Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011057.1 Corchorus olitorius cultivar O-4 contig11090, 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, 730
Length: 1218
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Found at i:448 original size:153 final size:153
Alignment explanation
Indices: 7--1218 Score: 1874
Period size: 154 Copynumber: 7.9 Consensus size: 153
1 TGCATC
*
7 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCC
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-TTTCCATTGTTTATGGCC
*
72 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGGAACACTTGTT
65 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
*
137 ATTTTGGGCCTATCGGAGACCATT
130 ATTTTGGGCCTATCGGGGACCATT
* *
161 AGTGACGTTTTGAATCGTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGGTC
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-TTTCCATTGTTTATGGCC
226 TAACTATAATCATTTTGGTGAGATTTA-TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
65 TAACTATAATCATTTTGGTGAGA-TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
*
290 TATTTTGGGCGTATCGGGGACCATT
129 TATTTTGGGCCTATCGGGGACCATT
* *
315 AGTGACGTTTTGAATCGTCTTCGATTTGGAAAACCTCAATGCTTTTTTTCCATTGTTTATGGTCT
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTGTTTATGGCCT
* *
380 AACTATAATCATTTTGGTGAGATTAGTCCGCTGTGAAGTTTTTGGCTCATTTGGAACACTTGTTA
66 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* * *
445 TTTTGTGCCTATCGAGGCCCATT
131 TTTTGGGCCTATCGGGGACCATT
** *
468 AGTTCCG-TTTGAATTGTCGTTCGATTTGGCAAACCTCAATGCTTTTTTTTCCATTGTTTATGGC
1 AGTGACGTTTTGAATCGTC-TTCGATTTGGCAAACCTCAATGC-TTTTTTTCCATTGTTTATGGC
* *
532 CTAACTATAATCATTTTGGTGAGATTAGTCCGCTGTGAAGTTTTTGGCTCATTTGGAACACTTGT
64 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * *
597 TATTTTGTGCCTATCGAGGCCCATT
129 TATTTTGGGCCTATCGGGGACCATT
** *
622 AGTTCCGTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTGTTTATGGCCT
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTGTTTATGGCCT
* *
687 AACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTA
66 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
752 TTTTGGGCCTATCGGGGACCATT
131 TTTTGGGCCTATCGGGGACCATT
* * *
775 AGTGACGTTTTGAATCTTGTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCTTTGTTTATGGCC
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-TTTCCATTGTTTATGGCC
*
840 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTT
65 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
905 AATTTTGGGCCTATCGGGGACCATT
130 -ATTTTGGGCCTATCGGGGACCATT
* *
930 AGTGACGTTCTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTATCCCATTGTTTATGGCC
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTT-TTCCATTGTTTATGGCC
995 TAACTATAATCATTTTGGTGATG-TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
65 TAACTATAATCATTTTGGTGA-GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
1059 TATTTTGTGCCTATCGAGGACCATT
129 TATTTTGGGCCTATCGGGGACCATT
** ** * * * **
1084 AGTTCCGTTTTGAATTATCTTCGATTTGGC-AACCTTCGATGCCTTTCTTTCCATTTTTTATTAC
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATG-CTTTTTTTCCATTGTTTATGGC
* * * *
1148 CTACCTATAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTCGCGCATTTGGAACACTTGT
64 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1213 TATTTT
129 TATTTT
Statistics
Matches: 990, Mismatches: 56, Indels: 24
0.93 0.05 0.02
Matches are distributed among these distances:
152 13 0.01
153 274 0.28
154 539 0.54
155 163 0.16
156 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (153 bp):
AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTGTTTATGGCCT
AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
TTTTGGGCCTATCGGGGACCATT
Found at i:570 original size:307 final size:307
Alignment explanation
Indices: 7--1218 Score: 1905
Period size: 307 Copynumber: 3.9 Consensus size: 307
1 TGCATC
*
7 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCC
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-TTTCCATTGTTTATGGCC
*
72 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGGAACACTTGTT
65 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* *
137 ATTTTGGGCCTATCG-GAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGAAAACCTCAAT
130 ATTTTGGGCCTATCGAG-GACCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACCTCAAT
*
201 GCTTTTCTTTCCATTGTTTATGGTCTAACTATAATCATTTTGGTGAGATTTA-TCCACTGTGAAG
194 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA-TTAGTCCACTGTGAAG
*
265 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCGTATCGGGGACCATT
258 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATT
* *
315 AGTGACGTTTTGAATCGTCTTCGATTTGGAAAACCTCAATGCTTTTTTTCCATTGTTTATGGTCT
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTGTTTATGGCCT
* *
380 AACTATAATCATTTTGGTGAGATTAGTCCGCTGTGAAGTTTTTGGCTCATTTGGAACACTTGTTA
66 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* * **
445 TTTTGTGCCTATCGAGGCCCATTAGTTCCG-TTTGAATTGTCGTTCGATTTGGCAAACCTCAATG
131 TTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATTGTC-TTCGATTTGGCAAACCTCAATG
* *
509 CTTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCGCTGTGAAGTT
195 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
* * * *
574 TTTGGCTCATTTGGAACACTTGTTATTTTGTGCCTATCGAGGCCCATT
260 TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATT
** *
622 AGTTCCGTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTGTTTATGGCCT
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTGTTTATGGCCT
* *
687 AACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTA
66 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* *
752 TTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCT-TGTTCGATTTGGCAAACCTCAATG
131 TTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAAT-TGTCTTCGATTTGGCAAACCTCAATG
*
816 CTTTTCTTTCCTTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
195 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
*
881 TTTACCTCATTTGGAACACTTGTTAATTTTGGGCCTATCGGGGACCATT
260 TTTAGCTCATTTGGAACACTTGTT-ATTTTGGGCCTATCGGGGACCATT
* *
930 AGTGACGTTCTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTATCCCATTGTTTATGGCC
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTT-TTCCATTGTTTATGGCC
995 TAACTATAATCATTTTGGTGATG-TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
65 TAACTATAATCATTTTGGTGA-GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* ** * *
1059 TATTTTGTGCCTATCGAGGACCATTAGTTCCGTTTTGAATTATCTTCGATTTGGC-AACCTTCGA
129 TATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACC-TCAA
* * ** * *
1123 TGCCTTTCTTTCCATTTTTTATTACCTACCTATAATCATTTTGCTGAGATTAGTCCACTGTGAAG
193 TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* *
1188 TTTTTCGCGCATTTGGAACACTTGTTATTTT
258 TTTTTAGCTCATTTGGAACACTTGTTATTTT
Statistics
Matches: 828, Mismatches: 66, Indels: 20
0.91 0.07 0.02
Matches are distributed among these distances:
306 13 0.02
307 478 0.58
308 127 0.15
309 209 0.25
310 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (307 bp):
AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTGTTTATGGCCT
AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
TTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGC
TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATT
Done.