Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 99 of 120
Found at i:29206641 original size:20 final size:19
Alignment explanation
Indices: 29206547--29206641 Score: 68
Period size: 21 Copynumber: 4.7 Consensus size: 19
29206537 AACTAGTAAA
29206547 AAAATATTCAAAAA-AATTT
1 AAAATATT-AAAAATAATTT
*
29206566 AAAATCTATTTAAAAA-AATTC
1 AAAA--TA-TTAAAAATAATTT
* * *
29206587 AAAAAATTTAAAATCTATTT
1 AAAATATTAAAAAT-AATTT
*
29206607 AAAAAAATTAAAAATAATTT
1 -AAAATATTAAAAATAATTT
29206627 AAAATATTGAAAAAT
1 AAAATATT-AAAAAT
29206642 TTGTAAAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
18 6 0.10
19 12 0.20
20 13 0.21
21 28 0.46
22 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAATATTAAAAATAATTT
Found at i:29207042 original size:28 final size:29
Alignment explanation
Indices: 29206999--29207057 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
29206989 CTAAGATAAA
*
29206999 TTTTAAAGATTATTATAATTTTTACAATT
1 TTTTAAAGATTATTATAATTTTCACAATT
* * *
29207028 TTTTAAA-ATTTTTATGATTTTCAGAATT
1 TTTTAAAGATTATTATAATTTTCACAATT
29207056 TT
1 TT
29207058 AAACTCTTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTTAAAGATTATTATAATTTTCACAATT
Found at i:29217041 original size:11 final size:11
Alignment explanation
Indices: 29217025--29217071 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
29217015 TGTTTCTCTG
29217025 TAAAAATAAAA
1 TAAAAATAAAA
29217036 TAAAAATAAAA
1 TAAAAATAAAA
*
29217047 TAAATAATAATA
1 TAAA-AATAAAA
*
29217059 TGAAAATTAAAA
1 T-AAAAATAAAA
29217071 T
1 T
29217072 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 15 0.48
12 13 0.42
13 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:29229507 original size:12 final size:12
Alignment explanation
Indices: 29229490--29229527 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
29229480 GAGCCCATCC
29229490 ATATTAATTTTT
1 ATATTAATTTTT
29229502 ATATT-ATTTTT
1 ATATTAATTTTT
*
29229513 ATA-TAATTTTA
1 ATATTAATTTTT
29229524 ATAT
1 ATAT
29229528 ATATATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 1 0.04
11 17 0.74
12 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:29229692 original size:30 final size:30
Alignment explanation
Indices: 29229648--29229707 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
29229638 ACTTAACAAG
29229648 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
29229678 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
29229708 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:29231024 original size:9 final size:9
Alignment explanation
Indices: 29230997--29231033 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
29230987 TGAGTTTTCG
29230997 AATTCGAAT
1 AATTCGAAT
* *
29231006 AACTCAAAT
1 AATTCGAAT
29231015 AATTCGAAT
1 AATTCGAAT
29231024 AATTCGAAT
1 AATTCGAAT
29231033 A
1 A
29231034 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29234063 original size:5 final size:5
Alignment explanation
Indices: 29234053--29234079 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
29234043 CTCAAAAATT
29234053 TTCGA TTCGA TTCGA TTCGA TTCGA TT
1 TTCGA TTCGA TTCGA TTCGA TTCGA TT
29234080 GAATGCTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTCGA
Found at i:29234506 original size:22 final size:22
Alignment explanation
Indices: 29234478--29234527 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
29234468 TGCAGAGGTA
29234478 ATTTCTGCTTCTTCTTCCATCG
1 ATTTCTGCTTCTTCTTCCATCG
29234500 ATTTCTGCTTCTTCTTCCATCG
1 ATTTCTGCTTCTTCTTCCATCG
*
29234522 TTTTCT
1 ATTTCT
29234528 TATTTGGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.08, C:0.30, G:0.08, T:0.54
Consensus pattern (22 bp):
ATTTCTGCTTCTTCTTCCATCG
Found at i:29236624 original size:16 final size:18
Alignment explanation
Indices: 29236586--29236623 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
29236576 ATATTAAGAA
29236586 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
29236604 TTTTATTAAATTATAT-T
1 TTTTATTAAATTATATAT
29236621 TTT
1 TTT
29236624 AATAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:29236834 original size:18 final size:18
Alignment explanation
Indices: 29236813--29236858 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
29236803 TATAGAATAT
29236813 TTAATATTA-AGAATTTTA
1 TTAA-ATTATAGAATTTTA
* *
29236831 TTAAATTATATATTTTTA
1 TTAAATTATAGAATTTTA
29236849 TTAAATTATA
1 TTAAATTATA
29236859 TTTAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTAAATTATAGAATTTTA
Found at i:29236940 original size:238 final size:238
Alignment explanation
Indices: 29236395--29236986 Score: 1016
Period size: 238 Copynumber: 2.5 Consensus size: 238
29236385 TTCAAATTTT
29236395 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC--TAAGAATATTT
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTAAGAATATTT
* * *
29236458 AATATCAATAATTTTATTAAATTATATATTTTTATTAAATTATATTTAA-AAATAATTAATTTAA
66 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAAATAAATAATTTAA
29236522 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAAT
131 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAAT
29236587 TTTATTAAATTATATATTTTTATTAAATTATATTTTTAATAATA
196 TTTATTAAATTATATATTTTTATTAAATTATA-TTTTAATAATA
*
29236631 ATTATTTTATATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATT
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCA-TTAAGAATATT
* *
29236696 TAATATTAAGAATTTTGTTAAATTATATATTTTTATTAAATTATATTTAATAAA-AAATATTTTA
65 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAAATAAATAATTTA
*
29236760 AATTATATTTTATAGTATTATATATTATGATTTTA-TTAATTCGTATAGAATATTTAATATTAAG
130 AATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC-TA-AGAATATTTAATATTAAG
29236824 AATTTTATTAAATTATATATTTTTATTAAATTATA-TTTAATAATA
193 AATTTTATTAAATTATATATTTTTATTAAATTATATTTTAATAATA
* *
29236869 ATTATGTTAAATTATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATT
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAT-TAAGAATATT
29236934 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAA
65 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAA
29236987 TAATTATGTT
Statistics
Matches: 338, Mismatches: 11, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
236 51 0.15
237 1 0.00
238 128 0.38
239 102 0.30
240 56 0.17
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (238 bp):
ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTAAGAATATTT
AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAAATAAATAATTTAA
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAAT
TTTATTAAATTATATATTTTTATTAAATTATATTTTAATAATA
Found at i:29236987 original size:120 final size:118
Alignment explanation
Indices: 29236395--29236999 Score: 1009
Period size: 120 Copynumber: 5.1 Consensus size: 118
29236385 TTCAAATTTT
29236395 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC-TAAGAATATTTA
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTTAAGAATATTTA
* * *
29236459 ATATCAATAATTTTATTAAATTATATATTTTTATTAAATTATATTTAAAAATA
66 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
*
29236512 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC-TAAGAATATTTA
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTTAAGAATATTTA
29236576 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTTTAATAATA
66 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATA
*
29236631 ATTATTTTATATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATT
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC--TTAAGAATATT
* *
29236696 TAATATTAAGAATTTTGTTAAATTATATATTTTTATTAAATTATATTTAATAAAA
64 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
* * *
29236751 AATATTTTAAATTATATTTTATAGTATTATATATTATGATTTTA-TTAATTCGTATAGAATATTT
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTTA-AGAATATTT
29236815 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
65 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
* *
29236869 ATTATGTTAAATTATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATT
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC-T-TAAGAATATT
29236934 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
64 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
*
29236989 ATTATGTTAAA
1 ATTATTTTAAA
29237000 ATATGATTAA
Statistics
Matches: 460, Mismatches: 19, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
117 106 0.23
118 103 0.22
119 70 0.15
120 125 0.27
121 2 0.00
122 54 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (118 bp):
ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTTAAGAATATTTA
ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
Found at i:29237223 original size:45 final size:44
Alignment explanation
Indices: 29237138--29237230 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 44
