Multiple sequence alignment - TraesCS7B01G283900

Loading Multiple Alignment...

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 TraesCS7B01G283900 chr7B 100.000 3136 0 0 1 3136 517934149 517931014 0.000000e+00 5792
1 TraesCS7B01G283900 chr7B 86.522 2263 250 36 47 2288 509737380 509735152 0.000000e+00 2438
2 TraesCS7B01G283900 chr7B 85.232 711 85 11 549 1247 577201287 577201989 0.000000e+00 713
3 TraesCS7B01G283900 chr7B 84.367 371 41 8 2772 3136 509733303 509732944 6.440000e-92 348
4 TraesCS7B01G283900 chr7B 87.727 220 15 7 2545 2756 509733452 509733237 2.420000e-61 246
5 TraesCS7B01G283900 chr7B 94.937 79 4 0 2693 2771 517931378 517931300 1.180000e-24 124
6 TraesCS7B01G283900 chr7B 94.937 79 4 0 2772 2850 517931457 517931379 1.180000e-24 124
7 TraesCS7B01G283900 chr7D 94.674 1840 86 5 587 2416 489302131 489300294 0.000000e+00 2844
8 TraesCS7B01G283900 chr7D 88.514 1541 132 14 161 1685 484072277 484070766 0.000000e+00 1823
9 TraesCS7B01G283900 chr7D 92.000 600 35 7 3 593 489311295 489310700 0.000000e+00 830
10 TraesCS7B01G283900 chr7D 86.319 709 77 14 549 1247 535510715 535511413 0.000000e+00 754
11 TraesCS7B01G283900 chr7D 91.733 375 17 3 2772 3136 489300054 489299684 2.790000e-140 508
12 TraesCS7B01G283900 chr7D 93.865 326 12 2 2454 2771 489300294 489299969 4.700000e-133 484
13 TraesCS7B01G283900 chr7D 83.799 358 40 8 2772 3125 484069180 484068837 1.080000e-84 324
14 TraesCS7B01G283900 chr7D 85.039 254 21 6 2302 2546 484069607 484069362 3.120000e-60 243
15 TraesCS7B01G283900 chr7D 86.364 220 15 7 2545 2756 484069328 484069116 3.150000e-55 226
16 TraesCS7B01G283900 chr7D 90.299 134 11 2 257 390 535510568 535510699 1.160000e-39 174
17 TraesCS7B01G283900 chr7D 76.842 190 34 10 68 250 56405406 56405592 7.160000e-17 99
18 TraesCS7B01G283900 chr7A 89.147 1465 125 19 161 1606 551543284 551541835 0.000000e+00 1794
19 TraesCS7B01G283900 chr7A 80.410 2047 302 59 262 2261 591023617 591025611 0.000000e+00 1467
20 TraesCS7B01G283900 chr7A 85.594 715 78 16 549 1247 615785795 615786500 0.000000e+00 726
21 TraesCS7B01G283900 chr7A 85.554 713 81 14 549 1247 616444049 616443345 0.000000e+00 726
22 TraesCS7B01G283900 chr7A 84.824 369 41 6 2772 3136 551540672 551540315 1.070000e-94 357
23 TraesCS7B01G283900 chr7A 88.716 257 19 3 2298 2546 551541124 551540870 3.930000e-79 305
24 TraesCS7B01G283900 chr7A 91.538 130 10 1 2628 2756 551540737 551540608 8.940000e-41 178
25 TraesCS7B01G283900 chr6B 81.642 2059 277 59 263 2267 121960706 121958695 0.000000e+00 1615
26 TraesCS7B01G283900 chr6B 85.894 1035 134 6 1265 2290 649832149 649831118 0.000000e+00 1092
27 TraesCS7B01G283900 chr6D 81.518 2056 278 54 261 2267 49182162 49184164 0.000000e+00 1598
