Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01185.F1
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: 3212
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Found at i:854 original size:357 final size:357
Alignment explanation
Indices: 199--912 Score: 1383
Period size: 357 Copynumber: 2.0 Consensus size: 357
189 CCGATCTCGA
*
199 CTCCTCTTGCCCGAATTCCATTTCTCCGTTGTTGTTGTGCCTTGAGTTGTGACTCCATAGTTCAC
1 CTCCTCTTGCCCGAATTCCATTTCTCCGTTGTGGTTGTGCCTTGAGTTGTGACTCCATAGTTCAC
*
264 CCTGGCAAAAACAAGCTCGTCTCTTCTGGTGATGAGAGGGTGTGGGTGTGCGAGTAGGCCAGGGA
66 CCTGGCAAAAACAAGCTCGTCTCTTCTCGTGATGAGAGGGTGTGGGTGTGCGAGTAGGCCAGGGA
329 CCTCAGCTGCAGTCACTTGCGATGCCCACATCCACTCTGCTAATCATCAGGCTCGTCGCTACCAT
131 CCTCAGCTGCAGTCACTTGCGATGCCCACATCCACTCTGCTAATCATCAGGCTCGTCGCTACCAT
*
394 CTTGTCCTTGTCGACCCTTTTCTTAATGCCAGTAATTGTCAACCAGATGAAGTGATAGGTTCTGG
196 CTTGTCCTTGTCGACCCTTTTCTTAATGCCAGTAATTGTCAACCAGATGAAGTGATAAGTTCTGG
459 GTCGTTGCCCAGTCCTACTCTTAATCCCTAAACTCACCATGGAAACTAATCATGTCAAAACTGTG
261 GTCGTTGCCCAGTCCTACTCTTAATCCCTAAACTCACCATGGAAACTAATCATGTCAAAACTGTG
524 CTTAGTTTGGGTTGTTGTTGTTGTGGAATAAG
326 CTTAGTTTGGGTTGTTGTTGTTGTGGAATAAG
556 CTCCTCTTGCCCGAATTCCATTTCTCCGTTGTGGTTGTGCCTTGAGTTGTGACTCCATAGTTCAC
1 CTCCTCTTGCCCGAATTCCATTTCTCCGTTGTGGTTGTGCCTTGAGTTGTGACTCCATAGTTCAC
621 CCTGGCAAAAACAAGCTCGTCTCTTCTCGTGATGAGAGGGTGTGGGTGTGCGAGTAGGCCAGGGA
66 CCTGGCAAAAACAAGCTCGTCTCTTCTCGTGATGAGAGGGTGTGGGTGTGCGAGTAGGCCAGGGA
*
686 CCTCAGCTGCCGTCACTTGCGATGCCCACATCCACTCTGCTAATCATCAGGCTCGTCGCTACCAT
131 CCTCAGCTGCAGTCACTTGCGATGCCCACATCCACTCTGCTAATCATCAGGCTCGTCGCTACCAT
*
751 CTTGTCCTTGTCGACCCTTTTCTTAATGCTAGTAATTGTCAACCAGATGAAGTGATAAGTTCTGG
196 CTTGTCCTTGTCGACCCTTTTCTTAATGCCAGTAATTGTCAACCAGATGAAGTGATAAGTTCTGG
816 GTCGTTGCCCAGTCCTACTCTTAATCCCTAAACTCACCATGGAAACTAATCATGTCAAAACTGTG
261 GTCGTTGCCCAGTCCTACTCTTAATCCCTAAACTCACCATGGAAACTAATCATGTCAAAACTGTG
881 CTTAGTTTGGGTTGTTGTTGTTGTGGAATAAG
326 CTTAGTTTGGGTTGTTGTTGTTGTGGAATAAG
913 GGGGTGGTTT
Statistics
Matches: 352, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
357 352 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.31
Consensus pattern (357 bp):
CTCCTCTTGCCCGAATTCCATTTCTCCGTTGTGGTTGTGCCTTGAGTTGTGACTCCATAGTTCAC
CCTGGCAAAAACAAGCTCGTCTCTTCTCGTGATGAGAGGGTGTGGGTGTGCGAGTAGGCCAGGGA
CCTCAGCTGCAGTCACTTGCGATGCCCACATCCACTCTGCTAATCATCAGGCTCGTCGCTACCAT
CTTGTCCTTGTCGACCCTTTTCTTAATGCCAGTAATTGTCAACCAGATGAAGTGATAAGTTCTGG
GTCGTTGCCCAGTCCTACTCTTAATCCCTAAACTCACCATGGAAACTAATCATGTCAAAACTGTG
CTTAGTTTGGGTTGTTGTTGTTGTGGAATAAG
Found at i:1435 original size:43 final size:43
Alignment explanation
Indices: 1374--1460 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
1364 TAATCCATAC
1374 CCTTCTCTAAGATTCTCAATCAAACCACCCTTCTCACCAGCTT
1 CCTTCTCTAAGATTCTCAATCAAACCACCCTTCTCACCAGCTT
1417 CCTTCTCTAAGATTCTCAATCAAACCACCCTTCTCACCAGCTT
1 CCTTCTCTAAGATTCTCAATCAAACCACCCTTCTCACCAGCTT
1460 C
1 C
1461 GTCCTCTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.40, G:0.05, T:0.30
Consensus pattern (43 bp):
CCTTCTCTAAGATTCTCAATCAAACCACCCTTCTCACCAGCTT
Found at i:2258 original size:2 final size:2
Alignment explanation
Indices: 2253--2311 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2243 CCCAAGGGGG
2253 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2295 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
2312 GTCTGGGTAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.