Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4786
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: 13460
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4774 original size:40 final size:40
Alignment explanation
Indices: 4719--4826 Score: 207
Period size: 40 Copynumber: 2.7 Consensus size: 40
4709 CTGGAAAAAA
4719 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCAGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCAGGTTAT
*
4759 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCAGGTTAT
4799 TATAACCGGGTTAAGTCCCGAAGGCATT
1 TATAACCGGGTTAAGTCCCGAAGGCATT
4827 TTTGCTGGTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCAGGTTAT
Found at i:6639 original size:46 final size:47
Alignment explanation
Indices: 6572--6756 Score: 213
Period size: 46 Copynumber: 4.0 Consensus size: 47
6562 CCATGTAACC
*
6572 CGAG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCT
1 CGAGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
6618 CGAG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CGAGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
* * * * *
6664 CGGATGCCTAGTT-ACAT--TTCA-CGAACTCGGACTCAACTCAACGAGTT
1 C-GA-GAC--GTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
* *
6711 CG-GACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAACAAGTT
1 CGAGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
6757 TAGATGCCCA
Statistics
Matches: 118, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 70 0.59
47 28 0.24
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (47 bp):
CGAGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
Found at i:6763 original size:93 final size:93
Alignment explanation
Indices: 6593--6764 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
6583 ATCCATAAGT
*
6593 GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
* *
6658 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CAAGTTCAGATGCCTAGTTACATTTCAC
*
6686 GAACTCGGACTCAACTCAACGAGTTCG-GACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGAG-CGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
6750 ACAAGTTTAGATGCC
65 ACAAGTTCAGATGCC
6765 CAAATATCCA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 72 0.99
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CAAGTTCAGATGCCTAGTTACATTTCAC
Found at i:10134 original size:42 final size:42
Alignment explanation
Indices: 10077--10231 Score: 179
Period size: 42 Copynumber: 3.7 Consensus size: 42
10067 CTAAGACTAT
* *
10077 GTGTAAGACCTTATCTGGGATATGGCATCTATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCTATAAGAGACTTC
* *
10119 GTGTAAGACCATATCTAGGATATGGCATCGATAAGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCTATAAGAGACTTC
* * * *
10161 GTGTAAGACCATAGCTGGGCTATTGGCAT-TGATACGAGA-TCCC
1 GTGTAAGACCATATCTGGGATA-TGGCATCT-ATAAGAGACT-TC
* *
10204 ATGTAAGACCATATATGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
10232 TGGTATGGTA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
42 64 0.67
43 32 0.33
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCTATAAGAGACTTC
Found at i:10428 original size:15 final size:16
Alignment explanation
Indices: 10402--10431 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10392 ATGAACCCTC
10402 AGTAAGGTTATGATTG
1 AGTAAGGTTATGATTG
10418 AGTAA-GTTATGATT
1 AGTAAGGTTATGATT
10432 ATAAGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (16 bp):
AGTAAGGTTATGATTG
Found at i:13414 original size:26 final size:25
Alignment explanation
Indices: 13384--13450 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
13374 TTATAAATTT
13384 CCTAAATAAAAAAAAAAAAAAAATAA
1 CCTAAATAAAAAAAAAAAAAAAA-AA
**
13410 CCTAAA-AATCTAAAAAAAAAAAAAA
1 CCTAAATAA-AAAAAAAAAAAAAAAA
*
13435 CC--ATTAAAAAAAAAAA
1 CCTAAATAAAAAAAAAAA
13451 TTTTTTAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 8 0.24
24 2 0.06
25 6 0.18
26 18 0.53
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (25 bp):
CCTAAATAAAAAAAAAAAAAAAAAA
Done.