Multiple sequence alignment - TraesCS2A01G313200

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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 TraesCS2A01G313200 chr2A 100.000 3704 0 0 1 3704 537548485 537552188 0.000000e+00 6841
1 TraesCS2A01G313200 chr2A 83.134 670 92 15 3 660 427335464 427336124 3.190000e-165 592
2 TraesCS2A01G313200 chr2A 86.321 424 46 9 3 415 693439346 693439768 5.640000e-123 451
3 TraesCS2A01G313200 chr2B 95.249 1747 67 9 792 2531 474856145 474857882 0.000000e+00 2752
4 TraesCS2A01G313200 chr2B 92.143 980 54 13 2731 3704 474892221 474893183 0.000000e+00 1362
5 TraesCS2A01G313200 chr2B 82.815 675 81 20 3 660 773943433 773942777 4.150000e-159 571
6 TraesCS2A01G313200 chr2B 96.744 215 7 0 2528 2742 474857974 474858188 3.520000e-95 359
7 TraesCS2A01G313200 chr2B 78.869 336 59 9 335 664 462935053 462935382 2.240000e-52 217
8 TraesCS2A01G313200 chr2D 97.139 1608 35 2 1471 3077 400512083 400513680 0.000000e+00 2704
9 TraesCS2A01G313200 chr2D 94.737 665 29 3 777 1440 400511427 400512086 0.000000e+00 1029
10 TraesCS2A01G313200 chr2D 91.796 646 38 6 3070 3704 400515112 400515753 0.000000e+00 885
11 TraesCS2A01G313200 chr2D 83.242 549 66 18 2 542 246550119 246549589 7.190000e-132 481
12 TraesCS2A01G313200 chr1D 82.794 680 91 16 2 660 404078428 404079102 5.330000e-163 584
13 TraesCS2A01G313200 chr1D 82.923 568 75 18 106 662 454295 454851 3.320000e-135 492
14 TraesCS2A01G313200 chr4D 82.138 683 82 19 2 660 44834890 44835556 1.940000e-152 549
15 TraesCS2A01G313200 chr5B 81.525 682 93 16 3 658 544396278 544396952 7.040000e-147 531
16 TraesCS2A01G313200 chr5B 80.588 680 96 25 2 661 417810146 417809483 3.320000e-135 492
17 TraesCS2A01G313200 chr7D 81.232 698 86 21 2 663 575422729 575422041 4.240000e-144 521
18 TraesCS2A01G313200 chr5D 80.659 698 90 18 2 661 403560919 403561609 1.990000e-137 499
19 TraesCS2A01G313200 chr5D 86.480 429 40 10 3 415 498930404 498929978 4.360000e-124 455
20 TraesCS2A01G313200 chr4A 87.324 426 38 8 2 415 12456252 12455831 1.200000e-129 473
21 TraesCS2A01G313200 chr3A 86.525 423 42 11 2 415 588444090 588444506 5.640000e-123 451
22 TraesCS2A01G313200 chr3A 83.565 359 50 9 305 658 503840974 503841328 9.920000e-86 327


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 TraesCS2A01G313200 chr2A 537548485 537552188 3703 False 6841.000000 6841 100.000000 1 3704 1 chr2A.!!$F2 3703
1 TraesCS2A01G313200 chr2A 427335464 427336124 660 False 592.000000 592 83.134000 3 660 1 chr2A.!!$F1 657
2 TraesCS2A01G313200 chr2B 474856145 474858188 2043 False 1555.500000 2752 95.996500 792 2742 2 chr2B.!!$F3 1950
3 TraesCS2A01G313200 chr2B 474892221 474893183 962 False 1362.000000 1362 92.143000 2731 3704 1 chr2B.!!$F2 973
4 TraesCS2A01G313200 chr2B 773942777 773943433 656 True 571.000000 571 82.815000 3 660 1 chr2B.!!$R1 657
5 TraesCS2A01G313200 chr2D 400511427 400515753 4326 False 1539.333333 2704 94.557333 777 3704 3 chr2D.!!$F1 2927
6 TraesCS2A01G313200 chr2D 246549589 246550119 530 True 481.000000 481 83.242000 2 542 1 chr2D.!!$R1 540
7 TraesCS2A01G313200 chr1D 404078428 404079102 674 False 584.000000 584 82.794000 2 660 1 chr1D.!!$F2 658
8 TraesCS2A01G313200 chr1D 454295 454851 556 False 492.000000 492 82.923000 106 662 1 chr1D.!!$F1 556
