Multiple sequence alignment - TraesCS6A01G088300

Loading Multiple Alignment...

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 TraesCS6A01G088300 chr6A 100.000 4727 0 0 1 4727 56256288 56251562 0.000000e+00 8730.0
1 TraesCS6A01G088300 chr6A 100.000 36 0 0 126 161 17672683 17672718 3.050000e-07 67.6
2 TraesCS6A01G088300 chrUn 98.348 4117 53 11 623 4727 20103498 20107611 0.000000e+00 7212.0
3 TraesCS6A01G088300 chrUn 79.699 133 23 4 4 134 34756892 34756762 5.040000e-15 93.5
4 TraesCS6A01G088300 chr6B 98.352 4006 54 7 731 4727 92760898 92756896 0.000000e+00 7022.0
5 TraesCS6A01G088300 chr5D 90.129 466 42 4 157 620 267622359 267622822 1.880000e-168 603.0
6 TraesCS6A01G088300 chr5D 100.000 36 0 0 126 161 255562146 255562181 3.050000e-07 67.6
7 TraesCS6A01G088300 chr5D 82.895 76 11 2 620 694 512537805 512537879 3.050000e-07 67.6
8 TraesCS6A01G088300 chr2D 89.744 468 44 2 157 620 15478196 15477729 3.150000e-166 595.0
9 TraesCS6A01G088300 chr4A 89.339 469 46 4 157 622 590188190 590187723 1.900000e-163 586.0
10 TraesCS6A01G088300 chr1D 89.247 465 40 6 157 620 316626723 316627178 1.480000e-159 573.0
11 TraesCS6A01G088300 chr1D 86.966 468 59 2 157 622 395349737 395349270 4.190000e-145 525.0
12 TraesCS6A01G088300 chr1D 100.000 36 0 0 126 161 316624392 316624427 3.050000e-07 67.6
13 TraesCS6A01G088300 chr7A 88.651 467 50 2 159 622 465796530 465796996 2.470000e-157 566.0
14 TraesCS6A01G088300 chr7A 88.817 465 47 5 157 619 632270832 632271293 2.470000e-157 566.0
15 TraesCS6A01G088300 chr7A 95.122 41 1 1 620 659 204671694 204671734 3.950000e-06 63.9
16 TraesCS6A01G088300 chr5B 88.034 468 54 2 157 622 560388488 560388021 1.920000e-153 553.0
17 TraesCS6A01G088300 chr4B 87.446 462 52 5 163 620 472885259 472884800 1.170000e-145 527.0
18 TraesCS6A01G088300 chr4B 83.486 109 9 9 30 134 562346878 562346775 5.040000e-15 93.5
19 TraesCS6A01G088300 chr3D 91.045 134 10 1 1 134 459493474 459493605 3.760000e-41 180.0
20 TraesCS6A01G088300 chr3D 84.733 131 20 0 4 134 80220366 80220236 1.070000e-26 132.0
21 TraesCS6A01G088300 chr1A 90.476 126 12 0 9 134 5830356 5830481 2.930000e-37 167.0
22 TraesCS6A01G088300 chr1A 100.000 36 0 0 126 161 564212720 564212755 3.050000e-07 67.6
23 TraesCS6A01G088300 chr2A 83.206 131 22 0 4 134 685488858 685488988 2.310000e-23 121.0
24 TraesCS6A01G088300 chr2A 83.784 74 12 0 620 693 89166676 89166603 2.360000e-08 71.3
25 TraesCS6A01G088300 chr1B 82.443 131 23 0 4 134 331426739 331426609 1.070000e-21 115.0
26 TraesCS6A01G088300 chr1B 86.667 75 9 1 620 693 582913061 582913135 1.090000e-11 82.4
27 TraesCS6A01G088300 chr1B 100.000 36 0 0 126 161 56461709 56461744 3.050000e-07 67.6
28 TraesCS6A01G088300 chr5A 87.838 74 8 1 620 692 522982067 522981994 8.430000e-13 86.1
29 TraesCS6A01G088300 chr7D 97.500 40 0 1 121 160 572593625 572593587 3.050000e-07 67.6
30 TraesCS6A01G088300 chr7D 82.667 75 11 2 620 693 501526768 501526841 1.100000e-06 65.8
31 TraesCS6A01G088300 chr6D 100.000 36 0 0 126 161 414267964 414267929 3.050000e-07 67.6
32 TraesCS6A01G088300 chr6D 100.000 36 0 0 126 161 445611076 445611041 3.050000e-07 67.6
33 TraesCS6A01G088300 chr6D 100.000 36 0 0 126 161 454174279 454174314 3.050000e-07 67.6
