Multiple sequence alignment - TraesCS3D01G477100

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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 TraesCS3D01G477100 chr3D 100.000 3092 0 0 1 3092 577381193 577384284 0.000000e+00 5710.0
1 TraesCS3D01G477100 chr3D 84.785 1045 140 11 1155 2181 577414679 577413636 0.000000e+00 1031.0
2 TraesCS3D01G477100 chr3D 85.774 963 123 10 1161 2116 577410531 577409576 0.000000e+00 1007.0
3 TraesCS3D01G477100 chr3D 76.502 932 183 32 1156 2066 577790177 577789261 2.790000e-130 475.0
4 TraesCS3D01G477100 chr3A 94.154 1608 69 9 662 2255 712698619 712700215 0.000000e+00 2425.0
5 TraesCS3D01G477100 chr3A 85.495 979 129 10 1161 2132 712726833 712725861 0.000000e+00 1009.0
6 TraesCS3D01G477100 chr3A 82.852 1108 150 21 1021 2101 712729476 712728382 0.000000e+00 957.0
7 TraesCS3D01G477100 chr3A 76.496 936 176 40 1156 2066 713535484 713534568 1.300000e-128 470.0
8 TraesCS3D01G477100 chr3A 84.577 402 32 14 1 386 712696445 712696832 3.770000e-99 372.0
9 TraesCS3D01G477100 chr3A 85.338 266 31 8 1 261 670662602 670662864 5.080000e-68 268.0
10 TraesCS3D01G477100 chr3B 91.304 1403 91 16 723 2100 770556449 770557845 0.000000e+00 1886.0
11 TraesCS3D01G477100 chr3B 89.301 916 45 23 715 1587 769398121 769399026 0.000000e+00 1099.0
12 TraesCS3D01G477100 chr3B 84.615 962 138 7 1160 2116 770610057 770609101 0.000000e+00 948.0
13 TraesCS3D01G477100 chr3B 84.672 959 130 8 1157 2101 770653295 770652340 0.000000e+00 941.0
14 TraesCS3D01G477100 chr3B 84.008 494 68 8 238 724 769397352 769397841 6.040000e-127 464.0
15 TraesCS3D01G477100 chr3B 87.786 262 26 5 4 261 769397089 769397348 5.010000e-78 302.0
16 TraesCS3D01G477100 chr3B 85.821 268 27 10 4 263 370166854 370166590 1.090000e-69 274.0
17 TraesCS3D01G477100 chr3B 86.826 167 12 5 2089 2255 770558191 770558347 8.810000e-41 178.0
18 TraesCS3D01G477100 chr3B 76.230 122 23 6 470 588 415043581 415043699 3.330000e-05 60.2
19 TraesCS3D01G477100 chr1B 85.356 717 44 16 2392 3080 568773134 568773817 0.000000e+00 686.0
20 TraesCS3D01G477100 chr1B 84.502 271 30 11 1 263 235381346 235381612 1.100000e-64 257.0
21 TraesCS3D01G477100 chr7D 83.476 351 34 16 1 332 486550369 486550024 3.870000e-79 305.0
22 TraesCS3D01G477100 chr6A 86.415 265 29 7 1 261 425897060 425897321 1.820000e-72 283.0
23 TraesCS3D01G477100 chr6B 85.019 267 32 8 1 261 638476187 638475923 6.570000e-67 265.0
24 TraesCS3D01G477100 chr6B 90.698 43 2 1 560 602 5039527 5039487 4.310000e-04 56.5
25 TraesCS3D01G477100 chr6B 88.636 44 5 0 543 586 47300988 47300945 2.000000e-03 54.7
26 TraesCS3D01G477100 chr6B 88.636 44 5 0 543 586 47330733 47330690 2.000000e-03 54.7
27 TraesCS3D01G477100 chr6B 88.636 44 5 0 543 586 47367198 47367155 2.000000e-03 54.7
28 TraesCS3D01G477100 chr2B 85.019 267 28 10 4 263 554726759 554726498 8.500000e-66 261.0
29 TraesCS3D01G477100 chr6D 80.165 363 48 11 1 345 27413770 27413414 1.840000e-62 250.0
30 TraesCS3D01G477100 chr7A 77.251 422 63 11 2586 2976 466668633 466669052 1.870000e-52 217.0
31 TraesCS3D01G477100 chr7A 75.772 421 67 11 2586 2973 243263543 243263961 2.450000e-41 180.0
32 TraesCS3D01G477100 chr7A 75.650 423 69 11 2586 2976 244316711 244317131 2.450000e-41 180.0
33 TraesCS3D01G477100 chr5A 97.500 40 1 0 548 587 705536277 705536316 5.530000e-08 69.4
