Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold214
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: 1307275
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 88184 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:891228 original size:15 final size:15
Alignment explanation
Indices: 891192--891270 Score: 51
Period size: 14 Copynumber: 5.5 Consensus size: 15
891182 TTAAAGGCCG
* *
891192 GGGTTTAAGGTTTAA
1 GGGTTTATGGGTTAA
* *
891207 AGG-TTATGTGTTAA
1 GGGTTTATGGGTTAA
*
891221 GGGTTTATGGGTTTA
1 GGGTTTATGGGTTAA
891236 GGGTTT-TAGGGTTTAA
1 GGGTTTAT-GGG-TTAA
*
891252 --GTTTATGGTTTAA
1 GGGTTTATGGGTTAA
891265 -GGTTTA
1 GGGTTTA
891271 GATTAACTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
13 4 0.08
14 22 0.44
15 21 0.42
16 3 0.06
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.46
Consensus pattern (15 bp):
GGGTTTATGGGTTAA
Found at i:891261 original size:13 final size:14
Alignment explanation
Indices: 891217--891271 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 14
891207 AGGTTATGTG
891217 TTAAGGGTTTATGGGT
1 TTAA-GGTTTA-GGGT
*
891233 TTAGGGTTTTAGGGT
1 TTAAGG-TTTAGGGT
*
891248 TTAA-GTTTATGGT
1 TTAAGGTTTAGGGT
891261 TTAAGGTTTAG
1 TTAAGGTTTAG
891272 ATTAACTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 11 0.33
14 6 0.18
15 9 0.27
16 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (14 bp):
TTAAGGTTTAGGGT
Found at i:891261 original size:21 final size:20
Alignment explanation
Indices: 891231--891270 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
891221 GGGTTTATGG
*
891231 GTTTAGGGTTTTAGGGTTTAA
1 GTTTAGGG-TTTAAGGTTTAA
*
891252 GTTTATGGTTTAAGGTTTA
1 GTTTAGGGTTTAAGGTTTA
891271 GATTAACTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (20 bp):
GTTTAGGGTTTAAGGTTTAA
Found at i:891592 original size:22 final size:21
Alignment explanation
Indices: 891562--891636 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
891552 TGGGATTTAA
*
891562 GGTTTAGGGGTTAGTAGTTAGG
1 GGTTAAGGGGTTAG-AGTTAGG
*
891584 GGTTAA-GGGTTAAGAGTTAGT
1 GGTTAAGGGGTT-AGAGTTAGG
* * *
891605 GATTTAGGGGTTAGGATTTAGG
1 GGTTAAGGGGTTA-GAGTTAGG
*
891627 GATTTAAGGG
1 G-GTTAAGGG
891637 TCGGGTTAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
21 16 0.39
22 19 0.46
23 6 0.15
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (21 bp):
GGTTAAGGGGTTAGAGTTAGG
Found at i:891624 original size:14 final size:14
Alignment explanation
Indices: 891564--891627 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
891554 GGATTTAAGG
*
891564 TTTAGGGGTTAGTA
1 TTTAGGGGTTAGGA
*
891578 GTTAGGGGTTAAGG-
1 TTTAGGGGTT-AGGA
* * *
891592 GTTAAGAGTTAGTGA
1 TTTAGGGGTTAG-GA
891607 TTTAGGGGTTAGGA
1 TTTAGGGGTTAGGA
891621 TTTAGGG
1 TTTAGGG
891628 ATTTAAGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
13 2 0.05
14 27 0.68
15 11 0.28
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (14 bp):
TTTAGGGGTTAGGA
Found at i:891637 original size:22 final size:21
Alignment explanation
Indices: 891547--891651 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
891537 GTTAATTTTG
* * *
891547 AGGGTTGGGATTTAAGGTTTA
1 AGGGTTAGGAGTTAGGGTTTA
* * *
891568 GGGGTTAGTAGTTAGGGGTTA
1 AGGGTTAGGAGTTAGGGTTTA
* *
891589 AGGGTTAAGAGTTAGTGATTTA
1 AGGGTTAGGAGTTAG-GGTTTA
* *
891611 GGGGTTAGGATTTAGGGATTTA
1 AGGGTTAGGAGTTAGGG-TTTA
*
891633 AGGG-TCGG-GTTAGGGTTTA
1 AGGGTTAGGAGTTAGGGTTTA
891652 GATTAATTAG
Statistics
Matches: 64, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
19 4 0.06
20 6 0.09
21 31 0.48
22 23 0.36
ACGTcount: A:0.23, C:0.01, G:0.41, T:0.35
Consensus pattern (21 bp):
AGGGTTAGGAGTTAGGGTTTA
Found at i:896365 original size:21 final size:21
Alignment explanation
Indices: 896341--896414 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
896331 CTACAACTTA
896341 AAGCAGAAGCAGCAGCGAGGG
1 AAGCAGAAGCAGCAGCGAGGG
* * *
896362 AAGCAGCAGCTGCAGCAAGGG
1 AAGCAGAAGCAGCAGCGAGGG
* *
896383 AAGCA-AAGGCTGCAGCGAGAG
1 AAGCAGAA-GCAGCAGCGAGGG
896404 AAGCAG-AGCAG
1 AAGCAGAAGCAG
896415 AGCAAAAAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.09
21 40 0.91
ACGTcount: A:0.38, C:0.20, G:0.39, T:0.03
Consensus pattern (21 bp):
AAGCAGAAGCAGCAGCGAGGG
Found at i:900752 original size:31 final size:31
Alignment explanation
Indices: 900717--900784 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
900707 TACAATTAAT
* * *
900717 AAAAATTAAAGTTTTATGTATATATTT-CAAC
1 AAAAATCAAACTTTAATGTATATATTTGC-AC
*
900748 AAAAATCAAACTTTAATGTGTATATTTGCAC
1 AAAAATCAAACTTTAATGTATATATTTGCAC
900779 AAAAAT
1 AAAAAT
900785 AAAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (31 bp):
AAAAATCAAACTTTAATGTATATATTTGCAC
Found at i:902040 original size:465 final size:466
Alignment explanation
Indices: 901158--902089 Score: 1857
Period size: 465 Copynumber: 2.0 Consensus size: 466
901148 TATTTTAAAA
901158 TTGTATCTTGAAATTTCTAGTTTCATAATTTAATTATTTAGATATAAAATATAATGCGATCATAA
1 TTGTATCTTGAAATTTCTAGTTTCATAATTTAATTATTTAGATATAAAATATAATGCGATCATAA
901223 TTTAAACATTTTGGAAAGTTTTTAATTTTGTACAATTTCTTTCTTTTTTTGTCACCTTTAATTAT
66 TTTAAACATTTTGGAAAGTTTTTAATTTTGTACAATTTCTTTCTTTTTTTGTCACCTTTAATTAT
901288 GTTGAAATTCATTTCCTATTTAATAGATGCATATTTAAATTCTCAAAAATAATCTTCCCCCACGC
131 GTTGAAATTCATTTCCTATTTAATAGATGCATATTTAAATTCTCAAAAATAATCTTCCCCCACGC
901353 TATAACTTGAACTCACAACATGAATAATGAGAACATTTATAACCAAATGGGATGAGGTAGGAGTG
196 TATAACTTGAACTCACAACATGAATAATGAGAACATTTATAACCAAATGGGATGAGGTAGGAGTG
901418 AACAAAATCCGATTCGATTTAAAAAACTCGATAAAATATTCAATTTTGAATTCAATAGTTCGAGT
261 AACAAAATCCGATTCGATTTAAAAAACTCGATAAAATATTCAATTTTGAATTCAATAGTTCGAGT
901483 TATTTGAGTTAATCGAGTTATTCGAATCAACTCGAATAAGAAAATTAAATTTTTCAGTTTAACTG
326 TATTTGAGTTAATCGAGTTATTCGAATCAACTCGAATAAGAAAATTAAATTTTTCAGTTTAACTG
901548 AATATGAATTACACAATTCGAGTTATCCGAAAATCCGAATAAGAAAAGGTAAAACTATGCCGTTT
391 AATATGAATTACACAATTCGAGTTATCCGAAAATCCGAATAAGAAAAGGTAAAACTATGCCGTTT
901613 TGATAAATATT
456 TGATAAATATT
901624 TTGTATCTTG-AATTTCTAGTTTCATAATTTAATTATTTAGATATAAAATATAATGCGATCATAA
1 TTGTATCTTGAAATTTCTAGTTTCATAATTTAATTATTTAGATATAAAATATAATGCGATCATAA
901688 TTTAAACATTTTGGAAAGTTTTTAATTTTGTACAATTTCTTTCTTTTTTTGTCACCTTTAATTAT
66 TTTAAACATTTTGGAAAGTTTTTAATTTTGTACAATTTCTTTCTTTTTTTGTCACCTTTAATTAT
901753 GTTGAAATTCATTTCCTATTTAATAGATGCATATTTAAATTCTCAAAAATAATCTTCCCCCACGC
131 GTTGAAATTCATTTCCTATTTAATAGATGCATATTTAAATTCTCAAAAATAATCTTCCCCCACGC
901818 TATAACTTGAACTCACAACATGAATAATGAGAACATTTATAACCAAATGGGATGAGGTAGGAGTG
196 TATAACTTGAACTCACAACATGAATAATGAGAACATTTATAACCAAATGGGATGAGGTAGGAGTG
901883 AACAAAATCCGATTCGATTTAAAAAACTCGATAAAATATTCAATTTTGAATTCAATAGTTCGAGT
261 AACAAAATCCGATTCGATTTAAAAAACTCGATAAAATATTCAATTTTGAATTCAATAGTTCGAGT
901948 TATTTGAGTTAATCGAGTTATTCGAATCAACTCGAATAAGAAAATTAAATTTTTCAGTTTAACTG
326 TATTTGAGTTAATCGAGTTATTCGAATCAACTCGAATAAGAAAATTAAATTTTTCAGTTTAACTG
902013 AATATGAATTACACAATTCGAGTTATCCGAAAATCCGAATAAGAAAAGGTAAAACTATGCCGTTT
391 AATATGAATTACACAATTCGAGTTATCCGAAAATCCGAATAAGAAAAGGTAAAACTATGCCGTTT
902078 TGATAAATATT
456 TGATAAATATT
902089 T
1 T
902090 ACCTTTTCTA
Statistics
Matches: 466, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
465 456 0.98
466 10 0.02
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (466 bp):
TTGTATCTTGAAATTTCTAGTTTCATAATTTAATTATTTAGATATAAAATATAATGCGATCATAA
TTTAAACATTTTGGAAAGTTTTTAATTTTGTACAATTTCTTTCTTTTTTTGTCACCTTTAATTAT
GTTGAAATTCATTTCCTATTTAATAGATGCATATTTAAATTCTCAAAAATAATCTTCCCCCACGC
TATAACTTGAACTCACAACATGAATAATGAGAACATTTATAACCAAATGGGATGAGGTAGGAGTG
AACAAAATCCGATTCGATTTAAAAAACTCGATAAAATATTCAATTTTGAATTCAATAGTTCGAGT
TATTTGAGTTAATCGAGTTATTCGAATCAACTCGAATAAGAAAATTAAATTTTTCAGTTTAACTG
AATATGAATTACACAATTCGAGTTATCCGAAAATCCGAATAAGAAAAGGTAAAACTATGCCGTTT
TGATAAATATT
Found at i:902127 original size:21 final size:21
Alignment explanation
Indices: 902103--902142 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
902093 TTTTCTAAAT
* *
902103 TTAAAAGTCAAAACTATTAAG
1 TTAAAAGACAAAACCATTAAG
902124 TTAAAAGACAAAACCATTA
1 TTAAAAGACAAAACCATTA
902143 TATTGTTTAT
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:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (21 bp):
TTAAAAGACAAAACCATTAAG
Found at i:902809 original size:2 final size:2
Alignment explanation
Indices: 902797--902836 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
902787 CAAATCTTCC
* *
902797 TA TA CA TA TA TA TA TA TA TA TA TA AA 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
902837 ATCAATTCAA
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:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:905297 original size:24 final size:26
Alignment explanation
Indices: 905252--905299 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
905242 CACATATTTT
*
905252 GTATAACTACTTTATTACTATTTTCA
1 GTATAACTACTGTATTACTATTTTCA
*
905278 GTATAACTA-TGTA-TAGTATTTT
1 GTATAACTACTGTATTACTATTTT
905300 TCTCTGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 3 0.15
26 9 0.45
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (26 bp):
GTATAACTACTGTATTACTATTTTCA
Found at i:909498 original size:34 final size:34
Alignment explanation
Indices: 909391--909490 Score: 139
Period size: 34 Copynumber: 2.9 Consensus size: 34
909381 CTAAGCTGAT
*
909391 CTATTATAAGCATA-TTACTTGTTACTGTATTGAA
1 CTATTATAAGCATATTTA-TTGATACTGTATTGAA
* * *
909425 CTGTTATAAGCATATTAATTGATATTGTATTGAA
1 CTATTATAAGCATATTTATTGATACTGTATTGAA
*
909459 CTATTATAAGCATATTTATTGCTACTGTATTG
1 CTATTATAAGCATATTTATTGATACTGTATTG
909491 TTCTATTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 55 0.96
35 2 0.04
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (34 bp):