34 TraesCS6A01G088300 chr6D 95.000 40 2 0 620 659 67871816 67871777 3.950000e-06 63.9
35 TraesCS6A01G088300 chr3B 89.796 49 5 0 620 668 768483159 768483207 3.950000e-06 63.9
36 TraesCS6A01G088300 chr3A 92.683 41 2 1 622 661 674068442 674068402 1.840000e-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 TraesCS6A01G088300 chr6A 56251562 56256288 4726 True 8730.0 8730 100.0000 1 4727 1 chr6A.!!$R1 4726
1 TraesCS6A01G088300 chrUn 20103498 20107611 4113 False 7212.0 7212 98.3480 623 4727 1 chrUn.!!$F1 4104
2 TraesCS6A01G088300 chr6B 92756896 92760898 4002 True 7022.0 7022 98.3520 731 4727 1 chr6B.!!$R1 3996
3 TraesCS6A01G088300 chr1D 316624392 316627178 2786 False 320.3 573 94.6235 126 620 2 chr1D.!!$F1 494

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
118 119 0.100503 GCGATGTGTATTTGGGGTGC 59.899 55.0 0.00 0.0 0.00 5.01 F
581 2883 0.164432 GCGCGCGGTAAAGTAGTTTT 59.836 50.0 33.06 0.0 0.00 2.43 F
619 2921 0.179062 GCGGATGTTGGAGATGCTCT 60.179 55.0 0.00 0.0 0.00 4.09 F
694 2996 0.253044 AGTGTCCATCCAACCATCCG 59.747 55.0 0.00 0.0 0.00 4.18 F
695 2997 0.748005 GTGTCCATCCAACCATCCGG 60.748 60.0 0.00 0.0 38.77 5.14 F
3084 5400 0.112412 TTTGGAGGGAAGCAAGGGAC 59.888 55.0 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1196 3512 2.586357 GGAAGGAGACGGCGATGC 60.586 66.667 16.62 7.14 0.00 3.91 R
2580 4896 6.936335 TGATCAAGCTCTTGTAAGTTGATTCA 59.064 34.615 9.20 7.09 37.84 2.57 R
2682 4998 0.544595 ACTGGTAGAGGCTTCGGGTT 60.545 55.000 0.00 0.00 0.00 4.11 R
3084 5400 4.988540 TCGATGCTCGGTATTAATCCTTTG 59.011 41.667 0.00 0.00 40.88 2.77 R
3180 5496 1.901464 GCGCCCTGTTTCCCTGAAA 60.901 57.895 0.00 0.00 0.00 2.69 R
3982 6299 0.034616 CATCCAGTAGGCAGGCTAGC 59.965 60.000 6.04 6.04 33.74 3.42 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 3.838795 CGCGCGCAACCTGTAGAC 61.839 66.667 32.61 0.00 0.00 2.59
27 28 2.736995 GCGCGCAACCTGTAGACA 60.737 61.111 29.10 0.00 0.00 3.41
28 29 2.314647 GCGCGCAACCTGTAGACAA 61.315 57.895 29.10 0.00 0.00 3.18
29 30 1.781555 CGCGCAACCTGTAGACAAG 59.218 57.895 8.75 0.00 0.00 3.16
30 31 1.497722 GCGCAACCTGTAGACAAGC 59.502 57.895 0.30 0.00 0.00 4.01
31 32 0.951040 GCGCAACCTGTAGACAAGCT 60.951 55.000 0.30 0.00 0.00 3.74
32 33 1.071605 CGCAACCTGTAGACAAGCTC 58.928 55.000 0.00 0.00 0.00 4.09
33 34 1.443802 GCAACCTGTAGACAAGCTCC 58.556 55.000 0.00 0.00 0.00 4.70
34 35 1.270839 GCAACCTGTAGACAAGCTCCA 60.271 52.381 0.00 0.00 0.00 3.86
35 36 2.693069 CAACCTGTAGACAAGCTCCAG 58.307 52.381 0.00 0.00 30.87 3.86
36 37 0.610687 ACCTGTAGACAAGCTCCAGC 59.389 55.000 0.00 0.00 42.49 4.85
74 75 2.400798 CGCGGCATGTGCAGTTAG 59.599 61.111 7.36 0.00 44.36 2.34
75 76 2.793946 GCGGCATGTGCAGTTAGG 59.206 61.111 7.36 0.00 44.36 2.69
76 77 2.793946 CGGCATGTGCAGTTAGGC 59.206 61.111 7.36 0.00 44.36 3.93
77 78 2.793946 GGCATGTGCAGTTAGGCG 59.206 61.111 7.36 0.00 44.36 5.52
78 79 2.100991 GCATGTGCAGTTAGGCGC 59.899 61.111 0.00 0.00 44.35 6.53
79 80 2.400798 CATGTGCAGTTAGGCGCG 59.599 61.111 0.00 0.00 46.96 6.86
80 81 3.499737 ATGTGCAGTTAGGCGCGC 61.500 61.111 25.94 25.94 46.96 6.86
95 96 3.427425 CGCGGTCCGAATTGCCAA 61.427 61.111 17.49 0.00 40.02 4.52
96 97 2.178273 GCGGTCCGAATTGCCAAC 59.822 61.111 17.49 0.00 0.00 3.77
