Multiple sequence alignment - TraesCS1B01G330800

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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 TraesCS1B01G330800 chr1B 100.000 2684 0 0 1 2684 556662045 556664728 0.000000e+00 4957.0
1 TraesCS1B01G330800 chr1B 93.688 1917 91 10 771 2684 556251123 556253012 0.000000e+00 2843.0
2 TraesCS1B01G330800 chr1B 89.312 2049 138 35 587 2625 556296878 556298855 0.000000e+00 2495.0
3 TraesCS1B01G330800 chr1B 88.499 1852 151 27 580 2414 556064794 556062988 0.000000e+00 2183.0
4 TraesCS1B01G330800 chr1B 100.000 494 0 0 2871 3364 556664915 556665408 0.000000e+00 913.0
5 TraesCS1B01G330800 chr1B 93.556 419 25 2 21 439 556263487 556263903 1.020000e-174 623.0
6 TraesCS1B01G330800 chr1B 91.827 208 10 3 580 787 556263895 556264095 1.980000e-72 283.0
7 TraesCS1B01G330800 chr1B 89.412 85 9 0 2875 2959 561989731 561989815 1.280000e-19 108.0
8 TraesCS1B01G330800 chr1D 91.151 2102 131 30 580 2651 412641710 412643786 0.000000e+00 2800.0
9 TraesCS1B01G330800 chr1D 91.151 2102 131 30 580 2651 412745688 412747764 0.000000e+00 2800.0
10 TraesCS1B01G330800 chr1D 91.151 2102 131 30 580 2651 412762851 412764927 0.000000e+00 2800.0
11 TraesCS1B01G330800 chr1D 93.537 1903 86 17 800 2684 412897463 412899346 0.000000e+00 2798.0
12 TraesCS1B01G330800 chr1D 92.992 1912 91 19 800 2684 412683757 412685652 0.000000e+00 2748.0
13 TraesCS1B01G330800 chr1D 92.635 1901 93 26 800 2684 412814151 412816020 0.000000e+00 2691.0
14 TraesCS1B01G330800 chr1D 93.326 1798 92 14 580 2367 412659979 412661758 0.000000e+00 2630.0
15 TraesCS1B01G330800 chr1D 91.823 1810 82 24 580 2367 412786362 412788127 0.000000e+00 2462.0
16 TraesCS1B01G330800 chr1D 90.534 412 37 2 2954 3364 249176265 249175855 8.210000e-151 544.0
17 TraesCS1B01G330800 chr1D 92.758 359 25 1 9 367 412785974 412786331 4.980000e-143 518.0
18 TraesCS1B01G330800 chr1D 92.098 367 28 1 1 367 412659583 412659948 1.790000e-142 516.0
19 TraesCS1B01G330800 chr1D 92.877 351 24 1 17 367 412854091 412854440 2.990000e-140 508.0
20 TraesCS1B01G330800 chr1D 88.089 403 47 1 2963 3364 327922924 327923326 8.440000e-131 477.0
21 TraesCS1B01G330800 chr1D 86.441 118 13 2 468 582 373113840 373113723 3.520000e-25 126.0
22 TraesCS1B01G330800 chr1D 92.941 85 6 0 2875 2959 327921757 327921841 1.270000e-24 124.0
23 TraesCS1B01G330800 chr1D 90.588 85 8 0 2875 2959 249226928 249226844 2.740000e-21 113.0
24 TraesCS1B01G330800 chr1A 92.012 1978 116 21 580 2546 509849923 509847977 0.000000e+00 2739.0
25 TraesCS1B01G330800 chr1A 92.711 1852 104 15 580 2426 509720398 509718573 0.000000e+00 2643.0
26 TraesCS1B01G330800 chr1A 92.549 1852 107 15 580 2426 509793778 509791953 0.000000e+00 2627.0
27 TraesCS1B01G330800 chr1A 90.073 2065 144 32 581 2625 509704017 509701994 0.000000e+00 2621.0
28 TraesCS1B01G330800 chr1A 91.572 439 34 2 1 439 509850350 509849915 1.340000e-168 603.0
29 TraesCS1B01G330800 chr1A 90.205 439 39 3 1 439 509720824 509720390 1.350000e-158 569.0
30 TraesCS1B01G330800 chr1A 90.205 439 38 4 1 439 509794203 509793770 4.870000e-158 568.0
