Multiple sequence alignment - TraesCS3D01G360100

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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 TraesCS3D01G360100 chr3D 100.000 4854 0 0 1 4854 473750505 473745652 0.000000e+00 8964
1 TraesCS3D01G360100 chr3D 96.512 86 3 0 2516 2601 404594183 404594098 5.060000e-30 143
2 TraesCS3D01G360100 chr3D 91.765 85 7 0 4441 4525 389633131 389633215 8.530000e-23 119
3 TraesCS3D01G360100 chr3D 89.362 94 7 3 4441 4531 136418857 136418764 1.100000e-21 115
4 TraesCS3D01G360100 chr3A 94.442 2447 96 11 44 2477 616254192 616251773 0.000000e+00 3729
5 TraesCS3D01G360100 chr3A 96.107 2055 61 12 2599 4640 616251531 616249483 0.000000e+00 3334
6 TraesCS3D01G360100 chr3A 92.523 321 19 2 4537 4854 616249481 616249163 5.730000e-124 455
7 TraesCS3D01G360100 chr3A 98.305 59 1 0 2461 2519 616251586 616251528 2.390000e-18 104
8 TraesCS3D01G360100 chr3B 93.263 2553 97 19 1 2519 630008085 630005574 0.000000e+00 3692
9 TraesCS3D01G360100 chr3B 93.436 1691 90 15 2670 4353 630005483 630003807 0.000000e+00 2488
10 TraesCS3D01G360100 chr3B 90.099 101 9 1 4441 4541 783474168 783474069 3.940000e-26 130
11 TraesCS3D01G360100 chr3B 89.474 95 10 0 4433 4527 482487892 482487798 2.370000e-23 121
12 TraesCS3D01G360100 chr7B 83.969 393 47 8 3823 4210 639215677 639215296 3.570000e-96 363
13 TraesCS3D01G360100 chr7B 95.506 89 4 0 2517 2605 657870646 657870558 5.060000e-30 143
14 TraesCS3D01G360100 chr7B 90.385 104 6 4 4422 4525 482484937 482485036 3.050000e-27 134
15 TraesCS3D01G360100 chr7B 87.619 105 10 3 4424 4525 482485055 482484951 8.530000e-23 119
16 TraesCS3D01G360100 chr4D 82.448 433 53 12 3585 4011 333467733 333467318 1.660000e-94 357
17 TraesCS3D01G360100 chr5D 81.755 433 61 12 3585 4011 371882009 371882429 3.600000e-91 346
18 TraesCS3D01G360100 chr5D 85.577 104 9 2 4087 4190 371882432 371882529 2.390000e-18 104
19 TraesCS3D01G360100 chr5B 83.582 268 36 7 3894 4157 365305686 365305949 1.350000e-60 244
20 TraesCS3D01G360100 chr5B 82.707 266 37 8 3896 4157 365321205 365321465 1.360000e-55 228
21 TraesCS3D01G360100 chr5B 92.857 98 6 1 2513 2609 507933379 507933476 1.820000e-29 141
22 TraesCS3D01G360100 chr5B 92.941 85 6 0 2517 2601 674658524 674658440 1.830000e-24 124
23 TraesCS3D01G360100 chr6D 89.080 174 16 2 4040 4210 193559503 193559676 3.810000e-51 213
24 TraesCS3D01G360100 chr6D 97.647 85 2 0 2517 2601 91174832 91174916 3.910000e-31 147
25 TraesCS3D01G360100 chr6B 88.506 174 15 3 4040 4210 300951529 300951358 6.370000e-49 206
26 TraesCS3D01G360100 chr1B 97.701 87 2 0 2515 2601 10762245 10762331 3.030000e-32 150
27 TraesCS3D01G360100 chr1A 95.294 85 4 0 4441 4525 568391203 568391287 8.470000e-28 135
28 TraesCS3D01G360100 chr1A 92.941 85 6 0 4441 4525 415638131 415638047 1.830000e-24 124
29 TraesCS3D01G360100 chr4A 91.579 95 8 0 2517 2611 464687280 464687374 1.100000e-26 132
30 TraesCS3D01G360100 chr1D 94.118 85 5 0 2517 2601 110500579 110500495 3.940000e-26 130
31 TraesCS3D01G360100 chr7A 91.011 89 7 1 2514 2602 548567139 548567226 8.530000e-23 119


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 TraesCS3D01G360100 chr3D 473745652 473750505 4853 True 8964.0 8964 100.00000 1 4854 1 chr3D.!!$R3 4853
1 TraesCS3D01G360100 chr3A 616249163 616254192 5029 True 1905.5 3729 95.34425 44 4854 4 chr3A.!!$R1 4810
2 TraesCS3D01G360100 chr3B 630003807 630008085 4278 True 3090.0 3692 93.34950 1 4353 2 chr3B.!!$R3 4352
3 TraesCS3D01G360100 chr5D 371882009 371882529 520 False 225.0 346 83.66600 3585 4190 2 chr5D.!!$F1 605

