Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013564.1 Corchorus olitorius cultivar O-4 contig13597, 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: 2586
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Found at i:478 original size:154 final size:153
Alignment explanation
Indices: 1--783 Score: 1275
Period size: 154 Copynumber: 5.1 Consensus size: 153
*
1 ACTTGTTATTTTGGGCCTATCTGGGCCCATTAGT-TCCGTTTTGAATCGTCTTCGATTTGGGAAA
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGT-CGTTTTGAATCGTCTTCGATTT-GGAAA
65 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
64 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
130 GTGAAGTTTTTAGCTCATTTGGAAC
129 GTGAAGTTTTTAGCTCATTTGGAAC
* * *
155 ACTTGTTATTTTAGGCCTTTCGGGG-CCATTAGT-TCCGTTCTGAATCGTCTTCGATTTGGCAAA
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGT-CGTTTTGAATCGTCTTCGATTTGG-AAA
* *
218 CCACAATGACTTTTCTTTTGTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
64 CCTCAATG-CTTTTC-TTT-CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
283 ACTGTGAAGTTTTTAGCTCATTTGGAAC
126 ACTGTGAAGTTTTTAGCTCATTTGGAAC
* *
311 ACTTGTTATTTTGGGCCTACCGGGGCCCATTAGTGTCGTTTTGAATCGTCTCCGATTTGAGAAAC
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCTTCGATTTG-GAAAC
* * *
376 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATTATCATTTTCGTGAGATTAGTCCATTG
65 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
441 TGAAGTTTTTAGCTCATTTGGAAC
130 TGAAGTTTTTAGCTCATTTGGAAC
* *
465 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGTCATTTTGAATCGTCTTTGATTTGGGAAAC
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCTTCGATTT-GGAAAC
*
530 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTACCTATAATCATTTTGGTGAGATTAGTCCACTG
65 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
595 TGAAGTTTTTAGCTCATTTGGAAC
130 TGAAGTTTTTAGCTCATTTGGAAC
* ** * *
619 ACTTGTTATTTTGTGCCTATCAAGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCAAAC
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCTTCGATTTGG-AAAC
*
684 CTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
65 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
749 TGAAGTTTTTAGCTCATTTGGAAC
130 TGAAGTTTTTAGCTCATTTGGAAC
773 ACTTGTTATTT
1 ACTTGTTATTT
784 GATGCGCCAA
Statistics
Matches: 587, Mismatches: 33, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
152 2 0.00
153 43 0.07
154 394 0.67
155 7 0.01
156 100 0.17
157 39 0.07
158 2 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (153 bp):
ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCTTCGATTTGGAAACC
TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
GAAGTTTTTAGCTCATTTGGAAC
Done.