Multiple sequence alignment - TraesCS7B01G015300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G015300 chr7B 100.000 5567 0 0 1 5567 12384882 12379316 0.000000e+00 10281
1 TraesCS7B01G015300 chr7B 81.373 1675 257 38 3494 5139 12211940 12210292 0.000000e+00 1314
2 TraesCS7B01G015300 chr7B 83.915 945 142 8 1584 2523 12366125 12365186 0.000000e+00 894
3 TraesCS7B01G015300 chr7B 82.609 851 129 13 1826 2668 12207409 12206570 0.000000e+00 734
4 TraesCS7B01G015300 chr7B 84.247 292 43 2 1166 1456 12198243 12197954 1.180000e-71 281
5 TraesCS7B01G015300 chr7B 78.286 350 66 10 4869 5213 12184308 12183964 3.380000e-52 217
6 TraesCS7B01G015300 chr7A 92.553 4915 285 41 675 5566 76428688 76423832 0.000000e+00 6974
7 TraesCS7B01G015300 chr7A 92.230 4929 288 43 678 5566 76402009 76397136 0.000000e+00 6892
8 TraesCS7B01G015300 chr7A 93.061 2623 145 16 2952 5566 76482730 76480137 0.000000e+00 3801
9 TraesCS7B01G015300 chr7A 91.785 2252 137 22 639 2870 76484948 76482725 0.000000e+00 3090
10 TraesCS7B01G015300 chr7A 82.283 2032 285 40 2928 4933 76292385 76290403 0.000000e+00 1688
11 TraesCS7B01G015300 chr7A 81.479 1663 254 39 3501 5141 76356113 76354483 0.000000e+00 1315
12 TraesCS7B01G015300 chr7A 83.927 983 151 5 1590 2568 76293686 76292707 0.000000e+00 933
13 TraesCS7B01G015300 chr7A 93.310 568 37 1 1 567 679310949 679311516 0.000000e+00 837
14 TraesCS7B01G015300 chr7A 89.628 646 46 8 4923 5566 76367178 76366552 0.000000e+00 802
15 TraesCS7B01G015300 chr7A 86.364 308 35 3 1164 1469 76293996 76293694 4.160000e-86 329
16 TraesCS7B01G015300 chr7D 89.096 3063 233 45 754 3751 69814326 69811300 0.000000e+00 3712
17 TraesCS7B01G015300 chr7D 96.419 1815 60 5 3754 5566 69811214 69809403 0.000000e+00 2987
18 TraesCS7B01G015300 chr7D 82.882 2033 269 50 2928 4933 69710731 69708751 0.000000e+00 1753
19 TraesCS7B01G015300 chr7D 81.484 1685 249 39 3494 5153 69782321 69780675 0.000000e+00 1325
20 TraesCS7B01G015300 chr7D 81.365 1685 251 39 3494 5153 69806016 69804370 0.000000e+00 1314
21 TraesCS7B01G015300 chr7D 84.372 979 148 3 1592 2567 69712028 69711052 0.000000e+00 955
22 TraesCS7B01G015300 chr7D 95.307 554 25 1 1 554 161408938 161408386 0.000000e+00 878
23 TraesCS7B01G015300 chr7D 95.126 554 23 3 1 554 14677242 14676693 0.000000e+00 870
24 TraesCS7B01G015300 chr7D 83.845 749 115 4 1584 2329 69807580 69806835 0.000000e+00 708
25 TraesCS7B01G015300 chr7D 87.379 309 30 5 1164 1469 69712340 69712038 4.130000e-91 346
26 TraesCS7B01G015300 chr7D 84.229 279 34 4 1167 1440 69720771 69720498 4.280000e-66 263
27 TraesCS7B01G015300 chr7D 81.155 329 33 17 1164 1466 69778846 69778521 2.590000e-58 237
28 TraesCS7B01G015300 chr7D 96.053 76 2 1 639 714 69814407 69814333 7.570000e-24 122
29 TraesCS7B01G015300 chrUn 92.932 1627 83 21 2549 4172 386059372 386057775 0.000000e+00 2338
30 TraesCS7B01G015300 chr6A 81.299 1524 230 38 3492 4994 106736887 106738376 0.000000e+00 1184
31 TraesCS7B01G015300 chr6A 85.102 933 134 3 1590 2521 106735195 106736123 0.000000e+00 948
32 TraesCS7B01G015300 chr6A 94.234 555 31 1 1 554 196332310 196332864 0.000000e+00 846
33 TraesCS7B01G015300 chr6A 84.641 306 40 3 1164 1467 106734885 106735185 1.170000e-76 298
