Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021939.1 Corchorus olitorius cultivar O-4 contig21972, 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: 4610
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Found at i:1211 original size:615 final size:616
Alignment explanation
Indices: 1--2336 Score: 3307
Period size: 621 Copynumber: 3.8 Consensus size: 616
*
1 AATTCATACCTTCAAAATAATATTTCTTCTGTGGTGATTTTCAAT-A--ACTATAATAGAGGCAA
1 AATTCATACCTTC-AAATAATATTTCTTCAGTGGTGATTTTCAATAACGACTATAATAGAGGCAA
* * * * *
63 GAGATCTACCAAGCAAAAACAAAGCATCAGGCATAAATACACCATGGTTACAAAATGCATGCCAA
65 GAGATCCACCATGCAAAATCAAAGCATCAGGCATAAGTACACCATGGTTACAAAATGCATGTCAA
* * *
128 AAGTTGCCGCTCCAACCACCATTTGTCCTAACACATAGAGACAATGACAACAACAAGCATCATTA
130 AAGTTGCCGCTCGAACCACCATTTGTCC-AA-ACACAGAGACAATGACAACAACAAGCATCACTA
* * * *
193 TATGTAGCATCTTCTCATGTGTCTTCGATAGTTTTCCCATACAGCACACATGGGCACCCCTTATC
193 TATGTAGCTTCTTCTCATGTGTCTTCGACATTTTTCCCATACAGCACACATGGGCACCCCTTACC
* * *
258 TGAAACAAGATGTACTGATATTAAAAACTATTGATATGAGGATGAAAATAACAATAAAATTATTA
258 TGAAACAAGATGTAATGATATTAAGAACTATTGATATGAGGATGAAAATAACAATAAAA-TATAA
* *
323 AATAAATTGGAAACTCACAACTACGAGACGCTTCATTACAACCGAAAAGTCTAGTGGTACAATCC
322 AATAAATTTGAAACTCACAACTACGAGACTCTTCATTACAACCGAAAAGTCTAGTGGTACAATCC
* * ** *
388 TCTTCAGTTGGTGGCTGTACAGATTGCTTTGTTCCACTTTCAATGCAAAAATCCATCATCACAAT
387 TCTTCAGTTGGTGGCTGTACAAATTGCCTTGGCCCACTTTCAATGCAAACATCCATCATCACAAT
*
453 ACTGAAAGGATTGTTTTCAGAGTTAACAATCTCTATACTAAGCA-CCATGAGTTAAAAGATATAT
452 ACTGAAAGGATTGTTTTCTGAGTTAACAATCTCTATACTAAGCACCCATGAGTTAAAAGATATAT
* * *
517 TTGGACTCTAATATCATATAAAATAAATAAAAATAAAAAATAATTTAATTTCAAATTTATACATA
517 TTGGACTCTAATATCATATAAAATAAATAAAAATAAAAAATAATTTATTTTCTAATATATACATA
582 TAAATTTTTATTCATTTTTTCCAATATTTATATATA
582 TAAA-TTTTATTCATTTTTTCCAATATTTATATATA
* * * *
618 AATTCATACATTCAAATAATATTTCTTCAGTGGTGATTTTCAATAACGACTATAGTATAGTCAAG
1 AATTCATACCTTCAAATAATATTTCTTCAGTGGTGATTTTCAATAACGACTATAATAGAGGCAAG
* * * *
683 AGATCCACCATGCAAAATCAAAGCATCAGGTATAAGTACAACATGGTTATAAAATGCATGTCAAT
66 AGATCCACCATGCAAAATCAAAGCATCAGGCATAAGTACACCATGGTTACAAAATGCATGTCAAA
* * *
748 AGTCGCCGCTCGAACCACCATTTGTCCTAACACAGAGACAATGATAACAACAAGCATCACTATAT
131 AGTTGCCGCTCGAACCACCATTTGTCCAAACACAGAGACAATGACAACAACAAGCATCACTATAT
* *
