Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010606.1 Corchorus capsularis cultivar CVL-1 contig10627, 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: 22356
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Found at i:123 original size:74 final size:74
Alignment explanation
Indices: 1--232 Score: 376
Period size: 74 Copynumber: 3.1 Consensus size: 74
* *
1 ACCTCGCTGAGAGTTATATGGGGCACCAGTCTAGGCGCTCAGCCGTCTGCGGGTGACGTCTGCTT
1 ACCTCGCTTAGAGTTATACGGGGCACCAGTCTAGGCGCTCAGCCGTCTGCGGGTGACGTCTGCTT
66 GGACGTTCG
66 GGACGTTCG
* * *
75 ACCTCGCTTAGAGTTATACGGGGCATCAGTCTAGGCGCTCAGCTGTCTGTGGGTGACGTCTGCTT
1 ACCTCGCTTAGAGTTATACGGGGCACCAGTCTAGGCGCTCAGCCGTCTGCGGGTGACGTCTGCTT
140 GGACAG-TCG
66 GGAC-GTTCG
* * *
149 ACCTCGCTTAGAGTTATACGGGGCACCGGTCTAGGCACTCAACCGTCTGCGGGTGACGTCTGCTT
1 ACCTCGCTTAGAGTTATACGGGGCACCAGTCTAGGCGCTCAGCCGTCTGCGGGTGACGTCTGCTT
214 GGACGTTCG
66 GGACGTTCG
223 ACCTCGCTTA
1 ACCTCGCTTA
233 AATGATTCAT
Statistics
Matches: 145, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
73 1 0.01
74 143 0.99
75 1 0.01
ACGTcount: A:0.16, C:0.27, G:0.31, T:0.25
Consensus pattern (74 bp):
ACCTCGCTTAGAGTTATACGGGGCACCAGTCTAGGCGCTCAGCCGTCTGCGGGTGACGTCTGCTT
GGACGTTCG
Found at i:1861 original size:75 final size:75
Alignment explanation
Indices: 1738--2221 Score: 756
Period size: 75 Copynumber: 6.5 Consensus size: 75
1728 GGATTCCTGT
* ** * * * *
1738 GGGTGACGTCTGTTTGGACGTTCGACCTCGCTTAGAGTTACGCAGGGGCGCCAATCTTGGCGCTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCACCAGTCTAGGCGCTC
*
1803 AGGCGTCTGC
66 AGCCGTCTGC
1813 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCACCAGTCTAGGCGCTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCACCAGTCTAGGCGCTC
1878 AGCCGTCTGC
66 AGCCGTCTGC
* * * *
1888 AGGTGACGTCTGCTTGGACGTTAGACCTCGCTTA-AGGTTATACGGGGGCACCAGTCTAGGTGTT
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGA-GTTATACGGGGGCACCAGTCTAGGCGCT
1952 CAGCCGTCTGC
65 CAGCCGTCTGC
* *
1963 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTGAGAGTTATATGGGGGCACCAGTCTAGGCGCTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCACCAGTCTAGGCGCTC
2028 AGCCGTCTGC
66 AGCCGTCTGC
*
2038 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCATCAGTCTAGGCGCTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCACCAGTCTAGGCGCTC
* *
2103 AGCTGTCTGT
66 AGCCGTCTGC
* *
2113 GGGTGACGTCTGCTTGGACAG-TCGACCTCGCTTAGAGTTATACGGGGGCACCGGTCTAGGCACT
1 GGGTGACGTCTGCTTGGAC-GTTCGACCTCGCTTAGAGTTATACGGGGGCACCAGTCTAGGCGCT
*
2177 CAACCGTCTGC
65 CAGCCGTCTGC
2188 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTA
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTA
2222 AATGATTCAT
Statistics
Matches: 376, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
74 2 0.01
75 372 0.99
76 2 0.01
ACGTcount: A:0.15, C:0.26, G:0.33, T:0.25
Consensus pattern (75 bp):
GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCACCAGTCTAGGCGCTC
AGCCGTCTGC
Found at i:5762 original size:15 final size:15
Alignment explanation
Indices: 5744--5776 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5734 GTGAGAAGCG
5744 CCAGAGTGCAGACCT
1 CCAGAGTGCAGACCT
5759 CCAGAGTGCAGACCT
1 CCAGAGTGCAGACCT
5774 CCA
1 CCA
5777 TGTCCGTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.36, G:0.24, T:0.12
Consensus pattern (15 bp):
CCAGAGTGCAGACCT
Found at i:9449 original size:28 final size:27
Alignment explanation
Indices: 9416--9471 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
