Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015365.1 Kokia drynarioides strain JFW-HI SEQ_130412, whole genome shotgun sequence
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: 483592
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 525 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5322 original size:2 final size:2
Alignment explanation
Indices: 5317--5349 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5307 TTTATTCTTT
5317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5350 TAATTAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11044 original size:2 final size:2
Alignment explanation
Indices: 11039--11071 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11029 TTTATTCTTT
11039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11072 TAATTAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18903 original size:16 final size:17
Alignment explanation
Indices: 18882--18914 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18872 AAAATTTCAC
*
18882 TTTTAATAA-TTTAAAA
1 TTTTAAAAATTTTAAAA
18898 TTTTAAAAATTTTAAAA
1 TTTTAAAAATTTTAAAA
18915 CATCTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAAAATTTTAAAA
Found at i:40598 original size:3 final size:3
Alignment explanation
Indices: 40590--40615 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40580 TTAAGAGTTT
40590 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
40616 TGGGATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:41018 original size:27 final size:24
Alignment explanation
Indices: 40988--41045 Score: 62
Period size: 27 Copynumber: 2.3 Consensus size: 24
40978 TTAAATAGGC
* *
40988 ATAAATTATTATTATTATTAAGTATAT
1 ATAAATTAATATAATTATT-A-TA-AT
*
41015 ATAAAATAATATAATTATTATAAT
1 ATAAATTAATATAATTATTATAAT
41039 ATAAATT
1 ATAAATT
41046 CCGATTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 8 0.30
25 2 0.07
26 1 0.04
27 16 0.59
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATAAATTAATATAATTATTATAAT
Found at i:41945 original size:17 final size:19
Alignment explanation
Indices: 41930--41970 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41920 GTGTATTTTT
41930 TGAGTTTTTATATTTTATA
1 TGAGTTTTTATATTTTATA
*
41949 TGATTTTTTATAAGTTTTATA
1 TGAGTTTTTAT-A-TTTTATA
41970 T
1 T
41971 AATTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (19 bp):
TGAGTTTTTATATTTTATA
Found at i:41958 original size:19 final size:21
Alignment explanation
Indices: 41934--41975 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41924 ATTTTTTGAG
*
41934 TTTTTAT-A-TTTTATATGAT
1 TTTTTATAAGTTTTATATAAT
41953 TTTTTATAAGTTTTATATAAT
1 TTTTTATAAGTTTTATATAAT
41974 TT
1 TT
41976 ATATATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTTATAAGTTTTATATAAT
Found at i:46233 original size:2 final size:2
Alignment explanation
Indices: 46226--46268 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
46216 CTAAACAATT
46226 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
46268 T
1 T
46269 TGTAATTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46920 original size:2 final size:2
Alignment explanation
Indices: 46913--46941 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46903 GTGTTTGAGT
46913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46942 TAAATTCTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60058 original size:20 final size:21
Alignment explanation
Indices: 60030--60069 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
60020 ACTTTATGTG
* *
60030 AAAAGCTAAATAAAT-AAATA
1 AAAAACTAAAGAAATGAAATA
60050 AAAAACTAAAGAAATGAAAT
1 AAAAACTAAAGAAATGAAAT
60070 TTGTGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAACTAAAGAAATGAAATA
Found at i:66563 original size:30 final size:28
Alignment explanation
Indices: 66529--66622 Score: 68
Period size: 30 Copynumber: 3.2 Consensus size: 28
66519 AAAATGCCAA
66529 TTTTGAGAGTTTCAAGGTCGAAAATGGGAT
1 TTTTGAGAG-TTCAAGGTC-AAAATGGGAT
*
66559 TTTTG-GAAGTTCAGAGGT-AAAATGGTAATT
1 TTTTGAG-AGTTCA-AGGTCAAAATGG-GA-T
**
66589 TTTTGA-AGGTTCGGGGTCAAAAATGGGAT
1 TTTTGAGA-GTTCAAGGTC-AAAATGGGAT
66618 TTTTG
1 TTTTG
66623 GATGTCCGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
28 7 0.13
29 16 0.31
30 22 0.42
31 7 0.13
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.36
Consensus pattern (28 bp):
TTTTGAGAGTTCAAGGTCAAAATGGGAT
Found at i:66571 original size:29 final size:28
Alignment explanation
Indices: 66543--67040 Score: 287
Period size: 29 Copynumber: 17.0 Consensus size: 28
66533 GAGAGTTTCA
66543 AGGTCGAAAATGGGATTTTTGGAAGTTCAG
1 AGGT-GAAAATGGGATTTTTGGAAGTTC-G
* *
66573 AGGT-AAAATGGTAATTTTTTGAAGGTTCG
1 AGGTGAAAATGG-GATTTTTGGAA-GTTCG
* * * *
66602 GGGTCAAAAATGGGATTTTTGGATGTCCG
1 AGGT-GAAAATGGGATTTTTGGAAGTTCG
* *
66631 AGG-GTAAAATGGTAATTTTTGGAAGATTTG
1 AGGTG-AAAATGG-GATTTTTGGAAG-TTCG
* *
66661 AGGTTAAAAATAGGA-TTTTGGAAGTTCG
1 AGG-TGAAAATGGGATTTTTGGAAGTTCG
** *
66689 AGG-GTAAAATGATAATTTTGGAAGGTTCG
1 AGGTG-AAAATGGGATTTTTGGAA-GTTCG
* * *
66718 GGGTTTAAAATGAGATTTTTGGAAGTTCG
1 AGG-TGAAAATGGGATTTTTGGAAGTTCG
* *
66747 -GGGGTAAAATGGTAATTTTTGGAAGGTTCG
1 AGGTG-AAAATGG-GATTTTTGGAA-GTTCG
* *
66777 AGGTTAAAAATGGCATTTTTGGAAGTTC-
1 AGG-TGAAAATGGGATTTTTGGAAGTTCG
* *
66805 ATGG-GTAAAATGGTAATTTTTTGAAGGTTCG
1 A-GGTG-AAAATGG-GATTTTTGGAA-GTTCG
*
66836 AGGTTAAAATGGGATTTTTGGAAGTTCG
1 AGGTGAAAATGGGATTTTTGGAAGTTCG
* *
66864 AGG-GTAGAATGGTAATTTTTGGAAGGTTCG
1 AGGTG-AAAATGG-GATTTTTGGAA-GTTCG
* * * *
66894 GGGTTAAAAATGAGATTTTTAGAAGTTCG
1 AGG-TGAAAATGGGATTTTTGGAAGTTCG
*
66923 AGG-GTAAAATGGTAATTTTTGGAAGGTTCG
1 AGGTG-AAAATGG-GATTTTTGGAA-GTTCG
* * *
66953 GGGTCAAAAATGAGATTTTTGGAAGTTCG
1 AGGT-GAAAATGGGATTTTTGGAAGTTCG
* * *
66982 AGGT-AAAAAGGTAATTTTTGGAAGGTTAG
1 AGGTGAAAATGG-GATTTTTGGAA-GTTCG
* * *
67011 GGGTTAAAAATGGGATTTTCTGAAAGTTCG
1 AGG-TGAAAATGGGATTTT-TGGAAGTTCG
67041 GGGGTAAAAT
Statistics
Matches: 362, Mismatches: 66, Indels: 80
0.71 0.13 0.16
Matches are distributed among these distances:
27 11 0.03
28 74 0.20
29 124 0.34
30 109 0.30
31 44 0.12
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (28 bp):
AGGTGAAAATGGGATTTTTGGAAGTTCG
Found at i:66691 original size:58 final size:58
Alignment explanation
Indices: 66549--67068 Score: 701
Period size: 59 Copynumber: 8.9 Consensus size: 58
66539 TTCAAGGTCG
* *
66549 AAAATGGGATTTTTGGAAGTTC-AGAGGTAAAATGGTAATTTTTTGAAGGTTCGGGGTCA
1 AAAAT-GGATTTTTGGAAGTTCGAG-GGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* * * * *
66608 AAAATGGGATTTTTGGATGTCCGAGGGTAAAATGGTAATTTTTGGAAGATTTGAGGTTA
1 AAAAT-GGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* *
66667 AAAATAGGA-TTTTGGAAGTTCGAGGGTAAAATGATAA-TTTTGGAAGGTTCGGGGTTT
1 AAAAT-GGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* *
66724 AAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTA
1 AAAATG-GATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* *
66783 AAAATGGCATTTTTGGAAGTTC-ATGGGTAAAATGGTAATTTTTTGAAGGTTCGAGGTT-
1 AAAATGG-ATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
*
66841 AAAATGGGATTTTTGGAAGTTCGAGGGTAGAATGGTAATTTTTGGAAGGTTCGGGGTTA
1 AAAAT-GGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* *
66900 AAAATGAGATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCA
1 AAAATG-GATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* *
66959 AAAATGAGATTTTTGGAAGTTCGA-GGTAAAAAGGTAATTTTTGGAAGGTTAGGGGTTA
1 AAAATG-GATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* * *
67017 AAAATGGGATTTTCTGAAAGTTCGGGGGTAAAATGGTAATTTTTGCAAGGTT
1 AAAAT-GGATTTT-TGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTT
67069 TAGGGACCTC
Statistics
Matches: 413, Mismatches: 35, Indels: 25
0.87 0.07 0.05
Matches are distributed among these distances:
56 1 0.00
57 23 0.06
58 145 0.35
59 218 0.53
60 26 0.06
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (58 bp):
AAAATGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
Found at i:66705 original size:117 final size:117
Alignment explanation
Indices: 66549--67068 Score: 712
Period size: 117 Copynumber: 4.4 Consensus size: 117
66539 TTCAAGGTCG
66549 AAAATGGGATTTTTGGAAGTTC-AGAGGTAAAATGGTAATTTTTTGAAGGTTCGGGGTCAAAAAT
1 AAAAT-GGATTTTTGGAAGTTCGAG-GGTAAAATGGTAATTTTTTGAAGGTTCGGGGTCAAAAAT
* * * * *
66613 GGGATTTTTGGATGTCCGAGGGTAAAATGGTAATTTTTGGAAGATTTGAGGTTA
64 GAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTA
* * **
66667 AAAATAGGA-TTTTGGAAGTTCGAGGGTAAAATGATAA-TTTTGGAAGGTTCGGGGTTTAAAATG
1 AAAAT-GGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTTGAAGGTTCGGGGTCAAAAATG
*
66730 AGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTA
65 AGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTA
* *
66783 AAAATGGCATTTTTGGAAGTTC-ATGGGTAAAATGGTAATTTTTTGAAGGTTCGAGGT-TAAAAT
1 AAAATGG-ATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTTGAAGGTTCGGGGTCAAAAAT
* * *
66846 GGGATTTTTGGAAGTTCGAGGGTAGAATGGTAATTTTTGGAAGGTTCGGGGTTA
64 GAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTA
* *
66900 AAAATGAGATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATG
1 AAAATG-GATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTTGAAGGTTCGGGGTCAAAAATG
