Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 237 of 240
Found at i:71770136 original size:18 final size:19
Alignment explanation
Indices: 71770115--71770162 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
71770105 GTAATAACTT
71770115 TATTTTAATTTAATAA-AC
1 TATTTTAATTTAATAACAC
* * *
71770133 TATTCTCATTTAATAACTC
1 TATTTTAATTTAATAACAC
71770152 TATTTTAATTT
1 TATTTTAATTT
71770163 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTAATTTAATAACAC
Found at i:71771126 original size:19 final size:19
Alignment explanation
Indices: 71771089--71771124 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
71771079 AAGATTTATT
*
71771089 TAAAATTTAAATTGATTTA
1 TAAAATTTAAAATGATTTA
71771108 TAAAATTTAAAAT-ATTT
1 TAAAATTTAAAATGATTT
71771125 TAATTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TAAAATTTAAAATGATTTA
Found at i:71773028 original size:24 final size:24
Alignment explanation
Indices: 71773001--71773052 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
71772991 TTAGTAAGTC
*
71773001 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
71773025 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
71773049 AAAT
1 AAAT
71773053 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:71774996 original size:24 final size:24
Alignment explanation
Indices: 71774969--71775018 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
71774959 TTAGTAAGTC
* *
71774969 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAAAAAATACT
* *
71774993 AAATATATTATACTAAAAAATACT
1 AAATAAACTATACTAAAAAATACT
71775017 AA
1 AA
71775019 GTCTTCTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATAAACTATACTAAAAAATACT
Found at i:71777059 original size:21 final size:21
Alignment explanation
Indices: 71776967--71777060 Score: 63
Period size: 21 Copynumber: 4.4 Consensus size: 21
71776957 TGAATGCTAT
71776967 TTAA-ATTTTAGAATAT-TTTAA
1 TTAATATTTTA-AATATATTT-A
* *
71776988 TTAATATTATATCAATAAGATTTA
1 TTAATATT-T-TAAAT-ATATTTA
71777012 TTTAA-ATTTTAAAT-TGATTTA
1 -TTAATATTTTAAATAT-ATTTA
*
71777033 -TAATATTTTAAATATTTTTA
1 TTAATATTTTAAATATATTTA
71777053 TTAATATT
1 TTAATATT
71777061 ATATCAATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
19 3 0.05
20 13 0.22
21 17 0.29
22 7 0.12
23 5 0.09
24 6 0.10
25 7 0.12
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
TTAATATTTTAAATATATTTA
Found at i:71777108 original size:65 final size:63
Alignment explanation
Indices: 71776965--71777111 Score: 154
Period size: 65 Copynumber: 2.3 Consensus size: 63
71776955 CATGAATGCT
***
71776965 ATTTAAATTTTAGAATATTTTAATTAATATTATATCAATAAGATTTATTTAAATTTTAAATTGA
1 ATTTAAATTTTA-AATATTTTAATTAATATTATATCAATAAGAACAATTTAAATTTTAAATTGA
* * *
71777029 TTTATAATATTTTAAATATTTTTATTAATATTATATCAATAA-AACAATTT-AATTTGTCTAATT
1 ATT-TAA-ATTTTAAATATTTTAATTAATATTATATCAATAAGAACAATTTAAATTT-T-AAATT
71777092 GTCA
62 G--A
*
71777096 ATTTAAACTTTAAATA
1 ATTTAAATTTTAAATA
71777112 ACAATTTGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
63 5 0.07
64 8 0.12
65 44 0.64
66 9 0.13
67 3 0.04
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (63 bp):
ATTTAAATTTTAAATATTTTAATTAATATTATATCAATAAGAACAATTTAAATTTTAAATTGA
Found at i:71782271 original size:18 final size:17
Alignment explanation
Indices: 71782243--71782277 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
71782233 ATTATTAAGA
*
71782243 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
71782260 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
71782278 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:71782415 original size:18 final size:17
Alignment explanation
Indices: 71782387--71782421 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
71782377 ATTATTAAGA
*
71782387 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
71782404 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
71782422 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:71782631 original size:44 final size:45
Alignment explanation
Indices: 71782582--71782676 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
71782572 TTACACCTCT
* *
71782582 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
71782626 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
71782671 ATTACA
1 ATTACA
71782677 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:71782676 original size:16 final size:16
Alignment explanation
Indices: 71782655--71782687 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
71782645 TTGATTTGCT
*
71782655 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
71782671 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
71782687 A
1 A
71782688 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:71782697 original size:21 final size:21
Alignment explanation
Indices: 71782668--71782710 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
71782658 ACACCTCTAT
*
71782668 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
71782689 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
71782710 T
1 T
71782711 GCAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:71785964 original size:9 final size:9
Alignment explanation
Indices: 71785952--71785977 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
71785942 TGCTGATATT
71785952 GATGATGAA
1 GATGATGAA
71785961 GATGATGAA
1 GATGATGAA
71785970 GATGATGA
1 GATGATGA
71785978 TGAGAAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (9 bp):
GATGATGAA
Found at i:71793651 original size:3 final size:3
Alignment explanation
Indices: 71793643--71793680 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
71793633 ATCACATGTT
71793643 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
71793681 TGGATGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:71793786 original size:58 final size:58
Alignment explanation
Indices: 71793696--71793806 Score: 204
Period size: 58 Copynumber: 1.9 Consensus size: 58
71793686 GTAATGATAT
*
71793696 AACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTTATTGATGA
1 AACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGAGGTGATTTATTGATGA
*
71793754 AACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTTATT
1 AACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGAGGTGATTTATT
71793807 TTAAGTGGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (58 bp):
AACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGAGGTGATTTATTGATGA
Found at i:71798075 original size:3 final size:3
Alignment explanation
Indices: 71798067--71798110 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
71798057 ATCACATGTT
71798067 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
71798111 TGGATGTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:71798210 original size:58 final size:58
Alignment explanation
Indices: 71798120--71798236 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
71798110 TTGGATGTAA
* *
71798120 TGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTTAT
1 TGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGAGGTGATTTAT
*
71798178 TGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTTAT
1 TGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGAGGTGATTTAT
71798236 T
1 T
71798237 TTAAGTGGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (58 bp):
TGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGAGGTGATTTAT
Found at i:71801098 original size:17 final size:19
Alignment explanation
Indices: 71801054--71801100 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
71801044 ATATGTAAAA
71801054 TAAATAATTAATAATATATT
1 TAAATAA-TAATAATATATT
71801074 TAAA-AATAA-AATAT-TT
1 TAAATAATAATAATATATT
71801090 TAAATAATAAT
1 TAAATAATAAT
71801101 TAAAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 3 0.12
19 2 0.08
20 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAATAATAATATATT
Found at i:71801608 original size:31 final size:30
Alignment explanation
Indices: 71801573--71801652 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
71801563 AATTTCAATA
*
71801573 AAAGGGTCTAATTAAAATTTATAAA-ACTATT
1 AAAGGGTCTAATTAAAATTTA-AAAGA-AATT
* *
