Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 110 of 175
Found at i:34857639 original size:11 final size:11
Alignment explanation
Indices: 34857625--34857662 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
34857615 GTAGTAAAAG
34857625 AGCAACATAAT
1 AGCAACATAAT
*
34857636 AGCAACAAAAT
1 AGCAACATAAT
*
34857647 AGCAACATAAC
1 AGCAACATAAT
34857658 AGCAA
1 AGCAA
34857663 TAAACAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.58, C:0.21, G:0.11, T:0.11
Consensus pattern (11 bp):
AGCAACATAAT
Found at i:34857645 original size:22 final size:22
Alignment explanation
Indices: 34857620--34857662 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34857610 AAATAGTAGT
*
34857620 AAAAGAGCAACATAATAGCAAC
1 AAAAGAGCAACATAACAGCAAC
*
34857642 AAAATAGCAACATAACAGCAA
1 AAAAGAGCAACATAACAGCAA
34857663 TAAACAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.19, G:0.12, T:0.09
Consensus pattern (22 bp):
AAAAGAGCAACATAACAGCAAC
Found at i:34858364 original size:14 final size:13
Alignment explanation
Indices: 34858345--34858383 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
34858335 TTTTCTTTTC
34858345 TTTTTAATTTTACT
1 TTTTTAATTTTA-T
*
34858359 TTTTTATTTTCTAT
1 TTTTTAATTT-TAT
34858373 TTTTTAATTTT
1 TTTTTAATTTT
34858384 TAATCAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.05
14 19 0.86
15 2 0.09
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTAATTTTAT
Found at i:34862176 original size:6 final size:6
Alignment explanation
Indices: 34862165--34862191 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34862155 TAAGAAGCAT
34862165 GGACAC GGACAC GGACAC GGACAC GGA
1 GGACAC GGACAC GGACAC GGACAC GGA
34862192 TATGCAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.37, T:0.00
Consensus pattern (6 bp):
GGACAC
Found at i:34864910 original size:24 final size:24
Alignment explanation
Indices: 34864859--34864910 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
34864849 TTCATAGGTC
* *
34864859 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
34864883 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
34864907 AAAT
1 AAAT
34864911 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:34865247 original size:21 final size:21
Alignment explanation
Indices: 34865222--34865262 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34865212 ACTCATATTC
* *
34865222 CCCTTCTTTTCTTTCTCATTA
1 CCCTTCTTTTCCTCCTCATTA
*
34865243 CCCTTTTTTTCCTCCTCATT
1 CCCTTCTTTTCCTCCTCATT
34865263 TACTGTCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (21 bp):
CCCTTCTTTTCCTCCTCATTA
Found at i:34870090 original size:64 final size:63
Alignment explanation
Indices: 34869990--34870118 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 63
34869980 CTATGCAGAA
*
34869990 AGCTAATGAATGAGAAAGTAGTAACATTGGCACTATTGTAAGGATTACAAGTGACAAAAGTTG
1 AGCTAATGAATGAGAAAGTAGTAACATTGGCACTATTGTAAGGATTACAACTGACAAAAGTTG
* *
34870053 AGCTAATGAATGAGAAAAGTAGTAACATTGGTACTATTGTAAGGATTAGAACTGACAAAAGTTG
1 AGCTAATGAATGAG-AAAGTAGTAACATTGGCACTATTGTAAGGATTACAACTGACAAAAGTTG
34870117 AG
1 AG
34870119 AGTTTGATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 14 0.23
64 48 0.77
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.26
Consensus pattern (63 bp):
AGCTAATGAATGAGAAAGTAGTAACATTGGCACTATTGTAAGGATTACAACTGACAAAAGTTG
Found at i:34871632 original size:261 final size:262
Alignment explanation
Indices: 34871081--34871807 Score: 922
Period size: 261 Copynumber: 2.8 Consensus size: 262
34871071 AATATTATTT
* * * *
34871081 TATCAAGAGTATAACTCTG-AAGTAATGAAACAAAACTTCTTAAATCTCATTAA-CTTTATAGAG
1 TATCAAGAGTATAACTGTGAAAGTAGTGAAACGAAACTCCTTAAATCTCATTAATC-TTATAGAG
*
34871144 ATTTGAAAAACT-AGCAGGCGATAAATAACATAAGATAGTTCAACCAATTATTATACACTGCGTA
65 ATTTGATAAACTGA-CAGGCGATAAATAACATAAGATAGTTCAACCAATTATTATACACTGCGTA
*
34871208 CTTTTCCCGCACAGCAAAAGCAACTTCCACAGCGTGGGGCCACCTCACCTTGCCGTTACATAATA
129 CTTTTCCCGCACAGCAAAAGCAACTTCCACAACGTGGGGCCACCTCACCTTGCCGTTACATAATA
* * * *
34871273 TATATTCTCTAAGAGTATATTATATTAAAAAACTGATTTTATTTTCAATTTTACTAGATACAGCA
194 TATATTCTCTAAGAGTATATCATATTAAAAAAC-AATTTAATTTTCAATTTTACTAGATACAACA
*
34871338 TTATT
258 TTATA
*
34871343 TATCAAGAGTGTAACTGTGAAA-TAGTGAAACGAAACTCCTTAAATCTCATTAATCTTATAGAGA
1 TATCAAGAGTATAACTGTGAAAGTAGTGAAACGAAACTCCTTAAATCTCATTAATCTTATAGAGA
* * *
34871407 TTTGATAAACTGACAGGCAATAAATAATATAAGATAGTTCAACCAATTATTATACACTGTGTA-T
66 TTTGATAAACTGACAGGCGATAAATAACATAAGATAGTTCAACCAATTATTATACACTGCGTACT
* * * * * * *
34871471 CTTCCAGCACATCAAAAGCAACTGT-CACAACGTGGAGCCACCTCACCTCGCCGTTACGTTATAT
131 TTTCCCGCACAGCAAAAGCAACT-TCCACAACGTGGGGCCACCTCACCTTGCCGTTACATAATAT
* * *
34871535 ATATTCTCTAAGAGTGTATCATATTAAAAAA-AATTTGAATTTTTCAGA-TTTGC-AGGATGCAA
195 ATATTCTCTAAGAGTATATCATATTAAAAAACAATTT-AA-TTTTCA-ATTTTACTA-GATACAA
34871597 CATTATA
256 CATTATA
* * * * * *
34871604 TATCAAGTA-TATAA-T-TGCAAAGTAGTGAAATGAAACTCCTCAAGTCTTAGT-ATCCTCATAG
1 TATCAAG-AGTATAACTGTG-AAAGTAGTGAAACGAAACTCCTTAAATCTCATTAAT-CTTATAG
* * * * * *
34871665 GGATTTGATAAATTGGCTGACGATAAATTAACATAAGATAGTTCAACCAATTATTATACACTGCA
63 AGATTTGATAAACTGACAGGCGATAAA-TAACATAAGATAGTTCAACCAATTATTATACACTGCG
34871730 TACTTTTCCCGCACAGCAAAAGCAACTTCCACAACGTGGGGCCACCTCACCTTGCCGTTACATAA
127 TACTTTTCCCGCACAGCAAAAGCAACTTCCACAACGTGGGGCCACCTCACCTTGCCGTTACATAA
34871795 TATATATTCTCTA
192 TATATATTCTCTA
34871808 GGGCCACTCG
Statistics
Matches: 402, Mismatches: 48, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
259 6 0.01
260 8 0.02
261 167 0.42
262 151 0.38
263 70 0.17
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (262 bp):
TATCAAGAGTATAACTGTGAAAGTAGTGAAACGAAACTCCTTAAATCTCATTAATCTTATAGAGA
TTTGATAAACTGACAGGCGATAAATAACATAAGATAGTTCAACCAATTATTATACACTGCGTACT
TTTCCCGCACAGCAAAAGCAACTTCCACAACGTGGGGCCACCTCACCTTGCCGTTACATAATATA
TATTCTCTAAGAGTATATCATATTAAAAAACAATTTAATTTTCAATTTTACTAGATACAACATTA
TA
Found at i:34874310 original size:16 final size:16
Alignment explanation
Indices: 34874286--34874335 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
34874276 TATAATTTTA
*
34874286 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
34874302 TTATAAATTATAAAA-T
1 TTATAAATT-TAAAATT
* *
34874318 GTCTAAA-TTAAAATT
1 TTATAAATTTAAAATT
34874333 TTA
1 TTA
34874336 CGAAAACATG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 5 0.19
15 3 0.11
16 14 0.52
17 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:34876704 original size:25 final size:25
Alignment explanation
Indices: 34876646--34876704 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
34876636 ATGAGCCTTT
*
34876646 AAATCAATT-GAATAAAATAAAATC
1 AAATTAATTGGAATAAAATAAAATC
* *
34876670 AAATTGATTGGAATCAAATAAAATC
1 AAATTAATTGGAATAAAATAAAATC
34876695 AAGA-TAATTG
1 AA-ATTAATTG
34876705 TCCTTTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
25 21 0.72
26 1 0.03
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (25 bp):
AAATTAATTGGAATAAAATAAAATC
Found at i:34877530 original size:18 final size:18
Alignment explanation
Indices: 34877507--34877550 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
34877497 AATTTTTATG
*
34877507 ATTGGGTTGGGTTGAGTA
1 ATTGGGTTGGGTTGAATA
34877525 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
34877543 CTTGGGTT
1 ATTGGGTT
34877551 TGGATTGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:34879008 original size:29 final size:29
Alignment explanation
Indices: 34878966--34879022 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
34878956 TATGTGACAT
34878966 AGTTTTGCACAAAAATGATAGTGTTTCAC
1 AGTTTTGCACAAAAATGATAGTGTTTCAC
34878995 AGTTTTGCACAAAAATGATAGTGTTTCA
1 AGTTTTGCACAAAAATGATAGTGTTTCA
34879023 TTCTTAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (29 bp):
AGTTTTGCACAAAAATGATAGTGTTTCAC
Found at i:34883520 original size:10 final size:11
Alignment explanation
Indices: 34883505--34883534 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
34883495 ATTGTTATTT
34883505 AAATAAAAT-A
1 AAATAAAATAA
34883515 AAATAAAATAA
1 AAATAAAATAA
34883526 AAATAAAAT
1 AAATAAAAT
34883535 CCATATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:34883530 original size:6 final size:5
Alignment explanation
Indices: 34883505--34883534 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
34883495 ATTGTTATTT
34883505 AAATA AAATA AAATA AAATAA AAATA AAAT
1 AAATA AAATA AAATA AAAT-A AAATA AAAT
34883535 CCATATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:34885335 original size:42 final size:42
Alignment explanation
Indices: 34885239--34885569 Score: 340
Period size: 42 Copynumber: 7.8 Consensus size: 42
34885229 CAACCAAAAA
* * *** * *
34885239 CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGAGAAAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTATAAG
* * * *
34885281 CGCCACTGAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTATAAG
*
34885323 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTATAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTATAAG
* * * *
34885365 CGCCACTAAAGAACATGATCTTTAGTGGCGTTTTTCTATAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTATAAG
* * *
34885407 CGCCGCTAAAGAATATGATCTTTAGTGGCG-TTTTTTATTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTA-TAAG
* * * * *
34885449 CGCCGCTAAAGAACATGTTCTTTAACGACGTTTTGTATAAAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT-TTTATAAG
* * * * * *
34885492 CGCTGTTAAAGAACATGTTCTTCAGCGGCGCTTTGTTTACAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTTATAAG
* *
34885535 TGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
34885570 GTACAAAAAC
Statistics
Matches: 242, Mismatches: 43, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
41 6 0.02
42 168 0.69
43 62 0.26
44 6 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTATAAG
Found at i:34885976 original size:21 final size:21
Alignment explanation
Indices: 34885952--34886023 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
34885942 TTCTTTTGAA
*
34885952 CCTCTGCTTCTCTCGCTGTAG
1 CCTCTGCTTCTCTCGCTGCAG
*
34885973 CCTCTGCTTCTCTCGTTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
* * *
34885994 CCTCTGCTTCCCTCGATGCCG
1 CCTCTGCTTCTCTCGCTGCAG
*
34886015 CGTCTGCTT
1 CCTCTGCTT
34886024 TAAGTTGTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.04, C:0.40, G:0.19, T:0.36
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:34888788 original size:18 final size:18
Alignment explanation
Indices: 34888758--34888831 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
34888748 GTATTATGTA
34888758 ATGTAAGTTATGTAATTT
1 ATGTAAGTTATGTAATTT
* * *
34888776 ATTTAATTTATGTAAGTT
1 ATGTAAGTTATGTAATTT
*
34888794 ATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAATTT
* *
34888812 ATGTAAATTATTTAATTT
1 ATGTAAGTTATGTAATTT
34888830 AT
1 AT
34888832 TGAAATGCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
ATGTAAGTTATGTAATTT
Found at i:34888789 original size:27 final size:27
Alignment explanation
Indices: 34888758--34888832 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
34888748 GTATTATGTA
34888758 ATGTAAGTTATGTAATTTATTTAATTT
1 ATGTAAGTTATGTAATTTATTTAATTT
*
34888785 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAATTTATTTAATTT
* *
34888812 ATGTAAATTATTTAATTTATT
1 ATGTAAGTTATGTAATTTATT
34888833 GAAATGCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.55
Consensus pattern (27 bp):
ATGTAAGTTATGTAATTTATTTAATTT
Found at i:34888832 original size:9 final size:9
Alignment explanation
Indices: 34888758--34888831 Score: 85
