Multiple sequence alignment - TraesCS2A01G271900

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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 TraesCS2A01G271900 chr2A 100.000 5702 0 0 1 5702 445035830 445030129 0.000000e+00 10530.0
1 TraesCS2A01G271900 chr2A 97.553 1185 27 2 2658 3841 8566647 8565464 0.000000e+00 2026.0
2 TraesCS2A01G271900 chr2B 95.406 2068 67 11 616 2666 402558729 402556673 0.000000e+00 3267.0
3 TraesCS2A01G271900 chr2B 97.172 990 20 1 3841 4830 402556685 402555704 0.000000e+00 1666.0
4 TraesCS2A01G271900 chr2B 95.262 591 15 5 4 583 402559308 402558720 0.000000e+00 924.0
5 TraesCS2A01G271900 chr2B 95.980 199 8 0 4886 5084 402555703 402555505 1.980000e-84 324.0
6 TraesCS2A01G271900 chr2D 97.189 1245 31 3 3841 5084 334264698 334263457 0.000000e+00 2102.0
7 TraesCS2A01G271900 chr2D 97.427 1205 27 3 1466 2666 334265890 334264686 0.000000e+00 2050.0
8 TraesCS2A01G271900 chr2D 93.403 576 23 7 22 583 334266834 334266260 0.000000e+00 839.0
9 TraesCS2A01G271900 chr2D 89.931 576 48 7 5132 5702 603212887 603213457 0.000000e+00 734.0
10 TraesCS2A01G271900 chr2D 89.796 392 18 8 616 995 334266269 334265888 3.090000e-132 483.0
11 TraesCS2A01G271900 chr7A 97.311 1190 32 0 2658 3847 649097300 649096111 0.000000e+00 2021.0
12 TraesCS2A01G271900 chr7A 95.943 1183 47 1 2658 3839 118153494 118154676 0.000000e+00 1917.0
13 TraesCS2A01G271900 chr7A 89.913 575 49 7 5133 5702 73800613 73801183 0.000000e+00 732.0
14 TraesCS2A01G271900 chr6A 97.382 1184 29 2 2658 3840 520810162 520808980 0.000000e+00 2013.0
15 TraesCS2A01G271900 chr6A 97.136 1187 32 2 2658 3843 520776523 520775338 0.000000e+00 2002.0
16 TraesCS2A01G271900 chr6A 97.126 1183 32 2 2658 3839 520822727 520821546 0.000000e+00 1995.0
17 TraesCS2A01G271900 chr6A 96.883 1187 35 2 2658 3843 520797593 520796408 0.000000e+00 1986.0
18 TraesCS2A01G271900 chr6A 95.561 1194 49 4 2658 3848 575099780 575100972 0.000000e+00 1908.0
19 TraesCS2A01G271900 chr6A 83.620 757 116 7 3842 4594 610275567 610276319 0.000000e+00 704.0
20 TraesCS2A01G271900 chr6A 86.817 622 72 10 5084 5702 33215433 33214819 0.000000e+00 686.0
21 TraesCS2A01G271900 chr6A 75.551 1362 275 37 1325 2665 610268509 610269833 8.120000e-173 617.0
22 TraesCS2A01G271900 chr5A 96.957 1183 34 2 2658 3840 674203349 674202169 0.000000e+00 1984.0
23 TraesCS2A01G271900 chr1D 91.896 617 50 0 5084 5700 111537779 111537163 0.000000e+00 863.0
24 TraesCS2A01G271900 chr1D 82.688 878 138 12 3841 4711 7028881 7029751 0.000000e+00 767.0
25 TraesCS2A01G271900 chr1D 82.069 870 146 10 3842 4706 7050958 7051822 0.000000e+00 734.0
26 TraesCS2A01G271900 chr1D 81.663 878 145 14 3841 4711 7082735 7083603 0.000000e+00 715.0
27 TraesCS2A01G271900 chr1D 76.282 624 127 17 1319 1934 7049737 7050347 4.290000e-81 313.0
28 TraesCS2A01G271900 chr5D 90.756 595 48 4 5111 5702 12175145 12175735 0.000000e+00 787.0
29 TraesCS2A01G271900 chr5D 81.257 875 142 18 3841 4704 510657686 510658549 0.000000e+00 688.0
30 TraesCS2A01G271900 chr5B 82.529 870 137 12 3841 4704 641715316 641716176 0.000000e+00 750.0
31 TraesCS2A01G271900 chr5B 96.000 50 1 1 579 627 591891224 591891273 4.740000e-11 80.5
32 TraesCS2A01G271900 chr7B 89.145 608 57 8 5094 5697 645528112 645527510 0.000000e+00 749.0
33 TraesCS2A01G271900 chr7B 86.188 181 18 5 5145 5319 588832294 588832115 7.540000e-44 189.0
