Multiple sequence alignment - TraesCS4A01G478800

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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 TraesCS4A01G478800 chr4A 100.000 5521 0 0 1 5521 735766460 735771980 0.000000e+00 10196
1 TraesCS4A01G478800 chr4A 94.853 3342 141 7 1 3316 736883293 736886629 0.000000e+00 5190
2 TraesCS4A01G478800 chr4A 89.275 3310 313 19 1 3282 736055261 736058556 0.000000e+00 4108
3 TraesCS4A01G478800 chr4A 88.147 2590 278 13 695 3277 735316356 735318923 0.000000e+00 3055
4 TraesCS4A01G478800 chr4A 86.093 2603 293 31 695 3288 735487907 735485365 0.000000e+00 2737
5 TraesCS4A01G478800 chr4A 85.627 2623 334 29 695 3282 735776450 735779064 0.000000e+00 2715
6 TraesCS4A01G478800 chr4A 85.951 2598 294 35 695 3282 735003469 735006005 0.000000e+00 2710
7 TraesCS4A01G478800 chr4A 85.426 2628 331 27 663 3275 736570748 736573338 0.000000e+00 2684
8 TraesCS4A01G478800 chr4A 85.312 2628 335 26 663 3275 734730671 734733262 0.000000e+00 2667
9 TraesCS4A01G478800 chr4A 85.374 2605 312 36 690 3282 734917491 734920038 0.000000e+00 2636
10 TraesCS4A01G478800 chr4A 84.975 2589 359 20 695 3275 736413254 736410688 0.000000e+00 2599
11 TraesCS4A01G478800 chr4A 84.527 2598 358 25 695 3282 736756370 736758933 0.000000e+00 2531
12 TraesCS4A01G478800 chr4A 84.002 2619 341 40 695 3282 736896814 736899385 0.000000e+00 2444
13 TraesCS4A01G478800 chr4A 86.196 2311 254 30 695 2998 734582680 734584932 0.000000e+00 2440
14 TraesCS4A01G478800 chr4A 86.208 2226 284 14 665 2884 734480156 734482364 0.000000e+00 2388
15 TraesCS4A01G478800 chr4A 86.416 2098 272 13 1190 3282 736724764 736726853 0.000000e+00 2283
16 TraesCS4A01G478800 chr4A 84.933 2177 293 16 1100 3266 735689506 735691657 0.000000e+00 2170
17 TraesCS4A01G478800 chr4A 95.923 981 38 1 4470 5450 736886894 736887872 0.000000e+00 1589
18 TraesCS4A01G478800 chr4A 95.244 799 33 3 4653 5450 736475524 736474730 0.000000e+00 1260
19 TraesCS4A01G478800 chr4A 85.082 972 134 7 4480 5450 734483710 734484671 0.000000e+00 981
20 TraesCS4A01G478800 chr4A 84.584 986 139 9 4470 5450 736467768 736466791 0.000000e+00 966
21 TraesCS4A01G478800 chr4A 84.334 983 148 4 4470 5450 734388101 734389079 0.000000e+00 957
22 TraesCS4A01G478800 chr4A 84.232 983 142 9 4470 5450 735559767 735558796 0.000000e+00 944
23 TraesCS4A01G478800 chr4A 83.418 983 150 9 4470 5450 736759241 736760212 0.000000e+00 900
24 TraesCS4A01G478800 chr4A 84.231 260 25 8 3626 3878 27665565 27665815 7.150000e-59 239
25 TraesCS4A01G478800 chr7A 87.688 3322 338 22 1 3285 7323008 7319721 0.000000e+00 3803
26 TraesCS4A01G478800 chr7A 87.332 2597 286 29 695 3277 7045454 7042887 0.000000e+00 2933
27 TraesCS4A01G478800 chr7A 85.787 985 123 13 4470 5450 6925722 6924751 0.000000e+00 1027
28 TraesCS4A01G478800 chr7A 80.602 598 87 15 3895 4470 705140670 705140080 8.490000e-118 435
29 TraesCS4A01G478800 chr7D 85.177 2604 355 19 702 3288 5638037 5635448 0.000000e+00 2641
30 TraesCS4A01G478800 chr7D 85.002 2607 336 29 695 3277 5449076 5446501 0.000000e+00 2597
31 TraesCS4A01G478800 chr7D 92.169 945 60 6 3532 4469 540646897 540645960 0.000000e+00 1323
32 TraesCS4A01G478800 chr7D 83.181 987 152 12 4470 5450 5483949 5482971 0.000000e+00 891
