Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 424860
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 46523 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:286261 original size:18 final size:18
Alignment explanation
Indices: 286238--286280 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
286228 AAAAAAAAAG
*
286238 AAAAAAATTCGAAATTAA
1 AAAAAAATTCAAAATTAA
286256 AAAAAAATTCAAAATTAA
1 AAAAAAATTCAAAATTAA
286274 AAAAAAA
1 AAAAAAA
286281 AGCCATGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAATTCAAAATTAA
Found at i:287245 original size:13 final size:12
Alignment explanation
Indices: 287214--287242 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
287204 GTGTGAGATA
287214 GAAAAGAAAATT
1 GAAAAGAAAATT
287226 GAAAAGAAAATT
1 GAAAAGAAAATT
287238 GAAAA
1 GAAAA
287243 AGAGAGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (12 bp):
GAAAAGAAAATT
Found at i:289060 original size:13 final size:13
Alignment explanation
Indices: 289039--289073 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
289029 ATAAGTTGCT
* *
289039 GTTAGTTAAATTA
1 GTTAATTAAATAA
289052 GTTAATTAAATAA
1 GTTAATTAAATAA
289065 GTTAATTAA
1 GTTAATTAA
289074 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:292842 original size:21 final size:21
Alignment explanation
Indices: 292816--292878 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
292806 TTGGTATTTG
292816 GGAATTGGCT-CGAAATGGTAT
1 GGAATTGG-TACGAAATGGTAT
292837 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* * *
292858 GGTATTTGGTATGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
292879 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.03
21 21 0.57
22 15 0.41
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:299538 original size:18 final size:18
Alignment explanation
Indices: 299496--299538 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
299486 CTCATTTCTT
299496 TTTTTTTTGAATCACTCTC
1 TTTTTTTT-AATCACTCTC
299515 TCTTTTTTT-ATCACTCATC
1 T-TTTTTTTAATCACTC-TC
299534 TTTTT
1 TTTTT
299539 GTTTTTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 11 0.50
19 4 0.18
20 7 0.32
ACGTcount: A:0.14, C:0.21, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTTTTTAATCACTCTC
Found at i:303118 original size:9 final size:10
Alignment explanation
Indices: 303094--303132 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
303084 TATGCAATAT
**
303094 ATTTTTTTCA
1 ATTTTTTTTG
303104 ATTTTTTTTG
1 ATTTTTTTTG
303114 ATTTTTTTTG
1 ATTTTTTTTG
303124 ATTTTTTTT
1 ATTTTTTTT
303133 CAAAAACTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (10 bp):
ATTTTTTTTG
Found at i:309617 original size:19 final size:20
Alignment explanation
Indices: 309593--309637 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
309583 CTTTTCATTC
*
309593 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
309612 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
309632 TCTTTT
1 TCTTTT
309638 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:313084 original size:20 final size:20
Alignment explanation
Indices: 313038--313084 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
313028 AGCTCGTTTC
*
313038 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
313058 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
313078 CAGCTCA
1 CAGCTCA
313085 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:316212 original size:12 final size:13
Alignment explanation
Indices: 316183--316216 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
316173 TTCATTTTCT
316183 CTTCTTTCTTCAA
1 CTTCTTTCTTCAA
316196 CTTCTTT-TTCAA
1 CTTCTTTCTTCAA
*
316208 TTTCTTTCT
1 CTTCTTTCT
316217 GTTTCACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTCTTTCTTCAA
Found at i:327310 original size:22 final size:22
Alignment explanation
