Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011789.1 Corchorus olitorius cultivar O-4 contig11822, 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, 720
Length: 1201
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Found at i:620 original size:154 final size:154
Alignment explanation
Indices: 158--1201 Score: 1716
Period size: 154 Copynumber: 6.7 Consensus size: 154
148 TGAGATTAAG
*
158 TTTTTAGTCTCATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
1 TTTTTAG-CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
*
223 TCGTCTTCGATTTGGCAAACCTCAAATGCTTTTGTTTCCATTGTTTATGGCCTAACTATAATCAT
65 TCGTCTTCGATTTGGCAAACCTC-AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAT
* *
288 TTTGGTGAGATTAGTCCATTGTGAAG
129 TTTGGTGAGATTAGTCCACTGTGAAC
* *
314 TTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCGTTTTGAA
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGA-CGTATTGAA
* *
379 TCGTCTTGGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGTCTAACTATAATCATT
65 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
* **
444 TTGGTGAGATTAATCCGTTGTGAAC
130 TTGGTGAGATTAGTCCACTGTGAAC
* *
469 TTTTTAGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
534 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
*
599 TGGTGAGATTAGTCCACTGTGAAG
131 TGGTGAGATTAGTCCACTGTGAAC
* * *
623 TTCTTAGCTCATTCGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
*
688 CGTCTTCGATTTGGCAAACCTCAGTGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
753 TGGTGAGATTAGTCCACTGTGAAC
131 TGGTGAGATTAGTCCACTGTGAAC
* *
777 TTTTTAGCTCCTTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TC-TATTTTGA
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA--TTGA
840 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAT
64 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAT
905 TTTGGTGAGATTAGTCCACTGTGAAC
129 TTTGGTGAGATTAGTCCACTGTGAAC
** * * *
931 TTTTTAGCTCATTTGGAACACTTGTTATTTTAAGCCTATCGGGACCCATTAGAT-CCGTTTTGAA
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAG-TGACGTATTGAA
*
995 TCGTCTTCGATTTGGCAAATCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
65 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
* * *
1060 TTGTTGACGATTAGTCGTACTGTGAAA
130 TTGGTGA-GATTAGTC-CACTGTGAAC
*
1087 TTTTTAGCTCATTTGGAGCACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
*
1152 CGTCTTCGATTTGCCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
Statistics
Matches: 832, Mismatches: 48, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
152 2 0.00
153 1 0.00
154 506 0.61
155 172 0.21
156 151 0.18
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
TGGTGAGATTAGTCCACTGTGAAC
Found at i:803 original size:308 final size:307
Alignment explanation
Indices: 1--1201 Score: 1895
Period size: 308 Copynumber: 3.9 Consensus size: 307
* *
1 AGTCCACTGTGAACTTTTTAGCTCATTTGTAACACTTGTTATTTTGGGCATATCGGGGCCCATTA
1 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * *
66 GTTCTGTTTTGAATCGTCATCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGTCT
66 GTAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
*
131 AACTATAATCATTTTGGTGAGATTA----A----G---TTTTTAGTCTCATTTGGAATACTTGTT
130 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAG-CTCATTTGGAACACTTGTT
*
185 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAAAT
194 ATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAATCGTCTTCGATTTGGCAAACCTC-AAT
*
250 GCTTTTGTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
258 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
* * *
300 AGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* *
365 GTGACCGTTTTGAATCGTCTTGGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGTC
66 GT-A-CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
* ** *
430 TAACTATAATCATTTTGGTGAGATTAATCCGTTGTGAACTTTTTAGCTCATTTGGAATACTTGTT
129 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTT
495 ATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAATCGTCTTCGATTTGGCAAACCTCAATG
194 ATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAATCGTCTTCGATTTGGCAAACCTCAATG
560 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
259 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
* * * *
609 AGTCCACTGTGAAGTTCTTAGCTCATTCGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* *
674 GTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAGTGCTTTTCTTTCCATTGTTTATGGCCT
66 GT-ACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
*
739 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCCTTTGGAACACTTGTTA
130 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTA
* *
804 TTTTGGGCCTATCGGGGCCCATTAGT-TCTATTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
195 TTTTGGGCCTATCGGGGCCCATTAGTGAC-ATATTGAATCGTCTTCGATTTGGCAAACCTCAATG
868 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
