Multiple sequence alignment - TraesCS3D01G377700

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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 TraesCS3D01G377700 chr3D 100.000 2954 0 0 1 2954 495279266 495276313 0.000000e+00 5456.0
1 TraesCS3D01G377700 chr3D 87.749 653 77 2 1528 2178 495234200 495233549 0.000000e+00 760.0
2 TraesCS3D01G377700 chr3D 97.059 68 2 0 2608 2675 147095430 147095497 6.690000e-22 115.0
3 TraesCS3D01G377700 chr3B 92.642 1930 87 15 1043 2954 654308520 654306628 0.000000e+00 2726.0
4 TraesCS3D01G377700 chr3B 86.524 653 85 2 1528 2178 654179065 654178414 0.000000e+00 715.0
5 TraesCS3D01G377700 chr3B 76.636 1070 229 16 1072 2129 654311447 654310387 3.300000e-159 571.0
6 TraesCS3D01G377700 chr3B 75.429 1050 239 13 1072 2112 654069089 654068050 2.650000e-135 492.0
7 TraesCS3D01G377700 chr3B 82.385 545 61 22 1 529 654310412 654309887 2.700000e-120 442.0
8 TraesCS3D01G377700 chr3B 93.617 94 6 0 2859 2952 821906956 821906863 1.100000e-29 141.0
9 TraesCS3D01G377700 chr3B 96.429 84 1 1 694 777 654308811 654308730 1.430000e-28 137.0
10 TraesCS3D01G377700 chr3B 93.750 80 3 1 598 677 654308869 654308792 5.170000e-23 119.0
11 TraesCS3D01G377700 chr3B 100.000 28 0 0 912 939 654308598 654308571 5.000000e-03 52.8
12 TraesCS3D01G377700 chr3A 90.901 1176 89 12 1043 2209 634667556 634666390 0.000000e+00 1563.0
13 TraesCS3D01G377700 chr3A 88.207 619 70 2 1562 2178 634661733 634661116 0.000000e+00 736.0
14 TraesCS3D01G377700 chr3A 90.022 451 34 6 1 447 634671539 634671096 9.180000e-160 573.0
15 TraesCS3D01G377700 chr3A 74.127 1059 252 16 1072 2118 634185515 634184467 4.550000e-113 418.0
16 TraesCS3D01G377700 chr3A 87.975 158 15 4 443 598 634668021 634667866 1.810000e-42 183.0
17 TraesCS3D01G377700 chr3A 82.609 115 11 4 772 883 634667805 634667697 3.130000e-15 93.5
18 TraesCS3D01G377700 chr3A 100.000 28 0 0 997 1024 634667581 634667554 5.000000e-03 52.8
19 TraesCS3D01G377700 chr5D 88.396 293 30 3 1888 2178 369027172 369027462 1.680000e-92 350.0
20 TraesCS3D01G377700 chr5D 97.059 68 2 0 2608 2675 6163701 6163768 6.690000e-22 115.0
21 TraesCS3D01G377700 chr5D 97.059 68 2 0 2608 2675 6261693 6261760 6.690000e-22 115.0
22 TraesCS3D01G377700 chr2A 80.184 217 41 2 1576 1791 759323321 759323536 8.470000e-36 161.0
23 TraesCS3D01G377700 chrUn 97.059 68 2 0 2608 2675 414537829 414537896 6.690000e-22 115.0
24 TraesCS3D01G377700 chr7D 97.059 68 2 0 2608 2675 530797376 530797443 6.690000e-22 115.0
25 TraesCS3D01G377700 chr7D 77.391 115 23 3 2839 2953 321935829 321935718 6.830000e-07 65.8
26 TraesCS3D01G377700 chr6D 97.059 68 2 0 2608 2675 79649987 79649920 6.690000e-22 115.0
27 TraesCS3D01G377700 chr6D 97.059 68 2 0 2608 2675 346731230 346731163 6.690000e-22 115.0
28 TraesCS3D01G377700 chr1D 97.059 68 2 0 2608 2675 254448249 254448182 6.690000e-22 115.0
29 TraesCS3D01G377700 chr7B 84.270 89 12 2 2853 2941 439594710 439594796 5.250000e-13 86.1
30 TraesCS3D01G377700 chr7B 84.091 88 12 1 2867 2954 474290554 474290639 1.890000e-12 84.2
31 TraesCS3D01G377700 chr1A 85.000 80 12 0 2875 2954 277643768 277643847 6.790000e-12 82.4
32 TraesCS3D01G377700 chr4B 92.157 51 1 3 2905 2954 462239485 462239437 5.280000e-08 69.4
33 TraesCS3D01G377700 chr2D 82.716 81 8 4 1651 1731 632958543 632958617 1.900000e-07 67.6
34 TraesCS3D01G377700 chr2B 80.000 90 17 1 2866 2954 730185382 730185293 6.830000e-07 65.8
35 TraesCS3D01G377700 chr4A 77.451 102 21 2 2853 2954 483962582 483962681 3.180000e-05 60.2


