Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 2 of 17
Found at i:176574 original size:13 final size:13
Alignment explanation
Indices: 176556--176580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
176546 TTTAACATAT
176556 TTATATTTTTATA
1 TTATATTTTTATA
176569 TTATATTTTTAT
1 TTATATTTTTAT
176581 TATTTTATAT
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:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:176574 original size:19 final size:20
Alignment explanation
Indices: 176531--176601 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 20
176521 TTAAAATATT
*
176531 TTATATTATATAAATTTTA-A
1 TTATATT-TATATATTTTATA
*
176551 -CATATTTATAT-TTTTATA
1 TTATATTTATATATTTTATA
*
176569 TTATATTTTTATTATTTTATA
1 TTATATTTATA-TATTTTATA
176590 TTATATTTATAT
1 TTATATTTATAT
176602 CGTATAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 13 0.31
20 2 0.05
21 17 0.40
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATATTTATATATTTTATA
Found at i:176583 original size:16 final size:16
Alignment explanation
Indices: 176526--176591 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 16
176516 TATGATTAAA
176526 ATATTTTATATTATA-T
1 ATATTTT-TATTATATT
* **
176542 A-AATTTTAACATATT
1 ATATTTTTATTATATT
*
176557 -TATATTT-TTATATT
1 ATATTTTTATTATATT
*
176571 ATATTTTTATTATTTT
1 ATATTTTTATTATATT
176587 ATATT
1 ATATT
176592 ATATTTATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
14 10 0.27
15 15 0.41
16 12 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATTTTTATTATATT
Found at i:176586 original size:21 final size:22
Alignment explanation
Indices: 176562--176622 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 22
176552 ATATTTATAT
*
176562 TTTTATATTATATTTTTAT-TA
1 TTTTATATTATATTTATATCTA
176583 TTTTATATTATATTTATATCGTA
1 TTTTATATTATATTTATATC-TA
*
176606 TAATTATATTATATTTA
1 T-TTTATATTATATTTA
176623 AAGTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 18 0.51
23 3 0.09
24 14 0.40
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTATATTATATTTATATCTA
Found at i:176593 original size:13 final size:11
Alignment explanation
Indices: 176552--176622 Score: 78
Period size: 11 Copynumber: 6.6 Consensus size: 11
176542 AAATTTTAAC
176552 ATATTTATA-T
1 ATATTTATATT
176562 -T-TTTATATT
1 ATATTTATATT
*
176571 ATATTTTTATT
1 ATATTTATATT
176582 AT-TTTATATT
1 ATATTTATATT
176592 ATATTTATATCGT
1 ATATTTATAT--T
*
176605 ATAATTATATT
1 ATATTTATATT
176616 ATATTTA
1 ATATTTA
176623 AAGTTAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
8 6 0.12
9 2 0.04
10 10 0.20
11 23 0.45
13 10 0.20
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (11 bp):
ATATTTATATT
Found at i:176599 original size:16 final size:16
Alignment explanation
Indices: 176552--176622 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
176542 AAATTTTAAC
176552 ATATTTATATT-T-TT
1 ATATTTATATTATATT
*
176566 ATA-TTATATTTTTATT
1 ATATTTATA-TTATATT
176582 AT-TTTATATTATATTT
1 ATATTTATATTATA-TT
*
176598 ATATCGTATAATTATATT
1 ATAT-TTAT-ATTATATT
176616 ATATTTA
1 ATATTTA
176623 AAGTTAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 5 0.11
16 13 0.28
17 3 0.07
18 9 0.20
19 6 0.13
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (16 bp):
ATATTTATATTATATT
Found at i:177894 original size:22 final size:21
Alignment explanation
Indices: 177846--177894 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
177836 CAACAAATTG
* *
177846 TAACAATTTAAAAAAATAATA
1 TAACAATTAAAAAAAATAAAA
177867 TAACAATTAAAAAAAATTAAAA
1 TAACAATTAAAAAAAA-TAAAA
*
177889 TTACAA
1 TAACAA
177895 AATTATGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (21 bp):
TAACAATTAAAAAAAATAAAA
Found at i:179839 original size:2 final size:2
Alignment explanation
Indices: 179832--179877 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
179822 ACATACATAC
179832 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
179874 AT AT
1 AT AT
179878 TTTATTACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180356 original size:3 final size:3
Alignment explanation
Indices: 180350--180375 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
180340 CAACAACAAC
180350 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
180376 AAGTAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:191295 original size:18 final size:18
Alignment explanation
Indices: 191244--191281 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
191234 GTTATATAAA
191244 AAAAG-AATTTAAATATT
1 AAAAGTAATTTAAATATT
191261 AAAAGTAATTTAAATATT
1 AAAAGTAATTTAAATATT
191279 AAA
1 AAA
191282 CAAGTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAAGTAATTTAAATATT
Found at i:191943 original size:90 final size:90
Alignment explanation
Indices: 191790--191965 Score: 325
Period size: 90 Copynumber: 2.0 Consensus size: 90
191780 ACAGTGAAGA
191790 TCATATGATAATATGTCTCAATTGGCCCAAAAGTAAAAAGATAGGACAGAAAAGCACCACCAGAT
1 TCATATGATAATATGTCTCAATTGGCCCAAAAGTAAAAAGATAGGACAGAAAAGCACCACCAGAT
191855 GGAGAAACAAAATAAAGTATTTTCT
66 GGAGAAACAAAATAAAGTATTTTCT
* *
191880 TCATATGATAATATGTCTCAATTGGCCCAAAAGTAAAATGATAGGACAGAAAAGTACCACCAGAT
1 TCATATGATAATATGTCTCAATTGGCCCAAAAGTAAAAAGATAGGACAGAAAAGCACCACCAGAT
*
191945 GGAGAGACAAAATAAAGTATT
66 GGAGAAACAAAATAAAGTATT
191966 CGTTTGTCGC
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (90 bp):
TCATATGATAATATGTCTCAATTGGCCCAAAAGTAAAAAGATAGGACAGAAAAGCACCACCAGAT
GGAGAAACAAAATAAAGTATTTTCT
Found at i:194599 original size:6 final size:6
Alignment explanation
Indices: 194559--194598 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
194549 AGCATGAGCA
* *
194559 TTGGAT TTGGAT TTGGAT TTGGAT TTGGCT TTGGCT TTGG
1 TTGGAT TTGGAT TTGGAT TTGGAT TTGGAT TTGGAT TTGG
194599 CATGGGTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.10, C:0.05, G:0.35, T:0.50
Consensus pattern (6 bp):
TTGGAT
Found at i:195185 original size:27 final size:27
Alignment explanation
Indices: 195155--195228 Score: 62
Period size: 28 Copynumber: 2.7 Consensus size: 27
195145 AGTTTGGCTC
195155 AAATTAGATAATATATTAT-AAAAAAA
1 AAATTAGATAATATATTATGAAAAAAA
* *
195181 TAAA-TATGTATAATATTATTATGTAAATAA
1 -AAATTA-G-ATAATA-TATTATGAAAAAAA
* *
195211 AAATTAAAAAATATATTA
1 AAATTAGATAATATATTA
195229 ATTATTTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
26 2 0.05
27 9 0.24
28 11 0.29
29 9 0.24
30 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (27 bp):
AAATTAGATAATATATTATGAAAAAAA
Found at i:198607 original size:34 final size:34
Alignment explanation
Indices: 198571--198702 Score: 176
Period size: 34 Copynumber: 3.9 Consensus size: 34
198561 AATTTCTTTG
* *
198571 TTAAGTGTGTTAGGTGATGTATTTGGTGAGAATG
1 TTAAGTGTGTTAGGTAATGTATTTGGTGAGAATA
* *
198605 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATA
1 TTAAGTGTGTTAGGTAATGTATTTGGTGAGAATA
* *
198639 TT-AGATGTATTAGGTAATGTATTTGGTGAAAATA
1 TTAAG-TGTGTTAGGTAATGTATTTGGTGAGAATA
* *
198673 TTAAGTGTGTTAGGTAATGTGTTAGGTGAG
1 TTAAGTGTGTTAGGTAATGTATTTGGTGAG
198703 TAAGATATTT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
33 1 0.01
34 83 0.97
35 2 0.02
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.41
Consensus pattern (34 bp):
TTAAGTGTGTTAGGTAATGTATTTGGTGAGAATA
Found at i:203450 original size:29 final size:32
Alignment explanation
Indices: 203403--203487 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 32
203393 TTAATTTCTT
*
203403 TGTTAAGT-TGTTAGTGATGTATTTGGTGAGAA
1 TGTT-AGTGTGTTAGTGATGTATTTGGTCAGAA
203435 T-TTAGTG-GTTA-TGATGTATTTGGTCAGAA
1 TGTTAGTGTGTTAGTGATGTATTTGGTCAGAA
*
203464 TGTTGGTGTGTTAGGTGATGTATT
1 TGTTAGTGTGTTA-GTGATGTATT
203488 AGTAGACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
29 18 0.39
30 12 0.26
31 6 0.13
32 1 0.02
33 9 0.20
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (32 bp):
TGTTAGTGTGTTAGTGATGTATTTGGTCAGAA
Found at i:204781 original size:20 final size:19
Alignment explanation
Indices: 204737--204783 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
204727 TGTTTTTTCT
204737 TTTATTTTTTACTCAAAATA
1 TTTATTTTTTAC-CAAAATA
204757 TTTATTTTTTA-CAAAATTA
1 TTTATTTTTTACCAAAA-TA
204776 TCTTATTT
1 T-TTATTT
204784 ATTATCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.20
19 3 0.12
20 17 0.68
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATTTTTTACCAAAATA
Found at i:205337 original size:23 final size:24
Alignment explanation
Indices: 205309--205358 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
205299 TACTAAATTC
* *
205309 TTAAATAATAATA-ATTGATAAAT
1 TTAAATAAAAATATATTAATAAAT
*
205332 TTAAATAAAAATATTTTAATAAAT
1 TTAAATAAAAATATATTAATAAAT
205356 TTA
1 TTA
205359 TTTCAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TTAAATAAAAATATATTAATAAAT
Found at i:205681 original size:30 final size:29
Alignment explanation
Indices: 205627--205699 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
205617 TAAATTTTAT
*
205627 AAAAATAAATGCATATTTTTT-AAAAGTTAA
1 AAAAATAAAT--ATATTTTTTAAAAAATTAA
**
205657 AAAAATAAATATATTTTTTATAAAAAATTTT
1 AAAAATAAATATA-TTTTT-TAAAAAATTAA
205688 AAAAATAAATAT
1 AAAAATAAATAT
205700 CTTCAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 5 0.14
30 11 0.30
31 18 0.49
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAAATAAATATATTTTTTAAAAAATTAA
Found at i:206280 original size:25 final size:25
Alignment explanation
Indices: 206229--206282 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
206219 ATTTACTTAT
* *
206229 TAATTATTAAAATTATATTTATAAA
1 TAATGATTAAAATTATATTAATAAA
206254 TAATGATTAAAATTATATTGAAT-AA
1 TAATGATTAAAATTATATT-AATAAA
206279 TAAT
1 TAAT
206283 AAATAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
TAATGATTAAAATTATATTAATAAA
Found at i:206289 original size:25 final size:25
Alignment explanation
Indices: 206236--206290 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
206226 TATTAATTAT
* * *
206236 TAAAATTATATTTATAAATAATGAT
1 TAAAATTATATTAATAAATAATAAA
206261 TAAAATTATATTGAAT-AATAATAAA
1 TAAAATTATATT-AATAAATAATAAA
206286 TAAAA
1 TAAAA
206291 GATAATGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TAAAATTATATTAATAAATAATAAA
Found at i:206664 original size:50 final size:50
Alignment explanation
Indices: 206595--206753 Score: 221
Period size: 50 Copynumber: 3.2 Consensus size: 50
206585 TATACTTAGA
*
206595 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
206645 GTTAACAATTATTGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
206695 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGATTAGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
206745 GTCAACAAT
1 GTCAACAAT
206754 GACAACAACT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
50 94 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:210873 original size:19 final size:18
Alignment explanation
Indices: 210849--210890 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
210839 TTTCACATGC
*
210849 ACAGTAACCGTATGTATGA
1 ACAGTAA-CGTATATATGA
*
210868 ACAGT-ACTTATATATGA
1 ACAGTAACGTATATATGA
210885 ACAGTA
1 ACAGTA
210891 CCTCGATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 14 0.70
18 1 0.05
19 5 0.25
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (18 bp):
ACAGTAACGTATATATGA
Found at i:211205 original size:50 final size:50
Alignment explanation
Indices: 211146--211290 Score: 245
Period size: 50 Copynumber: 2.9 Consensus size: 50
211136 TATACTTAGA
* *
211146 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
211196 GTCAACAATTATTGTCACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
