Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009157.1 Corchorus olitorius cultivar O-4 contig09185, 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: 1976
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:662 original size:323 final size:320
Alignment explanation
Indices: 1--1976 Score: 2408
Period size: 323 Copynumber: 6.1 Consensus size: 320
* * * * *
1 GCAAAACTGAGGCCGGGCCCCGAAACACGTTTTTAGCAAAAAAACTGTGATGTATGTAGCACACG
1 GCAAAACTGA-GCCGGGGCCCGAAACGCGTTTTTAGC-AAAAAACCGTGATG-GT-TAGTACACG
* *
66 ATTTCGGCTAAAAATTGACCCGAAAACTTCTTTTCTCA-TTTTTTGCCACATAACTCTAAAAAAA
62 ATTTCGGCTAAAAATTGACCTGAAAACTT-TTTTCTCATTTTTTTGCCACACAACTCTAAAAAAA
* * * * * *
130 TATATGATTCAACCCCCCAAAAAA-TGAAGGGTTTTTCACGCTTCTAATATCGATTTTTCA-ATT
126 TATATAATTCAA-CGCCAAAAAAATTGAAGGGTTTTTCACGCTTCGAATATCG-TTTTCCATTTT
* *
193 TTTTCTGAATTTATTTCTAATTAAATCGAAACAAATTTAAGATGCTCGTAAAAAGAAAT-CTATA
189 TTTTC-GAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCT-TA
* *
257 AATCCAAATTTGCTGAGATTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTG-CAAAAA
252 AATCCAAATTGGCTGAGATTTGGTTATATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAA
321 CTCAT
317 -TCAT
* * *
326 GCAATATTGAGCCGGGGTCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGGTTAGTACACGAT
1 GCAAAACTGAGCCGGGG-CCCGAAACGCGTTTTTAGCAAAAAACCGTGAT-GGTTAGTACACGAT
* * *
391 TTCGGCTAAAAGTTGACCTGAAAACTTTATTCTCATTTTTTTTGCCACACAACTCT-ACAAAATA
64 TTCGGCTAAAAATTGACCTGAAAACTTTTTTCTCA-TTTTTTTGCCACACAACTCTAAAAAAATA
* * *
455 TATAATTCAACGCCAAAAAAATTGAAGGGGTTTTCACGATTCCAATATTTC-TTTTCCATTTTTT
128 TATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCGAATA--TCGTTTTCCATTTTTT
* ** *
519 TTCGAATTTATTTTTAATTAAATCGAAACAAAATTCTTATGCTTGTAAAAAGAAATCCTTAAATC
191 TTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATC
* * * *
584 CAAATTGGCT-AGGATTTCGTTATATAAATATAAATATTTCAAGGAGTCTTTTTGCCAAAAATAA
256 CAAATTGGCTGA-GATTTGGTTATATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCA
648 T
320 T
** * * **
649 GCAAAACTGAGCCGGAACTTCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATAATT
1 GCAAAACTGAGCCGGGGC-CCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATT
* * * * * *
714 TCGGATAAAAATTGACC---CAATTTTTTTTTCATTTTTTTTCCACAAAACTCTAAAAAAATATA
65 TCGGCTAAAAATTGACCTGAAAACTTTTTTCTCATTTTTTTGCCACACAACTCTAAAAAAATATA
* * * *
776 TAATTCAATGCCAAAAAAATTGAAGGTTTTTTCACGCTTCCAATATCGTTTTCTCATTTCTTTTC
130 TAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTC-CATTT-TTTTT
* * *
841 CGAATTTATTTCTGATTAAATCGAAACAAAATTCAGATGCTCATAAAAGGAAATCCTTAAATCCA
193 CGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCA
* * *
906 AATTGGCTGAGATTTGGTTATATGAATATATATATTTCAAGGAGTCTATCTGCCAAAAATCAT
258 AATTGGCTGAGATTTGGTTATATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAT
** * * *
969 GCAAAACTGAGGTGGGGCCCAGAAACGCGTTTTTAGCAAAAAACCGTAATGGTTTGTATACGATT
1 GCAAAACTGAGCCGGGGCCC-GAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATT
*
1034 TCGGCTAAAAATTGA-CTCGAAAA-------CT--TTTTTTTGCCACACTACTCTAAAAAAATAT
