Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1421
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: 311925
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:9588 original size:19 final size:20
Alignment explanation
Indices: 9551--9605 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
9541 CGAATTCAAA
*
9551 AAAAAAAGAGTGAGCAAAAAA-
1 AAAAAAA-AGTGA-AAAAAAAC
*
9572 GAAAAAAAGT-AAAAAAAAC
1 AAAAAAAAGTGAAAAAAAAC
9591 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
9606 GTCTTGTGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.21
19 10 0.34
20 7 0.24
21 6 0.21
ACGTcount: A:0.76, C:0.04, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAAAGTGAAAAAAAAC
Found at i:14809 original size:13 final size:13
Alignment explanation
Indices: 14791--14836 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
14781 CATAAATCAC
14791 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
* *
14804 TTTTTTTTTGCAT
1 TTTTTTTTCGAAT
* *
14817 TGTTTTTTCAAAT
1 TTTTTTTTCGAAT
14830 TTTTTTT
1 TTTTTTT
14837 AACTTCTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:15505 original size:15 final size:15
Alignment explanation
Indices: 15485--15513 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15475 ACAACGGAAT
15485 GGTAGGAACAAAGGG
1 GGTAGGAACAAAGGG
15500 GGTAGGAACAAAGG
1 GGTAGGAACAAAGG
15514 ATATGAACAA
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:0.41, C:0.07, G:0.45, T:0.07
Consensus pattern (15 bp):
GGTAGGAACAAAGGG
Found at i:19114 original size:10 final size:10
Alignment explanation
Indices: 19101--19127 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
19091 GTGAGTGAAG
19101 TTGAGCTGAT
1 TTGAGCTGAT
19111 TTGAGCTGAT
1 TTGAGCTGAT
19121 TTGAGCT
1 TTGAGCT
19128 TGAGGAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:31388 original size:28 final size:29
Alignment explanation
Indices: 31331--31389 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
31321 GAGGATTCAA
* *
31331 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
31360 AGATGGATTTAT-GATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
31388 AG
1 AG
31390 GTTTGGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:32369 original size:14 final size:14
Alignment explanation
Indices: 32347--32389 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
32337 TTAAAGAAGC
32347 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
32361 AATTCATTAAAATA
1 AACTCATTAAATTA
*
32375 AACTCATTTAATTA
1 AACTCATTAAATTA
32389 A
1 A
32390 CTAAGATGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:32427 original size:45 final size:46
Alignment explanation
Indices: 32375--32486 Score: 133
Period size: 45 Copynumber: 2.5 Consensus size: 46
32365 CATTAAAATA
**
32375 AACTCATTTAATT-AACTAAGATGAGTTTGTA-TTAATG-ACCAGTGC
1 AACTCATTT-ATTAAACTAAGATGAG-TTGTATTTAATGAACCACAGC
* *
32420 AACTCATTTTATTAAACTCA-ATGAGTTGTATTTAATGAACCTCAGC
1 AACTCA-TTTATTAAACTAAGATGAGTTGTATTTAATGAACCACAGC
32466 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
32487 GGCTTAAATC
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
44 5 0.09
45 32 0.56
46 20 0.35
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (46 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTTAATGAACCACAGC
Found at i:33169 original size:30 final size:30
Alignment explanation
Indices: 33074--33170 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
33064 AGCTCACTCC
*
33074 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
* * * * **
33104 TATCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
33134 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
33164 TAGCTCA
1 TAGCTCA
33171 TTTTAGTTTT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 3 0.06
30 43 0.88
31 3 0.06
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:34854 original size:10 final size:10
Alignment explanation
Indices: 34839--34883 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
34829 AAGAGAGAAG
34839 AAATTAAAAA
1 AAATTAAAAA
34849 AAATT-AAAA
1 AAATTAAAAA
*
34858 AAATCGAAAAAA
1 AAAT--TAAAAA
34870 AAATTAAAAA
1 AAATTAAAAA
34880 AAAT
1 AAAT
34884 CGAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 8 0.27
10 14 0.47
12 8 0.27
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (10 bp):
AAATTAAAAA
Found at i:34858 original size:31 final size:31
Alignment explanation
Indices: 34820--34883 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
34810 ATTGTATTGG
* *
34820 ATTAAAAAAA-AGAGAGAAGAAATTAAAAAAA
1 ATTAAAAAAATAGA-AAAAAAAATTAAAAAAA
*
34851 ATTAAAAAAATCGAAAAAAAAATTAAAAAAA
1 ATTAAAAAAATAGAAAAAAAAATTAAAAAAA
34882 AT
1 AT
34884 CGAAATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (31 bp):
ATTAAAAAAATAGAAAAAAAAATTAAAAAAA
Found at i:34869 original size:22 final size:22
Alignment explanation
Indices: 34844--34888 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
34834 AGAAGAAATT
34844 AAAAAAAATT-AAAAAAATCGA
1 AAAAAAAATTAAAAAAAATCGA
34865 AAAAAAAATTAAAAAAAATCGA
1 AAAAAAAATTAAAAAAAATCGA
34887 AA
1 AA
34889 TATAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAAAAAATTAAAAAAAATCGA
Found at i:35782 original size:5 final size:5
Alignment explanation
Indices: 35772--35849 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
35762 AAAGAGAAAC
*
35772 AAGAA AAGAA AAGAA AAGAA AA-AGA AAGAA AAG-A AA-CA AAGAA AATGAA
1 AAGAA AAGAA AAGAA AAGAA AAGA-A AAGAA AAGAA AAGAA AAGAA AA-GAA
* *
35821 AA-CA AAGAA AA-AA TGAAAAA AAGAA AAGA
1 AAGAA AAGAA AAGAA --AAGAA AAGAA AAGA
35850 GAGGCAGAGG
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
4 12 0.20
5 38 0.63
6 8 0.13
7 2 0.03
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:35792 original size:15 final size:14
Alignment explanation
Indices: 35772--35849 Score: 77
Period size: 15 Copynumber: 5.3 Consensus size: 14
35762 AAAGAGAAAC
35772 AAGAAAAGAAAAGAA
1 AAGAAAA-AAAAGAA
35787 AAGAAAAAGAAAGAA
1 AAGAAAAA-AAAGAA
*
35802 AAG-AAACAAAGAA
1 AAGAAAAAAAAGAA
*
35815 AATGAAAACAAAGAA
1 AA-GAAAAAAAAGAA
*
35830 AAAATGAAAAAAAGAA
1 AAGA--AAAAAAAGAA
35846 AAGA
1 AAGA
35850 GAGGCAGAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
13 8 0.15
14 6 0.11
15 28 0.52
16 12 0.22
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:42080 original size:15 final size:16
Alignment explanation
Indices: 42060--42097 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
42050 CATTTCTTTT
42060 TCTTTTGAATCACTC-
1 TCTTTTGAATCACTCA
**
42075 TCTTTTTTATCACTCA
1 TCTTTTGAATCACTCA
42091 TCTTTTG
1 TCTTTTG
42098 TTTTTCTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (16 bp):