CTATTATAAGCATATTTATTGATACTGTATTGAA
Found at i:914704 original size:17 final size:18
Alignment explanation
Indices: 914672--914706 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
914662 TCATGATGTT
914672 CGCCCGTGTGGGCCCACA
1 CGCCCGTGTGGGCCCACA
*
914690 CGCCTGTGT-GGCCCACA
1 CGCCCGTGTGGGCCCACA
914707 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.43, G:0.31, T:0.14
Consensus pattern (18 bp):
CGCCCGTGTGGGCCCACA
Found at i:919085 original size:14 final size:14
Alignment explanation
Indices: 919066--919093 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
919056 AGAATTGAAA
919066 ATATTTAAAAAAAT
1 ATATTTAAAAAAAT
919080 ATATTTAAAAAAAT
1 ATATTTAAAAAAAT
919094 TTGTAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATTTAAAAAAAT
Found at i:919293 original size:29 final size:28
Alignment explanation
Indices: 919243--919298 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
919233 TTTATCAGCA
** *
919243 TTAACTAAGGATTAATTTTATTGAAACT
1 TTAACTAAGGATTAATAGTATTAAAACT
*
919271 TTAATTAAGGAATTAATAGTATTAAAAC
1 TTAACTAAGG-ATTAATAGTATTAAAAC
919299 ATAAAAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (28 bp):
TTAACTAAGGATTAATAGTATTAAAACT
Found at i:922380 original size:83 final size:81
Alignment explanation
Indices: 922236--922422 Score: 230
Period size: 83 Copynumber: 2.2 Consensus size: 81
922226 GTGTTACACC
* * *
922236 TTGGCCCCTCAAAAATGAAAATTTCAATTCAATCCTCTTATAAATAGAGAATTTATAAATTAATA
1 TTGGCCCCT-AAAAATGAAAATTTCAATACAATCCTCTTATAAATAAAGAAATTATAAATTAATA
* *
922301 TATAGTGAAATTGTACT
65 TATAGTAAAATTATACT
* * * * *
922318 TTGGCCCCTTAAAATTAAAATTTTTCAATACAGTCCTCTTATAAATAAAGAAATTGTTAATTAAT
1 TTGGCCCCTAAAAATGAAAA--TTTCAATACAATCCTCTTATAAATAAAGAAATTATAAATTAAT
922383 ATATAGTAAAATTATACT
64 ATATAGTAAAATTATACT
*
922401 TTAGCCCTCTAAAAATGGAAAA
1 TTGGCCC-CTAAAAAT-GAAAA
922423 ATATATGGTT
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
81 9 0.10
82 9 0.10
83 59 0.67
84 7 0.08
85 4 0.05
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (81 bp):
TTGGCCCCTAAAAATGAAAATTTCAATACAATCCTCTTATAAATAAAGAAATTATAAATTAATAT
ATAGTAAAATTATACT
Found at i:923381 original size:30 final size:30
Alignment explanation
Indices: 923355--923427 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 30
923345 AATTAAAATT
923355 TTAAAAATTCAA-AAAATTATTTTTAAAAAA
1 TTAAAAA-TCAATAAAATTATTTTTAAAAAA
*
923385 TTAAAAATCAATAAAATTA--TTTAAAAAG
1 TTAAAAATCAATAAAATTATTTTTAAAAAA
923413 TATAAAAATC-ATAAA
1 T-TAAAAATCAATAAA
923428 TAAATTAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 14 0.35
29 12 0.30
30 14 0.35
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (30 bp):
TTAAAAATCAATAAAATTATTTTTAAAAAA
Found at i:923435 original size:27 final size:28
Alignment explanation
Indices: 923377--923435 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
923367 AAAATTATTT
* *
923377 TTAAAAAATTAAAAATCAATAAAATTAT
1 TTAAAAAATTAAAAATCAATAAAATAAA
*
923405 TTAAAAAGTATAAAAATC-AT-AAATAAA
1 TTAAAAAAT-TAAAAATCAATAAAATAAA
923432 TTAA
1 TTAA
923436 TTAAATACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.33
28 10 0.37
29 8 0.30
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (28 bp):
TTAAAAAATTAAAAATCAATAAAATAAA
Found at i:929554 original size:1 final size:1
Alignment explanation
Indices: 929550--929579 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
929540 TTTTTAAACC
*
929550 AAAAAAAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
929580 GAAAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:929573 original size:15 final size:15
Alignment explanation
Indices: 929550--929590 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
929540 TTTTTAAACC
929550 AAAAA-AAAAAAAAA
1 AAAAAGAAAAAAAAA
929564 AAAAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
*
929579 AGAAAGATAAAA
1 AAAAAGA-AAAA
929591 GGTGATCCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 5 0.21
15 15 0.62
16 4 0.17
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:929591 original size:11 final size:11
Alignment explanation
Indices: 929550--929583 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
929540 TTTTTAAACC
929550 AAAAAAAAA-A
1 AAAAAAAAAGA
929560 AAAAAAAAAGA
1 AAAAAAAAAGA
929571 AAAAAAAAAGA
1 AAAAAAAAAGA
929582 AA
1 AA
929584 GATAAAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:931772 original size:18 final size:18
Alignment explanation
Indices: 931749--931784 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
931739 GTTTTATGCT
931749 GAGAAGAAGAAGATGAAG
1 GAGAAGAAGAAGATGAAG
*
931767 GAGAAGAAGATGATGAAG
1 GAGAAGAAGAAGATGAAG
931785 AGTATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.39, T:0.08
Consensus pattern (18 bp):
GAGAAGAAGAAGATGAAG
Found at i:933872 original size:162 final size:163
Alignment explanation
Indices: 933698--934011 Score: 569
Period size: 162 Copynumber: 1.9 Consensus size: 163
933688 AGGTACCAAC
* *
933698 TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAACCTATAAAAGTTTGATGATGTGGCATTAT
1 TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGATGTGGCACTAT
933763 GAGATTGTGCAACATCATCACTTGAAAA-TT-AAAAAATATATATGAATTTTCAGGTGATGATGT
66 GAGATTGTGCAACATCATCACTTGAAAATTTAAAAAAAT-TATATGAATTTTCAGGTGATGATGT
933826 GATACAATTTCAAAGTTTCACATGGCACTTAAAT
130 GATACAATTTCAAAGTTTCACATGGCACTTAAAT
933860 TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGATGTGGCACTAT
1 TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGATGTGGCACTAT
*
933925 GAGATTGTGCTACATCATCACTTGAAAATTTAAAAAAATTATATGAATTTTCAGGTGATGATGTG
66 GAGATTGTGCAACATCATCACTTGAAAATTTAAAAAAATTATATGAATTTTCAGGTGATGATGTG
*
933990 GTACAATTTCAAAGTTTCACAT
131 ATACAATTTCAAAGTTTCACAT
934012 ACAATATTTT
Statistics
Matches: 146, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
162 90 0.62
163 49 0.34
164 7 0.05
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (163 bp):
TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGATGTGGCACTAT
GAGATTGTGCAACATCATCACTTGAAAATTTAAAAAAATTATATGAATTTTCAGGTGATGATGTG
ATACAATTTCAAAGTTTCACATGGCACTTAAAT
Found at i:937531 original size:45 final size:46
Alignment explanation
Indices: 937469--937564 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
937459 CAATTTGACC
*
937469 TACTAAATAATTAACTAAATTACATAGTATATATT-TTAAATTATTTA
1 TACTAAAT-ATTAACTAAATTACATAGTATATATTATT-AATTATCTA
* *
937516 TACTAAAT-TTAACTAAATTAGATAGTATTTATTATTAATTATCTA
1 TACTAAATATTAACTAAATTACATAGTATATATTATTAATTATCTA
937561 TACT
1 TACT
937565 TGATCAAGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 35 0.78
46 2 0.04
47 8 0.18
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (46 bp):
TACTAAATATTAACTAAATTACATAGTATATATTATTAATTATCTA
Found at i:940694 original size:17 final size:18
Alignment explanation
Indices: 940674--940707 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
940664 ATGAATACAA
*
940674 TTTAAATTTG-AATTATT
1 TTTAAATGTGAAATTATT
940691 TTTAAATGTGAAATTAT
1 TTTAAATGTGAAATTAT
940708 CAAAACATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TTTAAATGTGAAATTATT
Found at i:944428 original size:3 final size:3
Alignment explanation
Indices: 944420--944461 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
944410 TGATATAAAA
* *
944420 AAT AAT AAT AA- ACT AAT AAT AAT AAT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
944462 TTAAACCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:945995 original size:45 final size:45
Alignment explanation
Indices: 945760--946682 Score: 558
Period size: 44 Copynumber: 20.7 Consensus size: 45
945750 ACTAGGCTTC
* * *
945760 AATCTGCCCCGCTGCAACTTCAGGGGGATAAGA-TTCGCTA----T
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTT
* * * * * * *
945801 GATCTACTCTACTGCAACTTCAGAGAGATAAAATCTGTAACCAGTCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-T-GCTA-TCTTT
* * * * * * *
945850 AATCTGCTCCACCGTAATTTCAGGGA-AGTGAGATTTGCTATATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGA-TAAGACTTGCTATCTTT
* * * * *
945895 AGTCTGC-CCTACTGCAACTTTAGGGGGATAGGACTTG---T-TAT
1 AATCTGCTCC-ACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
** * * ** *
945936 GGTCTGCTCTACTGCAACTTCAGAGAGATAAGACCCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * * * *
945981 AGTCTGCTCCACTGCAACTTCAGAGAGATAAGA-GTGGTGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * * * * *
946025 AATCCGCTCCACTACAACTTCAAGGAGAT-AGAATT-ATTTGCTGT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAT-CTTT
* * *
946069 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGC---C-AT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * *
946110 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TG--CTAT--CTTT
* * * *
946161 AATCTGTTCCACTACAACTTCAGAGAAATAAGA-TTCGCTATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTT
*
946206 AATCTGCTCCACTACAACTTCAGGGAGATAAGACTTG-TCA-CTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCT-ATCTTT
* * ** **
946250 AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTATTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * * * *
946294 AATTTACTCCACTGCAACTTCAAGGAGATAAGA-TTCACCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTT
* * * * * *
946339 ATTCTGCCCCACTGCAACTTTAGGGGGATAAGACTTGTTTTCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * *
946384 AGTCTGCTCCACTGTAACTTCAAGGAGATAAGACTTG-TAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * * * **
946428 AACCCGCTCCACTGTAACTTCAGGGAGATATGA-TTACTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* *
946472 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTT
* * * *
