Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1759
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: 45615
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Found at i:1540 original size:44 final size:47
Alignment explanation
Indices: 1447--1563 Score: 197
Period size: 45 Copynumber: 2.6 Consensus size: 47
1437 TGCAAATGTT
1447 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATC
1494 CG-AC-CGTTGAGTTGAGTCCGAGTTCGT-AAATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATC
1538 CGATACTCG-TGAGTTGAGTCCGAGTT
1 CGA-ACTCGTTGAGTTGAGTCCGAGTT
1564 ACTTATGGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
44 19 0.28
45 23 0.34
46 21 0.31
47 4 0.06
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (47 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATC
Found at i:8365 original size:11 final size:12
Alignment explanation
Indices: 8340--8365 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8330 TTTAGTTATT
8340 AAAATAAATTAA
1 AAAATAAATTAA
8352 AAAATAAATTAA
1 AAAATAAATTAA
8364 AA
1 AA
8366 GCCAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAAATTAA
Found at i:9337 original size:46 final size:46
Alignment explanation
Indices: 9287--9462 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
9277 TGGTTGAGCA
* * *
9287 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* * * *
9333 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA--A--CG
*
9380 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* *
9426 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
9463 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 64 0.59
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
Found at i:9443 original size:93 final size:93
Alignment explanation
Indices: 9284--9454 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
9274 GGATGGTTGA
* * *
9284 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
9349 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
** *
9377 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
9442 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
9455 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:11851 original size:15 final size:15
Alignment explanation
Indices: 11831--11862 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11821 ACGGGTTTTC
11831 CTAAAGCTTCATCCT
1 CTAAAGCTTCATCCT
11846 CTAAAGCTTCATCCT
1 CTAAAGCTTCATCCT
11861 CT
1 CT
11863 TTTTTCTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.34, G:0.06, T:0.34
Consensus pattern (15 bp):
CTAAAGCTTCATCCT
Found at i:14126 original size:11 final size:11
Alignment explanation
Indices: 14112--14155 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
14102 AGATAAATAT
14112 TATTTTATTAA
1 TATTTTATTAA
*
14123 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
14136 TATTTTTTTAA
1 TATTTTATTAA
14147 TATTTTATT
1 TATTTTATT
14156 TAATTAAGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 15 0.56
12 5 0.19
13 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:16510 original size:17 final size:16
Alignment explanation
Indices: 16481--16513 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
16471 ATGATGGTAC
16481 ATGAAATAATGATATA
1 ATGAAATAATGATATA
16497 ATGAAATGAATGATATA
1 ATGAAAT-AATGATATA
16514 TGTTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (16 bp):
ATGAAATAATGATATA
Done.