Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2676
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: 29269
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Found at i:437 original size:27 final size:27
Alignment explanation
Indices: 396--449 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
386 TGTCATGTGA
* *
396 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
423 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
450 GGTTGTATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:2292 original size:55 final size:53
Alignment explanation
Indices: 2167--2420 Score: 261
Period size: 53 Copynumber: 4.8 Consensus size: 53
2157 ATTAGGGTTT
* * * *
2167 AAGGATACCGTGTAAGACCATGCCAAGGCATGGAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAA-G-TTCATAAGGC
* * *
2221 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * * *
2276 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
*
2329 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT--TCAA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCAT-AAGGC
* * * *
2378 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
2421 GTACCCGTGT
Statistics
Matches: 172, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
49 40 0.23
51 1 0.01
52 8 0.05
53 44 0.26
54 36 0.21
55 39 0.23
56 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:2372 original size:108 final size:109
Alignment explanation
Indices: 2177--2373 Score: 317
Period size: 108 Copynumber: 1.8 Consensus size: 109
2167 AAGGATACCG
*
2177 TGTAAGACCATGCCAAGGCATGGAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCAT
1 TGTAAGACCATGCCAAGGCATGGAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
*
2242 GTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
* * *
2286 TGTAAGACCATGCCAAGGCATGGCATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACCA
*
2349 TGTCAAGACATGGCAATGGTAAGTT
65 TGTCAAGACATGGCAATGATAAGTT
2374 TCAAAAGGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
107 3 0.04
108 48 0.59
109 30 0.37
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (109 bp):
TGTAAGACCATGCCAAGGCATGGAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:2633 original size:16 final size:16
Alignment explanation
Indices: 2612--2642 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2602 ATAAATTTGA
2612 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
2628 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
2643 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:9701 original size:55 final size:54
Alignment explanation
Indices: 9613--9868 Score: 271
Period size: 55 Copynumber: 4.8 Consensus size: 54
9603 CATTAGGGTT
* *
9613 CAAGGATACCGTGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGG
* * * *
9668 CAAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTCTAAGG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGG
* * *
9723 CAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGG
1 C-AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGG
* *
9776 CAAGGCTACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA--
1 CAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGG
* * *
9826 -AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
9869 GTACCCGTGT
Statistics
Matches: 173, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
49 39 0.23
52 8 0.05
53 41 0.24
54 12 0.07
55 69 0.40
56 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (54 bp):
CAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGG
Found at i:9820 original size:108 final size:110
Alignment explanation
Indices: 9624--9821 Score: 312
Period size: 108 Copynumber: 1.8 Consensus size: 110
9614 AAGGATACCG
*
9624 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
*
9689 TGTCAAGACATGGCATTGATAAGTTACTCTAAGGCAAAGGTCCCA
66 TGTCAAGACATGGCAATGATAAGTTACTCTAAGGCAAAGGTCCCA
* **
9734 TGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGCTACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
*
9796 ATGTCAAGACATGGCAATGGTAAGTT
65 ATGTCAAGACATGGCAATGATAAGTT
9822 TCAAAAGGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.58
109 7 0.09
110 24 0.30
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
TGTCAAGACATGGCAATGATAAGTTACTCTAAGGCAAAGGTCCCA
Found at i:10081 original size:16 final size:16
Alignment explanation
Indices: 10060--10090 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10050 ATAAATTTGA
10060 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
10076 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
10091 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Done.