Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010917.1 Corchorus olitorius cultivar O-4 contig10949, 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: 3981
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:754 original size:332 final size:329
Alignment explanation
Indices: 101--1375 Score: 1483
Period size: 332 Copynumber: 3.9 Consensus size: 329
91 TTGGGTCAGT
* * ** * *
101 TTTTAGCCGAAATCATGTAC-AACCATCACGGTTTTTGCCTAAAAACGTATTTCGG-GCCCTCGA
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCC-CGG
* * * ** * ** *
164 CTCAGTTTTGCATGGTTTTTGACATAAAGACTCCTT-ATAATATCAATATTCATTTAACCCAATC
65 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGA-AATATCTATATTCATCGAACCAAATC
* * * * * * * * *
228 TCAGCCA-AGTTGGATTTAAGGTTTTGATTTTACGAGCATCTGAATCTTGTCTCGATTAAATTAG
129 TCAGCCACA-TTGCATATAAGGATTTG-TTTTTCGGGCATTTGAATCTTGTTTCCATTTAATTAG
** * * * *
292 AAAAAAATTCGGAAAAAAATATGAAAAATGATATTAGAAGCGTGAAAAACCC-TTAAGTTTTTAT
192 AAATTAATTCGGAAAAAAAT-TGAAAAACGATATTAGAAGTGTGAAAATCCCATCAA-TTTTT-T
* * * * * *
356 GGCGTTGAATTATATA-TTTTTCTGAGTACTGCGGCAAAAAATTGACAAAAAAATTATCGGGTCA
254 GGCATTGAATTATATATTTTTTCTGAGTATTGTGGGAAAAAATTGA-GAAAAAATTTTCGGGTCA
420 GTTTTTGCAAAA
318 GTTTTTGCAAAA
* * * ** *
432 TTTTAGCCGAAATCGTGTATTATCCATCACGGTTTTTGGCTACAAACGCGTTTTGGAGCCCCGGG
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGC
* * ** * *
497 TCAATTTTCCATGATTTTTGGTGCAATTACTCCTTGAAATATCTATATTCATTGAACCAAATCTA
66 TCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
562 AGCCACATTGCATATAAGGATTTGTTTTTCGGGCATTTGAATCTTGTTTCCATTTAATTAGAAAT
131 AGCCACATTGCATATAAGGATTTGTTTTTCGGGCATTTGAATCTTGTTTCCATTTAATTAGAAAT
*
627 TAATTCGGGAAAAAAATTGAAAAACGATATTAGAAGTGTGAAAATCCCATCAATATTATTGGCAT
196 TAATTC-GGAAAAAAATTGAAAAACGATATTAGAAGTGTGAAAATCCCATCAAT-TTTTTGGCAT
692 TGAATTATATATTTTTTCTGAGTATTGTGGGAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTT
259 TGAATTATATATTTTTTCTGAGTATTGTGGGAAAAAATTGA-GAAAAAATTTTCGGGTCAGTTTT
757 TGCAAAA
323 TGCAAAA
* * * *
764 TTTTAGTCGAAATCATGTACTAACCATCACGGTTTTTGGCTAGAAACGCGTTCCGGAGCCCCAGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGC
829 TCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
66 TCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
* * * * * * *
894 AGCCACATTGGAGATAAGGATTTGTTTTTACGGG-ATATGAATCTCGATTCTATTTAATTAAAAA
131 AGCCACATTGCATATAAGGATTTGTTTTT-CGGGCATTTGAATCTTGTTTCCATTTAATTAGAAA
* * * * * * *
958 TTAATACGG-AAAAAATTGAAAAAATGATATTAGAATTGTGAAAAGCCCGTCACTTCTTTTGGCG
195 TTAATTCGGAAAAAAATTG-AAAAACGATATTAGAAGTGTGAAAATCCCATCAATT-TTTTGGCA
* * * * * * * *
1022 TTGAAATAAATATTATTTCTGAGTATTGTGGTAAAAAATTGAG-AGAACTTTTTGGGCCAG----
258 TTGAATTATATATTTTTTCTGAGTATTGTGGGAAAAAATTGAGAAAAAATTTTCGGGTCAGTTTT
1082 T------
323 TGCAAAA
* * *
