Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2470
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: 44795
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:679 original size:28 final size:29
Alignment explanation
Indices: 636--703 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
626 TTTCAATCAC
*
636 TCTTTTTTTTTCAATTTTG-ATTTTTTTCT
1 TCTTTTTTTTTCAATTTCGAATTTTTTT-T
665 TCTTTTTTTTT-AATTTCGAATTTTTTTT
1 TCTTTTTTTTTCAATTTCGAATTTTTTTT
693 TCTTTTTTTTT
1 TCTTTTTTTTT
704 TCTTCAATAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 18 0.49
29 19 0.51
ACGTcount: A:0.10, C:0.09, G:0.03, T:0.78
Consensus pattern (29 bp):
TCTTTTTTTTTCAATTTCGAATTTTTTTT
Found at i:769 original size:15 final size:14
Alignment explanation
Indices: 744--797 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
734 AAATTGAATA
*
744 CAAACTTTTTTTTT
1 CAAATTTTTTTTTT
*
758 GAAA-TTTTTTTTT
1 CAAATTTTTTTTTT
771 CAAAATTTTTTTTTT
1 C-AAATTTTTTTTTT
786 CAAATTTTTTTT
1 CAAATTTTTTTT
798 ATATTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
13 9 0.25
14 17 0.47
15 10 0.28
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (14 bp):
CAAATTTTTTTTTT
Found at i:16648 original size:23 final size:22
Alignment explanation
Indices: 16597--16648 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
16587 CCTCGTCTTT
*
16597 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
16619 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
16642 TTCTTTT
1 TTCTTTT
16649 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:25578 original size:12 final size:11
Alignment explanation
Indices: 25555--25587 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
25545 GTTGTAAAGT
25555 TTTATT-TTTA
1 TTTATTATTTA
25565 TTTATTTATTTA
1 TTTA-TTATTTA
25577 TTTATTATTTA
1 TTTATTATTTA
25588 CTTAGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 9 0.43
12 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:33082 original size:16 final size:15
Alignment explanation
Indices: 33063--33092 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
33053 AGTATCAATT
33063 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
33079 TTTGATTGGGATGA
1 TTTGATTGGGATGA
33093 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:33789 original size:22 final size:22
Alignment explanation
Indices: 33759--33802 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33749 TTTGGTATTT
33759 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
33781 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
33803 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:35295 original size:23 final size:22
Alignment explanation
Indices: 35243--35295 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
35233 TCCACGTCTT
*
35243 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
35265 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
35288 TTTCTTTT
1 TTTCTTTT
35296 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:36882 original size:10 final size:10
Alignment explanation
Indices: 36866--36923 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
36856 CAACTCCGAC
36866 CAGCTCAATT
1 CAGCTCAATT
* *
36876 GAGCTCATTT
1 CAGCTCAATT
36886 CAGCTCAA-T
1 CAGCTCAATT
36895 CGAGCTCAATT
1 C-AGCTCAATT
*
36906 TAGCTACAATT
1 CAGCT-CAATT
36917 CAGCTCA
1 CAGCTCA
36924 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:36889 original size:20 final size:20
Alignment explanation
Indices: 36866--36926 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
36856 CAACTCCGAC
36866 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
36886 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
36907 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
36927 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Done.