Period size: 9 Copynumber: 8.2 Consensus size: 9
34888748 GTATTATGTA
*
34888758 ATGTAAGTT
1 ATGTAATTT
34888767 ATGTAATTT
1 ATGTAATTT
*
34888776 ATTTAATTT
1 ATGTAATTT
*
34888785 ATGTAAGTT
1 ATGTAATTT
*
34888794 ATGTAAGTT
1 ATGTAATTT
*
34888803 ATTTAATTT
1 ATGTAATTT
*
34888812 ATGTAAATT
1 ATGTAATTT
*
34888821 ATTTAATTT
1 ATGTAATTT
34888830 AT
1 AT
34888832 TGAAATGCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (9 bp):
ATGTAATTT
Found at i:34889065 original size:9 final size:9
Alignment explanation
Indices: 34889033--34889072 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
34889023 TTATGTCGTA
34889033 TTATGTAAG
1 TTATGTAAG
34889042 TTATGT-A-
1 TTATGTAAG
*
34889049 TTA-ATAAG
1 TTATGTAAG
34889057 TTATGTAAG
1 TTATGTAAG
34889066 TTATGTA
1 TTATGTA
34889073 TCATTTATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
6 1 0.04
7 4 0.15
8 4 0.15
9 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:34889094 original size:43 final size:43
Alignment explanation
Indices: 34889047--34889209 Score: 177
Period size: 43 Copynumber: 3.6 Consensus size: 43
34889037 GTAAGTTATG
34889047 TATTAATAAGTTATGTAAGTTATGTATCATTTATCCATAAATA
1 TATTAATAAGTTATGTAAGTTATGTATCATTTATCCATAAATA
* * * ** *
34889090 TATTAATAAGTTATGT-CGTATTATGTAAGTTATGTATTAAAAATGATA
1 TATTAATAAGTTATGTAAG--TTATGT-A-TCATTTATCCATAA--ATA
34889138 TGTATTAATAAGTTATGTAAGTTATGTATCATTTATCCATAAATA
1 --TATTAATAAGTTATGTAAGTTATGTATCATTTATCCATAAATA
34889183 TATTAATAAGTTATGTAA-TGTATGTAT
1 TATTAATAAGTTATGTAAGT-TATGTAT
34889210 TATAAATGGG
Statistics
Matches: 98, Mismatches: 12, Indels: 20
0.75 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 41 0.42
44 6 0.06
45 4 0.04
46 9 0.09
47 9 0.09
48 4 0.04
49 6 0.06
50 16 0.16
51 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (43 bp):
TATTAATAAGTTATGTAAGTTATGTATCATTTATCCATAAATA
Found at i:34889841 original size:15 final size:15
Alignment explanation
Indices: 34889813--34889848 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
34889803 TTAATAAAAG
*
34889813 GAAAA-AGTAGAAAT
1 GAAAACAGTACAAAT
34889827 GAAAACAGTACAAAT
1 GAAAACAGTACAAAT
34889842 GAAAACA
1 GAAAACA
34889849 AATTGGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (15 bp):
GAAAACAGTACAAAT
Found at i:34892027 original size:15 final size:15
Alignment explanation
Indices: 34892009--34892042 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
34891999 ATAAAACTCA
34892009 TAAACCACAAAACAC
1 TAAACCACAAAACAC
* *
34892024 TAAACCACCAAACCC
1 TAAACCACAAAACAC
34892039 TAAA
1 TAAA
34892043 ATCCAAGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.35, G:0.00, T:0.09
Consensus pattern (15 bp):
TAAACCACAAAACAC
Found at i:34892949 original size:190 final size:194
Alignment explanation
Indices: 34892651--34893202 Score: 478
Period size: 204 Copynumber: 2.8 Consensus size: 194
34892641 AAGCACCACT
* * ** * ** *
34892651 AATGACCA-TATACCTCTCCGCCAAAACGATGCGCCTTGGTTAAATACTTGCGGCGTTT-TTTGT
1 AATG-CCACTATACCTCACGGCC-AAACGATGCGTTTTGGTTAACTTTTTGCGGCGTTTATTAGT
* * * *
34892714 CAAGCGCCGTTAATACCGATATTTAGCGGCGATTTTATGTTAGCGCCGCG-AATGCCACAA-TGA
64 TAAGCGCCGTTAATACCGATCTTTAGCGGCGTTTTTA-ATTAGCGCCGCGAAAT-CCACAATTGA
* *
34892777 TCAACAA-CGAACGATGCGTTTAGTTTTAACATCTCTAGTGGC-ATT-TTTA-GGC-AAAGCGCC
127 TCAA-AATCGAACGATGCGTTTAGTTTTAACATATCTAGCGGCGATTCTTTAGGGCTAAAGCGCC
34892837 GCTA
191 GCTA
*
34892841 AATGCCACTATACCTCACGGCCAAACGATGCGTTTTGGTTAACTTTTTGCGGCGTTTACTAGTTA
1 AATGCCACTATACCTCACGGCCAAACGATGCGTTTTGGTTAACTTTTTGCGGCGTTTATTAGTTA
* * * *
34892906 AGCGTCGTTAATACCGATCTTTAGCGGCGTTTTTCAATTAGCGCCGTGAAATCCAGAATTTATCA
66 AGCGCCGTTAATACCGATCTTTAGCGGCGTTTTT-AATTAGCGCCGCGAAATCCACAATTGATCA
* * * * *
34892971 AAATCGAACGTTGTGTTTAGTTTTAACATATTTTGCGGCGTTTTCTTTAGTGGCGTTTGGTTTAA
130 AAATCGAACGATGCGTTTAGTTTTAACATATCTAGCGGCG-ATTCTTTAG-GGC--------TAA
34893036 AGCGCCGCTA
185 AGCGCCGCTA
* ** * * *
34893046 AATGCCACCATAAATCAAGGCCAAA-GATGCGTTTTGGTTAACTTTCTGCGGCGTTTATTCGTTA
1 AATGCCACTATACCTCACGGCCAAACGATGCGTTTTGGTTAACTTTTTGCGGCGTTTATTAGTTA
* * * * * * * *
34893110 AGCGCCGTTAATTCTGATCTTTCGCAGCGATTTTTTATTAGCGCCGCTGGAAT-CGCAATTGATT
66 AGCGCCGTTAATACCGATCTTTAGCGGCG-TTTTTAATTAGCGCCGC-GAAATCCACAATTGATC
* * * * *
34893174 AAAACCAAACGCTACATTTAGTTTTAACA
129 AAAATCGAACGATGCGTTTAGTTTTAACA
34893203 GACTCGGCGG
Statistics
Matches: 291, Mismatches: 49, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
189 33 0.11
190 68 0.23
191 39 0.13
193 2 0.01
194 4 0.01
196 3 0.01
204 100 0.34
205 42 0.14
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (194 bp):
AATGCCACTATACCTCACGGCCAAACGATGCGTTTTGGTTAACTTTTTGCGGCGTTTATTAGTTA
AGCGCCGTTAATACCGATCTTTAGCGGCGTTTTTAATTAGCGCCGCGAAATCCACAATTGATCAA
AATCGAACGATGCGTTTAGTTTTAACATATCTAGCGGCGATTCTTTAGGGCTAAAGCGCCGCTA
Found at i:34893196 original size:204 final size:204
Alignment explanation
Indices: 34892829--34893202 Score: 493
Period size: 204 Copynumber: 1.8 Consensus size: 204
34892819 ATTTTTAGGC
* ** * *
34892829 AAAGCGCCGCTAAATGCCACTATACCTCACGGCCAAACGATGCGTTTTGGTTAACTTTTTGCGGC
1 AAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAACGATGCGTTTTGGTTAACTTTCTGCGGC
* *
34892894 GTTTACTAGTTAAGCGTCGTTAATACCGATCTTTAGCGGCGTTTTTCAATTAGCGCCGTGAAATC
66 GTTTACTAGTTAAGCGCCGTTAATACCGATCTTTAGCAGCGTTTTTCAATTAGCGCCGTGAAATC
* * * * ***
34892959 CAGAATTTATCAAAATCGAACGTTGTGTTTAGTTTTAACATATTTTGCGGCGTTTTCTTTAGTGG
131 CA-AATTGATCAAAACCAAACGCTACATTTAGTTTTAACATATTTTGCGGCGTTTTCTTTAGTGG
34893024 CGTTTGGTTT
195 CGTTTGGTTT
34893034 AAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAA-GATGCGTTTTGGTTAACTTTCTGCGGC
1 AAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAACGATGCGTTTTGGTTAACTTTCTGCGGC
* * * * * * *
34893098 GTTTATTCGTTAAGCGCCGTTAATTCTGATCTTTCGCAGCGATTTTT-TATTAGCGCCGCTGGAA
66 GTTTACTAGTTAAGCGCCGTTAATACCGATCTTTAGCAGCG-TTTTTCAATTAGCGCCG-TGAAA
*
34893162 TCGC-AATTGATTAAAACCAAACGCTACATTTAGTTTTAACA
129 TC-CAAATTGATCAAAACCAAACGCTACATTTAGTTTTAACA
34893203 GACTCGGCGG
Statistics
Matches: 144, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
204 99 0.69
205 44 0.31
206 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (204 bp):
AAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAACGATGCGTTTTGGTTAACTTTCTGCGGC
GTTTACTAGTTAAGCGCCGTTAATACCGATCTTTAGCAGCGTTTTTCAATTAGCGCCGTGAAATC
CAAATTGATCAAAACCAAACGCTACATTTAGTTTTAACATATTTTGCGGCGTTTTCTTTAGTGGC
GTTTGGTTT
Found at i:34893426 original size:230 final size:226
Alignment explanation
Indices: 34893014--34893651 Score: 651
Period size: 230 Copynumber: 2.8 Consensus size: 226
34893004 TGCGGCGTTT
* * *
34893014 TCTTTAGTGGCGTTTGGTTTAAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAAGATGCGTT
1 TCTTTAGTGGCG-TTGGTTAAAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAAGATGCATT
* * *
34893079 TTGGTTAACTTTCTGCGGCGTTTATTCGTTAAGCGCCGTTAAT-TCTGATCTTTCGCAGCGATTT
65 TTGGTTAACTTTCTGAGGCGTTTA-TCGATAAGCGCCGTTAATATC-GATCTTTAGCAGCG-TTT
* * * * * * * * * *
34893143 TT-TATTAGCGCCGCTGGAA-TCGCAATTGATTAAAACCAAACGCTACATTTAGTTTTAACAGAC
127 TTATGTTAGCGCCGCT-AAAGCCACAATTGATCAACACCGAACACTGCGTTTAGTTTTAAC-GAC
* * *
34893206 -TCGGCGGCGTTTTAACGAAAACGAC-GTTAATGAAGA
190 TTCGGCGGCGCTATAACGAAAACG-CTGCTAATGAAGA
34893242 TCTTTAGTGGCGTTCAGGTTAAAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAACGATGCA
1 TCTTTAGTGGCGTT--GGTTAAAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAA-GATGCA
* * * *
34893307 TTTTGGTTAGCTTTCTGAGGCGTTTATCCGGTAAGCACCGTTAATATCGATTTTTAGCAGCGTTT
63 TTTTGGTTAACTTTCTGAGGCGTTTAT-CGATAAGCGCCGTTAATATCGATCTTTAGCAGCGTTT
* * **
34893372 TTATGTTTGCGCCGCTAAAGCCACAATTGATGAACACCGAACACTGCGTTTAGTTTTAACTTCTT
127 TTATGTTAGCGCCGCTAAAGCCACAATTGATCAACACCGAACACTGCGTTTAGTTTTAACGACTT
** *** *
34893437 TTGCGGCGCTATGGTGAAATCGCTGCTAATGAAGA
192 CGGCGGCGCTATAACGAAAACGCTGCTAATGAAGA
* * * *
34893472 TCTTTAGTGGCGTT-GTAACTAAAGCGCCGCTAAATGCCACTATACCTCGAGGCCAAATGATGCA
1 TCTTTAGTGGCGTTGGTTA--AAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAA-GATGCA
* * ** * * *
34893536 TTTTGGTTAAACTTTCTGTGGCATTTAGTATATAAGCGCCGTTAATACCGATCTTTGGCGGCGTT
63 TTTTGGTT-AACTTTCTGAGGCGTTTA-TCGATAAGCGCCGTTAATATCGATCTTTAGCAGCGTT
* * *
34893601 TCTA-GATTAGCGCCGCTAAAGCAACAATTGATCAACACCGAACCCTGCGTT
126 TTTATG-TTAGCGCCGCTAAAGCCACAATTGATCAACACCGAACACTGCGTT
34893652 CTGCTTTAAT
Statistics
Matches: 344, Mismatches: 52, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
227 5 0.01
228 12 0.03
229 99 0.29
230 225 0.65
231 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (226 bp):
TCTTTAGTGGCGTTGGTTAAAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAAGATGCATTT
TGGTTAACTTTCTGAGGCGTTTATCGATAAGCGCCGTTAATATCGATCTTTAGCAGCGTTTTTAT
GTTAGCGCCGCTAAAGCCACAATTGATCAACACCGAACACTGCGTTTAGTTTTAACGACTTCGGC
GGCGCTATAACGAAAACGCTGCTAATGAAGA
Found at i:34901823 original size:32 final size:32
Alignment explanation
Indices: 34901782--34901923 Score: 169
Period size: 32 Copynumber: 4.4 Consensus size: 32
34901772 TAGAGGAATA
*
34901782 TTGTTATCATTTAACAAAATTAAAGTTGATAT
1 TTGTTATCATTTCACAAAATTAAAGTTGATAT
* *
34901814 TTGTTATCATTTCACAAAATTAAAGTTGTTAA
1 TTGTTATCATTTCACAAAATTAAAGTTGATAT
* * * * *
34901846 TTGTTATTATTTCATAAAATTTAAGTCG-TAAC
1 TTGTTATCATTTCACAAAATTAAAGTTGAT-AT
* * *
34901878 TTGTTATTATTTCACAAAATGAAAGGTGATAT
1 TTGTTATCATTTCACAAAATTAAAGTTGATAT
34901910 TTGTTATCATTTCA
1 TTGTTATCATTTCA
34901924 TAGAACCGCG
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
31 1 0.01
32 91 0.98
33 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (32 bp):
TTGTTATCATTTCACAAAATTAAAGTTGATAT
Found at i:34904527 original size:23 final size:23
Alignment explanation
Indices: 34904496--34904546 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
34904486 ACCTACTTTC
* *
34904496 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
*
34904519 TTACAGTAGTAATTTTCGGTATA
1 TTACAGTAGTAATTTTCGGGATA
34904542 TTACA
1 TTACA
34904547 CTCACTATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:34905632 original size:20 final size:20
Alignment explanation
Indices: 34905604--34905643 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34905594 ATGTCAAGTT
*
34905604 TTTATTAACTAGT-TTAGCAA
1 TTTACTAAC-AGTGTTAGCAA
34905624 TTTACTAACAGTGTTAGCAA
1 TTTACTAACAGTGTTAGCAA
34905644 CAAGTACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (20 bp):
TTTACTAACAGTGTTAGCAA
Found at i:34905762 original size:63 final size:62
Alignment explanation
Indices: 34905647--34905765 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 62
34905637 TTAGCAACAA
* * * *
34905647 GTACCATAATAGAACACATATAGATAGTTTAGGTATCACATTGAATAATTTATGAATGTACAT
1 GTACAATAATAAAACACATATAGATAGTTTAAGTACCACATTGAAT-ATTTATGAATGTACAT
* *
34905710 GTACAATAATAAAACACATATTGATAGTTTAAGTACCATATTAGACAT-TTTATGAA
1 GTACAATAATAAAACACATATAGATAGTTTAAGTACCACATT-GA-ATATTTATGAA
34905766 AGTATAGGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 44 0.92
64 2 0.04
65 2 0.04
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (62 bp):
GTACAATAATAAAACACATATAGATAGTTTAAGTACCACATTGAATATTTATGAATGTACAT
Found at i:34906412 original size:20 final size:19
Alignment explanation
Indices: 34906384--34906443 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
34906374 ATAAAACCTT
*
34906384 AAAACATTTAAAAATTATAA
1 AAAATATTTAAAAA-TATAA
34906404 AAAATATTTAAAAA-ATCAA
1 AAAATATTTAAAAATAT-AA
34906423 AAAATATTTAAAAATATAA
1 AAAATATTTAAAAATATAA
34906442 AA
1 AA
34906444 TTAAAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 2 0.05
