Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009116.1 Corchorus olitorius cultivar O-4 contig09144, 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, 819
Length: 1365
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Found at i:355 original size:155 final size:154
Alignment explanation
Indices: 1--1365 Score: 2058
Period size: 155 Copynumber: 8.8 Consensus size: 154
* * *
1 ACTATAATCATTTTTGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCCTTTGGAACACTTGTTAT
1 ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* * * *
66 TTTGGGAATATCGAGGAACATTAGTTCCGTTTTGAATCGTCTTCGATTTTGCAACCCTCAATGCG
66 TTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
131 TTTCTTTCCATTGTTTATGGCCTA
131 TTTCTTTCCATTGTTTATGGCCTA
* *
155 AATATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTATTAT
1 ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* *
220 TTTGGGCATCTCGAGGACCATTAGTTCCGTTTAGAATCGTCTTCGATTTTGGCAACCCTCAATGC
66 TTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGA-TTTGGCAACCCTCAATGC
*
285 TTTTCTTTCCAATGTTTATGGCCTA
130 TTTTCTTTCCATTGTTTATGGCCTA
* * *
310 ACTATAATCATTTTGGTAAGAGTAGTCCACTTTGAAGTTTTTAGCTCCTTTGGAACACTTGTTAT
1 ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* * *
375 TTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
66 TTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
**
440 TTT-TTTATATTGTTTATGGCCTA
131 TTTCTTTCCATTGTTTATGGCCTA
*
463 ACTATAATCATTTTGGTGA-AATAGTCCA-TTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
1 ACTATAATCATTTTGGTGAGATTAGTCCACTT-TGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* * *
526 TTTTGGGCATATCTAGGACTATGAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGC
65 TTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGC
*
591 TTTTCTTTCCAATGTTTATGGCCTA
130 TTTTCTTTCCATTGTTTATGGCCTA
* * *
616 ACTATAATCATTTTGGTAAGATTATTCGACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
1 ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* * * *
681 TTTGGGCCTATTGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
66 TTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
*
746 TTTCGTTCCATTGTTTATGGCCTA
131 TTTCTTTCCATTGTTTATGGCCTA
* * * * *
770 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAATTTTTTTGGCTCATTAGGAACACTTTTTA
1 ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAA-GTTTTTAGCTCATTTGGAACACTTGTTA
* * * *
835 TTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGA
65 TTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGC
*
900 TTTTCGTTCCATTGTTTATGGCCTA
130 TTTTCTTTCCATTGTTTATGGCCTA
* * *
925 ACTATAATCATTTTGGTGAGATTATTCCACTTTGAAGGTTTTAGTCTCTATTTGGAACACTTATT
1 ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAG-CTC-ATTTGGAACACTTGTT
990 ATTTTGGGGCTATTGATCGAGGGACCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCC
64 ATTTT-GGGC-A-T-ATCGA-GGA-CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCC
*
1055 TCAATGCTTTT-GTTCCATTGTTTATGGCCTA
123 TCAATGCTTTTCTTTCCATTGTTTATGGCCTA
* *
1086 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTAT
1 ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* * * *
1151 TTTGGGCCTACCGGGGCCCATTAG-TCCGTTTTGAATCGTCTTCGATTTTGGCAACCCTCAATGC
66 TTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGA-TTTGGCAACCCTCAATGC
1215 -TTTCTTTCCATTGTTTATGGCCTA
130 TTTTCTTTCCATTGTTTATGGCCTA
** *
1239 ACTATAATCATTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTCGTTAT
1 ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
*
1304 TTTGGGGCATATCAAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAA
66 TTT-GGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAA
Statistics
Matches: 1106, Mismatches: 87, Indels: 36
0.90 0.07 0.03
Matches are distributed among these distances:
151 2 0.00
152 126 0.11
153 181 0.16
154 313 0.28
155 316 0.29
156 20 0.02
157 4 0.00
158 4 0.00
159 20 0.02
160 7 0.01
161 63 0.06
162 50 0.05
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
ACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
TTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
TTTCTTTCCATTGTTTATGGCCTA
