Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold587
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: 26253
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.32
Warning! 1855 characters in sequence are not A, C, G, or T
Found at i:9780 original size:14 final size:14
Alignment explanation
Indices: 9761--9810 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
9751 TCTTTTGAAG
*
9761 TTATAAATTATAGC
1 TTATAAATTATAGA
*
9775 TTATAATTTATAGA
1 TTATAAATTATAGA
* *
9789 TTATAAAAATATAAA
1 TTAT-AAATTATAGA
9804 TTATAAA
1 TTATAAA
9811 AATATATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (14 bp):
TTATAAATTATAGA
Found at i:9806 original size:15 final size:15
Alignment explanation
Indices: 9783--9823 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
9773 GCTTATAATT
*
9783 TATAGATTATAAAAA
1 TATAAATTATAAAAA
9798 TATAAATTATAAAAA
1 TATAAATTATAAAAA
*
9813 TATATATTATA
1 TATAAATTATA
9824 CTAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TATAAATTATAAAAA
Found at i:11287 original size:42 final size:42
Alignment explanation
Indices: 11223--11306 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
11213 GGTTGATGGG
11223 CATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTT
1 CATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTT
*
11265 CATTTCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTT
1 CATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTT
11307 GACGCAATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.30
Consensus pattern (42 bp):
CATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTT
Found at i:11398 original size:105 final size:105
Alignment explanation
Indices: 11265--11554 Score: 427
Period size: 105 Copynumber: 2.8 Consensus size: 105
11255 GGATATTGTT
*
11265 CATTTCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTTGACGCAATGATAAAGCGAGGCAT
1 CATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTTGACGCAATGATAAAGCGAGGCAT
* *
11330 TGGGCCTAATGTTGTCACATATAACACATTGGTTGATGCG
66 TGAGCCTAATGTTGTCACATATAACACATTGGTTGATGCA
* * *
11370 TATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTTGATGCAATGATAAAACGAGGCAT
1 CATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTTGACGCAATGATAAAGCGAGGCAT
* * *
11435 TGAGCCTGATGTTGTCACGTATAATACATTGGTTGATGCA
66 TGAGCCTAATGTTGTCACATATAACACATTGGTTGATGCA
* * * * ** * *
11475 CATTGCAAGCAAGGGATGGTTTTTAAAGCTGAGGATATCATTGACGCGATGATAAAGTGAGGCAT
1 CATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTTGACGCAATGATAAAGCGAGGCAT
11540 TGAGCCTAATGTTGT
66 TGAGCCTAATGTTGT
11555 TACCTATAGT
Statistics
Matches: 164, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 164 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (105 bp):
CATTGCAAGGAAGGGATGGTCTCTGAAGCTGAGGATATTGTTGACGCAATGATAAAGCGAGGCAT
TGAGCCTAATGTTGTCACATATAACACATTGGTTGATGCA
Found at i:16007 original size:16 final size:15
Alignment explanation
Indices: 15982--16011 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
15972 GACTAGAGTT
15982 AAGAAAGAAAAAAAA
1 AAGAAAGAAAAAAAA
15997 AAGAGAAGAAAAAAA
1 AAGA-AAGAAAAAAA
16012 GGGACAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAAAAAAA
Found at i:18419 original size:3 final size:3
Alignment explanation
Indices: 18411--18443 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
18401 GGCTGTTACA
18411 CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT -TT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
18444 GTTGCCCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:19087 original size:5 final size:5
Alignment explanation
Indices: 19073--19109 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
19063 TAAAATTATA
* *
19073 GTATA GTATC ATATC GTATC GTATC GTATC GTATC GT
1 GTATC GTATC GTATC GTATC GTATC GTATC GTATC GT
19110 GCTTTCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (5 bp):
GTATC
Found at i:19873 original size:5 final size:5
Alignment explanation
Indices: 19863--19895 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
19853 CTATTTTCAA
19863 AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
19896 CCCTAATCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:19888 original size:9 final size:9
Alignment explanation
Indices: 19864--19894 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
19854 TATTTTCAAA
19864 AAAGAAAAG
1 AAAGAAAAG
19873 AAAAGAAAAG
1 -AAAGAAAAG
19883 AAAGAAAAG
1 AAAGAAAAG
19892 AAA
1 AAA
19895 ACCCTAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:19888 original size:14 final size:15
Alignment explanation
Indices: 19863--19895 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
19853 CTATTTTCAA
19863 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
19878 AAAAG-AAAGAAAAG
1 AAAAGAAAAGAAAAG
19892 AAAA
1 AAAA
19896 CCCTAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:21451 original size:2 final size:2
Alignment explanation
Indices: 21444--21481 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
21434 TTTATGATTC
* *
21444 AT AT AT AT AC CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21482 GCCAGCAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25387 original size:123 final size:123
Alignment explanation
Indices: 25168--25420 Score: 407
Period size: 123 Copynumber: 2.1 Consensus size: 123
25158 GAAAATACAT
*
25168 TATAATATCATAATTGAATAATAATTACTATATATTCATATTTTACATATATATAACAATTGATA
1 TATAATTTCATAATTGAATAATAATTACTATATATTCATATTTTACATATATATAACAATTGATA
*
25233 TATTATATGTAGTTAAACATGTATGTATATATGTTTTTGTAATACAATATGTACTAAA
66 TATTATATGTAGTTAAACATGTATGTATATATGTTTTTATAATACAATATGTACTAAA
* * ** * * *
25291 TATAATTTTATAATTGTATAATAATTACTATATATTCATATTTTATGTATGTATAACAGTTGATG
1 TATAATTTCATAATTGAATAATAATTACTATATATTCATATTTTACATATATATAACAATTGATA
* *
25356 TATTATATGTAGTTAAACATGTATGTATATATGTTTTTATAATATAATTTGTACTAAA
66 TATTATATGTAGTTAAACATGTATGTATATATGTTTTTATAATACAATATGTACTAAA
25414 TATAATT
1 TATAATT
25421 ATATCCCATC
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (123 bp):
TATAATTTCATAATTGAATAATAATTACTATATATTCATATTTTACATATATATAACAATTGATA
TATTATATGTAGTTAAACATGTATGTATATATGTTTTTATAATACAATATGTACTAAA
Done.