Indices: 327280--327323 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
327270 TTTGGTATTT
327280 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
327302 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
327324 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:334206 original size:20 final size:20
Alignment explanation
Indices: 334183--334229 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
334173 GGGTTAAGAT
*
334183 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
334203 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
334223 TGAGCTG
1 TGAGCTG
334230 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:334388 original size:25 final size:25
Alignment explanation
Indices: 334343--334391 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
334333 ATGGTCGTAT
* *
334343 CAAGAATTTTCTTTGGGGTTTTCTC
1 CAAGAATTCTCTTTGGAGTTTTCTC
334368 CAAGAATTCTCTCTT-GAGTTTTCT
1 CAAGAATTCTCT-TTGGAGTTTTCT
334392 TTAGAAGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (25 bp):
CAAGAATTCTCTTTGGAGTTTTCTC
Found at i:335443 original size:17 final size:17
Alignment explanation
Indices: 335418--335472 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
335408 TCTCTTTTCA
*
335418 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
335435 TTCTTTTTTTTTTCATTT
1 TTC-TTTTTTTTTGAATT
* *
335453 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
335470 TTC
1 TTC
335473 GCTCTTTTCT
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:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:335446 original size:18 final size:18
Alignment explanation
Indices: 335423--335464 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
335413 TTTCATTCTC
*
335423 TTTTTTTGAATTTTCTTT
1 TTTTTTTCAATTTTCTTT
*
335441 TTTTTTTCATTTTTCTTT
1 TTTTTTTCAATTTTCTTT
335459 TCTTTT
1 T-TTTT
335465 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTCAATTTTCTTT
Found at i:340112 original size:13 final size:13
Alignment explanation
Indices: 340094--340142 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
340084 AAACCGTATG
340094 CAATTTTTTTTTT
1 CAATTTTTTTTTT
340107 CAA-TTTTTTTTT
1 CAATTTTTTTTTT
*
340119 CAAATTTTTTTTT
1 CAATTTTTTTTTT
340132 CAATTTTTTTT
1 CAATTTTTTTT
340143 ACATACCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 12 0.35
13 22 0.65
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:340115 original size:12 final size:12
Alignment explanation
Indices: 340098--340142 Score: 81
Period size: 12 Copynumber: 3.7 Consensus size: 12
340088 CGTATGCAAT
340098 TTTTTTTTTCAA
1 TTTTTTTTTCAA
340110 TTTTTTTTTCAAA
1 TTTTTTTTTC-AA
340123 TTTTTTTTTCAA
1 TTTTTTTTTCAA
340135 TTTTTTTT
1 TTTTTTTT
340143 ACATACCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 20 0.62
13 12 0.38
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:340471 original size:22 final size:22
Alignment explanation
Indices: 340441--340484 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
340431 TTTGGTATTT
340441 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
340463 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
340485 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:341932 original size:16 final size:16
Alignment explanation
Indices: 341893--341933 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
341883 GTATGCAATT
*
341893 TTTTTTTGTCTTTTCAA
1 TTTTTTT-TCCTTTCAA
341910 TTTTTTTTCCTTTCAA
1 TTTTTTTTCCTTTCAA
341926 TTTTTTTT
1 TTTTTTTT
341934 TTCGATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTTTTTCCTTTCAA
Found at i:341934 original size:17 final size:17
Alignment explanation
Indices: 341892--341934 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
341882 CGTATGCAAT
*
341892 TTTTTTTTGTCTTTTCAA
1 TTTTTTTT-TCCTTTCAA
341910 -TTTTTTTTCCTTTCAA
1 TTTTTTTTTCCTTTCAA
341926 TTTTTTTTT
1 TTTTTTTTT
