Multiple sequence alignment - TraesCS7D01G554600

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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 TraesCS7D01G554600 chr7D 100.000 2600 0 0 1 2600 638355609 638353010 0.000000e+00 4802.0
1 TraesCS7D01G554600 chr7D 98.202 890 15 1 1712 2600 83376844 83375955 0.000000e+00 1554.0
2 TraesCS7D01G554600 chr7D 97.848 883 17 2 1718 2600 492146358 492145478 0.000000e+00 1524.0
3 TraesCS7D01G554600 chr7D 87.883 751 68 11 878 1606 638344325 638343576 0.000000e+00 861.0
4 TraesCS7D01G554600 chr7D 77.104 511 74 35 95 577 176157917 176158412 3.320000e-64 255.0
5 TraesCS7D01G554600 chr7D 77.374 358 63 14 1128 1485 638268458 638268119 2.040000e-46 196.0
6 TraesCS7D01G554600 chr7D 87.805 123 7 3 1603 1719 638343535 638343415 1.250000e-28 137.0
7 TraesCS7D01G554600 chr7D 100.000 29 0 0 818 846 638382471 638382443 1.000000e-03 54.7
8 TraesCS7D01G554600 chr5D 98.423 888 14 0 1713 2600 381783326 381782439 0.000000e+00 1563.0
9 TraesCS7D01G554600 chr5D 97.961 883 18 0 1718 2600 331212246 331211364 0.000000e+00 1531.0
10 TraesCS7D01G554600 chr3D 98.194 886 16 0 1715 2600 438262468 438263353 0.000000e+00 1548.0
11 TraesCS7D01G554600 chr3D 82.542 590 82 18 2 581 545818220 545817642 1.390000e-137 499.0
12 TraesCS7D01G554600 chr3D 88.561 271 23 8 318 585 13411704 13411969 3.230000e-84 322.0
13 TraesCS7D01G554600 chr3D 82.197 264 38 9 318 576 451370484 451370743 4.360000e-53 219.0
14 TraesCS7D01G554600 chr6D 95.795 880 36 1 1718 2597 42534214 42535092 0.000000e+00 1419.0
15 TraesCS7D01G554600 chr6D 84.167 240 36 2 342 581 376008845 376008608 5.600000e-57 231.0
16 TraesCS7D01G554600 chr5A 93.905 886 48 4 1718 2600 377927998 377928880 0.000000e+00 1332.0
17 TraesCS7D01G554600 chr5A 91.516 884 73 2 1718 2600 11691691 11690809 0.000000e+00 1216.0
18 TraesCS7D01G554600 chr1A 93.092 883 57 4 1718 2600 589992097 589992975 0.000000e+00 1290.0
19 TraesCS7D01G554600 chr7B 87.467 758 84 8 851 1606 734365970 734366718 0.000000e+00 863.0
20 TraesCS7D01G554600 chr7B 77.847 641 104 27 992 1601 734379429 734380062 1.900000e-96 363.0
21 TraesCS7D01G554600 chr7B 88.350 103 7 2 621 721 734365710 734365809 4.550000e-23 119.0
22 TraesCS7D01G554600 chr7B 95.455 44 2 0 739 782 734365802 734365845 1.290000e-08 71.3
23 TraesCS7D01G554600 chr7B 100.000 29 0 0 818 846 734359935 734359963 1.000000e-03 54.7
24 TraesCS7D01G554600 chr7B 96.774 31 1 0 818 848 734365904 734365934 5.000000e-03 52.8
25 TraesCS7D01G554600 chr3B 91.438 584 44 6 2 583 575300939 575300360 0.000000e+00 797.0
26 TraesCS7D01G554600 chr6B 91.439 549 40 6 38 581 579697942 579698488 0.000000e+00 747.0
27 TraesCS7D01G554600 chr6B 89.483 542 53 4 42 581 350832933 350832394 0.000000e+00 682.0
28 TraesCS7D01G554600 chr2B 89.757 576 49 10 9 577 66963973 66963401 0.000000e+00 728.0
29 TraesCS7D01G554600 chr7A 81.995 772 117 15 852 1606 727583566 727584332 1.010000e-178 636.0
