Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024133.1 Corchorus olitorius cultivar O-4 contig24166, whole genome shotgun sequence
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: 31688
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Found at i:279 original size:23 final size:23
Alignment explanation
Indices: 253--325 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
243 TTTATTCTAC
253 TAAAAACTATATTTTTATTTAAT
1 TAAAAACTATATTTTTATTTAAT
** * * *
276 TAAATTCAATATTTTAAATTCAA-
1 TAAAAACTATATTTT-TATTTAAT
*
299 TAAAAACTCTATTTTTATTTAAT
1 TAAAAACTATATTTTTATTTAAT
322 TAAA
1 TAAA
326 TTTATAAATA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 5 0.14
23 27 0.73
24 5 0.14
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAAACTATATTTTTATTTAAT
Found at i:2381 original size:179 final size:178
Alignment explanation
Indices: 2065--2388 Score: 483
Period size: 179 Copynumber: 1.8 Consensus size: 178
2055 ATTATGTAAT
* * *
2065 ATATTAAGTAGACTGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCATTTTTTATAC
1 ATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGATAC
* * *
2130 CTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATTGAACAACCTTTCAA
66 CTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAACCTTTCAA
*
2195 GAGACACTTGAATCATCTAAATCAGACATCCGGAGCCAAAGTTATATA
131 GAGACACTTAAATCATCTAAATCAGACATCCGGAGCCAAAGTTATATA
* *
2243 ATATTAAGTGGACCGTCTA-TTCTCGTTAACCGAAACAACAAATT-TTTCGGAATCATTTTTGAT
1 ATATTAAGTAGACCGTCTATTTC-CGTTAACCGAAACAACAAATTCTTT-GGAAGCATTTTTGAT
*
2306 A-CTTAAAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAATCTT
64 ACCTT--AAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAACCTT
* *
2370 TTAATAGACACTTAAATCA
127 TCAAGAGACACTTAAATCA
2389 CCTTAATTGG
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
177 9 0.07
178 51 0.39
179 70 0.54
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (178 bp):
ATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGATAC
CTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAACCTTTCAA
GAGACACTTAAATCATCTAAATCAGACATCCGGAGCCAAAGTTATATA
Found at i:2421 original size:179 final size:178
Alignment explanation
Indices: 2065--2433 Score: 449
Period size: 179 Copynumber: 2.1 Consensus size: 178
2055 ATTATGTAAT
* * *
2065 ATATTAAGTAGACTGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCATTTTTTATAC
1 ATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGATAC
* * *
2130 CTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATTGAACAACCTTTCAA
66 CTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAACCTTTCAA
* * * * ** *
2195 GAGACACTTGAATCATCTAAATCAGACATCCGGAGCCAAAGTTATATA
131 GAGACACTTAAATCACCTAAATCAGAAATCCGAAAACAAAATTATATA
* *
2243 ATATTAAGTGGACCGTCTA-TTCTCGTTAACCGAAACAACAAATT-TTTCGGAATCATTTTTGAT
1 ATATTAAGTAGACCGTCTATTTC-CGTTAACCGAAACAACAAATTCTTT-GGAAGCATTTTTGAT
*
2306 A-CTTAAAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAATCTT
64 ACCTT--AAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAACCTT
* * * ** *
2370 TTAATAGACACTTAAATCACCTTAATTGGATAAT-CGAAAAGAAAATTATATA
127 TCAAGAGACACTTAAATCACCTAAATCAGA-AATCCGAAAACAAAATTATATA
* *
2422 ATGTTAAATAGA
1 ATATTAAGTAGA
2434 TCATTTAGCC
Statistics
Matches: 161, Mismatches: 25, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
177 9 0.06
178 51 0.32
179 99 0.61
180 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (178 bp):
ATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGATAC
CTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAACCTTTCAA
GAGACACTTAAATCACCTAAATCAGAAATCCGAAAACAAAATTATATA
Found at i:25040 original size:29 final size:29
Alignment explanation
Indices: 24998--25063 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
24988 ACCATTAAGT
24998 GGAAACACGCAAAAAGCGGAGCGGGTCAA
1 GGAAACACGCAAAAAGCGGAGCGGGTCAA
25027 GGAAACACGCAAAAAGCGGAGCGGGTCAA
1 GGAAACACGCAAAAAGCGGAGCGGGTCAA
25056 GGAAACAC
1 GGAAACAC
25064 CACTCCAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.42, C:0.21, G:0.33, T:0.03
Consensus pattern (29 bp):
GGAAACACGCAAAAAGCGGAGCGGGTCAA
Found at i:27330 original size:14 final size:14
Alignment explanation
Indices: 27311--27338 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27301 AAACTTTTCA
27311 GATTTCAAAAAGGC
1 GATTTCAAAAAGGC
27325 GATTTCAAAAAGGC
1 GATTTCAAAAAGGC
27339 AGAAGGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
GATTTCAAAAAGGC
Done.