Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 138 of 199
Found at i:40148315 original size:16 final size:16
Alignment explanation
Indices: 40148294--40148345 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
40148284 AGAATGGAAA
40148294 GAAAATTAGAAAGATG
1 GAAAATTAGAAAGATG
* *
40148310 GAAAATTA-AAAGGTA
1 GAAAATTAGAAAGATG
*
40148325 GAAAAAT-GAAAAGATG
1 GAAAATTAG-AAAGATG
40148341 GAAAA
1 GAAAA
40148346 ATATATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (16 bp):
GAAAATTAGAAAGATG
Found at i:40148346 original size:16 final size:16
Alignment explanation
Indices: 40148303--40148347 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
40148293 AGAAAATTAG
*
40148303 AAAGATGG-AAAATTA
1 AAAGATGGAAAAATGA
* *
40148318 AAAGGTAGAAAAATGA
1 AAAGATGGAAAAATGA
40148334 AAAGATGGAAAAAT
1 AAAGATGGAAAAAT
40148348 ATATATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
AAAGATGGAAAAATGA
Found at i:40150327 original size:12 final size:12
Alignment explanation
Indices: 40150310--40150343 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
40150300 AAGATGGAGT
40150310 AATAGGAATACG
1 AATAGGAATACG
40150322 AATAGGAATACG
1 AATAGGAATACG
*
40150334 AATGGGAATA
1 AATAGGAATA
40150344 GGAAAAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.26, T:0.18
Consensus pattern (12 bp):
AATAGGAATACG
Found at i:40153317 original size:12 final size:12
Alignment explanation
Indices: 40153300--40153334 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
40153290 TTTTAATTAT
40153300 TTATTATTAAAA
1 TTATTATTAAAA
40153312 TTATTATTAAAA
1 TTATTATTAAAA
*
40153324 TCATTTATTAA
1 TTA-TTATTAA
40153335 TTTTGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
TTATTATTAAAA
Found at i:40163626 original size:38 final size:38
Alignment explanation
Indices: 40163575--40163651 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
40163565 GGAGCCTTTG
40163575 ACCTTCCCTCACATATCTAAATCCTTTGTGTTTACCCT
1 ACCTTCCCTCACATATCTAAATCCTTTGTGTTTACCCT
40163613 ACCTTCCCTCACATATCTAAATCCTTTGTGTTTACCCT
1 ACCTTCCCTCACATATCTAAATCCTTTGTGTTTACCCT
40163651 A
1 A
40163652 AGCGATGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.22, C:0.34, G:0.05, T:0.39
Consensus pattern (38 bp):
ACCTTCCCTCACATATCTAAATCCTTTGTGTTTACCCT
Found at i:40169021 original size:44 final size:44
Alignment explanation
Indices: 40168948--40169446 Score: 225
Period size: 44 Copynumber: 10.7 Consensus size: 44
40168938 TTAAGCCACA
* * * *
40168948 AATCTTATCTTCCTGAGATTACAGCGGAGCACATAGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCACATTGAAGCCAGT
* * *** *
40168992 AATCCTATCTCCCTGAGATTACAGTGGAGCGA-ATTAAAATAAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGC-ACATTGAAGCCAGT
* * *
40169036 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGA
1 AATCTTATCTCCCTGAGA-TTACAGT---G--GA--GCA-C--ATTGAAGCCAGT
* ** *
40169090 AATCTTATCTCCCTGAAATTACAGCAGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCACATTGAAGCCAGT
* * * *** *
40169134 AATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCACATTGAAGCCAGT
* * *
40169178 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGAGA-TTACAGT---G--GA--GCA-C--ATTGAAGCCAGT
* *
40169232 AATCTTATTTCCCTGAGATTACAGTGGAGCAAATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCACATTGAAGCCAGT
* *** * ***
40169276 AATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGTGGAGCACATT-GAAGCCAGT
* * * * *
40169320 GATCTTATCTCTCT-AAAGTTACAATAGAGTAGATCGCATCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGAGA-TTAC-----AGTGGA--GCA-C--ATTGAAGCCAGT
* * *
40169374 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCACATTGAAGCCAGT
* *
40169418 AATCCTATCTCCCTGATATTACAGTGGAG
1 AATCTTATCTCCCTGAGATTACAGTGGAG
40169447 TGGATTAAAA
Statistics
Matches: 335, Mismatches: 80, Indels: 80
0.68 0.16 0.16
Matches are distributed among these distances:
43 4 0.01
44 211 0.63
45 5 0.01
47 11 0.03
49 17 0.05
50 1 0.00
51 7 0.02
53 4 0.01
54 71 0.21
55 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCACATTGAAGCCAGT
Found at i:40169196 original size:142 final size:142
Alignment explanation
Indices: 40168933--40169460 Score: 867
Period size: 142 Copynumber: 3.7 Consensus size: 142
40168923 TGTAAGGAAA
* * * * * *
40168933 CAGATTTAAGCCACAAATCTTATCTTCCTGAGATTACAGCGGAGCACATAGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCT
*
40168998 ATCTCCCTGAGATTACAGTGGAGCGAATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAG
40169063 AGTAGATCGCAT
131 AGTAGATCGCAT
* * *
40169075 CAAATTGAAGCCAGAAATCTTATCTCCCTGAAATTACAGCAGAGCAGATTGAAGCCAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCT
*
40169140 ATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAG
40169205 AGTAGATCGCAT
131 AGTAGATCGCAT
* * *
40169217 CAGATTGAAGCCAGAAATCTTATTTCCCTGAGATTACAGTGGAGCAAATTGAAGCCAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCT
* * * *
40169282 ATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAATAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAG
40169347 AGTAGATCGCAT
131 AGTAGATCGCAT
*
40169359 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCT
* *
40169424 ATCTCCCTGATATTACAGTGGAGTGGATTAAAATAAA
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
40169461 GGAAAAGAAC
Statistics
Matches: 359, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 359 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCGCAT
Found at i:40169298 original size:98 final size:98
Alignment explanation
Indices: 40169119--40169305 Score: 241
Period size: 98 Copynumber: 1.9 Consensus size: 98
40169109 TACAGCAGAG
* * * * *
40169119 CAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAATGATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGTGGAGCAAATTAAAACAAATAATCCT
*
40169184 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 ATCTCCCTGAAGTTACAGTAGAGTAGATCGCAT
* * * * * *
40169217 CAGATTGAAGCCAGAAATCTTATTTCCCTGAGATTACAGTGGAGCAAATTGAAGCCAGTAATCCT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGTGGAGCAAATTAAAACAAATAATCCT
*
40169282 ATCTCCCTG-AGATTACAGTGGAGT
66 ATCTCCCTGAAG-TTACAGTAGAGT
40169306 GGATTAAAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
97 2 0.03
98 73 0.97
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (98 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGTGGAGCAAATTAAAACAAATAATCCT
ATCTCCCTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:40172376 original size:7 final size:7
Alignment explanation
Indices: 40172366--40172404 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
40172356 CTCCTTTCTC
40172366 CTTTCAA
1 CTTTCAA
40172373 CTTTCAA
1 CTTTCAA
40172380 CTTTCAA
1 CTTTCAA
40172387 CTTTCAA
1 CTTTCAA
*
40172394 CTTTCAC
1 CTTTCAA
40172401 CTTT
1 CTTT
40172405 TTCCTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (7 bp):
CTTTCAA
Found at i:40172383 original size:21 final size:21
Alignment explanation
Indices: 40172359--40172411 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
40172349 AAGTTTTCTC
40172359 CTTTCTCCTTTCAACTTTCAA
1 CTTTCTCCTTTCAACTTTCAA
** *
40172380 CTTTCAACTTTCAACTTTCAC
1 CTTTCTCCTTTCAACTTTCAA
*
40172401 CTTTTTCCTTT
1 CTTTCTCCTTT
40172412 TTTTTTCTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (21 bp):
CTTTCTCCTTTCAACTTTCAA
Found at i:40175655 original size:23 final size:23
Alignment explanation
Indices: 40175621--40175668 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
40175611 GTTTGAATTA
40175621 TTTTGAGTTCGAGGCATTGAGGG
1 TTTTGAGTTCGAGGCATTGAGGG
*
40175644 TTTTAGAG-TCGAGTCATTGAGGG
1 TTTT-GAGTTCGAGGCATTGAGGG
40175667 TT
1 TT
40175669 ATAGTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.19, C:0.08, G:0.35, T:0.38
Consensus pattern (23 bp):
TTTTGAGTTCGAGGCATTGAGGG
Found at i:40180457 original size:15 final size:15
Alignment explanation
Indices: 40180437--40180470 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
40180427 CCAACAAAGA
40180437 AGATACTTGGTATGG
1 AGATACTTGGTATGG
40180452 AGATACTTGGTATGG
1 AGATACTTGGTATGG
40180467 AGAT
1 AGAT
40180471 TCTTAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (15 bp):
AGATACTTGGTATGG
Found at i:40184691 original size:6 final size:6
Alignment explanation
Indices: 40184680--40184854 Score: 332
Period size: 6 Copynumber: 29.2 Consensus size: 6
40184670 TTACCAAAAC
*
40184680 ATACAT ATACAT ATACAT ACACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
40184728 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
*
40184776 ATACAT ATACAT ATACAT ATACAT ATACAT ATGCAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
40184824 ATACAT ATACAT ATACAT ATACAT ATACAT A
1 ATACAT ATACAT ATACAT ATACAT ATACAT A
40184855 CGGACATTAA
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 165 1.00
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:40186470 original size:16 final size:17
Alignment explanation
Indices: 40186445--40186479 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40186435 TGAACATGAA
*
40186445 ATTTTTTTTTGT-TTTT
1 ATTTTATTTTGTCTTTT
40186461 ATTTTATTTTGTCTTTT
1 ATTTTATTTTGTCTTTT
40186478 AT
1 AT
40186480 AATTGTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (17 bp):
ATTTTATTTTGTCTTTT
Found at i:40186882 original size:20 final size:20
Alignment explanation
Indices: 40186857--40186907 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
40186847 GTATCAATCT
*
40186857 GGTATCGATACT-TTTCTTAA
1 GGTATCGATA-TATTTCCTAA
*
40186877 GGTATCTATATATTTCCTAA
1 GGTATCGATATATTTCCTAA
*
40186897 GATATCGATAT
1 GGTATCGATAT
40186908 TCCTGGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (20 bp):
GGTATCGATATATTTCCTAA
