Multiple sequence alignment - TraesCS3B01G450200

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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 TraesCS3B01G450200 chr3B 100.000 3191 0 0 1 3191 690720143 690716953 0.000000e+00 5893
1 TraesCS3B01G450200 chr3A 90.290 2554 135 43 25 2509 658598724 658596215 0.000000e+00 3238
2 TraesCS3B01G450200 chr3A 91.493 623 49 4 2569 3191 658596082 658595464 0.000000e+00 854
3 TraesCS3B01G450200 chr3A 84.167 360 37 10 1467 1817 6710761 6711109 6.600000e-87 331
4 TraesCS3B01G450200 chr3D 89.573 2273 118 48 1 2191 523635897 523633662 0.000000e+00 2774
5 TraesCS3B01G450200 chr3D 83.748 763 93 21 1059 1816 211943429 211944165 0.000000e+00 693
6 TraesCS3B01G450200 chr3D 89.167 360 39 0 2832 3191 601908860 601908501 1.750000e-122 449
7 TraesCS3B01G450200 chr3D 76.817 509 78 29 118 608 523641806 523641320 1.900000e-62 250
8 TraesCS3B01G450200 chr6D 83.398 777 101 17 1059 1831 436513818 436513066 0.000000e+00 695
9 TraesCS3B01G450200 chr7D 83.073 768 102 18 1059 1822 48463013 48463756 0.000000e+00 673
10 TraesCS3B01G450200 chr7D 88.611 360 41 0 2832 3191 198293878 198293519 3.780000e-119 438
11 TraesCS3B01G450200 chr7D 88.611 360 41 0 2832 3191 260004516 260004157 3.780000e-119 438
12 TraesCS3B01G450200 chr2D 90.801 337 31 0 2855 3191 196476839 196476503 4.850000e-123 451
13 TraesCS3B01G450200 chr2D 88.611 360 40 1 2832 3191 351709864 351710222 1.360000e-118 436
14 TraesCS3B01G450200 chr2D 85.854 410 43 9 1415 1821 187733870 187733473 3.810000e-114 422
15 TraesCS3B01G450200 chr2A 89.167 360 39 0 2832 3191 412270385 412270026 1.750000e-122 449
16 TraesCS3B01G450200 chr2A 83.889 360 38 11 1467 1817 409138399 409138747 3.070000e-85 326
17 TraesCS3B01G450200 chr5A 88.889 360 40 0 2832 3191 250436221 250436580 8.120000e-121 444
18 TraesCS3B01G450200 chr1D 88.333 360 42 0 2832 3191 368658983 368658624 1.760000e-117 433
19 TraesCS3B01G450200 chr4A 83.611 360 39 11 1467 1817 16885935 16885587 1.430000e-83 320


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 TraesCS3B01G450200 chr3B 690716953 690720143 3190 True 5893 5893 100.0000 1 3191 1 chr3B.!!$R1 3190
1 TraesCS3B01G450200 chr3A 658595464 658598724 3260 True 2046 3238 90.8915 25 3191 2 chr3A.!!$R1 3166
2 TraesCS3B01G450200 chr3D 523633662 523635897 2235 True 2774 2774 89.5730 1 2191 1 chr3D.!!$R1 2190
3 TraesCS3B01G450200 chr3D 211943429 211944165 736 False 693 693 83.7480 1059 1816 1 chr3D.!!$F1 757
4 TraesCS3B01G450200 chr6D 436513066 436513818 752 True 695 695 83.3980 1059 1831 1 chr6D.!!$R1 772
5 TraesCS3B01G450200 chr7D 48463013 48463756 743 False 673 673 83.0730 1059 1822 1 chr7D.!!$F1 763

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
295 347 0.036858 AAAGAAGCTCAGCTCCCGTC 60.037 55.0 0.0 0.0 38.25 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2303 0.248843 TGCAGTGTGGCGATATGTCA 59.751 50.0 0.0 0.0 36.28 3.58 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 2.851195 ACTGAATTATGGCCATCGTCC 58.149 47.619 24.80 11.16 0.00 4.79
49 50 6.719495 TCGTCCTCGCTGATCATTTGATCTA 61.719 44.000 18.60 7.13 42.60 1.98
65 66 9.516314 CATTTGATCTATCTGAACGTAACAGTA 57.484 33.333 17.84 11.06 36.81 2.74
90 91 0.833287 CACACTCGGATCCCTTCCAT 59.167 55.000 6.06 0.00 45.78 3.41
130 148 2.202703 CGGTCGGTCGTTGGGATC 60.203 66.667 0.00 0.00 0.00 3.36
162 184 1.179174 TCTCATCTCCGGGCCATACG 61.179 60.000 4.39 0.00 0.00 3.06
