Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 21 of 143
Found at i:6340880 original size:4 final size:4
Alignment explanation
Indices: 6340843--6340868 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6340833 TTAGGGTTTC
6340843 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
6340869 CAAGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:6340898 original size:45 final size:46
Alignment explanation
Indices: 6340806--6340906 Score: 118
Period size: 45 Copynumber: 2.2 Consensus size: 46
6340796 CCGTTAATTA
** **
6340806 ATTTATTTATTTATTTTTAGAGTTTTCTTAGGGTTTCTATTTATTT
1 ATTTATTTATTTATTTACAGAGTTTTCTTAGGGTTTCTAGGTATTT
*
6340852 ATTTATTTATTTATTTACA-AGTTTAT-TTAGGGTTTTTTAGGT-TTT
1 ATTTATTTATTTATTTACAGAGTTT-TCTTAGGG-TTTCTAGGTATTT
6340897 ATTTATTTAT
1 ATTTATTTAT
6340907 AAAATAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
45 24 0.50
46 24 0.50
ACGTcount: A:0.22, C:0.03, G:0.11, T:0.64
Consensus pattern (46 bp):
ATTTATTTATTTATTTACAGAGTTTTCTTAGGGTTTCTAGGTATTT
Found at i:6343571 original size:51 final size:52
Alignment explanation
Indices: 6343486--6343583 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 52
6343476 GCTATAAACG
6343486 AAAGAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
* *
6343538 AAAG-GTCTGATGACTAAGTGTCATTATGAGTAAATGAATCCTTTAC
1 AAAGAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTAC
6343584 CTGTGGATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 40 0.91
52 4 0.09
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (52 bp):
AAAGAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
Found at i:6346143 original size:22 final size:22
Alignment explanation
Indices: 6346089--6346144 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
6346079 TATACAAACG
* *
6346089 ATAACAATAAGATAGTAGCAAT
1 ATAACAATAAAATAGTAGCAAA
* * *
6346111 ATAATAGTAAAATGGTAGCAAA
1 ATAACAATAAAATAGTAGCAAA
6346133 ATAACAATAAAA
1 ATAACAATAAAA
6346145 CAACAGAGGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAA
Found at i:6355496 original size:35 final size:35
Alignment explanation
Indices: 6355450--6355525 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
6355440 GTGGCCCGAC
6355450 TTATGATCAAGTCTAGCTACATGCAATGAAGTGGA
1 TTATGATCAAGTCTAGCTACATGCAATGAAGTGGA
6355485 TTATGATCAAGTCTAGCTACATGCAATGAAGTGGA
1 TTATGATCAAGTCTAGCTACATGCAATGAAGTGGA
6355520 TTATGA
1 TTATGA
6355526 GATATCTTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (35 bp):
TTATGATCAAGTCTAGCTACATGCAATGAAGTGGA
Found at i:6359022 original size:25 final size:25
Alignment explanation
Indices: 6358993--6359040 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6358983 TATTTTTAAT
6358993 TTTATAT-TTAATAATTTTATATATC
1 TTTATATATTAA-AATTTTATATATC
*
6359018 TTTATTTATTAAAATTTTATATA
1 TTTATATATTAAAATTTTATATA
6359041 CATACATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTATATATTAAAATTTTATATATC
Found at i:6364069 original size:2 final size:2
Alignment explanation
Indices: 6364026--6364050 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6364016 AATAATATTT
6364026 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6364051 TAATATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6364279 original size:17 final size:18
Alignment explanation
Indices: 6364219--6364281 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 18
6364209 ACCCTCTTAT
6364219 TATATTATATAATACGCTATA
1 TATATTATATAATA---TATA
6364240 TCATATTATATAATATATAA
1 T-ATATTATATAATATAT-A
* *
6364260 TATATTA-ATAGTTTATA
1 TATATTATATAATATATA
6364277 TATAT
1 TATAT
6364282 GCATCAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 6 0.16
18 7 0.18
19 9 0.24
20 2 0.05
21 1 0.03
22 13 0.34
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (18 bp):
TATATTATATAATATATA
Found at i:6364997 original size:24 final size:24
Alignment explanation
Indices: 6364969--6365029 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
6364959 ATTCCCATTT
* *
6364969 AATTAGCAAATATATATTTTTAA-A
1 AATTA-CAAAAATATATTATTAATA
*
6364993 AATTATAAAAATATATTATTAATA
1 AATTACAAAAATATATTATTAATA
6365017 AATTTA-AAAAATA
1 AA-TTACAAAAATA
6365030 AATATGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 14 0.44
24 15 0.47
25 3 0.09
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
AATTACAAAAATATATTATTAATA
Found at i:6365014 original size:23 final size:23
Alignment explanation
Indices: 6364980--6365026 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
6364970 ATTAGCAAAT
*
6364980 ATATATTTTTAA-AAATTATAAAA
1 ATATATTATTAATAAATT-TAAAA
6365003 ATATATTATTAATAAATTTAAAA
1 ATATATTATTAATAAATTTAAAA
6365026 A
1 A
6365027 ATAAATATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATTATTAATAAATTTAAAA
Found at i:6365027 original size:25 final size:23
Alignment explanation
Indices: 6364980--6365042 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
6364970 ATTAGCAAAT
* *
6364980 ATATATTTTTAAAAATTATAAAA
1 ATATATTATTAAAAATTAAAAAA
*
6365003 ATATATTATTAATAAATTTAAAAA
1 ATATATTATTAA-AAATTAAAAAA
*
6365027 ATA-AATATGTAAAAAT
1 ATATATTAT-TAAAAAT
6365043 CACTTGCAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
ATATATTATTAAAAATTAAAAAA
Found at i:6365042 original size:23 final size:24
Alignment explanation
Indices: 6364988--6365042 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
6364978 ATATATATTT
*
6364988 TTAAAAA-TTATAAAAATATATTA
1 TTAAAAATTTATAAAAATATAATA
6365011 TTAATAAATTTA-AAAAATA-AATA
1 TTAA-AAATTTATAAAAATATAATA
6365034 TGTAAAAAT
1 T-TAAAAAT
6365043 CACTTGCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 12 0.43
24 13 0.46
25 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TTAAAAATTTATAAAAATATAATA
Found at i:6366239 original size:19 final size:19
Alignment explanation
Indices: 6366211--6366254 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
6366201 TTTCTCTCCA
*
6366211 TCTTCCTTCC-CTCTCTATC
1 TCTTCTTTCCTCTCT-TATC
*
6366230 TTTTCTTTCCTCTCTTATC
1 TCTTCTTTCCTCTCTTATC
6366249 TCTTCT
1 TCTTCT
6366255 GTGCCCTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.57
Consensus pattern (19 bp):
TCTTCTTTCCTCTCTTATC
Found at i:6378228 original size:51 final size:51
Alignment explanation
Indices: 6378173--6378313 Score: 183
Period size: 51 Copynumber: 2.8 Consensus size: 51
6378163 TCGTCTAGGA
* * * * *
6378173 ATTCATATACTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
* * **
6378224 ATTCATTTACTCATGATGACATTTAGTCATCGGACCTTTAATCTGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
* *
6378275 ATTCATTTACTCACGATGACACTTAATCATCGGATCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTT
6378314 TCGTTTATAG
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 77 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
Found at i:6380939 original size:19 final size:18
Alignment explanation
Indices: 6380866--6380943 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 18
6380856 TTAAAAAAAC
*
6380866 ATAAAACTGTATTAAATGT
1 ATAAAACT-TATTAAATTT
*
6380885 -TAAAA--TATTAAATTG
1 ATAAAACTTATTAAATTT
6380900 ATATAAACTTATTAAATTT
1 ATA-AAACTTATTAAATTT
6380919 ATGAAAACTTA-TAAATATT
1 AT-AAAACTTATTAAAT-TT
6380938 ATAAAA
1 ATAAAA
6380944 TATAAAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
15 8 0.16
16 2 0.04
17 3 0.06
18 14 0.28
19 22 0.44
20 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (18 bp):
ATAAAACTTATTAAATTT
Found at i:6381037 original size:19 final size:18
Alignment explanation
Indices: 6381002--6381092 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
6380992 AATAAAACTT
*
6381002 ATTTTAAATAT-T-TAAA
1 ATTTTAAAAATGTATAAA
6381018 ATTTTAAAAATGTATTAAA
1 ATTTTAAAAATGTA-TAAA
6381037 ATTCTTAAAAAAT-TATAAA
1 ATT-TT-AAAAATGTATAAA
* *
6381056 ATATTAAAATTG-ATATAA
1 ATTTTAAAAATGTATA-AA
6381074 ATTTATAAAAAT-TATAAA
1 ATTT-TAAAAATGTATAAA
6381092 A
1 A
6381093 AAATCATAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
16 10 0.16
17 9 0.15
18 10 0.16
19 22 0.36
20 4 0.07
21 6 0.10
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTTTAAAAATGTATAAA
Found at i:6381059 original size:47 final size:47
Alignment explanation
Indices: 6381007--6381103 Score: 115
Period size: 47 Copynumber: 2.1 Consensus size: 47
6380997 AACTTATTTT
* * * * *
6381007 AAATATTTAAAATT-TTAAAAATGTATTAAAATTCTTAAAAAATTATA
1 AAATA-TTAAAATTGATAAAAATGTATAAAAATTATAAAAAAATCATA
* *
6381054 AAATATTAAAATTGATATAAATTTATAAAAATTATAAAAAAATCATA
1 AAATATTAAAATTGATAAAAATGTATAAAAATTATAAAAAAATCATA
6381101 AAA
1 AAA
6381104 AATTGAACTG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 8 0.19
47 34 0.81
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (47 bp):
AAATATTAAAATTGATAAAAATGTATAAAAATTATAAAAAAATCATA
Found at i:6381079 original size:27 final size:27
Alignment explanation
Indices: 6381030--6381107 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
6381020 TTTAAAAATG
*
6381030 TATTAAAATTCTTAAAAAATTATAAAA
1 TATTAAAATTCATAAAAAATTATAAAA
* * *
6381057 TATTAAAATTGATATAAATTTATAAAAA
1 TATTAAAATTCATAAAAAATTAT-AAAA
* *
6381085 TTATAAAAAAATCATAAAAAATT
1 -TAT-TAAAATTCATAAAAAATT
6381108 GAACTGAACC
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
27 19 0.49
28 4 0.10
29 3 0.08
30 13 0.33
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (27 bp):
TATTAAAATTCATAAAAAATTATAAAA
Found at i:6381093 original size:9 final size:9
Alignment explanation
Indices: 6380894--6381093 Score: 63
Period size: 9 Copynumber: 21.3 Consensus size: 9
6380884 TTAAAATATT
6380894 AAATTGATATA
1 AAATT-ATA-A
* *
6380905 AACTTATTA
1 AAATTATAA
*
6380914 AATTTATGAA
1 AAATTAT-AA
