Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_27081
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: 2937
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:963 original size:144 final size:144
Alignment explanation
Indices: 541--992 Score: 701
Period size: 144 Copynumber: 3.1 Consensus size: 144
531 CTCAAGGAAC
* *
541 ATGCTTGTTGGTCCAATCCCATCTTCTATCAACAACTTAACCAATCTTGCATCGTTGGTTCTTAA
1 ATGCTTGTTGGTCCAATCCCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
606 T-GACAACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTG
66 TGGA-AACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTG
*
670 GAGCTATCTTCTAAT
130 GATCTATCTTCTAAT
* **
685 ATGCTTGTTGGTCCAATCCCATCTTCTGTCAACCACTTAACCAATCTTGCATCACTGGTTCTTTA
1 ATGCTTGTTGGTCCAATCCCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
*
750 TGGAAACCAACTTAATGGATCCATTCCACAAGAAATTGGGAGACTGACAAATTTGATTACATTGG
66 TGGAAACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTGG
815 ATCTATCTTCTAAT
131 ATCTATCTTCTAAT
829 ATGCTTGTTGGTCCAATCCCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
1 ATGCTTGTTGGTCCAATCCCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
* * * * * * **
894 TGGAAACCAACTCAATGGATCCATTCCGCATGAAATTGGGAGGCTAACGAATTTGGTTACATTAC
66 TGGAAACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTGG
** *
959 ATCTATCCGCCAAT
131 ATCTATCTTCTAAT
*
973 ATGCTT-TTGGGTCCCATCCC
1 ATGCTTGTT-GGTCCAATCCC
993 TTCCTCTTTG
Statistics
Matches: 283, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
143 2 0.01
144 279 0.99
145 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (144 bp):
ATGCTTGTTGGTCCAATCCCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
TGGAAACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTGG
ATCTATCTTCTAAT
Done.