Found at i:40191634 original size:79 final size:79
Alignment explanation
Indices: 40191503--40191666 Score: 328
Period size: 79 Copynumber: 2.1 Consensus size: 79
40191493 TACTGCTACA
40191503 AAATATATTGAATTGAGGAGGTGTCCTCAAGTATACGAGTTAGGTTGTAATATAGTTTGTTTACA
1 AAATATATTGAATTGAGGAGGTGTCCTCAAGTATACGAGTTAGGTTGTAATATAGTTTGTTTACA
40191568 ATGAAACACTTGGT
66 ATGAAACACTTGGT
40191582 AAATATATTGAATTGAGGAGGTGTCCTCAAGTATACGAGTTAGGTTGTAATATAGTTTGTTTACA
1 AAATATATTGAATTGAGGAGGTGTCCTCAAGTATACGAGTTAGGTTGTAATATAGTTTGTTTACA
40191647 ATGAAACACTTGGT
66 ATGAAACACTTGGT
40191661 AAATAT
1 AAATAT
40191667 TCCGAGGATT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 85 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (79 bp):
AAATATATTGAATTGAGGAGGTGTCCTCAAGTATACGAGTTAGGTTGTAATATAGTTTGTTTACA
ATGAAACACTTGGT
Found at i:40212408 original size:23 final size:22
Alignment explanation
Indices: 40212361--40212406 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
40212351 GGTTCATGAG
40212361 TTGAACCAAAAATGATGTTAGT
1 TTGAACCAAAAATGATGTTAGT
*
40212383 TTGAACCAAAAATGATGTTGGT
1 TTGAACCAAAAATGATGTTAGT
40212405 TT
1 TT
40212407 TGGATGTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (22 bp):
TTGAACCAAAAATGATGTTAGT
Found at i:40214604 original size:15 final size:15
Alignment explanation
Indices: 40214584--40214635 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
40214574 AAAAAGAGAC
40214584 TGAAAAAGAAACGAG
1 TGAAAAAGAAACGAG
40214599 TGAAAAAGAAA-GAGGG
1 TGAAAAAGAAACGA--G
40214615 CTTGAAAAAGAAACGAG
1 --TGAAAAAGAAACGAG
40214632 TGAA
1 TGAA
40214636 GAGAGTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.06
15 15 0.47
16 1 0.03
17 1 0.03
18 11 0.34
19 2 0.06
ACGTcount: A:0.56, C:0.06, G:0.29, T:0.10
Consensus pattern (15 bp):
TGAAAAAGAAACGAG
Found at i:40216287 original size:24 final size:24
Alignment explanation
Indices: 40216259--40216306 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
40216249 GTTTGAATGT
40216259 TTGTTTTATTTAATTAAGTGTGTA
1 TTGTTTTATTTAATTAAGTGTGTA
*
40216283 TTGTTTTATTTGATTAAGTGTGTA
1 TTGTTTTATTTAATTAAGTGTGTA
40216307 CTAGCTAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (24 bp):
TTGTTTTATTTAATTAAGTGTGTA
Found at i:40225532 original size:19 final size:19
Alignment explanation
Indices: 40225496--40225548 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
40225486 TATATCTACT
40225496 ATTTATATTATTAAATTAA
1 ATTTATATTATTAAATTAA
*
40225515 ATTTCATATT-TTATATT--
1 ATTT-ATATTATTAAATTAA
*
40225532 ATTTATATTATTGAATT
1 ATTTATATTATTAAATT
40225549 GTTTAGTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.17
17 9 0.31
19 10 0.34
20 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTATATTATTAAATTAA
Found at i:40236005 original size:36 final size:36
Alignment explanation
Indices: 40235926--40236005 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 36
40235916 GAGCTATGGG
* ** * **
40235926 TTTGTTATCTGATGGATTGGCTTTTATGAGCATCTGG
1 TTTGTT-TCAGATGGATTAACTCTTATGAGCATCTCA
*
40235963 TGTGTTTCAGATGGATTAACTCTTATGAGCATCTCA
1 TTTGTTTCAGATGGATTAACTCTTATGAGCATCTCA
40235999 TTTGTTT
1 TTTGTTT
40236006 TGGTTGAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
36 30 0.86
37 5 0.14
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (36 bp):
TTTGTTTCAGATGGATTAACTCTTATGAGCATCTCA
Found at i:40243790 original size:30 final size:30
Alignment explanation
Indices: 40243769--40243912 Score: 225
Period size: 30 Copynumber: 4.8 Consensus size: 30
40243759 TTCATAGCTC
* * * * *
40243769 GATAGTCGAAGTTATCCCTTTTTATAATTT
1 GATAGCCGAAGCTATCCCATTTCACAATTT
40243799 GATAGCCGAAGCTATCCCATTTCACAATTT
1 GATAGCCGAAGCTATCCCATTTCACAATTT
*
40243829 GATAGCCGAAGATATCCCATTTCACAATTT
1 GATAGCCGAAGCTATCCCATTTCACAATTT
40243859 GATAGCCGAAGCTATCCCATTTCACAATTT
1 GATAGCCGAAGCTATCCCATTTCACAATTT
*
40243889 GATAGCCGAAGCTATCCCTTTTCA
1 GATAGCCGAAGCTATCCCATTTCA
40243913 TTGTTCGATG
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 106 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (30 bp):
GATAGCCGAAGCTATCCCATTTCACAATTT
Found at i:40243934 original size:30 final size:29
Alignment explanation
Indices: 40243900--40243972 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
40243890 ATAGCCGAAG
*
40243900 CTATCCCTTTTCATTGTTCGATGGTCGTCA
1 CTATCCCTTTTCATTATT-GATGGTCGTCA
40243930 CTATCCCTTTTCATTATTGATGGTCGTCA
1 CTATCCCTTTTCATTATTGATGGTCGTCA
* *
40243959 CCAACCCTTTTCAT
1 CTATCCCTTTTCAT
40243973 AATTTGATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.16, C:0.29, G:0.12, T:0.42
Consensus pattern (29 bp):
CTATCCCTTTTCATTATTGATGGTCGTCA
Found at i:40243998 original size:30 final size:30
Alignment explanation
Indices: 40243963--40244033 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
40243953 TCGTCACCAA
* * *
40243963 CCCTTTTCATAATTTGATAGCTGAGGTTAT
1 CCCTTTTCATAATTTGATAGCCGAAGCTAT
* *
40243993 TCCTTTTCATTATTTTGATAGCCGAAGCTAT
1 CCCTTTTCA-TAATTTGATAGCCGAAGCTAT
40244024 CCCTTTTCAT
1 CCCTTTTCAT
40244034 TAGCCAATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (30 bp):
CCCTTTTCATAATTTGATAGCCGAAGCTAT
Found at i:40244013 original size:31 final size:31
Alignment explanation
Indices: 40243769--40244035 Score: 221
Period size: 30 Copynumber: 8.9 Consensus size: 31
40243759 TTCATAGCTC
* * *
40243769 GATAGTCGAAGTTATCCCTTTTTA-TAATTT
1 GATAGCCGAAGCTATCCCTTTTCATTAATTT
* *
40243799 GATAGCCGAAGCTATCCCATTTCA-CAATTT
1 GATAGCCGAAGCTATCCCTTTTCATTAATTT
* * *
40243829 GATAGCCGAAGATATCCCATTTCA-CAATTT
1 GATAGCCGAAGCTATCCCTTTTCATTAATTT
* *
40243859 GATAGCCGAAGCTATCCCATTTCA-CAATTT
1 GATAGCCGAAGCTATCCCTTTTCATTAATTT
* *
40243889 GATAGCCGAAGCTATCCCTTTTCATT-GTTC
1 GATAGCCGAAGCTATCCCTTTTCATTAATTT
* * *
40243919 GATGGTCGTCA-CTATCCCTTTTCATT-A-TT
1 GATAGCCG-AAGCTATCCCTTTTCATTAATTT
* * * * *
40243948 GATGGTCGTCA-CCAACCCTTTTCA-TAATTT
1 GATAGCCG-AAGCTATCCCTTTTCATTAATTT
* * * * *
40243978 GATAGCTGAGGTTATTCCTTTTCATTATTTT
1 GATAGCCGAAGCTATCCCTTTTCATTAATTT
40244009 GATAGCCGAAGCTATCCCTTTTCATTA
1 GATAGCCGAAGCTATCCCTTTTCATTA
40244036 GCCAATGATT
Statistics
Matches: 199, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 24 0.12
30 145 0.73
31 29 0.15
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
GATAGCCGAAGCTATCCCTTTTCATTAATTT
Found at i:40253419 original size:4 final size:4
Alignment explanation
Indices: 40253398--40253437 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
40253388 TTAATTAGTT
*
40253398 TTTA TTTA TATA TATTA TTTA TTTA TTTA TTTA TTT- TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
40253438 ACAAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.81
5 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:40257545 original size:9 final size:9
Alignment explanation
Indices: 40257531--40257567 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40257521 TATAGTTTGA
40257531 TATTCGAAT
1 TATTCGAAT
40257540 TATTCGAAT
1 TATTCGAAT
*
40257549 TATTCGAGT
1 TATTCGAAT
*
40257558 TATTTGAAT
1 TATTCGAAT
40257567 T
1 T
40257568 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40257638 original size:9 final size:9
Alignment explanation
Indices: 40257621--40257651 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40257611 TCGAGTTGAT
40257621 TCGAATAAC
1 TCGAATAAC
*
40257630 TCGATTAAC
1 TCGAATAAC
40257639 TCGAATAAC
1 TCGAATAAC
40257648 TCGA
1 TCGA
40257652 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:40259583 original size:11 final size:11
Alignment explanation
Indices: 40259569--40259598 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40259559 TTTTATTTTT
40259569 TAATTTTAAAA
1 TAATTTTAAAA
40259580 TAATTTTAAAA
1 TAATTTTAAAA
*
40259591 TATTTTTA
1 TAATTTTA
40259599 TTTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:40259636 original size:23 final size:25
Alignment explanation
Indices: 40259585--40259638 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
40259575 TAAAATAATT
* * *
40259585 TTAAAATATTTTTATTTTTTTATTT
1 TTAAAATATTTTTATTTGTGTATTA
40259610 TTAAAATATTTTT-TTTGTGT-TTA
1 TTAAAATATTTTTATTTGTGTATTA
40259633 TTAAAA
1 TTAAAA
40259639 ATCGGGCCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 8 0.31
24 5 0.19
25 13 0.50
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
TTAAAATATTTTTATTTGTGTATTA
Found at i:40261628 original size:39 final size:40
Alignment explanation
Indices: 40261424--40261646 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 40
40261414 TTGAATGCTG
* * * * * *
40261424 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
**
40261464 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40261504 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40261544 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40261584 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40261623 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40261647 TGAACGAGGA
Statistics
Matches: 165, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 35 0.21
40 123 0.75
41 7 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:40261666 original size:79 final size:80
Alignment explanation
Indices: 40261500--40261681 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 80
40261490 TGCGAGTTAT
** * *
40261500 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
** ** *
40261565 ATTCGTGCGAGTTGT
66 ATTCGAACGAGGAGC
* * *
40261580 TAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
*
40261644 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
* *
40261659 TATATCC-GGTTAAATCCCGAAGG
1 TAAATCCGGGTTAAGTCCCGAAGG
40261682 TACGTGATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:40269454 original size:40 final size:39
