Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 195 of 202
Found at i:59507324 original size:217 final size:217
Alignment explanation
Indices: 59506949--59507384 Score: 836
Period size: 217 Copynumber: 2.0 Consensus size: 217
59506939 TCATTGTTGA
59506949 AGTTAAACCCTTAAAAGGTTTTATGGAAAAGGTGGAGAACTTGTTTGTTGAGAGTTCACGATGAA
1 AGTTAAACCCTTAAAAGGTTTTATGGAAAAGGTGGAGAACTTGTTTGTTGAGAGTTCACGATGAA
*
59507014 GAACTTGTTCATTGAGAATTCGTGTCCAGGTGGAGACTGTTAGAATTAAGTGACCCGAATCCTTA
66 GAACTTGTTCATTGAGAATTCGTGTCAAGGTGGAGACTGTTAGAATTAAGTGACCCGAATCCTTA
*
59507079 TTTTTATTCCTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATTCCTATAGAAC
131 TTTGTATTCCTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATTCCTATAGAAC
59507144 TATACTTCTTTCATTTTATTTT
196 TATACTTCTTTCATTTTATTTT
* *
59507166 AGTTAAACCCTTAAAAGGTTTTATGGAAGAGGTGGAGAACTTGTTTGTTGAGAGTTCATGATGAA
1 AGTTAAACCCTTAAAAGGTTTTATGGAAAAGGTGGAGAACTTGTTTGTTGAGAGTTCACGATGAA
59507231 GAACTTGTTCATTGAGAATTCGTGTCAAGGTGGAGACTGTTAGAATTAAGTGACCCGAATCCTTA
66 GAACTTGTTCATTGAGAATTCGTGTCAAGGTGGAGACTGTTAGAATTAAGTGACCCGAATCCTTA
59507296 TTTGTATTCCTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATTCCTATAGAAC
131 TTTGTATTCCTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATTCCTATAGAAC
59507361 TATACTTCTTTCATTTTATTTT
196 TATACTTCTTTCATTTTATTTT
59507383 AG
1 AG
59507385 AATAAGGTTT
Statistics
Matches: 215, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
217 215 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (217 bp):
AGTTAAACCCTTAAAAGGTTTTATGGAAAAGGTGGAGAACTTGTTTGTTGAGAGTTCACGATGAA
GAACTTGTTCATTGAGAATTCGTGTCAAGGTGGAGACTGTTAGAATTAAGTGACCCGAATCCTTA
TTTGTATTCCTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATTCCTATAGAAC
TATACTTCTTTCATTTTATTTT
Found at i:59509082 original size:2 final size:2
Alignment explanation
Indices: 59509070--59509102 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
59509060 ACATTGAAAA
59509070 AT AT CAT 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
59509103 TAGAAAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59509633 original size:13 final size:13
Alignment explanation
Indices: 59509615--59509641 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59509605 ACTAATTGTC
59509615 ATTATTAAATATG
1 ATTATTAAATATG
59509628 ATTATTAAATATG
1 ATTATTAAATATG
59509641 A
1 A
59509642 AAGATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTATTAAATATG
Found at i:59510600 original size:59 final size:60
Alignment explanation
Indices: 59510499--59510622 Score: 223
Period size: 59 Copynumber: 2.1 Consensus size: 60
59510489 ATTAAGCATT
59510499 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATTAACATCAAATAATCACTC
1 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATTAACATCAAATAATCACTC
* *
59510559 AAAA-ATGCATTTAAGTGATTATGAGTATAAAATTCACAATTAACATCAAATAATCACTC
1 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATTAACATCAAATAATCACTC
59510618 AAAAC
1 AAAAC
59510623 GCATTAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 57 0.93
60 4 0.07
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (60 bp):
AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATTAACATCAAATAATCACTC
Found at i:59515088 original size:2 final size:2
Alignment explanation
Indices: 59515047--59515072 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59515037 TAATTAAATA
59515047 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
59515073 GAAAGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59516685 original size:3 final size:3
Alignment explanation
Indices: 59516677--59516703 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
59516667 CCTTGGGCTT
59516677 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
59516704 AGAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:59516919 original size:13 final size:14
Alignment explanation
Indices: 59516901--59516952 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
59516891 GGCCCACTTT
59516901 GCGCA-GCCCAGTA
1 GCGCAGGCCCAGTA
* *
59516914 GCGCAGGCCCACTTT
1 GCGCAGGCCCA-GTA
59516929 GCGCA-GCCCAGTA
1 GCGCAGGCCCAGTA
59516942 GCGCAGGCCCA
1 GCGCAGGCCCA
59516953 ACGCAGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 11 0.34
14 15 0.47
15 6 0.19
ACGTcount: A:0.19, C:0.40, G:0.31, T:0.10
Consensus pattern (14 bp):
GCGCAGGCCCAGTA
Found at i:59516920 original size:28 final size:28
Alignment explanation
Indices: 59516888--59516952 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
59516878 CAGGTCTGCA
59516888 GCAGGCCCACTTTGCGCAGCCCAGTAGC
1 GCAGGCCCACTTTGCGCAGCCCAGTAGC
59516916 GCAGGCCCACTTTGCGCAGCCCAGTAGC
1 GCAGGCCCACTTTGCGCAGCCCAGTAGC
59516944 GCAGGCCCA
1 GCAGGCCCA
59516953 ACGCAGGCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.18, C:0.40, G:0.29, T:0.12
Consensus pattern (28 bp):
GCAGGCCCACTTTGCGCAGCCCAGTAGC
Found at i:59516962 original size:28 final size:28
Alignment explanation
Indices: 59516901--59516989 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
59516891 GGCCCACTTT
***
59516901 GCGCAGCCCAGTAGCGCAGGCCCACTTT
1 GCGCAGCCCAGTAGCGCAGGCCCACGCA
59516929 GCGCAGCCCAGTAGCGCAGGCCCAACGCA
1 GCGCAGCCCAGTAGCGCAGGCCC-ACGCA
59516958 G-GCAGCCCAGCACTAGCAGCAGGCCCAC-CA
1 GCGCAGCCCAG---TAGC-GCAGGCCCACGCA
59516988 GC
1 GC
59516990 ATAAGCAGGC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
28 32 0.62
29 3 0.06
30 3 0.06
31 6 0.12
32 8 0.15
ACGTcount: A:0.22, C:0.42, G:0.29, T:0.07
Consensus pattern (28 bp):
GCGCAGCCCAGTAGCGCAGGCCCACGCA
Found at i:59517052 original size:14 final size:14
Alignment explanation
Indices: 59517033--59517084 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
59517023 GAAACAGGCC
59517033 AGAAAAAAGAGAGA
1 AGAAAAAAGAGAGA
* *
59517047 AGAAAAAAGAAAAA
1 AGAAAAAAGAGAGA
59517061 AGAAAAAA-A-AGA
1 AGAAAAAAGAGAGA
*
59517073 AAAAAAAAGAGA
1 AGAAAAAAGAGA
59517085 AAAAAAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 9 0.28
13 2 0.06
14 21 0.66
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAGAGAGA
Found at i:59517066 original size:28 final size:28
Alignment explanation
Indices: 59517034--59517145 Score: 122
Period size: 28 Copynumber: 3.9 Consensus size: 28
59517024 AAACAGGCCA
59517034 GAAAAAAGAGAGAAGAAAAAAGAAAAAA-
1 GAAAAAAGAGAGAA-AAAAAAGAAAAAAG
* *
59517062 GAAAAAAAAGAAAAAAAAAGAGAAAAAAAG
1 GAAAAAAGAGAGAAAAAAA-AG-AAAAAAG
*
59517092 GAAAAAAGAG-GAAAAAAGAGGAAAAAAG
1 GAAAAAAGAGAGAAAAAA-AAGAAAAAAG
59517120 GAAAAAA-AGAGAAAAATGAAAGAAAA
1 GAAAAAAGAGAGAAAAA--AAAGAAAA
59517146 GTTAAATTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
27 7 0.10
28 34 0.48
29 19 0.27
30 11 0.15
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (28 bp):
GAAAAAAGAGAGAAAAAAAAGAAAAAAG
Found at i:59517069 original size:10 final size:10
Alignment explanation
Indices: 59517056--59517145 Score: 76
Period size: 10 Copynumber: 9.1 Consensus size: 10
59517046 AAGAAAAAAG
59517056 AAAAAAG-AA
1 AAAAAAGAAA
59517065 AAAAAAGAAA
1 AAAAAAGAAA
*
59517075 AAAAAAGAGA
1 AAAAAAGAAA
*
59517085 AAAAAAGGAA
1 AAAAAAGAAA
* *
59517095 AAAAGAGGAA
1 AAAAAAGAAA
* *
59517105 AAAAGAG-GA
1 AAAAAAGAAA
*
59517114 AAAAAGGAAA
1 AAAAAAGAAA
*
59517124 AAAAGAGAAA
1 AAAAAAGAAA
*
59517134 AATGAAAGAAA
1 AA-AAAAGAAA
59517145 A
1 A
59517146 GTTAAATTTG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
9 13 0.20
10 46 0.70
11 7 0.11
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:59517098 original size:38 final size:38
Alignment explanation
Indices: 59517035--59517135 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