28 TraesCS7B01G283900 chr6D 82.825 1345 186 19 885 2197 50179809 50181140 0.000000e+00 1162
29 TraesCS7B01G283900 chr6D 82.220 1018 168 12 1256 2267 50605495 50606505 0.000000e+00 865
30 TraesCS7B01G283900 chr6D 80.614 521 80 14 312 816 50179282 50179797 1.760000e-102 383
31 TraesCS7B01G283900 chr6D 81.600 375 53 10 261 620 50604555 50604928 2.360000e-76 296
32 TraesCS7B01G283900 chrUn 80.704 1591 241 31 718 2267 277361152 277362717 0.000000e+00 1177
33 TraesCS7B01G283900 chr6A 82.259 1381 195 24 881 2228 64908445 64907082 0.000000e+00 1147
34 TraesCS7B01G283900 chr6A 85.850 947 123 6 1265 2202 577722912 577721968 0.000000e+00 996
35 TraesCS7B01G283900 chr2D 85.592 701 78 15 549 1241 89468726 89469411 0.000000e+00 713
36 TraesCS7B01G283900 chr2D 93.893 131 7 1 261 390 89468580 89468710 2.470000e-46 196
37 TraesCS7B01G283900 chr4A 77.559 254 27 17 2900 3129 30287257 30287010 3.280000e-25 126
38 TraesCS7B01G283900 chr4D 76.378 254 30 16 2900 3129 437818491 437818738 3.310000e-20 110
39 TraesCS7B01G283900 chr4B 75.591 254 32 15 2900 3129 540726082 540726329 7.160000e-17 99
40 TraesCS7B01G283900 chr2B 77.536 138 21 6 76 208 762512921 762512789 1.210000e-09 75


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 TraesCS7B01G283900 chr7B 517931014 517934149 3135 True 2013.333333 5792 96.624667 1 3136 3 chr7B.!!$R2 3135
1 TraesCS7B01G283900 chr7B 509732944 509737380 4436 True 1010.666667 2438 86.205333 47 3136 3 chr7B.!!$R1 3089
2 TraesCS7B01G283900 chr7B 577201287 577201989 702 False 713.000000 713 85.232000 549 1247 1 chr7B.!!$F1 698
3 TraesCS7B01G283900 chr7D 489299684 489302131 2447 True 1278.666667 2844 93.424000 587 3136 3 chr7D.!!$R3 2549
4 TraesCS7B01G283900 chr7D 489310700 489311295 595 True 830.000000 830 92.000000 3 593 1 chr7D.!!$R1 590
5 TraesCS7B01G283900 chr7D 484068837 484072277 3440 True 654.000000 1823 85.929000 161 3125 4 chr7D.!!$R2 2964
6 TraesCS7B01G283900 chr7D 535510568 535511413 845 False 464.000000 754 88.309000 257 1247 2 chr7D.!!$F2 990
7 TraesCS7B01G283900 chr7A 591023617 591025611 1994 False 1467.000000 1467 80.410000 262 2261 1 chr7A.!!$F1 1999
8 TraesCS7B01G283900 chr7A 615785795 615786500 705 False 726.000000 726 85.594000 549 1247 1 chr7A.!!$F2 698
9 TraesCS7B01G283900 chr7A 616443345 616444049 704 True 726.000000 726 85.554000 549 1247 1 chr7A.!!$R1 698
10 TraesCS7B01G283900 chr7A 551540315 551543284 2969 True 658.500000 1794 88.556250 161 3136 4 chr7A.!!$R2 2975
11 TraesCS7B01G283900 chr6B 121958695 121960706 2011 True 1615.000000 1615 81.642000 263 2267 1 chr6B.!!$R1 2004
12 TraesCS7B01G283900 chr6B 649831118 649832149 1031 True 1092.000000 1092 85.894000 1265 2290 1 chr6B.!!$R2 1025