33 TraesCS4A01G478800 chr7D 93.600 250 15 1 3315 3563 540647084 540646835 6.750000e-99 372
34 TraesCS4A01G478800 chr2B 96.886 1156 28 4 3315 4469 690966796 690965648 0.000000e+00 1929
35 TraesCS4A01G478800 chr2B 79.630 270 33 7 3626 3882 66199414 66199154 2.040000e-39 174
36 TraesCS4A01G478800 chr7B 96.710 1155 28 5 3317 4470 596683157 596682012 0.000000e+00 1914
37 TraesCS4A01G478800 chr6B 97.638 1016 16 4 3315 4329 51333565 51334573 0.000000e+00 1736
38 TraesCS4A01G478800 chr6B 83.559 517 61 12 3956 4469 411669289 411668794 3.900000e-126 462
39 TraesCS4A01G478800 chr4B 81.535 1186 159 39 3315 4469 245545866 245547022 0.000000e+00 922
40 TraesCS4A01G478800 chr1D 81.113 593 100 11 3885 4471 439835092 439835678 1.080000e-126 464
41 TraesCS4A01G478800 chr1D 83.669 447 50 16 4037 4469 434360384 434359947 3.100000e-107 399
42 TraesCS4A01G478800 chr1D 86.875 160 20 1 3859 4017 434360523 434360364 1.580000e-40 178
43 TraesCS4A01G478800 chr1D 79.845 258 31 6 3626 3870 439834670 439834919 9.510000e-38 169
44 TraesCS4A01G478800 chr6A 79.869 611 93 15 3884 4472 96150616 96150014 2.380000e-113 420
45 TraesCS4A01G478800 chr2A 88.108 185 20 2 4288 4471 23941281 23941098 9.310000e-53 219
46 TraesCS4A01G478800 chr2A 86.413 184 21 4 4289 4469 23948672 23948854 1.210000e-46 198
47 TraesCS4A01G478800 chr1A 86.264 182 21 3 4289 4469 533777259 533777437 1.570000e-45 195
48 TraesCS4A01G478800 chr6D 79.845 258 31 6 3626 3870 35018922 35019171 9.510000e-38 169


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 TraesCS4A01G478800 chr4A 735766460 735771980 5520 False 10196.0 10196 100.0000 1 5521 1 chr4A.!!$F9 5520
1 TraesCS4A01G478800 chr4A 736055261 736058556 3295 False 4108.0 4108 89.2750 1 3282 1 chr4A.!!$F11 3281
2 TraesCS4A01G478800 chr4A 736883293 736887872 4579 False 3389.5 5190 95.3880 1 5450 2 chr4A.!!$F17 5449
3 TraesCS4A01G478800 chr4A 735316356 735318923 2567 False 3055.0 3055 88.1470 695 3277 1 chr4A.!!$F7 2582
4 TraesCS4A01G478800 chr4A 735485365 735487907 2542 True 2737.0 2737 86.0930 695 3288 1 chr4A.!!$R1 2593
5 TraesCS4A01G478800 chr4A 735776450 735779064 2614 False 2715.0 2715 85.6270 695 3282 1 chr4A.!!$F10 2587
6 TraesCS4A01G478800 chr4A 735003469 735006005 2536 False 2710.0 2710 85.9510 695 3282 1 chr4A.!!$F6 2587
7 TraesCS4A01G478800 chr4A 736570748 736573338 2590 False 2684.0 2684 85.4260 663 3275 1 chr4A.!!$F12 2612
8 TraesCS4A01G478800 chr4A 734730671 734733262 2591 False 2667.0 2667 85.3120 663 3275 1 chr4A.!!$F4 2612
9 TraesCS4A01G478800 chr4A 734917491 734920038 2547 False 2636.0 2636 85.3740 690 3282 1 chr4A.!!$F5 2592
10 TraesCS4A01G478800 chr4A 736410688 736413254 2566 True 2599.0 2599 84.9750 695 3275 1 chr4A.!!$R3 2580
11 TraesCS4A01G478800 chr4A 736896814 736899385 2571 False 2444.0 2444 84.0020 695 3282 1 chr4A.!!$F14 2587
12 TraesCS4A01G478800 chr4A 734582680 734584932 2252 False 2440.0 2440 86.1960 695 2998 1 chr4A.!!$F3 2303
13 TraesCS4A01G478800 chr4A 736724764 736726853 2089 False 2283.0 2283 86.4160 1190 3282 1 chr4A.!!$F13 2092
14 TraesCS4A01G478800 chr4A 735689506 735691657 2151 False 2170.0 2170 84.9330 1100 3266 1 chr4A.!!$F8 2166
15 TraesCS4A01G478800 chr4A 736756370 736760212 3842 False 1715.5 2531 83.9725 695 5450 2 chr4A.!!$F16 4755
