Multiple sequence alignment - TraesCS2A01G193000

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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 TraesCS2A01G193000 chr2A 100.000 3187 0 0 1 3187 161327662 161330848 0.000000e+00 5886
1 TraesCS2A01G193000 chr2D 90.699 3161 136 56 94 3187 139530367 139527298 0.000000e+00 4063
2 TraesCS2A01G193000 chr2B 92.809 2058 89 26 412 2444 198635768 198637791 0.000000e+00 2926
3 TraesCS2A01G193000 chr2B 86.676 683 46 21 2493 3156 198637805 198638461 0.000000e+00 715
4 TraesCS2A01G193000 chr2B 93.431 137 7 2 280 416 198635395 198635529 5.390000e-48 202
5 TraesCS2A01G193000 chr3B 89.308 1141 74 21 1060 2188 402914850 402913746 0.000000e+00 1387
6 TraesCS2A01G193000 chr6B 86.050 724 54 23 1513 2224 492508887 492508199 0.000000e+00 734
7 TraesCS2A01G193000 chr6B 90.112 445 42 2 1059 1501 492521739 492521295 7.670000e-161 577
8 TraesCS2A01G193000 chr7D 86.881 404 51 1 1216 1619 150762116 150762517 4.850000e-123 451


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 TraesCS2A01G193000 chr2A 161327662 161330848 3186 False 5886 5886 100.000 1 3187 1 chr2A.!!$F1 3186
1 TraesCS2A01G193000 chr2D 139527298 139530367 3069 True 4063 4063 90.699 94 3187 1 chr2D.!!$R1 3093
2 TraesCS2A01G193000 chr2B 198635395 198638461 3066 False 1281 2926 90.972 280 3156 3 chr2B.!!$F1 2876
3 TraesCS2A01G193000 chr3B 402913746 402914850 1104 True 1387 1387 89.308 1060 2188 1 chr3B.!!$R1 1128
4 TraesCS2A01G193000 chr6B 492508199 492508887 688 True 734 734 86.050 1513 2224 1 chr6B.!!$R1 711

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
907 1170 0.035056 CGCACCCAATTCTTCCTCCT 60.035 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2822 3172 0.378962 TCGGTTGAACCAGCAAAACG 59.621 50.0 15.58 0.0 38.47 3.6 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
17 18 3.166434 AACACGGCCTCATTCCCA 58.834 55.556 0.00 0.00 0.00 4.37
18 19 1.303317 AACACGGCCTCATTCCCAC 60.303 57.895 0.00 0.00 0.00 4.61
19 20 1.779061 AACACGGCCTCATTCCCACT 61.779 55.000 0.00 0.00 0.00 4.00
20 21 1.450312 CACGGCCTCATTCCCACTC 60.450 63.158 0.00 0.00 0.00 3.51
21 22 1.613630 ACGGCCTCATTCCCACTCT 60.614 57.895 0.00 0.00 0.00 3.24
22 23 1.144936 CGGCCTCATTCCCACTCTC 59.855 63.158 0.00 0.00 0.00 3.20
23 24 1.617018 CGGCCTCATTCCCACTCTCA 61.617 60.000 0.00 0.00 0.00 3.27
24 25 0.620556 GGCCTCATTCCCACTCTCAA 59.379 55.000 0.00 0.00 0.00 3.02
25 26 1.004745 GGCCTCATTCCCACTCTCAAA 59.995 52.381 0.00 0.00 0.00 2.69
26 27 2.357569 GGCCTCATTCCCACTCTCAAAT 60.358 50.000 0.00 0.00 0.00 2.32
27 28 2.686915 GCCTCATTCCCACTCTCAAATG 59.313 50.000 0.00 0.00 0.00 2.32
28 29 3.285484 CCTCATTCCCACTCTCAAATGG 58.715 50.000 0.00 0.00 35.59 3.16
29 30 3.054139 CCTCATTCCCACTCTCAAATGGA 60.054 47.826 0.00 0.00 38.34 3.41
30 31 3.944015 CTCATTCCCACTCTCAAATGGAC 59.056 47.826 0.00 0.00 38.34 4.02
31 32 3.330405 TCATTCCCACTCTCAAATGGACA 59.670 43.478 0.00 0.00 38.34 4.02
32 33 3.874383 TTCCCACTCTCAAATGGACAA 57.126 42.857 0.00 0.00 38.34 3.18
33 34 3.874383 TCCCACTCTCAAATGGACAAA 57.126 42.857 0.00 0.00 38.34 2.83
34 35 4.177537 TCCCACTCTCAAATGGACAAAA 57.822 40.909 0.00 0.00 38.34 2.44
35 36 4.739793 TCCCACTCTCAAATGGACAAAAT 58.260 39.130 0.00 0.00 38.34 1.82
36 37 5.147032 TCCCACTCTCAAATGGACAAAATT 58.853 37.500 0.00 0.00 38.34 1.82
37 38 5.243730 TCCCACTCTCAAATGGACAAAATTC 59.756 40.000 0.00 0.00 38.34 2.17
