Multiple sequence alignment - TraesCS2D01G586100

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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 TraesCS2D01G586100 chr2D 100.000 3534 0 0 1 3534 644723966 644720433 0.000000e+00 6527.0
1 TraesCS2D01G586100 chr2D 84.127 378 53 5 1972 2347 565982384 565982012 3.350000e-95 359.0
2 TraesCS2D01G586100 chr2D 88.235 204 24 0 1753 1956 644722178 644721975 9.800000e-61 244.0
3 TraesCS2D01G586100 chr2D 88.235 204 24 0 1789 1992 644722214 644722011 9.800000e-61 244.0
4 TraesCS2D01G586100 chr2D 88.542 96 11 0 1897 1992 644722214 644722119 2.230000e-22 117.0
5 TraesCS2D01G586100 chr2D 95.000 60 3 0 1330 1389 324685520 324685461 1.040000e-15 95.3
6 TraesCS2D01G586100 chr2D 100.000 30 0 0 496 525 639611879 639611850 4.930000e-04 56.5
7 TraesCS2D01G586100 chr2A 92.975 1765 85 16 1789 3534 770013375 770011631 0.000000e+00 2536.0
8 TraesCS2D01G586100 chr2A 92.679 560 40 1 1391 1949 770013738 770013179 0.000000e+00 806.0
9 TraesCS2D01G586100 chr2A 83.806 846 79 17 10 838 770016184 770015380 0.000000e+00 750.0
10 TraesCS2D01G586100 chr2A 87.925 530 39 13 875 1391 770014282 770013765 5.050000e-168 601.0
11 TraesCS2D01G586100 chr2A 84.840 376 54 2 1972 2347 706217971 706217599 3.330000e-100 375.0
12 TraesCS2D01G586100 chr2B 92.312 1730 89 20 1809 3534 790751901 790753590 0.000000e+00 2418.0
13 TraesCS2D01G586100 chr2B 89.594 567 48 7 1401 1956 790751518 790752084 0.000000e+00 710.0
14 TraesCS2D01G586100 chr2B 91.507 471 28 3 904 1364 790750933 790751401 3.850000e-179 638.0
15 TraesCS2D01G586100 chr2B 88.747 391 30 10 3144 3534 790860607 790860983 1.920000e-127 466.0
16 TraesCS2D01G586100 chr2B 82.734 417 35 21 2999 3394 17481971 17482371 1.570000e-88 337.0
17 TraesCS2D01G586100 chr2B 85.333 75 4 4 1419 1491 118053017 118053086 1.760000e-08 71.3
18 TraesCS2D01G586100 chr3A 85.232 1808 148 57 1786 3534 718353383 718351636 0.000000e+00 1749.0
19 TraesCS2D01G586100 chr3A 84.658 541 65 14 1416 1951 718353709 718353182 1.120000e-144 523.0
20 TraesCS2D01G586100 chr3A 89.881 168 17 0 1825 1992 718353380 718353213 2.140000e-52 217.0
21 TraesCS2D01G586100 chr3A 90.184 163 16 0 1750 1912 718353347 718353185 2.760000e-51 213.0
22 TraesCS2D01G586100 chr3A 88.652 141 16 0 1750 1890 718353311 718353171 4.690000e-39 172.0
23 TraesCS2D01G586100 chr3D 85.569 1476 127 45 1822 3233 588318796 588317343 0.000000e+00 1467.0
24 TraesCS2D01G586100 chr3D 84.825 514 53 17 1416 1920 588319123 588318626 8.810000e-136 494.0
25 TraesCS2D01G586100 chr3D 89.136 359 23 9 3172 3529 588317345 588317002 1.950000e-117 433.0
26 TraesCS2D01G586100 chr3D 88.889 135 15 0 1750 1884 588318760 588318626 2.180000e-37 167.0
27 TraesCS2D01G586100 chr3D 85.185 135 20 0 1858 1992 588318796 588318662 4.760000e-29 139.0
28 TraesCS2D01G586100 chr3D 95.238 63 3 0 1329 1391 286679667 286679729 2.240000e-17 100.0
29 TraesCS2D01G586100 chr3D 93.443 61 4 0 1329 1389 573297250 573297310 1.350000e-14 91.6
30 TraesCS2D01G586100 chr3B 90.078 897 74 8 1822 2711 786724927 786724039 0.000000e+00 1149.0
31 TraesCS2D01G586100 chr3B 81.061 792 65 43 2794 3534 786724001 786723244 1.430000e-153 553.0
32 TraesCS2D01G586100 chr3B 82.066 513 59 19 1419 1920 786725247 786724757 1.180000e-109 407.0
33 TraesCS2D01G586100 chr3B 82.507 383 29 19 3008 3369 168990025 168989660 5.730000e-78 302.0
34 TraesCS2D01G586100 chr3B 85.185 135 20 0 1858 1992 786724927 786724793 4.760000e-29 139.0
35 TraesCS2D01G586100 chr4B 83.455 411 31 20 3008 3397 76501852 76501458 7.260000e-92 348.0
36 TraesCS2D01G586100 chr4B 83.088 408 32 20 3011 3397 592373048 592372657 1.570000e-88 337.0
