Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold728
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: 14961
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Found at i:151 original size:55 final size:56
Alignment explanation
Indices: 56--569 Score: 376
Period size: 55 Copynumber: 8.8 Consensus size: 56
46 GCCACCGACC
* * * *
56 GACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACT
1 GACTTGTGGGCTT-TGAAAAAGATGCCACTGACTTGTGGGCTTTGAAGGTTGCCACT
* *
113 GA-TTGTGGACTTTGAAAAAGATGCCACTGACTTATGGGCTTTGAAAGGTTGCCACT
1 GACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTG-AAGGTTGCCACT
* * ** *
169 GACTTGTGGGCTTTTG-AAAAGGTGCCACTAACTTGTGGGCTTAAAAGGAAAATAGTGCCACG
1 GACTTGTGGGC-TTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAGG----T--TGCCACT
* * * * ** *
231 GAGTTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATATGCCACC
1 GACTTGTGGGCTT-T----GAAAAAGA-TGCCACTGACTTGTGGGCTTT-GAAGGT-TGCCACT
* * *
295 GACTTGTGGGCTTCGGAAAAAGGGTGCCACTGATTTGTGGGC-TTGAAGGTTGCCACT
1 GACTTGTGGGCTT-TGAAAAA-GATGCCACTGACTTGTGGGCTTTGAAGGTTGCCACT
* *
352 GATTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACT
1 GACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTG-AAGGTTGCCACT
* * * * * * *
409 GAC-T-TGGGCTTTTGAAAAGGTTGCCACTAACTTCTGGGCTTAAAAGGAAAAAGGGTGCCACG
1 GACTTGTGGGC-TTTGAAAAAGATGCCACTGACTTGTGGGCTT----TG---AAGGTTGCCACT
* *
471 GAGTTGTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTGAA-GTTGCCA-T
1 GA-CT-TGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAGGTTGCCACT
* * * *
527 GACTTGTGGGCTTTTGAAAAGGGTGCCATTAACTTGTGGGCTT
1 GACTTGTGGGC-TTTGAAAAAGATGCCACTGACTTGTGGGCTT
570 AAAGGAAAAA
Statistics
Matches: 365, Mismatches: 60, Indels: 66
0.74 0.12 0.13
Matches are distributed among these distances:
54 7 0.02
55 77 0.21
56 66 0.18
57 69 0.19
58 10 0.03
59 2 0.01
60 23 0.06
61 4 0.01
62 30 0.08
64 18 0.05
65 30 0.08
66 6 0.02
67 5 0.01
68 16 0.04
69 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.29
Consensus pattern (56 bp):
GACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAGGTTGCCACT
Found at i:184 original size:29 final size:29
Alignment explanation
Indices: 56--569 Score: 339
Period size: 29 Copynumber: 17.4 Consensus size: 29
46 GCCACCGACC
* *
56 GACTTGTGGGCTTCGGAAAAGGGTGCCACT
1 GACTTGTGGGCTT-TGAAAAGGTTGCCACT
*
86 GATTTGTGGGCTTTG--AAGGTTGCCACT
1 GACTTGTGGGCTTTGAAAAGGTTGCCACT
* * *
113 GA-TTGTGGACTTTGAAAAAGATGCCACT
1 GACTTGTGGGCTTTGAAAAGGTTGCCACT
*
141 GACTTATGGGCTTTG-AAAGGTTGCCACT
1 GACTTGTGGGCTTTGAAAAGGTTGCCACT
169 GACTTGTGGGCTTTTGAAAAGG-TGCCACT
1 GACTTGTGGGC-TTTGAAAAGGTTGCCACT
* *
198 AACTTGTGGGC-TT-AAAAGGAAAATAGTGCCACG
1 GACTTGTGGGCTTTGAAAAGG----T--TGCCACT
* *
231 GAGTTGTGGGCTTATAAAAGAAAAAGAG-TGCCACG
1 GACTTGTGGGCTT-T----G-AAAAG-GTTGCCACT
* * *
266 GAGTTGTGGACTTTGGAAAA--TATGCCACC
1 GACTTGTGGGCTTT-GAAAAGGT-TGCCACT
* *
295 GACTTGTGGGCTTCGGAAAAAGGGTGCCACT
1 GACTTGTGGGCTT-TG-AAAAGGTTGCCACT
*
326 GATTTGTGGGC-TTG--AAGGTTGCCACT
1 GACTTGTGGGCTTTGAAAAGGTTGCCACT
* * * *
352 GATTTGTGGACTTTGAAAAAGATGCCACT
1 GACTTGTGGGCTTTGAAAAGGTTGCCACT
381 GACTTGTGGGCTTTG-AAAGGTTGCCACT
1 GACTTGTGGGCTTTGAAAAGGTTGCCACT
