Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016210.1 Corchorus capsularis cultivar CVL-1 contig16231, 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: 33138
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1999 original size:16 final size:16
Alignment explanation
Indices: 1972--2064 Score: 98
Period size: 16 Copynumber: 5.8 Consensus size: 16
1962 TAATATTCTT
1972 GGGTCATTCGGGTTTC
1 GGGTCATTCGGGTTTC
* * *
1988 GGATCATACGGGTCTC
1 GGGTCATTCGGGTTTC
* *
2004 GGGTCACTCGGGTTAC
1 GGGTCATTCGGGTTTC
*
2020 GGGTCATTCGGCTTTC
1 GGGTCATTCGGGTTTC
* *
2036 GAGTCA-TCTGGGTTAC
1 GGGTCATTC-GGGTTTC
2052 GGGTCATTCGGGT
1 GGGTCATTCGGGT
2065 CATCTGGGTT
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
15 2 0.03
16 56 0.93
17 2 0.03
ACGTcount: A:0.12, C:0.22, G:0.35, T:0.31
Consensus pattern (16 bp):
GGGTCATTCGGGTTTC
Found at i:2030 original size:25 final size:26
Alignment explanation
Indices: 1994--2090 Score: 78
Period size: 25 Copynumber: 3.7 Consensus size: 26
1984 TTTCGGATCA
1994 TACGGGTC--TCGGGTCACTC-GGGT
1 TACGGGTCATTCGGGTCACTCTGGGT
*
2017 TACGGGTCATTCGGCTTTCGAGTCATCTGGGT
1 TACGGGTCATTCGG--GTC-A--C-TCTGGGT
2049 TACGGGTCATTCGGGTCA-TCTGGGT
1 TACGGGTCATTCGGGTCACTCTGGGT
*
2074 TGCGGGTCACTT-GGGTC
1 TACGGGTCA-TTCGGGTC
2091 TCGGGTCGGG
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
23 8 0.13
25 24 0.39
26 2 0.03
27 2 0.03
28 1 0.02
29 1 0.02
30 3 0.05
31 2 0.03
32 18 0.30
ACGTcount: A:0.10, C:0.23, G:0.36, T:0.31
Consensus pattern (26 bp):
TACGGGTCATTCGGGTCACTCTGGGT
Found at i:2158 original size:25 final size:27
Alignment explanation
Indices: 2128--2177 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
2118 TTGGTCAAAT
*
2128 CGGGTTGGGCGGG-T-TCGGGTTCGGA
1 CGGGTTGGACGGGTTCTCGGGTTCGGA
2153 CGGGTTGGACGGGTTCTCGGGTTCG
1 CGGGTTGGACGGGTTCTCGGGTTCG
2178 TGTCAACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
26 1 0.05
27 9 0.41
ACGTcount: A:0.04, C:0.18, G:0.52, T:0.26
Consensus pattern (27 bp):
CGGGTTGGACGGGTTCTCGGGTTCGGA
Found at i:2471 original size:15 final size:17
Alignment explanation
Indices: 2451--2488 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2441 TGTTCAAATG
2451 TCGGGTC-ATT-TGGGT
1 TCGGGTCAATTCTGGGT
2466 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
2483 T-GGGTC
1 TCGGGTC
2489 GTTTTCGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Found at i:2562 original size:16 final size:16
Alignment explanation
Indices: 2541--2571 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2531 CAACCTCGGG
*
2541 TTTTCGGGTTTGGGTC
1 TTTTCGGGTTCGGGTC
2557 TTTTCGGGTTCGGGT
1 TTTTCGGGTTCGGGT
2572 TGTAACAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.13, G:0.39, T:0.48
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTC
Found at i:3563 original size:22 final size:22
Alignment explanation
Indices: 3511--3553 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3501 TAAATAAAAT
**
3511 ATTCATACGAAATTATGATAAC
1 ATTCATATTAAATTATGATAAC
3533 ATTCATATTAAATTATGATAA
1 ATTCATATTAAATTATGATAA
3554 TTACACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTCATATTAAATTATGATAAC
Found at i:3912 original size:23 final size:21
Alignment explanation
Indices: 3574--4204 Score: 184
Period size: 22 Copynumber: 29.1 Consensus size: 21
3564 TTTTATGATG
3574 TCCTCATGAAATTTTGATAACC
1 TCCT-ATGAAATTTTGATAACC
** *
3596 TTCCTATGAAATTTCAATAACGA
1 -TCCTATGAAATTTTGATAAC-C
* *
3619 TACTATGAAATTTCT-AGAACC
1 TCCTATGAAATTT-TGATAACC
* * **
3640 TTTCTAT-AATTTTTTTTTAACC
1 -TCCTATGAA-ATTTTGATAACC
* * *
3662 TTCTTATGAAATTTCGTTAACC
1 -TCCTATGAAATTTTGATAACC
* * *
3684 TCCCTAAGGAGTTTTGA-AGACC
