Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2305
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: 74675
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:76 original size:30 final size:30
Alignment explanation
Indices: 1--77 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
* * *
1 AGCTAAACCTTAGCTCAACTTTAGCTTAGG
1 AGCTAAAGCTTAGCTCAACTTTAGCTCACG
** *
31 AG-TTTAGCCTCAGCTCAACTTTAGCTCACG
1 AGCTAAAG-CTTAGCTCAACTTTAGCTCACG
61 AGCTAAAGCTTAGCTCA
1 AGCTAAAGCTTAGCTCA
78 TTTTTAGTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
29 2 0.06
30 31 0.86
31 3 0.08
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (30 bp):
AGCTAAAGCTTAGCTCAACTTTAGCTCACG
Found at i:1499 original size:21 final size:21
Alignment explanation
Indices: 1473--1535 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1463 TTGGTATTTG
1473 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
1494 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
1515 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
1536 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:6160 original size:10 final size:10
Alignment explanation
Indices: 6145--6182 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
6135 ATTTAGGAAT
6145 TGGTATGAAA
1 TGGTATGAAA
*
6155 TGGTATGGAAT
1 TGGTAT-GAAA
6166 TGGTATGAAA
1 TGGTATGAAA
6176 TGGTATG
1 TGGTATG
6183 GTATTTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (10 bp):
TGGTATGAAA
Found at i:6166 original size:21 final size:21
Alignment explanation
Indices: 6140--6202 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
6130 TTGGTATTTA
6140 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
6161 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
* * *
6182 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTATGAAATGGTA
6203 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 23 0.61
22 15 0.39
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (21 bp):
GGAATTGGTATGAAATGGTAT
Found at i:7603 original size:10 final size:10
Alignment explanation
Indices: 7588--7649 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
7578 TTTGAACCAT
*
7588 TACCAATTCG
1 TACCAATTCA
*
7598 TACCAAATACCA
1 TACC-AAT-TCA
*
7610 TACCATTTCA
1 TACCAATTCA
7620 TACCAATTCCA
1 TACCAATT-CA
* *
7631 TACCATTTCG
1 TACCAATTCA
7641 TACCAATTC
1 TACCAATTC
7650 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:7633 original size:21 final size:21
Alignment explanation
Indices: 7588--7650 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
7578 TTTGAACCAT
* *
7588 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
7610 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
7631 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
7651 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:14470 original size:20 final size:19
Alignment explanation
Indices: 14447--14492 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
14437 GGGTTAAAAT
14447 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGC-TGAG
* *
14467 TGAGTTGACTTGAGCTGAG
1 TGAGCTGAATTGAGCTGAG
14486 TGAGCTG
1 TGAGCTG
14493 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.22, C:0.11, G:0.37, T:0.30
Consensus pattern (19 bp):
TGAGCTGAATTGAGCTGAG
Found at i:14883 original size:14 final size:14
Alignment explanation
Indices: 14864--14908 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
14854 AACTCATCGT
*
14864 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
14878 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
14891 AATTTAATTTAATG
1 AGTTTAATTTAATG
14905 AGTT
1 AGTT
14909 GCTTCTTTAA
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:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:15914 original size:29 final size:29
Alignment explanation
Indices: 15881--15940 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
15871 ATAACCAAAC
*
15881 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
15910 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
15939 CT
1 CT
15941 TTGAATCCTT
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:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:15933 original size:15 final size:15
Alignment explanation
Indices: 15887--15934 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
15877 AAACCTACAA
*
15887 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
15902 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
15916 AAACTTCATATCCAT
1 AAACTTCATATCCAT
15931 AAAC
1 AAAC
15935 CCATCTTTGA
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:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:17277 original size:18 final size:18
Alignment explanation
Indices: 17254--17301 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
17244 GAAAGACAAA
* *
17254 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATAAGAGT
* *
17272 GAAAAAGAAAATAAGATT
1 GAAAAAGAGAATAAGAGT
17290 GAAAAAGAGAAT
1 GAAAAAGAGAAT
17302 GAAAAAGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (18 bp):
GAAAAAGAGAATAAGAGT
Found at i:17280 original size:24 final size:24
Alignment explanation
Indices: 17251--17328 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
17241 AATGAAAGAC
* *
17251 AAAGAAAAAGAGATTGAGAGTGAA
1 AAAGAAAAAGAGATTGAGAGAGAG
* *
17275 AAAGAAAATA-AGATTGAAAAAGAG
1 AAAGAAAA-AGAGATTGAGAGAGAG
* *
17299 AATGAAAAAGAGTTTGAGAGAGAG
1 AAAGAAAAAGAGATTGAGAGAGAG
17323 AAAGAA
1 AAAGAA
17329 TGTGAACAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (24 bp):
AAAGAAAAAGAGATTGAGAGAGAG
Found at i:18364 original size:21 final size:22
Alignment explanation
Indices: 18325--18368 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
18315 ATGCATACTC
18325 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
