Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold387
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: 37367
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:13454 original size:18 final size:18
Alignment explanation
Indices: 13431--13467 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13421 TAAAATTACT
13431 TAACTCATAAGTGATGTG
1 TAACTCATAAGTGATGTG
13449 TAACTCATAAGTGATGTG
1 TAACTCATAAGTGATGTG
13467 T
1 T
13468 CCCAACGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (18 bp):
TAACTCATAAGTGATGTG
Found at i:21879 original size:3 final size:3
Alignment explanation
Indices: 21871--21924 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
21861 AAGGGCTCAA
* * * *
21871 ATT ATT ATT ATC ATT ATC ATT ACT ATT ATT ATT AAAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
21917 ATT ATT AT
1 ATT ATT AT
21925 CTTTTTTTAC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:22408 original size:148 final size:149
Alignment explanation
Indices: 22248--22562 Score: 394
Period size: 148 Copynumber: 2.1 Consensus size: 149
22238 GATCTTGGGA
*
22248 ATTTTTTTAAAAAAAGGGAAAGTTTAGATTTTAAAAATAAAAAAAAAATAT-TTTTTTAGTCA-T
1 ATTTTTTTAAAAAAAGAGAAAGTTTAGATTTT-----TAAAAAAAAAATATGTTTTTTAGTCAGT
* *
22311 TTCAAAGG-AAATTTTAAA-ATTTTAAAACAAAGTTATGAT-TTTTTTAACTATTTCGAAATAAA
61 TT-AAAGGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAA
22373 AGCTTTGA-TTTTAAA-AAAATAAT-
125 A-CTTTGATTTTTAAAGAAAATAATG
* * *
22396 ATTTTTTTAAAAAAAAAGAGAAAGTTTAGATTTTTGAAATAAAAATATGTTTTTTAGTCAGTTTT
1 ATTTTTTT--AAAAAAAGAGAAAGTTTAGATTTTTAAAAAAAAAATATGTTTTTTAGTCAGTTTA
* *
22461 AAGGAAAAATTTAAATTTTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAACTT
64 AAGGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTT
* *
22526 TGATTTTTAAAGAAAGTAGTG
129 TGATTTTTAAAGAAAATAATG
22547 ATTTTTTTAAAGAAAA
1 ATTTTTTTAAA-AAAA
22563 CTTTGATTCT
Statistics
Matches: 146, Mismatches: 10, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
145 12 0.08
146 15 0.10
147 12 0.08
148 33 0.23
149 33 0.23
150 33 0.23
151 8 0.05
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (149 bp):
ATTTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAAAAAAATATGTTTTTTAGTCAGTTTAAA
GGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTTTG
ATTTTTAAAGAAAATAATG
Found at i:22569 original size:21 final size:21
Alignment explanation
Indices: 22519--22570 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
22509 ATTTCGAAAT
22519 AAAACTTTGA--TTTTTAAAG
1 AAAACTTTGATTTTTTTAAAG
* *
22538 -AAAGTAGTGATTTTTTTAAAG
1 AAAACT-TTGATTTTTTTAAAG
22559 AAAACTTTGATT
1 AAAACTTTGATT
22571 CTACAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
21 14 0.56
22 4 0.16
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (21 bp):
AAAACTTTGATTTTTTTAAAG
Found at i:30579 original size:20 final size:20
Alignment explanation
Indices: 30522--30588 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
30512 GCAAGTTAAG
*
30522 ATGAGCTGAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
* * *** *
30542 ATAAGCTAAGGACAAGCTCA
1 ATGAGCTAAAGTTGAGCTGA
30562 ATGAGCTAAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
30582 ATGAGCT
1 ATGAGCT
30589 TGAAGTAGAG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.22
Consensus pattern (20 bp):
ATGAGCTAAAGTTGAGCTGA
Found at i:34718 original size:20 final size:20
Alignment explanation
Indices: 34661--34727 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
34651 GCAAGCTAAG
*
34661 ATGAGCTGAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
* * *** *
34681 ATAAGCTAAGGACAAGCTCA
1 ATGAGCTAAAGTTGAGCTGA
34701 ATGAGCTAAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
34721 ATGAGCT
1 ATGAGCT
34728 TGAAGTAGAG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.22
Consensus pattern (20 bp):
ATGAGCTAAAGTTGAGCTGA
Done.