Multiple sequence alignment - TraesCS3B01G295700

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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 TraesCS3B01G295700 chr3B 100.000 4806 0 0 1 4806 474032767 474027962 0.000000e+00 8876
1 TraesCS3B01G295700 chr3D 94.267 2477 115 13 2342 4806 363870545 363868084 0.000000e+00 3762
2 TraesCS3B01G295700 chr3D 94.333 600 19 2 881 1474 363872399 363871809 0.000000e+00 905
3 TraesCS3B01G295700 chr3D 88.790 562 21 15 8 552 363873144 363872608 0.000000e+00 651
4 TraesCS3B01G295700 chr3D 89.270 466 31 7 1793 2252 363871406 363870954 2.510000e-157 566
5 TraesCS3B01G295700 chr3D 92.887 239 5 4 611 849 363872614 363872388 2.140000e-88 337
6 TraesCS3B01G295700 chr3A 90.290 2173 105 46 881 2960 485015133 485012974 0.000000e+00 2747
7 TraesCS3B01G295700 chr3A 93.348 1804 90 17 3022 4806 485012949 485011157 0.000000e+00 2639
8 TraesCS3B01G295700 chr3A 86.906 695 33 22 6 674 485015923 485015261 0.000000e+00 726
9 TraesCS3B01G295700 chr3A 93.750 128 3 1 725 847 485015251 485015124 2.280000e-43 187
10 TraesCS3B01G295700 chr1D 81.455 275 49 2 4533 4806 457074694 457074421 1.740000e-54 224
11 TraesCS3B01G295700 chr1A 81.685 273 47 3 4536 4806 549712735 549712464 1.740000e-54 224


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 TraesCS3B01G295700 chr3B 474027962 474032767 4805 True 8876.00 8876 100.0000 1 4806 1 chr3B.!!$R1 4805
1 TraesCS3B01G295700 chr3D 363868084 363873144 5060 True 1244.20 3762 91.9094 8 4806 5 chr3D.!!$R1 4798
2 TraesCS3B01G295700 chr3A 485011157 485015923 4766 True 1574.75 2747 91.0735 6 4806 4 chr3A.!!$R1 4800

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
861 899 0.179045 AGCACACACACACTCTTCCC 60.179 55.0 0.0 0.0 0.0 3.97 F
863 901 0.469917 CACACACACACTCTTCCCCT 59.530 55.0 0.0 0.0 0.0 4.79 F
2693 3183 0.179124 TTGCTTCACGGTTGCCAAAC 60.179 50.0 0.0 0.0 35.4 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2256 0.033208 ACAGTACCATGGCCCCATTG 60.033 55.0 13.04 4.52 33.90 2.82 R
2797 3287 0.908198 AACTCTGATGAGGAGGGTGC 59.092 55.0 0.00 0.00 44.29 5.01 R
4199 4714 0.321122 GAGTGGAGTGCTGAACTGGG 60.321 60.0 0.00 0.00 40.07 4.45 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
108 119 1.338136 CCTATCCAACCGGCAGGAGT 61.338 60.000 19.02 10.81 41.02 3.85
234 253 1.512926 CCTGCCCGTTCTGTATATGC 58.487 55.000 0.00 0.00 0.00 3.14
263 284 5.351740 AGGTTTATTACTTTTGCTCGAGCTC 59.648 40.000 35.27 11.03 42.66 4.09
311 338 1.065928 CTCGAGTACATGACCCGCC 59.934 63.158 3.62 0.00 0.00 6.13
439 466 1.923148 CCCCCATCCTAAAGACAACCT 59.077 52.381 0.00 0.00 0.00 3.50
495 522 1.446272 CGCCACGTTCTCTCCTTCC 60.446 63.158 0.00 0.00 0.00 3.46
502 529 3.193691 CACGTTCTCTCCTTCCACATACT 59.806 47.826 0.00 0.00 0.00 2.12
503 530 3.444388 ACGTTCTCTCCTTCCACATACTC 59.556 47.826 0.00 0.00 0.00 2.59
504 531 3.181485 CGTTCTCTCCTTCCACATACTCC 60.181 52.174 0.00 0.00 0.00 3.85
505 532 3.757947 TCTCTCCTTCCACATACTCCA 57.242 47.619 0.00 0.00 0.00 3.86
506 533 4.271807 TCTCTCCTTCCACATACTCCAT 57.728 45.455 0.00 0.00 0.00 3.41
507 534 5.403558 TCTCTCCTTCCACATACTCCATA 57.596 43.478 0.00 0.00 0.00 2.74
508 535 5.389520 TCTCTCCTTCCACATACTCCATAG 58.610 45.833 0.00 0.00 0.00 2.23
509 536 5.103473 TCTCTCCTTCCACATACTCCATAGT 60.103 44.000 0.00 0.00 39.91 2.12
