Multiple sequence alignment - TraesCS2B01G072200

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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 TraesCS2B01G072200 chr2B 100.000 3376 0 0 1 3376 38402293 38398918 0.000000e+00 6235.0
1 TraesCS2B01G072200 chr2B 95.320 1752 51 5 1 1731 37578029 37576288 0.000000e+00 2752.0
2 TraesCS2B01G072200 chr2B 95.724 1333 50 7 397 1726 37742707 37741379 0.000000e+00 2139.0
3 TraesCS2B01G072200 chr2B 96.524 1007 29 4 447 1448 38461491 38460486 0.000000e+00 1661.0
4 TraesCS2B01G072200 chr2B 91.521 861 40 14 1730 2574 38460218 38459375 0.000000e+00 1155.0
5 TraesCS2B01G072200 chr2B 90.308 877 33 16 1729 2574 37576256 37575401 0.000000e+00 1101.0
6 TraesCS2B01G072200 chr2B 95.064 628 25 5 2732 3357 37575403 37574780 0.000000e+00 983.0
7 TraesCS2B01G072200 chr2B 95.578 588 20 4 2732 3318 38459377 38458795 0.000000e+00 937.0
8 TraesCS2B01G072200 chr2B 94.380 605 27 6 2755 3357 37741369 37740770 0.000000e+00 922.0
9 TraesCS2B01G072200 chr2B 95.798 238 10 0 1494 1731 38460490 38460253 5.280000e-103 385.0
10 TraesCS2B01G072200 chr2B 96.273 161 6 0 2573 2733 124626275 124626435 7.180000e-67 265.0
11 TraesCS2B01G072200 chr2B 98.387 62 1 0 384 445 37580037 37579976 3.560000e-20 110.0
12 TraesCS2B01G072200 chrUn 95.578 588 20 4 2732 3318 341780604 341781186 0.000000e+00 937.0
13 TraesCS2B01G072200 chrUn 91.304 368 19 4 2220 2574 341780239 341780606 1.090000e-134 490.0
14 TraesCS2B01G072200 chrUn 93.617 47 3 0 2242 2288 341780195 341780241 1.680000e-08 71.3
15 TraesCS2B01G072200 chr2A 94.040 604 30 1 1134 1731 24433383 24433986 0.000000e+00 911.0
16 TraesCS2B01G072200 chr2A 89.535 516 40 7 2800 3315 24436530 24437031 2.840000e-180 641.0
17 TraesCS2B01G072200 chr2A 85.661 537 43 21 1726 2242 24434017 24434539 4.960000e-148 534.0
18 TraesCS2B01G072200 chr2A 94.156 154 8 1 2243 2395 24435937 24436090 2.030000e-57 233.0
19 TraesCS2B01G072200 chr2A 90.323 62 4 1 3317 3376 93888995 93889056 2.790000e-11 80.5
20 TraesCS2B01G072200 chr2D 93.677 601 37 1 1131 1731 22843568 22844167 0.000000e+00 898.0
21 TraesCS2B01G072200 chr2D 92.164 536 26 4 2045 2567 22844589 22845121 0.000000e+00 743.0
22 TraesCS2B01G072200 chr2D 87.500 576 40 14 2743 3315 22845137 22845683 1.320000e-178 636.0
23 TraesCS2B01G072200 chr2D 87.273 330 21 10 1726 2046 22844198 22844515 1.150000e-94 357.0
24 TraesCS2B01G072200 chr2D 94.118 170 9 1 2571 2740 56540993 56541161 1.200000e-64 257.0
25 TraesCS2B01G072200 chr3B 96.649 388 12 1 1 387 72208689 72208302 0.000000e+00 643.0
26 TraesCS2B01G072200 chr3B 95.679 162 6 1 2573 2734 748432770 748432610 3.340000e-65 259.0
27 TraesCS2B01G072200 chr7B 94.845 388 19 1 1 387 54269037 54269424 3.730000e-169 604.0
28 TraesCS2B01G072200 chr7B 91.667 60 2 1 3317 3376 85782876 85782932 2.790000e-11 80.5
29 TraesCS2B01G072200 chr7B 91.667 60 2 1 3317 3376 85782951 85782895 2.790000e-11 80.5
30 TraesCS2B01G072200 chr5A 94.845 388 19 1 1 387 535702357 535702744 3.730000e-169 604.0
31 TraesCS2B01G072200 chr7D 94.588 388 20 1 1 387 7488141 7488528 1.730000e-167 599.0
32 TraesCS2B01G072200 chr3D 93.299 388 25 1 1 387 85278077 85277690 3.780000e-159 571.0
33 TraesCS2B01G072200 chr3D 93.491 169 10 1 2571 2739 238999577 238999410 2.010000e-62 250.0
