Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2932
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: 34034
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:10935 original size:18 final size:19
Alignment explanation
Indices: 10904--10939 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
10894 TATTTAATAA
*
10904 TATTTTTATTTCAAAAAAT
1 TATTTTTATCTCAAAAAAT
10923 TATTTTT-TCTCAAAAAA
1 TATTTTTATCTCAAAAAA
10940 ATTTCTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTTTATCTCAAAAAAT
Found at i:11140 original size:28 final size:28
Alignment explanation
Indices: 11087--11140 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
11077 ATAGTGAATG
*
11087 ATTTAAAAATTTATATAAAATATATTTT
1 ATTTAAAAATTTATATAAAAGATATTTT
*
11115 ATTT-AAAATGTTATATAAAAGCTATT
1 ATTTAAAAAT-TTATATAAAAGATATT
11141 GATTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (28 bp):
ATTTAAAAATTTATATAAAAGATATTTT
Found at i:12321 original size:25 final size:25
Alignment explanation
Indices: 12271--12347 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
12261 GCCTAGTATT
* *
12271 AAACCTAAACCCAACTATCTATCCA
1 AAACCTAAACCCAACTATCAACCCA
*
12296 AAACCTAAACCCAATTA-CAAACCCA
1 AAACCTAAACCCAACTATC-AACCCA
* *
12321 AAA-CTCAAACCTAAATCATCAACCCA
1 AAACCT-AAACCCAACT-ATCAACCCA
12347 A
1 A
12348 TTAAACCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 3 0.07
25 31 0.72
26 8 0.19
27 1 0.02
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (25 bp):
AAACCTAAACCCAACTATCAACCCA
Found at i:13911 original size:26 final size:25
Alignment explanation
Indices: 13877--13938 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 25
13867 AATTTTCATG
* *
13877 TATAGTATTTAATTTAAACTGTTTTA
1 TATATTATTTAATTTAAAAT-TTTTA
* * *
13903 TATGTTATTCATTTTAAAATTTTTA
1 TATATTATTTAATTTAAAATTTTTA
13928 TATATT-TTTAA
1 TATATTATTTAA
13939 AGCTCTTTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 3 0.11
25 10 0.36
26 15 0.54
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (25 bp):
TATATTATTTAATTTAAAATTTTTA
Found at i:15285 original size:19 final size:17
Alignment explanation
Indices: 15251--15285 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
15241 CTAAAATTGT
15251 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
15268 AACAAGAATTATACAATA
1 AACAA-AATTA-ACAATA
15286 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:22809 original size:16 final size:16
Alignment explanation
Indices: 22790--22961 Score: 94
Period size: 17 Copynumber: 9.8 Consensus size: 16
22780 CGAAAGTTTT
*
22790 TTTTAAAACACGAGAAT
1 TTTTAAAACACGA-AAA
*
22807 TTTTGAAAACACGAGAA
1 TTTT-AAAACACGAAAA
22824 TTTGT-AAACACGAAAA
1 TTT-TAAAACACGAAAA
22840 TTTTAGAAACACGAAAA
1 TTTTA-AAACACGAAAA
* *
22857 TTTTTAGAAAAAACGAAAT
1 -TTTT--AAAACACGAAAA
**
22876 TTCCTTAAAACACGACATTTTT
1 TT--TTAAAACACGA-A---AA
* * *
22898 TTTTGAAACACGGGAAT
1 TTTTAAAACAC-GAAAA
* *
22915 TTTTAAAACAGGGAAA
1 TTTTAAAACACGAAAA
22931 TTTTAGAAACACGAAAA
1 TTTTA-AAACACGAAAA
22948 TTTTTAAAACACGA
1 -TTTTAAAACACGA
22962 CATTTTTTTG
Statistics
Matches: 124, Mismatches: 15, Indels: 32
0.73 0.09 0.19
Matches are distributed among these distances:
15 1 0.01
16 22 0.18
17 46 0.37
18 29 0.23
19 10 0.08
20 12 0.10
21 1 0.01
22 3 0.02
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (16 bp):
TTTTAAAACACGAAAA
Found at i:23222 original size:18 final size:18
Alignment explanation
Indices: 22788--23224 Score: 172
