Multiple sequence alignment - TraesCS2D01G407300

Loading Multiple Alignment...

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 TraesCS2D01G407300 chr2D 100.000 3401 0 0 1 3401 522688366 522691766 0.000000e+00 6281.0
1 TraesCS2D01G407300 chr2D 91.923 1461 114 2 990 2448 522749232 522750690 0.000000e+00 2041.0
2 TraesCS2D01G407300 chr2D 90.066 1520 141 8 906 2420 577609484 577607970 0.000000e+00 1962.0
3 TraesCS2D01G407300 chr2D 78.673 1402 266 22 1023 2403 522629719 522631108 0.000000e+00 902.0
4 TraesCS2D01G407300 chr2D 80.556 612 102 11 25 630 115150722 115150122 4.000000e-124 455.0
5 TraesCS2D01G407300 chr2D 87.560 209 10 4 2450 2656 522726235 522726429 9.490000e-56 228.0
6 TraesCS2D01G407300 chr2B 95.199 1708 72 4 742 2449 615735773 615737470 0.000000e+00 2691.0
7 TraesCS2D01G407300 chr2B 92.181 1458 114 0 991 2448 615788433 615789890 0.000000e+00 2061.0
8 TraesCS2D01G407300 chr2B 90.664 1521 133 7 906 2420 694943983 694945500 0.000000e+00 2013.0
9 TraesCS2D01G407300 chr2B 81.641 1389 235 14 1024 2402 615797455 615798833 0.000000e+00 1134.0
10 TraesCS2D01G407300 chr2B 82.166 757 103 23 2656 3401 585941907 585941172 3.730000e-174 621.0
11 TraesCS2D01G407300 chr2B 81.046 612 100 11 25 630 165779544 165778943 1.100000e-129 473.0
12 TraesCS2D01G407300 chr2B 80.229 612 103 12 25 630 165929224 165928625 8.660000e-121 444.0
13 TraesCS2D01G407300 chr2B 85.714 343 40 7 31 371 615734943 615735278 1.500000e-93 353.0
14 TraesCS2D01G407300 chr2B 83.624 287 44 2 339 624 99495278 99495562 2.010000e-67 267.0
15 TraesCS2D01G407300 chr2B 88.325 197 12 2 2453 2649 743320707 743320522 3.410000e-55 226.0
16 TraesCS2D01G407300 chr2B 87.019 208 15 2 2450 2657 615783954 615784149 1.230000e-54 224.0
17 TraesCS2D01G407300 chr2A 93.533 1732 96 5 930 2656 667959380 667961100 0.000000e+00 2564.0
18 TraesCS2D01G407300 chr2A 90.714 1443 133 1 979 2420 715806770 715808212 0.000000e+00 1921.0
19 TraesCS2D01G407300 chr2A 81.052 1388 237 20 1028 2402 667964302 667965676 0.000000e+00 1083.0
20 TraesCS2D01G407300 chr2A 78.914 1399 270 19 1022 2403 667942226 667943616 0.000000e+00 926.0
21 TraesCS2D01G407300 chr2A 86.424 604 47 15 22 625 667950344 667950912 2.230000e-176 628.0
22 TraesCS2D01G407300 chr2A 79.772 613 104 13 25 628 116832356 116831755 8.720000e-116 427.0
23 TraesCS2D01G407300 chr2A 78.583 593 107 11 25 608 116699488 116698907 1.150000e-99 374.0
24 TraesCS2D01G407300 chr3D 91.779 742 54 6 2656 3395 17881779 17882515 0.000000e+00 1026.0
25 TraesCS2D01G407300 chr3D 90.476 63 5 1 2656 2718 580334795 580334856 7.820000e-12 82.4
26 TraesCS2D01G407300 chr3D 90.741 54 4 1 2656 2709 600164675 600164623 1.690000e-08 71.3
27 TraesCS2D01G407300 chr7A 88.874 746 68 9 2656 3397 442278639 442277905 0.000000e+00 904.0
28 TraesCS2D01G407300 chr7A 89.348 460 49 0 2942 3401 634911865 634912324 2.280000e-161 579.0
29 TraesCS2D01G407300 chr7A 79.479 614 109 10 25 634 30157977 30157377 1.460000e-113 420.0