13 TraesCS7B01G283900 chr6D 49182162 49184164 2002 False 1598.000000 1598 81.518000 261 2267 1 chr6D.!!$F1 2006
14 TraesCS7B01G283900 chr6D 50179282 50181140 1858 False 772.500000 1162 81.719500 312 2197 2 chr6D.!!$F2 1885
15 TraesCS7B01G283900 chr6D 50604555 50606505 1950 False 580.500000 865 81.910000 261 2267 2 chr6D.!!$F3 2006
16 TraesCS7B01G283900 chrUn 277361152 277362717 1565 False 1177.000000 1177 80.704000 718 2267 1 chrUn.!!$F1 1549
17 TraesCS7B01G283900 chr6A 64907082 64908445 1363 True 1147.000000 1147 82.259000 881 2228 1 chr6A.!!$R1 1347
18 TraesCS7B01G283900 chr6A 577721968 577722912 944 True 996.000000 996 85.850000 1265 2202 1 chr6A.!!$R2 937
19 TraesCS7B01G283900 chr2D 89468580 89469411 831 False 454.500000 713 89.742500 261 1241 2 chr2D.!!$F1 980

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
286 289 1.272928 TGGAATGCTATGTTTGGGCCA 60.273 47.619 0.0 0.0 0.0 5.36 F
1433 1524 1.070134 CTCCGTTGTCCCTGTTGAAGA 59.930 52.381 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1717 0.666274 TGTTACTCTGGACAAGCGCG 60.666 55.0 0.0 0.0 0.0 6.86 R
2808 4782 0.033504 TGGTTCGAAGTGGAGCTGAC 59.966 55.0 0.0 0.0 0.0 3.51 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
26 27 6.489022 ACTTTGGAGTTTAACTATTGTCCACC 59.511 38.462 0.00 0.00 33.80 4.61
55 56 7.705325 TGTTTGCCTCTATTAGTCTCGTATTTC 59.295 37.037 0.00 0.00 0.00 2.17
245 248 1.843368 TAGTTACCAGGACGAGGGTG 58.157 55.000 0.00 0.00 38.06 4.61
271 274 5.941788 AGAACTAAGGAGTGTTGTTGGAAT 58.058 37.500 0.00 0.00 35.52 3.01
286 289 1.272928 TGGAATGCTATGTTTGGGCCA 60.273 47.619 0.00 0.00 0.00 5.36
537 554 5.652014 TCCGCATAAATGGTCAAATTTCTCT 59.348 36.000 0.00 0.00 32.16 3.10
572 591 5.119694 GTCTTGACCTCTTGAGTTGTTTCT 58.880 41.667 0.00 0.00 0.00 2.52
764 796 3.963383 AACACGAGGTTTGTTCATCAC 57.037 42.857 0.00 0.00 35.82 3.06
973 1031 4.574013 GTCCCTCTTAGCATTGACATTGAG 59.426 45.833 1.52 0.00 0.00 3.02
977 1035 5.125097 CCTCTTAGCATTGACATTGAGCTTT 59.875 40.000 1.52 0.00 36.80 3.51
980 1038 4.170292 AGCATTGACATTGAGCTTTCAC 57.830 40.909 1.52 0.00 29.98 3.18
1100 1164 2.686572 GCCCCTCGGGTAAATGGGT 61.687 63.158 0.55 0.00 46.51 4.51
1125 1192 4.511082 GCTGAAATCAGAGATCCTAGCAAC 59.489 45.833 14.43 0.00 46.59 4.17
1322 1413 2.751259 CAGCAGTCAACAACCATGCTAT 59.249 45.455 0.00 0.00 45.03 2.97
1323 1414 3.940852 CAGCAGTCAACAACCATGCTATA 59.059 43.478 0.00 0.00 45.03 1.31
1402 1493 3.987220 GCTTGATAACGTGCCATTTGTTT 59.013 39.130 0.00 0.00 0.00 2.83
1433 1524 1.070134 CTCCGTTGTCCCTGTTGAAGA 59.930 52.381 0.00 0.00 0.00 2.87
1461 1552 9.710900 CCTGTTATGAATATGTACTATGAGCAA 57.289 33.333 0.00 0.00 0.00 3.91
