Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold913
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: 5811
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Found at i:314 original size:59 final size:59
Alignment explanation
Indices: 1--3953 Score: 5198
Period size: 59 Copynumber: 67.0 Consensus size: 59
* *
1 CGTCCTGCTCTTTGAGGATTGGGAA-GTGCCACCAACTTGTGTGGGGCTTTAAAAG----GG
1 CGTCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGT-GGGCTTTAAAAGAAAAGG
* * * * * *
58 -GTCCTGCTCTATGGGGACGGAAAGGTGCCACCAACTTGTCTGGGCTTTAAAAGGAGAAGG
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGG
* * *
118 CGTCCTGCTCTTTGAGGATTGGGAA-GTGCCACCAACTTGTGTGGG-TTT--TA-AAAAGG
1 CGTCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * * *
174 -GTCCTGCTCTATGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* * *
234 CATCCCGGTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
*
293 CGTCCCGCTGTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* ** *
352 CGTCACGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGG
* * *
413 TG-CCCTGCTCTTTGAGGACTGGGATGTGCCACCAACTTGTGTGGGCTTTAAAAG----GG
1 CGTCCC-GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * *
469 -GTCCTGCTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGCGCTTTAAAAGGAGAAA-G
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GA-AAAGG
*
529 CGTCCTC-CTCTTTGAGGATTAGGAA-GTGCCACCAACTTGTGTGGGCTTT---A-AAAAGG
1 CGTCC-CGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * * *
585 -GTCCTGCTCTATGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* *
645 CATCCCGATCTTTGAGGACTGAAGGTAG-CACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGT-GCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* *
704 CGTCCCGCTCTTTTAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* *
763 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGAGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* * * *
823 CATCCTGCTCTTTGAGGACTGAATGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* *
882 CTTCCCGCTGTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
** * *
941 CGTCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTAAAAGGAGAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGG
* *
1002 TGTCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG----GG
1 CGTCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * *
1058 -GTCCTGCTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* * * * **
1118 CATCCTGCTCTTTGAGGACTGAAGGTGCCTCCAACTTGGGTGGGCTAGAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1177 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAA-G
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
*
1235 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCTACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
**
1294 CGTCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
** ** *
1354 CGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGG
*
1415 CGTCCTC-CTCTTTGAGGATTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG----GG
1 CGTCC-CGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * * *
1471 -GTCCTGCTCTATGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* *
1531 CATCCCAG-TGTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCC-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* *
1590 CGTCCCGCTCTTTTAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* *
1649 CGTCCCACTCTTTGAGGACTGAATGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * *
1708 CGTCCCGCTCTTTGAGGACTGAAGCTGCCAACAACTTGTGTGGGC-TT---CG-AAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * *
1762 GGTCCTGCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTGAGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGA-GGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* * *
1823 CATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * *
1882 CGTCCCGCTGTTTAAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
** *
1940 CGTCCCGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGG
* * *
2001 TGTCCTGCTCTTTGAGGACTGGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG----GG
1 CGTCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * * *
2058 GGTCCTGCTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* *
2119 CATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
2178 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
2237 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* *
2295 CATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAATAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
2354 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* **
2413 CATCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
** ** * *
2473 CGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* * *
2534 CATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * *
2593 CGT-CCG-TGTTTAAGGGATTGAATGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGA-GGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
** *
2651 CGTCCCGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGG
*
2712 TGTCCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG----GG
1 CGTCCC-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * *
2768 -GTCCTGCTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* *
2828 CATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
2887 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
2946 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * *
3005 CATTCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGC-TTAAAAGAATAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
3063 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* **
3122 CATCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
** ** * *
3182 CGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* * *
3243 CATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * *
3302 CGTCCCGCTGTTTAAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
** *
3361 CGTCCCGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGG
* *
3422 TGTCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG----GG
1 CGTCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * *
3478 -GTCCTGCTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 CGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGG
* *
3538 CATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
*
3597 CATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
3656 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* *
3715 CATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAATAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
3774 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* **
3833 CATCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
** ** *
3893 CGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGGGGGCTTTTAAAAGGAAAAG
1 CGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGC-TTTAAAA-GAAAAG
3954 TTATCTTGCT
Statistics
Matches: 3484, Mismatches: 287, Indels: 245
0.87 0.07 0.06
Matches are distributed among these distances:
53 6 0.00
54 47 0.01
55 302 0.09
56 103 0.03
57 29 0.01
58 243 0.07
59 1362 0.39
60 791 0.23
61 531 0.15
62 68 0.02
63 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (59 bp):
CGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
Found at i:4918 original size:14 final size:15
Alignment explanation
Indices: 4880--4933 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
4870 AGCTTAAGCA
4880 GCTTCT-TTTTCTTT
1 GCTTCTGTTTTCTTT
*
4894 TCTCTCT-TTTTCTTT
1 GCT-TCTGTTTTCTTT
* *
4909 G-TTTTGTTTTTTTT
1 GCTTCTGTTTTCTTT
4923 GCTTCTGTTTT
1 GCTTCTGTTTT
4934 TTTTTCTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 2 0.06
14 11 0.34
15 19 0.59
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (15 bp):
GCTTCTGTTTTCTTT
Found at i:4918 original size:15 final size:15
Alignment explanation
Indices: 4900--4937 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4890 CTTTTCTCTC
*
4900 TTTTTCTTTG-TTTTG
1 TTTTT-TTTGCTTCTG
4915 TTTTTTTTGCTTCTG
1 TTTTTTTTGCTTCTG
4930 TTTTTTTT
1 TTTTTTTT
4938 TCTTTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.82
Consensus pattern (15 bp):
TTTTTTTTGCTTCTG
Done.