TCTTTTGAATCACTCA
Found at i:42491 original size:20 final size:20
Alignment explanation
Indices: 42445--42491 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
42435 AGCTCGTTTC
*
42445 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
42465 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
42485 CAGCTCA
1 CAGCTCA
42492 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46914 original size:20 final size:20
Alignment explanation
Indices: 46868--46914 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46858 AGCTCGTTTC
*
46868 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
46888 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
46908 CAGCTCA
1 CAGCTCA
46915 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:48471 original size:22 final size:22
Alignment explanation
Indices: 48446--48490 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
48436 AGAAGTGAGC
*
48446 AAAAAAAGAAAAAAAAGTAAAA
1 AAAAAAACAAAAAAAAGTAAAA
* *
48468 AAAAGAACAAAAAAAAGTGAAA
1 AAAAAAACAAAAAAAAGTAAAA
48490 A
1 A
48491 GTCTTGTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.04
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAGTAAAA
Found at i:48490 original size:10 final size:9
Alignment explanation
Indices: 48446--48481 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
48436 AGAAGTGAGC
48446 AAAAAAAGA
1 AAAAAAAGA
48455 AAAAAAAGTA
1 AAAAAAAG-A
48465 AAAAAAAGA
1 AAAAAAAGA
48474 ACAAAAAA
1 A-AAAAAA
48482 AAGTGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:54396 original size:14 final size:14
Alignment explanation
Indices: 54379--54418 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
54369 CGAACGGAAT
54379 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
54393 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
54407 GATATGAACAAA
1 GGTAGGAACAAA
54419 TTGGTCAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.53, C:0.07, G:0.30, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:55578 original size:19 final size:19
Alignment explanation
Indices: 55526--55579 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
55516 AGCTGATCCT
55526 AGCTCATTTCCAGCTCCTCG
1 AGCTCATTT-CAGCTCCTCG
** *
55546 AGCTCCGTCCAGCTCCTCG
1 AGCTCATTTCAGCTCCTCG
*
55565 AGCTCATTTGAGCTC
1 AGCTCATTTCAGCTC
55580 GTTTCAGCTC
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.15, C:0.39, G:0.19, T:0.28
Consensus pattern (19 bp):
AGCTCATTTCAGCTCCTCG
Found at i:65348 original size:29 final size:29
Alignment explanation
Indices: 65303--65362 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
65293 AAGGATTCAA
* *
65303 AGATGGGTTTATAGATATGAAGTTTATGT
1 AGATGGATTTATAGATATAAAGTTTATGT
* *
65332 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATAGATATAAAGTTTATGT
65361 AG
1 AG
65363 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATAGATATAAAGTTTATGT
Found at i:66386 original size:14 final size:14
Alignment explanation
Indices: 66344--66388 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66334 TTAAAGAAGC
66344 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
66358 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
66371 AACTCATTTAATTA
1 AACTCATTAAATTA
66385 AACT
1 AACT
66389 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:68889 original size:23 final size:24
Alignment explanation
Indices: 68845--68890 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
68835 TTCACATTCT
*
68845 TTCTCTCTCTCAAACTCTTTTTCA
1 TTCTCTCTCTCAAACTCATTTTCA
* *
68869 TTCTCT-TTTCAATCTCATTTTC
1 TTCTCTCTCTCAAACTCATTTTC
68891 TTTTTCACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.54
Consensus pattern (24 bp):
TTCTCTCTCTCAAACTCATTTTCA
Found at i:70218 original size:29 final size:29
Alignment explanation
Indices: 70185--70244 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
70175 AAGGATTCAA
* *
70185 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
* *
70214 AGATGGATTTATTGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
70243 AG
1 AG
70245 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:71247 original size:14 final size:14
Alignment explanation
Indices: 71225--71269 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
71215 TTAAAGAAGC
71225 AACTCATTAAATTA
1 AACTCATTAAATTA
*
71239 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
71252 AACTCATTTAATTA
1 AACTCATTAAATTA
71266 AACT
1 AACT
71270 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:71307 original size:22 final size:22
Alignment explanation
Indices: 71281--71350 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
71271 AGATGAGTTG
71281 TATTAATGACCAGCAACTCATT
1 TATTAATGACCAGCAACTCATT
* *
71303 TATTAA--ACTA--AGA-TGAGTT
1 TATTAATGACCAGCA-ACTCA-TT
71322 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACCAGCAACTCATT
71345 TATTAA
1 TATTAA
71351 ACTAAGAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 9 0.25
22 15 0.42
23 3 0.08
24 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
TATTAATGACCAGCAACTCATT
Found at i:71313 original size:42 final size:42
Alignment explanation
Indices: 71252--71357 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
71242 TCATTAAATA
71252 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
71295 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
71337 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
71358 GGCTTAAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 54 0.86
43 9 0.14
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:74460 original size:20 final size:21
Alignment explanation
Indices: 74437--74502 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 21
74427 AGTTTTTCCC
74437 AGCTCGAA-TTAGCTCACTTG
1 AGCTCGAATTTAGCTCACTTG
* **
74457 AGCT-TAATTTAGCTCTTTTG
1 AGCTCGAATTTAGCTCACTTG
* *
74477 AGCTC-AATTTAGCTTACTTT
1 AGCTCGAATTTAGCTCACTTG
74497 AGCTCG
1 AGCTCG
74503 TTTGAGCTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.06
20 34 0.94
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (21 bp):
AGCTCGAATTTAGCTCACTTG
Found at i:74481 original size:30 final size:30
Alignment explanation
Indices: 74447--74510 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
74437 AGCTCGAATT
* *
74447 AGCTCACTTGAGCTTAATTTAGCTCTTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
* *
74477 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
74507 AGCT
1 AGCT
74511 TGGCTTAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAGCTCGTTTG
Found at i:76121 original size:14 final size:14