1504 1595 1.561542 CTGACTTGGGCTGGGAGTATT 59.438 52.381 0.00 0.00 0.00 1.89
1544 1635 2.852714 TCATCCATGGCTCCCATTTT 57.147 45.000 6.96 0.00 42.23 1.82
1656 1750 3.504906 TCCAGAGTAACACCTACAACTCG 59.495 47.826 0.00 0.00 42.51 4.18
1713 1807 5.277058 CGATTTCGAAGATTGGATGAGGTTC 60.277 44.000 0.00 0.00 43.02 3.62
1730 1824 2.880890 GGTTCTGTATGGATGATGGCAC 59.119 50.000 0.00 0.00 0.00 5.01
1816 1910 4.895297 ACCTTTGGAACTTTGATGACATGT 59.105 37.500 0.00 0.00 0.00 3.21
1818 1912 4.747540 TTGGAACTTTGATGACATGTCG 57.252 40.909 20.54 7.89 0.00 4.35
1908 2006 9.508567 GCAATTTGGATGTTTAGTCTAAGATTC 57.491 33.333 0.00 0.00 0.00 2.52
2072 2173 5.553123 TCTTTAGTAATCGACCCTTTTGCA 58.447 37.500 0.00 0.00 0.00 4.08
2256 2372 7.067494 GGCTGTTTAATTGGTGATAGAAGTGAT 59.933 37.037 0.00 0.00 0.00 3.06
2333 4229 7.646922 GTCTATAAGATGTTTGGTCGTTCGTAT 59.353 37.037 0.00 0.00 0.00 3.06
2419 4323 4.651503 TGTAAACAAAAAGGCCCAGATTGA 59.348 37.500 13.27 0.00 0.00 2.57
2443 4347 2.293399 GCCACGAACAACCTCAAAGAAT 59.707 45.455 0.00 0.00 0.00 2.40
2505 4417 1.835494 CCTAGGAACGAGACCAGACA 58.165 55.000 1.05 0.00 30.78 3.41
2522 4434 4.202336 CCAGACATGCTACTGATCTTGGAT 60.202 45.833 14.06 0.00 36.38 3.41
2561 4513 7.449704 GTGGAAATAAATAGCCCAAGAGATCAT 59.550 37.037 0.00 0.00 0.00 2.45
2584 4546 4.797868 TGAAACAAAACACAAGCATTCGAG 59.202 37.500 0.00 0.00 0.00 4.04
2709 4680 1.003003 GCTCCTCTTCTGCAGAAAGGT 59.997 52.381 33.20 0.00 33.07 3.50
2718 4689 5.131642 TCTTCTGCAGAAAGGTATCATCCAT 59.868 40.000 28.16 0.00 33.07 3.41
2756 4730 2.496070 TCCACTTCGAACCATACTGAGG 59.504 50.000 0.00 0.00 0.00 3.86
2757 4731 2.496070 CCACTTCGAACCATACTGAGGA 59.504 50.000 0.00 0.00 0.00 3.71
2758 4732 3.429547 CCACTTCGAACCATACTGAGGAG 60.430 52.174 0.00 0.00 0.00 3.69
2760 4734 4.082190 CACTTCGAACCATACTGAGGAGAA 60.082 45.833 0.00 0.00 0.00 2.87
2761 4735 4.082136 ACTTCGAACCATACTGAGGAGAAC 60.082 45.833 0.00 0.00 0.00 3.01
2762 4736 3.427573 TCGAACCATACTGAGGAGAACA 58.572 45.455 0.00 0.00 0.00 3.18
2765 4739 4.994852 CGAACCATACTGAGGAGAACAAAA 59.005 41.667 0.00 0.00 0.00 2.44
2767 4741 6.149474 CGAACCATACTGAGGAGAACAAAATT 59.851 38.462 0.00 0.00 0.00 1.82
2769 4743 8.934023 AACCATACTGAGGAGAACAAAATTTA 57.066 30.769 0.00 0.00 0.00 1.40
2770 4744 8.934023 ACCATACTGAGGAGAACAAAATTTAA 57.066 30.769 0.00 0.00 0.00 1.52
2771 4745 8.793592 ACCATACTGAGGAGAACAAAATTTAAC 58.206 33.333 0.00 0.00 0.00 2.01
2772 4746 8.244113 CCATACTGAGGAGAACAAAATTTAACC 58.756 37.037 0.00 0.00 0.00 2.85
2773 4747 9.014297 CATACTGAGGAGAACAAAATTTAACCT 57.986 33.333 0.00 0.00 0.00 3.50
2775 4749 7.290813 ACTGAGGAGAACAAAATTTAACCTCT 58.709 34.615 0.00 8.33 41.89 3.69
2777 4751 8.166422 TGAGGAGAACAAAATTTAACCTCTTC 57.834 34.615 0.00 14.58 41.89 2.87
