Multiple sequence alignment - TraesCS3B01G405900

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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 TraesCS3B01G405900 chr3B 100.000 2995 0 0 1 2995 641652984 641655978 0.000000e+00 5531.0
1 TraesCS3B01G405900 chr3B 85.137 693 77 20 801 1480 640832064 640832743 0.000000e+00 686.0
2 TraesCS3B01G405900 chr3B 84.168 619 78 14 877 1490 640693405 640694008 1.550000e-162 582.0
3 TraesCS3B01G405900 chr3B 84.854 548 71 9 1593 2133 640832755 640833297 2.630000e-150 542.0
4 TraesCS3B01G405900 chr3D 91.331 2884 175 29 77 2912 480836078 480838934 0.000000e+00 3871.0
5 TraesCS3B01G405900 chr3D 84.438 694 85 15 801 1490 480366550 480367224 0.000000e+00 662.0
6 TraesCS3B01G405900 chr3D 84.091 704 85 18 801 1490 480357809 480358499 0.000000e+00 654.0
7 TraesCS3B01G405900 chr3D 83.761 702 93 19 801 1490 480375618 480376310 0.000000e+00 645.0
8 TraesCS3B01G405900 chr3D 87.475 503 62 1 988 1490 480157917 480158418 2.000000e-161 579.0
9 TraesCS3B01G405900 chr3D 81.187 691 106 17 815 1488 480125118 480125801 4.390000e-148 534.0
10 TraesCS3B01G405900 chr3D 84.629 553 64 14 1594 2133 480376313 480376857 5.680000e-147 531.0
11 TraesCS3B01G405900 chr3D 88.834 403 45 0 1594 1996 480358502 480358904 2.070000e-136 496.0
12 TraesCS3B01G405900 chr3D 88.586 403 46 0 1594 1996 480158421 480158823 9.650000e-135 490.0
13 TraesCS3B01G405900 chr3D 83.202 506 82 1 990 1492 480120544 480121049 7.560000e-126 460.0
14 TraesCS3B01G405900 chr3D 84.864 403 42 5 1594 1996 480367227 480367610 3.620000e-104 388.0
15 TraesCS3B01G405900 chr3D 78.070 342 50 13 49 378 539556469 539556141 3.050000e-45 193.0
16 TraesCS3B01G405900 chr3A 92.222 2520 163 15 497 2995 623604611 623607118 0.000000e+00 3537.0
17 TraesCS3B01G405900 chr3A 84.357 684 88 18 815 1490 623389456 623390128 0.000000e+00 652.0
18 TraesCS3B01G405900 chr3A 83.024 701 94 20 801 1490 623354308 623354994 1.970000e-171 612.0
19 TraesCS3B01G405900 chr3A 87.234 517 63 2 977 1490 623340336 623340852 1.200000e-163 586.0
20 TraesCS3B01G405900 chr3A 85.165 546 69 9 1594 2132 623390131 623390671 1.570000e-152 549.0
21 TraesCS3B01G405900 chr3A 89.330 403 43 0 1594 1996 623340855 623341257 9.580000e-140 507.0
22 TraesCS3B01G405900 chr3A 88.089 403 48 0 1594 1996 623230095 623230497 2.090000e-131 479.0
23 TraesCS3B01G405900 chr3A 77.844 334 66 7 167 495 174277441 174277771 1.820000e-47 200.0
24 TraesCS3B01G405900 chr7D 81.844 347 51 8 49 385 72119274 72118930 6.320000e-72 281.0
25 TraesCS3B01G405900 chr6D 78.214 459 83 10 49 492 391567462 391567918 8.180000e-71 278.0
26 TraesCS3B01G405900 chr2D 78.139 462 79 14 49 494 3038779 3039234 1.060000e-69 274.0
27 TraesCS3B01G405900 chr2D 79.023 348 58 11 49 385 190094560 190094903 1.080000e-54 224.0
28 TraesCS3B01G405900 chr2D 76.316 456 83 20 58 506 7004723 7005160 1.400000e-53 220.0
29 TraesCS3B01G405900 chr2D 81.061 264 25 9 2741 2995 119846132 119846379 1.420000e-43 187.0
30 TraesCS3B01G405900 chr2D 92.000 50 4 0 1416 1465 560399508 560399557 1.490000e-08 71.3
31 TraesCS3B01G405900 chr6B 77.363 455 86 15 50 494 707852709 707853156 1.380000e-63 254.0
32 TraesCS3B01G405900 chr6B 75.652 460 84 17 51 501 194419693 194420133 1.410000e-48 204.0
33 TraesCS3B01G405900 chr6B 82.353 204 24 4 2758 2950 604705506 604705708 1.850000e-37 167.0
