Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1381
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: 32026
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2834 original size:46 final size:46
Alignment explanation
Indices: 2767--2941 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
2757 TGTAACCCGC
*
2767 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
2813 CCATAAGTGAACTCGGACTCAAGTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * * *
2863 -C-TCA-CGAACTCGGACTCAACTTAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
2906 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG
2942 ATGCTCAACC
Statistics
Matches: 103, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.57
47 24 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:2903 original size:93 final size:93
Alignment explanation
Indices: 2774--2945 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
2764 CGCCCATAAG
* * * * *
2774 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAAGTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
2839 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* *
2867 CGAACTCGGACTCAACTTAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
2932 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
2946 TCAACCATCC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:5437 original size:46 final size:46
Alignment explanation
Indices: 5387--5607 Score: 290
Period size: 46 Copynumber: 4.8 Consensus size: 46
5377 TGGTTGAGCA
*
5387 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
5433 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
5478 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
5526 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
5571 GCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5608 GCGGGTTACA
Statistics
Matches: 156, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
45 47 0.30
46 64 0.41
47 29 0.19
48 3 0.02
50 4 0.03
51 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:15379 original size:46 final size:46
Alignment explanation
Indices: 15320--15439 Score: 222
Period size: 46 Copynumber: 2.6 Consensus size: 46
15310 GCCCATAAAC
15320 GAACTCGGACTCAACTCAACGAGCTCGGCCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGCCGTTCGCATCCATAAGT
*
15366 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGCCGTTCGCATCCATAAGT
*
15412 GAACTCGGACTCAACTCAACGAGTTCGG
1 GAACTCGGACTCAACTCAACGAGCTCGG
15440 ATGCCTAGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCCGTTCGCATCCATAAGT
Found at i:17093 original size:38 final size:38
Alignment explanation
Indices: 17051--17179 Score: 188
Period size: 38 Copynumber: 3.4 Consensus size: 38
17041 GCAAGCTATA
*
17051 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGTTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
*
17089 TGCTGGTAA-TATATCCGGGTTAAATCCCACAGGCTTCG
1 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
17127 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
*
17165 TGCTGGTATTATATC
1 TGCTGGAATTATATC
17180 TGAGTTTAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
37 1 0.01
38 80 0.96
39 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:20642 original size:29 final size:29
Alignment explanation
Indices: 20574--20698 Score: 189
Period size: 29 Copynumber: 4.3 Consensus size: 29
20564 AAGTCTACAT
* *
20574 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
20602 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
**
20631 ACATTCGCATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
20660 ACATTCATACGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
20689 ACATTCATAT
1 ACATTCATAT
20699 ACATGCTTTC
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 21 0.24
29 65 0.76
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:27722 original size:13 final size:13
Alignment explanation
Indices: 27704--27729 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27694 TATTGTGCTA
27704 GAAAGAAGACTAG
1 GAAAGAAGACTAG
27717 GAAAGAAGACTAG
1 GAAAGAAGACTAG
27730 AAGTGCTTAC
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:0.54, C:0.08, G:0.31, T:0.08
Consensus pattern (13 bp):
GAAAGAAGACTAG
Found at i:29435 original size:51 final size:49
Alignment explanation
Indices: 29312--29544 Score: 259
Period size: 49 Copynumber: 4.7 Consensus size: 49
29302 TCTATTGTGA
* *
29312 GGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* * * * *
29361 GGTCGCATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCTGATAACTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TT
* * * * **
29411 CGATCACGTGTGTAGAACTAAGTGCAGACTACTATGTGTATCAGATGGTT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* * *
29461 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAACGGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
** * *
29511 GGTTGCATGTGTAGTACTAAGTACAGGCTACTAT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTAT
29545 ACCTACCAGA
Statistics
Matches: 150, Mismatches: 32, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
49 69 0.46
50 45 0.30
51 36 0.24
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
Done.