Multiple sequence alignment - TraesCS3A01G535200

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 TraesCS3A01G535200 chr3A 100.000 2783 0 0 1 2783 746899698 746902480 0.000000e+00 5140
1 TraesCS3A01G535200 chr3A 77.020 557 107 10 1020 1576 607234406 607233871 1.620000e-77 300
2 TraesCS3A01G535200 chr3A 76.661 557 112 7 1020 1576 607146283 607145745 2.710000e-75 292
3 TraesCS3A01G535200 chr3A 77.350 234 52 1 1016 1249 692677625 692677857 1.340000e-28 137
4 TraesCS3A01G535200 chr3D 91.809 1111 63 8 719 1807 612263425 612264529 0.000000e+00 1522
5 TraesCS3A01G535200 chr3D 93.014 501 31 1 2260 2760 612265140 612265636 0.000000e+00 728
6 TraesCS3A01G535200 chr3D 88.425 527 37 13 1798 2320 612264635 612265141 5.090000e-172 614
7 TraesCS3A01G535200 chr3D 91.765 340 19 3 347 677 612263076 612263415 5.430000e-127 464
8 TraesCS3A01G535200 chr3D 92.369 249 19 0 1 249 612262827 612263075 3.410000e-94 355
9 TraesCS3A01G535200 chr3D 89.209 139 15 0 2183 2321 8368057 8367919 1.020000e-39 174
10 TraesCS3A01G535200 chr3D 80.976 205 37 2 1046 1249 555532130 555532333 7.980000e-36 161
11 TraesCS3A01G535200 chr3B 92.909 973 51 11 851 1806 826919837 826918866 0.000000e+00 1399
12 TraesCS3A01G535200 chr3B 90.526 665 52 6 3 660 826747381 826746721 0.000000e+00 869
13 TraesCS3A01G535200 chr3B 91.216 444 32 4 2319 2760 826911119 826910681 5.130000e-167 597
14 TraesCS3A01G535200 chr3B 91.111 225 16 1 2536 2760 826746721 826746501 4.500000e-78 302
15 TraesCS3A01G535200 chr3B 89.474 228 17 4 1939 2164 826911326 826911104 5.870000e-72 281
16 TraesCS3A01G535200 chr3B 83.133 249 40 2 1329 1576 617439000 617438753 2.790000e-55 226
17 TraesCS3A01G535200 chr3B 90.566 159 7 3 1798 1953 826918760 826918607 1.310000e-48 204
18 TraesCS3A01G535200 chr3B 89.781 137 14 0 2183 2319 808100929 808101065 2.850000e-40 176
19 TraesCS3A01G535200 chr3B 80.976 205 37 2 1046 1249 738716934 738717137 7.980000e-36 161
20 TraesCS3A01G535200 chr6D 86.597 761 73 14 1021 1772 427170926 427171666 0.000000e+00 813
21 TraesCS3A01G535200 chr6D 90.441 136 13 0 2183 2318 18495463 18495598 2.200000e-41 180
22 TraesCS3A01G535200 chr6D 90.977 133 12 0 2186 2318 379339981 379339849 2.200000e-41 180
23 TraesCS3A01G535200 chr6B 87.482 711 74 7 1021 1725 643131466 643132167 0.000000e+00 806
24 TraesCS3A01G535200 chr6B 89.358 592 52 5 1021 1611 642989561 642990142 0.000000e+00 734
25 TraesCS3A01G535200 chr6B 90.441 136 13 0 2183 2318 27127333 27127198 2.200000e-41 180
26 TraesCS3A01G535200 chr6A 88.525 610 57 7 1021 1628 571881425 571882023 0.000000e+00 726
27 TraesCS3A01G535200 chr5D 90.580 138 13 0 2183 2320 375170784 375170921 1.700000e-42 183
28 TraesCS3A01G535200 chr7A 89.362 141 15 0 2183 2323 419932424 419932564 7.920000e-41 178
29 TraesCS3A01G535200 chr2A 90.370 135 13 0 2182 2316 564044875 564045009 7.920000e-41 178
30 TraesCS3A01G535200 chr4D 90.299 134 13 0 2183 2316 226455208 226455341 2.850000e-40 176


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 TraesCS3A01G535200 chr3A 746899698 746902480 2782 False 5140.0 5140 100.0000 1 2783 1 chr3A.!!$F2 2782