34 TraesCS2B01G072200 chr1A 93.299 388 25 1 1 387 324854030 324854417 3.780000e-159 571.0
35 TraesCS2B01G072200 chr1A 92.526 388 26 3 1 386 64911579 64911965 1.370000e-153 553.0
36 TraesCS2B01G072200 chr4D 93.041 388 25 2 1 387 10400154 10399768 1.760000e-157 566.0
37 TraesCS2B01G072200 chr4D 94.012 167 9 1 2571 2737 68663818 68663983 5.590000e-63 252.0
38 TraesCS2B01G072200 chr4B 95.062 162 8 0 2573 2734 483266379 483266540 4.320000e-64 255.0
39 TraesCS2B01G072200 chr3A 94.479 163 9 0 2572 2734 659527229 659527391 5.590000e-63 252.0
40 TraesCS2B01G072200 chr7A 92.941 170 12 0 2569 2738 727851289 727851120 7.230000e-62 248.0
41 TraesCS2B01G072200 chr5D 93.023 172 9 2 2572 2741 472290994 472291164 7.230000e-62 248.0
42 TraesCS2B01G072200 chr6A 82.550 149 22 4 587 733 12459893 12460039 9.830000e-26 128.0
43 TraesCS2B01G072200 chr1B 90.323 62 4 2 3293 3352 561503106 561503167 2.790000e-11 80.5
44 TraesCS2B01G072200 chr1B 89.394 66 1 2 3317 3376 120674610 120674675 1.000000e-10 78.7
45 TraesCS2B01G072200 chr4A 90.164 61 5 1 3317 3376 32114927 32114867 1.000000e-10 78.7
46 TraesCS2B01G072200 chr5B 86.957 69 6 3 3309 3376 296833899 296833833 1.300000e-09 75.0


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 TraesCS2B01G072200 chr2B 38398918 38402293 3375 True 6235.000000 6235 100.000000 1 3376 1 chr2B.!!$R1 3375
1 TraesCS2B01G072200 chr2B 37740770 37742707 1937 True 1530.500000 2139 95.052000 397 3357 2 chr2B.!!$R3 2960
2 TraesCS2B01G072200 chr2B 37574780 37580037 5257 True 1236.500000 2752 94.769750 1 3357 4 chr2B.!!$R2 3356
3 TraesCS2B01G072200 chr2B 38458795 38461491 2696 True 1034.500000 1661 94.855250 447 3318 4 chr2B.!!$R4 2871
4 TraesCS2B01G072200 chrUn 341780195 341781186 991 False 499.433333 937 93.499667 2220 3318 3 chrUn.!!$F1 1098
5 TraesCS2B01G072200 chr2A 24433383 24437031 3648 False 579.750000 911 90.848000 1134 3315 4 chr2A.!!$F2 2181
6 TraesCS2B01G072200 chr2D 22843568 22845683 2115 False 658.500000 898 90.153500 1131 3315 4 chr2D.!!$F2 2184

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
481 2512 0.459237 AAGTGAGAGCGAGCGGAATG 60.459 55.000 0.00 0.00 0.00 2.67 F
789 2825 0.616395 TCGACATGAGCCACCCCTTA 60.616 55.000 0.00 0.00 0.00 2.69 F
932 2968 1.751563 GGGTCAGATAGCTCCTGGC 59.248 63.158 13.95 12.54 42.19 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 3643 0.833834 ACCGATCCTAGATGCCCCAG 60.834 60.0 0.00 0.00 0.0 4.45 R
2297 5877 1.255882 TGCACGCCATTCCAAGAAAT 58.744 45.0 0.00 0.00 0.0 2.17 R
2809 6636 0.389426 AAGGAAATGACGACGTCCCG 60.389 55.0 24.33 1.95 0.0 5.14 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
83 2093 3.555586 CCCCAAGATTGCAAGTCCAAAAG 60.556 47.826 4.94 0.00 0.00 2.27
114 2124 6.239232 GGACAATTTAGACCGATAAGCCTCTA 60.239 42.308 0.00 0.00 0.00 2.43
183 2193 3.242867 AGCTCATTCTCCCCGATATCAA 58.757 45.455 3.12 0.00 0.00 2.57
206 2216 3.264947 TCTGAGGAACAATCAGCATTCG 58.735 45.455 0.00 0.00 43.20 3.34
297 2307 8.896722 AGGAAGGTAAAGAGTAACAGATTCTA 57.103 34.615 0.00 0.00 0.00 2.10
357 2367 7.978982 AGAATTGAGTGGAATTATCTTGAACG 58.021 34.615 0.00 0.00 0.00 3.95
467 2498 4.912586 AGTAGCTCTCTACAGTGAAGTGA 58.087 43.478 0.00 0.00 45.90 3.41
481 2512 0.459237 AAGTGAGAGCGAGCGGAATG 60.459 55.000 0.00 0.00 0.00 2.67
752 2788 4.467107 GAGCCTCCCCCTCCTCGT 62.467 72.222 0.00 0.00 0.00 4.18
