Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019113.1 Corchorus olitorius cultivar O-4 contig19146, 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: 11643
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:3056 original size:18 final size:18
Alignment explanation
Indices: 3006--3060 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 18
2996 AATTTATCTA
3006 ATCTTATCTTATCTTACT
1 ATCTTATCTTATCTTACT
*
3024 A-CTATATAAATTTATCTTACT
1 ATCT-TAT---CTTATCTTACT
3045 ATCTTATCTTATCTTA
1 ATCTTATCTTATCTTA
3061 TTTTACTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
17 2 0.07
18 12 0.40
21 14 0.47
22 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCTTATCTTACT
Found at i:3370 original size:15 final size:16
Alignment explanation
Indices: 3345--3374 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3335 AATAATTATT
3345 TTTAGATTATAATATA
1 TTTAGATTATAATATA
3361 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
3375 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:4439 original size:332 final size:328
Alignment explanation
Indices: 3843--5262 Score: 1367
Period size: 331 Copynumber: 4.3 Consensus size: 328
3833 GAAATGCGTA
* * * * * **
3843 AAAAGACCTCCAATCTTTTCGGCGTTGAATTTTATA-TTTTTATGAGTATTTTAGTAAAAAATTG
1 AAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG
* * * * * * *
3907 AGAAGAAATCTTTCGTGTCAATTTTTACAAAATTTTAGTCGAAATTGTGTACTAACAAACCATCG
66 AGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAA-TAACCATCA
* * * * *
3972 CGGTTTTCGGCTAAAATCGCGTTCTAGGTA--CCGTCTCAATTTTGCATGATTTTTGGCTCCAAG
127 CGGTTTTTGGCTAAAAACGCGTT-TAGG-AGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
* * *
4035 ACTACTTGAAATATCTATATTCATCTAATTAAATCTCAGTCACATTAGATTTAAGGGTTTGTTTT
190 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGTCACATTAGATTTAAGGATTT-TTTT
* * *
4100 TACAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGAT
254 TACAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGG-AAAAATATGAAAAACGAT
*
4165 ATTAGAAACGTC
318 ATTA-AAACATC
*
4177 AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG
1 AAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG
* * * *
4242 AGAAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGT
66 AGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGT
* * * * *
4307 TTTTGGCTAAAAATGCGATTTAGGACCCCGGCTCAGTTATGCCTGATTTTTGGCGCCAACACTCC
131 TTTTGGCTAAAAACGCG-TTTAGGAGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * *
4372 TTGAGATAT-TCATATTCATCTAATCAAATCTCAGTCACATTGGATTTAAGAATTTATTTTTACA
195 TTGAAATATCT-ATATTCATCTAATCAAATCTCAGTCACATTAGATTTAAGGATTT-TTTTTACA
*
4436 AGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAA-TTGTGAAAAATATGAAAAATGATATTA
258 AGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTG-GAAAAATATGAAAAACGATATTA
*
4500 AAAGCATG
322 AAA-CATC
* * *
4508 AAAAGTCCTTCAAT-TGTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTAATCCAAAAATT
1 AAAAGCCCTTCAATCT-TTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGCCAAAAATT
** * * * * * *
4572 GAGGAAAAAAT-TTTCGTATTATTTTTTTGCATAACTTTAGCCAAAATCGTGTACTAACCATCAC
65 GA-GAAAAAATCTTTCGGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCAC
* * * * * *
4636 TGTTTTT-GCTAAAAACGCGTTTCGGGGGTCCGGCTCAGTTTTGCATGATTTTTGGC-ACAGATA
128 GGTTTTTGGCTAAAAACGCGTTT-AGGAGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCA-AGA
* * * * *
4699 CTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTACATTTAAGGATTTGTTTTA
191 CTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGTCACATTAGATTTAAGGATTTTTTTTA
* * ** ** *
4764 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAGGGGTATT
256 CAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAAATATGAAAAACGATATT
*
4829 AAAA-GTGC
321 AAAACAT-C
* * * * *
4837 GAAAAGCCCTTCAAAT-TTTTTGGCGTCAAATTATATATTTTAT-TGAGTATTATGGCTAAAAAT
1 -AAAAGCCCTTC-AATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGCCAAAAAT
* * * ** * * **
4900 TAAGGAAATATCTTTTAGGTCAATTTTTGCAAAA-CTTAGCCAAAATCGTGTAATAATGATCACG
64 TGAGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACG
** * * * * * *
4964 GTTTTTGGCTAAAAACGCGTTCCGGGGCCGGGTTCAGTTTTGAATGATTTTTGGTGCCGAGAC-C
129 GTTTTTGGCTAAAAACGCGTTTAGGAGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
*
5028 CTTTGAAATATCTATATTCATCT-ATCCAAATCCCAG-C-C-----A-TT---G----TTTTTAC
194 C-TTGAAATATCTATATTCATCTAAT-CAAATCTCAGTCACATTAGATTTAAGGATTTTTTTTAC
* * *
5077 AAGCATCTGAATCATGTTTC-ATTTTAATTAAAAATTAATTTGGAAAAAGATAAGAAAAACGGTA
257 AAGCATCTGAATCTTGTTTCGA-TTTAATTAAAAATTAATTTGG-AAAA-ATATGAAAAACGATA
* *
5141 TTAGAAGCATG
319 TTA-AAACATC
* * * * * * *
5152 AAAAGCCCTTCAATCTTTTTTGCATTCAATTATATATTTTTTATAAGTATTGTGGCTAAAAATTG
1 AAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG
* *
5217 AAGAAAAAAAT-TTT-GGATCAATTTTTGCAAAATATTAGCCGAAATC
66 -AG-AAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
5263 TTTTTGGCGT
Statistics
Matches: 913, Mismatches: 141, Indels: 82
0.80 0.12 0.07
Matches are distributed among these distances:
311 1 0.00
312 42 0.05
313 7 0.01
314 48 0.05
315 37 0.04
316 18 0.02
317 5 0.01
319 2 0.00
320 1 0.00
325 1 0.00
326 5 0.01
327 89 0.10
328 32 0.04
329 22 0.02
330 109 0.12
331 215 0.24
332 177 0.19
334 32 0.04
335 70 0.08
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (328 bp):
AAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG
AGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGT
TTTTGGCTAAAAACGCGTTTAGGAGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
TGAAATATCTATATTCATCTAATCAAATCTCAGTCACATTAGATTTAAGGATTTTTTTTACAAGC
ATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAAATATGAAAAACGATATTAAAAC
ATC
Found at i:5279 original size:96 final size:96
Alignment explanation
Indices: 5163--5358 Score: 234
Period size: 96 Copynumber: 2.0 Consensus size: 96
5153 AAAGCCCTTC
* * * * *
5163 AATCTTTTTTGCATTCAATTATATATTTTTTATAAGTATTGT-GGCTAAAAATTGAAGAAAAAAA
1 AATCTTTTTGGCATTAAATTATATATATTTCATAAGTATTGTAGAC-AAAAATT-AAGAAAAAAA
