Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014259.1 Corchorus olitorius cultivar O-4 contig14292, 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: 73470
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1253 original size:58 final size:58
Alignment explanation
Indices: 1183--1299 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
1173 CGGCAGATCG
*
1183 CCACAATGCGTGTTTGGGTCGTAATTGTAAGAACCTCTTTTCCACAACATGTGCAGTT
1 CCACAATGCGTGTTTGGGTCGTAATTGTAAGAACCTCTTTTCCACAACATGCGCAGTT
*
1241 CCACAATGCGTGTTTGGGTCGTAATTGTAAGGACCTCTTTTCCACAACATGCGCAGTT
1 CCACAATGCGTGTTTGGGTCGTAATTGTAAGAACCTCTTTTCCACAACATGCGCAGTT
1299 C
1 C
1300 GATTTTCTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (58 bp):
CCACAATGCGTGTTTGGGTCGTAATTGTAAGAACCTCTTTTCCACAACATGCGCAGTT
Found at i:2348 original size:65 final size:65
Alignment explanation
Indices: 2239--2436 Score: 378
Period size: 65 Copynumber: 3.0 Consensus size: 65
2229 ATCATGAAGA
*
2239 GATGAGTTGTTAGAGTGGCTTATATATATATGAAAGACCCAATAAACCATTAGTCTAGACTTTTG
1 GATGGGTTGTTAGAGTGGCTTATATATATATGAAAGACCCAATAAACCATTAGTCTAGACTTTTG
2304 GATGGGTTGTTAGAGTGGCTTATATATATATGAAAGACCCAATAAACCATTAGTCTAGACTTTTG
1 GATGGGTTGTTAGAGTGGCTTATATATATATGAAAGACCCAATAAACCATTAGTCTAGACTTTTG
*
2369 GATGGGTTGTTAGAGTGACTTATATATATATGAAAGACCCAATAAACCATTAGTCTAGACTTTTG
1 GATGGGTTGTTAGAGTGGCTTATATATATATGAAAGACCCAATAAACCATTAGTCTAGACTTTTG
2434 GAT
1 GAT
2437 TCAGATTGAT
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 131 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (65 bp):
GATGGGTTGTTAGAGTGGCTTATATATATATGAAAGACCCAATAAACCATTAGTCTAGACTTTTG
Found at i:28868 original size:14 final size:14
Alignment explanation
Indices: 28851--28877 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28841 ACTTAAGTGA
28851 ATCCCAAATTCCAC
1 ATCCCAAATTCCAC
28865 ATCCCAAATTCCA
1 ATCCCAAATTCCA
28878 TCCCCATGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (14 bp):
ATCCCAAATTCCAC
Found at i:33386 original size:21 final size:21
Alignment explanation
Indices: 33362--33404 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33352 TTTATATTTG
33362 TTTTT-TTTTTCTCATTTCCC
1 TTTTTGTTTTTCTCATTTCCC
* *
33382 TTTTTGTTTTTCTCTTTTGCC
1 TTTTTGTTTTTCTCATTTCCC
33403 TT
1 TT
33405 GTAGAGGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.02, C:0.21, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTTGTTTTTCTCATTTCCC
Found at i:50101 original size:14 final size:14
Alignment explanation
Indices: 50082--50109 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50072 AGTTTAACGT
50082 GTAAATATACCGAA
1 GTAAATATACCGAA
50096 GTAAATATACCGAA
1 GTAAATATACCGAA
50110 AAAACAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