Alignment explanation
Indices: 76104--76151 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
76094 AAAAAAAATC
76104 AAAAAAAATTCGAA
1 AAAAAAAATTCGAA
*
76118 AAAAAAAATT-GATTG
1 AAAAAAAATTCGA--A
76133 AAAAAAAATTC-AA
1 AAAAAAAATTCGAA
76146 AAAAAA
1 AAAAAA
76152 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 8 0.28
14 10 0.34
15 11 0.38
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:77243 original size:12 final size:12
Alignment explanation
Indices: 77231--77348 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
77221 GAAAGAGATT
*
77231 GAAAAAGAAATT
1 GAAAAAGAAATA
77243 G--AAAGAAA-A
1 GAAAAAGAAATA
*
77252 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
77263 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
77276 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
77288 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
77300 GAAAAAGTGAGA
1 GAAAAAGAAATA
77312 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
77323 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
77339 GAAAAAGAAA
1 GAAAAAGAAA
77349 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:77274 original size:18 final size:18
Alignment explanation
Indices: 77248--77351 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
77238 AAATTGAAAG
*
77248 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
77266 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
77284 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
77302 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
77320 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
77341 AAAAGAAAAAG
1 AAAAGAAAAAG
77352 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:77276 original size:6 final size:6
Alignment explanation
Indices: 77244--77351 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
77234 AAAGAAATTG
* * ** *
77244 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
77291 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
77342 AAAGAA AAAG
1 AAAGAA AAAG
77352 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:77333 original size:14 final size:13
Alignment explanation
Indices: 77312--77349 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
77302 AAAAGTGAGA
77312 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
77324 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
77339 GAAAAAGAAAA
1 GAAAAAGAAAA
77350 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:77363 original size:21 final size:21
Alignment explanation
Indices: 77313--77363 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
77303 AAAGTGAGAG
*
77313 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
77334 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
77355 AAAAAGAAA
1 AAAAAGAAA
77364 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:77403 original size:33 final size:33
Alignment explanation
Indices: 77366--77428 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
77356 AAAAGAAATT
77366 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
77399 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
77429 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:79237 original size:20 final size:20
Alignment explanation
Indices: 79212--79257 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
79202 CCCAGCTCGA
*
79212 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
79232 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
79252 TTAGCT
1 TTAGCT
79258 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:79248 original size:30 final size:30
Alignment explanation
Indices: 79205--79277 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
79195 AGTTTTTCCC
*
79205 AGCTCGATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCGTTTGAGCTCA-ATTGAGCTTAATTT
* *
79234 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
79264 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
79278 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:81406 original size:23 final size:22
Alignment explanation
Indices: 81354--81406 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
81344 TCCACGTCTT
*
81354 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
81376 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
81399 TTTCTTTT
1 TTTCTTTT
81407 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:91389 original size:19 final size:19
Alignment explanation
Indices: 91365--91404 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
91355 AGCTCCCATG
91365 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
91384 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
91403 TA
1 TA
91405 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:93304 original size:30 final size:30
Alignment explanation
Indices: 93219--93315 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
93209 TAAACTAAAA
* *
93219 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
93249 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
93279 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
93308 ATGAGCTA
1 -TGAGCTA
93316 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:95598 original size:30 final size:30
Alignment explanation
Indices: 95527--95609 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
95517 CTTTTGTTTC
* *
95527 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
95558 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
95587 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
95610 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:95609 original size:18 final size:18
Alignment explanation
Indices: 95560--95615 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
95550 CACTCTCAAA
* *
95560 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
95577 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
95595 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
95614 TT
1 TT
95616 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:95616 original size:12 final size:12
Alignment explanation
Indices: 95585--95609 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
95575 TTTTTCAATC
95585 TCATTTTCTTTT
1 TCATTTTCTTTT
95597 TCATTTTCTTTT
1 TCATTTTCTTTT
95609 T
1 T
95610 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:95688 original size:5 final size:5
Alignment explanation
Indices: 95678--95734 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
95668 CTCTTGCCTC
*
95678 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
95725 TCTTT TCTTT
1 TCTTT TCTTT
