Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015047.1 Corchorus olitorius cultivar O-4 contig15080, 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: 1888
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Found at i:445 original size:154 final size:154
Alignment explanation
Indices: 1--621 Score: 938
Period size: 154 Copynumber: 4.0 Consensus size: 154
* *
1 ATAAATAATGGAAAGAAAAGCTTT-AGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACAAATG
1 ATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATG
* ** *
65 GGCCACGAAAGAACCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACATATCT
66 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCT
**
130 CACCAAAATGATTATAGTTAGTTC
131 CACCAAAATGATTATAGTTAGGCC
* *
154 ATAAACAATGGAAAGAAAAGTTTTGAGGTTTTGCCAAATCGATAGTCGATTCAAAACGGATCTAA
1 ATAAACAATGGAAAGAAAAGCTTTGAGG-TTTGCCAAATCGA-AGTCGATTCAAAACGGAACTAA
* * * *
219 TGGGCCCCCGAAAGGCCCCAAATTACAATTGTTCCAAATGAGCTAAAAACATCACAGTGGACATA
64 TGGG-CCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATA
284 TCTCACCAAAATGATTATAGTTAGGCC
128 TCTCACCAAAATGATTATAGTTAGGCC
*
311 ATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATG
1 ATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATG
* * * * * *
376 GGCCCCGAAAGGCCAAAAATTACAATTGTTCCAAATGTGCTAAAAACTTCACAGTGGACCTTTCT
66 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCT
441 CACCAAAATGATTATAGTTAGGCC
131 CACCAAAATGATTATAGTTAGGCC
* * *
465 CTAAACAATGGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATG
1 ATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATG
* ** * *
530 GTCCCCGAAAGGCCCAAAATAACAAGTGTTGAAAATGAGATAAAAACTTCATAGTGGACATATCT
66 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCT
*
595 CACCAAAATGATTATTGTTAGGCC
131 CACCAAAATGATTATAGTTAGGCC
619 ATA
1 ATA
622 CACATATCTC
Statistics
Matches: 426, Mismatches: 38, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
153 22 0.05
154 224 0.53
155 39 0.09
156 37 0.09
157 104 0.24
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (154 bp):
ATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATG
GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCT
CACCAAAATGATTATAGTTAGGCC
Found at i:629 original size:36 final size:36
Alignment explanation
Indices: 587--657 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
577 TTCATAGTGG
587 ACATATCTCACCAAAATGATTATTGTTAGGCCATAC
1 ACATATCTCACCAAAATGATTATTGTTAGGCCATAC
623 ACATATCTCACCAAAATGATTATTGTTAGGCCATA
1 ACATATCTCACCAAAATGATTATTGTTAGGCCATA
658 AACAACTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (36 bp):
ACATATCTCACCAAAATGATTATTGTTAGGCCATAC
Found at i:766 original size:190 final size:190
Alignment explanation
Indices: 438--805 Score: 569
Period size: 190 Copynumber: 1.9 Consensus size: 190
428 AGTGGACCTT
*
438 TCTCACCAAAATGATTATAGTTAGGCCCTAAACAATGGAAAGAAAAACTTTGAGGTTTGCCAAAT
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTGAGGTTTGCCAAAT
* * * *
503 CGAAGTCGATTCAAAATGGAACTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTGAAAATGA
66 CGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCAAAATGA
* *
568 GATAAAAACTTCATAGTGGAC-ATATCTCACCAAAATGATTATTGTTAGGCCATACACATA
131 GATAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATACACATA
* * *
628 TCTCACCAAAATGATTATTGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAA
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAACTTTGAGGTTTGCCAAA
* * * *
692 TTGAAGACGATTCAAAGCGGAACTAATGGGCCTCGAAAGGCCCAAAATAAGAAGTGTTCAAAATG
65 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCAAAATG
*
757 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
130 AGATAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
806 TACATGAACA
Statistics
Matches: 161, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
190 159 0.99
191 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (190 bp):
TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTGAGGTTTGCCAAAT
CGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCAAAATGA
GATAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATACACATA
Found at i:910 original size:154 final size:154
Alignment explanation
Indices: 627--1455 Score: 1265
Period size: 154 Copynumber: 5.4 Consensus size: 154
617 CCATACACAT
* *
627 ATCTCACCAAAATGATTATTGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAA
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGAGGTTTGCCAA