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 TraesCS3D01G377700 chr3D 495276313 495279266 2953 True 5456.000000 5456 100.0000 1 2954 1 chr3D.!!$R2 2953
1 TraesCS3D01G377700 chr3D 495233549 495234200 651 True 760.000000 760 87.7490 1528 2178 1 chr3D.!!$R1 650
2 TraesCS3D01G377700 chr3B 654178414 654179065 651 True 715.000000 715 86.5240 1528 2178 1 chr3B.!!$R2 650
3 TraesCS3D01G377700 chr3B 654306628 654311447 4819 True 674.633333 2726 90.3070 1 2954 6 chr3B.!!$R4 2953
4 TraesCS3D01G377700 chr3B 654068050 654069089 1039 True 492.000000 492 75.4290 1072 2112 1 chr3B.!!$R1 1040
5 TraesCS3D01G377700 chr3A 634661116 634661733 617 True 736.000000 736 88.2070 1562 2178 1 chr3A.!!$R2 616
6 TraesCS3D01G377700 chr3A 634666390 634671539 5149 True 493.060000 1563 90.3014 1 2209 5 chr3A.!!$R3 2208
7 TraesCS3D01G377700 chr3A 634184467 634185515 1048 True 418.000000 418 74.1270 1072 2118 1 chr3A.!!$R1 1046

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
974 6152 0.040646 TACACGGGTCCAGTCCAGAT 59.959 55.0 0.0 0.0 0.00 2.9 F
1155 6336 0.037232 GTACGAAAGCCTCTGCACCT 60.037 55.0 0.0 0.0 41.13 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 7001 0.316204 GCAGCCACAGCAATTCTTGT 59.684 50.0 0.0 0.0 43.56 3.16 R
2882 8088 0.976641 AAGACAAGGTGGATCAGCGA 59.023 50.0 0.0 0.0 36.92 4.93 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
96 1134 8.357402 AGGTTATAGTTTTGTTTTCATGTCACC 58.643 33.333 0.00 0.00 0.00 4.02
97 1135 8.138712 GGTTATAGTTTTGTTTTCATGTCACCA 58.861 33.333 0.00 0.00 0.00 4.17
98 1136 8.964150 GTTATAGTTTTGTTTTCATGTCACCAC 58.036 33.333 0.00 0.00 0.00 4.16
111 1149 1.040646 TCACCACTCACCAGTCAGTC 58.959 55.000 0.00 0.00 0.00 3.51
137 1175 4.696877 TGTGACTTGATGTTATGCCAGAAG 59.303 41.667 0.00 0.00 0.00 2.85
162 1201 8.667463 AGAACATTTTAATTGGTTGCATTATGC 58.333 29.630 10.65 10.65 45.29 3.14
204 1243 0.969894 GGATACATCGTGCCTAGCCT 59.030 55.000 0.00 0.00 0.00 4.58
246 1286 1.876156 CCAACTCAGAGAAGCAACACC 59.124 52.381 3.79 0.00 0.00 4.16
314 1361 5.583061 TGACGTGAACTTTGCTTTCTTTCTA 59.417 36.000 0.00 0.00 0.00 2.10
338 1385 2.623915 GCAGCAACTCAGGTGGCAG 61.624 63.158 0.00 0.00 44.47 4.85
378 1432 2.037251 GACCTGGACAGTCAAGCTACAA 59.963 50.000 0.00 0.00 0.00 2.41
395 1449 1.026718 CAAGATGGTGCCCTTCCGTC 61.027 60.000 0.00 0.00 40.24 4.79
414 1468 2.905546 GTCGTCGAAGATATCATCGCTG 59.094 50.000 22.15 16.82 40.67 5.18
422 1476 5.689514 CGAAGATATCATCGCTGAACTTTCT 59.310 40.000 16.43 0.00 34.37 2.52
474 4607 8.221766 CGTTGTTAGTTCCTATCTGAAACTTTC 58.778 37.037 0.00 0.00 0.00 2.62
488 4621 7.029563 TCTGAAACTTTCTTTTGTCAAGAAGC 58.970 34.615 3.22 0.00 37.54 3.86
526 4659 2.355132 GAGAGATCAACTGCAGCAATGG 59.645 50.000 15.27 0.00 0.00 3.16
527 4660 1.404391 GAGATCAACTGCAGCAATGGG 59.596 52.381 15.27 0.00 0.00 4.00
528 4661 0.179119 GATCAACTGCAGCAATGGGC 60.179 55.000 15.27 3.25 45.30 5.36
539 4672 2.994186 GCAATGGGCATGAGGAATTT 57.006 45.000 0.00 0.00 43.97 1.82
540 4673 3.271055 GCAATGGGCATGAGGAATTTT 57.729 42.857 0.00 0.00 43.97 1.82
541 4674 4.405116 GCAATGGGCATGAGGAATTTTA 57.595 40.909 0.00 0.00 43.97 1.52
542 4675 4.768583 GCAATGGGCATGAGGAATTTTAA 58.231 39.130 0.00 0.00 43.97 1.52
543 4676 4.812626 GCAATGGGCATGAGGAATTTTAAG 59.187 41.667 0.00 0.00 43.97 1.85
544 4677 5.395546 GCAATGGGCATGAGGAATTTTAAGA 60.396 40.000 0.00 0.00 43.97 2.10
545 4678 6.687139 GCAATGGGCATGAGGAATTTTAAGAT 60.687 38.462 0.00 0.00 43.97 2.40
546 4679 5.857471 TGGGCATGAGGAATTTTAAGATG 57.143 39.130 0.00 0.00 0.00 2.90
