Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 75 of 91
Found at i:12480403 original size:14 final size:14
Alignment explanation
Indices: 12480384--12480435 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
12480374 TTCAAACCTC
12480384 AAACCCTAAAATCA
1 AAACCCTAAAATCA
* *
12480398 AAACCC-CAAATCTC
1 AAACCCTAAAATC-A
*
12480412 AAACTCTAAAATCA
1 AAACCCTAAAATCA
*
12480426 AAAACCTAAA
1 AAACCCTAAA
12480436 CCCCAAAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 5 0.17
14 19 0.66
15 5 0.17
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:12483487 original size:19 final size:20
Alignment explanation
Indices: 12483460--12483510 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
12483450 GACTTTCCGG
* *
12483460 CCAACTTCCGGTG-AAATTT
1 CCAAATTCCGGCGAAAATTT
12483479 CCAAATTCCGGCGAAAATTT
1 CCAAATTCCGGCGAAAATTT
12483499 CCAGAA-TCCGGC
1 CCA-AATTCCGGC
12483511 ATCGGTGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 15 0.54
21 2 0.07
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (20 bp):
CCAAATTCCGGCGAAAATTT
Found at i:12483871 original size:13 final size:12
Alignment explanation
Indices: 12483833--12483882 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
12483823 CCGCTCCAGG
12483833 TTTT-TTTTTT-
1 TTTTATTTTTTA
*
12483843 TTTT-TTTTCTTT
1 TTTTATTTT-TTA
12483855 TTTTATTTGTTTA
1 TTTTATTT-TTTA
12483868 TTTTATTTTTTA
1 TTTTATTTTTTA
12483880 TTT
1 TTT
12483883 ATTAGATTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 8 0.23
11 2 0.06
12 11 0.31
13 13 0.37
14 1 0.03
ACGTcount: A:0.08, C:0.02, G:0.02, T:0.88
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:12483883 original size:16 final size:15
Alignment explanation
Indices: 12483837--12483885 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
12483827 TCCAGGTTTT
* *
12483837 TTTTTTTTTTTTTTC
1 TTTTTTTTTTATTTA
*
12483852 TTTTTTTATTTGTTTA
1 TTTTTTT-TTTATTTA
12483868 TTTTATTTTTTATTTA
1 TTTT-TTTTTTATTTA
12483884 TT
1 TT
12483886 AGATTAGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 7 0.24
16 19 0.66
17 3 0.10
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTATTTA
Found at i:12484046 original size:57 final size:57
Alignment explanation
Indices: 12483964--12484368 Score: 461
Period size: 57 Copynumber: 6.7 Consensus size: 57
12483954 AAAATTCCAA
* *
12483964 AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAATTAAATTTC
1 AAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* * *
12484022 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTAAAAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT------C
* * *
12484085 AAAAAAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* * *
12484142 CAAAAACTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTT-C
12484205 AAAAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAGAATCAAAATTTC
1 ---AAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AAT--AAATTTC
*
12484268 AAAAAAAAATATTTTTGGGGAAAAGTTGAAATTATCAATTTTCCTTAGAAATAAATTTTC
1 --AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
* *
12484328 AAAAAAATGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAT-ATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
12484369 TCCTAAAAAA
Statistics
Matches: 301, Mismatches: 24, Indels: 43
0.82 0.07 0.12
Matches are distributed among these distances:
57 86 0.29
58 13 0.04
59 32 0.11
60 6 0.02
61 40 0.13
62 23 0.08
63 54 0.18
64 6 0.02
66 5 0.02
67 36 0.12
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (57 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
Found at i:12484098 original size:120 final size:119
Alignment explanation
Indices: 12483962--12484368 Score: 516
Period size: 120 Copynumber: 3.4 Consensus size: 119
12483952 AAAAAATTCC
*
12483962 AAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAATTAAATTTCCAAAA
1 AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAATTAAATTTCCAAAA
* *
12484027 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTAAAA
66 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAATAAATTT-CAA
* * *
12484082 AAAAAAAAAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTCCAAAA
1 AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAATTAAATTTCCAAAA
* * *
12484147 ACTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCCA
66 AATATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTTCCT--AAG--AAATAAATTTCAA
* * * *
12484206 AAAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAATCAAAATTTCAAA
1 AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAT-TAAATTTC--C
* *
12484271 AAAAAATATTTTTGGGGAAAAGTTGAAATTATCAATTTTCCTTAGAAATAAATTTTC--
62 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAATAAA-TTTCAA
*** *
12484328 AAAAAAATGGT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
12484369 TCCTAAAAAA
Statistics
Matches: 253, Mismatches: 24, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
120 115 0.45
121 10 0.04
122 9 0.04
123 9 0.04
124 49 0.19
125 16 0.06
126 6 0.02
127 6 0.02
128 33 0.13
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (119 bp):
AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAATTAAATTTCCAAAA
AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAATAAATTTCAA
Found at i:12484274 original size:187 final size:180
Alignment explanation
Indices: 12483964--12484382 Score: 532
Period size: 187 Copynumber: 2.3 Consensus size: 180
12483954 AAAATTCCAA
* * *
12483964 AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AATTAAATTTCCA
1 AAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCCA
12484024 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTAAAAAAAAAAA
65 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTT---AAAAAAAA
12484089 AAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-ATTC
127 AAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATATTC
* *
12484142 CAAAAACTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCCAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCC--
* *
12484207 AAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT-TGAGAATCAAAATTT-CAA
64 --AAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGA-AAT--AAATTTAAAA
* * * *
12484270 AAAAAAATATTTTTGGGGAAAAGTTGAAATTATCAATTTTCCTTAGAAATAAATTTTC
123 AAAAAAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATATTC
* * *
12484328 AAAAAAATGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTAAAA-AAAAAT
1 AAAAAAAT-ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAAT
12484383 CATTCTCTCC
Statistics
Matches: 210, Mismatches: 16, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
177 35 0.17
178 5 0.02
180 2 0.01
182 11 0.05
185 52 0.25
186 23 0.11
187 76 0.36
189 6 0.03
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (180 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCCAA
AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTAAAAAAAAAAAC
ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATATTC
Found at i:12487055 original size:20 final size:20
Alignment explanation
Indices: 12487030--12487079 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
12487020 TATATAAAAA
*
12487030 TAATTTTTTAATTAATTATT
1 TAATTTTATAATTAATTATT
* *
12487050 TAATTTTATAATTATTTATA
1 TAATTTTATAATTAATTATT
*
12487070 TATTTTTATA
1 TAATTTTATA
12487080 TATATTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TAATTTTATAATTAATTATT
Found at i:12488240 original size:58 final size:58
Alignment explanation
Indices: 12488157--12488429 Score: 410
Period size: 58 Copynumber: 4.7 Consensus size: 58
12488147 TTTTTTTTAG
* *
12488157 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTTTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
* * *
12488215 GGAAAATTGATACTCTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
* *
12488272 GG-AAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAA-ATATTTTTTTTGAAATTTATTTCTAA
* * *
12488330 GG-AAATTGATACTTTCAACTTTTCCCCCAAAAGTA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTT-CCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
12488387 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
12488430 TGGAACTTTT
Statistics
Matches: 192, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
56 27 0.14
57 54 0.28
58 104 0.54
59 7 0.04
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
Found at i:12488368 original size:115 final size:116
Alignment explanation
Indices: 12488157--12488430 Score: 473
Period size: 115 Copynumber: 2.4 Consensus size: 116
12488147 TTTTTTTTAG
* *
12488157 GGAAAATTGATACTTTCAACTTTTCCCTAAAA-ATATTTTTTTTGAAATTTATTTTTGAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAAA
12488221 TTGATACTCTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
66 TTGATACTCTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
12488272 GG-AAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTTTTTGAAATTTATTTCTGAGG-AAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAAA
* *
12488335 TTGATACTTTCAACTTTTCCCCCAAAAGTATTTTTTGGAAATTTATTTCTAA
66 TTGATACTCTCAACTTTT-CCCCAAAAATATTTTTTGGAAATTTATTTCTAA
12488387 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAATATTTTTTTTT
12488431 GGAACTTTTG
Statistics
Matches: 151, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
114 49 0.32
115 62 0.41
116 25 0.17
117 15 0.10
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.46
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAAA
TTGATACTCTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:12488479 original size:16 final size:15
Alignment explanation
Indices: 12488453--12488607 Score: 57
Period size: 17 Copynumber: 9.6 Consensus size: 15
12488443 TTTTTTTATT
12488453 TAAAGAAAAATAGAAAA
1 TAAA-AAAAATA-AAAA
12488470 TAAAAAAAATAAAAA
1 TAAAAAAAATAAAAA
* * *
12488485 GAAAAGTAAAACAAAAC
1 TAAAA--AAAATAAAAA
*
12488502 TAAAAATAAAT-AAGA
1 TAAAAA-AAATAAAAA
*
12488517 T-AAAAAAATATTAAA
1 TAAAAAAAATA-AAAA
* ** *
12488532 TAAACCTAATCTAATAA
1 TAAA--AAAAATAAAAA
12488549 TAAAATAATAAATAAACAAA
1 T-AAA-AA-AAAT-AA-AAA
*
12488569 TAAAACAAATAAAAA
1 TAAAAAAAATAAAAA
12488584 TTCAAAAAAAA-AAAAA
1 -T-AAAAAAAATAAAAA
12488600 -AAAAAAAA
1 TAAAAAAAA
12488608 AAACCTGGAG
Statistics
Matches: 103, Mismatches: 21, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
13 12 0.12
