Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2519
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: 17509
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:1797 original size:20 final size:19
Alignment explanation
Indices: 1772--1834 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
1762 GAAAATTCAA
*
1772 TTCTTTATTTTCTTTTTGTT
1 TTCTTTATTGTCTTTTT-TT
1792 TTCTTTA-TGTCTTTTTCTTT
1 TTCTTTATTGTC-TTTT-TTT
*
1812 TTCTTT-TTGCCTTTTTTT
1 TTCTTTATTGTCTTTTTTT
1830 TTCTT
1 TTCTT
1835 CTTGTTCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 8 0.21
19 7 0.18
20 22 0.58
21 1 0.03
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (19 bp):
TTCTTTATTGTCTTTTTTT
Found at i:1812 original size:5 final size:6
Alignment explanation
Indices: 1779--1834 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
1769 CAATTCTTTA
* *
1779 TTTTCT TTTT-G TTTTCT TTATGTCT TTTTCT TTTTCT TTTTGCC TTTT-T
1 TTTTCT TTTTCT TTTTCT TT-T-TCT TTTTCT TTTTCT TTTT-CT TTTTCT
1828 TTTTCT T
1 TTTTCT T
1835 CTTGTTCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 8 0.20
6 21 0.51
7 7 0.17
8 5 0.12
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:3037 original size:220 final size:219
Alignment explanation
Indices: 2614--3037 Score: 500
Period size: 220 Copynumber: 1.9 Consensus size: 219
2604 TATTACTTTG
* * * *
2614 AAAATACGTTTTGTTTATTGAGAAAATAACTTTATTAGTATTAGATTAATCAAATTAGTATCTAT
1 AAAATACATTTTGTTTATTAAGAAAATAACTTTATTAGCATTAGATTAATCAAATTAATATCTAT
* * * * * * *
2679 TTAAGTTTACGTTAAATATTAAAAGTATAATCATTTATTATTTATATGTTTTTTTGTTTTGATCA
66 TTAAATATACGTTAAATATTAAAAATATAATCATTTATAATTTAAATGTTTATTTGTTTAGATCA
* * ** *
2744 ATTTTTTTATTGTTAAAGTTTTTTAAATGATGAGATTTAGTTATAAGAAAAATAACATAATATAT
131 ATTTATTTATTATTAAAGTTTTTTAAACAATGAGATTTAGTTATAAGAAAAATAACACAATATAT
2809 AAATCAATGTACATAATTAAATTA
196 AAATCAATGTACATAATTAAATTA
* * * *
2833 AAAATCACATTTTGTTTATTAAGAAAGTAACTTTGTTAGCATTA-AGTTAATCGAATTAATATTT
1 AAAAT-ACATTTTGTTTATTAAGAAAATAACTTTATTAGCATTAGA-TTAATCAAATTAATATCT
*
2897 ATTTAAATATACTTTAAATATTAAAAATATAATCATTTATAATTTTAAACT-TTTCATTT-TTTA
64 ATTTAAATATACGTTAAATATTAAAAATATAATCATTTATAA-TTTAAA-TGTTT-ATTTGTTTA
** * * **
2960 G-TCAATTTATTTATTATTAATTTTTTTTAAACAATGAGATTTATTTTTAA-TTAAA-AACACAA
126 GATCAATTTATTTATTATTAAAGTTTTTTAAACAATGAGATTTAGTTATAAGAAAAATAACACAA
3022 TATATTAATATCAATG
191 TATA-TAA-ATCAATG
3038 GTAGAAGATA
Statistics
Matches: 171, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
218 10 0.06
219 12 0.07
220 133 0.78
221 12 0.07
222 4 0.02
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (219 bp):
AAAATACATTTTGTTTATTAAGAAAATAACTTTATTAGCATTAGATTAATCAAATTAATATCTAT
TTAAATATACGTTAAATATTAAAAATATAATCATTTATAATTTAAATGTTTATTTGTTTAGATCA
ATTTATTTATTATTAAAGTTTTTTAAACAATGAGATTTAGTTATAAGAAAAATAACACAATATAT
AAATCAATGTACATAATTAAATTA
Found at i:9031 original size:59 final size:59
Alignment explanation
Indices: 8939--9059 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
8929 AAAAAAATTA
*
8939 CATGGCTTAAGAGGTAATTTACTTAAAAAAGAACAATCTGTACATTTATGTTCTTTTTT
1 CATGGCTTAAGAGGTAATTTACTCAAAAAAGAACAATCTGTACATTTATGTTCTTTTTT
8998 CATGGCTTAAGAGGTAATTTACTCAAAAAAGAACAATCTGTACATTTATGTTCTTTTTT
1 CATGGCTTAAGAGGTAATTTACTCAAAAAAGAACAATCTGTACATTTATGTTCTTTTTT
9057 CAT
1 CAT
9060 TTTTAACCTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (59 bp):
CATGGCTTAAGAGGTAATTTACTCAAAAAAGAACAATCTGTACATTTATGTTCTTTTTT
Found at i:10567 original size:15 final size:18
Alignment explanation
Indices: 10529--10568 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
10519 ATAATTATTA
10529 AAAATTATTTATAATGAT
1 AAAATTATTTATAATGAT
*
10547 ATAATT-TTT-TAAT-AT
1 AAAATTATTTATAATGAT
10562 AAAATTA
1 AAAATTA
10569 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
15 7 0.37
16 4 0.21
17 3 0.16
18 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAATTATTTATAATGAT
Found at i:11581 original size:13 final size:13
Alignment explanation
Indices: 11563--11588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11553 CAATTCAGAG
11563 AACCGGACAACTA
1 AACCGGACAACTA
11576 AACCGGACAACTA
1 AACCGGACAACTA
11589 CGCCATGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (13 bp):
AACCGGACAACTA
Done.