341935 TCGATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTTTTTCCTTTCAA
Found at i:342328 original size:22 final size:22
Alignment explanation
Indices: 342277--342334 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
342267 GGAATTGGCT
342277 CGAAATGGTATGG-AATCGGTA
1 CGAAATGGTATGGTAATCGGTA
* * *
342298 AGAAATGGTATGGTATTTGGTA
1 CGAAATGGTATGGTAATCGGTA
*
342320 CGAATTGGTAATGGT
1 CGAAATGGT-ATGGT
342335 TCAAAGAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 12 0.40
22 13 0.43
23 5 0.17
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (22 bp):
CGAAATGGTATGGTAATCGGTA
Found at i:344500 original size:20 final size:20
Alignment explanation
Indices: 344477--344523 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
344467 GGGTTAAGAT
*
344477 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* * *
344497 TGAGTTCACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
344517 TGAGCTG
1 TGAGCTG
344524 GAAACGAGCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:351987 original size:12 final size:11
Alignment explanation
Indices: 351947--351988 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 11
351937 TTATACTTCA
351947 ATTTTTTTTTG
1 ATTTTTTTTTG
351958 AATTTTTTTTTG
1 -ATTTTTTTTTG
*
351970 A-ATTTTTTTG
1 ATTTTTTTTTG
351980 ATTTTTTTT
1 ATTTTTTTT
351989 CAAATTTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
ATTTTTTTTTG
Found at i:351988 original size:10 final size:10
Alignment explanation
Indices: 351949--351988 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
351939 ATACTTCAAT
351949 TTTTTTTTGAA
1 TTTTTTTTG-A
351960 TTTTTTTTTGA
1 -TTTTTTTTGA
*
351971 ATTTTTTTGA
1 TTTTTTTTGA
351981 TTTTTTTT
1 TTTTTTTT
351989 CAAATTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 16 0.62
11 1 0.04
12 9 0.35
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:351994 original size:21 final size:22
Alignment explanation
Indices: 351950--351995 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
351940 TACTTCAATT
**
351950 TTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTGAATTTTTTTTCAAA
351972 TTTTTTTG-ATTTTTTTTCAAA
1 TTTTTTTGAATTTTTTTTCAAA
351993 TTT
1 TTT
351996 CCTCTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (22 bp):
TTTTTTTGAATTTTTTTTCAAA
Found at i:351995 original size:12 final size:12
Alignment explanation
Indices: 351946--351978 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
351936 TTTATACTTC
351946 AATTTTTTTTTG
1 AATTTTTTTTTG
351958 AATTTTTTTTTG
1 AATTTTTTTTTG
351970 AATTTTTTT
1 AATTTTTTT
351979 GATTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:355371 original size:21 final size:21
Alignment explanation
Indices: 355326--355388 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
355316 TTTGAACCAT
* *
355326 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
355348 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
355369 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
355389 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:355730 original size:17 final size:17
Alignment explanation
Indices: 355697--355756 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
355687 AAAAAAGAGT
* *
355697 TCAAAAAAAAGTCAAAA
1 TCAAAAAAAATTGAAAA
355714 TCAAAAAAAATTG--AA
1 TCAAAAAAAATTGAAAA
355729 --AAAAAAAATTGAAAA
1 TCAAAAAAAATTGAAAA
**
355744 GAAAAAAAAATTG
1 TCAAAAAAAATTG
355757 CATACGGTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 11 0.30
15 4 0.11
17 22 0.59
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (17 bp):
TCAAAAAAAATTGAAAA
Found at i:355733 original size:14 final size:13
Alignment explanation
Indices: 355716--355750 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
355706 AGTCAAAATC
355716 AAAAAAAATTGAA
1 AAAAAAAATTGAA
355729 AAAAAAAATTGAA
1 AAAAAAAATTGAA
355742 AAGAAAAAA
1 AA-AAAAAA
355751 AAATTGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (13 bp):
