Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00699.P1
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: 8434
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Found at i:4535 original size:19 final size:19
Alignment explanation
Indices: 4511--4550 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4501 TTCTTTGTGG
4511 CTGGAAAACTATTATGTTT
1 CTGGAAAACTATTATGTTT
4530 CTGGAAAACTATTATGTTT
1 CTGGAAAACTATTATGTTT
4549 CT
1 CT
4551 TTGTGGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (19 bp):
CTGGAAAACTATTATGTTT
Found at i:4554 original size:46 final size:49
Alignment explanation
Indices: 4498--4622 Score: 175
Period size: 54 Copynumber: 2.5 Consensus size: 49
4488 CAAGGAAGTT
4498 TGTTTCTTTGTGGCTGGAAAACTATTATG-TT-T-CTGGAAAACTATTA
1 TGTTTCTTTGTGGCTGGAAAACTATTATGTTTGTGCTGGAAAACTATTA
*
4544 TGTTTCTTTGTGGCTGGAAAACTATTATGTTTCTTTGTGGCTGGAAAATTATTA
1 TGTTTCTTTGTGGCTGGAAAACTATTATG----TTTGT-GCTGGAAAACTATTA
4598 TGTTTCTTTGTGGCTGGAAAACTAT
1 TGTTTCTTTGTGGCTGGAAAACTAT
4623 GTTTCTTTTG
Statistics
Matches: 70, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
46 29 0.41
51 2 0.03
52 1 0.01
54 38 0.54
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.45
Consensus pattern (49 bp):
TGTTTCTTTGTGGCTGGAAAACTATTATGTTTGTGCTGGAAAACTATTA
Found at i:4568 original size:27 final size:27
Alignment explanation
Indices: 4530--4622 Score: 177
Period size: 27 Copynumber: 3.4 Consensus size: 27
4520 TATTATGTTT
4530 CTGGAAAACTATTATGTTTCTTTGTGG
1 CTGGAAAACTATTATGTTTCTTTGTGG
4557 CTGGAAAACTATTATGTTTCTTTGTGG
1 CTGGAAAACTATTATGTTTCTTTGTGG
*
4584 CTGGAAAATTATTATGTTTCTTTGTGG
1 CTGGAAAACTATTATGTTTCTTTGTGG
4611 CTGGAAAACTAT
1 CTGGAAAACTAT
4623 GTTTCTTTTG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.43
Consensus pattern (27 bp):
CTGGAAAACTATTATGTTTCTTTGTGG
Found at i:5639 original size:126 final size:126
Alignment explanation
Indices: 5414--5663 Score: 396
Period size: 126 Copynumber: 2.0 Consensus size: 126
5404 GGGCCCGAAG
*
5414 AATCACCAATCGAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
1 AATCACCAATCAAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
*
5479 TATTTGTTGAAGACCCCGTAGCGTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
66 TATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
* * *
5540 AATCACCAATCAAGTATGAGAAAG-ATCTCTAAGTTTGTTTTGAATTAAGTTTTTTAGTAAATGT
1 AATCACCAATCAAGTATGAG--AGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGT
* * *
5604 A-TATTTGTTGAAGACCTCGTAGCCTTGTGTGGCTTAATTTGTAGTTTTGCAGTCATATAG
64 ATTATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAG
5664 GAAACTTCTG
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
126 74 0.65
127 38 0.33
128 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (126 bp):
AATCACCAATCAAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
TATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
Found at i:8109 original size:51 final size:51
Alignment explanation
Indices: 7960--8218 Score: 437
Period size: 51 Copynumber: 5.0 Consensus size: 51
7950 TCCATGGGAA
*
7960 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTGCACAATGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTC
8011 AATTAGGGGTCCTGAAAGGCTGTGTGTTCCTTACACAATGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGC--TGTGTTCCTTACACAATGGCAAAACTATGTC
* *
8064 AATTAGGGTTCCTGAAAGGCTGTGTTCCTTACACAGTGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTC
* *
8115 AATTAGGGGTCCTGAAAGGCTGTGTTCTTTACACAATGGCAAAACCATGTC
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTC
8166 AATTAGGGGTCCTGAAAGGCTGTGTATTCCTTACACAATGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGCTGTG--TTCCTTACACAATGGCAAAACTATGTC
8219 TTAATTTCAG
Statistics
Matches: 195, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
51 121 0.62
53 74 0.38
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (51 bp):
AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTC
Found at i:8196 original size:104 final size:103
Alignment explanation
Indices: 7960--8218 Score: 439
Period size: 104 Copynumber: 2.5 Consensus size: 103
7950 TCCATGGGAA
*
7960 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTGCACAATGGCAAAACTATGTCAATTAGGGGTCCTG
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTCAATTAGGGGTCCTG
*
8025 AAAGGCTGTGTGTTCCTTACACAATGGCAAAACTATGTC
66 AAAGGC-GTGTGTTCCTTACACAATGGCAAAACCATGTC
* *
8064 AATTAGGGTTCCTGAAAGGCTGTGTTCCTTACACAGTGGCAAAACTATGTCAATTAGGGGTCCTG
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTCAATTAGGGGTCCTG
*
8129 AAAGGC-TGTGTTCTTTACACAATGGCAAAACCATGTC
66 AAAGGCGTGTGTTCCTTACACAATGGCAAAACCATGTC
8166 AATTAGGGGTCCTGAAAGGCTGTGTATTCCTTACACAATGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGCTGTG--TTCCTTACACAATGGCAAAACTATGTC
8219 TTAATTTCAG
Statistics
Matches: 146, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
102 52 0.36
104 94 0.64
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (103 bp):
AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTCAATTAGGGGTCCTG
AAAGGCGTGTGTTCCTTACACAATGGCAAAACCATGTC
Done.