Multiple sequence alignment - TraesCS7D01G081000

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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 TraesCS7D01G081000 chr7D 100.000 2971 0 0 568 3538 47648320 47651290 0.000000e+00 5487
1 TraesCS7D01G081000 chr7D 100.000 173 0 0 1 173 47647753 47647925 1.580000e-83 320
2 TraesCS7D01G081000 chr7D 87.629 97 5 1 2862 2951 47510954 47510858 4.830000e-19 106
3 TraesCS7D01G081000 chrUn 88.711 1816 160 21 832 2611 49378790 49380596 0.000000e+00 2176
4 TraesCS7D01G081000 chrUn 93.772 578 36 0 2961 3538 28751380 28750803 0.000000e+00 869
5 TraesCS7D01G081000 chrUn 82.341 991 154 17 1529 2510 49323234 49324212 0.000000e+00 841
6 TraesCS7D01G081000 chrUn 81.250 1008 152 25 1529 2510 82309324 82310320 0.000000e+00 780
7 TraesCS7D01G081000 chrUn 81.294 1005 151 25 1532 2510 286813042 286812049 0.000000e+00 780
8 TraesCS7D01G081000 chrUn 92.982 171 9 3 1 169 49378475 49378644 2.730000e-61 246
9 TraesCS7D01G081000 chrUn 93.878 98 6 0 2859 2956 49380600 49380697 7.910000e-32 148
10 TraesCS7D01G081000 chr7A 87.693 1877 177 25 774 2616 50182810 50180954 0.000000e+00 2137
11 TraesCS7D01G081000 chr7A 86.166 253 26 5 2606 2855 106443962 106444208 7.530000e-67 265
12 TraesCS7D01G081000 chr4A 90.633 1580 124 12 832 2390 662626614 662625038 0.000000e+00 2076
13 TraesCS7D01G081000 chr4A 93.023 172 12 0 1 172 662627466 662627295 5.860000e-63 252
14 TraesCS7D01G081000 chr4A 88.835 206 19 4 2411 2614 662623797 662623594 2.110000e-62 250
15 TraesCS7D01G081000 chr4A 90.526 190 10 5 577 766 662626830 662626649 9.810000e-61 244
16 TraesCS7D01G081000 chr4A 81.944 216 32 4 2612 2827 11702952 11703160 3.630000e-40 176
17 TraesCS7D01G081000 chr4A 91.262 103 9 0 2854 2956 662623598 662623496 1.320000e-29 141
18 TraesCS7D01G081000 chr6D 94.464 578 31 1 2961 3538 368733522 368734098 0.000000e+00 889
19 TraesCS7D01G081000 chr6D 93.782 579 34 2 2961 3538 457702771 457702194 0.000000e+00 869
20 TraesCS7D01G081000 chr4D 94.301 579 32 1 2961 3538 354832390 354832968 0.000000e+00 885
21 TraesCS7D01G081000 chr4D 85.973 221 27 3 2613 2830 362407872 362407653 2.120000e-57 233
22 TraesCS7D01G081000 chr3D 94.291 578 33 0 2961 3538 317194283 317193706 0.000000e+00 885
23 TraesCS7D01G081000 chr3D 93.782 579 35 1 2961 3538 496064943 496064365 0.000000e+00 869
24 TraesCS7D01G081000 chr3D 89.500 200 12 5 2660 2855 385438089 385437895 9.810000e-61 244
25 TraesCS7D01G081000 chr2D 94.291 578 33 0 2961 3538 499719753 499719176 0.000000e+00 885
26 TraesCS7D01G081000 chr2D 93.782 579 35 1 2961 3538 249985098 249984520 0.000000e+00 869
27 TraesCS7D01G081000 chr2D 81.448 221 29 7 2613 2827 304397195 304397409 1.690000e-38 171
28 TraesCS7D01G081000 chr5D 93.772 578 36 0 2961 3538 297123532 297124109 0.000000e+00 869
29 TraesCS7D01G081000 chr5D 84.848 396 54 6 1031 1423 507769061 507768669 9.210000e-106 394
30 TraesCS7D01G081000 chr5D 85.488 379 51 4 1052 1428 507618671 507618295 3.310000e-105 392
31 TraesCS7D01G081000 chr5D 84.585 253 35 4 2609 2859 15661130 15660880 7.580000e-62 248
32 TraesCS7D01G081000 chr1B 81.366 1025 161 14 1505 2508 562564468 562563453 0.000000e+00 808
