Multiple sequence alignment - TraesCS7B01G421000

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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 TraesCS7B01G421000 chr7B 100.000 2166 0 0 1294 3459 690199501 690201666 0.000000e+00 4000.0
1 TraesCS7B01G421000 chr7B 87.055 2163 189 30 1367 3459 690094242 690096383 0.000000e+00 2359.0
2 TraesCS7B01G421000 chr7B 88.397 1715 144 18 1779 3459 690080898 690082591 0.000000e+00 2013.0
3 TraesCS7B01G421000 chr7B 100.000 1045 0 0 1 1045 690198208 690199252 0.000000e+00 1930.0
4 TraesCS7B01G421000 chr7B 85.666 1479 132 20 1367 2776 690119703 690121170 0.000000e+00 1483.0
5 TraesCS7B01G421000 chr7B 90.344 1046 84 7 2417 3459 690031465 690032496 0.000000e+00 1356.0
6 TraesCS7B01G421000 chr7B 86.686 1044 88 14 1367 2365 690030118 690031155 0.000000e+00 1110.0
7 TraesCS7B01G421000 chr7B 96.269 536 19 1 1 535 63023921 63023386 0.000000e+00 878.0
8 TraesCS7B01G421000 chr7B 96.255 534 20 0 1 534 703724863 703725396 0.000000e+00 876.0
9 TraesCS7B01G421000 chr7B 95.522 536 23 1 1 536 530444709 530444175 0.000000e+00 856.0
10 TraesCS7B01G421000 chr7B 94.972 537 26 1 1 536 32090478 32091014 0.000000e+00 841.0
11 TraesCS7B01G421000 chr7B 88.991 327 22 7 628 940 690119136 690119462 3.240000e-105 392.0
12 TraesCS7B01G421000 chr7B 88.957 326 23 6 628 940 690093676 690094001 1.160000e-104 390.0
13 TraesCS7B01G421000 chr7B 89.883 257 14 6 694 938 690029642 690029898 1.550000e-83 320.0
14 TraesCS7B01G421000 chr7B 79.681 251 39 9 704 943 690948605 690948854 1.650000e-38 171.0
15 TraesCS7B01G421000 chr7B 98.901 91 1 0 534 624 54533721 54533631 2.760000e-36 163.0
16 TraesCS7B01G421000 chr7D 94.484 2103 91 16 1365 3457 606301713 606303800 0.000000e+00 3217.0
17 TraesCS7B01G421000 chr7D 87.621 2165 185 33 1367 3459 606010727 606012880 0.000000e+00 2436.0
18 TraesCS7B01G421000 chr7D 88.523 1821 166 19 1673 3459 606107172 606108983 0.000000e+00 2165.0
19 TraesCS7B01G421000 chr7D 86.079 1293 108 16 1315 2545 605947226 605948508 0.000000e+00 1325.0
20 TraesCS7B01G421000 chr7D 90.841 928 73 4 2537 3459 605957465 605958385 0.000000e+00 1232.0
21 TraesCS7B01G421000 chr7D 90.960 885 68 6 2580 3459 606182717 606183594 0.000000e+00 1181.0
22 TraesCS7B01G421000 chr7D 87.171 951 79 7 1673 2591 606181497 606182436 0.000000e+00 1040.0
23 TraesCS7B01G421000 chr7D 84.453 521 49 13 1367 1862 606699833 606700346 5.190000e-133 484.0
24 TraesCS7B01G421000 chr7D 90.432 324 21 7 629 943 606301150 606301472 5.340000e-113 418.0
25 TraesCS7B01G421000 chr7D 88.615 325 25 8 628 940 606180304 606180628 5.420000e-103 385.0
26 TraesCS7B01G421000 chr7D 87.316 339 24 8 623 943 605946615 605946952 1.520000e-98 370.0
27 TraesCS7B01G421000 chr7D 91.189 227 16 3 1413 1635 606106837 606107063 4.340000e-79 305.0
28 TraesCS7B01G421000 chr7D 90.830 229 15 4 1413 1635 606181161 606181389 5.610000e-78 302.0
29 TraesCS7B01G421000 chr7A 86.816 2101 183 36 1415 3459 697975793 697977855 0.000000e+00 2259.0
30 TraesCS7B01G421000 chr7A 89.402 1104 82 15 2361 3459 697824554 697825627 0.000000e+00 1358.0
31 TraesCS7B01G421000 chr7A 89.836 305 14 11 654 943 697975122 697975424 3.260000e-100 375.0
32 TraesCS7B01G421000 chr7A 87.417 302 21 11 656 943 697822931 697823229 7.160000e-87 331.0
33 TraesCS7B01G421000 chr7A 87.375 301 22 13 657 943 697877568 697877866 7.160000e-87 331.0
34 TraesCS7B01G421000 chr7A 94.444 162 8 1 654 814 698131586 698131747 7.410000e-62 248.0