97 98 2.332654 GCGGTCCGAATTGCCAACT 61.333 57.895 17.49 0.00 0.00 3.16
98 99 1.794222 CGGTCCGAATTGCCAACTC 59.206 57.895 4.91 0.00 0.00 3.01
99 100 1.794222 GGTCCGAATTGCCAACTCG 59.206 57.895 0.57 0.57 0.00 4.18
100 101 1.134694 GTCCGAATTGCCAACTCGC 59.865 57.895 2.23 0.00 0.00 5.03
101 102 2.098298 CCGAATTGCCAACTCGCG 59.902 61.111 2.23 0.00 0.00 5.87
102 103 2.387445 CCGAATTGCCAACTCGCGA 61.387 57.895 9.26 9.26 0.00 5.87
103 104 1.705337 CCGAATTGCCAACTCGCGAT 61.705 55.000 10.36 0.00 34.13 4.58
104 105 0.587242 CGAATTGCCAACTCGCGATG 60.587 55.000 10.36 5.89 32.97 3.84
105 106 0.447801 GAATTGCCAACTCGCGATGT 59.552 50.000 10.36 7.38 32.97 3.06
106 107 0.168788 AATTGCCAACTCGCGATGTG 59.831 50.000 10.36 10.90 32.97 3.21
107 108 0.955428 ATTGCCAACTCGCGATGTGT 60.955 50.000 10.36 0.14 31.36 3.72
108 109 0.319986 TTGCCAACTCGCGATGTGTA 60.320 50.000 10.36 0.00 0.00 2.90
109 110 0.108377 TGCCAACTCGCGATGTGTAT 60.108 50.000 10.36 0.00 0.00 2.29
110 111 1.006832 GCCAACTCGCGATGTGTATT 58.993 50.000 10.36 0.00 0.00 1.89
111 112 1.396996 GCCAACTCGCGATGTGTATTT 59.603 47.619 10.36 0.00 0.00 1.40
112 113 2.787723 GCCAACTCGCGATGTGTATTTG 60.788 50.000 10.36 4.97 0.00 2.32
113 114 2.223021 CCAACTCGCGATGTGTATTTGG 60.223 50.000 10.36 10.16 0.00 3.28
114 115 1.651987 ACTCGCGATGTGTATTTGGG 58.348 50.000 10.36 0.00 0.00 4.12
115 116 0.937304 CTCGCGATGTGTATTTGGGG 59.063 55.000 10.36 0.00 0.00 4.96
116 117 0.250793 TCGCGATGTGTATTTGGGGT 59.749 50.000 3.71 0.00 0.00 4.95
117 118 0.376852 CGCGATGTGTATTTGGGGTG 59.623 55.000 0.00 0.00 0.00 4.61
118 119 0.100503 GCGATGTGTATTTGGGGTGC 59.899 55.000 0.00 0.00 0.00 5.01
119 120 0.738389 CGATGTGTATTTGGGGTGCC 59.262 55.000 0.00 0.00 0.00 5.01
120 121 1.111277 GATGTGTATTTGGGGTGCCC 58.889 55.000 0.00 0.00 45.71 5.36
183 2484 2.622942 GTTGAAGATCTTGCCAACACCA 59.377 45.455 24.55 9.30 38.84 4.17
184 2485 2.229792 TGAAGATCTTGCCAACACCAC 58.770 47.619 14.00 0.00 0.00 4.16
190 2491 2.958578 CTTGCCAACACCACCGGAGT 62.959 60.000 9.46 1.17 0.00 3.85
201 2502 1.068474 CACCGGAGTTTCACGTGATC 58.932 55.000 20.80 14.01 0.00 2.92
202 2503 0.966920 ACCGGAGTTTCACGTGATCT 59.033 50.000 20.80 19.73 0.00 2.75
204 2505 1.067846 CCGGAGTTTCACGTGATCTGA 60.068 52.381 20.80 0.31 0.00 3.27
209 2510 0.721154 TTTCACGTGATCTGATGCGC 59.279 50.000 20.80 0.00 0.00 6.09
219 2520 1.103398 TCTGATGCGCGATGAGGAGA 61.103 55.000 12.10 0.00 0.00 3.71
220 2521 0.249197 CTGATGCGCGATGAGGAGAA 60.249 55.000 12.10 0.00 0.00 2.87
221 2522 0.175531 TGATGCGCGATGAGGAGAAA 59.824 50.000 12.10 0.00 0.00 2.52
222 2523 1.290203 GATGCGCGATGAGGAGAAAA 58.710 50.000 12.10 0.00 0.00 2.29
237 2538 7.108847 TGAGGAGAAAAAGGAAGAATCATCTC 58.891 38.462 0.00 0.00 33.77 2.75
238 2539 7.037730 TGAGGAGAAAAAGGAAGAATCATCTCT 60.038 37.037 0.00 0.00 33.77 3.10
304 2605 1.391485 CGAGGCTTGATGTGTCTTTCG 59.609 52.381 0.00 0.00 0.00 3.46
331 2632 4.445385 GTGTCATGAACTTGGTTTGCATTC 59.555 41.667 0.00 0.00 0.00 2.67
341 2642 3.030291 TGGTTTGCATTCTGAACTTGGT 58.970 40.909 0.00 0.00 0.00 3.67
345 2646 2.942804 TGCATTCTGAACTTGGTTGGA 58.057 42.857 0.00 0.00 0.00 3.53
350 2651 5.337009 GCATTCTGAACTTGGTTGGATGAAT 60.337 40.000 0.00 0.00 0.00 2.57
375 2676 4.141756 TGTGGGCATGATTTTGAACTTGTT 60.142 37.500 0.00 0.00 0.00 2.83