37 TraesCS2D01G586100 chr7B 83.538 407 30 23 3008 3393 571235272 571234882 2.610000e-91 346.0
38 TraesCS2D01G586100 chr7B 95.238 63 3 0 1329 1391 505228417 505228355 2.240000e-17 100.0
39 TraesCS2D01G586100 chr5B 83.212 411 32 23 3008 3397 685680781 685680387 3.380000e-90 342.0
40 TraesCS2D01G586100 chr5B 82.968 411 33 22 3008 3397 534293394 534293000 1.570000e-88 337.0
41 TraesCS2D01G586100 chr5B 92.063 63 5 0 1329 1391 317049041 317049103 4.860000e-14 89.8
42 TraesCS2D01G586100 chr1B 82.974 417 34 23 2999 3394 10526242 10526642 3.380000e-90 342.0
43 TraesCS2D01G586100 chr1A 83.212 411 32 23 3008 3397 575302012 575301618 3.380000e-90 342.0
44 TraesCS2D01G586100 chrUn 82.014 417 38 21 2999 3394 34684941 34685341 1.580000e-83 320.0
45 TraesCS2D01G586100 chrUn 85.135 74 4 4 1419 1490 24211137 24211069 6.330000e-08 69.4
46 TraesCS2D01G586100 chrUn 87.500 64 3 2 1419 1482 68849933 68849991 6.330000e-08 69.4
47 TraesCS2D01G586100 chrUn 85.135 74 4 4 1419 1490 104162439 104162371 6.330000e-08 69.4
48 TraesCS2D01G586100 chrUn 85.135 74 4 4 1419 1490 271534927 271534859 6.330000e-08 69.4
49 TraesCS2D01G586100 chrUn 87.500 64 3 2 1419 1482 389851317 389851375 6.330000e-08 69.4
50 TraesCS2D01G586100 chr4A 84.211 247 16 12 2999 3225 655273189 655273432 5.940000e-53 219.0
51 TraesCS2D01G586100 chr6B 91.803 61 5 0 1329 1389 531730 531670 6.290000e-13 86.1
52 TraesCS2D01G586100 chr6B 89.831 59 3 1 1329 1387 166099855 166099910 4.890000e-09 73.1
53 TraesCS2D01G586100 chr7D 86.486 74 3 4 1419 1490 502808001 502808069 1.360000e-09 75.0


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 TraesCS2D01G586100 chr2D 644720433 644723966 3533 True 1783.000000 6527 91.253000 1 3534 4 chr2D.!!$R4 3533
1 TraesCS2D01G586100 chr2A 770011631 770016184 4553 True 1173.250000 2536 89.346250 10 3534 4 chr2A.!!$R2 3524
2 TraesCS2D01G586100 chr2B 790750933 790753590 2657 False 1255.333333 2418 91.137667 904 3534 3 chr2B.!!$F4 2630
3 TraesCS2D01G586100 chr3A 718351636 718353709 2073 True 574.800000 1749 87.721400 1416 3534 5 chr3A.!!$R1 2118
4 TraesCS2D01G586100 chr3D 588317002 588319123 2121 True 540.000000 1467 86.720800 1416 3529 5 chr3D.!!$R1 2113
5 TraesCS2D01G586100 chr3B 786723244 786725247 2003 True 562.000000 1149 84.597500 1419 3534 4 chr3B.!!$R2 2115

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
584 590 0.036105 CTTGGGAGCAAATTTGGCCC 60.036 55.0 19.47 13.3 39.29 5.80 F
1790 2998 0.033208 GCAGGATGGGTGGAAATGGA 60.033 55.0 0.00 0.0 35.86 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 3011 0.033208 TTTCCACCCATCCTGCCATC 60.033 55.0 0.0 0.0 0.00 3.51 R
2646 3867 1.160137 CAAAAGGAGAGGGAACTGCG 58.840 55.0 0.0 0.0 44.43 5.18 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
269 273 5.525012 TCATAAATGTTTGATCTGCCTCTCG 59.475 40.000 0.00 0.00 0.00 4.04
298 302 4.371855 TCATAAAGTCTCCGCACTACAG 57.628 45.455 0.00 0.00 0.00 2.74
300 304 4.461431 TCATAAAGTCTCCGCACTACAGAA 59.539 41.667 0.00 0.00 0.00 3.02
302 306 3.746045 AAGTCTCCGCACTACAGAAAA 57.254 42.857 0.00 0.00 0.00 2.29
355 359 0.179124 CAAGCAGTCTAGGACGAGCC 60.179 60.000 12.00 0.00 38.51 4.70
356 360 1.658686 AAGCAGTCTAGGACGAGCCG 61.659 60.000 12.00 0.00 43.43 5.52
379 383 1.827969 AGGAGTTCGAACCCATGAGAG 59.172 52.381 27.10 0.00 0.00 3.20
382 386 2.231478 GAGTTCGAACCCATGAGAGTGA 59.769 50.000 24.22 0.00 0.00 3.41
385 389 1.275291 TCGAACCCATGAGAGTGAACC 59.725 52.381 0.00 0.00 0.00 3.62
396 400 4.755411 TGAGAGTGAACCGCTATTTTAGG 58.245 43.478 0.00 0.00 0.00 2.69
410 416 5.685954 GCTATTTTAGGATTTTTACGCTGCC 59.314 40.000 0.00 0.00 0.00 4.85