Alignment explanation
Indices: 40269335--40269556 Score: 248
Period size: 40 Copynumber: 5.6 Consensus size: 39
40269325 TTGAATGCTG
* * * * *
40269335 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* *
40269375 TCCGGACTAAGAT-CCGAAGGCATTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTGTGCGAGTTACTAAA
* *
40269414 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
40269454 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * *
40269494 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
40269533 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
40269557 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
38 1 0.01
39 60 0.37
40 99 0.61
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:40269471 original size:79 final size:79
Alignment explanation
Indices: 40269335--40269556 Score: 259
Period size: 79 Copynumber: 2.8 Consensus size: 79
40269325 TTGAATGCTG
* * * * * *
40269335 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
40269399 -GTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* *
40269414 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTC
* **
40269479 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * * * *
40269494 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATT
40269557 TGAACGAGGA
Statistics
Matches: 123, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
78 1 0.01
79 83 0.67
80 39 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:40269576 original size:79 final size:80
Alignment explanation
Indices: 40269409--40269591 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
40269399 GTGCGAGATA
* * *
40269409 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
40269474 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
40269489 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
40269553 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
40269568 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
40269592 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:40277309 original size:40 final size:40
Alignment explanation
Indices: 40277227--40277448 Score: 193
Period size: 40 Copynumber: 5.6 Consensus size: 40
40277217 TTGAATGCTG
* * *
40277227 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGA-T-AATAAA
* * * *
40277266 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGATAATAAA
* * *
40277306 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGATAATAAA
* * **
40277346 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGATAATAAA
* * * * *
40277386 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGATAATAAA
* *
40277425 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
40277449 TGAACGAGGA
Statistics
Matches: 162, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 45 0.28
40 107 0.66
41 9 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGATAATAAA
Found at i:40277363 original size:80 final size:79
Alignment explanation
Indices: 40277227--40277450 Score: 236
Period size: 80 Copynumber: 2.8 Consensus size: 79
40277217 TTGAATGCTG
* * * * * * * * *
40277227 TCCGGGCTAAGT-CCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
40277290 TGTGCGAGATACTAAA
64 TGTGCGAGATACTAAA
* * * *
40277306 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* **
40277371 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
40277386 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
40277451 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
79 47 0.39
80 71 0.58
81 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:40277430 original size:39 final size:40
Alignment explanation
Indices: 40277279--40277448 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
40277269 GGACTAAGAT
* * *
40277279 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
*
40277319 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
40277359 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * *
40277399 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
40277438 CCGAAGGCATT
1 CCGAAGGCATT
40277449 TGAACGAGGA
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 34 0.29
40 85 0.71
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:40277468 original size:79 final size:80
Alignment explanation
Indices: 40277301--40277482 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
40277291 GTGCGAGATA
* * *
40277301 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
40277366 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
40277381 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
40277445 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
40277460 CTATATCC-GGTTAAAT-CCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
40277483 TACGTGATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
77 7 0.08
78 6 0.07
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:40279020 original size:17 final size:18
Alignment explanation
Indices: 40278998--40279031 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40278988 CAATTCAAGG
40278998 TCAATTT-CACAATTTTA
1 TCAATTTACACAATTTTA
*
40279015 TCAATTTACACCATTTT
1 TCAATTTACACAATTTT
40279032 TAATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (18 bp):
TCAATTTACACAATTTTA
Found at i:40279986 original size:66 final size:66
Alignment explanation
Indices: 40279880--40280006 Score: 211
Period size: 66 Copynumber: 1.9 Consensus size: 66
40279870 CAATTTAGCA
*
40279880 GATCCCTAGCAGTTAAATTAGAGTCAGCCCTGTATGCATAATACACCAGACCTGGCTTAGTCAGT
1 GATCCCTAGCAGTTAAATTAGAGTCAGCCCTGTATGCATAATACACCAGACCTAGCTTAGTCAGT
40279945 C
66 C
* *
40279946 GATCCCT-GACAGTTAAATTAGAGTTAGCCCTGTATGCATAATACACTAGACCTAGCTTAGT
1 GATCCCTAG-CAGTTAAATTAGAGTCAGCCCTGTATGCATAATACACCAGACCTAGCTTAGT
40280007 ATCTTAGGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 1 0.02
66 56 0.98
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (66 bp):
GATCCCTAGCAGTTAAATTAGAGTCAGCCCTGTATGCATAATACACCAGACCTAGCTTAGTCAGT
C
Found at i:40282726 original size:25 final size:23
Alignment explanation
Indices: 40282698--40282744 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
40282688 TTTCCCAATT
*
40282698 TAATTTTATTTCCAATTTATTTAAA
1 TAATGTTATTT-CAA-TTATTTAAA
*
40282723 TAATGTTGTTTCAATTATTTAA
1 TAATGTTATTTCAATTATTTAA
40282745 TTTCTAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 3 0.15
25 9 0.45
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
TAATGTTATTTCAATTATTTAAA
Found at i:40283976 original size:38 final size:37
Alignment explanation
Indices: 40283934--40284051 Score: 107
Period size: 38 Copynumber: 3.1 Consensus size: 37
40283924 ACACCCAATG
* *
40283934 CCTCATCAGAACATCTGAAGTATAATTTGTGCTTCACA
1 CCTCATCGGAACATCTGAAGT-TAATATGTGCTTCACA
* *
40283972 CCTCATCGGTATAAATC-GAAG-TAATATGTG-TTACGCA
1 CCTCATCGG-A-ACATCTGAAGTTAATATGTGCTT-CACA
* * *
40284009 CCTCATTGGAACATCTGAAGTGTAATATGTGCTCCACG
1 CCTCATCGGAACATCTGAAGT-TAATATGTGCTTCACA
40284047 CCTCA
1 CCTCA
40284052 ACGGCATAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
35 4 0.06
36 7 0.11
37 19 0.30
38 24 0.38
39 6 0.09
40 4 0.06
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (37 bp):
CCTCATCGGAACATCTGAAGTTAATATGTGCTTCACA
Found at i:40296488 original size:40 final size:40
Alignment explanation
Indices: 40296341--40296563 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
40296331 TTGAATGCTG
* * * *
40296341 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
**
40296381 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
40296420 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
40296459 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
40296499 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
40296538 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
40296564 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 22 0.14
39 59 0.37
40 67 0.42
41 10 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:40296525 original size:79 final size:78
Alignment explanation
Indices: 40296394--40296561 Score: 221
Period size: 79 Copynumber: 2.1 Consensus size: 78
40296384 GGACTAAGAT
* *
40296394 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGCCCGAAGGCCTTTGTGCGAGATACTAAA
1 CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGCCCGAAGGCCATTGTGCGAGATACTAAA
* *
40296459 TCCGGGTTAAGTC
66 ACCGGGCTAAGTC
* * * * *
40296472 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTA
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAG-CCCGAAGGCCATTGTGCGAGATACTA
*
40296536 AAACCGGGCTATGTC
64 AAACCGGGCTAAGTC
40296551 CCGAAGGCATT
1 CCGAAGGCATT
40296562 TGAACGAGGA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
78 20 0.26
79 50 0.64
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGCCCGAAGGCCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:40296581 original size:79 final size:80
Alignment explanation
Indices: 40296417--40296596 Score: 197
Period size: 79 Copynumber: 2.3 Consensus size: 80
40296407 TGCGAGATAC
* * *
40296417 AAATCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCA
1 AAATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCA
** * *
40296481 TTCGTGCGAGTTATT
66 TTCGAACGAGTGACT
* * * *
40296496 AAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCA
1 AAATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCA
*
40296560 TTTGAACGAG-GAGCT
66 TTCGAACGAGTGA-CT
* *
40296575 ATATCC-GGTTAAATCCCGAAGG
1 AAATCCGGGTTAAGTCCCGAAGG
40296597 TACGTGATTT
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 15 0.18
79 61 0.73
80 8 0.10
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
AAATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCA
TTCGAACGAGTGACT
Found at i:40304417 original size:40 final size:40
Alignment explanation
Indices: 40304287--40304508 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 40
40304277 TTGAATGCTG
* * * * *
40304287 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * *
40304327 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-TAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40304366 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
40304406 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * * *
40304446 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
40304485 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
40304509 TGAACGAGGA
Statistics
Matches: 162, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 66 0.41
40 87 0.54
41 8 0.05
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:40304423 original size:79 final size:79
Alignment explanation
Indices: 40304287--40304510 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 79
40304277 TTGAATGCTG
* * * * * *
40304287 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
40304351 TGTGCGAGAT-ATAAA
64 TGTGCGAGATGATAAA
* * *
40304366 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTT
* *
40304431 GTGCGAGTTGTTAAA
65 GTGCGAGATGATAAA
* * * * *
40304446 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTTG
40304511 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
78 1 0.01
79 92 0.74
80 31 0.25
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATGATAAA
Found at i:40304528 original size:79 final size:80
Alignment explanation
Indices: 40304362--40304543 Score: 224
Period size: 79 Copynumber: 2.3 Consensus size: 80
40304352 GTGCGAGATA
* * *
40304362 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
** ** *
40304427 ATTCGTGCGAGTTGT
66 ATTCGAACGAGGAGC
* * *
40304442 TAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
*
40304506 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
* *
40304521 TATATCC-GGTTAAATCCCGAAGG
1 TAAATCCGGGTTAAGTCCCGAAGG
40304544 TACGTGATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:40312440 original size:39 final size:40
Alignment explanation
Indices: 40312236--40312458 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 40
40312226 TTGAATGCTG
* * * * * *
40312236 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
**
40312276 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40312316 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40312356 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40312396 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40312435 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40312459 TGAACGAGGA
Statistics
Matches: 165, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 35 0.21
40 123 0.75
41 7 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:40312478 original size:79 final size:80
Alignment explanation
Indices: 40312312--40312493 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 80
40312302 TGCGAGTTAT
** * *
40312312 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
** ** *
40312377 ATTCGTGCGAGTTGT
66 ATTCGAACGAGGAGC
* * *
40312392 TAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
*
40312456 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
* *
40312471 TATATCC-GGTTAAATCCCGAAGG
1 TAAATCCGGGTTAAGTCCCGAAGG
40312494 TACGTGATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:40315483 original size:50 final size:50
Alignment explanation
Indices: 40315422--40315531 Score: 211
Period size: 50 Copynumber: 2.2 Consensus size: 50
40315412 ACGATTTCAA
40315422 TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCGTTCCTT
1 TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCGTTCCTT
*
40315472 TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCGTTTCTT
1 TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCGTTCCTT
40315522 TCCTTTTCAT
1 TCCTTTTCAT
40315532 GCCCGTTGAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.48
Consensus pattern (50 bp):
TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCGTTCCTT
Found at i:40323530 original size:17 final size:19
Alignment explanation
Indices: 40323498--40323532 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
40323488 ATTATTATTT
40323498 TTTCATTTTTCTTCTCATC
1 TTTCATTTTTCTTCTCATC
40323517 TTTC-TTTTTC-TCTCAT
1 TTTCATTTTTCTTCTCAT
40323533 ATTTTCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTCATTTTTCTTCTCATC
Found at i:40323538 original size:18 final size:18
Alignment explanation
Indices: 40323496--40323545 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
40323486 GAATTATTAT
40323496 TTTTTCATTTTTCTTCTCA
1 TTTTTC-TTTTTCTTCTCA
*
40323515 TCTTTCTTTTTC-TCTCA
1 TTTTTCTTTTTCTTCTCA
40323532 TATTTTCTCTTTTC
1 T-TTTTCT-TTTTC
40323546 CACCACCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 11 0.41
19 10 0.37
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTCTTTTTCTTCTCA
Found at i:40327120 original size:37 final size:37
Alignment explanation
Indices: 40327070--40327161 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
40327060 TAAATAGCCT
40327070 AGTGGTTAAGTGTGTGAATGTATTCCAAGTGGTTCCA
1 AGTGGTTAAGTGTGTGAATGTATTCCAAGTGGTTCCA
*
40327107 AGTGGTTAAGTGTGTGAATGTATTCGAAGTGGTTCCA
1 AGTGGTTAAGTGTGTGAATGTATTCCAAGTGGTTCCA
*
40327144 AGTGGTTAAGTGTCTGAA
1 AGTGGTTAAGTGTGTGAA
40327162 CACCCTTGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.25, C:0.09, G:0.32, T:0.35
Consensus pattern (37 bp):
AGTGGTTAAGTGTGTGAATGTATTCCAAGTGGTTCCA
Found at i:40336588 original size:14 final size:15
Alignment explanation
Indices: 40336564--40336592 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40336554 CATGTTATAA
40336564 AATATAAGAATAAAG
1 AATATAAGAATAAAG
40336579 AATA-AAGAATAAAG
1 AATATAAGAATAAAG
40336593 TTTAATTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (15 bp):
AATATAAGAATAAAG
Found at i:40336995 original size:51 final size:51
Alignment explanation
Indices: 40336832--40337016 Score: 189
Period size: 51 Copynumber: 3.6 Consensus size: 51
40336822 GAAGTTGCTA
* *
40336832 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGAAAAT
* * * * * ***
40336882 GGTCGCATGTGTAGTACTATGTGCAAGCTACTATGCGTA-CTAGAT-AGCTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GGATGAAAAT
* * *
40336932 CGATCACGTGTGTAGTACTATGTGCAGCCTACTACGTGTATCGGATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT
*
40336984 GGTCACATGTGTAGTACCATGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
40337017 TGTGAACCGG
Statistics
Matches: 105, Mismatches: 24, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
49 3 0.03
50 35 0.33
51 64 0.61
52 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT
Found at i:40346874 original size:20 final size:20
Alignment explanation
Indices: 40346851--40346891 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40346841 GCAAGTTTGG
*
40346851 TATCGTTTTCTCAAGTGTAT
1 TATCATTTTCTCAAGTGTAT
* *
40346871 TATCATTTTTTCAGGTGTAT
1 TATCATTTTCTCAAGTGTAT
40346891 T
1 T
40346892 GATACCACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.54
Consensus pattern (20 bp):
TATCATTTTCTCAAGTGTAT
Found at i:40349622 original size:58 final size:58
Alignment explanation
Indices: 40349577--40349697 Score: 181
Period size: 58 Copynumber: 2.1 Consensus size: 58
40349567 TATTTTTTCT
* * *
40349577 TTTTC-TTTTTCATTTTGGAGAAAACCACATTCATTTTCAAATATTTCCATTTCTCCA
1 TTTTCATTTTCCATTTTAGAGAAAACCACATTCATTTCCAAATATTTCCATTTCTCCA
* *
40349634 TTTTCATTTTCCTTTTTAGAGAAAACCACATTCATTTCCAAATGTTTCTCATTTCTCCA
1 TTTTCATTTTCCATTTTAGAGAAAACCACATTCATTTCCAAATATTTC-CATTTCTCCA
40349693 TTTTC
1 TTTTC
40349698 GCCATTTCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 5 0.09
58 37 0.65
59 15 0.26
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.48
Consensus pattern (58 bp):
TTTTCATTTTCCATTTTAGAGAAAACCACATTCATTTCCAAATATTTCCATTTCTCCA
Found at i:40352037 original size:20 final size:19
Alignment explanation
Indices: 40352028--40352107 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 19
40352018 TTATTAAATT
40352028 TTAGAAAAATATATAAAAA
1 TTAGAAAAATATATAAAAA
*
40352047 TTAGAAAAAATAAATAAAAA
1 TTAG-AAAAATATATAAAAA
40352067 TCGTA-AAAAAT-TATAAAATA
1 T--TAGAAAAATATATAAAA-A
* *
40352087 TATAGAAATATA-AGAAAAA
1 T-TAGAAAAATATATAAAAA
40352106 TT
1 TT
40352108 TTAAAATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.02
19 14 0.28
20 33 0.66
22 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.26
Consensus pattern (19 bp):
TTAGAAAAATATATAAAAA
Found at i:40352044 original size:19 final size:20
Alignment explanation
Indices: 40352012--40352055 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
40352002 TTCAAATATT
* **
40352012 AAAAATTTATTAAATTTTAG
1 AAAAATATATTAAAAATTAG
40352032 AAAAATATA-TAAAAATTAG
1 AAAAATATATTAAAAATTAG
40352051 AAAAA
1 AAAAA
40352056 ATAAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAAATATATTAAAAATTAG
Found at i:40352045 original size:10 final size:10
Alignment explanation
Indices: 40352005--40352098 Score: 54
Period size: 10 Copynumber: 9.7 Consensus size: 10
40351995 TAAAAAATTC
40352005 AAATAT-TAA
1 AAATATATAA
* *
40352014 AAATTTATTA
1 AAATATATAA
* * *
40352024 AATTTTAGAA
1 AAATATATAA
40352034 AAATATATAA
1 AAATATATAA
*
40352044 AAAT-TAGAAA
1 AAATATA-TAA
*
40352054 AAATAAATAA
1 AAATATATAA
*
40352064 AAATCGTA-AA
1 AAAT-ATATAA
40352074 AAAT-TAT-A
1 AAATATATAA
*
40352082 AAATATATAG
1 AAATATATAA
40352092 AAATATA
1 AAATATA
40352099 AGAAAAATTT
Statistics