547 4680 4.099881 TGGGCATGAGGAATTTTAAGATGC 59.900 41.667 0.00 0.00 35.14 3.91
560 4693 4.929819 TTAAGATGCGCCAGTAGTATCA 57.070 40.909 4.18 0.00 33.96 2.15
564 4720 2.979814 TGCGCCAGTAGTATCATTGT 57.020 45.000 4.18 0.00 0.00 2.71
619 5745 9.392506 TCAGTATTCCTATCCAATTCCAATCTA 57.607 33.333 0.00 0.00 0.00 1.98
628 5754 6.288941 TCCAATTCCAATCTACGTGACTTA 57.711 37.500 0.00 0.00 0.00 2.24
634 5760 9.962783 AATTCCAATCTACGTGACTTATACTAC 57.037 33.333 0.00 0.00 0.00 2.73
635 5761 8.743085 TTCCAATCTACGTGACTTATACTACT 57.257 34.615 0.00 0.00 0.00 2.57
696 5822 7.591421 TTTTTCCTTTTCTTTTACGGGAGAT 57.409 32.000 0.00 0.00 0.00 2.75
697 5823 8.694581 TTTTTCCTTTTCTTTTACGGGAGATA 57.305 30.769 0.00 0.00 0.00 1.98
698 5824 7.916914 TTTCCTTTTCTTTTACGGGAGATAG 57.083 36.000 0.00 0.00 0.00 2.08
699 5825 6.862469 TCCTTTTCTTTTACGGGAGATAGA 57.138 37.500 0.00 0.00 0.00 1.98
700 5826 7.433537 TCCTTTTCTTTTACGGGAGATAGAT 57.566 36.000 0.00 0.00 0.00 1.98
701 5827 7.858498 TCCTTTTCTTTTACGGGAGATAGATT 58.142 34.615 0.00 0.00 0.00 2.40
702 5828 7.769044 TCCTTTTCTTTTACGGGAGATAGATTG 59.231 37.037 0.00 0.00 0.00 2.67
703 5829 7.769044 CCTTTTCTTTTACGGGAGATAGATTGA 59.231 37.037 0.00 0.00 0.00 2.57
704 5830 8.718102 TTTTCTTTTACGGGAGATAGATTGAG 57.282 34.615 0.00 0.00 0.00 3.02
705 5831 7.419711 TTCTTTTACGGGAGATAGATTGAGT 57.580 36.000 0.00 0.00 0.00 3.41
706 5832 7.419711 TCTTTTACGGGAGATAGATTGAGTT 57.580 36.000 0.00 0.00 0.00 3.01
707 5833 7.848128 TCTTTTACGGGAGATAGATTGAGTTT 58.152 34.615 0.00 0.00 0.00 2.66
708 5834 8.319146 TCTTTTACGGGAGATAGATTGAGTTTT 58.681 33.333 0.00 0.00 0.00 2.43
709 5835 8.857694 TTTTACGGGAGATAGATTGAGTTTTT 57.142 30.769 0.00 0.00 0.00 1.94
747 5873 1.295792 GATCAAGATTTACCGCCGCA 58.704 50.000 0.00 0.00 0.00 5.69
788 5914 0.985549 CGCGTGTCTTAGTTGAGAGC 59.014 55.000 0.00 0.00 0.00 4.09
789 5915 1.351153 GCGTGTCTTAGTTGAGAGCC 58.649 55.000 0.00 0.00 0.00 4.70
831 5960 2.917971 CGTCTCGGCTTCAAGTTAAGAG 59.082 50.000 0.00 0.00 0.00 2.85
832 5961 3.612004 CGTCTCGGCTTCAAGTTAAGAGT 60.612 47.826 0.00 0.00 0.00 3.24
833 5962 3.921630 GTCTCGGCTTCAAGTTAAGAGTC 59.078 47.826 0.00 0.00 0.00 3.36
834 5963 3.056749 TCTCGGCTTCAAGTTAAGAGTCC 60.057 47.826 0.00 0.00 0.00 3.85
835 5964 2.631062 TCGGCTTCAAGTTAAGAGTCCA 59.369 45.455 0.00 0.00 0.00 4.02
836 5965 3.260884 TCGGCTTCAAGTTAAGAGTCCAT 59.739 43.478 0.00 0.00 0.00 3.41
876 6005 4.376008 GCGTTGTATGTTGGCGTCTATATG 60.376 45.833 0.00 0.00 0.00 1.78
877 6006 4.979815 CGTTGTATGTTGGCGTCTATATGA 59.020 41.667 0.00 0.00 0.00 2.15
878 6007 5.633601 CGTTGTATGTTGGCGTCTATATGAT 59.366 40.000 0.00 0.00 0.00 2.45
879 6008 6.804783 CGTTGTATGTTGGCGTCTATATGATA 59.195 38.462 0.00 0.00 0.00 2.15
880 6009 7.201325 CGTTGTATGTTGGCGTCTATATGATAC 60.201 40.741 0.00 0.00 0.00 2.24
949 6127 1.096416 GCACAGGAGCGTCTAGTACT 58.904 55.000 0.00 0.00 0.00 2.73
950 6128 1.064357 GCACAGGAGCGTCTAGTACTC 59.936 57.143 0.00 0.00 0.00 2.59
951 6129 2.634600 CACAGGAGCGTCTAGTACTCT 58.365 52.381 0.00 0.00 0.00 3.24
952 6130 2.353269 CACAGGAGCGTCTAGTACTCTG 59.647 54.545 0.00 0.08 0.00 3.35
953 6131 2.236644 ACAGGAGCGTCTAGTACTCTGA 59.763 50.000 0.00 0.00 0.00 3.27
954 6132 2.869801 CAGGAGCGTCTAGTACTCTGAG 59.130 54.545 0.00 2.45 0.00 3.35
955 6133 2.502538 AGGAGCGTCTAGTACTCTGAGT 59.497 50.000 15.57 15.57 0.00 3.41
956 6134 3.705579 AGGAGCGTCTAGTACTCTGAGTA 59.294 47.826 13.34 13.34 0.00 2.59
965 6143 2.119801 TACTCTGAGTACACGGGTCC 57.880 55.000 13.34 0.00 0.00 4.46
