Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1127
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: 2704
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Found at i:155 original size:88 final size:88
Alignment explanation
Indices: 1--1973 Score: 3356
Period size: 88 Copynumber: 22.4 Consensus size: 88
* * * * *
1 TCGACCTGCTTCGCTGTCAATGCAGGA-AGGCAGGATCTTTTATCTTCAATCAGCTCTATCACAA
1 TCGACCTGCTTCGCTGTCAATGCAGGATA-GCAAGATCTGTTCTCTTCAACCAGCTCTATCATAA
* *
65 CCGAGAGAGGGAAGGTTTGTGTCT
65 CCGAGGGAGGCAAGGTTTGTGTCT
89 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
154 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
177 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
242 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
265 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
330 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
353 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
418 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
441 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
506 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
529 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
594 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
617 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
682 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
705 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
770 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
793 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
858 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
881 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
946 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
969 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1034 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
1057 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1122 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
1145 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1210 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
1233 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1298 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
1321 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1386 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
1409 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1 TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
1474 CGAGGGAGGCAAGGTTTGTGTCT
66 CGAGGGAGGCAAGGTTTGTGTCT
* * * * * *
1497 TCGATCTGATTCGCTATCAATGCAGGA-AGCCAAGATCTGTTGTCTTCAACCAGCTTTATCACAA
1 TCGACCTGCTTCGCTGTCAATGCAGGATAG-CAAGATCTGTTCTCTTCAACCAGCTCTATCATAA
* *
1561 CCG-GAGAGGCAAGGTTTGTGTGT
65 CCGAGGGAGGCAAGGTTTGTGTCT
* * * * * * *
1584 TCGATCTGATTCGCTGTCAACGCAGG-TACGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAA
1 TCGACCTGCTTCGCTGTCAATGCAGGATA-GCAAGATCTGTTCTCTTCAACCAGCTCTATCATAA
* *
1648 CCGAGGAAGGCAAAGTTTGTGTCT
65 CCGAGGGAGGCAAGGTTTGTGTCT
* * * * *
1672 TAGACCTGCTTCGCTGTCAATGCAGG-TACGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAA
1 TCGACCTGCTTCGCTGTCAATGCAGGATA-GCAAGATCTGTTCTCTTCAACCAGCTCTATCATAA