Matches: 64, Mismatches: 14, Indels: 13
0.70 0.15 0.14
Matches are distributed among these distances:
8 7 0.11
9 10 0.16
10 45 0.70
11 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (10 bp):
AAATATATAA
Found at i:40352180 original size:20 final size:21
Alignment explanation
Indices: 40352110--40352180 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 21
40352100 GAAAAATTTT
* *
40352110 AAAATTTTAAA-AAGTCGTAAG
1 AAAATTATAAATAA-TCGTAAA
*
40352131 AAAATTATACATAAT-GTAAA
1 AAAATTATAAATAATCGTAAA
* *
40352151 GAAA-TATAAAT-TTCGTAAA
1 AAAATTATAAATAATCGTAAA
40352170 AAAATTATAAA
1 AAAATTATAAA
40352181 AATTATCGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.35
20 13 0.32
21 10 0.25
22 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (21 bp):
AAAATTATAAATAATCGTAAA
Found at i:40352239 original size:16 final size:17
Alignment explanation
Indices: 40352218--40352251 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40352208 AATTTTTCTA
40352218 TATTTTTAT-TCATTTT
1 TATTTTTATGTCATTTT
*
40352234 TATTTTTTTGTCATTTT
1 TATTTTTATGTCATTTT
40352251 T
1 T
40352252 CGCCAATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTTATGTCATTTT
Found at i:40352436 original size:19 final size:21
Alignment explanation
Indices: 40352405--40352451 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
40352395 AATTTTTTTA
40352405 TATTTTTATTAAAATTTAA-T
1 TATTTTTATTAAAATTTAATT
40352425 TATTTTTA-TAAAATTTAATT
1 TATTTTTATTAAAATTTAATT
40352445 TATTTTT
1 TATTTTT
40352452 TTTTCTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTTATTAAAATTTAATT
Found at i:40352659 original size:90 final size:88
Alignment explanation
Indices: 40352474--40352674 Score: 237
Period size: 89 Copynumber: 2.2 Consensus size: 88
40352464 TAATAAGAGT
* *
40352474 AGGGGCTTAATTGCTTTTTTTGAAAAATTTTGGAGGTCTTTTTGATGCATTTCGAAAGTTTAAGT
1 AGGGGCTTAATTGCTTTTTTT-AAAAAATTTGGAGGCCTTTTTGATGCATTTCGAAAGTTTAAGT
*
40352539 ACCCAATTGAGTGGAAAAAAAAGC
65 ACCCAATTGAGTGCAAAAAAAAGC
* * *
40352563 AAGGGCTTAATCGCTTTTTTTAAAGAAATTT-GAGGGCCTTTTTTGATGCATTTTG-AAGTTTAA
1 AGGGGCTTAATTGCTTTTTTTAAA-AAATTTGGA-GGCC-TTTTTGATGCATTTCGAAAGTTTAA
* * * *
40352626 GTGCTCAGTTGAGTGCAAAAAATGATG-
63 GTACCCAATTGAGTGCAAAAAA--AAGC
40352653 AGGGGCTTAATTGCTTTTTTTA
1 AGGGGCTTAATTGCTTTTTTTA
40352675 TTTTTTAAAG
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
88 5 0.05
89 53 0.56
90 35 0.37
91 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (88 bp):
AGGGGCTTAATTGCTTTTTTTAAAAAATTTGGAGGCCTTTTTGATGCATTTCGAAAGTTTAAGTA
CCCAATTGAGTGCAAAAAAAAGC
Found at i:40355288 original size:56 final size:56
Alignment explanation
Indices: 40355200--40355307 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
40355190 GGATTACAGG
* * *
40355200 TGTAAGACCATACCTTGGCTATGACATCCGTTAAAGTCTGCCATGACATTAACCAT
1 TGTAAGACCATACCTCGACTATGACATCCGTTAAAGTCTGCCAGGACATTAACCAT
* * * *
40355256 TGTAAGACCATAGCTCGACTATGGCATTCGTTAAAGTCTGCTAGGACATTAA
1 TGTAAGACCATACCTCGACTATGACATCCGTTAAAGTCTGCCAGGACATTAA
40355308 ACATGGGGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (56 bp):
TGTAAGACCATACCTCGACTATGACATCCGTTAAAGTCTGCCAGGACATTAACCAT
Found at i:40362560 original size:27 final size:27
Alignment explanation
Indices: 40362529--40362586 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
40362519 AGTTTCCTTA
*
40362529 TCTTGTACAAGTGGAATAACAGCTATT
1 TCTTGTACAAGTGGAATAACAACTATT
40362556 TCTTGTACAAGTGGAATAACAACTATT
1 TCTTGTACAAGTGGAATAACAACTATT
40362583 TCTT
1 TCTT
40362587 TGGGAGTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (27 bp):
TCTTGTACAAGTGGAATAACAACTATT
Found at i:40363505 original size:21 final size:22
Alignment explanation
Indices: 40363465--40363505 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40363455 AAATATATAA
*
40363465 TAATTTACAAAATTTTAAGTGT
1 TAATTTACAAAATTTCAAGTGT
*
40363487 TAATTTA-AGAATTTCAAGT
1 TAATTTACAAAATTTCAAGT
40363506 TTTATTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (22 bp):
TAATTTACAAAATTTCAAGTGT
Found at i:40365186 original size:21 final size:23
Alignment explanation
Indices: 40365138--40365186 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
40365128 TAGATGCTCT
*
40365138 TTGGCCATATGTATGATGTTCAG
1 TTGGCCATATGTAGGATGTTCAG
40365161 TTGGCCACTA-GTAGGA-GTTC-G
1 TTGGCCA-TATGTAGGATGTTCAG
40365182 TTGGC
1 TTGGC
40365187 ATGCTCTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 4 0.17
23 12 0.50
24 2 0.08
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (23 bp):
TTGGCCATATGTAGGATGTTCAG
Found at i:40370091 original size:23 final size:23
Alignment explanation
Indices: 40370063--40370107 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
40370053 CCACTATACC
*
40370063 AAATGAACATGCAAAATGCAACA
1 AAATGAACATACAAAATGCAACA
*
40370086 AAATGATCATACAAAATGCAAC
1 AAATGAACATACAAAATGCAAC
40370108 CTAGATGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.18, G:0.11, T:0.16
Consensus pattern (23 bp):
AAATGAACATACAAAATGCAACA
Found at i:40370868 original size:15 final size:16
Alignment explanation
Indices: 40370848--40370886 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
40370838 ATCTTACTAT
40370848 TATCATAAAACAT-TA
1 TATCATAAAACATATA
*
40370863 TATCATAATACATATA
1 TATCATAAAACATATA
*
40370879 TATAATAA
1 TATCATAA
40370887 TCCTATTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (16 bp):
TATCATAAAACATATA
Found at i:40373327 original size:12 final size:12
Alignment explanation
Indices: 40373310--40373335 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40373300 ATAAACACAA
40373310 AAAATATTTTTT
1 AAAATATTTTTT
40373322 AAAATATTTTTT
1 AAAATATTTTTT
40373334 AA
1 AA
40373336 CTCGGATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:40377644 original size:19 final size:19
Alignment explanation
Indices: 40377620--40377656 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40377610 TGTTGTCACT
40377620 GTTTAATAATAGATCATTC
1 GTTTAATAATAGATCATTC
40377639 GTTTAATAATAGATCATT
1 GTTTAATAATAGATCATT
40377657 GTTGTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (19 bp):
GTTTAATAATAGATCATTC
Found at i:40380390 original size:21 final size:21
Alignment explanation
Indices: 40380360--40380400 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40380350 TCCAACGGAA
*
40380360 GGATTTTCATTGAA-ATCATTT
1 GGATTATCATT-AAGATCATTT
40380381 GGATTATCATTAAGATCATT
1 GGATTATCATTAAGATCATT
40380401 CATGTTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (21 bp):
GGATTATCATTAAGATCATTT
Found at i:40388366 original size:14 final size:14
Alignment explanation
Indices: 40388347--40388376 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40388337 GTCATTTAGG
40388347 CCAACCAAACTGGC
1 CCAACCAAACTGGC
40388361 CCAACCAAACTGGC
1 CCAACCAAACTGGC
40388375 CC
1 CC
40388377 GGTGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.47, G:0.13, T:0.07
Consensus pattern (14 bp):
CCAACCAAACTGGC
Found at i:40393492 original size:14 final size:14
Alignment explanation
Indices: 40393473--40393502 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40393463 GTCATTTAGG
40393473 CCAACCAAACTGGC
1 CCAACCAAACTGGC
40393487 CCAACCAAACTGGC
1 CCAACCAAACTGGC
40393501 CC
1 CC
40393503 GGTGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.47, G:0.13, T:0.07
Consensus pattern (14 bp):
CCAACCAAACTGGC
Found at i:40413224 original size:68 final size:69
Alignment explanation
Indices: 40413004--40413430 Score: 431
Period size: 66 Copynumber: 6.4 Consensus size: 69
40412994 AGGTCCATTG
* * * * *
40413004 TTTGCAGATTCTGTTCC-AGCACCCCTGCCTACGCAGGTGACATGTTCCAA--GGAAGAGCTCAT
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTT-CAAGGGGAAGAGTTCAT
** *
40413066 CTGTT
65 CCATA
* * * * * *
40413071 TTTG-GGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCA-GGGAAG-GCTCAT-
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
* *
40413132 -TTT
66 CATA
* * *
40413135 TTTGCAGATTCTGTTCCAAGCACTCC-GCCTATGGCAGATAGCATGTTTAAGGGGAAGAGTTCGT
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTAT-GCAGATAACATGTTCAAGGGGAAGAGTTCAT
* *
40413199 CCTTG
65 CCATA
* * **
40413204 TTTGCAGA-TCTGTTCCAAGCACTCCTGCCTATGCAG-TAACTTGTTTAAGGGTCAG-GTTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
40413266 CATA
66 CATA
* * *
40413270 TTTG--GATTCTGTTCCAAGCACTCCTGCCTATG--GA-AACTTGTTCAAGGGGAAGGGTTCGTC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
40413330 CATA
66 CATA
*
40413334 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
*
40413399 TAT-
66 CATA
*
40413402 TTTGCAGATTCTGTTCCAAGCACCCCTGC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGC
40413431 TTATCATTGG
Statistics
Matches: 308, Mismatches: 35, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
63 16 0.05
64 27 0.09
65 57 0.19
66 64 0.21
67 53 0.17
68 51 0.17
69 40 0.13
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (69 bp):
TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
CATA
Found at i:40430418 original size:116 final size:116
Alignment explanation
Indices: 40430214--40430445 Score: 464
Period size: 116 Copynumber: 2.0 Consensus size: 116
40430204 CGATGTAGGA
40430214 TTATAGGTCCCCAAAAAAACCACGAGATGTCAGGTGGTGCATGTGGCTGGCAGACTAAGAATATC
1 TTATAGGTCCCCAAAAAAACCACGAGATGTCAGGTGGTGCATGTGGCTGGCAGACTAAGAATATC
40430279 TGATCCTGGGCGTAAGGATAACTACAAAATATTCAATCAAAAAACAAAGGT
66 TGATCCTGGGCGTAAGGATAACTACAAAATATTCAATCAAAAAACAAAGGT
40430330 TTATAGGTCCCCAAAAAAACCACGAGATGTCAGGTGGTGCATGTGGCTGGCAGACTAAGAATATC
1 TTATAGGTCCCCAAAAAAACCACGAGATGTCAGGTGGTGCATGTGGCTGGCAGACTAAGAATATC
40430395 TGATCCTGGGCGTAAGGATAACTACAAAATATTCAATCAAAAAACAAAGGT
66 TGATCCTGGGCGTAAGGATAACTACAAAATATTCAATCAAAAAACAAAGGT