34 TraesCS2A01G271900 chr1A 87.816 632 63 10 5083 5702 21209476 21208847 0.000000e+00 728.0
35 TraesCS2A01G271900 chr1A 74.970 1650 342 43 1043 2662 9129461 9127853 0.000000e+00 693.0
36 TraesCS2A01G271900 chr1A 72.890 1505 319 56 1204 2666 9149630 9148173 2.440000e-118 436.0
37 TraesCS2A01G271900 chr3A 87.898 628 61 11 5084 5701 102209911 102210533 0.000000e+00 725.0
38 TraesCS2A01G271900 chr1B 90.161 559 47 6 5134 5688 482169620 482170174 0.000000e+00 721.0
39 TraesCS2A01G271900 chr6B 81.214 873 136 20 3841 4708 707009177 707010026 0.000000e+00 678.0
40 TraesCS2A01G271900 chr6B 75.900 1361 272 39 1325 2666 707007866 707009189 0.000000e+00 645.0
41 TraesCS2A01G271900 chr6B 75.314 1353 270 36 1329 2666 706972968 706974271 1.770000e-164 590.0
42 TraesCS2A01G271900 chr6B 78.929 280 54 5 2384 2662 707195449 707195174 9.760000e-43 185.0
43 TraesCS2A01G271900 chr6D 75.461 1357 275 41 1328 2666 463756567 463755251 4.890000e-170 608.0
44 TraesCS2A01G271900 chr6D 72.818 1398 276 58 1328 2666 469603570 469604922 1.160000e-101 381.0
45 TraesCS2A01G271900 chr3B 94.118 51 2 1 579 628 712430526 712430576 6.130000e-10 76.8
46 TraesCS2A01G271900 chr3B 89.831 59 4 2 574 632 10116842 10116786 2.200000e-09 75.0
47 TraesCS2A01G271900 chrUn 92.308 52 3 1 579 630 281902718 281902668 7.920000e-09 73.1
48 TraesCS2A01G271900 chrUn 92.308 52 3 1 579 630 281923231 281923181 7.920000e-09 73.1
49 TraesCS2A01G271900 chrUn 92.308 52 3 1 579 630 297707829 297707779 7.920000e-09 73.1
50 TraesCS2A01G271900 chr7D 93.878 49 2 1 582 630 300888128 300888175 7.920000e-09 73.1
51 TraesCS2A01G271900 chr3D 92.308 52 3 1 582 633 137646846 137646796 7.920000e-09 73.1
52 TraesCS2A01G271900 chr3D 93.878 49 2 1 582 630 415447461 415447508 7.920000e-09 73.1


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 TraesCS2A01G271900 chr2A 445030129 445035830 5701 True 10530.00 10530 100.00000 1 5702 1 chr2A.!!$R2 5701
1 TraesCS2A01G271900 chr2A 8565464 8566647 1183 True 2026.00 2026 97.55300 2658 3841 1 chr2A.!!$R1 1183
2 TraesCS2A01G271900 chr2B 402555505 402559308 3803 True 1545.25 3267 95.95500 4 5084 4 chr2B.!!$R1 5080
3 TraesCS2A01G271900 chr2D 334263457 334266834 3377 True 1368.50 2102 94.45375 22 5084 4 chr2D.!!$R1 5062
4 TraesCS2A01G271900 chr2D 603212887 603213457 570 False 734.00 734 89.93100 5132 5702 1 chr2D.!!$F1 570
5 TraesCS2A01G271900 chr7A 649096111 649097300 1189 True 2021.00 2021 97.31100 2658 3847 1 chr7A.!!$R1 1189
6 TraesCS2A01G271900 chr7A 118153494 118154676 1182 False 1917.00 1917 95.94300 2658 3839 1 chr7A.!!$F2 1181
7 TraesCS2A01G271900 chr7A 73800613 73801183 570 False 732.00 732 89.91300 5133 5702 1 chr7A.!!$F1 569
8 TraesCS2A01G271900 chr6A 520808980 520810162 1182 True 2013.00 2013 97.38200 2658 3840 1 chr6A.!!$R4 1182
9 TraesCS2A01G271900 chr6A 520775338 520776523 1185 True 2002.00 2002 97.13600 2658 3843 1 chr6A.!!$R2 1185
10 TraesCS2A01G271900 chr6A 520821546 520822727 1181 True 1995.00 1995 97.12600 2658 3839 1 chr6A.!!$R5 1181
11 TraesCS2A01G271900 chr6A 520796408 520797593 1185 True 1986.00 1986 96.88300 2658 3843 1 chr6A.!!$R3 1185
12 TraesCS2A01G271900 chr6A 575099780 575100972 1192 False 1908.00 1908 95.56100 2658 3848 1 chr6A.!!$F1 1190
13 TraesCS2A01G271900 chr6A 610275567 610276319 752 False 704.00 704 83.62000 3842 4594 1 chr6A.!!$F3 752
