Multiple sequence alignment - TraesCS6D01G073900

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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 TraesCS6D01G073900 chr6D 100.000 2765 0 0 1 2765 37736841 37734077 0.000000e+00 5107.0
1 TraesCS6D01G073900 chr6D 92.676 1065 56 6 820 1876 37881368 37880318 0.000000e+00 1515.0
2 TraesCS6D01G073900 chr6D 95.383 888 28 6 1878 2765 454158239 454157365 0.000000e+00 1400.0
3 TraesCS6D01G073900 chr6D 90.874 1041 59 10 852 1876 37839236 37838216 0.000000e+00 1363.0
4 TraesCS6D01G073900 chr6D 96.552 58 2 0 793 850 37878032 37877975 2.270000e-16 97.1
5 TraesCS6D01G073900 chr6D 86.885 61 7 1 40 100 37878351 37878292 1.780000e-07 67.6
6 TraesCS6D01G073900 chr6B 93.199 1088 49 14 793 1876 88498704 88497638 0.000000e+00 1576.0
7 TraesCS6D01G073900 chr6B 91.846 1067 62 10 810 1868 88573017 88571968 0.000000e+00 1465.0
8 TraesCS6D01G073900 chr6B 89.933 149 11 3 41 188 88570591 88570446 3.640000e-44 189.0
9 TraesCS6D01G073900 chr6A 92.322 1055 64 7 827 1876 49132132 49131090 0.000000e+00 1483.0
10 TraesCS6D01G073900 chr7D 95.608 888 39 0 1878 2765 106381690 106380803 0.000000e+00 1424.0
11 TraesCS6D01G073900 chr7D 95.045 888 34 5 1878 2765 626964721 626963844 0.000000e+00 1387.0
12 TraesCS6D01G073900 chr7D 94.820 888 41 2 1878 2765 626959247 626958365 0.000000e+00 1380.0
13 TraesCS6D01G073900 chr7D 85.586 111 15 1 189 298 232942260 232942370 6.260000e-22 115.0
14 TraesCS6D01G073900 chr5D 95.495 888 38 1 1878 2765 434301833 434302718 0.000000e+00 1417.0
15 TraesCS6D01G073900 chr3D 95.388 889 38 2 1878 2765 527120774 527119888 0.000000e+00 1411.0
16 TraesCS6D01G073900 chr3D 95.383 888 31 4 1878 2765 509240852 509239975 0.000000e+00 1404.0
17 TraesCS6D01G073900 chr3D 95.158 888 33 3 1878 2765 167377910 167377033 0.000000e+00 1393.0
18 TraesCS6D01G073900 chr1D 94.625 893 46 1 1875 2765 458410911 458411803 0.000000e+00 1382.0
19 TraesCS6D01G073900 chr1D 90.994 322 26 3 182 501 488506069 488505749 5.470000e-117 431.0
20 TraesCS6D01G073900 chr3A 87.269 542 63 5 195 734 733433524 733434061 5.060000e-172 614.0
21 TraesCS6D01G073900 chr5B 88.454 511 54 5 191 699 545087671 545087164 1.820000e-171 612.0
22 TraesCS6D01G073900 chr5B 83.275 568 61 19 191 739 216660234 216659682 2.470000e-135 492.0
23 TraesCS6D01G073900 chr5B 83.871 155 22 3 442 594 21528516 21528363 7.980000e-31 145.0
24 TraesCS6D01G073900 chr1B 86.453 561 69 6 188 746 296493423 296492868 2.350000e-170 608.0
25 TraesCS6D01G073900 chr2A 85.500 400 54 4 202 600 92478157 92478553 5.510000e-112 414.0
26 TraesCS6D01G073900 chr1A 85.146 377 54 2 192 568 256960250 256959876 4.320000e-103 385.0
27 TraesCS6D01G073900 chr3B 83.284 341 36 5 193 515 788105304 788104967 7.490000e-76 294.0
28 TraesCS6D01G073900 chr2D 84.422 199 24 7 335 529 648289464 648289659 3.640000e-44 189.0


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 TraesCS6D01G073900 chr6D 37734077 37736841 2764 True 5107.0 5107 100.000000 1 2765 1 chr6D.!!$R1 2764
1 TraesCS6D01G073900 chr6D 454157365 454158239 874 True 1400.0 1400 95.383000 1878 2765 1 chr6D.!!$R3 887
2 TraesCS6D01G073900 chr6D 37838216 37839236 1020 True 1363.0 1363 90.874000 852 1876 1 chr6D.!!$R2 1024
3 TraesCS6D01G073900 chr6D 37877975 37881368 3393 True 559.9 1515 92.037667 40 1876 3 chr6D.!!$R4 1836