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
235 237 0.534203 TTCCGTTTGTGCTCCTGTCC 60.534 55.0 0.00 0.00 0.00 4.02 F
454 458 0.682292 TGCAATACCACTGACGTCCA 59.318 50.0 14.12 0.01 0.00 4.02 F
1397 1414 0.321298 TGGCGCTACTTTCCTTGTCC 60.321 55.0 7.64 0.00 0.00 4.02 F
1398 1415 1.025113 GGCGCTACTTTCCTTGTCCC 61.025 60.0 7.64 0.00 0.00 4.46 F
1399 1416 0.321298 GCGCTACTTTCCTTGTCCCA 60.321 55.0 0.00 0.00 0.00 4.37 F
2447 2499 2.040412 AGCCTTCTAGGGAACACAAAGG 59.960 50.0 0.00 0.00 35.37 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1362 1.923204 CTCTCTTCCATCGAAAGCACG 59.077 52.381 0.0 0.00 0.00 5.34 R
1986 2029 2.285220 CCTGATTTGCTTGTATCGTCCG 59.715 50.000 0.0 0.00 0.00 4.79 R
2583 2838 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.0 0.00 0.00 2.74 R
3094 3380 1.230635 CCCTGCACAACTGGTTCTCG 61.231 60.000 0.0 0.00 35.64 4.04 R
3338 3625 3.630312 TGTGAGGGTCTGCTAACAAAAAC 59.370 43.478 0.0 0.00 0.00 2.43 R
4356 4653 0.164432 GCACCGCGGTAAACAGTAAC 59.836 55.000 33.7 8.02 0.00 2.50 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
20 21 1.744320 GCGTTGCTTGTTTTCCCCCT 61.744 55.000 0.00 0.00 0.00 4.79
74 76 1.891060 GATCGATCCATGCCGCGTTC 61.891 60.000 14.76 0.00 0.00 3.95
94 96 3.747976 GCGCGGATTTTGGGCAGT 61.748 61.111 8.83 0.00 43.94 4.40
127 129 3.573491 GCGGCGCCACCTGATTAC 61.573 66.667 28.98 0.00 35.61 1.89
161 163 3.491447 GCGGCATTGGAATTAGCATTTCT 60.491 43.478 0.00 0.00 0.00 2.52
235 237 0.534203 TTCCGTTTGTGCTCCTGTCC 60.534 55.000 0.00 0.00 0.00 4.02
270 274 3.001736 CGCACCTTTAGATTCTGCTTAGC 59.998 47.826 0.00 0.00 0.00 3.09
288 292 1.887301 CTGTGCATGATTGGCTGCA 59.113 52.632 0.50 0.00 45.60 4.41
334 338 7.630242 TCAGATTATTCCTCGCTTGATTTTT 57.370 32.000 0.00 0.00 0.00 1.94
370 374 6.410540 AGGTTCAGAGAGTTGGAAATCATAC 58.589 40.000 0.00 0.00 0.00 2.39
410 414 6.628844 GCCAGAATTTCCTTCAGTGCATATTT 60.629 38.462 0.00 0.00 36.24 1.40
439 443 2.088423 AGTCACTTCGGTTTGTTGCAA 58.912 42.857 0.00 0.00 0.00 4.08
440 444 2.687935 AGTCACTTCGGTTTGTTGCAAT 59.312 40.909 0.59 0.00 0.00 3.56
441 445 3.880490 AGTCACTTCGGTTTGTTGCAATA 59.120 39.130 0.59 0.00 0.00 1.90
442 446 3.972502 GTCACTTCGGTTTGTTGCAATAC 59.027 43.478 0.59 1.42 0.00 1.89
443 447 3.003897 TCACTTCGGTTTGTTGCAATACC 59.996 43.478 0.59 10.14 0.00 2.73
444 448 2.952978 ACTTCGGTTTGTTGCAATACCA 59.047 40.909 21.05 6.64 0.00 3.25
445 449 3.243267 ACTTCGGTTTGTTGCAATACCAC 60.243 43.478 21.05 11.02 0.00 4.16
446 450 2.577700 TCGGTTTGTTGCAATACCACT 58.422 42.857 21.05 0.00 0.00 4.00
447 451 2.292016 TCGGTTTGTTGCAATACCACTG 59.708 45.455 21.05 14.55 0.00 3.66
448 452 2.292016 CGGTTTGTTGCAATACCACTGA 59.708 45.455 21.05 0.00 0.00 3.41
449 453 3.638484 GGTTTGTTGCAATACCACTGAC 58.362 45.455 18.16 5.77 0.00 3.51
450 454 3.296628 GTTTGTTGCAATACCACTGACG 58.703 45.455 0.59 0.00 0.00 4.35
451 455 2.248280 TGTTGCAATACCACTGACGT 57.752 45.000 0.59 0.00 0.00 4.34
452 456 2.139917 TGTTGCAATACCACTGACGTC 58.860 47.619 9.11 9.11 0.00 4.34
453 457 1.463444 GTTGCAATACCACTGACGTCC 59.537 52.381 14.12 0.00 0.00 4.79
454 458 0.682292 TGCAATACCACTGACGTCCA 59.318 50.000 14.12 0.01 0.00 4.02
455 459 1.277842 TGCAATACCACTGACGTCCAT 59.722 47.619 14.12 0.00 0.00 3.41
456 460 1.665679 GCAATACCACTGACGTCCATG 59.334 52.381 14.12 11.01 0.00 3.66
457 461 2.676750 GCAATACCACTGACGTCCATGA 60.677 50.000 14.12 0.00 0.00 3.07
458 462 3.595173 CAATACCACTGACGTCCATGAA 58.405 45.455 14.12 3.69 0.00 2.57
459 463 2.736144 TACCACTGACGTCCATGAAC 57.264 50.000 14.12 0.00 0.00 3.18
460 464 0.756294 ACCACTGACGTCCATGAACA 59.244 50.000 14.12 0.00 0.00 3.18