1 TraesCS3A01G535200 chr3A 607233871 607234406 535 True 300.0 300 77.0200 1020 1576 1 chr3A.!!$R2 556
2 TraesCS3A01G535200 chr3A 607145745 607146283 538 True 292.0 292 76.6610 1020 1576 1 chr3A.!!$R1 556
3 TraesCS3A01G535200 chr3D 612262827 612265636 2809 False 736.6 1522 91.4764 1 2760 5 chr3D.!!$F2 2759
4 TraesCS3A01G535200 chr3B 826918607 826919837 1230 True 801.5 1399 91.7375 851 1953 2 chr3B.!!$R4 1102
5 TraesCS3A01G535200 chr3B 826746501 826747381 880 True 585.5 869 90.8185 3 2760 2 chr3B.!!$R2 2757
6 TraesCS3A01G535200 chr3B 826910681 826911326 645 True 439.0 597 90.3450 1939 2760 2 chr3B.!!$R3 821
7 TraesCS3A01G535200 chr6D 427170926 427171666 740 False 813.0 813 86.5970 1021 1772 1 chr6D.!!$F2 751
8 TraesCS3A01G535200 chr6B 643131466 643132167 701 False 806.0 806 87.4820 1021 1725 1 chr6B.!!$F2 704
9 TraesCS3A01G535200 chr6B 642989561 642990142 581 False 734.0 734 89.3580 1021 1611 1 chr6B.!!$F1 590
10 TraesCS3A01G535200 chr6A 571881425 571882023 598 False 726.0 726 88.5250 1021 1628 1 chr6A.!!$F1 607

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
969 1010 0.109412 GAGTAGTAGCCGCACACGTT 60.109 55.0 0.0 0.0 37.7 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2355 0.393077 CAGTGGGAGGAGACGTTTGT 59.607 55.0 0.0 0.0 0.0 2.83 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
24 25 2.693069 CTGACAACTCATCACACCCTC 58.307 52.381 0.00 0.00 0.00 4.30
36 37 3.670625 TCACACCCTCGAACTTTATTGG 58.329 45.455 0.00 0.00 0.00 3.16
39 40 3.016736 CACCCTCGAACTTTATTGGCAT 58.983 45.455 0.00 0.00 0.00 4.40
77 78 7.661847 GCTAGTATTTGCTAGTGGATTAATGGT 59.338 37.037 0.00 0.00 40.29 3.55
86 87 3.206412 AGTGGATTAATGGTAATGGGGCA 59.794 43.478 0.00 0.00 29.69 5.36
191 192 1.791204 CAACTCATCGCCATCATCTCG 59.209 52.381 0.00 0.00 0.00 4.04
206 207 2.861147 TCTCGACTCTTCTGACAGGA 57.139 50.000 1.81 0.00 0.00 3.86
223 224 1.284198 AGGAGTTGCCATGAGCTCATT 59.716 47.619 26.70 11.33 44.23 2.57
243 244 8.760569 GCTCATTTGAAAAGTTTAAATTTCGGA 58.239 29.630 0.00 2.61 38.16 4.55
297 299 8.757164 AATAACCGAATTTTTGAGATTTGGAC 57.243 30.769 9.50 0.00 39.46 4.02
345 347 8.849168 TCAAAGTTCACTGACATGACAATAAAT 58.151 29.630 0.00 0.00 0.00 1.40
433 435 6.944557 TGATTTCAGTTACGTACACATCAG 57.055 37.500 0.00 0.00 0.00 2.90
466 468 1.602851 GGCATCACTCATCTCATGTGC 59.397 52.381 0.00 0.00 0.00 4.57
513 519 2.330286 TGTATACGCCAAGTTGTCACG 58.670 47.619 1.45 5.46 0.00 4.35
517 523 2.052237 GCCAAGTTGTCACGCGTG 60.052 61.111 32.76 32.76 0.00 5.34
561 567 9.672086 TTCGATACCAACTGAAAATAACAAAAG 57.328 29.630 0.00 0.00 0.00 2.27
568 574 8.807581 CCAACTGAAAATAACAAAAGTTCAGAC 58.192 33.333 16.32 0.00 45.16 3.51
642 654 4.814234 ACAACTCAGCGTGTCTTAATTCAA 59.186 37.500 0.00 0.00 0.00 2.69
677 689 1.148027 AGAGACCTGAGGTGAGGAACA 59.852 52.381 9.89 0.00 35.25 3.18
678 690 1.971357 GAGACCTGAGGTGAGGAACAA 59.029 52.381 9.89 0.00 35.25 2.83
680 692 2.104963 AGACCTGAGGTGAGGAACAAAC 59.895 50.000 9.89 0.00 35.25 2.93
681 693 2.104963 GACCTGAGGTGAGGAACAAACT 59.895 50.000 9.89 0.00 35.25 2.66
683 695 3.714798 ACCTGAGGTGAGGAACAAACTAA 59.285 43.478 1.77 0.00 36.51 2.24
