Multiple sequence alignment - TraesCS6A01G296400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G296400 chr6A 100.000 2598 0 0 1 2598 530044818 530047415 0.000000e+00 4798
1 TraesCS6A01G296400 chr6D 88.402 2647 148 61 10 2598 385559048 385561593 0.000000e+00 3040
2 TraesCS6A01G296400 chr6B 91.537 1477 61 22 643 2099 575637975 575639407 0.000000e+00 1977
3 TraesCS6A01G296400 chr6B 87.348 656 53 19 9 648 575637147 575637788 0.000000e+00 725
4 TraesCS6A01G296400 chr6B 90.097 414 19 8 2191 2598 575639429 575639826 3.830000e-143 518
5 TraesCS6A01G296400 chr7D 83.544 395 37 16 1015 1398 164534946 164534569 6.880000e-91 344
6 TraesCS6A01G296400 chr7A 83.291 395 38 15 1015 1398 165936823 165937200 3.200000e-89 339
7 TraesCS6A01G296400 chr7B 81.818 396 46 13 1013 1398 126833771 126833392 2.510000e-80 309


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G296400 chr6A 530044818 530047415 2597 False 4798.000000 4798 100.000000 1 2598 1 chr6A.!!$F1 2597
1 TraesCS6A01G296400 chr6D 385559048 385561593 2545 False 3040.000000 3040 88.402000 10 2598 1 chr6D.!!$F1 2588
2 TraesCS6A01G296400 chr6B 575637147 575639826 2679 False 1073.333333 1977 89.660667 9 2598 3 chr6B.!!$F1 2589

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
974 1204 0.595095 AACGAAACGAGCGTCTAGGT 59.405 50.0 0.0 0.0 41.75 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2211 0.584396 TGAACATGTTCGTTCGGCAC 59.416 50.0 28.55 7.51 46.77 5.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.801716 GCCCAACAGTATTAATCTTATGTCA 57.198 36.000 0.00 0.00 0.00 3.58
27 28 9.046296 CCCAACAGTATTAATCTTATGTCAGAC 57.954 37.037 0.00 0.00 0.00 3.51
211 214 3.495434 ACGGTTATGTGTTTTCCTCCA 57.505 42.857 0.00 0.00 0.00 3.86
217 220 5.461526 GTTATGTGTTTTCCTCCAAGAAGC 58.538 41.667 0.00 0.00 0.00 3.86
243 248 3.677190 TCCCTTATTTGTGTGGTAACCG 58.323 45.455 0.00 0.00 0.00 4.44
268 278 1.514087 CACATTGCTCACCCCATGC 59.486 57.895 0.00 0.00 0.00 4.06
269 279 1.683365 ACATTGCTCACCCCATGCC 60.683 57.895 0.00 0.00 0.00 4.40
270 280 2.042639 ATTGCTCACCCCATGCCC 60.043 61.111 0.00 0.00 0.00 5.36
271 281 2.933617 ATTGCTCACCCCATGCCCA 61.934 57.895 0.00 0.00 0.00 5.36
272 282 2.246513 ATTGCTCACCCCATGCCCAT 62.247 55.000 0.00 0.00 0.00 4.00
273 283 2.836360 GCTCACCCCATGCCCATG 60.836 66.667 1.28 1.28 38.51 3.66
296 306 6.690530 TGGAAAGCTTTCATTAACAGAATGG 58.309 36.000 33.88 0.96 38.72 3.16
302 312 7.168219 AGCTTTCATTAACAGAATGGTGTAGA 58.832 34.615 8.39 0.00 35.42 2.59