486 490 5.249780 TCCTGTGTTCTTGGGCTATTTTA 57.750 39.130 0.00 0.00 0.00 1.52
488 492 5.885912 TCCTGTGTTCTTGGGCTATTTTATC 59.114 40.000 0.00 0.00 0.00 1.75
489 493 5.652014 CCTGTGTTCTTGGGCTATTTTATCA 59.348 40.000 0.00 0.00 0.00 2.15
491 495 7.309744 CCTGTGTTCTTGGGCTATTTTATCAAA 60.310 37.037 0.00 0.00 0.00 2.69
511 515 3.753294 AAGTGGTCTGAACAATCGACT 57.247 42.857 0.00 0.00 32.96 4.18
532 536 9.982291 TCGACTTTATTGGAAAATATTTCTTCG 57.018 29.630 0.10 0.00 0.00 3.79
534 538 9.516314 GACTTTATTGGAAAATATTTCTTCGGG 57.484 33.333 0.10 0.00 0.00 5.14
557 561 7.469870 CGGGACAAAATTTATGGCAATATCTCA 60.470 37.037 0.00 0.00 0.00 3.27
635 641 6.042093 AGTCTGTTCTGACTTCTCCAACAATA 59.958 38.462 6.54 0.00 44.01 1.90
1389 1406 2.426381 GAGGTACTACTGGCGCTACTTT 59.574 50.000 7.64 0.00 41.55 2.66
1390 1407 2.426381 AGGTACTACTGGCGCTACTTTC 59.574 50.000 7.64 0.00 36.02 2.62
1392 1409 1.558233 ACTACTGGCGCTACTTTCCT 58.442 50.000 7.64 0.00 0.00 3.36
1395 1412 0.396811 ACTGGCGCTACTTTCCTTGT 59.603 50.000 7.64 0.00 0.00 3.16
1396 1413 1.079503 CTGGCGCTACTTTCCTTGTC 58.920 55.000 7.64 0.00 0.00 3.18
1397 1414 0.321298 TGGCGCTACTTTCCTTGTCC 60.321 55.000 7.64 0.00 0.00 4.02
1398 1415 1.025113 GGCGCTACTTTCCTTGTCCC 61.025 60.000 7.64 0.00 0.00 4.46
1399 1416 0.321298 GCGCTACTTTCCTTGTCCCA 60.321 55.000 0.00 0.00 0.00 4.37
1542 1582 8.925161 TTTGATTGCAAATTACTGTAATAGCC 57.075 30.769 23.52 14.73 38.99 3.93
1598 1638 5.185249 ACAAGATCTGCTGATTCATTTTGCT 59.815 36.000 7.59 0.00 32.19 3.91
1604 1644 3.057666 TGCTGATTCATTTTGCTTACGCA 60.058 39.130 0.00 0.00 46.24 5.24
1801 1844 5.866207 TGTGTGTATGTATGTTTGTACCCA 58.134 37.500 0.00 0.00 0.00 4.51
2075 2118 5.237344 CCATGTGGATTAGTAAAGCTACTGC 59.763 44.000 0.00 0.00 36.80 4.40
2099 2142 6.206438 GCTTTTTGGGGATCAGATATTCTCTC 59.794 42.308 0.00 0.00 29.16 3.20
2180 2230 9.261180 CGCTTATCTTAGATGATGTCCTTTTTA 57.739 33.333 4.78 0.00 0.00 1.52
2195 2245 6.095377 GTCCTTTTTAGTCCATTGCAATCTG 58.905 40.000 9.53 3.96 0.00 2.90
2208 2258 6.370442 CCATTGCAATCTGACATGAAAACAAT 59.630 34.615 9.53 0.00 0.00 2.71
2209 2259 7.094975 CCATTGCAATCTGACATGAAAACAATT 60.095 33.333 9.53 0.00 0.00 2.32
2417 2469 7.433425 GCTAATGTTGCATATTGTTCTTCCTTC 59.567 37.037 6.90 0.00 0.00 3.46
2447 2499 2.040412 AGCCTTCTAGGGAACACAAAGG 59.960 50.000 0.00 0.00 35.37 3.11
2516 2771 2.446435 ACCGCTTAATGCTTCCATTGT 58.554 42.857 0.00 0.00 41.58 2.71
2517 2772 3.616219 ACCGCTTAATGCTTCCATTGTA 58.384 40.909 0.00 0.00 41.58 2.41
2518 2773 3.377172 ACCGCTTAATGCTTCCATTGTAC 59.623 43.478 0.00 0.00 41.58 2.90
2519 2774 3.627577 CCGCTTAATGCTTCCATTGTACT 59.372 43.478 0.00 0.00 41.58 2.73
2520 2775 4.260784 CCGCTTAATGCTTCCATTGTACTC 60.261 45.833 0.00 0.00 41.58 2.59
2521 2776 4.260784 CGCTTAATGCTTCCATTGTACTCC 60.261 45.833 0.00 0.00 41.58 3.85
2522 2777 4.036852 GCTTAATGCTTCCATTGTACTCCC 59.963 45.833 0.00 0.00 41.58 4.30
2523 2778 5.440610 CTTAATGCTTCCATTGTACTCCCT 58.559 41.667 0.00 0.00 41.58 4.20
2524 2779 3.567478 ATGCTTCCATTGTACTCCCTC 57.433 47.619 0.00 0.00 0.00 4.30
2525 2780 2.551270 TGCTTCCATTGTACTCCCTCT 58.449 47.619 0.00 0.00 0.00 3.69
2526 2781 2.237143 TGCTTCCATTGTACTCCCTCTG 59.763 50.000 0.00 0.00 0.00 3.35
2527 2782 2.237392 GCTTCCATTGTACTCCCTCTGT 59.763 50.000 0.00 0.00 0.00 3.41
2528 2783 3.680196 GCTTCCATTGTACTCCCTCTGTC 60.680 52.174 0.00 0.00 0.00 3.51
2529 2784 3.474798 TCCATTGTACTCCCTCTGTCT 57.525 47.619 0.00 0.00 0.00 3.41
2530 2785 3.366396 TCCATTGTACTCCCTCTGTCTC 58.634 50.000 0.00 0.00 0.00 3.36
2531 2786 2.099921 CCATTGTACTCCCTCTGTCTCG 59.900 54.545 0.00 0.00 0.00 4.04
