Multiple sequence alignment - TraesCS7D01G357100

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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 TraesCS7D01G357100 chr7D 100.000 5591 0 0 1 5591 460278710 460284300 0.000000e+00 10325.0
1 TraesCS7D01G357100 chr7D 84.428 3166 466 22 896 4052 459752908 459749761 0.000000e+00 3090.0
2 TraesCS7D01G357100 chr7D 83.266 3215 499 28 865 4052 459790384 459787182 0.000000e+00 2920.0
3 TraesCS7D01G357100 chr7D 81.744 1709 287 15 2963 4664 460108978 460110668 0.000000e+00 1404.0
4 TraesCS7D01G357100 chr7D 92.479 851 48 11 4747 5588 168777857 168778700 0.000000e+00 1203.0
5 TraesCS7D01G357100 chr7D 82.955 528 72 8 1017 1538 460273364 460273879 1.420000e-125 460.0
6 TraesCS7D01G357100 chr7D 79.717 212 15 11 512 718 460114957 460115145 1.630000e-25 128.0
7 TraesCS7D01G357100 chr7D 100.000 54 0 0 375 428 460279032 460279085 3.560000e-17 100.0
8 TraesCS7D01G357100 chr7D 100.000 54 0 0 323 376 460279084 460279137 3.560000e-17 100.0
9 TraesCS7D01G357100 chr7D 90.000 50 5 0 228 277 99871580 99871531 1.300000e-06 65.8
10 TraesCS7D01G357100 chr7D 86.364 66 1 7 82 146 460272503 460272561 1.300000e-06 65.8
11 TraesCS7D01G357100 chr7D 91.489 47 4 0 231 277 572037663 572037617 1.300000e-06 65.8
12 TraesCS7D01G357100 chr7A 96.963 4379 111 12 381 4747 539326606 539322238 0.000000e+00 7330.0
13 TraesCS7D01G357100 chr7A 82.906 2106 342 17 1953 4049 539928023 539930119 0.000000e+00 1879.0
14 TraesCS7D01G357100 chr7A 76.260 3610 772 73 1170 4747 539449485 539445929 0.000000e+00 1840.0
15 TraesCS7D01G357100 chr7A 85.447 1017 137 5 901 1917 539926861 539927866 0.000000e+00 1048.0
16 TraesCS7D01G357100 chr7A 83.669 845 119 12 3909 4747 539403676 539402845 0.000000e+00 778.0
17 TraesCS7D01G357100 chr7A 86.534 401 22 8 4 376 539326955 539326559 4.030000e-111 412.0
18 TraesCS7D01G357100 chr7A 87.931 58 2 4 89 146 539368258 539368206 4.680000e-06 63.9
19 TraesCS7D01G357100 chr7B 97.039 3782 107 4 381 4161 482683739 482687516 0.000000e+00 6359.0
20 TraesCS7D01G357100 chr7B 84.317 3169 463 27 896 4052 481857159 481854013 0.000000e+00 3068.0
21 TraesCS7D01G357100 chr7B 83.420 2883 456 18 1178 4052 482078294 482075426 0.000000e+00 2656.0
22 TraesCS7D01G357100 chr7B 92.069 580 42 1 4159 4734 482687597 482688176 0.000000e+00 813.0
23 TraesCS7D01G357100 chr7B 88.529 340 11 9 1 328 482683395 482683718 2.440000e-103 387.0
24 TraesCS7D01G357100 chr7B 86.310 336 42 2 1203 1538 482664456 482664787 4.120000e-96 363.0
25 TraesCS7D01G357100 chr7B 97.917 48 1 0 329 376 482683739 482683786 3.590000e-12 84.2
26 TraesCS7D01G357100 chr2B 81.818 3531 580 42 1105 4591 784188703 784192215 0.000000e+00 2907.0
27 TraesCS7D01G357100 chr2B 80.940 3552 584 58 1105 4598 798128351 798131867 0.000000e+00 2723.0
28 TraesCS7D01G357100 chr2B 79.616 417 75 8 1574 1982 780594011 780594425 1.970000e-74 291.0
29 TraesCS7D01G357100 chr2A 80.724 3538 599 51 1105 4598 764309067 764312565 0.000000e+00 2678.0
30 TraesCS7D01G357100 chr2A 92.784 776 44 6 506 1273 208166413 208167184 0.000000e+00 1112.0