71801604 AAAGGGTTTAAAT-AAATTTAAAAGAAATT
1 AAAGGGTCTAATTAAAATTTAAAAGAAATT
*
71801633 -GAGGAGTCTAATTAAAATTT
1 AAAGG-GTCTAATTAAAATTT
71801653 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
28 3 0.08
29 12 0.30
30 14 0.35
31 11 0.28
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.34
Consensus pattern (30 bp):
AAAGGGTCTAATTAAAATTTAAAAGAAATT
Found at i:71808295 original size:21 final size:21
Alignment explanation
Indices: 71808269--71808309 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
71808259 TCCTCAATAT
71808269 CTGTTTATAACTTTTATGTCA
1 CTGTTTATAACTTTTATGTCA
71808290 CTGTTTATAACTTTTATGTC
1 CTGTTTATAACTTTTATGTC
71808310 GGGTTTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.54
Consensus pattern (21 bp):
CTGTTTATAACTTTTATGTCA
Found at i:71808758 original size:19 final size:19
Alignment explanation
Indices: 71808731--71808771 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
71808721 GAGGTTATGC
*
71808731 TTTACGATTTGTTATTATA
1 TTTACGATTTATTATTATA
*
71808750 TTTATGATTTATTATTATA
1 TTTACGATTTATTATTATA
71808769 TTT
1 TTT
71808772 TAGTTGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTACGATTTATTATTATA
Found at i:71817572 original size:16 final size:16
Alignment explanation
Indices: 71817547--71817594 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
71817537 TTAGCCAACA
*
71817547 AAATATATATAAATAT
1 AAATAAATATAAATAT
**
71817563 AAATAAATATTTATAT
1 AAATAAATATAAATAT
71817579 AAA-AAATA-AAATAT
1 AAATAAATATAAATAT
71817593 AA
1 AA
71817595 CTAGAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 6 0.22
15 5 0.19
16 16 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAAATATAAATAT
Found at i:71817572 original size:20 final size:19
Alignment explanation
Indices: 71817547--71817593 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
71817537 TTAGCCAACA
71817547 AAATATATATA-AATATAAAT
1 AAATATATATATAA-A-AAAT
*
71817567 AAATATTTATATAAAAAAT
1 AAATATATATATAAAAAAT
71817586 AAA-ATATA
1 AAATATATA
71817594 ACTAGAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 11 0.46
21 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATATATATATAAAAAAT
Found at i:71818006 original size:20 final size:21
Alignment explanation
Indices: 71817964--71818013 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
71817954 AGGAGCCAAC
*
71817964 AAATCAATTTGATTAAAAATT
1 AAATCAAATTGATTAAAAATT
*
71817985 AAATCAAATTGATT-AGAATT
1 AAATCAAATTGATTAAAAATT
*
71818005 AAATAAAAT
1 AAATCAAAT
71818014 AAGATAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (21 bp):
AAATCAAATTGATTAAAAATT
Found at i:71819136 original size:5 final size:5
Alignment explanation
Indices: 71819111--71819153 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
71819101 TTGATTTTTT
* *
71819111 ATTTA ATTT- ATTT- GTTCA ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
71819154 GGGGTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 6 0.18
5 27 0.82
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:71820460 original size:18 final size:18
Alignment explanation
Indices: 71820433--71820525 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
71820423 TACGACCGTT
71820433 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
71820451 TACGGCACTATTAACGTA
1 TACGGTACTATTCACGTA
*
71820469 TACGGTACTATTTACGTA
1 TACGGTACTATTCACGTA
*
71820487 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
71820505 TATGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
71820523 TAC
1 TAC
71820526 AGTAGTTGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:71820480 original size:36 final size:36
Alignment explanation
Indices: 71820433--71820525 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
71820423 TACGACCGTT
71820433 TACGGTACTATTCACGTATACGGCACTATTAACGTA
1 TACGGTACTATTCACGTATACGGCACTATTAACGTA
* *
71820469 TACGGTACTATTTACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTAACGTA
* *
71820505 TATGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
71820526 AGTAGTTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTAACGTA
Found at i:71840397 original size:30 final size:32
Alignment explanation
Indices: 71840363--71840422 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
71840353 CTCAAAGACA
*
71840363 TTTTA-TTTTCTACTTAATACCC-AAAAAATC
1 TTTTATTTTTCTACTTAAAACCCTAAAAAATC
71840393 TTTTATTTTTCTACTTAAAACCCTAAAAAA
1 TTTTATTTTTCTACTTAAAACCCTAAAAAA
71840423 ATCATAACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 5 0.19
31 16 0.59
32 6 0.22
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.43
Consensus pattern (32 bp):
TTTTATTTTTCTACTTAAAACCCTAAAAAATC
Found at i:71855620 original size:75 final size:75
Alignment explanation
Indices: 71855535--71855684 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
71855525 TTGTGCAGAA
71855535 ATTTCAATTTTGGATGACGCTGCAATTATATTATTAAGAGTAATAGCATTTTATTTATTATTAAC
1 ATTTCAATTTTGGATGACGCTGCAATTATATTATTAAGAGTAATAGCATTTTATTTATTATTAAC
71855600 ATATATTTGT
66 ATATATTTGT
71855610 ATTTCAATTTTGGATGACGCTGCAATTATATTATTAAGAGTAATAGCATTTTATTTATTATTAAC
1 ATTTCAATTTTGGATGACGCTGCAATTATATTATTAAGAGTAATAGCATTTTATTTATTATTAAC
71855675 ATATATTTGT
66 ATATATTTGT
71855685 TTATTGTATA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (75 bp):
ATTTCAATTTTGGATGACGCTGCAATTATATTATTAAGAGTAATAGCATTTTATTTATTATTAAC
ATATATTTGT
Found at i:71856176 original size:19 final size:17
Alignment explanation
Indices: 71856132--71856176 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
71856122 AATTGAATTA
71856132 ATAAAATTAAAATTTGT
1 ATAAAATTAAAATTTGT
*
71856149 ACAAAATTAAAATTCATGT
1 ATAAAATTAAAATT--TGT
*
71856168 ATAATATTA
1 ATAAAATTA
71856177 CATATTGGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 13 0.57
19 10 0.43
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (17 bp):
ATAAAATTAAAATTTGT
Found at i:71857090 original size:29 final size:31
Alignment explanation
Indices: 71857034--71857101 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 31
71857024 TTCATGAATA
*
71857034 TTGATGTAATGTGTAATTTGATACATG-AACT
1 TTGAT-TAATGTGTAATTTGATAAATGAAACT
71857065 TTGATTAA-GTGTAATTAT-ATAAATGAAACT
1 TTGATTAATGTGTAATT-TGATAAATGAAACT
*
71857095 TTAATTA
1 TTGATTA
71857102 TTATTCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 14 0.42
30 14 0.42
31 5 0.15
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (31 bp):
TTGATTAATGTGTAATTTGATAAATGAAACT
Found at i:71861482 original size:12 final size:13
Alignment explanation
Indices: 71861450--71861485 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
71861440 CCAATAAAAA
71861450 ATTTA-TTTATTT
1 ATTTATTTTATTT
71861462 ATTTATTTTATTT
1 ATTTATTTTATTT
71861475 A-TTATTTTATT
1 ATTTATTTTATT
71861486 ACTCTTCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTATTTTATTT
Found at i:71861872 original size:15 final size:15
Alignment explanation
Indices: 71861838--71861881 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
71861828 CAACTTTTAC
71861838 ATATATATATTATT-T
1 ATATAT-TATTATTGT
71861853 ATATATTATTATTGT
1 ATATATTATTATTGT
*
71861868 GTATATTATT-TTGT
1 ATATATTATTATTGT
71861882 TTTCTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (15 bp):
ATATATTATTATTGT
Found at i:71871345 original size:50 final size:50
Alignment explanation
Indices: 71871230--71871428 Score: 209
Period size: 50 Copynumber: 3.8 Consensus size: 50
71871220 GATAATAACA
* * * ** *
71871230 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGAGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCAG
* * **
71871281 TGCCCATACCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATATCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
*
71871331 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAAAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--AG
* * *
71871386 ATGCCAATGTCATGTCCCAGATATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
71871429 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
50 50 0.41
51 31 0.25
53 2 0.02
55 2 0.02
56 38 0.31
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
Found at i:71874103 original size:21 final size:21