765 2801 3.060615 CTCGTCGTCTTCCCCGGT 61.061 66.667 0.00 0.00 0.00 5.28
789 2825 0.616395 TCGACATGAGCCACCCCTTA 60.616 55.000 0.00 0.00 0.00 2.69
932 2968 1.751563 GGGTCAGATAGCTCCTGGC 59.248 63.158 13.95 12.54 42.19 4.85
1030 3066 4.687215 GGTCAGTGCTCTGCGCCA 62.687 66.667 18.11 0.00 40.23 5.69
1370 3406 4.281941 GCCACTAGATCTGTATGACCATGA 59.718 45.833 5.18 0.00 0.00 3.07
1576 3618 2.629617 CCACTGTCTTTGCTGGGATTTT 59.370 45.455 0.00 0.00 0.00 1.82
1601 3643 2.502510 CAGCAATGCGTTCGTGGC 60.503 61.111 0.00 0.00 0.00 5.01
1663 3705 6.056090 ACCCTCTGAGGTTTAAGAAGATTC 57.944 41.667 21.70 0.00 36.44 2.52
1739 3820 6.912591 GCAGGTAATGTCATGCATAACTAAAC 59.087 38.462 0.00 0.00 43.28 2.01
1782 3863 5.006386 GGGACAATAGGATGCTGGAATTAG 58.994 45.833 0.00 0.00 0.00 1.73
1924 4014 3.439129 TGCAGCATTGATCTCTTTGACTG 59.561 43.478 0.00 0.00 0.00 3.51
1947 4046 8.025445 ACTGCTTTAGTAATTCTTTGAATGCAG 58.975 33.333 17.19 17.19 44.61 4.41
1948 4047 7.885297 TGCTTTAGTAATTCTTTGAATGCAGT 58.115 30.769 0.00 0.00 0.00 4.40
1951 4050 5.064441 AGTAATTCTTTGAATGCAGTGCC 57.936 39.130 13.72 0.00 0.00 5.01
1967 4072 6.724263 TGCAGTGCCGTAATTTTAATCATAG 58.276 36.000 13.72 0.00 0.00 2.23
2026 4133 3.118956 TGGTTGTTGAGAATTTTTGGCGT 60.119 39.130 0.00 0.00 0.00 5.68
2033 4141 4.732784 TGAGAATTTTTGGCGTTCTATGC 58.267 39.130 0.00 0.00 32.67 3.14
2078 4261 7.846066 AGCCAAGATAATCACTAGATCCATAC 58.154 38.462 0.00 0.00 31.90 2.39
2297 5877 3.772387 TGGCAATGATTTCCACTTACCA 58.228 40.909 0.00 0.00 0.00 3.25
2401 5982 2.730382 TGTTCCGGTAGCTGAGATGTA 58.270 47.619 0.00 0.00 0.00 2.29
2474 6067 2.485426 TGGTCCGTGTAGAAACTAGTCG 59.515 50.000 0.00 0.00 0.00 4.18
2553 6146 5.062308 GTGTGGAACTAGTCAAATCGACATC 59.938 44.000 11.69 4.74 42.46 3.06
2573 6166 1.334870 CGCTTGCATTTGTGCTGTGTA 60.335 47.619 1.86 0.00 35.49 2.90
2574 6167 2.053627 GCTTGCATTTGTGCTGTGTAC 58.946 47.619 1.86 0.00 35.49 2.90
2575 6168 2.287788 GCTTGCATTTGTGCTGTGTACT 60.288 45.455 1.86 0.00 35.49 2.73
2576 6169 3.558505 CTTGCATTTGTGCTGTGTACTC 58.441 45.455 1.86 0.00 35.49 2.59
2577 6170 1.879380 TGCATTTGTGCTGTGTACTCC 59.121 47.619 1.86 0.00 35.49 3.85
2578 6171 1.200020 GCATTTGTGCTGTGTACTCCC 59.800 52.381 0.00 0.00 0.00 4.30
2579 6172 2.783135 CATTTGTGCTGTGTACTCCCT 58.217 47.619 0.00 0.00 0.00 4.20
2580 6173 2.543777 TTTGTGCTGTGTACTCCCTC 57.456 50.000 0.00 0.00 0.00 4.30
2581 6174 0.685097 TTGTGCTGTGTACTCCCTCC 59.315 55.000 0.00 0.00 0.00 4.30
2582 6175 1.215647 GTGCTGTGTACTCCCTCCG 59.784 63.158 0.00 0.00 0.00 4.63
2583 6176 1.228769 TGCTGTGTACTCCCTCCGT 60.229 57.895 0.00 0.00 0.00 4.69
2584 6177 0.830444 TGCTGTGTACTCCCTCCGTT 60.830 55.000 0.00 0.00 0.00 4.44
2585 6178 0.320697 GCTGTGTACTCCCTCCGTTT 59.679 55.000 0.00 0.00 0.00 3.60
2586 6179 1.270678 GCTGTGTACTCCCTCCGTTTT 60.271 52.381 0.00 0.00 0.00 2.43
2587 6180 2.809299 GCTGTGTACTCCCTCCGTTTTT 60.809 50.000 0.00 0.00 0.00 1.94
2588 6181 3.555586 GCTGTGTACTCCCTCCGTTTTTA 60.556 47.826 0.00 0.00 0.00 1.52
2589 6182 4.634199 CTGTGTACTCCCTCCGTTTTTAA 58.366 43.478 0.00 0.00 0.00 1.52
2590 6183 5.033589 TGTGTACTCCCTCCGTTTTTAAA 57.966 39.130 0.00 0.00 0.00 1.52
2591 6184 5.623169 TGTGTACTCCCTCCGTTTTTAAAT 58.377 37.500 0.00 0.00 0.00 1.40
2592 6185 6.767456 TGTGTACTCCCTCCGTTTTTAAATA 58.233 36.000 0.00 0.00 0.00 1.40
2593 6186 7.396418 TGTGTACTCCCTCCGTTTTTAAATAT 58.604 34.615 0.00 0.00 0.00 1.28
