Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006939.1 Corchorus capsularis cultivar CVL-1 contig06960, 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: 30977
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:125 original size:25 final size:25
Alignment explanation
Indices: 10--127 Score: 87
Period size: 25 Copynumber: 4.7 Consensus size: 25
1 GCCTAGCGG
* * *
10 GCGTTCTCTGCTTGTCGCTCGTCGA
1 GCGTTCTCCGCTTGGCGCCCGTCGA
* * * *
35 GCGTTCTCCCCTTGGCGCCTGGCAA
1 GCGTTCTCCGCTTGGCGCCCGTCGA
* *
60 GCAG-TCTCCGCTAGGC-CCTCGACGA
1 GC-GTTCTCCGCTTGGCGCC-CGTCGA
* * *
85 GCGTTCTCCACGTGGCGCCCGTCGG
1 GCGTTCTCCGCTTGGCGCCCGTCGA
*
110 GCGTTCTCTGCTTGGCGC
1 GCGTTCTCCGCTTGGCGC
128 TCAACGGGTG
Statistics
Matches: 69, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
24 3 0.04
25 63 0.91
26 3 0.04
ACGTcount: A:0.07, C:0.37, G:0.31, T:0.25
Consensus pattern (25 bp):
GCGTTCTCCGCTTGGCGCCCGTCGA
Found at i:180 original size:25 final size:25
Alignment explanation
Indices: 77--182 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 25
67 CCGCTAGGCC
* * *
77 CTCGACGAGCGTTCTCCACGTGGCG
1 CTCGACGGGTGTTCTCCACTTGGCG
* * * **
102 CCCGTCGGGCGTTCTCTGCTTGGCG
1 CTCGACGGGTGTTCTCCACTTGGCG
* *
127 CTCAACGGGTGTTCTACACTTGGCG
1 CTCGACGGGTGTTCTCCACTTGGCG
* *
152 CTCGGCGGGTATTCTCCACTTGGCG
1 CTCGACGGGTGTTCTCCACTTGGCG
177 CTCGAC
1 CTCGAC
183 CCACGTTCTC
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.09, C:0.34, G:0.31, T:0.25
Consensus pattern (25 bp):
CTCGACGGGTGTTCTCCACTTGGCG
Found at i:320 original size:25 final size:25
Alignment explanation
Indices: 292--344 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
282 TTGACGCTCT
* *
292 ACGGATGTTTTCTGCTTGGCGCTAG
1 ACGGATGTTCTCCGCTTGGCGCTAG
* *
317 ACGGGTGTTCTCCGCTTGGCGCTCG
1 ACGGATGTTCTCCGCTTGGCGCTAG
342 ACG
1 ACG
345 AGTGCTCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.09, C:0.26, G:0.34, T:0.30
Consensus pattern (25 bp):
ACGGATGTTCTCCGCTTGGCGCTAG
Found at i:446 original size:25 final size:25
Alignment explanation
Indices: 362--975 Score: 285
Period size: 25 Copynumber: 24.6 Consensus size: 25
352 TTCCCTTTGT
* *
362 GCCTGGCGGGCGTTCTCCACTTTGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
*** * * *
387 GCCCACCAGGCGTTCTCCACTTAGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
*
412 G-CTCGACGGGCGTTCTCCCCTTGGC
1 GCCT-GGCGGGCGTTCTCCCCTTGGC
*
437 GCCTGGCGGGCGTTCTCCGCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
** * * *
462 G-CTCGATGGGCATTCTCCGCTTAACGCAC
1 GCCT-GGCGGGCGTTCTCCCCTT---G-GC
* *
491 ATGCCTTGCGAGCGTTCTCCCCTTGGC
1 --GCCTGGCGGGCGTTCTCCCCTTGGC
*
518 GCCTAGCGGGCGTTCTCCCCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
*
543 GCCTAGCGGGCGTTCTCCCCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
* * ** * *
568 G-ATCGCCCAGCGTTCTTCCGTTGGC
1 GCCT-GGCGGGCGTTCTCCCCTTGGC
* * *
593 GCCTAGCCGGCGTTCTCCGC-T--C
1 GCCTGGCGGGCGTTCTCCCCTTGGC
* *
615 G-C---CAGGCATTCTCCCCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
** * ** **
636 GTGTGGCGAGCGAAC-CCTTTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
** * * **
660 -CCTCGAAGAGCGTTCTCCACTTAAC
1 GCCT-GGCGGGCGTTCTCCCCTTGGC
* * * *
685 TCCCGGCGGGCGTTTTCCGCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
* * *
710 G-CTCGACGGGTGTTCTCCCATTGGC
1 GCCT-GGCGGGCGTTCTCCCCTTGGC
*
735 GCCTGGCGGGCGTTCTCCGCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