33 TraesCS7D01G081000 chr1B 85.371 458 47 7 972 1428 562564903 562564465 1.160000e-124 457
34 TraesCS7D01G081000 chr1D 82.353 833 120 12 1699 2510 416228399 416227573 0.000000e+00 699
35 TraesCS7D01G081000 chr1A 81.274 769 117 11 1761 2510 513685737 513684977 6.540000e-167 597
36 TraesCS7D01G081000 chr1A 84.861 251 28 7 2610 2855 562621224 562620979 9.810000e-61 244
37 TraesCS7D01G081000 chr5A 85.606 396 52 5 1028 1421 635292519 635292127 9.140000e-111 411
38 TraesCS7D01G081000 chr5A 85.396 404 50 9 1018 1415 635337748 635337348 9.140000e-111 411
39 TraesCS7D01G081000 chr5A 89.055 201 15 3 2660 2857 34842099 34841903 3.530000e-60 243
40 TraesCS7D01G081000 chr5A 90.123 81 8 0 2662 2742 665598230 665598150 4.830000e-19 106
41 TraesCS7D01G081000 chr5B 85.530 387 51 5 1031 1415 638304543 638304160 1.980000e-107 399
42 TraesCS7D01G081000 chr2B 86.275 255 31 4 2607 2860 457730190 457730441 1.250000e-69 274
43 TraesCS7D01G081000 chr4B 89.163 203 15 3 2660 2859 398088693 398088495 2.730000e-61 246
44 TraesCS7D01G081000 chr6B 88.557 201 18 2 2661 2860 469709569 469709373 4.560000e-59 239


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 TraesCS7D01G081000 chr7D 47647753 47651290 3537 False 2903.500000 5487 100.0000 1 3538 2 chr7D.!!$F1 3537
1 TraesCS7D01G081000 chrUn 28750803 28751380 577 True 869.000000 869 93.7720 2961 3538 1 chrUn.!!$R1 577
2 TraesCS7D01G081000 chrUn 49378475 49380697 2222 False 856.666667 2176 91.8570 1 2956 3 chrUn.!!$F3 2955
3 TraesCS7D01G081000 chrUn 49323234 49324212 978 False 841.000000 841 82.3410 1529 2510 1 chrUn.!!$F1 981
4 TraesCS7D01G081000 chrUn 82309324 82310320 996 False 780.000000 780 81.2500 1529 2510 1 chrUn.!!$F2 981
5 TraesCS7D01G081000 chrUn 286812049 286813042 993 True 780.000000 780 81.2940 1532 2510 1 chrUn.!!$R2 978
6 TraesCS7D01G081000 chr7A 50180954 50182810 1856 True 2137.000000 2137 87.6930 774 2616 1 chr7A.!!$R1 1842
7 TraesCS7D01G081000 chr4A 662623496 662627466 3970 True 592.600000 2076 90.8558 1 2956 5 chr4A.!!$R1 2955
8 TraesCS7D01G081000 chr6D 368733522 368734098 576 False 889.000000 889 94.4640 2961 3538 1 chr6D.!!$F1 577
9 TraesCS7D01G081000 chr6D 457702194 457702771 577 True 869.000000 869 93.7820 2961 3538 1 chr6D.!!$R1 577
10 TraesCS7D01G081000 chr4D 354832390 354832968 578 False 885.000000 885 94.3010 2961 3538 1 chr4D.!!$F1 577
11 TraesCS7D01G081000 chr3D 317193706 317194283 577 True 885.000000 885 94.2910 2961 3538 1 chr3D.!!$R1 577
12 TraesCS7D01G081000 chr3D 496064365 496064943 578 True 869.000000 869 93.7820 2961 3538 1 chr3D.!!$R3 577
13 TraesCS7D01G081000 chr2D 499719176 499719753 577 True 885.000000 885 94.2910 2961 3538 1 chr2D.!!$R2 577
14 TraesCS7D01G081000 chr2D 249984520 249985098 578 True 869.000000 869 93.7820 2961 3538 1 chr2D.!!$R1 577
15 TraesCS7D01G081000 chr5D 297123532 297124109 577 False 869.000000 869 93.7720 2961 3538 1 chr5D.!!$F1 577
16 TraesCS7D01G081000 chr1B 562563453 562564903 1450 True 632.500000 808 83.3685 972 2508 2 chr1B.!!$R1 1536
17 TraesCS7D01G081000 chr1D 416227573 416228399 826 True 699.000000 699 82.3530 1699 2510 1 chr1D.!!$R1 811
18 TraesCS7D01G081000 chr1A 513684977 513685737 760 True 597.000000 597 81.2740 1761 2510 1 chr1A.!!$R1 749