34 TraesCS3B01G405900 chr1D 76.484 455 90 12 51 494 204143907 204144355 6.460000e-57 231.0
35 TraesCS3B01G405900 chr1D 80.240 167 21 5 2758 2913 370534537 370534372 6.780000e-22 115.0
36 TraesCS3B01G405900 chr1D 84.685 111 13 3 2574 2683 224144861 224144968 1.140000e-19 108.0
37 TraesCS3B01G405900 chr1B 76.380 453 74 16 49 494 546506915 546506489 2.340000e-51 213.0
38 TraesCS3B01G405900 chr1B 84.706 85 11 2 2912 2995 494071120 494071037 1.910000e-12 84.2
39 TraesCS3B01G405900 chr6A 75.699 465 87 19 49 494 457451555 457451098 3.030000e-50 209.0
40 TraesCS3B01G405900 chr6A 80.702 228 32 4 2737 2953 549621722 549621496 1.850000e-37 167.0
41 TraesCS3B01G405900 chr6A 78.027 223 39 1 2741 2953 1979001 1978779 6.740000e-27 132.0
42 TraesCS3B01G405900 chr6A 98.148 54 0 1 1 53 110493459 110493406 3.180000e-15 93.5
43 TraesCS3B01G405900 chr6A 98.148 54 0 1 1 53 150572041 150571988 3.180000e-15 93.5
44 TraesCS3B01G405900 chr7A 78.869 336 48 17 167 494 252192034 252192354 3.910000e-49 206.0
45 TraesCS3B01G405900 chr2A 83.333 228 25 4 2741 2956 122155887 122156113 6.550000e-47 198.0
46 TraesCS3B01G405900 chr2A 77.619 210 29 5 2804 2995 615745237 615745028 8.780000e-21 111.0
47 TraesCS3B01G405900 chr7B 76.807 332 67 9 167 492 621405575 621405902 8.530000e-41 178.0
48 TraesCS3B01G405900 chr7B 81.481 216 31 4 2741 2953 410631528 410631737 5.130000e-38 169.0
49 TraesCS3B01G405900 chr7B 98.182 55 0 1 1 54 158864920 158864974 8.840000e-16 95.3
50 TraesCS3B01G405900 chr7B 95.238 42 2 0 2738 2779 161229677 161229718 1.930000e-07 67.6
51 TraesCS3B01G405900 chr2B 79.545 264 28 9 2741 2995 172228180 172228426 6.640000e-37 165.0
52 TraesCS3B01G405900 chr2B 98.246 57 0 1 1 56 434776503 434776447 6.830000e-17 99.0
53 TraesCS3B01G405900 chr4A 83.974 156 24 1 2574 2729 669653980 669654134 6.690000e-32 148.0
54 TraesCS3B01G405900 chr4A 98.182 55 0 1 1 54 134347867 134347921 8.840000e-16 95.3
55 TraesCS3B01G405900 chr4A 98.182 55 0 1 1 54 685210750 685210804 8.840000e-16 95.3
56 TraesCS3B01G405900 chr4A 80.000 145 14 3 2866 2995 556802451 556802307 3.180000e-15 93.5
57 TraesCS3B01G405900 chr4A 98.148 54 0 1 1 53 722242345 722242292 3.180000e-15 93.5
58 TraesCS3B01G405900 chr5B 79.186 221 37 2 2741 2952 241266827 241266607 8.650000e-31 145.0
59 TraesCS3B01G405900 chr5B 80.000 145 24 4 2814 2953 547350370 547350226 5.280000e-18 102.0
60 TraesCS3B01G405900 chr5A 82.301 113 20 0 2814 2926 566292722 566292610 6.830000e-17 99.0
61 TraesCS3B01G405900 chr5A 98.182 55 0 1 1 54 367266550 367266604 8.840000e-16 95.3
62 TraesCS3B01G405900 chr5A 96.429 56 2 0 1 56 259344485 259344430 3.180000e-15 93.5
63 TraesCS3B01G405900 chr4D 79.310 145 15 4 2866 2995 43080424 43080568 1.480000e-13 87.9
64 TraesCS3B01G405900 chr4D 94.595 37 2 0 2815 2851 43080348 43080384 1.160000e-04 58.4
65 TraesCS3B01G405900 chr4B 93.750 48 3 0 2948 2995 139947956 139948003 4.140000e-09 73.1


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 TraesCS3B01G405900 chr3B 641652984 641655978 2994 False 5531.0 5531 100.0000 1 2995 1 chr3B.!!$F2 2994
1 TraesCS3B01G405900 chr3B 640832064 640833297 1233 False 614.0 686 84.9955 801 2133 2 chr3B.!!$F3 1332
2 TraesCS3B01G405900 chr3B 640693405 640694008 603 False 582.0 582 84.1680 877 1490 1 chr3B.!!$F1 613
3 TraesCS3B01G405900 chr3D 480836078 480838934 2856 False 3871.0 3871 91.3310 77 2912 1 chr3D.!!$F3 2835