259 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
** *
917 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTAAGCCTATCGGGACCCATTA
1 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* *
982 GATCCGTTTTGAATCGTCTTCGATTTGGCAAATCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
66 G-TACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
* * * *
1047 AACTATAATCATTTTGTTGACGATTAGTCGTACTGTGAAATTTTTAGCTCATTTGGAGCACTTGT
130 AACTATAATCATTTTGGTGA-GATTAGTC-CACTGTGAACTTTTTAGCTCATTTGGAACACTTGT
* *
1112 TATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGCCAAACCTCAAT
193 TATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAATCGTCTTCGATTTGGCAAACCTCAAT
1177 GCTTTTCTTTCCATTGTTTATGGCC
258 GCTTTTCTTTCCATTGTTTATGGCC
Statistics
Matches: 837, Mismatches: 47, Indels: 25
0.92 0.05 0.03
Matches are distributed among these distances:
299 62 0.07
300 83 0.10
301 1 0.00
307 1 0.00
308 363 0.43
309 125 0.15
310 194 0.23
311 8 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (307 bp):
AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
GTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTAT
TTTGGGCCTATCGGGGCCCATTAGTGACATATTGAATCGTCTTCGATTTGGCAAACCTCAATGCT
TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
Found at i:956 original size:462 final size:459
Alignment explanation
Indices: 1--1201 Score: 1934
Period size: 462 Copynumber: 2.6 Consensus size: 459
* *
1 AGTCCACTGTGAACTTTTTAGCTCATTTGTAACACTTGTTATTTTGGGCATATCGGGGCCCATTA
1 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * *
66 GTTCTGTTTTGAATCGTCATCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGTCT
66 GTAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
131 AACTATAATCATTTTGGTGAGATTA---A--GT---TTTTAGTCTCATTTGGAATACTTGTTATT
130 AACTATAATCATTTTGGTGAGATTAGTCACTGTGAATTTTAG-CTCATTTGGAATACTTGTTATT
188 TTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAAATGCT
194 TTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTC-AATGCT
* * *
253 TTTGTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTT
258 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTT
*
318 TAGCTCATTTGGAACACCTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCGTTTTGAATCGT
323 TAGCTCATTTGGAACACCTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCATTTTGAATCGT
* *
383 CTTGGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGTCTAACTATAATCATTTTGG
388 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
448 TGAGATT
453 TGAGATT
* ** *
455 AATCCGTTGTGAACTTTTTAGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* *
520 GTGACATATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
66 GT-ACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
*
585 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTCGGAATACTTGTTA
130 AACTATAATCATTTTGGTGAGATTAGT-CACTGTGAA-TT-TTAGCTCATTTGGAATACTTGTTA
*
650 TTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAGTGC
192 TTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGC
715 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTT
257 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTT
* * * *
780 TTAGCTCCTTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCTATTTTGAATCG
322 TTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCATTTTGAATCG
844 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
387 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
909 GTGAGATT
452 GTGAGATT
** *
917 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTAAGCCTATCGGGACCCATTA
1 AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* *
982 GATCCGTTTTGAATCGTCTTCGATTTGGCAAATCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
66 G-TACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
* **
1047 AACTATAATCATTTTGTTGACGATTAGTCGTACTGTGAAATTTTTAGCTCATTTGGAGCACTTGT
130 AACTATAATCATTTTGGTGA-GATTAGTC--ACTGTG-AA-TTTTAGCTCATTTGGAATACTTGT
*
1112 TATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGCCAAACCTCAAT
190 TATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAAT
1177 GCTTTTCTTTCCATTGTTTATGGCC
255 GCTTTTCTTTCCATTGTTTATGGCC
Statistics
Matches: 689, Mismatches: 41, Indels: 24
0.91 0.05 0.03
Matches are distributed among these distances:
454 142 0.21
455 1 0.00
458 1 0.00
460 2 0.00
462 219 0.32
463 122 0.18
464 194 0.28
465 8 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (459 bp):
AGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
GTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
ACTATAATCATTTTGGTGAGATTAGTCACTGTGAATTTTAGCTCATTTGGAATACTTGTTATTTT
GGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT
CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAG
CTCATTTGGAACACCTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCATTTTGAATCGTCTT
CGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGA
GATT
Done.