*
3261392 AGAAAAGA
1 AGAAAAAA
*
3261400 AGCAAAAA
1 AGAAAAAA
3261408 AGAAAAAA
1 AGAAAAAA
*
3261416 ACAAAAGAA
1 AGAAAA-AA
*
3261425 A-AAAGAA
1 AGAAAAAA
3261432 AGAACAAAA
1 AGAA-AAAA
3261441 A
1 A
3261442 TCAAAATGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
7 10 0.19
8 33 0.61
9 11 0.20
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:3261390 original size:7 final size:7
Alignment explanation
Indices: 3261373--3261432 Score: 77
Period size: 7 Copynumber: 8.3 Consensus size: 7
3261363 CAATCAGAAC
3261373 AAAAAGAA
1 AAAAAG-A
3261381 AAAAAGA
1 AAAAAGA
3261388 AAAAAGA
1 AAAAAGA
3261395 AAAGAAGCA
1 AAA-AAG-A
3261404 AAAAAGA
1 AAAAAGA
3261411 AAAAA-A
1 AAAAAGA
*
3261417 CAAAAGA
1 AAAAAGA
3261424 AAAAAGA
1 AAAAAGA
3261431 AA
1 AA
3261433 GAACAAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
6 5 0.11
7 26 0.55
8 12 0.26
9 4 0.09
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:3261411 original size:31 final size:31
Alignment explanation
Indices: 3261373--3261431 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3261363 CAATCAGAAC
*
3261373 AAAAAGAAAAAAAGAAAA-AAGAAAAGAAGCA
1 AAAAAGAAAAAAACAAAAGAA-AAAAGAAGCA
3261404 AAAAAGAAAAAAACAAAAGAAAAAAGAA
1 AAAAAGAAAAAAACAAAAGAAAAAAGAA
3261432 AGAACAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (31 bp):
AAAAAGAAAAAAACAAAAGAAAAAAGAAGCA
Found at i:3262134 original size:22 final size:22
Alignment explanation
Indices: 3262061--3262137 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
3262051 GCTACCCCAT
*
3262061 CAAACCATTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
3262083 CAAACCTATGAGCATCAAATAC
1 CAAACCTTTGAGCATCAAATGC
3262105 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
3262127 CAAACCTTTGA
1 CAAACCTTTGA
3262138 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:3262358 original size:24 final size:24
Alignment explanation
Indices: 3262325--3262392 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
3262315 TGAAAGGGAC
3262325 AACAT-TTTCAAAACTTTTAATTA
1 AACATCTTTCAAAACTTTTAATTA
* *
3262348 AACATCTTTCAAAACTCTTGATTA
1 AACATCTTTCAAAACTTTTAATTA
*
3262372 AACATCTTTCGAAACTCTTTA
1 AACATCTTTCAAAACT-TTTA
3262393 TTGATATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 5 0.13
24 31 0.82
25 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (24 bp):
AACATCTTTCAAAACTTTTAATTA
Found at i:3263912 original size:106 final size:106
Alignment explanation
Indices: 3262960--3263911 Score: 1508
Period size: 106 Copynumber: 9.0 Consensus size: 106
3262950 GAAGGATATT
* *
3262960 GACAACGCAAGTTCAACTTCACTACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
** *
3263025 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCGA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
3263066 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
3263131 AGAGCCAATTTCAACTTCACAGTGAAAGATATTGGACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* *
3263172 GACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * *
3263237 GGAGCCAATTTCAACTTCACAGCGATGGATATTGCACTTCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* * *
3263278 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTT
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
3263343 AGAGCCAATTTTAACTTCACAACGAAAGATATTGGACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
*
3263384 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
3263449 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* *
3263490 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
3263555 AGAGCCAATTTCAACTTCACAGTGAATGATATTGGACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
3263596 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
3263661 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
** ** * *
3263702 GATGACGCAAGTTCAACTTCAAAACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
3263767 GGAGACAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* * * * * *
3263808 GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
3263873 AGAGCTAATTTCAACTTCACAACGGAGGATATTGGACTC
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
3263912 GGAACAATCC
Statistics
Matches: 781, Mismatches: 65, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 781 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
Found at i:3264760 original size:37 final size:36
Alignment explanation
Indices: 3264661--3264762 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 36
3264651 CCTTTTCGTC
3264661 CTACTAGGATTCAAACTCCTAAAATTAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAA-TAGGATAGAATT
*
3264698 -T--TAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCT-AAAATAGGATAGAATT
* * *
3264732 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAA-ATAGGAT
3264763 TCACAAGCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
34 27 0.48
35 5 0.09
36 4 0.07
37 20 0.36
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
Found at i:3268693 original size:55 final size:55
Alignment explanation
Indices: 3268611--3269000 Score: 472
Period size: 55 Copynumber: 7.2 Consensus size: 55
3268601 GTATAGTGAT
* *
3268611 TTTC-GTATGGGCCCTTTGTGTACAAAACTAAGAAATTCATACTAAGTGTATGAA
1 TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * *
3268665 TTTCTGTATGGGCACTTGGTGTGAAAAACTAAGAAATTCATACTATGTGTATGAA
1 TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * *
3268720 TTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTTATACAAAGTGTATGAA
1 TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * *
3268775 TTT-TCATATGGGCACTTTGTCTTG-AAAACTAAGAAATTCATAATAAGTGTATGAA
1 TTTCT-GTATGGGCACTTTGT-GTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * * * *
3268830 TTTTTGTATAGGTACTTGGTGTGCAAAACTAAGAAATTCAAACTAAGTGTATGAA
1 TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* *
3268885 TTT-TCGTATGGGAACTTTGTGTGTAAAACTAAGAAATT--TA-TAAGTGTATGAA
1 TTTCT-GTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * * * *
3268937 TTT-TCATATGGGCACTTGGTGTGCAAAACTAAGAAATTCATAATAAGTATGTGAA
1 TTTCT-GTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
*
3268992 TTTCCGTAT
1 TTTCTGTAT
3269001 TGTTGGTGGG
Statistics
Matches: 289, Mismatches: 37, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
52 46 0.16
53 1 0.00
54 9 0.03
55 230 0.80
56 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (55 bp):
TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
Found at i:3268791 original size:110 final size:108
Alignment explanation
Indices: 3268609--3269000 Score: 520
Period size: 110 Copynumber: 3.6 Consensus size: 108
3268599 ATGTATAGTG
* * *
3268609 ATTTTCGTATGGGCCCTTTGTGTACAAAACTAAGAAATTCATACTAAGTGTATGAA-TTTCTGTA
1 ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTC-GTA
* *
3268673 TGGGCACTTGGTGTGAAAAACTAAGAAATTCATACTATGTGTATGA
65 TGGGCACTTTGTGTG-AAAACTAAGAAATTCATA-TAAGTGTATGA
* * * * *
3268719 ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTTATACAAAGTGTATGAATTTTCATAT
1 ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
*
3268784 GGGCACTTTGTCTTGAAAACTAAGAAATTCATAATAAGTGTATGA
66 GGGCACTTTGT-GTGAAAACTAAGAAATTCAT-ATAAGTGTATGA
* * * *
3268829 ATTTTTGTATAGGTACTTGGTGTGCAAAACTAAGAAATTCAAACTAAGTGTATGAATTTTCGTAT
1 ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
*
3268894 GGGAACTTTGTGTGTAAAACTAAGAAATT--TATAAGTGTATGA
66 GGGCACTTTGTGTG-AAAACTAAGAAATTCATATAAGTGTATGA
* * * * *
3268936 ATTTTCATATGGGCACTTGGTGTGCAAAACTAAGAAATTCATAATAAGTATGTGAATTTCCGTAT
1 ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
3269001 TGTTGGTGGG
Statistics
Matches: 249, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
107 68 0.27
108 1 0.00
109 2 0.01
110 171 0.69
111 7 0.03
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (108 bp):
ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
GGGCACTTTGTGTGAAAACTAAGAAATTCATATAAGTGTATGA
Found at i:3268895 original size:165 final size:161
Alignment explanation
Indices: 3268609--3269000 Score: 559
Period size: 165 Copynumber: 2.4 Consensus size: 161
3268599 ATGTATAGTG
* * ** *
3268609 ATTTTCGTATGGGCCCTTTGTGTACAAAACTAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
1 ATTTTCATATGGGCACTTTGT-TTGAAAACTAAGAAATTCATAATAAGTGTATGAATTTCTGTAT
* * * *
3268674 GGGCACTTGGTGTGAAAAACTAAGAAATTCATACTATGTGTATGAATTTCCGTATGGGCACTTTG
65 AGGCACTTGGTGTGAAAAACTAAGAAATTCAAACTAAGTGTATGAATTTCCGTATGGGAACTTTG
3268739 TGTGCAAAACTAAGAAATTTATACAAAGTGTATGA
130 TGTGCAAAACTAAGAAATTTAT---AAGTGTATGA
*
3268774 ATTTTCATATGGGCACTTTGTCTTGAAAACTAAGAAATTCATAATAAGTGTATGAATTTTTGTAT
1 ATTTTCATATGGGCACTTTGT-TTGAAAACTAAGAAATTCATAATAAGTGTATGAATTTCTGTAT
* * *
3268839 AGGTACTTGGTGTGCAAAACTAAGAAATTCAAACTAAGTGTATGAATTTTCGTATGGGAACTTTG
65 AGGCACTTGGTGTGAAAAACTAAGAAATTCAAACTAAGTGTATGAATTTCCGTATGGGAACTTTG
*
3268904 TGTGTAAAACTAAGAAATTTATAAGTGTATGA
130 TGTGCAAAACTAAGAAATTTATAAGTGTATGA
* * * * *
3268936 ATTTTCATATGGGCACTTGGTGTGCAAAACTAAGAAATTCATAATAAGTATGTGAATTTCCGTAT
1 ATTTTCATATGGGCACTTTGTTTG-AAAACTAAGAAATTCATAATAAGTGTATGAATTTCTGTAT
3269001 TGTTGGTGGG
Statistics
Matches: 205, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
161 2 0.01
162 66 0.32
165 137 0.67
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (161 bp):
ATTTTCATATGGGCACTTTGTTTGAAAACTAAGAAATTCATAATAAGTGTATGAATTTCTGTATA
GGCACTTGGTGTGAAAAACTAAGAAATTCAAACTAAGTGTATGAATTTCCGTATGGGAACTTTGT
GTGCAAAACTAAGAAATTTATAAGTGTATGA
Found at i:3275917 original size:55 final size:55
Alignment explanation
Indices: 3275688--3275901 Score: 306
Period size: 55 Copynumber: 3.9 Consensus size: 55
3275678 ATGTATGGTG
* *
3275688 ATTTACGTATGGGAACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
1 ATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
* * * *
3275743 ATTTCCGTATGGGCACTTTCTATGAAAAACTAAGAAATTCATACTAAGTGTATGA
1 ATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
*
3275798 ATTTTCGTATGGGTACTTTGTGTGCAAAACTAAGAAATGT-ATACTAAGTGTATGA
1 ATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAAT-TCATACTAAGTGTATGA
* * *
3275853 ATGTGT-GTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATAATAAGT
1 AT-TTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGT
3275902 ATGTGATTTT
Statistics
Matches: 142, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
54 1 0.01
55 138 0.97
56 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (55 bp):
ATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
Found at i:3277457 original size:32 final size:33
Alignment explanation
