Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014049.1 Corchorus olitorius cultivar O-4 contig14082, 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, 681
Length: 1136
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Found at i:590 original size:310 final size:307
Alignment explanation
Indices: 1--1136 Score: 1576
Period size: 310 Copynumber: 3.7 Consensus size: 307
* * *
1 TGTTCC-AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGGTTATAGTAAGTCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * * *
65 TAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATTGAAGACGATTCAAAACGTCACTTATGGG
66 AAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
* * * * * *
130 TCTCGATA-GGCCAAACTAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCA
131 CCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCA
* * * * *
194 CCAAAATGATCATAGTTAGGCCATAAACAA-TGGAAAGAAAATCATTGAGGTTTGCCAAATCGAA
196 CCAAAATGATTATAGTTAGGCCATAAA-AACT-TAAAGAAAAACTTTGAGCTTTGCCAAATCGAA
* *
258 GACGATTCAGAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAG
259 GACGATTCAGAACGTTACTAATGGGCCCTGATATGCCCAAAATAACAAG
307 TGTTCCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
1 TGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * * *
372 TAAAAAACTTG-AAGAAAAGCTTTAGAGCTTTGCCAAAATCGAAGACGATTCAAAACGTTACTAA
65 TAAAAAA-TGGAAAGAAAAGCATT-GAGGTTTGCC-AAATCGAAGACGATTCAAAACGTCACTAA
* * *
436 TGGGCCCCTATATGCCC-ATATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTTGACTAAT
127 TGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAAT
*
500 CTCACCAAAATGATTATAGTTAGGCCATTAAAAACTTAAAGAAAAACTTTGAGTTTTGCCAAATC
192 CTCACCAAAATGATTATAGTTAGGCCA-TAAAAACTTAAAGAAAAACTTTGAGCTTTGCCAAATC
* * *
565 GAAGACAATTCAAAACGTTACTAATGGGCCCCGATATGCCCAAAATAACAAG
256 GAAGACGATTCAGAACGTTACTAATGGGCCCTGATATGCCCAAAATAACAAG
* * *
617 TGCTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATCATAGTTAGGCCA-
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
681 AAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACGTCACTAATGG
66 AAAA-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG
* * *
746 GCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAG--AAAAACACTTCACACTGGACTAATC
130 GCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACA--TCACAGTGGACTAATC
* *
809 TGACCAAAATGATTATAGTTAGGCCATAAAAACTTAAAGAAAAGCTTTGAGCTTTGCCAAATCGA
193 TCACCAAAATGATTATAGTTAGGCCATAAAAACTTAAAGAAAAACTTTGAGCTTTGCCAAATCGA
* * *
874 AGACGATTCTGAACGTTACAAATGGGCCCCT-ATATGCCC-ATATAACAAG
258 AGACGATTCAGAACGTTACTAATGGG-CCCTGATATGCCCAAAATAACAAG
* * *
923 TGTTCCAAATGAGCTAAAAACATC-TAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * * * * * * *
987 TAAAACT-TAAAGAAAAACTTTGAGTTTTGCCAAATCGAAGACAATTCAAAACGTTACTAATGGG
66 AAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
* *
1051 CCCCGATATGCCCAAAATAACAAGTGTTCCAGATGAGCTAAAAACTTCACAGTGGACTAATCTCA
131 CCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCA
1116 CCAAAATGATTATAGTTAGGC
196 CCAAAATGATTATAGTTAGGC
Statistics
Matches: 739, Mismatches: 74, Indels: 36
0.87 0.09 0.04
Matches are distributed among these distances:
304 121 0.16
305 38 0.05
306 53 0.07
307 117 0.16
308 139 0.19
309 71 0.10
310 192 0.26
311 8 0.01
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (307 bp):
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
AAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
CCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCA
CCAAAATGATTATAGTTAGGCCATAAAAACTTAAAGAAAAACTTTGAGCTTTGCCAAATCGAAGA
CGATTCAGAACGTTACTAATGGGCCCTGATATGCCCAAAATAACAAG
Found at i:652 original size:154 final size:154
Alignment explanation
Indices: 1--1136 Score: 1569
Period size: 153 Copynumber: 7.4 Consensus size: 154
* * *
1 TGTTCC-AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGGTTATAGTAAGTCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * * * * *
65 TAATAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATTGAAGACGATTCAAAACGTCACTTATGG
66 TAAAAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTTACTAATGG
* * * *
129 GTCTCGATA-GGCCAAACTAACAAG
130 GCCCCGATATGCCCAAAATAACAAG
* *
153 TGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATCATAGTTAGGCCA-
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * * * *
217 TAAACAA-TGGAAAGAAAATCATTGAGGTTTGCCAAATCGAAGACGATTCAGAACGTCACTAATG
66 TAAA-AACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTTACTAATG
* *
281 GGCCCTGATAGGCCCAAAATAACAAG
129 GGCCCCGATATGCCCAAAATAACAAG
307 TGTTCCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
1 TGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * *
372 TAAAAAACTTGAAGAAAAGCTTTAGAGCTTTGCCAAAATCGAAGACGATTCAAAACGTTACTAAT
65 TTAAAAACTTAAAGAAAAGCTTT-GAGGTTTGCC-AAATCGAAGACGATTCAAAACGTTACTAAT
* *
437 GGGCCCCTATATGCCC-ATATAACAAG
128 GGGCCCCGATATGCCCAAAATAACAAG
* *
463 TGTTCCAAATGAGCTAAAAACATCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * *
528 TAAAAACTTAAAGAAAAACTTTGAGTTTTGCCAAATCGAAGACAATTCAAAACGTTACTAATGGG
66 TAAAAACTTAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTTACTAATGGG
593 CCCCGATATGCCCAAAATAACAAG
131 CCCCGATATGCCCAAAATAACAAG
* * *
617 TGCTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATCATAGTTAGGCCA-
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * * * * *
681 -AAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACGTCACTAATG
66 TAAAA-ACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTTACTAATG
*
745 GGCCCCGATAGGCCCAAAATAACAAG
129 GGCCCCGATATGCCCAAAATAACAAG
* * * *
771 TATTCCAAATGAG-AAAAACACTTCACACTGGACTAATCTGACCAAAATGATTATAGTTAGGCCA
1 TGTTCCAAATGAGCTAAAA-ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* ** *
835 -TAAAAACTTAAAGAAAAGCTTTGAGCTTTGCCAAATCGAAGACGATTCTGAACGTTACAAATGG
65 TTAAAAACTTAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTTACTAATGG
* *
899 GCCCCTATATGCCC-ATATAACAAG
130 GCCCCGATATGCCCAAAATAACAAG
* * *
923 TGTTCCAAATGAGCTAAAAACATC-TAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * *
987 T-AAAACTTAAAGAAAAACTTTGAGTTTTGCCAAATCGAAGACAATTCAAAACGTTACTAATGGG
66 TAAAAACTTAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTTACTAATGGG
1051 CCCCGATATGCCCAAAATAACAAG
131 CCCCGATATGCCCAAAATAACAAG
*
1075 TGTTCCAGATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
Statistics
Matches: 878, Mismatches: 89, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
151 104 0.12
152 70 0.08
153 264 0.30
154 232 0.26
155 130 0.15
156 37 0.04
157 41 0.05
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (154 bp):
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
TAAAAACTTAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTTACTAATGGG
CCCCGATATGCCCAAAATAACAAG
Done.