Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1241
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: 178731
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:164980 original size:21 final size:21
Alignment explanation
Indices: 164956--165019 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
164946 ATTCACCAAA
164956 TGTTTTCTAGTTAAATATAAT
1 TGTTTTCTAGTTAAATATAAT
* *
164977 TGTTTTCAAGGCTTAAA-ATGAT
1 TGTTTTCTA-G-TTAAATATAAT
*
164999 TGATTTCTAAGTTAAAATATA
1 TGTTTTCT-AGTT-AAATATA
165020 TAAAGTATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 10 0.30
22 15 0.45
23 8 0.24
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (21 bp):
TGTTTTCTAGTTAAATATAAT
Found at i:165241 original size:32 final size:33
Alignment explanation
Indices: 165200--165262 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
165190 AGCCAAACTT
* **
165200 GTATCGATACACCAAGTA-TGTATCGATACAAG
1 GTATCGATACACAAAAAATTGTATCGATACAAG
165232 GTATCGATACACAAAAAATTGTATCGATACA
1 GTATCGATACACAAAAAATTGTATCGATACA
165263 TTGGCCTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.25
Consensus pattern (33 bp):
GTATCGATACACAAAAAATTGTATCGATACAAG
Found at i:168471 original size:41 final size:41
Alignment explanation
Indices: 168413--168516 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
168403 TAATATAAGA
* * *
168413 CCATTTTATATCGATACAATGTTGATTGTATCCATACAAGG
1 CCATATTATATCGATACAATGTTCATTGTATCCATACAAAG
* * * ** *
168454 CCATATTGTATCAATACAATGCTCATTGTATTGATGCAAAG
1 CCATATTATATCGATACAATGTTCATTGTATCCATACAAAG
*
168495 CCATATTATATCGATAAAATGT
1 CCATATTATATCGATACAATGT
168517 CATGTTTTCA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (41 bp):
CCATATTATATCGATACAATGTTCATTGTATCCATACAAAG
Found at i:168483 original size:20 final size:20
Alignment explanation
Indices: 168421--168484 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
168411 GACCATTTTA
* * *
168421 TATCGATACAATGTTGATTG
1 TATCAATACAATGCTCATTG
* *
168441 TATCCATACAAGGC-CATATTG
1 TATCAATACAATGCTC--ATTG
168462 TATCAATACAATGCTCATTG
1 TATCAATACAATGCTCATTG
168482 TAT
1 TAT
168485 TGATGCAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 18 0.51
21 16 0.46
22 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (20 bp):
TATCAATACAATGCTCATTG
Found at i:169940 original size:58 final size:56
Alignment explanation
Indices: 169843--170062 Score: 149
Period size: 58 Copynumber: 3.8 Consensus size: 56
169833 TCATAAATTT
* * * * **
169843 TAGTCATTTTTTATGTTTTAGCGACTTTTATACAATTTCATGCATTTTAAAACCAATC
1 TAGTTATTTTTCAT-TTTTAGGGACTATTATGTAATTTCATGCATTTT-AAACCAATC
* * * *** *
169901 TAGTTATTTTTCATTAGTTAGGGACTATTATGTAATTTCATTCATCTTAGGGCTA-C
1 TAGTTATTTTTCATT-TTTAGGGACTATTATGTAATTTCATGCATTTTAAACCAATC
* * * * * *
169957 TAAG-AATTTGTCATGTTTTAGGGACTTTTATGCAATTTCATGCATTTTGAAACCATTT
1 T-AGTTATTTTTCAT-TTTTAGGGACTATTATGTAATTTCATGCATTTT-AAACCAATC
* * *
170015 TAGTTA-TTTTCTATTTTTTGGGGACTACTATGTAATTTCATACATTTT
1 TAGTTATTTTTC-A-TTTTTAGGGACTATTATGTAATTTCATGCATTTT
170063 TAGGTCATTT
Statistics
Matches: 121, Mismatches: 33, Indels: 16
0.71 0.19 0.09
Matches are distributed among these distances:
56 37 0.31
57 15 0.12
58 68 0.56
59 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (56 bp):
TAGTTATTTTTCATTTTTAGGGACTATTATGTAATTTCATGCATTTTAAACCAATC
Found at i:170257 original size:28 final size:28
Alignment explanation
Indices: 170224--170277 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
170214 TATATAGGTT
170224 ATTTTCAT-AATCTAAGGACCATTTAGTA
1 ATTTTCATGAATCTAA-GACCATTTAGTA
* *
170252 ATTTTCATGATTTTAAGACCATTTAG
1 ATTTTCATGAATCTAAGACCATTTAG
170278 GATAATTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (28 bp):
ATTTTCATGAATCTAAGACCATTTAGTA
Found at i:178580 original size:6 final size:7
Alignment explanation
Indices: 178561--178592 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
178551 TATAGACAAG
178561 GCAAAAA
1 GCAAAAA
178568 GCAAAAA
1 GCAAAAA
178575 GCAAAAA
1 GCAAAAA
178582 GC-AAAA
1 GCAAAAA
178588 GCAAA
1 GCAAA
178593 GTAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.69, C:0.16, G:0.16, T:0.00
Consensus pattern (7 bp):
GCAAAAA
Found at i:178580 original size:14 final size:13
Alignment explanation
Indices: 178561--178592 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
178551 TATAGACAAG
178561 GCAAAAAGCAAAAA
1 GCAAAAAGC-AAAA
178575 GCAAAAAGCAAAA
1 GCAAAAAGCAAAA
178588 GCAAA
1 GCAAA
178593 GTAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.69, C:0.16, G:0.16, T:0.00
Consensus pattern (13 bp):
GCAAAAAGCAAAA
Done.