Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1306
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: 54721
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:7195 original size:201 final size:201
Alignment explanation
Indices: 6850--7256 Score: 787
Period size: 201 Copynumber: 2.0 Consensus size: 201
6840 TAGTTTGCTT
*
6850 GATTTATGGCTGGCCACCCATGGAAGATTCTTCAAAGGATTAAAACTCCTATATTTAGTAAACTA
1 GATTTATGGCTGGCCACCCATGGAAGATTCTTCAAAGGATGAAAACTCCTATATTTAGTAAACTA
6915 TCCCCCTCTCCTTACCTATAAATAAGACCCTCTCATTCATTCTTCAAGCATCCCACAATCATTCT
66 TCCCCCTCTCCTTACCTATAAATAAGACCCTCTCATTCATTCTTCAAGCATCCCACAATCATTCT
*
6980 TCAATCATCCCTCAAGCACTATTCTCTCTTAGCCTTTTCCATTCCCAAGCCTAGCATCATCTCTT
131 TCAATCATCCCTCAAGCACCATTCTCTCTTAGCCTTTTCCATTCCCAAGCCTAGCATCATCTCTT
7045 CATAGA
196 CATAGA
*
7051 GATTTATGGCTGGCCACCCATGGAAGATTCTTCAAAGGATGAAAACTCTTATATTTAGTAAACTA
1 GATTTATGGCTGGCCACCCATGGAAGATTCTTCAAAGGATGAAAACTCCTATATTTAGTAAACTA
7116 TCCCCCTCTCCTTACCTATAAATAAGACCCTCTCATTCATTCTTCAAGCATCCCACAATCATTCT
66 TCCCCCTCTCCTTACCTATAAATAAGACCCTCTCATTCATTCTTCAAGCATCCCACAATCATTCT
7181 TCAATCATCCCTCAAGCACCATTCTCTCTTAGCCTTTTCCATTCCCAAGCCTAGCATCATCTCTT
131 TCAATCATCCCTCAAGCACCATTCTCTCTTAGCCTTTTCCATTCCCAAGCCTAGCATCATCTCTT
7246 CATAGA
196 CATAGA
7252 GATTT
1 GATTT
7257 TAGGAATTAA
Statistics
Matches: 203, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
201 203 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (201 bp):
GATTTATGGCTGGCCACCCATGGAAGATTCTTCAAAGGATGAAAACTCCTATATTTAGTAAACTA
TCCCCCTCTCCTTACCTATAAATAAGACCCTCTCATTCATTCTTCAAGCATCCCACAATCATTCT
TCAATCATCCCTCAAGCACCATTCTCTCTTAGCCTTTTCCATTCCCAAGCCTAGCATCATCTCTT
CATAGA
Found at i:20043 original size:22 final size:22
Alignment explanation
Indices: 20009--20052 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
19999 TTTTCACTTA
* *
20009 AATTATTAATATATTGAATTTT
1 AATTATTAATATAATAAATTTT
**
20031 AATTATTTTTATAATAAATTTT
1 AATTATTAATATAATAAATTTT
20053 CTCAAATTTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTATTAATATAATAAATTTT
Found at i:25750 original size:19 final size:19
Alignment explanation
Indices: 25728--25765 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25718 TCAATCATCC
25728 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
25747 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
25766 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:26576 original size:21 final size:22
Alignment explanation
Indices: 26535--26578 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
26525 CCTAGTTTAT
*
26535 TTATGTTATAATTGTTGTAAAA
1 TTATGTTATAATTGTTCTAAAA
26557 TTATGTT-TAATT-TTACTAAAA
1 TTATGTTATAATTGTT-CTAAAA
26578 T
1 T
26579 CTATTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 11 0.55
22 7 0.35
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (22 bp):
TTATGTTATAATTGTTCTAAAA
Found at i:38284 original size:25 final size:25
Alignment explanation
Indices: 38255--38315 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
38245 CCACCACTCA
* *
38255 TGAGAGCATAC-AGATTTGTAGCTTG
1 TGAGAGCATACTA-ATTTATAGCTCG
38280 TGAGAGCATACTAATTTATAGCTCG
1 TGAGAGCATACTAATTTATAGCTCG
38305 TGAGAGCATAC
1 TGAGAGCATAC
38316 CGATCTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (25 bp):
TGAGAGCATACTAATTTATAGCTCG
Found at i:39430 original size:30 final size:30
Alignment explanation
Indices: 39360--39419 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
39350 GTGTGTCTCT
* * * *
39360 CAGCTGTGTTTGACACATAGCTAGGTGACA
1 CAGCCGTGTGTGACACACAGCCAGGTGACA
39390 CAGCCGTGTGTGACACACAGCCAGGTGACA
1 CAGCCGTGTGTGACACACAGCCAGGTGACA
39420 TGGTCGTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (30 bp):
CAGCCGTGTGTGACACACAGCCAGGTGACA
Found at i:39708 original size:20 final size:20
Alignment explanation
Indices: 39669--39709 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
39659 CCCTAAAATA
*
39669 TTGAAAAATTTTACTGTTTT
1 TTGAAAAATTCTACTGTTTT
39689 TTGAAAAATTCT-CTGATTTT
1 TTGAAAAATTCTACTG-TTTT
39709 T
1 T
39710 CGATTTAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (20 bp):
TTGAAAAATTCTACTGTTTT
Found at i:52164 original size:25 final size:25
Alignment explanation
Indices: 52135--52195 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
52125 CCACCACTCA
* *
52135 TGAGAGCATAC-AGATTTGTAGCTTG
1 TGAGAGCATACTA-ATTTATAGCTCG
52160 TGAGAGCATACTAATTTATAGCTCG
1 TGAGAGCATACTAATTTATAGCTCG
52185 TGAGAGCATAC
1 TGAGAGCATAC
52196 CGATCTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (25 bp):
TGAGAGCATACTAATTTATAGCTCG
Found at i:53295 original size:30 final size:30
Alignment explanation
Indices: 53225--53284 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
53215 GTGTGTCTCT
* * * *
53225 CAGCTGTGTTTGACACATAGCTAGGTGACA
1 CAGCCGTGTGTGACACACAGCCAGGTGACA
53255 CAGCCGTGTGTGACACACAGCCAGGTGACA
1 CAGCCGTGTGTGACACACAGCCAGGTGACA
53285 TGGTCGTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (30 bp):
CAGCCGTGTGTGACACACAGCCAGGTGACA
Found at i:53572 original size:20 final size:20
Alignment explanation
Indices: 53533--53573 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
53523 CCCTAAAATA
*
53533 TTGAAAAATTTTACTGTTTT
1 TTGAAAAATTCTACTGTTTT
53553 TTGAAAAATTCT-CTGATTTT
1 TTGAAAAATTCTACTG-TTTT
53573 T
1 T
53574 CGATTTAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (20 bp):
TTGAAAAATTCTACTGTTTT
Done.