175 197 1.153529 CATACGTTGCGTGGGCCTA 60.154 57.895 4.53 0.00 41.39 3.93
179 207 3.431725 GTTGCGTGGGCCTACAGC 61.432 66.667 20.31 21.61 38.85 4.40
195 230 0.803768 CAGCCATCGTCCTCTTCACG 60.804 60.000 0.00 0.00 38.67 4.35
197 232 1.945354 GCCATCGTCCTCTTCACGGA 61.945 60.000 0.00 0.00 37.85 4.69
198 233 0.530744 CCATCGTCCTCTTCACGGAA 59.469 55.000 0.00 0.00 37.85 4.30
199 234 1.469940 CCATCGTCCTCTTCACGGAAG 60.470 57.143 7.17 7.17 40.65 3.46
200 235 0.173708 ATCGTCCTCTTCACGGAAGC 59.826 55.000 8.32 0.00 39.29 3.86
201 236 1.176619 TCGTCCTCTTCACGGAAGCA 61.177 55.000 8.32 0.00 39.29 3.91
202 237 1.009389 CGTCCTCTTCACGGAAGCAC 61.009 60.000 8.32 5.15 39.29 4.40
204 239 1.118965 TCCTCTTCACGGAAGCACCA 61.119 55.000 8.32 0.00 39.29 4.17
206 241 0.318441 CTCTTCACGGAAGCACCAGA 59.682 55.000 8.32 0.00 39.29 3.86
207 242 0.318441 TCTTCACGGAAGCACCAGAG 59.682 55.000 8.32 0.00 39.29 3.35
208 243 0.318441 CTTCACGGAAGCACCAGAGA 59.682 55.000 1.49 0.00 38.90 3.10
209 244 0.318441 TTCACGGAAGCACCAGAGAG 59.682 55.000 1.20 0.00 38.90 3.20
210 245 0.539669 TCACGGAAGCACCAGAGAGA 60.540 55.000 1.20 0.00 38.90 3.10
211 246 0.318441 CACGGAAGCACCAGAGAGAA 59.682 55.000 1.20 0.00 38.90 2.87
213 248 0.390472 CGGAAGCACCAGAGAGAACC 60.390 60.000 1.20 0.00 38.90 3.62
214 249 0.980423 GGAAGCACCAGAGAGAACCT 59.020 55.000 0.00 0.00 38.79 3.50
216 260 1.620819 GAAGCACCAGAGAGAACCTGA 59.379 52.381 0.00 0.00 33.65 3.86
217 261 1.722034 AGCACCAGAGAGAACCTGAA 58.278 50.000 0.00 0.00 33.65 3.02
221 265 0.247736 CCAGAGAGAACCTGAACCCG 59.752 60.000 0.00 0.00 33.65 5.28
229 273 4.577693 AGAGAACCTGAACCCGTTTAAAAC 59.422 41.667 0.00 0.00 0.00 2.43
252 304 4.201532 CGACATCACGTCATTCAGAAAGAC 60.202 45.833 8.26 8.26 45.70 3.01
261 313 0.959553 TTCAGAAAGACGACTCGCCT 59.040 50.000 0.00 0.00 0.00 5.52
282 334 5.291858 GCCTGAGAAAACAAACCAAAAGAAG 59.708 40.000 0.00 0.00 0.00 2.85
283 335 5.291858 CCTGAGAAAACAAACCAAAAGAAGC 59.708 40.000 0.00 0.00 0.00 3.86
284 336 6.036577 TGAGAAAACAAACCAAAAGAAGCT 57.963 33.333 0.00 0.00 0.00 3.74
286 338 6.036577 AGAAAACAAACCAAAAGAAGCTCA 57.963 33.333 0.00 0.00 0.00 4.26
287 339 6.101997 AGAAAACAAACCAAAAGAAGCTCAG 58.898 36.000 0.00 0.00 0.00 3.35
288 340 3.443099 ACAAACCAAAAGAAGCTCAGC 57.557 42.857 0.00 0.00 0.00 4.26
289 341 3.026694 ACAAACCAAAAGAAGCTCAGCT 58.973 40.909 0.00 0.00 42.56 4.24
290 342 3.067320 ACAAACCAAAAGAAGCTCAGCTC 59.933 43.478 0.00 0.00 38.25 4.09
293 345 0.801251 CAAAAGAAGCTCAGCTCCCG 59.199 55.000 0.00 0.00 38.25 5.14
294 346 0.398318 AAAAGAAGCTCAGCTCCCGT 59.602 50.000 0.00 0.00 38.25 5.28
295 347 0.036858 AAAGAAGCTCAGCTCCCGTC 60.037 55.000 0.00 0.00 38.25 4.79
312 365 1.808411 GTCGTTCATCTCTGCCCAAA 58.192 50.000 0.00 0.00 0.00 3.28
323 376 1.278699 TCTGCCCAAATTTTCCCATGC 59.721 47.619 0.00 0.00 0.00 4.06
325 378 0.327591 GCCCAAATTTTCCCATGCCA 59.672 50.000 0.00 0.00 0.00 4.92
376 430 4.363990 CACCTGTGCCGCGTCTCT 62.364 66.667 4.92 0.00 0.00 3.10
377 431 4.057428 ACCTGTGCCGCGTCTCTC 62.057 66.667 4.92 0.00 0.00 3.20
393 447 1.348036 CTCTCGGGTCCCAGAAAAACT 59.652 52.381 9.12 0.00 0.00 2.66
401 455 3.139077 GTCCCAGAAAAACTCACGACAT 58.861 45.455 0.00 0.00 0.00 3.06
427 485 2.032377 CGCTTTCGAGCAGGTTTTACAA 60.032 45.455 0.00 0.00 38.10 2.41
447 505 1.425428 CGCTTTTGAGCATCGTCCC 59.575 57.895 0.00 0.00 38.61 4.46
465 523 1.557269 CCTGGAGGTGGCAAGTAGCT 61.557 60.000 0.00 0.00 44.79 3.32
515 573 1.819632 CCGGAAATTCCCTCTGCCG 60.820 63.158 6.42 0.00 38.54 5.69