34 TraesCS7B01G015300 chr2D 94.784 556 24 3 1 554 591563498 591564050 0.000000e+00 861
35 TraesCS7B01G015300 chr5D 94.595 555 29 1 1 554 441123742 441123188 0.000000e+00 857
36 TraesCS7B01G015300 chr2B 94.414 555 30 1 1 554 157687716 157688270 0.000000e+00 852
37 TraesCS7B01G015300 chr1D 93.531 572 34 3 1 570 480620983 480620413 0.000000e+00 848
38 TraesCS7B01G015300 chr3D 93.322 569 34 3 1 568 75735825 75736390 0.000000e+00 837


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 TraesCS7B01G015300 chr7B 12379316 12384882 5566 True 10281.000000 10281 100.000000 1 5567 1 chr7B.!!$R4 5566
1 TraesCS7B01G015300 chr7B 12206570 12211940 5370 True 1024.000000 1314 81.991000 1826 5139 2 chr7B.!!$R5 3313
2 TraesCS7B01G015300 chr7B 12365186 12366125 939 True 894.000000 894 83.915000 1584 2523 1 chr7B.!!$R3 939
3 TraesCS7B01G015300 chr7A 76423832 76428688 4856 True 6974.000000 6974 92.553000 675 5566 1 chr7A.!!$R4 4891
4 TraesCS7B01G015300 chr7A 76397136 76402009 4873 True 6892.000000 6892 92.230000 678 5566 1 chr7A.!!$R3 4888
5 TraesCS7B01G015300 chr7A 76480137 76484948 4811 True 3445.500000 3801 92.423000 639 5566 2 chr7A.!!$R6 4927
6 TraesCS7B01G015300 chr7A 76354483 76356113 1630 True 1315.000000 1315 81.479000 3501 5141 1 chr7A.!!$R1 1640
7 TraesCS7B01G015300 chr7A 76290403 76293996 3593 True 983.333333 1688 84.191333 1164 4933 3 chr7A.!!$R5 3769
8 TraesCS7B01G015300 chr7A 679310949 679311516 567 False 837.000000 837 93.310000 1 567 1 chr7A.!!$F1 566
9 TraesCS7B01G015300 chr7A 76366552 76367178 626 True 802.000000 802 89.628000 4923 5566 1 chr7A.!!$R2 643
10 TraesCS7B01G015300 chr7D 69804370 69814407 10037 True 1768.600000 3712 89.355600 639 5566 5 chr7D.!!$R6 4927
11 TraesCS7B01G015300 chr7D 69708751 69712340 3589 True 1018.000000 1753 84.877667 1164 4933 3 chr7D.!!$R4 3769
12 TraesCS7B01G015300 chr7D 161408386 161408938 552 True 878.000000 878 95.307000 1 554 1 chr7D.!!$R3 553
13 TraesCS7B01G015300 chr7D 14676693 14677242 549 True 870.000000 870 95.126000 1 554 1 chr7D.!!$R1 553
14 TraesCS7B01G015300 chr7D 69778521 69782321 3800 True 781.000000 1325 81.319500 1164 5153 2 chr7D.!!$R5 3989
15 TraesCS7B01G015300 chrUn 386057775 386059372 1597 True 2338.000000 2338 92.932000 2549 4172 1 chrUn.!!$R1 1623
16 TraesCS7B01G015300 chr6A 196332310 196332864 554 False 846.000000 846 94.234000 1 554 1 chr6A.!!$F1 553
17 TraesCS7B01G015300 chr6A 106734885 106738376 3491 False 810.000000 1184 83.680667 1164 4994 3 chr6A.!!$F2 3830
18 TraesCS7B01G015300 chr2D 591563498 591564050 552 False 861.000000 861 94.784000 1 554 1 chr2D.!!$F1 553
19 TraesCS7B01G015300 chr5D 441123188 441123742 554 True 857.000000 857 94.595000 1 554 1 chr5D.!!$R1 553
20 TraesCS7B01G015300 chr2B 157687716 157688270 554 False 852.000000 852 94.414000 1 554 1 chr2B.!!$F1 553
21 TraesCS7B01G015300 chr1D 480620413 480620983 570 True 848.000000 848 93.531000 1 570 1 chr1D.!!$R1 569
22 TraesCS7B01G015300 chr3D 75735825 75736390 565 False 837.000000 837 93.322000 1 568 1 chr3D.!!$F1 567

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
107 108 0.462581 TATGTCGCCGTCGGTACTCT 60.463 55.000 13.94 6.49 36.13 3.24 F
1718 1770 0.396278 GGAGCTGGGATTTCCTTGGG 60.396 60.000 0.00 0.00 36.20 4.12 F