684 696 4.065789 CCTGAGGTGAGGAACAAACTAAC 58.934 47.826 0.00 0.00 34.69 2.34
685 697 4.065789 CTGAGGTGAGGAACAAACTAACC 58.934 47.826 0.00 0.00 0.00 2.85
686 698 3.456644 TGAGGTGAGGAACAAACTAACCA 59.543 43.478 2.04 0.00 0.00 3.67
687 699 4.104102 TGAGGTGAGGAACAAACTAACCAT 59.896 41.667 2.04 0.00 0.00 3.55
688 700 4.398319 AGGTGAGGAACAAACTAACCATG 58.602 43.478 2.04 0.00 0.00 3.66
689 701 3.057526 GGTGAGGAACAAACTAACCATGC 60.058 47.826 0.00 0.00 0.00 4.06
690 702 3.568007 GTGAGGAACAAACTAACCATGCA 59.432 43.478 0.00 0.00 0.00 3.96
691 703 4.218417 GTGAGGAACAAACTAACCATGCAT 59.782 41.667 0.00 0.00 0.00 3.96
692 704 4.832266 TGAGGAACAAACTAACCATGCATT 59.168 37.500 0.00 0.00 0.00 3.56
693 705 5.138125 AGGAACAAACTAACCATGCATTG 57.862 39.130 0.00 0.00 0.00 2.82
694 706 4.832266 AGGAACAAACTAACCATGCATTGA 59.168 37.500 4.52 0.00 0.00 2.57
695 707 5.047802 AGGAACAAACTAACCATGCATTGAG 60.048 40.000 4.52 0.00 0.00 3.02
696 708 4.178545 ACAAACTAACCATGCATTGAGC 57.821 40.909 4.52 0.00 45.96 4.26
697 709 3.828451 ACAAACTAACCATGCATTGAGCT 59.172 39.130 4.52 0.00 45.94 4.09
698 710 4.082571 ACAAACTAACCATGCATTGAGCTC 60.083 41.667 6.82 6.82 45.94 4.09
699 711 3.354948 ACTAACCATGCATTGAGCTCA 57.645 42.857 13.74 13.74 45.94 4.26
700 712 3.894759 ACTAACCATGCATTGAGCTCAT 58.105 40.909 19.04 4.99 45.94 2.90
701 713 3.630769 ACTAACCATGCATTGAGCTCATG 59.369 43.478 19.04 17.74 45.94 3.07
702 714 2.139323 ACCATGCATTGAGCTCATGT 57.861 45.000 19.04 6.79 45.94 3.21
703 715 2.022195 ACCATGCATTGAGCTCATGTC 58.978 47.619 19.04 9.76 45.94 3.06
704 716 1.337071 CCATGCATTGAGCTCATGTCC 59.663 52.381 19.04 7.20 45.94 4.02
705 717 2.298610 CATGCATTGAGCTCATGTCCT 58.701 47.619 19.04 0.00 45.94 3.85
706 718 3.473625 CATGCATTGAGCTCATGTCCTA 58.526 45.455 19.04 0.75 45.94 2.94
707 719 3.851458 TGCATTGAGCTCATGTCCTAT 57.149 42.857 19.04 3.60 45.94 2.57
708 720 3.736720 TGCATTGAGCTCATGTCCTATC 58.263 45.455 19.04 5.07 45.94 2.08
709 721 2.735663 GCATTGAGCTCATGTCCTATCG 59.264 50.000 19.04 3.54 41.15 2.92
710 722 3.801638 GCATTGAGCTCATGTCCTATCGT 60.802 47.826 19.04 0.00 41.15 3.73
711 723 4.559502 GCATTGAGCTCATGTCCTATCGTA 60.560 45.833 19.04 0.00 41.15 3.43
712 724 4.569761 TTGAGCTCATGTCCTATCGTAC 57.430 45.455 19.04 0.00 0.00 3.67
713 725 3.551846 TGAGCTCATGTCCTATCGTACA 58.448 45.455 13.74 0.00 0.00 2.90
714 726 3.315470 TGAGCTCATGTCCTATCGTACAC 59.685 47.826 13.74 0.00 0.00 2.90
715 727 3.288092 AGCTCATGTCCTATCGTACACA 58.712 45.455 0.00 0.00 0.00 3.72
716 728 3.891977 AGCTCATGTCCTATCGTACACAT 59.108 43.478 0.00 0.00 0.00 3.21
717 729 4.022762 AGCTCATGTCCTATCGTACACATC 60.023 45.833 0.00 0.00 0.00 3.06
725 737 5.465724 GTCCTATCGTACACATCCAAATTCC 59.534 44.000 0.00 0.00 0.00 3.01
733 745 4.658063 ACACATCCAAATTCCGAGGTTAA 58.342 39.130 0.00 0.00 0.00 2.01
734 746 5.074115 ACACATCCAAATTCCGAGGTTAAA 58.926 37.500 0.00 0.00 0.00 1.52
740 755 7.056844 TCCAAATTCCGAGGTTAAAACAAAT 57.943 32.000 0.00 0.00 0.00 2.32
764 779 3.045601 ACCTCCAAGATTCGTGTCAAG 57.954 47.619 0.00 0.00 0.00 3.02
766 781 3.071023 ACCTCCAAGATTCGTGTCAAGAA 59.929 43.478 3.60 3.60 0.00 2.52