38 39 5.010922 CCCACTCTCAAATGGACAAAATTCA 59.989 40.000 0.00 0.00 38.34 2.57
39 40 6.462768 CCCACTCTCAAATGGACAAAATTCAA 60.463 38.462 0.00 0.00 38.34 2.69
40 41 6.985645 CCACTCTCAAATGGACAAAATTCAAA 59.014 34.615 0.00 0.00 38.34 2.69
41 42 7.658575 CCACTCTCAAATGGACAAAATTCAAAT 59.341 33.333 0.00 0.00 38.34 2.32
42 43 9.695526 CACTCTCAAATGGACAAAATTCAAATA 57.304 29.630 0.00 0.00 0.00 1.40
51 52 7.832550 TGGACAAAATTCAAATAAAACGAACG 58.167 30.769 0.00 0.00 0.00 3.95
52 53 7.488471 TGGACAAAATTCAAATAAAACGAACGT 59.512 29.630 0.00 0.00 0.00 3.99
53 54 8.322428 GGACAAAATTCAAATAAAACGAACGTT 58.678 29.630 0.00 0.00 40.45 3.99
55 56 9.466741 ACAAAATTCAAATAAAACGAACGTTTG 57.533 25.926 22.45 14.14 46.22 2.93
56 57 9.466741 CAAAATTCAAATAAAACGAACGTTTGT 57.533 25.926 22.45 15.61 46.22 2.83
59 60 9.466741 AATTCAAATAAAACGAACGTTTGTTTG 57.533 25.926 35.59 30.36 46.22 2.93
60 61 6.979509 TCAAATAAAACGAACGTTTGTTTGG 58.020 32.000 35.59 24.66 46.22 3.28
61 62 6.805271 TCAAATAAAACGAACGTTTGTTTGGA 59.195 30.769 35.59 28.34 46.22 3.53
62 63 6.799786 AATAAAACGAACGTTTGTTTGGAG 57.200 33.333 35.59 10.62 46.22 3.86
63 64 2.182904 AACGAACGTTTGTTTGGAGC 57.817 45.000 25.05 0.00 42.77 4.70
64 65 0.379316 ACGAACGTTTGTTTGGAGCC 59.621 50.000 15.61 0.00 42.77 4.70
65 66 0.656205 CGAACGTTTGTTTGGAGCCG 60.656 55.000 0.46 0.00 38.78 5.52
66 67 0.933047 GAACGTTTGTTTGGAGCCGC 60.933 55.000 0.46 0.00 38.78 6.53
67 68 1.658686 AACGTTTGTTTGGAGCCGCA 61.659 50.000 0.00 0.00 33.53 5.69
68 69 1.657181 CGTTTGTTTGGAGCCGCAC 60.657 57.895 0.00 0.00 0.00 5.34
69 70 1.657181 GTTTGTTTGGAGCCGCACG 60.657 57.895 0.00 0.00 0.00 5.34
70 71 1.820056 TTTGTTTGGAGCCGCACGA 60.820 52.632 0.00 0.00 0.00 4.35
71 72 1.169661 TTTGTTTGGAGCCGCACGAT 61.170 50.000 0.00 0.00 0.00 3.73
72 73 1.851021 TTGTTTGGAGCCGCACGATG 61.851 55.000 0.00 0.00 0.00 3.84
73 74 2.745884 TTTGGAGCCGCACGATGG 60.746 61.111 0.00 0.00 0.00 3.51
74 75 3.247056 TTTGGAGCCGCACGATGGA 62.247 57.895 0.00 0.00 0.00 3.41
75 76 3.664025 TTGGAGCCGCACGATGGAG 62.664 63.158 0.00 0.00 0.00 3.86
76 77 4.148825 GGAGCCGCACGATGGAGT 62.149 66.667 0.00 0.00 0.00 3.85
77 78 2.125512 GAGCCGCACGATGGAGTT 60.126 61.111 0.00 0.00 0.00 3.01
78 79 2.434884 AGCCGCACGATGGAGTTG 60.435 61.111 0.00 0.00 0.00 3.16
79 80 3.499737 GCCGCACGATGGAGTTGG 61.500 66.667 0.00 0.00 0.00 3.77
80 81 3.499737 CCGCACGATGGAGTTGGC 61.500 66.667 0.00 0.00 0.00 4.52
81 82 3.499737 CGCACGATGGAGTTGGCC 61.500 66.667 0.00 0.00 0.00 5.36
82 83 2.045926 GCACGATGGAGTTGGCCT 60.046 61.111 3.32 0.00 0.00 5.19
83 84 2.401766 GCACGATGGAGTTGGCCTG 61.402 63.158 3.32 0.00 0.00 4.85
84 85 1.296392 CACGATGGAGTTGGCCTGA 59.704 57.895 3.32 0.00 0.00 3.86
85 86 0.107508 CACGATGGAGTTGGCCTGAT 60.108 55.000 3.32 0.00 0.00 2.90
86 87 0.620556 ACGATGGAGTTGGCCTGATT 59.379 50.000 3.32 0.00 0.00 2.57
87 88 1.004745 ACGATGGAGTTGGCCTGATTT 59.995 47.619 3.32 0.00 0.00 2.17
88 89 1.672881 CGATGGAGTTGGCCTGATTTC 59.327 52.381 3.32 0.00 0.00 2.17
89 90 2.726821 GATGGAGTTGGCCTGATTTCA 58.273 47.619 3.32 0.00 0.00 2.69
90 91 1.909700 TGGAGTTGGCCTGATTTCAC 58.090 50.000 3.32 0.00 0.00 3.18
91 92 0.804989 GGAGTTGGCCTGATTTCACG 59.195 55.000 3.32 0.00 0.00 4.35
92 93 0.804989 GAGTTGGCCTGATTTCACGG 59.195 55.000 3.32 0.00 0.00 4.94
103 104 4.509230 CCTGATTTCACGGTGTGATGATAG 59.491 45.833 8.17 0.35 42.40 2.08
104 105 4.441792 TGATTTCACGGTGTGATGATAGG 58.558 43.478 8.17 0.00 42.40 2.57
