Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009870.1 Corchorus capsularis cultivar CVL-1 contig09891, 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: 14505
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3113 original size:53 final size:53
Alignment explanation
Indices: 3033--3139 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
3023 TTGTTATCAT
* * *
3033 TTCACAGCAAAATTTGATTTCTTAACTGAATTTTCTTAAGAGAGTTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
* *
3086 TTCACAACAAAATTTGATTTTTTAACTGAATTTTCTTAAAATAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
3139 T
1 T
3140 AAAACAACCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
Found at i:3211 original size:19 final size:19
Alignment explanation
Indices: 3187--3224 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3177 GTTTAGATTG
3187 CTTTTGTCTTCTTCGTGAT
1 CTTTTGTCTTCTTCGTGAT
*
3206 CTTTTGTCTTCTTCTTGAT
1 CTTTTGTCTTCTTCGTGAT
3225 TGAATTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.21, G:0.13, T:0.61
Consensus pattern (19 bp):
CTTTTGTCTTCTTCGTGAT
Found at i:3888 original size:26 final size:25
Alignment explanation
Indices: 3841--3893 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
3831 TGCAAATACT
**
3841 CATAAATATATTATTTCTTTGAAGAA
1 CATAAATATATTAAATCTTTGAA-AA
3867 CATAAATATATTACAATC-TTGAAAA
1 CATAAATATATTA-AATCTTTGAAAA
3892 CA
1 CA
3894 GTAATGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.17
26 18 0.75
27 2 0.08
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (25 bp):
CATAAATATATTAAATCTTTGAAAA
Found at i:8420 original size:16 final size:16
Alignment explanation
Indices: 8373--8449 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
8363 ATAGATATAG
*
8373 ATAATAATTATTAATA
1 ATAATAATTATTATTA
* * *
8389 ATAAAAATAATAATTA
1 ATAATAATTATTATTA
*
8405 ATAATGATTATTATTA
1 ATAATAATTATTATTA
* * *
8421 ATAATAGTTAATAGTA
1 ATAATAATTATTATTA
8437 ATAATAATTATTA
1 ATAATAATTATTA
8450 ATTTTTAATT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
ATAATAATTATTATTA
Found at i:8451 original size:19 final size:19
Alignment explanation
Indices: 8373--8426 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
8363 ATAGATATAG
8373 ATAATAATTATTAATAATA
1 ATAATAATTATTAATAATA
* * *
8392 AAAATAATAATTAATAATG
1 ATAATAATTATTAATAATA
8411 AT--T-ATTATTAATAATA
1 ATAATAATTATTAATAATA
8427 GTTAATAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 11 0.38
17 1 0.03
19 17 0.59
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATAATTATTAATAATA
Found at i:9346 original size:23 final size:22
Alignment explanation
Indices: 9292--9350 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
9282 CCAGTTTTTG
* **
9292 ATAAAATTTTGATAAGCTTACT
1 ATAAAATTTTGATAACCACACT
9314 ATAAAATTTTGATAACCACACT
1 ATAAAATTTTGATAACCACACT
9336 ATGAAAATTTT-ATAA
1 AT-AAAATTTTGATAA
9351 TCTCCTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 25 0.76
23 8 0.24
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (22 bp):
ATAAAATTTTGATAACCACACT
Found at i:12129 original size:17 final size:17
Alignment explanation
Indices: 12107--12140 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12097 GATGTTATCC
12107 AGTACCTCATGCTACCT
1 AGTACCTCATGCTACCT
12124 AGTACCTCATGCTACCT
1 AGTACCTCATGCTACCT
12141 GGTATCGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.12, T:0.29
Consensus pattern (17 bp):
AGTACCTCATGCTACCT
Found at i:13106 original size:37 final size:37
Alignment explanation
Indices: 13061--13131 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
13051 TCGAACAATT
*
13061 GCACACCTGAACTATTATATTTGAACAATTGCAACAA
1 GCACACCTGAACTATTATATTCGAACAATTGCAACAA
*
13098 GCACACCTGAACTATTGTATTCGAACAATTGCAA
1 GCACACCTGAACTATTATATTCGAACAATTGCAA
13132 GTTTGCAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (37 bp):
GCACACCTGAACTATTATATTCGAACAATTGCAACAA
Found at i:13659 original size:186 final size:185
Alignment explanation
Indices: 13329--13668 Score: 572
Period size: 185 Copynumber: 1.8 Consensus size: 185
13319 AAACTTTTCA
* * * *
13329 TTGCGATCCTTATAAATATCACCCTAAAAACATCAGTTTTACCAATTAATGTCAAGCAAAGGTGC
1 TTGCGACCCTCATAAACATCACCCTAAAAACATCAGTTTTACCAATCAATGTCAAGCAAAGGTGC
* * *
13394 TGGTAGGCTTATTCAATCATTGATAGTGAAGTCAGTTTGATAAACAAAGAGCCAAGAGATTGTTT
66 TGCTAGGCTTATTCAATCATTGATAGTGAAGTCAGTTTAATAAACAAAGAGCCAAGAAATTGTTT
13459 GTGAGAATCTATACTAATTATAATTCTCACAAACATCACCTTATTCAATCAATGT
131 GTGAGAATCTATACTAATTATAATTCTCACAAACATCACCTTATTCAATCAATGT
* * * *
13514 TTGCGACCCTCATAAACATCACCCTGAAAACATCAGTTTTGCCAATCAATGTTAAGCAAAGTTGC
1 TTGCGACCCTCATAAACATCACCCTAAAAACATCAGTTTTACCAATCAATGTCAAGCAAAGGTGC
13579 TGCTAGGCTTATTCAATCATTGGATAGTGAAGTCAGTTTAATAAACAAAGAGCCAAGAAATTGTT
66 TGCTAGGCTTATTCAATCATT-GATAGTGAAGTCAGTTTAATAAACAAAGAGCCAAGAAATTGTT
13644 TGTGAGAATCTATACTAATTATAAT
130 TGTGAGAATCTATACTAATTATAAT
13669 GCGAGAACTT
Statistics
Matches: 143, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
185 77 0.54
186 66 0.46
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (185 bp):
TTGCGACCCTCATAAACATCACCCTAAAAACATCAGTTTTACCAATCAATGTCAAGCAAAGGTGC
TGCTAGGCTTATTCAATCATTGATAGTGAAGTCAGTTTAATAAACAAAGAGCCAAGAAATTGTTT
GTGAGAATCTATACTAATTATAATTCTCACAAACATCACCTTATTCAATCAATGT
Done.