Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2392
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: 45980
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1419 original size:22 final size:22
Alignment explanation
Indices: 1391--1434 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1381 TTTTGAACCA
1391 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
1413 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
1435 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:4143 original size:23 final size:22
Alignment explanation
Indices: 4091--4143 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4081 TCCACGTCTT
*
4091 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
4113 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
4136 TTTCTTTT
1 TTTCTTTT
4144 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:12503 original size:21 final size:23
Alignment explanation
Indices: 12458--12504 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12448 TCACCTGCAA
* *
12458 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
12481 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
12502 TAA
1 TAA
12505 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:18016 original size:20 final size:20
Alignment explanation
Indices: 17970--18016 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17960 AGCTCGTTTC
*
17970 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
17990 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18010 CAGCTCA
1 CAGCTCA
18017 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:19653 original size:30 final size:30
Alignment explanation
Indices: 19597--19653 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
19587 TGGGCTCAAA
* **
19597 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
19627 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
19654 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:20140 original size:327 final size:327
Alignment explanation
Indices: 19546--20198 Score: 1225
Period size: 327 Copynumber: 2.0 Consensus size: 327
19536 TTTTGAGGAA
*
19546 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTAAAATCAAGAAAATCAAG
* *
19611 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGT
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTCCTGTTCGGAGC
19676 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
*
19741 TGCAGCCAAAGCGTGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
*
19806 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAACCAAGAAATCCAT
19871 AT
326 AT
19873 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTAAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTAAAATCAAGAAAATCAAG
**
19938 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATTGAATCTTGGCCCAATTTTCCTGTTCGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTCCTGTTCGGAGC
*
20003 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
*
20068 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTTGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
20133 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAACCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAACCAAGAAATCCAT
20198 A
326 A
20199 CATATTTAGT
Statistics
Matches: 317, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
327 317 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (327 bp):
GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTAAAATCAAGAAAATCAAG
ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTCCTGTTCGGAGC
GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAACCAAGAAATCCAT
AT
Found at i:20509 original size:20 final size:20
Alignment explanation
Indices: 20463--20509 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20453 AGCTCGTTTC
*
20463 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
20483 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20503 CAGCTCA
1 CAGCTCA
20510 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:43872 original size:12 final size:12
Alignment explanation
Indices: 43857--43894 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
43847 AGGAAATTCG
43857 AAAAAAAATCGA
1 AAAAAAAATCGA
*
43869 AAAAAAAATTGA
1 AAAAAAAATCGA
*
43881 AAAAAAATTCGA
1 AAAAAAAATCGA
43893 AA
1 AA
43895 GTAAAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (12 bp):
AAAAAAAATCGA
Done.