4 TraesCS6D01G073900 chr6B 88497638 88498704 1066 True 1576.0 1576 93.199000 793 1876 1 chr6B.!!$R1 1083
5 TraesCS6D01G073900 chr6B 88570446 88573017 2571 True 827.0 1465 90.889500 41 1868 2 chr6B.!!$R2 1827
6 TraesCS6D01G073900 chr6A 49131090 49132132 1042 True 1483.0 1483 92.322000 827 1876 1 chr6A.!!$R1 1049
7 TraesCS6D01G073900 chr7D 106380803 106381690 887 True 1424.0 1424 95.608000 1878 2765 1 chr7D.!!$R1 887
8 TraesCS6D01G073900 chr7D 626963844 626964721 877 True 1387.0 1387 95.045000 1878 2765 1 chr7D.!!$R3 887
9 TraesCS6D01G073900 chr7D 626958365 626959247 882 True 1380.0 1380 94.820000 1878 2765 1 chr7D.!!$R2 887
10 TraesCS6D01G073900 chr5D 434301833 434302718 885 False 1417.0 1417 95.495000 1878 2765 1 chr5D.!!$F1 887
11 TraesCS6D01G073900 chr3D 527119888 527120774 886 True 1411.0 1411 95.388000 1878 2765 1 chr3D.!!$R3 887
12 TraesCS6D01G073900 chr3D 509239975 509240852 877 True 1404.0 1404 95.383000 1878 2765 1 chr3D.!!$R2 887
13 TraesCS6D01G073900 chr3D 167377033 167377910 877 True 1393.0 1393 95.158000 1878 2765 1 chr3D.!!$R1 887
14 TraesCS6D01G073900 chr1D 458410911 458411803 892 False 1382.0 1382 94.625000 1875 2765 1 chr1D.!!$F1 890
15 TraesCS6D01G073900 chr3A 733433524 733434061 537 False 614.0 614 87.269000 195 734 1 chr3A.!!$F1 539
16 TraesCS6D01G073900 chr5B 545087164 545087671 507 True 612.0 612 88.454000 191 699 1 chr5B.!!$R3 508
17 TraesCS6D01G073900 chr5B 216659682 216660234 552 True 492.0 492 83.275000 191 739 1 chr5B.!!$R2 548
18 TraesCS6D01G073900 chr1B 296492868 296493423 555 True 608.0 608 86.453000 188 746 1 chr1B.!!$R1 558

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
747 769 0.173708 AATGACTCTCGAAGCGGTCC 59.826 55.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2226 0.602106 CCGCATCGCCTTCATCATCT 60.602 55.0 0.0 0.0 0.0 2.9 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
30 31 3.853207 TCCACTAGGGAAACACTACACT 58.147 45.455 0.00 0.00 44.80 3.55
31 32 3.830755 TCCACTAGGGAAACACTACACTC 59.169 47.826 0.00 0.00 44.80 3.51
32 33 3.576982 CCACTAGGGAAACACTACACTCA 59.423 47.826 0.00 0.00 40.01 3.41
33 34 4.223032 CCACTAGGGAAACACTACACTCAT 59.777 45.833 0.00 0.00 40.01 2.90
34 35 5.411781 CACTAGGGAAACACTACACTCATC 58.588 45.833 0.00 0.00 0.00 2.92
35 36 5.047306 CACTAGGGAAACACTACACTCATCA 60.047 44.000 0.00 0.00 0.00 3.07
36 37 4.974645 AGGGAAACACTACACTCATCAA 57.025 40.909 0.00 0.00 0.00 2.57
37 38 5.505181 AGGGAAACACTACACTCATCAAT 57.495 39.130 0.00 0.00 0.00 2.57
38 39 5.880901 AGGGAAACACTACACTCATCAATT 58.119 37.500 0.00 0.00 0.00 2.32
39 40 6.306987 AGGGAAACACTACACTCATCAATTT 58.693 36.000 0.00 0.00 0.00 1.82
40 41 6.431234 AGGGAAACACTACACTCATCAATTTC 59.569 38.462 0.00 0.00 0.00 2.17
41 42 6.431234 GGGAAACACTACACTCATCAATTTCT 59.569 38.462 0.00 0.00 0.00 2.52
42 43 7.361286 GGGAAACACTACACTCATCAATTTCTC 60.361 40.741 0.00 0.00 0.00 2.87
43 44 6.712241 AACACTACACTCATCAATTTCTCG 57.288 37.500 0.00 0.00 0.00 4.04
44 45 5.784177 ACACTACACTCATCAATTTCTCGT 58.216 37.500 0.00 0.00 0.00 4.18
45 46 5.864474 ACACTACACTCATCAATTTCTCGTC 59.136 40.000 0.00 0.00 0.00 4.20
46 47 6.096036 CACTACACTCATCAATTTCTCGTCT 58.904 40.000 0.00 0.00 0.00 4.18
47 48 6.587990 CACTACACTCATCAATTTCTCGTCTT 59.412 38.462 0.00 0.00 0.00 3.01
48 49 7.116948 CACTACACTCATCAATTTCTCGTCTTT 59.883 37.037 0.00 0.00 0.00 2.52