31 TraesCS1B01G330800 chr1A 94.186 86 5 0 2875 2960 407134407 407134492 7.570000e-27 132.0
32 TraesCS1B01G330800 chr4B 87.794 1958 175 28 579 2518 633465587 633467498 0.000000e+00 2233.0
33 TraesCS1B01G330800 chr4B 87.404 1961 180 29 579 2518 633398455 633400369 0.000000e+00 2191.0
34 TraesCS1B01G330800 chr4B 100.000 36 0 0 2649 2684 633468427 633468462 2.170000e-07 67.6
35 TraesCS1B01G330800 chr4B 97.222 36 1 0 2649 2684 633401300 633401335 1.010000e-05 62.1
36 TraesCS1B01G330800 chr3B 92.839 391 27 1 2967 3356 663175159 663174769 1.750000e-157 566.0
37 TraesCS1B01G330800 chr3B 89.051 137 13 2 444 579 303122941 303123076 5.770000e-38 169.0
38 TraesCS1B01G330800 chr3B 90.588 85 8 0 2875 2959 663176331 663176247 2.740000e-21 113.0
39 TraesCS1B01G330800 chr4A 89.578 403 41 1 2954 3356 719287010 719287411 8.330000e-141 510.0
40 TraesCS1B01G330800 chr4A 89.578 403 41 1 2954 3356 719511765 719512166 8.330000e-141 510.0
41 TraesCS1B01G330800 chr4A 88.564 411 46 1 2954 3364 501781061 501781470 6.480000e-137 497.0
42 TraesCS1B01G330800 chr5D 89.055 402 44 0 2963 3364 437861279 437860878 1.800000e-137 499.0
43 TraesCS1B01G330800 chr5D 94.118 85 5 0 2875 2959 437862446 437862362 2.720000e-26 130.0
44 TraesCS1B01G330800 chr5D 82.222 135 19 4 444 578 383296503 383296374 9.870000e-21 111.0
45 TraesCS1B01G330800 chr2D 89.295 383 39 2 2954 3335 155472107 155472488 2.350000e-131 479.0
46 TraesCS1B01G330800 chr2D 86.352 403 54 1 2963 3364 544249781 544250183 3.980000e-119 438.0
47 TraesCS1B01G330800 chr2D 90.588 85 8 0 2875 2959 544248616 544248700 2.740000e-21 113.0
48 TraesCS1B01G330800 chr7B 88.235 136 13 2 444 579 581956620 581956752 3.470000e-35 159.0
49 TraesCS1B01G330800 chr7B 85.600 125 15 2 461 582 587901422 587901298 9.800000e-26 128.0
50 TraesCS1B01G330800 chr3A 87.234 141 14 3 444 581 654404057 654404196 1.250000e-34 158.0
51 TraesCS1B01G330800 chr6B 92.941 85 6 0 2875 2959 231575748 231575664 1.270000e-24 124.0
52 TraesCS1B01G330800 chr6B 81.818 110 20 0 260 369 699028087 699028196 3.570000e-15 93.5
53 TraesCS1B01G330800 chr5B 83.333 138 17 5 444 580 35248244 35248376 4.560000e-24 122.0
54 TraesCS1B01G330800 chr5B 83.200 125 19 2 457 579 459173299 459173175 2.740000e-21 113.0
55 TraesCS1B01G330800 chr2A 85.345 116 13 3 468 579 713644489 713644374 2.120000e-22 117.0
56 TraesCS1B01G330800 chr6D 89.412 85 8 1 2875 2959 315235803 315235886 4.590000e-19 106.0
57 TraesCS1B01G330800 chr7D 79.832 119 23 1 255 373 66397543 66397660 5.980000e-13 86.1


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 TraesCS1B01G330800 chr1B 556662045 556665408 3363 False 2935.00 4957 100.0000 1 3364 2 chr1B.!!$F5 3363
1 TraesCS1B01G330800 chr1B 556251123 556253012 1889 False 2843.00 2843 93.6880 771 2684 1 chr1B.!!$F1 1913
2 TraesCS1B01G330800 chr1B 556296878 556298855 1977 False 2495.00 2495 89.3120 587 2625 1 chr1B.!!$F2 2038
3 TraesCS1B01G330800 chr1B 556062988 556064794 1806 True 2183.00 2183 88.4990 580 2414 1 chr1B.!!$R1 1834
4 TraesCS1B01G330800 chr1B 556263487 556264095 608 False 453.00 623 92.6915 21 787 2 chr1B.!!$F4 766
