Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3569
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: 62044
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:4628 original size:40 final size:40
Alignment explanation
Indices: 4523--4745 Score: 221
Period size: 40 Copynumber: 5.7 Consensus size: 40
4513 TTGAATGATG
* *
4523 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
4562 ATCCGGACTAAGAT-CCGAAGGC-TTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
4602 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * * *
4642 TCCGGGCTAA-ACCCGAAGGCA-TTGTGCTAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
4680 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* * *
4719 AACCGGGCTATGTCCCGAAGGTATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
4746 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
38 24 0.15
39 40 0.26
40 89 0.57
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:4717 original size:78 final size:80
Alignment explanation
Indices: 4523--4739 Score: 248
Period size: 78 Copynumber: 2.8 Consensus size: 80
4513 TTGAATGATG
* * * * * *
4523 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATCCGGACTAAGATCCGAAGGCTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAATATCCGGACTAAGACCCGAAGGCAT
*
4586 TGTGCGAGATACTAAT
65 TGTGCGAGATACTAAA
*
4602 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-TCCGGGCTAA-ACCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTAATATCCGGACTAAGACCCGAAGGCAT
* *
4664 TGTGCTAGTTACTAAA
65 TGTGCGAGATACTAAA
* * * *
4680 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAATATCCGGACTAAGACCCGAAGG
4740 TATTTGAACG
Statistics
Matches: 119, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
77 3 0.03
78 66 0.55
79 39 0.33
80 10 0.08
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAATATCCGGACTAAGACCCGAAGGCATT
GTGCGAGATACTAAA
Found at i:4745 original size:118 final size:119
Alignment explanation
Indices: 4523--4745 Score: 276
Period size: 118 Copynumber: 1.9 Consensus size: 119
4513 TTGAATGATG
* * *
4523 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCTTTG
1 TCCGGGCTAAGACCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCTTTG
* *
4588 TGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
66 TGCGAGATACTAATACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * **
4642 TCCGGGCTAA-ACCCGAAGGCATTGTGCT-AGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGACCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGC-TT
* *
4704 TGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGTATTTG
64 TGTGCGAGA-TACTAAT-ACCGGGCTAAGTCCCGAAGGCATTTG
4746 AACGAGGAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
116 1 0.01
117 27 0.30
118 51 0.57
119 10 0.11
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (119 bp):
TCCGGGCTAAGACCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCTTTG
TGCGAGATACTAATACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:6148 original size:15 final size:16
Alignment explanation
Indices: 6128--6159 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
6118 AGAAAATGAA
6128 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
6143 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
6159 A
1 A
6160 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:13030 original size:21 final size:23
Alignment explanation
Indices: 12985--13031 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12975 TCACCTGCAA
* *
12985 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
13008 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
13029 TAA
1 TAA
13032 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:16516 original size:10 final size:11
Alignment explanation
Indices: 16482--16513 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
16472 AAAGGAAACC
16482 AATTCTTTTTTG
1 AATT-TTTTTTG
16494 AATTTTTTTTG
1 AATTTTTTTTG
16505 AATTTTTTT
1 AATTTTTTT
16514 GAAGAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:17880 original size:19 final size:20
Alignment explanation
Indices: 17846--17884 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
17836 TAGCACTGTG
17846 ATTGAATATAAAAAAATTAA
1 ATTGAATATAAAAAAATTAA
17866 ATTGAATAT-AAAAAATTAA
1 ATTGAATATAAAAAAATTAA
17885 TCCCGCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTGAATATAAAAAAATTAA
Found at i:19255 original size:23 final size:22
Alignment explanation
Indices: 19229--19281 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
19219 TTGAGAGTGA
*
19229 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
*
19252 AAAACAAATTAGAAAAAGAAAC
