Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1849
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: 37015
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:14665 original size:23 final size:22
Alignment explanation
Indices: 14613--14665 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
14603 TCCACGTCTT
*
14613 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
14635 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
14658 TTTCTTTT
1 TTTCTTTT
14666 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:19863 original size:12 final size:11
Alignment explanation
Indices: 19847--19901 Score: 94
Period size: 11 Copynumber: 5.0 Consensus size: 11
19837 AACCCAAATT
19847 TTTTTTTTGAA
1 TTTTTTTTGAA
19858 TTTTTTTTG-A
1 TTTTTTTTGAA
19868 TTTTTTTTGAAA
1 TTTTTTTTG-AA
19880 TTTTTTTTGAA
1 TTTTTTTTGAA
19891 TTTTTTTTGAA
1 TTTTTTTTGAA
19902 GAAACTACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.24
11 22 0.52
12 10 0.24
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:23000 original size:20 final size:20
Alignment explanation
Indices: 22954--23000 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22944 AGCTTGTTTC
*
22954 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
22974 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
22994 CAGCTCA
1 CAGCTCA
23001 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:28321 original size:22 final size:22
Alignment explanation
Indices: 28278--28320 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
28268 AAGGGCATAA
*
28278 AATGCTCTTTAAAACTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
*
28300 AATGATCTTT-AAGCTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
28321 TTTAACAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (22 bp):
AATGATCTTTAAAACTCCTTTT
Found at i:28471 original size:21 final size:23
Alignment explanation
Indices: 28426--28473 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
28416 TCACCTGCAA
* *
28426 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
28449 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
28470 TAAA
1 TAAA
28474 TCATAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 1 0.04
23 14 0.61
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:33937 original size:14 final size:14
Alignment explanation
Indices: 33918--33954 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
33908 ATGGAAAACC
33918 AAATTTTTTTTTTG
1 AAATTTTTTTTTTG
33932 AAA--TTTTTTTTG
1 AAATTTTTTTTTTG
33944 -AATTTTTTTTT
1 AAATTTTTTTTT
33955 ATTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.10
12 9 0.43
13 7 0.33
14 3 0.14
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (14 bp):
AAATTTTTTTTTTG
Found at i:33940 original size:12 final size:11
Alignment explanation
Indices: 33923--33973 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
33913 AAACCAAATT
33923 TTTTTTTTGAAA
1 TTTTTTTTG-AA
33935 TTTTTTTTGAA
1 TTTTTTTTGAA
* *
33946 TTTTTTTTTAT
1 TTTTTTTTGAA
33957 TTTTTTTTGAA
1 TTTTTTTTGAA
33968 TTTTTT
1 TTTTTT
33974 GAAAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
11 26 0.74
12 9 0.26
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Done.