30 TraesCS7D01G554600 chr7A 84.893 609 92 0 998 1606 727580820 727581428 1.320000e-172 616.0
31 TraesCS7D01G554600 chr7A 87.474 487 61 0 1120 1606 727710462 727710948 1.750000e-156 562.0
32 TraesCS7D01G554600 chr7A 88.889 324 36 0 1283 1606 727597236 727597559 1.450000e-107 399.0
33 TraesCS7D01G554600 chr7A 84.444 270 35 5 318 583 544898890 544898624 2.570000e-65 259.0
34 TraesCS7D01G554600 chr7A 87.162 148 12 3 582 727 727550732 727550874 7.450000e-36 161.0
35 TraesCS7D01G554600 chr7A 86.577 149 14 3 582 727 727586491 727586636 2.680000e-35 159.0
36 TraesCS7D01G554600 chr7A 90.598 117 9 2 1603 1719 727710989 727711103 1.250000e-33 154.0
37 TraesCS7D01G554600 chr7A 86.441 118 13 3 248 364 544899090 544898975 2.720000e-25 126.0
38 TraesCS7D01G554600 chr7A 82.667 150 19 4 582 727 727580182 727580328 2.720000e-25 126.0
39 TraesCS7D01G554600 chr6A 85.253 495 50 16 95 581 79238348 79238827 3.010000e-134 488.0
40 TraesCS7D01G554600 chr6A 87.966 349 23 11 1 330 42898577 42898925 6.740000e-106 394.0
41 TraesCS7D01G554600 chr6A 87.679 349 24 11 1 330 42848697 42849045 3.140000e-104 388.0
42 TraesCS7D01G554600 chr1B 93.031 287 19 1 2 287 538875985 538876271 4.000000e-113 418.0
43 TraesCS7D01G554600 chrUn 87.017 362 31 8 2 347 104896159 104895798 6.740000e-106 394.0
44 TraesCS7D01G554600 chr5B 84.016 244 36 3 339 581 27457013 27457254 5.600000e-57 231.0
45 TraesCS7D01G554600 chr5B 81.250 256 46 2 323 577 24112738 24112992 3.390000e-49 206.0
46 TraesCS7D01G554600 chr2A 92.500 80 6 0 248 327 71672918 71672839 5.880000e-22 115.0


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 TraesCS7D01G554600 chr7D 638353010 638355609 2599 True 4802.000 4802 100.0000 1 2600 1 chr7D.!!$R4 2599
1 TraesCS7D01G554600 chr7D 83375955 83376844 889 True 1554.000 1554 98.2020 1712 2600 1 chr7D.!!$R1 888
2 TraesCS7D01G554600 chr7D 492145478 492146358 880 True 1524.000 1524 97.8480 1718 2600 1 chr7D.!!$R2 882
3 TraesCS7D01G554600 chr7D 638343415 638344325 910 True 499.000 861 87.8440 878 1719 2 chr7D.!!$R6 841
4 TraesCS7D01G554600 chr5D 381782439 381783326 887 True 1563.000 1563 98.4230 1713 2600 1 chr5D.!!$R2 887
5 TraesCS7D01G554600 chr5D 331211364 331212246 882 True 1531.000 1531 97.9610 1718 2600 1 chr5D.!!$R1 882
6 TraesCS7D01G554600 chr3D 438262468 438263353 885 False 1548.000 1548 98.1940 1715 2600 1 chr3D.!!$F2 885
7 TraesCS7D01G554600 chr3D 545817642 545818220 578 True 499.000 499 82.5420 2 581 1 chr3D.!!$R1 579
8 TraesCS7D01G554600 chr6D 42534214 42535092 878 False 1419.000 1419 95.7950 1718 2597 1 chr6D.!!$F1 879
9 TraesCS7D01G554600 chr5A 377927998 377928880 882 False 1332.000 1332 93.9050 1718 2600 1 chr5A.!!$F1 882
10 TraesCS7D01G554600 chr5A 11690809 11691691 882 True 1216.000 1216 91.5160 1718 2600 1 chr5A.!!$R1 882
11 TraesCS7D01G554600 chr1A 589992097 589992975 878 False 1290.000 1290 93.0920 1718 2600 1 chr1A.!!$F1 882
12 TraesCS7D01G554600 chr7B 734379429 734380062 633 False 363.000 363 77.8470 992 1601 1 chr7B.!!$F2 609