544 602 2.664081 GCCTAGCTGCCAGTGTCCT 61.664 63.158 0.00 0.00 0.00 3.85
668 726 4.742649 TCCCGAGCGCCTCTGTCT 62.743 66.667 2.29 0.00 0.00 3.41
682 740 4.314440 GTCTGTGCCTGCCGGTGA 62.314 66.667 1.90 0.00 0.00 4.02
815 881 2.694760 GCTTGTAGCCAGCTGGTGC 61.695 63.158 32.81 22.04 34.48 5.01
1134 1218 2.106683 CCACGGCGAAATCCAGGAC 61.107 63.158 16.62 0.00 0.00 3.85
1146 1230 4.813526 CAGGACGTCGACGAGCCG 62.814 72.222 41.52 28.43 43.02 5.52
1482 1578 4.039357 CAGCAGCAGCAGCACCAC 62.039 66.667 12.92 0.00 45.49 4.16
1692 1796 1.006571 CGTGCTCACCGTGTACCTT 60.007 57.895 0.00 0.00 0.00 3.50
1822 1926 3.680786 CCGACCTCACCGTGCTGA 61.681 66.667 0.00 0.00 0.00 4.26
1827 1931 4.363990 CTCACCGTGCTGACCGCT 62.364 66.667 0.00 0.00 40.11 5.52
1831 1935 2.655364 CCGTGCTGACCGCTATCG 60.655 66.667 0.00 0.00 40.11 2.92
1849 1953 2.429930 CGAGCCCCAACACCAAGA 59.570 61.111 0.00 0.00 0.00 3.02
1901 2005 0.320374 CTGTACTTCGAGGGCCACAA 59.680 55.000 6.18 0.00 0.00 3.33
2062 2166 2.747855 GGCCCGTGAAGCTCAAGG 60.748 66.667 9.89 9.89 44.14 3.61
2199 2303 1.945387 CACGCTGCTGACCTCATATT 58.055 50.000 0.00 0.00 0.00 1.28
2269 2373 6.718522 TTTACTGAAGAAATTCCGGGTTTT 57.281 33.333 0.00 1.30 0.00 2.43
2324 2429 3.978164 AGGAGGATGCCTGGTAGC 58.022 61.111 0.00 0.00 36.76 3.58
2372 2477 8.068893 TCAGAAATTGTTCACGTAAAGACTAC 57.931 34.615 0.00 0.00 36.09 2.73
2417 2522 6.254804 TCACGAATGTAGTATGTGTTATGTGC 59.745 38.462 0.00 0.00 32.55 4.57
2421 2526 2.394930 AGTATGTGTTATGTGCGGCA 57.605 45.000 0.00 0.00 0.00 5.69
2436 2541 1.798813 GCGGCAGAAGGATATAAACGG 59.201 52.381 0.00 0.00 0.00 4.44
2437 2542 2.547218 GCGGCAGAAGGATATAAACGGA 60.547 50.000 0.00 0.00 0.00 4.69
2438 2543 3.318017 CGGCAGAAGGATATAAACGGAG 58.682 50.000 0.00 0.00 0.00 4.63
2462 2567 2.899900 GAGCCCAAGGATTCCTGTTTTT 59.100 45.455 5.84 0.00 32.13 1.94
2474 2579 6.204108 GGATTCCTGTTTTTCTCGACAAGTTA 59.796 38.462 0.00 0.00 0.00 2.24
2478 2583 7.414436 TCCTGTTTTTCTCGACAAGTTAAATG 58.586 34.615 0.00 0.00 0.00 2.32
2480 2585 7.700656 CCTGTTTTTCTCGACAAGTTAAATGTT 59.299 33.333 0.00 0.00 0.00 2.71
2482 2587 8.237949 TGTTTTTCTCGACAAGTTAAATGTTCA 58.762 29.630 0.00 0.00 0.00 3.18
2488 2593 8.218441 TCTCGACAAGTTAAATGTTCATAAACG 58.782 33.333 0.00 0.00 38.28 3.60
2535 2745 7.596248 GATTTTGCTTAAATTTCAGTCAGCTGA 59.404 33.333 13.74 13.74 41.72 4.26
2546 2756 5.728637 TCAGTCAGCTGAGATTTAGACAA 57.271 39.130 18.89 0.00 45.94 3.18
2547 2757 6.101650 TCAGTCAGCTGAGATTTAGACAAA 57.898 37.500 18.89 0.00 45.94 2.83
2548 2758 6.162079 TCAGTCAGCTGAGATTTAGACAAAG 58.838 40.000 18.89 0.00 45.94 2.77
2549 2759 5.931146 CAGTCAGCTGAGATTTAGACAAAGT 59.069 40.000 18.89 0.00 45.28 2.66
2550 2760 6.090628 CAGTCAGCTGAGATTTAGACAAAGTC 59.909 42.308 18.89 0.00 45.28 3.01
2551 2761 6.014669 AGTCAGCTGAGATTTAGACAAAGTCT 60.015 38.462 18.89 1.27 45.54 3.24
2552 2762 6.310224 GTCAGCTGAGATTTAGACAAAGTCTC 59.690 42.308 18.89 3.97 42.40 3.36
2553 2763 6.210385 TCAGCTGAGATTTAGACAAAGTCTCT 59.790 38.462 13.74 0.00 42.40 3.10
2554 2764 6.310956 CAGCTGAGATTTAGACAAAGTCTCTG 59.689 42.308 8.42 10.53 42.40 3.35
2555 2765 6.014669 AGCTGAGATTTAGACAAAGTCTCTGT 60.015 38.462 2.48 0.00 42.40 3.41
2556 2766 6.090628 GCTGAGATTTAGACAAAGTCTCTGTG 59.909 42.308 2.48 6.58 42.40 3.66
2557 2767 7.290110 TGAGATTTAGACAAAGTCTCTGTGA 57.710 36.000 2.48 0.00 42.40 3.58
2558 2768 7.374272 TGAGATTTAGACAAAGTCTCTGTGAG 58.626 38.462 2.48 0.00 42.40 3.51
2559 2769 6.696411 AGATTTAGACAAAGTCTCTGTGAGG 58.304 40.000 2.48 0.00 42.40 3.86