40430446 AGAGCACAGG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (116 bp):
TTATAGGTCCCCAAAAAAACCACGAGATGTCAGGTGGTGCATGTGGCTGGCAGACTAAGAATATC
TGATCCTGGGCGTAAGGATAACTACAAAATATTCAATCAAAAAACAAAGGT
Found at i:40456728 original size:31 final size:31
Alignment explanation
Indices: 40456666--40456728 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
40456656 TAGCCCGGTA
* * * *
40456666 ACTTAAATTAAAACTTTTAAATAGTTTAATG
1 ACTTAAATAAAAACTTTCAAATAATTCAATG
*
40456697 ACTTAAATAAAAACTTTCGAATAATTCAATG
1 ACTTAAATAAAAACTTTCAAATAATTCAATG
40456728 A
1 A
40456729 TCAAATTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTCAATG
Found at i:40459247 original size:16 final size:16
Alignment explanation
Indices: 40459228--40459290 Score: 105
Period size: 16 Copynumber: 4.1 Consensus size: 16
40459218 CCCAAATATA
40459228 TCCCTCAAAAAATTTC
1 TCCCTCAAAAAATTTC
40459244 TCCCTCAAAAAATTTC
1 TCCCTCAAAAAATTTC
40459260 T---TCAAAAAATTTC
1 TCCCTCAAAAAATTTC
40459273 TCCCTCAAAAAATTTC
1 TCCCTCAAAAAATTTC
40459289 TC
1 TC
40459291 AAAGAAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.30
16 31 0.70
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (16 bp):
TCCCTCAAAAAATTTC
Found at i:40459265 original size:29 final size:28
Alignment explanation
Indices: 40459231--40459300 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 28
40459221 AAATATATCC
40459231 CTCAAAAAATTTCTCCCTCAAAAAATTT
1 CTCAAAAAATTTCTCCCTCAAAAAATTT
40459259 CTTCAAAAAATTTCTCCCTCAAAAAATTT
1 C-TCAAAAAATTTCTCCCTCAAAAAATTT
40459288 CTCAAAGAAATTT
1 CTCAAA-AAATTT
40459301 TTTGAGGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.33
Consensus pattern (28 bp):
CTCAAAAAATTTCTCCCTCAAAAAATTT
Found at i:40461629 original size:51 final size:50
Alignment explanation
Indices: 40461561--40461755 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 50
40461551 TAAATGGTAC
* * * *
40461561 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCAT
* * * *
40461612 CCGATACACGTAGTAGCCTGCACATAGTACTACACACATGATCGA-AGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-AT
* * * * * *
40461663 CCGGTACGCTTAATAGCCTGCACATAATACTACACATGCGACC-TATCATT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATATCA-T
* *
40461713 CCGGTACATGTAGTAGCCTGCACATGGTACTACACACGTGACC
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC
40461756 TAGCAACTTC
Statistics
Matches: 114, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
49 1 0.01
50 40 0.35
51 71 0.62
52 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (50 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATATCAT
Found at i:40465418 original size:114 final size:113
Alignment explanation
Indices: 40465225--40465518 Score: 324
Period size: 113 Copynumber: 2.6 Consensus size: 113
40465215 TACAACCACA
* * * * * * * * *
40465225 CGCCGCAAAATCTCCTATCCAAAATGCAACG-TTTTCGTCTTTATGTATGCAAGAATTAGTGGCG
1 CGCCGTAAAATCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATACTAGAATTAGTGGCG
*
40465289 CTTCAAAAAACACGCCGCT-AAAGTGTCTTAGCAGCGTTTTACAACAACG
66 CTTCAAAAAACACGCCG-TAAAAGCGTCTTAGCAGCGTTTTACAA-AACG
* ** *
40465338 CGTCGTAATTTCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCG
1 CGCCGTAAAATCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATACTAGAATTAGTGGCG
* * * * * *
40465403 CTTCTCAAAAA-ACGCCGTAAAAGCGTCTTAGCGGCGTTTTGCGATATG
66 CTTC-AAAAAACACGCCGTAAAAGCGTCTTAGCAGCGTTTTACAAAACG
* * * *
40465451 CGCCGTAAAATATCTTAACCAAAACGCATCGTTTTTGGTGTTGATGTATACTAGATTTAGTGGCG
1 CGCCGTAAAATCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATACTAGAATTAGTGGCG
40465516 CTT
66 CTT
40465519 TGTGATATGC
Statistics
Matches: 151, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
113 87 0.58
114 59 0.39
115 5 0.03
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (113 bp):
CGCCGTAAAATCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATACTAGAATTAGTGGCG
CTTCAAAAAACACGCCGTAAAAGCGTCTTAGCAGCGTTTTACAAAACG
Found at i:40466267 original size:266 final size:266
Alignment explanation
Indices: 40465567--40466367 Score: 1253
Period size: 259 Copynumber: 3.0 Consensus size: 266
40465557 TCGTAGAAAG
* *
40465567 CGCCGC-AAAATATCTTTACTAAAACACGTAGTTTTAATTTTGATGTATACTTATATTAGTGGCG
1 CGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGTGGCG
* * *
40465631 CTTACTAGAAAACGCTGTTAAAGAATAGATTTAGCGGCGCTTGAGCCAAAGCGCCGCAACATATC
66 CTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCCGCAACGTATC
* *
40465696 TTAACAAAACACAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAAAAGCCG
131 TTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAAACGCCG
* * * *
40465761 TAAAAAATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTTAATTAGTGGCGTTGACG
196 CAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTGACG
40465826 TTAAAA
261 TTAAAA
40465832 CGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAA-TTT--TG---A-TTATATTAGTGGCG
1 CGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGTGGCG
* * *
40465890 CTTACTAGAAAACGCCGTTAAAGAATATCATTAGCGGCGCTTGAGCCAAAGCGCCGCAAAGTATC
66 CTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCCGCAACGTATC
* *
40465955 TTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCGTATAGTAAAACGCCG
131 TTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAAACGCCG
* *
40466020 CAAAATATCTGAAGCAAAACGCACCGTTTTGGTCTCAATGTATACTTCAATTAGTGGCGCTGACG
196 CAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTGACG
*
40466085 TTGAAA
261 TTAAAA
40466091 CGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGTGGCG
1 CGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGTGGCG
* * * *
40466156 CTTATTAGAAAACGCCGTTAAAAAATAGCTTTAGCGGCACTTTG-GATC-AAGCGCCGCAACGTA
66 CTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGC-TTGAG-CCAAAGCGCCGCAACGTA
* *
40466219 TCTTAACAAAACGCAGTGTTTTGTCTTAAGCTATGTTACATTTAGTGGCACTTATAGGAAAACGC
129 TCTTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAAACGC
* * * *
40466284 CGCAAAATATCTGAACCAAAATGCACCGTTTTGGTCTTGATGTATACTTCAATTAGTGGTGCTAA
194 CGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTGA
40466349 CGTTAAAA
259 CGTTAAAA
40466357 CGCCGCAAAAA
1 CGCCGCAAAAA
40466368 AGCAAAATAC
Statistics
Matches: 489, Mismatches: 37, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
259 236 0.48
260 4 0.01
262 2 0.00
263 2 0.00
265 10 0.02
266 231 0.47
267 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (266 bp):
CGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGTGGCG
CTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCCGCAACGTATC
TTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAAACGCCG
CAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTGACG
TTAAAA
Found at i:40466967 original size:15 final size:14
Alignment explanation
Indices: 40466947--40466996 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
40466937 TAAGGTTTGT
40466947 AGTTTAGGGTTTAA
1 AGTTTAGGGTTTAA
**
40466961 GAGTTTAAAGTTTAA
1 -AGTTTAGGGTTTAA
*
40466976 AGGTTACGGGTTTAA
1 AGTTTA-GGGTTTAA
40466991 AGTTTA
1 AGTTTA
40466997 AAGGTTACGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (14 bp):
AGTTTAGGGTTTAA
Found at i:40466972 original size:22 final size:21
Alignment explanation
Indices: 40466947--40467003 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
40466937 TAAGGTTTGT
*
40466947 AGTTTAGGGTTTAAGAGTTTAA
1 AGTTTAAGG-TTAAGAGTTTAA
* *
40466969 AGTTTAAAGGTTACGGGTTTAA
1 AGTTT-AAGGTTAAGAGTTTAA
40466991 AGTTTAAAGGTTA
1 AGTTT-AAGGTTA
40467004 CGGGTTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (21 bp):
AGTTTAAGGTTAAGAGTTTAA
Found at i:40466994 original size:29 final size:29
Alignment explanation
Indices: 40466917--40466999 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
40466907 TTTTGAGTGT
* * *
40466917 AAGGTTACGGGTTTAGAA-TGTAAGGTTTG
1 AAGGTTACGGGTTTA-AAGTTTAAAGTTTA
* *
40466946 TAGTTTA-GGGTTTAAGAGTTTAAAGTTTA
1 AAGGTTACGGGTTTAA-AGTTTAAAGTTTA
40466975 AAGGTTACGGGTTTAAAGTTTAAAG
1 AAGGTTACGGGTTTAAAGTTTAAAG
40467000 GTTACGGGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 1 0.02
28 8 0.18
29 27 0.61
30 8 0.18
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
AAGGTTACGGGTTTAAAGTTTAAAGTTTA
Found at i:40467002 original size:15 final size:15
Alignment explanation
Indices: 40466954--40467002 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
40466944 TGTAGTTTAG
40466954 GGTTTAAGAGTTTAAA
1 GGTTTAA-AGTTTAAA
* **
40466970 -GTTTAAAGGTTACG
1 GGTTTAAAGTTTAAA
40466984 GGTTTAAAGTTTAAA
1 GGTTTAAAGTTTAAA
40466999 GGTT
1 GGTT
40467003 ACGGGTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.39
Consensus pattern (15 bp):
GGTTTAAAGTTTAAA
Found at i:40467004 original size:22 final size:22
Alignment explanation
Indices: 40466963--40467015 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
40466953 GGGTTTAAGA
40466963 GTTTAAAGTTTAAAGGTTACGG
1 GTTTAAAGTTTAAAGGTTACGG
40466985 GTTTAAAGTTTAAAGGTTACGG
1 GTTTAAAGTTTAAAGGTTACGG
40467007 G-TTAAAGTT
1 GTTTAAAGTT
40467016 AGGGGCCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (22 bp):
GTTTAAAGTTTAAAGGTTACGG
Found at i:40467608 original size:39 final size:40
Alignment explanation
Indices: 40467553--40467631 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
40467543 TCCCTAATTT
* * *
40467553 CCCATTTCGTATTCCCCCA-ATTCCCCGATTTCATTTCCC
1 CCCAATTCCTATTCCCCCAGATTCCCCGATTTAATTTCCC
*
40467592 CCCAATTCCTATTCCCCCAGTTTCCCCGATTTAATTTCCC
1 CCCAATTCCTATTCCCCCAGATTCCCCGATTTAATTTCCC
40467632 TAAATCCCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 17 0.49
40 18 0.51
ACGTcount: A:0.16, C:0.43, G:0.05, T:0.35
Consensus pattern (40 bp):
