Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2173
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: 38051
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:4734 original size:22 final size:22
Alignment explanation
Indices: 4706--4750 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4696 TTAAATGATA
4706 ACCTTGTACTTGAAGAACATGT
1 ACCTTGTACTTGAAGAACATGT
4728 ACCTTGTACTTGAAGAACATGT
1 ACCTTGTACTTGAAGAACATGT
4750 A
1 A
4751 TACAAGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (22 bp):
ACCTTGTACTTGAAGAACATGT
Found at i:10953 original size:20 final size:19
Alignment explanation
Indices: 10928--10992 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
10918 CACATGCGTG
10928 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTT-GGTA
** * * *
10948 CCCCTGAATGCACATGCGTG
1 CCCCTGTTTGTACTTG-GTA
10968 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTAC-TTGGTA
10988 CCCCT
1 CCCCT
10993 AAATGCACAT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 1 0.03
20 30 0.91
21 2 0.06
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (19 bp):
CCCCTGTTTGTACTTGGTA
Found at i:10969 original size:40 final size:40
Alignment explanation
Indices: 10914--11156 Score: 326
Period size: 40 Copynumber: 6.1 Consensus size: 40
10904 TTATTGTCTA
* *
10914 AATGCACATGCGTGCCCCTGTTTGTACTTCGGTACCCCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTG
* *
10954 AATGCACATGCGTGCCCCTGTTTGTACTTTGGTACCCCTA
1 AATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTG
* *
10994 AATGCACATATGTGCCCCTGTTTGTATTTTGGT-CCCCTTG
1 AATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC-TG
* * *
11034 AATGCACATACGTGGCCCTTTTTGTACTTCGGTACCCCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTG
* *
11074 AATGCACATACCTGCCCCTGTTTGTACTTTGGTACCCCTA
1 AATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTG
* * * * *
11114 AATGCACCTACGTGCCCTTGTTTATACTTTGGTAACCTTG
1 AATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTG
11154 AAT
1 AAT
11157 CAAATAGCAT
Statistics
Matches: 178, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
39 4 0.02
40 170 0.96
41 4 0.02
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (40 bp):
AATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTG
Found at i:11129 original size:120 final size:120
Alignment explanation
Indices: 10914--11156 Score: 378
Period size: 120 Copynumber: 2.0 Consensus size: 120
10904 TTATTGTCTA
* * *
10914 AATGCACATGCGTGCCCCTGTTTGTACTTCGGTACCCCTGAATGCACATGCGTGCCCCTGTTTGT
1 AATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACCTGCCCCTGTTTGT
* * * **
10979 ACTTTGGTACCCCTAAATGCACATATGTGCCCCTGTTTGTATTTTGGTCCCCTTG
66 ACTTTGGTACCCCTAAATGCACATACGTGCCCCTGTTTATACTTTGGTAACCTTG
* *
11034 AATGCACATACGTGGCCCTTTTTGTACTTCGGTACCCCTGAATGCACATACCTGCCCCTGTTTGT
1 AATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACCTGCCCCTGTTTGT
* *
11099 ACTTTGGTACCCCTAAATGCACCTACGTGCCCTTGTTTATACTTTGGTAACCTTG
66 ACTTTGGTACCCCTAAATGCACATACGTGCCCCTGTTTATACTTTGGTAACCTTG
11154 AAT
1 AAT
11157 CAAATAGCAT
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 111 1.00
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (120 bp):
AATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACCTGCCCCTGTTTGT
ACTTTGGTACCCCTAAATGCACATACGTGCCCCTGTTTATACTTTGGTAACCTTG
Found at i:16011 original size:51 final size:51
Alignment explanation
Indices: 15925--16218 Score: 287
Period size: 51 Copynumber: 5.8 Consensus size: 51
15915 TATCGATGAA
*
15925 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATGATGGT
* * * * * * * *
15976 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTA-CTGAGAAGCT-TTCGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GATAA-ATGATGGT
** * *
16027 CACGTGTGTAGTACCGTGTGAAGGCTACTATGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATGATGGT
* * * * *
16078 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATG--ATGGT
* * * *
16129 CACGTGTGTAGTACTATGTGAAGGGTACTACGTGAACCG-TAAA--ACTAGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATGA-T-GGT
16179 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
16219 ATGATAAAAG
Statistics
Matches: 197, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
49 2 0.01
50 43 0.22
51 150 0.76
52 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATGATGGT
Found at i:16101 original size:102 final size:102
Alignment explanation
Indices: 15925--16206 Score: 408
Period size: 102 Copynumber: 2.8 Consensus size: 102
15915 TATCGATGAA
*
15925 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
15990 TAAGTGAAGGCTACAATGTGTACTGAGAAGCTTTCGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTCGT
* *
16027 CACGTGTGTAGTACCGTGTGAAGGCTACTATGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
16092 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTCGT
* * * * *
16129 CACGTGTGTAGTACTATGTGAAGGGTACTACGTGAACCG-TAAA--ACTAGATCACGTGTGTAGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGA-T-GGTCACATGTGTAGT
*
16191 ACTATGTGAAGGCTAC
64 ACTAAGTGAAGGCTAC
16207 TACGTGTATC
Statistics
Matches: 163, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