49 50 8.304596 ACTACACTCATCAATTTCTCGTCTTTA 58.695 33.333 0.00 0.00 0.00 1.85
50 51 7.588143 ACACTCATCAATTTCTCGTCTTTAG 57.412 36.000 0.00 0.00 0.00 1.85
51 52 7.378966 ACACTCATCAATTTCTCGTCTTTAGA 58.621 34.615 0.00 0.00 0.00 2.10
52 53 7.543868 ACACTCATCAATTTCTCGTCTTTAGAG 59.456 37.037 0.00 0.00 37.09 2.43
53 54 7.543868 CACTCATCAATTTCTCGTCTTTAGAGT 59.456 37.037 0.00 0.00 37.07 3.24
54 55 7.757624 ACTCATCAATTTCTCGTCTTTAGAGTC 59.242 37.037 0.00 0.00 37.07 3.36
55 56 6.747739 TCATCAATTTCTCGTCTTTAGAGTCG 59.252 38.462 0.00 0.00 37.07 4.18
56 57 5.399858 TCAATTTCTCGTCTTTAGAGTCGG 58.600 41.667 0.49 0.00 35.57 4.79
57 58 2.915738 TTCTCGTCTTTAGAGTCGGC 57.084 50.000 0.49 0.00 35.57 5.54
58 59 2.110901 TCTCGTCTTTAGAGTCGGCT 57.889 50.000 0.00 0.00 35.57 5.52
59 60 2.434428 TCTCGTCTTTAGAGTCGGCTT 58.566 47.619 0.00 0.00 35.57 4.35
60 61 2.818432 TCTCGTCTTTAGAGTCGGCTTT 59.182 45.455 0.00 0.00 35.57 3.51
61 62 3.255149 TCTCGTCTTTAGAGTCGGCTTTT 59.745 43.478 0.00 0.00 35.57 2.27
62 63 3.314553 TCGTCTTTAGAGTCGGCTTTTG 58.685 45.455 0.00 0.00 35.57 2.44
63 64 3.057734 CGTCTTTAGAGTCGGCTTTTGT 58.942 45.455 0.00 0.00 32.06 2.83
64 65 3.493503 CGTCTTTAGAGTCGGCTTTTGTT 59.506 43.478 0.00 0.00 32.06 2.83
65 66 4.376109 CGTCTTTAGAGTCGGCTTTTGTTC 60.376 45.833 0.00 0.00 32.06 3.18
66 67 4.750598 GTCTTTAGAGTCGGCTTTTGTTCT 59.249 41.667 0.00 0.00 0.00 3.01
67 68 5.236695 GTCTTTAGAGTCGGCTTTTGTTCTT 59.763 40.000 0.00 0.00 0.00 2.52
68 69 5.820947 TCTTTAGAGTCGGCTTTTGTTCTTT 59.179 36.000 0.00 0.00 0.00 2.52
69 70 5.668558 TTAGAGTCGGCTTTTGTTCTTTC 57.331 39.130 0.00 0.00 0.00 2.62
70 71 3.809905 AGAGTCGGCTTTTGTTCTTTCT 58.190 40.909 0.00 0.00 0.00 2.52
71 72 4.200092 AGAGTCGGCTTTTGTTCTTTCTT 58.800 39.130 0.00 0.00 0.00 2.52
72 73 4.640647 AGAGTCGGCTTTTGTTCTTTCTTT 59.359 37.500 0.00 0.00 0.00 2.52
73 74 4.921547 AGTCGGCTTTTGTTCTTTCTTTC 58.078 39.130 0.00 0.00 0.00 2.62
74 75 4.398044 AGTCGGCTTTTGTTCTTTCTTTCA 59.602 37.500 0.00 0.00 0.00 2.69
75 76 4.735338 GTCGGCTTTTGTTCTTTCTTTCAG 59.265 41.667 0.00 0.00 0.00 3.02
76 77 4.638421 TCGGCTTTTGTTCTTTCTTTCAGA 59.362 37.500 0.00 0.00 0.00 3.27
77 78 4.972440 CGGCTTTTGTTCTTTCTTTCAGAG 59.028 41.667 0.00 0.00 0.00 3.35
78 79 5.220854 CGGCTTTTGTTCTTTCTTTCAGAGA 60.221 40.000 0.00 0.00 0.00 3.10
79 80 6.564328 GGCTTTTGTTCTTTCTTTCAGAGAA 58.436 36.000 0.00 0.00 42.56 2.87
90 91 6.469782 TTCTTTCAGAGAAAAATGTTGGCT 57.530 33.333 0.00 0.00 41.34 4.75
91 92 6.469782 TCTTTCAGAGAAAAATGTTGGCTT 57.530 33.333 0.00 0.00 0.00 4.35
92 93 7.581213 TCTTTCAGAGAAAAATGTTGGCTTA 57.419 32.000 0.00 0.00 0.00 3.09
93 94 8.181904 TCTTTCAGAGAAAAATGTTGGCTTAT 57.818 30.769 0.00 0.00 0.00 1.73
94 95 8.084073 TCTTTCAGAGAAAAATGTTGGCTTATG 58.916 33.333 0.00 0.00 0.00 1.90
95 96 6.899393 TCAGAGAAAAATGTTGGCTTATGT 57.101 33.333 0.00 0.00 0.00 2.29
96 97 7.288810 TCAGAGAAAAATGTTGGCTTATGTT 57.711 32.000 0.00 0.00 0.00 2.71
97 98 7.370383 TCAGAGAAAAATGTTGGCTTATGTTC 58.630 34.615 0.00 0.00 0.00 3.18
98 99 6.587608 CAGAGAAAAATGTTGGCTTATGTTCC 59.412 38.462 0.00 0.00 0.00 3.62
99 100 6.494835 AGAGAAAAATGTTGGCTTATGTTCCT 59.505 34.615 0.00 0.00 0.00 3.36
100 101 7.669722 AGAGAAAAATGTTGGCTTATGTTCCTA 59.330 33.333 0.00 0.00 0.00 2.94
101 102 8.189119 AGAAAAATGTTGGCTTATGTTCCTAA 57.811 30.769 0.00 0.00 0.00 2.69
102 103 8.646900 AGAAAAATGTTGGCTTATGTTCCTAAA 58.353 29.630 0.00 0.00 0.00 1.85