16 TraesCS4A01G478800 chr4A 734480156 734484671 4515 False 1684.5 2388 85.6450 665 5450 2 chr4A.!!$F15 4785
17 TraesCS4A01G478800 chr4A 736474730 736475524 794 True 1260.0 1260 95.2440 4653 5450 1 chr4A.!!$R5 797
18 TraesCS4A01G478800 chr4A 736466791 736467768 977 True 966.0 966 84.5840 4470 5450 1 chr4A.!!$R4 980
19 TraesCS4A01G478800 chr4A 734388101 734389079 978 False 957.0 957 84.3340 4470 5450 1 chr4A.!!$F2 980
20 TraesCS4A01G478800 chr4A 735558796 735559767 971 True 944.0 944 84.2320 4470 5450 1 chr4A.!!$R2 980
21 TraesCS4A01G478800 chr7A 7319721 7323008 3287 True 3803.0 3803 87.6880 1 3285 1 chr7A.!!$R3 3284
22 TraesCS4A01G478800 chr7A 7042887 7045454 2567 True 2933.0 2933 87.3320 695 3277 1 chr7A.!!$R2 2582
23 TraesCS4A01G478800 chr7A 6924751 6925722 971 True 1027.0 1027 85.7870 4470 5450 1 chr7A.!!$R1 980
24 TraesCS4A01G478800 chr7A 705140080 705140670 590 True 435.0 435 80.6020 3895 4470 1 chr7A.!!$R4 575
25 TraesCS4A01G478800 chr7D 5635448 5638037 2589 True 2641.0 2641 85.1770 702 3288 1 chr7D.!!$R3 2586
26 TraesCS4A01G478800 chr7D 5446501 5449076 2575 True 2597.0 2597 85.0020 695 3277 1 chr7D.!!$R1 2582
27 TraesCS4A01G478800 chr7D 5482971 5483949 978 True 891.0 891 83.1810 4470 5450 1 chr7D.!!$R2 980
28 TraesCS4A01G478800 chr7D 540645960 540647084 1124 True 847.5 1323 92.8845 3315 4469 2 chr7D.!!$R4 1154
29 TraesCS4A01G478800 chr2B 690965648 690966796 1148 True 1929.0 1929 96.8860 3315 4469 1 chr2B.!!$R2 1154
30 TraesCS4A01G478800 chr7B 596682012 596683157 1145 True 1914.0 1914 96.7100 3317 4470 1 chr7B.!!$R1 1153
31 TraesCS4A01G478800 chr6B 51333565 51334573 1008 False 1736.0 1736 97.6380 3315 4329 1 chr6B.!!$F1 1014
32 TraesCS4A01G478800 chr4B 245545866 245547022 1156 False 922.0 922 81.5350 3315 4469 1 chr4B.!!$F1 1154
33 TraesCS4A01G478800 chr1D 439834670 439835678 1008 False 316.5 464 80.4790 3626 4471 2 chr1D.!!$F1 845
34 TraesCS4A01G478800 chr1D 434359947 434360523 576 True 288.5 399 85.2720 3859 4469 2 chr1D.!!$R1 610
35 TraesCS4A01G478800 chr6A 96150014 96150616 602 True 420.0 420 79.8690 3884 4472 1 chr6A.!!$R1 588

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
811 847 1.269726 CCACAATCTTGCCGCAGTTTT 60.270 47.619 0.00 0.00 0.0 2.43 F
874 910 1.490490 AGTTGGACAAGTGGCTTCAGA 59.510 47.619 0.00 0.00 0.0 3.27 F
1021 1057 1.575576 GAAGCCTCTGTGTGCTGCAG 61.576 60.000 10.11 10.11 38.0 4.41 F
2715 2868 1.265635 TCAAACAAAGAATCACGGCCG 59.734 47.619 26.86 26.86 0.0 6.13 F
3207 3990 3.125316 CGAACCTGAAGACATTACCTTGC 59.875 47.826 0.00 0.00 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2694 2847 2.095263 CGGCCGTGATTCTTTGTTTGAT 60.095 45.455 19.5 0.0 0.0 2.57 R
2715 2868 3.181531 GCTTGCCAATGTTACGAATTTGC 60.182 43.478 0.0 0.0 0.0 3.68 R
2841 2994 5.939883 CCCAGTGACATTCTCAAGATTTGTA 59.060 40.000 0.0 0.0 0.0 2.41 R
4164 5275 2.542595 CGAGCATTTATACGAACACCCC 59.457 50.000 0.0 0.0 0.0 4.95 R
5166 6366 1.833630 CCCAGGCTCTTGACAGATGTA 59.166 52.381 0.0 0.0 0.0 2.29 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
211 212 3.939066 ACTCCAACAGGTTTTCTATCCG 58.061 45.455 0.00 0.00 0.00 4.18
236 237 6.674760 GCTGTTATATTCACCGGTTGTTTCTC 60.675 42.308 2.97 0.00 0.00 2.87
257 258 4.584874 TCCTATCTCCGATCTAGAAGCAG 58.415 47.826 0.00 0.00 0.00 4.24
