Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011642.1 Corchorus olitorius cultivar O-4 contig11675, 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, 813
Length: 1356
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Found at i:508 original size:152 final size:152
Alignment explanation
Indices: 2--1349 Score: 2062
Period size: 153 Copynumber: 8.8 Consensus size: 152
1 T
2 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* *
67 AGCATTGAGGGTTGCCAAATCG-AGACGATTCAAAACGGAACTAATGGGCCCCGATAGAACCAAA
66 AGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG-GCCCAA
131 ATAACAAGTGTTCCAAATGAGCTA
129 ATAACAAGTGTTCCAAATGAGCTA
* * *
155 AAAACTTCATAGTGGACTAATCTCACCTAAATGATTATAGTTAGGCCGTAAACAATGGAAAGAAA
1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* * *
220 AGCATTGAGGGTTACAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGAACCAAAA
66 AGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG-GCCCAAA
285 TAACAAGTGTTCCAAATGAGCTA
130 TAACAAGTGTTCCAAATGAGCTA
* *
308 AAAACTTCACAGTGGACTAATCTCAACTAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* ** * *
373 AGCATTGAGCGTTGCAAATCGAAGACGATTCAAAACGTCACTAATGAGCCCCAATAGGCCCAAAT
66 AGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAT
* *
438 AAAAAGTGTTCCAAATGAACTA
131 AACAAGTGTTCCAAATGAGCTA
* * *
460 AAAATTTCATAGTGGACTAATCTCACCTAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* ** * * *
525 AGCATTGAGGGTTACAAATCGAAGACGATTCAAAACGTCACTGATGAGCCCCAATAGGCCCAAAT
66 AGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAT
* *
590 AAAAAGTGTTCCAAATGAGCTT
131 AACAAGTGTTCCAAATGAGCTA
* *
612 AAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAACAATGGAAAGAAA
1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
** *
677 AGCATTGAGGGTTGCAAATCGAATTCGATTCAAAACGGAACTAATGGGCCCCGATAGG--C--TT
66 AGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAT
738 AACAAGTGTTCCAAATGAGCTA
131 AACAAGTGTTCCAAATGAGCTA
*
760 AAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
825 AGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAA
66 AGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC-AA
890 ATAACAAGTGTTCCAAATGAGCTA
129 ATAACAAGTGTTCCAAATGAGCTA
* *
914 AAAACTTCACAGTGGA-TAAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAA-TA
1 AAAACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* ** * * *
977 AAGCATTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGGCCCTGATAGGTCCAA
65 AAGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGG-CCCA
1042 AATAACAAGTGTTCCAAATGAGCTA
128 AATAACAAGTGTTCCAAATGAGCTA
* *
1067 AAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAACAATGGAAAGAAA
1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* * * ** *
1132 ATCATTTAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGGCCCCGATAGGCCCAAA
66 AGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC-AA
1197 ATAACAAGTGTTCCAAATGAGCTA
129 ATAACAAGTGTTCCAAATGAGCTA
1221 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
** ** *
1286 AGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGTCACTAATGATCCCCAATAGGCCCAAA
66 AGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAA
1350 ACAAAAG
Statistics
Matches: 1110, Mismatches: 73, Indels: 25
0.92 0.06 0.02
Matches are distributed among these distances:
148 99 0.09
149 42 0.04
150 1 0.00
151 1 0.00
152 290 0.26
153 435 0.39
154 242 0.22
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (152 bp):
AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
AGCATTGAGGGTTGCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAT
AACAAGTGTTCCAAATGAGCTA
Done.