Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011576.1 Corchorus olitorius cultivar O-4 contig11609, 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, 798
Length: 1330
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Found at i:525 original size:154 final size:154
Alignment explanation
Indices: 1--1329 Score: 1745
Period size: 154 Copynumber: 8.6 Consensus size: 154
* * * * *
1 ATCGAAGACGATTCAAAACGTCATTGATGGACCCTGATAGGCCCAATATAACAAGTGTTCCAAAT
1 ATCGAAGACGATTCAAAACGTAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAT
66 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
66 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* *
131 AAGAAAAACATTGGGGTTTGCCAA
131 AAGAAAAGCATTGAGGTTTGCCAA
* * * * * *
155 ATCGAATACGATTTAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAATT
1 ATCGAAGACGATTCAAAACGTAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAT
* * * * **
220 GAGCTAAAAACTCCACAGTGGACTAATCTCCCCAAAATGGTTATAGTTAGG-CA-ATAC-A-CCA
66 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
281 AAGAAAAGCATTGAGGTTTGCCAA
131 AAGAAAAGCATTGAGGTTTGCCAA
* * * * *
305 ATCGAAGACGATTCAAAAACGTCATTGACGGGCCCTGATAGGCCCAAAATAGCAAGTGTTCCAAA
1 ATCGAAGACGATTC-AAAACGTAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAA
* ** * * *
370 TGAGCTAAAAACTTCTCAGTGGACTAATCTCACCAAAATGATTATAGTTAGATCGTACACTATGG
65 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
435 AAAGAAAAGCATTGAGGTTTGCCAA
130 AAAGAAAAGCATTGAGGTTTGCCAA
* * * * *
460 ATCGAAGACGACTCAAAACGTCATTGATGGGCCCTGATAGGCCCAAAATAGCAAGTGTTCCAAAT
1 ATCGAAGACGATTCAAAACGTAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAT
* *
525 GAGCTAAAAACTTCACAGTGGACTAATCTCA-CATAAATGATTATAGTTAGGCCGTACACAATGG
66 GAGCTAAAAACTTCACAGTGGACTAATCTCACCA-AAATGATTATAGTTAGGCCATAAACAATGG
* *
589 AAAGAAAAGCATTGGGGTTTGTCAA
130 AAAGAAAAGCATTGAGGTTTGCCAA
* * * * *
614 ATTGAAGATGATTCAAAACGGAACTAATGGGGCCC-GAAAGGCCCAAAATAACAAGTGTTCCAAT
1 ATCGAAGACGATTCAAAACGTAACTAAT-GGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAA
* *
678 TGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGCC--AAACAATTG
65 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
741 AAAGAAAAGCATTGAGGTTTGCCAA
130 AAAGAAAAGCATTGAGGTTTGCCAA
* * * *
766 ATCGAAGACGATTCAAAACGTCACTAATGGTCCATGATAGGCCCAAAAAAACAAGTGTTCCAAAT
1 ATCGAAGACGATTCAAAACGTAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAT
* * *
831 GAGTTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAATAATGGA
66 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
*
896 AAGAAAAGCTTTGAGGTTTGCCAA
131 AAGAAAAGCATTGAGGTTTGCCAA
* * *
920 ATCGAAGACAATTCAAAACAG-AACTAATGGG-CCTCAATAGGCCCAAAAAAATAACAAGTTTTC
1 ATCGAAGACGATTCAAAAC-GTAACTAATGGGCCCT-GATAGGCCC---AAAATAACAAGTGTTC
* * * *
983 CAAATGAGCTAAACACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGACATAAAGA
61 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA-C
*
1048 AATGG-AAGAAAAGCATTGGGGTTTAGCCAA
125 AATGGAAAGAAAAGCATTGAGGTTT-GCCAA
* * * * * *
1078 ATCGAAGATGATTCAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAATT
1 ATCGAAGACGATTCAAAACGTAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAT
* *
1143 GAGCTAAAAACTTCACAGAT-GACTAATCTCACCAAAATGATTATAATTAGGCCATAAACAAGGG
66 GAGCTAAAAACTTCACAG-TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
*
1207 AAAGAAAAGCATTGAGGTTTGCCGA
130 AAAGAAAAGCATTGAGGTTTGCCAA
* * *
1232 ATCGAAGACAATTCAAAACAG-AACTAATGGG-CCTCAATAGTCCCAAAA-AACAAGTGTTCCAA
1 ATCGAAGACGATTCAAAAC-GTAACTAATGGGCCCT-GATAGGCCCAAAATAACAAGTGTTCCAA
* *
1294 ATGAGCT-AAGACTTCACAGTAGACTAATCTCACCAA
64 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
1330 G
Statistics
Matches: 1033, Mismatches: 117, Indels: 52
0.86 0.10 0.04
Matches are distributed among these distances:
150 35 0.03
151 94 0.09
152 161 0.16
153 31 0.03
154 439 0.42
155 137 0.13
156 1 0.00
157 90 0.09
158 43 0.04
159 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
ATCGAAGACGATTCAAAACGTAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAT
GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
AAGAAAAGCATTGAGGTTTGCCAA
Found at i:571 original size:305 final size:304
Alignment explanation
Indices: 1--1329 Score: 1651
Period size: 305 Copynumber: 4.3 Consensus size: 304
* * * * *
1 ATCGAAGACGATTCAAAACGTCATTGATGGACCCTGATAGGCCCAATATAACAAGTGTTCCAAAT
1 ATCGAAGACGATTCAAAACG-AACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAT
*
66 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
65 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA-GACATAAACAATGGA
* * * *
131 AAGAAAAACATTGGGGTTTGCCAAATCGAATACGATTTAAAACGGAACTAATGGGCCCCGAAAGG
129 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGG
* * * *
196 CCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACTCCACAGTGGACTAATCTCCCCAAAATGGT
194 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
*
261 TATAGTTAGG-CAATACA-CCAAAGAAAAGCATTGAGGTTTGCCAA
259 TATAGTTAGGCCAATACAGCGAAAGAAAAGCATTGAGGTTTGCCAA
* * * * *
305 ATCGAAGACGATTCAAAAACGTCATTGACGGGCCCTGATAGGCCCAAAATAGCAAGTGTTCCAAA
1 ATCGAAGACGATTC-AAAACG-AACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAA
* * * *
370 TGAGCTAAAAACTTCTCAGTGGACTAATCTCACCAAAATGATTATAGTTAGATCGTACACTATGG
64 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGA-CATAAACAATGG
* ** * * * *
435 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGACTCAAAACGTCATTGATGGGCCCTGATAG
128 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAG
*
500 GCCCAAAATAGCAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CATAAATG
193 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA-AAATG
* * * *
564 ATTATAGTTAGGCCGTACACAATG-GAAAGAAAAGCATTGGGGTTTGTCAA
257 ATTATAGTTAGGCC-AATAC-A-GCGAAAGAAAAGCATTGAGGTTTGCCAA
* * * *
614 ATTGAAGATGATTCAAAACGGAACTAATGGGGCCC-GAAAGGCCCAAAATAACAAGTGTTCCAAT
1 ATCGAAGACGATTCAAAAC-GAACTAAT-GGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAA
* * * *
678 TGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGC-CAAACAATTGA
64 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGACATAAACAATGGA
** * ** *
742 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCATGATAGG
129 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGG
* * *
807 CCCAAAAAAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTAACCAAAATGAT
194 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
*
872 TATAGTTAGGCCATAAATA-ATG-GAAAGAAAAGCTTTGAGGTTTGCCAA
259 TATAGTTAGGCC---AATACA-GCGAAAGAAAAGCATTGAGGTTTGCCAA
* * *
920 ATCGAAGACAATTCAAAACAGAACTAATGGG-CCTCAATAGGCCCAAAAAAATAACAAGTTTTCC
1 ATCGAAGACGATTCAAAAC-GAACTAATGGGCCCT-GATAGGCCC---AAAATAACAAGTGTTCC
* * *
984 AAATGAGCTAAACACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGACATAAAGAA
61 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA-GACATAAA-CA
* * *
1049 ATGG-AAGAAAAGCATTGGGGTTTAGCCAAATCGAAGATGATTCAAAATGGAACTAATGGGCCCC
124 ATGGAAAGAAAAGCATTGAGGTTT-GCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
*
1113 GAAAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGAT-GACTAATCTCACCA
188 GAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG-TGGACTAATCTCACCA
* * * *
1177 AAATGATTATAATTAGGCCATAAACAAGGGAAAGAAAAGCATTGAGGTTTGCCGA
252 AAATGATTATAGTTAGGCCA-ATAC-AGCGAAAGAAAAGCATTGAGGTTTGCCAA
* * *
1232 ATCGAAGACAATTCAAAACAGAACTAATGGG-CCTCAATAGTCCCAAAA-AACAAGTGTTCCAAA
1 ATCGAAGACGATTCAAAAC-GAACTAATGGGCCCT-GATAGGCCCAAAATAACAAGTGTTCCAAA
* *
1295 TGAGCT-AAGACTTCACAGTAGACTAATCTCACCAA
64 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
1330 G
Statistics
Matches: 900, Mismatches: 98, Indels: 51
0.86 0.09 0.05
Matches are distributed among these distances:
304 19 0.02
305 229 0.25
306 195 0.22
307 32 0.04
308 106 0.12
309 112 0.12
310 4 0.00
311 22 0.02
312 180 0.20
313 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (304 bp):
ATCGAAGACGATTCAAAACGAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGACATAAACAATGGAAA
GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCC
CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
TAGTTAGGCCAATACAGCGAAAGAAAAGCATTGAGGTTTGCCAA
Done.