Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 74 of 207
Found at i:21437637 original size:38 final size:37
Alignment explanation
Indices: 21437581--21437668 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
21437571 TTGCATGTTC
* *
21437581 AGCATGCCTACTATTACTATTGAACCGAATACATATTA
1 AGCATGTCTACTACTACTATTG-ACCGAATACATATTA
* * * *
21437619 AGCATGTCTACTGCTACTATTGAGCTAATACATGTTA
1 AGCATGTCTACTACTACTATTGACCGAATACATATTA
*
21437656 AGAATGTCTACTA
1 AGCATGTCTACTA
21437669 GTTTTACATG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 23 0.55
38 19 0.45
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (37 bp):
AGCATGTCTACTACTACTATTGACCGAATACATATTA
Found at i:21447647 original size:24 final size:23
Alignment explanation
Indices: 21447620--21447674 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
21447610 TGTATCTGAT
21447620 TATGAAACTACATCTGAATATGTA
1 TATGAAA-TACATCTGAATATGTA
** *
21447644 TATGATAATATGTTTGAATATGTA
1 TATGA-AATACATCTGAATATGTA
*
21447668 TCTGAAA
1 TATGAAA
21447675 GTGTATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 22 0.85
25 2 0.08
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (23 bp):
TATGAAATACATCTGAATATGTA
Found at i:21451525 original size:21 final size:19
Alignment explanation
Indices: 21451501--21451565 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 19
21451491 AAGGAGAAAT
21451501 GAAAGAAGTAAAAAGACAAAA
1 GAAAGAAG-AAAAAGA-AAAA
*
21451522 GAAAG--GAAAAATAAAAA
1 GAAAGAAGAAAAAGAAAAA
* *
21451539 GAAAGAAAAGGAAAAGAAGAA
1 GAAAG--AAGAAAAAGAAAAA
21451560 GAAAGA
1 GAAAGA
21451566 GTACAGAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 9 0.25
18 6 0.17
19 2 0.06
21 19 0.53
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.03
Consensus pattern (19 bp):
GAAAGAAGAAAAAGAAAAA
Found at i:21451551 original size:22 final size:24
Alignment explanation
Indices: 21451495--21451553 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
21451485 ATCGAAAAGG
*
21451495 AGAAATGAAAGAAGTAAAAAGACAAA
1 AGAAAGGAAA-AA-TAAAAAGACAAA
*
21451521 AGAAAGGAAAAATAAAAAGA-AAG
1 AGAAAGGAAAAATAAAAAGACAAA
21451544 A-AAAGGAAAA
1 AGAAAGGAAAA
21451554 GAAGAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 9 0.29
23 3 0.10
24 8 0.26
25 2 0.06
26 9 0.29
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (24 bp):
AGAAAGGAAAAATAAAAAGACAAA
Found at i:21455775 original size:20 final size:19
Alignment explanation
Indices: 21455726--21455782 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
21455716 CAATTTTTAT
* *
21455726 AATTTTTAAAAATATTTTG
1 AATTTTTAAAATTATTTTC
*
21455745 AATTTTAAAAATTATTTTC
1 AATTTTTAAAATTATTTTC
21455764 AATTTTTTAAAATTATTTT
1 AA-TTTTTAAAATTATTTT
21455783 GATTATTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTC
Found at i:21455791 original size:20 final size:20
Alignment explanation
Indices: 21455729--21455791 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
21455719 TTTTTATAAT
*
21455729 TTTTAAAAATATTTTGA--A
1 TTTTAAAATTATTTTGATTA
*
21455747 TTTTAAAAATTATTTTCAATT-
1 TTTT-AAAATTATTTT-GATTA
21455768 TTTTAAAATTATTTTGATTA
1 TTTTAAAATTATTTTGATTA
21455788 TTTT
1 TTTT
21455792 GTAATTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.11
19 13 0.35
20 16 0.43
21 4 0.11
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTAAAATTATTTTGATTA
Found at i:21468911 original size:22 final size:24
Alignment explanation
Indices: 21468886--21468940 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
21468876 TTTATAAATT
21468886 TAATTTAA-AATATATAAT-ACAA
1 TAATTTAAGAATATATAATAACAA
* * *
21468908 TAATATCAAGCATATTTAATAACAA
1 TAAT-TTAAGAATATATAATAACAA
21468933 TAATTTAA
1 TAATTTAA
21468941 TCATAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.15
23 3 0.12
24 11 0.42
25 8 0.31
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
TAATTTAAGAATATATAATAACAA
Found at i:21469822 original size:17 final size:18
Alignment explanation
Indices: 21469787--21469825 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
21469777 GCTTTAATAA
21469787 TTTAAAAAATTATAGAATT
1 TTTAAAAAATTATA-AATT
21469806 TTTAAAAAATTAT-AATT
1 TTTAAAAAATTATAAATT
21469823 TTT
1 TTT
21469826 CTCATATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
19 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTAAAAAATTATAAATT
Found at i:21471513 original size:35 final size:35
Alignment explanation
Indices: 21471454--21471569 Score: 128
Period size: 35 Copynumber: 3.3 Consensus size: 35
21471444 AAAAAAAAGC
* *
21471454 TAGGATAGACTCGTCTAA-AGCAACCTTAAAGAGGT
1 TAGGATAGACCCGTCTAAGA-CAACCTTAAAAAGGT
* *
21471489 TAGGATAGACCCGTTTAAGACAACCGTAAAAAGGT
1 TAGGATAGACCCGTCTAAGACAACCTTAAAAAGGT
* * *
21471524 T-GAGATGGACCAGTCTAAGGCAACCTTAAAAAGGT
1 TAG-GATAGACCCGTCTAAGACAACCTTAAAAAGGT
*
21471559 TTGGATAGACC
1 TAGGATAGACC
21471570 TTGTTTGCAC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
34 1 0.01
35 65 0.96
36 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (35 bp):
TAGGATAGACCCGTCTAAGACAACCTTAAAAAGGT
Found at i:21477915 original size:37 final size:37
Alignment explanation
Indices: 21477865--21477938 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
21477855 GGTATAAGCC
21477865 CTAAAGCATGAGATCTATCACTCTGTTAGATTGAATT
1 CTAAAGCATGAGATCTATCACTCTGTTAGATTGAATT
*
21477902 CTAAAGCATGAGATCTGTCACTCTGTTAGATTGAATT
1 CTAAAGCATGAGATCTATCACTCTGTTAGATTGAATT
21477939 TGACGTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (37 bp):
CTAAAGCATGAGATCTATCACTCTGTTAGATTGAATT
Found at i:21481714 original size:38 final size:38
Alignment explanation
Indices: 21481663--21481739 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
21481653 AGGAGATGTT
21481663 AGCTAAATTTATGTCGATGTTAGAAACTCGATTTCAAA
1 AGCTAAATTTATGTCGATGTTAGAAACTCGATTTCAAA
*
21481701 AGCTAAATTTATGTCGGTGTTAGAAACTCGATTTCAAA
1 AGCTAAATTTATGTCGATGTTAGAAACTCGATTTCAAA
21481739 A
1 A
21481740 CACTGAGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (38 bp):
AGCTAAATTTATGTCGATGTTAGAAACTCGATTTCAAA
Found at i:21485434 original size:20 final size:20
Alignment explanation
Indices: 21485409--21485447 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21485399 TTTGTTTTAT
*
21485409 TATTTTTTTCTTTA-TTAGTA
1 TATTTTATT-TTTAGTTAGTA
21485429 TATTTTATTTTTAGTTAGT
1 TATTTTATTTTTAGTTAGT
21485448 TGGTTAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (20 bp):
TATTTTATTTTTAGTTAGTA
Found at i:21492133 original size:22 final size:22
Alignment explanation
Indices: 21492108--21492166 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 22
21492098 TAACTCTTCG
*
21492108 GAGTTACCTGTTAAACTCACAT
1 GAGTTTCCTGTTAAACTCACAT
* **
21492130 GAGTTTTCTGTTTCAAACTCTTAT
1 GAGTTTCCTG-TT-AAACTCACAT
21492154 GAGTTTCCTGTTA
1 GAGTTTCCTGTTA
21492167 TAGCCCGGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 9 0.30
23 4 0.13
24 17 0.57
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (22 bp):
GAGTTTCCTGTTAAACTCACAT
Found at i:21496008 original size:5 final size:5
Alignment explanation
Indices: 21496000--21496072 Score: 146
Period size: 5 Copynumber: 14.6 Consensus size: 5
21495990 TTAAGTATAA
21496000 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
21496050 ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATA
21496073 AAAGAAATAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 68 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:21497060 original size:25 final size:25
Alignment explanation
Indices: 21497032--21497108 Score: 109
Period size: 25 Copynumber: 3.1 Consensus size: 25
21497022 TAGCGCGCTA
* *
21497032 TCTGATTATTAGCATGTTGTTGCTC
1 TCTGATTATTAGCACGTTGGTGCTC
21497057 TCTGATTATTAGCACGTTGGTGCTC
1 TCTGATTATTAGCACGTTGGTGCTC
* **
21497082 TCTGATTACTAGCACGTCAGTGCTC
1 TCTGATTATTAGCACGTTGGTGCTC
21497107 TC
1 TC
21497109 CATTTAGCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (25 bp):
TCTGATTATTAGCACGTTGGTGCTC
Found at i:21509743 original size:15 final size:15
Alignment explanation
Indices: 21509719--21509748 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21509709 TCCATCCTAC
21509719 TTTCTACTATTTTTA
1 TTTCTACTATTTTTA
*
21509734 TTTCTCCTATTTTTA
1 TTTCTACTATTTTTA
21509749 AATTTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTCTACTATTTTTA
Found at i:21525372 original size:14 final size:14
Alignment explanation
Indices: 21525335--21525385 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
21525325 TGGAAAATAT
*
21525335 AAATA-AAAATAAA
1 AAATATAAATTAAA
*
21525348 AAATAT--TTTAAA
1 AAATATAAATTAAA
21525360 AAATATAAATTAAA
1 AAATATAAATTAAA
21525374 AAATATATAATT
1 AAATATA-AATT
21525386 TTCTTAGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 10 0.32
13 5 0.16
14 12 0.39
15 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATATAAATTAAA
Found at i:21526112 original size:26 final size:26
Alignment explanation
Indices: 21526083--21526135 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
21526073 GTGACAAAAT
* * * *
21526083 AAAAGTTAGGTACTATCTAGGTCCAA
1 AAAAATTAGGTACCAACTAGGTACAA
21526109 AAAAATTAGGTACCAACTAGGTACAA
