Multiple sequence alignment - TraesCS3B01G516900

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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 TraesCS3B01G516900 chr3B 100.000 4957 0 0 1 4957 760044274 760049230 0.000000e+00 9154.0
1 TraesCS3B01G516900 chr3B 84.817 764 89 12 2429 3192 759807306 759808042 0.000000e+00 743.0
2 TraesCS3B01G516900 chr3B 84.570 337 36 5 1331 1663 760445486 760445162 2.230000e-83 320.0
3 TraesCS3B01G516900 chr3B 94.495 109 4 2 4777 4884 764248078 764247971 3.070000e-37 167.0
4 TraesCS3B01G516900 chr3B 91.304 115 6 4 4777 4889 771101531 771101643 2.390000e-33 154.0
5 TraesCS3B01G516900 chr3B 93.878 98 3 2 4777 4872 828229358 828229262 1.440000e-30 145.0
6 TraesCS3B01G516900 chr3B 100.000 36 0 0 4922 4957 764247914 764247879 3.200000e-07 67.6
7 TraesCS3B01G516900 chr3B 100.000 36 0 0 4922 4957 771101691 771101726 3.200000e-07 67.6
8 TraesCS3B01G516900 chr3A 93.486 3408 194 16 420 3817 704684352 704687741 0.000000e+00 5038.0
9 TraesCS3B01G516900 chr3A 92.339 3446 190 29 413 3846 704588175 704584792 0.000000e+00 4833.0
10 TraesCS3B01G516900 chr3A 94.834 2865 132 6 986 3843 704766218 704769073 0.000000e+00 4457.0
11 TraesCS3B01G516900 chr3A 93.429 624 20 7 4334 4957 704771078 704771680 0.000000e+00 905.0
12 TraesCS3B01G516900 chr3A 91.074 661 26 11 4212 4872 704584151 704583524 0.000000e+00 863.0
13 TraesCS3B01G516900 chr3A 90.796 402 23 6 3893 4282 704688026 704688425 4.400000e-145 525.0
14 TraesCS3B01G516900 chr3A 93.827 324 15 4 3893 4214 704584616 704584296 2.680000e-132 483.0
15 TraesCS3B01G516900 chr3A 87.441 422 33 10 1 404 704683748 704684167 7.510000e-128 468.0
16 TraesCS3B01G516900 chr3A 92.500 280 18 1 1 280 704590764 704590488 1.000000e-106 398.0
17 TraesCS3B01G516900 chr3A 95.735 211 4 3 4055 4261 704770862 704771071 7.950000e-88 335.0
18 TraesCS3B01G516900 chr3A 100.000 31 0 0 4927 4957 704583492 704583462 1.930000e-04 58.4
19 TraesCS3B01G516900 chrUn 95.005 2943 121 11 910 3846 33131063 33128141 0.000000e+00 4597.0
20 TraesCS3B01G516900 chrUn 86.140 1443 151 17 1025 2453 132108132 132109539 0.000000e+00 1511.0
21 TraesCS3B01G516900 chrUn 81.579 1672 221 44 1867 3515 33174644 33173037 0.000000e+00 1301.0
22 TraesCS3B01G516900 chrUn 95.298 638 19 10 4251 4884 33127621 33126991 0.000000e+00 1002.0
23 TraesCS3B01G516900 chrUn 85.236 806 106 11 2461 3259 132109625 132110424 0.000000e+00 817.0
24 TraesCS3B01G516900 chrUn 84.540 815 103 7 1186 1981 132088895 132089705 0.000000e+00 785.0
25 TraesCS3B01G516900 chrUn 78.475 1115 197 27 1158 2252 33276109 33275018 0.000000e+00 689.0
26 TraesCS3B01G516900 chrUn 85.784 619 73 8 2600 3218 33172999 33172396 4.180000e-180 641.0
27 TraesCS3B01G516900 chrUn 86.237 574 71 4 3247 3819 132112018 132112584 2.540000e-172 616.0
28 TraesCS3B01G516900 chrUn 84.115 661 76 6 1966 2623 132091411 132092045 3.280000e-171 612.0
29 TraesCS3B01G516900 chrUn 94.241 382 17 3 3844 4223 33127993 33127615 3.330000e-161 579.0
30 TraesCS3B01G516900 chrUn 86.866 434 52 4 3128 3560 132100681 132101110 9.650000e-132 481.0
31 TraesCS3B01G516900 chrUn 83.529 510 80 3 1743 2252 431581707 431581202 1.610000e-129 473.0