4 TraesCS3B01G405900 chr3D 480375618 480376857 1239 False 588.0 645 84.1950 801 2133 2 chr3D.!!$F7 1332
5 TraesCS3B01G405900 chr3D 480357809 480358904 1095 False 575.0 654 86.4625 801 1996 2 chr3D.!!$F5 1195
6 TraesCS3B01G405900 chr3D 480157917 480158823 906 False 534.5 579 88.0305 988 1996 2 chr3D.!!$F4 1008
7 TraesCS3B01G405900 chr3D 480125118 480125801 683 False 534.0 534 81.1870 815 1488 1 chr3D.!!$F2 673
8 TraesCS3B01G405900 chr3D 480366550 480367610 1060 False 525.0 662 84.6510 801 1996 2 chr3D.!!$F6 1195
9 TraesCS3B01G405900 chr3D 480120544 480121049 505 False 460.0 460 83.2020 990 1492 1 chr3D.!!$F1 502
10 TraesCS3B01G405900 chr3A 623604611 623607118 2507 False 3537.0 3537 92.2220 497 2995 1 chr3A.!!$F4 2498
11 TraesCS3B01G405900 chr3A 623354308 623354994 686 False 612.0 612 83.0240 801 1490 1 chr3A.!!$F3 689
12 TraesCS3B01G405900 chr3A 623389456 623390671 1215 False 600.5 652 84.7610 815 2132 2 chr3A.!!$F6 1317
13 TraesCS3B01G405900 chr3A 623340336 623341257 921 False 546.5 586 88.2820 977 1996 2 chr3A.!!$F5 1019

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
790 817 0.096454 CAGCTTTACTTAACCGCGGC 59.904 55.0 28.58 6.83 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2522 2595 0.615544 CGTGGGAGTAGGGGTGGTTA 60.616 60.0 0.0 0.0 0.0 2.85 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
22 23 4.779987 GTCGTCAATACTCCAAAACCAAC 58.220 43.478 0.00 0.00 0.00 3.77
23 24 4.514066 GTCGTCAATACTCCAAAACCAACT 59.486 41.667 0.00 0.00 0.00 3.16
24 25 4.513692 TCGTCAATACTCCAAAACCAACTG 59.486 41.667 0.00 0.00 0.00 3.16
25 26 4.320202 CGTCAATACTCCAAAACCAACTGG 60.320 45.833 0.00 0.00 42.17 4.00
26 27 4.022329 GTCAATACTCCAAAACCAACTGGG 60.022 45.833 0.00 0.00 44.81 4.45
27 28 2.668144 TACTCCAAAACCAACTGGGG 57.332 50.000 0.00 0.00 42.91 4.96
28 29 0.634465 ACTCCAAAACCAACTGGGGT 59.366 50.000 0.00 0.00 41.84 4.95
29 30 1.039856 CTCCAAAACCAACTGGGGTG 58.960 55.000 0.00 0.00 41.32 4.61
30 31 0.397816 TCCAAAACCAACTGGGGTGG 60.398 55.000 0.00 0.00 41.32 4.61
31 32 1.445518 CAAAACCAACTGGGGTGGC 59.554 57.895 1.05 0.00 41.32 5.01
32 33 1.002274 AAAACCAACTGGGGTGGCA 59.998 52.632 1.05 0.00 41.32 4.92
33 34 1.334384 AAAACCAACTGGGGTGGCAC 61.334 55.000 9.70 9.70 41.32 5.01
34 35 2.236959 AAACCAACTGGGGTGGCACT 62.237 55.000 18.45 0.00 41.32 4.40
35 36 1.357272 AACCAACTGGGGTGGCACTA 61.357 55.000 18.45 3.68 41.32 2.74
36 37 1.002134 CCAACTGGGGTGGCACTAG 60.002 63.158 18.45 15.15 0.00 2.57
37 38 1.488705 CCAACTGGGGTGGCACTAGA 61.489 60.000 18.45 0.19 0.00 2.43
38 39 0.620556 CAACTGGGGTGGCACTAGAT 59.379 55.000 18.45 5.89 0.00 1.98
39 40 0.620556 AACTGGGGTGGCACTAGATG 59.379 55.000 18.45 7.06 0.00 2.90
52 53 3.786635 CACTAGATGCACTTACACCTCC 58.213 50.000 0.00 0.00 0.00 4.30
53 54 3.449018 CACTAGATGCACTTACACCTCCT 59.551 47.826 0.00 0.00 0.00 3.69
54 55 3.702045 ACTAGATGCACTTACACCTCCTC 59.298 47.826 0.00 0.00 0.00 3.71
55 56 2.826488 AGATGCACTTACACCTCCTCT 58.174 47.619 0.00 0.00 0.00 3.69
56 57 2.763448 AGATGCACTTACACCTCCTCTC 59.237 50.000 0.00 0.00 0.00 3.20
57 58 0.888619 TGCACTTACACCTCCTCTCG 59.111 55.000 0.00 0.00 0.00 4.04
58 59 0.173708 GCACTTACACCTCCTCTCGG 59.826 60.000 0.00 0.00 0.00 4.63
59 60 0.818296 CACTTACACCTCCTCTCGGG 59.182 60.000 0.00 0.00 0.00 5.14
60 61 0.702902 ACTTACACCTCCTCTCGGGA 59.297 55.000 0.00 0.00 42.77 5.14
96 97 3.069318 GACGGCCGTCTCCTCCTT 61.069 66.667 43.32 15.28 41.57 3.36