34 TraesCS3D01G477100 chr5A 92.683 41 3 0 546 586 623929600 623929560 3.330000e-05 60.2
35 TraesCS3D01G477100 chr5B 92.500 40 3 0 559 598 526221291 526221330 1.200000e-04 58.4


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 TraesCS3D01G477100 chr3D 577381193 577384284 3091 False 5710.000000 5710 100.000000 1 3092 1 chr3D.!!$F1 3091
1 TraesCS3D01G477100 chr3D 577409576 577414679 5103 True 1019.000000 1031 85.279500 1155 2181 2 chr3D.!!$R2 1026
2 TraesCS3D01G477100 chr3D 577789261 577790177 916 True 475.000000 475 76.502000 1156 2066 1 chr3D.!!$R1 910
3 TraesCS3D01G477100 chr3A 712696445 712700215 3770 False 1398.500000 2425 89.365500 1 2255 2 chr3A.!!$F2 2254
4 TraesCS3D01G477100 chr3A 712725861 712729476 3615 True 983.000000 1009 84.173500 1021 2132 2 chr3A.!!$R2 1111
5 TraesCS3D01G477100 chr3A 713534568 713535484 916 True 470.000000 470 76.496000 1156 2066 1 chr3A.!!$R1 910
6 TraesCS3D01G477100 chr3B 770556449 770558347 1898 False 1032.000000 1886 89.065000 723 2255 2 chr3B.!!$F3 1532
7 TraesCS3D01G477100 chr3B 770609101 770610057 956 True 948.000000 948 84.615000 1160 2116 1 chr3B.!!$R2 956
8 TraesCS3D01G477100 chr3B 770652340 770653295 955 True 941.000000 941 84.672000 1157 2101 1 chr3B.!!$R3 944
9 TraesCS3D01G477100 chr3B 769397089 769399026 1937 False 621.666667 1099 87.031667 4 1587 3 chr3B.!!$F2 1583
10 TraesCS3D01G477100 chr1B 568773134 568773817 683 False 686.000000 686 85.356000 2392 3080 1 chr1B.!!$F2 688

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
360 391 0.038744 AAGTGTGGAAGCCAGGGATG 59.961 55.0 0.00 0.00 32.34 3.51 F
365 396 0.255890 TGGAAGCCAGGGATGTAAGC 59.744 55.0 0.00 0.00 0.00 3.09 F
400 431 0.689055 ACTCTGCTGCTTGTGGATCA 59.311 50.0 0.00 0.00 0.00 2.92 F
884 2793 0.739813 AACTTCTTCGAATCCGGCCG 60.740 55.0 21.04 21.04 36.24 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 3662 0.034863 GATGTTGGGGTCGCCCTTTA 60.035 55.0 13.58 0.36 44.66 1.85 R
1719 3699 0.833409 TGGTGCTCTGCTGGAAGAGA 60.833 55.0 9.63 0.00 45.59 3.10 R
1785 3774 1.304509 TGTACACCGCGTCGACCATA 61.305 55.0 10.58 0.00 0.00 2.74 R
2650 9172 0.458543 TCAGGAAGAAGACGATGCGC 60.459 55.0 0.00 0.00 0.00 6.09 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
324 355 2.308722 ATGGGGGAGGACATGCGTT 61.309 57.895 0.00 0.00 0.00 4.84
360 391 0.038744 AAGTGTGGAAGCCAGGGATG 59.961 55.000 0.00 0.00 32.34 3.51
361 392 1.136329 AGTGTGGAAGCCAGGGATGT 61.136 55.000 0.00 0.00 32.34 3.06
365 396 0.255890 TGGAAGCCAGGGATGTAAGC 59.744 55.000 0.00 0.00 0.00 3.09
375 406 1.734465 GGGATGTAAGCAGATATGCGC 59.266 52.381 6.68 0.00 40.27 6.09
400 431 0.689055 ACTCTGCTGCTTGTGGATCA 59.311 50.000 0.00 0.00 0.00 2.92
413 2009 5.744300 GCTTGTGGATCAGTGGCTTATATCT 60.744 44.000 0.00 0.00 0.00 1.98
420 2016 6.070881 GGATCAGTGGCTTATATCTGTCTCAT 60.071 42.308 0.00 0.00 0.00 2.90
421 2017 6.737720 TCAGTGGCTTATATCTGTCTCATT 57.262 37.500 0.00 0.00 0.00 2.57
425 2021 7.714377 CAGTGGCTTATATCTGTCTCATTTCTT 59.286 37.037 0.00 0.00 0.00 2.52
519 2117 9.338622 ACATACTGGGTAATTTATAGCAACTTC 57.661 33.333 0.00 0.00 0.00 3.01
523 2121 6.964464 TGGGTAATTTATAGCAACTTCTGGA 58.036 36.000 0.00 0.00 0.00 3.86
524 2122 7.406916 TGGGTAATTTATAGCAACTTCTGGAA 58.593 34.615 0.00 0.00 0.00 3.53
607 2207 8.985805 AGATATATATGTGCGCATGTATGAATG 58.014 33.333 29.24 0.00 38.99 2.67