31 TraesCS7D01G357100 chr2D 80.767 3546 581 62 1105 4598 638724248 638727744 0.000000e+00 2676.0
32 TraesCS7D01G357100 chr2D 80.614 3549 588 65 1104 4598 638804386 638807888 0.000000e+00 2651.0
33 TraesCS7D01G357100 chr2D 92.000 50 4 0 228 277 584537946 584537897 2.790000e-08 71.3
34 TraesCS7D01G357100 chr3D 96.919 844 23 2 4748 5591 175552147 175552987 0.000000e+00 1411.0
35 TraesCS7D01G357100 chr3D 90.000 50 5 0 228 277 943265 943314 1.300000e-06 65.8
36 TraesCS7D01G357100 chr6B 94.090 846 44 4 4748 5591 390632046 390631205 0.000000e+00 1280.0
37 TraesCS7D01G357100 chr5A 94.909 766 30 6 4747 5505 41930590 41931353 0.000000e+00 1190.0
38 TraesCS7D01G357100 chr5A 95.882 170 7 0 5422 5591 41931312 41931481 5.520000e-70 276.0
39 TraesCS7D01G357100 chr3B 93.368 769 33 10 4744 5505 345004792 345005549 0.000000e+00 1122.0
40 TraesCS7D01G357100 chr3B 92.174 690 41 9 4748 5431 119075398 119076080 0.000000e+00 963.0
41 TraesCS7D01G357100 chr3B 91.489 47 4 0 231 277 628472741 628472695 1.300000e-06 65.8
42 TraesCS7D01G357100 chr4A 92.829 767 43 9 4747 5505 340501782 340501020 0.000000e+00 1101.0
43 TraesCS7D01G357100 chr4A 92.941 170 12 0 5422 5591 340501061 340500892 1.200000e-61 248.0
44 TraesCS7D01G357100 chr4B 94.876 644 32 1 4949 5591 295676014 295675371 0.000000e+00 1005.0
45 TraesCS7D01G357100 chr5D 92.433 674 41 8 4748 5419 288253303 288253968 0.000000e+00 953.0
46 TraesCS7D01G357100 chr6D 95.294 170 8 0 5422 5591 214551014 214551183 2.570000e-68 270.0
47 TraesCS7D01G357100 chr6D 92.941 170 12 0 5422 5591 464899045 464899214 1.200000e-61 248.0
48 TraesCS7D01G357100 chr6D 90.385 52 5 0 226 277 401153796 401153847 1.010000e-07 69.4
49 TraesCS7D01G357100 chr6D 91.489 47 4 0 231 277 304998272 304998318 1.300000e-06 65.8
50 TraesCS7D01G357100 chr6A 94.152 171 9 1 5422 5591 611463535 611463705 5.560000e-65 259.0
51 TraesCS7D01G357100 chr4D 90.196 51 5 0 227 277 51919869 51919919 3.610000e-07 67.6
52 TraesCS7D01G357100 chr1A 91.667 48 2 2 231 277 72565329 72565283 1.300000e-06 65.8


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 TraesCS7D01G357100 chr7D 460278710 460284300 5590 False 10325.0 10325 100.0000 1 5591 1 chr7D.!!$F4 5590
1 TraesCS7D01G357100 chr7D 459749761 459752908 3147 True 3090.0 3090 84.4280 896 4052 1 chr7D.!!$R2 3156
2 TraesCS7D01G357100 chr7D 459787182 459790384 3202 True 2920.0 2920 83.2660 865 4052 1 chr7D.!!$R3 3187
3 TraesCS7D01G357100 chr7D 460108978 460110668 1690 False 1404.0 1404 81.7440 2963 4664 1 chr7D.!!$F2 1701
4 TraesCS7D01G357100 chr7D 168777857 168778700 843 False 1203.0 1203 92.4790 4747 5588 1 chr7D.!!$F1 841
5 TraesCS7D01G357100 chr7D 460272503 460273879 1376 False 262.9 460 84.6595 82 1538 2 chr7D.!!$F5 1456
6 TraesCS7D01G357100 chr7A 539322238 539326955 4717 True 3871.0 7330 91.7485 4 4747 2 chr7A.!!$R4 4743
7 TraesCS7D01G357100 chr7A 539445929 539449485 3556 True 1840.0 1840 76.2600 1170 4747 1 chr7A.!!$R3 3577
8 TraesCS7D01G357100 chr7A 539926861 539930119 3258 False 1463.5 1879 84.1765 901 4049 2 chr7A.!!$F1 3148