Alignment explanation
Indices: 71874079--71874133 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
71874069 ATTCTTCATT
* *
71874079 TAATTTATAAATAATTTTTTA
1 TAATTTAAAAATAATCTTTTA
*
71874100 TAATATAAAAATAAATCTTTTA
1 TAATTTAAAAAT-AATCTTTTA
71874122 T-ATTTAAAAATA
1 TAATTTAAAAATA
71874134 GTGAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 19 0.66
22 9 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTTAAAAATAATCTTTTA
Found at i:71875625 original size:4 final size:4
Alignment explanation
Indices: 71875616--71875649 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
71875606 TCTAAGGGTA
71875616 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
71875650 TAACGCTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:71875998 original size:42 final size:42
Alignment explanation
Indices: 71875942--71876031 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
71875932 AAGAGTTCTT
71875942 TTTATTGAAGAAATATCATGAGAGAGCTTATAATTAAAATTA
1 TTTATTGAAGAAATATCATGAGAGAGCTTATAATTAAAATTA
71875984 TTTATTGAAGAAATATCATGAGAGAGCTTATAATTAAAATTA
1 TTTATTGAAGAAATATCATGAGAGAGCTTATAATTAAAATTA
71876026 TGTTAT
1 T-TTAT
71876032 ATAATAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 43 0.91
43 4 0.09
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.38
Consensus pattern (42 bp):
TTTATTGAAGAAATATCATGAGAGAGCTTATAATTAAAATTA
Found at i:71877206 original size:33 final size:34
Alignment explanation
Indices: 71877164--71877238 Score: 102
Period size: 33 Copynumber: 2.2 Consensus size: 34
71877154 TTAACATTAC
*
71877164 TTTTATCAAGAATTA-T-ATTTTTATGATAA-AAAG
1 TTTTATCAAGAATTATTAATGTTTAT--TAACAAAG
71877197 TTTTATCAAGAATTATTAATGTTTATTAACAAAG
1 TTTTATCAAGAATTATTAATGTTTATTAACAAAG
71877231 TTTTATCA
1 TTTTATCA
71877239 TTATTGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
33 18 0.47
34 13 0.34
35 7 0.18
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (34 bp):
TTTTATCAAGAATTATTAATGTTTATTAACAAAG
Found at i:71884249 original size:47 final size:49
Alignment explanation
Indices: 71884149--71884249 Score: 109
Period size: 49 Copynumber: 2.1 Consensus size: 49
71884139 TAAAATATTT
* ** * **
71884149 TAATATAAATATATTTGTAAAAATATTAAGATGATTAGATATAAAATTT
1 TAATAAAAATATATAAGTAAAAATATTAAGATGATTAAATATAAAATAA
*
71884198 TAATAAAAATATATAAGTAAAATTATTAA-AT-ATTAAAT-TAAAAATAA
1 TAATAAAAATATATAAGTAAAAATATTAAGATGATTAAATAT-AAAATAA
71884245 TAATA
1 TAATA
71884250 TGGACGAGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
46 1 0.02
47 16 0.36
48 2 0.05
49 25 0.57
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (49 bp):
TAATAAAAATATATAAGTAAAAATATTAAGATGATTAAATATAAAATAA
Found at i:71884586 original size:3 final size:3
Alignment explanation
Indices: 71884574--71884609 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
71884564 TGCTATTTTG
71884574 TTA TTA -TA TTA TTA TTA TTA TTA TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
71884610 GTTTAGATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:71884593 original size:14 final size:13
Alignment explanation
Indices: 71884567--71884608 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
71884557 GTTTTACTGC
*
71884567 TATTTTGTTATTA
1 TATTTTATTATTA
71884580 TATTATTATTATTA
1 TATT-TTATTATTA
71884594 TTATTTTATTATTA
1 -TATTTTATTATTA
71884608 T
1 T
71884609 TGTTTAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.19
14 17 0.65
15 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TATTTTATTATTA
Found at i:71884596 original size:17 final size:17
Alignment explanation
Indices: 71884574--71884609 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
71884564 TGCTATTTTG
71884574 TTATTATATTATTATTA
1 TTATTATATTATTATTA
*
71884591 TTATTATTTTATTATTA
1 TTATTATATTATTATTA
71884608 TT
1 TT
71884610 GTTTAGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATATTATTATTA
Found at i:71885278 original size:44 final size:42
Alignment explanation
Indices: 71885215--71885449 Score: 215
Period size: 44 Copynumber: 5.5 Consensus size: 42
71885205 CCGTTACACG
** *
71885215 GTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCA
1 GTGGAATCAGCACTTAGCAACCACCTCATAATC-AAGGAT-ACA
** *
71885259 GTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCA
1 GTGGAATCAGCACTTAGCAACCACCTCATAATC-AAGGAT-ACA
* * * * *
71885303 ATGGAATCAACACTTAGAAACCACCTTATAATCAATGATAC-
1 GTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGATACA
* * * *
71885344 GGGGAATCAGCACATAGCAACC-CCTTTCACAATCAAGGATACG
1 GTGGAATCAGCACTTAGCAACCACC--TCATAATCAAGGATACA
* *
71885387 GTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATAC-
1 GTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGATACA
* * *
71885428 GGGGAATCAGCACATAGTAACC
1 GTGGAATCAGCACTTAGCAACC
71885450 CCTTTTTGAT
Statistics
Matches: 163, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.01
41 36 0.22
42 27 0.17
43 25 0.15
44 73 0.45
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (42 bp):
GTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGATACA
Found at i:71885414 original size:84 final size:83
Alignment explanation
Indices: 71885304--71885495 Score: 280
Period size: 84 Copynumber: 2.3 Consensus size: 83
71885294 AGGATCCCAA
* *
71885304 TGGAATCAACACTTAGAAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
71885369 TTCACAATCAAGGATACGG
66 TT-ACAATCAAGGATACGG
*
71885388 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGTAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
*** * *
71885453 TTTTGATCAATGATTCGG
66 TTACAATCAAGGATACGG
*
71885471 -GGAATCTGCACTTAGCAACC-CCTTA
1 TGGAATCAGCACTTAGCAACCACCTTA
71885496 CATTCAAAGA
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
81 5 0.05
82 19 0.19
83 11 0.11
84 64 0.65
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (83 bp):
TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
TTACAATCAAGGATACGG
Found at i:71885462 original size:41 final size:41
Alignment explanation
Indices: 71885305--71885494 Score: 222
Period size: 41 Copynumber: 4.6 Consensus size: 41
71885295 GGATCCCAAT
* * *
71885305 GGAATCAACACTTAGAAACCACC-TTATAATCAATGATACGG
1 GGAATCAGCACATAGCAACC-CCTTTATAATCAATGATACGG
* *
71885346 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCCTTT-ATAATCAATGATACGG
*
71885388 TGGAATCAGCACTTAGCAACCACC-TTATAATCAATGATACGG
1 -GGAATCAGCACATAGCAACC-CCTTTATAATCAATGATACGG
* * * *
71885430 GGAATCAGCACATAGTAACCCCTTTTTGATCAATGATTCGG
1 GGAATCAGCACATAGCAACCCCTTTATAATCAATGATACGG
* *
71885471 GGAATCTGCACTTAGCAACCCCTT
1 GGAATCAGCACATAGCAACCCCTT
71885495 ACATTCAAAG
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
40 4 0.03
41 73 0.57
42 28 0.22
43 21 0.16
44 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
GGAATCAGCACATAGCAACCCCTTTATAATCAATGATACGG
Found at i:71887828 original size:2 final size:2
Alignment explanation
Indices: 71887821--71887847 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71887811 TTGACAACTG
71887821 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
71887848 TTGTAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71904016 original size:3 final size:3
Alignment explanation
Indices: 71904008--71904071 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
71903998 TTAGTATGGA
71904008 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
71904056 ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG A
71904072 CGACGACAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:71904984 original size:144 final size:144
Alignment explanation
Indices: 71904741--71905023 Score: 469
Period size: 144 Copynumber: 2.0 Consensus size: 144
71904731 GCCTCAAAAA
*
71904741 ATTAACAATAGGAGATTGCAAGGAGGTTGATTTCGAGGGCATGCAATGGGAACTCCTTAAGAATC
1 ATTAACAATAGGAGATTGCAAGGAGGTTGATTTAGAGGGCATGCAATGGGAACTCCTTAAGAATC
* ** * *
71904806 TCTCTCATTTGGAGATTAATAATAATCCGCAGCTGGTGTCTCTCCCCTTTTGGCTTCAACATCTT
66 TCTCTCATTTGGAGATTAAGAATAATCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCTT
71904871 GTTCAATTGAAAGG
131 GTTCAATTGAAAGG
*
71904885 ATTAACAGTAGGAGATTGCAAGGAGGTTGATTTAGAGGGCATGCAATGGGAAGC-CCTTAAGAAT