* * *
66965 AGATTTTTGGAAGTTCGA-GGTAAAAAGGTAATTTTTGGAAGGTTAGGGGTTA
65 AGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTA
* *
67017 AAAATGGGATTTTCTGAAAGTTCGGGGGTAAAATGGTAA-TTTTTGCAAGGTT
1 AAAAT-GGATTTT-TGGAAGTTCGAGGGTAAAATGGTAATTTTTTG-AAGGTT
67069 TAGGGACCTC
Statistics
Matches: 361, Mismatches: 30, Indels: 22
0.87 0.07 0.05
Matches are distributed among these distances:
115 2 0.01
116 77 0.21
117 202 0.56
118 80 0.22
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (117 bp):
AAAATGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTTGAAGGTTCGGGGTCAAAAATGA
GATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTA
Found at i:68653 original size:17 final size:16
Alignment explanation
Indices: 68633--68709 Score: 82
Period size: 17 Copynumber: 4.6 Consensus size: 16
68623 AAATAAACTT
68633 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
*
68650 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
68667 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
68684 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
68701 TAAATTTAA
1 TAAATTTAA
68710 GCTGATTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 1 0.02
17 47 0.94
18 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:68706 original size:34 final size:34
Alignment explanation
Indices: 68633--68709 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
68623 AAATAAACTT
* * * *
68633 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
* *
68667 CAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
68701 TAAATTTAA
1 TAAATTTAA
68710 GCTGATTGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
Found at i:68952 original size:19 final size:21
Alignment explanation
Indices: 68905--68950 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
68895 TTTCTCTCAA
68905 CAAAAATTACAAAATAAATTT
1 CAAAAATTACAAAATAAATTT
*
68926 CAAAAATTA-AAAATAATTTT
1 CAAAAATTACAAAATAAATTT
*
68946 TAAAA
1 CAAAA
68951 TTCACAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
CAAAAATTACAAAATAAATTT
Found at i:69003 original size:26 final size:24
Alignment explanation
Indices: 68957--69007 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
68947 AAAATTCACA
*
68957 ATATTTATAAAAAAATCAAAATTT
1 ATATTTATAAAAAAATAAAAATTT
*
68981 ATATTTTTAAAAAATTATAAAAATTT
1 ATATTTATAAAAAA--ATAAAAATTT
69007 A
1 A
69008 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
26 10 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATTTATAAAAAAATAAAAATTT
Found at i:75554 original size:17 final size:17
Alignment explanation
Indices: 75529--75567 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
75519 TTAAGTCGAT
* *
75529 ATAATATATTATTTATC
1 ATAAAATATTATCTATC
*
75546 ATAAAATATTATCTATT
1 ATAAAATATTATCTATC
75563 ATAAA
1 ATAAA
75568 CCAAATTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAAATATTATCTATC
Found at i:78162 original size:6 final size:6
Alignment explanation
Indices: 78151--78176 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
78141 TTGCAGCGTA
78151 CATGAG CATGAG CATGAG CATGAG CA
1 CATGAG CATGAG CATGAG CATGAG CA
78177 GTGCTATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (6 bp):
CATGAG
Found at i:83216 original size:18 final size:19
Alignment explanation
Indices: 83178--83224 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
83168 ATTGGCAATT
* *
83178 AATAATTTTTATTTTTTAA
1 AATAAATTTTATTTTTAAA
*
83197 AATAAATTTTATTTTAAAAA
1 AATAAATTTTATTTT-TAAA
83217 AATAAATT
1 AATAAATT
83225 ATAATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAAATTTTATTTTTAAA
Found at i:83541 original size:16 final size:17
Alignment explanation
Indices: 83510--83544 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
83500 TTCTTAAAAT
*
83510 AATAAAAAACTTTTTAA
1 AATAAAAAACTATTTAA
83527 AATAAAAAA-TATTTAA
1 AATAAAAAACTATTTAA
83543 AA
1 AA
83545 GTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAAAAACTATTTAA
Found at i:83955 original size:12 final size:13
Alignment explanation
Indices: 83926--83956 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
83916 ATAAATTTTT
83926 TTTTTCAAATTTA
1 TTTTTCAAATTTA
*
83939 TTTTTCGAATTTA
1 TTTTTCAAATTTA
83952 TTTTT
1 TTTTT
83957 TTGTCTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTTTCAAATTTA
Found at i:85987 original size:26 final size:27
Alignment explanation
Indices: 85935--85991 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
85925 GTATTGTTTA
* * **
85935 TTTAGTTTTTAAGAGACTCAATTTTTT
1 TTTAATTTTTAAGAGACCCAAAATTTT
85962 TTTAATTTTTAAG-GACCCAAAATTTT
1 TTTAATTTTTAAGAGACCCAAAATTTT
85988 TTTA
1 TTTA
85992 CCAATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.53
Consensus pattern (27 bp):
TTTAATTTTTAAGAGACCCAAAATTTT
Found at i:87378 original size:96 final size:96
Alignment explanation
Indices: 87200--87380 Score: 208
Period size: 96 Copynumber: 1.9 Consensus size: 96
87190 AGGATATCCA
* ** * *
87200 ATTATCTCGATTTGTAGAAAGGTTGCACCTAGTAAGTTAATACGCAATATTTCAGAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAATATTTCAGAATAGAAGAT
* *
87265 AAGGAAACATTGTCTTGATTAAGGGTATTCG
66 AAGAAAACATTGCCTTGATTAAGGGTATTCG
* *
87296 ATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGATGCAA-ATTTTC-GAAACTAGAA
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAATA-TTTCAG-AA-TAGAA
*
87359 -ATAA-AATAATATTGCCTTGATT
63 GATAAGAA-AACATTGCCTTGATT
87381 TTAAAGTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
95 3 0.04
96 64 0.90
97 4 0.06
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAATATTTCAGAATAGAAGAT
AAGAAAACATTGCCTTGATTAAGGGTATTCG
Found at i:87739 original size:59 final size:59
Alignment explanation
Indices: 87675--88294 Score: 519
Period size: 59 Copynumber: 10.7 Consensus size: 59
87665 GTAAAAGGGT
* * * *
87675 AATTTTT-GAGAGTTTCGAAGTTGAAAATGGAGATTTTGGAAGTTTGAGGGCAAAAATGG
1 AATTTTTGGA-AGTTTTGAGGTTAAAAATGGAGATTTTGGAAGTTTGAGGGTAAAAATGG
* * *
87734 AATTTTT----G----G-GGTTAAAAATGGCA-TTTTTGGAAGTTCGGGGGTAAAAATGG
1 AATTTTTGGAAGTTTTGAGGTTAAAAATGG-AGATTTTGGAAGTTTGAGGGTAAAAATGG
* *
87784 AATTTTTGGAAGTTTTGAGGTCAAAAAT-GAGATTTTTAGAAGTTT-AGGGGTAAAAATGG
1 AATTTTTGGAAGTTTTGAGGTTAAAAATGGAGA-TTTTGGAAGTTTGA-GGGTAAAAATGG
* * * *
87843 ATTTTTTGGAAGTTTCGAGGTTAAAAATGG-GATTTTTGGAAGTTCGAGGATAAAAATGG
1 AATTTTTGGAAGTTTTGAGGTTAAAAATGGAGA-TTTTGGAAGTTTGAGGGTAAAAATGG
* * *
87902 AATTTTTGGAAGTTTTTG-GGTCAAAAATGGCA-TTTTTGTAAGTTT-AGGGGTAAAAATGG
1 AATTTTTGGAAG-TTTTGAGGTTAAAAATGG-AGATTTTGGAAGTTTGA-GGGTAAAAATGG
* * * * *
87961 AATTTTTGGAAGTTTTGAGGTCAAGAAT-GAGATTTTTGGAAGTTCG-GTGATAAAAATGA
1 AATTTTTGGAAGTTTTGAGGTTAAAAATGGAGA-TTTTGGAAGTTTGAG-GGTAAAAATGG
* * * *
88020 AATTTTTGGAAG-TTTCAGGGTAAAAAAT-GACATTTTTGGAAGTTTGGGGGTAAAAATGG
1 AATTTTTGGAAGTTTTGA-GGTTAAAAATGGAGA-TTTTGGAAGTTTGAGGGTAAAAATGG
* * * *
88079 AATTTTTGGAAGTTTCGAGGTCAAAAGTGG-GAATTTTGGAAGTTT-AGGGGTAAAAATAG
1 AATTTTTGGAAGTTTTGAGGTTAAAAATGGAG-ATTTTGGAAGTTTGA-GGGTAAAAATGG
* * * * * *
88138 AATTTTTTGAAGTTTTGGGGTTAAAAATGGCA-TTTTTGGAAGTTTGGGGGTTAAAATGA
1 AATTTTTGGAAGTTTTGAGGTTAAAAATGG-AGATTTTGGAAGTTTGAGGGTAAAAATGG
88197 AATTTTTGGAAGTTTTGAGGTTAAAAATGGA-ATATTTGGAAGTTTCGA-GGTCAAAAATGG
1 AATTTTTGGAAGTTTTGAGGTTAAAAATGGAGAT-TTTGGAAGTTT-GAGGGT-AAAAATGG
* *
88257 -A--TTTGGAAG-TTCGAGGGTAAAAATGGA-ATTTTTGGAAG
1 AATTTTTGGAAGTTTTGAGGTTAAAAATGGAGA-TTTTGGAAG
88295 GTTTAAGGAC
Statistics
Matches: 462, Mismatches: 62, Indels: 77
0.77 0.10 0.13
Matches are distributed among these distances:
50 40 0.09
51 2 0.00
54 1 0.00
55 1 0.00
56 25 0.05
57 11 0.02
58 16 0.03
59 347 0.75
60 19 0.04
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (59 bp):
AATTTTTGGAAGTTTTGAGGTTAAAAATGGAGATTTTGGAAGTTTGAGGGTAAAAATGG
Found at i:87749 original size:109 final size:110
Alignment explanation
Indices: 87628--88087 Score: 330
Period size: 118 Copynumber: 4.0 Consensus size: 110
87618 TTTGGGAAAA
87628 TTTGGGGTTTAAAAATGGAATTTTTAGACA-TTCGGGGGT-AAAAGGGTAATTTTT-GAGAGTTT
1 TTTGGGGTTTAAAAATGGAATTTTTAGA-AGTTCGGGGGTAAAAAGGG-AATTTTTGGA-AGTTT
** *
87690 CGAAGTTGAAAATGGAGA-TTTTGGAAGTTT-GAGGGCAAAAATGGAATT
63 CGAAGTCAAAAAT-GAGATTTTTAGAAGTTTAG-GGGCAAAAATGGAATT
* * * *
87738 TTTGGGG-TTAAAAATGGCATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGA
1 TTTGGGGTTTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAAGGGAATTTTTGGAAGTTTCGA
* * *
87802 GGTCAAAAATGAGATTTTTAGAAGTTTAGGGGTAAAAATGGATTT
66 AGTCAAAAATGAGATTTTTAGAAGTTTAGGGGCAAAAATGGAATT
* * * * * *
87847 TTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGATAAAAATGGAATTTTTGGA
1 TTT-G--G----G-GTTTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAAGGGAATTTTTGGA
* * *
87912 AGTTTTTG-GGTCAAAAATG-GCATTTTT-GTAAGTTTAGGGGTAAAAATGGAATT
58 AG-TTTCGAAGTCAAAAATGAG-ATTTTTAG-AAGTTTAGGGGCAAAAATGGAATT
* * * * * *
87965 TTTGGAAGTTTTGAGGTCAAGAAT-GAGATTTTTGGAAGTTCGGTGATAAAAATGAAATTTTTGG
1 TTTGG--GGTTT-A----AA-AATGGA-ATTTTTAGAAGTTCGGGGGTAAAAAGGGAATTTTTGG
* * * * * *
88029 AAGTTTC-AGGGTAAAAAATGACATTTTTGGAAGTTTGGGGGTAAAAATGGAATT
57 AAGTTTCGA-AGTCAAAAATGAGATTTTTAGAAGTTTAGGGGCAAAAATGGAATT
88083 TTTGG
1 TTTGG
88088 AAGTTTCGAG
Statistics
Matches: 296, Mismatches: 26, Indels: 48
0.80 0.07 0.13
