Multiple sequence alignment - TraesCS6A01G091800

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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 TraesCS6A01G091800 chr6A 100.000 3535 0 0 1 3535 60394387 60397921 0.000000e+00 6529.0
1 TraesCS6A01G091800 chr6A 90.090 111 9 2 867 976 596589446 596589337 3.680000e-30 143.0
2 TraesCS6A01G091800 chr7A 97.593 2202 51 1 1336 3535 419044685 419042484 0.000000e+00 3771.0
3 TraesCS6A01G091800 chr7A 95.868 242 10 0 553 794 700807890 700808131 3.310000e-105 392.0
4 TraesCS6A01G091800 chr7A 93.750 256 15 1 541 795 429694496 429694751 1.990000e-102 383.0
5 TraesCS6A01G091800 chr2A 96.474 1957 54 5 1588 3535 705945433 705947383 0.000000e+00 3217.0
6 TraesCS6A01G091800 chr2A 98.267 1673 27 1 1865 3535 36893474 36895146 0.000000e+00 2928.0
7 TraesCS6A01G091800 chr2A 97.940 534 11 0 1336 1869 36883795 36884328 0.000000e+00 926.0
8 TraesCS6A01G091800 chr2A 94.048 252 15 0 542 793 135280107 135280358 1.990000e-102 383.0
9 TraesCS6A01G091800 chr2A 81.481 81 15 0 1336 1416 768679371 768679291 2.280000e-07 67.6
10 TraesCS6A01G091800 chr4A 98.556 554 8 0 1 554 638978938 638979491 0.000000e+00 979.0
11 TraesCS6A01G091800 chr4A 97.982 545 11 0 791 1335 638979489 638980033 0.000000e+00 946.0
12 TraesCS6A01G091800 chr4A 95.868 242 10 0 553 794 17027497 17027256 3.310000e-105 392.0
13 TraesCS6A01G091800 chr4B 97.248 545 15 0 791 1335 650324988 650324444 0.000000e+00 924.0
14 TraesCS6A01G091800 chr4B 98.125 320 5 1 1 319 650325702 650325383 1.110000e-154 556.0
15 TraesCS6A01G091800 chr4B 95.397 239 11 0 316 554 650325224 650324986 7.160000e-102 381.0
16 TraesCS6A01G091800 chr7B 97.070 546 14 2 791 1335 100044045 100044589 0.000000e+00 918.0
17 TraesCS6A01G091800 chr7B 98.750 320 3 1 1 319 100043358 100043677 5.120000e-158 568.0
18 TraesCS6A01G091800 chr7B 97.490 239 6 0 316 554 100043809 100044047 3.280000e-110 409.0
19 TraesCS6A01G091800 chr2B 96.881 545 17 0 791 1335 197573927 197573383 0.000000e+00 913.0
20 TraesCS6A01G091800 chr2B 95.825 527 18 2 1 527 197574557 197574035 0.000000e+00 848.0
21 TraesCS6A01G091800 chr2B 95.868 242 10 0 553 794 677810258 677810499 3.310000e-105 392.0
22 TraesCS6A01G091800 chr2B 95.868 242 10 0 552 793 752624529 752624770 3.310000e-105 392.0
23 TraesCS6A01G091800 chr2B 80.576 278 41 8 3254 3528 859686 859419 5.980000e-48 202.0
24 TraesCS6A01G091800 chr6B 85.731 841 106 11 1610 2441 664394216 664393381 0.000000e+00 876.0
25 TraesCS6A01G091800 chr3A 85.615 723 96 5 1763 2479 99582175 99582895 0.000000e+00 752.0
26 TraesCS6A01G091800 chr5B 98.015 403 8 0 933 1335 527471479 527471881 0.000000e+00 701.0
27 TraesCS6A01G091800 chr5B 98.746 319 3 1 1 319 527470656 527470973 1.840000e-157 566.0
28 TraesCS6A01G091800 chr5B 97.490 239 6 0 316 554 527471132 527471370 3.280000e-110 409.0
29 TraesCS6A01G091800 chr5B 96.429 112 3 1 791 901 527471368 527471479 2.170000e-42 183.0
30 TraesCS6A01G091800 chr5B 84.138 145 14 7 864 1005 146824724 146824862 7.960000e-27 132.0
31 TraesCS6A01G091800 chr5A 77.660 940 180 24 1483 2405 557068555 557067629 2.400000e-151 545.0
