Multiple sequence alignment - TraesCS3A01G447400

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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 TraesCS3A01G447400 chr3A 100.000 3717 0 0 1 3717 687480957 687484673 0.000000e+00 6865.0
1 TraesCS3A01G447400 chr3A 86.983 484 53 6 2692 3174 687476290 687475816 1.520000e-148 536.0
2 TraesCS3A01G447400 chr3A 88.949 371 40 1 3174 3543 693581527 693581157 1.220000e-124 457.0
3 TraesCS3A01G447400 chr3A 81.050 438 72 9 2737 3174 687501198 687501624 4.600000e-89 339.0
4 TraesCS3A01G447400 chr3A 97.778 45 1 0 3673 3717 56781384 56781428 1.110000e-10 78.7
5 TraesCS3A01G447400 chr3D 94.183 1616 64 13 899 2487 550457257 550458869 0.000000e+00 2436.0
6 TraesCS3A01G447400 chr3D 93.796 548 25 4 2470 3012 550458881 550459424 0.000000e+00 815.0
7 TraesCS3A01G447400 chr3D 88.272 486 46 5 2690 3174 550442693 550442218 4.160000e-159 571.0
8 TraesCS3A01G447400 chr3D 95.965 347 14 0 70 416 550455797 550456143 6.970000e-157 564.0
9 TraesCS3A01G447400 chr3D 91.538 260 17 3 486 745 550456424 550456678 1.640000e-93 353.0
10 TraesCS3A01G447400 chr3D 81.279 438 72 8 2735 3171 550471662 550472090 2.750000e-91 346.0
11 TraesCS3A01G447400 chr3D 94.690 113 2 1 3062 3174 550459926 550460034 4.940000e-39 172.0
12 TraesCS3A01G447400 chr3D 92.308 117 6 2 777 891 550456977 550457092 2.970000e-36 163.0
13 TraesCS3A01G447400 chr3D 100.000 32 0 0 2735 2766 550599835 550599866 4.010000e-05 60.2
14 TraesCS3A01G447400 chr3D 100.000 31 0 0 2735 2765 550599190 550599220 1.440000e-04 58.4
15 TraesCS3A01G447400 chr3B 93.357 1656 81 16 778 2405 729941050 729939396 0.000000e+00 2422.0
16 TraesCS3A01G447400 chr3B 86.792 742 67 15 1 740 729945895 729945183 0.000000e+00 798.0
17 TraesCS3A01G447400 chr3B 87.222 360 42 4 3172 3529 727792413 727792770 1.240000e-109 407.0
18 TraesCS3A01G447400 chr3B 82.432 444 66 7 2735 3178 729975881 729976312 9.740000e-101 377.0
19 TraesCS3A01G447400 chr3B 79.302 430 81 6 3174 3599 706858863 706858438 1.010000e-75 294.0
20 TraesCS3A01G447400 chr3B 97.778 45 1 0 3673 3717 747525367 747525411 1.110000e-10 78.7
21 TraesCS3A01G447400 chr3B 100.000 31 0 0 2735 2765 730163483 730163513 1.440000e-04 58.4
22 TraesCS3A01G447400 chr4A 84.982 546 52 9 3174 3717 578166113 578166630 9.140000e-146 527.0
23 TraesCS3A01G447400 chr5B 92.378 328 23 2 3169 3495 699981754 699981428 2.020000e-127 466.0
24 TraesCS3A01G447400 chr5B 93.488 215 12 1 3503 3715 699981457 699981243 5.990000e-83 318.0
25 TraesCS3A01G447400 chr2A 85.116 430 61 2 3174 3600 707270394 707270823 1.590000e-118 436.0
26 TraesCS3A01G447400 chr2A 82.488 434 64 9 3173 3600 39727634 39728061 1.630000e-98 370.0
27 TraesCS3A01G447400 chr2A 100.000 31 0 0 3568 3598 94419878 94419908 1.440000e-04 58.4
28 TraesCS3A01G447400 chr6B 84.884 430 61 4 3174 3600 38966828 38966400 7.370000e-117 431.0
29 TraesCS3A01G447400 chr6B 84.919 431 59 6 3174 3600 49670157 49670585 7.370000e-117 431.0
30 TraesCS3A01G447400 chr6B 97.727 44 1 0 3674 3717 34137248 34137205 3.980000e-10 76.8
31 TraesCS3A01G447400 chr7D 90.312 320 30 1 3174 3492 555156714 555156395 5.740000e-113 418.0
32 TraesCS3A01G447400 chr6A 85.012 407 58 2 3179 3582 115969836 115970242 9.610000e-111 411.0