1 AAAAATTAGGTACCAACTAGGTACAA
21526135 A
1 A
21526136 TGGACAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (26 bp):
AAAAATTAGGTACCAACTAGGTACAA
Found at i:21526329 original size:3 final size:3
Alignment explanation
Indices: 21526323--21526369 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
21526313 CATGGCATAA
21526323 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
21526370 ATAATAAGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:21526690 original size:12 final size:13
Alignment explanation
Indices: 21526662--21526696 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
21526652 TCACACTATT
*
21526662 TTCTTCATCTTTC
1 TTCTTCATCTGTC
21526675 TTCTTCA-CTGTC
1 TTCTTCATCTGTC
21526687 TTCTTCATCT
1 TTCTTCATCT
21526697 CCCATTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.09, C:0.31, G:0.03, T:0.57
Consensus pattern (13 bp):
TTCTTCATCTGTC
Found at i:21529071 original size:56 final size:56
Alignment explanation
Indices: 21528985--21529097 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
21528975 GAATTATAAG
* * *
21528985 TCAGAATGTGCTATAAATGTCTATATAATTTTTAGTTCTCACACCCTTAAACTTAA
1 TCAGAATGTGCTATAAATGTCTATATAATTTTGAGTTATCACACCCCTAAACTTAA
*
21529041 TCAGAATGTGTTATAAATGTCTATATAATTTTGAGTTATCACACCCCTAAACTTAA
1 TCAGAATGTGCTATAAATGTCTATATAATTTTGAGTTATCACACCCCTAAACTTAA
21529097 T
1 T
21529098 TCATTGTTCG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (56 bp):
TCAGAATGTGCTATAAATGTCTATATAATTTTGAGTTATCACACCCCTAAACTTAA
Found at i:21532378 original size:13 final size:13
Alignment explanation
Indices: 21532335--21532392 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
21532325 ATATATGTAA
21532335 ATGAAATGGTTAT
1 ATGAAATGGTTAT
* * *
21532348 ATGGAATGATTAC
1 ATGAAATGGTTAT
21532361 ATGAAATGGTTAT
1 ATGAAATGGTTAT
*
21532374 GTG-AATCGGTTAT
1 ATGAAAT-GGTTAT
*
21532387 GTGAAA
1 ATGAAA
21532393 ATATATATGT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 3 0.08
13 31 0.86
14 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.34
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:21549378 original size:17 final size:18
Alignment explanation
Indices: 21549340--21549389 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
21549330 GATTAAAATA
*
21549340 TTTATTTATGTATATATTAT
1 TTTATTTAT-TAAAT-TTAT
21549360 TTT-TTTATTAAATTTAT
1 TTTATTTATTAAATTTAT
*
21549377 TTTATTTTTTAAA
1 TTTATTTATTAAA
21549390 CATTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.26
18 12 0.44
19 5 0.19
20 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATTTATTAAATTTAT
Found at i:21550043 original size:9 final size:10
Alignment explanation
Indices: 21550018--21550051 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
21550008 TCATATACTT
21550018 TATAATTAAA
1 TATAATTAAA
21550028 TATAATTAAA
1 TATAATTAAA
*
21550038 -ATAATTATA
1 TATAATTAAA
21550047 TATAA
1 TATAA
21550052 ACTATTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TATAATTAAA
Found at i:21560134 original size:27 final size:28
Alignment explanation
Indices: 21560110--21560185 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
21560100 AATTTTTTTA
*
21560110 AAATATAAAAATTAAAATAAATTTTATAT
1 AAATAT-AAAATAAAAATAAATTTTATAT
* * *
21560139 TAATATTAAATAAAAATAAATTTAATACT
1 AAATATAAAATAAAAATAAATTTTATA-T
*
21560168 -AATATTAAATAAAAATAA
1 AAATATAAAATAAAAATAA
21560186 TGATTTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 36 0.86
29 6 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATATAAAATAAAAATAAATTTTATAT
Found at i:21560202 original size:28 final size:28
Alignment explanation
Indices: 21560118--21560185 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
21560108 TAAAATATAA
* * *
21560118 AAATTAAAATAAATTTTATATTAATATT
1 AAATAAAAATAAATTTAATACTAATATT
21560146 AAATAAAAATAAATTTAATACTAATATT
1 AAATAAAAATAAATTTAATACTAATATT
21560174 AAATAAAAATAA
1 AAATAAAAATAA
21560186 TGATTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATAAAAATAAATTTAATACTAATATT
Found at i:21562479 original size:18 final size:18
Alignment explanation
Indices: 21562452--21562489 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21562442 AAGAAAAAAA
*
21562452 AGAAGAGAGAGGGAAGAG
1 AGAAGAGAGAGAGAAGAG
*
21562470 AGAAGGGAGAGAGAAGAG
1 AGAAGAGAGAGAGAAGAG
21562488 AG
1 AG
21562490 GGGAATCCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (18 bp):
AGAAGAGAGAGAGAAGAG
Found at i:21562484 original size:11 final size:12
Alignment explanation
Indices: 21562453--21562485 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
21562443 AGAAAAAAAA
21562453 GAAGAGAG-AGG
1 GAAGAGAGAAGG
21562464 GAAGAGAGAAGG
1 GAAGAGAGAAGG
21562476 G-AGAGAGAAG
1 GAAGAGAGAAG
21562486 AGAGGGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:21566976 original size:20 final size:20
Alignment explanation
Indices: 21566951--21566991 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
21566941 CCCCTATAAG
*
21566951 TATGACCTATTTGATATGAA
1 TATGACATATTTGATATGAA
*
21566971 TATGACATATTTGATGTGAA
1 TATGACATATTTGATATGAA
21566991 T
1 T
21566992 GGCGAGCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (20 bp):
TATGACATATTTGATATGAA
Found at i:21567576 original size:18 final size:18
Alignment explanation
Indices: 21567534--21567583 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
21567524 AGGTGTAGAT
*
21567534 GAGGAAAAAGATGCGATC
1 GAGGAAGAAGATGCGATC
* *
21567552 GAGGAAGAAGATGTGGTC
1 GAGGAAGAAGATGCGATC
*
21567570 GAGGAAGAATATGC
1 GAGGAAGAAGATGC
21567584 AAGTGAGGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.38, T:0.14
Consensus pattern (18 bp):
GAGGAAGAAGATGCGATC
Found at i:21576939 original size:25 final size:25
Alignment explanation
Indices: 21576901--21576982 Score: 139
Period size: 25 Copynumber: 3.3 Consensus size: 25
21576891 ACAAATAAAA
*
21576901 ACCCAAAATC-AGCCCAACACCCCAC
1 ACCCAAAA-CAAGCCCAACACCTCAC
21576926 ACCCAAAACAAGCCCAACACCTCAC
1 ACCCAAAACAAGCCCAACACCTCAC
21576951 ACCCAAAACAAGCCCAACACCTCAC
1 ACCCAAAACAAGCCCAACACCTCAC
21576976 ACCCAAA
1 ACCCAAA
21576983 TAGAAAAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
24 1 0.02
25 54 0.98
ACGTcount: A:0.44, C:0.49, G:0.04, T:0.04
Consensus pattern (25 bp):
ACCCAAAACAAGCCCAACACCTCAC
Found at i:21582683 original size:24 final size:23
Alignment explanation
Indices: 21582617--21582703 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 23
21582607 TGGTTATTCG
* *
21582617 GAGCTTCTTGATTAATGGCTCTTC
1 GAGCTTCCTGATT-ATGGCTCTAC
* *
21582641 GGAGCTACC-CATTATTGGCTCGTAC
1 -GAGCTTCCTGATTA-TGGCTC-TAC
*
21582666 GAGCTTCCTGATTATGGCTCTTAT
1 GAGCTTCCTGATTATGGCTC-TAC
21582690 GAGCTTCCTG-TTAT
1 GAGCTTCCTGATTAT
21582704 ACAGCCCGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
23 5 0.10
24 34 0.67
25 12 0.24
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (23 bp):
GAGCTTCCTGATTATGGCTCTAC
Found at i:21584504 original size:20 final size:21
Alignment explanation
Indices: 21584467--21584506 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
21584457 TTATAATGAC
*
21584467 AAAAAAAATATTTTAATTTAT
1 AAAAAAAATATTTAAATTTAT
*
21584488 AAAAAAACT-TTTAAATTTA
1 AAAAAAAATATTTAAATTTA
21584507 ACTTGATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAAAATATTTAAATTTAT
Found at i:21589001 original size:69 final size:69
Alignment explanation
Indices: 21588917--21589057 Score: 203
Period size: 69 Copynumber: 2.0 Consensus size: 69
21588907 TTCCCTTCCT
* *
21588917 GAGGATTCCATCACAAAGAAGGTCTGTTTCAAGGAATC-GAACGTGAACCTTGAAGATGTGATGG
1 GAGGATTCCAACACAAAGAAGGTCTGTTTCAAGGAATCAG-ACGTGAACCTTGAAGATGTAATGG
*
21588981 TTGTG
65 TCGTG
* * **
21588986 GAGGATTCCAACACAAAGAAGGTCTGTTTCAAGGACTCAGATGTGATTCTTGAAGATGTAATGGT
1 GAGGATTCCAACACAAAGAAGGTCTGTTTCAAGGAATCAGACGTGAACCTTGAAGATGTAATGGT
21589051 CGTG
66 CGTG
21589055 GAG
1 GAG
21589058 TCATCACCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
69 63 0.98
70 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.26
Consensus pattern (69 bp):
GAGGATTCCAACACAAAGAAGGTCTGTTTCAAGGAATCAGACGTGAACCTTGAAGATGTAATGGT
CGTG
Found at i:21589406 original size:69 final size:69
Alignment explanation
Indices: 21589322--21589462 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
21589312 TTCTCTTACT
* *
21589322 GAGGATTCCATCACAAAGAAGGTCTGTTTCAAGGAATCGAACGTGAATCTTAAAGATGTGATGGT
1 GAGGATTCCAACACAAAGAAGGTCTGTTTCAAGGAATCGAACGTGAATCTTAAAGATGTAATGGT
*
21589387 TGTG
66 CGTG
* * * * *
21589391 GAGGATTCCAACACAAAGAAGGTCTGTTTCAAGGACTCGGATGTGATTCTTGAAGATGTAATGGT
1 GAGGATTCCAACACAAAGAAGGTCTGTTTCAAGGAATCGAACGTGAATCTTAAAGATGTAATGGT
21589456 CGTG
66 CGTG
21589460 GAG
1 GAG
21589463 TCATCACCAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.27
Consensus pattern (69 bp):
GAGGATTCCAACACAAAGAAGGTCTGTTTCAAGGAATCGAACGTGAATCTTAAAGATGTAATGGT
CGTG
Found at i:21589500 original size:405 final size:405
Alignment explanation
Indices: 21588749--21589563 Score: 1504
Period size: 405 Copynumber: 2.0 Consensus size: 405
21588739 ATGTCAACAA
*
21588749 AATTTAATGGTCAAACTCGGTCAACATTAACGAAGGGGATTAATTGATTAAATTTTCATCTTTAA