2594 6187 8.538701 TGTGTACTCCCTCCGTTTTTAAATATA 58.461 33.333 0.00 0.00 0.00 0.86
2595 6188 9.382275 GTGTACTCCCTCCGTTTTTAAATATAA 57.618 33.333 0.00 0.00 0.00 0.98
2596 6189 9.603921 TGTACTCCCTCCGTTTTTAAATATAAG 57.396 33.333 0.00 0.00 0.00 1.73
2597 6190 9.605275 GTACTCCCTCCGTTTTTAAATATAAGT 57.395 33.333 0.00 0.00 0.00 2.24
2598 6191 8.728337 ACTCCCTCCGTTTTTAAATATAAGTC 57.272 34.615 0.00 0.00 0.00 3.01
2599 6192 8.546322 ACTCCCTCCGTTTTTAAATATAAGTCT 58.454 33.333 0.00 0.00 0.00 3.24
2600 6193 9.392259 CTCCCTCCGTTTTTAAATATAAGTCTT 57.608 33.333 0.00 0.00 0.00 3.01
2601 6194 9.743581 TCCCTCCGTTTTTAAATATAAGTCTTT 57.256 29.630 0.00 0.00 0.00 2.52
2629 6222 7.877003 AGAGATTCCACTATGAACTACATACG 58.123 38.462 0.00 0.00 40.07 3.06
2630 6223 6.982852 AGATTCCACTATGAACTACATACGG 58.017 40.000 0.00 0.00 40.07 4.02
2631 6224 6.776116 AGATTCCACTATGAACTACATACGGA 59.224 38.462 0.00 0.00 40.07 4.69
2632 6225 6.387041 TTCCACTATGAACTACATACGGAG 57.613 41.667 0.00 0.00 38.29 4.63
2633 6226 4.277672 TCCACTATGAACTACATACGGAGC 59.722 45.833 0.00 0.00 40.07 4.70
2634 6227 4.037565 CCACTATGAACTACATACGGAGCA 59.962 45.833 0.00 0.00 40.07 4.26
2635 6228 5.451381 CCACTATGAACTACATACGGAGCAA 60.451 44.000 0.00 0.00 40.07 3.91
2636 6229 6.040247 CACTATGAACTACATACGGAGCAAA 58.960 40.000 0.00 0.00 40.07 3.68
2637 6230 6.533723 CACTATGAACTACATACGGAGCAAAA 59.466 38.462 0.00 0.00 40.07 2.44
2638 6231 7.224753 CACTATGAACTACATACGGAGCAAAAT 59.775 37.037 0.00 0.00 40.07 1.82
2639 6232 5.794687 TGAACTACATACGGAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
2640 6233 5.483811 TGAACTACATACGGAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
2641 6234 5.580691 TGAACTACATACGGAGCAAAATGAG 59.419 40.000 0.00 0.00 0.00 2.90
2642 6235 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2643 6236 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2644 6237 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2645 6238 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2646 6239 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2647 6240 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2648 6241 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2649 6242 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2650 6243 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2651 6244 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2652 6245 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2683 6276 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
2684 6277 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
2685 6278 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
2686 6279 6.918569 GCATCTATATACATCCGTATGTGGTC 59.081 42.308 3.56 0.00 45.99 4.02
2687 6280 7.426410 CATCTATATACATCCGTATGTGGTCC 58.574 42.308 3.56 0.00 45.99 4.46
2688 6281 6.486941 TCTATATACATCCGTATGTGGTCCA 58.513 40.000 3.56 0.00 45.99 4.02
2689 6282 7.123383 TCTATATACATCCGTATGTGGTCCAT 58.877 38.462 3.56 0.00 45.99 3.41
2690 6283 8.276477 TCTATATACATCCGTATGTGGTCCATA 58.724 37.037 3.56 0.00 45.99 2.74
2691 6284 5.661056 ATACATCCGTATGTGGTCCATAG 57.339 43.478 3.56 0.00 45.99 2.23
2692 6285 3.305720 ACATCCGTATGTGGTCCATAGT 58.694 45.455 0.00 0.00 44.79 2.12
2693 6286 3.069586 ACATCCGTATGTGGTCCATAGTG 59.930 47.826 0.00 0.00 44.79 2.74