59517025 AACAGGCCAG
* *
59517035 AAAAAAGAGAGAAGAAAAAAGAAAAAAGA-AAAAAAAGA
1 AAAAAAAAGAGAA-AAAAAGGAAAAAAGAGAAAAAAAGA
*
59517073 AAAAAAAAGAGAAAAAAAGGAAAAAAGAGGAAAAAAGA
1 AAAAAAAAGAGAAAAAAAGGAAAAAAGAGAAAAAAAGA
**
59517111 GGAAAAAAG-GAAAAAAAGAGAAAAA
1 AAAAAAAAGAGAAAAAAAG-GAAAAA
59517136 TGAAAGAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 23 0.41
38 33 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (38 bp):
AAAAAAAAGAGAAAAAAAGGAAAAAAGAGAAAAAAAGA
Found at i:59517146 original size:18 final size:17
Alignment explanation
Indices: 59517033--59517146 Score: 87
Period size: 18 Copynumber: 6.6 Consensus size: 17
59517023 GAAACAGGCC
59517033 AGAAAAAAGAGAGAAGAAA
1 AGAAAAAA-AGAGAA-AAA
59517052 A-AAGAAAAA-AGAAAAA
1 AGAA-AAAAAGAGAAAAA
* *
59517068 A-AAGAAAA-A-AAAAG
1 AGAAAAAAAGAGAAAAA
59517082 AGAAAAAAAG-GAAAAA
1 AGAAAAAAAGAGAAAAA
59517098 AGAGGAAAAAAGAGGAAAAA
1 AGA--AAAAAAGA-GAAAAA
59517118 AGGAAAAAAAGAGAAAAA
1 A-GAAAAAAAGAGAAAAA
*
59517136 TGAAAGAAAAG
1 AGAAA-AAAAG
59517147 TTAAATTTGT
Statistics
Matches: 80, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.06
15 11 0.14
16 13 0.16
17 8 0.10
18 21 0.26
19 13 0.16
20 7 0.09
21 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (17 bp):
AGAAAAAAAGAGAAAAA
Found at i:59517465 original size:13 final size:13
Alignment explanation
Indices: 59517447--59517471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59517437 TAATTGTCAT
59517447 TATTAAATATGAG
1 TATTAAATATGAG
59517460 TATTAAATATGA
1 TATTAAATATGA
59517472 AAGATAAATT
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
TATTAAATATGAG
Found at i:59522670 original size:2 final size:2
Alignment explanation
Indices: 59522663--59522691 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59522653 TAAGTTTAGA
59522663 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
59522692 GTTTTGGAAT
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:59536014 original size:14 final size:14
Alignment explanation
Indices: 59535995--59536030 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
59535985 ACTAGATCAC
59535995 TCTCCCACTAAGCT
1 TCTCCCACTAAGCT
59536009 TCTCCCACTAAGCT
1 TCTCCCACTAAGCT
*
59536023 TCTTCCAC
1 TCTCCCAC
59536031 GAAAACTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (14 bp):
TCTCCCACTAAGCT
Found at i:59536986 original size:98 final size:98
Alignment explanation
Indices: 59536817--59537011 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
59536807 ACAATAAAAT
* *
59536817 TTTAAAAGAAGATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
59536882 TCTAAAATCCCAAACTCGGAATATTTCATTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCATTTAC
59536915 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
59536980 TTTAAAATCCCAAACTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCATTTA
59537012 TTGTTTTTAG
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCATTTAC
Found at i:59542969 original size:98 final size:98
Alignment explanation
Indices: 59542797--59542991 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
59542787 ACAATAAAAT
* * *
59542797 TTTAAAAGAAGATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAAAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
59542862 TCTAGAATCCCAAACTCGGAATATTTCATTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCATTTAC
*
59542895 TTTAAAAAAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTATGGCACAATTCC
1 TTTAAAAAAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
59542960 TTTAAAATCCCAAACTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCATTTA
59542992 TTGTTTTTAG
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
TTTAAAAAAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCATTTAC
Found at i:59544475 original size:19 final size:19
Alignment explanation
Indices: 59544450--59544558 Score: 164
Period size: 19 Copynumber: 5.7 Consensus size: 19
59544440 TCATATATTA
59544450 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
* **
59544469 GAAGATTATATATCATATC
1 TAAGATTGCATATCATATC
*
59544488 TAAGATTACATATCATATC
1 TAAGATTGCATATCATATC
*
59544507 TAAGATTGCATATCATATT
1 TAAGATTGCATATCATATC
*
59544526 TAGGATTGCATATCATATC
1 TAAGATTGCATATCATATC
59544545 TAAGATTGCATATC
1 TAAGATTGCATATC
59544559 CTCAAAAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:59551425 original size:26 final size:26
Alignment explanation
Indices: 59551389--59551447 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
59551379 AAAAATAACT
59551389 AAAATATTATAACTTTTTTATTTACC
1 AAAATATTATAACTTTTTTATTTACC
*
59551415 AAAATATTATAATTTTTTTATTTACC
1 AAAATATTATAACTTTTTTATTTACC
59551441 AAAATAT
1 AAAATAT
59551448 ATCAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.49
Consensus pattern (26 bp):
AAAATATTATAACTTTTTTATTTACC
Found at i:59551555 original size:27 final size:27
Alignment explanation
Indices: 59551517--59551581 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
59551507 ATTGGCGGTT
*
59551517 TGGTGCCAAAGAGATTGGCGGCACCAA
1 TGGTGCCAAAGAGATTGGCAGCACCAA
*
59551544 TGGTGCCAAAGAGATTGGCAGCGCCAA
1 TGGTGCCAAAGAGATTGGCAGCACCAA
* *
59551571 TTGTGTCAAAG
1 TGGTGCCAAAG
59551582 GACTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.18
Consensus pattern (27 bp):
TGGTGCCAAAGAGATTGGCAGCACCAA
Found at i:59558746 original size:22 final size:21
Alignment explanation
Indices: 59558721--59558790 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
59558711 AATTACATAG
59558721 AATTTTACTCTTAATAAACATT
1 AATTTTA-TCTTAATAAACATT
*
59558743 AATTTTAAT-GTATATCAAACTATT
1 AATTTT-ATCTTA-AT-AAAC-ATT
59558767 --TTTTATCTTAATAAACATT
1 AATTTTATCTTAATAAACATT
*
59558786 CATTT
1 AATTT
59558791 AATAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
19 3 0.08
20 4 0.10
21 9 0.23
22 15 0.38
23 5 0.13
24 3 0.08
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (21 bp):
AATTTTATCTTAATAAACATT
Found at i:59559453 original size:14 final size:14
Alignment explanation
Indices: 59559434--59559472 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
59559424 TATCGTGTAA
59559434 AATAGAATTCAAAT
1 AATAGAATTCAAAT
59559448 AATAGAATTCAAAT
1 AATAGAATTCAAAT
59559462 AATAGAATTCA
1 AATAGAATTCA
59559473 TTATAGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (14 bp):
AATAGAATTCAAAT
Found at i:59560329 original size:11 final size:11
Alignment explanation
Indices: 59560313--59560339 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
59560303 CCTGTATGCA
59560313 TAGTACAAGAT
1 TAGTACAAGAT
59560324 TAGTACAAGAT
1 TAGTACAAGAT
59560335 TAGTA
1 TAGTA
59560340 TATTTAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (11 bp):
TAGTACAAGAT
Found at i:59563969 original size:52 final size:51
Alignment explanation
Indices: 59563879--59563980 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 51
59563869 CTATTGCATA
* * * *
59563879 CTTTAGCTTTGCAGCAATTTTTTGTTTCAAAACGAGTGATGTAGGATAAGG
1 CTTTAGCTTTGCAGAAATTTTGTGTTTCAAAACAAGTGATGTAAGATAAGG
59563930 CTTTAGCTTTGCA-AAATGTTGTGTGTTTCAAAACAAGTGATGTAAGATAAG
1 CTTTAGCTTTGCAGAAAT-TT-TGTGTTTCAAAACAAGTGATGTAAGATAAG
59563981 TAAGGAGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
50 3 0.07
51 15 0.33
52 27 0.60
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (51 bp):
CTTTAGCTTTGCAGAAATTTTGTGTTTCAAAACAAGTGATGTAAGATAAGG
Found at i:59564707 original size:6 final size:6
Alignment explanation
Indices: 59564687--59564717 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
59564677 TTTATCAATC