13 TraesCS7D01G554600 chr7B 734365710 734366718 1008 False 276.525 863 92.0115 621 1606 4 chr7B.!!$F3 985
14 TraesCS7D01G554600 chr3B 575300360 575300939 579 True 797.000 797 91.4380 2 583 1 chr3B.!!$R1 581
15 TraesCS7D01G554600 chr6B 579697942 579698488 546 False 747.000 747 91.4390 38 581 1 chr6B.!!$F1 543
16 TraesCS7D01G554600 chr6B 350832394 350832933 539 True 682.000 682 89.4830 42 581 1 chr6B.!!$R1 539
17 TraesCS7D01G554600 chr2B 66963401 66963973 572 True 728.000 728 89.7570 9 577 1 chr2B.!!$R1 568
18 TraesCS7D01G554600 chr7A 727580182 727586636 6454 False 384.250 636 84.0330 582 1606 4 chr7A.!!$F3 1024
19 TraesCS7D01G554600 chr7A 727710462 727711103 641 False 358.000 562 89.0360 1120 1719 2 chr7A.!!$F4 599

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
729 742 0.110295 CACCACTGATCACCACCCAA 59.89 55.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 4838 1.414181 CTTCTGGTGGTATGCCGAGAT 59.586 52.381 0.0 0.0 37.67 2.75 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
29 30 5.034852 TGAACTTGTGTGAAGATCTTCCA 57.965 39.130 28.40 22.49 38.77 3.53
30 31 5.624159 TGAACTTGTGTGAAGATCTTCCAT 58.376 37.500 28.40 12.81 38.77 3.41
142 145 8.735692 TCTCAATGAATATGAAACTATGTGCA 57.264 30.769 0.00 0.00 0.00 4.57
145 148 8.959548 TCAATGAATATGAAACTATGTGCAGTT 58.040 29.630 0.00 0.00 40.49 3.16
229 232 6.343716 TGCCAATTGTTCTTGTCAATATGT 57.656 33.333 4.43 0.00 34.92 2.29
333 337 2.109181 GACCCTACCGCCAGCATC 59.891 66.667 0.00 0.00 0.00 3.91
418 424 1.821759 CCTGGCCGTTTGTGTGACA 60.822 57.895 0.00 0.00 0.00 3.58
551 560 3.244770 GGGCCAGATCCCGAATTTATACA 60.245 47.826 4.39 0.00 36.38 2.29
552 561 3.751698 GGCCAGATCCCGAATTTATACAC 59.248 47.826 0.00 0.00 0.00 2.90
553 562 3.432252 GCCAGATCCCGAATTTATACACG 59.568 47.826 0.00 0.00 0.00 4.49
569 578 3.775661 ACACGAAAAGGGTCAAAACAG 57.224 42.857 0.00 0.00 0.00 3.16
577 586 6.238076 CGAAAAGGGTCAAAACAGGAAATTTG 60.238 38.462 0.00 0.00 37.77 2.32
593 602 3.622060 TTGGCCGCTCTTAGCACCC 62.622 63.158 0.00 0.00 42.58 4.61
601 610 2.159379 CGCTCTTAGCACCCCAATTTTC 60.159 50.000 0.00 0.00 42.58 2.29
604 613 4.380973 GCTCTTAGCACCCCAATTTTCTTC 60.381 45.833 0.00 0.00 41.89 2.87
608 617 7.007723 TCTTAGCACCCCAATTTTCTTCTTTA 58.992 34.615 0.00 0.00 0.00 1.85
609 618 5.728637 AGCACCCCAATTTTCTTCTTTAG 57.271 39.130 0.00 0.00 0.00 1.85
610 619 4.528206 AGCACCCCAATTTTCTTCTTTAGG 59.472 41.667 0.00 0.00 0.00 2.69
654 665 5.120208 GTGCTAAAGCGTGTCTCATCTTTTA 59.880 40.000 0.00 0.00 45.83 1.52
722 735 8.870879 GTTAGTACTATTTTCACCACTGATCAC 58.129 37.037 2.79 0.00 0.00 3.06
723 736 6.407202 AGTACTATTTTCACCACTGATCACC 58.593 40.000 0.00 0.00 0.00 4.02
724 737 5.241403 ACTATTTTCACCACTGATCACCA 57.759 39.130 0.00 0.00 0.00 4.17
725 738 5.003804 ACTATTTTCACCACTGATCACCAC 58.996 41.667 0.00 0.00 0.00 4.16
726 739 2.270352 TTTCACCACTGATCACCACC 57.730 50.000 0.00 0.00 0.00 4.61
727 740 0.400213 TTCACCACTGATCACCACCC 59.600 55.000 0.00 0.00 0.00 4.61