966 6144 0.111832 ACTCTGAGTACACGGGTCCA 59.888 55.000 8.91 0.00 0.00 4.02
967 6145 0.811915 CTCTGAGTACACGGGTCCAG 59.188 60.000 0.00 0.13 0.00 3.86
968 6146 0.111832 TCTGAGTACACGGGTCCAGT 59.888 55.000 0.00 0.00 0.00 4.00
969 6147 0.526662 CTGAGTACACGGGTCCAGTC 59.473 60.000 0.00 0.00 0.00 3.51
970 6148 0.896940 TGAGTACACGGGTCCAGTCC 60.897 60.000 0.00 0.00 0.00 3.85
971 6149 0.896940 GAGTACACGGGTCCAGTCCA 60.897 60.000 0.00 0.00 0.00 4.02
972 6150 0.898789 AGTACACGGGTCCAGTCCAG 60.899 60.000 0.00 0.00 0.00 3.86
973 6151 0.896940 GTACACGGGTCCAGTCCAGA 60.897 60.000 0.00 0.00 0.00 3.86
974 6152 0.040646 TACACGGGTCCAGTCCAGAT 59.959 55.000 0.00 0.00 0.00 2.90
975 6153 0.836400 ACACGGGTCCAGTCCAGATT 60.836 55.000 0.00 0.00 0.00 2.40
978 6156 0.613260 CGGGTCCAGTCCAGATTTCA 59.387 55.000 0.00 0.00 0.00 2.69
986 6164 6.931840 GGTCCAGTCCAGATTTCAGTTATATC 59.068 42.308 0.00 0.00 0.00 1.63
1024 6202 1.807981 TTTGCCGGCGTGTCTATCG 60.808 57.895 23.90 0.00 0.00 2.92
1034 6212 0.317938 GTGTCTATCGCCCGCTACAG 60.318 60.000 0.00 0.00 0.00 2.74
1055 6233 3.380671 CGACATCGCCCGTTACAC 58.619 61.111 0.00 0.00 0.00 2.90
1056 6234 2.162754 CGACATCGCCCGTTACACC 61.163 63.158 0.00 0.00 0.00 4.16
1057 6235 2.125832 ACATCGCCCGTTACACCG 60.126 61.111 0.00 0.00 0.00 4.94
1059 6237 4.825252 ATCGCCCGTTACACCGGC 62.825 66.667 0.00 0.00 46.71 6.13
1127 6305 2.669569 CCTGCTTGTGGTCACCGG 60.670 66.667 0.00 0.00 0.00 5.28
1154 6335 1.352156 CGTACGAAAGCCTCTGCACC 61.352 60.000 10.44 0.00 41.13 5.01
1155 6336 0.037232 GTACGAAAGCCTCTGCACCT 60.037 55.000 0.00 0.00 41.13 4.00
1156 6337 1.203994 GTACGAAAGCCTCTGCACCTA 59.796 52.381 0.00 0.00 41.13 3.08
1161 6342 1.196012 AAGCCTCTGCACCTACTACC 58.804 55.000 0.00 0.00 41.13 3.18
1228 6409 2.515523 CCATCCGCTGCTTCCCTG 60.516 66.667 0.00 0.00 0.00 4.45
1305 6486 2.758736 AAGATGTCACAGAGGCTGTC 57.241 50.000 0.00 0.00 43.43 3.51
1793 6976 2.125326 CGCTACCCGACATGGAGGA 61.125 63.158 9.92 0.00 42.00 3.71
1794 6977 1.464376 CGCTACCCGACATGGAGGAT 61.464 60.000 9.92 0.00 42.00 3.24
1809 6992 1.482593 GAGGATGACAACGTGGAGGAT 59.517 52.381 0.00 0.00 0.00 3.24
1818 7001 2.145397 ACGTGGAGGATAGAGAAGCA 57.855 50.000 0.00 0.00 0.00 3.91
1879 7062 5.047660 GCAGATAGATACGATCTCCAAAGGT 60.048 44.000 0.00 0.00 40.76 3.50
1885 7068 5.422331 AGATACGATCTCCAAAGGTTGAAGA 59.578 40.000 0.00 0.00 33.42 2.87
2136 7322 4.337274 ACAAAACCGGTTAGTTCCTGAAAG 59.663 41.667 22.60 1.04 0.00 2.62
2147 7333 4.003648 AGTTCCTGAAAGCCTATGTTTCG 58.996 43.478 0.00 0.00 36.81 3.46
2178 7364 3.006859 GCCTTACTTTCTTGCCACCATTT 59.993 43.478 0.00 0.00 0.00 2.32
2205 7398 8.846943 ATGTCATGTTGTTTGAGTAAGACATA 57.153 30.769 0.00 0.00 40.99 2.29
2247 7441 0.615331 AGGTGAAGGCGATGTGATGT 59.385 50.000 0.00 0.00 0.00 3.06
2275 7469 7.502696 TGTACAATGTAACTACATGATACCCC 58.497 38.462 0.00 0.00 45.55 4.95
2353 7549 7.452562 ACTAGTCATGGATTTTGGCAAATTTT 58.547 30.769 14.29 1.85 32.35 1.82
2354 7550 6.563222 AGTCATGGATTTTGGCAAATTTTG 57.437 33.333 14.29 4.72 32.35 2.44
2355 7551 5.474189 AGTCATGGATTTTGGCAAATTTTGG 59.526 36.000 14.29 2.92 32.35 3.28
2377 7573 3.436359 GCAAATTTGAACCGCCATTCAAT 59.564 39.130 22.31 0.00 45.55 2.57
2397 7593 5.657745 TCAATGAATGGGTGCACTTATGAAT 59.342 36.000 17.98 6.32 0.00 2.57
2412 7608 8.019669 GCACTTATGAATATCTATTGCTTGTGG 58.980 37.037 0.00 0.00 0.00 4.17
2421 7617 9.507329 AATATCTATTGCTTGTGGTCGATTAAT 57.493 29.630 0.00 0.00 0.00 1.40
2519 7715 6.731292 AAAATCCTCTGCCTAGTTTGTTTT 57.269 33.333 0.00 0.00 0.00 2.43
2540 7736 1.731720 GCTTTGGTTTGTTTGGTGCA 58.268 45.000 0.00 0.00 0.00 4.57