946517 AGTCTG-TCCCACTGCAACTTCAGGGGGATAAGACTTGCTTTCTTC
1 AATCTGCT-CCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * *
946562 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG-TAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* ** **
946606 AAT-TCGCTCCACTACAACTTCAGGGAGAT-AGTA-TTATTGGCTTT
1 AATCT-GCTCCACTGCAACTTCAGGGAGATAAG-ACTTGCTATCTTT
*
946650 AATCTGCTCCACTACAACTTCAGGGAGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
946683 TTCGCCATCT
Statistics
Matches: 683, Mismatches: 152, Indels: 91
0.74 0.16 0.10
Matches are distributed among these distances:
41 83 0.12
42 4 0.01
43 17 0.02
44 267 0.39
45 240 0.35
46 10 0.01
47 4 0.01
48 3 0.00
49 25 0.04
50 1 0.00
51 29 0.04
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
Found at i:946416 original size:178 final size:178
Alignment explanation
Indices: 945938--946694 Score: 824
Period size: 178 Copynumber: 4.2 Consensus size: 178
945928 CTTGTTATGG
* * ** * *
945938 TCTGCTCTACTGCAACTTCAGAGAGATAAGACCCGCTATCTTCAGTCTGCTCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCA
* * * * * * * * ** * * * **
946003 GAGAGATAAGA-GTGGTGTCTTCAATCCGCTCCACTACAACTTCAAGGAGAT-AGAATTATTTGC
66 GGGGGATAAGACTTGCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTT-GTAAC
* * * * ** *
946066 TGTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-T-TT-GCCATGA
130 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
* * * ** * * ** *
946112 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCACTACA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-CG--CCAT--CTTCAGTCTGCCCCACTGCA
* ** * * **
946177 ACTTCAGAGAAATAAGA-TTCGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGACT
60 ACTTCAGGGGGATAAGACTT-GCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACT
*
946241 TGTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
124 TGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
* * * * * *
946296 TTTACTCCACTGCAACTTCAAGGAGATAAGATTCACCATCTTCATTCTGCCCCACTGCAACTTTA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCA
* *
946361 GGGGGATAAGACTTGTTTTCTTTAGTCTGCTCCACTGTAACTTCAAGGAGATAAGACTTGTAACT
66 GGGGGATAAGACTTGCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACT
* * * *
946426 TTAACCCGCTCCACTGTAACTTCAGGGAGATATGATTACTGGCTTTAA
131 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
*
946474 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGTCCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCA
*
946539 GGGGGATAAGACTTGCTTTCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACT
66 GGGGGATAAGACTTGCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACT
* * *
946604 TTAATTCGCTCCACTACAACTTCAGGGAGATAGTATTATTGGCTTTAA
131 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
*
946652 TCTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATCTTC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTC
946695 TTCAATCCAT
Statistics
Matches: 498, Mismatches: 73, Indels: 20
0.84 0.12 0.03
Matches are distributed among these distances:
174 31 0.06
176 1 0.00
178 322 0.65
179 2 0.00
180 35 0.07
181 67 0.13
182 6 0.01
183 3 0.01
184 31 0.06
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (178 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCA
GGGGGATAAGACTTGCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACT
TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
Found at i:946661 original size:222 final size:221
Alignment explanation
Indices: 945892--946685 Score: 588
Period size: 225 Copynumber: 3.6 Consensus size: 221
945882 ATTTGCTATA
* * * * * * *
945892 TTCAGTCTGCCCTACTGCAACTTTAGGGGGATAGGACTTGTT-A---TGGTCTGCTCTACTGCAA
1 TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTTAGTCTGCTCCACTACAA
** * * * * * *
945953 CTTC-AGAGAGATAAGACCCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGAGTG
66 CTTCAAG-GAGATAAGACTTG-TAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGA-TT
* ** * * * * * * *
946017 GTGTCTTCAATCCGCTCCACTACAACTTCAAGGAGAT-AGAATTATTTG-CTGTAATCTGCTCCA
128 CTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAG-ATTA-TCGCCTTTAATTTACTCCA
* * **
946080 CTGTAACTTCAGGGAGATAAGATTTGCCA--
191 CTGCAACTTCAAGGAGATAAGATTCACCATC
* * * * * *
946109 -TGA-TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCA
1 TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGA-CT-TG--TTA-A-CTTTAGTCTGCTCCA
* *
946172 CTACAACTTC-AGAGAAATAAGA-TTCGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGAT
60 CTACAACTTCAAG-GAGATAAGACTT-G-TAACTTTAATCTGCTCCACTACAACTTCAGGGAGAT
* * * *
946235 AAGACTTGTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATTTA
122 AAGA-TTCTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGCCTTTAATTTA
946300 CTCCACTGCAACTTCAAGGAGATAAGATTCACCATC
186 CTCCACTGCAACTTCAAGGAGATAAGATTCACCATC
* * * ** **
946336 TTCATTCTGCCCCACTGCAACTTTAGGGGGATAAGACTTGTTTTCTTTAGTCTGCTCCACTGTAA
1 TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTTAGTCTGCTCCACTACAA
* * ** *
946401 CTTCAAGGAGATAAGACTTGTAACTTTAACCCGCTCCACTGTAACTTCAGGGAGATATGATTACT
66 CTTCAAGGAGATAAGACTTGTAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATT-CT
** * *
946466 GGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TCGCCATCTTCAGTCTGT-C-CC
130 CACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGCC-T-TT-AAT-T-TACTCC
* * * **
946527 ACTGCAACTTCAGGGGGATAAGACTT-GCTTTC
190 ACTGCAACTTCAAGGAGATAAGA-TTCACCATC
* * *
946559 TTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG-TAACTTTAAT-TCGCTCCACTACA
1 TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTTAGTCT-GCTCCACTACA
* * **
946622 ACTTCAGGGAGAT-AGTA-TTATTGGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATT
65 ACTTCAAGGAGATAAG-ACTT-GTAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATT
946685 C
128 C
946686 GCCATCTTCT
Statistics
Matches: 464, Mismatches: 84, Indels: 54
0.77 0.14 0.09
Matches are distributed among these distances:
215 26 0.06
216 4 0.01
217 2 0.00
219 2 0.00
220 3 0.01
221 11 0.02
222 136 0.29
223 93 0.20
224 11 0.02
225 143 0.31
226 1 0.00
227 2 0.00
228 4 0.01
229 26 0.06
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (221 bp):
TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTTAGTCTGCTCCACTACAA
CTTCAAGGAGATAAGACTTGTAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTCTC
ACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGCCTTTAATTTACTCCACTGCA
ACTTCAAGGAGATAAGATTCACCATC
Found at i:947038 original size:24 final size:24
Alignment explanation
Indices: 947011--947071 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
947001 CAGATTACCC
947011 CCACTGTAATTTTCAAGATTCAAT
1 CCACTGTAATTTTCAAGATTCAAT
* *
947035 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATTTTCAAGATTCAAT
*
947059 CCACTGTACTTTT
1 CCACTGTAATTTT
947072 GAGACATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (24 bp):
CCACTGTAATTTTCAAGATTCAAT
Found at i:948895 original size:6 final size:6
Alignment explanation
Indices: 948884--948928 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
948874 TGGCCTCTCA
* *
948884 TTTTTC TTTTTC -TTTTC TTTTTC CTTCTC -TTTTC TTTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
948929 ATCATTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 14 0.42
6 19 0.58
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:948899 original size:11 final size:11
Alignment explanation
Indices: 948885--948928 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
948875 GGCCTCTCAT
948885 TTTTCTTTTTC
1 TTTTCTTTTTC
948896 TTTTCTTTTTC
1 TTTTCTTTTTC
*
948907 -CTTCTCTTTTC
1 TTTTCT-TTTTC
*
948918 TTTTTTTTTTC
1 TTTTCTTTTTC
948929 ATCATTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 4 0.14
11 21 0.75
12 3 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:948906 original size:17 final size:17
Alignment explanation
Indices: 948884--948928 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
948874 TGGCCTCTCA
948884 TTTTTCTTTTTCTTTTC
1 TTTTTCTTTTTCTTTTC
* *
948901 TTTTTCCTTCTCTTTTC
1 TTTTTCTTTTTCTTTTC
948918 TTTTT-TTTTTC
1 TTTTTCTTTTTC
948929 ATCATTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTC
Found at i:948956 original size:29 final size:29
Alignment explanation
Indices: 948922--948980 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
948912 CTTTTCTTTT
948922 TTTTTTCATCATTTTCATTTTTTTGAAATA
1 TTTTTTCAT-ATTTTCATTTTTTTGAAATA
* * *
948952 TTTTTTGATTTTTTGATTTTTTTGAAATA
1 TTTTTTCATATTTTCATTTTTTTGAAATA
948981 CTCTTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (29 bp):
TTTTTTCATATTTTCATTTTTTTGAAATA
Found at i:953006 original size:13 final size:13
Alignment explanation
Indices: 952988--953012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
952978 TTTAAAACAT
952988 AGAATTTTAAAAG
1 AGAATTTTAAAAG
953001 AGAATTTTAAAA
1 AGAATTTTAAAA
953013 ATAAATATAT
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:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
AGAATTTTAAAAG
Found at i:954276 original size:47 final size:46
Alignment explanation
Indices: 954207--954300 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 46
954197 CACCACTAGA
* *
954207 GTTAGAATCAGATGTAAAGATCAAAGGGTTTTTGTTAGGTTGTAACG
1 GTTAGAATCAGATGCAAAGATCAAAGGG-TTTTGTTAGGTTATAACG
*
954254 GTTAGAATCGGATGCAAAGATCAAAGGGTTTTGTTAGGTTATAACG
1 GTTAGAATCAGATGCAAAGATCAAAGGGTTTTGTTAGGTTATAACG
954300 G
1 G
954301 GGCTTGGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 18 0.41
47 26 0.59
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (46 bp):
GTTAGAATCAGATGCAAAGATCAAAGGGTTTTGTTAGGTTATAACG
