Multiple sequence alignment - TraesCS3A01G408000

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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 TraesCS3A01G408000 chr3A 100.000 3948 0 0 1 3948 653240882 653244829 0.000000e+00 7291
1 TraesCS3A01G408000 chr3D 92.861 3306 159 37 1 3275 517274051 517277310 0.000000e+00 4726
2 TraesCS3A01G408000 chr3D 95.264 549 24 1 3400 3948 517278574 517279120 0.000000e+00 869
3 TraesCS3A01G408000 chr3D 93.651 252 12 3 3282 3532 517278324 517278572 1.340000e-99 374
4 TraesCS3A01G408000 chr3B 93.522 2408 107 29 1 2383 681097301 681099684 0.000000e+00 3537
5 TraesCS3A01G408000 chr3B 94.717 1571 66 9 2384 3948 681099770 681101329 0.000000e+00 2425


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 TraesCS3A01G408000 chr3A 653240882 653244829 3947 False 7291.000000 7291 100.000000 1 3948 1 chr3A.!!$F1 3947
1 TraesCS3A01G408000 chr3D 517274051 517279120 5069 False 1989.666667 4726 93.925333 1 3948 3 chr3D.!!$F1 3947
2 TraesCS3A01G408000 chr3B 681097301 681101329 4028 False 2981.000000 3537 94.119500 1 3948 2 chr3B.!!$F1 3947

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
166 168 0.104144 TGTTCAGAGGGGAAGGGGAA 60.104 55.0 0.00 0.00 0.00 3.97 F
1276 1314 0.249120 CTCACCGGTGTGCTCCAATA 59.751 55.0 32.74 10.49 42.46 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1556 1.962822 TGCTTCTCCGCTGTTGCTG 60.963 57.895 0.0 0.0 36.97 4.41 R
3027 3155 0.037232 CCAAGAACTCCTCCGTGGTC 60.037 60.000 0.0 0.0 37.07 4.02 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
45 47 2.689471 TGATTGGTATGTTCATGCCTGC 59.311 45.455 17.80 9.57 0.00 4.85
49 51 1.581934 GTATGTTCATGCCTGCGCTA 58.418 50.000 9.73 0.00 35.36 4.26
67 69 2.306255 TATTTGGGAGGCCTCGTCGC 62.306 60.000 26.36 13.35 0.00 5.19
90 92 3.636153 AGGGTCAAGCTATGGTTCTTC 57.364 47.619 0.00 0.00 0.00 2.87
101 103 2.251371 GTTCTTCGGGTTGCGTGC 59.749 61.111 0.00 0.00 0.00 5.34
142 144 3.845259 GGGTGCCATGCTGCCATG 61.845 66.667 0.00 1.20 46.70 3.66
164 166 0.548510 GATGTTCAGAGGGGAAGGGG 59.451 60.000 0.00 0.00 0.00 4.79
166 168 0.104144 TGTTCAGAGGGGAAGGGGAA 60.104 55.000 0.00 0.00 0.00 3.97
253 259 9.790344 CCTCTGATAAGAATGAATACTTCCAAT 57.210 33.333 0.00 0.00 0.00 3.16
262 268 8.917088 AGAATGAATACTTCCAATATTTGTGGG 58.083 33.333 0.00 0.00 36.73 4.61