32 TraesCS6A01G091800 chr5A 97.510 241 6 0 553 793 90623203 90622963 2.540000e-111 412.0
33 TraesCS6A01G091800 chr5A 95.492 244 11 0 550 793 536150051 536150294 1.190000e-104 390.0
34 TraesCS6A01G091800 chr1A 95.122 246 11 1 552 797 287684676 287684920 1.540000e-103 387.0
35 TraesCS6A01G091800 chr4D 96.744 215 7 0 1 215 215134780 215134994 3.360000e-95 359.0
36 TraesCS6A01G091800 chr2D 89.381 113 9 3 861 971 2310809 2310698 4.760000e-29 139.0
37 TraesCS6A01G091800 chr1B 89.381 113 7 5 864 974 654503000 654502891 1.710000e-28 137.0
38 TraesCS6A01G091800 chr6D 85.271 129 15 4 843 968 368755071 368755198 2.860000e-26 130.0


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 TraesCS6A01G091800 chr6A 60394387 60397921 3534 False 6529.000000 6529 100.000000 1 3535 1 chr6A.!!$F1 3534
1 TraesCS6A01G091800 chr7A 419042484 419044685 2201 True 3771.000000 3771 97.593000 1336 3535 1 chr7A.!!$R1 2199
2 TraesCS6A01G091800 chr2A 705945433 705947383 1950 False 3217.000000 3217 96.474000 1588 3535 1 chr2A.!!$F4 1947
3 TraesCS6A01G091800 chr2A 36893474 36895146 1672 False 2928.000000 2928 98.267000 1865 3535 1 chr2A.!!$F2 1670
4 TraesCS6A01G091800 chr2A 36883795 36884328 533 False 926.000000 926 97.940000 1336 1869 1 chr2A.!!$F1 533
5 TraesCS6A01G091800 chr4A 638978938 638980033 1095 False 962.500000 979 98.269000 1 1335 2 chr4A.!!$F1 1334
6 TraesCS6A01G091800 chr4B 650324444 650325702 1258 True 620.333333 924 96.923333 1 1335 3 chr4B.!!$R1 1334
7 TraesCS6A01G091800 chr7B 100043358 100044589 1231 False 631.666667 918 97.770000 1 1335 3 chr7B.!!$F1 1334
8 TraesCS6A01G091800 chr2B 197573383 197574557 1174 True 880.500000 913 96.353000 1 1335 2 chr2B.!!$R2 1334
9 TraesCS6A01G091800 chr6B 664393381 664394216 835 True 876.000000 876 85.731000 1610 2441 1 chr6B.!!$R1 831
10 TraesCS6A01G091800 chr3A 99582175 99582895 720 False 752.000000 752 85.615000 1763 2479 1 chr3A.!!$F1 716
11 TraesCS6A01G091800 chr5B 527470656 527471881 1225 False 464.750000 701 97.670000 1 1335 4 chr5B.!!$F2 1334
12 TraesCS6A01G091800 chr5A 557067629 557068555 926 True 545.000000 545 77.660000 1483 2405 1 chr5A.!!$R2 922

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
569 816 1.651770 TGGTACTCCCTCCTTCCATCT 59.348 52.381 0.00 0.0 0.0 2.90 F
1367 1615 1.338674 TGTCCTTCGCGTTCCATTCAT 60.339 47.619 5.77 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1674 0.812811 CGGTCATCGGTCCGACTCTA 60.813 60.000 18.08 0.0 46.67 2.43 R
2943 3204 1.822990 CAGTGGTCTTCGGCTAACCTA 59.177 52.381 0.00 0.0 34.05 3.08 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
557 804 9.708092 GGAGTATATAAACAAGAATGGTACTCC 57.292 37.037 10.81 10.81 44.62 3.85
558 805 9.708092 GAGTATATAAACAAGAATGGTACTCCC 57.292 37.037 0.00 0.00 33.02 4.30
559 806 9.448587 AGTATATAAACAAGAATGGTACTCCCT 57.551 33.333 0.00 0.00 0.00 4.20
560 807 9.708092 GTATATAAACAAGAATGGTACTCCCTC 57.292 37.037 0.00 0.00 0.00 4.30
561 808 4.302559 AAACAAGAATGGTACTCCCTCC 57.697 45.455 0.00 0.00 0.00 4.30
562 809 3.207044 ACAAGAATGGTACTCCCTCCT 57.793 47.619 0.00 0.00 0.00 3.69
563 810 3.532102 ACAAGAATGGTACTCCCTCCTT 58.468 45.455 0.00 0.00 0.00 3.36
564 811 3.519913 ACAAGAATGGTACTCCCTCCTTC 59.480 47.826 0.00 0.00 0.00 3.46