30 TraesCS2D01G407300 chr7A 77.905 611 112 17 25 628 421486691 421487285 3.230000e-95 359.0
31 TraesCS2D01G407300 chr7A 93.846 65 2 1 23 87 363982479 363982541 2.790000e-16 97.1
32 TraesCS2D01G407300 chr3A 87.567 748 81 6 2655 3397 639330525 639331265 0.000000e+00 856.0
33 TraesCS2D01G407300 chr3A 78.105 612 104 24 22 625 736102150 736102739 8.970000e-96 361.0
34 TraesCS2D01G407300 chr3A 77.381 420 74 14 25 442 492185558 492185158 2.640000e-56 230.0
35 TraesCS2D01G407300 chr7D 86.667 750 80 14 2656 3395 576064848 576064109 0.000000e+00 813.0
36 TraesCS2D01G407300 chr7D 92.593 54 2 2 2656 2709 176172894 176172945 3.640000e-10 76.8
37 TraesCS2D01G407300 chr6A 85.901 766 90 13 2641 3401 34679718 34680470 0.000000e+00 800.0
38 TraesCS2D01G407300 chr6A 78.818 609 114 10 24 628 73294518 73295115 2.460000e-106 396.0
39 TraesCS2D01G407300 chr1D 84.176 752 106 12 2656 3401 276728820 276729564 0.000000e+00 717.0
40 TraesCS2D01G407300 chr4D 81.389 763 120 16 2656 3401 339322867 339323624 1.350000e-168 603.0
41 TraesCS2D01G407300 chr4D 81.538 325 47 10 311 629 50807587 50807270 4.360000e-64 255.0
42 TraesCS2D01G407300 chr6D 78.748 607 109 17 24 624 57993412 57994004 4.120000e-104 388.0
43 TraesCS2D01G407300 chr6B 77.629 599 110 14 42 630 458572362 458571778 3.250000e-90 342.0
44 TraesCS2D01G407300 chr4A 79.392 296 51 8 22 315 188613554 188613267 2.070000e-47 200.0
45 TraesCS2D01G407300 chr3B 74.092 606 96 35 22 624 10723299 10723846 3.460000e-45 193.0
46 TraesCS2D01G407300 chr5A 88.148 135 12 4 2517 2649 550719872 550720004 1.260000e-34 158.0
47 TraesCS2D01G407300 chr5B 87.313 134 14 3 2517 2649 530263131 530263262 2.110000e-32 150.0
48 TraesCS2D01G407300 chr1B 89.706 68 5 2 2654 2721 554510453 554510518 6.050000e-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 TraesCS2D01G407300 chr2D 522688366 522691766 3400 False 6281.0 6281 100.0000 1 3401 1 chr2D.!!$F2 3400
1 TraesCS2D01G407300 chr2D 522749232 522750690 1458 False 2041.0 2041 91.9230 990 2448 1 chr2D.!!$F4 1458
2 TraesCS2D01G407300 chr2D 577607970 577609484 1514 True 1962.0 1962 90.0660 906 2420 1 chr2D.!!$R2 1514
3 TraesCS2D01G407300 chr2D 522629719 522631108 1389 False 902.0 902 78.6730 1023 2403 1 chr2D.!!$F1 1380
4 TraesCS2D01G407300 chr2D 115150122 115150722 600 True 455.0 455 80.5560 25 630 1 chr2D.!!$R1 605
5 TraesCS2D01G407300 chr2B 615788433 615789890 1457 False 2061.0 2061 92.1810 991 2448 1 chr2B.!!$F3 1457
6 TraesCS2D01G407300 chr2B 694943983 694945500 1517 False 2013.0 2013 90.6640 906 2420 1 chr2B.!!$F5 1514
7 TraesCS2D01G407300 chr2B 615734943 615737470 2527 False 1522.0 2691 90.4565 31 2449 2 chr2B.!!$F6 2418
8 TraesCS2D01G407300 chr2B 615797455 615798833 1378 False 1134.0 1134 81.6410 1024 2402 1 chr2B.!!$F4 1378
9 TraesCS2D01G407300 chr2B 585941172 585941907 735 True 621.0 621 82.1660 2656 3401 1 chr2B.!!$R3 745
10 TraesCS2D01G407300 chr2B 165778943 165779544 601 True 473.0 473 81.0460 25 630 1 chr2B.!!$R1 605
11 TraesCS2D01G407300 chr2B 165928625 165929224 599 True 444.0 444 80.2290 25 630 1 chr2B.!!$R2 605
