Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2686
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: 10808
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Found at i:4392 original size:19 final size:20
Alignment explanation
Indices: 4348--4401 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
4338 CTGCCAGTTT
* **
4348 CATGTATCGATACATTTGTT
1 CATGTATCGATACATATGAA
4368 CATGTATCGATACA-ATGAA
1 CATGTATCGATACATATGAA
*
4387 CATGTATTGATACAT
1 CATGTATCGATACAT
4402 TGTATCGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
CATGTATCGATACATATGAA
Found at i:4432 original size:33 final size:32
Alignment explanation
Indices: 4370--4434 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
4360 CATTTGTTCA
* *
4370 TGTATCGATACAATGAACATGTATTGATACAT
1 TGTATCGATACAAAGAACATGTATCGATACAT
4402 TGTATCGATACAAAGCATA-ATGTATCGATACAT
1 TGTATCGATACAAAG-A-ACATGTATCGATACAT
4435 CTGAAAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAT
Found at i:7725 original size:21 final size:21
Alignment explanation
Indices: 7677--7729 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
7667 ACAATTCTTG
*
7677 ATGTATCGATACAATTTTAAA
1 ATGTATCGATACAATTTCAAA
** *
7698 ACATATCGATACAATTTCAAC
1 ATGTATCGATACAATTTCAAA
7719 ATGTATCGATA
1 ATGTATCGATA
7730 AAATCGAGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (21 bp):
ATGTATCGATACAATTTCAAA
Found at i:7842 original size:33 final size:33
Alignment explanation
Indices: 7781--7843 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
7771 ATTTTAAGTG
** *
7781 TATCGATACAAAGCAATTTGTTTTGATACAATT
1 TATCGATACAAAGCAATTTGCATAGATACAATT
**
7814 TATCGATACTTAGCAATTTGCATAGATACA
1 TATCGATACAAAGCAATTTGCATAGATACA
7844 TATGAGTGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (33 bp):
TATCGATACAAAGCAATTTGCATAGATACAATT
Found at i:8310 original size:91 final size:91
Alignment explanation
Indices: 8154--8430 Score: 410
Period size: 91 Copynumber: 3.0 Consensus size: 91
8144 AAGCTTAACA
* * * *
8154 ATTTCCTTGGAGGCAAGGTGCAGCCCACATATTCCCCAATCACATCTCTTTCATCTAACCTCTAG
1 ATTTCCTTGGGGGCAAGGTGCAGCCCACACATTCCCCAATCATATCTCTTTCATCTAACCACTAG
* *
8219 ATGGTATTAATGCATCACAAAGCCTG
66 ATGGTATTGATGCATCACAAAGCTTG
*
8245 ATTTCCTTGGGGGCAAGGTGCAGCCCACACATTACCCAATCATATCTCTTTCATCTAACCACTAG
1 ATTTCCTTGGGGGCAAGGTGCAGCCCACACATTCCCCAATCATATCTCTTTCATCTAACCACTAG
* * *
8310 AAGATATTGATGCATCATAAAGCTTG
66 ATGGTATTGATGCATCACAAAGCTTG
* * * *
8336 ATTTCCATGGGGGCAAGGTGCAGCCCACACATTCCCCAATTATATCTCCTTCATCCAACCACTAG
1 ATTTCCTTGGGGGCAAGGTGCAGCCCACACATTCCCCAATCATATCTCTTTCATCTAACCACTAG
* *
8401 ATGGTATTGATGCATTAGAAAGCTTG
66 ATGGTATTGATGCATCACAAAGCTTG
8427 ATTT
1 ATTT
8431 TCCTAGGGCA
Statistics
Matches: 167, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 167 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (91 bp):
ATTTCCTTGGGGGCAAGGTGCAGCCCACACATTCCCCAATCATATCTCTTTCATCTAACCACTAG
ATGGTATTGATGCATCACAAAGCTTG
Found at i:10117 original size:20 final size:20
Alignment explanation
Indices: 10092--10146 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
10082 AAAAAAATTA
10092 TTTCAAAGTATCTCTATTTC
1 TTTCAAAGTATCTCTATTTC
10112 TTTCAAAGTATCTCTATTTC
1 TTTCAAAGTATCTCTATTTC
10132 TTTCAAAGTATCTCT
1 TTTCAAAGTATCTCT
10147 CTCTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTCAAAGTATCTCTATTTC
Found at i:10283 original size:17 final size:17
Alignment explanation
Indices: 10261--10295 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10251 TATGCAGAAA
10261 ATATATTGCATTCATGT
1 ATATATTGCATTCATGT
*
10278 ATATATTGGATTCATGT
1 ATATATTGCATTCATGT
10295 A
1 A
10296 GAAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (17 bp):
ATATATTGCATTCATGT
Done.