Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008990.1 Corchorus capsularis cultivar CVL-1 contig09011, 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: 21216
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Found at i:1167 original size:30 final size:30
Alignment explanation
Indices: 1131--1187 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1121 TCAATCTTGG
*
1131 ATCCTGCTGTAAACAAACTGTTGACTTTAA
1 ATCCTGCTGTAAACAAACAGTTGACTTTAA
* *
1161 ATCCTGCTGTAAATACACAGTTGACTT
1 ATCCTGCTGTAAACAAACAGTTGACTT
1188 ATTTCATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (30 bp):
ATCCTGCTGTAAACAAACAGTTGACTTTAA
Found at i:3332 original size:2 final size:2
Alignment explanation
Indices: 3325--3365 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3315 AAATCATTAC
*
3325 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3366 CTAAATTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4823 original size:2 final size:2
Alignment explanation
Indices: 4816--4852 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4806 TTGCCCACTC
4816 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4853 AATGACCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7303 original size:17 final size:17
Alignment explanation
Indices: 7281--7313 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7271 ATAGAGGGAC
7281 AATAAAATATGGAGAAG
1 AATAAAATATGGAGAAG
*
7298 AATAAAATATGTAGAA
1 AATAAAATATGGAGAA
7314 TGGCAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (17 bp):
AATAAAATATGGAGAAG
Found at i:9999 original size:22 final size:22
Alignment explanation
Indices: 9974--10095 Score: 75
Period size: 22 Copynumber: 5.6 Consensus size: 22
9964 ATGATCCCAT
9974 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
9996 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
10018 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
10040 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
10061 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
10083 TAAGGAATTTTGA
1 TATGAAATTTTGA
10096 AGACCTCAAT
Statistics
Matches: 71, Mismatches: 28, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
21 14 0.20
22 57 0.80
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:10366 original size:22 final size:22
Alignment explanation
Indices: 10341--10511 Score: 116
Period size: 22 Copynumber: 7.8 Consensus size: 22
10331 ATGATCCCAT
10341 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
10363 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
10385 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
10407 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
10428 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
10450 TAAGAAATTTTGA-AGACC-TCAG
1 TATGAAATTTTGATA-ACCTTC-C
10472 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
*
10494 AATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
10512 AACACTATAT
Statistics
Matches: 110, Mismatches: 32, Indels: 13
0.71 0.21 0.08
Matches are distributed among these distances:
21 17 0.15
22 90 0.82
23 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:10663 original size:378 final size:377
Alignment explanation
Indices: 9862--10912 Score: 1838
Period size: 378 Copynumber: 2.8 Consensus size: 377
9852 TACTAGTTTC
* * *
9862 AGCTTTCACGTGCGTTGCCCATGACCCAACGTGTTTAAATGGAATATTCATATGAAATTGTGATA
1 AGCTTTCACGTGCGTTGCCCGTGGCCCAACGTGTTT-AATGGAATATTCATATGAAATTATGATA
* *
9927 ACCTCTCTTTTAAATTATGTTAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAACC
65 ACCTCTCTATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAACC
9992 TTCCTATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAATTTTTTTTAACC
130 TTCCTATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAATTTTTTTTAACC
10057 TTCTTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTC------AA---T-ATAACT
195 TTCTTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCATATGAAATTTTGATAACT
* *
10112 TCCCAATGAAATTTTGATAACCAACATTATATGAGATGTTGATAACCTCCATATGATATATTGAT
260 TCCCAATGAAATTTTGATAACCAACACTATATGAGATGTTGATAACCTCCATATGATATACTGAT
10177 AACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATT
325 AACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATT
* * *
10230 AGCTTTCACGTGTGTTGCCCGTGGCCCAACATGTTTAATGGAATATTCATATGAAATTATGCTAA
