Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 110 of 204
Found at i:34207320 original size:18 final size:18
Alignment explanation
Indices: 34207297--34207344 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
34207287 ATTCAAGTTT
34207297 AATATTATTATATTATTA
1 AATATTATTATATTATTA
* *
34207315 AATATTTTTAT-TTTTTA
1 AATATTATTATATTATTA
*
34207332 AAGTATTAATATA
1 AA-TATTATTATA
34207345 AAATATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
AATATTATTATATTATTA
Found at i:34208199 original size:24 final size:22
Alignment explanation
Indices: 34208149--34208200 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
34208139 ATAAATACTC
*
34208149 AAAAATAAATATTTTTATAATA
1 AAAAATAAATATTTTAATAATA
* *
34208171 TAAAATATGAATATTTTAATTATA
1 -AAAA-ATAAATATTTTAATAATA
34208195 AAAAAT
1 AAAAAT
34208201 GGGTATTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 8 0.32
24 15 0.60
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAATAAATATTTTAATAATA
Found at i:34210342 original size:36 final size:36
Alignment explanation
Indices: 34210295--34210364 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
34210285 GCTCTTTTGA
34210295 TGCTGGAGAAACGTTGGTCAACTGTCTCCTAGGAGG
1 TGCTGGAGAAACGTTGGTCAACTGTCTCCTAGGAGG
34210331 TGCTGGAGAAACGTTGGTCAACTGTCTCCTAGGA
1 TGCTGGAGAAACGTTGGTCAACTGTCTCCTAGGA
34210365 TACAACAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (36 bp):
TGCTGGAGAAACGTTGGTCAACTGTCTCCTAGGAGG
Found at i:34217017 original size:36 final size:38
Alignment explanation
Indices: 34216965--34217035 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
34216955 CATTCTGAGC
*
34216965 AAATGTTCTTTTA-TTTTTT-CATTTCAATCATAACCA
1 AAATATTCTTTTATTTTTTTCCATTTCAATCATAACCA
*
34217001 AAATATTCTTTTATTTTTTTCCATTTCATTCATAA
1 AAATATTCTTTTATTTTTTTCCATTTCAATCATAA
34217036 TCATACTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 12 0.39
37 6 0.19
38 13 0.42
ACGTcount: A:0.30, C:0.15, G:0.01, T:0.54
Consensus pattern (38 bp):
AAATATTCTTTTATTTTTTTCCATTTCAATCATAACCA
Found at i:34217619 original size:19 final size:19
Alignment explanation
Indices: 34217595--34217640 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
34217585 TGCAGGAGAG
34217595 GCAAAAAAAA-AACAAATAA
1 GCAAAAAAAAGAACAAA-AA
*
34217614 GCAAAAAAAAGAGCAAAAA
1 GCAAAAAAAAGAACAAAAA
34217633 -CAAAAAAA
1 GCAAAAAAA
34217641 CAAAAACCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 12 0.48
20 5 0.20
ACGTcount: A:0.78, C:0.11, G:0.09, T:0.02
Consensus pattern (19 bp):
GCAAAAAAAAGAACAAAAA
Found at i:34219095 original size:45 final size:44
Alignment explanation
Indices: 34218991--34219103 Score: 133
Period size: 44 Copynumber: 2.5 Consensus size: 44
34218981 GCCACTAATT
* * * *
34218991 TTATCCCCCTAAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTC
1 TTATCTCCCTAAAGTTGTAGTGGAGCAGCTTGAAGATACAAGTC
34219035 TTATCTCCCTAAAGTTGTAGTGGAGCAGACTT-AAGATAGCGAA-TC
1 TTATCTCCCTAAAGTTGTAGTGGAGCAG-CTTGAAGATA-C-AAGTC
34219080 TTAAT-TCCCTAAAGTTGTAGTGGA
1 TT-ATCTCCCTAAAGTTGTAGTGGA
34219104 ATAGACTCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
44 31 0.51
45 26 0.43
46 4 0.07
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (44 bp):
TTATCTCCCTAAAGTTGTAGTGGAGCAGCTTGAAGATACAAGTC
Found at i:34219476 original size:143 final size:143
Alignment explanation
Indices: 34219215--34220012 Score: 960
Period size: 143 Copynumber: 5.6 Consensus size: 143
34219205 AGTTACAAGT
* * * ** ** *
34219215 CTTATCTCCTTGAAGATGCAGTGGAGCAGACTGAAGACAGTGAATCTTATTTCCCTAATGTTGTA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTAGCGTTGCA
* * * * * *
34219280 --AGAACAGGTTAAAGCTACAAATTATGGTGGATCTTATCTTCGTGAAGTTGCAGTGGAGCAGAT
66 GTGGAACAGATTAAAGCTACAAATTATAGCGGAACTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
34219343 TGAAGCCACCAGC
131 TGAAGCCACCAGC
* * * * * *
34219356 CTTATCTCCCTGAAGTCGCAGCGGAGTAGACTGAAGACAACAAATCTTATTTCCCTGGTGTTACA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTAGCGTTGCA
* * *
34219421 GTGGAACAGATTAAAGCTACAAATTATGGCGGAACTTATCTTCTTGAAGTTGCAGTGGAGCAAAT
66 GTGGAACAGATTAAAGCTACAAATTATAGCGGAACTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
*
34219486 TGAAGCCACCAGT
131 TGAAGCCACCAGC
* * *
34219499 CTTATCTCCATGAAGTTGCAGTGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTAGCGTTGCA
* *
34219564 GTGGAACAGATTAATGCTACAAATTATAGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
66 GTGGAACAGATTAAAGCTACAAATTATAGCGGAACTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
*
34219629 TGAAGTCACCAGC
131 TGAAGCCACCAGC
* * * *
34219642 CTTATCTCCCTGAAGTTGCAGCGGAGCGGACT-AAAAAAAGCGAATCTTATTTCCCTAGCGTTGT
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAA-CGAATCTTATTTCCCTAGCGTTGC
* ** *
34219706 AGTGGAATAGATTAAAATTACAAAAAATATAGCGGATA-TTATCTTCCTGAAGTTGCAGTGGAGC
65 AGTGGAACAGATTAAAGCTAC--AAATTATAGCGGA-ACTTATCTTCCTGAAGTTGCAGTGGAGC
*
34219770 AGATTGAAGCCACCAAC
127 AGATTGAAGCCACCAGC
* * * * * * *
34219787 CTTATCTCCCTGAAGTTGCAGTGGAGCATACTAAAAATAGCGAATCTTATTTCCCTGGCGTTGCA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTAGCGTTGCA
* ** * * *
34219852 GTGG-ATAGATTAAAATTACAAAATATAGCGGATA-TTATCTTCCTGAAGTCGCAGTGGAGCATA
66 GTGGAACAGATTAAAGCTACAAATTATAGCGGA-ACTTATCTTCCTGAAGTTGCAGTGGAGCAGA
34219915 TTGAAGCCACCAGC
130 TTGAAGCCACCAGC
* * * * * **
34219929 CTTATTTCCCTGAAGTTGCAGCGAAGCAGATTGAAGACAGCGAATCTTATTTTCCTAGTATTGCA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTAGCGTTGCA
* *
34219994 ATGGAACAGATTGAAGCTA
66 GTGGAACAGATTAAAGCTA
34220013 TAAAGTGCAG
Statistics
Matches: 574, Mismatches: 75, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
141 53 0.09
142 116 0.20
143 276 0.48
144 15 0.03
145 109 0.19
146 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (143 bp):
CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTAGCGTTGCA
GTGGAACAGATTAAAGCTACAAATTATAGCGGAACTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
TGAAGCCACCAGC
Found at i:34219563 original size:45 final size:44
Alignment explanation
Indices: 34219455--34219573 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
34219445 TATGGCGGAA
* * * * * *
34219455 CTTATCTTCTTGAAGTTGCAGTGGAGCAAATTGAAGCCACCAGT
1 CTTATCTCCATGAAGTTGCAGTGGAGCAGACTGAAGCAACCAAT
*
34219499 CTTATCTCCATGAAGTTGCAGTGGAGCAGACTGAAGACAACGAAT
1 CTTATCTCCATGAAGTTGCAGTGGAGCAGACTGAAG-CAACCAAT
* * ** *
34219544 CTTATTTCCCTGGCGTTGCAGTGGAACAGA
1 CTTATCTCCATGAAGTTGCAGTGGAGCAGA
34219574 TTAATGCTAC
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
44 32 0.52
45 30 0.48
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTATCTCCATGAAGTTGCAGTGGAGCAGACTGAAGCAACCAAT
Found at i:34227777 original size:19 final size:19
Alignment explanation
Indices: 34227753--34227789 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
34227743 TCCAACAATA
34227753 AAAAATTTGATTACGGTGC
1 AAAAATTTGATTACGGTGC
34227772 AAAAATTTGATTACGGTG
1 AAAAATTTGATTACGGTG
34227790 GGTGACAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (19 bp):
AAAAATTTGATTACGGTGC
Found at i:34230341 original size:35 final size:36
Alignment explanation
Indices: 34230302--34230374 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 36
34230292 TTGAGTAATT
34230302 AAATATTAATTAAATAGGA-TTTAATTGTAAAACAA
1 AAATATTAATTAAATAGGATTTTAATTGTAAAACAA
*
34230337 AAATATTACTTAAATAGGATTTTTAATTGTAAAACAA
1 AAATATTAATTAAATAGGA-TTTTAATTGTAAAACAA
34230374 A
1 A
34230375 GGAAGTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 18 0.51
37 17 0.49
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (36 bp):
AAATATTAATTAAATAGGATTTTAATTGTAAAACAA
Found at i:34233020 original size:14 final size:14
Alignment explanation
Indices: 34233001--34233028 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34232991 ATGACATGAA
34233001 CATAGTCGTTTAAT
1 CATAGTCGTTTAAT
34233015 CATAGTCGTTTAAT
1 CATAGTCGTTTAAT
34233029 GACACACGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
CATAGTCGTTTAAT
Found at i:34235082 original size:6 final size:6
Alignment explanation
Indices: 34235071--34235131 Score: 86
Period size: 6 Copynumber: 10.0 Consensus size: 6
34235061 TAATTTAGCC
*
34235071 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTTG TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA
* *
34235120 ATTTAA TTTTTA
1 TTTTTA TTTTTA
34235132 CATTCTAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
6 43 0.90
7 5 0.10
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:34238451 original size:6 final size:6
Alignment explanation
Indices: 34238425--34238492 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
34238415 AGTGATTTCA
* *
34238425 TTTAGT TTTATGT TTTA-- TTTATT TTTATT TTTACT TTTATT TTTATT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
34238472 GTTATT TATT-TT TTTATT TTT
1 TTTATT T-TTATT TTTATT TTT
34238493 CAAATTTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.08
5 2 0.04
6 39 0.75
7 7 0.13
ACGTcount: A:0.16, C:0.01, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:34240544 original size:29 final size:27
Alignment explanation