14 4 0.04
15 18 0.17
16 20 0.19
17 31 0.30
18 10 0.10
19 5 0.05
20 3 0.03
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.16
Consensus pattern (15 bp):
TAAAAAAAATAAAAA
Found at i:12488589 original size:21 final size:21
Alignment explanation
Indices: 12488565--12488604 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12488555 AATAAATAAA
* * *
12488565 CAAATAAAACAAATAAAAATT
1 CAAAAAAAAAAAAAAAAAATT
12488586 CAAAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAA
12488605 AAAAAACCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.10
Consensus pattern (21 bp):
CAAAAAAAAAAAAAAAAAATT
Found at i:12488969 original size:19 final size:20
Alignment explanation
Indices: 12488925--12488971 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
12488915 GAACACCGGT
* *
12488925 GCCGGATTCTGGAAAAATTC
1 GCCGGAATCTGGAAAAATTA
*
12488945 GCCGGAATCTGG-AAATTTA
1 GCCGGAATCTGGAAAAATTA
12488964 GCCGGAAT
1 GCCGGAAT
12488972 TTCGTCGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (20 bp):
GCCGGAATCTGGAAAAATTA
Found at i:12489689 original size:3 final size:3
Alignment explanation
Indices: 12489681--12489725 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12489671 AAAGATATAC
12489681 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12489726 GAATACATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12489739 original size:14 final size:14
Alignment explanation
Indices: 12489650--12489739 Score: 63
Period size: 12 Copynumber: 6.7 Consensus size: 14
12489640 ATCTAATCTG
*
12489650 AATAAAAATA-AAT
1 AATAATAATAGAAT
12489663 AAATAAATAA-AGATAT
1 -AAT-AATAATAGA-AT
12489679 ACATAATAAT--AAT
1 A-ATAATAATAGAAT
12489692 AATAATAAT--AAT
1 AATAATAATAGAAT
12489704 AATAATAAT--AAT
1 AATAATAATAGAAT
12489716 AATAATAATAGAAT
1 AATAATAATAGAAT
12489730 ACATAA-AATA
1 A-ATAATAATA
12489740 CAAAAGAAGA
Statistics
Matches: 67, Mismatches: 1, Indels: 16
0.80 0.01 0.19
Matches are distributed among these distances:
12 32 0.48
13 3 0.04
14 13 0.19
15 15 0.22
16 4 0.06
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (14 bp):
AATAATAATAGAAT
Found at i:12490301 original size:20 final size:20
Alignment explanation
Indices: 12490261--12490303 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12490251 GAGTGATTAA
* *
12490261 AAATTTTAATTTTTTTAAAT
1 AAATTTTAAATTTTATAAAT
*
12490281 AAATTTTAAATTTTATGAAT
1 AAATTTTAAATTTTATAAAT
12490301 AAA
1 AAA
12490304 AAAATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTTTAAATTTTATAAAT
Found at i:12490644 original size:17 final size:18
Alignment explanation
Indices: 12490612--12490646 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12490602 TTTTATATCA
*
12490612 AAATTTAAATTCTTTTAT
1 AAATTAAAATTCTTTTAT
12490630 AAATTAAAATT-TTTTAT
1 AAATTAAAATTCTTTTAT
12490647 TTTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTAAAATTCTTTTAT
Found at i:12492602 original size:3 final size:3
Alignment explanation
Indices: 12492594--12492634 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
12492584 CAATTCTTAT
**
12492594 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12492635 GTTTAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:12493886 original size:8 final size:8
Alignment explanation
Indices: 12493875--12493899 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12493865 TAAAAAATAA
12493875 TATTTTAT
1 TATTTTAT
12493883 TATTTTAT
1 TATTTTAT
12493891 TATTTTAT
1 TATTTTAT
12493899 T
1 T
12493900 TTTCCTGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:12494019 original size:3 final size:3
Alignment explanation
Indices: 12494011--12494043 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12494001 AATTAAAAAG
12494011 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12494044 ATTTTCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12494183 original size:13 final size:13
Alignment explanation
Indices: 12494165--12494326 Score: 74
Period size: 13 Copynumber: 11.4 Consensus size: 13
12494155 CATGTTTTCT
*
12494165 TTAAACCTTAAAA
1 TTAAACCCTAAAA
12494178 TTAAACCCTAAAA
1 TTAAACCCTAAAA
**
12494191 CCAAACCCTAAAA
1 TTAAACCCTAAAA
*
12494204 TTTTTAAACCCCAAAA
1 ---TTAAACCCTAAAA
* *
12494220 CCTCTAAACCTTCAAA
1 --T-TAAACCCTAAAA
* *
12494236 TTAAA-TCTCAAACC
1 TTAAACCCT-AAA-A
*
12494250 TTCAAACCCTATAA
1 TT-AAACCCTAAAA
* *
12494264 TTAAACCCCAAACC
1 TTAAACCCTAAA-A
12494278 TCTAAACCCTAAAA
1 T-TAAACCCTAAAA
12494292 TTAAACCCTAAATA
1 TTAAACCCTAAA-A
12494306 TTCTAAACCCCTAAAA
1 -T-TAAA-CCCTAAAA
*
12494322 CTAAA
1 TTAAA
12494327 ACTTCAAGCC
Statistics
Matches: 111, Mismatches: 24, Indels: 27
0.69 0.15 0.17
Matches are distributed among these distances:
12 1 0.01
13 48 0.43
14 12 0.11
15 17 0.15
16 26 0.23
17 7 0.06
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAACCCTAAAA
Found at i:12494373 original size:88 final size:88
Alignment explanation
Indices: 12494281--12494442 Score: 236
Period size: 88 Copynumber: 1.8 Consensus size: 88
12494271 CCAAACCTCT
* * * * * *
12494281 AAACCCTAAAAT-TAAACCCTAAATATTCTAAACCCCTAAAACTAAAACTTCAAGCCTCAAACCT
1 AAACCCAAAAATCAAAACCCTAAATACTCTAAA-CCCTAAAACCAAAACTTCAAACCTCAAACCC
12494345 TAAAATCAAATCTCTAAAACATTA
65 TAAAATCAAATCTCTAAAACATTA
* *
12494369 AAACCCAAAAATCAAAACCCTAAATCCTCTAAACCCTAAAACCAAAACTTCAAACCTTAAACCCT
1 AAACCCAAAAATCAAAACCCTAAATACTCTAAACCCTAAAACCAAAACTTCAAACCTCAAACCCT
12494434 AAAATCAAA
66 AAAATCAAA
12494443 ACCCTAAATC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
88 48 0.74
89 17 0.26
ACGTcount: A:0.51, C:0.28, G:0.01, T:0.20
Consensus pattern (88 bp):
AAACCCAAAAATCAAAACCCTAAATACTCTAAACCCTAAAACCAAAACTTCAAACCTCAAACCCT
AAAATCAAATCTCTAAAACATTA
Found at i:12494450 original size:88 final size:88
Alignment explanation
Indices: 12494243--12494450 Score: 235
Period size: 88 Copynumber: 2.4 Consensus size: 88
12494233 AAATTAAATC
* * * * * *
12494243 TCAAACCTTCAAACCCTATAAT-TAAACCC-CAAACCTCTAAACCCTAAAATTAAACCCTAAATA
1 TCAAACCTT-AAACCCTAAAATCAAAACCCTAAAACATCTAAACCCAAAAATAAAACCCTAAATA
* *
12494306 TTCTAAACCCCTAAAACTAAAACT
65 CTCTAAACCCCTAAAACCAAAACT
* * * * *
12494330 TCAAGCCTCAAACCTTAAAATCAAATCTCTAAAACAT-TAAAACCCAAAAATCAAAACCCTAAAT
1 TCAAACCTTAAACCCTAAAATCAAAACCCTAAAACATCT-AAACCCAAAAAT-AAAACCCTAAAT
*
12494394 CCTCTAAA-CCCTAAAACCAAAACT
64 ACTCTAAACCCCTAAAACCAAAACT
12494418 TCAAACCTTAAACCCTAAAATCAAAACCCTAAA
1 TCAAACCTTAAACCCTAAAATCAAAACCCTAAA
12494451 TCTCAAACTC
Statistics
Matches: 98, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
86 10 0.10
87 12 0.12
88 59 0.60
89 17 0.17
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (88 bp):
TCAAACCTTAAACCCTAAAATCAAAACCCTAAAACATCTAAACCCAAAAATAAAACCCTAAATAC
TCTAAACCCCTAAAACCAAAACT
Found at i:12494458 original size:28 final size:28
Alignment explanation
Indices: 12494167--12494485 Score: 141
Period size: 28 Copynumber: 11.1 Consensus size: 28
12494157 TGTTTTCTTT
* * *
12494167 AAACCTTAAAAT-TAAACCCTAAAAC-C
1 AAACCCTAAAATCAAAACCCTAAACCTC
* * *
12494193 AAACCCTAAAATTTTTAAACCCCAAAACCTC
1 AAACCCTAAAA---TCAAAACCCTAAACCTC
* * * * *
12494224 TAAACCTTCAAATTAAATCTC-AAACCTTC
1 -AAACCCTAAAATCAAAACCCTAAACC-TC
* * *
12494253 AAACCCTATAAT-TAAACCCCAAACCTC
1 AAACCCTAAAATCAAAACCCTAAACCTC
* **
12494280 TAAACCCTAAAAT-TAAACCCTAAATATTC
1 -AAACCCTAAAATCAAAACCCTAAA-CCTC
* *
12494309 TAAACCCCTAAAA-CTAAAA-CTTCAAGCCTC
1 -AAA-CCCTAAAATC-AAAACCCT-AAACCTC
* * * * *
12494339 AAACCTTAAAATCAAATCTCTAAAACATTA
1 AAACCCTAAAATCAAAACCCT-AAAC-CTC
*
12494369 AAACCCAAAAATCAAAACCCTAAATCCTC
1 AAACCCTAAAATCAAAACCCTAAA-CCTC
* * *
12494398 TAAACCCTAAAACCAAAA-CTTCAAACCTT
1 -AAACCCTAAAATCAAAACCCT-AAACCTC
*
12494427 AAACCCTAAAATCAAAACCCTAAATCTC
1 AAACCCTAAAATCAAAACCCTAAACCTC
* * * *
12494455 AAACTCTAAAATAAAAAACCTAAACCCC
1 AAACCCTAAAATCAAAACCCTAAACCTC
12494483 AAA
1 AAA
12494486 ATTTGAAACT
Statistics
Matches: 221, Mismatches: 51, Indels: 40
0.71 0.16 0.13
Matches are distributed among these distances:
26 10 0.05
27 6 0.03
28 97 0.44
29 35 0.16
30 58 0.26
31 6 0.03
32 9 0.04
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.21
Consensus pattern (28 bp):
AAACCCTAAAATCAAAACCCTAAACCTC
Found at i:12494466 original size:15 final size:14
Alignment explanation
Indices: 12494339--12494478 Score: 68
Period size: 14 Copynumber: 9.7 Consensus size: 14
12494329 TTCAAGCCTC
*
12494339 AAACCTTAAAATCA
1 AAACCCTAAAATCA
* * *
12494353 AATCTCTAAAACATTA
1 AAACCCT-AAA-ATCA
*
12494369 AAACCCAAAAATCA
1 AAACCCTAAAATCA
* *
12494383 AAACCCTAAATCCTCT
1 AAACCCTAAA--ATCA
*
12494399 AAACCCTAAAACCA
1 AAACCCTAAAATCA
* * * *
12494413 AAA-CTTCAAACCTT
1 AAACCCTAAAATC-A
12494427 AAACCCTAAAATCA
1 AAACCCTAAAATCA
*
12494441 AAACCCT-AAATCTC
1 AAACCCTAAAATC-A
* *
12494455 AAACTCTAAAATAA
1 AAACCCTAAAATCA
*
12494469 AAAACCTAAA
1 AAACCCTAAA
12494479 CCCCAAAATT
Statistics
Matches: 91, Mismatches: 27, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
13 12 0.13
14 44 0.48
15 16 0.18
16 19 0.21
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:12494579 original size:25 final size:24
Alignment explanation
Indices: 12494549--12494600 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
12494539 CAAAACTTGA
* * *
12494549 AAATCCCAATTTCTAAAAAGCCCAT
1 AAATCCAAAATTCTAAAAAACCC-T
12494574 AAATCCAAAATTCTAAAAAACCCT
1 AAATCCAAAATTCTAAAAAACCCT
12494598 AAA
1 AAA
12494601 AAATCATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.52, C:0.25, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATCCAAAATTCTAAAAAACCCT
Found at i:12498896 original size:13 final size:12
Alignment explanation
Indices: 12498865--12498898 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
12498855 ATTTTTATAC
12498865 TTTTTTATATTA
1 TTTTTTATATTA
12498877 -TTTTTATATTA
1 TTTTTTATATTA
12498888 TTTTATTATAT
1 TTTT-TTATAT
12498899 CATATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 3 0.15
13 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTATATTA
Found at i:12501540 original size:34 final size:35
Alignment explanation
Indices: 12501492--12501562 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 35
12501482 ATTTTATTTT
*
12501492 TTTTCATTCAAATTGAATCAAATTCGTATCTTTAA
1 TTTTCATTCAAATTGAATCAAATTCATATCTTTAA
*
12501527 TTTT-ATTCAAATTGAATCAATTTCATATCTTTAA
1 TTTTCATTCAAATTGAATCAAATTCATATCTTTAA
12501561 TT
1 TT