2532 2787 2.581216 TTGTACTCCCTCTGTCTCGT 57.419 50.000 0.00 0.00 0.00 4.18
2533 2788 3.708403 TTGTACTCCCTCTGTCTCGTA 57.292 47.619 0.00 0.00 0.00 3.43
2534 2789 3.708403 TGTACTCCCTCTGTCTCGTAA 57.292 47.619 0.00 0.00 0.00 3.18
2535 2790 4.232188 TGTACTCCCTCTGTCTCGTAAT 57.768 45.455 0.00 0.00 0.00 1.89
2536 2791 3.945921 TGTACTCCCTCTGTCTCGTAATG 59.054 47.826 0.00 0.00 0.00 1.90
2537 2792 3.088789 ACTCCCTCTGTCTCGTAATGT 57.911 47.619 0.00 0.00 0.00 2.71
2538 2793 4.232188 ACTCCCTCTGTCTCGTAATGTA 57.768 45.455 0.00 0.00 0.00 2.29
2539 2794 4.597004 ACTCCCTCTGTCTCGTAATGTAA 58.403 43.478 0.00 0.00 0.00 2.41
2540 2795 4.641094 ACTCCCTCTGTCTCGTAATGTAAG 59.359 45.833 0.00 0.00 0.00 2.34
2541 2796 4.851843 TCCCTCTGTCTCGTAATGTAAGA 58.148 43.478 0.00 0.00 0.00 2.10
2542 2797 4.639310 TCCCTCTGTCTCGTAATGTAAGAC 59.361 45.833 0.00 0.00 39.87 3.01
2543 2798 4.496010 CCCTCTGTCTCGTAATGTAAGACG 60.496 50.000 0.00 0.00 41.84 4.18
2544 2799 4.094590 CCTCTGTCTCGTAATGTAAGACGT 59.905 45.833 0.00 0.00 41.84 4.34
2545 2800 5.391736 CCTCTGTCTCGTAATGTAAGACGTT 60.392 44.000 0.00 0.00 41.84 3.99
2546 2801 6.005583 TCTGTCTCGTAATGTAAGACGTTT 57.994 37.500 0.00 0.00 41.84 3.60
2547 2802 6.441274 TCTGTCTCGTAATGTAAGACGTTTT 58.559 36.000 0.00 0.00 41.84 2.43
2548 2803 6.919662 TCTGTCTCGTAATGTAAGACGTTTTT 59.080 34.615 0.00 0.00 41.84 1.94
2549 2804 7.097342 TGTCTCGTAATGTAAGACGTTTTTC 57.903 36.000 0.00 0.00 41.84 2.29
2550 2805 6.129378 TGTCTCGTAATGTAAGACGTTTTTCG 60.129 38.462 0.00 0.00 41.84 3.46
2551 2806 6.086765 GTCTCGTAATGTAAGACGTTTTTCGA 59.913 38.462 0.00 0.00 42.86 3.71
2552 2807 6.086765 TCTCGTAATGTAAGACGTTTTTCGAC 59.913 38.462 0.00 0.00 42.86 4.20
2553 2808 5.685068 TCGTAATGTAAGACGTTTTTCGACA 59.315 36.000 0.00 0.00 42.86 4.35
2554 2809 5.775474 CGTAATGTAAGACGTTTTTCGACAC 59.225 40.000 0.00 0.00 42.86 3.67
2555 2810 5.978934 AATGTAAGACGTTTTTCGACACT 57.021 34.783 0.00 0.00 42.86 3.55
2556 2811 7.149144 CGTAATGTAAGACGTTTTTCGACACTA 60.149 37.037 0.00 0.00 42.86 2.74
2557 2812 6.686130 ATGTAAGACGTTTTTCGACACTAG 57.314 37.500 0.00 0.00 42.86 2.57
2558 2813 5.581605 TGTAAGACGTTTTTCGACACTAGT 58.418 37.500 0.00 0.00 42.86 2.57
2559 2814 5.456497 TGTAAGACGTTTTTCGACACTAGTG 59.544 40.000 21.44 21.44 42.86 2.74
2561 2816 5.173774 AGACGTTTTTCGACACTAGTGTA 57.826 39.130 27.98 11.50 45.05 2.90
2562 2817 5.210715 AGACGTTTTTCGACACTAGTGTAG 58.789 41.667 27.98 26.46 45.05 2.74
2563 2818 4.925068 ACGTTTTTCGACACTAGTGTAGT 58.075 39.130 27.98 14.12 45.05 2.73
2594 2849 8.848474 AAAATGTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
2595 2850 5.995565 TGTCTTATATTATGGGACGGAGG 57.004 43.478 0.00 0.00 0.00 4.30
2596 2851 4.775780 TGTCTTATATTATGGGACGGAGGG 59.224 45.833 0.00 0.00 0.00 4.30
2597 2852 5.021458 GTCTTATATTATGGGACGGAGGGA 58.979 45.833 0.00 0.00 0.00 4.20
2598 2853 5.127356 GTCTTATATTATGGGACGGAGGGAG 59.873 48.000 0.00 0.00 0.00 4.30
2614 2869 7.186972 ACGGAGGGAGTACCATATTAATCATA 58.813 38.462 0.00 0.00 43.89 2.15
2639 2894 5.805728 TCTTAAAGCTACCCTTTCCAGAAG 58.194 41.667 0.00 0.00 42.63 2.85
2706 2988 7.420002 TGCATTTACTGAAACATATGCTCATC 58.580 34.615 1.58 0.00 31.15 2.92
2803 3085 4.345854 TGTTGAGGTACCTTTTGTGGTTT 58.654 39.130 17.53 0.00 41.22 3.27
2940 3222 3.496160 GGCAACTTGGTGACTTCCTTCTA 60.496 47.826 0.00 0.00 0.00 2.10
2958 3240 5.452496 CCTTCTAGTCGGTGTTCATGATGAT 60.452 44.000 0.00 0.00 0.00 2.45
3338 3625 9.716531 ATTGTATTGTATATGACACAGAGATGG 57.283 33.333 0.00 0.00 37.96 3.51
3418 3705 4.118410 TCAACATTTCATTGGTTGTGCAC 58.882 39.130 10.75 10.75 41.87 4.57