Indices: 34240526--34240595 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
34240516 ATATTAAGTC
34240526 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
34240553 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
34240581 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
34240596 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:34240589 original size:28 final size:28
Alignment explanation
Indices: 34240526--34240623 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
34240516 ATATTAAGTC
*
34240526 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
34240553 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
34240581 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
34240610 CGCACACTTAGTGC
1 CGCACACTTAGTGC
34240624 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:34244095 original size:16 final size:16
Alignment explanation
Indices: 34244070--34244110 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
34244060 CCCCAAATTA
* *
34244070 TATTTTTTTTCTTTTT
1 TATTTATTTTCGTTTT
*
34244086 TATTTATTTTGGTTTT
1 TATTTATTTTCGTTTT
34244102 TATTTATTT
1 TATTTATTT
34244111 ATTATTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80
Consensus pattern (16 bp):
TATTTATTTTCGTTTT
Found at i:34245180 original size:4 final size:4
Alignment explanation
Indices: 34245146--34245219 Score: 57
Period size: 4 Copynumber: 18.5 Consensus size: 4
34245136 CCAAATAAGT
* *
34245146 AATA AAT- AATAA AATAA AATA AAGT- AATA AATA AAGTA AAGA AAAA
1 AATA AATA AAT-A AAT-A AATA AA-TA AATA AATA AA-TA AATA AATA
*
34245192 AAT- AATA AAT- AATA AATA AAAA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
34245220 AATAAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
3 10 0.17
4 35 0.60
5 13 0.22
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:34245222 original size:21 final size:22
Alignment explanation
Indices: 34245145--34245228 Score: 100
Period size: 22 Copynumber: 3.7 Consensus size: 22
34245135 TCCAAATAAG
34245145 TAATAAATAATAAAATAAAATAAA
1 TAATAAATAAT-AAATAAAA-AAA
*
34245169 GTAATAAATAAAGTAAAGAAAAAAA
1 -TAATAAAT-AA-TAAATAAAAAAA
34245194 TAATAAATAATAAATAAAAAAA
1 TAATAAATAATAAATAAAAAAA
34245216 TAA-AAATAA-AAAT
1 TAATAAATAATAAAT
34245229 TGGGTTGCCT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.07
21 6 0.11
22 14 0.25
23 2 0.04
24 8 0.15
25 11 0.20
26 9 0.16
27 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (22 bp):
TAATAAATAATAAATAAAAAAA
Found at i:34245226 original size:5 final size:6
Alignment explanation
Indices: 34245146--34245228 Score: 50
Period size: 6 Copynumber: 13.5 Consensus size: 6
34245136 CCAAATAAGT
* *
34245146 AATAAA TAAT-AA AAT-AA AAT-AA AGTAATA AAT-AA AGTAAA GAA-AAA
1 AATAAA -AATAAA AATAAA AATAAA AATAA-A AATAAA AATAAA -AATAAA
34245192 AATAATA AATAATA AATAAAAA AATAAA AATAAA AAT
1 AATAA-A AATAA-A AAT--AAA AATAAA AATAAA AAT
34245229 TGGGTTGCCT
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
5 17 0.27
6 23 0.36
7 18 0.28
8 4 0.06
9 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:34247654 original size:24 final size:24
Alignment explanation
Indices: 34247620--34247666 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
34247610 TCATGCTAAG
34247620 ACAAACAATATGAAGCTCTTTCAA
1 ACAAACAATATGAAGCTCTTTCAA
*
34247644 ACAAACCATATGAAGCTCTTTCA
1 ACAAACAATATGAAGCTCTTTCA
34247667 GATGCTTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (24 bp):
ACAAACAATATGAAGCTCTTTCAA
Found at i:34249183 original size:15 final size:14
Alignment explanation
Indices: 34249162--34249197 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
34249152 ATAATCTTTA
*
34249162 ATAATTATCTTAAT
1 ATAATTATCCTAAT
34249176 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
34249191 ATAATTA
1 ATAATTA
34249198 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:34250733 original size:16 final size:16
Alignment explanation
Indices: 34250712--34250777 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 16
34250702 GTCTCATAAT
34250712 CATTTCTCATATTTTC
1 CATTTCTCATATTTTC
*
34250728 CATTTC-AATATTTTC
1 CATTTCTCATATTTTC
34250743 TCA--TCTCATA--TT-
1 -CATTTCTCATATTTTC
*
34250755 CATTTCTCATCTTTTTC
1 CATTTCTCAT-ATTTTC
34250772 CATTTC
1 CATTTC
34250778 AATATCTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
11 2 0.05
13 8 0.21
14 2 0.05
15 11 0.28
16 10 0.26
17 6 0.15
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.55
Consensus pattern (16 bp):
CATTTCTCATATTTTC
Found at i:34250750 original size:43 final size:44
Alignment explanation
Indices: 34250696--34250782 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 44
34250686 TCATATCTCA
*
34250696 TTTCTCGTCTCATAATCATTTCTCAT-ATTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATCATTTTCCATTTCAATAT
* *
34250739 TTTCTCATCTCATATTCATTTCTCATCTTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATCATTTTCCATTTCAATAT
34250783 CTATCACATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 24 0.60
44 16 0.40
ACGTcount: A:0.22, C:0.24, G:0.01, T:0.53
Consensus pattern (44 bp):
TTTCTCATCTCATAATCATTTCTCATCATTTTCCATTTCAATAT
Found at i:34251949 original size:15 final size:15
Alignment explanation
Indices: 34251929--34251961 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
34251919 TGTTTTCATT
*
34251929 TTATTATCTTTATTA
1 TTATTATCATTATTA
34251944 TTATTATCATTATTA
1 TTATTATCATTATTA
34251959 TTA
1 TTA
34251962 AAGTTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTATCATTATTA
Found at i:34253278 original size:33 final size:33
Alignment explanation
Indices: 34253206--34253268 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
34253196 GGGTCACAAG
34253206 GCCGTGTGGCCAGGCCATTTGGAATCACCCCAA
1 GCCGTGTGGCCAGGCCATTTGGAATCACCCCAA
*
34253239 GCCGTGTGGCCAGGCCGTTTGGAATCACCC
1 GCCGTGTGGCCAGGCCATTTGGAATCACCC
34253269 TAGCCCGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.19
Consensus pattern (33 bp):
GCCGTGTGGCCAGGCCATTTGGAATCACCCCAA
Found at i:34253425 original size:30 final size:30
Alignment explanation
Indices: 34253381--34253453 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
34253371 CTCACAAATG
* *
34253381 ACACAGGCCATGTCACCAGGCTGTGTGTCTC
1 ACAC-GGCCGTGTCACCAGGCTGTATGTCTC
34253412 ACACGGCCGTGTCACCAGGCTGTATGTCTC
1 ACACGGCCGTGTCACCAGGCTGTATGTCTC
*
34253442 ACACGACCGTGT
1 ACACGGCCGTGT
34253454 GACAACCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 35 0.90
31 4 0.10
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.22
Consensus pattern (30 bp):
ACACGGCCGTGTCACCAGGCTGTATGTCTC
Found at i:34260768 original size:12 final size:12
Alignment explanation
Indices: 34260751--34260790 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
34260741 TTAAGCCTAA
34260751 ATTATAATATAG
1 ATTATAATATAG
34260763 ATTATAATATAG
1 ATTATAATATAG
34260775 --T-TAATATAG
1 ATTATAATATAG
34260784 TATTATA
1 -ATTATA
34260791 TGGTATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
9 8 0.33
10 1 0.04
12 13 0.54
13 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (12 bp):
ATTATAATATAG
Found at i:34262620 original size:20 final size:21
Alignment explanation
Indices: 34262595--34262652 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
34262585 AGAAATTTTG
*
34262595 AAATAATATTTTAATTACA-T
1 AAATAATATTTTAATTAAATT
*
34262615 AAATAAAATATTTTTATTAAATT
1 AAAT--AATATTTTAATTAAATT
*
34262638 AAAT-TTATTTTAATT
1 AAATAATATTTTAATT
34262653 GAAAATTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATAATATTTTAATTAAATT
Found at i:34262640 original size:23 final size:22
Alignment explanation
Indices: 34262599--34262641 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
34262589 ATTTTGAAAT
*
34262599 AATATTTTAATTACATAAATAA
1 AATATTTTAATTAAATAAATAA
*
34262621 AATATTTTTATTAAATTAAAT
1 AATATTTTAATTAAA-TAAAT
34262642 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATTTTAATTAAATAAATAA
Found at i:34271121 original size:20 final size:20
Alignment explanation
Indices: 34271096--34271139 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
34271086 TTTTGGGCAA
34271096 ATATTATTACCATAGCCTAG
1 ATATTATTACCATAGCCTAG
34271116 ATATTATTACCATAGCCTAG
1 ATATTATTACCATAGCCTAG
34271136 ATAT
1 ATAT
34271140 CCACATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATTATTACCATAGCCTAG
Found at i:34272513 original size:20 final size:19
Alignment explanation
Indices: 34272484--34272523 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
34272474 AATTTTTTAA
34272484 TTTTAAAATTATTTTGAAT
1 TTTTAAAATTATTTTGAAT
34272503 TTTTGAAAATTATTTTGAAT
1 TTTT-AAAATTATTTTGAAT
34272523 T
1 T
34272524 ATTTTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTTAAAATTATTTTGAAT
Found at i:34280102 original size:20 final size:20
Alignment explanation
Indices: 34280074--34280123 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
34280064 CATTTATCTT
* *
34280074 ATTTTATTTTATTCCAATCA
1 ATTTGATTTAATTCCAATCA
**
34280094 ATTTGATTTAATTTTAATCA
1 ATTTGATTTAATTCCAATCA
*
34280114 AATTGATTTA
1 ATTTGATTTA
34280124 TTGACTCCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (20 bp):
ATTTGATTTAATTCCAATCA