14 TraesCS2A01G271900 chr6A 33214819 33215433 614 True 686.00 686 86.81700 5084 5702 1 chr6A.!!$R1 618
15 TraesCS2A01G271900 chr6A 610268509 610269833 1324 False 617.00 617 75.55100 1325 2665 1 chr6A.!!$F2 1340
16 TraesCS2A01G271900 chr5A 674202169 674203349 1180 True 1984.00 1984 96.95700 2658 3840 1 chr5A.!!$R1 1182
17 TraesCS2A01G271900 chr1D 111537163 111537779 616 True 863.00 863 91.89600 5084 5700 1 chr1D.!!$R1 616
18 TraesCS2A01G271900 chr1D 7028881 7029751 870 False 767.00 767 82.68800 3841 4711 1 chr1D.!!$F1 870
19 TraesCS2A01G271900 chr1D 7082735 7083603 868 False 715.00 715 81.66300 3841 4711 1 chr1D.!!$F2 870
20 TraesCS2A01G271900 chr1D 7049737 7051822 2085 False 523.50 734 79.17550 1319 4706 2 chr1D.!!$F3 3387
21 TraesCS2A01G271900 chr5D 12175145 12175735 590 False 787.00 787 90.75600 5111 5702 1 chr5D.!!$F1 591
22 TraesCS2A01G271900 chr5D 510657686 510658549 863 False 688.00 688 81.25700 3841 4704 1 chr5D.!!$F2 863
23 TraesCS2A01G271900 chr5B 641715316 641716176 860 False 750.00 750 82.52900 3841 4704 1 chr5B.!!$F2 863
24 TraesCS2A01G271900 chr7B 645527510 645528112 602 True 749.00 749 89.14500 5094 5697 1 chr7B.!!$R2 603
25 TraesCS2A01G271900 chr1A 21208847 21209476 629 True 728.00 728 87.81600 5083 5702 1 chr1A.!!$R3 619
26 TraesCS2A01G271900 chr1A 9127853 9129461 1608 True 693.00 693 74.97000 1043 2662 1 chr1A.!!$R1 1619
27 TraesCS2A01G271900 chr1A 9148173 9149630 1457 True 436.00 436 72.89000 1204 2666 1 chr1A.!!$R2 1462
28 TraesCS2A01G271900 chr3A 102209911 102210533 622 False 725.00 725 87.89800 5084 5701 1 chr3A.!!$F1 617
29 TraesCS2A01G271900 chr1B 482169620 482170174 554 False 721.00 721 90.16100 5134 5688 1 chr1B.!!$F1 554
30 TraesCS2A01G271900 chr6B 707007866 707010026 2160 False 661.50 678 78.55700 1325 4708 2 chr6B.!!$F2 3383
31 TraesCS2A01G271900 chr6B 706972968 706974271 1303 False 590.00 590 75.31400 1329 2666 1 chr6B.!!$F1 1337
32 TraesCS2A01G271900 chr6D 463755251 463756567 1316 True 608.00 608 75.46100 1328 2666 1 chr6D.!!$R1 1338
33 TraesCS2A01G271900 chr6D 469603570 469604922 1352 False 381.00 381 72.81800 1328 2666 1 chr6D.!!$F1 1338

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
597 613 0.033796 TCGTACTCCCTTCGTCCCAT 60.034 55.0 0.00 0.00 0.00 4.00 F
1314 1342 0.107508 CCAAGATCACCATGCCGACT 60.108 55.0 0.00 0.00 0.00 4.18 F
2023 2083 0.601046 TGTGCTTGTCCGCTTCAGAG 60.601 55.0 0.00 0.00 0.00 3.35 F
2280 2358 0.604073 TGATTCCGCTGGAACGTGTA 59.396 50.0 11.39 0.00 45.07 2.90 F
3402 3516 0.920664 GTTGGTGTTTGCGCTTTGAC 59.079 50.0 9.73 2.39 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 2358 0.772124 AAGACCCTGGTCACCCACAT 60.772 55.0 18.12 0.0 46.76 3.21 R
3215 3329 2.223805 TGATTGTCTCATCCCGATCACG 60.224 50.0 0.00 0.0 39.43 4.35 R
3497 3612 0.039798 GTGAGTAGCGACCACGAACA 60.040 55.0 0.00 0.0 42.66 3.18 R
4209 4325 0.961753 CTTTGCTTTGGTCCCTGTCC 59.038 55.0 0.00 0.0 0.00 4.02 R
5265 5424 0.178992 GCATGTTATAGGCAGGGGCA 60.179 55.0 0.00 0.0 43.71 5.36 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
64 65 2.480802 ACGATCACGATATGGAGACTCG 59.519 50.000 0.00 11.71 42.66 4.18
98 99 5.508320 GCTCTAACCATAGTAGCAAGAGGAC 60.508 48.000 0.00 0.00 34.83 3.85
515 530 6.349300 AGTTTGCCTAAGTAATCATCGTGAT 58.651 36.000 0.00 0.00 39.09 3.06
562 578 3.710209 AGTAGCAAGAGGACTGCATTT 57.290 42.857 0.00 0.00 0.00 2.32
