Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015092.1 Corchorus capsularis cultivar CVL-1 contig15113, 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: 30721
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:3799 original size:26 final size:26
Alignment explanation
Indices: 3760--3820 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
3750 ATATAATTTG
*
3760 AAAATTGTAATATT-CATATTGTATAAA
1 AAAATT-TTATATTCCA-ATTGTATAAA
*
3787 TAAATTTTATATTCCCAATTGTATAAA
1 AAAATTTTATATT-CCAATTGTATAAA
3814 AAAATTT
1 AAAATTT
3821 ACAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 6 0.21
27 21 0.72
28 2 0.07
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (26 bp):
AAAATTTTATATTCCAATTGTATAAA
Found at i:15213 original size:6 final size:7
Alignment explanation
Indices: 15179--15211 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
15169 TTCATAAACC
15179 TAAAAAT
1 TAAAAAT
15186 TAAAAAT
1 TAAAAAT
15193 TAAAAAAT
1 T-AAAAAT
15201 T-AAAAT
1 TAAAAAT
15207 TAAAA
1 TAAAA
15212 TTGGGTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAAAT
Found at i:24506 original size:27 final size:27
Alignment explanation
Indices: 24474--24546 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
24464 AAGTGGACTT
24474 AAAATGACTAAAATGCCCCTGAATATG
1 AAAATGACTAAAATGCCCCTGAATATG
** * * * *
24501 CGAATGACCAAAATG-CCCTTAGTGTG
1 AAAATGACTAAAATGCCCCTGAATATG
24527 AAAATGACTAAAATGCCCCT
1 AAAATGACTAAAATGCCCCT
24547 ATGTGCCCTA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 20 0.56
27 16 0.44
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (27 bp):
AAAATGACTAAAATGCCCCTGAATATG
Found at i:25035 original size:60 final size:60
Alignment explanation
Indices: 24939--25083 Score: 213
Period size: 60 Copynumber: 2.5 Consensus size: 60
24929 TAAAAACTTA
* *
24939 CAGGAACTGTCTTCAG-ATCCATGTATGAGCTTTCTTCATACTCATTCTTAAATACCATT
1 CAGGAACTGTCTTCAGAATCCATCTATGAGCTGTCTTCATACTCATTCTTAAATACCATT
* * * *
24998 GAGGAACTATCTTCAGAATCCATCTTTGAGCTGTCTTCATACTCATTCTTAAATACCTTT
1 CAGGAACTGTCTTCAGAATCCATCTATGAGCTGTCTTCATACTCATTCTTAAATACCATT
*
25058 CAGGAACTGTCTTCAG-ATCCGTCTAT
1 CAGGAACTGTCTTCAGAATCCATCTAT
25084 ACCATTGTGG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
59 22 0.29
60 53 0.71
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (60 bp):
CAGGAACTGTCTTCAGAATCCATCTATGAGCTGTCTTCATACTCATTCTTAAATACCATT
Found at i:25309 original size:97 final size:97
Alignment explanation
Indices: 25184--25366 Score: 251
Period size: 97 Copynumber: 1.9 Consensus size: 97
25174 TTTATAAGCC
* *
25184 GTCTTCATACTCATTCTTAAATACCTTTCAAGAACTGTCTTCAAATCCGTTATCAAATATCTT-T
1 GTCTTCATACTCATTCTTAAATACCTTTCAAGAACTCTCTTCAAATCCATTATCAAATATCTTCT
25248 CAGGAACTGTCTTCAGATCCATCTTCATGAGCA
66 -AGGAACTGTCTTCAGATCCATCTTCATGAGCA
* * * * * * *
25281 GTCTTCATACTCATTCTTAAATATCTTTCAGGAATTCTCTTCAGATCCATTCTTAAATTTCTTCT
1 GTCTTCATACTCATTCTTAAATACCTTTCAAGAACTCTCTTCAAATCCATTATCAAATATCTTCT
* *
25346 AGGAGCTGTCTTTAGATCCAT
66 AGGAACTGTCTTCAGATCCAT
25367 TCTTAAAAGG
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 73 0.99
98 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.39
Consensus pattern (97 bp):
GTCTTCATACTCATTCTTAAATACCTTTCAAGAACTCTCTTCAAATCCATTATCAAATATCTTCT
AGGAACTGTCTTCAGATCCATCTTCATGAGCA
Found at i:25363 original size:36 final size:36
Alignment explanation
Indices: 25292--25373 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