33 TraesCS3A01G447400 chr1A 72.538 528 109 29 3174 3686 579735657 579735151 5.010000e-29 139.0
34 TraesCS3A01G447400 chr7B 97.778 45 1 0 3673 3717 670208327 670208283 1.110000e-10 78.7
35 TraesCS3A01G447400 chr6D 81.553 103 12 4 3568 3669 1366798 1366702 1.110000e-10 78.7


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 TraesCS3A01G447400 chr3A 687480957 687484673 3716 False 6865.0 6865 100.000000 1 3717 1 chr3A.!!$F2 3716
1 TraesCS3A01G447400 chr3D 550455797 550460034 4237 False 750.5 2436 93.746667 70 3174 6 chr3D.!!$F2 3104
2 TraesCS3A01G447400 chr3B 729939396 729941050 1654 True 2422.0 2422 93.357000 778 2405 1 chr3B.!!$R2 1627
3 TraesCS3A01G447400 chr3B 729945183 729945895 712 True 798.0 798 86.792000 1 740 1 chr3B.!!$R3 739
4 TraesCS3A01G447400 chr4A 578166113 578166630 517 False 527.0 527 84.982000 3174 3717 1 chr4A.!!$F1 543
5 TraesCS3A01G447400 chr5B 699981243 699981754 511 True 392.0 466 92.933000 3169 3715 2 chr5B.!!$R1 546

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
60 61 0.179018 AATTCCATACGGCCAGCCTC 60.179 55.0 2.24 0.00 0.00 4.70 F
310 312 0.240945 CGAGCCGGATTTGTTGCTTT 59.759 50.0 5.05 0.00 33.41 3.51 F
1054 1697 0.930742 ATCTCGATCTTTCGCGACGC 60.931 55.0 9.15 10.49 41.43 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 2335 0.365523 CGTTGTTGTAGCCGACGATG 59.634 55.0 0.00 0.0 41.23 3.84 R
2289 2968 0.309302 CAGGCCAGTCGATCTCTACG 59.691 60.0 5.01 0.0 0.00 3.51 R
3020 3737 0.609662 ATCAAACATGGCTTGCCACC 59.390 50.0 17.22 0.0 0.00 4.61 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
31 32 4.136796 CAGACATGTTTCTGGAGGTTCAA 58.863 43.478 0.00 0.00 39.59 2.69
59 60 0.466189 CAATTCCATACGGCCAGCCT 60.466 55.000 2.24 0.00 0.00 4.58
60 61 0.179018 AATTCCATACGGCCAGCCTC 60.179 55.000 2.24 0.00 0.00 4.70
62 63 1.344953 TTCCATACGGCCAGCCTCAT 61.345 55.000 2.24 0.00 0.00 2.90
79 81 0.695924 CATGGTGGTAGTTGGGGTGA 59.304 55.000 0.00 0.00 0.00 4.02
89 91 1.916181 AGTTGGGGTGATTACCTGGAG 59.084 52.381 6.62 0.00 46.66 3.86
160 162 2.551459 CTGGCTACTGATGCTATTTGCC 59.449 50.000 0.00 0.00 42.00 4.52
165 167 4.980434 GCTACTGATGCTATTTGCCAAATG 59.020 41.667 12.86 4.41 42.00 2.32
180 182 2.547211 CCAAATGTGCGGATTTTTGCAA 59.453 40.909 0.00 0.00 43.75 4.08
223 225 1.068264 GGCATGCTCGAGACGATATCA 60.068 52.381 18.75 2.46 34.61 2.15
310 312 0.240945 CGAGCCGGATTTGTTGCTTT 59.759 50.000 5.05 0.00 33.41 3.51
435 438 1.301423 TGGCCGTTGCGTTATAATCC 58.699 50.000 0.00 0.00 38.85 3.01
438 441 2.097791 GGCCGTTGCGTTATAATCCAAA 59.902 45.455 0.00 0.00 38.85 3.28
440 443 3.181504 GCCGTTGCGTTATAATCCAAAGT 60.182 43.478 10.59 0.00 0.00 2.66
441 444 4.339429 CCGTTGCGTTATAATCCAAAGTG 58.661 43.478 10.59 3.37 0.00 3.16
442 445 4.339429 CGTTGCGTTATAATCCAAAGTGG 58.661 43.478 3.29 0.00 39.43 4.00
443 446 4.668289 GTTGCGTTATAATCCAAAGTGGG 58.332 43.478 0.00 0.00 38.32 4.61
444 447 3.283751 TGCGTTATAATCCAAAGTGGGG 58.716 45.455 0.00 0.00 38.32 4.96
445 448 3.054287 TGCGTTATAATCCAAAGTGGGGA 60.054 43.478 0.00 0.00 38.32 4.81
446 449 3.949113 GCGTTATAATCCAAAGTGGGGAA 59.051 43.478 0.00 0.00 38.32 3.97
447 450 4.399934 GCGTTATAATCCAAAGTGGGGAAA 59.600 41.667 0.00 0.00 38.32 3.13
448 451 5.105675 GCGTTATAATCCAAAGTGGGGAAAA 60.106 40.000 0.00 0.00 38.32 2.29