728 741 0.766288 TCACCACTGATCACCACCCA 60.766 55.000 0.00 0.00 0.00 4.51
729 742 0.110295 CACCACTGATCACCACCCAA 59.890 55.000 0.00 0.00 0.00 4.12
730 743 0.110486 ACCACTGATCACCACCCAAC 59.890 55.000 0.00 0.00 0.00 3.77
731 744 0.401738 CCACTGATCACCACCCAACT 59.598 55.000 0.00 0.00 0.00 3.16
732 745 1.202927 CCACTGATCACCACCCAACTT 60.203 52.381 0.00 0.00 0.00 2.66
733 746 2.154462 CACTGATCACCACCCAACTTC 58.846 52.381 0.00 0.00 0.00 3.01
734 747 1.774254 ACTGATCACCACCCAACTTCA 59.226 47.619 0.00 0.00 0.00 3.02
735 748 2.174639 ACTGATCACCACCCAACTTCAA 59.825 45.455 0.00 0.00 0.00 2.69
736 749 3.221771 CTGATCACCACCCAACTTCAAA 58.778 45.455 0.00 0.00 0.00 2.69
737 750 3.636300 CTGATCACCACCCAACTTCAAAA 59.364 43.478 0.00 0.00 0.00 2.44
738 751 3.383185 TGATCACCACCCAACTTCAAAAC 59.617 43.478 0.00 0.00 0.00 2.43
739 752 2.808919 TCACCACCCAACTTCAAAACA 58.191 42.857 0.00 0.00 0.00 2.83
740 753 2.494073 TCACCACCCAACTTCAAAACAC 59.506 45.455 0.00 0.00 0.00 3.32
741 754 2.495669 CACCACCCAACTTCAAAACACT 59.504 45.455 0.00 0.00 0.00 3.55
742 755 2.495669 ACCACCCAACTTCAAAACACTG 59.504 45.455 0.00 0.00 0.00 3.66
743 756 2.757868 CCACCCAACTTCAAAACACTGA 59.242 45.455 0.00 0.00 0.00 3.41
744 757 3.384467 CCACCCAACTTCAAAACACTGAT 59.616 43.478 0.00 0.00 0.00 2.90
745 758 4.499696 CCACCCAACTTCAAAACACTGATC 60.500 45.833 0.00 0.00 0.00 2.92
746 759 4.097741 CACCCAACTTCAAAACACTGATCA 59.902 41.667 0.00 0.00 0.00 2.92
750 763 6.207417 CCCAACTTCAAAACACTGATCACTAT 59.793 38.462 0.00 0.00 0.00 2.12
782 798 4.841246 ACAACAGTGTCCCTAGATTCTTCT 59.159 41.667 0.00 0.00 29.49 2.85
784 800 5.669164 ACAGTGTCCCTAGATTCTTCTTC 57.331 43.478 0.00 0.00 33.17 2.87
785 801 5.337788 ACAGTGTCCCTAGATTCTTCTTCT 58.662 41.667 0.00 0.00 33.17 2.85
786 802 5.782845 ACAGTGTCCCTAGATTCTTCTTCTT 59.217 40.000 0.00 0.00 33.17 2.52
788 804 6.154363 CAGTGTCCCTAGATTCTTCTTCTTCT 59.846 42.308 0.00 0.00 33.17 2.85
790 806 7.039270 GTGTCCCTAGATTCTTCTTCTTCTTC 58.961 42.308 0.00 0.00 33.17 2.87
791 807 6.155393 TGTCCCTAGATTCTTCTTCTTCTTCC 59.845 42.308 0.00 0.00 33.17 3.46
792 808 6.382859 GTCCCTAGATTCTTCTTCTTCTTCCT 59.617 42.308 0.00 0.00 33.17 3.36
793 809 6.962902 TCCCTAGATTCTTCTTCTTCTTCCTT 59.037 38.462 0.00 0.00 33.17 3.36
794 810 7.047271 CCCTAGATTCTTCTTCTTCTTCCTTG 58.953 42.308 0.00 0.00 33.17 3.61
795 811 6.538381 CCTAGATTCTTCTTCTTCTTCCTTGC 59.462 42.308 0.00 0.00 33.17 4.01
798 814 6.947158 AGATTCTTCTTCTTCTTCCTTGCATT 59.053 34.615 0.00 0.00 0.00 3.56
799 815 6.566197 TTCTTCTTCTTCTTCCTTGCATTC 57.434 37.500 0.00 0.00 0.00 2.67
800 816 5.624159 TCTTCTTCTTCTTCCTTGCATTCA 58.376 37.500 0.00 0.00 0.00 2.57
801 817 6.243900 TCTTCTTCTTCTTCCTTGCATTCAT 58.756 36.000 0.00 0.00 0.00 2.57
802 818 5.892160 TCTTCTTCTTCCTTGCATTCATG 57.108 39.130 0.00 0.00 0.00 3.07
804 820 6.475504 TCTTCTTCTTCCTTGCATTCATGTA 58.524 36.000 0.00 0.00 0.00 2.29
806 822 5.809001 TCTTCTTCCTTGCATTCATGTACT 58.191 37.500 0.00 0.00 0.00 2.73
807 823 6.946340 TCTTCTTCCTTGCATTCATGTACTA 58.054 36.000 0.00 0.00 0.00 1.82