5 TraesCS1B01G330800 chr1D 412641710 412643786 2076 False 2800.00 2800 91.1510 580 2651 1 chr1D.!!$F1 2071
6 TraesCS1B01G330800 chr1D 412745688 412747764 2076 False 2800.00 2800 91.1510 580 2651 1 chr1D.!!$F3 2071
7 TraesCS1B01G330800 chr1D 412762851 412764927 2076 False 2800.00 2800 91.1510 580 2651 1 chr1D.!!$F4 2071
8 TraesCS1B01G330800 chr1D 412897463 412899346 1883 False 2798.00 2798 93.5370 800 2684 1 chr1D.!!$F7 1884
9 TraesCS1B01G330800 chr1D 412683757 412685652 1895 False 2748.00 2748 92.9920 800 2684 1 chr1D.!!$F2 1884
10 TraesCS1B01G330800 chr1D 412814151 412816020 1869 False 2691.00 2691 92.6350 800 2684 1 chr1D.!!$F5 1884
11 TraesCS1B01G330800 chr1D 412659583 412661758 2175 False 1573.00 2630 92.7120 1 2367 2 chr1D.!!$F9 2366
12 TraesCS1B01G330800 chr1D 412785974 412788127 2153 False 1490.00 2462 92.2905 9 2367 2 chr1D.!!$F10 2358
13 TraesCS1B01G330800 chr1D 327921757 327923326 1569 False 300.50 477 90.5150 2875 3364 2 chr1D.!!$F8 489
14 TraesCS1B01G330800 chr1A 509701994 509704017 2023 True 2621.00 2621 90.0730 581 2625 1 chr1A.!!$R1 2044
15 TraesCS1B01G330800 chr1A 509847977 509850350 2373 True 1671.00 2739 91.7920 1 2546 2 chr1A.!!$R4 2545
16 TraesCS1B01G330800 chr1A 509718573 509720824 2251 True 1606.00 2643 91.4580 1 2426 2 chr1A.!!$R2 2425
17 TraesCS1B01G330800 chr1A 509791953 509794203 2250 True 1597.50 2627 91.3770 1 2426 2 chr1A.!!$R3 2425
18 TraesCS1B01G330800 chr4B 633465587 633468462 2875 False 1150.30 2233 93.8970 579 2684 2 chr4B.!!$F2 2105
19 TraesCS1B01G330800 chr4B 633398455 633401335 2880 False 1126.55 2191 92.3130 579 2684 2 chr4B.!!$F1 2105
20 TraesCS1B01G330800 chr3B 663174769 663176331 1562 True 339.50 566 91.7135 2875 3356 2 chr3B.!!$R1 481
21 TraesCS1B01G330800 chr5D 437860878 437862446 1568 True 314.50 499 91.5865 2875 3364 2 chr5D.!!$R2 489
22 TraesCS1B01G330800 chr2D 544248616 544250183 1567 False 275.50 438 88.4700 2875 3364 2 chr2D.!!$F2 489

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
340 341 0.965363 TCTGGCTCAAAATTCCGGGC 60.965 55.0 0.0 0.0 0.0 6.13 F
1108 1187 0.178068 GAAGATGGCGTTGAGGGCTA 59.822 55.0 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1285 0.036448 TCTCCTTCCTCACGACGTCT 59.964 55.0 14.70 0.00 0.00 4.18 R
2873 4638 0.044092 TATTCAGGTGGGGAGCTCCA 59.956 55.0 33.29 12.97 37.91 3.86 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
51 52 9.626045 CCAAGCTTGAAACTTATAAAAACTAGG 57.374 33.333 28.05 0.00 0.00 3.02
108 109 9.119329 TGTTTGGAATTTAAACGTCATTATTCG 57.881 29.630 11.98 0.00 40.10 3.34
244 245 8.523915 AACAAAGCAATCTTGGATGACATATA 57.476 30.769 0.00 0.00 31.78 0.86
340 341 0.965363 TCTGGCTCAAAATTCCGGGC 60.965 55.000 0.00 0.00 0.00 6.13
364 398 6.455646 GCTTACAAGTATTTCAGACCACATCG 60.456 42.308 0.00 0.00 0.00 3.84
374 408 3.058293 TCAGACCACATCGAAATTTGCAC 60.058 43.478 0.00 0.00 0.00 4.57
414 448 7.660617 AGATCAAATGAATATAGCACTGACTGG 59.339 37.037 0.00 0.00 0.00 4.00
430 464 3.135712 TGACTGGGACTTAGCAAAACTGA 59.864 43.478 0.00 0.00 0.00 3.41
431 465 4.202461 TGACTGGGACTTAGCAAAACTGAT 60.202 41.667 0.00 0.00 0.00 2.90
432 466 4.729868 ACTGGGACTTAGCAAAACTGATT 58.270 39.130 0.00 0.00 0.00 2.57