211246 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA
211291 AGATAGTTAA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:219285 original size:2 final size:2
Alignment explanation
Indices: 219247--219275 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
219237 TAAGCAAAAC
219247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
219276 AAAGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219506 original size:14 final size:14
Alignment explanation
Indices: 219487--219513 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
219477 AAGAACTTCA
219487 ATTTTTTTTTTTTG
1 ATTTTTTTTTTTTG
219501 ATTTTTTTTTTTT
1 ATTTTTTTTTTTT
219514 TGTGGGTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.04, T:0.89
Consensus pattern (14 bp):
ATTTTTTTTTTTTG
Found at i:225003 original size:5 final size:5
Alignment explanation
Indices: 224983--225146 Score: 72
Period size: 5 Copynumber: 32.6 Consensus size: 5
224973 AATACAATTG
* * *
224983 ATTAT ATTTGT ATTAT A-T-T ATTAT ATTTT ATTAT ATTAT AATTAT ATTTAA
1 ATTAT A-TTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT -ATTAT A-TTAT
* * * * * *
225034 AATAT ATTAT ATTTAT ATAAT TTATAT ATTA- ATAAT -TTAT GTTAT A-TAA
1 ATTAT ATTAT A-TTAT ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT ATTAT
* ** * * *
225083 ATTGT AAAAT ATT-T A-TAT GTTTAT ATTAT ATTTT AATTAT TTTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT -ATTAT ATTAT ATTAT -ATTAT ATTAT ATTAT
225133 ATTTAT ATTAT ATT
1 A-TTAT ATTAT ATT
225147 TAATATTATT
Statistics
Matches: 115, Mismatches: 29, Indels: 30
0.66 0.17 0.17
Matches are distributed among these distances:
3 3 0.03
4 14 0.12
5 65 0.57
6 33 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:225028 original size:11 final size:11
Alignment explanation
Indices: 224983--225150 Score: 56
Period size: 11 Copynumber: 15.7 Consensus size: 11
224973 AATACAATTG
* *
224983 ATTATATTTGT
1 ATTATAATTAT
224994 ATTATATTATTAT
1 ATTATA--ATTAT
*
225007 ATT-TTATTAT
1 ATTATAATTAT
225017 ATTATAATTAT
1 ATTATAATTAT
*
225028 ATT-TAAAATAT
1 ATTAT-AATTAT
225039 ATTAT-ATT-T
1 ATTATAATTAT
225048 A-TATAATT-T
1 ATTATAATTAT
*
225057 ATATATTAATAAT
1 AT-TA-TAATTAT
*
225070 -TTAT-GTTAT
1 ATTATAATTAT
*
225079 A-TA-AATTGT
1 ATTATAATTAT
** *
225088 AAAATATTTAT
1 ATTATAATTAT
*
225099 ATGTTTATATTAT
1 AT-TATA-ATTAT
*
225112 ATTTTAATTAT
1 ATTATAATTAT
*
225123 TTTAT-ATTAT
1 ATTATAATTAT
225133 ATT-TATATTAT
1 ATTATA-ATTAT
225144 ATT-TAAT
1 ATTATAAT
225151 ATTATTAAAT
Statistics
Matches: 118, Mismatches: 21, Indels: 37
0.67 0.12 0.21
Matches are distributed among these distances:
8 3 0.03
9 17 0.14
10 22 0.19
11 50 0.42
12 13 0.11
13 13 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
ATTATAATTAT
Found at i:225127 original size:16 final size:16
Alignment explanation
Indices: 225103--225147 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
225093 ATTTATATGT
225103 TTATATTATATTTTAA
1 TTATATTATATTTTAA
* * *
225119 TTATTTTATATTATAT
1 TTATATTATATTTTAA
225135 TTATATTATATTT
1 TTATATTATATTT
225148 AATATTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTATATTTTAA
Found at i:225384 original size:2 final size:2
Alignment explanation
Indices: 225331--225364 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
225321 ATTGCTTTTG
225331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
225365 AATTGCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:225401 original size:27 final size:27
Alignment explanation
Indices: 225349--225401 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
225339 TATATATATA
* **
225349 TATATATATATATATAAATTGCTTTTG
1 TATATATATATATACAAAAGGCTTTTG
*
225376 TATATATATATATACAAAAGGTTTTT
1 TATATATATATATACAAAAGGCTTTT
225402 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (27 bp):
TATATATATATATACAAAAGGCTTTTG
Found at i:227549 original size:23 final size:23
Alignment explanation
Indices: 227522--227578 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
227512 ATCTATTAAG
* *
227522 TATCCAAATAAAAAGTTAAGATA
1 TATCCAAATAAAAAGTAAAAATA
***
227545 TATCCAAATAATTGGTAAAAATA
1 TATCCAAATAAAAAGTAAAAATA
227568 TATCCAAATAA
1 TATCCAAATAA
227579 GCATTAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (23 bp):
TATCCAAATAAAAAGTAAAAATA
Found at i:227586 original size:23 final size:23
Alignment explanation
Indices: 227522--227586 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
227512 ATCTATTAAG
** * *
227522 TATCCAAATAAAAAGTTAAGATA
1 TATCCAAATAAGCAGTAAAAATA
***
227545 TATCCAAATAATTGGTAAAAATA
1 TATCCAAATAAGCAGTAAAAATA
*
227568 TATCCAAATAAGCATTAAA
1 TATCCAAATAAGCAGTAAA
227587 GATGTTTGTT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.28
Consensus pattern (23 bp):
TATCCAAATAAGCAGTAAAAATA
Found at i:228656 original size:13 final size:13
Alignment explanation
Indices: 228638--228672 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
228628 TATTAAAATA
228638 AAATTTAATTATT
1 AAATTTAATTATT
228651 AAATTTAATTATT
1 AAATTTAATTATT
*
228664 -TATTTAATT
1 AAATTTAATT
228673 TAAGTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AAATTTAATTATT
Found at i:231451 original size:2 final size:2
Alignment explanation
Indices: 231444--231486 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
231434 ATTAGCTTGG
231444 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
231486 A
1 A
231487 GGTATTATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:232108 original size:20 final size:18
Alignment explanation
Indices: 232064--232130 Score: 84
Period size: 19 Copynumber: 3.7 Consensus size: 18
232054 AAATACTCAG
*
232064 ATGTATCGATACATTTTC
1 ATGTATCGATACATTCTC
232082 AATGTATCGATACATTCATAC
1 -ATGTATCGATACATTC-T-C
232103 ATGTATCGAT--ATTCTC
1 ATGTATCGATACATTCTC
232119 ATGTATCGATAC
1 ATGTATCGATAC
232131 TTGTCTTTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
16 11 0.26
17 1 0.02
18 4 0.09
19 15 0.35
20 11 0.26
21 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (18 bp):
ATGTATCGATACATTCTC
Found at i:243630 original size:12 final size:11
Alignment explanation
Indices: 243610--243677 Score: 66
Period size: 12 Copynumber: 5.9 Consensus size: 11
243600 CCTTCATACC
*
243610 AAAAAAAAATT
1 AAAAAAAAAAT
243621 AAATAAAAAAAT
1 AAA-AAAAAAAT
243633 AAAAAAATAAA-
1 AAAAAAA-AAAT
243644 AAACAAAAAAACT
1 AAA-AAAAAAA-T
*
243657 AAGAAAAAAAT
1 AAAAAAAAAAT
*
243668 AACAAAAAAA
1 AAAAAAAAAA
243678 CAGAAAGGGG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 23 0.47
12 24 0.49
13 2 0.04
ACGTcount: A:0.84, C:0.04, G:0.01, T:0.10
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:243631 original size:16 final size:15
Alignment explanation
Indices: 243610--243666 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
243600 CCTTCATACC
**
243610 AAAAAAAAATTAAAT
1 AAAAAAAAAAAAAAT
243625 AAAAAAATAAAAAAAT
1 AAAAAAA-AAAAAAAT
*
243641 AAAAAACAAAAAAACT
1 AAAAAA-AAAAAAAAT
243657 AAGAAAAAAA
1 AA-AAAAAAA
243667 TAACAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.19
16 24 0.67
17 5 0.14
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.11
Consensus pattern (15 bp):
AAAAAAAAAAAAAAT
Found at i:243638 original size:7 final size:8
Alignment explanation
Indices: 243621--243675 Score: 56
Period size: 8 Copynumber: 6.4 Consensus size: 8
243611 AAAAAAAATT
243621 AAATAAAA
1 AAATAAAA
243629 AAATAAAA
1 AAATAAAA
243637 AAATAAAA
1 AAATAAAA
*
243645 AACAAAAAA
1 AA-ATAAAA
*
243654 ACTAAGAAAA
1 A--AATAAAA
243664 AAATAACAA
1 AAATAA-AA
243673 AAA
1 AAA
243676 AACAGAAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
8 22 0.55
9 11 0.28
10 6 0.15
11 1 0.03
ACGTcount: A:0.84, C:0.05, G:0.02, T:0.09
Consensus pattern (8 bp):
AAATAAAA
Found at i:243671 original size:23 final size:24
Alignment explanation
Indices: 243625--243678 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
243615 AAAATTAAAT
243625 AAAAAAA-TAAAAAAATAAAAAAC
1 AAAAAAACTAAAAAAATAAAAAAC
* *
243648 AAAAAAACTAAGAAAA-AAATAAC
1 AAAAAAACTAAAAAAATAAAAAAC
243671 AAAAAAAC
1 AAAAAAAC
243679 AGAAAGGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.83, C:0.07, G:0.02, T:0.07
Consensus pattern (24 bp):
AAAAAAACTAAAAAAATAAAAAAC
Found at i:244939 original size:28 final size:28
Alignment explanation
Indices: 244899--245073 Score: 307
Period size: 28 Copynumber: 6.2 Consensus size: 28
244889 CGTTCATCTC
*
244899 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
244927 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
244955 TTCAAAGGCCACAAGTCAGTGGCACTCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
244984 TTCAAAGGCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
245012 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
245040 TTCAAAG-CCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
245067 TTCAAAG
1 TTCAAAG
245074 GCACCCTTTC
Statistics
Matches: 143, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
27 27 0.19
28 88 0.62
29 28 0.20
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:245042 original size:85 final size:83
Alignment explanation
Indices: 244899--245075 Score: 318
Period size: 85 Copynumber: 2.1 Consensus size: 83
244889 CGTTCATCTC
* *
244899 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGGC
1 TTCAAAGGCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA-GC
244964 CACAAGTCAGTGGCACTCCT
65 CACAAGTCAGTGGCAC-CCT
244984 TTCAAAGGCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGGCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
245049 ACAAGTCAGTGGCACCCT
66 ACAAGTCAGTGGCACCCT
245067 TTCAAAGGC
1 TTCAAAGGC
245076 ACCCTTTCAA
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
83 12 0.13
84 18 0.20
85 60 0.67
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (83 bp):
TTCAAAGGCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
ACAAGTCAGTGGCACCCT
Found at i:245078 original size:14 final size:14
Alignment explanation
Indices: 245059--245087 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
245049 ACAAGTCAGT
245059 GGCACCCTTTCAAA
1 GGCACCCTTTCAAA
245073 GGCACCCTTTCAAA
1 GGCACCCTTTCAAA
245087 G
1 G
245088 CCCACAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (14 bp):
GGCACCCTTTCAAA
Found at i:245105 original size:42 final size:41
Alignment explanation
Indices: 245032--245115 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 41
245022 ACAAGTCAGT
245032 GGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTTCAAA
1 GGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTTCAAA
245073 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
1 GGCACCCTTTCAAAG-CCACAAGTCAGTGGCACCCTTTCAAA
245115 G
1 G
245116 CCACAAGTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 15 0.36
42 27 0.64
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.19
Consensus pattern (41 bp):
GGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTTCAAA
Found at i:245113 original size:28 final size:28
Alignment explanation
Indices: 245073--245789 Score: 932
Period size: 28 Copynumber: 25.2 Consensus size: 28
245063 CCCTTTCAAA
245073 GGCACCCTTTCAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
245101 GGCACCCTTTCAAAG-CCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
*
245128 GGCACCCTTTCAAAGCCCATAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
*
245156 GGCACTCTTTTCAAAGCCCACAAGTCAGT
1 GGCAC-CCTTTCAAAGCCCACAAGTCAGT
*
245185 GGCATCCTTTCAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