616 2216 3.818387 GCATGTATGAATGCCGATCTTG 58.182 45.455 0.00 0.00 45.93 3.02
801 2709 4.957164 GGCACCTGGCTACCTAAC 57.043 61.111 0.00 0.00 44.01 2.34
811 2719 3.244582 TGGCTACCTAACAGAGTGGAAA 58.755 45.455 0.00 0.00 0.00 3.13
815 2723 4.021368 GCTACCTAACAGAGTGGAAACAGA 60.021 45.833 0.00 0.00 44.46 3.41
881 2790 1.130561 GCCAAACTTCTTCGAATCCGG 59.869 52.381 0.00 0.00 36.24 5.14
882 2791 1.130561 CCAAACTTCTTCGAATCCGGC 59.869 52.381 0.00 0.00 36.24 6.13
883 2792 1.130561 CAAACTTCTTCGAATCCGGCC 59.869 52.381 0.00 0.00 36.24 6.13
884 2793 0.739813 AACTTCTTCGAATCCGGCCG 60.740 55.000 21.04 21.04 36.24 6.13
936 2856 2.431782 ACACTTGCATGCAAAAGGAGTT 59.568 40.909 31.37 14.16 35.33 3.01
959 2879 2.159014 AGTACGTGCTCCAACTGTTTCA 60.159 45.455 0.00 0.00 0.00 2.69
969 2889 4.832248 TCCAACTGTTTCATAGCTACCTG 58.168 43.478 0.00 0.00 0.00 4.00
970 2890 4.530553 TCCAACTGTTTCATAGCTACCTGA 59.469 41.667 0.00 0.00 0.00 3.86
971 2891 4.872691 CCAACTGTTTCATAGCTACCTGAG 59.127 45.833 0.00 0.00 0.00 3.35
972 2892 4.744795 ACTGTTTCATAGCTACCTGAGG 57.255 45.455 0.00 0.00 0.00 3.86
973 2893 4.353777 ACTGTTTCATAGCTACCTGAGGA 58.646 43.478 4.99 0.00 0.00 3.71
983 2907 2.930950 CTACCTGAGGAGAGGAGAGTG 58.069 57.143 4.99 0.00 36.51 3.51
1460 3415 2.355363 CAACGAAGTGGACGGCGA 60.355 61.111 16.62 0.00 45.00 5.54
1644 3621 2.033757 CAGCTGCTCAAGGCCACT 59.966 61.111 5.01 0.00 40.92 4.00
1677 3654 0.971959 TCGCCAACGTGTACCCCTAT 60.972 55.000 0.00 0.00 41.18 2.57
1685 3662 1.202604 CGTGTACCCCTATTTCGCCAT 60.203 52.381 0.00 0.00 0.00 4.40
1719 3699 1.032657 ACATCGACCTCAGCTACGCT 61.033 55.000 0.00 0.00 40.77 5.07
1785 3774 0.603569 ACATCAACCTCTTCGACGCT 59.396 50.000 0.00 0.00 0.00 5.07
1938 8094 1.447838 CCTGATCAACCACGTCGGG 60.448 63.158 0.00 0.00 40.22 5.14
2136 8652 3.504906 TGCCTGCATACGTATCTACTACC 59.495 47.826 4.74 0.00 0.00 3.18
2137 8653 3.504906 GCCTGCATACGTATCTACTACCA 59.495 47.826 4.74 0.00 0.00 3.25
2138 8654 4.379603 GCCTGCATACGTATCTACTACCAG 60.380 50.000 4.74 4.13 0.00 4.00
2168 8684 9.524106 CTCAATAAGCTGCAAAATAATTCATGA 57.476 29.630 1.02 0.00 0.00 3.07
2210 8726 8.744652 AGGTAAGATCGGTGATATGAATAAGAG 58.255 37.037 0.00 0.00 0.00 2.85
2255 8771 4.614306 CGTTTCCCCTTCCGTACAAAAATC 60.614 45.833 0.00 0.00 0.00 2.17
2256 8772 4.376225 TTCCCCTTCCGTACAAAAATCT 57.624 40.909 0.00 0.00 0.00 2.40
2257 8773 5.502089 TTCCCCTTCCGTACAAAAATCTA 57.498 39.130 0.00 0.00 0.00 1.98
2258 8774 5.703730 TCCCCTTCCGTACAAAAATCTAT 57.296 39.130 0.00 0.00 0.00 1.98
2259 8775 5.677567 TCCCCTTCCGTACAAAAATCTATC 58.322 41.667 0.00 0.00 0.00 2.08
2260 8776 5.427481 TCCCCTTCCGTACAAAAATCTATCT 59.573 40.000 0.00 0.00 0.00 1.98
2261 8777 6.612456 TCCCCTTCCGTACAAAAATCTATCTA 59.388 38.462 0.00 0.00 0.00 1.98
2262 8778 7.291651 TCCCCTTCCGTACAAAAATCTATCTAT 59.708 37.037 0.00 0.00 0.00 1.98
2263 8779 7.603024 CCCCTTCCGTACAAAAATCTATCTATC 59.397 40.741 0.00 0.00 0.00 2.08
2264 8780 8.368668 CCCTTCCGTACAAAAATCTATCTATCT 58.631 37.037 0.00 0.00 0.00 1.98
2336 8852 8.808240 ACCTATACTAATTCTGGATTAACCCA 57.192 34.615 0.00 0.00 38.00 4.51
2348 8864 5.362263 TGGATTAACCCAGAGTATTAACGC 58.638 41.667 0.00 0.00 38.00 4.84
2349 8865 5.104859 TGGATTAACCCAGAGTATTAACGCA 60.105 40.000 0.00 0.00 38.00 5.24
2350 8866 5.818857 GGATTAACCCAGAGTATTAACGCAA 59.181 40.000 0.00 0.00 0.00 4.85
2351 8867 6.316890 GGATTAACCCAGAGTATTAACGCAAA 59.683 38.462 0.00 0.00 0.00 3.68
