Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011722.1 Corchorus olitorius cultivar O-4 contig11755, 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, 981
Length: 1635
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Found at i:285 original size:154 final size:154
Alignment explanation
Indices: 3--1634 Score: 2439
Period size: 154 Copynumber: 10.6 Consensus size: 154
1 CT
* * *
3 TTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTGAGGTTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
* *
68 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCACTT-GTTTCGTTTCGAATCATCTTC
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA-TTAGTTCCGTTTTGAATCATCTTC
132 GATTTGGCAAACCTCAATGCTTTTC
130 GATTTGGCAAACCTCAATGCTTTTC
* *
157 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTCTGAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
* * *
222 TCATTTGGAACACTTGTTATTACT-GGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTC
66 TCATTTGGAACACTTGTTATT-TTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTC
*
286 GATTTTGCAAACCTCAATGCTTTTC
130 GATTTGGCAAACCTCAATGCTTTTC
*
311 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
* * * *
376 TCATTTAGAACACTTGTTATATTGGGCCTATCAGGGCCCATTAGTTCCATTTTGAATCATCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCG
* *
441 ATTGGGCAAACTTCAATGCTTTTC
131 ATTTGGCAAACCTCAATGCTTTTC
*** * *
465 TTTATTTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
* ** * *
530 TCATATGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCG
595 ATTTGGCAAACCTCAATGCTTTTC
131 ATTTGGCAAACCTCAATGCTTTTC
* * *
619 TTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTGTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
* *
684 TCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCATCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCG
*
749 ATTTGGCAAACTTCAATGCTTTTC
131 ATTTGGCAAACCTCAATGCTTTTC
** **
773 TTTCTTTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
*
838 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCACTT-GTTCCGTTTCGAATCATCTTC
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA-TTAGTTCCGTTTTGAATCATCTTC
*
902 GGTTTGGCAAACCTCAATGCTTTTC
130 GATTTGGCAAACCTCAATGCTTTTC
*
927 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
* * * ** *
992 TCATTTGGAACACTTGTT-TTTTTGGCCTATCGGGGTCCATTTGTGACGTTTTGAATCGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCG
* *
1056 ATTTGGAAAACCTGAATGCTTTTC
131 ATTTGGCAAACCTCAATGCTTTTC
* * *
1080 TTTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTTTGAAGTTTCTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
* ** * ** **
1145 TCATTTGGAACACTTGTTATTTTGGGCCTATCTGGGTGCATTTGTGACGTTTTGAATGGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCG
1210 ATTTGGCAAACCTCAATGCTTTTC
131 ATTTGGCAAACCTCAATGCTTTTC
1234 TTTCCATTGTTTTATTGGCCTAACTATAATCATTTTGGTGAGATTATGTCCA-TTGTGAAGTTTT
1 TTTCCATTG-TTTA-TGGCCTAACTATAATCATTTTGGTGAGATTA-GTCCACTT-TGAAG-TTT
* ** * *
1298 TTAGCTCATTTGGAACACTTGTTATTTTGGGGCTATCGGGGCCCATTAGTGACGTATTGAATCTT
61 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCAT
*
1363 CTTCGATTTGGTAAACCTCAATGCTTTTC
126 CTTCGATTTGGCAAACCTCAATGCTTTTC
** * *
1392 TTTCTTTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTAAAGTTCTTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
* * * *
1457 TCATTTGGAACACTTGTTATTACT-GGCATATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTC
66 TCATTTGGAACACTTGTTATT-TTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTC
*
1521 GATTTTGCAAACCTCAATGCTTTTC
130 GATTTGGCAAACCTCAATGCTTTTC
*
1546 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGTGATTAGTCCACTTTGAAGTTTTTTAG
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAG-TTTTTAG
*
1611 CTCATTTGGAACACTTCTTATTTT
65 CTCATTTGGAACACTTGTTATTTT
1635 T
Statistics
Matches: 1343, Mismatches: 121, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
152 2 0.00
153 140 0.10
154 984 0.73
155 44 0.03
156 66 0.05
157 13 0.01
158 94 0.07
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (154 bp):
TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGC
TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCG
ATTTGGCAAACCTCAATGCTTTTC
Done.