2778 4752 7.998964 TGAGGAGAACAAAATTTAACCTCTTCT 59.001 33.333 0.00 10.82 41.89 2.85
2779 4753 8.171164 AGGAGAACAAAATTTAACCTCTTCTG 57.829 34.615 0.00 0.00 0.00 3.02
2780 4754 6.863645 GGAGAACAAAATTTAACCTCTTCTGC 59.136 38.462 0.00 0.00 0.00 4.26
2781 4755 7.346751 AGAACAAAATTTAACCTCTTCTGCA 57.653 32.000 0.00 0.00 0.00 4.41
2782 4756 7.428826 AGAACAAAATTTAACCTCTTCTGCAG 58.571 34.615 7.63 7.63 0.00 4.41
2783 4757 6.959639 ACAAAATTTAACCTCTTCTGCAGA 57.040 33.333 13.74 13.74 0.00 4.26
2784 4758 7.346751 ACAAAATTTAACCTCTTCTGCAGAA 57.653 32.000 26.87 26.87 0.00 3.02
2785 4759 7.781056 ACAAAATTTAACCTCTTCTGCAGAAA 58.219 30.769 28.16 17.93 33.07 2.52
2786 4760 7.922811 ACAAAATTTAACCTCTTCTGCAGAAAG 59.077 33.333 28.16 24.39 33.07 2.62
2787 4761 6.581171 AATTTAACCTCTTCTGCAGAAAGG 57.419 37.500 33.26 33.26 33.07 3.11
2788 4762 1.902938 AACCTCTTCTGCAGAAAGGC 58.097 50.000 34.03 0.00 33.07 4.35
2789 4763 0.767375 ACCTCTTCTGCAGAAAGGCA 59.233 50.000 34.03 19.72 42.53 4.75
2790 4764 1.353694 ACCTCTTCTGCAGAAAGGCAT 59.646 47.619 34.03 23.37 43.97 4.40
2791 4765 2.015587 CCTCTTCTGCAGAAAGGCATC 58.984 52.381 28.86 0.00 43.97 3.91
2792 4766 1.664659 CTCTTCTGCAGAAAGGCATCG 59.335 52.381 28.16 15.57 43.97 3.84
2793 4767 0.098376 CTTCTGCAGAAAGGCATCGC 59.902 55.000 28.16 0.00 43.97 4.58
2803 4777 2.573340 GGCATCGCCCAACCAAAG 59.427 61.111 0.00 0.00 44.06 2.77
2804 4778 1.976474 GGCATCGCCCAACCAAAGA 60.976 57.895 0.00 0.00 44.06 2.52
2805 4779 1.508088 GCATCGCCCAACCAAAGAG 59.492 57.895 0.00 0.00 0.00 2.85
2806 4780 0.960364 GCATCGCCCAACCAAAGAGA 60.960 55.000 0.00 0.00 0.00 3.10
2807 4781 1.533625 CATCGCCCAACCAAAGAGAA 58.466 50.000 0.00 0.00 0.00 2.87
2808 4782 1.470098 CATCGCCCAACCAAAGAGAAG 59.530 52.381 0.00 0.00 0.00 2.85
2809 4783 0.472471 TCGCCCAACCAAAGAGAAGT 59.528 50.000 0.00 0.00 0.00 3.01
2810 4784 0.875059 CGCCCAACCAAAGAGAAGTC 59.125 55.000 0.00 0.00 0.00 3.01
2811 4785 1.813862 CGCCCAACCAAAGAGAAGTCA 60.814 52.381 0.00 0.00 0.00 3.41
2812 4786 1.882623 GCCCAACCAAAGAGAAGTCAG 59.117 52.381 0.00 0.00 0.00 3.51
2813 4787 1.882623 CCCAACCAAAGAGAAGTCAGC 59.117 52.381 0.00 0.00 0.00 4.26
2814 4788 2.487986 CCCAACCAAAGAGAAGTCAGCT 60.488 50.000 0.00 0.00 0.00 4.24
2815 4789 2.810852 CCAACCAAAGAGAAGTCAGCTC 59.189 50.000 0.00 0.00 0.00 4.09
2816 4790 2.810852 CAACCAAAGAGAAGTCAGCTCC 59.189 50.000 0.00 0.00 32.82 4.70
2817 4791 2.050144 ACCAAAGAGAAGTCAGCTCCA 58.950 47.619 0.00 0.00 32.82 3.86
2818 4792 2.224402 ACCAAAGAGAAGTCAGCTCCAC 60.224 50.000 0.00 0.00 32.82 4.02
2855 4829 8.536175 ACTGAGGAGAACAAAATTTAAAACCAA 58.464 29.630 0.00 0.00 0.00 3.67
2890 4864 0.321210 TACGTACCCGTCTTGGTCGA 60.321 55.000 0.00 0.00 46.28 4.20
2891 4865 0.962356 ACGTACCCGTCTTGGTCGAT 60.962 55.000 0.00 0.00 46.28 3.59