*
760 G-CTCGACGGGCGTTCTCCCCTTGGC
1 GCCT-GGCGGGCGTTCTCCCCTTGGC
*
785 GCCTGGCGGGCGTTCTCCGCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
* * * *
810 GCTTGACGGGCGTTCTTCTCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
* * * *
835 ACCTGGCGAGCGTTCTTCGCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
* *
860 -CCTCGACGGGCGTTCTCCACTTGGC
1 GCCT-GGCGGGCGTTCTCCCCTTGGC
***
885 GGCC--GCTGGGCGTTCTCAAGTTGGC
1 -GCCTGGC-GGGCGTTCTCCCCTTGGC
* * * *
910 G-CTCGACAGGCGTTCTCCCCTTCGA
1 GCCT-GGCGGGCGTTCTCCCCTTGGC
* *
935 ACCTGGCGGGCGTTCTCCGCTTGGC
1 GCCTGGCGGGCGTTCTCCCCTTGGC
*
960 G-CTCGACGGGCGTTCT
1 GCCT-GGCGGGCGTTCT
976 ACACTTCACC
Statistics
Matches: 439, Mismatches: 115, Indels: 70
0.70 0.18 0.11
Matches are distributed among these distances:
18 11 0.03
19 1 0.00
21 3 0.01
22 2 0.00
23 2 0.00
24 29 0.07
25 358 0.82
26 12 0.03
27 3 0.01
28 2 0.00
29 1 0.00
31 13 0.03
32 2 0.00
ACGTcount: A:0.07, C:0.36, G:0.31, T:0.25
Consensus pattern (25 bp):
GCCTGGCGGGCGTTCTCCCCTTGGC
Found at i:581 original size:50 final size:50
Alignment explanation
Indices: 395--975 Score: 459
Period size: 50 Copynumber: 11.7 Consensus size: 50
385 GCGCCCACCA
* * *
395 GGCGTTCTCCACTTAGCGCTCGACGGGCGTTCTCCCCTTGGCGCCTGGCG
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGCGCCTGGCG
* * * * * *
445 GGCGTTCTCCGCTTGGCGCTCGATGGGCATTCTCCGCTTAACGCACATGCCTTGCG
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTT---G-GC--GCCTGGCG
* * * * *
501 AGCGTTCTCCCCTTGGCGC-CTAGCGGGCGTTCTCCCCTTGGCGCCTAGCG
1 GGCGTTCTCCGCTTGGCGCTCGA-CGAGCGTTCTCCCCTTGGCGCCTGGCG
* * * * * * * *
551 GGCGTTCTCCCCTTGGCGATCGCCCAGCGTTCTTCCGTTGGCGCCTAGCC
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGCGCCTGGCG
* **
601 GGCGTTCTCCGC-T--CGC-C-A-G-GCATTCTCCCCTTGGCGTGTGGCG
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGCGCCTGGCG
* ** ** * * * ** * *
644 AGCGAAC-CCTTTTGGCCCTCGAAGAGCGTTCTCCACTTAACTCCCGGCG
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGCGCCTGGCG
* * * *
693 GGCGTTTTCCGCTTGGCGCTCGACGGGTGTTCTCCCATTGGCGCCTGGCG
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGCGCCTGGCG
*
743 GGCGTTCTCCGCTTGGCGCTCGACGGGCGTTCTCCCCTTGGCGCCTGGCG
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGCGCCTGGCG
* * * * *
793 GGCGTTCTCCGCTTGGCGCTTGACGGGCGTTCTTCTCTTGGCACCTGGCG
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGCGCCTGGCG
* * * * *
843 AGCGTTCTTCGCTTGGCCCTCGACGGGCGTTCTCCACTTGGCGGCC--GCTG
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGC-GCCTGGC-G
* * **
893 GGCGTTCTCAAG-TTGGCGCTCGAC-AGGCGTTCTCCCCTTCGAACCTGGCG
1 GGCGTTCTC-CGCTTGGCGCTCGACGA-GCGTTCTCCCCTTGGCGCCTGGCG
*
943 GGCGTTCTCCGCTTGGCGCTCGACGGGCGTTCT
1 GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCT
976 ACACTTCACC
Statistics
Matches: 417, Mismatches: 90, Indels: 48
0.75 0.16 0.09
Matches are distributed among these distances:
42 2 0.00
43 22 0.05
45 2 0.00
46 2 0.00
47 3 0.01
48 1 0.00
49 25 0.06
50 311 0.75
51 6 0.01
52 1 0.00
53 2 0.00
54 1 0.00
55 2 0.00
56 37 0.09
ACGTcount: A:0.07, C:0.36, G:0.31, T:0.26
Consensus pattern (50 bp):
GGCGTTCTCCGCTTGGCGCTCGACGAGCGTTCTCCCCTTGGCGCCTGGCG
Found at i:1016 original size:19 final size:19
Alignment explanation
Indices: 992--1037 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
982 CACCCTCGCA
*
992 GCGCGTGGAAGTGTTGCCG
1 GCGCGTGGAAGTGTCGCCG
*
1011 GCGCGTGGAAGTGTCGTCG
