Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016248.1 Corchorus olitorius cultivar O-4 contig16281, 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: 23329
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Found at i:2352 original size:36 final size:36
Alignment explanation
Indices: 2274--2353 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
2264 ATCTCTCTCC
* ** *
2274 CTCTCCCTCTGAATTTGGGCAGCAGCAGCAGCCTCT
1 CTCTCCCTCTGAATCTGAACAGCAGCAGCAACCTCT
** *
2310 GACTCCCTCTGAGTCTGAACAGCAGCAGCAACCTCT
1 CTCTCCCTCTGAATCTGAACAGCAGCAGCAACCTCT
2346 CTCTCCCT
1 CTCTCCCT
2354 ATAGCTCCGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.24
Consensus pattern (36 bp):
CTCTCCCTCTGAATCTGAACAGCAGCAGCAACCTCT
Found at i:9612 original size:226 final size:225
Alignment explanation
Indices: 9218--9914 Score: 1052
Period size: 226 Copynumber: 3.0 Consensus size: 225
9208 CGATGCGCTG
*
9218 AGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTAAGGAACTAAAT
1 AGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACTAAAT
*
9283 AGCAGTTCTGTCGAGAAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACTTCAC
66 AGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACTTCAC
*
9348 TAGGGGTAGTAGATTTCCTGCATTCTTGACAGATTGTAAGCTCTGCTGGAACAAGCCCTTTCCAT
131 TAGGGGTAGTAGATTTCCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAACAAGCCCTTTCCAT
9413 CTAAAGTGTGGTACTCAATCACAGCAGGCTC
196 CTAAAGTG-GGTACTCAATCACAGCAGGCTC
*
9444 AGCATATTTGCACACTTCAATCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACTAAAT
1 AGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACTAAAT
*
9509 AGCAGTTCTTTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACTTCAC
66 AGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACTTCAC
* * * *
9574 TAGGGGTGGTAGACTTCCTGCATCCGTGACCGATTGTAAGCTCTGCTGGAACAAGCCCTTTCCAT
131 TAGGGGTAGTAGATTTCCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAACAAGCCCTTTCCAT
*
9639 CTAAAGTGGGGTACTCAACCGCACCAGACTCAATTGTTGGAGCAGGCTC
196 CTAAAGT-GGGTACT---------CA-A-TC-A------CAGCAGGCTC
*
9688 AGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAGAAAGCAGTCAACTTTAGGAACTAAAT
1 AGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACTAAAT
* *
9753 AGCAGTTCTGTCGAGGAGATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACCTCAC
66 AGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACTTCAC
* *
9818 TAGGGGTAGTAGATTTGCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAATAAGCCCTTTCCAT
131 TAGGGGTAGTAGATTTCCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAACAAGCCCTTTCCAT
* *
9883 CTAAAGTGGAGTACTCAATCGCACCAGGCTC
196 CTAAAGTGG-GTACTCAATCACAGCAGGCTC
9914 A
1 A
9915 ATTGTTGGAG
Statistics
Matches: 427, Mismatches: 24, Indels: 40
0.87 0.05 0.08
Matches are distributed among these distances:
226 208 0.49
227 1 0.00
233 2 0.00
234 1 0.00
235 4 0.01
236 1 0.00
237 2 0.00
238 1 0.00
243 2 0.00
244 205 0.48
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (225 bp):
AGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACTAAAT
AGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACTTCAC
TAGGGGTAGTAGATTTCCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAACAAGCCCTTTCCAT
CTAAAGTGGGTACTCAATCACAGCAGGCTC
Found at i:9864 original size:244 final size:244
Alignment explanation
Indices: 9435--9928 Score: 862
Period size: 244 Copynumber: 2.0 Consensus size: 244
9425 ACTCAATCAC
*
9435 AGCAGGCTCAGCATATTTGCACACTTCAATCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAG
1 AGCAGGCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAG
*
9500 GAACTAAATAGCAGTTCTTTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTC
66 GAACTAAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTC
* * *
9565 ACACTTCACTAGGGGTGGTAGACTTCCTGCATCCGTGACCGATTGTAAGCTCTGCTGGAACAAGC
131 ACACCTCACTAGGGGTAGTAGACTTCCTGCATCCGTGACAGATTGTAAGCTCTGCTGGAACAAGC
*
9630 CCTTTCCATCTAAAGTGGGGTACTCAACCGCACCAGACTCAATTGTTGG
196 CCTTTCCATCTAAAGTGGAGTACTCAACCGCACCAGACTCAATTGTTGG
*
9679 AGCAGGCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAGAAAGCAGTCAACTTTAG
1 AGCAGGCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAG
*
9744 GAACTAAATAGCAGTTCTGTCGAGGAGATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTC
66 GAACTAAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTC
* * * *
9809 ACACCTCACTAGGGGTAGTAGATTTGCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAATAAGC
131 ACACCTCACTAGGGGTAGTAGACTTCCTGCATCCGTGACAGATTGTAAGCTCTGCTGGAACAAGC
* *
9874 CCTTTCCATCTAAAGTGGAGTACTCAATCGCACCAGGCTCAATTGTTGG
196 CCTTTCCATCTAAAGTGGAGTACTCAACCGCACCAGACTCAATTGTTGG
9923 AGCAGG
1 AGCAGG
9929 TGCAAGAAAA
Statistics
Matches: 236, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
244 236 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (244 bp):
AGCAGGCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAG
GAACTAAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTC
ACACCTCACTAGGGGTAGTAGACTTCCTGCATCCGTGACAGATTGTAAGCTCTGCTGGAACAAGC
CCTTTCCATCTAAAGTGGAGTACTCAACCGCACCAGACTCAATTGTTGG
Found at i:19827 original size:3 final size:3
Alignment explanation
Indices: 19821--19863 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
19811 ATCATCATCA
19821 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
19864 AGAAACTAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:22946 original size:29 final size:31
Alignment explanation
Indices: 22881--22950 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 31
22871 AGTGAGCTAC
*
22881 TCGAGCTCGAGTTCGATCGATCGAACTTTGATTA
1 TCGAGCTCGAGTTCGA--GATCGAAC-TTGAGTA
*
22915 TCGAGCTCGAGTTCG-GCTCGAA-TTGAGTA
1 TCGAGCTCGAGTTCGAGATCGAACTTGAGTA
22944 TCGAGCT
1 TCGAGCT
22951 ATTCAAGCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 13 0.38
31 6 0.18
34 15 0.44
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (31 bp):
TCGAGCTCGAGTTCGAGATCGAACTTGAGTA
Found at i:23192 original size:27 final size:27
Alignment explanation
Indices: 23154--23208 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
23144 TAAACTCGAA
23154 CTCGGCTCGATTCGATACTCGAGCTAC
1 CTCGGCTCGATTCGATACTCGAGCTAC
23181 CTCGGCTCGATTCGATACTCGAGCTAC
1 CTCGGCTCGATTCGATACTCGAGCTAC
23208 C
1 C
23209 GAGCTCGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.35, G:0.22, T:0.25
Consensus pattern (27 bp):
CTCGGCTCGATTCGATACTCGAGCTAC
Done.