Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold525
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: 6687
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Found at i:1424 original size:18 final size:20
Alignment explanation
Indices: 1383--1425 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1373 AGTAAATTTC
1383 ATTATATAATATATTTTATT
1 ATTATATAATATATTTTATT
*
1403 -TTAT-TAATTTA-TTTATT
1 ATTATATAATATATTTTATT
1420 ATTATA
1 ATTATA
1426 AACTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
17 6 0.30
18 10 0.50
19 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTATATAATATATTTTATT
Found at i:4219 original size:232 final size:229
Alignment explanation
Indices: 3620--4307 Score: 1197
Period size: 232 Copynumber: 3.0 Consensus size: 229
3610 TTTAAATAAT
* *
3620 TACCTATAATTTA-TTATTAATAAAACTTATTGTTCCGTTGAAATAAATAAAATACATTATCAAA
1 TACCTATAATTGATTTATTAATAAAACTTATTATTCCGTTGAAATAAATAAAATACATTATCAAA
** *
3684 AAATAACAAAAAGTGATTATACTTAAAATAAAAGGAAGGGAAAACAAATGGAAAGCACTCATGTG
66 AAATAACAAAGGGTGATTATATTTAAAATAAAAGGAAGGGAAAACAAATGGAAAGCACTCATGTG
*
3749 GTTTCCTTTTAAAAGCACACTTCA-ATATGCCAATGTCAGTGAATAAAATTTTT-AATTTATTTG
131 GTTTCTTTTTAAAAGCACACTTCATATATGCCAATGTCAGTGAATAAAATTTTTAAATTTATTTG
3812 GAGTGTGTAAAATG-AAAAAGTAATTGTAAAAGA
196 GAGTGTGTAAAATGAAAAAAGTAATTGTAAAAGA
*
3845 T-CCTATAATTGATTTATTAATAAAATTTATTATTCCGTTGAAATAAATAAAATACATTATCAAA
1 TACCTATAATTGATTTATTAATAAAACTTATTATTCCGTTGAAATAAATAAAATACATTATC-AA
3909 AAAATAACAAAGGGTGATTATATTTAAAATAAAAGGAAGGGAAAACAAATGGAAAGCACTCATGT
65 AAAATAACAAAGGGTGATTATATTTAAAATAAAAGGAAGGGAAAACAAATGGAAAGCACTCATGT
* *
3974 GGTTTCTTTTTAAAAGCACACTTTATATATGCCAATGTCAGTAAATAAAATTTTTTAAATTTATT
130 GGTTTCTTTTTAAAAGCACACTTCATATATGCCAATGTCAGTGAATAAAA-TTTTTAAATTTATT
4039 TGGAGTGTGTAAAATGAAAAAAGTAATTGTAAAAGA
194 TGGAGTGTGTAAAATGAAAAAAGTAATTGTAAAAGA
*
4075 TACCTATAATTGATTTATTAATAAAACCTATTATTCCGTTGAAATAAATAAAAATACATTATCAA
1 TACCTATAATTGATTTATTAATAAAACTTATTATTCCGTTGAAATAAAT-AAAATACATTATCAA
4140 AAAATAACAAAGGGTGATTATATTTTAAAATAAAAGGAAGGGAAAACAAATGGAAAGCACTCATG
65 AAAATAACAAAGGGTGATTATA-TTTAAAATAAAAGGAAGGGAAAACAAATGGAAAGCACTCATG
4205 TGGTTTCTTTTTAAAAGCACACTTCATATATGCCAATGTCAGTGAATAAAAATTTTTAAATTTAT
129 TGGTTTCTTTTTAAAAGCACACTTCATATATGCCAATGTCAGTGAAT-AAAATTTTTAAATTTAT
4270 TTGGAGTGTGTAAAATGAAAAAAAGTAATTGTAAAAGA
193 TTGGAGTGTGTAAAATG-AAAAAAGTAATTGTAAAAGA
4308 AATAATAATA
Statistics
Matches: 439, Mismatches: 13, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
224 10 0.02
225 47 0.11
226 87 0.20
227 23 0.05
228 5 0.01
229 24 0.05
230 20 0.05
231 69 0.16
232 130 0.30
233 24 0.05
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (229 bp):
TACCTATAATTGATTTATTAATAAAACTTATTATTCCGTTGAAATAAATAAAATACATTATCAAA
AAATAACAAAGGGTGATTATATTTAAAATAAAAGGAAGGGAAAACAAATGGAAAGCACTCATGTG
GTTTCTTTTTAAAAGCACACTTCATATATGCCAATGTCAGTGAATAAAATTTTTAAATTTATTTG
GAGTGTGTAAAATGAAAAAAGTAATTGTAAAAGA
Found at i:5833 original size:14 final size:15
Alignment explanation
Indices: 5802--5834 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5792 GAAATAAATG
5802 AAAATACATTATCAA
1 AAAATACATTATCAA
5817 AAAATACATTATCAA
1 AAAATACATTATCAA
5832 AAA
1 AAA
5835 CTTAGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATACATTATCAA
Found at i:6575 original size:51 final size:52
Alignment explanation
Indices: 6445--6654 Score: 181
Period size: 51 Copynumber: 4.2 Consensus size: 52
6435 GAAAAGTGAT
* * * * * * * *
6445 AAAGATGCCAATATGTTGATTCACGGCCAACGATA-TGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* * *
6498 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
6551 AAAGGTGCCAA-ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
6593 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
6645 AAAGGTGCCA
1 AAAGGTGCCA
6655 CCGATTTGTG
Statistics
Matches: 126, Mismatches: 19, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
42 11 0.09
43 25 0.20
44 1 0.01
45 1 0.01
49 1 0.01
50 1 0.01
51 26 0.21
52 15 0.12
53 10 0.08
54 24 0.19
55 11 0.09
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:6616 original size:43 final size:42
Alignment explanation
Indices: 6551--6639 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 42
6541 TAAAGATGGA
*
6551 AAAGGTGCCAAATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAAATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
6593 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTT
1 AAAGGTGCCAA-ATGCTGATTCAAGGCCAGCTACATTGGACTT
6636 AAAG
1 AAAG
6640 ATGGAAAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 11 0.26
43 31 0.74
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (42 bp):
AAAGGTGCCAAATGCTGATTCAAGGCCAGCTACATTGGACTT
Done.