1 AATTTAATGGTCAAACTCGGTCAACATTAACGAAGGAGATTAATTGATTAAATTTTCATCTTTAA
* *
21588814 TGGCTCACTTGGGTGTTAAATTCCGTTGAGGGCAATTCTGAAAATGCTCTCGTCTTCTTCGGTTT
66 TGGCTCACTAGGGTGTTAAATTCCATTGAGGGCAATTCTGAAAATGCTCTCGTCTTCTTCGGTTT
* *
21588879 CTAATGTGGACAATAATGGAGAAGGTGATTCCCTTCCTGAGGATTCCATCACAAAGAAGGTCTGT
131 CTAATGTGGACAATAATGGAGAAAGTGATTCCCTTACTGAGGATTCCATCACAAAGAAGGTCTGT
*
21588944 TTCAAGGAATCGAACGTGAACCTTGAAGATGTGATGGTTGTGGAGGATTCCAACACAAAGAAGGT
196 TTCAAGGAATCGAACGTGAACCTTAAAGATGTGATGGTTGTGGAGGATTCCAACACAAAGAAGGT
21589009 CTGTTTCAAGGACTCAGATGTGATTCTTGAAGATGTAATGGTCGTGGAGTCATCACCAACGCCTT
261 CTGTTTCAAGGACTCAGATGTGATTCTTGAAGATGTAATGGTCGTGGAGTCATCACCAACGCCTT
* * *
21589074 CTTTTTCTTGAAAAGATATGCTAGTGGGGAAGGATACTCCTGTGCAGAATAATACAAAAAATGGG
326 CTTTTTCTTGAAAAGATATGCTAGCGGGGAAGGATACTCCTGTGCAAAATAATACAAAAAATGGC
21589139 CACTTCCTTGTTGAT
391 CACTTCCTTGTTGAT
21589154 AATTTAATGGTCAAACTCGGTCAACATTAACGAAGGAGATTAATTGATTAAATTTTCATCTTTAA
1 AATTTAATGGTCAAACTCGGTCAACATTAACGAAGGAGATTAATTGATTAAATTTTCATCTTTAA
21589219 TGGCTCACTAGGGTGTTAAATTCCATTGAGGGCAATTCTGAAAATGCTCTCGTCTTCTTCGGTTT
66 TGGCTCACTAGGGTGTTAAATTCCATTGAGGGCAATTCTGAAAATGCTCTCGTCTTCTTCGGTTT
*
21589284 CTAATGTGGACAATAATGGAGAAAGTGATTCTCTTACTGAGGATTCCATCACAAAGAAGGTCTGT
131 CTAATGTGGACAATAATGGAGAAAGTGATTCCCTTACTGAGGATTCCATCACAAAGAAGGTCTGT
*
21589349 TTCAAGGAATCGAACGTGAATCTTAAAGATGTGATGGTTGTGGAGGATTCCAACACAAAGAAGGT
196 TTCAAGGAATCGAACGTGAACCTTAAAGATGTGATGGTTGTGGAGGATTCCAACACAAAGAAGGT
*
21589414 CTGTTTCAAGGACTCGGATGTGATTCTTGAAGATGTAATGGTCGTGGAGTCATCACCAACGCCTT
261 CTGTTTCAAGGACTCAGATGTGATTCTTGAAGATGTAATGGTCGTGGAGTCATCACCAACGCCTT
* *
21589479 TTTTTTCTTGAAAAGATATGCTAGCGGGGAAGGATACTCCTGTGCAAAATAATACAAATAATGGC
326 CTTTTTCTTGAAAAGATATGCTAGCGGGGAAGGATACTCCTGTGCAAAATAATACAAAAAATGGC
21589544 CACTTCCTTGTTGAT
391 CACTTCCTTGTTGAT
21589559 AATTT
1 AATTT
21589564 TTCCCTCACT
Statistics
Matches: 396, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
405 396 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (405 bp):
AATTTAATGGTCAAACTCGGTCAACATTAACGAAGGAGATTAATTGATTAAATTTTCATCTTTAA
TGGCTCACTAGGGTGTTAAATTCCATTGAGGGCAATTCTGAAAATGCTCTCGTCTTCTTCGGTTT
CTAATGTGGACAATAATGGAGAAAGTGATTCCCTTACTGAGGATTCCATCACAAAGAAGGTCTGT
TTCAAGGAATCGAACGTGAACCTTAAAGATGTGATGGTTGTGGAGGATTCCAACACAAAGAAGGT
CTGTTTCAAGGACTCAGATGTGATTCTTGAAGATGTAATGGTCGTGGAGTCATCACCAACGCCTT
CTTTTTCTTGAAAAGATATGCTAGCGGGGAAGGATACTCCTGTGCAAAATAATACAAAAAATGGC
CACTTCCTTGTTGAT
Found at i:21595709 original size:21 final size:22
Alignment explanation
Indices: 21595665--21595731 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
21595655 TTTAATTTTC
* **
21595665 AAATTTTAAAAAAAATTTAAAA
1 AAATTATAAAAATTATTTAAAA
* *
21595687 AAGATTGT-AAAATTATTTTAAA
1 AA-ATTATAAAAATTATTTAAAA
21595709 AAATTATAAAAATTATTTAAAA
1 AAATTATAAAAATTATTTAAAA
21595731 A
1 A
21595732 TATAAAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 4 0.11
22 29 0.78
23 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (22 bp):
AAATTATAAAAATTATTTAAAA
Found at i:21596453 original size:19 final size:20
Alignment explanation
Indices: 21596421--21596462 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
21596411 TTTTGCTTAC
21596421 TTTGGTTTACTATTTTT-TT
1 TTTGGTTTACTATTTTTATT
21596440 TTTGTGTTTA-TATTTTTATT
1 TTTG-GTTTACTATTTTTATT
21596460 TTT
1 TTT
21596463 ATTTTACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (20 bp):
TTTGGTTTACTATTTTTATT
Found at i:21596468 original size:19 final size:20
Alignment explanation
Indices: 21596425--21596471 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
21596415 GCTTACTTTG
*
21596425 GTTTACTATTTTTTTTTTGT
1 GTTTACTATTTTTTTTTTAT
21596445 GTTTA-TATTTTTATTTTTAT
1 GTTTACTATTTTT-TTTTTAT
21596465 -TTTACTA
1 GTTTACTA
21596472 AAATATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.72
Consensus pattern (20 bp):
GTTTACTATTTTTTTTTTAT
Found at i:21599603 original size:18 final size:17
Alignment explanation
Indices: 21599573--21599606 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21599563 ATAATTGTAA
*
21599573 TTTAAATTTTAATTATT
1 TTTAAATTGTAATTATT
21599590 TTTAAATATGTAATTAT
1 TTTAAAT-TGTAATTAT
21599607 CACAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAATTGTAATTATT
Found at i:21599994 original size:15 final size:15
Alignment explanation
Indices: 21599974--21600006 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
21599964 TACCCGTTTC
21599974 ATTAAT-TTTTATATA
1 ATTAATATTTTA-ATA
21599989 ATTAATATTTTAATA
1 ATTAATATTTTAATA
21600004 ATT
1 ATT
21600007 CAATCGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTAATATTTTAATA
Found at i:21606617 original size:41 final size:41
Alignment explanation
Indices: 21606559--21606693 Score: 128
Period size: 41 Copynumber: 3.3 Consensus size: 41
21606549 TGAATTGCAA
* * * *
21606559 ATACGTACCCCTCTTTGTACTTCGGTACCCTTGAAATAG-GC
1 ATACGTGCCCCTATTTGTACTTCGGTACCCCT-AAATAGCAC
* * *
21606600 ATACGTGCCTCTATTTGTAATTCGGTACCCCTAAATTGCAC
1 ATACGTGCCCCTATTTGTACTTCGGTACCCCTAAATAGCAC
* * ** * *
21606641 ATATGTGCCCCTATTTGTACTTTGGTACCATTAACTTGCAC
1 ATACGTGCCCCTATTTGTACTTCGGTACCCCTAAATAGCAC
*
21606682 ATACATGCCCCT
1 ATACGTGCCCCT
21606694 GTTTAGACTT
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 5 0.06
41 72 0.94
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (41 bp):
ATACGTGCCCCTATTTGTACTTCGGTACCCCTAAATAGCAC
Found at i:21613032 original size:16 final size:16
Alignment explanation
Indices: 21613011--21613048 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
21613001 CATTAAAATT
* *
21613011 TAAAATAAATTATAAA
1 TAAAATAAAATAAAAA
21613027 TAAAATAAAATAAAAA
1 TAAAATAAAATAAAAA
21613043 TAAAAT
1 TAAAAT
21613049 TCAATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:21613531 original size:7 final size:7
Alignment explanation
Indices: 21613519--21613547 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
21613509 AATTAGGTAA
21613519 TTTTGTT
1 TTTTGTT
21613526 TTTTGTT
1 TTTTGTT
21613533 TTTTGTT
1 TTTTGTT
21613540 TTTTGTT
1 TTTTGTT
21613547 T
1 T
21613548 CTTAGTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTGTT
Found at i:21620715 original size:25 final size:25
Alignment explanation
Indices: 21620682--21620732 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
21620672 TCATATATCT
21620682 TCTTACTATATCAATAACCATTTCA
1 TCTTACTATATCAATAACCATTTCA
*
21620707 TCTTACTATATCAATATCCATTTCA
1 TCTTACTATATCAATAACCATTTCA
21620732 T
1 T
21620733 GCATTTCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (25 bp):
TCTTACTATATCAATAACCATTTCA
Found at i:21621134 original size:23 final size:23
Alignment explanation
Indices: 21621083--21621163 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
21621073 AATATACGAT
*
21621083 ACAT-AAGTACCTGAAA--CGAC
1 ACATAAAGTGCCTGAAATTCGAC
**
21621103 ACACGAAGTGCCTGAAATTCGAC
1 ACATAAAGTGCCTGAAATTCGAC
21621126 ACATAAAGTGCCTGAAATAT-GAC
1 ACATAAAGTGCCTGAAAT-TCGAC
*
21621149 ACATAAAGTGTCTGA
1 ACATAAAGTGCCTGA
21621164 TCAGCAAAGC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.06
21 11 0.21
23 37 0.71
24 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (23 bp):
ACATAAAGTGCCTGAAATTCGAC
Found at i:21630045 original size:6 final size:6
Alignment explanation
Indices: 21630034--21630067 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
21630024 ACTCATATCA
*
21630034 TTTCAT TTTCAT TTTCAT TTTCAT TTTCGT TTTC
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC
21630068 CAATAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.12, C:0.18, G:0.03, T:0.68
Consensus pattern (6 bp):
TTTCAT
Found at i:21639944 original size:34 final size:35
Alignment explanation
Indices: 21639897--21639963 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
21639887 AAAATGAGAT
* * * *
21639897 AAAAATAATAGTTTATATACTAAAATG-AGAAAAA
1 AAAAAAAAGAGTTTAAATAATAAAATGAAGAAAAA
*
21639931 AAAAAAAAGAGTTTAAATAATAAAGTGAAGAAA
1 AAAAAAAAGAGTTTAAATAATAAAATGAAGAAA
21639964 CCGTTATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 22 0.81
35 5 0.19
ACGTcount: A:0.64, C:0.01, G:0.12, T:0.22
Consensus pattern (35 bp):
AAAAAAAAGAGTTTAAATAATAAAATGAAGAAAAA
Found at i:21640974 original size:29 final size:28
Alignment explanation
Indices: 21640907--21640977 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 28
21640897 ATGTTTAAAT
21640907 TAAGATTGAAATTTTTTATAATAGTATTAG
1 TAAGATT-AAATTTTTTATAATAG-ATTAG
*
21640937 TAAGTTTAAATTGTTTCTATCAATAG-TTAG
1 TAAGATTAAATT-TTT-TAT-AATAGATTAG
21640967 -AAGATTAAATT
1 TAAGATTAAATT
21640978 AAGTGAGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
29 15 0.42
30 13 0.36
31 3 0.08
32 5 0.14
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (28 bp):
TAAGATTAAATTTTTTATAATAGATTAG
Found at i:21644658 original size:31 final size:31
Alignment explanation
Indices: 21644591--21644658 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
21644581 TCTTTTTATT
* * *
21644591 AATATATGAATTTTATTTTTGTTAATATATG
1 AATATATGAATATTATTTTGGATAATATATG
21644622 AATATATGAATATTATGTTTGGAT-AT-TATG
1 AATATATGAATATTAT-TTTGGATAATATATG
21644652 ACATATA