Matches are distributed among these distances:
108 5 0.02
109 76 0.26
110 17 0.06
112 3 0.01
113 2 0.01
115 1 0.00
116 1 0.00
117 10 0.03
118 175 0.59
119 6 0.02
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (110 bp):
TTTGGGGTTTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAAGGGAATTTTTGGAAGTTTCGA
AGTCAAAAATGAGATTTTTAGAAGTTTAGGGGCAAAAATGGAATT
Found at i:87901 original size:118 final size:118
Alignment explanation
Indices: 87743--88299 Score: 668
Period size: 118 Copynumber: 4.7 Consensus size: 118
87733 GAATTTTTGG
* * *
87743 GGTTAAAAATGGCATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAA
1 GGTTAAAAATGGGATTTTTGGAAGTTCGAGGATAAAAATGGAATTTTTGGAAGTTTTGAGGTCAA
* *
87808 AAATGAG-ATTTTTAGAAGTTTAGGGGTAAAAATGGATTTTTTGGAAGTTTCGA
66 AAATG-GCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGA
87861 GGTTAAAAATGGGATTTTTGGAAGTTCGAGGATAAAAATGGAATTTTTGGAAGTTTTTG-GGTCA
1 GGTTAAAAATGGGATTTTTGGAAGTTCGAGGATAAAAATGGAATTTTTGGAAG-TTTTGAGGTCA
* *
87925 AAAATGGCATTTTTGTAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGA
65 AAAATGGCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGA
* * * * * *
87979 GGTCAAGAATGAGATTTTTGGAAGTTCG-GTGATAAAAATGAAATTTTTGGAAG-TTTCAGGGTA
1 GGTTAAAAATGGGATTTTTGGAAGTTCGAG-GATAAAAATGGAATTTTTGGAAGTTTTGA-GGTC
* *
88042 AAAAATGACATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCGA
64 AAAAATGGCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGA
* * * * * * * * *
88097 GGTCAAAAGTGGGAATTTTGGAAGTT-TAGGGGTAAAAATAGAATTTTTTGAAGTTTTGGGGTTA
1 GGTTAAAAATGGGATTTTTGGAAGTTCGA-GGATAAAAATGGAATTTTTGGAAGTTTTGAGGTCA
* * * *
88161 AAAATGGCATTTTTGGAAGTTTGGGGGTTAAAATGAAATTTTTGGAAGTTTTGA
65 AAAATGGCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGA
* * *
88215 GGTTAAAAATGGAATATTTGGAAGTTTCGAGG-TCAAAAATGG-A--TTTGGAAG-TTCGAGGGT
1 GGTTAAAAATGGGATTTTTGGAAG-TTCGAGGAT-AAAAATGGAATTTTTGGAAGTTTTGA-GGT
*
88275 -AAAAATGGAATTTTTGGAAGGTTTA
63 CAAAAATGGCATTTTTGGAA-GTTTA
88300 AGGACCTCCA
Statistics
Matches: 381, Mismatches: 45, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
115 21 0.06
116 17 0.04
117 2 0.01
118 320 0.84
119 20 0.05
120 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (118 bp):
GGTTAAAAATGGGATTTTTGGAAGTTCGAGGATAAAAATGGAATTTTTGGAAGTTTTGAGGTCAA
AAATGGCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGA
Found at i:87992 original size:177 final size:176
Alignment explanation
Indices: 87731--88299 Score: 699
Period size: 177 Copynumber: 3.2 Consensus size: 176
87721 AGGGCAAAAA
* **
87731 TGGAA-TTTTTGGGGTTAAAAATGGCATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAA
1 TGGAAGTTTTT-GGGTCAAAAATGGCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAA
* * *
87795 GTTTTGAGGTCAAAAATGAGATTTTTAGAAGTTTAGGGGTAAAAATGGATTTTTTGGAAGTTTCG
65 GTTTTGAGGTCAAAAATGAGATTTTTGGAAGTTTAGGGGTAAAAATGAAATTTTTGGAAGTTTCG
*
87860 AGGTTAAAAATGGGATTTTTGGAAGTTCGAGGATAAAAATGGAATTTT
130 AGGTTAAAAATGGAATTTTTGGAAGTTCGAGG-TAAAAATGGAATTTT
*
87908 TGGAAGTTTTTGGGTCAAAAATGGCATTTTTGTAAGTTTAGGGGTAAAAATGGAATTTTTGGAAG
1 TGGAAGTTTTTGGGTCAAAAATGGCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAG
* * *
87973 TTTTGAGGTCAAGAATGAGATTTTTGGAAG-TTCGGTGATAAAAATGAAATTTTTGGAAGTTTC-
66 TTTTGAGGTCAAAAATGAGATTTTTGGAAGTTTAGG-GGTAAAAATGAAATTTTTGGAAGTTTCG
* * *
88036 AGGGTAAAAAAT-GACATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTT
130 A-GGTTAAAAATGGA-ATTTTTGGAAG-TTCGAGGTAAAAATGGAATTTT
* * * * * *
88085 TGGAAG-TTTCGAGGTCAAAAGTGGGAATTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTTGAA
1 TGGAAGTTTTTG-GGTCAAAAATGGCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAA
* * * * *
88149 GTTTTGGGGTTAAAAATG-GCATTTTTGGAAGTTTGGGGGTTAAAATGAAATTTTTGGAAGTTTT
65 GTTTTGAGGTCAAAAATGAG-ATTTTTGGAAGTTTAGGGGTAAAAATGAAATTTTTGGAAGTTTC
*
88213 GAGGTTAAAAATGGAATATTTGGAAGTTTCGAGGTCAAAAATGG-A--TT
129 GAGGTTAAAAATGGAATTTTTGGAAG-TTCGAGGT-AAAAATGGAATTTT
*** *
88260 TGGAAGTTCGAGGGT-AAAAATGGAATTTTTGGAAGGTTTA
1 TGGAAGTTTTTGGGTCAAAAATGGCATTTTTGGAA-GTTTA
88300 AGGACCTCCA
Statistics
Matches: 341, Mismatches: 38, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
174 16 0.05
175 16 0.05
176 13 0.04
177 271 0.79
178 25 0.07
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.36
Consensus pattern (176 bp):
TGGAAGTTTTTGGGTCAAAAATGGCATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAG
TTTTGAGGTCAAAAATGAGATTTTTGGAAGTTTAGGGGTAAAAATGAAATTTTTGGAAGTTTCGA
GGTTAAAAATGGAATTTTTGGAAGTTCGAGGTAAAAATGGAATTTT
Found at i:88279 original size:27 final size:26
Alignment explanation
Indices: 87759--88283 Score: 182
Period size: 30 Copynumber: 18.0 Consensus size: 26
87749 AAATGGCATT
*
87759 TTTGGAAG-TTCGGGGGTAAAAATGGAA
1 TTTGGAAGTTTC-GAGGTAAAAATGG-A
*
87786 TTTTTGGAAGTTTTGAGGTCAAAAATGAGA
1 --TTTGGAAGTTTCGAGGT-AAAAATG-GA
* * *
87816 TTTTTAGAAGTTTAGGGGTAAAAATGGA
1 --TTTGGAAGTTTCGAGGTAAAAATGGA
87844 TTTTTTGGAAGTTTCGAGGTTAAAAATGGGA
1 ---TTTGGAAGTTTCGAGG-TAAAAAT-GGA
87875 TTTTTGGAAG-TTCGAGGATAAAAATGGAA
1 --TTTGGAAGTTTCGAGG-TAAAAATGG-A
*
87904 TTTTTGGAAGTTTTTG-GGTCAAAAATGGCA
1 --TTTGGAAG-TTTCGAGGT-AAAAATGG-A
* * *
87934 TTTTTGTAAGTTTAGGGGTAAAAATGGAA
1 --TTTGGAAGTTTCGAGGTAAAAATGG-A
* *
87963 TTTTTGGAAGTTTTGAGGTCAAGAATGAGA
1 --TTTGGAAGTTTCGAGGT-AAAAATG-GA
*
87993 TTTTTGGAAG-TTCG-GTGATAAAAATGAAA
1 --TTTGGAAGTTTCGAG-G-TAAAAATG-GA
*
88022 TTTTTGGAAGTTTC-AGGGTAAAAAATGACA
1 --TTTGGAAGTTTCGA-GGT-AAAAATG-GA
* *
88052 TTTTTGGAAGTTTGGGGGTAAAAATGGAA
1 --TTTGGAAGTTTCGAGGTAAAAATGG-A
*
88081 TTTTTGGAAGTTTCGAGGTCAAAAGTGGGAA
1 --TTTGGAAGTTTCGAGGT-AAAAAT-GG-A
* * *
88112 TTTTGGAAGTTTAGGGGTAAAAATAGAA
1 -TTTGGAAGTTTCGAGGTAAAAAT-GGA
* * *
88140 TTTTTTGAAGTTTTGGGGTTAAAAATGGCA
1 --TTTGGAAGTTTCGAGG-TAAAAATGG-A
* * * *
88170 TTTTTGGAAGTTTGGGGGTTAAAATGAAA
1 --TTTGGAAGTTTCGAGGTAAAAATG-GA
*
88199 TTTTTGGAAGTTTTGAGGTTAAAAATGGAATA
1 --TTTGGAAGTTTCGAGG-TAAAAATGG---A
88231 TTTGGAAGTTTCGAGGTCAAAAATGGA
1 TTTGGAAGTTTCGAGGT-AAAAATGGA
88258 TTTGGAAG-TTCGAGGGTAAAAATGGA
1 TTTGGAAGTTTCGA-GGTAAAAATGGA
88284 ATTTTTGGAA
Statistics
Matches: 418, Mismatches: 45, Indels: 69
0.79 0.08 0.13
Matches are distributed among these distances:
26 14 0.03
27 12 0.03
28 6 0.01
29 184 0.44
30 188 0.45
31 13 0.03
32 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (26 bp):
TTTGGAAGTTTCGAGGTAAAAATGGA
Found at i:89363 original size:9 final size:9
Alignment explanation
Indices: 89335--89394 Score: 57
Period size: 9 Copynumber: 6.0 Consensus size: 9
89325 AAAACTTATT
89335 TATTATTAA
1 TATTATTAA
89344 TGATATCATTAA
1 T-AT-T-ATTAA
89356 TATTATTAA
1 TATTATTAA
*
89365 AATTATTAAAA
1 TATTATT--AA
89376 TAATTATTAA
1 T-ATTATTAA
89386 TATTATTAA
1 TATTATTAA
89395 GAATTATTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 20 0.47
10 6 0.14
11 5 0.12
12 12 0.28
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (9 bp):
TATTATTAA
Found at i:90106 original size:17 final size:17
Alignment explanation
Indices: 90068--90136 Score: 93
Period size: 17 Copynumber: 4.0 Consensus size: 17
90058 TTTGAACTTT
*
90068 TTTAATTTTAAAATTAAA
1 TTTAAATTTAAAATT-AA
*
90086 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATTAA
*
90103 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATTAA
*
90120 TCTAAATTTAAAATTAA
1 TTTAAATTTAAAATTAA
90137 AAATGGGTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
17 32 0.71
18 13 0.29
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATTAA
Found at i:90112 original size:6 final size:6
Alignment explanation
Indices: 90068--90137 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
90058 TTTGAACTTT
* *
90068 TTTAAT TTTAAA ATTAAA TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
* * *
90115 -ATAAA TCTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
90138 AATGGGTCAG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 44 0.83
7 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:90127 original size:23 final size:23
Alignment explanation
Indices: 90075--90138 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
90065 TTTTTTAATT
* *
90075 TTAAAATTAAATTTAAATTTAAGA
1 TTAAATTTAAATTTAAA-ATAAGA
90099 TT-AATTTAAATTTAAAATAA-A
1 TTAAATTTAAATTTAAAATAAGA
*
90120 TCTAAATTTAAAATTAAAA
1 T-TAAATTTAAATTTAAAA
90139 ATGGGTCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 4 0.11
23 27 0.77
24 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TTAAATTTAAATTTAAAATAAGA
Found at i:101265 original size:21 final size:20
Alignment explanation
Indices: 101216--101267 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
101206 AAGATTAAGC
*
101216 TTAATT-AAATAAATTAAGA
1 TTAATTAAAATAAATCAAGA
* * *
101235 TTGATAAAAACTAAATCATGA
1 TTAATTAAAA-TAAATCAAGA
101256 TTAATTAAAATA
1 TTAATTAAAATA
101268 TAAATAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 4 0.16
20 5 0.20
21 16 0.64
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (20 bp):
TTAATTAAAATAAATCAAGA
Found at i:107810 original size:32 final size:34
Alignment explanation
Indices: 107774--107852 Score: 117
Period size: 32 Copynumber: 2.4 Consensus size: 34
107764 AAATATAACA
107774 ATATTTGAAATATTTCACATATAAAA-A-TAATG
1 ATATTTGAAATATTTCACATATAAAACAGTAATG