268 274 9.500785 AATACTTCCAATATTTGTGGGTTTTTG 57.499 29.630 0.00 0.00 36.73 2.44
270 276 6.765512 ACTTCCAATATTTGTGGGTTTTTGTG 59.234 34.615 0.00 0.00 36.73 3.33
271 277 5.059833 TCCAATATTTGTGGGTTTTTGTGC 58.940 37.500 0.00 0.00 36.73 4.57
272 278 4.818546 CCAATATTTGTGGGTTTTTGTGCA 59.181 37.500 0.00 0.00 32.03 4.57
273 279 5.472820 CCAATATTTGTGGGTTTTTGTGCAT 59.527 36.000 0.00 0.00 32.03 3.96
275 281 3.902881 TTTGTGGGTTTTTGTGCATCT 57.097 38.095 0.00 0.00 0.00 2.90
276 282 3.451141 TTGTGGGTTTTTGTGCATCTC 57.549 42.857 0.00 0.00 0.00 2.75
277 283 2.382882 TGTGGGTTTTTGTGCATCTCA 58.617 42.857 0.00 0.00 0.00 3.27
278 284 2.762887 TGTGGGTTTTTGTGCATCTCAA 59.237 40.909 0.00 0.00 0.00 3.02
279 285 3.196469 TGTGGGTTTTTGTGCATCTCAAA 59.804 39.130 0.00 0.00 33.76 2.69
280 286 4.141756 TGTGGGTTTTTGTGCATCTCAAAT 60.142 37.500 2.22 0.00 35.25 2.32
283 289 5.163322 TGGGTTTTTGTGCATCTCAAATTCT 60.163 36.000 2.22 0.00 35.25 2.40
300 306 8.571461 TCAAATTCTCAATAGATTTGAGCAGT 57.429 30.769 9.87 0.00 44.08 4.40
303 309 9.852091 AAATTCTCAATAGATTTGAGCAGTTTC 57.148 29.630 9.87 0.00 44.08 2.78
322 328 2.100605 CCTGGTTCAGGCTTCAGTAC 57.899 55.000 0.61 0.00 45.13 2.73
323 329 1.625818 CCTGGTTCAGGCTTCAGTACT 59.374 52.381 0.61 0.00 45.13 2.73
346 368 8.860780 ACTTGCAGATTTATCTTCTTCTTTCT 57.139 30.769 0.00 0.00 34.22 2.52
450 473 4.386652 GTCTCCGCGTTTCTTGTGTATTAA 59.613 41.667 4.92 0.00 0.00 1.40
451 474 4.624024 TCTCCGCGTTTCTTGTGTATTAAG 59.376 41.667 4.92 0.00 0.00 1.85
452 475 4.309099 TCCGCGTTTCTTGTGTATTAAGT 58.691 39.130 4.92 0.00 0.00 2.24
453 476 4.386652 TCCGCGTTTCTTGTGTATTAAGTC 59.613 41.667 4.92 0.00 0.00 3.01
454 477 4.387862 CCGCGTTTCTTGTGTATTAAGTCT 59.612 41.667 4.92 0.00 0.00 3.24
455 478 5.107220 CCGCGTTTCTTGTGTATTAAGTCTT 60.107 40.000 4.92 0.00 0.00 3.01
456 479 6.089820 CCGCGTTTCTTGTGTATTAAGTCTTA 59.910 38.462 4.92 0.00 0.00 2.10
457 480 7.359431 CCGCGTTTCTTGTGTATTAAGTCTTAA 60.359 37.037 4.92 7.49 0.00 1.85
458 481 7.473411 CGCGTTTCTTGTGTATTAAGTCTTAAC 59.527 37.037 7.20 0.00 0.00 2.01
459 482 8.277713 GCGTTTCTTGTGTATTAAGTCTTAACA 58.722 33.333 7.20 0.42 0.00 2.41
620 654 1.535015 CGAGCTACTCCACTTGCTAGC 60.535 57.143 8.10 8.10 35.76 3.42
632 666 4.437930 CCACTTGCTAGCTGCTAAATGTTC 60.438 45.833 17.23 0.00 43.37 3.18
669 704 3.191162 TGCAACATGCTGTACAGAATTCC 59.809 43.478 27.08 8.71 45.31 3.01