2892 4866 1.016627 CGTACCCGTCTTGGTCGATA 58.983 55.000 0.00 0.00 39.91 2.92
2893 4867 1.401552 CGTACCCGTCTTGGTCGATAA 59.598 52.381 0.00 0.00 39.91 1.75
2894 4868 2.033801 CGTACCCGTCTTGGTCGATAAT 59.966 50.000 0.00 0.00 39.91 1.28
3015 4989 2.221299 AGGTAGCCGCCTTCCAACA 61.221 57.895 0.00 0.00 34.71 3.33
3053 5027 3.573772 CTTCTGCCGAGCCACGTCA 62.574 63.158 0.00 0.00 40.78 4.35
3071 5045 0.969894 CACTCCTCGTCTTCTTGGGT 59.030 55.000 0.00 0.00 0.00 4.51
3081 5055 4.659172 TCTTGGGTGCCGGCTTGG 62.659 66.667 29.70 11.62 42.50 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.913784 TGGGTGGACAATAGTTAAACTCC 58.086 43.478 0.00 0.00 0.00 3.85
11 12 5.047660 GCAAACATGGGTGGACAATAGTTAA 60.048 40.000 0.00 0.00 0.00 2.01
26 27 4.747108 CGAGACTAATAGAGGCAAACATGG 59.253 45.833 0.00 0.00 34.40 3.66
55 56 1.522668 TGTGGTCAGCCTTTGATTCG 58.477 50.000 0.00 0.00 38.29 3.34
65 66 9.379791 AGTTTACTAGTTAATTATGTGGTCAGC 57.620 33.333 0.00 0.00 0.00 4.26
200 202 6.840780 CCCCCTCATATTTTTGGTCATATC 57.159 41.667 0.00 0.00 0.00 1.63
225 227 2.385803 CACCCTCGTCCTGGTAACTAT 58.614 52.381 0.00 0.00 32.32 2.12
245 248 4.995487 CCAACAACACTCCTTAGTTCTACC 59.005 45.833 0.00 0.00 31.97 3.18
271 274 1.935799 AACATGGCCCAAACATAGCA 58.064 45.000 0.00 0.00 0.00 3.49
286 289 9.574516 AAATCTCTAAACAAACAGGAGTAACAT 57.425 29.630 0.00 0.00 0.00 2.71
497 514 3.086282 TGCGGATTTTCTACCCCTTTTC 58.914 45.455 0.00 0.00 0.00 2.29
537 554 1.754226 GGTCAAGACCCAAGCAAAACA 59.246 47.619 8.06 0.00 45.68 2.83
572 591 4.517453 GCACACCTACAACCATCTAACAAA 59.483 41.667 0.00 0.00 0.00 2.83
973 1031 4.671250 GCTTAAGTCATCTGCAGTGAAAGC 60.671 45.833 23.15 23.15 32.87 3.51
977 1035 3.329386 GTGCTTAAGTCATCTGCAGTGA 58.671 45.455 14.67 13.65 34.15 3.41
980 1038 2.703416 TGGTGCTTAAGTCATCTGCAG 58.297 47.619 7.63 7.63 34.15 4.41
1100 1164 4.162888 TGCTAGGATCTCTGATTTCAGCAA 59.837 41.667 2.60 0.00 43.46 3.91
1322 1413 4.667573 TGGGTACATGAAAGCATTTGGTA 58.332 39.130 0.00 0.00 39.27 3.25
1323 1414 3.505386 TGGGTACATGAAAGCATTTGGT 58.495 40.909 0.00 0.00 39.27 3.67
1458 1549 2.204237 CCAAAAGTGTTGCTTCCTTGC 58.796 47.619 0.00 0.00 36.17 4.01
1461 1552 1.410153 CAGCCAAAAGTGTTGCTTCCT 59.590 47.619 0.00 0.00 36.17 3.36
1626 1717 0.666274 TGTTACTCTGGACAAGCGCG 60.666 55.000 0.00 0.00 0.00 6.86
1713 1807 1.070601 TCGGTGCCATCATCCATACAG 59.929 52.381 0.00 0.00 0.00 2.74
1730 1824 1.354040 GCTATCAATCGGCTCATCGG 58.646 55.000 0.00 0.00 0.00 4.18
1816 1910 1.395608 GAAAAATTCGCCACGGATCGA 59.604 47.619 0.00 0.00 0.00 3.59
1818 1912 2.418628 TCAGAAAAATTCGCCACGGATC 59.581 45.455 0.00 0.00 34.02 3.36
2072 2173 1.065491 TGCCACACAGACAGTCAACTT 60.065 47.619 2.66 0.00 0.00 2.66