29237128 ATTACAACAT
*
29237138 CATTCCATTCAACCAAACACAATAATACTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACACAATAATACTATTACACCTCTATTC
* * *
29237182 CATTGCATTCAACCAAACA-ATTAAATTACTATTATACCTCTATTC
1 CATTCCATTCAACCAAACACAAT-AA-TACTATTACACCTCTATTC
29237227 CATT
1 CATT
29237231 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 2 0.05
44 20 0.47
45 21 0.49
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAATAATACTATTACACCTCTATTC
Found at i:29237238 original size:16 final size:16
Alignment explanation
Indices: 29237219--29237283 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
29237209 ACTATTATAC
29237219 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
* *
29237235 CTCTATTCCATTATAC
1 CTCTATTCCATTACAG
*
29237251 CTCTATTTCATTACAG
1 CTCTATTCCATTACAG
29237267 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
29237283 C
1 C
29237284 GAACCAAACG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.25, C:0.31, G:0.05, T:0.40
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:29237253 original size:32 final size:32
Alignment explanation
Indices: 29237212--29237279 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
29237202 TTAAATTACT
29237212 ATTATACCTCTATTCCATTACAGCTCTATTCC
1 ATTATACCTCTATTCCATTACAGCTCTATTCC
*
29237244 ATTATACCTCTATTTCATTACAGCTCTATTCC
1 ATTATACCTCTATTCCATTACAGCTCTATTCC
29237276 ATTA
1 ATTA
29237280 CAGCGAACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.03, T:0.43
Consensus pattern (32 bp):
ATTATACCTCTATTCCATTACAGCTCTATTCC
Found at i:29244412 original size:2 final size:2
Alignment explanation
Indices: 29244405--29244460 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
29244395 ATAAGTTCTC
* *
29244405 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29244447 AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT
29244461 CAGACTTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:29245696 original size:13 final size:13
Alignment explanation
Indices: 29245678--29245702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29245668 TTTTAAACCT
29245678 TTTTAAAAAATTC
1 TTTTAAAAAATTC
29245691 TTTTAAAAAATT
1 TTTTAAAAAATT
29245703 TATTGCATCT
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAAAAATTC
Found at i:29246584 original size:23 final size:23
Alignment explanation
Indices: 29246545--29246600 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
29246535 AGTATTAAAA
*
29246545 TAATATAATCAAGTATTATTATAT
1 TAAT-TAATCAAATATTATTATAT
*
29246569 TAATTAATCAAATATTGTTATAT
1 TAATTAATCAAATATTATTATAT
29246592 TAATTAATC
1 TAATTAATC
29246601 TAAAACAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (23 bp):
TAATTAATCAAATATTATTATAT
Found at i:29249856 original size:17 final size:16
Alignment explanation
Indices: 29249836--29249869 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29249826 TTTATTAAAT
*
29249836 TAATTAATTAATTATTC
1 TAATTAAATAA-TATTC
29249853 TAATTAAATAATATTC
1 TAATTAAATAATATTC
29249869 T
1 T
29249870 CAACCCAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTAAATAATATTC
Found at i:29249915 original size:23 final size:23
Alignment explanation
Indices: 29249888--29249940 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
29249878 TTCTAATTTT
29249888 ATTAAAGTCATGACAACTTTACC
1 ATTAAAGTCATGACAACTTTACC
* *
29249911 GTTAAAGTTATGACAACTTTACC
1 ATTAAAGTCATGACAACTTTACC
29249934 ATTAAAG
1 ATTAAAG
29249941 AATATATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (23 bp):
ATTAAAGTCATGACAACTTTACC
Found at i:29252021 original size:23 final size:23
Alignment explanation
Indices: 29251995--29252086 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 23
29251985 GGACTCACCA
29251995 CAGCTTGTATGAGCTTACCGTTT
1 CAGCTTGTATGAGCTTACCGTTT
* *
29252018 CAGC-TCTACGGAGCTTACCGTTT
1 CAGCTTGTA-TGAGCTTACCGTTT
*
29252041 CAGCTCGATAT-AGCTTACCGTTTAT
1 CAGCTTG-TATGAGCTTACCG-TT-T
* *
29252066 CAGCTCGGAATGAGCTTACCG
1 CAGCT-TGTATGAGCTTACCG
29252087 ATCATGGCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
22 3 0.05
23 30 0.55
24 2 0.04
25 10 0.18
26 10 0.18
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (23 bp):
CAGCTTGTATGAGCTTACCGTTT
Found at i:29254734 original size:22 final size:25
Alignment explanation
Indices: 29254688--29254734 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
29254678 AAAGTGATAG
29254688 GTGAAATGTATAATAAGAATTATTA
1 GTGAAATGTATAATAAGAATTATTA
*
29254713 GTGAAAT-TATGA-AAG-ATTATTA
1 GTGAAATGTATAATAAGAATTATTA
29254735 AATATTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 3 0.14
24 4 0.19
25 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (25 bp):
GTGAAATGTATAATAAGAATTATTA
Found at i:29262641 original size:2 final size:2
Alignment explanation
Indices: 29262634--29262661 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29262624 ATTAATTAGG
29262634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29262662 TCACATAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29271910 original size:6 final size:6
Alignment explanation
Indices: 29271892--29271927 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
29271882 GGTTTTCTCC
* *
29271892 AAAATG GAAATG AAGATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
29271928 GAGAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:29271989 original size:75 final size:76
Alignment explanation
Indices: 29271846--29271992 Score: 169
Period size: 75 Copynumber: 1.9 Consensus size: 76
29271836 AAAAATGATA
* * *
29271846 AAAATGAAGAAATGAGAAATATTTTGAAATGATTATGGTTTTCTCCAAAATGGAAATGAAGATGA
1 AAAATGAAGAAATGAGAAATATTTTGAAATGAATATCGTTTTCTCCAAAATGGAAATGAACATGA
29271911 AAATGAAAATG
66 AAATGAAAATG
* * *
29271922 AAAATGGAGAAAT-A-AAATCA-TTTGAAAATGAATATCGTTTTCTTCAAAA-GGAAAATG-ACC
1 AAAATGAAGAAATGAGAAAT-ATTTTG-AAATGAATATCGTTTTCTCCAAAATGG-AAATGAACA
29271982 TGAAAAATGAA
63 TG-AAAATGAA
29271993 TTTATGTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
74 13 0.21
75 36 0.59
76 12 0.20
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.27
Consensus pattern (76 bp):
AAAATGAAGAAATGAGAAATATTTTGAAATGAATATCGTTTTCTCCAAAATGGAAATGAACATGA
AAATGAAAATG
Found at i:29278332 original size:22 final size:21
Alignment explanation
Indices: 29278294--29278335 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29278284 TGAGTTTATA
*
29278294 ATAAAAAATACATTTTAATTC
1 ATAAAAAATACAATTTAATTC
*
29278315 ATAAAAAATTATAATTTAATT
1 ATAAAAAA-TACAATTTAATT
29278336 TTAACCCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAAAAATACAATTTAATTC
Found at i:29279797 original size:3 final size:3
Alignment explanation
Indices: 29279791--29279843 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
29279781 AACAAGATTA
29279791 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29279839 AAT AA
1 AAT AA
29279844 AGGTTGGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29281568 original size:26 final size:26
Alignment explanation
Indices: 29281539--29281596 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
29281529 TTGTAGTGGT
29281539 TGGTTTAACCAACTGATTCTACTAAC
1 TGGTTTAACCAACTGATTCTACTAAC
* * *
29281565 TGGTTTGACCAATTGATTCTATTAAC
1 TGGTTTAACCAACTGATTCTACTAAC
29281591 -GGTTTA
1 TGGTTTA
29281597 TTTAAAGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (26 bp):
TGGTTTAACCAACTGATTCTACTAAC
Found at i:29294675 original size:151 final size:151
Alignment explanation
Indices: 29294390--29294680 Score: 449
Period size: 151 Copynumber: 1.9 Consensus size: 151
29294380 TTTCACGGGT
* * *
29294390 CTGCTCACATAAGCTGTCAGGCTTTCGTTACTACTCAGTGTTGCTCACACAAGCTGTCAGGTATC
1 CTGCTCACACAAGCTGTCAGGCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGTCAGGTATC
* * *
29294455 CGCAACATATGCCGGTATACCTAGCCACTGGTAGAACTTAAGACTAGCACCCGAGTTCACATTAA
66 CGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAGTCCACATTAA
29294520 TCACAATTTCGCATCATGGGC
131 TCACAATTTCGCATCATGGGC
*
29294541 CTGCTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGTCAGGTATC
1 CTGCTCACACAAGCTGTCAGGCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGTCAGGTATC
* * * * *
29294606 CGCAGCATATGCTGGTATACCCAGCCACTGGTAGAACTTATGACCAGCACTCG-GATCCACTTTA
66 CGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAG-TCCACATTA
*
29294670 TTCACAATTTC
130 ATCACAATTTC
29294681 ACATAGGTCT
Statistics
Matches: 126, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
150 1 0.01
151 125 0.99
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (151 bp):
CTGCTCACACAAGCTGTCAGGCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGTCAGGTATC
CGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAGTCCACATTAA
TCACAATTTCGCATCATGGGC
Found at i:29297745 original size:25 final size:23