569 585 4.573900 CAAGAGGACTGCATTTACTCTGT 58.426 43.478 10.33 0.59 38.44 3.41
577 593 6.256757 GGACTGCATTTACTCTGTGAATACTC 59.743 42.308 0.00 0.00 0.00 2.59
578 594 6.940739 ACTGCATTTACTCTGTGAATACTCT 58.059 36.000 0.00 0.00 0.00 3.24
579 595 7.038659 ACTGCATTTACTCTGTGAATACTCTC 58.961 38.462 0.00 0.00 0.00 3.20
580 596 6.036470 TGCATTTACTCTGTGAATACTCTCG 58.964 40.000 0.00 0.00 0.00 4.04
581 597 6.037098 GCATTTACTCTGTGAATACTCTCGT 58.963 40.000 0.00 0.00 0.00 4.18
582 598 7.148137 TGCATTTACTCTGTGAATACTCTCGTA 60.148 37.037 0.00 0.00 0.00 3.43
583 599 7.166142 GCATTTACTCTGTGAATACTCTCGTAC 59.834 40.741 0.00 0.00 0.00 3.67
584 600 7.918536 TTTACTCTGTGAATACTCTCGTACT 57.081 36.000 0.00 0.00 0.00 2.73
585 601 7.536895 TTACTCTGTGAATACTCTCGTACTC 57.463 40.000 0.00 0.00 0.00 2.59
586 602 4.877251 ACTCTGTGAATACTCTCGTACTCC 59.123 45.833 0.00 0.00 0.00 3.85
587 603 4.197750 TCTGTGAATACTCTCGTACTCCC 58.802 47.826 0.00 0.00 0.00 4.30
588 604 4.080469 TCTGTGAATACTCTCGTACTCCCT 60.080 45.833 0.00 0.00 0.00 4.20
589 605 4.597004 TGTGAATACTCTCGTACTCCCTT 58.403 43.478 0.00 0.00 0.00 3.95
590 606 4.639310 TGTGAATACTCTCGTACTCCCTTC 59.361 45.833 0.00 0.00 0.00 3.46
591 607 3.875727 TGAATACTCTCGTACTCCCTTCG 59.124 47.826 0.00 0.00 0.00 3.79
592 608 3.557228 ATACTCTCGTACTCCCTTCGT 57.443 47.619 0.00 0.00 0.00 3.85
593 609 1.736612 ACTCTCGTACTCCCTTCGTC 58.263 55.000 0.00 0.00 0.00 4.20
594 610 1.015868 CTCTCGTACTCCCTTCGTCC 58.984 60.000 0.00 0.00 0.00 4.79
595 611 0.393537 TCTCGTACTCCCTTCGTCCC 60.394 60.000 0.00 0.00 0.00 4.46
596 612 0.679002 CTCGTACTCCCTTCGTCCCA 60.679 60.000 0.00 0.00 0.00 4.37
597 613 0.033796 TCGTACTCCCTTCGTCCCAT 60.034 55.000 0.00 0.00 0.00 4.00
598 614 1.212688 TCGTACTCCCTTCGTCCCATA 59.787 52.381 0.00 0.00 0.00 2.74
599 615 2.026641 CGTACTCCCTTCGTCCCATAA 58.973 52.381 0.00 0.00 0.00 1.90
600 616 2.626743 CGTACTCCCTTCGTCCCATAAT 59.373 50.000 0.00 0.00 0.00 1.28
601 617 3.822735 CGTACTCCCTTCGTCCCATAATA 59.177 47.826 0.00 0.00 0.00 0.98
602 618 4.461781 CGTACTCCCTTCGTCCCATAATAT 59.538 45.833 0.00 0.00 0.00 1.28
603 619 5.649395 CGTACTCCCTTCGTCCCATAATATA 59.351 44.000 0.00 0.00 0.00 0.86
604 620 6.151648 CGTACTCCCTTCGTCCCATAATATAA 59.848 42.308 0.00 0.00 0.00 0.98
605 621 6.607004 ACTCCCTTCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
606 622 6.320518 ACTCCCTTCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
607 623 6.785963 ACTCCCTTCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
608 624 7.001099 TCCCTTCGTCCCATAATATAAGAAC 57.999 40.000 0.00 0.00 0.00 3.01
609 625 5.867716 CCCTTCGTCCCATAATATAAGAACG 59.132 44.000 0.00 0.00 0.00 3.95
610 626 6.453092 CCTTCGTCCCATAATATAAGAACGT 58.547 40.000 0.00 0.00 0.00 3.99
611 627 6.927381 CCTTCGTCCCATAATATAAGAACGTT 59.073 38.462 0.00 0.00 0.00 3.99
612 628 7.440255 CCTTCGTCCCATAATATAAGAACGTTT 59.560 37.037 0.46 0.00 0.00 3.60
613 629 8.721019 TTCGTCCCATAATATAAGAACGTTTT 57.279 30.769 0.46 0.00 0.00 2.43
614 630 8.356533 TCGTCCCATAATATAAGAACGTTTTC 57.643 34.615 0.46 0.00 0.00 2.29
615 631 8.199449 TCGTCCCATAATATAAGAACGTTTTCT 58.801 33.333 0.46 0.00 44.53 2.52
616 632 9.467258 CGTCCCATAATATAAGAACGTTTTCTA 57.533 33.333 0.46 0.00 41.56 2.10
642 658 8.803235 ACACTACTAGTAATTTCTGTGACATCA 58.197 33.333 19.10 0.00 0.00 3.07
698 714 0.603065 GACAAGCATCCAACCAACCC 59.397 55.000 0.00 0.00 0.00 4.11
