Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1142
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: 23508
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:107 original size:27 final size:27
Alignment explanation
Indices: 74--253 Score: 183
Period size: 28 Copynumber: 6.7 Consensus size: 27
64 TTCAGACTAT
74 TAATCAACTCGCACACTTAGTGCCACA
1 TAATCAACTCGCACACTTAGTGCCACA
*
101 TAATCAAACTCGCACACTT-GTGCTACA
1 TAATC-AACTCGCACACTTAGTGCCACA
*
128 TAGTCAACTCGCA-ACTTAGTGCC-C-
1 TAATCAACTCGCACACTTAGTGCCACA
*
152 TAATC-ACTCGCACACTTAGTGCTACA
1 TAATCAACTCGCACACTTAGTGCCACA
* *
178 TAGTCAACTCGCACACTTAGTGCCGGCA
1 TAATCAACTCGCACACTTAGTGCC-ACA
** * *
206 TGGTCAATTCGCACACTTAG-GCAATCA
1 TAATCAACTCGCACACTTAGTGCCA-CA
**
233 TAATTCATTTCGCACACTTAG
1 TAA-TCAACTCGCACACTTAG
254 ATGCAAATAG
Statistics
Matches: 129, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
23 7 0.05
24 13 0.10
25 6 0.05
26 16 0.12
27 38 0.29
28 49 0.38
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.26
Consensus pattern (27 bp):
TAATCAACTCGCACACTTAGTGCCACA
Found at i:220 original size:28 final size:27
Alignment explanation
Indices: 77--282 Score: 167
Period size: 28 Copynumber: 7.7 Consensus size: 27
67 AGACTATTAA
* *
77 TCAACTCGCACACTTAGTGCCACATAA
1 TCAACTCGCACACTTAGTGCGACATAG
*
104 TCAAACTCGCACACTT-GTGCTACATAG
1 TC-AACTCGCACACTTAGTGCGACATAG
* *
131 TCAACTCGCA-ACTTAGTGC--CCTAA
1 TCAACTCGCACACTTAGTGCGACATAG
*
155 TC-ACTCGCACACTTAGTGCTACATAG
1 TCAACTCGCACACTTAGTGCGACATAG
* *
181 TCAACTCGCACACTTAGTGCCGGCATGG
1 TCAACTCGCACACTTAGTG-CGACATAG
* * *
209 TCAATTCGCACACTTAG-GCAATCATAAT
1 TCAACTCGCACACTTAGTGCGA-CAT-AG
** *
237 TCATTTCGCACACTTAGATGC-AAATAG
1 TCAACTCGCACACTTAG-TGCGACATAG
* *
264 TCAAATCGC-CACCTAGTGC
1 TCAACTCGCACACTTAGTGC
283 TGTACAATTA
Statistics
Matches: 148, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
23 7 0.05
24 14 0.09
25 7 0.05
26 24 0.16
27 41 0.28
28 52 0.35
29 1 0.01
30 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (27 bp):
TCAACTCGCACACTTAGTGCGACATAG
Found at i:3731 original size:13 final size:13
Alignment explanation
Indices: 3712--3750 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3702 TCTCTTTTTT
3712 AAATTTTTTTTCA
1 AAATTTTTTTTCA
**
3725 ATTTTTTTTTTCA
1 AAATTTTTTTTCA
3738 AAATTTTTTTTCA
1 AAATTTTTTTTCA
3751 CAACTTGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (13 bp):
AAATTTTTTTTCA
Found at i:6904 original size:20 final size:19
Alignment explanation
Indices: 6879--6918 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
6869 CAAAACACTG
*
6879 TTTCTCCCACTCTTTCTTTC
1 TTTCTCCCAATCTTT-TTTC
6899 TTTCTCCCAATCTTTTTTC
1 TTTCTCCCAATCTTTTTTC
6918 T
1 T
6919 CTTTTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.07, C:0.35, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTCTCCCAATCTTTTTTC
Found at i:7876 original size:13 final size:13
Alignment explanation
Indices: 7860--7885 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7850 TTTTTAATTT
7860 TTTTTTTTCACAA
1 TTTTTTTTCACAA
7873 TTTTTTTTCACAA
1 TTTTTTTTCACAA
7886 CTTGATATCC
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:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:15939 original size:27 final size:27
Alignment explanation
Indices: 15905--16137 Score: 279
Period size: 27 Copynumber: 8.6 Consensus size: 27
15895 TAAATTGTAC
*
15905 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* ** *
15932 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGACTATGT
* * *
15958 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAGTTGACTATGT
*
15986 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
16013 AGCACTAAGTGTGCGAGTTTGATTATGC
1 AGCACTAAGTGTGCGAG-TTGACTATGT
*
16041 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
16068 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* * *
16096 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
16123 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16138 GACTTAATAT
Statistics
Matches: 178, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
27 129 0.72
28 49 0.28
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:16055 original size:55 final size:54
Alignment explanation
Indices: 15905--16137 Score: 315
Period size: 55 Copynumber: 4.3 Consensus size: 54
15895 TAAATTGTAC
** ** *
15905 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGCGGCACTAAGTGTGCGAGTTGACTATGT
* *
15958 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGCGGCACTAAGTGTGCGAGTTGACTATGT
*
16013 AGCACTAAGTGTGCGAGTTTGATTATGCGGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGCGGCACTAAGTGTGCGAGTTGACTATGT
* * * *
16068 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTTGACTATGCGGCACTAAGTGTGCGAGTTGACTATGT
*
16123 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16138 GACTTAATAT
Statistics
Matches: 163, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.01
54 60 0.37
55 102 0.63
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGCGGCACTAAGTGTGCGAGTTGACTATGT
Found at i:16128 original size:82 final size:81
Alignment explanation
Indices: 15904--16137 Score: 301
Period size: 82 Copynumber: 2.9 Consensus size: 81
15894 GTAAATTGTA
* ** *
15904 CAGCACTAAGTGTGCGA-TTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAG
1 CAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGATTAT-ATGCACTAAG
15968 TGTGCGAATTGACCATG
65 TGTGCGAATTGACCATG
* **
15985 CGGCACTAAGTGTGCGAG-TTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGCGGCACTAA
1 CAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAG-TTGATTAT-ATGCACTAA
* *
16049 GTGTGCGAGTTGACTATG
64 GTGTGCGAATTGACCATG
* * * *
16067 TAGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTATATAGCACTGAG
1 CAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGATTATAT-GCACTAAG
16132 TGTGCG
65 TGTGCG
16138 GACTTAATAT
Statistics
Matches: 133, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
81 41 0.31
82 67 0.50
83 25 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (81 bp):
CAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGATTATATGCACTAAGT
GTGCGAATTGACCATG
Found at i:21064 original size:45 final size:45
Alignment explanation
Indices: 21013--21243 Score: 394
Period size: 45 Copynumber: 5.2 Consensus size: 45
21003 TCGACCATGG
* * * *
21013 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
21058 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
21103 TGCTTCCTCAAATTCTT-CATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
21147 TGCTTCCTCAAATTC-TCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
21191 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
21236 TGCTTCCT
1 TGCTTCCT
21244 TAATTTCATG
Statistics
Matches: 177, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
43 1 0.01
44 84 0.47
45 92 0.52
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Done.