2560 2770 5.871396 TTTAGACAAAGTCTCTGTGAGGT 57.129 39.130 2.48 0.00 42.40 3.85
2561 2771 6.971726 TTTAGACAAAGTCTCTGTGAGGTA 57.028 37.500 2.48 0.00 42.40 3.08
2562 2772 6.576662 TTAGACAAAGTCTCTGTGAGGTAG 57.423 41.667 2.48 0.00 42.40 3.18
2563 2773 4.730966 AGACAAAGTCTCTGTGAGGTAGA 58.269 43.478 0.00 0.00 38.71 2.59
2564 2774 4.521256 AGACAAAGTCTCTGTGAGGTAGAC 59.479 45.833 0.00 0.00 38.71 2.59
2565 2775 3.253677 ACAAAGTCTCTGTGAGGTAGACG 59.746 47.826 0.00 0.00 43.51 4.18
2566 2776 2.116827 AGTCTCTGTGAGGTAGACGG 57.883 55.000 0.00 0.00 43.51 4.79
2567 2777 1.629353 AGTCTCTGTGAGGTAGACGGA 59.371 52.381 0.00 0.00 43.51 4.69
2585 2795 1.270907 GAGATCATGCGGGAGGGTAT 58.729 55.000 0.00 0.00 0.00 2.73
2594 2804 1.890489 GCGGGAGGGTATGTTTTGTTT 59.110 47.619 0.00 0.00 0.00 2.83
2635 2845 6.634436 CGGAGTTCTTGAAACAGAAAAATCTG 59.366 38.462 4.36 4.36 43.03 2.90
2682 2892 2.158519 AGTCGAATCAAACCCCAACCTT 60.159 45.455 0.00 0.00 0.00 3.50
2689 2899 6.295067 CGAATCAAACCCCAACCTTAAAATCT 60.295 38.462 0.00 0.00 0.00 2.40
2690 2900 6.605471 ATCAAACCCCAACCTTAAAATCTC 57.395 37.500 0.00 0.00 0.00 2.75
2704 2914 6.655003 CCTTAAAATCTCTGAAACTAGCACCA 59.345 38.462 0.00 0.00 0.00 4.17
2716 2926 3.947868 ACTAGCACCACGTACTCTCTAA 58.052 45.455 0.00 0.00 0.00 2.10
2731 2941 6.531503 ACTCTCTAATTCTGACAATTCCGA 57.468 37.500 0.00 0.00 0.00 4.55
2732 2942 7.118496 ACTCTCTAATTCTGACAATTCCGAT 57.882 36.000 0.00 0.00 0.00 4.18
2736 2946 3.931907 ATTCTGACAATTCCGATGGGA 57.068 42.857 0.00 0.00 41.83 4.37
2740 2950 3.392285 TCTGACAATTCCGATGGGATCAT 59.608 43.478 0.00 0.00 43.41 2.45
2746 2956 5.474532 ACAATTCCGATGGGATCATACATTG 59.525 40.000 12.47 12.47 43.41 2.82
2749 2959 3.005554 CCGATGGGATCATACATTGCTC 58.994 50.000 0.00 0.00 32.98 4.26
2759 2969 6.989169 GGATCATACATTGCTCTCACTTACTT 59.011 38.462 0.00 0.00 0.00 2.24
2807 3017 4.609301 TGCTAGTTAAGGGCATTTCCAAT 58.391 39.130 0.00 0.00 36.21 3.16
2815 3025 1.029681 GGCATTTCCAATACCGACCC 58.970 55.000 0.00 0.00 34.01 4.46
2830 3040 4.019174 ACCGACCCGTAAATTCTCTTAGA 58.981 43.478 0.00 0.00 0.00 2.10
2838 3048 6.346096 CCGTAAATTCTCTTAGACATCCCAA 58.654 40.000 0.00 0.00 0.00 4.12
2849 3059 2.762327 AGACATCCCAACATGGCATTTC 59.238 45.455 0.00 0.00 33.69 2.17
2853 3063 3.173953 TCCCAACATGGCATTTCTTCT 57.826 42.857 0.00 0.00 35.79 2.85
2854 3064 2.827322 TCCCAACATGGCATTTCTTCTG 59.173 45.455 0.00 0.00 35.79 3.02
2858 3068 1.822990 ACATGGCATTTCTTCTGCTGG 59.177 47.619 0.00 0.00 39.60 4.85
2863 3073 2.498885 GGCATTTCTTCTGCTGGGAAAT 59.501 45.455 14.49 14.49 39.36 2.17
2876 3086 3.760684 GCTGGGAAATGTGAAAGACATCT 59.239 43.478 0.00 0.00 45.12 2.90
2883 3093 7.174946 GGGAAATGTGAAAGACATCTTGAACTA 59.825 37.037 0.00 0.00 45.12 2.24
2884 3094 8.734386 GGAAATGTGAAAGACATCTTGAACTAT 58.266 33.333 0.00 0.00 45.12 2.12
2898 3108 5.874810 TCTTGAACTATTGACAATCCTTCGG 59.125 40.000 3.36 4.68 0.00 4.30
2900 3110 5.175859 TGAACTATTGACAATCCTTCGGAC 58.824 41.667 3.36 0.00 32.98 4.79
2901 3111 4.819105 ACTATTGACAATCCTTCGGACA 57.181 40.909 3.36 0.00 32.98 4.02
2908 3118 3.756434 GACAATCCTTCGGACAATTCCAA 59.244 43.478 0.00 0.00 43.00 3.53
2932 3142 4.737855 TGTATGCAACTTCTCCTCTACC 57.262 45.455 0.00 0.00 0.00 3.18
2950 3160 8.383175 TCCTCTACCTTCAAGAATTTTGTATGT 58.617 33.333 0.00 0.00 0.00 2.29
2957 3167 7.703621 CCTTCAAGAATTTTGTATGTGCCTATG 59.296 37.037 0.00 0.00 0.00 2.23
2977 3187 3.686016 TGAATCTGGGTGCTAACTTTCC 58.314 45.455 0.00 0.00 0.00 3.13