417 423 1.249407 TTTTTACGCTGCCCCGATTT 58.751 45.000 0.00 0.00 0.00 2.17
437 443 6.566564 CGATTTGATTATAGTGCCATTCGCTT 60.567 38.462 0.00 0.00 38.78 4.68
438 444 5.422666 TTGATTATAGTGCCATTCGCTTG 57.577 39.130 0.00 0.00 38.78 4.01
440 446 2.254546 TATAGTGCCATTCGCTTGGG 57.745 50.000 5.73 0.00 37.24 4.12
441 447 0.255890 ATAGTGCCATTCGCTTGGGT 59.744 50.000 5.73 0.00 37.24 4.51
442 448 0.676466 TAGTGCCATTCGCTTGGGTG 60.676 55.000 5.73 0.00 37.24 4.61
443 449 3.372730 TGCCATTCGCTTGGGTGC 61.373 61.111 5.73 0.00 37.24 5.01
444 450 4.133796 GCCATTCGCTTGGGTGCC 62.134 66.667 5.73 0.00 37.24 5.01
445 451 2.361610 CCATTCGCTTGGGTGCCT 60.362 61.111 0.00 0.00 32.80 4.75
446 452 1.077787 CCATTCGCTTGGGTGCCTA 60.078 57.895 0.00 0.00 32.80 3.93
447 453 1.376609 CCATTCGCTTGGGTGCCTAC 61.377 60.000 0.00 0.00 32.80 3.18
448 454 1.077716 ATTCGCTTGGGTGCCTACC 60.078 57.895 0.00 0.00 46.76 3.18
481 487 1.743995 GTTGGGCTTCCGTATGCGT 60.744 57.895 1.69 0.00 36.15 5.24
486 492 1.804326 GCTTCCGTATGCGTCGTGT 60.804 57.895 1.69 0.00 36.15 4.49
489 495 2.186350 TTCCGTATGCGTCGTGTCGT 62.186 55.000 1.69 0.00 36.15 4.34
491 497 1.335836 CGTATGCGTCGTGTCGTTG 59.664 57.895 0.00 0.00 0.00 4.10
561 567 3.063704 CTCGCAAGCCCCATGCAA 61.064 61.111 0.00 0.00 44.01 4.08
584 590 0.036105 CTTGGGAGCAAATTTGGCCC 60.036 55.000 19.47 13.30 39.29 5.80
595 601 0.606096 ATTTGGCCCGTTTGGTTAGC 59.394 50.000 0.00 0.00 36.04 3.09
602 608 0.596082 CCGTTTGGTTAGCTGGGTTG 59.404 55.000 0.00 0.00 0.00 3.77
606 612 2.008242 TTGGTTAGCTGGGTTGCATT 57.992 45.000 0.00 0.00 34.99 3.56
607 613 1.255882 TGGTTAGCTGGGTTGCATTG 58.744 50.000 0.00 0.00 34.99 2.82
633 639 1.561643 TGGGCCACACAAACTTTGAA 58.438 45.000 0.00 0.00 0.00 2.69
655 661 1.371512 CATCTCAGGCTAGCGCTCG 60.372 63.158 16.34 9.56 36.09 5.03
679 685 1.429463 ACGCCTGAGTCGATTGTTTC 58.571 50.000 0.00 0.00 0.00 2.78
681 687 0.721718 GCCTGAGTCGATTGTTTCCG 59.278 55.000 0.00 0.00 0.00 4.30
718 724 2.508526 ACATGCAGGGAGAGAAAACAC 58.491 47.619 2.31 0.00 0.00 3.32
720 726 0.250295 TGCAGGGAGAGAAAACACGG 60.250 55.000 0.00 0.00 0.00 4.94
721 727 1.578206 GCAGGGAGAGAAAACACGGC 61.578 60.000 0.00 0.00 0.00 5.68
722 728 1.004918 AGGGAGAGAAAACACGGCG 60.005 57.895 4.80 4.80 0.00 6.46
723 729 1.005394 GGGAGAGAAAACACGGCGA 60.005 57.895 16.62 0.00 0.00 5.54
724 730 1.289800 GGGAGAGAAAACACGGCGAC 61.290 60.000 16.62 0.00 0.00 5.19
725 731 0.599204 GGAGAGAAAACACGGCGACA 60.599 55.000 16.62 0.00 0.00 4.35
726 732 0.784778 GAGAGAAAACACGGCGACAG 59.215 55.000 16.62 5.45 0.00 3.51
727 733 0.600255 AGAGAAAACACGGCGACAGG 60.600 55.000 16.62 2.12 0.00 4.00
728 734 1.566018 GAGAAAACACGGCGACAGGG 61.566 60.000 16.62 0.00 0.00 4.45
729 735 3.249973 GAAAACACGGCGACAGGGC 62.250 63.158 16.62 0.00 37.98 5.19
730 736 3.767630 AAAACACGGCGACAGGGCT 62.768 57.895 16.62 0.00 39.52 5.19
731 737 3.767630 AAACACGGCGACAGGGCTT 62.768 57.895 16.62 0.00 39.52 4.35
732 738 4.988598 ACACGGCGACAGGGCTTG 62.989 66.667 16.62 0.05 44.76 4.01
733 739 4.988598 CACGGCGACAGGGCTTGT 62.989 66.667 16.62 0.23 44.55 3.16
734 740 4.988598 ACGGCGACAGGGCTTGTG 62.989 66.667 16.62 0.78 41.05 3.33
737 743 3.286751 GCGACAGGGCTTGTGCAA 61.287 61.111 7.11 0.00 41.05 4.08
761 767 4.101790 GGATGGCACCAACACGCG 62.102 66.667 3.53 3.53 0.00 6.01
797 810 0.105453 ATGGCGGGAGTATCACCTCT 60.105 55.000 0.00 0.00 32.04 3.69
802 815 1.409427 CGGGAGTATCACCTCTGGTTC 59.591 57.143 0.00 0.00 32.04 3.62
808 821 2.698855 ATCACCTCTGGTTCATTCCG 57.301 50.000 0.00 0.00 31.02 4.30
809 822 1.348064 TCACCTCTGGTTCATTCCGT 58.652 50.000 0.00 0.00 31.02 4.69
838 856 2.758852 TAACCCCCTTCGGCTCACCT 62.759 60.000 0.00 0.00 0.00 4.00
839 857 3.330720 CCCCCTTCGGCTCACCTT 61.331 66.667 0.00 0.00 0.00 3.50