* *
107806 ATATTTAAAATATTTTACATATAAAACTAGTAATG
1 ATATTTGAAATATTTCACATATAAAAC-AGTAATG
107841 ATATTTGAAATA
1 ATATTTGAAATA
107853 ATTATTTGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
32 24 0.59
34 1 0.02
35 16 0.39
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.39
Consensus pattern (34 bp):
ATATTTGAAATATTTCACATATAAAACAGTAATG
Found at i:116279 original size:13 final size:13
Alignment explanation
Indices: 116261--116286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
116251 AAGAGAAGTT
116261 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
116274 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
116287 GTAATGGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:122274 original size:2 final size:2
Alignment explanation
Indices: 122267--122298 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
122257 TTTTTCATGG
122267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
122299 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:129565 original size:14 final size:15
Alignment explanation
Indices: 129536--129567 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
129526 TTTCAATTGG
*
129536 AATAATTTTTCAAAA
1 AATAATTTTACAAAA
129551 AATAATTTTACAAAA
1 AATAATTTTACAAAA
129566 AA
1 AA
129568 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATTTTACAAAA
Found at i:135794 original size:24 final size:24
Alignment explanation
Indices: 135765--135815 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
135755 AGAAATAATC
135765 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAATTCTGTTTATTTG
*
135789 TTTCAATTAAATTTTGTTTATTTG
1 TTTCAATTAAATTCTGTTTATTTG
135813 TTT
1 TTT
135816 GAGTAAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.63
Consensus pattern (24 bp):
TTTCAATTAAATTCTGTTTATTTG
Found at i:136040 original size:23 final size:23
Alignment explanation
Indices: 136010--136060 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
136000 TCTTCATTTT
136010 TTTGCCATTATAGTAAAACTATC
1 TTTGCCATTATAGTAAAACTATC
136033 TTTGCCATTATAGTAAAACTATC
1 TTTGCCATTATAGTAAAACTATC
136056 TTTGC
1 TTTGC
136061 TTGTGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (23 bp):
TTTGCCATTATAGTAAAACTATC
Found at i:136237 original size:19 final size:22
Alignment explanation
Indices: 136195--136239 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
136185 TTATAAAATA
*
136195 AATTCATATATAATATTATTTT
1 AATTCATATATAATATTATGTT
136217 AATT-ATATA-AATATTA-GTT
1 AATTCATATATAATATTATGTT
136236 AATT
1 AATT
136240 TTTTGGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 7 0.32
21 5 0.23
22 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTCATATATAATATTATGTT
Found at i:136485 original size:21 final size:21
Alignment explanation
Indices: 136443--136485 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
136433 ATTAAAAAAA
* *
136443 ACATTTTTATTATGTTTTTGT
1 ACATTTTTATTATATTTGTGT
136464 ACATTATTTATTA-ATTTGTGT
1 ACATT-TTTATTATATTTGTGT
136485 A
1 A
136486 AACACTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (21 bp):
ACATTTTTATTATATTTGTGT
Found at i:141247 original size:18 final size:19
Alignment explanation
Indices: 141224--141286 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 19
141214 TTTGTCAAAT
141224 ATATATAAAGAT-TAAAAA
1 ATATATAAAGATATAAAAA
*
141242 ATATATAAATATATAAAAA
1 ATATATAAAGATATAAAAA
** *
141261 AT-CCTAAAGATCTAAAAA
1 ATATATAAAGATATAAAAA
141279 A-ATATAAA
1 ATATATAAA
141287 AAAAAAACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
18 28 0.78
19 8 0.22
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (19 bp):
ATATATAAAGATATAAAAA
Found at i:146019 original size:25 final size:24
Alignment explanation
Indices: 145972--146022 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
145962 ATATCATATT
145972 TAAAATAAAAACATTAAATTTAAA
1 TAAAATAAAAACATTAAATTTAAA
*
145996 TAAAATAGAAA-ATTATAATATTAAA
1 TAAAATAAAAACATTA-AAT-TTAAA
146021 TA
1 TA
146023 TTTAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 13 0.54
25 7 0.29
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
TAAAATAAAAACATTAAATTTAAA
Found at i:155552 original size:17 final size:19
Alignment explanation
Indices: 155532--155570 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
155522 TTAACTTTGG
*
155532 TTTTTAT-TTAAAAATA-T
1 TTTTTATGTCAAAAATACT
155549 TTTTTATGTCAAAAATACT
1 TTTTTATGTCAAAAATACT
155568 TTT
1 TTT
155571 AAAAAGTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 8 0.42
19 4 0.21
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTTATGTCAAAAATACT
Found at i:163128 original size:14 final size:14
Alignment explanation
Indices: 163097--163125 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
163087 TTAAACTAAG
163097 AATAAAGATAAAAT
1 AATAAAGATAAAAT
163111 AATAAA-ATAAAAT
1 AATAAAGATAAAAT
163124 AA
1 AA
163126 ATACTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAAGATAAAAT
Found at i:165777 original size:20 final size:19
Alignment explanation
Indices: 165745--165782 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
165735 GAAAGGAAAC
*
165745 AATGTCATCAATGTACAGA
1 AATGTCATAAATGTACAGA
165764 AATGATCATAAATGTACAG
1 AATG-TCATAAATGTACAG
165783 TGCGATGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (19 bp):
AATGTCATAAATGTACAGA
Found at i:167858 original size:36 final size:36
Alignment explanation
Indices: 167818--167890 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
167808 TAACCAAATT
167818 TTAGTCAAGATCGTGCACTCAAATGACAAATGACTA
1 TTAGTCAAGATCGTGCACTCAAATGACAAATGACTA
167854 TTAGTCAAGATCGTGCACTCAAATGACAAATGACTA
1 TTAGTCAAGATCGTGCACTCAAATGACAAATGACTA
167890 T
1 T
167891 GTTACCATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (36 bp):
TTAGTCAAGATCGTGCACTCAAATGACAAATGACTA
Found at i:175136 original size:25 final size:24
Alignment explanation
Indices: 175050--175128 Score: 113
Period size: 25 Copynumber: 3.2 Consensus size: 24
175040 CGAAATACTT
* *
175050 AACAAAAGCGCATAAGTGCTAGGGA
1 AACAGAAGCACATAAGTGCT-GGGA
*
175075 AACAGAAACACATAAGTGCTGGAGA
1 AACAGAAGCACATAAGTGCTGG-GA
175100 AACAGAAGCACATAAGTGCTGGGA
1 AACAGAAGCACATAAGTGCTGGGA
175124 AACAG
1 AACAG
175129 TAGGCACACA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
24 9 0.18
25 40 0.82
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (24 bp):
AACAGAAGCACATAAGTGCTGGGA
Found at i:178329 original size:23 final size:23
Alignment explanation
Indices: 178288--178337 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
178278 TTGAACTGAA
*
178288 ATTTTTTTATTTTAAAATATTTT
1 ATTTTTTTATTTTAAAATAATTT
*
178311 ATTTTTTATATTTT-TAATAATTT
1 ATTTTTT-TATTTTAAAATAATTT
178334 ATTT
1 ATTT
178338 AATCGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTTTTATTTTAAAATAATTT
Found at i:178498 original size:45 final size:47
Alignment explanation
Indices: 178434--178534 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 47
178424 GAGCTTCCAC
178434 TTCTACCTAACAACTTCCTAAAATTATA-TTAGTT-G-AACTTGCCCT
1 TTCTACCTAACAACTTCCTAAAATT-TAGTTAGTTGGTAACTTGCCCT
*
178479 TTCTACTTAACAACTTCCTAAAATTTAGTTAGTTGGTTCAACTTGCCCT
1 TTCTACCTAACAACTTCCTAAAATTTAGTTAGTTGG-T-AACTTGCCCT
178528 TTCTACC
1 TTCTACC
178535 GGTCTTCCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
44 2 0.04
45 30 0.61
46 1 0.02
49 16 0.33
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.40
Consensus pattern (47 bp):
TTCTACCTAACAACTTCCTAAAATTTAGTTAGTTGGTAACTTGCCCT
Found at i:189560 original size:3 final size:3
Alignment explanation
Indices: 189552--189591 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
189542 AATTACTGGT
189552 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
189592 AAAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:189608 original size:13 final size:13
Alignment explanation
Indices: 189590--189617 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
189580 TATTATTATT
189590 ATAAAAAATAAAA
1 ATAAAAAATAAAA
189603 ATAAAAAATAAAA
1 ATAAAAAATAAAA
189616 AT
1 AT
189618 TTTCTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:204094 original size:18 final size:16
Alignment explanation
Indices: 204071--204112 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
204061 TTTTATTATA
204071 TTTATCAGTATAATCTTT
1 TTTATCAGTA-AATC-TT
*
204089 TTTATCA-TAATTCTT
1 TTTATCAGTAAATCTT
204104 TTTATCAGT
1 TTTATCAGT
204113 GTAAACCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 4 0.18
17 2 0.09
18 7 0.32
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTATCAGTAAATCTT
Found at i:210150 original size:15 final size:17
Alignment explanation
Indices: 210132--210164 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
210122 TTATAATTTT
210132 AAATAT-TAT-ATTAAA
1 AAATATATATGATTAAA
210147 AAATATATATGATTAAA
1 AAATATATATGATTAAA
210164 A
1 A
210165 TTTATAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATATATATGATTAAA
Found at i:223658 original size:52 final size:48
Alignment explanation
Indices: 223596--223695 Score: 164
Period size: 52 Copynumber: 2.0 Consensus size: 48
223586 CCTTAATGCT
223596 ACCTACATCTTTTATTTCTTGAATATGAGAAAGATAGTTGACAGTCTATTCA