19 20 0.54
20 15 0.41
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATATTTAAAAATATAA
Found at i:34912408 original size:26 final size:26
Alignment explanation
Indices: 34912360--34912435 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
34912350 TCTTATCCCT
* *
34912360 ATTTTACCCCTAA-AAAATTTTTGACG
1 ATTTTACCCATAATAAAA-ATTTGACG
* *
34912386 ATTTTACCCTTAGTAAAAATTTGACG
1 ATTTTACCCATAATAAAAATTTGACG
* *
34912412 ATTTTGCCCATAATAAAATTTTGA
1 ATTTTACCCATAATAAAAATTTGA
34912436 GAAAATATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 38 0.90
27 4 0.10
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (26 bp):
ATTTTACCCATAATAAAAATTTGACG
Found at i:34916813 original size:25 final size:25
Alignment explanation
Indices: 34916785--34916876 Score: 120
Period size: 25 Copynumber: 3.8 Consensus size: 25
34916775 GTGTTATAAT
34916785 GTTCATGTTTTGGTTTCTGTATTAA
1 GTTCATGTTTTGGTTTCTGTATTAA
34916810 GTTCATGTTTTGGTTTCTGTATTAA
1 GTTCATGTTTTGGTTTCTGTATTAA
*
34916835 GTTGATG--TT--TTTCTGTATTAA
1 GTTCATGTTTTGGTTTCTGTATTAA
* *
34916856 GTTGATGTTTTCCGTTTCTGT
1 GTTCATGTTTT-GGTTTCTGT
34916877 TTATGGATTA
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
21 19 0.31
23 4 0.07
25 31 0.51
26 7 0.11
ACGTcount: A:0.14, C:0.09, G:0.21, T:0.57
Consensus pattern (25 bp):
GTTCATGTTTTGGTTTCTGTATTAA
Found at i:34916847 original size:21 final size:21
Alignment explanation
Indices: 34916798--34916866 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 21
34916788 CATGTTTTGG
*
34916798 TTTCTGTATTAAGTTCATGTTTT
1 TTTCTGTATTAAGTTGATG--TT
34916821 GGTTTCTGTATTAAGTTGATGTT
1 --TTTCTGTATTAAGTTGATGTT
34916844 TTTCTGTATTAAGTTGATGTT
1 TTTCTGTATTAAGTTGATGTT
34916865 TT
1 TT
34916867 CCGTTTCTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 23 0.53
23 2 0.05
25 18 0.42
ACGTcount: A:0.17, C:0.06, G:0.19, T:0.58
Consensus pattern (21 bp):
TTTCTGTATTAAGTTGATGTT
Found at i:34918042 original size:38 final size:38
Alignment explanation
Indices: 34918000--34918118 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 38
34917990 GCAATTGTTT
34918000 TTCAATTTACTAAATAATGCATTTGTTTATTTTTGTAA
1 TTCAATTTACTAAATAATGCATTTGTTTATTTTTGTAA
* * * * * *
34918038 TTCAA-GTA--AAGT-TTGGATTATTTTTTATTTTT-AATA
1 TTCAATTTACTAAATAATGCA-T-TTGTTTATTTTTGTA-A
34918074 TTCCAATTTACTAAATAATGCATTTGTTTATTTTTGTAA
1 TT-CAATTTACTAAATAATGCATTTGTTTATTTTTGTAA
34918113 TTCAAT
1 TTCAAT
34918119 AAAGTTTGGA
Statistics
Matches: 60, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
34 3 0.05
35 5 0.08
36 14 0.23
37 5 0.08
38 11 0.18
39 14 0.23
40 5 0.08
41 3 0.05
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (38 bp):
TTCAATTTACTAAATAATGCATTTGTTTATTTTTGTAA
Found at i:34918170 original size:73 final size:75
Alignment explanation
Indices: 34918002--34918174 Score: 323
Period size: 73 Copynumber: 2.3 Consensus size: 75
34917992 AATTGTTTTT
34918002 CAATTTACTAAATAATGCATTTGTTTATTTTTGTAATTCAAGTAAAGTTTGGATTATTTTTTATT
1 CAATTTACTAAATAATGCATTTGTTTATTTTTGTAATTCAAGTAAAGTTTGGATTATTTTTTATT
34918067 TTTAATATTC
66 TTTAATATTC
34918077 CAATTTACTAAATAATGCATTTGTTTATTTTTGTAATTCAA-TAAAGTTTGGA-TATTTTTTATT
1 CAATTTACTAAATAATGCATTTGTTTATTTTTGTAATTCAAGTAAAGTTTGGATTATTTTTTATT
34918140 TTTAATATTC
66 TTTAATATTC
*
34918150 CAATTTATTAAATAATGCATTTGTT
1 CAATTTACTAAATAATGCATTTGTT
34918175 AAAATAAAAA
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
73 45 0.46
74 11 0.11
75 41 0.42
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.53
Consensus pattern (75 bp):
CAATTTACTAAATAATGCATTTGTTTATTTTTGTAATTCAAGTAAAGTTTGGATTATTTTTTATT
TTTAATATTC
Found at i:34918263 original size:16 final size:16
Alignment explanation
Indices: 34918242--34918278 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
34918232 ATATTATATT
34918242 ATATTTTTTATTTTTA
1 ATATTTTTTATTTTTA
34918258 ATATTTTTTATTTTTA
1 ATATTTTTTATTTTTA
34918274 ATATT
1 ATATT
34918279 CCAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATATTTTTTATTTTTA
Found at i:34920676 original size:49 final size:49
Alignment explanation
Indices: 34920619--34920722 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
34920609 TCATGTGTTA
* *
34920619 TAATTTTATAAAGTGTTGA-TATTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACT-TTTTGATTCATGATATTAAACTTAATTT
34920668 TAATTTTATAAAGTGTTCACTTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACTTTTTGATTCATGATATTAAACTTAATTT
34920717 TAATTT
1 TAATTT
34920723 GTTTTTTTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 51 0.98
50 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACTTTTTGATTCATGATATTAAACTTAATTT
Found at i:34922197 original size:17 final size:17
Alignment explanation
Indices: 34922177--34922210 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34922167 AATATTAAGA
34922177 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
34922194 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
34922211 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:34922382 original size:120 final size:120
Alignment explanation
Indices: 34922108--34923029 Score: 1554
Period size: 120 Copynumber: 7.7 Consensus size: 120
34922098 AAGTAGATTA
* *
34922108 TAAATTATATTTTATAATATTATATATTATGATTTTAGTAAATACATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
34922173 AAGAATTTTATTAAATTATATA-TTTTATTAAATTATATTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* *
34922227 TAGATTATATTTTATAGTATTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
34922292 AAGAATTTTATTAAATTATATATTTTTAATAAATTATATTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
34922347 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
34922412 AAGAATTTTATTAAATTAGATATTTTTATTAAATTATATTTAA-AATAATTAATT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
*
34922466 TAAGTTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
34922528 AAGAATTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTT
34922585 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* * *
34922647 AATAATTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATTATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTT
* * *
34922704 TAAATTATATTTTATAGTATTATATATTATGATTTTATTATATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
34922769 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATCTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
*
34922824 TAAATTATATTTTATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
34922889 AAGAATTTTATTAAATTTTATATTTTTATTAAATTATATTTAATAATAATTATGT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* * *
34922944 TAAATTATATTTTATAGTATTATATTTTATGATTTTAGAAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
34923009 AAGAATTTTATTAAATTATAT
66 AAGAATTTTATTAAATTATAT
34923030 TTAAAAATAA
Statistics
Matches: 763, Mismatches: 33, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
116 53 0.07
118 5 0.01
119 306 0.40
120 346 0.45
122 53 0.07
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
Found at i:34922554 original size:18 final size:17
Alignment explanation
Indices: 34922533--34922570 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
34922523 ATATTAAGAA
*
34922533 TTTTATTAAATTATATAT
1 TTTTACTAAATTATAT-T
34922551 TTTTACTAAATTATATT
1 TTTTACTAAATTATATT
34922568 TTT
1 TTT
34922571 AATAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTACTAAATTATATT
Found at i:34922673 original size:18 final size:18
Alignment explanation
Indices: 34922639--34922689 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
34922629 CTAAGAATAT
*
34922639 TTAATATTA-ATAATTTTA
1 TTAA-ATTATATATTTTTA
34922657 TTAAATTATATATTTTTA
1 TTAAATTATATATTTTTA
*
34922675 CTAAATTATAT-TTTT
1 TTAAATTATATATTTT
34922690 AATAATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATTATATATTTTTA
Found at i:34922696 original size:15 final size:15
Alignment explanation
Indices: 34922665--34922716 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
34922655 TATTAAATTA
*
34922665 TATATTTTTACTAAAT
1 TATATTTTTAAT-AAT
34922681 TATATTTTTAATAAT
1 TATATTTTTAATAAT
34922696 TAT-TATTTT-A-AAT
1 TATAT-TTTTAATAAT
34922709 TATATTTT
1 TATATTTT
34922717 ATAGTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 9 0.27
14 3 0.09
15 10 0.30
16 11 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTTTTAATAAT
Found at i:34922700 original size:18 final size:18
Alignment explanation
Indices: 34922660--34922701 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
34922650 AATTTTATTA
*
34922660 AATTA-TATATTTTTACT
1 AATTATTATATTTTTAAT
34922677 AA--ATTATATTTTTAAT
1 AATTATTATATTTTTAAT
34922693 AATTATTAT
1 AATTATTAT
34922702 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 2 0.10
18 5 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTATTATATTTTTAAT
Found at i:34922725 original size:28 final size:29
Alignment explanation
Indices: 34922676--34922731 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
34922666 ATATTTTTAC
34922676 TAAATTATATTTTTAATAATTAT-TATTT
1 TAAATTATATTTTTAATAATTATATATTT
*
34922704 TAAATTATATTTTATAGT-ATTATATATT
1 TAAATTATATTTT-TAATAATTATATATT
34922732 ATGATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TAAATTATATTTTTAATAATTATATATTT
Found at i:34922927 original size:16 final size:17
Alignment explanation
Indices: 34922894--34922929 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
34922884 ATATTAAGAA
34922894 TTTTATTAAATTTTATAT
1 TTTTATTAAA-TTTATAT
34922912 TTTTATTAAA-TTATAT
1 TTTTATTAAATTTATAT
34922928 TT
1 TT
34922930 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTAAATTTATAT
Found at i:34923022 original size:102 final size:99
Alignment explanation
Indices: 34922912--34923128 Score: 355
Period size: 102 Copynumber: 2.2 Consensus size: 99
34922902 AATTTTATAT
* *
34922912 TTTTATTAAATTATATTTAATAATAATT-ATGTTAAATTATATTTTATAGTATTATATTTTATGA
1 TTTTATTAAATTATATTTAAAAATAATTAAT-TTAAATTATATTTTATAGTATTATATATTATGA
34922976 TTTTAGAAAATTCATTTAAGAATATTTAATATTAAGAA
65 TTTTAGAAAATTC---TAAGAATATTTAATATTAAGAA
*
34923014 TTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATATTTTATAGTATTCTATATTATGAT
1 TTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATATTTTATAGTATTATATATTATGAT
*
34923079 TTTAGTAAATTCTAAGAATATTTAATATTAAGAA
66 TTTAGAAAATTCTAAGAATATTTAATATTAAGAA
34923113 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
34923129 ATTTTTACTA
Statistics
Matches: 110, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
99 38 0.35
102 70 0.64
103 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (99 bp):
TTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATATTTTATAGTATTATATATTATGAT
TTTAGAAAATTCTAAGAATATTTAATATTAAGAA
Found at i:34923279 original size:460 final size:468
Alignment explanation
Indices: 34922108--34923407 Score: 2144
Period size: 477 Copynumber: 2.8 Consensus size: 468
34922098 AAGTAGATTA
* *
34922108 TAAATTATATTTTATAATATTATATATTATGATTTTAGTAAATACATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAAT---TCTAAGAATATTTAATATT
* *
34922173 AAGAATTTTATTAAATTATATA-TTTTATTAAATTATA-TTTAATAATAATTATTTTAGATTATA
63 AAGAATTTTATTAAATTATATATTTTTACTAAATTATATTTTAATAATAATTATTTTAAATTATA
* * *
34922236 TTTTATAGTATTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAGAATTTT
128 TTTTATAGTATTATATATTATGATTTTATTATATTCATTTAAGAATATTTAATATTAAGAATTTT
*
34922301 ATTAAATTATATATTTTTAATAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
193 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