109 110 0.882042 CGGTGTGATGATAGGCCAGC 60.882 60.000 5.01 0.00 0.00 4.85
125 130 0.169672 CAGCGCAGAAACATCCAAGG 59.830 55.000 11.47 0.00 0.00 3.61
126 131 0.036732 AGCGCAGAAACATCCAAGGA 59.963 50.000 11.47 0.00 0.00 3.36
127 132 0.169009 GCGCAGAAACATCCAAGGAC 59.831 55.000 0.30 0.00 0.00 3.85
128 133 1.813513 CGCAGAAACATCCAAGGACT 58.186 50.000 0.00 0.00 0.00 3.85
129 134 2.154462 CGCAGAAACATCCAAGGACTT 58.846 47.619 0.00 0.00 0.00 3.01
130 135 2.095567 CGCAGAAACATCCAAGGACTTG 60.096 50.000 5.09 5.09 40.13 3.16
156 161 4.477975 CGACTCGGAGCCGACACC 62.478 72.222 8.06 0.00 44.01 4.16
157 162 3.371063 GACTCGGAGCCGACACCA 61.371 66.667 7.66 0.00 44.01 4.17
179 184 2.771435 GGGCATGCAAAAATGCTCC 58.229 52.632 21.36 3.89 46.50 4.70
186 191 0.681175 GCAAAAATGCTCCTGTGGGT 59.319 50.000 0.00 0.00 0.00 4.51
195 200 1.674962 GCTCCTGTGGGTACGTACTAG 59.325 57.143 24.07 16.19 0.00 2.57
196 201 2.943199 GCTCCTGTGGGTACGTACTAGT 60.943 54.545 24.07 0.00 0.00 2.57
197 202 3.682718 GCTCCTGTGGGTACGTACTAGTA 60.683 52.174 24.07 0.00 0.00 1.82
198 203 3.873910 TCCTGTGGGTACGTACTAGTAC 58.126 50.000 24.07 21.06 44.50 2.73
216 221 5.824904 AGTACGTGGTAGTATGATTCGTT 57.175 39.130 0.00 0.00 0.00 3.85
217 222 5.575957 AGTACGTGGTAGTATGATTCGTTG 58.424 41.667 0.00 0.00 0.00 4.10
218 223 4.445452 ACGTGGTAGTATGATTCGTTGT 57.555 40.909 0.00 0.00 0.00 3.32
230 235 3.484285 TGATTCGTTGTGTATATGACGCG 59.516 43.478 3.53 3.53 41.82 6.01
575 826 3.068881 CTGAACTCTTCGCCCCCA 58.931 61.111 0.00 0.00 0.00 4.96
576 827 1.376037 CTGAACTCTTCGCCCCCAC 60.376 63.158 0.00 0.00 0.00 4.61
578 829 3.952628 GAACTCTTCGCCCCCACCG 62.953 68.421 0.00 0.00 0.00 4.94
696 948 3.162858 TTTCCGACGGTGGGTGGT 61.163 61.111 14.79 0.00 0.00 4.16
718 970 4.547367 CGGGGCCGTCTGATTCCC 62.547 72.222 0.00 3.99 38.03 3.97
773 1025 1.797025 AGCGGCAGAAAAGTAGTGAC 58.203 50.000 1.45 0.00 0.00 3.67
862 1117 1.512926 CCCCCTCGCTTATTTCATCG 58.487 55.000 0.00 0.00 0.00 3.84
907 1170 0.035056 CGCACCCAATTCTTCCTCCT 60.035 55.000 0.00 0.00 0.00 3.69
908 1171 1.756430 GCACCCAATTCTTCCTCCTC 58.244 55.000 0.00 0.00 0.00 3.71
909 1172 1.683319 GCACCCAATTCTTCCTCCTCC 60.683 57.143 0.00 0.00 0.00 4.30
910 1173 1.635487 CACCCAATTCTTCCTCCTCCA 59.365 52.381 0.00 0.00 0.00 3.86
927 1193 2.287896 ATTCCATCCCCCAGCCCA 60.288 61.111 0.00 0.00 0.00 5.36
928 1194 2.397902 ATTCCATCCCCCAGCCCAG 61.398 63.158 0.00 0.00 0.00 4.45
938 1210 2.433994 CCAGCCCAGCTCTCTCTCC 61.434 68.421 0.00 0.00 36.40 3.71
961 1233 2.726351 CCTCCGAGGTTCTCTGCCC 61.726 68.421 6.24 0.00 0.00 5.36
997 1269 4.208686 GGTAGAGCACGGCGGAGG 62.209 72.222 13.24 0.77 0.00 4.30
1414 1686 3.119096 GCGACGAGAACAAGGCCC 61.119 66.667 0.00 0.00 0.00 5.80
1845 2117 2.501610 GAGATGGTGGAGGTCGGC 59.498 66.667 0.00 0.00 0.00 5.54
2022 2322 2.159627 ACCAATCGTTCGAAGCACAATC 59.840 45.455 0.00 0.00 0.00 2.67
2066 2366 5.551760 AACAGAATTTACAGCTTCCGATG 57.448 39.130 0.00 0.00 0.00 3.84
2097 2397 5.116069 ACTAATTTGTTTTGCGATTCCGT 57.884 34.783 0.00 0.00 38.24 4.69
2198 2498 1.755161 CGGAGTGATGATACCGTTCG 58.245 55.000 0.00 0.00 40.42 3.95
2200 2500 1.488527 GAGTGATGATACCGTTCGGC 58.511 55.000 11.32 0.00 0.00 5.54
2398 2709 2.266554 CTCAACCTCAAGCGAGATGAC 58.733 52.381 0.00 0.00 42.34 3.06
2402 2713 0.526524 CCTCAAGCGAGATGACGACC 60.527 60.000 0.00 0.00 42.34 4.79
2448 2759 3.855599 TCCCTGTAAATTCATTCTCCCCA 59.144 43.478 0.00 0.00 0.00 4.96