Found at i:964868 original size:16 final size:16
Alignment explanation
Indices: 964847--964877 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
964837 CCACTACAGA
964847 AAATATTACAATTTCT
1 AAATATTACAATTTCT
*
964863 AAATATTGCAATTTC
1 AAATATTACAATTTC
964878 ATTATTCGAT
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:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (16 bp):
AAATATTACAATTTCT
Found at i:964953 original size:114 final size:114
Alignment explanation
Indices: 964753--964997 Score: 411
Period size: 114 Copynumber: 2.1 Consensus size: 114
964743 TACAGAAAAA
*
964753 ATTGCAATTCCATTATTTAATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTA
1 ATTGCAATTCCATTATTCAATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTA
964818 GATATTATTTAACATCCATCCA-CTACAGAAAATATTACAATTTCTAAAT
66 GATATTATTTAACATCCATCCATC-ACAGAAAATATTACAATTTCTAAAT
* * * *
964867 ATTGCAATTTCATTATTCGATATTTTAGTCTCAATCAATGTGTACATCTTTGATTTGATAAAGTA
1 ATTGCAATTCCATTATTCAATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTA
* *
964932 GATATTATTTGACATCCATCCATCATAGAAAATATTACAATTTCTAAAT
66 GATATTATTTAACATCCATCCATCACAGAAAATATTACAATTTCTAAAT
964981 ATTGCAATTCCATTATT
1 ATTGCAATTCCATTATT
964998 AAAACTTAAG
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 121 0.99
115 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (114 bp):
ATTGCAATTCCATTATTCAATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTA
GATATTATTTAACATCCATCCATCACAGAAAATATTACAATTTCTAAAT
Found at i:973155 original size:16 final size:16
Alignment explanation
Indices: 973136--973167 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
973126 GCAAGGACAT
*
973136 ATCGATGCATATTTTA
1 ATCGATGCACATTTTA
973152 ATCGATGCACATTTTA
1 ATCGATGCACATTTTA
973168 TAAAGTTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (16 bp):
ATCGATGCACATTTTA
Found at i:979908 original size:16 final size:16
Alignment explanation
Indices: 979871--979901 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
979861 TGAGAGCTAA
*
979871 GAGAGTTGAGAGAATT
1 GAGAGATGAGAGAATT
979887 GAGAGATGAGAGAAT
1 GAGAGATGAGAGAAT
979902 GATGAGAAGT
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:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (16 bp):
GAGAGATGAGAGAATT
Found at i:989606 original size:14 final size:14
Alignment explanation
Indices: 989587--989616 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
989577 ACACAGTCGT
989587 TATCAAGTAATAAG
1 TATCAAGTAATAAG
989601 TATCAAGTAATAAG
1 TATCAAGTAATAAG
989615 TA
1 TA
989617 AGTATCGAGT
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:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (14 bp):
TATCAAGTAATAAG
Found at i:1004767 original size:14 final size:14
Alignment explanation
Indices: 1004748--1004777 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1004738 ACACAGTCGT
1004748 TATCAAGTAATAAG
1 TATCAAGTAATAAG
1004762 TATCAAGTAATAAG
1 TATCAAGTAATAAG
1004776 TA
1 TA
1004778 AGTATCGAGT
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:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (14 bp):
TATCAAGTAATAAG
Found at i:1009481 original size:130 final size:130
Alignment explanation
Indices: 1009332--1009609 Score: 522
Period size: 130 Copynumber: 2.1 Consensus size: 130
1009322 GAAATTTTTA
1009332 ATAATATTTTATAATTTACACTTTTTAACAATTTTTCATATATACTTTTTATTTTTATAGATTTC
1 ATAATATTTT-TAATTTACACTTTTTAACAATTTTTCATATATACTTTTTATTTTTATAGATTTC
1009397 TTAAACTTTTAATACTTTTAATATTAATTCTTTTATATTTTTTGAAATTTTTATATTTTTTAGGA
65 TTAAACTTTTAATACTTTTAATATTAATTCTTTTATATTTTTTGAAATTTTTATATTTTTTAGGA
1009462 T
130 T
1009463 ATAATATTTTTAATTTACACTTTTTAACAATTTTTCATATATACTTTTTATTTTTATAGATTTCT
1 ATAATATTTTTAATTTACACTTTTTAACAATTTTTCATATATACTTTTTATTTTTATAGATTTCT
1009528 TAAACTTTTAATACTTTTAATATTAATTCTTTTATATTTTTTGAAATTTTTATATTTTTTAGGAT
66 TAAACTTTTAATACTTTTAATATTAATTCTTTTATATTTTTTGAAATTTTTATATTTTTTAGGAT
1009593 ATTGAAT-TTTTTAATTT
1 A-T-AATATTTTTAATTT
1009610 TTGAAAATAA
Statistics
Matches: 145, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
130 121 0.83
131 21 0.14
132 3 0.02
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (130 bp):
ATAATATTTTTAATTTACACTTTTTAACAATTTTTCATATATACTTTTTATTTTTATAGATTTCT
TAAACTTTTAATACTTTTAATATTAATTCTTTTATATTTTTTGAAATTTTTATATTTTTTAGGAT
Found at i:1013248 original size:16 final size:16
Alignment explanation
Indices: 1013227--1013259 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1013217 GTGGCAGAAG
1013227 GAAAGCGCACCACGTA
1 GAAAGCGCACCACGTA
1013243 GAAAGCGCACCACGTA
1 GAAAGCGCACCACGTA
1013259 G
1 G
1013260 GACGAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.27, T:0.06
Consensus pattern (16 bp):
GAAAGCGCACCACGTA
Found at i:1017448 original size:20 final size:20
Alignment explanation
Indices: 1017423--1017463 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1017413 AATGACATAC
1017423 TTTTATGTGTTAATTGTATA
1 TTTTATGTGTTAATTGTATA
1017443 TTTTATGTGTTAATTGTATA
1 TTTTATGTGTTAATTGTATA
1017463 T
1 T
1017464 ATATTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (20 bp):
TTTTATGTGTTAATTGTATA
Found at i:1017913 original size:20 final size:20
Alignment explanation
Indices: 1017888--1017954 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
1017878 TGTTCCTTTT
* *
1017888 ATTTATTCAGTAAAATTCTA
1 ATTTATTCAATAAAATTCCA
* *
1017908 ATTTATTCAATGAATTTCCA
1 ATTTATTCAATAAAATTCCA
*
1017928 ATTTATTCAATAAATTTCCA
1 ATTTATTCAATAAAATTCCA
*
1017948 TTTTATT
1 ATTTATT
1017955 AAACTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTTATTCAATAAAATTCCA
Found at i:1023893 original size:17 final size:18
Alignment explanation
Indices: 1023861--1023896 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1023851 TAAGTAAACA
*
1023861 AAAATATTCATTAAAAAT
1 AAAATATTCATCAAAAAT
1023879 AAAATATTCA-CAAAAAT
1 AAAATATTCATCAAAAAT
1023896 A
1 A
1023897 GTCAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATTCATCAAAAAT
Found at i:1034053 original size:3 final size:3
Alignment explanation
Indices: 1034047--1034073 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1034037 AATAATAATA
1034047 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1034074 CATTCACTTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1039273 original size:43 final size:43
Alignment explanation
Indices: 1039204--1039308 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
1039194 AATACCAACA
** * ** *
1039204 TCCCACACGTGGTCTTACATGTAATTACGTAGCGATGCCGCTG
1 TCCCACACAAGGTCTTACATGCAATTACAAAGCGATGCCACTG
* **
1039247 TCCCACACAAGGTCTTAC-TCGCAATTATAAATTGATGCCACTG
1 TCCCACACAAGGTCTTACAT-GCAATTACAAAGCGATGCCACTG
1039290 TCCCACACAAGGTCTTACA
1 TCCCACACAAGGTCTTACA
1039309 CTGTAACATT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 50 0.98
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (43 bp):
TCCCACACAAGGTCTTACATGCAATTACAAAGCGATGCCACTG
Found at i:1039813 original size:29 final size:29
Alignment explanation
Indices: 1039780--1039847 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1039770 AGCTTATATA
*
1039780 AGTCCTCAC-ATTTCATT-TTTTCACATTTT
1 AGTCC-CACAATTT-ATTATTTTCACAATTT
*
1039809 AGTCCCCCAATTTATTATTTTCACAATTT
1 AGTCCCACAATTTATTATTTTCACAATTT
1039838 AG-CCCA-AATT
1 AGTCCCACAATT
1039848 ACTCAAATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.12
28 8 0.24
29 22 0.65
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.44
Consensus pattern (29 bp):
AGTCCCACAATTTATTATTTTCACAATTT
Found at i:1045711 original size:67 final size:67
Alignment explanation
Indices: 1045611--1045896 Score: 267
Period size: 67 Copynumber: 4.3 Consensus size: 67
1045601 CCATCGTAGC
* * * *
1045611 CGAGCTATGGTCTTACACAACAT--ACCATGTGTTTATTGTCCTGGC-GAAATTTTTATGCTGCC
1 CGAGCTATGGTCTTACACAACATACACCA--TGTTTACTGTCCTGGCAG-ACTCTCTATGCTGCC
1045673 ATAGT
63 ATAGT
*
1045678 CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCCT-GCAGACTCTCTATGTTGCCAT
1 CGAGCTATGGTCTTACACAACATACACCATGTTTACTGT-CCTGGCAGACTCTCTATGCTGCCAT
1045742 AGT
65 AGT
* * * * * * * * *
1045745 CAAGCTTTGGTCTTACGCAACATACCCCGTGTTTACTCTCCCGACAGACTCTCTGTGCTGCCATA
1 CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCTGGCAGACTCTCTATGCTGCCATA
*
1045810 GC
66 GT
* * * * * * ** *
1045812 CGAACTATGATCATACATAACATAC-CTCATGTTTACTATCTTGGTGGACTCTTTATGCTGCCAT
1 CGAGCTATGGTCTTACACAACATACAC-CATGTTTACTGTCCTGGCAGACTCTCTATGCTGCCAT
1045876 AGT
65 AGT
*
1045879 CGAGTTATGGTCTTACAC
1 CGAGCTATGGTCTTACAC
1045897 CTTATACCTC
Statistics
Matches: 175, Mismatches: 38, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
66 3 0.02
67 164 0.94
68 4 0.02
69 4 0.02
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.33
Consensus pattern (67 bp):
CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCTGGCAGACTCTCTATGCTGCCATA
GT
Found at i:1048506 original size:37 final size:37
Alignment explanation
Indices: 1048456--1048527 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
1048446 TTGGAACGCC
1048456 CAAAGGAAAATACACCTAGTGCTTATCGACATATAGT
1 CAAAGGAAAATACACCTAGTGCTTATCGACATATAGT
1048493 CAAAGGAAAATACACCTAGTGCTTATCGACATATA
1 CAAAGGAAAATACACCTAGTGCTTATCGACATATA
1048528 ATACTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (37 bp):
CAAAGGAAAATACACCTAGTGCTTATCGACATATAGT
Found at i:1055227 original size:32 final size:33
Alignment explanation
Indices: 1055191--1055299 Score: 79
Period size: 32 Copynumber: 3.5 Consensus size: 33
1055181 TAATAACTCA
1055191 CATATATATA-TGTATATATATACAACCCCACT
1 CATATATATACTGTATATATATACAACCCCACT
* * * * *
1055223 CATATGTA-AATGCATAT-TA-CCAACCCCTC-
1 CATATATATACTGTATATATATACAACCCCACT
