Multiple sequence alignment - TraesCS1B01G310700

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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 TraesCS1B01G310700 chr1B 100.000 2981 0 0 1 2981 533814225 533817205 0.000000e+00 5505
1 TraesCS1B01G310700 chr1B 80.041 982 122 43 862 1814 533747586 533748522 0.000000e+00 660
2 TraesCS1B01G310700 chr1B 82.581 798 91 20 973 1761 533759781 533760539 0.000000e+00 660
3 TraesCS1B01G310700 chr1B 90.291 103 8 1 327 429 286354876 286354776 1.860000e-27 134
4 TraesCS1B01G310700 chr1B 84.848 132 13 5 326 454 286354790 286354917 3.120000e-25 126
5 TraesCS1B01G310700 chr1D 91.076 2622 149 38 411 2981 398379106 398381693 0.000000e+00 3467
6 TraesCS1B01G310700 chr1D 84.569 836 84 23 845 1673 398121296 398122093 0.000000e+00 787
7 TraesCS1B01G310700 chr1D 83.256 866 107 22 958 1814 398246149 398246985 0.000000e+00 761
8 TraesCS1B01G310700 chr1D 85.016 634 69 15 1142 1763 398093790 398094409 3.260000e-174 621
9 TraesCS1B01G310700 chr1D 91.793 329 23 3 3 328 398378780 398379107 3.500000e-124 455
10 TraesCS1B01G310700 chr1A 88.857 2082 157 34 943 2981 495332256 495334305 0.000000e+00 2490
11 TraesCS1B01G310700 chr1A 84.411 866 102 18 958 1814 495320043 495320884 0.000000e+00 821
12 TraesCS1B01G310700 chr1A 82.283 254 31 7 493 737 495329686 495329934 1.080000e-49 207
13 TraesCS1B01G310700 chr5D 84.686 542 60 12 1130 1667 409454515 409455037 1.220000e-143 520
14 TraesCS1B01G310700 chr5D 91.000 100 9 0 325 424 174013452 174013353 5.180000e-28 135
15 TraesCS1B01G310700 chr5B 88.155 439 46 3 1232 1667 491246031 491246466 4.400000e-143 518
16 TraesCS1B01G310700 chr5B 80.723 166 27 5 448 611 559760531 559760369 1.120000e-24 124
17 TraesCS1B01G310700 chr5B 77.778 198 38 6 422 617 277030401 277030208 1.880000e-22 117
18 TraesCS1B01G310700 chr7D 81.250 192 34 2 422 612 611352742 611352552 1.430000e-33 154
19 TraesCS1B01G310700 chr2D 93.000 100 6 1 314 412 174430845 174430746 8.610000e-31 145
20 TraesCS1B01G310700 chr2D 80.663 181 27 6 431 610 34682310 34682483 1.860000e-27 134
21 TraesCS1B01G310700 chr2A 94.624 93 4 1 321 412 24958954 24958862 3.100000e-30 143
22 TraesCS1B01G310700 chr2A 91.000 100 9 0 327 426 762155350 762155251 5.180000e-28 135
23 TraesCS1B01G310700 chr6A 93.684 95 4 2 321 413 535818388 535818482 1.110000e-29 141
24 TraesCS1B01G310700 chr7B 79.592 196 37 3 422 616 700575422 700575229 1.440000e-28 137
25 TraesCS1B01G310700 chr4A 90.476 105 7 2 324 428 615436794 615436895 5.180000e-28 135
26 TraesCS1B01G310700 chr4A 80.606 165 29 2 448 611 674359806 674359644 1.120000e-24 124
27 TraesCS1B01G310700 chr6D 79.558 181 34 3 436 616 304115590 304115767 3.120000e-25 126
28 TraesCS1B01G310700 chr3B 84.091 132 14 5 326 454 694097178 694097305 1.450000e-23 121