9 TraesCS2A01G313200 chr4D 44834890 44835556 666 False 549.000000 549 82.138000 2 660 1 chr4D.!!$F1 658
10 TraesCS2A01G313200 chr5B 544396278 544396952 674 False 531.000000 531 81.525000 3 658 1 chr5B.!!$F1 655
11 TraesCS2A01G313200 chr5B 417809483 417810146 663 True 492.000000 492 80.588000 2 661 1 chr5B.!!$R1 659
12 TraesCS2A01G313200 chr7D 575422041 575422729 688 True 521.000000 521 81.232000 2 663 1 chr7D.!!$R1 661
13 TraesCS2A01G313200 chr5D 403560919 403561609 690 False 499.000000 499 80.659000 2 661 1 chr5D.!!$F1 659

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
690 857 0.038983 TGGGTATGTGACGTGTCGTG 60.039 55.000 0.00 0.00 41.37 4.35 F
693 860 0.433492 GTATGTGACGTGTCGTGCAC 59.567 55.000 6.82 6.82 41.37 4.57 F
871 1039 1.412343 TCCATCAGAAATCCATCGCGA 59.588 47.619 13.09 13.09 0.00 5.87 F
2679 2984 0.608130 TGTCACCAGTTGAGATCGGG 59.392 55.000 0.00 0.00 33.71 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1773 2.587522 ACCTTTTCCTTGCAGGAGTTC 58.412 47.619 0.00 0.0 46.73 3.01 R
2158 2368 2.961536 TGTCAGGGGGAAGATAAGGA 57.038 50.000 0.00 0.0 0.00 3.36 R
2700 3005 1.972660 CTGCAGGTACCAGGCCCTAC 61.973 65.000 21.55 0.0 0.00 3.18 R
3677 5435 2.614057 CCCTTGGCAAACGTATCTGATC 59.386 50.000 0.00 0.0 0.00 2.92 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
47 50 1.689273 ACCGTGACTCTCAAGAAAGCT 59.311 47.619 0.00 0.00 0.00 3.74
128 146 1.942677 TTCGTTTTCAAGAGGCACGA 58.057 45.000 0.00 0.00 38.07 4.35
131 149 1.305201 GTTTTCAAGAGGCACGACCA 58.695 50.000 0.00 0.00 43.14 4.02
136 154 0.320683 CAAGAGGCACGACCATGACA 60.321 55.000 0.00 0.00 43.14 3.58
252 380 2.359107 TACGGCCGTGACTCTCGT 60.359 61.111 40.02 13.03 37.78 4.18
263 391 2.802816 GTGACTCTCGTGAAAGCACAAT 59.197 45.455 0.00 0.00 45.41 2.71
295 423 2.409371 GCGAAAGTAAAACCGTGACTCG 60.409 50.000 0.00 0.00 39.52 4.18
299 427 1.130955 GTAAAACCGTGACTCGCGAA 58.869 50.000 11.33 0.00 39.94 4.70
301 429 0.580104 AAAACCGTGACTCGCGAAAG 59.420 50.000 11.33 1.10 39.94 2.62
416 546 0.899232 CGTTACTCTCGCGAAAGACG 59.101 55.000 17.91 12.80 45.66 4.18
570 737 0.396435 TTCAGAGAAAGCGCCCAGAA 59.604 50.000 2.29 0.00 0.00 3.02
573 740 1.668151 GAGAAAGCGCCCAGAACGT 60.668 57.895 2.29 0.00 0.00 3.99
663 830 2.675889 CGTTAACTAATGGCTCCCGTGT 60.676 50.000 3.71 0.00 0.00 4.49
664 831 2.676342 GTTAACTAATGGCTCCCGTGTG 59.324 50.000 0.00 0.00 0.00 3.82
665 832 0.690762 AACTAATGGCTCCCGTGTGT 59.309 50.000 0.00 0.00 0.00 3.72
666 833 0.249398 ACTAATGGCTCCCGTGTGTC 59.751 55.000 0.00 0.00 0.00 3.67
667 834 0.249120 CTAATGGCTCCCGTGTGTCA 59.751 55.000 0.00 0.00 0.00 3.58
668 835 0.249120 TAATGGCTCCCGTGTGTCAG 59.751 55.000 0.00 0.00 0.00 3.51
669 836 2.469465 AATGGCTCCCGTGTGTCAGG 62.469 60.000 0.00 0.00 0.00 3.86
671 838 4.008933 GCTCCCGTGTGTCAGGCT 62.009 66.667 0.00 0.00 0.00 4.58
672 839 2.047844 CTCCCGTGTGTCAGGCTG 60.048 66.667 8.58 8.58 0.00 4.85
673 840 3.596066 CTCCCGTGTGTCAGGCTGG 62.596 68.421 15.73 0.00 0.00 4.85
674 841 4.704833 CCCGTGTGTCAGGCTGGG 62.705 72.222 15.73 6.45 0.00 4.45
675 842 3.941188 CCGTGTGTCAGGCTGGGT 61.941 66.667 15.73 0.00 0.00 4.51
676 843 2.579657 CCGTGTGTCAGGCTGGGTA 61.580 63.158 15.73 0.00 0.00 3.69
677 844 1.596934 CGTGTGTCAGGCTGGGTAT 59.403 57.895 15.73 0.00 0.00 2.73