Found at i:34280488 original size:227 final size:224
Alignment explanation
Indices: 34280096--34280551 Score: 691
Period size: 227 Copynumber: 2.0 Consensus size: 224
34280086 TCCAATCAAT
* *
34280096 TTGATTTAATTTTAATCAAATTGATTTATTGACTCCTTTAAAGGTATTTTTTTTGGAAATTTCCA
1 TTGATTTAATTTTAATCAAATTGATTTATTGACTCCATTAAAGGTATTTTTTTTGGAAATTTCAA
* *
34280161 AAATTTCACCATGCTAAATGGCTATAAAAGGCTATGAATTCTAAAGAATTTTTCTACACTCATAC
66 AAATTTCACCATACTAAATGCCTATAAAAGGCTATGAATTCTAAAGAATTTTTCTACACTCATAC
*
34280226 TCTTTCACACCAAATTTATTTTCCTCTCAAAATTAT-TCTTTTCCTTTCTATATTTTTCAACGTT
131 TCTTTCACACCAAATTTATTTTACTCTCAAAATTATAT-TTTTCCTTTCTATATTTTTCAACGTT
* * * * *
34280290 TTGGTAATAGAAAAAGGAAATGTTTGTTCG
195 CTAGTAATAGAAAAAAGAAATGTGTGCTCG
*
34280320 TTGATTTAATTTTAATCAAATTGATTTATTGGCTCCATTAAAGGTAATTTTTTTTGGAAATTTCA
1 TTGATTTAATTTTAATCAAATTGATTTATTGACTCCATTAAAGGT-ATTTTTTTTGGAAATTTCA
* * *
34280385 AAAATTTCACCATACTGAATGCCTATAAAAGGCTATATGAATTTTGAAGAATTTTTCTACACTCA
65 AAAATTTCACCATACTAAATGCCTATAAAAGGC--TATGAATTCTAAAGAATTTTTCTACACTCA
* ***
34280450 TACT-TTCTCACACCGAATTTATTTTACTCTCAAAATTATATTTTTCCTTTCTATATTTTTTGGC
128 TACTCTT-TCACACCAAATTTATTTTACTCTCAAAATTATATTTTTCCTTTCTATATTTTTCAAC
34280514 GTTCTAGTAATAGAAAAAAGAAATGTGTGCTCG
192 GTTCTAGTAATAGAAAAAAGAAATGTGTGCTCG
34280547 TTGAT
1 TTGAT
34280552 CGCTATAGAG
Statistics
Matches: 209, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
224 43 0.21
225 48 0.23
226 2 0.01
227 115 0.55
228 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (224 bp):
TTGATTTAATTTTAATCAAATTGATTTATTGACTCCATTAAAGGTATTTTTTTTGGAAATTTCAA
AAATTTCACCATACTAAATGCCTATAAAAGGCTATGAATTCTAAAGAATTTTTCTACACTCATAC
TCTTTCACACCAAATTTATTTTACTCTCAAAATTATATTTTTCCTTTCTATATTTTTCAACGTTC
TAGTAATAGAAAAAAGAAATGTGTGCTCG
Found at i:34283467 original size:22 final size:20
Alignment explanation
Indices: 34283437--34283477 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
34283427 TAGCAGTTGT
34283437 AAATCAAAAGAATAAAAACCCC
1 AAATC-AAA-AATAAAAACCCC
*
34283459 AAATTAAAAATAAAAACCC
1 AAATCAAAAATAAAAACCC
34283478 AAAGAGGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 3 0.17
22 4 0.22
ACGTcount: A:0.66, C:0.20, G:0.02, T:0.12
Consensus pattern (20 bp):
AAATCAAAAATAAAAACCCC
Found at i:34288959 original size:21 final size:21
Alignment explanation
Indices: 34288934--34288977 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
34288924 ATCAATGACA
*
34288934 TTCCATATCAATGACAACTCT
1 TTCCACATCAATGACAACTCT
34288955 TTCCACATCAATGACAACTCT
1 TTCCACATCAATGACAACTCT
34288976 TT
1 TT
34288978 ATCATCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.34
Consensus pattern (21 bp):
TTCCACATCAATGACAACTCT
Found at i:34288985 original size:20 final size:20
Alignment explanation
Indices: 34288940--34288986 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
34288930 GACATTCCAT
34288940 ATCAATGACAACTCTTTCCAC
1 ATCAATGACAACTCTTT-CAC
34288961 ATCAATGACAACTCTTT-ATC
1 ATCAATGACAACTCTTTCA-C
34288981 ATCAAT
1 ATCAAT
34288987 CAACTACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 7 0.28
21 17 0.68
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (20 bp):
ATCAATGACAACTCTTTCAC
Found at i:34296250 original size:41 final size:41
Alignment explanation
Indices: 34296187--34296290 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
34296177 GTTAATTATT
* * * *
34296187 CCCTGAATTGCACATATGTGCCCCTGTTTGTACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTGATTATACTTCGGTAC
* * *
34296228 CCTTAAATTGCACATACATGCCCCTGATTATACTTTGGTAC
1 CCCTAAATTGCACATACGTGCCCCTGATTATACTTCGGTAC
*
34296269 CCCTGAATTGCACATACGTGCC
1 CCCTAAATTGCACATACGTGCC
34296291 ATGTTTACAC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (41 bp):
CCCTAAATTGCACATACGTGCCCCTGATTATACTTCGGTAC
Found at i:34300315 original size:7 final size:7
Alignment explanation
Indices: 34300303--34300336 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
34300293 TTCGAACTTA
34300303 ATCAAAT
1 ATCAAAT
34300310 ATCAAAT
1 ATCAAAT
34300317 ATCAAAT
1 ATCAAAT
34300324 ATCAAAT
1 ATCAAAT
34300331 ATCAAA
1 ATCAAA
34300337 GAACTACTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (7 bp):
ATCAAAT
Found at i:34303061 original size:21 final size:22
Alignment explanation
Indices: 34303008--34303070 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
34302998 AATAAAAATT
* *
34303008 TTAAATATTTCTAAATAATTAATG
1 TTAAATATTTATAAA-ATTTAA-G
*
34303032 TTAATTATTTATAAAATTTAA-
1 TTAAATATTTATAAAATTTAAG
* *
34303053 TTAAATATTAATACAATT
1 TTAAATATTTATAAAATT
34303071 GTATTATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.45
23 5 0.15
24 13 0.39
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAATATTTATAAAATTTAAG
Found at i:34309607 original size:57 final size:57
Alignment explanation
Indices: 34309525--34309662 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 57
34309515 TTTTTATAGT
** * * *
34309525 ATTATATATTATGATTTTCGTAAATTCATA-TAAAAATAGTTATATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTTATTAAATT-ATATTAAAAATAATTATATTAA-AATATGATTAA
* *
34309585 ATTATATATTA-TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
1 ATTATATATTATTTTTATTAAATTATA-TTAAAAATAATTATATTAAAATATGATTAA
*
34309642 ATTATTTATTATTTTTATTAA
1 ATTATATATTATTTTTATTAA
34309663 TAATCTTATT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
56 3 0.04
57 29 0.43
58 24 0.36
60 11 0.16
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (57 bp):
ATTATATATTATTTTTATTAAATTATATTAAAAATAATTATATTAAAATATGATTAA
Found at i:34310394 original size:15 final size:15
Alignment explanation
Indices: 34310374--34310428 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
34310364 AAAATTAAAA
34310374 ATTTATATTTATATT
1 ATTTATATTTATATT
34310389 ATTTATAATTTA-A-T
1 ATTTAT-ATTTATATT
*
34310403 ATTTAATAATTATATT
1 ATTT-ATATTTATATT
34310419 -TTT-TATTTAT
1 ATTTATATTTAT
34310429 TAAAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
13 6 0.18
14 9 0.26
15 13 0.38
16 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATATTTATATT
Found at i:34311449 original size:7 final size:7
Alignment explanation
Indices: 34311437--34311485 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
34311427 TAAATATATT
34311437 TTTTTTA
1 TTTTTTA
34311444 TTTTTTA
1 TTTTTTA
*
34311451 TTTTTAAAA
1 TTTTT--TA
34311460 TATTTTTA
1 T-TTTTTA
34311468 -TTTTTA
1 TTTTTTA
34311474 TTTTTTA
1 TTTTTTA
34311481 TTTTT
1 TTTTT
34311486 AAAATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 6 0.17
7 23 0.64
8 1 0.03
9 2 0.06
10 4 0.11
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTA
Found at i:34311474 original size:30 final size:29
Alignment explanation
Indices: 34311428--34311498 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 29
34311418 CAAATATAAT
*
34311428 AAATATATTTTTTTTATTTTTTATTTTTA
1 AAATATTTTTTTTTTATTTTTTATTTTTA
34311457 AAATATTTTTATTTTTATTTTTTATTTTTA
1 AAATATTTTT-TTTTTATTTTTTATTTTTA
*
34311487 AAATAATTTTTT
1 AAATATTTTTTT
34311499 AATGTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 11 0.28
30 28 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (29 bp):
AAATATTTTTTTTTTATTTTTTATTTTTA
Found at i:34311495 original size:19 final size:18
Alignment explanation
Indices: 34311442--34311499 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 18
34311432 ATATTTTTTT
34311442 TATTTTTTATTTTTAAAA
1 TATTTTTTATTTTTAAAA
34311460 TA-TTTTTA-TTTT----
1 TATTTTTTATTTTTAAAA
34311472 TATTTTTTATTTTTAAAA
1 TATTTTTTATTTTTAAAA
34311490 TAATTTTTTA
1 T-ATTTTTTA
34311500 ATGTTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
12 2 0.06
13 6 0.18
14 4 0.12
16 4 0.12
17 6 0.18
18 3 0.09
19 8 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTTTTATTTTTAAAA
Found at i:34312369 original size:25 final size:23
Alignment explanation
Indices: 34312341--34312388 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
34312331 ACACACACAT
34312341 AAATTTTAAAAATGAAAAATAGAGG
1 AAATTTTAAAAAT-AAAAA-AGAGG
* *
34312366 AAATTTTCAAACTAAAAAAGAGG
1 AAATTTTAAAAATAAAAAAGAGG
34312389 GCTCAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 5 0.24
25 11 0.52
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.23
Consensus pattern (23 bp):
AAATTTTAAAAATAAAAAAGAGG
Found at i:34312816 original size:132 final size:132
Alignment explanation
Indices: 34312579--34312828 Score: 387
Period size: 132 Copynumber: 1.9 Consensus size: 132
34312569 AGAAAAATAG
* * * *
34312579 ATAGAAGAGATGAACAAGAGAAGGCGGCGTCTATCGGTTGAGAGAGCCAGATATTTAAAGGGGAA
1 ATAGAAGAGATGAACAAGAGAAGGCGGCGACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAAA
*
34312644 GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATTATGACAAATTTAACCTTTTACCTCTTCTAT
66 GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATAATGACAAATTTAACCTTTTACCTCTTCTAT
34312709 CA
131 CA
* *
34312711 ATAGAAGAGATGAACAGGAGAAGGCGGCGGAC-AACGGTTAAGATAGCCAGATATTTAAAGGGAA
1 ATAGAAGAGATGAACAAGAGAAGGCGGC-GACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAA
* *
34312775 AGAAATGAGAAGGTATAGGGTTTAA-TATTAGGTGTAATGACAATTTTAACCTTT