565 812 2.765502 AGAATGGTACTCCCTCCTTCC 58.234 52.381 0.00 0.00 0.00 3.46
566 813 2.045885 AGAATGGTACTCCCTCCTTCCA 59.954 50.000 0.00 0.00 0.00 3.53
567 814 2.897823 ATGGTACTCCCTCCTTCCAT 57.102 50.000 0.00 0.00 0.00 3.41
568 815 2.176247 TGGTACTCCCTCCTTCCATC 57.824 55.000 0.00 0.00 0.00 3.51
569 816 1.651770 TGGTACTCCCTCCTTCCATCT 59.348 52.381 0.00 0.00 0.00 2.90
570 817 2.863238 TGGTACTCCCTCCTTCCATCTA 59.137 50.000 0.00 0.00 0.00 1.98
571 818 3.471306 TGGTACTCCCTCCTTCCATCTAT 59.529 47.826 0.00 0.00 0.00 1.98
572 819 4.673132 TGGTACTCCCTCCTTCCATCTATA 59.327 45.833 0.00 0.00 0.00 1.31
573 820 5.318889 TGGTACTCCCTCCTTCCATCTATAT 59.681 44.000 0.00 0.00 0.00 0.86
574 821 6.511445 TGGTACTCCCTCCTTCCATCTATATA 59.489 42.308 0.00 0.00 0.00 0.86
575 822 7.064229 GGTACTCCCTCCTTCCATCTATATAG 58.936 46.154 3.10 3.10 0.00 1.31
576 823 6.098716 ACTCCCTCCTTCCATCTATATAGG 57.901 45.833 9.89 0.00 0.00 2.57
577 824 5.042979 ACTCCCTCCTTCCATCTATATAGGG 60.043 48.000 9.89 4.49 43.23 3.53
578 825 3.970640 CCCTCCTTCCATCTATATAGGGC 59.029 52.174 9.89 0.00 36.30 5.19
579 826 3.970640 CCTCCTTCCATCTATATAGGGCC 59.029 52.174 9.89 0.00 0.00 5.80
580 827 4.327332 CCTCCTTCCATCTATATAGGGCCT 60.327 50.000 12.58 12.58 0.00 5.19
581 828 5.103043 CCTCCTTCCATCTATATAGGGCCTA 60.103 48.000 17.16 17.16 0.00 3.93
582 829 6.432190 TCCTTCCATCTATATAGGGCCTAA 57.568 41.667 18.91 7.61 0.00 2.69
583 830 7.009960 TCCTTCCATCTATATAGGGCCTAAT 57.990 40.000 18.91 14.19 0.00 1.73
584 831 6.846505 TCCTTCCATCTATATAGGGCCTAATG 59.153 42.308 18.91 15.42 0.00 1.90
585 832 6.465035 CCTTCCATCTATATAGGGCCTAATGC 60.465 46.154 18.91 0.00 40.16 3.56
586 833 4.588951 TCCATCTATATAGGGCCTAATGCG 59.411 45.833 18.91 10.04 42.61 4.73
587 834 4.345257 CCATCTATATAGGGCCTAATGCGT 59.655 45.833 18.91 2.76 42.61 5.24
588 835 5.163301 CCATCTATATAGGGCCTAATGCGTT 60.163 44.000 18.91 1.94 42.61 4.84
589 836 6.349300 CATCTATATAGGGCCTAATGCGTTT 58.651 40.000 18.91 1.12 42.61 3.60
590 837 6.368779 TCTATATAGGGCCTAATGCGTTTT 57.631 37.500 18.91 0.30 42.61 2.43
591 838 6.775708 TCTATATAGGGCCTAATGCGTTTTT 58.224 36.000 18.91 0.00 42.61 1.94
620 867 8.515414 AGGTTAACTTTGATCAAATGTTAGAGC 58.485 33.333 25.24 23.73 31.87 4.09
621 868 8.296713 GGTTAACTTTGATCAAATGTTAGAGCA 58.703 33.333 25.24 16.78 31.87 4.26
622 869 9.677567 GTTAACTTTGATCAAATGTTAGAGCAA 57.322 29.630 25.24 17.54 38.26 3.91
638 885 9.723601 TGTTAGAGCAATAATATATGACATGCA 57.276 29.630 10.78 0.00 34.89 3.96
641 888 8.859236 AGAGCAATAATATATGACATGCAACT 57.141 30.769 10.78 7.52 34.89 3.16
642 889 9.293404 AGAGCAATAATATATGACATGCAACTT 57.707 29.630 10.78 0.00 34.89 2.66
651 898 3.963665 TGACATGCAACTTACACAAAGC 58.036 40.909 0.00 0.00 38.93 3.51
652 899 3.379688 TGACATGCAACTTACACAAAGCA 59.620 39.130 0.00 0.00 38.93 3.91
653 900 4.037803 TGACATGCAACTTACACAAAGCAT 59.962 37.500 0.00 0.00 42.82 3.79
654 901 5.240403 TGACATGCAACTTACACAAAGCATA 59.760 36.000 0.00 0.00 40.38 3.14
655 902 5.460646 ACATGCAACTTACACAAAGCATAC 58.539 37.500 0.00 0.00 40.38 2.39
656 903 4.497473 TGCAACTTACACAAAGCATACC 57.503 40.909 0.00 0.00 38.93 2.73
657 904 3.885901 TGCAACTTACACAAAGCATACCA 59.114 39.130 0.00 0.00 38.93 3.25