678 845 0.740868 CGTGTGTCAGGCTGGGTATG 60.741 60.000 15.73 1.05 0.00 2.39
679 846 0.324943 GTGTGTCAGGCTGGGTATGT 59.675 55.000 15.73 0.00 0.00 2.29
680 847 0.324614 TGTGTCAGGCTGGGTATGTG 59.675 55.000 15.73 0.00 0.00 3.21
681 848 0.613260 GTGTCAGGCTGGGTATGTGA 59.387 55.000 15.73 0.00 0.00 3.58
682 849 0.613260 TGTCAGGCTGGGTATGTGAC 59.387 55.000 15.73 3.41 38.41 3.67
683 850 0.460284 GTCAGGCTGGGTATGTGACG 60.460 60.000 15.73 0.00 0.00 4.35
684 851 0.902984 TCAGGCTGGGTATGTGACGT 60.903 55.000 15.73 0.00 0.00 4.34
685 852 0.740868 CAGGCTGGGTATGTGACGTG 60.741 60.000 6.61 0.00 0.00 4.49
686 853 1.192146 AGGCTGGGTATGTGACGTGT 61.192 55.000 0.00 0.00 0.00 4.49
687 854 0.739813 GGCTGGGTATGTGACGTGTC 60.740 60.000 0.00 0.00 0.00 3.67
688 855 1.076533 GCTGGGTATGTGACGTGTCG 61.077 60.000 0.00 0.00 0.00 4.35
689 856 0.242825 CTGGGTATGTGACGTGTCGT 59.757 55.000 0.00 0.00 45.10 4.34
690 857 0.038983 TGGGTATGTGACGTGTCGTG 60.039 55.000 0.00 0.00 41.37 4.35
691 858 1.349259 GGGTATGTGACGTGTCGTGC 61.349 60.000 0.00 0.00 41.37 5.34
692 859 0.665068 GGTATGTGACGTGTCGTGCA 60.665 55.000 0.00 0.00 41.37 4.57
693 860 0.433492 GTATGTGACGTGTCGTGCAC 59.567 55.000 6.82 6.82 41.37 4.57
732 899 2.556287 CGAAGCACAGCCGTTTCC 59.444 61.111 0.00 0.00 0.00 3.13
733 900 2.954611 GAAGCACAGCCGTTTCCC 59.045 61.111 0.00 0.00 0.00 3.97
734 901 1.600916 GAAGCACAGCCGTTTCCCT 60.601 57.895 0.00 0.00 0.00 4.20
735 902 1.578206 GAAGCACAGCCGTTTCCCTC 61.578 60.000 0.00 0.00 0.00 4.30
736 903 3.056328 GCACAGCCGTTTCCCTCC 61.056 66.667 0.00 0.00 0.00 4.30
737 904 2.359975 CACAGCCGTTTCCCTCCC 60.360 66.667 0.00 0.00 0.00 4.30
738 905 4.016706 ACAGCCGTTTCCCTCCCG 62.017 66.667 0.00 0.00 0.00 5.14
739 906 3.702048 CAGCCGTTTCCCTCCCGA 61.702 66.667 0.00 0.00 0.00 5.14
740 907 3.391382 AGCCGTTTCCCTCCCGAG 61.391 66.667 0.00 0.00 0.00 4.63
742 909 3.391382 CCGTTTCCCTCCCGAGCT 61.391 66.667 0.00 0.00 0.00 4.09
743 910 2.663196 CGTTTCCCTCCCGAGCTT 59.337 61.111 0.00 0.00 0.00 3.74
744 911 1.448013 CGTTTCCCTCCCGAGCTTC 60.448 63.158 0.00 0.00 0.00 3.86
745 912 1.448013 GTTTCCCTCCCGAGCTTCG 60.448 63.158 0.00 0.00 40.07 3.79
757 924 3.909019 CGAGCTTCGGACTTAAATCAC 57.091 47.619 0.00 0.00 36.00 3.06
758 925 3.512680 CGAGCTTCGGACTTAAATCACT 58.487 45.455 0.00 0.00 36.00 3.41
759 926 3.927142 CGAGCTTCGGACTTAAATCACTT 59.073 43.478 0.00 0.00 36.00 3.16
760 927 5.100259 CGAGCTTCGGACTTAAATCACTTA 58.900 41.667 0.00 0.00 36.00 2.24
761 928 5.575606 CGAGCTTCGGACTTAAATCACTTAA 59.424 40.000 0.00 0.00 36.00 1.85
762 929 6.453922 CGAGCTTCGGACTTAAATCACTTAAC 60.454 42.308 0.00 0.00 36.00 2.01
763 930 6.228258 AGCTTCGGACTTAAATCACTTAACA 58.772 36.000 0.00 0.00 0.00 2.41
764 931 6.147328 AGCTTCGGACTTAAATCACTTAACAC 59.853 38.462 0.00 0.00 0.00 3.32
765 932 6.073440 GCTTCGGACTTAAATCACTTAACACA 60.073 38.462 0.00 0.00 0.00 3.72
766 933 7.416154 TTCGGACTTAAATCACTTAACACAG 57.584 36.000 0.00 0.00 0.00 3.66
767 934 6.751157 TCGGACTTAAATCACTTAACACAGA 58.249 36.000 0.00 0.00 0.00 3.41
768 935 6.643770 TCGGACTTAAATCACTTAACACAGAC 59.356 38.462 0.00 0.00 0.00 3.51
769 936 6.128634 CGGACTTAAATCACTTAACACAGACC 60.129 42.308 0.00 0.00 0.00 3.85
770 937 6.128634 GGACTTAAATCACTTAACACAGACCG 60.129 42.308 0.00 0.00 0.00 4.79