* *
245213 GGCACCCTTTCAAAGCCTACAAGTCATT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
** *
245241 GGCACATTTTCAAAGCCCACAAGTTAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
* * *
245269 AGCATCCTTTCAAAGCCCGCAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
* * *
245297 GGCACCCTTTTTAAAGCTCACAAGTCAAT
1 GGCACCC-TTTCAAAGCCCACAAGTCAGT
*
245326 GGCACCCTTTGAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
*
245354 GGCACCCTTTGAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
*
245382 GGCACTCTTTTCAAAGCCCACAAGTCAGT
1 GGCAC-CCTTTCAAAGCCCACAAGTCAGT
*
245411 GGCATCCTTTCAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
*
245439 GACACCCTTTCAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
* * *
245467 GGTACCCTTTTAAAGCCCATAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
*
245495 GGCATCCTTTCAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
245523 GGCACCCTTTCAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
* **
245551 GGCACTCTTTTCAAAGCCCACAAGTTGGT
1 GGCAC-CCTTTCAAAGCCCACAAGTCAGT
* * * *
245580 GGTAACTCTTTTCAAAGACCACAAGTTAGT
1 GG-CAC-CCTTTCAAAGCCCACAAGTCAGT
*
245610 GGCACCCTTTCAAAGCCCATAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
* * *
245638 GGCGCCCTTTCAAAACCCACAAGTTAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
* *
245666 GGTATCCTTTCAAAGCCCACAAGTCAGT
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
* * *
245694 GGCACCATTTCAAAGCCCACAAGTCGGC
1 GGCACCCTTTCAAAGCCCACAAGTCAGT
*
245722 GGCACTCTTTTCAAAGCCCACACGAGTCAGT
1 GGCAC-CCTTTCAAAGCCCACA--AGTCAGT
* *
245753 GGCAACTCTTTTCAAAGCCCACAGAAGTTAGT
1 GGC-AC-CCTTTCAAAGCCCAC--AAGTCAGT
245785 GGCAC
1 GGCAC
245790 TTTTTTTTTT
Statistics
Matches: 605, Mismatches: 72, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
27 27 0.04
28 401 0.66
29 113 0.19
30 26 0.04
31 10 0.02
32 27 0.04
34 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
GGCACCCTTTCAAAGCCCACAAGTCAGT
Found at i:245115 original size:69 final size:69
Alignment explanation
Indices: 245004--245142 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
244994 ACAAGTCAGT
245004 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTT
1 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTT
245069 CAAA
66 CAAA
245073 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTT
1 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTT
245138 CAAA
66 CAAA
245142 G
1 G
245143 CCCATAAGTC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.19
Consensus pattern (69 bp):
GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTT
CAAA
Found at i:245251 original size:84 final size:84
Alignment explanation
Indices: 245073--245789 Score: 932
Period size: 85 Copynumber: 8.4 Consensus size: 84
245063 CCCTTTCAAA
245073 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CCACAAGTCAGTGGCACCCTT
1 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTT
*
245137 TCAAAGCCCATAAGTCAGT
66 TCAAAGCCCACAAGTCAGT
* *
245156 GGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
1 GGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
245221 TTCAAAGCCTACAAGTCATT
65 TTCAAAGCCCACAAGTCAGT
** * * * *
245241 GGCACATTTTCAAAGCCCACAAGTTAGTAGCATCCTTTCAAAGCCCGCAAGTCAGTGGCACCCTT
1 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC-T
* * *
245306 TTTAAAGCTCACAAGTCAAT
65 TTCAAAGCCCACAAGTCAGT
* * *
245326 GGCACCCTTTGAAAGCCCACAAGTCAGTGGCACCCTTTGAAAGCCCACAAGTCAGTGGCACTCTT
1 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
245391 TTCAAAGCCCACAAGTCAGT
65 TTCAAAGCCCACAAGTCAGT
* * *
245411 GGCATCCTTTCAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCACAAGTCAGTGGTACCCTT
1 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
245476 TTAAAGCCCATAAGTCAGT
66 TCAAAGCCCACAAGTCAGT
* *
245495 GGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
**
245560 TTCAAAGCCCACAAGTTGGT
65 TTCAAAGCCCACAAGTCAGT
* * * * * *
245580 GGTAACTCTTTTCAAAGACCACAAGTTAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCGCCC
1 GG-CAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
245645 TTTCAAAACCCACAAGTTAGT
64 TTTCAAAGCCCACAAGTCAGT
* * * * * *
245666 GGTATCCTTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTCGGCGGCACTCTT
1 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
245731 TTCAAAGCCCACACGAGTCAGT
65 TTCAAAGCCCACA--AGTCAGT
* *
245753 GGCAACTCTTTTCAAAGCCCACAGAAGTTAGTGGCAC
1 GGC-AC-CCTTTCAAAGCCCAC--AAGTCAGTGGCAC
245790 TTTTTTTTTT
Statistics
Matches: 553, Mismatches: 67, Indels: 20
0.86 0.10 0.03
Matches are distributed among these distances:
83 5 0.01
84 217 0.39
85 221 0.40
86 24 0.04
87 59 0.11
88 1 0.00
89 14 0.03
91 12 0.02
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (84 bp):
GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTT
TCAAAGCCCACAAGTCAGT
Found at i:245913 original size:44 final size:47
Alignment explanation
Indices: 245857--245977 Score: 122
Period size: 49 Copynumber: 2.6 Consensus size: 47
245847 CTATCTGACA
*
245857 TCGCTAGCATTGAATCAGCATATTGGCAC-CAT-T-TTAGCTCAATG
1 TCGCTGGCATTGAATCAGCATATTGGCACTCATCTCTTAGCTCAATG
* * * * **
245901 TTGCTGGCATTGAATCAACACATTGATCCACTTTTCTCTTAGCTCAATG
1 TCGCTGGCATTGAATCAGCATATTG--GCACTCATCTCTTAGCTCAATG
* *
245950 TCGCTGGCCTTGAATTAGCATATTGGCA
1 TCGCTGGCATTGAATCAGCATATTGGCA
245978 TTCTTTTCAT
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
44 21 0.36
46 3 0.05
47 3 0.05
48 1 0.02
49 31 0.53
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (47 bp):
TCGCTGGCATTGAATCAGCATATTGGCACTCATCTCTTAGCTCAATG
Found at i:246748 original size:20 final size:20
Alignment explanation
Indices: 246672--246747 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
246662 AAGTACCCAG
* *
246672 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTCATAA
*
246692 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCATAA
* *
246712 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCATAA
246732 ATGTATCGATACATTC
1 ATGTATCGATACATTC
246748 TGTCTTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTCATAA
Found at i:250972 original size:20 final size:20
Alignment explanation
Indices: 250947--251046 Score: 110
Period size: 20 Copynumber: 4.8 Consensus size: 20
250937 TTTTACCCAG
*
250947 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
250967 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
250987 ATATATTGATACATTCTACCCA
1 ATGTATCGATACATTCT--TCA
* * *
251009 GATGTATCGATGCATTCATCC
1 -ATGTATCGATACATTCTTCA
251030 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
251047 ACATAGATGT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
20 49 0.75
21 1 0.02
22 2 0.03
23 13 0.20
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:251017 original size:43 final size:43
Alignment explanation
Indices: 250967--251048 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
250957 ACATTTTTCA
* *
250967 ATGTATCGATACATTCTTCAATATATTGATACATTCTACCCAG
1 ATGTATCGATACATTCATCAATATATCGATACATTCTACCCAG
* * *
251010 ATGTATCGATGCATTCATCCATGTATCGATACATTCTAC
1 ATGTATCGATACATTCATCAATATATCGATACATTCTAC
251049 ATAGATGTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (43 bp):
ATGTATCGATACATTCATCAATATATCGATACATTCTACCCAG
Found at i:251056 original size:43 final size:41
Alignment explanation
Indices: 250947--251049 Score: 118
Period size: 43 Copynumber: 2.5 Consensus size: 41
250937 TTTTACCCAG
* * *
250947 ATGTATCGATACATTTTTCA-ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTACAGATGTATCGATACATTCATCA
* * * *
250987 ATATATTGATACATTCTACCCAGATGTATCGATGCATTCATCC
1 ATGTATCGATACATTCTA--CAGATGTATCGATACATTCATCA
251030 ATGTATCGATACATTCTACA
1 ATGTATCGATACATTCTACA
251050 TAGATGTCGT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
40 14 0.27
41 2 0.04
42 2 0.04
43 33 0.65
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATTCTACAGATGTATCGATACATTCATCA
Found at i:252913 original size:13 final size:13
Alignment explanation
Indices: 252895--252943 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
252885 TTTTAGAATA
252895 AAATTTAATTTTT
1 AAATTTAATTTTT
252908 AAATTTAATTATTT
1 AAATTTAATT-TTT
252922 --ATTTAA--TTT
1 AAATTTAATTTTT
*
252931 AAATTCAATTTTT
1 AAATTTAATTTTT
252944 GACTCATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
9 3 0.10
11 5 0.17
12 6 0.20
13 13 0.43
14 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
AAATTTAATTTTT
Found at i:255454 original size:2 final size:2
Alignment explanation
Indices: 255449--255478 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
255439 CTATTATACT
255449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
255479 GGTATATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:267725 original size:12 final size:12
Alignment explanation
Indices: 267707--267774 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 12
267697 TTCCTACCAA
267707 AAAAAAATTAAAT
1 AAAAAAA-TAAAT
267720 AAAAAAAT-AAT
1 AAAAAAATAAAT
267731 AAAAAAATAAA-
1 AAAAAAATAAAT
*
267742 AAACAAAAAAAACT
1 AAA-AAAATAAA-T
*
267756 AAGAAAA-AAAT
1 AAAAAAATAAAT
267767 AACAAAAA
1 AA-AAAAA
267775 AAAACAGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
11 17 0.36
12 17 0.36
13 11 0.23
14 2 0.04
ACGTcount: A:0.82, C:0.04, G:0.01, T:0.12
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:267749 original size:24 final size:25
Alignment explanation
Indices: 267707--267777 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 25
267697 TTCCTACCAA
*
267707 AAAAAAATTAAATAA-AAAAATAA-T
1 AAAAAAA-TAAATAACAAAAAAAACT
*
267731 AAAAAAATAAAAAACAAAAAAAACT
1 AAAAAAATAAATAACAAAAAAAACT
*
267756 AAGAAAA-AAATAACAAAAAAAA
1 AAAAAAATAAATAACAAAAAAAA
267778 ACAGAAAGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.15
24 28 0.68
25 7 0.17
ACGTcount: A:0.83, C:0.04, G:0.01, T:0.11
Consensus pattern (25 bp):
AAAAAAATAAATAACAAAAAAAACT
Found at i:267751 original size:28 final size:27
Alignment explanation
Indices: 267720--267778 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
267710 AAAATTAAAT
*
267720 AAAAAAATAATAAAAAAATAAAAAACAA
1 AAAAAAATAAGAAAAAAATAAAAAA-AA
* *
267748 AAAAAACTAAGAAAAAAATAACAAAAA
1 AAAAAAATAAGAAAAAAATAAAAAAAA
267775 AAAA
1 AAAA
267779 CAGAAAGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.85, C:0.05, G:0.02, T:0.08
Consensus pattern (27 bp):
AAAAAAATAAGAAAAAAATAAAAAAAA
Found at i:269124 original size:58 final size:57
Alignment explanation
Indices: 269017--269177 Score: 193
Period size: 58 Copynumber: 2.8 Consensus size: 57
269007 TTTCATCTCT
* * * *
269017 TCAAAGCCCACACGTTAGTGG-ACCCTTTTTAAAAGCCCACAAGTCCAGTGGCACCCTT-
1 TCAAAGCCCACAAGTCAGTGGCACCC--TTTCAAAGCCCACAAGTCCAGT-GAACCCTTC
* * *
269075 TCAAAGGCCACAAGTCAGTGGCACTCCTTTCCAAAGGCCACAA-TTCAGTGAACCCTTC
1 TCAAAGCCCACAAGTCAGTGGCAC-CCTTT-CAAAGCCCACAAGTCCAGTGAACCCTTC
269133 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCC
1 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCC
269178 CGGGCCCCCT
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
56 11 0.12
57 14 0.16
58 49 0.56
59 12 0.14
60 2 0.02
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (57 bp):
TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCCAGTGAACCCTTC
Found at i:269188 original size:28 final size:28
Alignment explanation
Indices: 269016--269176 Score: 191
Period size: 28 Copynumber: 5.6 Consensus size: 28
269006 CTTTCATCTC
* *
269016 TTCAAAGCCCACACGTTAGTGG-ACCCTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCC--T
*