2449 2760 3.954258 CCCTGTAAATTCATTCTCCCCAC 59.046 47.826 0.00 0.00 0.00 4.61
2450 2761 4.325344 CCCTGTAAATTCATTCTCCCCACT 60.325 45.833 0.00 0.00 0.00 4.00
2451 2762 4.641989 CCTGTAAATTCATTCTCCCCACTG 59.358 45.833 0.00 0.00 0.00 3.66
2454 2765 5.710099 TGTAAATTCATTCTCCCCACTGTTC 59.290 40.000 0.00 0.00 0.00 3.18
2455 2766 4.664688 AATTCATTCTCCCCACTGTTCT 57.335 40.909 0.00 0.00 0.00 3.01
2456 2767 4.664688 ATTCATTCTCCCCACTGTTCTT 57.335 40.909 0.00 0.00 0.00 2.52
2457 2768 3.703001 TCATTCTCCCCACTGTTCTTC 57.297 47.619 0.00 0.00 0.00 2.87
2458 2769 3.251484 TCATTCTCCCCACTGTTCTTCT 58.749 45.455 0.00 0.00 0.00 2.85
2459 2770 3.652869 TCATTCTCCCCACTGTTCTTCTT 59.347 43.478 0.00 0.00 0.00 2.52
2460 2771 3.771577 TTCTCCCCACTGTTCTTCTTC 57.228 47.619 0.00 0.00 0.00 2.87
2461 2772 2.977808 TCTCCCCACTGTTCTTCTTCT 58.022 47.619 0.00 0.00 0.00 2.85
2462 2773 3.318313 TCTCCCCACTGTTCTTCTTCTT 58.682 45.455 0.00 0.00 0.00 2.52
2463 2774 3.325135 TCTCCCCACTGTTCTTCTTCTTC 59.675 47.826 0.00 0.00 0.00 2.87
2464 2775 3.318313 TCCCCACTGTTCTTCTTCTTCT 58.682 45.455 0.00 0.00 0.00 2.85
2465 2776 3.716872 TCCCCACTGTTCTTCTTCTTCTT 59.283 43.478 0.00 0.00 0.00 2.52
2466 2777 4.068599 CCCCACTGTTCTTCTTCTTCTTC 58.931 47.826 0.00 0.00 0.00 2.87
2467 2778 4.202409 CCCCACTGTTCTTCTTCTTCTTCT 60.202 45.833 0.00 0.00 0.00 2.85
2468 2779 5.372373 CCCACTGTTCTTCTTCTTCTTCTT 58.628 41.667 0.00 0.00 0.00 2.52
2469 2780 5.468409 CCCACTGTTCTTCTTCTTCTTCTTC 59.532 44.000 0.00 0.00 0.00 2.87
2470 2781 6.287525 CCACTGTTCTTCTTCTTCTTCTTCT 58.712 40.000 0.00 0.00 0.00 2.85
2471 2782 6.765512 CCACTGTTCTTCTTCTTCTTCTTCTT 59.234 38.462 0.00 0.00 0.00 2.52
2472 2783 7.042119 CCACTGTTCTTCTTCTTCTTCTTCTTC 60.042 40.741 0.00 0.00 0.00 2.87
2473 2784 6.989759 ACTGTTCTTCTTCTTCTTCTTCTTCC 59.010 38.462 0.00 0.00 0.00 3.46
2514 2825 5.243060 AGTTTCTAGTACCATTTTGGGTTGC 59.757 40.000 0.00 0.00 43.37 4.17
2516 2827 4.993028 TCTAGTACCATTTTGGGTTGCTT 58.007 39.130 0.00 0.00 43.37 3.91
2518 2829 2.897326 AGTACCATTTTGGGTTGCTTCC 59.103 45.455 0.00 0.00 43.37 3.46
2519 2830 2.101640 ACCATTTTGGGTTGCTTCCT 57.898 45.000 0.00 0.00 43.37 3.36
2522 2833 1.969923 CATTTTGGGTTGCTTCCTGGA 59.030 47.619 0.00 0.00 0.00 3.86
2523 2834 2.397044 TTTTGGGTTGCTTCCTGGAT 57.603 45.000 0.00 0.00 0.00 3.41
2524 2835 1.923356 TTTGGGTTGCTTCCTGGATC 58.077 50.000 0.00 0.00 0.00 3.36
2525 2836 0.776810 TTGGGTTGCTTCCTGGATCA 59.223 50.000 0.00 0.00 0.00 2.92
2582 2893 1.849976 GCTGTGCTGTTGGAGTGAGC 61.850 60.000 0.00 0.00 0.00 4.26
2586 2897 1.595382 GCTGTTGGAGTGAGCGTGT 60.595 57.895 0.00 0.00 0.00 4.49
2587 2898 1.160329 GCTGTTGGAGTGAGCGTGTT 61.160 55.000 0.00 0.00 0.00 3.32
2588 2899 0.861837 CTGTTGGAGTGAGCGTGTTC 59.138 55.000 0.00 0.00 0.00 3.18
2589 2900 0.464036 TGTTGGAGTGAGCGTGTTCT 59.536 50.000 0.00 0.00 0.00 3.01
2590 2901 0.861837 GTTGGAGTGAGCGTGTTCTG 59.138 55.000 0.00 0.00 0.00 3.02
2591 2902 0.249868 TTGGAGTGAGCGTGTTCTGG 60.250 55.000 0.00 0.00 0.00 3.86
2617 2956 3.517901 TGGTTTCTTCTGGTGGATACGAT 59.482 43.478 0.00 0.00 42.51 3.73
2632 2971 6.978659 GTGGATACGATAGAAAGATTGTGTGA 59.021 38.462 0.00 0.00 42.51 3.58
2638 2977 8.226819 ACGATAGAAAGATTGTGTGATCTCTA 57.773 34.615 0.00 0.00 36.07 2.43
2646 2985 9.434420 AAAGATTGTGTGATCTCTAGAAGAAAG 57.566 33.333 0.00 0.00 37.61 2.62
2690 3029 2.083774 GAACTGCAATCCAATCCACGA 58.916 47.619 0.00 0.00 0.00 4.35