2997 3207 5.118729 TCCTTTAACACCAAACCTCTTGA 57.881 39.130 0.00 0.00 0.00 3.02
3004 3214 2.744202 CACCAAACCTCTTGATTCCTCG 59.256 50.000 0.00 0.00 0.00 4.63
3048 3258 0.037303 TCGGTCTCCCACTTCGTACT 59.963 55.000 0.00 0.00 0.00 2.73
3078 3288 4.271533 CCTTGCGTTTACTATCGGCATAAA 59.728 41.667 0.00 0.00 0.00 1.40
3089 3299 6.219473 ACTATCGGCATAAATCTTCTGTCTG 58.781 40.000 0.00 0.00 0.00 3.51
3094 3304 4.574013 GGCATAAATCTTCTGTCTGGACTG 59.426 45.833 2.38 2.15 0.00 3.51
3117 3327 4.285020 AGCTATCTTGAGTCTGTCATGGA 58.715 43.478 0.00 0.00 34.17 3.41
3121 3331 5.688814 ATCTTGAGTCTGTCATGGATCAA 57.311 39.130 0.00 0.00 34.17 2.57
3122 3332 4.825422 TCTTGAGTCTGTCATGGATCAAC 58.175 43.478 0.00 0.00 34.17 3.18
3124 3334 4.897509 TGAGTCTGTCATGGATCAACTT 57.102 40.909 0.00 0.00 0.00 2.66
3125 3335 4.572909 TGAGTCTGTCATGGATCAACTTG 58.427 43.478 0.00 0.00 0.00 3.16
3126 3336 4.284234 TGAGTCTGTCATGGATCAACTTGA 59.716 41.667 0.00 0.00 0.00 3.02
3137 3347 4.347876 TGGATCAACTTGACCTTCTCTTCA 59.652 41.667 0.00 0.00 0.00 3.02
3146 3356 6.951198 ACTTGACCTTCTCTTCAGAATCTCTA 59.049 38.462 0.00 0.00 38.02 2.43
3157 3367 7.598278 TCTTCAGAATCTCTAATAAGATCGGC 58.402 38.462 0.00 0.00 34.90 5.54
3177 3387 3.517602 GCACCAAAAAGTTTTCGGTCTT 58.482 40.909 8.04 0.00 32.85 3.01
3184 3394 4.365899 AAAGTTTTCGGTCTTCAACACC 57.634 40.909 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.070018 GAGGACGATGGCCATAATTCAG 58.930 50.000 20.84 8.60 0.00 3.02
18 19 3.157252 AGCGAGGACGATGGCCAT 61.157 61.111 20.96 20.96 42.66 4.40
49 50 5.919141 GTGTCTGTTACTGTTACGTTCAGAT 59.081 40.000 21.42 11.52 36.81 2.90
65 66 0.608640 GGGATCCGAGTGTGTCTGTT 59.391 55.000 5.45 0.00 0.00 3.16
113 114 2.202703 GATCCCAACGACCGACCG 60.203 66.667 0.00 0.00 0.00 4.79
114 115 2.202703 CGATCCCAACGACCGACC 60.203 66.667 0.00 0.00 0.00 4.79
116 117 0.961857 TCTTCGATCCCAACGACCGA 60.962 55.000 0.00 0.00 39.46 4.69
130 148 1.336440 AGATGAGATGCTCGGTCTTCG 59.664 52.381 0.00 0.00 40.90 3.79
162 184 3.431725 GCTGTAGGCCCACGCAAC 61.432 66.667 11.76 0.00 36.38 4.17
175 197 0.247736 GTGAAGAGGACGATGGCTGT 59.752 55.000 0.00 0.00 0.00 4.40
179 207 0.530744 TTCCGTGAAGAGGACGATGG 59.469 55.000 0.00 0.00 39.21 3.51
195 230 0.980423 AGGTTCTCTCTGGTGCTTCC 59.020 55.000 0.00 0.00 0.00 3.46
197 232 1.722034 TCAGGTTCTCTCTGGTGCTT 58.278 50.000 0.00 0.00 33.36 3.91
198 233 1.346068 GTTCAGGTTCTCTCTGGTGCT 59.654 52.381 0.00 0.00 33.36 4.40
199 234 1.609320 GGTTCAGGTTCTCTCTGGTGC 60.609 57.143 0.00 0.00 33.36 5.01
200 235 1.002544 GGGTTCAGGTTCTCTCTGGTG 59.997 57.143 0.00 0.00 33.36 4.17
201 236 1.353091 GGGTTCAGGTTCTCTCTGGT 58.647 55.000 0.00 0.00 33.36 4.00
202 237 0.247736 CGGGTTCAGGTTCTCTCTGG 59.752 60.000 0.00 0.00 33.36 3.86
204 239 1.718280 AACGGGTTCAGGTTCTCTCT 58.282 50.000 0.00 0.00 0.00 3.10
206 241 4.426736 TTTAAACGGGTTCAGGTTCTCT 57.573 40.909 0.00 0.00 0.00 3.10
207 242 4.852138 GTTTTAAACGGGTTCAGGTTCTC 58.148 43.478 0.00 0.00 0.00 2.87
208 243 4.906065 GTTTTAAACGGGTTCAGGTTCT 57.094 40.909 0.00 0.00 0.00 3.01
238 282 2.342948 GCGAGTCGTCTTTCTGAATGAC 59.657 50.000 20.49 20.49 34.45 3.06
252 304 1.497991 TTGTTTTCTCAGGCGAGTCG 58.502 50.000 8.54 8.54 40.44 4.18
254 306 1.947456 GGTTTGTTTTCTCAGGCGAGT 59.053 47.619 6.32 0.00 40.44 4.18
261 313 6.036577 AGCTTCTTTTGGTTTGTTTTCTCA 57.963 33.333 0.00 0.00 0.00 3.27
282 334 2.507324 GAACGACGGGAGCTGAGC 60.507 66.667 0.00 0.00 0.00 4.26
283 335 0.526524 GATGAACGACGGGAGCTGAG 60.527 60.000 0.00 0.00 0.00 3.35