9 TraesCS7D01G357100 chr7A 539402845 539403676 831 True 778.0 778 83.6690 3909 4747 1 chr7A.!!$R2 838
10 TraesCS7D01G357100 chr7B 481854013 481857159 3146 True 3068.0 3068 84.3170 896 4052 1 chr7B.!!$R1 3156
11 TraesCS7D01G357100 chr7B 482075426 482078294 2868 True 2656.0 2656 83.4200 1178 4052 1 chr7B.!!$R2 2874
12 TraesCS7D01G357100 chr7B 482683395 482688176 4781 False 1910.8 6359 93.8885 1 4734 4 chr7B.!!$F2 4733
13 TraesCS7D01G357100 chr2B 784188703 784192215 3512 False 2907.0 2907 81.8180 1105 4591 1 chr2B.!!$F2 3486
14 TraesCS7D01G357100 chr2B 798128351 798131867 3516 False 2723.0 2723 80.9400 1105 4598 1 chr2B.!!$F3 3493
15 TraesCS7D01G357100 chr2A 764309067 764312565 3498 False 2678.0 2678 80.7240 1105 4598 1 chr2A.!!$F2 3493
16 TraesCS7D01G357100 chr2A 208166413 208167184 771 False 1112.0 1112 92.7840 506 1273 1 chr2A.!!$F1 767
17 TraesCS7D01G357100 chr2D 638724248 638727744 3496 False 2676.0 2676 80.7670 1105 4598 1 chr2D.!!$F1 3493
18 TraesCS7D01G357100 chr2D 638804386 638807888 3502 False 2651.0 2651 80.6140 1104 4598 1 chr2D.!!$F2 3494
19 TraesCS7D01G357100 chr3D 175552147 175552987 840 False 1411.0 1411 96.9190 4748 5591 1 chr3D.!!$F2 843
20 TraesCS7D01G357100 chr6B 390631205 390632046 841 True 1280.0 1280 94.0900 4748 5591 1 chr6B.!!$R1 843
21 TraesCS7D01G357100 chr5A 41930590 41931481 891 False 733.0 1190 95.3955 4747 5591 2 chr5A.!!$F1 844
22 TraesCS7D01G357100 chr3B 345004792 345005549 757 False 1122.0 1122 93.3680 4744 5505 1 chr3B.!!$F2 761
23 TraesCS7D01G357100 chr3B 119075398 119076080 682 False 963.0 963 92.1740 4748 5431 1 chr3B.!!$F1 683
24 TraesCS7D01G357100 chr4A 340500892 340501782 890 True 674.5 1101 92.8850 4747 5591 2 chr4A.!!$R1 844
25 TraesCS7D01G357100 chr4B 295675371 295676014 643 True 1005.0 1005 94.8760 4949 5591 1 chr4B.!!$R1 642
26 TraesCS7D01G357100 chr5D 288253303 288253968 665 False 953.0 953 92.4330 4748 5419 1 chr5D.!!$F1 671

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
282 327 0.035317 GCATCAGTCAGGACACCACA 59.965 55.000 1.84 0.0 0.00 4.17 F
320 372 0.107897 TGGTCGTTCTGTGCACAGTT 60.108 50.000 38.41 0.0 44.12 3.16 F
963 1258 0.168348 AGTCGTCAGTCCGTTCATCG 59.832 55.000 0.00 0.0 39.52 3.84 F
1132 1442 1.000993 ACCGACCTCCATGCTCTCT 59.999 57.895 0.00 0.0 0.00 3.10 F
2462 2945 0.034059 CAAGGAGTCTTGCCGAGTGT 59.966 55.000 0.00 0.0 43.10 3.55 F
3903 4401 0.322816 TGAAGCCCAGCAATGTCCTC 60.323 55.000 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 1442 2.305635 TGAGATGGAGTTTAAGGCAGCA 59.694 45.455 0.00 0.00 0.00 4.41 R
2280 2763 2.676632 TGCCATGGAATGCATTGTTC 57.323 45.000 18.59 2.91 44.97 3.18 R
2462 2945 0.667993 CTTTGAAAGGCCTGCAACGA 59.332 50.000 18.12 6.77 0.00 3.85 R
3020 3503 4.494091 TGAGGGATTCTTCCATGAAGAC 57.506 45.455 6.05 0.00 46.54 3.01 R
3732 4225 0.321996 AGAGCCAACTTTCGAGGTCC 59.678 55.000 0.00 0.00 0.00 4.46 R
5565 6298 0.318441 AGCGTCTACTTGCAGCTTCA 59.682 50.000 0.00 0.00 34.05 3.02 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
37 38 4.212214 GCATGGATCTTCGCTAAGTTAAGG 59.788 45.833 0.00 0.00 34.13 2.69