32 TraesCS3B01G516900 chrUn 82.276 536 75 11 2158 2685 33275019 33274496 3.520000e-121 446.0
33 TraesCS3B01G516900 chrUn 89.189 185 18 1 1323 1505 132203938 132204122 3.860000e-56 230.0
34 TraesCS3B01G516900 chrUn 92.949 156 11 0 2630 2785 132099405 132099560 1.390000e-55 228.0
35 TraesCS3B01G516900 chrUn 100.000 36 0 0 4922 4957 33126927 33126892 3.200000e-07 67.6
36 TraesCS3B01G516900 chr4B 94.690 113 4 2 4777 4889 593666424 593666534 1.830000e-39 174.0
37 TraesCS3B01G516900 chr7B 93.805 113 3 3 4777 4889 214868665 214868773 3.070000e-37 167.0
38 TraesCS3B01G516900 chr7B 97.917 96 1 1 4777 4872 566538524 566538618 1.100000e-36 165.0
39 TraesCS3B01G516900 chr7B 96.875 96 2 1 4777 4872 647529716 647529810 5.140000e-35 159.0
40 TraesCS3B01G516900 chr7B 100.000 36 0 0 4922 4957 647529866 647529901 3.200000e-07 67.6
41 TraesCS3B01G516900 chr6B 95.789 95 3 1 4777 4871 250003889 250003982 8.590000e-33 152.0
42 TraesCS3B01G516900 chr6B 95.402 87 3 1 4777 4863 178836400 178836315 2.410000e-28 137.0
43 TraesCS3B01G516900 chr2B 100.000 36 0 0 4922 4957 290277258 290277293 3.200000e-07 67.6


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 TraesCS3B01G516900 chr3B 760044274 760049230 4956 False 9154.000000 9154 100.000000 1 4957 1 chr3B.!!$F2 4956
1 TraesCS3B01G516900 chr3B 759807306 759808042 736 False 743.000000 743 84.817000 2429 3192 1 chr3B.!!$F1 763
2 TraesCS3B01G516900 chr3A 704683748 704688425 4677 False 2010.333333 5038 90.574333 1 4282 3 chr3A.!!$F1 4281
3 TraesCS3B01G516900 chr3A 704766218 704771680 5462 False 1899.000000 4457 94.666000 986 4957 3 chr3A.!!$F2 3971
4 TraesCS3B01G516900 chr3A 704583462 704590764 7302 True 1327.080000 4833 93.948000 1 4957 5 chr3A.!!$R1 4956
5 TraesCS3B01G516900 chrUn 33126892 33131063 4171 True 1561.400000 4597 96.136000 910 4957 4 chrUn.!!$R2 4047
6 TraesCS3B01G516900 chrUn 132108132 132112584 4452 False 981.333333 1511 85.871000 1025 3819 3 chrUn.!!$F4 2794
7 TraesCS3B01G516900 chrUn 33172396 33174644 2248 True 971.000000 1301 83.681500 1867 3515 2 chrUn.!!$R3 1648
8 TraesCS3B01G516900 chrUn 132088895 132092045 3150 False 698.500000 785 84.327500 1186 2623 2 chrUn.!!$F2 1437
9 TraesCS3B01G516900 chrUn 33274496 33276109 1613 True 567.500000 689 80.375500 1158 2685 2 chrUn.!!$R4 1527
10 TraesCS3B01G516900 chrUn 431581202 431581707 505 True 473.000000 473 83.529000 1743 2252 1 chrUn.!!$R1 509
11 TraesCS3B01G516900 chrUn 132099405 132101110 1705 False 354.500000 481 89.907500 2630 3560 2 chrUn.!!$F3 930

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
373 2394 0.029834 CCCTCTTATTGCGCACATGC 59.970 55.0 11.12 0.00 37.78 4.06 F
1462 3695 0.109458 TGCTCGATACTTTGACGCGT 60.109 50.0 13.85 13.85 0.00 6.01 F
2847 7442 0.165295 CACTGCATGTCACTGAAGCG 59.835 55.0 0.00 0.00 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 4123 0.176680 AAAGACCATCTGCGCGAGAT 59.823 50.0 12.10 12.79 42.7 2.75 R
3045 8038 1.167851 ACACATTTCATCAGGCACGG 58.832 50.0 0.00 0.00 0.0 4.94 R
4135 12764 0.179054 GAGGTAATGAAGGGCGTCCC 60.179 60.0 0.08 4.26 45.9 4.46 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
