Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015835.1 Corchorus capsularis cultivar CVL-1 contig15856, 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: 11302
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Found at i:541 original size:57 final size:58
Alignment explanation
Indices: 436--553 Score: 177
Period size: 57 Copynumber: 2.1 Consensus size: 58
426 ATCCCAATGG
*
436 AAACATGTACAATACTACAAATATTGCATCATATATTGCTTTG-AAAAAAATGTAGAA
1 AAACATGTACAATACTACAAATATTGCATCACATATTGCTTTGAAAAAAAATGTAGAA
* * *
493 AAACATGTACACTACTACAAATATTGCATCACATCTTTGCTTT-TAAAAAAATGTAGAA
1 AAACATGTACAATACTACAAATATTGCATCACAT-ATTGCTTTGAAAAAAAATGTAGAA
551 AAA
1 AAA
554 AAATATATTG
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 32 0.57
58 24 0.43
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (58 bp):
AAACATGTACAATACTACAAATATTGCATCACATATTGCTTTGAAAAAAAATGTAGAA
Found at i:1443 original size:33 final size:33
Alignment explanation
Indices: 1401--1465 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1391 TTTATCTTGA
1401 GACCACCATGACAAATCAGG-TCATTTGCTTTGT
1 GACCACCATGACAAA-CAGGATCATTTGCTTTGT
*
1434 GACCACCATGACAAACTGGATCATTTGCTTTG
1 GACCACCATGACAAACAGGATCATTTGCTTTG
1466 CAAGAAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (33 bp):
GACCACCATGACAAACAGGATCATTTGCTTTGT
Found at i:1886 original size:22 final size:22
Alignment explanation
Indices: 1758--2144 Score: 101
Period size: 22 Copynumber: 17.6 Consensus size: 22
1748 AAACTTCCCA
*
1758 ATGAAATTTTGATAACCAACACT
1 ATGAAATTTTGATAATC-ACACT
*
1781 ATGAGAGATGTTGATAACCTC-CA-T
1 ATGA-A-ATTTTGATAA--TCACACT
* * * **
1805 ATGATATATTGATAACCACGTT
1 ATGAAATTTTGATAATCACACT
* * * *
1827 ATGAAAATTTAAAAATCTC-CAT
1 ATGAAATTTTGATAATCACAC-T
1849 ATG-AATTGTT-AGTAATCACACT
1 ATGAAATT-TTGA-TAATCACACT
* *
1871 CTGAAATTTTGATAATCACATT
1 ATGAAATTTTGATAATCACACT
* * * *
1893 ATGAAATTGTGATAACCTCGCT
1 ATGAAATTTTGATAATCACACT
*
1915 ATGAAATTTTGATAAATCTTC-CT
1 ATGAAATTTTGAT-AATC-ACACT
** * *
1938 AAAAAATTTTGATAAAC-CTCCTT
1 ATGAAATTTTGATAATCAC-AC-T
* * *
1961 ATAAAATTTTGATAA-CATTATT
1 ATGAAATTTTGATAATCA-CACT
*
1983 ATGAAATCTTG---AT-A-AC-
1 ATGAAATTTTGATAATCACACT
* * *
1999 -TGCAAATTTTGATAACCTCCCT
1 ATG-AAATTTTGATAATCACACT
** * * *
2021 ATGATTTTTTGATAACCTCATT
1 ATGAAATTTTGATAATCACACT
* * *
2043 ATGAAATTTTGTTAATCTCCCT
1 ATGAAATTTTGATAATCACACT
* *
2065 ATGAAATTTTGAT-CTACATACT
1 ATGAAATTTTGATAAT-CACACT
* *
2087 ATGAAATTTTGATAA-CCCTCTT
1 ATGAAATTTTGATAATCACAC-T
*
2109 ATGAAATTTTGA-AAACTA-ATCT
1 ATGAAATTTTGATAATC-ACA-CT
2131 ATGAAATTTTGATA
1 ATGAAATTTTGATA
2145 TCCTCCCTGA
Statistics
Matches: 267, Mismatches: 62, Indels: 70
0.67 0.16 0.18
Matches are distributed among these distances:
15 2 0.01
16 7 0.03
17 1 0.00
19 3 0.01
20 2 0.01
21 11 0.04
22 176 0.66
23 45 0.17
24 8 0.03
25 11 0.04
27 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAATCACACT
Found at i:1946 original size:23 final size:23
Alignment explanation
Indices: 1918--1975 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
1908 CCTCGCTATG
*
1918 AAATTTTGATAAATCTTCC-TAAA
1 AAATTTTGATAAA-CCTCCTTAAA
*
1941 AAATTTTGATAAACCTCCTTATA
1 AAATTTTGATAAACCTCCTTAAA
1964 AAATTTTGATAA
1 AAATTTTGATAA
1976 CATTATTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCTTAAA
Found at i:1996 original size:45 final size:44
Alignment explanation
Indices: 1874--1997 Score: 105
Period size: 46 Copynumber: 2.8 Consensus size: 44
1864 TCACACTCTG
* *
1874 AAATTTTGATAATCA-CATTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAA-CATTATTATGAAATT-TGATAAACCTCGCTATA
**
1918 AAATTTTGATAA-ATCT-TCCTAAAAAATTTTGATAAACCTC-CTTATA
1 AAATTTTGATAACAT-TAT--TATGAAA-TTTGATAAACCTCGC-TATA
1964 AAATTTTGATAACATTATTATGAAATCTTGATAA
1 AAATTTTGATAACATTATTATGAAAT-TTGATAA
1998 CTGCAAATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
42 1 0.02
43 1 0.02
44 13 0.20
45 22 0.34
46 24 0.38
47 3 0.05
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (44 bp):
AAATTTTGATAACATTATTATGAAATTTGATAAACCTCGCTATA
Found at i:2090 original size:44 final size:44
Alignment explanation
Indices: 2002--2163 Score: 142
Period size: 44 Copynumber: 3.7 Consensus size: 44
1992 TGATAACTGC
* ** * * *
2002 AAATTTTGATAACCTCCCTATGATTTTTTGAT-AACCTCATTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGATCTACAT-ACTATG
*
2046 AAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATACTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGATCTACATACTATG
*
2090 AAATTTTGATAA-C-CCTCTTATGAAATTTTGAAAACTA-AT-CTATG