1 ACCTACATCTTTTATTTCTTGAATATGAGAAAG-T--TT-ACAGTCTATTCA
223648 ACCTACATCTTTTATTTCTTGAATATGAGAAAGTTTACAGTCTATTCA
1 ACCTACATCTTTTATTTCTTGAATATGAGAAAGTTTACAGTCTATTCA
223696 TACTGTAAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
48 12 0.25
49 2 0.04
51 1 0.02
52 33 0.69
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (48 bp):
ACCTACATCTTTTATTTCTTGAATATGAGAAAGTTTACAGTCTATTCA
Found at i:224248 original size:33 final size:33
Alignment explanation
Indices: 224211--224277 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
224201 TACATTTATG
224211 TATGGCTCATATATGTTTGAATAGATGGTTGGC
1 TATGGCTCATATATGTTTGAATAGATGGTTGGC
224244 TATGGCTCATATATGTTTGAATAGATGGTTGGC
1 TATGGCTCATATATGTTTGAATAGATGGTTGGC
224277 T
1 T
224278 TCTCCAATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (33 bp):
TATGGCTCATATATGTTTGAATAGATGGTTGGC
Found at i:228728 original size:36 final size:36
Alignment explanation
Indices: 228671--228746 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
228661 TATTAACCTT
** * *
228671 AGAATTTTATTGGGAAAGAAACACATAATTCGATTC
1 AGAATTTTATCAGGAAAGAAACACATAATTCCATGC
* *
228707 AGAATTTTATCAGGAAGGAAACATATAATTCCATGC
1 AGAATTTTATCAGGAAAGAAACACATAATTCCATGC
228743 AGAA
1 AGAA
228747 CAATTATCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (36 bp):
AGAATTTTATCAGGAAAGAAACACATAATTCCATGC
Found at i:234806 original size:24 final size:25
Alignment explanation
Indices: 234779--234832 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
234769 ACATGAATTA
* *
234779 TATATATATATAA-TAAAGTTCTT-T
1 TATATA-AAATAATTAAAGTGCTTAT
234803 TATATAAAATAATTAAAGTGCTTAT
1 TATATAAAATAATTAAAGTGCTTAT
234828 TATAT
1 TATAT
234833 GTAAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 15 0.58
25 6 0.23
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (25 bp):
TATATAAAATAATTAAAGTGCTTAT
Found at i:235790 original size:231 final size:229
Alignment explanation
Indices: 235383--235812 Score: 524
Period size: 231 Copynumber: 1.9 Consensus size: 229
235373 TCATATAGTG
* * * * * * * *
235383 TTGTTTATTATGATACTGGTCGAAATATGCTTTAAACCCCTATATTTTTCTTACATTGGAAATTT
1 TTGTTTATTATGATACTAGTCGAAATATACTCTAAACCCCTATATCTTTCGTAAATTGAAAAGTT
* *
235448 AGCCCTCTTACTATATTATATAATGTTATAACATATCATATATTAATAGTTTATATATGCATAAA
66 AGCACTCTTACTATATTATATAATGTTATAACATATAATATATTAATAGTTTATATATGCATAAA
* * * *
235513 TAATTAAATATTATAGTATCATGTAATACTATACCTATTGTTATAATCTATACTATAATAATAGT
131 TAATTAAACAGTATAATATCATGTAATACTATACCTATTATTATAATCTATACTATAATAATAGT
235578 TATATATAATAGTATTACTTATTATTTTATATTA
196 TATATATAATAGTATTACTTATTATTTTATATTA
* * * * *
235612 TTGTTTATTATTATATTAGTTGAAATATACTCTAAATCCCTA-ATCTTTCGTAAATTTAAAAGTT
1 TTGTTTATTATGATACTAGTCGAAATATACTCTAAACCCCTATATCTTTCGTAAATTGAAAAGTT
* *
235676 AGCACTCTTAGTATATTATATAATGCTATATCATATTATATAATATATTAATAG-TT-TATATGC
66 AGCACTCTTACTATATTATATAATG-T-TAT-A-A-CATATAATATATTAATAGTTTATATATGC
* ** * * * * * *
235739 ATTAATGTTTAGACAGTATAATTTCTTGTAATACTATATCTTTTATTATAATCTATATTATAATA
126 ATAAATAATTAAACAGTATAATATCATGTAATACTATACCTATTATTATAATCTATACTATAATA
235804 ATAGTTATA
191 ATAGTTATA
235813 CGTGTATTAA
Statistics
Matches: 166, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
228 39 0.23
229 36 0.22
230 3 0.02
231 69 0.42
232 3 0.02
233 16 0.10
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (229 bp):
TTGTTTATTATGATACTAGTCGAAATATACTCTAAACCCCTATATCTTTCGTAAATTGAAAAGTT
AGCACTCTTACTATATTATATAATGTTATAACATATAATATATTAATAGTTTATATATGCATAAA
TAATTAAACAGTATAATATCATGTAATACTATACCTATTATTATAATCTATACTATAATAATAGT
TATATATAATAGTATTACTTATTATTTTATATTA
Found at i:236017 original size:8 final size:8
Alignment explanation
Indices: 236004--236037 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
235994 CATTAAAGTT
236004 TAATTTTA
1 TAATTTTA
236012 TAATTTTAA
1 TAATTTT-A
236021 TAATTTT-
1 TAATTTTA
236028 TAATTTTA
1 TAATTTTA
236036 TA
1 TA
236038 TATACTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.29
8 9 0.38
9 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TAATTTTA
Found at i:239711 original size:16 final size:17
Alignment explanation
Indices: 239685--239716 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
239675 AACTGAAATT
239685 AAAAAAGGAAAAAGAAG
1 AAAAAAGGAAAAAGAAG
239702 AAAAAA-GAAAAAGAA
1 AAAAAAGGAAAAAGAA
239717 AAATTGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAAAAAGAAG
Found at i:240000 original size:3 final size:3
Alignment explanation
Indices: 239994--240028 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
239984 AAAAAAAAAA
*
239994 AAG AAG AAA AAG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
240029 TGAAAAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:240003 original size:9 final size:9
Alignment explanation
Indices: 239979--240019 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
239969 AAACCAAATT
*
239979 AAGAAAAAA
1 AAGAAAAAG
*
239988 AAAAAAAAG
1 AAGAAAAAG
239997 AAGAAAAAG
1 AAGAAAAAG
*
240006 AAGAAGAAG
1 AAGAAAAAG
240015 AAGAA
1 AAGAA
240020 GAAAAGAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:240009 original size:12 final size:12
Alignment explanation
Indices: 239988--240022 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
239978 TAAGAAAAAA
*
239988 AAAAAAAAGAAG
1 AAAAAGAAGAAG
240000 AAAAAGAAGAAG
1 AAAAAGAAGAAG
*
240012 AAGAAGAAGAA
1 AAAAAGAAGAA
240023 AAGAAGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:248939 original size:15 final size:16
Alignment explanation
Indices: 248919--248953 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
248909 CTTTATAAAT
248919 AAAATAAA-ATATTAA
1 AAAATAAATATATTAA
*
248934 AAAATAAATATTTTAA
1 AAAATAAATATATTAA
248950 AAAA
1 AAAA
248954 GAAACACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAAATATATTAA
Found at i:250525 original size:4 final size:4
Alignment explanation
Indices: 250506--250558 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
250496 AAATAAACGG
* * * *
250506 GAAA AAAA GAAAA GAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
250556 GAA
1 GAA
250559 TAATTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 33 0.80
5 8 0.20
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:250851 original size:16 final size:16
Alignment explanation
Indices: 250830--250879 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
250820 TGATGGGGAT
250830 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
250846 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
250861 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
250876 ATTA
1 ATTA
250880 GCTAAGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:251087 original size:20 final size:21
Alignment explanation
Indices: 251062--251104 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
251052 TACTTACTAC
251062 TACTAAC-AACAAAATTAAAT
1 TACTAACTAACAAAATTAAAT
*
251082 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATTAAAT
251103 TA
1 TA
251105 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (21 bp):
TACTAACTAACAAAATTAAAT
Found at i:251483 original size:7 final size:7
Alignment explanation
Indices: 251453--251499 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
251443 TTTTTTCCTC
251453 TCCTTCT
1 TCCTTCT
*
251460 TCC-CCT
1 TCCTTCT
251466 T-CTTC-
1 TCCTTCT
251471 TCCTTCT
1 TCCTTCT
251478 TCCTTCT
1 TCCTTCT
251485 TCCTTCT
1 TCCTTCT
*
251492 TCTTTCT
1 TCCTTCT
251499 T
1 T
251500 TCTTTCTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 2 0.06
6 8 0.24
7 24 0.71
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
TCCTTCT
Found at i:251498 original size:4 final size:4
Alignment explanation
Indices: 251491--251533 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
251481 TTCTTCCTTC
*
251491 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
251534 CTTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:251502 original size:25 final size:24
Alignment explanation
Indices: 251453--251528 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 24
251443 TTTTTTCCTC
* *
251453 TCCTTCTTCCCCTTCTTCTCCTTCT
1 TCCTTCTTCCTCTTCTT-TCTTTCT
251478 TCCTTCTTCCTTCTTCTTTCTTTCTT
1 TCCTTCTTCC-TCTTCTTTCTTTC-T
* * *
251504 TCTTTCTTTCTCTTTTTTCTTTCT
1 TCCTTCTTCCTCTTCTTTCTTTCT
251528 T
1 T
251529 TTTTCCTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.05
25 27 0.61
26 15 0.34
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (24 bp):
TCCTTCTTCCTCTTCTTTCTTTCT
Found at i:251507 original size:29 final size:28
Alignment explanation
Indices: 251453--251537 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 28
251443 TTTTTTCCTC
* *
251453 TCCTTCTTCCCCTTC-TTC--TCCTTCT
1 TCCTTCTTCCTCTTCTTTCTTTCTTTCT
251478 TCCTTCTTCCTTCTTCTTTCTTTCTTTC-
1 TCCTTCTTCC-TCTTCTTTCTTTCTTTCT
* * *
251506 T--TTCTTTCTCTTTTTTCTTTCTTTTT
1 TCCTTCTTCCTCTTCTTTCTTTCTTTCT
251532 TCCTTC
1 TCCTTC
251538 ATTTTTCGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
25 25 0.52
26 11 0.23
27 3 0.06
28 4 0.08
29 5 0.10
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (28 bp):
TCCTTCTTCCTCTTCTTTCTTTCTTTCT
Found at i:251542 original size:12 final size:11
Alignment explanation
Indices: 251477--251544 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