Period size: 18 Copynumber: 25.0 Consensus size: 18
22778 AACGAAAGTT
* *
22788 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
22806 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
22824 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
22840 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
22857 TTTTTAGAAAAAACG-AAA
1 TTTTT-GAAAACACGAAAA
**
22875 TTTCCTT-AAAACACGACATTTT
1 TTT--TTGAAAACACGA-A--AA
**
22897 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACACGAAAA
* *
22914 TTTTT-AAAACAGGGAAA
1 TTTTTGAAAACACGAAAA
*
22931 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
22948 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
22966 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
*
22980 --TTT-AAAAAAC-AAAA
1 TTTTTGAAAACACGAAAA
* ** *
22994 --ATTG-AAATGCGAGAA
1 TTTTTGAAAACACGAAAA
**
23009 TATTTTG-AAACACGAATTT
1 T-TTTTGAAAACACGAA-AA
** * *
23028 TTTTTTTAAACGCGAGAA
1 TTTTTGAAAACACGAAAA
* *
23046 TTTTTGAAAACATGGAAA
1 TTTTTGAAAACACGAAAA
* * *
23064 -CTTTG-AAACACTG-GAG
1 TTTTTGAAAACAC-GAAAA
*
23080 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
23098 TTTGTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
23115 TTTGTGAAAACATGTAAACTT
1 TTTTTGAAAACACG-AAA--A
** *
23136 TTTTTTTAAACACAAAAA
1 TTTTTGAAAACACGAAAA
* * *
23154 TTTTTG-AAACGCCAGAA
1 TTTTTGAAAACACGAAAA
*
23171 TTTCTGAAAACAC-AAAGA
1 TTTTTGAAAACACGAAA-A
23189 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
23207 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
23225 CACAAAATTT
Statistics
Matches: 313, Mismatches: 68, Indels: 76
0.68 0.15 0.17
Matches are distributed among these distances:
12 8 0.03
14 7 0.02
15 3 0.01
16 20 0.06
17 95 0.30
18 133 0.42
19 20 0.06
20 15 0.05
21 9 0.03
22 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:23302 original size:9 final size:9
Alignment explanation
Indices: 23288--23321 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
23278 ATTCACGAGA
23288 ATTTTTTTT
1 ATTTTTTTT
23297 ATTTTTTTT
1 ATTTTTTTT
23306 A--TTTTTT
1 ATTTTTTTT
23313 ATTTTTTTT
1 ATTTTTTTT
23322 GAAACACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
9 16 0.70
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:23312 original size:16 final size:16
Alignment explanation
Indices: 23291--23321 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
23281 CACGAGAATT
23291 TTTTTTATTTTTTTTA
1 TTTTTTATTTTTTTTA
23307 TTTTTTATTTTTTTT
1 TTTTTTATTTTTTTT
23322 GAAACACGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTATTTTTTTTA
Found at i:23335 original size:19 final size:20
Alignment explanation
Indices: 23313--23350 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
23303 TTTATTTTTT
23313 ATTTTTTTTG-AAACACGAG
1 ATTTTTTTTGAAAACACGAG
23332 ATTTTTTTTGAAAACACGA
1 ATTTTTTTTGAAAACACGA
23351 AAACACGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTTTTTTTGAAAACACGAG
Found at i:23398 original size:17 final size:16
Alignment explanation
Indices: 23349--23396 Score: 64
Period size: 15 Copynumber: 3.0 Consensus size: 16
23339 TTGAAAACAC
23349 GAAAACACGAATTTTT
1 GAAAACACGAATTTTT
23365 G-AAACACGGAAATTTTT
1 GAAAACAC-G-AATTTTT
23382 GAAAACACG-ATTTTT
1 GAAAACACGAATTTTT
23397 TTAGAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 2 0.07
17 9 0.31
18 6 0.21
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (16 bp):
GAAAACACGAATTTTT
Found at i:24732 original size:29 final size:29
Alignment explanation