Alignment explanation
Indices: 29297712--29297757 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
29297702 AATTAATAAC
*
29297712 ATTATAAATTATAATATCTAAATAT
1 ATTAGAAATTA-AATATC-AAATAT
29297737 ATTAGAAATTAAATATCAAAT
1 ATTAGAAATTAAATATCAAAT
29297758 TTTAACATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 6 0.30
25 10 0.50
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTAGAAATTAAATATCAAATAT
Found at i:29299365 original size:14 final size:14
Alignment explanation
Indices: 29299342--29299381 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29299332 ACAGAAAAGT
*
29299342 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
29299356 AAATCATTTTACGG
1 AAAACATTTTACAG
29299370 AAAACATTTTAC
1 AAAACATTTTAC
29299382 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:29299366 original size:34 final size:35
Alignment explanation
Indices: 29299307--29299373 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
29299297 CAAACAGCAG
* * *
29299307 AAAATATTTTCTAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
29299342 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
29299374 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:29301339 original size:5 final size:5
Alignment explanation
Indices: 29301329--29301354 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29301319 AAAATACATT
29301329 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
29301355 GATATAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:29301882 original size:18 final size:19
Alignment explanation
Indices: 29301839--29301882 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
29301829 AAATTTTATT
*
29301839 TTTTTTTCCAAATTTTTAA
1 TTTTTTTCCAAATTTTCAA
*
29301858 TTTTTTT-CAACTTTTCAA
1 TTTTTTTCCAAATTTTCAA
29301876 TTTTTTT
1 TTTTTTT
29301883 AAAAAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTTCCAAATTTTCAA
Found at i:29304712 original size:16 final size:16
Alignment explanation
Indices: 29304669--29304731 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
29304659 AAACAAACGA
*
29304669 AAAATAAAATAAAATTT
1 AAAATAAAA-AAAAATT
* *
29304686 AGAAT-ATAAAAAATT
1 AAAATAAAAAAAAATT
* *
29304701 AAATTAAAAAAATATT
1 AAAATAAAAAAAAATT
29304717 AAAATAAAAATAAAA
1 AAAATAAAAA-AAAA
29304732 AATGGCAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
15 9 0.26
16 19 0.54
17 7 0.20
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAATAAAAAAAAATT
Found at i:29304720 original size:23 final size:22
Alignment explanation
Indices: 29304688--29304733 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
29304678 TAAAATTTAG
* *
29304688 AATATAAAAAATTAAATTAAAAA
1 AATAT-AAAAATAAAAATAAAAA
*
29304711 AATATTAAAATAAAAATAAAAA
1 AATATAAAAATAAAAATAAAAA
29304733 A
1 A
29304734 TGGCAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AATATAAAAATAAAAATAAAAA
Found at i:29304725 original size:14 final size:15
Alignment explanation
Indices: 29304679--29304728 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
29304669 AAAATAAAAT
29304679 AAAAT-TTAGAATATA
1 AAAATATTA-AATATA
*
29304694 AAAA-ATTAAATTAAA
1 AAAATATTAAA-TATA
29304709 AAAATATTAAA-ATA
1 AAAATATTAAATATA
29304723 AAAATA
1 AAAATA
29304729 AAAAATGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 10 0.33
15 14 0.47
16 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (15 bp):
AAAATATTAAATATA
Found at i:29309148 original size:51 final size:50
Alignment explanation
Indices: 29309079--29309274 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 50
29309069 CAATGATGTT
* *
29309079 CGGTTCACATAGTAGCCTGCACATAGTACCACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACCACACATGTGACCA-TACCATC
* * * * * * *
29309130 TGATACACGTAGTTGCCTGCACATAGTACCACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACCACACATGTGA-CCATACCATC
* * * * * *
29309181 CGGTACGCATGGTAGCCTACACATAGTACTACACATGTGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACCACACATGTGACCATACCA-TC
* * *
29309231 CGGTACACGTAGTAGCCTGCACATAATACTACACAAGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACCACACATGTGACCAT
29309275 CACTTTCACT
Statistics
Matches: 114, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.34
51 71 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACCACACATGTGACCATACCATC
Found at i:29310602 original size:16 final size:15
Alignment explanation
Indices: 29310581--29310634 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 15
29310571 GTTTGGTTCA
29310581 CTGTAATGAAATAGAG
1 CTGTAATG-AATAGAG
29310597 CTGTAATTGAATAGAG
1 CTGTAA-TGAATAGAG
*
29310613 CTGTAATGGAATAAAG
1 CTGTAAT-GAATAGAG
29310629 CTGTAA
1 CTGTAA
29310635 ACAGTAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 1 0.03
16 32 0.91
17 2 0.06
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (15 bp):
CTGTAATGAATAGAG
Found at i:29311270 original size:2 final size:2
Alignment explanation
Indices: 29311263--29311312 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
29311253 ATACCATCCA
29311263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29311305 AT AT AT AT
1 AT AT AT AT
29311313 TATTTTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29313682 original size:18 final size:17
Alignment explanation
Indices: 29313644--29313680 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
29313634 GTTGAAATGG
29313644 AAATCATAAAGAAGGAA
1 AAATCATAAAGAAGGAA
29313661 AAATCATAAAGAAGGAA
1 AAATCATAAAGAAGGAA
29313678 AAA
1 AAA
29313681 ATAAATTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (17 bp):
AAATCATAAAGAAGGAA
Found at i:29323382 original size:2 final size:2
Alignment explanation
Indices: 29323377--29323415 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
29323367 AGATAGATAG
29323377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29323416 TGACTTCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29325893 original size:3 final size:3
Alignment explanation
Indices: 29325878--29325914 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
29325868 GTAAAATAAA
29325878 AAG AAG -AG AAAG AAG -AG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29325915 AAGCATAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 25 0.81
4 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29325900 original size:17 final size:17
Alignment explanation
Indices: 29325878--29325910 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29325868 GTAAAATAAA
29325878 AAGAAG-AGAAAGAAGAG
1 AAGAAGAAG-AAGAAGAG
29325895 AAGAAGAAGAAGAAGA
1 AAGAAGAAGAAGAAGA
29325911 AGAAAAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAGAAGAAGAAGAAGAG
Found at i:29325956 original size:12 final size:13
Alignment explanation
Indices: 29325941--29325973 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
29325931 ATGTTGAGAG
29325941 AGAAAAAGAT-GA
1 AGAAAAAGATAGA
29325953 AGAAAAAGATAAGA
1 AGAAAAAGAT-AGA
29325967 AGAAAAA
1 AGAAAAA
29325974 AAAGGAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
14 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (13 bp):
AGAAAAAGATAGA
Found at i:29325970 original size:14 final size:14
Alignment explanation
Indices: 29325878--29325973 Score: 56
Period size: 14 Copynumber: 6.8 Consensus size: 14
29325868 GTAAAATAAA
*
29325878 AAGAAGAGAAAGA-
1 AAGAAGAAAAAGAT
* *
29325891 AGAGAAGAAGAAGAAG
1 A-AGAAGAAAAAG-AT
29325907 AAGAAG-AAAAGCAT
1 AAGAAGAAAAAG-AT
* * *
29325921 AAGGAGAAAGATGTT
1 AAGAAGAAA-AAGAT
*
29325936 GAGAGAGAAAAAGAT
1 AAGA-AGAAAAAGAT
29325951 --GAAGAAAAAGAT
1 AAGAAGAAAAAGAT
29325963 AAGAAGAAAAA
1 AAGAAGAAAAA
29325974 AAAGGAGAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
12 10 0.16
13 3 0.05
14 28 0.44
15 14 0.22
16 8 0.13
ACGTcount: A:0.64, C:0.01, G:0.29, T:0.06
Consensus pattern (14 bp):
AAGAAGAAAAAGAT
Found at i:29332936 original size:2 final size:2
Alignment explanation
Indices: 29332929--29332957 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29332919 AATTTTAACT
29332929 TA 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 TA T
29332958 TTAGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29333018 original size:20 final size:19
Alignment explanation
Indices: 29332986--29333045 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 19
29332976 TTTTTAAAAA
29332986 TATAAAA-TTTGAATTTTT
1 TATAAAATTTTGAATTTTT
29333004 TATAAATATTTTGAA-TTTT
1 TATAAA-ATTTTGAATTTTT
29333023 TA-AAAATTATTGTAATTTTT
1 TATAAAATT-TTG-AATTTTT
29333043 TAT
1 TAT
29333046 TGTAATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.08
18 12 0.33
19 9 0.25
20 12 0.33
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAAATTTTGAATTTTT
Found at i:29333022 original size:19 final size:17
