Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1841
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: 19442
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3175 original size:13 final size:13
Alignment explanation
Indices: 3157--3182 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3147 TACAGCAAGT
3157 ATGTATCGATACA
1 ATGTATCGATACA
3170 ATGTATCGATACA
1 ATGTATCGATACA
3183 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5771 original size:23 final size:21
Alignment explanation
Indices: 5729--5771 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
5719 GTTTAATGTT
**
5729 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
5750 TTTGCATTGTACTTTGAATTTT
1 TTTGC-TTG-ACTTTGAATTTT
5772 TAATCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.60
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:6693 original size:13 final size:13
Alignment explanation
Indices: 6675--6700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6665 TACACAAAGT
6675 ATGTATCGATACA
1 ATGTATCGATACA
6688 ATGTATCGATACA
1 ATGTATCGATACA
6701 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:6719 original size:34 final size:32
Alignment explanation
Indices: 6657--6721 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
6647 TAGCCAAACT
**
6657 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
6689 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
6722 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:8291 original size:27 final size:27
Alignment explanation
Indices: 8249--8307 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
8239 CATTCACATA
*
8249 AAAAAACTACCTATTAATTTCACTTTT
1 AAAAAACTACCCATTAATTTCACTTTT
*
8276 AAAAAACTGCCCATTAATTTCACTTTT
1 AAAAAACTACCCATTAATTTCACTTTT
8303 AAAAA
1 AAAAA
8308 GATTGCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.36
Consensus pattern (27 bp):
AAAAAACTACCCATTAATTTCACTTTT
Found at i:8383 original size:80 final size:78
Alignment explanation
Indices: 8269--8414 Score: 229
Period size: 80 Copynumber: 1.8 Consensus size: 78
8259 CTATTAATTT
* * *
8269 CACTTTTAAAAAACTGCCCATTAATTTCACTTTTAAAAAGATTGCTTATATTTTTTTACATATTA
1 CACTTTTAAAAAACTACCCATTAATTTCACTTTTAAAAAAATTACTTATA-TTTTTTACATATTA
8334 ATCTAATAATCTTG
65 ATCTAATAATCTTG
* *
8348 CACTTTTAAAAGAACTACCTATTAATTTCATTTTTAAAAAAATTACTTATATTTTTTACATATTA
1 CACTTTTAAAA-AACTACCCATTAATTTCACTTTTAAAAAAATTACTTATATTTTTTACATATTA
8413 AT
65 AT
8415 AAATAATATT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 27 0.44
80 34 0.56
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.45
Consensus pattern (78 bp):
CACTTTTAAAAAACTACCCATTAATTTCACTTTTAAAAAAATTACTTATATTTTTTACATATTAA
TCTAATAATCTTG
Found at i:10773 original size:29 final size:30
Alignment explanation
Indices: 10547--10789 Score: 316
Period size: 30 Copynumber: 8.2 Consensus size: 30
10537 AGCGCCTTTA
* *
10547 AGAGCACCTGCTCCATGAGCA-CTGGCACCA
1 AGAGCACCTGCTCCGTGAGCAGC-GGCACCG
* * * * *
10577 ATAGAACCAAGCTCCATGAGCAGTGGCACCG
1 AGAGCACC-TGCTCCGTGAGCAGCGGCACCG
*
10608 AGAGCACCTGC-CCATGAGCAGCGGCACCG
1 AGAGCACCTGCTCCGTGAGCAGCGGCACCG
*
10637 AGAGCTCCTGCT-CGTGA-CAGCGGCACCG
1 AGAGCACCTGCTCCGTGAGCAGCGGCACCG
10665 AGAGCACCTGCTCCGTGAGCAGCGGCACCG
1 AGAGCACCTGCTCCGTGAGCAGCGGCACCG
*
10695 AGGGCACCTGCTCCGTGAGCAGCGGCACCG
1 AGAGCACCTGCTCCGTGAGCAGCGGCACCG
10725 AGAGCACCTGCTCCGTGAGCAGCGGCACCG
1 AGAGCACCTGCTCCGTGAGCAGCGGCACCG
** *
10755 AG-GGTCCTGCTCCGTGAGCTGCGGCACCG
1 AGAGCACCTGCTCCGTGAGCAGCGGCACCG
10784 AGAGCA
1 AGAGCA
10790 GCGGCACCGA
Statistics