97 98 1.751927 GACGGCCGTCTCCTCCTTA 60.752 63.158 43.32 0.00 41.57 2.69
114 115 1.046472 TTAGGACCGCGTGGGATGAT 61.046 55.000 21.14 0.00 40.75 2.45
127 128 0.312416 GGATGATCCCAGAGTCGACG 59.688 60.000 10.46 0.00 0.00 5.12
129 130 0.106669 ATGATCCCAGAGTCGACGGA 60.107 55.000 10.46 11.12 0.00 4.69
134 135 0.748367 CCCAGAGTCGACGGATCTGA 60.748 60.000 26.35 0.00 42.48 3.27
155 156 1.321074 GGTGAAGGACTCGGATCCGT 61.321 60.000 32.15 15.85 44.22 4.69
162 163 0.526662 GACTCGGATCCGTTGTCAGT 59.473 55.000 34.89 29.48 40.45 3.41
171 172 1.667830 CGTTGTCAGTCATGCCGGT 60.668 57.895 1.90 0.00 0.00 5.28
202 203 1.529713 GGAGTTTGGGTGGCGGAAA 60.530 57.895 0.00 0.00 0.00 3.13
212 213 3.771160 GGCGGAAAGGAGCGGAGA 61.771 66.667 0.00 0.00 0.00 3.71
240 241 2.038557 GAGTGAAGTGGCTAGGGTTTGA 59.961 50.000 0.00 0.00 0.00 2.69
244 245 0.541863 AGTGGCTAGGGTTTGATCCG 59.458 55.000 0.00 0.00 0.00 4.18
247 248 1.887707 GCTAGGGTTTGATCCGGCG 60.888 63.158 0.00 0.00 0.00 6.46
249 250 0.177141 CTAGGGTTTGATCCGGCGAA 59.823 55.000 9.30 0.00 0.00 4.70
251 252 2.746803 GGGTTTGATCCGGCGAACG 61.747 63.158 9.30 0.00 43.80 3.95
264 265 0.463833 GCGAACGGATGGGAAGGAAT 60.464 55.000 0.00 0.00 0.00 3.01
269 270 5.394883 GCGAACGGATGGGAAGGAATATATA 60.395 44.000 0.00 0.00 0.00 0.86
271 272 7.470981 GCGAACGGATGGGAAGGAATATATATA 60.471 40.741 0.00 0.00 0.00 0.86
272 273 8.585881 CGAACGGATGGGAAGGAATATATATAT 58.414 37.037 0.00 0.00 0.00 0.86
275 276 7.237679 ACGGATGGGAAGGAATATATATATGGG 59.762 40.741 6.00 0.00 0.00 4.00
276 277 7.457852 CGGATGGGAAGGAATATATATATGGGA 59.542 40.741 6.00 0.00 0.00 4.37
277 278 9.356649 GGATGGGAAGGAATATATATATGGGAT 57.643 37.037 6.00 0.00 0.00 3.85
279 280 8.435931 TGGGAAGGAATATATATATGGGATCG 57.564 38.462 6.00 0.00 0.00 3.69
280 281 7.457852 TGGGAAGGAATATATATATGGGATCGG 59.542 40.741 6.00 0.00 0.00 4.18
281 282 7.678598 GGGAAGGAATATATATATGGGATCGGA 59.321 40.741 6.00 0.00 0.00 4.55
282 283 9.273137 GGAAGGAATATATATATGGGATCGGAT 57.727 37.037 6.00 0.00 0.00 4.18
290 291 0.400525 ATGGGATCGGATGGGTCAGT 60.401 55.000 0.00 0.00 0.00 3.41
291 292 1.337384 TGGGATCGGATGGGTCAGTG 61.337 60.000 0.00 0.00 0.00 3.66
299 300 2.521958 GATGGGTCAGTGTGGGTCGG 62.522 65.000 0.00 0.00 0.00 4.79
304 305 3.238497 CAGTGTGGGTCGGGTCCA 61.238 66.667 0.00 0.00 0.00 4.02
311 312 3.932483 GGTCGGGTCCAACGTGGT 61.932 66.667 0.00 0.00 39.03 4.16
346 347 1.526887 CCGCATATCCGCCCCATAT 59.473 57.895 0.00 0.00 0.00 1.78
420 421 1.591248 CCGTCTGCGTCGAATTTTTG 58.409 50.000 0.00 0.00 36.15 2.44
422 423 1.962547 CGTCTGCGTCGAATTTTTGTG 59.037 47.619 0.00 0.00 0.00 3.33
431 432 5.113529 GCGTCGAATTTTTGTGAACAGTTAG 59.886 40.000 0.00 0.00 0.00 2.34
436 437 6.413818 CGAATTTTTGTGAACAGTTAGTGACC 59.586 38.462 0.00 0.00 0.00 4.02
437 438 4.868450 TTTTGTGAACAGTTAGTGACCG 57.132 40.909 0.00 0.00 0.00 4.79
438 439 3.804786 TTGTGAACAGTTAGTGACCGA 57.195 42.857 0.00 0.00 0.00 4.69
467 468 2.322830 GGACGTTTGAGGCGGGTTC 61.323 63.158 0.00 0.00 0.00 3.62
548 574 4.092968 GTCCATAAACTAAAGTGCCGTCTG 59.907 45.833 0.00 0.00 0.00 3.51
550 576 4.454504 CCATAAACTAAAGTGCCGTCTGTT 59.545 41.667 0.00 0.00 0.00 3.16
585 612 0.108662 CATGCGCTCTGTCTGGTACA 60.109 55.000 9.73 0.00 36.42 2.90
646 673 1.596709 CGCACGCATTGTTGAGTTTCA 60.597 47.619 0.00 0.00 33.19 2.69
711 738 7.600375 TCATTCACTACTCTTTGATGAACACTC 59.400 37.037 0.00 0.00 32.42 3.51
790 817 0.096454 CAGCTTTACTTAACCGCGGC 59.904 55.000 28.58 6.83 0.00 6.53