409 GAC-T-TGGGCTTTTGAAAAGGTTGCCACT
1 GACTTGTGGGC-TTTGAAAAGGTTGCCACT
* * * * *
437 AACTTCTGGGCTTAAAAGGAAAAAGGGTGCCACG
1 GACTTGTGGGCTT----TG-AAAAGGTTGCCACT
* * *
471 GAGTTGTGTGGGCTTTGAAAAAGATGCCACT
1 GA-CT-TGTGGGCTTTGAAAAGGTTGCCACT
*
502 AACTTGTGGGCTTTG--AA-GTTGCCA-T
1 GACTTGTGGGCTTTGAAAAGGTTGCCACT
* *
527 GACTTGTGGGCTTTTGAAAAGGGTGCCATT
1 GACTTGTGGGC-TTTGAAAAGGTTGCCACT
*
557 AACTTGTGGGCTT
1 GACTTGTGGGCTT
570 AAAGGAAAAA
Statistics
Matches: 388, Mismatches: 50, Indels: 93
0.73 0.09 0.18
Matches are distributed among these distances:
25 11 0.03
26 53 0.14
27 25 0.06
28 64 0.16
29 96 0.25
30 43 0.11
31 29 0.07
32 1 0.00
33 16 0.04
34 15 0.04
35 21 0.05
36 8 0.02
41 5 0.01
42 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.29
Consensus pattern (29 bp):
GACTTGTGGGCTTTGAAAAGGTTGCCACT
Found at i:261 original size:35 final size:33
Alignment explanation
Indices: 201--274 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 33
191 TGCCACTAAC
* *
201 TTGTGGGCTTAAAAGGAAAATAGTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
234 TTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGGC-T-TAAAAGAAAAAGAGTGCCACGGAG
269 TTGTGG
1 TTGTGG
275 ACTTTGGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 8 0.22
34 1 0.03
35 28 0.76
ACGTcount: A:0.32, C:0.11, G:0.34, T:0.23
Consensus pattern (33 bp):
TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
Found at i:469 original size:240 final size:241
Alignment explanation
Indices: 3--478 Score: 829
Period size: 240 Copynumber: 2.0 Consensus size: 241
1 AC
3 AAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATATGCCACCGACCGACTTGTGGGCT
1 AAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATATG-C-CCGACCGACTTGTGGGCT
68 TCGGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTGTGGACTTTGAAAAAG
64 TCGGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTGTGGACTTTGAAAAAG
133 ATGCCACTGACTTATGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGTGCCACT
129 ATGCCACTGACTTATGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGTGCCACT
*
198 AACTTGTGGGCTTAAAAGGAAAATAGTGCCACGGAGTTGTGGGCTTAT
194 AACTTCTGGGCTTAAAAGGAAAATAGTGCCACGGAGTTGTGGGCTTAT
246 AAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATATG-CC-ACCGACTTGTGGGCTTC
1 AAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATATGCCCGACCGACTTGTGGGCTTC
309 GGAAAAAGGGTGCCACTGATTTGTGGGC-TTGAAGGTTGCCACTGATTTGTGGACTTTGAAAAAG
66 GG-AAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGA-TTGTGGACTTTGAAAAAG
*
373 ATGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACTGAC-T-TGGGCTTTTGAAAAGGTTGCCAC
129 ATGCCACTGACTTATGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGG-TGCCAC
436 TAACTTCTGGGCTTAAAAGGAAAA-AGGGTGCCACGGAGTTGTG
193 TAACTTCTGGGCTTAAAAGGAAAATA--GTGCCACGGAGTTGTG
479 TGGGCTTTGA
Statistics
Matches: 226, Mismatches: 2, Indels: 13
0.94 0.01 0.05
Matches are distributed among these distances:
238 17 0.08
239 66 0.29
240 99 0.44
243 44 0.19
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.26
Consensus pattern (241 bp):
AAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATATGCCCGACCGACTTGTGGGCTTC
GGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTGTGGACTTTGAAAAAGAT
GCCACTGACTTATGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGTGCCACTAA
CTTCTGGGCTTAAAAGGAAAATAGTGCCACGGAGTTGTGGGCTTAT
Found at i:580 original size:120 final size:118
Alignment explanation
Indices: 116--633 Score: 475
Period size: 120 Copynumber: 4.4 Consensus size: 118
106 TGCCACTGAT
* *
116 TGTGGACTTTGAAAAAGATGCCACTGACTTATGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTG-AA-GTTGCCACTGAC-T-TGGGCT
* *
181 TTTGAAAA-GGTGCCACTAACTTGTGGGCTTAAAAGGAAAATA--GTGCCACGGAGT-
62 TTTGAAAAGGGTGCCACTAACTTCTGGGCTTAAAAGGAAAA-AGGGTGCCACGGATTG
* * * * *
235 TGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATATGCCACCGACTT
1 TGTGGGCTT-T----GAAAAAGA-TGCCACTGACTTGTGGGCTTT-G-AAGT-TGCCACTGAC-T
** * * * * *
300 GTGGGCTTCGGAAAAAGGGTGCCACTGATTTGTGGGCTT-----G---AAGGTTGCCACTGATT-
56 -TGGGCTTTTG-AAAAGGGTGCCACTAACTTCTGGGCTTAAAAGGAAAAAGGGTGCCACGGATTG
*
356 TGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACTGACTTGGGCTTT
1 TGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTG-AA-GTTGCCACTGACTTGGGCTTT
*
421 TGAAAAGGTTGCCACTAACTTCTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTG
64 TGAAAAGGGTGCCACTAACTTCTGGGCTTAAAAGGAAAAAGGGTGCCACGGA-TTG
*
477 TGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTGAAGTTGCCA-TGACTTGTGGGCTTT
1 TGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAGTTGCCACTGAC-T-TGGGCTTT
* * *
541 TGAAAAGGGTGCCATTAACTTGTGGGCTT-AAAGGAAAAAAGAGTGCCACGGA--G
64 TGAAAAGGGTGCCACTAACTTCTGGGCTTAAAAGG-AAAAAGGGTGCCACGGATTG
594 TGT-GGC-TTGAAAAAGATGCC-CTGACTTGT-GGCTTTTGAAG
1 TGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGC-TTTGAAG
634 GGTGAGGAAT
Statistics
Matches: 337, Mismatches: 35, Indels: 59
0.78 0.08 0.14
Matches are distributed among these distances:
111 23 0.07
112 8 0.02
113 4 0.01
114 28 0.08
115 33 0.10
116 12 0.04
117 4 0.01
118 4 0.01
119 34 0.10
120 57 0.17
121 55 0.16
123 1 0.00
124 8 0.02
125 18 0.05
126 24 0.07
127 4 0.01
128 20 0.06
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (118 bp):
TGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAGTTGCCACTGACTTGGGCTTTTG
AAAAGGGTGCCACTAACTTCTGGGCTTAAAAGGAAAAAGGGTGCCACGGATTG
Found at i:2069 original size:7 final size:7
Alignment explanation
Indices: 2059--2116 Score: 86
Period size: 7 Copynumber: 8.6 Consensus size: 7
2049 TTGTTGTTTG
2059 TTTTGTT
1 TTTTGTT
2066 TTTTGTT
1 TTTTGTT
2073 TTTTGTT
1 TTTTGTT
2080 TTTTGTT
1 TTTTGTT
2087 TTTT-TT
1 TTTTGTT
2093 TGTTT-TT
1 T-TTTGTT
2100 TTTTGTT
1 TTTTGTT
2107 TTTT-TT
1 TTTTGTT
2113 TTTT
1 TTTT
2117 TTTGTGGAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.24
7 37 0.76
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (7 bp):
TTTTGTT
Found at i:2075 original size:1 final size:1
Alignment explanation
Indices: 2059--2119 Score: 68
Period size: 1 Copynumber: 61.0 Consensus size: 1
2049 TTGTTGTTTG
* * * * * *
2059 TTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2120 GTGGAGGACG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:2078 original size:14 final size:13
Alignment explanation
Indices: 2044--2116 Score: 85
Period size: 14 Copynumber: 5.3 Consensus size: 13