469 472 8.570123 GAAAACTCGTTTTCGTCATATGTTAG 57.430 34.615 16.62 0.00 45.76 2.34
474 477 6.032094 TCGTTTTCGTCATATGTTAGACTCC 58.968 40.000 1.90 0.00 44.46 3.85
477 480 6.525578 TTTCGTCATATGTTAGACTCCTGT 57.474 37.500 1.90 0.00 32.68 4.00
479 482 6.862711 TCGTCATATGTTAGACTCCTGTAG 57.137 41.667 1.90 0.00 32.68 2.74
480 483 5.763698 TCGTCATATGTTAGACTCCTGTAGG 59.236 44.000 1.90 0.00 32.68 3.18
481 484 5.531659 CGTCATATGTTAGACTCCTGTAGGT 59.468 44.000 1.90 0.00 36.34 3.08
482 485 6.513556 CGTCATATGTTAGACTCCTGTAGGTG 60.514 46.154 1.90 0.00 36.34 4.00
483 486 5.302059 TCATATGTTAGACTCCTGTAGGTGC 59.698 44.000 1.90 0.00 36.34 5.01
484 487 3.170991 TGTTAGACTCCTGTAGGTGCT 57.829 47.619 0.00 1.05 36.34 4.40
490 704 1.142870 ACTCCTGTAGGTGCTTGCAAA 59.857 47.619 0.00 0.00 36.34 3.68
503 717 3.928992 TGCTTGCAAATTTTTGTGACGAA 59.071 34.783 0.00 0.00 40.24 3.85
559 773 7.775561 GGATCTAGAAATTATTTCACACCACCT 59.224 37.037 18.37 0.00 42.10 4.00
562 776 8.328758 TCTAGAAATTATTTCACACCACCTGAT 58.671 33.333 18.37 0.00 42.10 2.90
574 788 4.702131 ACACCACCTGATAATTTGAAGCTC 59.298 41.667 0.00 0.00 0.00 4.09
578 792 5.416952 CCACCTGATAATTTGAAGCTCAGTT 59.583 40.000 0.00 0.00 33.16 3.16
579 793 6.071728 CCACCTGATAATTTGAAGCTCAGTTT 60.072 38.462 0.00 0.00 33.16 2.66
622 836 5.278907 CCTCTGATCTCATCTAAGCACGAAT 60.279 44.000 0.00 0.00 0.00 3.34
640 854 4.681025 ACGAATTTTTGCAAGCATGTAGTG 59.319 37.500 0.00 0.00 0.00 2.74
641 855 4.681025 CGAATTTTTGCAAGCATGTAGTGT 59.319 37.500 0.00 0.00 0.00 3.55
642 856 5.855925 CGAATTTTTGCAAGCATGTAGTGTA 59.144 36.000 0.00 0.00 0.00 2.90
643 857 6.183359 CGAATTTTTGCAAGCATGTAGTGTAC 60.183 38.462 0.00 0.00 0.00 2.90
671 885 5.470098 AGTTGAGCGTCTTTGATGTACAAAT 59.530 36.000 0.00 0.00 45.63 2.32
740 1014 2.104111 TCATCGGGAACATATGACCCAC 59.896 50.000 28.10 12.23 43.40 4.61
763 1040 7.094334 CCACGGATCAGCTAGTACTATGAATTA 60.094 40.741 9.65 0.00 0.00 1.40
875 1355 3.812053 GAGTCGGAATAGTACTAAGCCGA 59.188 47.826 30.19 30.19 40.21 5.54
876 1356 3.814283 AGTCGGAATAGTACTAAGCCGAG 59.186 47.826 32.55 16.08 41.80 4.63
878 1358 4.455190 GTCGGAATAGTACTAAGCCGAGAT 59.545 45.833 32.55 7.11 41.80 2.75
879 1359 5.048852 GTCGGAATAGTACTAAGCCGAGATT 60.049 44.000 32.55 14.00 41.80 2.40
892 1373 9.227777 ACTAAGCCGAGATTAAATTACAAAAGT 57.772 29.630 0.00 0.00 0.00 2.66
995 1638 4.933064 CGGCGCCCTCTGATCGAC 62.933 72.222 23.46 0.00 0.00 4.20
1019 1662 4.813161 CAGCAACGAATCATCCAAGATAGT 59.187 41.667 0.00 0.00 0.00 2.12
1054 1697 0.930742 ATCTCGATCTTTCGCGACGC 60.931 55.000 9.15 10.49 41.43 5.19
1063 1706 2.424705 TTTCGCGACGCCCACTTACT 62.425 55.000 9.15 0.00 0.00 2.24
1065 1708 1.585521 CGCGACGCCCACTTACTAG 60.586 63.158 15.34 0.00 0.00 2.57
1066 1709 1.226888 GCGACGCCCACTTACTAGG 60.227 63.158 9.14 0.00 0.00 3.02
1251 1903 2.058595 CGACCCATCCTTCCTCCGT 61.059 63.158 0.00 0.00 0.00 4.69
1542 2209 3.626924 GACGTGGACCACCTGGCT 61.627 66.667 19.11 0.00 39.32 4.75
1666 2333 1.366366 CCGACGTCCTTCAAGGTGT 59.634 57.895 10.58 3.40 36.53 4.16
1668 2335 1.137513 CGACGTCCTTCAAGGTGTTC 58.862 55.000 10.58 0.00 36.53 3.18
1713 2380 2.202623 CAGCAGTACGACCTCCGC 60.203 66.667 0.00 0.00 43.32 5.54
2076 2755 3.267860 GAGCATTGCGGCCGAGAG 61.268 66.667 33.48 16.22 0.00 3.20