35 TraesCS7B01G421000 chr4B 96.269 536 19 1 1 535 68661124 68661659 0.000000e+00 878.0
36 TraesCS7B01G421000 chr1A 96.262 535 20 0 1 535 78542228 78542762 0.000000e+00 878.0
37 TraesCS7B01G421000 chr4A 95.677 532 23 0 1 532 712652214 712651683 0.000000e+00 856.0
38 TraesCS7B01G421000 chr1B 94.972 537 25 2 1 536 36283013 36282478 0.000000e+00 841.0
39 TraesCS7B01G421000 chr5B 94.953 535 27 0 1 535 392111163 392111697 0.000000e+00 839.0
40 TraesCS7B01G421000 chr5B 100.000 90 0 0 534 623 355621426 355621515 2.140000e-37 167.0
41 TraesCS7B01G421000 chr5B 100.000 90 0 0 534 623 554767331 554767420 2.140000e-37 167.0
42 TraesCS7B01G421000 chr3B 82.000 850 107 22 1367 2180 760055925 760055086 0.000000e+00 680.0
43 TraesCS7B01G421000 chr3B 100.000 89 0 0 535 623 802662908 802662996 7.680000e-37 165.0
44 TraesCS7B01G421000 chr3A 81.616 854 108 22 1367 2180 704695770 704694926 0.000000e+00 662.0
45 TraesCS7B01G421000 chr5D 100.000 91 0 0 534 624 220689305 220689395 5.940000e-38 169.0
46 TraesCS7B01G421000 chr5D 100.000 90 0 0 534 623 220683856 220683945 2.140000e-37 167.0
47 TraesCS7B01G421000 chr5D 86.667 60 5 3 629 685 496276555 496276614 2.880000e-06 63.9
48 TraesCS7B01G421000 chr2D 98.925 93 1 0 534 626 159330664 159330572 2.140000e-37 167.0
49 TraesCS7B01G421000 chr2B 98.936 94 0 1 534 626 242985153 242985246 2.140000e-37 167.0
50 TraesCS7B01G421000 chr3D 98.889 90 1 0 534 623 1138503 1138592 9.930000e-36 161.0
51 TraesCS7B01G421000 chr4D 93.220 59 4 0 638 696 248956509 248956567 1.710000e-13 87.9


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 TraesCS7B01G421000 chr7B 690198208 690201666 3458 False 2965.000000 4000 100.0000 1 3459 2 chr7B.!!$F8 3458
1 TraesCS7B01G421000 chr7B 690080898 690082591 1693 False 2013.000000 2013 88.3970 1779 3459 1 chr7B.!!$F2 1680
2 TraesCS7B01G421000 chr7B 690093676 690096383 2707 False 1374.500000 2359 88.0060 628 3459 2 chr7B.!!$F6 2831
3 TraesCS7B01G421000 chr7B 690119136 690121170 2034 False 937.500000 1483 87.3285 628 2776 2 chr7B.!!$F7 2148
4 TraesCS7B01G421000 chr7B 690029642 690032496 2854 False 928.666667 1356 88.9710 694 3459 3 chr7B.!!$F5 2765
5 TraesCS7B01G421000 chr7B 63023386 63023921 535 True 878.000000 878 96.2690 1 535 1 chr7B.!!$R2 534
6 TraesCS7B01G421000 chr7B 703724863 703725396 533 False 876.000000 876 96.2550 1 534 1 chr7B.!!$F4 533
7 TraesCS7B01G421000 chr7B 530444175 530444709 534 True 856.000000 856 95.5220 1 536 1 chr7B.!!$R3 535
8 TraesCS7B01G421000 chr7B 32090478 32091014 536 False 841.000000 841 94.9720 1 536 1 chr7B.!!$F1 535
9 TraesCS7B01G421000 chr7D 606010727 606012880 2153 False 2436.000000 2436 87.6210 1367 3459 1 chr7D.!!$F2 2092
10 TraesCS7B01G421000 chr7D 606301150 606303800 2650 False 1817.500000 3217 92.4580 629 3457 2 chr7D.!!$F7 2828
11 TraesCS7B01G421000 chr7D 606106837 606108983 2146 False 1235.000000 2165 89.8560 1413 3459 2 chr7D.!!$F5 2046
12 TraesCS7B01G421000 chr7D 605957465 605958385 920 False 1232.000000 1232 90.8410 2537 3459 1 chr7D.!!$F1 922
13 TraesCS7B01G421000 chr7D 605946615 605948508 1893 False 847.500000 1325 86.6975 623 2545 2 chr7D.!!$F4 1922
14 TraesCS7B01G421000 chr7D 606180304 606183594 3290 False 727.000000 1181 89.3940 628 3459 4 chr7D.!!$F6 2831
15 TraesCS7B01G421000 chr7D 606699833 606700346 513 False 484.000000 484 84.4530 1367 1862 1 chr7D.!!$F3 495
16 TraesCS7B01G421000 chr7A 697975122 697977855 2733 False 1317.000000 2259 88.3260 654 3459 2 chr7A.!!$F4 2805
17 TraesCS7B01G421000 chr7A 697822931 697825627 2696 False 844.500000 1358 88.4095 656 3459 2 chr7A.!!$F3 2803
