Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009558.1 Corchorus olitorius cultivar O-4 contig09590, 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: 4184
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:2297 original size:328 final size:325
Alignment explanation
Indices: 1324--3961 Score: 1515
Period size: 328 Copynumber: 8.1 Consensus size: 325
1314 ATTTTTGACG
* * * *
1324 TTTTATAAGTATTGTGGCCATAAATTGAGCAGAAAATGT-T-TCTGG-TATATTTTTGCAAAATT
1 TTTTATGAGTATCGTGGCCAAAAATTGAG--GAAAAT-TCTATC-GGTTAAATTTTTGCAAAATT
* * * * ** * *
1386 TTAGCCGACATCGTGTACTAACCATCAC-GATTTTT-GTTAAAAACGCGTTCCGGGGCTCTGGCT
62 TTAGCCGAAATCATGTAC--A-CATCACAG-TTTTTGGCTAAAAACACGTTTAGGAGC-C-AGCT
* * * * * * * * ** *
1449 CAGTTTTGCATGAATTTTGGCGCCATGACTCATAGAAATATCTATATTTATCTAAAGAAATCTAA
121 CAGTTTTACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTA-TAATTTAACCAAATCTCA
* ** * * * *
1514 GCCACATTGGATTTAAGGATTTCCTTTTACGAGCATCTAAATCCGGTTTCGATTTAATTAGAAGT
185 TCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTTCGATTCAATTAGAAAT
* * * * * * *
1579 TAATTCGG--GAAA-A--AAAA-TGATACTAGAAGCATGAGAAGCCCTTCAATTTTTTTGGCGTT
250 TAATTCGGAAAAAATAGGAAAACCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGC-TT
*
1638 GAGTTATATATT
314 GAATTATATATT
* * * * * *
1650 TTTTATGAGTATTGTAGCCAAAAATTGAGGTGATATGT-T-TCGGGTAAATTTTTGAAAAATTTT
1 TTTTATGAGTATCGTGGCCAAAAATTGAGG-AAAAT-TCTATCGGTTAAATTTTTGCAAAATTTT
* *** * * * ** ** * *
1713 AGCCGAAATCGTGTA-TGTTAACTA-TTTTTGACCAAAAACGTGTTCCGGAGCCCCGACTCTGTT
64 AGCCGAAATCATGTACACATCAC-AGTTTTTGGCTAAAAACACGTTTAGGAG-CCAG-CTCAGTT
* * * * * * * * *
1776 TTGA-ATGACTTTTGGTGACAAGACTCATTGAAATATCTATATCCATCTAACGAAATCTCA-GC-
126 TT-ACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTAT-AATTTAACCAAATCTCATCCA
* * * *
1838 CA---GATTTTAGGATTTGTTTTT-CAGAGCATCTGAAT-CATGTTTCGATTTAATTAGAAATTT
189 CATTGGATTTAAGGATTTGTTTTTAC-GAGCATCTCAATCCA-GTTTCGATTCAATTAGAAATTA
* * * * ** *
1898 ATTCGGAAAAAA-AGGATAAACAGATATTGGAAGCTTCAATTGCCTTTCAATCTTTTTGGTGTTG
252 ATTCGGAAAAAATAGGA-AAACCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGG-CTTG
1962 AATTATATATT
315 AATTATATATT
* * * * *
1973 TTTTATGAGTATCGTGTCCAAAAATTTACGAAAATTCTATCGGTTAAAATTTCT-CAAATTTTTA
1 TTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTATCGGTT-AAATTTTTGCAAAATTTTA
* * *
2037 GCCAAAATCATGTAC-CATTACAGTTTTGGGCTAAAAACACGTTCTAGG-GCCAGACTCAGTTTT
65 GCCGAAATCATGTACACATCACAGTTTTTGGCTAAAAACACGTT-TAGGAGCCAG-CTCAGTTTT
2100 ACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTATACATTTAACCAAATCTCATCCACAT
128 ACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTATA-ATTTAACCAAATCTCATCCACAT
* ** * ** * * ***
2165 CGGGCTTAAGGATTTGGTTTTACGAGCATCAAAATCCAGTTTCGATTTTAGTTAGTTTTTAATTC
192 TGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTTCGA-TTCAATTAGAAATTAATTC
* *
2230 GGAAAAAATAGGAAATCCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCATGAAATTA
256 GGAAAAAATAGGAAAACCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCTTG-AATTA
2295 TATATT
320 TATATT
* * * *
2301 TTTTATGAGTATCGTGGCCCAAAATTGAGGAAAATTCTTTTGGGTAAATTTTTGCAAAATTTTAG
1 TTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTATCGGTTAAATTTTTGCAAAATTTTAG
* * * ** *
2366 CCGAAATCGTGTACAAACTATAAC-GATTTTTGACTAAAAACAC-TTTCTGAGGCTTAGCCTCAG
66 CCGAAATCATGTAC--AC-ATCACAG-TTTTTGGCTAAAAACACGTTTAGGA-GC-CAG-CTCAG
* * * * * *
2429 TTTTGCATAATTTTTGGAGTCAAGACTCCTTGAAATATATATATATATATATATCTAATCAAATC
124 TTTTACATGATTTTTGGCGCCAAGACTCCTTG-AA-ATATCT-T-TATA-AT-T-TAACCAAATC
* * * ** *
2494 TCATCCAAATTGGATTCAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
182 TCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTTCGATTCAATTAGA
* * * * *
2559 AATTAATTCGGGCAAAAAAAAAAGACAGGAAACACAATATTAGAAGCGTGAAAATCCCTTCAATC
247 AATTAATTC-GG---AAAAAATAG---GAAAAC-CGATATTAGAAGCGTGAAAAGCCTTTCAATC
* *
2624 TTTTTGATG-TTGAATTTAAATATA
304 TTTTTG--GCTTGAA-TTATATATT
* * * * * * *
2648 ATTTATGAGAATTGTGGCTAAAAATTGAGGGAGAAACT-TA-CGGTTAATTTTTTGCAAAAATTT
1 TTTTATGAGTATCGTGGCCAAAAATTGA-GGA-AAATTCTATCGGTTAAATTTTTGCAAAATTTT
* * * * * *
2711 AGCCGAAATCATGTACTAACATCACGGTGTTTGGCAAAAAACGCG-TTACGGAGCCCTGGCTCTG
64 AGCCGAAATCATGTAC--ACATCACAGTTTTTGGCTAAAAACACGTTTA-GGAG-CC-AGCTCAG
* * * * *
2775 TTTTACATGATTTGTGGTGCAAAGA--CC---------C---AT-A--TAACGAAATCTCAGCCA
124 TTTTACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTATAATTTAACCAAATCTCATCCA
** * * *
2823 CATTGGATTTTGGGATTTGTTTTTAGGAGCATCTCAATCCGGTTTCGATTCAAATAGAAATTAAT
189 CATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTTCGATTCAATTAGAAATTAAT
* ** * * *
2888 TCGG-AAAAATGGGAAAACAAATATTAGAAGCTTGAACAA-TCTTTCAATCTTTTTGGTGTTGAA
254 TCGGAAAAAATAGGAAAACCGATATTAGAAGCGTGAA-AAGCCTTTCAATCTTTTTGG-CTTGAA
2951 TTATATATT
317 TTATATATT
** *
2960 TTTTATGAGTATCGTGGCCAAAAATTGTTGAAAATTCTATCAGG-TCAATTTTTGC-AAATTTTC
1 TTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTATC-GGTTAAATTTTTGCAAAATTTT-
* ** * *
3023 AGCCGAAATCGTGTACGTTATCACAGTTTTTGGCTAAAAACACGTTTCGGAACCCATGCTCAGTT
64 AGCCGAAATCATGTAC-ACATCACAGTTTTTGGCTAAAAACACGTTTAGG-AGCCA-GCTCAGTT
* * ** * * * *
3088 TTGCATGATTTTTGACGTTAAGACTCCTTGAAATATCTATATAAATCTAATCAAATTTCATCCAC
126 TTACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTAT-AATTTAACCAAATCTCATCCAC
* *
3153 ATTGGATTTAAGGATTT-TTTTTATGAGCATCTCAAT-CAGGTTTAGATTTC-ATTAGAAATTAA
190 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCA-GTTTCGA-TTCAATTAGAAATTAA
* * * * *
3215 TTCGG-AAAAATACGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAG
253 TTCGGAAAAAATAGGAAAACCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGC-TTGAA
3279 TTATATATT
317 TTATATATT
* * * *
3288 TTTTATGAGTATTGCGGCCAAAAATTGAGGAGAAATGT-T-TCGGGTAAATTTTCGC-AAA---T