2034 ATCCGGACCC
*
2044 TTTTGTTGTTGTTTG
1 TTTTGTT-TT-TTTT
2059 TTTTGTTTTTTGTT
1 TTTTGTTTTTT-TT
2073 TTTTGTTTTTTGTT
1 TTTTGTTTTTT-TT
2087 TTTT-TTTGTTTTT
1 TTTTGTTT-TTTTT
2100 TTTTGTTTTTTTT
1 TTTTGTTTTTTTT
2113 TTTT
1 TTTT
2117 TTTGTGGAGG
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
13 20 0.37
14 27 0.50
15 7 0.13
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (13 bp):
TTTTGTTTTTTTT
Found at i:2085 original size:26 final size:25
Alignment explanation
Indices: 2044--2121 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 25
2034 ATCCGGACCC
*
2044 TTTTGTTGTTGTTTGTTTTGTTTTTTG
1 TTTT-TTGTTTTTTGTTTT-TTTTTTG
2071 TTTTTTGTTTTTTG-TTTTTTTTTG
1 TTTTTTGTTTTTTGTTTTTTTTTTG
* *
2095 TTTTTTTTTGTTTTTTTTTTTTTTTG
1 TTTTTTGTT-TTTTGTTTTTTTTTTG
2121 T
1 T
2122 GGAGGACGCC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
24 15 0.33
25 7 0.15
26 20 0.43
27 4 0.09
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (25 bp):
TTTTTTGTTTTTTGTTTTTTTTTTG
Found at i:2113 original size:10 final size:10
Alignment explanation
Indices: 2044--2119 Score: 93
Period size: 10 Copynumber: 7.4 Consensus size: 10
2034 ATCCGGACCC
*
2044 TTTTGTTGTT
1 TTTTTTTGTT
2054 GTTTGTTTTGTT
1 -TTT-TTTTGTT
2066 TTTTGTTT-TT
1 TTTT-TTTGTT
2076 TGTTTTTTGTT
1 T-TTTTTTGTT
2087 TTTTTTTGTT
1 TTTTTTTGTT
2097 TTTTTTTGTT
1 TTTTTTTGTT
2107 TTTTTTT-TT
1 TTTTTTTGTT
2116 TTTT
1 TTTT
2120 GTGGAGGACG
Statistics
Matches: 60, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
9 6 0.10
10 33 0.55
11 15 0.25
12 6 0.10
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:2118 original size:36 final size:36
Alignment explanation
Indices: 2044--2121 Score: 108
Period size: 34 Copynumber: 2.2 Consensus size: 36
2034 ATCCGGACCC
2044 TTTTGTTGTTGTTTGTTTTGTTTTTTGTTTTTTGTT
1 TTTTGTTGTTGTTTGTTTTGTTTTTTGTTTTTTGTT
* *
2080 TTTTGTTTTTTTTTG-TTT-TTTTTTGTTTTTT-TT
1 TTTTGTTGTTGTTTGTTTTGTTTTTTGTTTTTTGTT
*
2113 TTTTTTTGT
1 TTTTGTTGT
2122 GGAGGACGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 9 0.24
34 13 0.34
35 3 0.08
36 13 0.34
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (36 bp):
TTTTGTTGTTGTTTGTTTTGTTTTTTGTTTTTTGTT
Found at i:4047 original size:19 final size:19
Alignment explanation
Indices: 4023--4090 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
4013 AATTCAACAA
4023 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
4042 TTTGTATCGATGC--AA--
1 TTTGTATCGATACATAAGT
4057 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
4074 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
4091 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4147 original size:13 final size:13
Alignment explanation
Indices: 4129--4154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4119 ACATTTTCTG
4129 TGTATCGATACAT
1 TGTATCGATACAT
4142 TGTATCGATACAT
1 TGTATCGATACAT
4155 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4171 original size:33 final size:32
Alignment explanation
Indices: 4110--4175 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
4100 GCCAAGAAAA
**
4110 TGTATCGATACATTTTCTGTGTATCGATACAT
1 TGTATCGATACATGATCTGTGTATCGATACAT
*
