Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1687
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: 72752
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:882 original size:21 final size:23
Alignment explanation
Indices: 837--883 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
827 TCACCTGCAA
* *
837 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
860 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
881 TAA
1 TAA
884 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:6228 original size:16 final size:16
Alignment explanation
Indices: 6207--6248 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
6197 TAGCTTCTTC
6207 TTTTTTTCACGAAAAT
1 TTTTTTTCACGAAAAT
**
6223 TTTTTTTCCACGAATTT
1 TTTTTTT-CACGAAAAT
6240 TTTTTTTCA
1 TTTTTTTCA
6249 ACTTGATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTTTTCACGAAAAT
Found at i:6229 original size:17 final size:16
Alignment explanation
Indices: 6207--6248 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
6197 TAGCTTCTTC
6207 TTTTTTTCACGAAAATT
1 TTTTTTTCACG-AAATT
* *
6224 TTTTTTCCACGAATTT
1 TTTTTTTCACGAAATT
6240 TTTTTTTCA
1 TTTTTTTCA
6249 ACTTGATATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:6238 original size:15 final size:15
Alignment explanation
Indices: 6207--6244 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6197 TAGCTTCTTC
6207 TTTTTTTCACGAAAAT
1 TTTTTTTCACG-AAAT
6223 TTTTTTTCCACG-AAT
1 TTTTTTT-CACGAAAT
6238 TTTTTTT
1 TTTTTTT
6245 TTCAACTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 7 0.33
17 4 0.19
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.61
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:6309 original size:11 final size:11
Alignment explanation
Indices: 6295--6338 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
6285 AAATTTTTTT
6295 TTTTTTTTGAA
1 TTTTTTTTGAA
*
6306 TTTTTTTTCAA
1 TTTTTTTTGAA
*
6317 TTTTTTTTAAA
1 TTTTTTTTGAA
6328 TTTTTTTTGAA
1 TTTTTTTTGAA
6339 GAAACTACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:7273 original size:21 final size:23
Alignment explanation
Indices: 7228--7274 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
7218 TCACCTGCAA
* *
7228 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
7251 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
7272 TAA
1 TAA
7275 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:11703 original size:40 final size:39
Alignment explanation
Indices: 11650--11780 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
11640 TAACTCATTC
* * * *
11650 AATGCCTTTGGGACTTAACCCGGATTTTAAAACTCACACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAAAACTCGCACA
* *
11690 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTA-AAACTCGCACA
*
11730 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAA-AACTCGCACA
*
11770 AATACCTTCGG
1 AATGCCTTCGG
11781 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 75 0.96
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCACA
Found at i:11793 original size:80 final size:80
Alignment explanation
Indices: 11653--11832 Score: 192
Period size: 80 Copynumber: 2.3 Consensus size: 80
11643 CTCATTCAAT
* * * *
11653 GCCTTTGGGACTTAACCCGGATTTTAAAACTCACACGAATGCCTTCGGGACTTAACCCGGA-ATT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCACACAAATACCTTCGGGACTTAACCCGGATA-T
*
11717 AGT-A-TCTCGCACAAA
65 AGTCACT-TAGCACAAA
* **
11732 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAGTCCGGAT
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCACACAAATACCTTCGGGA-CTTAACCCGGAT
11795 ATAGTCACTTAGCACAAA
63 ATAGTCACTTAGCACAAA
*
11813 GCCTTC-GGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
11833 CAACATTCAA
Statistics
Matches: 86, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
79 20 0.23
80 55 0.64
81 10 0.12
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCACACAAATACCTTCGGGACTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:15877 original size:10 final size:10
Alignment explanation
Indices: 15862--15926 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
15852 AGTTTTTCCC
15862 AGCTCAATTT
1 AGCTCAATTT
*
15872 AGCTCACA-TG
1 AGCTCA-ATTT
*
15882 AGCTTAATTT
1 AGCTCAATTT
*
15892 AGCTC-GTTT
1 AGCTCAATTT
15901 GAGCTCAATTT
1 -AGCTCAATTT
* *
15912 AGCTTACTTT
1 AGCTCAATTT
15922 AGCTC
1 AGCTC
15927 GTTTGAGCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 4 0.10
10 34 0.81
11 4 0.10
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (10 bp):
AGCTCAATTT
Found at i:15885 original size:20 final size:20
Alignment explanation
Indices: 15862--15915 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
15852 AGTTTTTCCC
15862 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
15882 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
15902 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
15916 TACTTTAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:15896 original size:30 final size:30
Alignment explanation
Indices: 15862--15935 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