768 783 4.515191 CCTCCAAGATTCGTGTCAAGAAAA 59.485 41.667 5.28 0.00 0.00 2.29
769 784 5.008613 CCTCCAAGATTCGTGTCAAGAAAAA 59.991 40.000 5.28 0.00 0.00 1.94
770 785 5.816919 TCCAAGATTCGTGTCAAGAAAAAC 58.183 37.500 5.28 1.53 0.00 2.43
771 786 4.976116 CCAAGATTCGTGTCAAGAAAAACC 59.024 41.667 5.28 0.00 0.00 3.27
772 787 4.830826 AGATTCGTGTCAAGAAAAACCC 57.169 40.909 5.28 0.00 0.00 4.11
773 788 4.204012 AGATTCGTGTCAAGAAAAACCCA 58.796 39.130 5.28 0.00 0.00 4.51
816 831 4.272489 TGGAAATAATGAACCCTGCTCAG 58.728 43.478 0.00 0.00 0.00 3.35
826 841 1.012841 CCCTGCTCAGATCTTTTCGC 58.987 55.000 0.00 0.00 0.00 4.70
873 888 6.789262 AGAAGAGTGATAAAAATTGCATCGG 58.211 36.000 0.00 0.00 0.00 4.18
961 998 0.791422 CGATCCTCGAGTAGTAGCCG 59.209 60.000 12.31 1.35 43.74 5.52
962 999 0.518195 GATCCTCGAGTAGTAGCCGC 59.482 60.000 12.31 0.00 0.00 6.53
967 1008 1.582937 CGAGTAGTAGCCGCACACG 60.583 63.158 0.00 0.00 39.67 4.49
969 1010 0.109412 GAGTAGTAGCCGCACACGTT 60.109 55.000 0.00 0.00 37.70 3.99
978 1019 1.445582 CGCACACGTTCCTACCTCC 60.446 63.158 0.00 0.00 33.53 4.30
979 1020 1.669440 GCACACGTTCCTACCTCCA 59.331 57.895 0.00 0.00 0.00 3.86
981 1022 0.388134 CACACGTTCCTACCTCCACG 60.388 60.000 0.00 0.00 38.62 4.94
1007 1051 1.208052 TCTAGTCTCTGGCATGGCAAC 59.792 52.381 23.47 17.89 0.00 4.17
1659 1706 1.447314 GGGCGGTACCTTCGAGTTG 60.447 63.158 10.90 0.00 39.10 3.16
1924 2094 5.411361 CCTTCAATTGTGATTTGTCTCGGTA 59.589 40.000 5.13 0.00 32.48 4.02
2007 2181 4.300803 TGCATGCAAGAATGTTTTCTGTC 58.699 39.130 20.30 0.00 41.42 3.51
2023 2197 7.870954 TGTTTTCTGTCAATCAGTACTCGTTAT 59.129 33.333 0.00 0.00 43.97 1.89
2125 2301 3.070748 CACACGTGTTATGTTCATCCCA 58.929 45.455 20.79 0.00 0.00 4.37
2192 2368 3.366440 ACACAGTACAAACGTCTCCTC 57.634 47.619 0.00 0.00 0.00 3.71
2208 2384 1.425066 TCCTCCCACTGAAAGCACATT 59.575 47.619 0.00 0.00 37.60 2.71
2209 2385 2.642311 TCCTCCCACTGAAAGCACATTA 59.358 45.455 0.00 0.00 37.60 1.90
2213 2389 1.468520 CCACTGAAAGCACATTACCGG 59.531 52.381 0.00 0.00 37.60 5.28
2226 2402 5.977129 GCACATTACCGGAAATCCTAAAATG 59.023 40.000 9.46 6.14 34.64 2.32
2233 2409 7.475137 ACCGGAAATCCTAAAATGAATTCAA 57.525 32.000 13.09 0.00 0.00 2.69
2248 2424 5.572211 TGAATTCAAGAATAATGCGAGCAC 58.428 37.500 5.45 0.00 0.00 4.40
2250 2426 1.933181 TCAAGAATAATGCGAGCACCG 59.067 47.619 0.00 0.00 42.21 4.94
2261 2437 1.371558 GAGCACCGGGACTTGAACT 59.628 57.895 6.32 0.00 0.00 3.01
2265 2441 0.679505 CACCGGGACTTGAACTCTGA 59.320 55.000 6.32 0.00 0.00 3.27
2267 2443 1.276421 ACCGGGACTTGAACTCTGATG 59.724 52.381 6.32 0.00 0.00 3.07
2268 2444 1.276421 CCGGGACTTGAACTCTGATGT 59.724 52.381 0.00 0.00 0.00 3.06
2272 2448 2.740981 GGACTTGAACTCTGATGTGCTG 59.259 50.000 0.00 0.00 0.00 4.41
2273 2449 3.555795 GGACTTGAACTCTGATGTGCTGA 60.556 47.826 0.00 0.00 0.00 4.26
2275 2451 3.323115 ACTTGAACTCTGATGTGCTGAGA 59.677 43.478 0.00 0.00 43.14 3.27
2279 2455 5.414360 TGAACTCTGATGTGCTGAGAATAC 58.586 41.667 0.00 0.00 43.14 1.89
2283 2459 3.771479 TCTGATGTGCTGAGAATACCACT 59.229 43.478 0.00 0.00 0.00 4.00
2365 2600 7.507616 ACACAAGGGTAGGAATTGTTTTATGAA 59.492 33.333 0.00 0.00 35.04 2.57
2395 2630 3.706594 TGCCCAACAAAATTGAAGGTACA 59.293 39.130 0.00 0.33 0.00 2.90
