Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00699.M1
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: 4789
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:1259 original size:19 final size:19
Alignment explanation
Indices: 1235--1274 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1225 TTCTTTGTGG
1235 CTGGAAAACTATTATGTTT
1 CTGGAAAACTATTATGTTT
1254 CTGGAAAACTATTATGTTT
1 CTGGAAAACTATTATGTTT
1273 CT
1 CT
1275 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:1278 original size:46 final size:49
Alignment explanation
Indices: 1222--1346 Score: 175
Period size: 54 Copynumber: 2.5 Consensus size: 49
1212 CAAGGAAGTT
1222 TGTTTCTTTGTGGCTGGAAAACTATTATG-TT-T-CTGGAAAACTATTA
1 TGTTTCTTTGTGGCTGGAAAACTATTATGTTTGTGCTGGAAAACTATTA
*
1268 TGTTTCTTTGTGGCTGGAAAACTATTATGTTTCTTTGTGGCTGGAAAATTATTA
1 TGTTTCTTTGTGGCTGGAAAACTATTATG----TTTGT-GCTGGAAAACTATTA
1322 TGTTTCTTTGTGGCTGGAAAACTAT
1 TGTTTCTTTGTGGCTGGAAAACTAT
1347 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:1292 original size:27 final size:27
Alignment explanation
Indices: 1254--1346 Score: 177
Period size: 27 Copynumber: 3.4 Consensus size: 27
1244 TATTATGTTT
1254 CTGGAAAACTATTATGTTTCTTTGTGG
1 CTGGAAAACTATTATGTTTCTTTGTGG
1281 CTGGAAAACTATTATGTTTCTTTGTGG
1 CTGGAAAACTATTATGTTTCTTTGTGG
*
1308 CTGGAAAATTATTATGTTTCTTTGTGG
1 CTGGAAAACTATTATGTTTCTTTGTGG
1335 CTGGAAAACTAT
1 CTGGAAAACTAT
1347 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:2363 original size:126 final size:126
Alignment explanation
Indices: 2138--2387 Score: 396
Period size: 126 Copynumber: 2.0 Consensus size: 126
2128 GGGCCCGAAG
*
2138 AATCACCAATCGAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
1 AATCACCAATCAAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
*
2203 TATTTGTTGAAGACCCCGTAGCGTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
66 TATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
* * *
2264 AATCACCAATCAAGTATGAGAAAG-ATCTCTAAGTTTGTTTTGAATTAAGTTTTTTAGTAAATGT
1 AATCACCAATCAAGTATGAG--AGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGT
* * *
2328 A-TATTTGTTGAAGACCTCGTAGCCTTGTGTGGCTTAATTTGTAGTTTTGCAGTCATATAG
64 ATTATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAG
2388 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:4464 original size:51 final size:51
Alignment explanation
Indices: 4315--4573 Score: 437
Period size: 51 Copynumber: 5.0 Consensus size: 51
4305 TCCATGGGAA
*
4315 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTGCACAATGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTC
4366 AATTAGGGGTCCTGAAAGGCTGTGTGTTCCTTACACAATGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGC--TGTGTTCCTTACACAATGGCAAAACTATGTC
* *
4419 AATTAGGGTTCCTGAAAGGCTGTGTTCCTTACACAGTGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTC
* *
4470 AATTAGGGGTCCTGAAAGGCTGTGTTCTTTACACAATGGCAAAACCATGTC
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTC
4521 AATTAGGGGTCCTGAAAGGCTGTGTATTCCTTACACAATGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGCTGTG--TTCCTTACACAATGGCAAAACTATGTC
4574 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:4551 original size:104 final size:103
Alignment explanation
Indices: 4315--4573 Score: 439
Period size: 104 Copynumber: 2.5 Consensus size: 103
4305 TCCATGGGAA
*
4315 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTGCACAATGGCAAAACTATGTCAATTAGGGGTCCTG
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTCAATTAGGGGTCCTG
*
4380 AAAGGCTGTGTGTTCCTTACACAATGGCAAAACTATGTC
66 AAAGGC-GTGTGTTCCTTACACAATGGCAAAACCATGTC
* *
4419 AATTAGGGTTCCTGAAAGGCTGTGTTCCTTACACAGTGGCAAAACTATGTCAATTAGGGGTCCTG
1 AATTAGGGGTCCTGAAAGGCTGTGTTCCTTACACAATGGCAAAACTATGTCAATTAGGGGTCCTG
*
4484 AAAGGC-TGTGTTCTTTACACAATGGCAAAACCATGTC
66 AAAGGCGTGTGTTCCTTACACAATGGCAAAACCATGTC
4521 AATTAGGGGTCCTGAAAGGCTGTGTATTCCTTACACAATGGCAAAACTATGTC
1 AATTAGGGGTCCTGAAAGGCTGTG--TTCCTTACACAATGGCAAAACTATGTC
4574 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.