9406 CAATCTTACA
*
9416 AGTAGAGGGATTAAATTGATCTTTTTTT
1 AGTAGAGGGACTAAATTGAT-TTTTTTT
*
9444 AGTAGAGGGACTAGATTGATTTTTTTT
1 AGTAGAGGGACTAAATTGATTTTTTTT
9471 A
1 A
9472 TAAGTAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.45
Consensus pattern (27 bp):
AGTAGAGGGACTAAATTGATTTTTTTT
Found at i:10311 original size:18 final size:18
Alignment explanation
Indices: 10290--10343 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
10280 TCACAACTCC
10290 AACTTATCACACAAATTA
1 AACTTATCACACAAATTA
* **
10308 AAC-T-T--CACAACTCC
1 AACTTATCACACAAATTA
10322 AACTTATCACACAAATTA
1 AACTTATCACACAAATTA
10340 AACT
1 AACT
10344 GGCCTACATT
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
14 9 0.35
15 1 0.04
16 2 0.08
17 1 0.04
18 13 0.50
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (18 bp):
AACTTATCACACAAATTA
Found at i:10315 original size:32 final size:32
Alignment explanation
Indices: 10279--10343 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
10269 AAATCATATA
10279 TTCACAACTCCAACTTATCACACAAATTAAAC
1 TTCACAACTCCAACTTATCACACAAATTAAAC
10311 TTCACAACTCCAACTTATCACACAAATTAAAC
1 TTCACAACTCCAACTTATCACACAAATTAAAC
10343 T
1 T
10344 GGCCTACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (32 bp):
TTCACAACTCCAACTTATCACACAAATTAAAC
Found at i:16551 original size:61 final size:61
Alignment explanation
Indices: 16476--16597 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
16466 ATCTTTCACT
16476 TAACCAAACATGTGCCAATTAATTTGAATTCAATTATGATTTACCATTTATAAACCAACAA
1 TAACCAAACATGTGCCAATTAATTTGAATTCAATTATGATTTACCATTTATAAACCAACAA
16537 TAACCAAACATGTGCCAATTAATTTGAATTCAATTATGATTTACCATTTATAAACCAACAA
1 TAACCAAACATGTGCCAATTAATTTGAATTCAATTATGATTTACCATTTATAAACCAACAA
16598 ATTAGTATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (61 bp):
TAACCAAACATGTGCCAATTAATTTGAATTCAATTATGATTTACCATTTATAAACCAACAA
Found at i:16784 original size:6 final size:7
Alignment explanation
Indices: 16767--16793 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
16757 GGTAAACCCC
16767 AAAAATT
1 AAAAATT
16774 AAAAATT
1 AAAAATT
16781 AAAAATT
1 AAAAATT
16788 AAAAAT
1 AAAAAT
16794 CTTTCAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:17320 original size:30 final size:31
Alignment explanation
Indices: 17260--17332 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
17250 ATTTGGTGAA
17260 GGACCCAATTGCTCAATAAACTCAACTTCAG
1 GGACCCAATTGCTCAATAAACTCAACTTCAG
* * **
17291 GGACTCAATTGCTCATTAAGTTC-ACTTCAG
1 GGACCCAATTGCTCAATAAACTCAACTTCAG
*
17321 GGACCCATTTGC
1 GGACCCAATTGC
17333 ACATTTGCCC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 17 0.47
31 19 0.53
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (31 bp):
GGACCCAATTGCTCAATAAACTCAACTTCAG
Found at i:18107 original size:17 final size:17
Alignment explanation
Indices: 18085--18117 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18075 GAAAATGATT
18085 TAAAAAA-AACGAAAAAA
1 TAAAAAAGAA-GAAAAAA
18102 TAAAAAAGAAGAAAAA
1 TAAAAAAGAAGAAAAA
18118 TGAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (17 bp):
TAAAAAAGAAGAAAAAA
Found at i:19569 original size:7 final size:7
Alignment explanation
Indices: 19559--19597 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
19549 CACCCATCCC
19559 ATTTTTA
1 ATTTTTA
19566 ATTTTTA
1 ATTTTTA
19573 ATTTTTA
1 ATTTTTA
19580 ATTTTTA
1 ATTTTTA
*
19587 ATTTTTC
1 ATTTTTA
19594 ATTT
1 ATTT
19598 CATATATAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Done.