59564687 TCTGAT TCATGAT TCTGAT TCTGAT TCTGAT
1 TCTGAT TC-TGAT TCTGAT TCTGAT TCTGAT
59564718 ATGCTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
TCTGAT
Found at i:59566177 original size:20 final size:20
Alignment explanation
Indices: 59566152--59566198 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
59566142 CATCCAAACA
59566152 CTAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCATTTT
59566172 CTAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCATTTT
*
59566192 CCAGAAA
1 CTAGAAA
59566199 TCATTTTCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (20 bp):
CTAGAAAAGTAAATCATTTT
Found at i:59566218 original size:14 final size:14
Alignment explanation
Indices: 59566182--59566219 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
59566172 CTAGAAAAGT
*
59566182 AAATCATTTTCCAG
1 AAATCATTTTCCAA
59566196 AAATCATTTTCCGAA
1 AAATCATTTTCC-AA
59566211 AAAT-ATTTT
1 AAATCATTTT
59566220 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:59567076 original size:68 final size:66
Alignment explanation
Indices: 59566996--59567133 Score: 231
Period size: 68 Copynumber: 2.1 Consensus size: 66
59566986 TCAAGTTTGT
*
59566996 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATATAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
59567061 AAA
64 AAA
*
59567064 TTTACTGATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
59567129 T
66 A
59567130 TTTA
1 TTTA
59567134 TTAACAATTA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 23 0.34
67 1 0.01
68 43 0.64
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:59567147 original size:16 final size:16
Alignment explanation
Indices: 59567126--59567167 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
59567116 AATAATTTGA
*
59567126 TAATTTTATTAACAAT
1 TAATTTTAATAACAAT
59567142 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
59567158 TAGTTTTAAT
1 TAATTTTAAT
59567168 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:59573389 original size:23 final size:23
Alignment explanation
Indices: 59573346--59573389 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
59573336 GAAATTAAAT
* *
59573346 TGTAATTTTTATAATAGTAAAAC
1 TGTAATTTTTAAAAGAGTAAAAC
*
59573369 TGTAATTTTTAAAAGATTAAA
1 TGTAATTTTTAAAAGAGTAAA
59573390 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TGTAATTTTTAAAAGAGTAAAAC
Found at i:59582572 original size:9 final size:9
Alignment explanation
Indices: 59582558--59582597 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
59582548 TTTGGTTAAA
59582558 AATTAACCG
1 AATTAACCG
59582567 AATTAACCG
1 AATTAACCG
59582576 AATT-ACCTG
1 AATTAACC-G
*
59582585 AATTACCCG
1 AATTAACCG
59582594 AATT
1 AATT
59582598 GAATAACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 3 0.11
9 23 0.82
10 2 0.07
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:59584344 original size:17 final size:17
Alignment explanation
Indices: 59584308--59584340 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59584298 AGACTGTGTG
*
59584308 ATTTAAATATTTTAAAT
1 ATTTAAATATTATAAAT
59584325 ATTTAAAT-TTATAAAT
1 ATTTAAATATTATAAAT
59584341 TATTGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAAATATTATAAAT
Found at i:59585164 original size:16 final size:16
Alignment explanation
Indices: 59585126--59585165 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
59585116 AATATGTGAA
59585126 TAATATTATTTAAAAT
1 TAATATTATTTAAAAT
*
59585142 TATTATT-TTTAAAATT
1 TAATATTATTTAAAA-T
59585158 TAATATTA
1 TAATATTA
59585166 AAATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATATTATTTAAAAT
Found at i:59585174 original size:18 final size:19
Alignment explanation
Indices: 59585151--59585186 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
59585141 TTATTATTTT
59585151 TAAAATTT-AATATTAAAA
1 TAAAATTTAAATATTAAAA
59585169 TAAAATTTAAATATTAAA
1 TAAAATTTAAATATTAAA
59585187 TAATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTTAAATATTAAAA
Found at i:59586337 original size:21 final size:22
Alignment explanation
Indices: 59586294--59586338 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
59586284 CAAATGGCCA
* *
59586294 AATGCCATTTTTTTAATGGTAG
1 AATGCCATTTTTTAAATGATAG
*
59586316 AATGCCA-TTTTTAAATTATAG
1 AATGCCATTTTTTAAATGATAG
59586337 AA
1 AA
59586339 GTAGTTGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
AATGCCATTTTTTAAATGATAG
Found at i:59594855 original size:27 final size:28
Alignment explanation
Indices: 59594823--59594883 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
59594813 AAACTTTTGA
* *
59594823 AAATTTAAATTATACCTTTAATTTTTTT
1 AAATTTAAATTAAACCTTCAATTTTTTT
* *
59594851 -AATTT-AATTAAATCTTCATTTTTTTT
1 AAATTTAAATTAAACCTTCAATTTTTTT
59594877 AAATTTA
1 AAATTTA
59594884 TTATTGAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (28 bp):
AAATTTAAATTAAACCTTCAATTTTTTT
Found at i:59594979 original size:17 final size:17
Alignment explanation
Indices: 59594930--59594981 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
59594920 TTTTTTTTTG
*
59594930 TAAATTTTCATAAATCTC
1 TAAATTTTCATAAA-ATC
* * *
59594948 TAAAATTTAAAAAAATC
1 TAAATTTTCATAAAATC
59594965 TAAATTTTCATAAAATC
1 TAAATTTTCATAAAATC
59594982 AGTATCCTAG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTTCATAAAATC
Found at i:59597076 original size:51 final size:50
Alignment explanation
Indices: 59597000--59597177 Score: 163
Period size: 51 Copynumber: 3.6 Consensus size: 50
59596990 ACTAGACCTG
59597000 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCTC-TA
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTA-AAATCTTATTTC-CGTA
* * *
59597051 AAGTTTCAGTGGAGCAGATTGAAGCTACAAG------TCTTATTTCCGTA
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTAAAATCTTATTTCCGTA
* * * * * *
59597095 AAGTTGAAGTGGAACAAATTAAAGATACAAGTTATAAATCTTATCTCCTTG
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTA-AAATCTTATTTCCGTA
* * * *
59597146 AAGTTACAGTGGAGCAGATTGAAGTTACAAGT
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGT
59597178 CTTATCTCCC
Statistics
Matches: 101, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.01
44 36 0.36
51 64 0.63
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (50 bp):
AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTAAAATCTTATTTCCGTA
Found at i:59597097 original size:44 final size:43
Alignment explanation
Indices: 59597032--59597219 Score: 142
Period size: 44 Copynumber: 4.1 Consensus size: 43
59597022 AGCTACAAGT
* * *
59597032 TACAAATCTTATTTCTCTAAAGTTTCAGTGGAGCAGATTGAAGC
1 TACAAGTCTTATCTC-CTAAAGTTGCAGTGGAGCAGATTGAAGC
* * * * * *
59597076 TACAAGTCTTATTTCCGTAAAGTTGAAGTGGAACAAATTAAAGA
1 TACAAGTCTTATCTCC-TAAAGTTGCAGTGGAGCAGATTGAAGC
* * *
59597120 TACAAGTTATAAATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGT
1 TACAAG-------TCTTATCTCC-TAAAGTTGCAGTGGAGCAGATTGAAGC
* * *
59597171 TACAAGTCTTATCTCCCTAAAGTAGCAGTGGAGTAGATTGAAAC
1 TACAAGTCTTATCT-CCTAAAGTTGCAGTGGAGCAGATTGAAGC
59597215 TACAA
1 TACAA
59597220 TTCCTATACC
Statistics
Matches: 113, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
43 1 0.01
44 75 0.66
45 2 0.02
51 35 0.31
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (43 bp):
TACAAGTCTTATCTCCTAAAGTTGCAGTGGAGCAGATTGAAGC
Found at i:59597219 original size:95 final size:95
Alignment explanation
Indices: 59597000--59597219 Score: 291
Period size: 95 Copynumber: 2.3 Consensus size: 95
59596990 ACTAGACCTG
* *
59597000 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCTCTAAAGTTTCAGTGGAG
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTCCTCTAAAGTTACAGTGGAG