1 T-CCTATGAAATTTTGATA-ACC
* *
3706 TCATTATGAAATTTTGATAACT
1 TC-CTATGAAATTTTGATAACC
* *
3728 TCCAAATGAAATTTTAATAACC
1 TCC-TATGAAATTTTGATAACC
* *
3750 AACACTAT-AAGATGTTGATAACC
1 -TC-CTATGAA-ATTTTGATAACC
* *
3773 TCCATATGATATATTGATAACC
1 TCC-TATGAAATTTTGATAACC
* * * * * *
3795 ACGTTAAGAAAATTTAAAAACC
1 TC-CTATGAAATTTTGATAACC
* * * *
3817 T-CTATATAAATTGTCAGTAATC
1 TCCTAT-GAAATTTTGA-TAACC
* * *
3839 ACACTCTGAAATTTTGATAATC
1 TC-CTATGAAATTTTGATAACC
* *
3861 ACACTATGAAATTGTGATAACC
1 TC-CTATGAAATTTTGATAACC
3883 TCGCTATGAAATTTTGATAAACC
1 TC-CTATGAAATTTTGAT-AACC
* *
3906 TTCCTATAAAATTTTGATAAATC
1 -TCCTATGAAATTTTGAT-AACC
*
3929 TCCCTATAAAATTTTGATAACC
1 T-CCTATGAAATTTTGATAACC
** *
3951 TCCTTATGAAATCCTGATGA--
1 TCC-TATGAAATTTTGATAACC
*
3971 --CTA-CAAATTTTGATAACC
1 TCCTATGAAATTTTGATAACC
** * *
3989 TCTCTATGATTTTTTTTATTACC
1 TC-CTATGA-AATTTTGATAACC
* *
4012 TCATTATGAAATTTTGATAATC
1 TC-CTATGAAATTTTGATAACC
* *
4034 TCCCTATGAAATTTTGATCTACA
1 T-CCTATGAAATTTTGAT-AACC
* * *
4057 TACTATAAAATTTTAATAACCC
1 TCCTATGAAATTTTGATAA-CC
* *
4079 TCTTATGAAATTTTGA-AAAC
1 TCCTATGAAATTTTGATAACC
* *
4099 TAAACTATGAAATTTTGATATCC
1 T--CCTATGAAATTTTGATAACC
* *
4122 TCC-CTGAAA-TTTGATTA-C
1 TCCTATGAAATTTTGATAACC
* * *
4140 TCCATAATAAAAGTTTAATAACC
1 TCC-T-ATGAAATTTTGATAACC
*
4163 TTCC--T--AA-TTTGGTAACC
1 -TCCTATGAAATTTTGATAACC
*
4180 ATACTATGAAATTTTGATAACC
1 -TCCTATGAAATTTTGATAACC
4202 TCC
1 TCC
4205 CCAGAAATAC
Statistics
Matches: 438, Mismatches: 121, Indels: 100
0.66 0.18 0.15
Matches are distributed among these distances:
16 9 0.02
17 12 0.03
18 7 0.02
19 7 0.02
20 10 0.02
21 30 0.07
22 265 0.61
23 89 0.20
24 9 0.02
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAACC
Found at i:3951 original size:45 final size:45
Alignment explanation
Indices: 3847--3951 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 45
3837 TCACACTCTG
* * * *
3847 AAATTTTGATAATC-ACACTATGAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTACACTATAAAATTGTGATAACCTCCCTATA
* * *
3891 AAATTTTGATAAACCTTC-CTATAAAATTTTGATAAATCTCCCTATA
1 AAATTTTGAT-AACCTACACTATAAAATTGTGAT-AACCTCCCTATA
3937 AAATTTTGATAACCT
1 AAATTTTGATAACCT
3952 CCTTATGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
44 10 0.20
45 21 0.41
46 20 0.39
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (45 bp):
AAATTTTGATAACCTACACTATAAAATTGTGATAACCTCCCTATA
Found at i:4331 original size:22 final size:22
Alignment explanation
Indices: 4218--4344 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
4208 GAAATACCAC
* *
4218 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCACAT
* * ***
4240 TTTGAAAATTTGATAACCTTTT
1 TATGAAATTTTGATAACCACAT
*
4262 TATGAAATTTTGATAACCTC-T
1 TATGAAATTTTGATAACCACAT
* * *
4283 CTATAAAATTTTGTTGACGC-C-T
1 -TATGAAATTTTGATAAC-CACAT
*
4305 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAACCACAT
* *
4328 TATGTAATTTTAATAAC
1 TATGAAATTTTGATAAC
4345 GTCGCTTTGA
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
21 2 0.02
22 77 0.95
23 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAT
Found at i:4337 original size:44 final size:44
Alignment explanation
Indices: 4217--4362 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 44
4207 AGAAATACCA
* * * *
4217 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTTT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * * *
4261 TTATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACGC-CT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAAC-CTCT
* * * *
4305 CTATGAAATTTTGATAATCACATTATGTAATTTTAATAACGTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
*
4349 CTTTGAAATTTTGA
1 CTATGAAATTTTGA