64 66 1.658095 GATCTTGCTTCTGTCGACTGC 59.342 52.381 17.92 15.21 0.00 4.40
116 119 4.796312 GTCTCTTTCGCTCTTGTCATCTAC 59.204 45.833 0.00 0.00 0.00 2.59
117 120 4.702612 TCTCTTTCGCTCTTGTCATCTACT 59.297 41.667 0.00 0.00 0.00 2.57
118 121 5.880887 TCTCTTTCGCTCTTGTCATCTACTA 59.119 40.000 0.00 0.00 0.00 1.82
164 179 3.603532 CCAGTTGACATGCTGACATAGT 58.396 45.455 8.57 0.00 33.67 2.12
165 180 3.620374 CCAGTTGACATGCTGACATAGTC 59.380 47.826 8.57 0.00 36.08 2.59
176 191 2.231478 CTGACATAGTCGTGGAAGTGGT 59.769 50.000 0.00 0.00 34.95 4.16
206 221 4.006989 TCCTGGATGTACAATTTGGTTCG 58.993 43.478 0.00 0.00 0.00 3.95
260 305 2.032071 CGCCGACCCTCAAACCTT 59.968 61.111 0.00 0.00 0.00 3.50
282 327 0.035317 GCATCAGTCAGGACACCACA 59.965 55.000 1.84 0.00 0.00 4.17
319 371 0.530650 CTGGTCGTTCTGTGCACAGT 60.531 55.000 38.41 0.00 44.12 3.55
320 372 0.107897 TGGTCGTTCTGTGCACAGTT 60.108 50.000 38.41 0.00 44.12 3.16
322 374 2.206750 GGTCGTTCTGTGCACAGTTTA 58.793 47.619 38.41 25.00 44.12 2.01
323 375 2.221055 GGTCGTTCTGTGCACAGTTTAG 59.779 50.000 38.41 28.11 44.12 1.85
324 376 1.864711 TCGTTCTGTGCACAGTTTAGC 59.135 47.619 38.41 23.96 44.12 3.09
325 377 1.867233 CGTTCTGTGCACAGTTTAGCT 59.133 47.619 38.41 0.00 44.12 3.32
327 379 2.169832 TCTGTGCACAGTTTAGCTCC 57.830 50.000 38.41 0.96 44.12 4.70
357 431 7.050377 CACCAATGTGATGTTCTACTCCTATT 58.950 38.462 0.00 0.00 45.76 1.73
358 432 7.011763 CACCAATGTGATGTTCTACTCCTATTG 59.988 40.741 0.00 0.00 45.76 1.90
359 433 7.050377 CCAATGTGATGTTCTACTCCTATTGT 58.950 38.462 0.00 0.00 0.00 2.71
360 434 8.204160 CCAATGTGATGTTCTACTCCTATTGTA 58.796 37.037 0.00 0.00 0.00 2.41
361 435 9.254133 CAATGTGATGTTCTACTCCTATTGTAG 57.746 37.037 0.00 0.00 38.85 2.74
362 436 6.806751 TGTGATGTTCTACTCCTATTGTAGC 58.193 40.000 0.00 0.00 37.78 3.58
363 437 6.379988 TGTGATGTTCTACTCCTATTGTAGCA 59.620 38.462 0.00 0.00 37.78 3.49
364 438 7.069950 TGTGATGTTCTACTCCTATTGTAGCAT 59.930 37.037 0.00 0.00 37.78 3.79
365 439 7.383572 GTGATGTTCTACTCCTATTGTAGCATG 59.616 40.741 0.00 0.00 37.78 4.06
366 440 7.287696 TGATGTTCTACTCCTATTGTAGCATGA 59.712 37.037 0.00 0.00 37.78 3.07
367 441 7.043961 TGTTCTACTCCTATTGTAGCATGAG 57.956 40.000 0.00 0.00 37.78 2.90
368 442 6.040955 TGTTCTACTCCTATTGTAGCATGAGG 59.959 42.308 0.00 0.00 37.78 3.86
369 443 5.953571 TCTACTCCTATTGTAGCATGAGGA 58.046 41.667 0.00 0.00 37.78 3.71
370 444 6.373759 TCTACTCCTATTGTAGCATGAGGAA 58.626 40.000 0.00 0.00 35.90 3.36
371 445 5.543507 ACTCCTATTGTAGCATGAGGAAG 57.456 43.478 0.00 0.00 35.90 3.46
372 446 5.211973 ACTCCTATTGTAGCATGAGGAAGA 58.788 41.667 0.00 0.00 35.90 2.87
373 447 5.304101 ACTCCTATTGTAGCATGAGGAAGAG 59.696 44.000 0.00 0.00 35.90 2.85
374 448 5.458595 TCCTATTGTAGCATGAGGAAGAGA 58.541 41.667 0.00 0.00 33.33 3.10
375 449 5.538053 TCCTATTGTAGCATGAGGAAGAGAG 59.462 44.000 0.00 0.00 33.33 3.20
376 450 3.533606 TTGTAGCATGAGGAAGAGAGC 57.466 47.619 0.00 0.00 0.00 4.09
377 451 2.744760 TGTAGCATGAGGAAGAGAGCT 58.255 47.619 0.00 0.00 36.20 4.09
378 452 2.692557 TGTAGCATGAGGAAGAGAGCTC 59.307 50.000 5.27 5.27 33.83 4.09