840 858 2.757077 CCCCTTCGGCTCACCTTT 59.243 61.111 0.00 0.00 0.00 3.11
841 859 1.074951 CCCCTTCGGCTCACCTTTT 59.925 57.895 0.00 0.00 0.00 2.27
842 860 0.539669 CCCCTTCGGCTCACCTTTTT 60.540 55.000 0.00 0.00 0.00 1.94
843 861 0.598065 CCCTTCGGCTCACCTTTTTG 59.402 55.000 0.00 0.00 0.00 2.44
962 2041 3.003480 CAAGAAGGAAAGACGGCCTAAG 58.997 50.000 0.00 0.00 33.20 2.18
1044 2129 1.149627 CGGATCTCGTCCTCCTCCT 59.850 63.158 0.00 0.00 45.46 3.69
1195 2284 0.461135 CCCTTCCATTGCATTTCCCG 59.539 55.000 0.00 0.00 0.00 5.14
1226 2315 4.522405 ACTCGATCCAGATCCATCTAACTG 59.478 45.833 0.00 0.00 34.85 3.16
1230 2319 2.702478 TCCAGATCCATCTAACTGGCAG 59.298 50.000 14.16 14.16 46.36 4.85
1241 2330 4.018490 TCTAACTGGCAGTACGATGGTAA 58.982 43.478 22.37 0.00 0.00 2.85
1243 2332 2.176889 ACTGGCAGTACGATGGTAACT 58.823 47.619 20.61 0.00 37.61 2.24
1256 2345 6.127793 ACGATGGTAACTAGGTAGACTGAAT 58.872 40.000 0.00 0.00 37.61 2.57
1281 2377 5.119898 CGAATCTTGAACTGAAACAGAGAGG 59.880 44.000 5.76 0.00 35.18 3.69
1284 2380 6.672266 TCTTGAACTGAAACAGAGAGGTAT 57.328 37.500 5.76 0.00 35.18 2.73
1296 2392 6.811253 ACAGAGAGGTATGATAGATTCGTC 57.189 41.667 0.00 0.00 0.00 4.20
1301 2397 5.182950 AGAGGTATGATAGATTCGTCAGCTG 59.817 44.000 7.63 7.63 0.00 4.24
1364 2460 6.887013 TGTAATTTCATTTCATGGGGAATGG 58.113 36.000 13.61 1.76 36.86 3.16
1380 2476 5.297029 GGGGAATGGATAGAAGAAGAAAACG 59.703 44.000 0.00 0.00 0.00 3.60
1495 2682 6.149308 TGTTGACCACAAATCTTGCTACTATG 59.851 38.462 0.00 0.00 37.77 2.23
1588 2795 5.049129 AGTTTTGCTTAGACATGAACAGAGC 60.049 40.000 0.00 7.38 0.00 4.09
1661 2869 4.421515 CAGGGCCCACTGCAGGAG 62.422 72.222 27.56 10.12 43.89 3.69
1786 2994 1.076549 GTGGCAGGATGGGTGGAAA 59.923 57.895 0.00 0.00 35.86 3.13
1787 2995 0.324645 GTGGCAGGATGGGTGGAAAT 60.325 55.000 0.00 0.00 35.86 2.17
1788 2996 0.324552 TGGCAGGATGGGTGGAAATG 60.325 55.000 0.00 0.00 35.86 2.32
1789 2997 1.044790 GGCAGGATGGGTGGAAATGG 61.045 60.000 0.00 0.00 35.86 3.16
1790 2998 0.033208 GCAGGATGGGTGGAAATGGA 60.033 55.000 0.00 0.00 35.86 3.41
1791 2999 1.412074 GCAGGATGGGTGGAAATGGAT 60.412 52.381 0.00 0.00 35.86 3.41
1792 3000 2.956385 GCAGGATGGGTGGAAATGGATT 60.956 50.000 0.00 0.00 35.86 3.01
1793 3001 2.961062 CAGGATGGGTGGAAATGGATTC 59.039 50.000 0.00 0.00 37.31 2.52
1794 3002 2.586838 AGGATGGGTGGAAATGGATTCA 59.413 45.455 0.00 0.00 39.98 2.57
1795 3003 2.695147 GGATGGGTGGAAATGGATTCAC 59.305 50.000 0.00 0.00 39.98 3.18
1796 3004 2.988636 TGGGTGGAAATGGATTCACA 57.011 45.000 0.00 0.00 39.98 3.58
1797 3005 2.806434 TGGGTGGAAATGGATTCACAG 58.194 47.619 0.00 0.00 39.98 3.66
1798 3006 1.478105 GGGTGGAAATGGATTCACAGC 59.522 52.381 0.00 0.00 39.98 4.40
1799 3007 1.478105 GGTGGAAATGGATTCACAGCC 59.522 52.381 0.00 0.00 39.98 4.85
1800 3008 2.170166 GTGGAAATGGATTCACAGCCA 58.830 47.619 0.00 0.00 39.98 4.75
1801 3009 2.165030 GTGGAAATGGATTCACAGCCAG 59.835 50.000 0.00 0.00 39.98 4.85
1802 3010 1.135721 GGAAATGGATTCACAGCCAGC 59.864 52.381 0.00 0.00 39.98 4.85
1803 3011 0.813184 AAATGGATTCACAGCCAGCG 59.187 50.000 0.00 0.00 37.64 5.18
1804 3012 0.035152 AATGGATTCACAGCCAGCGA 60.035 50.000 0.00 0.00 37.64 4.93
1805 3013 0.182061 ATGGATTCACAGCCAGCGAT 59.818 50.000 0.00 0.00 37.64 4.58
1806 3014 0.745486 TGGATTCACAGCCAGCGATG 60.745 55.000 0.00 0.00 0.00 3.84
1807 3015 1.442526 GGATTCACAGCCAGCGATGG 61.443 60.000 17.26 17.26 0.00 3.51
1816 3024 2.593725 CAGCGATGGCAGGATGGG 60.594 66.667 1.50 0.00 43.41 4.00
1817 3025 3.092511 AGCGATGGCAGGATGGGT 61.093 61.111 1.50 0.00 43.41 4.51
1818 3026 2.903855 GCGATGGCAGGATGGGTG 60.904 66.667 0.00 0.00 39.62 4.61
1819 3027 2.203252 CGATGGCAGGATGGGTGG 60.203 66.667 0.00 0.00 35.86 4.61