AAAAAAAATTGAA
Found at i:355735 original size:30 final size:30
Alignment explanation
Indices: 355699--355756 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
355689 AAAAGAGTTC
**
355699 AAAAAAAAGTCAAAATCAAAAAAAATTGAA
1 AAAAAAAAGTCAAAAGAAAAAAAAATTGAA
* *
355729 AAAAAAAATTGAAAAGAAAAAAAAATTG
1 AAAAAAAAGTCAAAAGAAAAAAAAATTG
355757 CATACGGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (30 bp):
AAAAAAAAGTCAAAAGAAAAAAAAATTGAA
Found at i:357991 original size:17 final size:17
Alignment explanation
Indices: 357946--357999 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
357936 AGAAAAGAGC
* *
357946 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
357963 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
357980 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
357997 GAA
1 GAA
358000 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:360942 original size:20 final size:21
Alignment explanation
Indices: 360907--360945 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
360897 CAACTCGTTG
360907 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
360928 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
360946 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:361353 original size:13 final size:13
Alignment explanation
Indices: 361335--361360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
361325 TGTGTCCTAA
361335 TATGAATTAAATT
1 TATGAATTAAATT
361348 TATGAATTAAATT
1 TATGAATTAAATT
361361 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:362482 original size:11 final size:11
Alignment explanation
Indices: 362466--362506 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
362456 ACGGTATTGT
362466 AAAAAAATTAA
1 AAAAAAATTAA
* *
362477 AAAAAAACTCA
1 AAAAAAATTAA
362488 AAAAAAATTCAA
1 AAAAAAATT-AA
362500 AAAAAAA
1 AAAAAAA
362507 GTTTGTATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:362597 original size:29 final size:29
Alignment explanation
Indices: 362551--362623 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 29
362541 AGTATTGAAG
362551 GAAAAAAAATAAGAAAAAAAAATTCGAAATT
1 GAAAAAAAA-AAGAAAAAAAAA-TCGAAATT
362582 -AAAAAAAAGAAGAAAAAAAAATCGAAATT
1 GAAAAAAAA-AAGAAAAAAAAATCGAAATT
362611 GAAAAAAAAAAGA
1 GAAAAAAAAAAGA
362624 GTGATTGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 12 0.30
30 28 0.70
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (29 bp):
GAAAAAAAAAAGAAAAAAAAATCGAAATT
Found at i:363472 original size:6 final size:6
Alignment explanation
Indices: 363447--363545 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
363437 TAATGAATTC
** * * *
363447 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA GAAAAC GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
363495 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
363546 TATGAAAATG
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
5 1 0.01
6 57 0.81
7 8 0.11
8 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:363528 original size:14 final size:13
Alignment explanation
Indices: 363507--363544 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
363497 AAAAGTGAGA
363507 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
363519 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
363534 GAAAAAGAAAA
1 GAAAAAGAAAA
363545 ATATGAAAAT
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:363588 original size:17 final size:18
Alignment explanation
Indices: 363563--363602 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
363553 ATGAGATTTC
363563 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
363580 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
363598 AAAAA
1 AAAAA
363603 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:363594 original size:18 final size:17
Alignment explanation