65 TCGGCTAAAAATTGACCT-GAAAACTTTTTTCTCATTTTTTTGCCACACAACTCTAAAAAAATAT
* * * *
1089 ATGATTCAACGCCAAAAAAAATTTAATGGTTTTTCACGTTTCGAATATCGTTTTGCCAATTTTTT
129 ATAATTCAACGCC-AAAAAAATTGAAGGGTTTTTCACGCTTCGAATATCGTTTT-CC-ATTTTTT
* * * *
1154 TTCAGAATTTATTTCTAATTAAATCGAAACAAATTTCAGATACTTGTAAAAATAAATCCTTAAAT
191 TTC-GAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
1219 CCAAATTGGCTGAGATTTGGTTATA-AGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC
255 CCAAATTGGCTGAGATTTGGTTATATA-AATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC
1283 AT
319 AT
* * *
1285 ACAAAACTGAGCCGGGGCCCTGAAACGTGTTTTTAGCAAAAAACCGTGATGGTTAGTACATGATT
1 GCAAAACTGAGCCGGGGCCC-GAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATT
* * *
1350 TCGGCTAAAAATTAACCAGAAAACTTTTTTTCTCATTTTTTTGCCACACAACTCTAAAAAAATAC
65 TCGGCTAAAAATTGACCTGAAAAC-TTTTTTCTCATTTTTTTGCCACACAACTCTAAAAAAATAT
** * * * *
1415 ACGATTCAACCCCAATGAAAA-T-AA-GGCTTTTCACACTTCGAATATCGTTTTTCCAATTTTTT
129 ATAATTCAACGCCAA-AAAAATTGAAGGGTTTTTCACGCTTCGAATATCG-TTTTCC-ATTTTTT
* * * *
1477 TTCCGAATTTATTTCTAATTAAATGGAAACAAGATTGAGATACTCGTAAAAAGAAATCCTTAAAT
191 TT-CGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
* * * * *
1542 CCAAATTGGCTGAGATTTTGTTATATAAATATTGATATTTCAAGGAGTCTTTTTGCCAAAACTAA
255 CCAAATTGGCTGAGATTTGGTTATATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCA
1607 T
320 T
* * *
1608 GCAAAATTGAGCCGGGGCGCCGAAACGCGATTTTATG-AAAAAACCGTGAT-GTTTGTACACGAT
1 GCAAAACTGAGCCGGGGC-CCGAAACGCGTTTTTA-GCAAAAAACCGTGATGGTTAGTACACGAT
* * * *
1671 TTCGTCTAAAAATTGACTTGAAAACTTTTTTATCTCA-TTTTTTGCCACACTACT-TTAAAAAAT
64 TTCGGCTAAAAATTGACCTGAAAAC-TTTTT-TCTCATTTTTTTGCCACACAACTCTAAAAAAAT
* * ** *
1734 ATATGATTCAACGCGAAAAATTTTTTAAGGGTTTTTCACGCTTCGAATATCGTTATTCCATTTTT
127 ATATAATTCAACGCCAAAAA-AATTGAAGGGTTTTTCACGCTTCGAATATCGTT-TTCCA--TTT
*
1799 CTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAAATTAAGATGCTCGTAAAAAGAAATCCTT
188 -TTTTTC-GAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTT
*
1864 AAATCCAAATTGGCTGAGATTTGGTTATATAAATATAGATATTTCAAGGAGTCTATCTGCCAAAA
251 AAATCCAAATTGGCTGAGATTTGGTTATATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
1929 ATCAT
316 ATCAT
*
1934 GCAATACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAA
1 GCAAAACTGAGCCGGGG-CCCGAAACGCGTTTTTAGCAAAAAA
Statistics
Matches: 1429, Mismatches: 166, Indels: 111
0.84 0.10 0.07
Matches are distributed among these distances:
314 38 0.03
315 41 0.03
316 197 0.14
317 3 0.00
318 23 0.02
319 67 0.05
320 185 0.13
321 22 0.02
322 101 0.07
323 424 0.30
324 89 0.06
325 37 0.03
326 201 0.14
327 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (320 bp):
GCAAAACTGAGCCGGGGCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTT
CGGCTAAAAATTGACCTGAAAACTTTTTTCTCATTTTTTTGCCACACAACTCTAAAAAAATATAT
AATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTCCATTTTTTTTCGA
ATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAAT
TGGCTGAGATTTGGTTATATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAT
Done.