2352 8868 7.148205 GGATTAACCCAGAGTATTAACGCAAAA 60.148 37.037 0.00 0.00 0.00 2.44
2353 8869 5.622770 AACCCAGAGTATTAACGCAAAAG 57.377 39.130 0.00 0.00 0.00 2.27
2354 8870 4.901868 ACCCAGAGTATTAACGCAAAAGA 58.098 39.130 0.00 0.00 0.00 2.52
2355 8871 5.310451 ACCCAGAGTATTAACGCAAAAGAA 58.690 37.500 0.00 0.00 0.00 2.52
2356 8872 5.766174 ACCCAGAGTATTAACGCAAAAGAAA 59.234 36.000 0.00 0.00 0.00 2.52
2357 8873 6.433093 ACCCAGAGTATTAACGCAAAAGAAAT 59.567 34.615 0.00 0.00 0.00 2.17
2358 8874 7.039993 ACCCAGAGTATTAACGCAAAAGAAATT 60.040 33.333 0.00 0.00 0.00 1.82
2359 8875 7.484959 CCCAGAGTATTAACGCAAAAGAAATTC 59.515 37.037 0.00 0.00 0.00 2.17
2360 8876 7.484959 CCAGAGTATTAACGCAAAAGAAATTCC 59.515 37.037 0.00 0.00 0.00 3.01
2361 8877 7.484959 CAGAGTATTAACGCAAAAGAAATTCCC 59.515 37.037 0.00 0.00 0.00 3.97
2362 8878 7.175990 AGAGTATTAACGCAAAAGAAATTCCCA 59.824 33.333 0.00 0.00 0.00 4.37
2363 8879 7.836842 AGTATTAACGCAAAAGAAATTCCCAT 58.163 30.769 0.00 0.00 0.00 4.00
2364 8880 6.966435 ATTAACGCAAAAGAAATTCCCATG 57.034 33.333 0.00 0.00 0.00 3.66
2365 8881 4.335400 AACGCAAAAGAAATTCCCATGT 57.665 36.364 0.00 0.00 0.00 3.21
2366 8882 4.335400 ACGCAAAAGAAATTCCCATGTT 57.665 36.364 0.00 0.00 0.00 2.71
2367 8883 5.461032 ACGCAAAAGAAATTCCCATGTTA 57.539 34.783 0.00 0.00 0.00 2.41
2368 8884 5.848406 ACGCAAAAGAAATTCCCATGTTAA 58.152 33.333 0.00 0.00 0.00 2.01
2369 8885 6.463360 ACGCAAAAGAAATTCCCATGTTAAT 58.537 32.000 0.00 0.00 0.00 1.40
2370 8886 7.607250 ACGCAAAAGAAATTCCCATGTTAATA 58.393 30.769 0.00 0.00 0.00 0.98
2371 8887 7.544217 ACGCAAAAGAAATTCCCATGTTAATAC 59.456 33.333 0.00 0.00 0.00 1.89
2372 8888 7.543868 CGCAAAAGAAATTCCCATGTTAATACA 59.456 33.333 0.00 0.00 38.95 2.29
2373 8889 9.213799 GCAAAAGAAATTCCCATGTTAATACAA 57.786 29.630 0.00 0.00 37.91 2.41
2380 8896 8.980143 AATTCCCATGTTAATACAAGAAAACG 57.020 30.769 0.00 0.00 37.91 3.60
2381 8897 7.747155 TTCCCATGTTAATACAAGAAAACGA 57.253 32.000 0.00 0.00 37.91 3.85
2382 8898 7.747155 TCCCATGTTAATACAAGAAAACGAA 57.253 32.000 0.00 0.00 37.91 3.85
2383 8899 8.167605 TCCCATGTTAATACAAGAAAACGAAA 57.832 30.769 0.00 0.00 37.91 3.46
2384 8900 8.630917 TCCCATGTTAATACAAGAAAACGAAAA 58.369 29.630 0.00 0.00 37.91 2.29
2385 8901 9.250624 CCCATGTTAATACAAGAAAACGAAAAA 57.749 29.630 0.00 0.00 37.91 1.94
2426 8942 2.536761 TTGGGACTGTGTTTCTACCG 57.463 50.000 0.00 0.00 0.00 4.02
2429 8945 1.337541 GGGACTGTGTTTCTACCGTCC 60.338 57.143 9.98 9.98 40.04 4.79
2448 8965 4.441415 CGTCCAGATCTAAACTACAATCGC 59.559 45.833 0.00 0.00 0.00 4.58
2492 9009 5.163405 GGAGTGCATGGACTAAGTTATCTGA 60.163 44.000 20.79 0.00 0.00 3.27
2503 9020 5.753921 ACTAAGTTATCTGATAGCAAACCGC 59.246 40.000 13.02 0.00 42.91 5.68
2549 9069 6.594744 AGCAATCAAATCCCAACTTTCTTTT 58.405 32.000 0.00 0.00 0.00 2.27
2629 9151 3.133901 TGCGTTATCTTCATGGCTTCCTA 59.866 43.478 0.00 0.00 0.00 2.94
2645 9167 1.137086 TCCTAGCACGCATCTCCTTTC 59.863 52.381 0.00 0.00 0.00 2.62
2650 9172 0.807667 CACGCATCTCCTTTCCCTCG 60.808 60.000 0.00 0.00 0.00 4.63
2657 9179 3.264897 CCTTTCCCTCGCGCATCG 61.265 66.667 8.75 0.00 40.15 3.84
2658 9180 2.509336 CTTTCCCTCGCGCATCGT 60.509 61.111 8.75 0.00 39.67 3.73
2668 9190 1.746727 CGCGCATCGTCTTCTTCCTG 61.747 60.000 8.75 0.00 0.00 3.86
2669 9191 0.458543 GCGCATCGTCTTCTTCCTGA 60.459 55.000 0.30 0.00 0.00 3.86
2670 9192 1.554392 CGCATCGTCTTCTTCCTGAG 58.446 55.000 0.00 0.00 0.00 3.35
