Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010443.1 Corchorus olitorius cultivar O-4 contig10475, 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, 993
Length: 1655
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Found at i:620 original size:154 final size:154
Alignment explanation
Indices: 1--1138 Score: 1714
Period size: 154 Copynumber: 7.5 Consensus size: 154
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA-
* *
66 TAGTTAGGCC----AC--T-AAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAT
65 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
** * * ** *
124 GGAACTAATAGGTCCTAATAAGCCC
130 GTCACTAATGGGCCCCGATAGGCCC
*
149 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGGCTAATCTCACCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
214 AGTTAGGCCATAAACGATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAAC
66 AGTTAGGCCATAAAC-AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
279 GTCACTAATGGGCCCCGATAGGCCC
130 GTCACTAATGGGCCCCGATAGGCCC
304 AAAATAACAAGTGTTCCAAATGAGC-AAAAACCTTCACAGTGGACTAATCTCACCAAAATGATTA
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAA-CTTCACAGTGGACTAATCTCACCAAAATGATTA
** *
368 TAGTTAGGCCATAAACAAT-G---G-AAAG--TTGAGATTTGCCAAATTGAAGACGATTCAAAAC
65 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
*
426 GTCCCTAATGGGCCCCGATAGGCCC
130 GTCACTAATGGGCCCCGATAGGCCC
* * *
451 AAAATAATAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTGGACTAATCTCATCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* * *
516 AGTTAGGCCATAAACAATGAAAAGAAAATCATTGAGGGTTGCCCAATCGAAGACGATTCAAAACG
66 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
*
581 TCACTAATGGGGCCCGATAGGCCC
131 TCACTAATGGGCCCCGATAGGCCC
*
605 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
670 AGTTAGGCCATAAACGATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAACG
66 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
** * * *
735 GAACTAATGAGCCCCGGATAGACTC
131 TCACTAATGGGCCCC-GATAGGCCC
* *
760 AAAATAACAAGTGTTCCAAATGCGCTAAAAACTTCTCAGTGGACTAATCTCACCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
825 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTAGCCAAATCGAAGACGATTCAAAACA
66 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC-
* *
890 G-AACTAATGGGCCCCTATAGGCCC
130 GTCACTAATGGGCCCCGATAGGCCC
* * * *
914 AAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCTCAGTGGACTAATCTTATCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
979 AGTTAAGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCCAATCGAAGACGATTCAAAACG
66 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
*
1044 TCACTAATGGGGCCCGATAGGCCC
131 TCACTAATGGGCCCCGATAGGCCC
* *
1068 AAAATATCAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTGGACTAATCTCACCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
1133 AGTTAG
66 AGTTAG
1139 TGATGCGCTA
Statistics
Matches: 901, Mismatches: 69, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
147 137 0.15
148 68 0.08
149 4 0.00
150 1 0.00
151 3 0.00
152 3 0.00
153 2 0.00
154 406 0.45
155 276 0.31
156 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
TCACTAATGGGCCCCGATAGGCCC
Found at i:885 original size:309 final size:307
Alignment explanation
Indices: 1--1138 Score: 1696
Period size: 309 Copynumber: 3.7 Consensus size: 307
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA-
* *
66 TAGTTAGGCC----AC--TAAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAATG
65 TAGTTAGGCCATAAACAATGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
* ** *
125 GAACTAAT-AGGTCCTAATA-AGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
130 GAACTAATGA-GCCCCGATAGA-CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCTCAG
* *
188 TGGGCTAATCTCACCAAAATGATTATAGTTAGGCCATAAACGATTGGAAAGAAAAGCATTGAGGG
193 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-AATGGAAAGAAAAGCATTGAGGG
*
253 TTGCCAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
257 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
304 AAAATAACAAGTGTTCCAAATGAGC-AAAAACCTTCACAGTGGACTAATCTCACCAAAATGATTA
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAA-CTTCACAGTGGACTAATCTCACCAAAATGATTA
** *
368 TAGTTAGGCCATAAACAATG---G-AAAG--TTGAGATTTGCCAAATTGAAGACGATTCAAAACG
65 TAGTTAGGCCATAAACAATGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
*** * * *
427 TCCCTAATGGGCCCCGATAGGCCCAAAATAATAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTG
130 GAACTAATGAGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTG
* * *
492 GACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAATGAAAAGAAAATCATTGAGGGTTG
195 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG
* *
557 CCCAATCGAAGACGATTCAAAACGTCACTAATGGGGCCCGATAGGCCC
260 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
*
605 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
670 AGTTAGGCCATAAACGATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAACG
66 AGTTAGGCCATAAACAAT-GAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
* *
735 GAACTAATGAGCCCCGGATAGACTCAAAATAACAAGTGTTCCAAATGCGCTAAAAACTTCTCAGT
130 GAACTAATGAGCCCC-GATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCTCAGT
*
800 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTA
194 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTT
* *
865 GCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCTATAGGCCC
259 GCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCCCGATAGGCCC
* * * *
914 AAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCTCAGTGGACTAATCTTATCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
979 AGTTAAGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCCAATCGAAGACGATTCAAAACG
66 AGTTAGGCCATAAACAAT-GAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
** * * * *
1044 TCACTAATGGGGCCCGATAGGCCCAAAATATCAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTG
130 GAACTAATGAGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTG
1109 GACTAATCTCACCAAAATGATTATAGTTAG
195 GACTAATCTCACCAAAATGATTATAGTTAG
1139 TGATGCGCTA
Statistics
Matches: 754, Mismatches: 62, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
301 143 0.19
302 141 0.19
303 58 0.08
304 4 0.01
305 2 0.00
306 6 0.01
308 118 0.16
309 281 0.37
310 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (307 bp):
AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
AGTTAGGCCATAAACAATGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
AACTAATGAGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTGG
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
Done.