658 905 4.522405 TGCAACTTACACAAAGCATACCAT 59.478 37.500 0.00 0.00 38.93 3.55
659 906 5.095490 GCAACTTACACAAAGCATACCATC 58.905 41.667 0.00 0.00 38.93 3.51
660 907 5.335583 GCAACTTACACAAAGCATACCATCA 60.336 40.000 0.00 0.00 38.93 3.07
661 908 6.676950 CAACTTACACAAAGCATACCATCAA 58.323 36.000 0.00 0.00 38.93 2.57
662 909 6.892658 ACTTACACAAAGCATACCATCAAA 57.107 33.333 0.00 0.00 38.93 2.69
663 910 7.466746 ACTTACACAAAGCATACCATCAAAT 57.533 32.000 0.00 0.00 38.93 2.32
664 911 7.895759 ACTTACACAAAGCATACCATCAAATT 58.104 30.769 0.00 0.00 38.93 1.82
665 912 8.028938 ACTTACACAAAGCATACCATCAAATTC 58.971 33.333 0.00 0.00 38.93 2.17
666 913 5.401550 ACACAAAGCATACCATCAAATTCG 58.598 37.500 0.00 0.00 0.00 3.34
667 914 5.048083 ACACAAAGCATACCATCAAATTCGT 60.048 36.000 0.00 0.00 0.00 3.85
668 915 6.150307 ACACAAAGCATACCATCAAATTCGTA 59.850 34.615 0.00 0.00 0.00 3.43
669 916 7.148086 ACACAAAGCATACCATCAAATTCGTAT 60.148 33.333 0.00 0.00 0.00 3.06
670 917 7.166307 CACAAAGCATACCATCAAATTCGTATG 59.834 37.037 0.00 0.00 40.55 2.39
671 918 6.942532 AAGCATACCATCAAATTCGTATGT 57.057 33.333 0.00 0.00 40.02 2.29
672 919 6.304356 AGCATACCATCAAATTCGTATGTG 57.696 37.500 0.00 0.00 40.02 3.21
673 920 6.054941 AGCATACCATCAAATTCGTATGTGA 58.945 36.000 0.00 0.00 40.02 3.58
674 921 6.542005 AGCATACCATCAAATTCGTATGTGAA 59.458 34.615 0.00 0.00 40.02 3.18
675 922 7.066887 AGCATACCATCAAATTCGTATGTGAAA 59.933 33.333 0.00 0.00 40.02 2.69
676 923 7.376866 GCATACCATCAAATTCGTATGTGAAAG 59.623 37.037 0.00 0.00 40.02 2.62
677 924 6.817765 ACCATCAAATTCGTATGTGAAAGT 57.182 33.333 0.00 0.00 31.82 2.66
678 925 7.915293 ACCATCAAATTCGTATGTGAAAGTA 57.085 32.000 0.00 0.00 31.82 2.24
679 926 7.974675 ACCATCAAATTCGTATGTGAAAGTAG 58.025 34.615 0.00 0.00 31.82 2.57
680 927 7.822334 ACCATCAAATTCGTATGTGAAAGTAGA 59.178 33.333 0.00 0.00 31.82 2.59
681 928 8.830580 CCATCAAATTCGTATGTGAAAGTAGAT 58.169 33.333 0.00 0.00 31.82 1.98
719 966 8.686397 TTTTTCACATTATGCATGTCATGTAC 57.314 30.769 10.16 0.00 43.17 2.90
720 967 7.628769 TTTCACATTATGCATGTCATGTACT 57.371 32.000 10.16 3.51 43.17 2.73
721 968 8.729805 TTTCACATTATGCATGTCATGTACTA 57.270 30.769 10.16 2.43 43.17 1.82
722 969 8.907222 TTCACATTATGCATGTCATGTACTAT 57.093 30.769 10.16 4.57 43.17 2.12
723 970 8.907222 TCACATTATGCATGTCATGTACTATT 57.093 30.769 10.16 0.00 43.17 1.73
724 971 9.995003 TCACATTATGCATGTCATGTACTATTA 57.005 29.630 10.16 0.00 43.17 0.98
731 978 8.962884 TGCATGTCATGTACTATTAATCTTGT 57.037 30.769 14.26 0.00 0.00 3.16
732 979 9.045223 TGCATGTCATGTACTATTAATCTTGTC 57.955 33.333 14.26 0.00 0.00 3.18
733 980 9.045223 GCATGTCATGTACTATTAATCTTGTCA 57.955 33.333 14.26 0.00 0.00 3.58
747 994 6.727824 AATCTTGTCAATAGTCAAAGACGG 57.272 37.500 0.00 0.00 37.67 4.79
748 995 5.209818 TCTTGTCAATAGTCAAAGACGGT 57.790 39.130 0.00 0.00 37.67 4.83
749 996 5.227908 TCTTGTCAATAGTCAAAGACGGTC 58.772 41.667 0.00 0.00 37.67 4.79
750 997 4.866508 TGTCAATAGTCAAAGACGGTCT 57.133 40.909 4.45 4.45 37.67 3.85
751 998 5.209818 TGTCAATAGTCAAAGACGGTCTT 57.790 39.130 17.38 17.38 38.59 3.01
752 999 4.988540 TGTCAATAGTCAAAGACGGTCTTG 59.011 41.667 23.05 16.41 36.71 3.02
753 1000 5.221362 TGTCAATAGTCAAAGACGGTCTTGA 60.221 40.000 23.05 18.16 36.71 3.02