12501563 ATTTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (35 bp):
TTTTCATTCAAATTGAATCAAATTCATATCTTTAA
Found at i:12502322 original size:22 final size:22
Alignment explanation
Indices: 12502268--12502322 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
12502258 AGACTATGTA
* *
12502268 ATTTGTATATTTTTTAATATAT
1 ATTTATATATTTTATAATATAT
* *
12502290 TTTTATATATTTTATCATATAAT
1 ATTTATATATTTTATAATAT-AT
12502313 ATTT-TATATT
1 ATTTATATATT
12502323 CACTTTCTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTATATATTTTATAATATAT
Found at i:12504930 original size:17 final size:17
Alignment explanation
Indices: 12504908--12504944 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12504898 AGATATTCAC
* *
12504908 GTATTATATTATCATTT
1 GTATTATATCATCATAT
12504925 GTATTATATCATCATAT
1 GTATTATATCATCATAT
12504942 GTA
1 GTA
12504945 ATACATGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (17 bp):
GTATTATATCATCATAT
Found at i:12508930 original size:31 final size:29
Alignment explanation
Indices: 12508895--12508954 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
12508885 AAGGATAATT
* *
12508895 TTTAAATTATAGTAAAATATTTAATTTGATA
1 TTTAAATTATA--AAAATATCTAATGTGATA
*
12508926 TTTAAATTTTAAAAATATCTAATGTGATA
1 TTTAAATTATAAAAATATCTAATGTGATA
12508955 GCTGAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.62
31 10 0.38
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (29 bp):
TTTAAATTATAAAAATATCTAATGTGATA
Found at i:12509107 original size:29 final size:31
Alignment explanation
Indices: 12509068--12509137 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
12509058 TAATAAATTC
*
12509068 ATAATTTAAATACCATATTAAAAATTTT-TT
1 ATAATTTAAATACCACATTAAAAATTTTATT
* *
12509098 AT-ATTTAAATATCACATTAAATATTTTATT
1 ATAATTTAAATACCACATTAAAAATTTTATT
12509128 ATAATTTAAA
1 ATAATTTAAA
12509138 AATCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 22 0.63
30 6 0.17
31 7 0.20
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (31 bp):
ATAATTTAAATACCACATTAAAAATTTTATT
Found at i:12509144 original size:29 final size:28
Alignment explanation
Indices: 12509084--12509144 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
12509074 TAAATACCAT
*
12509084 ATTAAAAATTTTTTATATTTAAATATCAC
1 ATTAAAAATTTTTTATATTTAAAAAT-AC
*
12509113 ATTAAATATTTTATTATAATTTAAAAAT-C
1 ATTAAAAATTTT-TTAT-ATTTAAAAATAC
12509142 ATT
1 ATT
12509145 TATGATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 15 0.54
30 4 0.14
31 9 0.32
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTAAAAATTTTTTATATTTAAAAATAC
Found at i:12511367 original size:3 final size:3
Alignment explanation
Indices: 12511353--12511383 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
12511343 ATCAAGCACT
*
12511353 ACA ACA ATA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
12511384 ACTATGCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
ACA
Found at i:12517042 original size:2 final size:2
Alignment explanation
Indices: 12517035--12517077 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
12517025 GCAAAAGAAT
* *
12517035 TA TA TA TA T- TA TA TA TA CA TA CA 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
12517076 TA
1 TA
12517078 GAATTTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12520069 original size:145 final size:147
Alignment explanation
Indices: 12519796--12520089 Score: 448
Period size: 145 Copynumber: 2.0 Consensus size: 147
12519786 AAAATAGATA
**
12519796 TTCAAATTAAATTTAACATTTTAAAATAAGATACAATAATACCAAACGAATGTGATATAAAAATA
1 TTCAAATTAAATTTAACATTTTAAAATAAGATACAATAATACCAAACGAATACGATATAAAAATA
* * *
12519861 GGATACAAAAATAATATGACCTAAAATTTTAATAATAATTATATATGAGTTCAATAAAATTAAAA
66 AGATACAAAAATAATATGACCTAAAATTTTAACAATAATTATATATGAGTTCAACAAAATTAAAA
12519926 ATAT-T-TTTTATATTT
131 ATATATATTTTATATTT
* ** * *
12519941 TTCAAATTAAATTTAATATTTTAAAATAAGATATGATGATACTAAACGAATACGATATAAAAATA
1 TTCAAATTAAATTTAACATTTTAAAATAAGATACAATAATACCAAACGAATACGATATAAAAATA
* * *
12520006 AGATACAAAAATAATATGACTTAAAATTTTAACAATAATTATATATGAGTTTAACAAATTTAAAA
66 AGATACAAAAATAATATGACCTAAAATTTTAACAATAATTATATATGAGTTCAACAAAATTAAAA
*
12520071 ATATATATTTTATTTTT
131 ATATATATTTTATATTT
12520088 TT
1 TT
12520090 ATATCGATAC
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
145 121 0.91
146 1 0.01
147 11 0.08
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.37
Consensus pattern (147 bp):
TTCAAATTAAATTTAACATTTTAAAATAAGATACAATAATACCAAACGAATACGATATAAAAATA
AGATACAAAAATAATATGACCTAAAATTTTAACAATAATTATATATGAGTTCAACAAAATTAAAA
ATATATATTTTATATTT
Found at i:12520362 original size:14 final size:15
Alignment explanation
Indices: 12520340--12520368 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12520330 TATTTTTTTA
12520340 ATTGTATTATTAATT
1 ATTGTATTATTAATT
12520355 ATTG-ATTATTAATT
1 ATTGTATTATTAATT
12520369 TATTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
ATTGTATTATTAATT
Found at i:12521335 original size:32 final size:33
Alignment explanation
Indices: 12521289--12521375 Score: 113
Period size: 32 Copynumber: 2.6 Consensus size: 33
12521279 AAAGAAATTT
** *
12521289 ACTTTATTTTATTATAAGTAATAAAGCAAATAG
1 ACTTTATTTTATTATAAAAAATAAAACAAATAG
* *
12521322 ATTTTA-TTTATTATAAAAAATAAAACAAATCG
1 ACTTTATTTTATTATAAAAAATAAAACAAATAG
12521354 ACTTTATTTTATTATAATAAAA
1 ACTTTATTTTATTATAA-AAAA
12521376 ATATATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 27 0.59
33 15 0.33
34 4 0.09
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (33 bp):
ACTTTATTTTATTATAAAAAATAAAACAAATAG
Found at i:12521963 original size:15 final size:15
Alignment explanation
Indices: 12521936--12521964 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12521926 TCGAGCTACG
12521936 CAAATTCGAGCTTGT
1 CAAATTCGAGCTTGT
12521951 CAAATTCGAGCTTG
1 CAAATTCGAGCTTG
12521965 ATTCGATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (15 bp):
CAAATTCGAGCTTGT
Found at i:12522512 original size:2 final size:2
Alignment explanation
Indices: 12522505--12522532 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12522495 CTCAAATTCC
12522505 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
12522533 GAGAGAGAGA
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):
TA
Found at i:12522537 original size:2 final size:2
Alignment explanation
Indices: 12522532--12522556 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12522522 ATATATATAT
12522532 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12522557 TCCTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12525099 original size:3 final size:3
Alignment explanation
Indices: 12525093--12525131 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
12525083 TATTTACAAC
* *
12525093 AAT AAT AAT AAT AAC AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12525132 TTATCATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:12525940 original size:30 final size:30
Alignment explanation
Indices: 12525886--12525980 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
12525876 TCAAGGATTC
* * *
12525886 AATTGGAGTGAAAATAGATGTTTAAAAGT-TT
1 AATTGGA-TAAAAATAAATATTTAAAA-TCTT
12525917 AATTGGATAAAAATAAATATTTAAAATCTT
1 AATTGGATAAAAATAAATATTTAAAATCTT
* *
12525947 AATT-GATCCAAAATAAA-ATTT-TAATGCTT
1 AATTGGAT-AAAAATAAATATTTAAAAT-CTT
12525976 AATTG
1 AATTG
12525981 ATTTTAATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
28 3 0.05
29 15 0.27
30 30 0.55
31 7 0.13
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (30 bp):
AATTGGATAAAAATAAATATTTAAAATCTT
Found at i:12525977 original size:29 final size:30
Alignment explanation
Indices: 12525896--12525982 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 30
12525886 AATTGGAGTG
* * *
12525896 AAAATAGATGTTTAAAAGT-TTAATTGGAT-A
1 AAAATAAATATTTAAAA-TCTTAATT-GATCC
12525926 AAAATAAATATTTAAAATCTTAATTGATCC
1 AAAATAAATATTTAAAATCTTAATTGATCC
*
12525956 AAAATAAA-ATTT-TAATGCTTAATTGAT
1 AAAATAAATATTTAAAAT-CTTAATTGAT
12525983 TTTAATAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.06
29 18 0.36
30 29 0.58
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (30 bp):
AAAATAAATATTTAAAATCTTAATTGATCC
Found at i:12526077 original size:23 final size:23
Alignment explanation
Indices: 12526033--12526078 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12526023 GTTCGAGAGT
* *
12526033 TTTATTGACTATTTTATCTTAAA
1 TTTATTGAATATTTTATATTAAA
12526056 TTTATTGAATATTATT-TATTAAA
1 TTTATTGAATATT-TTATATTAAA
12526079 AATAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTATTGAATATTTTATATTAAA
Found at i:12531039 original size:22 final size:22
Alignment explanation
Indices: 12531011--12531053 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12531001 GAACTAAATT
12531011 CCAATAACACAAGTATTAGTTA
1 CCAATAACACAAGTATTAGTTA
12531033 CCAATAACACAAGTATTAGTT
1 CCAATAACACAAGTATTAGTT
12531054 GTAAGTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (22 bp):
CCAATAACACAAGTATTAGTTA
Found at i:12539607 original size:10 final size:10
Alignment explanation
Indices: 12539592--12539616 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12539582 CTTTCCAATC
12539592 TTTCCATCAT
1 TTTCCATCAT
12539602 TTTCCATCAT
1 TTTCCATCAT
12539612 TTTCC
1 TTTCC
12539617 CCATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTCCATCAT
Found at i:12539675 original size:28 final size:27
Alignment explanation
Indices: 12539619--12539670 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
12539609 CATTTTCCCC
* *
12539619 ATTTTATTTTTTTATTTCATAAAGAAG
1 ATTTTAATTTTTTATTTCATAAAAAAG
12539646 ATTTTAATTTTTTATTT-ATAAAAAA
1 ATTTTAATTTTTTATTTCATAAAAAA
12539671 TAGATACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (27 bp):
ATTTTAATTTTTTATTTCATAAAAAAG
Found at i:12541826 original size:98 final size:99
Alignment explanation
Indices: 12541656--12541852 Score: 324
Period size: 98 Copynumber: 2.0 Consensus size: 99
12541646 GTATCCTTAA
* *
12541656 TAATTTCACTTGGGAAATTATCTTGTTGCTATGATGTTAGATCATACTCTGTTATAATATTGGTA
1 TAATTTCACTTGGGAAATTATCTTGTTGCTATAATGTTAGAGCATACTCTGTTATAATATTGGTA
* **
12541721 TCTATCTTGTTGTTTATGGTTAAA-GGAAAAGCT
66 TCCATCTTGTCATTTATGGTTAAATGGAAAAGCT
* *
12541754 TAATTTCATTTGGGAAATTATCTTGTTGCTATAATGTTAGAGCATACTCTGTTATAATATTGGTG
1 TAATTTCACTTGGGAAATTATCTTGTTGCTATAATGTTAGAGCATACTCTGTTATAATATTGGTA