26 27 1.004436 GGGGAGATGGGTGGGTTTAA 58.996 55.000 0.00 0.00 0.00 1.52
33 34 5.023452 GAGATGGGTGGGTTTAAAGGAATT 58.977 41.667 0.00 0.00 0.00 2.17
39 40 5.478407 GGTGGGTTTAAAGGAATTGACATG 58.522 41.667 0.00 0.00 0.00 3.21
60 61 2.483745 CGCGGCAGACGTAGAAGA 59.516 61.111 0.00 0.00 46.52 2.87
68 69 2.732597 GCAGACGTAGAAGAGCGACAAT 60.733 50.000 0.00 0.00 0.00 2.71
94 101 0.341258 AAGATGGCAGGAGGAGGAGA 59.659 55.000 0.00 0.00 0.00 3.71
95 102 0.567182 AGATGGCAGGAGGAGGAGAT 59.433 55.000 0.00 0.00 0.00 2.75
171 178 5.164606 TCGACTAGTGCCAAAAAGAAAAC 57.835 39.130 0.00 0.00 0.00 2.43
202 209 2.639347 CCACATATAGCCAGGGATGTCA 59.361 50.000 0.00 0.00 30.13 3.58
327 2336 7.772332 AGCTATTTTTCCATTCAGTACTACG 57.228 36.000 0.00 0.00 0.00 3.51
340 2353 2.114825 GTACTACGAGCGGTGCATAAC 58.885 52.381 0.00 0.00 0.00 1.89
345 2358 1.447140 GAGCGGTGCATAACGGTGA 60.447 57.895 15.82 0.00 41.25 4.02
373 2394 0.029834 CCCTCTTATTGCGCACATGC 59.970 55.000 11.12 0.00 37.78 4.06
410 2431 2.736197 TGCCTGAATGCACTGCTTT 58.264 47.368 1.98 1.94 36.04 3.51
411 2432 0.315886 TGCCTGAATGCACTGCTTTG 59.684 50.000 6.87 0.00 36.04 2.77
508 2708 4.598062 CCTTTCCGAGACAACTTGAAAAC 58.402 43.478 0.00 0.00 31.72 2.43
515 2715 6.540914 TCCGAGACAACTTGAAAACAACTAAT 59.459 34.615 0.00 0.00 0.00 1.73
543 2744 2.428187 TGGAACAATCGCCACGGT 59.572 55.556 0.00 0.00 31.92 4.83
555 2757 1.734137 CCACGGTGAGGGTCTATCG 59.266 63.158 10.28 0.00 0.00 2.92
559 2761 2.100916 CACGGTGAGGGTCTATCGAAAT 59.899 50.000 0.74 0.00 0.00 2.17
560 2762 3.317149 CACGGTGAGGGTCTATCGAAATA 59.683 47.826 0.74 0.00 0.00 1.40
563 2765 5.162075 CGGTGAGGGTCTATCGAAATATTC 58.838 45.833 0.00 0.00 0.00 1.75
587 2791 1.346062 TTCTGAAGTGAGCTGCTCCT 58.654 50.000 25.61 18.63 0.00 3.69
590 2794 1.824230 CTGAAGTGAGCTGCTCCTAGT 59.176 52.381 25.61 9.19 0.00 2.57
618 2823 1.306141 AGCCCTCCCTGATCGTTCA 60.306 57.895 0.00 0.00 0.00 3.18
636 2841 1.151810 AGCAGGGGAAGGGACAAGA 60.152 57.895 0.00 0.00 0.00 3.02
798 3006 6.162777 GCCACTTTATGAAAAATGCCAAGTA 58.837 36.000 0.00 0.00 0.00 2.24
868 3076 2.509336 GTGCGACGGTGATGGGAG 60.509 66.667 0.00 0.00 0.00 4.30
917 3125 5.705609 AACGTCAGCCAAATAACATTTCT 57.294 34.783 0.00 0.00 0.00 2.52
928 3136 7.172361 GCCAAATAACATTTCTGCCTAACAAAA 59.828 33.333 0.00 0.00 0.00 2.44
929 3137 9.050601 CCAAATAACATTTCTGCCTAACAAAAA 57.949 29.630 0.00 0.00 0.00 1.94
954 3162 4.000988 GTGTGAGCGGAAGGATAGAAAAA 58.999 43.478 0.00 0.00 0.00 1.94
958 3167 2.614057 AGCGGAAGGATAGAAAAATGCG 59.386 45.455 0.00 0.00 0.00 4.73
966 3175 7.226720 GGAAGGATAGAAAAATGCGACTCATTA 59.773 37.037 0.00 0.00 44.23 1.90
971 3180 9.387123 GATAGAAAAATGCGACTCATTATTTCC 57.613 33.333 14.91 4.92 44.23 3.13
974 3183 5.409643 AAATGCGACTCATTATTTCCTCG 57.590 39.130 0.00 0.00 44.23 4.63
1012 3221 4.016706 AGTTTGGGACCCTCGCCG 62.017 66.667 13.00 0.00 0.00 6.46
1034 3243 3.236003 AACTCCGTGGAGAACCGCC 62.236 63.158 22.36 0.00 44.53 6.13
1035 3244 4.796231 CTCCGTGGAGAACCGCCG 62.796 72.222 10.50 0.00 44.53 6.46
1137 3348 3.072468 CCGCACTTCCTACCCGGA 61.072 66.667 0.73 0.00 41.34 5.14
1432 3665 3.214123 CGCCCGGACGTGATCCTA 61.214 66.667 0.73 0.00 46.69 2.94