740 776 7.086230 ACGAGACTATGACCTTAGTTTGTAG 57.914 40.000 0.00 0.00 32.59 2.74
741 777 6.658391 ACGAGACTATGACCTTAGTTTGTAGT 59.342 38.462 0.00 0.00 32.59 2.73
880 918 1.122227 AGAGAGGCTGCTGATCCTTC 58.878 55.000 0.00 0.00 31.71 3.46
902 940 6.061022 TCCTTGTCTTATTGTAGGCATCAA 57.939 37.500 0.00 0.00 28.36 2.57
908 946 8.402798 TGTCTTATTGTAGGCATCAAAGAAAA 57.597 30.769 0.00 0.00 0.00 2.29
910 948 9.860898 GTCTTATTGTAGGCATCAAAGAAAATT 57.139 29.630 0.00 0.00 0.00 1.82
911 949 9.859427 TCTTATTGTAGGCATCAAAGAAAATTG 57.141 29.630 0.00 0.00 0.00 2.32
912 950 6.973229 ATTGTAGGCATCAAAGAAAATTGC 57.027 33.333 0.00 0.00 0.00 3.56
913 951 5.465532 TGTAGGCATCAAAGAAAATTGCA 57.534 34.783 0.00 0.00 35.04 4.08
915 953 6.465948 TGTAGGCATCAAAGAAAATTGCATT 58.534 32.000 0.00 0.00 35.04 3.56
916 954 5.873179 AGGCATCAAAGAAAATTGCATTG 57.127 34.783 0.00 0.00 35.04 2.82
919 957 4.456566 GCATCAAAGAAAATTGCATTGGGT 59.543 37.500 0.00 0.00 33.58 4.51
980 1018 0.465460 TATTTAGCTTGGCAGGCCCG 60.465 55.000 18.73 0.00 35.87 6.13
1031 1069 1.673808 GGGCGAGTAGACCCGTCAAT 61.674 60.000 0.00 0.00 44.51 2.57
1110 1148 2.816087 TGCAAGAAGATTTGGCTCTGAC 59.184 45.455 0.00 0.00 0.00 3.51
1202 1240 1.309950 CCATCTGCTGCATTCCAGAG 58.690 55.000 1.31 8.65 44.64 3.35
1276 1314 0.249120 CTCACCGGTGTGCTCCAATA 59.751 55.000 32.74 10.49 42.46 1.90
1278 1316 1.134521 TCACCGGTGTGCTCCAATATC 60.135 52.381 32.74 0.00 42.46 1.63
1414 1452 4.498241 TGGAGATGACATCTTGTTCGAAG 58.502 43.478 18.89 0.00 40.38 3.79
1478 1516 2.957680 TGAAGGATGTCTTGCTTGCAAA 59.042 40.909 9.39 0.00 35.93 3.68
1518 1556 1.541147 TCAAGCATTAGTTGTGCAGGC 59.459 47.619 0.00 0.00 44.87 4.85
1569 1607 1.945394 CAGTTGCTCTTTGACTGTGCT 59.055 47.619 0.00 0.00 36.81 4.40
1755 1793 0.038744 CATGCAAGGACCCTCCAACT 59.961 55.000 0.00 0.00 39.61 3.16
1941 1979 5.252969 TGCAGTTTATGAAAGATGATGCC 57.747 39.130 0.00 0.00 0.00 4.40
2307 2345 2.886523 TGCTCCATTTCAGACAAGGTTG 59.113 45.455 0.00 0.00 0.00 3.77
2344 2382 6.058833 TCCAATTCTATTGCGGCAGTAATTA 58.941 36.000 5.41 0.00 34.54 1.40
2345 2383 6.017440 TCCAATTCTATTGCGGCAGTAATTAC 60.017 38.462 7.57 7.57 34.54 1.89
2350 2388 1.810959 TGCGGCAGTAATTACGGTTT 58.189 45.000 15.72 0.00 0.00 3.27
2374 2412 5.637006 TTGTGGATTGGATAGTTTTTCCG 57.363 39.130 0.00 0.00 35.94 4.30