5227 TTTT-GGATCAATTTTTGCAAAATATTAGCCGA
64 TTTTCGGATCAATTTTTGCAAAATATTAGCCGA
* * * * *
5259 AATCTTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGACAAAAATTAAGGAAAAATTT
1 AATCTTTTTGGCATTAAATTATATATATTTCATAAGTATTGTAGACAAAAATTAAGAAAAAAATT
* * * *
5324 TTCTGATCATTTTTTGCAAACTTTTAGCCGA
66 TTCGGATCAATTTTTGCAAAATATTAGCCGA
5355 AATC
1 AATC
5359 GTGTACTAAC
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
95 12 0.14
96 70 0.83
97 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (96 bp):
AATCTTTTTGGCATTAAATTATATATATTTCATAAGTATTGTAGACAAAAATTAAGAAAAAAATT
TTCGGATCAATTTTTGCAAAATATTAGCCGA
Found at i:7425 original size:333 final size:328
Alignment explanation
Indices: 6257--7961 Score: 1681
Period size: 332 Copynumber: 5.1 Consensus size: 328
6247 CTTTTTGGCA
* * * *
6257 TTATGAGTATTTTAGTCAAAAATTGTTGGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGC
1 TTATGAGTATTTT-GGCTAAAATTG-AGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGC
* * * * ** *
6322 CGAAATCGTGTACTAACCATCAC-GGTTTTTAGCTAAAAACGTGTTTCGAGACCCCGACTTAGTT
64 CGAAATC-TGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCG-GGGCCCGACTCAGTT
* * * * *
6386 TTGCATGATTTTTT-TGCACTGAGACTTCTTGAAATATCTTTATTTATCTAATCAAATCTCAGCC
127 TTGCATGATTTTTTGTGC-C-AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* ** *
6450 ACATTGAATCTAAGGATTTGTTTTTACGAGCCTCTGAATCTTGTTTCAATTTAATTAAAAATTAA
190 ACATTG-ATTTAAGGATTTGTTTTTACGA-ATTCTGAATCTTGTTTCAATTTAATTAGAAATTAA
* * * * * *
6515 -TT-CAGAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTCCTCCAGTCTTTTTGGTGTTGA
253 TTTGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGGCCTCCA-TCTTTTTGGCGTTGA
*
6578 ATTATATATATT
317 ATTATATATTTT
* * * *
6590 TTATGAGTGTTGTGGCCTAAAATTGAGAAAAAAATATTTCGGGTCATTTTTTGCAAAATTTTAGC
1 TTATGAGTATTTTGG-CTAAAATTGAG-GAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGC
* * * * *
6655 CGAAATC-GT-GT-ACCATCACAGTTTTTTGGCTAAAAACGCATTCCGTGGCCCCAGGTCAGTTT
64 CGAAATCTGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGGGCCCGA-CTCAGTTT
* * * *
6717 TGCATGATTTTTTGTGGCAAAACTCCTTGAAATATCTATATTTATCTAACCAAATCTTAGCCACA
128 TGCATGATTTTTTGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA
* *
6782 CTTGATTTAAGGATTTGTTTTTGCGAGCATT-TGAATCATGTTTCAATTTAATTAGAAATTAATT
193 -TTGATTTAAGGATTTGTTTTTACGA--ATTCTGAATCTTGTTTCAATTTAATTAGAAATTAATT
** * *
6846 TGG--AAAAATAGGAAAAATTATATTAGAAGCGTGAGAA-G-C-CCACTCTTTTTGGCGTTGAAT
255 TGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGGCCTCCA-TCTTTTTGGCGTTGAAT
6906 TATATATTTT
319 TATATATTTT
* * * *
6916 TAATGAGTATTGTGGCTAAAAATTGA-GAAAAATATTTCGTGTCAATTTTTGCAAAATTTTAGCT
1 TTATGAGTATTTTGGCT-AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCC
* ** ** * ** *
6980 GAAATC-GT-GT-ACCATCATTGTTTTTAAGCTAAAAACGCGTTCCGGGGTCCTGGGTCAATTTT
65 GAAATCTGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGGG-CCCGACTCAGTTTT
* *
7042 GCATGATTTTTGGTGCCAAGACTCCTTAAAATATATCTATATTCATCTAACCAAATCTCAGCCAC
129 GCATGATTTTTTGTGCCAAGACTCCTT-GAA-ATATCTATATTCATCTAACCAAATCTCAGCCAC