4142 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACAT-GATCTGTGTATCGATACAT
4175 T
1 T
4176 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGATCTGTGTATCGATACAT
Found at i:6598 original size:51 final size:48
Alignment explanation
Indices: 6530--6646 Score: 130
Period size: 51 Copynumber: 2.4 Consensus size: 48
6520 AATTCTCCGC
* * *
6530 AATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACACTGATTTTCTAT
1 AATCAGGGATACT-CCAACTCCGATTTCATTTCT-AAAACA-TCAATTT-T-T
*
6581 AATCAGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTT
1 AATCAGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTT
*
6629 CATCAGGGATACTCCAAC
1 AATCAGGGATACTCCAAC
6647 CCCGTTAATC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
48 18 0.31
49 1 0.02
50 5 0.08
51 33 0.56
52 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (48 bp):
AATCAGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTT
Found at i:6665 original size:27 final size:26
Alignment explanation
Indices: 6628--6679 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
6618 CATCAATTTT
6628 TCATCAGGGATACTCCAACCCCGTTAA
1 TCATCAGGGATACTCC-ACCCCGTTAA
*
6655 TCATTAGGGATACTCCACCCCGTTA
1 TCATCAGGGATACTCCACCCCGTTA
6680 TTTTCGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (26 bp):
TCATCAGGGATACTCCACCCCGTTAA
Found at i:6789 original size:80 final size:78
Alignment explanation
Indices: 6661--6841 Score: 231
Period size: 80 Copynumber: 2.3 Consensus size: 78
6651 TTAATCATTA
* * *
6661 GGGATACTCC-ACCCCGTTATTTTCGAGAGGATACTCCAACCCCCGCTTTATTTCTAAAATATTA
1 GGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCCGCTTTATTCCCAAAATATTA
6725 ATTTCTCCATAATCG
66 A-TTCT-CATAATCG
* * *
6740 GGGATACTCCAACCCCGTTACTTTCCGAGGGGATACTCC-ACCTCGGCTTTATTCCCAAAATATT
1 GGGATACTCCAACCCCGTTA-TTTCCGAGAGGATACTCCAACCCCCGCTTTATTCCCAAAATATT
* *
6804 GATTCTCATAATTG
65 AATTCTCATAATCG
*
6818 GGGATACTCCATCGCCCGTTATTT
1 GGGATACTCCAAC-CCCGTTATTT
6842 TCAAAGGAAC
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
78 22 0.24
79 21 0.23
80 31 0.34
81 16 0.18
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCCGCTTTATTCCCAAAATATTA
ATTCTCATAATCG
Found at i:6856 original size:78 final size:77
Alignment explanation
Indices: 6661--6891 Score: 216
Period size: 78 Copynumber: 2.9 Consensus size: 77
6651 TTAATCATTA
* * *
6661 GGGATACTCCACCCCGTTATTTTCGAGAGGATACTCCAACCCCCGCTTTATTTCTAAAATATTAA
1 GGGATACTCCACCCCGTTATTTTC-AAAGGATACTCC-ACCCCCGCTTTATTCCCAAAATATTAA
6726 TTTCTCCATAATCG
64 TTTCTCCATAATCG
* ** * * *
6740 GGGATACTCCAACCCCGTTACTTTCCGAGGGGATACTCCACCTCGGCTTTATTCCCAAAATATTG
1 GGGATACTCC-ACCCCGTTA-TTTTC-AAAGGATACTCCACCCCCGCTTTATTCCCAAAATATTA
*
6805 A-TTCT-CATAATTG
63 ATTTCTCCATAATCG
* * * *
6818 GGGATACTCCATCGCCCGTTATTTTCAAAGGAACACTCCAACCCTGTTATTA-TCTCCAAAATAT
1 GGGATACTCCA-C-CCCGTTATTTTCAAAGG-ATACTCCACCCCCGCT-TTATTC-CCAAAATAT
6882 TAAATTTCTC
61 T-AATTTCTC
6892 ATTGGGAAAT
Statistics
Matches: 125, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
77 4 0.03
78 35 0.28
79 34 0.27
80 32 0.26
81 20 0.16
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (77 bp):
GGGATACTCCACCCCGTTATTTTCAAAGGATACTCCACCCCCGCTTTATTCCCAAAATATTAATT
TCTCCATAATCG
Done.