Indices: 24694--24809 Score: 101
Period size: 30 Copynumber: 3.9 Consensus size: 29
24684 TGTAATTTTT
* *
24694 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAGTTTAGGGTTAAAATGAAATTTAA
* * *
24723 TGAAGGTTTAGGGTCT-AAGTGAAATTTAA
1 AGAAAGTTTAGGGT-TAAAATGAAATTTAA
*
24752 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAGTTT-AGGGTTAAAATGAAATTTAA
* * *
24781 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AG-AAAGTTTA-GGGTTAAAATGAAATTT
24810 TTATTTTTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
29 32 0.45
30 39 0.55
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAGTTTAGGGTTAAAATGAAATTTAA
Found at i:24776 original size:30 final size:30
Alignment explanation
Indices: 24709--24809 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 30
24699 ATTTAGGATT
* *
24709 AAAATGAAATTTAATGAAGGTTT-AGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
24738 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
24768 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
24798 AAAATGCAATTT
1 AAAATGAAATTT
24810 TTATTTTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 21 0.34
30 40 0.66
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:24840 original size:14 final size:15
Alignment explanation
Indices: 24805--24840 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
24795 GTCAAAATGC
24805 AATTTTTATTTTTAA
1 AATTTTTATTTTTAA
* *
24820 AATTTTTTTTTTTGA
1 AATTTTTATTTTTAA
24835 AATTTT
1 AATTTT
24841 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
AATTTTTATTTTTAA
Found at i:25164 original size:55 final size:55
Alignment explanation
Indices: 25080--25302 Score: 281
Period size: 55 Copynumber: 4.1 Consensus size: 55
25070 CACGTGAGCC
* * *
25080 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTG-AA
****** *
25135 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-TTTTTGAAAAATAGAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTG-AA
*
25190 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTTGAAAAACAAAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTT-GATTTTTGAAAAACAAAAATTGAA
* *
25245 AAGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAA
25300 AAG
1 AAG
25303 TAGAAATTGA
Statistics
Matches: 143, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
54 19 0.13
55 112 0.78
56 6 0.04
57 6 0.04
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAA
Found at i:25273 original size:110 final size:109
Alignment explanation
Indices: 25080--25282 Score: 327
Period size: 110 Copynumber: 1.8 Consensus size: 109
25070 CACGTGAGCC
* * *
25080 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAAATT-CAAAAGGCTCAAC
25145 TCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAATAGAAA
65 TCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAATAGAAA
* *
25190 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTTGAAAAACAAAAATT-AAAAGGCTCAG
1 AAGGCTCAACTCACCTCTCGCAATATGAGTT-GATTTTTG-AAAACAAAAATTCAAAAGGCTCAA
25254 CTCACCTCTCGCAATATGAGTTGATTTTT
64 CTCACCTCTCGCAATATGAGTTGATTTTT
25283 GAAAAACAGA
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
110 69 0.80
111 7 0.08
112 10 0.12
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (109 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAAATTCAAAAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAATAGAAA
Found at i:25300 original size:14 final size:14
Alignment explanation