* * *
1055252 CATTTATATATTTTATATATATAGC-A-CCCACT
1 CATATATATACTGTATATATATA-CAACCCCACT
*
1055284 AATATATATACTGTAT
1 CATATATATACTGTAT
1055300 GCACAATAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
29 6 0.11
30 14 0.25
31 9 0.16
32 26 0.46
33 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (33 bp):
CATATATATACTGTATATATATACAACCCCACT
Found at i:1055746 original size:32 final size:32
Alignment explanation
Indices: 1055702--1055770 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
1055692 GAAATTCTAT
1055702 TTTTACGAATTGATTAGGATTTTATGGGATA-
1 TTTTACGAATTGATTAGGATTTTATGGGATAC
*
1055733 TTTTATGAGATTGATTAGGATTTTATGGGATAC
1 TTTTACGA-ATTGATTAGGATTTTATGGGATAC
1055766 TTTTA
1 TTTTA
1055771 AAAGGGGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 7 0.20
32 23 0.66
33 5 0.14
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.48
Consensus pattern (32 bp):
TTTTACGAATTGATTAGGATTTTATGGGATAC
Found at i:1056612 original size:21 final size:21
Alignment explanation
Indices: 1056586--1056634 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1056576 AAATGTAACT
1056586 GACTGGACTAACAGGACATTA
1 GACTGGACTAACAGGACATTA
** * *
1056607 GACTGGACTGGCAGGATATTG
1 GACTGGACTAACAGGACATTA
1056628 GACTGGA
1 GACTGGA
1056635 TCCAAGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (21 bp):
GACTGGACTAACAGGACATTA
Found at i:1058482 original size:78 final size:78
Alignment explanation
Indices: 1058395--1058550 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 78
1058385 ACAGCTTCTA
* * *
1058395 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAATAAAACA
1 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAACTCAAAGAGAATTATTATTAACTAAAAAAAACA
*
1058460 TAAATCAATTGTG
66 TAAATAAATTGTG
1058473 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAACTCAAAGAGAATTATTATTAACTAAAAAAAACA
1 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAACTCAAAGAGAATTATTATTAACTAAAAAAAACA
1058538 TAAATAAATTGTG
66 TAAATAAATTGTG
1058551 TGTATAACAG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.24
Consensus pattern (78 bp):
AAAGAAACTCAAGAGCAATTCTTGAAGAAAAACTCAAAGAGAATTATTATTAACTAAAAAAAACA
TAAATAAATTGTG
Found at i:1071202 original size:28 final size:28
Alignment explanation
Indices: 1071171--1071227 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1071161 ACTAAGACAT
1071171 TGGATCAAAACACTAGGCAAGTAAAATG
1 TGGATCAAAACACTAGGCAAGTAAAATG
*
1071199 TGGATCAAAACATTAGGCAAGTAAAATG
1 TGGATCAAAACACTAGGCAAGTAAAATG
1071227 T
1 T
1071228 AAGTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (28 bp):
TGGATCAAAACACTAGGCAAGTAAAATG
Found at i:1076833 original size:21 final size:21
Alignment explanation
Indices: 1076795--1076877 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
1076785 CAAATATGTC
*
1076795 AACAGAAGCT--TGAAAGCTA
1 AACAGAAGCTCGTAAAAGCTA
* *
1076814 AACAAAAGCTCGTAAAAGCTG
1 AACAGAAGCTCGTAAAAGCTA
* *
1076835 AACAGTAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAAAGCTA
* *
1076856 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCGTAAAAGCTA
1076877 A
1 A
1076878 TTCACCCAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.17
21 44 0.83
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAAAGCTA
Found at i:1079324 original size:15 final size:15
Alignment explanation
Indices: 1079304--1079358 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
1079294 ATAAAACAAC
1079304 AAATTTAAAGATAAA
1 AAATTTAAAGATAAA
* *
1079319 AAATTTGAGGA-AGAA
1 AAATTTAAAGATA-AA
1079334 AATATTATAAAGAT-AA
1 AA-ATT-TAAAGATAAA
1079350 AAATTTAAA
1 AAATTTAAA
1079359 TAAAATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 16 0.50
16 7 0.22
17 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (15 bp):
AAATTTAAAGATAAA
Found at i:1079809 original size:2 final size:2
Alignment explanation
Indices: 1079802--1079828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1079792 CAAGAAGATA
1079802 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1079829 CGCGCGCGCG
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:1081298 original size:51 final size:51
Alignment explanation
Indices: 1081181--1081311 Score: 136
Period size: 51 Copynumber: 2.6 Consensus size: 51
1081171 GTATATGGCA
* * * * * *
1081181 TAAGACTATGGATGAAAAATGCTATGGTAGTCTAGTATAAGGTATATAGTG
1 TAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAAGGTACATAGTG
** * * * *
1081232 TAAGACCATATATGAAAGACGCTATGGCAATTTGGTATGAGGTACGTAGTG
1 TAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAAGGTACATAGTG
* *
1081283 TAAGACCATGGATGAAAGACACCATGGCA
1 TAAGACCATGGATGAAAGACGCTATGGCA
1081312 GCATGGTACA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (51 bp):
TAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAAGGTACATAGTG
Found at i:1081326 original size:51 final size:51
Alignment explanation
Indices: 1081227--1081326 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 51
1081217 ATAAGGTATA
* * * ** **
1081227 TAGTGTAAGACCATATATGAAAGACGCTATGGCAATTTGGTATGAGGTACG
1 TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTACG
* *
1081278 TAGTGTAAGACCATGGATGAAAGACACCATGGCAGCATGGTACAAGGTA
1 TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTA
1081327 TAAGGTATAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (51 bp):
TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTACG
Found at i:1084298 original size:23 final size:23
Alignment explanation
Indices: 1084221--1084308 Score: 65
Period size: 23 Copynumber: 3.9 Consensus size: 23
1084211 GATATTTTAT
* * *
1084221 TGTTGT-AATTGAGGTGTATAAA
1 TGTTGTAAATTAAAGTGTTTAAA
*
1084243 TGTTGTTAA-TAAAGATG-TTAAA
1 TGTTGTAAATTAAAG-TGTTTAAA
* **
1084265 GTGCTACAAATTAAAGTGTTTAAA
1 -TGTTGTAAATTAAAGTGTTTAAA
*
1084289 TGTTGTAAATTGAAGTGTTT
1 TGTTGTAAATTAAAGTGTTT
1084309 TAAGTATCGC
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
22 13 0.26
23 27 0.54
24 10 0.20
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (23 bp):
TGTTGTAAATTAAAGTGTTTAAA
Found at i:1084400 original size:138 final size:138
Alignment explanation
Indices: 1084152--1084415 Score: 449
Period size: 138 Copynumber: 1.9 Consensus size: 138
1084142 TCTGTCTTAA
1084152 GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
1 GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
*
1084217 TTATTGTTGTAATTGAGGTGTATAAATGTTGTTAATAAAGATGTTAAAGTGCTACAAATTAAAGT
66 TTATTGTTGTAACTGAGGTGTATAAATGTTGTTAATAAAGATGTTAAAGTGCTACAAATTAAAGT
1084282 GTTTAAAT
131 GTTTAAAT
* * *
1084290 GTTGTAAATTGAAGTGTTTTAAGTA-TCGCAAATTGAATTGTTTAGTTTCTGGAAATTGAGATGT
1 GTTGTAAATTGAAGTGTTTTAAGTACT-GCAAATTGAATTATTTAGTTGCTGGAAATTGAGATAT
* * *
1084354 TTTATTGTTGTAACTGAGGTGTATAAATGTTGTTAATAGAGATGTTAAAGTGTTGCAAATTA
65 TTTATTGTTGTAACTGAGGTGTATAAATGTTGTTAATAAAGATGTTAAAGTGCTACAAATTA
1084416 CTGAAGCTCT
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
137 1 0.01
138 117 0.99
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.42
Consensus pattern (138 bp):
GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
TTATTGTTGTAACTGAGGTGTATAAATGTTGTTAATAAAGATGTTAAAGTGCTACAAATTAAAGT
GTTTAAAT
Found at i:1086265 original size:16 final size:16
Alignment explanation
Indices: 1086244--1086308 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
1086234 TGAGTTACTG
*
1086244 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
1086260 ATTACAGCTC---T--
1 ATTACAGCTCTATTCC
*
1086271 ATT-CAGCTCTATTCA
1 ATTACAGCTCTATTCC
1086286 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
1086302 ATTACAG
1 ATTACAG
1086309 TGAACCAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.15
11 3 0.07
13 2 0.05
15 3 0.07
16 27 0.66
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:1086277 original size:26 final size:26
Alignment explanation
Indices: 1086248--1086300 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1086238 TTACTGATTA
* *
1086248 CAGCTTTATTCCATTACAGCTCTATT
1 CAGCTCTATTCAATTACAGCTCTATT
1086274 CAGCTCTATTCAATTACAGCTCTATT
1 CAGCTCTATTCAATTACAGCTCTATT
1086300 C
1 C
1086301 CATTACAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.40
Consensus pattern (26 bp):
CAGCTCTATTCAATTACAGCTCTATT
Found at i:1093719 original size:9 final size:9
Alignment explanation
Indices: 1093702--1093738 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1093692 TGAGTTTTCG
1093702 AATTCGAAT
1 AATTCGAAT
*
1093711 AACTCGAAT
1 AATTCGAAT
1093720 AATTCGAAT
1 AATTCGAAT
1093729 AATTCGAAT
1 AATTCGAAT
1093738 A
1 A
1093739 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1094895 original size:14 final size:14
Alignment explanation
Indices: 1094872--1094905 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1094862 TACAATCTCC
1094872 AAATAATAACAATA
1 AAATAATAACAATA
*
1094886 AAATAGTAACAATA
1 AAATAATAACAATA
*
1094900 TAATAA
1 AAATAA
1094906 CGAAACGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:1094962 original size:1 final size:1
Alignment explanation
Indices: 1094956--1094983 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1094946 AGCAAATTTG
1094956 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1094984 AAAAATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1098181 original size:12 final size:11
Alignment explanation
Indices: 1098153--1098182 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1098143 AATTTTTTAA
1098153 TTTTTAAGAAT
1 TTTTTAAGAAT
1098164 TTTTTAAGAAT
1 TTTTTAAGAAT
1098175 TTATTTAA
1 TT-TTTAA
1098183 TTAAAATTAG
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:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