284 336 0.965866 AGATGAACGACGGGAGCTGA 60.966 55.000 0.00 0.00 0.00 4.26
286 338 0.681564 AGAGATGAACGACGGGAGCT 60.682 55.000 0.00 0.00 0.00 4.09
287 339 0.526524 CAGAGATGAACGACGGGAGC 60.527 60.000 0.00 0.00 0.00 4.70
288 340 0.526524 GCAGAGATGAACGACGGGAG 60.527 60.000 0.00 0.00 0.00 4.30
289 341 1.511305 GCAGAGATGAACGACGGGA 59.489 57.895 0.00 0.00 0.00 5.14
290 342 1.519455 GGCAGAGATGAACGACGGG 60.519 63.158 0.00 0.00 0.00 5.28
293 345 1.808411 TTTGGGCAGAGATGAACGAC 58.192 50.000 0.00 0.00 0.00 4.34
294 346 2.787473 ATTTGGGCAGAGATGAACGA 57.213 45.000 0.00 0.00 0.00 3.85
295 347 3.855689 AAATTTGGGCAGAGATGAACG 57.144 42.857 0.00 0.00 0.00 3.95
312 365 2.618794 TGGAAAGTGGCATGGGAAAAT 58.381 42.857 0.00 0.00 0.00 1.82
372 426 1.346722 GTTTTTCTGGGACCCGAGAGA 59.653 52.381 5.91 0.00 0.00 3.10
374 428 1.346722 GAGTTTTTCTGGGACCCGAGA 59.653 52.381 5.91 7.29 0.00 4.04
376 430 1.133363 TGAGTTTTTCTGGGACCCGA 58.867 50.000 5.91 3.36 0.00 5.14
377 431 1.235724 GTGAGTTTTTCTGGGACCCG 58.764 55.000 5.91 0.63 0.00 5.28
379 433 1.871676 GTCGTGAGTTTTTCTGGGACC 59.128 52.381 0.00 0.00 0.00 4.46
380 434 2.557317 TGTCGTGAGTTTTTCTGGGAC 58.443 47.619 0.00 0.00 0.00 4.46
381 435 2.992124 TGTCGTGAGTTTTTCTGGGA 57.008 45.000 0.00 0.00 0.00 4.37
393 447 1.794076 CGAAAGCGCTCTATGTCGTGA 60.794 52.381 12.06 0.00 0.00 4.35
447 505 1.134670 GTAGCTACTTGCCACCTCCAG 60.135 57.143 16.88 0.00 44.23 3.86
465 523 0.955428 CAGAGCTTTGCTTGCCGGTA 60.955 55.000 1.90 0.00 39.88 4.02
539 597 0.035152 CTTAGCCATGGCACAGGACA 60.035 55.000 37.18 12.17 46.40 4.02
540 598 0.035056 ACTTAGCCATGGCACAGGAC 60.035 55.000 37.18 7.37 46.40 3.85
544 602 0.251297 AGCAACTTAGCCATGGCACA 60.251 50.000 37.18 22.36 44.88 4.57
668 726 3.952508 ACATCACCGGCAGGCACA 61.953 61.111 0.00 0.00 42.76 4.57
1482 1578 2.494918 GTCGACCCCTGGTGATCG 59.505 66.667 3.51 5.42 35.25 3.69
1692 1796 4.151582 GGCTGCGGGCGGTAGTAA 62.152 66.667 2.13 0.00 42.94 2.24
1738 1842 2.356075 CACGTACCCGGCGTTCAA 60.356 61.111 6.01 0.00 40.90 2.69
1827 1931 2.185867 GTGTTGGGGCTCGCGATA 59.814 61.111 10.36 0.00 0.00 2.92
1831 1935 3.365265 CTTGGTGTTGGGGCTCGC 61.365 66.667 0.00 0.00 0.00 5.03
1849 1953 3.724478 TGTACCAGAGGACCATCTTCAT 58.276 45.455 0.00 0.00 0.00 2.57
1901 2005 2.341101 ACCGTCGAAGTGCCGATCT 61.341 57.895 0.00 0.00 40.91 2.75
2062 2166 0.942884 GTGTGGAACTTCCCGACGAC 60.943 60.000 5.30 0.00 38.04 4.34
2140 2244 3.550431 CGGCGGGTCCATCCAGAT 61.550 66.667 0.00 0.00 38.11 2.90
2199 2303 0.248843 TGCAGTGTGGCGATATGTCA 59.751 50.000 0.00 0.00 36.28 3.58
2240 2344 8.862085 ACCCGGAATTTCTTCAGTAAAATTAAA 58.138 29.630 0.73 0.00 35.72 1.52
2241 2345 8.411991 ACCCGGAATTTCTTCAGTAAAATTAA 57.588 30.769 0.73 0.00 35.72 1.40
2242 2346 8.411991 AACCCGGAATTTCTTCAGTAAAATTA 57.588 30.769 0.73 0.00 35.72 1.40
2243 2347 6.911250 ACCCGGAATTTCTTCAGTAAAATT 57.089 33.333 0.73 0.00 37.69 1.82
2244 2348 6.911250 AACCCGGAATTTCTTCAGTAAAAT 57.089 33.333 0.73 0.00 32.70 1.82
2246 2350 6.718522 AAAACCCGGAATTTCTTCAGTAAA 57.281 33.333 0.73 0.00 32.70 2.01
2324 2429 8.737168 TGAATTAGTTTCTCCAATGTCCTATG 57.263 34.615 0.00 0.00 35.23 2.23
2330 2435 9.918630 CAATTTCTGAATTAGTTTCTCCAATGT 57.081 29.630 0.00 0.00 33.78 2.71
2372 2477 5.392874 CGTGATTCGACAATACTTCTAGACG 59.607 44.000 0.00 0.00 42.86 4.18
2417 2522 3.243771 ACTCCGTTTATATCCTTCTGCCG 60.244 47.826 0.00 0.00 0.00 5.69
2421 2526 5.477637 GGCTCTACTCCGTTTATATCCTTCT 59.522 44.000 0.00 0.00 0.00 2.85