303 313 7.665559 AGCTTTCATTAACAGAATGGTGTAGAA 59.334 33.333 8.39 0.00 35.42 2.10
304 314 7.965107 GCTTTCATTAACAGAATGGTGTAGAAG 59.035 37.037 0.00 0.00 35.42 2.85
349 359 1.204113 AACTCCTCCCAGCCTCCAAG 61.204 60.000 0.00 0.00 0.00 3.61
371 381 5.971763 AGGTTGAAAATAGTGCACACAAAA 58.028 33.333 21.04 0.97 0.00 2.44
395 405 6.554334 TTTTCCTATGTTGCAAGTAGACAC 57.446 37.500 16.56 0.00 0.00 3.67
396 406 4.202245 TCCTATGTTGCAAGTAGACACC 57.798 45.455 16.56 0.00 0.00 4.16
452 462 9.352784 CTATAGAAAATCCAAAATGACGCAAAA 57.647 29.630 0.00 0.00 0.00 2.44
492 503 3.677121 CGATCTAGCACTGCAATATGACC 59.323 47.826 3.30 0.00 0.00 4.02
493 504 3.097877 TCTAGCACTGCAATATGACCG 57.902 47.619 3.30 0.00 0.00 4.79
502 513 1.869767 GCAATATGACCGGAGAGCAAG 59.130 52.381 9.46 0.00 0.00 4.01
503 514 2.743183 GCAATATGACCGGAGAGCAAGT 60.743 50.000 9.46 0.00 0.00 3.16
504 515 2.868583 CAATATGACCGGAGAGCAAGTG 59.131 50.000 9.46 0.00 0.00 3.16
548 562 4.670765 AGACCAGCTCAAATTTCCTTCAT 58.329 39.130 0.00 0.00 0.00 2.57
549 563 5.819991 AGACCAGCTCAAATTTCCTTCATA 58.180 37.500 0.00 0.00 0.00 2.15
550 564 5.649831 AGACCAGCTCAAATTTCCTTCATAC 59.350 40.000 0.00 0.00 0.00 2.39
551 565 5.324409 ACCAGCTCAAATTTCCTTCATACA 58.676 37.500 0.00 0.00 0.00 2.29
553 567 5.416952 CCAGCTCAAATTTCCTTCATACAGT 59.583 40.000 0.00 0.00 0.00 3.55
555 569 7.414540 CCAGCTCAAATTTCCTTCATACAGTAC 60.415 40.741 0.00 0.00 0.00 2.73
556 570 6.599638 AGCTCAAATTTCCTTCATACAGTACC 59.400 38.462 0.00 0.00 0.00 3.34
569 594 5.886474 TCATACAGTACCACAGAAGGAGTAG 59.114 44.000 0.00 0.00 0.00 2.57
579 604 5.163258 CCACAGAAGGAGTAGCTAATTCCAT 60.163 44.000 21.50 13.38 33.32 3.41
603 628 1.529418 GCGAAACAAAACGACCGTTCA 60.529 47.619 8.30 0.00 37.35 3.18
604 629 2.359598 CGAAACAAAACGACCGTTCAG 58.640 47.619 8.30 6.79 37.35 3.02
606 631 2.027003 AACAAAACGACCGTTCAGGA 57.973 45.000 8.30 0.00 45.00 3.86
617 642 3.881089 GACCGTTCAGGAAGGAAAGAAAA 59.119 43.478 3.46 0.00 45.00 2.29
652 677 1.742768 CTGTGCTCGGATCCTACCC 59.257 63.158 10.75 0.00 0.00 3.69
671 887 4.003788 CCCCTGTCCGTGAACGCT 62.004 66.667 0.00 0.00 38.18 5.07
788 1006 4.447342 CCCATGCTCCACCCCCAC 62.447 72.222 0.00 0.00 0.00 4.61
948 1178 4.040706 AGCATCCATCTCTCATCTTCTTCC 59.959 45.833 0.00 0.00 0.00 3.46
973 1203 0.982673 CAACGAAACGAGCGTCTAGG 59.017 55.000 0.00 0.00 41.75 3.02
974 1204 0.595095 AACGAAACGAGCGTCTAGGT 59.405 50.000 0.00 0.00 41.75 3.08
975 1205 0.595095 ACGAAACGAGCGTCTAGGTT 59.405 50.000 0.00 0.00 37.42 3.50
976 1206 1.806542 ACGAAACGAGCGTCTAGGTTA 59.193 47.619 0.00 0.00 37.42 2.85