CCCAATTCCTATTCCCCCAGATTCCCCGATTTAATTTCCC
Found at i:40469270 original size:22 final size:23
Alignment explanation
Indices: 40469245--40469290 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
40469235 TTATGAATTC
40469245 GGTTTATAAACT-ACTCATTTAT
1 GGTTTATAAACTGACTCATTTAT
* * *
40469267 GGTTTGTAACCTGATTCATTTAT
1 GGTTTATAAACTGACTCATTTAT
40469290 G
1 G
40469291 AATTCAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (23 bp):
GGTTTATAAACTGACTCATTTAT
Found at i:40469607 original size:32 final size:32
Alignment explanation
Indices: 40469568--40469713 Score: 99
Period size: 32 Copynumber: 4.7 Consensus size: 32
40469558 TTCTAAACAA
40469568 TTATAAATATTGTTTTAATATCTATATAAGTT
1 TTATAAATATTGTTTTAATATCTATATAAGTT
* * * * *
40469600 TTCT-AA-A-T-TTATAAGGTTTCTATATTAGTA
1 TTATAAATATTGTTTTAA--TATCTATATAAGTT
* * * * *
40469630 TTA-AATTTATTACTATTAA-ATTTATA-AAATT
1 TTATAA-ATATT-GTTTTAATATCTATATAAGTT
* *
40469661 TTATAAATATTGTTTTAATATCTATATTAGTA
1 TTATAAATATTGTTTTAATATCTATATAAGTT
40469693 TTATAAATATTGTTTTAATAT
1 TTATAAATATTGTTTTAATAT
40469714 AACCTATAAA
Statistics
Matches: 82, Mismatches: 21, Indels: 22
0.66 0.17 0.18
Matches are distributed among these distances:
28 5 0.06
29 1 0.01
30 20 0.24
31 17 0.21
32 34 0.41
33 1 0.01
35 4 0.05
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (32 bp):
TTATAAATATTGTTTTAATATCTATATAAGTT
Found at i:40469646 original size:15 final size:15
Alignment explanation
Indices: 40469622--40469654 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40469612 AAGGTTTCTA
*
40469622 TATTAGTATTAAATT
1 TATTACTATTAAATT
40469637 TATTACTATTAAATT
1 TATTACTATTAAATT
40469652 TAT
1 TAT
40469655 AAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:40469669 original size:93 final size:92
Alignment explanation
Indices: 40469568--40469858 Score: 352
Period size: 93 Copynumber: 3.2 Consensus size: 92
40469558 TTCTAAACAA
40469568 TTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCTATATTAGTATTA
1 TTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCTATATTAGTATTA
40469633 AATTTATTACTATTAAATTTATAAAATT
66 AATTTATTA-TATTAAATTTATAAAATT
* * * * * *
40469661 TTATAAATATTGTTTTAATATCTATATTAGTATTATAAA--TAT--TGTTT-TAATATAACCTAT
1 TTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCT-ATATTA-GTAT
* ** * *
40469721 AAAATTTA--A-A--AGTTTTCT-AAATAA
64 TAAATTTATTATATTAAATTTATAAAAT-T
*
40469745 TTATAAATATTGTTTTAATATCTATATAAATTTTCTAAATTTATAAGGTTTCTATATTAGTATTA
1 TTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCTATATTAGTATTA
40469810 AATTTATTAGTATTAAATTTATAAAATT
66 AATTTATTA-TATTAAATTTATAAAATT
40469838 TTATAAATATTGTTTTAATAT
1 TTATAAATATTGTTTTAATAT
40469859 AACCTATAAA
Statistics
Matches: 160, Mismatches: 23, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
83 4 0.03
84 40 0.25
86 4 0.03
87 10 0.06
88 11 0.07
89 11 0.07
90 10 0.06
91 4 0.03
93 62 0.39
94 4 0.03
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (92 bp):
TTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCTATATTAGTATTA
AATTTATTATATTAAATTTATAAAATT
Found at i:40469819 original size:15 final size:15
Alignment explanation
Indices: 40469799--40469831 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
40469789 AAGGTTTCTA
40469799 TATTAGTATTAAATT
1 TATTAGTATTAAATT
40469814 TATTAGTATTAAATT
1 TATTAGTATTAAATT
40469829 TAT
1 TAT
40469832 AAAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TATTAGTATTAAATT
Found at i:40470000 original size:24 final size:26
Alignment explanation
Indices: 40469973--40470027 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
40469963 TATATATCTT
*
40469973 ACATAATACATAAC-TACATAACAA-
1 ACATAATAAATAACTTACATAACAAC
*
40469997 ACATAATAAATAACTTACATAATAAC
1 ACATAATAAATAACTTACATAACAAC
40470023 ACATA
1 ACATA
40470028 CCGTACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 13 0.48
25 9 0.33
26 5 0.19
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (26 bp):
ACATAATAAATAACTTACATAACAAC
Found at i:40470149 original size:9 final size:9
Alignment explanation
Indices: 40470117--40470333 Score: 131
Period size: 9 Copynumber: 25.8 Consensus size: 9
40470107 TAGTGAATAA
40470117 TACAT-ACT
1 TACATAACT
*
40470125 TACATAAAT
1 TACATAACT
* *
40470134 TAAATAAGT
1 TACATAACT
40470143 TACATAA--
1 TACATAACT
* *
40470150 TACACAAAT
1 TACATAACT
40470159 TACATAACT
1 TACATAACT
40470168 TACATAA--
1 TACATAACT
*
40470175 TACATAATT
1 TACATAACT
40470184 TACATAA--
1 TACATAACT
* *
40470191 TACACACCT
1 TACATAACT
*
40470200 GACATAACT
1 TACATAACT
40470209 TACATAA--
1 TACATAACT
**
40470216 TACATATTT
1 TACATAACT
*
40470225 TACATCACT
1 TACATAACT
40470234 TACATAA--
1 TACATAACT
*
40470241 GACATAACT
1 TACATAACT
40470250 TACATAA--
1 TACATAACT
*
40470257 TACACAACT
1 TACATAACT
*
40470266 TACATAAGT
1 TACATAACT
*
40470275 TTCATAA--
1 TACATAACT
*
40470282 TACACAACT
1 TACATAACT
* *
40470291 TACACAGCT
1 TACATAACT
40470300 TACATAACT
1 TACATAACT
* *
40470309 TACACAAGT
1 TACATAACT
40470318 TACATAACT
1 TACATAACT
*
40470327 TAGATAA
1 TACATAA
40470334 TAAATAACTT
Statistics
Matches: 160, Mismatches: 34, Indels: 29
0.72 0.15 0.13
Matches are distributed among these distances:
7 41 0.26
8 5 0.03
9 114 0.71
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (9 bp):
TACATAACT
Found at i:40470178 original size:16 final size:16
Alignment explanation
Indices: 40470159--40470272 Score: 106
Period size: 16 Copynumber: 7.0 Consensus size: 16
40470149 ATACACAAAT
40470159 TACATAACTTACATAA
1 TACATAACTTACATAA
*
40470175 TACATAATTTACATAA
1 TACATAACTTACATAA
* * *
40470191 TACACACCTGACATAA
1 TACATAACTTACATAA
*
40470207 CTTACATAA--TACATATTT
1 --TACATAACTTACATA--A
*
40470225 TACATCACTTACATAA
1 TACATAACTTACATAA
*
40470241 GACATAACTTACATAA
1 TACATAACTTACATAA
*
40470257 TACACAACTTACATAA
1 TACATAACTTACATAA
40470273 GTTTCATAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
16 66 0.86
18 11 0.14
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:40470192 original size:41 final size:41
Alignment explanation
Indices: 40470118--40470272 Score: 163
Period size: 41 Copynumber: 3.8 Consensus size: 41
40470108 AGTGAATAAT
* * *
40470118 ACAT-ACTTACATAAATTAAATAAGTTACATAATACACAAATT
1 ACATAACTTACAT-AA-TACATAATTTACATAATACACAAATG
**
40470160 ACATAACTTACATAATACATAATTTACATAATACACACCTG
1 ACATAACTTACATAATACATAATTTACATAATACACAAATG
* * *
40470201 ACATAACTTACATAATACATATTTTACATCACTTACA-TAA-G
1 ACATAACTTACATAATACATAATTTACAT-A-ATACACAAATG
* *
40470242 ACATAACTTACATAATACACAACTTACATAA
1 ACATAACTTACATAATACATAATTTACATAA
40470273 GTTTCATAAT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
40 1 0.01
41 76 0.79
42 7 0.07
43 12 0.12
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.30
Consensus pattern (41 bp):
ACATAACTTACATAATACATAATTTACATAATACACAAATG
Found at i:40470229 original size:25 final size:25
Alignment explanation
Indices: 40470113--40470333 Score: 109
Period size: 25 Copynumber: 8.8 Consensus size: 25
40470103 AAATTAGTGA
* *
40470113 ATAATACAT-ACTTACATAAATTAA
1 ATAATACATAACTTACATAACTTAC
* *
40470137 ATAAGTTACATAA--TACACAAATTAC
1 ATAA--TACATAACTTACATAACTTAC
*
40470162 ATAACTTACATAA--TACATAATTTAC
1 ATAA--TACATAACTTACATAACTTAC
* * *
40470187 ATAATACACACCTGACATAACTTAC
1 ATAATACATAACTTACATAACTTAC
** *
40470212 ATAATACATATTTTACATCACTTAC
1 ATAATACATAACTTACATAACTTAC
*
40470237 ATAAGACATAACTTACATAA--TAC
1 ATAATACATAACTTACATAACTTAC
* * *
40470260 ACAACTTACATAAGTTTCATAA--TAC
1 ATAA--TACATAACTTACATAACTTAC
* * *
40470285 ACAACTTACACAGCTTACATAACTTAC
1 ATAA--TACATAACTTACATAACTTAC
* *
40470312 ACAAGTTACATAACTTAGATAA
1 ATAA--TACATAACTTACATAA
40470334 TAAATAACTT
Statistics
Matches: 158, Mismatches: 30, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
23 11 0.07
24 4 0.03
25 116 0.73
26 5 0.03
27 22 0.14
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.30
Consensus pattern (25 bp):
ATAATACATAACTTACATAACTTAC
Found at i:40470281 original size:41 final size:40
Alignment explanation
Indices: 40470160--40470294 Score: 146
Period size: 41 Copynumber: 3.3 Consensus size: 40
40470150 TACACAAATT
* *
40470160 ACATAACTTACATAATACATAATTTACATAA-TACACACCTG
1 ACATAACTTACATAATACATAATTTACATAATTACATA--AG
* *
40470201 ACATAACTTACATAATACATATTTTACATCACTTACATAAG
1 ACATAACTTACATAATACATAATTTACAT-AATTACATAAG
* * * *
40470242 ACATAACTTACATAATACACAACTTACATAAGTTTCATAAT
1 ACATAACTTACATAATACATAATTTACATAA-TTACATAAG
*
40470283 ACACAACTTACA
1 ACATAACTTACA
40470295 CAGCTTACAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 1 0.01
41 73 0.91
42 1 0.01
43 5 0.06
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.30
Consensus pattern (40 bp):
ACATAACTTACATAATACATAATTTACATAATTACATAAG
Found at i:40471667 original size:21 final size:21
Alignment explanation
Indices: 40471643--40471691 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
40471633 GGCAGTAAGG
*
40471643 GAAGCAGAGGCTACAGCGAGA
1 GAAGCAGAGGCCACAGCGAGA
*
40471664 GAAGCAGAGGCCGCAGCGAGA
1 GAAGCAGAGGCCACAGCGAGA
40471685 GAAGCAG
1 GAAGCAG
40471692 CGAGAGAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.41, T:0.02
Consensus pattern (21 bp):
GAAGCAGAGGCCACAGCGAGA
Found at i:40471693 original size:12 final size:12
Alignment explanation
Indices: 40471656--40471715 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
40471646 GCAGAGGCTA
40471656 CAGCGAGAGAAG
1 CAGCGAGAGAAG
**
40471668 CA--GAG-GCCG
1 CAGCGAGAGAAG
40471677 CAGCGAGAGAAG
1 CAGCGAGAGAAG
40471689 CAGCGAGAGAAG
1 CAGCGAGAGAAG
* *
40471701 CAGCAATAGAAG
1 CAGCGAGAGAAG
40471713 CAG
1 CAG
40471716 TGGTTCAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 29 0.74