Alignment explanation
Indices: 29332989--29333042 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 17
29332979 TTAAAAATAT
29332989 AAAA-TTTGAATTTTTTA
1 AAAATTTTGAA-TTTTTA
29333006 TAAATATTTTGAATTTTTA
1 -AAA-ATTTTGAATTTTTA
29333025 AAAATTATTGTAATTTTT
1 AAAATT-TTG-AATTTTT
29333043 TATTGTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.09
18 9 0.28
19 14 0.44
20 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
AAAATTTTGAATTTTTA
Found at i:29333047 original size:13 final size:13
Alignment explanation
Indices: 29333029--29333061 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29333019 TTTTTAAAAA
29333029 TTATTGTAATTTT
1 TTATTGTAATTTT
29333042 TTATTGTAATTTT
1 TTATTGTAATTTT
*
29333055 TTGTTGT
1 TTATTGT
29333062 GAGAGAGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (13 bp):
TTATTGTAATTTT
Found at i:29342310 original size:38 final size:38
Alignment explanation
Indices: 29342259--29342333 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
29342249 TCTAACTTCC
*
29342259 TTTTGCTTGTTAACAGCTTCTTTAAAAATTTTACATAA
1 TTTTGCTTGTTAACAACTTCTTTAAAAATTTTACATAA
*
29342297 TTTTGTTTGTTAACAACTTCTTTAAAAATTTTACATA
1 TTTTGCTTGTTAACAACTTCTTTAAAAATTTTACATA
29342334 CTTTGACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (38 bp):
TTTTGCTTGTTAACAACTTCTTTAAAAATTTTACATAA
Found at i:29344582 original size:23 final size:23
Alignment explanation
Indices: 29344556--29344608 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
29344546 ATAAGTGCCA
29344556 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
29344579 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
29344602 CACTGAT
1 CACTGAT
29344609 CAATAACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:29344708 original size:8 final size:8
Alignment explanation
Indices: 29344695--29344723 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
29344685 ACCCGGGACT
29344695 CACTGTAA
1 CACTGTAA
29344703 CACTGTAA
1 CACTGTAA
29344711 CACTGTAA
1 CACTGTAA
29344719 CACTG
1 CACTG
29344724 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:29344854 original size:18 final size:17
Alignment explanation
Indices: 29344828--29344866 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
29344818 ATTTTCCTTC
29344828 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
29344845 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
29344863 CACA
1 CACA
29344867 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:29348898 original size:19 final size:18
Alignment explanation
Indices: 29348853--29348908 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
29348843 ATAATTTTCA
* *
29348853 AAAATTTAAAATAATTTTT
1 AAAATTTCAAAT-ATTTAT
*
29348872 AAATTTTCAAATATTTAT
1 AAAATTTCAAATATTTAT
29348890 ACAAATTTCAAA-ATTTAT
1 A-AAATTTCAAATATTTAT
29348908 A
1 A
29348909 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 13 0.41
19 19 0.59
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTTCAAATATTTAT
Found at i:29348903 original size:28 final size:28
Alignment explanation
Indices: 29348845--29348905 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
29348835 AAAATAAAAT
**
29348845 AATTTTCAAAAATTTAAAATAATTTTTA
1 AATTTTCAAAAATTTAAAATAATTTCAA
* *
29348873 AATTTTCAAATATTTATACA-AATTTCAA
1 AATTTTCAAAAATTTA-AAATAATTTCAA
29348901 AATTT
1 AATTT
29348906 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTTTCAAAAATTTAAAATAATTTCAA
Found at i:29351543 original size:43 final size:43
Alignment explanation
Indices: 29351495--29351618 Score: 167
Period size: 43 Copynumber: 2.9 Consensus size: 43
29351485 ATGCCGCTAT
*
29351495 AGAACATGACATGTAGCGGCGCTTTTATCACAAACGCCACTAA
1 AGAACATGACATTTAGCGGCGCTTTTATCACAAACGCCACTAA
* ** * * *
29351538 AGAACATGACATTTCGCAACACTTTTATCACAAACACCGCTAA
1 AGAACATGACATTTAGCGGCGCTTTTATCACAAACGCCACTAA
* *
29351581 AGAACATGACCTTTAGTGGCGCTTTTATCACAAACGCC
1 AGAACATGACATTTAGCGGCGCTTTTATCACAAACGCC
29351619 GTTAAAAGTA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (43 bp):
AGAACATGACATTTAGCGGCGCTTTTATCACAAACGCCACTAA
Found at i:29361334 original size:19 final size:19
Alignment explanation
Indices: 29361310--29361358 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
29361300 TAAAATTATA
29361310 ATTTTTAGTTTTTGTATTTT
1 ATTTTTA-TTTTTGTATTTT
29361330 ATTTTTATTTTTGTATTTT
1 ATTTTTATTTTTGTATTTT
29361349 ATTTTTATTT
1 ATTTTTATTT
29361359 GTTATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (19 bp):
ATTTTTATTTTTGTATTTT
Found at i:29361335 original size:6 final size:6
Alignment explanation
Indices: 29361310--29361363 Score: 54
Period size: 6 Copynumber: 8.3 Consensus size: 6
29361300 TAAAATTATA
* *
29361310 ATTTTT AGTTTTT GTATTTT ATTTTT ATTTTT GTATTTT ATTTTT ATTTGTT
1 ATTTTT A-TTTTT AT-TTTT ATTTTT ATTTTT AT-TTTT ATTTTT ATTT-TT
29361362 AT
1 AT
29361364 AATTTGGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 21 0.52
7 19 0.47
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:29361363 original size:13 final size:12
Alignment explanation
Indices: 29361310--29361363 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
29361300 TAAAATTATA
29361310 ATTTTTAGTTTTT
1 ATTTTTA-TTTTT
*
29361323 GTATTTTATTTTT
1 AT-TTTTATTTTT
*
29361336 ATTTTTGTATTTT
1 ATTTTTAT-TTTT
29361349 ATTTTTATTTGTT
1 ATTTTTATTT-TT
29361362 AT
1 AT
29361364 AATTTGGTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 7 0.21
13 22 0.65
14 5 0.15
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:29364123 original size:36 final size:35
Alignment explanation
Indices: 29364078--29364153 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
29364068 ACCCCTAACT
* *
29364078 CCTATCCCCTAAACCCTAAATCATAAAACATAAATC
1 CCTAACCCCTAAACCCCAAATCATAAAACAT-AATC
* * *
29364114 CCTAACCCCTAAACCCCAACTCTTAAACCATAATC
1 CCTAACCCCTAAACCCCAAATCATAAAACATAATC
29364149 CCTAA
1 CCTAA
29364154 ACTCATAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 9 0.26
36 26 0.74
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (35 bp):
CCTAACCCCTAAACCCCAAATCATAAAACATAATC
Found at i:29364162 original size:15 final size:14
Alignment explanation
Indices: 29364137--29364171 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
29364127 CCCCAACTCT
29364137 TAAACCATAATCCC
1 TAAACCATAATCCC
*
29364151 TAAACTCATAATCCT
1 TAAAC-CATAATCCC
29364166 TAAACC
1 TAAACC
29364172 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:29364176 original size:22 final size:22
Alignment explanation
Indices: 29364151--29364221 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
29364141 CCATAATCCC
29364151 TAAACTCATAATCCTTAAACCT
1 TAAACTCATAATCCTTAAACCT
*
29364173 TAAAAT-AGTAA-CTCTTAAACCT
1 TAAACTCA-TAATC-CTTAAACCT
* * * *
29364195 TAAAC-CCTAATCCATATACCC
1 TAAACTCATAATCCTTAAACCT
29364216 TAAACT
1 TAAACT
29364222 ATAGAGCCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
21 16 0.42
22 22 0.58
ACGTcount: A:0.42, C:0.27, G:0.01, T:0.30
Consensus pattern (22 bp):
TAAACTCATAATCCTTAAACCT
Found at i:29364795 original size:41 final size:40
Alignment explanation
Indices: 29364690--29364778 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 40
29364680 TAATTTTTTT
* *
29364690 GCGGCATTTTTCAAGAAGCG--GCTAATGGTCGACCTATA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
*
29364728 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
29364768 GCGGCATTTTT
1 GCGGCATTTTT
29364779 TATCCAAACG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 19 0.41
40 27 0.59
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (40 bp):
GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
Found at i:29367156 original size:18 final size:18
Alignment explanation
Indices: 29367135--29367179 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29367125 ATGAAATGAA
29367135 ATAT-TTAATATAAATAAT
1 ATATATTAATAT-AATAAT
*
29367153 ATATATTTATATAATAAT
1 ATATATTAATATAATAAT
*
29367171 ATATGTTAA
1 ATATATTAA
29367180 AAGGGTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATATTAATATAATAAT
Found at i:29367160 original size:20 final size:18
Alignment explanation
Indices: 29367135--29367174 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 18
29367125 ATGAAATGAA
29367135 ATATTTAATATAAATAATAT
1 ATATTT-ATAT-AATAATAT
29367155 ATATTTATATAATAATAT
1 ATATTTATATAATAATAT
29367173 AT
1 AT
29367175 GTTAAAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTATATAATAATAT
Found at i:29371049 original size:17 final size:17
Alignment explanation
Indices: 29371024--29371056 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29371014 TGGGATCTTT
*
29371024 TTTTTAGGTTGTTTTGG
1 TTTTAAGGTTGTTTTGG
29371041 TTTTAAGGTTGTTTTG
1 TTTTAAGGTTGTTTTG