808 824 6.818644 TCTTCTTCCTTGCATTCATGTACTAC 59.181 38.462 0.00 0.00 0.00 2.73
809 825 6.299805 TCTTCCTTGCATTCATGTACTACT 57.700 37.500 0.00 0.00 0.00 2.57
811 827 8.023021 TCTTCCTTGCATTCATGTACTACTAT 57.977 34.615 0.00 0.00 0.00 2.12
812 828 8.486210 TCTTCCTTGCATTCATGTACTACTATT 58.514 33.333 0.00 0.00 0.00 1.73
813 829 8.437360 TTCCTTGCATTCATGTACTACTATTG 57.563 34.615 0.00 0.00 0.00 1.90
816 855 5.063204 TGCATTCATGTACTACTATTGCCC 58.937 41.667 0.00 0.00 0.00 5.36
819 858 5.950544 TTCATGTACTACTATTGCCCAGT 57.049 39.130 0.00 0.00 0.00 4.00
848 887 3.205338 CGTGCATGGACAAATATCCTGA 58.795 45.455 18.05 0.00 39.75 3.86
854 893 4.235079 TGGACAAATATCCTGAAGTGGG 57.765 45.455 0.00 0.00 39.75 4.61
855 894 2.952310 GGACAAATATCCTGAAGTGGGC 59.048 50.000 0.00 0.00 35.68 5.36
856 895 2.952310 GACAAATATCCTGAAGTGGGCC 59.048 50.000 0.00 0.00 0.00 5.80
857 896 2.310538 CAAATATCCTGAAGTGGGCCC 58.689 52.381 17.59 17.59 0.00 5.80
858 897 0.474184 AATATCCTGAAGTGGGCCCG 59.526 55.000 19.37 0.17 0.00 6.13
859 898 1.418908 ATATCCTGAAGTGGGCCCGG 61.419 60.000 19.37 11.44 0.00 5.73
913 983 2.283529 ACCACCCCACTGACGCTAG 61.284 63.158 0.00 0.00 0.00 3.42
941 1013 3.626924 ACCCTCACAGTCCACGGC 61.627 66.667 0.00 0.00 0.00 5.68
947 1019 1.003355 CACAGTCCACGGCCAGAAT 60.003 57.895 2.24 0.00 0.00 2.40
954 1026 1.361668 CCACGGCCAGAATTCAGACG 61.362 60.000 18.94 18.94 0.00 4.18
959 1031 2.359900 GGCCAGAATTCAGACGAACAT 58.640 47.619 8.44 0.00 32.81 2.71
965 1037 5.464722 CCAGAATTCAGACGAACATATCTGG 59.535 44.000 8.44 3.83 42.25 3.86
976 1048 5.118990 CGAACATATCTGGTCCAGTCAAAT 58.881 41.667 18.65 7.35 35.54 2.32
981 1053 6.613271 ACATATCTGGTCCAGTCAAATCTAGT 59.387 38.462 18.65 4.16 32.61 2.57
987 1059 6.698380 TGGTCCAGTCAAATCTAGTTCTTAC 58.302 40.000 0.00 0.00 0.00 2.34
988 1060 6.497259 TGGTCCAGTCAAATCTAGTTCTTACT 59.503 38.462 0.00 0.00 38.44 2.24
989 1061 7.016268 TGGTCCAGTCAAATCTAGTTCTTACTT 59.984 37.037 0.00 0.00 35.78 2.24
990 1062 7.546316 GGTCCAGTCAAATCTAGTTCTTACTTC 59.454 40.741 0.00 0.00 35.78 3.01
1053 1177 4.547367 GCCCTTATCGCTGCCGGT 62.547 66.667 1.90 0.00 34.56 5.28
1056 1180 1.740285 CCTTATCGCTGCCGGTACT 59.260 57.895 1.90 0.00 34.56 2.73
1063 1187 3.082579 GCTGCCGGTACTGGAGAGG 62.083 68.421 25.59 10.98 0.00 3.69
1065 1189 3.851128 GCCGGTACTGGAGAGGCC 61.851 72.222 25.59 0.00 41.81 5.19
1087 1405 4.717629 CGTCGTCGCCTGCCTCAA 62.718 66.667 0.00 0.00 0.00 3.02
1094 1412 3.368571 GCCTGCCTCAACACAGCC 61.369 66.667 0.00 0.00 32.37 4.85
1098 1416 2.203337 GCCTCAACACAGCCACCA 60.203 61.111 0.00 0.00 0.00 4.17
1138 1459 1.080093 GCGTTGGACTCGGACATGA 60.080 57.895 0.00 0.00 0.00 3.07
1152 1473 1.221566 CATGACGGTCATCCTGGCA 59.778 57.895 20.27 0.00 34.28 4.92
1245 1566 0.617249 CCAGCTCCACTTCCTCCTCT 60.617 60.000 0.00 0.00 0.00 3.69
1256 1586 1.082206 CCTCCTCTAACCCACCCCA 59.918 63.158 0.00 0.00 0.00 4.96
1257 1587 0.549169 CCTCCTCTAACCCACCCCAA 60.549 60.000 0.00 0.00 0.00 4.12