741 757 2.680339 GAGCAGCCAATAAGTCACCTTC 59.320 50.000 0.00 0.00 31.89 3.46
748 764 1.120530 ATAAGTCACCTTCCGGCGAT 58.879 50.000 9.30 0.00 31.89 4.58
759 775 2.474266 CGGCGATGGTCAAACACG 59.526 61.111 0.00 0.00 0.00 4.49
797 819 3.068560 GCGTGGTATGGTTGTGAACTTA 58.931 45.455 0.00 0.00 0.00 2.24
807 829 3.686726 GGTTGTGAACTTAGGATGCTGAG 59.313 47.826 4.36 4.36 0.00 3.35
837 859 2.866762 GACGAAGACTTGTTGACTGCTT 59.133 45.455 0.00 0.00 0.00 3.91
844 872 2.614057 ACTTGTTGACTGCTTCTTTCCG 59.386 45.455 0.00 0.00 0.00 4.30
879 907 4.633126 TCTGCTTCACTGATTCTGCATAAC 59.367 41.667 0.00 0.00 0.00 1.89
882 910 3.998913 TCACTGATTCTGCATAACCCA 57.001 42.857 0.00 0.00 0.00 4.51
892 920 2.437281 CTGCATAACCCAGGTGAGATCT 59.563 50.000 0.00 0.00 0.00 2.75
902 930 3.055819 CCAGGTGAGATCTTTTTCTCCGA 60.056 47.826 0.00 0.00 41.24 4.55
972 1000 6.492772 TCCTTTTCTCTCCTAAAGTCGTAAGT 59.507 38.462 0.00 0.00 39.48 2.24
1095 1123 2.575893 TTTCGACTACCCCGCAGCA 61.576 57.895 0.00 0.00 0.00 4.41
1104 1132 3.121030 CCCGCAGCAAACCTCTCG 61.121 66.667 0.00 0.00 0.00 4.04
1119 1147 0.817654 TCTCGACGCTGTGGATCAAT 59.182 50.000 0.00 0.00 0.00 2.57
1314 1342 0.107508 CCAAGATCACCATGCCGACT 60.108 55.000 0.00 0.00 0.00 4.18
1368 1396 3.760035 GCTCGCCCCGTCAGAGAA 61.760 66.667 0.00 0.00 34.13 2.87
1539 1569 2.481795 GCAACAGTGTGGCAGTCATTTT 60.482 45.455 18.12 0.00 31.84 1.82
1653 1686 7.498900 AGAATCAGTTGTACATGACAGTTCAAA 59.501 33.333 0.00 0.00 39.88 2.69
1686 1719 3.777106 ATGCTTATGTCGGATCCACAT 57.223 42.857 24.12 24.12 38.13 3.21
1736 1775 5.929415 GGTGAACAAAAACAAGACAGGAAAA 59.071 36.000 0.00 0.00 0.00 2.29
2023 2083 0.601046 TGTGCTTGTCCGCTTCAGAG 60.601 55.000 0.00 0.00 0.00 3.35
2176 2239 2.603135 GATGCCAGCCACATCGTTGC 62.603 60.000 0.00 0.00 35.03 4.17
2269 2347 1.537202 GTATGGCCAGAATGATTCCGC 59.463 52.381 13.05 4.03 39.69 5.54
2280 2358 0.604073 TGATTCCGCTGGAACGTGTA 59.396 50.000 11.39 0.00 45.07 2.90
2434 2545 1.550976 AGGTGCTACACTTGGAGCTAC 59.449 52.381 14.57 10.37 39.54 3.58
2507 2621 8.606830 AGGAAAAAGTACCAAGAGTTAGATGAT 58.393 33.333 0.00 0.00 0.00 2.45
2585 2699 3.326006 TGAGAGAATGCACTGGAGACTTT 59.674 43.478 0.00 0.00 0.00 2.66
2654 2768 6.820656 GGAAAATAGATGAAGAGAGAGTTGCA 59.179 38.462 0.00 0.00 0.00 4.08
2655 2769 7.011295 GGAAAATAGATGAAGAGAGAGTTGCAG 59.989 40.741 0.00 0.00 0.00 4.41
2656 2770 6.543430 AATAGATGAAGAGAGAGTTGCAGT 57.457 37.500 0.00 0.00 0.00 4.40
2720 2834 6.830873 CTTTCTGGAAAGGACTGATGAAAT 57.169 37.500 13.48 0.00 42.96 2.17
3304 3418 5.890334 ACGGTCCACATTGCTTTTAATATG 58.110 37.500 0.00 0.00 0.00 1.78
3359 3473 4.464008 GACATGGCTTAATGGGATTGAGA 58.536 43.478 0.00 0.00 31.46 3.27
3402 3516 0.920664 GTTGGTGTTTGCGCTTTGAC 59.079 50.000 9.73 2.39 0.00 3.18
3519 3634 2.632544 CGTGGTCGCTACTCACCCA 61.633 63.158 5.00 0.00 0.00 4.51
3563 3678 1.860641 TACTGGATCTTTCCGCTGGA 58.139 50.000 0.00 0.00 45.89 3.86
3655 3770 1.272807 ACCTAGTTTTAGCCAGCCGA 58.727 50.000 0.00 0.00 0.00 5.54
3897 4013 4.213564 AGAATTCTTGGCTGAAGTCGAT 57.786 40.909 0.88 0.00 43.25 3.59
4151 4267 7.655328 TCATTTGGACATCAAACCACAAAATAC 59.345 33.333 0.00 0.00 46.72 1.89
4159 4275 9.520515 ACATCAAACCACAAAATACTCTCTTAT 57.479 29.630 0.00 0.00 0.00 1.73
4180 4296 8.902806 TCTTATATGAGAATTTCAACGCCAAAT 58.097 29.630 0.00 0.00 39.77 2.32
4209 4325 8.502387 GCTGATTTTGGACTATCTAAGCTAATG 58.498 37.037 0.00 0.00 0.00 1.90
