Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011937.1 Corchorus olitorius cultivar O-4 contig11970, 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, 725
Length: 1209
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Found at i:591 original size:154 final size:154
Alignment explanation
Indices: 133--1209 Score: 1796
Period size: 154 Copynumber: 7.0 Consensus size: 154
123 ATCGGGGTCC
* *
133 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * * * * * ** * *
198 TGGAACAATTGTTATTTTGCGCCAATCGGGGCCCATTAATGACGTATTGAATCTTCTTCGATTTG
66 TAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
263 GCTAACCTCAATGCTTTTCTTTCA
131 GCAAACCTCAATGCTTTTCTTTCA
287 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGTCTCAT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTCAT
* ** * *
352 TTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGATTT
65 TTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTT
417 GGCAAACCTCAATGCTTTTCTTTCA
130 GGCAAACCTCAATGCTTTTCTTTCA
442 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* *
507 TAGAACACTTGTTATTTTGGGTCTATCGGTGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
66 TAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
572 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCA
* *
596 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGATCATT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* ** * *
661 TAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTTCGATTT
66 TAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTC-TTCGATTT
726 GGCAAACCTCAATGCTTTTCTTTCA
130 GGCAAACCTCAATGCTTTTCTTTCA
*
751 ATTGTTTATGGCCTAACAATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* *
816 TAGAACACTTGTTATTTTGCGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTC
66 TAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
881 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCA
905 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
970 TAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
66 TAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
1035 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCA
*
1059 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTTAGCTCAA
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCAT
1124 TTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCCG-TTTGAATCGTCTTCGATT
65 TTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTT-CCGTTTTGAATCGTCTTCGATT
*
1188 TGGCAAACCTCAATGATTTTCT
129 TGGCAAACCTCAATGCTTTTCT
Statistics
Matches: 877, Mismatches: 42, Indels: 7
0.95 0.05 0.01
Matches are distributed among these distances:
154 490 0.56
155 384 0.44
156 3 0.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (154 bp):
ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
TAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
GCAAACCTCAATGCTTTTCTTTCA
Found at i:620 original size:309 final size:308
Alignment explanation
Indices: 133--1209 Score: 1850
Period size: 309 Copynumber: 3.5 Consensus size: 308
123 ATCGGGGTCC
* *
133 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * * * * ** * *
198 TGGAACAATTGTTATTTTGCGCCAATCGGGGCCCATTAATGACGTATTGAATCTTCTTCGATTTG
66 TAGAACACTTGTTATTTTGCGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
* *
263 GCTAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGT
131 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGT
328 CCACTGTGAAGTTTTTAGTCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
196 CCACTGTGAAGTTTTTAG-CTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
393 GACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCA
260 GACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCA
442 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * *
507 TAGAACACTTGTTATTTTGGGTCTATCGGTGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
66 TAGAACACTTGTTATTTTGCGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
572 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
131 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGT
*
637 CCACTGTGAAGTTTTTAGATCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTG
196 CCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTG
702 ACGTATTGAATCTTCTTTCGATTTGGCAAACCTCAATGCTTTTCTTTCA
261 ACGTATTGAATCTTC-TTCGATTTGGCAAACCTCAATGCTTTTCTTTCA
*
751 ATTGTTTATGGCCTAACAATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
*
816 TAGAACACTTGTTATTTTGCGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTC
66 TAGAACACTTGTTATTTTGCGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
881 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGT
131 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGT
* *
946 CCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTT
196 CCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTG
* * * *
1011 CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
261 ACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCA
*
1059 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTTAGCTCAA
1 ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCAT
*
1124 TTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCCG-TTTGAATCGTCTTCGATT
65 TTAGAACACTTGTTATTTTGCGCCTATCGGGGTCCATTAGTT-CCGTTTTGAATCGTCTTCGATT
*
1188 TGGCAAACCTCAATGATTTTCT
129 TGGCAAACCTCAATGCTTTTCT
Statistics
Matches: 729, Mismatches: 36, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
308 144 0.20
309 582 0.80
310 3 0.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (308 bp):
ATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
TAGAACACTTGTTATTTTGCGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGT
CCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTG
ACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCA
Found at i:922 original size:463 final size:463
Alignment explanation
Indices: 130--1209 Score: 1885
Period size: 463 Copynumber: 2.3 Consensus size: 463
120 CCTATCGGGG
*
130 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTC
1 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* * * * *
195 ATTTGGAACAATTGTTATTTTGCGCCAATCGGGGCCCATTAATGACGTATTGAATCTTCTTCGAT
66 ATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGAT
*
260 TTGGCTAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATT
131 TTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATT
*
325 AGTCCACTGTGAAGTTTTTAGTCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
196 AGTCCACTGTGAAGTTTTTAGTCTCATTTAGAACACTTGTTATTTTGCGCCTATCGGGGCCCATT
* *
390 AGTGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCC
261 AGTGACGTATTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCC
455 TAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTT
326 TAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTT
* *
520 ATTTTGGGTCTATCGGTGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
391 ATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
585 CTTTTCTT
456 CTTTTCTT
*
593 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGATC
1 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
658 ATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTTCGA
66 ATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTC-TTCGA
*
723 TTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACAATAATCATTTTTGTGAGAT
130 TTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACAATAATCATTTTGGTGAGAT
*
788 TAGTCCACTGTGAAGTTTTTAG-CTCATTTAGAACACTTGTTATTTTGCGCCTATCGGGGTCCAT
195 TAGTCCACTGTGAAGTTTTTAGTCTCATTTAGAACACTTGTTATTTTGCGCCTATCGGGGCCCAT
** * *
852 TAGTTCCGTTTTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
260 TAGTGACGTATTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGC
917 CTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGT
325 CTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGT
982 TATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
390 TATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
1047 GCTTTTCTT
455 GCTTTTCTT
*
1056 TCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTTAGCT
1 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCT
* * ** *
1121 CAATTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCCGT-TTGAATCGTCTTCG
65 CATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAG-TGACGTATTGAATCTTCTTCG
*
1185 ATTTGGCAAACCTCAATGATTTTCT
129 ATTTGGCAAACCTCAATGCTTTTCT
Statistics
Matches: 587, Mismatches: 27, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
463 435 0.74
464 148 0.25
465 4 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (463 bp):
TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
ATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGAT
TTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATT
AGTCCACTGTGAAGTTTTTAGTCTCATTTAGAACACTTGTTATTTTGCGCCTATCGGGGCCCATT
AGTGACGTATTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCC
TAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTT
ATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
CTTTTCTT
Done.