Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016505.1 Corchorus capsularis cultivar CVL-1 contig16526, 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: 15603
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:3997 original size:23 final size:23
Alignment explanation
Indices: 3925--4026 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 23
3915 TCACACTCTG
* * * *
3925 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* * **
3947 AAATTGTGAT-AACCTCGCTAGG
1 AAATTTTGATAAACCTCCCTATA
* * *
3969 AAATTTTGATAAATCTTCCTTTA
1 AAATTTTGATAAACCTCCCTATA
3992 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
4015 AAATTTTGATAA
1 AAATTTTGATAA
4027 CTTTCTTATG
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
22 26 0.41
23 38 0.59
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:4082 original size:22 final size:22
Alignment explanation
Indices: 3757--4871 Score: 358
Period size: 22 Copynumber: 51.2 Consensus size: 22
3747 TTTATTTTAT
* *
3757 TAACCTCCCTAAGGAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
**
3779 -AGACCTCAATATGAAATTTTGA
1 TA-ACCTCCCTATGAAATTTTGA
* *
3801 TAACTTCCCAATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * * *
3823 TAACCAACACTATGAGATGTTGA
1 TAACC-TCCCTATGAAATTTTGA
* * * *
3846 TAACCTCCATATGATATATTGG
1 TAACCTCCCTATGAAATTTTGA
** * *
3868 TAA-CTACATTATGAAAATTTAA
1 TAACCT-CCCTATGAAATTTTGA
* *
3890 AAACCTCCATATG-AATTGTT-A
1 TAACCTCCCTATGAAATT-TTGA
* * * *
3911 GTAATCACACTCTGAAATTTTGA
1 -TAACCTCCCTATGAAATTTTGA
* * * *
3934 TAATCACACTATGAAATTGTGA
1 TAACCTCCCTATGAAATTTTGA
* *
3956 TAACCTCGCTAGGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * * *
3978 TAAATCTTCCTTTAAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
*
4001 TAAACCTCCCTATAAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
* * * *
4024 TAACTTTCTTATGAAATCTTGA
1 TAACCTCCCTATGAAATTTTGA
*
4046 TAA-----CTA-CAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
**
4062 TAACCTCCCTATGATTTTTTGA
1 TAACCTCCCTATGAAATTTTGA
** *
4084 TAACCTCATTATGAAATTTTGT
1 TAACCTCCCTATGAAATTTTGA
*
4106 TAATCTCCCTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
** * * *
4128 TCTGCAT-ACTATGAAATTTTAA
1 T-AACCTCCCTATGAAATTTTGA
*
4150 TAACC-CTCTTATGAAATTTTGA
1 TAACCTC-CCTATGAAATTTTGA
** **
4172 -AAATTAAACTATGAAATTTTGA
1 TAACCT-CCCTATGAAATTTTGA
*
4194 TATCCTCCC--TGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * * * *
4214 TTA-CTCCATAATAAAAGTTTAA
1 TAACCTCCCT-ATGAAATTTTGA
* *
4236 TAACCTTCC--T--AA-TTTGG
1 TAACCTCCCTATGAAATTTTGA
*
4253 TAACCAT-ACTATGAAATTTTTGA
1 TAACC-TCCCTATGAAA-TTTTGA
4276 TAACCT--CTATGAAATTTTTG-
1 TAACCTCCCTATGAAA-TTTTGA
* * ** * *
4296 TAATCACATTCTGAAAATTTGA
1 TAACCTCCCTATGAAATTTTGA
**
4318 TAACCTCTTTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
** * *
4340 TAACCTCTTTATAAAATTTTGT
1 TAACCTCCCTATGAAATTTTGA
*
4362 TGACC-CCTCTATGAAATTTTGA
1 TAACCTCC-CTATGAAATTTTGA
* * ** *
4384 TAATCACATTATGTAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* *
4406 TAACCTCGCTTTGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* ** *
4428 TGACAACACTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* *
4450 TAATCTTCCTAT-AAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* *
4471 TAATCCGATCTCTATGAAATTTCGA
1 TAA-CC--TCCCTATGAAATTTTGA
* * * * *
