Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011746.1 Corchorus olitorius cultivar O-4 contig11779, 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, 884
Length: 1474
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Found at i:559 original size:309 final size:306
Alignment explanation
Indices: 1--889 Score: 1402
Period size: 309 Copynumber: 2.9 Consensus size: 306
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
*
66 GCAAACCTCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
66 GCAAACCTCAATGCTTTTCTTT-CATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
131 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT
130 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT
* *
196 CCGTATTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGACCTAAC
195 -CGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
261 TATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCAGT
259 TATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCAGT
* * ** *
309 TGGAACACTTGTTATTTTAGGCCTATCGGGGCCCATTAAATTCCGTTTTGAATCGTCTTCGATTT
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT-AGTGACGTATTGAATCGTCTTCGATTT
*
374 GGCAAACCTCAACGCTTTTCTTTCATCTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
65 GGCAAACCTCAATGCTTTTCTTTCAT-TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
*
439 TCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
129 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
*
504 TCTGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAA
194 TC-GTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAA
* * *
569 CTATAATAATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
258 CTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCAGT
* * * * *
618 TGGAACACTTCTTATTTTGGGCTTATTGGGGTCCATTAGTGACGTATTGAATCGTCTTCGATTTA
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
* * * * * *
683 TCAGACCTTAATGCCTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTCGTGAGATTAGT
66 GCAAACCTCAATGCTTTTC-TTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
* *
748 CCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCAATCGGGGCCCATTAGTG
130 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-
* * * * *
813 ACGTATTGAATCTTCTTCGAATTGGCAAGA-CTCAATGCTTTTGTTTCCATTGTTTATGGCCTAC
194 TCGTATTGAATCGTCTTCGATTTGGCAA-ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAA
*
877 CTATATTCATTTT
258 CTATAATCATTTT
890 TTTTATATTA
Statistics
Matches: 533, Mismatches: 42, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
308 242 0.45
309 291 0.55
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (306 bp):
TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
GCAAACCTCAATGCTTTTCTTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTC
GTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
TAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCAGT
Found at i:901 original size:154 final size:154
Alignment explanation
Indices: 1--889 Score: 1406
Period size: 154 Copynumber: 5.8 Consensus size: 154
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
*
66 GCAAACCTCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
66 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
131 CCACTGTGAAGTTTTTAGCTCATT
131 CCACTGTGAAGTTTTTAGCTCATT
** *
155 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTATTGAATCGTATTCGATTTG
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
*
220 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGT
66 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
* *
285 CCACTGTGAACTTTTTAGCTCAGT
131 CCACTGTGAAGTTTTTAGCTCATT
* * ** *
309 TGGAACACTTGTTATTTTAGGCCTATCGGGGCCCATTAAATTCCGTTTTGAATCGTCTTCGATTT
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT-AGTGACGTATTGAATCGTCTTCGATTT
*
374 GGCAAACCTCAACGCTTTTCTTT-CATCTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
65 GGCAAACCTCAATGCTTTTCTTTCCAT-TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
*
438 GTCCACTGTGAACTTTTTAGCTCATT
129 GTCCACTGTGAAGTTTTTAGCTCATT
* *
464 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCTGTTTTGAATCGTCTTCGATTT
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGAC-GTATTGAATCGTCTTCGATTT
*
528 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATAATTTTGGTGAGATTAG
65 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
593 TCCACTGTGAAGTTTTTAGCTCATT
130 TCCACTGTGAAGTTTTTAGCTCATT
* * * * *
618 TGGAACACTTCTTATTTTGGGCTTATTGGGGTCCATTAGTGACGTATTGAATCGTCTTCGATTTA
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
* * * * * *
683 TCAGACCTTAATGCCTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTCGTGAGATTAGT
66 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
*
748 CCACTGTGAAGTTTTTAGCTAATT
131 CCACTGTGAAGTTTTTAGCTCATT
* * *
772 TGGAACACTTGTTATTTTGGGCCAATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGAATTG
1 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
* * *
837 GCAAGA-CTCAATGCTTTTGTTTCCATTGTTTATGGCCTACCTATATTCATTTT
66 GCAA-ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
890 TTTTATATTA
Statistics
Matches: 678, Mismatches: 51, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
153 1 0.00
154 529 0.78
155 148 0.22
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTG
GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
CCACTGTGAAGTTTTTAGCTCATT
Found at i:1037 original size:21 final size:21
Alignment explanation
Indices: 1011--1052 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1001 TAAGGAAGAA
1011 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
1032 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
1053 CCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Done.