Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005494.1 Corchorus capsularis cultivar CVL-1 contig05512, 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: 6046
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Found at i:57 original size:29 final size:29
Alignment explanation
Indices: 1--239 Score: 306
Period size: 29 Copynumber: 8.3 Consensus size: 29
* * *
1 GGTAGTACGCCC-CCAACGGCTCACGAAGT
1 GGTAGTACTCCCTCCAA-AGCTCAAGAAGT
* *
30 GGTAGTACTCCCTTCAAAGTTCAAGAAGT
1 GGTAGTACTCCCTCCAAAGCTCAAGAAGT
59 GGTAGTACTCCCTCCAAAGCTCAAGAAGT
1 GGTAGTACTCCCTCCAAAGCTCAAGAAGT
* **
88 GGTAGTACTCCCTCCAAAGTTCCCGAAGT
1 GGTAGTACTCCCTCCAAAGCTCAAGAAGT
*
117 GGTAGTACTCCCTCCAAAGTTCAAGAAGT
1 GGTAGTACTCCCTCCAAAGCTCAAGAAGT
*
146 GGTAGTACTCCCTCCAAAGCTCAAAAAGT
1 GGTAGTACTCCCTCCAAAGCTCAAGAAGT
* *
175 GGTAGTA-TGTCCTCCAAAGCTCATGAAGT
1 GGTAGTACT-CCCTCCAAAGCTCAAGAAGT
*
204 GGTAGTA-TGCCCTCC-AAGCTCATGAAGT
1 GGTAGTACT-CCCTCCAAAGCTCAAGAAGT
232 GGTAGTAC
1 GGTAGTAC
240 ACCCCCTAGA
Statistics
Matches: 189, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
28 21 0.11
29 165 0.87
30 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (29 bp):
GGTAGTACTCCCTCCAAAGCTCAAGAAGT
Found at i:407 original size:29 final size:29
Alignment explanation
Indices: 366--750 Score: 386
Period size: 29 Copynumber: 14.0 Consensus size: 29
356 ATATCAAAAG
366 AGAGAGCGCCGTACATCCACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
* *
395 AGAGAACGCCGTACATCCACCATTTTGG-
1 AGAGAGCGCCGTACATCCACCATCTTGGA
*
423 A-CGAGCGCCGTACA---ACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
*
448 AGAAAGCGCCGT--A--CACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
*
473 AGAGAGCGCCGTACATCCACCATTTTGG-
1 AGAGAGCGCCGTACATCCACCATCTTGGA
* *
501 A-CGAGCGTCGTACA---ACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
*
526 AGAGAGCGCCGTACA---ACCATTTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
* *
552 CGAGAGCGCCGTACATCCACTATCTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
*
581 AGAGAGCGCCGTACATCCACCATTTTGG-
1 AGAGAGCGCCGTACATCCACCATCTTGGA
* * * *
609 A-CGAGCGCTGTACATCTACCATTTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
*
637 CA-AGAGCGCCGTACATCCACCATTTTGGA
1 -AGAGAGCGCCGTACATCCACCATCTTGGA
* **
666 CGAGAGCGTTGTACATCCACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
695 AGAGAGCGCCGTACAT-CA--ATCTTGGA
1 AGAGAGCGCCGTACATCCACCATCTTGGA
* * *
721 AGAGGGCGCCATAC-GCCAACCATCTTGGA
1 AGAGAGCGCCGTACATCC-ACCATCTTGGA
750 A
1 A
751 ATGGGCGCCG
Statistics
Matches: 300, Mismatches: 37, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
24 19 0.06
25 24 0.08
26 64 0.21
27 47 0.16
28 5 0.02
29 141 0.47
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (29 bp):
AGAGAGCGCCGTACATCCACCATCTTGGA
Found at i:435 original size:56 final size:57
Alignment explanation
Indices: 366--711 Score: 395
Period size: 56 Copynumber: 6.3 Consensus size: 57
356 ATATCAAAAG
* * *
366 AGAGAGCGCCGTACATCCACCATCTTGGAAGAGAACGCCGTACATCCACCATTTTGG-
1 AGAGAGCGCCGTACATCCACCATTTTGGACGAG-ACGCCGTACATCCACCATCTTGGA
* * * *
423 A-CGAGCGCCGTACA---ACCATCTTGGAAGAAAGCGCCGT--A--CACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGACGAGA-CGCCGTACATCCACCATCTTGGA
*
473 AGAGAGCGCCGTACATCCACCATTTTGGACGAG-CGTCGTACA---ACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGACGAGACGCCGTACATCCACCATCTTGGA
*
526 AGAGAGCGCCGTACA---ACCATTTTGGACGAGAGCGCCGTACATCCACTATCTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGACGAGA-CGCCGTACATCCACCATCTTGGA
* * *
581 AGAGAGCGCCGTACATCCACCATTTTGGACGAG-CGCTGTACATCTACCATTTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGACGAGACGCCGTACATCCACCATCTTGGA
**
637 CA-AGAGCGCCGTACATCCACCATTTTGGACGAGAGCGTTGTACATCCACCATCTTGGA
1 -AGAGAGCGCCGTACATCCACCATTTTGGACGAGA-CGCCGTACATCCACCATCTTGGA
695 AGAGAGCGCCGTACATC
1 AGAGAGCGCCGTACATC
712 AATCTTGGAA
Statistics
Matches: 252, Mismatches: 17, Indels: 39
0.82 0.06 0.13
Matches are distributed among these distances:
49 10 0.04
50 16 0.06
51 13 0.05
52 14 0.06
53 46 0.18
54 13 0.05
55 25 0.10
56 62 0.25
57 3 0.01
58 50 0.20
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (57 bp):
AGAGAGCGCCGTACATCCACCATTTTGGACGAGACGCCGTACATCCACCATCTTGGA