65 AGAAATGAGAAGGTATAGGGTTTAAGT-TTAGGTATAATGACAAATTTAACCTTT
34312829 AATTTTTACA
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
131 1 0.01
132 104 0.97
133 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.26
Consensus pattern (132 bp):
ATAGAAGAGATGAACAAGAGAAGGCGGCGACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAAA
GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATAATGACAAATTTAACCTTTTACCTCTTCTAT
CA
Found at i:34313158 original size:13 final size:13
Alignment explanation
Indices: 34313126--34313157 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
34313116 CACTAACATC
34313126 GTTAAAATTTTTA
1 GTTAAAATTTTTA
34313139 GTTAAAATTTTTA
1 GTTAAAATTTTTA
34313152 -TTAAAA
1 GTTAAAA
34313158 ACTAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
GTTAAAATTTTTA
Found at i:34317193 original size:19 final size:19
Alignment explanation
Indices: 34317152--34317201 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
34317142 ATTGATGTTT
* * *
34317152 TTTTATTGCTTTCTTGTTT
1 TTTTATTGTTTTCTTGCTA
*
34317171 TTTTATTGTTTTGTTGCTA
1 TTTTATTGTTTTCTTGCTA
*
34317190 TTTTCTTGTTTT
1 TTTTATTGTTTT
34317202 TTTTCACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.06, C:0.08, G:0.12, T:0.74
Consensus pattern (19 bp):
TTTTATTGTTTTCTTGCTA
Found at i:34317215 original size:32 final size:31
Alignment explanation
Indices: 34317161--34317231 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
34317151 TTTTTATTGC
* * *
34317161 TTTCTTG-TTTTTTTATTGTTTTGTTGCTAT
1 TTTCTTGTTTTTTTTACTATTTTGTTACTAT
34317191 TTTCTTGTTTTTTTTCACTATTTTGTTACTAT
1 TTTCTTGTTTTTTTT-ACTATTTTGTTACTAT
*
34317223 TTTGTTGTT
1 TTTCTTGTT
34317232 ATTGTTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 7 0.20
31 7 0.20
32 21 0.60
ACGTcount: A:0.08, C:0.08, G:0.11, T:0.72
Consensus pattern (31 bp):
TTTCTTGTTTTTTTTACTATTTTGTTACTAT
Found at i:34318230 original size:19 final size:17
Alignment explanation
Indices: 34318206--34318249 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
34318196 AAAAAATTTA
34318206 AAATATATTTGTCTTTTT
1 AAATATATTT-TCTTTTT
*
34318224 AATATATACTTTCTTTTT
1 AA-ATATATTTTCTTTTT
34318242 AAATATAT
1 AAATATAT
34318250 AATAAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
19 7 0.30
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (17 bp):
AAATATATTTTCTTTTT
Found at i:34318250 original size:19 final size:20
Alignment explanation
Indices: 34318202--34318250 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
34318192 TTCCAAAAAA
*
34318202 TTTAAA-ATATATTTGTCTT
1 TTTAAATATATACTTGTCTT
34318221 TTT-AATATATACTT-TCTT
1 TTTAAATATATACTTGTCTT
34318239 TTTAAATATATA
1 TTTAAATATATA
34318251 ATAAAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTAAATATATACTTGTCTT
Found at i:34318532 original size:29 final size:29
Alignment explanation
Indices: 34318499--34318562 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
34318489 GGCTAAATTG
* *
34318499 AAAGATTGAAGATTTGGAGTTGGCTAGAT
1 AAAGATTGAAGATTTGAAATTGGCTAGAT
* *
34318528 AAAGATTGAAGATTTGAAATTGGTTGGAT
1 AAAGATTGAAGATTTGAAATTGGCTAGAT
34318557 AAAGAT
1 AAAGAT
34318563 CAAATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.28, T:0.31
Consensus pattern (29 bp):
AAAGATTGAAGATTTGAAATTGGCTAGAT
Found at i:34318623 original size:18 final size:18
Alignment explanation
Indices: 34318600--34318634 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34318590 ATGTAATTAC
34318600 TTTAAAGTTGATCTTTAG
1 TTTAAAGTTGATCTTTAG
* *
34318618 TTTAAATTTGATTTTTA
1 TTTAAAGTTGATCTTTA
34318635 AAATTTTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTAAAGTTGATCTTTAG
Found at i:34323341 original size:20 final size:20
Alignment explanation
Indices: 34323316--34323362 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
34323306 TTGAATTCGT
34323316 AAAAAACAACAAAAAAGTA-A
1 AAAAAACAACAAAAAA-TATA
* *
34323336 AAAAAATAATAAAAAATATA
1 AAAAAACAACAAAAAATATA
34323356 AAAAAAC
1 AAAAAAC
34323363 GTCAAGTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAAACAACAAAAAATATA
Found at i:34323941 original size:29 final size:29
Alignment explanation
Indices: 34323869--34323929 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
34323859 AAAAAAGAGT
* *
34323869 GCTAGATTGAAAGATTGAAGATTTGAAGTTG
1 GCTAGA-T-AAAGATTGAAGATTTGAAATTA
34323900 GCTAGATAAAGATTGAAGATTTGAAATTA
1 GCTAGATAAAGATTGAAGATTTGAAATTA
34323929 G
1 G
34323930 TTGGGTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.75
30 1 0.04
31 6 0.21
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.31
Consensus pattern (29 bp):
GCTAGATAAAGATTGAAGATTTGAAATTA
Found at i:34323996 original size:18 final size:18
Alignment explanation
Indices: 34323975--34324013 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
34323965 AATTCTATAA
34323975 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
34323993 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
34324011 TTA
1 TTA
34324014 AAATTTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (18 bp):
TTAGTTTAAATTTGATCT
Found at i:34330022 original size:18 final size:17
Alignment explanation
Indices: 34329989--34330027 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
34329979 TTTTATAAAT
34329989 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
34330007 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
34330024 TGTG
1 TGTG
34330028 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:34330280 original size:23 final size:23
Alignment explanation
Indices: 34330253--34330374 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
34330243 AGTGTTATTG
34330253 ATCAGTGGTAGCTTCGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
* *
34330275 ATTCAGTGGTAGCTACGGCTCCAT
1 A-TCAGTGGTAGCTTCGGCTACAT
34330299 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
34330322 TTCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
34330345 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
34330368 ATCAGTG
1 ATCAGTG
34330375 TGGCACTTAT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.01
23 84 0.98
24 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:34330306 original size:46 final size:46
Alignment explanation
Indices: 34330253--34330374 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
34330243 AGTGTTATTG
* *
34330253 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTCCAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
* *
34330299 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
34330345 ATCAGTGGTAGCTTCGGCTAC-ATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACAAT-TCAGTG
34330375 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.01
46 69 0.99
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
Found at i:34340094 original size:8 final size:8
Alignment explanation
Indices: 34340081--34340106 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
34340071 CACTAGAGAC
34340081 CAGTGTTA
1 CAGTGTTA
34340089 CAGTGTTA
1 CAGTGTTA
34340097 CAGTGTTA
1 CAGTGTTA
34340105 CA
1 CA
34340107 ATGAGTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (8 bp):
CAGTGTTA
Found at i:34340313 original size:23 final size:23
Alignment explanation
Indices: 34340196--34340317 Score: 122
Period size: 23 Copynumber: 5.3 Consensus size: 23
34340186 AGTGTTATTG
*
34340196 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* * * *
34340219 TTTAATGGTAGCTATGA-CTACAT
1 ATCAGTGGTAGCT-TCAGCTACAT
* *
34340242 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* * *
34340265 TTCAGTGGTAGCTATGA-CTACGT
1 ATCAGTGGTAGCT-TCAGCTACAT
34340288 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
34340311 ATCAGTG
1 ATCAGTG
34340318 TGGCACTTAT
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
22 3 0.04
23 73 0.94
24 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCAGCTACAT
Found at i:34340316 original size:46 final size:46
Alignment explanation
Indices: 34340196--34340317 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
34340186 AGTGTTATTG
* *
34340196 ATCAGTGGTAGCTTCGGCTACATTTTAATGGTAGCTATGACTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGACTACAT
* *
34340242 ATCAATGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGACTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGACTACAT
* *
34340288 ATCAGTGGTAGCTTCAGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
34340318 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGACTACAT
Found at i:34350109 original size:29 final size:30
Alignment explanation
Indices: 34350067--34350125 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
34350057 TATGGTTTAA
*
34350067 TGTGTAATAGTATACAT-GAATTTTGATTT
1 TGTGTAATAGTATACATAAAATTTTGATTT
** *
34350096 TGTGTAATTTTATATATAAAATTTTGATTT
1 TGTGTAATAGTATACATAAAATTTTGATTT
34350126 GAATTCTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGTAATAGTATACATAAAATTTTGATTT
Found at i:34357074 original size:23 final size:22
Alignment explanation
Indices: 34357029--34357076 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
34357019 CAAGTATTAC
*
34357029 TAAAATGTTAGAATGATAAATA
1 TAAAATGTTAAAATGATAAATA