269045 TTAAAAGCCCACAAGTCCAGTGGCACCCT
1 TTCAAAGCCCACAAGT-CAGTGGCACCCT
*
269074 TTCAAAGGCCACAAGTCAGTGGCACTCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
269103 TTCCAAAGGCCACAATTCAGT-GAACCCT
1 TT-CAAAGCCCACAAGTCAGTGGCACCCT
269131 TCTCAAAGCCCACAAGTCAGTGGCACCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACCCT
269160 TTCAAAGCCCACAAGTC
1 TTCAAAGCCCACAAGTC
269177 CCGGGCCCCC
Statistics
Matches: 116, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
28 45 0.39
29 45 0.39
30 22 0.19
31 4 0.03
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:269334 original size:27 final size:28
Alignment explanation
Indices: 269195--269681 Score: 285
Period size: 28 Copynumber: 17.1 Consensus size: 28
269185 CCTTCAAAGT
269195 CACCCTTTCAAAAGCCCA-AAGTCAGTGG
1 CACCCTTTC-AAAGCCCACAAGTCAGTGG
* *
269223 CACCCTTTACAAAACCGCCACACGTCAGTGG
1 CACCCTTT-C-AAAGC-CCACAAGTCAGTGG
* *
269254 CCCCACCCTTCCAAAG-CCATTAAGTCAAGTGG
1 ---CACCCTTTCAAAGCCCA-CAAGTC-AGTGG
269286 CACCCTTTTCAAAAGCCCACAAGTC-GTGG
1 CACCC-TTTC-AAAGCCCACAAGTCAGTGG
*
269315 CATCCTTTCAAAGCCCACAAAGTCAAGTGG
1 CACCCTTTCAAAGCCCAC-AAGTC-AGTGG
* * *
269345 AACCCCTTTTC-AAG-CTA-AAGTCATTGGCG
1 CA-CCC-TTTCAAAGCCCACAAGTCAGT-G-G
** * * *
269374 CACATTTTCAAAGCCCACCAGT-TGTAG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* *
269401 CATCCTTTCAAAGGCCGAC-AGT-AGTGG
1 CACCCTTTCAAA-GCCCACAAGTCAGTGG
* * * *
269428 CCACCCTTTTTAAAGCTCA-AATTCATATGG
1 -CACCC-TTTCAAAGCCCACAAGTCA-GTGG
* *
269458 CACCCTTTGAAAGCCCACAAGTCCGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
269486 CACCCTTTGC--AG-CCACAAGTCAAGTGG
1 CACCCTTT-CAAAGCCCACAAGTC-AGTGG
* *
269513 CACTCTTTTCAAAGCCCACAAGTCA-TTG
1 CAC-CCTTTCAAAGCCCACAAGTCAGTGG
* *
269541 CATCCTTTCAAAG-CCACAAGTCAGTGA
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
269568 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* * *
269596 TACCCTTTTAAAGCCC-CTACGTTCAGTGG
1 CACCCTTTCAAAGCCCAC-AAG-TCAGTGG
* * *
269625 CATCCTTTCAAA--CCACACGTCCGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* *
269651 CA--CTTTCTAACAGCCCAAAAGTCCGTGG
1 CACCCTTTC-AA-AGCCCACAAGTCAGTGG
269679 CAC
1 CAC
269682 TTTTTCACGC
Statistics
Matches: 358, Mismatches: 57, Indels: 87
0.71 0.11 0.17
Matches are distributed among these distances:
24 5 0.01
25 2 0.01
26 28 0.08
27 69 0.19
28 114 0.32
29 59 0.16
30 31 0.09
31 27 0.08
32 15 0.04
33 1 0.00
34 7 0.02
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (28 bp):
CACCCTTTCAAAGCCCACAAGTCAGTGG
Found at i:269530 original size:56 final size:54
Alignment explanation
Indices: 269458--269653 Score: 175
Period size: 55 Copynumber: 3.6 Consensus size: 54
269448 ATTCATATGG
* *
269458 CACCCTTTGAAAGCCCACAAGTCCGTGGCACCCTTTGC-AGCCACAAGTCAAGTGG
1 CACCCTTTCAAAGCCCACAAGTCCGTGGCACCCTTT-CAAGCCACAAGTC-AGTGA
* * * *
269513 CACTCTTTTCAAAGCCCACAAGT-CATTGCATCCTTTCAAAGCCACAAGTCAGTGA
1 CAC-CCTTTCAAAGCCCACAAGTCCGTGGCACCCTTTC-AAGCCACAAGTCAGTGA
* * * * * *
269568 CACCCTTTCAAAGCCCACAAGTCAGTGGTACCCTTTTAAAGCCCCTACGTTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCCGTGGCACCC-TTTCAAGCCAC-AAG-TCAGTGA
* *
269625 CATCCTTTCAAA--CCACACGTCCGTGGCAC
1 CACCCTTTCAAAGCCCACAAGTCCGTGGCAC
269654 TTTCTAACAG
Statistics
Matches: 114, Mismatches: 20, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
54 19 0.17
55 45 0.39
56 33 0.29
57 17 0.15
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.22
Consensus pattern (54 bp):
CACCCTTTCAAAGCCCACAAGTCCGTGGCACCCTTTCAAGCCACAAGTCAGTGA
Found at i:276143 original size:23 final size:23
Alignment explanation
Indices: 276116--276172 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
276106 ATCTATTAAG
* *
276116 TATCCAAATAAAAAGTTAAGATA
1 TATCCAAATAAAAAGTAAAAATA
***
276139 TATCCAAATAATTGGTAAAAATA
1 TATCCAAATAAAAAGTAAAAATA
276162 TATCCAAATAA
1 TATCCAAATAA
276173 GCATTAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (23 bp):
TATCCAAATAAAAAGTAAAAATA
Found at i:276180 original size:23 final size:23
Alignment explanation
Indices: 276116--276180 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
276106 ATCTATTAAG
** * *
276116 TATCCAAATAAAAAGTTAAGATA
1 TATCCAAATAAGCAGTAAAAATA
***
276139 TATCCAAATAATTGGTAAAAATA
1 TATCCAAATAAGCAGTAAAAATA
*
276162 TATCCAAATAAGCATTAAA
1 TATCCAAATAAGCAGTAAA
276181 GATGTTTGTT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.28
Consensus pattern (23 bp):
TATCCAAATAAGCAGTAAAAATA
Found at i:280035 original size:2 final size:2
Alignment explanation
Indices: 280028--280070 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
280018 ATTAGCTTGG
280028 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
280070 A
1 A
280071 GGTATTATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:280679 original size:20 final size:20
Alignment explanation
Indices: 280656--280731 Score: 118
Period size: 20 Copynumber: 3.8 Consensus size: 20
280646 AAAATACCCA
*
280656 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTCTTC
*
280676 AATGTATCGATACATTCAT-
1 AATGTATCGATACATTCTTC
280695 ACATGTATCGATACATTCTTC
1 A-ATGTATCGATACATTCTTC
280716 AATGTATCGATACATT
1 AATGTATCGATACATT
280732 TTGTCTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 49 0.96
21 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:294676 original size:15 final size:15
Alignment explanation
Indices: 294656--294715 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
294646 TCCTTCATAC
294656 AAAAAAAAAATAAAT
1 AAAAAAAAAATAAAT
*
294671 AAAAAAACAAAAAAAT
1 AAAAAAA-AAATAAAT
*
294687 AAAAAACAAAA-AAACC
1 AAAAAA-AAAATAAA-T
*
294703 AAGAAAAAAATAA
1 AAAAAAAAAATAA
294716 CAAAAAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 14 0.37
16 23 0.61
17 1 0.03
ACGTcount: A:0.85, C:0.07, G:0.02, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAATAAAT
Found at i:294677 original size:16 final size:15
Alignment explanation
Indices: 294656--294723 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
294646 TCCTTCATAC
*
294656 AAAAAAAAAATAAAT
1 AAAAAAAAAAAAAAT
294671 AAAAAAACAAAAAAAT
1 AAAAAAA-AAAAAAAT
* *
294687 AAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAT
* * * *
294702 CAAGAAAAAAATAAC
1 AAAAAAAAAAAAAAT
294717 AAAAAAA
1 AAAAAAA
294724 CAGAAAGGGG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
15 30 0.70
16 13 0.30
ACGTcount: A:0.85, C:0.07, G:0.01, T:0.06
Consensus pattern (15 bp):
AAAAAAAAAAAAAAT
Found at i:294680 original size:23 final size:23
Alignment explanation
Indices: 294654--294725 Score: 94
Period size: 23 Copynumber: 3.1 Consensus size: 23
294644 CGTCCTTCAT
*
294654 ACAAAAAAAAAATAAATAAAAAA
1 ACAAAAAAAAAATAAACAAAAAA
294677 ACAAAAAAATAAA-AAACAAAAAA
1 ACAAAAAAA-AAATAAACAAAAAA
*
294700 ACCAAGAAAAAAAT-AACAAAAAA
1 A-CAAAAAAAAAATAAACAAAAAA
294723 ACA
1 ACA
294726 GAAAGGGGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.05
23 32 0.73
24 10 0.23
ACGTcount: A:0.83, C:0.10, G:0.01, T:0.06
Consensus pattern (23 bp):
ACAAAAAAAAAATAAACAAAAAA
Found at i:295983 original size:28 final size:28
Alignment explanation
Indices: 295939--296794 Score: 1138
Period size: 28 Copynumber: 30.1 Consensus size: 28
295929 CTAGAACGTT
* *
295939 CACCCTTTCAAAACCCACAAGTTAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
295967 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
**
295995 CACCCTTTCAAAGCTTACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
296023 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
296051 CACTCCTTTCAAAGCCCACAAGTCAGTGG
1 CAC-CCTTTCAAAGCCCACAAGTCAGTGG
296080 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
296108 CACCCTTTCAAAG-CCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* *
296135 CACCCTTTCAAATCCCATAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* *
296163 CACTCTTTTCAAAGCTCACAAGTCAGTGG
1 CAC-CCTTTCAAAGCCCACAAGTCAGTGG
*
296192 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* * *
296220 CACTCTTTCAAAGCCTACAAGTCATTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* * *
296248 CACACTTTCAAAGCCCGCAAGTTAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* * *
296276 TATCCTTTCAAAGCCCGCAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* *
296304 CACCTTTTTTAAAGCCCACAAGTCAGTGG
1 CACC-CTTTCAAAGCCCACAAGTCAGTGG
* *
296333 CACCCTTTGAAAGCCAACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
*
296361 CACCCTTTGAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
*
296389 CACTCTTTTCAAAGCCCACAAGTCAGTGG
1 CAC-CCTTTCAAAGCCCACAAGTCAGTGG
* *
296418 CATCCTTTCAAAGCCCACAAGTCAGTGA
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
296446 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* * *
296474 TACCCTTTTAAAGCCCATAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* *
296502 CATCCTTTCAAAGCCCACAAGTTAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
296530 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* *
296558 GACTCTTTTCAAAGCCCACAAGTCAGTGG
1 CAC-CCTTTCAAAGCCCACAAGTCAGTGG
* * *
296587 TAACTCTTTTCAAAACCCACAAGTCAGTGG
1 -CAC-CCTTTCAAAGCCCACAAGTCAGTGG
*
296617 CACCCTTTCAAAGCCCACATGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* * * *
296645 CGCCCTTTCAAAACCCATAAGTTAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* *
296673 TATCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
* * *
296701 CACCCTTTCAAAGCCCACAAGTCGGCGA
1 CACCCTTTCAAAGCCCACAAGTCAGTGG
*
296729 CACTCTTTTCAAAGCCCACACGAGTCAGTGG
1 CAC-CCTTTCAAAGCCCACA--AGTCAGTGG
* *
296760 CAACTCTTTTCAAAGCCCACAGAAGTTAGTGG
1 C-AC-CCTTTCAAAGCCCAC--AAGTCAGTGG
296792 CAC
1 CAC
296795 TTTTTTTTTT
Statistics
Matches: 732, Mismatches: 83, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
27 26 0.04
28 500 0.68
29 142 0.19
30 27 0.04
31 9 0.01
32 27 0.04
34 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
CACCCTTTCAAAGCCCACAAGTCAGTGG
Found at i:296331 original size:113 final size:113
Alignment explanation
Indices: 295942--296794 Score: 1165
Period size: 113 Copynumber: 7.5 Consensus size: 113
295932 GAACGTTCAC
* *
295942 CCTTTCAAAACCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
**
296007 GCTTACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
66 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
296055 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
* *
296120 G-CCACAAGTCAGTGGCACCCTTTCAAATCCCATAAGTCAGTGGCACT
66 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
296167 CTTTTCAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
* * * * * *
296232 GCCTACAAGTCATTGGCACACTTTCAAAGCCCGCAAGTTAGTGGTA-T
66 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
296279 CCTTTCAAAGCCCGCAAGTCAGTGGCACCTTTTTTAAAGCCCACAAGTCAGTGGCACCCTTTGAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACC-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
* *
296344 AGCCAACAAGTCAGTGGCACCCTTTGAAAGCCCACAAGTCAGTGGCACT
65 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
296393 CTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGACACCCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
* * *
296458 GCCCACAAGTCAGTGGTACCCTTTTAAAGCCCATAAGTCAGTGGCA-T
66 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
296505 CCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGGACTCTTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAA
* * *
296570 AGCCCACAAGTCAGTGGTAACTCTTTTCAAAACCCACAAGTCAGTGGCAC-
65 AGCCCACAAGTCAGTGG-CAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * * * *
296620 CCTTTCAAAGCCCACATGTCAGTGGCGCCCTTTCAAAACCCATAAGTTAGTGGTATCCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