4402 4520 5.311265 AGAGTGTTCAGCTCATCAAATTGA 58.689 37.500 0.00 0.00 35.55 2.57
4727 4856 5.111293 TGGGCGCTACTGTAACTTATAAAC 58.889 41.667 7.64 0.00 0.00 2.01
4728 4857 5.105228 TGGGCGCTACTGTAACTTATAAACT 60.105 40.000 7.64 0.00 0.00 2.66
4729 4858 5.814188 GGGCGCTACTGTAACTTATAAACTT 59.186 40.000 7.64 0.00 0.00 2.66
4730 4859 6.980397 GGGCGCTACTGTAACTTATAAACTTA 59.020 38.462 7.64 0.00 0.00 2.24
4731 4860 7.654923 GGGCGCTACTGTAACTTATAAACTTAT 59.345 37.037 7.64 0.00 0.00 1.73
4732 4861 9.683069 GGCGCTACTGTAACTTATAAACTTATA 57.317 33.333 7.64 0.00 0.00 0.98
4881 5011 6.268566 ACTCATGACTTCAAAGCAAGAAAAC 58.731 36.000 0.00 0.00 0.00 2.43
4892 5022 2.226437 AGCAAGAAAACATGTAGCACCG 59.774 45.455 0.00 0.00 0.00 4.94
4896 5026 3.997762 AGAAAACATGTAGCACCGTGTA 58.002 40.909 0.00 0.00 33.52 2.90
4972 5102 8.900983 AGGAAGAAATATTCTAAGAGCACATC 57.099 34.615 0.00 0.00 39.61 3.06
5120 5250 1.336755 GTGTCAAACATCTTTGGGCGT 59.663 47.619 0.00 0.00 37.87 5.68
5125 5255 3.823873 TCAAACATCTTTGGGCGTATTGT 59.176 39.130 0.00 0.00 37.87 2.71
5127 5257 4.957759 AACATCTTTGGGCGTATTGTAC 57.042 40.909 0.00 0.00 0.00 2.90
5128 5258 3.945346 ACATCTTTGGGCGTATTGTACA 58.055 40.909 0.00 0.00 0.00 2.90
5140 5279 7.094248 TGGGCGTATTGTACATACGTATCTTAT 60.094 37.037 25.02 7.00 46.30 1.73
5149 5288 9.557061 TGTACATACGTATCTTATCAAGAGTCT 57.443 33.333 4.74 0.00 41.61 3.24
5175 5331 4.344390 CGGTTAGGCTAGGAGGTTTATCTT 59.656 45.833 0.00 0.00 0.00 2.40
5228 5386 6.857437 TGATCTCCAAGTTGTAATCTCTCA 57.143 37.500 1.45 0.00 0.00 3.27
5265 5424 0.833287 ATGCGCTATCAGGGACTTGT 59.167 50.000 9.73 0.00 34.60 3.16
5421 5580 1.409802 CCAGTTCCTCCTCGCCTAGTA 60.410 57.143 0.00 0.00 0.00 1.82
5451 5610 5.955355 AGTCAGGTTACAGAGAAGCTATCTT 59.045 40.000 0.00 0.00 38.96 2.40
5663 5822 3.821033 ACCTGCTGAATAACCTCACAAAC 59.179 43.478 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.371558 GGATATGGAGGTCGCCCAC 59.628 63.158 0.00 0.00 36.36 4.61
2 3 1.568504 TATGGATATGGAGGTCGCCC 58.431 55.000 0.00 0.00 0.00 6.13
98 99 0.677288 TCGAAGTATATGGTGGGGCG 59.323 55.000 0.00 0.00 0.00 6.13
249 251 1.138859 CATGGTAGGTGAAGATCCGCA 59.861 52.381 0.00 0.00 0.00 5.69
577 593 0.679002 TGGGACGAAGGGAGTACGAG 60.679 60.000 0.00 0.00 0.00 4.18
578 594 0.033796 ATGGGACGAAGGGAGTACGA 60.034 55.000 0.00 0.00 0.00 3.43
579 595 1.683943 TATGGGACGAAGGGAGTACG 58.316 55.000 0.00 0.00 0.00 3.67
580 596 5.997384 ATATTATGGGACGAAGGGAGTAC 57.003 43.478 0.00 0.00 0.00 2.73
581 597 7.472741 TCTTATATTATGGGACGAAGGGAGTA 58.527 38.462 0.00 0.00 0.00 2.59
582 598 6.320518 TCTTATATTATGGGACGAAGGGAGT 58.679 40.000 0.00 0.00 0.00 3.85
583 599 6.852420 TCTTATATTATGGGACGAAGGGAG 57.148 41.667 0.00 0.00 0.00 4.30
584 600 6.294899 CGTTCTTATATTATGGGACGAAGGGA 60.295 42.308 0.00 0.00 0.00 4.20
585 601 5.867716 CGTTCTTATATTATGGGACGAAGGG 59.132 44.000 0.00 0.00 0.00 3.95
586 602 6.453092 ACGTTCTTATATTATGGGACGAAGG 58.547 40.000 14.76 0.00 0.00 3.46
587 603 7.941795 AACGTTCTTATATTATGGGACGAAG 57.058 36.000 14.76 0.00 0.00 3.79
588 604 8.721019 AAAACGTTCTTATATTATGGGACGAA 57.279 30.769 0.00 0.00 0.00 3.85
589 605 8.199449 AGAAAACGTTCTTATATTATGGGACGA 58.801 33.333 0.00 0.00 41.55 4.20
590 606 8.361592 AGAAAACGTTCTTATATTATGGGACG 57.638 34.615 0.00 9.33 41.55 4.79
613 629 9.511272 TGTCACAGAAATTACTAGTAGTGTAGA 57.489 33.333 13.29 0.00 0.00 2.59