1451 3684 2.011741 ATGGAACGCCGTGCTCGATA 62.012 55.000 10.21 0.00 39.71 2.92
1454 3687 0.801067 GAACGCCGTGCTCGATACTT 60.801 55.000 10.21 0.00 39.71 2.24
1462 3695 0.109458 TGCTCGATACTTTGACGCGT 60.109 50.000 13.85 13.85 0.00 6.01
1507 3740 4.776322 CTGTTCCGGCGGATGGCA 62.776 66.667 31.59 25.16 46.16 4.92
1710 3969 0.534203 TCGGAGGCTGTGTTTTGGAC 60.534 55.000 0.00 0.00 0.00 4.02
1864 4123 3.071457 TGTCTTCTGTCCTTTCAGCATCA 59.929 43.478 0.00 0.00 35.63 3.07
1932 4191 2.513753 TGTGGTCAAGCTTGGTTATGG 58.486 47.619 25.73 0.00 0.00 2.74
2473 6652 9.726438 ACTTTGACTACTATAATTGCTGTTCTT 57.274 29.630 0.00 0.00 0.00 2.52
2737 6916 1.795162 GCCTTTCGGTTCATGCATTCG 60.795 52.381 0.00 0.00 0.00 3.34
2809 7404 4.082571 GCATGTGGAACTCTTAAACTGCAT 60.083 41.667 0.00 0.00 38.04 3.96
2847 7442 0.165295 CACTGCATGTCACTGAAGCG 59.835 55.000 0.00 0.00 0.00 4.68
2970 7896 6.429385 GGAGATATAAATTTGTGCTCCTGGAG 59.571 42.308 19.55 19.55 37.91 3.86
3045 8038 7.222611 GCAGTTCTATCAGAAGATTGAAGACTC 59.777 40.741 3.29 0.00 43.34 3.36
3259 9889 4.281435 TCCTCTGCTGAAAAATCAATTGCA 59.719 37.500 0.00 0.00 0.00 4.08
3468 10098 6.552008 AGAAATTTGGGATTACTCCAACAGA 58.448 36.000 0.00 0.00 43.20 3.41
3755 10704 6.811665 GGTTAGGGACATTTTGCAAGATAAAC 59.188 38.462 1.59 1.83 0.00 2.01
3876 11054 1.464608 ACGCTGTTTGTGGATTGATCG 59.535 47.619 0.00 0.00 0.00 3.69
3887 11082 4.081697 TGTGGATTGATCGCTCTTGAACTA 60.082 41.667 0.00 0.00 0.00 2.24
3888 11083 4.870426 GTGGATTGATCGCTCTTGAACTAA 59.130 41.667 0.00 0.00 0.00 2.24
3889 11084 5.525378 GTGGATTGATCGCTCTTGAACTAAT 59.475 40.000 0.00 0.00 0.00 1.73
3890 11085 6.037610 GTGGATTGATCGCTCTTGAACTAATT 59.962 38.462 0.00 0.00 0.00 1.40
3891 11086 6.599244 TGGATTGATCGCTCTTGAACTAATTT 59.401 34.615 0.00 0.00 0.00 1.82
3892 11087 7.121168 TGGATTGATCGCTCTTGAACTAATTTT 59.879 33.333 0.00 0.00 0.00 1.82
3893 11088 7.641802 GGATTGATCGCTCTTGAACTAATTTTC 59.358 37.037 0.00 0.00 0.00 2.29
3894 11089 7.433708 TTGATCGCTCTTGAACTAATTTTCA 57.566 32.000 0.00 0.00 33.55 2.69
3895 11090 7.615582 TGATCGCTCTTGAACTAATTTTCAT 57.384 32.000 0.00 0.00 35.42 2.57
3896 11091 8.044060 TGATCGCTCTTGAACTAATTTTCATT 57.956 30.769 0.00 0.00 35.42 2.57
3897 11092 8.177663 TGATCGCTCTTGAACTAATTTTCATTC 58.822 33.333 0.00 0.00 35.42 2.67
3898 11093 7.672983 TCGCTCTTGAACTAATTTTCATTCT 57.327 32.000 0.00 0.00 35.42 2.40
3899 11094 8.099364 TCGCTCTTGAACTAATTTTCATTCTT 57.901 30.769 0.00 0.00 35.42 2.52
3900 11095 8.017373 TCGCTCTTGAACTAATTTTCATTCTTG 58.983 33.333 0.00 0.00 35.42 3.02
3901 11096 8.017373 CGCTCTTGAACTAATTTTCATTCTTGA 58.983 33.333 0.00 0.00 35.42 3.02
3902 11097 9.683069 GCTCTTGAACTAATTTTCATTCTTGAA 57.317 29.630 0.00 0.00 40.09 2.69
3972 11185 2.649531 ACTCCAATGGTTTTCGTCCA 57.350 45.000 0.00 0.00 39.41 4.02
3983 11196 6.767524 TGGTTTTCGTCCATTAAGCAATAT 57.232 33.333 0.00 0.00 0.00 1.28
3984 11197 7.867305 TGGTTTTCGTCCATTAAGCAATATA 57.133 32.000 0.00 0.00 0.00 0.86
4027 11243 1.945394 GAGGGCAAGCTGTGATGTATG 59.055 52.381 0.00 0.00 0.00 2.39
4067 12692 3.754965 TCTGAGCCAAACAAGCTTATGT 58.245 40.909 0.00 0.00 41.75 2.29
4120 12745 9.708222 GTATGTTAATGAGCTCAAGTGTTTATG 57.292 33.333 22.50 0.00 0.00 1.90
