Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023470.1 Corchorus olitorius cultivar O-4 contig23503, 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: 2143
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Found at i:269 original size:21 final size:21
Alignment explanation
Indices: 245--399 Score: 208
Period size: 21 Copynumber: 7.4 Consensus size: 21
235 CTTAGGCAAT
*
245 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
266 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
287 TCCAATGAACTTGGAACCGTC
1 TCCAATGAGCTTGGAACCTTC
*
308 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
329 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
350 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
*
371 TCCAAAGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
392 TCCAATGA
1 TCCAATGA
400 ACTTCTAGCA
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
20 3 0.02
21 122 0.98
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:1161 original size:153 final size:154
Alignment explanation
Indices: 506--1278 Score: 1187
Period size: 154 Copynumber: 5.0 Consensus size: 154
496 TGGCGCATCA
506 CAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCG
1 CAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCG
* *
571 AATGAGCTAAGAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
66 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
636 GGAAAGAAAAGCATTG-AGGTTTGC
131 GGAAAGAAAAGCATCGAAGG-TTGC
* * * *
660 CAAATCGAAGACGATTCAAAAAGTCTCTAATGGTCCCCGATAGGCCCAAAATAACAAGTTTTCCA
1 CAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCG
*
725 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGCCCATAAACAAT
66 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
790 GGAAAGAAAAGCGTCGAAGGTTGC
131 GGAAAGAAAAGCATCGAAGGTTGC
* ** * * *
814 CAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAGGGCCAAAATAACAAGTGTTCCA
1 CAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCG
*
879 AATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
66 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* *
944 GGAAAGAAAGGCATCGAAGGTTAC
131 GGAAAGAAAAGCATCGAAGGTTGC
* * *
968 CAAATCGAAGACGATTAAAAATGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCTG
1 CAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCG
* **
1033 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAATGACTATAGTTAGGCCATACGCAAT
66 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
1097 GGAAAGAAAAGCATCGAAGGTTTC
131 GGAAAGAAAAGCATCGAAGGTTGC
** *** * *
1121 CAAATCGAAGACGATTCAAAACGAAACTAATGGGATCCGATAGAG--AAAAATAATAAGTGTT-C
1 CAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAG-GCCCAAAATAACAAGTGTTCC
1183 GAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
65 G-AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
*
1248 ATGGAAAGAAAGGCATCGAAGGTTGC
129 ATGGAAAGAAAAGCATCGAAGGTTGC
1274 CAAAT
1 CAAAT
1279 TGATACGAAT
Statistics
Matches: 566, Mismatches: 49, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
151 1 0.00
152 50 0.09
153 135 0.24
154 377 0.67
155 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
CAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCG
AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATCGAAGGTTGC
Found at i:2100 original size:21 final size:21
Alignment explanation
Indices: 2076--2143 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
2066 CTTAGGCAAT
* *
2076 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
2097 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
2118 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
2139 TCCAA
1 TCCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Done.