29371057 AATCTCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.00, G:0.27, T:0.64
Consensus pattern (17 bp):
TTTTAAGGTTGTTTTGG
Found at i:29371275 original size:80 final size:80
Alignment explanation
Indices: 29371181--29371342 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
29371171 AACTGGCTTA
29371181 CCTGAATTCAGCATTTGAGATGCCAATTTGCATCCCTAGATCTGGTTATGAGGTGCCAAGTGTCC
1 CCTGAATTCAGCATTTGAGATGCCAATTTGCATCCCTAGATCTGGTTATGAGGTGCCAAGTGTCC
29371246 CTCACATACCACACC
66 CTCACATACCACACC
29371261 CCTGAATTCAGCATTTGAGATGCCAATTTGCATCCCTAGATCTGGTTATGAGGTGCCAAGTGTCC
1 CCTGAATTCAGCATTTGAGATGCCAATTTGCATCCCTAGATCTGGTTATGAGGTGCCAAGTGTCC
29371326 CTCACATACCACACC
66 CTCACATACCACACC
29371341 CC
1 CC
29371343 CATATTATTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (80 bp):
CCTGAATTCAGCATTTGAGATGCCAATTTGCATCCCTAGATCTGGTTATGAGGTGCCAAGTGTCC
CTCACATACCACACC
Found at i:29375537 original size:10 final size:10
Alignment explanation
Indices: 29375524--29375551 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
29375514 TAAAGAACAA
29375524 AAAAGAAAGT
1 AAAAGAAAGT
29375534 AAAAGAAAGT
1 AAAAGAAAGT
29375544 AAAAGAAA
1 AAAAGAAA
29375552 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (10 bp):
AAAAGAAAGT
Found at i:29375537 original size:24 final size:24
Alignment explanation
Indices: 29375495--29375542 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29375485 TAGAGGGATA
* * *
29375495 AACAGAAAAGAATGGAAAATAAAG
1 AACAAAAAAGAAAGGAAAAGAAAG
*
29375519 AACAAAAAAGAAAGTAAAAGAAAG
1 AACAAAAAAGAAAGGAAAAGAAAG
29375543 TAAAAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (24 bp):
AACAAAAAAGAAAGGAAAAGAAAG
Found at i:29380108 original size:72 final size:72
Alignment explanation
Indices: 29380008--29380183 Score: 208
Period size: 72 Copynumber: 2.4 Consensus size: 72
29379998 CATGTGTTGT
** *
29380008 GGATTCTTTGAAGCTTGTGTGAGCAGCATCAAATCATTATTTATCAATGGCTTGAGATCCAACAC
1 GGATTCTTTGAAGCTTGTGTGAGCAGCATCAAATCACCATTTACCAATGGCTTGAGATCCAACAC
29380073 GTGTTAC
66 GTGTTAC
* * * * * * * * *
29380080 GGATTCTTTGAAGCTTGTGTAAGTAGCATCGAATTACCCTTTACCGATGGCTTGAGGTTCAGCAC
1 GGATTCTTTGAAGCTTGTGTGAGCAGCATCAAATCACCATTTACCAATGGCTTGAGATCCAACAC
**
29380145 GTGTTGT
66 GTGTTAC
* *
29380152 GAATTCTTTGAAGCTTGTTTGAGCAGCATCAA
1 GGATTCTTTGAAGCTTGTGTGAGCAGCATCAA
29380184 GTAAAACTTG
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 85 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (72 bp):
GGATTCTTTGAAGCTTGTGTGAGCAGCATCAAATCACCATTTACCAATGGCTTGAGATCCAACAC
GTGTTAC
Found at i:29384263 original size:12 final size:12
Alignment explanation
Indices: 29384248--29384282 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29384238 TATGGAGGAT
29384248 ATAGAGGTGGAA
1 ATAGAGGTGGAA
*
29384260 ATAGAGGTGTAA
1 ATAGAGGTGGAA
29384272 ATAGAGGTGGA
1 ATAGAGGTGGA
29384283 TGAGGAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (12 bp):
ATAGAGGTGGAA
Found at i:29390301 original size:12 final size:12
Alignment explanation
Indices: 29390282--29390316 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
29390272 CTGTTTTTGA
29390282 TAATTATTAATT
1 TAATTATTAATT
*
29390294 TCATTATTAATT
1 TAATTATTAATT
29390306 TAATTTATTAA
1 TAA-TTATTAA
29390317 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (12 bp):
TAATTATTAATT
Found at i:29391723 original size:17 final size:17
Alignment explanation
Indices: 29391701--29391734 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29391691 AAAATAATTT
29391701 TTAAAAATTAGAAAATA
1 TTAAAAATTAGAAAATA
*
29391718 TTAAAAATTTGAAAATA
1 TTAAAAATTAGAAAATA
29391735 AATTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAAAAATTAGAAAATA
Found at i:29399743 original size:3 final size:3
Alignment explanation
Indices: 29399735--29399763 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29399725 CTCTCAAGGT
29399735 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
29399764 CAGGTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:29401249 original size:34 final size:35
Alignment explanation
Indices: 29401185--29401258 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
29401175 TAAAAAATAG
* *
29401185 TAAAAAAATATTCAAATTATGTATACTAGTAAAAA
1 TAAAAAAATATTCAAATTAAGAATACTAGTAAAAA
* *
29401220 TTAAAAAAA-A-TCAAATTAAGAATATTAGTAACAA
1 -TAAAAAAATATTCAAATTAAGAATACTAGTAAAAA
29401254 TAAAA
1 TAAAA
29401259 TATTTACACT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 5 0.15
34 20 0.59
35 1 0.03
36 8 0.24
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.28
Consensus pattern (35 bp):
TAAAAAAATATTCAAATTAAGAATACTAGTAAAAA
Found at i:29401655 original size:47 final size:48
Alignment explanation
Indices: 29401581--29401682 Score: 190
Period size: 47 Copynumber: 2.2 Consensus size: 48
29401571 CATTAGCAAG
29401581 CCAA-AAAGAGTCATATATATACATGATAAGCATGGAAAATAAATCAA
1 CCAATAAAGAGTCATATATATACATGATAAGCATGGAAAATAAATCAA
29401628 CCAATAAA-AGTCATATATATACATGATAAGCATGGAAAATAAATCAA
1 CCAATAAAGAGTCATATATATACATGATAAGCATGGAAAATAAATCAA
29401675 CCAATAAA
1 CCAATAAA
29401683 TCTATGTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 51 0.94
48 3 0.06
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22
Consensus pattern (48 bp):
CCAATAAAGAGTCATATATATACATGATAAGCATGGAAAATAAATCAA
Found at i:29418162 original size:7 final size:7
Alignment explanation
Indices: 29418122--29418148 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29418112 CAATAAGTTT
29418122 AAAAATA
1 AAAAATA
29418129 AAAAATA
1 AAAAATA
29418136 AAAAATA
1 AAAAATA
29418143 AAAAAT
1 AAAAAT
29418149 CTTTAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:29419969 original size:43 final size:43
Alignment explanation
Indices: 29419907--29419993 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
29419897 AGCTTTTATC
29419907 TCACATTTAATAACACATTAAATCTG-CATAACTTTCATGCATT
1 TCACATTTAATAACACATTAAATCTGAC-TAACTTTCATGCATT
* * *
29419950 TCACATTTAATAACTCATTACATCTGACTAACTTTCTTGCATT
1 TCACATTTAATAACACATTAAATCTGACTAACTTTCATGCATT
29419993 T
1 T
29419994 AATTATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 39 0.98
44 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (43 bp):
TCACATTTAATAACACATTAAATCTGACTAACTTTCATGCATT
Found at i:29420991 original size:36 final size:35
Alignment explanation
Indices: 29420945--29421018 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 35
29420935 AAAAGATACT
* ***
29420945 AAAAAATATTCAATTTATTTATACCAGTAACAATA
1 AAAAAATATTCAAATTAAGAATACCAGTAACAATA
*
29420980 AAAAAATTATTCAAATTAAGAATACTAGTAACAATA
1 AAAAAA-TATTCAAATTAAGAATACCAGTAACAATA
29421016 AAA
1 AAA
29421019 TATTTATACT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (35 bp):
AAAAAATATTCAAATTAAGAATACCAGTAACAATA
Found at i:29423232 original size:24 final size:24
Alignment explanation
Indices: 29423202--29423251 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
29423192 TAACATATAA
** *
29423202 AATTTTTAAAAATTAGAAAATTTT
1 AATTTTTAAAAACCAGAAAATATT
29423226 AATTTTTAAAAACCAGAAAATATT
1 AATTTTTAAAAACCAGAAAATATT
29423250 AA
1 AA
29423252 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
AATTTTTAAAAACCAGAAAATATT
Found at i:29424363 original size:12 final size:13
Alignment explanation
Indices: 29424346--29424392 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
29424336 TTTTGATAAG
*
29424346 TATTAATTTCA-T
1 TATTAATTTAATT
29424358 TATTAATTTAATT
1 TATTAATTTAATT
*
29424371 TATTAA-ATAATT
1 TATTAATTTAATT
29424383 TATTTAATTT
1 TA-TTAATTT
29424393 TTATTTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 17 0.59
13 11 0.38
14 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTAATTTAATT
Found at i:29425940 original size:2 final size:2
Alignment explanation
Indices: 29425933--29425963 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29425923 ATTTAGCTAT
29425933 TA TA 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 TA TA T
29425964 TTGTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29426158 original size:18 final size:17
Alignment explanation
Indices: 29426135--29426169 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
29426125 AAATTAATTT
29426135 TTAAAAAATTAGAAAATA
1 TTAAAAAATTA-AAAATA
29426153 TTAAAAAATTAAAAATA
1 TTAAAAAATTAAAAATA
29426170 AATTTAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TTAAAAAATTAAAAATA
Found at i:29433850 original size:42 final size:43
Alignment explanation
Indices: 29433744--29433898 Score: 109
Period size: 43 Copynumber: 3.6 Consensus size: 43
29433734 CTCGTACAAT
* * * ** *
29433744 GCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACGAT
1 GCCAATGTCCCAAACATGGTCTTACACATAATCAAATAACGAC
* * * * * *
29433787 GCCACTGTCCCATATAGGGTCTTACACATAATGATATAA-GAC
1 GCCAATGTCCCAAACATGGTCTTACACATAATCAAATAACGAC
