Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002150.1 Corchorus olitorius cultivar O-4 contig02150, 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, 740
Length: 1234
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:519 original size:273 final size:272
Alignment explanation
Indices: 13--520 Score: 752
Period size: 273 Copynumber: 1.9 Consensus size: 272
3 ACCCCTTCAG
**
13 ACATATATATTCATCTAACCAAATTTCAGCCACGTTGGACTTAAGGATTTGTTTTTACGAGCATT
1 ACATATATATTCATCTAACCAAAGCTCAGCCACGTTGGACTTAAGGATTTGTTTTTACGAGCATT
* * * *
78 TTAATCTAGTTTCGATTTAATTAGAAATTAATTCAGGAAAAATGGAAAAACGATATTAGATGCTC
66 TGAATCTAGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATGAAAAAACGATATTAGATACTC
*
143 AAAAAGCCCTTCAATCTTTTTGGCATTAAATTATATATATTTTTATGAGAATTGTGGTCAAAAAT
131 AAAAAGCCCTTCAATCTTTTTGGCATTAAATTATATATATTTATATGAGAATTGTGGTCAAAAAT
** **
208 TGAGGAAAATCTTTTCGGTTGTTTTTTCGCAAAATTTTAGCCGAAATCATGTATTTTTGGTGGCC
196 TGAGGAAAAAATTTTCGGTCATTTTTTCGCAAAATTTTAGCCGAAATCATGTATTTTTGGTGGCC
273 AAACTCCTTGAA
261 AAACTCCTTGAA
* * *
285 ACATATATATTCATCTAACCAAAGCTCAGCCATGTTGTATTTAAGGATTT-TCTTTT-CGAGCAT
1 ACATATATATTCATCTAACCAAAGCTCAGCCACGTTGGACTTAAGGATTTGT-TTTTACGAGCAT
* *
348 TTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAATGAAAAAACGATATTATATA
65 TTGAATCTAGTTTCGATTTAATTAGAAATTAATTCAG--AAAAAATGAAAAAACGATATTAGATA
** * * *
413 CTTGAAAATCCCTTCAATCTTTTTGGCGTTGAATTATATATATTTATATGAGAATTGTGGTCAAA
128 CTCAAAAAGCCCTTCAATCTTTTTGGCATTAAATTATATATATTTATATGAGAATTGTGGTCAAA
* *
478 ATTTGAGGAAAAAATTTTCGGGTCATTTTTT-GCAGAATTTTAG
193 AATTGAGGAAAAAATTTTC-GGTCATTTTTTCGCAAAATTTTAG
521 ATGAAATCGT
Statistics
Matches: 209, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
271 43 0.21
272 49 0.23
273 108 0.52
274 9 0.04
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (272 bp):
ACATATATATTCATCTAACCAAAGCTCAGCCACGTTGGACTTAAGGATTTGTTTTTACGAGCATT
TGAATCTAGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATGAAAAAACGATATTAGATACTC
AAAAAGCCCTTCAATCTTTTTGGCATTAAATTATATATATTTATATGAGAATTGTGGTCAAAAAT
TGAGGAAAAAATTTTCGGTCATTTTTTCGCAAAATTTTAGCCGAAATCATGTATTTTTGGTGGCC
AAACTCCTTGAA
Found at i:887 original size:334 final size:330
Alignment explanation
Indices: 271--1232 Score: 1220
Period size: 335 Copynumber: 2.9 Consensus size: 330
261 TTTTTGGTGG
* * *
271 CCAAACTCCTTGAAACATATATATTCATCTAACCAAAGCTCAGCCATGTTGTATTTAAGGATTT-
1 CCAAACTCCTTGAAACATATATATTCATCTAACCAAATCTCAGCCATGTTGGAATTAAGGATTTA
*
335 TCTTTTCGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAAAATGAAAA
66 T-TTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAAATGAAAA
* * *
399 AACGATATTATATACTTGAAAATCCCTTCAATCTTTTTGGCGTTGAATTATATATATTTATATGA
