Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1767
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: 13385
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Found at i:2579 original size:20 final size:20
Alignment explanation
Indices: 2556--2602 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2546 TACAGAAGAA
2556 TCTAGAACACTT-TGGAATGT
1 TCTAGAA-ACTTCTGGAATGT
**
2576 TCTAGAATGTTCTGGAATGT
1 TCTAGAAACTTCTGGAATGT
2596 TCTAGAA
1 TCTAGAA
2603 TATCGTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
TCTAGAAACTTCTGGAATGT
Found at i:2585 original size:10 final size:10
Alignment explanation
Indices: 2570--2603 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2560 GAACACTTTG
2570 GAATGTTCTA
1 GAATGTTCTA
*
2580 GAATGTTCTG
1 GAATGTTCTA
2590 GAATGTTCTA
1 GAATGTTCTA
2600 GAAT
1 GAAT
2604 ATCGTGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (10 bp):
GAATGTTCTA
Found at i:2611 original size:20 final size:19
Alignment explanation
Indices: 2568--2702 Score: 74
Period size: 20 Copynumber: 6.8 Consensus size: 19
2558 TAGAACACTT
*
2568 TGGAATGTTCTAGAATGTTC
1 TGGAATGTTCTAGAAT-ATC
2588 TGGAATGTTCTAGAATATC
1 TGGAATGTTCTAGAATATC
* * *
2607 GTGGAAGGCTT-TGGAAGATTC
1 -TGGAATG-TTCTAGAATA-TC
* *
2628 TAGAATGTTCTAGAATATTG
1 TGGAATGTTCTAGAATA-TC
* * * * *
2648 TGGGAGGCTCTGGAAGATTC
1 TGGAATGTTCTAGAATA-TC
* *
2668 TAGAATGTTCTAGAATAATG
1 TGGAATGTTCTAGAAT-ATC
*
2688 TGGAAGGTTCTAGAA
1 TGGAATGTTCTAGAA
2703 CTTTATGGAG
Statistics
Matches: 85, Mismatches: 25, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
19 4 0.05
20 76 0.89
21 5 0.06
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (19 bp):
TGGAATGTTCTAGAATATC
Found at i:2612 original size:40 final size:39
Alignment explanation
Indices: 2568--2702 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 39
2558 TAGAACACTT
* *
2568 TGGAATGTTCTAGAATG-TTCTGGAATGTTCTAGAATATCG
1 TGGAAGGTTCTAGAA-GATTCTAGAATGTTCTAGAATAT-G
*
2608 TGGAAGGCTT-TGGAAGATTCTAGAATGTTCTAGAATATTG
1 TGGAAGG-TTCTAGAAGATTCTAGAATGTTCTAGAATA-TG
* * *
2648 TGGGAGGCTCTGGAAGATTCTAGAATGTTCTAGAATAATG
1 TGGAAGGTTCTAGAAGATTCTAGAATGTTCTAGAAT-ATG
2688 TGGAAGGTTCTAGAA
1 TGGAAGGTTCTAGAA
2703 CTTTATGGAG
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.02
40 76 0.93
41 4 0.05
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (39 bp):
TGGAAGGTTCTAGAAGATTCTAGAATGTTCTAGAATATG
Found at i:6012 original size:33 final size:33
Alignment explanation
Indices: 5975--6041 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5965 TTCAACGATT
5975 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
6008 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
6041 T
1 T
6042 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:6013 original size:13 final size:13
Alignment explanation
Indices: 5995--6019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5985 CATAAAATGT
5995 TGTATCGATACAA
1 TGTATCGATACAA
6008 TGTATCGATACA
1 TGTATCGATACA
6020 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6102 original size:13 final size:13
Alignment explanation
Indices: 6084--6108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6074 ATTACTCACA
6084 TGTATCGATACAT
1 TGTATCGATACAT
6097 TGTATCGATACA
1 TGTATCGATACA
6109 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6245 original size:52 final size:52
Alignment explanation
Indices: 6117--6237 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
6107 CACTGATCTT
6117 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATCATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATCATAAAA
*
6169 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA-CTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATC-ATAAAA
6221 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
6238 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
51 1 0.01
52 66 0.99
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATCATAAAA
Done.