2375 2413 4.912586 TGTGGATTGGATAGTTTTTCCGA 58.087 39.130 0.00 0.00 35.94 4.55
2383 2421 6.509418 TGGATAGTTTTTCCGAATCCTTTG 57.491 37.500 0.00 0.00 37.57 2.77
2388 2426 9.110502 GATAGTTTTTCCGAATCCTTTGTAGAT 57.889 33.333 0.00 0.00 0.00 1.98
2390 2428 8.494016 AGTTTTTCCGAATCCTTTGTAGATAG 57.506 34.615 0.00 0.00 0.00 2.08
2393 2431 9.947433 TTTTTCCGAATCCTTTGTAGATAGTAA 57.053 29.630 0.00 0.00 0.00 2.24
2394 2432 8.937634 TTTCCGAATCCTTTGTAGATAGTAAC 57.062 34.615 0.00 0.00 0.00 2.50
2396 2434 8.985315 TCCGAATCCTTTGTAGATAGTAACTA 57.015 34.615 0.00 0.00 0.00 2.24
2415 2540 9.790389 AGTAACTATTTCTTCGTAGATTCTGTG 57.210 33.333 0.00 0.00 35.04 3.66
2419 2544 9.953697 ACTATTTCTTCGTAGATTCTGTGTATC 57.046 33.333 0.00 0.00 35.04 2.24
2430 2555 3.217599 TCTGTGTATCGACTCTTGTGC 57.782 47.619 0.00 0.00 0.00 4.57
2446 2571 0.036022 GTGCTTCTCTTCCCACTGCT 59.964 55.000 0.00 0.00 0.00 4.24
2557 2682 1.850345 ACACTTCCAAGGGAAAGTCCA 59.150 47.619 0.00 0.00 41.54 4.02
2560 2685 2.989571 ACTTCCAAGGGAAAGTCCAGAT 59.010 45.455 0.00 0.00 41.54 2.90
2575 2700 6.566079 AGTCCAGATAGAATGAATGTGGAA 57.434 37.500 3.77 0.00 45.37 3.53
2602 2727 0.667184 GCCTTGCACGGGAAATTGTG 60.667 55.000 11.75 0.00 39.10 3.33
2652 2780 2.159085 GCGTGGAGAGGTAATAGTGCTT 60.159 50.000 0.00 0.00 0.00 3.91
2658 2786 5.447624 GAGAGGTAATAGTGCTTCTCTCC 57.552 47.826 12.05 0.00 38.86 3.71
2666 2794 6.798427 AATAGTGCTTCTCTCCACTCATAA 57.202 37.500 0.00 0.00 41.13 1.90
2668 2796 3.118811 AGTGCTTCTCTCCACTCATAAGC 60.119 47.826 0.00 0.00 37.77 3.09
2679 2807 5.199723 TCCACTCATAAGCCATGCAAATTA 58.800 37.500 0.00 0.00 34.35 1.40
2683 2811 6.643770 CACTCATAAGCCATGCAAATTATTCC 59.356 38.462 0.00 0.00 34.35 3.01
2684 2812 6.100404 TCATAAGCCATGCAAATTATTCCC 57.900 37.500 0.00 0.00 34.35 3.97
2685 2813 3.457610 AAGCCATGCAAATTATTCCCG 57.542 42.857 0.00 0.00 0.00 5.14
2686 2814 2.387757 AGCCATGCAAATTATTCCCGT 58.612 42.857 0.00 0.00 0.00 5.28
2687 2815 2.765699 AGCCATGCAAATTATTCCCGTT 59.234 40.909 0.00 0.00 0.00 4.44
2688 2816 3.197549 AGCCATGCAAATTATTCCCGTTT 59.802 39.130 0.00 0.00 0.00 3.60
2731 2859 2.251818 ACTCCATGTAGCTGACAGTGT 58.748 47.619 3.99 0.00 42.79 3.55
2761 2889 1.019805 GCTCCAGGTACGAAGTTGCC 61.020 60.000 0.00 0.00 37.78 4.52
2938 3066 4.193334 CTCATCGTCGCCTCCGCA 62.193 66.667 0.00 0.00 34.03 5.69