*
6380924 AACTTATAA
1 AAATTATAA
*
6380933 ATATTAT-A
1 AAATTATAA
6380941 AAA-TATAAA
1 AAATTAT-AA
*
6380950 AAATTCTAA
1 AAATTATAA
* * *
6380959 CCAATTCTAT
1 -AAATTATAA
*
6380969 ACATTATAAA
1 AAATTAT-AA
6380979 AAATTAT-A
1 AAATTATAA
6380987 AAATTAATAA
1 AAATT-ATAA
*
6380997 AACTTATTTTAA
1 AA---ATTATAA
*
6381009 ATATT-T-A
1 AAATTATAA
*
6381016 AAATTTTAA
1 AAATTATAA
*
6381025 AAATGTATTA
1 AAAT-TATAA
*
6381035 AAATTCTTAAA
1 AAATT-AT-AA
6381046 AAATTAT-A
1 AAATTATAA
*
6381054 AAA-TATTA
1 AAATTATAA
6381062 AAATTGATATA
1 AAATT-ATA-A
*
6381073 AATTTATAA
1 AAATTATAA
6381082 AAATTATAA
1 AAATTATAA
6381091 AAA
1 AAA
6381094 AATCATAAAA
Statistics
Matches: 142, Mismatches: 27, Indels: 42
0.67 0.13 0.20
Matches are distributed among these distances:
7 11 0.08
8 19 0.13
9 48 0.34
10 42 0.30
11 15 0.11
12 4 0.03
13 3 0.02
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (9 bp):
AAATTATAA
Found at i:6381585 original size:10 final size:9
Alignment explanation
Indices: 6381522--6381673 Score: 93
Period size: 9 Copynumber: 17.0 Consensus size: 9
6381512 TGATAATTTC
6381522 TTTTTATAA
1 TTTTTATAA
*
6381531 TTTTTATGA
1 TTTTTATAA
* *
6381540 TTTTCAGAA
1 TTTTTATAA
* *
6381549 TTTTAATACG
1 TTTTTATA-A
*
6381559 TTTTTGTAAA
1 TTTTTAT-AA
*
6381569 ATTTTATAA
1 TTTTTATAA
6381578 TTTATTAT-A
1 TTT-TTATAA
*
6381587 TATTTATAA
1 TTTTTATAA
6381596 TTTTTATAAA
1 TTTTTAT-AA
* *
6381606 TTTATATCA
1 TTTTTATAA
6381615 TTTTTAT--
1 TTTTTATAA
6381622 TTTTT-TAA
1 TTTTTATAA
*
6381630 TATTTAATAA
1 T-TTTTATAA
*
6381640 TATTTAT-A
1 TTTTTATAA
6381648 TTTTTGATAA
1 TTTTT-ATAA
6381658 TTTTT-T-A
1 TTTTTATAA
6381665 TTTTTATAA
1 TTTTTATAA
6381674 ATTTCTATGT
Statistics
Matches: 108, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
6 1 0.01
7 11 0.10
8 12 0.11
9 51 0.47
10 32 0.30
11 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:6381602 original size:27 final size:26
Alignment explanation
Indices: 6381570--6381672 Score: 90
Period size: 25 Copynumber: 4.0 Consensus size: 26
6381560 TTTTGTAAAA
6381570 TTTTATAATTTATTATATATTTATAAT
1 TTTTATAATTTATTATATATTTAT-AT
* *
6381597 TTTTATAAATTTA-TATCATTTTTATTT
1 TTTTAT-AATTTATTAT-ATATTTATAT
*
6381624 TTTTA-ATATTTAATA-ATATTTATAT
1 TTTTATA-ATTTATTATATATTTATAT
*
6381649 TTTTGATAATTT-TT-TATTTTTATA
1 TTTT-ATAATTTATTATATATTTATA
6381673 AATTTCTATG
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
25 22 0.35
26 10 0.16
27 18 0.29
28 13 0.21
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTATAATTTATTATATATTTATAT
Found at i:6381608 original size:17 final size:17
Alignment explanation
Indices: 6381571--6381677 Score: 78
Period size: 17 Copynumber: 6.2 Consensus size: 17
6381561 TTTGTAAAAT
*
6381571 TTTATAATTTATTATATA
1 TTTATAATTT-TTATAAA
6381589 TTTATAATTTTTATAAA
1 TTTATAATTTTTATAAA
*
6381606 TTTATATCATTTTTAT--T
1 TTTATA--ATTTTTATAAA
* *
6381623 TTTTTAATATTTAATAATA
1 TTTATAAT-TTTTATAA-A
6381642 TTTAT-ATTTTTGAT-AA
1 TTTATAATTTTT-ATAAA
* *
6381658 TTTTTTATTTTTATAAA
1 TTTATAATTTTTATAAA
6381675 TTT
1 TTT
6381678 CTATGTTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
15 2 0.03
16 12 0.17
17 32 0.44
18 14 0.19
19 12 0.17
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (17 bp):
TTTATAATTTTTATAAA
Found at i:6381619 original size:19 final size:18
Alignment explanation
Indices: 6381571--6381687 Score: 77
Period size: 18 Copynumber: 6.7 Consensus size: 18
6381561 TTTGTAAAAT
*
6381571 TTTATA-ATTTATTATATA
1 TTTATATATTT-TTATAAA
6381589 TTTATA-ATTTTTATAAA
1 TTTATATATTTTTATAAA
***
6381606 TTTATATCATTTTTATTTT
1 TTTATAT-ATTTTTATAAA
*
6381625 TTTA-ATA-TTTAATAATA
1 TTTATATATTTTTATAA-A
*
6381642 TTTATAT-TTTTGAT-AA
1 TTTATATATTTTTATAAA
*
6381658 TTT-TTTATTTTTATAAA
1 TTTATATATTTTTATAAA
* *
6381675 TTTCTATGTTTTT
1 TTTATATATTTTT
6381688 TGTGTTTTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.03
16 15 0.19
17 23 0.29
18 26 0.33
19 12 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATATATTTTTATAAA
Found at i:6397553 original size:18 final size:18
Alignment explanation
Indices: 6397532--6397568 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6397522 ATGCAGAAAG
6397532 CTGTAAAGTTTCAGACAA
1 CTGTAAAGTTTCAGACAA
6397550 CTGTAAAGTTTCAGACAA
1 CTGTAAAGTTTCAGACAA
6397568 C
1 C
6397569 AATACTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (18 bp):
CTGTAAAGTTTCAGACAA
Found at i:6398598 original size:15 final size:16
Alignment explanation
Indices: 6398573--6398612 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
6398563 TGGGGGCCCC
6398573 TAAAGTTTAATTTTTT-
1 TAAA-TTTAATTTTTTG
6398589 TAAATTTAATTTTTTG
1 TAAATTTAATTTTTTG
6398605 TAAATTTA
1 TAAATTTA
6398613 CACCATGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (16 bp):
TAAATTTAATTTTTTG
Found at i:6400063 original size:21 final size:22
Alignment explanation
Indices: 6400038--6400079 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
6400028 TTTTAACTTT
6400038 AAAAATTACTTTAAA-TTTTTG
1 AAAAATTACTTTAAACTTTTTG
*
6400059 AAAAATTATTTTAAACTTTTT
1 AAAAATTACTTTAAACTTTTT
6400080 TTGTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAAATTACTTTAAACTTTTTG
Found at i:6404781 original size:45 final size:45
Alignment explanation
Indices: 6404717--6404808 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
6404707 AAAGCATACA
6404717 TTTAAATAAACACAAAAATAGGGTTAAAGAAAGCTTAATTATTTC
1 TTTAAATAAACACAAAAATAGGGTTAAAGAAAGCTTAATTATTTC
6404762 TTTAAATAAACACAAAAATAGGGTTAAAGAAAGCTTAATTATTTC
1 TTTAAATAAACACAAAAATAGGGTTAAAGAAAGCTTAATTATTTC
6404807 TT
1 TT
6404809 GATGATTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (45 bp):
TTTAAATAAACACAAAAATAGGGTTAAAGAAAGCTTAATTATTTC
Found at i:6407222 original size:22 final size:22
Alignment explanation
Indices: 6407194--6407237 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6407184 TAATGAAATT
6407194 CTGCATACTAGTTTCGGTAGAA
1 CTGCATACTAGTTTCGGTAGAA
*
6407216 CTGCATACTAGTTTTGGTAGAA
1 CTGCATACTAGTTTCGGTAGAA
6407238 TTACTGCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGCATACTAGTTTCGGTAGAA
Found at i:6414366 original size:22 final size:22
Alignment explanation
Indices: 6414324--6414367 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6414314 TAATGAAATT
* *
6414324 CTGCATACTAGTTTTGGTAGAA
1 CTGCATACTAGTTTCGATAGAA
6414346 CTGCATACTAGTTTCGATAGAA
1 CTGCATACTAGTTTCGATAGAA
6414368 TTATTGCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (22 bp):
CTGCATACTAGTTTCGATAGAA
Found at i:6416444 original size:11 final size:11
Alignment explanation
Indices: 6416397--6416447 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 11
6416387 GGGATTATAA
6416397 ATAAATATTA-
1 ATAAATATTAT
6416407 ATAAAT-TTAT
1 ATAAATATTAT
* * *
6416417 TTGAATATAAT
1 ATAAATATTAT
6416428 -TAAATATTAT
1 ATAAATATTAT
6416438 ATAAATATTA
1 ATAAATATTA
6416448 ATATTATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
9 3 0.09
10 18 0.55
11 12 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
ATAAATATTAT
Found at i:6416835 original size:4 final size:4
Alignment explanation
Indices: 6416826--6416853 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6416816 TTGGGATTTA
6416826 CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT
6416854 ATATATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:6419199 original size:5 final size:5
Alignment explanation
Indices: 6419189--6419221 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
6419179 ACATTTTTCA
*
6419189 CCTCT CCTCT CCTCT CGTCT CCTCT CCTCT CCT
1 CCTCT CCTCT CCTCT CCTCT CCTCT CCTCT CCT
6419222 ACCCTATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.03, T:0.39
Consensus pattern (5 bp):
CCTCT
Found at i:6419428 original size:40 final size:41
Alignment explanation
Indices: 6419353--6419440 Score: 160
Period size: 41 Copynumber: 2.1 Consensus size: 41
6419343 TAAGGTGTGA
6419353 TATATATGATAAAATATATAAAAAAAATATATACGGAAGTTT
1 TATA-ATGATAAAATATATAAAAAAAATATATACGGAAGTTT
6419395 TATAATGATAAAATATATAAAAAAAA-ATATACGGAAGTTT
1 TATAATGATAAAATATATAAAAAAAATATATACGGAAGTTT
6419435 TATAAT
1 TATAAT
6419441 TTCGAACTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 20 0.43
41 22 0.48
42 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (41 bp):
TATAATGATAAAATATATAAAAAAAATATATACGGAAGTTT
Found at i:6421292 original size:21 final size:20
Alignment explanation
Indices: 6421267--6421318 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
6421257 TAAAGTTATT
6421267 TATATTATATATACAATAATA
1 TATATTATAT-TACAATAATA
* **
6421288 TATATTAT-TTATAATTTTA
1 TATATTATATTACAATAATA
6421307 TATATTATATTA
1 TATATTATATTA
6421319 TAATGTTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.56
20 4 0.15
21 8 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTATATTACAATAATA
Found at i:6427952 original size:21 final size:21
Alignment explanation
Indices: 6427902--6427952 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
6427892 TAAAAGAGAT
* * *
6427902 GGAGAAGAAAGGGAAATAGAG
1 GGAGAAGCAAGGAAAATAAAG
* *
6427923 AGAGCAGCAAGGAAAATAAAG
1 GGAGAAGCAAGGAAAATAAAG
6427944 GGAGAAGCA
1 GGAGAAGCA
6427953 GAAGAGAATG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.53, C:0.06, G:0.37, T:0.04
Consensus pattern (21 bp):
GGAGAAGCAAGGAAAATAAAG
Found at i:6437455 original size:20 final size:20
Alignment explanation
Indices: 6437430--6437470 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
6437420 TTGCAATCAA
6437430 TTTCTTCTTC-TTCTTCCTCT
1 TTTCTTCTTCGTT-TTCCTCT
6437450 TTTCTTCTTCGTTTTCCTCT
1 TTTCTTCTTCGTTTTCCTCT
6437470 T
1 T