2694 6287 3.021177 TCCGTATGTGGTCCATAGTGA 57.979 47.619 0.00 0.00 36.71 3.41
2695 6288 3.367321 TCCGTATGTGGTCCATAGTGAA 58.633 45.455 0.00 0.00 36.71 3.18
2696 6289 3.770388 TCCGTATGTGGTCCATAGTGAAA 59.230 43.478 0.00 0.00 36.71 2.69
2697 6290 4.407621 TCCGTATGTGGTCCATAGTGAAAT 59.592 41.667 0.00 0.00 36.71 2.17
2698 6291 4.511454 CCGTATGTGGTCCATAGTGAAATG 59.489 45.833 0.00 0.00 36.71 2.32
2699 6292 5.116180 CGTATGTGGTCCATAGTGAAATGT 58.884 41.667 0.00 0.00 36.71 2.71
2700 6293 5.234329 CGTATGTGGTCCATAGTGAAATGTC 59.766 44.000 0.00 0.00 36.71 3.06
2701 6294 4.908601 TGTGGTCCATAGTGAAATGTCT 57.091 40.909 0.00 0.00 0.00 3.41
2702 6295 6.560003 ATGTGGTCCATAGTGAAATGTCTA 57.440 37.500 0.00 0.00 29.82 2.59
2703 6296 6.560003 TGTGGTCCATAGTGAAATGTCTAT 57.440 37.500 0.00 0.00 0.00 1.98
2704 6297 7.669089 TGTGGTCCATAGTGAAATGTCTATA 57.331 36.000 0.00 0.00 0.00 1.31
2705 6298 8.084985 TGTGGTCCATAGTGAAATGTCTATAA 57.915 34.615 0.00 0.00 0.00 0.98
2706 6299 8.544622 TGTGGTCCATAGTGAAATGTCTATAAA 58.455 33.333 0.00 0.00 0.00 1.40
2707 6300 9.046296 GTGGTCCATAGTGAAATGTCTATAAAG 57.954 37.037 0.00 0.00 0.00 1.85
2708 6301 8.988060 TGGTCCATAGTGAAATGTCTATAAAGA 58.012 33.333 0.00 0.00 0.00 2.52
2729 6322 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2730 6323 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2731 6324 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2732 6325 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2809 6636 9.035607 CACATCTTGTTATCAGGTAGTGTATTC 57.964 37.037 0.00 0.00 0.00 1.75
2814 6641 5.068198 TGTTATCAGGTAGTGTATTCGGGAC 59.932 44.000 0.00 0.00 0.00 4.46
2897 6724 2.703798 CCGCCACTTCCCTTGCATG 61.704 63.158 0.00 0.00 0.00 4.06
2988 6817 7.763172 TTTTGGTAATATTATTTGCTTGGCG 57.237 32.000 0.00 0.00 0.00 5.69
3078 6908 2.797177 AAGGTTCAGGAATCAGGAGC 57.203 50.000 0.00 0.00 0.00 4.70
3203 7033 2.760092 GGGCATAACCTGAAGCATTTCA 59.240 45.455 0.00 0.00 41.10 2.69
3334 7164 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
3354 7184 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
3360 7190 7.959658 ACTTGTCATCAAAATGGATTATCCA 57.040 32.000 16.99 16.99 41.03 3.41
3374 7204 7.959658 TGGATTATCCATTTTGATGACAAGT 57.040 32.000 10.29 0.00 42.67 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.800072 AATCCTCTCCCTTTAGAACACTAG 57.200 41.667 0.00 0.00 0.00 2.57
3 4 5.186942 GGAAATCCTCTCCCTTTAGAACAC 58.813 45.833 0.00 0.00 0.00 3.32
83 2093 8.496751 GCTTATCGGTCTAAATTGTCCTAAATC 58.503 37.037 0.00 0.00 0.00 2.17
94 2104 6.726490 TTGTAGAGGCTTATCGGTCTAAAT 57.274 37.500 0.00 0.00 0.00 1.40
114 2124 4.456911 ACGCAATCTTGAAGATCACATTGT 59.543 37.500 8.32 0.00 32.89 2.71
183 2193 3.996921 ATGCTGATTGTTCCTCAGAGT 57.003 42.857 4.57 0.00 42.22 3.24
206 2216 1.268234 CGTGATAAGACGTCCCGGTAC 60.268 57.143 13.01 5.90 34.56 3.34
297 2307 9.582431 CTTTCATCATATCAAGTTTCAAAGCAT 57.418 29.630 0.00 0.00 0.00 3.79
331 2341 9.098355 CGTTCAAGATAATTCCACTCAATTCTA 57.902 33.333 0.00 0.00 0.00 2.10
333 2343 7.189512 CCGTTCAAGATAATTCCACTCAATTC 58.810 38.462 0.00 0.00 0.00 2.17
334 2344 6.095440 CCCGTTCAAGATAATTCCACTCAATT 59.905 38.462 0.00 0.00 0.00 2.32
335 2345 5.590259 CCCGTTCAAGATAATTCCACTCAAT 59.410 40.000 0.00 0.00 0.00 2.57
336 2346 4.941263 CCCGTTCAAGATAATTCCACTCAA 59.059 41.667 0.00 0.00 0.00 3.02
337 2347 4.019681 ACCCGTTCAAGATAATTCCACTCA 60.020 41.667 0.00 0.00 0.00 3.41