95735 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:95718 original size:15 final size:14
Alignment explanation
Indices: 95678--95734 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
95668 CTCTTGCCTC
*
95678 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
95693 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
95708 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
95725 TCTTTTCTTT
1 TCTTTTCTTT
95735 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:95735 original size:21 final size:21
Alignment explanation
Indices: 95678--95745 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
95668 CTCTTGCCTC
* *
95678 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
95699 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
95720 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
95740 CTCTTT
1 -TCTTT
95746 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:96942 original size:28 final size:28
Alignment explanation
Indices: 96909--96965 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
96899 TCGGGATTAA
96909 ATGATACGAATC-GCCTCGGGGAGAGTCG
1 ATGATACG-ATCTGCCTCGGGGAGAGTCG
*
96937 ATGATACGATCTGCCTCGGGGTGAGTCG
1 ATGATACGATCTGCCTCGGGGAGAGTCG
96965 A
1 A
96966 GTCGTATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (28 bp):
ATGATACGATCTGCCTCGGGGAGAGTCG
Found at i:97139 original size:29 final size:29
Alignment explanation
Indices: 97073--97129 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
97063 GATTCAAAGA
*
97073 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
97102 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
97130 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:98760 original size:17 final size:16
Alignment explanation
Indices: 98734--98767 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
98724 TTAAGAGCTG
98734 TAACTAAATAACTAAT
1 TAACTAAATAACTAAT
*
98750 TAACTTAAATAATTAAT
1 TAAC-TAAATAACTAAT
98767 T
1 T
98768 TATTCCAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
TAACTAAATAACTAAT
Found at i:101449 original size:12 final size:12
Alignment explanation
Indices: 101434--101467 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
101424 AATGTGAAAC
101434 AAAAAGAAATTG
1 AAAAAGAAATTG
*
101446 AAAAAGAAGTTG
1 AAAAAGAAATTG
101458 AAGAAAGAAA
1 AA-AAAGAAA
101468 ATGAGTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.12
Consensus pattern (12 bp):
AAAAAGAAATTG
Found at i:104550 original size:15 final size:15
Alignment explanation
Indices: 104530--104577 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
104520 TCAAAGATGG
104530 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
104545 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
104559 GTTTATGGATATAAA
1 GTTTATGGATATGAA
104574 GTTT
1 GTTT
104578 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:104564 original size:14 final size:14
Alignment explanation
Indices: 104524--104567 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
104514 AAGGATTCAA
104524 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
104538 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
104553 AGATGGGTTTATGG
1 AGATGGGTTTATGG
104567 A
1 A
104568 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:104593 original size:29 final size:29
Alignment explanation
Indices: 104524--104583 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
104514 AAGGATTCAA
*
104524 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
104553 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
104582 AG
1 AG
104584 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:106582 original size:20 final size:21
Alignment explanation
Indices: 106552--106600 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
106542 TTTTCAGAAT
106552 TTTTGTTTGAA-TTTTTTTTCG
1 TTTT-TTTGAATTTTTTTTTCG
106573 TTTTTTTGAATTTTTTTTTCG
1 TTTTTTTGAATTTTTTTTTCG
106594 TTTTTTT
1 TTTTTTT
106601 AAAACTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.08, C:0.04, G:0.10, T:0.78
Consensus pattern (21 bp):
TTTTTTTGAATTTTTTTTTCG
Found at i:106885 original size:29 final size:29
Alignment explanation
Indices: 106819--106875 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
106809 GATTCAAAGA
*
106819 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
106848 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
106876 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:107968 original size:14 final size:14
Alignment explanation
Indices: 107926--107970 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
107916 TTAAAGAAGC
107926 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
107940 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
107953 AACTCATTTAATTA
1 AACTCATTAAATTA
107967 AACT
1 AACT
107971 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:111374 original size:30 final size:30
Alignment explanation
Indices: 111289--111385 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
111279 TAAACTAAAA
* *
111289 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
111319 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
111349 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
111378 ATGAGCTA
1 -TGAGCTA
111386 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:118585 original size:5 final size:5
Alignment explanation
Indices: 118575--118631 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
118565 CTCTTGCCTC
*
118575 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
118622 TCTTT TCTTT
1 TCTTT TCTTT
118632 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:118615 original size:15 final size:14
Alignment explanation
Indices: 118575--118631 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
118565 CTCTTGCCTC
*
118575 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
118590 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
118605 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
118622 TCTTTTCTTT
1 TCTTTTCTTT
118632 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:118632 original size:21 final size:21
Alignment explanation
Indices: 118575--118642 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
118565 CTCTTGCCTC
* *
118575 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
118596 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
118617 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
118637 CTCTTT
1 -TCTTT
118643 ATAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:119559 original size:10 final size:11
Alignment explanation
Indices: 119544--119616 Score: 80
