Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2297
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: 12166
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:4967 original size:21 final size:21
Alignment explanation
Indices: 4949--5008 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
4939 TATTAAAAGT
* *
4949 TGCATTTTTTTATCCAAAAAA
1 TGCATTCTTTCATCCAAAAAA
**
4970 TGCATTCTTTCATCCAATCAA
1 TGCATTCTTTCATCCAAAAAA
4991 TGCA-TCATTTCATCCAAA
1 TGCATTC-TTTCATCCAAA
5009 GATACTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (21 bp):
TGCATTCTTTCATCCAAAAAA
Found at i:8345 original size:21 final size:21
Alignment explanation
Indices: 8321--8365 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8311 TTAAAAGTTA
8321 CATT-TTTTCATCCAAAAAATG
1 CATTCTTTT-ATCCAAAAAATG
**
8342 CATTCTTTTATCCAATCAATG
1 CATTCTTTTATCCAAAAAATG
8363 CAT
1 CAT
8366 CATTTCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (21 bp):
CATTCTTTTATCCAAAAAATG
Found at i:8626 original size:3 final size:3
Alignment explanation
Indices: 8618--8681 Score: 119
Period size: 3 Copynumber: 21.0 Consensus size: 3
8608 GGATTAACAC
8618 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8666 ATA ATA ATAA ATA ATA
1 ATA ATA AT-A ATA ATA
8682 TTAGACACAA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8706 original size:31 final size:32
Alignment explanation
Indices: 8664--8723 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
8654 ATAATAATAA
*
8664 TAATAATAATAAATAATAT-TAGACACAATTAC
1 TAATAATAATAAATAAAATATA-ACACAATTAC
*
8696 TAATAA-AATAATTAAAATATAACACAAT
1 TAATAATAATAAATAAAATATAACACAAT
8724 ATGAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (32 bp):
TAATAATAATAAATAAAATATAACACAATTAC
Found at i:9232 original size:2 final size:2
Alignment explanation
Indices: 9227--9261 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9217 TACATAACAA
9227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9262 CACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9500 original size:15 final size:14
Alignment explanation
Indices: 9464--9511 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
9454 TAATTTTTCT
9464 AATTTATTTTTT-A
1 AATTTATTTTTTAA
*
9477 AATATATTTTTTAA
1 AATTTATTTTTTAA
*
9491 AATTTAATTTTTAA
1 AATTTATTTTTTAA
9505 TAATTTA
1 -AATTTA
9512 ATAATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 11 0.37
14 13 0.43
15 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTATTTTTTAA
Found at i:9501 original size:14 final size:14
Alignment explanation
Indices: 9453--9513 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
9443 TCATTTCATA
**
9453 TTAATTTTTCTAAT
1 TTAATTTTTAAAAT
*
9467 TT-ATTTTTTAAAT
1 TTAATTTTTAAAAT
* *
9480 ATATTTTTTAAAAT
1 TTAATTTTTAAAAT
9494 TTAATTTTTAATAAT
1 TTAATTTTTAA-AAT
9509 TTAAT
1 TTAAT
9514 AATTTAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.26
14 20 0.53
15 8 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATTTTTAAAAT
Found at i:9513 original size:8 final size:8
Alignment explanation
Indices: 9486--9526 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
9476 AAATATATTT
9486 TTTAA-AA
1 TTTAATAA
*
9493 TTTAAT-T
1 TTTAATAA
9500 TTTAATAA
1 TTTAATAA
9508 TTTAATAA
1 TTTAATAA
9516 TTTAATAA
1 TTTAATAA
9524 TTT
1 TTT
9527 TCTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 11 0.37
8 19 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTAATAA
Found at i:9998 original size:22 final size:21
Alignment explanation
Indices: 9960--10001 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
9950 AAATTTTATT
9960 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
9981 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
10001 T
1 T
10002 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:10053 original size:90 final size:89
Alignment explanation
Indices: 9947--10114 Score: 293
Period size: 90 Copynumber: 1.9 Consensus size: 89
9937 ATTCTTCAAA
9947 TAAAAATTTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAAAT-ATTTTTTTAAT
1 TAAAAATTTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAAATAATTTTTTT-AT
*
10011 ATTTTAAACTTTTAAAAGAGACTTG
65 AGTTTAAACTTTTAAAAGAGACTTG
*
10036 TAAAAATTTTTATTTAAATTTTATTATAAAATATATAAATATTAATATAAAAATAATTTTTTTAT
1 TAAAAA-TTTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAAATAATTTTTTTAT
10101 AGTTTAAACTTTTA
65 AGTTTAAACTTTTA
10115 GGATTGGCTT
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
89 6 0.08
90 61 0.81
91 8 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (89 bp):
TAAAAATTTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAAATAATTTTTTTATA
GTTTAAACTTTTAAAAGAGACTTG
Found at i:11797 original size:15 final size:16
Alignment explanation
Indices: 11771--11800 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11761 TTCTTTTTTG
11771 TTTCTTTCTTTCCTTA
1 TTTCTTTCTTTCCTTA
11787 TTTCTTT-TTTCCTT
1 TTTCTTTCTTTCCTT
11801 CCTCCCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCTTTCTTTCCTTA
Done.