Indices: 363563--363612 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
363553 ATGAGATTTC
363563 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
363580 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
363598 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
363613 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:363618 original size:36 final size:34
Alignment explanation
Indices: 363549--363644 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
363539 AGAAAAATAT
* *
363549 GAAAATGAGATTTCAAAAACAAAAGAGAG-TGAAAA
1 GAAAATGAGA-TTGAAAAA-GAAAGAGAGTTGAAAA
363584 GCAAAATGAGATTGAAAAAGAAAGAGAGTTTGAAAA
1 G-AAAATGAGATTGAAAAAGAAAGAGAG-TTGAAAA
* *
363620 GAAAACGAG--TGAAGAAG-AAGAGAGT
1 GAAAATGAGATTGAAAAAGAAAGAGAGT
363645 GCTCAAACAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.02
32 7 0.13
33 7 0.13
34 8 0.15
35 15 0.28
36 16 0.30
ACGTcount: A:0.56, C:0.04, G:0.26, T:0.14
Consensus pattern (34 bp):
GAAAATGAGATTGAAAAAGAAAGAGAGTTGAAAA
Found at i:363621 original size:17 final size:16
Alignment explanation
Indices: 363570--363644 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
363560 TTCAAAAACA
363570 AAAGAGAG-TGAAAAG
1 AAAGAGAGTTGAAAAG
363585 CAAA-ATGAGATTGAAAAAG
1 -AAAGA-GAG-TTG-AAAAG
363604 AAAGAGAGTTTGAAAAG
1 AAAGAGAG-TTGAAAAG
363621 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAA-AAG
363637 -AAGAGAGT
1 AAAGAGAGT
363645 GCTCAAACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
15 10 0.20
16 11 0.22
17 11 0.22
18 11 0.22
19 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (16 bp):
AAAGAGAGTTGAAAAG
Found at i:364538 original size:21 final size:21
Alignment explanation
Indices: 364523--364574 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
364513 GAATTGGCTC
364523 GAAATGGTATGGAATTGGTAA
1 GAAATGGTATGGAATTGGTAA
* *
364544 GAAATGGTATGGTATTTGGTAC
1 GAAATGGTATGG-AATTGGTAA
*
364566 GAATTGGTA
1 GAAATGGTA
364575 ATGGTTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.33
Consensus pattern (21 bp):
GAAATGGTATGGAATTGGTAA
Found at i:366918 original size:13 final size:13
Alignment explanation
Indices: 366900--366925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
366890 TGTGTCCTAA
366900 TATGAATTAAATT
1 TATGAATTAAATT
366913 TATGAATTAAATT
1 TATGAATTAAATT
366926 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:369410 original size:21 final size:21
Alignment explanation
Indices: 369365--369427 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
369355 TTTGAACCAT
* *
369365 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
369387 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
369408 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
369428 CAAATACAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:372223 original size:11 final size:10
Alignment explanation
Indices: 372207--372236 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
372197 TTCGTAATGT
372207 AAAAAAAAGTC
1 AAAAAAAA-TC
372218 AAAAAAAATC
1 AAAAAAAATC
372228 AAAAAAAAT
1 AAAAAAAAT
372237 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:373454 original size:6 final size:6
Alignment explanation
Indices: 373422--373529 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
373412 AAAGAAATTG
* * ** *
373422 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
373469 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
373520 AAAGAA AAAG
1 AAAGAA AAAG
373530 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:373509 original size:14 final size:13
Alignment explanation
Indices: 373490--373527 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
373480 AAAAGTGAGA
373490 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
373502 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
373517 GAAAAAGAAAA
1 GAAAAAGAAAA
373528 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:373564 original size:12 final size:12