Found at i:885 original size:461 final size:461
Alignment explanation
Indices: 1--1365 Score: 2105
Period size: 461 Copynumber: 2.9 Consensus size: 461
* *
1 ACTATAATCATTTTTGT-AAGATTAGTCCACTTTGAAGTTTTTAGCTCCTTTGGAACACTTGTTA
1 ACTATAATCATTTTGGTGAA-A-TAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* *
65 TTTTGGGAATATCGAGGAACATTAGTTCCGTTTTGAATCGTCTTCGATTTTGCAACCCTCAATGC
64 TTTTGGGCATATCGAGG-ACATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGC
* *
130 GTTTCTTTCCATTGTTTATGGCCTAAATATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTT
128 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTT
* * * * * *
195 TTAGCTCATTTGGAACACTTATTATTTTGGGCATCTCGAGGACCATTAGTTCCGTTTAGAATCGT
193 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
*
260 CTTCGATTTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTG
258 CTTCGATTTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
* * * *
325 GTAAGAGTAGTCCACTTTGAAGTTTTTAGCTCCTTTGGAACACTTGTTATTTTGGGCCTATCGGG
323 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
* * *
390 GCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT-TTTATATTGTT
388 GCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGATTTTCGTTACATTGTT
454 TATGGCCTA
453 TATGGCCTA
463 ACTATAATCATTTTGGTGAAATAGTCCA-TTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
1 ACTATAATCATTTTGGTGAAATAGTCCACTT-TGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* *
527 TTTGGGCATATCTAGGACTATGAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
65 TTTGGGCATATCGAGGAC-ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
* * * *
592 TTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTAAGATTATTCGACTTTGAAGTTTT
129 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
*
657 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATTGGGGCCCATTAGTTCCGTTTTGAATCGTC
194 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
*
722 TTCGA-TTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
259 TTCGATTTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* * * *
786 TGAGATTAGTCCACTGTGAATTTTTTTGGCTCATTAGGAACACTTTTTATTTTGGGCCTATCGGG
324 TGAGATTAGTCCACTGTGAA-GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
*
851 GCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGATTTTCGTTCCATTGTT
388 GCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGATTTTCGTTACATTGTT
916 TATGGCCTA
453 TATGGCCTA
* * * *
925 ACTATAATCATTTTGGTGAGATTATTCCACTTTGAAGGTTTTAGTCTCTATTTGGAACACTTATT
1 ACTATAATCATTTTGGTGA-AATAGTCCACTTTGAAGTTTTTAG-CTC-ATTTGGAACACTTGTT
990 ATTTTGGGGCTATTGATCGAGGGACCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCC
63 ATTTT-GGGC-A-T-ATCGA-GGA--CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCC
* *
1055 TCAATGCTTTT-GTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
121 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTT
* *
1119 GAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTACCGGGGCCCATTAG-TCCGTTTT
186 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTT
1183 GAATCGTCTTCGATTTTGGCAACCCTCAATGC-TTTCTTTCCATTGTTTATGGCCTAACTATAAT
251 GAATCGTCTTCGATTTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
* *
1247 CATTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGGC
316 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGGC
* ** *
1312 ATATCAAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAA
380 CTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAA
Statistics
Matches: 826, Mismatches: 59, Indels: 29
0.90 0.06 0.03
Matches are distributed among these distances:
460 78 0.09
461 310 0.38
462 53 0.06
463 20 0.02
464 5 0.01
465 20 0.02
466 4 0.00
467 1 0.00
468 28 0.03
469 137 0.17
470 121 0.15
471 48 0.06
472 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (461 bp):
ACTATAATCATTTTGGTGAAATAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
TTGGGCATATCGAGGACATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTT
TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTA
GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTT
CGATTTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGATTTTCGTTACATTGTTTAT
GGCCTA
Done.