Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020657.1 Corchorus olitorius cultivar O-4 contig20690, 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: 7841
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Found at i:1549 original size:2 final size:2
Alignment explanation
Indices: 1542--1586 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1532 ATTATTTTTC
* * *
1542 TA TA TA TA TA TA TA TG TG TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1584 TA T
1 TA T
1587 CTTGCTACCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1565 original size:16 final size:16
Alignment explanation
Indices: 1544--1586 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1534 TATTTTTCTA
*
1544 TATATATATATATGTG
1 TATATATATATATATG
1560 TATATATATATATATG
1 TATATATATATATATG
1576 TATATATATAT
1 TATATATATAT
1587 CTTGCTACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:1565 original size:18 final size:18
Alignment explanation
Indices: 1542--1586 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1532 ATTATTTTTC
*
1542 TATATATATATATATGTG
1 TATATATATATATATGTA
1560 TATATATATATATATGTA
1 TATATATATATATATGTA
1578 TATATATAT
1 TATATATAT
1587 CTTGCTACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
TATATATATATATATGTA
Found at i:5921 original size:71 final size:70
Alignment explanation
Indices: 5826--5963 Score: 190
Period size: 71 Copynumber: 2.0 Consensus size: 70
5816 TCTAAAGTTG
* *
5826 CCATTTAAGTAAACCTGCTTAGGT-CCTTGTCTAGAATT-TCCGTTTAAACAAACCTGCTTAGGT
1 CCATTCAAGTAAACCTGCTTAGGTCCCTT-TCTAGAATTCT-CGTTCAAACAAACCTGCTTAGGT
5889 CTTCGTT
64 CTTCGTT
** *
5896 CCATTCAAGTAAAACCTGCTTAGGTCCCTTTCTAGAATTCTCGTTCAAGTAAACTTGCTTAGGTC
1 CCATTCAAGT-AAACCTGCTTAGGTCCCTTTCTAGAATTCTCGTTCAAACAAACCTGCTTAGGTC
5961 TTC
65 TTC
5964 ATTTAGAAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
70 9 0.15
71 46 0.77
72 5 0.08
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (70 bp):
CCATTCAAGTAAACCTGCTTAGGTCCCTTTCTAGAATTCTCGTTCAAACAAACCTGCTTAGGTCT
TCGTT
Found at i:6081 original size:38 final size:38
Alignment explanation
Indices: 6039--6303 Score: 243
Period size: 38 Copynumber: 6.9 Consensus size: 38
6029 AGGCGTCTGC
*
6039 TTAGAGCTTCGTTTAA-TCAAACCTGCTTAGGTCTATGT
1 TTAGAGCTTCATTTAAGT-AAACCTGCTTAGGTCTATGT
* * *
6077 TTAGA-ATCTCTATTTAAGTAAACCTGCTTAGGTCTCTAT
1 TTAGAGCT-TC-ATTTAAGTAAACCTGCTTAGGTCTATGT
* * * * * *
6116 TTAGAGCTTCCATTCAAGTGAATCTACTTATGTCTCTGT
1 TTAGAGCTT-CATTTAAGTAAACCTGCTTAGGTCTATGT
*
6155 TTAGAG-TGTCGTTTAA-TCAAACCTGCTTAGGTCTATGT
1 TTAGAGCT-TCATTTAAGT-AAACCTGCTTAGGTCTATGT
* *
6193 TTAGA-ATTCCCTTTTAAGTAAACCTGCTTAGGTCTATGT
1 TTAGAGCTT--CATTTAAGTAAACCTGCTTAGGTCTATGT
* * *
6232 CTAGAACTTCATTTAAGTGAACCTGCTTAGGTCTATGT
1 TTAGAGCTTCATTTAAGTAAACCTGCTTAGGTCTATGT
** * *
6270 TTAGAATTTCATTTAAGAAAACATGCTTAGGTCT
1 TTAGAGCTTCATTTAAGTAAACCTGCTTAGGTCT
6304 CCGTTCCGTT
Statistics
Matches: 187, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
37 3 0.02
38 90 0.48
39 88 0.47
40 6 0.03
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (38 bp):
TTAGAGCTTCATTTAAGTAAACCTGCTTAGGTCTATGT
Found at i:6102 original size:39 final size:39
Alignment explanation
Indices: 6057--6303 Score: 238
Period size: 39 Copynumber: 6.4 Consensus size: 39
6047 TCGTTTAATC
6057 AAACCTGCTTAGGTCTATGTTTAGAATCTCTATTTAAGT
1 AAACCTGCTTAGGTCTATGTTTAGAATCTCTATTTAAGT
* * * * *
6096 AAACCTGCTTAGGTCTCTATTTAG-AGCTTCCATTCAAGT
1 AAACCTGCTTAGGTCTATGTTTAGAATC-TCTATTTAAGT
* * * * * * * *
6135 GAATCTACTTATGTCTCTGTTTAGAGTGTC-GTTTAA-T