3462 3749 8.154856 TGGTTCTGCTGTAAGTTCTTAATTACT 58.845 33.333 0.00 0.00 35.30 2.24
3486 3773 7.984050 ACTGTCTAAAATGTATCCTGATGTCAG 59.016 37.037 3.01 3.01 43.40 3.51
3534 3821 5.192927 ACTGAACTTGAAACTTCATGGACA 58.807 37.500 9.40 7.80 37.00 4.02
3711 4001 9.368674 TGTGATTTGCCTGATAAATACAAATTG 57.631 29.630 0.00 0.00 40.13 2.32
3932 4225 7.978414 TCTCTGCATTGAAGAGTTATTCTACAG 59.022 37.037 19.22 0.00 41.64 2.74
4022 4317 5.979517 GGAATCGGCTCAAGGAAATAAATTG 59.020 40.000 0.00 0.00 0.00 2.32
4057 4352 5.598417 ACATTCTTCTACTGTTGCCCTTTTT 59.402 36.000 0.00 0.00 0.00 1.94
4205 4501 5.944007 GGTATTACTGGGTTTGTGAAGTGAT 59.056 40.000 0.00 0.00 0.00 3.06
4213 4509 4.022329 GGGTTTGTGAAGTGATTAGGGTTG 60.022 45.833 0.00 0.00 0.00 3.77
4232 4528 6.068670 GGGTTGGCATACTTCCTAATTGTAT 58.931 40.000 0.00 0.00 0.00 2.29
4283 4579 5.181748 GCTGAGAAACAACCTAGTGATGAT 58.818 41.667 0.00 0.00 0.00 2.45
4319 4615 8.463930 TTGTTTGATTTGTCTAACCAGAGAAT 57.536 30.769 0.00 0.00 34.31 2.40
4356 4653 5.720371 TCCTTGTTCATTGGTATTTGGTG 57.280 39.130 0.00 0.00 0.00 4.17
4370 4667 3.967203 TTTGGTGTTACTGTTTACCGC 57.033 42.857 0.00 0.00 35.98 5.68
4377 4682 0.945265 TACTGTTTACCGCGGTGCAC 60.945 55.000 40.02 32.29 0.00 4.57
4387 4692 1.503542 GCGGTGCACTGGAGATTTG 59.496 57.895 26.55 2.61 0.00 2.32
4413 4718 7.118390 GTCTGTGCAGAATGTCAGTAGTATTTT 59.882 37.037 3.19 0.00 39.48 1.82
4449 4754 7.872113 AAGAAATAATTAAGCACTCCCTCTG 57.128 36.000 0.00 0.00 0.00 3.35
4465 4770 7.605691 CACTCCCTCTGATCCATATTAATTGTC 59.394 40.741 0.00 0.00 0.00 3.18
4489 4794 9.079833 GTCGCTGATTTAGTACAACTTTATACA 57.920 33.333 0.00 0.00 0.00 2.29
4520 4825 5.696724 GCGATAATTAATATGGATCGGAGGG 59.303 44.000 16.92 0.00 39.74 4.30
4565 4870 2.173356 TGTTGGCTGCTTAGCTCCATAT 59.827 45.455 16.48 0.00 33.67 1.78
4566 4871 3.390967 TGTTGGCTGCTTAGCTCCATATA 59.609 43.478 16.48 3.18 33.67 0.86
4567 4872 3.685139 TGGCTGCTTAGCTCCATATAC 57.315 47.619 13.01 0.00 34.73 1.47
4568 4873 2.029020 TGGCTGCTTAGCTCCATATACG 60.029 50.000 13.01 0.00 34.73 3.06
4569 4874 1.996191 GCTGCTTAGCTCCATATACGC 59.004 52.381 5.60 0.00 0.00 4.42
4624 5030 6.855836 TGTGATTCACTCAAATAGCATTTCC 58.144 36.000 17.26 0.00 35.07 3.13
4640 5046 5.183904 AGCATTTCCTTTGTACTGGTGAATC 59.816 40.000 0.00 0.00 0.00 2.52
4671 5077 3.365969 GCTGGGACCGTTTGTATTTTGAG 60.366 47.826 0.00 0.00 0.00 3.02
4685 5091 8.761575 TTGTATTTTGAGAAATGATTTCCAGC 57.238 30.769 13.88 5.40 40.54 4.85
4692 5098 1.197812 AATGATTTCCAGCCCTTGCC 58.802 50.000 0.00 0.00 38.69 4.52
4694 5100 0.899717 TGATTTCCAGCCCTTGCCAC 60.900 55.000 0.00 0.00 38.69 5.01
4703 5109 0.032540 GCCCTTGCCACAGTGAAAAG 59.967 55.000 0.62 5.24 0.00 2.27
4704 5110 1.402787 CCCTTGCCACAGTGAAAAGT 58.597 50.000 0.62 0.00 0.00 2.66
4716 5122 6.378582 CACAGTGAAAAGTTAAGTGTTGTGT 58.621 36.000 0.00 0.00 0.00 3.72
4741 5147 4.608948 TTCTGAGAGGTTTGGAGTCTTC 57.391 45.455 0.00 0.00 0.00 2.87
4790 5196 6.855763 AAAGGATCATGGTTTAAATCTGCA 57.144 33.333 0.00 0.00 0.00 4.41
4851 5260 4.380843 AGGTGGTGGTGAAATTACATGA 57.619 40.909 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.285144 GAACGGAGGGAAGGGGGA 60.285 66.667 0.00 0.00 0.00 4.81
74 76 4.536687 GCCCAAAATCCGCGCTCG 62.537 66.667 5.56 0.00 0.00 5.03
79 81 1.079888 CCAACTGCCCAAAATCCGC 60.080 57.895 0.00 0.00 0.00 5.54
86 88 4.992740 ATGCGCCCAACTGCCCAA 62.993 61.111 4.18 0.00 0.00 4.12
120 122 2.474526 CGCAAACGGCAGAAGTAATCAG 60.475 50.000 0.00 0.00 45.17 2.90
161 163 2.002018 GCCCGAATTCCCCCACCATA 62.002 60.000 0.00 0.00 0.00 2.74
235 237 2.978010 GTGCGTGGGTCCAACAGG 60.978 66.667 0.00 0.00 0.00 4.00
270 274 1.887301 TGCAGCCAATCATGCACAG 59.113 52.632 0.00 0.00 46.97 3.66