2541 7737 2.079925 GCTTTGGTTTGTTTGGTGCAA 58.920 42.857 0.00 0.00 0.00 4.08
2559 7755 6.990939 TGGTGCAAAATGATTCAAATGAAGAA 59.009 30.769 1.98 0.00 37.48 2.52
2614 7810 3.310774 CCATGTTGATCGAGTTGACCATC 59.689 47.826 0.00 0.00 0.00 3.51
2647 7843 1.227263 CGCGGGACCCACTATCAAG 60.227 63.158 12.15 0.00 0.00 3.02
2648 7844 1.672854 CGCGGGACCCACTATCAAGA 61.673 60.000 12.15 0.00 0.00 3.02
2649 7845 0.539986 GCGGGACCCACTATCAAGAA 59.460 55.000 12.15 0.00 0.00 2.52
2650 7846 1.473434 GCGGGACCCACTATCAAGAAG 60.473 57.143 12.15 0.00 0.00 2.85
2651 7847 1.831736 CGGGACCCACTATCAAGAAGT 59.168 52.381 12.15 0.00 0.00 3.01
2652 7848 2.418746 CGGGACCCACTATCAAGAAGTG 60.419 54.545 12.15 0.00 43.26 3.16
2653 7849 2.572104 GGGACCCACTATCAAGAAGTGT 59.428 50.000 5.33 0.00 42.30 3.55
2654 7850 3.773119 GGGACCCACTATCAAGAAGTGTA 59.227 47.826 5.33 0.00 42.30 2.90
2655 7851 4.409247 GGGACCCACTATCAAGAAGTGTAT 59.591 45.833 5.33 0.00 42.30 2.29
2656 7852 5.453480 GGGACCCACTATCAAGAAGTGTATC 60.453 48.000 5.33 0.42 42.30 2.24
2657 7853 5.453480 GGACCCACTATCAAGAAGTGTATCC 60.453 48.000 2.86 5.25 42.30 2.59
2658 7854 5.030147 ACCCACTATCAAGAAGTGTATCCA 58.970 41.667 2.86 0.00 42.30 3.41
2678 7874 1.234615 TGGCTTCTTGTACCAAGCGC 61.235 55.000 0.00 0.00 45.13 5.92
2697 7893 7.308408 CCAAGCGCTGTGTATACTATACTAGAA 60.308 40.741 12.58 0.00 0.00 2.10
2763 7969 3.496130 CCATGGATCTTTCGTGCTCATAC 59.504 47.826 5.56 0.00 0.00 2.39
2793 7999 6.832520 TCACAGTGGCATATATTTTGTTGT 57.167 33.333 0.00 0.00 0.00 3.32
2901 8107 0.976641 TCGCTGATCCACCTTGTCTT 59.023 50.000 0.00 0.00 0.00 3.01
2916 8122 1.229400 TCTTCGGTGGCCTTAGGGT 60.229 57.895 3.32 0.00 34.45 4.34
2925 8131 1.149401 GCCTTAGGGTCATGGAGGC 59.851 63.158 0.00 0.00 45.21 4.70
2927 8133 1.227674 CTTAGGGTCATGGAGGCGC 60.228 63.158 0.00 0.00 34.52 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 1113 7.068103 TGAGTGGTGACATGAAAACAAAACTAT 59.932 33.333 0.00 0.00 46.14 2.12
89 1127 1.345741 CTGACTGGTGAGTGGTGACAT 59.654 52.381 0.00 0.00 46.14 3.06
92 1130 1.040646 GACTGACTGGTGAGTGGTGA 58.959 55.000 0.00 0.00 30.16 4.02
93 1131 0.752658 TGACTGACTGGTGAGTGGTG 59.247 55.000 0.00 0.00 30.16 4.17
94 1132 1.043816 CTGACTGACTGGTGAGTGGT 58.956 55.000 0.00 0.00 30.16 4.16
95 1133 1.043816 ACTGACTGACTGGTGAGTGG 58.956 55.000 0.00 0.00 32.82 4.00
96 1134 2.145958 CACTGACTGACTGGTGAGTG 57.854 55.000 0.00 0.59 42.72 3.51
97 1135 1.410517 CACACTGACTGACTGGTGAGT 59.589 52.381 0.00 0.00 34.22 3.41
98 1136 1.683385 TCACACTGACTGACTGGTGAG 59.317 52.381 0.00 0.00 34.28 3.51
111 1149 3.752747 TGGCATAACATCAAGTCACACTG 59.247 43.478 0.00 0.00 0.00 3.66
122 1160 9.807649 ATTAAAATGTTCTTCTGGCATAACATC 57.192 29.630 14.15 0.00 40.66 3.06
137 1175 7.635587 CGCATAATGCAACCAATTAAAATGTTC 59.364 33.333 0.00 0.00 45.36 3.18
162 1201 5.062558 CCAAATTATTTCTTGCCAAAGCTCG 59.937 40.000 0.00 0.00 40.80 5.03
164 1203 6.112927 TCCAAATTATTTCTTGCCAAAGCT 57.887 33.333 0.00 0.00 40.80 3.74
230 1270 1.071385 ACAGGGTGTTGCTTCTCTGAG 59.929 52.381 0.00 0.00 0.00 3.35
246 1286 4.202161 ACACTTAAGGCGAGATATGACAGG 60.202 45.833 7.53 0.00 0.00 4.00
288 1328 4.695217 AGAAAGCAAAGTTCACGTCAAA 57.305 36.364 0.00 0.00 0.00 2.69
290 1330 4.394920 AGAAAGAAAGCAAAGTTCACGTCA 59.605 37.500 0.00 0.00 0.00 4.35
294 1335 7.592903 CCTGAATAGAAAGAAAGCAAAGTTCAC 59.407 37.037 0.00 0.00 0.00 3.18
303 1344 3.441572 TGCTGCCTGAATAGAAAGAAAGC 59.558 43.478 0.00 0.00 0.00 3.51
314 1361 0.403271 ACCTGAGTTGCTGCCTGAAT 59.597 50.000 0.00 0.00 0.00 2.57