2136 2248 7.437565 ACATTCAGAAATGATAGAGACGACATG 59.562 37.037 5.22 0.00 44.25 3.21
2409 4313 1.031571 TCGTGGCAATCAATCTGGGC 61.032 55.000 0.00 0.00 0.00 5.36
2419 4323 1.686355 TTGAGGTTGTTCGTGGCAAT 58.314 45.000 0.00 0.00 0.00 3.56
2443 4347 9.020731 TGTTGTGAGTATAGATTAAGACTGACA 57.979 33.333 0.00 0.00 34.80 3.58
2505 4417 6.893583 AGTTGTAATCCAAGATCAGTAGCAT 58.106 36.000 0.00 0.00 32.51 3.79
2522 4434 5.769484 TTATTTCCACCGCAAAGTTGTAA 57.231 34.783 0.00 0.00 0.00 2.41
2561 4513 4.738124 TCGAATGCTTGTGTTTTGTTTCA 58.262 34.783 0.00 0.00 0.00 2.69
2584 4546 1.461127 GTAGATTGATTGATCGGCCGC 59.539 52.381 23.51 8.29 0.00 6.53
2709 4680 6.687393 GCTGACTTCTCTTTGGATGGATGATA 60.687 42.308 0.00 0.00 0.00 2.15
2718 4689 2.037772 GTGGAGCTGACTTCTCTTTGGA 59.962 50.000 0.00 0.00 0.00 3.53
2756 4730 7.425606 TGCAGAAGAGGTTAAATTTTGTTCTC 58.574 34.615 0.00 0.00 0.00 2.87
2757 4731 7.285401 TCTGCAGAAGAGGTTAAATTTTGTTCT 59.715 33.333 15.67 0.00 0.00 3.01
2758 4732 7.425606 TCTGCAGAAGAGGTTAAATTTTGTTC 58.574 34.615 15.67 0.00 0.00 3.18
2760 4734 6.959639 TCTGCAGAAGAGGTTAAATTTTGT 57.040 33.333 15.67 0.00 0.00 2.83
2761 4735 7.383300 CCTTTCTGCAGAAGAGGTTAAATTTTG 59.617 37.037 30.13 14.10 35.91 2.44
2762 4736 7.436933 CCTTTCTGCAGAAGAGGTTAAATTTT 58.563 34.615 30.13 0.00 35.91 1.82
2765 4739 4.460731 GCCTTTCTGCAGAAGAGGTTAAAT 59.539 41.667 33.85 0.00 35.91 1.40
2767 4741 3.181445 TGCCTTTCTGCAGAAGAGGTTAA 60.181 43.478 33.85 25.07 36.04 2.01
2769 4743 1.143684 TGCCTTTCTGCAGAAGAGGTT 59.856 47.619 33.85 0.00 36.04 3.50
2770 4744 0.767375 TGCCTTTCTGCAGAAGAGGT 59.233 50.000 33.85 0.00 36.04 3.85
2771 4745 2.015587 GATGCCTTTCTGCAGAAGAGG 58.984 52.381 32.10 32.10 45.93 3.69
2772 4746 1.664659 CGATGCCTTTCTGCAGAAGAG 59.335 52.381 27.02 23.92 45.93 2.85
2773 4747 1.730501 CGATGCCTTTCTGCAGAAGA 58.269 50.000 27.02 17.41 45.93 2.87
2775 4749 1.308069 GGCGATGCCTTTCTGCAGAA 61.308 55.000 25.16 25.16 46.69 3.02
2777 4751 2.796651 GGCGATGCCTTTCTGCAG 59.203 61.111 7.63 7.63 46.69 4.41
2787 4761 0.960364 TCTCTTTGGTTGGGCGATGC 60.960 55.000 0.00 0.00 0.00 3.91
2788 4762 1.470098 CTTCTCTTTGGTTGGGCGATG 59.530 52.381 0.00 0.00 0.00 3.84
2789 4763 1.073923 ACTTCTCTTTGGTTGGGCGAT 59.926 47.619 0.00 0.00 0.00 4.58
2790 4764 0.472471 ACTTCTCTTTGGTTGGGCGA 59.528 50.000 0.00 0.00 0.00 5.54
2791 4765 0.875059 GACTTCTCTTTGGTTGGGCG 59.125 55.000 0.00 0.00 0.00 6.13
2792 4766 1.882623 CTGACTTCTCTTTGGTTGGGC 59.117 52.381 0.00 0.00 0.00 5.36
2793 4767 1.882623 GCTGACTTCTCTTTGGTTGGG 59.117 52.381 0.00 0.00 0.00 4.12
2794 4768 2.810852 GAGCTGACTTCTCTTTGGTTGG 59.189 50.000 0.00 0.00 0.00 3.77
2795 4769 2.810852 GGAGCTGACTTCTCTTTGGTTG 59.189 50.000 0.00 0.00 0.00 3.77