2499 2735 8.523915 AATAGATAACAAAATGTGATGCCTCA 57.476 30.769 0.00 0.00 0.00 3.86
2526 2762 7.601073 TGCAGTAATGTCAAGTTAATCTCAG 57.399 36.000 0.00 0.00 0.00 3.35
2534 2770 6.533730 TGTCAAGTTAATCTCAGTTGGACAT 58.466 36.000 0.00 0.00 0.00 3.06
2588 2824 0.527565 CCAGTGGTAAATGGCAGTGC 59.472 55.000 6.55 6.55 0.00 4.40
2601 2837 0.235926 GCAGTGCGTTGAGGAAAGAC 59.764 55.000 0.00 0.00 0.00 3.01
2602 2838 1.871080 CAGTGCGTTGAGGAAAGACT 58.129 50.000 0.00 0.00 0.00 3.24
2608 2844 3.246699 TGCGTTGAGGAAAGACTTTAACG 59.753 43.478 21.23 21.23 40.77 3.18
2670 2906 3.117776 ACTGGATTATTCATGAGCTGCCA 60.118 43.478 0.00 1.17 0.00 4.92
2687 2923 3.702548 CTGCCATTTCATTTGGAGGATGA 59.297 43.478 0.00 0.00 36.26 2.92
2688 2924 4.291792 TGCCATTTCATTTGGAGGATGAT 58.708 39.130 0.00 0.00 36.26 2.45
2689 2925 5.456779 TGCCATTTCATTTGGAGGATGATA 58.543 37.500 0.00 0.00 36.26 2.15
2690 2926 6.079336 TGCCATTTCATTTGGAGGATGATAT 58.921 36.000 0.00 0.00 36.26 1.63
2728 2964 5.308825 AGTACCAATGCTAATGCTGGATAC 58.691 41.667 3.81 3.57 37.77 2.24
2761 2997 2.047002 TGGATGACACCTCATGCATG 57.953 50.000 21.07 21.07 46.94 4.06
2762 2998 0.666913 GGATGACACCTCATGCATGC 59.333 55.000 22.25 11.82 43.15 4.06
2763 2999 1.385528 GATGACACCTCATGCATGCA 58.614 50.000 25.04 25.04 37.24 3.96
2764 3000 1.954382 GATGACACCTCATGCATGCAT 59.046 47.619 27.46 27.46 37.24 3.96
2765 3001 2.713863 TGACACCTCATGCATGCATA 57.286 45.000 31.73 18.59 34.91 3.14
2766 3002 3.217681 TGACACCTCATGCATGCATAT 57.782 42.857 31.73 15.34 34.91 1.78
2767 3003 2.882137 TGACACCTCATGCATGCATATG 59.118 45.455 31.73 25.95 34.91 1.78
2768 3004 2.882761 GACACCTCATGCATGCATATGT 59.117 45.455 31.73 28.49 36.65 2.29
2769 3005 2.621526 ACACCTCATGCATGCATATGTG 59.378 45.455 32.93 32.93 36.65 3.21
2770 3006 2.621526 CACCTCATGCATGCATATGTGT 59.378 45.455 31.73 21.91 36.65 3.72
2771 3007 2.621526 ACCTCATGCATGCATATGTGTG 59.378 45.455 31.73 20.29 36.65 3.82
2772 3008 2.621526 CCTCATGCATGCATATGTGTGT 59.378 45.455 31.73 6.60 36.65 3.72
2773 3009 3.067601 CCTCATGCATGCATATGTGTGTT 59.932 43.478 31.73 5.79 36.65 3.32
2774 3010 4.440940 CCTCATGCATGCATATGTGTGTTT 60.441 41.667 31.73 4.96 36.65 2.83
2775 3011 5.221087 CCTCATGCATGCATATGTGTGTTTA 60.221 40.000 31.73 5.15 36.65 2.01
2776 3012 6.205101 TCATGCATGCATATGTGTGTTTAA 57.795 33.333 31.73 2.46 36.65 1.52
2777 3013 6.807789 TCATGCATGCATATGTGTGTTTAAT 58.192 32.000 31.73 3.67 36.65 1.40
2778 3014 7.266400 TCATGCATGCATATGTGTGTTTAATT 58.734 30.769 31.73 2.95 36.65 1.40
2779 3015 7.764901 TCATGCATGCATATGTGTGTTTAATTT 59.235 29.630 31.73 2.53 36.65 1.82
2780 3016 9.032420 CATGCATGCATATGTGTGTTTAATTTA 57.968 29.630 31.73 0.00 36.65 1.40
2781 3017 8.631676 TGCATGCATATGTGTGTTTAATTTAG 57.368 30.769 18.46 0.00 36.65 1.85
2782 3018 7.222417 TGCATGCATATGTGTGTTTAATTTAGC 59.778 33.333 18.46 0.00 36.65 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 7.255381 CCATTAGCTAGCTCAATTGCAATTACT 60.255 37.037 23.26 21.12 34.99 2.24
191 192 2.611722 GGCAACTCCTGTCAGAAGAGTC 60.612 54.545 10.96 2.32 39.92 3.36
206 207 2.799017 TCAAATGAGCTCATGGCAACT 58.201 42.857 29.34 10.26 44.79 3.16