754 1001 5.694910 GTCAATAGTCAAAGACGGTCTTGAA 59.305 40.000 23.05 11.96 36.71 2.69
755 1002 6.202188 GTCAATAGTCAAAGACGGTCTTGAAA 59.798 38.462 23.05 13.66 36.71 2.69
756 1003 6.764085 TCAATAGTCAAAGACGGTCTTGAAAA 59.236 34.615 23.05 13.38 36.71 2.29
757 1004 7.281324 TCAATAGTCAAAGACGGTCTTGAAAAA 59.719 33.333 23.05 10.33 36.71 1.94
779 1026 8.814038 AAAAAGCATTAGGCCCTATATAGATG 57.186 34.615 11.53 6.87 46.50 2.90
780 1027 6.506538 AAGCATTAGGCCCTATATAGATGG 57.493 41.667 11.53 6.04 46.50 3.51
781 1028 5.792858 AGCATTAGGCCCTATATAGATGGA 58.207 41.667 11.53 0.00 46.50 3.41
782 1029 6.212773 AGCATTAGGCCCTATATAGATGGAA 58.787 40.000 11.53 0.00 46.50 3.53
783 1030 6.853983 AGCATTAGGCCCTATATAGATGGAAT 59.146 38.462 11.53 2.08 46.50 3.01
784 1031 6.939163 GCATTAGGCCCTATATAGATGGAATG 59.061 42.308 11.53 13.14 36.11 2.67
785 1032 7.202130 GCATTAGGCCCTATATAGATGGAATGA 60.202 40.741 11.53 0.00 36.11 2.57
786 1033 7.921041 TTAGGCCCTATATAGATGGAATGAG 57.079 40.000 11.53 0.00 0.00 2.90
787 1034 5.222870 AGGCCCTATATAGATGGAATGAGG 58.777 45.833 11.53 1.87 0.00 3.86
788 1035 4.349342 GGCCCTATATAGATGGAATGAGGG 59.651 50.000 11.53 3.52 44.52 4.30
789 1036 5.219739 GCCCTATATAGATGGAATGAGGGA 58.780 45.833 11.53 0.00 44.48 4.20
790 1037 5.306678 GCCCTATATAGATGGAATGAGGGAG 59.693 48.000 11.53 0.00 44.48 4.30
791 1038 6.448202 CCCTATATAGATGGAATGAGGGAGT 58.552 44.000 11.53 0.00 44.48 3.85
792 1039 7.596407 CCCTATATAGATGGAATGAGGGAGTA 58.404 42.308 11.53 0.00 44.48 2.59
958 1206 4.041198 AGACACTTATTTTGGGACGGAAGA 59.959 41.667 0.00 0.00 0.00 2.87
1240 1488 4.133078 GGACAAGCCATGGAGATTTAGAG 58.867 47.826 18.40 0.00 36.34 2.43
1367 1615 1.338674 TGTCCTTCGCGTTCCATTCAT 60.339 47.619 5.77 0.00 0.00 2.57
1426 1674 1.750399 GTTGCATGTCGGCCAGGAT 60.750 57.895 2.24 0.00 0.00 3.24
1432 1680 1.000283 CATGTCGGCCAGGATAGAGTC 60.000 57.143 2.24 0.00 0.00 3.36
1572 1822 7.170965 TCTTCCTCATTTGTCTCTAGCAAAAT 58.829 34.615 0.00 0.00 38.98 1.82
1854 2106 3.777522 AGATTCCGGATCCAGAGTTCTTT 59.222 43.478 13.41 0.00 35.21 2.52
1855 2107 4.962995 AGATTCCGGATCCAGAGTTCTTTA 59.037 41.667 13.41 0.00 35.21 1.85
2260 2519 6.430007 AGGAGCAATATGGAGATTGAAAACT 58.570 36.000 0.00 0.00 38.83 2.66
2484 2745 6.971527 TTGTATGACCATTAAGTTACACCG 57.028 37.500 0.00 0.00 0.00 4.94
2943 3204 3.181443 ACGGTTCATTCTCTTTCCCAACT 60.181 43.478 0.00 0.00 0.00 3.16
2952 3213 3.518303 TCTCTTTCCCAACTAGGTTAGCC 59.482 47.826 0.00 0.00 34.66 3.93
3239 3507 6.908870 TCAGATCGTGAACTTATTCCATTG 57.091 37.500 0.00 0.00 33.49 2.82
3305 3573 3.057596 GCTGCTGCAACACCTACAATTTA 60.058 43.478 11.11 0.00 39.41 1.40
3405 3673 9.790344 TTGTTGGTGGATTTGATGAATTTTTAT 57.210 25.926 0.00 0.00 0.00 1.40
3463 3731 5.105310 ACACCGACTAGTCAGCTTGATAAAT 60.105 40.000 22.37 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
435 599 8.568794 ACTACCTTTCTAGAAAAATTGTTCAGC 58.431 33.333 18.25 0.00 0.00 4.26
554 801 5.463154 CCCTATATAGATGGAAGGAGGGAG 58.537 50.000 11.53 0.00 44.48 4.30
555 802 4.327010 GCCCTATATAGATGGAAGGAGGGA 60.327 50.000 11.53 0.00 44.48 4.20
556 803 3.970640 GCCCTATATAGATGGAAGGAGGG 59.029 52.174 11.53 3.52 44.52 4.30
