Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_18189
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, 936
Length: 1560
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Found at i:662 original size:144 final size:144
Alignment explanation
Indices: 402--680 Score: 332
Period size: 144 Copynumber: 1.9 Consensus size: 144
392 CAATCCCTCA
* * * *
402 TGAAATTGGAAACTTAAAGAATTTGGTTGCATTGAATTTAAGTAACAACAATCTCAAGCATCGGA
1 TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAAGCATCGGA
* * * *
467 TTCCTCAATCCCTAACTACTTTATCCAAATTGAGCTACTTGTACTTGGATTCAAAT-TTTCTACA
66 TCCCTCAATCACTAACTAATTTATCCAAATTGAGCTACTTGTACTTGGATTCAAATCTTT-TAAA
531 AGGTCCAATTCCTAG
130 AGGTCCAATTCCTAG
* * * **
546 TGAAATTGGAAACTTGAAGAATTTGTTTGAATTGAATCTAAGTAAAAACAAGCTCAATG-GTTTG
1 TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAA-GCATCGG
* * * * *
610 ATCCCTTC-ATCACTAGCTAATTTATCTAGATTGAGCTATTTGTTCCTT-GATTCAAATCTTTTA
65 ATCCC-TCAATCACTAACTAATTTATCCAAATTGAGCTACTTG-TACTTGGATTCAAATCTTTTA
673 AAAGGTCC
128 AAAGGTCC
681 CTTACCATCT
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
144 103 0.91
145 10 0.09
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (144 bp):
TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAAGCATCGGA
TCCCTCAATCACTAACTAATTTATCCAAATTGAGCTACTTGTACTTGGATTCAAATCTTTTAAAA
GGTCCAATTCCTAG
Done.