GTAAATATACCGAA
Found at i:65295 original size:83 final size:86
Alignment explanation
Indices: 65156--65353 Score: 224
Period size: 83 Copynumber: 2.3 Consensus size: 86
65146 ACAGTGGCGC
* * * ** * * * *
65156 TCCTATTATACATCAAGGTATAATGGCGCATCTGAATAAAAGTTGGTGATGGGAATTTCTAT-TT
1 TCCTACTATACATCAAGGTATAGTGGTGCATCCAAATAAAAGTTGGTAATGAGAATTCCTATAAT
65220 GCAG-CAAA-AG-AGATGGCAT
66 GCAGTCAAACAGTAG-TGGCAT
*
65239 TCCTACTATACATCAAGGTATAGTGGTGCATCCAAATAAAGGTTGGTAATGAGAATTCCTATAAT
1 TCCTACTATACATCAAGGTATAGTGGTGCATCCAAATAAAAGTTGGTAATGAGAATTCCTATAAT
* * *
65304 GCAGTTAAACTGTTGTGGCAT
66 GCAGTCAAACAGTAGTGGCAT
* *
65325 TCCTACTATACTTAAAGGTATAGTGGTGC
1 TCCTACTATACATCAAGGTATAGTGGTGC
65354 CAGTTCGTGT
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
83 53 0.55
84 5 0.05
85 3 0.03
86 34 0.35
87 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (86 bp):
TCCTACTATACATCAAGGTATAGTGGTGCATCCAAATAAAAGTTGGTAATGAGAATTCCTATAAT
GCAGTCAAACAGTAGTGGCAT
Found at i:71800 original size:209 final size:209
Alignment explanation
Indices: 71440--71840 Score: 802
Period size: 209 Copynumber: 1.9 Consensus size: 209
71430 AGAGGGATGT
71440 AATGATCACAGCTGTTTCTGACCATGGAGAGTCCCAGGAAGCTTTGGTTTAATTCTCAAAGATGC
1 AATGATCACAGCTGTTTCTGACCATGGAGAGTCCCAGGAAGCTTTGGTTTAATTCTCAAAGATGC
71505 GGAAGGAAGGAATTAAACCAAACCAGATTACATTCAATGGTCTACTTAATGCCTGCAGTGCATGG
66 GGAAGGAAGGAATTAAACCAAACCAGATTACATTCAATGGTCTACTTAATGCCTGCAGTGCATGG
71570 TGGATTATATCCATTTGACCTGATGGCACAAAACTTTTGTTCCCTTAAATGAGCACCTTACTGCT
131 TGGATTATATCCATTTGACCTGATGGCACAAAACTTTTGTTCCCTTAAATGAGCACCTTACTGCT
71635 GTTTCTTACAGCAC
196 GTTTCTTACAGCAC
71649 AATGATCACAGCTGTTTCTGACCATGGAGAGTCCCAGGAAGCTTTGGTTTAATTCTCAAAGATGC
1 AATGATCACAGCTGTTTCTGACCATGGAGAGTCCCAGGAAGCTTTGGTTTAATTCTCAAAGATGC
71714 GGAAGGAAGGAATTAAACCAAACCAGATTACATTCAATGGTCTACTTAATGCCTGCAGTGCATGG
66 GGAAGGAAGGAATTAAACCAAACCAGATTACATTCAATGGTCTACTTAATGCCTGCAGTGCATGG
71779 TGGATTATATCCATTTGACCTGATGGCACAAAACTTTTGTTCCCTTAAATGAGCACCTTACT
131 TGGATTATATCCATTTGACCTGATGGCACAAAACTTTTGTTCCCTTAAATGAGCACCTTACT
71841 TGAATATGAA
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 192 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (209 bp):
AATGATCACAGCTGTTTCTGACCATGGAGAGTCCCAGGAAGCTTTGGTTTAATTCTCAAAGATGC
GGAAGGAAGGAATTAAACCAAACCAGATTACATTCAATGGTCTACTTAATGCCTGCAGTGCATGG
TGGATTATATCCATTTGACCTGATGGCACAAAACTTTTGTTCCCTTAAATGAGCACCTTACTGCT
GTTTCTTACAGCAC
Found at i:72233 original size:1 final size:1
Alignment explanation
Indices: 72227--72262 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
72217 TGTCTCTTAG
72227 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
72263 CACCATGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.