2241 2920 2.105128 GCCATGGAGGAGACGACG 59.895 66.667 18.40 0.00 41.22 5.12
2318 2997 0.034670 GACTGGCCTGCCTTCTTCAT 60.035 55.000 9.95 0.00 36.94 2.57
2351 3030 6.817765 TGGTGGAAAGTCAGATGTTTAATC 57.182 37.500 0.00 0.00 0.00 1.75
2405 3087 8.574251 TTACAATAATGCTTCTGGCTTCTTTA 57.426 30.769 0.00 0.00 42.39 1.85
2406 3088 7.093322 ACAATAATGCTTCTGGCTTCTTTAG 57.907 36.000 0.00 0.00 42.39 1.85
2407 3089 6.886459 ACAATAATGCTTCTGGCTTCTTTAGA 59.114 34.615 0.00 0.00 42.39 2.10
2498 3210 9.367444 GAGAATTAGGACTTCGAAATAAGACAA 57.633 33.333 0.00 0.00 0.00 3.18
2504 3216 8.068892 AGGACTTCGAAATAAGACAACTCTAT 57.931 34.615 0.00 0.00 0.00 1.98
2551 3263 9.781633 AAAATTTGAATTCTCAATCATGGTGAA 57.218 25.926 7.05 0.00 41.22 3.18
2552 3264 8.997621 AATTTGAATTCTCAATCATGGTGAAG 57.002 30.769 7.05 0.00 41.22 3.02
2570 3282 7.609960 TGGTGAAGCAAAGATAAAATATGCAA 58.390 30.769 0.00 0.00 39.42 4.08
2572 3284 9.101655 GGTGAAGCAAAGATAAAATATGCAAAT 57.898 29.630 0.00 0.00 39.42 2.32
2697 3410 0.321919 GCACATGCTCCTTGTCTCCA 60.322 55.000 0.00 0.00 38.21 3.86
2789 3505 7.429374 TGATGAGGTCAAGAGTGAATATTCT 57.571 36.000 16.24 0.00 34.87 2.40
2790 3506 8.539117 TGATGAGGTCAAGAGTGAATATTCTA 57.461 34.615 16.24 0.74 34.87 2.10
2791 3507 8.417106 TGATGAGGTCAAGAGTGAATATTCTAC 58.583 37.037 16.24 12.09 34.87 2.59
2792 3508 6.796426 TGAGGTCAAGAGTGAATATTCTACG 58.204 40.000 16.24 0.41 34.87 3.51
2870 3586 1.821216 TTCAATTCCCTCGACTTGCC 58.179 50.000 0.00 0.00 30.70 4.52
2898 3614 4.530857 CTCGGACCGCACCCATCC 62.531 72.222 9.66 0.00 0.00 3.51
2912 3628 2.352371 CCCATCCTTCCATACCCTCAT 58.648 52.381 0.00 0.00 0.00 2.90
2914 3630 3.521126 CCCATCCTTCCATACCCTCATAG 59.479 52.174 0.00 0.00 0.00 2.23
2961 3677 5.885912 GCTTGGTCCAAAGTTCAAGGATATA 59.114 40.000 5.64 0.00 37.61 0.86
3012 3729 5.395682 TTTTCTTTCTCAAGGATGCATGG 57.604 39.130 2.46 0.00 0.00 3.66
3013 3730 3.008835 TCTTTCTCAAGGATGCATGGG 57.991 47.619 2.46 0.00 0.00 4.00
3014 3731 2.577563 TCTTTCTCAAGGATGCATGGGA 59.422 45.455 2.46 0.00 0.00 4.37
3015 3732 3.010472 TCTTTCTCAAGGATGCATGGGAA 59.990 43.478 2.46 0.10 34.33 3.97
3016 3733 2.425143 TCTCAAGGATGCATGGGAAC 57.575 50.000 2.46 0.00 0.00 3.62
3017 3734 1.019673 CTCAAGGATGCATGGGAACG 58.980 55.000 2.46 0.00 0.00 3.95
3018 3735 0.394216 TCAAGGATGCATGGGAACGG 60.394 55.000 2.46 0.00 0.00 4.44
3019 3736 1.076777 AAGGATGCATGGGAACGGG 60.077 57.895 2.46 0.00 0.00 5.28
3020 3737 2.519302 GGATGCATGGGAACGGGG 60.519 66.667 2.46 0.00 0.00 5.73
3021 3738 2.519302 GATGCATGGGAACGGGGG 60.519 66.667 2.46 0.00 0.00 5.40
3022 3739 3.346734 ATGCATGGGAACGGGGGT 61.347 61.111 0.00 0.00 0.00 4.95
3023 3740 3.660422 ATGCATGGGAACGGGGGTG 62.660 63.158 0.00 0.00 0.00 4.61
3042 3759 3.488778 TGGCAAGCCATGTTTGATTTT 57.511 38.095 10.24 0.00 41.89 1.82
3043 3760 4.613925 TGGCAAGCCATGTTTGATTTTA 57.386 36.364 10.24 0.00 41.89 1.52
3044 3761 4.965814 TGGCAAGCCATGTTTGATTTTAA 58.034 34.783 10.24 0.00 41.89 1.52
3045 3762 5.558818 TGGCAAGCCATGTTTGATTTTAAT 58.441 33.333 10.24 0.00 41.89 1.40
3046 3763 6.002704 TGGCAAGCCATGTTTGATTTTAATT 58.997 32.000 10.24 0.00 41.89 1.40
3047 3764 6.072618 TGGCAAGCCATGTTTGATTTTAATTG 60.073 34.615 10.24 0.00 41.89 2.32
3048 3765 6.316319 GCAAGCCATGTTTGATTTTAATTGG 58.684 36.000 10.42 0.00 0.00 3.16