257 258 3.692101 CGGTTATTTAGTGTGGCATTCCA 59.308 43.478 0.00 0.00 40.85 3.53
262 263 5.968528 AAATTCGGTTATTTAGTGTGGCA 57.031 34.783 0.00 0.00 0.00 4.92
396 398 9.530129 GTAACTGAAATCATTGTAAGTTCGAAG 57.470 33.333 0.00 0.00 0.00 3.79
402 404 8.706035 GTGTACGTAACTGAAATCATTGTAAGT 58.294 33.333 0.00 0.00 0.00 2.24
410 412 6.683715 TCTGATGTGTACGTAACTGAAATCA 58.316 36.000 0.00 1.21 0.00 2.57
415 417 3.119602 GCCTCTGATGTGTACGTAACTGA 60.120 47.826 0.00 0.00 0.00 3.41
466 468 7.753132 GTGTTCATTCAGTAGTAGAGAGACAAG 59.247 40.741 0.00 0.00 0.00 3.16
513 519 2.292292 ACATTTGTAACCTGGAACACGC 59.708 45.455 0.00 0.00 0.00 5.34
517 523 5.427036 TCGAAACATTTGTAACCTGGAAC 57.573 39.130 0.00 0.00 0.00 3.62
642 654 1.134965 GTCTCTGGTCACGCTTGCTAT 60.135 52.381 0.00 0.00 0.00 2.97
677 689 4.081406 TGAGCTCAATGCATGGTTAGTTT 58.919 39.130 15.67 0.00 45.94 2.66
678 690 3.689347 TGAGCTCAATGCATGGTTAGTT 58.311 40.909 15.67 0.00 45.94 2.24
680 692 3.630769 ACATGAGCTCAATGCATGGTTAG 59.369 43.478 22.50 0.00 45.94 2.34
681 693 3.623703 ACATGAGCTCAATGCATGGTTA 58.376 40.909 22.50 0.00 45.94 2.85
683 695 2.022195 GACATGAGCTCAATGCATGGT 58.978 47.619 22.50 10.08 45.94 3.55
684 696 1.337071 GGACATGAGCTCAATGCATGG 59.663 52.381 22.50 0.00 45.94 3.66
685 697 2.298610 AGGACATGAGCTCAATGCATG 58.701 47.619 22.50 16.34 45.94 4.06
686 698 2.730934 AGGACATGAGCTCAATGCAT 57.269 45.000 22.50 7.45 45.94 3.96
687 699 3.736720 GATAGGACATGAGCTCAATGCA 58.263 45.455 22.50 8.62 45.94 3.96
688 700 2.735663 CGATAGGACATGAGCTCAATGC 59.264 50.000 22.50 16.97 43.29 3.56
689 701 3.987547 ACGATAGGACATGAGCTCAATG 58.012 45.455 22.50 20.10 43.77 2.82
702 714 5.607477 GGAATTTGGATGTGTACGATAGGA 58.393 41.667 0.00 0.00 43.77 2.94
703 715 4.447724 CGGAATTTGGATGTGTACGATAGG 59.552 45.833 0.00 0.00 43.77 2.57
704 716 5.286438 TCGGAATTTGGATGTGTACGATAG 58.714 41.667 0.00 0.00 46.19 2.08
705 717 5.265350 TCGGAATTTGGATGTGTACGATA 57.735 39.130 0.00 0.00 0.00 2.92
706 718 4.119862 CTCGGAATTTGGATGTGTACGAT 58.880 43.478 0.00 0.00 0.00 3.73
707 719 3.517602 CTCGGAATTTGGATGTGTACGA 58.482 45.455 0.00 0.00 0.00 3.43
708 720 2.607635 CCTCGGAATTTGGATGTGTACG 59.392 50.000 0.00 0.00 0.00 3.67
709 721 3.606687 ACCTCGGAATTTGGATGTGTAC 58.393 45.455 0.00 0.00 0.00 2.90
710 722 3.992943 ACCTCGGAATTTGGATGTGTA 57.007 42.857 0.00 0.00 0.00 2.90
711 723 2.879103 ACCTCGGAATTTGGATGTGT 57.121 45.000 0.00 0.00 0.00 3.72
712 724 5.637006 TTTAACCTCGGAATTTGGATGTG 57.363 39.130 0.00 0.00 0.00 3.21
713 725 5.536916 TGTTTTAACCTCGGAATTTGGATGT 59.463 36.000 0.00 0.00 0.00 3.06
714 726 6.019779 TGTTTTAACCTCGGAATTTGGATG 57.980 37.500 0.00 0.00 0.00 3.51
715 727 6.658188 TTGTTTTAACCTCGGAATTTGGAT 57.342 33.333 0.00 0.00 0.00 3.41
716 728 6.466885 TTTGTTTTAACCTCGGAATTTGGA 57.533 33.333 0.00 0.00 0.00 3.53
717 729 8.996024 ATATTTGTTTTAACCTCGGAATTTGG 57.004 30.769 0.00 0.00 0.00 3.28
725 737 8.271312 TGGAGGTAATATTTGTTTTAACCTCG 57.729 34.615 18.55 0.00 41.37 4.63
733 745 8.458843 CACGAATCTTGGAGGTAATATTTGTTT 58.541 33.333 0.00 0.00 0.00 2.83
734 746 7.610305 ACACGAATCTTGGAGGTAATATTTGTT 59.390 33.333 0.00 0.00 0.00 2.83
