Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011055.1 Corchorus olitorius cultivar O-4 contig11088, 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, 721
Length: 1202
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Found at i:289 original size:154 final size:154
Alignment explanation
Indices: 1--1190 Score: 1804
Period size: 154 Copynumber: 7.7 Consensus size: 154
* * * *
1 AACCTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTACAATCATTTTGGTAAGATTAGTCCA
1 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
* * * *
66 CTGTAAAGTTTTTACCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTACTGACG
66 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCAGGGCCCATTAGTGACG
131 TTTTGAATCGTCTTCGATTTGGCA
131 TTTTGAATCGTCTTCGATTTGGCA
*
155 AACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
1 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
* * ** *
220 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTCCA
66 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCAGGGCCCATTAGTGACG
*
285 TTTTGAATCGTCTTTGATTTGGCA
131 TTTTGAATCGTCTTCGATTTGGCA
*
309 AACCTCGATGCTTTTCTTTCCATTTGTTTATGATGGCCTAACTATAATCATTTTAGTGAGATTAG
1 AACCTCAATGCTTTTCTTTCCA-TTG-TT-T-ATGGCCTAACTATAATCATTTTAGTGAGATTAG
* * * *
374 TCCACTGTGAAATTTTAAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGT
62 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCAGGGCCCATTAGT
** * *
439 TCCATTTGGAATCGTCTTCGATTTGGCA
127 GACGTTTTGAATCGTCTTCGATTTGGCA
* * *
467 AACCTCGATACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
1 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
* *
532 CTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGTGCCTATCAGAGCCCATTAGTGACG
66 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCAGGGCCCATTAGTGACG
* * *
597 TTTTCAACCGTCTTCGATTTCGCA
131 TTTTGAATCGTCTTCGATTTGGCA
*
621 AACTTCAATGCTTTTCTTTCCATTGTTTATGATGGCCTAACTATAATCATTTTAGTGAGATTAGT
1 AACCTCAATGCTTTTCTTTCCATTG-TT-T-ATGGCCTAACTATAATCATTTTAGTGAGATTAGT
* * * * * * * * *
686 CCACTGTGGAGGTTTTAGCTAATTTTGAACACTTGTTATTTTATGCCTTTCGGGGTCCATTAGTT
63 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCAGGGCCCATTAGTG
*
751 CCGTTTTGAATCGTCTTCGATTTGGCA
128 ACGTTTTGAATCGTCTTCGATTTGGCA
* * *
778 AACCTCAAAGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
1 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
* * * *
843 CTGTAAAGTTTTTAGCTCATTTGGAGCACTTGTTATTTTGGGCCTATCAGGGCCCATTAATGACG
66 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCAGGGCCCATTAGTGACG
908 TTTTGAATCGTCTTCGATTTGGCA
131 TTTTGAATCGTCTTCGATTTGGCA
* * *
932 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCGAAGTAAAATCATTTTAGTGAGATTAGTCCA
1 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
* *
997 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCAATTAGTGACG
66 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCAGGGCCCATTAGTGACG
1062 TTTTGAATCGTCTTCGATTTGGCA
131 TTTTGAATCGTCTTCGATTTGGCA
* *
1086 AACCTTAATGGTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
1 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
1151 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
66 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
1191 GACATATCAG
Statistics
Matches: 943, Mismatches: 86, Indels: 14
0.90 0.08 0.01
Matches are distributed among these distances:
154 650 0.69
155 7 0.01
156 7 0.01
157 136 0.14
158 143 0.15
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (154 bp):
AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTATCAGGGCCCATTAGTGACG
TTTTGAATCGTCTTCGATTTGGCA
Found at i:798 original size:311 final size:308
Alignment explanation
Indices: 1--1190 Score: 1772
Period size: 311 Copynumber: 3.8 Consensus size: 308
* * * *
1 AACCTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTACAATCATTTTGGTAAGATTAGTCCA
1 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
* * *
66 CTGTAAAGTTTTTACCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTACTGACG
66 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACG
* * *
131 TTTTGAATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
131 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCGTTTCTTTCCATTGTTTATGGCCTAACTAT
196 AATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGT
196 AATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGT
* * ** * *
261 GCCTTTCGGGGCCCATTAGTTCCATTTTGAATCGTCTTTGATTTGGCA
261 GCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
*
309 AACCTCGATGCTTTTCTTTCCATTTGTTTATGATGGCCTAACTATAATCATTTTAGTGAGATTAG
1 AACCTCAATGCTTTTCTTTCCA-TTG-TT-T-ATGGCCTAACTATAATCATTTTAGTGAGATTAG
* * * * *
374 TCCACTGTGAAATTTTAAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGT
62 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGT
** * * * *
439 TCCATTTGGAATCGTCTTCGATTTGGCAAACCTCGATA-CTTTTCTTTCCATTGTTTATGGCCTA
127 GACGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AAAGCGTTTCTTTCCATTGTTTATGGCCTA
* *
503 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTAT
191 ACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* * * *
568 TTTGTGCCTATCAGAGCCCATTAGTGACGTTTTCAACCGTCTTCGATTTCGCA
256 TTTGTGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
*
621 AACTTCAATGCTTTTCTTTCCATTGTTTATGATGGCCTAACTATAATCATTTTAGTGAGATTAGT
1 AACCTCAATGCTTTTCTTTCCATTG-TT-T-ATGGCCTAACTATAATCATTTTAGTGAGATTAGT
* * * * ** * * * *
686 CCACTGTGGAGGTTTTAGCTAATTTTGAACACTTGTTATTTTATGCCTTTCGGGGTCCATTAGTT
63 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTG
*
751 CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCGTTTCTTTCCATTGTTTATGGCCTAAC
128 ACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCGTTTCTTTCCATTGTTTATGGCCTAAC
* * *
816 TATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAGCACTTGTTATTT
193 TATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
881 TGGGCCTATCAGGGCCCATTAATGACGTTTTGAATCGTCTTCGATTTGGCA
258 TGTGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
* * *
932 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCGAAGTAAAATCATTTTAGTGAGATTAGTCCA
1 AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
*
997 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCAATTAGTGACG
66 CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACG
* *
1062 TTTTGAATCGTCTTCGATTTGGCAAACCTTAATG-GTTTTCTTTCCATTGTTTATGGCCTAACTA
131 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCG-TTTCTTTCCATTGTTTATGGCCTAACTA
1126 TAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
195 TAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
1191 GACATATCAG
Statistics
Matches: 799, Mismatches: 76, Indels: 14
0.90 0.09 0.02
Matches are distributed among these distances:
307 1 0.00
308 229 0.29
309 4 0.01
310 6 0.01
311 290 0.36
312 269 0.34
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (308 bp):
AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCA
CTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACG
TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCGTTTCTTTCCATTGTTTATGGCCTAACTAT
AATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGT
GCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
Done.