* *
34357051 TAAAATTTTAAAATTGATACATA
1 TAAAATGTTAAAA-TGATAAATA
34357074 TAA
1 TAA
34357077 TGTAACCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
TAAAATGTTAAAATGATAAATA
Found at i:34361663 original size:69 final size:69
Alignment explanation
Indices: 34361552--34361691 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
34361542 GGAGAAGGGC
* * *
34361552 TAATAGGGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGGGTCTCTCATTGTATTGGGCA
1 TAATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGGGCCTCTCATTGTATTGAGCA
34361617 CAAT
66 CAAT
* * *
34361621 TAATAGAGTGTGTTTCCCCTTATATGTATTATGATCG-GGATTCGGGCCTTTCATTGTATTGAGC
1 TAATAGAGTGTGATTCCCCTCATATGTATTATGAT-GAGGATTCGGGCCTCTCATTGTATTGAGC
34361685 ACAAT
65 ACAAT
34361690 TA
1 TA
34361692 TATGTGTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 63 0.98
70 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (69 bp):
TAATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGGGCCTCTCATTGTATTGAGCA
CAAT
Found at i:34366448 original size:93 final size:93
Alignment explanation
Indices: 34366289--34366473 Score: 352
Period size: 93 Copynumber: 2.0 Consensus size: 93
34366279 TTTTGGTTTC
*
34366289 AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACTAAAATGATACTTTTT
1 AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTT
34366354 TTATGAATAATAAAGATATGGATTTTAT
66 TTATGAATAATAAAGATATGGATTTTAT
34366382 AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTT
1 AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTT
*
34366447 TTATGAATAATAATGATATGGATTTTA
66 TTATGAATAATAAAGATATGGATTTTA
34366474 CTTTAACTAC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.38
Consensus pattern (93 bp):
AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTT
TTATGAATAATAAAGATATGGATTTTAT
Found at i:34366495 original size:93 final size:92
Alignment explanation
Indices: 34366305--34366502 Score: 267
Period size: 93 Copynumber: 2.1 Consensus size: 92
34366295 TGGTTGAGTG
*
34366305 ATTAAAATTAAATTAAATTAAAAATTTGGGAACTAAAATGATACTTTTTTTATGAATAATAAAGA
1 ATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTTTTATGAATAATAAAGA
** * **
34366370 TATGGATTTTATAGGTGATGGTTGAGTG
66 TATGGATTTTATAACTCATGG-TGAGAA
*
34366398 ATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTTTTATGAATAATAATGA
1 ATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTTTTATGAATAATAAAGA
34366463 TATGGATTTTACTTTAACTACAT-G-GA-AA
66 TATGGATTTTA---TAACT-CATGGTGAGAA
34366491 ATTAAAATTAAA
1 ATTAAAATTAAA
34366503 ATTTAAAAGA
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
93 86 0.91
94 2 0.02
96 4 0.04
97 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (92 bp):
ATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTTTTATGAATAATAAAGA
TATGGATTTTATAACTCATGGTGAGAA
Found at i:34368517 original size:15 final size:15
Alignment explanation
Indices: 34368497--34368527 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34368487 ATGATGTACT
*
34368497 ATCTATGTAAAAATC
1 ATCTATGCAAAAATC
34368512 ATCTATGCAAAAATC
1 ATCTATGCAAAAATC
34368527 A
1 A
34368528 AATGAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (15 bp):
ATCTATGCAAAAATC
Found at i:34374869 original size:21 final size:22
Alignment explanation
Indices: 34374844--34374887 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
34374834 CAAATATAAG
*
34374844 TATTGTAT-TAACCAAATCATT
1 TATTGAATATAACCAAATCATT
34374865 TATTGAATATAACCAAATCATT
1 TATTGAATATAACCAAATCATT
34374887 T
1 T
34374888 TCATATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTGAATATAACCAAATCATT
Found at i:34375494 original size:13 final size:13
Alignment explanation
Indices: 34375476--34375500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34375466 ATACTCAAAT
34375476 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
34375489 TTCTCAAAAGCA
1 TTCTCAAAAGCA
34375501 ATAAAGAACT
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:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:34377300 original size:3 final size:3
Alignment explanation
Indices: 34377292--34377321 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34377282 CTGAAGTTGG
34377292 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
34377322 ATCATTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:34386876 original size:26 final size:26
Alignment explanation
Indices: 34386840--34386891 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
34386830 AAGCCCATGT
34386840 ATGCAAATCAGACAGAGTGTGAAGAA
1 ATGCAAATCAGACAGAGTGTGAAGAA
*
34386866 ATGCAAATCAGATAGAGTGTGAAGAA
1 ATGCAAATCAGACAGAGTGTGAAGAA
34386892 CTTGATGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.27, T:0.17
Consensus pattern (26 bp):
ATGCAAATCAGACAGAGTGTGAAGAA
Found at i:34392102 original size:18 final size:18
Alignment explanation
Indices: 34392067--34392100 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34392057 TAAAATACTA
34392067 TAAATATAAGTATTAAAT
1 TAAATATAAGTATTAAAT
*
34392085 TAAATTTAA-TATTAAA
1 TAAATATAAGTATTAAA
34392101 ATATTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAATATAAGTATTAAAT
Found at i:34394181 original size:38 final size:38
Alignment explanation
Indices: 34394080--34394190 Score: 116
Period size: 38 Copynumber: 2.9 Consensus size: 38
34394070 GTAATAGAAA
* * * *
34394080 AATTCAACACTACCAGTAAACATGCTTAACATGTATTC
1 AATTCAACATTAGCAATCAACATGCTTAACATGTATTC
*
34394118 AATTCAACATTGGCAATCAACATGCTTAACATGTATTC
1 AATTCAACATTAGCAATCAACATGCTTAACATGTATTC
* * * * *
34394156 ACTTTAACATTAGTAAT-AGATATGCTTAACGTGTA
1 AATTCAACATTAGCAATCA-ACATGCTTAACATGTA
34394191 CTTCGAAAGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 1 0.02
38 60 0.98
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (38 bp):
AATTCAACATTAGCAATCAACATGCTTAACATGTATTC
Found at i:34394619 original size:21 final size:21
Alignment explanation
Indices: 34394594--34394635 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
34394584 CATGGTGCAC
34394594 AAAAATAAATAAAAAA-AGAAA
1 AAAAATAAA-AAAAAAGAGAAA
34394615 AAAAATAAAAAAAAAGAGAAA
1 AAAAATAAAAAAAAAGAGAAA
34394636 GAAGAGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAATAAAAAAAAAGAGAAA
Found at i:34394620 original size:17 final size:18
Alignment explanation
Indices: 34394594--34394627 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
34394584 CATGGTGCAC
34394594 AAAAATAAATAAAAAAAG
1 AAAAATAAATAAAAAAAG
34394612 AAAAA-AAATAAAAAAA
1 AAAAATAAATAAAAAAA
34394628 AAGAGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (18 bp):
AAAAATAAATAAAAAAAG
Found at i:34395077 original size:21 final size:21
Alignment explanation
Indices: 34395055--34395104 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
34395045 AAATAGCTTA
*
34395055 TATATTAATTAAA-A-TTTAC
1 TATATTTATTAAATATTTTAC
34395074 TATATTTATTAAATATTTTAC
1 TATATTTATTAAATATTTTAC
34395095 TAT-TTTATTA
1 TATATTTATTA
34395105 GAGTAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.43
20 8 0.29
21 8 0.29
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTTATTAAATATTTTAC
Found at i:34395385 original size:16 final size:16
Alignment explanation
Indices: 34395364--34395398 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34395354 ATTACTGATG
*
34395364 ACAACTCGATTCTATT
1 ACAACTCGATTATATT
*
34395380 ACAACTCTATTATATT
1 ACAACTCGATTATATT
34395396 ACA
1 ACA
34395399 GCCCTACTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (16 bp):
ACAACTCGATTATATT
Found at i:34397477 original size:9 final size:9
Alignment explanation
Indices: 34397460--34397496 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
34397450 TTCGAGTTCG
34397460 AATTCGAAT
1 AATTCGAAT
*
34397469 AACTCGAAT
1 AATTCGAAT
34397478 AATTCGAAT
1 AATTCGAAT
34397487 AATTCGAAT
1 AATTCGAAT
34397496 A
1 A
34397497 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34398531 original size:5 final size:5
Alignment explanation
Indices: 34398521--34398546 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34398511 CTCGAAAATT
34398521 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
34398547 CGAATGCTCA
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:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:34400273 original size:7 final size:7
Alignment explanation
Indices: 34400261--34400285 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34400251 CTTCTTTTTC
34400261 TTTTCTT
1 TTTTCTT
34400268 TTTTCTT
1 TTTTCTT
34400275 TTTTCTT
1 TTTTCTT
34400282 TTTT
1 TTTT
34400286 AATCTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:34405989 original size:50 final size:51
Alignment explanation
Indices: 34405863--34406109 Score: 223
Period size: 50 Copynumber: 4.8 Consensus size: 51
34405853 GATAATAACA
* * * * ** * * *
34405863 TGCCAAAGCCATGTCCTAGACGTGGTCTTACATGAGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCCGG
* * * * **
34405912 TGCCAATTCCATATCCCATATATGGTCTTACATGGGAGTTCTCATAT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCCGG
* ** *
34405962 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCCGG
* *
