Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018150.1 Corchorus olitorius cultivar O-4 contig18183, 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: 3395
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:1911 original size:334 final size:322
Alignment explanation
Indices: 1210--3395 Score: 2097
Period size: 334 Copynumber: 6.7 Consensus size: 322
1200 ATAAAATTGG
* ** *
1210 CTCAGTTTTGCATGAGTTTTGGCAGAAAGACTTGTCGAAATATCTATATTCATCTAATCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATCTAATGAAA--T
* * * * * * * *
1275 CTCAGCCACAATGGATTTACGGATTTATTTTTACAAGTATCTGAAACTTGTTTCGATTTAATTAG
64 CTCAG-CATATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTATTTAG
* * * ** ** *
1340 AAATGTATTGTGGCAGAAAATGGAAAAACGATATTAGAAACGTGAAAAACCCTAAAATATTTTTG
128 AAAT-TATT-AGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTG
** * * * *
1405 GAATTGAATTATATGATTTTTCTAAGTATTGTCAATTGTGGCAAATAATTG-GGGAAAAGCTTTT
191 GCGTTGAATTATA-GATTTTTCT--G-A-AGT--ATTGTGACAAAAAATTGAGGGAAAA-TTTTT
* * * *
1469 CGGGTCAGTTTTTCGCAAAATTTTATCTGAAATCGTGTACTAACCATCACAG-TTTTTGGCTGAA
248 CGGGTCAG------GC----TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAA
*
1533 AACGCGTTTC-GGGGCCCTGA
303 AACGCGTTCCAGGGG-CCTGA
* * * * *
1553 CTCAATTTTGCATGATTCTTGGCAGAAAGACTTCTCAAAATATCTATATTCATCTAATCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATCTAATGAAATCT
* * * * * * *
1618 CAGACATGTTGGATTTACGGATTTATTTTTACTAGTATTTGAATCTTGTTTCGATTTAATTAGAA
66 CAG-CATATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTATTTAGAA
* * * * * ** * *
1683 ATGTATTGTGGCAGAAAATGGAAAAACAATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGT
130 AT-TATT-AGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGC
* * *
1748 ATTGAATTATACGATTATTCT-AAGTATTGTGGCAAAAAATTG-GGGAAAATCTTTTCGGGTCAG
193 GTTGAATTATA-GATTTTTCTGAAGTATTGTGACAAAAAATTGAGGGAAAAT-TTTTCGGGTCAG
*
1811 TTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGGCTGAAAACGCGTT
256 ------GC----TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTT
*
1875 TC-GGGGCCCTGA
311 CCAGGGG-CCTGA
* * * *
1887 CTCATTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATATATATTCATTTAATTAAATCT
1 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATCTAATGAAATCT
* ** * * * * * *
1952 TAGCGGCAATGGATTTAAGGATTTATTTTTACTAGTATCTAAATCTTGTTTCGATTTAATTAGAA
66 CAGC-ATATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTATTTAG-A
** ** * * *
2017 AAAAATTCA-GAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCTTCATTGTTTTTGGC
129 AATTATT-AGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGC
* * * *
2081 TTTGAATTATATGATTTTTCTG-AGTATTATGGCAAAAAATTG-GGGAAAAGCTTTTCGGGTCAG
193 GTTGAATTATA-GATTTTTCTGAAGTATTGTGACAAAAAATTGAGGGAAAA-TTTTTCGGGTCAG
* * * * *
2144 TTTTTTACAAAATTTTAGCCGAAATCGTGAACTAACCATCATGGTTTTTTTGCTAAAAACGAGTT
256 ------GC----TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTT
* *
2209 CC-GGGGCATCGG
311 CCAGGGGCCT-GA
* * *
2221 CTCAGTTTTGCATAATTTTTGGC-GTAAAGACTCATTGAAATATCTATATTCATCTAATGAAATC
1 CTCAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTCGAAATATCTATATTCATCTAATGAAATC