2671 9193 1.135257 CGCATCGTCTTCTTCCTGAGT 60.135 52.381 0.00 0.00 0.00 3.41
2672 9194 2.535331 GCATCGTCTTCTTCCTGAGTC 58.465 52.381 0.00 0.00 0.00 3.36
2673 9195 2.165437 GCATCGTCTTCTTCCTGAGTCT 59.835 50.000 0.00 0.00 0.00 3.24
2674 9196 3.768406 CATCGTCTTCTTCCTGAGTCTG 58.232 50.000 0.00 0.00 0.00 3.51
2675 9197 2.163509 TCGTCTTCTTCCTGAGTCTGG 58.836 52.381 9.74 9.74 0.00 3.86
2676 9198 2.163509 CGTCTTCTTCCTGAGTCTGGA 58.836 52.381 14.37 14.37 0.00 3.86
2717 9239 2.266055 GGCAGGTCACTTCTCCCG 59.734 66.667 0.00 0.00 0.00 5.14
2783 9305 0.392193 CTCAGTCCTGTGGTGCCATC 60.392 60.000 0.00 0.00 0.00 3.51
2792 9314 2.042639 GGTGCCATCAGCCCCATT 60.043 61.111 0.00 0.00 39.19 3.16
2797 9319 1.197812 GCCATCAGCCCCATTCTTTT 58.802 50.000 0.00 0.00 34.35 2.27
2798 9320 1.556451 GCCATCAGCCCCATTCTTTTT 59.444 47.619 0.00 0.00 34.35 1.94
2815 9361 6.698008 TCTTTTTGAGATTGTCAAGCAGAA 57.302 33.333 3.27 0.00 46.09 3.02
2849 9395 2.264794 CCGCCGCCAAGTTCTACT 59.735 61.111 0.00 0.00 0.00 2.57
2854 9400 0.392998 CCGCCAAGTTCTACTGCCAT 60.393 55.000 0.00 0.00 0.00 4.40
2885 9431 0.102481 CTCGAGGGATGGTGTTACCG 59.898 60.000 3.91 0.00 42.58 4.02
2900 9446 2.857575 TACCGCTGCAGCCAGACATG 62.858 60.000 32.07 16.19 41.77 3.21
2910 9456 0.179181 GCCAGACATGATGTTGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
2913 9459 2.094258 CCAGACATGATGTTGCGTGTAC 59.906 50.000 0.00 0.00 38.09 2.90
2955 9501 0.821517 TATGGCTGGTCGTCGAACAT 59.178 50.000 14.43 0.93 0.00 2.71
3005 9551 4.694233 CTGCAGGTCACCGCTGCT 62.694 66.667 5.57 0.00 43.74 4.24
3085 9631 2.515757 TGCCGCTGCAACAGTCAA 60.516 55.556 0.00 0.00 46.66 3.18
3086 9632 2.050985 GCCGCTGCAACAGTCAAC 60.051 61.111 0.00 0.00 37.47 3.18
3087 9633 2.833533 GCCGCTGCAACAGTCAACA 61.834 57.895 0.00 0.00 37.47 3.33
3088 9634 1.951510 CCGCTGCAACAGTCAACAT 59.048 52.632 0.00 0.00 33.43 2.71
3089 9635 0.311790 CCGCTGCAACAGTCAACATT 59.688 50.000 0.00 0.00 33.43 2.71
3090 9636 1.401530 CGCTGCAACAGTCAACATTG 58.598 50.000 0.00 0.00 33.43 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
257 260 2.425668 CGGGGTTTCACTCAACTGTTTT 59.574 45.455 0.00 0.00 0.00 2.43
261 264 0.817634 TGCGGGGTTTCACTCAACTG 60.818 55.000 0.00 0.00 0.00 3.16
264 267 0.179004 ATGTGCGGGGTTTCACTCAA 60.179 50.000 0.00 0.00 34.49 3.02
265 268 0.888736 CATGTGCGGGGTTTCACTCA 60.889 55.000 0.00 0.00 34.49 3.41
299 330 0.327480 TGTCCTCCCCCATGTATGCT 60.327 55.000 0.00 0.00 0.00 3.79
324 355 7.348033 TCCACACTTTTTAACTCCCTTTTCTA 58.652 34.615 0.00 0.00 0.00 2.10
360 391 1.264288 GGTTGGCGCATATCTGCTTAC 59.736 52.381 10.83 0.00 46.65 2.34
361 392 1.134250 TGGTTGGCGCATATCTGCTTA 60.134 47.619 10.83 0.00 46.65 3.09
365 396 0.940126 GAGTGGTTGGCGCATATCTG 59.060 55.000 10.83 0.00 0.00 2.90
375 406 4.488790 AAGCAGCAGAGTGGTTGG 57.511 55.556 0.00 0.00 36.79 3.77
400 431 7.372260 AGAAATGAGACAGATATAAGCCACT 57.628 36.000 0.00 0.00 0.00 4.00
421 2017 8.357402 GCCATCCTACTTTCTTGTTTTAAAGAA 58.643 33.333 0.00 0.00 42.89 2.52
425 2021 7.286775 AGTTGCCATCCTACTTTCTTGTTTTAA 59.713 33.333 0.00 0.00 0.00 1.52
434 2030 5.705609 TCAAAAGTTGCCATCCTACTTTC 57.294 39.130 0.00 0.00 44.78 2.62
444 2040 4.392921 TTTTTCGGATCAAAAGTTGCCA 57.607 36.364 0.00 0.00 0.00 4.92
488 2086 8.880244 TGCTATAAATTACCCAGTATGTCATCT 58.120 33.333 0.00 0.00 0.00 2.90
