Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g01741.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: 5277
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:3096 original size:210 final size:209
Alignment explanation
Indices: 2734--3378 Score: 1042
Period size: 210 Copynumber: 3.1 Consensus size: 209
2724 AATATTTGGA
*
2734 GTTGTCCTAATTTAAGTTCAATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
1 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
* *
2799 GAAAGCTGCGCTGAGTTGGAAGTTATTT-CGATGACCGGGGGATGTTCATCTCTTGAAAAGCTTA
66 GAAAGGTGCGCTGAGTTGGAAGTT-TTTCCGATAACCGGGGGATGTTCATCTCTTGAAAAGCTTA
* **
2863 GCATTCTTTTTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAA
130 ACATTC-CATTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAA
2928 GAATTAGATCTATATG
194 GAATTAGATCTATATG
2944 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
1 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
3009 GAAAGGTGCGCTGAGTTGGAAGTTTTTCCGATAACCGGGGGATGTTCATCTCTTGAAAAGCTTAA
66 GAAAGGTGCGCTGAGTTGGAAGTTTTTCCGATAACCGGGGGATGTTCATCTCTTGAAAAGCTTAA
*
3074 CATTCACCTTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAAG
131 CATTC-CATTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAAG
3139 AATTAGATCTATATG
195 AATTAGATCTATATG
3154 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
1 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
* ** * * **
3219 GAAACGTGCAATGAGTTGGAAGTTCTTCCGATTACCGGAAGATGTTCATCTCTTGAAAAAG-TTA
66 GAAAGGTGCGCTGAGTTGGAAGTTTTTCCGATAACCGGGGGATGTTCATCTCTTG-AAAAGCTTA
* * *
3283 ACATTTCCAGTTGCAAAAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTATCTCAAA
130 ACA-TTCCATTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAA
* * *
3348 TATTTACATCTATATG
194 GAATTAGATCTATATG
*
3364 ATTGTCCTAATTTAA
1 GTTGTCCTAATTTAA
3379 AGCCCATTCC
Statistics
Matches: 410, Mismatches: 22, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
209 3 0.01
210 399 0.97
211 8 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (209 bp):
GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
GAAAGGTGCGCTGAGTTGGAAGTTTTTCCGATAACCGGGGGATGTTCATCTCTTGAAAAGCTTAA
CATTCCATTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAAGA
ATTAGATCTATATG
Found at i:3857 original size:144 final size:144
Alignment explanation
Indices: 3655--3939 Score: 365
Period size: 144 Copynumber: 2.0 Consensus size: 144
3645 TCCCTTCGAG
* * * * *
3655 TTCTAAAGTTGATTGGTTGGGAAAAGCTAAAGAGTCTTCCCCCCCAACTTCAATTCCTCACTTCC
1 TTCTAAAGTTGAGTGGTTGGGAAAAGCTAAAGAGCCTTCCCCACCAACTTCAACTCCTCACTGCC
* *
3720 CTTGAAGCTTTGACGATAAAAGAGTTTCA-AGGAATAGAAGCCTTACCGAAGTGGTTGGGAAATC
66 CTTAAAGCTTTGACGATAAAAGAGTTTCATA-AAATAGAAGCCTTACCGAAGTGGTTGGGAAATC
3784 TCTCTTCTCTAAGGT
130 TCTCTTCTCTAAGGT
* ** *
3799 TTCTAAATTTGAGTGGTTTTGAAAAGCTAAAGAGCCTTCCTCACCAACTTCAACTCCTCACTGCC
1 TTCTAAAGTTGAGTGGTTGGGAAAAGCTAAAGAGCCTTCCCCACCAACTTCAACTCCTCACTGCC
* ** **** * * *
3864 CTTAAAGTTTTGATTATGTCGGGGTTTCATAAAATAGAAGCCTTGCCGGAGTGGTTGGGAAATCT
66 CTTAAAGCTTTGACGATAAAAGAGTTTCATAAAATAGAAGCCTTACCGAAGTGGTTGGGAAATCT
3929 CTCTTCTCTAA
131 CTCTTCTCTAA
3940 CGCGCCTGCA
Statistics
Matches: 119, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
144 118 0.99
145 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (144 bp):
TTCTAAAGTTGAGTGGTTGGGAAAAGCTAAAGAGCCTTCCCCACCAACTTCAACTCCTCACTGCC
CTTAAAGCTTTGACGATAAAAGAGTTTCATAAAATAGAAGCCTTACCGAAGTGGTTGGGAAATCT
CTCTTCTCTAAGGT
Done.