251467 CTTCTCCTTC
**
251477 TTCCTTCTTCC
1 TTCCTTCTTTT
251488 TT-CTTCTTTCT
1 TTCCTTCTTT-T
*
251499 TTCTTTCTTTCT
1 TTCCTTCTTT-T
251511 TT-C-TCTTTT
1 TTCCTTCTTTT
*
251520 TTCTTTCTTTT
1 TTCCTTCTTTT
*
251531 TTCCTTCATTT
1 TTCCTTCTTTT
251542 TTC
1 TTC
251545 GTTCGTCACC
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
9 3 0.07
10 11 0.24
11 22 0.48
12 10 0.22
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (11 bp):
TTCCTTCTTTT
Found at i:254558 original size:15 final size:15
Alignment explanation
Indices: 254538--254582 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
254528 AAACCAAGAA
*
254538 GCTGTTGTTGCTGCT
1 GCTGTTGTTGTTGCT
254553 GCTGTTGTTGTTGCT
1 GCTGTTGTTGTTGCT
* *
254568 GTTGCTGTTGTTGCT
1 GCTGTTGTTGTTGCT
254583 CTTGTTCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.00, C:0.16, G:0.33, T:0.51
Consensus pattern (15 bp):
GCTGTTGTTGTTGCT
Found at i:254563 original size:18 final size:18
Alignment explanation
Indices: 254540--254580 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
254530 ACCAAGAAGC
254540 TGTTGTTGCTGCTGCTGT
1 TGTTGTTGCTGCTGCTGT
*
254558 TGTTGTTGCTGTTGCTGT
1 TGTTGTTGCTGCTGCTGT
254576 TGTTG
1 TGTTG
254581 CTCTTGTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.34, T:0.54
Consensus pattern (18 bp):
TGTTGTTGCTGCTGCTGT
Found at i:254564 original size:6 final size:6
Alignment explanation
Indices: 254543--254577 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
254533 AAGAAGCTGT
* *
254543 TGTTGC TGCTGC TGTTGT TGTTGC TGTTGC TGTTG
1 TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTG
254578 TTGCTCTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.14, G:0.34, T:0.51
Consensus pattern (6 bp):
TGTTGC
Found at i:257889 original size:20 final size:19
Alignment explanation
Indices: 257864--257903 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
257854 ATAATCGTAA
257864 TATTTTTAATATTTTAATAT
1 TATTTTTAATA-TTTAATAT
**
257884 TATTTTTGTTATTTAATAT
1 TATTTTTAATATTTAATAT
257903 T
1 T
257904 TTAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TATTTTTAATATTTAATAT
Found at i:260494 original size:23 final size:23
Alignment explanation
Indices: 260468--260525 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
260458 AAAGCTATGT
* *
260468 CTGATAAATTAAAAAATTAAGTG
1 CTGAAAAATTAAAAAATTAAATG
*
260491 CTGAAAAATTAAAAACTTAAATG
1 CTGAAAAATTAAAAAATTAAATG
*
260514 TTGAAAAATTAA
1 CTGAAAAATTAA
260526 GTATTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.29
Consensus pattern (23 bp):
CTGAAAAATTAAAAAATTAAATG
Found at i:260520 original size:15 final size:15
Alignment explanation
Indices: 260502--260540 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
260492 TGAAAAATTA
*
260502 AAAACTTAAATGTTG
1 AAAACTTAAATATTG
* *
260517 AAAAATTAAGTATTG
1 AAAACTTAAATATTG
260532 AAAACTTAA
1 AAAACTTAA
260541 TCATTGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (15 bp):
AAAACTTAAATATTG
Found at i:264903 original size:29 final size:30
Alignment explanation
Indices: 264855--264914 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
264845 AAAATCAAAT
*
264855 AAAATAAAAATTTCATGTATAAAATTACAC
1 AAAATAAAAATTTCAAGTATAAAATTACAC
*
264885 AAAATAAAAA-TTCAAGTATAATATTACAC
1 AAAATAAAAATTTCAAGTATAAAATTACAC
264914 A
1 A
264915 TTATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.28
Consensus pattern (30 bp):
AAAATAAAAATTTCAAGTATAAAATTACAC
Found at i:266387 original size:19 final size:18
Alignment explanation
Indices: 266363--266431 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 18
266353 TTTCTTCCTT
266363 AAATATTTATATATATTTC
1 AAATA-TTATATATATTTC
266382 AAATATTCATAT-TCATATTC
1 AAATATT-ATATAT-AT-TTC
266402 --ATATT-TA-ATATTT-
1 AAATATTATATATATTTC
266415 AAATATTATATATATTT
1 AAATATTATATATATTT
266432 TTTACTTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 18
0.70 0.00 0.30
Matches are distributed among these distances:
14 2 0.05
15 7 0.17
16 5 0.12
17 6 0.14
18 8 0.19
19 11 0.26
20 3 0.07
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (18 bp):
AAATATTATATATATTTC
Found at i:266393 original size:25 final size:23
Alignment explanation
Indices: 266365--266431 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
266355 TCTTCCTTAA
266365 ATATTTATATATATTTCAAATATTC
1 ATATTTATATATATTT--AATATTC
* *
266390 ATATTCATATTCATATTTAATATTT
1 ATATTTATA-T-ATATTTAATATTC
*
266415 AAATATTATATATATTT
1 ATAT-TTATATATATTT
266432 TTTACTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
24 6 0.17
25 18 0.51
26 5 0.14
27 6 0.17
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTTATATATATTTAATATTC
Found at i:274954 original size:29 final size:30
Alignment explanation
Indices: 274912--274968 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
274902 TGATCAAATA
274912 TGCAATGTCATACAT-AAACTTTGATTTTG
1 TGCAATGTCATACATGAAACTTTGATTTTG
* * *
274941 TGCAATTTTATACATGAAATTTTGATTT
1 TGCAATGTCATACATGAAACTTTGATTT
274969 GATTCTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.46
Consensus pattern (30 bp):
TGCAATGTCATACATGAAACTTTGATTTTG
Found at i:277753 original size:26 final size:26
Alignment explanation
Indices: 277715--277765 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
277705 CATTACTTCT
*
277715 GAAAAATATTTTTAAAAAGTGCTTTG
1 GAAAAATATTTTTAAAAAGTACTTTG
*
277741 GAAAAATGA-TTTTGAAAAGTACTTT
1 GAAAAAT-ATTTTTAAAAAGTACTTT
277766 TAAAAAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (26 bp):
GAAAAATATTTTTAAAAAGTACTTTG
Found at i:277771 original size:26 final size:26
Alignment explanation
Indices: 277708--277771 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
277698 AGTTTAACAT
277708 TACTTCTG-AAAAATATTTTTAAAAAG
1 TACTT-TGAAAAAATATTTTTAAAAAG
* * *
277734 TGCTTTGGAAAAATGA-TTTTGAAAAG
1 TACTTTGAAAAAAT-ATTTTTAAAAAG
*
277760 TACTTTTAAAAA
1 TACTTTGAAAAA
277772 GCTTGGTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 2 0.06
26 28 0.90
27 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (26 bp):
TACTTTGAAAAAATATTTTTAAAAAG
Found at i:278191 original size:18 final size:18
Alignment explanation
Indices: 278160--278199 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
278150 TTTAATATTA
278160 TTTTTTGTTCAAAAGTAC
1 TTTTTTGTTCAAAAGTAC
*
278178 TTTTTATGTT-AAAAGTGC
1 TTTTT-TGTTCAAAAGTAC
278196 TTTT
1 TTTT
278200 GAAAAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (18 bp):
TTTTTTGTTCAAAAGTAC
Found at i:280398 original size:25 final size:24
Alignment explanation
Indices: 280370--280431 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
280360 TGGGTGCATG
*
280370 AATATTTTATATTTGAAATTTATTT
1 AATATTTTATATTTGAAATTTA-TA
* *
280395 AATATAATT-TATTTGATATTTATA
1 AATAT-TTTATATTTGAAATTTATA
280419 AATATTTTTATAT
1 AATA-TTTTATAT
280432 GCATATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
24 7 0.23
25 21 0.70
26 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (24 bp):
AATATTTTATATTTGAAATTTATA
Found at i:290214 original size:45 final size:44
Alignment explanation
Indices: 290159--290249 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 44
290149 TTGAGTTTTG
* ** * *
290159 TTTACTTCAAGTGTAAATTTTGGGTCATTAAAAGTTCGGATTATT
1 TTTACTTCAAG-ATAAATTTTGAATAATTAAAAGATCGGATTATT
* * *
290204 TTTAGTTCAAGATAATTTTTGAATAATTTAAAGATCGGATTATT
1 TTTACTTCAAGATAAATTTTGAATAATTAAAAGATCGGATTATT
290248 TT
1 TT
290250 AGGATTGGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 28 0.74
45 10 0.26
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (44 bp):
TTTACTTCAAGATAAATTTTGAATAATTAAAAGATCGGATTATT
Found at i:293879 original size:183 final size:183
Alignment explanation
Indices: 293565--293932 Score: 574
Period size: 183 Copynumber: 2.0 Consensus size: 183
293555 CTCAGTCTCC
* * *
293565 TACAGTAAATTCTATATCTTTTCTCTTAAGATCTGCATACGACTTATGTCGGGCAGACGCTGCTT
1 TACAGCAAATTCTATATCTTTTCTCTTAAGATCTGCATACGACTTATGTCAGACAGACGCTGCTT
* *
293630 CCAAACAATCACGAATTACCCACAATTTGTCCTCAGTCTCATGAACCAAATCAGTTTCAATCAAC
66 CCAAACAATCACGAATTACCCACAATTTGTCATCAGTCTCATGAACCAAATCAGTTCCAATCAAC
* * *
293695 TTAGACTCGCTCAATTCTGACTAGTACAAAAGTGTCCTGCACTTCCGACCATA
131 TTAGACTCGCTCAATTCTGACCAATACAAAAGTATCCTGCACTTCCGACCATA
* * *
293748 TACAGCAAATTCTATATCTTTTCTTTTAAGATCTGCATACGACTTATGTCAGATAGACGTTGCTT
1 TACAGCAAATTCTATATCTTTTCTCTTAAGATCTGCATACGACTTATGTCAGACAGACGCTGCTT
** * * *
293813 TTAAACAATCACGAATTACCCGCACTTTGTCATTAGTCTCATGAACCAAATCAGTTCCAATCAAC
66 CCAAACAATCACGAATTACCCACAATTTGTCATCAGTCTCATGAACCAAATCAGTTCCAATCAAC
* *
293878 TTAGACTCGCTCAATTCTGACCAATACAAAGGTATCTTGCACTTCCGACCATA
131 TTAGACTCGCTCAATTCTGACCAATACAAAAGTATCCTGCACTTCCGACCATA
293931 TA
1 TA
293933 ATGCTTCGAA
Statistics
Matches: 167, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
183 167 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (183 bp):
TACAGCAAATTCTATATCTTTTCTCTTAAGATCTGCATACGACTTATGTCAGACAGACGCTGCTT
CCAAACAATCACGAATTACCCACAATTTGTCATCAGTCTCATGAACCAAATCAGTTCCAATCAAC
TTAGACTCGCTCAATTCTGACCAATACAAAAGTATCCTGCACTTCCGACCATA
Found at i:295735 original size:22 final size:22
Alignment explanation