806 833 1.006832 CGGCCACTCTCGGTAAATTG 58.993 55.000 2.24 0.00 0.00 2.32
983 1025 2.158943 GGTTCCTGTACCATCTAGGCAC 60.159 54.545 0.00 0.00 43.14 5.01
984 1026 1.399714 TCCTGTACCATCTAGGCACG 58.600 55.000 0.00 0.00 43.14 5.34
1038 1097 1.834856 CTCCCTTCCAGCTCACTGCA 61.835 60.000 0.00 0.00 45.94 4.41
1224 1283 1.529244 GAACCTTGCCAGCCACTGT 60.529 57.895 0.00 0.00 0.00 3.55
1250 1309 2.745492 GTCAGGTGGCTGCAGAGC 60.745 66.667 20.43 7.26 45.40 4.09
1380 1439 2.831526 GGTTGCCATGTACCTTTGGAAT 59.168 45.455 9.99 0.00 34.81 3.01
1537 1600 3.048941 GCGCCGTCCGAACTAGTCT 62.049 63.158 0.00 0.00 40.02 3.24
1538 1601 1.505353 CGCCGTCCGAACTAGTCTT 59.495 57.895 0.00 0.00 40.02 3.01
1539 1602 0.797249 CGCCGTCCGAACTAGTCTTG 60.797 60.000 0.00 0.00 40.02 3.02
1540 1603 0.243095 GCCGTCCGAACTAGTCTTGT 59.757 55.000 0.00 0.00 0.00 3.16
1541 1604 1.731750 GCCGTCCGAACTAGTCTTGTC 60.732 57.143 0.00 0.00 0.00 3.18
1585 1648 3.337358 CTCATGTATATTGGCGCCATGA 58.663 45.455 33.25 26.34 39.51 3.07
1586 1649 3.749226 TCATGTATATTGGCGCCATGAA 58.251 40.909 33.25 17.27 39.02 2.57
1730 1793 3.561143 TGTTTGGGTGCAGTTCTACAAT 58.439 40.909 0.00 0.00 0.00 2.71
1907 1970 0.478072 TGTTGCCACTCATCAAGGGT 59.522 50.000 0.00 0.00 0.00 4.34
1932 1995 2.489971 CAAAGTACGGTGGTGTCATGT 58.510 47.619 0.00 0.00 0.00 3.21
1985 2048 1.220206 CAGCTCCGCCATCAAGAGT 59.780 57.895 0.00 0.00 0.00 3.24
2171 2244 3.318275 CACTAGATGGTAGCGGTGTGTAT 59.682 47.826 0.00 0.00 0.00 2.29
2182 2255 4.827692 AGCGGTGTGTATCAGTATTTCAA 58.172 39.130 0.00 0.00 0.00 2.69
2202 2275 7.706281 TTCAACACAATAAAAATCACGCAAT 57.294 28.000 0.00 0.00 0.00 3.56
2276 2349 7.169158 TCTTCTTTCTTTCTTCCTTTTTGCA 57.831 32.000 0.00 0.00 0.00 4.08
2305 2378 0.831307 AACTCGTTGGCCCCTCTATC 59.169 55.000 0.00 0.00 0.00 2.08
2321 2394 4.366586 CTCTATCGATTGATGCACACACT 58.633 43.478 9.98 0.00 35.99 3.55
2323 2396 5.178061 TCTATCGATTGATGCACACACTTT 58.822 37.500 1.71 0.00 35.99 2.66
2336 2409 7.503521 TGCACACACTTTCATCTTTATTGTA 57.496 32.000 0.00 0.00 0.00 2.41
2414 2487 4.017499 AGGGATAGCCATTTTTACAGTGGT 60.017 41.667 0.00 0.00 35.44 4.16
2456 2529 3.933542 GAGGAGGGACAGGGGCAGT 62.934 68.421 0.00 0.00 0.00 4.40
2466 2539 1.355720 ACAGGGGCAGTTAGATGCTTT 59.644 47.619 0.00 0.00 45.75 3.51
2501 2574 3.732048 AAACAGGTTATCCCCAATCGT 57.268 42.857 0.00 0.00 0.00 3.73
2508 2581 4.461431 AGGTTATCCCCAATCGTGAAAAAC 59.539 41.667 0.00 0.00 0.00 2.43
2511 2584 2.938838 TCCCCAATCGTGAAAAACTGT 58.061 42.857 0.00 0.00 0.00 3.55
2512 2585 2.882137 TCCCCAATCGTGAAAAACTGTC 59.118 45.455 0.00 0.00 0.00 3.51
2514 2587 2.546368 CCCAATCGTGAAAAACTGTCGA 59.454 45.455 0.00 0.00 35.14 4.20
2515 2588 3.188460 CCCAATCGTGAAAAACTGTCGAT 59.812 43.478 0.00 0.00 41.82 3.59
2522 2595 0.949105 AAAAACTGTCGATCGGCGCT 60.949 50.000 15.94 0.00 40.61 5.92
2534 2607 2.188731 GGCGCTAACCACCCCTAC 59.811 66.667 7.64 0.00 0.00 3.18
2535 2608 2.364780 GGCGCTAACCACCCCTACT 61.365 63.158 7.64 0.00 0.00 2.57
2539 2612 0.619543 GCTAACCACCCCTACTCCCA 60.620 60.000 0.00 0.00 0.00 4.37
2555 2628 3.943034 CACGTCGCGGGCAAAACA 61.943 61.111 6.13 0.00 0.00 2.83
2556 2629 3.203412 ACGTCGCGGGCAAAACAA 61.203 55.556 6.13 0.00 0.00 2.83
2589 2666 2.041922 TGCACCTAGCCGATCCCT 60.042 61.111 0.00 0.00 44.83 4.20
2591 2668 1.227674 GCACCTAGCCGATCCCTTG 60.228 63.158 0.00 0.00 37.23 3.61
2633 2710 6.500684 AACTGCATATGTTTTGTGTCCTAG 57.499 37.500 4.29 0.00 0.00 3.02