1 A-ATATA
21644659 AACTAATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 5 0.16
31 22 0.69
32 5 0.16
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.49
Consensus pattern (31 bp):
AATATATGAATATTATTTTGGATAATATATG
Found at i:21644885 original size:21 final size:21
Alignment explanation
Indices: 21644840--21644886 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
21644830 AAAAAATAAA
*
21644840 ATAG-ATTATATATTATTTTT
1 ATAGTATTATATATTATATTT
21644860 ATAGTATTATATATTATGATTT
1 ATAGTATTATATATTAT-ATTT
21644882 -TAGTA
1 ATAGTA
21644887 AATTCATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 17 0.71
22 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATAGTATTATATATTATATTT
Found at i:21644928 original size:17 final size:18
Alignment explanation
Indices: 21644903--21644948 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
21644893 TATAAGAATA
*
21644903 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
21644920 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
21644938 ATTAAATTATA
1 ATTAAATTATA
21644949 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:21644945 original size:55 final size:54
Alignment explanation
Indices: 21644879--21644984 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 54
21644869 TATATTATGA
* *
21644879 TTTTAGTAAATTCATA-TAAGAATAATTATATTAAGAATTTTATTAAATTATATAT
1 TTTTAGTAAATT-ATATTAAGAATAATTATATTAA-AATATGATTAAATTATATAT
* * *
21644934 TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAAATTAT
1 TTTTAGTAAATTATA-TTAAGAATAATTATATTAAAATATGATTAAATTAT
21644985 TTACTATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
54 3 0.07
55 25 0.57
56 16 0.36
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (54 bp):
TTTTAGTAAATTATATTAAGAATAATTATATTAAAATATGATTAAATTATATAT
Found at i:21645160 original size:39 final size:43
Alignment explanation
Indices: 21645117--21645206 Score: 107
Period size: 45 Copynumber: 2.1 Consensus size: 43
21645107 TTACAACATC
*
21645117 ATTCCATT-CAATCAA-ACACAA-GAA-TACTATTACAGTTCT
1 ATTCCATTCCAATCAACAAACAATGAATTACTATTACAGTTCT
* *
21645156 ATTCCATTCCATTCAACCAAACAATTGAATTACTATTGCAGTTCT
1 ATTCCATTCCAATCAA-CAAACAA-TGAATTACTATTACAGTTCT
21645201 ATTCCA
1 ATTCCA
21645207 AAACACCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 8 0.19
40 6 0.14
42 5 0.12
44 3 0.07
45 20 0.48
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (43 bp):
ATTCCATTCCAATCAACAAACAATGAATTACTATTACAGTTCT
Found at i:21645204 original size:45 final size:44
Alignment explanation
Indices: 21645116--21645206 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 44
21645106 ATTACAACAT
*
21645116 CATTCCATTCAATCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
* *
21645160 CATTCCATTCAACCAAACA-ATTGAATTACTATTGCAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
21645205 CA
1 CA
21645207 AAACACCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.50
45 20 0.48
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:21645219 original size:16 final size:16
Alignment explanation
Indices: 21645198--21645260 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
21645188 CTATTGCAGT
* *
21645198 TCTATTCCAAAACACC
1 TCTATTCCAATACAGC
*
21645214 TCTATTCCATTACAGC
1 TCTATTCCAATACAGC
21645230 TCTATT-CAATTACAGC
1 TCTATTCCAA-TACAGC
*
21645246 TCTATTCCATTACAG
1 TCTATTCCAATACAG
21645261 TGAACCAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 2 0.05
16 36 0.90
17 2 0.05
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (16 bp):
TCTATTCCAATACAGC
Found at i:21645234 original size:32 final size:32
Alignment explanation
Indices: 21645198--21645260 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
21645188 CTATTGCAGT
21645198 TCTATTCCAA-AACACCTCTATTCCATTACAGC
1 TCTATT-CAATAACACCTCTATTCCATTACAGC
* *
21645230 TCTATTCAATTACAGCTCTATTCCATTACAG
1 TCTATTCAATAACACCTCTATTCCATTACAG
21645261 TGAACCAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (32 bp):
TCTATTCAATAACACCTCTATTCCATTACAGC
Found at i:21648829 original size:24 final size:24
Alignment explanation
Indices: 21648802--21648847 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
21648792 AGAACAATCC
*
21648802 CAAAAGAAAATGCAGGAGCAGCTT
1 CAAAAGAAAATGAAGGAGCAGCTT
* *
21648826 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGAAAATGAAGGAGCAGC
21648848 AAAAGATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (24 bp):
CAAAAGAAAATGAAGGAGCAGCTT
Found at i:21656902 original size:45 final size:45
Alignment explanation
Indices: 21656799--21657218 Score: 297
Period size: 45 Copynumber: 9.5 Consensus size: 45
21656789 ACAGATCGAG
* *
21656799 TCTTATCTTCCTGAAGTTGCAGTG-GAGCAGACTAAG-TAGGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTAAGAT-GGCAAA
* *
21656843 TCTTATC-CTTCTGAAGTTGCAGTGAG-GCAAACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGAGAGCAGACT-AAGATGGCAAA
* * * *
21656888 TCTTATCTCCCTGAACTTGCAGTG-GAGTAGATTAA-A-GCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTAAGATGGC-A-AA
21656932 TCTTATCTCCCTGAAGTTGCAGTGAG-GCAGACTGAAGATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACT-AAGATGGCAAA
* * * * *** *
21656977 TCTTATCTCTCTGAAGTTACAGTG-GAGCAGATTAAAACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTAAGATGGCAAA
* * * * *
21657021 TCTTATCTCTCTGAAGTT--A-TAGAGAGCAGA-TCACAT--CTAG
1 TCTTATCTCCCTGAAGTTGCAGT-GAGAGCAGACTAAGATGGCAAA
* ** * *
21657061 TCTTATCTCCCTGAAGTTGCAGT-AGAGTAGACTAAGTAAAGTAAG
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTAAG-ATGGCAAA
*
21657106 TCTTATC-CTCCTGAAGTTGCGGTGAG-GCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGAGAGCAGACT-AAGATGGCAAA
* * *
21657151 TCTTATCTCCTTGAAGTTGCAGTG-GAGCAGATTAA-A-GCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTAAGATGGC-A-AA
* *
21657195 TCCTATCTCCCTGAAGTTGTAGTG
1 TCTTATCTCCCTGAAGTTGCAGTG
21657219 GAGTGGATTA
Statistics
Matches: 299, Mismatches: 48, Indels: 58
0.74 0.12 0.14
Matches are distributed among these distances:
40 18 0.06
41 8 0.03
42 12 0.04
43 13 0.04
44 112 0.37
45 124 0.41
46 10 0.03
47 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTAAGATGGCAAA
Found at i:21656936 original size:89 final size:89
Alignment explanation
Indices: 21656799--21657218 Score: 428
Period size: 89 Copynumber: 4.8 Consensus size: 89
21656789 ACAGATCGAG
* * ** * *
21656799 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT-AAGTAGGCAAGTCTTATC-CTTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA-TCTTATCTC-CCTGAAGTTG
*
21656862 CAGTGAGGCAAACTGAAGATGGCAAA
64 CAGTGAGGCAGACTGAAGATGGCAAA
* *
21656888 TCTTATCTCCCTGAACTTGCAGTGGAGTAGATTAAAGCCGACAATCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCTTATCTCCCTGAAGTTGCA
21656953 GTGAGGCAGACTGAAGATGGCAAA
66 GTGAGGCAGACTGAAGATGGCAAA
* * * * * **
21656977 TCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAACC-TCAGATCTTATCTCTCTGAAGTTAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA-ATCTTATCTCCCTGAAGTTGC
* * * * *
21657041 AGAGA-GCAGA-T-CACAT--CTAG
65 AGTGAGGCAGACTGAAGATGGCAAA
* * * *** *
21657061 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGACT-AAGTAAAGTAAGTCTTATC-CTCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-CAA-TCTTATCTC-CCTGAAGTT
*
21657124 GCGGTGAGGCAGACTGAAGATGGCAAA
63 GCAGTGAGGCAGACTGAAGATGGCAAA
* * *
21657151 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCTTATCTCCCTGAAGTTGCA
21657216 GTG
66 GTG
21657219 GAGTGGATTA
Statistics
Matches: 264, Mismatches: 53, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
83 2 0.01
84 32 0.12
85 19 0.07
86 8 0.03
87 2 0.01
88 10 0.04
89 145 0.55
90 42 0.16
91 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (89 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCTTATCTCCCTGAAGTTGCA
GTGAGGCAGACTGAAGATGGCAAA
Found at i:21657152 original size:174 final size:173
Alignment explanation
Indices: 21656888--21657212 Score: 460
Period size: 174 Copynumber: 1.9 Consensus size: 173
21656878 AGATGGCAAA
* * **
21656888 TCTTATCTCCCTGAACTTGCAGTGGAGTAGATTAAAGCCGACAATCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAACTTGCAGTAGAGTAGACTAAAGCAAACAATCTTATCTCCCTGAAGTTGCA
21656953 GTGAGGCAGACTGAAGATGGCAAATCTTATCT-CTCTGAAGTTACAGTGGAGCAGATTAAAACC-
66 GTGAGGCAGACTGAAGATGGCAAATCTTATCTCCT-TGAAGTTACAGTGGAGCAGATTAAAACCG
* * *
21657016 TCAGATCTTATCTCTCTGAAGTTATAGAGAGCAGATCACATCTAG
130 ACA-ATCCTATCTCCCTGAAGTTATAGAGAGCAGATCACATCTAG
* * *
21657061 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGACT-AAGTAAAGTAAGTCTTATC-CTCCTGAAGTT
1 TCTTATCTCCCTGAACTTGCAGTAGAGTAGACTAAAGCAAA-CAA-TCTTATCTC-CCTGAAGTT
* * *
21657124 GCGGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGC
63 GCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAAC
21657189 CGACAATCCTATCTCCCTGAAGTT
128 CGACAATCCTATCTCCCTGAAGTT
21657213 GTAGTGGAGT
Statistics
Matches: 134, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
172 4 0.03
173 33 0.25
174 93 0.69
175 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (173 bp):
TCTTATCTCCCTGAACTTGCAGTAGAGTAGACTAAAGCAAACAATCTTATCTCCCTGAAGTTGCA
GTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAACCGA
CAATCCTATCTCCCTGAAGTTATAGAGAGCAGATCACATCTAG
Found at i:21658722 original size:17 final size:17
Alignment explanation
Indices: 21658702--21658753 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
21658692 ATTTTCTTTA
21658702 TTTTTTATTAATTAGTT
1 TTTTTTATTAATTAGTT
21658719 TTTTTTATT--TT-GTT
1 TTTTTTATTAATTAGTT
*
21658733 TTTTATATTTAATTA-TT
1 TTTTTTA-TTAATTAGTT
21658750 TTTT
1 TTTT
21658754 AAAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 9 0.30
15 4 0.13
17 17 0.57
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTTATTAATTAGTT
Found at i:21658733 original size:14 final size:14
Alignment explanation
Indices: 21658693--21658754 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
21658683 TCCTTTTTCA
*
21658693 TTTTCTTTA-TTTT
1 TTTTATTTAGTTTT
*
21658706 TTATTAATTAGTTTT
1 TT-TTATTTAGTTTT
*
21658721 TTTTATTTTGTTTT
1 TTTTATTTAGTTTT
* *
21658735 TTATATTTAATTATT
1 TTTTATTTAGTT-TT
21658750 TTTTA
1 TTTTA
21658755 AAAAATATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 12 0.32
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTATTTAGTTTT
Found at i:21658862 original size:22 final size:21
Alignment explanation
Indices: 21658811--21658863 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
21658801 TGTAGTATAA
*
21658811 TATATATTTTTTTGTTTATATG
1 TATATA-TTTTTTGTCTATATG
21658833 TA-ATTATTTTTTGATCTATATG
1 TATA-TATTTTTTG-TCTATATG
21658855 TATATATTT
1 TATATATTT
21658864 ATTTTAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 8 0.30
22 18 0.67
23 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (21 bp):
TATATATTTTTTGTCTATATG
Found at i:21682050 original size:16 final size:16
Alignment explanation
Indices: 21682029--21682074 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
21682019 TTATTAAATT
21682029 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
21682045 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
21682060 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
21682075 CTTTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:21682148 original size:120 final size:120
Alignment explanation
Indices: 21681935--21682192 Score: 491
Period size: 120 Copynumber: 2.1 Consensus size: 120
21681925 GGCAGTTGTC
21681935 TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
1 TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
21682000 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
66 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
21682055 TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATAATAA-
1 TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCAT-ATAAG
21682119 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
65 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
21682175 TAATAATTATGTTTAAAT
1 TAATAATTATG-TTAAAT
21682193 ATGATTAAAT
Statistics
Matches: 136, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
120 126 0.93
121 10 0.07
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAA
Found at i:21682170 original size:16 final size:16
Alignment explanation
Indices: 21682149--21682190 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21682139 TTATTAAATT
*
21682149 ATATATTTTAATTATA
1 ATATATTTTAATAATA
21682165 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
21682180 AT-TATGTTTAA
1 ATATAT-TTTAA
21682191 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:21682175 original size:15 final size:15
Alignment explanation
Indices: 21682140--21682181 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21682130 TTAAGAATTT
*
21682140 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21682154 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21682168 TATTTAATAATAAT
1 TATTTAATTATAAT
21682182 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:21682417 original size:45 final size:44
Alignment explanation
Indices: 21682335--21682425 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
21682325 ACCTCTATTC
* *
21682335 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCAATTA
*** * *
21682379 CATTCAACCAAACAGTTGATTTGCTATTACATCTCTATTCAATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCAATTA
21682424 CA
1 CA
21682426 CCTCTATTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 16 0.41
45 23 0.59
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCAATTA
Found at i:21682452 original size:16 final size:16
Alignment explanation
Indices: 21682404--21682457 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
21682394 TTGATTTGCT
* *
21682404 ATTACATCTCTATTCA
1 ATTACACCTCTATTCC
21682420 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
21682436 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
21682452 AATACA
1 ATTACA
21682458 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:21687200 original size:16 final size:15
Alignment explanation
Indices: 21687146--21687243 Score: 56
Period size: 16 Copynumber: 6.3 Consensus size: 15
21687136 AACATTAAAT
*
21687146 TTAATTTAATTTAAGA
1 TTAA-TTAATTTAATA
*
21687162 -TAATTACTTTAATA
1 TTAATTAATTTAATA
*
21687176 TTGATTTAATTTAATA
1 TT-AATTAATTTAATA
**
21687192 CTTAATTAATAAAATA
1 -TTAATTAATTTAATA
* **
21687208 CT-ATTAAGATAAGTA
1 TTAATTAATTTAA-TA
21687223 TTAAATTAAATTTAATA
1 TT-AATT-AATTTAATA
21687240 TTAA
1 TTAA
21687244 ACTATTAAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 14
0.70 0.15 0.16
Matches are distributed among these distances:
14 17 0.27
15 8 0.13
16 23 0.37
17 9 0.15
18 5 0.08
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (15 bp):
TTAATTAATTTAATA
Found at i:21688389 original size:35 final size:35
Alignment explanation
Indices: 21688340--21688407 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
21688330 CTGTTGCTAG
*
21688340 TAAAGCCATTCCATACATAAGTCATATACCCAAAC
1 TAAAGCCATGCCATACATAAGTCATATACCCAAAC
*
21688375 TAAAGCCATGCCATACATAAGTCATGTACCCAA
1 TAAAGCCATGCCATACATAAGTCATATACCCAA
21688408 CATACCAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (35 bp):
TAAAGCCATGCCATACATAAGTCATATACCCAAAC
Found at i:21693422 original size:10 final size:10
Alignment explanation
Indices: 21693415--21693447 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
21693405 ATAATAAATA
21693415 AAATTAAAAG
1 AAATTAAAAG
21693425 AAATTAAAAG
1 AAATTAAAAG
21693435 AAA-TAGAAAG
1 AAATTA-AAAG
21693445 AAA
1 AAA
21693448 GAGGAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 2 0.09
10 20 0.91
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (10 bp):
AAATTAAAAG
Found at i:21695979 original size:48 final size:48
Alignment explanation
Indices: 21695895--21695987 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
21695885 TCAAGAGGGA
* * *
21695895 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAAAG
1 ATAAATAGTGATAAAAGTGTAGACAGTGAAAAACCAAGTTTAGCAAAG
*
21695943 ATAAATAGTGATAAAAGTGTAGATAGTGAAAAACCAAGTTTAGCA
1 ATAAATAGTGATAAAAGTGTAGACAGTGAAAAACCAAGTTTAGCA
21695988 TTGCATAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.23
Consensus pattern (48 bp):
ATAAATAGTGATAAAAGTGTAGACAGTGAAAAACCAAGTTTAGCAAAG
Found at i:21700552 original size:21 final size:21
Alignment explanation
Indices: 21700528--21700570 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
21700518 CTTTTAGTAT
21700528 TTAGGTTAGAATTGATTTGAC
1 TTAGGTTAGAATTGATTTGAC
21700549 TTAGGTTAGAATTGATTTGAC
1 TTAGGTTAGAATTGATTTGAC
21700570 T
1 T
21700571 CTCGCCTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (21 bp):
TTAGGTTAGAATTGATTTGAC
Found at i:21704293 original size:24 final size:24
Alignment explanation
Indices: 21704261--21704308 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
21704251 TAAACTTAAA
*
21704261 AATTGAGTTTAAACAATTTAAAAC
1 AATTCAGTTTAAACAATTTAAAAC
21704285 AATTCAGTTTAAACAATTTAAAAC
1 AATTCAGTTTAAACAATTTAAAAC
21704309 TTAAAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AATTCAGTTTAAACAATTTAAAAC
Found at i:21708545 original size:45 final size:45
Alignment explanation
Indices: 21708486--21708641 Score: 197
Period size: 45 Copynumber: 3.5 Consensus size: 45
21708476 ATATAAATAT
*
21708486 AGGTACTATGTACCAGTGTTGGCTATCATGCTATATGCATACAAC
1 AGGTACTATGTACCAGTGTTGGCTATCATGCTATATACATACAAC
* * * * *
21708531 AGGTACTATTTACCAGTGTTGGCTTTCATG-TCACATAAATACAAA
1 AGGTACTATGTACCAGTGTTGGCTATCATGCT-ATATACATACAAC
** *
21708576 AGGTACTATGTACTGGTGTTGGCTATCATGCCATATACATACAAC
1 AGGTACTATGTACCAGTGTTGGCTATCATGCTATATACATACAAC
* *
21708621 AGGTACTATGTATCGGTGTTG
1 AGGTACTATGTACCAGTGTTG
21708642 ATTTTCTTAT
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.01
45 92 0.99
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (45 bp):
AGGTACTATGTACCAGTGTTGGCTATCATGCTATATACATACAAC
Found at i:21710612 original size:91 final size:91
Alignment explanation
Indices: 21710451--21710638 Score: 205
Period size: 91 Copynumber: 2.1 Consensus size: 91
21710441 ATTTAATAAT
* * * *
21710451 CTGCAAACACTAGTGGTTTATCCACAATTTTTACTAACAACTTTAATCTGCAAAAAAGTTGTGCA
1 CTGCAAACACTAGTGGTTTATCCACAATTTATACTAACAAATTTAATCTACAAAAAAGTTATGCA
* * * *