12 TraesCS2D01G407300 chr2A 715806770 715808212 1442 False 1921.0 1921 90.7140 979 2420 1 chr2A.!!$F3 1441
13 TraesCS2D01G407300 chr2A 667959380 667965676 6296 False 1823.5 2564 87.2925 930 2656 2 chr2A.!!$F4 1726
14 TraesCS2D01G407300 chr2A 667942226 667943616 1390 False 926.0 926 78.9140 1022 2403 1 chr2A.!!$F1 1381
15 TraesCS2D01G407300 chr2A 667950344 667950912 568 False 628.0 628 86.4240 22 625 1 chr2A.!!$F2 603
16 TraesCS2D01G407300 chr2A 116831755 116832356 601 True 427.0 427 79.7720 25 628 1 chr2A.!!$R2 603
17 TraesCS2D01G407300 chr2A 116698907 116699488 581 True 374.0 374 78.5830 25 608 1 chr2A.!!$R1 583
18 TraesCS2D01G407300 chr3D 17881779 17882515 736 False 1026.0 1026 91.7790 2656 3395 1 chr3D.!!$F1 739
19 TraesCS2D01G407300 chr7A 442277905 442278639 734 True 904.0 904 88.8740 2656 3397 1 chr7A.!!$R2 741
20 TraesCS2D01G407300 chr7A 30157377 30157977 600 True 420.0 420 79.4790 25 634 1 chr7A.!!$R1 609
21 TraesCS2D01G407300 chr7A 421486691 421487285 594 False 359.0 359 77.9050 25 628 1 chr7A.!!$F2 603
22 TraesCS2D01G407300 chr3A 639330525 639331265 740 False 856.0 856 87.5670 2655 3397 1 chr3A.!!$F1 742
23 TraesCS2D01G407300 chr3A 736102150 736102739 589 False 361.0 361 78.1050 22 625 1 chr3A.!!$F2 603
24 TraesCS2D01G407300 chr7D 576064109 576064848 739 True 813.0 813 86.6670 2656 3395 1 chr7D.!!$R1 739
25 TraesCS2D01G407300 chr6A 34679718 34680470 752 False 800.0 800 85.9010 2641 3401 1 chr6A.!!$F1 760
26 TraesCS2D01G407300 chr6A 73294518 73295115 597 False 396.0 396 78.8180 24 628 1 chr6A.!!$F2 604
27 TraesCS2D01G407300 chr1D 276728820 276729564 744 False 717.0 717 84.1760 2656 3401 1 chr1D.!!$F1 745
28 TraesCS2D01G407300 chr4D 339322867 339323624 757 False 603.0 603 81.3890 2656 3401 1 chr4D.!!$F1 745
29 TraesCS2D01G407300 chr6D 57993412 57994004 592 False 388.0 388 78.7480 24 624 1 chr6D.!!$F1 600
30 TraesCS2D01G407300 chr6B 458571778 458572362 584 True 342.0 342 77.6290 42 630 1 chr6B.!!$R1 588

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
915 1105 0.037303 CTCCTTTGCTGGCTTCTGGA 59.963 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 2749 0.109412 GCTTCACATCAGCAACTGCC 60.109 55.0 0.0 0.0 43.38 4.85 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
17 18 3.880846 GCTTGGCTGGATTCCGCG 61.881 66.667 0.00 0.00 0.00 6.46
18 19 2.436646 CTTGGCTGGATTCCGCGT 60.437 61.111 4.92 0.00 0.00 6.01
19 20 2.435938 TTGGCTGGATTCCGCGTC 60.436 61.111 4.92 0.00 0.00 5.19
20 21 3.247056 TTGGCTGGATTCCGCGTCA 62.247 57.895 4.92 4.66 0.00 4.35
146 148 2.514803 GAATGCCTGTAAGTGGTGGTT 58.485 47.619 0.00 0.00 0.00 3.67
147 149 1.909700 ATGCCTGTAAGTGGTGGTTG 58.090 50.000 0.00 0.00 0.00 3.77
148 150 0.179004 TGCCTGTAAGTGGTGGTTGG 60.179 55.000 0.00 0.00 0.00 3.77
149 151 0.179001 GCCTGTAAGTGGTGGTTGGT 60.179 55.000 0.00 0.00 0.00 3.67
150 152 1.604604 CCTGTAAGTGGTGGTTGGTG 58.395 55.000 0.00 0.00 0.00 4.17
151 153 1.604604 CTGTAAGTGGTGGTTGGTGG 58.395 55.000 0.00 0.00 0.00 4.61