379 453 1.122227 AGCATGAGGAAGAGAGCTCC 58.878 55.000 10.93 1.70 0.00 4.70
380 454 0.249405 GCATGAGGAAGAGAGCTCCG 60.249 60.000 10.93 0.00 0.00 4.63
381 455 1.397672 CATGAGGAAGAGAGCTCCGA 58.602 55.000 10.93 0.00 0.00 4.55
382 456 1.753649 CATGAGGAAGAGAGCTCCGAA 59.246 52.381 10.93 0.00 0.00 4.30
383 457 1.924731 TGAGGAAGAGAGCTCCGAAA 58.075 50.000 10.93 0.00 0.00 3.46
384 458 1.546476 TGAGGAAGAGAGCTCCGAAAC 59.454 52.381 10.93 0.00 0.00 2.78
385 459 1.546476 GAGGAAGAGAGCTCCGAAACA 59.454 52.381 10.93 0.00 0.00 2.83
386 460 1.273886 AGGAAGAGAGCTCCGAAACAC 59.726 52.381 10.93 0.00 0.00 3.32
387 461 1.673329 GGAAGAGAGCTCCGAAACACC 60.673 57.143 10.93 1.73 0.00 4.16
388 462 1.000955 GAAGAGAGCTCCGAAACACCA 59.999 52.381 10.93 0.00 0.00 4.17
389 463 1.048601 AGAGAGCTCCGAAACACCAA 58.951 50.000 10.93 0.00 0.00 3.67
390 464 1.625818 AGAGAGCTCCGAAACACCAAT 59.374 47.619 10.93 0.00 0.00 3.16
391 465 1.734465 GAGAGCTCCGAAACACCAATG 59.266 52.381 10.93 0.00 0.00 2.82
392 466 1.072331 AGAGCTCCGAAACACCAATGT 59.928 47.619 10.93 0.00 42.46 2.71
394 468 1.202758 AGCTCCGAAACACCAATGTGA 60.203 47.619 0.00 0.00 45.76 3.58
395 469 1.812571 GCTCCGAAACACCAATGTGAT 59.187 47.619 0.00 0.00 45.76 3.06
396 470 2.414559 GCTCCGAAACACCAATGTGATG 60.415 50.000 0.00 0.00 45.76 3.07
397 471 2.813754 CTCCGAAACACCAATGTGATGT 59.186 45.455 0.00 0.00 45.76 3.06
398 472 3.218453 TCCGAAACACCAATGTGATGTT 58.782 40.909 0.00 0.00 45.76 2.71
399 473 3.252215 TCCGAAACACCAATGTGATGTTC 59.748 43.478 0.00 0.41 45.76 3.18
400 474 3.253188 CCGAAACACCAATGTGATGTTCT 59.747 43.478 0.00 0.00 45.76 3.01
401 475 4.454161 CCGAAACACCAATGTGATGTTCTA 59.546 41.667 0.00 0.00 45.76 2.10
402 476 5.382303 CGAAACACCAATGTGATGTTCTAC 58.618 41.667 0.00 0.00 45.76 2.59
403 477 5.179368 CGAAACACCAATGTGATGTTCTACT 59.821 40.000 0.00 0.00 45.76 2.57
404 478 6.560253 AAACACCAATGTGATGTTCTACTC 57.440 37.500 0.00 0.00 45.76 2.59
405 479 4.579869 ACACCAATGTGATGTTCTACTCC 58.420 43.478 0.00 0.00 45.76 3.85
406 480 4.287067 ACACCAATGTGATGTTCTACTCCT 59.713 41.667 0.00 0.00 45.76 3.69
407 481 5.483937 ACACCAATGTGATGTTCTACTCCTA 59.516 40.000 0.00 0.00 45.76 2.94
408 482 6.156949 ACACCAATGTGATGTTCTACTCCTAT 59.843 38.462 0.00 0.00 45.76 2.57
730 856 9.354673 TCTCAAAGTTGAATTGGAAGAATAACT 57.645 29.630 0.00 0.00 36.64 2.24
788 914 1.040339 TTCAACACAAGGCCGCCTTT 61.040 50.000 22.62 11.02 41.69 3.11
881 1176 4.477975 GGTGTCGCGAGAGGACGG 62.478 72.222 10.24 0.00 43.49 4.79
960 1255 1.105167 ACCAGTCGTCAGTCCGTTCA 61.105 55.000 0.00 0.00 0.00 3.18
963 1258 0.168348 AGTCGTCAGTCCGTTCATCG 59.832 55.000 0.00 0.00 39.52 3.84
983 1278 2.391879 GACTAAACTGTCGAAGCGTGT 58.608 47.619 0.00 0.00 0.00 4.49
1132 1442 1.000993 ACCGACCTCCATGCTCTCT 59.999 57.895 0.00 0.00 0.00 3.10
1175 1488 1.611851 CCTCTGCTGGACTCCTGGT 60.612 63.158 4.27 0.00 0.00 4.00
2318 2801 3.198417 GGCATTGTTCCATCTTTTGGGAT 59.802 43.478 0.00 0.00 46.45 3.85
2462 2945 0.034059 CAAGGAGTCTTGCCGAGTGT 59.966 55.000 0.00 0.00 43.10 3.55
3903 4401 0.322816 TGAAGCCCAGCAATGTCCTC 60.323 55.000 0.00 0.00 0.00 3.71
