Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3180
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: 51228
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:1595 original size:29 final size:29
Alignment explanation
Indices: 1561--1634 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
1551 TAATCAACCG
*
1561 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
1590 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
1619 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
1635 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:9717 original size:29 final size:29
Alignment explanation
Indices: 9683--9756 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
9673 TAATCAACCG
*
9683 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
9712 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
9741 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
9757 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:15231 original size:20 final size:20
Alignment explanation
Indices: 15206--15277 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
15196 TAACTAGGCA
15206 TCCGAGCTCATTGAGTTGAG
1 TCCGAGCTCATTGAGTTGAG
* * *
15226 TCCGAGTTCACTTATAGATGCAAATG
1 TCCGAGCTCA-TT-GAGTTG---A-G
*
15252 CCCGAGCTCATTGAGTTGAG
1 TCCGAGCTCATTGAGTTGAG
15272 TCCGAG
1 TCCGAG
15278 TTCGTTTATG
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
20 15 0.39
21 3 0.08
22 4 0.11
24 4 0.11
25 3 0.08
26 9 0.24
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (20 bp):
TCCGAGCTCATTGAGTTGAG
Found at i:24636 original size:58 final size:58
Alignment explanation
Indices: 24546--24661 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
24536 CTCGATCAAG
24546 ACCCATATCTCATTTTTCTTGATATATAATGCCAAATTTAACTTGTTTAATAATCATA
1 ACCCATATCTCATTTTTCTTGATATATAATGCCAAATTTAACTTGTTTAATAATCATA
*
24604 ACCCATATCTCATTTTTCTTGATCTATAATGCCAAATTTAACTTGTTTAATAATCATA
1 ACCCATATCTCATTTTTCTTGATATATAATGCCAAATTTAACTTGTTTAATAATCATA
24662 TTGGCCAAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (58 bp):
ACCCATATCTCATTTTTCTTGATATATAATGCCAAATTTAACTTGTTTAATAATCATA
Found at i:33320 original size:33 final size:34
Alignment explanation
Indices: 33228--33320 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 34
33218 GTTCAGTTAA
* *
33228 GGCCTTAGCCCATTTCAGAATCAGA-AACAATGTG
1 GGCCTAAGCCCATTACAGAATCA-ATAACAATGTG
* * *
33262 GGCCTGAGCCCATTCCAGTAA-CAATATCAATG-G
1 GGCCTAAGCCCATTACAG-AATCAATAACAATGTG
33295 GGCCTAAGCCCATTACAGAATCAATA
1 GGCCTAAGCCCATTACAGAATCAATA
33321 CCGTATGCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
32 2 0.04
33 23 0.45
34 24 0.47
35 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (34 bp):
GGCCTAAGCCCATTACAGAATCAATAACAATGTG
Found at i:44296 original size:27 final size:27
Alignment explanation
Indices: 44266--44470 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
44256 ATATTGAGTC
* * * *
44266 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
44293 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44320 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
44348 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
44375 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
44402 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44429 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44456 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44471 GTACAATTTA
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Done.