152 154 0.920438 TGTAAGTGGTGGTTGGTGGT 59.080 50.000 0.00 0.00 0.00 4.16
183 185 0.249489 CCTTCCGTCACGATGATCCC 60.249 60.000 0.00 0.00 0.00 3.85
593 735 4.335594 CGAAACATGATCTCCCCCTTTAAC 59.664 45.833 0.00 0.00 0.00 2.01
609 752 7.088272 CCCCTTTAACGAGATTTGGTTTTTAG 58.912 38.462 0.00 0.00 0.00 1.85
616 759 5.773176 ACGAGATTTGGTTTTTAGTGGGAAT 59.227 36.000 0.00 0.00 0.00 3.01
631 774 9.581289 TTTAGTGGGAATGAGAAAAATCAGTAA 57.419 29.630 0.00 0.00 31.44 2.24
632 775 7.693969 AGTGGGAATGAGAAAAATCAGTAAG 57.306 36.000 0.00 0.00 31.44 2.34
635 778 7.607991 GTGGGAATGAGAAAAATCAGTAAGAGA 59.392 37.037 0.00 0.00 31.44 3.10
636 779 8.331740 TGGGAATGAGAAAAATCAGTAAGAGAT 58.668 33.333 0.00 0.00 31.44 2.75
637 780 8.835439 GGGAATGAGAAAAATCAGTAAGAGATC 58.165 37.037 0.00 0.00 31.44 2.75
643 833 9.308318 GAGAAAAATCAGTAAGAGATCTGGTAC 57.692 37.037 0.00 1.90 33.13 3.34
644 834 8.261522 AGAAAAATCAGTAAGAGATCTGGTACC 58.738 37.037 4.43 4.43 33.13 3.34
648 838 3.068873 CAGTAAGAGATCTGGTACCAGGC 59.931 52.174 35.94 27.94 43.75 4.85
661 851 1.446016 ACCAGGCTACCAACTTTCCT 58.554 50.000 0.00 0.00 0.00 3.36
666 856 4.263331 CCAGGCTACCAACTTTCCTTTCTA 60.263 45.833 0.00 0.00 0.00 2.10
667 857 5.501156 CAGGCTACCAACTTTCCTTTCTAT 58.499 41.667 0.00 0.00 0.00 1.98
668 858 5.946377 CAGGCTACCAACTTTCCTTTCTATT 59.054 40.000 0.00 0.00 0.00 1.73
669 859 7.110155 CAGGCTACCAACTTTCCTTTCTATTA 58.890 38.462 0.00 0.00 0.00 0.98
670 860 7.610305 CAGGCTACCAACTTTCCTTTCTATTAA 59.390 37.037 0.00 0.00 0.00 1.40
671 861 7.610692 AGGCTACCAACTTTCCTTTCTATTAAC 59.389 37.037 0.00 0.00 0.00 2.01
672 862 7.610692 GGCTACCAACTTTCCTTTCTATTAACT 59.389 37.037 0.00 0.00 0.00 2.24
675 865 8.405418 ACCAACTTTCCTTTCTATTAACTTCC 57.595 34.615 0.00 0.00 0.00 3.46
676 866 7.450634 ACCAACTTTCCTTTCTATTAACTTCCC 59.549 37.037 0.00 0.00 0.00 3.97
677 867 7.093902 CCAACTTTCCTTTCTATTAACTTCCCC 60.094 40.741 0.00 0.00 0.00 4.81
678 868 7.344599 ACTTTCCTTTCTATTAACTTCCCCT 57.655 36.000 0.00 0.00 0.00 4.79
679 869 7.766628 ACTTTCCTTTCTATTAACTTCCCCTT 58.233 34.615 0.00 0.00 0.00 3.95
680 870 8.232412 ACTTTCCTTTCTATTAACTTCCCCTTT 58.768 33.333 0.00 0.00 0.00 3.11
681 871 8.645814 TTTCCTTTCTATTAACTTCCCCTTTC 57.354 34.615 0.00 0.00 0.00 2.62
682 872 6.728411 TCCTTTCTATTAACTTCCCCTTTCC 58.272 40.000 0.00 0.00 0.00 3.13
683 873 5.892119 CCTTTCTATTAACTTCCCCTTTCCC 59.108 44.000 0.00 0.00 0.00 3.97
685 875 6.730001 TTCTATTAACTTCCCCTTTCCCTT 57.270 37.500 0.00 0.00 0.00 3.95
686 876 7.834100 TTCTATTAACTTCCCCTTTCCCTTA 57.166 36.000 0.00 0.00 0.00 2.69
687 877 7.204243 TCTATTAACTTCCCCTTTCCCTTAC 57.796 40.000 0.00 0.00 0.00 2.34
688 878 2.873094 AACTTCCCCTTTCCCTTACG 57.127 50.000 0.00 0.00 0.00 3.18
689 879 2.034436 ACTTCCCCTTTCCCTTACGA 57.966 50.000 0.00 0.00 0.00 3.43
690 880 1.907255 ACTTCCCCTTTCCCTTACGAG 59.093 52.381 0.00 0.00 0.00 4.18
691 881 1.907255 CTTCCCCTTTCCCTTACGAGT 59.093 52.381 0.00 0.00 0.00 4.18
692 882 2.925966 TCCCCTTTCCCTTACGAGTA 57.074 50.000 0.00 0.00 0.00 2.59