4122 12747 7.806690 TGTTAATGAGCTCAAGTGTTTATGTC 58.193 34.615 22.50 8.45 0.00 3.06
4123 12748 7.443879 TGTTAATGAGCTCAAGTGTTTATGTCA 59.556 33.333 22.50 10.58 0.00 3.58
4124 12749 8.454106 GTTAATGAGCTCAAGTGTTTATGTCAT 58.546 33.333 22.50 0.00 0.00 3.06
4127 12752 8.743085 ATGAGCTCAAGTGTTTATGTCATATT 57.257 30.769 22.50 0.00 0.00 1.28
4128 12753 9.836864 ATGAGCTCAAGTGTTTATGTCATATTA 57.163 29.630 22.50 0.00 0.00 0.98
4129 12754 9.665719 TGAGCTCAAGTGTTTATGTCATATTAA 57.334 29.630 15.67 0.00 0.00 1.40
4268 13044 3.694566 CCTGTTAACCAGCCACTTAATCC 59.305 47.826 2.48 0.00 40.06 3.01
4272 13048 6.727394 TGTTAACCAGCCACTTAATCCTATT 58.273 36.000 2.48 0.00 0.00 1.73
4337 13113 4.752101 GCGTAGAGGCAATCTTGTGATAAT 59.248 41.667 0.00 0.00 39.64 1.28
4587 13366 1.608590 CGAGAGCCAAGGAAAAGCAAA 59.391 47.619 0.00 0.00 0.00 3.68
4651 13430 2.352715 GCCAAAATTCGCAGTTTAGGCT 60.353 45.455 11.66 0.00 34.28 4.58
4674 13453 2.749621 GCATGCTACAGCTAGTTTTGGT 59.250 45.455 11.37 0.00 42.66 3.67
4816 13595 3.206150 ACAGCCATTAATCATCACCGTC 58.794 45.455 0.00 0.00 0.00 4.79
4862 13641 1.122227 GCTTGCCAGGATCTCTCTCT 58.878 55.000 0.00 0.00 0.00 3.10
4863 13642 1.069049 GCTTGCCAGGATCTCTCTCTC 59.931 57.143 0.00 0.00 0.00 3.20
4864 13643 2.669781 CTTGCCAGGATCTCTCTCTCT 58.330 52.381 0.00 0.00 0.00 3.10
4865 13644 2.363306 TGCCAGGATCTCTCTCTCTC 57.637 55.000 0.00 0.00 0.00 3.20
4866 13645 1.852309 TGCCAGGATCTCTCTCTCTCT 59.148 52.381 0.00 0.00 0.00 3.10
4867 13646 2.158623 TGCCAGGATCTCTCTCTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
4868 13647 2.107204 GCCAGGATCTCTCTCTCTCTCT 59.893 54.545 0.00 0.00 0.00 3.10
4869 13648 3.808618 GCCAGGATCTCTCTCTCTCTCTC 60.809 56.522 0.00 0.00 0.00 3.20
4870 13649 3.649981 CCAGGATCTCTCTCTCTCTCTCT 59.350 52.174 0.00 0.00 0.00 3.10
4871 13650 4.262808 CCAGGATCTCTCTCTCTCTCTCTC 60.263 54.167 0.00 0.00 0.00 3.20
4872 13651 3.576118 AGGATCTCTCTCTCTCTCTCTCG 59.424 52.174 0.00 0.00 0.00 4.04
4873 13652 3.306364 GGATCTCTCTCTCTCTCTCTCGG 60.306 56.522 0.00 0.00 0.00 4.63
4874 13653 2.747177 TCTCTCTCTCTCTCTCTCGGT 58.253 52.381 0.00 0.00 0.00 4.69
4875 13654 2.693591 TCTCTCTCTCTCTCTCTCGGTC 59.306 54.545 0.00 0.00 0.00 4.79
4876 13655 1.760613 TCTCTCTCTCTCTCTCGGTCC 59.239 57.143 0.00 0.00 0.00 4.46
4877 13656 1.762957 CTCTCTCTCTCTCTCGGTCCT 59.237 57.143 0.00 0.00 0.00 3.85
4878 13657 1.760613 TCTCTCTCTCTCTCGGTCCTC 59.239 57.143 0.00 0.00 0.00 3.71
4879 13658 1.762957 CTCTCTCTCTCTCGGTCCTCT 59.237 57.143 0.00 0.00 0.00 3.69
4880 13659 1.760613 TCTCTCTCTCTCGGTCCTCTC 59.239 57.143 0.00 0.00 0.00 3.20
4881 13660 1.762957 CTCTCTCTCTCGGTCCTCTCT 59.237 57.143 0.00 0.00 0.00 3.10
4882 13661 1.760613 TCTCTCTCTCGGTCCTCTCTC 59.239 57.143 0.00 0.00 0.00 3.20
4883 13662 1.762957 CTCTCTCTCGGTCCTCTCTCT 59.237 57.143 0.00 0.00 0.00 3.10
4884 13663 1.484653 TCTCTCTCGGTCCTCTCTCTG 59.515 57.143 0.00 0.00 0.00 3.35
4885 13664 0.544223 TCTCTCGGTCCTCTCTCTGG 59.456 60.000 0.00 0.00 0.00 3.86
4886 13665 0.544223 CTCTCGGTCCTCTCTCTGGA 59.456 60.000 0.00 0.00 0.00 3.86
4887 13666 0.544223 TCTCGGTCCTCTCTCTGGAG 59.456 60.000 0.00 0.00 40.73 3.86
4888 13667 0.254747 CTCGGTCCTCTCTCTGGAGT 59.745 60.000 0.00 0.00 40.29 3.85