1 AAAAGAAATTAGAAAAAGAAAC
19274 AAAAGAAA
1 AAAAGAAA
19282 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.31
23 15 0.58
24 3 0.12
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.08
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:27077 original size:33 final size:33
Alignment explanation
Indices: 27040--27103 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
27030 TGATTACTCA
27040 TTTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTT
1 TTTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTT
*
27073 TTTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTTCACTCGATTTCTTTTCAAGCTCTCTTTC
27104 AATTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 17 0.61
34 10 0.36
35 1 0.04
ACGTcount: A:0.12, C:0.27, G:0.06, T:0.55
Consensus pattern (33 bp):
TTTCACTCGATTTCTTTTCAAGCTCTCTTTCTT
Found at i:27166 original size:27 final size:27
Alignment explanation
Indices: 27121--27187 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 27
27111 TTTGTCGCTT
* *
27121 TTTCTTTTTTAATTTTTTTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
27151 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
27178 TTTCTTTTTC
1 TTTCTTTTTC
27188 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
30 20 0.59
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:27171 original size:12 final size:12
Alignment explanation
Indices: 27147--27277 Score: 63
Period size: 12 Copynumber: 10.9 Consensus size: 12
27137 TTTTTCATTC
27147 TCAATTTCTTTT
1 TCAATTTCTTTT
27159 TCAATTTTCTTTTCT
1 TCAA-TTTC-TTT-T
*
27174 TCATTTTCTTTT
1 TCAATTTCTTTT
** **
27186 TCTCTCACTTTT
1 TCAATTTCTTTT
27198 TCAATTTCTTTT
1 TCAATTTCTTTT
* **
27210 TC-TTTTGCAATT
1 TCAATTT-CTTTT
**
27222 TCTTTTTCTTTT
1 TCAATTTCTTTT
**
27234 TCGTTTTCTTTT
1 TCAATTTCTTTT
* *
27246 T--GTTT-TCTT
1 TCAATTTCTTTT
27255 TCAATTTCTTTT
1 TCAATTTCTTTT
*
27267 TCAATCTCTTT
1 TCAATTTCTTT
27278 CTCCTTTTCT
Statistics
Matches: 91, Mismatches: 20, Indels: 16
0.72 0.16 0.13
Matches are distributed among these distances:
9 4 0.04
10 3 0.03
11 6 0.07
12 56 0.62
13 11 0.12
14 7 0.08
15 4 0.04
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (12 bp):
TCAATTTCTTTT
Found at i:27186 original size:45 final size:45
Alignment explanation
Indices: 27102--27187 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
27092 AAGCTCTCTT
**
27102 TCAATTTCTTTTGTCGCTTTTTCTTTTTTAATTTTTTTTTCATTC
1 TCAATTTCTTTTGTCGAATTTTCTTTTTTAATTTTTTTTTCATTC
*
27147 TCAATTTCTTTT-TC-AATTTTCTTTTCTTCATTTTCTTTTTC
1 TCAATTTCTTTTGTCGAATTTTCTTTT-TTAATTTT-TTTTTC
27188 TCTCACTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 9 0.25
44 9 0.25
45 18 0.50
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.69
Consensus pattern (45 bp):
TCAATTTCTTTTGTCGAATTTTCTTTTTTAATTTTTTTTTCATTC
Found at i:27246 original size:18 final size:18
Alignment explanation
Indices: 27133--27251 Score: 87
Period size: 18 Copynumber: 6.5 Consensus size: 18
27123 TCTTTTTTAA
* *
27133 TTTT-TTTTTCATTCTCA
1 TTTTCTTTTTCATTTTCT
*
27150 ATTTCTTTTTCAATTTTCTT
1 TTTTCTTTTTC-ATTTTC-T
* *
27170 TTCTTCATTTTCTTTTTCT
1 TT-TTCTTTTTCATTTTCT
* ** *
27189 CTCACTTTTTCAATTTCT
1 TTTTCTTTTTCATTTTCT
* *
27207 TTTTCTTTTGCAATTTCT
1 TTTTCTTTTTCATTTTCT
*
27225 TTTTCTTTTTCGTTTTCT
1 TTTTCTTTTTCATTTTCT
*
27243 TTTTGTTTT
1 TTTTCTTTT
27252 CTTTCAATTT
Statistics
Matches: 78, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
17 3 0.04
18 54 0.69
19 7 0.09
20 6 0.08
21 8 0.10
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTCTTTTTCATTTTCT
Found at i:27268 original size:6 final size:6
Alignment explanation
Indices: 27151--27255 Score: 68
Period size: 6 Copynumber: 17.2 Consensus size: 6
27141 TCATTCTCAA
* * * ** **
27151 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCAA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** * *
27202 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
27249 TTTCTT T
1 TTTCTT T
27256 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 25, Indels: 6
0.70 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 55 0.77
7 9 0.13
8 3 0.04
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:28343 original size:11 final size:11
Alignment explanation
Indices: 28320--28359 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
28310 TTGTCACTTC
*
28320 TTTTTTTC-CT
1 TTTTTTTCAAT
28330 TTTTTTTCAAT
1 TTTTTTTCAAT
*
28341 TTTTTTTGAAT
1 TTTTTTTCAAT
28352 TTTTTTTC
1 TTTTTTTC
28360 TGAATTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:35681 original size:12 final size:11
Alignment explanation
Indices: 35641--35683 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