693 883 2.743553 TCCCCTTTCCCTTACGAGTAG 58.256 52.381 0.00 0.00 0.00 2.57
694 884 2.312741 TCCCCTTTCCCTTACGAGTAGA 59.687 50.000 0.00 0.00 0.00 2.59
695 885 2.694109 CCCCTTTCCCTTACGAGTAGAG 59.306 54.545 0.00 0.00 0.00 2.43
696 886 3.626729 CCCCTTTCCCTTACGAGTAGAGA 60.627 52.174 0.00 0.00 0.00 3.10
697 887 4.216708 CCCTTTCCCTTACGAGTAGAGAT 58.783 47.826 0.00 0.00 0.00 2.75
698 888 4.278919 CCCTTTCCCTTACGAGTAGAGATC 59.721 50.000 0.00 0.00 0.00 2.75
699 889 5.134661 CCTTTCCCTTACGAGTAGAGATCT 58.865 45.833 0.00 0.00 0.00 2.75
700 890 5.009210 CCTTTCCCTTACGAGTAGAGATCTG 59.991 48.000 0.00 0.00 0.00 2.90
713 903 8.714179 CGAGTAGAGATCTGGTAAGTGTATTAG 58.286 40.741 0.00 0.00 0.00 1.73
715 905 9.563748 AGTAGAGATCTGGTAAGTGTATTAGTC 57.436 37.037 0.00 0.00 0.00 2.59
716 906 7.499321 AGAGATCTGGTAAGTGTATTAGTCG 57.501 40.000 0.00 0.00 0.00 4.18
717 907 6.487331 AGAGATCTGGTAAGTGTATTAGTCGG 59.513 42.308 0.00 0.00 0.00 4.79
718 908 4.644103 TCTGGTAAGTGTATTAGTCGGC 57.356 45.455 0.00 0.00 0.00 5.54
719 909 3.065786 TCTGGTAAGTGTATTAGTCGGCG 59.934 47.826 0.00 0.00 0.00 6.46
720 910 3.016031 TGGTAAGTGTATTAGTCGGCGA 58.984 45.455 4.99 4.99 0.00 5.54
721 911 3.443329 TGGTAAGTGTATTAGTCGGCGAA 59.557 43.478 12.92 0.00 0.00 4.70
722 912 3.793492 GGTAAGTGTATTAGTCGGCGAAC 59.207 47.826 12.92 6.42 0.00 3.95
723 913 3.863142 AAGTGTATTAGTCGGCGAACT 57.137 42.857 12.92 13.96 0.00 3.01
724 914 3.146618 AGTGTATTAGTCGGCGAACTG 57.853 47.619 12.92 0.00 0.00 3.16
725 915 1.587034 GTGTATTAGTCGGCGAACTGC 59.413 52.381 12.92 0.00 45.38 4.40
736 926 4.814294 GAACTGCGACCCGGCGAT 62.814 66.667 9.30 0.00 35.06 4.58
737 927 4.388499 AACTGCGACCCGGCGATT 62.388 61.111 9.30 0.00 35.06 3.34
770 960 3.812053 GAGCCATGACGATAAGCATTTCT 59.188 43.478 0.00 0.00 0.00 2.52
782 972 6.694411 CGATAAGCATTTCTTGGAAGATTTGG 59.306 38.462 0.00 0.00 36.25 3.28
792 982 8.189378 TTCTTGGAAGATTTGGCTTGGTAAGC 62.189 42.308 5.02 5.02 43.41 3.09
809 999 4.921515 GGTAAGCGTATTATCTGCGAATCA 59.078 41.667 0.00 0.00 34.56 2.57
811 1001 5.769967 AAGCGTATTATCTGCGAATCATC 57.230 39.130 0.00 0.00 34.56 2.92
834 1024 4.868171 CGTCGACCCAGAGAAAATAAATGA 59.132 41.667 10.58 0.00 0.00 2.57
859 1049 1.065854 AGATTTGGAGCTTCACCCGAG 60.066 52.381 0.00 0.00 0.00 4.63
872 1062 0.962356 ACCCGAGATTTGCTGGCTTG 60.962 55.000 0.00 0.00 0.00 4.01
885 1075 1.526917 GGCTTGCACTGTGACCTGT 60.527 57.895 12.86 0.00 0.00 4.00
891 1081 1.510480 GCACTGTGACCTGTTCTGCC 61.510 60.000 12.86 0.00 0.00 4.85
893 1083 0.546122 ACTGTGACCTGTTCTGCCAA 59.454 50.000 0.00 0.00 0.00 4.52
901 1091 1.072965 CCTGTTCTGCCAACTCTCCTT 59.927 52.381 0.00 0.00 0.00 3.36
915 1105 0.037303 CTCCTTTGCTGGCTTCTGGA 59.963 55.000 0.00 0.00 0.00 3.86
955 1152 1.686325 ATAGCCCGCCTACACTGTGG 61.686 60.000 13.09 0.00 0.00 4.17
972 1169 0.171231 TGGCGTTCAGTCTCATCTCG 59.829 55.000 0.00 0.00 0.00 4.04
1006 1205 1.377202 CACAGAACGGTGATGGGGG 60.377 63.158 0.00 0.00 41.32 5.40
1968 2181 1.668151 GAGCCGCCACGAGAAGTTT 60.668 57.895 0.00 0.00 0.00 2.66
2148 2361 3.726558 ATGGCCCATGCACTGCGAT 62.727 57.895 0.00 0.00 40.13 4.58