1 TTTTATGAGTATCGTGGCCAAAAATTGAGGA-AAAT-TCTATCGGTTAAATTTTTGCAAAATTTT
* * * * *
3347 A--C----T-A---AC-CATCA-AGATTTTT-GCTAAAAACGCG-TTACGGGGCCCTGGTTTAGT
64 AGCCGAAATCATGTACACATCACAG-TTTTTGGCTAAAAACACGTTTA-GGAG-CC-AGCTCAGT
* * * * * * *
3398 TTTGCATGAATTTTGGCGCCATGACTCATTGAAATAT-TTATATTTATCTAATCAAATCTCATCC
125 TTTACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTT-TA-TAATTTAACCAAATCTCATCC
* * ** *
3462 AAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
188 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTTCGATTCAATTAGAAATTAA
* * * *
3527 TTCGGACAAAAAAAAAACAGG-AAACACAATATTAGAAGCGTGAAAATCCCTTCAATCTTTTTGA
253 TTCGG------AAAAAATAGGAAAAC-CGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTG-
* *
3591 TG-TTGAATTTAAATATA
310 -GCTTGAA-TTATATATT
* * * * * * *
3608 ATTTATGAGAATTGTGGCTAAAAATTGAGGGAGAAACT-TA-CGGTTAATTTTTTGCAAAAATTT
1 TTTTATGAGTATCGTGGCCAAAAATTGA-GGA-AAATTCTATCGGTTAAATTTTTGCAAAATTTT
* * * * *
3671 AGCCGAAATCATGTACTAACCATCACGGTGTTTGGC-CAAAA-ATGTGTTACGGAGCCCTGGCTC
64 AGCCGAAATCATGTAC--A-CATCACAGTTTTTGGCTAAAAACACGT-TTA-GGAG-CC-AGCTC
* * * * *
3734 TGTTTTACATGATTTTTGGTGCAAAGA--CC---------C---AT-A--TAACGAAATCTCAGC
122 AGTTTTACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTATAATTTAACCAAATCTCATC
** * * *
3782 CACATTGGATTTTGGGATTTGTTTTTAGGAGCATCTCAATCCGGTTTCGATTCAAATAGAAATTA
187 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTTCGATTCAATTAGAAATTA
* ** * * *
3847 ATTCGG-AAAAATGGGAAAACAAATATTAGAAGCTTGAACAA-TCTTTCAATCTTTTTGGTGTTG
252 ATTCGGAAAAAATAGGAAAACCGATATTAGAAGCGTGAA-AAGCCTTTCAATCTTTTTGG-CTTG
3910 AATTATATATT
315 AATTATATATT
**
3921 TTTTATGAGTATCGTGGCCAAAAATTGTTGAAAATTCTATC
1 TTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTATC
3962 AGGTCAAAAA
Statistics
Matches: 1815, Mismatches: 342, Indels: 323
0.73 0.14 0.13
Matches are distributed among these distances:
310 7 0.00
311 157 0.09
312 113 0.06
313 70 0.04
314 51 0.03
315 6 0.00
316 2 0.00
317 59 0.03
318 4 0.00
319 49 0.03
320 47 0.03
321 101 0.06
322 210 0.12
323 113 0.06
324 18 0.01
325 43 0.02
326 28 0.02
327 47 0.03
328 267 0.15
329 41 0.02
330 4 0.00
331 5 0.00
332 21 0.01
333 35 0.02
334 4 0.00
335 5 0.00
336 1 0.00
337 8 0.00
338 29 0.02
339 94 0.05
342 8 0.00
344 2 0.00
345 4 0.00
346 79 0.04
347 74 0.04
348 5 0.00
349 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (325 bp):
TTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTATCGGTTAAATTTTTGCAAAATTTTAG
CCGAAATCATGTACACATCACAGTTTTTGGCTAAAAACACGTTTAGGAGCCAGCTCAGTTTTACA
TGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTATAATTTAACCAAATCTCATCCACATTGGA
TTTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTTCGATTCAATTAGAAATTAATTCGGAAA
AAATAGGAAAACCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCTTGAATTATATATT
Done.