813 GTAGCTTCTTCTCATGTGTTTTCGACATTTTTCCCATACAGCACATATGGGCACCACC-TACCTG
196 GTAGCTTCTTCTCATGTGTCTTCGACATTTTTCCCATACAGCACACATGGGCACC-CCTTACCTG
* *
877 AAACAAGATGTAATTATATTAAGAACTATTGATATTAGGATGAAAATAACAATAAAA-ATAAAAT
260 AAACAAGATGTAATGATATTAAGAACTATTGATATGAGGATGAAAATAACAATAAAATATAAAAT
** ** *
941 AAATTACAAACTCACAACTACGAGACTCTTCATTGTAACCGACAAA-TGTAGTGGTACAATCCTC
325 AAATTTGAAACTCACAACTACGAGACTCTTCATTACAACCGA-AAAGTCTAGTGGTACAATCCTC
* * *
1005 ATCAGTTGG-GGACTGCACAAATTTCCTTGGCCCACTTTCAATGCAAACATCCATCATCACAATA
389 TTCAGTTGGTGG-CTGTACAAATTGCCTTGGCCCACTTTCAATGCAAACATCCATCATCACAATA
* * * * *
1069 CTGAAAGGATTGTTTTGTTAGTTGACAATCTCTATACTAAGCACCCATAAGTGAAAAGATATATT
453 CTGAAAGGATTGTTTTCTGAGTTAACAATCTCTATACTAAGCACCCATGAGTTAAAAGATATATT
* ** * * *
1134 TGGACTCTGATATCATATAAAATAAATAAAAATTTTAAAA-AGTTT-TTTTCTAATAAATACTTA
518 TGGACTCTAATATCATATAAAATAAATAAAAA-TAAAAAATAATTTATTTTCTAATATATACATA
*
1197 TAAACTTTTATTCATTTCTTCCAATATTTATATATATGA
582 TAAA-TTTTATTCATTTTTTCCAATA-TT-TATATAT-A
* * * * *
1236 AATTCTATACCTTCAAATAAGGATTTTTTTCTGTGGTGATTTTGAATAACGACTATAGTAGAGGC
1 AATTC-ATACCTTCAAATAA-TA-TTTCTTCAGTGGTGATTTTCAATAACGACTATAATAGAGGC
* *
1301 TAGAGATCCACCACGCAAAATCAAAGCATCAGGCATAAGTACACCATGGTTACAAAATGCATGAT
63 AAGAGATCCACCATGCAAAATCAAAGCATCAGGCATAAGTACACCATGGTTACAAAATGCATG-T
** * * ** *
1366 -TTAAGTTGCCGCTTGAACCATCATTTGTCTCAAAACACAGAGACAATGACAACGGCAATCATCA
127 CAAAAGTTGCCGCTCGAACCACCATTTGTC-C-AAACACAGAGACAATGACAACAACAAGCATCA
* * * * *
1430 CTATATGTAGCTTATTCTCATGCGTCTTCGACTTTTTTCTCATACAGCACACATTGGCACCACC-
190 CTATATGTAGCTTCTTCTCATGTGTCTTCGACATTTTTCCCATACAGCACACATGGGCACC-CCT
*
1494 TACCTGAAACAAGATGTAATGATATTAAGAACTATTGATATGAGGATGAAAATAACAGTAAAATA
254 TACCTGAAACAAGATGTAATGATATTAAGAACTATTGATATGAGGATGAAAATAACAATAAAATA
* * * *
1559 TAAAATAAATTTGAAATTCACATCTACGAGACTCTTCATTACAACCGAAAATTCTTGTGGTACAA
319 TAAAATAAATTTGAAACTCACAACTACGAGACTCTTCATTACAACCGAAAAGTCTAGTGGTACAA
* *
1624 TCCTTTTCAGTTGGTGGCTGTACAGAA-TGCCTTGGCCCACGTTCAATGCAAACATCCATCATCA
384 TCCTCTTCAGTTGGTGGCTGTACA-AATTGCCTTGGCCCACTTTCAATGCAAACATCCATCATCA
* * *
1688 CAATACTGAAAGGATTGATTTATGAGTTAACAATCTCTATACTAAGTACCCATGAGTTAAAAGAT
448 CAATACTGAAAGGATTGTTTTCTGAGTTAACAATCTCTATACTAAGCACCCATGAGTTAAAAGAT
* *
1753 ATAGTTGGACTTTAATATCATATAAAATAAATAAAAAAATAAAAAATAATTTATTTTCTAATATA