* *
59597065 CAGATTGAAGCTACAAGTCTTATTTCCGTA
66 CAGATTGAAGCTACAAGTCTTATCTCCCTA
* * * * *
59597095 AAGTTGAAGTGGAACAAATTAAAGATACAAGTTATAAATCTTATCTCCT-TGAAGTTACAGTGGA
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTAT-TCCTCTAAAGTTACAGTGGA
*
59597159 GCAGATTGAAGTTACAAGTCTTATCTCCCTA
65 GCAGATTGAAGCTACAAGTCTTATCTCCCTA
* **
59597190 AAGTAGCAGTGGAGTAGATTGAAA-CTACAA
1 AAGTTGCAGTGGAACAGATT-AAAGCTACAA
59597220 TTCCTATACC
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
95 101 0.94
96 6 0.06
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (95 bp):
AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTCCTCTAAAGTTACAGTGGAG
CAGATTGAAGCTACAAGTCTTATCTCCCTA
Found at i:59597766 original size:26 final size:26
Alignment explanation
Indices: 59597736--59597799 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
59597726 AACTTTTGAA
*
59597736 AAATTTAGTTATACCTTTAA-TTTTTT
1 AAATTTA-TTATACCTTCAATTTTTTT
* *
59597762 AAATTTAATTAAATCTTCAATTTTTTT
1 AAATTT-ATTATACCTTCAATTTTTTT
59597789 AAATTTATTAT
1 AAATTTATTAT
59597800 TGAACATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (26 bp):
AAATTTATTATACCTTCAATTTTTTT
Found at i:59597891 original size:17 final size:17
Alignment explanation
Indices: 59597842--59597893 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
59597832 TTTTTTTTTG
*
59597842 TAAATTTTCATAAATCTC
1 TAAATTTTCATAAA-ATC
* * *
59597860 TAAAATTTAAAAAAATC
1 TAAATTTTCATAAAATC
59597877 TAAATTTTCATAAAATC
1 TAAATTTTCATAAAATC
59597894 AGTATCCTAG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTTCATAAAATC
Found at i:59599018 original size:30 final size:31
Alignment explanation
Indices: 59598984--59599067 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 31
59598974 CCAATATCTC
*
59598984 GATACTCATATCTTTGACTTTCCAAAT-TTT
1 GATACCCATATCTTTGACTTTCCAAATATTT
* *
59599014 GATACCCATATCTTTGACTTT-CTATTATTT
1 GATACCCATATCTTTGACTTTCCAAATATTT
59599044 GATACCCATATCTTTGACTTTCCA
1 GATACCCATATCTTTGACTTTCCA
59599068 TAAATATGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
29 3 0.06
30 44 0.92
31 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (31 bp):
GATACCCATATCTTTGACTTTCCAAATATTT
Found at i:59599029 original size:15 final size:15
Alignment explanation
Indices: 59598984--59599060 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
59598974 CCAATATCTC
*
59598984 GATACTCATATCTTT
1 GATACCCATATCTTT
** *
59598999 GACTTTCCAAAT-TTT
1 GA-TACCCATATCTTT
59599014 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
59599029 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
59599044 GATACCCATATCTTT
1 GATACCCATATCTTT
59599059 GA
1 GA
59599061 CTTTCCATAA
Statistics
Matches: 43, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
14 10 0.23
15 24 0.56
16 9 0.21
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:59600746 original size:5 final size:5
Alignment explanation
Indices: 59600736--59600790 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
59600726 AATCTTAGAT
59600736 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
59600786 TATTA
1 TATTA
59600791 AATAAACTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:59601388 original size:22 final size:24
Alignment explanation
Indices: 59601360--59601403 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
59601350 TATGGCAAGA
59601360 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
59601382 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
59601404 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:59602721 original size:2 final size:2
Alignment explanation
Indices: 59602716--59602770 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
59602706 TATATATATA
59602716 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
59602758 TG TG TG TG TG TG T
1 TG TG TG TG TG TG T
59602771 TTTGGGCTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:59606059 original size:30 final size:31
Alignment explanation
Indices: 59606025--59606108 Score: 154
Period size: 30 Copynumber: 2.8 Consensus size: 31
59606015 CCAATATCTC
59606025 GATACCCATATCTTTGACTTTCCAATT-TTT
1 GATACCCATATCTTTGACTTTCCAATTATTT
59606055 GATACCCATATCTTTGACTTTCC-ATTATTT
1 GATACCCATATCTTTGACTTTCCAATTATTT
59606085 GATACCCATATCTTTGACTTTCCA
1 GATACCCATATCTTTGACTTTCCA
59606109 TAAATATGGA
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
29 3 0.06
30 49 0.94
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (31 bp):
GATACCCATATCTTTGACTTTCCAATTATTT
Found at i:59606070 original size:15 final size:15
Alignment explanation
Indices: 59606025--59606101 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
59606015 CCAATATCTC
59606025 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
59606040 GACTTTCCA-ATTTTT
1 GA-TACCCATATCTTT
59606055 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
59606070 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
59606085 GATACCCATATCTTT
1 GATACCCATATCTTT
59606100 GA
1 GA
59606102 CTTTCCATAA
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.20
15 28 0.61
16 9 0.20
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:59607312 original size:32 final size:32
Alignment explanation
Indices: 59607272--59607336 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
59607262 TCATGGAGTT
59607272 AGGCAAAATACAATACATTAGAGTTTTAATAC
1 AGGCAAAATACAATACATTAGAGTTTTAATAC
*
59607304 AGGCAAAATACAATGCATTAGAGTTTTAATAC
1 AGGCAAAATACAATACATTAGAGTTTTAATAC
59607336 A
1 A
59607337 ATTAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (32 bp):
AGGCAAAATACAATACATTAGAGTTTTAATAC
Found at i:59609223 original size:5 final size:5
Alignment explanation
Indices: 59609213--59609240 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
59609203 TGAAATATAC
59609213 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
59609241 ATATTATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:59618777 original size:18 final size:19
Alignment explanation
Indices: 59618754--59618792 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
59618744 TAAAAAGTTG
59618754 AAATAAA-ATCTAAT-TTAA
1 AAATAAATA-CTAATATTAA
59618772 AAATAAATACTAATATTAA
1 AAATAAATACTAATATTAA
59618791 AA
1 AA
59618793 GTATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAAATACTAATATTAA
Found at i:59618912 original size:16 final size:16
Alignment explanation
Indices: 59618883--59618921 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
59618873 AAATCGAGAA
59618883 AAAAAATAAATGAAACT
1 AAAAAATAAATGAAA-T
*
59618900 AAAAAA-AATTGAAAT
1 AAAAAATAAATGAAAT
59618915 AAAAAAT
1 AAAAAAT
59618922 TTGAGGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 7 0.35
16 7 0.35
17 6 0.30
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAAATAAATGAAAT
Found at i:59625989 original size:2 final size:2
Alignment explanation
Indices: 59625984--59626029 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
59625974 TTTTTTATTT
59625984 TA TA TA TA 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 TA TA TA TA
59626026 TA TA
1 TA TA
59626030 GGCAAAAGCA
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):
TA
Found at i:59628428 original size:2 final size:2
Alignment explanation
Indices: 59628421--59628447 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59628411 TATTATAATT
59628421 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59628448 GTTTAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59629532 original size:16 final size:16
Alignment explanation