Indices: 3277421--3277504 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 33
3277411 AAGGTGACCC
*
3277421 TTGGGTAGGCTCTTAGGCCCCAAGGTACT-CCT
1 TTGGGTAGGCTCTTAGGCCCCAAGGCACTACCT
* *
3277453 TTGGGTAGGCTCTAAGGCCCTAAGGCACTACCT
1 TTGGGTAGGCTCTTAGGCCCCAAGGCACTACCT
* * *
3277486 TAGGTTA-GCTCTTATGCCC
1 TTGGGTAGGCTCTTAGGCCC
3277505 AACGGGTATA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 36 0.82
33 8 0.18
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (33 bp):
TTGGGTAGGCTCTTAGGCCCCAAGGCACTACCT
Found at i:3277793 original size:31 final size:32
Alignment explanation
Indices: 3277751--3277827 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
3277741 CCTAAGCTGA
* * *
3277751 CCCTTGGGTAGGCTCTTAGGCCCCAAGGTA-T
1 CCCTTAGGTAGGCTCTAAGGCCCCAAGGCACT
*
3277782 TCCTTAGGTAGGCTCTAAGGCCCCAAGGCACT
1 CCCTTAGGTAGGCTCTAAGGCCCCAAGGCACT
*
3277814 CCCTTAGGTTGGCT
1 CCCTTAGGTAGGCT
3277828 TCTACACCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 26 0.67
32 13 0.33
ACGTcount: A:0.17, C:0.30, G:0.27, T:0.26
Consensus pattern (32 bp):
CCCTTAGGTAGGCTCTAAGGCCCCAAGGCACT
Found at i:3282331 original size:55 final size:55
Alignment explanation
Indices: 3282212--3282424 Score: 293
Period size: 55 Copynumber: 3.9 Consensus size: 55
3282202 ATGTATAGTG
* *
3282212 ATTTCCATATGGGAACTTTGTGTGCAAAACTAAGAAA-TCATACTAAGTGTATGA
1 ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
* * * *
3282266 ATTTTCGTATGGGCACTTTGTATGAAAAACTAAGAAATTCATACTAACTGTATGA
1 ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
* *
3282321 ATTTCCGTATGGGTACTTTGTGTGCAAAACTAAGAAATGCATACTAAGTGTATGA
1 ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
* * * * * *
3282376 ATGTCTGTATGGGCACTTGGTGTGTACAACTAAGAAATTCATAATAAGT
1 ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGT
3282425 ATGTGATTTT
Statistics
Matches: 138, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
54 32 0.23
55 106 0.77
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (55 bp):
ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
Found at i:3282408 original size:110 final size:109
Alignment explanation
Indices: 3282212--3282418 Score: 326
Period size: 110 Copynumber: 1.9 Consensus size: 109
3282202 ATGTATAGTG
*
3282212 ATTTCCATATGGGAACTTTGTGTGCAAAACTAAGAAATCATACTAAGTGTATGAATTTTCGTATG
1 ATTTCCATATGGGAACTTTGTGTGCAAAACTAAGAAATCATACTAAGTGTATGAATTCTCGTATG
*
3282277 GGCACTTTGTATGAAAAACTAAGAAATTCATACTAACTGTATGA
66 GGCACTTGGTATGAAAAACTAAGAAATTCATACTAACTGTATGA
* *
3282321 ATTTCCGTATGGGTACTTTGTGTGCAAAACTAAGAAATGCATACTAAGTGTATGAATGTCT-GTA
1 ATTTCCATATGGGAACTTTGTGTGCAAAACTAAGAAAT-CATACTAAGTGTATGAAT-TCTCGTA
* * *
3282385 TGGGCACTTGGTGTGTACAACTAAGAAATTCATA
64 TGGGCACTTGGTATGAAAAACTAAGAAATTCATA
3282419 ATAAGTATGT
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
109 36 0.40
110 51 0.57
111 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (109 bp):
ATTTCCATATGGGAACTTTGTGTGCAAAACTAAGAAATCATACTAAGTGTATGAATTCTCGTATG
GGCACTTGGTATGAAAAACTAAGAAATTCATACTAACTGTATGA
Found at i:3283974 original size:32 final size:32
Alignment explanation
Indices: 3283938--3283999 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
3283928 AAGGTGACCC
* * *
3283938 TTGGGTAGGCTCTTATGCCCCAAGGTACTCAT
1 TTGGGTAGGCTCTAAGGCCCCAAGGCACTCAT
3283970 TTGGGTAGGCTCTAAGGCCCCAAGGCACTC
1 TTGGGTAGGCTCTAAGGCCCCAAGGCACTC
3284000 CCTTATGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.26
Consensus pattern (32 bp):
TTGGGTAGGCTCTAAGGCCCCAAGGCACTCAT
Found at i:3290293 original size:18 final size:19
Alignment explanation
Indices: 3290272--3290311 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3290262 GAAGAGAGAT
3290272 AAAA-GAAAGTAGA-AAAAG
1 AAAAGGAAAG-AGACAAAAG
3290290 AAAAGGAAAGAGACAAAAG
1 AAAAGGAAAGAGACAAAAG
3290309 AAA
1 AAA
3290312 GCAAAAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (19 bp):
AAAAGGAAAGAGACAAAAG
Found at i:3290342 original size:18 final size:17
Alignment explanation
Indices: 3290272--3290342 Score: 54
Period size: 18 Copynumber: 4.1 Consensus size: 17
3290262 GAAGAGAGAT
*
3290272 AAAAGAAAGTAGAAAAA
1 AAAAGAAAATAGAAAAA
* *
3290289 GAAAAGGAAAGAGACAAAA
1 -AAAAGAAAATAGA-AAAA
* *
3290308 GAAAGCAAAA-AGGAAAA
1 AAAAG-AAAATAGAAAAA
*
3290325 AAAAGAAAATAGATAAA
1 AAAAGAAAATAGAAAAA
3290342 A
1 A
3290343 TACTTCAAGA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
16 4 0.10
17 14 0.34
18 16 0.39
19 7 0.17
ACGTcount: A:0.73, C:0.03, G:0.20, T:0.04
Consensus pattern (17 bp):
AAAAGAAAATAGAAAAA
Found at i:3291009 original size:28 final size:29
Alignment explanation
Indices: 3290966--3291034 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
3290956 CAAATAAACC
* * * *
3290966 AACCCGAAACATATTACCTCC-CCAAATT
1 AACCTGAAACACATTACCACCTCAAAATT
*
3290994 AACCTTAAACACATTACCACCTCAAAATT
1 AACCTGAAACACATTACCACCTCAAAATT
3291023 AACCTGAAACAC
1 AACCTGAAACAC
3291035 GTTAGCTTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 17 0.50
29 17 0.50
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (29 bp):
AACCTGAAACACATTACCACCTCAAAATT
Found at i:3292432 original size:57 final size:57
Alignment explanation
Indices: 3292332--3292439 Score: 135
Period size: 57 Copynumber: 1.9 Consensus size: 57
3292322 ATTACTTCCG
* * **