557 804 3.970640 GGCCCTATATAGATGGAAGGAGG 59.029 52.174 11.53 1.87 0.00 4.30
558 805 4.889780 AGGCCCTATATAGATGGAAGGAG 58.110 47.826 11.53 0.00 0.00 3.69
559 806 4.994411 AGGCCCTATATAGATGGAAGGA 57.006 45.455 11.53 0.00 0.00 3.36
560 807 6.465035 GCATTAGGCCCTATATAGATGGAAGG 60.465 46.154 11.53 3.94 36.11 3.46
561 808 6.529220 GCATTAGGCCCTATATAGATGGAAG 58.471 44.000 11.53 0.00 36.11 3.46
562 809 5.070446 CGCATTAGGCCCTATATAGATGGAA 59.930 44.000 11.53 0.00 40.31 3.53
563 810 4.588951 CGCATTAGGCCCTATATAGATGGA 59.411 45.833 11.53 0.00 40.31 3.41
564 811 4.345257 ACGCATTAGGCCCTATATAGATGG 59.655 45.833 11.53 6.04 40.31 3.51
565 812 5.537300 ACGCATTAGGCCCTATATAGATG 57.463 43.478 11.53 6.87 40.31 2.90
566 813 6.561519 AAACGCATTAGGCCCTATATAGAT 57.438 37.500 11.53 0.00 40.31 1.98
567 814 6.368779 AAAACGCATTAGGCCCTATATAGA 57.631 37.500 11.53 0.00 40.31 1.98
594 841 8.515414 GCTCTAACATTTGATCAAAGTTAACCT 58.485 33.333 24.17 4.83 33.32 3.50
595 842 8.296713 TGCTCTAACATTTGATCAAAGTTAACC 58.703 33.333 24.17 18.70 33.32 2.85
596 843 9.677567 TTGCTCTAACATTTGATCAAAGTTAAC 57.322 29.630 24.17 19.73 33.32 2.01
612 859 9.723601 TGCATGTCATATATTATTGCTCTAACA 57.276 29.630 0.00 0.00 0.00 2.41
615 862 9.948964 AGTTGCATGTCATATATTATTGCTCTA 57.051 29.630 0.00 0.00 0.00 2.43
616 863 8.859236 AGTTGCATGTCATATATTATTGCTCT 57.141 30.769 0.00 0.00 0.00 4.09
625 872 8.131100 GCTTTGTGTAAGTTGCATGTCATATAT 58.869 33.333 0.00 0.00 36.19 0.86
626 873 7.120432 TGCTTTGTGTAAGTTGCATGTCATATA 59.880 33.333 0.00 0.00 36.19 0.86
627 874 6.072008 TGCTTTGTGTAAGTTGCATGTCATAT 60.072 34.615 0.00 0.00 36.19 1.78
628 875 5.240403 TGCTTTGTGTAAGTTGCATGTCATA 59.760 36.000 0.00 0.00 36.19 2.15
629 876 4.037803 TGCTTTGTGTAAGTTGCATGTCAT 59.962 37.500 0.00 0.00 36.19 3.06
630 877 3.379688 TGCTTTGTGTAAGTTGCATGTCA 59.620 39.130 0.00 0.00 36.19 3.58
631 878 3.963665 TGCTTTGTGTAAGTTGCATGTC 58.036 40.909 0.00 0.00 36.19 3.06
632 879 4.589216 ATGCTTTGTGTAAGTTGCATGT 57.411 36.364 0.00 0.00 39.30 3.21
633 880 4.858692 GGTATGCTTTGTGTAAGTTGCATG 59.141 41.667 8.29 0.00 40.65 4.06
634 881 4.522405 TGGTATGCTTTGTGTAAGTTGCAT 59.478 37.500 0.00 0.00 42.64 3.96
635 882 3.885901 TGGTATGCTTTGTGTAAGTTGCA 59.114 39.130 0.00 0.00 36.19 4.08
636 883 4.497473 TGGTATGCTTTGTGTAAGTTGC 57.503 40.909 0.00 0.00 36.19 4.17
637 884 6.252967 TGATGGTATGCTTTGTGTAAGTTG 57.747 37.500 0.00 0.00 36.19 3.16
638 885 6.892658 TTGATGGTATGCTTTGTGTAAGTT 57.107 33.333 0.00 0.00 36.19 2.66
639 886 6.892658 TTTGATGGTATGCTTTGTGTAAGT 57.107 33.333 0.00 0.00 36.19 2.24
640 887 7.218773 CGAATTTGATGGTATGCTTTGTGTAAG 59.781 37.037 0.00 0.00 36.90 2.34
641 888 7.026562 CGAATTTGATGGTATGCTTTGTGTAA 58.973 34.615 0.00 0.00 0.00 2.41
642 889 6.150307 ACGAATTTGATGGTATGCTTTGTGTA 59.850 34.615 0.00 0.00 0.00 2.90
643 890 5.048083 ACGAATTTGATGGTATGCTTTGTGT 60.048 36.000 0.00 0.00 0.00 3.72
644 891 5.401550 ACGAATTTGATGGTATGCTTTGTG 58.598 37.500 0.00 0.00 0.00 3.33
645 892 5.643379 ACGAATTTGATGGTATGCTTTGT 57.357 34.783 0.00 0.00 0.00 2.83
646 893 7.166307 CACATACGAATTTGATGGTATGCTTTG 59.834 37.037 0.00 0.00 43.66 2.77
647 894 7.066887 TCACATACGAATTTGATGGTATGCTTT 59.933 33.333 0.00 0.00 43.66 3.51
