Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021922.1 Corchorus olitorius cultivar O-4 contig21955, 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: 11618
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:1398 original size:52 final size:52
Alignment explanation
Indices: 1318--1450 Score: 239
Period size: 52 Copynumber: 2.6 Consensus size: 52
1308 AAAAAAAAAT
1318 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAA
1 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAA
*
1370 GCCTGCTAAGTTGAAAACCCCATCGGGGCGGCTTAGGCAAAAGTTAAGGCAA
1 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAA
* *
1422 GACTGCTAGGTTGAAAACCCCATTGGGGC
1 GCCTGCTAAGTTGAAAACCCCATTGGGGC
1451 AGCCTAAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 77 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.19
Consensus pattern (52 bp):
GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAA
Found at i:5153 original size:45 final size:45
Alignment explanation
Indices: 5102--5187 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
5092 AAGTCGAAGA
* * *
5102 GTCCGATGCAGAGGTAGAGGGTGAT-AAGAATCAACCCCGCCAAGT
1 GTCCGATACAAAGGTAGAGGGCGATGAA-AATCAACCCCGCCAAGT
5147 GTCCGATACAAAGGTAGAGGGCGATGAAAATCAACCCCGCC
1 GTCCGATACAAAGGTAGAGGGCGATGAAAATCAACCCCGCC
5188 GAGAGTGAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 35 0.95
46 2 0.05
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.14
Consensus pattern (45 bp):
GTCCGATACAAAGGTAGAGGGCGATGAAAATCAACCCCGCCAAGT
Found at i:5208 original size:37 final size:37
Alignment explanation
Indices: 5158--5230 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
5148 TCCGATACAA
* *
5158 AGGTAGAGGGCGATGAAAATCAACCCCGCCGAGAGTG
1 AGGTAGAGGGCGATAAAAATCAACCCCGCCAAGAGTG
5195 AGGTAGAGGGCGATAAAAATCAACCCCGCCAAGAGT
1 AGGTAGAGGGCGATAAAAATCAACCCCGCCAAGAGT
5231 ACAATCAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.32, T:0.11
Consensus pattern (37 bp):
AGGTAGAGGGCGATAAAAATCAACCCCGCCAAGAGTG
Found at i:6371 original size:36 final size:36
Alignment explanation
Indices: 6299--6374 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
6289 TGAGAAAAGG
* ** *
6299 CCAAGTACATAATTAAGTTGGCTTAATTCTATTGGC
1 CCAAATACATAATTAAGTTGGCCCAATTCTACTGGC
6335 CCAAATACATAATTAAGTTGGCCCAACTT-TACTGGC
1 CCAAATACATAATTAAGTTGGCCCAA-TTCTACTGGC
6371 CCAA
1 CCAA
6375 TACTACCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (36 bp):
CCAAATACATAATTAAGTTGGCCCAATTCTACTGGC
Found at i:6530 original size:13 final size:13
Alignment explanation
Indices: 6499--6658 Score: 83
Period size: 13 Copynumber: 12.8 Consensus size: 13
6489 GTGAAACAAG
*
6499 TCTTCATCAAAAT
1 TCTTCATCAAAGT
*
6512 TATTCATCAAAGT
1 TCTTCATCAAAGT
*
6525 TCTTCAAC-AAGT
1 TCTTCATCAAAGT
6537 TAC--CA-CGAAAGT
1 T-CTTCATC-AAAGT
*
6549 TATTCATCAAAGT
1 TCTTCATCAAAGT
*
6562 TCTTCAAC-AAGT
1 TCTTCATCAAAGT
* * *
6574 CCCT-ACCAAAGT
1 TCTTCATCAAAGT
*
6586 TATTCATCAAAGT
1 TCTTCATCAAAGT
*
6599 TCTTCAAC-AAG-
1 TCTTCATCAAAGT
6610 TCTTCATC-AAGT
1 TCTTCATCAAAGT
* *
6622 TGTTCTTCAACAAGT
1 TCTTCATC-A-AAGT
6637 T-TTCACTC--AGT
1 TCTTCA-TCAAAGT
6648 TCTTCATCAAA
1 TCTTCATCAAA
6659 TTTTCCACCA
Statistics
Matches: 111, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
10 1 0.01
11 20 0.18
12 34 0.31
13 45 0.41
14 4 0.04
15 7 0.06
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (13 bp):
TCTTCATCAAAGT
Found at i:6534 original size:37 final size:37
Alignment explanation
Indices: 6493--6619 Score: 170
Period size: 37 Copynumber: 3.4 Consensus size: 37
6483 CCAAGAGTGA
* *
6493 AACAAGTCTTCATCAAAATTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
6530 AACAAGT-TACCA-CGAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCT-CCATC-AAAGTTATTCATCAAAGTTCTTC
*
6567 AACAAGTC-CCTACCAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCC-ATCAAAGTTATTCATCAAAGTTCTTC
*
6604 AACAAGTCTTCATCAA
1 AACAAGTCTCCATCAA
6620 GTTGTTCTTC
Statistics
Matches: 80, Mismatches: 4, Indels: 12
0.83 0.04 0.12
Matches are distributed among these distances:
36 4 0.05
37 74 0.93
38 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.31
Consensus pattern (37 bp):
AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
Done.