18 TraesCS7B01G421000 chr4B 68661124 68661659 535 False 878.000000 878 96.2690 1 535 1 chr4B.!!$F1 534
19 TraesCS7B01G421000 chr1A 78542228 78542762 534 False 878.000000 878 96.2620 1 535 1 chr1A.!!$F1 534
20 TraesCS7B01G421000 chr4A 712651683 712652214 531 True 856.000000 856 95.6770 1 532 1 chr4A.!!$R1 531
21 TraesCS7B01G421000 chr1B 36282478 36283013 535 True 841.000000 841 94.9720 1 536 1 chr1B.!!$R1 535
22 TraesCS7B01G421000 chr5B 392111163 392111697 534 False 839.000000 839 94.9530 1 535 1 chr5B.!!$F2 534
23 TraesCS7B01G421000 chr3B 760055086 760055925 839 True 680.000000 680 82.0000 1367 2180 1 chr3B.!!$R1 813
24 TraesCS7B01G421000 chr3A 704694926 704695770 844 True 662.000000 662 81.6160 1367 2180 1 chr3A.!!$R1 813

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
832 850 0.321653 CCTGGCTACCGAACAAAGCT 60.322 55.0 0.0 0.0 36.48 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2812 3978 0.32336 TCATGCCACCCTAGCAAACC 60.323 55.0 0.0 0.0 44.83 3.27 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
92 94 3.302344 GGCGCATGGTGGTGGTTT 61.302 61.111 10.83 0.00 0.00 3.27
312 314 2.441375 TCTTGGAGGTGTTGATTGGTGA 59.559 45.455 0.00 0.00 0.00 4.02
313 315 3.117701 TCTTGGAGGTGTTGATTGGTGAA 60.118 43.478 0.00 0.00 0.00 3.18
314 316 3.304911 TGGAGGTGTTGATTGGTGAAA 57.695 42.857 0.00 0.00 0.00 2.69
396 398 3.571828 TCTTCATTTTTGTTGATCCGCCA 59.428 39.130 0.00 0.00 0.00 5.69
542 546 3.953712 CCTTTTTCGGTAAAGGCCAAT 57.046 42.857 5.01 0.00 45.46 3.16
544 548 4.740268 CCTTTTTCGGTAAAGGCCAATAC 58.260 43.478 5.01 7.52 45.46 1.89
545 549 4.218852 CCTTTTTCGGTAAAGGCCAATACA 59.781 41.667 16.88 0.00 45.46 2.29
546 550 5.105513 CCTTTTTCGGTAAAGGCCAATACAT 60.106 40.000 16.88 0.00 45.46 2.29
547 551 6.095720 CCTTTTTCGGTAAAGGCCAATACATA 59.904 38.462 16.88 4.48 45.46 2.29
548 552 7.201875 CCTTTTTCGGTAAAGGCCAATACATAT 60.202 37.037 16.88 0.00 45.46 1.78
549 553 8.749026 TTTTTCGGTAAAGGCCAATACATATA 57.251 30.769 16.88 1.00 0.00 0.86
550 554 7.733402 TTTCGGTAAAGGCCAATACATATAC 57.267 36.000 16.88 3.85 0.00 1.47
551 555 6.422344 TCGGTAAAGGCCAATACATATACA 57.578 37.500 16.88 0.00 0.00 2.29
552 556 7.011499 TCGGTAAAGGCCAATACATATACAT 57.989 36.000 16.88 0.00 0.00 2.29
553 557 6.876789 TCGGTAAAGGCCAATACATATACATG 59.123 38.462 16.88 0.00 38.21 3.21
555 559 7.360861 CGGTAAAGGCCAATACATATACATGTG 60.361 40.741 9.11 0.00 45.17 3.21
556 560 7.447238 GGTAAAGGCCAATACATATACATGTGT 59.553 37.037 9.11 4.04 45.17 3.72
557 561 9.496873 GTAAAGGCCAATACATATACATGTGTA 57.503 33.333 9.11 6.70 45.17 2.90
558 562 8.621532 AAAGGCCAATACATATACATGTGTAG 57.378 34.615 9.11 3.35 45.17 2.74
559 563 6.711277 AGGCCAATACATATACATGTGTAGG 58.289 40.000 9.11 10.82 45.17 3.18
560 564 5.880332 GGCCAATACATATACATGTGTAGGG 59.120 44.000 16.94 12.39 45.17 3.53
561 565 6.472887 GCCAATACATATACATGTGTAGGGT 58.527 40.000 16.94 14.38 45.17 4.34
562 566 7.310796 GGCCAATACATATACATGTGTAGGGTA 60.311 40.741 16.94 15.75 45.17 3.69
563 567 8.098286 GCCAATACATATACATGTGTAGGGTAA 58.902 37.037 16.94 4.47 45.17 2.85
568 572 6.990349 ACATATACATGTGTAGGGTAAAGTGC 59.010 38.462 16.94 0.00 43.89 4.40
569 573 3.780804 ACATGTGTAGGGTAAAGTGCA 57.219 42.857 0.00 0.00 0.00 4.57
570 574 4.093472 ACATGTGTAGGGTAAAGTGCAA 57.907 40.909 0.00 0.00 0.00 4.08
571 575 4.072131 ACATGTGTAGGGTAAAGTGCAAG 58.928 43.478 0.00 0.00 0.00 4.01
572 576 4.202419 ACATGTGTAGGGTAAAGTGCAAGA 60.202 41.667 0.00 0.00 0.00 3.02
573 577 4.002906 TGTGTAGGGTAAAGTGCAAGAG 57.997 45.455 0.00 0.00 0.00 2.85