* * * *
2285 TCAGCCATA-TGAGATTTAAGGATTTGTTATTACGAGCATCTGCATCTTGTTTCGTTTTATTTAA
65 TCAG-CATATTG-GATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTATTTAG
2349 AAATTAATTAGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGG
128 AAATT-ATTAGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGG
*
2414 CGTTGAATTATATATTTTTTCTGAACG--TTGTGACAAAAAATTGAGGGAAAATTTTTCGGGTCA
192 CGTTGAATTATAGA-TTTTTCTGAA-GTATTGTGACAAAAAATTGAGGGAAAATTTTTCGGGTCA
* * * * * * *
2477 GG-TTTAAGCCGAAATCGTGTATTAACCATCACGGATTTTTGGCTAAAAACGC-TTTCTGGTGCA
255 GGCTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCAGGGGCC
2540 TCGA
320 T-GA
* * *
2544 CTCAGTTTTGCATGATTTTTGGCATAAA-A--ACTC-AAATTATTTATATTCATCTAATGAAATC
1 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAA-TATCTATATTCATCTAATGAAATC
* * * * *
2605 TCAGCAATATGGGATTTAAGGATTTGTTTTTATGATTATATGAATCTTGTTTCGTTTTATTTAAA
65 TCAGC-ATATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTATTTAGA
* *
2670 AATTAATTAGG---AAAATGGAAAAACGATATTAGAAGTGTGAAAACCCCGTCAATATTCTTGGC
129 AATT-ATTAGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGC
* * * * *
2732 GTTGAATTATATATTTTTTCTGAA-TGTTATGACAAAAAATTGTGGGAAAATTTTCCGGGTCA-G
193 GTTGAATTATAGA-TTTTTCTGAAGTATTGTGACAAAAAATTGAGGGAAAATTTTTCGGGTCAGG
* *
2795 -TTTTAGCCGAAATCGTGTA-T----GTCACGGTTTTTTGGCTGAAAACGCGTTCCAGGGTGCCT
257 CTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCAGGG-GCCT
2854 G-
321 GA
** *
2855 CTCAGTTTTGCATGATTTTTGGCTTAAAGACTCCTTGAAATATCTATATTCATCTAATGAAATCT
1 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATCTAATGAAATCT
* * *
2920 CAGCAATATGGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAA
66 CAGC-ATATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTATTTAGAA
*
2985 ATTAATTAGGAAAAAAATGGCAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCG
130 ATT-ATTAGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCG
* * *
3050 TTGAATTATATATTTTTCTGAA-TGTTGTGAAAAAAAATTGAGGGAAAATTTTTCGGGTCA-GCT
194 TTGAATTATAGATTTTTCTGAAGTATTGTGACAAAAAATTGAGGGAAAATTTTTCGGGTCAGGCT
* *
3113 TTTAGCCGAAATCGTGTATTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCAGGGTGCC-GA
259 TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCAGGG-GCCTGA
* * * *
3177 CTCAGATTTGAATGAACTTTTGGC-GTAAAGACTCCTAGAAATATCTATATTCATCTAATGAAAT
1 CTCAGTTTTGCATG-ATTTTTGGCAG-AAAGACTCCTCGAAATATCTATATTCATCTAATGAAAT
** * * * * * *
3241 CTCAGCCATATAAGATTTAGGGATTTGTTATTACGAGCATCTAAATCCTGTTTTGTTTTATTTAG
64 CTCAG-CATATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTATTTAG
* *
3306 AAATTAATTAGGAAAAAAATGGGAAAACAATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGG
128 AAATT-ATTAGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGG
* *
3371 CGTTGAATTAAATATTTTTTCTGAA
192 CGTTGAATTATAGA-TTTTTCTGAA
Statistics
Matches: 1632, Mismatches: 168, Indels: 105
0.86 0.09 0.06
Matches are distributed among these distances:
311 49 0.03
312 7 0.00
313 3 0.00
314 95 0.06
315 4 0.00
316 64 0.04
317 186 0.11
318 1 0.00
319 4 0.00
320 89 0.05
321 2 0.00
322 51 0.03