103 104 9.267084 GAAAAATGTTGGCTTATGTTCCTAAAA 57.733 29.630 0.00 0.00 0.00 1.52
104 105 9.620259 AAAAATGTTGGCTTATGTTCCTAAAAA 57.380 25.926 0.00 0.00 0.00 1.94
105 106 8.831715 AAATGTTGGCTTATGTTCCTAAAAAG 57.168 30.769 0.00 0.00 0.00 2.27
106 107 7.775053 ATGTTGGCTTATGTTCCTAAAAAGA 57.225 32.000 0.00 0.00 0.00 2.52
107 108 7.589958 TGTTGGCTTATGTTCCTAAAAAGAA 57.410 32.000 0.00 0.00 0.00 2.52
108 109 8.189119 TGTTGGCTTATGTTCCTAAAAAGAAT 57.811 30.769 0.00 0.00 0.00 2.40
109 110 9.303116 TGTTGGCTTATGTTCCTAAAAAGAATA 57.697 29.630 0.00 0.00 0.00 1.75
161 162 9.911788 ATTTTGGATTAGACTAGATGTTCATGT 57.088 29.630 0.00 0.00 0.00 3.21
162 163 8.722480 TTTGGATTAGACTAGATGTTCATGTG 57.278 34.615 0.00 0.00 0.00 3.21
163 164 6.283694 TGGATTAGACTAGATGTTCATGTGC 58.716 40.000 0.00 0.00 0.00 4.57
164 165 6.127083 TGGATTAGACTAGATGTTCATGTGCA 60.127 38.462 0.00 0.00 0.00 4.57
165 166 6.201806 GGATTAGACTAGATGTTCATGTGCAC 59.798 42.308 10.75 10.75 0.00 4.57
166 167 3.515630 AGACTAGATGTTCATGTGCACG 58.484 45.455 13.13 0.00 0.00 5.34
167 168 3.056536 AGACTAGATGTTCATGTGCACGT 60.057 43.478 13.13 9.52 0.00 4.49
168 169 4.157840 AGACTAGATGTTCATGTGCACGTA 59.842 41.667 12.10 0.00 0.00 3.57
169 170 5.011090 ACTAGATGTTCATGTGCACGTAT 57.989 39.130 12.10 0.95 0.00 3.06
170 171 4.805719 ACTAGATGTTCATGTGCACGTATG 59.194 41.667 12.10 11.00 0.00 2.39
264 265 1.685148 GCCAGATCCAAGTTCCATCC 58.315 55.000 0.00 0.00 0.00 3.51
288 289 2.091588 CGGTGCACAACGTACATCTTAC 59.908 50.000 20.43 0.00 36.64 2.34
290 291 4.487948 GGTGCACAACGTACATCTTACTA 58.512 43.478 20.43 0.00 30.59 1.82
315 316 0.677731 CACCTGATTCGTGGCACCAT 60.678 55.000 12.86 4.20 0.00 3.55
331 332 0.385751 CCATATGACTCAGTCCGCGT 59.614 55.000 4.92 0.00 0.00 6.01
408 409 3.632145 AGAAATCCTTTCGCAACAACACT 59.368 39.130 0.00 0.00 44.29 3.55
480 483 1.825090 TGCAGAAGTCATTCCGCAAT 58.175 45.000 0.00 0.00 43.99 3.56
565 586 3.177997 AGTCATTTTGCAACAACACCC 57.822 42.857 0.00 0.00 0.00 4.61
568 589 3.494251 GTCATTTTGCAACAACACCCATC 59.506 43.478 0.00 0.00 0.00 3.51
572 594 5.543507 TTTTGCAACAACACCCATCTTAT 57.456 34.783 0.00 0.00 0.00 1.73
662 684 7.446625 ACATATGGTCTATTGCAAAGAAGGATC 59.553 37.037 1.71 0.00 0.00 3.36
669 691 2.811410 TGCAAAGAAGGATCCTGCAAT 58.189 42.857 22.61 7.39 40.20 3.56
700 722 2.622942 GTTGCAATGGTGAGGAAAGACA 59.377 45.455 0.59 0.00 0.00 3.41
706 728 1.228657 GGTGAGGAAAGACACGTGCC 61.229 60.000 17.22 3.99 37.82 5.01
707 729 1.300620 TGAGGAAAGACACGTGCCG 60.301 57.895 17.22 0.00 0.00 5.69
730 752 2.290641 GCTGGATAACGCCGAATCAAAT 59.709 45.455 0.00 0.00 0.00 2.32
735 757 4.318831 GGATAACGCCGAATCAAATGACTC 60.319 45.833 0.00 0.00 0.00 3.36
740 762 2.930040 GCCGAATCAAATGACTCTCGAA 59.070 45.455 11.01 0.00 0.00 3.71
743 765 3.301451 CGAATCAAATGACTCTCGAAGCG 60.301 47.826 5.81 0.00 0.00 4.68
746 768 1.656095 CAAATGACTCTCGAAGCGGTC 59.344 52.381 0.00 0.00 0.00 4.79
747 769 0.173708 AATGACTCTCGAAGCGGTCC 59.826 55.000 0.00 0.00 0.00 4.46
748 770 1.994507 ATGACTCTCGAAGCGGTCCG 61.995 60.000 6.99 6.99 0.00 4.79
766 788 4.508128 CCGGCCGACGTGTAGCAT 62.508 66.667 30.73 0.00 42.24 3.79
767 789 2.954868 CGGCCGACGTGTAGCATC 60.955 66.667 24.07 0.00 37.93 3.91
768 790 2.585247 GGCCGACGTGTAGCATCC 60.585 66.667 0.00 0.00 0.00 3.51
769 791 2.585247 GCCGACGTGTAGCATCCC 60.585 66.667 0.00 0.00 0.00 3.85
770 792 3.077519 GCCGACGTGTAGCATCCCT 62.078 63.158 0.00 0.00 0.00 4.20