12541819 TCCATCTTGTCATTTATGGTTAAATGGAAAAGCT
66 TCCATCTTGTCATTTATGGTTAAATGGAAAAGCT
12541853 CGTATGATTT
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 82 0.90
99 9 0.10
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (99 bp):
TAATTTCACTTGGGAAATTATCTTGTTGCTATAATGTTAGAGCATACTCTGTTATAATATTGGTA
TCCATCTTGTCATTTATGGTTAAATGGAAAAGCT
Found at i:12558911 original size:17 final size:17
Alignment explanation
Indices: 12558889--12558924 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12558879 TCATTCATTC
12558889 TATTTATTTTTAAAAGA
1 TATTTATTTTTAAAAGA
12558906 TATTTATTTTTAAAAGA
1 TATTTATTTTTAAAAGA
12558923 TA
1 TA
12558925 GATTATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTTATTTTTAAAAGA
Found at i:12558930 original size:18 final size:17
Alignment explanation
Indices: 12558892--12558930 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
12558882 TTCATTCTAT
*
12558892 TTATTTTTAAAAGATAT
1 TTATTTTTAAAAGATAA
12558909 TTATTTTTAAAAGATAGA
1 TTATTTTTAAAAGATA-A
12558927 TTAT
1 TTAT
12558931 GGAAAAAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
TTATTTTTAAAAGATAA
Found at i:12559784 original size:8 final size:8
Alignment explanation
Indices: 12559771--12559872 Score: 51
Period size: 8 Copynumber: 12.4 Consensus size: 8
12559761 ATTACACACA
12559771 TATATATG
1 TATATATG
*
12559779 TATATATA
1 TATATATG
* * *
12559787 AACATATA
1 TATATATG
12559795 TAATATATATG
1 T-ATAT--ATG
*
12559806 TACATATG
1 TATATATG
**
12559814 TATATACA
1 TATATATG
* * *
12559822 CATGTATA
1 TATATATG
12559830 TATATATG
1 TATATATG
*
12559838 TATGTATG
1 TATATATG
*
12559846 TATGTATG
1 TATATATG
*
12559854 TATGTATG
1 TATATATG
*
12559862 TATGTATG
1 TATATATG
12559870 TAT
1 TAT
12559873 GTTTGCTACA
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
8 65 0.88
9 3 0.04
10 3 0.04
11 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (8 bp):
TATATATG
Found at i:12559821 original size:12 final size:12
Alignment explanation
Indices: 12559791--12559840 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
12559781 TATATAAACA
*
12559791 TATATA-ATATA
1 TATATACATATG
*
12559802 TATGTACATATG
1 TATATACATATG
*
12559814 TATATACACATG
1 TATATACATATG
*
12559826 TATATATATATG
1 TATATACATATG
12559838 TAT
1 TAT
12559841 GTATGTATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 5 0.16
12 27 0.84
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (12 bp):
TATATACATATG
Found at i:12559841 original size:4 final size:4
Alignment explanation
Indices: 12559823--12559874 Score: 86
Period size: 4 Copynumber: 13.0 Consensus size: 4
12559813 GTATATACAC
* *
12559823 ATGT ATAT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
12559871 ATGT
1 ATGT
12559875 TTGCTACATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:12561451 original size:28 final size:28
Alignment explanation
Indices: 12561411--12561466 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
12561401 CTCTTTTTTG
*
12561411 ATTATCGAGGAATCTCTTTTACTTGTAA
1 ATTATCGAGGAATCTCCTTTACTTGTAA
*
12561439 ATTATTGAGGAATCTCCTTTACTTGTAA
1 ATTATCGAGGAATCTCCTTTACTTGTAA
12561467 TACATGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (28 bp):
ATTATCGAGGAATCTCCTTTACTTGTAA
Found at i:12561812 original size:14 final size:15
Alignment explanation
Indices: 12561795--12561824 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12561785 AAAATTTTAA
12561795 ATCGTGTCAT-TTTT
1 ATCGTGTCATATTTT
12561809 ATCGTGTCATATTTT
1 ATCGTGTCATATTTT
12561824 A
1 A
12561825 AATTGATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (15 bp):
ATCGTGTCATATTTT
Found at i:12565768 original size:32 final size:29
Alignment explanation
Indices: 12565710--12565770 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
12565700 CTACTTCCAA
*
12565710 AGAGAAAAAGAAGACAAGGGGGCATTTTT
1 AGAGAAAAAGAAGACAAGGGGACATTTTT
12565739 AGAGAAAAAGAAGACAATAAGGGGACATTTTT
1 AGAGAAAAAGAAGAC---AAGGGGACATTTTT
12565771 TTTAAGTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 15 0.54
32 13 0.46
ACGTcount: A:0.48, C:0.07, G:0.28, T:0.18
Consensus pattern (29 bp):
AGAGAAAAAGAAGACAAGGGGACATTTTT
Found at i:12566203 original size:11 final size:11
Alignment explanation
Indices: 12566187--12566217 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12566177 TCATCAATCT
12566187 AGAATATTACC
1 AGAATATTACC
*
12566198 AGAATATTACT
1 AGAATATTACC
12566209 AGAATATTA
1 AGAATATTA
12566218 TTGATCAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (11 bp):
AGAATATTACC
Found at i:12573724 original size:16 final size:16
Alignment explanation
Indices: 12573705--12573769 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
12573695 TTAATTAAGA
12573705 TATTAAATAATAATTT
1 TATTAAATAATAATTT
*
12573721 TATTAATATAATATATATA
1 TATTAA-ATAATA-AT-TT
*
12573740 TATATAAAT-ATAAATT
1 TAT-TAAATAATAATTT
*
12573756 TAGATAAATAATAA
1 TA-TTAAATAATAA
12573770 AATATATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
16 14 0.36
17 11 0.28
18 5 0.13
19 6 0.15
20 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TATTAAATAATAATTT
Found at i:12573736 original size:29 final size:32
Alignment explanation
Indices: 12573659--12573739 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 32
12573649 AACTATTATT
*
12573659 TTTAATATAAATTATATATAAATTTAATATTTTTA
1 TTTAATAT-AA-TATATATAAA-TTAATAATTTTA
*
12573694 TTTAAT-TAAGATAT-TAAA-TAATAATTTTA
1 TTTAATATAATATATATAAATTAATAATTTTA
12573723 -TTAATATAATATATATA
1 TTTAATATAATATATATA
12573740 TATATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.12
29 17 0.41
30 2 0.05
31 4 0.10
32 4 0.10
33 2 0.05
34 1 0.02
35 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
TTTAATATAATATATATAAATTAATAATTTTA
Found at i:12574300 original size:18 final size:18
Alignment explanation
Indices: 12574277--12574311 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12574267 ATGCTTTTAT
*
12574277 TAAATTAATTTATAAAAA
1 TAAATTAATTAATAAAAA
*
12574295 TAAATTTATTAATAAAA
1 TAAATTAATTAATAAAA
12574312 TTATATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTAATTAATAAAAA
Found at i:12574327 original size:16 final size:16
Alignment explanation
Indices: 12574306--12574344 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12574296 AAATTTATTA
*
12574306 ATAAAATTATATAAAT
1 ATAAAATTAAATAAAT
*
12574322 ATAAAATTAAATAACT
1 ATAAAATTAAATAAAT
12574338 ATAAAAT
1 ATAAAAT
12574345 ATAATTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAATTAAATAAAT
Found at i:12574334 original size:26 final size:25
Alignment explanation
Indices: 12574275--12574335 Score: 61
Period size: 28 Copynumber: 2.4 Consensus size: 25
12574265 TAATGCTTTT
*
12574275 ATTAAAT-TAATTTATAAAAATAAA
1 ATTAAATAAAATTTATAAAAATAAA
* *
12574299 TTTATTAATAAAATTATATAAATATAAA
1 ATTA--AATAAAATT-TATAAAAATAAA
12574327 ATTAAATAA
1 ATTAAATAA
12574336 CTATAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
24 3 0.10
26 8 0.28
27 4 0.14
28 14 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTAAATAAAATTTATAAAAATAAA
Found at i:12575664 original size:28 final size:28
Alignment explanation
Indices: 12575625--12575685 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
12575615 ATTTAATGAC
12575625 ATATATATAAAAAATAAAAATAAAAATT
1 ATATATATAAAAAATAAAAATAAAAATT
* * *
12575653 ATATATGTAAAAATTAAAAGTAAAAATT
1 ATATATATAAAAAATAAAAATAAAAATT
12575681 ATATA
1 ATATA
12575686 AAAATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (28 bp):
ATATATATAAAAAATAAAAATAAAAATT
Found at i:12575677 original size:13 final size:13
Alignment explanation
Indices: 12575632--12575681 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
12575622 GACATATATA
* *
12575632 TAAAAAATAAAAA
1 TAAAAATTAAAAG
*
12575645 TAAAAATTATATATG
1 TAAAAATTA-A-AAG
12575660 TAAAAATTAAAAG
1 TAAAAATTAAAAG
12575673 TAAAAATTA
1 TAAAAATTA
12575682 TATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 19 0.61
14 2 0.06
15 10 0.32
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (13 bp):
TAAAAATTAAAAG
Found at i:12575700 original size:13 final size:13
Alignment explanation
Indices: 12575631--12575700 Score: 50
Period size: 13 Copynumber: 4.9 Consensus size: 13
12575621 TGACATATAT
*
12575631 ATAAAAAATAAAA
1 ATAAAAATTAAAA
*
12575644 ATAAAAATTATATAT
1 ATAAAAATTA-A-AA
*
12575659 GTAAAAATTAAAA
1 ATAAAAATTAAAA
*
12575672 GTAAAAATTATATAAAA
1 AT-AAAA--AT-TAAAA
12575689 ATAAAAATTAAA
1 ATAAAAATTAAA
12575701 TTTGATAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
13 16 0.35
14 8 0.17
15 10 0.22
16 6 0.13
17 6 0.13
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
ATAAAAATTAAAA
Found at i:12575725 original size:22 final size:22
Alignment explanation
Indices: 12575638--12575720 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
12575628 TATATAAAAA
* *
12575638 ATAAAAATAAAAATTATATATG
1 ATAAAAATAAAAATTAAATTTG
* *
12575660 -TAAAAATTAAAAGTAAAAATTAT-
1 ATAAAAA-TAAAAAT-TAAATT-TG
12575683 ATAAAAATAAAAATTAAATTTG
1 ATAAAAATAAAAATTAAATTTG
*
12575705 ATAAAATATTAAAATT
1 ATAAAA-ATAAAAATT
12575721 TATTTTTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
21 7 0.15
22 17 0.35
23 17 0.35
24 7 0.15
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAAAAATAAAAATTAAATTTG
Found at i:12584578 original size:22 final size:22
Alignment explanation
Indices: 12584553--12584623 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
12584543 AGACTAAGAC
12584553 TTTTCATAGAAATTAAGGGAAG
1 TTTTCATAGAAATTAAGGGAAG
* * *
12584575 TTTTATATAGCAAAAACTAA--G-AC
1 TTTT-CATAG---AAATTAAGGGAAG
12584598 TTTTCATAGAAATTAAGGGAAG
1 TTTTCATAGAAATTAAGGGAAG
12584620 TTTT
1 TTTT
12584624 AAAAAGAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 6 0.17
21 1 0.03
22 13 0.36
23 9 0.25
24 1 0.03
26 6 0.17
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (22 bp):
TTTTCATAGAAATTAAGGGAAG
Found at i:12584597 original size:45 final size:45
Alignment explanation
Indices: 12584533--12584624 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
12584523 CAGAAATAAG
*
12584533 TATATAGCAAAGACTAAGACTTTTCATAGAAATTAAGGGAAGTTT
1 TATATAGCAAAAACTAAGACTTTTCATAGAAATTAAGGGAAGTTT
12584578 TATATAGCAAAAACTAAGACTTTTCATAGAAATTAAGGGAAGTTT
1 TATATAGCAAAAACTAAGACTTTTCATAGAAATTAAGGGAAGTTT
12584623 TA
1 TA
12584625 AAAAGAAAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (45 bp):