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 TraesCS1B01G310700 chr1B 533814225 533817205 2980 False 5505.0 5505 100.0000 1 2981 1 chr1B.!!$F4 2980
1 TraesCS1B01G310700 chr1B 533747586 533748522 936 False 660.0 660 80.0410 862 1814 1 chr1B.!!$F2 952
2 TraesCS1B01G310700 chr1B 533759781 533760539 758 False 660.0 660 82.5810 973 1761 1 chr1B.!!$F3 788
3 TraesCS1B01G310700 chr1D 398378780 398381693 2913 False 1961.0 3467 91.4345 3 2981 2 chr1D.!!$F4 2978
4 TraesCS1B01G310700 chr1D 398121296 398122093 797 False 787.0 787 84.5690 845 1673 1 chr1D.!!$F2 828
5 TraesCS1B01G310700 chr1D 398246149 398246985 836 False 761.0 761 83.2560 958 1814 1 chr1D.!!$F3 856
6 TraesCS1B01G310700 chr1D 398093790 398094409 619 False 621.0 621 85.0160 1142 1763 1 chr1D.!!$F1 621
7 TraesCS1B01G310700 chr1A 495329686 495334305 4619 False 1348.5 2490 85.5700 493 2981 2 chr1A.!!$F2 2488
8 TraesCS1B01G310700 chr1A 495320043 495320884 841 False 821.0 821 84.4110 958 1814 1 chr1A.!!$F1 856
9 TraesCS1B01G310700 chr5D 409454515 409455037 522 False 520.0 520 84.6860 1130 1667 1 chr5D.!!$F1 537

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
528 531 0.179129 CGAGCATGGCAAATTCACCC 60.179 55.0 0.00 0.0 0.00 4.61 F
1011 3228 0.385751 AGTGTGACAGACAGACACGG 59.614 55.0 5.43 0.0 44.25 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 4077 0.329261 AGCTTGGGCATGCAGAAGTA 59.671 50.0 21.36 0.0 41.7 2.24 R
2640 4955 0.308376 GATCGAGCTAGACCGTCCAC 59.692 60.0 0.00 0.0 0.0 4.02 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
63 64 1.903404 CATCCCCCAATAAGCCGCC 60.903 63.158 0.00 0.00 0.00 6.13
117 118 3.925630 CTTGCCCCATGACGTGCCT 62.926 63.158 0.00 0.00 0.00 4.75
136 137 0.319555 TTGACGACGGCAAGAGAAGG 60.320 55.000 13.22 0.00 0.00 3.46
137 138 2.048127 ACGACGGCAAGAGAAGGC 60.048 61.111 0.00 0.00 0.00 4.35
161 162 1.896122 GCTAGGGTACGGCAACCACT 61.896 60.000 8.16 5.59 41.67 4.00
164 165 1.058284 AGGGTACGGCAACCACTTTA 58.942 50.000 8.16 0.00 41.67 1.85
166 167 1.271001 GGGTACGGCAACCACTTTAGT 60.271 52.381 8.16 0.00 41.67 2.24
167 168 2.497138 GGTACGGCAACCACTTTAGTT 58.503 47.619 1.29 0.00 39.50 2.24
170 171 0.879090 CGGCAACCACTTTAGTTCCC 59.121 55.000 0.00 0.00 0.00 3.97
172 173 2.160205 GGCAACCACTTTAGTTCCCTC 58.840 52.381 0.00 0.00 0.00 4.30
173 174 1.804748 GCAACCACTTTAGTTCCCTCG 59.195 52.381 0.00 0.00 0.00 4.63
174 175 1.804748 CAACCACTTTAGTTCCCTCGC 59.195 52.381 0.00 0.00 0.00 5.03
177 178 2.158726 ACCACTTTAGTTCCCTCGCAAA 60.159 45.455 0.00 0.00 0.00 3.68
194 196 6.204108 CCTCGCAAAGTTACTTCCTTCTTTTA 59.796 38.462 0.00 0.00 0.00 1.52
195 197 7.186021 TCGCAAAGTTACTTCCTTCTTTTAG 57.814 36.000 0.00 0.00 0.00 1.85
206 208 5.422214 TCCTTCTTTTAGGTCTAGCAAGG 57.578 43.478 0.00 0.00 36.63 3.61