433 467 5.140454 ACTGGGACTTAGCAAAACTGATTT 58.860 37.500 0.00 0.00 0.00 2.17
435 469 4.280677 TGGGACTTAGCAAAACTGATTTGG 59.719 41.667 11.59 0.00 46.93 3.28
436 470 4.321974 GGGACTTAGCAAAACTGATTTGGG 60.322 45.833 11.59 0.00 46.93 4.12
437 471 4.522789 GGACTTAGCAAAACTGATTTGGGA 59.477 41.667 11.59 0.00 46.93 4.37
438 472 5.185828 GGACTTAGCAAAACTGATTTGGGAT 59.814 40.000 11.59 0.00 46.93 3.85
439 473 6.272822 ACTTAGCAAAACTGATTTGGGATC 57.727 37.500 11.59 0.00 46.93 3.36
440 474 5.774690 ACTTAGCAAAACTGATTTGGGATCA 59.225 36.000 11.59 0.00 46.93 2.92
441 475 4.796038 AGCAAAACTGATTTGGGATCAG 57.204 40.909 13.01 13.01 46.93 2.90
449 483 5.747951 CTGATTTGGGATCAGTTAAGCTC 57.252 43.478 7.66 0.00 40.34 4.09
450 484 4.526970 TGATTTGGGATCAGTTAAGCTCC 58.473 43.478 0.00 0.00 0.00 4.70
451 485 4.228210 TGATTTGGGATCAGTTAAGCTCCT 59.772 41.667 0.00 0.00 0.00 3.69
452 486 5.428457 TGATTTGGGATCAGTTAAGCTCCTA 59.572 40.000 0.00 0.00 0.00 2.94
453 487 4.755266 TTGGGATCAGTTAAGCTCCTAC 57.245 45.455 0.00 0.00 0.00 3.18
454 488 3.719871 TGGGATCAGTTAAGCTCCTACA 58.280 45.455 0.00 0.00 0.00 2.74
455 489 4.101114 TGGGATCAGTTAAGCTCCTACAA 58.899 43.478 0.00 0.00 0.00 2.41
456 490 4.534500 TGGGATCAGTTAAGCTCCTACAAA 59.466 41.667 0.00 0.00 0.00 2.83
457 491 5.191722 TGGGATCAGTTAAGCTCCTACAAAT 59.808 40.000 0.00 0.00 0.00 2.32
458 492 6.385759 TGGGATCAGTTAAGCTCCTACAAATA 59.614 38.462 0.00 0.00 0.00 1.40
459 493 7.072454 TGGGATCAGTTAAGCTCCTACAAATAT 59.928 37.037 0.00 0.00 0.00 1.28
460 494 8.594550 GGGATCAGTTAAGCTCCTACAAATATA 58.405 37.037 0.00 0.00 0.00 0.86
469 503 7.856145 AGCTCCTACAAATATATAATGCAGC 57.144 36.000 0.00 0.00 0.00 5.25
470 504 7.397221 AGCTCCTACAAATATATAATGCAGCA 58.603 34.615 0.00 0.00 0.00 4.41
471 505 7.884877 AGCTCCTACAAATATATAATGCAGCAA 59.115 33.333 0.00 0.00 0.00 3.91
472 506 7.965107 GCTCCTACAAATATATAATGCAGCAAC 59.035 37.037 0.00 0.00 0.00 4.17
473 507 8.916628 TCCTACAAATATATAATGCAGCAACA 57.083 30.769 0.00 0.00 0.00 3.33
474 508 9.348476 TCCTACAAATATATAATGCAGCAACAA 57.652 29.630 0.00 0.00 0.00 2.83
475 509 9.964303 CCTACAAATATATAATGCAGCAACAAA 57.036 29.630 0.00 0.00 0.00 2.83
511 545 9.793259 AAATTAGGACAAGAACAATAGACTTCA 57.207 29.630 0.00 0.00 0.00 3.02
512 546 9.793259 AATTAGGACAAGAACAATAGACTTCAA 57.207 29.630 0.00 0.00 0.00 2.69
513 547 9.793259 ATTAGGACAAGAACAATAGACTTCAAA 57.207 29.630 0.00 0.00 0.00 2.69
514 548 7.497925 AGGACAAGAACAATAGACTTCAAAC 57.502 36.000 0.00 0.00 0.00 2.93
515 549 7.054124 AGGACAAGAACAATAGACTTCAAACA 58.946 34.615 0.00 0.00 0.00 2.83
516 550 7.227512 AGGACAAGAACAATAGACTTCAAACAG 59.772 37.037 0.00 0.00 0.00 3.16
517 551 7.226720 GGACAAGAACAATAGACTTCAAACAGA 59.773 37.037 0.00 0.00 0.00 3.41
518 552 8.147642 ACAAGAACAATAGACTTCAAACAGAG 57.852 34.615 0.00 0.00 0.00 3.35
519 553 7.770897 ACAAGAACAATAGACTTCAAACAGAGT 59.229 33.333 0.00 0.00 0.00 3.24
520 554 7.721286 AGAACAATAGACTTCAAACAGAGTG 57.279 36.000 0.00 0.00 0.00 3.51
521 555 6.708054 AGAACAATAGACTTCAAACAGAGTGG 59.292 38.462 0.00 0.00 0.00 4.00
522 556 6.174720 ACAATAGACTTCAAACAGAGTGGA 57.825 37.500 0.00 0.00 0.00 4.02