264 265 4.938080 TCCGATCTAGAAGCAGTTTCATC 58.062 43.478 0.00 0.00 38.31 2.92
388 390 8.680903 CATTGCAGTTGACTAATTTATCTCCTT 58.319 33.333 0.00 0.00 0.00 3.36
436 438 4.133820 TCAATCACACGTCCAACAATTCT 58.866 39.130 0.00 0.00 0.00 2.40
443 445 4.242475 CACGTCCAACAATTCTAGTGCTA 58.758 43.478 0.00 0.00 0.00 3.49
465 467 6.258947 GCTAGTCTTTCGATTTATTCAAGCCT 59.741 38.462 0.00 0.00 0.00 4.58
515 517 4.160329 AGGAAAAGAGGGGAAATTTGTCC 58.840 43.478 0.00 0.00 36.90 4.02
525 527 7.128883 AGAGGGGAAATTTGTCCTTATAGCTTA 59.871 37.037 9.50 0.00 37.85 3.09
547 572 4.672587 TGTTCATCTCCATACTAGGTGC 57.327 45.455 0.00 0.00 0.00 5.01
612 642 6.841781 TTCCTCTATAAACAGCCCCTTTAT 57.158 37.500 0.00 0.00 0.00 1.40
613 643 6.841781 TCCTCTATAAACAGCCCCTTTATT 57.158 37.500 0.00 0.00 0.00 1.40
624 654 2.766263 GCCCCTTTATTTCCCTTTCAGG 59.234 50.000 0.00 0.00 34.30 3.86
811 847 1.269726 CCACAATCTTGCCGCAGTTTT 60.270 47.619 0.00 0.00 0.00 2.43
874 910 1.490490 AGTTGGACAAGTGGCTTCAGA 59.510 47.619 0.00 0.00 0.00 3.27
1021 1057 1.575576 GAAGCCTCTGTGTGCTGCAG 61.576 60.000 10.11 10.11 38.00 4.41
1157 1195 5.823861 TCTGGTTATAATGCAGATAGCCA 57.176 39.130 19.53 19.53 44.83 4.75
1167 1205 3.853475 TGCAGATAGCCACATCATATCG 58.147 45.455 0.00 0.00 44.83 2.92
1174 1212 2.893489 AGCCACATCATATCGTCAGCTA 59.107 45.455 0.00 0.00 0.00 3.32
1283 1327 6.239396 AGACAACAGCTACTACTGAGTCTAA 58.761 40.000 16.64 0.00 45.50 2.10
1467 1511 1.839424 TCATCGAGTCTGCCTCTCAA 58.161 50.000 0.00 0.00 38.11 3.02
1674 1719 2.662866 TCTCGACGGGATACATTTCCT 58.337 47.619 0.00 0.00 35.97 3.36
1817 1881 4.928615 ACTCGAAGATTTTGCAGAGAAGAG 59.071 41.667 2.69 1.78 33.89 2.85
2041 2105 5.163513 CAAAAGGCCACAAGTATGTCATTC 58.836 41.667 5.01 0.00 37.82 2.67
2456 2577 5.532557 ACTACAAAATTTGAAGAAGCTGCC 58.467 37.500 13.19 0.00 0.00 4.85
2474 2595 2.017049 GCCGGTGCTATCTTTGTCATT 58.983 47.619 1.90 0.00 33.53 2.57
2665 2794 5.580691 TGCAATCTAAGGAAGTTACGACATG 59.419 40.000 0.00 0.00 0.00 3.21
2669 2798 9.314321 CAATCTAAGGAAGTTACGACATGTTAT 57.686 33.333 0.00 0.00 0.00 1.89
2715 2868 1.265635 TCAAACAAAGAATCACGGCCG 59.734 47.619 26.86 26.86 0.00 6.13
2841 2994 4.072131 AGATTCGTGGCAGTTTATGTGTT 58.928 39.130 0.00 0.00 0.00 3.32
3024 3807 6.093404 GCCTCAACTTAAGCACCTTAAAATC 58.907 40.000 1.29 0.00 35.82 2.17
3207 3990 3.125316 CGAACCTGAAGACATTACCTTGC 59.875 47.826 0.00 0.00 0.00 4.01
3307 4102 4.017591 ACCACAATATCATGAGGGGAAACA 60.018 41.667 7.92 0.00 35.60 2.83
4249 5443 5.763204 ACATCTGTTTAACGTGGAGTCAAAT 59.237 36.000 0.00 0.00 0.00 2.32
5065 6265 6.127310 ACTCCAAGTTAGCAGTCCTGTAATAG 60.127 42.308 0.00 0.00 0.00 1.73
5120 6320 4.346418 AGTTCCAACATGTCTCTCTCTTGT 59.654 41.667 0.00 0.00 0.00 3.16
5149 6349 5.990996 TGCAAGGAACCATTCTTTTCATTTC 59.009 36.000 0.00 0.00 0.00 2.17
5185 6385 3.616956 TTACATCTGTCAAGAGCCTGG 57.383 47.619 0.00 0.00 35.37 4.45
5192 6392 1.556911 TGTCAAGAGCCTGGGATTCTC 59.443 52.381 0.00 0.00 0.00 2.87
5224 6424 6.771749 TCAAATGATTTCCTTGCCAACAAATT 59.228 30.769 0.00 0.00 34.74 1.82
5260 6460 4.914504 CCAATCTGACTAATCTCGTCATCG 59.085 45.833 0.00 0.00 40.30 3.84
5311 6511 2.367377 TGCCATCCTCCCTCCTGG 60.367 66.667 0.00 0.00 0.00 4.45
5400 6600 1.069022 CCAAAGATTGCGCATATCCGG 60.069 52.381 12.75 13.30 0.00 5.14
5423 6627 6.379386 GGTGGAAGACAATTAGTTAAAGTGC 58.621 40.000 0.00 0.00 36.63 4.40