338 1385 0.734889 CACCCATCGCCATGACTTTC 59.265 55.000 0.00 0.00 30.57 2.62
395 1449 3.188895 TCAGCGATGATATCTTCGACG 57.811 47.619 33.12 24.59 43.48 5.12
414 1468 7.201478 CCACTAATCATCGTTCAGAGAAAGTTC 60.201 40.741 0.00 0.00 0.00 3.01
422 1476 6.037786 AGAAACCACTAATCATCGTTCAGA 57.962 37.500 0.00 0.00 0.00 3.27
474 4607 6.581166 GGTAAAATACGGCTTCTTGACAAAAG 59.419 38.462 0.00 0.00 0.00 2.27
488 4621 6.715718 TGATCTCTCTCTAGGGTAAAATACGG 59.284 42.308 0.00 0.00 0.00 4.02
526 4659 4.293415 CGCATCTTAAAATTCCTCATGCC 58.707 43.478 0.00 0.00 33.14 4.40
527 4660 3.732721 GCGCATCTTAAAATTCCTCATGC 59.267 43.478 0.30 0.00 33.35 4.06
528 4661 4.202040 TGGCGCATCTTAAAATTCCTCATG 60.202 41.667 10.83 0.00 0.00 3.07
529 4662 3.953612 TGGCGCATCTTAAAATTCCTCAT 59.046 39.130 10.83 0.00 0.00 2.90
530 4663 3.351740 TGGCGCATCTTAAAATTCCTCA 58.648 40.909 10.83 0.00 0.00 3.86
531 4664 3.378427 ACTGGCGCATCTTAAAATTCCTC 59.622 43.478 10.83 0.00 0.00 3.71
532 4665 3.356290 ACTGGCGCATCTTAAAATTCCT 58.644 40.909 10.83 0.00 0.00 3.36
533 4666 3.782889 ACTGGCGCATCTTAAAATTCC 57.217 42.857 10.83 0.00 0.00 3.01
534 4667 5.485662 ACTACTGGCGCATCTTAAAATTC 57.514 39.130 10.83 0.00 0.00 2.17
535 4668 6.765989 TGATACTACTGGCGCATCTTAAAATT 59.234 34.615 10.83 0.00 0.00 1.82
536 4669 6.288294 TGATACTACTGGCGCATCTTAAAAT 58.712 36.000 10.83 0.00 0.00 1.82
537 4670 5.666462 TGATACTACTGGCGCATCTTAAAA 58.334 37.500 10.83 0.00 0.00 1.52
538 4671 5.270893 TGATACTACTGGCGCATCTTAAA 57.729 39.130 10.83 0.00 0.00 1.52
539 4672 4.929819 TGATACTACTGGCGCATCTTAA 57.070 40.909 10.83 0.00 0.00 1.85
540 4673 5.221441 ACAATGATACTACTGGCGCATCTTA 60.221 40.000 10.83 0.00 0.00 2.10
541 4674 4.060900 CAATGATACTACTGGCGCATCTT 58.939 43.478 10.83 0.00 0.00 2.40
542 4675 3.070159 ACAATGATACTACTGGCGCATCT 59.930 43.478 10.83 0.00 0.00 2.90
543 4676 3.393800 ACAATGATACTACTGGCGCATC 58.606 45.455 10.83 1.68 0.00 3.91
544 4677 3.475566 ACAATGATACTACTGGCGCAT 57.524 42.857 10.83 0.00 0.00 4.73
545 4678 2.979814 ACAATGATACTACTGGCGCA 57.020 45.000 10.83 0.00 0.00 6.09
546 4679 4.588278 GAAAACAATGATACTACTGGCGC 58.412 43.478 0.00 0.00 0.00 6.53
547 4680 4.260212 CCGAAAACAATGATACTACTGGCG 60.260 45.833 0.00 0.00 0.00 5.69
560 4693 6.270064 CCAAACTGTTCTAACCGAAAACAAT 58.730 36.000 0.00 0.00 32.89 2.71
564 4720 3.695060 TGCCAAACTGTTCTAACCGAAAA 59.305 39.130 0.00 0.00 32.41 2.29
593 4749 8.280258 AGATTGGAATTGGATAGGAATACTGA 57.720 34.615 0.00 0.00 0.00 3.41
594 4750 9.442047 GTAGATTGGAATTGGATAGGAATACTG 57.558 37.037 0.00 0.00 0.00 2.74
619 5745 9.701098 TGAATTTGAAAGTAGTATAAGTCACGT 57.299 29.630 0.00 0.00 0.00 4.49
634 5760 6.422701 TCTGCAGCTTTGATTGAATTTGAAAG 59.577 34.615 9.47 0.00 0.00 2.62
635 5761 6.282167 TCTGCAGCTTTGATTGAATTTGAAA 58.718 32.000 9.47 0.00 0.00 2.69
677 5803 7.769044 TCAATCTATCTCCCGTAAAAGAAAAGG 59.231 37.037 0.00 0.00 0.00 3.11
678 5804 8.718102 TCAATCTATCTCCCGTAAAAGAAAAG 57.282 34.615 0.00 0.00 0.00 2.27
679 5805 8.319146 ACTCAATCTATCTCCCGTAAAAGAAAA 58.681 33.333 0.00 0.00 0.00 2.29
680 5806 7.848128 ACTCAATCTATCTCCCGTAAAAGAAA 58.152 34.615 0.00 0.00 0.00 2.52
681 5807 7.419711 ACTCAATCTATCTCCCGTAAAAGAA 57.580 36.000 0.00 0.00 0.00 2.52
682 5808 7.419711 AACTCAATCTATCTCCCGTAAAAGA 57.580 36.000 0.00 0.00 0.00 2.52
683 5809 8.494016 AAAACTCAATCTATCTCCCGTAAAAG 57.506 34.615 0.00 0.00 0.00 2.27
684 5810 8.857694 AAAAACTCAATCTATCTCCCGTAAAA 57.142 30.769 0.00 0.00 0.00 1.52
709 5835 6.395780 TGATCCCCCAGTCTACATTAAAAA 57.604 37.500 0.00 0.00 0.00 1.94