TATATAGCAAAAACTAAGACTTTTCATAGAAATTAAGGGAAGTTT
Found at i:12584746 original size:214 final size:214
Alignment explanation
Indices: 12584364--12584783 Score: 671
Period size: 214 Copynumber: 2.0 Consensus size: 214
12584354 AAAAAATAAG
*
12584364 TATAAAGCAAAGACTAAGACTTATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAGTAAAACCA
1 TATAAAGCAAAAACTAAGACTTATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAGTAAAACCA
* * * * * *
12584429 AAGAAAGAATGATAAGTCTTAGTCTTTGCTTTATATTTAGTCTTGGCATGAAGCATGCAAATGTC
66 AAAAAAGAACGATAAGTCCTAGTCTTTGCTTTATATTTAGTCTTGACATGAAACATGCAAATGTA
* * * *
12584494 TCAATCTTTTTGCCCTCATCTTTACTTCACAGAAATAAGTATATAGCAAAGACTA-AGACTTTTC
131 TCAATCTTTTTGCCCTCATCTTTACTTCACAAAAATAAGTACAAAGCAAAGACTACA-ACTTATC
12584558 ATAGAAATTAAGGGAAGTTT
195 ATAGAAATTAAGGGAAGTTT
* *
12584578 TATATAGCAAAAACTAAGACTTTTCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAGTAAAACCA
1 TATAAAGCAAAAACTAAGACTTATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAGTAAAACCA
12584643 AAAAAAGAACGATAAGTCCTAGTCTTTGCTTTATATTTAGTCTTGACATGAAACATGCAAATGTA
66 AAAAAAGAACGATAAGTCCTAGTCTTTGCTTTATATTTAGTCTTGACATGAAACATGCAAATGTA
* * * *
12584708 TCAGTCTTTTTGTCCTCATCTTTACTTTACAAAAATAAGTACAAAGCGAAGACTACAACTTATCA
131 TCAATCTTTTTGCCCTCATCTTTACTTCACAAAAATAAGTACAAAGCAAAGACTACAACTTATCA
12584773 TAGAAATTAAG
196 TAGAAATTAAG
12584784 AAAAGTTTAA
Statistics
Matches: 188, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
214 187 0.99
215 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (214 bp):
TATAAAGCAAAAACTAAGACTTATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAGTAAAACCA
AAAAAAGAACGATAAGTCCTAGTCTTTGCTTTATATTTAGTCTTGACATGAAACATGCAAATGTA
TCAATCTTTTTGCCCTCATCTTTACTTCACAAAAATAAGTACAAAGCAAAGACTACAACTTATCA
TAGAAATTAAGGGAAGTTT
Found at i:12584816 original size:15 final size:15
Alignment explanation
Indices: 12584781--12584819 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
12584771 CATAGAAATT
12584781 AAGAAAAGTTTAAAAC
1 AAGAAAAG-TTAAAAC
12584797 AAGAAAAG-TAAAACC
1 AAGAAAAGTTAAAA-C
12584812 AAGAAAAG
1 AAGAAAAG
12584820 AATGATAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.23
15 9 0.41
16 8 0.36
ACGTcount: A:0.67, C:0.08, G:0.15, T:0.10
Consensus pattern (15 bp):
AAGAAAAGTTAAAAC
Found at i:12591264 original size:58 final size:58
Alignment explanation
Indices: 12591194--12591394 Score: 293
Period size: 58 Copynumber: 3.5 Consensus size: 58
12591184 TTGTGCAGGA
12591194 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGG
* * * * **
12591252 AAAATTGATACTTTCAACTTTTCCTC-AAAA-ATCCCTTTGAAAATTT-ATCTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAAT-TTCGAGG
12591308 AAAATTGATACTTTCAACTTTTCCCCAAAAATATT-TTTTGAAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTG-AAACTTTAATTTCGAGG
*
12591366 AAAATTGATACTTTCAACTTTTCCTCAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAA
12591395 GAAGAAAAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
55 2 0.02
56 43 0.34
57 12 0.10
58 66 0.53
59 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGG
Found at i:12591509 original size:9 final size:9
Alignment explanation
Indices: 12591492--12591536 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
12591482 TATTTAAAGA
*
12591492 AAATGAAAT
1 AAATAAAAT
12591501 AAATAAAAT
1 AAATAAAAT
12591510 AAAT-AAAT
1 AAATAAAAT
12591518 AAAATGAAAAT
1 -AAAT-AAAAT
12591529 AAATAAAA
1 AAATAAAA
12591537 AATAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 4 0.12
9 20 0.62
10 4 0.12
11 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:12591546 original size:19 final size:18
Alignment explanation
Indices: 12591501--12591538 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
12591491 AAAATGAAAT
12591501 AAAT-AAAATAAATAAATA
1 AAATGAAAATAAATAAA-A
12591519 AAATGAAAATAAATAAAA
1 AAATGAAAATAAATAAAA
12591537 AA
1 AA
12591539 TAGAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATGAAAATAAATAAAA
Found at i:12592442 original size:31 final size:32
Alignment explanation
Indices: 12592390--12592450 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
12592380 TTAGCCGAAT
*
12592390 AAATAAAAAAAATCAAATAAAAATATTAATGA
1 AAATAAAAAAAATCAAATAAAAAAATTAATGA
* *
12592422 AAATAAATAAGAT-AAATAAAAAAATTAAT
1 AAATAAAAAAAATCAAATAAAAAAATTAAT
12592451 AGATAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (32 bp):
AAATAAAAAAAATCAAATAAAAAAATTAATGA
Found at i:12592451 original size:21 final size:20
Alignment explanation
Indices: 12592421--12592503 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 20
12592411 AATATTAATG
12592421 AAAATAAATAAGATAAATAAA
1 AAAATAAAT-AGATAAATAAA
*
12592442 AAAATTAATAGATAAATTAAA
1 AAAATAAATAGATAAA-TAAA
* * *
12592463 ATTAAAT-AACAGATAAATTAT
1 A--AAATAAATAGATAAATAAA
*
12592484 AACATATAATATGATAAATA
1 AAAATA-AATA-GATAAATA
12592504 TACATATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
19 3 0.06
20 7 0.14
21 19 0.39
22 16 0.33
23 4 0.08
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATAAATAGATAAATAAA
Found at i:12592469 original size:31 final size:29
Alignment explanation
Indices: 12592397--12592471 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
12592387 AATAAATAAA
* *
12592397 AAAAATCAAATAAAAATATTAATGAAAAT
1 AAAAATTAAATAAAAAAATTAATGAAAAT
*
12592426 AAATAAGATAAATAAAAAAATTAATAGATAAAT
1 AAA-AA-TTAAATAAAAAAATTAAT-GA-AAAT
*
12592459 TAAAATTAAATAA
1 AAAAATTAAATAA
12592472 CAGATAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
29 3 0.08
30 2 0.05
31 22 0.59
32 4 0.11
33 6 0.16
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (29 bp):
AAAAATTAAATAAAAAAATTAATGAAAAT
Found at i:12592479 original size:22 final size:21
Alignment explanation
Indices: 12592431--12592482 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
12592421 AAAATAAATA
*
12592431 AGATAAA-TAAAAAAATTAAT
1 AGATAAATTAAAAAAATTAAC
12592451 AGATAAATTAAAATTAAA-TAAC
1 AGATAAATTAAAA--AAATTAAC
12592473 AGATAAATTA
1 AGATAAATTA
12592483 TAACATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.25
21 5 0.18
22 13 0.46
23 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (21 bp):
AGATAAATTAAAAAAATTAAC
Found at i:12592577 original size:6 final size:6
Alignment explanation
Indices: 12592566--12592647 Score: 51
Period size: 6 Copynumber: 13.2 Consensus size: 6
12592556 AATACATAAG
* * * *
12592566 ATAAAA ATAAAA GAAAAAA ATATATAA A-AACA ATAATA ATAATA ATAAAA
1 ATAAAA ATAAAA -ATAAAA ATA-A-AA ATAAAA ATAAAA ATAAAA ATAAAA
* *
12592616 AT-AAA ATAAAA ATGTAAAA ATATAT ATAAAA A
1 ATAAAA ATAAAA A--TAAAA ATAAAA ATAAAA A
12592648 ATAGACTTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
5 7 0.12
6 37 0.62
7 7 0.12
8 9 0.15
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.22
Consensus pattern (6 bp):
ATAAAA
Found at i:12600016 original size:32 final size:32
Alignment explanation
Indices: 12599975--12600038 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
12599965 TTTTTCTTTC
* *
12599975 ATCCTATTATTTTCAAATAATTGGAAATTTAG
1 ATCCTATTATTTTCAAATAAATGAAAATTTAG
12600007 ATCCTATTATTTTCAAATAAATGAAAATTTAG
1 ATCCTATTATTTTCAAATAAATGAAAATTTAG
12600039 GTATCTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (32 bp):
ATCCTATTATTTTCAAATAAATGAAAATTTAG
Found at i:12601115 original size:23 final size:23
Alignment explanation
Indices: 12601072--12601130 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
12601062 TAAGATTACA
12601072 TATAATATTTTATAGAAAAAATTAT
1 TATAAT-TTTT-TAGAAAAAATTAT
12601097 TATAATTTTTTA-AAGAAAATTAT
1 TATAATTTTTTAGAA-AAAATTAT
*
12601120 AATAATTTTTT
1 TATAATTTTTT
12601131 TTCAGTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 2 0.06
23 20 0.62
24 4 0.12
25 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
TATAATTTTTTAGAAAAAATTAT
Found at i:12608745 original size:22 final size:22
Alignment explanation
Indices: 12608727--12608831 Score: 124
Period size: 22 Copynumber: 4.9 Consensus size: 22
12608717 ACAAAATCAG
*
12608727 TAATAACTTTATACTAAATTAA
1 TAATAACTTTATAGTAAATTAA
* *
12608749 TGATAACTGTATAGTAAATT-A
1 TAATAACTTTATAGTAAATTAA
* * *
12608770 TGATAACTTAATAGTAAAATAA
1 TAATAACTTTATAGTAAATTAA
* *
12608792 TAATAACTTAATAGTAAATAAA
1 TAATAACTTTATAGTAAATTAA
12608814 TAATAA-TTTATAGTAAAT
1 TAATAACTTTATAGTAAAT
12608832 AATTGATAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
21 29 0.40
22 43 0.60
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (22 bp):
TAATAACTTTATAGTAAATTAA
Found at i:12608776 original size:43 final size:43
Alignment explanation
Indices: 12608727--12609062 Score: 134
Period size: 43 Copynumber: 8.0 Consensus size: 43
12608717 ACAAAATCAG
* *
12608727 TAATAACTTTATACTAAATTAATGATAACTGT-ATAGTAAAT-TA
1 TAATAACTTTATAGTAAA-TAATGATAACT-TAATAGTAAATAAA
* * *
12608770 TGATAACTTAATAGTAAAATAATAATAACTTAATAGTAAATAAA
1 TAATAACTTTATAGT-AAATAATGATAACTTAATAGTAAATAAA
*
12608814 TAATAA-TTTATAGTAAATAATTGATAA---AATAGT--GT--A
1 TAATAACTTTATAGTAAATAA-TGATAACTTAATAGTAAATAAA
* * * * * * *
12608850 TGATAACATAATAATAAATACATAATAACATAGTAG-AAATAACA
1 TAATAACTTTATAGTAAATA-ATGATAACTTAATAGTAAATAA-A
* * * * * **
12608894 -AATAACTTAACAGTAAATCAT--TTA-TATAATTGTAAATGTA
1 TAATAACTTTATAGTAAATAATGATAACT-TAATAGTAAATAAA
* * ** *
12608934 TAA-CAC-ATATTAGTAAATTAA-GATAACTTAATAAAAAATAAG
1 TAATAACTTTA-TAGTAAA-TAATGATAACTTAATAGTAAATAAA
* * * * * *
12608976 TGATAAC-TTAGTAGTTAATTATTGATAACTTAGTAATAAATCAA
1 TAATAACTTTA-TAG-TAAATAATGATAACTTAATAGTAAATAAA
* *
12609020 TGATAACTTAATAGTAAATTAATGATAACTTAATAGTAAATAA
1 TAATAACTTTATAGTAAA-TAATGATAACTTAATAGTAAATAA
12609063 GATTCAGTTT
Statistics
Matches: 211, Mismatches: 55, Indels: 53
0.66 0.17 0.17
Matches are distributed among these distances:
36 6 0.03
37 15 0.07
38 2 0.01
39 1 0.00
40 25 0.12
41 9 0.04
42 21 0.10
43 70 0.33
44 60 0.28
45 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.34
Consensus pattern (43 bp):
TAATAACTTTATAGTAAATAATGATAACTTAATAGTAAATAAA
Found at i:12608981 original size:22 final size:21
Alignment explanation
Indices: 12608947--12609062 Score: 108
Period size: 22 Copynumber: 5.3 Consensus size: 21
12608937 CACATATTAG
12608947 TAAATTAA-GATAACTTAATAA
1 TAAA-TAATGATAACTTAATAA
* * *
12608968 AAAATAAGTGATAACTTAGTAGT
1 TAAATAA-TGATAACTTAATA-A
* * *