34406012 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCCCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-AT-CC---GG
*
34406068 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34406110 TTACCCAAAT
Statistics
Matches: 160, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 35 0.22
50 81 0.51
51 1 0.01
53 1 0.01
56 41 0.26
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCCGG
Found at i:34411751 original size:53 final size:53
Alignment explanation
Indices: 34411674--34411778 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
34411664 CAATTTGTTA
*
34411674 TTTCCAAATTCAACTTGTTATAAGTTAAAATAAACCTGAAATCACTTATATAT
1 TTTCCAAATTCAACTTATTATAAGTTAAAATAAACCTGAAATCACTTATATAT
*
34411727 TTTCCAAATTCAACTTATTATAAGTTAAAATAGACCTGAAATCACTTATATA
1 TTTCCAAATTCAACTTATTATAAGTTAAAATAAACCTGAAATCACTTATATA
34411779 CATTCTTATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (53 bp):
TTTCCAAATTCAACTTATTATAAGTTAAAATAAACCTGAAATCACTTATATAT
Found at i:34411803 original size:53 final size:53
Alignment explanation
Indices: 34411691--34411803 Score: 138
Period size: 53 Copynumber: 2.1 Consensus size: 53
34411681 ATTCAACTTG
** * **
34411691 TTATAAGTTAAAATAAACCTGAAATCACTTATATATTTTCCAAATTCAACTTA
1 TTATAAGTTAAAATAAACCTGAAATCACTTATATACATTCCAAATGCAACCAA
* **
34411744 TTATAAGTTAAAATAGACCTGAAATCACTTATATACATT-CTTATGCAACCAA
1 TTATAAGTTAAAATAAACCTGAAATCACTTATATACATTCCAAATGCAACCAA
34411796 TTCATAAG
1 TT-ATAAG
34411804 CTTACCAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 10 0.20
53 41 0.80
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (53 bp):
TTATAAGTTAAAATAAACCTGAAATCACTTATATACATTCCAAATGCAACCAA
Found at i:34413763 original size:30 final size:30
Alignment explanation
Indices: 34413707--34413763 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
34413697 TACGAGCCTA
* *
34413707 GGGGCAAAATCGTAATTTTGTGAAACTTTT
1 GGGGCAAAAACGTAATTTTGTCAAACTTTT
34413737 GGGGCAAAAACGTAATTTT-TCCAAACT
1 GGGGCAAAAACGTAATTTTGT-CAAACT
34413764 ATGATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (30 bp):
GGGGCAAAAACGTAATTTTGTCAAACTTTT
Found at i:34414124 original size:51 final size:51
Alignment explanation
Indices: 34413990--34414174 Score: 216
Period size: 51 Copynumber: 3.6 Consensus size: 51
34413980 AGTGAAAGTG
* * *
34413990 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACT-GA-AATG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
* * * *
34414039 ATAGGTCGCATGTATAGTACTATGTGCAGGCTACTATGCGTACTGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
* * * *
34414090 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-TCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACT-GGATAGTA
34414142 ATGGTCACATGTGTAGTACTATGTGCAGGCTAC
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTAC
34414175 CACCGGACAT
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.02
50 37 0.33
51 71 0.63
52 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
Found at i:34420509 original size:51 final size:51
Alignment explanation
Indices: 34420421--34420539 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
34420411 ATAGAAATGG
* *
34420421 TGAAAATAGAG-AATGAGAAATCATTTGAAAATTATTATGGTTTTCTCCAAAA
1 TGAAAATAGAGAAATG-G-AATCATTTGAAAATGATTATGGTTTTCTACAAAA
*
34420473 TGAAAATAGAGAAATGGAATCATTTGGAAATGATTATGGTTTTCTACAAAA
1 TGAAAATAGAGAAATGGAATCATTTGAAAATGATTATGGTTTTCTACAAAA
*
34420524 TCAAAATA-A-AAATGGA
1 TGAAAATAGAGAAATGGA
34420540 TAAATGGAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
49 7 0.11
50 1 0.02
51 38 0.61
52 12 0.19
53 4 0.06
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (51 bp):
TGAAAATAGAGAAATGGAATCATTTGAAAATGATTATGGTTTTCTACAAAA
Found at i:34420580 original size:51 final size:51
Alignment explanation
Indices: 34420423--34420580 Score: 147
Period size: 57 Copynumber: 3.0 Consensus size: 51
34420413 AGAAATGGTG
* * *
34420423 AAAATAGAG-AATGAGAAATCATTTGAAAATTATTATGGTTTTCTCCAAAATG
1 AAAATAGAGAAATG-G-AATCATTTGAAAATAATTATGGTTTTCACCAAAATA
* *
34420475 AAAATAGAGAAATGGAATCATTTGGAAATGATTATGGTTTTCTACAAAATCAAAATA
1 AAAATAGAGAAATGGAATCATTTGAAAATAATTATGGTTTTC-AC-----CAAAATA
* * * * *
34420532 AAAATGGATAAATGGAGTCATTTGAAAATAAATGTGGTTTTCACCAAAA
1 AAAATAGAGAAATGGAATCATTTGAAAATAATTATGGTTTTCACCAAAA
34420581 AATGAAAATG
Statistics
Matches: 88, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
51 30 0.34
52 11 0.12
53 4 0.05
56 2 0.02
57 41 0.47
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (51 bp):
AAAATAGAGAAATGGAATCATTTGAAAATAATTATGGTTTTCACCAAAATA
Found at i:34420604 original size:59 final size:59
Alignment explanation
Indices: 34420468--34420638 Score: 188
Period size: 59 Copynumber: 2.9 Consensus size: 59
34420458 TGGTTTTCTC
* * *
34420468 CAAAATGAAAATAGAGAAATGGAATCATTTGGAAATGATTATGGTTTTCTA-C--AAAAT
1 CAAAATGAAAATAGTGAAATGGAATCATTTGGAAATGAATGTGGTTTTC-ACCAAAAAAT
* * * * *
34420525 CAAAATAAAAATGGAT-AAATGGAGTCATTTGAAAATAAATGTGGTTTTCACCAAAAAAT
1 CAAAATGAAAATAG-TGAAATGGAATCATTTGGAAATGAATGTGGTTTTCACCAAAAAAT
* * * *
34420584 GAAAATGAAAATAGTGAAATGGAATCAATTGGAAATGAATGTGATTTTCTCCAAA
1 CAAAATGAAAATAGTGAAATGGAATCATTTGGAAATGAATGTGGTTTTCACCAAA
34420639 TTGATAATGA
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
56 1 0.01
57 41 0.45
58 1 0.01
59 49 0.53
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.28
Consensus pattern (59 bp):
CAAAATGAAAATAGTGAAATGGAATCATTTGGAAATGAATGTGGTTTTCACCAAAAAAT
Found at i:34422365 original size:183 final size:183
Alignment explanation
Indices: 34422057--34422427 Score: 724
Period size: 183 Copynumber: 2.0 Consensus size: 183
34422047 AAAATGGTCA
34422057 AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCCATGGTGACAAAATTGAAGAT
1 AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCCATGGTGACAAAATTGAAGAT
34422122 CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
66 CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
34422187 GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
131 GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
**
34422240 AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCGGTGGTGACAAAATTGAAGAT
1 AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCCATGGTGACAAAATTGAAGAT
34422305 CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
66 CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
34422370 GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
131 GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
34422423 AAAAA
1 AAAAA
34422428 TGGTGATATT
Statistics
Matches: 186, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 186 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (183 bp):
AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCCATGGTGACAAAATTGAAGAT
CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
Found at i:34431386 original size:105 final size:105
Alignment explanation
Indices: 34431250--34431456 Score: 387
Period size: 105 Copynumber: 2.0 Consensus size: 105
34431240 GATGTCATCT
*
34431250 GTTTAGGCTCCTCAGCAATAGTTTCCTCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
1 GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
34431315 CTGGCAGTAGGAGTTTGAGCTGGCTCCTCTGCAGCTTTAG
66 CTGGCAGTAGGAGTTTGAGCTGGCTCCTCTGCAGCTTTAG
*
34431355 GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCGAAATTCACTGATTCGACT
1 GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
*
34431420 CTGGCAGTATGAGTTTGAGCTGGCTCCTCTGCAGCTT
66 CTGGCAGTAGGAGTTTGAGCTGGCTCCTCTGCAGCTT
34431457 CAGGAATTGG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 99 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (105 bp):
GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
CTGGCAGTAGGAGTTTGAGCTGGCTCCTCTGCAGCTTTAG
Found at i:34438853 original size:29 final size:28
Alignment explanation
Indices: 34438785--34438853 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
34438775 CATAAAAGTG
34438785 AGCCTTTTGGCTATCTCTATTAAAAAGA
1 AGCCTTTTGGCTATCTCTATTAAAAAGA
* **
34438813 AGCCCTTATGGCTATCTCTATTAAATGGA
1 AG-CCTTTTGGCTATCTCTATTAAAAAGA
34438842 AGCCTTTGTGGC
1 AGCCTTT-TGGC
34438854 GAGACTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (28 bp):
AGCCTTTTGGCTATCTCTATTAAAAAGA
Found at i:34443034 original size:24 final size:25
Alignment explanation
Indices: 34442988--34443034 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
34442978 ATAAATAACT
**
34442988 GAAAAAAAAAATCTAAAGCCTAAAA
1 GAAAAAAAAAATCTAAAAACTAAAA
*
34443013 GAAAAGAAAAA-CTAAAAACTAA
1 GAAAAAAAAAATCTAAAAACTAA
34443035 TTACAGAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.70, C:0.11, G:0.09, T:0.11
Consensus pattern (25 bp):
GAAAAAAAAAATCTAAAAACTAAAA
Found at i:34454709 original size:48 final size:48
Alignment explanation
Indices: 34454569--34454702 Score: 234
Period size: 48 Copynumber: 2.8 Consensus size: 48
34454559 ATATGACGGA
34454569 CCACTGGTAGGGCATGTTAGTGCTAATCAAGTTAGCGGAGATGAGGGG
1 CCACTGGTAGGGCATGTTAGTGCTAATCAAGTTAGCGGAGATGAGGGG
34454617 CCACTGGTAGGGCATGTTAGTGCTAATCAAGTTAGCGGAGATGAGGGG
1 CCACTGGTAGGGCATGTTAGTGCTAATCAAGTTAGCGGAGATGAGGGG
*
34454665 CCACTGGTAGGGCATGTTAGTTTCTAATC-AGCTTAGCG