Matches: 188, Mismatches: 19, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
28 22 0.12
29 62 0.33
30 80 0.43
31 24 0.13
ACGTcount: A:0.22, C:0.35, G:0.32, T:0.12
Consensus pattern (30 bp):
AGAGCACCTGCTCCGTGAGCAGCGGCACCG
Found at i:10819 original size:89 final size:88
Alignment explanation
Indices: 10587--10803 Score: 260
Period size: 89 Copynumber: 2.5 Consensus size: 88
10577 ATAGAACCAA
* * * * *
10587 GCTCCATGAGCAGTGGCACCGAGAGCACCTGC-CC-ATGAGCAGCGGCACCGAGAGCTCCTGCTC
1 GCTCCGTGAGCAGCGGCACCGAGAGCACCGGCACCGA-GAGCACCGGCACCGAGAGCACCTGCTC
10650 GTGACAGCGGCACCGAGAGCACCT
65 GTGACAGCGGCACCGAGAGCACCT
* * * * *
10674 GCTCCGTGAGCAGCGGCACCGAGGGCACCTGCTCCGTGAGCAGCGGCACCGAGAGCACCTGCTCC
1 GCTCCGTGAGCAGCGGCACCGAGAGCACCGGCACCGAGAGCACCGGCACCGAGAGCACCTGCT-C
**
10739 GTGAGCAGCGGCACCGAG-GGTCCT
65 GTGA-CAGCGGCACCGAGAGCACCT
* *
10763 GCTCCGTGAGCTGCGGCACCGAGAGCAGCGGCACCGAGAGC
1 GCTCCGTGAGCAGCGGCACCGAGAGCACCGGCACCGAGAGC
10804 TCCTGCTCCG
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
87 29 0.26
88 27 0.24
89 44 0.39
90 13 0.12
ACGTcount: A:0.19, C:0.35, G:0.35, T:0.11
Consensus pattern (88 bp):
GCTCCGTGAGCAGCGGCACCGAGAGCACCGGCACCGAGAGCACCGGCACCGAGAGCACCTGCTCG
TGACAGCGGCACCGAGAGCACCT
Found at i:10833 original size:15 final size:15
Alignment explanation
Indices: 10594--10920 Score: 172
Period size: 15 Copynumber: 22.3 Consensus size: 15
10584 CAAGCTCCAT
*
10594 GAGCAGTGGCACCGA
1 GAGCAGCGGCACCGA
* *
10609 GAGCACCTGC-CC-A
1 GAGCAGCGGCACCGA
10622 TGAGCAGCGGCACCGA
1 -GAGCAGCGGCACCGA
** * * *
10638 GAGCTCCTGC-TCGT
1 GAGCAGCGGCACCGA
10652 GA-CAGCGGCACCGA
1 GAGCAGCGGCACCGA
* * * *
10666 GAGCACCTGCTCCGT
1 GAGCAGCGGCACCGA
10681 GAGCAGCGGCACCGA
1 GAGCAGCGGCACCGA
* * * * *
10696 GGGCACCTGCTCCGT
1 GAGCAGCGGCACCGA
10711 GAGCAGCGGCACCGA
1 GAGCAGCGGCACCGA
* * * *
10726 GAGCACCTGCTCCGT
1 GAGCAGCGGCACCGA
10741 GAGCAGCGGCACCGA
1 GAGCAGCGGCACCGA
* * * *
10756 GGGTC--CTGCTCCGT
1 GAG-CAGCGGCACCGA
*
10770 GAGCTGCGGCACCGA
1 GAGCAGCGGCACCGA
10785 GAGCAGCGGCACCGA
1 GAGCAGCGGCACCGA
** * * *
10800 GAGCTCCTGCTCCGT
1 GAGCAGCGGCACCGA
*
10815 GAGCAGCGGCACGGA
1 GAGCAGCGGCACCGA
* *
10830 GAGCAGCTGCTCC-A
1 GAGCAGCGGCACCGA
*
10844 CCAGCAGCGGCACC-A
1 -GAGCAGCGGCACCGA
* * *
10859 GAG-AGCTGCTCCGT
1 GAGCAGCGGCACCGA
10873 GAGCAGCGGCA-CGA
1 GAGCAGCGGCACCGA
* *
10887 GAGCAGCTGCTCC-A
1 GAGCAGCGGCACCGA
*
10901 CCAGCAGCGGCACCGA
1 -GAGCAGCGGCACCGA
10917 GAGC
1 GAGC
10921 TCCTGCTCCA
Statistics
Matches: 218, Mismatches: 80, Indels: 28
0.67 0.25 0.09
Matches are distributed among these distances:
13 13 0.06
14 44 0.20
15 158 0.72
16 3 0.01
ACGTcount: A:0.20, C:0.35, G:0.35, T:0.10
Consensus pattern (15 bp):
GAGCAGCGGCACCGA
Found at i:10897 original size:87 final size:88
Alignment explanation
Indices: 10785--10945 Score: 225
Period size: 87 Copynumber: 1.8 Consensus size: 88
10775 GCGGCACCGA
* *** * *
10785 GAGCAGCGGCACCGAGAGCTCCTGCTCCGTGAGCAGCGGCACGGAGAGCAGCTGCTCCACCAGCA
1 GAGCAGCGGCACCGAGAGCACCTGCTCCACCAGCAGCGGCACCGAGAGCACCTGCTCCACCAGCA
*
10850 GCGGCACCAGAGAGCTGCTCCGT
66 GCAGCACCAGAGAGCTGCTCCGT
* * *
10873 GAGCAGCGGCA-CGAGAGCAGCTGCTCCACCAGCAGCGGCACCGAGAGCTCCTGCTCCACCTGCA
1 GAGCAGCGGCACCGAGAGCACCTGCTCCACCAGCAGCGGCACCGAGAGCACCTGCTCCACCAGCA
10937 GCAGCACCA
66 GCAGCACCA
10946 AGACCAACAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
87 52 0.83
88 11 0.17
ACGTcount: A:0.22, C:0.37, G:0.32, T:0.09
Consensus pattern (88 bp):
GAGCAGCGGCACCGAGAGCACCTGCTCCACCAGCAGCGGCACCGAGAGCACCTGCTCCACCAGCA
GCAGCACCAGAGAGCTGCTCCGT
Found at i:10906 original size:57 final size:57
Alignment explanation