*
1736 CCGAGAGG-GG-ATAGGTTTGTGTAT
65 CCGAG-GGAGGCA-AGGTTTGTGTCT
* * * * *
1760 TCGACCTGCCTCGCTGTCCATGCAGGA-AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAA
1 TCGACCTGCTTCGCTGTCAATGCAGGATA-GCAAGATCTGTTCTCTTCAACCAGCTCTATCATAA
*
1824 CCGAGAGAGGC-AGGTTTGTGTCT
65 CCGAGGGAGGCAAGGTTTGTGTCT
* * ** * * * *
1847 TCAACCTGTTTCGCTGTCAATAAAGGA-AGGCAAGATCCGTTGTCTTCAACCAGCTCCATCACAA
1 TCGACCTGCTTCGCTGTCAATGCAGGATA-GCAAGATCTGTTCTCTTCAACCAGCTCTATCATAA
* *
1911 CCGAGAGAGGCAAGGTTTGTGTCG
65 CCGAGGGAGGCAAGGTTTGTGTCT
* *
1935 TCGAGCTGCTTCGCTGTCACTGCAGGA-AGGCAAGATCTG
1 TCGACCTGCTTCGCTGTCAATGCAGGATA-GCAAGATCTG
1974 CTTCACTGTC
Statistics
Matches: 1821, Mismatches: 53, Indels: 22
0.96 0.03 0.01
Matches are distributed among these distances:
87 160 0.09
88 1659 0.91
89 2 0.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (88 bp):
TCGACCTGCTTCGCTGTCAATGCAGGATAGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAAC
CGAGGGAGGCAAGGTTTGTGTCT
Found at i:1983 original size:31 final size:31
Alignment explanation
Indices: 1940--2003 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1930 TGTCGTCGAG
* * * *
1940 CTGCTTCGCTGTCACTGCAGGAAGGCAAGAT
1 CTGCTTCACTGTCAATCCAGGAACGCAAGAT
*
1971 CTGCTTCACTGTCAATCCAGGAACGCATGAT
1 CTGCTTCACTGTCAATCCAGGAACGCAAGAT
2002 CT
1 CT
2004 TTTGTCTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (31 bp):
CTGCTTCACTGTCAATCCAGGAACGCAAGAT
Found at i:2168 original size:207 final size:206
Alignment explanation
Indices: 1773--2180 Score: 487
Period size: 207 Copynumber: 2.0 Consensus size: 206
1763 ACCTGCCTCG
* * * *
1773 CTGTCCATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAGG
1 CTGTCAATCCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGAAGG
* * * *
1838 TTTGTGTCTTCAACCTGTTTCGCTGTCAATAAAGGAAGGCAAGATCCGTTGTCTTCAACCAGCTC
66 CTTGTGTCTTCAACCTGCTTCGCTGTCAATAAAGGAAGGCAAGATACGTTCTCTTCAACCAGCTC
* * * * * * *
1903 CATCACAACCGAGAGAGGCAAGGTTTGTGTCGTCGAGCTGCTTCGCTGTCACTGCAGGAAGGCAA
131 CATCACAACCGAGAGAGGCAAGGTTTGTATAGTCGACCTGCCTCGCTATAAATGCAGGAAGGCAA
1968 GATCTGCTTCA
196 GATCTGCTTCA
* * *
1979 CTGTCAATCCAGGAACGCATGATCTTTTGTCTTCAACCAGCTCCATCACAGCCG-GTAGAGGTAA
1 CTGTCAATCCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAG-AGAGG-AA
* * * ** * **
2043 GGCTTGTGTCTTCGACTTGCTTCGTTGTCAATGCAGGAAGGTAAGATATTTTCTCTTCAACCAGC
64 GGCTTGTGTCTTCAACCTGCTTCGCTGTCAATAAAGGAAGGCAAGATACGTTCTCTTCAACCAGC
* ** * *
2108 TCCATCGCAACCGAGATTGG-ATAGGTTTGTATATTCGCCCTGCCTCGCTATAAATGCAGGAAGG
129 TCCATCACAACCGAGAGAGGCA-AGGTTTGTATAGTCGACCTGCCTCGCTATAAATGCAGGAAGG
*
2172 CAAGTTCTG
193 CAAGATCTG
2181 TTGTCTGCAT
Statistics
Matches: 167, Mismatches: 32, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
205 1 0.01
206 54 0.32
207 112 0.67
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (206 bp):
CTGTCAATCCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGAAGG
CTTGTGTCTTCAACCTGCTTCGCTGTCAATAAAGGAAGGCAAGATACGTTCTCTTCAACCAGCTC
CATCACAACCGAGAGAGGCAAGGTTTGTATAGTCGACCTGCCTCGCTATAAATGCAGGAAGGCAA
GATCTGCTTCA
Found at i:2451 original size:88 final size:88
Alignment explanation