12608991 TAATTATTGATAACTTAGTAA
1 TAAATAATGATAACTTAATAA
*
12609012 TAAATCAATGATAACTTAATAG
1 TAAAT-AATGATAACTTAATAA
*
12609034 TAAATTAATGATAACTTAATAG
1 TAAA-TAATGATAACTTAATAA
12609056 TAAATAA
1 TAAATAA
12609063 GATTCAGTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
20 3 0.04
21 10 0.13
22 61 0.77
23 5 0.06
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.34
Consensus pattern (21 bp):
TAAATAATGATAACTTAATAA
Found at i:12609004 original size:44 final size:44
Alignment explanation
Indices: 12608944--12609063 Score: 163
Period size: 44 Copynumber: 2.8 Consensus size: 44
12608934 TAACACATAT
* *
12608944 TAGTAAATTAA-GATAACTTAATAAAAAATAAGTGATAACTTAG
1 TAGTAAATTAATGATAACTTAATAATAAATAAGTGATAACTTAA
* * *
12608987 TAGTTAATTATTGATAACTTAGTAATAAATCAA-TGATAACTTAA
1 TAGTAAATTAATGATAACTTAATAATAAAT-AAGTGATAACTTAA
*
12609031 TAGTAAATTAATGATAACTTAATAGTAAATAAG
1 TAGTAAATTAATGATAACTTAATAATAAATAAG
12609064 ATTCAGTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
43 11 0.17
44 52 0.80
45 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (44 bp):
TAGTAAATTAATGATAACTTAATAATAAATAAGTGATAACTTAA
Found at i:12609920 original size:22 final size:22
Alignment explanation
Indices: 12609895--12610250 Score: 108
Period size: 22 Copynumber: 15.9 Consensus size: 22
12609885 AGCAAATGCA
*
12609895 TAATAGTATAGTAGTAAATCAT
1 TAATAATATAGTAGTAAATCAT
* *
12609917 TAATAATTTAGTAGTAAATTAT
1 TAATAATATAGTAGTAAATCAT
* *
12609939 CAATAACT-TAGTAGTAAATCAC
1 TAATAA-TATAGTAGTAAATCAT
*
12609961 TAATAATATAATAGTAAAAT-AT
1 TAATAATATAGTAGT-AAATCAT
* * *
12609983 TGATAACT-TAGTTGTAAATCAG
1 TAATAA-TATAGTAGTAAATCAT
* * * *
12610005 TGATAATTTTATTA-TAAATCAA
1 TAATAA-TATAGTAGTAAATCAT
* * * *
12610027 TGATAATTTAGTTGTAAATTAGT
1 TAATAATATAGTAGTAAATCA-T
**
12610050 TAATTATTAATAATTTTATAGTAAATCAT
1 T-A--A-TAAT-A--TAGTAGTAAATCAT
* * * *
12610079 CAATAACTTTA-TAGTAAATAAG
1 TAATAA-TATAGTAGTAAATCAT
* * *
12610101 TAATAACATTA-TAATAAATTAT
1 TAATAATA-TAGTAGTAAATCAT
* *
12610123 TAATAACT-TAATAGTAAATTAT
1 TAATAA-TATAGTAGTAAATCAT
* *
12610145 CAATAACT-TAGTAATAAATCAT
1 TAATAA-TATAGTAGTAAATCAT
*
12610167 TTATAACT-TAGTAGTAAATCAT
1 TAATAA-TATAGTAGTAAATCAT
*
12610189 CT-ATAACT-TAATGAG-AAATCA-
1 -TAATAA-TATAGT-AGTAAATCAT
* * *
12610210 TGATAATTTAGTAGTAAATCAG
1 TAATAATATAGTAGTAAATCAT
* *
12610232 TGATAAGATAGTAGTAAAT
1 TAATAATATAGTAGTAAAT
12610251 GAGTAGTGAC
Statistics
Matches: 258, Mismatches: 51, Indels: 50
0.72 0.14 0.14
Matches are distributed among these distances:
20 4 0.02
21 25 0.10
22 194 0.75
23 14 0.05
25 3 0.01
26 3 0.01
27 4 0.02
28 1 0.00
29 1 0.00
30 9 0.03
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (22 bp):
TAATAATATAGTAGTAAATCAT
Found at i:12609951 original size:44 final size:43
Alignment explanation
Indices: 12609790--12610250 Score: 195
Period size: 44 Copynumber: 10.3 Consensus size: 43
12609780 TTAAATTACA
* * * * *
12609790 AATTTAGTAGTAAATTATAAATAACTTAGCAATAAATCAATCAT
1 AATTTAGTAGTAAATCAT-AATAACTTAGTAGTAAATCATTAAT
* * * * *
12609834 AATTTAATAGCT-AATCACTAA-AACTTAGTAATAAATTAATGAT
1 AATTTAGTAG-TAAATCA-TAATAACTTAGTAGTAAATCATTAAT
** * * *
12609877 AATAAAGCAGCAAATGCATAAT-AGTATAGTAGTAAATCATTAAT
1 AATTTAGTAGTAAAT-CATAATAACT-TAGTAGTAAATCATTAAT
* *
12609921 AATTTAGTAGTAAATTATCAATAACTTAGTAGTAAATCACTAAT
1 AATTTAGTAGTAAATCAT-AATAACTTAGTAGTAAATCATTAAT
* * * * * *
12609965 AATATAATAGTAAAAT-ATTGATAACTTAGTTGTAAATCAGTGAT
1 AATTTAGTAGT-AAATCA-TAATAACTTAGTAGTAAATCATTAAT
* * * * *
12610009 AATTTTATTA-TAAATCAATGATAATTTAGTTGTAAATTAGTTAATTATTAAT
1 AA-TTTAGTAGTAAATC-ATAATAACTTA---G-----TAGTAAATCATTAAT
* *
12610061 AATTTTA-TAGTAAATCATCAATAACTTTA-TAGTAAATAAGTAAT
1 AA-TTTAGTAGTAAATCAT-AATAAC-TTAGTAGTAAATCATTAAT
* * * * * *
12610105 AACATTA-TAATAAATTATTAATAACTTAATAGTAAATTATCAAT
1 AA-TTTAGTAGTAAATCA-TAATAACTTAGTAGTAAATCATTAAT
* * *
12610149 AACTTAGTAATAAATCATTTATAACTTAGTAGTAAATCATCT-AT
1 AATTTAGTAGTAAATCA-TAATAACTTAGTAGTAAATCAT-TAAT
* * * * * *
12610193 AACTTAATGAG-AAATCATGATAATTTAGTAGTAAATCAGTGAT
1 AATTTAGT-AGTAAATCATAATAACTTAGTAGTAAATCATTAAT
**
12610236 AAGATAGTAGTAAAT
1 AATTTAGTAGTAAAT
12610251 GAGTAGTGAC
Statistics
Matches: 324, Mismatches: 62, Indels: 63
0.72 0.14 0.14
Matches are distributed among these distances:
42 3 0.01
43 75 0.23
44 194 0.60
45 17 0.05
47 1 0.00
51 4 0.01
52 27 0.08
53 3 0.01
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.36
Consensus pattern (43 bp):
AATTTAGTAGTAAATCATAATAACTTAGTAGTAAATCATTAAT
Found at i:12609965 original size:66 final size:65
Alignment explanation
Indices: 12609793--12610250 Score: 222
Period size: 66 Copynumber: 6.8 Consensus size: 65
12609783 AATTACAAAT
* * * * * *
12609793 TTAGTAGTAAATTATAAATAACTTAGCAATAAATCAATCATAATTTAATAGCT-AATCACTAA-A
1 TTAGTAGTAAATTAT-AATAACTTAGTAGTAAATCAATAATAATATAGTAG-TAAATCATTAATA
12609856 AC
64 AC
* * * * * *
12609858 TTAGTAATAAATTAATGATAA-TAAAGCAGCAAATGC-ATAATAGTATAGTAGTAAATCATTAAT
1 TTAGTAGTAAATT-ATAATAACT-TAGTAGTAAAT-CAATAATAATATAGTAGTAAATCATTAAT
*
12609921 AAT
63 AAC
* * *
12609924 TTAGTAGTAAATTATCAATAACTTAGTAGTAAATCACTAATAATATAATAGTAAAAT-ATTGATA
1 TTAGTAGTAAATTAT-AATAACTTAGTAGTAAATCAATAATAATATAGTAGT-AAATCATTAATA
12609988 AC
64 AC
* * * * * * * *
12609990 TTAGTTGTAAATCAGTGATAATTTTATTA-TAAATCAATGATAATTTAGTTGTAAATTAGTTAAT
1 TTAGTAGTAAATTA-TAATAA-CTTAGTAGTAAATCAATAATAA--TA----T--AGTAGTAAAT
* *
12610054 TATTAATAATT
56 CATTAATAA-C
* * * *
12610065 TTA-TAGTAAATCATCAATAACTTTA-TAGTAAAT-AAGTAATAACATTA-TAATAAATTATTAA
1 TTAGTAGTAAATTAT-AATAAC-TTAGTAGTAAATCAA-TAATAATA-TAGTAGTAAATCATTAA
12610126 TAAC
62 TAAC
* * * *
12610130 TTAATAGTAAATTATCAATAACTTAGTAATAAATCATTTATAACT-TAGTAGTAAATCATCT-AT
1 TTAGTAGTAAATTAT-AATAACTTAGTAGTAAATCAATAATAA-TATAGTAGTAAATCAT-TAAT
12610193 AAC
63 AAC
* * * * * * *
12610196 TTAATGAG-AAATCATGATAATTTAGTAGTAAATCAGTGATAAGATAGTAGTAAAT
1 TTAGT-AGTAAATTATAATAACTTAGTAGTAAATCAATAATAATATAGTAGTAAAT
12610251 GAGTAGTGAC
Statistics
Matches: 305, Mismatches: 55, Indels: 66
0.72 0.13 0.15
Matches are distributed among these distances:
64 2 0.01
65 87 0.29
66 146 0.48
67 16 0.05
68 2 0.01
69 1 0.00
72 2 0.01
73 8 0.03
74 38 0.12
75 3 0.01
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.36
Consensus pattern (65 bp):
TTAGTAGTAAATTATAATAACTTAGTAGTAAATCAATAATAATATAGTAGTAAATCATTAATAAC
Found at i:12610156 original size:19 final size:21
Alignment explanation
Indices: 12610046--12610198 Score: 119
Period size: 22 Copynumber: 7.0 Consensus size: 21
12610036 AGTTGTAAAT
* * *
12610046 TAGTTAATTATTAATAATTTTA
1 TAGTAAATTATCAATAA-CTTA
*
12610068 TAGTAAATCATCAATAACTTTA
1 TAGTAAATTATCAATAAC-TTA
*
12610090 TAGTAAATAAGT-AATAACATTA
1 TAGTAAATTA-TCAATAAC-TTA
* *
12610112 TAATAAATTATTAATAACTTAA
1 TAGTAAATTATCAATAACTT-A
12610134 TAGTAAATTATCAATAACTTA
1 TAGTAAATTATCAATAACTTA
* * **
12610155 GTAATAAATCATTTATAACTTA
1 -TAGTAAATTATCAATAACTTA
* *
12610177 GTAGTAAATCATCTATAACTTA
1 -TAGTAAATTATCAATAACTTA
12610199 ATGAGAAATC
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
21 4 0.04
22 105 0.95
23 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (21 bp):
TAGTAAATTATCAATAACTTA
Found at i:12610178 original size:140 final size:140
Alignment explanation
Indices: 12609906--12610185 Score: 316
Period size: 140 Copynumber: 2.0 Consensus size: 140
12609896 AATAGTATAG
* * *
12609906 TAGTAAATCATTAATAATTTAGTAGTAAATTATCAATAACTTAGTAGTAAATCACTAATAATATA
1 TAGTAAATCATTAATAATTTAGTAGTAAATCATCAATAACTTAGTAGTAAATAACTAATAACATA
* * * * * * * *
12609971 ATAGTAAAATATTGATAACTTAGTTGTAAATCAGTGATAATTTTATTATAAATCAATGATAATTT
66 ATAATAAAATATTAATAACTTAATAGTAAATCAGTAATAATCTTATAATAAATCAATGATAACTT
*
12610036 AGTTGTAAAT
131 AGTAGTAAAT
* * *
12610046 TAGTTAATTATTAATAATTTTA-TAGTAAATCATCAATAACTTTA-TAGTAAATAAGTAATAACA
1 TAGTAAATCATTAATAA-TTTAGTAGTAAATCATCAATAAC-TTAGTAGTAAATAACTAATAACA
* * * * *
12610109 TTATAATAAATTATTAATAACTTAATAGTAAATTA-TCAATAA-CTTAGTAATAAATCATTTATA
64 TAATAATAAAATATTAATAACTTAATAGTAAATCAGT-AATAATCTTA-TAATAAATCAATGATA
12610172 ACTTAGTAGTAAAT
127 ACTTAGTAGTAAAT
12610186 CATCTATAAC
Statistics
Matches: 116, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
139 4 0.03
140 105 0.91
141 7 0.06
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (140 bp):
TAGTAAATCATTAATAATTTAGTAGTAAATCATCAATAACTTAGTAGTAAATAACTAATAACATA
ATAATAAAATATTAATAACTTAATAGTAAATCAGTAATAATCTTATAATAAATCAATGATAACTT
AGTAGTAAAT
Found at i:12610181 original size:25 final size:22
Alignment explanation
Indices: 12610068--12610230 Score: 122
Period size: 22 Copynumber: 7.5 Consensus size: 22
12610058 AATAATTTTA
*
12610068 TAGTAAATCATCAATAACTTTA-
1 TAGTAAATCATCTATAAC-TTAG
* *
12610090 TAGTAAATAAGT-AATAACATTA-
1 TAGTAAATCA-TCTATAAC-TTAG
* * *
12610112 TAATAAATTAT-TAATAACTTAA
1 TAGTAAATCATCT-ATAACTTAG
* *
12610134 TAGTAAATTATCAATAACTTAG
1 TAGTAAATCATCTATAACTTAG
* *
12610156 TAATAAATCATTTATAACTTAG
1 TAGTAAATCATCTATAACTTAG
*
12610178 TAGTAAATCATCTATAACTTAA
1 TAGTAAATCATCTATAACTTAG
* *
12610200 TGAG-AAATCAT-GATAATTTAG
1 T-AGTAAATCATCTATAACTTAG
12610221 TAGTAAATCA
1 TAGTAAATCA
12610231 GTGATAAGAT
Statistics
Matches: 117, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.02
21 18 0.15
22 94 0.80
23 3 0.03
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (22 bp):
TAGTAAATCATCTATAACTTAG
Found at i:12610514 original size:22 final size:21
Alignment explanation
Indices: 12610489--12610807 Score: 91
Period size: 22 Copynumber: 14.8 Consensus size: 21
12610479 TATATCATAA
*
12610489 ATAACTTAGTAGTAATTCAATG
1 ATAACTTAGTAGTAAAT-AATG
*
12610511 ATAATTTAGTAGTAAATAATTG
1 ATAACTTAGTAGTAAATAA-TG
* * *
12610533 ATAACTTAATAGCTAACTATTG
1 ATAACTTAGTAG-TAAATAATG
* *
12610555 AAAACTTAGTAATAAATCAATG
1 ATAACTTAGTAGTAAAT-AATG
* * *
12610577 GTAA--T--TAGTAAATGCATA
1 ATAACTTAGTAGTAAAT-AATG
* *
12610595 ATAA-TATAATAGTAAATCACTG
1 ATAACT-TAGTAGTAAAT-AATG
* * *
12610617 --AATTTAGTAGTAAATCACTA
1 ATAACTTAGTAGTAAAT-AATG
* * * *
12610637 ATAA-TATAGTAATAAGTCACTT
1 ATAACT-TAGTAGTAAAT-AATG
* *
12610659 ATAACTTAGTTGTATATCAATG
1 ATAACTTAGTAGTAAAT-AATG
* * *
12610681 ATAATTTTGTAGTAAATCATCG
1 ATAACTTAGTAGTAAATAAT-G
* *
12610703 ATAACTTCA-TAGTAAATTAGTT
1 ATAACTT-AGTAGTAAA-TAATG
* * *
12610725 ATAACTTTA-TAATAAATTATTA
1 ATAAC-TTAGTAGTAAA-TAATG
* * *
12610747 ATAACTTAGTACTAAATCATCA
1 ATAACTTAGTAGTAAATAAT-G