Indices: 25281--25315 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
25271 GAGTTGATTT
25281 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
25295 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
25309 TTGAAAA
1 TTGAAAA
25316 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:25368 original size:87 final size:85
Alignment explanation
Indices: 25246--25457 Score: 302
Period size: 84 Copynumber: 2.5 Consensus size: 85
25236 AAAAATTAAA
* * *
25246 AGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGTAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAA-CAGAAATG
* *
25311 GAAAATACCTCAGCGTGCCCTG
65 GAAAATACCTCAACATG-CCTG
* * *
25333 AGGCTCAACTCACCTCTTGCAATATGAATTGATTTTTG-AAAACATAAATTGAAAACAGAAATGG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAACAGAAATGG
*
25397 AAAATACCTCAACATGTCTG
66 AAAATACCTCAACATGCCTG
*
25417 AGGCTCAACTCACCTCTCGCAGTATGAGTTGA-TTTTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
25458 CATACAAAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
83 5 0.04
84 35 0.31
85 21 0.19
86 16 0.14
87 35 0.31
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (85 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAACAGAAATGG
AAAATACCTCAACATGCCTG
Found at i:25443 original size:84 final size:86
Alignment explanation
Indices: 25246--25461 Score: 312
Period size: 87 Copynumber: 2.5 Consensus size: 86
25236 AAAAATTAAA
* * * *
25246 AGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGTAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACATAAATTGAAAAGCAGAAATG
* *
25311 GAAAATACCTCAGCGTGCCCTG
65 GAAAATACCTCAACATGCCCTG
* *
25333 AGGCTCAACTCACCTCTTGCAATATGAATTGATTTTTGAAAACATAAATTGAAAA-CAGAAATGG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATAAATTGAAAAGCAGAAATGG
*
25397 AAAATACCTCAACATG-TCTG
66 AAAATACCTCAACATGCCCTG
*
25417 AGGCTCAACTCACCTCTCGCAGTATGAGTTGA-TTTTGAAAACATA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATA
25462 CAAAAATTGA
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
83 13 0.11
84 32 0.27
85 21 0.18
86 16 0.14
87 35 0.30
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (86 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATAAATTGAAAAGCAGAAATGG
AAAATACCTCAACATGCCCTG
Found at i:25578 original size:72 final size:71
Alignment explanation
Indices: 25381--25905 Score: 623
Period size: 72 Copynumber: 7.2 Consensus size: 71
25371 AAAACATAAA
* * ** *
25381 TTGAAAACAGAAATGGAAAATACCTCAACATGT-CTGAGGCTCAACTCACCTCTCGCAGTATGAG
1 TTGAAAACAGAAATTG-AAATACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAG
25445 TTG-ATT
65 TTGAATT
* *
25451 TTGAAAACATACAAAAATTGACAATACCT-AA-GTATGTCTTGAGGCTCAACTCATTTCTCGCAA
1 TTG--AA-A-ACAGAAATTGA-AATACCTCAACG--TGTCCTGAGGCTCAACTCATTTCTCGCAA
25514 TATGAGTTGAATT
59 TATGAGTTGAATT
* * *
25527 TTGAAAAGCAGAAATTGAAATACCTCAACTTGTCTTGAGGCTCAACTCATTTCTCACAATATGAG
1 TTGAAAA-CAGAAATTGAAATACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAG
25592 TTGAATT
65 TTGAATT
*
25599 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAA-TACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAG
25664 TTGAATT
65 TTGAATT
* *
25671 TTGAAAAGCAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA-TTCTCGCAATATAA
1 TTGAAAA-CAGAAATTG-AAATACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGA
25735 GTTGAATT
64 GTTGAATT
*
25743 TTGAAAACAGAAATTGAAATTA-CTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAA-TACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAG
*
25807 TTGATTTTTTT
65 TTGA----ATT
* * * ** *
25818 TTTAACAACAGAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGA
1 TTGAA-AACAGAAATTGAAA-TACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGA
25883 GTTG-ATT
64 GTTGAATT
*
25890 TTGAAAAACATAAATT
1 TTG-AAAACAGAAATT
25906 AAAAGGCTTA
Statistics
Matches: 406, Mismatches: 25, Indels: 46
0.85 0.05 0.10
Matches are distributed among these distances:
70 32 0.08
71 41 0.10
72 156 0.38
73 54 0.13
74 23 0.06
75 36 0.09
76 22 0.05
77 42 0.10
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (71 bp):
TTGAAAACAGAAATTGAAATACCTCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGT
TGAATT
Found at i:25881 original size:292 final size:289
Alignment explanation
Indices: 25381--25905 Score: 690
Period size: 292 Copynumber: 1.8 Consensus size: 289
25371 AAAACATAAA
* *
25381 TTGAAAACAGAAATGGAAAATACCTCAACATGTCTGAGGCTCAACTCACCTCTCGCAGTATGAGT
1 TTGAAAACAGAAATGGAAAATACCTCAACATGTCTGAGGCTCAACTCACCTCTCGCAATATAAGT
* *
25446 TGATTTTGAAAACATACAAAAATTGACAATACCTAAGTATGTCTTGAGGCTCAACTCATTTCTCG
66 TGATTTTG-AAACATACAAAAATTGACAATACCTAAGCATGTCCTGAGGCTCAACTCATTTCTCG
* * *
25511 CAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAATACCTCAACTTGTCTTGAGGCTCAACTCA
130 CAATATGAGTTGAATTTTGAAAAGCAGAAATTAAAATACCTCAACGTGTCCTGAGGCTCAACTCA
**
25576 TTTCTCACAATATGAGTTGAATTTTG-AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGC
195 CCTCTCACAATATGAGTTG-ATTTTGAAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGC
25640 TCAACTCATTTCTCGCAATATGAGTTGAATT
259 TCAACTCATTTCTCGCAATATGAGTTGAATT
* * * *
25671 TTGAAAAGCAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA-TTCTCGCAATATAA
1 TTGAAAA-CAGAAATGGAAAATACCTCAACATGT-CTGAGGCTCAACTCACCTCTCGCAATATAA
* * *
25735 GTTGAATTTTG-AA-A-ACAGAAATTGA-AATTA-CTCAGCGTGTCCTGAGGCTCAACTCATTTC
64 GTTG-ATTTTGAAACATACAAAAATTGACAA-TACCTAAGCATGTCCTGAGGCTCAACTCATTTC
* * *
25795 TCGCAATATGAGTTGATTTTTTTTTTAACAA-CAGAAATTAAAATTACCTCAGCGTGTCCTGAGG
127 TCGCAATATGAGTTGA----ATTTTGAA-AAGCAGAAATTAAAA-TACCTCAACGTGTCCTGAGG
*
25859 CTCAACTCACCTCT-AGCAATATGAGTTGATTTTGAAAAACATAAATT
186 CTCAACTCACCTCTCA-CAATATGAGTTGATTTTGAAAAACAGAAATT
25906 AAAAGGCTTA
Statistics
Matches: 203, Mismatches: 20, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
287 44 0.22
288 12 0.06
289 1 0.00
290 9 0.04
291 62 0.31
292 75 0.37
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (289 bp):
TTGAAAACAGAAATGGAAAATACCTCAACATGTCTGAGGCTCAACTCACCTCTCGCAATATAAGT
TGATTTTGAAACATACAAAAATTGACAATACCTAAGCATGTCCTGAGGCTCAACTCATTTCTCGC
AATATGAGTTGAATTTTGAAAAGCAGAAATTAAAATACCTCAACGTGTCCTGAGGCTCAACTCAC
CTCTCACAATATGAGTTGATTTTGAAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTC
AACTCATTTCTCGCAATATGAGTTGAATT
Found at i:26057 original size:52 final size:56
Alignment explanation
Indices: 25977--26081 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 56
25967 GGCGTGCCCT
25977 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAA-AACAGAAATTAAA
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAATAACAGAAATTAAA
26031 AGGCTC-ACTCAC-TCTCGCAATATGAGTTGATTTTTGAAAATAACAGAAATT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAATAACAGAAATT
26082 GAAATACCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
52 24 0.49
53 9 0.18
54 16 0.33
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (56 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAATAACAGAAATTAAA
Done.