523 557 5.992217 ACAATAGACTTCAAACAGAGTGGAC 59.008 40.000 0.00 0.00 0.00 4.02
524 558 5.808366 ATAGACTTCAAACAGAGTGGACA 57.192 39.130 0.00 0.00 0.00 4.02
525 559 4.696479 AGACTTCAAACAGAGTGGACAT 57.304 40.909 0.00 0.00 0.00 3.06
526 560 4.636249 AGACTTCAAACAGAGTGGACATC 58.364 43.478 0.00 0.00 0.00 3.06
527 561 4.101585 AGACTTCAAACAGAGTGGACATCA 59.898 41.667 0.00 0.00 0.00 3.07
528 562 4.780815 ACTTCAAACAGAGTGGACATCAA 58.219 39.130 0.00 0.00 0.00 2.57
529 563 4.818546 ACTTCAAACAGAGTGGACATCAAG 59.181 41.667 0.00 0.00 0.00 3.02
530 564 4.422073 TCAAACAGAGTGGACATCAAGT 57.578 40.909 0.00 0.00 0.00 3.16
531 565 4.780815 TCAAACAGAGTGGACATCAAGTT 58.219 39.130 0.00 0.00 0.00 2.66
532 566 5.924356 TCAAACAGAGTGGACATCAAGTTA 58.076 37.500 0.00 0.00 0.00 2.24
533 567 5.991606 TCAAACAGAGTGGACATCAAGTTAG 59.008 40.000 0.00 0.00 0.00 2.34
534 568 5.808366 AACAGAGTGGACATCAAGTTAGA 57.192 39.130 0.00 0.00 0.00 2.10
535 569 6.365970 AACAGAGTGGACATCAAGTTAGAT 57.634 37.500 0.00 0.00 0.00 1.98
577 611 8.324163 ACATTTAGATGTGTCTTAAACAGACC 57.676 34.615 0.00 0.00 44.64 3.85
725 759 3.726517 CCGCAGTTTGCTCCGTGG 61.727 66.667 0.00 0.00 42.25 4.94
856 907 4.323477 GCCGGTGTACCTGCCACA 62.323 66.667 1.90 0.00 39.91 4.17
878 929 2.419324 GCAAAGATTCCAGAGAGTGCAG 59.581 50.000 0.00 0.00 0.00 4.41
900 958 6.459573 GCAGACAAGGAACAACTCATTAAACA 60.460 38.462 0.00 0.00 0.00 2.83
925 983 2.356135 GAATTTTACCTGCTGCTCCGA 58.644 47.619 0.00 0.00 0.00 4.55
995 1054 4.552365 CCGGCGCCAGTCCATCAT 62.552 66.667 28.98 0.00 0.00 2.45
1003 1062 0.818445 CCAGTCCATCATCAGCAGCC 60.818 60.000 0.00 0.00 0.00 4.85
1100 1179 0.320374 TTGACCGAGAAGATGGCGTT 59.680 50.000 0.00 0.00 0.00 4.84
1108 1187 0.178068 GAAGATGGCGTTGAGGGCTA 59.822 55.000 0.00 0.00 0.00 3.93
1109 1188 0.179000 AAGATGGCGTTGAGGGCTAG 59.821 55.000 0.00 0.00 0.00 3.42
1117 1196 0.530870 GTTGAGGGCTAGGACGATGC 60.531 60.000 0.00 0.00 0.00 3.91
1312 1391 1.798079 GCTTCGTCAGGGTAAGCTACG 60.798 57.143 0.00 0.00 41.85 3.51
1338 1423 0.473755 TGCATGTTGTCTGTCCCTGT 59.526 50.000 0.00 0.00 0.00 4.00
1342 1427 0.758734 TGTTGTCTGTCCCTGTCCTG 59.241 55.000 0.00 0.00 0.00 3.86
1355 1446 1.898574 GTCCTGCCCTGTTGTGTGG 60.899 63.158 0.00 0.00 0.00 4.17
1401 1492 0.034574 ATTAATGCAGGGGTGCGACA 60.035 50.000 0.00 0.00 37.69 4.35
1535 1626 2.989824 CCCGACACGGTCTCCTGT 60.990 66.667 9.28 0.00 46.80 4.00
1585 1676 1.069204 CGCAGTATGGCTGGTGAGTAT 59.931 52.381 0.00 0.00 45.14 2.12
1594 1689 4.207955 TGGCTGGTGAGTATAGACTACTG 58.792 47.826 0.00 0.00 35.45 2.74
1595 1690 3.570550 GGCTGGTGAGTATAGACTACTGG 59.429 52.174 0.00 0.00 35.45 4.00
2108 2212 3.948719 GACCCCTTCACCCGTGCA 61.949 66.667 0.00 0.00 0.00 4.57
2144 3007 3.717294 ACCGGCGCCTTCAAGGAT 61.717 61.111 26.68 5.77 37.67 3.24
2290 3919 2.665165 AGGCTGTTTGGATTTGTGACA 58.335 42.857 0.00 0.00 0.00 3.58
2348 3990 4.414337 AGATCCTTTCTCTCCCAAATCG 57.586 45.455 0.00 0.00 0.00 3.34
2356 3998 5.941948 TTCTCTCCCAAATCGTTTTCTTC 57.058 39.130 0.00 0.00 0.00 2.87
2459 4105 3.452264 TCGTCCATTGTCATCTGGAGATT 59.548 43.478 5.17 0.00 42.10 2.40
2460 4106 4.649218 TCGTCCATTGTCATCTGGAGATTA 59.351 41.667 5.17 0.00 42.10 1.75
