Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1658
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: 8054
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Found at i:3761 original size:20 final size:20
Alignment explanation
Indices: 3738--3784 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3728 TAGTTCATTT
3738 AAAGCTCATTTTCTTGCTTC
1 AAAGCTCATTTTCTTGCTTC
3758 AAAGCTCATTTTCTTGCTTC
1 AAAGCTCATTTTCTTGCTTC
*
3778 CAAGCTC
1 AAAGCTC
3785 TCTTTACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.40
Consensus pattern (20 bp):
AAAGCTCATTTTCTTGCTTC
Found at i:7540 original size:6 final size:6
Alignment explanation
Indices: 7529--7632 Score: 97
Period size: 6 Copynumber: 17.8 Consensus size: 6
7519 TTAGGCATAT
* * * * * *
7529 AATAAC AATAAC AACAAC AATAAT AATAAC AACAAT AACAAT AATAAC
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC
* * * *
7577 AATAAT AATAAC AATAA- AA-AAC AAAAAT AATAAT AATAA- AATAAC
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC
7622 AATAAC AATAA
1 AATAAC AATAA
7633 TAATGATAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
4 2 0.02
5 9 0.11
6 72 0.87
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAC
Found at i:7544 original size:26 final size:26
Alignment explanation
Indices: 7476--7544 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
7466 CAATAATAAC
* *
7476 AATAACAATAACAATAACTAGGCGTAT
1 AATAACAATAACAA-CACTAGGCATAT
* * * * *
7503 AAGAAAAAAAATAACATTAGGCATAT
1 AATAACAATAACAACACTAGGCATAT
7529 AATAACAATAACAACA
1 AATAACAATAACAACA
7545 ACAATAATAA
Statistics
Matches: 31, Mismatches: 11, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.19
Consensus pattern (26 bp):
AATAACAATAACAACACTAGGCATAT
Found at i:7574 original size:3 final size:3
Alignment explanation
Indices: 7527--7642 Score: 85
Period size: 3 Copynumber: 39.7 Consensus size: 3
7517 CATTAGGCAT
* * * * * * *
7527 ATA ATA ACA ATA ACA ACA ACA ATA ATA ATA ACA ACA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
7575 ACA ATA ATA ATA ACA ATA A-A A-A ACA AAA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
7620 ACA ATA ACA ATA ATA ATG ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
7643 TGAGCATATA
Statistics
Matches: 91, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
2 6 0.07
3 85 0.93
ACGTcount: A:0.68, C:0.10, G:0.01, T:0.21
Consensus pattern (3 bp):
ATA
Found at i:7722 original size:9 final size:9
Alignment explanation
Indices: 7699--7738 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
7689 AATTGGGCAT
*
7699 ATAACAACA
1 ATAACAATA
*
7708 ACAACAATA
1 ATAACAATA
7717 ATAACAATA
1 ATAACAATA
7726 ATAACAATA
1 ATAACAATA
7735 ATAA
1 ATAA
7739 TTAGGTGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (9 bp):
ATAACAATA
Found at i:7800 original size:3 final size:3
Alignment explanation
Indices: 7757--7791 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7747 TTAAGAAAAT
7757 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7792 GCTAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7850 original size:13 final size:13
Alignment explanation
Indices: 7832--7857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7822 AATTGGACAT
7832 ATAATAATAATAA
1 ATAATAATAATAA
7845 ATAATAATAATAA
1 ATAATAATAATAA
7858 TTGGGCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:7913 original size:29 final size:30
Alignment explanation
Indices: 7837--7913 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 30
7827 GACATATAAT
* * *
7837 AATAATAAATAATAATAATAATTGGGCATATA
1 AATAA-AAAAAAT-ATAATAATTGAGCATAGA
*
7869 AGA-AAAAAAAACATAATAA-TGAGCATAGA
1 A-ATAAAAAAAATATAATAATTGAGCATAGA
*
7898 AATAAAAACAATATAA
1 AATAAAAAAAATATAA
7914 CAATACTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.03
29 20 0.54
30 7 0.19
31 5 0.14
32 3 0.08
33 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.22
Consensus pattern (30 bp):
AATAAAAAAAATATAATAATTGAGCATAGA
Found at i:7928 original size:3 final size:3
Alignment explanation
Indices: 7910--7953 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
7900 TAAAAACAAT
* *
7910 ATA ACA ATA CTA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA A
7954 GTGAGCCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:7942 original size:16 final size:16
Alignment explanation
Indices: 7921--7953 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
7911 TAACAATACT
7921 AATAATAATAATAATA
1 AATAATAATAATAATA
7937 AATAATAATAATAATA
1 AATAATAATAATAATA
7953 A
1 A
7954 GTGAGCCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:8003 original size:3 final size:3
Alignment explanation
Indices: 7989--8034 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
7979 AATTGGGCGT
* *
7989 ATA ATA ACA ATA ATA ATA ATTA AT- ATA ACA ATA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
8033 AT
1 AT
8035 CAATTGCGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:8007 original size:27 final size:26
Alignment explanation
Indices: 7937--8009 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
7927 AATAATAATA
*
7937 AATAATAATAATAATAAGTGAGCCTAT
1 AATAA-AATAATAATAATTGAGCCTAT
* * * * *
7964 AAGAAAAAAACATATAATTGGGCGTAT
1 AATAAAATAATA-ATAATTGAGCCTAT
7991 AATAACAATAATAATAATT
1 AATAA-AATAATAATAATT
8010 AATATAACAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
26 5 0.14
27 25 0.71
28 5 0.14
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (26 bp):
AATAAAATAATAATAATTGAGCCTAT
Found at i:8016 original size:21 final size:19
Alignment explanation
Indices: 7992--8032 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
7982 TGGGCGTATA
7992 ATAACAATAATAATAATTAAT
1 ATAACAATAATAA-AA-TAAT
8013 ATAACAATAATAAAATAAT
1 ATAACAATAATAAAATAAT
8032 A
1 A
8033 ATCAATTGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAACAATAATAAAATAAT
Done.