* *
12610769 ATAACTTAGTAGTAAATCATTC
1 ATAACTTAGTAGTAAAT-AATG
*
12610791 ATAACTTAATAGTAAAT
1 ATAACTTAGTAGTAAAT
12610808 CATTAATAAT
Statistics
Matches: 224, Mismatches: 54, Indels: 38
0.71 0.17 0.12
Matches are distributed among these distances:
18 12 0.05
20 18 0.08
21 15 0.07
22 168 0.75
23 11 0.05
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (21 bp):
ATAACTTAGTAGTAAATAATG
Found at i:12610539 original size:44 final size:44
Alignment explanation
Indices: 12610489--12610845 Score: 150
Period size: 44 Copynumber: 8.2 Consensus size: 44
12610479 TATATCATAA
* *
12610489 ATAACTTAGTAGTAATTCAATGATAATTTAGTAGTAAATAATTG
1 ATAACTTAGTAGTAATTCAATAATAATTTAGTAATAAATAATTG
* * * *
12610533 ATAACTTAATAGCTAACT-ATTGAA-AACTTAGTAATAAATCAA-TG
1 ATAACTTAGTAG-TAATTCAAT-AATAATTTAGTAATAAAT-AATTG
* * * * * * *
12610577 GTAA-TTAGTA--AATGC-ATAATAATATAATAGTAAATCACTG
1 ATAACTTAGTAGTAATTCAATAATAATTTAGTAATAAATAATTG
* * * * * *
12610617 --AATTTAGTAGTAAATCACTAATAATATAGTAATAAGTCACTT-
1 ATAACTTAGTAGTAATTCAATAATAATTTAGTAATAAAT-AATTG
* * * * * *
12610659 ATAACTTAGTTGT-ATATCAATGATAATTTTGTAGTAAATCATCG
1 ATAACTTAGTAGTAAT-TCAATAATAATTTAGTAATAAATAATTG
* * * *
12610703 ATAACTTCA-TAGTAAATT-AGTTATAACTTTA-TAATAAATTATTA
1 ATAACTT-AGTAGT-AATTCAATAATAA-TTTAGTAATAAATAATTG
* * * * * *
12610747 ATAACTTAGTACTAAATC-ATCAATAACTTAGTAGTAAATCATTC
1 ATAACTTAGTAGTAATTCAAT-AATAATTTAGTAATAAATAATTG
* * * * * *
12610791 ATAACTTAATAGTAAATCATTAATAATTTAATAATAAATTACTG
1 ATAACTTAGTAGTAATTCAATAATAATTTAGTAATAAATAATTG
*
12610835 ATAACATAGTA
1 ATAACTTAGTA
12610846 ATAAATTAGT
Statistics
Matches: 225, Mismatches: 64, Indels: 48
0.67 0.19 0.14
Matches are distributed among these distances:
38 2 0.01
39 9 0.04
40 16 0.07
41 3 0.01
42 16 0.07
43 16 0.07
44 148 0.66
45 13 0.06
46 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (44 bp):
ATAACTTAGTAGTAATTCAATAATAATTTAGTAATAAATAATTG
Found at i:12610648 original size:19 final size:19
Alignment explanation
Indices: 12610597--12610648 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
12610587 AATGCATAAT
12610597 AATATAATAGTAAATCACTG
1 AATAT-ATAGTAAATCACTG
*
12610617 AATTTAGTAGTAAATCACT-
1 AATATA-TAGTAAATCACTG
12610636 AATAATATAGTAA
1 AAT-ATATAGTAA
12610649 TAAGTCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.33
Consensus pattern (19 bp):
AATATATAGTAAATCACTG
Found at i:12610748 original size:11 final size:11
Alignment explanation
Indices: 12610715--12610860 Score: 64
Period size: 11 Copynumber: 13.3 Consensus size: 11
12610705 AACTTCATAG
*
12610715 TAAATTAGTTA
1 TAAATTAGTAA
*
12610726 TAACTTTA-TAA
1 TAA-ATTAGTAA
*
12610737 TAAATTATTAA
1 TAAATTAGTAA
* *
12610748 TAACTTAGTAC
1 TAAATTAGTAA
*
12610759 TAAATCA-TCAA
1 TAAATTAGT-AA
* *
12610770 TAACTTAGTAG
1 TAAATTAGTAA
* * *
12610781 TAAATCATTCA
1 TAAATTAGTAA
* * *
12610792 TAACTTAATAG
1 TAAATTAGTAA
* *
12610803 TAAATCATTAA
1 TAAATTAGTAA
* *
12610814 TAATTTAATAA
1 TAAATTAGTAA
* *
12610825 TAAATTACTGA
1 TAAATTAGTAA
12610836 TAACA-TAGTAA
1 TAA-ATTAGTAA
12610847 TAAATTAGTAA
1 TAAATTAGTAA
12610858 TAA
1 TAA
12610861 CTTAATTGTC
Statistics
Matches: 95, Mismatches: 34, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
10 5 0.05
11 85 0.89
12 5 0.05
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (11 bp):
TAAATTAGTAA
Found at i:12610808 original size:22 final size:22
Alignment explanation
Indices: 12610690--12610829 Score: 124
Period size: 22 Copynumber: 6.4 Consensus size: 22
12610680 GATAATTTTG
*
12610690 TAGTAAATCA-TCGATAACTTCA
1 TAGTAAATCATTC-ATAACTTAA
* *
12610712 TAGTAAATTAGTT-ATAACTTTA
1 TAGTAAATCA-TTCATAACTTAA
* * * *
12610734 TAATAAATTATTAATAACTTAG
1 TAGTAAATCATTCATAACTTAA
* *
12610756 TACTAAATCA-TCAATAACTTAG
1 TAGTAAATCATTC-ATAACTTAA
12610778 TAGTAAATCATTCATAACTTAA
1 TAGTAAATCATTCATAACTTAA
* *
12610800 TAGTAAATCATTAATAATTTAA
1 TAGTAAATCATTCATAACTTAA
*
12610822 TAATAAAT
1 TAGTAAAT
12610830 TACTGATAAC
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.03
22 94 0.94
23 2 0.02
24 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (22 bp):
TAGTAAATCATTCATAACTTAA
Found at i:12610839 original size:66 final size:65
Alignment explanation
Indices: 12610693--12610866 Score: 181
Period size: 66 Copynumber: 2.6 Consensus size: 65
12610683 AATTTTGTAG
* * *
12610693 TAAATCATCGATAACTTCA-TAGTAAATTAGTTATAACTTTATAATAAATTATTAATAACTTAGT
1 TAAATCATCGATAACTT-AGTAGTAAATTA-TTATAACTTAATAATAAATCATTAATAACTTAAT
*
12610757 AC
64 AA
* * * *
12610759 TAAATCATCAATAACTTAGTAGTAAATCATTCATAACTTAATAGTAAATCATTAATAATTTAATA
1 TAAATCATCGATAACTTAGTAGTAAATTATT-ATAACTTAATAATAAATCATTAATAACTTAATA
12610824 A
65 A
* * * *
12610825 TAAATTA-CTGATAACATAGTAATAAATTAGTAATAACTTAAT
1 TAAATCATC-GATAACTTAGTAGTAAATTA-TTATAACTTAAT
12610867 TGTCAATTGA
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
65 4 0.04
66 85 0.94
67 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (65 bp):
TAAATCATCGATAACTTAGTAGTAAATTATTATAACTTAATAATAAATCATTAATAACTTAATAA
Found at i:12610851 original size:44 final size:44
Alignment explanation
Indices: 12610725--12610866 Score: 149
Period size: 44 Copynumber: 3.2 Consensus size: 44
12610715 TAAATTAGTT
* * *
12610725 ATAACTTTATAATAAATTATTAATAACTTAGTACTAAATCATCA
1 ATAACTTAATAATAAATTATTAATAACTTAGTAATAAATCATTA
* * * * * *
12610769 ATAACTTAGTAGTAAATCATTCATAACTTAATAGTAAATCATTA
1 ATAACTTAATAATAAATTATTAATAACTTAGTAATAAATCATTA
* * * * * *
12610813 ATAATTTAATAATAAATTACTGATAACATAGTAATAAATTAGTA
1 ATAACTTAATAATAAATTATTAATAACTTAGTAATAAATCATTA
12610857 ATAACTTAAT
1 ATAACTTAAT
12610867 TGTCAATTGA
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 78 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (44 bp):
ATAACTTAATAATAAATTATTAATAACTTAGTAATAAATCATTA
Found at i:12610860 original size:22 final size:22
Alignment explanation
Indices: 12610715--12610864 Score: 133
Period size: 22 Copynumber: 6.8 Consensus size: 22
12610705 AACTTCATAG
12610715 TAAATTAGTT-ATAACTTTA-TAA
1 TAAATTA-TTAATAAC-TTAGTAA
*
12610737 TAAATTATTAATAACTTAGTAC
1 TAAATTATTAATAACTTAGTAA
* * *
12610759 TAAATCATCAATAACTTAGTAG
1 TAAATTATTAATAACTTAGTAA
* * * *
12610781 TAAATCATTCATAACTTAATAG
1 TAAATTATTAATAACTTAGTAA
* * *
12610803 TAAATCATTAATAATTTAATAA
1 TAAATTATTAATAACTTAGTAA
* * *
12610825 TAAATTACTGATAACATAGTAA
1 TAAATTATTAATAACTTAGTAA
*
12610847 TAAATTAGTAATAACTTA
1 TAAATTATTAATAACTTA
12610865 ATTGTCAATT
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.05
22 102 0.95
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (22 bp):
TAAATTATTAATAACTTAGTAA
Found at i:12611079 original size:22 final size:22
Alignment explanation
Indices: 12611045--12611121 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
12611035 AAATCAGTGA
*
12611045 TAATAATAAATCAATGATAACT
1 TAATAGTAAATCAATGATAACT
* ** *
12611067 TATTAGTAAATCAATTTTAGCT
1 TAATAGTAAATCAATGATAACT
*
12611089 TAGTAGTAAAGTC--TGGATAACT
1 TAATAGTAAA-TCAAT-GATAACT
12611111 TAATAGTAAAT
1 TAATAGTAAAT
12611122 TATTCATATT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 2 0.05
22 39 0.91
23 2 0.05
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (22 bp):
TAATAGTAAATCAATGATAACT
Found at i:12611152 original size:22 final size:22
Alignment explanation
Indices: 12611110--12611152 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12611100 TCTGGATAAC
* *
12611110 TTAATAGTAAATTATTCATATT
1 TTAATAATAAATTAGTCATATT
*
12611132 TTAATAATAAATTAGTGATAT
1 TTAATAATAAATTAGTCATAT
12611153 AACTTAGCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (22 bp):
TTAATAATAAATTAGTCATATT
Found at i:12612717 original size:15 final size:16
Alignment explanation
Indices: 12612697--12612726 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12612687 TTATAGTCAA
12612697 AAAAAT-TAAAAAAAG
1 AAAAATATAAAAAAAG
12612712 AAAAATATAAAAAAA
1 AAAAATATAAAAAAA
12612727 AGAATGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAATATAAAAAAAG
Found at i:12616509 original size:26 final size:26
Alignment explanation
Indices: 12616480--12616533 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
12616470 AAATTTAGAT
12616480 AAAATTT-CTCACTTAGAAATTT-TATA
1 AAAATTTACT-ACTTA-AAATTTCTATA
*
12616506 AAAATTTACTATTTAAAATTTCTATA
1 AAAATTTACTACTTAAAATTTCTATA
12616532 AA
1 AA
12616534 TTCCATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 6 0.24
26 17 0.68
27 2 0.08
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
AAAATTTACTACTTAAAATTTCTATA
Found at i:12616948 original size:14 final size:13
Alignment explanation
Indices: 12616931--12616975 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
12616921 AAATCTCCCC
12616931 TTTCCCTTCTTTCT
1 TTTCCCTT-TTTCT
*
12616945 TTTCCCCTTTTCT
1 TTTCCCTTTTTCT
*
12616958 TTTCTCTTTTTCT
1 TTTCCCTTTTTCT
12616971 CTTTC
1 -TTTC
12616976 TAGAACCAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTCCCTTTTTCT
Found at i:12624548 original size:24 final size:23
Alignment explanation
Indices: 12624493--12624546 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 23
12624483 TTTTCTTTTG
12624493 TATTTTATGTATTCTATTATTAT
1 TATTTTATGTATTCTATTATTAT
12624516 TATTATTATGTATATCT-TTATTCATT
1 TATT-TTATGTAT-TCTATTATT-A-T
12624542 TATTT
1 TATTT
12624547 ATTTTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 5 0.19
26 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATGTATTCTATTATTAT
Found at i:12624605 original size:3 final size:3
Alignment explanation
Indices: 12624597--12624622 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12624587 AGTTATATAT
12624597 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12624623 TTTGTAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12625282 original size:20 final size:20
Alignment explanation
Indices: 12625239--12625283 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12625229 CCGGCCAACT
*
12625239 TCCGGCGAAAAAACCCAGAT
1 TCCGGCGAAAAAACCCAGAA
***
12625259 TCCGGCGAAAATTTCCAGAA
1 TCCGGCGAAAAAACCCAGAA
12625279 TCCGG
1 TCCGG
12625284 TGAATCTTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (20 bp):
TCCGGCGAAAAAACCCAGAA
Found at i:12625670 original size:13 final size:13
Alignment explanation
Indices: 12625654--12625678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12625644 TTTTTTTTTT