2272 2485 0.397675 AGTCATCGAGGAGGCCATGA 60.398 55.000 5.01 0.35 0.00 3.07
2331 2544 3.833645 CTCGGGGATGCCGTTCGA 61.834 66.667 0.00 0.00 0.00 3.71
2604 2817 5.532779 ACTTCTTTTAGGTTCTTTCTGCTGG 59.467 40.000 0.00 0.00 0.00 4.85
2617 2830 3.586470 TCTGCTGGTAAAAGTTGGGAA 57.414 42.857 0.00 0.00 0.00 3.97
2636 2849 3.305199 GGAATGCCATAGAGATGCTTTGC 60.305 47.826 0.00 0.00 0.00 3.68
2722 4292 1.546773 GGGGCAACACAAGTCACCATA 60.547 52.381 0.00 0.00 42.67 2.74
2895 6121 4.279671 CCGAACTAAGCCAGAGAGTATCAT 59.720 45.833 0.00 0.00 37.82 2.45
2929 6460 1.070289 ACCACCGGTCTCTTGTTCTTC 59.930 52.381 2.59 0.00 0.00 2.87
2931 6462 2.610727 CCACCGGTCTCTTGTTCTTCTC 60.611 54.545 2.59 0.00 0.00 2.87
2946 6493 3.520696 TCTTCTCTCCCTCACCAATCAA 58.479 45.455 0.00 0.00 0.00 2.57
2953 6500 1.453155 CCTCACCAATCAACCCGAAG 58.547 55.000 0.00 0.00 0.00 3.79
3037 6732 2.223200 CTGAGCAGCTCGCCTCTTCA 62.223 60.000 17.81 0.00 44.04 3.02
3044 6739 2.010582 GCTCGCCTCTTCACCGATCT 62.011 60.000 0.00 0.00 0.00 2.75
3067 6901 2.816958 CTGAAGGCAGCGTCGCAT 60.817 61.111 21.09 1.30 34.95 4.73
3120 6955 4.462834 TCTTCCATTGATGTAGAGACACGT 59.537 41.667 0.00 0.00 38.76 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.880846 CGCGGAATCCAGCCAAGC 61.881 66.667 0.00 0.00 0.00 4.01
1 2 2.436646 ACGCGGAATCCAGCCAAG 60.437 61.111 12.47 0.00 0.00 3.61
2 3 2.435938 GACGCGGAATCCAGCCAA 60.436 61.111 12.47 0.00 0.00 4.52
3 4 2.923426 GATGACGCGGAATCCAGCCA 62.923 60.000 12.47 0.00 0.00 4.75
4 5 2.203070 ATGACGCGGAATCCAGCC 60.203 61.111 12.47 0.00 0.00 4.85
5 6 2.247437 GGATGACGCGGAATCCAGC 61.247 63.158 27.79 13.59 41.78 4.85
6 7 0.179073 AAGGATGACGCGGAATCCAG 60.179 55.000 31.59 0.00 44.17 3.86
8 9 1.865340 GTTAAGGATGACGCGGAATCC 59.135 52.381 26.32 26.32 42.39 3.01
9 10 1.521423 CGTTAAGGATGACGCGGAATC 59.479 52.381 12.47 12.92 31.57 2.52
10 11 1.135527 TCGTTAAGGATGACGCGGAAT 59.864 47.619 12.47 2.60 38.33 3.01
11 12 0.527113 TCGTTAAGGATGACGCGGAA 59.473 50.000 12.47 0.00 38.33 4.30
13 14 1.352114 TTTCGTTAAGGATGACGCGG 58.648 50.000 12.47 0.00 38.33 6.46
14 15 3.306166 AGAATTTCGTTAAGGATGACGCG 59.694 43.478 3.53 3.53 38.33 6.01
15 16 4.859629 AGAATTTCGTTAAGGATGACGC 57.140 40.909 0.00 0.00 38.33 5.19
16 17 6.128661 TGTCAAGAATTTCGTTAAGGATGACG 60.129 38.462 16.45 0.71 39.67 4.35
17 18 7.129109 TGTCAAGAATTTCGTTAAGGATGAC 57.871 36.000 15.43 15.43 35.30 3.06
18 19 7.921786 ATGTCAAGAATTTCGTTAAGGATGA 57.078 32.000 0.00 0.00 0.00 2.92
19 20 8.970691 AAATGTCAAGAATTTCGTTAAGGATG 57.029 30.769 0.00 0.00 0.00 3.51
151 153 2.126031 GAAGGCTGGTCGTCGGAC 60.126 66.667 0.00 0.00 42.66 4.79
152 154 3.379445 GGAAGGCTGGTCGTCGGA 61.379 66.667 0.00 0.00 0.00 4.55
288 292 7.500720 TTTCTTATGGACATATGCATCTGTG 57.499 36.000 21.12 12.72 38.04 3.66
564 701 2.352960 GGGAGATCATGTTTCGTGCTTC 59.647 50.000 0.00 0.00 0.00 3.86
571 709 4.335594 CGTTAAAGGGGGAGATCATGTTTC 59.664 45.833 0.00 0.00 0.00 2.78
577 715 3.110293 TCTCGTTAAAGGGGGAGATCA 57.890 47.619 0.00 0.00 31.00 2.92
