Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011705.1 Corchorus olitorius cultivar O-4 contig11738, 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, 850
Length: 1418
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Found at i:288 original size:154 final size:154
Alignment explanation
Indices: 3--1418 Score: 1988
Period size: 154 Copynumber: 9.2 Consensus size: 154
1 AA
* * *
3 GGTTG-CAAATTGAAGACGATTCAAAA-AATCACTAATGGGCCCCGATAGGGCCAAAATAAAAAG
1 GGTTGCCAAATCGAAGACGATTCAAAACAA-AACTAATGGGCCCCGATAGGCCCAAAATAAAAAG
* * *
66 TGTTCCTAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCAT
65 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCAT
* *
131 AAACATTGGAATGAAAAGCATTGAG
130 AAACAATGGAAAGAAAAGCATTGAG
* * *** *
156 GGTTGCCAAATCGAAGATGATTCCAAATGGAACTAATGGGCCCTGATAGGCCCAAAATAAAAAGT
1 GGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGT
* * * *
221 GTTTCAATTGAGCTAAAAACTTCATAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATA
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCATA
* *
286 AACAATGGAAAGAAAAGCATTAAA
131 AACAATGGAAAGAAAAGCATTGAG
***
310 GGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACTTGT
1 GGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGT
375 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT-TTCACCAAAATGATTATAGTTAGGGCAT
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTT-ACCAAAATGATTATAGTTAGGGCAT
*
439 AAACAATGGAAAGAAAGGCATTGAG
130 AAACAATGGAAAGAAAAGCATTGAG
* *
464 GGTCGCCAAATCGAAGACGATTCAAAACAAAGACTAATGGGCCCCGATAGGCCCAAAATAACAAG
1 GGTTGCCAAATCGAAGACGATTCAAAACAAA-ACTAATGGGCCCCGATAGGCCCAAAATAAAAAG
* * * *
529 TGTTCCAAATGAGCTAAAAACTTCACAGTGCACTAATCTCACCAAAATGATAACAGTTAGGGCAT
65 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCAT
* * *
594 AAACATTGGAAAGAAACGCATTGAA
130 AAACAATGGAAAGAAAAGCATTGAG
* * ** * * *
619 GGTTG-CAAATAGAAGGCGATTCAAAGA-ATCACTAATTGGCCCCAATAGGGCCAAAATAAAAAG
1 GGTTGCCAAATCGAAGACGATTCAAA-ACAAAACTAATGGGCCCCGATAGGCCCAAAATAAAAAG
* * * *
682 TGTTCCAATTGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAACGATTATAGTTAGGGCAT
65 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCAT
*
747 AAACAATGGAAAGAAAAGCATTGAC
130 AAACAATGGAAAGAAAAGCATTGAG
*
772 GGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGT
1 GGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGT
* * *
837 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATA
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCATA
* *
902 AACAATGGAAAGCAAAGCATTGAC
131 AACAATGGAAAGAAAAGCATTGAG
* *
926 GGTTGCCAAATCGAAGACGATTCAAAAC-AAACTAATTGGCCCCGATAGGCCC-AAATAACAAGT
1 GGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGT
* *
989 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGGCATA
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCATA
*
1054 AACAATGGAAAGAAAGGCATTGAG
131 AACAATGGAAAGAAAAGCATTGAG
* ** * *
1078 CGTCACC-AATAGAAGACGATT-AAAA-AAATCACTAATGGGCCCCGATAGGGCCAAAATAAAAA
1 GGTTGCCAAATCGAAGACGATTCAAAACAAA--ACTAATGGGCCCCGATAGGCCCAAAATAAAAA
* *
1140 GTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCA
64 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCA
*
1205 TAAACATTGGAAAGAAAAGCATTGAG
129 TAAACAATGGAAAGAAAAGCATTGAG
* * *** ** *
1231 GGTTGCCAAATCGAAGATGATTCCAAATGGAACTAATGGGCCCTAATAGGCCCAATATAAAAAGT
1 GGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGT
* * * *
1296 GTTTCAATTGAGCTAAAAACTTCATAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATA
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCATA
* * * *
1361 CACAATGGAAAGAAAAGCGTTAAA
131 AACAATGGAAAGAAAAGCATTGAG
1385 GGTTGCCAAATCGAAGACGATTCAAAACAAAACT
1 GGTTGCCAAATCGAAGACGATTCAAAACAAAACT
Statistics
Matches: 1127, Mismatches: 121, Indels: 29
0.88 0.09 0.02
Matches are distributed among these distances:
150 6 0.01
151 13 0.01
152 118 0.10
153 243 0.22
154 625 0.55
155 120 0.11
156 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
GGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGT
GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGGCATA
AACAATGGAAAGAAAAGCATTGAG
