Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_34095
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: 4551
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Found at i:4042 original size:159 final size:159
Alignment explanation
Indices: 3812--4122 Score: 439
Period size: 159 Copynumber: 2.0 Consensus size: 159
3802 TCATCACAAG
* * *
3812 CTGATGATGCTGAAGCCAGTCAAGTTGCATCCAAGAATTGCTTGGTACCTAGAATTGAAGCTGAT
1 CTGATGATGCTGAAGCCAGTCAAGTTGCATCAAAGAATTGCTTGGTACCAAAAATTGAAGCTGAT
* * * * *
3877 GATGATTTTGGCAATTGTTATGCTGGAAATTCTGGCCCTGCTGCCCAACTCACTACTATAGAATA
66 GATGATTTTGGCAAATGTCATGCTGGAAATTCTAGCCCCGCTGCCCAACTCACTACCATAGAATA
3942 TCAAGAAAATGAAGAGGAAGTCAATCTTA
131 TCAAGAAAATGAAGAGGAAGTCAATCTTA
*
3971 CTGATGATGCT-ATAGCCAGTCAAGTTGCATCTAAAG-ATTGGC-TGGTTCCAAAAATTGAAGCT
1 CTGATGATGCTGA-AGCCAGTCAAGTTGCATC-AAAGAATT-GCTTGGTACCAAAAATTGAAGCT
* * * * *
4033 GATGATGATTTTGGCAAATGTCATGTTGGAAATTCTAGCCCCGCTGCCCAATTCCCTGCCATAGG
63 GATGATGATTTTGGCAAATGTCATGCTGGAAATTCTAGCCCCGCTGCCCAACTCACTACCATAGA
*
4098 ATATCAAGAAACTGAAGAGGAAGTC
128 ATATCAAGAAAATGAAGAGGAAGTC
4123 CAACCTACTA
Statistics
Matches: 134, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
158 1 0.01
159 128 0.96
160 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (159 bp):
CTGATGATGCTGAAGCCAGTCAAGTTGCATCAAAGAATTGCTTGGTACCAAAAATTGAAGCTGAT
GATGATTTTGGCAAATGTCATGCTGGAAATTCTAGCCCCGCTGCCCAACTCACTACCATAGAATA
TCAAGAAAATGAAGAGGAAGTCAATCTTA
Done.