Period size: 10 Copynumber: 6.6 Consensus size: 11
119534 ATAAATCACT
119544 TTTTTTTC-AA
1 TTTTTTTCGAA
119554 TTTTTTT-GAA
1 TTTTTTTCGAA
*
119564 TTTTTTTCGAT
1 TTTTTTTCGAA
119575 TTCTTTTTCGAAA
1 TT-TTTTTCG-AA
119588 TTTTTTTTCGAA
1 -TTTTTTTCGAA
*
119600 TTTTTTTC-AG
1 TTTTTTTCGAA
119610 TTTTTTT
1 TTTTTTT
119617 TAAACTTGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
10 24 0.44
11 12 0.22
12 9 0.16
13 8 0.15
14 2 0.04
ACGTcount: A:0.15, C:0.08, G:0.07, T:0.70
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:119570 original size:13 final size:13
Alignment explanation
Indices: 119564--119606 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
119554 TTTTTTTGAA
119564 TTTTTTTCG-ATT
1 TTTTTTTCGAATT
* *
119576 TCTTTTTCGAAAT
1 TTTTTTTCGAATT
119589 TTTTTTTCGAATT
1 TTTTTTTCGAATT
119602 TTTTT
1 TTTTT
119607 CAGTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:119590 original size:14 final size:13
Alignment explanation
Indices: 119564--119606 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
119554 TTTTTTTGAA
119564 TTTTTTTCG--AT
1 TTTTTTTCGAAAT
119575 TTCTTTTTCGAAAT
1 TT-TTTTTCGAAAT
119589 TTTTTTTCG-AAT
1 TTTTTTTCGAAAT
119601 TTTTTT
1 TTTTTT
119607 CAGTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.07
12 16 0.55
13 7 0.24
14 4 0.14
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTTTTCGAAAT
Found at i:123832 original size:23 final size:22
Alignment explanation
Indices: 123780--123832 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
123770 TCCACGTCTT
*
123780 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
123802 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
123825 TTTCTTTT
1 TTTCTTTT
123833 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:127231 original size:24 final size:24
Alignment explanation
Indices: 127198--127279 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
127188 AAGAAATGAA
127198 AGAAAAAGAAAATGAGATTGAGAG
1 AGAAAAAGAAAATGAGATTGAGAG
* * *
127222 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAATGAGATTGAGAG
* * * *
127246 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAATGAGATTGAGAG
127270 AGAAAAAGAA
1 AGAAAAAGAA
127280 TGTGAACAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (24 bp):
AGAAAAAGAAAATGAGATTGAGAG
Found at i:127237 original size:18 final size:18
Alignment explanation
Indices: 127216--127254 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
127206 AAAATGAGAT
127216 TGAGAGTGAAAAAGAAAA
1 TGAGAGTGAAAAAGAAAA
* *
127234 TGAGATTGAAAAAGAGAA
1 TGAGAGTGAAAAAGAAAA
127252 TGA
1 TGA
127255 AAAAGAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (18 bp):
TGAGAGTGAAAAAGAAAA
Found at i:127308 original size:18 final size:19
Alignment explanation
Indices: 127272--127310 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
127262 TTTGAGAGAG
*
127272 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
127291 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
127309 AA
1 AA
127311 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:128921 original size:20 final size:20
Alignment explanation
Indices: 128898--128945 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
128888 AGCTCCGTCC
128898 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
128918 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
128938 AGCTCAAC
1 AGCTCAAC
128946 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:131465 original size:24 final size:24
Alignment explanation
Indices: 131432--131513 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
131422 AAGAAATGAA
131432 AGAAAAAGAAAATGAGATTGAGAG
1 AGAAAAAGAAAATGAGATTGAGAG
* * *
131456 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAATGAGATTGAGAG
* * * *
131480 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAATGAGATTGAGAG
131504 AGAAAAAGAA
1 AGAAAAAGAA
131514 TGCGAACAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (24 bp):
AGAAAAAGAAAATGAGATTGAGAG
Found at i:131471 original size:18 final size:18
Alignment explanation
Indices: 131450--131488 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
131440 AAAATGAGAT
131450 TGAGAGTGAAAAAGAAAA
1 TGAGAGTGAAAAAGAAAA
* *
131468 TGAGATTGAAAAAGAGAA
1 TGAGAGTGAAAAAGAAAA
131486 TGA
1 TGA
131489 AAAAGAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (18 bp):
TGAGAGTGAAAAAGAAAA
Found at i:137359 original size:18 final size:18
Alignment explanation
Indices: 137336--137385 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
137326 GAAAGAAAAA
* *
137336 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGACT
*
137354 GAAAAAGAAAATGAGACT
1 GAAAAAGAGAATGAGACT
137372 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
137386 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.02, G:0.28, T:0.12
Consensus pattern (18 bp):
GAAAAAGAGAATGAGACT
Found at i:137361 original size:24 final size:24
Alignment explanation
Indices: 137329--137410 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
137319 AAGAAATGAA
137329 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * * *
137353 TGAAAAAGAAAATGAGACTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
137377 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
137401 AGAAAAAGAA
1 AGAAAAAGAA
137411 TGCGAACAAG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.61, C:0.01, G:0.27, T:0.11
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:137815 original size:30 final size:30
Alignment explanation
Indices: 137779--137875 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
137769 AGCTCACTCC
137779 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
137809 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
137839 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
137869 TAGCTCA
1 TAGCTCA
137876 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:143132 original size:17 final size:17
Alignment explanation
Indices: 143086--143132 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
143076 AAAGCAAGCG
*
143086 AGAAAAGAAGAAGATGAAA
1 AGAAAAG-AG-AGATCAAA
143105 AGCAAAA-AGAGATCAAA
1 AG-AAAAGAGAGATCAAA
143122 AGAAAAGAGAG
1 AGAAAAGAGAG
143133 GCAAGAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 13 0.52
18 2 0.08
19 2 0.08
20 4 0.16
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.04
Consensus pattern (17 bp):
AGAAAAGAGAGATCAAA
Found at i:143234 original size:18 final size:18
Alignment explanation
Indices: 143209--143258 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
143199 GAAAGAAAAA
*