2691 3030 1.453155 ACTGCAATCCAATCCACGAC 58.547 50.000 0.00 0.00 0.00 4.34
2692 3031 0.374758 CTGCAATCCAATCCACGACG 59.625 55.000 0.00 0.00 0.00 5.12
2721 3060 3.857052 TGTTACATTCAGGTTCTAGCGG 58.143 45.455 0.00 0.00 0.00 5.52
2728 3067 3.795623 TCAGGTTCTAGCGGTGTTATC 57.204 47.619 0.00 0.00 0.00 1.75
2737 3076 2.111384 AGCGGTGTTATCACTCCATCT 58.889 47.619 4.02 0.00 43.41 2.90
2740 3079 4.021894 AGCGGTGTTATCACTCCATCTATC 60.022 45.833 4.02 0.00 43.41 2.08
2746 3085 7.319646 GTGTTATCACTCCATCTATCTCATCC 58.680 42.308 0.00 0.00 40.98 3.51
2760 3099 4.115199 ATCCCAGGTTCCTGCGGC 62.115 66.667 12.88 0.00 33.07 6.53
2810 3160 2.431601 AGCGAGCGAGTGACTTGC 60.432 61.111 16.97 16.97 43.68 4.01
2897 3248 2.601666 TCTGCTCGCTGGGTCAGT 60.602 61.111 13.02 0.00 33.43 3.41
2898 3249 2.125753 CTGCTCGCTGGGTCAGTC 60.126 66.667 7.95 0.00 33.43 3.51
2899 3250 3.978723 CTGCTCGCTGGGTCAGTCG 62.979 68.421 7.95 0.00 33.43 4.18
2900 3251 3.749064 GCTCGCTGGGTCAGTCGA 61.749 66.667 11.52 11.52 37.55 4.20
2919 3270 4.383602 CGGTCGTTGCCGCCAAAG 62.384 66.667 3.36 0.00 45.47 2.77
2940 3291 3.808656 GGCTTCTTCTGCCGCTGC 61.809 66.667 0.00 0.00 41.03 5.25
2964 3315 1.134280 TGGCCTAGAAGAAGATGCAGC 60.134 52.381 3.32 0.00 0.00 5.25
3073 3425 1.462670 CTGAAAAGGACGCTGCTCTTC 59.537 52.381 0.00 0.00 0.00 2.87
3156 3519 3.399181 GCCCATCCTCCCACACGA 61.399 66.667 0.00 0.00 0.00 4.35
3158 3521 2.184322 CCATCCTCCCACACGACG 59.816 66.667 0.00 0.00 0.00 5.12
3159 3522 2.509336 CATCCTCCCACACGACGC 60.509 66.667 0.00 0.00 0.00 5.19
3160 3523 3.771160 ATCCTCCCACACGACGCC 61.771 66.667 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.303317 GTGGGAATGAGGCCGTGTT 60.303 57.895 0.00 0.00 0.00 3.32
1 2 2.185310 GAGTGGGAATGAGGCCGTGT 62.185 60.000 0.00 0.00 0.00 4.49
3 4 1.613630 AGAGTGGGAATGAGGCCGT 60.614 57.895 0.00 0.00 0.00 5.68
4 5 1.144936 GAGAGTGGGAATGAGGCCG 59.855 63.158 0.00 0.00 0.00 6.13
5 6 0.620556 TTGAGAGTGGGAATGAGGCC 59.379 55.000 0.00 0.00 0.00 5.19
6 7 2.496899 TTTGAGAGTGGGAATGAGGC 57.503 50.000 0.00 0.00 0.00 4.70
7 8 3.054139 TCCATTTGAGAGTGGGAATGAGG 60.054 47.826 0.00 0.00 36.15 3.86
8 9 3.944015 GTCCATTTGAGAGTGGGAATGAG 59.056 47.826 0.00 0.00 36.15 2.90
9 10 3.330405 TGTCCATTTGAGAGTGGGAATGA 59.670 43.478 0.00 0.00 36.15 2.57
10 11 3.689347 TGTCCATTTGAGAGTGGGAATG 58.311 45.455 0.00 0.00 36.15 2.67
11 12 4.387026 TTGTCCATTTGAGAGTGGGAAT 57.613 40.909 0.00 0.00 36.15 3.01
12 13 3.874383 TTGTCCATTTGAGAGTGGGAA 57.126 42.857 0.00 0.00 36.15 3.97
13 14 3.874383 TTTGTCCATTTGAGAGTGGGA 57.126 42.857 0.00 0.00 36.15 4.37
14 15 5.010922 TGAATTTTGTCCATTTGAGAGTGGG 59.989 40.000 0.00 0.00 36.15 4.61
15 16 6.088016 TGAATTTTGTCCATTTGAGAGTGG 57.912 37.500 0.00 0.00 36.82 4.00
16 17 8.597662 ATTTGAATTTTGTCCATTTGAGAGTG 57.402 30.769 0.00 0.00 0.00 3.51
25 26 8.484008 CGTTCGTTTTATTTGAATTTTGTCCAT 58.516 29.630 0.00 0.00 0.00 3.41
26 27 7.488471 ACGTTCGTTTTATTTGAATTTTGTCCA 59.512 29.630 0.00 0.00 0.00 4.02
27 28 7.833539 ACGTTCGTTTTATTTGAATTTTGTCC 58.166 30.769 0.00 0.00 0.00 4.02
28 29 9.678247 AAACGTTCGTTTTATTTGAATTTTGTC 57.322 25.926 15.92 0.00 35.10 3.18
29 30 9.466741 CAAACGTTCGTTTTATTTGAATTTTGT 57.533 25.926 18.46 0.00 36.35 2.83
30 31 9.466741 ACAAACGTTCGTTTTATTTGAATTTTG 57.533 25.926 18.46 7.93 36.35 2.44
33 34 9.466741 CAAACAAACGTTCGTTTTATTTGAATT 57.533 25.926 29.15 16.07 40.08 2.17