1 ATTAACAATAGGAGATTGCAAGGAGGTTGATTTAGAGGGCATGCAATGGGAA-CTCCTTAAGAAT
* *
71904949 CTCTCTCGTTTGGAGATTAAGAATATTCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCT
65 CTCTCTCATTTGGAGATTAAGAATAATCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCT
71905014 TGTTCAATTG
130 TGTTCAATTG
71905024 GAAACATTAG
Statistics
Matches: 129, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
144 128 0.99
145 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (144 bp):
ATTAACAATAGGAGATTGCAAGGAGGTTGATTTAGAGGGCATGCAATGGGAACTCCTTAAGAATC
TCTCTCATTTGGAGATTAAGAATAATCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCTT
GTTCAATTGAAAGG
Found at i:71909884 original size:30 final size:30
Alignment explanation
Indices: 71909848--71909908 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
71909838 TAATATCAAG
71909848 TTTACTCCAGGGATTCAACTATTTCGTTAA
1 TTTACTCCAGGGATTCAACTATTTCGTTAA
71909878 TTTACTCCAGGGATTCAACTATTTCGTTAA
1 TTTACTCCAGGGATTCAACTATTTCGTTAA
71909908 T
1 T
71909909 CTATTAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (30 bp):
TTTACTCCAGGGATTCAACTATTTCGTTAA
Found at i:71911160 original size:17 final size:18
Alignment explanation
Indices: 71911138--71911171 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
71911128 TTAAGGGTTC
71911138 AATTTAAAT-TAGTTTTT
1 AATTTAAATCTAGTTTTT
*
71911155 AATTTAATTCTAGTTTT
1 AATTTAAATCTAGTTTT
71911172 CGATTTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (18 bp):
AATTTAAATCTAGTTTTT
Found at i:71919529 original size:21 final size:21
Alignment explanation
Indices: 71919500--71919540 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
71919490 ATCTGCTCAA
* *
71919500 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
*
71919521 ACTCTACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
71919541 TTGCTCGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:71922089 original size:21 final size:21
Alignment explanation
Indices: 71922048--71922089 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
71922038 TCGGGTCACC
*
71922048 TAGAAATTTGGGTTGTTTTAA
1 TAGAAATTTGGGTTGTATTAA
*
71922069 TAGAACATTTTGGTT-TATTAA
1 TAGAA-ATTTGGGTTGTATTAA
71922090 AACAATGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (21 bp):
TAGAAATTTGGGTTGTATTAA
Found at i:71928338 original size:20 final size:20
Alignment explanation
Indices: 71928315--71928352 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
71928305 CACGTGTATT
71928315 AAATAAAAATTTAATAATTA
1 AAATAAAAATTTAATAATTA
*
71928335 AAATATAAATTTAATAAT
1 AAATAAAAATTTAATAAT
71928353 AATTTAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAAAAATTTAATAATTA
Found at i:71935854 original size:22 final size:23
Alignment explanation
Indices: 71935810--71935854 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
71935800 CAATGTTATG
**
71935810 TTTATATTTAAAATATATCATAT
1 TTTATATTTAAAATATAAAATAT
*
71935833 TTTATA-TTAAATTATAAAATAT
1 TTTATATTTAAAATATAAAATAT
71935855 ACATAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTATATTTAAAATATAAAATAT
Found at i:71937217 original size:28 final size:27
Alignment explanation
Indices: 71937158--71937217 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
71937148 TTTAAATTAA
*
71937158 TAAA-AATAAAATTATATTTTAATCTT
1 TAAATAATAAAATTATAATTTAATCTT
71937184 TAAAATAATAAAAATT-TAATTTAATCCTT
1 T-AAATAAT-AAAATTATAATTTAAT-CTT
71937213 TAAAT
1 TAAAT
71937218 CTATCATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 1 0.03
27 3 0.10
28 15 0.52
29 10 0.34
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAATAATAAAATTATAATTTAATCTT
Found at i:71946116 original size:13 final size:13
Alignment explanation
Indices: 71946098--71946122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71946088 GGGTTGTAGT
71946098 TTAAATCTGTGCA
1 TTAAATCTGTGCA
71946111 TTAAATCTGTGC
1 TTAAATCTGTGC
71946123 CAAGGTTTCA
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTAAATCTGTGCA
Found at i:71983488 original size:3 final size:3
Alignment explanation
Indices: 71983480--71983504 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
71983470 TACCATTACA
71983480 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
71983505 CTCAATGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:71993235 original size:24 final size:24
Alignment explanation
Indices: 71993189--71993235 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
71993179 GTACACGCTA
*
71993189 TTATTTTATTTTTCATTTCATTTT
1 TTATTTTATTTTTCAATTCATTTT
*
71993213 TTATTTATATTTTT-AATTGATTT
1 TTATTT-TATTTTTCAATTCATTT
71993236 AAGGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (24 bp):
TTATTTTATTTTTCAATTCATTTT
Found at i:71998504 original size:29 final size:30
Alignment explanation
Indices: 71998461--71998524 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
71998451 AATTTGGAAT
*
71998461 TTTAGTCATTATACTTTT-A-TTTTCAAGAA
1 TTTAGTCATTATACTTTTCAGATTTCAA-AA
* *
71998490 TTTAGTTATTTTACTTTTCAGATTTCAAAA
1 TTTAGTCATTATACTTTTCAGATTTCAAAA
71998520 TTTAG
1 TTTAG
71998525 GCCCAATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 16 0.53
30 8 0.27
31 6 0.20
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTAGTCATTATACTTTTCAGATTTCAAAA
Found at i:72003524 original size:10 final size:10
Alignment explanation
Indices: 72003509--72003542 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
72003499 ACAGTTAAAT
72003509 CAGCAATTGA
1 CAGCAATTGA
72003519 CAGCAATTGA
1 CAGCAATTGA
72003529 CAGCAATTGA
1 CAGCAATTGA
72003539 CAGC
1 CAGC
72003543 TTTTAGGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (10 bp):
CAGCAATTGA
Found at i:72004006 original size:29 final size:28
Alignment explanation
Indices: 72003974--72004045 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
72003964 TATAGACTGT
*
72003974 ATCAAATTAGTCC-ATTTGTTATTAAATGA
1 ATCAAATTAGTCCGA--TATTATTAAATGA
*
72004003 ATCAACTTAGTTCCGATATTATTAAATGA
1 ATCAAATTAG-TCCGATATTATTAAATGA
*
72004032 ATTAAATTAGTCCG
1 ATCAAATTAGTCCG
72004046 CATAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.11
29 29 0.78
30 3 0.08
31 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (28 bp):
ATCAAATTAGTCCGATATTATTAAATGA
Found at i:72015718 original size:29 final size:29
Alignment explanation
Indices: 72015673--72015731 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
72015663 GGCTGAAATT
*
72015673 AAGATTAAATTAAAATTTTATTATTT-TTA
1 AAGATTAAAATAAAATTTTATT-TTTATTA
*
72015702 AAGATTAAAATATAATTTTATTTTTATTA
1 AAGATTAAAATAAAATTTTATTTTTATTA
72015731 A
1 A
72015732 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
AAGATTAAAATAAAATTTTATTTTTATTA
Found at i:72028619 original size:3 final size:3
Alignment explanation
Indices: 72028611--72028644 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
72028601 GAAAGGGTCA
72028611 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
72028645 AGGATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:72032073 original size:19 final size:21
Alignment explanation
Indices: 72032049--72032089 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
72032039 ACACTTCACT
72032049 TTCTTTGC-TTTC-TTTTCTC
1 TTCTTTGCTTTTCATTTTCTC
*
72032068 TTCTTTTCTTTTCATTTTCTC
1 TTCTTTGCTTTTCATTTTCTC
72032089 T
1 T
72032090 CGATTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCTTTGCTTTTCATTTTCTC
Found at i:72032843 original size:29 final size:29
Alignment explanation
Indices: 72032811--72032887 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
72032801 CAAATTTGGG
* *
72032811 AAATTCTCATTAAGCCTTCAAT-TTTTTGA
1 AAATTTTCATTAAGCCCTCAATCTTTTT-A
* *
72032840 AAATTTTAATTAAACTCCTCAATCTTTTTA
1 AAATTTTCATTAAGC-CCTCAATCTTTTTA
*
72032870 AAATTTTCACTAAGCCCT
1 AAATTTTCATTAAGCCCT
72032888 TTAATAGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 15 0.38
30 19 0.49
31 5 0.13
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (29 bp):
AAATTTTCATTAAGCCCTCAATCTTTTTA
Found at i:72035569 original size:120 final size:120
Alignment explanation
Indices: 72035356--72035601 Score: 474
Period size: 120 Copynumber: 2.0 Consensus size: 120
72035346 CGTTGGAATC
* *