574 578 3.644265 TGTGTAGGGTAAAGTGCAAGAGA 59.356 43.478 0.00 0.00 0.00 3.10
575 579 3.995048 GTGTAGGGTAAAGTGCAAGAGAC 59.005 47.826 0.00 0.00 0.00 3.36
576 580 2.861147 AGGGTAAAGTGCAAGAGACC 57.139 50.000 0.00 0.00 0.00 3.85
577 581 1.351350 AGGGTAAAGTGCAAGAGACCC 59.649 52.381 16.75 16.75 45.87 4.46
578 582 1.613520 GGGTAAAGTGCAAGAGACCCC 60.614 57.143 14.49 5.14 40.65 4.95
579 583 1.351350 GGTAAAGTGCAAGAGACCCCT 59.649 52.381 0.00 0.00 0.00 4.79
580 584 2.224793 GGTAAAGTGCAAGAGACCCCTT 60.225 50.000 0.00 0.00 0.00 3.95
581 585 3.008704 GGTAAAGTGCAAGAGACCCCTTA 59.991 47.826 0.00 0.00 0.00 2.69
582 586 4.324331 GGTAAAGTGCAAGAGACCCCTTAT 60.324 45.833 0.00 0.00 0.00 1.73
583 587 5.104652 GGTAAAGTGCAAGAGACCCCTTATA 60.105 44.000 0.00 0.00 0.00 0.98
584 588 4.489306 AAGTGCAAGAGACCCCTTATAC 57.511 45.455 0.00 0.00 0.00 1.47
585 589 3.450904 AGTGCAAGAGACCCCTTATACA 58.549 45.455 0.00 0.00 0.00 2.29
586 590 3.844211 AGTGCAAGAGACCCCTTATACAA 59.156 43.478 0.00 0.00 0.00 2.41
587 591 4.475016 AGTGCAAGAGACCCCTTATACAAT 59.525 41.667 0.00 0.00 0.00 2.71
588 592 4.576463 GTGCAAGAGACCCCTTATACAATG 59.424 45.833 0.00 0.00 0.00 2.82
589 593 4.137543 GCAAGAGACCCCTTATACAATGG 58.862 47.826 0.00 0.00 0.00 3.16
590 594 4.718961 CAAGAGACCCCTTATACAATGGG 58.281 47.826 0.00 0.00 43.43 4.00
599 603 5.007682 CCCTTATACAATGGGGATAAACCG 58.992 45.833 0.00 0.00 41.25 4.44
600 604 5.221966 CCCTTATACAATGGGGATAAACCGA 60.222 44.000 0.00 0.00 41.25 4.69
601 605 6.300703 CCTTATACAATGGGGATAAACCGAA 58.699 40.000 0.00 0.00 40.11 4.30
602 606 6.773685 CCTTATACAATGGGGATAAACCGAAA 59.226 38.462 0.00 0.00 40.11 3.46
603 607 7.285858 CCTTATACAATGGGGATAAACCGAAAA 59.714 37.037 0.00 0.00 40.11 2.29
604 608 6.709018 ATACAATGGGGATAAACCGAAAAG 57.291 37.500 0.00 0.00 40.11 2.27
606 610 2.517998 TGGGGATAAACCGAAAAGGG 57.482 50.000 0.00 0.00 46.96 3.95
607 611 1.108776 GGGGATAAACCGAAAAGGGC 58.891 55.000 0.00 0.00 46.96 5.19
608 612 1.341679 GGGGATAAACCGAAAAGGGCT 60.342 52.381 0.00 0.00 46.96 5.19
609 613 2.092267 GGGGATAAACCGAAAAGGGCTA 60.092 50.000 0.00 0.00 46.96 3.93
610 614 3.436035 GGGGATAAACCGAAAAGGGCTAT 60.436 47.826 0.00 0.00 46.96 2.97
611 615 4.202493 GGGGATAAACCGAAAAGGGCTATA 60.202 45.833 0.00 0.00 46.96 1.31
612 616 4.758674 GGGATAAACCGAAAAGGGCTATAC 59.241 45.833 0.00 0.00 46.96 1.47
613 617 5.370679 GGATAAACCGAAAAGGGCTATACA 58.629 41.667 0.00 0.00 46.96 2.29
614 618 5.237996 GGATAAACCGAAAAGGGCTATACAC 59.762 44.000 0.00 0.00 46.96 2.90
615 619 3.706600 AACCGAAAAGGGCTATACACA 57.293 42.857 0.00 0.00 46.96 3.72
616 620 3.926058 ACCGAAAAGGGCTATACACAT 57.074 42.857 0.00 0.00 46.96 3.21
617 621 3.805207 ACCGAAAAGGGCTATACACATC 58.195 45.455 0.00 0.00 46.96 3.06
618 622 3.454812 ACCGAAAAGGGCTATACACATCT 59.545 43.478 0.00 0.00 46.96 2.90
619 623 4.652421 ACCGAAAAGGGCTATACACATCTA 59.348 41.667 0.00 0.00 46.96 1.98
620 624 5.129815 ACCGAAAAGGGCTATACACATCTAA 59.870 40.000 0.00 0.00 46.96 2.10
621 625 5.465724 CCGAAAAGGGCTATACACATCTAAC 59.534 44.000 0.00 0.00 35.97 2.34
622 626 6.046593 CGAAAAGGGCTATACACATCTAACA 58.953 40.000 0.00 0.00 0.00 2.41
623 627 6.706270 CGAAAAGGGCTATACACATCTAACAT 59.294 38.462 0.00 0.00 0.00 2.71
624 628 7.307396 CGAAAAGGGCTATACACATCTAACATG 60.307 40.741 0.00 0.00 0.00 3.21
625 629 6.747414 AAGGGCTATACACATCTAACATGA 57.253 37.500 0.00 0.00 0.00 3.07
626 630 6.942163 AGGGCTATACACATCTAACATGAT 57.058 37.500 0.00 0.00 0.00 2.45
642 646 4.713553 ACATGATGTGTGTGTGTTCCTAA 58.286 39.130 0.00 0.00 40.28 2.69