143209 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* * *
143227 GGAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
143245 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
143259 AAAAGAGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:143312 original size:18 final size:19
Alignment explanation
Indices: 143276--143314 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
143266 TTTGAGAGAG
*
143276 AAAAAGAATGCGAACAAGA
1 AAAAAGAATGCGAAAAAGA
*
143295 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGCGAAAAAGA
143313 AA
1 AA
143315 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.05, G:0.23, T:0.05
Consensus pattern (19 bp):
AAAAAGAATGCGAAAAAGA
Found at i:147965 original size:24 final size:23
Alignment explanation
Indices: 147911--147988 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
147901 GGATAATTAA
**
147911 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
147934 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
147958 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
147979 GAAATAGTAT
1 GAAATGGTAT
147989 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:147973 original size:21 final size:21
Alignment explanation
Indices: 147947--148013 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
147937 TTGGTATTTG
147947 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
147968 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
147989 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
148012 GG
1 GG
148014 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:152282 original size:17 final size:17
Alignment explanation
Indices: 152257--152311 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
152247 TCTCTTTTCA
*
152257 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
152274 TTCTTTTTTTTATCATTT
1 TTCTTTTTTTT-TGAATT
* *
152292 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
152309 TTC
1 TTC
152312 GGTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:154552 original size:13 final size:13
Alignment explanation
Indices: 154534--154582 Score: 80
Period size: 13 Copynumber: 3.7 Consensus size: 13
154524 CGTATGCAAT
154534 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
154547 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
*
154560 TTTTTTTTTTGAA
1 TTTTTTTTTTCAA
154573 CTTTTTTTTT
1 -TTTTTTTTT
154583 ACGCACCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 25 0.74
14 9 0.26
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:154898 original size:24 final size:23
Alignment explanation
Indices: 154844--154921 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
154834 GGATAATTAA
**
154844 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
154867 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
154891 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
154912 GAAATAGTAT
1 GAAATGGTAT
154922 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:154906 original size:21 final size:21
Alignment explanation
Indices: 154880--154946 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
154870 TTGGTATTTG
154880 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
154901 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
154922 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
154945 GG
1 GG
154947 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:159148 original size:30 final size:30
Alignment explanation
Indices: 159063--159159 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
159053 TAAACTAAAA
* * *
159063 TGAGCTAAGCTTTAGCTCGTGAACTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
159093 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
159123 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
159152 ATGAGCTA
1 -TGAGCTA
159160 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:160939 original size:8 final size:8
Alignment explanation
Indices: 160926--160954 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
160916 GATTTTTCAC
160926 TCACTATT
1 TCACTATT
160934 TCACTATT
1 TCACTATT
160942 TCACTATT
1 TCACTATT
160950 TCACT
1 TCACT
160955 CAAAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (8 bp):
TCACTATT
Found at i:163853 original size:68 final size:64
Alignment explanation
Indices: 163736--163988 Score: 226
Period size: 68 Copynumber: 3.9 Consensus size: 64
163726 ATACAAATGG
* ** * * * *
163736 TATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGT-GTACAAGAGAGCTACGAGACA
1 TATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAG-ACAAGAGAGCTACGAG--A
163800 TTA
63 -TA
* * *
163803 TGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATA
1 T-ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATA
* * * * *
163868 TATGTAGCTAGGTCGCATGCGTGGTTCCAGGTAAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 TATGTAGCTAGGTCGCATGGGTGGTACTAAGT---GTACACCATGTAGACAAGAGAGCTACGAGA
163933 TA
63 TA
* * *
163935 AACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 TA-TGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAG-ACAAGAGAGC
163989 CAAAATTATG
Statistics
Matches: 154, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.12
64 26 0.17
65 3 0.02
66 22 0.14
67 32 0.21
68 50 0.32
69 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATA
Found at i:164183 original size:28 final size:28
Alignment explanation
Indices: 164151--164208 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
164141 AAATGAAATT
164151 GTGTAAGACTTTGTGATGATAAGTGTAA
1 GTGTAAGACTTTGTGATGATAAGTGTAA
164179 GTGTAAGACTTTGTGATGATAAGTGTAA
1 GTGTAAGACTTTGTGATGATAAGTGTAA
164207 GT
1 GT
164209 ATATACGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.36
Consensus pattern (28 bp):
GTGTAAGACTTTGTGATGATAAGTGTAA
Found at i:167907 original size:30 final size:30
Alignment explanation
Indices: 167861--167921 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
167851 TTCCTGAGCC
167861 TAGGAGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGAGCAAAAGTGTAAATATGCAAAAGTT
* * * * *
167891 TAGGGGCAAAATTGTAATTGTGCCAAAGTT
1 TAGGAGCAAAAGTGTAAATATGCAAAAGTT
167921 T
1 T
167922 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGAGCAAAAGTGTAAATATGCAAAAGTT
Found at i:168810 original size:30 final size:30
Alignment explanation
Indices: 168776--168876 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
168766 AGCTCACTCC
*
168776 TAGCTCATTTTCAACTCACGAGCTAAACCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
** * * * * *
168806 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
* * *