510 537 6.102762 TCTCTCCTTCCACATACTCCATAGTA 59.897 42.308 0.00 0.00 42.35 1.82
511 538 6.069331 TCTCCTTCCACATACTCCATAGTAC 58.931 44.000 0.00 0.00 40.98 2.73
541 568 3.946558 GACTCCTAGTTCTCTTCGCCTAA 59.053 47.826 0.00 0.00 0.00 2.69
561 588 5.308237 CCTAACCTAAACCATCTCTAGCCAT 59.692 44.000 0.00 0.00 0.00 4.40
571 598 5.132648 ACCATCTCTAGCCATCCATTTACAA 59.867 40.000 0.00 0.00 0.00 2.41
574 601 5.674525 TCTCTAGCCATCCATTTACAACTG 58.325 41.667 0.00 0.00 0.00 3.16
575 602 5.189736 TCTCTAGCCATCCATTTACAACTGT 59.810 40.000 0.00 0.00 0.00 3.55
578 605 4.603131 AGCCATCCATTTACAACTGTGAT 58.397 39.130 0.00 0.00 0.00 3.06
658 691 6.890979 AAAGAAGGGAGAAATCTTTCACTG 57.109 37.500 5.53 0.00 38.65 3.66
674 707 3.747521 CTGGTTGGCCACCCACCAA 62.748 63.158 24.60 11.61 46.68 3.67
677 710 2.119391 TTGGCCACCCACCAATCC 59.881 61.111 3.88 0.00 42.23 3.01
678 711 2.783535 TTGGCCACCCACCAATCCA 61.784 57.895 3.88 0.00 42.23 3.41
679 712 2.679996 GGCCACCCACCAATCCAC 60.680 66.667 0.00 0.00 0.00 4.02
680 713 2.679996 GCCACCCACCAATCCACC 60.680 66.667 0.00 0.00 0.00 4.61
681 714 2.850290 CCACCCACCAATCCACCA 59.150 61.111 0.00 0.00 0.00 4.17
719 752 1.445582 GGACGACGACCGCAGAATT 60.446 57.895 0.00 0.00 43.32 2.17
849 887 5.616270 TCCAACACTAGAATTAAGCACACA 58.384 37.500 0.00 0.00 0.00 3.72
850 888 5.468746 TCCAACACTAGAATTAAGCACACAC 59.531 40.000 0.00 0.00 0.00 3.82
851 889 5.238432 CCAACACTAGAATTAAGCACACACA 59.762 40.000 0.00 0.00 0.00 3.72
852 890 5.924475 ACACTAGAATTAAGCACACACAC 57.076 39.130 0.00 0.00 0.00 3.82
853 891 5.364778 ACACTAGAATTAAGCACACACACA 58.635 37.500 0.00 0.00 0.00 3.72
854 892 5.236478 ACACTAGAATTAAGCACACACACAC 59.764 40.000 0.00 0.00 0.00 3.82
855 893 5.466728 CACTAGAATTAAGCACACACACACT 59.533 40.000 0.00 0.00 0.00 3.55
856 894 5.696724 ACTAGAATTAAGCACACACACACTC 59.303 40.000 0.00 0.00 0.00 3.51
857 895 4.708177 AGAATTAAGCACACACACACTCT 58.292 39.130 0.00 0.00 0.00 3.24
858 896 5.126067 AGAATTAAGCACACACACACTCTT 58.874 37.500 0.00 0.00 0.00 2.85
859 897 5.237344 AGAATTAAGCACACACACACTCTTC 59.763 40.000 0.00 0.00 0.00 2.87
860 898 1.668419 AAGCACACACACACTCTTCC 58.332 50.000 0.00 0.00 0.00 3.46
861 899 0.179045 AGCACACACACACTCTTCCC 60.179 55.000 0.00 0.00 0.00 3.97
862 900 1.166531 GCACACACACACTCTTCCCC 61.167 60.000 0.00 0.00 0.00 4.81
863 901 0.469917 CACACACACACTCTTCCCCT 59.530 55.000 0.00 0.00 0.00 4.79
864 902 0.759346 ACACACACACTCTTCCCCTC 59.241 55.000 0.00 0.00 0.00 4.30
865 903 0.758734 CACACACACTCTTCCCCTCA 59.241 55.000 0.00 0.00 0.00 3.86
866 904 1.140852 CACACACACTCTTCCCCTCAA 59.859 52.381 0.00 0.00 0.00 3.02
867 905 1.843851 ACACACACTCTTCCCCTCAAA 59.156 47.619 0.00 0.00 0.00 2.69
868 906 2.241176 ACACACACTCTTCCCCTCAAAA 59.759 45.455 0.00 0.00 0.00 2.44
869 907 3.287222 CACACACTCTTCCCCTCAAAAA 58.713 45.455 0.00 0.00 0.00 1.94
906 944 0.655733 CACACTCGCCACGAAAAGTT 59.344 50.000 0.00 0.00 34.74 2.66
958 1019 1.305633 TCCTCTCTGCTCCCACCAG 60.306 63.158 0.00 0.00 0.00 4.00
959 1020 2.365586 CCTCTCTGCTCCCACCAGG 61.366 68.421 0.00 0.00 0.00 4.45
960 1021 3.005539 TCTCTGCTCCCACCAGGC 61.006 66.667 0.00 0.00 34.51 4.85
961 1022 4.106925 CTCTGCTCCCACCAGGCC 62.107 72.222 0.00 0.00 34.51 5.19
962 1023 4.980592 TCTGCTCCCACCAGGCCA 62.981 66.667 5.01 0.00 34.51 5.36