3027 3155 3.317993 CAGAGGTTGTAAAAAGGGTGTGG 59.682 47.826 0.00 0.00 0.00 4.17
3098 3226 6.647334 TTGTCAGAATAATTGAGTTTGGCA 57.353 33.333 0.00 0.00 0.00 4.92
3149 3277 1.798813 GCAGCAACTGGTTGTGTTGTC 60.799 52.381 13.85 2.07 44.54 3.18
3236 3368 8.630917 GCTAGAACATACTCCTAAGTACAATGA 58.369 37.037 0.00 0.00 40.74 2.57
3336 4475 7.367285 TCATGTAAATACTTGCAAAAGTCCAC 58.633 34.615 0.00 0.00 34.37 4.02
3654 4927 3.179443 TGAAGGCAAGGTATAAGCTCG 57.821 47.619 0.00 0.00 0.00 5.03
3692 4965 0.310543 GCTGTGCCGTGAATTCAACA 59.689 50.000 10.35 9.94 0.00 3.33
3862 5135 0.472471 ACAGGTGGTCCGTTTGACAT 59.528 50.000 0.00 0.00 46.38 3.06
3873 5146 5.440685 GTCCGTTTGACATTCTGTTACTTG 58.559 41.667 0.00 0.00 43.85 3.16
3917 5190 3.607078 GCTTGAACTTTCCGTAGTGCTTG 60.607 47.826 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 1.595382 CGAGGCCTCCCAAATAGCG 60.595 63.158 27.20 8.81 0.00 4.26
49 51 2.584608 CGACGAGGCCTCCCAAAT 59.415 61.111 27.20 7.49 0.00 2.32
67 69 2.431057 AGAACCATAGCTTGACCCTACG 59.569 50.000 0.00 0.00 0.00 3.51
142 144 1.065126 CCTTCCCCTCTGAACATCACC 60.065 57.143 0.00 0.00 0.00 4.02
164 166 7.315142 TGCATCAAAGATCAAATAAGGTGTTC 58.685 34.615 0.00 0.00 0.00 3.18
166 168 6.839124 TGCATCAAAGATCAAATAAGGTGT 57.161 33.333 0.00 0.00 0.00 4.16
173 175 8.909923 TCATGAACTATGCATCAAAGATCAAAT 58.090 29.630 0.19 0.00 36.70 2.32
174 176 8.283699 TCATGAACTATGCATCAAAGATCAAA 57.716 30.769 0.19 0.00 36.70 2.69
175 177 7.868906 TCATGAACTATGCATCAAAGATCAA 57.131 32.000 0.19 0.00 36.70 2.57
176 178 8.459911 AATCATGAACTATGCATCAAAGATCA 57.540 30.769 0.19 6.42 36.70 2.92
177 179 9.745880 AAAATCATGAACTATGCATCAAAGATC 57.254 29.630 0.19 0.00 36.70 2.75
209 215 2.621998 GAGGACATGAGATGCCAATTGG 59.378 50.000 20.81 20.81 38.53 3.16
220 226 9.421806 GTATTCATTCTTATCAGAGGACATGAG 57.578 37.037 0.00 0.00 0.00 2.90
253 259 5.069648 TGAGATGCACAAAAACCCACAAATA 59.930 36.000 0.00 0.00 0.00 1.40
258 264 3.451141 TTGAGATGCACAAAAACCCAC 57.549 42.857 0.00 0.00 0.00 4.61
261 267 5.984926 TGAGAATTTGAGATGCACAAAAACC 59.015 36.000 5.21 0.00 39.95 3.27
262 268 7.467557 TTGAGAATTTGAGATGCACAAAAAC 57.532 32.000 5.21 3.52 39.95 2.43
268 274 9.234384 CAAATCTATTGAGAATTTGAGATGCAC 57.766 33.333 0.00 0.00 34.98 4.57
270 276 9.666626 CTCAAATCTATTGAGAATTTGAGATGC 57.333 33.333 23.09 0.00 45.73 3.91