377 2678 4.100653 TGGGCATGATTTTGAACTTGTTGA 59.899 37.500 0.00 0.00 0.00 3.18
443 2744 7.123160 TGTCATGTTCATTGCATTTTGAATG 57.877 32.000 9.58 6.30 34.60 2.67
454 2756 7.747155 TTGCATTTTGAATGTTGAAATCCAT 57.253 28.000 0.00 0.00 0.00 3.41
489 2791 2.945447 CAATATATGCAATGCCCCGG 57.055 50.000 1.53 0.00 0.00 5.73
490 2792 2.170166 CAATATATGCAATGCCCCGGT 58.830 47.619 1.53 0.00 0.00 5.28
494 2796 1.920734 TATGCAATGCCCCGGTGAGT 61.921 55.000 1.53 0.00 0.00 3.41
495 2797 3.134127 GCAATGCCCCGGTGAGTC 61.134 66.667 0.00 0.00 0.00 3.36
512 2814 0.723129 GTCGCGCGTGTTGCATTTTA 60.723 50.000 30.98 1.78 46.97 1.52
513 2815 0.451957 TCGCGCGTGTTGCATTTTAG 60.452 50.000 30.98 0.00 46.97 1.85
514 2816 1.696083 GCGCGTGTTGCATTTTAGC 59.304 52.632 8.43 0.00 46.97 3.09
515 2817 1.972801 CGCGTGTTGCATTTTAGCG 59.027 52.632 0.00 9.05 46.97 4.26
516 2818 1.696083 GCGTGTTGCATTTTAGCGC 59.304 52.632 0.00 0.00 45.45 5.92
517 2819 1.972801 CGTGTTGCATTTTAGCGCG 59.027 52.632 0.00 0.00 37.31 6.86
518 2820 1.395068 CGTGTTGCATTTTAGCGCGG 61.395 55.000 8.83 0.00 37.31 6.46
519 2821 1.443533 TGTTGCATTTTAGCGCGGC 60.444 52.632 8.83 0.29 37.31 6.53
520 2822 1.154035 GTTGCATTTTAGCGCGGCT 60.154 52.632 8.83 8.38 43.41 5.52
521 2823 1.154054 TTGCATTTTAGCGCGGCTG 60.154 52.632 8.83 0.00 40.10 4.85
522 2824 1.861542 TTGCATTTTAGCGCGGCTGT 61.862 50.000 8.83 0.00 40.10 4.40
523 2825 1.154035 GCATTTTAGCGCGGCTGTT 60.154 52.632 8.83 0.00 40.10 3.16
524 2826 1.405469 GCATTTTAGCGCGGCTGTTG 61.405 55.000 8.83 0.00 40.10 3.33
525 2827 0.798009 CATTTTAGCGCGGCTGTTGG 60.798 55.000 8.83 0.00 40.10 3.77
526 2828 0.958382 ATTTTAGCGCGGCTGTTGGA 60.958 50.000 8.83 0.00 40.10 3.53
527 2829 1.573829 TTTTAGCGCGGCTGTTGGAG 61.574 55.000 8.83 0.00 40.10 3.86
562 2864 4.653555 GCAAAACCAAGCGAAGGG 57.346 55.556 0.00 0.00 0.00 3.95
563 2865 1.664649 GCAAAACCAAGCGAAGGGC 60.665 57.895 0.00 0.00 44.05 5.19
574 2876 3.861263 GAAGGGCGCGCGGTAAAG 61.861 66.667 33.06 1.90 0.00 1.85
575 2877 4.692475 AAGGGCGCGCGGTAAAGT 62.692 61.111 33.06 2.35 0.00 2.66
576 2878 3.299524 AAGGGCGCGCGGTAAAGTA 62.300 57.895 33.06 0.00 0.00 2.24
577 2879 3.259751 GGGCGCGCGGTAAAGTAG 61.260 66.667 33.06 0.00 0.00 2.57
578 2880 2.507769 GGCGCGCGGTAAAGTAGT 60.508 61.111 33.06 0.00 0.00 2.73
579 2881 2.096442 GGCGCGCGGTAAAGTAGTT 61.096 57.895 33.06 0.00 0.00 2.24
580 2882 1.629345 GGCGCGCGGTAAAGTAGTTT 61.629 55.000 33.06 0.37 0.00 2.66
581 2883 0.164432 GCGCGCGGTAAAGTAGTTTT 59.836 50.000 33.06 0.00 0.00 2.43
582 2884 1.398832 GCGCGCGGTAAAGTAGTTTTT 60.399 47.619 33.06 0.00 0.00 1.94
583 2885 2.159854 GCGCGCGGTAAAGTAGTTTTTA 60.160 45.455 33.06 0.00 0.00 1.52
584 2886 3.652478 CGCGCGGTAAAGTAGTTTTTAG 58.348 45.455 24.84 0.00 0.00 1.85
585 2887 3.410850 GCGCGGTAAAGTAGTTTTTAGC 58.589 45.455 8.83 3.96 37.55 3.09
590 2892 4.388790 GGTAAAGTAGTTTTTAGCGCACG 58.611 43.478 11.47 0.00 33.13 5.34
591 2893 3.531262 AAAGTAGTTTTTAGCGCACGG 57.469 42.857 11.47 0.00 0.00 4.94
592 2894 0.794473 AGTAGTTTTTAGCGCACGGC 59.206 50.000 11.47 0.00 44.05 5.68
610 2912 4.481870 GCATTGTGCGGATGTTGG 57.518 55.556 0.00 0.00 31.71 3.77
611 2913 1.882311 GCATTGTGCGGATGTTGGA 59.118 52.632 0.00 0.00 31.71 3.53