963 1024 4.729918 CTGCTCCCACCAGGCCAC 62.730 72.222 5.01 0.00 34.51 5.01
966 1027 4.351054 CTCCCACCAGGCCACCAC 62.351 72.222 5.01 0.00 34.51 4.16
969 1030 4.974721 CCACCAGGCCACCACCAC 62.975 72.222 5.01 0.00 0.00 4.16
970 1031 4.974721 CACCAGGCCACCACCACC 62.975 72.222 5.01 0.00 0.00 4.61
972 1033 4.351054 CCAGGCCACCACCACCTC 62.351 72.222 5.01 0.00 0.00 3.85
973 1034 4.351054 CAGGCCACCACCACCTCC 62.351 72.222 5.01 0.00 0.00 4.30
974 1035 4.918360 AGGCCACCACCACCTCCA 62.918 66.667 5.01 0.00 0.00 3.86
1191 1257 1.075374 CTCCTCATCCCCGAGATCTCT 59.925 57.143 20.26 0.00 34.79 3.10
1509 1606 1.227999 TTGCGGCTGAGAAGTTTCCG 61.228 55.000 0.00 0.00 42.68 4.30
1560 1657 2.220653 AGGTGCGTACTGGGTAGTAA 57.779 50.000 3.01 0.00 40.89 2.24
1588 1697 7.013178 TGGATATGTGGTGTGCATTTATTAGTG 59.987 37.037 0.00 0.00 0.00 2.74
1597 1709 7.850982 GGTGTGCATTTATTAGTGTTAGATTCG 59.149 37.037 0.00 0.00 0.00 3.34
1610 1722 4.873827 TGTTAGATTCGGTGTGCCTATTTC 59.126 41.667 0.00 0.00 0.00 2.17
1624 1736 3.445096 GCCTATTTCTGATTGGTTGCTGT 59.555 43.478 0.00 0.00 0.00 4.40
1635 1747 5.819379 TGATTGGTTGCTGTAATTTTGCAAA 59.181 32.000 8.05 8.05 46.22 3.68
1648 1760 5.638530 ATTTTGCAAAAGGGGGTTTTCTA 57.361 34.783 27.08 2.43 36.11 2.10
1653 1765 8.437274 TTTGCAAAAGGGGGTTTTCTATATTA 57.563 30.769 10.02 0.00 36.11 0.98
1660 1772 6.549242 AGGGGGTTTTCTATATTATTTCGGG 58.451 40.000 0.00 0.00 0.00 5.14
1678 1801 8.996651 ATTTCGGGGTAAGATCATCTTATTTT 57.003 30.769 10.40 0.00 40.64 1.82
1682 1805 6.017109 CGGGGTAAGATCATCTTATTTTGGTG 60.017 42.308 10.40 0.00 40.64 4.17
1683 1806 6.239036 GGGGTAAGATCATCTTATTTTGGTGC 60.239 42.308 10.40 0.00 40.64 5.01
1705 1831 1.350351 ACTTCACTGCTGCAGATCCTT 59.650 47.619 34.28 10.32 35.18 3.36
1708 1834 3.701205 TCACTGCTGCAGATCCTTTTA 57.299 42.857 34.28 8.44 35.18 1.52
1721 1847 8.299570 TGCAGATCCTTTTAGACTCAAATTTTC 58.700 33.333 0.00 0.00 0.00 2.29
1746 1872 6.088085 CGAATTGCACACAAGATAAGGAAAAC 59.912 38.462 0.00 0.00 39.69 2.43
1747 1873 5.843673 TTGCACACAAGATAAGGAAAACA 57.156 34.783 0.00 0.00 0.00 2.83
1750 1876 6.634805 TGCACACAAGATAAGGAAAACAAAA 58.365 32.000 0.00 0.00 0.00 2.44
1783 1910 8.150945 ACTAGTATTAGTGCGGATGAAATTCAT 58.849 33.333 8.39 8.39 38.03 2.57
1799 1959 9.643693 ATGAAATTCATCTGTATTTGTTGGTTC 57.356 29.630 2.07 0.00 29.59 3.62
1803 1963 4.458989 TCATCTGTATTTGTTGGTTCCTGC 59.541 41.667 0.00 0.00 0.00 4.85
1814 1974 4.010349 GTTGGTTCCTGCTTAGCACTATT 58.990 43.478 1.39 0.00 33.79 1.73
1939 2101 9.326413 CCGTATCAGTCCATTAGTTTAGAAAAT 57.674 33.333 0.00 0.00 0.00 1.82
1948 2110 7.980099 TCCATTAGTTTAGAAAATCTCGACCTC 59.020 37.037 0.00 0.00 0.00 3.85
1956 2118 9.938280 TTTAGAAAATCTCGACCTCATTTCTAA 57.062 29.630 15.60 15.60 42.75 2.10
1957 2119 9.938280 TTAGAAAATCTCGACCTCATTTCTAAA 57.062 29.630 16.46 7.53 42.10 1.85
2032 2197 3.201290 ACAGCAGAAACTCTGTGACTTG 58.799 45.455 5.61 0.94 45.94 3.16
2203 2371 7.108847 AGAAACTTTTCGAATGATGAGGAGAT 58.891 34.615 0.00 0.00 41.92 2.75
2277 2445 6.407187 CCAATGTGCCAGATGATTGGAATTAA 60.407 38.462 0.00 0.00 45.26 1.40
2322 2491 2.273776 CCACACCACCCACACACA 59.726 61.111 0.00 0.00 0.00 3.72
2336 2505 2.910482 CACACACACGCTTGATTTATGC 59.090 45.455 0.00 0.00 0.00 3.14
2356 2843 5.401531 TGCTCAAAGTTAGTACCCTACAG 57.598 43.478 0.00 0.00 0.00 2.74
2361 2848 7.463961 TCAAAGTTAGTACCCTACAGAAGAG 57.536 40.000 0.00 0.00 0.00 2.85