* * *
296685 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCGGCGACACT
66 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
296733 CTTTTCAAAGCCCACACGAGTCAGTGGCAACTCTTTTCAAAGCCCACAGAAGTTAGTGGCAC
1 CCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAGCCCAC--AAGTCAGTGGCAC
296795 TTTTTTTTTT
Statistics
Matches: 648, Mismatches: 78, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
112 205 0.32
113 286 0.44
114 53 0.08
115 80 0.12
116 1 0.00
117 12 0.02
119 11 0.02
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (113 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:296932 original size:45 final size:47
Alignment explanation
Indices: 296862--296990 Score: 154
Period size: 49 Copynumber: 2.7 Consensus size: 47
296852 CTATCTGACA
* *
296862 TCGCTAGCATTGAATCAGCATATTGGCAC-CTT-TATTAGCCCAATG
1 TCGCTGGCATTGAATCAGCACATTGGCACTCTTCTATTAGCCCAATG
* * *
296907 TTGCTGGCATTGAATCAGCACATTGGTCCACTTTTCTCTTAGCCCAATG
1 TCGCTGGCATTGAATCAGCACATTGG--CACTCTTCTATTAGCCCAATG
* * *
296956 TCGCTGGCCTTGAATTAGCACATTGGCATTCTTCT
1 TCGCTGGCATTGAATCAGCACATTGGCACTCTTCT
296991 CATCTCTAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
45 23 0.33
47 10 0.14
48 2 0.03
49 35 0.50
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.34
Consensus pattern (47 bp):
TCGCTGGCATTGAATCAGCACATTGGCACTCTTCTATTAGCCCAATG
Found at i:297793 original size:20 final size:20
Alignment explanation
Indices: 297677--297793 Score: 155
Period size: 20 Copynumber: 5.8 Consensus size: 20
297667 AAGTACCCAG
****
297677 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTCTTCA
* *
297697 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
297717 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
297737 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
297757 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
297777 ATGTATCGATACTTTCT
1 ATGTATCGATACATTCT
297794 GTCTTTTTAC
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
19 1 0.01
20 88 0.98
21 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:298285 original size:13 final size:14
Alignment explanation
Indices: 298263--298291 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
298253 ATATCTTAGC
298263 AAAACATCAACACA
1 AAAACATCAACACA
298277 AAAAC-TCAACACA
1 AAAACATCAACACA
298290 AA
1 AA
298292 GTCTATTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.66, C:0.28, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACATCAACACA
Found at i:308305 original size:32 final size:34
Alignment explanation
Indices: 308263--308328 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 34
308253 TTCTAAAGCT
*
308263 GTTAAATTTGATC-ACATAT-TTATATATTTTTG
1 GTTAAATTTGATCAAAATATATTATATATTTTTG
*
308295 GTTAACTTTGATCATAAATATATTATATATTTTT
1 GTTAAATTTGATCA-AAATATATTATATATTTTT
308329 TATTTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 12 0.41
34 5 0.17
35 12 0.41
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (34 bp):
GTTAAATTTGATCAAAATATATTATATATTTTTG
Found at i:308341 original size:35 final size:34
Alignment explanation
Indices: 308278--308343 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
308268 ATTTGATCAC
* *
308278 ATATTTATATATTTTTGGTTAACTTTGATCATAA
1 ATATTTATATATTTTTGATTAACATTGATCATAA
* *
308312 ATATATTATATATTTTTTATTTACATTGATCA
1 ATAT-TTATATATTTTTGATTAACATTGATCA
308344 AATTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 4 0.15
35 23 0.85
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (34 bp):
ATATTTATATATTTTTGATTAACATTGATCATAA
Found at i:309702 original size:19 final size:19
Alignment explanation
Indices: 309661--309703 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
309651 TGCGTTTGCT
* **
309661 GTCTTCTTTTCCATTTACT
1 GTCTTCTTTTCCACTTAAA
309680 GTCTTCTTTTCCACTTAAA
1 GTCTTCTTTTCCACTTAAA
309699 GTCTT
1 GTCTT
309704 AACAACTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.07, T:0.53
Consensus pattern (19 bp):
GTCTTCTTTTCCACTTAAA
Found at i:315510 original size:13 final size:13
Alignment explanation
Indices: 315492--315517 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
315482 CATTATTAAA
315492 TGTATCGATACAT
1 TGTATCGATACAT
315505 TGTATCGATACAT
1 TGTATCGATACAT
315518 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:315581 original size:20 final size:19
Alignment explanation
Indices: 315556--315629 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
315546 TTTACCCAGA
315556 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
315576 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
315596 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
*
315616 TGTATTGATACATT
1 TGTATCGATACATT
315630 CAGGCATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:317980 original size:51 final size:50
Alignment explanation
Indices: 317905--318083 Score: 191
Period size: 51 Copynumber: 3.5 Consensus size: 50
317895 AAATTTCTAG
* * * *
317905 ATTTTTCAT-CTCGGGGATACTCCAATCTCGATTTCATTTCTAAAATATCA
1 ATTTTTCATAATCGGGGATACTCCAA-CTCGATTTTATTTCTAAAACACCA
* * *
317955 ATTTTTCTTAATCGGGGATACTCCAACTTTGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCGGGGATACTCCAAC-TCGATTTTATTTCTAAAACACCA
* * * *
318006 ATTTTCCATAATCGGGGAAACTCTAACTCCGATTTTATTT-TCAAAACACCG
1 ATTTTTCATAATCGGGGATACTCCAACT-CGATTTTATTTCT-AAAACACCA
* *
318057 ACTTTTCACAATCGGGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
318084 CCCATTATTT
Statistics
Matches: 107, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 11 0.10
51 96 0.90
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.36
Consensus pattern (50 bp):
ATTTTTCATAATCGGGGATACTCCAACTCGATTTTATTTCTAAAACACCA
Found at i:318114 original size:79 final size:79
Alignment explanation
Indices: 318019--318346 Score: 400
Period size: 79 Copynumber: 4.2 Consensus size: 79
318009 TTCCATAATC
* * * *
318019 GGGGAAACTCTAACTCCGATTTTATTT-TCAAAACACCGACTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCT-AAAACATCGAATTTTCACAATCGGGGATACTCCAA
*
318083 CCCCATTATTTTCGA
65 CCCCGTTATTTTCGA
* * *
318098 GGGGACACCCCAACTCCGATTTTATTTCTAAAACATC-AATTTT-TC-ATCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAAC
*
318160 CCCGTTATTTTTGA
66 CCCGTTATTTTCGA
* * * * *
318174 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATAT-TAATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCTAAAACATCGAATTT-TCACAATCGGGGATACTCCAA
*
318238 CCCCGTTA-TTTCTGT
65 CCCCGTTATTTTC-GA
* * *
318253 GGGGATACTCCAA-TCCTGATTTTATTTATAAATCATCGATTTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCC-GATTTTATTTCTAAAACATCGA-ATTTTCACAATCGGGGATACTCCA
318317 ACCCCGTTATTTTCGA
64 ACCCCGTTATTTTCGA
318333 GGGGATACTCCAAC
1 GGGGATACTCCAAC
318347 CCCGTTATTA
Statistics
Matches: 212, Mismatches: 26, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
76 65 0.31
77 2 0.01
78 10 0.05
79 84 0.40
80 44 0.21
81 7 0.03
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACTCCGATTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:318366 original size:159 final size:156
Alignment explanation
Indices: 318066--318378 Score: 436
Period size: 159 Copynumber: 2.0 Consensus size: 156
318056 GACTTTTCAC
*
318066 AATCGGGGATACTCCAACCCCATTATTTTCGAGGGGACACCCCAACTCCGATTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCATTATTTTCGAGGGGACACCCCAACTCCGATTTTATTTATAAAA
*
318131 CATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTT
66 CATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTT
* *
318196 TATTTCTAAAATATT-AATTTCTCAT
131 TATCTCCAAAATATTAAATTTCTCAT
* * * *
318221 AATCGGGGATACTCCAACCCCGTTA-TTTCTGTGGGGATACTCCAA-TCCTGATTTTATTTATAA
1 AATCGGGGATACTCCAACCCCATTATTTTC-GAGGGGACACCCCAACTCC-GATTTTATTTATAA
* *
318284 ATCATCGATTTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
64 AACATC-AATTTTT--C-ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
*
318349 C-GTTATTATCTCCAAAATCTTAAATTTCTC
125 CGGTT-TTATCTCCAAAATATTAAATTTCTC
318379 GTCGGGAGAT
Statistics
Matches: 139, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
154 7 0.05
155 54 0.39
156 6 0.04
158 4 0.03
159 60 0.43
160 8 0.06
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (156 bp):
AATCGGGGATACTCCAACCCCATTATTTTCGAGGGGACACCCCAACTCCGATTTTATTTATAAAA
CATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTT
TATCTCCAAAATATTAAATTTCTCAT
Found at i:324679 original size:55 final size:58
Alignment explanation
Indices: 324510--324783 Score: 297
Period size: 64 Copynumber: 4.5 Consensus size: 58
324500 CTTTTTTAGC
* *
324510 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTTCTTTTTAAAGCCCATACAACTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCC-----TCTTTTTAAAGCCCACACAAGTTGGTGGCA
*
324573 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTCAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCC---TCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *
324633 CCTT-TCAGTCCTCAAAGAGTAGGACG-C-C-TTTTAAAGCCCACACAAGTTGGTCGCA
1 CCTTCT-AGTCCTCAAAGAGCAGGACGCCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *
324688 CCCTCTAGTCCTCAAAGAGCAGGATGCCTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCC------TCTTTTTAAAGCCCACACAAGTTGGTGGCA
*
324752 CCTTCTAGTCCTTAAAGAGCAGGACGCTCTCT
1 CCTTCTAGTCCTCAAAGAGCAGGACGC-CTCT
324784 CCTTTCACCC
Statistics
Matches: 186, Mismatches: 13, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
55 46 0.25
56 3 0.02
59 3 0.02
60 36 0.19
61 19 0.10
62 23 0.12
63 5 0.03
64 50 0.27
65 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (58 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:324750 original size:119 final size:115
Alignment explanation
Indices: 324546--324778 Score: 342
Period size: 119 Copynumber: 2.0 Consensus size: 115
324536 CCTTTTTTCT
* * * *
324546 TTTTAAAGCCCATACAACTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTC
1 TTTTAAAGCCCACACAACTTGGTCGCACCTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTA
*
324611 AAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGTAGGACGCC
66 AAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGACGCC
* *
324661 TTTTAAAGCCCACACAAGTTGGTCGCACCCTCTAGTCCTCAAAGAGCAGGATGCCTTTTTTTCTT
1 TTTTAAAGCCCACACAACTTGGTCGCA-CCTCTAGTCCTCAAAGAGCAGGACGCC---TTTTCTT
*
324726 TTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTTAAAGAGCAGGACGC
62 TTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGC
324779 TCTCTCCTTT
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
115 24 0.23
116 25 0.24
119 55 0.52
120 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (115 bp):
TTTTAAAGCCCACACAACTTGGTCGCACCTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTA
AAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCC
Found at i:325085 original size:120 final size:121
Alignment explanation
Indices: 324817--325113 Score: 463
Period size: 120 Copynumber: 2.5 Consensus size: 121
324807 GAGGAGGACG
**
324817 CCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACCTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
* *
324882 CAAAGTCCACACAAGTTGGTGGCACCTTTTAATCCTCAAAGAGCAGGACGCCTTTT
66 CAAAGTCCACACAAGATGGTGGCACCTTTTAATCCTCAAAGAGCAGGACACCTTTT
*
324938 CCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACGCCTTTTTCTT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCA-CCTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
* * *
325003 TTAAAG-CCACATAAGATGGTGGCACC-TTTAGTCCTCAAAGAGCAGGACACCTTTT