996 1227 5.234543 GGTTAACAGCTAGCTAAAGATTCGG 59.765 44.000 18.86 4.01 0.00 4.30
1429 1661 2.109834 TCTTGCCCCCTTCATTTCTTGA 59.890 45.455 0.00 0.00 0.00 3.02
1430 1662 1.923356 TGCCCCCTTCATTTCTTGAC 58.077 50.000 0.00 0.00 32.84 3.18
1433 1665 1.533625 CCCCTTCATTTCTTGACGCA 58.466 50.000 0.00 0.00 32.84 5.24
1434 1666 1.470098 CCCCTTCATTTCTTGACGCAG 59.530 52.381 0.00 0.00 32.84 5.18
1462 1694 2.507407 TAGGAACCAAGAACATGCCC 57.493 50.000 0.00 0.00 0.00 5.36
1679 1919 4.681978 GGGAGCGAGCACCAACGT 62.682 66.667 13.20 0.00 0.00 3.99
1680 1920 3.112709 GGAGCGAGCACCAACGTC 61.113 66.667 6.67 0.00 0.00 4.34
1681 1921 3.112709 GAGCGAGCACCAACGTCC 61.113 66.667 0.00 0.00 0.00 4.79
1823 2065 2.111878 GGGCTGGGATCCACGATG 59.888 66.667 15.23 0.00 0.00 3.84
1824 2066 2.111878 GGCTGGGATCCACGATGG 59.888 66.667 15.23 0.00 39.43 3.51
1825 2067 2.592861 GCTGGGATCCACGATGGC 60.593 66.667 15.23 4.23 37.47 4.40
1826 2068 2.910360 CTGGGATCCACGATGGCA 59.090 61.111 15.23 0.00 37.47 4.92
1827 2069 1.524621 CTGGGATCCACGATGGCAC 60.525 63.158 15.23 0.00 37.47 5.01
1828 2070 2.588877 GGGATCCACGATGGCACG 60.589 66.667 15.23 7.71 37.47 5.34
1829 2071 3.272334 GGATCCACGATGGCACGC 61.272 66.667 6.95 0.00 37.47 5.34
1830 2072 3.630148 GATCCACGATGGCACGCG 61.630 66.667 3.53 3.53 37.47 6.01
1864 2106 1.585006 GTCGACGCTTTCCTGAGGA 59.415 57.895 0.00 0.00 0.00 3.71
1866 2108 1.153745 CGACGCTTTCCTGAGGAGG 60.154 63.158 0.00 0.00 41.39 4.30
1867 2109 1.448717 GACGCTTTCCTGAGGAGGC 60.449 63.158 15.40 15.40 39.57 4.70
1869 2111 2.821810 GCTTTCCTGAGGAGGCGC 60.822 66.667 11.56 0.00 39.57 6.53
1870 2112 2.665000 CTTTCCTGAGGAGGCGCA 59.335 61.111 10.83 0.00 39.57 6.09
1871 2113 1.449246 CTTTCCTGAGGAGGCGCAG 60.449 63.158 10.83 0.00 39.57 5.18
1872 2114 1.892819 CTTTCCTGAGGAGGCGCAGA 61.893 60.000 10.83 0.00 39.57 4.26
1881 2126 4.406173 AGGCGCAGAGTCGTCGTG 62.406 66.667 10.83 0.00 39.34 4.35
1932 2177 4.098654 AGAAATGTGTGAGGTAGAGATCGG 59.901 45.833 0.00 0.00 0.00 4.18
1953 2198 2.557372 GCGAACGGGGCAGGAAAAA 61.557 57.895 0.00 0.00 0.00 1.94
1981 2236 0.531974 ACAGTGCCGAACGAACATGT 60.532 50.000 0.00 0.00 0.00 3.21
2050 2307 8.776680 ATTGTAAATTAAATTAAGTAGCCGCG 57.223 30.769 0.00 0.00 0.00 6.46
2067 2324 2.243957 CGTCTTTGTGGCACGCTCA 61.244 57.895 13.77 0.00 40.97 4.26
2078 2335 2.492881 TGGCACGCTCAATCAATCAAAT 59.507 40.909 0.00 0.00 0.00 2.32
2082 2339 4.348656 CACGCTCAATCAATCAAATGAGG 58.651 43.478 4.06 0.00 39.69 3.86
2087 2344 6.292757 CGCTCAATCAATCAAATGAGGACTAG 60.293 42.308 4.06 0.00 39.69 2.57