2453 2941 2.966516 GGAGGTCTACAGGGAAGGTATG 59.033 54.545 0.00 0.00 0.00 2.39
2467 2957 4.982295 GGAAGGTATGTTTGTGTTTTCTGC 59.018 41.667 0.00 0.00 0.00 4.26
2484 2974 8.067784 TGTTTTCTGCTTCATCTTTAACTTACG 58.932 33.333 0.00 0.00 0.00 3.18
2486 2976 6.706055 TCTGCTTCATCTTTAACTTACGTG 57.294 37.500 0.00 0.00 0.00 4.49
2494 2984 4.069304 TCTTTAACTTACGTGGCAATGCT 58.931 39.130 4.82 0.00 0.00 3.79
2501 2991 4.094887 ACTTACGTGGCAATGCTAATCTTG 59.905 41.667 4.82 0.00 0.00 3.02
2642 3132 8.680903 CCAGATGAGGATATAATTTTGTATGGC 58.319 37.037 0.00 0.00 0.00 4.40
2693 3183 0.179124 TTGCTTCACGGTTGCCAAAC 60.179 50.000 0.00 0.00 35.40 2.93
2720 3210 0.886490 CTGTGGTTCTGCACAGTCCC 60.886 60.000 0.00 0.08 42.62 4.46
2741 3231 6.098409 GTCCCATTTTATCTGGACTGAGAGTA 59.902 42.308 0.00 0.00 43.16 2.59
2756 3246 7.174253 GGACTGAGAGTACTATATCCAGTCAAG 59.826 44.444 26.31 9.93 46.27 3.02
2797 3287 9.619316 TGACATTTACAAGGTAAATTCGATTTG 57.381 29.630 10.72 4.05 33.82 2.32
2799 3289 8.085296 ACATTTACAAGGTAAATTCGATTTGCA 58.915 29.630 10.72 0.00 36.71 4.08
2808 3304 0.690192 TTCGATTTGCACCCTCCTCA 59.310 50.000 0.00 0.00 0.00 3.86
2809 3305 0.911769 TCGATTTGCACCCTCCTCAT 59.088 50.000 0.00 0.00 0.00 2.90
2818 3314 1.209019 CACCCTCCTCATCAGAGTTGG 59.791 57.143 0.00 0.00 40.40 3.77
2827 3326 7.202038 CCTCCTCATCAGAGTTGGTGATAAATA 60.202 40.741 0.00 0.00 43.27 1.40
2861 3361 7.610580 TTTTCCCTCCATTTTGTAGAATGTT 57.389 32.000 0.00 0.00 35.68 2.71
2947 3447 7.460082 ACCCTACCCTCTTCTTTTTCAATACTA 59.540 37.037 0.00 0.00 0.00 1.82
2961 3461 4.953667 TCAATACTATCTGCCTCTTGCTG 58.046 43.478 0.00 0.00 42.00 4.41
2971 3471 2.086869 GCCTCTTGCTGTCTTGCATTA 58.913 47.619 0.00 0.00 42.96 1.90
3002 3502 4.081697 GGTGGGATAGTGGGATTTGTTTTG 60.082 45.833 0.00 0.00 0.00 2.44
3035 3536 5.171339 ACCACTACATTGAGAAGCTGAAT 57.829 39.130 0.00 0.00 0.00 2.57
3039 3541 8.486210 ACCACTACATTGAGAAGCTGAATATAA 58.514 33.333 0.00 0.00 0.00 0.98
3085 3587 8.301002 TCACCAAGCCAAGTATGTAAAAATTAC 58.699 33.333 0.00 0.00 0.00 1.89
3117 3619 7.053316 TGAACCAAATGAACAATCAGATGTT 57.947 32.000 0.00 0.00 45.82 2.71
3142 3644 4.464008 AGTTGCTGGGGTGATATAACATG 58.536 43.478 0.00 0.00 0.00 3.21
3250 3760 2.467566 ACGTAGTTGATTGGTCCCAC 57.532 50.000 0.00 0.00 37.78 4.61
3385 3895 0.667993 TGTCGAGCCTTGGCAAAAAG 59.332 50.000 14.54 0.00 0.00 2.27
3388 3898 0.954452 CGAGCCTTGGCAAAAAGTCT 59.046 50.000 14.54 0.00 0.00 3.24
3421 3931 3.560068 ACTTGAAAGAGTTACCAGCAACG 59.440 43.478 0.00 0.00 33.50 4.10
3436 3946 1.935300 GCAACGGAAGACACATCTCGT 60.935 52.381 0.00 0.00 37.08 4.18
3467 3977 5.419542 CAGAATCTGTATCCTCGGACAAAA 58.580 41.667 1.31 0.00 0.00 2.44
3490 4000 1.799258 AAGAAGCTGCAAAGTGCCGG 61.799 55.000 1.02 0.00 44.23 6.13
3511 4021 0.102120 AGATCTCGCGGAAGAGCTTG 59.898 55.000 9.53 0.00 38.87 4.01
3623 4133 3.355378 TGCTTGGTTTGGTGATCTATGG 58.645 45.455 0.00 0.00 0.00 2.74
3656 4166 4.202357 TGCACAGTTCATGGAGTAGTTTCT 60.202 41.667 0.00 0.00 0.00 2.52
3659 4169 5.636965 CACAGTTCATGGAGTAGTTTCTGAG 59.363 44.000 0.00 0.00 0.00 3.35
3691 4201 1.197721 GGGAATCAAGCAACTGTGTCG 59.802 52.381 0.00 0.00 0.00 4.35
3714 4224 2.159282 AGTGTATAGCGAGGAACAACGG 60.159 50.000 0.00 0.00 0.00 4.44
3725 4235 0.878961 GAACAACGGCGACAGTTCCT 60.879 55.000 16.62 0.00 35.52 3.36