710 5836 6.216662 TCTTGATCCCCCAGTCTACATTAAAA 59.783 38.462 0.00 0.00 0.00 1.52
711 5837 5.729229 TCTTGATCCCCCAGTCTACATTAAA 59.271 40.000 0.00 0.00 0.00 1.52
712 5838 5.285401 TCTTGATCCCCCAGTCTACATTAA 58.715 41.667 0.00 0.00 0.00 1.40
713 5839 4.890988 TCTTGATCCCCCAGTCTACATTA 58.109 43.478 0.00 0.00 0.00 1.90
714 5840 3.736094 TCTTGATCCCCCAGTCTACATT 58.264 45.455 0.00 0.00 0.00 2.71
747 5873 4.086457 GGACAGGTTGGTTATTTGGACAT 58.914 43.478 0.00 0.00 0.00 3.06
788 5914 0.179073 CATGGAGACTAACCAGCCGG 60.179 60.000 0.00 0.00 40.89 6.13
789 5915 0.537188 ACATGGAGACTAACCAGCCG 59.463 55.000 0.00 0.00 40.89 5.52
831 5960 0.322322 TAACACACCCGGACATGGAC 59.678 55.000 0.73 0.00 0.00 4.02
832 5961 0.322322 GTAACACACCCGGACATGGA 59.678 55.000 0.73 0.00 0.00 3.41
833 5962 1.017177 CGTAACACACCCGGACATGG 61.017 60.000 0.73 0.00 0.00 3.66
834 5963 1.017177 CCGTAACACACCCGGACATG 61.017 60.000 0.73 0.00 44.41 3.21
835 5964 1.294138 CCGTAACACACCCGGACAT 59.706 57.895 0.73 0.00 44.41 3.06
836 5965 2.735883 CCGTAACACACCCGGACA 59.264 61.111 0.73 0.00 44.41 4.02
876 6005 4.026558 CACATCACGCTGTGTATGTGTATC 60.027 45.833 24.50 0.00 41.39 2.24
877 6006 3.865164 CACATCACGCTGTGTATGTGTAT 59.135 43.478 24.50 7.74 41.39 2.29
878 6007 3.057174 TCACATCACGCTGTGTATGTGTA 60.057 43.478 27.29 20.24 45.40 2.90
879 6008 2.068519 CACATCACGCTGTGTATGTGT 58.931 47.619 24.50 13.54 41.39 3.72
880 6009 2.336667 TCACATCACGCTGTGTATGTG 58.663 47.619 25.49 25.49 45.40 3.21
946 6124 1.352017 TGGACCCGTGTACTCAGAGTA 59.648 52.381 6.15 6.15 0.00 2.59
949 6127 0.111832 ACTGGACCCGTGTACTCAGA 59.888 55.000 0.00 0.00 0.00 3.27
950 6128 0.526662 GACTGGACCCGTGTACTCAG 59.473 60.000 0.00 0.00 0.00 3.35
951 6129 0.896940 GGACTGGACCCGTGTACTCA 60.897 60.000 0.00 0.00 0.00 3.41
952 6130 0.896940 TGGACTGGACCCGTGTACTC 60.897 60.000 0.00 0.00 0.00 2.59
953 6131 0.898789 CTGGACTGGACCCGTGTACT 60.899 60.000 0.00 0.00 0.00 2.73
954 6132 0.896940 TCTGGACTGGACCCGTGTAC 60.897 60.000 0.00 0.00 0.00 2.90
955 6133 0.040646 ATCTGGACTGGACCCGTGTA 59.959 55.000 0.00 0.00 0.00 2.90
956 6134 0.836400 AATCTGGACTGGACCCGTGT 60.836 55.000 0.00 0.00 0.00 4.49
958 6136 0.613777 GAAATCTGGACTGGACCCGT 59.386 55.000 0.00 0.00 0.00 5.28
959 6137 0.613260 TGAAATCTGGACTGGACCCG 59.387 55.000 0.00 0.00 0.00 5.28
960 6138 1.630878 ACTGAAATCTGGACTGGACCC 59.369 52.381 0.00 0.00 0.00 4.46
961 6139 3.425162 AACTGAAATCTGGACTGGACC 57.575 47.619 0.00 0.00 0.00 4.46
963 6141 6.846505 AGGATATAACTGAAATCTGGACTGGA 59.153 38.462 0.00 0.00 0.00 3.86
964 6142 6.933521 CAGGATATAACTGAAATCTGGACTGG 59.066 42.308 1.56 0.00 38.20 4.00
965 6143 6.426328 GCAGGATATAACTGAAATCTGGACTG 59.574 42.308 10.27 0.00 38.20 3.51
966 6144 6.465035 GGCAGGATATAACTGAAATCTGGACT 60.465 42.308 10.27 0.00 38.20 3.85
967 6145 5.703130 GGCAGGATATAACTGAAATCTGGAC 59.297 44.000 10.27 0.00 38.20 4.02
968 6146 5.221925 GGGCAGGATATAACTGAAATCTGGA 60.222 44.000 10.27 0.00 38.20 3.86
969 6147 5.006386 GGGCAGGATATAACTGAAATCTGG 58.994 45.833 10.27 0.00 38.20 3.86
970 6148 4.692625 CGGGCAGGATATAACTGAAATCTG 59.307 45.833 10.27 0.00 38.20 2.90
971 6149 4.348168 ACGGGCAGGATATAACTGAAATCT 59.652 41.667 10.27 0.00 38.20 2.40
972 6150 4.642429 ACGGGCAGGATATAACTGAAATC 58.358 43.478 10.27 0.00 38.20 2.17
973 6151 4.505039 GGACGGGCAGGATATAACTGAAAT 60.505 45.833 10.27 0.00 38.20 2.17
974 6152 3.181458 GGACGGGCAGGATATAACTGAAA 60.181 47.826 10.27 0.00 38.20 2.69
975 6153 2.367567 GGACGGGCAGGATATAACTGAA 59.632 50.000 10.27 0.00 38.20 3.02