288 292 8.308931 TCTGATTCTTAGCTCAAATTTTGCATT 58.691 29.630 13.37 0.00 0.00 3.56
334 338 5.010719 ACTCTCTGAACCTCGAATTGTAACA 59.989 40.000 0.00 0.00 0.00 2.41
370 374 1.419012 TCTGGCAGAATAGGGAGCATG 59.581 52.381 16.28 0.00 0.00 4.06
410 414 5.047306 ACAAACCGAAGTGACTGATCATCTA 60.047 40.000 0.00 0.00 37.14 1.98
439 443 2.565391 TGTTCATGGACGTCAGTGGTAT 59.435 45.455 18.91 0.00 0.00 2.73
440 444 1.964933 TGTTCATGGACGTCAGTGGTA 59.035 47.619 18.91 4.77 0.00 3.25
441 445 0.756294 TGTTCATGGACGTCAGTGGT 59.244 50.000 18.91 0.00 0.00 4.16
442 446 1.733912 CATGTTCATGGACGTCAGTGG 59.266 52.381 18.91 3.65 0.00 4.00
443 447 2.416747 ACATGTTCATGGACGTCAGTG 58.583 47.619 18.91 14.84 0.00 3.66
444 448 2.839486 ACATGTTCATGGACGTCAGT 57.161 45.000 18.91 1.51 0.00 3.41
445 449 2.416547 GGAACATGTTCATGGACGTCAG 59.583 50.000 33.42 6.72 41.20 3.51
446 450 2.038426 AGGAACATGTTCATGGACGTCA 59.962 45.455 33.42 3.91 41.20 4.35
447 451 2.416547 CAGGAACATGTTCATGGACGTC 59.583 50.000 34.57 18.48 44.71 4.34
448 452 2.426522 CAGGAACATGTTCATGGACGT 58.573 47.619 34.57 12.44 44.71 4.34
457 461 2.958355 CCCAAGAACACAGGAACATGTT 59.042 45.455 11.78 11.78 41.53 2.71
458 462 2.586425 CCCAAGAACACAGGAACATGT 58.414 47.619 0.00 0.00 0.00 3.21
459 463 1.270550 GCCCAAGAACACAGGAACATG 59.729 52.381 0.00 0.00 0.00 3.21
460 464 1.145738 AGCCCAAGAACACAGGAACAT 59.854 47.619 0.00 0.00 0.00 2.71
475 479 6.152661 CAGACCACTTTTGATAAAATAGCCCA 59.847 38.462 0.00 0.00 0.00 5.36
486 490 5.049405 GTCGATTGTTCAGACCACTTTTGAT 60.049 40.000 0.00 0.00 0.00 2.57
488 492 4.273480 AGTCGATTGTTCAGACCACTTTTG 59.727 41.667 0.00 0.00 35.65 2.44
489 493 4.451900 AGTCGATTGTTCAGACCACTTTT 58.548 39.130 0.00 0.00 35.65 2.27
491 495 3.753294 AGTCGATTGTTCAGACCACTT 57.247 42.857 0.00 0.00 35.65 3.16
511 515 9.026121 TGTCCCGAAGAAATATTTTCCAATAAA 57.974 29.630 1.43 0.00 0.00 1.40
532 536 7.725251 TGAGATATTGCCATAAATTTTGTCCC 58.275 34.615 0.00 0.00 0.00 4.46
534 538 9.199982 CCATGAGATATTGCCATAAATTTTGTC 57.800 33.333 0.00 0.00 0.00 3.18
557 561 4.036518 ACTAGTGGAGCTCAAGAATCCAT 58.963 43.478 17.19 0.00 44.59 3.41
781 787 6.321181 TGACTCAAAAGTAGATGTGCCTTTTT 59.679 34.615 0.00 0.00 36.53 1.94
1350 1362 1.923204 CTCTCTTCCATCGAAAGCACG 59.077 52.381 0.00 0.00 0.00 5.34
1392 1409 9.253832 AACAGAATAATGTATTTCATGGGACAA 57.746 29.630 0.00 0.00 35.28 3.18
1395 1412 9.473007 TGAAACAGAATAATGTATTTCATGGGA 57.527 29.630 0.00 0.00 36.81 4.37
1542 1582 8.714179 GCATGAGAAGATTAGAAGAGAATCATG 58.286 37.037 0.00 0.00 41.87 3.07
1598 1638 4.534794 TCGACGATATAGTTGTGCGTAA 57.465 40.909 0.00 0.00 35.09 3.18
1604 1644 7.700505 TGTAACTTCATCGACGATATAGTTGT 58.299 34.615 28.87 16.91 31.81 3.32
1801 1844 4.652421 TCCACTAACAAGTGTCAACCTAGT 59.348 41.667 4.94 0.00 38.07 2.57
1812 1855 5.768164 CACCCACTTTAATCCACTAACAAGT 59.232 40.000 0.00 0.00 0.00 3.16
1986 2029 2.285220 CCTGATTTGCTTGTATCGTCCG 59.715 50.000 0.00 0.00 0.00 4.79
2075 2118 6.426328 CGAGAGAATATCTGATCCCCAAAAAG 59.574 42.308 0.00 0.00 38.84 2.27
2167 2217 5.076182 TGCAATGGACTAAAAAGGACATCA 58.924 37.500 0.00 0.00 0.00 3.07
2180 2230 3.959293 TCATGTCAGATTGCAATGGACT 58.041 40.909 27.75 14.92 0.00 3.85
2195 2245 6.198966 GTGTGGACAGAAATTGTTTTCATGTC 59.801 38.462 15.18 15.18 43.09 3.06
2417 2469 4.428294 TCCCTAGAAGGCTGATCAAATG 57.572 45.455 0.00 0.00 32.73 2.32
2447 2499 5.767168 AGACAAAGATATAGCAGGCCATTTC 59.233 40.000 5.01 0.00 0.00 2.17
2516 2771 4.232188 ACATTACGAGACAGAGGGAGTA 57.768 45.455 0.00 0.00 0.00 2.59
2517 2772 3.088789 ACATTACGAGACAGAGGGAGT 57.911 47.619 0.00 0.00 0.00 3.85
