Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1018
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: 3327
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.30
Warning! 307 characters in sequence are not A, C, G, or T
Found at i:184 original size:8 final size:8
Alignment explanation
Indices: 161--190 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
151 TGGCCTCTCC
161 TTTTTCTT
1 TTTTTCTT
169 TTTGTTCTT
1 TTT-TTCTT
178 TTTTTCTT
1 TTTTTCTT
186 TTTTT
1 TTTTT
191 TGTTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTCTT
Found at i:627 original size:1 final size:1
Alignment explanation
Indices: 621--738 Score: 65
Period size: 1 Copynumber: 118.0 Consensus size: 1
611 CCGGTAGAGG
* * * * * * * * * **
621 TTTTTTTCTTATTTTTTATTTTTTATTTTTTGTTTTTTTTCTTTTGTTTTCTCTTTTTTTTTGCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * ** *
686 TCTTTTTTTTACTTTTTTTGTTTTTTTGTTTTTTACTTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
739 GTTCTTTTGC
Statistics
Matches: 82, Mismatches: 35, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.05, C:0.07, G:0.04, T:0.84
Consensus pattern (1 bp):
T
Found at i:670 original size:26 final size:25
Alignment explanation
Indices: 641--741 Score: 84
Period size: 26 Copynumber: 4.1 Consensus size: 25
631 ATTTTTTATT
641 TTTTATTTTTTGTTTTTTTTCTTTTG
1 TTTTATTTTTT-TTTTTTTTCTTTTG
* **
667 TTTTCTCTTTTTTTTTGCTTCTTTT-
1 TTTTAT-TTTTTTTTTTTTTCTTTTG
* *
692 TTTTACTTTTTTTGTTTTTT-TGTT-
1 TTTTA-TTTTTTTTTTTTTTCTTTTG
* *
716 TTTTACTTTTTTTTTATTT-TTTTG
1 TTTTATTTTTTTTTTTTTTCTTTTG
740 TT
1 TT
742 CTTTTGCCTC
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
23 14 0.23
24 10 0.17
25 14 0.23
26 17 0.28
27 5 0.08
ACGTcount: A:0.04, C:0.07, G:0.06, T:0.83
Consensus pattern (25 bp):
TTTTATTTTTTTTTTTTTTCTTTTG
Found at i:710 original size:59 final size:58
Alignment explanation
Indices: 626--738 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 58
616 AGAGGTTTTT
*
626 TTCTTATTTTTTATTTTTTATTTTTTGTT-TTTTTT-CTTTTGTTTTCTCTTTTTTTTTGC
1 TTCTTATTTTTTATTTTTTATTTTTT-TTGTTTTTTACTTTT-TTTT-TATTTTTTTTTGC
685 TTCTT-TTTTTTACTTTTTT-TGTTTTTTTGTTTTTTACTTTTTTTTTATTTTTTT
1 TTCTTATTTTTTA-TTTTTTAT-TTTTTTTGTTTTTTACTTTTTTTTTATTTTTTT
739 GTTCTTTTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
58 18 0.37
59 26 0.53
60 5 0.10
ACGTcount: A:0.05, C:0.07, G:0.04, T:0.83
Consensus pattern (58 bp):
TTCTTATTTTTTATTTTTTATTTTTTTTGTTTTTTACTTTTTTTTTATTTTTTTTTGC
Found at i:712 original size:34 final size:32
Alignment explanation
Indices: 632--746 Score: 101
Period size: 35 Copynumber: 3.4 Consensus size: 32
622 TTTTTTCTTA
* * *
632 TTTTTTATTTTTTATTTTTTGTTTTTTTT-CT
1 TTTTTTGTTTTTTTTTTTTTCTTTTTTTTACT
663 TTTGTTT-TCTCTTTTTTTTTGCTTCTTTTTTTTACT
1 TTT-TTTGT-T-TTTTTTTTT--TTCTTTTTTTTACT
699 TTTTTTGTTTTTTTGTTTTTTACTTTTTTTTTA-T
1 TTTTTTGTTTTTTT-TTTTTT-C-TTTTTTTTACT
*
733 TTTTTTGTTCTTTT
1 TTTTTTGTTTTTTT
747 GCCTCCATTG
Statistics
Matches: 71, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
31 4 0.06
32 4 0.06
33 10 0.14
34 20 0.28
35 27 0.38
36 6 0.08
ACGTcount: A:0.04, C:0.07, G:0.05, T:0.83
Consensus pattern (32 bp):
TTTTTTGTTTTTTTTTTTTTCTTTTTTTTACT
Done.