819 837 2.896039 AGTAAGAAGACACTCCTGGCT 58.104 47.619 0.00 0.00 37.35 4.75
832 850 0.321653 CCTGGCTACCGAACAAAGCT 60.322 55.000 0.00 0.00 36.48 3.74
833 851 1.066430 CCTGGCTACCGAACAAAGCTA 60.066 52.381 0.00 0.00 36.48 3.32
945 975 2.693074 TGGTTTTGCTTTCCTCTCAACC 59.307 45.455 0.00 0.00 34.05 3.77
946 976 2.693074 GGTTTTGCTTTCCTCTCAACCA 59.307 45.455 0.00 0.00 33.71 3.67
947 977 3.132111 GGTTTTGCTTTCCTCTCAACCAA 59.868 43.478 0.00 0.00 33.71 3.67
950 980 3.228188 TGCTTTCCTCTCAACCAACAT 57.772 42.857 0.00 0.00 0.00 2.71
951 981 3.565307 TGCTTTCCTCTCAACCAACATT 58.435 40.909 0.00 0.00 0.00 2.71
952 982 3.318839 TGCTTTCCTCTCAACCAACATTG 59.681 43.478 0.00 0.00 0.00 2.82
1015 1313 9.337091 GAAATTAAGTTGTAGAAATAAGCGCAA 57.663 29.630 11.47 0.00 0.00 4.85
1016 1314 8.669394 AATTAAGTTGTAGAAATAAGCGCAAC 57.331 30.769 11.47 0.29 37.18 4.17
1028 1351 2.230264 GCGCAACAACACAAGCACC 61.230 57.895 0.30 0.00 0.00 5.01
1032 1355 1.379309 AACAACACAAGCACCGGGT 60.379 52.632 6.32 0.00 0.00 5.28
1340 1717 3.797039 CGAGGAAGCCATTGTAAGATCA 58.203 45.455 0.00 0.00 0.00 2.92
1347 1724 2.357154 GCCATTGTAAGATCAGGTGGGT 60.357 50.000 0.00 0.00 0.00 4.51
1363 1740 4.426023 AGGTGGGTAAGGAGGGATCTAATA 59.574 45.833 0.00 0.00 0.00 0.98
1615 2050 1.459450 GGTGCAAATACCACCGTGAT 58.541 50.000 0.00 0.00 42.86 3.06
1823 2370 3.531207 CCTCGAGCTCATCCGCCA 61.531 66.667 15.40 0.00 0.00 5.69
1873 2422 5.480073 ACTCTCACTGCTCAATTCTAAGTCT 59.520 40.000 0.00 0.00 0.00 3.24
1876 2425 7.896811 TCTCACTGCTCAATTCTAAGTCTTAA 58.103 34.615 0.00 0.00 0.00 1.85
1972 2529 7.127032 ACAGAGAGAGGATATTCATTCCTTTGT 59.873 37.037 0.00 0.00 43.75 2.83
1999 2556 7.761704 GCAACACGTGAGATCCTATATATTCAT 59.238 37.037 25.01 0.00 0.00 2.57
2037 2594 1.509644 AAGACACATGCACGCCACAG 61.510 55.000 0.00 0.00 0.00 3.66
2122 2687 3.181443 GGGATCCCATCTAACCGTTCATT 60.181 47.826 26.95 0.00 35.81 2.57
2130 2695 3.404899 TCTAACCGTTCATTGGTCCAAC 58.595 45.455 6.41 0.00 39.29 3.77
2149 2722 2.675242 CGGATGGCCAGTGGGGTAA 61.675 63.158 13.05 0.00 39.65 2.85
2205 2782 1.451927 GGGTGCTGGATCGCATGAA 60.452 57.895 0.00 0.00 42.62 2.57
2212 2789 1.802960 CTGGATCGCATGAACCATAGC 59.197 52.381 0.00 0.00 44.98 2.97
2227 2804 2.612212 CCATAGCGGTATCGTTTGCTTT 59.388 45.455 3.66 0.00 38.82 3.51
2228 2805 3.546020 CCATAGCGGTATCGTTTGCTTTG 60.546 47.826 3.66 0.00 38.82 2.77
2241 2818 1.112315 TGCTTTGCCGAACCAATGGT 61.112 50.000 0.00 0.00 37.65 3.55
2287 2865 1.453928 GAATGGCTAGTGGGGGCAC 60.454 63.158 0.00 0.00 41.82 5.01
2300 2878 1.029947 GGGGCACGGTAATGGAAGTG 61.030 60.000 0.00 0.00 37.63 3.16
2301 2879 1.029947 GGGCACGGTAATGGAAGTGG 61.030 60.000 0.00 0.00 35.35 4.00
2302 2880 0.035820 GGCACGGTAATGGAAGTGGA 60.036 55.000 0.00 0.00 35.35 4.02
2303 2881 1.084289 GCACGGTAATGGAAGTGGAC 58.916 55.000 0.00 0.00 35.35 4.02
2304 2882 1.609580 GCACGGTAATGGAAGTGGACA 60.610 52.381 0.00 0.00 35.35 4.02
2305 2883 2.346803 CACGGTAATGGAAGTGGACAG 58.653 52.381 0.00 0.00 0.00 3.51
2437 3302 2.981898 AGGAACCGGTTCTATTTTCGG 58.018 47.619 38.59 0.00 46.95 4.30
2613 3773 3.134623 TCCTATGCAATGTAGACCCACTG 59.865 47.826 0.00 0.00 0.00 3.66
2619 3781 3.531538 CAATGTAGACCCACTGCGTATT 58.468 45.455 0.00 0.00 33.97 1.89
2789 3951 2.484264 GTGTAGTCCTTGCAATCACACC 59.516 50.000 0.00 0.00 30.99 4.16
2812 3978 3.531538 AGTATAGAATTGCACCACACCG 58.468 45.455 0.00 0.00 0.00 4.94
2939 4105 8.983307 AAAACTACTTACTTCTGAGAATACCG 57.017 34.615 0.00 0.00 0.00 4.02
3041 4216 7.175641 AGCTTTATTGACTTTGAACTAGCACAT 59.824 33.333 0.00 0.00 0.00 3.21