771 938 6.518493 ACTTAAATCACTTAACACAGACCGA 58.482 36.000 0.00 0.00 0.00 4.69
772 939 6.987992 ACTTAAATCACTTAACACAGACCGAA 59.012 34.615 0.00 0.00 0.00 4.30
773 940 7.660208 ACTTAAATCACTTAACACAGACCGAAT 59.340 33.333 0.00 0.00 0.00 3.34
774 941 6.877611 AAATCACTTAACACAGACCGAATT 57.122 33.333 0.00 0.00 0.00 2.17
775 942 5.862924 ATCACTTAACACAGACCGAATTG 57.137 39.130 0.00 0.00 0.00 2.32
803 970 9.394832 GTCTAGGAAGAAAATTGGAGCCCAAAC 62.395 44.444 10.21 4.16 39.23 2.93
818 985 2.648059 CCAAACCTGCCATTCTCCTAG 58.352 52.381 0.00 0.00 0.00 3.02
839 1007 7.455008 TCCTAGTCTCCATTGTTAGAGAAAGTT 59.545 37.037 0.00 0.00 40.69 2.66
846 1014 3.746045 TGTTAGAGAAAGTTGTCCGCT 57.254 42.857 0.00 0.00 0.00 5.52
858 1026 2.028420 TGTCCGCTCAAATCCATCAG 57.972 50.000 0.00 0.00 0.00 2.90
871 1039 1.412343 TCCATCAGAAATCCATCGCGA 59.588 47.619 13.09 13.09 0.00 5.87
886 1054 4.493747 CGACGTCCTCCCGGAAGC 62.494 72.222 10.58 0.00 41.83 3.86
940 1108 1.773653 AGCCCAATCCATCTCTCTTCC 59.226 52.381 0.00 0.00 0.00 3.46
1231 1399 4.624024 TCCGATTCATGTCGTGTTTAGAAC 59.376 41.667 5.17 0.00 39.89 3.01
1285 1453 4.047627 AGTTCAGTGGGGGAAATTTAGG 57.952 45.455 0.00 0.00 0.00 2.69
1348 1516 5.012975 TGCTTAAAAGGGCCTGATTTTGAAT 59.987 36.000 6.92 0.00 31.41 2.57
1349 1517 6.212388 TGCTTAAAAGGGCCTGATTTTGAATA 59.788 34.615 6.92 0.00 31.41 1.75
1388 1556 5.582689 AATTTACTTAGCATTCCAGCACC 57.417 39.130 0.00 0.00 36.85 5.01
1422 1590 8.792633 CAAAGGATTCAAGGAACACTTTACATA 58.207 33.333 8.46 0.00 37.29 2.29
1437 1605 9.840427 ACACTTTACATACATTAATTCAAGCAC 57.160 29.630 0.00 0.00 0.00 4.40
1438 1606 9.289303 CACTTTACATACATTAATTCAAGCACC 57.711 33.333 0.00 0.00 0.00 5.01
1439 1607 9.243105 ACTTTACATACATTAATTCAAGCACCT 57.757 29.630 0.00 0.00 0.00 4.00
1440 1608 9.507280 CTTTACATACATTAATTCAAGCACCTG 57.493 33.333 0.00 0.00 0.00 4.00
1441 1609 8.574251 TTACATACATTAATTCAAGCACCTGT 57.426 30.769 0.00 0.00 0.00 4.00
1442 1610 7.466746 ACATACATTAATTCAAGCACCTGTT 57.533 32.000 0.00 0.00 0.00 3.16
1443 1611 8.574251 ACATACATTAATTCAAGCACCTGTTA 57.426 30.769 0.00 0.00 0.00 2.41
1444 1612 9.189156 ACATACATTAATTCAAGCACCTGTTAT 57.811 29.630 0.00 0.00 0.00 1.89
1445 1613 9.454585 CATACATTAATTCAAGCACCTGTTATG 57.545 33.333 0.00 0.00 0.00 1.90
1446 1614 6.866480 ACATTAATTCAAGCACCTGTTATGG 58.134 36.000 0.00 0.00 0.00 2.74
1447 1615 6.663093 ACATTAATTCAAGCACCTGTTATGGA 59.337 34.615 0.00 0.00 0.00 3.41
1448 1616 7.178274 ACATTAATTCAAGCACCTGTTATGGAA 59.822 33.333 0.00 0.00 0.00 3.53
1449 1617 7.531857 TTAATTCAAGCACCTGTTATGGAAA 57.468 32.000 0.00 0.00 0.00 3.13
1450 1618 4.846779 TTCAAGCACCTGTTATGGAAAC 57.153 40.909 0.00 0.00 0.00 2.78
1468 1636 7.604657 TGGAAACAAAATAATAACAGTGGGT 57.395 32.000 0.00 0.00 37.44 4.51
1469 1637 8.024145 TGGAAACAAAATAATAACAGTGGGTT 57.976 30.769 0.00 0.00 39.78 4.11
1508 1710 4.221703 AGAGAAGTGGTGATGGTTGACTAG 59.778 45.833 0.00 0.00 0.00 2.57
1570 1773 6.583806 GTGCAACAGAGTATGAGGAAAAATTG 59.416 38.462 0.00 0.00 36.32 2.32
1578 1781 7.609532 AGAGTATGAGGAAAAATTGAACTCCTG 59.390 37.037 3.34 0.00 38.45 3.86
1598 1801 3.096092 TGCAAGGAAAAGGTTGACAAGT 58.904 40.909 0.00 0.00 0.00 3.16
1891 2094 2.464157 GCTGAAGGCACAGTAAGTCT 57.536 50.000 11.94 0.00 41.35 3.24
1941 2151 4.568152 ACATTTTGCTTTCGTAACTGCT 57.432 36.364 0.00 0.00 0.00 4.24