72035356 ATCATCGATTGGTTTTGTCGTCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGTT
1 ATCATCAATTGGTTTTGTCGTCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGAT
72035421 GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGGCTATT
66 GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGGCTATT
72035476 ATCATCAATTGGTTTTGTCGTCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGAT
1 ATCATCAATTGGTTTTGTCGTCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGAT
72035541 GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGGCTATT
66 GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGGCTATT
72035596 ATCATC
1 ATCATC
72035602 CATGTACTCC
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 124 1.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.35
Consensus pattern (120 bp):
ATCATCAATTGGTTTTGTCGTCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGAT
GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGGCTATT
Found at i:72039266 original size:20 final size:19
Alignment explanation
Indices: 72039243--72039290 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
72039233 TTTTCTTATA
72039243 ATTTTTTTAATTTTTAAAAT
1 ATTTTTTTAATTTTT-AAAT
* *
72039263 ATTTTTTTGATTTTTTAAT
1 ATTTTTTTAATTTTTAAAT
72039282 -TTTTTTTAA
1 ATTTTTTTAA
72039291 AAATAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.32
19 3 0.12
20 14 0.56
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
ATTTTTTTAATTTTTAAAT
Found at i:72048668 original size:16 final size:16
Alignment explanation
Indices: 72048647--72048677 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
72048637 CTTCAAAAAT
72048647 TATATTACAAATTAAA
1 TATATTACAAATTAAA
72048663 TATATTACAAATTAA
1 TATATTACAAATTAA
72048678 TATTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
TATATTACAAATTAAA
Found at i:72049742 original size:3 final size:3
Alignment explanation
Indices: 72049734--72049791 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
72049724 TTTGATAAGA
72049734 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
72049782 TAT TAT TAT T
1 TAT TAT TAT T
72049792 TGCTTTGGGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:72054352 original size:21 final size:23
Alignment explanation
Indices: 72054328--72054369 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
72054318 TTCACTGGAT
*
72054328 ACGACGGTG-CCTA-TGGTTGCA
1 ACGACGGCGTCCTAGTGGTTGCA
72054349 ACGACGGCGTCCTAGTGGTTG
1 ACGACGGCGTCCTAGTGGTTG
72054370 GTGGCAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.17, C:0.24, G:0.36, T:0.24
Consensus pattern (23 bp):
ACGACGGCGTCCTAGTGGTTGCA
Found at i:72058022 original size:42 final size:42
Alignment explanation
Indices: 72057971--72058114 Score: 225
Period size: 42 Copynumber: 3.4 Consensus size: 42
72057961 ATAGTCAGCT
72057971 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
* *
72058013 ATGGCCTTACATGAATCTCATATCGATGCCAATGTCCCAAAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
* * * *
72058055 ATGGTCTTACATGAATCACATAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
72058097 ATGGTCTTACACGTAATC
1 ATGGTCTTACACG-AATC
72058115 ACATCTTTGT
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 90 0.96
43 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (42 bp):
ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
Found at i:72067423 original size:21 final size:21
Alignment explanation
Indices: 72067391--72067431 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
72067381 AGGCTCGAGG
72067391 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
72067412 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
72067432 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:72073686 original size:31 final size:30
Alignment explanation
Indices: 72073650--72073722 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
72073640 ATTAATAATG
*
72073650 ATAAAATTATAATTTAA-TCCTCTAAAAATTT
1 ATAAAAATATAATTTAACT-CTCTAAAAA-TT
* *
72073681 ATAAAAAAATTAATTTAACTCTTTAAAAATT
1 ATAAAAATA-TAATTTAACTCTCTAAAAATT
72073712 ATAAAAATATA
1 ATAAAAATATA
72073723 CTACTATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 2 0.06
31 17 0.47
32 16 0.44
33 1 0.03
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (30 bp):
ATAAAAATATAATTTAACTCTCTAAAAATT
Found at i:72073697 original size:32 final size:31
Alignment explanation
Indices: 72073659--72073718 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
72073649 GATAAAATTA
72073659 TAATTTAA-TCCTCTAAAAATTTATAAAAAAAT
1 TAATTTAACT-CTCTAAAAA-TTATAAAAAAAT
*
72073691 TAATTTAACTCTTTAAAAATTATAAAAA
1 TAATTTAACTCTCTAAAAATTATAAAAA
72073719 TATACTACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.35
32 16 0.62
33 1 0.04
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (31 bp):
TAATTTAACTCTCTAAAAATTATAAAAAAAT
Found at i:72080610 original size:9 final size:9
Alignment explanation
Indices: 72080596--72080622 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
72080586 TTTCTTATTA
72080596 TTTTTTAAT
1 TTTTTTAAT
72080605 TTTTTTAAT
1 TTTTTTAAT
72080614 TTTTTTAAT
1 TTTTTTAAT
72080623 GTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:72080635 original size:20 final size:21
Alignment explanation
Indices: 72080612--72080652 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
72080602 AATTTTTTTA
*
72080612 ATTTTTTTAATG-TTTAAAAT
1 ATTTTTTAAATGTTTTAAAAT
72080632 ATTTTTTAAATGTTTTAAAAT
1 ATTTTTTAAATGTTTTAAAAT
72080653 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTTTAAATGTTTTAAAAT
Found at i:72082249 original size:15 final size:15
Alignment explanation
Indices: 72082229--72082261 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
72082219 AATTCTAATG
72082229 TAATAAA-AGTAAAAA
1 TAATAAAGA-TAAAAA
72082244 TAATAAAGATAAAAA
1 TAATAAAGATAAAAA
72082259 TAA
1 TAA
72082262 GCAAAAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
TAATAAAGATAAAAA
Found at i:72090621 original size:12 final size:12
Alignment explanation
Indices: 72090603--72090637 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
72090593 TCCCTTAAAC
72090603 AAAGGAATTAAT
1 AAAGGAATTAAT
*
72090615 GAAGGAATTAAT
1 AAAGGAATTAAT
72090627 AAAGG-ATTAAT
1 AAAGGAATTAAT
72090638 TGATATGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (12 bp):
AAAGGAATTAAT
Found at i:72093089 original size:31 final size:31
Alignment explanation
Indices: 72093051--72093116 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
72093041 AAAATATTAA
72093051 AAAATATTTTCTTAT-AA-TTTTTTAAAATTTT
1 AAAATATTTT-TT-TGAATTTTTTTAAAATTTT
72093082 AAAATATTTTTTTGAATTTTTTTAAAATTTT
1 AAAATATTTTTTTGAATTTTTTTAAAATTTT
72093113 AAAA
1 AAAA
72093117 ATAATTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 1 0.03
30 4 0.12
31 28 0.85
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
AAAATATTTTTTTGAATTTTTTTAAAATTTT
Found at i:72096402 original size:24 final size:24
Alignment explanation
Indices: 72096345--72096396 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
72096335 TTTTTAGAAA
* **
72096345 ATTTAGTATTTATTAATATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
72096369 GTTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
72096393 ATTT
1 ATTT
72096397 GACATTGATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:72096407 original size:24 final size:24
Alignment explanation
Indices: 72096362--72096408 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
72096352 ATTTATTAAT
* *
72096362 ATAATATGTTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
72096386 ATAATATATTT-GACATTGATTAG
1 ATAATATATTTAG-CATTGATTAG
72096409 AATTAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:72097298 original size:40 final size:40
Alignment explanation
Indices: 72097254--72097329 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
72097244 AGCAGCGCAA
72097254 AAAAACAAACGCCACAATAGACCTACATTAGCGGCGCTCG
1 AAAAACAAACGCCACAATAGACCTACATTAGCGGCGCTCG
* * *
72097294 AAAAACAAACGCCACAATAGGCCTGCCTTAGCGGCG
1 AAAAACAAACGCCACAATAGACCTACATTAGCGGCG
72097330 ATTTCTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.38, C:0.30, G:0.20, T:0.12