593 735 5.699097 TTCCCACTAAAAACCAAATCTCG 57.301 39.130 0.00 0.00 0.00 4.04
609 752 7.607991 TCTCTTACTGATTTTTCTCATTCCCAC 59.392 37.037 0.00 0.00 0.00 4.61
616 759 7.911651 ACCAGATCTCTTACTGATTTTTCTCA 58.088 34.615 0.00 0.00 36.38 3.27
631 774 2.425102 GGTAGCCTGGTACCAGATCTCT 60.425 54.545 38.35 28.18 46.30 3.10
632 775 1.964933 GGTAGCCTGGTACCAGATCTC 59.035 57.143 38.35 24.64 46.30 2.75
643 833 2.586648 AAGGAAAGTTGGTAGCCTGG 57.413 50.000 0.00 0.00 0.00 4.45
644 834 3.756117 AGAAAGGAAAGTTGGTAGCCTG 58.244 45.455 0.00 0.00 0.00 4.85
661 851 6.730001 AGGGAAAGGGGAAGTTAATAGAAA 57.270 37.500 0.00 0.00 0.00 2.52
666 856 4.537288 TCGTAAGGGAAAGGGGAAGTTAAT 59.463 41.667 0.00 0.00 38.47 1.40
667 857 3.909364 TCGTAAGGGAAAGGGGAAGTTAA 59.091 43.478 0.00 0.00 38.47 2.01
668 858 3.516700 CTCGTAAGGGAAAGGGGAAGTTA 59.483 47.826 0.00 0.00 44.69 2.24
669 859 2.305052 CTCGTAAGGGAAAGGGGAAGTT 59.695 50.000 0.00 0.00 44.69 2.66
670 860 1.907255 CTCGTAAGGGAAAGGGGAAGT 59.093 52.381 0.00 0.00 44.69 3.01
671 861 1.907255 ACTCGTAAGGGAAAGGGGAAG 59.093 52.381 0.00 0.00 44.69 3.46
672 862 2.034436 ACTCGTAAGGGAAAGGGGAA 57.966 50.000 0.00 0.00 44.69 3.97
674 864 2.694109 CTCTACTCGTAAGGGAAAGGGG 59.306 54.545 0.00 0.00 44.69 4.79
675 865 3.629087 TCTCTACTCGTAAGGGAAAGGG 58.371 50.000 0.00 0.00 44.69 3.95
676 866 5.009210 CAGATCTCTACTCGTAAGGGAAAGG 59.991 48.000 0.00 0.00 44.69 3.11
677 867 5.009210 CCAGATCTCTACTCGTAAGGGAAAG 59.991 48.000 0.00 0.00 44.69 2.62
678 868 4.888239 CCAGATCTCTACTCGTAAGGGAAA 59.112 45.833 0.00 0.00 44.69 3.13
679 869 4.079901 ACCAGATCTCTACTCGTAAGGGAA 60.080 45.833 0.00 0.00 44.69 3.97
680 870 3.458857 ACCAGATCTCTACTCGTAAGGGA 59.541 47.826 0.00 0.00 44.69 4.20
682 872 6.017770 CACTTACCAGATCTCTACTCGTAAGG 60.018 46.154 13.56 5.90 36.90 2.69
683 873 6.539464 ACACTTACCAGATCTCTACTCGTAAG 59.461 42.308 0.00 0.00 37.99 2.34
685 875 5.987098 ACACTTACCAGATCTCTACTCGTA 58.013 41.667 0.00 0.00 0.00 3.43
686 876 4.846040 ACACTTACCAGATCTCTACTCGT 58.154 43.478 0.00 0.00 0.00 4.18
687 877 7.499321 AATACACTTACCAGATCTCTACTCG 57.501 40.000 0.00 0.00 0.00 4.18
688 878 9.563748 ACTAATACACTTACCAGATCTCTACTC 57.436 37.037 0.00 0.00 0.00 2.59
689 879 9.563748 GACTAATACACTTACCAGATCTCTACT 57.436 37.037 0.00 0.00 0.00 2.57
690 880 8.497554 CGACTAATACACTTACCAGATCTCTAC 58.502 40.741 0.00 0.00 0.00 2.59
691 881 7.660617 CCGACTAATACACTTACCAGATCTCTA 59.339 40.741 0.00 0.00 0.00 2.43
692 882 6.487331 CCGACTAATACACTTACCAGATCTCT 59.513 42.308 0.00 0.00 0.00 3.10
693 883 6.670233 CCGACTAATACACTTACCAGATCTC 58.330 44.000 0.00 0.00 0.00 2.75
694 884 5.009811 GCCGACTAATACACTTACCAGATCT 59.990 44.000 0.00 0.00 0.00 2.75
695 885 5.221130 GCCGACTAATACACTTACCAGATC 58.779 45.833 0.00 0.00 0.00 2.75
696 886 4.261489 CGCCGACTAATACACTTACCAGAT 60.261 45.833 0.00 0.00 0.00 2.90
697 887 3.065786 CGCCGACTAATACACTTACCAGA 59.934 47.826 0.00 0.00 0.00 3.86
698 888 3.065786 TCGCCGACTAATACACTTACCAG 59.934 47.826 0.00 0.00 0.00 4.00
699 889 3.016031 TCGCCGACTAATACACTTACCA 58.984 45.455 0.00 0.00 0.00 3.25
