Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011895.1 Corchorus olitorius cultivar O-4 contig11928, 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, 1000
Length: 2196
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Found at i:307 original size:154 final size:154
Alignment explanation
Indices: 1--2192 Score: 3190
Period size: 154 Copynumber: 14.3 Consensus size: 154
* * *
1 ACTTGTTATTTTGGGTCTTTCGGGG-CCATTAGATCCGTTTTGAATCGACATCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* * * *
65 CTCAATGCTTTTCTATCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATATGTCAACTG
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTG
* *
130 CGAAGTTTTTAGCTCATTGGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* * *
154 AATTCTAATTTTGGGCCTTACGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
219 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT-TAGTCCACT
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATAT-GTCCACT
* *
283 GTGGAGTTTTTAACTCATTTGGAAC
130 GTGAAGTTTTTAGCTCATTTGGAAC
* *
308 ACTTGTAATTTTGGGCCTTTCGGGGTCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* * *
373 CTCAAAGATTTTATATCCATTGTTTAT-GACATAACTATAATCATTTTGGTGAGATATGTCCACT
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGAC-TAACTATAATCATTTTGGTGAGATATGTCCACT
437 GTGAAGTTTTTAGCTCATTTGGAAC
130 GTGAAGTTTTTAGCTCATTTGGAAC
* * * *
462 ACTAGTAATTTTGCGCCTTTCGGGGACCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* *
527 CTCAAAGCTTTTCTTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTG
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTG
592 TGAAGTTTTTAGCTCATTTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* * *
616 AATTGTAATTTTGGGCCTTTCGGGGTCCATTAGGTCCGTTTTGAATCGACTTCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* *
681 CTCAAAGCTTTTCTTTCCATTATTTATGAACTAACTATAATCATTTTGGTGAGATATGTCCACTG
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTG
746 TGAAGTTTTTAGCTCATTTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* * * * * *
770 ACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATAGATTTCGTTTTGGAAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* * * * * *
835 CTAAAAGCTTTTCATTCCATTGCTTATGGCCTAACTCTAATCATTTTGGAGAGATATGTCCACTG
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTG
* *
900 TGAAATTTTTAGCACATTTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* ** *
924 ACTTGTTA-TTTGGGCCTTTTAGGGCCCATTAG-TACCGTTTTGAATCGACTTTGATTTGGCAAA
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGAT-CCGTTTTGAATCGACTTCGATTTGGCAAA
*
987 CCTCAAAGCTTTTCTATCCATTGTTTAT-GACTTAACTATAATCATTTTGGTGAGATATGTCCAC
65 CCTCAAAGCTTTTCTTTCCATTGTTTATGGAC-TAACTATAATCATTTTGGTGAGATATGTCCAC
* *
1051 TATGAAGTTTTTAAC-CAATTTGGAAC
129 TGTGAAGTTTTTAGCTC-ATTTGGAAC
*
1077 ACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
1142 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT-TAGTCCACT
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATAT-GTCCACT
** *
1206 GTGGTGTTTTTAACTCATTTGGAAC
130 GTGAAGTTTTTAGCTCATTTGGAAC
*
1231 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* *
1296 CTCAAAGATTTTCTATCCATTGTTTAT-GACATAACTATAATCATTTTGGTGAGATATGTCCACT
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGAC-TAACTATAATCATTTTGGTGAGATATGTCCACT
* *
1360 GTGAAATTTTTAGTTCATTTGGAAC
130 GTGAAGTTTTTAGCTCATTTGGAAC
* * * *
1385 AATTGTAATTTTGGGTCTTTCGGGGCCCATTAGATTCGTTTTGAATCGACATCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* * *
1450 CTCAAAACTTTTCTTTCTATTTTTTATGGACTAACTATAATCATTTTGGTGAGAT-TAGTCCACT
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATAT-GTCCACT
1514 GTGAAGTTTTTAGCTCATTTGGAAC
130 GTGAAGTTTTTAGCTCATTTGGAAC
* * * * * *
1539 ACTTCTTATTTTGGGTCTTTCGGGGCTCATTAGTTCCGTTTTGAATCGACTTCGATTCGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* * * * * *
1604 CTAAAAGCTTTTCATTCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATATATCCAATG
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTG
1669 TGAAGTTTTTAGCTCATTTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* *
1693 ACTTGTTATTTTGGGCCTTTCGGGGACCATT--A--------GAATCGACTTCGATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
*
1748 CTCAAAG-TTTTCTTTCCATTGTTTATGAACTAACTATAATCATTTTGGTGAGATATGTCCACTG
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTG
1812 TGAAGTTTTTAGCTCATTTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* * * *
1836 ACTTGTTATTTTGGGCCTTTCGAGGCCCATTAGATCCGTTTTGAATCGACATCGATTTCGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* *
1901 CTCAAAGCTTTTCTTTCTATTTTTTATGGACTAACTATAATCATTTTGGTGAGAT-TAGTCCACT
66 CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATAT-GTCCACT
1965 GTGAAGTTTTTAGCTCATTTGGAAC
130 GTGAAGTTTTTAGCTCATTTGGAAC
* * * * * *
1990 ACTTCTTATTTTGGGTCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCCATTTGGCAAAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
* * * * * * *
2055 CTCAAAGCTTTTCTTT-AAGTTGATTATGGCCTAACAATAATAATTTTGGTGAGATAT-ACCAAT
66 CTCAAAGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACT
2118 GTGAAGTTTTTAGCTCATTTGGAAC
130 GTGAAGTTTTTAGCTCATTTGGAAC
* * *
2143 AATTGTAATTTTGGGACTTTCGGGGCCCATTAGATCCATTTTGAATCGAC
1 ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGAC
2193 CTCG
Statistics
Matches: 1843, Mismatches: 164, Indels: 64
0.89 0.08 0.03
Matches are distributed among these distances:
143 104 0.06
144 28 0.02
145 1 0.00
152 4 0.00
153 260 0.14
154 1432 0.78
155 14 0.01
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (154 bp):
ACTTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAAC
CTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTG
TGAAGTTTTTAGCTCATTTGGAAC
Done.