3292332 ATGAATTTTTAAAGAAGCTAAGTTTAATTTTTAGGGGTCTCTTGATGATAACTATAA
1 ATGAATTTTTAAAGAAGCCAAGTCTAATTTTTAAAGGTCTCTTGATGATAACTATAA
* * * * *
3292389 ATGAATTTTTAATGAAGCCAAGTCTGATTTTTAAATGTTTCTTGTTGATAA
1 ATGAATTTTTAAAGAAGCCAAGTCTAATTTTTAAAGGTCTCTTGATGATAA
3292440 GTCCTTTGGA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 42 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (57 bp):
ATGAATTTTTAAAGAAGCCAAGTCTAATTTTTAAAGGTCTCTTGATGATAACTATAA
Found at i:3294168 original size:43 final size:43
Alignment explanation
Indices: 3294110--3294211 Score: 168
Period size: 43 Copynumber: 2.4 Consensus size: 43
3294100 AGTTCGTTTC
* *
3294110 CATCACATAAGGAGTTAGAACAACACTAATATTTTGGCTCATT
1 CATCGCATATGGAGTTAGAACAACACTAATATTTTGGCTCATT
*
3294153 CATCGCATATGGAGTTAGAATAACACTAATATTTTGGCTCATT
1 CATCGCATATGGAGTTAGAACAACACTAATATTTTGGCTCATT
*
3294196 CATCGTATATGGAGTT
1 CATCGCATATGGAGTT
3294212 TGATTAGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (43 bp):
CATCGCATATGGAGTTAGAACAACACTAATATTTTGGCTCATT
Found at i:3294637 original size:117 final size:116
Alignment explanation
Indices: 3294426--3294672 Score: 361
Period size: 117 Copynumber: 2.1 Consensus size: 116
3294416 CAACATCATC
* *
3294426 ACCTTGTTTGATTTCATCACAGAAGGAGCTGGATCGACATTTCCAGTGGAGATTTCATAGTGAAA
1 ACCTTGTTTGATTTCATCACAGAAGGAGCTGGATCGACATTTCCAGTGGAGAGTTCATAATGAAA
*
3294491 AGAACTCATCCGAGGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
66 AGAACTCATACGAGGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * *
3294542 CCCTTGGTTTGATTTCATCACAGCAA-GAGGTGGATCGACATTTCTAGTGGAGAGTTCGTAATGA
1 ACCTT-GTTTGATTTCATCACAG-AAGGAGCTGGATCGACATTTCCAGTGGAGAGTTCATAATGA
* * *
3294606 GAAGAACTCATACGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
64 AAAGAACTCATACGAGGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
3294659 ACCTTAGATTGATT
1 ACCTT-GTTTGATT
3294673 CTATCACCTT
Statistics
Matches: 116, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
116 4 0.03
117 110 0.95
118 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (116 bp):
ACCTTGTTTGATTTCATCACAGAAGGAGCTGGATCGACATTTCCAGTGGAGAGTTCATAATGAAA
AGAACTCATACGAGGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
Found at i:3294980 original size:3 final size:3
Alignment explanation
Indices: 3294974--3295029 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
3294964 TTATTATCCT
3294974 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3295022 TAA TAA TA
1 TAA TAA TA
3295030 TTATTATTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3296469 original size:18 final size:18
Alignment explanation
Indices: 3296427--3296484 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 18
3296417 TTTGGTTCAC
* *
3296427 GGAATGTATGATTACCAGTG
1 GGAATATATGATTACTA--G
3296447 GGAATATATGATTACTAG
1 GGAATATATGATTACTAG
3296465 GGAATA-A-GATTACT-G
1 GGAATATATGATTACTAG
3296480 GGAAT
1 GGAAT
3296485 GTTGTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
15 6 0.17
16 7 0.19
17 1 0.03
18 7 0.19
20 15 0.42
ACGTcount: A:0.36, C:0.07, G:0.28, T:0.29
Consensus pattern (18 bp):
GGAATATATGATTACTAG
Found at i:3296477 original size:16 final size:17
Alignment explanation
Indices: 3296445--3296484 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
3296435 TGATTACCAG
3296445 TGGGAATATATGATTAC
1 TGGGAATATATGATTAC
3296462 TAGGGAATA-A-GATTAC
1 T-GGGAATATATGATTAC
3296478 TGGGAAT
1 TGGGAAT
3296485 GTTGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 7 0.32
17 2 0.09
18 7 0.32
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.30
Consensus pattern (17 bp):
TGGGAATATATGATTAC
Found at i:3299310 original size:23 final size:23
Alignment explanation
Indices: 3299278--3299335 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
3299268 TTATGACATG
*
3299278 TTCTCCACCTTTATGGAAC-ATT
1 TTCTCTACCTTTATGGAACGATT
* *
3299300 TATCTCTACCTTTGTGGCACGATT
1 T-TCTCTACCTTTATGGAACGATT
*
3299324 TTCTCTGCCTTT
1 TTCTCTACCTTT
3299336 TGGTAGCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.03
23 25 0.83
24 4 0.13
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.45
Consensus pattern (23 bp):
TTCTCTACCTTTATGGAACGATT
Found at i:3304450 original size:14 final size:13
Alignment explanation
Indices: 3304421--3304457 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
3304411 AAATTTAATA
3304421 ATTTAATAATAAG
1 ATTTAATAATAAG
*
3304434 ATTTGATAATAAAG
1 ATTTAATAAT-AAG
3304448 ATTTAATAAT
1 ATTTAATAAT
3304458 GATTTGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (13 bp):
ATTTAATAATAAG
Found at i:3304483 original size:26 final size:26
Alignment explanation
Indices: 3304413--3304492 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
3304403 AATTTTATAA
*
3304413 ATTTAATAATTTAATAATAAGATTTGAT
1 ATTTAATGATTTAATAAT--GATTTGAT
* *
3304441 A-ATAAAGATTTAATAATGATTTGAT
1 ATTTAATGATTTAATAATGATTTGAT
* *
3304466 ATTTAATGATTTAGTAATGATATGAT
1 ATTTAATGATTTAATAATGATTTGAT
3304492 A
1 A
3304493 GTAGTGATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 9 0.20
26 21 0.48
27 13 0.30
28 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.44
Consensus pattern (26 bp):
ATTTAATGATTTAATAATGATTTGAT
Found at i:3304571 original size:8 final size:8
Alignment explanation