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
768 833 0.329596 GAATCTTGGTCCAGGCCTGT 59.670 55.0 30.63 9.34 0.00 4.00 F
824 889 0.537371 CAAAGTCCCTGTCCCACCAC 60.537 60.0 0.00 0.00 0.00 4.16 F
2352 2489 0.110644 CGACGGCTCTTTTGACAAGC 60.111 55.0 0.00 0.00 35.27 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2078 0.099082 CTTCCCAGAGCGACGTAGAC 59.901 60.000 0.00 0.0 0.00 2.59 R
2514 3874 0.316278 CTCGTCGATGTACTGCTCCG 60.316 60.000 4.21 0.0 0.00 4.63 R
3209 4572 1.850441 CCGTTTTCGTATGAGTAGGCG 59.150 52.381 0.00 0.0 42.35 5.52 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
25 26 3.488489 GTTTGCAACAGCGTTACATAGG 58.512 45.455 0.00 0.00 0.00 2.57
44 47 2.190578 GCATCCCCTCAGAACCCG 59.809 66.667 0.00 0.00 0.00 5.28
47 50 2.058595 ATCCCCTCAGAACCCGACG 61.059 63.158 0.00 0.00 0.00 5.12
89 92 3.702555 GCGCGTTGTGCTCGAACT 61.703 61.111 8.43 0.00 43.27 3.01
169 172 3.191162 CGGATCAGAGCTAGAGAGGATTG 59.809 52.174 0.00 0.00 0.00 2.67
172 175 3.831323 TCAGAGCTAGAGAGGATTGGAG 58.169 50.000 0.00 0.00 0.00 3.86
601 666 2.226674 GCAAGCTGTGAAGGAGGTTTAC 59.773 50.000 0.00 0.00 0.00 2.01
633 698 3.981071 ATCAGTCGGTTGAAATGGAGA 57.019 42.857 0.00 0.00 0.00 3.71
634 699 3.319137 TCAGTCGGTTGAAATGGAGAG 57.681 47.619 0.00 0.00 0.00 3.20
645 710 5.924475 TGAAATGGAGAGTTTTTCGAGAC 57.076 39.130 0.00 0.00 33.15 3.36
650 715 4.777463 TGGAGAGTTTTTCGAGACCTTTT 58.223 39.130 0.00 0.00 0.00 2.27
713 778 9.528489 GGATAATAAACAAAATAGCCCCAGATA 57.472 33.333 0.00 0.00 0.00 1.98
757 822 1.086696 ATGTTGCGTCGGAATCTTGG 58.913 50.000 1.49 0.00 0.00 3.61
766 831 1.915078 CGGAATCTTGGTCCAGGCCT 61.915 60.000 0.00 0.00 34.56 5.19
767 832 0.394899 GGAATCTTGGTCCAGGCCTG 60.395 60.000 26.87 26.87 35.05 4.85
768 833 0.329596 GAATCTTGGTCCAGGCCTGT 59.670 55.000 30.63 9.34 0.00 4.00
769 834 1.559682 GAATCTTGGTCCAGGCCTGTA 59.440 52.381 30.63 13.99 0.00 2.74
770 835 0.912486 ATCTTGGTCCAGGCCTGTAC 59.088 55.000 30.63 25.31 0.00 2.90
771 836 1.079127 CTTGGTCCAGGCCTGTACG 60.079 63.158 30.63 16.20 0.00 3.67
772 837 2.521958 CTTGGTCCAGGCCTGTACGG 62.522 65.000 30.63 16.26 0.00 4.02
781 846 2.746277 CCTGTACGGTGCAAGGCC 60.746 66.667 0.00 0.00 0.00 5.19
794 859 3.580319 AGGCCCACCCTTGTGACC 61.580 66.667 0.00 0.00 43.06 4.02
799 864 0.895100 CCCACCCTTGTGACCACATG 60.895 60.000 3.47 6.39 45.76 3.21
818 883 2.035783 GGGGCAAAGTCCCTGTCC 59.964 66.667 0.00 0.00 45.53 4.02
820 885 2.840753 GGGCAAAGTCCCTGTCCCA 61.841 63.158 0.00 0.00 43.13 4.37
822 887 1.603739 GCAAAGTCCCTGTCCCACC 60.604 63.158 0.00 0.00 0.00 4.61
823 888 1.843421 CAAAGTCCCTGTCCCACCA 59.157 57.895 0.00 0.00 0.00 4.17
824 889 0.537371 CAAAGTCCCTGTCCCACCAC 60.537 60.000 0.00 0.00 0.00 4.16
825 890 1.716028 AAAGTCCCTGTCCCACCACC 61.716 60.000 0.00 0.00 0.00 4.61
826 891 2.529389 GTCCCTGTCCCACCACCT 60.529 66.667 0.00 0.00 0.00 4.00
827 892 2.203938 TCCCTGTCCCACCACCTC 60.204 66.667 0.00 0.00 0.00 3.85
828 893 2.203998 CCCTGTCCCACCACCTCT 60.204 66.667 0.00 0.00 0.00 3.69
829 894 1.080354 CCCTGTCCCACCACCTCTA 59.920 63.158 0.00 0.00 0.00 2.43
886 966 2.408050 AGTTAGCTCGTGTTGCTCAAG 58.592 47.619 0.00 0.00 41.46 3.02
889 978 1.719600 AGCTCGTGTTGCTCAAGATC 58.280 50.000 0.00 0.00 35.67 2.75