65 TCAAAGTCCACACAAGATGGTGGCACCTTTTAATCCTCAAAGAGCAGGACACCTTTT
* * *
325058 CCTTTTAAAGCGCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACCTCC-AGTCCTCAAAGAGCAGGACGC
325114 TCTCTCCTTT
Statistics
Matches: 163, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
119 4 0.02
120 75 0.46
121 47 0.29
122 37 0.23
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (121 bp):
CCTTTTAAAGCCCACACGAGTTGGTGGCACCTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
CAAAGTCCACACAAGATGGTGGCACCTTTTAATCCTCAAAGAGCAGGACACCTTTT
Found at i:325123 original size:61 final size:59
Alignment explanation
Indices: 324817--325113 Score: 425
Period size: 61 Copynumber: 4.9 Consensus size: 59
324807 GAGGAGGACG
*
324817 CCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAG-CCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
324877 CCTTTCAAAGTCCACACAAGTTGGTGGCACCTTTTAATCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAG-CCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAGAGCAGGACGCCTTTT
* **
324938 CCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAG-CCACACAAGTTGGTGGCA-CCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
324999 TCTTTTAAAGCCACATAAGATGGTGGCACCTTTAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTTAAAGCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
325058 CCTTTTAAAGCGCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
1 CCTTTTAAAGC-CACACAAGTTGGTGGCACCTT--TAGTCCTCAAAGAGCAGGACGC
325114 TCTCTCCTTT
Statistics
Matches: 211, Mismatches: 21, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
59 41 0.19
60 58 0.27
61 110 0.52
62 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (59 bp):
CCTTTTAAAGCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:325125 original size:335 final size:335
Alignment explanation
Indices: 324510--325374 Score: 1111
Period size: 335 Copynumber: 2.6 Consensus size: 335
324500 CTTTTTTAGC
* * *
324510 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTTCTTTTTAAAGCCCATACAACTTGGTGGCACC
1 CCTT-TAGTCCTCAAAGAGCAGGACGCC--TTTTCCTTTCAAAGCCCATACAAGTTGGTGGCACC
* * *
324575 -TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTCAAGCCCACACAAGTTGGTGGCACCTTTC
63 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC
* * * *
324639 AGTCCTCAAAGAGTAGGACG-C---CTTTTAAAGCCCACACAAGTTGGTCGCACCCTCTAGTCCT
128 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGATGGTGGCA-CCTTTAGTCCT
** * *
324700 CAAAGAGCAGGATGCCTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTT
192 CAAAGAGCAGGACACC--TTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTC
324765 AAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGGAGGACGCCTTTTAAAGCCC
255 AAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGGAGGACGCCTTTTAAAGCCC
*
324830 ACACGAGTTGGTGGCA
320 ACACAAGTTGGTGGCA
* *
324846 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGTCCACACAAGTTGGTGGCACCTTT
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCATACAAGTTGGTGGCACCTTT
* * *
324911 TAATCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAGT
66 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGT
*
324976 CCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAG-CCACATAAGATGGTGGCACCTTTAGTCCTCA
131 CCTCAAAGAGCAGGACGCC--TTTCTTTTAAAGCCCACACAAGATGGTGGCACCTTTAGTCCTCA
*
325040 AAGAGCAGGACACC-TTTTCCTTTTAAAGCGCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAA
194 AAGAGCAGGACACCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAA
* * * *
325103 GAGCAGGACGCTCTCTCCTTTCACCTTTTTGTCCTCAAAGAGTAGGATGCCTTTTAAAGCCCACA
258 GAGCAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGGAGGACGCCTTTTAAAGCCCACA
325168 CAAGTTGGTGGCA
323 CAAGTTGGTGGCA
* * *
325181 -TTTTCCAGTCCTCAAAGAGCAGGA---C---ACCTTTCAAAACCCATACAAGTTGGTGGCA--T
1 CCTTT--AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCATACAAGTTGGTGGCACCT
* * * **
325237 TTTCCAGTCCTCAAAGAGCAAGATG-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTT
64 TTT--AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTT
* *
325301 CTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAA-ACTGGTGGCACTTTTCA
126 CCAGTCCTCAAAGAGCAGGACGCCTT-T-CTTTTAAAGCCCACACAAGA-TGGTGGCACCTTT-A
325365 GTCCTCAAAG
187 GTCCTCAAAG
325375 GGCTGGATGC
Statistics
Matches: 469, Mismatches: 42, Indels: 40
0.85 0.08 0.07
Matches are distributed among these distances:
328 6 0.01
329 11 0.02
330 99 0.21
331 19 0.04
332 11 0.02
333 31 0.07
334 83 0.18
335 139 0.30
336 22 0.05
338 24 0.05
339 15 0.03
340 9 0.02
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (335 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCATACAAGTTGGTGGCACCTTT
TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGT
CCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGATGGTGGCACCTTTAGTCCTCAAA
GAGCAGGACACCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAG
CAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGGAGGACGCCTTTTAAAGCCCACACAA
GTTGGTGGCA
Found at i:325226 original size:55 final size:55
Alignment explanation
Indices: 325133--325896 Score: 797
Period size: 55 Copynumber: 13.3 Consensus size: 55
325123 TCACCTTTTT
* * *
325133 GTCCTCAAAGAGTAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCA
1 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * *
325188 GTCCTCAAAGAGCAGGACACCTTTCAAAACCCATACAAGTTGGTGGCATTTTCCA
1 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * *
325243 GTCCTCAAAGAGCAAGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTA
1 GTCCTCAAAGAGCAGGACGC-----C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
**
325304 GTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAACTGGTGGCACTTTT-CA
1 GTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCA-TTTTCCA
* * * * * *
325365 GTCCTCAAAGGGCTGGATGCTTTCTTTTTGCAAAGCCCACACTGAGTCGGTGGCATTTTCTA
1 GTCCTCAAAGAGCAGGACGC---C--TTT-CAAAGCCCACAC-AAGTTGGTGGCATTTTCCA
*
325427 GTCC-CTAAAGAGCAGGACACCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGGCATTTTCCA
1 GTCCTC-AAAGAGCAGGACGCC-TTTC------AAAGCCCACACAAGTTGGTGGCATTTTCCA
*
325489 GTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCCA
1 GTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * *
325544 TTCCTCAAAGAGCATGACGCCTCTT-AAAGCCCACAAAAGTTGGTGGCATTTTCCA
1 GTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * *
325599 GTCCTCAAAGAGCAGGACGCCTCTT-AAAGCCCACAAAAGTTAGTGGCATTTTCTA
1 GTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* *
325654 GTCCTCAAAGAGTAGGACGCCTCTT-AAAGTCCACACAAGTTGGTGGCATTTTCCA
1 GTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
*
325709 GTCCTCAAAGAGCAAGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCCA
1 GTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
**
325764 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCA
1 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * * *
325819 GTCCTCAAAGAGCAAGATGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TA
1 GTCCTCAAAGAGC-AG--GAC--GCC-TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCA
*
325880 GTCTTCAAAGAGCAGGA
1 GTCCTCAAAGAGCAGGA
325897 TGCACTTTAT
Statistics
Matches: 612, Mismatches: 60, Indels: 71
0.82 0.08 0.10
Matches are distributed among these distances:
54 2 0.00
55 364 0.59
56 4 0.01
57 2 0.00
58 7 0.01
59 1 0.00
60 5 0.01
61 144 0.24
62 66 0.11
63 12 0.02
64 1 0.00
65 2 0.00
66 2 0.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (55 bp):
GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
Found at i:325318 original size:210 final size:211
Alignment explanation
Indices: 324938--325333 Score: 532
Period size: 210 Copynumber: 1.9 Consensus size: 211
324928 GACGCCTTTT
* *
324938 CCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACGCCTTTTTCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACACC-TTTTC--
* * * *
325003 TTAAAGCCACATAAGATGGTGGCACCTTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAG
63 TAAAACCCACACAAGATGGTGGCACCTTTAGTCCTCAAAGAGCAAGACACCTTTTCCTTTTAAAG
*
325068 CGCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG-CTCTCTCCTTTCACCTTTT
128 CCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCT-TCTCCTTTCACCTTTT
325132 TGTCCTCAAAGAGTAGGATG
192 TGTCCTCAAAGAGTAGGATG
***
325152 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TTTC-AA
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACACCTTTTCTAA
* * * ** *
325215 AACCCATACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGA-TGCTTTTTCTTTTCAAAG
66 AACCCACACAAGATGGTGGCACCTTT--AGTCCTCAAAGAGCAAGACACCTTTTCCTTTT-AAAG
* *
325278 CCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
128 CCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
325334 TAAAGCCCAC
Statistics
Matches: 160, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
208 3 0.02
209 28 0.17
210 71 0.44
211 2 0.01
212 4 0.03
214 52 0.32
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (211 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACACCTTTTCTAA
AACCCACACAAGATGGTGGCACCTTTAGTCCTCAAAGAGCAAGACACCTTTTCCTTTTAAAGCCC
ACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTCACCTTTTTGTC
CTCAAAGAGTAGGATG
Found at i:325607 original size:27 final size:27
Alignment explanation
Indices: 325577--325717 Score: 75
Period size: 27 Copynumber: 5.1 Consensus size: 27
325567 TTAAAGCCCA
*
325577 CAAAAGTTGGTGGCATTTTCCAGTCCT
1 CAAAAGTTGGTGGCATTTTCAAGTCCT
** ** * * * * *
325604 CAAAGAGCAGGACGCCTCTTAAAGCCCA
1 CAAA-AGTTGGTGGCATTTTCAAGTCCT
* *
325632 CAAAAGTTAGTGGCATTTTCTAGTCCT
1 CAAAAGTTGGTGGCATTTTCAAGTCCT
* ** * * * *
325659 CAAAGAGTAGGACGCCTCTTAAAGTCCA
1 CAAA-AGTTGGTGGCATTTTCAAGTCCT
* *
325687 CACAAGTTGGTGGCATTTTCCAGTCCT
1 CAAAAGTTGGTGGCATTTTCAAGTCCT
325714 CAAA
1 CAAA
325718 GAGCAAGACG
Statistics
Matches: 72, Mismatches: 40, Indels: 4
0.62 0.34 0.03
Matches are distributed among these distances:
27 38 0.53
28 34 0.47
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (27 bp):
CAAAAGTTGGTGGCATTTTCAAGTCCT
Found at i:325685 original size:28 final size:28
Alignment explanation
Indices: 325545--325685 Score: 74
Period size: 28 Copynumber: 5.1 Consensus size: 28
325535 CATTTTCCAT
* *
325545 TCCTCAAAGAGCATGACGCCTCTTAAAG
1 TCCTCAAAGAGTAGGACGCCTCTTAAAG
* * * ** * * **
325573 CCCACAAA-AGTTGGTGGCATTTTCCAG
1 TCCTCAAAGAGTAGGACGCCTCTTAAAG
*
325600 TCCTCAAAGAGCAGGACGCCTCTTAAAG
1 TCCTCAAAGAGTAGGACGCCTCTTAAAG
* * * * **
325628 CCCACAAA-AGTTAGTG--GCATTTTCTAG
1 TCCTCAAAGAG-TAG-GACGCCTCTTAAAG
325655 TCCTCAAAGAGTAGGACGCCTCTTAAAG
1 TCCTCAAAGAGTAGGACGCCTCTTAAAG
325683 TCC
1 TCC
325686 ACACAAGTTG
Statistics
Matches: 73, Mismatches: 34, Indels: 12
0.61 0.29 0.10
Matches are distributed among these distances:
26 1 0.01
27 34 0.47
28 37 0.51
29 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (28 bp):
TCCTCAAAGAGTAGGACGCCTCTTAAAG
Found at i:326860 original size:13 final size:13
Alignment explanation
Indices: 326842--326867 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
326832 CATTATTAAA
326842 TGTATCGATACAT
1 TGTATCGATACAT
326855 TGTATCGATACAT
1 TGTATCGATACAT
326868 CGATATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:326962 original size:13 final size:13
Alignment explanation
Indices: 326943--326973 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
326933 ATACATTGCT
326943 CATTGTATCGATA
1 CATTGTATCGATA
*
326956 TATTGTATCGATA
1 CATTGTATCGATA
326969 CATTG
1 CATTG
326974 CTCATTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:326970 original size:33 final size:33
Alignment explanation