498 2096 7.054124 TCCAGAAGTTGCTATAAATTACCCAG 58.946 38.462 0.00 0.00 0.00 4.45
499 2097 6.964464 TCCAGAAGTTGCTATAAATTACCCA 58.036 36.000 0.00 0.00 0.00 4.51
533 2133 3.867771 GCTTCTGGCAGTCTGTCG 58.132 61.111 15.27 0.00 41.35 4.35
589 2189 2.410785 GCATTCATACATGCGCACAT 57.589 45.000 14.90 6.30 40.30 3.21
596 2196 6.148315 ACATACAAGATCGGCATTCATACATG 59.852 38.462 0.00 0.00 0.00 3.21
607 2207 5.402568 CACAGTACATACATACAAGATCGGC 59.597 44.000 0.00 0.00 0.00 5.54
608 2208 6.504398 ACACAGTACATACATACAAGATCGG 58.496 40.000 0.00 0.00 0.00 4.18
609 2209 7.987268 AACACAGTACATACATACAAGATCG 57.013 36.000 0.00 0.00 0.00 3.69
800 2708 5.440610 ACTTCAAATCTGTTTCCACTCTGT 58.559 37.500 0.00 0.00 0.00 3.41
801 2709 5.528690 TGACTTCAAATCTGTTTCCACTCTG 59.471 40.000 0.00 0.00 0.00 3.35
811 2719 4.039245 TCTCGTTCCTGACTTCAAATCTGT 59.961 41.667 0.00 0.00 0.00 3.41
815 2723 5.997746 TCAATTCTCGTTCCTGACTTCAAAT 59.002 36.000 0.00 0.00 0.00 2.32
881 2790 3.613432 GCGGCCTATATATACATACCGGC 60.613 52.174 0.00 12.23 39.75 6.13
882 2791 3.365666 CGCGGCCTATATATACATACCGG 60.366 52.174 0.00 0.00 39.75 5.28
883 2792 3.251729 ACGCGGCCTATATATACATACCG 59.748 47.826 12.47 10.28 42.19 4.02
884 2793 4.518211 AGACGCGGCCTATATATACATACC 59.482 45.833 9.25 0.00 0.00 2.73
936 2856 1.037493 ACAGTTGGAGCACGTACTCA 58.963 50.000 17.37 1.39 38.50 3.41
959 2879 3.330701 CTCTCCTCTCCTCAGGTAGCTAT 59.669 52.174 0.00 0.00 34.76 2.97
969 2889 2.643551 CTGACTCACTCTCCTCTCCTC 58.356 57.143 0.00 0.00 0.00 3.71
970 2890 1.340991 GCTGACTCACTCTCCTCTCCT 60.341 57.143 0.00 0.00 0.00 3.69
971 2891 1.102978 GCTGACTCACTCTCCTCTCC 58.897 60.000 0.00 0.00 0.00 3.71
972 2892 1.745087 CAGCTGACTCACTCTCCTCTC 59.255 57.143 8.42 0.00 0.00 3.20
973 2893 1.838112 CAGCTGACTCACTCTCCTCT 58.162 55.000 8.42 0.00 0.00 3.69
983 2907 1.558741 CATCTTCGAGCAGCTGACTC 58.441 55.000 20.43 20.97 0.00 3.36
1045 2975 1.949847 ATGGGTGCGAAGACTCCGAG 61.950 60.000 0.00 0.00 0.00 4.63
1449 3404 4.338539 GTGTCGTCGCCGTCCACT 62.339 66.667 4.65 0.00 35.58 4.00
1460 3415 2.431942 GGATGTTCCGCGTGTCGT 60.432 61.111 4.92 0.00 36.19 4.34
1607 3584 1.080366 GCCACGTCCGTCATGTACA 60.080 57.895 0.00 0.00 0.00 2.90
1685 3662 0.034863 GATGTTGGGGTCGCCCTTTA 60.035 55.000 13.58 0.36 44.66 1.85
1719 3699 0.833409 TGGTGCTCTGCTGGAAGAGA 60.833 55.000 9.63 0.00 45.59 3.10
1785 3774 1.304509 TGTACACCGCGTCGACCATA 61.305 55.000 10.58 0.00 0.00 2.74
1906 3895 2.631062 TGATCAGGTTCTGGTTGTACGT 59.369 45.455 0.00 0.00 31.51 3.57
1938 8094 2.482326 CCTCTTGGGCGTTCCATTC 58.518 57.895 0.68 0.00 46.52 2.67
1973 8129 3.326836 TGAACATGGCGAAGATGTACA 57.673 42.857 0.00 0.00 32.74 2.90
2136 8652 5.571784 TTTTGCAGCTTATTGAGATCCTG 57.428 39.130 0.00 0.00 0.00 3.86
2137 8653 7.886629 TTATTTTGCAGCTTATTGAGATCCT 57.113 32.000 0.00 0.00 0.00 3.24
2138 8654 9.189723 GAATTATTTTGCAGCTTATTGAGATCC 57.810 33.333 0.00 0.00 0.00 3.36
2210 8726 6.208644 ACGATTCTTTATGCAACATAATGGC 58.791 36.000 11.20 0.00 0.00 4.40
2310 8826 9.901651 TGGGTTAATCCAGAATTAGTATAGGTA 57.098 33.333 2.36 0.00 38.11 3.08
2311 8827 8.808240 TGGGTTAATCCAGAATTAGTATAGGT 57.192 34.615 2.36 0.00 38.11 3.08
2325 8841 5.104859 TGCGTTAATACTCTGGGTTAATCCA 60.105 40.000 7.38 7.38 38.11 3.41
2326 8842 5.362263 TGCGTTAATACTCTGGGTTAATCC 58.638 41.667 0.00 0.00 0.00 3.01
2327 8843 6.913873 TTGCGTTAATACTCTGGGTTAATC 57.086 37.500 0.00 0.00 0.00 1.75