Consensus pattern (40 bp):
AAAAACAAACGCCACAATAGACCTACATTAGCGGCGCTCG
Found at i:72098920 original size:15 final size:16
Alignment explanation
Indices: 72098890--72098924 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
72098880 ATTTATCAAT
*
72098890 TTTAATATTGATAGTA
1 TTTAATATTGAGAGTA
72098906 TTTAA-ATTGAGAGTA
1 TTTAATATTGAGAGTA
72098921 TTTA
1 TTTA
72098925 TAAATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTAATATTGAGAGTA
Found at i:72103930 original size:23 final size:23
Alignment explanation
Indices: 72103883--72103934 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
72103873 ACCTACTTTC
* ** *
72103883 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCAAGATA
72103906 TTACAGTAGTAATTTTCAAGATA
1 TTACAGTAGTAATTTTCAAGATA
72103929 TTACAG
1 TTACAG
72103935 GTGCTCATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCAAGATA
Found at i:72104921 original size:19 final size:20
Alignment explanation
Indices: 72104899--72104939 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
72104889 ATATTTTCTT
72104899 ATATTTTTTAA-TTTTTAAA
1 ATATTTTTTAATTTTTTAAA
72104918 ATATTTTTTAATTTTTTAAA
1 ATATTTTTTAATTTTTTAAA
72104938 AT
1 AT
72104940 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTTTAATTTTTTAAA
Found at i:72104921 original size:29 final size:28
Alignment explanation
Indices: 72104876--72104946 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 28
72104866 ATTATTTAAA
72104876 AAAATATTTAAAAATATTTTCTTATATTTTTT
1 AAAAT-TTTAAAA-TATTTT-TTA-ATTTTTT
*
72104908 -AATTTTTAAAATATTTTTTAATTTTTT
1 AAAATTTTAAAATATTTTTTAATTTTTT
72104935 AAAATTTTAAAA
1 AAAATTTTAAAA
72104947 AATAATTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 7 0.19
28 13 0.36
29 6 0.17
30 7 0.19
31 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
AAAATTTTAAAATATTTTTTAATTTTTT
Found at i:72118289 original size:20 final size:20
Alignment explanation
Indices: 72118231--72118289 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
72118221 TAATACTTTC
72118231 AAAACTTAATTAA-AATATTTT
1 AAAA-TTAATTAATAA-ATTTT
* * * *
72118252 ATAATTTATAAATTAATTTT
1 AAAATTAATTAATAAATTTT
72118272 AAAATTAATTAATAAATT
1 AAAATTAATTAATAAATT
72118290 GAGAATATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATTAATTAATAAATTTT
Found at i:72120979 original size:3 final size:3
Alignment explanation
Indices: 72120971--72121003 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
72120961 AAGTGACTTC
*
72120971 TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
72121004 GAATCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:72124303 original size:31 final size:29
Alignment explanation
Indices: 72124267--72124333 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
72124257 ATTAATAGTG
*
72124267 ATAAAATTATAATTTGA-TCATCTAAAAAATT
1 ATAAAATT-TAATTTAATTC-T-TAAAAAATT
*
72124298 ATAAAAATTTAATTTAATTCTTTAAAAATT
1 AT-AAAATTTAATTTAATTCTTAAAAAATT
72124328 ATAAAA
1 ATAAAA
72124334 ATACATTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 4 0.12
30 10 0.31
31 10 0.31
32 8 0.25
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAAAATTTAATTTAATTCTTAAAAAATT
Found at i:72125796 original size:28 final size:28
Alignment explanation
Indices: 72125752--72125812 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
72125742 TTAAAATAGT
* *
72125752 TTTTAATAATTTTTATACTTTTTAAAAC
1 TTTTAATAAGTTGTATACTTTTTAAAAC
* *
72125780 TTTTAATAAGTTGTATACTTTTTTAAAT
1 TTTTAATAAGTTGTATACTTTTTAAAAC
72125808 TTTTA
1 TTTTA
72125813 TATTTAGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTAATAAGTTGTATACTTTTTAAAAC
Found at i:72129016 original size:21 final size:21
Alignment explanation
Indices: 72128990--72129030 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
72128980 ATCTGCTCAA
*
72128990 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
72129011 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
72129031 TTGCTCGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:72133317 original size:31 final size:32
Alignment explanation
Indices: 72133273--72133332 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
72133263 AAGAAGAAGA
*
72133273 AAGAAGAAAGAAAAAAGAAGAAGAAAAAGGGG
1 AAGAAGAAAGAAAAAAGAAAAAGAAAAAGGGG
*
72133305 AAGAA-AAAGAAAAAAGAAAAAGAGAAAG
1 AAGAAGAAAGAAAAAAGAAAAAGAAAAAG
72133333 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (32 bp):
AAGAAGAAAGAAAAAAGAAAAAGAAAAAGGGG
Found at i:72133321 original size:25 final size:25
Alignment explanation
Indices: 72133266--72133342 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
72133256 CGGCCCGAAG
*
72133266 AAGAAGAAAGAAGAAAGAAAAA-AGAAG
1 AAGAA-AAAG-AGAAAGAAAAAGA-AAA
* *
72133293 AAGAAAAAGGGGAAGAAAAAGAAAA
1 AAGAAAAAGAGAAAGAAAAAGAAAA
72133318 AAGAAAAAGAGAAAGAAAAA-AAAA
1 AAGAAAAAGAGAAAGAAAAAGAAAA
72133342 A
1 A
72133343 TTTTAAAGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
24 5 0.11
25 29 0.66
26 5 0.11
27 5 0.11
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (25 bp):
AAGAAAAAGAGAAAGAAAAAGAAAA
Found at i:72133332 original size:6 final size:6
Alignment explanation
Indices: 72133266--72133342 Score: 66
Period size: 6 Copynumber: 12.3 Consensus size: 6
72133256 CGGCCCGAAG
* ***
72133266 AAGAAGA AAGAAGA AAGAAAA AAGAAG AAGAAA AAGGGG AAGAAA AAGAAAA
1 AAGAA-A AAGAA-A AAG-AAA AAGAAA AAGAAA AAGAAA AAGAAA AAG-AAA
*
72133318 AAGAAA AAGAGA AAGAAA AA-AAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AA
72133343 TTTTAAAGTC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
5 5 0.09
6 31 0.53
7 20 0.34
8 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:72134169 original size:18 final size:17
Alignment explanation
Indices: 72134124--72134173 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
72134114 TAAAGAAAAA
*
72134124 TCGTGTTTCAAAAATTT
1 TCGTATTTCAAAAATTT
**
72134141 TTATATCTTCAAAAATTT
1 TCGTAT-TTCAAAAATTT
72134159 CTCGTATTTCAAAAA
1 -TCGTATTTCAAAAA
72134174 ATCTTCACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (17 bp):
TCGTATTTCAAAAATTT
Found at i:72134315 original size:18 final size:18
Alignment explanation
Indices: 72134284--72134351 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
72134274 TTTCGTGTTT
72134284 TCATGTTCTCAAAAAATTC
1 TCATGTT-TCAAAAAATTC
**
72134303 TCATGTTTCAAAAAGCT-
1 TCATGTTTCAAAAAATTC
* *
72134320 TCGTGTTTTC-AAAAATCC
1 TCATG-TTTCAAAAAATTC
72134338 TCATGTTTCAAAAA
1 TCATGTTTCAAAAA
72134352 TTTTCGTGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 12 0.31
18 20 0.51
19 7 0.18
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (18 bp):
TCATGTTTCAAAAAATTC
Found at i:72134326 original size:17 final size:18
Alignment explanation
Indices: 72134308--72134535 Score: 112
Period size: 18 Copynumber: 12.6 Consensus size: 18
72134298 AATTCTCATG
*
72134308 TTTCAAAAAGCTTCGTGT
1 TTTCAAAAATCTTCGTGT
* *
72134326 TTTCAAAAATCCTCATG-
1 TTTCAAAAATCTTCGTGT
*
72134343 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATCTTCGTGT
* *
72134361 TTTCAAAATTC-TAGTG-
1 TTTCAAAAATCTTCGTGT
** * *
72134377 TAACAAAAATTTTCATGT
1 TTTCAAAAATCTTCGTGT
72134395 TTTCAAAAAT-TTCCCGTGT
1 TTTCAAAAATCTT--CGTGT
*
72134414 TTTCAAACAT-TCTCGT-T
1 TTTCAAAAATCT-TCGTGT
* * *
72134431 TTTCGAAAATTTTCTTGT
1 TTTCAAAAATCTTCGTGT
72134449 TTTCAGAAAAAAAT-TTCCGTGT
1 TTTC----AAAAATCTT-CGTGT
* *
72134471 TTT-ATAAATTTTCGTGT
1 TTTCAAAAATCTTCGTGT
*** **
72134488 TTTCAAAAAAAAATCCCGT
1 TTTC-AAAAATCTTCGTGT
*
72134507 CTTTCAAAAATTTTCGTGT
1 -TTTCAAAAATCTTCGTGT
72134526 TTTCAAAAAT
1 TTTCAAAAAT
72134536 TGACCGTGTT
Statistics
Matches: 157, Mismatches: 36, Indels: 34
0.69 0.16 0.15
Matches are distributed among these distances:
16 7 0.04
17 48 0.31
18 52 0.33
19 31 0.20
20 5 0.03
21 2 0.01
22 12 0.08
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (18 bp):
TTTCAAAAATCTTCGTGT
Found at i:72134341 original size:35 final size:35
Alignment explanation
Indices: 72134295--72134368 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
72134285 CATGTTCTCA
*
72134295 AAAAATTCTCATGTTTCAAAAAGCTTCGTGTTTTC
1 AAAAATCCTCATGTTTCAAAAAGCTTCGTGTTTTC