6437471 CTTAAATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTCTTCTTCGTTTTCCTCT
Found at i:6440675 original size:21 final size:22
Alignment explanation
Indices: 6440651--6440693 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6440641 ATTTATTCAA
*
6440651 ATCATGATATTATT-ATAATTT
1 ATCATGAAATTATTGATAATTT
*
6440672 ATCATTAAATTATTGATAATTT
1 ATCATGAAATTATTGATAATTT
6440694 GAATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
ATCATGAAATTATTGATAATTT
Found at i:6443854 original size:17 final size:17
Alignment explanation
Indices: 6443832--6443870 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6443822 TCTCACCTTG
* * *
6443832 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACAA
6443849 ACAAGAACTCTCAACAA
1 ACAAGAACTCTCAACAA
6443866 ACAAG
1 ACAAG
6443871 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACAA
Found at i:6460066 original size:21 final size:21
Alignment explanation
Indices: 6460041--6460091 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
6460031 ATAAAACATT
*
6460041 ATGTTTGTAACTCTTCTCATA
1 ATGTTTGTAACTCTCCTCATA
*
6460062 ATGTTTTGTAACTCTCCTCATT
1 ATG-TTTGTAACTCTCCTCATA
6460084 ATGTTTGT
1 ATGTTTGT
6460092 TTTAAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.51
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:6460237 original size:25 final size:23
Alignment explanation
Indices: 6460189--6460236 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
6460179 ACTTTTGTTC
*
6460189 TCTCTCAAAATTTGTTCATATTT
1 TCTCTCAAAATTAGTTCATATTT
6460212 TCTCTCAAAATTCCAGTTC-TATTT
1 TCTCTCAAAATT--AGTTCATATTT
6460236 T
1 T
6460237 TAGTGATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 12 0.55
24 6 0.27
25 4 0.18
ACGTcount: A:0.25, C:0.21, G:0.04, T:0.50
Consensus pattern (23 bp):
TCTCTCAAAATTAGTTCATATTT
Found at i:6460483 original size:11 final size:12
Alignment explanation
Indices: 6460456--6460489 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
6460446 TTATTTGTTT
*
6460456 TTAAATTTATTA
1 TTAAATTTATAA
6460468 TTAAATTTA-AA
1 TTAAATTTATAA
6460479 TTAAATTTATA
1 TTAAATTTATA
6460490 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATTTATAA
Found at i:6463782 original size:21 final size:21
Alignment explanation
Indices: 6463756--6463806 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
6463746 ACAAAACATT
*
6463756 ATGTTTGTAACTCTCCTTATA
1 ATGTTTGTAACTCTCCTCATA
*
6463777 ATGTTTTGTAACTCTCCTCATT
1 ATG-TTTGTAACTCTCCTCATA
6463799 ATGTTTGT
1 ATGTTTGT
6463807 TTTAAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.51
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:6464198 original size:11 final size:11
Alignment explanation
Indices: 6464171--6464206 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
6464161 TTATTTGTTT
*
6464171 TTAAATTTATTA
1 TTAAATTTA-AA
6464183 TTAAATTTAAA
1 TTAAATTTAAA
6464194 TTAAATTTAAA
1 TTAAATTTAAA
6464205 TT
1 TT
6464207 TTTTATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:6464591 original size:13 final size:13
Alignment explanation
Indices: 6464573--6464597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6464563 TTGAACCATT
6464573 CCACATGGCCAGA
1 CCACATGGCCAGA
6464586 CCACATGGCCAG
1 CCACATGGCCAG
6464598 GTGATCCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.40, G:0.24, T:0.08
Consensus pattern (13 bp):
CCACATGGCCAGA
Found at i:6467827 original size:30 final size:31
Alignment explanation
Indices: 6467791--6467854 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
6467781 TTTAATACGT
*
6467791 AAATTTTAATT-TGGTGT-AATTATATACATG
1 AAATTTTAATTGTGGT-TCAAATATATACATG
* *
6467821 AAATTTTGATTGTGGTTCAAATGTATACATG
1 AAATTTTAATTGTGGTTCAAATATATACATG
6467852 AAA
1 AAA
6467855 CTCTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.42
Consensus pattern (31 bp):
AAATTTTAATTGTGGTTCAAATATATACATG
Found at i:6468057 original size:29 final size:30
Alignment explanation
Indices: 6468021--6468085 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
6468011 AAATTTCTTG
** *
6468021 TATAAAATTGTACA-AAATTAAAGTTCATA
1 TATAAAATTACACATAAACTAAAGTTCATA
*
6468050 TATAAAATTACACATTAAACTAAAGTTCATG
1 TATAAAATTACACA-TAAACTAAAGTTCATA
6468081 TATAA
1 TATAA
6468086 TTTGAGATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.40
31 18 0.60
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (30 bp):
TATAAAATTACACATAAACTAAAGTTCATA
Found at i:6473266 original size:29 final size:29
Alignment explanation
Indices: 6473234--6473292 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
6473224 TCCACCTTGA
* * *
6473234 CACGAATTCTCTACAAACAAGTTCTTCAC
1 CACGAACTCTCAACAAACAAGTTCTCCAC
*
6473263 CACGAACTCTCAACGAACAAGTTCTCCAC
1 CACGAACTCTCAACAAACAAGTTCTCCAC
6473292 C
1 C
6473293 TTTTCCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.36, G:0.08, T:0.22
Consensus pattern (29 bp):
CACGAACTCTCAACAAACAAGTTCTCCAC
Found at i:6490872 original size:42 final size:42
Alignment explanation
Indices: 6490798--6490982 Score: 262
Period size: 42 Copynumber: 4.4 Consensus size: 42
6490788 TATGCTCTAA
* * * * * * *
6490798 CGAGTCATAAGTCTTCCTATAATCGTATTCTCATTCCCATCC
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
* *
6490840 CGAGACATGAGTTTTCCTTTAATCATAATCTCATTCTCTTCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
6490882 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
* *
6490924 CGAGACATTAGTCTTCCTTTAATCATAATCTCATTCTCTTCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
*
6490966 CAAGACATGAGTCTTCC
1 CGAGACATGAGTCTTCC
6490983 CTTTTATACA
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 128 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
Found at i:6493326 original size:91 final size:91
Alignment explanation
Indices: 6493171--6493347 Score: 345
Period size: 91 Copynumber: 1.9 Consensus size: 91
6493161 GCTCATTAAT
6493171 GTACAACAAGGAATGAGTACTAAGGAGAGAGGGGTGGTTGCTATGAAAGACGGTTCACCCAATCT
1 GTACAACAAGGAATGAGTACTAAGGAGAGAGGGGTGGTTGCTATGAAAGACGGTTCACCCAATCT
6493236 AGGTGGAAAGTTTTGTCACATATAAC
66 AGGTGGAAAGTTTTGTCACATATAAC
*
6493262 GTACAACAAGGAATGAGTACTAATGAGAGAGGGGTGGTTGCTATGAAAGACGGTTCACCCAATCT
1 GTACAACAAGGAATGAGTACTAAGGAGAGAGGGGTGGTTGCTATGAAAGACGGTTCACCCAATCT
6493327 AGGTGGAAAGTTTTGTCACAT
66 AGGTGGAAAGTTTTGTCACAT
6493348 CCTAAAAATC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (91 bp):
GTACAACAAGGAATGAGTACTAAGGAGAGAGGGGTGGTTGCTATGAAAGACGGTTCACCCAATCT
AGGTGGAAAGTTTTGTCACATATAAC
Found at i:6495124 original size:46 final size:47
Alignment explanation
Indices: 6495031--6495133 Score: 136
Period size: 47 Copynumber: 2.2 Consensus size: 47
6495021 GTGGTTTAAC
* * *
6495031 CACATATCTGTTCTGACATCTTGGCTGTAATTATAGTGGCTCAACCA
1 CACATATCTGTTCTGACAGCTTGACTGCAATTATAGTGGCTCAACCA
* **
6495078 CACATATCTGTTCTGGCAGCTTGACTGCAA-TATAGTGGCTTGACCA
1 CACATATCTGTTCTGACAGCTTGACTGCAATTATAGTGGCTCAACCA
*
6495124 CATATATCTG
1 CACATATCTG
6495134 ATTTAGCAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 23 0.47
47 26 0.53
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (47 bp):
CACATATCTGTTCTGACAGCTTGACTGCAATTATAGTGGCTCAACCA
Found at i:6495151 original size:46 final size:47
Alignment explanation
Indices: 6495031--6495162 Score: 117
Period size: 46 Copynumber: 2.8 Consensus size: 47
6495021 GTGGTTTAAC
* ** * *
6495031 CACATATCTGTTCT-GACATCTTGGCTGTAATTATAGTGGCTCAACCA
1 CACATATCTGTTCTAG-CAGCTTAACTGCAACTATAGTGGCTCAACCA
* * **
6495078 CACATATCTGTTCTGGCAGCTTGACTGCAA-TATAGTGGCTTGACCA
1 CACATATCTGTTCTAGCAGCTTAACTGCAACTATAGTGGCTCAACCA
* * *
6495124 CATATATCTGATT-TAGCAGTTTAACTGCAACTCTAGTGG
1 CACATATCTG-TTCTAGCAGCTTAACTGCAACTATAGTGG
6495163 TAATGTCCAC
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
46 37 0.51
47 34 0.47
48 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (47 bp):
CACATATCTGTTCTAGCAGCTTAACTGCAACTATAGTGGCTCAACCA
Found at i:6497674 original size:19 final size:19
Alignment explanation
Indices: 6497652--6497688 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6497642 TACAAATTCT
*
6497652 TTATTTATTTTTTAATTTC
1 TTATGTATTTTTTAATTTC
*
6497671 TTATGTATTTTTTTATTT
1 TTATGTATTTTTTAATTT
6497689 TTGACACATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (19 bp):
TTATGTATTTTTTAATTTC
Found at i:6500513 original size:32 final size:32
Alignment explanation
Indices: 6500477--6500543 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
6500467 CTATCATGGA
*
6500477 TTAAAGGTTCGATGACTATGTGTCATCGTGAG
1 TTAAAGGTTCGATAACTATGTGTCATCGTGAG
*
6500509 TTAAAGGTTTGATAACTATGTGTCATCGTGAG
1 TTAAAGGTTCGATAACTATGTGTCATCGTGAG
6500541 TTA
1 TTA
6500544 TATGAATCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.37
Consensus pattern (32 bp):
TTAAAGGTTCGATAACTATGTGTCATCGTGAG
Found at i:6500575 original size:85 final size:85
Alignment explanation
Indices: 6500438--6500593 Score: 260
Period size: 85 Copynumber: 1.8 Consensus size: 85
6500428 AAGTCCGATG
* *
6500438 ACTATGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAAAGGTTCGATGA-CTATGTGTCA
1 ACTATGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAAAGGTCCGATGACCT-TGTGTCA
6500502 TCGTGAGTTAAAGGTTTGATA
65 TCGTGAGTTAAAGGTTTGATA
* *
6500523 ACTATGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAGGGTCCGATGACCTTGTGTCAT
1 ACTATGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAAAGGTCCGATGACCTTGTGTCAT
6500588 CGTGAG
66 CGTGAG
6500594 ATATACGAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
85 64 0.97
86 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.35
Consensus pattern (85 bp):
ACTATGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAAAGGTCCGATGACCTTGTGTCAT