2328 8844 7.608761 TCTTTTGCGTTAATACTCTGGGTTAAT 59.391 33.333 0.00 0.00 0.00 1.40
2329 8845 6.935771 TCTTTTGCGTTAATACTCTGGGTTAA 59.064 34.615 0.00 0.00 0.00 2.01
2330 8846 6.465948 TCTTTTGCGTTAATACTCTGGGTTA 58.534 36.000 0.00 0.00 0.00 2.85
2331 8847 5.310451 TCTTTTGCGTTAATACTCTGGGTT 58.690 37.500 0.00 0.00 0.00 4.11
2332 8848 4.901868 TCTTTTGCGTTAATACTCTGGGT 58.098 39.130 0.00 0.00 0.00 4.51
2333 8849 5.873179 TTCTTTTGCGTTAATACTCTGGG 57.127 39.130 0.00 0.00 0.00 4.45
2334 8850 7.484959 GGAATTTCTTTTGCGTTAATACTCTGG 59.515 37.037 0.00 0.00 0.00 3.86
2335 8851 7.484959 GGGAATTTCTTTTGCGTTAATACTCTG 59.515 37.037 0.00 0.00 0.00 3.35
2336 8852 7.175990 TGGGAATTTCTTTTGCGTTAATACTCT 59.824 33.333 0.00 0.00 0.00 3.24
2337 8853 7.309920 TGGGAATTTCTTTTGCGTTAATACTC 58.690 34.615 0.00 0.00 0.00 2.59
2338 8854 7.222000 TGGGAATTTCTTTTGCGTTAATACT 57.778 32.000 0.00 0.00 0.00 2.12
2339 8855 7.544217 ACATGGGAATTTCTTTTGCGTTAATAC 59.456 33.333 0.00 0.00 0.00 1.89
2340 8856 7.607250 ACATGGGAATTTCTTTTGCGTTAATA 58.393 30.769 0.00 0.00 0.00 0.98
2341 8857 6.463360 ACATGGGAATTTCTTTTGCGTTAAT 58.537 32.000 0.00 0.00 0.00 1.40
2342 8858 5.848406 ACATGGGAATTTCTTTTGCGTTAA 58.152 33.333 0.00 0.00 0.00 2.01
2343 8859 5.461032 ACATGGGAATTTCTTTTGCGTTA 57.539 34.783 0.00 0.00 0.00 3.18
2344 8860 4.335400 ACATGGGAATTTCTTTTGCGTT 57.665 36.364 0.00 0.00 0.00 4.84
2345 8861 4.335400 AACATGGGAATTTCTTTTGCGT 57.665 36.364 0.00 0.00 0.00 5.24
2346 8862 6.966435 ATTAACATGGGAATTTCTTTTGCG 57.034 33.333 0.00 0.00 0.00 4.85
2347 8863 8.770438 TGTATTAACATGGGAATTTCTTTTGC 57.230 30.769 0.00 0.00 0.00 3.68
2354 8870 9.418045 CGTTTTCTTGTATTAACATGGGAATTT 57.582 29.630 0.00 0.00 34.97 1.82
2355 8871 8.798402 TCGTTTTCTTGTATTAACATGGGAATT 58.202 29.630 0.00 0.00 34.97 2.17
2356 8872 8.343168 TCGTTTTCTTGTATTAACATGGGAAT 57.657 30.769 0.00 0.00 34.97 3.01
2357 8873 7.747155 TCGTTTTCTTGTATTAACATGGGAA 57.253 32.000 0.00 0.00 34.97 3.97
2358 8874 7.747155 TTCGTTTTCTTGTATTAACATGGGA 57.253 32.000 0.00 0.00 34.97 4.37
2359 8875 8.804688 TTTTCGTTTTCTTGTATTAACATGGG 57.195 30.769 0.00 0.00 34.97 4.00
2413 8929 3.193691 AGATCTGGACGGTAGAAACACAG 59.806 47.826 0.00 0.00 0.00 3.66
2414 8930 3.162666 AGATCTGGACGGTAGAAACACA 58.837 45.455 0.00 0.00 0.00 3.72
2426 8942 5.593010 AGCGATTGTAGTTTAGATCTGGAC 58.407 41.667 5.18 3.82 0.00 4.02
2429 8945 5.689514 CCTGAGCGATTGTAGTTTAGATCTG 59.310 44.000 5.18 0.00 0.00 2.90
2448 8965 2.541588 CCACGTTTTTGCAAGTCCTGAG 60.542 50.000 0.00 0.00 0.00 3.35
2516 9033 4.141367 TGGGATTTGATTGCTACCCGATAA 60.141 41.667 0.00 0.00 40.08 1.75
2574 9094 7.775053 ATACAGTTGGGATTAGCTTCAAAAA 57.225 32.000 0.00 0.00 0.00 1.94
2575 9095 7.775053 AATACAGTTGGGATTAGCTTCAAAA 57.225 32.000 0.00 0.00 0.00 2.44
2576 9096 7.556275 CCTAATACAGTTGGGATTAGCTTCAAA 59.444 37.037 0.00 0.00 33.59 2.69
2577 9097 7.054124 CCTAATACAGTTGGGATTAGCTTCAA 58.946 38.462 0.00 0.00 33.59 2.69
2578 9098 6.591935 CCTAATACAGTTGGGATTAGCTTCA 58.408 40.000 0.00 0.00 33.59 3.02
2579 9099 5.470437 GCCTAATACAGTTGGGATTAGCTTC 59.530 44.000 0.00 0.00 33.59 3.86
2580 9100 5.104109 TGCCTAATACAGTTGGGATTAGCTT 60.104 40.000 0.00 0.00 33.59 3.74
2581 9101 4.412199 TGCCTAATACAGTTGGGATTAGCT 59.588 41.667 0.00 0.00 33.59 3.32
2582 9102 4.714632 TGCCTAATACAGTTGGGATTAGC 58.285 43.478 1.54 0.00 33.59 3.09