130 AACGATATTAGATACTT-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTCATATGA
*
464 GAATTGTGGTCAAAATTTGAGGAAAAAATTTTCGGGTCATTTTTTGCAGAATTTTAGATGAAATC
193 GAATTGTGGTCAAAAATTGAGGAAAAAATTTTCGGGTCATTTTTTGCA-AATTTTAGATGAAATC
* *
529 GTGTACTAACAATCACGGTTTTGGCTAAAAACGCGTTCC-GAGGACCGA-CTCAGTTTTGCTTGA
257 GTGTACTAACAATCACGTTTTTGGCTAAAAACGCGTTCCGGA-GACCCAGCTCAGTTTTGCTTGA
592 TTTTTAGCGC
321 TTTTTAGCGC
* * * * **
602 CCAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCGGCCACATTGGAATTAAGGATTTG
1 CCAAACTCCTTGAAACATATATATTCATCTAACCAAATCTCAGCCATGTTGGAATTAAGGATTT-
* * * *
667 ATTTTACGAGCATCTGAAT-TATGTTTGGATTTAATCAGAAATTAATTCAGAAAACAAAAATAGG
65 ATTTTACGAGCATTTGAATCT-TGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AAAAAT-GA
* * * * *
731 AAAATCGATATTAGATGCTTCAAAAGCCTTTCAATCTTTTTGGCGTTGAGTTACATATTTCATAT
127 AAAAACGATATTAGATACTT-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTCATAT
* * * * * **
796 GAGTATTGTGGGCAAAAATTGAGGAAAAATTTTTCTGGTCCTTTTTTGC-AATGTTTAGCCGAAA
191 GAGAATTGTGGTCAAAAATTGAGGAAAAAATTTTCGGGTCATTTTTTGCAAAT-TTTAGATGAAA
* * *
860 TCGTGTACTAACCATCACAGTTTTTGGCCAAAAACGCGTTCCGGAGCCCCAGCTCAGTTTTGCTT
255 TCGTGTACTAACAATCAC-GTTTTTGGCTAAAAACGCGTTCCGGAGACCCAGCTCAGTTTTGCTT
**
925 GATTTTTTTCGC
319 GATTTTTAGCGC
* *
937 CCAAAC-CCTTGGAAACATATATATTCATCTAACCAAATCTCAGCCATGTTGGACTTAAGGATCT
1 CCAAACTCCTT-GAAACATATATATTCATCTAACCAAATCTCAGCCATGTTGGAATTAAGGATTT
* * * *
1001 ATATGTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATTAATTTAGAAAAAAAAAATGCA
65 AT-TTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAAAAATGAA
* * *
1066 AAAACGATATTAGATACTTGAAAGTCCCTTCAAAT-TCTTTTGGCGTTGAATTATATATATCTTT
128 AAAACGATATTAGATACTTAAAAG-CCCTTC-AATCT-TTTTGGCGTTGAATTATATATTTC-AT
* *
1130 ATGAGAATTTTGGTCAAAAATTGAGAAAAAAATTTTCGGGTCATTTTTTGCAAAAATTTTAGATG
189 ATGAGAATTGTGGTCAAAAATTGAGGAAAAAATTTTCGGGTCATTTTTTGC--AAATTTTAGATG
* *
1195 AAATCGTGTACAAACTATCACGGTTTTTGGCTAAAAAC
252 AAATCGTGTACTAACAATCAC-GTTTTTGGCTAAAAAC
1233 TC
Statistics
Matches: 536, Mismatches: 74, Indels: 35
0.83 0.11 0.05
Matches are distributed among these distances:
331 56 0.10
332 45 0.08
333 34 0.06
334 111 0.21
335 197 0.37
336 50 0.09
338 40 0.07
339 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (330 bp):
CCAAACTCCTTGAAACATATATATTCATCTAACCAAATCTCAGCCATGTTGGAATTAAGGATTTA
TTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAAATGAAAAA
ACGATATTAGATACTTAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTCATATGAGAA
TTGTGGTCAAAAATTGAGGAAAAAATTTTCGGGTCATTTTTTGCAAATTTTAGATGAAATCGTGT
ACTAACAATCACGTTTTTGGCTAAAAACGCGTTCCGGAGACCCAGCTCAGTTTTGCTTGATTTTT
AGCGC
Done.