Alignment explanation
Indices: 373533--373564 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
373523 GAAAAAGCGA
*
373533 AAAAAGAATTTG
1 AAAAAGAGTTTG
373545 AAAAAGAGTTTG
1 AAAAAGAGTTTG
373557 AAAAAGAG
1 AAAAAGAG
373565 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:376846 original size:17 final size:17
Alignment explanation
Indices: 376826--376871 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
376816 AGTCAAAATC
376826 GAAAAAAAAATTG-AAA
1 GAAAAAAAAATTGAAAA
*
376842 GGAAAAAAAATTGAAAA
1 GAAAAAAAAATTGAAAA
376859 GAAAAAAAAATTG
1 GAAAAAAAAATTG
376872 CATACGGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (17 bp):
GAAAAAAAAATTGAAAA
Found at i:376847 original size:16 final size:16
Alignment explanation
Indices: 376828--376867 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
376818 TCAAAATCGA
*
376828 AAAAAAAATTGAAAGG
1 AAAAAAAATTGAAAAG
376844 AAAAAAAATTGAAAAG
1 AAAAAAAATTGAAAAG
376860 AAAAAAAA
1 AAAAAAAA
376868 ATTGCATACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (16 bp):
AAAAAAAATTGAAAAG
Found at i:379389 original size:85 final size:85
Alignment explanation
Indices: 379246--379419 Score: 321
Period size: 85 Copynumber: 2.0 Consensus size: 85
379236 GAAAAAGCTT
379246 TTCAAACACTAAAAGATAAGTTATGTCCTGCTCCTCTTCTCAAATTACTTGATTTTTCTAATACT
1 TTCAAACACTAAAAGATAAGTTATGTCCTGCTCCTCTTCTCAAATTACTTGATTTTTCTAATACT
379311 TTTGAGCTTGAGTGTAATAC
66 TTTGAGCTTGAGTGTAATAC
* *
379331 TTCAAACACTAAAAGATAAGTTATGTTCTGCTTCTCTTCTCAAATTACTTGATTTTTCTAATACT
1 TTCAAACACTAAAAGATAAGTTATGTCCTGCTCCTCTTCTCAAATTACTTGATTTTTCTAATACT
*
379396 TTTGAGCTTGAGTGTAATGC
66 TTTGAGCTTGAGTGTAATAC
379416 TTCA
1 TTCA
379420 GGAATTGGAA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (85 bp):
TTCAAACACTAAAAGATAAGTTATGTCCTGCTCCTCTTCTCAAATTACTTGATTTTTCTAATACT
TTTGAGCTTGAGTGTAATAC
Found at i:381695 original size:29 final size:28
Alignment explanation
Indices: 381636--381703 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
381626 GTATTGAAGA
* * *
381636 AAAAAAAGAAG-AAAAAAATTTGGAATT
1 AAAAAAAGAAGAAAAAAAAATCGAAATT
381663 AAAAAAAGAAGAAAAAAAAATCGAAATT
1 AAAAAAAGAAGAAAAAAAAATCGAAATT
*
381691 GAAAAAAAAAAGA
1 -AAAAAAAGAAGA
381704 GTGATTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 11 0.31
28 13 0.37
29 11 0.31
ACGTcount: A:0.74, C:0.01, G:0.13, T:0.12
Consensus pattern (28 bp):
AAAAAAAGAAGAAAAAAAAATCGAAATT
Found at i:382652 original size:4 final size:4
Alignment explanation
Indices: 382643--382670 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
382633 TTAAACTAAG
382643 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
382671 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:383262 original size:22 final size:22
Alignment explanation
Indices: 383232--383275 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
383222 TTTGGTATTT
383232 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
383254 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
383276 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:387569 original size:19 final size:19
Alignment explanation
Indices: 387545--387586 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
387535 TTCATTCTCT
*
387545 TTTTTTGAATTTTCTTTTC
1 TTTTTTCAATTTTCTTTTC
*
387564 TTTTTTCATTTTTCTTTTC
1 TTTTTTCAATTTTCTTTTC
387583 TTTT
1 TTTT
387587 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTCAATTTTCTTTTC
Found at i:390063 original size:22 final size:22
Alignment explanation
Indices: 390033--390076 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
390023 TTTGGTATTT
390033 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
390055 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
390077 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:392245 original size:10 final size:10
