Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1525
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: 38751
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:2392 original size:19 final size:19
Alignment explanation
Indices: 2359--2408 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2349 TTAGTAAAAA
2359 TAAAA-TATAAAAAAACA-T
1 TAAAATTATAAAAAAA-ATT
*
2377 TAAAATTATTAAAAAAATT
1 TAAAATTATAAAAAAAATT
2396 TAAAATTTATAAA
1 TAAAA-TTATAAA
2409 CTTACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.22
19 15 0.56
20 6 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATTATAAAAAAAATT
Found at i:3464 original size:22 final size:22
Alignment explanation
Indices: 3437--3487 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
3427 ATGGTTTTAA
*
3437 GGTTAATTAATTAATCAAATT-T
1 GGTTAATTAAATAAT-AAATTAT
*
3459 GTTTAATTAAATAATAAATTAT
1 GGTTAATTAAATAATAAATTAT
3481 GGTTAAT
1 GGTTAAT
3488 GAAGCTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (22 bp):
GGTTAATTAAATAATAAATTAT
Found at i:16541 original size:18 final size:18
Alignment explanation
Indices: 16510--16560 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
16500 TCTATTATAA
16510 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
16528 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
*
16546 TATTATTTAATAAAA
1 TATTAATTAATAAAA
16561 AAATTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:17648 original size:42 final size:42
Alignment explanation
Indices: 17598--17692 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
17588 CTTTGATTAG
* * *
17598 CCGATGATGCACTTATGTGCTAGTATATTTACTTCGATTTAT
1 CCGATGATGCACTTATATGCTAGTATAATTACTTCGATATAT
** *
17640 CTTATGATGCACTTATATGCTAGTATAATTGCTTCGATATAT
1 CCGATGATGCACTTATATGCTAGTATAATTACTTCGATATAT
17682 CCGATGATGCA
1 CCGATGATGCA
17693 TATATGTTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (42 bp):
CCGATGATGCACTTATATGCTAGTATAATTACTTCGATATAT
Found at i:17714 original size:42 final size:42
Alignment explanation
Indices: 17598--17715 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 42
17588 CTTTGATTAG
* *
17598 CCGATGATGCACT-TATGTGCTAGTATATTTACTTCGATTTAT
1 CCGATGATGCACTATATGT-CTAGTATATTTGCTTCGATATAT
** *
17640 CTTATGATGCACTTATATG-CTAGTATAATTGCTTCGATATAT
1 CCGATGATGCAC-TATATGTCTAGTATATTTGCTTCGATATAT
* *
17682 CCGATGATGCA-TATATGTTCCAATATATTTGCTT
1 CCGATGATGCACTATATG-TCTAGTATATTTGCTT
17716 TAGTTTATCT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
40 6 0.10
42 51 0.82
43 1 0.02
44 4 0.06
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.42
Consensus pattern (42 bp):
CCGATGATGCACTATATGTCTAGTATATTTGCTTCGATATAT
Found at i:19268 original size:41 final size:41
Alignment explanation
Indices: 19216--19375 Score: 171
Period size: 41 Copynumber: 4.0 Consensus size: 41
19206 GTAAGGCATA
* *
19216 AAGCCTAATATAATACACCGGCACAGAGCCTGTTAGGCAAT
1 AAGCCTAATATAATACACCGGCACAAAGCCTGATAGGCAAT
* * *
19257 AAGCCTGATATAATACATCGGCACAAAGGCTGATAGGCAAT
1 AAGCCTAATATAATACACCGGCACAAAGCCTGATAGGCAAT
* * ** * *
19298 AGGCCTGATATTTTACACCGGCACAAAGCTTGCTAGGCAAT
1 AAGCCTAATATAATACACCGGCACAAAGCCTGATAGGCAAT
* * * *
19339 AGGCCTAATATTATACACC-G-ACACAGCCTGCTAGGCA
1 AAGCCTAATATAATACACCGGCACAAAGCCTGATAGGCA
19376 TAAAGCCCGA
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 15 0.15
40 1 0.01
41 87 0.84
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (41 bp):
AAGCCTAATATAATACACCGGCACAAAGCCTGATAGGCAAT
Found at i:20768 original size:42 final size:42
Alignment explanation
Indices: 20670--20798 Score: 159
Period size: 42 Copynumber: 3.1 Consensus size: 42
20660 TATATACCAA
* * * *
20670 TATAATTGCTTCGGCATATCCAATGACGCACTTATGTGTCAG
1 TATATTTGCTTCAGTATATCCAATGATGCACTTATGTGTCAG
*
20712 CATATTTGCTTCAGTATATCCAATGATGCACTTATGTGTCAG
1 TATATTTGCTTCAGTATATCCAATGATGCACTTATGTGTCAG
* * * * **
20754 TATATTTGCTTCAGTACATTCGATAATGCACTTACATGTCAG
1 TATATTTGCTTCAGTATATCCAATGATGCACTTATGTGTCAG
20796 TAT
1 TAT
20799 GATTACTTCG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (42 bp):
TATATTTGCTTCAGTATATCCAATGATGCACTTATGTGTCAG
Found at i:23803 original size:32 final size:32
Alignment explanation
Indices: 23767--23827 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
23757 GTAAAGTGAA
23767 AATTGTTAGTTTTGAACTTAGGGACTAAAATG
1 AATTGTTAGTTTTGAACTTAGGGACTAAAATG
23799 AATTGTTAGTTTTGAACTTAGGGACTAAA
1 AATTGTTAGTTTTGAACTTAGGGACTAAA
23828 GTGTATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (32 bp):
AATTGTTAGTTTTGAACTTAGGGACTAAAATG
Found at i:34396 original size:30 final size:29
Alignment explanation
Indices: 34350--34408 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
34340 TTCCCGAGCC
*
34350 TAGGGGAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAATGTAATTATGCAAAAGTT
* *
34379 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGG-AAAAATGTAATTATGCAAAAGTT
34409 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (29 bp):
TAGGGGAAAAATGTAATTATGCAAAAGTT
Done.