616 632 8.803235 TGATGTCACAGAAATTACTAGTAGTGT 58.197 33.333 13.29 3.20 0.00 3.55
617 633 9.639601 TTGATGTCACAGAAATTACTAGTAGTG 57.360 33.333 13.29 6.99 0.00 2.74
618 634 9.640963 GTTGATGTCACAGAAATTACTAGTAGT 57.359 33.333 8.14 8.14 0.00 2.73
622 638 8.310406 TGTGTTGATGTCACAGAAATTACTAG 57.690 34.615 0.00 0.00 40.26 2.57
674 690 1.079503 GGTTGGATGCTTGTCTCGTC 58.920 55.000 0.00 0.00 0.00 4.20
698 714 1.926511 GCAGGCCCAAGTCATTGTCG 61.927 60.000 0.00 0.00 34.39 4.35
741 757 2.867472 GTGTTTGACCATCGCCGG 59.133 61.111 0.00 0.00 0.00 6.13
748 764 2.539338 GGCGCTTCGTGTTTGACCA 61.539 57.895 7.64 0.00 0.00 4.02
759 775 2.050442 CGGTGTTTTGGGCGCTTC 60.050 61.111 7.64 0.02 0.00 3.86
807 829 5.405571 TCAACAAGTCTTCGTCTTGCTATTC 59.594 40.000 5.72 0.00 43.97 1.75
837 859 1.888436 ATGTGAGCTCCGCGGAAAGA 61.888 55.000 30.53 13.77 0.00 2.52
844 872 1.427592 GAAGCAGATGTGAGCTCCGC 61.428 60.000 12.15 4.78 40.90 5.54
879 907 3.615155 GGAGAAAAAGATCTCACCTGGG 58.385 50.000 0.00 0.00 46.24 4.45
882 910 4.467795 TCATCGGAGAAAAAGATCTCACCT 59.532 41.667 0.00 0.00 46.24 4.00
892 920 4.396166 GGATGAGCTTTCATCGGAGAAAAA 59.604 41.667 9.20 0.00 45.41 1.94
902 930 0.749454 GTGCGGGGATGAGCTTTCAT 60.749 55.000 0.00 0.00 0.00 2.57
931 959 1.078637 GGAGCAAGTAACCGGGGTC 60.079 63.158 6.32 1.00 0.00 4.46
932 960 1.131928 AAGGAGCAAGTAACCGGGGT 61.132 55.000 6.32 0.00 0.00 4.95
933 961 0.037734 AAAGGAGCAAGTAACCGGGG 59.962 55.000 6.32 0.00 0.00 5.73
934 962 1.810755 GAAAAGGAGCAAGTAACCGGG 59.189 52.381 6.32 0.00 0.00 5.73
935 963 2.742589 GAGAAAAGGAGCAAGTAACCGG 59.257 50.000 0.00 0.00 0.00 5.28
936 964 3.665190 AGAGAAAAGGAGCAAGTAACCG 58.335 45.455 0.00 0.00 0.00 4.44
937 965 4.004314 GGAGAGAAAAGGAGCAAGTAACC 58.996 47.826 0.00 0.00 0.00 2.85
938 966 4.900684 AGGAGAGAAAAGGAGCAAGTAAC 58.099 43.478 0.00 0.00 0.00 2.50
939 967 6.681729 TTAGGAGAGAAAAGGAGCAAGTAA 57.318 37.500 0.00 0.00 0.00 2.24
940 968 6.270231 ACTTTAGGAGAGAAAAGGAGCAAGTA 59.730 38.462 0.00 0.00 37.09 2.24
941 969 5.072464 ACTTTAGGAGAGAAAAGGAGCAAGT 59.928 40.000 0.00 0.00 37.09 3.16
972 1000 4.039730 ACTGTAAGAAGAAGCAGCTCTTGA 59.960 41.667 10.70 0.00 35.76 3.02
1022 1050 2.412065 GCAAGCACGATGAACAAGAGAC 60.412 50.000 0.00 0.00 0.00 3.36
1095 1123 1.006102 CCACAGCGTCGAGAGGTTT 60.006 57.895 0.00 0.00 0.00 3.27
1104 1132 4.651994 CTTTGTTATTGATCCACAGCGTC 58.348 43.478 0.00 0.00 0.00 5.19
1119 1147 3.219281 GTGTGGGAGGAAAGCTTTGTTA 58.781 45.455 18.30 0.00 0.00 2.41
1314 1342 3.067011 CACCTGTGGAGTCCCAGTA 57.933 57.895 20.04 0.00 44.55 2.74
1359 1387 1.615107 GGGTCGCGTTTTCTCTGACG 61.615 60.000 5.77 0.00 41.89 4.35
1368 1396 0.818040 AAAGCTCAAGGGTCGCGTTT 60.818 50.000 5.77 0.00 0.00 3.60
1445 1475 1.608717 CTACAGACCGCCCAGAGCTT 61.609 60.000 0.00 0.00 40.39 3.74
1539 1569 2.171237 CCAATGCATCAGTAGGGTGAGA 59.829 50.000 0.00 0.00 0.00 3.27
1653 1686 5.698089 CGACATAAGCATACAATCCATCAGT 59.302 40.000 0.00 0.00 0.00 3.41
1686 1719 6.928979 TTTCGAAAAATAGAGTTGTGGTGA 57.071 33.333 8.44 0.00 0.00 4.02
1736 1775 5.070685 GTGAAGGTAACCTTTGTTGGATCT 58.929 41.667 0.00 0.00 44.82 2.75
2023 2083 8.384365 GCTTGAAGTAGCTTGAACTAGAATTAC 58.616 37.037 0.00 0.00 38.15 1.89
2176 2239 2.223144 TCTTCTCCGTTTGTTGCATTCG 59.777 45.455 0.00 0.00 0.00 3.34
2269 2347 1.001520 TCACCCACATACACGTTCCAG 59.998 52.381 0.00 0.00 0.00 3.86