612 2914 0.179156 GCATTGTGCGGATGTTGGAG 60.179 55.000 0.00 0.00 31.71 3.86
613 2915 1.452110 CATTGTGCGGATGTTGGAGA 58.548 50.000 0.00 0.00 0.00 3.71
614 2916 2.019249 CATTGTGCGGATGTTGGAGAT 58.981 47.619 0.00 0.00 0.00 2.75
615 2917 1.452110 TTGTGCGGATGTTGGAGATG 58.548 50.000 0.00 0.00 0.00 2.90
616 2918 1.026182 TGTGCGGATGTTGGAGATGC 61.026 55.000 0.00 0.00 0.00 3.91
617 2919 0.745845 GTGCGGATGTTGGAGATGCT 60.746 55.000 0.00 0.00 0.00 3.79
618 2920 0.462581 TGCGGATGTTGGAGATGCTC 60.463 55.000 0.00 0.00 0.00 4.26
619 2921 0.179062 GCGGATGTTGGAGATGCTCT 60.179 55.000 0.00 0.00 0.00 4.09
620 2922 1.069204 GCGGATGTTGGAGATGCTCTA 59.931 52.381 0.00 0.00 0.00 2.43
621 2923 2.483714 GCGGATGTTGGAGATGCTCTAA 60.484 50.000 0.00 0.00 0.00 2.10
624 2926 4.818546 CGGATGTTGGAGATGCTCTAAATT 59.181 41.667 0.00 0.00 33.06 1.82
628 2930 6.053632 TGTTGGAGATGCTCTAAATTCAGA 57.946 37.500 0.00 0.00 33.06 3.27
642 2944 8.158169 TCTAAATTCAGAATAAATGCGAGCAT 57.842 30.769 4.52 4.52 38.46 3.79
651 2953 2.988010 AATGCGAGCATCAGGACTTA 57.012 45.000 11.26 0.00 35.31 2.24
654 2956 2.346803 TGCGAGCATCAGGACTTAAAC 58.653 47.619 0.00 0.00 33.17 2.01
667 2969 5.590818 AGGACTTAAACCCTGATAGACTGA 58.409 41.667 0.00 0.00 0.00 3.41
673 2975 9.440761 ACTTAAACCCTGATAGACTGAGAATAT 57.559 33.333 0.00 0.00 0.00 1.28
694 2996 0.253044 AGTGTCCATCCAACCATCCG 59.747 55.000 0.00 0.00 0.00 4.18
695 2997 0.748005 GTGTCCATCCAACCATCCGG 60.748 60.000 0.00 0.00 38.77 5.14
716 3029 2.347697 TCGTGAAGATGTTGGAGTCG 57.652 50.000 0.00 0.00 0.00 4.18
718 3031 1.986378 CGTGAAGATGTTGGAGTCGAC 59.014 52.381 7.70 7.70 0.00 4.20
724 3037 1.469308 GATGTTGGAGTCGACTCGTCT 59.531 52.381 33.07 18.67 43.76 4.18
741 3054 1.815003 GTCTTGCAAACATCTCCCCAG 59.185 52.381 0.00 0.00 0.00 4.45
857 3170 2.551912 AAACCCAACCTCGCGCAAG 61.552 57.895 8.75 0.00 43.44 4.01
1086 3399 2.915659 ACCTTCTCGGCGTCCACA 60.916 61.111 6.85 0.00 35.61 4.17
1878 4194 1.148157 CCGCTGGCTCTATTGTCACG 61.148 60.000 0.00 0.00 0.00 4.35
2331 4647 1.623811 GAGGCTTGTCTGGTACTGGAA 59.376 52.381 0.00 0.00 0.00 3.53
3084 5400 0.112412 TTTGGAGGGAAGCAAGGGAC 59.888 55.000 0.00 0.00 0.00 4.46
3180 5496 8.571461 ACAGTGTTGTGAAGATTATTGATGAT 57.429 30.769 0.00 0.00 35.83 2.45
3708 6024 2.217112 GCGACCGCATGATCAGTAC 58.783 57.895 9.73 0.00 41.49 2.73
3982 6299 4.698276 CACTTTATTTTGGACTCGTCACG 58.302 43.478 0.00 0.00 0.00 4.35
4640 6962 3.243636 GCAATGCAGGTTCCTTATCATGG 60.244 47.826 0.00 0.00 0.00 3.66
4711 7033 3.954258 GCAGGTAGCTGGTCCAAATTATT 59.046 43.478 22.69 0.00 41.15 1.40
4713 7035 5.440610 CAGGTAGCTGGTCCAAATTATTCT 58.559 41.667 14.29 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.838795 GTCTACAGGTTGCGCGCG 61.839 66.667 28.44 28.44 0.00 6.86
10 11 2.227968 CTTGTCTACAGGTTGCGCGC 62.228 60.000 27.26 27.26 0.00 6.86
11 12 1.781555 CTTGTCTACAGGTTGCGCG 59.218 57.895 0.00 0.00 0.00 6.86
12 13 0.951040 AGCTTGTCTACAGGTTGCGC 60.951 55.000 0.00 0.00 0.00 6.09
13 14 1.071605 GAGCTTGTCTACAGGTTGCG 58.928 55.000 0.00 0.00 0.00 4.85
14 15 1.270839 TGGAGCTTGTCTACAGGTTGC 60.271 52.381 0.00 0.00 30.44 4.17
15 16 2.839486 TGGAGCTTGTCTACAGGTTG 57.161 50.000 0.00 0.00 30.44 3.77
20 21 1.591703 CCGCTGGAGCTTGTCTACA 59.408 57.895 0.00 0.00 39.32 2.74
