Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold548
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: 31065
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:140 original size:13 final size:14
Alignment explanation
Indices: 113--141 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
103 ACTAATTTTG
113 TTTGTTTTTTCAAT
1 TTTGTTTTTTCAAT
127 TTTGTTTTTT-AAT
1 TTTGTTTTTTCAAT
140 TT
1 TT
142 GTAACCACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTGTTTTTTCAAT
Found at i:1655 original size:2 final size:2
Alignment explanation
Indices: 1648--1678 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1638 TCCTTCTCAT
1648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1679 TTTAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2195 original size:22 final size:20
Alignment explanation
Indices: 2170--2220 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2160 AAAATATTAA
2170 AATATAAATTTATTTTTATATT
1 AATATAAATTTATTTTT-TA-T
*
2192 AATATTAA--TATTTTTTAT
1 AATATAAATTTATTTTTTAT
2210 AAT-TAAATTTA
1 AATATAAATTTA
2221 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
17 3 0.12
18 4 0.16
19 4 0.16
20 7 0.28
22 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATAAATTTATTTTTTAT
Found at i:6322 original size:2 final size:2
Alignment explanation
Indices: 6311--6344 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6301 ATCATAATTG
6311 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6345 GACTTGACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15855 original size:15 final size:15
Alignment explanation
Indices: 15835--15864 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15825 TGTTTTTATA
15835 CAAAATTAAAGAAAT
1 CAAAATTAAAGAAAT
*
15850 CAAAATTGAAGAAAT
1 CAAAATTAAAGAAAT
15865 TAATATATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (15 bp):
CAAAATTAAAGAAAT
Found at i:16795 original size:16 final size:16
Alignment explanation
Indices: 16774--16807 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16764 AGATTATAAA
*
16774 TATTTTTTTATTATAT
1 TATTTTTTAATTATAT
*
16790 TATTTTTTAATTTTAT
1 TATTTTTTAATTATAT
16806 TA
1 TA
16808 AATATATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTTAATTATAT
Found at i:17144 original size:50 final size:50
Alignment explanation
Indices: 17069--17278 Score: 334
Period size: 50 Copynumber: 4.2 Consensus size: 50
17059 AGTTGTTGTC
*
17069 ATTGTTGACTATCCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
*
17119 ATTGTTGA-TGATTCTTCACCAACCTTTGACAATAGAAG-GAGGTGACCATA
1 ATTGTTGACT-ATTCTTCACCAACCTTTGACAATA-AAGAGAGGTGGCCATA
*
17169 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
* * *
17219 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
17269 ATTGTTGACT
1 ATTGTTGACT
17279 CTAAGTATAT
Statistics
Matches: 149, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
49 3 0.02
50 142 0.95
51 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
Found at i:21720 original size:50 final size:50
Alignment explanation
Indices: 21645--21902 Score: 403
Period size: 50 Copynumber: 5.2 Consensus size: 50
21635 AGTTGTTGTC
* * *
21645 ATTGTTGACTATCCTTCACCAACCTTTGATAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
21695 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
21745 ATTATTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
21795 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* * *
21845 ATTGTTGACAATTCTTCACCAACTTTTAACAATAGAGTGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
21895 ATTGTTGA
1 ATTGTTGA
21903 TTCTAAGTAT
Statistics
Matches: 194, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
49 2 0.01
50 191 0.98
51 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:23279 original size:26 final size:24
Alignment explanation
Indices: 23249--23301 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
23239 CAAGATATTA
**
23249 TTAAAATTAATATTTTAAAATATTTT
1 TTAAAATTAAT-TAATAAAA-ATTTT
23275 TTAAAATTAATTAATAAAAATTTT
1 TTAAAATTAATTAATAAAAATTTT
23299 TTA
1 TTA
23302 CTTATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.32
25 6 0.24
26 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAAAATTAATTAATAAAAATTTT
Found at i:25007 original size:15 final size:14
Alignment explanation
Indices: 24983--25012 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
24973 TAATATAGAC
24983 TTTTATTTTTAAAT
1 TTTTATTTTTAAAT
24997 TTTTCATTTTTAAAT
1 TTTT-ATTTTTAAAT
25012 T
1 T
25013 GGTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTATTTTTAAAT
Found at i:25132 original size:14 final size:14
Alignment explanation
Indices: 25106--25142 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
25096 GTCAATAGTA
25106 ATATA-TATA-TAT
1 ATATATTATACTAT
25118 ATATATTATACTAT
1 ATATATTATACTAT
25132 ATATATTATAC
1 ATATATTATAC
25143 AAATTATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.22
13 4 0.17
14 14 0.61
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTATACTAT
Found at i:25248 original size:13 final size:14
Alignment explanation
Indices: 25222--25272 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
25212 CATTAGTGAT
*
25222 ATTAA-TTATTAAA
1 ATTAAGTTATAAAA
25235 ATTAAGTTA-AAAA
1 ATTAAGTTATAAAA
*
25248 ATCAAGTTATAAAA
1 ATTAAGTTATAAAA
*
25262 A-TAAGTAATAA
1 ATTAAGTTATAA
25273 TTATAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 24 0.75
14 8 0.25
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (14 bp):
ATTAAGTTATAAAA
Found at i:29254 original size:22 final size:21
Alignment explanation
Indices: 29236--29274 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29226 TAAATTAATT
*
29236 ATAAAAA-ATATTTATATTAA
1 ATAAAAATAAATTTATATTAA
29256 ATAAAAATAAATTTATATT
1 ATAAAAATAAATTTATATT
29275 TTATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAAAATAAATTTATATTAA
Done.