1952 2162 1.739466 CGTAACTGCTCACATGCCATT 59.261 47.619 0.00 0.00 0.00 3.16
2158 2368 4.887071 TGAATTTGGATAATGCTACCGCTT 59.113 37.500 0.00 0.00 36.97 4.68
2472 2682 8.986477 ATCCTTTCAATATGTTACTGTTTTGC 57.014 30.769 0.00 0.00 0.00 3.68
2519 2729 3.376234 TCAGTTTCTACCTATGGACGTCG 59.624 47.826 9.92 0.00 0.00 5.12
2679 2984 0.608130 TGTCACCAGTTGAGATCGGG 59.392 55.000 0.00 0.00 33.71 5.14
2700 3005 4.248058 GGGACAAGCTTTGGAAAATGATG 58.752 43.478 0.00 0.00 34.12 3.07
3055 3360 9.959749 GGATGTTTTTGTCACTTTTACTTGATA 57.040 29.630 0.00 0.00 0.00 2.15
3261 5005 6.227298 TGACCAACAATTTGTGTAACCATT 57.773 33.333 2.13 0.00 40.60 3.16
3265 5009 9.099454 GACCAACAATTTGTGTAACCATTTTAA 57.901 29.630 2.13 0.00 40.60 1.52
3298 5042 7.255035 GCGATGCAGATATATATCATTGGCTTT 60.255 37.037 21.95 12.15 35.17 3.51
3391 5135 7.872483 GGATGTATTGTGGATTTTGAAAGTTGT 59.128 33.333 0.00 0.00 0.00 3.32
3432 5176 2.158900 ACGGAAGGAATATGGCACTCTG 60.159 50.000 0.00 0.00 0.00 3.35
3519 5264 6.183360 CCAGGTGCTTTAGCTAGTGTTAATTC 60.183 42.308 3.10 0.00 42.66 2.17
3529 5274 2.980568 AGTGTTAATTCGAATGGCCGA 58.019 42.857 12.25 0.00 36.70 5.54
3539 5285 2.623889 TCGAATGGCCGAAAAGGAAAAA 59.376 40.909 0.00 0.00 45.00 1.94
3591 5337 0.169672 CCAGGAAAGTGAAGCGCATG 59.830 55.000 11.47 0.00 0.00 4.06
3624 5372 7.431249 TGAATTAACTAGTTGACAGAGAACGT 58.569 34.615 18.56 0.00 0.00 3.99
3632 5380 0.873054 GACAGAGAACGTCGTGAGGA 59.127 55.000 0.00 0.00 0.00 3.71
3633 5381 0.592148 ACAGAGAACGTCGTGAGGAC 59.408 55.000 0.00 0.00 42.48 3.85
3634 5382 0.591659 CAGAGAACGTCGTGAGGACA 59.408 55.000 0.00 0.00 46.42 4.02
3690 5448 6.716934 ATGTAGGACAGATCAGATACGTTT 57.283 37.500 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 146 1.291877 GCTTTCGCGAGTGTCATGGT 61.292 55.000 9.59 0.00 0.00 3.55
131 149 0.599991 TGTGCTTTCGCGAGTGTCAT 60.600 50.000 9.59 0.00 39.65 3.06
136 154 0.944311 ACGATTGTGCTTTCGCGAGT 60.944 50.000 9.59 0.00 38.91 4.18
160 285 0.378962 CACGGTTTTGCTTCCACGAA 59.621 50.000 0.00 0.00 0.00 3.85
222 350 0.664166 GGCCGTACGTCTCGAAAACA 60.664 55.000 15.21 0.00 0.00 2.83
233 361 2.099831 GAGAGTCACGGCCGTACG 59.900 66.667 33.70 20.65 40.31 3.67
235 363 2.359107 ACGAGAGTCACGGCCGTA 60.359 61.111 33.70 16.87 44.19 4.02
263 391 1.579964 TACTTTCGCGAGAGGCACGA 61.580 55.000 27.80 7.36 43.84 4.35
364 494 0.238553 GAGAGGCACGGTTTTGCTTC 59.761 55.000 0.28 0.28 46.31 3.86
445 601 6.300354 TGTCTTCCTTAGCTTTTCGAAAAG 57.700 37.500 35.51 35.51 46.25 2.27
448 604 4.202326 ACCTGTCTTCCTTAGCTTTTCGAA 60.202 41.667 0.00 0.00 0.00 3.71
573 740 0.943673 CAGCCATTTGTCACGTGTCA 59.056 50.000 16.51 13.90 0.00 3.58
582 749 1.302752 TGCGCTCTCAGCCATTTGT 60.303 52.632 9.73 0.00 38.18 2.83
663 830 0.613260 GTCACATACCCAGCCTGACA 59.387 55.000 0.00 0.00 32.99 3.58
664 831 0.460284 CGTCACATACCCAGCCTGAC 60.460 60.000 0.00 0.00 0.00 3.51
665 832 0.902984 ACGTCACATACCCAGCCTGA 60.903 55.000 0.00 0.00 0.00 3.86
666 833 0.740868 CACGTCACATACCCAGCCTG 60.741 60.000 0.00 0.00 0.00 4.85
667 834 1.192146 ACACGTCACATACCCAGCCT 61.192 55.000 0.00 0.00 0.00 4.58
668 835 0.739813 GACACGTCACATACCCAGCC 60.740 60.000 0.00 0.00 0.00 4.85
669 836 1.076533 CGACACGTCACATACCCAGC 61.077 60.000 0.00 0.00 0.00 4.85
670 837 0.242825 ACGACACGTCACATACCCAG 59.757 55.000 0.00 0.00 33.69 4.45