Found at i:1415 original size:459 final size:459
Alignment explanation
Indices: 1--1414 Score: 2071
Period size: 459 Copynumber: 3.1 Consensus size: 459
* * *
1 AAGGTTG-CAAATTGAAGACGATTCAAAA-AATCACTAATGGGCCCCGATAGGGCCAAAATAAAA
1 AAGGTTGCCAAATCGAAGACGATTCAAAACAA-CACTAATGGGCCCCGATA-GGCCCAAATAACA
* * * *
64 AGTGTTCCTAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTC
64 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGC
* * * * ****
129 ATAAACATTGGAATGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCCAAATGGAACTAATG
129 ATAAACATTGGAAAGAAAAGCATTGA-GGTTGCC-AATAGAAGACGATTCAAAAAATCACTAATG
* * * *
194 GGCCCTGATAGGCCCAAAATAAAAAGTGTTTCAATTGAGCTAAAAACTTCATAGTGGACTAATCT
192 GGCCCCGATAGGGCCAAAATAAAAAGTGTTCCAATTGAGCTAAAAACTTCAAAGTGGACTAATCT
*
259 TACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAAGGTTGCCAAATCGA
257 TACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGA
**
324 AGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACTTGTGTTCCAAATGAGCT
322 AGACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
*
389 AAAAACTTCACAGTGGACTAAT-TTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGA
387 AAAAACTTCACAGTGGACTAATCTT-ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
*
453 AAGGCATTG
451 AAAGCATTG
* * *
462 AGGGTCGCCAAATCGAAGACGATTCAAAACAAAGACTAATGGGCCCCGATAGGCCCAAAATAACA
1 AAGGTTGCCAAATCGAAGACGATTCAAAAC-AACACTAATGGGCCCCGATAGGCCC-AAATAACA
* * *
527 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGCACTAATCTCACCAAAATGATAACAGTTAGGGC
64 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGC
* * * * *
592 ATAAACATTGGAAAGAAACGCATTGAAGGTTGCAAATAGAAGGCGATTCAAAGAATCACTAATTG
129 ATAAACATTGGAAAGAAAAGCATTG-AGGTTGCCAATAGAAGACGATTCAAAAAATCACTAATGG
* * * *
657 GCCCCAATAGGGCCAAAATAAAAAGTGTTCCAATTGAGCTAAAAACATCACAGTGGACTAATCTC
193 GCCCCGATAGGGCCAAAATAAAAAGTGTTCCAATTGAGCTAAAAACTTCAAAGTGGACTAATCTT
* * *
722 ACCAAAACGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGACGGTTGCCAAATCGAA
258 ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAA
787 GACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
323 GACGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
* * *
852 AAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGCAA
388 AAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
917 AGCATTG
453 AGCATTG
* *
924 ACGGTTGCCAAATCGAAGACGATTCAAAACAA-ACTAATTGGCCCCGATAGGCCCAAATAACAAG
1 AAGGTTGCCAAATCGAAGACGATTCAAAACAACACTAATGGGCCCCGATAGGCCCAAATAACAAG
*
988 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGGCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCAT
* * ** *
1053 AAACAATGGAAAGAAAGGCATTGAGCGTCACCAATAGAAGACGATTAAAAAAATCACTAATGGGC
131 AAACATTGGAAAGAAAAGCATTGAG-GTTGCCAATAGAAGACGATTCAAAAAATCACTAATGGGC
*
1118 CCCGATAGGGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTAC
195 CCCGATAGGGCCAAAATAAAAAGTGTTCCAATTGAGCTAAAAACTTCAAAGTGGACTAATCTTAC
* * *
1183 CAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGA
260 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGA
* * *** ** * * * *
1248 TGATTCCAAATGGAACTAATGGGCCCTAATAGGCCCAATATAAAAAGTGTTTCAATTGAGCTAAA
325 CGATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* *
1313 AACTTCATAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATACACAATGGAAAGAAAAG
390 AACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
1378 CGTTA
455 CATTG
1383 AAGGTTGCCAAATCGAAGACGATTCAAAACAA
1 AAGGTTGCCAAATCGAAGACGATTCAAAACAA
1415 AACT
Statistics
Matches: 858, Mismatches: 88, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
458 2 0.00
459 393 0.46
460 21 0.02
461 7 0.01
462 320 0.37
463 112 0.13
464 3 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (459 bp):
AAGGTTGCCAAATCGAAGACGATTCAAAACAACACTAATGGGCCCCGATAGGCCCAAATAACAAG
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCAT
AAACATTGGAAAGAAAAGCATTGAGGTTGCCAATAGAAGACGATTCAAAAAATCACTAATGGGCC
CCGATAGGGCCAAAATAAAAAGTGTTCCAATTGAGCTAAAAACTTCAAAGTGGACTAATCTTACC
AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGAC
GATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
ATTG
Done.