323 254 0.16
324 11 0.01
333 154 0.09
334 443 0.27
335 12 0.01
336 3 0.00
337 1 0.00
341 142 0.09
343 57 0.03
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (322 bp):
CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATCTAATGAAATCT
CAGCATATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGTTTTATTTAGAAA
TTATTAGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTT
GAATTATAGATTTTTCTGAAGTATTGTGACAAAAAATTGAGGGAAAATTTTTCGGGTCAGGCTTT
TAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCAGGGGCCTGA
Found at i:3304 original size:323 final size:321
Alignment explanation
Indices: 1497--3395 Score: 2133
Period size: 334 Copynumber: 5.9 Consensus size: 321
1487 AATTTTATCT
* * * *
1497 GAAATCGTGTACTAACCATCACAG-TTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAATTT
1 GAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGG-CCTGACTCAGTTT
* * * *
1561 TGCATGATTCTTGGCAG-AAAGACTTCTCA-AAATATCTATATTCATCTAATCAAATCTCAGACA
65 TGCATGATTTTTGGC-GTAAAGACTCCT-AGAAATATCTATATTCATCTAATGAAATCTCAGCCA
* * * * * * * * * *
1624 TGTTGGATTTACGGATTTATTTTTACTAGTATTTGAATCTTGTTTCGATTTAATTAGAAATGT-A
128 TATGGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAAAT-TAA
* * * * * ** * **
1688 TTGTGGCAGAAAATGGAAAAACAATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGTATTGA
192 TT-AGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGA
* * * *
1753 ATTATACGA-TTATTCT-AAGTATTGTGGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTT
256 ATTATA-TATTTTTTCTGAA-TGTTGTGACAAAAAATTGGGGAAAAT-TTTTCGGGTCA------
1816 TGCAAAATTTTAGCC
312 -GC----TTTTAGCC
* * *
1831 GAAATCGTGTACTAACCATCACGG-TTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCATTTT
1 GAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGG-CCTGACTCAGTTT
* * * * *
1895 TGCATGATTTTTGGCAG-AAAGACTCCTCGAAATATATATATTCATTTAATTAAATCTTAGCGGC
65 TGCATGATTTTTGGC-GTAAAGACTCCTAGAAATATCTATATTCATCTAATGAAATCTCAGC--C
* * * * * * * **
1959 A-AT-GGATTTAAGGATTTATTTTTACTAGTATCTAAATCTTGTTTCGATTTAATTAGAAAAAAA
127 ATATGGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAAATTAA
** * * * *
2022 TTCA-GAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCTTCATTGTTTTTGGCTTTGA
192 TT-AGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGA
* * * * *
2086 ATTATATGA-TTTTTCTGAGTATTATGGCAAAAAATTGGGGAAAAGCTTTTCGGGTCAGTTTTTT
256 ATTATAT-ATTTTTTCTGAATGTTGTGACAAAAAATTGGGGAAAA-TTTTTCGGGTCAG------
2150 ACAAAATTTTAGCC
313 -C----TTTTAGCC
* * * * * *
2164 GAAATCGTGAACTAACCATCATGGTTTTTTTGCTAAAAACGAGTTCCGGGGCATCGGCTCAGTTT
1 GAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGCCT-GACTCAGTTT
* * *
2229 TGCATAATTTTTGGCGTAAAGACTCATTGAAATATCTATATTCATCTAATGAAATCTCAGCCATA
65 TGCATGATTTTTGGCGTAAAGACTCCTAGAAATATCTATATTCATCTAATGAAATCTCAGCCATA
* * *
2294 TGAGATTTAAGGATTTGTTATTACGAGCATCTGCATCTTGTTTCGTTTTATTTAAAAATTAATTA
130 TGGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAAATTAATTA
2359 GGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGAATTA
195 GGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGAATTA
* * *