513 ATATTTGGACTCTAATATCATATAAAATAAAT--AAAAATAAAAAATAATTTATTTTCTAATATA
*
1818 TACATCTAAATTTCTATTCATTTTTTCCAATATTTATATATA
576 TACATATAAATTT-TATTCATTTTTTCCAATATTTATATATA
* *
1860 AATTCATACCTTCAAATAATATTTCTTCTA-TGGTGATTTTCAATAACAACTATAATATAGGCAA
1 AATTCATACCTTCAAATAATATTTCTTC-AGTGGTGATTTTCAATAACGACTATAATAGAGGCAA
* * *
1924 GAAATCAACCATGCAAAATCAAAGCATCAGGCATAAGTACACCATGGTTACAAAATGAATGTCAA
65 GAGATCCACCATGCAAAATCAAAGCATCAGGCATAAGTACACCATGGTTACAAAATGCATGTCAA
* * * *
1989 AAGTTACCGCTCGAACCATCATTTGTCCCAAGACATAGAGACAATGTCAACAACAAGCATCACTA
130 AAGTTGCCGCTCGAACCACCATTTGT-CCAA-ACACAGAGACAATGACAACAACAAGCATCACTA
*
2054 TATGTAGCTTCTTCTCATGTGTCTTCGAC-TATTTTCCCATACAGCACACATGGGCACCCCTTTC
193 TATGTAGCTTCTTCTCATGTGTCTTCGACAT-TTTTCCCATACAGCACACATGGGCACCCCTTAC
* *
2118 CTGAAACAAGATGTAATGATATTAAGAACTATTGATATGAAGATGAATATAACAATAAAATATAA
257 CTGAAACAAGATGTAATGATATTAAGAACTATTGATATGAGGATGAAAATAACAATAAAATATAA
* *
2183 AATAAATTTGAAACTCACAACTACGAGACTTTTCATTACAACCAAAAAGTCTAGTGGTACAATCC
322 AATAAATTTGAAACTCACAACTACGAGACTCTTCATTACAACCGAAAAGTCTAGTGGTACAATCC
* * * *
2248 TTTTCAGTTGGTGGCTGTACAGATTTCCTTGGCCCACTTTCAATGCAAACATCCATCACCACAAT
387 TCTTCAGTTGGTGGCTGTACAAATTGCCTTGGCCCACTTTCAATGCAAACATCCATCATCACAAT
2313 ACTGAAAGGATTGTTTTCTGAGTT
452 ACTGAAAGGATTGTTTTCTGAGTT
2337 GAAATCATCC
Statistics
Matches: 1520, Mismatches: 166, Indels: 62
0.87 0.09 0.04
Matches are distributed among these distances:
614 2 0.00
615 189 0.12
616 89 0.06
617 166 0.11
618 9 0.01
619 108 0.07
620 8 0.01
621 518 0.34
622 4 0.00
623 161 0.11
624 200 0.13
625 16 0.01
626 14 0.01
627 36 0.02
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.31
Consensus pattern (616 bp):
AATTCATACCTTCAAATAATATTTCTTCAGTGGTGATTTTCAATAACGACTATAATAGAGGCAAG
AGATCCACCATGCAAAATCAAAGCATCAGGCATAAGTACACCATGGTTACAAAATGCATGTCAAA
AGTTGCCGCTCGAACCACCATTTGTCCAAACACAGAGACAATGACAACAACAAGCATCACTATAT
GTAGCTTCTTCTCATGTGTCTTCGACATTTTTCCCATACAGCACACATGGGCACCCCTTACCTGA
AACAAGATGTAATGATATTAAGAACTATTGATATGAGGATGAAAATAACAATAAAATATAAAATA
AATTTGAAACTCACAACTACGAGACTCTTCATTACAACCGAAAAGTCTAGTGGTACAATCCTCTT
CAGTTGGTGGCTGTACAAATTGCCTTGGCCCACTTTCAATGCAAACATCCATCATCACAATACTG
AAAGGATTGTTTTCTGAGTTAACAATCTCTATACTAAGCACCCATGAGTTAAAAGATATATTTGG
ACTCTAATATCATATAAAATAAATAAAAATAAAAAATAATTTATTTTCTAATATATACATATAAA
TTTTATTCATTTTTTCCAATATTTATATATA
Done.