338 2348 4.332819 CACCCGTTCAAGATAATTCCACTC 59.667 45.833 0.00 0.00 0.00 3.51
339 2349 4.019681 TCACCCGTTCAAGATAATTCCACT 60.020 41.667 0.00 0.00 0.00 4.00
340 2350 4.258543 TCACCCGTTCAAGATAATTCCAC 58.741 43.478 0.00 0.00 0.00 4.02
357 2367 2.999331 TGCCTAGTTTTAGCATCACCC 58.001 47.619 0.00 0.00 0.00 4.61
457 2488 1.069924 CGCTCGCTCTCACTTCACTG 61.070 60.000 0.00 0.00 0.00 3.66
467 2498 2.055042 ACTCCATTCCGCTCGCTCT 61.055 57.895 0.00 0.00 0.00 4.09
481 2512 5.129485 TCTCTGTTCCAGAATATTCCACTCC 59.871 44.000 11.92 0.00 40.18 3.85
752 2788 2.678934 CCTCACCGGGGAAGACGA 60.679 66.667 8.34 0.00 0.00 4.20
765 2801 1.591703 GTGGCTCATGTCGACCTCA 59.408 57.895 14.12 0.00 0.00 3.86
789 2825 2.363795 TCGAGGGAGGGCGTGAAT 60.364 61.111 0.00 0.00 0.00 2.57
921 2957 1.460305 ATCCCACGCCAGGAGCTAT 60.460 57.895 0.00 0.00 40.39 2.97
922 2958 2.041922 ATCCCACGCCAGGAGCTA 60.042 61.111 0.00 0.00 40.39 3.32
932 2968 4.508128 CGGTCACCGGATCCCACG 62.508 72.222 8.94 0.42 44.15 4.94
1067 3103 2.225343 ACCTTGAATGGGCTGGAATTGA 60.225 45.455 0.00 0.00 0.00 2.57
1336 3372 6.255287 ACAGATCTAGTGGCATCTCTATCAT 58.745 40.000 0.00 0.00 0.00 2.45
1370 3406 5.643421 AGTCATGAAGGAGCTGGATTTAT 57.357 39.130 0.00 0.00 0.00 1.40
1576 3618 2.125552 CGCATTGCTGTCCTCGGA 60.126 61.111 7.12 0.00 0.00 4.55
1601 3643 0.833834 ACCGATCCTAGATGCCCCAG 60.834 60.000 0.00 0.00 0.00 4.45
1663 3705 5.543405 AGATACAGAGATCCCTCCTTTCATG 59.457 44.000 0.00 0.00 40.30 3.07
1739 3820 6.649973 TGTCCCATTATCAAAAAGCAAATGTG 59.350 34.615 0.00 0.00 0.00 3.21
1767 3848 1.849039 AGGCACTAATTCCAGCATCCT 59.151 47.619 0.00 0.00 36.02 3.24
1810 3891 2.512692 TGGATGATTGAACCACCAGG 57.487 50.000 0.00 0.00 42.21 4.45
1813 3903 7.352079 AGATTTAATGGATGATTGAACCACC 57.648 36.000 0.00 0.00 36.49 4.61
1907 3997 7.375106 ACTAAAGCAGTCAAAGAGATCAATG 57.625 36.000 0.00 0.00 28.33 2.82
1914 4004 9.604626 CAAAGAATTACTAAAGCAGTCAAAGAG 57.395 33.333 0.00 0.00 38.80 2.85
1924 4014 7.201384 GCACTGCATTCAAAGAATTACTAAAGC 60.201 37.037 0.00 0.00 0.00 3.51
1967 4072 8.383318 ACTCCATAACATGTTGCAAGTATATC 57.617 34.615 21.42 0.00 0.00 1.63
2026 4133 5.105595 CCTCCTATGACATCGATGCATAGAA 60.106 44.000 37.87 29.62 41.73 2.10
2033 4141 3.616076 GCTTCCCTCCTATGACATCGATG 60.616 52.174 23.68 23.68 0.00 3.84
2085 4268 5.817816 GCTGGACACTTATTGCAACTACTAT 59.182 40.000 0.00 0.00 0.00 2.12
2297 5877 1.255882 TGCACGCCATTCCAAGAAAT 58.744 45.000 0.00 0.00 0.00 2.17
2401 5982 3.181490 TGCAATAGTAAGACGACATCGCT 60.181 43.478 0.14 0.00 44.43 4.93
2474 6067 5.296780 TCAGAAGCGGATACAAATTCATTCC 59.703 40.000 0.00 0.00 0.00 3.01
2523 6116 6.401474 CGATTTGACTAGTTCCACACAGATTG 60.401 42.308 0.00 0.00 0.00 2.67
2573 6166 8.546322 AGACTTATATTTAAAAACGGAGGGAGT 58.454 33.333 0.00 0.00 0.00 3.85
2574 6167 8.959705 AGACTTATATTTAAAAACGGAGGGAG 57.040 34.615 0.00 0.00 0.00 4.30
2575 6168 9.743581 AAAGACTTATATTTAAAAACGGAGGGA 57.256 29.630 0.00 0.00 0.00 4.20
2603 6196 9.000486 CGTATGTAGTTCATAGTGGAATCTCTA 58.000 37.037 0.00 0.00 39.36 2.43
2604 6197 7.040340 CCGTATGTAGTTCATAGTGGAATCTCT 60.040 40.741 3.20 0.00 39.36 3.10
2605 6198 7.040617 TCCGTATGTAGTTCATAGTGGAATCTC 60.041 40.741 7.73 0.00 39.60 2.75
2606 6199 6.776116 TCCGTATGTAGTTCATAGTGGAATCT 59.224 38.462 7.73 0.00 39.60 2.40
2607 6200 6.978338 TCCGTATGTAGTTCATAGTGGAATC 58.022 40.000 7.73 0.00 39.60 2.52
