Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_30327
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, 768
Length: 1281
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Found at i:705 original size:177 final size:179
Alignment explanation
Indices: 459--920 Score: 664
Period size: 177 Copynumber: 2.6 Consensus size: 179
449 GGGTGTATGC
** * * * * * **
459 AAAAAGGCAATCTGCTAGGCGTAAAACCCAAG---CAGAAACAACTGAAGATGTAATTGAGGTAG
1 AAAAAGGCAATCTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTTTGAGGTAG
521 ATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTCTGATATC
66 ATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTCTGATATC
* *
586 AAACCAGTCCAAGCTAAGGAAGGGATTGACAACAAA-AG-GGTTTGTTT
131 AAACCAGTCCAAACCAAGGAAGGGATTGACAACAAAGAGTGGTTTGTTT
* *
633 AAGAAGGCAATCTGCTAGGTTTAAATCCCAAGAACCTGAAACTACTGAATATATGTTTGAGGTAG
1 AAAAAGGCAATCTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTTTGAGGTAG
698 ATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTCTGATATC
66 ATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTCTGATATC
* *
763 AAACCAGTCCAAACCAAGGAGGGGATTGACAACAAAGGGTTTTTGGTTTGTTT
131 AAACCAGTCCAAACCAAGGAAGGGATTGACAACAAAGAG----TGGTTTGTTT
* **
816 AAAAAGGCTATCTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTGCGAGGTAG
1 AAAAAGGCAATCTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTTTGAGGTAG
* * *
881 ATGATACAAAATCTTTTGCTCCTATCTGTGATGATAAGGT
66 ATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGT
921 GTGTAAAAGT
Statistics
Matches: 257, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
174 28 0.11
177 122 0.47
178 1 0.00
183 106 0.41
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (179 bp):
AAAAAGGCAATCTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTTTGAGGTAG
ATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTCTGATATC
AAACCAGTCCAAACCAAGGAAGGGATTGACAACAAAGAGTGGTTTGTTT
Found at i:944 original size:183 final size:177
Alignment explanation
Indices: 514--920 Score: 652
Period size: 183 Copynumber: 2.3 Consensus size: 177
504 AGATGTAATT
514 GAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTC
1 GAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTC
* * *
579 TGATATCAAACCAGTCCAAGCTAAGGAAGGGATTGACAACAAAAGGGTTTGTTTAAGAAGGCAAT
66 TGATATCAAACCAGTCCAAACCAAGGAAGGGATTGACAACAAAAGGGTTTGTTTAAAAAGGCAAT
* **
644 CTGCTAGGTTTAAATCCCAAGAACCTGAAACTACTGAATATATGTTT
131 CTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTGC
691 GAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTC
1 GAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTC
* *
756 TGATATCAAACCAGTCCAAACCAAGGAGGGGATTGACAACAAAGGGTTTTTGGTTTGTTTAAAAA
66 TGATATCAAACCAGTCCAAACCAAGGAAGGGATTGACAACAAA-AG-----GGTTTGTTTAAAAA
*
821 GGCTATCTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTGC
125 GGCAATCTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTGC
* * *
874 GAGGTAGATGATACAAAATCTTTTGCTCCTATCTGTGATGATAAGGT
1 GAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGT
921 GTGTAAAAGT
Statistics
Matches: 212, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
177 105 0.50
178 1 0.00
183 106 0.50
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (177 bp):
GAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCTTC
TGATATCAAACCAGTCCAAACCAAGGAAGGGATTGACAACAAAAGGGTTTGTTTAAAAAGGCAAT
CTGCTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTGC
Done.