2424 TATATTTTTTCTGAACGTTGTGACAAAAAATTGAGGGAAAATTTTTCGGGTCAGGTTTAAGCC
260 TATATTTTTTCTGAATGTTGTGACAAAAAATTG-GGGAAAATTTTTCGGGTCAGCTTTTAGCC
* * * * * *
2487 GAAATCGTGTATTAACCATCACGGATTTTTGGCTAAAAACGCTTTCTGGTGCATCGACTCAGTTT
1 GAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGCCT-GACTCAGTTT
* * * * *
2552 TGCATGATTTTTGGCATAAAAACT-C-A-AATTATTTATATTCATCTAATGAAATCTCAGCAATA
65 TGCATGATTTTTGGCGTAAAGACTCCTAGAAATATCTATATTCATCTAATGAAATCTCAGCCATA
* * ** * *
2614 TGGGATTTAAGGATTTGTTTTTATGATTATATGAATCTTGTTTCGTTTTATTTAAAAATTAATTA
130 TGGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAAATTAATTA
* *
2679 GG---AAAATGGAAAAACGATATTAGAAGTGTGAAAACCCCGTCAATATTCTTGGCGTTGAATTA
195 GGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGAATTA
* *
2741 TATATTTTTTCTGAATGTTATGACAAAAAATTGTGGGAAAATTTTCCGGGTCAG-TTTTAGCC
260 TATATTTTTTCTGAATGTTGTGACAAAAAATTG-GGGAAAATTTTTCGGGTCAGCTTTTAGCC
* *
2803 GAAATCGTGTA-T----GTCACGGTTTTTTGGCTGAAAACGCGTTCCAGGGTGCCTG-CTCAGTT
1 GAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCC-GGG-GCCTGACTCAGTT
* * *
2862 TTGCATGATTTTTGGCTTAAAGACTCCTTGAAATATCTATATTCATCTAATGAAATCTCAGCAAT
64 TTGCATGATTTTTGGCGTAAAGACTCCTAGAAATATCTATATTCATCTAATGAAATCTCAGCCAT
2927 ATGGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAAATTAATT
129 ATGGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAAATTAATT
*
2992 AGGAAAAAAATGGCAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGAATT
194 AGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGAATT
*
3057 ATATA-TTTTTCTGAATGTTGTGAAAAAAAATTGAGGGAAAATTTTTCGGGTCAGCTTTTAGCC
259 ATATATTTTTTCTGAATGTTGTGACAAAAAATTG-GGGAAAATTTTTCGGGTCAGCTTTTAGCC
* * *
3120 GAAATCGTGTATTAACCATCACAGTTTTTTGGCTAAAAACGCGTTCCAGGGTGCC-GACTCAGAT
1 GAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCC-GGG-GCCTGACTCAGTT
* *
3184 TTGAATGAACTTTTGGCGTAAAGACTCCTAGAAATATCTATATTCATCTAATGAAATCTCAGCCA
64 TTGCATG-ATTTTTGGCGTAAAGACTCCTAGAAATATCTATATTCATCTAATGAAATCTCAGCCA
** * * * *
3249 TATAAGATTTAGGGATTTGTTATTACGAGCATCTAAATCCTGTTTTGTTTTATTTAGAAATTAAT
128 TATGGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAAATTAAT
* *
3314 TAGGAAAAAAATGGGAAAACAATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGAAT
193 TAGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGAAT
*
3379 TAAATATTTTTTCTGAA
258 TATATATTTTTTCTGAA
Statistics
Matches: 1376, Mismatches: 150, Indels: 88
0.85 0.09 0.05
Matches are distributed among these distances:
311 55 0.04
312 4 0.00
313 3 0.00
314 95 0.07
315 1 0.00
316 63 0.05
317 188 0.14
318 1 0.00
320 93 0.07
321 1 0.00
322 47 0.03
323 263 0.19
324 10 0.01
326 1 0.00
332 2 0.00
333 140 0.10
334 399 0.29
335 8 0.01
336 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36
Consensus pattern (321 bp):
GAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGCCTGACTCAGTTTT
GCATGATTTTTGGCGTAAAGACTCCTAGAAATATCTATATTCATCTAATGAAATCTCAGCCATAT
GGGATTTAAGGATTTGTTATTACGAGCATCTGAATCTTGTTTCGTTTTATTTAGAAATTAATTAG
GAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATATTCTTGGCGTTGAATTAT
ATATTTTTTCTGAATGTTGTGACAAAAAATTGGGGAAAATTTTTCGGGTCAGCTTTTAGCC
Done.