5454 6658 8.990163 AGTTTCCCACTTACAAATAAAGAAGA 57.010 30.769 0.00 0.00 27.32 2.87
5455 6659 9.416284 AGTTTCCCACTTACAAATAAAGAAGAA 57.584 29.630 0.00 0.00 27.32 2.52
5456 6660 9.678941 GTTTCCCACTTACAAATAAAGAAGAAG 57.321 33.333 0.00 0.00 0.00 2.85
5457 6661 7.448748 TCCCACTTACAAATAAAGAAGAAGC 57.551 36.000 0.00 0.00 0.00 3.86
5458 6662 7.231467 TCCCACTTACAAATAAAGAAGAAGCT 58.769 34.615 0.00 0.00 0.00 3.74
5459 6663 7.390718 TCCCACTTACAAATAAAGAAGAAGCTC 59.609 37.037 0.00 0.00 0.00 4.09
5460 6664 7.174946 CCCACTTACAAATAAAGAAGAAGCTCA 59.825 37.037 0.00 0.00 0.00 4.26
5461 6665 8.017946 CCACTTACAAATAAAGAAGAAGCTCAC 58.982 37.037 0.00 0.00 0.00 3.51
5462 6666 8.778358 CACTTACAAATAAAGAAGAAGCTCACT 58.222 33.333 0.00 0.00 0.00 3.41
5463 6667 9.998106 ACTTACAAATAAAGAAGAAGCTCACTA 57.002 29.630 0.00 0.00 0.00 2.74
5465 6669 7.674471 ACAAATAAAGAAGAAGCTCACTACC 57.326 36.000 0.00 0.00 0.00 3.18
5466 6670 7.224297 ACAAATAAAGAAGAAGCTCACTACCA 58.776 34.615 0.00 0.00 0.00 3.25
5467 6671 7.885399 ACAAATAAAGAAGAAGCTCACTACCAT 59.115 33.333 0.00 0.00 0.00 3.55
5468 6672 8.394121 CAAATAAAGAAGAAGCTCACTACCATC 58.606 37.037 0.00 0.00 0.00 3.51
5469 6673 5.489792 AAAGAAGAAGCTCACTACCATCA 57.510 39.130 0.00 0.00 0.00 3.07
5470 6674 5.690464 AAGAAGAAGCTCACTACCATCAT 57.310 39.130 0.00 0.00 0.00 2.45
5471 6675 5.021033 AGAAGAAGCTCACTACCATCATG 57.979 43.478 0.00 0.00 0.00 3.07
5472 6676 3.191078 AGAAGCTCACTACCATCATGC 57.809 47.619 0.00 0.00 0.00 4.06
5473 6677 2.158842 AGAAGCTCACTACCATCATGCC 60.159 50.000 0.00 0.00 0.00 4.40
5474 6678 0.105593 AGCTCACTACCATCATGCCG 59.894 55.000 0.00 0.00 0.00 5.69
5475 6679 0.882042 GCTCACTACCATCATGCCGG 60.882 60.000 0.00 0.00 0.00 6.13
5476 6680 0.465705 CTCACTACCATCATGCCGGT 59.534 55.000 1.90 10.32 39.41 5.28
5477 6681 0.908910 TCACTACCATCATGCCGGTT 59.091 50.000 10.68 0.00 36.69 4.44
5478 6682 1.280710 TCACTACCATCATGCCGGTTT 59.719 47.619 10.68 0.00 36.69 3.27
5479 6683 2.502130 TCACTACCATCATGCCGGTTTA 59.498 45.455 10.68 0.00 36.69 2.01
5480 6684 2.872245 CACTACCATCATGCCGGTTTAG 59.128 50.000 10.68 6.44 36.69 1.85
5481 6685 1.873591 CTACCATCATGCCGGTTTAGC 59.126 52.381 10.68 0.00 36.69 3.09
5482 6686 0.255890 ACCATCATGCCGGTTTAGCT 59.744 50.000 1.90 0.00 28.43 3.32
5483 6687 0.947244 CCATCATGCCGGTTTAGCTC 59.053 55.000 1.90 0.00 0.00 4.09
5484 6688 1.667236 CATCATGCCGGTTTAGCTCA 58.333 50.000 1.90 0.00 0.00 4.26
5485 6689 1.600957 CATCATGCCGGTTTAGCTCAG 59.399 52.381 1.90 0.00 0.00 3.35
5486 6690 0.107703 TCATGCCGGTTTAGCTCAGG 60.108 55.000 1.90 0.00 0.00 3.86
5488 6692 2.824489 GCCGGTTTAGCTCAGGCC 60.824 66.667 1.90 0.00 41.81 5.19
5489 6693 2.511600 CCGGTTTAGCTCAGGCCG 60.512 66.667 0.00 10.68 41.82 6.13
5490 6694 3.195698 CGGTTTAGCTCAGGCCGC 61.196 66.667 0.00 0.00 39.73 6.53
5491 6695 2.824489 GGTTTAGCTCAGGCCGCC 60.824 66.667 0.00 0.00 39.73 6.13
5492 6696 2.046314 GTTTAGCTCAGGCCGCCA 60.046 61.111 13.15 0.00 39.73 5.69
5493 6697 1.674322 GTTTAGCTCAGGCCGCCAA 60.674 57.895 13.15 0.00 39.73 4.52
5494 6698 1.674322 TTTAGCTCAGGCCGCCAAC 60.674 57.895 13.15 0.00 39.73 3.77
5495 6699 2.404566 TTTAGCTCAGGCCGCCAACA 62.405 55.000 13.15 0.00 39.73 3.33
5496 6700 2.196997 TTAGCTCAGGCCGCCAACAT 62.197 55.000 13.15 0.00 39.73 2.71
5497 6701 1.334384 TAGCTCAGGCCGCCAACATA 61.334 55.000 13.15 0.00 39.73 2.29