700 890 3.698029 TCGCCGACTAATACACTTACC 57.302 47.619 0.00 0.00 0.00 2.85
719 909 4.814294 ATCGCCGGGTCGCAGTTC 62.814 66.667 2.18 0.00 0.00 3.01
720 910 4.388499 AATCGCCGGGTCGCAGTT 62.388 61.111 2.18 0.00 0.00 3.16
732 922 2.020131 CTCAGGTCATGGCAATCGC 58.980 57.895 0.00 0.00 37.44 4.58
733 923 1.442526 GGCTCAGGTCATGGCAATCG 61.443 60.000 0.00 0.00 0.00 3.34
734 924 0.394762 TGGCTCAGGTCATGGCAATC 60.395 55.000 0.00 0.00 33.38 2.67
735 925 0.260816 ATGGCTCAGGTCATGGCAAT 59.739 50.000 0.00 0.00 36.31 3.56
736 926 1.693034 ATGGCTCAGGTCATGGCAA 59.307 52.632 0.00 0.00 36.31 4.52
737 927 3.418687 ATGGCTCAGGTCATGGCA 58.581 55.556 0.00 0.00 36.31 4.92
746 936 2.229675 TGCTTATCGTCATGGCTCAG 57.770 50.000 0.00 0.00 0.00 3.35
782 972 6.747379 TTCGCAGATAATACGCTTACCAAGC 61.747 44.000 0.71 0.71 44.40 4.01
809 999 4.730949 TTATTTTCTCTGGGTCGACGAT 57.269 40.909 9.92 0.00 0.00 3.73
811 1001 4.868171 TCATTTATTTTCTCTGGGTCGACG 59.132 41.667 9.92 0.00 0.00 5.12
812 1002 5.064834 GGTCATTTATTTTCTCTGGGTCGAC 59.935 44.000 7.13 7.13 0.00 4.20
817 1007 4.523083 TCCGGTCATTTATTTTCTCTGGG 58.477 43.478 0.00 0.00 0.00 4.45
820 1010 7.067494 CCAAATCTCCGGTCATTTATTTTCTCT 59.933 37.037 0.00 0.00 0.00 3.10
834 1024 0.984230 TGAAGCTCCAAATCTCCGGT 59.016 50.000 0.00 0.00 0.00 5.28
872 1062 1.510480 GGCAGAACAGGTCACAGTGC 61.510 60.000 0.00 0.00 0.00 4.40
885 1075 1.143684 AGCAAAGGAGAGTTGGCAGAA 59.856 47.619 0.00 0.00 0.00 3.02
891 1081 1.538950 GAAGCCAGCAAAGGAGAGTTG 59.461 52.381 0.00 0.00 0.00 3.16
893 1083 1.063183 AGAAGCCAGCAAAGGAGAGT 58.937 50.000 0.00 0.00 0.00 3.24
901 1091 0.251474 AGCAATCCAGAAGCCAGCAA 60.251 50.000 0.00 0.00 0.00 3.91
955 1152 1.540407 GACGAGATGAGACTGAACGC 58.460 55.000 0.00 0.00 0.00 4.84
972 1169 4.314440 TGGTGCTGAGTGGCCGAC 62.314 66.667 0.00 0.00 0.00 4.79
1338 1537 2.590645 CCGGAGAGGTCCTCGAGA 59.409 66.667 15.71 0.00 42.89 4.04
1968 2181 3.578282 TGTGCTTGGTGAACTCTGATAGA 59.422 43.478 0.00 0.00 0.00 1.98
2272 2485 1.408822 GGCCATTCCTTTGTCGGAGAT 60.409 52.381 0.00 0.00 40.67 2.75
2536 2749 0.109412 GCTTCACATCAGCAACTGCC 60.109 55.000 0.00 0.00 43.38 4.85
2575 2788 7.201741 GCAGAAAGAACCTAAAAGAAGTTCAGT 60.202 37.037 5.50 0.00 41.86 3.41
2617 2830 1.878088 CGCAAAGCATCTCTATGGCAT 59.122 47.619 4.88 4.88 33.38 4.40
2701 3479 1.152756 GGTGACTTGTGTTGCCCCT 60.153 57.895 0.00 0.00 0.00 4.79
2722 4292 3.057456 AGACTCGATCGCTTGTAACAGTT 60.057 43.478 11.09 0.00 0.00 3.16
2895 6121 2.219458 CGGTGGTCGCTCTATTCTCTA 58.781 52.381 0.00 0.00 0.00 2.43
2929 6460 1.065126 GGGTTGATTGGTGAGGGAGAG 60.065 57.143 0.00 0.00 0.00 3.20
2931 6462 0.392998 CGGGTTGATTGGTGAGGGAG 60.393 60.000 0.00 0.00 0.00 4.30
3037 6732 1.698506 CCTTCAGCTCCTAGATCGGT 58.301 55.000 0.00 0.00 0.00 4.69
3088 6923 3.379372 ACATCAATGGAAGATCCTTTGCG 59.621 43.478 16.20 12.91 45.82 4.85
3120 6955 2.110578 TGCGATCTTGGAGAGGATCAA 58.889 47.619 0.00 0.00 38.47 2.57


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

AutoCloner maintained by Alex Coulton.