4189 4797 9.834628 AATTAACGGTTTCAATAACTACACATG 57.165 29.630 0.00 0.00 0.00 3.21
4327 4935 7.175104 AGATGGTCTGAGCCTTTACAAATTTA 58.825 34.615 4.17 0.00 0.00 1.40
4377 4988 6.013379 TGGCGAGATTCTAGATCCTAGAATT 58.987 40.000 22.65 15.44 42.44 2.17
4556 5170 2.224113 ACGTTTACATTGAGGTCACCGT 60.224 45.455 0.00 0.00 0.00 4.83
4641 5258 1.236616 TTGCTGGTTCATGACGGCTG 61.237 55.000 15.80 0.00 0.00 4.85
4667 5284 8.345724 ACGTCTAGTTTTCTCTACATAAGGAA 57.654 34.615 0.00 0.00 0.00 3.36
4668 5285 8.800332 ACGTCTAGTTTTCTCTACATAAGGAAA 58.200 33.333 0.00 0.00 0.00 3.13
4669 5286 9.635520 CGTCTAGTTTTCTCTACATAAGGAAAA 57.364 33.333 0.00 0.00 34.62 2.29
4704 5325 2.916111 CAGCCGTGTTATGTTGTGAAC 58.084 47.619 0.00 0.00 0.00 3.18
4707 5328 2.916111 CCGTGTTATGTTGTGAACTGC 58.084 47.619 0.00 0.00 0.00 4.40
4716 5337 2.622942 TGTTGTGAACTGCCTTCCATTC 59.377 45.455 0.00 0.00 0.00 2.67
4991 5625 3.190744 TCGTCGTAGCATGAAGAGTCTTT 59.809 43.478 6.88 0.00 0.00 2.52
5162 5798 0.251564 ATGGCCCATGAAAACCGACA 60.252 50.000 0.00 0.00 0.00 4.35
5327 5968 2.879103 ATCAACGGATTTGGTGGACT 57.121 45.000 0.00 0.00 35.69 3.85
5448 6138 2.358737 CTCCCGTGTTGTGCTCCC 60.359 66.667 0.00 0.00 0.00 4.30
5456 6146 1.961277 GTTGTGCTCCCGACTGTGG 60.961 63.158 0.00 0.00 0.00 4.17
5481 6213 2.435586 CAAGCAGAGCTCCCGTGG 60.436 66.667 10.93 0.00 38.25 4.94
5531 6264 5.590259 GTCTCTCTGAGCTAGAAGAGTCAAT 59.410 44.000 16.22 0.00 40.70 2.57
5565 6298 3.049344 AGAACCTGGTGAAGAAGAACCT 58.951 45.455 0.00 0.00 37.36 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.101331 CAGAAGCAAGATCTTGGGCC 58.899 55.000 31.41 17.92 40.74 5.80
64 66 2.274437 CGAATGATGTGGACTGGACAG 58.726 52.381 0.00 0.00 0.00 3.51
116 119 4.564769 GCTTCTGAGACTTGGAACGAATAG 59.435 45.833 0.00 0.00 0.00 1.73
117 120 4.021456 TGCTTCTGAGACTTGGAACGAATA 60.021 41.667 0.00 0.00 0.00 1.75
118 121 3.244215 TGCTTCTGAGACTTGGAACGAAT 60.244 43.478 0.00 0.00 0.00 3.34
181 196 4.934356 ACCAAATTGTACATCCAGGACAT 58.066 39.130 0.00 0.00 0.00 3.06
206 221 3.119495 AGGCGCCAATTTGTTCAACTATC 60.119 43.478 31.54 0.00 0.00 2.08
260 305 1.591703 GTGTCCTGACTGATGCGGA 59.408 57.895 0.00 0.00 0.00 5.54
282 327 1.146544 AGCCATTGGGTTAGGTGGGT 61.147 55.000 0.36 0.00 37.61 4.51
319 371 3.252215 CACATTGGTGTTTCGGAGCTAAA 59.748 43.478 0.00 0.00 40.24 1.85
320 372 2.811431 CACATTGGTGTTTCGGAGCTAA 59.189 45.455 0.00 0.00 40.24 3.09
322 374 1.202758 TCACATTGGTGTTTCGGAGCT 60.203 47.619 0.00 0.00 45.45 4.09
323 375 1.234821 TCACATTGGTGTTTCGGAGC 58.765 50.000 0.00 0.00 45.45 4.70
324 376 2.813754 ACATCACATTGGTGTTTCGGAG 59.186 45.455 0.00 0.00 38.88 4.63
325 377 2.857483 ACATCACATTGGTGTTTCGGA 58.143 42.857 0.00 0.00 38.88 4.55
357 431 2.692557 GAGCTCTCTTCCTCATGCTACA 59.307 50.000 6.43 0.00 0.00 2.74
358 432 2.035832 GGAGCTCTCTTCCTCATGCTAC 59.964 54.545 14.64 0.00 0.00 3.58
359 433 2.315176 GGAGCTCTCTTCCTCATGCTA 58.685 52.381 14.64 0.00 0.00 3.49
360 434 1.122227 GGAGCTCTCTTCCTCATGCT 58.878 55.000 14.64 0.00 0.00 3.79
361 435 0.249405 CGGAGCTCTCTTCCTCATGC 60.249 60.000 14.64 0.00 0.00 4.06
362 436 1.397672 TCGGAGCTCTCTTCCTCATG 58.602 55.000 14.64 0.00 0.00 3.07