**
72134330 AAAAATCCTCATGTTTCAAAAATTTTCGTGTTTTC
1 AAAAATCCTCATGTTTCAAAAAGCTTCGTGTTTTC
72134365 AAAA
1 AAAA
72134369 TTCTAGTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (35 bp):
AAAAATCCTCATGTTTCAAAAAGCTTCGTGTTTTC
Found at i:72134384 original size:34 final size:34
Alignment explanation
Indices: 72134296--72134402 Score: 108
Period size: 34 Copynumber: 3.1 Consensus size: 34
72134286 ATGTTCTCAA
* ** **
72134296 AAAATTCTCATGTTTCAAAAAGCTTCGTGTTTTC
1 AAAATCCTCATGTAACAAAAATTTTCGTGTTTTC
**
72134330 AAAAATCCTCATGTTTCAAAAATTTTCGTGTTTTC
1 -AAAATCCTCATGTAACAAAAATTTTCGTGTTTTC
* *
72134365 AAAATTCT-AGTGTAACAAAAATTTTCATGTTTTC
1 AAAATCCTCA-TGTAACAAAAATTTTCGTGTTTTC
72134399 AAAA
1 AAAA
72134403 ATTTCCCGTG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
33 1 0.02
34 32 0.50
35 31 0.48
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (34 bp):
AAAATCCTCATGTAACAAAAATTTTCGTGTTTTC
Found at i:72134518 original size:38 final size:38
Alignment explanation
Indices: 72134431--72134534 Score: 136
Period size: 38 Copynumber: 2.7 Consensus size: 38
72134421 CATTCTCGTT
* * * * *
72134431 TTTCGAAAATTTTCTTGTTTTCAGAAAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTGTTTTCA-AAAAAAAATCCCGTC
* *
72134470 TTTTATAAATTTTCGTGTTTTCAAAAAAAAATCCCGTC
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAATCCCGTC
72134508 TTTCAAAAATTTTCGTGTTTTCAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAA
72134535 TTGACCGTGT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
38 37 0.66
39 19 0.34
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (38 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAAATCCCGTC
Found at i:72134585 original size:21 final size:21
Alignment explanation
Indices: 72134561--72134632 Score: 119
Period size: 21 Copynumber: 3.4 Consensus size: 21
72134551 AATTTCCGTA
*
72134561 TTTCAAAA-AAATCTTTTGTGT
1 TTTCAAAATAAA-ATTTTGTGT
72134582 TTTCAAAATAAAATTTTGTGT
1 TTTCAAAATAAAATTTTGTGT
72134603 TTTCAAAATAAAATTTTGTGT
1 TTTCAAAATAAAATTTTGTGT
72134624 TTTCAAAAT
1 TTTCAAAAT
72134633 TTTTGTGTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
21 46 0.94
22 3 0.06
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (21 bp):
TTTCAAAATAAAATTTTGTGT
Found at i:72134633 original size:16 final size:16
Alignment explanation
Indices: 72134612--72134647 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
72134602 TTTTCAAAAT
72134612 AAAA-TTTTGTGTTTTC
1 AAAATTTTTGTG-TTTC
72134628 AAAATTTTTGTGTTTC
1 AAAATTTTTGTGTTTC
72134644 AAAA
1 AAAA
72134648 AGAAAATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (16 bp):
AAAATTTTTGTGTTTC
Found at i:72134661 original size:37 final size:37
Alignment explanation
Indices: 72134591--72134668 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
72134581 TTTTCAAAAT
* *
72134591 AAAATTTTGTGTTTTCAAAATAAAATTTTGTGTTTTC
1 AAAATTTTGTGTTTTCAAAATAAAAATTCGTGTTTTC
*
72134628 AAAATTTT-TGTGTTTCAAAA-AGAAAATTCGTGTTTTG
1 AAAATTTTGTGT-TTTCAAAATA-AAAATTCGTGTTTTC
72134665 AAAA
1 AAAA
72134669 AATTCTCGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 4 0.11
37 32 0.89
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (37 bp):
AAAATTTTGTGTTTTCAAAATAAAAATTCGTGTTTTC
Found at i:72134728 original size:17 final size:17
Alignment explanation
Indices: 72134705--72134815 Score: 91
Period size: 17 Copynumber: 6.3 Consensus size: 17
72134695 TTTTTTTTTT
72134705 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
72134722 TAAAATTCTTGCGT-TTTAA
1 AAAAATT-TT-CGTGTTT-C
*
72134741 AAAAAATTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
72134758 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
**
72134776 AAAAATTGACCGTGTTT-
1 AAAAATT-TTCGTGTTTC
* *
72134793 AATAAATTTCCGTATTTC
1 AA-AAATTTTCGTGTTTC
72134811 AAAAA
1 AAAAA
72134816 AAATCTTTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
17 33 0.43
18 31 0.41
19 12 0.16
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:72134774 original size:36 final size:36
Alignment explanation
Indices: 72134654--72134928 Score: 134
Period size: 36 Copynumber: 7.2 Consensus size: 36
72134644 AAAAAGAAAA
* *
72134654 TTCGTGTTTT-GAAAAAATTCTCGTGTTTC-AAATTT
1 TTCGTGTTTTAAAAAAAATT-TCGTGTTTCAAAAATT
** * *
72134689 TTCGTGTTTTTTTTTTAAAAATTTTCGTGTTTCTAAAATT
1 TTCGTG----TTTTAAAAAAAATTTCGTGTTTCAAAAATT
*
72134729 CTT-GCGTTTTAAAAAAAATTTCGTGTTTCAAAAATT
1 -TTCGTGTTTTAAAAAAAATTTCGTGTTTCAAAAATT
* *
72134765 TTCGTGTTTT--CAAAAATTGACCGTGTTT-AATAAATT
1 TTCGTGTTTTAAAAAAAATT--TCGTGTTTCAA-AAATT
* * * *
72134801 TCCGTATTTCAAAAAAAATCTTTTGTGTTTTCAAAATAAAATT
1 TTCGTGTTTTAAAAAAAA--TTTCGTG-TTTC---A-AAAATT
*
72134844 TT-GTGTTTTCAAAATAAAATTTTGTGTTTTC-AAAATT
1 TTCGTGTTTT-AAAA-AAAATTTCGTG-TTTCAAAAATT
* * *
72134881 TTCGTGTTTCAAAAAGAAAATTCGTGTTTTGAAAAAATT
1 TTCGTGTTTTAAAAA-AAATTTCGTG-TTT-CAAAAATT
*
72134920 CTCGTGTTT
1 TTCGTGTTT
72134929 CAAATTTTTC
Statistics
Matches: 188, Mismatches: 25, Indels: 50
0.71 0.10 0.19
Matches are distributed among these distances:
34 7 0.04
35 10 0.05
36 52 0.28
37 24 0.13
38 14 0.07
39 30 0.16
40 16 0.09
41 2 0.01
42 17 0.09
43 11 0.06
44 5 0.03
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (36 bp):
TTCGTGTTTTAAAAAAAATTTCGTGTTTCAAAAATT
Found at i:72134845 original size:21 final size:21
Alignment explanation
Indices: 72134807--72134879 Score: 121
Period size: 21 Copynumber: 3.4 Consensus size: 21
72134797 AATTTCCGTA
72134807 TTTCAAAA-AAAATCTTTTGTGT
1 TTTCAAAATAAAA--TTTTGTGT
72134829 TTTCAAAATAAAATTTTGTGT
1 TTTCAAAATAAAATTTTGTGT
72134850 TTTCAAAATAAAATTTTGTGT
1 TTTCAAAATAAAATTTTGTGT
72134871 TTTCAAAAT
1 TTTCAAAAT
72134880 TTTCGTGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
21 38 0.76
22 8 0.16
23 4 0.08
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (21 bp):
TTTCAAAATAAAATTTTGTGT
Found at i:72134880 original size:16 final size:16
Alignment explanation
Indices: 72134859--72134894 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
72134849 TTTTCAAAAT
72134859 AAAATTTT-GTGTTTTC
1 AAAATTTTCGTG-TTTC
72134875 AAAATTTTCGTGTTTC
1 AAAATTTTCGTGTTTC
72134891 AAAA
1 AAAA
72134895 AGAAAATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.47
Consensus pattern (16 bp):
AAAATTTTCGTGTTTC
Found at i:72134994 original size:246 final size:246
Alignment explanation
Indices: 72134457--72135009 Score: 959
Period size: 247 Copynumber: 2.2 Consensus size: 246
72134447 GTTTTCAGAA
* * ** *
72134457 AAAAATTTCCGTGTTT-TATAAATT-TTCGTGTTTTCAAAAAAAAATCCCGTCTTTCAAAAATTT
1 AAAAATTTTCGTGTTTCTA-AAATTCTT-GCGTTTT--AAAAAAAATTTCGTGTTTCAAAAATTT
*
72134520 TCGTGTTTTCAAAAATTGACCGTGTTTCATAAATTTCCGTATTTCAAAAAAATCTTTTGTGTTTT
62 TCGTGTTTTCAAAAATTGACCGTGTTTAATAAATTTCCGTATTTCAAAAAAATCTTTTGTGTTTT
*
72134585 CAAAATAAAATTTTGTGTTTTCAAAATAAAATTTTGTGTTTTCAAAATTTTTGTGTTTCAAAAAG
127 CAAAATAAAATTTTGTGTTTTCAAAATAAAATTTTGTGTTTTCAAAATTTTCGTGTTTCAAAAAG
72134650 AAAATTCGTGTTTTGAAAAAATTCTCGTGTTTCAAATTTTTCGTGTTTTTTTTTT
192 AAAATTCGTGTTTTGAAAAAATTCTCGTGTTTCAAATTTTTCGTGTTTTTTTTTT
72134705 AAAAATTTTCGTGTTTCTAAAATTCTTGCGTTTTAAAAAAAATTTCGTGTTTCAAAAATTTTCGT
1 AAAAATTTTCGTGTTTCTAAAATTCTTGCGTTTTAAAAAAAATTTCGTGTTTCAAAAATTTTCGT
72134770 GTTTTCAAAAATTGACCGTGTTTAATAAATTTCCGTATTTCAAAAAAAATCTTTTGTGTTTTCAA
66 GTTTTCAAAAATTGACCGTGTTTAATAAATTTCCGTATTTC-AAAAAAATCTTTTGTGTTTTCAA
72134835 AATAAAATTTTGTGTTTTCAAAATAAAATTTTGTGTTTTCAAAATTTTCGTGTTTCAAAAAGAAA
130 AATAAAATTTTGTGTTTTCAAAATAAAATTTTGTGTTTTCAAAATTTTCGTGTTTCAAAAAGAAA
72134900 ATTCGTGTTTTGAAAAAATTCTCGTGTTTCAAATTTTTCGTGTTTTTTTTTT
195 ATTCGTGTTTTGAAAAAATTCTCGTGTTTCAAATTTTTCGTGTTTTTTTTTT
*
72134952 -AAATTTTTCGTGTTTCTAAAATTCTTGCGTTTTAAAAAAAATTTCGTGTTTTCAAAAA
1 AAAAATTTTCGTGTTTCTAAAATTCTTGCGTTTTAAAAAAAATTTCGTG-TTTCAAAAA
72135010 AAAAGGGTTA
Statistics
Matches: 293, Mismatches: 8, Indels: 9
0.95 0.03 0.03
Matches are distributed among these distances:
246 115 0.39
247 148 0.51
248 26 0.09
249 4 0.01
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.46
Consensus pattern (246 bp):
AAAAATTTTCGTGTTTCTAAAATTCTTGCGTTTTAAAAAAAATTTCGTGTTTCAAAAATTTTCGT