3049 3766 6.623331 GCAAGCCATGTTTGATTTTAATTGGG 60.623 38.462 10.42 0.00 0.00 4.12
3050 3767 6.371595 AGCCATGTTTGATTTTAATTGGGA 57.628 33.333 0.00 0.00 0.00 4.37
3051 3768 6.961042 AGCCATGTTTGATTTTAATTGGGAT 58.039 32.000 0.00 0.00 0.00 3.85
3052 3769 7.049754 AGCCATGTTTGATTTTAATTGGGATC 58.950 34.615 0.00 0.00 0.00 3.36
3053 3770 7.049754 GCCATGTTTGATTTTAATTGGGATCT 58.950 34.615 0.00 0.00 0.00 2.75
3054 3771 7.553760 GCCATGTTTGATTTTAATTGGGATCTT 59.446 33.333 0.00 0.00 0.00 2.40
3055 3772 8.885722 CCATGTTTGATTTTAATTGGGATCTTG 58.114 33.333 0.00 0.00 0.00 3.02
3056 3773 8.885722 CATGTTTGATTTTAATTGGGATCTTGG 58.114 33.333 0.00 0.00 0.00 3.61
3057 3774 6.878389 TGTTTGATTTTAATTGGGATCTTGGC 59.122 34.615 0.00 0.00 0.00 4.52
3058 3775 6.872585 TTGATTTTAATTGGGATCTTGGCT 57.127 33.333 0.00 0.00 0.00 4.75
3059 3776 7.969690 TTGATTTTAATTGGGATCTTGGCTA 57.030 32.000 0.00 0.00 0.00 3.93
3060 3777 7.969690 TGATTTTAATTGGGATCTTGGCTAA 57.030 32.000 0.00 0.00 0.00 3.09
3088 4257 5.234752 ACATTTGTCGTGTCAGCAGTTATA 58.765 37.500 0.00 0.00 0.00 0.98
3089 4258 5.874810 ACATTTGTCGTGTCAGCAGTTATAT 59.125 36.000 0.00 0.00 0.00 0.86
3090 4259 7.039270 ACATTTGTCGTGTCAGCAGTTATATA 58.961 34.615 0.00 0.00 0.00 0.86
3091 4260 7.710907 ACATTTGTCGTGTCAGCAGTTATATAT 59.289 33.333 0.00 0.00 0.00 0.86
3121 4290 5.404366 GCGTGTAGAAGTTTGTATTGTCTCA 59.596 40.000 0.00 0.00 0.00 3.27
3188 4357 0.172578 CAGACACTACCGGATTCGCA 59.827 55.000 9.46 0.00 34.56 5.10
3407 4576 2.293122 CGGCAGAAATTTTCACCTGACA 59.707 45.455 11.53 0.00 34.44 3.58
3414 4583 4.734398 AATTTTCACCTGACAGCAACAA 57.266 36.364 0.00 0.00 0.00 2.83
3444 4613 2.076100 TCAAAAGCGCTGACGAATCAT 58.924 42.857 12.58 0.00 43.93 2.45
3447 4616 0.108186 AAGCGCTGACGAATCATGGA 60.108 50.000 12.58 0.00 43.93 3.41
3513 4682 2.684001 TGAAAATCTATGCCGACGGT 57.316 45.000 16.73 0.00 0.00 4.83
3516 4685 2.225068 AAATCTATGCCGACGGTCAG 57.775 50.000 16.73 10.18 0.00 3.51
3615 4786 0.536724 AGATGCTGCCACGTGTCATA 59.463 50.000 15.65 0.11 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.743521 TGAACCTCCAGAAACATGTCTG 58.256 45.455 0.00 2.89 43.98 3.51
26 27 2.432510 TGGAATTGTGGTGGGTTTGAAC 59.567 45.455 0.00 0.00 0.00 3.18
31 32 2.442413 CGTATGGAATTGTGGTGGGTT 58.558 47.619 0.00 0.00 0.00 4.11
35 36 0.738389 GGCCGTATGGAATTGTGGTG 59.262 55.000 4.73 0.00 37.49 4.17
42 43 1.344953 TGAGGCTGGCCGTATGGAAT 61.345 55.000 4.73 0.00 41.95 3.01
59 60 0.695924 CACCCCAACTACCACCATGA 59.304 55.000 0.00 0.00 0.00 3.07
60 61 0.695924 TCACCCCAACTACCACCATG 59.304 55.000 0.00 0.00 0.00 3.66
62 63 1.451449 AATCACCCCAACTACCACCA 58.549 50.000 0.00 0.00 0.00 4.17
79 81 8.275187 TGAATATTCCATACACTCCAGGTAAT 57.725 34.615 12.90 0.00 0.00 1.89
160 162 3.248125 AGTTGCAAAAATCCGCACATTTG 59.752 39.130 0.00 0.00 38.00 2.32
165 167 2.923020 CCATAGTTGCAAAAATCCGCAC 59.077 45.455 0.00 0.00 38.00 5.34
180 182 3.878778 CTTGCTAAGTGGCTTCCATAGT 58.121 45.455 0.00 0.00 35.28 2.12
223 225 0.836400 AGGTCCACGGTGATCTGGTT 60.836 55.000 10.28 0.00 0.00 3.67
302 304 5.983540 ACCCTGAATAAAAACAAAGCAACA 58.016 33.333 0.00 0.00 0.00 3.33
310 312 6.926272 GCATAACACAACCCTGAATAAAAACA 59.074 34.615 0.00 0.00 0.00 2.83
435 438 3.793797 AAACGAGTTTTCCCCACTTTG 57.206 42.857 0.00 0.00 0.00 2.77