1 AAATTTTGATAATCTCC-C-TATGAAATTTTG--ATCTACATACTATG
2134 AAATTTTGAT-ATCCTCCC--TGAAATTTTGAT
1 AAATTTTGATAAT-CTCCCTATGAAATTTTGAT
2164 TACTCCATGA
Statistics
Matches: 100, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
40 1 0.01
42 12 0.12
43 3 0.03
44 71 0.71
45 7 0.07
46 6 0.06
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (44 bp):
AAATTTTGATAATCTCCCTATGAAATTTTGATCTACATACTATG
Found at i:2321 original size:22 final size:22
Alignment explanation
Indices: 2269--2515 Score: 105
Period size: 22 Copynumber: 11.3 Consensus size: 22
2259 AATCACATTT
* * *
2269 TGAAAATTTGACAACCTTTTTA
1 TGAAATTTTGATAACCTCTTTA
2291 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
2313 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * **
2335 TGAAATTCTGATAATCACAATA
1 TGAAATTTTGATAACCTCTTTA
* *
2357 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
2379 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
2401 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
* * *
2423 -AAAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTTTA
* * * *
2447 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
2469 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
2489 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
2509 TGAAATT
1 TGAAATT
2516 GAGACTTTTA
Statistics
Matches: 166, Mismatches: 47, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
19 2 0.01
20 17 0.10
21 26 0.16
22 104 0.63
23 1 0.01
24 2 0.01
25 11 0.07
26 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:2385 original size:66 final size:66
Alignment explanation
Indices: 2289--2416 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
2279 ACAACCTTTT
* * * ** *
2289 TATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACA
1 TATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCACA
2354 A
66 A
* * *
2355 TATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
2417 TTCCTAAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (66 bp):
TATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCACA
A
Found at i:2653 original size:22 final size:22
Alignment explanation
Indices: 2595--2653 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2585 ATATTAGCTA
*
2595 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
* *
2617 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCACACT
*
2639 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
2654 TCTCTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:2772 original size:22 final size:22
Alignment explanation
Indices: 2699--2872 Score: 108
Period size: 22 Copynumber: 7.8 Consensus size: 22
2689 TAACCACCCA
**
2699 ATGAAATTTCAATAACCA-ATCT
1 ATGAAATTTTGATAACCATA-CT
* *
2721 AAGAAATTTTAATAACCCGAT-CTT
1 ATGAAATTTTGATAA-CC-ATAC-T
*
2745 ATGAAATTTTGGTAACCATACT
1 ATGAAATTTTGATAACCATACT
* * *
2767 ATGAAATTTTGGTAA-CTTCCAT
1 ATGAAATTTTGATAACCATAC-T
* *
2789 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAACCATACT
* *
2811 ATGGAATTTTGATATCC-TCCAC-
1 ATGAAATTTTGATAACCAT--ACT
* *
2833 ATGAAATTATAATAACCAT-CTT
1 ATGAAATTTTGATAACCATAC-T
2855 ATGAAATTTTGATAACCA
1 ATGAAATTTTGATAACCA
2873 CATAGAGACA
Statistics
Matches: 120, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 91 0.76
23 11 0.09
24 14 0.12
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAACCATACT
Found at i:2801 original size:44 final size:44
Alignment explanation
Indices: 2744--2871 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 44
2734 AACCCGATCT
* *
2744 TATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACTTCCA
1 TATGAAATTTTGGTAACCATACTATGAAATTTTGATAACCTCCA
* * *
2788 TATGAAATTTTGGTAACCACACTATGGAATTTTGATATCCTCCA
1 TATGAAATTTTGGTAACCATACTATGAAATTTTGATAACCTCCA
* * **
2832 CATGAAATTATAATAACCAT-CTTATGAAATTTTGATAACC
1 TATGAAATTTTGGTAACCATAC-TATGAAATTTTGATAACC
2872 ACATAGAGAC
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 1 0.01
44 70 0.99
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCATACTATGAAATTTTGATAACCTCCA
Found at i:4517 original size:29 final size:31
Alignment explanation
Indices: 4484--4547 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
4474 TGGCAATTTA
*
4484 GAAATATGTTTT-AAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
4513 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
4544 GAAA
1 GAAA
4548 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 12 0.38
30 4 0.12
31 16 0.50
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Done.