21710516 TTCACAACTACTAGTAGCGTATTAAC
66 ATCACAAATACTAGCAGCGTATGAAC
* *** * *** *
21710542 CTGCAAACACTAGTGGTTTATCCATAATTTATACTGGTAAATTTTATCTACAAACCCGTTATGTA
1 CTGCAAACACTAGTGGTTTATCCACAATTTATACTAACAAATTTAATCTACAAAAAAGTTATGCA
* *
21710607 ATCACAAATACTGGCAGTGTATGAAC
66 ATCACAAATACTAGCAGCGTATGAAC
21710633 CTGCAA
1 CTGCAA
21710639 TACTGGCGGC
Statistics
Matches: 78, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (91 bp):
CTGCAAACACTAGTGGTTTATCCACAATTTATACTAACAAATTTAATCTACAAAAAAGTTATGCA
ATCACAAATACTAGCAGCGTATGAAC
Found at i:21711151 original size:9 final size:9
Alignment explanation
Indices: 21711134--21711167 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
21711124 TGAGTTTTCG
21711134 AATTCGAAT
1 AATTCGAAT
*
21711143 AACTCGAAT
1 AATTCGAAT
21711152 AATTCGAAT
1 AATTCGAAT
21711161 AATTCGA
1 AATTCGA
21711168 TTATCAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:21711285 original size:29 final size:29
Alignment explanation
Indices: 21711225--21711287 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
21711215 TTTTACTTTT
* *
21711225 CCCT-CAAAACTTTTACTCCTTCCCACTT
1 CCCTCCAAAACTTTTACTCCCTCCCACTC
21711253 CCCTCCAAAACTTTTACTCTCCTCCC-CTC
1 CCCTCCAAAACTTTTACTC-CCTCCCACTC
21711282 CCCTCC
1 CCCTCC
21711288 CCTCTCAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 4 0.13
29 22 0.71
30 5 0.16
ACGTcount: A:0.17, C:0.51, G:0.00, T:0.32
Consensus pattern (29 bp):
CCCTCCAAAACTTTTACTCCCTCCCACTC
Found at i:21712695 original size:25 final size:25
Alignment explanation
Indices: 21712667--21712722 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
21712657 ATTTCAGTGA
*
21712667 CTAATGTAGTCTCTTGAATTTGGGT
1 CTAATATAGTCTCTTGAATTTGGGT
21712692 CTAATATAGTCTCTTGAATTTGGGT
1 CTAATATAGTCTCTTGAATTTGGGT
21712717 CTAATA
1 CTAATA
21712723 GCTTGCAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (25 bp):
CTAATATAGTCTCTTGAATTTGGGT
Found at i:21712783 original size:23 final size:23
Alignment explanation
Indices: 21712757--21712810 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
21712747 GATCATGAAC
*
21712757 ATATTTATGAAAATATGTGTTTA
1 ATATTTATGAAAATATGTATTTA
** * *
21712780 ATATACATGAATATATTTATTTA
1 ATATTTATGAAAATATGTATTTA
*
21712803 ATGTTTAT
1 ATATTTAT
21712811 ACAAGTTTTC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (23 bp):
ATATTTATGAAAATATGTATTTA
Found at i:21712876 original size:44 final size:42
Alignment explanation
Indices: 21712793--21712877 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 42
21712783 TACATGAATA
* *
21712793 TATTTATTTAATGTTTATACAAGTTTTCATTTAACTGAAACC
1 TATTTATTTAATGTTTAAACAAGTTTTCATTGAACTGAAACC
* **
21712835 TATTTATTTAATGTTTACAAAGAAGTTTTTGTTGAACTGAAAC
1 TATTTATTTAATGTTT--AAACAAGTTTTCATTGAACTGAAAC
21712878 AAATGAGGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 16 0.44
44 20 0.56
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (42 bp):
TATTTATTTAATGTTTAAACAAGTTTTCATTGAACTGAAACC
Found at i:21714068 original size:19 final size:20
Alignment explanation
Indices: 21714034--21714073 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
21714024 AAAAAATTGA
21714034 ATATTTTAAGTTTTTTATAT
1 ATATTTTAAGTTTTTTATAT
*
21714054 ATATTTTTA-TTTTTTATAT
1 ATATTTTAAGTTTTTTATAT
21714073 A
1 A
21714074 ATTAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATATTTTAAGTTTTTTATAT
Found at i:21716347 original size:27 final size:27
Alignment explanation
Indices: 21716292--21716344 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21716282 AGTTTAAATT
** *
21716292 TTATATTAATATTAATATTAAATATAA
1 TTATATTAATATTAATAAAAAATAAAA
21716319 TTATATTAATATTAA-AAAAAATAAAA
1 TTATATTAATATTAATAAAAAATAAAA
21716345 ATTCCCCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TTATATTAATATTAATAAAAAATAAAA
Found at i:21725010 original size:61 final size:61
Alignment explanation
Indices: 21724915--21725046 Score: 255
Period size: 61 Copynumber: 2.2 Consensus size: 61
21724905 TCTTTCCCCT
21724915 CCAATTCCCAGAGGGTCGAGGGAGAAAAGACTAAGTCTGTCAGTTGTTATTATTGTTAATC
1 CCAATTCCCAGAGGGTCGAGGGAGAAAAGACTAAGTCTGTCAGTTGTTATTATTGTTAATC
*
21724976 CCAATTCCCAGAGGGTCGAGGGAGAAAAGACTAAGTCTGTCAGTTGTTATTATTGTTAGTC
1 CCAATTCCCAGAGGGTCGAGGGAGAAAAGACTAAGTCTGTCAGTTGTTATTATTGTTAATC
21725037 CCAATTCCCA
1 CCAATTCCCA
21725047 AAGAGTCATG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (61 bp):
CCAATTCCCAGAGGGTCGAGGGAGAAAAGACTAAGTCTGTCAGTTGTTATTATTGTTAATC
Found at i:21726950 original size:22 final size:22
Alignment explanation
Indices: 21726925--21726967 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21726915 TTAAAAGAGA
* *
21726925 CATAATTATTCAACTAATATTT
1 CATAACTATTCAAATAATATTT
21726947 CATAACTATTCAAATAATATT
1 CATAACTATTCAAATAATATT
21726968 ACTTGTATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (22 bp):
CATAACTATTCAAATAATATTT
Found at i:21732459 original size:33 final size:33
Alignment explanation
Indices: 21732415--21732613 Score: 137
Period size: 33 Copynumber: 5.5 Consensus size: 33
21732405 ATCAGTGGAT
21732415 TCAGCACTTAGCAACCACCAATGAATCGGGGAA
1 TCAGCACTTAGCAACCACCAATGAATCGGGGAA
* * * *
21732448 TCAGCATTTAGCAACCCCTTTCACATTTAAGATACGGTGGGA
1 TCAGCACTTAGCAACCAC---CA-A--TGA-AT-CGG-GGAA
* *
21732490 TCAGCACTTAGCAACCACCAATGATTCAGGGAA
1 TCAGCACTTAGCAACCACCAATGAATCGGGGAA
* * * *
21732523 TCAACACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAA
1 TCAGCACTTAGCAA-CCAC--CA-A--T-GAAT-CGG-GGAA
*
21732565 TCAGCACTTAGCAACCATCAATGAATCGGGGAA
1 TCAGCACTTAGCAACCACCAATGAATCGGGGAA
21732598 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
21732614 CCCTTTATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
33 52 0.41
34 7 0.06
35 4 0.03
36 7 0.06
37 2 0.02
38 2 0.02
39 7 0.06
40 4 0.03
41 6 0.05
42 36 0.28
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGAATCGGGGAA
Found at i:21732538 original size:75 final size:75
Alignment explanation
Indices: 21732409--21732618 Score: 330
Period size: 75 Copynumber: 2.8 Consensus size: 75
21732399 TTCGTTATCA
* * *
21732409 GTGGATTCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCATTTAGCAACCCCTTTCACAT
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTCACAT
*
21732474 TTAAGATACG
66 TTAAAATACG
* * * *
21732484 GTGGGATCAGCACTTAGCAACCACCAATGATTCAGGGAATCAACACTTAGCAACCCCCTTCACAT
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTCACAT
*
21732549 TTAAAATATG
66 TTAAAATACG
*
21732559 GTGGAATCAGCACTTAGCAACCATCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTT
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTT
21732619 TATATTCAAT
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 121 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (75 bp):
GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTCACAT
TTAAAATACG
Found at i:21737273 original size:21 final size:22
Alignment explanation
Indices: 21737244--21737290 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
21737234 CAGAAGGAGT
*
21737244 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
21737266 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
21737287 GAGT
1 GAGT
21737291 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:21740627 original size:11 final size:11
Alignment explanation
Indices: 21740613--21740637 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21740603 CAAGTGAAGA
21740613 ATGAATGAATG
1 ATGAATGAATG
21740624 ATGAATGAATG
1 ATGAATGAATG
21740635 ATG
1 ATG
21740638 TTTGGAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (11 bp):
ATGAATGAATG
Found at i:21744156 original size:24 final size:24
Alignment explanation
Indices: 21744124--21744171 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
21744114 AATTTGGGTC
21744124 TCAAAATAATTAAAACGTAAAAAA
1 TCAAAATAATTAAAACGTAAAAAA
21744148 TCAAAATAATTAAAACGTAAAAAA
1 TCAAAATAATTAAAACGTAAAAAA
21744172 ACTATCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (24 bp):
TCAAAATAATTAAAACGTAAAAAA
Found at i:21745372 original size:7 final size:7
Alignment explanation
Indices: 21745360--21745387 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21745350 ATGGAGGCCT
21745360 GGTATAA
1 GGTATAA
21745367 GGTATAA
1 GGTATAA
21745374 GGTATAA
1 GGTATAA
21745381 GGTATAA
1 GGTATAA
21745388 ATATACTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
GGTATAA
Found at i:21745583 original size:35 final size:35
Alignment explanation
Indices: 21745544--21745613 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
21745534 GTAAATACAG
*
21745544 AATAGAGATAAAGTCTGCCAAGACAATAAACACGA
1 AATAGAAATAAAGTCTGCCAAGACAATAAACACGA
* * ** *
21745579 AATAGAAATAAATTTTTTCAGGACAATAAACACGA
1 AATAGAAATAAAGTCTGCCAAGACAATAAACACGA
21745614 GGTAAGTTCG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.20
Consensus pattern (35 bp):
AATAGAAATAAAGTCTGCCAAGACAATAAACACGA
Found at i:21745931 original size:20 final size:20
Alignment explanation
Indices: 21745906--21745944 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
21745896 GCGAAGACCC
21745906 AATGAGAATTAGAGAAAGAT
1 AATGAGAATTAGAGAAAGAT
21745926 AATGAGAATTAGAGAAAGA
1 AATGAGAATTAGAGAAAGA