* * * * * *
691 ATTGAAGACGATTCAAAGCGGAACTAATGGGCCTCGAAAGGCCCAAAATAAGAAGTGTTCAAAAT
65 ATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
756 GAGCTAAAAACTTCACAGTGGACTA
130 GAGCTAAAAACTTCACAGTGGACTA
** * *
781 ATCTCACCAAAATGATTATAGTTAGTACATGAACAATGGAAAGAAAAGTTTTGAGGTTTGCCAAA
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAA
* * *
846 TCGATGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAGTAACAAGTGTTCCAAATG
66 TCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
911 ATCTAAAAATTTAACAGTGGAC-A
131 AGCTAAAAACTTCACAGTGGACTA
934 TATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAA
1 -ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAA
* *
999 ATCGAAGTCGATTTAAAACAGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
65 ATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
*
1064 GAGTTAAAAACTTCACAGTGGACTA
130 GAGCTAAAAACTTCACAGTGGACTA
* *
1089 ATGTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAA-CTTTTGAGGTTTGCCAA
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC-TTTGAGGTTTGCCAA
* * * * * *
1153 ATCGATGTCGATTCGAAATGGATCTATTGGGCCCCGAAAGGCCCAATATTAA-AAGTGTTCCAAA
65 ATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAA-AATAACAAGTGTTCCAAA
*
1217 TGAGCTAAAAACATCACAGTGGAC-A
129 TGAGCTAAAAACTTCACAGTGGACTA
1242 TATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAA
1 -ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAA
*
1307 ATCGAAGTCGATTCAAAACGGAAGTAATGGGCCCCGAAAGGCCC-AAATAACAAGTGTTCCAAAT
65 ATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
*
1371 GAGCTAAAAACTTCATAGTGGACTA
130 GAGCTAAAAACTTCACAGTGGACTA
* *
1396 ATCTCACCAAAATGATTATAGTCAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTG
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTG
1456 TGATGCGCCA
Statistics
Matches: 610, Mismatches: 56, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
152 4 0.01
153 97 0.16
154 503 0.82
155 6 0.01
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (154 bp):
ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAA
TCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGACTA
Found at i:932 original size:344 final size:344
Alignment explanation
Indices: 279--965 Score: 1045
Period size: 344 Copynumber: 2.0 Consensus size: 344
269 ATCACAGTGG
279 ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
1 ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
* * * * *
344 CAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCAAAAATTACAATTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCAAAAATAACAAGTGTTCAA
* * * *
409 AATGTGCTAAAAACTTCACAGTGGACCTTTCTCACCAAAATGATTATAGTTAGGCCCTAAACAAT
131 AATGAGCTAAAAACTTCACAGTGGACCTATCTCACCAAAATGATTATAGTTAGGACATAAACAAT
* *
474 GGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGTCCCCGAA
196 GGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* * *
539 AGGCCCAAAATAACAAGTGTTGAAAATGAGATAAAAACTTCATAGTGGACATATCTCACCAAAAT
261 AGGCCCAAAATAACAAGTGTTCAAAATGAGATAAAAACTTAACAGTGGACATATCTCACCAAAAT
*
604 GATTATTGTTAGGCCATAC
326 GATTATAGTTAGGCCATAC
* *
623 ACATATCTCACCAAAATGATTATTGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTG
1 ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGAGGTTTG
* * * * *
687 CCAAATTGAAGACGATTCAAAGCGGAACTAATGGGCCTCGAAAGGCCCAAAATAAGAAGTGTTCA
65 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCAAAAATAACAAGTGTTCA
* *
752 AAATGAGCTAAAAACTTCACAGTGGA-CTAATCTCACCAAAATGATTATAGTTAGTACATGAACA
130 AAATGAGCTAAAAACTTCACAGTGGACCT-ATCTCACCAAAATGATTATAGTTAGGACATAAACA
** * *
816 ATGGAAAGAAAAGTTTTGAGGTTTGCCAAATCGATGTCGATTCAAAACGGATCTAATGGGCCCCG
194 ATGGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCG
* * ** *
881 AAAGGCCCAAAGTAACAAGTGTTCCAAATGATCTAAAAATTTAACAGTGGACATATCTCACCAAA
259 AAAGGCCCAAAATAACAAGTGTTCAAAATGAGATAAAAACTTAACAGTGGACATATCTCACCAAA
946 ATGATTATAGTTAGGCCATA
324 ATGATTATAGTTAGGCCATA
966 AACAATGGAA
Statistics
Matches: 308, Mismatches: 33, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
343 2 0.01
344 305 0.99
345 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (344 bp):
ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCAAAAATAACAAGTGTTCAA
AATGAGCTAAAAACTTCACAGTGGACCTATCTCACCAAAATGATTATAGTTAGGACATAAACAAT
GGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
AGGCCCAAAATAACAAGTGTTCAAAATGAGATAAAAACTTAACAGTGGACATATCTCACCAAAAT
GATTATAGTTAGGCCATAC
Done.