Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011796.1 Corchorus olitorius cultivar O-4 contig11829, 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, 660
Length: 1100
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Found at i:286 original size:154 final size:154
Alignment explanation
Indices: 1--1100 Score: 1683
Period size: 154 Copynumber: 7.1 Consensus size: 154
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGA
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGA
** * * * *
66 GGGTTGCCAAATCGAAGATTATTCAAAACGGAACTAATGGTCCTCAATATGCCCAAAATAACAAG
66 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
131 TGTTCCAAATGAGCTAAAAACTTC
131 TGTTCCAAATGAGCTAAAAACTTC
*
155 ACAGTGTACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGA
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGA
* ** *
220 GGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAAAAG
66 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
*
285 TGTTCCAAGTGAGCTAAAAACTTC
131 TGTTCCAAATGAGCTAAAAACTTC
* * *
309 ACAGTGGAATAATCTCACCAAAATGATTATACTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGA
374 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAAGGCCCAAAATAACAA
66 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT-AGGCCCAAAATAACAA
439 GTGTTCCAAATAGAGCTAAAAACTTC
130 GTGTTCCAAAT-GAGCTAAAAACTTC
*
465 -CAAGTGGACTAA-CTTACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTG
1 AC-AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTG
* ** *
528 AGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAAAA
65 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA
* * * * * *
593 ATGTTCCTAGTGAACCAAAAAATTC
130 GTGTTCCAAATGAGCTAAAAACTTC
* * * *
618 ACAGTGGACTAATCTGACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGGAAAGCATTGA
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGA
* * *
683 GGGTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGG-CCTGATAGGCCCAAAATAACGAG
66 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
747 TGTTCCAAATGAGCTAAAAACTTC
131 TGTTCCAAATGAGCTAAAAACTTC
*
771 ACAGTGGACTAATCTCACCAAAATGATTATACGTTAGGCCAT-AACAATGG-AAG-AAAGCATTG
1 ACAGTGGACTAATCTCACCAAAATGATTATA-GTTAGGCCATAAACATTGGAAAGAAAAGCATTG
* * *
833 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCTCGATATGCCCAAAATAACAA
65 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA
*
898 GTGTTCCAATTTGAGCTAAAAACTTC
130 GTGTTCCAA-ATGAGCTAAAAACTTC
* * *
924 AAAGTTGGACTAATCTTACCAAAATGATTATAGTTAGGCTATAAACATTGGAAAGAAAAGCATTG
1 ACAG-TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTG
* * * *
989 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCTCGATATGCCCAAAATAACGA
65 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA
1054 GTGTTCCAAATGAGCTAAAAACTT-
130 GTGTTCCAAATGAGCTAAAAACTTC
1078 ACAAGTGGACTAATCTCACCAAA
1 AC-AGTGGACTAATCTCACCAAA
Statistics
Matches: 866, Mismatches: 67, Indels: 26
0.90 0.07 0.03
Matches are distributed among these distances:
151 49 0.06
152 29 0.03
153 124 0.14
154 420 0.48
155 139 0.16
156 105 0.12
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (154 bp):
ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGA
GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
TGTTCCAAATGAGCTAAAAACTTC
Found at i:559 original size:309 final size:308
Alignment explanation
Indices: 1--1100 Score: 1737
Period size: 309 Copynumber: 3.6 Consensus size: 308
*
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGA
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
** * * * *
66 GGGTTGCCAAATCGAAGATTATTCAAAACGGAACTAATGGTCCTCAATATGCCCAAAATAACAAG
66 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
*
131 TGTTCCAAATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTTAGGCCAT
131 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
196 AAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGG
196 AAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGG
261 CCCCGATAGGCCCAAAATAAAAAGTGTTCCAAGTGAGCTAAAAACTTC
261 CCCCGATAGGCCCAAAATAAAAAGTGTTCCAAGTGAGCTAAAAACTTC
* *
309 ACAGTGGAATAATCTCACCAAAATGATTATACTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
374 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAAGGCCCAAAATAACAA
66 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT-AGGCCCAAAATAACAA
*
439 GTGTTCCAAATAGAGCTAAAAACTTC-CAAGTGGACTAA-CTTACCAAAATGATTATAGTTAGGC
130 GTGTTCCAAAT-GAGCTAAAAACTTCAC-AGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
502 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAAT
193 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAAT
* * * * *
567 GGGCCCCGATAGGCCCAAAATAAAAAATGTTCCTAGTGAACCAAAAAATTC
258 GGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAGTGAGCTAAAAACTTC
* * *
618 ACAGTGGACTAATCTGACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGGAAAGCATTGA
1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
* * *
683 GGGTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGG-CCTGATAGGCCCAAAATAACGAG
66 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
747 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATACGTTAGGCCA
131 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA-GTTAGGCCA
* * **
812 T-AACAATGG-AAG-AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
195 TAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGG
* * * * *
874 TCCTCGATATGCCCAAAATAACAAGTGTTCCAATTTGAGCTAAAAACTTC
260 GCCCCGATAGGCCCAAAATAAAAAGTGTTCCAA-GTGAGCTAAAAACTTC
* * * *
924 AAAGTTGGACTAATCTTACCAAAATGATTATAGTTAGGCTATAAACATTGGAAAGAAAAGCATTG
1 ACAG-TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
* * * *
989 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCTCGATATGCCCAAAATAACGA
65 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA
1054 GTGTTCCAAATGAGCTAAAAACTT-ACAAGTGGACTAATCTCACCAAA
130 GTGTTCCAAATGAGCTAAAAACTTCAC-AGTGGACTAATCTCACCAAA
Statistics
Matches: 732, Mismatches: 50, Indels: 20
0.91 0.06 0.02
Matches are distributed among these distances:
305 74 0.10
306 42 0.06
307 148 0.20
308 183 0.25
309 262 0.36
310 23 0.03
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (308 bp):
ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
AAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGG
CCCCGATAGGCCCAAAATAAAAAGTGTTCCAAGTGAGCTAAAAACTTC
Done.