Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011920.1 Corchorus olitorius cultivar O-4 contig11953, 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, 1000
Length: 2251
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Found at i:588 original size:153 final size:154
Alignment explanation
Indices: 1--2176 Score: 3198
Period size: 154 Copynumber: 14.2 Consensus size: 154
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
* *
66 ACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGGTCATTTGGAACACTTGTTAT
66 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* * * *
131 TTTGGGCCTTTCGGGGCTCATGAA
131 TTTGGGCCTATCGGGGCCCATTAG
* * * *
155 T-TCTGTTTTGAATCGTCTTCAATTTGGCAAACCCCAATGCTTTTCTTTCTATTGTTTATGGCCT
1 TGAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
* * * *
219 AACTATAATCCTTTTGGTGAGATTCGACCACTGTGAAGTTTTTAGCTCACTTGGAACACTTGTTA
65 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* * *
284 TTTTGGGCCTTTCGGGACCCATTCG
130 TTTTGGGCCTATCGGGGCCCATTAG
** * * * * *
309 TTCCGTTTTGAATCGCCTTCGATTTGGCAAATCC-CAATGCTTTTCTTTCAATTATTTGTGGCCA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAA-CCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
* *
373 AACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTCGCTCATTTGGAACACTTGTTA
65 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* *
438 TTTTGGGCCTATCGGAGCCCGTTAG
130 TTTTGGGCCTATCGGGGCCCATTAG
463 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-TTTCCATTGTTTATGGCCTA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
*
527 ACTATAATCATTTGGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
66 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* * *
592 TTTGGGCCTTTCGGGGCACATTCG
131 TTTGGGCCTATCGGGGCCCATTAG
** * * *
616 TTCCGTTTTGAATCGCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTCTTTATGGCCTA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
* *
681 ACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGTTCATTTGGAACACTTGTTAT
66 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* *
745 TTTGGGCCTTTCGGGGCCCGTTAG
131 TTTGGGCCTATCGGGGCCCATTAG
** * * **
769 TTCCATTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGGATA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
* *
834 ACTATAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTAT
66 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
*
899 TTTAGGCCTATCGGGGCCCATTAG
131 TTTGGGCCTATCGGGGCCCATTAG
* * *
923 TGACGTTTTGAATCGTCATCGATTTGGCAAACCGCAATGCATTTTTTTTTCCATTGTTTATGGCC
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC--TTTTCTTTCCATTGTTTATGGCC
* *
988 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACAGTTGTT
64 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* *
1053 GTTTTTGGGCCTATTGGGGCCCATTAG
129 -ATTTTGGGCCTATCGGGGCCCATTAG
* * * * *
1080 TGACGTTTTGAATCCTCTTCAATTTGGTCAAACCACAATGCTTTTCTTTCAATTGTTTATTGCCT
1 TGACGTTTTGAATCGTCTTCGATTTGG-CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
*
1145 AACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
65 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
*
1210 TTTTGGGCCTTTCGGGGCCCATTAG
130 TTTTGGGCCTATCGGGGCCCATTAG
* * * * * *
1235 TGACGTATTGAATAGCCTTCGATTTGGCAAACAC-CAATGCTTTTCTTTCAATTGTTTGTGGCCA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAAC-CTCAATGCTTTTCTTTCCATTGTTTATGGCCT
* *
1299 AACTATAATCCTTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTA
65 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* *
1364 TTTTGGGCTTATTGGGGCCCATTAG
130 TTTTGGGCCTATCGGGGCCCATTAG
* * *
1389 TGACGTTTTGAATCCTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTGTATGGCCTA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
*
1454 ACTATAATCATTTTGGTGAGATTAGTCAACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
66 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
1519 TTTGGGCCTATCGGGGCCCATTAG
131 TTTGGGCCTATCGGGGCCCATTAG
* * * *
1543 TGACGTATTGAATCTTCTTCGAATTGGCAAGCCTCAATG-TGTTTCTTTCCATTGTTTATGGCCT
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCT-TTTCTTTCCATTGTTTATGGCCT
1607 AACTATAATCATTTTGGTGAGA-TAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTA
65 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* *
1670 -TTTGGGCCTATCGGGGACCGTTAG
130 TTTTGGGCCTATCGGGGCCCATTAG
* * *
1694 TGACG-TTTGAATCGTCTTCGATTTGGC-AACCTTCGATGCCTTACTTTCCATTGTTTATGGCCT
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCT
* *
1757 AACTATAATCATTTTTGTGAGATTAGTCCATTGTGAAGTTTTTTAGCTCATTTGGAACACTTG-T
65 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCATTTGGAACACTTGTT
*
1821 ATTTT--GCTCTATC-GGTCCCATTAG
129 ATTTTGGGC-CTATCGGGGCCCATTAG
*
1845 TTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
*
1910 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTGTTTAGCTCATTTGGAACACTTG-TAT
66 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
*
1974 TTTGGGCCTATCAGGGCCCATTAG
131 TTTGGGCCTATCGGGGCCCATTAG
*
1998 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCGTTTCTTTCCATTGTTTATGGCCTA
1 TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
* ** * *
2063 ACTATAATCATTTTAGACAGATTCGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
66 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
*
2128 TTTGTGTCCT-TCGGGGCCCATTAG
131 TTTG-GGCCTATCGGGGCCCATTAG
** *
2152 TTCCATTTTGAATCGTCTTCGATTT
1 TGACGTTTTGAATCGTCTTCGATTT
2177 TGGTGAGATT
Statistics
Matches: 1835, Mismatches: 160, Indels: 54
0.90 0.08 0.03
Matches are distributed among these distances:
149 3 0.00
150 67 0.04
151 84 0.05
152 124 0.07
153 458 0.25
154 822 0.45
155 53 0.03
156 165 0.09
157 47 0.03
158 12 0.01
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (154 bp):
TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
TTTGGGCCTATCGGGGCCCATTAG
Found at i:654 original size:307 final size:308
Alignment explanation
Indices: 3--2176 Score: 3208
Period size: 307 Copynumber: 7.1 Consensus size: 308
1 TG
*
3 ACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
*
68 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGGTCATTTGGAACACTTGTTATTT
66 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * * * * * *
133 TGGGCCTTTCGGGGCTCATGAAT-TCTGTTTTGAATCGTCTTCAATTTGGCAAACCCCAATGCTT
131 TGGGCCTATCGGGGCCCATTAGTGAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT
* * * *
197 TTCTTTCTATTGTTTATGGCCTAACTATAATCCTTTTGGTGAGATTCGACCACTGTGAAGTTTTT
195 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* * *
262 AGCTCACTTGGAACACTTGTTATTTTGGGCCTTTCGGGACCCATTCGTT
260 AGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTT
* * * * * * *
311 CCGTTTTGAATCGCCTTCGATTTGGCAAATCCCAATGCTTTTCTTTCAATTATTTGTGGCCAAAC
1 ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
*
376 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTCGCTCATTTGGAACACTTGTTATTT
66 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
441 TGGGCCTATCGGAGCCCGTTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
131 TGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
*
506 T-TTTCCATTGTTTATGGCCTAACTATAATCATTTGGGTGAGATTAGTCCACTGTGAAGTTTTTA
196 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
* *
570 GCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCACATTCGTT
261 GCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTT
* * *
618 CCGTTTTGAATCGCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTCTTTATGGCCTAAC
1 ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
*
683 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGTTCATTTGGAACACTTGTTATTT
66 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * ** * *
747 TGGGCCTTTCGGGGCCCGTTAGTTCCATTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTT
131 TGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
** *
812 TCTTTCCATTGTTTATGGGATAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTA
196 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
* * * *
877 ACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGGCCCATTAGTG
261 GCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTT
* * *
925 ACGTTTTGAATCGTCATCGATTTGGCAAACCGCAATGCATTTTTTTTTCCATTGTTTATGGCCTA
1 ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGC--TTTTCTTTCCATTGTTTATGGCCTA
* * * *
990 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACAGTTGTTGT
64 ACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT-A
* * * *
1055 TTTTGGGCCTATTGGGGCCCATTAGTGACGTTTTGAATCCTCTTCAATTTGGTCAAACCACAATG
128 TTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGG-CAAACCTCAATG
* * *
1120 CTTTTCTTTCAATTGTTTATTGCCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTT
192 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
*
1185 TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTG
257 TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTT
* * * * * * *
1237 ACGTATTGAATAGCCTTCGATTTGGCAAACACCAATGCTTTTCTTTCAATTGTTTGTGGCCAAAC
1 ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
*
1302 TATAATCCTTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
66 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * * *
1367 TGGGCTTATTGGGGCCCATTAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCACAATGCTTT
131 TGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
* *
1432 TCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTGTGAAGTTTTTA
196 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
* *
1497 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTG
261 GCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTT
* * * * *
1545 ACGTATTGAATCTTCTTCGAATTGGCAAGCCTCAATG-TGTTTCTTTCCATTGTTTATGGCCTAA
1 ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCT-TTTCTTTCCATTGTTTATGGCCTAA
*
1609 CTATAATCATTTTGGTGAGA-TAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTA-T
65 CTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
* * * *
1671 TTGGGCCTATCGGGGACCGTTAGTGACG-TTTGAATCGTCTTCGATTTGGC-AACCTTCGATGCC
130 TTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCT
* * *
1734 TTACTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTCCATTGTGAAGTTTT
194 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTT
* *
1799 TTAGCTCATTTGGAACACTTG-TATTTT--GCTCTATC-GGTCCCATTAGTT
258 TTAGCTCATTTGGAACACTTGTTATTTTGGGC-CTTTCGGGGCCCATTAGTT
*
1847 ACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
* *
1912 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTGTTTAGCTCATTTGGAACACTTG-TATTT
66 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
1976 TGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCGTT
131 TGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
* ** * *
2041 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGACAGATTCGTCCACTATGAAGTTTTTA
196 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
*
2106 GCTCATTTGGAACACTTGTTATTTTGTGTCC-TTCGGGGCCCATTAGTT
261 GCTCATTTGGAACACTTGTTATTTTG-GGCCTTTCGGGGCCCATTAGTT
* *
2154 CCATTTTGAATCGTCTTCGATTT
1 ACGTTTTGAATCGTCTTCGATTT
2177 TGGTGAGATT
Statistics
Matches: 1693, Mismatches: 151, Indels: 45
0.90 0.08 0.02
Matches are distributed among these distances:
302 91 0.05
303 27 0.02
304 160 0.09
305 137 0.08
306 119 0.07
307 382 0.23
308 370 0.22
309 110 0.06
310 102 0.06
311 44 0.03
312 151 0.09
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (308 bp):
ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
TGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
GCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTT
Done.