21 22 1.153549 CCCGCTGGAGCTTGTCTAC 60.154 63.158 0.00 0.00 39.32 2.59
22 23 3.019003 GCCCGCTGGAGCTTGTCTA 62.019 63.158 0.00 0.00 39.32 2.59
23 24 4.400961 GCCCGCTGGAGCTTGTCT 62.401 66.667 0.00 0.00 39.32 3.41
56 57 3.723364 CTAACTGCACATGCCGCGC 62.723 63.158 0.00 0.00 41.18 6.86
57 58 2.400798 CTAACTGCACATGCCGCG 59.599 61.111 0.00 0.00 41.18 6.46
58 59 2.793946 CCTAACTGCACATGCCGC 59.206 61.111 0.49 0.00 41.18 6.53
59 60 2.793946 GCCTAACTGCACATGCCG 59.206 61.111 0.49 0.00 41.18 5.69
60 61 2.793946 CGCCTAACTGCACATGCC 59.206 61.111 0.49 0.00 41.18 4.40
61 62 2.100991 GCGCCTAACTGCACATGC 59.899 61.111 0.00 0.00 42.50 4.06
62 63 2.400798 CGCGCCTAACTGCACATG 59.599 61.111 0.00 0.00 0.00 3.21
63 64 3.499737 GCGCGCCTAACTGCACAT 61.500 61.111 23.24 0.00 0.00 3.21
78 79 3.427425 TTGGCAATTCGGACCGCG 61.427 61.111 9.66 0.00 0.00 6.46
79 80 2.178273 GTTGGCAATTCGGACCGC 59.822 61.111 9.66 0.00 0.00 5.68
80 81 1.794222 GAGTTGGCAATTCGGACCG 59.206 57.895 7.84 7.84 0.00 4.79
81 82 1.794222 CGAGTTGGCAATTCGGACC 59.206 57.895 30.19 5.52 37.04 4.46
82 83 1.134694 GCGAGTTGGCAATTCGGAC 59.865 57.895 35.29 21.78 40.46 4.79
83 84 2.387445 CGCGAGTTGGCAATTCGGA 61.387 57.895 35.29 0.00 40.46 4.55
84 85 1.705337 ATCGCGAGTTGGCAATTCGG 61.705 55.000 35.29 27.07 40.46 4.30
85 86 0.587242 CATCGCGAGTTGGCAATTCG 60.587 55.000 32.44 32.44 42.62 3.34
86 87 0.447801 ACATCGCGAGTTGGCAATTC 59.552 50.000 16.66 12.28 35.16 2.17
87 88 0.168788 CACATCGCGAGTTGGCAATT 59.831 50.000 16.66 0.00 35.16 2.32
88 89 0.955428 ACACATCGCGAGTTGGCAAT 60.955 50.000 16.66 0.00 35.16 3.56
89 90 0.319986 TACACATCGCGAGTTGGCAA 60.320 50.000 16.66 0.00 35.16 4.52
90 91 0.108377 ATACACATCGCGAGTTGGCA 60.108 50.000 16.66 6.84 35.16 4.92
91 92 1.006832 AATACACATCGCGAGTTGGC 58.993 50.000 16.66 0.00 35.16 4.52
92 93 2.223021 CCAAATACACATCGCGAGTTGG 60.223 50.000 16.66 11.50 35.16 3.77
93 94 2.223021 CCCAAATACACATCGCGAGTTG 60.223 50.000 16.66 16.31 36.87 3.16
94 95 2.006888 CCCAAATACACATCGCGAGTT 58.993 47.619 16.66 0.00 0.00 3.01
95 96 1.651987 CCCAAATACACATCGCGAGT 58.348 50.000 16.66 10.04 0.00 4.18
96 97 0.937304 CCCCAAATACACATCGCGAG 59.063 55.000 16.66 9.51 0.00 5.03
97 98 0.250793 ACCCCAAATACACATCGCGA 59.749 50.000 13.09 13.09 0.00 5.87
98 99 0.376852 CACCCCAAATACACATCGCG 59.623 55.000 0.00 0.00 0.00 5.87
99 100 0.100503 GCACCCCAAATACACATCGC 59.899 55.000 0.00 0.00 0.00 4.58
100 101 0.738389 GGCACCCCAAATACACATCG 59.262 55.000 0.00 0.00 0.00 3.84
183 2484 0.966920 AGATCACGTGAAACTCCGGT 59.033 50.000 24.13 2.48 31.75 5.28
184 2485 1.067846 TCAGATCACGTGAAACTCCGG 60.068 52.381 24.13 10.88 31.75 5.14
190 2491 0.721154 GCGCATCAGATCACGTGAAA 59.279 50.000 24.13 8.99 0.00 2.69
201 2502 0.249197 TTCTCCTCATCGCGCATCAG 60.249 55.000 8.75 0.00 0.00 2.90
202 2503 0.175531 TTTCTCCTCATCGCGCATCA 59.824 50.000 8.75 0.00 0.00 3.07
204 2505 1.667724 CTTTTTCTCCTCATCGCGCAT 59.332 47.619 8.75 0.00 0.00 4.73
209 2510 5.877012 TGATTCTTCCTTTTTCTCCTCATCG 59.123 40.000 0.00 0.00 0.00 3.84
219 2520 6.012157 TCCTCCAGAGATGATTCTTCCTTTTT 60.012 38.462 0.00 0.00 30.30 1.94
220 2521 5.490357 TCCTCCAGAGATGATTCTTCCTTTT 59.510 40.000 0.00 0.00 30.30 2.27
221 2522 5.035556 TCCTCCAGAGATGATTCTTCCTTT 58.964 41.667 0.00 0.00 30.30 3.11