671 838 0.038983 CACGACACGTCACATACCCA 60.039 55.000 0.00 0.00 38.32 4.51
672 839 1.349259 GCACGACACGTCACATACCC 61.349 60.000 0.00 0.00 38.32 3.69
673 840 0.665068 TGCACGACACGTCACATACC 60.665 55.000 0.00 0.00 38.32 2.73
674 841 0.433492 GTGCACGACACGTCACATAC 59.567 55.000 0.00 1.94 40.07 2.39
675 842 2.803979 GTGCACGACACGTCACATA 58.196 52.632 0.00 0.00 40.07 2.29
676 843 3.625232 GTGCACGACACGTCACAT 58.375 55.556 0.00 0.00 40.07 3.21
713 880 3.911155 GAAACGGCTGTGCTTCGCG 62.911 63.158 0.00 0.00 0.00 5.87
714 881 2.127232 GAAACGGCTGTGCTTCGC 60.127 61.111 0.00 0.00 0.00 4.70
715 882 2.556287 GGAAACGGCTGTGCTTCG 59.444 61.111 0.00 0.00 0.00 3.79
716 883 1.578206 GAGGGAAACGGCTGTGCTTC 61.578 60.000 0.00 0.00 0.00 3.86
717 884 1.600916 GAGGGAAACGGCTGTGCTT 60.601 57.895 0.00 0.00 0.00 3.91
718 885 2.032681 GAGGGAAACGGCTGTGCT 59.967 61.111 0.00 0.00 0.00 4.40
719 886 3.056328 GGAGGGAAACGGCTGTGC 61.056 66.667 0.00 0.00 0.00 4.57
720 887 2.359975 GGGAGGGAAACGGCTGTG 60.360 66.667 0.00 0.00 0.00 3.66
721 888 4.016706 CGGGAGGGAAACGGCTGT 62.017 66.667 0.00 0.00 0.00 4.40
722 889 3.665675 CTCGGGAGGGAAACGGCTG 62.666 68.421 0.00 0.00 0.00 4.85
723 890 3.391382 CTCGGGAGGGAAACGGCT 61.391 66.667 0.00 0.00 0.00 5.52
725 892 2.854187 GAAGCTCGGGAGGGAAACGG 62.854 65.000 0.00 0.00 0.00 4.44
726 893 1.448013 GAAGCTCGGGAGGGAAACG 60.448 63.158 0.00 0.00 0.00 3.60
727 894 1.448013 CGAAGCTCGGGAGGGAAAC 60.448 63.158 0.00 0.00 36.00 2.78
728 895 2.978824 CGAAGCTCGGGAGGGAAA 59.021 61.111 0.00 0.00 36.00 3.13
736 903 9.243551 GTTAAGTGATTTAAGTCCGAAGCTCGG 62.244 44.444 15.77 15.77 44.95 4.63
737 904 3.512680 AGTGATTTAAGTCCGAAGCTCG 58.487 45.455 0.00 0.00 40.07 5.03
738 905 6.367969 TGTTAAGTGATTTAAGTCCGAAGCTC 59.632 38.462 0.00 0.00 32.07 4.09
739 906 6.147328 GTGTTAAGTGATTTAAGTCCGAAGCT 59.853 38.462 0.00 0.00 32.07 3.74
740 907 6.073440 TGTGTTAAGTGATTTAAGTCCGAAGC 60.073 38.462 0.00 0.00 32.07 3.86
741 908 7.384115 TCTGTGTTAAGTGATTTAAGTCCGAAG 59.616 37.037 0.00 0.00 32.07 3.79
742 909 7.170320 GTCTGTGTTAAGTGATTTAAGTCCGAA 59.830 37.037 0.00 0.00 32.07 4.30
743 910 6.643770 GTCTGTGTTAAGTGATTTAAGTCCGA 59.356 38.462 0.00 0.00 32.07 4.55
744 911 6.128634 GGTCTGTGTTAAGTGATTTAAGTCCG 60.129 42.308 0.00 0.00 32.07 4.79
745 912 6.128634 CGGTCTGTGTTAAGTGATTTAAGTCC 60.129 42.308 0.00 0.00 32.07 3.85
746 913 6.643770 TCGGTCTGTGTTAAGTGATTTAAGTC 59.356 38.462 0.00 0.00 32.07 3.01
747 914 6.518493 TCGGTCTGTGTTAAGTGATTTAAGT 58.482 36.000 0.00 0.00 32.07 2.24
748 915 7.416154 TTCGGTCTGTGTTAAGTGATTTAAG 57.584 36.000 0.00 0.00 32.07 1.85
749 916 7.972832 ATTCGGTCTGTGTTAAGTGATTTAA 57.027 32.000 0.00 0.00 0.00 1.52
750 917 7.094975 CCAATTCGGTCTGTGTTAAGTGATTTA 60.095 37.037 0.00 0.00 0.00 1.40
751 918 6.293955 CCAATTCGGTCTGTGTTAAGTGATTT 60.294 38.462 0.00 0.00 0.00 2.17
752 919 5.181245 CCAATTCGGTCTGTGTTAAGTGATT 59.819 40.000 0.00 0.00 0.00 2.57
753 920 4.695455 CCAATTCGGTCTGTGTTAAGTGAT 59.305 41.667 0.00 0.00 0.00 3.06
754 921 4.062293 CCAATTCGGTCTGTGTTAAGTGA 58.938 43.478 0.00 0.00 0.00 3.41
755 922 3.188460 CCCAATTCGGTCTGTGTTAAGTG 59.812 47.826 0.00 0.00 0.00 3.16
756 923 3.181448 ACCCAATTCGGTCTGTGTTAAGT 60.181 43.478 0.00 0.00 0.00 2.24
757 924 3.408634 ACCCAATTCGGTCTGTGTTAAG 58.591 45.455 0.00 0.00 0.00 1.85
