Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1798
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: 17168
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Found at i:4015 original size:6 final size:6
Alignment explanation
Indices: 4004--4029 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3994 TCCCATTATT
4004 ATTCAA ATTCAA ATTCAA ATTCAA AT
1 ATTCAA ATTCAA ATTCAA ATTCAA AT
4030 CAAGTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTCAA
Found at i:5845 original size:23 final size:25
Alignment explanation
Indices: 5793--5847 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
5783 ATGTAAATAT
5793 TAATTAAAATTTTAAATATATTTTA
1 TAATTAAAATTTTAAATATATTTTA
* *
5818 T-ATTAATA-TTTATATA-ATTTTA
1 TAATTAAAATTTTAAATATATTTTA
5840 TAATTAAA
1 TAATTAAA
5848 TTAATACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.27
23 12 0.46
24 6 0.23
25 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TAATTAAAATTTTAAATATATTTTA
Found at i:5859 original size:22 final size:21
Alignment explanation
Indices: 5807--5870 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
5797 TAAAATTTTA
5807 AATATATTTTATATTAATATT
1 AATATATTTTATATTAATATT
*
5828 TATATAATTTTATAATTAA-ATT
1 AATAT-ATTTTAT-ATTAATATT
*
5850 AATACTATTTAAATATTAATA
1 AATA-TATTT-TATATTAATA
5871 AAAATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.11
22 22 0.63
23 9 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATATTTTATATTAATATT
Found at i:6294 original size:18 final size:18
Alignment explanation
Indices: 6271--6310 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
6261 ATTTTTAAAA
6271 AATT-AATTATAAAATTTT
1 AATTAAATTATAAAA-TTT
*
6289 AATTAAATTATTAAATTT
1 AATTAAATTATAAAATTT
6307 AATT
1 AATT
6311 TCATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTAAATTATAAAATTT
Found at i:12217 original size:32 final size:32
Alignment explanation
Indices: 12171--12252 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
12161 TTAATTGGAA
12171 AAAAAAAAACAGAAAGAAAGAGGGAAAA-G-AAAG
1 AAAAAAAAA-AGAAA-AAA-AGGGAAAAGGAAAAG
*
12204 AAAAAAAAAAGAAAAAAATGGAAAATGGAAAAG
1 AAAAAAAAAAGAAAAAAAGGGAAAA-GGAAAAG
*
12237 AAAAGAAAAAGAAAAA
1 AAAAAAAAAAGAAAAA
12253 TGGAAAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
30 7 0.16
31 3 0.07
32 6 0.14
33 28 0.64
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.02
Consensus pattern (32 bp):
AAAAAAAAAAGAAAAAAAGGGAAAAGGAAAAG
Found at i:15793 original size:2 final size:2
Alignment explanation
Indices: 15786--15820 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
15776 CTTGGAATTC
* *
15786 TA TA TA TA TA TA TC TA TA TA TA TA TC TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15821 GCTTTTAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15805 original size:12 final size:12
Alignment explanation
Indices: 15788--15820 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
15778 TGGAATTCTA
15788 TATATATATATC
1 TATATATATATC
15800 TATATATATATC
1 TATATATATATC
15812 TATATATAT
1 TATATATAT
15821 GCTTTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATATATC
Found at i:16727 original size:22 final size:22
Alignment explanation
Indices: 16684--16729 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
16674 GCAGGCTTCA
*
16684 AAAAAAATTATTAAAATTTTTT
1 AAAAAAATTATTAAAATATTTT
* **
16706 AAAAAATTTATTTTAATATTTT
1 AAAAAAATTATTAAAATATTTT
16728 AA
1 AA
16730 TATCTTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAAAAATTATTAAAATATTTT
Done.