894 983 3.579709 TCGTGTTGCTCAAGATCTTCTC 58.420 45.455 4.57 0.00 30.27 2.87
895 984 3.005791 TCGTGTTGCTCAAGATCTTCTCA 59.994 43.478 4.57 0.90 30.27 3.27
896 985 3.742882 CGTGTTGCTCAAGATCTTCTCAA 59.257 43.478 4.57 7.17 0.00 3.02
897 986 4.212004 CGTGTTGCTCAAGATCTTCTCAAA 59.788 41.667 4.57 0.00 0.00 2.69
899 988 6.498304 GTGTTGCTCAAGATCTTCTCAAAAA 58.502 36.000 4.57 0.43 0.00 1.94
928 1017 2.839486 AAAGCTCGTGTTCCTCATGA 57.161 45.000 0.00 0.00 39.45 3.07
931 1020 3.126001 AGCTCGTGTTCCTCATGAAAA 57.874 42.857 0.00 0.00 40.93 2.29
934 1023 5.431765 AGCTCGTGTTCCTCATGAAAATAT 58.568 37.500 0.00 0.00 40.93 1.28
935 1024 6.582636 AGCTCGTGTTCCTCATGAAAATATA 58.417 36.000 0.00 0.00 40.93 0.86
936 1025 6.703607 AGCTCGTGTTCCTCATGAAAATATAG 59.296 38.462 0.00 0.00 40.93 1.31
937 1026 6.480320 GCTCGTGTTCCTCATGAAAATATAGT 59.520 38.462 0.00 0.00 40.93 2.12
938 1027 7.652105 GCTCGTGTTCCTCATGAAAATATAGTA 59.348 37.037 0.00 0.00 40.93 1.82
939 1028 8.867112 TCGTGTTCCTCATGAAAATATAGTAC 57.133 34.615 0.00 0.00 38.89 2.73
940 1029 7.646526 TCGTGTTCCTCATGAAAATATAGTACG 59.353 37.037 0.00 0.00 38.89 3.67
941 1030 7.434307 CGTGTTCCTCATGAAAATATAGTACGT 59.566 37.037 0.00 0.00 33.94 3.57
996 1098 1.227943 GGCCCATTGCGAGCAGATA 60.228 57.895 0.00 0.00 42.61 1.98
1068 1170 4.572571 TTCCCGTGGCTGGCGTTT 62.573 61.111 0.00 0.00 0.00 3.60
1429 1531 1.078426 GCCGACCAGCACAAGGTAT 60.078 57.895 0.00 0.00 40.09 2.73
1432 1534 1.338674 CCGACCAGCACAAGGTATCAA 60.339 52.381 0.00 0.00 40.09 2.57
1454 1556 1.964223 CTGTACGCCATCTCCACCTAT 59.036 52.381 0.00 0.00 0.00 2.57
1463 1568 3.320626 CATCTCCACCTATGCACGTATG 58.679 50.000 0.00 0.00 0.00 2.39
1661 1777 1.553690 CCACCGTCTTCCTCCACCAT 61.554 60.000 0.00 0.00 0.00 3.55
1814 1930 2.398754 TGTTCACCCTCCTCTCTGAA 57.601 50.000 0.00 0.00 0.00 3.02
1853 1969 2.109799 CCTGCCGGTATCCTGCTG 59.890 66.667 1.90 3.57 34.81 4.41
1884 2000 1.791283 GACGACCGTGACGAAGACG 60.791 63.158 6.54 5.53 45.75 4.18
1887 2003 1.573436 GACCGTGACGAAGACGACT 59.427 57.895 6.54 0.00 42.66 4.18
1943 2074 2.583441 CGACCAGCCTCCCAAGTCA 61.583 63.158 0.00 0.00 0.00 3.41
1947 2078 1.079543 CAGCCTCCCAAGTCAGTCG 60.080 63.158 0.00 0.00 0.00 4.18
1958 2089 0.669932 AGTCAGTCGTCTACGTCGCT 60.670 55.000 0.00 0.00 40.80 4.93
2027 2158 2.516460 GGACTAGAGCTCGCCGGA 60.516 66.667 5.05 0.00 0.00 5.14
2350 2487 1.938861 GCGACGGCTCTTTTGACAA 59.061 52.632 0.00 0.00 35.83 3.18
2352 2489 0.110644 CGACGGCTCTTTTGACAAGC 60.111 55.000 0.00 0.00 35.27 4.01
2390 2527 3.179265 CGACGCGTCATGGTGGAC 61.179 66.667 35.71 9.36 34.42 4.02
2403 2540 3.646715 TGGACGGCCAAGGGAAGG 61.647 66.667 8.12 0.00 42.49 3.46
2430 3790 4.043168 CGACCAACGCCAAGAAGT 57.957 55.556 0.00 0.00 34.51 3.01
2486 3846 1.132453 CAGTACATCCACGAGCTCGAA 59.868 52.381 40.58 24.91 43.02 3.71
2514 3874 1.337823 TGAGACGCTACAAAGAAGCCC 60.338 52.381 0.00 0.00 36.60 5.19
2559 3919 9.784824 GTTGATTTGATCTCGTTTATCTTATCG 57.215 33.333 0.00 0.00 0.00 2.92
2560 3920 9.529325 TTGATTTGATCTCGTTTATCTTATCGT 57.471 29.630 0.00 0.00 0.00 3.73
2563 3924 7.694388 TTGATCTCGTTTATCTTATCGTTGG 57.306 36.000 0.00 0.00 0.00 3.77
2601 3963 4.576053 TGTTCTGATAAAGGGCAATCGATG 59.424 41.667 0.00 0.00 0.00 3.84
2616 3978 6.144724 GGCAATCGATGAAGTTGATACTACTC 59.855 42.308 0.00 0.00 33.17 2.59