34 35 8.111224 CCAAACAAACGTTCGTTTTATTTGAAT 58.889 29.630 31.54 14.82 40.08 2.57
35 36 7.327761 TCCAAACAAACGTTCGTTTTATTTGAA 59.672 29.630 31.54 22.19 40.08 2.69
36 37 6.805271 TCCAAACAAACGTTCGTTTTATTTGA 59.195 30.769 31.54 22.28 40.08 2.69
37 38 6.979509 TCCAAACAAACGTTCGTTTTATTTG 58.020 32.000 27.79 27.79 38.98 2.32
38 39 6.237622 GCTCCAAACAAACGTTCGTTTTATTT 60.238 34.615 14.44 17.50 36.35 1.40
39 40 5.230516 GCTCCAAACAAACGTTCGTTTTATT 59.769 36.000 14.44 13.55 36.35 1.40
40 41 4.736307 GCTCCAAACAAACGTTCGTTTTAT 59.264 37.500 14.44 8.97 36.35 1.40
41 42 4.097012 GCTCCAAACAAACGTTCGTTTTA 58.903 39.130 14.44 5.69 36.35 1.52
42 43 2.918600 GCTCCAAACAAACGTTCGTTTT 59.081 40.909 14.44 5.40 36.35 2.43
43 44 2.521996 GCTCCAAACAAACGTTCGTTT 58.478 42.857 11.47 11.47 38.67 3.60
44 45 1.202211 GGCTCCAAACAAACGTTCGTT 60.202 47.619 0.00 0.00 0.00 3.85
45 46 0.379316 GGCTCCAAACAAACGTTCGT 59.621 50.000 0.00 0.00 0.00 3.85
46 47 0.656205 CGGCTCCAAACAAACGTTCG 60.656 55.000 0.00 0.00 0.00 3.95
47 48 0.933047 GCGGCTCCAAACAAACGTTC 60.933 55.000 0.00 0.00 0.00 3.95
48 49 1.065109 GCGGCTCCAAACAAACGTT 59.935 52.632 0.00 0.00 0.00 3.99
49 50 2.115911 TGCGGCTCCAAACAAACGT 61.116 52.632 0.00 0.00 0.00 3.99
50 51 1.657181 GTGCGGCTCCAAACAAACG 60.657 57.895 0.00 0.00 0.00 3.60
51 52 1.657181 CGTGCGGCTCCAAACAAAC 60.657 57.895 0.00 0.00 0.00 2.93
52 53 1.169661 ATCGTGCGGCTCCAAACAAA 61.170 50.000 0.00 0.00 0.00 2.83
53 54 1.599518 ATCGTGCGGCTCCAAACAA 60.600 52.632 0.00 0.00 0.00 2.83
54 55 2.031919 ATCGTGCGGCTCCAAACA 59.968 55.556 0.00 0.00 0.00 2.83
55 56 2.480555 CATCGTGCGGCTCCAAAC 59.519 61.111 0.00 0.00 0.00 2.93
56 57 2.745884 CCATCGTGCGGCTCCAAA 60.746 61.111 0.00 0.00 0.00 3.28
57 58 3.664025 CTCCATCGTGCGGCTCCAA 62.664 63.158 0.00 0.00 0.00 3.53
58 59 4.147449 CTCCATCGTGCGGCTCCA 62.147 66.667 0.00 0.00 0.00 3.86
59 60 3.665675 AACTCCATCGTGCGGCTCC 62.666 63.158 0.00 0.00 0.00 4.70
60 61 2.125512 AACTCCATCGTGCGGCTC 60.126 61.111 0.00 0.00 0.00 4.70
61 62 2.434884 CAACTCCATCGTGCGGCT 60.435 61.111 0.00 0.00 0.00 5.52
62 63 3.499737 CCAACTCCATCGTGCGGC 61.500 66.667 0.00 0.00 0.00 6.53
63 64 3.499737 GCCAACTCCATCGTGCGG 61.500 66.667 0.00 0.00 0.00 5.69
64 65 3.499737 GGCCAACTCCATCGTGCG 61.500 66.667 0.00 0.00 0.00 5.34
65 66 2.045926 AGGCCAACTCCATCGTGC 60.046 61.111 5.01 0.00 0.00 5.34
66 67 0.107508 ATCAGGCCAACTCCATCGTG 60.108 55.000 5.01 0.00 0.00 4.35
67 68 0.620556 AATCAGGCCAACTCCATCGT 59.379 50.000 5.01 0.00 0.00 3.73
68 69 1.672881 GAAATCAGGCCAACTCCATCG 59.327 52.381 5.01 0.00 0.00 3.84
69 70 2.424956 GTGAAATCAGGCCAACTCCATC 59.575 50.000 5.01 0.00 0.00 3.51
70 71 2.450476 GTGAAATCAGGCCAACTCCAT 58.550 47.619 5.01 0.00 0.00 3.41
71 72 1.881925 CGTGAAATCAGGCCAACTCCA 60.882 52.381 5.01 0.00 0.00 3.86
72 73 0.804989 CGTGAAATCAGGCCAACTCC 59.195 55.000 5.01 0.00 0.00 3.85
73 74 0.804989 CCGTGAAATCAGGCCAACTC 59.195 55.000 5.01 0.00 0.00 3.01
74 75 0.110486 ACCGTGAAATCAGGCCAACT 59.890 50.000 5.01 0.00 0.00 3.16
75 76 0.240945 CACCGTGAAATCAGGCCAAC 59.759 55.000 5.01 0.00 0.00 3.77
76 77 0.179004 ACACCGTGAAATCAGGCCAA 60.179 50.000 5.01 0.00 0.00 4.52
77 78 0.888736 CACACCGTGAAATCAGGCCA 60.889 55.000 5.01 0.00 35.23 5.36
78 79 0.605319 TCACACCGTGAAATCAGGCC 60.605 55.000 5.28 0.00 39.78 5.19
79 80 1.131126 CATCACACCGTGAAATCAGGC 59.869 52.381 5.28 0.00 45.96 4.85