GTTTTCAAAAATTGACCGTGTTTAATAAATTTCCGTATTTCAAAAAAATCTTTTGTGTTTTCAAA
ATAAAATTTTGTGTTTTCAAAATAAAATTTTGTGTTTTCAAAATTTTCGTGTTTCAAAAAGAAAA
TTCGTGTTTTGAAAAAATTCTCGTGTTTCAAATTTTTCGTGTTTTTTTTTT
Found at i:72137830 original size:31 final size:31
Alignment explanation
Indices: 72137791--72137873 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 31
72137781 GTTGGACTTG
**
72137791 AATT-TTAAAATTTAAAAAATATAGGAACTA
1 AATTCTTAAAATTTAAAAAATATACAAACTA
*
72137821 AATTCTTAAAA-AT-AAAAATATACAAACTA
1 AATTCTTAAAATTTAAAAAATATACAAACTA
* *
72137850 AATTC-TAAACTTACAAAAAATATA
1 AATTCTTAAAATT-TAAAAAATATA
72137874 TAGGACTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 4 0.09
29 19 0.44
30 5 0.12
31 15 0.35
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.30
Consensus pattern (31 bp):
AATTCTTAAAATTTAAAAAATATACAAACTA
Found at i:72138497 original size:13 final size:13
Alignment explanation
Indices: 72138401--72138503 Score: 55
Period size: 13 Copynumber: 7.5 Consensus size: 13
72138391 ATTATAATAT
*
72138401 AAAGTAAAGAAATA
1 AAAG-AAAGAAAGA
* *
72138415 AAAGAAA-CAAGG
1 AAAGAAAGAAAGA
*
72138427 AAATAAAGAAAGA
1 AAAGAAAGAAAGA
72138440 AAAGAACAGAGAAGTA
1 AAAGAA-AGA-AAG-A
* * *
72138456 GAACGAAACAGAGA
1 -AAAGAAAGAAAGA
* **
72138470 AAGGAAAGAGGGA
1 AAAGAAAGAAAGA
72138483 AAAGAAAGAAAGAA
1 AAAGAAAGAAAG-A
72138497 AAAGAAA
1 AAAGAAA
72138504 AAGGAAAATT
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
12 8 0.12
13 30 0.45
14 16 0.24
15 5 0.07
16 3 0.04
17 5 0.07
ACGTcount: A:0.68, C:0.04, G:0.24, T:0.04
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:72140727 original size:20 final size:21
Alignment explanation
Indices: 72140685--72140725 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
72140675 ATTATATCAA
72140685 ATTGTAACAGAATTAACATTT
1 ATTGTAACAGAATTAACATTT
72140706 ATTGTAACA-AATTTAACATT
1 ATTGTAACAGAA-TTAACATT
72140726 ATCAGAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTGTAACAGAATTAACATTT
Found at i:72142877 original size:30 final size:30
Alignment explanation
Indices: 72142843--72142906 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
72142833 CAAATTTGGG
* *
72142843 AAATTCGAATTAAGC-CTTCAATTTTTTTGA
1 AAATTCGAATTAAACTCCTCAATTTTTTT-A
**
72142873 AAATTTTAATTAAACTCCTCAATTTTTTTA
1 AAATTCGAATTAAACTCCTCAATTTTTTTA
72142903 AAAT
1 AAAT
72142907 CTTCACTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (30 bp):
AAATTCGAATTAAACTCCTCAATTTTTTTA
Found at i:72143056 original size:15 final size:15
Alignment explanation
Indices: 72143017--72143060 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 15
72143007 TTTCGCTACC
72143017 TTGTTGAAAATTACA
1 TTGTTGAAAATTACA
72143032 TT-TT---AATTACA
1 TTGTTGAAAATTACA
72143043 TTGTTGAAAATTAC-
1 TTGTTGAAAATTACA
72143057 TTGT
1 TTGT
72143061 ATTTTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
14 6 0.24
15 8 0.32
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (15 bp):
TTGTTGAAAATTACA
Found at i:72148282 original size:39 final size:39
Alignment explanation
Indices: 72148228--72148304 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
72148218 AATTAAATAA
*
72148228 AAAGTATTGTTGATTGGTGGGAAATGGTCCCTCCATGTT
1 AAAGTACTGTTGATTGGTGGGAAATGGTCCCTCCATGTT
72148267 AAAGTACTGTTGATTGGTGGGAAATGGTCCCTCCATGT
1 AAAGTACTGTTGATTGGTGGGAAATGGTCCCTCCATGT
72148305 GACACAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (39 bp):
AAAGTACTGTTGATTGGTGGGAAATGGTCCCTCCATGTT
Found at i:72150732 original size:20 final size:21
Alignment explanation
Indices: 72150694--72150733 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72150684 AATATTTTCT
72150694 TATAATTTTTTAAATTTTTAA
1 TATAATTTTTTAAATTTTTAA
* *
72150715 TATATTTTTTTGAATTTTT
1 TATAATTTTTTAAATTTTT
72150734 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TATAATTTTTTAAATTTTTAA
Found at i:72151324 original size:30 final size:31
Alignment explanation
Indices: 72151290--72151373 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 31
72151280 ATTTTAATTT
* * *
72151290 ATAAATAAATTTATTTTTTATAATA-TAAAA
1 ATAAATAAATTTATATTTAAAAATAGTAAAA
* *
72151320 ATAAAT-ATTTTATATTTAAAAATAGTGAAA
1 ATAAATAAATTTATATTTAAAAATAGTAAAA
**
72151350 ATAAATAAATAAAT-TTTAAAAATA
1 ATAAATAAATTTATATTTAAAAATA
72151374 TTATATAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 14 0.32
30 26 0.59
31 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (31 bp):
ATAAATAAATTTATATTTAAAAATAGTAAAA
Found at i:72156059 original size:216 final size:216
Alignment explanation
Indices: 72155789--72156229 Score: 801
Period size: 216 Copynumber: 2.0 Consensus size: 216
72155779 ATAACTCCAG
*
72155789 CTCCTTGCAGTCCTCTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGTG
1 CTCCTTGCAGTCCTCTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGCG
72155854 ACCTCAATCCATTGCAGTTATGAATTTTTAATCTTTTCAATTGAACAAGATGTTGAAGCCCAATG
66 ACCTCAATCCATTGCAGTTATGAATTTTTAATCTTTTCAATTGAACAAGATGTTGAAGCCCAATG
* *
72155919 GGGAGAGACACCAGCTTTGGAATATTATCAATCTTCAAATGAGAGAGATTCTTAAGGGGTTCCCA
131 GGGAGAGACACCAGCGTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
72155984 TTGCATGCCCTCTAAATCAAC
196 TTGCATGCCCTCTAAATCAAC
* * *
72156005 CTCCTTGCAGTCCTTTACTTTAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAGCAGCG
1 CTCCTTGCAGTCCTCTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGCG
* *
72156070 ACCTCAATCCATTGCAGTTATGAATTTTTAATGTTTTCAATTGAAGAAGATGTTGAAGCCCAATG
66 ACCTCAATCCATTGCAGTTATGAATTTTTAATCTTTTCAATTGAACAAGATGTTGAAGCCCAATG
72156135 GGGAGAGACACCAGCGTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
131 GGGAGAGACACCAGCGTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
*
72156200 TTGCATGCCCTCTAAATCAGC
196 TTGCATGCCCTCTAAATCAAC
72156221 CTCCTTGCA
1 CTCCTTGCA
72156230 ATCTCTTATT
Statistics
Matches: 216, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
216 216 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (216 bp):
CTCCTTGCAGTCCTCTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGCG
ACCTCAATCCATTGCAGTTATGAATTTTTAATCTTTTCAATTGAACAAGATGTTGAAGCCCAATG
GGGAGAGACACCAGCGTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
TTGCATGCCCTCTAAATCAAC
Found at i:72163658 original size:30 final size:31
Alignment explanation
Indices: 72163598--72163672 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 31
72163588 AATTATTTAA
72163598 AAAATATTTAAAAATATTTTCTTATAATTTTTT
1 AAAAT-TTT-AAAATATTTTCTTATAATTTTTT
* *
72163631 TAATTTTTAAAATATATTT-TT-TAATTTTTT
1 AAAATTTTAAAATAT-TTTCTTATAATTTTTT
72163661 AAAATTTTAAAA
1 AAAATTTTAAAA
72163673 AATAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 19 0.51
31 9 0.24
32 6 0.16
33 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
AAAATTTTAAAATATTTTCTTATAATTTTTT
Found at i:72164001 original size:21 final size:20
Alignment explanation
Indices: 72163959--72163999 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
72163949 AATTCTATTC
72163959 TTTATTTAATTTATAAATAAA
1 TTTATTT-ATTTATAAATAAA
72163980 TTTATTT-TTTATAATATAAA
1 TTTATTTATTTATAA-ATAAA
72164000 ATAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATTTATTTATAAATAAA
Found at i:72164003 original size:29 final size:31
Alignment explanation
Indices: 72163971--72164053 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 31
72163961 TATTTAATTT
* *
72163971 ATAAATAAATTTATTTTTTATAATA-T-AAA
1 ATAAATAAATTTATTTTTAAAAATAGTGAAA
* *
72164000 ATAAAT-ATTTTATATTTAAAAATAGTGAAA
1 ATAAATAAATTTATTTTTAAAAATAGTGAAA
* *
72164030 ATGAATAAATATA-TTTTAAAAATA
1 ATAAATAAATTTATTTTTAAAAATA
72164054 TTATATAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 14 0.33
29 7 0.16
30 18 0.42
31 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (31 bp):
ATAAATAAATTTATTTTTAAAAATAGTGAAA
Found at i:72165384 original size:19 final size:20
Alignment explanation
Indices: 72165360--72165398 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
72165350 TATTTATGTC
72165360 ACTCTAT-CCCCTATTTAGA
1 ACTCTATCCCCCTATTTAGA
72165379 ACTCTATCCCCCTATTTAGA
1 ACTCTATCCCCCTATTTAGA
72165399 GTACATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (20 bp):
ACTCTATCCCCCTATTTAGA
Done.