2090 2347 9.605275 CTCAATCAATCAAATGAGGACTAGTAA 57.395 33.333 0.00 0.00 36.50 2.24
2104 2361 9.964354 TGAGGACTAGTAATACTTACTGTACAA 57.036 33.333 0.00 0.00 45.58 2.41
2111 2368 8.517062 AGTAATACTTACTGTACAATCTCCGT 57.483 34.615 0.00 0.00 44.43 4.69
2112 2369 8.619546 AGTAATACTTACTGTACAATCTCCGTC 58.380 37.037 0.00 0.00 44.43 4.79
2113 2370 7.642082 AATACTTACTGTACAATCTCCGTCT 57.358 36.000 0.00 0.00 33.45 4.18
2114 2371 5.312120 ACTTACTGTACAATCTCCGTCTG 57.688 43.478 0.00 0.00 0.00 3.51
2121 2378 5.657474 TGTACAATCTCCGTCTGGAATTAC 58.343 41.667 0.00 0.00 45.87 1.89
2139 2396 0.603569 ACCTGTCGTCGAAATGAGCT 59.396 50.000 0.00 0.00 0.00 4.09
2146 2403 2.097629 TCGTCGAAATGAGCTAGTGGAG 59.902 50.000 0.00 0.00 0.00 3.86
2156 2413 6.892658 ATGAGCTAGTGGAGTACTATTCTG 57.107 41.667 0.00 0.00 40.94 3.02
2157 2414 5.756918 TGAGCTAGTGGAGTACTATTCTGT 58.243 41.667 0.00 0.00 40.94 3.41
2165 2422 4.219944 TGGAGTACTATTCTGTCACCACAC 59.780 45.833 0.00 0.00 0.00 3.82
2167 2424 5.279306 GGAGTACTATTCTGTCACCACACAA 60.279 44.000 0.00 0.00 0.00 3.33
2168 2425 6.169557 AGTACTATTCTGTCACCACACAAA 57.830 37.500 0.00 0.00 0.00 2.83
2169 2426 6.769512 AGTACTATTCTGTCACCACACAAAT 58.230 36.000 0.00 0.00 0.00 2.32
2170 2427 7.224297 AGTACTATTCTGTCACCACACAAATT 58.776 34.615 0.00 0.00 0.00 1.82
2171 2428 6.560253 ACTATTCTGTCACCACACAAATTC 57.440 37.500 0.00 0.00 0.00 2.17
2173 2430 3.576078 TCTGTCACCACACAAATTCCT 57.424 42.857 0.00 0.00 0.00 3.36
2186 2443 7.401080 CACACAAATTCCTGCAAAAGTAAAAG 58.599 34.615 0.00 0.00 0.00 2.27
2223 2482 6.480320 ACCGCTATATCTGTTTGATCAGAAAC 59.520 38.462 3.71 3.71 45.65 2.78
2254 2518 2.350522 CACGCCATTAGACTTGCTCTT 58.649 47.619 0.00 0.00 0.00 2.85
2271 2539 2.349590 TCTTGGACAGCAACATCGATG 58.650 47.619 23.68 23.68 0.00 3.84
2299 2567 2.303676 CGCTAATTCCTCTCCGCGC 61.304 63.158 0.00 0.00 34.05 6.86
2350 2618 2.236223 CTGTCCTGTCCTGCTGCGAT 62.236 60.000 0.00 0.00 0.00 4.58
2386 2654 1.860950 CATTATCACCGCAACCGAGAG 59.139 52.381 0.00 0.00 36.29 3.20
2387 2655 1.179152 TTATCACCGCAACCGAGAGA 58.821 50.000 0.00 0.00 36.29 3.10
2388 2656 0.738975 TATCACCGCAACCGAGAGAG 59.261 55.000 0.00 0.00 36.29 3.20
2389 2657 0.965866 ATCACCGCAACCGAGAGAGA 60.966 55.000 0.00 0.00 36.29 3.10
2390 2658 1.176619 TCACCGCAACCGAGAGAGAA 61.177 55.000 0.00 0.00 36.29 2.87
2391 2659 0.319555 CACCGCAACCGAGAGAGAAA 60.320 55.000 0.00 0.00 36.29 2.52
2392 2660 0.038159 ACCGCAACCGAGAGAGAAAG 60.038 55.000 0.00 0.00 36.29 2.62