1979 2038 1.336795 CGGTGGAAAGGAAAATGCCAC 60.337 52.381 0.00 0.00 46.28 5.01 F
2839 2970 1.064979 AGTGACGTTCAAACCAACCCT 60.065 47.619 0.00 0.00 0.00 4.34 F
3534 3755 0.476771 AATCCGGTGGTGAAGGTGTT 59.523 50.000 0.00 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2038 0.508641 CGTTGAACTTCTCGCCACTG 59.491 55.0 0.0 0.0 0.00 3.66 R
2807 2926 0.102481 ACGTCACTTTCGTGCTCAGT 59.898 50.0 0.0 0.0 40.99 3.41 R
2888 3034 0.449388 GGAGAACAAGCAATGCCTCG 59.551 55.0 0.0 0.0 34.59 4.63 R
4071 4397 0.323629 CGGCTAGTTTCCTTGGGACA 59.676 55.0 0.0 0.0 0.00 4.02 R
5314 5647 0.114364 GACAACCTTTGGACCCCCAT 59.886 55.0 0.0 0.0 43.12 4.00 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
44 45 3.249687 GAAGCCACGTCTTCCCAAT 57.750 52.632 5.85 0.00 37.17 3.16
107 108 0.462581 TATGTCGCCGTCGGTACTCT 60.463 55.000 13.94 6.49 36.13 3.24
137 138 2.060980 GGCATCTCCTCACCGGTCT 61.061 63.158 2.59 0.00 0.00 3.85
191 192 2.218454 TGACGGATCCAAACGGGGT 61.218 57.895 13.41 0.00 37.22 4.95
397 399 2.512896 GCCGCCTCAGATGGGATT 59.487 61.111 0.00 0.00 0.00 3.01
585 588 3.384532 GCCCCGTCGTAGTGGGAA 61.385 66.667 8.34 0.00 44.76 3.97
586 589 2.575461 CCCCGTCGTAGTGGGAAC 59.425 66.667 0.00 0.00 44.76 3.62
603 606 2.688446 GGAACCAACTAAGGGCATAAGC 59.312 50.000 0.00 0.00 41.10 3.09
604 607 3.352648 GAACCAACTAAGGGCATAAGCA 58.647 45.455 0.00 0.00 44.61 3.91
605 608 3.669939 ACCAACTAAGGGCATAAGCAT 57.330 42.857 0.00 0.00 44.61 3.79
606 609 4.788925 ACCAACTAAGGGCATAAGCATA 57.211 40.909 0.00 0.00 44.61 3.14
607 610 5.124036 ACCAACTAAGGGCATAAGCATAA 57.876 39.130 0.00 0.00 44.61 1.90
608 611 5.515106 ACCAACTAAGGGCATAAGCATAAA 58.485 37.500 0.00 0.00 44.61 1.40
609 612 5.955355 ACCAACTAAGGGCATAAGCATAAAA 59.045 36.000 0.00 0.00 44.61 1.52
610 613 6.439058 ACCAACTAAGGGCATAAGCATAAAAA 59.561 34.615 0.00 0.00 44.61 1.94
630 633 4.635699 AAAACCCTAGAATGAACGTCCT 57.364 40.909 0.00 0.00 0.00 3.85
631 634 5.750352 AAAACCCTAGAATGAACGTCCTA 57.250 39.130 0.00 0.00 0.00 2.94
632 635 5.340439 AAACCCTAGAATGAACGTCCTAG 57.660 43.478 0.00 0.00 0.00 3.02
633 636 2.694109 ACCCTAGAATGAACGTCCTAGC 59.306 50.000 0.00 0.00 0.00 3.42
634 637 2.693591 CCCTAGAATGAACGTCCTAGCA 59.306 50.000 0.00 0.00 0.00 3.49
635 638 3.322254 CCCTAGAATGAACGTCCTAGCAT 59.678 47.826 0.00 0.00 0.00 3.79
636 639 4.551388 CCTAGAATGAACGTCCTAGCATC 58.449 47.826 0.00 0.00 0.00 3.91
637 640 4.038042 CCTAGAATGAACGTCCTAGCATCA 59.962 45.833 0.00 0.00 0.00 3.07
656 659 4.191033 TCAAACTTACCGCGGAAGATTA 57.809 40.909 35.90 10.80 0.00 1.75
694 697 3.837731 TCAGGTCATTACATCAGACACCA 59.162 43.478 0.00 0.00 34.04 4.17
733 739 1.222113 GCTAAGTCCTGGCAGACCC 59.778 63.158 17.94 2.85 37.49 4.46
744 750 0.749454 GGCAGACCCGATCAAAGCAT 60.749 55.000 0.00 0.00 0.00 3.79
792 798 3.367932 CACGGTGCTTTGTATACAGACAG 59.632 47.826 5.56 5.23 0.00 3.51
865 871 6.410540 AGCAACACAAACAATCCCTTAAAAA 58.589 32.000 0.00 0.00 0.00 1.94
883 889 5.659440 AAAAAGGAAGAGAAACAGCAACA 57.341 34.783 0.00 0.00 0.00 3.33
911 917 5.994668 AGACAAATTCCTCTGAACTGTTCTC 59.005 40.000 20.18 6.10 32.68 2.87
923 949 4.142534 TGAACTGTTCTCGTTATACCTCCG 60.143 45.833 20.18 0.00 0.00 4.63
941 967 1.676006 CCGTGCTTGTTCTTGTTCCTT 59.324 47.619 0.00 0.00 0.00 3.36
