Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold625
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: 27390
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Found at i:6398 original size:28 final size:27
Alignment explanation
Indices: 6341--6492 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
6331 TAAATTGTGC
*
6341 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
6368 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
6396 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
6423 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCG-AGTTGACTATGT
* *
6451 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
6478 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6493 GACTTAATAT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 65 0.56
28 52 0.44
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:6405 original size:55 final size:55
Alignment explanation
Indices: 6341--6492 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
6331 TAAATTGTGC
* *
6341 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAATTTGACTATGT
*
6396 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAATTTGACTATGT
* * *
6451 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
6493 GACTTAATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAATTTGACTATGT
Found at i:9200 original size:40 final size:40
Alignment explanation
Indices: 9148--9360 Score: 376
Period size: 40 Copynumber: 5.4 Consensus size: 40
9138 CAAATGCCTT
*
9148 ACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGG
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
*
9188 ACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGG
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
*
9228 ACTTGGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
9268 ACTTAGCCC-GTTATAGTAACTCGCACAAATGCCTTCGGG
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
*
9307 ACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
9347 -CTTAGCCCGGTTAT
1 ACTTAGCCCGGTTAT
9361 CAATCCGAAT
Statistics
Matches: 167, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
39 52 0.31
40 115 0.69
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
Found at i:9323 original size:79 final size:80
Alignment explanation
Indices: 9148--9360 Score: 376
Period size: 79 Copynumber: 2.7 Consensus size: 80
9138 CAAATGCCTT
*
9148 ACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGC
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGC
*
9213 ACAATTGCCTTCGGG
66 ACAAATGCCTTCGGG
*
9228 ACTTGGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-GTTATAGTAACTCGC
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGC
9292 ACAAATGCCTTCGGG
66 ACAAATGCCTTCGGG
*
9307 ACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
9361 CAATCCGAAT
Statistics
Matches: 127, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
78 8 0.06
79 72 0.57
80 47 0.37
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (80 bp):
ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGC
ACAAATGCCTTCGGG
Found at i:17318 original size:40 final size:40
Alignment explanation
Indices: 17232--17452 Score: 349
Period size: 40 Copynumber: 5.6 Consensus size: 40
17222 AAACCAAGTA
** * *
17232 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
17270 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
17310 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
17350 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
17390 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
17430 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
17453 CAATCCGAAT
Statistics
Matches: 172, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
38 13 0.08
39 16 0.09
40 143 0.83
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:25372 original size:40 final size:40
Alignment explanation
Indices: 25303--25523 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
25293 AAACCAAGTA
* * *
25303 CCTTCGGG-TTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
25341 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
25381 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
25421 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
25461 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
25501 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
25524 CAATCCGAAT
Statistics
Matches: 173, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
38 8 0.05
39 5 0.03
40 160 0.92
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Done.