771 793 1.731433 GCCGACGTGTAGCATCCCTA 61.731 60.000 0.00 0.00 0.00 3.53
772 794 0.959553 CCGACGTGTAGCATCCCTAT 59.040 55.000 0.00 0.00 0.00 2.57
773 795 2.156917 CCGACGTGTAGCATCCCTATA 58.843 52.381 0.00 0.00 0.00 1.31
774 796 2.753452 CCGACGTGTAGCATCCCTATAT 59.247 50.000 0.00 0.00 0.00 0.86
775 797 3.192844 CCGACGTGTAGCATCCCTATATT 59.807 47.826 0.00 0.00 0.00 1.28
776 798 4.397103 CCGACGTGTAGCATCCCTATATTA 59.603 45.833 0.00 0.00 0.00 0.98
777 799 5.067413 CCGACGTGTAGCATCCCTATATTAT 59.933 44.000 0.00 0.00 0.00 1.28
778 800 6.261603 CCGACGTGTAGCATCCCTATATTATA 59.738 42.308 0.00 0.00 0.00 0.98
779 801 7.040617 CCGACGTGTAGCATCCCTATATTATAT 60.041 40.741 0.00 0.00 0.00 0.86
780 802 8.350722 CGACGTGTAGCATCCCTATATTATATT 58.649 37.037 0.00 0.00 0.00 1.28
781 803 9.680315 GACGTGTAGCATCCCTATATTATATTC 57.320 37.037 0.00 0.00 0.00 1.75
782 804 8.639761 ACGTGTAGCATCCCTATATTATATTCC 58.360 37.037 0.00 0.00 0.00 3.01
783 805 8.638873 CGTGTAGCATCCCTATATTATATTCCA 58.361 37.037 0.00 0.00 0.00 3.53
854 882 1.395954 GTTCTTTGGTTCGTATCCGCC 59.604 52.381 0.00 0.00 0.00 6.13
892 920 0.601841 ACGTAAACTTGGGGCGTGAG 60.602 55.000 0.00 0.00 34.36 3.51
893 921 0.601841 CGTAAACTTGGGGCGTGAGT 60.602 55.000 0.00 0.00 0.00 3.41
894 922 0.872388 GTAAACTTGGGGCGTGAGTG 59.128 55.000 0.00 0.00 0.00 3.51
895 923 0.250553 TAAACTTGGGGCGTGAGTGG 60.251 55.000 0.00 0.00 0.00 4.00
923 951 1.424493 CTGATCCGTTTCAGGCTCGC 61.424 60.000 4.38 0.00 39.58 5.03
1691 1728 0.824109 CTGGAGATGGCCAACTACGA 59.176 55.000 19.57 8.64 37.52 3.43
1702 1739 1.088306 CAACTACGAGCTCGGACTCT 58.912 55.000 36.93 20.02 44.95 3.24
1797 1842 7.465353 TGAATGCTGTTTTGATTCCAAGATA 57.535 32.000 0.00 0.00 33.23 1.98
1876 1921 7.714813 TCTCGATGGAATTCAATGCAATAGTTA 59.285 33.333 7.93 0.00 0.00 2.24
1949 1995 4.751060 AGCATGGCATTGACACAAATAAG 58.249 39.130 0.00 0.00 0.00 1.73
1958 2004 6.714492 CATTGACACAAATAAGCGCATACTA 58.286 36.000 11.47 0.00 0.00 1.82
2046 2092 5.763698 GGCTAAAACAGAAAACAGTAGGAGT 59.236 40.000 0.00 0.00 0.00 3.85
2108 2154 3.688159 GGCTTTGGTGGCAGCAGG 61.688 66.667 19.65 16.59 37.81 4.85
2180 2226 4.077184 GGCGTCGGTGGACATGGA 62.077 66.667 0.00 0.00 43.61 3.41
2195 2241 2.371179 ACATGGAGATGATGAAGGCGAT 59.629 45.455 0.00 0.00 33.36 4.58
2283 2329 0.981277 CCCTCACCCCGTACAGGAAT 60.981 60.000 5.95 0.00 45.00 3.01
2331 2377 3.422303 CCCGTCGACCGTGTACGA 61.422 66.667 10.58 0.00 43.02 3.43
2483 2531 2.341101 GGAGAGACGTGGGCTCGAA 61.341 63.158 0.00 0.00 37.46 3.71
2524 2572 1.725557 CCCACGATCCGACGTCTCAT 61.726 60.000 14.70 4.84 44.76 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.830755 GAGTGTAGTGTTTCCCTAGTGGA 59.169 47.826 0.00 0.00 43.18 4.02
10 11 3.576982 TGAGTGTAGTGTTTCCCTAGTGG 59.423 47.826 0.00 0.00 0.00 4.00
11 12 4.866508 TGAGTGTAGTGTTTCCCTAGTG 57.133 45.455 0.00 0.00 0.00 2.74
12 13 5.084519 TGATGAGTGTAGTGTTTCCCTAGT 58.915 41.667 0.00 0.00 0.00 2.57
13 14 5.661056 TGATGAGTGTAGTGTTTCCCTAG 57.339 43.478 0.00 0.00 0.00 3.02
14 15 6.620877 ATTGATGAGTGTAGTGTTTCCCTA 57.379 37.500 0.00 0.00 0.00 3.53
15 16 4.974645 TTGATGAGTGTAGTGTTTCCCT 57.025 40.909 0.00 0.00 0.00 4.20
16 17 6.431234 AGAAATTGATGAGTGTAGTGTTTCCC 59.569 38.462 0.00 0.00 0.00 3.97
17 18 7.440523 AGAAATTGATGAGTGTAGTGTTTCC 57.559 36.000 0.00 0.00 0.00 3.13
18 19 7.095607 ACGAGAAATTGATGAGTGTAGTGTTTC 60.096 37.037 0.00 0.00 0.00 2.78