CGTGAGTTAAAGGTTTGATA
Found at i:6500636 original size:52 final size:53
Alignment explanation
Indices: 6500509--6500645 Score: 170
Period size: 52 Copynumber: 2.6 Consensus size: 53
6500499 TCATCGTGAG
** * * * * *
6500509 TTAAAGGTTTGATAACTATGTGTCATCGTGAGTTATATGAATCCTATTACGGA
1 TTAAAGGTCCGATGACTCTGTGTCATCGTGAGATATACGAATCCTATCACGGA
* *
6500562 TTAAGGGTCCGATGAC-CTTGTGTCATCGTGAGATATACGAAT-CTATCATGGA
1 TTAAAGGTCCGATGACTC-TGTGTCATCGTGAGATATACGAATCCTATCACGGA
6500614 TTAAAGGTCCGATGACTCTGTGTCATCGTGAG
1 TTAAAGGTCCGATGACTCTGTGTCATCGTGAG
6500646 TTTTCAAATG
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
52 37 0.51
53 35 0.49
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (53 bp):
TTAAAGGTCCGATGACTCTGTGTCATCGTGAGATATACGAATCCTATCACGGA
Found at i:6501262 original size:53 final size:53
Alignment explanation
Indices: 6501143--6501442 Score: 406
Period size: 53 Copynumber: 5.7 Consensus size: 53
6501133 CACATTTGAA
* * * * *
6501143 AACTCACGATGACACAGAGTTATCGGACCTTTAATCCATGAT-GGATTCGTAT
1 AACTCACAATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCATAT
* * * * *
6501195 ATCTCACGATGACACA-AGCTCATCGAACCCTTAATCCGTAATAGGATTCATAT
1 AACTCACAATGACACATAG-TCATCGAACCTTTAATCCATGATAGGATTCATAT
* * *
6501248 AACTCACAATGACACATAGTCATTGAACCTTTAATCCGTAATAGGATTCATAT
1 AACTCACAATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCATAT
6501301 AACTCACAATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCATAT
1 AACTCACAATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCATAT
* * *
6501354 AACTCACAATGACACATAGTCATCGGACCTTTAATCCATGATAAGATCCATAT
1 AACTCACAATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCATAT
* * *
6501407 AACTCACGATGACACATAGTCATCGGACTTTTAATC
1 AACTCACAATGACACATAGTCATCGAACCTTTAATC
6501443 TTTGGCACAA
Statistics
Matches: 226, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
51 2 0.01
52 33 0.15
53 189 0.84
54 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (53 bp):
AACTCACAATGACACATAGTCATCGAACCTTTAATCCATGATAGGATTCATAT
Found at i:6508115 original size:41 final size:41
Alignment explanation
Indices: 6508046--6508263 Score: 274
Period size: 41 Copynumber: 5.2 Consensus size: 41
6508036 TCAAGTTATA
* * * **
6508046 AGTCTTCCTTTAACCATATTCTCATTCTCAACTCGAGACATG
1 AGTCTTCC-TTAATCAAAATCTCATTCTCATTTCGAGACATG
6508088 AGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGACATG
1 AGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGACATG
* *
6508129 AGTCTTCCTTATTCATAATCTCATTCTCATTTCGAGACATG
1 AGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGACATG
*
6508170 AGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAAACATG
1 AGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGACATG
* ** * ***
6508211 AGTCTTCCATTTATACAATTTCTCATGCTCAACCCGAGACATG
1 AGTCTTCC-TTAAT-CAAAATCTCATTCTCATTTCGAGACATG
6508254 AGTCTTCCTT
1 AGTCTTCCTT
6508264 TTTATACACC
Statistics
Matches: 156, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
41 113 0.72
42 14 0.09
43 29 0.19
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (41 bp):
AGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGACATG
Found at i:6508156 original size:82 final size:83
Alignment explanation
Indices: 6508046--6508263 Score: 325
Period size: 82 Copynumber: 2.6 Consensus size: 83
6508036 TCAAGTTATA
6508046 AGTCTTCCTTTA-ACCATATTCTCATTCTCAACTCGAGACATGAGTCTTCCTTAATCAAAATCTC
1 AGTCTTCCTTTATA-CATATTCTCATTCTCAACTCGAGACATGAGTCTTCCTTAATCAAAATCTC
*
6508110 ATTCTCATTTCGAGACATG
65 ATTCTCATTTCGAAACATG
* * **
6508129 AGTCTTCC-TTATTCATAATCTCATTCTCATTTCGAGACATGAGTCTTCCTTAATCAAAATCTCA
1 AGTCTTCCTTTATACATATTCTCATTCTCAACTCGAGACATGAGTCTTCCTTAATCAAAATCTCA
6508193 TTCTCATTTCGAAACATG
66 TTCTCATTTCGAAACATG
* *
6508211 AGTCTTCCATTTATACA-ATTTCTCATGCTCAACCCGAGACATGAGTCTTCCTT
1 AGTCTTCC-TTTATACATA-TTCTCATTCTCAACTCGAGACATGAGTCTTCCTT
6508264 TTTATACACC
Statistics
Matches: 120, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
82 76 0.63
83 9 0.08
84 35 0.29
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (83 bp):
AGTCTTCCTTTATACATATTCTCATTCTCAACTCGAGACATGAGTCTTCCTTAATCAAAATCTCA
TTCTCATTTCGAAACATG
Found at i:6512074 original size:22 final size:22
Alignment explanation
Indices: 6512044--6512098 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
6512034 AGGTTTATTC
6512044 AGTTCGTTTATGTTCACGAACA
1 AGTTCGTTTATGTTCACGAACA
*
6512066 AGTTTGTTTATGTTCACGAACA
1 AGTTCGTTTATGTTCACGAACA
6512088 AGTTCGTTTAT
1 AGTTCGTTTAT
6512099 TGACTCGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (22 bp):
AGTTCGTTTATGTTCACGAACA
Found at i:6512182 original size:15 final size:15
Alignment explanation
Indices: 6512162--6512195 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6512152 TGTCTGTATG
6512162 TATTTATTTATTTAT
1 TATTTATTTATTTAT
*
6512177 TATTTATTTGTTTAT
1 TATTTATTTATTTAT
6512192 TATT
1 TATT
6512196 CATCAAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TATTTATTTATTTAT
Found at i:6517434 original size:111 final size:111
Alignment explanation
Indices: 6517240--6517465 Score: 452
Period size: 111 Copynumber: 2.0 Consensus size: 111
6517230 ACATTCAAAT
6517240 CTCAAAAGAGACTGCATTATAACCAAATTTACTTCAATTGGGAGTCAACAGAACCAATAATAACA
1 CTCAAAAGAGACTGCATTATAACCAAATTTACTTCAATTGGGAGTCAACAGAACCAATAATAACA
6517305 TGAGCCTCAGCCTCAAAAATTCCTCAAAACACAGTAGTTTGTATCC
66 TGAGCCTCAGCCTCAAAAATTCCTCAAAACACAGTAGTTTGTATCC
6517351 CTCAAAAGAGACTGCATTATAACCAAATTTACTTCAATTGGGAGTCAACAGAACCAATAATAACA
1 CTCAAAAGAGACTGCATTATAACCAAATTTACTTCAATTGGGAGTCAACAGAACCAATAATAACA
6517416 TGAGCCTCAGCCTCAAAAATTCCTCAAAACACAGTAGTTTGTATCC
66 TGAGCCTCAGCCTCAAAAATTCCTCAAAACACAGTAGTTTGTATCC
6517462 CTCA
1 CTCA
6517466 GCCAGTAGGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 115 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (111 bp):
CTCAAAAGAGACTGCATTATAACCAAATTTACTTCAATTGGGAGTCAACAGAACCAATAATAACA
TGAGCCTCAGCCTCAAAAATTCCTCAAAACACAGTAGTTTGTATCC
Found at i:6518272 original size:30 final size:30
Alignment explanation
Indices: 6518232--6518289 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6518222 ATTGTTTACC
6518232 TTTCAGCTTCATCAATTTGACAGAAAAATG
1 TTTCAGCTTCATCAATTTGACAGAAAAATG
* * *
6518262 TTTCATCTTCATCAGTTTGATAGAAAAA
1 TTTCAGCTTCATCAATTTGACAGAAAAA
6518290 ATATCAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (30 bp):
TTTCAGCTTCATCAATTTGACAGAAAAATG
Found at i:6518311 original size:21 final size:20
Alignment explanation
Indices: 6518272--6518310 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6518262 TTTCATCTTC
*
6518272 ATCAGTTTGATAGAAAAAAT
1 ATCAGTTTGACAGAAAAAAT
6518292 ATCAGTTTGACAGAAAAAA
1 ATCAGTTTGACAGAAAAAA
6518311 AAAAGTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCAGTTTGACAGAAAAAAT
Found at i:6518317 original size:19 final size:19
Alignment explanation
Indices: 6518275--6518332 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
6518265 CATCTTCATC
* **
6518275 AGTTTGATAGAAAAAATATC
1 AGTTTGACAGAAAAAA-AAA
6518295 AGTTTGACAGAAAAAAAAA
1 AGTTTGACAGAAAAAAAAA
* *
6518314 AGTTTCAGAGAAGAAAAAA
1 AGTTTGACAGAA-AAAAAA
6518333 GAAAAAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.21
Consensus pattern (19 bp):
AGTTTGACAGAAAAAAAAA
Found at i:6526006 original size:25 final size:25
Alignment explanation
Indices: 6525970--6526020 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
6525960 TATAATTCAA
6525970 AGAACAAGAATAAAGTGAAAGAATG
1 AGAACAAGAATAAAGTGAAAGAATG
* * *
6525995 AGAACAATAATAAATTGAAGGAATG
1 AGAACAAGAATAAAGTGAAAGAATG
6526020 A
1 A
6526021 AAAATGATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.16
Consensus pattern (25 bp):
AGAACAAGAATAAAGTGAAAGAATG
Found at i:6526809 original size:30 final size:29
Alignment explanation
Indices: 6526744--6526811 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
6526734 AAATTTTAAA
* *
6526744 TTAATAAA-AATAAAATTATACTTTCACCT
1 TTAA-AAATAATAAAATTATAATTTAACCT
*
6526773 TCTAAAAATAATAAAATTTTAATTTAATCCT
1 T-TAAAAATAATAAAATTATAATTTAA-CCT
6526804 TTAAAAAT
1 TTAAAAAT
6526812 CATATTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 4 0.12
30 25 0.76
31 4 0.12
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (29 bp):
TTAAAAATAATAAAATTATAATTTAACCT
Found at i:6530196 original size:16 final size:16
Alignment explanation
Indices: 6530154--6530198 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
6530144 ATAATGTATT
6530154 ATTTTAATATT-TTAC
1 ATTTTAATATTATTAC
*
6530169 -TTTTAAAATTATTAC
1 ATTTTAATATTATTAC
*
6530184 ATTTTAATTTTATTA
1 ATTTTAATATTATTA
6530199 TCATATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 12 0.48
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAATATTATTAC
Found at i:6530345 original size:25 final size:25
Alignment explanation
Indices: 6530317--6530448 Score: 88
Period size: 25 Copynumber: 5.6 Consensus size: 25
6530307 AATTTGAAAA
6530317 GAAAAAACAAAAAAATAATAAAAGG
1 GAAAAAACAAAAAAATAATAAAAGG
* * *
6530342 GAAAAAAC-CAAAAAGAATTAAA--
1 GAAAAAACAAAAAAATAATAAAAGG
*
6530364 -ACAAAAC-AAAAAATAATAAAAGG
1 GAAAAAACAAAAAAATAATAAAAGG
*
6530387 GAACAAACCAAAAAGAAT--TAAAA--
1 GAA-AAAACAAAAA-AATAATAAAAGG
* *
6530410 CAAAACAA-AAAATAAATAACAAAAGG
1 GAAAA-AACAAAA-AAATAATAAAAGG
6530436 GAAAAAA-AAAAAA
1 GAAAAAACAAAAAA
6530449 GAATTAAAAC
Statistics
Matches: 82, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
21 17 0.21
22 9 0.11
23 4 0.05
24 18 0.22
25 23 0.28
26 8 0.10
27 3 0.04
ACGTcount: A:0.75, C:0.08, G:0.09, T:0.08
Consensus pattern (25 bp):
GAAAAAACAAAAAAATAATAAAAGG
Found at i:6530375 original size:20 final size:20