2436 2541 2.103941 CAGGAATCCTTGGGCTCTACTC 59.896 54.545 0.00 0.00 0.00 2.59
2437 2542 2.122768 CAGGAATCCTTGGGCTCTACT 58.877 52.381 0.00 0.00 0.00 2.57
2438 2543 1.840635 ACAGGAATCCTTGGGCTCTAC 59.159 52.381 0.00 0.00 0.00 2.59
2462 2567 8.218441 CGTTTATGAACATTTAACTTGTCGAGA 58.782 33.333 0.95 0.00 35.44 4.04
2474 2579 7.425606 AGTCTGCTTTTCGTTTATGAACATTT 58.574 30.769 0.95 0.00 35.44 2.32
2480 2585 9.817809 AGATATTAGTCTGCTTTTCGTTTATGA 57.182 29.630 0.00 0.00 0.00 2.15
2508 2718 6.583806 AGCTGACTGAAATTTAAGCAAAATCG 59.416 34.615 2.11 0.00 36.76 3.34
2535 2745 6.268847 ACCTCACAGAGACTTTGTCTAAATCT 59.731 38.462 0.00 0.00 43.53 2.40
2536 2746 6.459923 ACCTCACAGAGACTTTGTCTAAATC 58.540 40.000 0.00 0.00 43.53 2.17
2537 2747 6.426646 ACCTCACAGAGACTTTGTCTAAAT 57.573 37.500 0.00 0.00 43.53 1.40
2538 2748 5.871396 ACCTCACAGAGACTTTGTCTAAA 57.129 39.130 0.00 0.00 43.53 1.85
2539 2749 6.207025 GTCTACCTCACAGAGACTTTGTCTAA 59.793 42.308 0.00 0.00 43.53 2.10
2540 2750 5.706369 GTCTACCTCACAGAGACTTTGTCTA 59.294 44.000 0.00 0.00 43.53 2.59
2541 2751 4.521256 GTCTACCTCACAGAGACTTTGTCT 59.479 45.833 0.00 0.00 46.42 3.41
2542 2752 4.614078 CGTCTACCTCACAGAGACTTTGTC 60.614 50.000 0.00 0.00 37.95 3.18
2543 2753 3.253677 CGTCTACCTCACAGAGACTTTGT 59.746 47.826 0.00 0.00 37.95 2.83
2544 2754 3.366476 CCGTCTACCTCACAGAGACTTTG 60.366 52.174 0.00 0.00 37.95 2.77
2545 2755 2.820787 CCGTCTACCTCACAGAGACTTT 59.179 50.000 0.00 0.00 37.95 2.66
2546 2756 2.040012 TCCGTCTACCTCACAGAGACTT 59.960 50.000 0.00 0.00 37.95 3.01
2547 2757 1.629353 TCCGTCTACCTCACAGAGACT 59.371 52.381 0.00 0.00 37.95 3.24
2548 2758 2.011222 CTCCGTCTACCTCACAGAGAC 58.989 57.143 0.00 0.00 36.95 3.36
2549 2759 1.907255 TCTCCGTCTACCTCACAGAGA 59.093 52.381 0.00 0.00 0.00 3.10
2550 2760 2.404923 TCTCCGTCTACCTCACAGAG 57.595 55.000 0.00 0.00 0.00 3.35
2551 2761 2.238898 TGATCTCCGTCTACCTCACAGA 59.761 50.000 0.00 0.00 0.00 3.41
2552 2762 2.644676 TGATCTCCGTCTACCTCACAG 58.355 52.381 0.00 0.00 0.00 3.66
2553 2763 2.801077 TGATCTCCGTCTACCTCACA 57.199 50.000 0.00 0.00 0.00 3.58
2554 2764 2.287909 GCATGATCTCCGTCTACCTCAC 60.288 54.545 0.00 0.00 0.00 3.51
2555 2765 1.957177 GCATGATCTCCGTCTACCTCA 59.043 52.381 0.00 0.00 0.00 3.86
2556 2766 1.068885 CGCATGATCTCCGTCTACCTC 60.069 57.143 0.00 0.00 0.00 3.85
2557 2767 0.955178 CGCATGATCTCCGTCTACCT 59.045 55.000 0.00 0.00 0.00 3.08
2558 2768 0.039074 CCGCATGATCTCCGTCTACC 60.039 60.000 0.00 0.00 0.00 3.18
2559 2769 0.039074 CCCGCATGATCTCCGTCTAC 60.039 60.000 0.00 0.00 0.00 2.59
2560 2770 0.179001 TCCCGCATGATCTCCGTCTA 60.179 55.000 0.00 0.00 0.00 2.59
2561 2771 1.455773 TCCCGCATGATCTCCGTCT 60.456 57.895 0.00 0.00 0.00 4.18
2562 2772 1.006805 CTCCCGCATGATCTCCGTC 60.007 63.158 0.00 0.00 0.00 4.79
2563 2773 2.502492 CCTCCCGCATGATCTCCGT 61.502 63.158 0.00 0.00 0.00 4.69
2564 2774 2.341543 CCTCCCGCATGATCTCCG 59.658 66.667 0.00 0.00 0.00 4.63
2565 2775 0.832135 TACCCTCCCGCATGATCTCC 60.832 60.000 0.00 0.00 0.00 3.71
2566 2776 1.066573 CATACCCTCCCGCATGATCTC 60.067 57.143 0.00 0.00 0.00 2.75
2567 2777 0.979665 CATACCCTCCCGCATGATCT 59.020 55.000 0.00 0.00 0.00 2.75
2585 2795 0.102120 CTGGCCAGCGAAACAAAACA 59.898 50.000 22.33 0.00 0.00 2.83
2608 2818 3.553828 TTCTGTTTCAAGAACTCCGGT 57.446 42.857 0.00 0.00 31.19 5.28
2665 2875 7.004555 AGATTTTAAGGTTGGGGTTTGATTC 57.995 36.000 0.00 0.00 0.00 2.52
2682 2892 5.637810 CGTGGTGCTAGTTTCAGAGATTTTA 59.362 40.000 0.00 0.00 0.00 1.52