363 437 2.151502 TTCGGAGCTCTCTTCCTCAT 57.848 50.000 14.64 0.00 0.00 2.90
364 438 1.546476 GTTTCGGAGCTCTCTTCCTCA 59.454 52.381 14.64 0.00 0.00 3.86
365 439 1.546476 TGTTTCGGAGCTCTCTTCCTC 59.454 52.381 14.64 0.00 0.00 3.71
366 440 1.273886 GTGTTTCGGAGCTCTCTTCCT 59.726 52.381 14.64 0.00 0.00 3.36
367 441 1.673329 GGTGTTTCGGAGCTCTCTTCC 60.673 57.143 14.64 4.14 0.00 3.46
368 442 1.000955 TGGTGTTTCGGAGCTCTCTTC 59.999 52.381 14.64 0.00 0.00 2.87
369 443 1.048601 TGGTGTTTCGGAGCTCTCTT 58.951 50.000 14.64 0.00 0.00 2.85
370 444 1.048601 TTGGTGTTTCGGAGCTCTCT 58.951 50.000 14.64 0.00 0.00 3.10
371 445 1.734465 CATTGGTGTTTCGGAGCTCTC 59.266 52.381 14.64 2.76 0.00 3.20
372 446 1.072331 ACATTGGTGTTTCGGAGCTCT 59.928 47.619 14.64 0.00 34.01 4.09
373 447 1.197721 CACATTGGTGTTTCGGAGCTC 59.802 52.381 4.71 4.71 40.24 4.09
374 448 1.202758 TCACATTGGTGTTTCGGAGCT 60.203 47.619 0.00 0.00 45.45 4.09
375 449 1.234821 TCACATTGGTGTTTCGGAGC 58.765 50.000 0.00 0.00 45.45 4.70
376 450 2.813754 ACATCACATTGGTGTTTCGGAG 59.186 45.455 0.00 0.00 38.88 4.63
377 451 2.857483 ACATCACATTGGTGTTTCGGA 58.143 42.857 0.00 0.00 38.88 4.55
383 457 4.287067 AGGAGTAGAACATCACATTGGTGT 59.713 41.667 0.00 0.00 44.93 4.16
384 458 4.836825 AGGAGTAGAACATCACATTGGTG 58.163 43.478 0.00 0.00 46.66 4.17
385 459 6.814954 ATAGGAGTAGAACATCACATTGGT 57.185 37.500 0.00 0.00 0.00 3.67
386 460 7.050377 ACAATAGGAGTAGAACATCACATTGG 58.950 38.462 0.00 0.00 0.00 3.16
387 461 9.254133 CTACAATAGGAGTAGAACATCACATTG 57.746 37.037 0.00 0.00 41.07 2.82
388 462 7.928706 GCTACAATAGGAGTAGAACATCACATT 59.071 37.037 4.66 0.00 41.07 2.71
389 463 7.069950 TGCTACAATAGGAGTAGAACATCACAT 59.930 37.037 4.66 0.00 41.07 3.21
390 464 6.379988 TGCTACAATAGGAGTAGAACATCACA 59.620 38.462 4.66 0.00 41.07 3.58
391 465 6.806751 TGCTACAATAGGAGTAGAACATCAC 58.193 40.000 4.66 0.00 41.07 3.06
392 466 7.287696 TCATGCTACAATAGGAGTAGAACATCA 59.712 37.037 4.66 0.00 41.07 3.07
393 467 7.661968 TCATGCTACAATAGGAGTAGAACATC 58.338 38.462 4.66 0.00 41.07 3.06
394 468 7.256119 CCTCATGCTACAATAGGAGTAGAACAT 60.256 40.741 4.66 0.00 41.07 2.71
395 469 6.040955 CCTCATGCTACAATAGGAGTAGAACA 59.959 42.308 4.66 0.00 41.07 3.18
396 470 6.265649 TCCTCATGCTACAATAGGAGTAGAAC 59.734 42.308 4.66 0.00 41.07 3.01
397 471 6.373759 TCCTCATGCTACAATAGGAGTAGAA 58.626 40.000 4.66 0.00 41.07 2.10
398 472 5.953571 TCCTCATGCTACAATAGGAGTAGA 58.046 41.667 4.66 0.00 41.07 2.59
399 473 6.491745 TCTTCCTCATGCTACAATAGGAGTAG 59.508 42.308 0.00 0.00 41.41 2.57
400 474 6.373759 TCTTCCTCATGCTACAATAGGAGTA 58.626 40.000 0.00 0.00 37.63 2.59
401 475 5.211973 TCTTCCTCATGCTACAATAGGAGT 58.788 41.667 0.00 0.00 37.63 3.85
402 476 5.538053 TCTCTTCCTCATGCTACAATAGGAG 59.462 44.000 0.00 0.00 37.63 3.69
403 477 5.458595 TCTCTTCCTCATGCTACAATAGGA 58.541 41.667 0.00 0.00 34.56 2.94
404 478 5.538053 TCTCTCTTCCTCATGCTACAATAGG 59.462 44.000 0.00 0.00 0.00 2.57
405 479 6.647334 TCTCTCTTCCTCATGCTACAATAG 57.353 41.667 0.00 0.00 0.00 1.73
406 480 5.010516 GCTCTCTCTTCCTCATGCTACAATA 59.989 44.000 0.00 0.00 0.00 1.90