1 CCACTGGTAGGGCATGTTAG-TGCTAATCAAG-TTAGCG
34454703 TTATGAGTGA
Statistics
Matches: 83, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
48 70 0.84
49 13 0.16
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.25
Consensus pattern (48 bp):
CCACTGGTAGGGCATGTTAGTGCTAATCAAGTTAGCGGAGATGAGGGG
Found at i:34459626 original size:28 final size:28
Alignment explanation
Indices: 34459594--34459651 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
34459584 ATGTAAGCTA
34459594 CACGATGCTACTCACACGAATTGTGGAG
1 CACGATGCTACTCACACGAATTGTGGAG
34459622 CACGATGCTACTCACACGAATTGTGGAG
1 CACGATGCTACTCACACGAATTGTGGAG
34459650 CA
1 CA
34459652 TACGCAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (28 bp):
CACGATGCTACTCACACGAATTGTGGAG
Found at i:34465278 original size:19 final size:19
Alignment explanation
Indices: 34465254--34465298 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
34465244 ATATATTTGA
34465254 TTATTTGATTT-CTTGAATT
1 TTATTT-ATTTACTTGAATT
* *
34465273 TTATTTATTTACTTTACTT
1 TTATTTATTTACTTGAATT
34465292 TTATTTA
1 TTATTTA
34465299 CTTTCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (19 bp):
TTATTTATTTACTTGAATT
Found at i:34465296 original size:15 final size:14
Alignment explanation
Indices: 34465276--34465312 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
34465266 TTGAATTTTA
34465276 TTTATTTACTTTACT
1 TTTATTTACTTT-CT
34465291 TTTATTTACTTTCT
1 TTTATTTACTTTCT
34465305 TATTATTT
1 T-TTATTT
34465313 TTAGTATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTACTTTCT
Found at i:34469426 original size:40 final size:40
Alignment explanation
Indices: 34469365--34469603 Score: 325
Period size: 40 Copynumber: 6.0 Consensus size: 40
34469355 GTTAATTATA
* * *
34469365 CCTGAATTGCACATACGTGCCCTTGTTTGTACTTCAGTGCC
1 CCTG-ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACC
* *
34469406 CCTGATTGCACATACATGCCCCTGTTTGTACTTCGATACC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACC
* * * * *
34469446 CTTGATTGCACATATGTGCCCTTGTTTTTACATCGGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACC
* * *
34469486 CTTGATTGCACATACGTGCCCCTATTTGTACTTCGGTATC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACC
*
34469526 CCTGATTGCACCTACGTGCCCCTGTTTGTACTTCGGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACC
**
34469566 CCTGATTGCACATACGTGCCCCTGTTTACACTTCGGTA
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
34469604 ACTTTAATCG
Statistics
Matches: 173, Mismatches: 25, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
40 169 0.98
41 4 0.02
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35
Consensus pattern (40 bp):
CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACC
Found at i:34469469 original size:20 final size:20
Alignment explanation
Indices: 34469370--34469506 Score: 91
Period size: 20 Copynumber: 6.8 Consensus size: 20
34469360 TTATACCTGA
34469370 ATTGCACATACGTGCCCTTG
1 ATTGCACATACGTGCCCTTG
* * * *
34469390 TTTGTAC-TTCAGTGCCCCTG
1 ATTGCACATAC-GTGCCCTTG
* *
34469410 ATTGCACATACATGCCCCTG
1 ATTGCACATACGTGCCCTTG
* * * *
34469430 TTTGTAC-TTCGATACCCTTG
1 ATTGCACATACG-TGCCCTTG
*
34469450 ATTGCACATATGTGCCCTTG
1 ATTGCACATACGTGCCCTTG
* ** *
34469470 TTTTTACAT-CGGTACCCTTG
1 ATTGCACATAC-GTGCCCTTG
34469490 ATTGCACATACGTGCCC
1 ATTGCACATACGTGCCC
34469507 CTATTTGTAC
Statistics
Matches: 83, Mismatches: 28, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
19 4 0.05
20 74 0.89
21 5 0.06
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (20 bp):
ATTGCACATACGTGCCCTTG
Found at i:34469567 original size:20 final size:20
Alignment explanation
Indices: 34469504--34469569 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
34469494 CACATACGTG
*
34469504 CCCCTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* * * * *
34469524 TCCCTGATTGCACCTAC-GTG
1 CCCCTGTTTGTA-CTTCGGTA
34469544 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
34469564 CCCCTG
1 CCCCTG
34469570 ATTGCACATA
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.12, C:0.35, G:0.18, T:0.35
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:34473472 original size:27 final size:27
Alignment explanation
Indices: 34473434--34473714 Score: 295
Period size: 27 Copynumber: 10.5 Consensus size: 27
34473424 GGCAACTGAC
**
34473434 CGAAATACCCCTGGAGGGTAAAATGAT
1 CGAAATACCCCTAAAGGGTAAAATGAT
* *
34473461 CGAAATACCCCTAGAGGGTAAAATGAC
1 CGAAATACCCCTAAAGGGTAAAATGAT
* *
34473488 CGAAATACCCCCAAAAGGTAAAATGAT
1 CGAAATACCCCTAAAGGGTAAAATGAT
**
34473515 CGAAATACCCCTAAA-AATAAAATGA-
1 CGAAATACCCCTAAAGGGTAAAATGAT
*
34473540 CTGAAATA-CCCTCAGAGGGTAAAATGAT
1 C-GAAATACCCCT-AAAGGGTAAAATGAT
*
34473568 CGAAATACCCTTAAAGGGTAAAATGAT
1 CGAAATACCCCTAAAGGGTAAAATGAT
** * *
34473595 CGAAATACTGCTAGAGGGTAAAATGAC
1 CGAAATACCCCTAAAGGGTAAAATGAT
***
34473622 CGAAATACCCCCGGAGGGTAAAATGA-
1 CGAAATACCCCTAAAGGGTAAAATGAT
* *
34473648 CTGAAATACCTCTGAAGGGTAAAATGAT
1 C-GAAATACCCCTAAAGGGTAAAATGAT
*
34473676 CGAAATA-CCCTGAAGGGTAAAATGA-
1 CGAAATACCCCTAAAGGGTAAAATGAT
*
34473701 CTGAAATAACCCTA
1 C-GAAATACCCCTA
34473715 GGTGATGAAA
Statistics
Matches: 217, Mismatches: 28, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
25 6 0.03
26 40 0.18
27 166 0.76
28 5 0.02
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (27 bp):
CGAAATACCCCTAAAGGGTAAAATGAT
Found at i:34473494 original size:54 final size:54
Alignment explanation
Indices: 34473430--34473715 Score: 330
Period size: 54 Copynumber: 5.3 Consensus size: 54
34473420 CGTGGGCAAC
*
34473430 TGACCGAAATACCCCTGGAGGGTAAAATGATCGAAATACCCCTAGAGGGTAAAA
1 TGACCGAAATACCCCTAGAGGGTAAAATGATCGAAATACCCCTAGAGGGTAAAA
* * * ***
34473484 TGACCGAAATACCCCCAAAAGGTAAAATGATCGAAATACCCCTA-AAAATAAAA
1 TGACCGAAATACCCCTAGAGGGTAAAATGATCGAAATACCCCTAGAGGGTAAAA
* * *
34473537 TGACTGAAATA-CCCTCAGAGGGTAAAATGATCGAAATACCCTTAAAGGGTAAAA
1 TGACCGAAATACCCCT-AGAGGGTAAAATGATCGAAATACCCCTAGAGGGTAAAA
* ** * **
34473591 TGATCGAAATACTGCTAGAGGGTAAAATGACCGAAATACCCCCGGAGGGTAAAA
1 TGACCGAAATACCCCTAGAGGGTAAAATGATCGAAATACCCCTAGAGGGTAAAA
* *
34473645 TGACTGAAATACCTCT-GAAGGGTAAAATGATCGAAATA-CCCT-GAAGGGTAAAA
1 TGACCGAAATACCCCTAG-AGGGTAAAATGATCGAAATACCCCTAG-AGGGTAAAA
* *
34473698 TGACTGAAATAACCCTAG
1 TGACCGAAATACCCCTAG
34473716 GTGATGAAAT
Statistics
Matches: 194, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
52 4 0.02
53 68 0.35
54 120 0.62
55 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (54 bp):
TGACCGAAATACCCCTAGAGGGTAAAATGATCGAAATACCCCTAGAGGGTAAAA
Found at i:34473546 original size:80 final size:80
Alignment explanation
Indices: 34473434--34473715 Score: 345
Period size: 80 Copynumber: 3.5 Consensus size: 80
34473424 GGCAACTGAC
*
34473434 CGAAATACCCCTGGAGGGTAAAATGA-TCGAAATACCCCTAGAGGGTAAAATGACCGAAATACCC
1 CGAAATACCCCT-AAGGGTAAAATGACT-GAAATACCCCTAGAGGGTAAAATGACCGAAATACCC
* *
34473498 CCAAAAGGTAAAATGAT
64 CTAAAGGGTAAAATGAT
*** * *
34473515 CGAAATACCCCTAAAAATAAAATGACTGAAATA-CCCTCAGAGGGTAAAATGATCGAAATACCCT
1 CGAAATACCCCTAAGGGTAAAATGACTGAAATACCCCT-AGAGGGTAAAATGACCGAAATACCCC
34473579 TAAAGGGTAAAATGAT
65 TAAAGGGTAAAATGAT
** * ** * *
34473595 CGAAATACTGCTAGAGGGTAAAATGACCGAAATACCCCCGGAGGGTAAAATGACTGAAATACCTC
1 CGAAATACCCCTA-AGGGTAAAATGACTGAAATACCCCTAGAGGGTAAAATGACCGAAATACCCC
*
34473660 TGAAGGGTAAAATGAT
65 TAAAGGGTAAAATGAT
*
34473676 CGAAATA-CCCTGAAGGGTAAAATGACTGAAATAACCCTAG
1 CGAAATACCCCT-AAGGGTAAAATGACTGAAATACCCCTAG
34473716 GTGATGAAAT
Statistics
Matches: 169, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
79 4 0.02
80 89 0.53
81 73 0.43
82 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (80 bp):
CGAAATACCCCTAAGGGTAAAATGACTGAAATACCCCTAGAGGGTAAAATGACCGAAATACCCCT
AAAGGGTAAAATGAT
Found at i:34473626 original size:107 final size:106
Alignment explanation
Indices: 34473430--34473708 Score: 330
Period size: 107 Copynumber: 2.6 Consensus size: 106
34473420 CGTGGGCAAC
* * *
34473430 TGACCGAAATACCC-CTGGAGGGTAAAATGATCGAAATACCCCTAGAGGGTAAAATGACCGAAAT
1 TGACTGAAATACCCTC-AGAGGGTAAAATGATCGAAATA-CCCTAAAGGGTAAAATGA-CGAAAT
* *
34473494 ACCCCCAAAAGGTAAAATGATCGAAATA-CCCCTAAAAATAAAA
63 ACCCCCAAAAGGTAAAATGACCGAAATACCCCCGAAAAATAAAA
34473537 TGACTGAAATACCCTCAGAGGGTAAAATGATCGAAATACCCTTAAAGGGTAAAATGATCGAAATA
1 TGACTGAAATACCCTCAGAGGGTAAAATGATCGAAATACCC-TAAAGGGTAAAATGA-CGAAATA
** * * * * ***
34473602 CTGCTAGAGGGTAAAATGACCGAAATACCCCCGGAGGGTAAAA
64 CCCCCAAAAGGTAAAATGACCGAAATACCCCCGAAAAATAAAA
* *
34473645 TGACTGAAATA-CCTCTGAAGGGTAAAATGATCGAAATACCCTGAAGGGTAAAATGACTGAAATA
1 TGACTGAAATACCCTCAG-AGGGTAAAATGATCGAAATACCCTAAAGGGTAAAATGAC-GAAATA
34473709 ACCCTAGGTG
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
106 4 0.03
107 101 0.67
108 45 0.30
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (106 bp):
TGACTGAAATACCCTCAGAGGGTAAAATGATCGAAATACCCTAAAGGGTAAAATGACGAAATACC
CCCAAAAGGTAAAATGACCGAAATACCCCCGAAAAATAAAA
Found at i:34474101 original size:28 final size:28
Alignment explanation
Indices: 34474055--34474135 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
34474045 ACTGTACTGG
* *