2617 3979 6.144724 GCAATCGATGAAGTTGATACTACTCC 59.855 42.308 0.00 0.00 33.17 3.85
2618 3980 5.769484 TCGATGAAGTTGATACTACTCCC 57.231 43.478 0.00 0.00 33.17 4.30
2619 3981 5.446860 TCGATGAAGTTGATACTACTCCCT 58.553 41.667 0.00 0.00 33.17 4.20
2620 3982 5.531659 TCGATGAAGTTGATACTACTCCCTC 59.468 44.000 0.00 0.00 33.17 4.30
2621 3983 5.278561 CGATGAAGTTGATACTACTCCCTCC 60.279 48.000 0.00 0.00 33.17 4.30
2622 3984 3.952323 TGAAGTTGATACTACTCCCTCCG 59.048 47.826 0.00 0.00 33.17 4.63
2623 3985 3.666345 AGTTGATACTACTCCCTCCGT 57.334 47.619 0.00 0.00 31.21 4.69
2624 3986 3.978610 AGTTGATACTACTCCCTCCGTT 58.021 45.455 0.00 0.00 31.21 4.44
2625 3987 4.351127 AGTTGATACTACTCCCTCCGTTT 58.649 43.478 0.00 0.00 31.21 3.60
2626 3988 4.401837 AGTTGATACTACTCCCTCCGTTTC 59.598 45.833 0.00 0.00 31.21 2.78
2627 3989 4.246712 TGATACTACTCCCTCCGTTTCT 57.753 45.455 0.00 0.00 0.00 2.52
2628 3990 4.607239 TGATACTACTCCCTCCGTTTCTT 58.393 43.478 0.00 0.00 0.00 2.52
2629 3991 5.021458 TGATACTACTCCCTCCGTTTCTTT 58.979 41.667 0.00 0.00 0.00 2.52
2630 3992 5.482878 TGATACTACTCCCTCCGTTTCTTTT 59.517 40.000 0.00 0.00 0.00 2.27
2631 3993 4.701651 ACTACTCCCTCCGTTTCTTTTT 57.298 40.909 0.00 0.00 0.00 1.94
2632 3994 5.813513 ACTACTCCCTCCGTTTCTTTTTA 57.186 39.130 0.00 0.00 0.00 1.52
2633 3995 6.178607 ACTACTCCCTCCGTTTCTTTTTAA 57.821 37.500 0.00 0.00 0.00 1.52
2634 3996 6.776744 ACTACTCCCTCCGTTTCTTTTTAAT 58.223 36.000 0.00 0.00 0.00 1.40
2635 3997 6.877855 ACTACTCCCTCCGTTTCTTTTTAATC 59.122 38.462 0.00 0.00 0.00 1.75
2636 3998 5.877491 ACTCCCTCCGTTTCTTTTTAATCT 58.123 37.500 0.00 0.00 0.00 2.40
2637 3999 5.705905 ACTCCCTCCGTTTCTTTTTAATCTG 59.294 40.000 0.00 0.00 0.00 2.90
2638 4000 4.457949 TCCCTCCGTTTCTTTTTAATCTGC 59.542 41.667 0.00 0.00 0.00 4.26
2639 4001 4.459337 CCCTCCGTTTCTTTTTAATCTGCT 59.541 41.667 0.00 0.00 0.00 4.24
2640 4002 5.048013 CCCTCCGTTTCTTTTTAATCTGCTT 60.048 40.000 0.00 0.00 0.00 3.91
2641 4003 6.150474 CCCTCCGTTTCTTTTTAATCTGCTTA 59.850 38.462 0.00 0.00 0.00 3.09
2642 4004 7.148069 CCCTCCGTTTCTTTTTAATCTGCTTAT 60.148 37.037 0.00 0.00 0.00 1.73
2643 4005 8.889717 CCTCCGTTTCTTTTTAATCTGCTTATA 58.110 33.333 0.00 0.00 0.00 0.98
2660 4022 9.113838 TCTGCTTATAAGATTTGATCAAAGTCC 57.886 33.333 24.17 15.80 33.32 3.85
2661 4023 8.806429 TGCTTATAAGATTTGATCAAAGTCCA 57.194 30.769 24.17 11.34 33.32 4.02
2662 4024 9.241919 TGCTTATAAGATTTGATCAAAGTCCAA 57.758 29.630 24.17 12.65 33.32 3.53
2663 4025 9.508567 GCTTATAAGATTTGATCAAAGTCCAAC 57.491 33.333 24.17 11.77 33.32 3.77
2872 4234 4.439016 GGAGTACTAGCTAGCACAACTGAC 60.439 50.000 23.14 11.87 0.00 3.51
2911 4273 2.017782 TGAAGAGCTAGCTACAGACGG 58.982 52.381 19.38 0.00 0.00 4.79
2942 4304 3.697045 CACACAACAAACTAAGGTCCCAA 59.303 43.478 0.00 0.00 0.00 4.12
2952 4314 2.380064 AAGGTCCCAAATTCTGTGCA 57.620 45.000 0.00 0.00 0.00 4.57
2956 4318 2.299867 GGTCCCAAATTCTGTGCACATT 59.700 45.455 22.00 9.37 0.00 2.71
2957 4319 3.578688 GTCCCAAATTCTGTGCACATTC 58.421 45.455 22.00 0.00 0.00 2.67
2958 4320 3.005684 GTCCCAAATTCTGTGCACATTCA 59.994 43.478 22.00 7.64 0.00 2.57
2959 4321 3.833650 TCCCAAATTCTGTGCACATTCAT 59.166 39.130 22.00 9.78 0.00 2.57
2974 4336 5.293079 GCACATTCATTCTCTCAAGTACTCC 59.707 44.000 0.00 0.00 0.00 3.85
