Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010957.1 Corchorus olitorius cultivar O-4 contig10989, 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, 726
Length: 1210
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Found at i:245 original size:135 final size:135
Alignment explanation
Indices: 25--267 Score: 468
Period size: 135 Copynumber: 1.8 Consensus size: 135
15 ATATCAAGGA
*
25 CCATTCGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTA
1 CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTA
90 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACACTCGTTATTTTGGGCCTAAT
66 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACACTCGTTATTTTGGGCCTAAT
155 GGGGC
131 GGGGC
*
160 CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTA
1 CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTA
225 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
66 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
268 GTTTTTAGCT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
135 106 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.40
Consensus pattern (135 bp):
CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTA
TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACACTCGTTATTTTGGGCCTAAT
GGGGC
Found at i:470 original size:78 final size:78
Alignment explanation
Indices: 341--498 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 78
331 AATCGTCTTC
*
341 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
406 ATTAGTCCACTGT
66 ATTAGTCCACTGT
419 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
484 ATTAGTCCACTGT
66 ATTAGTCCACTGT
497 GA
1 GA
499 AGTTTTTAGC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (78 bp):
GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGT
Found at i:593 original size:232 final size:231
Alignment explanation
Indices: 187--651 Score: 831
Period size: 232 Copynumber: 2.0 Consensus size: 231
177 AATCGTCTTC
*
187 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* *
252 ATTAGTCCACTGTGAAGTTTTTAGCTCACTTGGAACACTTGATAATTTGGGCATATCGAGGACCA
66 ATTAGTCCACTGTGAAGTTTTTAGCTCACTTGGAACACTCGATAATTTGGGCATACCGAGGACCA
*
317 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
131 TTAGTTCCGTTTTGAATCGTCTTCGATTTGACAACCCTCAATGC-TTTCTTTCCATTGTTTATGG
382 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
195 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
419 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* * * * * *
484 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTACCGGGGCCCA
66 ATTAGTCCACTGTGAAGTTTTTAGCTCACTTGGAACACTCGATAATTTGGGCATACCGAGGACCA
549 TTAGTTCCGTTTTGAATCGTCTTCGATTTGACAACCCTCAATGCTTTCTTTCCATTGTTTATGGC
131 TTAGTTCCGTTTTGAATCGTCTTCGATTTGACAACCCTCAATGCTTTCTTTCCATTGTTTATGGC
614 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
196 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
650 GA
1 GA
652 AGTTTTTAGC
Statistics
Matches: 223, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
231 59 0.26
232 164 0.74
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (231 bp):
GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCTCACTTGGAACACTCGATAATTTGGGCATACCGAGGACCA
TTAGTTCCGTTTTGAATCGTCTTCGATTTGACAACCCTCAATGCTTTCTTTCCATTGTTTATGGC
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
Found at i:1016 original size:308 final size:309
Alignment explanation
Indices: 419--1210 Score: 1344
Period size: 308 Copynumber: 2.6 Consensus size: 309
409 AGTCCACTGT
419 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* *
484 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTACCGGGGCCCA
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
*
549 TTAGTTCCGTTTTGAATCGTCTTCGATTTGACAACCCTCAATGC-TTTCTTTCCATTGTTTATGG
131 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
613 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCG
196 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCG
678 TTATTTTGGGCATATCGAGGACCTATTAGTTCCGTTTTGAATCGTCTTC
261 TTATTTTGGGCATATCGAGGACCTATTAGTTCCGTTTTGAATCGTCTTC
* * *
727 GATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTAAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* * * *
792 ATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTATTGGGCATATCGAGGACC
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT-TTGGGCCTATCGGGGCCC
* *
857 ACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTC-TTCCCTTCGTTTAT
130 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT-GTTTAT
921 GGCCT-ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
194 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
*
985 TGTTATTTTGGGCATATCGAGGACC-ATTAGTTCCGTTTTGAATCGTCTTC
259 CGTTATTTTGGGCATATCGAGGACCTATTAGTTCCGTTTTGAATCGTCTTC
1035 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* * * *
1100 ATTAGTCCACTGTGAA-TTTTTGGTTCATTAGGAACTCTT-TTATTTTGGGCCTATCGGGGCCCA
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
** *
1163 TTAGTGACGTTTTGAATCATCTTCGATTTGGCAACCCTCAATGCTTTT
131 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT
Statistics
Matches: 453, Mismatches: 28, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
305 60 0.13
306 5 0.01
307 19 0.04
308 208 0.46
309 146 0.32
310 15 0.03
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (309 bp):
GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCG
TTATTTTGGGCATATCGAGGACCTATTAGTTCCGTTTTGAATCGTCTTC
Found at i:1084 original size:154 final size:154
Alignment explanation
Indices: 419--1210 Score: 1306
Period size: 153 Copynumber: 5.2 Consensus size: 154
409 AGTCCACTGT
419 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* * * * *
484 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTACCGGGGCCCA
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA
549 TTAGTTCCGTTTTGAATCGTCTTC
131 TTAGTTCCGTTTTGAATCGTCTTC
* *
573 GATTTGACAACCCTCAATGC-TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
*
637 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCATATCGAGGACCT
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACC-
702 ATTAGTTCCGTTTTGAATCGTCTTC
130 ATTAGTTCCGTTTTGAATCGTCTTC
* * *
727 GATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTAAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
*
792 ATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTATTGGGCATATCGAGGACC
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT-TTGGGCATATCGAGGACC
*
857 ACTAGTTCCGTTTTGAATCGTCTTC
130 ATTAGTTCCGTTTTGAATCGTCTTC
*
882 GATTTGGCAACCCTCAATGCTTTTC-TTCCCTTCGTTTATGGCCT-ACTATAATCATTTTGGTGA
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATT-GTTTATGGCCTAACTATAATCATTTTGGTGA
945 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACC
65 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACC
1010 ATTAGTTCCGTTTTGAATCGTCTTC
130 ATTAGTTCCGTTTTGAATCGTCTTC
1035 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* * * * * * *
1100 ATTAGTCCACTGTGAA-TTTTTGGTTCATTAGGAACTCTT-TTATTTTGGGCCTATCGGGGCCCA
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA
** *
1163 TTAGTGACGTTTTGAATCATCTTC
131 TTAGTTCCGTTTTGAATCGTCTTC
1187 GATTTGGCAACCCTCAATGCTTTT
1 GATTTGGCAACCCTCAATGCTTTT
Statistics
Matches: 604, Mismatches: 28, Indels: 14
0.93 0.04 0.02
Matches are distributed among these distances:
152 66 0.11
153 200 0.33
154 174 0.29
155 146 0.24
156 18 0.03
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (154 bp):
GATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCA
TTAGTTCCGTTTTGAATCGTCTTC
Done.