1820 3028 2.745308 CGATGGCAGGATGGGTGGA 61.745 63.158 0.00 0.00 35.86 4.02
1821 3029 1.614711 GATGGCAGGATGGGTGGAA 59.385 57.895 0.00 0.00 35.86 3.53
1836 3044 0.109532 TGGAAACGGATTCACAGCCA 59.890 50.000 0.36 0.00 39.98 4.75
1870 3078 1.544759 GGGTGGAAACGGATTCACAGT 60.545 52.381 3.88 0.00 39.98 3.55
1889 3097 2.520260 GGTGATGGCAGGATGGGC 60.520 66.667 0.00 0.00 35.86 5.36
1941 3149 2.524306 TGGGTGGAATTGGATTCACAC 58.476 47.619 3.39 7.87 41.03 3.82
2060 3268 3.442076 AGTAAAGAGGGACGTTCTCCAT 58.558 45.455 13.83 0.00 41.63 3.41
2093 3301 2.505405 GGGAAGAAGACCTTTGTGACC 58.495 52.381 0.00 0.00 34.68 4.02
2240 3448 1.353694 AGCAAGATTGGCCTCAAGTCT 59.646 47.619 3.32 0.00 36.19 3.24
2244 3452 1.980765 AGATTGGCCTCAAGTCTGTCA 59.019 47.619 3.32 0.00 36.19 3.58
2306 3514 0.040058 AGGTGATCATGGGCTTTGCA 59.960 50.000 0.00 0.00 0.00 4.08
2646 3867 2.151881 TGTTCATGGTTGCATTGCAC 57.848 45.000 11.66 6.75 38.71 4.57
2755 3976 8.519492 TTCAAGAAGTGAAAAAGTTTGAAGTG 57.481 30.769 0.00 0.00 43.43 3.16
2838 4059 1.004745 TGGCTCTGTCCCCTCATTTTC 59.995 52.381 0.00 0.00 0.00 2.29
2871 4092 6.969828 ACCGACAAGAAAATATTCTGAGAC 57.030 37.500 0.00 0.00 45.19 3.36
2873 4094 6.814146 ACCGACAAGAAAATATTCTGAGACTC 59.186 38.462 0.00 0.00 45.19 3.36
2914 4144 3.814842 TCTGCGATTCTTTCAAGCAAGAA 59.185 39.130 0.00 0.00 44.90 2.52
2994 4227 6.402222 TCTCCTCTCACTAAAATTTCTCTGC 58.598 40.000 0.00 0.00 0.00 4.26
3101 4361 3.855858 AGGAGCGACTTCTCTGATTTTC 58.144 45.455 0.00 0.00 33.70 2.29
3109 4369 5.388890 CGACTTCTCTGATTTTCTTGGTTCG 60.389 44.000 0.00 0.00 0.00 3.95
3204 4497 3.910568 TCATACACAGACCATGCATGA 57.089 42.857 28.31 5.54 0.00 3.07
3205 4498 3.800531 TCATACACAGACCATGCATGAG 58.199 45.455 28.31 19.16 0.00 2.90
3246 4598 9.599866 TCCATGATTTTATTACTGACAGTGTAG 57.400 33.333 18.58 0.00 0.00 2.74
3252 4604 8.615878 TTTTATTACTGACAGTGTAGCACATT 57.384 30.769 18.58 0.00 36.74 2.71
3253 4605 9.713713 TTTTATTACTGACAGTGTAGCACATTA 57.286 29.630 18.58 0.00 36.74 1.90
3254 4606 9.884636 TTTATTACTGACAGTGTAGCACATTAT 57.115 29.630 18.58 0.00 36.74 1.28
3257 4609 9.698309 ATTACTGACAGTGTAGCACATTATATC 57.302 33.333 18.58 0.00 36.74 1.63
3258 4610 7.112452 ACTGACAGTGTAGCACATTATATCA 57.888 36.000 7.47 0.00 36.74 2.15
3260 4612 7.112452 TGACAGTGTAGCACATTATATCAGT 57.888 36.000 0.00 0.00 36.74 3.41
3262 4614 8.691797 TGACAGTGTAGCACATTATATCAGTTA 58.308 33.333 0.00 0.00 36.74 2.24
3263 4615 8.873215 ACAGTGTAGCACATTATATCAGTTAC 57.127 34.615 0.00 0.00 36.74 2.50
3264 4616 8.696374 ACAGTGTAGCACATTATATCAGTTACT 58.304 33.333 0.00 0.00 36.74 2.24
3265 4617 9.186323 CAGTGTAGCACATTATATCAGTTACTC 57.814 37.037 2.01 0.00 36.74 2.59
3266 4618 9.137459 AGTGTAGCACATTATATCAGTTACTCT 57.863 33.333 2.01 0.00 36.74 3.24
3308 4660 6.638468 GCTTATGTTCATAATAGCAAAGCCAC 59.362 38.462 5.83 0.00 32.65 5.01
3310 4662 5.309323 TGTTCATAATAGCAAAGCCACAC 57.691 39.130 0.00 0.00 0.00 3.82
3312 4664 4.963276 TCATAATAGCAAAGCCACACAC 57.037 40.909 0.00 0.00 0.00 3.82
3313 4665 4.331108 TCATAATAGCAAAGCCACACACA 58.669 39.130 0.00 0.00 0.00 3.72
3316 4668 4.399004 AATAGCAAAGCCACACACAAAA 57.601 36.364 0.00 0.00 0.00 2.44
3317 4669 2.758736 AGCAAAGCCACACACAAAAA 57.241 40.000 0.00 0.00 0.00 1.94
3318 4670 2.345876 AGCAAAGCCACACACAAAAAC 58.654 42.857 0.00 0.00 0.00 2.43
3319 4671 2.028203 AGCAAAGCCACACACAAAAACT 60.028 40.909 0.00 0.00 0.00 2.66
3320 4672 2.741517 GCAAAGCCACACACAAAAACTT 59.258 40.909 0.00 0.00 0.00 2.66
3321 4673 3.929610 GCAAAGCCACACACAAAAACTTA 59.070 39.130 0.00 0.00 0.00 2.24
3322 4674 4.032786 GCAAAGCCACACACAAAAACTTAG 59.967 41.667 0.00 0.00 0.00 2.18
3323 4675 5.406649 CAAAGCCACACACAAAAACTTAGA 58.593 37.500 0.00 0.00 0.00 2.10