445 448 8.219105 GTCTAACATATGACGAAAACGAGTTTT 58.781 33.333 10.38 13.06 44.59 2.43
446 449 7.597743 AGTCTAACATATGACGAAAACGAGTTT 59.402 33.333 10.38 0.00 38.16 2.66
447 450 7.088905 AGTCTAACATATGACGAAAACGAGTT 58.911 34.615 10.38 0.00 38.16 3.01
448 451 6.618811 AGTCTAACATATGACGAAAACGAGT 58.381 36.000 10.38 0.00 38.16 4.18
458 461 6.736243 GCACCTACAGGAGTCTAACATATGAC 60.736 46.154 10.38 0.00 38.94 3.06
469 472 0.321671 TGCAAGCACCTACAGGAGTC 59.678 55.000 1.29 0.00 38.94 3.36
474 477 4.810491 ACAAAAATTTGCAAGCACCTACAG 59.190 37.500 0.00 0.00 41.79 2.74
477 480 4.808364 GTCACAAAAATTTGCAAGCACCTA 59.192 37.500 0.00 0.00 41.79 3.08
479 482 3.543852 CGTCACAAAAATTTGCAAGCACC 60.544 43.478 0.00 0.00 41.79 5.01
480 483 3.305629 TCGTCACAAAAATTTGCAAGCAC 59.694 39.130 0.00 0.00 41.79 4.40
481 484 3.515630 TCGTCACAAAAATTTGCAAGCA 58.484 36.364 0.00 0.00 41.79 3.91
482 485 4.513000 TTCGTCACAAAAATTTGCAAGC 57.487 36.364 0.00 0.00 41.79 4.01
483 486 6.624526 GTCATTTCGTCACAAAAATTTGCAAG 59.375 34.615 0.00 0.00 41.79 4.01
484 487 6.456181 GGTCATTTCGTCACAAAAATTTGCAA 60.456 34.615 5.82 0.00 41.79 4.08
490 704 5.163457 ACCAAGGTCATTTCGTCACAAAAAT 60.163 36.000 0.00 0.00 0.00 1.82
503 717 7.654022 TGTTTTTCTTTCTACCAAGGTCATT 57.346 32.000 0.00 0.00 0.00 2.57
539 753 8.877864 TTATCAGGTGGTGTGAAATAATTTCT 57.122 30.769 0.00 0.00 40.32 2.52
546 760 7.537596 TTCAAATTATCAGGTGGTGTGAAAT 57.462 32.000 0.00 0.00 0.00 2.17
622 836 5.506686 TGTACACTACATGCTTGCAAAAA 57.493 34.783 0.00 0.00 32.89 1.94
640 854 4.049186 TCAAAGACGCTCAACTCTTGTAC 58.951 43.478 0.00 0.00 0.00 2.90
641 855 4.316205 TCAAAGACGCTCAACTCTTGTA 57.684 40.909 0.00 0.00 0.00 2.41
642 856 3.179443 TCAAAGACGCTCAACTCTTGT 57.821 42.857 0.00 0.00 0.00 3.16
643 857 3.496130 ACATCAAAGACGCTCAACTCTTG 59.504 43.478 0.00 0.00 0.00 3.02
671 885 9.950680 GCAAAAATATCGAAAGGATCTGAAATA 57.049 29.630 0.00 0.00 36.55 1.40
703 917 9.450807 GTTCCCGATGAATAGTAAATTCAAATG 57.549 33.333 4.67 0.00 40.84 2.32
740 1014 7.251994 GGTAATTCATAGTACTAGCTGATCCG 58.748 42.308 8.85 0.00 0.00 4.18
763 1040 9.962783 CACTTAAGTAAATACTATAAGCTCGGT 57.037 33.333 8.04 0.00 34.99 4.69
892 1373 3.991773 GTCACGGTTCATAAAGTGTGCTA 59.008 43.478 0.00 0.00 36.16 3.49
995 1638 2.358957 TCTTGGATGATTCGTTGCTGG 58.641 47.619 0.00 0.00 0.00 4.85
1019 1662 1.273606 GAGATGCGGGATTAGCTGCTA 59.726 52.381 5.02 5.02 35.28 3.49
1054 1697 3.063997 CACGTACGTACCTAGTAAGTGGG 59.936 52.174 22.34 0.00 44.70 4.61
1063 1706 2.112198 CCCCGCACGTACGTACCTA 61.112 63.158 22.34 0.00 0.00 3.08
1065 1708 2.668261 GATCCCCGCACGTACGTACC 62.668 65.000 22.34 13.91 0.00 3.34
1066 1709 1.298638 GATCCCCGCACGTACGTAC 60.299 63.158 22.34 15.19 0.00 3.67
1281 1933 3.418744 GAAGCCGAGGAGCGAGGAC 62.419 68.421 0.00 0.00 44.57 3.85
1434 2086 4.812476 CGGTCGAAGATGCCGGCA 62.812 66.667 34.80 34.80 40.67 5.69
1593 2260 0.458025 CGTAGTCGAAGAACCAGCCC 60.458 60.000 0.00 0.00 39.69 5.19
1666 2333 2.063266 GTTGTTGTAGCCGACGATGAA 58.937 47.619 0.00 0.00 0.00 2.57
1668 2335 0.365523 CGTTGTTGTAGCCGACGATG 59.634 55.000 0.00 0.00 41.23 3.84
1900 2567 1.686110 CCGGGAGCTTCTGTAGGGT 60.686 63.158 0.00 0.00 0.00 4.34
1995 2662 0.601057 TGAACAGGCAGATCGACGAA 59.399 50.000 0.00 0.00 0.00 3.85
2085 2764 3.077556 AGCTCCACCACCCTAGCG 61.078 66.667 0.00 0.00 39.94 4.26