1305 1635 2.593956 GCTCCCCACCGTCTCCTTT 61.594 63.158 0.00 0.00 0.00 3.11
1523 1874 2.567497 CGGTGGTGGTCGTAGTGGT 61.567 63.158 0.00 0.00 0.00 4.16
1583 1934 3.661648 GGCTGGTGGTGGGGACAT 61.662 66.667 0.00 0.00 46.14 3.06
1606 1957 7.611467 ACATCACATTCTTGCCTTAATCAGTTA 59.389 33.333 0.00 0.00 0.00 2.24
1607 1958 7.615582 TCACATTCTTGCCTTAATCAGTTAG 57.384 36.000 0.00 0.00 0.00 2.34
1608 1959 6.599244 TCACATTCTTGCCTTAATCAGTTAGG 59.401 38.462 0.00 0.00 0.00 2.69
1611 1962 5.950544 TCTTGCCTTAATCAGTTAGGCTA 57.049 39.130 12.96 5.29 45.20 3.93
1612 1963 6.500589 TCTTGCCTTAATCAGTTAGGCTAT 57.499 37.500 12.96 0.00 45.20 2.97
1650 2313 7.886405 AGTTTTCTTTGGTTAGTCGAGTATC 57.114 36.000 0.00 0.11 0.00 2.24
1653 2316 9.583765 GTTTTCTTTGGTTAGTCGAGTATCTAT 57.416 33.333 0.00 0.00 0.00 1.98
1710 3844 9.165035 ACTTAGTTAAGTAGAGTAGTAGCACTG 57.835 37.037 2.80 0.00 44.18 3.66
2019 4295 2.079158 CCCTTACTACACGAGACGACA 58.921 52.381 0.00 0.00 0.00 4.35
2137 4474 4.641645 CCACCCTCGCAGCACCAA 62.642 66.667 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.463995 TGAAAGGCACAAGACAAACTAAAT 57.536 33.333 0.00 0.00 0.00 1.40
30 31 5.906113 TGAAAGGCACAAGACAAACTAAA 57.094 34.783 0.00 0.00 0.00 1.85
311 315 2.285818 TGGCGGTAGGGTCCCATT 60.286 61.111 11.55 0.00 0.00 3.16
333 337 1.380785 TACAGACCTACCGCCAGGG 60.381 63.158 5.62 0.00 43.47 4.45
418 424 1.612442 TAGGGAAACGGCAGAGGCT 60.612 57.895 0.00 0.00 40.87 4.58
551 560 3.007473 TCCTGTTTTGACCCTTTTCGT 57.993 42.857 0.00 0.00 0.00 3.85
552 561 4.379339 TTTCCTGTTTTGACCCTTTTCG 57.621 40.909 0.00 0.00 0.00 3.46
553 562 6.038161 CCAAATTTCCTGTTTTGACCCTTTTC 59.962 38.462 0.00 0.00 35.34 2.29
569 578 1.202302 GCTAAGAGCGGCCAAATTTCC 60.202 52.381 2.24 0.00 0.00 3.13
577 586 4.858680 GGGGTGCTAAGAGCGGCC 62.859 72.222 0.00 0.00 46.26 6.13
593 602 7.148018 TGCTATGCTCCTAAAGAAGAAAATTGG 60.148 37.037 0.00 0.00 0.00 3.16
601 610 4.046938 TCGTGCTATGCTCCTAAAGAAG 57.953 45.455 0.00 0.00 0.00 2.85
604 613 4.250116 AGATCGTGCTATGCTCCTAAAG 57.750 45.455 0.00 0.00 0.00 1.85
608 617 4.100189 ACTTTTAGATCGTGCTATGCTCCT 59.900 41.667 0.00 0.00 0.00 3.69
609 618 4.210120 CACTTTTAGATCGTGCTATGCTCC 59.790 45.833 0.00 0.00 0.00 4.70
610 619 5.321983 CACTTTTAGATCGTGCTATGCTC 57.678 43.478 0.00 0.00 0.00 4.26
654 665 6.203338 CCAACTATTAAACCACAGTACGTGTT 59.797 38.462 13.98 7.56 44.78 3.32
698 711 7.179516 TGGTGATCAGTGGTGAAAATAGTACTA 59.820 37.037 4.77 4.77 35.88 1.82
699 712 6.013725 TGGTGATCAGTGGTGAAAATAGTACT 60.014 38.462 0.00 0.00 35.88 2.73
700 713 6.092259 GTGGTGATCAGTGGTGAAAATAGTAC 59.908 42.308 0.00 0.00 35.88 2.73
722 735 2.757868 TCAGTGTTTTGAAGTTGGGTGG 59.242 45.455 0.00 0.00 0.00 4.61
723 736 4.097741 TGATCAGTGTTTTGAAGTTGGGTG 59.902 41.667 0.00 0.00 0.00 4.61
724 737 4.097892 GTGATCAGTGTTTTGAAGTTGGGT 59.902 41.667 0.00 0.00 0.00 4.51
725 738 4.339247 AGTGATCAGTGTTTTGAAGTTGGG 59.661 41.667 1.14 0.00 0.00 4.12
726 739 5.505173 AGTGATCAGTGTTTTGAAGTTGG 57.495 39.130 1.14 0.00 0.00 3.77