* *
29433829 GCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAAAT--CGAT
1 GCCAATGTCCCAAACATGGTCTTACACAT-AA--TCAAATAACGAC
* **
29433873 GCCAACGTCCCAAATGTGGTCTTACA
1 GCCAATGTCCCAAACATGGTCTTACA
29433899 TGATATAACA
Statistics
Matches: 86, Mismatches: 22, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
42 26 0.30
43 31 0.36
44 25 0.29
45 4 0.05
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
GCCAATGTCCCAAACATGGTCTTACACATAATCAAATAACGAC
Found at i:29434455 original size:18 final size:20
Alignment explanation
Indices: 29434418--29434456 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29434408 TTTCATTTTC
*
29434418 AATTCAACCCAAAATACTCA
1 AATTCAACCAAAAATACTCA
29434438 AATTC-ACCAAAAAT-CTCA
1 AATTCAACCAAAAATACTCA
29434456 A
1 A
29434457 TAAAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (20 bp):
AATTCAACCAAAAATACTCA
Found at i:29437852 original size:22 final size:23
Alignment explanation
Indices: 29437824--29437868 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29437814 AGGCAATCTT
29437824 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
29437846 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
29437869 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:29440547 original size:19 final size:19
Alignment explanation
Indices: 29440523--29440567 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29440513 CATTTCTTTT
*
29440523 TGCATT-CATTCCATGCATC
1 TGCATTACATTCCAT-CATA
*
29440542 TGCATTACATTGCATCATA
1 TGCATTACATTCCATCATA
29440561 TGCATTA
1 TGCATTA
29440568 GATTTTCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (19 bp):
TGCATTACATTCCATCATA
Found at i:29445229 original size:45 final size:45
Alignment explanation
Indices: 29445126--29445593 Score: 350
Period size: 45 Copynumber: 10.5 Consensus size: 45
29445116 CCACAAATCC
* * * **
29445126 TATCTCCTTGAAGTTGCAGTGGAGCGA-ATTAAAGTTA-CAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAG-GAGACTGAAGAAAGCAAGTCT
* *
29445170 TATCTCCATGAAGTTACAGTGGAGGAGACTGAAGAAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGGAGACTGAAGAAAGCAAGTCT
* * * ** *
29445215 TATCCCCCTAAAGTTACAGTGG-GGCAGACTGAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGG-AGACTGAAGAAAGCAAGTCT
* *
29445260 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAACAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGGAGACTGAAGAAAGCAAGTCT
* * *
29445305 TATCCCCCTGAAGTTGCAGTGG-GGCAAACTGAA-AATGGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGG-AGACTGAAGAA-AGCAAGTCT
* * * *
29445350 TATCCCCCTGAAGTTGCAGTGG-GGCAAACTGAA-AATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGG-AGACTGAAGAA-AGCAAGTCT
* * * * * * *
29445395 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCAA-TAATTC-
1 TATCTCCCTGAAGTTGCAGTGGAGGAGACTGAAG-AAAGCAAGTCT
* ** * **
29445439 TATCTCCCTAAAGTTGCAGTGGAGCG-GGTTAAAGTTA-CAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAG-GAGACTGAAGAAAGCAAGTCT
* ** *
29445483 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGGAGACTGAAGAAAGCAAGTCT
* * * * ** * *
29445528 TATCTCCCTGAAGTTTCAGTGGAGCAGATTAAAGTTA-CAAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGGAGACTGAAGAAAGCAAGTCT
29445572 TATCT-CCTGAAGTTGCAGTGGA
1 TATCTCCCTGAAGTTGCAGTGGA
29445594 ATGGATTAAA
Statistics
Matches: 354, Mismatches: 57, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
43 23 0.06
44 104 0.29
45 224 0.63
46 2 0.01
47 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGGAGACTGAAGAAAGCAAGTCT
Found at i:29445289 original size:90 final size:90
Alignment explanation
Indices: 29445167--29445555 Score: 439
Period size: 90 Copynumber: 4.3 Consensus size: 90
29445157 AAGTTACAAG
* * * *
29445167 TCTTATCTCCATGAAGTTACAGTGGAGGAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTGC
*
29445232 AGTGGGGCAGACTGAAGATGGCAAA
66 AGTGGAGCAGACTGAAGATGGCAAA
* *
29445257 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAACAAGTCTTATCCCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTGC
* * * *
29445322 AGTGGGGCAAACTGAAAATGGCAAG
66 AGTGGAGCAGACTGAAGATGGCAAA
* * * * * *
29445347 TCTTATCCCCCTGAAGTTGCAGTGGGGCAAACTGAA-AATGGCAAATCTTATCTCCCTAAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAA-AGCAAGTCTTATCCCCCTAAAGTTG
* *
29445411 CAGTGGAGCAGA-TTAA-A-GTCAATAA
65 CAGTGGAGCAGACTGAAGATGGC-A-AA
* * ** * ** * *
29445436 T-TCTATCTCCCTAAAGTTGCAGTGGAGCGGGTTAAAGTTA-CAAGTCTTATCTCCCTGAAGTTG
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTG
29445499 CAGTGGAGCAGACTGAAGATGGCAAA
65 CAGTGGAGCAGACTGAAGATGGCAAA
*
29445525 TCTTATCTCCCTGAAGTTTCAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
29445556 TTAAAGTTAC
Statistics
Matches: 249, Mismatches: 41, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
87 2 0.01
88 36 0.14
89 62 0.25
90 147 0.59
91 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (90 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTGC
AGTGGAGCAGACTGAAGATGGCAAA
Found at i:29445491 original size:88 final size:89
Alignment explanation
Indices: 29445118--29445593 Score: 408
Period size: 90 Copynumber: 5.3 Consensus size: 89
29445108 CAGTGAAACC
* * * * ** * * *
29445118 ACAAATCCTATCTCCTTGAAGTTGCAGTGGAGC-GAATTAA-AGTTACAAGTCTTATCTCCATGA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-TGGCAAATCTTATCTCCCTAA
* * * * **
29445181 AGTTACAGTGGAGGAGACTGAAGAA
65 AGTTGCAGTGGAGCAGATTAAAGTT
* * * * * *
29445206 AGCAAGTCTTATCCCCCTAAAGTTACAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAATCTTATCTCCCTAA
* * **
29445271 AGTTGCAGTGGAGCAGACTGAAGAAA
65 AGTTGCAGTGGAGCAGATTAAAG-TT
* * * * * * * *
29445297 ACAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAAACTGAAAATGGCAAGTCTTATCCCCCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAATCTTATCTCCCTAAA
* * * * *
29445362 GTTGCAGTGGGGCAAACTGAAAATG
66 GTTGCAGTGGAGCAGA-TTAAAGTT
* * * *
29445387 GCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTAA-A-GTCAATAAT-TCTATCTCCCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGC-A-AATCT-TATCTCCCT
* *
29445448 AAAGTTGCAGTGGAGCGGGTTAAAGTT
63 AAAGTTGCAGTGGAGCAGATTAAAGTT
* *
29445475 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAATCTTATCTCCCTAAA
*
29445540 GTTTCAGTGGAGCAGATTAAAGTT
66 GTTGCAGTGGAGCAGATTAAAGTT
*
29445564 ACAAATCCTATCT-CCTGAAGTTGCAGTGGA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGA
29445594 ATGGATTAAA
Statistics
Matches: 318, Mismatches: 58, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
87 2 0.01
88 59 0.19
89 101 0.32
90 148 0.47
91 8 0.03
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (89 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAATCTTATCTCCCTAAA
GTTGCAGTGGAGCAGATTAAAGTT
Found at i:29445521 original size:133 final size:132
Alignment explanation
Indices: 29445119--29445617 Score: 554
Period size: 135 Copynumber: 3.7 Consensus size: 132
29445109 AGTGAAACCA
* * * * * *
29445119 CAAATCCTATCTCCTTGAAGTTGCAGTGGAGC-GAATTAAAGTTACAAGTCTTATCTCCATGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGTAAAAATTC-TATCTCCCTGAAG
* * * ** * *
29445183 TTACAGTGGAG-GAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTACAGTGGGGCAGACTGA
64 TTGCAGTGGAGCG-GATTAAAGTTA-CAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGA
29445247 AGATGG
127 AGATGG
* * * * *
29445253 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAACAAGTCTTATCCCCCTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAAA-AATTC-TATCTCCCTGAAG
* ** * * ** *
29445318 TTGCAGTGGGGCAAACTGAAAATGGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAAACTGAA
64 TTGCAGTGGAGCGGA-TTAAAGTTACAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAA
*
29445383 AATGG
128 GATGG
* * *
29445388 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCAATAATTCTATCTCCCTAAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-AAAAATTCTATCTCCCTGAAGT
* * *
29445453 TGCAGTGGAGCGGGTTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
65 TGCAGTGGAGCGGATTAAAGTTACAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGA
29445518 TGG
130 TGG
* * *
29445521 CAAATCTTATCTCCCTGAAGTTTCAGTGGAGCAGATTAAAGTTACAAATCCTATCT-CCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAAAAATTCTATCTCCCTGAAGT
**
29445585 TGCAGTGGAATGGATTAAAGTTACAAGTCTTAT
65 TGCAGTGGAGCGGATTAAAGTTACAAGTCTTAT
29445618 TGAAGAAAGC
Statistics
Matches: 306, Mismatches: 53, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
132 37 0.12
133 95 0.31
134 59 0.19
135 111 0.36
136 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (132 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAAAAATTCTATCTCCCTGAAGTT
GCAGTGGAGCGGATTAAAGTTACAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGAT
GG