Indices: 10786--10921 Score: 229
Period size: 57 Copynumber: 2.3 Consensus size: 57
10776 CGGCACCGAG
10786 AGCAGCGGCACCGAGAGCTCCTGCTCCGTGAGCAGCGGCACGGAGAGCAGCTGCTCCACC
1 AGCAGCGGCACCGAGAG---CTGCTCCGTGAGCAGCGGCACGGAGAGCAGCTGCTCCACC
10846 AGCAGCGGCACCAGAGAGCTGCTCCGTGAGCAGCGGCAC-GAGAGCAGCTGCTCCACC
1 AGCAGCGGCACC-GAGAGCTGCTCCGTGAGCAGCGGCACGGAGAGCAGCTGCTCCACC
10903 AGCAGCGGCACCGAGAGCT
1 AGCAGCGGCACCGAGAGCT
10922 CCTGCTCCAC
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
56 7 0.09
57 30 0.40
58 21 0.28
60 12 0.16
61 5 0.07
ACGTcount: A:0.22, C:0.35, G:0.34, T:0.09
Consensus pattern (57 bp):
AGCAGCGGCACCGAGAGCTGCTCCGTGAGCAGCGGCACGGAGAGCAGCTGCTCCACC
Found at i:10932 original size:30 final size:30
Alignment explanation
Indices: 10786--10944 Score: 171
Period size: 30 Copynumber: 5.4 Consensus size: 30
10776 CGGCACCGAG
* ***
10786 AGCAGCGGCACCGAGAGCTCCTGCTCCGTG
1 AGCAGCGGCACCGAGAGCACCTGCTCCACC
* *
10816 AGCAGCGGCACGGAGAGCAGCTGCTCCACC
1 AGCAGCGGCACCGAGAGCACCTGCTCCACC
* ***
10846 AGCAGCGGCACC-AGAG-AGCTGCTCCGTG
1 AGCAGCGGCACCGAGAGCACCTGCTCCACC
*
10874 AGCAGCGGCA-CGAGAGCAGCTGCTCCACC
1 AGCAGCGGCACCGAGAGCACCTGCTCCACC
*
10903 AGCAGCGGCACCGAGAGCTCCTGCTCCACC
1 AGCAGCGGCACCGAGAGCACCTGCTCCACC
* *
10933 TGCAGCAGCACC
1 AGCAGCGGCACC
10945 AAGACCAACA
Statistics
Matches: 109, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
27 1 0.01
28 23 0.21
29 23 0.21
30 62 0.57
ACGTcount: A:0.21, C:0.38, G:0.31, T:0.09
Consensus pattern (30 bp):
AGCAGCGGCACCGAGAGCACCTGCTCCACC
Found at i:11284 original size:2 final size:2
Alignment explanation
Indices: 11279--11307 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11269 GATATAATAT
11279 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11308 AGGGGCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11727 original size:17 final size:16
Alignment explanation
Indices: 11705--11748 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
11695 TATATATTTA
11705 TTAATAAATTATTTTTT
1 TTAAT-AATTATTTTTT
*
11722 TTAATATTTATTTTTT
1 TTAATAATTATTTTTT
11738 AATTAATAATT
1 --TTAATAATT
11749 CAATTGAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATAATTATTTTTT
Found at i:12225 original size:19 final size:19
Alignment explanation
Indices: 12198--12245 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 19
12188 ATTAATTGAT
* *
12198 TTAAAAAATAATTTTAATA
1 TTAATAAATAATTTAAATA
12217 TTAATAAAT-A-TTAAATA
1 TTAATAAATAATTTAAATA
12234 -TAATAAATAATT
1 TTAATAAATAATT
12246 AATAAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 2 0.08
19 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAATAAATAATTTAAATA
Found at i:12237 original size:16 final size:18
Alignment explanation
Indices: 12198--12247 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
12188 ATTAATTGAT
* *
12198 TTAAAAAATAATTTTAATA
1 TTAATAAATAA-TTAAATA
12217 TTAATAAAT-ATTAAATA
1 TTAATAAATAATTAAATA
12234 -TAATAAATAATTAA
1 TTAATAAATAATTAA
12248 TAAACATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.29
17 11 0.39
18 1 0.04
19 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATAAATAATTAAATA
Found at i:12249 original size:16 final size:16
Alignment explanation
Indices: 12211--12249 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12201 AAAAATAATT
12211 TTAATATTAATAAATA
1 TTAATATTAATAAATA
12227 TTAA-ATATAATAAATAA
1 TTAATAT-TAATAAAT-A
12244 TTAATA
1 TTAATA
12250 AACATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 12 0.60
17 5 0.25
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAATATTAATAAATA
Done.