1 AAACCTGCTTAGGTCTATGTTTAGAATCTCTATTTAAGT
*
6172 CAAACCTGCTTAGGTCTATGTTTAGAATTCCCT-TTTAAGT
1 -AAACCTGCTTAGGTCTATGTTTAGAA-TCTCTATTTAAGT
*
6212 AAACCTGCTTAGGTCTATGTCTAGAA-CT-TCATTTAAGT
1 AAACCTGCTTAGGTCTATGTTTAGAATCTCT-ATTTAAGT
* * *
6250 GAACCTGCTTAGGTCTATGTTTAGAATTTC-ATTTAAGA
1 AAACCTGCTTAGGTCTATGTTTAGAATCTCTATTTAAGT
*
6288 AAACATGCTTAGGTCT
1 AAACCTGCTTAGGTCT
6304 CCGTTCCGTT
Statistics
Matches: 167, Mismatches: 31, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
36 1 0.01
37 2 0.01
38 78 0.47
39 85 0.51
40 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (39 bp):
AAACCTGCTTAGGTCTATGTTTAGAATCTCTATTTAAGT
Found at i:6179 original size:116 final size:114
Alignment explanation
Indices: 6034--6303 Score: 344
Period size: 116 Copynumber: 2.3 Consensus size: 114
6024 TGCATAGGCG
* *
6034 TCTGCTTAGAGCTTCGTTTAATCAAACCTGCTTAGGTCTATGTTTAGAA-TCTCTATTTAAGTAA
1 TCTGTTTAGAG-TTCGTTTAATCAAACCTGCTTAGGTCTATGTTTAGAATTCCCT-TTTAAGTAA
* * * * *
6098 ACCTGCTTAGGTCTCTATTTAGAGCTTCCATTCAAGTGAATCTACTTATGTC
64 ACCTGCTTAGGTCTATATCTAGAACTT-CATTCAAGTGAACCTACTTAGGTC
6150 TCTGTTTAGAGTGTCGTTTAATCAAACCTGCTTAGGTCTATGTTTAGAATTCCCTTTTAAGTAAA
1 TCTGTTTAGAGT-TCGTTTAATCAAACCTGCTTAGGTCTATGTTTAGAATTCCCTTTTAAGTAAA
* * *
6215 CCTGCTTAGGTCTATGTCTAGAACTTCATTTAAGTGAACCTGCTTAGGTC
65 CCTGCTTAGGTCTATATCTAGAACTTCATTCAAGTGAACCTACTTAGGTC
* * * ** *
6265 TATGTTTAGAATTTCATTTAAGAAAACATGCTTAGGTCT
1 TCTGTTTAG-AGTTCGTTTAATCAAACCTGCTTAGGTCT
6304 CCGTTCCGTT
Statistics
Matches: 135, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
115 51 0.38
116 80 0.59
117 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.40
Consensus pattern (114 bp):
TCTGTTTAGAGTTCGTTTAATCAAACCTGCTTAGGTCTATGTTTAGAATTCCCTTTTAAGTAAAC
CTGCTTAGGTCTATATCTAGAACTTCATTCAAGTGAACCTACTTAGGTC
Found at i:6247 original size:77 final size:76
Alignment explanation
Indices: 6057--6303 Score: 273
Period size: 77 Copynumber: 3.2 Consensus size: 76
6047 TCGTTTAATC
* *
6057 AAACCTGCTTAGGTCTATGTTTAGAATCTCTATTTAAGTAAACCTGCTTAGGTCTCTATTTAGAG
1 AAACCTGCTTAGGTCTATGTTTAGAATCTC-ATTTAAGTAAACCTGCTTAGGTCTATGTTTAGA-
* *
6122 CTTCCATTCAAGT
64 ATTCCATTTAAGT
* * * * * * * *
6135 GAATCTACTTATGTCTCTGTTTAGAGTGTCGTTTAA-TCAAACCTGCTTAGGTCTATGTTTAGAA
1 AAACCTGCTTAGGTCTATGTTTAGAATCTCATTTAAGT-AAACCTGCTTAGGTCTATGTTTAGAA
*
6199 TTCCCTTTTAAGT
65 TT-CCATTTAAGT
* *
6212 AAACCTGCTTAGGTCTATGTCTAGAA-CTTCATTTAAGTGAACCTGCTTAGGTCTATGTTTAGAA
1 AAACCTGCTTAGGTCTATGTTTAGAATC-TCATTTAAGTAAACCTGCTTAGGTCTATGTTTAGAA
* *
6276 TTTCATTTAAGA
65 TTCCATTTAAGT
*
6288 AAACATGCTTAGGTCT
1 AAACCTGCTTAGGTCT
6304 CCGTTCCGTT
Statistics
Matches: 138, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
76 25 0.18
77 89 0.64
78 24 0.17
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (76 bp):
AAACCTGCTTAGGTCTATGTTTAGAATCTCATTTAAGTAAACCTGCTTAGGTCTATGTTTAGAAT
TCCATTTAAGT
Found at i:6389 original size:38 final size:38
Alignment explanation
Indices: 6310--6449 Score: 192
Period size: 39 Copynumber: 3.6 Consensus size: 38
6300 GTCTCCGTTC
* * *
6310 CGTTTAAGT-AAACTTGTTTAGGACTTCTGCTTAGAGTTT
1 CGTTTAA-TCAAACCTGCTTAGGTCTTC-GCTTAGAGTTT
*
6349 CGTTTAATTAAACCTGCTTAGGTCTTCGCTTAGAGTTT
1 CGTTTAATCAAACCTGCTTAGGTCTTCGCTTAGAGTTT
*
6387 CGTTTAAATCGAACCTGCTTAGGTCTTCGCTTAGAGTTT
1 CGTTT-AATCAAACCTGCTTAGGTCTTCGCTTAGAGTTT
*
6426 CGTTTAATCAAACCTGCTCAGGTC
1 CGTTTAATCAAACCTGCTTAGGTC
6450 CATCTTTAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
38 34 0.37
39 58 0.63
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (38 bp):
CGTTTAATCAAACCTGCTTAGGTCTTCGCTTAGAGTTT
Done.