271 277 9.666626 GCTCAAATCTATTGAGAATTTGAGATG 57.333 33.333 28.10 12.68 45.73 2.90
272 278 9.404848 TGCTCAAATCTATTGAGAATTTGAGAT 57.595 29.630 28.10 0.20 45.73 2.75
273 279 8.797350 TGCTCAAATCTATTGAGAATTTGAGA 57.203 30.769 28.10 16.60 45.73 3.27
275 281 8.571461 ACTGCTCAAATCTATTGAGAATTTGA 57.429 30.769 19.39 8.84 46.57 2.69
276 282 9.635520 AAACTGCTCAAATCTATTGAGAATTTG 57.364 29.630 19.39 3.14 46.57 2.32
277 283 9.852091 GAAACTGCTCAAATCTATTGAGAATTT 57.148 29.630 19.39 14.73 46.57 1.82
278 284 8.465201 GGAAACTGCTCAAATCTATTGAGAATT 58.535 33.333 19.39 3.24 46.57 2.17
279 285 7.833183 AGGAAACTGCTCAAATCTATTGAGAAT 59.167 33.333 19.39 3.66 45.61 2.40
280 286 7.170965 AGGAAACTGCTCAAATCTATTGAGAA 58.829 34.615 19.39 10.00 45.61 2.87
319 325 9.980780 GAAAGAAGAAGATAAATCTGCAAGTAC 57.019 33.333 0.81 0.00 37.19 2.73
320 326 9.950496 AGAAAGAAGAAGATAAATCTGCAAGTA 57.050 29.630 0.81 0.00 37.19 2.24
322 328 8.115520 CGAGAAAGAAGAAGATAAATCTGCAAG 58.884 37.037 0.81 0.00 37.19 4.01
323 329 7.819415 TCGAGAAAGAAGAAGATAAATCTGCAA 59.181 33.333 0.81 0.00 37.19 4.08
346 368 6.096673 TCCTAAATAACATGCTATGCTCGA 57.903 37.500 0.00 0.00 0.00 4.04
388 411 0.725784 GCTCATTCGCACCACAAACG 60.726 55.000 0.00 0.00 0.00 3.60
598 632 1.216710 GCAAGTGGAGTAGCTCGCT 59.783 57.895 0.00 0.00 0.00 4.93
658 693 4.125703 CTGATGGAGCTGGAATTCTGTAC 58.874 47.826 5.23 0.00 0.00 2.90
669 704 5.105554 ACTCACTAGTTAACTGATGGAGCTG 60.106 44.000 18.56 8.06 29.00 4.24
740 776 8.015185 TCCCTGTTCATATACCTAACTTGTAC 57.985 38.462 0.00 0.00 0.00 2.90
741 777 8.612486 TTCCCTGTTCATATACCTAACTTGTA 57.388 34.615 0.00 0.00 0.00 2.41
755 793 6.436027 TCAGTCTAGTAGATTCCCTGTTCAT 58.564 40.000 2.51 0.00 0.00 2.57
791 829 4.142026 ACAGGATGCCATTTGATGATGTTG 60.142 41.667 0.00 0.00 42.53 3.33
880 918 6.599244 TCTTTGATGCCTACAATAAGACAAGG 59.401 38.462 0.00 0.00 0.00 3.61
902 940 5.046288 TCCAAACCCAATGCAATTTTCTT 57.954 34.783 0.00 0.00 31.22 2.52
908 946 6.824704 CAGATTAAATCCAAACCCAATGCAAT 59.175 34.615 0.00 0.00 0.00 3.56
910 948 5.483231 TCAGATTAAATCCAAACCCAATGCA 59.517 36.000 0.00 0.00 0.00 3.96
911 949 5.976458 TCAGATTAAATCCAAACCCAATGC 58.024 37.500 0.00 0.00 0.00 3.56
912 950 6.155049 ACCTCAGATTAAATCCAAACCCAATG 59.845 38.462 0.00 0.00 0.00 2.82
913 951 6.263754 ACCTCAGATTAAATCCAAACCCAAT 58.736 36.000 0.00 0.00 0.00 3.16
