Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_26962
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, 727
Length: 1212
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Found at i:613 original size:201 final size:201
Alignment explanation
Indices: 285--646 Score: 453
Period size: 201 Copynumber: 1.8 Consensus size: 201
275 GTGTTGATGT
* * * *
285 CATAAGGAAAGAACAATCCAATGAGCAAAACATCTCAAGAGCTCATGGGTTTGAAAATGTTCGGA
1 CATAAGGAAAGAAAAATCCAATGAACAAAACATCCCAAGAGCTAATGGGTTTGAAAATGTTCGGA
* * * * ** * *
350 ACGGAGAAATGATGGAGGAAGTTGAAGAAGATTCTTCTGATAGTGGAGGCGATGACATTGGTGAG
66 ACAGAGAAAGGATGGAGGAAGATGAAGAAGATTCTTCTGATAATGGAAACGATGAAATTGGTGAC
*
415 GGCCAACAGCAA-AAGCGACCATCCAGTTCAAGCGGTGTAAGAACTGTAGAAGAAACACAGGGTG
131 GACCAACAGCAATAA-CGACCATCCAGTTCAAGCGGTGTAAGAACTGTAGAAGAAACACAGGGTG
479 TTGCATC
195 TTGCATC
** * * *
486 CATAAGGAAAGAAAAATCTGATGAACAAAACCTCCCTATG-GCTAATGGGTTTGAAAATGTTGGG
1 CATAAGGAAAGAAAAATCCAATGAACAAAACATCCC-AAGAGCTAATGGGTTTGAAAATGTTCGG
* *
550 AACAGAGAAAGGATGGAGGAAGAT-ATAGAA-ATTTCTTCTGATAATGGAAATGCTGAAATTGGT
65 AACAGAGAAAGGATGGAGGAAGATGA-AGAAGA-TTCTTCTGATAATGGAAACGATGAAATTGGT
* * *
613 GACGACCGACAGCAATTACGACCATCTAGTTCAA
128 GACGACCAACAGCAATAACGACCATCCAGTTCAA
647 AAGTGCCTGT
Statistics
Matches: 134, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
200 2 0.01
201 129 0.96
202 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (201 bp):
CATAAGGAAAGAAAAATCCAATGAACAAAACATCCCAAGAGCTAATGGGTTTGAAAATGTTCGGA
ACAGAGAAAGGATGGAGGAAGATGAAGAAGATTCTTCTGATAATGGAAACGATGAAATTGGTGAC
GACCAACAGCAATAACGACCATCCAGTTCAAGCGGTGTAAGAACTGTAGAAGAAACACAGGGTGT
TGCATC
Done.