3737 4247 1.686110 AGTTCCTGCGGTAGAGGGG 60.686 63.158 0.00 0.00 0.00 4.79
3750 4260 4.161102 GGTAGAGGGGATAATAGCTGTGT 58.839 47.826 0.00 0.00 0.00 3.72
3778 4288 4.107072 TGTGGGAGAAGAAGAATCAGGAT 58.893 43.478 0.00 0.00 0.00 3.24
3864 4375 0.610785 AACCTGTATTGCAACCCCCG 60.611 55.000 0.00 0.00 0.00 5.73
4078 4589 1.082756 CGTTGCGTCTTTCTGCACC 60.083 57.895 0.00 0.00 41.57 5.01
4137 4652 1.065199 TGTTGGGGCTGCAGAATAGAG 60.065 52.381 20.43 0.00 0.00 2.43
4212 4727 5.602561 TGTATCATATACCCAGTTCAGCACT 59.397 40.000 0.00 0.00 35.35 4.40
4234 4749 2.607635 CCACTCCAATGTACGTATGCAC 59.392 50.000 0.00 0.00 0.00 4.57
4328 4845 0.738975 AAGAATCGTCGGATCGCTCA 59.261 50.000 0.00 0.00 30.81 4.26
4358 4875 2.593257 GCAAGCAAATCTCTCAACAGC 58.407 47.619 0.00 0.00 0.00 4.40
4467 4989 3.077907 CACCGTGTTGGGGGAGAT 58.922 61.111 0.00 0.00 44.64 2.75
4522 5044 1.507141 CGTCTTTGTGACCCAGGCAC 61.507 60.000 0.00 0.00 42.49 5.01
4561 5083 2.526873 ACGTCCAGCACCTCCCTT 60.527 61.111 0.00 0.00 0.00 3.95
4657 5179 3.214845 GCCGGGTCCGACTCGTAT 61.215 66.667 19.18 0.00 41.30 3.06
4660 5182 2.550101 CGGGTCCGACTCGTATCCC 61.550 68.421 12.87 10.81 37.30 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.198150 ATGTGCACAGCCACCCAA 59.802 55.556 25.84 0.00 34.85 4.12
1 2 2.598099 CATGTGCACAGCCACCCA 60.598 61.111 25.84 0.00 34.85 4.51
2 3 3.376078 CCATGTGCACAGCCACCC 61.376 66.667 25.84 0.00 34.85 4.61
3 4 1.660560 GATCCATGTGCACAGCCACC 61.661 60.000 25.84 10.31 34.85 4.61
4 5 0.961857 TGATCCATGTGCACAGCCAC 60.962 55.000 25.84 14.76 36.28 5.01
108 119 3.120338 GGACGCAACAATCGATCTTTTCA 60.120 43.478 0.00 0.00 0.00 2.69
140 151 4.436998 CCGTCCGTCCCAGAGTGC 62.437 72.222 0.00 0.00 0.00 4.40
220 235 3.243301 ACCTACACGCATATACAGAACGG 60.243 47.826 0.00 0.00 0.00 4.44
234 253 6.089820 TCGAGCAAAAGTAATAAACCTACACG 59.910 38.462 0.00 0.00 0.00 4.49
311 338 1.089481 TTTAGCTGCGCTTCATCGGG 61.089 55.000 9.73 0.00 40.44 5.14
436 463 6.971726 AGTTTCCCGATAAAAGAAAAAGGT 57.028 33.333 0.00 0.00 31.71 3.50
495 522 6.434340 TCCAGCTATGTACTATGGAGTATGTG 59.566 42.308 0.00 0.00 40.32 3.21
502 529 4.106502 AGGAGTCCAGCTATGTACTATGGA 59.893 45.833 12.86 0.00 37.71 3.41
503 530 4.411927 AGGAGTCCAGCTATGTACTATGG 58.588 47.826 12.86 0.00 0.00 2.74
504 531 6.242396 ACTAGGAGTCCAGCTATGTACTATG 58.758 44.000 12.86 0.00 0.00 2.23
505 532 6.457159 ACTAGGAGTCCAGCTATGTACTAT 57.543 41.667 12.86 0.00 0.00 2.12
506 533 5.908562 ACTAGGAGTCCAGCTATGTACTA 57.091 43.478 12.86 0.00 0.00 1.82
507 534 4.799715 ACTAGGAGTCCAGCTATGTACT 57.200 45.455 12.86 0.00 0.00 2.73
508 535 5.134661 AGAACTAGGAGTCCAGCTATGTAC 58.865 45.833 12.86 0.00 0.00 2.90
509 536 5.132985 AGAGAACTAGGAGTCCAGCTATGTA 59.867 44.000 12.86 0.00 0.00 2.29
510 537 4.079443 AGAGAACTAGGAGTCCAGCTATGT 60.079 45.833 12.86 0.00 0.00 2.29
511 538 4.469657 AGAGAACTAGGAGTCCAGCTATG 58.530 47.826 12.86 0.00 0.00 2.23
541 568 3.648545 GGATGGCTAGAGATGGTTTAGGT 59.351 47.826 0.00 0.00 0.00 3.08
561 588 5.814481 TGGATCATCACAGTTGTAAATGGA 58.186 37.500 0.00 0.00 0.00 3.41
599 630 5.678583 TCAAAATGGATTTGCCTCAACAAA 58.321 33.333 0.00 0.00 46.53 2.83
674 707 3.138653 AGACTAGTCGGTCTATGGTGGAT 59.861 47.826 17.07 0.00 43.76 3.41
675 708 2.508716 AGACTAGTCGGTCTATGGTGGA 59.491 50.000 17.07 0.00 43.76 4.02