2461 4107 5.305386 TCGTCCATTGTCATCTGGAGATTAT 59.695 40.000 5.17 0.00 42.10 1.28
2484 4130 5.600908 TCATGTTGCGGTTACTAGTTTTC 57.399 39.130 0.00 0.00 0.00 2.29
2936 4701 5.010922 AGGCAGCAATCACAGAATTACAAAA 59.989 36.000 0.00 0.00 0.00 2.44
2960 4725 4.368756 CGCAGCGTGTAGAGAGTC 57.631 61.111 6.65 0.00 0.00 3.36
2961 4726 1.226435 CGCAGCGTGTAGAGAGTCC 60.226 63.158 6.65 0.00 0.00 3.85
3063 5912 0.387202 CCGCGGAGATGAGAATGAGT 59.613 55.000 24.07 0.00 0.00 3.41
3076 5925 2.166459 AGAATGAGTCGATCGCCTTTGA 59.834 45.455 11.09 0.00 0.00 2.69
3078 5927 0.888619 TGAGTCGATCGCCTTTGACT 59.111 50.000 11.09 7.47 41.99 3.41
3096 5945 0.873743 CTAGCAGCTTAGCTCGCCAC 60.874 60.000 19.41 3.21 45.26 5.01
3102 5951 3.310860 CTTAGCTCGCCACCCGGTT 62.311 63.158 0.00 0.00 37.59 4.44
3165 6014 1.414685 GGTGGAGGCTTAGTAGGGGAT 60.415 57.143 0.00 0.00 0.00 3.85
3227 6078 3.095421 CCCATGGCAAGGGTGGTA 58.905 61.111 19.65 0.00 41.61 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.065600 TTTCAAGCTTGGCACGTGC 59.934 52.632 32.15 32.15 41.14 5.34
72 73 8.378421 CGTTTAAATTCCAAACACGGTTTAAAA 58.622 29.630 13.18 1.73 35.97 1.52
76 77 5.409211 ACGTTTAAATTCCAAACACGGTTT 58.591 33.333 13.18 0.00 35.97 3.27
132 133 8.251026 CCCAAAAGACCAGGAGAATTTAAATAC 58.749 37.037 0.01 0.00 0.00 1.89
340 341 6.811665 TCGATGTGGTCTGAAATACTTGTAAG 59.188 38.462 0.00 0.00 0.00 2.34
364 398 3.163594 CGTGAAGATCCGTGCAAATTTC 58.836 45.455 0.00 0.00 0.00 2.17
396 430 4.290093 AGTCCCAGTCAGTGCTATATTCA 58.710 43.478 0.00 0.00 0.00 2.57
414 448 4.522789 TCCCAAATCAGTTTTGCTAAGTCC 59.477 41.667 0.00 0.00 42.85 3.85
430 464 4.870021 AGGAGCTTAACTGATCCCAAAT 57.130 40.909 0.00 0.00 43.01 2.32
431 465 4.534500 TGTAGGAGCTTAACTGATCCCAAA 59.466 41.667 0.00 0.00 43.01 3.28
432 466 4.101114 TGTAGGAGCTTAACTGATCCCAA 58.899 43.478 0.00 0.00 43.01 4.12
433 467 3.719871 TGTAGGAGCTTAACTGATCCCA 58.280 45.455 0.00 0.00 43.01 4.37
434 468 4.755266 TTGTAGGAGCTTAACTGATCCC 57.245 45.455 0.00 0.00 43.01 3.85
443 477 9.383519 GCTGCATTATATATTTGTAGGAGCTTA 57.616 33.333 12.28 0.00 0.00 3.09
444 478 7.884877 TGCTGCATTATATATTTGTAGGAGCTT 59.115 33.333 0.00 0.00 0.00 3.74
445 479 7.397221 TGCTGCATTATATATTTGTAGGAGCT 58.603 34.615 0.00 0.00 0.00 4.09
446 480 7.615582 TGCTGCATTATATATTTGTAGGAGC 57.384 36.000 0.00 0.00 0.00 4.70
447 481 9.002600 TGTTGCTGCATTATATATTTGTAGGAG 57.997 33.333 1.84 0.00 0.00 3.69
448 482 8.916628 TGTTGCTGCATTATATATTTGTAGGA 57.083 30.769 1.84 8.58 0.00 2.94
449 483 9.964303 TTTGTTGCTGCATTATATATTTGTAGG 57.036 29.630 1.84 0.60 0.00 3.18
485 519 9.793259 TGAAGTCTATTGTTCTTGTCCTAATTT 57.207 29.630 0.00 0.00 0.00 1.82
486 520 9.793259 TTGAAGTCTATTGTTCTTGTCCTAATT 57.207 29.630 0.00 0.00 0.00 1.40
487 521 9.793259 TTTGAAGTCTATTGTTCTTGTCCTAAT 57.207 29.630 0.00 0.00 0.00 1.73
488 522 9.052759 GTTTGAAGTCTATTGTTCTTGTCCTAA 57.947 33.333 0.00 0.00 0.00 2.69
489 523 8.208224 TGTTTGAAGTCTATTGTTCTTGTCCTA 58.792 33.333 0.00 0.00 0.00 2.94
490 524 7.054124 TGTTTGAAGTCTATTGTTCTTGTCCT 58.946 34.615 0.00 0.00 0.00 3.85
491 525 7.226720 TCTGTTTGAAGTCTATTGTTCTTGTCC 59.773 37.037 0.00 0.00 0.00 4.02