2280 2358 0.772124 AAGACCCTGGTCACCCACAT 60.772 55.000 18.12 0.00 46.76 3.21
2434 2545 9.457110 CAATGACTAGCAGTACAAGAATAGTAG 57.543 37.037 0.00 0.00 0.00 2.57
2507 2621 8.313292 CCAGGAATTTGGTCAAAATCTAATTCA 58.687 33.333 10.23 0.00 37.51 2.57
2585 2699 2.901839 ACCACCTCCGAGCTTTTTACTA 59.098 45.455 0.00 0.00 0.00 1.82
2654 2768 5.757988 TGTAACCTGGGACAAAGTTTTACT 58.242 37.500 0.00 0.00 38.70 2.24
2655 2769 5.591472 ACTGTAACCTGGGACAAAGTTTTAC 59.409 40.000 0.00 0.00 38.70 2.01
2656 2770 5.757988 ACTGTAACCTGGGACAAAGTTTTA 58.242 37.500 0.00 0.00 38.70 1.52
3182 3296 4.960469 CCTAGTAGGTCCTGTCCAATTACA 59.040 45.833 8.17 0.00 0.00 2.41
3215 3329 2.223805 TGATTGTCTCATCCCGATCACG 60.224 50.000 0.00 0.00 39.43 4.35
3304 3418 4.726876 GCGTTAACAGAATTCGGTGGATTC 60.727 45.833 12.13 0.00 0.00 2.52
3359 3473 3.670895 CGAATGTGTCTCGCTAAGTCAGT 60.671 47.826 0.00 0.00 0.00 3.41
3402 3516 1.204704 TGCAAGTCCAGATAGTCCACG 59.795 52.381 0.00 0.00 0.00 4.94
3497 3612 0.039798 GTGAGTAGCGACCACGAACA 60.040 55.000 0.00 0.00 42.66 3.18
3563 3678 4.054359 AGATATCCCGAGCTACCATCTT 57.946 45.455 0.00 0.00 0.00 2.40
3655 3770 2.835764 AGCCATGAAAAGATGCCACAAT 59.164 40.909 0.00 0.00 0.00 2.71
3897 4013 4.331108 TGTGTTCAATGCTGCCAATAGTA 58.669 39.130 0.00 0.00 0.00 1.82
3989 4105 3.370104 CACCTATCAAGTGACCCTCTCT 58.630 50.000 0.00 0.00 37.42 3.10
4061 4177 7.991084 CCTTTGGCAATATCTAGAATGATCA 57.009 36.000 0.00 0.00 0.00 2.92
4151 4267 7.439356 TGGCGTTGAAATTCTCATATAAGAGAG 59.561 37.037 7.66 1.59 44.78 3.20
4159 4275 6.098679 CCAATTTGGCGTTGAAATTCTCATA 58.901 36.000 1.71 0.00 31.96 2.15
4180 4296 5.590259 GCTTAGATAGTCCAAAATCAGCCAA 59.410 40.000 0.00 0.00 0.00 4.52
4209 4325 0.961753 CTTTGCTTTGGTCCCTGTCC 59.038 55.000 0.00 0.00 0.00 4.02
4402 4520 9.118300 CTGATTATCTTCAGCCTTTTTCTGTAT 57.882 33.333 0.00 0.00 36.96 2.29
4730 4859 8.919777 AAGTAGTTACAAAGCCTGAAGTTTAT 57.080 30.769 0.00 0.00 0.00 1.40
4731 4860 8.741603 AAAGTAGTTACAAAGCCTGAAGTTTA 57.258 30.769 0.00 0.00 0.00 2.01
4732 4861 7.640597 AAAGTAGTTACAAAGCCTGAAGTTT 57.359 32.000 0.00 0.00 0.00 2.66
4733 4862 7.122204 ACAAAAGTAGTTACAAAGCCTGAAGTT 59.878 33.333 0.00 0.00 0.00 2.66
4734 4863 6.602009 ACAAAAGTAGTTACAAAGCCTGAAGT 59.398 34.615 0.00 0.00 0.00 3.01
4777 4906 9.646427 GGTGCCATTTAAATCATACTTACAAAA 57.354 29.630 0.00 0.00 0.00 2.44
4881 5011 4.260212 GCTTACATTACACGGTGCTACATG 60.260 45.833 8.30 7.80 0.00 3.21
4892 5022 7.041644 TGGTGTTTCAACTAGCTTACATTACAC 60.042 37.037 0.00 0.00 0.00 2.90
4896 5026 8.100791 TCTATGGTGTTTCAACTAGCTTACATT 58.899 33.333 0.00 0.00 0.00 2.71
5127 5257 9.108449 CGAAAGACTCTTGATAAGATACGTATG 57.892 37.037 13.97 0.00 36.82 2.39
5128 5258 8.291032 CCGAAAGACTCTTGATAAGATACGTAT 58.709 37.037 8.05 8.05 36.82 3.06
5140 5279 2.897969 AGCCTAACCGAAAGACTCTTGA 59.102 45.455 0.00 0.00 0.00 3.02
5149 5288 2.242882 ACCTCCTAGCCTAACCGAAA 57.757 50.000 0.00 0.00 0.00 3.46
5228 5386 4.747108 GCGCATACAGTTGAGATCTTACAT 59.253 41.667 0.30 0.00 0.00 2.29
5265 5424 0.178992 GCATGTTATAGGCAGGGGCA 60.179 55.000 0.00 0.00 43.71 5.36
5421 5580 5.788450 CTTCTCTGTAACCTGACTGTTGAT 58.212 41.667 0.00 0.00 0.00 2.57
5589 5748 2.104669 ATAGGGTGGAGAGGGTTAGC 57.895 55.000 0.00 0.00 0.00 3.09
5591 5750 4.141990 CCATATAGGGTGGAGAGGGTTA 57.858 50.000 0.00 0.00 39.12 2.85
5663 5822 2.989824 ACCGTGACCAGGACCTCG 60.990 66.667 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.