Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold259
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: 30216
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Found at i:1762 original size:29 final size:28
Alignment explanation
Indices: 1726--1803 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
1716 TCATGAGATT
1726 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
1756 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
1783 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
1804 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:1925 original size:22 final size:22
Alignment explanation
Indices: 1897--1944 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1887 TTGGACAGCG
*
1897 GAAAAGGTAAGTGTGCGAACTT
1 GAAAAGGTAAGTGTACGAACTT
1919 GAAAAGGTAAGTGTACGAACTT
1 GAAAAGGTAAGTGTACGAACTT
1941 GAAA
1 GAAA
1945 TGCAAGCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.29, T:0.21
Consensus pattern (22 bp):
GAAAAGGTAAGTGTACGAACTT
Found at i:20164 original size:27 final size:27
Alignment explanation
Indices: 20134--20338 Score: 196
Period size: 27 Copynumber: 7.6 Consensus size: 27
20124 ATATTAAGTC
* * *
20134 CGCACGCTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
20161 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
20189 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
20216 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
20243 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
20270 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
20297 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
20324 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20339 GTACAATTTA
Statistics
Matches: 154, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
27 128 0.83
28 26 0.17
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:20273 original size:54 final size:54
Alignment explanation
Indices: 20134--20337 Score: 248
Period size: 54 Copynumber: 3.8 Consensus size: 54
20124 ATATTAAGTC
* * * * **
20134 CGCACGCTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
20189 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
20243 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
20297 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
20338 TGTACAATTT
Statistics
Matches: 127, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.63
55 46 0.36
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:20300 original size:81 final size:81
Alignment explanation
Indices: 20188--20337 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
20178 ATAATCAAAC
* * * * * *
20188 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
20253 GTGCATCATTTTCATT
66 GTGCATCATTTTCATT
* *
20269 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
20334 GTGC
66 GTGC
20338 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTTCATT
Found at i:28298 original size:27 final size:27
Alignment explanation
Indices: 28268--28471 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
28258 ATATTAAGTC
* *
28268 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
28295 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
28323 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
28350 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
28377 CGCACACTTAGTGC-ATCAT-TTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
28403 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
28430 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
28457 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28472 GTACAATTTA
Statistics
Matches: 155, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 22 0.14
27 108 0.70
28 25 0.16
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28423 original size:53 final size:54
Alignment explanation
Indices: 28268--28470 Score: 257
Period size: 53 Copynumber: 3.8 Consensus size: 54
28258 ATATTAAGTC
* * * **
28268 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
28323 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* ** *
28377 CGCACACTTAGTGC-ATCAT-TTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
28430 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
28471 TGTACAATTT
Statistics
Matches: 128, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
53 46 0.36
54 36 0.28
55 46 0.36
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:28436 original size:80 final size:80
Alignment explanation
Indices: 28322--28470 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 80
28312 ATAATCAAAC
* * * * * *
28322 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
28387 GTGCATCATTTCATT
66 GTGCATCATTTCATT
* *
28402 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
28467 GTGC
66 GTGC
28471 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (80 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTCATT
Done.