945 971 2.358898 TGCTTGTTCTTGTTCCTTGCTC 59.641 45.455 0.00 0.00 0.00 4.26
951 977 6.121776 TGTTCTTGTTCCTTGCTCCTATAA 57.878 37.500 0.00 0.00 0.00 0.98
955 981 8.831550 GTTCTTGTTCCTTGCTCCTATAAATAG 58.168 37.037 0.00 0.00 0.00 1.73
957 983 8.938883 TCTTGTTCCTTGCTCCTATAAATAGAT 58.061 33.333 0.00 0.00 32.05 1.98
959 985 8.034313 TGTTCCTTGCTCCTATAAATAGATGT 57.966 34.615 0.00 0.00 32.05 3.06
963 989 7.044798 CCTTGCTCCTATAAATAGATGTAGGC 58.955 42.308 0.00 0.00 34.91 3.93
965 991 6.936279 TGCTCCTATAAATAGATGTAGGCAC 58.064 40.000 0.00 0.00 34.91 5.01
972 999 5.991328 AAATAGATGTAGGCACAACGATG 57.009 39.130 0.00 0.00 38.42 3.84
1017 1044 3.744942 CAGATATGGATTCCAGAACAGCG 59.255 47.826 11.78 0.00 36.75 5.18
1018 1045 3.643320 AGATATGGATTCCAGAACAGCGA 59.357 43.478 11.78 0.00 36.75 4.93
1047 1074 0.605083 CTCTGCTGCTACTGGTGACA 59.395 55.000 0.00 0.00 39.59 3.58
1048 1075 1.206610 CTCTGCTGCTACTGGTGACAT 59.793 52.381 0.00 0.00 41.51 3.06
1101 1128 3.900601 AGGTAAGATCCATGCTCGATTCT 59.099 43.478 0.00 0.00 0.00 2.40
1107 1134 4.344679 AGATCCATGCTCGATTCTTCTTCT 59.655 41.667 0.00 0.00 0.00 2.85
1119 1146 6.533012 TCGATTCTTCTTCTCACAGCATTTAG 59.467 38.462 0.00 0.00 0.00 1.85
1141 1168 4.458642 AGCTCAGCTTCTTTCCAATCTTTC 59.541 41.667 0.00 0.00 33.89 2.62
1147 1174 6.008960 AGCTTCTTTCCAATCTTTCACTGAT 58.991 36.000 0.00 0.00 0.00 2.90
1218 1246 3.055080 GCACGATGACCCGTCCGTA 62.055 63.158 0.00 0.00 41.29 4.02
1242 1270 2.703409 GCGTCGCACCATGACATC 59.297 61.111 13.44 0.00 36.11 3.06
1251 1279 2.880890 GCACCATGACATCCTAACATCC 59.119 50.000 0.00 0.00 0.00 3.51
1259 1287 5.067273 TGACATCCTAACATCCGTTTTTGT 58.933 37.500 0.00 0.00 36.52 2.83
1292 1321 3.123804 GGATACGAGTTCATGTCGCATT 58.876 45.455 4.28 0.00 41.26 3.56
1313 1342 7.041780 CGCATTGTAGAAGTATTAGCAGGAAAT 60.042 37.037 0.00 0.00 0.00 2.17
1469 1506 5.057819 TCGCAAGTAAGTAATTGTCAACCA 58.942 37.500 1.04 0.00 34.12 3.67
1511 1553 2.593725 CCCGGCCTCTGCATCATG 60.594 66.667 0.00 0.00 40.13 3.07
1588 1630 1.770658 AGGTGGCATGAGCTTGCTATA 59.229 47.619 10.12 0.00 42.38 1.31
1718 1770 0.396278 GGAGCTGGGATTTCCTTGGG 60.396 60.000 0.00 0.00 36.20 4.12
1735 1787 5.191722 TCCTTGGGCTTGACTATAATCAACT 59.808 40.000 0.00 0.00 34.84 3.16
1870 1928 3.652057 TCCCAAGACCAGGAATCAATC 57.348 47.619 0.00 0.00 0.00 2.67
1871 1929 2.918934 TCCCAAGACCAGGAATCAATCA 59.081 45.455 0.00 0.00 0.00 2.57
1873 1931 3.635373 CCCAAGACCAGGAATCAATCATG 59.365 47.826 0.00 0.00 39.54 3.07
1904 1962 4.823989 GGATGCACATGCTTCTTTATAGGT 59.176 41.667 16.56 0.00 42.66 3.08
1979 2038 1.336795 CGGTGGAAAGGAAAATGCCAC 60.337 52.381 0.00 0.00 46.28 5.01
2054 2113 2.203195 TATGGCCGTGGCATCAGC 60.203 61.111 13.76 0.00 45.69 4.26
2622 2721 2.568623 AGTGTTACCTTGCCCTTCTG 57.431 50.000 0.00 0.00 0.00 3.02
2659 2758 8.580024 AAACCCCATGGAAAATATTAATGGAT 57.420 30.769 15.22 0.00 40.23 3.41
2713 2813 3.321111 GGATAAGACGTGCTCCAATCCTA 59.679 47.826 0.00 0.00 32.03 2.94
2722 2822 6.646267 ACGTGCTCCAATCCTAAAATAGTTA 58.354 36.000 0.00 0.00 0.00 2.24
2723 2823 7.107542 ACGTGCTCCAATCCTAAAATAGTTAA 58.892 34.615 0.00 0.00 0.00 2.01
2724 2824 7.773690 ACGTGCTCCAATCCTAAAATAGTTAAT 59.226 33.333 0.00 0.00 0.00 1.40
2725 2825 9.268268 CGTGCTCCAATCCTAAAATAGTTAATA 57.732 33.333 0.00 0.00 0.00 0.98
