Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011694.1 Corchorus capsularis cultivar CVL-1 contig11715, 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: 27393
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5742 original size:2 final size:2
Alignment explanation
Indices: 5735--5767 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5725 AATCATATCA
5735 AT AT AT AT -T A- 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 A
5768 ACATCAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8017 original size:14 final size:15
Alignment explanation
Indices: 7998--8028 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7988 TTATAAAATA
7998 TTTTT-CCTTTTATT
1 TTTTTCCCTTTTATT
8012 TTTTTCCCTTTTATT
1 TTTTTCCCTTTTATT
8027 TT
1 TT
8029 CTTTTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCCCTTTTATT
Found at i:12541 original size:79 final size:79
Alignment explanation
Indices: 12426--12585 Score: 275
Period size: 79 Copynumber: 2.0 Consensus size: 79
12416 CTTGGCTAAA
*
12426 GACTTGACGGGTTGGGCCGCACAGGGGAGAGACGAGGACTCACAAGTGAATCGGGGGAAATTGTT
1 GACTTGACGGGTTGGGCCGCACAGGGGAGAGACGAGGACTCACAAGTGAATCGAGGGAAATTGTT
12491 AAGGATTCACATGT
66 AAGGATTCACATGT
* * * *
12505 GACTTGACGGGTTGGGCCGCATAGGGGAGAGACGAGGACTCACAAGTGAATTGATGGAGATTGTT
1 GACTTGACGGGTTGGGCCGCACAGGGGAGAGACGAGGACTCACAAGTGAATCGAGGGAAATTGTT
12570 AAGGATTCACATGT
66 AAGGATTCACATGT
12584 GA
1 GA
12586 GGAAACATCC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.21
Consensus pattern (79 bp):
GACTTGACGGGTTGGGCCGCACAGGGGAGAGACGAGGACTCACAAGTGAATCGAGGGAAATTGTT
AAGGATTCACATGT
Found at i:12913 original size:260 final size:260
Alignment explanation
Indices: 12452--12972 Score: 961
Period size: 260 Copynumber: 2.0 Consensus size: 260
12442 CCGCACAGGG
12452 GAGAGACGAGGACTCACAAGTGAATCGGGGGAAATTGTTAAGGATTCACATGTGACTTGACGGGT
1 GAGAGACGAGGACTCACAAGTGAATCGGGGGAAATTGTTAAGGATTCACATGTGACTTGACGGGT
* * *
12517 TGGGCCGCATAGGGGAGAGACGAGGACTCACAAGTGAATTGATGGAGATTGTTAAGGATTCACAT
66 TGGCCCGCATAAGGGAGAGACGAGGACTCACAAGTGAATCGATGGAGATTGTTAAGGATTCACAT
12582 GTGAGGAAACATCCCCCATCATGAAGAGATGGATTGTTAGAGTAGCTTGTATACATGAAGGACCC
131 GTGAGGAAACATCCCCCATCATGAAGAGATGGATTGTTAGAGTAGCTTGTATACATGAAGGACCC
*
12647 AAGAAACCATCAATCTAGGCTTTTGGGTTCGGGTTAGTGTCCGACATGTATATGGGCTAATCAGT
196 AAGAAACCATCAATCTAGGCTTTTGGGTTCGGATTAGTGTCCGACATGTATATGGGCTAATCAGT
12712 GAGAGACGAGGACTCACAAGTGAATCGGGGGAAATTGTTAAGGATTCACATGTGACTTGACGGGT
1 GAGAGACGAGGACTCACAAGTGAATCGGGGGAAATTGTTAAGGATTCACATGTGACTTGACGGGT
12777 TGGCCCGCATAAGGGAGAGACGAGGACTCACAAGTGAATCGATGGAGATTGTTAAGGATTCACAT
66 TGGCCCGCATAAGGGAGAGACGAGGACTCACAAGTGAATCGATGGAGATTGTTAAGGATTCACAT
* *
12842 GTGAGGGAACATCCCCCATCATGAAGAGATGGGTTGTTAGAGTAGCTTGTATACATGAAGGACCC