99 1 0.01
100 1 0.01
101 32 0.20
102 129 0.79
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTCGT
Found at i:21039 original size:100 final size:100
Alignment explanation
Indices: 20861--21056 Score: 347
Period size: 100 Copynumber: 2.0 Consensus size: 100
20851 TCCTTGGGCA
* * * *
20861 ACAAGAAACGTTTTGATTCACAAAATCGCTCTTTTCTTTCTGTCCCAAATCCCTAGATCTAATTC
1 ACAAAAAACGTTTTGATTCACAAAATCCCTCTTTTCTTGCCGTCCCAAATCCCTAGATCTAATTC
*
20926 CAATTGATTTCGCAATCTGATTGTTAATTTGATTC
66 CAATTGATTTCGCAATCTAATTGTTAATTTGATTC
20961 ACAAAAAACGTTTTGATTCACAAAATCCCTCTTTTCTTGCCGTCCCAAATCCCTAGATCTAATTC
1 ACAAAAAACGTTTTGATTCACAAAATCCCTCTTTTCTTGCCGTCCCAAATCCCTAGATCTAATTC
21026 CAATTGATTTCGCAATCTAATTGTTAATTTG
66 CAATTGATTTCGCAATCTAATTGTTAATTTG
21057 TTTGCCGTTT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 91 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (100 bp):
ACAAAAAACGTTTTGATTCACAAAATCCCTCTTTTCTTGCCGTCCCAAATCCCTAGATCTAATTC
CAATTGATTTCGCAATCTAATTGTTAATTTGATTC
Found at i:22901 original size:21 final size:22
Alignment explanation
Indices: 22856--22901 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
22846 AGAGAAAAAT
*
22856 AAAAGTGAAAAATAAGAAAATG
1 AAAAGTGAAAAATAAGAAAAGG
**
22878 AAAA-TGAAAAATGCGAAAAGG
1 AAAAGTGAAAAATAAGAAAAGG
22899 AAA
1 AAA
22902 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAGTGAAAAATAAGAAAAGG
Found at i:27170 original size:101 final size:101
Alignment explanation
Indices: 27039--27230 Score: 332
Period size: 101 Copynumber: 1.9 Consensus size: 101
27029 GGGCAACAAG
* *
27039 AAACGTTTTGATTCAGAAAATCACTCTTTTCTT-TCTGTTCCAAATCCCTAGATCTAATTCCAAT
1 AAACGTTTTGATTCACAAAATCACTCTTTTCTTGTC-GTCCCAAATCCCTAGATCTAATTCCAAT
*
27103 TGATTTCGCAATCTGATTGTTAATTTGATTCACAAAA
65 TGATTTCGCAATCTGATTATTAATTTGATTCACAAAA
*
27140 AAACGTTTTGATTCACAAAATCCCTCTTTTCTTGTCGTCCCAAATCCCTAGATCTAATTCCAATT
1 AAACGTTTTGATTCACAAAATCACTCTTTTCTTGTCGTCCCAAATCCCTAGATCTAATTCCAATT
27205 GATTTCGCAATCTGATTATTAATTTG
66 GATTTCGCAATCTGATTATTAATTTG
27231 TTTGCTGCTT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
101 84 0.98
102 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (101 bp):
AAACGTTTTGATTCACAAAATCACTCTTTTCTTGTCGTCCCAAATCCCTAGATCTAATTCCAATT
GATTTCGCAATCTGATTATTAATTTGATTCACAAAA
Found at i:32342 original size:102 final size:100
Alignment explanation
Indices: 32166--32508 Score: 431
Period size: 102 Copynumber: 3.4 Consensus size: 100
32156 TATTGATGAA
* * * * *
32166 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATCAATGATAGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
32231 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTCGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTT-GT
*
32268 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
32333 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTT-GT
* * * *** * *
32370 CACATGTGTAGTACTATGTGAAGGGTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAG-AC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* * * *
32433 TATGTGAAGGCTACTACGTGAACCGTAAAAC-TTGAT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTG-T
*
32469 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
32509 ATGATAAAAG
Statistics
Matches: 214, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
98 1 0.00
99 38 0.18
100 28 0.13
101 17 0.08
102 129 0.60
103 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (100 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGT
Found at i:32442 original size:49 final size:50
Alignment explanation
Indices: 32166--32502 Score: 326
Period size: 51 Copynumber: 6.7 Consensus size: 50
32156 TATTGATGAA
* * ** * *
32166 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATCAATGA-TAG-T
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-T-AA-AACTTGAT
* * * * * *
32217 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTCG-T
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TT-GAT
* * *** *
32268 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
* * * * *
32319 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
* *
32370 CACATGTGTAGTACTATGTGAAGGGTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
32420 CACGTGTGTAG-ACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
32469 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
32503 TATCGAATGA
Statistics
Matches: 239, Mismatches: 36, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
48 1 0.00
49 52 0.22
50 38 0.16
51 141 0.59
52 6 0.03
53 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:33867 original size:48 final size:48
Alignment explanation
Indices: 33794--33893 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
33784 CACTTCTTAC
*
33794 TTTGTTTCGATGATGAATACGGGTAAAAGGTGTTACACACCAAGTCTG
1 TTTGTTTCGATGATGAATACAGGTAAAAGGTGTTACACACCAAGTCTG
*
33842 TTTGTTTCGATGATGAATACAGGTAAGAGGTGTTACACACCAAGTCTG
1 TTTGTTTCGATGATGAATACAGGTAAAAGGTGTTACACACCAAGTCTG
33890 TTTG
1 TTTG
33894 AAGTAGTTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (48 bp):
TTTGTTTCGATGATGAATACAGGTAAAAGGTGTTACACACCAAGTCTG
Done.