3261 4438 7.732025 TCTTCAGGTTCATCAGTACTTAAACA 58.268 34.615 0.00 0.00 0.00 2.83
3294 4472 7.335627 TGATTTACCTAGTTAGAACATGGTGG 58.664 38.462 15.23 0.00 37.35 4.61
3404 4584 7.166851 TCCATTTAATTTGCATTGGAACACAT 58.833 30.769 0.00 0.00 39.29 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 0.898320 CACCAAACAAACCACCACCA 59.102 50.000 0.00 0.00 0.00 4.17
92 94 1.375396 CGGATCTCGCCACCAAACA 60.375 57.895 0.00 0.00 0.00 2.83
312 314 0.951040 CCAAGACTCCGAAGCGCTTT 60.951 55.000 25.84 7.69 0.00 3.51
313 315 1.374758 CCAAGACTCCGAAGCGCTT 60.375 57.895 25.35 25.35 0.00 4.68
314 316 2.219325 CTCCAAGACTCCGAAGCGCT 62.219 60.000 2.64 2.64 0.00 5.92
396 398 4.024977 GCAAAAGAAACAAATGCCGACAAT 60.025 37.500 0.00 0.00 0.00 2.71
536 540 5.880332 CCCTACACATGTATATGTATTGGCC 59.120 44.000 4.64 0.00 45.53 5.36
537 541 6.472887 ACCCTACACATGTATATGTATTGGC 58.527 40.000 4.64 0.00 45.53 4.52
542 546 8.145767 GCACTTTACCCTACACATGTATATGTA 58.854 37.037 4.64 0.00 45.53 2.29
544 548 6.989759 TGCACTTTACCCTACACATGTATATG 59.010 38.462 0.00 0.00 40.24 1.78
545 549 7.131907 TGCACTTTACCCTACACATGTATAT 57.868 36.000 0.00 0.00 0.00 0.86
546 550 6.547930 TGCACTTTACCCTACACATGTATA 57.452 37.500 0.00 0.00 0.00 1.47
547 551 5.429681 TGCACTTTACCCTACACATGTAT 57.570 39.130 0.00 0.00 0.00 2.29
548 552 4.893829 TGCACTTTACCCTACACATGTA 57.106 40.909 0.00 0.00 0.00 2.29
549 553 3.780804 TGCACTTTACCCTACACATGT 57.219 42.857 0.00 0.00 0.00 3.21
550 554 4.323417 TCTTGCACTTTACCCTACACATG 58.677 43.478 0.00 0.00 0.00 3.21
551 555 4.286032 TCTCTTGCACTTTACCCTACACAT 59.714 41.667 0.00 0.00 0.00 3.21
552 556 3.644265 TCTCTTGCACTTTACCCTACACA 59.356 43.478 0.00 0.00 0.00 3.72
553 557 3.995048 GTCTCTTGCACTTTACCCTACAC 59.005 47.826 0.00 0.00 0.00 2.90
554 558 3.007614 GGTCTCTTGCACTTTACCCTACA 59.992 47.826 0.00 0.00 0.00 2.74
555 559 3.597255 GGTCTCTTGCACTTTACCCTAC 58.403 50.000 0.00 0.00 0.00 3.18
556 560 2.570302 GGGTCTCTTGCACTTTACCCTA 59.430 50.000 15.93 0.00 42.74 3.53
557 561 1.351350 GGGTCTCTTGCACTTTACCCT 59.649 52.381 15.93 0.00 42.74 4.34
558 562 1.613520 GGGGTCTCTTGCACTTTACCC 60.614 57.143 15.20 15.20 44.86 3.69
559 563 1.351350 AGGGGTCTCTTGCACTTTACC 59.649 52.381 0.00 0.00 0.00 2.85
560 564 2.861147 AGGGGTCTCTTGCACTTTAC 57.139 50.000 0.00 0.00 0.00 2.01
561 565 5.486063 TGTATAAGGGGTCTCTTGCACTTTA 59.514 40.000 0.00 0.00 0.00 1.85
562 566 4.288626 TGTATAAGGGGTCTCTTGCACTTT 59.711 41.667 0.00 0.00 0.00 2.66
563 567 3.844211 TGTATAAGGGGTCTCTTGCACTT 59.156 43.478 0.00 0.00 0.00 3.16
564 568 3.450904 TGTATAAGGGGTCTCTTGCACT 58.549 45.455 0.00 0.00 0.00 4.40
565 569 3.906720 TGTATAAGGGGTCTCTTGCAC 57.093 47.619 0.00 0.00 0.00 4.57
566 570 4.385199 CCATTGTATAAGGGGTCTCTTGCA 60.385 45.833 0.00 0.00 34.16 4.08
567 571 4.137543 CCATTGTATAAGGGGTCTCTTGC 58.862 47.826 0.00 0.00 34.16 4.01
576 580 5.007682 CGGTTTATCCCCATTGTATAAGGG 58.992 45.833 0.00 0.00 42.44 3.95
577 581 5.871834 TCGGTTTATCCCCATTGTATAAGG 58.128 41.667 0.00 0.00 0.00 2.69
578 582 7.811117 TTTCGGTTTATCCCCATTGTATAAG 57.189 36.000 0.00 0.00 0.00 1.73
579 583 7.285858 CCTTTTCGGTTTATCCCCATTGTATAA 59.714 37.037 0.00 0.00 0.00 0.98
580 584 6.773685 CCTTTTCGGTTTATCCCCATTGTATA 59.226 38.462 0.00 0.00 0.00 1.47
581 585 5.596772 CCTTTTCGGTTTATCCCCATTGTAT 59.403 40.000 0.00 0.00 0.00 2.29
582 586 4.951094 CCTTTTCGGTTTATCCCCATTGTA 59.049 41.667 0.00 0.00 0.00 2.41
583 587 3.767131 CCTTTTCGGTTTATCCCCATTGT 59.233 43.478 0.00 0.00 0.00 2.71
584 588 3.132111 CCCTTTTCGGTTTATCCCCATTG 59.868 47.826 0.00 0.00 0.00 2.82