492 526 8.142994 TCTGTTTGAAGTCTATTGTTCTTGTC 57.857 34.615 0.00 0.00 0.00 3.18
493 527 7.770897 ACTCTGTTTGAAGTCTATTGTTCTTGT 59.229 33.333 0.00 0.00 0.00 3.16
494 528 8.066595 CACTCTGTTTGAAGTCTATTGTTCTTG 58.933 37.037 0.00 0.00 0.00 3.02
495 529 7.227512 CCACTCTGTTTGAAGTCTATTGTTCTT 59.772 37.037 0.00 0.00 0.00 2.52
496 530 6.708054 CCACTCTGTTTGAAGTCTATTGTTCT 59.292 38.462 0.00 0.00 0.00 3.01
497 531 6.706270 TCCACTCTGTTTGAAGTCTATTGTTC 59.294 38.462 0.00 0.00 0.00 3.18
498 532 6.483640 GTCCACTCTGTTTGAAGTCTATTGTT 59.516 38.462 0.00 0.00 0.00 2.83
499 533 5.992217 GTCCACTCTGTTTGAAGTCTATTGT 59.008 40.000 0.00 0.00 0.00 2.71
500 534 5.991606 TGTCCACTCTGTTTGAAGTCTATTG 59.008 40.000 0.00 0.00 0.00 1.90
501 535 6.174720 TGTCCACTCTGTTTGAAGTCTATT 57.825 37.500 0.00 0.00 0.00 1.73
502 536 5.808366 TGTCCACTCTGTTTGAAGTCTAT 57.192 39.130 0.00 0.00 0.00 1.98
503 537 5.304357 TGATGTCCACTCTGTTTGAAGTCTA 59.696 40.000 0.00 0.00 0.00 2.59
504 538 4.101585 TGATGTCCACTCTGTTTGAAGTCT 59.898 41.667 0.00 0.00 0.00 3.24
505 539 4.380531 TGATGTCCACTCTGTTTGAAGTC 58.619 43.478 0.00 0.00 0.00 3.01
506 540 4.422073 TGATGTCCACTCTGTTTGAAGT 57.578 40.909 0.00 0.00 0.00 3.01
507 541 4.818546 ACTTGATGTCCACTCTGTTTGAAG 59.181 41.667 0.00 0.00 0.00 3.02
508 542 4.780815 ACTTGATGTCCACTCTGTTTGAA 58.219 39.130 0.00 0.00 0.00 2.69
509 543 4.422073 ACTTGATGTCCACTCTGTTTGA 57.578 40.909 0.00 0.00 0.00 2.69
510 544 5.991606 TCTAACTTGATGTCCACTCTGTTTG 59.008 40.000 0.00 0.00 0.00 2.93
511 545 6.174720 TCTAACTTGATGTCCACTCTGTTT 57.825 37.500 0.00 0.00 0.00 2.83
512 546 5.808366 TCTAACTTGATGTCCACTCTGTT 57.192 39.130 0.00 0.00 0.00 3.16
513 547 5.728471 CATCTAACTTGATGTCCACTCTGT 58.272 41.667 0.00 0.00 39.05 3.41
577 611 0.880278 CCACACGCTATCCCGAATGG 60.880 60.000 0.00 0.00 33.19 3.16
591 625 5.290158 CCGTATATTTATATCGGCACCACAC 59.710 44.000 0.00 0.00 35.01 3.82
628 662 6.183360 TGGTAGTTTGAAGACTGAAGACATGA 60.183 38.462 0.00 0.00 0.00 3.07
632 666 5.602628 ACTGGTAGTTTGAAGACTGAAGAC 58.397 41.667 0.00 0.00 0.00 3.01
633 667 5.871396 ACTGGTAGTTTGAAGACTGAAGA 57.129 39.130 0.00 0.00 0.00 2.87
634 668 6.159988 CCTACTGGTAGTTTGAAGACTGAAG 58.840 44.000 6.96 0.00 0.00 3.02
635 669 5.601313 ACCTACTGGTAGTTTGAAGACTGAA 59.399 40.000 6.96 0.00 46.43 3.02
636 670 5.010719 CACCTACTGGTAGTTTGAAGACTGA 59.989 44.000 6.96 0.00 46.60 3.41
637 671 5.230942 CACCTACTGGTAGTTTGAAGACTG 58.769 45.833 6.96 0.00 46.60 3.51
638 672 4.283722 CCACCTACTGGTAGTTTGAAGACT 59.716 45.833 6.96 0.00 46.60 3.24
787 835 0.600255 AGCCAGACGGAAGAACAACG 60.600 55.000 0.00 0.00 0.00 4.10
789 837 0.468226 ACAGCCAGACGGAAGAACAA 59.532 50.000 0.00 0.00 0.00 2.83
793 841 2.636412 CGGACAGCCAGACGGAAGA 61.636 63.158 0.00 0.00 0.00 2.87
856 907 2.039480 TGCACTCTCTGGAATCTTTGCT 59.961 45.455 0.00 0.00 0.00 3.91
868 919 2.042464 TGTTCCTTGTCTGCACTCTCT 58.958 47.619 0.00 0.00 0.00 3.10
878 929 7.382218 CCATTGTTTAATGAGTTGTTCCTTGTC 59.618 37.037 1.80 0.00 45.21 3.18
900 958 3.444029 AGCAGCAGGTAAAATTCCCATT 58.556 40.909 0.00 0.00 0.00 3.16
925 983 1.075482 CATGTGGTGGGCTGTCCTT 59.925 57.895 0.00 0.00 36.20 3.36