740 755 5.925506 TGACACGAATCTTGGAGGTAATA 57.074 39.130 0.00 0.00 0.00 0.98
756 771 5.006261 GGAATTTTGGGTTTTTCTTGACACG 59.994 40.000 0.00 0.00 0.00 4.49
757 772 5.877564 TGGAATTTTGGGTTTTTCTTGACAC 59.122 36.000 0.00 0.00 0.00 3.67
764 779 7.995289 AGTTTTGATGGAATTTTGGGTTTTTC 58.005 30.769 0.00 0.00 0.00 2.29
766 781 7.613411 TGAAGTTTTGATGGAATTTTGGGTTTT 59.387 29.630 0.00 0.00 0.00 2.43
768 783 6.657875 TGAAGTTTTGATGGAATTTTGGGTT 58.342 32.000 0.00 0.00 0.00 4.11
769 784 6.245890 TGAAGTTTTGATGGAATTTTGGGT 57.754 33.333 0.00 0.00 0.00 4.51
770 785 7.308710 CCATTGAAGTTTTGATGGAATTTTGGG 60.309 37.037 7.09 0.00 41.20 4.12
771 786 7.444792 TCCATTGAAGTTTTGATGGAATTTTGG 59.555 33.333 11.28 0.00 43.65 3.28
772 787 8.380743 TCCATTGAAGTTTTGATGGAATTTTG 57.619 30.769 11.28 0.00 43.65 2.44
826 841 2.094539 CATGAGTTGTCACGCGCG 59.905 61.111 30.96 30.96 34.75 6.86
873 888 3.865164 TGTACATGACAACTCATCATCGC 59.135 43.478 0.00 0.00 34.65 4.58
961 998 0.669625 GTGGAGGTAGGAACGTGTGC 60.670 60.000 0.00 0.00 0.00 4.57
962 999 0.388134 CGTGGAGGTAGGAACGTGTG 60.388 60.000 0.00 0.00 0.00 3.82
967 1008 0.108756 GACTGCGTGGAGGTAGGAAC 60.109 60.000 0.00 0.00 0.00 3.62
969 1010 0.680280 GAGACTGCGTGGAGGTAGGA 60.680 60.000 0.00 0.00 0.00 2.94
978 1019 1.400142 CCAGAGACTAGAGACTGCGTG 59.600 57.143 0.00 0.00 0.00 5.34
979 1020 1.745232 CCAGAGACTAGAGACTGCGT 58.255 55.000 0.00 0.00 0.00 5.24
981 1022 1.468985 TGCCAGAGACTAGAGACTGC 58.531 55.000 0.00 0.00 0.00 4.40
1173 1217 3.379445 GGGGAGAAGACGACGGCA 61.379 66.667 2.19 0.00 0.00 5.69
1308 1352 4.947147 GCCAGGTTGCGGTCACCA 62.947 66.667 0.00 0.00 0.00 4.17
1395 1439 2.045045 TTTGCCATGGCCTCCTCG 60.045 61.111 33.44 0.00 41.09 4.63
1536 1580 3.496309 CTGGAGCACCTGGTTGGCA 62.496 63.158 11.24 0.00 40.22 4.92
1613 1657 2.007113 CTGTTGCTGCTGTTGGTGCA 62.007 55.000 0.00 0.00 38.81 4.57
1659 1706 4.912395 TTGGTGCTGGTGCCACCC 62.912 66.667 12.25 0.00 37.50 4.61
1740 1793 1.669999 GCACCATGTCCATTCCTGGC 61.670 60.000 0.00 0.00 42.80 4.85
1791 1844 9.727859 CAGATAGATGGATCATTCATCTTCTTT 57.272 33.333 14.06 0.00 46.33 2.52
1859 2026 4.032355 CACAACGCAACGACAATAAAAGT 58.968 39.130 0.00 0.00 0.00 2.66
1894 2064 4.281688 ACAAATCACAATTGAAGGACCCAG 59.718 41.667 13.59 1.70 34.61 4.45
1924 2094 7.775561 AGGGCTTTTATTTCATTAATCTCGAGT 59.224 33.333 13.13 0.00 0.00 4.18
1956 2126 1.742761 TGTTGCCAGCAGAGATAAGC 58.257 50.000 0.00 0.00 0.00 3.09
2007 2181 7.757097 ACAAGCTTATAACGAGTACTGATTG 57.243 36.000 0.00 0.80 0.00 2.67
2023 2197 6.115446 CAGATCCACCATCTTAACAAGCTTA 58.885 40.000 0.00 0.00 40.20 3.09
2125 2301 6.828785 AGTTTTGTGTAGACTGTCCAGAAATT 59.171 34.615 3.76 0.00 0.00 1.82
2169 2345 3.131577 AGGAGACGTTTGTACTGTGTTGA 59.868 43.478 0.00 0.00 0.00 3.18
2170 2346 3.454375 AGGAGACGTTTGTACTGTGTTG 58.546 45.455 0.00 0.00 0.00 3.33
2171 2347 3.492137 GGAGGAGACGTTTGTACTGTGTT 60.492 47.826 0.00 0.00 0.00 3.32
2172 2348 2.035576 GGAGGAGACGTTTGTACTGTGT 59.964 50.000 0.00 0.00 0.00 3.72
2173 2349 2.609737 GGGAGGAGACGTTTGTACTGTG 60.610 54.545 0.00 0.00 0.00 3.66
2174 2350 1.617357 GGGAGGAGACGTTTGTACTGT 59.383 52.381 0.00 0.00 0.00 3.55
