Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020206.1 Corchorus olitorius cultivar O-4 contig20239, 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: 20957
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:93 original size:2 final size:2
Alignment explanation
Indices: 86--115 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
76 ATCCCTCCTC
*
86 CT CT CT CT CT CT AT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
116 ATATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:120 original size:2 final size:2
Alignment explanation
Indices: 115--139 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
105 TCTCTCTCTC
115 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
140 GTATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:144 original size:4 final size:4
Alignment explanation
Indices: 137--333 Score: 331
Period size: 4 Copynumber: 48.0 Consensus size: 4
127 TATATATATA
137 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
185 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAATG TATG TAATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T-ATG TATG T-ATG
235 TATG TAATG TATG TAATG TATG TATG TAATG TATG TATG TATG TATG TATG
1 TATG T-ATG TATG T-ATG TATG TATG T-ATG TATG TATG TATG TATG TATG
* *
286 TATG CATG TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
334 AACCCATCAC
Statistics
Matches: 184, Mismatches: 4, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
4 164 0.89
5 20 0.11
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:403 original size:4 final size:4
Alignment explanation
Indices: 394--418 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
384 ATCCCATCCT
394 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
419 CAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:7619 original size:26 final size:28
Alignment explanation
Indices: 7566--7619 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
7556 CAAAAGTATA
7566 GAGATGGAGATAAAAACAAATTGTTGTT
1 GAGATGGAGATAAAAACAAATTGTTGTT
*
7594 GAGATGGAGA-GAAAA-AAATTGTTGTT
1 GAGATGGAGATAAAAACAAATTGTTGTT
7620 AAGCAGTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.44
27 4 0.16
28 10 0.40
ACGTcount: A:0.43, C:0.02, G:0.28, T:0.28
Consensus pattern (28 bp):
GAGATGGAGATAAAAACAAATTGTTGTT
Found at i:19401 original size:55 final size:55
Alignment explanation
Indices: 19310--19478 Score: 212
Period size: 65 Copynumber: 2.9 Consensus size: 55
19300 GAAAGGTAAA
*
19310 ATCATGACAACTTCTGGTGTCAATTGAATAATATTATGACATCTTCAAGAAATTT
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGAAATTT
* *
19365 ATTATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATTTTCAAGTGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACA---TC---T-TC-A--AGAAATTT
*
19430 ATCATGACAATTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAG
19479 TGTCTATTGG
Statistics
Matches: 98, Mismatches: 6, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
55 40 0.41
57 1 0.01
58 4 0.04
59 1 0.01
61 1 0.01
62 4 0.04
63 1 0.01
65 46 0.47
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (55 bp):
ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGAAATTT
Found at i:19437 original size:33 final size:33
Alignment explanation
Indices: 19400--19503 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
19390 GAATAAAATT
19400 ATGACATTTTCAAGTGTCTATTGGAAATTTATC
1 ATGACATTTTCAAGTGTCTATTGGAAATTTATC
* ** * ** *
19433 ATGACAATTTCTGGTGTCAATT-G-AATAAAATT
1 ATGACATTTTCAAGTGTCTATTGGAAAT-TTATC
*
19465 ATGACATCTTCAAGTGTCTATTGGAAATTTATC
1 ATGACATTTTCAAGTGTCTATTGGAAATTTATC
19498 ATGACA
1 ATGACA
19504 ACTTCTGCTG
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
31 3 0.06
32 20 0.38
33 27 0.51
34 3 0.06
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (33 bp):
ATGACATTTTCAAGTGTCTATTGGAAATTTATC
Found at i:19462 original size:65 final size:65
Alignment explanation
Indices: 19358--19520 Score: 281
Period size: 65 Copynumber: 2.5 Consensus size: 65
19348 ACATCTTCAA
* *
19358 GAAATTTATTATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATTTTCAAGTGTCTATTG
1 GAAATTTATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCTATTG
*
19423 GAAATTTATCATGACAATTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCTATTG
1 GAAATTTATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCTATTG
* *
19488 GAAATTTATCATGACAACTTCTGCTGACAATTG
1 GAAATTTATCATGACAACTTCTGGTGTCAATTG
19521 CAACATCATG
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 92 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (65 bp):
GAAATTTATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCTATTG
Found at i:19530 original size:30 final size:30
Alignment explanation
Indices: 19497--19795 Score: 384
Period size: 30 Copynumber: 9.7 Consensus size: 30
19487 GGAAATTTAT
* * * *
19497 CATGACAACTTCTGCTGACAATTGCAACAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
19527 CATGACAGCTTCTGGTGTCAATTGCAAGAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * * *
19557 CATGACAGCTTCTAGTGTCAATTGCAACAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
19587 CATGACAGCTTTTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
19617 CATGACAACTTCTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
19647 CATGACAACTTCTGGTGTCAATTGCAAATTGCAAGGC
1 CATGACAACTTCTGGTGTCAATTGC-AA--G--A--C
*
19684 CATGACAACTTCTGGTGTCAATTGCAAGGC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
19714 CATGACAACTTCTGGTGTCAATTGCAA-AGC
1 CATGACAACTTCTGGTGTCAATTGCAAGA-C
* *
19744 CATGACAACTTCTGGTGTCATTTGCAAGGC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
19774 CATGACAACTTCTGGTGTCAAT
1 CATGACAACTTCTGGTGTCAAT
19796 GTATATTAGC
Statistics
Matches: 243, Mismatches: 17, Indels: 18
0.87 0.06 0.06
Matches are distributed among these distances:
30 210 0.86
31 2 0.01
33 1 0.00
34 1 0.00
35 1 0.00
36 2 0.01
37 26 0.11
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (30 bp):
CATGACAACTTCTGGTGTCAATTGCAAGAC
Found at i:19733 original size:127 final size:120
Alignment explanation
Indices: 19497--19795 Score: 384
Period size: 127 Copynumber: 2.4 Consensus size: 120
19487 GGAAATTTAT
* * * * * *
19497 CATGACAACTTCTGCTGACAATTGCAACATCATGACAGCTTCTGGTGTCAATTGCAAGATCATGA
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
* * * *
19562 CAGCTTCTAGTGTCAATTGCAACATCATGACAGCTTTTGGTGTCAATTGC-AAGAC
66 CAACTTCTAGTGTCAATTGCAACACCATGACAACTTCTGGTGTCAATTGCAAAG-C
19617 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAATTGCAAG
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGC-AA--G--A-
* **
19682 GCCATGACAACTTCTGGTGTCAATTGCAAGGCCATGACAACTTCTGGTGTCAATTGCAAAGC
60 -CCATGACAACTTCTAGTGTCAATTGCAACACCATGACAACTTCTGGTGTCAATTGCAAAGC
* *
19744 CATGACAACTTCTGGTGTCATTTGCAAGGCCATGACAACTTCTGGTGTCAAT
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAAT
19796 GTATATTAGC
Statistics
Matches: 156, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
120 50 0.32
121 2 0.01
123 1 0.01
125 1 0.01
127 99 0.63
128 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (120 bp):
CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
CAACTTCTAGTGTCAATTGCAACACCATGACAACTTCTGGTGTCAATTGCAAAGC
Found at i:20934 original size:2 final size:2
Alignment explanation
Indices: 20927--20957 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20917 ATTCCATAAC
20927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.