19 20 6.706270 ACGAGAAATTGATGAGTGTAGTGTTT 59.294 34.615 0.00 0.00 0.00 2.83
20 21 6.223852 ACGAGAAATTGATGAGTGTAGTGTT 58.776 36.000 0.00 0.00 0.00 3.32
21 22 5.784177 ACGAGAAATTGATGAGTGTAGTGT 58.216 37.500 0.00 0.00 0.00 3.55
22 23 6.096036 AGACGAGAAATTGATGAGTGTAGTG 58.904 40.000 0.00 0.00 0.00 2.74
23 24 6.274157 AGACGAGAAATTGATGAGTGTAGT 57.726 37.500 0.00 0.00 0.00 2.73
24 25 7.588143 AAAGACGAGAAATTGATGAGTGTAG 57.412 36.000 0.00 0.00 0.00 2.74
25 26 8.520351 TCTAAAGACGAGAAATTGATGAGTGTA 58.480 33.333 0.00 0.00 0.00 2.90
26 27 7.378966 TCTAAAGACGAGAAATTGATGAGTGT 58.621 34.615 0.00 0.00 0.00 3.55
27 28 7.543868 ACTCTAAAGACGAGAAATTGATGAGTG 59.456 37.037 0.00 0.00 32.87 3.51
28 29 7.607250 ACTCTAAAGACGAGAAATTGATGAGT 58.393 34.615 0.00 0.00 32.87 3.41
29 30 7.044380 CGACTCTAAAGACGAGAAATTGATGAG 60.044 40.741 0.00 0.00 42.15 2.90
30 31 6.747739 CGACTCTAAAGACGAGAAATTGATGA 59.252 38.462 0.00 0.00 42.15 2.92
31 32 6.020281 CCGACTCTAAAGACGAGAAATTGATG 60.020 42.308 0.00 0.00 42.15 3.07
32 33 6.037098 CCGACTCTAAAGACGAGAAATTGAT 58.963 40.000 0.00 0.00 42.15 2.57
33 34 5.399858 CCGACTCTAAAGACGAGAAATTGA 58.600 41.667 0.00 0.00 42.15 2.57
34 35 4.031878 GCCGACTCTAAAGACGAGAAATTG 59.968 45.833 0.00 0.00 42.15 2.32
35 36 4.082136 AGCCGACTCTAAAGACGAGAAATT 60.082 41.667 0.00 0.00 42.15 1.82
36 37 3.444388 AGCCGACTCTAAAGACGAGAAAT 59.556 43.478 0.00 0.00 42.15 2.17
37 38 2.818432 AGCCGACTCTAAAGACGAGAAA 59.182 45.455 0.00 0.00 42.15 2.52
38 39 2.434428 AGCCGACTCTAAAGACGAGAA 58.566 47.619 0.00 0.00 42.15 2.87
39 40 2.110901 AGCCGACTCTAAAGACGAGA 57.889 50.000 0.00 0.00 42.15 4.04
40 41 2.923605 AAGCCGACTCTAAAGACGAG 57.076 50.000 0.00 0.00 42.15 4.18
41 42 3.243636 ACAAAAGCCGACTCTAAAGACGA 60.244 43.478 0.00 0.00 42.15 4.20
42 43 3.057734 ACAAAAGCCGACTCTAAAGACG 58.942 45.455 0.00 0.00 39.81 4.18
43 44 4.750598 AGAACAAAAGCCGACTCTAAAGAC 59.249 41.667 0.00 0.00 0.00 3.01
44 45 4.957296 AGAACAAAAGCCGACTCTAAAGA 58.043 39.130 0.00 0.00 0.00 2.52
45 46 5.674933 AAGAACAAAAGCCGACTCTAAAG 57.325 39.130 0.00 0.00 0.00 1.85
46 47 5.820947 AGAAAGAACAAAAGCCGACTCTAAA 59.179 36.000 0.00 0.00 0.00 1.85
47 48 5.365619 AGAAAGAACAAAAGCCGACTCTAA 58.634 37.500 0.00 0.00 0.00 2.10
48 49 4.957296 AGAAAGAACAAAAGCCGACTCTA 58.043 39.130 0.00 0.00 0.00 2.43
49 50 3.809905 AGAAAGAACAAAAGCCGACTCT 58.190 40.909 0.00 0.00 0.00 3.24
50 51 4.553756 AAGAAAGAACAAAAGCCGACTC 57.446 40.909 0.00 0.00 0.00 3.36
51 52 4.398044 TGAAAGAAAGAACAAAAGCCGACT 59.602 37.500 0.00 0.00 0.00 4.18
52 53 4.668289 TGAAAGAAAGAACAAAAGCCGAC 58.332 39.130 0.00 0.00 0.00 4.79
53 54 4.638421 TCTGAAAGAAAGAACAAAAGCCGA 59.362 37.500 0.00 0.00 42.31 5.54
54 55 4.920376 TCTGAAAGAAAGAACAAAAGCCG 58.080 39.130 0.00 0.00 42.31 5.52
55 56 6.136541 TCTCTGAAAGAAAGAACAAAAGCC 57.863 37.500 0.00 0.00 46.34 4.35
66 67 6.877236 AGCCAACATTTTTCTCTGAAAGAAA 58.123 32.000 0.00 0.00 46.34 2.52
67 68 6.469782 AGCCAACATTTTTCTCTGAAAGAA 57.530 33.333 0.00 0.00 46.34 2.52
68 69 6.469782 AAGCCAACATTTTTCTCTGAAAGA 57.530 33.333 0.00 0.00 43.69 2.52
69 70 7.869429 ACATAAGCCAACATTTTTCTCTGAAAG 59.131 33.333 0.00 0.00 0.00 2.62
70 71 7.725251 ACATAAGCCAACATTTTTCTCTGAAA 58.275 30.769 0.00 0.00 0.00 2.69
71 72 7.288810 ACATAAGCCAACATTTTTCTCTGAA 57.711 32.000 0.00 0.00 0.00 3.02
72 73 6.899393 ACATAAGCCAACATTTTTCTCTGA 57.101 33.333 0.00 0.00 0.00 3.27
