Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1676
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: 24423
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:564 original size:12 final size:12
Alignment explanation
Indices: 547--573 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
537 ATTCCGAAGT
547 ATATATATATAC
1 ATATATATATAC
559 ATATATATATAC
1 ATATATATATAC
571 ATA
1 ATA
574 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:1080 original size:26 final size:31
Alignment explanation
Indices: 1013--1070 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
1003 CTGAGAATTG
1013 GCACTAAGTGTGGCGAGTTGATTATATATAA
1 GCACTAAGTGTGGCGAGTTGATTATATATAA
1044 GCACTAAGTGT-GCGAGTTGATTATATA
1 GCACTAAGTGTGGCGAGTTGATTATATA
1071 GACTGAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (31 bp):
GCACTAAGTGTGGCGAGTTGATTATATATAA
Found at i:8934 original size:12 final size:12
Alignment explanation
Indices: 8917--8943 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
8907 ATTCCGAAGT
8917 ATATATATATAC
1 ATATATATATAC
8929 ATATATATATAC
1 ATATATATATAC
8941 ATA
1 ATA
8944 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:9474 original size:27 final size:28
Alignment explanation
Indices: 9390--9487 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
9380 CATGAGATTG
* * * *
9390 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
9419 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
9447 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
9474 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
9488 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:9498 original size:27 final size:27
Alignment explanation
Indices: 9418--9500 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
9408 TAAATTGTAC
* *
9418 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
9446 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
9473 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
9500 A
1 A
9501 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:15987 original size:19 final size:19
Alignment explanation
Indices: 15950--15987 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
15940 ACCTGTCAGA
*
15950 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
15969 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
15988 TAAATTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:18527 original size:69 final size:70
Alignment explanation
Indices: 18416--18563 Score: 228
Period size: 70 Copynumber: 2.1 Consensus size: 70
18406 CGGGAATCAT
* *
18416 CACTTAGCAACCCTCGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATGGA
1 CACTTAGCAACCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGGA
18480 TATCG
66 TATCG
***
18485 CACTTAGCAACCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGTGG
1 CACTTAGCAACCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
18549 ATATCG
65 ATATCG
18555 CACTTAGCA
1 CACTTAGCA
18564 CCACCAATGA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 22 0.31
70 50 0.69
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (70 bp):
CACTTAGCAACCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGGA
TATCG
Found at i:18602 original size:102 final size:102
Alignment explanation
Indices: 18484--18701 Score: 359
Period size: 102 Copynumber: 2.1 Consensus size: 102
18474 AATGGATATC
18484 GCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
18548 GAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATCA-CGCACATAGCACCACC-ATAAACCGGGGAATCA
18586 GCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
*
18651 GATCACGCACATAGCACCACCATAAATCGGGGAATCA
66 GATCACGCACATAGCACCACCATAAACCGGGGAATCA
**
18688 GCACACAGCAACCC
1 GCACTTAGCAACCC
18702 CTTTTATATA
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
102 63 0.58
103 45 0.41
104 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (102 bp):
GCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATCACGCACATAGCACCACCATAAACCGGGGAATCA
Found at i:19065 original size:29 final size:29
Alignment explanation
Indices: 19032--19095 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
19022 TAATCCACCA
19032 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
19061 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
19091 CCCAA
1 CCCAA
19096 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:19069 original size:30 final size:30
Alignment explanation
Indices: 19039--19095 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19029 CCACCCAACT
19039 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
19068 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
19096 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Done.