80 81 2.698803 TCATCACACCGTGAAATCAGG 58.301 47.619 5.28 0.00 45.96 3.86
81 82 4.509230 CCTATCATCACACCGTGAAATCAG 59.491 45.833 5.28 0.00 45.96 2.90
82 83 4.441792 CCTATCATCACACCGTGAAATCA 58.558 43.478 5.28 0.00 45.96 2.57
83 84 3.248602 GCCTATCATCACACCGTGAAATC 59.751 47.826 5.28 0.00 45.96 2.17
84 85 3.206150 GCCTATCATCACACCGTGAAAT 58.794 45.455 5.28 1.49 45.96 2.17
85 86 2.627945 GCCTATCATCACACCGTGAAA 58.372 47.619 5.28 0.00 45.96 2.69
86 87 1.134521 GGCCTATCATCACACCGTGAA 60.135 52.381 5.28 0.00 45.96 3.18
87 88 0.464036 GGCCTATCATCACACCGTGA 59.536 55.000 5.28 0.00 46.90 4.35
88 89 0.177836 TGGCCTATCATCACACCGTG 59.822 55.000 3.32 0.00 34.45 4.94
89 90 0.465705 CTGGCCTATCATCACACCGT 59.534 55.000 3.32 0.00 0.00 4.83
90 91 0.882042 GCTGGCCTATCATCACACCG 60.882 60.000 3.32 0.00 0.00 4.94
91 92 0.882042 CGCTGGCCTATCATCACACC 60.882 60.000 3.32 0.00 0.00 4.16
92 93 1.502163 GCGCTGGCCTATCATCACAC 61.502 60.000 3.32 0.00 0.00 3.82
103 104 2.486966 GATGTTTCTGCGCTGGCC 59.513 61.111 14.70 0.00 38.85 5.36
104 105 1.865788 TTGGATGTTTCTGCGCTGGC 61.866 55.000 14.70 6.03 40.52 4.85
109 110 1.813513 AGTCCTTGGATGTTTCTGCG 58.186 50.000 0.00 0.00 0.00 5.18
125 130 2.126031 GTCGCCCGAGTCCAAGTC 60.126 66.667 0.00 0.00 0.00 3.01
126 131 2.600769 AGTCGCCCGAGTCCAAGT 60.601 61.111 0.00 0.00 0.00 3.16
127 132 2.182030 GAGTCGCCCGAGTCCAAG 59.818 66.667 13.13 0.00 38.33 3.61
128 133 3.744719 CGAGTCGCCCGAGTCCAA 61.745 66.667 17.08 0.00 40.47 3.53
157 162 0.394625 GCATTTTTGCATGCCCCCAT 60.395 50.000 16.68 0.00 43.38 4.00
195 200 5.228635 CACAACGAATCATACTACCACGTAC 59.771 44.000 0.00 0.00 32.45 3.67
196 201 5.106197 ACACAACGAATCATACTACCACGTA 60.106 40.000 0.00 0.00 32.45 3.57
197 202 4.171005 CACAACGAATCATACTACCACGT 58.829 43.478 0.00 0.00 0.00 4.49
198 203 4.171005 ACACAACGAATCATACTACCACG 58.829 43.478 0.00 0.00 0.00 4.94
199 204 8.912658 CATATACACAACGAATCATACTACCAC 58.087 37.037 0.00 0.00 0.00 4.16
200 205 8.852135 TCATATACACAACGAATCATACTACCA 58.148 33.333 0.00 0.00 0.00 3.25
201 206 9.125906 GTCATATACACAACGAATCATACTACC 57.874 37.037 0.00 0.00 0.00 3.18
204 209 6.362551 GCGTCATATACACAACGAATCATACT 59.637 38.462 0.00 0.00 37.31 2.12
216 221 3.549423 GCTTCTACCGCGTCATATACACA 60.549 47.826 4.92 0.00 0.00 3.72
217 222 2.978489 GCTTCTACCGCGTCATATACAC 59.022 50.000 4.92 0.00 0.00 2.90
218 223 2.030540 GGCTTCTACCGCGTCATATACA 60.031 50.000 4.92 0.00 0.00 2.29
287 292 2.779506 GTCGTGAAAGTGAGGGGAATT 58.220 47.619 0.00 0.00 0.00 2.17
667 919 2.812178 CGGAAAGGTACGTGGCGG 60.812 66.667 0.00 0.00 0.00 6.13
670 922 1.444895 CCGTCGGAAAGGTACGTGG 60.445 63.158 4.91 0.00 34.90 4.94
698 950 2.762459 AATCAGACGGCCCCGCTA 60.762 61.111 6.63 0.00 44.19 4.26
862 1117 4.816984 TCGGGGAGGAGACGAGCC 62.817 72.222 0.00 0.00 32.29 4.70
907 1170 2.394506 GGCTGGGGGATGGAATGGA 61.395 63.158 0.00 0.00 0.00 3.41
908 1171 2.199535 GGCTGGGGGATGGAATGG 59.800 66.667 0.00 0.00 0.00 3.16
909 1172 2.199535 GGGCTGGGGGATGGAATG 59.800 66.667 0.00 0.00 0.00 2.67
910 1173 2.287896 TGGGCTGGGGGATGGAAT 60.288 61.111 0.00 0.00 0.00 3.01
927 1193 2.123897 GGCGAGGGAGAGAGAGCT 60.124 66.667 0.00 0.00 0.00 4.09
928 1194 2.123897 AGGCGAGGGAGAGAGAGC 60.124 66.667 0.00 0.00 0.00 4.09
997 1269 4.222847 GGCGTCCGAGTCCATCCC 62.223 72.222 0.00 0.00 0.00 3.85
1167 1439 2.725008 GAGATGGAGCCGTCGGAG 59.275 66.667 17.49 0.00 37.08 4.63
1218 1490 4.225340 CGGAGCGAGTCGACCGAG 62.225 72.222 32.36 14.40 45.05 4.63
