Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011460.1 Corchorus olitorius cultivar O-4 contig11493, 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: 1825
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Found at i:294 original size:154 final size:154
Alignment explanation
Indices: 1--882 Score: 1409
Period size: 154 Copynumber: 5.7 Consensus size: 154
* *
1 GAATCGTCTTCGATTTGGCAATTCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 GAATTGTCTTCGATTTGGCAATACCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
131 ATCGAGGCCCATTAGTTCCGTTTT
131 ATCGAGGCCCATTAGTTCCGTTTT
* *
155 GAGTTGTCTTTGATTTGGCAA-ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
1 GAATTGTCTTCGATTTGGCAATACC-CAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
* * * *
219 CACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAATT-GGAACACTTGTTATTTTGGGC
65 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTCGGAACACTTGTTATTCTGTGC
* *
283 CTTTCGGGGCCCATTAGTTCCGTTTT
129 CTATCGAGGCCCATTAGTTCCGTTTT
* * * *
309 GAATCGTCTTCAATTTGTCAATTCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 GAATTGTCTTCGATTTGGCAATACCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
374 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
439 ATCGAGGCCCATTAGTTCCGTTTT
131 ATCGAGGCCCATTAGTTCCGTTTT
*
463 GAATTGTCTTTGATTTGGCAA-ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
1 GAATTGTCTTCGATTTGGCAATACC-CAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
* * * * *
527 CACTTTGTTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAATT-GGAACACTTGTTATTTTGGGC
65 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTCGGAACACTTGTTATTCTGTGC
*
591 CTATCGGGGCCCATTAGTTCCGTTTT
129 CTATCGAGGCCCATTAGTTCCGTTTT
* * *
617 GAATTATCTTCGATTTGGCAATTCCCAATGCTTTT-TTTCCATTCTTTATGGCCTAACTATAATC
1 GAATTGTCTTCGATTTGGCAATACCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
*
681 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCGTTCGGAACACTTGTTATTCTGTGCCT
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
* *
746 ATCAAGGCCTATTAGTTCCGTTTT
131 ATCGAGGCCCATTAGTTCCGTTTT
770 GAATTGTCTTCGATTTGGCAA-ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
1 GAATTGTCTTCGATTTGGCAATACC-CAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
*
834 CATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCAATT-GGAACA
65 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTCGGAACA
883 TGATACGAAT
Statistics
Matches: 666, Mismatches: 51, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
152 4 0.01
153 142 0.21
154 508 0.76
155 12 0.02
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (154 bp):
GAATTGTCTTCGATTTGGCAATACCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
ATCGAGGCCCATTAGTTCCGTTTT
Found at i:559 original size:308 final size:308
Alignment explanation
Indices: 1--882 Score: 1622
Period size: 308 Copynumber: 2.9 Consensus size: 308
1 GAATCGTCTTCGATTTGGCAATTCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 GAATCGTCTTCGATTTGGCAATTCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
*
131 ATCGAGGCCCATTAGTTCCGTTTTGAGTTGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCC
131 ATCGAGGCCCATTAGTTCCGTTTTGAATTGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCC
196 ATTGTTTATGGCCTAACTATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAAT
196 ATTGTTTATGGCCTAACTATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAAT
*
261 TGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTT
261 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTT
* *
309 GAATCGTCTTCAATTTGTCAATTCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 GAATCGTCTTCGATTTGGCAATTCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
374 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
439 ATCGAGGCCCATTAGTTCCGTTTTGAATTGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCC
131 ATCGAGGCCCATTAGTTCCGTTTTGAATTGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCC
*
504 ATTGTTTATGGCCTAACTATAATCACTTTGTTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAAT
196 ATTGTTTATGGCCTAACTATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAAT
569 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTT
261 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTT
** *
617 GAATTATCTTCGATTTGGCAATTCCCAATGCTTTT-TTTCCATTCTTTATGGCCTAACTATAATC
1 GAATCGTCTTCGATTTGGCAATTCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
*
681 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCGTTCGGAACACTTGTTATTCTGTGCCT
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
* * *
746 ATCAAGGCCTATTAGTTCCGTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
131 ATCGAGGCCCATTAGTTCCGTTTTGAATTGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCC
* * *
811 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCAAT
196 ATTGTTTATGGCCTAACTATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAAT
876 TGGAACA
261 TGGAACA
883 TGATACGAAT
Statistics
Matches: 556, Mismatches: 18, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
307 222 0.40
308 334 0.60
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (308 bp):
GAATCGTCTTCGATTTGGCAATTCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTCTGTGCCT
ATCGAGGCCCATTAGTTCCGTTTTGAATTGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCC
ATTGTTTATGGCCTAACTATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAAT
TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTT
Done.