Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1902
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: 10836
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Found at i:2332 original size:27 final size:26
Alignment explanation
Indices: 2301--2477 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
2291 TAAATTGTAC
2301 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
2328 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
2354 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
2382 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
2410 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
2437 GGCACTAAGTGTGCGAGTTGA-TATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
2463 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2478 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
26 17 0.14
27 83 0.66
28 25 0.20
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:2417 original size:82 final size:81
Alignment explanation
Indices: 2302--2457 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
2292 AAATTGTACA
* * *
2302 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
2366 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2383 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
2448 TGCGAGTTGA
65 TGCGAATTGA
2458 TATATAGCAC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2425 original size:55 final size:53
Alignment explanation
Indices: 2301--2477 Score: 205
Period size: 55 Copynumber: 3.3 Consensus size: 53
2291 TAAATTGTAC
* **
2301 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCGAGTTG-ATATGT
* *
2354 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTGACTATGT
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-TGA-TATGT
* * * *
2410 AGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGTTGATATAT
1 AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTTGATATGT
*
2463 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2478 GGCTCAATAT
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
53 19 0.18
54 39 0.36
55 48 0.45
56 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (53 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTTGATATGT
Found at i:10262 original size:27 final size:27
Alignment explanation
Indices: 10232--10380 Score: 99
Period size: 27 Copynumber: 5.6 Consensus size: 27
10222 AAATTGTACA
*
10232 GCACTAAGTGTGCGATTCGATTATGTT
1 GCACTAAGTGTGCGATTCGATTATGTG
*** *
10259 GCACTAAGTGTGCGAAAAGAATATGAT-
1 GCACTAAGTGTGCGATTCGATTATG-TG
* * *
10286 GCACTAATGTGTG-AATT-GA-CATGCG
1 GCACTAA-GTGTGCGATTCGATTATGTG
* * * *
10311 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGATTC-GATTATGTG
* * * *
10339 ACACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTCGATTATGTG
10366 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
10381 GTTGAGTGAA
Statistics
Matches: 90, Mismatches: 25, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
24 5 0.06
25 12 0.13
26 2 0.02
27 48 0.53
28 23 0.26
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTCGATTATGTG
Done.