* * ** *
7107 ATTGTATTTAAGGATTTGTTTTTACAAATTTCTAAATCTTGTTTTGATTTAATCAGAAATTAATT
192 ATTG-ATTTAAGGATTTGTTTTTACGAA-TTCTGAATCTTGTTTCAATTTAATTAGAAATTAATT
* * * * * *
7172 TGGAAATAAAATAGGGAAAACGATACTAAAAGCGTGAAAAAGGCTTTCATTTTTTTGGCGTTAAA
255 TGGAAA-AAAATAGGAAAAACGATATTAAAAGCGTG-AAAAGGCCTCCATCTTTTTGGCGTTGAA
7237 TTATATATTTT
318 TTATATATTTT
* * * *
7248 TTATGAGTATTTTCGCTAGAAATCGAGGAAAAATATTTCGGGTCAATTTTTGGAAAATTTTAGCT
1 TTATGAGTATTTTGGCTA-AAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * * * *
7313 GAAATCTTGTATTAATCATCACAG-TTTTCGGCTAAAAACGCGTTCCGGGGTCTGACTCAGTTTT
65 GAAATC-TGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGGGCCCGACTCAGTTTT
* *
7377 GCTTGATTTTTTGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAGCCACAT
129 GCATGATTTTTTGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAT
* * * * *
7442 TAGATTTAAGGATTTATTTTTACGAGCA-TCTGAATCTTGGTTCGATTTAATTAGAACTTAATTC
194 T-GATTTAAGGATTTGTTTTTACGA--ATTCTGAATCTTGTTTCAATTTAATTAGAAATTAATTT
* * * * * * *** *
7506 GGAAAGAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATATTGAATC
256 GGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGGCC-TCCATCTTTTTGGCGTTGAATT
7571 ATATATTTT
320 ATATATTTT
* * * * * * * *
7580 TCATGAGTATTTTAGCCAAAAACTGAGGAAATATCTTTCAGGTCAATTTTTGGAAAATTTTAGCC
1 TTATGAGTATTTT-GGCTAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * *** ** *
7645 AAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCAAAGCCACGGTTCTGTTT
65 GAAATC-TGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGGGCC-CGACTCAGTTT
* * * * * * * ** *
7710 TGCATGATTTTTGGCGCCGAGATTTCTTAAAATATCTTTATTCATCTAATAAAATCTCAGCCACG
128 TGCATGATTTTTTGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA
* * *
7775 TTGGATTTAAGGATTTGTTTTTATGCGCA-TCTAAATCTTGTATCAATTTAATTAGAAATTAATT
193 TT-GATTTAAGGATTTGTTTTTA--CGAATTCTGAATCTTGTTTCAATTTAATTAGAAATTAATT
* * * * * *
7839 TAGAAAAAAAT--GAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTTGCATTTAAT
255 TGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGGCCTCC-ATCTTTTTGGCGTTGAAT
*
7902 TATATATATT
319 TATATATTTT
* * *
7912 TTATGAGTATTTTTGTCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTT
1 TTATGAGTA-TTTTGGCTAAAATTGAGGAAAAATATTTCGGGTCAATTTT
7962 ACCATTATGG
Statistics
Matches: 1140, Mismatches: 192, Indels: 81
0.81 0.14 0.06
Matches are distributed among these distances:
324 108 0.09
325 11 0.01
326 132 0.12
327 1 0.00
328 1 0.00
329 154 0.14
330 50 0.04
331 14 0.01
332 251 0.22
333 223 0.20
334 123 0.11
335 38 0.03
336 27 0.02
337 7 0.01
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (328 bp):
TTATGAGTATTTTGGCTAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCG
AAATCTGTACTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGC
ATGATTTTTTGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTG
ATTTAAGGATTTGTTTTTACGAATTCTGAATCTTGTTTCAATTTAATTAGAAATTAATTTGGAAA
AAAATAGGAAAAACGATATTAAAAGCGTGAAAAGGCCTCCATCTTTTTGGCGTTGAATTATATAT
TTT
Done.