4889 13668 0.034960 TCGGTCCTCTCTCTGGAGTG 60.035 60.000 0.00 0.00 40.29 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.322538 GCGGCCCATGTCAATTCCTT 61.323 55.000 0.00 0.00 0.00 3.36
55 56 6.214191 TCTTCTTCATATTGTCGCTCTTCT 57.786 37.500 0.00 0.00 0.00 2.85
60 61 3.812053 GCCATCTTCTTCATATTGTCGCT 59.188 43.478 0.00 0.00 0.00 4.93
68 69 3.645212 CTCCTCCTGCCATCTTCTTCATA 59.355 47.826 0.00 0.00 0.00 2.15
94 101 2.615227 GATGGCGTGCCTTCCTCCAT 62.615 60.000 12.84 0.00 39.99 3.41
95 102 3.329542 GATGGCGTGCCTTCCTCCA 62.330 63.158 12.84 0.00 35.10 3.86
128 135 7.230712 AGTCGAATTAATTTTCCAGGTTGTCTT 59.769 33.333 1.43 0.00 0.00 3.01
133 140 7.361799 GCACTAGTCGAATTAATTTTCCAGGTT 60.362 37.037 1.43 0.00 0.00 3.50
171 178 6.231211 CCTGGCTATATGTGGTTTACCTTAG 58.769 44.000 0.00 0.00 36.82 2.18
202 209 6.165700 AGAGTCATGGTTTTCTTTTTGCAT 57.834 33.333 0.00 0.00 0.00 3.96
252 265 6.259608 AGCTCATATTCCATTCTCAGTTTTCG 59.740 38.462 0.00 0.00 0.00 3.46
312 2321 1.674441 CCGCTCGTAGTACTGAATGGA 59.326 52.381 5.39 0.00 0.00 3.41
327 2336 0.810031 ATCACCGTTATGCACCGCTC 60.810 55.000 0.00 0.00 0.00 5.03
340 2353 0.541863 AGAGGGGCTTAACATCACCG 59.458 55.000 0.00 0.00 0.00 4.94
345 2358 3.214328 CGCAATAAGAGGGGCTTAACAT 58.786 45.455 0.00 0.00 42.10 2.71
373 2394 5.920273 CAGGCACAAACCATAACTTTTGTAG 59.080 40.000 0.00 0.00 42.67 2.74
475 2673 5.067273 TGTCTCGGAAAGGCTTCATTTAAA 58.933 37.500 0.00 0.00 32.75 1.52
476 2674 4.647611 TGTCTCGGAAAGGCTTCATTTAA 58.352 39.130 0.00 0.00 32.75 1.52
477 2675 4.280436 TGTCTCGGAAAGGCTTCATTTA 57.720 40.909 0.00 0.00 32.75 1.40
481 2679 1.416401 AGTTGTCTCGGAAAGGCTTCA 59.584 47.619 0.00 0.00 32.75 3.02
482 2680 2.171341 AGTTGTCTCGGAAAGGCTTC 57.829 50.000 0.00 0.00 0.00 3.86
483 2681 2.158813 TCAAGTTGTCTCGGAAAGGCTT 60.159 45.455 2.11 0.00 0.00 4.35
491 2691 4.616181 AGTTGTTTTCAAGTTGTCTCGG 57.384 40.909 2.11 0.00 40.13 4.63
532 2733 3.310860 GACCCTCACCGTGGCGATT 62.311 63.158 0.00 0.00 0.00 3.34
533 2734 2.849096 TAGACCCTCACCGTGGCGAT 62.849 60.000 0.00 0.00 0.00 4.58
573 2777 1.930251 TCACTAGGAGCAGCTCACTT 58.070 50.000 24.09 11.13 31.08 3.16
587 2791 1.480954 GGAGGGCTGATTCGTTCACTA 59.519 52.381 0.00 0.00 0.00 2.74
590 2794 0.909610 AGGGAGGGCTGATTCGTTCA 60.910 55.000 0.00 0.00 0.00 3.18
618 2823 1.151810 TCTTGTCCCTTCCCCTGCT 60.152 57.895 0.00 0.00 0.00 4.24
636 2841 1.152652 TGGACCATTGCGGGTTTGT 60.153 52.632 0.00 0.00 42.53 2.83
756 2961 4.883006 AGTGGCATTGCAGTTTTCATTTTT 59.117 33.333 11.39 0.00 0.00 1.94
761 2966 3.540314 AAAGTGGCATTGCAGTTTTCA 57.460 38.095 11.39 0.00 0.00 2.69
762 2967 5.229423 TCATAAAGTGGCATTGCAGTTTTC 58.771 37.500 11.39 0.00 0.00 2.29
764 2969 4.870123 TCATAAAGTGGCATTGCAGTTT 57.130 36.364 11.39 13.18 0.00 2.66
767 2972 6.539324 CATTTTTCATAAAGTGGCATTGCAG 58.461 36.000 11.39 0.00 29.96 4.41
768 2973 5.106634 GCATTTTTCATAAAGTGGCATTGCA 60.107 36.000 11.39 0.00 33.11 4.08
798 3006 9.904198 AAAGTAGCATGGCCATTTTATAAATTT 57.096 25.926 17.92 7.58 0.00 1.82
826 3034 5.733091 GCATCTTGACGCCATAGCATTTTTA 60.733 40.000 0.00 0.00 39.83 1.52
889 3097 0.598065 ATTTGGCTGACGTTTCCTGC 59.402 50.000 0.00 0.00 0.00 4.85
917 3125 4.367450 GCTCACACAATTTTTGTTAGGCA 58.633 39.130 0.52 0.00 43.23 4.75
