Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011774.1 Corchorus olitorius cultivar O-4 contig11807, 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: 2078
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--2078 Score: 3218
Period size: 154 Copynumber: 13.5 Consensus size: 154
* *
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGGCGATTCAAAA-GT
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG-
** * *
65 TCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTG
65 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
* *
130 GACTAATTTCACCAAAATCATTATA
130 GACTAATCTCACCAAAATGATTATA
* * *
155 GTTAGGCCATAAACAATGGAAAGAAAAAGCACTAAGGTTTGCCAAATCGAAGACGATTC-AAACG
1 GTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
*
219 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTG
65 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
*
284 GACTAATCTCACCAAAACGATTATA
130 GACTAATCTCACCAAAATGATTATA
*
309 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAATCAAAACGG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
374 AACT-ATGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
66 AACTAAT-GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
438 GACTAATCTCACCAAAATGATTATA
130 GACTAATCTCACCAAAATGATTATA
* * * *
463 GATAGGCCATATAGAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGT
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
* * *
528 CACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTGG
66 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
593 ACTAATCTCACCAAAATGATTATA
131 ACTAATCTCACCAAAATGATTATA
* * *
617 GTTAGGCCATAAACAATGGAATGAAAGGCATTGAGGGTTGCCAAATCGAAGACGAATCAAAACGG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
*
682 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGG
66 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
*
747 ACTAATCTCATCAAAATGATTATA
131 ACTAATCTCACCAAAATGATTATA
* * *
771 GTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGCCGAATCAAAACGG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
* *
836 AACTAAGGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
66 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
901 ACTAATCTCACCAAAATGATTATA
131 ACTAATCTCACCAAAATGATTATA
*
925 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAACACGATT-AAATACG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA-ACG
*
989 GAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
65 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
* *
1054 TACTAATCTCAACAAAATGATTATA
130 GACTAATCTCACCAAAATGATTATA
* * *
1079 GTTAGGCCATATACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGGCGATTCAAAA-GG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
* * * *
1143 TCACTAATGGGCCCAGATAGGCTCAAAAT-ACAAGTGTTCCAAATGAGCTAAATACTTCACAGTG
66 -AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
1207 GACTAATCTCACCAAAATGATTATA
130 GACTAATCTCACCAAAATGATTATA
* *
1232 GTTAGGCCATAAACAATGGAAAAGAAAAGCATTGAGGGTTTGCCCAAATCGAAAACGATTCAATA
1 GTTAGGCCATAAACAATGG-AAAGAAAAGCATTGAGGG-TTG-CCAAATCGAAGACGATTCAAAA
** * *
1297 CGTCACTAATGGGCCCCCGATAAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAAGTTCGA
63 CGGAACTAATGGG-CCCCGAT-AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC-A
* *
1362 CAGTGGACTAATCTAAACAAAATGATTATA
125 CAGTGGACTAATCTCACCAAAATGATTATA
* *
1392 GGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAATCAAAACGG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
** *
1457 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATTTGCTAAAAACTTGACAGTGG
66 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
*
1522 ACTAATATCACCAAAATGATTATA
131 ACTAATCTCACCAAAATGATTATA
* * * *
1546 GTTAGGTCGTAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGAATCAAAACGG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
* * * * *
1611 AACTAATGGGACCCAATAGGCCAAAAATAACAAGTGTTCCAAATGA-TTAAAAAACTTCAGAGTG
66 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTG
*
1675 CACTAATCTCACCAAAATGATTATA
130 GACTAATCTCACCAAAATGATTATA
* * * * *
1700 GTAAAGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTCCAAATCGAAGGCGATTTAAAACGG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
** * *
1764 AACTAATAAGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTGG
66 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
1829 ACTAATCTCACCAAAATGATTATA
131 ACTAATCTCACCAAAATGATTATA
* * * *
1853 GTTAGGCCATAAACATTGGTAAGAAAAGCATTGAGGGTTGCCAAATCGAAGTCGATTCAAAACAG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
* ** * * *
1918 AACTAATGGGCCCGGATATTCCCAAAATAACAAGTGTTCCAAATGAACTAAAAACTTTATAGTGG
66 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
1983 ACTAATCTCACCAAAATGATTATA
131 ACTAATCTCACCAAAATGATTATA
*
2007 GTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGG
1 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
2072 AACTAAT
66 AACTAAT
Statistics
Matches: 1762, Mismatches: 143, Indels: 38
0.91 0.07 0.02
Matches are distributed among these distances:
153 249 0.14
154 1259 0.71
155 77 0.04
156 36 0.02
157 37 0.02
158 13 0.01
159 44 0.02
160 47 0.03
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
ACTAATCTCACCAAAATGATTATA
Done.