585 589 3.371034 CCCTTTTCGGTTTATCCCCATT 58.629 45.455 0.00 0.00 0.00 3.16
586 590 2.953161 GCCCTTTTCGGTTTATCCCCAT 60.953 50.000 0.00 0.00 0.00 4.00
587 591 1.617533 GCCCTTTTCGGTTTATCCCCA 60.618 52.381 0.00 0.00 0.00 4.96
588 592 1.108776 GCCCTTTTCGGTTTATCCCC 58.891 55.000 0.00 0.00 0.00 4.81
589 593 2.139323 AGCCCTTTTCGGTTTATCCC 57.861 50.000 0.00 0.00 0.00 3.85
590 594 5.237996 GTGTATAGCCCTTTTCGGTTTATCC 59.762 44.000 0.00 0.00 0.00 2.59
591 595 5.818857 TGTGTATAGCCCTTTTCGGTTTATC 59.181 40.000 0.00 0.00 0.00 1.75
592 596 5.747342 TGTGTATAGCCCTTTTCGGTTTAT 58.253 37.500 0.00 0.00 0.00 1.40
593 597 5.163281 TGTGTATAGCCCTTTTCGGTTTA 57.837 39.130 0.00 0.00 0.00 2.01
594 598 4.023726 TGTGTATAGCCCTTTTCGGTTT 57.976 40.909 0.00 0.00 0.00 3.27
595 599 3.706600 TGTGTATAGCCCTTTTCGGTT 57.293 42.857 0.00 0.00 0.00 4.44
596 600 3.454812 AGATGTGTATAGCCCTTTTCGGT 59.545 43.478 0.00 0.00 0.00 4.69
597 601 4.073293 AGATGTGTATAGCCCTTTTCGG 57.927 45.455 0.00 0.00 0.00 4.30
598 602 6.046593 TGTTAGATGTGTATAGCCCTTTTCG 58.953 40.000 0.00 0.00 0.00 3.46
599 603 7.715249 TCATGTTAGATGTGTATAGCCCTTTTC 59.285 37.037 0.00 0.00 0.00 2.29
600 604 7.573710 TCATGTTAGATGTGTATAGCCCTTTT 58.426 34.615 0.00 0.00 0.00 2.27
601 605 7.136822 TCATGTTAGATGTGTATAGCCCTTT 57.863 36.000 0.00 0.00 0.00 3.11
602 606 6.747414 TCATGTTAGATGTGTATAGCCCTT 57.253 37.500 0.00 0.00 0.00 3.95
603 607 6.705302 CATCATGTTAGATGTGTATAGCCCT 58.295 40.000 0.00 0.00 40.35 5.19
604 608 6.974932 CATCATGTTAGATGTGTATAGCCC 57.025 41.667 0.00 0.00 40.35 5.19
615 619 5.412594 GGAACACACACACATCATGTTAGAT 59.587 40.000 0.00 0.00 40.64 1.98
616 620 4.754618 GGAACACACACACATCATGTTAGA 59.245 41.667 0.00 0.00 40.64 2.10
617 621 4.756642 AGGAACACACACACATCATGTTAG 59.243 41.667 0.00 0.00 40.64 2.34
618 622 4.713553 AGGAACACACACACATCATGTTA 58.286 39.130 0.00 0.00 40.64 2.41
619 623 3.554934 AGGAACACACACACATCATGTT 58.445 40.909 0.00 0.00 40.64 2.71
620 624 3.213206 AGGAACACACACACATCATGT 57.787 42.857 0.00 0.00 44.81 3.21
621 625 4.154737 CCTTAGGAACACACACACATCATG 59.845 45.833 0.00 0.00 0.00 3.07
622 626 4.326826 CCTTAGGAACACACACACATCAT 58.673 43.478 0.00 0.00 0.00 2.45
623 627 3.738982 CCTTAGGAACACACACACATCA 58.261 45.455 0.00 0.00 0.00 3.07
624 628 2.484264 GCCTTAGGAACACACACACATC 59.516 50.000 0.69 0.00 0.00 3.06
625 629 2.106511 AGCCTTAGGAACACACACACAT 59.893 45.455 0.69 0.00 0.00 3.21
626 630 1.488812 AGCCTTAGGAACACACACACA 59.511 47.619 0.69 0.00 0.00 3.72
642 646 3.492102 ACACAAACATACACTCAGCCT 57.508 42.857 0.00 0.00 0.00 4.58
707 712 2.744202 GTGACAATGTGTGAGGCCTAAG 59.256 50.000 4.42 0.00 0.00 2.18
819 837 2.165845 GAGGCTCTAGCTTTGTTCGGTA 59.834 50.000 7.40 0.00 41.70 4.02
832 850 8.862325 TTGAATTACAAAAATGAGAGGCTCTA 57.138 30.769 18.75 6.58 35.39 2.43
833 851 7.765695 TTGAATTACAAAAATGAGAGGCTCT 57.234 32.000 18.80 18.80 35.39 4.09
917 947 2.344521 GAAAGCAAAACCACGGGCGT 62.345 55.000 0.00 0.00 0.00 5.68
918 948 1.660264 GAAAGCAAAACCACGGGCG 60.660 57.895 0.00 0.00 0.00 6.13
998 1116 5.209240 GTGTTGTTGCGCTTATTTCTACAA 58.791 37.500 9.73 3.69 0.00 2.41
999 1117 4.273724 TGTGTTGTTGCGCTTATTTCTACA 59.726 37.500 9.73 1.89 0.00 2.74
1003 1125 3.121362 GCTTGTGTTGTTGCGCTTATTTC 60.121 43.478 9.73 0.00 0.00 2.17
1007 1305 0.735471 TGCTTGTGTTGTTGCGCTTA 59.265 45.000 9.73 0.00 0.00 3.09
1008 1306 0.801836 GTGCTTGTGTTGTTGCGCTT 60.802 50.000 9.73 0.00 33.71 4.68
1015 1313 0.534203 CTACCCGGTGCTTGTGTTGT 60.534 55.000 0.00 0.00 0.00 3.32
1016 1314 1.234615 CCTACCCGGTGCTTGTGTTG 61.235 60.000 0.00 0.00 0.00 3.33