35631 TAGTAGTTTC
*
35641 TCAAAAAAAAC
1 TCAAAAAAAAT
35652 TCGAAAAAAAAT
1 TC-AAAAAAAAT
*
35664 TC-AAAAAATT
1 TCAAAAAAAAT
35674 TCAAAAAAAA
1 TCAAAAAAAA
35684 AACTAGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.33
11 8 0.30
12 10 0.37
ACGTcount: A:0.70, C:0.12, G:0.02, T:0.16
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:35743 original size:12 final size:12
Alignment explanation
Indices: 35726--35772 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
35716 TATCAAGTTG
35726 TGAAAAAAAATT
1 TGAAAAAAAATT
35738 TGAAAAAAAATT
1 TGAAAAAAAATT
*
35750 GTGAAAAAAAAAT
1 -TGAAAAAAAATT
35763 TGAAAAAAAA
1 TGAAAAAAAA
35773 GAGAGCTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
12 22 0.67
13 11 0.33
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (12 bp):
TGAAAAAAAATT
Found at i:35751 original size:25 final size:25
Alignment explanation
Indices: 35723--35772 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
35713 GGATATCAAG
*
35723 TTGTGAAAAAAAATTTGAAAAAAAA
1 TTGTGAAAAAAAAATTGAAAAAAAA
35748 TTGTGAAAAAAAAATTGAAAAAAAA
1 TTGTGAAAAAAAAATTGAAAAAAAA
35773 GAGAGCTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (25 bp):
TTGTGAAAAAAAAATTGAAAAAAAA
Found at i:36721 original size:11 final size:10
Alignment explanation
Indices: 36697--36721 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
36687 GTGACGAGAG
36697 AAAAAGAAAC
1 AAAAAGAAAC
36707 AAAAAGAAAC
1 AAAAAGAAAC
36717 AAAAA
1 AAAAA
36722 TTGAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAC
Found at i:58934 original size:12 final size:12
Alignment explanation
Indices: 58917--58963 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
58907 TATCAAGTTG
58917 TGAAAAAAAATT
1 TGAAAAAAAATT
58929 TG-AAAAAAATT
1 TGAAAAAAAATT
58940 GTGAAAAAAAAATT
1 -TG-AAAAAAAATT
58954 TGAAAAAAAA
1 TGAAAAAAAA
58964 AGAAGAAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.28
12 12 0.38
13 2 0.06
14 9 0.28
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (12 bp):
TGAAAAAAAATT
Found at i:58937 original size:13 final size:13
Alignment explanation
Indices: 58919--58964 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
58909 TCAAGTTGTG
58919 AAAAAAAATTTG-
1 AAAAAAAATTTGA
58931 -AAAAAAATTGTGA
1 AAAAAAAATT-TGA
58944 AAAAAAAATTTGA
1 AAAAAAAATTTGA
58957 AAAAAAAA
1 AAAAAAAA
58965 GAAGAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 11 0.35
14 9 0.29
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:58941 original size:24 final size:25
Alignment explanation
Indices: 58914--58962 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
58904 GGATATCAAG
58914 TTGTG-AAAAAAAATTTGAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAA
58938 TTGTGAAAAAAAAATTTGAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAA
58963 AAGAAGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (25 bp):
TTGTGAAAAAAAAATTTGAAAAAAA
Found at i:61089 original size:13 final size:13
Alignment explanation
Indices: 61059--61110 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
61049 TAGCTCTCTC
* *
61059 TTTTTTTCAGAAAA
1 TTTTTTTCA-CAAT
61073 TTTTTTTCACAAT
1 TTTTTTTCACAAT
61086 TTTTTTTCA-AATT
1 TTTTTTTCACAA-T
61099 TTTTTTTCACAA
1 TTTTTTTCACAA
61111 CTTGATATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 2 0.06
13 21 0.62
14 11 0.32
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.60
Consensus pattern (13 bp):
TTTTTTTCACAAT
Found at i:61102 original size:26 final size:27
Alignment explanation
Indices: 61059--61110 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
61049 TAGCTCTCTC
61059 TTTTTTTCAGAAAATTTTTTTCACAAT
1 TTTTTTTCAGAAAATTTTTTTCACAAT
**
61086 TTTTTTTCA-AATTTTTTTTTCACAA
1 TTTTTTTCAGAAAATTTTTTTCACAA
61111 CTTGATATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTTTTCAGAAAATTTTTTTCACAAT
Found at i:61104 original size:12 final size:12
Alignment explanation
Indices: 61059--61104 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
61049 TAGCTCTCTC
*
61059 TTTTTTTCAGAAAA
1 TTTTTTTC--AAAT
61073 TTTTTTTCACAAT
1 TTTTTTTCA-AAT
61086 TTTTTTTCAAAT
1 TTTTTTTCAAAT
61098 TTTTTTT
1 TTTTTTT
61105 TCACAACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.37
13 11 0.37
14 8 0.27
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:61161 original size:12 final size:12
Alignment explanation
Indices: 61144--61174 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
61134 ATGGAACTAG
61144 TTTTTTTTTAAT
1 TTTTTTTTTAAT
*
61156 TTTTTTTTTGAT
1 TTTTTTTTTAAT
61168 TTTTTTT
1 TTTTTTT
61175 GAAGAACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTAAT
Done.