73 74 6.587608 GGAACATAAGCCAACATTTTTCTCTG 59.412 38.462 0.00 0.00 0.00 3.35
74 75 6.494835 AGGAACATAAGCCAACATTTTTCTCT 59.505 34.615 0.00 0.00 0.00 3.10
75 76 6.691508 AGGAACATAAGCCAACATTTTTCTC 58.308 36.000 0.00 0.00 0.00 2.87
76 77 6.670695 AGGAACATAAGCCAACATTTTTCT 57.329 33.333 0.00 0.00 0.00 2.52
77 78 8.825667 TTTAGGAACATAAGCCAACATTTTTC 57.174 30.769 0.00 0.00 0.00 2.29
78 79 9.620259 TTTTTAGGAACATAAGCCAACATTTTT 57.380 25.926 0.00 0.00 0.00 1.94
79 80 9.271828 CTTTTTAGGAACATAAGCCAACATTTT 57.728 29.630 0.00 0.00 0.00 1.82
80 81 8.646900 TCTTTTTAGGAACATAAGCCAACATTT 58.353 29.630 0.00 0.00 0.00 2.32
81 82 8.189119 TCTTTTTAGGAACATAAGCCAACATT 57.811 30.769 0.00 0.00 0.00 2.71
82 83 7.775053 TCTTTTTAGGAACATAAGCCAACAT 57.225 32.000 0.00 0.00 0.00 2.71
83 84 7.589958 TTCTTTTTAGGAACATAAGCCAACA 57.410 32.000 0.00 0.00 0.00 3.33
135 136 9.911788 ACATGAACATCTAGTCTAATCCAAAAT 57.088 29.630 0.00 0.00 0.00 1.82
136 137 9.166173 CACATGAACATCTAGTCTAATCCAAAA 57.834 33.333 0.00 0.00 0.00 2.44
137 138 7.280876 GCACATGAACATCTAGTCTAATCCAAA 59.719 37.037 0.00 0.00 0.00 3.28
138 139 6.763135 GCACATGAACATCTAGTCTAATCCAA 59.237 38.462 0.00 0.00 0.00 3.53
139 140 6.127083 TGCACATGAACATCTAGTCTAATCCA 60.127 38.462 0.00 0.00 0.00 3.41
140 141 6.201806 GTGCACATGAACATCTAGTCTAATCC 59.798 42.308 13.17 0.00 0.00 3.01
141 142 6.074623 CGTGCACATGAACATCTAGTCTAATC 60.075 42.308 18.64 0.00 0.00 1.75
142 143 5.750547 CGTGCACATGAACATCTAGTCTAAT 59.249 40.000 18.64 0.00 0.00 1.73
143 144 5.102313 CGTGCACATGAACATCTAGTCTAA 58.898 41.667 18.64 0.00 0.00 2.10
144 145 4.157840 ACGTGCACATGAACATCTAGTCTA 59.842 41.667 18.64 0.00 0.00 2.59
145 146 3.056536 ACGTGCACATGAACATCTAGTCT 60.057 43.478 18.64 0.00 0.00 3.24
146 147 3.254060 ACGTGCACATGAACATCTAGTC 58.746 45.455 18.64 0.00 0.00 2.59
147 148 3.319137 ACGTGCACATGAACATCTAGT 57.681 42.857 18.64 0.00 0.00 2.57
148 149 5.320607 CATACGTGCACATGAACATCTAG 57.679 43.478 18.64 0.00 0.00 2.43
163 164 7.134163 CCATATAATATTGCCATGCATACGTG 58.866 38.462 0.00 0.00 38.76 4.49
164 165 6.262944 CCCATATAATATTGCCATGCATACGT 59.737 38.462 0.00 0.00 38.76 3.57
165 166 6.486320 TCCCATATAATATTGCCATGCATACG 59.514 38.462 0.00 0.00 38.76 3.06
166 167 7.822161 TCCCATATAATATTGCCATGCATAC 57.178 36.000 0.00 0.00 38.76 2.39
167 168 8.835550 TTTCCCATATAATATTGCCATGCATA 57.164 30.769 0.00 0.00 38.76 3.14
168 169 7.736881 TTTCCCATATAATATTGCCATGCAT 57.263 32.000 0.00 0.00 38.76 3.96
169 170 7.399478 TCATTTCCCATATAATATTGCCATGCA 59.601 33.333 0.00 0.00 36.47 3.96
170 171 7.784037 TCATTTCCCATATAATATTGCCATGC 58.216 34.615 0.00 0.00 0.00 4.06
174 175 9.971922 GCTAATCATTTCCCATATAATATTGCC 57.028 33.333 0.00 0.00 0.00 4.52
180 181 8.910944 GCTGATGCTAATCATTTCCCATATAAT 58.089 33.333 0.00 0.00 41.97 1.28
181 182 7.340232 GGCTGATGCTAATCATTTCCCATATAA 59.660 37.037 0.00 0.00 41.97 0.98
182 183 6.830324 GGCTGATGCTAATCATTTCCCATATA 59.170 38.462 0.00 0.00 41.97 0.86
183 184 5.655532 GGCTGATGCTAATCATTTCCCATAT 59.344 40.000 0.00 0.00 41.97 1.78
184 185 5.012239 GGCTGATGCTAATCATTTCCCATA 58.988 41.667 0.00 0.00 41.97 2.74
185 186 3.830755 GGCTGATGCTAATCATTTCCCAT 59.169 43.478 0.00 0.00 41.97 4.00
186 187 3.225104 GGCTGATGCTAATCATTTCCCA 58.775 45.455 0.00 0.00 41.97 4.37
264 265 1.279527 ATGTACGTTGTGCACCGTCG 61.280 55.000 21.72 20.06 38.43 5.12
288 289 3.364964 GCCACGAATCAGGTGTTTTGTAG 60.365 47.826 0.00 0.00 33.56 2.74