1083 TTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCAG-TCCGGAGCCCCG
1 TTTTAGCCGAAATCGTGTACTAACCATCACG-GTTTTTGGCTAAAAACGC-GTTCCGGAGCCCCG
* *
1147 GCTCAATTTTGCATGATTTTTGACACAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATC
64 GCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATC
* *
1212 TCAGCCACATTGCATATAAGGACTTTTTTTTTCGGGCTTTTGAATCTTGTTTCCATTTAATTAGA
129 TCAGCCACATTGCATATAAGGA-TTTGTTTTTCGGGCATTTGAATCTTGTTTCCATTTAATTAGA
* *
1277 AATTAATTCGGGAAAAAATTTGAAAAACGATATTAGAAGTGTGAAAATCCCATCTATATTTTTGG
193 AATTAATTC-GGAAAAAAATTGAAAAACGATATTAGAAGTGTGAAAATCCCATCAAT-TTTTTGG
1342 CATTGAATTATATATTTTTTCTGAGTATTGTGGG
256 CATTGAATTATATATTTTTTCTGAGTATTGTGGG
1376 CAGGCAAAGG
Statistics
Matches: 811, Mismatches: 115, Indels: 45
0.84 0.12 0.05
Matches are distributed among these distances:
319 28 0.03
320 113 0.14
321 39 0.05
322 66 0.08
323 9 0.01
325 1 0.00
329 13 0.02
330 11 0.01
331 178 0.22
332 343 0.42
333 10 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (329 bp):
TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGC
TCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
AGCCACATTGCATATAAGGATTTGTTTTTCGGGCATTTGAATCTTGTTTCCATTTAATTAGAAAT
TAATTCGGAAAAAAATTGAAAAACGATATTAGAAGTGTGAAAATCCCATCAATTTTTTGGCATTG
AATTATATATTTTTTCTGAGTATTGTGGGAAAAAATTGAGAAAAAATTTTCGGGTCAGTTTTTGC
AAAA
Found at i:1943 original size:13 final size:13
Alignment explanation
Indices: 1925--1949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1915 ACCTTGTTCG
1925 TCTTTCTTCTATA
1 TCTTTCTTCTATA
1938 TCTTTCTTCTAT
1 TCTTTCTTCTAT
1950 GGAAAGACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTTTCTTCTATA
Found at i:3652 original size:319 final size:319
Alignment explanation
Indices: 2734--3981 Score: 1345
Period size: 319 Copynumber: 3.8 Consensus size: 319
2724 AATCATGTAC
* *
2734 TAACCATCACGGTTTTTGGCTAGAAACGCGTTCCGGAGCCCCAGCTCAATTTTGCATGATTTTTG
1 TAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGCTCAATTTTGCATGATTTTTG
*
2799 GCGCAAAGTCTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATATAAGGA
66 GCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATATAAGGA
* * * * *
2864 TTTGTTTTTTCGGGCATTTGAATCTTGTTTCCATTTAATTAGAAATTAATTCTGGAAAAAATTTG
131 TTTGTTTTTACGGGCATCTGAATCTTGTTTCTATTTAATTAGAAATTAATAC-GGAAAAAA-TGG
* * * * *
2929 -AAAAACGATATTAGAAGTGTGAAAATCCCGTCAATATTTTTGGCATTGAATTAAATATTTTTTC
194 AAAAAACGATATTAGAAGCGTGAAAATCCCATCAATATTTTTGGCGTTGAATTATATATATTTTC
* * * * *
2993 TGAGTATTGTGGAAAAAAATTAAG-GAAAAAATTTTTGGGTCAGTTTTT-GCAAAATTTTATTCA
259 TGAGTATTGTGGTAAAAAATTGAGAG-AAAACTTTTCGGGTCAGTTTTTAGC----------T-G
*
3056 AAATCATGTAC
312 AAATC--GT-G
* *
3067 TAACCATCACAGTTTTTGGCTAGAAACGCGTTCCGGAGCCCCATCTCAATTTTGCATGATTTTTG
1 TAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGCTCAATTTTGCATGATTTTTG
* * * * * *
3132 ACGCAAAGACTCCTTGAAATATTTATATTCATCAAACAAAATCTCAGCCACATTGGAGATAAGGA
66 GCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATATAAGGA
* *
3197 TTTGTTTTTACGGGCATCTGAATCTTGATTCTATTTAATTAGAAATTAATACGGGAAAAATGGAA
131 TTTGTTTTTACGGGCATCTGAATCTTGTTTCTATTTAATTAGAAATTAATACGGAAAAAATGGAA
* * *
3262 AAAACAATATTAGAAGCGTGAAAATCCCATCAATTTTTTTGGCGTTGAAATATATATTATTTT-T
196 AAAACGATATTAGAAGCGTGAAAATCCCATCAATATTTTTGGCGTTGAATTATATA-TATTTTCT
*
3326 GAGTATTGTGGTAAAAAATTGAGAGAAAACTTTTCGGGCCAGTTTTTAGCTGAAATCGTG
260 GAGTATTGTGGTAAAAAATTGAGAGAAAACTTTTCGGGTCAGTTTTTAGCTGAAATCGTG
* * * * * *
3386 TAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTG
1 TAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGCTCAATTTTGCATGATTTTTG
** * * * * * * * *
3451 GCGCCGACACTCCTTGAAATTTCTATATTCATTTAATCAAATCTCAACCACATTGAATTTAATGA
66 GCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATATAAGGA
* * * * * *
3516 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTAAATTAGAAATCAATTCGGAAAAAATATG-
131 TTTGTTTTTACGGGCATCTGAATCTTGTTTCTATTTAATTAGAAATTAATACGGAAAAAAT-GGA
*** * * **
3580 AAAAACGATATTAGAAGCGTGAAAAAGTC-TTAAGTCTTTTCCGCGTTGAATTATATATATTTTC
195 AAAAACGATATTAGAAGCGTGAAAATCCCATCAA-TATTTTTGGCGTTGAATTATATATATTTTC
* *
3644 AT-AGTATTGTGGCT-AAAAATTGACGA-AAACCTTTTCGGGTCAGTTTTTGCAAAATTTTAGCC
259 -TGAGTATTGTGG-TAAAAAATTGA-GAGAAAACTTTTCGGGTCAG----T------TTTTAGCT
3706 GAAATCGTG
311 GAAATCGTG
3715 TACTAGCCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCC-GACTCAATTTTGCATGATT
1 TA--A-CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAG-CTCAATTTTGCATGATT
* * * *
3779 ATTT-GTGCAAAGACTCCTTGAAATATCTTTATTCATCGAACCAAATGTCAGCCACATTGCATAT
62 -TTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATAT
* * * *
3843 AAGGATTT-TTTTTTCGGGCATCTGAATCTTGTTTCTATTTAATAACAAATTAATACGGGAAAAA
126 AAGGATTTGTTTTTACGGGCATCTGAATCTTGTTTCTATTTAATTAGAAATTAATACGGAAAAAA
* * * * *
3907 CGGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAAT-TTTTCTGCCGTTGAAATATATATTA
191 TGGAAAAAACGATATTAGAAGCGTGAAAATCCCATCAATATTTT-TGGCGTTGAATTATATA-TA
3971 TTTT-TGAGTAT
254 TTTTCTGAGTAT
Statistics
Matches: 773, Mismatches: 112, Indels: 62
0.82 0.12 0.07
Matches are distributed among these distances:
318 9 0.01
319 239 0.31
320 7 0.01
322 5 0.01
323 2 0.00
329 18 0.02
330 6 0.01
331 96 0.12
332 212 0.27
333 179 0.23
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (319 bp):
TAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAGCTCAATTTTGCATGATTTTTG
GCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATATAAGGA
TTTGTTTTTACGGGCATCTGAATCTTGTTTCTATTTAATTAGAAATTAATACGGAAAAAATGGAA
AAAACGATATTAGAAGCGTGAAAATCCCATCAATATTTTTGGCGTTGAATTATATATATTTTCTG
AGTATTGTGGTAAAAAATTGAGAGAAAACTTTTCGGGTCAGTTTTTAGCTGAAATCGTG
Done.