Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011009.1 Corchorus olitorius cultivar O-4 contig11041, 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: 1701
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Found at i:350 original size:154 final size:154
Alignment explanation
Indices: 1--1701 Score: 2488
Period size: 154 Copynumber: 11.1 Consensus size: 154
* * *
1 TGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCTATTG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* * * *
66 GGGCTCATTAGTGACGTTTTGAATC-ATCGTCGATTTGGCAAACCTCATTGC-TTTCTTTCCAGT
66 GGGCCCATTAGTGACGTTTTGAATCGA-CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
129 -TTTATGGCCTAACTATAATCATTT
130 GTTTATGGCCTAACTATAATCATTT
* * * *
153 TGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCA
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* * *
218 GGGCCCAATAGTGACGTTTTGAATCGACTTCGATTTGGCAAAGCTCAATGCTTTTCTTT-AAGTT
66 GGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-TT
* *
282 GTTTATGGCCAAACTATAATCCTTT
130 GTTTATGGCCTAACTATAATCATTT
*
307 TGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* * * *
372 GGGCCCATTAGTGACGTTTTAAATC-ATCGTCGATTTGGCAAACCTCATTGCTTTTCTTTCTATT
66 GGGCCCATTAGTGACGTTTTGAATCGA-CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
*
436 GTTTATGGCCTAACTATAATCATAT
130 GTTTATGGCCTAACTATAATCATTT
*
461 TGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* * *
526 GGGCCCATTAGTGACGTTTTAAATC-ATCTTCGATTTGGCAAGCCTCATTGCTTTTCTTTCCATT
66 GGGCCCATTAGTGACGTTTTGAATCGA-CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
*
590 GTTTATGGCCTAACTATAATAATTT
130 GTTTATGGCCTAACTATAATCATTT
* *
615 TGGTGAGACTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACATTTGTTATTTTGGGCCTATCG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* * * ***
680 GGGCCCATTAGTGACGTTTTCAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTATGTTG
66 GGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
745 TTTATGGCCTAACTATAATCATTT
131 TTTATGGCCTAACTATAATCATTT
* * *
769 TTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGTCTTTCG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* ** * * *
834 GGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTCGGCAACCCTCAATGCTTTTCTTTCCATTG
66 GGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
*
899 TTTATGGCCTAACTATAATAATTT
131 TTTATGGCCTAACTATAATCATTT
* * * *
923 TGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTAATTTGCAACACTTGTTATTTTGGGCCTATTG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* * ** * *
988 GGGACCATTCGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAATTCTTTTATTTCCATTG
66 GGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
* *
1053 TGTATGGCCTAACTATAATTATTT
131 TTTATGGCCTAACTATAATCATTT
*
1077 TGGTGAGATTAGTCCACTGTGAGGTTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
1 TGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
* * *
1142 GGGGCCCATTAGTGACGTTTTCAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT-AAGT
65 GGGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-T
*
1206 TGTTTATGGCCTAACTATAATTATTT
129 TGTTTATGGCCTAACTATAATCATTT
1232 TGGTGAGATTAGTCCACTGTGAA-TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* * * * *
1296 GGGCCCATTAGTGACGTTTCGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTT-AAGTA
66 GGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-TT
*
1360 GTTTATGGCCTAACTATAATCCTTT
130 GTTTATGGCCTAACTATAATCATTT
* *
1385 TGGTGAGTTTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
** ** * * *
1450 GGGAGCATTAGTTCCGTTTTGAAACGTCTTCGATTTGGC-AACCATAAATGCTTTTTCTTTCCAT
66 GGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACC-TCAATGC-TTTTCTTTCCAT
* *
1514 TGTTTATCGCCTAATTATAATCATTT
129 TGTTTATGGCCTAACTATAATCATTT
*
1540 TGGTGAGATTAGTCC-CTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
**
1604 GGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
66 GGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
* *
1669 TTTATGGCCTAACTATAATAATAT
131 TTTATGGCCTAACTATAATCATTT
1693 TGGTGAGAT
1 TGGTGAGAT
Statistics
Matches: 1408, Mismatches: 127, Indels: 27
0.90 0.08 0.02
Matches are distributed among these distances:
152 105 0.07
153 203 0.14
154 912 0.65
155 187 0.13
156 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (154 bp):
TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
GGGCCCATTAGTGACGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
TTTATGGCCTAACTATAATCATTT
Done.