Indices: 326924--326988 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
326914 TACATTTTGC
326924 ATTGTATCAATACATTGCTCATTGTATCGATAT
1 ATTGTATCAATACATTGCTCATTGTATCGATAT
*
326957 ATTGTATCGATACATTGCTCATTGTATCGATA
1 ATTGTATCAATACATTGCTCATTGTATCGATA
326989 CTTTTTACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (33 bp):
ATTGTATCAATACATTGCTCATTGTATCGATAT
Found at i:326982 original size:20 final size:20
Alignment explanation
Indices: 326923--326989 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
326913 ATACATTTTG
*
326923 CATTGTATCAATACATTGCT
1 CATTGTATCGATACATTGCT
326943 CATTGTATCGAT--A----T
1 CATTGTATCGATACATTGCT
326957 -ATTGTATCGATACATTGCT
1 CATTGTATCGATACATTGCT
326976 CATTGTATCGATAC
1 CATTGTATCGATAC
326990 TTTTTACAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 24 0.62
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (20 bp):
CATTGTATCGATACATTGCT
Found at i:328290 original size:56 final size:56
Alignment explanation
Indices: 328223--328336 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
328213 CCAAAACAAG
328223 ATTTTAAGGACATCCCCAAGCCAAGCTCATGCTACCTCCCATACATGGAGAATAAC
1 ATTTTAAGGACATCCCCAAGCCAAGCTCATGCTACCTCCCATACATGGAGAATAAC
328279 ATTTTAAGGACATCCCCAAGCCAAGCTCATGCTACCTCCCATACATGGAGAATAAC
1 ATTTTAAGGACATCCCCAAGCCAAGCTCATGCTACCTCCCATACATGGAGAATAAC
328335 AT
1 AT
328337 GAACTTATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (56 bp):
ATTTTAAGGACATCCCCAAGCCAAGCTCATGCTACCTCCCATACATGGAGAATAAC
Found at i:329451 original size:51 final size:51
Alignment explanation
Indices: 329360--329539 Score: 202
Period size: 51 Copynumber: 3.5 Consensus size: 51
329350 TAAATTTCTA
* * * * **
329360 AATTTTTCAT-CTCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAAAGATT
1 AATTTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACC
* *
329410 AATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACC
1 AATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACC
* * * *
329461 CATTTTCCATAATCGAGGAAACTCCAACTCCGATTTTATTTCCAAAACACC
1 AATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACC
* * *
329512 GACTTTTCACAATCGGGGATACTCCAAC
1 AATTTTTCATAATCGGGGATACTCCAAC
329540 CTCGTTATTT
Statistics
Matches: 108, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
50 9 0.08
51 98 0.91
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
AATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACC
Found at i:329790 original size:80 final size:79
Alignment explanation
Indices: 329481--329800 Score: 384
Period size: 79 Copynumber: 4.1 Consensus size: 79
329471 AATCGAGGAA
* * * *
329481 ACTCCAACTCC-GATTTTATTTCCAAAACACCGACTTTTCACAATCGGGGATACTCCAACCTCGT
1 ACTCCAA-TCCTGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTCGT
*
329545 TATTTTCGAGGGGAC
65 TATTTTCGAGGGGAT
* * *
329560 ACCCCAA-CCTCAGTTTTATTTCTAAAACATCAATTTTT--C-ATCGGGGATACTCCAACCCCGT
1 ACTCCAATCCTGA-TTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTCGT
329621 TA-TTTCGAGGGGAT
65 TATTTTCGAGGGGAT
* * * * * * * *
329635 ACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAACC-CTAT
1 ACTCCAATCCTGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTC-GT
*
329699 TATTTTCGAGGGGGT
65 TATTTTCGAGGGGAT
* *
329714 ACTCCAATCCTGATTTTATTTCTAAATCATCAATTTTTTCACAATCAGGGATACTCCAACCTCGT
1 ACTCCAATCCTGATTTTATTTCTAAAACATCAA-TTTTTCACAATCGGGGATACTCCAACCTCGT
329779 TATTTTCGAGGGGAT
65 TATTTTCGAGGGGAT
329794 ACTCCAA
1 ACTCCAA
329801 CCCCGTTATT
Statistics
Matches: 202, Mismatches: 29, Indels: 19
0.81 0.12 0.08
Matches are distributed among these distances:
75 39 0.19
76 25 0.12
77 4 0.02
78 22 0.11
79 65 0.32
80 46 0.23
81 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (79 bp):
ACTCCAATCCTGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTCGTT
ATTTTCGAGGGGAT
Found at i:335753 original size:41 final size:42
Alignment explanation
Indices: 335706--335889 Score: 146
Period size: 41 Copynumber: 4.5 Consensus size: 42
335696 AGTTTAAGCG
** *
335706 AGATGAAATTATACGAGTTAATAAATGAGAAGAGCTT-ACTA
1 AGATGAAACCATACGAGTTAATGAATGAGAAGAGCTTGACTA
* * * *
335747 GGATGAAACCATACGAGTCAACGAA-GA-AAGAGGTTGACTA
1 AGATGAAACCATACGAGTTAATGAATGAGAAGAGCTTGACTA
* * *
335787 AGATGAAACCATATGAGTTAATGAATGAGAAAAG-TTGA-TT
1 AGATGAAACCATACGAGTTAATGAATGAGAAGAGCTTGACTA
* * * * * * *
335827 AGTATGAAACTATATGAGTCAATGAAT-AAAAGGGGTTGACCA
1 AG-ATGAAACCATACGAGTTAATGAATGAGAAGAGCTTGACTA
* *
335869 AGATGAAATCATATGAGTTAA
1 AGATGAAACCATACGAGTTAA
335890 CAAATGTAAA
Statistics
Matches: 114, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
39 7 0.06
40 34 0.30
41 67 0.59
42 6 0.05
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.24
Consensus pattern (42 bp):
AGATGAAACCATACGAGTTAATGAATGAGAAGAGCTTGACTA
Found at i:335791 original size:81 final size:82
Alignment explanation
Indices: 335586--336015 Score: 254
Period size: 81 Copynumber: 5.3 Consensus size: 82
335576 GTTAACCGGA
* * * * * * * *
335586 ATGAAACCATACGATTCAACGAATTAGATG-GGTTGACCAAGACGAAACCATATAAGTCAACAAA
1 ATGAAACCATACGAGTCAACGAA-TAAAAGAGGTTGACCAAGATGAAATCATATGAGTTAATAAA
* ** *
335650 TGA-AAAGGGTTGACCCGA
65 TGAGAAA-AGTTGACTAGG
* * ** * * * * * *
335668 ATGAAACCATTCGAGT-AAAGAATAAGCGAGTTTAAGCGAGATGAAATTATACGAGTTAATAAAT
1 ATGAAACCATACGAGTCAACGAATAAAAGAGGTTGACCAAGATGAAATCATATGAGTTAATAAAT
*
335732 GAGAAGAGCTT-ACTAGG
66 GAGAAAAG-TTGACTAGG
* * * *
335749 ATGAAACCATACGAGTCAACGAA-GAAAGAGGTTGACTAAGATGAAACCATATGAGTTAATGAAT
1 ATGAAACCATACGAGTCAACGAATAAAAGAGGTTGACCAAGATGAAATCATATGAGTTAATAAAT
* *
335813 GAGAAAAGTTGATTAGT
66 GAGAAAAGTTGACTAGG
* * * * *
335830 ATGAAACTATATGAGTCAATGAATAAAAGGGGTTGACCAAGATGAAATCATATGAGTTAACAAAT
1 ATGAAACCATACGAGTCAACGAATAAAAGAGGTTGACCAAGATGAAATCATATGAGTTAATAAAT
* * *
335895 GTA-AAGATTTAACCTA-G
66 G-AGAAAAGTTGA-CTAGG
* * * *** * * *
335912 ATTAAAGCATACGAGTCAACTAATAAGAAG-GGTTTTTCGAGATGAAA-CTATATGAG-CAAAAA
1 ATGAAACCATACGAGTCAACGAATAA-AAGAGGTTGACCAAGATGAAATC-ATATGAGTTAATAA
* *
335974 ATGA-AAAGAGTTCA-TAGA
64 ATGAGAAA-AGTTGACTAGG
* *
335992 ATGAAACCATACAAGTCAATGAAT
1 ATGAAACCATACGAGTCAACGAAT
336016 GAGATGGATT
Statistics
Matches: 262, Mismatches: 74, Indels: 26
0.72 0.20 0.07
Matches are distributed among these distances:
79 2 0.01
80 27 0.10
81 122 0.47
82 105 0.40
83 6 0.02
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.23
Consensus pattern (82 bp):
ATGAAACCATACGAGTCAACGAATAAAAGAGGTTGACCAAGATGAAATCATATGAGTTAATAAAT
GAGAAAAGTTGACTAGG
Found at i:336120 original size:41 final size:40
Alignment explanation
Indices: 336075--336191 Score: 117
Period size: 41 Copynumber: 2.9 Consensus size: 40
336065 TGACCGAGAG
** *
336075 GAAACCATAAAAGTCAAAGAATGAGACAGGTTGATTGGGAT
1 GAAACCATACGAGT-AAAGAATGAGAGAGGTTGATTGGGAT
* * * * * *
336116 GAAACTATACGAGTTAATGAATAAGAGAAGTTAACTGGGAT
1 GAAACCATACGAG-TAAAGAATGAGAGAGGTTGATTGGGAT
*
336157 GAAACCATACGAGTAAATGAATGAGAGGGGTTGAT
1 GAAACCATACGAGTAAA-GAATGAGAGAGGTTGAT
336192 CAAGAAGAAA
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
40 3 0.05
41 54 0.93
42 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.21
Consensus pattern (40 bp):
GAAACCATACGAGTAAAGAATGAGAGAGGTTGATTGGGAT
Found at i:336202 original size:82 final size:82
Alignment explanation
Indices: 335992--336215 Score: 213
Period size: 82 Copynumber: 2.7 Consensus size: 82
335982 AGTTCATAGA
* * * *
335992 ATGAAACCATACAAGTCAATGAATGAGATGGATTGATCGAGACA-AAAC-CTACGAGTCAACGAA
1 ATGAAACCATACAAGTAAATGAATGAGACGGGTTGATCGAGA-AGAAACTATACGAGTCAACGAA
*
336055 TAAGAAGAACTGACCGAG
65 TAAGAAGAACTAACCGAG
* * * * * * * *
336073 AGGAAACCATAAAAGTCAAA-GAATGAGACAGGTTGATTGGGATGAAACTATACGAGTTAATGAA
1 ATGAAACCATACAAGT-AAATGAATGAGACGGGTTGATCGAGAAGAAACTATACGAGTCAACGAA
* * *
336137 TAAG-AGAAGTTAACTGGG
65 TAAGAAGAA-CTAACCGAG
* * * *
336155 ATGAAACCATACGAGTAAATGAATGAGAGGGGTTGATCAAGAAGAAACTATACAAGTCAAC
1 ATGAAACCATACAAGTAAATGAATGAGACGGGTTGATCGAGAAGAAACTATACGAGTCAAC
336216 AAAGAGTGAC
Statistics
Matches: 110, Mismatches: 28, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
81 42 0.38
82 68 0.62
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (82 bp):
ATGAAACCATACAAGTAAATGAATGAGACGGGTTGATCGAGAAGAAACTATACGAGTCAACGAAT
AAGAAGAACTAACCGAG
Found at i:336377 original size:41 final size:41
Alignment explanation
Indices: 336343--336767 Score: 196
Period size: 41 Copynumber: 10.4 Consensus size: 41
336333 TGATCGGGAT
**
336343 AAAACCATATGAGTCAATGAATGAAAGGGGTTGATCGGGAC
1 AAAACCATATGAGTCAATGAATGAAAGGGGTTGATCAAGAC
** ** * ** * * *
336384 AAAATTATAAAAGTTAACAAATGAAAAGAGTTGATCGAGAC
1 AAAACCATATGAGTCAATGAATGAAAGGGGTTGATCAAGAC
* ** * * * *
336425 GAAACCATACAAGTTAATGAATGAGAA-AGGTTGA-CTAGGAT
1 AAAACCATATGAGTCAATGAATGA-AAGGGGTTGATC-AAGAC
* *
336466 AAAACCATATGAGT-AATGAATGGGAA-GGGTT-AACTAAGAC
1 AAAACCATATGAGTCAATGAAT-GAAAGGGGTTGATC-AAGAC
* * *
336506 AAAACTATATGAATCAATGAA-AAAGAGGGGTTGATCAAGAC
1 AAAACCATATGAGTCAATGAATGAA-AGGGGTTGATCAAGAC
* * ** ** * *
336547 AAAACCATATAAGTGAACAAATGAGAA-GAATTGACCTA-A-
1 AAAACCATATGAGTCAATGAATGA-AAGGGGTTGATCAAGAC
* * * * *
336586 TAAAGC-TATGCAAAGTCAATGAAT-AAGAGGGGTTGACCGAGAT
1 AAAACCATATG---AGTCAATGAATGAA-AGGGGTTGATCAAGAC
* * * * *
336629 GAAACCATA-GAGTCAATGAATGAGACGAGTTGACCAAGAC
1 AAAACCATATGAGTCAATGAATGAAAGGGGTTGATCAAGAC
* *
336669 AAAATCATACGAGTCAATGAATGAAAGGGGTTGATCAAGAC
1 AAAACCATATGAGTCAATGAATGAAAGGGGTTGATCAAGAC
* * *
336710 AAAACCATACT-AATCAATGAAT-AAGAGGGGTT-AACAGTGAC
1 AAAACCATA-TGAGTCAATGAATGAA-AGGGGTTGATCA-AGAC
*
336751 AAAACCATATAAGTCAA
1 AAAACCATATGAGTCAA
336768 CGAAAAGCAA
Statistics
Matches: 288, Mismatches: 72, Indels: 48
0.71 0.18 0.12
Matches are distributed among these distances:
38 3 0.01
39 7 0.02
40 71 0.25
41 192 0.67
42 7 0.02
43 6 0.02
44 2 0.01
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAACCATATGAGTCAATGAATGAAAGGGGTTGATCAAGAC
Found at i:336510 original size:40 final size:40
Alignment explanation
Indices: 336421--336526 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 40
336411 GAGTTGATCG
* ** *
336421 AGACGAAACCATACAAGTTAATGAATGAGAAAGGTTGACTA
1 AGACAAAACCATATGAG-TAATGAATGAGAAAGGTTAACTA
* * * *
336462 GGATAAAACCATATGAGTAATGAATGGGAAGGGTTAACTA
1 AGACAAAACCATATGAGTAATGAATGAGAAAGGTTAACTA
* *
336502 AGACAAAACTATATGAATCAATGAA
1 AGACAAAACCATATGAGT-AATGAA
336527 AAAGAGGGGT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 34 0.65
41 18 0.35
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.21
Consensus pattern (40 bp):
AGACAAAACCATATGAGTAATGAATGAGAAAGGTTAACTA
Found at i:337109 original size:41 final size:41
Alignment explanation
Indices: 336976--337119 Score: 100
Period size: 41 Copynumber: 3.5 Consensus size: 41
336966 AATTAACTAG
* * * *
336976 GACAAAATCATACGAGTCAACAAA-AAAAAGGGAGTTGATC-A
1 GACAAAACCATACAAGTCAATAAATGAAAA-GG-GTTGATCGA
* ** * * *
337017 GGACAAAATCATA-TGGTCAATGAATGATAGGGGTTGATCGA
1 -GACAAAACCATACAAGTCAATAAATGAAAAGGGTTGATCGA
* *
337058 GATAAGACCATACTAA-TCAATAAATGAAAAGGGTTGATCGTA
1 GACAAAACCATAC-AAGTCAATAAATGAAAAGGGTTGATCG-A
337100 -ACAAAACCATACAAGTCAAT
1 GACAAAACCATACAAGTCAAT
337120 GAATAAGAAG
Statistics
Matches: 79, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
40 18 0.23
41 46 0.58
42 15 0.19
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (41 bp):
GACAAAACCATACAAGTCAATAAATGAAAAGGGTTGATCGA
Found at i:337243 original size:41 final size:41
Alignment explanation
Indices: 337154--337260 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 41
337144 AAATCATACG
* * * *
337154 AGTCAACAAATAAGAGAAGTTTAACCAGGATAAAACCATATG