2170 2849 2.354259 GTGAAGGTCCTTGATGAGCAG 58.646 52.381 9.46 0.00 35.23 4.24
2241 2920 0.594796 CACGGCAAAACTGCTTGTCC 60.595 55.000 0.00 0.00 34.73 4.02
2262 2941 2.811317 GTCTTGCAGCCGTCGAGG 60.811 66.667 0.00 0.00 44.97 4.63
2289 2968 0.309302 CAGGCCAGTCGATCTCTACG 59.691 60.000 5.01 0.00 0.00 3.51
2292 2971 2.430610 GGCAGGCCAGTCGATCTCT 61.431 63.158 5.01 0.00 35.81 3.10
2318 2997 0.817634 CTTTCCACCAAGGCGACACA 60.818 55.000 0.00 0.00 37.29 3.72
2464 3146 6.390721 TCGAAGTCCTAATTCTCAAGAACAG 58.609 40.000 0.00 0.00 36.80 3.16
2525 3237 9.781633 TTCACCATGATTGAGAATTCAAATTTT 57.218 25.926 8.44 0.00 45.82 1.82
2539 3251 8.712285 ATTTTATCTTTGCTTCACCATGATTG 57.288 30.769 0.00 0.00 0.00 2.67
2575 3287 7.931578 TTTGACCGATTGTCCAGTTTATAAT 57.068 32.000 0.00 0.00 43.78 1.28
2583 3295 2.778299 TCCTTTTGACCGATTGTCCAG 58.222 47.619 0.00 0.00 43.78 3.86
2593 3305 9.087424 GCTTGAATATGTTTTATCCTTTTGACC 57.913 33.333 0.00 0.00 0.00 4.02
2598 3310 9.034800 TCCAAGCTTGAATATGTTTTATCCTTT 57.965 29.630 28.05 0.00 0.00 3.11
2601 3313 8.225603 TCTCCAAGCTTGAATATGTTTTATCC 57.774 34.615 28.05 0.00 0.00 2.59
2697 3410 9.877178 TTCATGTTTTATTGTTACCAAAAGTGT 57.123 25.926 0.00 0.00 33.44 3.55
2728 3441 5.424895 AGCAAGTGATAGAGGAAGAGAACAT 59.575 40.000 0.00 0.00 0.00 2.71
2789 3505 3.132925 GGCAAAAGAAGTGTGGTACGTA 58.867 45.455 0.00 0.00 0.00 3.57
2790 3506 1.944709 GGCAAAAGAAGTGTGGTACGT 59.055 47.619 0.00 0.00 0.00 3.57
2791 3507 1.265905 GGGCAAAAGAAGTGTGGTACG 59.734 52.381 0.00 0.00 0.00 3.67
2792 3508 1.611977 GGGGCAAAAGAAGTGTGGTAC 59.388 52.381 0.00 0.00 0.00 3.34
2870 3586 4.899239 GTCCGAGCTGATGCCCCG 62.899 72.222 0.00 0.00 40.80 5.73
2898 3614 6.382282 TGATCATAGCTATGAGGGTATGGAAG 59.618 42.308 33.44 7.41 45.01 3.46
2912 3628 7.011763 GCAAGAACAAGACAATGATCATAGCTA 59.988 37.037 9.04 0.00 0.00 3.32
2914 3630 5.970023 GCAAGAACAAGACAATGATCATAGC 59.030 40.000 9.04 1.51 0.00 2.97
3017 3734 4.702274 ACATGGCTTGCCACCCCC 62.702 66.667 17.22 0.00 0.00 5.40
3018 3735 2.216331 AAACATGGCTTGCCACCCC 61.216 57.895 17.22 0.00 0.00 4.95
3019 3736 1.004679 CAAACATGGCTTGCCACCC 60.005 57.895 17.22 0.00 0.00 4.61
3020 3737 0.609662 ATCAAACATGGCTTGCCACC 59.390 50.000 17.22 0.00 0.00 4.61
3021 3738 2.460757 AATCAAACATGGCTTGCCAC 57.539 45.000 17.22 0.00 0.00 5.01
3022 3739 3.488778 AAAATCAAACATGGCTTGCCA 57.511 38.095 17.19 17.19 0.00 4.92
3023 3740 6.316319 CAATTAAAATCAAACATGGCTTGCC 58.684 36.000 4.43 4.43 0.00 4.52
3024 3741 6.316319 CCAATTAAAATCAAACATGGCTTGC 58.684 36.000 0.00 0.00 0.00 4.01
3025 3742 6.654161 TCCCAATTAAAATCAAACATGGCTTG 59.346 34.615 0.00 0.19 0.00 4.01
3026 3743 6.777782 TCCCAATTAAAATCAAACATGGCTT 58.222 32.000 0.00 0.00 0.00 4.35
3027 3744 6.371595 TCCCAATTAAAATCAAACATGGCT 57.628 33.333 0.00 0.00 0.00 4.75
3028 3745 7.049754 AGATCCCAATTAAAATCAAACATGGC 58.950 34.615 0.00 0.00 0.00 4.40
3029 3746 8.885722 CAAGATCCCAATTAAAATCAAACATGG 58.114 33.333 0.00 0.00 0.00 3.66
3030 3747 8.885722 CCAAGATCCCAATTAAAATCAAACATG 58.114 33.333 0.00 0.00 0.00 3.21
3031 3748 7.553760 GCCAAGATCCCAATTAAAATCAAACAT 59.446 33.333 0.00 0.00 0.00 2.71
3032 3749 6.878389 GCCAAGATCCCAATTAAAATCAAACA 59.122 34.615 0.00 0.00 0.00 2.83
3033 3750 7.105588 AGCCAAGATCCCAATTAAAATCAAAC 58.894 34.615 0.00 0.00 0.00 2.93