2518 2773 4.882427 TCTTACATTACGAGACAGAGGGAG 59.118 45.833 0.00 0.00 0.00 4.30
2519 2774 4.639310 GTCTTACATTACGAGACAGAGGGA 59.361 45.833 0.00 0.00 39.59 4.20
2520 2775 4.496010 CGTCTTACATTACGAGACAGAGGG 60.496 50.000 0.00 0.00 41.55 4.30
2521 2776 4.094590 ACGTCTTACATTACGAGACAGAGG 59.905 45.833 1.45 0.00 41.55 3.69
2522 2777 5.219226 ACGTCTTACATTACGAGACAGAG 57.781 43.478 1.45 0.00 41.55 3.35
2523 2778 5.618056 AACGTCTTACATTACGAGACAGA 57.382 39.130 1.45 0.00 41.55 3.41
2524 2779 6.686130 AAAACGTCTTACATTACGAGACAG 57.314 37.500 1.45 0.00 41.55 3.51
2525 2780 6.129378 CGAAAAACGTCTTACATTACGAGACA 60.129 38.462 1.45 0.00 41.55 3.41
2526 2781 6.086765 TCGAAAAACGTCTTACATTACGAGAC 59.913 38.462 1.45 0.00 41.55 3.36
2527 2782 6.086765 GTCGAAAAACGTCTTACATTACGAGA 59.913 38.462 1.45 0.00 41.55 4.04
2528 2783 6.129378 TGTCGAAAAACGTCTTACATTACGAG 60.129 38.462 1.45 0.00 41.55 4.18
2529 2784 5.685068 TGTCGAAAAACGTCTTACATTACGA 59.315 36.000 1.45 0.00 41.55 3.43
2530 2785 5.775474 GTGTCGAAAAACGTCTTACATTACG 59.225 40.000 0.00 0.00 44.47 3.18
2531 2786 6.870517 AGTGTCGAAAAACGTCTTACATTAC 58.129 36.000 0.00 0.00 43.13 1.89
2532 2787 7.862372 ACTAGTGTCGAAAAACGTCTTACATTA 59.138 33.333 0.00 0.00 43.13 1.90
2533 2788 5.978934 AGTGTCGAAAAACGTCTTACATT 57.021 34.783 0.00 0.00 43.13 2.71
2534 2789 6.143438 CACTAGTGTCGAAAAACGTCTTACAT 59.857 38.462 15.06 0.00 43.13 2.29
2535 2790 5.456497 CACTAGTGTCGAAAAACGTCTTACA 59.544 40.000 15.06 0.00 43.13 2.41
2536 2791 5.456822 ACACTAGTGTCGAAAAACGTCTTAC 59.543 40.000 22.95 0.00 40.24 2.34
2537 2792 5.581605 ACACTAGTGTCGAAAAACGTCTTA 58.418 37.500 22.95 0.00 40.24 2.10
2538 2793 4.427312 ACACTAGTGTCGAAAAACGTCTT 58.573 39.130 22.95 0.00 40.24 3.01
2539 2794 4.037858 ACACTAGTGTCGAAAAACGTCT 57.962 40.909 22.95 0.00 40.24 4.18
2540 2795 4.972440 ACTACACTAGTGTCGAAAAACGTC 59.028 41.667 31.11 0.00 43.74 4.34
2541 2796 4.925068 ACTACACTAGTGTCGAAAAACGT 58.075 39.130 31.11 13.23 43.74 3.99
2568 2823 9.284968 CTCCGTCCCATAATATAAGACATTTTT 57.715 33.333 0.00 0.00 0.00 1.94
2569 2824 7.883311 CCTCCGTCCCATAATATAAGACATTTT 59.117 37.037 0.00 0.00 0.00 1.82
2570 2825 7.394816 CCTCCGTCCCATAATATAAGACATTT 58.605 38.462 0.00 0.00 0.00 2.32
2571 2826 6.070194 CCCTCCGTCCCATAATATAAGACATT 60.070 42.308 0.00 0.00 0.00 2.71
2572 2827 5.425539 CCCTCCGTCCCATAATATAAGACAT 59.574 44.000 0.00 0.00 0.00 3.06
2573 2828 4.775780 CCCTCCGTCCCATAATATAAGACA 59.224 45.833 0.00 0.00 0.00 3.41
2574 2829 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
2575 2830 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2576 2831 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2577 2832 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2578 2833 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2579 2834 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2580 2835 3.501019 GGTACTCCCTCCGTCCCATAATA 60.501 52.174 0.00 0.00 0.00 0.98
2581 2836 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
2582 2837 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
2583 2838 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
2584 2839 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
2585 2840 1.882189 ATGGTACTCCCTCCGTCCCA 61.882 60.000 0.00 0.00 0.00 4.37
2586 2841 0.186873 TATGGTACTCCCTCCGTCCC 59.813 60.000 0.00 0.00 0.00 4.46
2587 2842 2.305858 ATATGGTACTCCCTCCGTCC 57.694 55.000 0.00 0.00 0.00 4.79
2588 2843 5.479375 TGATTAATATGGTACTCCCTCCGTC 59.521 44.000 0.00 0.00 0.00 4.79
2589 2844 5.399991 TGATTAATATGGTACTCCCTCCGT 58.600 41.667 0.00 0.00 0.00 4.69