727 740 7.800380 GTGATAGTGATCAGTGTTTTGAAGTTG 59.200 37.037 13.54 0.00 42.87 3.16
728 741 7.716998 AGTGATAGTGATCAGTGTTTTGAAGTT 59.283 33.333 13.54 0.00 42.98 2.66
729 742 7.220030 AGTGATAGTGATCAGTGTTTTGAAGT 58.780 34.615 13.54 0.00 42.98 3.01
730 743 7.386025 TGAGTGATAGTGATCAGTGTTTTGAAG 59.614 37.037 13.54 0.00 44.33 3.02
731 744 7.216494 TGAGTGATAGTGATCAGTGTTTTGAA 58.784 34.615 13.54 0.00 44.33 2.69
732 745 6.758254 TGAGTGATAGTGATCAGTGTTTTGA 58.242 36.000 13.54 0.00 44.33 2.69
733 746 7.058298 CTGAGTGATAGTGATCAGTGTTTTG 57.942 40.000 13.54 0.00 44.33 2.44
740 753 6.856895 TGTTGTACTGAGTGATAGTGATCAG 58.143 40.000 0.00 0.00 42.87 2.90
741 754 6.434340 ACTGTTGTACTGAGTGATAGTGATCA 59.566 38.462 0.00 0.00 39.88 2.92
742 755 6.749578 CACTGTTGTACTGAGTGATAGTGATC 59.250 42.308 13.11 0.00 39.64 2.92
743 756 6.209589 ACACTGTTGTACTGAGTGATAGTGAT 59.790 38.462 20.25 8.88 39.64 3.06
744 757 5.535030 ACACTGTTGTACTGAGTGATAGTGA 59.465 40.000 20.25 0.00 39.64 3.41
745 758 5.773575 ACACTGTTGTACTGAGTGATAGTG 58.226 41.667 19.78 15.29 39.64 2.74
746 759 5.047943 GGACACTGTTGTACTGAGTGATAGT 60.048 44.000 19.78 0.00 39.64 2.12
750 763 2.364324 GGGACACTGTTGTACTGAGTGA 59.636 50.000 19.78 0.00 39.64 3.41
782 798 6.240894 AGTACATGAATGCAAGGAAGAAGAA 58.759 36.000 0.00 0.00 0.00 2.52
784 800 6.820656 AGTAGTACATGAATGCAAGGAAGAAG 59.179 38.462 0.00 0.00 0.00 2.85
785 801 6.711277 AGTAGTACATGAATGCAAGGAAGAA 58.289 36.000 0.00 0.00 0.00 2.52
786 802 6.299805 AGTAGTACATGAATGCAAGGAAGA 57.700 37.500 0.00 0.00 0.00 2.87
788 804 7.012327 GCAATAGTAGTACATGAATGCAAGGAA 59.988 37.037 0.00 0.00 0.00 3.36
790 806 6.293626 GGCAATAGTAGTACATGAATGCAAGG 60.294 42.308 0.00 0.00 33.14 3.61
791 807 6.293626 GGGCAATAGTAGTACATGAATGCAAG 60.294 42.308 0.00 0.00 33.14 4.01
792 808 5.530915 GGGCAATAGTAGTACATGAATGCAA 59.469 40.000 0.00 0.00 33.14 4.08
793 809 5.063204 GGGCAATAGTAGTACATGAATGCA 58.937 41.667 0.00 0.00 33.14 3.96
794 810 5.063204 TGGGCAATAGTAGTACATGAATGC 58.937 41.667 0.00 5.69 0.00 3.56
795 811 6.291377 ACTGGGCAATAGTAGTACATGAATG 58.709 40.000 0.00 0.00 0.00 2.67
798 814 5.670485 CAACTGGGCAATAGTAGTACATGA 58.330 41.667 0.00 0.00 0.00 3.07
799 815 4.273480 GCAACTGGGCAATAGTAGTACATG 59.727 45.833 2.52 0.00 0.00 3.21
800 816 4.451900 GCAACTGGGCAATAGTAGTACAT 58.548 43.478 2.52 0.00 0.00 2.29
801 817 3.370103 GGCAACTGGGCAATAGTAGTACA 60.370 47.826 2.52 0.00 42.77 2.90
802 818 3.203716 GGCAACTGGGCAATAGTAGTAC 58.796 50.000 0.00 0.00 42.77 2.73
804 820 2.420058 GGCAACTGGGCAATAGTAGT 57.580 50.000 0.00 0.00 42.77 2.73
816 855 4.029186 ATGCACGCGTGGCAACTG 62.029 61.111 37.47 13.78 45.60 3.16
848 887 4.710167 GTAACGCCGGGCCCACTT 62.710 66.667 24.92 9.02 0.00 3.16
857 896 2.125673 CCTGGACTGGTAACGCCG 60.126 66.667 0.00 0.00 41.21 6.46
858 897 2.267961 CCCTGGACTGGTAACGCC 59.732 66.667 0.00 0.00 42.51 5.68
859 898 2.267961 CCCCTGGACTGGTAACGC 59.732 66.667 0.00 0.00 42.51 4.84
860 899 2.267961 GCCCCTGGACTGGTAACG 59.732 66.667 0.00 0.00 42.51 3.18