Found at i:29445987 original size:132 final size:131
Alignment explanation
Indices: 29445814--29446227 Score: 548
Period size: 132 Copynumber: 3.1 Consensus size: 131
29445804 CTCTGAATTT
* *
29445814 GCAGTAGAGTAGGTTGAAGATTGTAGATCCTGTCTCTCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
** * *
29445879 AGTGAATCTTATCTTCCTAAGATAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCTCACTGAG
66 AGTGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCTC-CTAAG
29445944 CA
130 CA
* * * *
29445946 GCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTCCCTAAGCAGTAGTAGAGCAGATCGAACAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
*
29446011 -GATGAATCTTATCTTCCCGAGGTAGTA-GGAAGCAGATTTAAGCCACCAGTCCTATCTTCCTAA
66 AG-TGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATC-TCCTAA
29446074 GCA
129 GCA
* * * *
29446077 GTAGTGGAGTAGGTTGAAGATTGTATATCCTGTCTCCTTAA-CAAGTAGTGTAGCAGATCAAAGA
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGC-AGTAGTGGAGCAGATCAAAGA
* * *
29446141 -AGGCGAGTCTTATCTTCCCGAGGTAGTAGGGAAGCAAATTTAAGCCACCAGTCTTATCTCCCTA
65 CA-GTGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCT-CCT-
**
29446205 AAGTT
127 AAGCA
*
29446210 GCAGTGGAGCAGGTTGAA
1 GCAGTGGAGTAGGTTGAA
29446228 ATTACCAATT
Statistics
Matches: 247, Mismatches: 27, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
130 1 0.00
131 113 0.46
132 114 0.46
133 19 0.08
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (131 bp):
GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
AGTGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCTCCTAAGC
A
Found at i:29453052 original size:45 final size:45
Alignment explanation
Indices: 29452993--29453124 Score: 183
Period size: 45 Copynumber: 2.9 Consensus size: 45
29452983 GCAGACAAGT
* * *
29452993 TGCTAGTACAGTGTGGATGAACCACTCATCGGTGCAGATAAAAGC
1 TGCTAATACGGTGTGGATAAACCACTCATCGGTGCAGATAAAAGC
*
29453038 TGCTAATACGGTGTGGATAAACCACTCATCGGTGCAGATAAAAGT
1 TGCTAATACGGTGTGGATAAACCACTCATCGGTGCAGATAAAAGC
* * * * *
29453083 TTCTAATAAGGTGTGGGTAAACCACTCAACGGTGTAGATAAA
1 TGCTAATACGGTGTGGATAAACCACTCATCGGTGCAGATAAA
29453125 TTGCTCATAC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (45 bp):
TGCTAATACGGTGTGGATAAACCACTCATCGGTGCAGATAAAAGC
Found at i:29453077 original size:21 final size:21
Alignment explanation
Indices: 29453012--29453079 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
29453002 AGTGTGGATG
29453012 AACCACTCATCGGTGCAGATAA
1 AACCACTCATCGGTGCAGAT-A
** * **
29453034 AAGCTGCTAATACGGTGTGGATA
1 AA-CCACTCAT-CGGTGCAGATA
29453057 AACCACTCATCGGTGCAGATA
1 AACCACTCATCGGTGCAGATA
29453078 AA
1 AA
29453080 AGTTTCTAAT
Statistics
Matches: 34, Mismatches: 10, Indels: 5
0.69 0.20 0.10
Matches are distributed among these distances:
21 11 0.32
22 7 0.21
23 8 0.24
24 8 0.24
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (21 bp):
AACCACTCATCGGTGCAGATA
Found at i:29455461 original size:20 final size:20
Alignment explanation
Indices: 29455416--29455462 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29455406 CTTTCTTTTG
*
29455416 TATTTTATTTACTTAAATTT
1 TATTTTATTTACTTAAATTC
*
29455436 TCTTTTATTTAC-TAAATTAC
1 TATTTTATTTACTTAAATT-C
29455456 TATTTTA
1 TATTTTA
29455463 ACCTTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTATTTACTTAAATTC
Found at i:29456443 original size:17 final size:17
Alignment explanation
Indices: 29456403--29456445 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
29456393 TCTAGCTTTC
29456403 ACAATTTAAGTTTTCAA
1 ACAATTTAAGTTTTCAA
*
29456420 ACTATTTAAGTTTTTCAA
1 ACAATTTAAG-TTTTCAA
29456438 A-AATTTAA
1 ACAATTTAA
29456446 ATTTAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (17 bp):
ACAATTTAAGTTTTCAA
Found at i:29458757 original size:30 final size:31
Alignment explanation
Indices: 29458703--29458762 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
29458693 TTGATCATTA
29458703 AACTATTAAAAAATTTTCATTTAAGTCACTG
1 AACTATTAAAAAATTTTCATTTAAGTCACTG
*
29458734 AACTATTCAAAAATTTT-ATTTAAGTCACT
1 AACTATTAAAAAATTTTCATTTAAGTCACT
29458763 AGGTTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (31 bp):
AACTATTAAAAAATTTTCATTTAAGTCACTG
Found at i:29459889 original size:123 final size:124
Alignment explanation
Indices: 29459621--29459925 Score: 375
Period size: 123 Copynumber: 2.4 Consensus size: 124
29459611 TTAAAATTTT
* *
29459621 AAAAGAAATACTCATTTGATTA-CAATGTAACATTCCTAAGTTAAGGTAGGTTCAGTGCCCCAAA
1 AAAAAAAATACTCACTTGA-TAGCAATGTAACATTCCTAAGTTAAGGTAGGTTCAGT----CAAA
** * * *
29459685 AGAGTCAATAGTTGTTAGACTAGCTTTGGCTTGATGGCAATGGTGTAGGTAGGGGGCTAGCAGG
61 AGAACCAATAGTTGTTAGACTAGCTTTGGCTTGATGGCAATGGCGTAAGTAGAGGGCTAGCAGG
* * *
29459749 AAAAAAAATACTTACTTGATAGCAATGTAACATTCCTAAGTTAAGGTAAGTTCAGT-ACAAGAAC
1 AAAAAAAATACTCACTTGATAGCAATGTAACATTCCTAAGTTAAGGTAGGTTCAGTCAAAAGAAC
* * * *
29459813 CGATAGTTGTTAGACTAGCTTTGGCTTGATGGC-ATAGGCGTAATTAGAAGGGTTGGCAGG
66 CAATAGTTGTTAGACTAGCTTTGGCTTGATGGCAAT-GGCGTAAGTAG-AGGGCTAGCAGG
* *
29459873 -GAAAAAATACTCACTTGATAGCAATGTAACATTCCTAAGTTAAGCTAGGTTCA
1 AAAAAAAATACTCACTTGATAGCAATGTAACATTCCTAAGTTAAGGTAGGTTCA
29459926 ATGTCTCAGA
Statistics
Matches: 156, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
122 2 0.01
123 94 0.60
124 9 0.06
127 2 0.01
128 49 0.31
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (124 bp):
AAAAAAAATACTCACTTGATAGCAATGTAACATTCCTAAGTTAAGGTAGGTTCAGTCAAAAGAAC
CAATAGTTGTTAGACTAGCTTTGGCTTGATGGCAATGGCGTAAGTAGAGGGCTAGCAGG
Found at i:29467516 original size:6 final size:6
Alignment explanation
Indices: 29467507--29467540 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
29467497 AATTATTTTG
29467507 TTATAT TTATAT TTATAT TTATAT TTATAT TTAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTAT
29467541 CATAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:29467548 original size:18 final size:18
Alignment explanation
Indices: 29467509--29467549 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29467499 TTATTTTGTT
*
29467509 ATATTTATATTTATATTT
1 ATATTTATATTTATATTA
29467527 ATATTTATATTTATCA-TA
1 ATATTTATATTTAT-ATTA
29467545 ATATT
1 ATATT
29467550 ATTTTTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTATATTTATATTA
Found at i:29469990 original size:16 final size:16
Alignment explanation
Indices: 29469965--29470004 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
29469955 AATATTAAAA
* **
29469965 ATTTTCTTAAATTTTT
1 ATTTTATTAAATAATT
29469981 ATTTTATTAAATAATT
1 ATTTTATTAAATAATT
29469997 ATTTTATT
1 ATTTTATT
29470005 TAAAACGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTATTAAATAATT
Found at i:29471727 original size:28 final size:28
Alignment explanation
Indices: 29471696--29471786 Score: 114
Period size: 27 Copynumber: 3.2 Consensus size: 28
29471686 GAGCTAACGA
* *
29471696 AAAAAAGGAGTTAGCCTGATGAGTTGCT
1 AAAAAAGGAGTTAGCCAGAAGAGTTGCT
*
29471724 -AAAAAGGAGTTAGCCAGAAGAGTTTGCC
1 AAAAAAGGAGTTAGCCAGAAGAG-TTGCT
29471752 AAAAAAGG-GTTAGCCAGAAGAGTTAGACT
1 AAAAAAGGAGTTAGCCAGAAGAGTT-G-CT
29471781 AAAAAA
1 AAAAAA
29471787 AAGGCTAGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
27 22 0.40
28 19 0.35
29 14 0.25
ACGTcount: A:0.44, C:0.11, G:0.26, T:0.19
Consensus pattern (28 bp):
AAAAAAGGAGTTAGCCAGAAGAGTTGCT
Found at i:29471731 original size:27 final size:28
Alignment explanation
Indices: 29471697--29471785 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 28
29471687 AGCTAACGAA
* *
29471697 AAAAAGGAGTTAGCCTGATGAGTTG-CT
1 AAAAAGGAGTTAGCCAGAAGAGTTGACT
* *
29471724 AAAAAGGAGTTAGCCAGAAGAGTTTGCCA
1 AAAAAGGAGTTAGCCAGAAGAG-TTGACT
29471753 AAAAAGG-GTTAGCCAGAAGAGTTAGACT
1 AAAAAGGAGTTAGCCAGAAGAGTT-GACT
29471781 AAAAA
1 AAAAA
29471786 AAAGGCTAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 22 0.41
28 24 0.44
29 8 0.15
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19
Consensus pattern (28 bp):
AAAAAGGAGTTAGCCAGAAGAGTTGACT
Found at i:29471752 original size:13 final size:13
Alignment explanation
Indices: 29471730--29471777 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
29471720 TGCTAAAAAG
29471730 GAGTTAGCCAGAA
1 GAGTTAGCCAGAA
* *
29471743 GAGTTTGCCAAAAAA
1 GAGTTAGCC--AGAA
*
29471758 GGGTTAGCCAGAA
1 GAGTTAGCCAGAA
29471771 GAGTTAG
1 GAGTTAG
29471778 ACTAAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 17 0.63
15 10 0.37
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.19
Consensus pattern (13 bp):
GAGTTAGCCAGAA
Found at i:29471812 original size:28 final size:28
Alignment explanation
Indices: 29471734--29471813 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 28
29471724 AAAAAGGAGT
* * *
29471734 TAGCCAGAAGAGTTTGCCAAAAAAGGGT
1 TAGCCAGAAGAGTTTGCAAAAAAAAGGC
*
29471762 TAGCCAGAAGAGTTAGACTAAAAAAAAGGC