2393 2661 1.355066 CCGCAACCGAGAGAGAAAGC 61.355 60.000 0.00 0.00 36.29 3.51
2394 2662 0.389166 CGCAACCGAGAGAGAAAGCT 60.389 55.000 0.00 0.00 36.29 3.74
2400 2668 2.563179 ACCGAGAGAGAAAGCTAAGCAA 59.437 45.455 0.00 0.00 0.00 3.91
2457 2731 1.521450 CGAGTGGAGTACGTGGTGGT 61.521 60.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.715249 TCTGACATAAGATTAATACTGTTGGGC 59.285 37.037 0.00 0.00 0.00 5.36
1 2 9.046296 GTCTGACATAAGATTAATACTGTTGGG 57.954 37.037 2.24 0.00 0.00 4.12
2 3 9.823647 AGTCTGACATAAGATTAATACTGTTGG 57.176 33.333 10.88 0.00 0.00 3.77
126 128 4.020307 AGTTTTGCCCCAAATCGAATGATT 60.020 37.500 3.34 0.00 46.75 2.57
142 144 4.702831 TGGAAAAGGGAAATGAGTTTTGC 58.297 39.130 0.00 0.00 35.09 3.68
184 186 4.806775 GGAAAACACATAACCGTTTTTGCT 59.193 37.500 0.00 0.00 43.46 3.91
185 187 4.806775 AGGAAAACACATAACCGTTTTTGC 59.193 37.500 0.00 0.00 43.46 3.68
186 188 5.460748 GGAGGAAAACACATAACCGTTTTTG 59.539 40.000 0.00 0.00 43.46 2.44
187 189 5.127356 TGGAGGAAAACACATAACCGTTTTT 59.873 36.000 0.00 0.00 43.46 1.94
211 214 5.944007 ACACAAATAAGGGATAACGCTTCTT 59.056 36.000 5.55 0.56 45.64 2.52
217 220 6.183360 GGTTACCACACAAATAAGGGATAACG 60.183 42.308 0.00 0.00 0.00 3.18
243 248 1.373570 GGTGAGCAATGTGGAGCTAC 58.626 55.000 0.00 0.00 42.04 3.58
268 278 5.185635 TCTGTTAATGAAAGCTTTCCATGGG 59.814 40.000 31.14 17.07 36.36 4.00
269 279 6.271488 TCTGTTAATGAAAGCTTTCCATGG 57.729 37.500 31.14 4.97 36.36 3.66
270 280 7.277098 CCATTCTGTTAATGAAAGCTTTCCATG 59.723 37.037 31.14 17.50 36.36 3.66
271 281 7.038799 ACCATTCTGTTAATGAAAGCTTTCCAT 60.039 33.333 31.14 22.83 36.36 3.41
272 282 6.267471 ACCATTCTGTTAATGAAAGCTTTCCA 59.733 34.615 31.14 21.27 36.36 3.53
273 283 6.587608 CACCATTCTGTTAATGAAAGCTTTCC 59.412 38.462 31.14 18.25 36.36 3.13
274 284 7.147976 ACACCATTCTGTTAATGAAAGCTTTC 58.852 34.615 28.61 28.61 37.69 2.62
275 285 7.054491 ACACCATTCTGTTAATGAAAGCTTT 57.946 32.000 12.53 12.53 0.00 3.51
296 306 3.185797 CCACGTGGCTTTTACTTCTACAC 59.814 47.826 24.02 0.00 0.00 2.90
302 312 4.010667 TCATACCACGTGGCTTTTACTT 57.989 40.909 34.26 14.75 39.32 2.24
303 313 3.688694 TCATACCACGTGGCTTTTACT 57.311 42.857 34.26 15.54 39.32 2.24
304 314 3.423907 CGTTCATACCACGTGGCTTTTAC 60.424 47.826 34.26 23.37 39.32 2.01
349 359 6.843069 ATTTTGTGTGCACTATTTTCAACC 57.157 33.333 19.41 0.00 0.00 3.77
371 381 6.151144 GGTGTCTACTTGCAACATAGGAAAAT 59.849 38.462 11.38 0.00 0.00 1.82
395 405 4.144297 TGTGAAAGGAAAGACAAGATGGG 58.856 43.478 0.00 0.00 0.00 4.00
396 406 5.300286 ACTTGTGAAAGGAAAGACAAGATGG 59.700 40.000 15.64 0.00 45.38 3.51