3324 4676 4.632538 AGCCACACACAAAAACTTAGAC 57.367 40.909 0.00 0.00 0.00 2.59
3325 4677 3.380320 AGCCACACACAAAAACTTAGACC 59.620 43.478 0.00 0.00 0.00 3.85
3346 4698 3.621715 CCGAAAGCATAGTTAACCCAGAC 59.378 47.826 0.88 0.00 0.00 3.51
3400 4753 1.081892 GCACACACTACTGCATCCAG 58.918 55.000 0.00 0.00 44.80 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.753669 AAACATGATTTTTGAAAAACTTCGAAC 57.246 25.926 5.08 0.00 0.00 3.95
259 263 0.598562 GAACTGACACGAGAGGCAGA 59.401 55.000 15.07 0.00 34.46 4.26
261 265 0.969149 ATGAACTGACACGAGAGGCA 59.031 50.000 0.00 0.00 0.00 4.75
269 273 3.368236 GCGGAGACTTTATGAACTGACAC 59.632 47.826 0.00 0.00 0.00 3.67
298 302 4.110482 GCTGGTGAGCATTCATGATTTTC 58.890 43.478 0.00 0.00 45.46 2.29
300 304 3.795623 GCTGGTGAGCATTCATGATTT 57.204 42.857 0.00 0.00 45.46 2.17
323 327 0.520404 CTGCTTGTTGCTAGCCACTG 59.480 55.000 18.75 12.66 43.37 3.66
350 354 2.196382 TTCGAACTCCTGACGGCTCG 62.196 60.000 0.00 0.00 0.00 5.03
355 359 0.246635 ATGGGTTCGAACTCCTGACG 59.753 55.000 24.92 0.00 0.00 4.35
356 360 1.275291 TCATGGGTTCGAACTCCTGAC 59.725 52.381 26.28 10.95 0.00 3.51
359 363 1.827969 CTCTCATGGGTTCGAACTCCT 59.172 52.381 24.92 13.10 0.00 3.69
360 364 1.550976 ACTCTCATGGGTTCGAACTCC 59.449 52.381 24.92 23.18 0.00 3.85
379 383 7.427318 CGTAAAAATCCTAAAATAGCGGTTCAC 59.573 37.037 0.00 0.00 0.00 3.18
382 386 6.094464 AGCGTAAAAATCCTAAAATAGCGGTT 59.906 34.615 0.00 0.00 0.00 4.44
385 389 5.395486 GCAGCGTAAAAATCCTAAAATAGCG 59.605 40.000 0.00 0.00 0.00 4.26
396 400 1.021968 ATCGGGGCAGCGTAAAAATC 58.978 50.000 0.00 0.00 0.00 2.17
410 416 5.390885 CGAATGGCACTATAATCAAATCGGG 60.391 44.000 0.00 0.00 0.00 5.14
437 443 3.095421 CCCATTGGTAGGCACCCA 58.905 61.111 1.20 0.00 45.11 4.51
443 449 4.355151 GGTTGGCCCATTGGTAGG 57.645 61.111 0.00 0.00 0.00 3.18
481 487 0.025256 GCGTCAAAACAACGACACGA 59.975 50.000 0.00 0.00 42.62 4.35
486 492 3.301906 CACATTTTGCGTCAAAACAACGA 59.698 39.130 16.31 0.00 44.40 3.85
489 495 3.301906 CGACACATTTTGCGTCAAAACAA 59.698 39.130 16.31 0.46 44.40 2.83
491 497 2.849473 ACGACACATTTTGCGTCAAAAC 59.151 40.909 16.31 6.34 44.40 2.43
548 554 1.255667 AAGAGCTTGCATGGGGCTTG 61.256 55.000 1.34 0.00 45.15 4.01
584 590 0.039527 GCAACCCAGCTAACCAAACG 60.040 55.000 0.00 0.00 0.00 3.60
595 601 2.546373 CCACTTTGACAATGCAACCCAG 60.546 50.000 0.00 0.00 0.00 4.45
602 608 0.319813 GTGGCCCACTTTGACAATGC 60.320 55.000 6.63 0.00 0.00 3.56
606 612 0.323816 TTGTGTGGCCCACTTTGACA 60.324 50.000 16.23 8.08 44.81 3.58
607 613 0.820871 TTTGTGTGGCCCACTTTGAC 59.179 50.000 16.23 5.23 44.81 3.18
633 639 1.440893 CGCTAGCCTGAGATGTGCT 59.559 57.895 9.66 0.00 39.10 4.40
655 661 0.173708 AATCGACTCAGGCGTTCCTC 59.826 55.000 0.00 0.00 41.93 3.71
679 685 2.856039 TAGTGAGTCTGGCTCCCCGG 62.856 65.000 6.84 0.00 43.48 5.73
681 687 0.614979 TGTAGTGAGTCTGGCTCCCC 60.615 60.000 6.84 0.00 43.48 4.81
720 726 3.259425 CTTGCACAAGCCCTGTCGC 62.259 63.158 0.00 4.88 41.13 5.19
721 727 2.949106 CTTGCACAAGCCCTGTCG 59.051 61.111 0.00 0.00 41.13 4.35
783 790 2.467880 TGAACCAGAGGTGATACTCCC 58.532 52.381 0.00 0.00 38.26 4.30
797 810 1.646912 TAGGGTGACGGAATGAACCA 58.353 50.000 0.00 0.00 34.18 3.67
802 815 3.881089 GGGTTAAATAGGGTGACGGAATG 59.119 47.826 0.00 0.00 0.00 2.67
808 821 3.683564 CGAAGGGGGTTAAATAGGGTGAC 60.684 52.174 0.00 0.00 0.00 3.67
809 822 2.506644 CGAAGGGGGTTAAATAGGGTGA 59.493 50.000 0.00 0.00 0.00 4.02
883 1910 7.040478 CCCACATCAAATTTTCTGACTTGTCTA 60.040 37.037 2.35 0.00 0.00 2.59
892 1971 4.261578 AGTGCCCACATCAAATTTTCTG 57.738 40.909 0.82 0.00 0.00 3.02
897 1976 3.056891 CCGTTTAGTGCCCACATCAAATT 60.057 43.478 0.82 0.00 0.00 1.82