Alignment explanation
Indices: 392229--392277 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
392219 AGCTCGTTTC
*
392229 CAGCTCACTT
1 CAGCTCAATT
* *
392239 GAGCTCAAGT
1 CAGCTCAATT
*
392249 CAGCTCATTT
1 CAGCTCAATT
*
392259 GAGCTCAATT
1 CAGCTCAATT
392269 CAGCTCAAT
1 CAGCTCAAT
392278 CTTAACCCAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:392254 original size:20 final size:20
Alignment explanation
Indices: 392229--392275 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
392219 AGCTCGTTTC
392229 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTTGAGCTCAAGT
* *
392249 CAGCTCATTTGAGCTCAATT
1 CAGCTCACTTGAGCTCAAGT
392269 CAGCTCA
1 CAGCTCA
392276 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (20 bp):
CAGCTCACTTGAGCTCAAGT
Found at i:395296 original size:21 final size:18
Alignment explanation
Indices: 395272--395316 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
395262 ACGAGAGTAC
395272 AAAAGAAATGAGTGATGTGA
1 AAAAGAAA-GAG-GATGTGA
*
395292 TAAAAGAAAGAGGATTTGA
1 -AAAAGAAAGAGGATGTGA
395311 AAAAGA
1 AAAAGA
395317 GTTTGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.18
Consensus pattern (18 bp):
AAAAGAAAGAGGATGTGA
Found at i:399800 original size:46 final size:46
Alignment explanation
Indices: 399748--399841 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
399738 CAAAGAAAAG
*
399748 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
399794 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
399840 AC
1 AC
399842 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:409687 original size:20 final size:20
Alignment explanation
Indices: 409664--409710 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
409654 GGGTTAAGAT
*
409664 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
409684 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
409704 TGAGCTG
1 TGAGCTG
409711 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:412522 original size:12 final size:12
Alignment explanation
Indices: 412505--412546 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
412495 GACTTTTCAC
412505 TTTTTTTTCTTT
1 TTTTTTTTCTTT
412517 TTTTTTTTCACTTT
1 TTTTTTTT--CTTT
*
412531 TTTTCTTTCTTT
1 TTTTTTTTCTTT
412543 TTTT
1 TTTT
412547 GCTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:412523 original size:22 final size:22
Alignment explanation
Indices: 412498--412568 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 22
412488 CTCGCAAGAC
412498 TTTTCACTTTTTTTTCTTTTTTT
1 TTTTCACTTTTTTTTC-TTTTTT
412521 TTTTCAC-TTTTTTTCTTTCTTT
1 TTTTCACTTTTTTTTCTTT-TTT
* **
412543 TTTTGCTCTTTTTTCACTTTTTT
1 TTTT-CACTTTTTTTTCTTTTTT
412566 TTT
1 TTT
412569 GAATTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.07
22 15 0.36
23 15 0.36
24 9 0.21
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.79
Consensus pattern (22 bp):
TTTTCACTTTTTTTTCTTTTTT
Found at i:412525 original size:23 final size:23
Alignment explanation
Indices: 412498--412568 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
412488 CTCGCAAGAC
412498 TTTTCACTTTTTTTTCTTTTTTT
1 TTTTCACTTTTTTTTCTTTTTTT
412521 TTTTCAC-TTTTTTTCTTTCTTTT
1 TTTTCACTTTTTTTTCTTT-TTTT
* * **
412544 TTTGCTCTTTTTTCACTTTTTTT
1 TTTTCACTTTTTTTTCTTTTTTT
412567 TT
1 TT
412569 GAATTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.26
23 22 0.52
24 9 0.21
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.79
Consensus pattern (23 bp):
TTTTCACTTTTTTTTCTTTTTTT
Found at i:412555 original size:12 final size:11
Alignment explanation
Indices: 412498--412556 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
412488 CTCGCAAGAC
*
412498 TTTTCACTTTT
1 TTTTCTCTTTT
*
412509 TTTTCTTTTTTT
1 TTTTC-TCTTTT
*
412521 TTTTCACTTTT
1 TTTTCTCTTTT
*
412532 TTTCTTTCTTTT
1 TTT-TCTCTTTT
*
412544 TTTGCTCTTTT
1 TTTTCTCTTTT
412555 TT
1 TT