Alignment explanation
Indices: 6530345--6530420 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
6530335 TAAAAGGGAA
6530345 AAAACCAAAAAGAATTAAAAC
1 AAAA-CAAAAAGAATTAAAAC
* *
6530366 AAAACAAAAAATAATAAAAGGGAAC
1 AAAAC-AAAAAGAAT-TAA---AAC
*
6530391 AAACCAAAAAGAATTAAAAC
1 AAAACAAAAAGAATTAAAAC
6530411 AAAACAAAAA
1 AAAACAAAAA
6530421 ATAAATAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
20 13 0.30
21 12 0.27
22 2 0.05
23 2 0.05
24 8 0.18
25 7 0.16
ACGTcount: A:0.74, C:0.12, G:0.07, T:0.08
Consensus pattern (20 bp):
AAAACAAAAAGAATTAAAAC
Found at i:6530375 original size:45 final size:44
Alignment explanation
Indices: 6530320--6530615 Score: 301
Period size: 45 Copynumber: 6.3 Consensus size: 44
6530310 TTGAAAAGAA
6530320 AAAACAAAAAAATAATAAAAGGGAAAAAACCAAAAAGAATTAAAAC
1 AAAAC-AAAAAATAATAAAAGGGAAAAAA-CAAAAAGAATTAAAAC
*
6530366 AAAACAAAAAATAATAAAAGGGAACAAACCAAAAAGAATTAAAAC
1 AAAACAAAAAATAATAAAAGGGAA-AAAACAAAAAGAATTAAAAC
*
6530411 AAAACAAAAAATAAATAACAAAAGGGAAAAAAAAAAAAGAATTAAAAC
1 AAAACAAAAAAT-AAT---AAAAGGGAAAAAACAAAAAGAATTAAAAC
** * * * * *
6530459 AAAAC-AAAAATAAT--GGGGGAAACATTTTTAGGGAAAAAACAAAAATATTAAA
1 AAAACAAAAAATAATAAAAGGGAAA-A-----A---ACAAAA-AGAATTA-AAAC
6530511 ACAAAACAAAAAATAATAAAAGGGAAAAAACAAAAAGAATTAAAAC
1 A--AAACAAAAAATAATAAAAGGGAAAAAACAAAAAGAATTAAAAC
6530557 AAAACAAAAAATAATAAAAGGGAAAAAACCAAAAAGAATTAAAAC
1 AAAACAAAAAATAATAAAAGGGAAAAAA-CAAAAAGAATTAAAAC
6530602 AAAACAAAAAATAA
1 AAAACAAAAAATAA
6530616 AGGGGGAAAC
Statistics
Matches: 212, Mismatches: 16, Indels: 45
0.78 0.06 0.16
Matches are distributed among these distances:
41 6 0.03
42 1 0.00
44 27 0.13
45 77 0.36
46 17 0.08
47 12 0.06
48 28 0.13
49 9 0.04
50 6 0.03
51 6 0.03
52 3 0.01
54 4 0.02
55 9 0.04
56 1 0.00
57 6 0.03
ACGTcount: A:0.72, C:0.08, G:0.09, T:0.10
Consensus pattern (44 bp):
AAAACAAAAAATAATAAAAGGGAAAAAACAAAAAGAATTAAAAC
Found at i:6530385 original size:98 final size:95
Alignment explanation
Indices: 6530273--6530576 Score: 277
Period size: 98 Copynumber: 3.2 Consensus size: 95
6530263 TGCATAAGAT
*
6530273 AAAAACATAA-AAAAGAAAAGAAAAGAAAAAGAAAAATTTGAAAAGAAAAAACAAAAAAATAATA
1 AAAAA-ATAATAAAAGAAAACAAAAGAAAAAGAAAAATTT-AAAA-AAAAAACAAAAAAATAATA
6530337 AAAGGGAAAAAACCAAAAAGAATTAAAACAAAAC
63 AAAGGGAAAAAA-CAAAAAGAATTAAAACAAAAC
** ** *
6530371 AAAAAATAATAAAAGGGAACAAACCAAAAAG---AA-TTAAAACAAAACAA-AAAATAAATAACA
1 AAAAAATAATAAAAGAAAACAAAAGAAAAAGAAAAATTTAAAA-AAAA-AACAAAA-AAATAATA
*
6530431 AAAGGGAAAAAAAAAAAAGAATTAAAACAAAAC
63 AAAGGGAAAAAACAAAAAGAATTAAAACAAAAC
*** * ** * *
6530464 -AAAAATAAT-GGGGGAAACATTTTTAGGGAAAAAACAAAAATATT-AAAACAAAAC-AAAAAAT
1 AAAAAATAATAAAAGAAAACA-----AAAG-AAAAAGAAAAAT-TTAAAAAAAAAACAAAAAAAT
6530525 AATAAAAGGGAAAAAACAAAAAGAATTAAAACAAAAC
59 AATAAAAGGGAAAAAACAAAAAGAATTAAAACAAAAC
6530562 AAAAAATAATAAAAG
1 AAAAAATAATAAAAG
6530577 GGAAAAAACC
Statistics
Matches: 167, Mismatches: 22, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
91 6 0.04
92 9 0.05
93 32 0.19
94 23 0.14
95 2 0.01
96 1 0.01
97 9 0.05
98 60 0.36
99 14 0.08
100 6 0.04
101 3 0.02
102 2 0.01
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.11
Consensus pattern (95 bp):
AAAAAATAATAAAAGAAAACAAAAGAAAAAGAAAAATTTAAAAAAAAAACAAAAAAATAATAAAA
GGGAAAAAACAAAAAGAATTAAAACAAAAC
Found at i:6530540 original size:24 final size:21
Alignment explanation
Indices: 6530492--6530615 Score: 92
Period size: 21 Copynumber: 5.8 Consensus size: 21
6530482 ATTTTTAGGG
*
6530492 AAAAAAC-AAAAAT-ATTAAA
1 AAAAAACAAAAAATAATAAAA
*
6530511 ACAAAACAAAAAATAATAAAA
1 AAAAAACAAAAAATAATAAAA
* *
6530532 GGGAAAAAAC-AAAAAGAATTAAA
1 ---AAAAAACAAAAAATAATAAAA
*
6530555 ACAAAACAAAAAATAATAAAA
1 AAAAAACAAAAAATAATAAAA
* * *
6530576 GGGAAAAAACCAAAAAGAATTAAA
1 ---AAAAAACAAAAAATAATAAAA
*
6530600 ACAAAACAAAAAATAA
1 AAAAAACAAAAAATAA
6530616 AGGGGGAAAC
Statistics
Matches: 81, Mismatches: 15, Indels: 16
0.72 0.13 0.14
Matches are distributed among these distances:
19 6 0.07
20 12 0.15
21 29 0.36
23 11 0.14
24 23 0.28
ACGTcount: A:0.76, C:0.08, G:0.06, T:0.10
Consensus pattern (21 bp):
AAAAAACAAAAAATAATAAAA
Found at i:6530640 original size:144 final size:142
Alignment explanation
Indices: 6530339--6530733 Score: 623
Period size: 144 Copynumber: 2.7 Consensus size: 142
6530329 AAATAATAAA
* *
6530339 AGGGAAAAAACCAAAAAGAATTAAAACAAAACAAAAAATAATAAAAGGGAACAAACCAAAAAGAA
1 AGGGAAAAAA-CAAAAA-TATTAAAACAAAACAAAAAATAATAAAAGGGAA-AAAACAAAAAGAA
*
6530404 TTAAAACAAAACAAAAAATAAATAACAAAAGGGAAAAAAAAAAAAGAATTAAAACAAAACAAAAA
63 TTAAAACAAAACAAAAAAT-AAT---AAAAGGGAAAAAACAAAAAGAATTAAAACAAAACAAAAA
*
6530469 TAATGGGGGAAACATTTTT
124 TAAAGGGGGAAACATTTTT
6530488 AGGGAAAAAACAAAAATATTAAAACAAAACAAAAAATAATAAAAGGGAAAAAACAAAAAGAATTA
1 AGGGAAAAAACAAAAATATTAAAACAAAACAAAAAATAATAAAAGGGAAAAAACAAAAAGAATTA
6530553 AAACAAAACAAAAAATAATAAAAGGGAAAAAACCAAAAAGAATTAAAACAAAACAAAAAATAAAG
66 AAACAAAACAAAAAATAATAAAAGGGAAAAAA-CAAAAAGAATTAAAACAAAAC-AAAAATAAAG
6530618 GGGGAAACATTTTT
129 GGGGAAACATTTTT
6530632 AGGGAAAAAAACAAAAATGATTAAAACAAAACAAAAAATAATAAAA-GG-AAAAACAAAAAGAAT
1 AGGG-AAAAAACAAAAAT-ATTAAAACAAAACAAAAAATAATAAAAGGGAAAAAACAAAAAGAAT
* *
6530695 TAAAATAAAACAAAAAATAATAAAAGGGTAAAAACAAAA
64 TAAAACAAAACAAAAAATAATAAAAGGGAAAAAACAAAA
6530734 CAAAAAATGA
Statistics
Matches: 236, Mismatches: 6, Indels: 14
0.92 0.02 0.05
Matches are distributed among these distances:
142 13 0.06
143 25 0.11
144 74 0.31
145 18 0.08
146 58 0.25
147 32 0.14
148 6 0.03
149 10 0.04
ACGTcount: A:0.70, C:0.08, G:0.11, T:0.11
Consensus pattern (142 bp):
AGGGAAAAAACAAAAATATTAAAACAAAACAAAAAATAATAAAAGGGAAAAAACAAAAAGAATTA
AAACAAAACAAAAAATAATAAAAGGGAAAAAACAAAAAGAATTAAAACAAAACAAAAATAAAGGG
GGAAACATTTTT
Found at i:6530668 original size:21 final size:21
Alignment explanation
Indices: 6530639--6530712 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
6530629 TTTAGGGAAA
6530639 AAAAC-AAAAATGATTAAAAC
1 AAAACAAAAAATGATTAAAAC
* *
6530659 AAAACAAAAAAT-AATAAAAGG
1 AAAACAAAAAATGATTAAAA-C
*
6530680 AAAA-ACAAAAA-GAATTAAAAT
1 AAAACA-AAAAATG-ATTAAAAC
6530701 AAAACAAAAAAT
1 AAAACAAAAAAT
6530713 AATAAAAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 12 0.28
21 24 0.56
22 7 0.16
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAACAAAAAATGATTAAAAC
Found at i:6530684 original size:42 final size:44
Alignment explanation
Indices: 6530638--6530733 Score: 153
Period size: 42 Copynumber: 2.2 Consensus size: 44
6530628 TTTTAGGGAA
6530638 AAAAACAAAAATG-ATTAAAACAAAACAAAAAATAATAAAA-GG-
1 AAAAACAAAAA-GAATTAAAACAAAACAAAAAATAATAAAAGGGT
*
6530680 AAAAACAAAAAGAATTAAAATAAAACAAAAAATAATAAAAGGGT
1 AAAAACAAAAAGAATTAAAACAAAACAAAAAATAATAAAAGGGT
6530724 AAAAACAAAA
1 AAAAACAAAA
6530734 CAAAAAATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
41 1 0.02
42 37 0.74
43 2 0.04
44 10 0.20
ACGTcount: A:0.75, C:0.06, G:0.07, T:0.11
Consensus pattern (44 bp):
AAAAACAAAAAGAATTAAAACAAAACAAAAAATAATAAAAGGGT
Found at i:6530718 original size:20 final size:20
Alignment explanation
Indices: 6530636--6530719 Score: 82
Period size: 20 Copynumber: 4.1 Consensus size: 20
6530626 ATTTTTAGGG
*
6530636 AAAAAAAC-AAAAATGATTAA
1 AAAAAAACAAAAAAT-AATAA
*
6530656 AACAAAACAAAAAATAATAA
1 AAAAAAACAAAAAATAATAA
*
6530676 AAGGAAAAACAAAAAGA-ATTAA
1 AA--AAAAACAAAAA-ATAATAA
*
6530698 AATAAAACAAAAAATAATAA
1 AAAAAAACAAAAAATAATAA
6530718 AA
1 AA
6530720 GGGTAAAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.02
20 29 0.55
21 6 0.11
22 16 0.30
23 1 0.02
ACGTcount: A:0.77, C:0.06, G:0.05, T:0.12
Consensus pattern (20 bp):
AAAAAAACAAAAAATAATAA
Found at i:6530718 original size:102 final size:101
Alignment explanation
Indices: 6530531--6530714 Score: 313
Period size: 102 Copynumber: 1.8 Consensus size: 101
6530521 AAATAATAAA
6530531 AGGGAAAAAACAAAAAGAATTAAAACAAAACAAAAAATAATAAAAGGGAAAAAACCAAAAAGAAT
1 AGGGAAAAAACAAAAAGAATTAAAACAAAACAAAAAATAATAAAAGGGAAAAAACCAAAAAGAAT
6530596 TAAAACAAAACAAAAAATAAAGGGGGAAACATTTTT
66 TAAAACAAAACAAAAAATAAAGGGGGAAACATTTTT
6530632 AGGGAAAAAAACAAAAATG-ATTAAAACAAAACAAAAAATAATAAAA-GG-AAAAA-CAAAAAGA
1 AGGG-AAAAAACAAAAA-GAATTAAAACAAAACAAAAAATAATAAAAGGGAAAAAACCAAAAAGA
*
6530693 ATTAAAATAAAACAAAAAATAA
64 ATTAAAACAAAACAAAAAATAA
6530715 TAAAAGGGTA
Statistics
Matches: 80, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
99 29 0.36
100 5 0.06
101 6 0.08
102 39 0.49
103 1 0.01
ACGTcount: A:0.71, C:0.07, G:0.11, T:0.11
Consensus pattern (101 bp):
AGGGAAAAAACAAAAAGAATTAAAACAAAACAAAAAATAATAAAAGGGAAAAAACCAAAAAGAAT
TAAAACAAAACAAAAAATAAAGGGGGAAACATTTTT
Found at i:6530903 original size:27 final size:25
Alignment explanation
Indices: 6530853--6530903 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
6530843 CTTTTTATAA
*
6530853 CAATTTTTTTCATAAAATTCTTTTC
1 CAATTTTTTTCATAAAATTATTTTC
*
6530878 CAATTTTTTTCTAATAAATTTATTTT
1 CAATTTTTTTC--ATAAAATTATTTT
6530904 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
27 11 0.50
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (25 bp):
CAATTTTTTTCATAAAATTATTTTC
Found at i:6530909 original size:27 final size:25
Alignment explanation
Indices: 6530854--6530910 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
6530844 TTTTTATAAC
* *
6530854 AATTTTTTTCATAAAATTCTTTTCC
1 AATTTTTTTCATAAAATTATTTTCA
* *
6530879 AATTTTTTTCTAATAAATTTATTTTTA
1 AATTTTTTTC--ATAAAATTATTTTCA
6530906 AATTT
1 AATTT
6530911 AAAATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 10 0.38
27 16 0.62
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (25 bp):
AATTTTTTTCATAAAATTATTTTCA
Found at i:6532111 original size:24 final size:24