648 895 6.542005 TCACATACGAATTTGATGGTATGCTT 59.458 34.615 0.00 0.00 43.66 3.91
649 896 6.054941 TCACATACGAATTTGATGGTATGCT 58.945 36.000 0.00 0.00 43.66 3.79
650 897 6.299023 TCACATACGAATTTGATGGTATGC 57.701 37.500 0.00 0.00 43.66 3.14
651 898 8.397906 ACTTTCACATACGAATTTGATGGTATG 58.602 33.333 0.00 8.12 44.76 2.39
652 899 8.506168 ACTTTCACATACGAATTTGATGGTAT 57.494 30.769 0.00 0.00 0.00 2.73
653 900 7.915293 ACTTTCACATACGAATTTGATGGTA 57.085 32.000 0.00 0.00 0.00 3.25
654 901 6.817765 ACTTTCACATACGAATTTGATGGT 57.182 33.333 0.00 0.00 0.00 3.55
655 902 8.196802 TCTACTTTCACATACGAATTTGATGG 57.803 34.615 0.00 0.00 0.00 3.51
705 952 9.565090 ACAAGATTAATAGTACATGACATGCAT 57.435 29.630 15.49 0.00 37.85 3.96
706 953 8.962884 ACAAGATTAATAGTACATGACATGCA 57.037 30.769 15.49 0.00 0.00 3.96
707 954 9.045223 TGACAAGATTAATAGTACATGACATGC 57.955 33.333 15.49 0.11 0.00 4.06
721 968 8.883731 CCGTCTTTGACTATTGACAAGATTAAT 58.116 33.333 0.00 0.00 0.00 1.40
722 969 7.876068 ACCGTCTTTGACTATTGACAAGATTAA 59.124 33.333 0.00 0.00 0.00 1.40
723 970 7.383687 ACCGTCTTTGACTATTGACAAGATTA 58.616 34.615 0.00 0.00 0.00 1.75
724 971 6.231211 ACCGTCTTTGACTATTGACAAGATT 58.769 36.000 0.00 0.00 0.00 2.40
725 972 5.794894 ACCGTCTTTGACTATTGACAAGAT 58.205 37.500 0.00 0.00 0.00 2.40
726 973 5.010719 AGACCGTCTTTGACTATTGACAAGA 59.989 40.000 0.00 0.00 0.00 3.02
727 974 5.230942 AGACCGTCTTTGACTATTGACAAG 58.769 41.667 0.00 0.00 0.00 3.16
728 975 5.209818 AGACCGTCTTTGACTATTGACAA 57.790 39.130 0.00 0.00 0.00 3.18
729 976 4.866508 AGACCGTCTTTGACTATTGACA 57.133 40.909 0.00 0.00 0.00 3.58
730 977 5.227908 TCAAGACCGTCTTTGACTATTGAC 58.772 41.667 11.24 0.00 33.78 3.18
731 978 5.462530 TCAAGACCGTCTTTGACTATTGA 57.537 39.130 11.24 1.39 33.78 2.57
732 979 6.539649 TTTCAAGACCGTCTTTGACTATTG 57.460 37.500 11.24 0.00 33.78 1.90
733 980 7.562454 TTTTTCAAGACCGTCTTTGACTATT 57.438 32.000 11.24 0.00 33.78 1.73
754 1001 7.836183 CCATCTATATAGGGCCTAATGCTTTTT 59.164 37.037 18.91 0.30 40.92 1.94
755 1002 7.184570 TCCATCTATATAGGGCCTAATGCTTTT 59.815 37.037 18.91 1.12 40.92 2.27
756 1003 6.678411 TCCATCTATATAGGGCCTAATGCTTT 59.322 38.462 18.91 1.94 40.92 3.51
757 1004 6.212773 TCCATCTATATAGGGCCTAATGCTT 58.787 40.000 18.91 2.76 40.92 3.91
758 1005 5.792858 TCCATCTATATAGGGCCTAATGCT 58.207 41.667 18.91 3.18 40.92 3.79
759 1006 6.500589 TTCCATCTATATAGGGCCTAATGC 57.499 41.667 18.91 0.00 40.16 3.56
760 1007 8.267620 TCATTCCATCTATATAGGGCCTAATG 57.732 38.462 18.91 15.42 0.00 1.90
761 1008 7.515514 CCTCATTCCATCTATATAGGGCCTAAT 59.484 40.741 18.91 14.19 0.00 1.73
762 1009 6.846505 CCTCATTCCATCTATATAGGGCCTAA 59.153 42.308 18.91 7.61 0.00 2.69
763 1010 6.385443 CCTCATTCCATCTATATAGGGCCTA 58.615 44.000 17.16 17.16 0.00 3.93
764 1011 5.222870 CCTCATTCCATCTATATAGGGCCT 58.777 45.833 12.58 12.58 0.00 5.19
765 1012 4.349342 CCCTCATTCCATCTATATAGGGCC 59.651 50.000 9.89 0.00 36.30 5.80
766 1013 5.219739 TCCCTCATTCCATCTATATAGGGC 58.780 45.833 9.89 0.00 41.88 5.19
767 1014 6.448202 ACTCCCTCATTCCATCTATATAGGG 58.552 44.000 9.89 4.49 43.23 3.53
768 1015 9.087871 CATACTCCCTCATTCCATCTATATAGG 57.912 40.741 9.89 0.00 0.00 2.57
769 1016 9.087871 CCATACTCCCTCATTCCATCTATATAG 57.912 40.741 3.10 3.10 0.00 1.31