222 2523 4.629122 TCCTCCAGAGATGATTCTTCCTT 58.371 43.478 0.00 0.00 30.30 3.36
237 2538 2.383855 AGACGATTCTTCCTCCTCCAG 58.616 52.381 0.00 0.00 0.00 3.86
238 2539 2.534042 AGACGATTCTTCCTCCTCCA 57.466 50.000 0.00 0.00 0.00 3.86
260 2561 3.430931 CTCGTCTTCGTCCTCATCTTTC 58.569 50.000 0.00 0.00 38.33 2.62
261 2562 2.164624 CCTCGTCTTCGTCCTCATCTTT 59.835 50.000 0.00 0.00 38.33 2.52
304 2605 4.032786 GCAAACCAAGTTCATGACACAAAC 59.967 41.667 0.00 0.00 0.00 2.93
331 2632 5.693104 CACAAATTCATCCAACCAAGTTCAG 59.307 40.000 0.00 0.00 0.00 3.02
341 2642 3.171528 TCATGCCCACAAATTCATCCAA 58.828 40.909 0.00 0.00 0.00 3.53
345 2646 5.806818 TCAAAATCATGCCCACAAATTCAT 58.193 33.333 0.00 0.00 0.00 2.57
350 2651 4.686191 AGTTCAAAATCATGCCCACAAA 57.314 36.364 0.00 0.00 0.00 2.83
443 2744 6.917217 TTTGGACACAAAATGGATTTCAAC 57.083 33.333 0.00 0.00 43.21 3.18
488 2790 4.059459 CAACACGCGCGACTCACC 62.059 66.667 39.36 0.00 0.00 4.02
489 2791 4.702826 GCAACACGCGCGACTCAC 62.703 66.667 39.36 18.63 0.00 3.51
494 2796 0.451957 CTAAAATGCAACACGCGCGA 60.452 50.000 39.36 14.00 46.97 5.87
495 2797 1.972801 CTAAAATGCAACACGCGCG 59.027 52.632 30.96 30.96 46.97 6.86
501 2803 1.443533 GCCGCGCTAAAATGCAACA 60.444 52.632 5.56 0.00 0.00 3.33
503 2805 1.154054 CAGCCGCGCTAAAATGCAA 60.154 52.632 5.56 0.00 36.40 4.08
545 2847 1.664649 GCCCTTCGCTTGGTTTTGC 60.665 57.895 0.00 0.00 0.00 3.68
546 2848 1.371635 CGCCCTTCGCTTGGTTTTG 60.372 57.895 0.00 0.00 34.21 2.44
547 2849 3.039134 CGCCCTTCGCTTGGTTTT 58.961 55.556 0.00 0.00 34.21 2.43
557 2859 3.861263 CTTTACCGCGCGCCCTTC 61.861 66.667 27.36 0.00 0.00 3.46
558 2860 3.299524 TACTTTACCGCGCGCCCTT 62.300 57.895 27.36 12.48 0.00 3.95
559 2861 3.711541 CTACTTTACCGCGCGCCCT 62.712 63.158 27.36 13.33 0.00 5.19
560 2862 3.259751 CTACTTTACCGCGCGCCC 61.260 66.667 27.36 0.00 0.00 6.13
561 2863 1.629345 AAACTACTTTACCGCGCGCC 61.629 55.000 27.36 8.11 0.00 6.53
562 2864 0.164432 AAAACTACTTTACCGCGCGC 59.836 50.000 27.36 23.91 0.00 6.86
563 2865 2.582446 AAAAACTACTTTACCGCGCG 57.418 45.000 25.67 25.67 0.00 6.86
564 2866 3.410850 GCTAAAAACTACTTTACCGCGC 58.589 45.455 0.00 0.00 0.00 6.86
565 2867 3.652478 CGCTAAAAACTACTTTACCGCG 58.348 45.455 0.00 0.00 33.67 6.46
566 2868 3.120580 TGCGCTAAAAACTACTTTACCGC 60.121 43.478 9.73 8.21 42.27 5.68
567 2869 4.388790 GTGCGCTAAAAACTACTTTACCG 58.611 43.478 9.73 0.00 0.00 4.02
568 2870 4.388790 CGTGCGCTAAAAACTACTTTACC 58.611 43.478 9.73 0.00 0.00 2.85
569 2871 4.388790 CCGTGCGCTAAAAACTACTTTAC 58.611 43.478 9.73 0.00 0.00 2.01
570 2872 3.120580 GCCGTGCGCTAAAAACTACTTTA 60.121 43.478 9.73 0.00 0.00 1.85
571 2873 2.350102 GCCGTGCGCTAAAAACTACTTT 60.350 45.455 9.73 0.00 0.00 2.66
572 2874 1.196127 GCCGTGCGCTAAAAACTACTT 59.804 47.619 9.73 0.00 0.00 2.24
573 2875 0.794473 GCCGTGCGCTAAAAACTACT 59.206 50.000 9.73 0.00 0.00 2.57
574 2876 3.285306 GCCGTGCGCTAAAAACTAC 57.715 52.632 9.73 0.00 0.00 2.73
593 2895 0.179156 CTCCAACATCCGCACAATGC 60.179 55.000 0.00 0.00 40.69 3.56
594 2896 1.452110 TCTCCAACATCCGCACAATG 58.548 50.000 0.00 0.00 0.00 2.82
595 2897 2.019249 CATCTCCAACATCCGCACAAT 58.981 47.619 0.00 0.00 0.00 2.71
596 2898 1.452110 CATCTCCAACATCCGCACAA 58.548 50.000 0.00 0.00 0.00 3.33