2608 6201 6.516860 GCTCCGTATGTAGTTCATAGTGGAAT 60.517 42.308 10.20 0.00 40.80 3.01
2609 6202 5.221185 GCTCCGTATGTAGTTCATAGTGGAA 60.221 44.000 10.20 0.00 40.80 3.53
2610 6203 4.277672 GCTCCGTATGTAGTTCATAGTGGA 59.722 45.833 9.16 9.16 39.94 4.02
2611 6204 4.037565 TGCTCCGTATGTAGTTCATAGTGG 59.962 45.833 2.99 2.99 39.36 4.00
2612 6205 5.183014 TGCTCCGTATGTAGTTCATAGTG 57.817 43.478 0.00 0.00 39.36 2.74
2613 6206 5.847111 TTGCTCCGTATGTAGTTCATAGT 57.153 39.130 0.00 0.00 39.36 2.12
2614 6207 7.438160 TCATTTTGCTCCGTATGTAGTTCATAG 59.562 37.037 0.00 0.00 39.36 2.23
2615 6208 7.269316 TCATTTTGCTCCGTATGTAGTTCATA 58.731 34.615 0.00 0.00 37.91 2.15
2616 6209 6.112734 TCATTTTGCTCCGTATGTAGTTCAT 58.887 36.000 0.00 0.00 40.25 2.57
2617 6210 5.483811 TCATTTTGCTCCGTATGTAGTTCA 58.516 37.500 0.00 0.00 0.00 3.18
2618 6211 5.581085 ACTCATTTTGCTCCGTATGTAGTTC 59.419 40.000 0.00 0.00 0.00 3.01
2619 6212 5.351465 CACTCATTTTGCTCCGTATGTAGTT 59.649 40.000 0.00 0.00 0.00 2.24
2620 6213 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2621 6214 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2622 6215 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2623 6216 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2624 6217 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2625 6218 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2626 6219 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2627 6220 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2628 6221 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2629 6222 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2630 6223 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2631 6224 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
2632 6225 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
2636 6229 9.846248 GCATTTTAAAGTGTAGATTCACTCATT 57.154 29.630 11.77 0.00 46.25 2.57
2637 6230 9.013229 TGCATTTTAAAGTGTAGATTCACTCAT 57.987 29.630 11.77 0.00 46.25 2.90
2638 6231 8.389779 TGCATTTTAAAGTGTAGATTCACTCA 57.610 30.769 11.77 0.00 46.25 3.41
2639 6232 9.495754 GATGCATTTTAAAGTGTAGATTCACTC 57.504 33.333 11.77 0.00 46.25 3.51
2656 6249 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
2657 6250 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
2658 6251 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
2659 6252 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
2660 6253 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
2661 6254 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
2662 6255 7.068226 TGGACCACATACGGATGTATATAGATG 59.932 40.741 14.23 0.00 44.82 2.90
2663 6256 7.123383 TGGACCACATACGGATGTATATAGAT 58.877 38.462 14.23 0.00 44.82 1.98
2664 6257 6.486941 TGGACCACATACGGATGTATATAGA 58.513 40.000 14.23 0.00 44.82 1.98
2665 6258 6.769134 TGGACCACATACGGATGTATATAG 57.231 41.667 14.23 0.00 44.82 1.31
2666 6259 8.057011 ACTATGGACCACATACGGATGTATATA 58.943 37.037 14.23 7.10 44.82 0.86
2667 6260 6.895756 ACTATGGACCACATACGGATGTATAT 59.104 38.462 14.23 1.16 44.82 0.86
2668 6261 6.152154 CACTATGGACCACATACGGATGTATA 59.848 42.308 14.23 6.48 44.82 1.47
2669 6262 5.047306 CACTATGGACCACATACGGATGTAT 60.047 44.000 14.23 4.48 44.82 2.29
2670 6263 4.279922 CACTATGGACCACATACGGATGTA 59.720 45.833 14.23 0.00 44.82 2.29