3034 3751 7.256494 AGCCAAGATCCCAATTAAAATCAAA 57.744 32.000 0.00 0.00 0.00 2.69
3035 3752 6.872585 AGCCAAGATCCCAATTAAAATCAA 57.127 33.333 0.00 0.00 0.00 2.57
3036 3753 7.069826 CCTTAGCCAAGATCCCAATTAAAATCA 59.930 37.037 0.00 0.00 33.20 2.57
3037 3754 7.069950 ACCTTAGCCAAGATCCCAATTAAAATC 59.930 37.037 0.00 0.00 33.20 2.17
3038 3755 6.902974 ACCTTAGCCAAGATCCCAATTAAAAT 59.097 34.615 0.00 0.00 33.20 1.82
3039 3756 6.260663 ACCTTAGCCAAGATCCCAATTAAAA 58.739 36.000 0.00 0.00 33.20 1.52
3040 3757 5.837829 ACCTTAGCCAAGATCCCAATTAAA 58.162 37.500 0.00 0.00 33.20 1.52
3041 3758 5.466127 ACCTTAGCCAAGATCCCAATTAA 57.534 39.130 0.00 0.00 33.20 1.40
3042 3759 6.069323 TGTTACCTTAGCCAAGATCCCAATTA 60.069 38.462 0.00 0.00 33.20 1.40
3043 3760 5.201243 GTTACCTTAGCCAAGATCCCAATT 58.799 41.667 0.00 0.00 33.20 2.32
3044 3761 4.229582 TGTTACCTTAGCCAAGATCCCAAT 59.770 41.667 0.00 0.00 33.20 3.16
3045 3762 3.589735 TGTTACCTTAGCCAAGATCCCAA 59.410 43.478 0.00 0.00 33.20 4.12
3046 3763 3.186283 TGTTACCTTAGCCAAGATCCCA 58.814 45.455 0.00 0.00 33.20 4.37
3047 3764 3.926058 TGTTACCTTAGCCAAGATCCC 57.074 47.619 0.00 0.00 33.20 3.85
3048 3765 5.652452 ACAAATGTTACCTTAGCCAAGATCC 59.348 40.000 0.00 0.00 33.20 3.36
3049 3766 6.456988 CGACAAATGTTACCTTAGCCAAGATC 60.457 42.308 0.00 0.00 33.20 2.75
3050 3767 5.354234 CGACAAATGTTACCTTAGCCAAGAT 59.646 40.000 0.00 0.00 33.20 2.40
3051 3768 4.693566 CGACAAATGTTACCTTAGCCAAGA 59.306 41.667 0.00 0.00 33.20 3.02
3052 3769 4.454504 ACGACAAATGTTACCTTAGCCAAG 59.545 41.667 0.00 0.00 0.00 3.61
3053 3770 4.214545 CACGACAAATGTTACCTTAGCCAA 59.785 41.667 0.00 0.00 0.00 4.52
3054 3771 3.749088 CACGACAAATGTTACCTTAGCCA 59.251 43.478 0.00 0.00 0.00 4.75
3055 3772 3.749609 ACACGACAAATGTTACCTTAGCC 59.250 43.478 0.00 0.00 0.00 3.93
3056 3773 4.449743 TGACACGACAAATGTTACCTTAGC 59.550 41.667 0.00 0.00 0.00 3.09
3057 3774 5.389516 GCTGACACGACAAATGTTACCTTAG 60.390 44.000 0.00 0.00 0.00 2.18
3058 3775 4.449743 GCTGACACGACAAATGTTACCTTA 59.550 41.667 0.00 0.00 0.00 2.69
3059 3776 3.250040 GCTGACACGACAAATGTTACCTT 59.750 43.478 0.00 0.00 0.00 3.50
3060 3777 2.806244 GCTGACACGACAAATGTTACCT 59.194 45.455 0.00 0.00 0.00 3.08
3088 4257 5.932303 ACAAACTTCTACACGCTCAACATAT 59.068 36.000 0.00 0.00 0.00 1.78
3089 4258 5.294356 ACAAACTTCTACACGCTCAACATA 58.706 37.500 0.00 0.00 0.00 2.29
3090 4259 4.127171 ACAAACTTCTACACGCTCAACAT 58.873 39.130 0.00 0.00 0.00 2.71
3091 4260 3.527533 ACAAACTTCTACACGCTCAACA 58.472 40.909 0.00 0.00 0.00 3.33
3121 4290 3.888323 TGACATTGTGCATTGGTTGTACT 59.112 39.130 0.00 0.00 41.13 2.73
3304 4473 0.108329 AAACTATGCCGACGGTCTGG 60.108 55.000 16.73 10.15 0.00 3.86
3357 4526 2.055310 CTATGCCGACAGCCGTACGA 62.055 60.000 18.76 0.00 42.71 3.43
3392 4561 4.734398 TGTTGCTGTCAGGTGAAAATTT 57.266 36.364 1.14 0.00 0.00 1.82
3490 4659 4.038763 ACCGTCGGCATAGATTTTCATCTA 59.961 41.667 12.28 0.00 44.61 1.98
3491 4660 3.181465 ACCGTCGGCATAGATTTTCATCT 60.181 43.478 12.28 0.00 42.83 2.90
3597 4766 0.933097 CTATGACACGTGGCAGCATC 59.067 55.000 30.46 12.35 35.91 3.91
3598 4767 1.091771 GCTATGACACGTGGCAGCAT 61.092 55.000 30.46 21.72 35.91 3.79


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

AutoCloner maintained by Alex Coulton.