131 GTGAGGAAACATCCCCCATCATGAAGAGATGGATTGTTAGAGTAGCTTGTATACATGAAGGACCC
* * *
12907 AAGAAACCATCAATCTAGGTTTTTGGGTTCGGATTGGTGTCCGACATGTATATGGGCTACTCAGT
196 AAGAAACCATCAATCTAGGCTTTTGGGTTCGGATTAGTGTCCGACATGTATATGGGCTAATCAGT
12972 G
1 G
12973 GACCTTGCTG
Statistics
Matches: 252, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
260 252 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (260 bp):
GAGAGACGAGGACTCACAAGTGAATCGGGGGAAATTGTTAAGGATTCACATGTGACTTGACGGGT
TGGCCCGCATAAGGGAGAGACGAGGACTCACAAGTGAATCGATGGAGATTGTTAAGGATTCACAT
GTGAGGAAACATCCCCCATCATGAAGAGATGGATTGTTAGAGTAGCTTGTATACATGAAGGACCC
AAGAAACCATCAATCTAGGCTTTTGGGTTCGGATTAGTGTCCGACATGTATATGGGCTAATCAGT
Found at i:19727 original size:237 final size:237
Alignment explanation
Indices: 19312--19787 Score: 952
Period size: 237 Copynumber: 2.0 Consensus size: 237
19302 GACATCTATT
19312 ATGAGAGAGGTTTTGAGTTCGAATTCTGAGATGAGCGGGGTGGGATTTGGGATAGGAGGGGGCTA
1 ATGAGAGAGGTTTTGAGTTCGAATTCTGAGATGAGCGGGGTGGGATTTGGGATAGGAGGGGGCTA
19377 TCTCCTATTATGTAGCCCAATTAAATATCATGTTCATGAGTAGCAAAAATATAAGTATTGTTATC
66 TCTCCTATTATGTAGCCCAATTAAATATCATGTTCATGAGTAGCAAAAATATAAGTATTGTTATC
19442 TCAACTGATAGGAGCACCGACCATAGGATCCTAGGTTCAAATATCACGGAATTTGAGTTTAATTT
131 TCAACTGATAGGAGCACCGACCATAGGATCCTAGGTTCAAATATCACGGAATTTGAGTTTAATTT
19507 ACTTGTTTGTTTGTTTGTTTGGTAGGTAATAATTTATATAAG
196 ACTTGTTTGTTTGTTTGTTTGGTAGGTAATAATTTATATAAG
19549 ATGAGAGAGGTTTTGAGTTCGAATTCTGAGATGAGCGGGGTGGGATTTGGGATAGGAGGGGGCTA
1 ATGAGAGAGGTTTTGAGTTCGAATTCTGAGATGAGCGGGGTGGGATTTGGGATAGGAGGGGGCTA
19614 TCTCCTATTATGTAGCCCAATTAAATATCATGTTCATGAGTAGCAAAAATATAAGTATTGTTATC
66 TCTCCTATTATGTAGCCCAATTAAATATCATGTTCATGAGTAGCAAAAATATAAGTATTGTTATC
19679 TCAACTGATAGGAGCACCGACCATAGGATCCTAGGTTCAAATATCACGGAATTTGAGTTTAATTT
131 TCAACTGATAGGAGCACCGACCATAGGATCCTAGGTTCAAATATCACGGAATTTGAGTTTAATTT
19744 ACTTGTTTGTTTGTTTGTTTGGTAGGTAATAATTTATATAAG
196 ACTTGTTTGTTTGTTTGTTTGGTAGGTAATAATTTATATAAG
19786 AT
1 AT
19788 AGTTTCTTAG
Statistics
Matches: 239, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 239 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (237 bp):
ATGAGAGAGGTTTTGAGTTCGAATTCTGAGATGAGCGGGGTGGGATTTGGGATAGGAGGGGGCTA
TCTCCTATTATGTAGCCCAATTAAATATCATGTTCATGAGTAGCAAAAATATAAGTATTGTTATC
TCAACTGATAGGAGCACCGACCATAGGATCCTAGGTTCAAATATCACGGAATTTGAGTTTAATTT
ACTTGTTTGTTTGTTTGTTTGGTAGGTAATAATTTATATAAG
Found at i:24850 original size:16 final size:17
Alignment explanation
Indices: 24826--24859 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24816 ACATACTACT
*
24826 ATTATATGTAGAT-TAG
1 ATTAGATGTAGATGTAG
24842 ATTAGATGTAGATGTAG
1 ATTAGATGTAGATGTAG
24859 A
1 A
24860 CAGTTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (17 bp):
ATTAGATGTAGATGTAG
Done.