168836 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTC-ATTTTCAGCTCACGAGCTAAACCT
168866 TAGCTCATTTT
1 TAGCTCATTTT
168877 AGTTTAAACT
Statistics
Matches: 51, Mismatches: 19, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
29 4 0.08
30 44 0.86
31 3 0.06
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (30 bp):
TAGCTCATTTTCAGCTCACGAGCTAAACCT
Found at i:169298 original size:13 final size:13
Alignment explanation
Indices: 169280--169304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169270 GTATTGATCA
169280 TGTGTTCACACCT
1 TGTGTTCACACCT
169293 TGTGTTCACACC
1 TGTGTTCACACC
169305 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:171270 original size:5 final size:5
Alignment explanation
Indices: 171260--171310 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
171250 AAGAGAAAAC
*
171260 AAAGA AAAGA AAAGCA AAAGA AGA-A AAAGAA AAAGA AATA-A AAAGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAGA AA-AGA AAAGA
171306 AAAGA
1 AAAGA
171311 GCGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.10
5 24 0.62
6 11 0.28
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:171614 original size:30 final size:30
Alignment explanation
Indices: 171580--171676 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
171570 AGCTCACTCC
*
171580 TAGCTC-ACTTTTAACTCACGAGCTAAACCT
1 TAGCTCAAC-TTTAGCTCACGAGCTAAACCT
* * * * * *
171610 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
171640 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
171670 TAGCTCA
1 TAGCTCA
171677 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 48 0.96
31 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:173396 original size:19 final size:18
Alignment explanation
Indices: 173361--173395 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
173351 AAAAAAATTC
*
173361 AAAAAAAAATTTGAAAAG
1 AAAAAAAAATCTGAAAAG
173379 AAAAAAAAATCTGAAAA
1 AAAAAAAAATCTGAAAA
173396 AAAGTGTTTA
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:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAAAAAAATCTGAAAAG
Found at i:174320 original size:9 final size:10
Alignment explanation
Indices: 174313--174369 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
174303 AAGAGAAAAC
174313 AAAGAAAAGA
1 AAAGAAAAGA
174323 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
174335 AAAGAAGA-A
1 AAAGAAAAGA
174344 AAAGAAAATGA
1 AAAGAAAA-GA
174355 AATA-AAAAGA
1 AA-AGAAAAGA
174365 AAAGA
1 AAAGA
174370 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:174336 original size:21 final size:20
Alignment explanation
Indices: 174302--174369 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
174292 ACATTCTTGT
174302 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
174323 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
174344 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
174365 AAAGA
1 AAAGA
174370 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:174337 original size:6 final size:5
Alignment explanation
Indices: 174313--174369 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
174303 AAGAGAAAAC
*
174313 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
174360 AAAGA AAAGA
1 AAAGA AAAGA
174370 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:174344 original size:15 final size:14
Alignment explanation
Indices: 174313--174369 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
174303 AAGAGAAAAC
174313 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
174329 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
174344 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
174360 AAAGAAAAGA
1 AAAGAAAAGA
174370 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:174446 original size:12 final size:12
Alignment explanation
Indices: 174438--174462 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
174428 TTTGAAAAGC
174438 AAAAAGAAAATG
1 AAAAAGAAAATG
174450 AAAAAGAAAATG
1 AAAAAGAAAATG
174462 A
1 A
174463 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:174459 original size:18 final size:18
Alignment explanation
Indices: 174432--174487 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
174422 AAAGCCTTTG
174432 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
174451 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
174469 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
174486 AA
1 AA
174488 TTTGAGAGCG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:174472 original size:30 final size:31
Alignment explanation
Indices: 174438--174519 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
174428 TTTGAAAAGC
**
174438 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGCG
* * *
174468 AAAAAGAGAACG-AAAAGAAATTTGAGAGCG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGCG
*
174498 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
174520 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.02, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGCG
Found at i:181584 original size:30 final size:30
Alignment explanation
Indices: 181550--181654 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
181540 AGCTCACTCC
181550 TAGCTCATA-TTTAGTTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGTTCACGAGCTAAACCT
* * * * *
181580 TAGCTCAACTTCAGCTT-AGGAGTTTAGCCT
1 TAGCTCAACTTTAG-TTCACGAGCTAAACCT
* * *
181610 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGTTCACGAGCTAAACCT
*
181640 TAGCTC-ATTTTAGTT
1 TAGCTCAACTTTAGTT
181655 TAAACTCGGT
Statistics
Matches: 56, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
29 9 0.16
30 45 0.80
31 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (30 bp):
TAGCTCAACTTTAGTTCACGAGCTAAACCT
Found at i:185295 original size:22 final size:20
Alignment explanation
Indices: 185263--185311 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
185253 TGCCAATTTA
185263 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
185286 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
185306 TGAACA
1 TGAACA
185312 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:185866 original size:30 final size:30
Alignment explanation
Indices: 185823--185879 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
185813 TATCAGAAAA
*
185823 TGAGATTGAAAAAG-AGAATGAAAAAGAGTT
1 TGAGAGTGAAAAAGAAG-ATGAAAAAGAGTT
*
185853 TGAGAGTGGAAAAGAAGATGAAAAAGA
1 TGAGAGTGAAAAAGAAGATGAAAAAGA
185880 AATCGAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.30, T:0.16
Consensus pattern (30 bp):
TGAGAGTGAAAAAGAAGATGAAAAAGAGTT
Found at i:188514 original size:13 final size:13