5498 6702 2.182842 GCTCAGGCCGCCAACATAG 61.183 63.158 13.15 2.33 0.00 2.23
5499 6703 1.522092 CTCAGGCCGCCAACATAGA 59.478 57.895 13.15 0.00 0.00 1.98
5500 6704 0.107703 CTCAGGCCGCCAACATAGAA 60.108 55.000 13.15 0.00 0.00 2.10
5501 6705 0.107703 TCAGGCCGCCAACATAGAAG 60.108 55.000 13.15 0.00 0.00 2.85
5502 6706 1.452108 AGGCCGCCAACATAGAAGC 60.452 57.895 13.15 0.00 0.00 3.86
5503 6707 1.452108 GGCCGCCAACATAGAAGCT 60.452 57.895 3.91 0.00 0.00 3.74
5504 6708 1.032114 GGCCGCCAACATAGAAGCTT 61.032 55.000 3.91 0.00 0.00 3.74
5505 6709 0.811281 GCCGCCAACATAGAAGCTTT 59.189 50.000 0.00 0.00 0.00 3.51
5506 6710 1.202348 GCCGCCAACATAGAAGCTTTT 59.798 47.619 0.00 0.00 0.00 2.27
5507 6711 2.867429 CCGCCAACATAGAAGCTTTTG 58.133 47.619 0.00 0.05 0.00 2.44
5508 6712 2.228822 CCGCCAACATAGAAGCTTTTGT 59.771 45.455 0.00 2.49 0.00 2.83
5509 6713 3.492313 CGCCAACATAGAAGCTTTTGTC 58.508 45.455 0.00 0.00 0.00 3.18
5510 6714 3.189287 CGCCAACATAGAAGCTTTTGTCT 59.811 43.478 0.00 0.00 0.00 3.41
5511 6715 4.391830 CGCCAACATAGAAGCTTTTGTCTA 59.608 41.667 0.00 0.00 0.00 2.59
5512 6716 5.065218 CGCCAACATAGAAGCTTTTGTCTAT 59.935 40.000 0.00 0.00 37.52 1.98
5513 6717 6.403636 CGCCAACATAGAAGCTTTTGTCTATT 60.404 38.462 0.00 0.00 35.35 1.73
5514 6718 6.749118 GCCAACATAGAAGCTTTTGTCTATTG 59.251 38.462 0.00 0.46 35.35 1.90
5515 6719 7.362056 GCCAACATAGAAGCTTTTGTCTATTGA 60.362 37.037 0.00 0.00 35.35 2.57
5516 6720 8.680903 CCAACATAGAAGCTTTTGTCTATTGAT 58.319 33.333 0.00 0.00 35.35 2.57
5517 6721 9.499585 CAACATAGAAGCTTTTGTCTATTGATG 57.500 33.333 0.00 0.00 35.35 3.07
5518 6722 8.798859 ACATAGAAGCTTTTGTCTATTGATGT 57.201 30.769 0.00 0.00 35.35 3.06
5519 6723 8.887717 ACATAGAAGCTTTTGTCTATTGATGTC 58.112 33.333 0.00 0.00 35.35 3.06
5520 6724 8.886719 CATAGAAGCTTTTGTCTATTGATGTCA 58.113 33.333 0.00 0.00 35.35 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 212 4.957759 AACAACCGGTGAATATAACAGC 57.042 40.909 8.52 0.00 0.00 4.40
236 237 4.331968 ACTGCTTCTAGATCGGAGATAGG 58.668 47.826 15.01 0.00 45.12 2.57
257 258 5.643339 AAATGATAGACGAGCGATGAAAC 57.357 39.130 0.00 0.00 0.00 2.78
264 265 5.223382 ACCTGAATAAATGATAGACGAGCG 58.777 41.667 0.00 0.00 0.00 5.03
388 390 5.446143 AAAACATGTTGGAGTGCGAAATA 57.554 34.783 12.82 0.00 0.00 1.40
393 395 3.077229 TGAAAAACATGTTGGAGTGCG 57.923 42.857 12.82 0.00 0.00 5.34
436 438 9.302345 CTTGAATAAATCGAAAGACTAGCACTA 57.698 33.333 0.00 0.00 46.97 2.74
443 445 7.362142 GGAAAGGCTTGAATAAATCGAAAGACT 60.362 37.037 0.00 0.00 46.97 3.24
465 467 1.562008 TCTTGGTGTGGACTGTGGAAA 59.438 47.619 0.00 0.00 0.00 3.13
525 527 4.904251 AGCACCTAGTATGGAGATGAACAT 59.096 41.667 0.00 0.00 0.00 2.71
578 603 8.874816 GCTGTTTATAGAGGAAAGTAAGAACAG 58.125 37.037 0.00 0.00 41.69 3.16
585 610 5.286221 AGGGGCTGTTTATAGAGGAAAGTA 58.714 41.667 0.00 0.00 0.00 2.24
586 611 4.112331 AGGGGCTGTTTATAGAGGAAAGT 58.888 43.478 0.00 0.00 0.00 2.66
587 612 4.779993 AGGGGCTGTTTATAGAGGAAAG 57.220 45.455 0.00 0.00 0.00 2.62
588 613 5.530176 AAAGGGGCTGTTTATAGAGGAAA 57.470 39.130 0.00 0.00 0.00 3.13
811 847 3.055602 TCTGCTGCTTCAATCAAGAGCTA 60.056 43.478 0.00 0.00 36.75 3.32
874 910 6.127786 GCCAGATAGAATGCTTCTTTGAGTTT 60.128 38.462 4.15 0.00 41.14 2.66
1021 1057 1.068055 CAGATTGGACAACCTGCTTGC 60.068 52.381 0.00 0.00 37.04 4.01
