Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006415.1 Corchorus capsularis cultivar CVL-1 contig06436, 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, 766
Length: 1278
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:996 original size:330 final size:332
Alignment explanation
Indices: 1--1214 Score: 1220
Period size: 335 Copynumber: 3.6 Consensus size: 332
* * *
1 AATCTTGTTTCGATTTAATTAAAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAACGTG
1 AATCTTGTTTCGATTTAATTAAAAATTAATTAAG-AAAAATATGAAAAACGATATTAAAAGCGTG
* * * * * * * *
66 AAAAGTCCTTCTATCTTTTGGTA--TTGACTTATATATTCTTTTATGAGTA---T-GCCAAAAAT
65 AAAAGTCCTCCAATCTTTTTG-ACGTTAAATTATA-AATATTTTATGAGTATTTTATCCAAAAAT
* * * * * * * *
125 TGATGAAATATCTTTCCGGTCAATTTTTACAAGATTTTAGCCGATATCG--TAATAATCATCAC-
128 TGAGGAAAAATTTTTCCGGTCATTTTTTTCAAAATTTTAGCCGAAATCGTATAATAACCATCACA
* * * *** ** * *
187 GATTTTTGGCTAAAAAAGCATTACAGGCCCTGCCGCCCTGGGGCAGTTTTGCATTATTTTTCGCG
193 GATTTTTGGCTAAAAACGCATTTC-GG----G--GCACTGACTCAGCATTGCATGATTTTTGGCG
** * * *
252 CTAAAACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTT
251 CCGACACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTT
*
317 GTTTTTACGAGCATTTG
316 GTTTTTACGAGCATCTG
* * * * *
334 AATCTTATTTCAATTTAATTAAAAAGTAATTCAA-AAAAAAATGAAAAACGATATGAAAAGCGTG
1 AATCTTGTTTCGATTTAATTAAAAATTAATT-AAGAAAAATATGAAAAACGATATTAAAAGCGTG
** * *
398 AAAAGTCCTCCAATCTTTTTGGA-AATAAATTATATATATTTCATGAGTATTTTATCCAAAAATT
65 AAAAGTCCTCCAATCTTTTT-GACGTTAAATTATAAATATTTTATGAGTATTTTATCCAAAAATT
* ** * * *** * * *
462 TAGG-AAAATATTTTCTAGTAATTTTTTTTTGCAAAACTTTATTTGAAATCATGTATTAACCATC
129 GAGGAAAAAT-TTTTCCGGTCA--TTTTTTT-CAAAATTTTAGCCGAAATCGTATAATAACCATC
* * ** *
526 ACAGTTTTTTTGCTAAAAACG-AGTTTCGGGGCACTGACTCAGTTTTGCATGATTTTTGGCGTCG
190 ACAGATTTTTGGCTAAAAACGCA-TTTCGGGGCACTGACTCAGCATTGCATGATTTTTGGCGCCG
* * * * * *
590 AGACTCCTTGAAATATTTATAGTCATCTAATCAAATATCAGCCACATTGGATTAAAGGATTTGTT
254 ACACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTT
* **
655 TTTAGGAGCATCAA
319 TTTACGAGCATCTG
* *
669 AATCTTGTTTCGATTTAATTAGAAATTAATTAAGAAAAATATGAAAAACGATATTAAAAGCTTGA
1 AATCTTGTTTCGATTTAATTAAAAATTAATTAAGAAAAATATGAAAAACGATATTAAAAGCGTGA
* * *
734 AAAGTCCCCCAATATTTTTTACGTTAAATTATAAATATTTTATGAGTATTTTATCCAAAAATTGA
66 AAAGTCCTCCAATCTTTTTGACGTTAAATTATAAATATTTTATGAGTATTTTATCCAAAAATTGA
* * * *
799 GGAAAAATTTTTCGGGGCA-TTTTTTCAAAATTTTAGCCAAAATCGTATAGTAACCATCACAG-T
131 GGAAAAATTTTTCCGGTCATTTTTTTCAAAATTTTAGCCGAAATCGTATAATAACCATCACAGAT
862 TTTTGGCTAAAAACGCATTTCGGGGC-CTTGACTCAGCATTGCATGATTTTTGGCGCCGACACTC
196 TTTTGGCTAAAAACGCATTTCGGGGCAC-TGACTCAGCATTGCATGATTTTTGGCGCCGACACTC
* * *
926 CTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGTTTTTACG
260 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACG
991 AGCATCTG
325 AGCATCTG
* * * *
999 AATCTTGTTTCGATTTAAATAAAAATTAATTCAGAAAAAATATGAAAAACAATATTAAAAACGTG
1 AATCTTGTTTCGATTTAATTAAAAATTAATTAAG-AAAAATATGAAAAACGATATTAAAAGCGTG
* * * * * * *
1064 AAAAGTCCTTCTATCTTTTTGGCGTTGAATTATATATTCTTTTATGAGTATTTTAGCCAAAAATT
65 AAAAGTCCTCCAATCTTTTTGACGTTAAATTATA-AATATTTTATGAGTATTTTATCCAAAAATT
* * * * * * *
1129 GAGGAAATATCTTTCCGTTCAACTTTTTACAAAATTTTAGCCGAAATCGTATAAAAATCATCAC-
129 GAGGAAAAATTTTTCCGGTC-ATTTTTTTCAAAATTTTAGCCGAAATCGTATAATAACCATCACA
*
1193 GATTTTTGGCTAAAAAAGCATT
193 GATTTTTGGCTAAAAACGCATT
1215 ACAGTCCCAG
Statistics
Matches: 724, Mismatches: 132, Indels: 49
0.80 0.15 0.05
Matches are distributed among these distances:
329 1 0.00
330 149 0.21
331 84 0.12
332 103 0.14
333 38 0.05
334 59 0.08
335 216 0.30
336 23 0.03
337 1 0.00
338 5 0.01
339 13 0.02
341 14 0.02
342 18 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (332 bp):
AATCTTGTTTCGATTTAATTAAAAATTAATTAAGAAAAATATGAAAAACGATATTAAAAGCGTGA
AAAGTCCTCCAATCTTTTTGACGTTAAATTATAAATATTTTATGAGTATTTTATCCAAAAATTGA
GGAAAAATTTTTCCGGTCATTTTTTTCAAAATTTTAGCCGAAATCGTATAATAACCATCACAGAT
TTTTGGCTAAAAACGCATTTCGGGGCACTGACTCAGCATTGCATGATTTTTGGCGCCGACACTCC
TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGA
GCATCTG
Done.