Indices: 59629498--59629550 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
59629488 ATGGCATCAG
59629498 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
59629514 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
59629530 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
59629546 TCATG
1 TCATG
59629551 AGTATAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:59629816 original size:41 final size:41
Alignment explanation
Indices: 59629739--59629879 Score: 157
Period size: 41 Copynumber: 3.6 Consensus size: 41
59629729 ACCAGTTTGG
* * * *
59629739 CACCCAATGCCTCATCGGAT-AATTCGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
59629779 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
* * ** *
59629820 CACACAGTATCTCATCGGTTAAA-CCG-A--AGTAAATTGG
1 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
*
59629857 CACCCAGTGTCTCATCGATTAAA
1 CACCCAGTGTCTCATCGAATAAA
59629880 CCAATAAACC
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
37 29 0.33
39 1 0.01
40 20 0.23
41 38 0.43
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
Found at i:59630885 original size:2 final size:2
Alignment explanation
Indices: 59630878--59630917 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
59630868 TATTATATTT
* *
59630878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59630918 AAAGGAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:59630945 original size:15 final size:17
Alignment explanation
Indices: 59630915--59630947 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
59630905 AGATATAAAT
59630915 ATAAAAGGAGAAAGAAA
1 ATAAAAGGAGAAAGAAA
59630932 ATAAAA-GA-AAAGAAA
1 ATAAAAGGAGAAAGAAA
59630947 A
1 A
59630948 GAGAGGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (17 bp):
ATAAAAGGAGAAAGAAA
Found at i:59633786 original size:14 final size:15
Alignment explanation
Indices: 59633762--59633795 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
59633752 AGCTGGCGGA
59633762 GTTTATAAAATAGTT
1 GTTTATAAAATAGTT
*
59633777 GTTT-TAAAATATTT
1 GTTTATAAAATAGTT
59633791 GTTTA
1 GTTTA
59633796 ACTTTACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
GTTTATAAAATAGTT
Found at i:59634529 original size:21 final size:22
Alignment explanation
Indices: 59634496--59634538 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
59634486 CATCTACCAT
*
59634496 ATCACTCCGGA-TTGTAAATAA
1 ATCACTCCGGATTTGCAAATAA
* *
59634517 ATCACTGCTGATTTGCAAATAA
1 ATCACTCCGGATTTGCAAATAA
59634539 TTGCCACTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (22 bp):
ATCACTCCGGATTTGCAAATAA
Found at i:59634875 original size:27 final size:28
Alignment explanation
Indices: 59634822--59634875 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
59634812 TAGATATGGG
59634822 AAATATATATAGTTTTATAAAAATATTA
1 AAATATATATAGTTTTATAAAAATATTA
*
59634850 AAATATA-ATA-TTTTAATAAATATATT
1 AAATATATATAGTTTT-ATAAAAATATT
59634876 TATCTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 13 0.54
28 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATATATATAGTTTTATAAAAATATTA
Found at i:59635842 original size:2 final size:2
Alignment explanation
Indices: 59635835--59635862 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59635825 TAATCAGAAC
59635835 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
59635863 GCACATATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59640603 original size:22 final size:23
Alignment explanation
Indices: 59640572--59640615 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
59640562 ACATCACTAA
* *
59640572 TAAAATAATATTTTTA-AAAAAG
1 TAAAAAAATAATTTTAGAAAAAG
59640594 TAAAAAAATAATTTTAGAAAAA
1 TAAAAAAATAATTTTAGAAAAA
59640616 AAAATGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
TAAAAAAATAATTTTAGAAAAAG
Found at i:59641886 original size:22 final size:23
Alignment explanation
Indices: 59641846--59641891 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
59641836 ATAATATTTA
** *
59641846 AACAATAACAACACCAAAATAAT
1 AACAATAACAACAAAAAAAAAAT
59641869 AACAA-AACAACAAAAAAAAAAT
1 AACAATAACAACAAAAAAAAAAT
59641891 A
1 A
59641892 GCAGTTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.74, C:0.17, G:0.00, T:0.09
Consensus pattern (23 bp):
AACAATAACAACAAAAAAAAAAT
Found at i:59653414 original size:111 final size:111
Alignment explanation
Indices: 59653287--59653492 Score: 313
Period size: 111 Copynumber: 1.9 Consensus size: 111
59653277 ACATTATGAA
** * *
59653287 CAACAGAGATACTGTTTCTGTCCTCCATGTTTGCAGGCTCAGAAGAAACCTTATCGAGTTCAGGA
1 CAACAGAGATACTGTTTCCATCCTCCATGGTTGCAGGCTCAGAAGAAACCTTATCAAGTTCAGGA
*
59653352 GCAGCTTCTTCTGATCGATTTTCACTATCATCTGAAATGTTATTAG
66 GCAGATTCTTCTGATCGATTTTCACTATCATCTGAAATGTTATTAG
* * * *
59653398 CAACAGAGATATTGTTTCCATCCTCCTTGGTTGCAGGCTCGGAAGAAACGTTATCAAGTTCAGGA
1 CAACAGAGATACTGTTTCCATCCTCCATGGTTGCAGGCTCAGAAGAAACCTTATCAAGTTCAGGA
* *
59653463 GCAGATTCTTCTGATTGATTTTCGCTATCA
66 GCAGATTCTTCTGATCGATTTTCACTATCA
59653493 CGAGTTCCTT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
111 84 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (111 bp):
CAACAGAGATACTGTTTCCATCCTCCATGGTTGCAGGCTCAGAAGAAACCTTATCAAGTTCAGGA
GCAGATTCTTCTGATCGATTTTCACTATCATCTGAAATGTTATTAG
Found at i:59660081 original size:15 final size:15
Alignment explanation
Indices: 59660038--59660101 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
59660028 ATTATAAAAA
*
59660038 TAATTATTTTTA-TT
1 TAATTATTTATATTT
*
59660052 TATTTCATATTATATTT
1 TAATT-AT-TTATATTT
59660069 TAATTATTTATATTT
1 TAATTATTTATATTT
* *
59660084 AAATTA-TTACATTT
1 TAATTATTTATATTT
59660098 TAAT
1 TAAT
59660102 CACTTACATT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
14 14 0.34
15 15 0.37
16 6 0.15
17 6 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTATTTATATTT
Found at i:59660081 original size:20 final size:20
Alignment explanation
Indices: 59660040--59660082 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
59660030 TATAAAAATA
*
59660040 ATTATTTTTATTTATTTCAT
1 ATTATTTTTAATTATTTCAT
59660060 ATTATATTTTAATTATTT-AT
1 ATTAT-TTTTAATTATTTCAT
59660080 ATT
1 ATT
59660083 TAAATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATTTTTAATTATTTCAT
Found at i:59662665 original size:29 final size:29
Alignment explanation
Indices: 59662633--59662693 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
59662623 ACTCGATTCA
59662633 AAAAAATTCAAATCAAATTAGAATTGATT
1 AAAAAATTCAAATCAAATTAGAATTGATT
* *
59662662 AAAAAATTCGAGTCAAATTAGAATTGATT
1 AAAAAATTCAAATCAAATTAGAATTGATT
59662691 AAA
1 AAA
59662694 TAGGACTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.30
Consensus pattern (29 bp):
AAAAAATTCAAATCAAATTAGAATTGATT
Found at i:59666073 original size:18 final size:18
Alignment explanation
Indices: 59666047--59666084 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
59666037 ACTTTTTAAC
*
59666047 TTTTAAATAT-TTTTTAT
1 TTTTAAATATATTTTGAT
59666064 TTTTAGAATATATTTTGAT
1 TTTTA-AATATATTTTGAT
59666083 TT
1 TT
59666085 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTAAATATATTTTGAT
Found at i:59668320 original size:15 final size:17
Alignment explanation
Indices: 59668300--59668337 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
59668290 AATAAATAAC
59668300 ATAAATTT-AA-TAAAA
1 ATAAATTTGAAGTAAAA
59668315 ATAAATTTGAAGTAAAA
1 ATAAATTTGAAGTAAAA
59668332 ATAAAT
1 ATAAAT
59668338 GAAACTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
ATAAATTTGAAGTAAAA
Found at i:59674140 original size:23 final size:24
Alignment explanation