2778 2880 4.058817 GTCAATCTGGCGTTTCCCTATAG 58.941 47.826 0.00 0.00 0.00 1.31
2839 2970 1.064979 AGTGACGTTCAAACCAACCCT 60.065 47.619 0.00 0.00 0.00 4.34
2900 3046 9.618890 ATTCAATATATATACGAGGCATTGCTT 57.381 29.630 8.82 0.00 0.00 3.91
2920 3066 5.045942 TGCTTGTTCTCCACCAACTATATCA 60.046 40.000 0.00 0.00 0.00 2.15
3128 3336 5.912892 AGGACGAAACCATGTTCAATTTTT 58.087 33.333 0.00 0.00 0.00 1.94
3331 3544 2.158623 ACAATCTTGACAGCCTGGTTGA 60.159 45.455 17.92 0.00 0.00 3.18
3456 3669 4.771590 ACTGCAGTGTGAACATATTTGG 57.228 40.909 20.97 0.00 0.00 3.28
3457 3670 3.507233 ACTGCAGTGTGAACATATTTGGG 59.493 43.478 20.97 0.00 0.00 4.12
3534 3755 0.476771 AATCCGGTGGTGAAGGTGTT 59.523 50.000 0.00 0.00 0.00 3.32
3645 3866 7.275779 CGGCATACTCAAGGTGTATATCATTAC 59.724 40.741 0.00 0.00 0.00 1.89
3897 4207 1.670087 CGATGCTCAAGTCGGTTCACT 60.670 52.381 0.00 0.00 34.39 3.41
3932 4242 1.342174 GCCATGATCAAATCGGCCATT 59.658 47.619 14.63 0.00 36.73 3.16
4021 4347 8.849168 ACTAACTTGATTGTTCATTGTCATTGA 58.151 29.630 0.00 0.00 0.00 2.57
4039 4365 3.421919 TGATTGAAGCATCTGTGACCA 57.578 42.857 0.00 0.00 0.00 4.02
4149 4475 2.349755 GCCGTTGACCCTGGCTTA 59.650 61.111 0.00 0.00 45.40 3.09
4198 4524 2.874849 ACAAGTTTTTCAACTGCACCG 58.125 42.857 0.00 0.00 42.89 4.94
4211 4537 2.943033 ACTGCACCGTTGGATATTTAGC 59.057 45.455 0.00 0.00 0.00 3.09
4233 4559 4.597004 CTGGTTGTGAGTCCTACTACCTA 58.403 47.826 12.97 2.86 42.13 3.08
4316 4642 0.034337 GTGACTAACGTTGGGCCAGA 59.966 55.000 15.59 0.00 0.00 3.86
4345 4671 7.538575 AGCAACATATCATTTAGTGGTTGAAC 58.461 34.615 0.00 0.00 37.03 3.18
4568 4894 7.880195 AGACTTTGTTGCAGATACATCTTAAGT 59.120 33.333 1.63 5.06 34.22 2.24
4635 4961 7.094377 TGGTTGGCATAAGAAAATGTAGAAGAC 60.094 37.037 0.00 0.00 0.00 3.01
4771 5103 7.488187 AACCACAGATCATATCGAATGAAAG 57.512 36.000 12.24 8.79 0.00 2.62
4894 5226 4.844349 TCTTAGCTAGGCCAAAATCACT 57.156 40.909 5.01 0.00 0.00 3.41
4935 5267 4.320608 AATGTCCAAAATGCTCGTGTTT 57.679 36.364 0.00 0.00 0.00 2.83
5025 5357 6.420604 ACAAAATTTATGCCTCGTTGTTCTTG 59.579 34.615 0.00 0.00 0.00 3.02
5040 5372 2.623416 GTTCTTGGGGTCCAAACTTCAG 59.377 50.000 0.84 0.00 43.44 3.02
5079 5411 6.855914 GCGTTTGTCAATTAATTGTTCTGAGA 59.144 34.615 23.95 4.25 38.84 3.27
5120 5452 3.904339 TCTATTGCTCCAGATAGGGTTCC 59.096 47.826 0.00 0.00 38.24 3.62
5211 5544 4.568072 TGTAATGATGGATTATCCCCCG 57.432 45.455 8.98 0.00 35.03 5.73
5314 5647 4.624364 CTGTGTGAGCCACCCGCA 62.624 66.667 3.33 0.00 43.85 5.69
5334 5667 1.289982 TGGGGGTCCAAAGGTTGTCA 61.290 55.000 0.00 0.00 40.73 3.58
5390 5723 4.494199 CGGCGTTCTAAGTTCCATGAAATC 60.494 45.833 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.243902 GTGGCTTCCGGTGAAAATCA 58.756 50.000 0.00 0.00 0.00 2.57
42 43 4.845580 CCAGCCAGCCGCGAGATT 62.846 66.667 8.23 0.00 44.76 2.40
173 174 2.218454 ACCCCGTTTGGATCCGTCA 61.218 57.895 7.39 0.00 37.49 4.35
191 192 1.003839 GGTCACTGCGGATCCAACA 60.004 57.895 13.41 8.45 0.00 3.33
570 573 1.818959 TTGGTTCCCACTACGACGGG 61.819 60.000 0.00 0.00 44.60 5.28
571 574 0.668401 GTTGGTTCCCACTACGACGG 60.668 60.000 0.00 0.00 30.78 4.79
572 575 0.316204 AGTTGGTTCCCACTACGACG 59.684 55.000 0.00 0.00 30.78 5.12
573 576 3.582780 CTTAGTTGGTTCCCACTACGAC 58.417 50.000 2.83 0.00 30.78 4.34