978 6156 0.966920 CGGACGGGCAGGATATAACT 59.033 55.000 0.00 0.00 0.00 2.24
1048 6226 3.167945 GACGTCGCCGGTGTAACG 61.168 66.667 23.06 23.06 38.12 3.18
1049 6227 3.167945 CGACGTCGCCGGTGTAAC 61.168 66.667 26.59 5.79 38.78 2.50
1154 6335 0.318784 GATCGCCTTGCCGGTAGTAG 60.319 60.000 1.90 0.00 34.25 2.57
1155 6336 1.737816 GATCGCCTTGCCGGTAGTA 59.262 57.895 1.90 0.00 34.25 1.82
1156 6337 2.499685 GATCGCCTTGCCGGTAGT 59.500 61.111 1.90 0.00 34.25 2.73
1228 6409 3.562779 TTTCCGAGGTGTCGCCGTC 62.563 63.158 0.00 0.00 45.41 4.79
1305 6486 3.003480 GCTAAAGGAGTACTGCACCTTG 58.997 50.000 17.34 6.08 45.44 3.61
1416 6597 6.017357 GGTCGACTCTGTTCCAAAAATACTTT 60.017 38.462 16.46 0.00 0.00 2.66
1431 6612 1.395608 GACTTCTCGAGGTCGACTCTG 59.604 57.143 16.46 5.35 44.22 3.35
1793 6976 3.632333 TCTCTATCCTCCACGTTGTCAT 58.368 45.455 0.00 0.00 0.00 3.06
1794 6977 3.081710 TCTCTATCCTCCACGTTGTCA 57.918 47.619 0.00 0.00 0.00 3.58
1818 7001 0.316204 GCAGCCACAGCAATTCTTGT 59.684 50.000 0.00 0.00 43.56 3.16
1828 7011 2.643272 CAAGTGCTGCAGCCACAG 59.357 61.111 34.64 22.19 41.18 3.66
2136 7322 3.426292 GGCTTCAACTTCGAAACATAGGC 60.426 47.826 0.00 2.34 0.00 3.93
2147 7333 5.215903 GCAAGAAAGTAAGGCTTCAACTTC 58.784 41.667 14.12 8.83 36.17 3.01
2178 7364 6.765512 TGTCTTACTCAAACAACATGACATCA 59.234 34.615 0.00 0.00 0.00 3.07
2205 7398 1.457346 CTGCCGCCTGAAAGAGAAAT 58.543 50.000 0.00 0.00 34.07 2.17
2209 7402 1.743252 GACCTGCCGCCTGAAAGAG 60.743 63.158 0.00 0.00 34.07 2.85
2217 7411 4.329545 TTCACCTGACCTGCCGCC 62.330 66.667 0.00 0.00 0.00 6.13
2247 7441 8.418662 GGTATCATGTAGTTACATTGTACAGGA 58.581 37.037 17.07 7.11 43.99 3.86
2275 7469 7.278646 TCAACAATATCTTTGAGAACGGATCAG 59.721 37.037 0.00 0.00 0.00 2.90
2354 7550 1.731709 GAATGGCGGTTCAAATTTGCC 59.268 47.619 13.54 11.06 45.91 4.52
2355 7551 2.411904 TGAATGGCGGTTCAAATTTGC 58.588 42.857 13.54 1.00 35.31 3.68
2362 7558 3.507103 CATTCATTGAATGGCGGTTCA 57.493 42.857 25.33 1.53 43.78 3.18
2377 7573 6.604171 AGATATTCATAAGTGCACCCATTCA 58.396 36.000 14.63 0.00 0.00 2.57
2397 7593 9.990360 TTATTAATCGACCACAAGCAATAGATA 57.010 29.630 0.00 0.00 0.00 1.98
2488 7684 7.676683 ACTAGGCAGAGGATTTTACATCTTA 57.323 36.000 0.00 0.00 0.00 2.10
2495 7691 7.308348 CGAAAACAAACTAGGCAGAGGATTTTA 60.308 37.037 0.00 0.00 0.00 1.52
2519 7715 1.737363 GCACCAAACAAACCAAAGCGA 60.737 47.619 0.00 0.00 0.00 4.93
2647 7843 9.894518 TGGTACAAGAAGCCATGGATACACTTC 62.895 44.444 18.40 17.46 45.66 3.01
2648 7844 8.220021 TGGTACAAGAAGCCATGGATACACTT 62.220 42.308 18.40 13.09 45.66 3.16
2649 7845 6.811174 TGGTACAAGAAGCCATGGATACACT 61.811 44.000 18.40 7.21 45.66 3.55
2650 7846 4.625324 TGGTACAAGAAGCCATGGATACAC 60.625 45.833 18.40 4.71 45.66 2.90
2651 7847 3.521531 TGGTACAAGAAGCCATGGATACA 59.478 43.478 18.40 0.00 46.99 2.29
2652 7848 4.150897 TGGTACAAGAAGCCATGGATAC 57.849 45.455 18.40 2.28 31.92 2.24
2678 7874 9.383462 CGTTTGCTTCTAGTATAGTATACACAG 57.617 37.037 19.98 15.85 40.38 3.66
2716 7912 6.249260 GCATAACAACATCAATGAAAGACGAC 59.751 38.462 0.00 0.00 0.00 4.34
2763 7969 2.696989 TATGCCACTGTGATGTCCAG 57.303 50.000 9.86 0.00 36.01 3.86
2793 7999 6.892658 ACTAATTCATGTTTAGCACCAACA 57.107 33.333 14.22 0.00 38.49 3.33
2882 8088 0.976641 AAGACAAGGTGGATCAGCGA 59.023 50.000 0.00 0.00 36.92 4.93
2885 8091 1.276421 ACCGAAGACAAGGTGGATCAG 59.724 52.381 0.00 0.00 39.66 2.90
2901 8107 1.306654 ATGACCCTAAGGCCACCGA 60.307 57.895 5.01 0.00 36.11 4.69


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

AutoCloner maintained by Alex Coulton.