1414 1686 4.899239 GCCGGCCTCGACCATGAG 62.899 72.222 18.11 0.00 39.00 2.90
2022 2322 2.160615 TGTGATTGTAATGGCCGAAACG 59.839 45.455 0.00 0.00 0.00 3.60
2066 2366 6.011277 CGCAAAACAAATTAGTACTCCGTAC 58.989 40.000 0.00 0.00 39.10 3.67
2097 2397 3.461773 GACCAGCGCCTCAGCCTA 61.462 66.667 2.29 0.00 38.01 3.93
2198 2498 1.474330 CCAAGGTGGAATTGGTAGCC 58.526 55.000 0.00 0.00 40.96 3.93
2448 2759 6.989759 GGAAGAAGAAGAAGAAGAAGAACAGT 59.010 38.462 0.00 0.00 0.00 3.55
2449 2760 7.216494 AGGAAGAAGAAGAAGAAGAAGAACAG 58.784 38.462 0.00 0.00 0.00 3.16
2450 2761 7.130681 AGGAAGAAGAAGAAGAAGAAGAACA 57.869 36.000 0.00 0.00 0.00 3.18
2451 2762 8.445275 AAAGGAAGAAGAAGAAGAAGAAGAAC 57.555 34.615 0.00 0.00 0.00 3.01
2510 2821 2.496899 TCCTTGATCCAGGAAGCAAC 57.503 50.000 13.07 0.00 40.26 4.17
2516 2827 0.826715 CTCGCTTCCTTGATCCAGGA 59.173 55.000 11.48 11.48 41.60 3.86
2518 2829 0.813210 GGCTCGCTTCCTTGATCCAG 60.813 60.000 0.00 0.00 0.00 3.86
2519 2830 1.221840 GGCTCGCTTCCTTGATCCA 59.778 57.895 0.00 0.00 0.00 3.41
2522 2833 2.134789 ATTTGGCTCGCTTCCTTGAT 57.865 45.000 0.00 0.00 0.00 2.57
2523 2834 1.812571 GAATTTGGCTCGCTTCCTTGA 59.187 47.619 0.00 0.00 0.00 3.02
2524 2835 1.466360 CGAATTTGGCTCGCTTCCTTG 60.466 52.381 0.00 0.00 0.00 3.61
2525 2836 0.804989 CGAATTTGGCTCGCTTCCTT 59.195 50.000 0.00 0.00 0.00 3.36
2533 2844 1.154225 CCACACGCGAATTTGGCTC 60.154 57.895 15.93 0.00 0.00 4.70
2582 2893 2.561569 AGAAACCAAGTCCAGAACACG 58.438 47.619 0.00 0.00 0.00 4.49
2586 2897 3.202151 ACCAGAAGAAACCAAGTCCAGAA 59.798 43.478 0.00 0.00 0.00 3.02
2587 2898 2.777692 ACCAGAAGAAACCAAGTCCAGA 59.222 45.455 0.00 0.00 0.00 3.86
2588 2899 2.880890 CACCAGAAGAAACCAAGTCCAG 59.119 50.000 0.00 0.00 0.00 3.86
2589 2900 2.422803 CCACCAGAAGAAACCAAGTCCA 60.423 50.000 0.00 0.00 0.00 4.02
2590 2901 2.158667 TCCACCAGAAGAAACCAAGTCC 60.159 50.000 0.00 0.00 0.00 3.85
2591 2902 3.208747 TCCACCAGAAGAAACCAAGTC 57.791 47.619 0.00 0.00 0.00 3.01
2617 2956 9.467796 TCTTCTAGAGATCACACAATCTTTCTA 57.532 33.333 0.00 0.00 36.13 2.10
2690 3029 1.296056 GAATGTAACAGCACGGCCGT 61.296 55.000 28.70 28.70 0.00 5.68
2691 3030 1.295357 TGAATGTAACAGCACGGCCG 61.295 55.000 26.86 26.86 0.00 6.13
2692 3031 0.447801 CTGAATGTAACAGCACGGCC 59.552 55.000 0.00 0.00 0.00 6.13
2721 3060 7.319646 GGATGAGATAGATGGAGTGATAACAC 58.680 42.308 0.00 0.00 46.24 3.32
2728 3067 3.514706 CCTGGGATGAGATAGATGGAGTG 59.485 52.174 0.00 0.00 0.00 3.51
2737 3076 2.050144 GCAGGAACCTGGGATGAGATA 58.950 52.381 20.38 0.00 43.77 1.98
2740 3079 4.972875 GCAGGAACCTGGGATGAG 57.027 61.111 20.38 0.00 43.77 2.90
2781 3120 4.803426 CTCGCTCACCCACGGCTC 62.803 72.222 0.00 0.00 0.00 4.70
2822 3172 0.378962 TCGGTTGAACCAGCAAAACG 59.621 50.000 15.58 0.00 38.47 3.60
2940 3291 2.941720 GCATCTTCTTCTAGGCCACAAG 59.058 50.000 5.01 3.51 0.00 3.16
2996 3347 1.656095 CGAGCGCGAGATCTTTCTTTT 59.344 47.619 12.10 0.00 46.11 2.27
2997 3348 1.272781 CGAGCGCGAGATCTTTCTTT 58.727 50.000 12.10 0.00 46.11 2.52
2998 3349 1.142778 GCGAGCGCGAGATCTTTCTT 61.143 55.000 15.92 0.00 46.11 2.52
2999 3350 1.587613 GCGAGCGCGAGATCTTTCT 60.588 57.895 15.92 0.00 46.11 2.52
3000 3351 2.917161 GCGAGCGCGAGATCTTTC 59.083 61.111 15.92 0.00 46.11 2.62
3162 3525 3.430374 CCGTTTCCCACACTCGAAGATAT 60.430 47.826 0.00 0.00 33.89 1.63


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

AutoCloner maintained by Alex Coulton.