Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_20267
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: 3888
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Found at i:2998 original size:210 final size:209
Alignment explanation
Indices: 2636--3280 Score: 1042
Period size: 210 Copynumber: 3.1 Consensus size: 209
2626 AATATTTGGA
*
2636 GTTGTCCTAATTTAAGTTCAATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
1 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
* *
2701 GAAAGCTGCGCTGAGTTGGAAGTTATTT-CGATGACCGGGGGATGTTCATCTCTTGAAAAGCTTA
66 GAAAGGTGCGCTGAGTTGGAAGTT-TTTCCGATAACCGGGGGATGTTCATCTCTTGAAAAGCTTA
* **
2765 GCATTCTTTTTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAA
130 ACATTC-CATTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAA
2830 GAATTAGATCTATATG
194 GAATTAGATCTATATG
2846 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
1 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
2911 GAAAGGTGCGCTGAGTTGGAAGTTTTTCCGATAACCGGGGGATGTTCATCTCTTGAAAAGCTTAA
66 GAAAGGTGCGCTGAGTTGGAAGTTTTTCCGATAACCGGGGGATGTTCATCTCTTGAAAAGCTTAA
*
2976 CATTCACCTTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAAG
131 CATTC-CATTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAAG
3041 AATTAGATCTATATG
195 AATTAGATCTATATG
3056 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
1 GTTGTCCTAATTTAAGTTCGATTCCAGAGTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATT
* ** * * **
3121 GAAACGTGCAATGAGTTGGAAGTTCTTCCGATTACCGGAAGATGTTCATCTCTTGAAAAAG-TTA
66 GAAAGGTGCGCTGAGTTGGAAGTTTTTCCGATAACCGGGGGATGTTCATCTCTTG-AAAAGCTTA
* * *
3185 ACATTTCCAGTTGCAAAAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTATCTCAAA
130 ACA-TTCCATTTGCAAGAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAA
* * *
3250 TATTTACATCTATATG
194 GAATTAGATCTATATG
*
3266 ATTGTCCTAATTTAA
1 GTTGTCCTAATTTAA
3281 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
Done.