Alignment explanation
Indices: 6532083--6532157 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
6532073 AGAAATAATC
* *
6532083 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTATTTATTTG
*
6532107 TTTCAATTAAACTCTATTTATTTA
1 TTTCAATTAAACTCTATTTATTTG
6532131 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
6532155 TTT
1 TTT
6532158 GGTCAAACTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:6533361 original size:13 final size:13
Alignment explanation
Indices: 6533310--6533376 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
6533300 ATTATGTGTT
**
6533310 AAATGATTATACA
1 AAATGATTATATG
*
6533323 AAAT-CTTATATG
1 AAATGATTATATG
**
6533335 AAAAAATATATATG
1 AAATGAT-TATATG
6533349 AAATGATTATATG
1 AAATGATTATATG
* *
6533362 AAGTGTTTATATG
1 AAATGATTATATG
6533375 AA
1 AA
6533377 GTAGTGGTAG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 8 0.19
13 24 0.56
14 11 0.26
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (13 bp):
AAATGATTATATG
Found at i:6535520 original size:2 final size:2
Alignment explanation
Indices: 6535513--6535547 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6535503 AAAAATCAAG
6535513 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6535548 GAAAAATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6536125 original size:158 final size:158
Alignment explanation
Indices: 6535837--6536135 Score: 411
Period size: 158 Copynumber: 1.9 Consensus size: 158
6535827 ACAGTTACAG
* * * ** * *
6535837 CTCGTGTGAGCATTACAGGTTATATGGTTATTGGTTTTAGATGTCGTACCGATGGCTGAGGTCCT
1 CTCGTGTGAGAATTACAAGTTATATGGGTATTGGTCCTAGATGTCGTACCGATGGCTAAGGTCCG
* * * *
6535902 GTATTGGTTACGGATTCTTCATAGCTCGTGTGAGCAGCATCGCGTAGCCTAACATCTCGACCCAC
66 GTATTGATTACGGATTCTCCACAGCTCGTGTGAGCAACATCGCGTAGCCTAACATCTCGACCCAC
*
6535967 AGTTCGTGTGACTAGGCCCATTTCACAA
131 AGCTCGTGTGACTAGGCCCATTTCACAA
* * **
6535995 CTCGTGTGAGAATTACAAGTTATATGGGTGTTGGTCCTAGATGTCTTATTGATGGCTAAGGTCCG
1 CTCGTGTGAGAATTACAAGTTATATGGGTATTGGTCCTAGATGTCGTACCGATGGCTAAGGTCCG
* * *
6536060 GTATTTATTACGGATTCTCCACAGCTCGTGTGAGCAACATCGTGTAGTCC-CACATCTCGACCCA
66 GTATTGATTACGGATTCTCCACAGCTCGTGTGAGCAACATCGCGTAG-CCTAACATCTCGACCCA
6536124 CAGCTCGTGTGA
130 CAGCTCGTGTGA
6536136 GCATATATGG
Statistics
Matches: 121, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
158 119 0.98
159 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (158 bp):
CTCGTGTGAGAATTACAAGTTATATGGGTATTGGTCCTAGATGTCGTACCGATGGCTAAGGTCCG
GTATTGATTACGGATTCTCCACAGCTCGTGTGAGCAACATCGCGTAGCCTAACATCTCGACCCAC
AGCTCGTGTGACTAGGCCCATTTCACAA
Found at i:6547614 original size:12 final size:13
Alignment explanation
Indices: 6547597--6547629 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6547587 ACAAATTGAG
6547597 TTAGTTTTTA-TT
1 TTAGTTTTTAGTT
*
6547609 TTAGTTCTTAGTT
1 TTAGTTTTTAGTT
6547622 TTAGTTTT
1 TTAGTTTT
6547630 CATGCATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.15, C:0.03, G:0.12, T:0.70
Consensus pattern (13 bp):
TTAGTTTTTAGTT
Found at i:6547697 original size:34 final size:34
Alignment explanation
Indices: 6547654--6547721 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
6547644 AGTTATAATG
* *
6547654 TAATTGTCACCACAT-TCCTTTTGTCATTGCATTT
1 TAATTGTCACCACATCTAC-ATTGTCATTGCATTT
*
6547688 TAATTGTCACTACATCTACATTGTCATTGCATTT
1 TAATTGTCACCACATCTACATTGTCATTGCATTT
6547722 CCATTGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.46
Consensus pattern (34 bp):
TAATTGTCACCACATCTACATTGTCATTGCATTT
Found at i:6547726 original size:17 final size:17
Alignment explanation
Indices: 6547674--6547733 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
6547664 CACATTCCTT
6547674 TTGTCATTGCATTTTA-A
1 TTGTCATTGCA-TTTACA
* * *
6547691 TTGTCACTACATCTACA
1 TTGTCATTGCATTTACA
*
6547708 TTGTCATTGCATTTCCA
1 TTGTCATTGCATTTACA
*
6547725 TTGTTATTG
1 TTGTCATTG
6547734 TAAATTAATG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 3 0.09
17 31 0.91
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (17 bp):
TTGTCATTGCATTTACA
Found at i:6553411 original size:9 final size:8
Alignment explanation
Indices: 6553395--6553420 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6553385 GTTAATAATA
6553395 TATTTTTT
1 TATTTTTT
6553403 TATTTTTT
1 TATTTTTT
6553411 TATTTTTT
1 TATTTTTT
6553419 TA
1 TA
6553421 ATTATTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:6559953 original size:29 final size:29
Alignment explanation
Indices: 6559916--6559975 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
6559906 ATTTGCATCA
6559916 ACTTCCCAATAACGTTCCAAACCACAACT
1 ACTTCCCAATAACGTTCCAAACCACAACT
*
6559945 ACTTCCCAATAATGTTCCAAACCACAACT
1 ACTTCCCAATAACGTTCCAAACCACAACT
6559974 AC
1 AC
6559976 AGATGGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.37, G:0.03, T:0.22
Consensus pattern (29 bp):
ACTTCCCAATAACGTTCCAAACCACAACT
Found at i:6567529 original size:15 final size:16
Alignment explanation
Indices: 6567504--6567533 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6567494 CCCCTGATCG
6567504 AATACTTATTTATTAT
1 AATACTTATTTATTAT
6567520 AATA-TTATTTATTA
1 AATACTTATTTATTA
6567534 AGTTCGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
AATACTTATTTATTAT
Found at i:6571188 original size:2 final size:2
Alignment explanation
Indices: 6571181--6571207 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6571171 GCATAATAGC
6571181 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6571208 CGTAATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6571267 original size:9 final size:9
Alignment explanation
Indices: 6571249--6571279 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6571239 GTATTATACC
*
6571249 AAATATTTA
1 AAATAATTA
6571258 AAATAATTA
1 AAATAATTA
6571267 AAATAATTA
1 AAATAATTA
6571276 AAAT
1 AAAT
6571280 TTAAAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATAATTA
Found at i:6571797 original size:6 final size:6
Alignment explanation
Indices: 6571775--6571866 Score: 77
Period size: 6 Copynumber: 16.0 Consensus size: 6
6571765 AAGTTTGATA
*
6571775 TAAATT TAGATT T--ATT TAAATT TAAATT TAAA-T TAAACTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA-TT TAAATT
* * * * * *
6571821 TGAATT TGAGTC TAAATT T-ATTT TAAATT TAAAAT T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
6571867 AAAGACCAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
4 4 0.06
5 13 0.19
6 47 0.68
7 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:6571818 original size:18 final size:17
Alignment explanation
Indices: 6571775--6571866 Score: 69
Period size: 17 Copynumber: 5.4 Consensus size: 17
6571765 AAGTTTGATA
* *
6571775 TAAATTTAGATTT-ATT
1 TAAATTTAAATTTAAAT
6571791 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAT
*
6571808 TAAACTTTAAATTTGAATT
1 TAAA-TTTAAATTT-AAAT
* * * **
6571827 TGAGTCTAAATTTATTT
1 TAAATTTAAATTTAAAT
* *
6571844 TAAATTTAAAATTAATT
1 TAAATTTAAATTTAAAT
6571861 TAAATT
1 TAAATT
6571867 AAAGACCAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
16 12 0.20
17 27 0.44
18 17 0.28
19 5 0.08
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTAAAT
Found at i:6572889 original size:14 final size:14
Alignment explanation
Indices: 6572870--6572897 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6572860 ATGTTTAGAA
6572870 ATTTCCAGATCTGG
1 ATTTCCAGATCTGG
6572884 ATTTCCAGATCTGG
1 ATTTCCAGATCTGG
6572898 GATGGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
ATTTCCAGATCTGG
Found at i:6573648 original size:30 final size:30
Alignment explanation
Indices: 6573608--6573694 Score: 149
Period size: 30 Copynumber: 2.9 Consensus size: 30
6573598 CTCTGTAAGT
6573608 CCCT-AAACTTTTCCAAAATTATATTTTAA
1 CCCTAAAACTTTTCCAAAATTATATTTTAA
*
6573637 CCCTAAAACTTTTCCAAAATTACATTTTAA
1 CCCTAAAACTTTTCCAAAATTATATTTTAA
*
6573667 CCCTAAAATTTTTCCAAAATTATATTTT
1 CCCTAAAACTTTTCCAAAATTATATTTT
6573695 GACCTCAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 4 0.07
30 50 0.93
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (30 bp):
CCCTAAAACTTTTCCAAAATTATATTTTAA
Found at i:6573716 original size:60 final size:58
Alignment explanation
Indices: 6573608--6573746 Score: 160
Period size: 60 Copynumber: 2.4 Consensus size: 58
6573598 CTCTGTAAGT
6573608 CCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTTCCAAAATTACATTTTAA
1 CCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAAC-TTTCCAAAATTACATTTTAA
* * *
6573667 CCCTAAAATTTTTCCAAAATTATATTTTGA-CCTCAAAA-TTTCCAAAAAATTGCATTTTAA
1 CCCT-AAACTTTTCCAAAATTATATTTTAACCCT-AAAACTTTCC--AAAATTACATTTTAA
*
6573727 CCTCAAAAC-TTT-CAAAATTA
1 CC-CTAAACTTTTCCAAAATTA
6573747 CCATTTTACC
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
58 13 0.19
59 10 0.14
60 46 0.66
61 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.37
Consensus pattern (58 bp):
CCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTCCAAAATTACATTTTAA
Found at i:6573762 original size:29 final size:29
Alignment explanation
Indices: 6573612--6573762 Score: 144
Period size: 30 Copynumber: 5.1 Consensus size: 29
6573602 GTAAGTCCCT
* *
6573612 AAACTTTTCCAAAATTATATTTTAACCCTA
1 AAAC-TTTCCAAAATTACATTTTAACCCCA
*
6573642 AAACTTTTCCAAAATTACATTTTAACCCTA
1 AAAC-TTTCCAAAATTACATTTTAACCCCA
* * * *
6573672 AAATTTTTCCAAAATTATATTTTGACCTCA
1 AAA-CTTTCCAAAATTACATTTTAACCCCA
* *
6573702 AAA-TTTCCAAAAAATTGCATTTTAACCTCA
1 AAACTTTCC--AAAATTACATTTTAACCCCA
*
6573732 AAACTTT-CAAAATTACCATTTTACCCCCA
1 AAACTTTCCAAAATTA-CATTTTAACCCCA
6573761 AA
1 AA
6573763 CTTCCTAAAT
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.11