574 577 2.564062 CCTTAGTTGGTTCCCACTACGA 59.436 50.000 7.73 0.00 30.78 3.43
575 578 2.354403 CCCTTAGTTGGTTCCCACTACG 60.354 54.545 2.83 2.07 30.78 3.51
576 579 2.617276 GCCCTTAGTTGGTTCCCACTAC 60.617 54.545 2.83 0.00 30.78 2.73
577 580 1.631898 GCCCTTAGTTGGTTCCCACTA 59.368 52.381 0.00 0.00 30.78 2.74
578 581 0.404426 GCCCTTAGTTGGTTCCCACT 59.596 55.000 1.39 1.39 30.78 4.00
579 582 0.111639 TGCCCTTAGTTGGTTCCCAC 59.888 55.000 0.00 0.00 30.78 4.61
580 583 1.080638 ATGCCCTTAGTTGGTTCCCA 58.919 50.000 0.00 0.00 0.00 4.37
581 584 3.288092 CTTATGCCCTTAGTTGGTTCCC 58.712 50.000 0.00 0.00 0.00 3.97
582 585 2.688446 GCTTATGCCCTTAGTTGGTTCC 59.312 50.000 0.00 0.00 0.00 3.62
583 586 3.352648 TGCTTATGCCCTTAGTTGGTTC 58.647 45.455 0.00 0.00 38.71 3.62
584 587 3.449746 TGCTTATGCCCTTAGTTGGTT 57.550 42.857 0.00 0.00 38.71 3.67
585 588 3.669939 ATGCTTATGCCCTTAGTTGGT 57.330 42.857 0.00 0.00 38.71 3.67
586 589 6.463995 TTTTATGCTTATGCCCTTAGTTGG 57.536 37.500 0.00 0.00 38.71 3.77
608 611 4.981812 AGGACGTTCATTCTAGGGTTTTT 58.018 39.130 0.00 0.00 0.00 1.94
609 612 4.635699 AGGACGTTCATTCTAGGGTTTT 57.364 40.909 0.00 0.00 0.00 2.43
610 613 4.382793 GCTAGGACGTTCATTCTAGGGTTT 60.383 45.833 0.00 0.00 32.23 3.27
611 614 3.132467 GCTAGGACGTTCATTCTAGGGTT 59.868 47.826 0.00 0.00 32.23 4.11
612 615 2.694109 GCTAGGACGTTCATTCTAGGGT 59.306 50.000 0.00 0.00 32.23 4.34
613 616 2.693591 TGCTAGGACGTTCATTCTAGGG 59.306 50.000 0.00 0.00 32.23 3.53
614 617 4.038042 TGATGCTAGGACGTTCATTCTAGG 59.962 45.833 0.00 0.00 32.23 3.02
615 618 5.188327 TGATGCTAGGACGTTCATTCTAG 57.812 43.478 0.00 2.04 34.09 2.43
616 619 5.592104 TTGATGCTAGGACGTTCATTCTA 57.408 39.130 0.00 0.00 0.00 2.10
617 620 4.471904 TTGATGCTAGGACGTTCATTCT 57.528 40.909 0.00 0.00 0.00 2.40
618 621 4.631813 AGTTTGATGCTAGGACGTTCATTC 59.368 41.667 0.00 0.00 0.00 2.67
619 622 4.579869 AGTTTGATGCTAGGACGTTCATT 58.420 39.130 0.00 0.00 0.00 2.57
620 623 4.207891 AGTTTGATGCTAGGACGTTCAT 57.792 40.909 0.00 0.00 0.00 2.57
621 624 3.678056 AGTTTGATGCTAGGACGTTCA 57.322 42.857 0.00 0.00 0.00 3.18
622 625 4.329256 GGTAAGTTTGATGCTAGGACGTTC 59.671 45.833 0.00 0.00 0.00 3.95
623 626 4.251268 GGTAAGTTTGATGCTAGGACGTT 58.749 43.478 0.00 0.00 0.00 3.99
624 627 3.675228 CGGTAAGTTTGATGCTAGGACGT 60.675 47.826 0.00 0.00 0.00 4.34
625 628 2.858344 CGGTAAGTTTGATGCTAGGACG 59.142 50.000 0.00 0.00 0.00 4.79
626 629 2.608090 GCGGTAAGTTTGATGCTAGGAC 59.392 50.000 0.00 0.00 0.00 3.85
627 630 2.737359 CGCGGTAAGTTTGATGCTAGGA 60.737 50.000 0.00 0.00 0.00 2.94
628 631 1.593006 CGCGGTAAGTTTGATGCTAGG 59.407 52.381 0.00 0.00 0.00 3.02
629 632 1.593006 CCGCGGTAAGTTTGATGCTAG 59.407 52.381 19.50 0.00 0.00 3.42
630 633 1.205179 TCCGCGGTAAGTTTGATGCTA 59.795 47.619 27.15 0.00 0.00 3.49
631 634 0.036765 TCCGCGGTAAGTTTGATGCT 60.037 50.000 27.15 0.00 0.00 3.79
632 635 0.800012 TTCCGCGGTAAGTTTGATGC 59.200 50.000 27.15 0.00 0.00 3.91
633 636 2.343101 TCTTCCGCGGTAAGTTTGATG 58.657 47.619 27.15 5.38 0.00 3.07
634 637 2.754946 TCTTCCGCGGTAAGTTTGAT 57.245 45.000 27.15 0.00 0.00 2.57
635 638 2.754946 ATCTTCCGCGGTAAGTTTGA 57.245 45.000 27.15 9.18 0.00 2.69
636 639 5.479716 AATAATCTTCCGCGGTAAGTTTG 57.520 39.130 27.15 2.99 0.00 2.93
637 640 5.644636 TCAAATAATCTTCCGCGGTAAGTTT 59.355 36.000 27.15 25.08 0.00 2.66