2796 4770 2.439507 TGGAGCTGACTTCTCTTTGGTT 59.560 45.455 0.00 0.00 0.00 3.67
2797 4771 2.050144 TGGAGCTGACTTCTCTTTGGT 58.950 47.619 0.00 0.00 0.00 3.67
2798 4772 2.038295 AGTGGAGCTGACTTCTCTTTGG 59.962 50.000 0.00 0.00 0.00 3.28
2799 4773 3.399440 AGTGGAGCTGACTTCTCTTTG 57.601 47.619 0.00 0.00 0.00 2.77
2800 4774 3.553922 CGAAGTGGAGCTGACTTCTCTTT 60.554 47.826 23.42 0.00 44.83 2.52
2801 4775 2.029470 CGAAGTGGAGCTGACTTCTCTT 60.029 50.000 23.42 8.34 44.83 2.85
2802 4776 1.543802 CGAAGTGGAGCTGACTTCTCT 59.456 52.381 23.42 0.51 44.83 3.10
2803 4777 1.542030 TCGAAGTGGAGCTGACTTCTC 59.458 52.381 23.42 8.19 44.83 2.87
2804 4778 1.621992 TCGAAGTGGAGCTGACTTCT 58.378 50.000 23.42 1.39 44.83 2.85
2805 4779 2.062519 GTTCGAAGTGGAGCTGACTTC 58.937 52.381 19.13 19.13 43.97 3.01
2806 4780 1.270358 GGTTCGAAGTGGAGCTGACTT 60.270 52.381 0.00 7.33 36.33 3.01
2807 4781 0.318762 GGTTCGAAGTGGAGCTGACT 59.681 55.000 0.00 0.00 0.00 3.41
2808 4782 0.033504 TGGTTCGAAGTGGAGCTGAC 59.966 55.000 0.00 0.00 0.00 3.51
2809 4783 0.976641 ATGGTTCGAAGTGGAGCTGA 59.023 50.000 0.00 0.00 0.00 4.26
2810 4784 2.093973 AGTATGGTTCGAAGTGGAGCTG 60.094 50.000 0.00 0.00 0.00 4.24
2811 4785 2.093973 CAGTATGGTTCGAAGTGGAGCT 60.094 50.000 0.00 0.00 0.00 4.09
2812 4786 2.094182 TCAGTATGGTTCGAAGTGGAGC 60.094 50.000 0.00 0.00 36.16 4.70
2813 4787 3.429547 CCTCAGTATGGTTCGAAGTGGAG 60.430 52.174 0.00 0.00 36.16 3.86
2814 4788 2.496070 CCTCAGTATGGTTCGAAGTGGA 59.504 50.000 0.00 0.00 36.16 4.02
2815 4789 2.496070 TCCTCAGTATGGTTCGAAGTGG 59.504 50.000 0.00 0.00 36.16 4.00
2816 4790 3.444034 TCTCCTCAGTATGGTTCGAAGTG 59.556 47.826 0.00 0.00 36.16 3.16
2817 4791 3.698289 TCTCCTCAGTATGGTTCGAAGT 58.302 45.455 0.00 0.00 36.16 3.01
2818 4792 4.082190 TGTTCTCCTCAGTATGGTTCGAAG 60.082 45.833 0.00 0.00 36.16 3.79
2855 4829 4.448732 GGTACGTACAAACTCGAAATGGTT 59.551 41.667 26.02 0.00 0.00 3.67
2890 4864 1.349688 TCGCCTCCCGCCATTAATTAT 59.650 47.619 0.00 0.00 36.73 1.28
2891 4865 0.759959 TCGCCTCCCGCCATTAATTA 59.240 50.000 0.00 0.00 36.73 1.40
2892 4866 0.535102 CTCGCCTCCCGCCATTAATT 60.535 55.000 0.00 0.00 36.73 1.40
2893 4867 1.071471 CTCGCCTCCCGCCATTAAT 59.929 57.895 0.00 0.00 36.73 1.40
2894 4868 2.504032 CTCGCCTCCCGCCATTAA 59.496 61.111 0.00 0.00 36.73 1.40
3000 4974 2.221299 AGGTGTTGGAAGGCGGCTA 61.221 57.895 13.71 0.00 0.00 3.93
3001 4975 3.570212 AGGTGTTGGAAGGCGGCT 61.570 61.111 5.25 5.25 0.00 5.52
3053 5027 0.969894 CACCCAAGAAGACGAGGAGT 59.030 55.000 0.00 0.00 0.00 3.85
3081 5055 4.549516 GTACTCGTCGCCTCCGCC 62.550 72.222 0.00 0.00 0.00 6.13
3091 5065 1.406539 ACGTGTGGTTCAAGTACTCGT 59.593 47.619 0.00 0.00 38.98 4.18


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

AutoCloner maintained by Alex Coulton.