2709 2786 6.942886 AAAACATGCATAACATAACCGTTG 57.057 33.333 0.00 0.00 36.64 4.10
2804 2881 4.079253 TCTTCCAAAACATAGCCTTGGTC 58.921 43.478 0.35 0.00 40.47 4.02
2821 2908 1.750778 GGTCCAATCGTTGCATCCATT 59.249 47.619 0.00 0.00 0.00 3.16
2863 2950 2.481969 GCATAGAGCAACATCCTCGACA 60.482 50.000 0.00 0.00 44.79 4.35
2864 2951 3.785486 CATAGAGCAACATCCTCGACAA 58.215 45.455 0.00 0.00 34.56 3.18
2882 2969 7.545965 CCTCGACAAGATTATAGTTGTGAGTTT 59.454 37.037 2.83 0.00 37.02 2.66
2883 2970 8.462143 TCGACAAGATTATAGTTGTGAGTTTC 57.538 34.615 2.83 0.00 37.02 2.78
2928 3015 1.376037 CGGCCACCTCCTCAACTTC 60.376 63.158 2.24 0.00 0.00 3.01
2935 3022 0.171455 CCTCCTCAACTTCGTCTCCG 59.829 60.000 0.00 0.00 0.00 4.63
2938 3025 0.596577 CCTCAACTTCGTCTCCGTCA 59.403 55.000 0.00 0.00 35.01 4.35
2953 3040 1.254284 CGTCAGCCACCTCCTCTTCT 61.254 60.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.514066 AGTTGGTTTTGGAGTATTGACGAC 59.486 41.667 0.00 0.00 0.00 4.34
2 3 4.320202 CCAGTTGGTTTTGGAGTATTGACG 60.320 45.833 0.00 0.00 36.55 4.35
3 4 4.022329 CCCAGTTGGTTTTGGAGTATTGAC 60.022 45.833 0.00 0.00 36.55 3.18
5 6 3.258123 CCCCAGTTGGTTTTGGAGTATTG 59.742 47.826 0.00 0.00 36.55 1.90
6 7 3.116900 ACCCCAGTTGGTTTTGGAGTATT 60.117 43.478 0.00 0.00 33.91 1.89
7 8 2.449345 ACCCCAGTTGGTTTTGGAGTAT 59.551 45.455 0.00 0.00 33.91 2.12
9 10 0.634465 ACCCCAGTTGGTTTTGGAGT 59.366 50.000 0.00 0.00 33.91 3.85
10 11 1.039856 CACCCCAGTTGGTTTTGGAG 58.960 55.000 0.00 0.00 36.12 3.86
11 12 0.397816 CCACCCCAGTTGGTTTTGGA 60.398 55.000 4.65 0.00 36.12 3.53
12 13 2.038814 GCCACCCCAGTTGGTTTTGG 62.039 60.000 0.00 2.08 36.12 3.28
13 14 1.333636 TGCCACCCCAGTTGGTTTTG 61.334 55.000 0.00 0.00 36.12 2.44
14 15 1.002274 TGCCACCCCAGTTGGTTTT 59.998 52.632 0.00 0.00 36.12 2.43
15 16 1.760480 GTGCCACCCCAGTTGGTTT 60.760 57.895 0.00 0.00 36.12 3.27
16 17 1.357272 TAGTGCCACCCCAGTTGGTT 61.357 55.000 0.00 0.00 36.12 3.67
17 18 1.772567 TAGTGCCACCCCAGTTGGT 60.773 57.895 0.00 0.00 39.96 3.67
18 19 1.002134 CTAGTGCCACCCCAGTTGG 60.002 63.158 0.00 0.00 0.00 3.77
19 20 0.620556 ATCTAGTGCCACCCCAGTTG 59.379 55.000 0.00 0.00 0.00 3.16
20 21 0.620556 CATCTAGTGCCACCCCAGTT 59.379 55.000 0.00 0.00 0.00 3.16
21 22 2.300996 CATCTAGTGCCACCCCAGT 58.699 57.895 0.00 0.00 0.00 4.00
31 32 3.449018 AGGAGGTGTAAGTGCATCTAGTG 59.551 47.826 0.00 0.00 28.54 2.74
32 33 3.702045 GAGGAGGTGTAAGTGCATCTAGT 59.298 47.826 0.00 0.00 28.54 2.57
33 34 3.957497 AGAGGAGGTGTAAGTGCATCTAG 59.043 47.826 0.00 0.00 28.54 2.43
34 35 3.954904 GAGAGGAGGTGTAAGTGCATCTA 59.045 47.826 0.00 0.00 28.54 1.98
35 36 2.763448 GAGAGGAGGTGTAAGTGCATCT 59.237 50.000 0.00 0.00 31.56 2.90
36 37 2.480416 CGAGAGGAGGTGTAAGTGCATC 60.480 54.545 0.00 0.00 0.00 3.91
37 38 1.478510 CGAGAGGAGGTGTAAGTGCAT 59.521 52.381 0.00 0.00 0.00 3.96
38 39 0.888619 CGAGAGGAGGTGTAAGTGCA 59.111 55.000 0.00 0.00 0.00 4.57
39 40 3.723554 CGAGAGGAGGTGTAAGTGC 57.276 57.895 0.00 0.00 0.00 4.40
96 97 1.456892 ATCATCCCACGCGGTCCTA 60.457 57.895 12.47 0.00 0.00 2.94
97 98 2.764128 ATCATCCCACGCGGTCCT 60.764 61.111 12.47 0.00 0.00 3.85
114 115 0.748367 CAGATCCGTCGACTCTGGGA 60.748 60.000 20.16 16.28 34.17 4.37
118 119 1.340211 ACCTTCAGATCCGTCGACTCT 60.340 52.381 14.70 7.00 0.00 3.24
127 128 2.159170 CGAGTCCTTCACCTTCAGATCC 60.159 54.545 0.00 0.00 0.00 3.36
129 130 1.827969 CCGAGTCCTTCACCTTCAGAT 59.172 52.381 0.00 0.00 0.00 2.90