*
34922366 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTAG
258 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTAT
*
34922431 ATATTTTTATTAAATTATATTTAA-AATAATTAAT-TTAAGTTATATTTTATAGTATTATATATT
323 ATATTTTTATTAAATTATATTTAATAATAATT-ATGTTAAATTATATTTTATAGTATTATATATT
*
34922494 ATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTACTA
387 ATGATTTTAGAAAATTCTAAGAATATTTAATATTAAGAATTTTATTAAATTATATA--TTTA-TA
34922559 AATTATATTTTTAATAATAATTATTT
449 AA-TATA---TTAAT-ATAA-TATTT
*
34922585 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAG
*
34922650 AATTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATTATTATTTTAAATTATATT
66 AATTTTATTAAATTATATATTTTTACTAAATTATA-TTTTAATAATAATTATTTTAAATTATATT
34922715 TTATAGTATTATATATTATGATTTTATTATATTCATTTAAGAATATTTAATATTAAGAATTTTAT
130 TTATAGTATTATATATTATGATTTTATTATATTCATTTAAGAATATTTAATATTAAGAATTTTAT
*
34922780 TAAATTATATATTTTTATTAAATTATATCTAATAATAATTATTTTAAATTATATTTTATAGTATT
195 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
* *
34922845 ATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTTTAT
260 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
*
34922910 ATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATTTTATG
325 ATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATG
34922975 ATTTTAGAAAATTCATTTAAGAATATTTAATATTAAGAATTTTATTAAA-T-TATA-TT-TAAA-
390 ATTTTAGAAAATTC---TAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTATAAAT
34923035 A-A-TAAT-T-A-A-TT
452 ATATTAATATAATATTT
*
34923046 TAAATTATATTTTATAGTATTCTATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAG
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAG
*
34923111 AATTTTATTAAATTATATATTTTTACTAAATTATATTTTAATAATAATTAATTTAAATTATATTT
66 AATTTTATTAAATTATATATTTTTACTAAATTATATTTTAATAATAATTATTTTAAATTATATTT
34923176 TATAGTATTATATATTATGATTTTATTATATTCATTTAAGAATATTTAATATTAAGAATTTTATT
131 TATAGTATTATATATTATGATTTTATTATATTCATTTAAGAATATTTAATATTAAGAATTTTATT
*
34923241 AAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTA
196 AAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
* *
34923306 TATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATCAAGAATTTTATTAAATTATATA
261 TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
34923371 TTTTTATTAAATTATATTTAATAATAATTATGTTAAA
326 TTTTTATTAAATTATATTTAATAATAATTATGTTAAA
34923408 ATATGATAAA
Statistics
Matches: 788, Mismatches: 27, Indels: 33
0.93 0.03 0.04
Matches are distributed among these distances:
460 254 0.32
461 100 0.13
462 1 0.00
464 1 0.00
465 1 0.00
467 4 0.01
471 1 0.00
472 1 0.00
474 43 0.05
475 14 0.02
476 2 0.00
477 279 0.35
478 50 0.06
479 4 0.01
480 1 0.00
481 32 0.04
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (468 bp):
TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTACTAAATTATATTTTAATAATAATTATTTTAAATTATATTT
TATAGTATTATATATTATGATTTTATTATATTCATTTAAGAATATTTAATATTAAGAATTTTATT
AAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATA
TTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGA
TTTTAGAAAATTCTAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTATAAATATAT
TAATATAATATTT
Found at i:34923407 original size:120 final size:119
Alignment explanation
Indices: 34923014--34923400 Score: 654
Period size: 120 Copynumber: 3.2 Consensus size: 119
34923004 ATATTAAGAA
* *
34923014 TTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATATTTTATAGTATTCTATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTAATTTAAATTATATTTTATAGTATTATATATTATGAT
34923079 TTTAGTAAATTC--TAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
66 TTTAGTAAATTCATTAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
*
34923131 TTTTACTAAATTATATTTTAATAATAATTAATTTAAATTATATTTTATAGTATTATATATTATGA
1 TTTTATTAAATTATA-TTTAATAATAATTAATTTAAATTATATTTTATAGTATTATATATTATGA
* *
34923196 TTTTATTATATTCATTTAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
65 TTTTAGTAAATTCA-TTAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
34923252 TTTTATTAAATTATATTTAATAATAATT-ATGTTAAATTATATTTTATAGTATTATATATTATGA
1 TTTTATTAAATTATATTTAATAATAATTAAT-TTAAATTATATTTTATAGTATTATATATTATGA
* *
34923316 TTTTAGAAAATTCATATAAGAATATTTAATATCAAGAATTTTATTAAATTATATAT
65 TTTTAGTAAATTCAT-TAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
34923372 TTTTATTAAATTATATTTAATAATAATTA
1 TTTTATTAAATTATATTTAATAATAATTA
34923401 TGTTAAAATA
Statistics
Matches: 253, Mismatches: 10, Indels: 10
0.93 0.04 0.04
Matches are distributed among these distances:
117 14 0.06
118 58 0.23
119 3 0.01
120 124 0.49
121 54 0.21
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (119 bp):
TTTTATTAAATTATATTTAATAATAATTAATTTAAATTATATTTTATAGTATTATATATTATGAT
TTTAGTAAATTCATTAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
Found at i:34923603 original size:16 final size:16
Alignment explanation
Indices: 34923581--34923643 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
34923571 ACTATTACGC
34923581 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
* * *
34923597 CTATATTCTATTACAC
1 CTCTATTCCATTACAG
34923613 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
34923629 CTCTATTCCATTACA
1 CTCTATTCCATTACA
34923644 ACGAATCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.40
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:34923616 original size:32 final size:32
Alignment explanation
Indices: 34923572--34923643 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
34923562 CACAAGAATA
*
34923572 CTATTACGCCTCTATTCCATTACAGCTATATT
1 CTATTACACCTCTATTCCATTACAGCTATATT
*
34923604 CTATTACACCTCTATTCCATTACAGCTCTATT
1 CTATTACACCTCTATTCCATTACAGCTATATT
*
34923636 CCATTACA
1 CTATTACA
34923644 ACGAATCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.26, C:0.31, G:0.04, T:0.39
Consensus pattern (32 bp):
CTATTACACCTCTATTCCATTACAGCTATATT
Found at i:34932758 original size:22 final size:23
Alignment explanation
Indices: 34932705--34932758 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
34932695 GAAATTCTAA
* **
34932705 AAAAAGAAATATGAAATATATTG
1 AAAAAGAAATATGAAATAAAAAG
* *
34932728 TAAAGGAAATAT-AAATAAAAAG
1 AAAAAGAAATATGAAATAAAAAG
34932750 AAAAAGAAA
1 AAAAAGAAA
34932759 AAGTGTTGAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.19
Consensus pattern (23 bp):
AAAAAGAAATATGAAATAAAAAG
Found at i:34934862 original size:17 final size:20
Alignment explanation
Indices: 34934826--34934864 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
34934816 ACGCAAGTTC
34934826 TTTTAGCCTAGATCCAATTA
1 TTTTAGCCTAGATCCAATTA
34934846 TTTTA-CCTA-AT-CAATTA
1 TTTTAGCCTAGATCCAATTA
34934863 TT
1 TT
34934865 GATGTAGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 4 0.21
20 5 0.26
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (20 bp):
TTTTAGCCTAGATCCAATTA
Found at i:34943845 original size:12 final size:12
Alignment explanation
Indices: 34943830--34943867 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
34943820 ACTAATAGTT
*
34943830 ATAATAACATTA
1 ATAATAACAATA
34943842 ATAATAACAATA
1 ATAATAACAATA
34943854 ATAATGAA-AATA
1 ATAAT-AACAATA
34943866 AT
1 AT
34943868 TGAGTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 22 0.92
13 2 0.08
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (12 bp):
ATAATAACAATA
Found at i:34945396 original size:43 final size:43
Alignment explanation
Indices: 34945349--34945490 Score: 115
Period size: 43 Copynumber: 3.2 Consensus size: 43
34945339 TGCTGCTCAC
*
34945349 GGAGACAAGACTGAGGTCTTCGATCTGCTCCACTACTGCTTAG
1 GGAGACAAGACTGAGGTCTTCAATCTGCTCCACTACTGCTTAG
* ** * * * * **
34945392 GGAGATAAGAGCTGTAATTTTTTTAACCTACTCCACTGTTGCTCT-G
1 GGAGACAAGA-CTG--AGGTCTTCAATCTGCTCCACTACTGCT-TAG
* * *
34945438 GGAGACAAGGCTGGGGTCTTCAATATGCTCCACTACTGCTTAG
1 GGAGACAAGACTGAGGTCTTCAATCTGCTCCACTACTGCTTAG
*
34945481 GGAGATAAGA
1 GGAGACAAGA
34945491 TCTGTAATTT
Statistics
Matches: 70, Mismatches: 24, Indels: 10
0.67 0.23 0.10
Matches are distributed among these distances:
42 1 0.01
43 35 0.50
44 3 0.04
45 3 0.04
46 27 0.39
47 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (43 bp):
GGAGACAAGACTGAGGTCTTCAATCTGCTCCACTACTGCTTAG
Found at i:34945478 original size:89 final size:87
Alignment explanation
Indices: 34945311--34945520 Score: 294
Period size: 89 Copynumber: 2.4 Consensus size: 87
34945301 ACAGGAAGAC
* * * * * *
34945311 AAGATCTGTTATTTTCAACCTACTCCATTGCTGCTCACGGAGACAAGACTGAGGTCTTCGATCTG
1 AAGAGCTGTAATTTTCAACCTACTCCACTGTTGCTCACGGAGACAAGACTGAGGTCTTCAATATG
34945376 CTCCACTACTGCTTAGGGAGAT
66 CTCCACTACTGCTTAGGGAGAT
* ** * *
34945398 AAGAGCTGTAATTTTTTTAACCTACTCCACTGTTGCTCTGGGAGACAAGGCTGGGGTCTTCAATA
1 AAGAGCTGTAA--TTTTCAACCTACTCCACTGTTGCTCACGGAGACAAGACTGAGGTCTTCAATA
34945463 TGCTCCACTACTGCTTAGGGAGAT
64 TGCTCCACTACTGCTTAGGGAGAT
*
34945487 AAGATCTGTAATTTTCAACCTACTCCACTGTTGC
1 AAGAGCTGTAATTTTCAACCTACTCCACTGTTGC
34945521 ATAGGGAGAT
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
87 31 0.29
89 77 0.71
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (87 bp):
AAGAGCTGTAATTTTCAACCTACTCCACTGTTGCTCACGGAGACAAGACTGAGGTCTTCAATATG
CTCCACTACTGCTTAGGGAGAT
Found at i:34945544 original size:44 final size:44
Alignment explanation
Indices: 34945523--34946726 Score: 1640
Period size: 44 Copynumber: 27.4 Consensus size: 44
34945513 ACTGTTGCAT
* * * ** *
34945523 AGGGAGATAGGACTTACAATTTTTTGCCTATTCCACTGCCGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
*
34945567 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTAGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * *
34945611 AAGGAGCTAGGATTTACAATCTTCCGCCTATTCCATTACTGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* *
34945655 AGGGAGCTAGGATTTACAATCTTCCTCCTATTCCACTGCTAGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
*
34945699 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* *
34945743 AGGGAGCTAGGATTTACAATCTTTCACCTATTCCACTGCTGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* ** *
34945787 AGGGAGCTAGGATTTACAACCTTCCGCCTATTCCACTATTGTTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * *
34945831 AGGGAGCTAGGATTTACAATCTTTCACCTATTCCACTGCTGCTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* **
34945875 AGGGAGCTAGGATTTACAATCTTTCGCCTATTCCACTGCTATTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* ** *
34945919 AGGGAGCTAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * * * * *
34945963 AGGGAGCTAGAACTTACAGTCTTCCACCTATTCCATTGCTGTTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
*
34946007 AGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
*
34946051 AGGGAGCTAGGATTTACAATCTTCTGCCTATTCCACTGCTGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* *
34946095 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGTTGTTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
34946139 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * * *
34946183 AGGGAGCTAGGATTTACAATCTTCTGCCTATTCTACTGTTGTTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* ** * *
34946227 AGGGAGCTAGGACTTACAATCTTCAACCTATTCCACTGCTGTTG
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * * *
34946271 AGGGATCTAGGACTTACAATCTTCCACCTATTCCACTGCCGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
34946315 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * *
34946359 AAGGAGCTAGGATTTACAATCTTCTGCCTATTCCACTGCTGTTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * * *
34946403 AGAGATCTAGGATTTACAATCTTCCACCTATTCCACTACTGGTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * *
34946447 AGGGAGCTAGAATTTACAATCTTCCACCTATTCCACTGCTGTTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * *
34946491 AGGGAGCTAGAACTTT-CAGTCTTCCACCTATTCCACTGCTGGTC
1 AGGGAGCTAGGA-TTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * *
34946535 AGGGAGCTAGTATTTACAATCTTCCGCCTATTCCACTACTGTTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * * *
34946579 AGGAAGCTAGGACTTT-TAGTCTTCCACCTATTCCACTGCTGGTC
1 AGGGAGCTAGGA-TTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * **
34946623 AGGAAGCTAGGATTTACAATCTTCTGCCTATTCCACTGCTATTC
1 AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
* * *
34946667 AGGGAGCTAGGACTTT-CAGTCTTCCACCTATTCCACTGCTGTTC
1 AGGGAGCTAGGA-TTTACAATCTTCCGCCTATTCCACTGCTGGTC
*
34946711 AGGGAGCTAAGATTTA
1 AGGGAGCTAGGATTTA
34946727 TAGTTTCACC
Statistics
Matches: 1032, Mismatches: 122, Indels: 12
0.89 0.10 0.01
Matches are distributed among these distances:
43 9 0.01
44 1014 0.98
45 9 0.01
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (44 bp):
AGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGGTC
Found at i:34948079 original size:46 final size:45
Alignment explanation
Indices: 34948021--34948109 Score: 133
Period size: 46 Copynumber: 2.0 Consensus size: 45
34948011 TCATTTTTTA
* *
34948021 TTTTTTTGACTCAAAGTGCCCTTTGAGGGTTTTCACTTTGATCTT
1 TTTTTTTGACTCAAAGCGCCCTTTGAGGGTTTTCACCTTGATCTT
* *
34948066 TTTTTTTGGACTCAAAGCGCTCTTTGTGGGTTTTCACCTTGATC
1 TTTTTTT-GACTCAAAGCGCCCTTTGAGGGTTTTCACCTTGATC
34948110 CTTTCTCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 7 0.18
46 32 0.82
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (45 bp):
TTTTTTTGACTCAAAGCGCCCTTTGAGGGTTTTCACCTTGATCTT
Found at i:34953460 original size:12 final size:12
Alignment explanation
Indices: 34953445--34953482 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
34953435 ACTAATAGTT
*
34953445 ATAATAACATTA
1 ATAATAACAATA
34953457 ATAATAACAATA
1 ATAATAACAATA
34953469 ATAATGAA-AATA
1 ATAAT-AACAATA
34953481 AT
1 AT
34953483 TGAGTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 22 0.92
13 2 0.08
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (12 bp):
ATAATAACAATA
Found at i:34958218 original size:41 final size:39
Alignment explanation
Indices: 34958165--34958271 Score: 110
Period size: 41 Copynumber: 2.7 Consensus size: 39
34958155 TATATTAGTC
34958165 TAAATAAGTAATATATATAAAATGAAAAGTTTAATAATAATA
1 TAAATAA-TAATATATATAAAAT-AAAAGTTTAATAA-AATA
* * *
34958207 TAAATAATAATATATAATGATATAAAAGTTTAATAACATA
1 TAAATAATAATATAT-ATAAAATAAAAGTTTAATAAAATA
* *
34958247 T-AATAAT-ATGTATAAAAAATCAAAA
1 TAAATAATAATATATATAAAAT-AAAA
34958272 TAAAATAGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
37 4 0.07
38 9 0.16
39 6 0.11
40 4 0.07
41 21 0.38
42 12 0.21
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (39 bp):
TAAATAATAATATATATAAAATAAAAGTTTAATAAAATA
Found at i:34964774 original size:45 final size:45
Alignment explanation
Indices: 34964702--34964887 Score: 293
Period size: 45 Copynumber: 4.1 Consensus size: 45
34964692 TGGTAGTCCT
* * *
34964702 ACTGCTCGTAGGCTT-AATGAAATGAGAGGTGAATGTACCAGCCCC
1 ACTGCTCGTAAG-TTGAATGAATTGAGAGCTGAATGTACCAGCCCC
* *
34964747 ACAGCTCGTAAGTTGAATGAATGGAGAGCTGAATGTACCAGCCCC
1 ACTGCTCGTAAGTTGAATGAATTGAGAGCTGAATGTACCAGCCCC
*
34964792 ACTGCTCGTAAGTTGAATGAATTGAGAGCTGAATGTACCGGCCCC
1 ACTGCTCGTAAGTTGAATGAATTGAGAGCTGAATGTACCAGCCCC
*
34964837 ACTGCTCGTAGGTTGAATGAATTGAGAGCTGAATGTACCAGCCCC
1 ACTGCTCGTAAGTTGAATGAATTGAGAGCTGAATGTACCAGCCCC
34964882 ACTGCT
1 ACTGCT
34964888 TGTAGTCTTA
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
44 2 0.02
45 128 0.98
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (45 bp):
ACTGCTCGTAAGTTGAATGAATTGAGAGCTGAATGTACCAGCCCC
Found at i:34972578 original size:24 final size:24
Alignment explanation
Indices: 34972563--34972614 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
34972553 AATCAAAGTC
34972563 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
34972587 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
34972611 AAAT
1 AAAT
34972615 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:34976340 original size:137 final size:135
Alignment explanation
Indices: 34976043--34976462 Score: 531
Period size: 138 Copynumber: 3.1 Consensus size: 135
34976033 ATAACATAGG
*
34976043 TATAATTAATATATGAGTTTGATTCATACAAAATATCAATTGTATATATTTTA-TCGAATTTATT
1 TATAATTAATATATGAATTTGATTCATACAAAATAT-AATTGTATATATTTTACT-GAATTTATT
* * * *
34976107 AATATAAA-ACGTTATATTAATTAATTTCAGTCAAAATATAAAAGAAATAGAAATTAATATTTTT
64 AATATAAACA-ATTATATTAA-TAATTTCAGTCAAAATATTAAA-AAATGGAAATTAATATTATT
*
34976171 TTGGAAAAAA
126 TTGGAAAGAA
* * * * * *
34976181 TACAATTAATATATGGATTTGATTCATACAAAATACTAGTTGTATATAGTTTACTAAATTAATTA
1 TATAATTAATATATGAATTTGATTCATACAAAATA-TAATTGTATATATTTTACTGAATTTATTA
* * *
34976246 ATATAAACATTTATATTAATAATTTCGGTCAAAATATTTAAAAAATGGAAATTAATATTATTTTA
65 ATATAAACAATTATATTAATAATTTCAGTCAAAATA-TTAAAAAATGGAAATTAATATTATTTTG
*
34976311 GAAAGAG
129 GAAAGAA
*
34976318 TATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTA
1 TATAATTAATATATGAATTTGATTCATACAAAATA-TAATTGTATATATTTTACTGAATTTATTA
* * * *
34976383 ATATAAACAATTATATTAAATAATTTCAATCAAAATA-TAAAAGATATGAAAATTAATATTCTGT
65 ATATAAACAATTATATT-AATAATTTCAGTCAAAATATTAAAA-A-ATGGAAATTAATATTATTT
34976447 TGGAAAGAA
127 TGGAAAGAA
34976456 TATAATT
1 TATAATT
34976463 TTTTTTTAAC
Statistics
Matches: 244, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
136 5 0.02
137 115 0.47
138 121 0.50
139 3 0.01
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (135 bp):
TATAATTAATATATGAATTTGATTCATACAAAATATAATTGTATATATTTTACTGAATTTATTAA
TATAAACAATTATATTAATAATTTCAGTCAAAATATTAAAAAATGGAAATTAATATTATTTTGGA
AAGAA
Found at i:34977635 original size:17 final size:17
Alignment explanation
Indices: 34977613--34977649 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
34977603 GTTGAGATAA
34977613 AAATAAATAACG-AAAAT
1 AAATAAATAA-GAAAAAT
34977630 AAATAAATAAGAAAAAT
1 AAATAAATAAGAAAAAT
34977647 AAA
1 AAA
34977650 CAGACGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
AAATAAATAAGAAAAAT
Found at i:34979276 original size:3 final size:3
Alignment explanation
Indices: 34979270--34979316 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
34979260 GATGAAAATT
* *
34979270 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG ATG TTA TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
34979317 TATATATGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.04, C:0.00, G:0.30, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:34980821 original size:38 final size:38
Alignment explanation
Indices: 34980778--34980894 Score: 157
Period size: 38 Copynumber: 3.1 Consensus size: 38
34980768 TGAATTATAT
* * *
34980778 TGTTATTCAGGTTTTGTACCTAGTAGGCTTTGTGCCGG
1 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGG
*
34980816 TGTTATTCAGGCTTCGTGCCTAGCAGGCTTAT-TGCCGG
1 TGTTATTCAGGCTTTGTGCCTAGCAGGCTT-TGTGCCGG
*
34980854 TGTTATTCAGGCTTTGTGCCCAGCAGG-TTTAGTGCCGG
1 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTT-GTGCCGG
34980892 TGT
1 TGT
34980895 ATTAAAAGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
36 1 0.01
37 2 0.03
38 66 0.94
39 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.30, T:0.38
Consensus pattern (38 bp):
TGTTATTCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGG
Found at i:34980873 original size:22 final size:22
Alignment explanation
Indices: 34980802--34980873 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
34980792 TGTACCTAGT
34980802 AGGCTTTGTGCCGGTGTTATTC
1 AGGCTTTGTGCCGGTGTTATTC
* *
34980824 AGGCTTCGTGCC-----TA-GC
1 AGGCTTTGTGCCGGTGTTATTC
34980840 AGGCTTAT-TGCCGGTGTTATTC
1 AGGCTT-TGTGCCGGTGTTATTC
34980862 AGGCTTTGTGCC
1 AGGCTTTGTGCC
34980874 CAGCAGGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
16 11 0.29
17 2 0.05
21 3 0.08
22 22 0.58
ACGTcount: A:0.11, C:0.22, G:0.31, T:0.36
Consensus pattern (22 bp):
AGGCTTTGTGCCGGTGTTATTC
Found at i:34986769 original size:21 final size:20
Alignment explanation
Indices: 34986741--34986782 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
34986731 TTTCCACAAT
34986741 TGATTTTAATCTTATCATTA
1 TGATTTTAATCTTATCATTA
* *
34986761 TGATATTTAATTTTATTATTA
1 TGAT-TTTAATCTTATCATTA
34986782 T
1 T
34986783 ATTAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TGATTTTAATCTTATCATTA
Found at i:34994394 original size:15 final size:15
Alignment explanation
Indices: 34994374--34994403 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34994364 TGAACAACTG
34994374 CATAAATTATATATA
1 CATAAATTATATATA
*
34994389 CATAAATTGTATATA
1 CATAAATTATATATA
34994404 AACACCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (15 bp):
CATAAATTATATATA
Found at i:34997627 original size:19 final size:19
Alignment explanation
Indices: 34997599--34997652 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
34997589 AATCTTCGAG
34997599 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
34997618 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
34997637 GATATATAATCTTAGA
1 GATATACAATCTTAGA
34997653 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:34998225 original size:35 final size:35
Alignment explanation
Indices: 34998156--34998225 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
34998146 TTACAGTTCA
**
34998156 AATTAGTTTTTTTTCATTTTCTTTATTTTTTTATT
1 AATTAGTTTTTTTTCATTTTCTTTATTTAGTTATT
34998191 AATTAGTTTTTTATTC-TTTT-TTATATTTAGTTATT
1 AATTAGTTTTTT-TTCATTTTCTT-TATTTAGTTATT
34998226 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 2 0.06
35 26 0.84
36 3 0.10
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (35 bp):
AATTAGTTTTTTTTCATTTTCTTTATTTAGTTATT
Found at i:34998347 original size:26 final size:26
Alignment explanation
Indices: 34998282--34998350 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
34998272 TTTTTTGTAG
*
34998282 TATA-ATATAATTATTTTTTTATTTA
1 TATATATATAATTATTTTTTTATCTA
* *
34998307 TTTATATGTAATTATTTTTTTATCTA
1 TATATATATAATTATTTTTTTATCTA
* *
34998333 TATGTATATATTTATTTT
1 TATATATATAATTATTTT
34998351 AGTATACATA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 3 0.08
26 33 0.92
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.65
Consensus pattern (26 bp):
TATATATATAATTATTTTTTTATCTA
Found at i:34998356 original size:22 final size:22
Alignment explanation
Indices: 34998298--34998351 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
34998288 ATAATTATTT
*
34998298 TTTTATTTATTTATATGTAATTA
1 TTTT-TTTATCTATATGTAATTA
34998321 TTTTTTTATCTATATGT-ATATA
1 TTTTTTTATCTATATGTAAT-TA
34998343 TTTATTTTA
1 TTT-TTTTA
34998352 GTATACATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 17 0.61
23 9 0.32
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTTTATCTATATGTAATTA
Found at i:35005790 original size:44 final size:44
Alignment explanation
Indices: 35005701--35006231 Score: 457
Period size: 44 Copynumber: 12.1 Consensus size: 44
35005691 TCAGATCAGT
* * * * *
35005701 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAGGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
35005745 GAAGATGCAGATCTTATCTTCCCATATTGGTGGCGGAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * *
35005789 GAAGATGTAGATCTTATCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
35005832 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* *
35005877 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * ***