Indices: 3304545--3304621 Score: 56
Period size: 8 Copynumber: 9.9 Consensus size: 8
3304535 CTAATTATTA
3304545 ATTTAATG
1 ATTTAATG
*
3304553 ATTTTAT-
1 ATTTAATG
3304560 ATTTAATG
1 ATTTAATG
3304568 ATTTAGTAATG
1 A-TT--TAATG
3304579 ATTTAATG
1 ATTTAATG
3304587 ATTTAAT-
1 ATTTAATG
* *
3304594 A-ATAATT
1 ATTTAATG
3304601 ATTTAA--
1 ATTTAATG
*
3304607 CTTTAATG
1 ATTTAATG
3304615 ATTTAAT
1 ATTTAAT
3304622 AATAATTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
6 9 0.16
7 8 0.15
8 28 0.51
9 2 0.04
10 2 0.04
11 6 0.11
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.52
Consensus pattern (8 bp):
ATTTAATG
Found at i:3304584 original size:19 final size:17
Alignment explanation
Indices: 3304545--3304597 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
3304535 CTAATTATTA
3304545 ATTTAATGATTT-T-AT
1 ATTTAATGATTTATAAT
3304560 ATTTAATGATTTAGTAAT
1 ATTTAATGATTTA-TAAT
3304578 GATTTAATGATTTAATAAT
1 -ATTTAATGATTT-ATAAT
3304597 A
1 A
3304598 ATTATTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 12 0.36
17 1 0.03
18 3 0.09
19 16 0.48
20 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (17 bp):
ATTTAATGATTTATAAT
Found at i:3304633 original size:42 final size:42
Alignment explanation
Indices: 3304582--3304791 Score: 230
Period size: 42 Copynumber: 5.0 Consensus size: 42
3304572 AGTAATGATT
*
3304582 TAATGATTTAATAATAATTATTTAACTTTAATGATTTAA-TAA
1 TAATGATTTAATAATAATGATTTAACTTTAATGATTTAACT-A
* * * *
3304624 TAATTATTTAACT-TTAATGATTTAGCTTTAATAATTTAA-TAA
1 TAATGATTTAA-TAATAATGATTTAACTTTAATGATTTAACT-A
* * ** *
3304666 TAATAATTTAACT-TTAATGATTTAACAATAATGATTTAACTT
1 TAATGATTTAA-TAATAATGATTTAACTTTAATGATTTAACTA
* * *
3304708 TAATGATTTAATAATAATTATTTAACTTAAATGATTTAACTT
1 TAATGATTTAATAATAATGATTTAACTTTAATGATTTAACTA
*
3304750 TAATGATTTAATAATAATAATTTAACTTTAATGATTTAACTA
1 TAATGATTTAATAATAATGATTTAACTTTAATGATTTAACTA
3304792 CAGTTGGCGA
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 142 0.98
43 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (42 bp):
TAATGATTTAATAATAATGATTTAACTTTAATGATTTAACTA
Found at i:3304789 original size:14 final size:14
Alignment explanation
Indices: 3304580--3304790 Score: 207
Period size: 14 Copynumber: 15.1 Consensus size: 14
3304570 TTAGTAATGA
3304580 TTTAATGATTTAA-
1 TTTAATGATTTAAC
* *
3304593 TAATAATTATTTAAC
1 T-TTAATGATTTAAC
3304608 TTTAATGATTTAA-
1 TTTAATGATTTAAC
* *
3304621 TAATAATTATTTAAC
1 T-TTAATGATTTAAC
*
3304636 TTTAATGATTTAGC
1 TTTAATGATTTAAC
*
3304650 TTTAATAATTTAA-
1 TTTAATGATTTAAC
* *
3304663 TAATAATAATTTAAC
1 T-TTAATGATTTAAC
3304678 TTTAATGATTTAAC
1 TTTAATGATTTAAC
**
3304692 AATAATGATTTAAC
1 TTTAATGATTTAAC
3304706 TTTAATGATTTAA-
1 TTTAATGATTTAAC
* *
3304719 TAATAATTATTTAAC
1 T-TTAATGATTTAAC
*
3304734 TTAAATGATTTAAC
1 TTTAATGATTTAAC
3304748 TTTAATGATTTAA-
1 TTTAATGATTTAAC
* *
3304761 TAATAATAATTTAAC
1 T-TTAATGATTTAAC
3304776 TTTAATGATTTAAC
1 TTTAATGATTTAAC
3304790 T
1 T
3304791 ACAGTTGGCG
Statistics
Matches: 160, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
13 5 0.03
14 150 0.94
15 5 0.03
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (14 bp):
TTTAATGATTTAAC
Found at i:3308673 original size:32 final size:31
Alignment explanation
Indices: 3308632--3308694 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
3308622 GGTCCAAAGC
*
3308632 TTATTTCAAATTATGTAACAACATATACATCA
1 TTATTTCAAAGTATGTAACAACATATA-ATCA
*
3308664 TTATTTCAAAGTATGTAATAACATATAATCA
1 TTATTTCAAAGTATGTAACAACATATAATCA
3308695 CAAAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (31 bp):
TTATTTCAAAGTATGTAACAACATATAATCA
Found at i:3309181 original size:20 final size:20
Alignment explanation
Indices: 3309156--3309193 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3309146 CAACTCTCTG
*
3309156 CTCACCCCATGATTTCCCTA
1 CTCACCCCATGAATTCCCTA
*
3309176 CTCACCCCGTGAATTCCC
1 CTCACCCCATGAATTCCC
3309194 ACGTCTAGCC
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:0.18, C:0.47, G:0.08, T:0.26
Consensus pattern (20 bp):
CTCACCCCATGAATTCCCTA
Found at i:3314790 original size:20 final size:20
Alignment explanation
Indices: 3314761--3314839 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
3314751 CAAGCTGCAA
3314761 GAACAATATCGGTACTAGAT
1 GAACAATATCGGTACTAGAT
* * * *
3314781 GAACAGTATCGATATTGAGCAA
1 GAACAATATCGGTACT-AG-AT
*
3314803 GAACAATATCGGTACTGGAT
1 GAACAATATCGGTACTAGAT
* *
3314823 GAACAGTACCGGTACTA
1 GAACAATATCGGTACTA
3314840 AGTGCACATA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
20 28 0.62
21 3 0.07
22 14 0.31
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (20 bp):
GAACAATATCGGTACTAGAT
Found at i:3320643 original size:21 final size:21
Alignment explanation
Indices: 3320617--3320693 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
3320607 CAAAAGGAGC
3320617 AGTATCGGTACCATAACTAAG
1 AGTATCGGTACCATAACTAAG
* *
3320638 AGTATCGGTACTACCACACTAAG
1 AGTATCGGTACCA-TA-ACTAAG
*
3320661 TAGTATCGATACCA-AA-TAAG
1 -AGTATCGGTACCATAACTAAG
*
3320681 -GTATCAGTACCAT
1 AGTATCGGTACCAT
3320694 TTTAGCATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
18 10 0.22
20 4 0.09
21 13 0.28
22 2 0.04
23 6 0.13
24 11 0.24
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (21 bp):
AGTATCGGTACCATAACTAAG