4363 AATTGGACCA
Statistics
Matches: 77, Mismatches: 21, Indels: 8
0.73 0.20 0.08
Matches are distributed among these distances:
43 1 0.01
44 74 0.96
45 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
Found at i:4712 original size:31 final size:31
Alignment explanation
Indices: 4647--4712 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
4637 TGGCAATTTA
* *
4647 GAAATATGTTTTTTAAAAAAGGGTAAACTTG
1 GAAATATGTTTTTAAAAAAAGGGTAAACTCG
4678 GAAATATG-TTTTAAAAATAAGGGTACAA-TCG
1 GAAATATGTTTTTAAAAA-AAGGGTA-AACTCG
4709 GAAA
1 GAAA
4713 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 8 0.26
31 21 0.68
32 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (31 bp):
GAAATATGTTTTTAAAAAAAGGGTAAACTCG
Found at i:11332 original size:21 final size:21
Alignment explanation
Indices: 11306--11347 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11296 ACACTAGGAG
11306 AAATTAATAATAATAATTAAT
1 AAATTAATAATAATAATTAAT
* * *
11327 AAATTATTATTATTAATTAAT
1 AAATTAATAATAATAATTAAT
11348 TTAATCATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTAATAATAATAATTAAT
Found at i:18911 original size:23 final size:25
Alignment explanation
Indices: 18879--18925 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
18869 AAACATTCTT
18879 AAAAATTCAAAGCAATC-ATCAATC
1 AAAAATTCAAAGCAATCGATCAATC
*
18903 AAAAA-TCAAATCAATCGATCAAT
1 AAAAATTCAAAGCAATCGATCAAT
18926 ACATGCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.21
Consensus pattern (25 bp):
AAAAATTCAAAGCAATCGATCAATC
Found at i:19639 original size:23 final size:23
Alignment explanation
Indices: 19609--19661 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
19599 GCATAAGCCG
19609 GGCATGGTGCGCGGACAAGGCCA
1 GGCATGGTGCGCGGACAAGGCCA
* **
19632 GGCATGGTGCGTGGACAAGGCTG
1 GGCATGGTGCGCGGACAAGGCCA
19655 GGCATGG
1 GGCATGG
19662 CACGGTGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.47, T:0.13
Consensus pattern (23 bp):
GGCATGGTGCGCGGACAAGGCCA
Found at i:25593 original size:21 final size:21
Alignment explanation
Indices: 25567--25642 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
25557 TAATCCTATG
25567 TTGGAGGTTTCTTATTTATAT
1 TTGGAGGTTTCTTATTTATAT
* *
25588 TTGGAGGTCTCTTATTTGTAT
1 TTGGAGGTTTCTTATTTATAT
* *
25609 TTGGAGGTTTCTTATTCATAA
1 TTGGAGGTTTCTTATTTATAT
*
25630 TTAGAGGTTTCTT
1 TTGGAGGTTTCTT
25643 TCATATATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.18, C:0.08, G:0.21, T:0.53
Consensus pattern (21 bp):
TTGGAGGTTTCTTATTTATAT
Found at i:25652 original size:42 final size:42
Alignment explanation
Indices: 25567--25652 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
25557 TAATCCTATG
* * * * *
25567 TTGGAGGTTTCTTATTTATATTTGGAGGTCTCTTATTTGTAT
1 TTGGAGGTTTCTTATTCATAATTAGAGGTCTCTTATATATAT
*
25609 TTGGAGGTTTCTTATTCATAATTAGAGGTTTCTT-TCATATAT
1 TTGGAGGTTTCTTATTCATAATTAGAGGTCTCTTAT-ATATAT
25651 TT
1 TT
25653 AGGTTTTCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.03
42 36 0.97
ACGTcount: A:0.20, C:0.08, G:0.19, T:0.53
Consensus pattern (42 bp):
TTGGAGGTTTCTTATTCATAATTAGAGGTCTCTTATATATAT
Found at i:25654 original size:21 final size:20
Alignment explanation
Indices: 25607--25670 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
25597 TCTTATTTGT
*
25607 ATTTGGAGGTTTCTTATTCATA
1 ATTTAGAGGTTTC-T-TTCATA
25629 A-TTAGAGGTTTCTTTCATA
1 ATTTAGAGGTTTCTTTCATA
*
25648 TATTTAG-GTTTTCTTT-ATA
1 -ATTTAGAGGTTTCTTTCATA
25667 ATTT
1 ATTT
25671 GCTTTAGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 9 0.24
20 10 0.26
21 14 0.37
22 1 0.03
ACGTcount: A:0.23, C:0.08, G:0.14, T:0.55
Consensus pattern (20 bp):
ATTTAGAGGTTTCTTTCATA
Done.