29 13 0.12
30 77 0.74
31 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.36
Consensus pattern (29 bp):
AAACTTTCCAAAATTACATTTTAACCCCA
Found at i:6573830 original size:29 final size:29
Alignment explanation
Indices: 6573741--6573830 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
6573731 AAAACTTTCA
**
6573741 AAATTACCATTTTACCCCCAAACTT-CCT
1 AAATTACCATTTTACCCTTAAACTTCCCT
* * * *
6573769 AAA-T-CCTATTTTTAACCTT-GATTTCACT
1 AAATTACC-A-TTTTACCCTTAAACTTCCCT
6573797 AAAATTACCATTTTACCCTTAAACTTCCCT
1 -AAATTACCATTTTACCCTTAAACTTCCCT
6573827 AAAT
1 AAAT
6573831 CTCATTTTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 13
0.66 0.15 0.19
Matches are distributed among these distances:
26 2 0.04
27 5 0.11
28 12 0.27
29 16 0.36
30 8 0.18
31 2 0.04
ACGTcount: A:0.33, C:0.28, G:0.01, T:0.38
Consensus pattern (29 bp):
AAATTACCATTTTACCCTTAAACTTCCCT
Found at i:6573853 original size:58 final size:57
Alignment explanation
Indices: 6573739--6573875 Score: 195
Period size: 58 Copynumber: 2.4 Consensus size: 57
6573729 TCAAAACTTT
* **
6573739 CAAAATTACCATTTTACCCCCAAACTTCCTAAATCCTATTTTTAACCTTGATTTCAC
1 CAAAATTACCATTTTACCCTCAAACTTCCTAAATCCTATTTTTAACCCCGATTTCAC
* *
6573796 TAAAATTACCATTTTACCCTTAAACTTCCCTAAAT-CTCATTTTTAACCCCGATTTCAC
1 CAAAATTACCATTTTACCCTCAAACTT-CCTAAATCCT-ATTTTTAACCCCGATTTCAC
6573854 CAAAATTTACCATTTTACCCTC
1 CAAAA-TTACCATTTTACCCTC
6573876 GAGTATCCAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
57 26 0.37
58 29 0.41
59 15 0.21
ACGTcount: A:0.31, C:0.30, G:0.01, T:0.37
Consensus pattern (57 bp):
CAAAATTACCATTTTACCCTCAAACTTCCTAAATCCTATTTTTAACCCCGATTTCAC
Found at i:6576853 original size:49 final size:49
Alignment explanation
Indices: 6576800--6576958 Score: 171
Period size: 49 Copynumber: 3.2 Consensus size: 49
6576790 GCCGTCGTGG
*
6576800 CTTAAATCTTTCCCTTCATGCTTCTAAGGTGTGAGGTTCGTCGTTGCGA
1 CTTAAATCTTTCCCTTCATGCTTCTAAGGTATGAGGTTCGTCGTTGCGA
* * * * * *
6576849 CTTAAA-CATTTCCCTCCATTATCTTC-ATGGTATTG-GATTCGCCGTTGCGG
1 CTTAAATC-TTTCCCTTCA-T-GCTTCTAAGGTA-TGAGGTTCGTCGTTGCGA
* *
6576899 CTTAAATCTTTCCCTTCATGCTTCTAAGGTACGAGGTTCGTCGTTACGA
1 CTTAAATCTTTCCCTTCATGCTTCTAAGGTATGAGGTTCGTCGTTGCGA
*
6576948 CTTAAACCTTT
1 CTTAAATCTTT
6576959 TCCTCCATTA
Statistics
Matches: 87, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
48 6 0.07
49 42 0.48
50 32 0.37
51 7 0.08
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (49 bp):
CTTAAATCTTTCCCTTCATGCTTCTAAGGTATGAGGTTCGTCGTTGCGA
Found at i:6576887 original size:99 final size:99
Alignment explanation
Indices: 6576769--6577307 Score: 374
Period size: 99 Copynumber: 5.5 Consensus size: 99
6576759 CTTCCTCTTG
* * **
6576769 TATCTTCGTGGTACTGGATTCGCCGTCGTGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTGTGA
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACGA
*
6576834 GGTTCGTCGTTGCGACTTAAACATTTCCCTCCAT
66 GGTTCGTCGTTACGACTTAAACATTTCCCTCCAT
* *
6576868 TATCTTCATGGTATTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACGA
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACGA
* *
6576933 GGTTCGTCGTTACGACTTAAACCTTTTCCTCCAT
66 GGTTCGTCGTTACGACTTAAACATTTCCCTCCAT
* * * **
6576967 TAGT-TTCGCGGTACTGGATTCGCCGTTGCGGCTTAAA----T--CATCAT-CTGC---GGTATA
1 TA-TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACG
* * * *
6577021 AGGTTCGCCATTGCGACTTAAACTTTTCCCT---T
65 AGGTTCGTCGTTACGACTTAAACATTTCCCTCCAT
* * * ** * *
6577053 TGTACTTTCGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCTTCACGTCCCCTGAGTTA
1 TAT-C-TTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTAAGGTA
** ** * ** * **
6577118 TAAGGTTCAACATTGGGACTTAAACCTTTCCCTTTGTATTTTT
63 CGAGGTTCGTCGTTACGACTTAAACATTTCCC--TCCA----T
* * * * * * **
6577161 GTATTTTCATGGTACTGGATTAGCCGTTGCGGCTTGAATCTTTCCCTTCGT-C-TCTATGGTATA
1 -TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACG
* * * * **
6577224 AGGTTCGCCATTGCGACTTAAACCTTTCCCT-TTT
65 AGGTTCGTCGTTACGACTTAAACATTTCCCTCCAT
* * * *
6577258 GTGTCTTCTTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCA
1 -TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCA
6577308 CGTCTTCATG
Statistics
Matches: 358, Mismatches: 57, Indels: 52
0.77 0.12 0.11
Matches are distributed among these distances:
85 1 0.00
86 2 0.01
88 31 0.09
89 30 0.08
92 4 0.01
93 5 0.01
94 4 0.01
95 1 0.00
96 2 0.01
97 43 0.12
99 153 0.43
100 1 0.00
101 2 0.01
102 1 0.00
104 34 0.09
105 1 0.00
107 40 0.11
108 1 0.00
109 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (99 bp):
TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACGA
GGTTCGTCGTTACGACTTAAACATTTCCCTCCAT
Found at i:6576903 original size:50 final size:48
Alignment explanation
Indices: 6576738--6577003 Score: 132
Period size: 49 Copynumber: 5.4 Consensus size: 48
6576728 AGGTACAAGG
* * * **
6576738 TTCGCCATTGTGACTTAAACTCTT-CCT-CTTGTATCTTCGTGGTACTGGA
1 TTCGCCGTTGCGACTTAAACT-TTCCCTCCAT-TATCTTCAAGGTA-TGGA
* * * * * * *
6576787 TTCGCCGTCGTGGCTTAAATCTTTCCCTTCA-T-GCTTCTAAGGTGTGAGG
1 TTCGCCGTTGCGACTTAAA-CTTTCCCTCCATTATCTTC-AAGGTATG-GA
* *
6576836 TTCGTCGTTGCGACTTAAACATTTCCCTCCATTATCTTCATGGTATTGGA
1 TTCGCCGTTGCGACTTAAAC-TTTCCCTCCATTATCTTCAAGGTA-TGGA
* * * * *
6576886 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCA-T-GCTTCTAAGGTACGAGG
1 TTCGCCGTTGCGACTTAAA-CTTTCCCTCCATTATCTTC-AAGGTATG-GA
* * * **
6576935 TTCGTCGTTACGACTTAAACCTTTTCCTCCATTAGT-TTCGCGGTACTGGA
1 TTCGCCGTTGCGACTTAAA-CTTTCCCTCCATTA-TCTTCAAGGTA-TGGA
*
6576985 TTCGCCGTTGCGGCTTAAA
1 TTCGCCGTTGCGACTTAAA
6577004 TCATCATCTG
Statistics
Matches: 162, Mismatches: 39, Indels: 31
0.70 0.17 0.13
Matches are distributed among these distances:
48 12 0.07
49 79 0.49
50 59 0.36
51 12 0.07
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (48 bp):
TTCGCCGTTGCGACTTAAACTTTCCCTCCATTATCTTCAAGGTATGGA
Found at i:6577305 original size:97 final size:97
Alignment explanation
Indices: 6577015--6577306 Score: 311
Period size: 97 Copynumber: 2.9 Consensus size: 97
6577005 CATCATCTGC
* * *
6577015 GGTATAAGGTTCGCCATTGCGACTTAAACTTTTCCC-TTTGTACTTTCGTGGTACTGGATTCGCC
1 GGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTTGTTC-TTCATGGTACTGGATTCGCC
*
6577079 GTTACGGCTTAAATCTTTCCCTTCACGTCCCCTGA
65 GTTGCGGCTTAAATCTTTCCCTT--CGTCCCCTGA
* ** * *
6577114 GTTATAAGGTTCAACATTGGGACTTAAACCTTTCCCTTTGTATTTTTGTATTTTCATGGTACTGG
1 GGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCC-------TTTTGT-TCTTCATGGTACTGG
* * *
6577179 ATTAGCCGTTGCGGCTTGAATCTTTCCCTTCGT-CTCT-A
58 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCGTCCCCTGA
* *
6577217 TGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTTGTGTCTTCTTGGTACTAGATTCGC
1 -GGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTTGT-TCTTCATGGTACTGGATTCGC
*
6577282 CATTGCGGCTTAAATCTTTCCCTTC
64 CGTTGCGGCTTAAATCTTTCCCTTC
6577307 ACGTCTTCAT
Statistics
Matches: 160, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
97 46 0.29
99 31 0.19
103 1 0.01
104 35 0.22
105 3 0.02
107 44 0.28
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.40
Consensus pattern (97 bp):
GGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTTGTTCTTCATGGTACTGGATTCGCCG
TTGCGGCTTAAATCTTTCCCTTCGTCCCCTGA
Found at i:6578122 original size:409 final size:410
Alignment explanation
Indices: 6577357--6578183 Score: 1453
Period size: 409 Copynumber: 2.0 Consensus size: 410
6577347 GGGCCTTTAA
* *
6577357 GCCAAATTGTTTAGGATGTCATGATCAAAATGAGTCAAATGCTCCTAATTAGATGAATGTGCATG
1 GCCAGATTGTTTAGGATGTCATGATCAAAATGAGTCAAATGCTCCTAACTAGATGAATGTGCATG
*
6577422 ATTAATGTTAATTTCTTTTGCTTTAGGATTATCTCTTTATGTCTTCTCAAATCTATGACGAGATT
66 ATTAATGTTAATTTCTTTTGCTTTAGGATTATCTCTTTATGTCTTCTCAAATCTACGACGAGATT
*
6577487 TGACAGAATATTTTTATCTTGAACCATTCTTTCCAGGTTTGATTCTTTTAACTGGTGGTCCTGTT
131 TGACAGAATATTTTTATCTTGAACCATTCTTTCCAGGTTTGATTCTTTTAACTGGTGGTCATGTT
*
6577552 TAGGGTCCCTGTATCGTTTAGGAATTTTCTAAATAAGACACGCAGACCCTTCTTATGATATTAGT
196 TAGGGTCCCTGTATCGTTTAGGAATTTTCTAAATAACACACGCAGACCCTTCTTATGATATTAGT
* *
6577617 CTATTATCCATTATCTTAGTATGAAAATACTTGGGCAATGTGGGGAAAGAATAAGATTTTATTAG
261 CTATTATCCATTATCTTAGTATGAAAATACTTGGGCAATATGGGGAAAGAATAAGATTGTATTAG
* *
6577682 AGTCAAAGCTCGAAGAATCATTGGCCATAGAGAAATTTCCAATTATTTACAAGGAACAAAATAAT
326 AGTCAAAGCTCGAAGAATCATTAGCCATAGAGAAATTGCCAATTATTTACAAGGAACAAAATAAT
6577747 TAAAAGGAATAATATCAGAT
391 TAAAAGGAATAATATCAGAT
6577767 GCCAGATTGTTTAGGATGTCATGATCAAAATGAGTCAAATGCTCCTAACTAGATGAATGTGCATG
1 GCCAGATTGTTTAGGATGTCATGATCAAAATGAGTCAAATGCTCCTAACTAGATGAATGTGCATG
*
6577832 ATTAATGTTAATTTCTTTTGCTTT-GGAATTATCT-TCTTATGTCTTCTCAAATCTACGACGGGA
66 ATTAATGTTAATTTCTTTTGCTTTAGG-ATTATCTCT-TTATGTCTTCTCAAATCTACGACGAGA
* *
6577895 TTTGGCAGAATATTTTTATCTTGAACCATTCTTTCTA-GTTTGATTCTTTTAACTGGTGGTCATG
129 TTTGACAGAATATTTTTATCTTGAACCATTCTTTCCAGGTTTGATTCTTTTAACTGGTGGTCATG
*
6577959 TTTAGGGTCCCTGTATCGTTTAGGAATTTTTTAAATAACACACGCAGACCCTTCTTATGATATTA
194 TTTAGGGTCCCTGTATCGTTTAGGAATTTTCTAAATAACACACGCAGACCCTTCTTATGATATTA
* *
6578024 GTCTATTATCCATTATCTTAGTATGAAAATACTTGGGCAATATGGTGAAAGAATGAGATTGTATT
259 GTCTATTATCCATTATCTTAGTATGAAAATACTTGGGCAATATGGGGAAAGAATAAGATTGTATT
6578089 AGAGTCAAAGCTCGAAGAATCATTAGCCATAGAGAAATTGCCAATTATTTACAAGGAACAAAATA
324 AGAGTCAAAGCTCGAAGAATCATTAGCCATAGAGAAATTGCCAATTATTTACAAGGAACAAAATA
* *
6578154 ATTACAAGGAATAATATTAGAT
389 ATTAAAAGGAATAATATCAGAT
6578176 GCCTAGAT
1 GCC-AGAT
6578184 ATCAAATATG
Statistics
Matches: 397, Mismatches: 17, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
409 239 0.60
410 158 0.40
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (410 bp):