35005921 GAAGAAAGAAGATCTTGTCTTCATGTATTGG-CATGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * *
35005965 AAAGATAGCAGGTCATATCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
35006009 GAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
35006053 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * *
35006097 GAAAATAACAGGTCATGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* *
35006141 GAAGATGCAGATCTTGTCTTACC-ATACTGGTGGCAAAGTAGATC
1 GAAGATGCAGATCTTGTCTT-CCTATATTGGTGGCGAAGTAGATC
* * * * *
35006185 GAAGAAAGCAGATCTTGTCTTCATTTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
35006229 GAA
1 GAA
35006232 AATAGCAGGT
Statistics
Matches: 386, Mismatches: 87, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
43 81 0.21
44 228 0.59
45 77 0.20
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (44 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
Found at i:35006003 original size:132 final size:133
Alignment explanation
Indices: 35005702--35006242 Score: 876
Period size: 132 Copynumber: 4.1 Consensus size: 133
35005692 CAGATCAGTG
* *
35005702 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAGGTGGATCGAAGATGCAGATCTTATCTTCC
1 AAGATAGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCC
* * * * *
35005767 CATATTGGTGGCGGAGTAGATCGAAG-ATGTAGATCTTATCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
35005831 CG-
131 CGA
* * *
35005833 AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 AAGATAGCAGGTCATGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTATCTTC
* *
35005898 CCATACTGGTGGCGAAGTAGATCGAAGAAAGAAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
65 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
35005963 TC-A
130 TCGA
*
35005966 AAGATAGCAGGTCATATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCC
1 AAGATAGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCC
35006031 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
35006096 CGA
131 CGA
* * *
35006099 AA-ATAACAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTAC
1 AAGATAGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCC
* *
35006163 CATACTGGTGGCAAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
35006228 CGA
131 CGA
35006231 AA-ATAGCAGGTC
1 AAGATAGCAGGTC
35006243 TTACCTTCCT
Statistics
Matches: 384, Mismatches: 22, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
131 32 0.08
132 284 0.74
133 68 0.18
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (133 bp):
AAGATAGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCC
CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
CGA
Found at i:35006964 original size:21 final size:21
Alignment explanation
Indices: 35006939--35006993 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
35006929 ATCTTCGAGG
35006939 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
35006960 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
35006981 ATAT--AATCTTAGA
1 ATATGCAATCTTAGA
35006994 AGATATGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.26
21 25 0.74
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:35007550 original size:24 final size:24
Alignment explanation
Indices: 35007517--35007573 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
35007507 TTTTTTTTCA
35007517 TTTTCTTTATT-TTTTTATTAATTAG
1 TTTT-TTTATTCTTTTTA-TAATTAG
*
35007542 TTTTTTTATTCTTTTTATATTTAG
1 TTTTTTTATTCTTTTTATAATTAG
35007566 TTATTTTT
1 TT-TTTTT
35007574 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTTTATTCTTTTTATAATTAG
Found at i:35007712 original size:35 final size:38
Alignment explanation
Indices: 35007657--35007749 Score: 120
Period size: 41 Copynumber: 2.4 Consensus size: 38
35007647 TTATTTATTT
35007657 ATATGTAATTATTTTTAC-T-ATA-CATATGCATGTACAC
1 ATAT-TAA-TATTTTTACATAATAGCATATGCATGTACAC
35007694 ATATTAATATTTTTACTATACATATGCATATGCATGTACAC
1 ATATTAATATTTTTAC-ATA-ATA-GCATATGCATGTACAC
35007735 ATATTAATATTTTTA
1 ATATTAATATTTTTA
35007750 ACTAATTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
35 9 0.18
36 3 0.06
37 5 0.10
39 3 0.06
41 30 0.60
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (38 bp):
ATATTAATATTTTTACATAATAGCATATGCATGTACAC
Found at i:35023529 original size:24 final size:24
Alignment explanation
Indices: 35023502--35023547 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
35023492 CTTGAAACCA
*
35023502 TTTCCACAGCTCCTTTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
35023526 TTTCCACAGCTCCTCTCTTCAC
1 TTTCCACAGCTCCTCTCTTCAC
35023548 TCTCTTCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.46, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTCCACAGCTCCTCTCTTCACCC
Found at i:35023773 original size:14 final size:13
Alignment explanation
Indices: 35023738--35023764 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35023728 GTAGTAGATG
35023738 TGTTTTCTGCAAA
1 TGTTTTCTGCAAA
35023751 TGTTTTCTGCAAA
1 TGTTTTCTGCAAA
35023764 T
1 T
35023765 CAGTTTCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (13 bp):
TGTTTTCTGCAAA
Found at i:35025429 original size:17 final size:15
Alignment explanation
Indices: 35025395--35025437 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
35025385 AATGGCATGG
*
35025395 CATTTGTTTTTGAAA
1 CATTTGTTTTTCAAA
35025410 CATTTGTTTCATTCAAA
1 CATTTGTTT--TTCAAA
35025427 CATTTGTTTTT
1 CATTTGTTTTT
35025438 ATATATACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (15 bp):
CATTTGTTTTTCAAA
Found at i:35026473 original size:20 final size:20
Alignment explanation
Indices: 35026409--35026485 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
35026399 AAATCATTGC
35026409 AATATATGTAAAAACAATTT
1 AATATATGTAAAAACAATTT
* ** *
35026429 AA-A-ATATAAAAATTTATTA
1 AATATATGTAAAAA-CAATTT
35026448 ATATATATGTAAAAACAATTT
1 A-ATATATGTAAAAACAATTT
35026469 AATATATGTAAAAACAA
1 AATATATGTAAAAACAA
35026486 CTTTTCCGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.18
19 5 0.11
20 19 0.42
21 5 0.11
22 8 0.18
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (20 bp):
AATATATGTAAAAACAATTT
Found at i:35026597 original size:20 final size:20
Alignment explanation
Indices: 35026572--35026611 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35026562 AATATTTTCC
*
35026572 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
35026592 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
35026612 TCATTTTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:35026618 original size:14 final size:14
Alignment explanation
Indices: 35026595--35026630 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
35026585 ACAGAAAAGT
35026595 AAAACATTTTCCAG
1 AAAACATTTTCCAG
* *
35026609 AAATCATTTTCCGG
1 AAAACATTTTCCAG
35026623 AAAACATT
1 AAAACATT
35026631 CTACTTCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (14 bp):
AAAACATTTTCCAG
Found at i:35028143 original size:24 final size:24
Alignment explanation
Indices: 35028115--35028166 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
35028105 TTTCTAGAAG
* *
35028115 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
35028139 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
35028163 ATTT
1 ATTT
35028167 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:35028894 original size:106 final size:105
Alignment explanation
Indices: 35028713--35028904 Score: 271
Period size: 106 Copynumber: 1.8 Consensus size: 105
35028703 AAAAACTGTC
* *
35028713 GAGCTTTGGTGGCCTAAGCGACGCTTTTATAAAAACGCCGCTATAGATCAAGCATTAGCGGCACT
1 GAGCTTTGGTGGCATAAGCGACGCTTTTAGAAAAACGCCGCTATAGATCAAGCATTAGCGGCACT
*
35028778 TTTTGAAAAACACCGCGAAAAAAATTTAGCACAACGCTATT
66 TTTTAAAAAACACCGC-AAAAAAATTTAGCACAACGCTATT
* * * *
35028819 GAGCTTTGGTGGCATTAGCGGCGCTTTT-GAAAATCGCCGCTATAGATCAAGCA-TAGCGGCGCT
1 GAGCTTTGGTGGCATAAGCGACGCTTTTAGAAAAACGCCGCTATAGATCAAGCATTAGCGGCACT
*
35028882 TTCTTAAAAAAACGCCGCAAAAA
66 TT-TT-AAAAAACACCGCAAAAA
35028905 TTATTTCTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
104 11 0.14
105 30 0.39
106 35 0.46
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (105 bp):
GAGCTTTGGTGGCATAAGCGACGCTTTTAGAAAAACGCCGCTATAGATCAAGCATTAGCGGCACT
TTTTAAAAAACACCGCAAAAAAATTTAGCACAACGCTATT
Found at i:35032848 original size:18 final size:18
Alignment explanation
Indices: 35032825--35032884 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
35032815 TATGTATTCT
35032825 AATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
* * **
35032843 AATGTAA-AC-AATTTTCT
1 AATGTAATTCTAA-TATAG
*
35032860 TATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
35032878 AATGTAA
1 AATGTAA
35032885 CTTGTTTTAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 2 0.07
17 9 0.31
18 16 0.55
19 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (18 bp):
AATGTAATTCTAATATAG
Found at i:35033123 original size:43 final size:43
Alignment explanation
Indices: 35033059--35033285 Score: 314
Period size: 43 Copynumber: 5.3 Consensus size: 43
35033049 AAGTCATGTT
* *
35033059 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
35033102 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
35033145 -TTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * *
35033187 TTTAGCGGCGATTGCGGGAAAAGCGTCGTTAAAGGT-TGTGGTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGGTC
* *
35033230 TTTAGCGGCGTTTGCGAGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
35033273 TTTAGCAGCGTTT
1 TTTAGCGGCGTTT
35033286 TTTCCGAAGC
Statistics
Matches: 162, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 40 0.25
43 121 0.75
44 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:35033208 original size:85 final size:86
Alignment explanation
Indices: 35033060--35033278 Score: 307
Period size: 85 Copynumber: 2.6 Consensus size: 86
35033050 AGTCATGTTT
* * * *
35033060 TTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTTTGGTCTTTAGCGGCGTTTGTGAGAAAAG
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGATTGCGAGAAAAG
35033125 CGCCGCTAAAGGTCT-TGG-TC
66 CGCCGCTAAAGGT-TGTGGTTC
* * *
35033145 TTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTAGTCTTTAGCGGCGATTGCGGGAAAAG
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGATTGCGAGAAAAG
* * *
35033210 CGTCGTTAAAGGTTGTGGTTT
66 CGCCGCTAAAGGTTGTGGTTC
* *
35033231 TTAGCGGCGTTTGCGAGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGC
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGC
35033279 AGCGTTTTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
84 1 0.01
85 72 0.61
86 45 0.38
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (86 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGATTGCGAGAAAAG
CGCCGCTAAAGGTTGTGGTTC
Found at i:35036382 original size:40 final size:40
Alignment explanation
Indices: 35036333--35036447 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 40
35036323 GTTTGGATAA
*
35036333 AAAACGCCGCTAAAGATCGAGTATTAGCGGCGCTTT-TCGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTAT-GG
* *
35036373 AAAATGCCGCTAAAGATCGAACATTAGCGGCGCTTTATGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATGG
* *
35036413 AAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTT
35036448 CCAAAAAAGC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 16 0.24
40 50 0.75
41 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATGG
Found at i:35036461 original size:40 final size:40
Alignment explanation
Indices: 35036331--35036474 Score: 132
Period size: 40 Copynumber: 3.6 Consensus size: 40