2672 6265 3.320826 TCACTATGGACCACATACGGATG 59.679 47.826 5.94 5.94 41.03 3.51
2673 6266 3.572642 TCACTATGGACCACATACGGAT 58.427 45.455 0.00 0.00 41.03 4.18
2674 6267 3.021177 TCACTATGGACCACATACGGA 57.979 47.619 0.00 0.00 41.03 4.69
2675 6268 3.812156 TTCACTATGGACCACATACGG 57.188 47.619 0.00 0.00 41.03 4.02
2676 6269 5.116180 ACATTTCACTATGGACCACATACG 58.884 41.667 0.00 0.00 41.03 3.06
2677 6270 6.349300 AGACATTTCACTATGGACCACATAC 58.651 40.000 0.00 0.00 41.03 2.39
2678 6271 6.560003 AGACATTTCACTATGGACCACATA 57.440 37.500 0.00 0.00 41.03 2.29
2679 6272 5.441718 AGACATTTCACTATGGACCACAT 57.558 39.130 0.00 0.00 43.68 3.21
2680 6273 4.908601 AGACATTTCACTATGGACCACA 57.091 40.909 0.00 0.00 0.00 4.17
2681 6274 8.958119 TTTATAGACATTTCACTATGGACCAC 57.042 34.615 0.00 0.00 32.57 4.16
2682 6275 8.988060 TCTTTATAGACATTTCACTATGGACCA 58.012 33.333 0.00 0.00 32.57 4.02
2703 6296 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
2704 6297 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2705 6298 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2706 6299 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2707 6300 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2708 6301 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2709 6302 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2710 6303 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2711 6304 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2712 6305 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2713 6306 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2714 6307 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2715 6308 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2716 6309 4.414846 AGATACTACTCCCTCCGTTCCTAA 59.585 45.833 0.00 0.00 0.00 2.69
2717 6310 3.979347 AGATACTACTCCCTCCGTTCCTA 59.021 47.826 0.00 0.00 0.00 2.94
2718 6311 2.784682 AGATACTACTCCCTCCGTTCCT 59.215 50.000 0.00 0.00 0.00 3.36
2719 6312 3.226682 AGATACTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
2720 6313 4.756135 CAGTAGATACTACTCCCTCCGTTC 59.244 50.000 8.25 0.00 34.13 3.95
2721 6314 4.165758 ACAGTAGATACTACTCCCTCCGTT 59.834 45.833 8.25 0.00 34.13 4.44
2722 6315 3.715834 ACAGTAGATACTACTCCCTCCGT 59.284 47.826 8.25 1.30 34.13 4.69
2723 6316 4.354893 ACAGTAGATACTACTCCCTCCG 57.645 50.000 8.25 0.77 34.13 4.63
2724 6317 5.532032 GTCAACAGTAGATACTACTCCCTCC 59.468 48.000 8.25 0.00 34.13 4.30
2725 6318 6.358991 AGTCAACAGTAGATACTACTCCCTC 58.641 44.000 8.25 1.05 34.13 4.30
2726 6319 6.159046 AGAGTCAACAGTAGATACTACTCCCT 59.841 42.308 13.38 1.88 38.23 4.20
2727 6320 6.358991 AGAGTCAACAGTAGATACTACTCCC 58.641 44.000 13.38 0.00 38.23 4.30
2728 6321 7.049133 TGAGAGTCAACAGTAGATACTACTCC 58.951 42.308 13.38 8.41 38.23 3.85
2729 6322 8.671384 ATGAGAGTCAACAGTAGATACTACTC 57.329 38.462 8.25 10.63 37.97 2.59
2809 6636 0.389426 AAGGAAATGACGACGTCCCG 60.389 55.000 24.33 1.95 0.00 5.14
2814 6641 0.673644 AGGGCAAGGAAATGACGACG 60.674 55.000 0.00 0.00 0.00 5.12
2988 6817 2.620115 CAATGCCACCATGGTAGTCATC 59.380 50.000 19.28 3.82 40.46 2.92
3078 6908 3.560068 GGATAAGTGTGCTAATTCACCCG 59.440 47.826 0.00 0.00 36.17 5.28
3334 7164 9.645128 TGGATAATCCATTTTGATGACAAGTAT 57.355 29.630 0.00 0.00 42.67 2.12


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

AutoCloner maintained by Alex Coulton.