2986 4348 2.030958 GTACTCCGGGCCAAACACG 61.031 63.158 4.39 0.00 0.00 4.49
3017 4379 5.012148 ACAGTCTTGCAGAACTTATACAGGT 59.988 40.000 0.62 0.00 0.00 4.00
3078 4440 1.876849 ATGAGATCACCTGGCACTCT 58.123 50.000 0.00 0.00 0.00 3.24
3183 4545 5.482908 GAAATAGTCATCATAGCCGACCAT 58.517 41.667 0.00 0.00 0.00 3.55
3209 4572 5.811100 CCCTCTCTAATACGGTTGAAAAGAC 59.189 44.000 0.00 0.00 0.00 3.01
3230 4593 2.733227 CGCCTACTCATACGAAAACGGT 60.733 50.000 0.00 0.00 0.00 4.83
3234 4597 1.270412 ACTCATACGAAAACGGTGGCA 60.270 47.619 0.00 0.00 0.00 4.92
3301 4664 4.605640 CTTTCAAAGAAGGAAATGCCCA 57.394 40.909 0.00 0.00 37.37 5.36
3380 4743 3.368571 GCTGGCTGTTGAGGTGGC 61.369 66.667 0.00 0.00 0.00 5.01
3410 4773 0.179048 CACGGCAGCCAATATCTCCA 60.179 55.000 13.30 0.00 0.00 3.86
3417 4780 2.119495 AGCCAATATCTCCACCTCGTT 58.881 47.619 0.00 0.00 0.00 3.85
3452 4815 0.511653 GTCGGAGTCGCAAAGGAAAC 59.488 55.000 0.00 0.00 36.13 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.529309 GGGTTCTGAGGGGATGCTC 59.471 63.158 0.00 0.00 0.00 4.26
44 47 0.527817 CTACAACCCCGCATCTCGTC 60.528 60.000 0.00 0.00 36.19 4.20
47 50 1.653151 GTTCTACAACCCCGCATCTC 58.347 55.000 0.00 0.00 0.00 2.75
89 92 0.180642 TTGTGGTGCTACAAACCGGA 59.819 50.000 9.46 0.00 40.86 5.14
124 127 2.599597 GGCTGGCCATGGATCTGT 59.400 61.111 18.40 0.00 35.81 3.41
125 128 2.593725 CGGCTGGCCATGGATCTG 60.594 66.667 18.40 11.61 35.37 2.90
574 577 3.259425 CTTCACAGCTTGCCACGGC 62.259 63.158 0.00 0.00 42.35 5.68
575 578 2.620112 CCTTCACAGCTTGCCACGG 61.620 63.158 0.00 0.00 0.00 4.94
617 682 4.830826 AAAACTCTCCATTTCAACCGAC 57.169 40.909 0.00 0.00 0.00 4.79
645 710 5.982516 TTCATTGAACATGAAACCGAAAAGG 59.017 36.000 0.00 0.00 38.32 3.11
650 715 5.404968 GCAATTTCATTGAACATGAAACCGA 59.595 36.000 11.27 0.00 46.67 4.69
722 787 4.496336 ATTGCGAGGGCCAGGAGC 62.496 66.667 6.18 5.91 38.85 4.70
725 790 2.361610 AACATTGCGAGGGCCAGG 60.362 61.111 6.18 0.00 38.85 4.45
726 791 2.879907 CAACATTGCGAGGGCCAG 59.120 61.111 6.18 0.00 38.85 4.85
727 792 3.372730 GCAACATTGCGAGGGCCA 61.373 61.111 6.18 0.00 45.11 5.36
736 801 2.508867 CAAGATTCCGACGCAACATTG 58.491 47.619 0.00 0.00 0.00 2.82
757 822 2.264794 CACCGTACAGGCCTGGAC 59.735 66.667 34.97 34.97 46.52 4.02
766 831 3.561241 TGGGCCTTGCACCGTACA 61.561 61.111 4.53 0.00 0.00 2.90
767 832 3.053896 GTGGGCCTTGCACCGTAC 61.054 66.667 4.53 0.00 0.00 3.67
768 833 4.338710 GGTGGGCCTTGCACCGTA 62.339 66.667 13.15 0.00 0.00 4.02
771 836 4.621087 AAGGGTGGGCCTTGCACC 62.621 66.667 18.61 18.61 38.22 5.01
772 837 3.305516 CAAGGGTGGGCCTTGCAC 61.306 66.667 4.53 1.68 38.24 4.57
781 846 0.895100 CCATGTGGTCACAAGGGTGG 60.895 60.000 15.29 11.04 44.11 4.61
804 869 1.603739 GGTGGGACAGGGACTTTGC 60.604 63.158 0.00 0.00 41.80 3.68
818 883 1.141053 GCTACCCAATAGAGGTGGTGG 59.859 57.143 0.00 0.00 38.11 4.61
820 885 1.508256 GGCTACCCAATAGAGGTGGT 58.492 55.000 0.00 0.00 38.11 4.16
907 996 3.476552 TCATGAGGAACACGAGCTTTTT 58.523 40.909 0.00 0.00 0.00 1.94
908 997 3.126001 TCATGAGGAACACGAGCTTTT 57.874 42.857 0.00 0.00 0.00 2.27
909 998 2.839486 TCATGAGGAACACGAGCTTT 57.161 45.000 0.00 0.00 0.00 3.51
910 999 2.839486 TTCATGAGGAACACGAGCTT 57.161 45.000 0.00 0.00 0.00 3.74
920 1009 7.145985 GCTGACGTACTATATTTTCATGAGGA 58.854 38.462 0.00 0.00 0.00 3.71