35036321 GCGTTTGGAT
* * * *
35036331 AAAAAACGCCGCTAAAGATCGAGTATTAGCGGCGCTTTTC
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTAC
** * * *
35036371 GGAAAATGCCGCTAAAGATCGAA-CATTAGCGGCGCTTTAT
1 AAAAAACGCCGCTAAAAATC-AAGCATTAGCGGCGCTTTAC
** *
35036411 GGAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTTCC
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTAC
35036450 AAAAAAGCGCCGC-AAAAATCTAAGC
1 AAAAAA-CGCCGCTAAAAATC-AAGC
35036475 CCAACGACGC
Statistics
Matches: 86, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 25 0.29
40 54 0.63
41 5 0.06
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTAC
Found at i:35036613 original size:41 final size:41
Alignment explanation
Indices: 35036556--35036685 Score: 154
Period size: 41 Copynumber: 3.2 Consensus size: 41
35036546 CATTAGCAGT
* *
35036556 GTTTTTGAGGAAGCGCCACTAATGCCCAAGGCTTTAGTGGC
1 GTTTTTGAGGAAGCGCCGCTAATGCCCAAGGCTTTAGCGGC
* *
35036597 GTTTTTGAGGAAGCGCCGCTAATTCCCAGGGCTTTAGCGGC
1 GTTTTTGAGGAAGCGCCGCTAATGCCCAAGGCTTTAGCGGC
* * * * * *
35036638 GTTTCTAAGGAATCGCTGCTAATGCTC-AGGTCTTTAGCGGT
1 GTTTTTGAGGAAGCGCCGCTAATGCCCAAGG-CTTTAGCGGC
35036679 GTTTTTG
1 GTTTTTG
35036686 TATTAGCGCT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 2 0.03
41 72 0.97
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (41 bp):
GTTTTTGAGGAAGCGCCGCTAATGCCCAAGGCTTTAGCGGC
Found at i:35037287 original size:14 final size:15
Alignment explanation
Indices: 35037257--35037295 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
35037247 AGGGCGTATA
35037257 TATGGATTTAAGGAT
1 TATGGATTTAAGGAT
*
35037272 TATGGA-TTAGGGAT
1 TATGGATTTAAGGAT
35037286 TATGG-TTTAA
1 TATGGATTTAA
35037296 TTAATGGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:35037647 original size:15 final size:15
Alignment explanation
Indices: 35037627--35037692 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
35037617 GGGATTTAAG
35037627 GTTTAGGGGTTAGGA
1 GTTTAGGGGTTAGGA
35037642 GTTTAGGGGTTA-GA
1 GTTTAGGGGTTAGGA
** * *
35037656 CATTAGTGGTTAAGA
1 GTTTAGGGGTTAGGA
*
35037671 G-TTAGGGATTTAGG-
1 GTTTAGGG-GTTAGGA
35037685 GTTTAGGG
1 GTTTAGGG
35037693 TTTTAAAGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 17 0.41
15 24 0.59
ACGTcount: A:0.23, C:0.02, G:0.41, T:0.35
Consensus pattern (15 bp):
GTTTAGGGGTTAGGA
Found at i:35038162 original size:47 final size:47
Alignment explanation
Indices: 35038098--35038202 Score: 183
Period size: 47 Copynumber: 2.2 Consensus size: 47
35038088 AAAAATGAAA
* *
35038098 TAAAAACACTAAAATTTTTAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAA-ACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAAAT
35038146 TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAAAT
1 TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAAAT
35038193 TAAAAAACTA
1 TAAAAAACTA
35038203 TGTATTAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
47 49 0.89
48 6 0.11
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.45
Consensus pattern (47 bp):
TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAAAT
Found at i:35038668 original size:25 final size:25
Alignment explanation
Indices: 35038640--35038689 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
35038630 AAATTATAGG
* *
35038640 AAATAAAATTAAAATACAAAAATAA
1 AAATAAAATAAAAACACAAAAATAA
* *
35038665 AAATGAAATAAAAACACTAAAATAA
1 AAATAAAATAAAAACACAAAAATAA
35038690 TTTTATCTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (25 bp):
AAATAAAATAAAAACACAAAAATAA
Found at i:35038673 original size:19 final size:18
Alignment explanation
Indices: 35038640--35038678 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
35038630 AAATTATAGG
*
35038640 AAATAAAATTAAAATACAA
1 AAATAAAAATAAAATA-AA
*
35038659 AAATAAAAATGAAATAAA
1 AAATAAAAATAAAATAAA
35038677 AA
1 AA
35038679 CACTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAAAATAAAATAAA
Found at i:35041549 original size:42 final size:43
Alignment explanation
Indices: 35041452--35041755 Score: 377
Period size: 43 Copynumber: 7.2 Consensus size: 43
35041442 TGTTTTTAGT
* * * * **
35041452 GGCGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* *
35041494 -GCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGAGATATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
*
35041536 GGCGTTTGT-GGAAAAGGCGCCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGGAAAA-GCGCCGCTAAAGGTCTTGAGCTATAGC
* *
35041579 GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * *
35041622 GGTGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* * * *
35041665 GGCGTTTGT-GCAAAAACGCCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
*
35041707 GGCGTTTGTGGGAAAAGCGCCGCT-AAGGTCATG-GTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAG-CTATAGC
35041749 GGCGTTT
1 GGCGTTT
35041756 ATTTCTAAAA
Statistics
Matches: 228, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
41 24 0.11
42 75 0.33
43 123 0.54
44 6 0.03
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
Found at i:35041722 original size:128 final size:128
Alignment explanation
Indices: 35041452--35041755 Score: 409
Period size: 128 Copynumber: 2.4 Consensus size: 128
35041442 TGTTTTTAGT
* * * **
35041452 GGCGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTGTTCTATAGCGCGTTTGTGGGAAAAGCACCGC
1 GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGCGTTTGTGGGAAAAGCACCGC
* * *
35041516 TAAAGGTCTTGAGATATAGCGGCGTTTGTGGAAAAGGCGCCGCTAAAGGTCTTGATCTATAGC
66 TAAAGGTCTTGAGATATAGCGGCGTTTGTGCAAAAGACGCCGCTAAAGGTCCTGATCTATAGC
* * * *
35041579 GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGTGGTGTTTGTGTGAAAAGCGCCG
1 GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAG-CGCGTTTGTGGGAAAAGCACCG
**
35041644 CTAAAGGTCTTGATCTATAGCGGCGTTTGTGCAAAA-ACGCCGCTAAAGGTCCTGATCTATAGC
65 CTAAAGGTCTTGAGATATAGCGGCGTTTGTGCAAAAGACGCCGCTAAAGGTCCTGATCTATAGC
* *
35041707 GGCGTTTGTGGGAAAAGCGCCGCT-AAGGTCATG-GTCTATAGCGGCGTTT
1 GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGAG-CTATAGC-GCGTTT
35041756 ATTTCTAAAA
Statistics
Matches: 155, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
126 1 0.01
127 46 0.30
128 57 0.37
129 51 0.33
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (128 bp):
GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGCGTTTGTGGGAAAAGCACCGC
TAAAGGTCTTGAGATATAGCGGCGTTTGTGCAAAAGACGCCGCTAAAGGTCCTGATCTATAGC
Found at i:35043187 original size:24 final size:26
Alignment explanation
Indices: 35043155--35043204 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
35043145 AAATTATAGA
* *
35043155 TTAAGTACCTAGTT-AAAAAAGAATT
1 TTAAGTACCTAATTGAAAAAAAAATT
35043180 TTAA-TACCTAATTGAAAAAAAAATT
1 TTAAGTACCTAATTGAAAAAAAAATT
35043205 AATTTGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (26 bp):
TTAAGTACCTAATTGAAAAAAAAATT
Found at i:35043206 original size:23 final size:24
Alignment explanation
Indices: 35043154--35043207 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
35043144 GAAATTATAG
*
35043154 ATTAAGTACCTAGTTAAAAAAGAAT
1 ATTAA-TACCTAATTAAAAAAGAAT
*
35043179 TTTAATACCTAATTGAAAAAA-AA-
1 ATTAATACCTAATT-AAAAAAGAAT
35043202 ATTAAT
1 ATTAAT
35043208 TTGAAGGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 5 0.20
24 10 0.40
25 10 0.40
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.31
Consensus pattern (24 bp):
ATTAATACCTAATTAAAAAAGAAT
Found at i:35044269 original size:15 final size:15
Alignment explanation
Indices: 35044249--35044281 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
35044239 TATATAAAAT
35044249 TTATA-TTAAAATTAA
1 TTATATTTAAAA-TAA
35044264 TTATATTTAAAATAA
1 TTATATTTAAAATAA
35044279 TTA
1 TTA
35044282 AGTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATATTTAAAATAA
Found at i:35045853 original size:11 final size:11
Alignment explanation
Indices: 35045837--35045915 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 11
35045827 ATTTTTATTA
35045837 TTTTAAAATAT
1 TTTTAAAATAT
35045848 TTTTAAAATACT
1 TTTTAAAATA-T
**** *
35045860 TTTTTCTTTTT
1 TTTTAAAATAT
35045871 TTATATTAAAATAT
1 TT-T-T-AAAATAT
35045885 TTTTAAAATACT
1 TTTTAAAATA-T
*
35045897 CTTTTAAAATTT
1 -TTTTAAAATAT
35045909 TTTTAAA
1 TTTTAAA
35045916 TTTTAAAATA
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
11 26 0.51
12 10 0.20
13 11 0.22
14 4 0.08
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:35045901 original size:39 final size:38
Alignment explanation
Indices: 35045821--35045902 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 38
35045811 AAATTTTTTA
*
35045821 TTTTTTATTTTTATTATTTTAAAATATTTTTAAAATAC
1 TTTTTTATTTTTATTATATTAAAATATTTTTAAAATAC
*
35045859 TTTTTTCTTTTT-TTATATTAAAATATTTTTAAAATAC
1 TTTTTTATTTTTATTATATTAAAATATTTTTAAAATAC
*
35045896 TCTTTTA
1 TTTTTTA
35045903 AAATTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 29 0.73
38 11 0.28
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (38 bp):
TTTTTTATTTTTATTATATTAAAATATTTTTAAAATAC
Found at i:35045903 original size:13 final size:11
Alignment explanation
Indices: 35045876--35045915 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
35045866 TTTTTTTATA
35045876 TTAAAATATTT
1 TTAAAATATTT
35045887 TTAAAATACTCTT
1 TTAAAATA-T-TT
*
35045900 TTAAAATTTTT
1 TTAAAATATTT
35045911 TTAAA
1 TTAAA
35045916 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 15 0.58
12 2 0.08
13 9 0.35
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAAATATTT
Found at i:35051041 original size:29 final size:28
Alignment explanation
Indices: 35050999--35051110 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 28
35050989 GTCGTGTATT
*
35050999 CCCTTTTTTTAAAATTTTACAATTTTGTC
1 CCCTATTTTTAAAATTTTACAATTTTG-C
* *
35051028 CCCTATTTTCAAAATTTTATAATTTTGC
1 CCCTATTTTTAAAATTTTACAATTTTGC
* * * *
35051056 CCTTATTTTTTAGATTTTACAGTTTTGC
1 CCCTATTTTTAAAATTTTACAATTTTGC
* * *
35051084 CTCTATTTTTTAGATTTTACAATTTTG
1 CCCTATTTTTAAAATTTTACAATTTTG
35051111 TCCAAAATTT
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 47 0.66
29 24 0.34
ACGTcount: A:0.23, C:0.15, G:0.06, T:0.55
Consensus pattern (28 bp):
CCCTATTTTTAAAATTTTACAATTTTGC
Found at i:35051120 original size:29 final size:28
Alignment explanation
Indices: 35051041--35051121 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 28
35051031 TATTTTCAAA
* ***
35051041 ATTTTATAATTTTGCCCTTATTTTTTAG
1 ATTTTACAATTTTGCCAAAATTTTTTAG
* ***
35051069 ATTTTACAGTTTTGCCTCTATTTTTTAG
1 ATTTTACAATTTTGCCAAAATTTTTTAG
35051097 ATTTTACAATTTTGTCCAAAATTTT
1 ATTTTACAATTTTG-CCAAAATTTT
35051122 ACGTTTTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 37 0.84
29 7 0.16
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.57
Consensus pattern (28 bp):
ATTTTACAATTTTGCCAAAATTTTTTAG
Found at i:35051746 original size:85 final size:84
Alignment explanation
Indices: 35051629--35051792 Score: 274
Period size: 85 Copynumber: 1.9 Consensus size: 84
35051619 AAACAGTGTA
* *
35051629 GTTCGATTATGAACCAGCGGCAGTTTGTTTAATCTGTAAATATGTTGTGCACTCACAACAAGTGG
1 GTTCGATCATGAACCAGCGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGG
* *
35051694 CAGTAATTGCAAATATGTG
66 CAATAACTGCAAATATGTG
*
35051713 GTTCGATCATGAACCAAGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTG
1 GTTCGATCATGAACC-AGCGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTG
35051778 GCAATAACTGCAAAT
65 GCAATAACTGCAAAT
35051793 GTAACAGCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 14 0.19
85 60 0.81