TTTTTAAGAAT
Found at i:1108494 original size:21 final size:21
Alignment explanation
Indices: 1108468--1108512 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1108458 AATGGAGGAA
*
1108468 GTTGAGTAGTTTATCTACACC
1 GTTGAGTAGTTTATCCACACC
* *
1108489 GTTGAGTGGTTTATCCATACC
1 GTTGAGTAGTTTATCCACACC
1108510 GTT
1 GTT
1108513 TGAATAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (21 bp):
GTTGAGTAGTTTATCCACACC
Found at i:1116136 original size:18 final size:20
Alignment explanation
Indices: 1116096--1116137 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1116086 TGTTAAAAAC
*
1116096 AAATTGAGCTAAAAAAATTT
1 AAATTGAGCTAAAAAAATAT
*
1116116 AAATTGA-C-AAAAATATAT
1 AAATTGAGCTAAAAAAATAT
1116134 AAAT
1 AAAT
1116138 ATGGGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 1 0.05
20 7 0.35
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATTGAGCTAAAAAAATAT
Found at i:1116422 original size:30 final size:32
Alignment explanation
Indices: 1116388--1116451 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 32
1116378 TCATTTTCTG
* *
1116388 TTTTTTTAATAAATGGCTCAATAT-TTT-TAC
1 TTTTTTGAATAAATGGCCCAATATGTTTATAC
**
1116418 TTTTTTGCTTAAATGGCCCAATATGTTTATAC
1 TTTTTTGAATAAATGGCCCAATATGTTTATAC
1116450 TT
1 TT
1116452 CTTCTTTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 20 0.71
31 3 0.11
32 5 0.18
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (32 bp):
TTTTTTGAATAAATGGCCCAATATGTTTATAC
Found at i:1141306 original size:22 final size:22
Alignment explanation
Indices: 1141277--1141354 Score: 104
Period size: 22 Copynumber: 3.5 Consensus size: 22
1141267 GAAATAGAAG
* *
1141277 CATA-GCATAATATGTTAGTTA
1 CATATGCATATTATGATAGTTA
1141298 CATATGCATATTATGATAGTTA
1 CATATGCATATTATGATAGTTA
*
1141320 CATATGCATATTATGATAGATA
1 CATATGCATATTATGATAGTTA
*
1141342 CAGAATGCATATT
1 CA-TATGCATATT
1141355 TCCTACCCCC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.08
22 38 0.75
23 9 0.18
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
CATATGCATATTATGATAGTTA
Found at i:1141519 original size:22 final size:22
Alignment explanation
Indices: 1141489--1141556 Score: 100
Period size: 22 Copynumber: 3.0 Consensus size: 22
1141479 TAACTGTCCA
*
1141489 TATGTTAGTTACATATGCATAT
1 TATGATAGTTACATATGCATAT
1141511 TATGATAGTTACATATGCATAT
1 TATGATAGTTACATATGCATAT
* *
1141533 TATGATAGATACAGAATGCATAT
1 TATGATAGTTACA-TATGCATAT
1141556 T
1 T
1141557 TCCTACCCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 33 0.79
23 9 0.21
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TATGATAGTTACATATGCATAT
Found at i:1141632 original size:202 final size:202
Alignment explanation
Indices: 1141286--1141688 Score: 797
Period size: 202 Copynumber: 2.0 Consensus size: 202
1141276 GCATAGCATA
1141286 ATATGTTAGTTACATATGCATATTATGATAGTTACATATGCATATTATGATAGATACAGAATGCA
1 ATATGTTAGTTACATATGCATATTATGATAGTTACATATGCATATTATGATAGATACAGAATGCA
1141351 TATTTCCTACCCCCCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCG
66 TATTTCCTACCCCCCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCG
*
1141416 AGTACCCATCCATCCCTGCAAACCACATAGTGATTGTATGTCACGTTCAAAACTACTGCAGACTA
131 AGTACCCATCCATCCCTGCAAACCACATAATGATTGTATGTCACGTTCAAAACTACTGCAGACTA
1141481 ACTGTCC
196 ACTGTCC
1141488 ATATGTTAGTTACATATGCATATTATGATAGTTACATATGCATATTATGATAGATACAGAATGCA
1 ATATGTTAGTTACATATGCATATTATGATAGTTACATATGCATATTATGATAGATACAGAATGCA
1141553 TATTTCCTACCCCCCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCG
66 TATTTCCTACCCCCCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCG
1141618 AGTACCCATCCATCCCTGCAAACCACATAATGATTGTATGTCACGTTCAAAACTACTGCAGACTA
131 AGTACCCATCCATCCCTGCAAACCACATAATGATTGTATGTCACGTTCAAAACTACTGCAGACTA
1141683 ACTGTC
196 ACTGTC
1141689 AGAACAGAAT
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 200 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (202 bp):
ATATGTTAGTTACATATGCATATTATGATAGTTACATATGCATATTATGATAGATACAGAATGCA
TATTTCCTACCCCCCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCG
AGTACCCATCCATCCCTGCAAACCACATAATGATTGTATGTCACGTTCAAAACTACTGCAGACTA
ACTGTCC
Found at i:1155896 original size:31 final size:29
Alignment explanation
Indices: 1155826--1155899 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
1155816 GGCTCAGGTT
* *
1155826 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
1155855 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
1155886 ACATTTTAGTCACT
1 ACATTTTAGTCACT
1155900 AAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:1157487 original size:42 final size:43
Alignment explanation
Indices: 1157356--1157490 Score: 191
Period size: 43 Copynumber: 3.2 Consensus size: 43
1157346 ACGTCGCTAA
* *
1157356 CTTTAGCGGCGCTTCTCCCACGAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
* *
1157399 CTTTAGCGGCGCGTATACCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
* * * *
1157442 CTTTAGCGTCGCTTTTCCCAC-AACGCCGCTAAAGACCAGGTC
1 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
1157484 CTTTAGC
1 CTTTAGC
1157491 AGCACCGCTA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 26 0.32
43 56 0.68
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.19
Consensus pattern (43 bp):
CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:1157556 original size:43 final size:43
Alignment explanation
Indices: 1157495--1157675 Score: 254
Period size: 43 Copynumber: 4.2 Consensus size: 43
1157485 TTTAGCAGCA
* ** ** *
1157495 CCGCTAAAGACCAGGACCTTTAGCGGTACTTTTTTCAAAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG
* *
1157538 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTATACCACGAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG
*
1157581 CCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTACCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG
* *
1157624 CCGCTAAAGACCAAAACCTTTAGCGGCGCTTTTTATCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTACCACAAACG
1157668 CCGCTAAA
1 CCGCTAAA
1157676 AACATAATCT
Statistics
Matches: 123, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 102 0.83
44 21 0.17
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (43 bp):
CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG
Found at i:1163220 original size:28 final size:29
Alignment explanation
Indices: 1163176--1163232 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1163166 CCCCAGATCT
* *
1163176 CTAAACCCTAAATCACTAA-CTCTTAACC
1 CTAAACCCTAAACCACTAACCTCTAAACC
1163204 CTAAATCCC-AAACCACTAACCTCTAAACC
1 CTAAA-CCCTAAACCACTAACCTCTAAACC
1163233 TTATTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.21
Consensus pattern (29 bp):
CTAAACCCTAAACCACTAACCTCTAAACC
Found at i:1163312 original size:82 final size:82
Alignment explanation
Indices: 1163210--1163368 Score: 239
Period size: 82 Copynumber: 1.9 Consensus size: 82
1163200 AACCCTAAAT
* * *
1163210 CCCAAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATC
1 CCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACC
1163275 ATAAACCCTAACATGAC
66 ATAAACCCTAACATGAC
* * *
1163292 CCCAAATCC-CTAACCCCTAAACATTATTTAATATATAAATTAAAACACGCTAATTAATCTAAAC
1 CCCAAA-CCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAAC
*
1163356 CCTAAACCCTAAC
65 CATAAACCCTAAC
1163369 CTAACACTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
82 67 0.97
83 2 0.03
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (82 bp):
CCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACC
ATAAACCCTAACATGAC
Found at i:1163392 original size:82 final size:82
Alignment explanation
Indices: 1163221--1163394 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 82
1163211 CCAAACCACT
* *
1163221 AACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATCATAAACCCTAA
1 AACC-CTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAA
* * *
1163286 CATGACCCCAAATCCCTA
65 CATAACACCAAATCCATA
* * * * *
1163304 ACCCCTAAACATTATTTAATATATAAATTAAAACACGCTAATTAATCTAAACCCTAAACCCTAAC
1 AACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAAC
* * *
1163369 CTAACACTAAATCTATA
66 ATAACACCAAATCCATA
1163386 AACCCTAAA
1 AACCCTAAA
1163395 TCCCTAACTC
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
82 74 0.96
83 3 0.04
ACGTcount: A:0.47, C:0.25, G:0.02, T:0.26
Consensus pattern (82 bp):
AACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAAC
ATAACACCAAATCCATA
Found at i:1163415 original size:14 final size:14
Alignment explanation
Indices: 1163386--1163464 Score: 63
Period size: 14 Copynumber: 5.6 Consensus size: 14
1163376 TAAATCTATA
*
1163386 AACCCTAAATCCCT
1 AACCCTTAATCCCT
* *
1163400 AACTCTTAATCTCT
1 AACCCTTAATCCCT
*
1163414 AACCCTTAACCCCT
1 AACCCTTAATCCCT
*
1163428 AACCCCTAA-CCCAT
1 AACCCTTAATCCC-T
* *
1163442 AAACCTTAAATCAC-
1 AACCCTT-AATCCCT
1163456 AACCCTTAA
1 AACCCTTAA
1163465 ATCAGAATCC
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
13 5 0.10
14 42 0.82
15 2 0.04
16 2 0.04
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCCTTAATCCCT
Found at i:1163487 original size:14 final size:15
Alignment explanation
Indices: 1163470--1163501 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1163460 CTTAAATCAG
1163470 AATCCCTAATT-CAT
1 AATCCCTAATTCCAT
1163484 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
1163499 AAT
1 AAT
1163502 TTATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:1164032 original size:42 final size:41
Alignment explanation
Indices: 1163878--1164036 Score: 273
Period size: 41 Copynumber: 3.9 Consensus size: 41
1163868 AAATGTTTTT
*
1163878 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1163919 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