1152 1190 2.893489 AGCTGACGATATGATGTGGCTA 59.107 45.455 0.00 0.00 0.00 3.93
1157 1195 5.928839 GGAACAATAGCTGACGATATGATGT 59.071 40.000 0.00 0.00 0.00 3.06
1167 1205 3.055819 TGGTCTCAGGAACAATAGCTGAC 60.056 47.826 0.00 0.00 36.07 3.51
1174 1212 3.328931 AGTGATGTGGTCTCAGGAACAAT 59.671 43.478 0.00 0.00 41.23 2.71
1283 1327 4.202223 CCAAACCCGAGTACATAGCTGTAT 60.202 45.833 0.00 0.00 39.93 2.29
1534 1579 3.421844 ACACAAGTAGGAATTTCCCTGC 58.578 45.455 11.92 2.98 37.19 4.85
1674 1719 2.097954 CACTTCACAACAAAGAGCAGCA 59.902 45.455 0.00 0.00 0.00 4.41
1817 1881 5.106515 GGAGATTGTCCAAGTCTTTTAGCAC 60.107 44.000 0.00 0.00 46.10 4.40
1933 1997 3.318191 AGCTCTCATGGGCTCACC 58.682 61.111 0.00 0.00 40.81 4.02
2041 2105 6.987992 CCCATCCAAAGATAAACCAAATCATG 59.012 38.462 0.00 0.00 0.00 3.07
2456 2577 6.176975 TGTAAAATGACAAAGATAGCACCG 57.823 37.500 0.00 0.00 0.00 4.94
2474 2595 6.584488 TCTGGCAACTTACTACTGTTGTAAA 58.416 36.000 14.07 0.72 43.66 2.01
2694 2847 2.095263 CGGCCGTGATTCTTTGTTTGAT 60.095 45.455 19.50 0.00 0.00 2.57
2715 2868 3.181531 GCTTGCCAATGTTACGAATTTGC 60.182 43.478 0.00 0.00 0.00 3.68
2841 2994 5.939883 CCCAGTGACATTCTCAAGATTTGTA 59.060 40.000 0.00 0.00 0.00 2.41
3024 3807 4.630894 TTTTGGATATTTGTAGCCGCAG 57.369 40.909 0.00 0.00 0.00 5.18
3097 3880 2.203401 TGCACTGCAATCAACAAAAGC 58.797 42.857 0.00 0.00 34.76 3.51
3207 3990 4.302559 AAGTTTAAGGCCTAGTGGAAGG 57.697 45.455 5.16 0.00 39.87 3.46
3285 4068 4.535781 TGTTTCCCCTCATGATATTGTGG 58.464 43.478 0.00 0.00 0.00 4.17
3307 4102 0.667993 CACCACGATGTTGCCAAGTT 59.332 50.000 0.00 0.00 0.00 2.66
3720 4581 3.782443 GCCCCTTGGATCCGTCGT 61.782 66.667 7.39 0.00 0.00 4.34
3760 4621 3.176578 TCGCGTCGGATTTGTCGC 61.177 61.111 5.77 0.00 44.23 5.19
4163 5274 2.876550 GAGCATTTATACGAACACCCCC 59.123 50.000 0.00 0.00 0.00 5.40
4164 5275 2.542595 CGAGCATTTATACGAACACCCC 59.457 50.000 0.00 0.00 0.00 4.95
4165 5276 3.450578 TCGAGCATTTATACGAACACCC 58.549 45.455 0.00 0.00 0.00 4.61
4317 5511 4.828939 AGCCATTTGAGTGAATTTCTGACA 59.171 37.500 0.00 0.00 0.00 3.58
5044 6244 6.631016 TGACTATTACAGGACTGCTAACTTG 58.369 40.000 0.00 0.00 0.00 3.16
5065 6265 2.056094 GCCAAGAGCATGTTGTTGAC 57.944 50.000 19.08 5.54 37.73 3.18
5120 6320 4.591321 AAGAATGGTTCCTTGCATCCTA 57.409 40.909 0.00 0.00 0.00 2.94
5149 6349 8.752766 ACAGATGTAAAATTTGCAGATTCTTG 57.247 30.769 2.51 0.00 0.00 3.02
5166 6366 1.833630 CCCAGGCTCTTGACAGATGTA 59.166 52.381 0.00 0.00 0.00 2.29
5185 6385 8.401709 GGAAATCATTTGACAACTAGAGAATCC 58.598 37.037 0.00 0.00 33.66 3.01
5192 6392 6.095377 GGCAAGGAAATCATTTGACAACTAG 58.905 40.000 0.00 0.00 30.18 2.57
5224 6424 2.108075 TCAGATTGGGGAAGCACTTCAA 59.892 45.455 12.21 0.00 41.20 2.69
5260 6460 3.281727 TGACAATCTGGGGCAGTTATC 57.718 47.619 0.00 0.00 32.61 1.75
5311 6511 6.059787 AGAACAATCCCATAGAGATATGCC 57.940 41.667 0.00 0.00 0.00 4.40
5320 6520 6.586344 TCAAGAGCTTAGAACAATCCCATAG 58.414 40.000 0.00 0.00 0.00 2.23
5400 6600 6.073440 TCGCACTTTAACTAATTGTCTTCCAC 60.073 38.462 0.00 0.00 0.00 4.02
5450 6654 3.559242 GCATGATGGTAGTGAGCTTCTTC 59.441 47.826 0.00 0.00 0.00 2.87
5451 6655 3.539604 GCATGATGGTAGTGAGCTTCTT 58.460 45.455 0.00 0.00 0.00 2.52
5452 6656 2.158842 GGCATGATGGTAGTGAGCTTCT 60.159 50.000 0.00 0.00 0.00 2.85
5453 6657 2.216898 GGCATGATGGTAGTGAGCTTC 58.783 52.381 0.00 0.00 0.00 3.86