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (84 bp):
GTTCGATCATGAACCAGCGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGG
CAATAACTGCAAATATGTG
Found at i:35053065 original size:16 final size:16
Alignment explanation
Indices: 35053044--35053076 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35053034 ATTACTTATC
35053044 TATATGTGTATA-TAAA
1 TATATGT-TATAGTAAA
35053060 TATATGTTATAGTAAA
1 TATATGTTATAGTAAA
35053076 T
1 T
35053077 CATAACAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (16 bp):
TATATGTTATAGTAAA
Found at i:35053133 original size:45 final size:45
Alignment explanation
Indices: 35053084--35053171 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
35053074 AATCATAACA
*
35053084 GAAACAAATAAGACCATAGTTGA-AAGACTCTATAGCATCATGATG
1 GAAACAAATAAGACCATAGCT-ACAAGACTCTATAGCATCATGATG
*
35053129 GAAACAAATAAGACCATAGCTACAAGACTCTATGGCATCATGA
1 GAAACAAATAAGACCATAGCTACAAGACTCTATAGCATCATGA
35053172 AGGGAGTGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (45 bp):
GAAACAAATAAGACCATAGCTACAAGACTCTATAGCATCATGATG
Found at i:35053511 original size:13 final size:13
Alignment explanation
Indices: 35053492--35053558 Score: 89
Period size: 13 Copynumber: 5.2 Consensus size: 13
35053482 TGAGTTTTGT
35053492 TGAAATGGTTATA
1 TGAAATGGTTATA
*
35053505 CGAAATGGTTATA
1 TGAAATGGTTATA
* *
35053518 TGAAATGGCTACA
1 TGAAATGGTTATA
*
35053531 TGAAATGGTTAAA
1 TGAAATGGTTATA
*
35053544 TGAATTGGTTATA
1 TGAAATGGTTATA
35053557 TG
1 TG
35053559 GTAATAGATG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (13 bp):
TGAAATGGTTATA
Found at i:35055135 original size:14 final size:15
Alignment explanation
Indices: 35055116--35055148 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
35055106 TTTAAATAAT
35055116 AATATGAAT-GATTA
1 AATATGAATAGATTA
35055130 AATATGAATAGATTA
1 AATATGAATAGATTA
35055145 AATA
1 AATA
35055149 ATACAAGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (15 bp):
AATATGAATAGATTA
Found at i:35057338 original size:44 final size:44
Alignment explanation
Indices: 35057152--35057513 Score: 137
Period size: 44 Copynumber: 8.3 Consensus size: 44
35057142 GTCTGATGTG
* * * ** *
35057152 ATCTGCTCTACTGCAACTTCAGAGAGATGAGAACCATCG-TCTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGT-GATTTTA
* * * *
35057196 ATCTGCTCCACTGTAACTTCA-AGAAGATAGGAT-TG-GTTTCTTTT
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCTGTG-AT-TTTA
* * * * * **
35057240 GTCTGCTCCACTGTAACTTTA-AGGAGATAAGA-C--TAAATGCA
1 ATCTGCTCCACTGCAACTTCAGA-GAGATAAGATCTGTGATTTTA
*
35057281 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGATTTTA
* *
35057325 ATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TG-G-TTTCTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGATTT-TA
* ** * *
35057367 CGATCTGCTCCACTACTGCTT-AGGGAGATAAGATCTGTAATTTTCA
1 --ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGATTTT-A
* ** * * * * **
35057413 ACCTAG-TCCACTGCTGCTTAAG-GAGATAAGGT-TGGGGTCTTCG
1 ATCT-GCTCCACTGCAACTTCAGAGAGATAAGATCTGTGAT-TTTA
* ** *
35057456 ATCTGCTCCACTACTGCTT-AG-GCAGATAAGATCTGTAATTTTCA
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCTGTGATTTT-A
*
35057500 ATCTACTCCACTGC
1 ATCTGCTCCACTGC
35057514 CAACCAGGGA
Statistics
Matches: 241, Mismatches: 52, Indels: 50
0.70 0.15 0.15
Matches are distributed among these distances:
41 31 0.13
42 9 0.04
43 45 0.19
44 147 0.61
45 5 0.02
46 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGATTTTA
Found at i:35057525 original size:87 final size:88
Alignment explanation
Indices: 35057305--35057527 Score: 292
Period size: 87 Copynumber: 2.6 Consensus size: 88
35057295 AACTTCAGAG
* * **
35057305 AGATAAGATCTGTGATTTT-AATCTGCTCCACTGCAACTTCAGGGAGAT-AGGATTGGTTTCTAC
1 AGATAAGATCTGTAATTTTCAATCTACTCCACTGCAAC-TCAGGGAGATAAGGATTGGGGTCTAC
*
35057368 GATCTGCTCCACTACTGCTTAGGG
65 GATCTGCTCCACTACTGCTTAGGC
* * ** * * *
35057392 AGATAAGATCTGTAATTTTCAACCTAGTCCACTGCTGCTTAAGGAGATAAGG-TTGGGGTCTTCG
1 AGATAAGATCTGTAATTTTCAATCTACTCCACTGCAACTCAGGGAGATAAGGATTGGGGTCTACG
35057456 ATCTGCTCCACTACTGCTTAGGC
66 ATCTGCTCCACTACTGCTTAGGC
35057479 AGATAAGATCTGTAATTTTCAATCTACTCCACTGCCAAC-CAGGGAGATA
1 AGATAAGATCTGTAATTTTCAATCTACTCCACTG-CAACTCAGGGAGATA
35057528 GAATTACTGG
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
87 97 0.84
88 18 0.16
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (88 bp):
AGATAAGATCTGTAATTTTCAATCTACTCCACTGCAACTCAGGGAGATAAGGATTGGGGTCTACG
ATCTGCTCCACTACTGCTTAGGC
Found at i:35057787 original size:44 final size:44
Alignment explanation
Indices: 35057479--35057927 Score: 142
Period size: 44 Copynumber: 10.2 Consensus size: 44
35057469 CTGCTTAGGC
* * *
35057479 AGATAAGATCTGTAATTTTCAATCTACTCCACTGCCAACCAGGG
1 AGATAAAATCTGAAATCTTCAATCTACTCCACTGCCAACCAGGG
* * * *
35057523 AGATAGAATTACTG---GCTTCAATGTACTCCACTG-TAACCTCAGGG
1 AGATA-AAAT-CTGAAATCTTCAATCTACTCCACTGCCAA-C-CAGGG
* * * * * * ** *
35057567 AGGTAAAATC-CACCATCTTCGATCTACTTCACT-ACTGCTTAGGG
1 AGATAAAATCTGA-AATCTTCAATCTACTCCACTGCCAAC-CAGGG
* * * *
35057611 AGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAACCAGAG
1 AGATAAAATCTGAAATCTTCAATCTACTCCACTGCCAACCAGGG
* * * * *
35057655 AGATAGAATTACTG---GCTTCAATGTACTCCACTG-TAACCAAAGTG
1 AGATA-AAAT-CTGAAATCTTCAATCTACTCCACTGCCAACC--AGGG
* ** * * * ** *
35057699 A-AGTAAAATCCGCCATCTTCGATCTGCTCCACT-ACTGCTTAGGG
1 AGA-TAAAATCTGAAATCTTCAATCTACTCCACTGCCAAC-CAGGG
* *
35057743 AGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGG
1 AGATAAAATCTGAAATCTTCAATCTACTCCACTGCCAACCAGGG
* * *
35057787 AGATAAAATTACTG---GCTTCAATGC-ACTCCACTG-TAACCATAAGG
1 AGATAAAA-T-CTGAAATCTTCAAT-CTACTCCACTGCCAACC--AGGG
* * ** * * * ** *
35057831 AGGTAAAATCCGCCATCTTCGATCTGCTCCACT-ACTGCTTAGGG
1 AGATAAAATCTGAAATCTTCAATCTACTCCACTGCCAAC-CAGGG
* * *
35057875 AGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACTAGGG
1 AGATAAAATCTGAAATCTTCAATCTACTCCACTGCCAACCAGGG
35057919 AGATAAAAT
1 AGATAAAAT
35057928 TACTGGCTTC
Statistics
Matches: 284, Mismatches: 86, Indels: 70
0.65 0.20 0.16
Matches are distributed among these distances:
42 15 0.05
43 56 0.20
44 149 0.52
45 55 0.19
46 9 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (44 bp):
AGATAAAATCTGAAATCTTCAATCTACTCCACTGCCAACCAGGG
Found at i:35058111 original size:132 final size:132
Alignment explanation
Indices: 35057450--35058104 Score: 1049
Period size: 132 Copynumber: 5.0 Consensus size: 132
35057440 AAGGTTGGGG
* * * *
35057450 TCTTCGATCTGCTCCACTACTGCTTAGGCAGATAAGATCTGTAATTTTCAATCTACTCCACTGCC
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
* *
35057515 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCAC
66 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGC
35057580 CA
131 CA
* * *
35057582 TCTTCGATCTACTTCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCC
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
* * * *
35057647 AACCAGAGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCAAAGTGAAGTAAAATCCGC
66 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGC
35057712 CA
131 CA
35057714 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
* * * *
35057779 AACCAGGGAGATAAAATTACTGGCTTCAATGCACTCCACTGTAACCATAAGGAGGTAAAATCCGC
66 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGC
35057844 CA
131 CA
35057846 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
* * * ** *
35057911 AACTAGGGAGATAAAATTACTGGCTTCAATGTAATCCACTGTAACCACAATGAGGTAAAATCTGC
66 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGC
35057976 CA
131 CA
* * *
35057978 TCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACAGCT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
** *
35058043 GCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATC
66 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATC
35058105 TACCATCAAC
Statistics
Matches: 485, Mismatches: 38, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 485 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (132 bp):
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGC
CA
Found at i:35064739 original size:38 final size:38
Alignment explanation
Indices: 35064687--35064767 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
35064677 TTTTGAAATA
* *
35064687 ATATATAAAAAATTTATACTAAATAATATAT-ATACAT
1 ATATAAAAAAAATTTAAACTAAATAATATATAATACAT
35064724 ATATAAAAAACAATTTAAACTAAATAATATATACATACAT
1 ATATAAAAAA-AATTTAAACTAAATAATATATA-ATACAT
35064764 ATAT
1 ATAT
35064768 TAAACTAGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
37 9 0.23
38 20 0.51
40 10 0.26
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (38 bp):
ATATAAAAAAAATTTAAACTAAATAATATATAATACAT
Found at i:35073839 original size:216 final size:215
Alignment explanation
Indices: 35073458--35073892 Score: 789
Period size: 216 Copynumber: 2.0 Consensus size: 215
35073448 GAGGATATAG
*
35073458 TTTGGGGATTTTTTTTACCAAGACTTTACTAACTATAGAGTTTTCAGGGAAACATGTGGAGAGGA
1 TTTGGGGATTTGTTTTACCAAGACTTTACTAACTATAGAGTTTTCAGGGAAACATGTGGAGAGGA
*
35073523 TAGGAATGCAAAACATGACTCATCCACTTCACTAGGGCAAATAGGAGACTGTTGGATATAGTGCC
66 TAGGAATGCAAAACATGACTCATCCACTTCACTAGGGCAAATAGAAGACTGTTGGATATAGTGCC
* *
35073588 CTAAGTGTAGTATTTTCGTCTAAGTACATTTGTAATTTTTTTCAAACGGATTGGTTAATAAAATT
131 CTAAGTGTAGTATTTTCGTCTAAGTACACTTGTAA-TTTTTTCAAACGGATGGGTTAATAAAATT
*
35073653 ATTCATGAATTACATTAATAC
195 ATTCATGAATTACATTAACAC
* *
35073674 TTTGGGGATTTGTTTTACCAAGACTTTACTAGCTATAGAGTTTTCAGGGAAACATGTGGAGATGA
1 TTTGGGGATTTGTTTTACCAAGACTTTACTAACTATAGAGTTTTCAGGGAAACATGTGGAGAGGA
35073739 TAGGAATGCAAAACATGACTCATCCACTTCACTAGGGCAAATAGAAGACTGTTGGATATAGTGCC
66 TAGGAATGCAAAACATGACTCATCCACTTCACTAGGGCAAATAGAAGACTGTTGGATATAGTGCC
*
35073804 CTAAGTGTAGTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAATGGATGGGTTAATAAAATTA
131 CTAAGTGTAGTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACGGATGGGTTAATAAAATTA
35073869 TTCATGAATTACATTAACAC
196 TTCATGAATTACATTAACAC
35073889 TTTG
1 TTTG
35073893 TATATTGTCT
Statistics
Matches: 211, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
215 51 0.24
216 160 0.76
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (215 bp):
TTTGGGGATTTGTTTTACCAAGACTTTACTAACTATAGAGTTTTCAGGGAAACATGTGGAGAGGA
TAGGAATGCAAAACATGACTCATCCACTTCACTAGGGCAAATAGAAGACTGTTGGATATAGTGCC
CTAAGTGTAGTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACGGATGGGTTAATAAAATTA
TTCATGAATTACATTAACAC
Found at i:35077024 original size:26 final size:27
Alignment explanation
Indices: 35076985--35077047 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
35076975 AACAGAAACG
**
35076985 CCAAAAAATCCAAT-ATAGTTAGT-TGA
1 CCAAAAAAGACAATGATAGTT-GTGTGA
35077011 CCAAAAAAGACAATGGAATAGTTGTGTGA
1 CCAAAAAAGACAAT-G-ATAGTTGTGTGA
35077040 CCAAAAAA
1 CCAAAAAA
35077048 AATACCAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 12 0.39
28 2 0.06
29 17 0.55
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (27 bp):
CCAAAAAAGACAATGATAGTTGTGTGA
Found at i:35083285 original size:42 final size:42
Alignment explanation
Indices: 35083226--35083320 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
35083216 TTGCTTCTAC
* * *
35083226 GTTGCTTCCTTTTTTGTCT-GAACCTGTATGTTGTTTTCCCAA
1 GTTGCTTCCTTTTTTGTCTAG-ACATGGATGTTGCTTTCCCAA
*
35083268 GTTGCTTCCTTTTTTGTCTAGACATGGATGTTGCTTTCCCAT
1 GTTGCTTCCTTTTTTGTCTAGACATGGATGTTGCTTTCCCAA
*
35083310 GTTGTTTCCTT
1 GTTGCTTCCTT
35083321 GATATTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.51
Consensus pattern (42 bp):
GTTGCTTCCTTTTTTGTCTAGACATGGATGTTGCTTTCCCAA
Done.