431 441 8.559222 AAATTTTTGCGTCATTTTGGATTTTC 57.441 26.923 0.00 0.00 0.00 2.29
432 442 7.647318 GGAAATTTTTGCGTCATTTTGGATTTT 59.353 29.630 0.00 0.00 0.00 1.82
439 449 5.509771 GCAAGGAAATTTTTGCGTCATTTT 58.490 33.333 10.87 0.00 40.09 1.82
441 451 4.730600 GCAAGGAAATTTTTGCGTCATT 57.269 36.364 10.87 0.00 40.09 2.57
464 474 0.864455 GCAGTGCTAGATCGCAATCC 59.136 55.000 8.18 0.00 42.32 3.01
492 503 3.381908 AGAGTAATACCACTTGCTCTCCG 59.618 47.826 0.00 0.00 42.32 4.63
493 504 6.265649 TCATAGAGTAATACCACTTGCTCTCC 59.734 42.308 7.54 0.00 42.32 3.71
502 513 9.886132 TCTTTTCCTTTCATAGAGTAATACCAC 57.114 33.333 0.00 0.00 0.00 4.16
503 514 9.886132 GTCTTTTCCTTTCATAGAGTAATACCA 57.114 33.333 0.00 0.00 0.00 3.25
504 515 9.327628 GGTCTTTTCCTTTCATAGAGTAATACC 57.672 37.037 0.00 0.00 0.00 2.73
548 562 4.015084 GCTACTCCTTCTGTGGTACTGTA 58.985 47.826 0.00 0.00 0.00 2.74
549 563 2.826725 GCTACTCCTTCTGTGGTACTGT 59.173 50.000 0.00 0.00 0.00 3.55
550 564 3.093057 AGCTACTCCTTCTGTGGTACTG 58.907 50.000 0.00 0.00 0.00 2.74
551 565 3.459710 AGCTACTCCTTCTGTGGTACT 57.540 47.619 0.00 0.00 0.00 2.73
553 567 5.363005 GGAATTAGCTACTCCTTCTGTGGTA 59.637 44.000 12.15 0.00 0.00 3.25
555 569 4.162320 TGGAATTAGCTACTCCTTCTGTGG 59.838 45.833 17.92 0.00 0.00 4.17
556 570 5.344743 TGGAATTAGCTACTCCTTCTGTG 57.655 43.478 17.92 0.00 0.00 3.66
569 594 2.159393 TGTTTCGCTGCATGGAATTAGC 60.159 45.455 0.00 0.00 32.30 3.09
579 604 0.248296 GGTCGTTTTGTTTCGCTGCA 60.248 50.000 0.00 0.00 0.00 4.41
603 628 5.871396 GGTTTTCCTTTTCTTTCCTTCCT 57.129 39.130 0.00 0.00 36.94 3.36
652 677 2.261671 CGTTCACGGACAGGGGAG 59.738 66.667 0.00 0.00 35.37 4.30
671 887 4.175337 GAGGTAGGGCATGGCGCA 62.175 66.667 10.83 0.00 44.06 6.09
738 954 4.918201 AGATTAGCTGGGCGCGGC 62.918 66.667 26.39 26.39 45.59 6.53
785 1003 1.078001 GGTCGTAACATGGGGGTGG 60.078 63.158 0.00 0.00 0.00 4.61
788 1006 1.411612 GAGTAGGTCGTAACATGGGGG 59.588 57.143 0.00 0.00 0.00 5.40
948 1178 0.449507 CGCTCGTTTCGTTGCAAGAG 60.450 55.000 0.00 2.78 0.00 2.85
973 1203 6.019720 GTCCGAATCTTTAGCTAGCTGTTAAC 60.020 42.308 27.68 10.96 0.00 2.01
974 1204 6.040878 GTCCGAATCTTTAGCTAGCTGTTAA 58.959 40.000 27.68 16.25 0.00 2.01
975 1205 5.589192 GTCCGAATCTTTAGCTAGCTGTTA 58.411 41.667 27.68 9.61 0.00 2.41
976 1206 4.434520 GTCCGAATCTTTAGCTAGCTGTT 58.565 43.478 27.68 13.14 0.00 3.16
1257 1488 1.817099 GAGCACCTTGCCCATCTCG 60.817 63.158 0.00 0.00 46.52 4.04
1401 1632 1.228675 AAGGGGGCAAGAAGCTGTG 60.229 57.895 0.00 0.00 44.79 3.66