Indices: 2327--2617 Score: 415
Period size: 88 Copynumber: 3.3 Consensus size: 88
2317 GTTGTCTGCA
* * * * *
2327 TTCGATCTGATTCGTTGTCAATGCAGG-AAGGTAAGATATTTTCTCTTCAACCAGCTCCATCACG
1 TTCGACCTGCTTCGCTGTCAATGCAGGTACGG-AAGATATTTTGTCTTCAACCAGCTCCATCACG
2391 ACCGAGGAACGTAAAGTTTGTGTC
65 ACCGAGGAACGTAAAGTTTGTGTC
*
2415 TTCGCCCTGCTTCGCTGTCAATGCAGGTACGGAAGATATTTTGTCTTCAACCAGCTCCATCACGA
1 TTCGACCTGCTTCGCTGTCAATGCAGGTACGGAAGATATTTTGTCTTCAACCAGCTCCATCACGA
2480 CCGAGGAACGTAAAGTTTGTGTC
66 CCGAGGAACGTAAAGTTTGTGTC
*
2503 TTCGACCTGCTTCGCTGTCAATGCAGGTACGGAAGATATTTTGTCTTCAACCAGCTCCATCACAA
1 TTCGACCTGCTTCGCTGTCAATGCAGGTACGGAAGATATTTTGTCTTCAACCAGCTCCATCACGA
** * * *
2568 CCGA-GATTGGATAGGTTTGTGTA
66 CCGAGGAACGTA-AAGTTTGTGTC
* * *
2591 TTCGACCTGCCTCGCTATAAATGCAGG
1 TTCGACCTGCTTCGCTGTCAATGCAGG
2618 AAGGCAAGTT
Statistics
Matches: 185, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
87 4 0.02
88 178 0.96
89 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (88 bp):
TTCGACCTGCTTCGCTGTCAATGCAGGTACGGAAGATATTTTGTCTTCAACCAGCTCCATCACGA
CCGAGGAACGTAAAGTTTGTGTC
Found at i:2460 original size:137 final size:137
Alignment explanation
Indices: 2063--2396 Score: 650
Period size: 137 Copynumber: 2.4 Consensus size: 137
2053 TTCGACTTGC
2063 TTCGTTGTCAATGCAGGAAGGTAAGATATTTTCTCTTCAACCAGCTCCATCGCAACCGAGATTGG
1 TTCGTTGTCAATGCAGGAAGGTAAGATATTTTCTCTTCAACCAGCTCCATCGCAACCGAGATTGG
2128 ATAGGTTTGTATATTCGCCCTGCCTCGCTATAAATGCAGGAAGGCAAGTTCTGTTGTCTGCATTC
66 ATAGGTTTGTATATTCGCCCTGCCTCGCTATAAATGCAGGAAGGCAAGTTCTGTTGTCTGCATTC
2193 GATCTGA
131 GATCTGA
2200 TTCGTTGTCAATGCAGGAAGGTAAGATATTTTCTCTTCAACCAGCTCCATCGCAACCGAGATTGG
1 TTCGTTGTCAATGCAGGAAGGTAAGATATTTTCTCTTCAACCAGCTCCATCGCAACCGAGATTGG
2265 ATAGGTTTGTATATTCGCCCTGCCTCGCTATAAATGCAGGAAGGCAAGTTCTGTTGTCTGCATTC
66 ATAGGTTTGTATATTCGCCCTGCCTCGCTATAAATGCAGGAAGGCAAGTTCTGTTGTCTGCATTC
2330 GATCTGA
131 GATCTGA
* *
2337 TTCGTTGTCAATGCAGGAAGGTAAGATATTTTCTCTTCAACCAGCTCCATCACGACCGAG
1 TTCGTTGTCAATGCAGGAAGGTAAGATATTTTCTCTTCAACCAGCTCCATCGCAACCGAG
2397 GAACGTAAAG
Statistics
Matches: 195, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 195 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (137 bp):
TTCGTTGTCAATGCAGGAAGGTAAGATATTTTCTCTTCAACCAGCTCCATCGCAACCGAGATTGG
ATAGGTTTGTATATTCGCCCTGCCTCGCTATAAATGCAGGAAGGCAAGTTCTGTTGTCTGCATTC
GATCTGA
Found at i:2505 original size:43 final size:43
Alignment explanation
Indices: 2370--2505 Score: 118
Period size: 43 Copynumber: 3.1 Consensus size: 43
2360 AGATATTTTC
2370 TCTTCAACCAGCTCCATCACGACCGAGGAACGTAAAGTTTGTG
1 TCTTCAACCAGCTCCATCACGACCGAGGAACGTAAAGTTTGTG
** * * * * * *
2413 TCTTCGCCCTGCTTCGCTGTCA--A-TGCAGGTACG-GAAGATATTTTG
1 TCTTCAACCAGC-TC-C-ATCACGACCG-AGGAACGTAAAG-T-TTGTG
2458 TCTTCAACCAGCTCCATCACGACCGAGGAACGTAAAGTTTGTG
1 TCTTCAACCAGCTCCATCACGACCGAGGAACGTAAAGTTTGTG
2501 TCTTC
1 TCTTC
2506 GACCTGCTTC
Statistics
Matches: 67, Mismatches: 16, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
42 3 0.04
43 23 0.34
44 20 0.30
45 18 0.27
46 3 0.04
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (43 bp):
TCTTCAACCAGCTCCATCACGACCGAGGAACGTAAAGTTTGTG
Done.