Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4601.1
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: 51980
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Warning! 339 characters in sequence are not A, C, G, or T
Found at i:826 original size:21 final size:21
Alignment explanation
Indices: 788--827 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
778 CCACGTCTTT
*
788 TTCATTTGTTTCTTTTTCTAA
1 TTCATTTGTCTCTTTTTCTAA
809 TTCATTT-TCTCTTCTTTCT
1 TTCATTTGTCTCTT-TTTCT
828 TCATTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.68
Consensus pattern (21 bp):
TTCATTTGTCTCTTTTTCTAA
Found at i:7049 original size:18 final size:18
Alignment explanation
Indices: 7026--7062 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
7016 TTCTCATCTC
*
7026 TTCACTTCTCTCTCATTT
1 TTCACTTCCCTCTCATTT
7044 TTCACTTCCCTCTCATTT
1 TTCACTTCCCTCTCATTT
7062 T
1 T
7063 CCTCTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.35, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCACTTCCCTCTCATTT
Found at i:8033 original size:5 final size:5
Alignment explanation
Indices: 8023--8047 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
8013 GCATTGGAAC
8023 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
8048 CTTTGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:20538 original size:21 final size:21
Alignment explanation
Indices: 20500--20539 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20490 CAAAATCTCC
**
20500 GTAAAAGTTTTCCAAAATTGA
1 GTAAAAGTCATCCAAAATTGA
*
20521 GTAAAAGTCATCCGAAATT
1 GTAAAAGTCATCCAAAATT
20540 TCTTTAAGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (21 bp):
GTAAAAGTCATCCAAAATTGA
Found at i:29678 original size:56 final size:56
Alignment explanation
Indices: 29573--29679 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
29563 ATTAATGCCA
* * * * *
29573 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
*
29629 TCCATACATGG-GAACATCTTATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
29680 CAGCAAGCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
55 20 0.45
56 24 0.55
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:36785 original size:29 final size:28
Alignment explanation
Indices: 36719--36810 Score: 139
Period size: 29 Copynumber: 3.2 Consensus size: 28
36709 AAGTCTACAT
* *
36719 ACATGCATATGGCCCACTAGGCCCAATC
1 ACATTCATATGGCCCATTAGGCCCAATC
*
36747 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCC-AATC
36776 ACATTCATATGGCCCATTAGGCCCCAATC
1 ACATTCATATGGCCCATTAGG-CCCAATC
36805 ACATTC
1 ACATTC
36811 TTACACATGC
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
28 21 0.36
29 34 0.59
30 3 0.05
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (28 bp):
ACATTCATATGGCCCATTAGGCCCAATC
Found at i:37661 original size:108 final size:108
Alignment explanation
Indices: 37472--37687 Score: 432
Period size: 108 Copynumber: 2.0 Consensus size: 108
37462 ATTTAGGGCC
37472 AAAACGGAACAGTGGTTTCGAAACCACGAATCTGAGGTTGAAAAAAATTATTATTTTGATTAAGT
1 AAAACGGAACAGTGGTTTCGAAACCACGAATCTGAGGTTGAAAAAAATTATTATTTTGATTAAGT
37537 TTTAGTGTTTATATTATGATTGCATAATCGTGTGAAAATTTCA
66 TTTAGTGTTTATATTATGATTGCATAATCGTGTGAAAATTTCA
37580 AAAACGGAACAGTGGTTTCGAAACCACGAATCTGAGGTTGAAAAAAATTATTATTTTGATTAAGT
1 AAAACGGAACAGTGGTTTCGAAACCACGAATCTGAGGTTGAAAAAAATTATTATTTTGATTAAGT
37645 TTTAGTGTTTATATTATGATTGCATAATCGTGTGAAAATTTCA
66 TTTAGTGTTTATATTATGATTGCATAATCGTGTGAAAATTTCA
37688 TTGCGAAATT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (108 bp):
AAAACGGAACAGTGGTTTCGAAACCACGAATCTGAGGTTGAAAAAAATTATTATTTTGATTAAGT
TTTAGTGTTTATATTATGATTGCATAATCGTGTGAAAATTTCA
Found at i:44863 original size:22 final size:22
Alignment explanation
Indices: 44833--44876 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
44823 TTTGGTATTT
44833 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
44855 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
44877 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:46413 original size:67 final size:68
Alignment explanation
Indices: 46278--46418 Score: 185
Period size: 67 Copynumber: 2.0 Consensus size: 68
46268 CGGGTCGTAT
* * * *
46278 CAGATATTGTGGCTAAGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG--A-ATATATGTAGCGAAGCCACCAGATTACAGCGA
46343 GGCTGC
63 GGCTGC
* * *
46349 CAGATATTGTGACGAAGTCACCAGAACAG-ATATATGTAGCGAGGCCACTAGATTACAGCGAGGC
1 CAGATATTGTGACGAAGCCACCAGAACAGAATATATGTAGCGAAGCCACCAGATTACAGCGAGGC
46413 TGC
66 TGC
46416 CAG
1 CAG
46419 GACGCTTCGT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 37 0.59
71 26 0.41
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (68 bp):
CAGATATTGTGACGAAGCCACCAGAACAGAATATATGTAGCGAAGCCACCAGATTACAGCGAGGC
TGC
Done.