758 925 3.495434 ACCCAATTCGGTCTGTGTTAA 57.505 42.857 0.00 0.00 0.00 2.01
767 934 2.829023 TCTTCCTAGACCCAATTCGGT 58.171 47.619 0.00 0.00 39.49 4.69
768 935 3.906720 TTCTTCCTAGACCCAATTCGG 57.093 47.619 0.00 0.00 0.00 4.30
769 936 6.404734 CCAATTTTCTTCCTAGACCCAATTCG 60.405 42.308 0.00 0.00 0.00 3.34
770 937 6.663523 TCCAATTTTCTTCCTAGACCCAATTC 59.336 38.462 0.00 0.00 0.00 2.17
771 938 6.561294 TCCAATTTTCTTCCTAGACCCAATT 58.439 36.000 0.00 0.00 0.00 2.32
772 939 6.152638 TCCAATTTTCTTCCTAGACCCAAT 57.847 37.500 0.00 0.00 0.00 3.16
773 940 5.570320 CTCCAATTTTCTTCCTAGACCCAA 58.430 41.667 0.00 0.00 0.00 4.12
774 941 4.567747 GCTCCAATTTTCTTCCTAGACCCA 60.568 45.833 0.00 0.00 0.00 4.51
775 942 3.948473 GCTCCAATTTTCTTCCTAGACCC 59.052 47.826 0.00 0.00 0.00 4.46
782 949 3.557054 GGTTTGGGCTCCAATTTTCTTCC 60.557 47.826 7.39 0.00 43.55 3.46
783 950 3.324846 AGGTTTGGGCTCCAATTTTCTTC 59.675 43.478 7.39 0.00 43.55 2.87
785 952 2.634453 CAGGTTTGGGCTCCAATTTTCT 59.366 45.455 7.39 1.95 43.55 2.52
803 970 1.691434 GGAGACTAGGAGAATGGCAGG 59.309 57.143 0.00 0.00 0.00 4.85
818 985 6.147985 GGACAACTTTCTCTAACAATGGAGAC 59.852 42.308 0.00 0.00 42.21 3.36
839 1007 1.554617 TCTGATGGATTTGAGCGGACA 59.445 47.619 0.00 0.00 0.00 4.02
846 1014 4.276678 GCGATGGATTTCTGATGGATTTGA 59.723 41.667 0.00 0.00 0.00 2.69
858 1026 0.527817 AGGACGTCGCGATGGATTTC 60.528 55.000 30.24 18.66 0.00 2.17
1231 1399 0.387367 CGTCTTCACCACACGAGGAG 60.387 60.000 0.00 0.00 35.49 3.69
1285 1453 3.733443 ACTCAAAAATTGCCAGTGACC 57.267 42.857 0.00 0.00 0.00 4.02
1373 1541 0.038021 TGCAGGTGCTGGAATGCTAA 59.962 50.000 3.18 0.00 42.66 3.09
1388 1556 4.272489 TCCTTGAATCCTTTGGTATGCAG 58.728 43.478 0.00 0.00 0.00 4.41
1422 1590 6.663093 TCCATAACAGGTGCTTGAATTAATGT 59.337 34.615 0.00 0.00 0.00 2.71
1442 1610 9.315363 ACCCACTGTTATTATTTTGTTTCCATA 57.685 29.630 0.00 0.00 0.00 2.74
1443 1611 8.201242 ACCCACTGTTATTATTTTGTTTCCAT 57.799 30.769 0.00 0.00 0.00 3.41
1444 1612 7.604657 ACCCACTGTTATTATTTTGTTTCCA 57.395 32.000 0.00 0.00 0.00 3.53
1445 1613 9.414295 GTAACCCACTGTTATTATTTTGTTTCC 57.586 33.333 0.00 0.00 41.33 3.13
1446 1614 9.414295 GGTAACCCACTGTTATTATTTTGTTTC 57.586 33.333 0.00 0.00 41.33 2.78
1447 1615 9.150028 AGGTAACCCACTGTTATTATTTTGTTT 57.850 29.630 0.00 0.00 41.33 2.83
1448 1616 8.715190 AGGTAACCCACTGTTATTATTTTGTT 57.285 30.769 0.00 0.00 41.33 2.83
1449 1617 8.715190 AAGGTAACCCACTGTTATTATTTTGT 57.285 30.769 0.00 0.00 41.33 2.83
1450 1618 9.418045 CAAAGGTAACCCACTGTTATTATTTTG 57.582 33.333 0.00 0.00 41.33 2.44
1451 1619 9.369672 TCAAAGGTAACCCACTGTTATTATTTT 57.630 29.630 0.00 0.00 41.33 1.82
1452 1620 8.943594 TCAAAGGTAACCCACTGTTATTATTT 57.056 30.769 0.00 0.00 41.33 1.40
1453 1621 8.943594 TTCAAAGGTAACCCACTGTTATTATT 57.056 30.769 0.00 0.00 41.33 1.40
1454 1622 8.943594 TTTCAAAGGTAACCCACTGTTATTAT 57.056 30.769 0.00 0.00 41.33 1.28
1455 1623 8.943594 ATTTCAAAGGTAACCCACTGTTATTA 57.056 30.769 0.00 0.00 41.33 0.98
1456 1624 7.849322 ATTTCAAAGGTAACCCACTGTTATT 57.151 32.000 0.00 0.00 41.33 1.40
1457 1625 8.943594 TTATTTCAAAGGTAACCCACTGTTAT 57.056 30.769 0.00 0.00 41.33 1.89
1458 1626 8.943594 ATTATTTCAAAGGTAACCCACTGTTA 57.056 30.769 0.00 0.00 38.42 2.41
1459 1627 7.849322 ATTATTTCAAAGGTAACCCACTGTT 57.151 32.000 0.00 0.00 41.11 3.16
