Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1995
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: 24249
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:9317 original size:30 final size:30
Alignment explanation
Indices: 9283--9379 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
9273 TAAACTAAAA
9283 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
9313 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
9343 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
9372 ATGAGCTA
1 -TGAGCTA
9380 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:11602 original size:5 final size:5
Alignment explanation
Indices: 11592--11664 Score: 53
Period size: 5 Copynumber: 14.0 Consensus size: 5
11582 CTCTTGCCTC
* *
11592 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTCTT GCTTTT TCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCT-TT TC-TTT TC-TTT
11640 TCTTT TCTTT TCTTT T-TTT CTCTTT
1 TCTTT TCTTT TCTTT TCTTT -TCTTT
11665 ACAAGAATGT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
4 7 0.12
5 29 0.52
6 18 0.32
7 2 0.04
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:11621 original size:6 final size:6
Alignment explanation
Indices: 11605--11656 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
11595 TTTCTTTTTA
*
11605 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
11654 TTT
1 TTT
11657 TTCTCTTTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 10 0.24
6 22 0.54
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:11651 original size:37 final size:36
Alignment explanation
Indices: 11594--11663 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
11584 CTTGCCTCTC
11594 TTTTCTTTTTATTTCATTTTCTTTTTCTTCTCTTGCT
1 TTTTCTTTTTATTTCATTTTCTTTTT-TTCTCTTGCT
*
11631 TTTTCTTTTTCTTTTC-TTTTCTTTTTTTCTCTT
1 TTTTCTTTTT-ATTTCATTTTCTTTTTTTCTCTT
11664 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 7 0.23
37 20 0.65
38 4 0.13
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (36 bp):
TTTTCTTTTTATTTCATTTTCTTTTTTTCTCTTGCT
Found at i:12535 original size:10 final size:10
Alignment explanation
Indices: 12520--12560 Score: 64
Period size: 10 Copynumber: 3.9 Consensus size: 10
12510 ATATACTTCG
12520 ATTTTTTTTA
1 ATTTTTTTTA
12530 ATTTTTTTTCA
1 ATTTTTTTT-A
12541 ATTTTTTTTTA
1 A-TTTTTTTTA
12552 ATTTTTTTT
1 ATTTTTTTT
12561 TTCGAATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.59
11 4 0.14
12 8 0.28
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:12537 original size:11 final size:11
Alignment explanation
Indices: 12521--12561 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
12511 TATACTTCGA
12521 TTTTTTTTAAT
1 TTTTTTTTAAT
*
12532 TTTTTTTCAAT
1 TTTTTTTTAAT
12543 TTTTTTTTAAT
1 TTTTTTTTAAT
12554 TTTTTTTT
1 TTTTTTTT
12562 TCGAATTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:14296 original size:30 final size:30
Alignment explanation
Indices: 14262--14358 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
14252 AAAACTAAAA
14262 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
14292 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
14322 TGAGCTAAGCTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
14351 ATGAGCTA
1 -TGAGCTA
14359 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:17335 original size:21 final size:23
Alignment explanation
Indices: 17290--17336 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
17280 TCACCTGCAA
* *
17290 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
17313 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
17334 TAA
1 TAA
17337 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Done.