770 1017 8.801645 TCCATACTCCCTCATTCCATCTATATA 58.198 37.037 0.00 0.00 0.00 0.86
771 1018 7.665922 TCCATACTCCCTCATTCCATCTATAT 58.334 38.462 0.00 0.00 0.00 0.86
772 1019 7.056522 TCCATACTCCCTCATTCCATCTATA 57.943 40.000 0.00 0.00 0.00 1.31
773 1020 5.920347 TCCATACTCCCTCATTCCATCTAT 58.080 41.667 0.00 0.00 0.00 1.98
774 1021 5.162826 ACTCCATACTCCCTCATTCCATCTA 60.163 44.000 0.00 0.00 0.00 1.98
775 1022 4.166539 CTCCATACTCCCTCATTCCATCT 58.833 47.826 0.00 0.00 0.00 2.90
776 1023 3.906846 ACTCCATACTCCCTCATTCCATC 59.093 47.826 0.00 0.00 0.00 3.51
777 1024 3.946824 ACTCCATACTCCCTCATTCCAT 58.053 45.455 0.00 0.00 0.00 3.41
778 1025 3.421394 ACTCCATACTCCCTCATTCCA 57.579 47.619 0.00 0.00 0.00 3.53
779 1026 4.841246 ACATACTCCATACTCCCTCATTCC 59.159 45.833 0.00 0.00 0.00 3.01
780 1027 5.336055 CGACATACTCCATACTCCCTCATTC 60.336 48.000 0.00 0.00 0.00 2.67
781 1028 4.524714 CGACATACTCCATACTCCCTCATT 59.475 45.833 0.00 0.00 0.00 2.57
782 1029 4.082845 CGACATACTCCATACTCCCTCAT 58.917 47.826 0.00 0.00 0.00 2.90
783 1030 3.137728 TCGACATACTCCATACTCCCTCA 59.862 47.826 0.00 0.00 0.00 3.86
784 1031 3.502979 GTCGACATACTCCATACTCCCTC 59.497 52.174 11.55 0.00 0.00 4.30
785 1032 3.117625 TGTCGACATACTCCATACTCCCT 60.118 47.826 15.76 0.00 0.00 4.20
786 1033 3.220110 TGTCGACATACTCCATACTCCC 58.780 50.000 15.76 0.00 0.00 4.30
787 1034 4.913335 TTGTCGACATACTCCATACTCC 57.087 45.455 20.80 0.00 0.00 3.85
788 1035 6.588756 TGTTTTTGTCGACATACTCCATACTC 59.411 38.462 20.80 1.80 0.00 2.59
789 1036 6.460781 TGTTTTTGTCGACATACTCCATACT 58.539 36.000 20.80 0.00 0.00 2.12
790 1037 6.715344 TGTTTTTGTCGACATACTCCATAC 57.285 37.500 20.80 9.52 0.00 2.39
791 1038 7.156000 TCTTGTTTTTGTCGACATACTCCATA 58.844 34.615 20.80 0.00 0.00 2.74
792 1039 5.995282 TCTTGTTTTTGTCGACATACTCCAT 59.005 36.000 20.80 0.00 0.00 3.41
1240 1488 2.930040 TCTAGCTAGATGTTTTGCACGC 59.070 45.455 19.72 0.00 0.00 5.34
1367 1615 2.499205 CGGACTGGATTGCCGCTA 59.501 61.111 0.00 0.00 38.46 4.26
1426 1674 0.812811 CGGTCATCGGTCCGACTCTA 60.813 60.000 18.08 0.00 46.67 2.43
1572 1822 1.134995 CAGCTCGTGGTCAATGCTCTA 60.135 52.381 0.00 0.00 0.00 2.43
1854 2106 5.953571 TGTGGAGAGGAAGTATCTATGCTA 58.046 41.667 0.00 0.00 0.00 3.49
1855 2107 4.809193 TGTGGAGAGGAAGTATCTATGCT 58.191 43.478 0.00 0.00 0.00 3.79
1901 2153 3.211045 ACGAAAGCCACTTTTCTTGCTA 58.789 40.909 0.00 0.00 33.49 3.49
2260 2519 2.171659 TCAACTTGTTGACCACCTGCTA 59.828 45.455 11.62 0.00 0.00 3.49
2484 2745 7.328277 TGGCACATACAGAATAAAACATACC 57.672 36.000 0.00 0.00 0.00 2.73
2767 3028 4.713553 TGATGACAGGAAGCAACAAACTA 58.286 39.130 0.00 0.00 0.00 2.24
2837 3098 2.287915 GCATAAGCACCATCGTAGTTGG 59.712 50.000 0.00 0.00 41.58 3.77
2943 3204 1.822990 CAGTGGTCTTCGGCTAACCTA 59.177 52.381 0.00 0.00 34.05 3.08
2952 3213 2.093306 TATGTTGGCAGTGGTCTTCG 57.907 50.000 0.00 0.00 0.00 3.79
3305 3573 7.904205 AGCAGTGTACTAGGTATTTTTACAGT 58.096 34.615 0.00 0.00 0.00 3.55
3405 3673 3.701542 GTCATGAGATCACTGACCCTACA 59.298 47.826 0.00 0.00 34.55 2.74
3463 3731 0.468226 ACTTGCAAGTCTCCGACCAA 59.532 50.000 26.36 0.00 32.86 3.67


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

AutoCloner maintained by Alex Coulton.