2590 2845 5.995565 TGATTAATATGGTACTCCCTCCG 57.004 43.478 0.00 0.00 0.00 4.63
2614 2869 6.388619 TCTGGAAAGGGTAGCTTTAAGATT 57.611 37.500 0.00 0.00 0.00 2.40
2622 2877 2.979678 TGTTCTTCTGGAAAGGGTAGCT 59.020 45.455 0.00 0.00 35.51 3.32
2626 2881 5.701224 TGTAAATGTTCTTCTGGAAAGGGT 58.299 37.500 0.00 0.00 35.51 4.34
2706 2988 2.097038 CGAAGGAGCCTGAACGCAG 61.097 63.158 0.00 0.00 41.93 5.18
2940 3222 3.196469 ACTGATCATCATGAACACCGACT 59.804 43.478 0.00 0.00 0.00 4.18
2958 3240 8.141298 TGTTAAATAAGTACCTGATGGACTGA 57.859 34.615 0.00 0.00 37.04 3.41
3094 3380 1.230635 CCCTGCACAACTGGTTCTCG 61.231 60.000 0.00 0.00 35.64 4.04
3329 3616 5.239525 GTCTGCTAACAAAAACCATCTCTGT 59.760 40.000 0.00 0.00 0.00 3.41
3338 3625 3.630312 TGTGAGGGTCTGCTAACAAAAAC 59.370 43.478 0.00 0.00 0.00 2.43
3418 3705 1.378250 ACCCTCGACTACTGTCCCG 60.378 63.158 0.00 0.00 39.94 5.14
3462 3749 7.981789 GTCTGACATCAGGATACATTTTAGACA 59.018 37.037 8.99 0.00 43.91 3.41
3486 3773 3.922850 GTGCCAACTACGTTAGGTAAGTC 59.077 47.826 0.00 0.00 0.00 3.01
3534 3821 2.267174 ACTTCACTCTGCAGCAATGT 57.733 45.000 9.47 2.21 0.00 2.71
3932 4225 3.508762 CTGAGGAATTGTTGCAATCTGC 58.491 45.455 0.59 0.00 45.29 4.26
4022 4317 3.051081 AGAAGAATGTGGCAGTCTGTC 57.949 47.619 0.00 0.00 37.84 3.51
4205 4501 5.987019 ATTAGGAAGTATGCCAACCCTAA 57.013 39.130 0.00 0.00 34.43 2.69
4258 4554 4.415881 TCACTAGGTTGTTTCTCAGCAA 57.584 40.909 0.00 0.00 0.00 3.91
4283 4579 5.426504 ACAAATCAAACAAATGCCAACAGA 58.573 33.333 0.00 0.00 0.00 3.41
4319 4615 5.592282 TGAACAAGGAAAGCTGAACATAACA 59.408 36.000 0.00 0.00 0.00 2.41
4356 4653 0.164432 GCACCGCGGTAAACAGTAAC 59.836 55.000 33.70 8.02 0.00 2.50
4370 4667 0.798776 GACAAATCTCCAGTGCACCG 59.201 55.000 14.63 2.26 0.00 4.94
4377 4682 3.049708 TCTGCACAGACAAATCTCCAG 57.950 47.619 0.00 0.00 30.42 3.86
4387 4692 3.919216 ACTACTGACATTCTGCACAGAC 58.081 45.455 6.74 0.00 37.14 3.51
4415 4720 8.987890 GTGCTTAATTATTTCTTTTTGGCAAGA 58.012 29.630 0.00 0.00 0.00 3.02
4421 4726 9.358872 GAGGGAGTGCTTAATTATTTCTTTTTG 57.641 33.333 0.00 0.00 0.00 2.44
4423 4728 8.743714 CAGAGGGAGTGCTTAATTATTTCTTTT 58.256 33.333 0.00 0.00 0.00 2.27
4449 4754 9.979270 CTAAATCAGCGACAATTAATATGGATC 57.021 33.333 0.00 0.00 0.00 3.36
4520 4825 3.577649 TGTGCTCAGCTAACAGTACTC 57.422 47.619 0.00 0.00 0.00 2.59
4565 4870 6.804770 TTTTGGCTATCTTTTACTTGCGTA 57.195 33.333 0.00 0.00 0.00 4.42
4566 4871 5.699097 TTTTGGCTATCTTTTACTTGCGT 57.301 34.783 0.00 0.00 0.00 5.24
4567 4872 8.856490 ATATTTTTGGCTATCTTTTACTTGCG 57.144 30.769 0.00 0.00 0.00 4.85
4601 5007 7.093322 AGGAAATGCTATTTGAGTGAATCAC 57.907 36.000 5.02 5.02 37.77 3.06
4611 5017 6.808212 CACCAGTACAAAGGAAATGCTATTTG 59.192 38.462 6.09 0.00 38.35 2.32
4624 5030 4.862574 TCGATTCGATTCACCAGTACAAAG 59.137 41.667 4.29 0.00 0.00 2.77
4640 5046 1.951130 CGGTCCCAGCATCGATTCG 60.951 63.158 0.00 0.00 0.00 3.34
4671 5077 2.419159 GGCAAGGGCTGGAAATCATTTC 60.419 50.000 0.97 0.97 40.87 2.17
4685 5091 1.402787 ACTTTTCACTGTGGCAAGGG 58.597 50.000 18.19 0.00 0.00 3.95
4692 5098 6.305399 CACACAACACTTAACTTTTCACTGTG 59.695 38.462 0.17 0.17 37.16 3.66
4694 5100 6.607689 TCACACAACACTTAACTTTTCACTG 58.392 36.000 0.00 0.00 0.00 3.66
4703 5109 7.246674 TCTCAGAAATCACACAACACTTAAC 57.753 36.000 0.00 0.00 0.00 2.01
4704 5110 6.483307 CCTCTCAGAAATCACACAACACTTAA 59.517 38.462 0.00 0.00 0.00 1.85
4716 5122 4.594920 AGACTCCAAACCTCTCAGAAATCA 59.405 41.667 0.00 0.00 0.00 2.57
4764 5170 6.536224 GCAGATTTAAACCATGATCCTTTTGG 59.464 38.462 0.00 0.00 42.21 3.28


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

AutoCloner maintained by Alex Coulton.