Found at i:3323681 original size:22 final size:22
Alignment explanation
Indices: 3323653--3323697 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3323643 CACTGGTTAT
3323653 TATATATGATGTTTATCATGAA
1 TATATATGATGTTTATCATGAA
*
3323675 TATATATGATGTTTATTATGAA
1 TATATATGATGTTTATCATGAA
3323697 T
1 T
3323698 GTTATTTCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
TATATATGATGTTTATCATGAA
Found at i:3323959 original size:61 final size:61
Alignment explanation
Indices: 3323881--3324024 Score: 218
Period size: 61 Copynumber: 2.4 Consensus size: 61
3323871 CTATGTGTAT
* *
3323881 GTGGTGGGCACGACTTTATGTGTCATAT-CAGGATCAACACTAGAGTGTAAACTTAGTGCAG
1 GTGGTGGGCACGACTTTATGTGTCATATCCA-GATCAACACTAGAATGTAAACTTAGTACAG
3323942 GTGGTGGGCACGACTTTATGTGTCATATCCAGATCAACACTAGAATGTAAACTTAGTACAG
1 GTGGTGGGCACGACTTTATGTGTCATATCCAGATCAACACTAGAATGTAAACTTAGTACAG
* * * *
3324003 GAGATGGGCACAACCTTATGTG
1 GTGGTGGGCACGACTTTATGTG
3324025 GAAGCACTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
61 74 0.97
62 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (61 bp):
GTGGTGGGCACGACTTTATGTGTCATATCCAGATCAACACTAGAATGTAAACTTAGTACAG
Found at i:3324508 original size:21 final size:20
Alignment explanation
Indices: 3324484--3324525 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3324474 TACAAACTAT
3324484 TAATATAGT-TAGTAGCAAATA
1 TAATATAGTAT-GT-GCAAATA
*
3324505 TAATTTAGTATGTGCAAATA
1 TAATATAGTATGTGCAAATA
3324525 T
1 T
3324526 TATGATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 10 0.53
22 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATATAGTATGTGCAAATA
Found at i:3328989 original size:2 final size:2
Alignment explanation
Indices: 3328949--3328974 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3328939 GCTTTGTATG
3328949 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
3328975 CTTACATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3331080 original size:23 final size:22
Alignment explanation
Indices: 3331054--3331100 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
3331044 ATTAAGCACA
* *
3331054 ATAATATATTAGGTAGCGTTTAT
1 ATAATATAATAGGTAGAG-TTAT
*
3331077 ATAATGTAATAGGTAGAGTTAT
1 ATAATATAATAGGTAGAGTTAT
3331099 AT
1 AT
3331101 TAGACTGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (22 bp):
ATAATATAATAGGTAGAGTTAT
Found at i:3331117 original size:72 final size:73
Alignment explanation
Indices: 3331032--3331174 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 73
3331022 TAGGTTAATT
* * *
3331032 ACTGAAAACATTATTAAGCACAATAATATATTAGGTAGCGTTTATATAATGTAATAGGTAGAG-T
1 ACTGAAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGAGCT
3331096 TATATTAG
66 TATATTAG
* * *
3331104 ACTGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGTGCT
1 ACTGAAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGAGCT
3331169 TATATT
66 TATATT
3331175 GACATATTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 57 0.89
73 7 0.11
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (73 bp):
ACTGAAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGAGCT
TATATTAG
Found at i:3331614 original size:197 final size:198
Alignment explanation
Indices: 3331186--3331851 Score: 923
Period size: 200 Copynumber: 3.4 Consensus size: 198
3331176 ACATATTCTA
* **
3331186 TCATAAAACCGGTATATTTATACCGGTAATATTACAAATTTA-CTATTACATTATAATTATCAGT
1 TCATAAAACCGGTATATTTATACCGGT-ACATTGTAAATTTACCTATTACATTATAATTATCAGT
* *
3331250 TTCGATGTTTTTGGGATTGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCGTTG
65 TTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTG
* * * *
3331313 GACATTCATTCTGG-AAAAAGTATCGACACAAACTTAAAACGTGTTGATATATTATATAGACCTA
129 GACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTA
*
3331377 TTTTT
194 TTTTC
* * * *
3331382 TCATAAAATCGGTATATTTGTACCGGGTACATTGTAAATTTACCTATTA-ATTGTAATTATCGGT
1 TCATAAAACCGGTATATTTATACC-GGTACATTGTAAATTTACCTATTACATTATAATTATCAGT
* * *
3331446 TTGGAT-TTTTTGGGATCGATACTTTTAATAAATGTATCGACATTTTATGTGTGCACCTCGTTGG
65 TTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGG
3331510 ACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTAT
130 ACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTAT
3331575 TTTC
195 TTTC
* * * *
3331579 TCATAAAACCGATATATTTCTATCGAGTACATTGTAAATTTACCTATTACATTATAATTATCAAT
1 TCATAAAACCGGTATATTTATACCG-GTACATTGTAAATTTACCTATTACATTATAATTATCAGT
* *
3331644 TTTGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTG
65 TTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGG
* * *** *
3331709 ACATTCATTTTGGACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACATTATGTAGACCT
130 ACATTCATTCTGGA-AAAAAGTATCGACACAAACTTAAA-ATGTGTCGATACATTATGTAGACCT
*
3331773 ATTCTC
193 ATTTTC
* * *
3331779 TCATAAAAACGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGT
1 TCATAAAACCGGTATATTTATACCGG-TACATTGTAAATTTACCTATTACATTATAATTATCAGT
3331844 TTCGATGT
65 TTCGATGT
3331852 AACATATGTG
Statistics
Matches: 416, Mismatches: 43, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
194 3 0.01
195 15 0.04
196 99 0.24
197 102 0.25
198 17 0.04
199 74 0.18
200 106 0.25
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (198 bp):
TCATAAAACCGGTATATTTATACCGGTACATTGTAAATTTACCTATTACATTATAATTATCAGTT
TCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGA
CATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTATT
TTC
Found at i:3331812 original size:200 final size:198
Alignment explanation
Indices: 3331179--3331851 Score: 919
Period size: 196 Copynumber: 3.4 Consensus size: 198
3331169 TATATTGACA
* * * **
3331179 TATTCTATCATAAAACCGGTATATTTATACCGGTAATATTACAAATTTA-CTATTACATTATAAT
1 TATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAAT
* *
3331243 TATCAGTTTCGATGTTTTTGGGATTGATACAATTT--TAAATGTATCGACACTTTATGCGTGCAC
66 TATCAGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCAC
* * * *
3331306 CTCGTTGGACATTCATTCTGGAAAAAGTATCGACACAAACTTAAAACGTGTTGATATATTATATA
130 CTCGTTGGACATTCATTCTGGAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTA
3331371 GACC
195 GACC
* * * * * *
3331375 TATTTTTTCATAAAATCGGTATATTTGTACCGGGTACATTGTAAATTTACCTATTA-ATTGTAAT
1 TATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAAT
* * * *
3331439 TATCGGTTTGGAT-TTTTTGGGATCGATACTTTTAATAAATGTATCGACATTTTATGTGTGCACC
66 TATCAGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC
3331503 TCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTA
131 TCGTTGGACATTCATTCTGG-AAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTA
3331568 GACC
195 GACC
* * * *
3331572 TATTTTCTCATAAAACCGATATATTTCTATCGAG-TACATTGTAAATTTACCTATTACATTATAA
1 TATTCTCTCATAAAACCGGTATATTTATACCG-GTTACATTGTAAATTTACCTATTACATTATAA
* *
3331636 TTATCAATTTTGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCAC
65 TTATCAGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCAC
* * *** *
3331701 CTCGTTTGACATTCATTTTGGACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACATTAT
130 CTCGTTGGACATTCATTCTGGA-AAAA-GTATCGACACAAACTTAAA-ATGTGTCGATACATTAT
3331765 GTAGACC
192 GTAGACC
* *
3331772 TATTCTCTCATAAAAACGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAAT
1 TATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAAT
*
3331837 TATCGGTTTCGATGT
66 TATCAGTTTCGATGT
3331852 AACATATGTG
Statistics
Matches: 420, Mismatches: 46, Indels: 18
0.87 0.10 0.04
Matches are distributed among these distances:
194 3 0.01
195 15 0.04
196 105 0.25
197 99 0.24
198 19 0.05
199 77 0.18
200 102 0.24
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (198 bp):
TATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAAT
TATCAGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC
TCGTTGGACATTCATTCTGGAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAG
ACC
Found at i:3331993 original size:31 final size:30
Alignment explanation
Indices: 3331952--3332045 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
3331942 TTGTAATAAA
*
3331952 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
3331982 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
3332012 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
3332040 TAATAA
1 TAATAA
3332046 TATTGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:3332045 original size:14 final size:14
Alignment explanation
Indices: 3331963--3332049 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
3331953 AATAAATATA
**
3331963 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
3331978 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
3331991 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
3332005 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
3332019 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
3332033 ATTTTAATAATAAT
1 ATTTTAATAATAAT
3332047 ATT
1 ATT
3332050 GACATAAATA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 38 0.72
15 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:3332045 original size:28 final size:28
Alignment explanation
Indices: 3331977--3332045 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
3331967 ATAATAATTT
*
3331977 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
3332004 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
3332032 TATTTTAATAATAA
1 TATTTTAATAATAA
3332046 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:3332132 original size:24 final size:25
Alignment explanation
Indices: 3332064--3332132 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
3332054 TAAATAATAT
*
3332064 TAAATAA-ATTATTCTAATATT-TTAA
1 TAAATAATATTA-T-TATTATTGTTAA
3332089 -AAATAATATTATTATT-TTGTTAA
1 TAAATAATATTATTATTATTGTTAA
3332112 TAAATAATATTATT-TTATTGT
1 TAAATAATATTATTATTATTGT
3332133 ATTTGATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 9 0.23
24 24 0.62
25 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATAATATTATTATTATTGTTAA
Found at i:3332221 original size:2 final size:2
Alignment explanation
Indices: 3332214--3332256 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3332204 ATATGGTAAT
3332214 TA 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 TA
3332256 T
1 T
3332257 TCTTTTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3332796 original size:31 final size:30
Alignment explanation
Indices: 3332759--3332849 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
3332749 TAAAAAATAA
*
3332759 AAAATATAATTTATAATAATTTTATT-TTAAT
1 AAAATATAA-TAATAATAATTTT-TTATTAAT
* *
3332790 AAAATATAATAATCATAATTTTTTATTTAT
1 AAAATATAATAATAATAATTTTTTATTAAT
* *