597 2899 1.026182 GCATCTCCAACATCCGCACA 61.026 55.000 0.00 0.00 0.00 4.57
598 2900 0.745845 AGCATCTCCAACATCCGCAC 60.746 55.000 0.00 0.00 0.00 5.34
599 2901 0.462581 GAGCATCTCCAACATCCGCA 60.463 55.000 0.00 0.00 0.00 5.69
600 2902 2.315246 GAGCATCTCCAACATCCGC 58.685 57.895 0.00 0.00 0.00 5.54
612 2914 8.285394 TCGCATTTATTCTGAATTTAGAGCATC 58.715 33.333 8.38 0.00 0.00 3.91
613 2915 8.158169 TCGCATTTATTCTGAATTTAGAGCAT 57.842 30.769 8.38 0.00 0.00 3.79
614 2916 7.552458 TCGCATTTATTCTGAATTTAGAGCA 57.448 32.000 8.38 0.00 0.00 4.26
615 2917 6.576684 GCTCGCATTTATTCTGAATTTAGAGC 59.423 38.462 8.38 14.70 38.12 4.09
616 2918 7.633621 TGCTCGCATTTATTCTGAATTTAGAG 58.366 34.615 8.38 9.86 0.00 2.43
617 2919 7.552458 TGCTCGCATTTATTCTGAATTTAGA 57.448 32.000 8.38 0.00 0.00 2.10
618 2920 8.071967 TGATGCTCGCATTTATTCTGAATTTAG 58.928 33.333 8.38 0.00 36.70 1.85
619 2921 7.929159 TGATGCTCGCATTTATTCTGAATTTA 58.071 30.769 8.38 0.00 36.70 1.40
620 2922 6.798482 TGATGCTCGCATTTATTCTGAATTT 58.202 32.000 8.38 0.00 36.70 1.82
621 2923 6.381481 TGATGCTCGCATTTATTCTGAATT 57.619 33.333 8.38 0.00 36.70 2.17
624 2926 3.811497 CCTGATGCTCGCATTTATTCTGA 59.189 43.478 5.79 0.00 36.70 3.27
628 2930 3.813443 AGTCCTGATGCTCGCATTTATT 58.187 40.909 5.79 0.00 36.70 1.40
651 2953 7.921041 TGATATTCTCAGTCTATCAGGGTTT 57.079 36.000 0.00 0.00 30.47 3.27
667 2969 4.474651 TGGTTGGATGGACACTGATATTCT 59.525 41.667 0.00 0.00 0.00 2.40
673 2975 1.281867 GGATGGTTGGATGGACACTGA 59.718 52.381 0.00 0.00 0.00 3.41
676 2978 0.748005 CCGGATGGTTGGATGGACAC 60.748 60.000 0.00 0.00 0.00 3.67
694 2996 2.737252 GACTCCAACATCTTCACGAACC 59.263 50.000 0.00 0.00 0.00 3.62
695 2997 2.408704 CGACTCCAACATCTTCACGAAC 59.591 50.000 0.00 0.00 0.00 3.95
697 2999 1.883926 TCGACTCCAACATCTTCACGA 59.116 47.619 0.00 0.00 0.00 4.35
698 3000 1.986378 GTCGACTCCAACATCTTCACG 59.014 52.381 8.70 0.00 0.00 4.35
699 3001 3.246619 GAGTCGACTCCAACATCTTCAC 58.753 50.000 31.24 5.34 37.02 3.18
700 3002 2.095212 CGAGTCGACTCCAACATCTTCA 60.095 50.000 33.85 0.00 39.79 3.02
701 3003 2.095161 ACGAGTCGACTCCAACATCTTC 60.095 50.000 33.85 11.38 39.79 2.87
716 3029 2.413453 GGAGATGTTTGCAAGACGAGTC 59.587 50.000 0.00 0.00 0.00 3.36
718 3031 1.734465 GGGAGATGTTTGCAAGACGAG 59.266 52.381 0.00 0.00 0.00 4.18
724 3037 1.547675 GGACTGGGGAGATGTTTGCAA 60.548 52.381 0.00 0.00 0.00 4.08
741 3054 1.826487 AACTTGCGTTGGTGGGGAC 60.826 57.895 0.00 0.00 30.67 4.46
857 3170 2.822701 GGTCGCGGGTGGGAAATC 60.823 66.667 6.13 0.00 38.96 2.17
1196 3512 2.586357 GGAAGGAGACGGCGATGC 60.586 66.667 16.62 7.14 0.00 3.91
2331 4647 7.682787 AAAGTATCCATCTTCCATAGACTGT 57.317 36.000 0.00 0.00 35.19 3.55
2580 4896 6.936335 TGATCAAGCTCTTGTAAGTTGATTCA 59.064 34.615 9.20 7.09 37.84 2.57
2682 4998 0.544595 ACTGGTAGAGGCTTCGGGTT 60.545 55.000 0.00 0.00 0.00 4.11
3084 5400 4.988540 TCGATGCTCGGTATTAATCCTTTG 59.011 41.667 0.00 0.00 40.88 2.77
3180 5496 1.901464 GCGCCCTGTTTCCCTGAAA 60.901 57.895 0.00 0.00 0.00 2.69
3982 6299 0.034616 CATCCAGTAGGCAGGCTAGC 59.965 60.000 6.04 6.04 33.74 3.42
4640 6962 7.548427 TGCTAAGCTTCTAGATAATGATGATGC 59.452 37.037 0.00 0.00 0.00 3.91
4693 7015 7.556635 ACCTAAAGAATAATTTGGACCAGCTAC 59.443 37.037 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.