Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011073.1 Corchorus olitorius cultivar O-4 contig11106, 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, 886
Length: 1477
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1477 Score: 2330
Period size: 154 Copynumber: 9.6 Consensus size: 154
* **
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
*
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
* **
131 CTGTGAAGTTTTTAGCTTATTTAA
131 CTGTGAAGTTTTTAGCTCATTTGG
* **
155 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
* *
220 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCTTAACTATAATCATTTTGGTGAGATTAGTCAA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
* * **
285 CTTTGAAGTTTCTAGCTCATTTAA
131 CTGTGAAGTTTTTAGCTCATTTGG
* * *
309 AACACTTGTTTTTTTGGGCCTATTGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGAA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
* * * * *
374 AACCTGAATGCTTTTCTTTTCATTGTTTATGGCTTAACTATAAACATTTTGGTGAGATTAGTCAA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
* *
439 CTTTGAAGTTTCTAGCTCATTTGG
131 CTGTGAAGTTTTTAGCTCATTTGG
* *
463 AACACTTGTTATTTTGGGCCTATCGGGGTGCATTTGTGACGTTTTGAATGGTCTTCGATTTGGCA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
*
528 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATAAGTCCA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
*
593 CCGTGAAGTTTTTAGCTCATTTGG
131 CTGTGAAGTTTTTAGCTCATTTGG
* * * *
617 AACACTTGTTATTTTGGGCCAATCGGTGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
* *
682 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCTTAACTATAATTATTTTGGTGAGATTAGTCCA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
* * *
747 CTATGAAGTTTCTAGCTCATTTCG
131 CTGTGAAGTTTTTAGCTCATTTGG
* * * ** * *
771 AACACTTGTTATTTTGGGTCTATCGGTGTCCACTTGTTCCGTTTCGAATCATCTTCGATTTGGCA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
* * *
836 AACCTCAATGCTTTTCTTTCCATTCTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCTA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
**
901 CTGTGAAGTTTTTAGCTCATTTAA
131 CTGTGAAGTTTTTAGCTCATTTGG
* **
925 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
990 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
1055 CTGTGAAGTTTTTAGCTCATTTGG
131 CTGTGAAGTTTTTAGCTCATTTGG
1079 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
1144 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
*
1209 CTGTGAAG-TTTTACCTCATTTGG
131 CTGTGAAGTTTTTAGCTCATTTGG
* * **
1232 AACACCTGTTATTTTGGGGCTATCGGGGTCCATTTGTTCCG-TTTGAATCGTCTTCGATTTGGCA
1 AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
1296 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
66 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
* * *
1361 CTTTAAAGTTATTAGCTCATTTGG
131 CTGTGAAGTTTTTAGCTCATTTGG
**
1385 AACACTTGTTATTATT-GGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCTTTTTGGC
1 AACACTTGTTATT-TTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGC
* *
1449 AAACTTCAATGCTTTTCTTTCTATTGTTT
65 AAACCTCAATGCTTTTCTTTCCATTGTTT
Statistics
Matches: 1228, Mismatches: 92, Indels: 6
0.93 0.07 0.00
Matches are distributed among these distances:
152 94 0.08
153 98 0.08
154 1036 0.84
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (154 bp):
AACACTTGTTATTTTGGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCA
AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
CTGTGAAGTTTTTAGCTCATTTGG
Done.