891 961 4.660938 GTCAGTGGGGTGGTGGCC 62.661 72.222 0.00 0.00 0.00 5.36
920 992 2.147387 GTGGACTGTGAGGGTGGGT 61.147 63.158 0.00 0.00 0.00 4.51
922 994 2.343758 CGTGGACTGTGAGGGTGG 59.656 66.667 0.00 0.00 0.00 4.61
923 995 2.343758 CCGTGGACTGTGAGGGTG 59.656 66.667 0.00 0.00 0.00 4.61
924 996 3.626924 GCCGTGGACTGTGAGGGT 61.627 66.667 0.00 0.00 0.00 4.34
926 998 3.596066 CTGGCCGTGGACTGTGAGG 62.596 68.421 0.00 0.00 0.00 3.86
927 999 2.047844 CTGGCCGTGGACTGTGAG 60.048 66.667 0.00 0.00 0.00 3.51
930 1002 0.321653 GAATTCTGGCCGTGGACTGT 60.322 55.000 0.00 0.00 0.00 3.55
941 1013 5.464722 CCAGATATGTTCGTCTGAATTCTGG 59.535 44.000 11.89 0.00 43.50 3.86
947 1019 3.767131 TGGACCAGATATGTTCGTCTGAA 59.233 43.478 4.08 0.00 43.50 3.02
954 1026 6.352516 AGATTTGACTGGACCAGATATGTTC 58.647 40.000 28.56 13.92 35.18 3.18
959 1031 6.897966 AGAACTAGATTTGACTGGACCAGATA 59.102 38.462 28.56 12.97 35.18 1.98
965 1037 8.088981 TGAAGTAAGAACTAGATTTGACTGGAC 58.911 37.037 0.00 0.00 33.75 4.02
976 1048 4.082895 GGTGTCGCTGAAGTAAGAACTAGA 60.083 45.833 0.00 0.00 33.75 2.43
981 1053 3.325870 CATGGTGTCGCTGAAGTAAGAA 58.674 45.455 0.00 0.00 0.00 2.52
987 1059 2.780643 CGCATGGTGTCGCTGAAG 59.219 61.111 0.00 0.00 0.00 3.02
988 1060 3.422303 GCGCATGGTGTCGCTGAA 61.422 61.111 0.30 0.00 46.92 3.02
1041 1165 1.452953 CTCCAGTACCGGCAGCGATA 61.453 60.000 0.00 0.00 0.00 2.92
1042 1166 2.758327 TCCAGTACCGGCAGCGAT 60.758 61.111 0.00 0.00 0.00 4.58
1043 1167 3.449227 CTCCAGTACCGGCAGCGA 61.449 66.667 0.00 0.00 0.00 4.93
1047 1171 3.075005 GCCTCTCCAGTACCGGCA 61.075 66.667 0.00 0.00 40.41 5.69
1053 1177 1.451567 CGACGAGGCCTCTCCAGTA 60.452 63.158 29.73 0.00 36.70 2.74
1056 1180 2.750637 GACGACGAGGCCTCTCCA 60.751 66.667 29.73 0.00 36.70 3.86
1087 1405 3.941188 CTCCGGTGGTGGCTGTGT 61.941 66.667 0.00 0.00 0.00 3.72
1123 1444 1.183030 ACCGTCATGTCCGAGTCCAA 61.183 55.000 8.71 0.00 0.00 3.53
1138 1459 2.501128 CGATGCCAGGATGACCGT 59.499 61.111 0.00 0.00 39.69 4.83
1256 1586 2.881734 CCTTCTTCTTGAGGCCCTTTT 58.118 47.619 0.00 0.00 0.00 2.27
1257 1587 1.548809 GCCTTCTTCTTGAGGCCCTTT 60.549 52.381 0.00 0.00 41.28 3.11
1523 1874 1.373435 CCGCACCTGTTGTTCCCTA 59.627 57.895 0.00 0.00 0.00 3.53
1581 1932 6.446781 ACTGATTAAGGCAAGAATGTGATG 57.553 37.500 0.00 0.00 0.00 3.07
1583 1934 6.599244 CCTAACTGATTAAGGCAAGAATGTGA 59.401 38.462 0.00 0.00 0.00 3.58
1624 2176 6.997239 ACTCGACTAACCAAAGAAAACTTT 57.003 33.333 0.00 0.00 0.00 2.66
1627 2179 7.886405 AGATACTCGACTAACCAAAGAAAAC 57.114 36.000 0.00 0.00 0.00 2.43
1635 2187 6.149640 GCTGATGATAGATACTCGACTAACCA 59.850 42.308 0.00 0.00 0.00 3.67
1636 2188 6.373216 AGCTGATGATAGATACTCGACTAACC 59.627 42.308 0.00 0.00 0.00 2.85
2019 4295 4.681978 GTTCGTGGTCTGCGGGCT 62.682 66.667 0.00 0.00 0.00 5.19
2110 4447 2.430367 GAGGGTGGCCAGTTCGTT 59.570 61.111 5.11 0.00 0.00 3.85
2258 4838 1.414181 CTTCTGGTGGTATGCCGAGAT 59.586 52.381 0.00 0.00 37.67 2.75


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

AutoCloner maintained by Alex Coulton.