Found at i:503 original size:78 final size:79
Alignment explanation
Indices: 383--730 Score: 382
Period size: 78 Copynumber: 4.3 Consensus size: 79
373 GCCGTACATC
*
383 CACCATCTTGGAAGAGAACGCCGTACATCCACCATTTTGGACGAGCGCCGTACA-ACCATCTTGG
1 CACCATCTTGGAAGAGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACACACCATCTTGG
*
447 AAGAAAGCGCCGTA
66 AAGAGAGCGCCGTA
*
461 CACCATCTTGGAAGAGAGCGCCGTACATCCACCATTTTGGACGAGCGTCGTACA-ACCATCTTGG
1 CACCATCTTGGAAGAGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACACACCATCTTGG
525 AAGAGAGCGCCGTA
66 AAGAGAGCGCCGTA
* * * * *
539 CAACCATTTTGGACGAGAGCGCCGTACATCCACTATCTTGGAAGAGAGCGCCGTACATCCACCAT
1 C-ACCATCTTGGAAGAGAGCGCCGTACATCCACCATTTTGG-A-CGAGCGCCGTACA--CACCAT
* * *
604 TTTGG-A-CGAGCGCTGTACA
61 CTTGGAAGAGAGCGCCGT--A
* **
623 TCTACCATTTTGGACA-AGAGCGCCGTACATCCACCATTTTGGACGAGAGCGTTGTACATCCACC
1 -C-ACCATCTTGGA-AGAGAGCGCCGTACATCCACCATTTTGGAC--GAGCGCCGTACA--CACC
687 ATCTTGGAAGAGAGCGCCGTA
59 ATCTTGGAAGAGAGCGCCGTA
* *
708 CATCAATCTTGGAAGAGGGCGCC
1 CA-CCATCTTGGAAGAGAGCGCC
731 ATACGCCAAC
Statistics
Matches: 229, Mismatches: 25, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
78 76 0.33
79 35 0.15
80 1 0.00
81 11 0.05
82 8 0.03
83 3 0.01
84 27 0.12
85 59 0.26
86 1 0.00
87 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.20
Consensus pattern (79 bp):
CACCATCTTGGAAGAGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACACACCATCTTGG
AAGAGAGCGCCGTA
Found at i:905 original size:28 final size:28
Alignment explanation
Indices: 865--1028 Score: 193
Period size: 28 Copynumber: 6.2 Consensus size: 28
855 AAAATAGAGT
*
865 GCTCCCAATGACCGCGAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
*
893 GCTCCCAACGACCACGAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
* *
921 GCTCCCAATGACCGCAAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
*
949 GCTCCAAATGACCACGAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
977 GCT-CC--T----A--AAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
* * *
996 GCTCCCAATGACCGCAAAGCGATAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
1024 GCTCC
1 GCTCC
1029 AAAAGCGGTA
Statistics
Matches: 116, Mismatches: 11, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
19 15 0.13
20 2 0.02
21 1 0.01
22 1 0.01
25 1 0.01
27 1 0.01
28 95 0.82
ACGTcount: A:0.28, C:0.32, G:0.25, T:0.15
Consensus pattern (28 bp):
GCTCCCAATGACCACGAAGCGGTAGTAC
Found at i:1006 original size:47 final size:47
Alignment explanation
Indices: 936--1050 Score: 176
Period size: 47 Copynumber: 2.4 Consensus size: 47
926 CAATGACCGC
* * *
936 AAAGCGGTAGTACGCTCCAAATGACCACGAAGCGGTAGTACGCTCCT
1 AAAGCGGTAGTACGCTCCAAATGACCACAAAGCGATAGTACGCTCCA
* *
983 AAAGCGGTAGTACGCTCCCAATGACCGCAAAGCGATAGTACGCTCCA
1 AAAGCGGTAGTACGCTCCAAATGACCACAAAGCGATAGTACGCTCCA
*
1030 AAAGCGGTAGAACGCTCCAAA
1 AAAGCGGTAGTACGCTCCAAA
1051 AATAAATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (47 bp):
AAAGCGGTAGTACGCTCCAAATGACCACAAAGCGATAGTACGCTCCA
Found at i:1035 original size:19 final size:19
Alignment explanation
Indices: 1011--1051 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1001 CAATGACCGC
*
1011 AAAGCGATAGTACGCTCCA
1 AAAGCGATAGAACGCTCCA
*
1030 AAAGCGGTAGAACGCTCCA
1 AAAGCGATAGAACGCTCCA
1049 AAA
1 AAA
1052 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.12
Consensus pattern (19 bp):
AAAGCGATAGAACGCTCCA
Found at i:1142 original size:24 final size:24
Alignment explanation
Indices: 1110--1171 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
1100 TCACCATGAG
1110 AGAACGCTCACCATCAAATGTGGT
1 AGAACGCTCACCATCAAATGTGGT
1134 AGAACGCTCACCATCAAATGTGGT
1 AGAACGCTCACCATCAAATGTGGT
*
1158 AGAATGCTCACCAT
1 AGAACGCTCACCAT
1172 GTAAGCGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (24 bp):
AGAACGCTCACCATCAAATGTGGT
Found at i:1839 original size:6 final size:6
Alignment explanation
Indices: 1828--1865 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
1818 AACAGTAATA
1828 TATCTT TATCTT TATCTT TATCTT TATCTT TATCTT TA
1 TATCTT TATCTT TATCTT TATCTT TATCTT TATCTT TA
1866 CTATATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (6 bp):
TATCTT
Done.