1460 1628 7.849322 AATTATTTCAAAGGTAACCCACTGT 57.151 32.000 0.00 0.00 37.17 3.55
1461 1629 9.238368 TCTAATTATTTCAAAGGTAACCCACTG 57.762 33.333 0.00 0.00 37.17 3.66
1462 1630 9.462606 CTCTAATTATTTCAAAGGTAACCCACT 57.537 33.333 0.00 0.00 37.17 4.00
1463 1631 9.457436 TCTCTAATTATTTCAAAGGTAACCCAC 57.543 33.333 0.00 0.00 37.17 4.61
1490 1692 3.646162 TCAACTAGTCAACCATCACCACT 59.354 43.478 0.00 0.00 0.00 4.00
1508 1710 7.437862 TGCCACTTTTATTGTCAAATTCTCAAC 59.562 33.333 0.00 0.00 0.00 3.18
1559 1762 4.853924 TGCAGGAGTTCAATTTTTCCTC 57.146 40.909 0.00 0.00 37.97 3.71
1570 1773 2.587522 ACCTTTTCCTTGCAGGAGTTC 58.412 47.619 0.00 0.00 46.73 3.01
1578 1781 3.130340 TGACTTGTCAACCTTTTCCTTGC 59.870 43.478 0.44 0.00 0.00 4.01
1589 1792 5.160641 TGTTTCAGCTTTTGACTTGTCAAC 58.839 37.500 14.80 5.33 34.94 3.18
1591 1794 4.458989 ACTGTTTCAGCTTTTGACTTGTCA 59.541 37.500 0.00 0.00 34.94 3.58
1598 1801 6.542005 TCATCAGTAACTGTTTCAGCTTTTGA 59.458 34.615 0.00 0.00 34.37 2.69
1891 2094 7.342769 ACATGTACTCGGTGATACAAATCTA 57.657 36.000 0.00 0.00 35.05 1.98
1941 2151 3.088532 GTTTCCCACTAATGGCATGTGA 58.911 45.455 16.94 0.00 45.76 3.58
1952 2162 5.251932 TGACCATCCAAATAGTTTCCCACTA 59.748 40.000 0.00 0.00 42.49 2.74
2158 2368 2.961536 TGTCAGGGGGAAGATAAGGA 57.038 50.000 0.00 0.00 0.00 3.36
2564 2869 3.372869 CACACAAGTTTTGTTTGCTGC 57.627 42.857 0.00 0.00 43.23 5.25
2679 2984 4.886579 ACATCATTTTCCAAAGCTTGTCC 58.113 39.130 0.00 0.00 0.00 4.02
2700 3005 1.972660 CTGCAGGTACCAGGCCCTAC 61.973 65.000 21.55 0.00 0.00 3.18
2937 3242 5.456763 GGTGCTGATATAAGGGAGATTTGGT 60.457 44.000 0.00 0.00 0.00 3.67
3055 3360 8.584157 TGATTTTAAACAATACAGGTGAGCAAT 58.416 29.630 0.00 0.00 0.00 3.56
3179 4923 9.106070 ACGTTAATTATGGACAGAGGAAAATAC 57.894 33.333 0.00 0.00 0.00 1.89
3187 4931 8.627403 TCTACCTTACGTTAATTATGGACAGAG 58.373 37.037 0.00 0.00 0.00 3.35
3261 5005 6.866010 ATATCTGCATCGCACAATCTTAAA 57.134 33.333 0.00 0.00 33.79 1.52
3265 5009 7.495055 TGATATATATCTGCATCGCACAATCT 58.505 34.615 20.74 0.00 33.79 2.40
3298 5042 4.819088 TGATCTTTTCAACATCAACCGTCA 59.181 37.500 0.00 0.00 0.00 4.35
3369 5113 7.516627 GCACACAACTTTCAAAATCCACAATAC 60.517 37.037 0.00 0.00 0.00 1.89
3391 5135 3.000041 GTCCAGAAATACACGATGCACA 59.000 45.455 0.00 0.00 0.00 4.57
3501 5245 7.126398 GCCATTCGAATTAACACTAGCTAAAG 58.874 38.462 8.21 0.00 0.00 1.85
3519 5264 2.715737 TTTTCCTTTTCGGCCATTCG 57.284 45.000 2.24 0.00 0.00 3.34
3539 5285 8.585471 AGATGATACCATGAATCAAGTGTTTT 57.415 30.769 12.80 0.00 36.95 2.43
3543 5289 7.713942 TGAGAAGATGATACCATGAATCAAGTG 59.286 37.037 12.80 0.00 36.95 3.16
3544 5290 7.799081 TGAGAAGATGATACCATGAATCAAGT 58.201 34.615 12.80 0.00 36.95 3.16
3554 5300 3.963374 CCTGGTCTGAGAAGATGATACCA 59.037 47.826 0.00 0.00 34.52 3.25
3556 5302 5.860941 TTCCTGGTCTGAGAAGATGATAC 57.139 43.478 0.00 0.00 0.00 2.24
3557 5303 5.960811 ACTTTCCTGGTCTGAGAAGATGATA 59.039 40.000 0.00 0.00 0.00 2.15
3591 5337 5.351740 GTCAACTAGTTAATTCAGGTGCTCC 59.648 44.000 8.04 0.00 0.00 4.70
3661 5418 9.776158 CGTATCTGATCTGTCCTACATTAATAC 57.224 37.037 0.00 0.00 0.00 1.89
3662 5419 9.516546 ACGTATCTGATCTGTCCTACATTAATA 57.483 33.333 0.00 0.00 0.00 0.98
3677 5435 2.614057 CCCTTGGCAAACGTATCTGATC 59.386 50.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.