134 135 1.196012 GGATCCGAGTCCTTCACCTT 58.804 55.000 0.00 0.00 35.32 3.50
155 156 0.324614 ATCACCGGCATGACTGACAA 59.675 50.000 0.00 0.00 0.00 3.18
171 172 1.541310 AAACTCCTGTCCGGCGATCA 61.541 55.000 9.30 6.11 0.00 2.92
180 181 1.966451 CGCCACCCAAACTCCTGTC 60.966 63.158 0.00 0.00 0.00 3.51
202 203 1.063567 ACTCCACTAATCTCCGCTCCT 60.064 52.381 0.00 0.00 0.00 3.69
209 210 3.196685 AGCCACTTCACTCCACTAATCTC 59.803 47.826 0.00 0.00 0.00 2.75
212 213 3.452627 CCTAGCCACTTCACTCCACTAAT 59.547 47.826 0.00 0.00 0.00 1.73
244 245 2.513897 CCTTCCCATCCGTTCGCC 60.514 66.667 0.00 0.00 0.00 5.54
247 248 9.712305 CATATATATATTCCTTCCCATCCGTTC 57.288 37.037 2.28 0.00 0.00 3.95
249 250 7.237679 CCCATATATATATTCCTTCCCATCCGT 59.762 40.741 2.28 0.00 0.00 4.69
251 252 8.757307 TCCCATATATATATTCCTTCCCATCC 57.243 38.462 2.28 0.00 0.00 3.51
264 265 6.869930 TGACCCATCCGATCCCATATATATA 58.130 40.000 0.00 0.00 0.00 0.86
269 270 2.191400 CTGACCCATCCGATCCCATAT 58.809 52.381 0.00 0.00 0.00 1.78
271 272 0.400525 ACTGACCCATCCGATCCCAT 60.401 55.000 0.00 0.00 0.00 4.00
272 273 1.002921 ACTGACCCATCCGATCCCA 59.997 57.895 0.00 0.00 0.00 4.37
275 276 0.179073 CCACACTGACCCATCCGATC 60.179 60.000 0.00 0.00 0.00 3.69
276 277 1.626356 CCCACACTGACCCATCCGAT 61.626 60.000 0.00 0.00 0.00 4.18
277 278 2.290287 CCCACACTGACCCATCCGA 61.290 63.158 0.00 0.00 0.00 4.55
278 279 2.268920 CCCACACTGACCCATCCG 59.731 66.667 0.00 0.00 0.00 4.18
279 280 1.299976 GACCCACACTGACCCATCC 59.700 63.158 0.00 0.00 0.00 3.51
280 281 1.079127 CGACCCACACTGACCCATC 60.079 63.158 0.00 0.00 0.00 3.51
281 282 2.592993 CCGACCCACACTGACCCAT 61.593 63.158 0.00 0.00 0.00 4.00
282 283 3.238497 CCGACCCACACTGACCCA 61.238 66.667 0.00 0.00 0.00 4.51
283 284 4.016706 CCCGACCCACACTGACCC 62.017 72.222 0.00 0.00 0.00 4.46
290 291 3.931247 CGTTGGACCCGACCCACA 61.931 66.667 1.01 0.00 32.58 4.17
291 292 3.932483 ACGTTGGACCCGACCCAC 61.932 66.667 1.01 0.00 32.58 4.61
346 347 0.852842 CCCCTCATATCCAGCCCAAA 59.147 55.000 0.00 0.00 0.00 3.28
378 379 4.243008 TCAAACGAGCCACGCCCA 62.243 61.111 0.00 0.00 46.94 5.36
411 412 6.413818 GGTCACTAACTGTTCACAAAAATTCG 59.586 38.462 0.00 0.00 0.00 3.34
420 421 2.798847 GGTTCGGTCACTAACTGTTCAC 59.201 50.000 0.00 0.00 35.58 3.18
422 423 2.056577 CGGTTCGGTCACTAACTGTTC 58.943 52.381 0.00 0.00 35.58 3.18
467 468 4.514577 CTACAGCCGGACGCCCAG 62.515 72.222 5.05 0.00 38.78 4.45
473 474 4.740235 GAGCATCTACAGCCGGAC 57.260 61.111 5.05 0.00 0.00 4.79
548 574 4.442073 CGCATGCATATTCAAAGCCTTAAC 59.558 41.667 19.57 0.00 0.00 2.01
550 576 3.550639 GCGCATGCATATTCAAAGCCTTA 60.551 43.478 19.57 0.00 42.15 2.69
585 612 4.228210 TCCTCTATTTTCTGTCCCAGCAAT 59.772 41.667 0.00 0.00 0.00 3.56
646 673 1.177256 ACGCTCCACCGTACTCAACT 61.177 55.000 0.00 0.00 40.08 3.16
790 817 4.188247 TGTCTCAATTTACCGAGAGTGG 57.812 45.455 0.00 0.00 38.91 4.00
806 833 2.202987 CCGCTCCTGCCATGTCTC 60.203 66.667 0.00 0.00 35.36 3.36
983 1025 3.944250 ATGGCTGGGTTCAAGGGCG 62.944 63.158 0.00 0.00 0.00 6.13
984 1026 2.037847 ATGGCTGGGTTCAAGGGC 59.962 61.111 0.00 0.00 0.00 5.19
1038 1097 3.591254 GAGCGCCACGAAGAGGGTT 62.591 63.158 2.29 0.00 39.19 4.11
1197 1256 2.747855 GCAAGGTTCAGCTCCGGG 60.748 66.667 0.00 0.00 0.00 5.73
1250 1309 2.089980 CTTTGATGTCCTTGCTCTGGG 58.910 52.381 0.00 0.00 0.00 4.45
1380 1439 1.324740 ACGCGCCATCCAGGTAGTTA 61.325 55.000 5.73 0.00 40.61 2.24