1429 1661 3.244422 TGGTTCCTAATTTGACTCTGCGT 60.244 43.478 0.00 0.00 0.00 5.24
1430 1662 3.334691 TGGTTCCTAATTTGACTCTGCG 58.665 45.455 0.00 0.00 0.00 5.18
1433 1665 6.601332 TGTTCTTGGTTCCTAATTTGACTCT 58.399 36.000 0.00 0.00 0.00 3.24
1434 1666 6.877611 TGTTCTTGGTTCCTAATTTGACTC 57.122 37.500 0.00 0.00 0.00 3.36
1448 1680 3.421844 GTTTAGAGGGCATGTTCTTGGT 58.578 45.455 0.00 0.00 0.00 3.67
1462 1694 5.347635 TCAATCGGAAATCACACGTTTAGAG 59.652 40.000 0.00 0.00 0.00 2.43
1808 2050 2.592861 GCCATCGTGGATCCCAGC 60.593 66.667 9.90 0.00 40.96 4.85
1864 2106 4.406173 CACGACGACTCTGCGCCT 62.406 66.667 4.18 0.00 33.86 5.52
1881 2126 2.027460 CCATTATTTGCCGCGCCC 59.973 61.111 0.00 0.00 0.00 6.13
1883 2128 2.027460 CCCCATTATTTGCCGCGC 59.973 61.111 0.00 0.00 0.00 6.86
1932 2177 3.894547 TTCCTGCCCCGTTCGCTTC 62.895 63.158 0.00 0.00 0.00 3.86
1953 2198 2.540769 CGTTCGGCACTGTTTTGTCATT 60.541 45.455 0.00 0.00 0.00 2.57
1954 2199 1.002900 CGTTCGGCACTGTTTTGTCAT 60.003 47.619 0.00 0.00 0.00 3.06
1965 2211 0.584396 TGAACATGTTCGTTCGGCAC 59.416 50.000 28.55 7.51 46.77 5.01
1981 2236 5.639506 CAGAGCCTAAAGAAAGAATCGTGAA 59.360 40.000 0.00 0.00 0.00 3.18
2037 2292 2.671396 CACAAAGACGCGGCTACTTAAT 59.329 45.455 18.71 0.00 0.00 1.40
2050 2307 0.593128 ATTGAGCGTGCCACAAAGAC 59.407 50.000 0.00 0.00 0.00 3.01
2090 2347 6.039493 CCAGACGGAGATTGTACAGTAAGTAT 59.961 42.308 0.00 0.00 34.67 2.12
2095 2352 3.959293 TCCAGACGGAGATTGTACAGTA 58.041 45.455 0.00 0.00 35.91 2.74
2096 2353 2.803956 TCCAGACGGAGATTGTACAGT 58.196 47.619 0.00 0.00 35.91 3.55
2097 2354 3.868757 TTCCAGACGGAGATTGTACAG 57.131 47.619 0.00 0.00 44.10 2.74
2098 2355 4.819105 AATTCCAGACGGAGATTGTACA 57.181 40.909 0.00 0.00 44.10 2.90
2099 2356 5.048507 GGTAATTCCAGACGGAGATTGTAC 58.951 45.833 0.00 0.00 44.10 2.90
2100 2357 4.960469 AGGTAATTCCAGACGGAGATTGTA 59.040 41.667 0.00 0.00 44.10 2.41
2101 2358 3.775316 AGGTAATTCCAGACGGAGATTGT 59.225 43.478 0.00 0.00 44.10 2.71
2102 2359 4.122776 CAGGTAATTCCAGACGGAGATTG 58.877 47.826 0.00 0.00 44.10 2.67
2103 2360 3.775316 ACAGGTAATTCCAGACGGAGATT 59.225 43.478 0.00 0.00 44.10 2.40
2104 2361 3.375699 ACAGGTAATTCCAGACGGAGAT 58.624 45.455 0.00 0.00 44.10 2.75
2105 2362 2.758979 GACAGGTAATTCCAGACGGAGA 59.241 50.000 0.00 0.00 44.10 3.71
2106 2363 2.479730 CGACAGGTAATTCCAGACGGAG 60.480 54.545 0.00 0.00 44.10 4.63
2107 2364 1.475280 CGACAGGTAATTCCAGACGGA 59.525 52.381 0.00 0.00 40.60 4.69
2108 2365 1.203994 ACGACAGGTAATTCCAGACGG 59.796 52.381 12.35 0.00 42.55 4.79