962 2041 0.592754 GAGTGCGTCTCTCGTATGGC 60.593 60.000 2.12 0.00 42.13 4.40
1195 2284 2.386661 TCTGGATCGAGTTTCTTGCC 57.613 50.000 4.53 0.00 0.00 4.52
1226 2315 2.692041 ACCTAGTTACCATCGTACTGCC 59.308 50.000 0.00 0.00 0.00 4.85
1230 2319 6.051717 TCAGTCTACCTAGTTACCATCGTAC 58.948 44.000 0.00 0.00 0.00 3.67
1241 2330 6.829298 TCAAGATTCGATTCAGTCTACCTAGT 59.171 38.462 9.78 0.00 0.00 2.57
1243 2332 7.339721 AGTTCAAGATTCGATTCAGTCTACCTA 59.660 37.037 9.78 0.00 0.00 3.08
1256 2345 5.842907 TCTCTGTTTCAGTTCAAGATTCGA 58.157 37.500 0.00 0.00 32.61 3.71
1281 2377 4.489810 CCCAGCTGACGAATCTATCATAC 58.510 47.826 17.39 0.00 0.00 2.39
1284 2380 1.069204 GCCCAGCTGACGAATCTATCA 59.931 52.381 17.39 0.00 0.00 2.15
1364 2460 5.480205 ACACCTCCGTTTTCTTCTTCTATC 58.520 41.667 0.00 0.00 0.00 2.08
1380 2476 2.300437 AGAACAGCAGTAGAACACCTCC 59.700 50.000 0.00 0.00 0.00 4.30
1469 2655 3.996150 AGCAAGATTTGTGGTCAACAG 57.004 42.857 0.00 0.00 40.74 3.16
1495 2682 5.533903 AGATCACACAATAAGATTCATGGCC 59.466 40.000 0.00 0.00 0.00 5.36
1572 2779 2.094182 GGACCGCTCTGTTCATGTCTAA 60.094 50.000 0.00 0.00 0.00 2.10
1588 2795 3.198068 CACCAGATAACAAGATGGACCG 58.802 50.000 0.00 0.00 36.62 4.79
1786 2994 0.182061 ATCGCTGGCTGTGAATCCAT 59.818 50.000 11.70 0.00 38.81 3.41
1787 2995 0.745486 CATCGCTGGCTGTGAATCCA 60.745 55.000 11.70 0.00 38.81 3.41
1788 2996 1.442526 CCATCGCTGGCTGTGAATCC 61.443 60.000 11.70 0.00 38.81 3.01
1789 2997 2.020131 CCATCGCTGGCTGTGAATC 58.980 57.895 11.70 0.00 38.81 2.52
1790 2998 4.230603 CCATCGCTGGCTGTGAAT 57.769 55.556 11.70 0.00 38.81 2.57
1799 3007 2.593725 CCCATCCTGCCATCGCTG 60.594 66.667 0.00 0.00 35.36 5.18
1800 3008 3.092511 ACCCATCCTGCCATCGCT 61.093 61.111 0.00 0.00 35.36 4.93
1801 3009 2.903855 CACCCATCCTGCCATCGC 60.904 66.667 0.00 0.00 0.00 4.58
1802 3010 2.203252 CCACCCATCCTGCCATCG 60.203 66.667 0.00 0.00 0.00 3.84
1803 3011 0.033208 TTTCCACCCATCCTGCCATC 60.033 55.000 0.00 0.00 0.00 3.51
1804 3012 0.324645 GTTTCCACCCATCCTGCCAT 60.325 55.000 0.00 0.00 0.00 4.40
1805 3013 1.076549 GTTTCCACCCATCCTGCCA 59.923 57.895 0.00 0.00 0.00 4.92
1806 3014 2.046285 CGTTTCCACCCATCCTGCC 61.046 63.158 0.00 0.00 0.00 4.85
1807 3015 2.046285 CCGTTTCCACCCATCCTGC 61.046 63.158 0.00 0.00 0.00 4.85
1808 3016 0.255890 ATCCGTTTCCACCCATCCTG 59.744 55.000 0.00 0.00 0.00 3.86
1809 3017 0.999712 AATCCGTTTCCACCCATCCT 59.000 50.000 0.00 0.00 0.00 3.24
1810 3018 1.340600 TGAATCCGTTTCCACCCATCC 60.341 52.381 0.00 0.00 33.04 3.51
1811 3019 1.743394 GTGAATCCGTTTCCACCCATC 59.257 52.381 0.00 0.00 33.04 3.51
1812 3020 1.074727 TGTGAATCCGTTTCCACCCAT 59.925 47.619 0.00 0.00 33.04 4.00
1813 3021 0.474614 TGTGAATCCGTTTCCACCCA 59.525 50.000 0.00 0.00 33.04 4.51
1814 3022 1.165270 CTGTGAATCCGTTTCCACCC 58.835 55.000 0.00 0.00 33.04 4.61
1815 3023 0.521735 GCTGTGAATCCGTTTCCACC 59.478 55.000 0.00 0.00 33.04 4.61
1816 3024 0.521735 GGCTGTGAATCCGTTTCCAC 59.478 55.000 0.00 0.00 33.04 4.02
1817 3025 0.109532 TGGCTGTGAATCCGTTTCCA 59.890 50.000 0.00 0.00 33.04 3.53
1818 3026 0.804989 CTGGCTGTGAATCCGTTTCC 59.195 55.000 0.00 0.00 33.04 3.13
1819 3027 1.523758 ACTGGCTGTGAATCCGTTTC 58.476 50.000 0.00 0.00 34.72 2.78
1820 3028 3.725754 ACTGGCTGTGAATCCGTTT 57.274 47.368 0.00 0.00 0.00 3.60
1836 3044 1.611419 CACCCATCCTGCCATCACT 59.389 57.895 0.00 0.00 0.00 3.41
1870 3078 2.745308 CCCATCCTGCCATCACCGA 61.745 63.158 0.00 0.00 0.00 4.69
1889 3097 1.402968 CCGGCTGTGAATCCAATTCTG 59.597 52.381 0.00 0.00 39.96 3.02
1890 3098 1.004745 ACCGGCTGTGAATCCAATTCT 59.995 47.619 0.00 0.00 39.96 2.40
2033 3241 1.888736 GTCCCTCTTTACTCGCGGT 59.111 57.895 6.13 5.79 0.00 5.68
2060 3268 1.118965 TCTTCCCCTTGAGCGTGACA 61.119 55.000 0.00 0.00 0.00 3.58
