Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_15878
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: 3164
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Found at i:1181 original size:36 final size:36
Alignment explanation
Indices: 1141--1252 Score: 188
Period size: 36 Copynumber: 3.1 Consensus size: 36
1131 GATGTAAAAA
* *
1141 ATGGTACTACGAATGAAGTGGTTTCATTTGATGTTG
1 ATGGTACTACGAACGAAGTGGTTTCATCTGATGTTG
*
1177 ATGGTACAACGAACGAAGTGGTTTCATCTGATGTTG
1 ATGGTACTACGAACGAAGTGGTTTCATCTGATGTTG
*
1213 ATGGTACTATGAACGAAGTGGTTTCATCTGATGTTG
1 ATGGTACTACGAACGAAGTGGTTTCATCTGATGTTG
1249 ATGG
1 ATGG
1253 GGGTAATAGG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.35
Consensus pattern (36 bp):
ATGGTACTACGAACGAAGTGGTTTCATCTGATGTTG
Found at i:1460 original size:285 final size:285
Alignment explanation
Indices: 939--1465 Score: 788
Period size: 285 Copynumber: 1.8 Consensus size: 285
929 TGATGCTACA
* *
939 AACGCAGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCC
1 AACGAAGTGGTTGCATCTGATGTTGATGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCC
* * * * *
1004 TGTTGGGACTGATGATTCGAGTACGGCGAAACAGGAATCTCAAGGATGCTCTGGTTATGATTCTC
66 TGTTGAGACTGATGATTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTC
* **
1069 AAAAGGATTCTTTTGATAATATTTCTGTGGGAAGTGAAGAGTCGCCTACTAAAGAACCTCAAGAT
131 AAAAGGATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGACTAAAGAACCTCAAGAT
* * * **
1134 GTAAAAAATGGTACTACGAATGAAGTGGTTTCATTTGATGTTGATGGTACAACGAACGAAGTGGT
196 ATAAAAAATGATAATACGAATGAAGTGGTTTCACCTGATGTTGATGGTACAACGAACGAAGTGGT
1199 TTCATCTGATGTTGATGGTACTATG
261 TTCATCTGATGTTGATGGTACTATG
* * *
1224 AACGAAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGACATC-AGAACCGTGC
1 AACGAAGTGGTTGCATCTGATGTTGATGGGGGTAATAAGATGACTTCAGAC-TCAAGAACCATGC
1288 CTGTTGAGACTGATGACTT-GAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTC
65 CTGTTGAGACTGATGA-TTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTC
* * * * * *
1352 TCCAAAGGATTCTTTTGATACTATTTCTGTGAGAAGTGAAGAGTTGCAGGCTAAGGAACCTCAGG
129 TCAAAAGGATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGACTAAAGAACCTCAAG
* *
1417 ATATAAAAGATGATAATACGAATGATGTGGTTTCACCTGATGTTGATGG
194 ATATAAAAAATGATAATACGAATGAAGTGGTTTCACCTGATGTTGATGG
1466 GGGTAATAGG
Statistics
Matches: 214, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
285 210 0.98
286 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (285 bp):
AACGAAGTGGTTGCATCTGATGTTGATGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCC
TGTTGAGACTGATGATTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTC
AAAAGGATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGACTAAAGAACCTCAAGAT
ATAAAAAATGATAATACGAATGAAGTGGTTTCACCTGATGTTGATGGTACAACGAACGAAGTGGT
TTCATCTGATGTTGATGGTACTATG
Done.