2109 2366 2.527100 GACGACAGGTAATTCCAGACG 58.473 52.381 0.00 8.55 43.42 4.18
2110 2367 2.163010 TCGACGACAGGTAATTCCAGAC 59.837 50.000 0.00 0.00 39.02 3.51
2111 2368 2.439409 TCGACGACAGGTAATTCCAGA 58.561 47.619 0.00 0.00 39.02 3.86
2112 2369 2.933495 TCGACGACAGGTAATTCCAG 57.067 50.000 0.00 0.00 39.02 3.86
2113 2370 3.663995 TTTCGACGACAGGTAATTCCA 57.336 42.857 0.00 0.00 39.02 3.53
2114 2371 4.178540 TCATTTCGACGACAGGTAATTCC 58.821 43.478 0.00 0.00 0.00 3.01
2121 2378 2.159366 ACTAGCTCATTTCGACGACAGG 60.159 50.000 0.00 0.00 0.00 4.00
2139 2396 5.651139 GTGGTGACAGAATAGTACTCCACTA 59.349 44.000 14.26 3.33 44.46 2.74
2146 2403 7.360946 GGAATTTGTGTGGTGACAGAATAGTAC 60.361 40.741 0.00 0.00 44.46 2.73
2156 2413 1.680735 TGCAGGAATTTGTGTGGTGAC 59.319 47.619 0.00 0.00 0.00 3.67
2157 2414 2.064434 TGCAGGAATTTGTGTGGTGA 57.936 45.000 0.00 0.00 0.00 4.02
2214 2473 3.180387 GTGCGCAACTTTTGTTTCTGATC 59.820 43.478 14.00 0.00 41.35 2.92
2223 2482 1.214373 AATGGCGTGCGCAACTTTTG 61.214 50.000 14.00 0.00 44.11 2.44
2254 2518 1.725641 GACATCGATGTTGCTGTCCA 58.274 50.000 30.46 0.00 41.95 4.02
2278 2546 1.491505 GCGGAGAGGAATTAGCGTGC 61.492 60.000 0.00 0.00 0.00 5.34
2286 2554 2.202756 GAACGCGCGGAGAGGAAT 60.203 61.111 35.22 7.19 0.00 3.01
2299 2567 2.874780 CGAGAACGGCCGAGAACG 60.875 66.667 35.90 25.62 36.18 3.95
2350 2618 5.827797 GTGATAATGCAAGGGAATAGGAACA 59.172 40.000 0.00 0.00 0.00 3.18
2386 2654 5.051891 TCAATGCTTTGCTTAGCTTTCTC 57.948 39.130 5.60 0.00 41.76 2.87
2387 2655 5.656213 ATCAATGCTTTGCTTAGCTTTCT 57.344 34.783 5.60 0.86 41.76 2.52
2388 2656 6.034683 CAGAATCAATGCTTTGCTTAGCTTTC 59.965 38.462 5.60 7.16 41.76 2.62
2389 2657 5.867716 CAGAATCAATGCTTTGCTTAGCTTT 59.132 36.000 5.60 8.49 41.76 3.51
2390 2658 5.047519 ACAGAATCAATGCTTTGCTTAGCTT 60.048 36.000 5.60 3.38 41.76 3.74
2391 2659 4.461781 ACAGAATCAATGCTTTGCTTAGCT 59.538 37.500 5.60 0.00 41.76 3.32
2392 2660 4.741342 ACAGAATCAATGCTTTGCTTAGC 58.259 39.130 7.44 0.00 41.59 3.09
2393 2661 5.803967 GGAACAGAATCAATGCTTTGCTTAG 59.196 40.000 7.44 4.03 32.61 2.18
2394 2662 5.619757 CGGAACAGAATCAATGCTTTGCTTA 60.620 40.000 7.44 0.00 32.61 3.09
2400 2668 2.163010 CAGCGGAACAGAATCAATGCTT 59.837 45.455 0.00 0.00 0.00 3.91
2457 2731 0.615331 CCTGTAGCAGCTTCCTTCCA 59.385 55.000 0.00 0.00 0.00 3.53
2486 2765 0.941463 GGACGTGCGAGCATATCCAG 60.941 60.000 19.38 4.66 34.72 3.86
2491 2770 1.153647 CCTTGGACGTGCGAGCATA 60.154 57.895 18.32 0.00 0.00 3.14


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.