2689 2899 2.889045 AGTACGTGGTGCTAGTTTCAGA 59.111 45.455 0.00 0.00 0.00 3.27
2690 2900 3.057456 AGAGTACGTGGTGCTAGTTTCAG 60.057 47.826 0.00 0.00 0.00 3.02
2704 2914 7.259161 GGAATTGTCAGAATTAGAGAGTACGT 58.741 38.462 0.00 0.00 0.00 3.57
2716 2926 3.931907 TCCCATCGGAATTGTCAGAAT 57.068 42.857 0.00 0.00 34.19 2.40
2731 2941 4.350225 AGTGAGAGCAATGTATGATCCCAT 59.650 41.667 0.00 0.00 45.73 4.00
2732 2942 3.713248 AGTGAGAGCAATGTATGATCCCA 59.287 43.478 0.00 0.00 45.73 4.37
2736 2946 6.259608 GCAAGTAAGTGAGAGCAATGTATGAT 59.740 38.462 0.00 0.00 0.00 2.45
2740 2950 3.926527 CGCAAGTAAGTGAGAGCAATGTA 59.073 43.478 0.00 0.00 0.00 2.29
2746 2956 0.037232 ACCCGCAAGTAAGTGAGAGC 60.037 55.000 0.00 0.00 0.00 4.09
2749 2959 0.320374 TGGACCCGCAAGTAAGTGAG 59.680 55.000 0.00 0.00 0.00 3.51
2759 2969 0.836606 ATATGACACATGGACCCGCA 59.163 50.000 0.00 0.00 0.00 5.69
2807 3017 5.066505 GTCTAAGAGAATTTACGGGTCGGTA 59.933 44.000 0.00 0.00 0.00 4.02
2815 3025 6.816640 TGTTGGGATGTCTAAGAGAATTTACG 59.183 38.462 0.00 0.00 0.00 3.18
2838 3048 1.822990 CCAGCAGAAGAAATGCCATGT 59.177 47.619 0.00 0.00 44.97 3.21
2849 3059 3.822735 TCTTTCACATTTCCCAGCAGAAG 59.177 43.478 0.00 0.00 0.00 2.85
2853 3063 2.942804 TGTCTTTCACATTTCCCAGCA 58.057 42.857 0.00 0.00 0.00 4.41
2854 3064 3.760684 AGATGTCTTTCACATTTCCCAGC 59.239 43.478 0.00 0.00 46.53 4.85
2858 3068 6.974965 AGTTCAAGATGTCTTTCACATTTCC 58.025 36.000 0.00 0.00 46.53 3.13
2863 3073 7.714813 TGTCAATAGTTCAAGATGTCTTTCACA 59.285 33.333 0.00 0.00 40.18 3.58
2898 3108 5.772521 AGTTGCATACAAGTTGGAATTGTC 58.227 37.500 7.96 0.00 41.08 3.18
2900 3110 6.449698 AGAAGTTGCATACAAGTTGGAATTG 58.550 36.000 7.96 0.00 46.95 2.32
2901 3111 6.294731 GGAGAAGTTGCATACAAGTTGGAATT 60.295 38.462 7.96 0.00 46.95 2.17
2908 3118 4.899352 AGAGGAGAAGTTGCATACAAGT 57.101 40.909 0.00 0.00 41.32 3.16
2932 3142 8.461222 TCATAGGCACATACAAAATTCTTGAAG 58.539 33.333 7.18 0.00 0.00 3.02
2950 3160 1.216064 AGCACCCAGATTCATAGGCA 58.784 50.000 0.00 0.00 0.00 4.75
2957 3167 3.956744 AGGAAAGTTAGCACCCAGATTC 58.043 45.455 0.00 0.00 0.00 2.52
2977 3187 6.265422 AGGAATCAAGAGGTTTGGTGTTAAAG 59.735 38.462 0.00 0.00 0.00 1.85
2997 3207 2.248248 TGTGTCTCCACTTCGAGGAAT 58.752 47.619 0.00 0.00 42.34 3.01
3004 3214 3.902881 ATCTCCATGTGTCTCCACTTC 57.097 47.619 0.00 0.00 42.34 3.01
3048 3258 5.104374 CGATAGTAAACGCAAGGAGGTAAA 58.896 41.667 0.00 0.00 46.39 2.01
3078 3288 2.818921 AGCTCAGTCCAGACAGAAGAT 58.181 47.619 0.00 0.00 0.00 2.40
3089 3299 3.699038 ACAGACTCAAGATAGCTCAGTCC 59.301 47.826 13.73 1.12 35.10 3.85
3094 3304 4.340666 TCCATGACAGACTCAAGATAGCTC 59.659 45.833 0.00 0.00 30.60 4.09
3117 3327 5.815233 TCTGAAGAGAAGGTCAAGTTGAT 57.185 39.130 9.18 0.00 0.00 2.57
3121 3331 5.779771 AGAGATTCTGAAGAGAAGGTCAAGT 59.220 40.000 0.00 0.00 41.62 3.16
3122 3332 6.284891 AGAGATTCTGAAGAGAAGGTCAAG 57.715 41.667 0.00 0.00 41.62 3.02
3124 3334 7.969690 ATTAGAGATTCTGAAGAGAAGGTCA 57.030 36.000 0.00 0.00 41.62 4.02
3125 3335 9.965824 CTTATTAGAGATTCTGAAGAGAAGGTC 57.034 37.037 0.00 0.00 41.62 3.85
3126 3336 9.707957 TCTTATTAGAGATTCTGAAGAGAAGGT 57.292 33.333 0.00 0.00 41.62 3.50
3137 3347 5.540337 TGGTGCCGATCTTATTAGAGATTCT 59.460 40.000 0.00 0.00 36.54 2.40
3146 3356 5.722021 AACTTTTTGGTGCCGATCTTATT 57.278 34.783 0.00 0.00 0.00 1.40
3157 3367 4.739195 TGAAGACCGAAAACTTTTTGGTG 58.261 39.130 25.24 4.15 34.23 4.17


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

AutoCloner maintained by Alex Coulton.