1084 1155 0.108615 CTCAACGCCATCTTCTCGGT 60.109 55.000 0.00 0.00 0.00 4.69
1100 1179 1.075970 AGCATCGTCCTAGCCCTCA 60.076 57.895 0.00 0.00 0.00 3.86
1176 1255 0.388134 GGCACGACTCGCTGTAGAAA 60.388 55.000 0.00 0.00 0.00 2.52
1206 1285 0.036448 TCTCCTTCCTCACGACGTCT 59.964 55.000 14.70 0.00 0.00 4.18
1275 1354 0.608130 AGCAGTCGTGGAAGTGCATA 59.392 50.000 6.49 0.00 46.04 3.14
1312 1391 2.727798 GACAGACAACATGCATGCAAAC 59.272 45.455 26.68 15.10 0.00 2.93
1338 1423 2.382770 ACCACACAACAGGGCAGGA 61.383 57.895 0.00 0.00 0.00 3.86
1342 1427 2.489275 CCACACCACACAACAGGGC 61.489 63.158 0.00 0.00 0.00 5.19
1355 1446 1.598130 GTCACTGGTCAGGCCACAC 60.598 63.158 5.01 0.00 43.61 3.82
1401 1492 1.882989 GAGTCCAGCAGAACCGAGCT 61.883 60.000 0.00 0.00 42.94 4.09
1478 1569 1.339151 GCCTTCACCCTCTCGACAAAT 60.339 52.381 0.00 0.00 0.00 2.32
1526 1617 1.153549 GATGTCGGCACAGGAGACC 60.154 63.158 0.00 0.00 35.41 3.85
1585 1676 2.307392 TGCAAAATGGCCCAGTAGTCTA 59.693 45.455 0.00 0.00 0.00 2.59
1594 1689 1.805943 GTGTCATTTGCAAAATGGCCC 59.194 47.619 17.19 4.63 31.59 5.80
1595 1690 1.460359 CGTGTCATTTGCAAAATGGCC 59.540 47.619 17.19 0.00 31.59 5.36
2051 2155 4.332543 TGGAAGAGGCCCCTCCGT 62.333 66.667 10.64 0.00 43.70 4.69
2108 2212 2.588877 GCATGGCGCTGGACGTAT 60.589 61.111 7.64 0.00 46.11 3.06
2144 3007 0.386858 CGAAGTCGGCGAAGAACTCA 60.387 55.000 12.92 0.00 35.37 3.41
2211 3827 4.841422 CACTTCTTCCTGATCTCACCATT 58.159 43.478 0.00 0.00 0.00 3.16
2213 3829 2.027745 GCACTTCTTCCTGATCTCACCA 60.028 50.000 0.00 0.00 0.00 4.17
2318 3960 8.337118 TGGGAGAGAAAGGATCTATAACAATT 57.663 34.615 0.00 0.00 38.96 2.32
2329 3971 4.576330 AACGATTTGGGAGAGAAAGGAT 57.424 40.909 0.00 0.00 0.00 3.24
2356 3998 8.803799 GGTTGTAGCGAAACAATAAATTAATGG 58.196 33.333 6.33 0.00 41.18 3.16
2375 4017 6.932400 TGTACAAGGAACTAACATGGTTGTAG 59.068 38.462 0.00 0.00 38.49 2.74
2459 4105 7.604927 AGAAAACTAGTAACCGCAACATGAATA 59.395 33.333 0.00 0.00 0.00 1.75
2460 4106 6.430000 AGAAAACTAGTAACCGCAACATGAAT 59.570 34.615 0.00 0.00 0.00 2.57
2461 4107 5.761234 AGAAAACTAGTAACCGCAACATGAA 59.239 36.000 0.00 0.00 0.00 2.57
2613 4268 4.099419 CCATCCTGCCCCAAATAACTAAAC 59.901 45.833 0.00 0.00 0.00 2.01
2873 4638 0.044092 TATTCAGGTGGGGAGCTCCA 59.956 55.000 33.29 12.97 37.91 3.86
2921 4686 3.304391 GCCGTGCTTTTGTAATTCTGTGA 60.304 43.478 0.00 0.00 0.00 3.58
2961 4726 1.214923 ACCCTAGACTCCCTTCGTAGG 59.785 57.143 0.14 0.14 41.60 3.18
3063 5912 0.815095 TGCTAGTCAAAGGCGATCGA 59.185 50.000 21.57 0.00 0.00 3.59
3076 5925 1.323271 TGGCGAGCTAAGCTGCTAGT 61.323 55.000 0.90 0.00 44.17 2.57
3078 5927 1.141881 GTGGCGAGCTAAGCTGCTA 59.858 57.895 0.90 0.00 44.17 3.49
3102 5951 3.826754 CGGTCTCGCAGGCTGCTA 61.827 66.667 34.17 24.42 42.25 3.49
3109 5958 0.378962 CTCCTAGAACGGTCTCGCAG 59.621 60.000 6.06 0.00 40.63 5.18
3117 5966 2.257691 TCGATCCTCTCCTAGAACGG 57.742 55.000 0.00 0.00 0.00 4.44
3165 6014 0.185416 CTTACCTCGGCCTCCCTCTA 59.815 60.000 0.00 0.00 0.00 2.43
3227 6078 3.403038 GGATGATACCATTGCTAACGCT 58.597 45.455 0.00 0.00 32.93 5.07
3242 6093 1.405526 GCCACACTACACACGGATGAT 60.406 52.381 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.