676 709 2.933573 AGACTAGTCGGTCTATGGTGG 58.066 52.381 17.07 0.00 43.76 4.61
677 710 4.706035 AGTAGACTAGTCGGTCTATGGTG 58.294 47.826 17.07 0.00 46.29 4.17
678 711 5.011943 CCTAGTAGACTAGTCGGTCTATGGT 59.988 48.000 17.07 0.00 46.29 3.55
679 712 5.245751 TCCTAGTAGACTAGTCGGTCTATGG 59.754 48.000 17.07 18.46 46.29 2.74
680 713 6.158598 GTCCTAGTAGACTAGTCGGTCTATG 58.841 48.000 17.07 15.37 46.29 2.23
681 714 5.048083 CGTCCTAGTAGACTAGTCGGTCTAT 60.048 48.000 17.07 1.30 46.29 1.98
696 729 1.079197 TGCGGTCGTCGTCCTAGTA 60.079 57.895 6.94 0.00 41.72 1.82
699 732 1.028330 ATTCTGCGGTCGTCGTCCTA 61.028 55.000 6.94 0.00 41.72 2.94
700 733 1.874345 AATTCTGCGGTCGTCGTCCT 61.874 55.000 6.94 0.00 41.72 3.85
701 734 1.445582 AATTCTGCGGTCGTCGTCC 60.446 57.895 0.00 0.00 41.72 4.79
702 735 1.683790 CCAATTCTGCGGTCGTCGTC 61.684 60.000 0.00 0.00 41.72 4.20
849 887 3.662759 TTTTTGAGGGGAAGAGTGTGT 57.337 42.857 0.00 0.00 0.00 3.72
877 915 3.638484 GTGGCGAGTGTGCTTAATTTTT 58.362 40.909 0.00 0.00 34.52 1.94
878 916 2.350388 CGTGGCGAGTGTGCTTAATTTT 60.350 45.455 0.00 0.00 34.52 1.82
879 917 1.196808 CGTGGCGAGTGTGCTTAATTT 59.803 47.619 0.00 0.00 34.52 1.82
880 918 0.796312 CGTGGCGAGTGTGCTTAATT 59.204 50.000 0.00 0.00 34.52 1.40
881 919 0.037697 TCGTGGCGAGTGTGCTTAAT 60.038 50.000 0.00 0.00 34.52 1.40
882 920 0.249531 TTCGTGGCGAGTGTGCTTAA 60.250 50.000 0.00 0.00 37.14 1.85
883 921 0.249531 TTTCGTGGCGAGTGTGCTTA 60.250 50.000 0.00 0.00 37.14 3.09
884 922 1.092921 TTTTCGTGGCGAGTGTGCTT 61.093 50.000 0.00 0.00 37.14 3.91
885 923 1.498865 CTTTTCGTGGCGAGTGTGCT 61.499 55.000 0.00 0.00 37.14 4.40
886 924 1.082756 CTTTTCGTGGCGAGTGTGC 60.083 57.895 0.00 0.00 37.14 4.57
887 925 0.655733 AACTTTTCGTGGCGAGTGTG 59.344 50.000 0.00 0.00 37.14 3.82
888 926 0.935196 GAACTTTTCGTGGCGAGTGT 59.065 50.000 0.00 0.00 37.14 3.55
889 927 3.729004 GAACTTTTCGTGGCGAGTG 57.271 52.632 0.00 0.00 37.14 3.51
958 1019 4.660938 GTGGAGGTGGTGGTGGCC 62.661 72.222 0.00 0.00 0.00 5.36
959 1020 4.660938 GGTGGAGGTGGTGGTGGC 62.661 72.222 0.00 0.00 0.00 5.01
960 1021 2.291402 TTTGGTGGAGGTGGTGGTGG 62.291 60.000 0.00 0.00 0.00 4.61
961 1022 1.106944 GTTTGGTGGAGGTGGTGGTG 61.107 60.000 0.00 0.00 0.00 4.17
962 1023 1.229076 GTTTGGTGGAGGTGGTGGT 59.771 57.895 0.00 0.00 0.00 4.16
963 1024 1.530655 GGTTTGGTGGAGGTGGTGG 60.531 63.158 0.00 0.00 0.00 4.61
964 1025 1.530655 GGGTTTGGTGGAGGTGGTG 60.531 63.158 0.00 0.00 0.00 4.17
965 1026 1.699930 AGGGTTTGGTGGAGGTGGT 60.700 57.895 0.00 0.00 0.00 4.16
966 1027 1.074951 GAGGGTTTGGTGGAGGTGG 59.925 63.158 0.00 0.00 0.00 4.61
967 1028 1.074951 GGAGGGTTTGGTGGAGGTG 59.925 63.158 0.00 0.00 0.00 4.00
968 1029 2.526046 CGGAGGGTTTGGTGGAGGT 61.526 63.158 0.00 0.00 0.00 3.85
969 1030 1.562672 ATCGGAGGGTTTGGTGGAGG 61.563 60.000 0.00 0.00 0.00 4.30
970 1031 0.107654 GATCGGAGGGTTTGGTGGAG 60.108 60.000 0.00 0.00 0.00 3.86
971 1032 1.559065 GGATCGGAGGGTTTGGTGGA 61.559 60.000 0.00 0.00 0.00 4.02
972 1033 1.077716 GGATCGGAGGGTTTGGTGG 60.078 63.158 0.00 0.00 0.00 4.61
973 1034 0.037590 TTGGATCGGAGGGTTTGGTG 59.962 55.000 0.00 0.00 0.00 4.17
974 1035 0.774908 TTTGGATCGGAGGGTTTGGT 59.225 50.000 0.00 0.00 0.00 3.67
1509 1606 0.986527 TCCCGGAAGTTTCCCCTAAC 59.013 55.000 0.73 0.00 44.67 2.34
1533 1630 2.093128 CCCAGTACGCACCTTTCCTAAT 60.093 50.000 0.00 0.00 0.00 1.73