928 3136 2.496899 ATCCTTCCGCTCACACAATT 57.503 45.000 0.00 0.00 0.00 2.32
929 3137 2.766263 TCTATCCTTCCGCTCACACAAT 59.234 45.455 0.00 0.00 0.00 2.71
930 3138 2.176045 TCTATCCTTCCGCTCACACAA 58.824 47.619 0.00 0.00 0.00 3.33
931 3139 1.847328 TCTATCCTTCCGCTCACACA 58.153 50.000 0.00 0.00 0.00 3.72
958 3167 3.810386 GGAAGGCGAGGAAATAATGAGTC 59.190 47.826 0.00 0.00 0.00 3.36
966 3175 1.177401 GCAAAGGAAGGCGAGGAAAT 58.823 50.000 0.00 0.00 0.00 2.17
974 3183 0.383949 TGTCAAACGCAAAGGAAGGC 59.616 50.000 0.00 0.00 0.00 4.35
1012 3221 0.320508 GGTTCTCCACGGAGTTCCAC 60.321 60.000 12.77 6.08 41.61 4.02
1137 3348 4.189231 GTGGAATAATGCTACGTGAAGGT 58.811 43.478 0.00 0.00 0.00 3.50
1219 3443 4.101448 ATGGAGCTGGCCCGTGTC 62.101 66.667 0.00 0.00 0.00 3.67
1432 3665 2.011741 TATCGAGCACGGCGTTCCAT 62.012 55.000 11.19 3.13 40.21 3.41
1451 3684 2.027625 GGCAGCTACGCGTCAAAGT 61.028 57.895 18.63 0.00 0.00 2.66
1522 3755 1.153168 CAGGGTGGCCGAATCGAAT 60.153 57.895 3.36 0.00 0.00 3.34
1710 3969 2.358125 TGTCCCAACACGGCATCG 60.358 61.111 0.00 0.00 43.02 3.84
1864 4123 0.176680 AAAGACCATCTGCGCGAGAT 59.823 50.000 12.10 12.79 42.70 2.75
2462 6641 3.428532 AGCATGAAGGAAGAACAGCAAT 58.571 40.909 0.00 0.00 0.00 3.56
2473 6652 2.259917 TCTGGACAAGAGCATGAAGGA 58.740 47.619 0.00 0.00 0.00 3.36
2737 6916 4.686839 GTCAGGATTTACTGGCAAAGAC 57.313 45.455 0.00 0.00 42.51 3.01
2809 7404 2.844348 GTGGATGGACTTTCCTAGGGAA 59.156 50.000 9.46 5.42 40.27 3.97
2926 7550 6.996180 TCTCCGGGACTATAAAAGATTGAT 57.004 37.500 0.00 0.00 0.00 2.57
2970 7896 3.691118 TGCAAAGCCAGAGATCATACAAC 59.309 43.478 0.00 0.00 0.00 3.32
3045 8038 1.167851 ACACATTTCATCAGGCACGG 58.832 50.000 0.00 0.00 0.00 4.94
3468 10098 1.933181 CGATGCATACATGGTGTTCGT 59.067 47.619 0.00 0.00 36.35 3.85
3595 10543 5.801531 TCTTGAGTTCAGCCTTGTTACTA 57.198 39.130 0.00 0.00 0.00 1.82
3755 10704 0.956633 CCATGGGGCTTCATCAATCG 59.043 55.000 2.85 0.00 0.00 3.34
3857 11035 1.791555 GCGATCAATCCACAAACAGCG 60.792 52.381 0.00 0.00 0.00 5.18
3876 11054 9.683069 TTCAAGAATGAAAATTAGTTCAAGAGC 57.317 29.630 0.00 0.00 42.47 4.09
3890 11085 9.598517 ACTTGCAAAATTAGTTCAAGAATGAAA 57.401 25.926 0.00 0.00 46.66 2.69
3899 11094 9.891828 CAGTAACATACTTGCAAAATTAGTTCA 57.108 29.630 0.00 0.00 36.76 3.18
3900 11095 9.341899 CCAGTAACATACTTGCAAAATTAGTTC 57.658 33.333 0.00 0.00 36.76 3.01
3901 11096 8.303876 CCCAGTAACATACTTGCAAAATTAGTT 58.696 33.333 0.00 5.03 36.76 2.24
3902 11097 7.093945 CCCCAGTAACATACTTGCAAAATTAGT 60.094 37.037 0.00 0.00 36.76 2.24
3903 11098 7.122055 TCCCCAGTAACATACTTGCAAAATTAG 59.878 37.037 0.00 0.00 36.76 1.73
3904 11099 6.948886 TCCCCAGTAACATACTTGCAAAATTA 59.051 34.615 0.00 0.00 36.76 1.40
3960 11173 6.767524 ATATTGCTTAATGGACGAAAACCA 57.232 33.333 0.00 0.00 41.83 3.67
4001 11217 1.598130 ACAGCTTGCCCTCACGTTC 60.598 57.895 0.00 0.00 0.00 3.95
4006 11222 0.983467 TACATCACAGCTTGCCCTCA 59.017 50.000 0.00 0.00 0.00 3.86
4027 11243 7.650104 GGCTCAGAACAATAACAGAGTAGTATC 59.350 40.741 0.00 0.00 0.00 2.24
4044 11265 4.022849 ACATAAGCTTGTTTGGCTCAGAAC 60.023 41.667 9.86 0.00 39.30 3.01
4067 12692 6.370442 TCGTTTCAACTTTTCTTTCTCACAGA 59.630 34.615 0.00 0.00 0.00 3.41
