Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2443
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: 52330
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:10744 original size:24 final size:24
Alignment explanation
Indices: 10720--10766 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
10710 AAACTACTTC
10720 TAAAGAAAACTCAAGAGAGAATTCT
1 TAAAGAAAACTCAA-AGAGAATTCT
** *
10745 TGGAGAAAATTCAAAGAGAATT
1 TAAAGAAAACTCAAAGAGAATT
10767 TCTACTCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (24 bp):
TAAAGAAAACTCAAAGAGAATTCT
Found at i:14767 original size:10 final size:10
Alignment explanation
Indices: 14752--14810 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
14742 TTGGGTTAAG
14752 ATTGAGCTGA
1 ATTGAGCTGA
14762 ATTGAGCTCGA
1 ATTGAGCT-GA
14773 A-TGAGCTGA
1 ATTGAGCTGA
* *
14782 CTTGAGCTCA
1 ATTGAGCTGA
*
14792 AGTGAGCTGGA
1 ATTGAGCT-GA
*
14803 AATGAGCT
1 ATTGAGCT
14811 AAACGGAGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.05
10 27 0.68
11 11 0.28
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:14777 original size:20 final size:20
Alignment explanation
Indices: 14754--14810 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
14744 GGGTTAAGAT
14754 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
14774 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
*
14794 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
14811 AAACGGAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 22 0.69
21 8 0.25
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.25
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:19608 original size:17 final size:18
Alignment explanation
Indices: 19586--19622 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
19576 TGGAATAAAC
19586 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
19603 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
19621 TT
1 TT
19623 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:25220 original size:9 final size:9
Alignment explanation
Indices: 25206--25239 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
25196 GAATTTCATA
*
25206 TTTTTTGAT
1 TTTTTTGAC
25215 TTTTTTGAC
1 TTTTTTGAC
25224 TTTTTTGAC
1 TTTTTTGAC
25233 TTATTTT
1 TT-TTTT
25240 TTTGCGGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTTGAC
Found at i:26830 original size:30 final size:30
Alignment explanation
Indices: 26796--26869 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
26786 AGATTCGGTT
26796 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
26826 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
26856 TCTTGATTTTCTTG
1 TCTTGATTTTCTTG
26870 TTCTCTCGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (30 bp):
TCTTGATTTTCTTGAAAACAAGAAAGTGAA
Found at i:30713 original size:45 final size:45
Alignment explanation
Indices: 30649--30836 Score: 322
Period size: 45 Copynumber: 4.2 Consensus size: 45
30639 CATGAAATTA
*
30649 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
30694 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
30739 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
30784 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
30829 AGGAAGCA
1 AGGAAGCA
30837 CCATGGCCGA
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:38153 original size:14 final size:15
Alignment explanation
Indices: 38134--38162 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38124 ACAAAGAACG
38134 AATT-AAATCTGGAA
1 AATTAAAATCTGGAA
38148 AATTAAAATCTGGAA
1 AATTAAAATCTGGAA
38163 TAAGAACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (15 bp):
AATTAAAATCTGGAA
Found at i:40549 original size:23 final size:22
Alignment explanation
Indices: 40497--40549 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40487 TCCACGTCTT
*
40497 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40519 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40542 TTTCTTTT
1 TTTCTTTT
40550 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:44591 original size:23 final size:22
Alignment explanation
Indices: 44539--44591 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
44529 TCCACGTCTT
*
44539 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
44561 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
44584 TTTCTTTT
1 TTTCTTTT
44592 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:49625 original size:14 final size:14
Alignment explanation
Indices: 49606--49632 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49596 AGGGTTCTTA
49606 TTCCAGATTTAATT
1 TTCCAGATTTAATT
49620 TTCCAGATTTAAT
1 TTCCAGATTTAAT
49633 CTCGTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (14 bp):
TTCCAGATTTAATT
Done.