15852 AGTTTTTCCC
15862 AGCTCAATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTC-ATTTGAGCTCA-ATTGAGCTTAATTT
* * *
15892 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCATTTGAGCTCAATTGAGCTTAATTT
*
15922 AGCTCGTTTGAGCT
1 AGCTCATTTGAGCT
15936 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (30 bp):
AGCTCATTTGAGCTCAATTGAGCTTAATTT
Found at i:15925 original size:20 final size:20
Alignment explanation
Indices: 15862--15926 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
15852 AGTTTTTCCC
* * *
15862 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
15882 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
15901 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
15922 AGCTC
1 AGCTC
15927 GTTTGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 29 0.81
21 4 0.11
22 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:23665 original size:15 final size:16
Alignment explanation
Indices: 23640--23669 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23630 AGAGAAAAAT
23640 AAAAGTGAAAATGAAG
1 AAAAGTGAAAATGAAG
23656 AAAA-TGAAAATGAA
1 AAAAGTGAAAATGAA
23670 AAAGGCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
AAAAGTGAAAATGAAG
Found at i:26117 original size:12 final size:12
Alignment explanation
Indices: 26039--26118 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
26029 GAAGAAATTC
26039 GAAAAAAAAA-T
1 GAAAAAAAAAGT
*
26050 TAAAAAAAAAG-
1 GAAAAAAAAAGT
*
26061 AAAAAAAAGAAGT
1 GAAAAAAA-AAGT
26074 GACAAAAAAATCGAGT
1 GA-AAAAAAA---AGT
* **
26090 TAAAAAAAAAAA
1 GAAAAAAAAAGT
26102 GAAAAAAAAAGT
1 GAAAAAAAAAGT
26114 GAAAA
1 GAAAA
26119 GTCTTACGAG
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
11 16 0.30
12 18 0.34
13 2 0.04
14 6 0.11
15 7 0.13
16 4 0.08
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (12 bp):
GAAAAAAAAAGT
Found at i:28564 original size:18 final size:18
Alignment explanation
Indices: 28543--28577 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28533 AGAAAAGAAA
28543 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
28561 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
28578 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:35180 original size:20 final size:20
Alignment explanation
Indices: 35157--35210 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
35147 AGTTTTTCCC
*
35157 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
35177 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
35197 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
35211 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:35192 original size:30 final size:30
Alignment explanation
Indices: 35157--35230 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
35147 AGTTTTTCCC
35157 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
35187 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
35217 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
35231 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:35220 original size:20 final size:20
Alignment explanation
Indices: 35157--35221 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
35147 AGTTTTTCCC
* * * *
35157 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
35177 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
35196 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
35217 AGCTC
1 AGCTC
35222 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:40590 original size:13 final size:13
Alignment explanation
Indices: 40574--40598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40564 AAAAAAAATC
40574 GAAAAAAAATTGA
1 GAAAAAAAATTGA
40587 GAAAAAAAATTG
1 GAAAAAAAATTG
40599 CATACGGTCT
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
GAAAAAAAATTGA
Found at i:42867 original size:16 final size:17
Alignment explanation
Indices: 42829--42867 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
42819 AAGAAGAAAA
42829 ACAAAAAGATGAGTGAT
1 ACAAAAAGATGAGTGAT
*
42846 AAAAAAAGA-GAGTGAT
1 ACAAAAAGATGAGTGAT
*
42862 TCAAAA
1 ACAAAA
42868 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (17 bp):
ACAAAAAGATGAGTGAT
Found at i:47088 original size:34 final size:33
Alignment explanation
Indices: 47024--47089 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
47014 TTAAAGATGT
* *
47024 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
47057 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
47090 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:50274 original size:13 final size:14
Alignment explanation
Indices: 50256--50319 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
50246 ACGGTATTGT
50256 AAAAAAAAAT--AA
1 AAAAAAAAATCAAA
*
50268 AAAAAAAATTCGAAA
1 AAAAAAAAATC-AAA
**
50283 AAAAAAAAATTTAA
1 AAAAAAAAATCAAA
*
50297 AAAAAAAATTCAAA
1 AAAAAAAAATCAAA
50311 AAAAAAAAA
1 AAAAAAAAA
50320 GAAGTTTGTA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 9 0.22
14 21 0.51
15 11 0.27
ACGTcount: A:0.83, C:0.03, G:0.02, T:0.12
Consensus pattern (14 bp):