1 TAGCCAGAAGAGTTTG-C-AAAAAAAAGGC
*
29471792 TAGCTAGAAGAGTTTGCAAAAA
1 TAGCCAGAAGAGTTTGCAAAAA
29471814 TGGGAGTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 20 0.45
29 2 0.05
30 22 0.50
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.17
Consensus pattern (28 bp):
TAGCCAGAAGAGTTTGCAAAAAAAAGGC
Found at i:29471843 original size:58 final size:58
Alignment explanation
Indices: 29471734--29471843 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
29471724 AAAAAGGAGT
*
29471734 TAGCCAGAAGAGTTTGCCAAAAAAGGGTTAGCCAGAAGAGTTAGACTAAAAAAAAGGC
1 TAGCCAGAAGAGTTTGCCAAAAAAGGGTTAGCAAGAAGAGTTAGACTAAAAAAAAGGC
* * * *
29471792 TAGCTAGAAGAGTTTG-CAAAAATGGGAGTTAGTAAGAATAGTTAGAC-AAAAA
1 TAGCCAGAAGAGTTTGCCAAAAA-AGG-GTTAGCAAGAAGAGTTAGACTAAAAA
29471844 GGAGGTAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
57 6 0.13
58 22 0.49
59 17 0.38
ACGTcount: A:0.45, C:0.10, G:0.25, T:0.19
Consensus pattern (58 bp):
TAGCCAGAAGAGTTTGCCAAAAAAGGGTTAGCAAGAAGAGTTAGACTAAAAAAAAGGC
Found at i:29473505 original size:52 final size:52
Alignment explanation
Indices: 29473437--29473536 Score: 200
Period size: 52 Copynumber: 1.9 Consensus size: 52
29473427 TTTTTTTACA
29473437 ATTTTAACATTTATTTTGAATAAACCATTCTTGTTTAGAATATTTTTTTGTT
1 ATTTTAACATTTATTTTGAATAAACCATTCTTGTTTAGAATATTTTTTTGTT
29473489 ATTTTAACATTTATTTTGAATAAACCATTCTTGTTTAGAATATTTTTT
1 ATTTTAACATTTATTTTGAATAAACCATTCTTGTTTAGAATATTTTTT
29473537 GTCCAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (52 bp):
ATTTTAACATTTATTTTGAATAAACCATTCTTGTTTAGAATATTTTTTTGTT
Found at i:29474549 original size:21 final size:21
Alignment explanation
Indices: 29474525--29474643 Score: 76
Period size: 21 Copynumber: 5.7 Consensus size: 21
29474515 ATAAGTGCTA
*
29474525 AACAAAAACCCGTAAGGGTTG
1 AACAAAAACCCATAAGGGTTG
* * * *
29474546 AACAAAAGCTCATAAGAGCTG
1 AACAAAAACCCATAAGGGTTG
* *
29474567 AACGAAAACCCATAAGGGTTA
1 AACAAAAACCCATAAGGGTTG
* * * * * *
29474588 AACACAAGCTCAAAAGAGCTG
1 AACAAAAACCCATAAGGGTTG
* * *
29474609 AACAGAAACCCATTAGAGTTG
1 AACAAAAACCCATAAGGGTTG
* *
29474630 AACAGAAACTCATA
1 AACAAAAACCCATA
29474644 TAAGTTAAAC
Statistics
Matches: 71, Mismatches: 27, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.14
Consensus pattern (21 bp):
AACAAAAACCCATAAGGGTTG
Found at i:29474576 original size:42 final size:41
Alignment explanation
Indices: 29474515--29474643 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 41
29474505 AAATAAGTAT
* * *
29474515 ATAAGTGCTAAACAAAAACCCGTAAGGGTTGAACAAAAGCTC
1 ATAAGAGCTGAAC-AAAACCCATAAGGGTTGAACAAAAGCTC
* *
29474557 ATAAGAGCTGAACGAAAACCCATAAGGGTTAAACACAAGCTC
1 ATAAGAGCTGAAC-AAAACCCATAAGGGTTGAACAAAAGCTC
* * *
29474599 AAAAGAGCTGAACAGAAACCCATTAGAGTTGAACAGAAA-CTC
1 ATAAGAGCTGAACA-AAACCCATAAGGGTTGAACA-AAAGCTC
29474641 ATA
1 ATA
29474644 TAAGTTAAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 70 0.96
43 2 0.03
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (41 bp):
ATAAGAGCTGAACAAAACCCATAAGGGTTGAACAAAAGCTC
Found at i:29474649 original size:21 final size:21
Alignment explanation
Indices: 29474602--29474657 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
29474592 CAAGCTCAAA
*
29474602 AGAGCTGAACAGAAACCCATT
1 AGAGTTGAACAGAAACCCATT
*
29474623 AGAGTTGAACAGAAACTCATAT
1 AGAGTTGAACAGAAACCCAT-T
*
29474645 A-AGTTAAACAGAA
1 AGAGTTGAACAGAA
29474658 GCTCGTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (21 bp):
AGAGTTGAACAGAAACCCATT
Found at i:29479791 original size:2 final size:2
Alignment explanation
Indices: 29479784--29479810 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29479774 CATTACCAGT
29479784 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
29479811 CTTAATCCAT
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:29480430 original size:2 final size:2
Alignment explanation
Indices: 29480423--29480457 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29480413 TATATTCATC
29480423 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29480458 CTTACAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29480445 original size:17 final size:17
Alignment explanation
Indices: 29480425--29480457 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29480415 TATTCATCAT
29480425 ATATATATATATATATA
1 ATATATATATATATATA
29480442 ATATATATATATATAT
1 ATATATATATATATAT
29480458 CTTACAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:29480782 original size:43 final size:42
Alignment explanation
Indices: 29480730--29480861 Score: 160
Period size: 43 Copynumber: 3.1 Consensus size: 42
29480720 ACATGTATTT
* *
29480730 ACAAATCGATGCCACTGTCCTAGACAGGGTCTTACACGTAAAC
1 ACAAGTCGATGCCAC-GTCCCAGACAGGGTCTTACACGTAAAC
* *
29480773 ACAAGTCGATGCTAACGTCCCAGACATGGTCTTACACGTAAAC
1 ACAAGTCGATGC-CACGTCCCAGACAGGGTCTTACACGTAAAC
*
29480816 ACAAGTCGATGCCAACGTCCCAGGC-GTGGTCTTACACG-AAATC
1 ACAAGTCGATGCC-ACGTCCCAGACAG-GGTCTTACACGTAAA-C
29480859 ACA
1 ACA
29480862 TATCAGAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
42 3 0.04
43 73 0.94
44 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (42 bp):
ACAAGTCGATGCCACGTCCCAGACAGGGTCTTACACGTAAAC
Found at i:29481802 original size:47 final size:48
Alignment explanation
Indices: 29481748--29481848 Score: 161
Period size: 49 Copynumber: 2.1 Consensus size: 48
29481738 ATAATTGGTT
*
29481748 TACTTTAT-TAACCTTTATATAAATATAT-ACACATATATATAAGGCTA
1 TACTTTATATAA-ATTTATATAAATATATAACACATATATATAAGGCTA
29481795 TACTTTATATAAATTTATATAAATATATACACACATATATATAAGGCTA
1 TACTTTATATAAATTTATATAAATATATA-ACACATATATATAAGGCTA
29481844 TACTT
1 TACTT
29481849 GTACTTTGCC
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
47 23 0.46
48 3 0.06
49 24 0.48
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.41
Consensus pattern (48 bp):
TACTTTATATAAATTTATATAAATATATAACACATATATATAAGGCTA
Found at i:29483786 original size:42 final size:42
Alignment explanation
Indices: 29483739--29483839 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
29483729 AGTGCGAAAT
* * * * *
29483739 AGAAACCCGTAAGGGTTGAAC-GAAAGCTCATAAGAGCTGAAC
1 AGAAACCCATAAAGGTTAAACAGAAA-CTCAAAAGAGATGAAC
*
29483781 GGAAACCCATAAAGGTTAAACAGAAACTCAAAAGAGATGAAC
1 AGAAACCCATAAAGGTTAAACAGAAACTCAAAAGAGATGAAC
*
29483823 AGAAACCCATTAAGGTT
1 AGAAACCCATAAAGGTT
29483840 GAATGGAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
42 46 0.92
43 4 0.08
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (42 bp):
AGAAACCCATAAAGGTTAAACAGAAACTCAAAAGAGATGAAC
Found at i:29483791 original size:21 final size:21
Alignment explanation
Indices: 29483739--29483868 Score: 86
Period size: 21 Copynumber: 6.2 Consensus size: 21
29483729 AGTGCGAAAT
* *
29483739 AGAAACCCGTAAGGGTTGAAC
1 AGAAACCCATAAGAGTTGAAC
* *
29483760 -GAAAGCTCATAAGAGCTGAAC
1 AGAAA-CCCATAAGAGTTGAAC
* *
29483781 GGAAACCCATAA-AGGTTAAAC
1 AGAAACCCATAAGA-GTTGAAC
* * *
29483802 AGAAACTCAAAAGAGATGAAC
1 AGAAACCCATAAGAGTTGAAC
*
29483823 AGAAACCCATTAAG-GTTGAAT
1 AGAAACCCA-TAAGAGTTGAAC
* * * *
29483844 GGAAACTCATATGAGTTAAAC
1 AGAAACCCATAAGAGTTGAAC
29483865 AGAA
1 AGAA
29483869 GCTTGTGAGA
Statistics
Matches: 81, Mismatches: 22, Indels: 12
0.70 0.19 0.10
Matches are distributed among these distances:
20 8 0.10
21 65 0.80
22 8 0.10
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (21 bp):
AGAAACCCATAAGAGTTGAAC
Found at i:29483866 original size:42 final size:41
Alignment explanation
Indices: 29483739--29483868 Score: 118
Period size: 42 Copynumber: 3.1 Consensus size: 41
29483729 AGTGCGAAAT
* * *
29483739 AGAAACCC-GTAAGGGTTGAACGAAAGCTCATAAGAGCTGAAC
1 AGAAACCCATTAA-GGTTGAAAGAAA-CTCATAAGAGATGAAC
* * * *
29483781 GGAAACCCATAAAGGTTAAACAGAAACTCAAAAGAGATGAAC
1 AGAAACCCATTAAGGTTGAA-AGAAACTCATAAGAGATGAAC
* * * *
29483823 AGAAACCCATTAAGGTTGAATGGAAACTCATATGAGTTAAAC
1 AGAAACCCATTAAGGTTGAA-AGAAACTCATAAGAGATGAAC
29483865 AGAA
1 AGAA
29483869 GCTTGTGAGA
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
42 64 0.91
43 6 0.09
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (41 bp):
AGAAACCCATTAAGGTTGAAAGAAACTCATAAGAGATGAAC
Found at i:29494628 original size:24 final size:24
Alignment explanation
Indices: 29494559--29494651 Score: 66
Period size: 24 Copynumber: 3.9 Consensus size: 24
29494549 CATTCATTCT
* *
29494559 TCAGAGGATAAGATTTCACATCCT
1 TCAGGGGATAAGATTTCACATCCA
* *
29494583 TTATGGGAT---ATTATCATTCATCCA
1 TCAGGGGATAAGATT-TCA--CATCCA
*
29494607 TCAGGGGATAAGATTTCACATCCC
1 TCAGGGGATAAGATTTCACATCCA
* * *
29494631 TCAAGGGATCATATTTCACAT
1 TCAGGGGATAAGATTTCACAT
29494652 TCTTAAGGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
24 41 0.77
26 3 0.06
27 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (24 bp):
TCAGGGGATAAGATTTCACATCCA
Done.