1536 1633 1.125711 ACCCAGTACGCACCTTTCCT 61.126 55.000 0.00 0.00 0.00 3.36
1560 1657 6.982160 ATAAATGCACACCACATATCCATT 57.018 33.333 0.00 0.00 0.00 3.16
1588 1697 5.006746 CAGAAATAGGCACACCGAATCTAAC 59.993 44.000 0.00 0.00 42.76 2.34
1597 1709 3.356290 ACCAATCAGAAATAGGCACACC 58.644 45.455 0.00 0.00 0.00 4.16
1610 1722 4.989797 TGCAAAATTACAGCAACCAATCAG 59.010 37.500 0.00 0.00 34.97 2.90
1624 1736 6.007485 AGAAAACCCCCTTTTGCAAAATTA 57.993 33.333 24.06 3.39 31.81 1.40
1635 1747 7.008332 CCCGAAATAATATAGAAAACCCCCTT 58.992 38.462 0.00 0.00 0.00 3.95
1653 1765 8.850156 CAAAATAAGATGATCTTACCCCGAAAT 58.150 33.333 16.47 0.00 41.27 2.17
1660 1772 7.573968 AGCACCAAAATAAGATGATCTTACC 57.426 36.000 16.47 0.20 41.27 2.85
1678 1801 0.603707 GCAGCAGTGAAGTAGCACCA 60.604 55.000 0.00 0.00 39.59 4.17
1682 1805 1.932511 GATCTGCAGCAGTGAAGTAGC 59.067 52.381 22.10 0.35 30.06 3.58
1683 1806 2.168106 AGGATCTGCAGCAGTGAAGTAG 59.832 50.000 22.10 0.00 30.06 2.57
1705 1831 7.918033 TGTGCAATTCGAAAATTTGAGTCTAAA 59.082 29.630 12.90 0.00 32.69 1.85
1708 1834 5.687285 GTGTGCAATTCGAAAATTTGAGTCT 59.313 36.000 12.90 0.00 32.69 3.24
1721 1847 4.944962 TCCTTATCTTGTGTGCAATTCG 57.055 40.909 0.00 0.00 33.65 3.34
1746 1872 9.017669 CCGCACTAATACTAGTAACTAGTTTTG 57.982 37.037 14.49 12.41 43.82 2.44
1747 1873 8.960591 TCCGCACTAATACTAGTAACTAGTTTT 58.039 33.333 14.49 5.53 43.82 2.43
1757 1883 7.497595 TGAATTTCATCCGCACTAATACTAGT 58.502 34.615 0.00 0.00 39.04 2.57
1783 1910 4.098914 AGCAGGAACCAACAAATACAGA 57.901 40.909 0.00 0.00 0.00 3.41
1793 1920 4.301072 AATAGTGCTAAGCAGGAACCAA 57.699 40.909 0.00 0.00 40.08 3.67
1799 1959 6.203723 GGACAGATTAAATAGTGCTAAGCAGG 59.796 42.308 0.00 0.00 40.08 4.85
1803 1963 6.203723 GGCTGGACAGATTAAATAGTGCTAAG 59.796 42.308 3.00 0.00 0.00 2.18
1814 1974 6.855763 AATTTTCATGGCTGGACAGATTAA 57.144 33.333 3.00 0.00 0.00 1.40
1939 2101 9.534565 CATCTAATTTTAGAAATGAGGTCGAGA 57.465 33.333 4.26 0.00 42.55 4.04
1956 2118 8.037166 GCCTGTTTTCTGAAATCCATCTAATTT 58.963 33.333 3.31 0.00 0.00 1.82
1957 2119 7.550712 GCCTGTTTTCTGAAATCCATCTAATT 58.449 34.615 3.31 0.00 0.00 1.40
2027 2192 7.660208 TGGAACTGGAACTATTAAACTCAAGTC 59.340 37.037 0.00 0.00 0.00 3.01
2089 2256 0.033208 ACAGTACCATGGCCCCATTG 60.033 55.000 13.04 4.52 33.90 2.82
2203 2371 4.209307 TGCCTCGAAATACAACATACCA 57.791 40.909 0.00 0.00 0.00 3.25
2259 2427 4.581824 TCTGCTTAATTCCAATCATCTGGC 59.418 41.667 0.00 0.00 36.32 4.85
2262 2430 6.264744 CCATGTCTGCTTAATTCCAATCATCT 59.735 38.462 0.00 0.00 0.00 2.90
2277 2445 1.211457 GTCTTGGGATCCATGTCTGCT 59.789 52.381 15.23 0.00 31.53 4.24
2322 2491 5.376854 AACTTTGAGCATAAATCAAGCGT 57.623 34.783 0.00 0.00 0.00 5.07
2336 2505 7.177041 ACTCTTCTGTAGGGTACTAACTTTGAG 59.823 40.741 0.00 0.00 35.16 3.02
2453 2941 6.892310 AAAGATGAAGCAGAAAACACAAAC 57.108 33.333 0.00 0.00 0.00 2.93
2484 2974 4.202040 TGCATACAAGATTAGCATTGCCAC 60.202 41.667 4.70 0.00 0.00 5.01
2486 2976 4.572985 TGCATACAAGATTAGCATTGCC 57.427 40.909 4.70 0.00 0.00 4.52
2501 2991 8.870160 TTGTCCATTAAAATATGCTTGCATAC 57.130 30.769 16.29 4.57 0.00 2.39
2693 3183 1.864862 CAGAACCACAGCTCGCAAG 59.135 57.895 0.00 0.00 0.00 4.01
2797 3287 0.908198 AACTCTGATGAGGAGGGTGC 59.092 55.000 0.00 0.00 44.29 5.01
2799 3289 1.203364 ACCAACTCTGATGAGGAGGGT 60.203 52.381 9.58 5.73 44.29 4.34