AAAAAAAAATCAAA
Found at i:50285 original size:16 final size:15
Alignment explanation
Indices: 50266--50319 Score: 76
Period size: 13 Copynumber: 3.7 Consensus size: 15
50256 AAAAAAAAAT
50266 AAAAAAAAAATTCGAA
1 AAAAAAAAAATTC-AA
*
50282 AAAAAAAAAATT--T
1 AAAAAAAAAATTCAA
50295 AAAAAAAAAATTCAA
1 AAAAAAAAAATTCAA
50310 AAAAAAAAAA
1 AAAAAAAAAA
50320 GAAGTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 12 0.35
15 10 0.29
16 12 0.35
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (15 bp):
AAAAAAAAAATTCAA
Found at i:50297 original size:29 final size:26
Alignment explanation
Indices: 50256--50319 Score: 101
Period size: 29 Copynumber: 2.3 Consensus size: 26
50246 ACGGTATTGT
50256 AAAAAAAAATAAAAAAAAAATTCGAAA
1 AAAAAAAAATAAAAAAAAAATTC-AAA
50283 AAAAAAAAATTTAAAAAAAAAATTCAAA
1 AAAAAAAAA--TAAAAAAAAAATTCAAA
50311 AAAAAAAAA
1 AAAAAAAAA
50320 GAAGTTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 9 0.26
28 12 0.34
29 14 0.40
ACGTcount: A:0.83, C:0.03, G:0.02, T:0.12
Consensus pattern (26 bp):
AAAAAAAAATAAAAAAAAAATTCAAA
Found at i:50382 original size:14 final size:14
Alignment explanation
Indices: 50363--50389 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50353 ATTTAGTATT
50363 GAAGAAAAAAAAAA
1 GAAGAAAAAAAAAA
50377 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
50390 TTCGGAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
GAAGAAAAAAAAAA
Found at i:50440 original size:32 final size:32
Alignment explanation
Indices: 50366--50444 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 32
50356 TAGTATTGAA
* **
50366 GAAAAAAAAAAGAAGAAAAAAAAATTCGGAATT
1 GAAAAAAAAAA-AAGAAAAAAAAAATCAAAATT
50399 -AAAAGAAAAAAAAGAAAAAAAAAATCAAAATT
1 GAAAA-AAAAAAAAGAAAAAAAAAATCAAAATT
50431 GAAAAAAAAAAAAG
1 GAAAAAAAAAAAAG
50445 TGATTGAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 31 0.76
33 10 0.24
ACGTcount: A:0.77, C:0.03, G:0.11, T:0.09
Consensus pattern (32 bp):
GAAAAAAAAAAAAGAAAAAAAAAATCAAAATT
Found at i:51359 original size:21 final size:20
Alignment explanation
Indices: 51330--51375 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
51320 AATCTTGAAT
*
51330 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
51351 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
51371 GAAAA
1 GAAAA
51376 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:51402 original size:12 final size:12
Alignment explanation
Indices: 51382--51417 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
51372 AAAAAAGAAT
*
51382 TTGAGATTGAGA
1 TTGATATTGAGA
*
51394 TTGATATTGATA
1 TTGATATTGAGA
51406 TTGATATTGAGA
1 TTGATATTGAGA
51418 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:55396 original size:13 final size:13
Alignment explanation
Indices: 55378--55414 Score: 56
Period size: 13 Copynumber: 2.7 Consensus size: 13
55368 ATCAAAAGTC
55378 AAAAAAAAATTTG
1 AAAAAAAAATTTG
55391 AAAAAAAAATTTG
1 AAAAAAAAATTTG
55404 ATTAAAAAAAA
1 A--AAAAAAAA
55415 AATTTAGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.64
15 8 0.36
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:55901 original size:12 final size:12
Alignment explanation
Indices: 55886--55922 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
55876 TTTTTGCTCG
*
55886 TTTTTTTTTCAC
1 TTTTTTTTTCAA
*
55898 TTTTTTTTTGAA
1 TTTTTTTTTCAA
55910 TTTTTTTTTCAA
1 TTTTTTTTTCAA
55922 T
1 T
55923 CAAATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:55914 original size:13 final size:13
Alignment explanation
Indices: 55898--55956 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
55888 TTTTTTTCAC
55898 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
55911 TTTTTTTTCAATCAAAT
1 TTTTTTTT---T-GAAT
*
55928 TTTTTTTTCGAAT
1 TTTTTTTTTGAAT
*
55941 TTTTTTTTTGACT
1 TTTTTTTTTGAAT
55954 TTT
1 TTT
55957 GATCATTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 25 0.68
16 1 0.03
17 11 0.30
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:60357 original size:9 final size:10
Alignment explanation
Indices: 60331--60369 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
60321 TGTAGGTATA
60331 AAAAAGAAAAG
1 AAAAA-AAAAG
*
60342 AAAAAAATAG
1 AAAAAAAAAG
60352 AAAAAAAAAG
1 AAAAAAAAAG
60362 AAAAAAAA
1 AAAAAAAA
60370 TGCATAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 21 0.81
11 5 0.19
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:69979 original size:20 final size:20
Alignment explanation
Indices: 69937--69980 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
69927 GTGAAATTAC
*
69937 AAAAGAAAAGAAAAATGAGA
1 AAAAGAAAAGAAAAATGAAA
*
69957 AAAAG-AAAGAAAATTTGAAA
1 AAAAGAAAAGAAAA-ATGAAA
69977 AAAA
1 AAAA
69981 AGAGTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATGAAA
Found at i:71207 original size:6 final size:6
Alignment explanation
Indices: 71196--71221 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
71186 GTAAATAAAT
71196 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
71222 CTTACAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Done.