4120 12745 5.286438 GGGCGTCCCAAAAATTAATATGAC 58.714 41.667 9.72 0.00 44.65 3.06
4135 12764 0.179054 GAGGTAATGAAGGGCGTCCC 60.179 60.000 0.08 4.26 45.90 4.46
4292 13068 4.692625 GCATACTGGATAGCGATGTCAATT 59.307 41.667 0.00 0.00 0.00 2.32
4293 13069 4.248859 GCATACTGGATAGCGATGTCAAT 58.751 43.478 0.00 0.00 0.00 2.57
4294 13070 3.653344 GCATACTGGATAGCGATGTCAA 58.347 45.455 0.00 0.00 0.00 3.18
4337 13113 1.340889 GCAGAATGGTGCAAAGTTGGA 59.659 47.619 0.00 0.00 43.41 3.53
4521 13300 7.501507 ACCTCTGGTTAGCATCTTCTGCAAA 62.502 44.000 0.00 0.00 43.43 3.68
4587 13366 5.278660 GCAGAATTTTCACACAGTTGGATCT 60.279 40.000 0.00 0.00 0.00 2.75
4651 13430 2.749076 CAAAACTAGCTGTAGCATGCCA 59.251 45.455 15.66 5.15 45.16 4.92
4674 13453 5.178096 TGTCTGCTCCTCCATTTATCAAA 57.822 39.130 0.00 0.00 0.00 2.69
4734 13513 1.812922 CATGCTCCGTGTCTGCCTC 60.813 63.158 0.00 0.00 0.00 4.70
4735 13514 2.267006 CATGCTCCGTGTCTGCCT 59.733 61.111 0.00 0.00 0.00 4.75
4809 13588 0.989602 TGTAGAGAGAGGGACGGTGA 59.010 55.000 0.00 0.00 0.00 4.02
4816 13595 1.754226 GCTGGAGTTGTAGAGAGAGGG 59.246 57.143 0.00 0.00 0.00 4.30
4862 13641 1.760613 GAGAGAGGACCGAGAGAGAGA 59.239 57.143 0.00 0.00 0.00 3.10
4863 13642 1.762957 AGAGAGAGGACCGAGAGAGAG 59.237 57.143 0.00 0.00 0.00 3.20
4864 13643 1.484653 CAGAGAGAGGACCGAGAGAGA 59.515 57.143 0.00 0.00 0.00 3.10
4865 13644 1.475034 CCAGAGAGAGGACCGAGAGAG 60.475 61.905 0.00 0.00 0.00 3.20
4866 13645 0.544223 CCAGAGAGAGGACCGAGAGA 59.456 60.000 0.00 0.00 0.00 3.10
4867 13646 0.544223 TCCAGAGAGAGGACCGAGAG 59.456 60.000 0.00 0.00 0.00 3.20
4868 13647 0.544223 CTCCAGAGAGAGGACCGAGA 59.456 60.000 0.00 0.00 43.39 4.04
4869 13648 0.254747 ACTCCAGAGAGAGGACCGAG 59.745 60.000 0.70 0.00 43.39 4.63
4870 13649 0.034960 CACTCCAGAGAGAGGACCGA 60.035 60.000 0.70 0.00 43.39 4.69
4871 13650 2.487918 CACTCCAGAGAGAGGACCG 58.512 63.158 0.70 0.00 43.39 4.79
4876 13655 3.137176 AGAGAGATCCACTCCAGAGAGAG 59.863 52.174 12.10 0.00 45.96 3.20
4877 13656 3.122480 AGAGAGATCCACTCCAGAGAGA 58.878 50.000 12.10 0.00 45.96 3.10
4878 13657 3.137176 AGAGAGAGATCCACTCCAGAGAG 59.863 52.174 12.10 0.00 45.96 3.20
4879 13658 3.122480 AGAGAGAGATCCACTCCAGAGA 58.878 50.000 12.10 0.00 45.96 3.10
4880 13659 3.137176 AGAGAGAGAGATCCACTCCAGAG 59.863 52.174 12.10 0.00 45.96 3.35
4881 13660 3.122480 AGAGAGAGAGATCCACTCCAGA 58.878 50.000 12.10 0.00 45.96 3.86
4882 13661 3.137176 AGAGAGAGAGAGATCCACTCCAG 59.863 52.174 12.10 0.00 45.96 3.86
4883 13662 3.122480 AGAGAGAGAGAGATCCACTCCA 58.878 50.000 12.10 0.00 45.96 3.86
4884 13663 3.392616 AGAGAGAGAGAGAGATCCACTCC 59.607 52.174 12.10 6.11 45.96 3.85
4885 13664 4.346418 AGAGAGAGAGAGAGAGATCCACTC 59.654 50.000 8.83 8.83 45.22 3.51
4886 13665 4.302067 AGAGAGAGAGAGAGAGATCCACT 58.698 47.826 0.00 0.00 0.00 4.00
4887 13666 4.346418 AGAGAGAGAGAGAGAGAGATCCAC 59.654 50.000 0.00 0.00 0.00 4.02
4888 13667 4.560739 AGAGAGAGAGAGAGAGAGATCCA 58.439 47.826 0.00 0.00 0.00 3.41
4889 13668 4.837860 AGAGAGAGAGAGAGAGAGAGATCC 59.162 50.000 0.00 0.00 0.00 3.36
4890 13669 5.774690 AGAGAGAGAGAGAGAGAGAGAGATC 59.225 48.000 0.00 0.00 0.00 2.75
4891 13670 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.