21745945 CAGGTCTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (20 bp):
AATGAGAATTAGAGAAAGAT
Found at i:21750714 original size:74 final size:74
Alignment explanation
Indices: 21750590--21750741 Score: 295
Period size: 74 Copynumber: 2.1 Consensus size: 74
21750580 GTCTTACAAA
21750590 CCTCAGACTCAATTTTCCTTTTTGACAAAACCAAATAATCTTTTTACATAGAGAGACCTTTAGAA
1 CCTCAGACTCAATTTTCCTTTTTGACAAAACCAAATAATCTTTTTACATAGAGAGACCTTTAGAA
21750655 ATACTTTAT
66 ATACTTTAT
*
21750664 CCTCAGACTCAATTTTCCTTTTTGACAAAACCAAATAATCTTTTTCCATAGAGAGACCTTTAGAA
1 CCTCAGACTCAATTTTCCTTTTTGACAAAACCAAATAATCTTTTTACATAGAGAGACCTTTAGAA
21750729 ATACTTTAT
66 ATACTTTAT
21750738 CCTC
1 CCTC
21750742 TAAATTCAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (74 bp):
CCTCAGACTCAATTTTCCTTTTTGACAAAACCAAATAATCTTTTTACATAGAGAGACCTTTAGAA
ATACTTTAT
Found at i:21753783 original size:62 final size:59
Alignment explanation
Indices: 21753675--21753875 Score: 163
Period size: 62 Copynumber: 3.2 Consensus size: 59
21753665 ATCACTTTAA
* * *
21753675 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
21753734 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATGTTAAGATAATC
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAACATTAAATTAAATTTAATATT---A-AAT-
21753799 ACTT
58 -C-T
* * * ** *
21753803 TAACATTAAACTAATAAAATA-TTATTAAGATAAGTATTAAATTTAATTTAATATTAAAT-T
1 T---ATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
*
21753863 TATTAAAATAATA
1 TATTAAATTAATA
21753876 TTATTTTTAG
Statistics
Matches: 116, Mismatches: 13, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
57 11 0.09
59 20 0.17
60 2 0.02
61 1 0.01
62 27 0.23
64 3 0.03
65 2 0.02
66 3 0.03
68 26 0.22
69 3 0.03
71 3 0.03
72 15 0.13
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:21753872 original size:17 final size:17
Alignment explanation
Indices: 21753837--21753869 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21753827 TTAAGATAAG
*
21753837 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
21753854 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
21753870 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:21765168 original size:91 final size:91
Alignment explanation
Indices: 21765043--21765523 Score: 854
Period size: 91 Copynumber: 5.3 Consensus size: 91
21765033 AAGATTTTAG
* * *
21765043 TAAATTAATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
21765108 ATTTAATATTAATTATTTTAAATTATA
65 ATTTAATATTAATTATTTTAAATTATA
21765135 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
21765200 TTTAATATTAATTCTTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
21765226 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
21765291 TTTAATATTAATTCTTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
21765317 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
21765382 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* * *
21765408 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGCAATTATATATTAGTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* *
21765473 TTTAATAATAACTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
21765499 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
21765524 GTTATAATTA
Statistics
Matches: 378, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
91 363 0.96
92 15 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:21765490 original size:47 final size:45
Alignment explanation
Indices: 21765075--21765498 Score: 126
Period size: 44 Copynumber: 9.3 Consensus size: 45
21765065 ATTATTAAGA
* * *
21765075 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATG-AATTATATATTA-TATTAAATTATATTTAATAATAACT
* * **
21765122 ATTTTA--AATTATATAAATTCATA-TAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAATTATAT--ATT-ATATTAA-ATTATATTTAATAAT-AACT
* * *
21765166 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATG-AATTATATATTA-TATTAAATTATATTTAATAATAACT
* * * **
21765213 CTTTTA--AATTATATAAATTCATA-TAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAATTATAT--ATT-ATATTAA-ATTATATTTAATAAT-AACT
* * *
21765257 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATG-AATTATATATTA-TATTAAATTATATTTAATAATAACT
* * * **
21765304 CTTTTA--AATTATATAAATTCATA-TAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAATTATAT--ATT-ATATTAA-ATTATATTTAATAAT-AACT
* * *
21765348 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATG-AATTATATATTA-TATTAAATTATATTTAATAATAACT
* * **
21765395 ATTTTA--AATTATATAAATTCATA-TAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAATTATAT--ATT-ATATTAA-ATTATATTTAATAAT-AACT
21765439 ATTTTATGCAATTATATATTAGTATTAAATTATATTTAATAATAACT
1 ATTTTATG-AATTATATATTA-TATTAAATTATATTTAATAATAACT
21765486 ATTTTA--AATTATA
1 ATTTTATGAATTATA
21765499 CAAATTCATA
Statistics
Matches: 275, Mismatches: 50, Indels: 107
0.64 0.12 0.25
Matches are distributed among these distances:
43 12 0.04
44 93 0.34
45 33 0.12
46 32 0.12
47 92 0.33
48 13 0.05
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (45 bp):
ATTTTATGAATTATATATTATATTAAATTATATTTAATAATAACT
Found at i:21765615 original size:59 final size:58
Alignment explanation
Indices: 21765550--21765738 Score: 154
Period size: 59 Copynumber: 3.2 Consensus size: 58
21765540 ATTTTATTAA
21765550 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTA-TTCAAATTATATTTTATAGT
* * ** * *
21765609 ATCATATATTATGATTTTAGTAAACTCATATAAGAATATTGATTATT--AA-GA-ATTTTATTA-
1 ATCATATATT-TTA-ATTA--AAA-T-ATAT-TTAATATTAATTATTCAAATTATATTTTA-TAG
*
21765669 A
58 T
* * * *
21765670 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGCTAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTC-AAATTATATTTTATAGT
21765729 ATCATATATT
1 ATCATATATT
21765739 ATGATTTGAG
Statistics
Matches: 97, Mismatches: 19, Indels: 28
0.67 0.13 0.19
Matches are distributed among these distances:
54 10 0.10
55 4 0.04
56 1 0.01
57 5 0.05
58 3 0.03
59 27 0.28
60 4 0.04
61 18 0.19
62 3 0.03
63 5 0.05
64 1 0.01
65 6 0.06
66 10 0.10
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTCAAATTATATTTTATAGT
Found at i:21765688 original size:18 final size:17
Alignment explanation
Indices: 21765660--21765694 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21765650 ATTATTAAGA
*
21765660 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
21765677 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
21765695 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:21765796 original size:59 final size:59
Alignment explanation
Indices: 21765613--21765796 Score: 148
Period size: 56 Copynumber: 3.1 Consensus size: 59
21765603 TATAGTATCA
* * *
21765613 TATATTATGATTTTAGTAAACTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAAATCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* ** * *
21765672 TATA-TAT--TTTAATTAAAAT-ATAT-TTAATAATAATTATGCTAA-ATTATCTTT-TATAGTA
1 TATATTATGATTTAAGTAAAATCATATAAGAATATTAATTAT--TAAGA--AT-TTTAT-TA-AA
21765730 T
59 T
* *
21765731 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAAATCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
21765792 TATAT
1 TATAT
21765797 ATTTTAATTA
Statistics
Matches: 94, Mismatches: 15, Indels: 32
0.67 0.11 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 12 0.13
57 3 0.03
58 8 0.09
59 11 0.12
61 6 0.06
62 8 0.09
63 3 0.03
64 12 0.13
65 5 0.05
66 11 0.12
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (59 bp):
TATATTATGATTTAAGTAAAATCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:21765814 original size:16 final size:16
Alignment explanation
Indices: 21765793--21765834 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21765783 TTATTAAATT
*
21765793 ATATATTTTAATTATA
1 ATATATTTTAATAATA
21765809 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
21765824 AT-TATGTTTAA
1 ATATAT-TTTAA
21765835 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:21765819 original size:15 final size:15
Alignment explanation
Indices: 21765784--21765825 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21765774 TTAAGAATTT
*
21765784 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21765798 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21765812 TATTTAATAATAAT
1 TATTTAATTATAAT
21765826 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:21765829 original size:120 final size:121
Alignment explanation
Indices: 21765539--21765829 Score: 496
Period size: 120 Copynumber: 2.4 Consensus size: 121
21765529 AATTATTTTA
* * *
21765539 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGCTCAAATTATATTT
* *
21765603 TATAGTATCATATATTATGATTTTAGTAAACTCATATAAGAATATTGATTATTAAG
66 TATAGTATCATATATTATGATTTGAGTAAACTCATATAAGAATATTAATTATTAAG
*
21765659 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGCT-AAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGCTCAAATTATATTT
*
21765723 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 TATAGTATCATATATTATGATTTGAGTAAACTCATATAAGAATATTAATTATTAAG
*
21765779 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG
21765830 TTTAAATATG
Statistics
Matches: 162, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 161 0.99