1 AGTCAACAAATAAGAG-AGGTTGACAAGGATAAAACCATATA
337196 AGTCAACAAATAAGAG-GGATTGACAAGGACT-AAACCATATA
1 AGTCAACAAATAAGAGAGG-TTGACAAGGA-TAAAACCATATA
*
337237 AGTCAACAATTAAGAGAGGTTGAC
1 AGTCAACAAATAAGAGAGGTTGAC
337261 CGAGCTGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
40 1 0.02
41 37 0.65
42 19 0.33
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.19
Consensus pattern (41 bp):
AGTCAACAAATAAGAGAGGTTGACAAGGATAAAACCATATA
Found at i:338691 original size:15 final size:14
Alignment explanation
Indices: 338666--338721 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
338656 TTTCATCTGA
*
338666 TTTTTTCTTTTTTT
1 TTTTTTATTTTTTT
*
338680 GTTTTTATTTTTATT
1 TTTTTTATTTTT-TT
* *
338695 TTTATTATTTTTGT
1 TTTTTTATTTTTTT
*
338709 TTTTTGATTTTTT
1 TTTTTTATTTTTT
338722 ATTGAATTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.09, C:0.02, G:0.05, T:0.84
Consensus pattern (14 bp):
TTTTTTATTTTTTT
Found at i:345923 original size:21 final size:21
Alignment explanation
Indices: 345894--345933 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
345884 TATGTACACA
* *
345894 TATGTGTATATGTATGCATGG
1 TATGAGTATATGAATGCATGG
345915 TATGAGTATATGAATGCAT
1 TATGAGTATATGAATGCAT
345934 TTGTAGGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (21 bp):
TATGAGTATATGAATGCATGG
Found at i:351437 original size:19 final size:21
Alignment explanation
Indices: 351415--351459 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
351405 TTTTTTTAAA
*
351415 ATTTTTTTATTT-TTA-TTTG
1 ATTTTTTTATTTATTACTTAG
351434 ATTTTTTTATTTATTACTTAG
1 ATTTTTTTATTTATTACTTAG
351455 ATTTT
1 ATTTT
351460 GATTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 3 0.13
21 8 0.35
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (21 bp):
ATTTTTTTATTTATTACTTAG
Found at i:352758 original size:13 final size:13
Alignment explanation
Indices: 352740--352765 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
352730 TACATAAGTT
352740 ATGTATCGATACA
1 ATGTATCGATACA
352753 ATGTATCGATACA
1 ATGTATCGATACA
352766 TAATTAGCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:352826 original size:13 final size:13
Alignment explanation
Indices: 352808--352833 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
352798 CATTTTTCTG
352808 TGTATCGATACAT
1 TGTATCGATACAT
352821 TGTATCGATACAT
1 TGTATCGATACAT
352834 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:352830 original size:33 final size:33
Alignment explanation
Indices: 352788--352854 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
352778 GCCAAGGAAA
***
352788 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
352821 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
352854 T
1 T
352855 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:355284 original size:51 final size:50
Alignment explanation
Indices: 355207--355329 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 50
355197 CAATTCTCCG
* *
355207 CAATCGGGGATATTCCATCTCCGATTTTATTTTC-AAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACAC-AATTTTC-A
*
355258 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAAACACAATTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC---AAAAACACAATTTTCA
*
355311 CAATCGAGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
355330 CTCGTTATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
51 31 0.49
53 18 0.29
54 7 0.11
55 7 0.11
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.33
Consensus pattern (50 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACAATTTTCA
Found at i:360698 original size:10 final size:10
Alignment explanation
Indices: 360683--360712 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
360673 GTTCTTTTCT
360683 ACAAAAAAAA
1 ACAAAAAAAA
360693 ACAAAAAAAA
1 ACAAAAAAAA
360703 ACCAAAAAAA
1 A-CAAAAAAA
360713 TCCCTCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:361959 original size:60 final size:55
Alignment explanation
Indices: 361662--363101 Score: 1520
Period size: 55 Copynumber: 25.3 Consensus size: 55
361652 AGCTCTTCGT
* *
361662 AGTCCTCAAAGAGCGGGACACCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCC---TCT-TTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* *
361722 AGTCCCCAAAGAGCAGGACACCT-TTTAAAGCCCACACAAGTTGGTGGCA-TTCTCC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTT-T-C
* * *
361777 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTTTC
* * *
361831 TAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 -AGTCCTCAAAGAGCAGGACGC-----CTCTTTAAAGCCCACACAAGTTGGTGGCACTT-TC
*
361893 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCC---TCTTT-AAAGCCCACACAAGTTGGTGGCACTTT-C
* * * *
361953 AATCCTCAAAGAGCAGGATGCCTTTTCTTGCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCC---TCTT-TAAAGCCCACACAAGTTGGTGGCACTTT-C
* * * *
362013 AATCCTCAAAGAGCAGGATGCCT-TTTAAAGCCCACCCAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTTTC
* * *
362067 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGC---CTC-TTT-AAAGCCCACACAAGTTGGTGGCACTTT-C
362128 AGTCCTCAAAGAGCAGGACGCCTC-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * * *
362183 AGTCCTCAAAGAGCAGGATGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCAC-TTTC
*
362238 AGTCCTCAAAGAGCAGGACACCTC-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* *
362293 AGTCCTCAAAGAGCAAGATGCCTC-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * * *
362348 AGTCCTCAAAGAGCAAGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCAC-TTTC
*
362403 AGTCCTCAAAGAGTAGGACGCCTC-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
*
362458 AGTCCTCAAAGAGCAGGACGCCT-TTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTT-TC
*
362513 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 AGTCCTCAAAGAGCAGGACG-C--CT-C-TTTAAAGCCCACACAAGTTGGTGGCACTTTC
* *
362573 TAGTCCTCAGAGAGCAGGACGCCTC-TTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 -AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTT-TC
* *
362629 AGTCCTCAAAAAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACG-C--C-TCTTT-AAAGCCCACACAAGTTGGTGGCACTTT-C
* * * * * *
362690 AATCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGCTGGTGGTATTTTCC
1 AGTCCTCAAAGAGCAGGACGC---CTC-TTT-AAAGCCCACACAAGTTGGTGGCACTTT-C
* * *
362751 AGTCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACGCAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCC---TC-TTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * * * *
362811 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGC---CTC-TTTAAAGCCCACACAAGTTGGTGGCACTTTC
362870 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCC---TCT-TTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* **
362930 AGTCCTCAAAGAGCAGGACACCT-TTCGAAGCCCACACAAGTTGGTGG------C
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTTTC
* *
362978 A-TCCTCAAAGAGCAGGACACCTC-TTAAAGCCCACACAAGTTGGCGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * *
363032 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCAC-TTTC
363087 AGTCCTCAAAGAGCA
1 AGTCCTCAAAGAGCA
363102 AGATACACTT
Statistics
Matches: 1213, Mismatches: 92, Indels: 155
0.83 0.06 0.11
Matches are distributed among these distances:
47 41 0.03
48 2 0.00
53 2 0.00
54 31 0.03
55 578 0.48
56 18 0.01
57 5 0.00
58 8 0.01
59 57 0.05
60 250 0.21
61 220 0.18
62 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTTTC
Found at i:363008 original size:47 final size:48
Alignment explanation
Indices: 362929--363080 Score: 182
Period size: 47 Copynumber: 3.0 Consensus size: 48
362919 TGGCACCTTT
*
362929 CAGTCCTCAAAGAGCAGGACACCTTTCGAAGCCCACACAAGTTGGTGG
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
*
362977 CA-TCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGCGG
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGG
* *
363024 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGG
1 -------CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
363079 CA
1 CA
363081 CTTTTTAGTC
Statistics
Matches: 89, Mismatches: 5, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
47 40 0.45
48 6 0.07
54 4 0.04
55 39 0.44
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (48 bp):
CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:363056 original size:102 final size:102
Alignment explanation
Indices: 362896--363080 Score: 334
Period size: 102 Copynumber: 1.8 Consensus size: 102
362886 GACGCCTTTT
* *
362896 CTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCGAAGC
1 CTCTTAAAGCCCACACAAGTTGGCGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
362961 CCACACAAGTTGGTGGCATCCTCAAAGAGCAGGACAC
66 CCACACAAGTTGGTGGCATCCTCAAAGAGCAGGACAC
*
362998 CTCTTAAAGCCCACACAAGTTGGCGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
1 CTCTTAAAGCCCACACAAGTTGGCGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
*
363063 CCACACGAGTTGGTGGCA
66 CCACACAAGTTGGTGGCA
363081 CTTTTTAGTC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 79 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (102 bp):
CTCTTAAAGCCCACACAAGTTGGCGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
CCACACAAGTTGGTGGCATCCTCAAAGAGCAGGACAC
Found at i:363972 original size:13 final size:13
Alignment explanation
Indices: 363954--363979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
363944 CATTTTTCTG
363954 TGTATCGATACAT
1 TGTATCGATACAT
363967 TGTATCGATACAT
1 TGTATCGATACAT
363980 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:366428 original size:51 final size:53
Alignment explanation
Indices: 366351--366474 Score: 153
Period size: 54 Copynumber: 2.4 Consensus size: 53
366341 CAATTCTCTG
* * * *
366351 CAATCGGGGATATTCCATCTCCGATTTTA-TT-AACAAAACACTAATTTTCAA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTAAAAAAAACACAAATTTTCAA
* **
366402 TAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAAAAACACAAATTTTTTA
1 CAATCGGGGATACTCCAACTCCGATTTTA-TTTAAAAAAAACACAAATTTTCAA
*
366456 CAATCGAGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
366475 CTCGTTATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 26 0.43
53 2 0.03
54 33 0.54
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.31
Consensus pattern (53 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTAAAAAAAACACAAATTTTCAA
Found at i:371715 original size:13 final size:13
Alignment explanation
Indices: 371697--371721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
371687 CATTTTATGG
371697 TGTATCGATACAA
1 TGTATCGATACAA
371710 TGTATCGATACA
1 TGTATCGATACA
371722 TACTTTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:371737 original size:32 final size:33
Alignment explanation
Indices: 371674--371741 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
371664 CGTTACAAGC
*
371674 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATCTTATGGTGTATCGATA
371707 CAATGTATCGATACATACTT-T-GTGTATCGATA
1 CAATGTATCGATACAT-CTTATGGTGTATCGATA
371739 CAA
1 CAA
371742 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATCTTATGGTGTATCGATA
Found at i:373800 original size:21 final size:20
Alignment explanation
Indices: 373771--373809 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
373761 GGCTAGTGTG
*
373771 GGGACTGCCCGGTTGCGACTT
1 GGGACTG-CCGGTCGCGACTT
*
373792 GGGAGTGCCGGTCGCGAC
1 GGGACTGCCGGTCGCGAC
373810 CTGGTGGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.10, C:0.28, G:0.44, T:0.18
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACTT
Done.