Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002312.1 Corchorus olitorius cultivar O-4 contig02312, 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: 2324
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1473 original size:178 final size:179
Alignment explanation
Indices: 1141--1482 Score: 485
Period size: 178 Copynumber: 1.9 Consensus size: 179
1131 TAAGCGAAAC
* * * *
1141 TTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTTGGAAGCATTT
** * * * *
1206 TTTTTCACATTCAACATTAAATTTAGTTTTTGAGTCCTTCATGAAAGTCGTAGATAATGGAACAG
66 TTGATCACATTAAACATTAAATTCAATTTTCGAGTCCTTCATGAAAGTCGTAGATAATGGAACAG
*
1271 CTTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGCAAAAG
131 CTTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTGGAGCAAAAG
*
1320 TTATATAATATTAAGTGGACCGTCTATTCCCATTAACCGAAACAACAAATT-TTTCGGAAGCATT
1 TTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTT-GGAAGCATT
* *
1384 TTTGAT-AC-TTGAAACATTAAATTCAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
65 TTTGATCACATT-AAACATTAAATTCAATTTTCGAGTCCTTCATGAAAGTCGTAGATAATGGAAC
* *
1447 AGTCTTTT-AATAGACACTTAAATCATCTTAATCAGA
129 AG-CTTTTCAAGAGACACTTAAATCATCTCAATCAGA
1483 TAACCAGAGA
Statistics
Matches: 144, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
177 2 0.01
178 78 0.54
179 64 0.44
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (179 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTTGGAAGCATTT
TTGATCACATTAAACATTAAATTCAATTTTCGAGTCCTTCATGAAAGTCGTAGATAATGGAACAG
CTTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTGGAGCAAAAG
Found at i:1504 original size:178 final size:177
Alignment explanation
Indices: 1136--1520 Score: 481
Period size: 178 Copynumber: 2.2 Consensus size: 177
1126 CACCGTAAGC
* * * * *
1136 GAAACTTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAG
1 GAAAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTTGGAAG
** * * * *
1201 CATTTTTTTTCACATTCAACATTAAATTTAGTTTTTGAGTCCTTCATGAAAGTCGTAGATAATGG
66 CATTTTTGATCACATTAAACATTAAATTCAATTTTCGAGTCCTTCATGAAAGTCGTAGATAATGG
* * * *
1266 AACAGCTTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGA
131 AACAGCTTTTCAAGAGACACTTAAATCATCTCAATCAGAAACCAGGA
*
1313 GCAAAAGTTATATAATATTAAGTGGACCGTCTATTCCCATTAACCGAAACAACAAATT-TTTCGG
1 G-AAAA-TTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTT-GG
* *
1377 AAGCATTTTTGAT-AC-TTGAAACATTAAATTCAATTTTCGAGTCCTTCATGAAAGTTGTAGATC
63 AAGCATTTTTGATCACATT-AAACATTAAATTCAATTTTCGAGTCCTTCATGAAAGTCGTAGATA
* *
1440 ATGGAACAGTCTTTT-AATAGACACTTAAATCATCTTAATCAGATAACCAGAGA
127 ATGGAACAG-CTTTTCAAGAGACACTTAAATCATCTCAATCAGA-AACCAG-GA
* *
1493 GAAAATTATATAATGTTAAATAGACCGT
1 GAAAATTATATAATATTAAGTAGACCGT
1521 TTAGCCAAAC
Statistics
Matches: 178, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
177 3 0.02
178 101 0.57
179 71 0.40
180 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (177 bp):
GAAAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTTGGAAG
CATTTTTGATCACATTAAACATTAAATTCAATTTTCGAGTCCTTCATGAAAGTCGTAGATAATGG
AACAGCTTTTCAAGAGACACTTAAATCATCTCAATCAGAAACCAGGA
Found at i:1654 original size:16 final size:17
Alignment explanation
Indices: 1633--1668 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1623 GACGGAAAAA
1633 AATC-AAGCTAAATAGT
1 AATCAAAGCTAAATAGT
1649 AATCAAAGCTAAATAGT
1 AATCAAAGCTAAATAGT
1666 AAT
1 AAT
1669 TAAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (17 bp):
AATCAAAGCTAAATAGT
Done.