121 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (121 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGCTCAAATTATATTT
TATAGTATCATATATTATGATTTGAGTAAACTCATATAAGAATATTAATTATTAAG
Found at i:21766075 original size:16 final size:16
Alignment explanation
Indices: 21766056--21766097 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
21766046 GCTATTACGT
21766056 CTCTATTCCATTACT-C
1 CTCTATTCCATTA-TGC
*
21766072 CTCTATTTCATTATGC
1 CTCTATTCCATTATGC
*
21766088 CTCCATTCCA
1 CTCTATTCCA
21766098 ATACAGCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.19, C:0.36, G:0.02, T:0.43
Consensus pattern (16 bp):
CTCTATTCCATTATGC
Found at i:21768875 original size:29 final size:29
Alignment explanation
Indices: 21768838--21768898 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
21768828 AATTGTTCTT
21768838 TTAATGGAGTTCATCTTGGTTTAACTTTC
1 TTAATGGAGTTCATCTTGGTTTAACTTTC
21768867 TTAATGGAGTTCATCTTGGTTTAACTTTC
1 TTAATGGAGTTCATCTTGGTTTAACTTTC
21768896 TTA
1 TTA
21768899 GGAGAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.49
Consensus pattern (29 bp):
TTAATGGAGTTCATCTTGGTTTAACTTTC
Found at i:21780438 original size:2 final size:2
Alignment explanation
Indices: 21780431--21780458 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21780421 GTTAAAACTC
21780431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21780459 TCACAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21783344 original size:21 final size:22
Alignment explanation
Indices: 21783316--21783379 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
21783306 GCTTTGCCGG
21783316 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
* ** *
21783338 T-AGGCACCACGTGTGTCAT-T
1 TCAGGCACTATATGTGTCGTAT
* *
21783358 TCGGGCACTTTATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
21783380 ACTGCTTCTG
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAGGCACTATATGTGTCGTAT
Found at i:21783641 original size:23 final size:23
Alignment explanation
Indices: 21783615--21783771 Score: 137
Period size: 23 Copynumber: 7.1 Consensus size: 23
21783605 GGATTCGCTG
*
21783615 ATCAGGCACTTTATGTGTCATAT
1 ATCAGGCACTTTATGTGTCGTAT
*
21783638 ATCAGGAACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* ****
21783661 TTCAGGCACCACGTGTGTCGT-T
1 ATCAGGCACTTTATGTGTCGTAT
*
21783683 -TCAGGCAC-TTATGTGTTGTAT
1 ATCAGGCACTTTATGTGTCGTAT
*
21783704 ATCAAGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* * * **
21783727 TTCAGACACCTCGTGTGTCG--T
1 ATCAGGCACTTTATGTGTCGTAT
*
21783748 ATCAGGCAC-TTATGTATCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
21783770 AT
1 AT
21783772 TGATCAGGTA
Statistics
Matches: 104, Mismatches: 25, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
20 14 0.13
21 17 0.16
22 11 0.11
23 62 0.60
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:21783721 original size:43 final size:46
Alignment explanation
Indices: 21783615--21783771 Score: 130
Period size: 43 Copynumber: 3.5 Consensus size: 46
21783605 GGATTCGCTG
*
21783615 ATCAGGCACTTTATGTGTCATATATCAGGAACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTATATCAGGAACTTTATGTGTCGTAT
* **** * *
21783661 TTCAGGCACCACGTGTGTCGT-T-TCAGGCAC-TTATGTGTTGTAT
1 ATCAGGCACTTTATGTGTCGTATATCAGGAACTTTATGTGTCGTAT
* * * **
21783704 ATCAAGCACTTTATGTGTCGTATTTCA-GACACCTCGTGTGTCG--T
1 ATCAGGCACTTTATGTGTCGTATATCAGGA-ACTTTATGTGTCGTAT
*
21783748 ATCAGGCAC-TTATGTATCGTATAT
1 ATCAGGCACTTTATGTGTCGTATAT
21783772 TGATCAGGTA
Statistics
Matches: 86, Mismatches: 21, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
43 40 0.47
44 18 0.21
45 6 0.07
46 22 0.26
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (46 bp):
ATCAGGCACTTTATGTGTCGTATATCAGGAACTTTATGTGTCGTAT
Found at i:21783723 original size:66 final size:66
Alignment explanation
Indices: 21783615--21783771 Score: 233
Period size: 66 Copynumber: 2.4 Consensus size: 66
21783605 GGATTCGCTG
* * *
21783615 ATCAGGCACTTTATGTGTCATATATCAGGAACTTTATGTGTCGTATTTCAGGCACCACGTGTGTC
1 ATCAGGCAC-TTATGTGTCGTATATCAAGAACTTTATGTGTCGTATTTCAGACACCACGTGTGTC
21783680 GT
65 GT
* * * *
21783682 TTCAGGCACTTATGTGTTGTATATCAAGCACTTTATGTGTCGTATTTCAGACACCTCGTGTGTCG
1 ATCAGGCACTTATGTGTCGTATATCAAGAACTTTATGTGTCGTATTTCAGACACCACGTGTGTCG
21783747 T
66 T
*
21783748 ATCAGGCACTTATGTATCGTATAT
1 ATCAGGCACTTATGTGTCGTATAT
21783772 TGATCAGGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
66 72 0.90
67 8 0.10
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (66 bp):
ATCAGGCACTTATGTGTCGTATATCAAGAACTTTATGTGTCGTATTTCAGACACCACGTGTGTCG
T
Found at i:21788751 original size:45 final size:45
Alignment explanation
Indices: 21788687--21788845 Score: 158
Period size: 45 Copynumber: 3.6 Consensus size: 45
21788677 TACTGAGTAT
* ***
21788687 CATTGATTATAAAGGTGGTTGCTATATGTTGATTCCACCGGGTAC
1 CATTGATTATAAAGGTGGTTGCTATATGATGATTCCACCGAAAAC
* * * * *
21788732 CATTGATTATAAAAGTGGTTGCTATGTGCTGACTCCACCGAAAAT
1 CATTGATTATAAAGGTGGTTGCTATATGATGATTCCACCGAAAAC
** * * *
21788777 CATTGAAAATAAAGGTGGTTGCCATATGATGATTCCACCGAATAT
1 CATTGATTATAAAGGTGGTTGCTATATGATGATTCCACCGAAAAC
* * *
21788822 AATTAATTATAAGGGTGG-TGCTAT
1 CATTGATTATAAAGGTGGTTGCTAT
21788846 GTGCTGATCC
Statistics
Matches: 92, Mismatches: 22, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
44 5 0.05
45 87 0.95
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (45 bp):
CATTGATTATAAAGGTGGTTGCTATATGATGATTCCACCGAAAAC
Found at i:21788840 original size:90 final size:88
Alignment explanation
Indices: 21788685--21788857 Score: 229
Period size: 90 Copynumber: 1.9 Consensus size: 88
21788675 TGTACTGAGT
** * * ** * *
21788685 ATCATTGATTATAAAGGTGGTTGCTATATGTTGATTCCACCGGGTACCATTGATTATAAAAGTGG
1 ATCATTGAAAATAAAGGTGGTTGCCATATGATGATTCCACCGAATACAATTAATTATAAAAGTGG
21788750 TTGCTATGTGCTGACTCCACCGAAA
66 -TGCTATGTGCTGA-TCCACCGAAA
* **
21788775 ATCATTGAAAATAAAGGTGGTTGCCATATGATGATTCCACCGAATATAATTAATTATAAGGGTGG
1 ATCATTGAAAATAAAGGTGGTTGCCATATGATGATTCCACCGAATACAATTAATTATAAAAGTGG
21788840 TGCTATGTGCTGATCCAC
66 TGCTATGTGCTGATCCAC
21788858 AGTGTAACGG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
88 5 0.07
89 13 0.18
90 54 0.75
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (88 bp):
ATCATTGAAAATAAAGGTGGTTGCCATATGATGATTCCACCGAATACAATTAATTATAAAAGTGG
TGCTATGTGCTGATCCACCGAAA
Found at i:21793564 original size:23 final size:25
Alignment explanation
Indices: 21793513--21793565 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
21793503 TCTTTGTGAG
* *
21793513 CTTCCTGATTAGTGGCTCTCCTGAG
1 CTTCCTGATTAGTGGCTCGCCTGAA
*
21793538 CTTCCTGA-TA-TGGCTCGCTTGAA
1 CTTCCTGATTAGTGGCTCGCCTGAA
21793561 CTTCC
1 CTTCC
21793566 CAATATATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.60
24 2 0.08
25 8 0.32
ACGTcount: A:0.13, C:0.30, G:0.21, T:0.36
Consensus pattern (25 bp):
CTTCCTGATTAGTGGCTCGCCTGAA
Found at i:21793635 original size:24 final size:24
Alignment explanation
Indices: 21793608--21793725 Score: 87
Period size: 25 Copynumber: 4.8 Consensus size: 24
21793598 GTTTGTTCGA
*
21793608 AGCTACCCGTTATTGGCT-TGTATG
1 AGCTTCCCGTTATTGGCTCT-TATG
21793632 AGCTTCCCGATTA-TGGCTCTTATG
1 AGCTTCCCG-TTATTGGCTCTTATG
* * * ** *
21793656 AGCTTCTCGTTATATAGCCCGAATA
1 AGCTTCCCGTTAT-TGGCTCTTATG
* *
21793681 AGCTTCCTGTTATATGGCTCATATG
1 AGCTTCCCGTTAT-TGGCTCTTATG
*
21793706 AGCTTCCTGTTATATGGCTC
1 AGCTTCCCGTTAT-TGGCTC
21793726 GAGAGAGAGC
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
23 3 0.04
24 25 0.33
25 48 0.63
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.37
Consensus pattern (24 bp):
AGCTTCCCGTTATTGGCTCTTATG
Found at i:21793709 original size:25 final size:25
Alignment explanation
Indices: 21793628--21793725 Score: 103
Period size: 25 Copynumber: 4.0 Consensus size: 25
21793618 TATTGGCTTG
* * *
21793628 TATGAGCTTCCCGAT-TATGGCTCT
1 TATGAGCTTCCTGTTATATGGCTCA
* *
21793652 TATGAGCTT-CTCGTTATATAGCCCGA
1 TATGAGCTTCCT-GTTATATGGCTC-A
*
21793678 -ATAAGCTTCCTGTTATATGGCTCA
1 TATGAGCTTCCTGTTATATGGCTCA
21793702 TATGAGCTTCCTGTTATATGGCTC
1 TATGAGCTTCCTGTTATATGGCTC
21793726 GAGAGAGAGC
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
23 1 0.02
24 12 0.20
25 45 0.75
26 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.38
Consensus pattern (25 bp):
TATGAGCTTCCTGTTATATGGCTCA
Found at i:21794744 original size:31 final size:32
Alignment explanation
Indices: 21794699--21794761 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
21794689 AGATAATTTT
21794699 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
21794731 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
21794762 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTG
Found at i:21800881 original size:31 final size:32
Alignment explanation
Indices: 21800836--21800898 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
21800826 AGATAATTTT
21800836 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
21800868 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
21800899 GAATTGGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTG
Done.