1 GCGCGTGGAAGTGTCGCCG
1030 GCGCGTGG
1 GCGCGTGG
1038 CAAGCTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.09, C:0.22, G:0.50, T:0.20
Consensus pattern (19 bp):
GCGCGTGGAAGTGTCGCCG
Found at i:2931 original size:38 final size:37
Alignment explanation
Indices: 2879--2956 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 37
2869 TAACACCCGA
*
2879 ACCTCATCATTTAGAACACCACATTCCCATAGCATAGG
1 ACCTCATCAATTAGAACACCACATTCCCAT-GCATAGG
*
2917 ACCTCATCAATTAGAACACCACGTTCCCATGCATAGG
1 ACCTCATCAATTAGAACACCACATTCCCATGCATAGG
2954 ACC
1 ACC
2957 CTGTTTCTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 10 0.26
38 28 0.74
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.22
Consensus pattern (37 bp):
ACCTCATCAATTAGAACACCACATTCCCATGCATAGG
Found at i:3616 original size:26 final size:26
Alignment explanation
Indices: 3555--3625 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
3545 TAAGTCGCAT
3555 AGGGGCATTTTGGTCATTTTTGCACCC
1 AGGGGCATTTTGGTCA-TTTTGCACCC
* * *
3582 AAGGACATTTTGGTCATTTTGCA-CT
1 AGGGGCATTTTGGTCATTTTGCACCC
3607 AGGGGGCATTTTGGTCATT
1 A-GGGGCATTTTGGTCATT
3626 CTTAATTCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
25 2 0.05
26 22 0.58
27 14 0.37
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (26 bp):
AGGGGCATTTTGGTCATTTTGCACCC
Found at i:6730 original size:49 final size:49
Alignment explanation
Indices: 6661--6979 Score: 433
Period size: 49 Copynumber: 6.5 Consensus size: 49
6651 ACTTGTTTCC
*
6661 CCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTT
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTATTT
* * * * *
6710 CCTAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTTGCTATTT
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTATTT
* * *
6759 CCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTGCTTGCTATTT
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTATTT
* *
6808 CCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGTTATTT
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTATTT
* **
6857 CCCAAAACGCCCTTCCCAGACGAAAGCCATTCATCTTTACTTGCTATCC
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTATTT
* * * * * *
6906 CCCAAAACACCCTTCCCAGACGGAAGGCACT-AACTTTAATTGCTTTTT
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTATTT
* *
6954 CCTAAAACGCCCTTCCCGGACGGAAG
1 CCCAAAACGCCCTTCCCAGACGGAAG
6980 GCGTTAGTTT
Statistics
Matches: 244, Mismatches: 26, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
48 35 0.14
49 209 0.86
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.28
Consensus pattern (49 bp):
CCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTATTT
Found at i:24989 original size:2 final size:2
Alignment explanation
Indices: 24982--25015 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
24972 AGTGTCCGAC
24982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25016 TTGCTACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25546 original size:17 final size:17
Alignment explanation
Indices: 25507--25558 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
25497 TATCGATATG
*
25507 ATATTTTATT-ATCAA-
1 ATATTATATTAATCAAT
25522 AT-TTATATTAATCAAT
1 ATATTATATTAATCAAT
*
25538 ATATTATATTAATTAAT
1 ATATTATATTAATCAAT
25555 ATAT
1 ATAT
25559 GTAGAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 2 0.06
17 17 0.53
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTATATTAATCAAT
Done.