Indices: 59674096--59674140 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
59674086 CAAACCCAAA
* **
59674096 TTTCACCACATGACAATGCAACTC
1 TTTCACCACATGAAAACCCAACTC
59674120 TTTC-CCACATGAAAACCCAAC
1 TTTCACCACATGAAAACCCAAC
59674141 ATTTCTGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.22
Consensus pattern (24 bp):
TTTCACCACATGAAAACCCAACTC
Found at i:59681371 original size:41 final size:39
Alignment explanation
Indices: 59681295--59681371 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 39
59681285 TCACCTACAC
* *
59681295 AATTTTAATTAATAATAAAATTAGTTTTTAATATTTTTA
1 AATTTTAAATAATAATAAAATTAGTTTTAAATATTTTTA
*
59681334 AATTTATAAATAATATATAATATTA-TTTTCAAATATTT
1 AATTT-TAAATAATA-ATAAAATTAGTTTT-AAATATTT
59681372 AATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.16
40 12 0.38
41 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (39 bp):
AATTTTAAATAATAATAAAATTAGTTTTAAATATTTTTA
Found at i:59685063 original size:22 final size:22
Alignment explanation
Indices: 59685037--59685087 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
59685027 GTTCGAATAG
*
59685037 TTTAATTACTTAAATAAAAAAA
1 TTTAATTAATTAAATAAAAAAA
* * * *
59685059 TTTAAATAATTTAATGACAAAA
1 TTTAATTAATTAAATAAAAAAA
59685081 TTTAATT
1 TTTAATT
59685088 TTTTAATTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTAATTAATTAAATAAAAAAA
Found at i:59685095 original size:13 final size:14
Alignment explanation
Indices: 59685079--59685107 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59685069 TTAATGACAA
59685079 AATT-TAATTTTTT
1 AATTGTAATTTTTT
59685092 AATTGTAATTTTTT
1 AATTGTAATTTTTT
59685106 AA
1 AA
59685108 AATTGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
AATTGTAATTTTTT
Found at i:59689648 original size:31 final size:31
Alignment explanation
Indices: 59689613--59689674 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
59689603 TTACAAAATG
**
59689613 ATCACTAAATTGTTCAAAAGTTTTCATTTAA
1 ATCACTAAATTACTCAAAAGTTTTCATTTAA
* *
59689644 ATCACTAAATTACTCAAAATTTTTTATTTAA
1 ATCACTAAATTACTCAAAAGTTTTCATTTAA
59689675 GTCATTGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (31 bp):
ATCACTAAATTACTCAAAAGTTTTCATTTAA
Found at i:59693231 original size:15 final size:15
Alignment explanation
Indices: 59693213--59693249 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
59693203 CGCAAGCTAC
59693213 TGAAGAATGAAACCG
1 TGAAGAATGAAACCG
*
59693228 TGAAGAATGAAATCG
1 TGAAGAATGAAACCG
59693243 TGGAAGA
1 T-GAAGA
59693250 TGCTTCTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.46, C:0.08, G:0.30, T:0.16
Consensus pattern (15 bp):
TGAAGAATGAAACCG
Found at i:59693781 original size:22 final size:23
Alignment explanation
Indices: 59693747--59693790 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
59693737 CTTTCTTCTC
*
59693747 AAAAAATAAAGAAAAAATAAAAT
1 AAAAAATAAAGAAAAAAAAAAAT
*
59693770 AAAAAA-AGAGAAAAAAAAAAA
1 AAAAAATAAAGAAAAAAAAAAA
59693791 AACAGCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAAAATAAAGAAAAAAAAAAAT
Found at i:59693783 original size:20 final size:18
Alignment explanation
Indices: 59693747--59693792 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
59693737 CTTTCTTCTC
*
59693747 AAAAAATAAAGAAAAAATA
1 AAAAAAAAAAGAAAAAA-A
59693766 AAATAAAAAAAGAGAAAAAA
1 AAA-AAAAAAAGA-AAAAAA
59693786 AAAAAAA
1 AAAAAAA
59693793 CAGCACTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 12 0.50
21 5 0.21
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAAA
Found at i:59698917 original size:22 final size:23
Alignment explanation
Indices: 59698873--59698921 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
59698863 GAAAGATCTA
59698873 AAACAAAGTTGAATCAAAAACTG
1 AAACAAAGTTGAATCAAAAACTG
59698896 AAACAAAGTTGAATC-AAAACTG
1 AAACAAAGTTGAATCAAAAACTG
59698918 AAAC
1 AAAC
59698922 TTTAGATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.16
Consensus pattern (23 bp):
AAACAAAGTTGAATCAAAAACTG
Found at i:59709666 original size:4 final size:4
Alignment explanation
Indices: 59709649--59709697 Score: 89
Period size: 4 Copynumber: 12.2 Consensus size: 4
59709639 GTTAGAATGA
*
59709649 ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59709697 A
1 A
59709698 TACATATGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:59709725 original size:14 final size:14
Alignment explanation
Indices: 59709706--59709735 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
59709696 TATACATATG
59709706 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
59709720 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
59709734 TG
1 TG
59709736 CAAGGTCACC
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:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (14 bp):
TGTGTGTGTGTGTA
Found at i:59711609 original size:17 final size:17
Alignment explanation
Indices: 59711583--59711616 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59711573 ATATAATATA
59711583 TATATAGTTTTAGTATT
1 TATATAGTTTTAGTATT
* *
59711600 TATATTGTTTTATTATT
1 TATATAGTTTTAGTATT
59711617 ATTTATCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
TATATAGTTTTAGTATT
Found at i:59715312 original size:15 final size:16
Alignment explanation
Indices: 59715279--59715309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59715269 TGTAAAACTA
59715279 ATGTATGATATTTTTT
1 ATGTATGATATTTTTT
*
59715295 ATGTTTGATATTTTT
1 ATGTATGATATTTTT
59715310 ATGCTATGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (16 bp):
ATGTATGATATTTTTT
Found at i:59717453 original size:20 final size:20
Alignment explanation
Indices: 59717425--59717462 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59717415 TGCTCTGGGT
59717425 GAGAA-TTTTGCTGGCATGTG
1 GAGAATTTTTG-TGGCATGTG
*
59717445 GAGAGTTTTTGTGGCATG
1 GAGAATTTTTGTGGCATG
59717463 AATCTTGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.18, C:0.08, G:0.37, T:0.37
Consensus pattern (20 bp):
GAGAATTTTTGTGGCATGTG
Found at i:59717776 original size:29 final size:30
Alignment explanation
Indices: 59717744--59717801 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
59717734 TTAATCCAAT
*
59717744 GTACAATATC-ATATACA-AACTTTGATTTG
1 GTACAAT-TCTATATACACAACTTTAATTTG
*
59717773 GTACAATTCTATATATACAACTTTAATTT
1 GTACAATTCTATATACACAACTTTAATTT
59717802 CGATTCAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 13 0.52
30 10 0.40
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (30 bp):
GTACAATTCTATATACACAACTTTAATTTG
Found at i:59718554 original size:13 final size:13
Alignment explanation
Indices: 59718536--59718570 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
59718526 TTGTCAATAC
59718536 AAAAACAAAAAAA
1 AAAAACAAAAAAA
59718549 AAAAACAAAAAAA
1 AAAAACAAAAAAA
59718562 AAAAACAAA
1 AAAAACAAA
59718571 TTACACATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAA
Found at i:59722408 original size:20 final size:20
Alignment explanation
Indices: 59722371--59722413 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
59722361 AAATTTACTA
* *
59722371 TAAAATAAATTGATTTTTTT
1 TAAAAAAAATTGATTTTTAT
59722391 TAAAAAAAATT-ATGTTTTAT
1 TAAAAAAAATTGAT-TTTTAT
59722411 TAA
1 TAA
59722414 CAAGGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TAAAAAAAATTGATTTTTAT
Found at i:59733222 original size:20 final size:21
Alignment explanation
Indices: 59733197--59733235 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59733187 ATATAATTTC
*
59733197 ATTTAAT-GAATATTATTTTT
1 ATTTAATAAAATATTATTTTT
59733217 ATTTAATAAAATATTATTT
1 ATTTAATAAAATATTATTT
59733236 ATACAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