1340 1717 1.027815 AGATCCCTCCTTACCCACCT 58.972 55.000 0.00 0.00 0.00 4.00
1347 1724 6.782988 CACAACCTCTATTAGATCCCTCCTTA 59.217 42.308 0.00 0.00 0.00 2.69
1363 1740 3.584848 AGCCATCTAAGAACACAACCTCT 59.415 43.478 0.00 0.00 0.00 3.69
1555 1990 1.739562 CTTGAGGCAGACGCTGTCC 60.740 63.158 7.66 9.09 36.67 4.02
1615 2050 4.202264 GCGGAGGGATAAGATTCAAGAGAA 60.202 45.833 0.00 0.00 38.31 2.87
1823 2370 1.739338 GACGGGCAGATCCATCTCGT 61.739 60.000 4.36 4.36 37.52 4.18
1889 2438 7.108194 TCAAAGAGAATTGTCAGCTCATACAT 58.892 34.615 5.28 0.00 0.00 2.29
1972 2529 4.937201 ATATAGGATCTCACGTGTTGCA 57.063 40.909 16.51 0.00 0.00 4.08
1999 2556 5.823570 TGTCTTTGGTTTCCTAAAATCGTGA 59.176 36.000 0.00 0.00 0.00 4.35
2037 2594 7.696992 TTCTCATGGTTAAAAATAGGGTGAC 57.303 36.000 0.00 0.00 0.00 3.67
2149 2722 1.609555 GTCGATTCACCTCCGCTCTAT 59.390 52.381 0.00 0.00 0.00 1.98
2212 2789 0.520412 CGGCAAAGCAAACGATACCG 60.520 55.000 0.00 0.00 42.50 4.02
2223 2800 0.885196 TACCATTGGTTCGGCAAAGC 59.115 50.000 14.78 0.00 37.09 3.51
2227 2804 0.916086 AGGATACCATTGGTTCGGCA 59.084 50.000 14.78 0.00 37.09 5.69
2228 2805 2.490991 GTAGGATACCATTGGTTCGGC 58.509 52.381 14.78 1.29 37.09 5.54
2241 2818 4.458256 TGGATGAACGGTAGGTAGGATA 57.542 45.455 0.00 0.00 0.00 2.59
2287 2865 1.406887 CCCTGTCCACTTCCATTACCG 60.407 57.143 0.00 0.00 0.00 4.02
2290 2868 2.504175 GCTACCCTGTCCACTTCCATTA 59.496 50.000 0.00 0.00 0.00 1.90
2300 2878 1.224592 CCCACATGCTACCCTGTCC 59.775 63.158 0.00 0.00 0.00 4.02
2301 2879 0.328258 AACCCACATGCTACCCTGTC 59.672 55.000 0.00 0.00 0.00 3.51
2302 2880 1.663911 TAACCCACATGCTACCCTGT 58.336 50.000 0.00 0.00 0.00 4.00
2303 2881 2.172505 TCATAACCCACATGCTACCCTG 59.827 50.000 0.00 0.00 0.00 4.45
2304 2882 2.439507 CTCATAACCCACATGCTACCCT 59.560 50.000 0.00 0.00 0.00 4.34
2305 2883 2.438021 TCTCATAACCCACATGCTACCC 59.562 50.000 0.00 0.00 0.00 3.69
2346 2930 8.746922 ACACATGACAATCAACACAATTATTC 57.253 30.769 0.00 0.00 0.00 1.75
2406 3036 2.121948 ACCGGTTCCTATAGGGGAAAC 58.878 52.381 18.97 14.80 46.45 2.78
2498 3363 9.590451 CAATTCAGGCATTATGTATTGAAGTTT 57.410 29.630 11.41 3.35 37.52 2.66
2562 3430 6.183360 ACACATACTCACACTAAGCTAGCTAC 60.183 42.308 19.70 0.00 0.00 3.58
2563 3431 5.886474 ACACATACTCACACTAAGCTAGCTA 59.114 40.000 19.70 5.71 0.00 3.32
2564 3432 4.707448 ACACATACTCACACTAAGCTAGCT 59.293 41.667 12.68 12.68 0.00 3.32
2565 3433 5.000012 ACACATACTCACACTAAGCTAGC 58.000 43.478 6.62 6.62 0.00 3.42
2613 3773 1.735571 ACCCACATCGAACAAATACGC 59.264 47.619 0.00 0.00 0.00 4.42
2619 3781 1.269174 CAATGCACCCACATCGAACAA 59.731 47.619 0.00 0.00 0.00 2.83
2770 3932 1.732259 CGGTGTGATTGCAAGGACTAC 59.268 52.381 4.94 5.26 0.00 2.73
2789 3951 3.555956 GGTGTGGTGCAATTCTATACTCG 59.444 47.826 0.00 0.00 0.00 4.18
2812 3978 0.323360 TCATGCCACCCTAGCAAACC 60.323 55.000 0.00 0.00 44.83 3.27
2927 4093 8.216423 ACTCCTACTTTATACGGTATTCTCAGA 58.784 37.037 5.89 0.00 0.00 3.27
2939 4105 8.782339 TTAAAAGTGGCACTCCTACTTTATAC 57.218 34.615 22.31 0.00 39.99 1.47
2989 4164 7.770433 TGCAGGATTGTAGATATTATACATGGC 59.230 37.037 0.00 0.00 33.36 4.40
3147 4324 7.395190 TGCATTGTTCTAAGCATGTTAAGAT 57.605 32.000 0.00 0.00 31.05 2.40
3148 4325 6.127925 CCTGCATTGTTCTAAGCATGTTAAGA 60.128 38.462 0.00 0.00 36.28 2.10
3294 4472 5.356751 TGACACAATGCCTAAACCATCATAC 59.643 40.000 0.00 0.00 0.00 2.39
3436 4616 5.635549 GGAAGCAAACATGTTTTACACAC 57.364 39.130 21.10 10.34 38.61 3.82


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

AutoCloner maintained by Alex Coulton.