922 1011 6.856426 TCGCTGACGTACTATATTTTCATGAG 59.144 38.462 0.00 0.00 41.18 2.90
926 1015 5.740569 GTGTCGCTGACGTACTATATTTTCA 59.259 40.000 0.00 0.00 41.18 2.69
928 1017 5.039333 GGTGTCGCTGACGTACTATATTTT 58.961 41.667 0.00 0.00 41.18 1.82
931 1020 3.208594 TGGTGTCGCTGACGTACTATAT 58.791 45.455 0.00 0.00 41.18 0.86
934 1023 1.198408 CTTGGTGTCGCTGACGTACTA 59.802 52.381 0.00 0.00 41.18 1.82
935 1024 0.039437 CTTGGTGTCGCTGACGTACT 60.039 55.000 0.00 0.00 41.18 2.73
936 1025 1.615107 GCTTGGTGTCGCTGACGTAC 61.615 60.000 0.00 0.00 41.18 3.67
937 1026 1.372499 GCTTGGTGTCGCTGACGTA 60.372 57.895 0.00 0.00 41.18 3.57
938 1027 2.661866 GCTTGGTGTCGCTGACGT 60.662 61.111 0.00 0.00 41.18 4.34
939 1028 3.414700 GGCTTGGTGTCGCTGACG 61.415 66.667 4.65 0.00 42.01 4.35
940 1029 2.029844 GAGGCTTGGTGTCGCTGAC 61.030 63.158 0.00 2.32 0.00 3.51
941 1030 2.210013 AGAGGCTTGGTGTCGCTGA 61.210 57.895 0.00 0.00 0.00 4.26
1365 1467 4.081254 CAGAAGTCAAGGATGATCCAGTCA 60.081 45.833 14.90 0.00 39.61 3.41
1463 1568 0.238289 CTGTCAAACATGACCCGCAC 59.762 55.000 0.00 0.00 37.99 5.34
1467 1572 0.605319 TCCGCTGTCAAACATGACCC 60.605 55.000 0.00 0.00 37.99 4.46
1521 1626 0.813210 GCGGCATGGAAGAAGAGGAG 60.813 60.000 0.00 0.00 0.00 3.69
1527 1632 2.751436 GCTGGCGGCATGGAAGAA 60.751 61.111 13.85 0.00 41.35 2.52
1791 1907 2.093235 CAGAGAGGAGGGTGAACATTCC 60.093 54.545 0.00 0.00 0.00 3.01
1793 1909 2.907892 TCAGAGAGGAGGGTGAACATT 58.092 47.619 0.00 0.00 0.00 2.71
1884 2000 1.448189 CTGAGCTGCTCTGCCAGTC 60.448 63.158 28.04 2.84 35.28 3.51
1887 2003 2.926779 ACCTGAGCTGCTCTGCCA 60.927 61.111 28.04 9.69 0.00 4.92
1947 2078 0.099082 CTTCCCAGAGCGACGTAGAC 59.901 60.000 0.00 0.00 0.00 2.59
1982 2113 4.440802 GCGAGTTCATGGATGTTCTCTAGT 60.441 45.833 0.00 0.00 31.83 2.57
2027 2158 2.985847 GCCCAAAGGAAGCGCACT 60.986 61.111 11.47 0.88 33.47 4.40
2062 2193 1.392589 CTCCTGCTTGTTGTTGGTGT 58.607 50.000 0.00 0.00 0.00 4.16
2120 2257 1.151450 CCCTGTGCAGACCAAACCT 59.849 57.895 0.02 0.00 0.00 3.50
2124 2261 2.515398 CCACCCTGTGCAGACCAA 59.485 61.111 0.02 0.00 31.34 3.67
2342 2479 1.353804 GACGCCGTGCTTGTCAAAA 59.646 52.632 0.00 0.00 32.91 2.44
2390 2527 3.330720 ACCTCCTTCCCTTGGCCG 61.331 66.667 0.00 0.00 0.00 6.13
2392 2529 0.609406 GAACACCTCCTTCCCTTGGC 60.609 60.000 0.00 0.00 0.00 4.52
2393 2530 0.321653 CGAACACCTCCTTCCCTTGG 60.322 60.000 0.00 0.00 0.00 3.61
2401 2538 2.504274 TTGGTCGCGAACACCTCCT 61.504 57.895 29.42 0.00 34.66 3.69
2402 2539 2.029964 TTGGTCGCGAACACCTCC 59.970 61.111 29.42 15.69 34.66 4.30
2403 2540 2.654912 CGTTGGTCGCGAACACCTC 61.655 63.158 29.42 18.59 34.66 3.85
2430 3790 0.843309 TCCACCACAAGCTCCTTCAA 59.157 50.000 0.00 0.00 0.00 2.69
2486 3846 0.609406 TGTAGCGTCTCAGGTGCTCT 60.609 55.000 0.00 0.00 40.06 4.09
2514 3874 0.316278 CTCGTCGATGTACTGCTCCG 60.316 60.000 4.21 0.00 0.00 4.63
2577 3939 4.584874 TCGATTGCCCTTTATCAGAACAA 58.415 39.130 0.00 0.00 0.00 2.83
2579 3941 4.816385 TCATCGATTGCCCTTTATCAGAAC 59.184 41.667 0.00 0.00 0.00 3.01
2594 3956 6.551601 AGGGAGTAGTATCAACTTCATCGATT 59.448 38.462 0.00 0.00 37.15 3.34
2601 3963 3.952967 ACGGAGGGAGTAGTATCAACTTC 59.047 47.826 0.00 0.00 37.15 3.01
2616 3978 4.459337 AGCAGATTAAAAAGAAACGGAGGG 59.541 41.667 0.00 0.00 0.00 4.30