3332820 AAAAT-T-ATAGAT-ATAATATTTTAATAAT
1 AAAATATAATA-ATAATAATTTTTTATTAAT
3332848 AA
1 AA
3332850 TATTTACATA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.35
29 5 0.10
30 20 0.38
31 9 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
AAAATATAATAATAATAATTTTTTATTAAT
Found at i:3332849 original size:14 final size:14
Alignment explanation
Indices: 3332767--3332868 Score: 57
Period size: 14 Copynumber: 7.2 Consensus size: 14
3332757 AAAAAATATA
**
3332767 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
3332782 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
3332795 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
3332809 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
3332823 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
3332837 ATTTTAATAATAAT
1 ATTTTAATAATAAT
3332851 A-TTTACATAAATAAT
1 ATTTTA-AT-AATAAT
3332866 ATT
1 ATT
3332869 AAATAAATTA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
13 14 0.22
14 38 0.58
15 12 0.18
16 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:3332849 original size:28 final size:28
Alignment explanation
Indices: 3332781--3332849 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
3332771 ATAATAATTT
*
3332781 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
3332808 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
3332836 TATTTTAATAATAA
1 TATTTTAATAATAA
3332850 TATTTACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:3332874 original size:14 final size:15
Alignment explanation
Indices: 3332832--3332876 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
3332822 AATTATAGAT
*
3332832 ATAATATTTTAAT-A
1 ATAATATTTAAATAA
*
3332846 ATAATATTTACATAA
1 ATAATATTTAAATAA
3332861 ATAATA-TTAAATAA
1 ATAATATTTAAATAA
3332875 AT
1 AT
3332877 TATTCTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATTTAAATAA
Found at i:3333239 original size:23 final size:23
Alignment explanation
Indices: 3333189--3333233 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3333179 AGCATATTTT
*
3333189 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
3333212 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
3333234 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:3333302 original size:23 final size:23
Alignment explanation
Indices: 3333267--3333317 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3333257 CAAGTAATTA
** *
3333267 ACCTATTTTATTATATAAGCGTT
1 ACCTATTACATTATATAAGCGAT
3333290 ACCTATTACATTATATAAGCGAT
1 ACCTATTACATTATATAAGCGAT
3333313 ACCTA
1 ACCTA
3333318 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGAT
Found at i:3333320 original size:87 final size:86
Alignment explanation
Indices: 3333169--3333403 Score: 389
Period size: 87 Copynumber: 2.7 Consensus size: 86
3333159 TAATAACAAA
* * *
3333169 TTAAATAATTAGCATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATA
1 TTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATA
3333234 TGTTATTGTGCTTGATAATGT
66 TGTTATTGTGCTTGATAATGT
* *
3333255 TTCAAGTAATTAACCTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGATACCTAAT
1 TT-AAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAAT
3333320 ATGTTATTGTGCTTGATAATGT
65 ATGTTATTGTGCTTGATAATGT
* * *
3333342 TTTAGTAATTAACCTATTTTATTATATAAACGCTACCTATTACATTATATAAACGCTACCTA
1 TTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTA
3333404 TTACATTATA
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
86 57 0.41
87 81 0.59
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (86 bp):
TTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATA
TGTTATTGTGCTTGATAATGT
Found at i:3333422 original size:46 final size:46
Alignment explanation
Indices: 3333353--3333569 Score: 173
Period size: 46 Copynumber: 4.8 Consensus size: 46
3333343 TTAGTAATTA
* *
3333353 ACCTATTTTATTATATAAACGCTACCTATTACATTATATAAACGCT
1 ACCTATTATATTATATAAGCGCTACCTATTACATTATATAAACGCT
* * * *
3333399 ACCTATTACATTATATAAGCGCTATCTATTACATTATATAAGCGGT
1 ACCTATTATATTATATAAGCGCTACCTATTACATTATATAAACGCT
* * * ** * * * *
3333445 ACCTAATATGTTAT-T--GTGCTTGAAAATTTTCCAGTA-ATTAAC-CT
1 ACCTATTATATTATATAAGCGC-T--ACCTATTACATTATATAAACGCT
*
3333489 A--T-TT-TATTATATAAGCGCTACCTATTACATTATATAAGCGCT
1 ACCTATTATATTATATAAGCGCTACCTATTACATTATATAAACGCT
* * *
3333531 ACCTATTACATTATATAAGTGCTACCTATTACATCATAT
1 ACCTATTATATTATATAAGCGCTACCTATTACATTATAT
3333570 TTTTACATGT
Statistics
Matches: 128, Mismatches: 31, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
40 13 0.10
41 6 0.05
42 5 0.04
43 6 0.05
44 4 0.03
45 7 0.05
46 87 0.68
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (46 bp):
ACCTATTATATTATATAAGCGCTACCTATTACATTATATAAACGCT
Found at i:3333458 original size:23 final size:23
Alignment explanation
Indices: 3333353--3333449 Score: 140
Period size: 23 Copynumber: 4.2 Consensus size: 23
3333343 TTAGTAATTA
**
3333353 ACCTATTTTATTATATAAACGCT
1 ACCTATTACATTATATAAACGCT
3333376 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAACGCT
*
3333399 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAACGCT
* * *
3333422 ATCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAACGCT
3333445 ACCTA
1 ACCTA
3333450 ATATGTTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAACGCT
Done.