656 659 5.491070 TGACCTGATCATCGTCTTTCAAAT 58.509 37.500 18.71 0.00 29.99 2.32
718 721 1.613630 ATCGGGTCTGCCAGGACTT 60.614 57.895 0.00 0.00 36.55 3.01
720 723 1.899437 TTGATCGGGTCTGCCAGGAC 61.899 60.000 0.00 0.00 36.17 3.85
744 750 2.259917 TCCATCTGAGAAGAAGCACCA 58.740 47.619 0.00 0.00 0.00 4.17
758 764 1.244019 GCACCGTGCCTTTTCCATCT 61.244 55.000 12.80 0.00 37.42 2.90
792 798 4.618378 AGGAGGACCATAGATAGATCCC 57.382 50.000 0.00 0.00 38.94 3.85
865 871 2.213499 CGTGTTGCTGTTTCTCTTCCT 58.787 47.619 0.00 0.00 0.00 3.36
872 878 0.376852 TGTCTGCGTGTTGCTGTTTC 59.623 50.000 0.00 0.00 46.63 2.78
878 884 1.001378 AGGAATTTGTCTGCGTGTTGC 60.001 47.619 0.00 0.00 46.70 4.17
881 887 2.146342 CAGAGGAATTTGTCTGCGTGT 58.854 47.619 5.36 0.00 34.15 4.49
883 889 2.808543 GTTCAGAGGAATTTGTCTGCGT 59.191 45.455 11.42 0.00 40.13 5.24
911 917 2.288961 ACAAGCACGGAGGTATAACG 57.711 50.000 0.00 0.00 0.00 3.18
923 949 2.099756 AGCAAGGAACAAGAACAAGCAC 59.900 45.455 0.00 0.00 0.00 4.40
941 967 6.496911 TGTGCCTACATCTATTTATAGGAGCA 59.503 38.462 0.27 0.00 37.02 4.26
945 971 7.375834 TCGTTGTGCCTACATCTATTTATAGG 58.624 38.462 0.00 0.00 36.53 2.57
951 977 4.100963 TCCATCGTTGTGCCTACATCTATT 59.899 41.667 0.00 0.00 36.53 1.73
955 981 2.205074 CTCCATCGTTGTGCCTACATC 58.795 52.381 0.00 0.00 36.53 3.06
957 983 0.249120 CCTCCATCGTTGTGCCTACA 59.751 55.000 0.00 0.00 34.31 2.74
959 985 0.616395 TCCCTCCATCGTTGTGCCTA 60.616 55.000 0.00 0.00 0.00 3.93
963 989 1.156736 GTGTTCCCTCCATCGTTGTG 58.843 55.000 0.00 0.00 0.00 3.33
965 991 1.276421 AGAGTGTTCCCTCCATCGTTG 59.724 52.381 0.00 0.00 31.53 4.10
972 999 1.546961 TCGAGAAGAGTGTTCCCTCC 58.453 55.000 0.00 0.00 31.53 4.30
1017 1044 4.887987 AGCAGAGCGCCGCAGATC 62.888 66.667 13.36 0.00 44.04 2.75
1038 1065 0.607489 GAGGCAGCAATGTCACCAGT 60.607 55.000 0.00 0.00 0.00 4.00
1119 1146 4.217118 TGAAAGATTGGAAAGAAGCTGAGC 59.783 41.667 0.00 0.00 0.00 4.26
1122 1149 5.240183 TCAGTGAAAGATTGGAAAGAAGCTG 59.760 40.000 0.00 0.00 0.00 4.24
1218 1246 3.356639 ATGGTGCGACGCGATGACT 62.357 57.895 15.93 0.00 0.00 3.41
1242 1270 3.818773 ACCTCACAAAAACGGATGTTAGG 59.181 43.478 4.94 4.94 43.46 2.69
1251 1279 2.289547 CCAGTGGTACCTCACAAAAACG 59.710 50.000 14.36 0.00 39.93 3.60
1259 1287 2.025605 ACTCGTATCCAGTGGTACCTCA 60.026 50.000 14.36 0.00 0.00 3.86
1292 1321 8.350722 CGACTATTTCCTGCTAATACTTCTACA 58.649 37.037 0.00 0.00 0.00 2.74
1348 1385 2.877097 TGGCTTCATCCTTGCTGTTA 57.123 45.000 0.00 0.00 0.00 2.41
1485 1523 2.365237 GAGGCCGGGGAGTAACCT 60.365 66.667 2.18 0.00 38.98 3.50
1491 1532 4.247380 GATGCAGAGGCCGGGGAG 62.247 72.222 2.18 0.00 40.13 4.30
1511 1553 7.548780 ACAAATATGGTTGTGTAAATGGCAATC 59.451 33.333 0.00 0.00 40.22 2.67
1546 1588 8.285394 CACCTCAGGATTGACAATTAATATTCG 58.715 37.037 0.00 0.00 0.00 3.34
1718 1770 4.635765 TGTGGCAGTTGATTATAGTCAAGC 59.364 41.667 10.65 11.15 38.68 4.01
1871 1929 0.559205 ATGTGCATCCATGGGGTCAT 59.441 50.000 13.02 10.59 34.93 3.06
1873 1931 1.741327 GCATGTGCATCCATGGGGTC 61.741 60.000 13.02 1.38 42.01 4.46
1904 1962 3.324846 AGCTTCGTGATTCAGGCCATATA 59.675 43.478 5.01 0.00 0.00 0.86
1979 2038 0.508641 CGTTGAACTTCTCGCCACTG 59.491 55.000 0.00 0.00 0.00 3.66