2617 3979 5.629079 AGCAGATTAAAAAGAAACGGAGG 57.371 39.130 0.00 0.00 0.00 4.30
2634 3996 9.113838 GGACTTTGATCAAATCTTATAAGCAGA 57.886 33.333 20.76 3.53 0.00 4.26
2635 3997 8.896744 TGGACTTTGATCAAATCTTATAAGCAG 58.103 33.333 20.76 7.48 0.00 4.24
2636 3998 8.806429 TGGACTTTGATCAAATCTTATAAGCA 57.194 30.769 20.76 9.27 0.00 3.91
2637 3999 9.508567 GTTGGACTTTGATCAAATCTTATAAGC 57.491 33.333 20.76 7.31 0.00 3.09
2840 4202 4.406326 GCTAGCTAGTACTCCCTCCTTTTT 59.594 45.833 21.62 0.00 0.00 1.94
2841 4203 3.962063 GCTAGCTAGTACTCCCTCCTTTT 59.038 47.826 21.62 0.00 0.00 2.27
2842 4204 3.052793 TGCTAGCTAGTACTCCCTCCTTT 60.053 47.826 21.62 0.00 0.00 3.11
2843 4205 2.514582 TGCTAGCTAGTACTCCCTCCTT 59.485 50.000 21.62 0.00 0.00 3.36
2844 4206 2.136863 TGCTAGCTAGTACTCCCTCCT 58.863 52.381 21.62 0.00 0.00 3.69
2845 4207 2.232399 GTGCTAGCTAGTACTCCCTCC 58.768 57.143 28.52 8.22 36.23 4.30
2846 4208 2.933573 TGTGCTAGCTAGTACTCCCTC 58.066 52.381 32.97 13.85 39.30 4.30
2847 4209 3.025262 GTTGTGCTAGCTAGTACTCCCT 58.975 50.000 32.97 0.00 39.30 4.20
2848 4210 3.025262 AGTTGTGCTAGCTAGTACTCCC 58.975 50.000 32.97 22.86 39.30 4.30
2849 4211 3.695060 TCAGTTGTGCTAGCTAGTACTCC 59.305 47.826 32.97 24.77 39.30 3.85
2850 4212 4.439016 GGTCAGTTGTGCTAGCTAGTACTC 60.439 50.000 32.97 26.16 39.30 2.59
2851 4213 3.444388 GGTCAGTTGTGCTAGCTAGTACT 59.556 47.826 32.97 21.89 39.30 2.73
2852 4214 3.192844 TGGTCAGTTGTGCTAGCTAGTAC 59.807 47.826 28.93 28.93 39.06 2.73
2853 4215 3.192844 GTGGTCAGTTGTGCTAGCTAGTA 59.807 47.826 21.62 15.16 0.00 1.82
2854 4216 2.028930 GTGGTCAGTTGTGCTAGCTAGT 60.029 50.000 21.62 1.49 0.00 2.57
2855 4217 2.232452 AGTGGTCAGTTGTGCTAGCTAG 59.768 50.000 16.84 16.84 0.00 3.42
2856 4218 2.231478 GAGTGGTCAGTTGTGCTAGCTA 59.769 50.000 17.23 1.87 0.00 3.32
2857 4219 1.001406 GAGTGGTCAGTTGTGCTAGCT 59.999 52.381 17.23 0.00 0.00 3.32
2872 4234 1.066002 CACAGCTTGTTGTTGGAGTGG 59.934 52.381 0.00 0.00 0.00 4.00
2942 4304 5.708697 TGAGAGAATGAATGTGCACAGAATT 59.291 36.000 25.84 21.76 0.00 2.17
2952 4314 5.394663 CCGGAGTACTTGAGAGAATGAATGT 60.395 44.000 0.00 0.00 0.00 2.71
2956 4318 3.024547 CCCGGAGTACTTGAGAGAATGA 58.975 50.000 0.73 0.00 0.00 2.57
2957 4319 2.482142 GCCCGGAGTACTTGAGAGAATG 60.482 54.545 0.73 0.00 0.00 2.67
2958 4320 1.757699 GCCCGGAGTACTTGAGAGAAT 59.242 52.381 0.73 0.00 0.00 2.40
2959 4321 1.183549 GCCCGGAGTACTTGAGAGAA 58.816 55.000 0.73 0.00 0.00 2.87
2986 4348 2.169832 TCTGCAAGACTGTTACTGCC 57.830 50.000 7.08 0.00 38.67 4.85
3017 4379 3.139850 GCGAGTCTACATGCCTAGAGTA 58.860 50.000 0.00 0.00 0.00 2.59
3078 4440 2.359848 GCCATCTGAATGCTTGCATACA 59.640 45.455 8.61 0.00 0.00 2.29
3183 4545 3.675348 TCAACCGTATTAGAGAGGGGA 57.325 47.619 0.00 0.00 0.00 4.81
3209 4572 1.850441 CCGTTTTCGTATGAGTAGGCG 59.150 52.381 0.00 0.00 42.35 5.52
3230 4593 6.111382 TGTTCAAACATCAAAAATTCTGCCA 58.889 32.000 0.00 0.00 33.17 4.92
3234 4597 6.257630 CCCGTTGTTCAAACATCAAAAATTCT 59.742 34.615 0.00 0.00 38.95 2.40
3328 4691 3.406595 CTCCATTCCGGGCCACCTC 62.407 68.421 4.39 0.00 34.36 3.85
3380 4743 2.358125 TGCCGTGTTGGTCCATCG 60.358 61.111 0.00 0.00 41.21 3.84


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

AutoCloner maintained by Alex Coulton.