Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023560.1 Corchorus olitorius cultivar O-4 contig23593, 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, 636
Length: 1061
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Found at i:463 original size:154 final size:154
Alignment explanation
Indices: 1--1061 Score: 1603
Period size: 154 Copynumber: 6.9 Consensus size: 154
*
1 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAG
1 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* *
66 TTTTTAGCTCATTT-GTAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
66 TTTTTAGCTCATTTAG-AACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAA
* *
130 TCTTTCTTCGGATTTGGCAAACCTTAA
130 TC-GTCTTC-GATTTGGCAAACCTCAA
*
157 TGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
1 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
**
222 TTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAA
66 -TTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAA
287 TCGTCTTCGATTTGGCAAACCTCAA
130 TCGTCTTCGATTTGGCAAACCTCAA
* *
312 TGCTTTTCTTTCCACTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAG
1 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* *
377 TTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
66 TTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAAT
* *
442 CTTCTTCGATTTGTCAAACCTCAA
131 CGTCTTCGATTTGGCAAACCTCAA
* * *
466 TACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTTTGAAG
1 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* * * **
531 TTTCTAGCACATTTGGAACACTTGTTATTTTGGGCCTA-C--GGTCCATTAGTTCCGTTTTGAAT
66 TTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAAT
*
593 CGTCTTCGATTTGGCTAACCTCAA
131 CGTCTTCGATTTGGCAAACCTCAA
* * * * *
617 TGCTTTTCTTTCCATTGTTTTTGACCTAACTATAATCATTTTGGTGGGATTAGTCAACTTTGAAG
1 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* * * * *
682 TTTCTAGCTCATTTGGAACACTAGTTATTTTGGGCCTATCAGGGTCCATTTGTGACGTTTTGAAT
66 TTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAAT
*
747 CGTATTCGATTTGGCAAACCTCAA
131 CGTCTTCGATTTGGCAAACCTCAA
* *
771 TGCTTTTCTTTCCATTG-TTATGGCCTAACTATAATCAATTTGGTGAGATTAGTCCACCGTGAAG
1 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* *
835 TTTTTAGCTCATTT-GTAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
66 TTTTTAGCTCATTTAG-AACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAA
* *
899 TCTTCTTCGATTTGGCAAACCTGAA
130 TCGTCTTCGATTTGGCAAACCTCAA
* * * *
924 TGCTTTTCTTTCCATTGCTTATGGCCTAACAATAATAATTTTGGTGAGATTAGTCCACTGTGTAG
1 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* * **
989 TTTTTAGCCCATTTAGAATACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAAT
66 TTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAAT
1054 CGTCTTCG
131 CGTCTTCG
Statistics
Matches: 826, Mismatches: 71, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
151 137 0.17
152 2 0.00
153 136 0.16
154 343 0.42
155 79 0.10
156 68 0.08
157 60 0.07
158 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
TTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAAT
CGTCTTCGATTTGGCAAACCTCAA
Found at i:885 original size:458 final size:462
Alignment explanation
Indices: 3--1061 Score: 1669
Period size: 458 Copynumber: 2.3 Consensus size: 462
1 TG
*
3 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTT
1 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
* * * ** *
68 TTTAGCTCATTTGTAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCT
66 TTTAGCACATTTGGAACACTTGTTATTTTGGGCCTATC-GGGTCCATTAGTTCCGTTTTGAATC-
* * *
133 TTCTTCGGATTTGGCAAACCTTAATGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCATTT
129 GTCTTC-GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACAATAATCATTT
* * *
198 TGGTGAGATTAGTCCACTGTGAAGTTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATC
193 TGGTGAGATTAGTCAACTGTGAAGTTTTCTAGCTCATTTAGAACACTAGTTATTTTGGGCCTATC
* ** *
263 GGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACT
258 AGGGTCCATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACT
* *
328 GTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAG
323 GTTTATGGCCTAACTATAATCAATTTAGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATTTAG
*
393 AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGATTTGTCA
388 AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCA
458 AACCTCAATA
453 AACCTCAATA
* *
468 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTTTGAAGTT
1 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
*
533 TCTAGCACATTTGGAACACTTGTTATTTTGGGCCTA-C-GGTCCATTAGTTCCGTTTTGAATCGT
66 TTTAGCACATTTGGAACACTTGTTATTTTGGGCCTATCGGGTCCATTAGTTCCGTTTTGAATCGT
* * *
596 CTTCGATTTGGCTAACCTCAATGCTTTTCTTTCCATTGTTTTTGACCTAACTATAATCATTTTGG
131 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACAATAATCATTTTGG
* * *
661 TGGGATTAGTCAACTTTGAAG-TTTCTAGCTCATTTGGAACACTAGTTATTTTGGGCCTATCAGG
196 TGAGATTAGTCAACTGTGAAGTTTTCTAGCTCATTTAGAACACTAGTTATTTTGGGCCTATCAGG
* *
725 GTCCATTTGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG-T
261 GTCCATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACTGTT
*
789 TATGGCCTAACTATAATCAATTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATTT-GTAA
326 TATGGCCTAACTATAATCAATTTAGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATTTAG-AA
853 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAA
390 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAA
* *
918 CCTGAATG
455 CCTCAATA
* * * *
926 CTTTTCTTTCCATTGCTTATGGCCTAACAATAATAATTTTGGTGAGATTAGTCCACTGTGTAGTT
1 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
* * *
991 TTTAGCCCATTTAGAATACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCG
66 TTTAGCACATTTGGAACACTTGTTATTTTGGGCCTATC-GGGTCCATTAGTTCCGTTTTGAATCG
1056 TCTTCG
130 TCTTCG
Statistics
Matches: 546, Mismatches: 44, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
457 1 0.00
458 221 0.40
459 98 0.18
460 74 0.14
461 36 0.07
462 20 0.04
464 1 0.00
465 95 0.17
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (462 bp):
CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
TTTAGCACATTTGGAACACTTGTTATTTTGGGCCTATCGGGTCCATTAGTTCCGTTTTGAATCGT
CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACAATAATCATTTTGG
TGAGATTAGTCAACTGTGAAGTTTTCTAGCTCATTTAGAACACTAGTTATTTTGGGCCTATCAGG
GTCCATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACTGTT
TATGGCCTAACTATAATCAATTTAGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATTTAGAAC
ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAAC
CTCAATA
Done.