412557 CACTTTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 20 0.53
12 18 0.47
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:412565 original size:11 final size:11
Alignment explanation
Indices: 412498--412567 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
412488 CTCGCAAGAC
412498 TTTTCACTTTT
1 TTTTCACTTTT
**
412509 TTTTCTTTTTTT
1 TTTTC-ACTTTT
412521 TTTTCAC-TTT
1 TTTTCACTTTT
*
412531 TTTTC-TTTCTT
1 TTTTCACTT-TT
** *
412542 TTTTTGCTCTT
1 TTTTCACTTTT
412553 TTTTCACTTTT
1 TTTTCACTTTT
412564 TTTT
1 TTTT
412568 TGAATTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
10 9 0.20
11 25 0.57
12 10 0.23
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTTCACTTTT
Found at i:412575 original size:10 final size:10
Alignment explanation
Indices: 412562--412588 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
412552 TTTTTCACTT
412562 TTTTTTTGAA
1 TTTTTTTGAA
412572 TTTTTTTGAA
1 TTTTTTTGAA
412582 TTTTTTT
1 TTTTTTT
412589 TTTGATACTC
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:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:412576 original size:22 final size:22
Alignment explanation
Indices: 412506--412593 Score: 90
Period size: 22 Copynumber: 4.0 Consensus size: 22
412496 ACTTTTCACT
* *
412506 TTTTTTTCTTTTTTTTTTTCAC
1 TTTTTTTCATTTTTTTTTTGAC
412528 TTTTTTTC-TTTCTTTTTTTG-C
1 TTTTTTTCATTT-TTTTTTTGAC
* *
412549 TCTTTTTTCACTTTTTTTTTGAA
1 T-TTTTTTCATTTTTTTTTTGAC
*
412572 TTTTTTTGAATTTTTTTTTTGA
1 TTTTTTT-CATTTTTTTTTTGA
412594 TACTCCAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
21 5 0.09
22 36 0.64
23 15 0.27
ACGTcount: A:0.08, C:0.10, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTTTTTCATTTTTTTTTTGAC
Found at i:412576 original size:32 final size:32
Alignment explanation
Indices: 412519--412579 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
412509 TTTTCTTTTT
**
412519 TTTTTTCACTTTTTTTCTTTCTTTTTTTGCTC
1 TTTTTTCACTTTTTTTCTTAATTTTTTTGCTC
412551 TTTTTTCACTTTTTTT-TTGAATTTTTTTG
1 TTTTTTCACTTTTTTTCTT-AATTTTTTTG
412580 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.07, C:0.13, G:0.05, T:0.75
Consensus pattern (32 bp):
TTTTTTCACTTTTTTTCTTAATTTTTTTGCTC
Found at i:412587 original size:32 final size:31
Alignment explanation
Indices: 412518--412588 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
412508 TTTTTCTTTT
** *
412518 TTTTTTTCACTTTTTTTCTTTCTTTTTTTGC
1 TTTTTTTCACTTTTTTTCTTAATTTTTTTGA
412549 TCTTTTTTCACTTTTTTT-TTGAATTTTTTTGAA
1 T-TTTTTTCACTTTTTTTCTT-AATTTTTTTG-A
412582 TTTTTTT
1 TTTTTTT
412589 TTTGATACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.09
32 30 0.88
33 1 0.03
ACGTcount: A:0.08, C:0.11, G:0.04, T:0.76
Consensus pattern (31 bp):
TTTTTTTCACTTTTTTTCTTAATTTTTTTGA
Found at i:414082 original size:20 final size:20
Alignment explanation
Indices: 414059--414105 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
414049 GGGTTAAGAT
*
414059 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
414079 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
414099 TGAGCTG
1 TGAGCTG
414106 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:421918 original size:24 final size:23
Alignment explanation
Indices: 421886--421930 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
421876 ACGTGAGAGT
421886 GAAAAAGAAATT-GAAGAAAGAAGA
1 GAAAAAG-AATTAGAA-AAAGAAGA
421910 GAAAAAGAATTAGAAAAAGAA
1 GAAAAAGAATTAGAAAAAGAA
421931 ACAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (23 bp):
GAAAAAGAATTAGAAAAAGAAGA
Found at i:423271 original size:17 final size:17
Alignment explanation
Indices: 423249--423282 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
423239 TTGAAAATGA
423249 GGCCAAA-TTGTCAAAGT
1 GGCCAAAGTTGT-AAAGT
423266 GGCCAAAGTTGTAAAGT
1 GGCCAAAGTTGTAAAGT
423283 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (17 bp):
GGCCAAAGTTGTAAAGT
Done.