2054 2113 1.134530 CGCTCTTTAGTGACTCGGCG 61.135 60.000 0.00 0.00 35.06 6.46
2120 2179 1.219664 CCCACCGGCGATAGTTGAA 59.780 57.895 9.30 0.00 39.35 2.69
2622 2721 2.375014 TGGGGTTTTTCTGTCCCTTC 57.625 50.000 0.00 0.00 40.88 3.46
2629 2728 9.904198 ATTAATATTTTCCATGGGGTTTTTCTG 57.096 29.630 13.02 0.00 34.93 3.02
2667 2766 8.141268 TCCAATAACATCTTTCACCTGTTTTTC 58.859 33.333 0.00 0.00 35.00 2.29
2668 2767 8.017418 TCCAATAACATCTTTCACCTGTTTTT 57.983 30.769 0.00 0.00 35.00 1.94
2726 2826 9.492730 TCCTCCACATTCATGCTATCTTATATA 57.507 33.333 0.00 0.00 0.00 0.86
2801 2920 1.683917 ACTTTCGTGCTCAGTGAGTCT 59.316 47.619 21.06 0.00 31.39 3.24
2807 2926 0.102481 ACGTCACTTTCGTGCTCAGT 59.898 50.000 0.00 0.00 40.99 3.41
2839 2970 6.432403 AGGAGCAAACCATTTATTTTTCCA 57.568 33.333 0.00 0.00 0.00 3.53
2888 3034 0.449388 GGAGAACAAGCAATGCCTCG 59.551 55.000 0.00 0.00 34.59 4.63
2900 3046 8.727100 AGATATGATATAGTTGGTGGAGAACA 57.273 34.615 0.00 0.00 0.00 3.18
2920 3066 7.070571 AGCTAACTGAGGAAAGCTACAAGATAT 59.929 37.037 4.03 0.00 43.29 1.63
3128 3336 4.380444 GGGTCGCATCTGCTCAAAATTTTA 60.380 41.667 2.44 0.00 39.32 1.52
3143 3351 1.153369 CAGTGATTCCGGGTCGCAT 60.153 57.895 18.98 6.02 0.00 4.73
3331 3544 2.624838 CAAGGCATAAATCCCTCGCATT 59.375 45.455 0.00 0.00 0.00 3.56
3354 3567 2.359900 GATCTCAAAATCCACCAGCGT 58.640 47.619 0.00 0.00 0.00 5.07
3457 3670 0.807496 GGAGATGGCAAACTGACTGC 59.193 55.000 0.00 0.00 39.16 4.40
3534 3755 1.944024 CAACAACACTTACAGCCGGAA 59.056 47.619 5.05 0.00 0.00 4.30
3897 4207 0.837691 ATGGCAGGTGACCACTGAGA 60.838 55.000 3.63 0.00 40.82 3.27
3932 4242 2.404559 ACTTTCCTACCTGTGGTGACA 58.595 47.619 0.00 0.00 36.19 3.58
4011 4337 6.152154 TCACAGATGCTTCAATCAATGACAAT 59.848 34.615 2.07 0.00 37.92 2.71
4021 4347 3.376234 CGATTGGTCACAGATGCTTCAAT 59.624 43.478 2.07 0.00 0.00 2.57
4071 4397 0.323629 CGGCTAGTTTCCTTGGGACA 59.676 55.000 0.00 0.00 0.00 4.02
4149 4475 3.440173 CCCTTGCATCAACATCGTAAACT 59.560 43.478 0.00 0.00 0.00 2.66
4198 4524 5.648092 ACTCACAACCAGCTAAATATCCAAC 59.352 40.000 0.00 0.00 0.00 3.77
4211 4537 3.432378 AGGTAGTAGGACTCACAACCAG 58.568 50.000 0.00 0.00 0.00 4.00
4233 4559 3.721087 ATTGACGGGAGGTTGAGATTT 57.279 42.857 0.00 0.00 0.00 2.17
4316 4642 6.426587 ACCACTAAATGATATGTTGCTTCCT 58.573 36.000 0.00 0.00 0.00 3.36
4688 5019 4.404185 AACCTCCCCTTAGCAAAGAATT 57.596 40.909 0.00 0.00 34.37 2.17
4771 5103 3.354467 TCCTTCGTTCTCCCTTAGTCTC 58.646 50.000 0.00 0.00 0.00 3.36
4881 5213 4.773674 TCATGAATTCAGTGATTTTGGCCT 59.226 37.500 14.54 0.00 0.00 5.19
4894 5226 5.361571 ACATTAGCAGCCATTCATGAATTCA 59.638 36.000 18.41 11.26 0.00 2.57
5025 5357 1.341089 GGATCCTGAAGTTTGGACCCC 60.341 57.143 3.84 2.25 34.90 4.95
5040 5372 5.465935 TGACAAACGCAAAAATAAGGATCC 58.534 37.500 2.48 2.48 0.00 3.36
5079 5411 7.558604 CAATAGAATTGAAATGGACATGGGTT 58.441 34.615 0.00 0.00 0.00 4.11
5120 5452 6.391227 AGATTATTATTTTCACCCGCCAAG 57.609 37.500 0.00 0.00 0.00 3.61
5314 5647 0.114364 GACAACCTTTGGACCCCCAT 59.886 55.000 0.00 0.00 43.12 4.00
5334 5667 0.842635 GCCAGAAGGAGATGATGGGT 59.157 55.000 0.00 0.00 36.89 4.51
5390 5723 6.942005 TCAAGTGTTGGGATAATATGGCATAG 59.058 38.462 13.39 0.00 0.00 2.23
5468 5801 0.613012 ACCCCCTCTTTGAATGCAGC 60.613 55.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.