Alignment explanation
Indices: 188496--188520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
188486 GTATTGATCA
188496 TGTGTTCACACCT
1 TGTGTTCACACCT
188509 TGTGTTCACACC
1 TGTGTTCACACC
188521 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:191959 original size:22 final size:21
Alignment explanation
Indices: 191928--191978 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
191918 ACCTCTTTGA
*
191928 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCCTACC-AAT
*
191951 ACCATACCATTTCCTACCAAT
1 ACCATACCAATTCCTACCAAT
*
191972 TCCATAC
1 ACCATAC
191979 TATTTCGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.35, C:0.35, G:0.02, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCCTACCAAT
Found at i:191978 original size:21 final size:21
Alignment explanation
Indices: 191933--191995 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
191923 TTTGAACCAT
* *
191933 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
191955 TACCATTTCCTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
191976 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
191996 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:192328 original size:13 final size:13
Alignment explanation
Indices: 192312--192346 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
192302 GAGTTCGAAA
192312 AAAAAAAATTATT
1 AAAAAAAATTATT
192325 -AAAAAAATTATT
1 AAAAAAAATTATT
192337 AAAAAAAATT
1 AAAAAAAATT
192347 GCATACGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAAAAATTATT
Found at i:194602 original size:17 final size:17
Alignment explanation
Indices: 194557--194610 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
194547 AGAAAAGAGC
* *
194557 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
194574 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
194591 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
194608 GAA
1 GAA
194611 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:197097 original size:30 final size:30
Alignment explanation
Indices: 197063--197159 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
197053 TAAACTAAAA
*
197063 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
197093 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
197123 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
197152 ATGAGCTA
1 -TGAGCTA
197160 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:199353 original size:12 final size:12
Alignment explanation
Indices: 199338--199368 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
199328 TTCTTTTTGC
199338 TTTTCAAAGGCT
1 TTTTCAAAGGCT
199350 TTTTCAAAGGCT
1 TTTTCAAAGGCT
199362 TTTTCAA
1 TTTTCAA
199369 GTTCTTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:199444 original size:6 final size:6
Alignment explanation
Indices: 199428--199477 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
199418 TTTCTTTTTA
*
199428 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
199477 T
1 T
199478 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:199460 original size:37 final size:37
Alignment explanation
Indices: 199417--199487 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
199407 CTTGCCTCTC
199417 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
199454 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
199488 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:199488 original size:16 final size:16
Alignment explanation
Indices: 199413--199473 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
199403 GCCTCTTGCC
*
199413 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
199429 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
199445 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
199461 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
199474 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:200410 original size:18 final size:18
Alignment explanation
Indices: 200387--200424 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
200377 TTTAACTCGA
200387 TTTTTTTGTC-ACTTTTTT
1 TTTTTTTGTCGA-TTTTTT
*
200405 TTTTTTTTTCGATTTTTT
1 TTTTTTTGTCGATTTTTT
200423 TT
1 TT
200425 GAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTTTGTCGATTTTTT
Found at i:200420 original size:11 final size:12
Alignment explanation
Indices: 200406--200443 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
200396 CACTTTTTTT
200406 TTTTTTTTCG-A
1 TTTTTTTTCGAA
200417 TTTTTTTT-GAA
1 TTTTTTTTCGAA
200428 TTTTTTTTCTGAA
1 TTTTTTTTC-GAA
200441 TTT
1 TTT
200444 CTTCTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 17 0.71
13 6 0.25
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:201421 original size:30 final size:30
Alignment explanation
Indices: 201387--201483 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
201377 TAAACTAAAA
*
201387 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
201417 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
201447 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
201476 ATGAGCTA
1 -TGAGCTA
201484 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:203677 original size:12 final size:12
Alignment explanation
Indices: 203662--203692 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
203652 TTCTTTTTGC
203662 TTTTCAAAGGCT
1 TTTTCAAAGGCT
203674 TTTTCAAAGGCT
1 TTTTCAAAGGCT
203686 TTTTCAA
1 TTTTCAA
203693 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:203769 original size:6 final size:6
Alignment explanation
Indices: 203753--203802 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
203743 TTTCTTTTTA
*
203753 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
203802 T
1 T
203803 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:203785 original size:37 final size:37
Alignment explanation
Indices: 203742--203812 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
203732 CTTGCCTCTC
203742 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
203779 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
203813 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:203813 original size:16 final size:16
Alignment explanation
Indices: 203738--203798 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
203728 GCCTCTTGCC
*
203738 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
203754 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
203770 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
203786 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
203799 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Done.