18347 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
18368 C
1 C
18369 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:21389 original size:14 final size:14
Alignment explanation
Indices: 21370--21414 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
21360 AACTCATCGT
*
21370 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
21384 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
21397 AATTTAATTTAATG
1 AGTTTAATTTAATG
21411 AGTT
1 AGTT
21415 GCTTCTTTAA
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:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:22420 original size:29 final size:29
Alignment explanation
Indices: 22387--22446 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
22377 ATAACCAAAC
*
22387 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
22416 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
22445 CT
1 CT
22447 TTGAATCCTT
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:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:22439 original size:15 final size:15
Alignment explanation
Indices: 22393--22440 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
22383 AAACCTACAA
*
22393 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
22408 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
22422 AAACTTCATATCCAT
1 AAACTTCATATCCAT
22437 AAAC
1 AAAC
22441 CCATCTTTGA
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:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:23314 original size:19 final size:19
Alignment explanation
Indices: 23290--23329 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23280 AGCTCCCATG
23290 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
23309 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
23328 TA
1 TA
23330 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:37863 original size:55 final size:55
Alignment explanation
Indices: 37779--37915 Score: 267
Period size: 55 Copynumber: 2.5 Consensus size: 55
37769 AGCAGCAAGG
37779 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
1 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
37834 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
1 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
37889 GAGATGTTCCCATGCATGG-ACGGCATT
1 GAGATGTTCCCATGCATGGAACGGCATT
37916 AATGAAAGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
54 8 0.10
55 74 0.90
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (55 bp):
GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
Found at i:39037 original size:17 final size:17
Alignment explanation
Indices: 39015--39069 Score: 87
Period size: 16 Copynumber: 3.4 Consensus size: 17
39005 AAAAAAATAT
39015 AAAAAAAATTCGAAAAA
1 AAAAAAAATTCGAAAAA
*
39032 AAAAAAAATTTG-AAAA
1 AAAAAAAATTCGAAAAA
39048 AAAAAAAATTC-AAAAA
1 AAAAAAAATTCGAAAAA
39064 AAAAAA
1 AAAAAA
39070 GTTTGTATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
16 24 0.69
17 11 0.31
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.13
Consensus pattern (17 bp):
AAAAAAAATTCGAAAAA
Found at i:39152 original size:31 final size:30
Alignment explanation
Indices: 39107--39186 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 30
39097 TGTATTTAGT
**
39107 ATTGAAGAAAAAAAAGAAGAAAAAAAATTCGGA
1 ATTGAA-AAAAAAAAGAA-AAAAAAAA-TCAAA
39140 ATT-AAAAAAAAAAGAAAAAAAAAATCAAA
1 ATTGAAAAAAAAAAGAAAAAAAAAATCAAA
39169 ATTGAAAAAAAAAA-AAAA
1 ATTGAAAAAAAAAAGAAAA
39187 GTGATTGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
29 10 0.23
30 18 0.41
31 11 0.25
32 2 0.05
33 3 0.07
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.11
Consensus pattern (30 bp):
ATTGAAAAAAAAAAGAAAAAAAAAATCAAA
Found at i:39158 original size:29 final size:29
Alignment explanation
Indices: 39114--39186 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
39104 AGTATTGAAG
**
39114 AAAAAAAAGAAGAAAAAAAATTCGGAATTAA
1 AAAAAAAAGAA-AAAAAAAA-TCAAAATTAA
*
39145 AAAAAAAAGAAAAAAAAAATCAAAATTGA
1 AAAAAAAAGAAAAAAAAAATCAAAATTAA
39174 AAAAAAAA-AAAAA
1 AAAAAAAAGAAAAA
39187 GTGATTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.13
29 15 0.38
30 8 0.21
31 11 0.28
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (29 bp):
AAAAAAAAGAAAAAAAAAATCAAAATTAA
Found at i:39176 original size:28 final size:30
Alignment explanation
Indices: 39112--39186 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 30
39102 TTAGTATTGA
**
39112 AGAAAAAAAAGAAGAAAAAAAATTCGGAATT
1 AGAAAAAAAAGAA-AAAAAAAATTCAAAATT
*
39143 AAAAAAAAAAGAAAAAAAAAA-TCAAAATT
1 AGAAAAAAAAGAAAAAAAAAATTCAAAATT
39172 -GAAAAAAAA-AAAAAA
1 AGAAAAAAAAGAAAAAA
39187 GTGATTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 6 0.15
28 8 0.20
29 6 0.15
30 8 0.20
31 12 0.30
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (30 bp):
AGAAAAAAAAGAAAAAAAAAATTCAAAATT
Found at i:40113 original size:21 final size:21
Alignment explanation
Indices: 40073--40131 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
40063 AATCTTGAAT
*
40073 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
40094 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
40115 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
40132 TGAAAATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:40123 original size:15 final size:14
Alignment explanation
Indices: 40084--40131 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
40074 AAATTGAGAG
40084 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
40098 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
40113 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
40128 AAGA
1 AAGA
40132 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:42580 original size:51 final size:53
