Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2215
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: 11426
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:214 original size:21 final size:21
Alignment explanation
Indices: 182--242 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
172 AGTTTTCATT
*
182 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATCAAA-AA
*
204 TTTCTCCCCTTTAATCAAAAA
1 TTTCTCCCCCTTAATCAAAAA
225 TTTCTCCCCCTTAATCAA
1 TTTCTCCCCCTTAATCAA
243 GGCATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.30, C:0.31, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTCTCCCCCTTAATCAAAAA
Found at i:5441 original size:19 final size:19
Alignment explanation
Indices: 5397--5469 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
5387 CTGCCAATCT
* **
5397 CATGTATCAATACAATTGTC
1 CATGTATCGATACAA-TGAA
5417 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
5436 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
5457 -ATGTATCGATACA
1 CATGTATCGATACA
5470 TCTGAGTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.38
20 28 0.60
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:8967 original size:52 final size:51
Alignment explanation
Indices: 8889--9037 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
8879 CGAAATATGA
8889 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
8941 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
8993 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
9038 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:9128 original size:33 final size:33
Alignment explanation
Indices: 9091--9157 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
9081 AGTAGCTTAA
9091 ATTGTATCGATACAAAAAGATATGTATCGATAC
1 ATTGTATCGATACAAAAAGATATGTATCGATAC
* ***
9124 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAGATATGTATCGATAC
9157 A
1 A
9158 AACTGTTGAA
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:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAGATATGTATCGATAC
Found at i:9131 original size:13 final size:13
Alignment explanation
Indices: 9113--9137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9103 CAAAAAGATA
9113 TGTATCGATACAT
1 TGTATCGATACAT
9126 TGTATCGATACA
1 TGTATCGATACA
9138 ACATTTTATG
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:10375 original size:52 final size:51
Alignment explanation
Indices: 10307--10429 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 51
10297 TGCATGTGTT
* * *
10307 GATACATTGAAGAATGTATCGATACATTTGGGTCAAAAAGCTAGA-ATATATC
1 GATACAATGAAAAATGTATCGATACATTTGGG-CAAAAACCTA-ACATATATC
* *
10359 GATACAATGAAAAATGTATCGATACATTTGGGCTAAAACCTAACATGTATC
1 GATACAATGAAAAATGTATCGATACATTTGGGCAAAAACCTAACATATATC
*
10410 GATACAATAAAAAATGTATC
1 GATACAATGAAAAATGTATC
10430 TAAAAAAATG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 33 0.52
52 30 0.47
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (51 bp):
GATACAATGAAAAATGTATCGATACATTTGGGCAAAAACCTAACATATATC
Found at i:10479 original size:65 final size:65
Alignment explanation
Indices: 10368--10494 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
10358 CGATACAATG
*
10368 AAAAATGTATCGATACATTTGGGCTAAAACCTAACATGTATCGATACAATAAAAAATGTATCTAA
1 AAAAATGTATCGATACATTTGGGCTAAAACCCAACATGTATCGATACAATAAAAAATGTATCTAA
* *
10433 AAAAATGTATCGATACATTTGGGCTAAAACCCAACATTTATTGATACAATAAAAAATGTATC
1 AAAAATGTATCGATACATTTGGGCTAAAACCCAACATGTATCGATACAATAAAAAATGTATC
10495 GATACATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (65 bp):
AAAAATGTATCGATACATTTGGGCTAAAACCCAACATGTATCGATACAATAAAAAATGTATCTAA
Done.