1526 1589 1.196354 ACGACGACAAGACTAGTTCGG 59.804 52.381 16.67 4.99 0.00 4.30
1554 1617 2.663826 TATACATGAGCACGCACACA 57.336 45.000 0.00 0.00 0.00 3.72
1559 1622 1.136252 CGCCAATATACATGAGCACGC 60.136 52.381 0.00 0.00 0.00 5.34
1585 1648 0.765510 GTCCTTGAGGTCCCTGTGTT 59.234 55.000 0.00 0.00 36.34 3.32
1586 1649 1.128188 GGTCCTTGAGGTCCCTGTGT 61.128 60.000 2.29 0.00 37.42 3.72
1730 1793 4.556233 CACTGAACTGACATTCCTCGTTA 58.444 43.478 0.00 0.00 0.00 3.18
1907 1970 1.764134 ACACCACCGTACTTTGGAGAA 59.236 47.619 14.79 0.00 36.28 2.87
1932 1995 3.322541 TCGTCATAGAACTTGGACCACAA 59.677 43.478 0.00 0.00 37.55 3.33
1985 2048 0.666274 GCCACGAGAATCACACGTCA 60.666 55.000 0.00 0.00 43.10 4.35
2095 2168 6.639563 TCCGAGACATCAACAAAGAATATGA 58.360 36.000 0.00 0.00 0.00 2.15
2182 2255 8.698854 CAAACTATTGCGTGATTTTTATTGTGT 58.301 29.630 0.00 0.00 0.00 3.72
2202 2275 8.764524 AACATAAAACAACAACTTGCAAACTA 57.235 26.923 0.00 0.00 0.00 2.24
2209 2282 7.707104 AGGAGAGAACATAAAACAACAACTTG 58.293 34.615 0.00 0.00 0.00 3.16
2212 2285 9.447040 GTTTAGGAGAGAACATAAAACAACAAC 57.553 33.333 0.00 0.00 30.10 3.32
2276 2349 3.181479 GGGCCAACGAGTTTTCTCTTTTT 60.181 43.478 4.39 0.00 44.16 1.94
2305 2378 3.541071 TGAAAGTGTGTGCATCAATCG 57.459 42.857 0.00 0.00 0.00 3.34
2352 2425 1.411977 CCTGCATCCAACCAAACACAA 59.588 47.619 0.00 0.00 0.00 3.33
2390 2463 5.192923 ACCACTGTAAAAATGGCTATCCCTA 59.807 40.000 0.00 0.00 36.96 3.53
2483 2556 2.193127 TCACGATTGGGGATAACCTGT 58.807 47.619 0.00 0.00 40.03 4.00
2488 2561 5.074115 ACAGTTTTTCACGATTGGGGATAA 58.926 37.500 0.00 0.00 0.00 1.75
2501 2574 0.787787 CGCCGATCGACAGTTTTTCA 59.212 50.000 18.66 0.00 41.67 2.69
2508 2581 1.944676 GGTTAGCGCCGATCGACAG 60.945 63.158 18.66 8.36 41.67 3.51
2511 2584 2.103538 GTGGTTAGCGCCGATCGA 59.896 61.111 18.66 0.00 41.67 3.59
2512 2585 2.960129 GGTGGTTAGCGCCGATCG 60.960 66.667 8.51 8.51 42.12 3.69
2514 2587 4.171103 GGGGTGGTTAGCGCCGAT 62.171 66.667 2.29 0.00 0.00 4.18
2515 2588 3.961225 TAGGGGTGGTTAGCGCCGA 62.961 63.158 2.29 0.00 42.84 5.54
2522 2595 0.615544 CGTGGGAGTAGGGGTGGTTA 60.616 60.000 0.00 0.00 0.00 2.85
2539 2612 2.065906 AATTGTTTTGCCCGCGACGT 62.066 50.000 8.23 0.00 0.00 4.34
2555 2628 7.148069 GCTAGGTGCACCTATAAACAGAAAATT 60.148 37.037 39.06 16.01 46.71 1.82
2556 2629 6.318900 GCTAGGTGCACCTATAAACAGAAAAT 59.681 38.462 39.06 16.64 46.71 1.82
2619 2696 4.203226 TCATGCAACTAGGACACAAAACA 58.797 39.130 0.00 0.00 0.00 2.83
2633 2710 6.529829 TGTAAAGTGTTTGAAGTTCATGCAAC 59.470 34.615 6.36 8.98 34.86 4.17
2683 2760 8.916654 CAACGGTTATGTTATGCATGTTTTAAA 58.083 29.630 10.16 0.00 38.47 1.52
2709 2786 8.694975 AACTCGTGATGATATATATGCTTGTC 57.305 34.615 0.00 0.00 0.00 3.18
2804 2881 4.898829 TCTTAATGGATGCAACGATTGG 57.101 40.909 13.30 7.15 0.00 3.16
2821 2908 5.683681 TGCTATGCTTGGATGAACATCTTA 58.316 37.500 13.34 2.49 37.92 2.10
2860 2947 9.424319 TCAGAAACTCACAACTATAATCTTGTC 57.576 33.333 0.00 0.00 0.00 3.18
2863 2950 8.598041 AGGTCAGAAACTCACAACTATAATCTT 58.402 33.333 0.00 0.00 0.00 2.40
2864 2951 8.140112 AGGTCAGAAACTCACAACTATAATCT 57.860 34.615 0.00 0.00 0.00 2.40
2882 2969 2.254471 CGAGGTCGTCAAGGTCAGA 58.746 57.895 0.00 0.00 34.11 3.27
2883 2970 4.870305 CGAGGTCGTCAAGGTCAG 57.130 61.111 0.00 0.00 34.11 3.51
2935 3022 0.980423 AAGAAGAGGAGGTGGCTGAC 59.020 55.000 0.00 0.00 0.00 3.51
2938 3025 1.261238 CCGAAGAAGAGGAGGTGGCT 61.261 60.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.