ACGTcount: A:0.40, C:0.20, G:0.38, T:0.02
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:40472300 original size:42 final size:42
Alignment explanation
Indices: 40472137--40472300 Score: 226
Period size: 42 Copynumber: 3.9 Consensus size: 42
40472127 TGTGAAATAG
* **
40472137 GCGCCGCTAAAGAACACT-A-CTTTTAGCGGCATTTTTGAGC-AA
1 GCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TTCTAA
* *
40472179 GCGCCACTAAAGAACATGATCTTTAGCGGCGATTTTTTCTAA
1 GCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAA
*
40472221 GCGCCGCTAAAGAACATGATCTTTAGCGGAGTTTTTTTCTAA
1 GCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAA
40472263 GCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 GCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
40472301 ATGTAAGCAC
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.02
42 107 0.97
43 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
GCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAA
Found at i:40472421 original size:22 final size:22
Alignment explanation
Indices: 40472390--40472432 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40472380 TAGTGGAGTT
* *
40472390 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
40472412 AAAAAACGCCGCTAAAAACCT
1 AAAAAACGCCGCTAAAAACCT
40472433 GTTTTGCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:40476723 original size:138 final size:138
Alignment explanation
Indices: 40476475--40476752 Score: 547
Period size: 138 Copynumber: 2.0 Consensus size: 138
40476465 TATACTTTAT
40476475 AAGTATTTGGTGATAATATGTGTATTCTTCGATTCTCCTTAGAAATACAATCATTCTTCTTTATA
1 AAGTATTTGGTGATAATATGTGTATTCTTCGATTCTCCTTAGAAATACAATCATTCTTCTTTATA
40476540 ACAACCAAAATTATTATAGATATTTTAATAAATGATATTAATTATCAATAAAATTTTATAGGTAT
66 ACAACCAAAATTATTATAGATATTTTAATAAATGATATTAATTATCAATAAAATTTTATAGGTAT
40476605 TTGAATAA
131 TTGAATAA
40476613 AAGTATTTGGTGATAATATGTGTATTCTTCGATTCTCCTTAGAAATACAATCATTCTTCTTTATA
1 AAGTATTTGGTGATAATATGTGTATTCTTCGATTCTCCTTAGAAATACAATCATTCTTCTTTATA
*
40476678 ACAACCAAAATTATTATAGGTATTTTAATAAATGATATTAATTATCAATAAAATTTTATAGGTAT
66 ACAACCAAAATTATTATAGATATTTTAATAAATGATATTAATTATCAATAAAATTTTATAGGTAT
40476743 TTGAATAA
131 TTGAATAA
40476751 AA
1 AA
40476753 TGTTATAGGT
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (138 bp):
AAGTATTTGGTGATAATATGTGTATTCTTCGATTCTCCTTAGAAATACAATCATTCTTCTTTATA
ACAACCAAAATTATTATAGATATTTTAATAAATGATATTAATTATCAATAAAATTTTATAGGTAT
TTGAATAA
Found at i:40476749 original size:22 final size:22
Alignment explanation
Indices: 40476722--40476776 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
40476712 ATATTAATTA
*
40476722 TCAATAAAATTTTATAGGTATT
1 TCAATAAAATTTTATAGGTAGT
* *
40476744 TGAATAAAATGTTATAGGTAGT
1 TCAATAAAATTTTATAGGTAGT
40476766 TCAATAAAATT
1 TCAATAAAATT
40476777 AATCATGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (22 bp):
TCAATAAAATTTTATAGGTAGT
Found at i:40478171 original size:20 final size:20
Alignment explanation
Indices: 40478132--40478185 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
40478122 AGGAAAAACT
* *
40478132 TTTATCAAAATATTTCTAAAAC
1 TTTACCAAAATA--TCTAAAAA
*
40478154 TTTACTAAAATATCTAAAAA
1 TTTACCAAAATATCTAAAAA
40478174 TTTACCAAAATA
1 TTTACCAAAATA
40478186 AATCCTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 18 0.64
22 10 0.36
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTACCAAAATATCTAAAAA
Found at i:40483330 original size:30 final size:30
Alignment explanation
Indices: 40483273--40483332 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40483263 GCTTTTTGAA
* *
40483273 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACACCAAATTTTT
40483303 AATATTTACAAAAAGAGTA-ACCAAATTTTT
1 AATATTTACAAAAAGAG-ACACCAAATTTTT
40483333 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTTT
Found at i:40495201 original size:41 final size:41
Alignment explanation
Indices: 40495105--40495202 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
40495095 AATCACAATG
* * * *
40495105 CTCACACGAGCTGTCGGTCGAAACGTAGCTACACGATACTG
1 CTCACACGAGCTGTGGGTCAAAACATAGCTACACGATACTA
* * *
40495146 CTCACACAAGCTGTGGGTTAAAACATAGCTACACGATGCTA
1 CTCACACGAGCTGTGGGTCAAAACATAGCTACACGATACTA
40495187 CTCACACGAGCTGTGG
1 CTCACACGAGCTGTGG
40495203 AGTATCCGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (41 bp):
CTCACACGAGCTGTGGGTCAAAACATAGCTACACGATACTA
Found at i:40500324 original size:18 final size:17
Alignment explanation
Indices: 40500282--40500325 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
40500272 TAGAAACTTA
40500282 TAAGTTTAGAAAAAGGAC
1 TAAGTTT-GAAAAAGGAC
*
40500300 TAA-TTTGTAAAAAGGTC
1 TAAGTTTG-AAAAAGGAC
40500317 TAAGTTTGA
1 TAAGTTTGA
40500326 GTCTTTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 15 0.65
18 7 0.30
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (17 bp):
TAAGTTTGAAAAAGGAC
Found at i:40505253 original size:50 final size:51
Alignment explanation
Indices: 40505136--40505382 Score: 209
Period size: 50 Copynumber: 4.8 Consensus size: 51
40505126 GATAATAACA
* * * **
40505136 TGCCAAAT-CCATGTCCCAGACATGGTCTTACATGAGATG-TTTC-T-TGTAC
1 TGCC-AATGCCATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATATATGG
* * *
40505185 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-TGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATATGG
* ** * * *
40505235 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGAACTCTCATCT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATATGG
* * * *
40505285 TGCCAACGCTATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT-A--T--ATGG
* *
40505341 TGCTAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCT
40505383 TTCCCCAAAT
Statistics
Matches: 160, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
48 4 0.03
49 33 0.21
50 82 0.51
51 1 0.01
53 1 0.01
56 39 0.24
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATATGG
Found at i:40512529 original size:21 final size:20
Alignment explanation
Indices: 40512505--40512572 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
40512495 GTTGTTGAGA
40512505 AGGAAGTTGATGTTGCAGAAG
1 AGGAAGTTG-TGTTGCAGAAG
40512526 AGGAAG-T-TGTTGCAGAAG
1 AGGAAGTTGTGTTGCAGAAG
* *
40512544 AGGAAGTTGTTTCTGAAGAAG
1 AGGAAGTTGTGT-TGCAGAAG
40512565 AGGAAGTT
1 AGGAAGTT
40512573 ATTGAAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 17 0.40
19 1 0.02
20 3 0.07
21 21 0.50
ACGTcount: A:0.34, C:0.04, G:0.37, T:0.25
Consensus pattern (20 bp):
AGGAAGTTGTGTTGCAGAAG
Found at i:40512562 original size:18 final size:18
Alignment explanation
Indices: 40512515--40512554 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
40512505 AGGAAGTTGA
40512515 TGTTGCAGAAGAGGAAGT
1 TGTTGCAGAAGAGGAAGT
40512533 TGTTGCAGAAGAGGAAGT
1 TGTTGCAGAAGAGGAAGT
40512551 TGTT
1 TGTT
40512555 TCTGAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.38, T:0.28
Consensus pattern (18 bp):
TGTTGCAGAAGAGGAAGT
Found at i:40512578 original size:18 final size:18
Alignment explanation
Indices: 40512521--40512578 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
40512511 TTGATGTTGC
* *
40512521 AGAAGAGGAAGTTGTTGC
1 AGAAGAGGAAGTTATTGA
*
40512539 AGAAGAGGAAGTTGTTTCTGA
1 AGAAGAGGAAG-T-TAT-TGA
40512560 AGAAGAGGAAGTTATTGA
1 AGAAGAGGAAGTTATTGA
40512578 A
1 A
40512579 AATGAGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 15 0.44
19 3 0.09
20 3 0.09
21 13 0.38
ACGTcount: A:0.38, C:0.03, G:0.34, T:0.24
Consensus pattern (18 bp):
AGAAGAGGAAGTTATTGA
Found at i:40515989 original size:67 final size:67
Alignment explanation
Indices: 40515910--40516058 Score: 217
Period size: 67 Copynumber: 2.2 Consensus size: 67
40515900 GCTCAAGTGC
* * * *
40515910 CAAATTATCTTAAATTATGAGTTTGTGTGTATTGTGATATGTGTTTATATGACATGCGACCATTA
1 CAAATTATCTTAAATTATGAATATGTGTGTATTATGATATGTGTTTATATGACATGCGACCACTA
40515975 TG
66 TG
* * *
40515977 CAAATTATCTTAACTTATGAATATGTGTGTATTATGATATGTGTTTTTATGACATGTGACCACTA
1 CAAATTATCTTAAATTATGAATATGTGTGTATTATGATATGTGTTTATATGACATGCGACCACTA
40516042 TG
66 TG
*
40516044 CAATTTATCTATAAA
1 CAAATTATCT-TAAA
40516059 ATGTTTTAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 69 0.96
68 3 0.04
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (67 bp):
CAAATTATCTTAAATTATGAATATGTGTGTATTATGATATGTGTTTATATGACATGCGACCACTA
TG
Found at i:40516028 original size:15 final size:16
Alignment explanation
Indices: 40515991--40516034 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
40515981 TTATCTTAAC
40515991 TTATGAATATGTGTGTA
1 TTATG-ATATGTGTGTA
*
40516008 TTATGATATGTGT-TT
1 TTATGATATGTGTGTA
*
40516023 TTATGACATGTG
1 TTATGATATGTG
40516035 ACCACTATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 8 0.32
17 5 0.20
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.50
Consensus pattern (16 bp):
TTATGATATGTGTGTA
Found at i:40517312 original size:17 final size:18
Alignment explanation
Indices: 40517280--40517315 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40517270 AGGGTGTTAC
*
40517280 ATTTAGGTTGTGTTAATT
1 ATTTAGGTTGTATTAATT
40517298 ATTTA-GTTGTATTAATT
1 ATTTAGGTTGTATTAATT
40517315 A
1 A
40517316 ATTAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (18 bp):
ATTTAGGTTGTATTAATT
Found at i:40522111 original size:22 final size:22
Alignment explanation
Indices: 40522085--40522133 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40522075 TCAAAACATC
*
40522085 TAATACTTATACATATGACCAA
1 TAATAATTATACATATGACCAA
* * *
40522107 TAATAATTCTACCTATTACCAA
1 TAATAATTATACATATGACCAA
40522129 TAATA
1 TAATA
40522134 GTTCATTACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATAATTATACATATGACCAA
Done.