915 953 5.269554 ACCTCAGATTAAATCCAAACCCA 57.730 39.130 0.00 0.00 0.00 4.51
916 954 5.952347 AGAACCTCAGATTAAATCCAAACCC 59.048 40.000 0.00 0.00 0.00 4.11
919 957 8.163408 TCTTCAGAACCTCAGATTAAATCCAAA 58.837 33.333 0.00 0.00 0.00 3.28
980 1018 1.220477 GCTCCTCTCAAGCACCTCC 59.780 63.158 0.00 0.00 39.61 4.30
995 1033 1.666189 GCCCGACAAAAGACATAGCTC 59.334 52.381 0.00 0.00 0.00 4.09
1031 1069 9.292846 GTACATAAATATTATCCGCGTATGTCA 57.707 33.333 14.09 2.83 33.83 3.58
1202 1240 2.608016 GCTTGCTGGTTGTAAAAGGAGC 60.608 50.000 0.00 0.00 0.00 4.70
1276 1314 3.513515 GACTGGGAGTTCTGTTGAGAGAT 59.486 47.826 0.00 0.00 0.00 2.75
1278 1316 2.896685 AGACTGGGAGTTCTGTTGAGAG 59.103 50.000 0.00 0.00 0.00 3.20
1494 1532 4.157289 CCTGCACAACTAATGCTTGATTCT 59.843 41.667 0.00 0.00 43.77 2.40
1518 1556 1.962822 TGCTTCTCCGCTGTTGCTG 60.963 57.895 0.00 0.00 36.97 4.41
1569 1607 8.745590 TCTACATTATATTCAGCTAATGCCGTA 58.254 33.333 4.85 0.00 38.38 4.02
1590 1628 2.857186 TTGCCTGTGCTTCATCTACA 57.143 45.000 0.00 0.00 38.71 2.74
1755 1793 3.528532 CATTGCTGACAGCTGATACAGA 58.471 45.455 28.90 17.42 42.97 3.41
1941 1979 2.126467 CTCAAATGGCGTGGTTTGTTG 58.874 47.619 7.88 0.00 36.83 3.33
2103 2141 3.416119 CAATCTAGCATTGCAGGTGTG 57.584 47.619 11.91 0.00 0.00 3.82
2274 2312 9.982651 GTCTGAAATGGAGCAGTATTAGTATTA 57.017 33.333 0.00 0.00 33.90 0.98
2350 2388 6.265649 TCGGAAAAACTATCCAATCCACAAAA 59.734 34.615 0.00 0.00 36.74 2.44
2370 2408 8.302515 AGTTACTATCTACAAAGGATTCGGAA 57.697 34.615 0.00 0.00 0.00 4.30
2390 2428 9.570488 ACACAGAATCTACGAAGAAATAGTTAC 57.430 33.333 0.00 0.00 34.73 2.50
2393 2431 9.953697 GATACACAGAATCTACGAAGAAATAGT 57.046 33.333 0.00 0.00 34.73 2.12
2394 2432 9.108449 CGATACACAGAATCTACGAAGAAATAG 57.892 37.037 0.00 0.00 34.73 1.73
2396 2434 7.644551 GTCGATACACAGAATCTACGAAGAAAT 59.355 37.037 0.00 0.00 34.73 2.17
2399 2524 5.816258 AGTCGATACACAGAATCTACGAAGA 59.184 40.000 0.00 0.00 35.80 2.87
2403 2528 5.660629 AGAGTCGATACACAGAATCTACG 57.339 43.478 0.00 0.00 39.60 3.51
2415 2540 4.364415 AGAGAAGCACAAGAGTCGATAC 57.636 45.455 0.00 0.00 0.00 2.24
2419 2544 2.333014 GGAAGAGAAGCACAAGAGTCG 58.667 52.381 0.00 0.00 0.00 4.18
2430 2555 1.675415 GCTCAGCAGTGGGAAGAGAAG 60.675 57.143 0.00 0.00 0.00 2.85
2446 2571 4.938575 TTCAGGTATTTTTAGGGGCTCA 57.061 40.909 0.00 0.00 0.00 4.26