290 291 1.336755 GCCACGAATCAGGTGTTTTGT 59.663 47.619 0.00 0.00 33.56 2.83
315 316 1.138883 GCACGCGGACTGAGTCATA 59.861 57.895 15.33 0.00 33.68 2.15
339 340 0.698238 TGTTAAGGTGGCAGAGGCAT 59.302 50.000 0.00 0.00 43.71 4.40
390 391 2.571212 TGAGTGTTGTTGCGAAAGGAT 58.429 42.857 0.00 0.00 0.00 3.24
471 474 2.733956 ACATGGGTGTTATTGCGGAAT 58.266 42.857 7.49 7.49 34.01 3.01
549 553 4.420522 AAGATGGGTGTTGTTGCAAAAT 57.579 36.364 0.00 0.00 0.00 1.82
552 556 6.656632 TTAATAAGATGGGTGTTGTTGCAA 57.343 33.333 0.00 0.00 0.00 4.08
615 637 2.060284 TGCAGAAACATTCGCAATTGC 58.940 42.857 20.76 20.76 36.68 3.56
617 639 3.715495 TGTTGCAGAAACATTCGCAATT 58.285 36.364 18.04 0.00 43.96 2.32
676 698 3.896888 TCTTTCCTCACCATTGCAACAAT 59.103 39.130 0.00 0.00 0.00 2.71
723 745 2.932614 CCGCTTCGAGAGTCATTTGATT 59.067 45.455 0.00 0.00 0.00 2.57
730 752 2.687805 CGGACCGCTTCGAGAGTCA 61.688 63.158 0.00 0.00 0.00 3.41
749 771 4.508128 ATGCTACACGTCGGCCGG 62.508 66.667 27.83 13.23 42.24 6.13
750 772 2.954868 GATGCTACACGTCGGCCG 60.955 66.667 22.12 22.12 44.03 6.13
751 773 2.585247 GGATGCTACACGTCGGCC 60.585 66.667 0.00 0.00 34.88 6.13
752 774 1.731433 TAGGGATGCTACACGTCGGC 61.731 60.000 0.00 0.00 34.88 5.54
753 775 0.959553 ATAGGGATGCTACACGTCGG 59.040 55.000 0.00 0.00 34.88 4.79
754 776 4.436242 AATATAGGGATGCTACACGTCG 57.564 45.455 0.00 0.00 34.88 5.12
755 777 9.680315 GAATATAATATAGGGATGCTACACGTC 57.320 37.037 0.00 0.00 0.00 4.34
756 778 8.639761 GGAATATAATATAGGGATGCTACACGT 58.360 37.037 0.00 0.00 0.00 4.49
757 779 8.638873 TGGAATATAATATAGGGATGCTACACG 58.361 37.037 0.00 0.00 0.00 4.49
788 810 0.738389 CTGTGTGCCCGTGTCTTTTT 59.262 50.000 0.00 0.00 0.00 1.94
789 811 1.724582 GCTGTGTGCCCGTGTCTTTT 61.725 55.000 0.00 0.00 35.15 2.27
790 812 2.186826 GCTGTGTGCCCGTGTCTTT 61.187 57.895 0.00 0.00 35.15 2.52
791 813 2.591715 GCTGTGTGCCCGTGTCTT 60.592 61.111 0.00 0.00 35.15 3.01
798 820 2.469465 TAGGAAGCTGCTGTGTGCCC 62.469 60.000 1.35 0.00 42.00 5.36
854 882 2.202298 GGTCGGCGCGTTTTGATG 60.202 61.111 8.43 0.00 0.00 3.07
892 920 2.167861 GGATCAGAAGTCGCGCCAC 61.168 63.158 0.00 0.00 0.00 5.01
893 921 2.184322 GGATCAGAAGTCGCGCCA 59.816 61.111 0.00 0.00 0.00 5.69
894 922 2.956964 CGGATCAGAAGTCGCGCC 60.957 66.667 0.00 0.00 0.00 6.53
895 923 1.352156 AAACGGATCAGAAGTCGCGC 61.352 55.000 0.00 0.00 0.00 6.86
940 968 2.449450 GGCCCCGGTACTTATGGCT 61.449 63.158 14.21 0.00 41.84 4.75
1691 1728 3.768922 GCAGCCAGAGTCCGAGCT 61.769 66.667 0.00 0.00 35.52 4.09
1949 1995 5.406780 AGCTTGACTGAATATTAGTATGCGC 59.593 40.000 0.00 0.00 0.00 6.09
1958 2004 7.504403 ACTATGTGCTAGCTTGACTGAATATT 58.496 34.615 17.23 0.00 0.00 1.28
2046 2092 4.590222 GGAGGGTATAACTCGTTTATCCCA 59.410 45.833 18.07 0.00 38.63 4.37
2180 2226 0.602106 CCGCATCGCCTTCATCATCT 60.602 55.000 0.00 0.00 0.00 2.90
2195 2241 1.065926 TCTACTTCCTCTACGTCCGCA 60.066 52.381 0.00 0.00 0.00 5.69
2283 2329 1.301401 CGAAACCACGCCCTTCTGA 60.301 57.895 0.00 0.00 0.00 3.27
2331 2377 4.779733 ACTCCATCCCGTCCGCCT 62.780 66.667 0.00 0.00 0.00 5.52
2524 2572 1.960040 CTGACAGCTGGGCCACGATA 61.960 60.000 19.93 0.00 0.00 2.92
2727 2828 5.191124 TGGACCTCCTTATAAGGGTTTCTTC 59.809 44.000 27.65 16.05 46.47 2.87
2728 2829 5.105853 TGGACCTCCTTATAAGGGTTTCTT 58.894 41.667 27.65 9.51 46.47 2.52


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

AutoCloner maintained by Alex Coulton.