2175 2351 1.616865 TGGGAGGAGACGTTTGTACTG 59.383 52.381 0.00 0.00 0.00 2.74
2176 2352 1.617357 GTGGGAGGAGACGTTTGTACT 59.383 52.381 0.00 0.00 0.00 2.73
2177 2353 1.617357 AGTGGGAGGAGACGTTTGTAC 59.383 52.381 0.00 0.00 0.00 2.90
2178 2354 1.616865 CAGTGGGAGGAGACGTTTGTA 59.383 52.381 0.00 0.00 0.00 2.41
2179 2355 0.393077 CAGTGGGAGGAGACGTTTGT 59.607 55.000 0.00 0.00 0.00 2.83
2180 2356 0.679505 TCAGTGGGAGGAGACGTTTG 59.320 55.000 0.00 0.00 0.00 2.93
2192 2368 1.468520 CGGTAATGTGCTTTCAGTGGG 59.531 52.381 0.00 0.00 0.00 4.61
2208 2384 8.582657 TTGAATTCATTTTAGGATTTCCGGTA 57.417 30.769 9.40 0.00 42.08 4.02
2209 2385 7.396055 TCTTGAATTCATTTTAGGATTTCCGGT 59.604 33.333 9.40 0.00 42.08 5.28
2226 2402 4.972440 GGTGCTCGCATTATTCTTGAATTC 59.028 41.667 0.00 0.00 0.00 2.17
2233 2409 0.532862 CCCGGTGCTCGCATTATTCT 60.533 55.000 0.00 0.00 37.59 2.40
2248 2424 1.276421 ACATCAGAGTTCAAGTCCCGG 59.724 52.381 0.00 0.00 0.00 5.73
2250 2426 2.079925 GCACATCAGAGTTCAAGTCCC 58.920 52.381 0.00 0.00 0.00 4.46
2261 2437 3.771479 AGTGGTATTCTCAGCACATCAGA 59.229 43.478 8.01 0.00 46.81 3.27
2265 2441 3.369892 GGACAGTGGTATTCTCAGCACAT 60.370 47.826 8.01 0.00 46.81 3.21
2267 2443 2.622436 GGACAGTGGTATTCTCAGCAC 58.378 52.381 0.00 0.00 45.19 4.40
2268 2444 1.555075 GGGACAGTGGTATTCTCAGCA 59.445 52.381 0.00 0.00 0.00 4.41
2272 2448 4.099727 GGTTAGAGGGACAGTGGTATTCTC 59.900 50.000 0.00 0.00 0.00 2.87
2273 2449 4.031611 GGTTAGAGGGACAGTGGTATTCT 58.968 47.826 0.00 0.00 0.00 2.40
2275 2451 3.798515 TGGTTAGAGGGACAGTGGTATT 58.201 45.455 0.00 0.00 0.00 1.89
2279 2455 1.486726 GGATGGTTAGAGGGACAGTGG 59.513 57.143 0.00 0.00 0.00 4.00
2283 2459 1.913419 GGTTGGATGGTTAGAGGGACA 59.087 52.381 0.00 0.00 0.00 4.02
2316 2492 5.062809 GTCTATCAACTAGTTTGCTCAGTGC 59.937 44.000 5.07 0.00 43.25 4.40
2365 2600 7.823799 CCTTCAATTTTGTTGGGCATACTTATT 59.176 33.333 0.00 0.00 0.00 1.40
2395 2630 5.841267 AACCTTTTTATTTCATTGGGGCT 57.159 34.783 0.00 0.00 0.00 5.19
2499 2735 9.013229 TGAGATTAACTTGACATTACTGCAAAT 57.987 29.630 0.00 0.00 0.00 2.32
2526 2762 6.313658 GGCCTTGATGAAAAATTATGTCCAAC 59.686 38.462 0.00 0.00 0.00 3.77
2534 2770 4.594970 TCGAGGGCCTTGATGAAAAATTA 58.405 39.130 19.96 0.00 0.00 1.40
2540 2776 1.203237 TGATCGAGGGCCTTGATGAA 58.797 50.000 35.78 22.46 35.00 2.57
2588 2824 4.758561 CACGTTAAAGTCTTTCCTCAACG 58.241 43.478 21.23 21.23 42.04 4.10
2601 2837 2.480419 ACTAGCTTGCAGCACGTTAAAG 59.520 45.455 0.00 0.00 45.56 1.85
2602 2838 2.489971 ACTAGCTTGCAGCACGTTAAA 58.510 42.857 0.00 0.00 45.56 1.52
2608 2844 2.158449 CACTGTTACTAGCTTGCAGCAC 59.842 50.000 0.00 0.00 45.56 4.40
2621 2857 6.978343 TTGTATCCTAATGTGCACTGTTAC 57.022 37.500 19.41 10.21 0.00 2.50
2625 2861 8.124823 CAGTAATTTGTATCCTAATGTGCACTG 58.875 37.037 19.41 5.64 0.00 3.66
2689 2925 9.273016 GCATTGGTACTTCATAAGTGTGTATAT 57.727 33.333 2.59 0.00 42.84 0.86
2690 2926 8.482943 AGCATTGGTACTTCATAAGTGTGTATA 58.517 33.333 2.59 0.00 42.84 1.47
2709 2945 3.187227 GTCGTATCCAGCATTAGCATTGG 59.813 47.826 0.00 0.00 45.49 3.16
2728 2964 2.029244 GTCATCCAGCATTGTTACGTCG 59.971 50.000 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.