1163960 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
1164001 GCGACGCTTTTTTTAAAAACGCCGCTAAAGATCTGA
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAGATCTGA
1164037 AAGGTACAAG
Statistics
Matches: 112, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 86 0.77
42 26 0.23
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:1164125 original size:40 final size:40
Alignment explanation
Indices: 1164081--1164159 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
1164071 TTGTGGCGTT
*
1164081 TTTCCAAAAAAACGCCACTAATGCT-AATTTTTAGCGGCGC
1 TTTCC-AAAAAACGCCACTAATGCTCAATCTTTAGCGGCGC
* * *
1164121 TTTCCTAAAAACGCCTCTAATGCTCGATCTTTAGCGGCG
1 TTTCCAAAAAACGCCACTAATGCTCAATCTTTAGCGGCG
1164160 TTTTACGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (40 bp):
TTTCCAAAAAACGCCACTAATGCTCAATCTTTAGCGGCGC
Found at i:1164181 original size:40 final size:40
Alignment explanation
Indices: 1164088--1164203 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
1164078 GTTTTTCCAA
* *
1164088 AAAAACGCCACTAATGCT-AATTTTTAGCGGCGCTTTCCT
1 AAAAACGCCACTAATGCTCGATTTTTAGCGGCGTTTTCCT
* * *
1164127 AAAAACGCCTCTAATGCTCGATCTTTAGCGGCGTTTTACGT
1 AAAAACGCCACTAATGCTCGATTTTTAGCGGCGTTTT-CCT
* * *
1164168 -AAAGCGCCGCTAATGCTCGATTTTTAGTGGCGTTTT
1 AAAAACGCCACTAATGCTCGATTTTTAGCGGCGTTTT
1164204 TTATCCAAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
39 17 0.26
40 47 0.71
41 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (40 bp):
AAAAACGCCACTAATGCTCGATTTTTAGCGGCGTTTTCCT
Found at i:1164227 original size:12 final size:12
Alignment explanation
Indices: 1164210--1164235 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1164200 TTTTTTATCC
1164210 AAACGCCGCTAA
1 AAACGCCGCTAA
1164222 AAACGCCGCTAA
1 AAACGCCGCTAA
1164234 AA
1 AA
1164236 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:1168478 original size:30 final size:30
Alignment explanation
Indices: 1168442--1168522 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
1168432 GGTCCATTTT
1168442 TATTTTAAAAAT-TTTAAAAATTTTAAAAAA
1 TATTTTAAAAATATTTAAAAA-TTTAAAAAA
*
1168472 TATTTTAAAAATATTTTAAAATTTAAAAAA
1 TATTTTAAAAATATTTAAAAATTTAAAAAA
* *
1168502 -AATTTAAAAAGTATGTAAAAA
1 TATTTTAAAAA-TATTTAAAAA
1168523 ATATTTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 9 0.20
30 29 0.64
31 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TATTTTAAAAATATTTAAAAATTTAAAAAA
Found at i:1168481 original size:11 final size:11
Alignment explanation
Indices: 1168442--1168533 Score: 81
Period size: 11 Copynumber: 8.9 Consensus size: 11
1168432 GGTCCATTTT
1168442 TATTTT-AAAA
1 TATTTTAAAAA
1168452 -ATTTTAAAAA
1 TATTTTAAAAA
*
1168462 T-TTTAAAAAA
1 TATTTTAAAAA
1168472 TATTTTAAAAA
1 TATTTTAAAAA
1168483 TATTTT--AAA
1 TATTTTAAAAA
1168492 -A-TTTAAAAA
1 TATTTTAAAAA
* *
1168501 AAATTTAAAAA
1 TATTTTAAAAA
* *
1168512 GTATGTAAAAAA
1 -TATTTTAAAAA
1168524 TATTTTAAAA
1 TATTTTAAAA
1168534 TTAAAAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
7 3 0.05
8 1 0.02
9 11 0.17
10 14 0.21
11 30 0.45
12 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:1168488 original size:41 final size:42
Alignment explanation
Indices: 1168442--1168544 Score: 133
Period size: 41 Copynumber: 2.5 Consensus size: 42
1168432 GGTCCATTTT
* * * *
1168442 TATTTTAAAAATTT-TAAAAATTTTAAAAAATATTTTAAAAA
1 TATTTTAAAAATTTAAAAAAAATTTAAAAAATATGTAAAAAA
*
1168483 TATTTT-AAAATTTAAAAAAAATTTAAAAAGTATGTAAAAAA
1 TATTTTAAAAATTTAAAAAAAATTTAAAAAATATGTAAAAAA
1168524 TATTTT-AAAA-TTAAAAAAAAT
1 TATTTTAAAAATTTAAAAAAAAT
1168545 AAATATATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
40 18 0.32
41 38 0.68
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (42 bp):
TATTTTAAAAATTTAAAAAAAATTTAAAAAATATGTAAAAAA
Found at i:1168500 original size:8 final size:9
Alignment explanation
Indices: 1168443--1168511 Score: 66
Period size: 9 Copynumber: 7.1 Consensus size: 9
1168433 GTCCATTTTT
1168443 ATTTTAAAA
1 ATTTTAAAA
1168452 ATTTTAAAA
1 ATTTTAAAA
1168461 ATTTTAAAAAA
1 ATTTT--AAAA
1168472 TATTTTAAAA
1 -ATTTTAAAA
*
1168482 ATATTTTAAA
1 AT-TTTAAAA
*
1168492 ATTTAAAAAA
1 ATTT-TAAAA
*
1168502 AATTTAAAA
1 ATTTTAAAA
1168511 A
1 A
1168512 GTATGTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
9 23 0.46
10 18 0.36
11 4 0.08
12 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:1169005 original size:31 final size:31
Alignment explanation
Indices: 1168967--1169034 Score: 106
Period size: 28 Copynumber: 2.3 Consensus size: 31
1168957 TTTAATAGAA
1168967 GACTAATTTTTTCTTTAATCCAATGTGCAAG
1 GACTAATTTTTTCTTTAATCCAATGTGCAAG
*
1168998 GACTAA---TTTGTTTAATCCAATGTGCAAG
1 GACTAATTTTTTCTTTAATCCAATGTGCAAG
1169026 GACTAATTT
1 GACTAATTT
1169035 GTCTAACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 27 0.82
31 6 0.18
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (31 bp):
GACTAATTTTTTCTTTAATCCAATGTGCAAG
Found at i:1169016 original size:28 final size:28
Alignment explanation
Indices: 1168980--1169036 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1168970 TAATTTTTTC
1168980 TTTAATCCAATGTGCAAGGACTAATTTG
1 TTTAATCCAATGTGCAAGGACTAATTTG
1169008 TTTAATCCAATGTGCAAGGACTAATTTG
1 TTTAATCCAATGTGCAAGGACTAATTTG
1169036 T
1 T
1169037 CTAACTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (28 bp):
TTTAATCCAATGTGCAAGGACTAATTTG
Found at i:1177696 original size:16 final size:16
Alignment explanation
Indices: 1177675--1177713 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1177665 TTGATTTGCT
*
1177675 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
1177691 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
1177707 ATTACAC
1 ATTACAC
1177714 CTCTAATCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:1177714 original size:16 final size:16
Alignment explanation
Indices: 1177688--1177744 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
1177678 ACACAGCTTT
* *
1177688 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
1177704 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
*
1177720 TCTAATACACCTCTAA
1 TCCAATACACCTCTAA
1177736 TCCAATACA
1 TCCAATACA
1177745 GCGAACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.32
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:1178513 original size:25 final size:25
Alignment explanation
Indices: 1178479--1178528 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1178469 AAGCCCAACT
1178479 CCTCAGCCACCGTCACTGCTTGGAG
1 CCTCAGCCACCGTCACTGCTTGGAG
1178504 CCTCAGCCACCGTCACTGCTTGGAG
1 CCTCAGCCACCGTCACTGCTTGGAG
1178529 GCACGCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (25 bp):
CCTCAGCCACCGTCACTGCTTGGAG
Found at i:1183521 original size:19 final size:18
Alignment explanation
Indices: 1183493--1183541 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1183483 AAATCTGACA
* *
1183493 ATTTATATATTTATATTAT
1 ATTTAAATATTTA-AATAT
1183512 ATTTAAATATTTAAATAT
1 ATTTAAATATTTAAATAT
*
1183530 AGTT-AATATTTA
1 ATTTAAATATTTA
1183542 CATAGCTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTAAATATTTAAATAT
Found at i:1187588 original size:5 final size:5
Alignment explanation
Indices: 1187574--1187604 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1187564 ATGAATGACA
*
1187574 TATGG GATGG TATGG TATGG TATGG TATGG T
1 TATGG TATGG TATGG TATGG TATGG TATGG T
1187605 TAAGTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.39
Consensus pattern (5 bp):
TATGG
Found at i:1200017 original size:18 final size:18
Alignment explanation
Indices: 1199982--1200033 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1199972 ACATAGCTTT
*
1199982 TAAAAATAAAAACTAAAA
1 TAAAAATAAAAACAAAAA
*
1200000 TAAAAATAAAACCAAAAA
1 TAAAAATAAAAACAAAAA
* *
1200018 GAAAAAAAATAAACAA
1 TAAAAATAA-AAACAA
1200034 TAAAGTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.79, C:0.08, G:0.02, T:0.12
Consensus pattern (18 bp):
TAAAAATAAAAACAAAAA
Found at i:1207483 original size:25 final size:24
Alignment explanation
Indices: 1207455--1207546 Score: 105
Period size: 25 Copynumber: 3.7 Consensus size: 24
1207445 TCCGACCCAC
1207455 AGCTCGTGTGAGCATACCGATTCA
1 AGCTCGTGTGAGCATACCGATTCA
*
1207479 TAGCTCGTGAGAGCATACCGATCTACA
1 -AGCTCGTGTGAGCATACCGAT-T-CA
* *
1207506 A-CTCGAGTGAGCATACCAATTCA
1 AGCTCGTGTGAGCATACCGATTCA
*
1207529 CAGCTCGTTTGAGCATAC
1 -AGCTCGTGTGAGCATAC
1207547 ATGTACATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 49 0.86
26 2 0.04
27 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (24 bp):
AGCTCGTGTGAGCATACCGATTCA
Found at i:1215287 original size:25 final size:25
Alignment explanation
Indices: 1215254--1215327 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
1215244 GCTACGCTTT
*
1215254 GATCCACAGCTCGTGTGAGCATACC
1 GATCTACAGCTCGTGTGAGCATACC
* *
1215279 GATCTACAGCTCGAGTGAGCAAACC
1 GATCTACAGCTCGTGTGAGCATACC
* *
1215304 GAT-TCACAGCTTGTATGAGCATAC
1 GATCT-ACAGCTCGTGTGAGCATAC
1215328 ATGTACATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (25 bp):
GATCTACAGCTCGTGTGAGCATACC
Found at i:1217920 original size:16 final size:17
Alignment explanation
Indices: 1217896--1217931 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1217886 AACCATAATT
*
1217896 TTTTTAATTT-ATTTAA
1 TTTTGAATTTAATTTAA
1217912 TTTTGAATTTAATTTAA
1 TTTTGAATTTAATTTAA
1217929 TTT
1 TTT
1217932 ATGTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTGAATTTAATTTAA
Found at i:1221316 original size:85 final size:84
Alignment explanation
Indices: 1221173--1221387 Score: 261
Period size: 85 Copynumber: 2.5 Consensus size: 84