25282 TCTTCATACT
*
25292 CATTCTTAAATATCTTTCAGGAATTCTCTTCAGATC
1 CATTCTTAAATATCTTTCAGGAACTCTCTTCAGATC
* * * *
25328 CATTCTTAAATTTC-TTCTAGGAGCTGTCTTTAGATC
1 CATTCTTAAATATCTTTC-AGGAACTCTCTTCAGATC
25364 CATTCTTAAA
1 CATTCTTAAA
25374 AGGAAAGTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 3 0.08
36 37 0.93
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.43
Consensus pattern (36 bp):
CATTCTTAAATATCTTTCAGGAACTCTCTTCAGATC
Found at i:25420 original size:22 final size:22
Alignment explanation
Indices: 25392--25435 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25382 CTTCGAAGTA
25392 TGCCCGGAGGCAATCAGAATTG
1 TGCCCGGAGGCAATCAGAATTG
*
25414 TGCCCGGAGGCTATCAGAATTG
1 TGCCCGGAGGCAATCAGAATTG
25436 CCTTATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (22 bp):
TGCCCGGAGGCAATCAGAATTG
Found at i:25620 original size:64 final size:65
Alignment explanation
Indices: 25435--25634 Score: 330
Period size: 65 Copynumber: 3.1 Consensus size: 65
25425 TATCAGAATT
* *
25435 GCCTTATAACATGCCTGAGGGCTATCAGAATTGCTACCCGGAGGTTTCTGACGTCGTGCCCGGAG
1 GCCTTATAACATGCCTGGGGGCTATCAGAATTGCTACCCGGAGGTTTCTGACGTCGCGCCCGGAG
* * *
25500 GCCTTATAACATGCCTGGAGGCCATCAGAATTGCTACCCGGAGGTTTCCGACGTCGCGCCCGGAG
1 GCCTTATAACATGCCTGGGGGCTATCAGAATTGCTACCCGGAGGTTTCTGACGTCGCGCCCGGAG
*
25565 GCCTTATAACATGCC-GGGGGCTATCAGAATTGCTACCCGGAGGTTTCTGAAGTCGCGCCCGGAG
1 GCCTTATAACATGCCTGGGGGCTATCAGAATTGCTACCCGGAGGTTTCTGACGTCGCGCCCGGAG
*
25629 GACTTA
1 GCCTTA
25635 CCAAATGTAA
Statistics
Matches: 125, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
64 50 0.40
65 75 0.60
ACGTcount: A:0.20, C:0.28, G:0.29, T:0.23
Consensus pattern (65 bp):
GCCTTATAACATGCCTGGGGGCTATCAGAATTGCTACCCGGAGGTTTCTGACGTCGCGCCCGGAG
Found at i:27833 original size:17 final size:17
Alignment explanation
Indices: 27807--27842 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27797 ACATTCCATC
* *
27807 TTTTCTTTCTTTCTTCT
1 TTTTCCTTCTTGCTTCT
27824 TTTTCCTTCTTGCTTCT
1 TTTTCCTTCTTGCTTCT
27841 TT
1 TT
27843 CATATCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTCCTTCTTGCTTCT
Found at i:28105 original size:22 final size:23
Alignment explanation
Indices: 28077--28120 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28067 TTAGGCCAAG
28077 TTTTTTTTCTTCTCTT-TTTTCC
1 TTTTTTTTCTTCTCTTCTTTTCC
* *
28099 TTTTTTTTGTTGTCTTCTTTTC
1 TTTTTTTTCTTCTCTTCTTTTC
28121 TTTGAGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (23 bp):
TTTTTTTTCTTCTCTTCTTTTCC
Found at i:28825 original size:13 final size:13
Alignment explanation
Indices: 28777--28832 Score: 67
Period size: 14 Copynumber: 4.2 Consensus size: 13
28767 CTCAAAAACC
28777 TTTTGAAAATCCAT
1 TTTTGAAAA-CCAT
*
28791 TTTTGAAAACCTT
1 TTTTGAAAACCAT
*
28804 TTCTTGAAAACAAT
1 TT-TTGAAAACCAT
*
28818 TTTTGAAAAACAT
1 TTTTGAAAACCAT
28831 TT
1 TT
28833 CTTATTTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 16 0.44
14 20 0.56
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (13 bp):
TTTTGAAAACCAT
Found at i:28826 original size:27 final size:28
Alignment explanation
Indices: 28779--28835 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
28769 CAAAAACCTT
* * *
28779 TTGAAAATCCATTTTTGAAAACCTTTTC
1 TTGAAAATCAATTTTTGAAAAACATTTC
28807 TTGAAAA-CAATTTTTGAAAAACATTTC
1 TTGAAAATCAATTTTTGAAAAACATTTC
28834 TT
1 TT
28836 ATTTTGACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (28 bp):
TTGAAAATCAATTTTTGAAAAACATTTC
Done.