1 AGCTTTCACGTGCGTTGCCCGTGGCCCAACGTGTTTAATGGAATATTCATATGAAATTATGATAA
10295 CCTCTCTATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAACCT
66 CCTCTCTATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAACCT
10360 TCCTATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAATTTTTTTTAACCT
131 TCCTATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAATTTTTTTTAACCT
*
10425 TCTTATGAAATTTTGTTAACCTCCCTAAGAAATTTTGAAGACCTCAGTATGAAATTTTGATAACT
196 TCTTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCA-TATGAAATTTTGATAACT
10490 TCCCAATGAAATTTTGATAACCAACACTATATGAGATGTTGATAACCTCCATATGATATACTGAT
260 TCCCAATGAAATTTTGATAACCAACACTATATGAGATGTTGATAACCTCCATATGATATACTGAT
10555 AACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATT
325 AACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATT
10608 AGCTTTCACGTGCGTTGCCCGTGGCCCAACGTGTTTAATGGAATATTCATATGAAATTATGATAA
1 AGCTTTCACGTGCGTTGCCCGTGGCCCAACGTGTTTAATGGAATATTCATATGAAATTATGATAA
*
10673 CCTCTCTATTAAATAATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAACCT
66 CCTCTCTATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAACCT
* *
10738 TCCTATAAAATTTTAATAATGATACTATGGAATTTCGAGAACCATTTTATAAATTTTTTTTAACC
131 TCCTATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTAT-AATTTTTTTTAACC
*
10803 TTCTCATGAAATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCAATATGAAATTTTGATAAC
195 TTCTTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTC-ATATGAAATTTTGATAAC
*
10868 TTCCCAATAAAATTTTGATAACCAACAC--TATGAGATGTTGATAAC
259 TTCCCAATGAAATTTTGATAACCAACACTATATGAGATGTTGATAAC
10913 TTTCTTATAA
Statistics
Matches: 650, Mismatches: 20, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
367 199 0.31
368 32 0.05
374 2 0.00
377 18 0.03
378 296 0.46
379 102 0.16
380 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (377 bp):
AGCTTTCACGTGCGTTGCCCGTGGCCCAACGTGTTTAATGGAATATTCATATGAAATTATGATAA
CCTCTCTATTAAATTATGATAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAACCT
TCCTATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAATTTTTTTTAACCT
TCTTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCATATGAAATTTTGATAACTT
CCCAATGAAATTTTGATAACCAACACTATATGAGATGTTGATAACCTCCATATGATATACTGATA
ACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATT
Found at i:10748 original size:22 final size:22
Alignment explanation
Indices: 10719--11055 Score: 130
Period size: 22 Copynumber: 15.6 Consensus size: 22
10709 ATGATCCCAT
10719 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *** *
10741 TATAAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * *
10763 TATGGAATTTCGAGAACCATT-T
1 TATGAAATTTTGATAACC-TTCC
**
10785 TAT-AAATTTTTTTTAACCTT-C
1 TATGAAA-TTTTGATAACCTTCC
* *
10806 TCATGAAATTTTGTTAACCTCCC
1 T-ATGAAATTTTGATAACCTTCC
* * *
10829 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
10851 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * **
10873 AATAAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * * *
10896 TATGAGATGTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
10918 TATAAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
10935 TA-AAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
10956 TATGATATTTTGAT-ACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
10977 TACGAAATTTTGTTAATCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
10999 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
*
11021 TATGAAATTTTGATAAACC-TCT
1 TATGAAATTTTGAT-AACCTTCC
11043 TATGAAATTTTGA
1 TATGAAATTTTGA
11056 AAACTAAACT
Statistics
Matches: 226, Mismatches: 66, Indels: 46
0.67 0.20 0.14
Matches are distributed among these distances:
16 12 0.05
17 2 0.01
20 1 0.00
21 25 0.11
22 158 0.70
23 28 0.12
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:11306 original size:27 final size:26
Alignment explanation
Indices: 11252--11304 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
11242 TGATTAAAAA
11252 AGTAATGGAATAATTAAAATATTATTT
1 AGTAATGGAAT-ATTAAAATATTATTT
11279 AGTAATGGTAAT-TTAGAAATA-TATTT
1 AGTAATGG-AATATTA-AAATATTATTT
11305 TAAAAAAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 8 0.33
27 13 0.54
28 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (26 bp):
AGTAATGGAATATTAAAATATTATTT
Done.