407 481 4.202243 GCTCTCTCTTCCTCATGCTACAAT 60.202 45.833 0.00 0.00 0.00 2.71
408 482 3.131933 GCTCTCTCTTCCTCATGCTACAA 59.868 47.826 0.00 0.00 0.00 2.41
729 855 7.202016 TCAGCCAATCAAACACTAGTTTAAG 57.798 36.000 0.00 0.00 45.80 1.85
730 856 7.255451 CCTTCAGCCAATCAAACACTAGTTTAA 60.255 37.037 0.00 0.00 45.80 1.52
738 864 2.070262 GCCTTCAGCCAATCAAACAC 57.930 50.000 0.00 0.00 34.35 3.32
788 914 3.031013 TGTAGAGCTGCAGCACCTAATA 58.969 45.455 38.24 24.48 45.16 0.98
963 1258 2.153247 CACACGCTTCGACAGTTTAGTC 59.847 50.000 0.00 0.00 35.19 2.59
983 1278 7.851228 AGGAGACATGTAATTTCTATCACACA 58.149 34.615 0.00 0.00 32.55 3.72
1132 1442 2.305635 TGAGATGGAGTTTAAGGCAGCA 59.694 45.455 0.00 0.00 0.00 4.41
1175 1488 3.686241 CAGCGAGTCATTTTTCCATGAGA 59.314 43.478 0.00 0.00 33.69 3.27
2280 2763 2.676632 TGCCATGGAATGCATTGTTC 57.323 45.000 18.59 2.91 44.97 3.18
2318 2801 3.132289 CAGATCGACTAGGCTGGGTAAAA 59.868 47.826 2.02 0.00 0.00 1.52
2462 2945 0.667993 CTTTGAAAGGCCTGCAACGA 59.332 50.000 18.12 6.77 0.00 3.85
3020 3503 4.494091 TGAGGGATTCTTCCATGAAGAC 57.506 45.455 6.05 0.00 46.54 3.01
3732 4225 0.321996 AGAGCCAACTTTCGAGGTCC 59.678 55.000 0.00 0.00 0.00 4.46
3903 4401 1.267806 GCGCCCATGACATCATTTAGG 59.732 52.381 0.00 0.00 33.61 2.69
4189 4797 2.760092 TCCCAAAGCCATATTCTGCAAC 59.240 45.455 0.00 0.00 0.00 4.17
4327 4935 9.933723 AATCTTTTCTGGAAATGATTTTTCGAT 57.066 25.926 21.11 7.35 45.12 3.59
4395 5006 2.015587 CCTCCTGCTTCTTCATCTTGC 58.984 52.381 0.00 0.00 0.00 4.01
4556 5170 6.864685 CAGTGCTGAAAATGCTTCTTTGATTA 59.135 34.615 0.00 0.00 0.00 1.75
4641 5258 7.983307 TCCTTATGTAGAGAAAACTAGACGTC 58.017 38.462 7.70 7.70 0.00 4.34
4670 5287 1.412343 ACGGCTGCAACCAAGATTTTT 59.588 42.857 6.99 0.00 0.00 1.94
4672 5289 0.314935 CACGGCTGCAACCAAGATTT 59.685 50.000 6.99 0.00 0.00 2.17
4674 5291 0.823356 AACACGGCTGCAACCAAGAT 60.823 50.000 6.99 0.00 0.00 2.40
4704 5325 4.487714 TTACCAGTAGAATGGAAGGCAG 57.512 45.455 2.45 0.00 43.57 4.85
4707 5328 8.432805 ACATAGATTTACCAGTAGAATGGAAGG 58.567 37.037 2.45 0.00 43.57 3.46
4716 5337 7.606456 ACACCACAAACATAGATTTACCAGTAG 59.394 37.037 0.00 0.00 0.00 2.57
4738 5359 5.240844 AGTTGCTTTCCTAACAACATACACC 59.759 40.000 7.73 0.00 44.77 4.16
4905 5534 8.796475 AGTATTACACTTCTTCAAATGCAATGT 58.204 29.630 0.00 0.00 31.59 2.71
4947 5581 3.069586 ACACTCTCAAGACACGGATTTGA 59.930 43.478 0.00 0.00 0.00 2.69
4991 5625 2.343506 TGGCGACTCGACAGGTTTA 58.656 52.632 1.80 0.00 41.22 2.01
5162 5798 2.811317 CGCCGAGCTTCTTTCGCT 60.811 61.111 0.00 0.00 41.15 4.93
5327 5968 7.788026 TCCTAGTTTTCTATAATTTCCGCTGA 58.212 34.615 0.00 0.00 0.00 4.26
5448 6138 2.513026 CTTGGCCCTCTCCACAGTCG 62.513 65.000 0.00 0.00 35.50 4.18
5456 6146 2.124778 GCTCTGCTTGGCCCTCTC 60.125 66.667 0.00 0.00 0.00 3.20
5481 6213 1.069204 TCTTCACAGTCAGGAGCACAC 59.931 52.381 0.00 0.00 0.00 3.82
5531 6264 1.053424 AGGTTCTGCCGGTCTTGTTA 58.947 50.000 1.90 0.00 43.70 2.41
5565 6298 0.318441 AGCGTCTACTTGCAGCTTCA 59.682 50.000 0.00 0.00 34.05 3.02


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

AutoCloner maintained by Alex Coulton.