GCCAGATTGTTTAGGATGTCATGATCAAAATGAGTCAAATGCTCCTAACTAGATGAATGTGCATG
ATTAATGTTAATTTCTTTTGCTTTAGGATTATCTCTTTATGTCTTCTCAAATCTACGACGAGATT
TGACAGAATATTTTTATCTTGAACCATTCTTTCCAGGTTTGATTCTTTTAACTGGTGGTCATGTT
TAGGGTCCCTGTATCGTTTAGGAATTTTCTAAATAACACACGCAGACCCTTCTTATGATATTAGT
CTATTATCCATTATCTTAGTATGAAAATACTTGGGCAATATGGGGAAAGAATAAGATTGTATTAG
AGTCAAAGCTCGAAGAATCATTAGCCATAGAGAAATTGCCAATTATTTACAAGGAACAAAATAAT
TAAAAGGAATAATATCAGAT
Found at i:6583330 original size:9 final size:9
Alignment explanation
Indices: 6583316--6583344 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
6583306 ACTCGCTGTG
6583316 TTTCAAGAA
1 TTTCAAGAA
6583325 TTTCAAGAA
1 TTTCAAGAA
6583334 TTTCAAGAA
1 TTTCAAGAA
6583343 TT
1 TT
6583345 CTTTTGCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (9 bp):
TTTCAAGAA
Found at i:6591338 original size:16 final size:15
Alignment explanation
Indices: 6591316--6591355 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
6591306 AAACGATCAT
*
6591316 AAATTTTAAAATTTT
1 AAATTTTAAAATTTC
*
6591331 AGAATTTTCAAATTTC
1 A-AATTTTAAAATTTC
6591347 AAATTTTAA
1 AAATTTTAA
6591356 TTGACTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATTTTAAAATTTC
Found at i:6594079 original size:59 final size:58
Alignment explanation
Indices: 6593972--6594174 Score: 198
Period size: 59 Copynumber: 3.4 Consensus size: 58
6593962 TTGGATACCT
* ** *
6593972 GGGGGCAAAATGGTAATTTTTTAAAAGGTTCGAGGTCAAAAATGAAATTTTTAGACA-TTC
1 GGGGGTAAAATGGTAA-TTTTTGGAAGGTTC-AGGTCAAAAATGAAATTTTTGGA-AGTTC
6594032 GGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGATCAAAAATGAAATTTTTGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCAGG-TCAAAAATGAAATTTTTGGAAGTTC
** *** * *
6594091 ACGGGTAAAAAT-GTAATTTTTGGAAAAATCGGGGTCAAAAATTG-AA-TTTTGGAAAGTTT
1 GGGGGT-AAAATGGTAATTTTTGGAAGGTTC-AGGTCAAAAA-TGAAATTTTTGG-AAGTTC
*
6594150 GGGGGTAAAATGGTAATTTTGGGAA
1 GGGGGTAAAATGGTAATTTTTGGAA
6594175 AAAATAAGGG
Statistics
Matches: 122, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
58 15 0.12
59 83 0.68
60 24 0.20
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGTCAAAAATGAAATTTTTGGAAGTTC
Found at i:6594091 original size:29 final size:30
Alignment explanation
Indices: 6594046--6594115 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
6594036 GTAAAATGGT
6594046 AATTTTTGGAAGGTTCA-GGATCAAAAATGA
1 AATTTTTGGAAGGTTCACGGAT-AAAAATGA
* *
6594076 AATTTTTGGAA-GTTCACGGGTAAAAATGT
1 AATTTTTGGAAGGTTCACGGATAAAAATGA
6594105 AATTTTTGGAA
1 AATTTTTGGAA
6594116 AAATCGGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (30 bp):
AATTTTTGGAAGGTTCACGGATAAAAATGA
Found at i:6594125 original size:29 final size:29
Alignment explanation
Indices: 6594093--6594258 Score: 126
Period size: 29 Copynumber: 5.7 Consensus size: 29
6594083 GGAAGTTCAC
**
6594093 GGGT-AAAAATGTAATTTTTGGAAAAATCG
1 GGGTCAAAAATGTAA-TTTTGGAAAAATAA
** **
6594122 GGGTCAAAAAT-TGAATTTTGGAAAGTTTGG
1 GGGTCAAAAATGT-AATTTTGGAAA-AATAA
6594152 GGGT--AAAATGGTAATTTTGGGAAAAAATAA
1 GGGTCAAAAAT-GTAATTTT-GG-AAAAATAA
* **
6594182 GGGTCAAAAATGGAATTTTGGAAATTTTAA
1 GGGTCAAAAATGTAATTTTGGAAA-AATAA
*
6594212 GGGT-AAAAATGTAATTTTGGAAAAATTA
1 GGGTCAAAAATGTAATTTTGGAAAAATAA
* *
6594240 GGGTAAAAAATGGAATTTT
1 GGGTCAAAAATGTAATTTT
6594259 TGAAGTTCGA
Statistics
Matches: 111, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
28 11 0.10
29 54 0.49
30 31 0.28
31 10 0.09
32 5 0.05
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.31
Consensus pattern (29 bp):
GGGTCAAAAATGTAATTTTGGAAAAATAA
Found at i:6594175 original size:59 final size:59
Alignment explanation
Indices: 6594033--6594258 Score: 244
Period size: 59 Copynumber: 3.8 Consensus size: 59
6594023 TAGACATTCG
*** * * *
6594033 GGGGT-AAAATGGTAATTTTTGGAAGGTTCAGGATCAAAAATGAAATTTTTGG-AAGTTCA
1 GGGGTAAAAAT-GTAATTTTTGGAAAAATCAGGGTCAAAAATGGAA-TTTTGGAAAGTTTA
* * * *
6594092 CGGGTAAAAATGTAATTTTTGGAAAAATCGGGGTCAAAAATTGAATTTTGGAAAGTTTG
1 GGGGTAAAAATGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTA
* * *
6594151 GGGGT-AAAATGGTAATTTTGGGAAAAAATAAGGGTCAAAAATGGAATTTTGGAAATTTTA
1 GGGGTAAAAAT-GTAATTTTTGG-AAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTA
* * *
6594211 AGGGTAAAAATGTAA-TTTTGGAAAAATTAGGGTAAAAAATGGAATTTT
1 GGGGTAAAAATGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAATTTT
6594259 TGAAGTTCGA
Statistics
Matches: 141, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
58 36 0.26
59 55 0.39
60 45 0.32
61 5 0.04
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (59 bp):
GGGGTAAAAATGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTA
Found at i:6595359 original size:3 final size:3
Alignment explanation
Indices: 6595351--6595417 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
6595341 GTATTTTGTA
* * * * * *
6595351 TAT TAT TAT TAA TAT TAT AAT AAT AAT TAT TAAT TAA TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
*
6595397 TAT TAT TAAA TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TA
6595418 CTGATTCATT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 47 0.90
4 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:6595398 original size:19 final size:19
Alignment explanation
Indices: 6595350--6595417 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
6595340 CGTATTTTGT
*
6595350 ATATTATTATTAATATTATA
1 ATATTATTATTATTATTA-A
*
6595370 ATA--ATAATTATTAATT-A
1 ATATTATTATTATT-ATTAA
*
6595387 ATGTTATTATTATTATTAA
1 ATATTATTATTATTATTAA
6595406 ATATTATTATTA
1 ATATTATTATTA
6595418 CTGATTCATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 3 0.08
18 10 0.26
19 23 0.59
20 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (19 bp):
ATATTATTATTATTATTAA
Found at i:6595933 original size:25 final size:25
Alignment explanation
Indices: 6595905--6595959 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
6595895 GTGGCGGTGA
*
6595905 TGGCAGAGCAGGTTAAAGCTAGTGG
1 TGGCAGAGCAAGTTAAAGCTAGTGG
* *
6595930 TGGCAGAGCAAGTTGAAGCTGGTGG
1 TGGCAGAGCAAGTTAAAGCTAGTGG
6595955 TGGCA
1 TGGCA
6595960 CTGCTGGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.42, T:0.20
Consensus pattern (25 bp):
TGGCAGAGCAAGTTAAAGCTAGTGG
Found at i:6596200 original size:18 final size:17
Alignment explanation
Indices: 6596179--6596254 Score: 73
Period size: 18 Copynumber: 4.4 Consensus size: 17
6596169 TGGACTTTGT
6596179 AATAAATTTAAATTTTAA
1 AATAAATTTAAA-TTTAA
* *
6596197 AATAAATTTAAACTCAA
1 AATAAATTTAAATTTAA
* *
6596214 AGTAAGTTTAAATTTAA
1 AATAAATTTAAATTTAA
**
6596231 AATAAAATAAAAATTTAA
1 AAT-AAATTTAAATTTAA
6596249 AA-AAAT
1 AATAAAT
6596255 CCAGAATTGG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
16 4 0.09
17 18 0.38
18 25 0.53
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:6600713 original size:30 final size:30
Alignment explanation
Indices: 6600679--6600738 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
6600669 GCCAAGTTCA
6600679 TCTAGCAACCCACTTAACCAAACAATTTTT
1 TCTAGCAACCCACTTAACCAAACAATTTTT
6600709 TCTAGCAACCCACTTAACCAAACAATTTTT
1 TCTAGCAACCCACTTAACCAAACAATTTTT
6600739 GCAATTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (30 bp):
TCTAGCAACCCACTTAACCAAACAATTTTT
Found at i:6602801 original size:13 final size:13
Alignment explanation
Indices: 6602757--6602814 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
6602747 TAATAATAAA
*
6602757 ATAATACTA-ATT
1 ATAATATTATATT
6602769 A-AATAATTAT-TT
1 ATAAT-ATTATATT
*
6602781 ATATTATTATATT
1 ATAATATTATATT
6602794 ATAATATT-TATTT
1 ATAATATTATA-TT
6602807 ATAATATT
1 ATAATATT
6602815 TTAAATCATG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 3 0.08
12 14 0.37
13 21 0.55
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAATATTATATT
Found at i:6602804 original size:26 final size:25
Alignment explanation
Indices: 6602757--6602814 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
6602747 TAATAATAAA
*
6602757 ATAATACTA-ATTAAATAATTATTT
1 ATAATATTATATTAAATAATTATTT
* *
6602781 ATATTATTATATTATAATATTTATTT
1 ATAATATTATATTA-AATAATTATTT
6602807 ATAATATT
1 ATAATATT
6602815 TTAAATCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 7 0.25
25 4 0.14
26 17 0.61
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATAATATTATATTAAATAATTATTT
Found at i:6602815 original size:13 final size:13
Alignment explanation
Indices: 6602770--6602815 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
6602760 ATACTAATTA
*
6602770 AATAATTATTTAT
1 AATATTTATTTAT
*
6602783 ATTA-TTATATTAT
1 AATATTTAT-TTAT
6602796 AATATTTATTTAT
1 AATATTTATTTAT
6602809 AATATTT
1 AATATTT
6602816 TAAATCATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.14
13 21 0.72
14 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTTATTTAT
Found at i:6609834 original size:2 final size:2
Alignment explanation
Indices: 6609827--6609885 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
6609817 CTTTTATTTC
6609827 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6609869 AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT A
6609886 GATTAGTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6609950 original size:13 final size:13
Alignment explanation
Indices: 6609906--6609963 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
6609896 TAATAATAAA
*
6609906 ATAATACTA-ATT
1 ATAATATTATATT
6609918 A-AATAATTAT-TT
1 ATAAT-ATTATATT
*
6609930 ATATTATTATATT
1 ATAATATTATATT
6609943 ATAATATT-TATTT
1 ATAATATTATA-TT
6609956 ATAATATT
1 ATAATATT
6609964 TTAAATCATG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 3 0.08
12 14 0.37
13 21 0.55
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAATATTATATT
Done.