ATTTAATAAAATATTATTTTT
Found at i:59733421 original size:18 final size:18
Alignment explanation
Indices: 59733394--59733432 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
59733384 TATTTTAGTT
* *
59733394 TTGAAAACTGTTGTTTTC
1 TTGAAAACTGTGGGTTTC
*
59733412 TTGAAGACTGTGGGTTTC
1 TTGAAAACTGTGGGTTTC
59733430 TTG
1 TTG
59733433 CATGCATGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (18 bp):
TTGAAAACTGTGGGTTTC
Found at i:59734442 original size:28 final size:28
Alignment explanation
Indices: 59734405--59734468 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
59734395 GATTTAGTTA
*
59734405 ATTAAATTAGT-TTCTTTATTATTAAATT
1 ATTAAATTAGTCTT-TATATTATTAAATT
* *
59734433 ATTAATTTAGTCTTTATATTATTAAATAA
1 ATTAAATTAGTCTTTATATTATTAAAT-T
59734462 ATTAAAT
1 ATTAAAT
59734469 ATTTACTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTAAATTAGTCTTTATATTATTAAATT
Found at i:59735998 original size:2 final size:2
Alignment explanation
Indices: 59735991--59736017 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59735981 ATCTTTTTAA
59735991 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 A
59736018 CACATTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59737935 original size:7 final size:7
Alignment explanation
Indices: 59737925--59737952 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
59737915 TTCTATGACG
59737925 CGCCGCC
1 CGCCGCC
59737932 CGCCGCC
1 CGCCGCC
59737939 CGCCGCC
1 CGCCGCC
59737946 CGCCGCC
1 CGCCGCC
59737953 GGGTACTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.71, G:0.29, T:0.00
Consensus pattern (7 bp):
CGCCGCC
Found at i:59743203 original size:10 final size:10
Alignment explanation
Indices: 59743190--59743224 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
59743180 ATAAAATGAC
*
59743190 TAAAAAGTCA
1 TAAAAAGTTA
59743200 TAAAAAGTTA
1 TAAAAAGTTA
59743210 TAAAAA-TTA
1 TAAAAAGTTA
59743219 TAAAAA
1 TAAAAA
59743225 ATTAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (10 bp):
TAAAAAGTTA
Found at i:59743235 original size:17 final size:18
Alignment explanation
Indices: 59743210--59743251 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
59743200 TAAAAAGTTA
*
59743210 TAAAAATTATAAAAA-AT
1 TAAAAATTAGAAAAACAT
*
59743227 TAAATATTAGAAAAACAT
1 TAAAAATTAGAAAAACAT
59743245 TAAAAAT
1 TAAAAAT
59743252 ATTAAAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATTAGAAAAACAT
Found at i:59743316 original size:19 final size:19
Alignment explanation
Indices: 59743279--59743338 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
59743269 CTTATTAAAC
59743279 TTAT-AAAA-TATAAAAAAA
1 TTATAAAAACTAT-AAAAAA
* *
59743297 TTATAAAAATTATAATAAA
1 TTATAAAAACTATAAAAAA
*
59743316 TCTA-ATAAACTATAAAAAA
1 T-TATAAAAACTATAAAAAA
59743335 TTAT
1 TTAT
59743339 GGAACTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 6 0.18
19 23 0.68
20 5 0.15
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TTATAAAAACTATAAAAAA
Found at i:59743746 original size:19 final size:17
Alignment explanation
Indices: 59743722--59743758 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
59743712 CATCCAGTTC
59743722 AATTAAATAAAATATTAAA
1 AATTAAA-AAAA-ATTAAA
59743741 AATTAAAAAAAATTAAA
1 AATTAAAAAAAATTAAA
59743758 A
1 A
59743759 TCGGTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAAAAAAATTAAA
Found at i:59755831 original size:11 final size:11
Alignment explanation
Indices: 59755811--59755840 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
59755801 TAAAAAATAA
59755811 AAAAAGTATTTT
1 AAAAA-TATTTT
59755823 AAAAATATTTT
1 AAAAATATTTT
59755834 AAAAATA
1 AAAAATA
59755841 AAAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:59759836 original size:21 final size:23
Alignment explanation
Indices: 59759810--59759851 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
59759800 TAAGTTATTT
59759810 TAAAA-TTATAAAAA-TTATAAA
1 TAAAATTTATAAAAACTTATAAA
59759831 TAAAATTTATAAAAACTTATA
1 TAAAATTTATAAAAACTTATA
59759852 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAATTTATAAAAACTTATAAA
Found at i:59759987 original size:13 final size:13
Alignment explanation
Indices: 59759951--59759992 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
59759941 TCTGTATTGT
59759951 TTTTTTTAATAAA
1 TTTTTTTAATAAA
* **
59759964 ATAATTT-ATAAA
1 TTTTTTTAATAAA
59759976 TTTTTTTAATAAA
1 TTTTTTTAATAAA
59759989 TTTT
1 TTTT
59759993 GTATATAGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTTTAATAAA
Found at i:59767797 original size:9 final size:9
Alignment explanation
Indices: 59767783--59767885 Score: 134
Period size: 9 Copynumber: 11.4 Consensus size: 9
59767773 TTTGGTTAAA
59767783 AATTAACCG
1 AATTAACCG
*
59767792 AATTAACCA
1 AATTAACCG
59767801 AATTAACCG
1 AATTAACCG
*
59767810 AATTACCCG
1 AATTAACCG
*
59767819 ACTTAACCG
1 AATTAACCG
*
59767828 AATTACCCG
1 AATTAACCG
59767837 AATTAACCG
1 AATTAACCG
*
59767846 AATTACCCG
1 AATTAACCG
*
59767855 AATTACCCG
1 AATTAACCG
*
59767864 AATTAACCA
1 AATTAACCG
*
59767873 AATTAACCT
1 AATTAACCG
59767882 AATT
1 AATT
59767886 GAATCATACA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 82 1.00
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:59767935 original size:6 final size:6
Alignment explanation
Indices: 59767924--59767952 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
59767914 ACTTTTATAC
59767924 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
59767953 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:59767976 original size:20 final size:20
Alignment explanation
Indices: 59767924--59767965 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
59767914 ACTTTTATAC
59767924 TTTAGTTTTAG--TTTTAGT
1 TTTAGTTTTAGAATTTTAGT
*
59767942 TTTAGTTTTAGAATTTTATT
1 TTTAGTTTTAGAATTTTAGT
59767962 TTTA
1 TTTA
59767966 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTAGTTTTAGAATTTTAGT
Found at i:59773387 original size:78 final size:79
Alignment explanation
Indices: 59773279--59773436 Score: 230
Period size: 78 Copynumber: 2.0 Consensus size: 79
59773269 AATTCAAAGA
**
59773279 AAAATAAAGTTAAAGAAGAAAGGGTTTCAACAGATTGAGGTAGG-AGGCGGTTGTG-ACAGTTAT
1 AAAATAAAGTTAAAGAAGAAAGGGTTTCAACAGATTGAGGT-GGAAGGCGACTGTGCACAGTTAT
* *
59773342 GAAGAGGATGCACAT
65 CAAGAGGACGCACAT
**
59773357 AAAATAAAGTTAAAGAAGATGGGGTTTCAACAGATTGAGGTGGAAGGCGACTGTGCCACAGTTAT
1 AAAATAAAGTTAAAGAAGAAAGGGTTTCAACAGATTGAGGTGGAAGGCGACTGTG-CACAGTTAT
59773422 CAAGAGGACGCACAT
65 CAAGAGGACGCACAT
59773437 CATGTAAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
77 2 0.03
78 48 0.68
80 21 0.30
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.21
Consensus pattern (79 bp):
AAAATAAAGTTAAAGAAGAAAGGGTTTCAACAGATTGAGGTGGAAGGCGACTGTGCACAGTTATC
AAGAGGACGCACAT
Found at i:59792008 original size:109 final size:111
Alignment explanation
Indices: 59791841--59792042 Score: 306
Period size: 109 Copynumber: 1.8 Consensus size: 111
59791831 TTTCAGAATA
*
59791841 AGATATAAATATACGAAAAAGTAAAAAAAAAATTTGGTGCTGGCCTGTCAATGTCCGGCACCCAG
1 AGATATAAATATACGAAAAAGT--AAAAAAAATTGGGTGCTGGCCTGTCAATGTCCGGCACCCAG
59791906 TACAATTTAAAAAAATA-TT-TTTTTTTTCTTTTTTCGTAGTAAGAGTC
64 TACAATTTAAAAAAA-ACTTCTTTTTTTTCTTTTTTCGTAGTAAGAGTC
*
59791953 AGATATAATTATACGAAAAA-T-AAAAAAATTGGGTGACTGGCCTGTCAAT-TGCCGGCACCCAG
1 AGATATAAATATACGAAAAAGTAAAAAAAATTGGGTG-CTGGCCTGTCAATGT-CCGGCACCCAG
59792015 TACAATTTAAAAAAAACTTCTTTTTTTT
64 TACAATTTAAAAAAAACTTCTTTTTTTT
59792043 ACGNNNNNNN
Statistics
Matches: 84, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