4496 TAATCACTCTATGAGA-TTTAA
1 TAACCTCCCTATGAAATTTTGA
* * *
4517 TAACCT-TCTATCAAATTTTGG
1 TAACCTCCCTATGAAATTTTGA
* *
4538 T-A-CTCCTTATGAAATTGAGACTTTTA
1 TAACCTCCCTATGAAA-T-----TTTGA
* *
4564 TAACCTTCATATTG-AATTTTGA
1 TAACCTCCCTA-TGAAATTTTGA
* * *
4586 TAACCACACTATAAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
4608 TAATCTCCCCATGAAATATT-A
1 TAACCTCCCTATGAAATTTTGA
*
4629 GTAACATCTCCTAATGAAATTTT-A
1 -TAACCTC-CCT-ATGAAATTTTGA
* *
4653 TTAACCACACTATGAAATTCTT-A
1 -TAACCTCCCTATGAAATT-TTGA
* * *
4676 CAACCTCGCTATGACATTTCT-A
1 TAACCTCCCTATGAAATTT-TGA
** * *
4698 TAAAAT---TGTGAAA--AT--
1 TAACCTCCCTATGAAATTTTGA
* **
4713 TAACCACCCTATGAAATTTCAA
1 TAACCTCCCTATGAAATTTTGA
** * *
4735 TAACCAACCTAAGAAATTTTGG
1 TAACCTCCCTATGAAATTTTGA
* *
4757 TAACCACACTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
4779 TAACTTCCATATGAAATTTTGG
1 TAACCTCCCTATGAAATTTTGA
* * *
4801 TAACCACACTATGGAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
4823 TAACCT-CCTCAAGAAATTATAA
1 TAACCTCCCT-ATGAAATTTTGA
*
4845 TAACCAT-CTTATGAAATTTTGA
1 TAACC-TCCCTATGAAATTTTGA
4867 TAACC
1 TAACC
4872 ACATAGAGAC
Statistics
Matches: 790, Mismatches: 235, Indels: 136
0.68 0.20 0.12
Matches are distributed among these distances:
15 3 0.00
16 12 0.02
17 11 0.01
18 9 0.01
19 12 0.02
20 31 0.04
21 63 0.08
22 515 0.65
23 87 0.11
24 21 0.03
25 11 0.01
26 4 0.01
27 2 0.00
28 7 0.01
29 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
TAACCTCCCTATGAAATTTTGA
Found at i:5227 original size:15 final size:15
Alignment explanation
Indices: 5209--5259 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
5199 TATATAATCT
5209 AATAATTAATAATGG
1 AATAATTAATAATGG
* *
5224 AATAATTTATAAT-T
1 AATAATTAATAATGG
*
5238 AA-AA-AAATAATGG
1 AATAATTAATAATGG
5251 AATAATTAA
1 AATAATTAA
5260 AATATTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 5 0.19
13 4 0.15
14 4 0.15
15 14 0.52
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (15 bp):
AATAATTAATAATGG
Found at i:9143 original size:29 final size:28
Alignment explanation
Indices: 9072--9144 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
9062 CCATGTATTC
*
9072 ACAAAGGCAGAGAA-TATTTTGGTGAAA
1 ACAAAGGTAGAGAATTATTTTGGTGAAA
*
9099 ACAAAGGTAG-GAAATTTTTTTGGGTGAAA
1 ACAAAGGTAGAG-AATTATTTT-GGTGAAA
9128 ACAAAGGTAGAGAATTA
1 ACAAAGGTAGAGAATTA
9145 GAGTAAGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 1 0.03
27 11 0.28
28 5 0.13
29 21 0.54
30 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (28 bp):
ACAAAGGTAGAGAATTATTTTGGTGAAA
Found at i:10039 original size:19 final size:19
Alignment explanation
Indices: 10015--10054 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
10005 TTGCCCTTCT
10015 TCTCTCTCCCCCCACTAAG
1 TCTCTCTCCCCCCACTAAG
* *
10034 TCTCTCTCCTCCCACTTAG
1 TCTCTCTCCCCCCACTAAG
10053 TC
1 TC
10055 AAGATGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.50, G:0.05, T:0.33
Consensus pattern (19 bp):
TCTCTCTCCCCCCACTAAG
Found at i:12244 original size:12 final size:14
Alignment explanation
Indices: 12213--12249 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12203 ACGAGAACTA
*
12213 GAGAGGGAGAAGGG
1 GAGAGAGAGAAGGG
12227 GAGAGAGAGAAGGG
1 GAGAGAGAGAAGGG
12241 GAGAGAGAG
1 GAGAGAGAG
12250 GAGCGGCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGAAGGG
Done.