2808 3304 7.129457 TCAGCTATTTATCACCAACTCTGAT 57.871 36.000 0.00 0.00 32.91 2.90
2809 3305 6.544928 TCAGCTATTTATCACCAACTCTGA 57.455 37.500 0.00 0.00 0.00 3.27
2827 3326 7.786464 ACAAAATGGAGGGAAAATATATCAGCT 59.214 33.333 0.00 0.00 0.00 4.24
2837 3337 7.288852 TCAACATTCTACAAAATGGAGGGAAAA 59.711 33.333 2.11 0.00 40.28 2.29
2841 3341 5.476599 TGTCAACATTCTACAAAATGGAGGG 59.523 40.000 2.11 0.00 40.28 4.30
2988 3488 7.977789 ATTACAAATCCAAAACAAATCCCAC 57.022 32.000 0.00 0.00 0.00 4.61
3002 3502 8.958119 TCTCAATGTAGTGGTATTACAAATCC 57.042 34.615 0.00 0.00 34.92 3.01
3039 3541 9.504708 TTGGTGAGCATTTAAAAATGAATCATT 57.495 25.926 17.46 2.07 46.72 2.57
3085 3587 8.396390 TGATTGTTCATTTGGTTCATTTTTGTG 58.604 29.630 0.00 0.00 0.00 3.33
3097 3599 7.149973 ACTTCAACATCTGATTGTTCATTTGG 58.850 34.615 0.00 0.00 37.73 3.28
3117 3619 4.018870 TGTTATATCACCCCAGCAACTTCA 60.019 41.667 0.00 0.00 0.00 3.02
3235 3745 0.768622 TTCCGTGGGACCAATCAACT 59.231 50.000 0.00 0.00 0.00 3.16
3250 3760 2.997899 CTCCCATAGCTGCTTTCCG 58.002 57.895 7.79 0.00 0.00 4.30
3385 3895 6.539103 ACTCTTTCAAGTCAGGTTTTGTAGAC 59.461 38.462 0.00 0.00 0.00 2.59
3388 3898 7.281549 GGTAACTCTTTCAAGTCAGGTTTTGTA 59.718 37.037 0.00 0.00 0.00 2.41
3436 3946 5.505819 CGAGGATACAGATTCTGCGTCTTTA 60.506 44.000 13.64 0.00 41.41 1.85
3454 3964 1.702957 TCTTGGGTTTTGTCCGAGGAT 59.297 47.619 0.00 0.00 36.63 3.24
3467 3977 1.035139 CACTTTGCAGCTTCTTGGGT 58.965 50.000 0.00 0.00 0.00 4.51
3490 4000 1.948635 GCTCTTCCGCGAGATCTGC 60.949 63.158 8.23 3.35 32.74 4.26
3511 4021 3.117888 TGGATTTCCCAACTCTGCTATCC 60.118 47.826 0.00 0.00 43.29 2.59
3623 4133 2.672714 TGAACTGTGCAGACGTCATAC 58.327 47.619 19.50 13.41 0.00 2.39
3691 4201 4.033684 CGTTGTTCCTCGCTATACACTAC 58.966 47.826 0.00 0.00 0.00 2.73
3725 4235 2.176889 GCTATTATCCCCTCTACCGCA 58.823 52.381 0.00 0.00 0.00 5.69
3728 4238 4.161102 ACACAGCTATTATCCCCTCTACC 58.839 47.826 0.00 0.00 0.00 3.18
3737 4247 8.220755 TCCCACATTTAAACACAGCTATTATC 57.779 34.615 0.00 0.00 0.00 1.75
3750 4260 7.394359 CCTGATTCTTCTTCTCCCACATTTAAA 59.606 37.037 0.00 0.00 0.00 1.52
3778 4288 7.555914 TGATAAATAACAGCTTATTCACCAGCA 59.444 33.333 0.00 0.00 38.61 4.41
3864 4375 1.947456 GATGGAAATCCTAACGCCACC 59.053 52.381 0.44 0.00 36.82 4.61
3871 4382 8.877864 ACACTTTTACATGATGGAAATCCTAA 57.122 30.769 3.26 0.00 28.96 2.69
4026 4537 8.428852 AGTTCCTTTTAAGCCACAAAACATATT 58.571 29.630 0.00 0.00 0.00 1.28
4137 4652 3.766591 TGTTCTCCTGATCCTGAGTTCTC 59.233 47.826 8.07 0.00 0.00 2.87
4199 4714 0.321122 GAGTGGAGTGCTGAACTGGG 60.321 60.000 0.00 0.00 40.07 4.45
4212 4727 2.498078 TGCATACGTACATTGGAGTGGA 59.502 45.455 0.00 0.00 0.00 4.02
4277 4792 6.122277 CCTTCCAGGTGATGTAAATATGTGT 58.878 40.000 0.00 0.00 0.00 3.72
4328 4845 3.282021 AGATTTGCTTGCCGTGTATGAT 58.718 40.909 0.00 0.00 0.00 2.45
4358 4875 2.286184 CCGGCCGAGTTTTATTTCATCG 60.286 50.000 30.73 0.00 0.00 3.84
4467 4989 2.748058 GAAGGACTTTGCCGAGCCCA 62.748 60.000 0.00 0.00 0.00 5.36
4522 5044 1.058428 TCAGGGCCATCCAGGATGAG 61.058 60.000 28.79 19.34 42.09 2.90
4561 5083 4.357947 GAGATGCGCCCGCCGATA 62.358 66.667 4.18 0.00 41.09 2.92
4657 5179 3.311110 GTGGACGTGGAGCTGGGA 61.311 66.667 0.00 0.00 0.00 4.37
4660 5182 2.047844 CTGGTGGACGTGGAGCTG 60.048 66.667 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.