2583 9103 7.066284 GCATATGCCTAATACAGTTGGGATTAG 59.934 40.741 17.26 0.00 34.36 1.73
2584 9104 6.884295 GCATATGCCTAATACAGTTGGGATTA 59.116 38.462 17.26 0.00 32.91 1.75
2585 9105 5.711976 GCATATGCCTAATACAGTTGGGATT 59.288 40.000 17.26 0.00 32.91 3.01
2586 9106 5.256474 GCATATGCCTAATACAGTTGGGAT 58.744 41.667 17.26 0.00 34.97 3.85
2587 9107 4.651778 GCATATGCCTAATACAGTTGGGA 58.348 43.478 17.26 0.00 34.31 4.37
2588 9108 3.436704 CGCATATGCCTAATACAGTTGGG 59.563 47.826 21.77 0.00 37.91 4.12
2589 9109 4.065088 ACGCATATGCCTAATACAGTTGG 58.935 43.478 21.77 5.56 37.91 3.77
2590 9110 5.673337 AACGCATATGCCTAATACAGTTG 57.327 39.130 21.77 5.76 37.91 3.16
2591 9111 7.386851 AGATAACGCATATGCCTAATACAGTT 58.613 34.615 21.77 17.62 37.91 3.16
2592 9112 6.936279 AGATAACGCATATGCCTAATACAGT 58.064 36.000 21.77 8.34 37.91 3.55
2593 9113 7.545615 TGAAGATAACGCATATGCCTAATACAG 59.454 37.037 21.77 7.69 37.91 2.74
2594 9114 7.382898 TGAAGATAACGCATATGCCTAATACA 58.617 34.615 21.77 9.87 37.91 2.29
2595 9115 7.827819 TGAAGATAACGCATATGCCTAATAC 57.172 36.000 21.77 9.26 37.91 1.89
2596 9116 7.495606 CCATGAAGATAACGCATATGCCTAATA 59.504 37.037 21.77 9.94 37.91 0.98
2629 9151 1.078143 GGGAAAGGAGATGCGTGCT 60.078 57.895 0.00 0.00 0.00 4.40
2633 9155 1.884926 GCGAGGGAAAGGAGATGCG 60.885 63.158 0.00 0.00 0.00 4.73
2645 9167 2.890847 AAGAAGACGATGCGCGAGGG 62.891 60.000 12.10 0.00 44.57 4.30
2650 9172 0.458543 TCAGGAAGAAGACGATGCGC 60.459 55.000 0.00 0.00 0.00 6.09
2657 9179 4.953579 AGTATCCAGACTCAGGAAGAAGAC 59.046 45.833 0.00 0.00 38.93 3.01
2658 9180 4.952957 CAGTATCCAGACTCAGGAAGAAGA 59.047 45.833 0.00 0.00 38.93 2.87
2668 9190 3.011119 ACTCGTGTCAGTATCCAGACTC 58.989 50.000 0.00 0.00 35.81 3.36
2669 9191 3.074675 ACTCGTGTCAGTATCCAGACT 57.925 47.619 0.00 0.00 35.81 3.24
2670 9192 3.851976 AACTCGTGTCAGTATCCAGAC 57.148 47.619 0.00 0.00 35.37 3.51
2671 9193 4.840271 TCTAACTCGTGTCAGTATCCAGA 58.160 43.478 0.00 0.00 0.00 3.86
2672 9194 5.297029 TGATCTAACTCGTGTCAGTATCCAG 59.703 44.000 0.00 0.00 0.00 3.86
2673 9195 5.190677 TGATCTAACTCGTGTCAGTATCCA 58.809 41.667 0.00 0.00 0.00 3.41
2674 9196 5.278071 CCTGATCTAACTCGTGTCAGTATCC 60.278 48.000 0.00 0.00 35.66 2.59
2675 9197 5.753744 CCTGATCTAACTCGTGTCAGTATC 58.246 45.833 0.00 0.00 35.66 2.24
2676 9198 4.036971 GCCTGATCTAACTCGTGTCAGTAT 59.963 45.833 0.00 0.00 35.66 2.12
2717 9239 4.202151 GGGGTGGAGCAATACAAATCAATC 60.202 45.833 0.00 0.00 0.00 2.67
2769 9291 2.352422 GCTGATGGCACCACAGGA 59.648 61.111 16.05 0.00 41.35 3.86
2783 9305 4.020839 ACAATCTCAAAAAGAATGGGGCTG 60.021 41.667 0.00 0.00 38.94 4.85
2792 9314 6.543465 TCTTCTGCTTGACAATCTCAAAAAGA 59.457 34.615 0.00 0.00 38.47 2.52
2797 9319 5.410746 GTCATCTTCTGCTTGACAATCTCAA 59.589 40.000 0.00 0.00 39.59 3.02
2798 9320 4.934001 GTCATCTTCTGCTTGACAATCTCA 59.066 41.667 0.00 0.00 39.59 3.27
2849 9395 2.190313 GCACCGGAGATCATGGCA 59.810 61.111 9.46 0.00 0.00 4.92
2854 9400 2.121538 CCTCGAGCACCGGAGATCA 61.122 63.158 17.29 3.86 39.14 2.92
2885 9431 1.030488 ACATCATGTCTGGCTGCAGC 61.030 55.000 30.88 30.88 41.14 5.25
2910 9456 2.001159 TGACGTTGGTGTTGTGTGTAC 58.999 47.619 0.00 0.00 0.00 2.90
2913 9459 1.364721 TCTGACGTTGGTGTTGTGTG 58.635 50.000 0.00 0.00 0.00 3.82
2985 9531 4.694233 AGCGGTGACCTGCAGCAG 62.694 66.667 16.23 16.23 45.15 4.24
3005 9551 2.668632 GCGGTGGTGATGAAGGGA 59.331 61.111 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.