108 15 0.18
109 41 0.49
110 8 0.10
111 1 0.01
112 19 0.23
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (111 bp):
AGATATAAATATACGAAAAAGTAAAAAAAATTGGGTGCTGGCCTGTCAATGTCCGGCACCCAGTA
CAATTTAAAAAAAACTTCTTTTTTTTCTTTTTTCGTAGTAAGAGTC
Found at i:59798799 original size:2 final size:2
Alignment explanation
Indices: 59798792--59798844 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
59798782 AAAACTGTAA
* * *
59798792 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
59798834 AC AC AT AT AT A
1 AT AT AT AT AT A
59798845 CTGACCTGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:59800211 original size:42 final size:42
Alignment explanation
Indices: 59800165--59800255 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
59800155 TTAAGCATAA
59800165 ATAATTTAAA-AGTTTTTATTATATATTTAATTTCCATAAAAT
1 ATAATTTAAACA-TTTTTATTATATATTTAATTTCCATAAAAT
59800207 ATAATTTAAACATTTTTATTATATATTTAATTTCCATAAAAT
1 ATAATTTAAACATTTTTATTATATATTTAATTTCCATAAAAT
59800249 ATAATTT
1 ATAATTT
59800256 TCAATCCGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (42 bp):
ATAATTTAAACATTTTTATTATATATTTAATTTCCATAAAAT
Found at i:59802385 original size:52 final size:52
Alignment explanation
Indices: 59802329--59802467 Score: 217
Period size: 52 Copynumber: 2.7 Consensus size: 52
59802319 TTGTCTCTTA
** *
59802329 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATTTATTCTTATCTCG
1 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATGAATTCTTATCCCG
*
59802381 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATGAATTCTTATCCCT
1 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATGAATTCTTATCCCG
*
59802433 GTGAAGCTTGCATATGGTGTTTGTA-ATTCCATAGG
1 GTGAAGCATGCATATGGTGTTTG-ACATTCCATAGG
59802468 TGTGTTTTAT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 80 0.99
53 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (52 bp):
GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATGAATTCTTATCCCG
Found at i:59808757 original size:50 final size:51
Alignment explanation
Indices: 59808631--59808765 Score: 200
Period size: 51 Copynumber: 2.7 Consensus size: 51
59808621 TGTCTGCGAA
* * * * *
59808631 CACGTGTGCAGTACTAAGTGCAGGCTACTATGTGAACCGGAAGGCCTTGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGAACCGGAAAGCCTTGAT
*
59808682 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTGAACCGGAAAG-CTTGAT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGAACCGGAAAGCCTTGAT
*
59808732 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTG
59808766 TATCGAATGA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 37 0.48
51 40 0.52
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGAACCGGAAAGCCTTGAT
Found at i:59813450 original size:27 final size:26
Alignment explanation
Indices: 59813414--59813464 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
59813404 GAATATAAAG
*
59813414 GGGGTTGGTAATTGCTGATTTCCCCAA
1 GGGGTTGGTAAGTGCTGA-TTCCCCAA
59813441 GGGGTTGGTAAGTGCTGATTCCCC
1 GGGGTTGGTAAGTGCTGATTCCCC
59813465 GAATCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.16, C:0.20, G:0.33, T:0.31
Consensus pattern (26 bp):
GGGGTTGGTAAGTGCTGATTCCCCAA
Found at i:59813486 original size:33 final size:33
Alignment explanation
Indices: 59813443--59813608 Score: 188
Period size: 33 Copynumber: 4.7 Consensus size: 33
59813433 TTCCCCAAGG
*
59813443 GGTTGGTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
59813476 GGTTGCTAAGTGCTGATTCCACCGTATCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
59813518 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
59813551 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
59813584 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
59813609 GTAACAGATA
Statistics
Matches: 115, Mismatches: 8, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
33 70 0.61
34 10 0.09
36 2 0.02
37 2 0.02
38 2 0.02
39 2 0.02
41 6 0.05
42 21 0.18
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:59815654 original size:28 final size:28
Alignment explanation
Indices: 59815611--59815673 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
59815601 GTTCGAATGG
59815611 ATTGATAAATGTCAACTAAGTTTTGAGAA
1 ATTGA-AAATGTCAACTAAGTTTTGAGAA
59815640 ATTGAAAATGTCAACTAAGTTTTGAGAA
1 ATTGAAAATGTCAACTAAGTTTTGAGAA
59815668 ATTGAA
1 ATTGAA
59815674 GGCATTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.33
Consensus pattern (28 bp):
ATTGAAAATGTCAACTAAGTTTTGAGAA
Found at i:59816660 original size:26 final size:26
Alignment explanation
Indices: 59816580--59816660 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
59816570 TGCGAACACG
*
59816580 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCCACTA
* * * *
59816606 CGTGTA-T-CGATAAAT-AATGGTCAC-A
1 TGTGTAGTAC--TAAGTGCA-GGCCACTA
59816631 TGTGTAGTACTAAGTGCAGGCCACTA
1 TGTGTAGTACTAAGTGCAGGCCACTA
59816657 TGTG
1 TGTG
59816661 AACTGGAAGG
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
24 1 0.03
25 17 0.44
26 20 0.51
27 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGCAGGCCACTA
Found at i:59816744 original size:50 final size:50
Alignment explanation
Indices: 59816576--59816761 Score: 185
Period size: 51 Copynumber: 3.7 Consensus size: 50
59816566 TGTCTGCGAA
* * *** *
59816576 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGA-AAAGCTTGAT
* * * * * *
59816627 CACATGTGTAGTACTAAGTGCAGGCCACTATGTGAACTGGAAGGCCTT-ATT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAAAAG-CTTGA-T
* * *
59816678 CACGTGTGTAGTACTATGTGTAGGCAACTACGTGAACCGAAAAGCTTGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAAAAGCTTGAT
* *
59816728 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTG
59816762 TATCGGATGA
Statistics
Matches: 110, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 38 0.35
51 72 0.65
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAAAAGCTTGAT
Found at i:59821909 original size:25 final size:26
Alignment explanation
Indices: 59821881--59821946 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
59821871 ACCATTTCAC
59821881 TATTATATTACTATTATTTTATTG-T
1 TATTATATTACTATTATTTTATTGTT
* *
59821906 TATTGTATAACT-TATATTTTATTGTT
1 TATTATATTACTAT-TATTTTATTGTT
*
59821932 TATTTTATTACTATT
1 TATTATATTACTATT
59821947 TTAGAGACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.03
25 20 0.59
26 12 0.35
27 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (26 bp):
TATTATATTACTATTATTTTATTGTT
Found at i:59830004 original size:4 final size:4
Alignment explanation
Indices: 59829995--59830020 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
59829985 CATCAAAGCA
59829995 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
59830021 GAGCTGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:59831393 original size:21 final size:21
Alignment explanation
Indices: 59831363--59831402 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59831353 TGAGTTTGGG
59831363 ATTCGAGATTCAGGATTCTAA
1 ATTCGAGATTCAGGATTCTAA
* *
59831384 ATTCGGGATTCAGGGTTCT
1 ATTCGAGATTCAGGATTCT
59831403 GGAATAAAAA
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:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
ATTCGAGATTCAGGATTCTAA
Found at i:59831639 original size:15 final size:16
Alignment explanation
Indices: 59831621--59831650 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59831611 TAAAGGACTA
59831621 AAAAATAAA-AATTAC
1 AAAAATAAATAATTAC
59831636 AAAAATAAATAATTA
1 AAAAATAAATAATTA
59831651 ACCAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATAAATAATTAC
Done.