1221163 ATGCCGTTAT
* *
1221173 AGAACATGACCTTTAGCGGCACCTTTCCCACAAACGCCACTAAAGAATTGACCTTTAGCGGCA-C
1 AGAACATGACCTTTAGCGGC-GCTTTCCCACAAACGCCACTAAAGAAATGACCTTTAGCGG-AGC
1221237 TTTCCCCACAAACGCTGCTAA
64 TTTCCCCACAAACGCTGCTAA
* * *** *
1221258 AGAACATGACCTTTGGCGGCGCTTTCCCACAAATGTTGCTATAGAACATGACCTTTAGCGGAGCT
1 AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAGAA-ATGACCTTTAGCGGAGCT
**
1221323 TTTTCCACAAACGCTGCTAA
65 TTCCCCACAAACGCTGCTAA
* * * *
1221343 AGATCATGACCTTTAGCAGCGCTTTCCCCAGAAACGCCGCTAAAG
1 AGAACATGACCTTTAGCGGCGCTTT-CCCACAAACGCCACTAAAG
1221388 GTCATGTTCT
Statistics
Matches: 109, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
84 21 0.19
85 74 0.68
86 14 0.13
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (84 bp):
AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAGAAATGACCTTTAGCGGAGCTT
TCCCCACAAACGCTGCTAA
Found at i:1221393 original size:43 final size:42
Alignment explanation
Indices: 1221173--1221387 Score: 252
Period size: 43 Copynumber: 5.0 Consensus size: 42
1221163 ATGCCGTTAT
* **
1221173 AGAACATGACCTTTAGCGGCACCTTTCCCACAAACGCCACTAA
1 AGAACATGACCTTTAGCGGC-GCTTTCCCACAAACGCTGCTAA
* *
1221216 AGAA-TTGACCTTTAGCGGCACTTTCCCCACAAACGCTGCTAA
1 AGAACATGACCTTTAGCGGCGCTTT-CCCACAAACGCTGCTAA
* * * *
1221258 AGAACATGACCTTTGGCGGCGCTTTCCCACAAATGTTGCTAT
1 AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCTGCTAA
* *
1221300 AGAACATGACCTTTAGCGGAGCTTTTTCCACAAACGCTGCTAA
1 AGAACATGACCTTTAGCGGCGC-TTTCCCACAAACGCTGCTAA
* * * *
1221343 AGATCATGACCTTTAGCAGCGCTTTCCCCAGAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTT-CCCACAAACGCTGCTAA
1221386 AG
1 AG
1221388 GTCATGTTCT
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.03
42 70 0.48
43 72 0.49
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (42 bp):
AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCTGCTAA
Found at i:1221762 original size:21 final size:21
Alignment explanation
Indices: 1221737--1221777 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1221727 TGCTTTGCTC
* *
1221737 TGCTTCTCTTGCTGCTGCCTT
1 TGCTTCCCTCGCTGCTGCCTT
1221758 TGCTTCCCTCGCTGCTGCCT
1 TGCTTCCCTCGCTGCTGCCT
1221778 CCGCTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.39, G:0.20, T:0.41
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCTGCCTT
Found at i:1221783 original size:21 final size:21
Alignment explanation
Indices: 1221738--1221783 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1221728 GCTTTGCTCT
* * **
1221738 GCTTCTCTTGCTGCTGCCTTT
1 GCTTCCCTCGCTGCTGCCTCC
1221759 GCTTCCCTCGCTGCTGCCTCC
1 GCTTCCCTCGCTGCTGCCTCC
1221780 GCTT
1 GCTT
1221784 TAAGTTCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.41, G:0.20, T:0.39
Consensus pattern (21 bp):
GCTTCCCTCGCTGCTGCCTCC
Found at i:1227149 original size:21 final size:22
Alignment explanation
Indices: 1227111--1227151 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1227101 TTAATTATAC
**
1227111 TTTTTTAATTTATAAATTTATG
1 TTTTTTAATAAATAAATTTATG
1227133 TTTTTTAATAAAT-AATTTA
1 TTTTTTAATAAATAAATTTA
1227152 AATAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTTAATAAATAAATTTATG
Found at i:1227330 original size:66 final size:66
Alignment explanation
Indices: 1227224--1227355 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
1227214 CCATTAATAT
*
1227224 ACAAGTATTTATATTATTCAAAGATATACCATTAATATAAAAGCTATCCGAAACCCTAATAGGAG
1 ACAAGTAATTATATTATTCAAAGATATACCATTAATATAAAAGCTATCCGAAACCCTAATAGGAG
1227289 A
66 A
1227290 ACAAGTAATTATATTATTCAAAGATATACCATTAATATAAAAGCTATCCGAAACCCTAATAGGAG
1 ACAAGTAATTATATTATTCAAAGATATACCATTAATATAAAAGCTATCCGAAACCCTAATAGGAG
1227355 A
66 A
1227356 TTCAAGGTGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (66 bp):
ACAAGTAATTATATTATTCAAAGATATACCATTAATATAAAAGCTATCCGAAACCCTAATAGGAG
A
Found at i:1228177 original size:24 final size:24
Alignment explanation
Indices: 1228150--1228202 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1228140 TGTATTTTAT
1228150 AATATAATATTAATTTTAGATACA
1 AATATAATATTAATTTTAGATACA
* *
1228174 AATATAATATTAATTTTAGTTAGA
1 AATATAATATTAATTTTAGATACA
1228198 AATAT
1 AATAT
1228203 TATACAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:1228648 original size:17 final size:17
Alignment explanation
Indices: 1228628--1228665 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1228618 TTAAAGTTCA
1228628 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
*
1228645 CAAGGAAGTAGAGGCTG
1 CAAGGAAGTAAAGGCTG
1228662 CAAG
1 CAAG
1228666 TTCCTGGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.37, T:0.11
Consensus pattern (17 bp):
CAAGGAAGTAAAGGCTG
Found at i:1228953 original size:33 final size:33
Alignment explanation
Indices: 1228906--1228973 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
1228896 ATATACATGT
*
1228906 ATTCATACCTAACACTAATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
*
1228939 ATTCATACCCAACACTTATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
1228972 AT
1 AT
1228974 AACATAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (33 bp):
ATTCATACCCAACACTAATCTCATTTAACTCGA
Found at i:1229627 original size:15 final size:14
Alignment explanation
Indices: 1229595--1229634 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1229585 AATTGGGAAA
*
1229595 TTGGGGAAAATAAT
1 TTGGGGAAAATAAC
1229609 TTGGGGAAGAATAAC
1 TTGGGGAA-AATAAC
*
1229624 TTGGGGGAAAT
1 TTGGGGAAAAT
1229635 TGGGGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.25
Consensus pattern (14 bp):
TTGGGGAAAATAAC
Found at i:1229638 original size:25 final size:22
Alignment explanation
Indices: 1229609--1229665 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
1229599 GGAAAATAAT
*
1229609 TTGGGGAAGAATAACTTGGGGGAAA
1 TTGGGGAA-AAGAACTT--GGGAAA
*
1229634 TTGGGGGAAAAGAAGTTGGGAAA
1 TT-GGGGAAAAGAACTTGGGAAA
1229657 TTGGGGAAA
1 TTGGGGAAA
1229666 TGAAATCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
25 8 0.28
26 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.42, T:0.19
Consensus pattern (22 bp):
TTGGGGAAAAGAACTTGGGAAA
Found at i:1229678 original size:23 final size:23
Alignment explanation
Indices: 1229628--1229681 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1229618 AATAACTTGG
* *
1229628 GGGAAATTGGGGGAAAAGAAGTT
1 GGGAAATTGGGGGAAAAGAAATC
*
1229651 GGGAAATT-GGGGAAATGAAATC
1 GGGAAATTGGGGGAAAAGAAATC
1229673 GTGGAAATT
1 G-GGAAATT
1229682 TGACTTGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.39, C:0.02, G:0.39, T:0.20
Consensus pattern (23 bp):
GGGAAATTGGGGGAAAAGAAATC
Found at i:1229905 original size:12 final size:11
Alignment explanation
Indices: 1229888--1229921 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
1229878 ACAGCATTTT
1229888 AGTAAAAACGCC
1 AGTAAAAACG-C
1229900 AGTAAAAACGC
1 AGTAAAAACGC
1229911 AGATAAAAACG
1 AG-TAAAAACG
1229922 TCAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 3 0.14
12 18 0.86
ACGTcount: A:0.56, C:0.18, G:0.18, T:0.09
Consensus pattern (11 bp):
AGTAAAAACGC
Found at i:1230163 original size:116 final size:113
Alignment explanation
Indices: 1229785--1230193 Score: 374
Period size: 116 Copynumber: 3.5 Consensus size: 113
1229775 CACTAATGCA
* * * * *
1229785 ACTAAAAATGCAGCTTAAAACGACAACATTTTGCAAACTCTTAAAACATATTTGCAGTGTTTTTT
1 ACTAAAAACGCAGC-TAAAACGACAACGTTTTGCAAACTCTTAATACATATTCGCAGCG-TTTTT
** * *
1229850 TGTGAAAA-CCACTAACTTATATCCTTTTACAGCATTTTAGTAAAAACGCC
64 TGTGAAAAGCCACTAACGCATATCCTTTTGCGGCATTTTAGT-AAAACGCC
* * * ** * * *
1229900 AGTAAAAACGCAGATAAAAACGTCAAATTTTTGCAAACTCTTAA-ACCAAATTCGCGGCATTTTT
1 ACTAAAAACGCAGCT-AAAACGACAACGTTTTGCAAACTCTTAATA-CATATTCGCAGCGTTTTT
* ** *
1229964 TGTGAAAAGGCCACTAACGCATATCCTTTTGTGGTTTTTTAGTAAAAGTGCC
64 TGTGAAAA-GCCACTAACGCATATCCTTTTGCGGCATTTTAGTAAAA-CGCC
* ** *
1230016 ACCAAAAGTGCAGCTGAAAACGAC-ACTGTTTTGCAAACTCTTAATACATATTTGCAGCGTTTTT
1 ACTAAAAACGCAGCT-AAAACGACAAC-GTTTTGCAAACTCTTAATACATATTCGCAGCGTTTTT
* * *
1230080 GGTGAAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAACGCC
64 TGTGAAAA-GCCACTAACGCATATCCTTTTGCGGCATTTTAGT-AAAACGCC
** * ** * *
1230132 ACTAAAAACATAGCTACAAATGACAACGTTTTGCATTCTTTTAATACATATTCGCCGCGTTT
1 ACTAAAAACGCAGCTA-AAACGACAACGTTTTGCAAACTCTTAATACATATTCGCAGCGTTT
1230194 GGACCAAAAA
Statistics
Matches: 234, Mismatches: 50, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
114 15 0.06
115 50 0.21
116 162 0.69
117 7 0.03
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (113 bp):
ACTAAAAACGCAGCTAAAACGACAACGTTTTGCAAACTCTTAATACATATTCGCAGCGTTTTTTG
TGAAAAGCCACTAACGCATATCCTTTTGCGGCATTTTAGTAAAACGCC
Found at i:1230725 original size:7 final size:7
Alignment explanation
Indices: 1230715--1230777 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
1230705 AAATTTATTT
1230715 TTTAGGG
1 TTTAGGG
*
1230722 TTTATGG
1 TTTAGGG
* *
1230729 TATATGGT
1 TTTA-GGG
1230737 TTTAGGG
1 TTTAGGG
1230744 TTTAGGG
1 TTTAGGG
*
1230751 TTTAAGG
1 TTTAGGG
* *
1230758 TCTAAAGG
1 T-TTAGGG
1230766 TTTAGGG
1 TTTAGGG
1230773 TTTAG
1 TTTAG
1230778 AGAAAGCCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
7 34 0.77
8 10 0.23
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:1230747 original size:29 final size:29
Alignment explanation
Indices: 1230715--1230777 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1230705 AAATTTATTT
* *
1230715 TTTAGGGTTTATGGTAT-ATGGTTTTAGGG
1 TTTAGGGTTTAAGGTATAAAGG-TTTAGGG
*
1230744 TTTAGGGTTTAAGGTCTAAAGGTTTAGGG
1 TTTAGGGTTTAAGGTATAAAGGTTTAGGG
1230773 TTTAG
1 TTTAG
1230778 AGAAAGCCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (29 bp):
TTTAGGGTTTAAGGTATAAAGGTTTAGGG
Done.