2240 3448 4.163441 TCCTTTCACCTTCACAATGACA 57.837 40.909 0.00 0.00 0.00 3.58
2306 3514 1.698067 TTTCACCCCGGAAACCGTCT 61.698 55.000 0.73 0.00 46.80 4.18
2321 3529 1.343465 GACGGGGTTCTCACTCTTTCA 59.657 52.381 0.00 0.00 0.00 2.69
2510 3719 5.614308 TCCAGGCTCATGACATTATTACAG 58.386 41.667 0.00 0.00 0.00 2.74
2646 3867 1.160137 CAAAAGGAGAGGGAACTGCG 58.840 55.000 0.00 0.00 44.43 5.18
2755 3976 3.864540 GCAACCCTTCCAAATTACTTGCC 60.865 47.826 0.00 0.00 33.27 4.52
2921 4151 7.559533 TGCATATTTTGGCCTATAAAGAGTTCA 59.440 33.333 3.32 0.00 0.00 3.18
2922 4152 7.940850 TGCATATTTTGGCCTATAAAGAGTTC 58.059 34.615 3.32 0.00 0.00 3.01
2930 4160 6.003950 GGAGTTCTGCATATTTTGGCCTATA 58.996 40.000 3.32 0.00 0.00 1.31
2931 4161 4.829492 GGAGTTCTGCATATTTTGGCCTAT 59.171 41.667 3.32 0.00 0.00 2.57
2994 4227 6.521151 AATTAACTGCAAAAGGGATCTCAG 57.479 37.500 0.00 0.00 0.00 3.35
3101 4361 4.822026 ACTACATTCTTCTCCGAACCAAG 58.178 43.478 0.00 0.00 0.00 3.61
3109 4369 7.556844 TCCTTCACAATACTACATTCTTCTCC 58.443 38.462 0.00 0.00 0.00 3.71
3204 4497 8.941995 AAATCATGGAATCATTCATCTCATCT 57.058 30.769 0.00 0.00 0.00 2.90
3235 4587 7.205992 ACTGATATAATGTGCTACACTGTCAG 58.794 38.462 0.00 0.00 35.11 3.51
3255 4607 9.372369 GTTGTTAGCAATTCTAGAGTAACTGAT 57.628 33.333 0.00 0.00 36.92 2.90
3256 4608 8.585881 AGTTGTTAGCAATTCTAGAGTAACTGA 58.414 33.333 0.00 0.00 36.92 3.41
3257 4609 8.651588 CAGTTGTTAGCAATTCTAGAGTAACTG 58.348 37.037 9.19 9.19 36.92 3.16
3258 4610 7.332182 GCAGTTGTTAGCAATTCTAGAGTAACT 59.668 37.037 0.00 0.00 36.92 2.24
3260 4612 7.386851 AGCAGTTGTTAGCAATTCTAGAGTAA 58.613 34.615 0.00 0.00 36.92 2.24
3262 4614 5.799213 AGCAGTTGTTAGCAATTCTAGAGT 58.201 37.500 0.00 0.00 36.92 3.24
3263 4615 6.734104 AAGCAGTTGTTAGCAATTCTAGAG 57.266 37.500 0.00 0.00 36.92 2.43
3264 4616 7.824289 ACATAAGCAGTTGTTAGCAATTCTAGA 59.176 33.333 0.00 0.00 36.92 2.43
3265 4617 7.978982 ACATAAGCAGTTGTTAGCAATTCTAG 58.021 34.615 0.00 0.00 36.92 2.43
3266 4618 7.921786 ACATAAGCAGTTGTTAGCAATTCTA 57.078 32.000 0.00 0.00 36.92 2.10
3267 4619 6.824305 ACATAAGCAGTTGTTAGCAATTCT 57.176 33.333 0.00 0.00 36.92 2.40
3268 4620 7.083858 TGAACATAAGCAGTTGTTAGCAATTC 58.916 34.615 0.00 0.00 36.25 2.17
3277 4629 7.864108 TGCTATTATGAACATAAGCAGTTGT 57.136 32.000 13.67 0.70 36.79 3.32
3308 4660 4.733405 GCTTTCGGTCTAAGTTTTTGTGTG 59.267 41.667 0.00 0.00 0.00 3.82
3310 4662 4.915704 TGCTTTCGGTCTAAGTTTTTGTG 58.084 39.130 0.00 0.00 0.00 3.33
3312 4664 6.899114 ACTATGCTTTCGGTCTAAGTTTTTG 58.101 36.000 0.00 0.00 0.00 2.44
3313 4665 7.506328 AACTATGCTTTCGGTCTAAGTTTTT 57.494 32.000 0.00 0.00 0.00 1.94
3316 4668 6.592994 GGTTAACTATGCTTTCGGTCTAAGTT 59.407 38.462 5.42 0.00 0.00 2.66
3317 4669 6.104665 GGTTAACTATGCTTTCGGTCTAAGT 58.895 40.000 5.42 0.00 0.00 2.24
3318 4670 5.522824 GGGTTAACTATGCTTTCGGTCTAAG 59.477 44.000 5.42 0.00 0.00 2.18
3319 4671 5.046448 TGGGTTAACTATGCTTTCGGTCTAA 60.046 40.000 5.42 0.00 0.00 2.10
3320 4672 4.467082 TGGGTTAACTATGCTTTCGGTCTA 59.533 41.667 5.42 0.00 0.00 2.59
3321 4673 3.262405 TGGGTTAACTATGCTTTCGGTCT 59.738 43.478 5.42 0.00 0.00 3.85
3322 4674 3.602483 TGGGTTAACTATGCTTTCGGTC 58.398 45.455 5.42 0.00 0.00 4.79
3323 4675 3.262405 TCTGGGTTAACTATGCTTTCGGT 59.738 43.478 5.42 0.00 0.00 4.69
3324 4676 3.621715 GTCTGGGTTAACTATGCTTTCGG 59.378 47.826 5.42 0.00 0.00 4.30
3325 4677 4.504858 AGTCTGGGTTAACTATGCTTTCG 58.495 43.478 5.42 0.00 0.00 3.46
3346 4698 4.739716 GTGTTGTCTGCATTTTGGTTGTAG 59.260 41.667 0.00 0.00 0.00 2.74
3400 4753 4.591202 CATTCATGTACAAGCCGAATGAC 58.409 43.478 23.05 0.00 43.55 3.06


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

AutoCloner maintained by Alex Coulton.