5454 6658 1.473965 CGGCATGATGGTAGTGAGCTT 60.474 52.381 0.00 0.00 0.00 3.74
5455 6659 0.105593 CGGCATGATGGTAGTGAGCT 59.894 55.000 0.00 0.00 0.00 4.09
5456 6660 0.882042 CCGGCATGATGGTAGTGAGC 60.882 60.000 0.00 0.00 0.00 4.26
5457 6661 0.465705 ACCGGCATGATGGTAGTGAG 59.534 55.000 0.00 0.00 36.50 3.51
5458 6662 0.908910 AACCGGCATGATGGTAGTGA 59.091 50.000 0.00 0.00 37.54 3.41
5459 6663 1.750193 AAACCGGCATGATGGTAGTG 58.250 50.000 0.00 0.00 37.54 2.74
5460 6664 2.745152 GCTAAACCGGCATGATGGTAGT 60.745 50.000 0.00 4.48 37.54 2.73
5461 6665 1.873591 GCTAAACCGGCATGATGGTAG 59.126 52.381 0.00 6.09 37.54 3.18
5462 6666 1.488812 AGCTAAACCGGCATGATGGTA 59.511 47.619 0.00 0.00 37.54 3.25
5463 6667 0.255890 AGCTAAACCGGCATGATGGT 59.744 50.000 0.00 0.00 41.20 3.55
5464 6668 0.947244 GAGCTAAACCGGCATGATGG 59.053 55.000 0.00 0.00 0.00 3.51
5465 6669 1.600957 CTGAGCTAAACCGGCATGATG 59.399 52.381 0.00 0.00 0.00 3.07
5466 6670 1.475751 CCTGAGCTAAACCGGCATGAT 60.476 52.381 0.00 0.00 0.00 2.45
5467 6671 0.107703 CCTGAGCTAAACCGGCATGA 60.108 55.000 0.00 0.00 0.00 3.07
5468 6672 1.718757 GCCTGAGCTAAACCGGCATG 61.719 60.000 0.00 0.00 40.41 4.06
5469 6673 1.452108 GCCTGAGCTAAACCGGCAT 60.452 57.895 0.00 0.00 40.41 4.40
5470 6674 2.046314 GCCTGAGCTAAACCGGCA 60.046 61.111 0.00 0.00 40.41 5.69
5471 6675 2.824489 GGCCTGAGCTAAACCGGC 60.824 66.667 0.00 0.00 39.73 6.13
5472 6676 2.511600 CGGCCTGAGCTAAACCGG 60.512 66.667 0.00 0.00 40.18 5.28
5473 6677 3.195698 GCGGCCTGAGCTAAACCG 61.196 66.667 7.70 7.70 46.50 4.44
5474 6678 2.824489 GGCGGCCTGAGCTAAACC 60.824 66.667 12.87 0.00 39.73 3.27
5475 6679 1.674322 TTGGCGGCCTGAGCTAAAC 60.674 57.895 21.46 0.00 39.73 2.01
5476 6680 1.674322 GTTGGCGGCCTGAGCTAAA 60.674 57.895 21.46 0.54 36.86 1.85
5477 6681 2.046314 GTTGGCGGCCTGAGCTAA 60.046 61.111 21.46 1.36 39.73 3.09
5478 6682 1.334384 TATGTTGGCGGCCTGAGCTA 61.334 55.000 21.46 2.89 39.73 3.32
5479 6683 2.599645 CTATGTTGGCGGCCTGAGCT 62.600 60.000 21.46 3.87 39.73 4.09
5480 6684 2.124736 TATGTTGGCGGCCTGAGC 60.125 61.111 21.46 3.21 38.76 4.26
5481 6685 0.107703 TTCTATGTTGGCGGCCTGAG 60.108 55.000 21.46 9.82 0.00 3.35
5482 6686 0.107703 CTTCTATGTTGGCGGCCTGA 60.108 55.000 21.46 6.04 0.00 3.86
5483 6687 1.718757 GCTTCTATGTTGGCGGCCTG 61.719 60.000 21.46 3.74 0.00 4.85
5484 6688 1.452108 GCTTCTATGTTGGCGGCCT 60.452 57.895 21.46 1.61 0.00 5.19
5485 6689 1.032114 AAGCTTCTATGTTGGCGGCC 61.032 55.000 13.32 13.32 0.00 6.13
5486 6690 0.811281 AAAGCTTCTATGTTGGCGGC 59.189 50.000 0.00 0.00 0.00 6.53
5487 6691 2.228822 ACAAAAGCTTCTATGTTGGCGG 59.771 45.455 11.46 0.00 0.00 6.13
5488 6692 3.189287 AGACAAAAGCTTCTATGTTGGCG 59.811 43.478 11.46 0.00 32.28 5.69
5489 6693 4.773323 AGACAAAAGCTTCTATGTTGGC 57.227 40.909 11.46 8.76 0.00 4.52
5490 6694 8.044060 TCAATAGACAAAAGCTTCTATGTTGG 57.956 34.615 11.46 2.21 35.61 3.77
5491 6695 9.499585 CATCAATAGACAAAAGCTTCTATGTTG 57.500 33.333 0.00 2.52 35.61 3.33
5492 6696 9.236006 ACATCAATAGACAAAAGCTTCTATGTT 57.764 29.630 0.00 0.77 35.61 2.71
5493 6697 8.798859 ACATCAATAGACAAAAGCTTCTATGT 57.201 30.769 0.00 5.78 35.61 2.29
5494 6698 8.886719 TGACATCAATAGACAAAAGCTTCTATG 58.113 33.333 0.00 2.17 35.61 2.23


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

AutoCloner maintained by Alex Coulton.