Indices: 295703--295746 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
295693 ATGAAAGAAA
295703 AACCATAATAATTTCTCACATT
1 AACCATAATAATTTCTCACATT
*
295725 AACCATCATAATTTCTCACATT
1 AACCATAATAATTTCTCACATT
295747 CTTCTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (22 bp):
AACCATAATAATTTCTCACATT
Found at i:296119 original size:51 final size:51
Alignment explanation
Indices: 296043--296206 Score: 249
Period size: 51 Copynumber: 3.2 Consensus size: 51
296033 AAACGAAAGG
* *
296043 GTCCGATAACTAAGTGTCATCGTGAGTAAATGAAACATTTACGGATTAAAA
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCATTTACGGATTAAAA
* *
296094 GTCCGATGACTAAGTGTCATCGTGAGAAAATGAATCCTTTACGGATTAAAA
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCATTTACGGATTAAAA
* * *
296145 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCA-TGATGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCATTTACGGATTAAAA
296196 GTCCGATGACT
1 GTCCGATGACT
296207 CCCTATTATC
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 101 0.98
52 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCATTTACGGATTAAAA
Found at i:296251 original size:102 final size:101
Alignment explanation
Indices: 296033--296283 Score: 238
Period size: 102 Copynumber: 2.4 Consensus size: 101
296023 TTCGAGCTAT
* *
296033 AAACGAAAGGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAAACATTTACGGATTAAAAGTCC
1 AAAC-AAA-GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAACATTGACGGATTAAAAGTCC
* * * *
296098 GATGACTAAGTGTCATCGTGAGAAAATGAATCCTTTACG
64 GATGACTAACTATCATCGTGAG-AAATGAATCCTATACA
* ** * * * *
296137 GATTAAAAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCA-TGATGGATTAAAGGTCCG
1 AAACAAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-ACATTGACGGATTAAAAGTCCG
** * *
296201 ATGACTCCCTATTATCGTGAG-TATGAATTCCTATACA
65 ATGACTAACTATCATCGTGAGAAATGAA-TCCTATACA
*
296238 AAACAAGAGGTCCGATGACTATA-TGTCATCGTTAGTATTAATGAAA
1 AAACAA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA--AATGAAA
296284 TGAGTTTCAA
Statistics
Matches: 118, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
100 5 0.04
101 10 0.08
102 90 0.76
103 6 0.05
104 7 0.06
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (101 bp):
AAACAAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAACATTGACGGATTAAAAGTCCGA
TGACTAACTATCATCGTGAGAAATGAATCCTATACA
Found at i:303121 original size:14 final size:11
Alignment explanation
Indices: 303089--303123 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
303079 AAATGAGTCT
303089 TTCTCTTCTTC
1 TTCTCTTCTTC
303100 TTCTCTTCTTC
1 TTCTCTTCTTC
* *
303111 GTCTCTCCTTC
1 TTCTCTTCTTC
303122 TT
1 TT
303124 TTTCCTCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.37, G:0.03, T:0.60
Consensus pattern (11 bp):
TTCTCTTCTTC
Found at i:304243 original size:24 final size:24
Alignment explanation
Indices: 304216--304266 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
304206 TTCTCCTTCT
304216 CCTCCTCCTTCCCCCTTCTTAAAC
1 CCTCCTCCTTCCCCCTTCTTAAAC
304240 CCTCCTCCTTCCCCCTTCTTAAAC
1 CCTCCTCCTTCCCCCTTCTTAAAC
304264 CCT
1 CCT
304267 AAAATATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.55, G:0.00, T:0.33
Consensus pattern (24 bp):
CCTCCTCCTTCCCCCTTCTTAAAC
Found at i:305929 original size:15 final size:15
Alignment explanation
Indices: 305909--305947 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
305899 AACTCTATAA
305909 CATCATCATCATCTT
1 CATCATCATCATCTT
* *
305924 CATCATTATCTTCTT
1 CATCATCATCATCTT
*
305939 CACCATCAT
1 CATCATCAT
305948 TGTTATCGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (15 bp):
CATCATCATCATCTT
Found at i:307476 original size:15 final size:15
Alignment explanation
Indices: 307456--307484 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
307446 CTCTTCTTCC
307456 TCATCATCCTCATCG
1 TCATCATCCTCATCG
307471 TCATCATCCTCATC
1 TCATCATCCTCATC
307485 CTCTACCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.41, G:0.03, T:0.34
Consensus pattern (15 bp):
TCATCATCCTCATCG
Found at i:307850 original size:15 final size:15
Alignment explanation
Indices: 307830--307866 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
307820 CTGGATCATA
307830 TTCATCATCATCCTC
1 TTCATCATCATCCTC
* *
307845 TTCATCTTCCTCCTC
1 TTCATCATCATCCTC
307860 TTCATCA
1 TTCATCA
307867 GACTCCGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.43
Consensus pattern (15 bp):
TTCATCATCATCCTC
Found at i:312845 original size:218 final size:218
Alignment explanation
Indices: 312470--312864 Score: 621
Period size: 218 Copynumber: 1.8 Consensus size: 218
312460 TGAAATGAAC
*
312470 ATTCCAACCTAATTGCAACACCCTGGCAAATGTCACTTAATTGGAGCTTCAAATTCTAGAGGGGA
1 ATTCCAACCTAATTGCAACACCCTGGCAAATGTCACTTAATTGGAGCTTCAAAGTCTAGAGGGGA
* * * *
312535 AAAAGCCTAGAAAAAGATTAACTACAGCTTTAACAGAACTGATTTCACCCATCTGTACAGACCAA
66 AAAAGCCCAGAAAAAGATTAACTACAGCTTTAACAGAACTGATTTCACACACCTCTACAGACCAA
* * *
312600 GAGGCACTTTGCACTCATCATGGTCTAGTGTGCATTATAGAAAAAAATCTTACAGCTTCATTCCC
131 GAGGCACTTTGCACTCATCACGGTCTAGCGTGAATTATAGAAAAAAATCTTACAGCTTCATTCCC
312665 ATCCAAAATTTTGCAAAATAAAT
196 ATCCAAAATTTTGCAAAATAAAT
* * *
312688 ATTCCAACCTAATTGCAACACCTTGGCAAATGTCACTTAATTGGAGCTTCAAAGTGTAGA-GGGT
1 ATTCCAACCTAATTGCAACACCCTGGCAAATGTCACTTAATTGGAGCTTCAAAGTCTAGAGGGGA
* *
312752 AAAAGCCCAGAAAAAGATTAACTACAGCTTTTACAGAACTGATTTCACACACCTCTACAGATCAA
66 AAAAGCCCAGAAAAAGATTAACTACAGCTTTAACAGAACTGATTTCACACACCTCTACAGACCAA
* * **
312817 GAGGCTCCTTTGCATTCATTGCGGTCTAGCGTGAATTATAGAAAAAAA
131 GAGGC-ACTTTGCACTCATCACGGTCTAGCGTGAATTATAGAAAAAAA
312865 AAACTTGAAC
Statistics
Matches: 159, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
217 67 0.42
218 92 0.58
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (218 bp):
ATTCCAACCTAATTGCAACACCCTGGCAAATGTCACTTAATTGGAGCTTCAAAGTCTAGAGGGGA
AAAAGCCCAGAAAAAGATTAACTACAGCTTTAACAGAACTGATTTCACACACCTCTACAGACCAA
GAGGCACTTTGCACTCATCACGGTCTAGCGTGAATTATAGAAAAAAATCTTACAGCTTCATTCCC
ATCCAAAATTTTGCAAAATAAAT
Found at i:317899 original size:3 final size:3
Alignment explanation
Indices: 317886--317920 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
317876 AGGAGTGAAT
*
317886 AAG AA- AAG AAG AAG AAG AAT AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
317921 GAGGAGGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:319979 original size:52 final size:52
Alignment explanation
Indices: 319901--320006 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
319891 TAAATGCAAA
*
319901 AGGTCTGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* *
319953 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
320005 AG
1 AG
320007 TATATGAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
Found at i:320006 original size:26 final size:26
Alignment explanation
Indices: 319977--320029 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
319967 TGTGTCATCG
319977 TGAGTATATGAATCCTTTACGGATTA
1 TGAGTATATGAATCCTTTACGGATTA
320003 TGAGTATATGAATCCTTTACGGATTA
1 TGAGTATATGAATCCTTTACGGATTA
320029 T
1 T
320030 AAGGTCCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (26 bp):
TGAGTATATGAATCCTTTACGGATTA
Found at i:320054 original size:78 final size:78
Alignment explanation
Indices: 319925--320084 Score: 275
Period size: 78 Copynumber: 2.1 Consensus size: 78
319915 TGTGTCATCG
* *
319925 TGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
1 TGAGTATATGAATCCTTTACGAATTATAAGGTCCGATGACAATGTGTCATCGTGAGTATATGAAT
*
319990 CCTTTACGGATTA
66 CCTTTACGAATTA
* *
320003 TGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACAATGTGTCATCGTGAGTATCTGAAT
1 TGAGTATATGAATCCTTTACGAATTATAAGGTCCGATGACAATGTGTCATCGTGAGTATATGAAT
320068 CCTTTACGAATTA
66 CCTTTACGAATTA
320081 TGAG
1 TGAG
320085 GTCCGATGAC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (78 bp):
TGAGTATATGAATCCTTTACGAATTATAAGGTCCGATGACAATGTGTCATCGTGAGTATATGAAT
CCTTTACGAATTA
Found at i:320081 original size:52 final size:52
Alignment explanation
Indices: 320003--320165 Score: 245
Period size: 52 Copynumber: 3.1 Consensus size: 52
319993 TTACGGATTA
*
320003 TGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACAATGTGTCATCG
1 TGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACAATGTGTCATCG
* * * *
320055 TGAGTATCTGAATCCTTTACGAATTATGAGGTCCGATGACCATGTGTCATCA
1 TGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACAATGTGTCATCG
* * * *
320107 TGAGCATATGAATCCTTTTCGGATTATGAGGTTCGATGACTATGTGTCATCG
1 TGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACAATGTGTCATCG
320159 TGAGTAT
1 TGAGTAT
320166 CAAATGAGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 98 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (52 bp):
TGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACAATGTGTCATCG
Found at i:320133 original size:130 final size:130
Alignment explanation
Indices: 319900--320136 Score: 402
Period size: 130 Copynumber: 1.8 Consensus size: 130
319890 GTAAATGCAA
* *
319900 AAGGTCTGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGAC
1 AAGGTCCGATAACAATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGAC
* * *
319965 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGTATATGAATCCTTTACGGATTAT
66 CATGTGTCATCATGAGCATATGAATCCTTTACGGATTATGAGTATATGAATCCTTTACGGATTAT
* *
320030 AAGGTCCGATGACAATGTGTCATCGTGAGTATCTGAATCCTTTACGAATTATGAGGTCCGATGAC
1 AAGGTCCGATAACAATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGAC
*
320095 CATGTGTCATCATGAGCATATGAATCCTTTTCGGATTATGAG
66 CATGTGTCATCATGAGCATATGAATCCTTTACGGATTATGAG
320137 GTTCGATGAC
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 99 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (130 bp):
AAGGTCCGATAACAATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGAC
CATGTGTCATCATGAGCATATGAATCCTTTACGGATTATGAGTATATGAATCCTTTACGGATTAT
Found at i:321630 original size:30 final size:31
Alignment explanation
Indices: 321559--321630 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
321549 GAGGGAGTTG
*
321559 AGTTG-GTGACTGTTTTGTCACTTTTCAATA
1 AGTTGAGTGACTATTTTGTCACTTTTCAATA
321589 ACGTT-AGTGACTATTTTGTCACATTTTC-A-A
1 A-GTTGAGTGACTATTTTGTCAC-TTTTCAATA
321619 AGTTGAGTGACT
1 AGTTGAGTGACT
321631 GTTGTGTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
29 3 0.08
30 10 0.27
31 19 0.51
32 5 0.14
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (31 bp):
AGTTGAGTGACTATTTTGTCACTTTTCAATA
Found at i:322553 original size:32 final size:32
Alignment explanation
Indices: 322474--322561 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 32
322464 TTTAAATCTC
*
322474 TTAAAAGTTGGTAAAAAAAA-TTTGGGGCCCT
1 TTAAAAGTTGATAAAAAAAATTTTGGGGCCCT
* * ** *
322505 TAAAAACTAAAAAAAAAAATATTTTGGGG-CCT
1 TTAAAAGTTGATAAAAAAA-ATTTTGGGGCCCT
322537 TTAAAAGTTGATAAAAAAAATTTTG
1 TTAAAAGTTGATAAAAAAAATTTTG
322562 ACCTGTAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
31 19 0.43
32 18 0.41
33 7 0.16
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.30
Consensus pattern (32 bp):
TTAAAAGTTGATAAAAAAAATTTTGGGGCCCT
Found at i:322553 original size:33 final size:32
Alignment explanation
Indices: 322473--322561 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
322463 ATTTAAATCT
*
322473 CTTAAAAGTTGGT-AAAAAAA-ATTTGGGGCC
1 CTTAAAAGTTGATAAAAAAAATATTTGGGGCC
** * *
322503 CTTAAAAACTAAAAAAAAAAATATTTTGGGGCC
1 CTTAAAAGTTGATAAAAAAAATA-TTTGGGGCC
*
322536 TTTAAAAGTTGATAAAAAAAAT-TTTG
1 CTTAAAAGTTGATAAAAAAAATATTTG
322562 ACCTGTAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
30 8 0.17
31 11 0.24
32 1 0.02
33 26 0.57
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (32 bp):
CTTAAAAGTTGATAAAAAAAATATTTGGGGCC
Found at i:322598 original size:28 final size:26
Alignment explanation
Indices: 322537--322613 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 26
322527 TTTGGGGCCT
* *
322537 TTAAAAGTTGATAAAAAAAATTTTGACC
1 TTAAAAGTT-A-AAAAAAAAATTGGACC
322565 TGTAAAAGTTAAAAAAAAAATTGGATCTC
1 T-TAAAAGTTAAAAAAAAAATTGGA-C-C
* *
322594 TTAAAAATAAAAAACAAAAA
1 TTAAAAGTTAAAAA-AAAAA
322614 CAAAAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 12 0.29
28 14 0.34
29 15 0.37
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.26
Consensus pattern (26 bp):
TTAAAAGTTAAAAAAAAAATTGGACC
Found at i:333596 original size:31 final size:30
Alignment explanation
Indices: 333558--333617 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
333548 TGGCAAATTC
333558 ATTGTAATTTGACTTTAAAATCATCAAAAAG
1 ATTGTAATTTGACTTTAAAATCAT-AAAAAG
*
333589 ATTGTAATTTGACTTTATAATCATAAAAA
1 ATTGTAATTTGACTTTAAAATCATAAAAA
333618 TGAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.38
Consensus pattern (30 bp):
ATTGTAATTTGACTTTAAAATCATAAAAAG
Found at i:341001 original size:23 final size:24
Alignment explanation
Indices: 340975--341032 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
340965 CAGTCAATTG
* * *
340975 CTTGGGGTTTAGGA-GTTTAGAAC
1 CTTGAGGTTTAGGAGGTTCAAAAC
340998 CTTGAGGTTTAGGAGGTTCAAAAC
1 CTTGAGGTTTAGGAGGTTCAAAAC
341022 CTTGAGGTTTA
1 CTTGAGGTTTA
341033 TTTGGGCATC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.34
Consensus pattern (24 bp):
CTTGAGGTTTAGGAGGTTCAAAAC
Found at i:341783 original size:18 final size:20
Alignment explanation
Indices: 341760--341805 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
341750 TTTTGGTTGC
341760 TGTTTT-TG-TGTTTTTTAT
1 TGTTTTGTGCTGTTTTTTAT
*
341778 TGTTTTGGTGCTTTTTTTTAT
1 TGTTTT-GTGCTGTTTTTTAT
341799 TGTTTTG
1 TGTTTTG
341806 GTTGTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
20 3 0.12
21 15 0.62
ACGTcount: A:0.04, C:0.02, G:0.20, T:0.74
Consensus pattern (20 bp):
TGTTTTGTGCTGTTTTTTAT
Found at i:341796 original size:30 final size:30
Alignment explanation
Indices: 341740--341795 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
341730 TTGGTGCTAT
341740 TTTTTTACTGTTTTGGTTGCTGTTTTTGTG
1 TTTTTTACTGTTTTGGTTGCTGTTTTTGTG
* *
341770 TTTTTTATTGTTTTGG-TGCTTTTTTT
1 TTTTTTACTGTTTTGGTTGCTGTTTTT
341796 TATTGTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.04, C:0.05, G:0.20, T:0.71
Consensus pattern (30 bp):
TTTTTTACTGTTTTGGTTGCTGTTTTTGTG
Found at i:341809 original size:51 final size:53
Alignment explanation
Indices: 341725--341827 Score: 156
Period size: 51 Copynumber: 2.0 Consensus size: 53
341715 AATTATATTG
* *
341725 TTGTTTTGGTGCTATTTTTTTACTGTTTTGGTTGCTGTTTTTGTGTT-TTTTA
1 TTGTTTTGGTGCTATTTTTTTACTGTTTTGGTTGCTATTTTCGTGTTATTTTA
* *
341777 TTGTTTTGGTGCT-TTTTTTTATTGTTTTGGTTGTTATTTTCGTGTTATTTT
1 TTGTTTTGGTGCTATTTTTTTACTGTTTTGGTTGCTATTTTCGTGTTATTTT
341828 TACTGTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 29 0.63
52 17 0.37
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.69
Consensus pattern (53 bp):
TTGTTTTGGTGCTATTTTTTTACTGTTTTGGTTGCTATTTTCGTGTTATTTTA
Found at i:341816 original size:12 final size:12
Alignment explanation
Indices: 341801--341913 Score: 60
Period size: 12 Copynumber: 9.9 Consensus size: 12
341791 TTTTTTATTG
*
341801 TTTTGGTTGTTA
1 TTTTTGTTGTTA
*
341813 TTTTCG-TGTTA
1 TTTTTGTTGTTA
**
341824 TTTTTACTGTTA
1 TTTTTGTTGTTA
*
341836 TTTTTGTTGCTA
1 TTTTTGTTGTTA
341848 --TTT-TTGTTA
1 TTTTTGTTGTTA
**
341857 TTTTTAATG-T-
1 TTTTTGTTGTTA
* *
341867 TGTTTGCTGTTA
1 TTTTTGTTGTTA
* *
341879 TTTTTGCTGCTA
1 TTTTTGTTGTTA
*
341891 -TTTTGATTGCTA
1 TTTTTG-TTGTTA
341903 TTTTTGTTGTT
1 TTTTTGTTGTT
341914 TGGATGTTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
9 5 0.06
10 9 0.12
11 19 0.24
12 40 0.51
13 5 0.06
ACGTcount: A:0.11, C:0.06, G:0.17, T:0.66
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:341816 original size:21 final size:21
Alignment explanation
Indices: 341771--341816 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
341761 GTTTTTGTGT
*
341771 TTTTTATTGTTTTGGTGCTTT
1 TTTTTATTGTTTTGGTGCTTA
341792 TTTTTATTGTTTTGGTTG-TTA
1 TTTTTATTGTTTTGG-TGCTTA
341813 TTTT
1 TTTT
341817 CGTGTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.07, C:0.02, G:0.17, T:0.74
Consensus pattern (21 bp):
TTTTTATTGTTTTGGTGCTTA
Found at i:341911 original size:43 final size:43
Alignment explanation
Indices: 341830--341927 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
341820 GTTATTTTTA
* *
341830 CTGTTATTTTTGTTGCTATTTTTGTTATTTTTAATGTTGTTT-G
1 CTGTTATTTTTGCTGCTATTTTTGCTATTTTT-ATGTTGTTTGG
341873 CTGTTATTTTTGCTGCTATTTTGATTGCTA-TTTT-TGTTGTTTGG
1 CTGTTATTTTTGCTGCTA-TTT--TTGCTATTTTTATGTTGTTTGG
*
341917 ATGTTATTTTT
1 CTGTTATTTTT
341928 ATGCGTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 25 0.52
44 14 0.29
45 4 0.08
46 5 0.10
ACGTcount: A:0.11, C:0.06, G:0.17, T:0.65
Consensus pattern (43 bp):
CTGTTATTTTTGCTGCTATTTTTGCTATTTTTATGTTGTTTGG
Found at i:346246 original size:18 final size:18
Alignment explanation
Indices: 346223--346257 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
346213 AGCTCCAGCT
*
346223 CCGGCACCAGCACCGGCA
1 CCGGCACCACCACCGGCA
346241 CCGGCACCACCACCGGC
1 CCGGCACCACCACCGGC
346258 TGGCTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.54, G:0.26, T:0.00
Consensus pattern (18 bp):
CCGGCACCACCACCGGCA
Found at i:351867 original size:156 final size:153
Alignment explanation
Indices: 351554--351836 Score: 365
Period size: 156 Copynumber: 1.8 Consensus size: 153
351544 GGTTAAAGCA
* * *
351554 GGAGGTTGAGGAGGTTGTATGCTTGCAGATACAGTTGAGGAGGCAAATAAGCTTGAAAATACACC
1 GGAGGTTGAGGAGGTCGTATGCTTGCAGATACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
* * **
351619 ACTCCTGCTGCTACTGCTAGCACCATTGCCAACCAGGCTCATGCTACCGCTACAACTTCCATTTA
66 ACTCCTGCTGCTAC--CTA-CACCACTGCCAACCAAGCTCACACTACCGCTACAACTTCCATTTA
* *
351684 AGCCAGCAGATGGTGGAGCTGGTGCC
128 AGCCAGCAGATGGCGGAGCCGGTGCC
* *
351710 GGAGGTTGAGGAGGTCGTATGGTTGCAGATACAGTCGAGGAGGCAAATAAGCTCGAGAATACACC
1 GGAGGTTGAGGAGGTCGTATGCTTGCAGATACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
* * * * * *
351775 GCTGCTGCTGCTA-C-A-ACCACTGCTAATCAAGCTGACACTACTGCTACAACTTCCATTTAAGC
66 ACTCCTGCTGCTACCTACACCACTGCCAACCAAGCTCACACTACCGCTACAACTTCCATTTAAGC
351837 TAGCCGGAGG
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
150 39 0.35
152 1 0.01
153 1 0.01
156 71 0.63
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (153 bp):
GGAGGTTGAGGAGGTCGTATGCTTGCAGATACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
ACTCCTGCTGCTACCTACACCACTGCCAACCAAGCTCACACTACCGCTACAACTTCCATTTAAGC
CAGCAGATGGCGGAGCCGGTGCC
Done.