12625654 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
12625667 TTTTTTTTTTGA
1 TTTTTTTTTTGA
12625679 CTTTGATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:12625676 original size:1 final size:1
Alignment explanation
Indices: 12625632--12625663 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
12625622 CCGCTCCAGG
12625632 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12625664 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12626112 original size:152 final size:152
Alignment explanation
Indices: 12625701--12626158 Score: 715
Period size: 152 Copynumber: 3.0 Consensus size: 152
12625691 CATGATTTTT
* * * *
12625701 TTTTTCTTTTTTTTTAATTAATGCCGACGACAGAGCCTCT-TACAGTGAAACAGTAGTTTTTCCT
1 TTTTTGTTTTTTTTTAATAAAT-CCGACGACGGAGCCTCTGCA-AGTGAAACAGTAGTTTTT-CT
12625765 TGCAATACTCTTGAGGTGAGGGAATTTTCTCAA-TTTCTGCTAAAAAGTATTAGAGTCAATTGAG
63 TGC-ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCT-AAAAGTATTAGAGTCAATTGAG
12625829 AATAAATTTTCCAATAATTAATTGGATGA
126 AAT-AA-TTTCCAATAATTAATTGGATGA
12625858 TTTTTGTATTTTTTTTAATAAATCCGACGACGGGAGGCCTCTGCAAGTGAAACAGTAGTTTTTCT
1 TTTTTGT-TTTTTTTTAATAAATCCGACGAC-GGA-GCCTCTGCAAGTGAAACAGTAGTTTTTCT
*
12625923 TGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAA
63 TGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
12625988 TAATTTCCAATAATTAATTGGATGA
128 TAATTTCCAATAATTAATTGGATGA
*
12626013 -TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTG
1 TTTTTGTTTTTT-TTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
*
12626077 CATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATA
65 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATA
* *
12626142 ATTTCCAACAACTAATT
130 ATTTCCAATAATTAATT
12626159 ACTTGGTAAA
Statistics
Matches: 285, Mismatches: 10, Indels: 17
0.91 0.03 0.05
Matches are distributed among these distances:
152 108 0.38
153 8 0.03
154 24 0.08
155 22 0.08
156 2 0.01
157 67 0.24
158 29 0.10
159 24 0.08
160 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (152 bp):
TTTTTGTTTTTTTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
TTTCCAATAATTAATTGGATGA
Found at i:12629386 original size:1 final size:1
Alignment explanation
Indices: 12629382--12629406 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12629372 GTAATTTTTG
12629382 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12629407 CACCACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12629819 original size:10 final size:10
Alignment explanation
Indices: 12629804--12629840 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
12629794 AGAAGATGAT
12629804 GAAAAAAAAA
1 GAAAAAAAAA
*
12629814 GAAAAAAATA
1 GAAAAAAAAA
*
12629824 GAAAAAAAAG
1 GAAAAAAAAA
12629834 GAAAAAA
1 GAAAAAA
12629841 TGAGAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:12629846 original size:20 final size:20
Alignment explanation
Indices: 12629780--12629848 Score: 74
Period size: 19 Copynumber: 3.6 Consensus size: 20
12629770 ACAATGGATG
12629780 AAAAATGAG--AAAAAAGAA
1 AAAAATGAGAAAAAAAAGAA
* **
12629798 GATGATGA-AAAAAAAAGAA
1 AAAAATGAGAAAAAAAAGAA
*
12629817 AAAAAT-AGAAAAAAAAGGA
1 AAAAATGAGAAAAAAAAGAA
12629836 AAAAATGAGAAAA
1 AAAAATGAGAAAA
12629849 TGAAAAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 6 0.15
19 28 0.70
20 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AAAAATGAGAAAAAAAAGAA
Found at i:12631122 original size:41 final size:41
Alignment explanation
Indices: 12631071--12631605 Score: 751
Period size: 41 Copynumber: 13.0 Consensus size: 41
12631061 GTCTAGGAGT
*
12631071 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
12631112 ATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
12631154 ATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
*
12631195 ATTTATTTTTCAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCA
* *
12631236 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
12631277 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
12631318 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGTA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
12631359 ATTTAATTTCCAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCA
* * *
12631400 ATTTATTTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
12631442 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTT-TAGAGGAGCA
* *
12631484 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
12631525 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * *
12631566 ATTTAC-TTTCAAAAGTCGTTGAGTCTCTGTTTAGAGGAGC
1 ATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGC
12631606 TTCGGCAAAA
Statistics
Matches: 450, Mismatches: 31, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.01
40 19 0.04
41 306 0.68
42 110 0.24
43 12 0.03
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:12631227 original size:124 final size:122
Alignment explanation
Indices: 12631071--12631605 Score: 708
Period size: 124 Copynumber: 4.3 Consensus size: 122
12631061 GTCTAGGAGT
* *
12631071 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGGTG
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTG
* * *
12631136 CCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
65 CCTCTGTTGAGAGGAGCAATTTAC-TTTTCAAAG-TCGTGTACCTCTGTTGAGAGGAGCA
*
12631195 ATTTATTTTTCAAAGTTCCGT-TGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGT
1 ATTTACTTTTCAAAG-T-CGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGT
* * * *
12631258 ACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
64 GCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGT-GTACCTCTGTTGAGAGGAGCA
* * *
12631318 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGTAATTTA-ATTTCCAAAGTTCCGT--
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAG-T-CGTGG
* *
12631380 TGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
63 TGCCTCTGTTGAGAGGAGCAATTTA-CTTTTCAAAGTCGT-GTACCTCTGTTGAGAGGAGCA
*
12631442 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAAGAGGAGCAATTTAC-TTTCCAAAGTCGTGGT
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTT-TAGAGGAGCAATTTACTTTTCCAAAGTCGTGGT
12631506 GCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
64 GCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGT-GTACCTCTGTTGAGAGGAGCA
* *
12631566 ATTTAC-TTTCAAAAGTCGTTGAGTCTCTGTTTAGAGGAGC
1 ATTTACTTTTC-AAAGTCG-TGTGCCTCTGTTTAGAGGAGC
12631606 TTCGGCAAAA
Statistics
Matches: 372, Mismatches: 23, Indels: 33
0.87 0.05 0.08
Matches are distributed among these distances:
121 7 0.02
122 12 0.03
123 134 0.36
124 165 0.44
125 51 0.14
126 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (122 bp):
ATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGC
CTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGTACCTCTGTTGAGAGGAGCA
Found at i:12631618 original size:1 final size:1
Alignment explanation
Indices: 12631612--12631730 Score: 85
Period size: 1 Copynumber: 119.0 Consensus size: 1
12631602 GAGCTTCGGC
* * ** ** **
12631612 AAAAAAAAAAAAAACAAAAAAAACAAAAAAAAAAAAAAAATCAAAAAAAAAAAATCAAAAAAATC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * * ** *
12631677 AGAAAAAATCAAAAAAATAAAAAAACAAAAATAAAAAAAATCAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12631731 TGTTGAGTTG
Statistics
Matches: 89, Mismatches: 29, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 89 1.00
ACGTcount: A:0.86, C:0.07, G:0.01, T:0.07
Consensus pattern (1 bp):
A
Found at i:12631674 original size:51 final size:52
Alignment explanation
Indices: 12631617--12631724 Score: 143
Period size: 51 Copynumber: 2.1 Consensus size: 52
12631607 TCGGCAAAAA
12631617 AAAAAAAAACA-AAAAAAACAAAAAAA-AAAAAAA-AATCAAAAAAAAAAAATC
1 AAAAAAAAACAGAAAAAAACAAAAAAATAAAAAAACAA--AAAAAAAAAAAATC
* * *
12631668 -AAAAAAATCAGAAAAAATCAAAAAAATAAAAAAACAAAAATAAAAAAAATC
1 AAAAAAAAACAGAAAAAAACAAAAAAATAAAAAAACAAAAAAAAAAAAAATC
12631719 AAAAAA
1 AAAAAA
12631725 TAAAAATGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
50 9 0.18
51 27 0.54
52 12 0.24
53 2 0.04
ACGTcount: A:0.85, C:0.07, G:0.01, T:0.06
Consensus pattern (52 bp):
AAAAAAAAACAGAAAAAAACAAAAAAATAAAAAAACAAAAAAAAAAAAAATC
Found at i:12631729 original size:13 final size:14
Alignment explanation
Indices: 12631613--12631731 Score: 107
Period size: 14 Copynumber: 7.9 Consensus size: 14
12631603 AGCTTCGGCA
*
12631613 AAAAAAAAAAAAAC
1 AAAAAAAAAAAATC
12631627 AAAAAAAACAAAA--
1 AAAAAAAA-AAAATC
12631640 AAAAAAAAAAAATC
1 AAAAAAAAAAAATC
12631654 AAAAAAAAAAAATC
1 AAAAAAAAAAAATC
12631668 AAAAAAATCAGAAAAAATC
1 --AAAAA--A-AAAAAATC
*
12631687 AAAAAAATAAAAAAAC
1 -AAAAAA-AAAAAATC
12631703 AAAAATAAAAAAAATC
1 -AAAA-AAAAAAAATC
*
12631719 AAAAAATAAAAAT
1 AAAAAAAAAAAAT
12631732 GTTGAGTTGA
Statistics
Matches: 92, Mismatches: 4, Indels: 18
0.81 0.04 0.16
Matches are distributed among these distances:
12 4 0.04
13 8 0.09
14 30 0.33
15 8 0.09
16 25 0.27
17 2 0.02
18 7 0.08
19 8 0.09
ACGTcount: A:0.85, C:0.07, G:0.01, T:0.08
Consensus pattern (14 bp):
AAAAAAAAAAAATC
Found at i:12631731 original size:23 final size:22
Alignment explanation
Indices: 12631611--12631731 Score: 112
Period size: 23 Copynumber: 5.6 Consensus size: 22
12631601 GGAGCTTCGG
12631611 CAAAAAAAAAAA-AAACAAAAA-
1 CAAAAAAAAAAATAAA-AAAAAT
12631632 -AAACAAAAAAAA-AAAAAAAAT
1 CAAA-AAAAAAAATAAAAAAAAT
*
12631653 CAAAAAAAAAAAATCAAAAAAAT
1 C-AAAAAAAAAAATAAAAAAAAT
* *
12631676 C---AGAAAAAATCAAAAAAAT
1 CAAAAAAAAAAATAAAAAAAAT
*
12631695 AAAAAAACAAAAATAAAAAAAAT
1 CAAAAAA-AAAAATAAAAAAAAT
12631718 CAAAAAATAAAAAT
1 CAAAAAA-AAAAAT
12631732 GTTGAGTTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 16
0.79 0.07 0.15
Matches are distributed among these distances:
19 17 0.20
20 8 0.10
21 11 0.13
22 10 0.12
23 38 0.45
ACGTcount: A:0.84, C:0.07, G:0.01, T:0.07
Consensus pattern (22 bp):
CAAAAAAAAAAATAAAAAAAAT
Found at i:12631955 original size:24 final size:23
Alignment explanation
Indices: 12631900--12631953 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 23
12631890 TTTTCTTTTG
12631900 TATTTTATGTATTCTATTATTAT
1 TATTTTATGTATTCTATTATTAT
12631923 TATTATTATGTATATCT-TTATTCATT
1 TATT-TTATGTAT-TCTATTATT-A-T
12631949 TATTT
1 TATTT
12631954 ATTTTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 5 0.19
26 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATGTATTCTATTATTAT
Done.