2557 2682 5.759059 TGCCTTTCCACATTCATTCTATCT 58.241 37.500 0.00 0.00 0.00 1.98
2560 2685 5.394443 GCATTGCCTTTCCACATTCATTCTA 60.394 40.000 0.00 0.00 0.00 2.10
2593 2718 4.525912 AGCCAAGATGTTCACAATTTCC 57.474 40.909 0.00 0.00 0.00 3.13
2602 2727 1.135575 CCTTCGCAAGCCAAGATGTTC 60.136 52.381 0.85 0.00 37.18 3.18
2652 2780 2.103771 GCATGGCTTATGAGTGGAGAGA 59.896 50.000 0.00 0.00 39.21 3.10
2658 2786 6.643770 GGAATAATTTGCATGGCTTATGAGTG 59.356 38.462 0.00 0.00 39.21 3.51
2666 2794 2.387757 ACGGGAATAATTTGCATGGCT 58.612 42.857 0.00 0.00 0.00 4.75
2668 2796 5.064579 GGAAAAACGGGAATAATTTGCATGG 59.935 40.000 0.00 0.00 0.00 3.66
2679 2807 4.282195 TGCATAGTTTGGAAAAACGGGAAT 59.718 37.500 0.00 0.00 37.71 3.01
2683 2811 5.799936 CAGTATGCATAGTTTGGAAAAACGG 59.200 40.000 11.49 0.00 37.71 4.44
2684 2812 6.853279 CAGTATGCATAGTTTGGAAAAACG 57.147 37.500 11.49 0.00 37.71 3.60
2720 2848 4.452455 GCATAAACAACTACACTGTCAGCT 59.548 41.667 0.00 0.00 0.00 4.24
2731 2859 4.463539 TCGTACCTGGAGCATAAACAACTA 59.536 41.667 0.00 0.00 0.00 2.24
2761 2889 0.392461 TTCTCGCCCTCCATTTTCCG 60.392 55.000 0.00 0.00 0.00 4.30
2938 3066 1.671261 GCGAGCTCGATCTATTGCCAT 60.671 52.381 38.74 0.00 43.02 4.40
2948 3076 1.140589 CCAAGTCAGCGAGCTCGAT 59.859 57.895 38.74 31.68 43.02 3.59
3027 3155 0.037232 CCAAGAACTCCTCCGTGGTC 60.037 60.000 0.00 0.00 37.07 4.02
3098 3226 3.782443 GGTTCACCCGGGCGATCT 61.782 66.667 24.08 0.00 0.00 2.75
3236 3368 4.974645 TCTAGTTCCCAAACAGACACAT 57.025 40.909 0.00 0.00 37.88 3.21
3275 3407 0.823460 AAACCTGTGGCCAAACTGTG 59.177 50.000 7.24 0.00 0.00 3.66
3277 3409 1.067516 CAGAAACCTGTGGCCAAACTG 59.932 52.381 7.24 0.55 0.00 3.16
3336 4475 9.853177 ACTCTATTGGTTATAAGAAAATCTGGG 57.147 33.333 0.00 0.00 0.00 4.45
3429 4570 9.599322 GTTGTAATTTCACAAGATTACTCTGTG 57.401 33.333 7.49 0.00 39.02 3.66
3502 4643 4.767578 ATCTGGAGAGCATATGTGTGTT 57.232 40.909 4.29 0.00 0.00 3.32
3545 4818 8.049117 AGATTCTTGAGATTATAGTGTTGCCAA 58.951 33.333 0.00 0.00 0.00 4.52
3548 4821 8.654230 TCAGATTCTTGAGATTATAGTGTTGC 57.346 34.615 0.00 0.00 0.00 4.17
3654 4927 5.988561 CACAGCCTACCTTGAAGATAAGATC 59.011 44.000 0.00 0.00 0.00 2.75
3692 4965 3.006323 CGACCTGGCTCTGATTATAGCTT 59.994 47.826 0.00 0.00 38.80 3.74
3862 5135 5.008613 GGTCAGAAATGCACAAGTAACAGAA 59.991 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.