Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold10423.1
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: 3643
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Found at i:490 original size:20 final size:19
Alignment explanation
Indices: 467--531 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
457 AAGCTCAAAC
467 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
487 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
507 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
527 GAGCT
1 GAGCT
532 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:2346 original size:33 final size:33
Alignment explanation
Indices: 2309--2371 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2299 GATTACTCAC
2309 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
2342 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
2372 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:2398 original size:21 final size:21
Alignment explanation
Indices: 2369--2424 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
2359 CAAGCTCTCT
*
2369 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
2390 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
2411 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
2425 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:2417 original size:14 final size:14
Alignment explanation
Indices: 2368--2424 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
2358 TCAAGCTCTC
2368 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
2381 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
2395 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
2409 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
2423 TT
1 TT
2425 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:2452 original size:18 final size:18
Alignment explanation
Indices: 2431--2489 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
2421 TTTTCTCTCA
2431 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
2449 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
2467 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
2485 GTTTT
1 CTTTT
2490 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:2506 original size:6 final size:6
Alignment explanation
Indices: 2386--2493 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
2376 TCTTTTTTCG
* * * **
2386 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
2437 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
2485 -GTTTT CTTT
1 CTTTTT CTTT
2494 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Done.