Alignment explanation
Indices: 42505--42638 Score: 222
Period size: 55 Copynumber: 2.6 Consensus size: 53
42495 AGCAGCAAGG
42505 GAGAT-TTCCCATGCATGGAACGGCATTAAAGG-AGC-AGACATGGATTTAAT
1 GAGATGTTCCCATGCATGGAACGGCATTAAAGGAAGCAAGACATGGATTTAAT
42555 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
1 GAGATGTTCCCATGCATGGAACGGCA-TTAAAGGAAGC-AAGACATGGATTTAAT
42610 GAGATGTTCCCATGCATGG-ACGGCATTAA
1 GAGATGTTCCCATGCATGGAACGGCATTAA
42639 TGAAAGCATG
Statistics
Matches: 79, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
50 5 0.06
51 20 0.25
52 7 0.09
53 7 0.09
54 6 0.08
55 34 0.43
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (53 bp):
GAGATGTTCCCATGCATGGAACGGCATTAAAGGAAGCAAGACATGGATTTAAT
Found at i:49905 original size:22 final size:22
Alignment explanation
Indices: 49874--49917 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
49864 TTTTGAACCA
*
49874 TTACCTTTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
49896 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
49918 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:51920 original size:22 final size:22
Alignment explanation
Indices: 51890--51933 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
51880 TTTGGTATTT
51890 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
51912 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
51934 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:52751 original size:20 final size:20
Alignment explanation
Indices: 52705--52751 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
52695 AGCTCGTTTC
*
52705 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
52725 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
52745 CAGCTCA
1 CAGCTCA
52752 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:55432 original size:48 final size:47
Alignment explanation
Indices: 55353--55458 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
55343 GAGTGTCATG
*
55353 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
55401 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
55449 GAAAAAGAAA
1 GAAAAAGAAA
55459 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:57173 original size:20 final size:20
Alignment explanation
Indices: 57127--57173 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
57117 AGCTCGTTTC
*
57127 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
57147 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
57167 CAGCTCA
1 CAGCTCA
57174 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:62063 original size:17 final size:17
Alignment explanation
Indices: 62038--62091 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
62028 TCTCTTTTCA
*
62038 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
62055 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
62072 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
62089 TTC
1 TTC
62092 GCTCTTTTCT
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:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:64278 original size:13 final size:12
Alignment explanation
Indices: 64260--64309 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
64250 AACCGTATGC
64260 AATTTTTTTTTAA
1 AATTTTTTTTT-A
*
64273 AATTTTTTTTTC
1 AATTTTTTTTTA
*
64285 AATTTTTTTTGA
1 AATTTTTTTTTA
*
64297 ACTCTTTTTTTTA
1 AAT-TTTTTTTTA
64310 CGTACCTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 12 0.39
13 19 0.61
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (12 bp):
AATTTTTTTTTA
Found at i:64636 original size:22 final size:22
Alignment explanation
Indices: 64606--64649 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
64596 TTTGGTATTT
64606 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
64628 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
64650 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:71604 original size:18 final size:19
Alignment explanation
Indices: 71572--71610 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
71562 ATCAGACTGA
*
71572 AATTAAAATCCCCAA-AAC
1 AATTAAAATACCCAAGAAC
*
71590 AATTAAAATAGCCAAGAAC
1 AATTAAAATACCCAAGAAC
71609 AA
1 AA
71611 AGAAGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15
Consensus pattern (19 bp):
AATTAAAATACCCAAGAAC
Found at i:74461 original size:24 final size:22
Alignment explanation
Indices: 74433--74480 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
74423 TCTCTTTCAT
*
74433 TTCTTTTCCACTCTTTCTTTTTGC
1 TTCTTTTCCAATC--TCTTTTTGC
*
74457 TTCTTTTTCAATCTCTTTTTGC
1 TTCTTTTCCAATCTCTTTTTGC
74479 TT
1 TT
74481 TCACTCTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
24 11 0.50
ACGTcount: A:0.06, C:0.25, G:0.04, T:0.65
Consensus pattern (22 bp):
TTCTTTTCCAATCTCTTTTTGC
Found at i:74532 original size:21 final size:21
Alignment explanation
Indices: 74514--74570 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
74504 CTCATTTTCA
74514 TCTTTTGCT-T-ATTTCTTTT
1 TCTTTTGCTCTCATTTCTTTT
*
74533 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTGCTCTCATTTCTTTT
74554 T-TTTCT-CTCTCAATTTC
1 TCTTT-TGCTCTC-ATTTC
74571 ATTCAAGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.24
20 9 0.27
21 16 0.48
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.68
Consensus pattern (21 bp):
TCTTTTGCTCTCATTTCTTTT
Found at i:74553 original size:20 final size:22
Alignment explanation
Indices: 74524--74570 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
74514 TCTTTTGCTT
74524 ATTTCTTTTTCTTTT-TCTCTC-
1 ATTTCTTTTT-TTTTCTCTCTCA
74545 ATTTC-TTTTTTTTCTCTCTCA
1 ATTTCTTTTTTTTTCTCTCTCA
74566 ATTTC
1 ATTTC
74571 ATTCAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 10 0.42
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTTCTTTTTTTTTCTCTCTCA
Done.