34474055 TTACTATATTAGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
* *
34474083 TTGCTGTATTGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTA
* *
34474111 TTACTGTTTTGGGCTAAGTCCCACA
1 TTACTGTATTGGGCTAAGGCCCACA
34474136 TTGTACTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTA
Found at i:34479800 original size:55 final size:55
Alignment explanation
Indices: 34479716--34479884 Score: 311
Period size: 55 Copynumber: 3.1 Consensus size: 55
34479706 CAAGTCTTGC
*
34479716 CCTTGGCAAAATTTTTAGTTTTGTTCTTAAATGAATCTGGACATTGGTATATAGG
1 CCTTGGCAGAATTTTTAGTTTTGTTCTTAAATGAATCTGGACATTGGTATATAGG
*
34479771 CCTTGGCAGAATTTTTAGTTTTGTTCTTAAATGAATCAGGACATTGGTATATAGG
1 CCTTGGCAGAATTTTTAGTTTTGTTCTTAAATGAATCTGGACATTGGTATATAGG
*
34479826 CCTTGGCAGAATTTTTACTTTTGTTCTTAAATGAATCTGGACATTGGTATATAGG
1 CCTTGGCAGAATTTTTAGTTTTGTTCTTAAATGAATCTGGACATTGGTATATAGG
34479881 CCTT
1 CCTT
34479885 ATAAATAATA
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 110 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.41
Consensus pattern (55 bp):
CCTTGGCAGAATTTTTAGTTTTGTTCTTAAATGAATCTGGACATTGGTATATAGG
Found at i:34480174 original size:19 final size:20
Alignment explanation
Indices: 34480139--34480176 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
34480129 CAAGCTGATT
34480139 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
*
34480159 TTAGCTC-ATTTTAGCTCC
1 TTAGCTCAATTTCAGCTCC
34480177 AACCAGCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:34482713 original size:27 final size:26
Alignment explanation
Indices: 34482674--34482767 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 26
34482664 GATTCGTGGG
34482674 AAAATGACTGAAATACCCTCAGAGGGT
1 AAAATGACTGAAATACCCTC-GAGGGT
* *
34482701 AAAATGA-TCGAAATACCTTCGAAGGAT
1 AAAATGACT-GAAATACCCTCG-AGGGT
*
34482728 AAAATGACTGAAATACCCCTGGAGGGT
1 AAAATGACTGAAATA-CCCTCGAGGGT
34482755 AAAATGACTGAAA
1 AAAATGACTGAAA
34482768 ATGGTAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.03
27 51 0.88
28 5 0.09
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (26 bp):
AAAATGACTGAAATACCCTCGAGGGT
Found at i:34482828 original size:27 final size:28
Alignment explanation
Indices: 34482770--34482834 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
34482760 GACTGAAAAT
* *
34482770 GGTAAAATGATCGAAATACCCCCCGAAG
1 GGTAAAATGAACGAAATACCCCCAGAAG
* *
34482798 GGTAAACTGAACGAAATACCCCCATAA-
1 GGTAAAATGAACGAAATACCCCCAGAAG
34482825 GGTAAAATGA
1 GGTAAAATGA
34482835 CTGTTATACT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (28 bp):
GGTAAAATGAACGAAATACCCCCAGAAG
Found at i:34482829 original size:73 final size:72
Alignment explanation
Indices: 34482698--34482837 Score: 183
Period size: 73 Copynumber: 1.9 Consensus size: 72
34482688 ACCCTCAGAG
** ** *
34482698 GGTAAAATGATCGAAATACCTTCGAAGGATAAAATGACTGAAATACCCCTGGAGGGTAAAATGAC
1 GGTAAAATGATCGAAATACCCCCGAAGGATAAAATGACTGAAATACCCCCAGAAGGTAAAATGAC
34482763 TGAAAAT
66 TGAAAAT
* * *
34482770 GGTAAAATGATCGAAATACCCCCCGAAGGGTAAACTGAAC-GAAATACCCCCATAAGGTAAAATG
1 GGTAAAATGATCGAAATA-CCCCCGAAGGATAAAATG-ACTGAAATACCCCCAGAAGGTAAAATG
34482834 ACTG
64 ACTG
34482838 TTATACTCCT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 18 0.31
73 38 0.66
74 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (72 bp):
GGTAAAATGATCGAAATACCCCCGAAGGATAAAATGACTGAAATACCCCCAGAAGGTAAAATGAC
TGAAAAT
Found at i:34483263 original size:33 final size:33
Alignment explanation
Indices: 34483178--34483281 Score: 121
Period size: 27 Copynumber: 3.3 Consensus size: 33
34483168 TACATTATTG
34483178 CACTGTACTGGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTACT-GTTACTGTATTGGGCTAAGGCCCA
34483212 CAC--TA---TT-CTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
* *
34483239 CACTGTACTGTTACTGTATAGGGCTCAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
*
34483272 AACTGATACT
1 CACTG-TACT
34483282 ACATGGCTAC
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
27 23 0.38
28 2 0.03
29 2 0.03
32 4 0.07
33 22 0.37
34 7 0.12
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (33 bp):
CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:34488046 original size:35 final size:35
Alignment explanation
Indices: 34487987--34488068 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
34487977 TAGGCAATCC
*
34487987 AACACACCAGAAGCTCATAAGAGCTAATCCATCCGA
1 AACACACCA-AAGCTCATAAGAGCTAATCCATCCAA
* *
34488023 AACACACCAATGCTCATACGAGCTAATCCATCCAA
1 AACACACCAAAGCTCATAAGAGCTAATCCATCCAA
34488058 AACACACCAAA
1 AACACACCAAA
34488069 ACAGAGAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 33 0.79
36 9 0.21
ACGTcount: A:0.44, C:0.33, G:0.10, T:0.13
Consensus pattern (35 bp):
AACACACCAAAGCTCATAAGAGCTAATCCATCCAA
Found at i:34489669 original size:24 final size:22
Alignment explanation
Indices: 34489628--34489671 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
34489618 CATTATTCAA
*
34489628 ATTTCATATACATGTATCATAC
1 ATTTCATATACATATATCATAC
34489650 ATTTCATATATCAATATATCAT
1 ATTTCATATA-C-ATATATCAT
34489672 GTAACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTCATATACATATATCATAC
Found at i:34497361 original size:24 final size:22
Alignment explanation
Indices: 34497320--34497363 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
34497310 CATTATTCAA
*
34497320 ATTTCATATATATGTATCATAC
1 ATTTCATATATATATATCATAC
34497342 ATTTCATATATCAATATATCAT
1 ATTTCATATAT--ATATATCAT
34497364 GTAACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTCATATATATATATCATAC
Found at i:34497865 original size:14 final size:15
Alignment explanation
Indices: 34497846--34497874 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34497836 GAAGAAGAAA
34497846 ACTTATTTTT-TTTT
1 ACTTATTTTTGTTTT
34497860 ACTTATTTTTGTTTT
1 ACTTATTTTTGTTTT
34497875 GATTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (15 bp):
ACTTATTTTTGTTTT
Found at i:34499454 original size:40 final size:39
Alignment explanation
Indices: 34499363--34499545 Score: 197
Period size: 40 Copynumber: 4.6 Consensus size: 39
34499353 TCCTCGTTCA
* * *
34499363 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* *
34499402 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* *
34499441 GAATGCCTTCGGGACTTAACCCGGATTTAGTACCTCGCAC
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* * * * * *
34499481 AAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCAC
*
34499522 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
34499546 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
39 37 0.30
40 77 0.63
41 8 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
Found at i:34499554 original size:41 final size:41
Alignment explanation
Indices: 34499477--34499554 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
34499467 TTAGTACCTC
* * *
34499477 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
34499518 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
34499555 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:34507114 original size:25 final size:24
Alignment explanation
Indices: 34507083--34507129 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
34507073 TTTTCTTTAA
34507083 TTTTA-TTAACCTTTATTTAATAATT
1 TTTTATTTAACC-TTA-TTAATAATT
34507108 TTTTATTTAACCTTATTAATAA
1 TTTTATTTAACCTTATTAATAA
34507130 CCTTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.33
25 8 0.38
26 6 0.29
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATTTAACCTTATTAATAATT
Found at i:34513615 original size:27 final size:27
Alignment explanation
Indices: 34513537--34513769 Score: 259
Period size: 27 Copynumber: 8.5 Consensus size: 27
34513527 TCAGATTCGT
* * *
34513537 GGGTAAAATGATCGAAATACCCCCGAA
1 GGGTAAAATGACCGAAATACCCTCAAA
34513564 GGGTAAAATGACCGACCGAAATACCCTCAAA
1 GGGTAAAAT----GACCGAAATACCCTCAAA
* *
34513595 GGGTAAAATGACCGAAATACCCCCGAA
1 GGGTAAAATGACCGAAATACCCTCAAA
* *
34513622 GGGTAAAATGACTGAAATACCCTTAAA
1 GGGTAAAATGACCGAAATACCCTCAAA
* ** **
34513649 GGGTAAAATAACAAAAATACCCTTGAA
1 GGGTAAAATGACCGAAATACCCTCAAA
* * **
34513676 GGGTAAAATGATCAAAATACCCTTGAA
1 GGGTAAAATGACCGAAATACCCTCAAA
* *
34513703 GGGTAAAATGATCGAAATACCCTCACA
1 GGGTAAAATGACCGAAATACCCTCAAA
*
34513730 GGGTAAAATGACCGAAATACCCTCATA
1 GGGTAAAATGACCGAAATACCCTCAAA
34513757 GGGTAAAATGACC
1 GGGTAAAATGACC
34513770 ATTATACCCC
Statistics
Matches: 180, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
27 156 0.87
31 24 0.13
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (27 bp):
GGGTAAAATGACCGAAATACCCTCAAA
Found at i:34514118 original size:28 final size:28
Alignment explanation
Indices: 34514086--34514174 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 28
34514076 GGTTGCATTA
34514086 CCACATTGTTACTATAATGGGCTAAGGC
1 CCACATTGTTACTATAATGGGCTAAGGC
* *
34514114 CCACATTGTTTCTATATTGGGCTAAGGC
1 CCACATTGTTACTATAATGGGCTAAGGC
* *
34514142 CCTCATTATTAC-AGT-ATCGGGCTAAGGC
1 CCACATTGTTACTA-TAAT-GGGCTAAGGC
34514170 CCACA
1 CCACA
34514175 CTGTGCTATT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.04
28 50 0.96
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (28 bp):
CCACATTGTTACTATAATGGGCTAAGGC
Done.