216 218 4.020543 AGGTCTAGCAAGGAGTTCAGTAG 58.979 47.826 0.00 0.00 0.00 2.57
255 257 2.223386 ACGTTGTTTTATTGTGTGCGCT 60.223 40.909 9.73 0.00 0.00 5.92
270 273 2.199652 CGCTCCCTAGGCTCTCTGG 61.200 68.421 2.05 0.00 0.00 3.86
296 299 3.144120 ATAGCCGACCGAGCTGCAG 62.144 63.158 10.11 10.11 41.71 4.41
302 305 1.805945 GACCGAGCTGCAGTTACCG 60.806 63.158 16.64 10.08 0.00 4.02
328 331 9.146984 GGTTCAAAGCCCATTATTTAAAACTAC 57.853 33.333 0.00 0.00 0.00 2.73
329 332 9.923143 GTTCAAAGCCCATTATTTAAAACTACT 57.077 29.630 0.00 0.00 0.00 2.57
331 334 9.528489 TCAAAGCCCATTATTTAAAACTACTCT 57.472 29.630 0.00 0.00 0.00 3.24
334 337 9.755122 AAGCCCATTATTTAAAACTACTCTCTT 57.245 29.630 0.00 0.00 0.00 2.85
335 338 9.397280 AGCCCATTATTTAAAACTACTCTCTTC 57.603 33.333 0.00 0.00 0.00 2.87
336 339 8.336080 GCCCATTATTTAAAACTACTCTCTTCG 58.664 37.037 0.00 0.00 0.00 3.79
337 340 9.379791 CCCATTATTTAAAACTACTCTCTTCGT 57.620 33.333 0.00 0.00 0.00 3.85
348 351 9.760077 AAACTACTCTCTTCGTTTCAAAATAGA 57.240 29.630 0.00 0.00 0.00 1.98
349 352 9.930693 AACTACTCTCTTCGTTTCAAAATAGAT 57.069 29.630 0.00 0.00 0.00 1.98
350 353 9.360093 ACTACTCTCTTCGTTTCAAAATAGATG 57.640 33.333 0.00 0.00 0.00 2.90
351 354 9.574458 CTACTCTCTTCGTTTCAAAATAGATGA 57.426 33.333 0.00 0.00 0.00 2.92
352 355 8.245701 ACTCTCTTCGTTTCAAAATAGATGAC 57.754 34.615 0.00 0.00 0.00 3.06
353 356 7.332182 ACTCTCTTCGTTTCAAAATAGATGACC 59.668 37.037 0.00 0.00 0.00 4.02
354 357 6.594159 TCTCTTCGTTTCAAAATAGATGACCC 59.406 38.462 0.00 0.00 0.00 4.46
355 358 6.234920 TCTTCGTTTCAAAATAGATGACCCA 58.765 36.000 0.00 0.00 0.00 4.51
356 359 6.712998 TCTTCGTTTCAAAATAGATGACCCAA 59.287 34.615 0.00 0.00 0.00 4.12
357 360 6.249035 TCGTTTCAAAATAGATGACCCAAC 57.751 37.500 0.00 0.00 0.00 3.77
358 361 6.001460 TCGTTTCAAAATAGATGACCCAACT 58.999 36.000 0.00 0.00 0.00 3.16
359 362 6.488683 TCGTTTCAAAATAGATGACCCAACTT 59.511 34.615 0.00 0.00 0.00 2.66
360 363 7.013846 TCGTTTCAAAATAGATGACCCAACTTT 59.986 33.333 0.00 0.00 0.00 2.66
361 364 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
362 365 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
363 366 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
364 367 8.106247 TCAAAATAGATGACCCAACTTTGTAC 57.894 34.615 0.00 0.00 0.00 2.90
365 368 7.721842 TCAAAATAGATGACCCAACTTTGTACA 59.278 33.333 0.00 0.00 0.00 2.90
366 369 8.356657 CAAAATAGATGACCCAACTTTGTACAA 58.643 33.333 3.59 3.59 0.00 2.41
367 370 8.472007 AAATAGATGACCCAACTTTGTACAAA 57.528 30.769 19.53 19.53 0.00 2.83
368 371 8.472007 AATAGATGACCCAACTTTGTACAAAA 57.528 30.769 20.89 5.14 0.00 2.44
369 372 6.391227 AGATGACCCAACTTTGTACAAAAG 57.609 37.500 20.89 16.42 0.00 2.27
370 373 5.891551 AGATGACCCAACTTTGTACAAAAGT 59.108 36.000 20.89 16.98 41.82 2.66
372 375 7.558444 AGATGACCCAACTTTGTACAAAAGTTA 59.442 33.333 20.89 11.84 45.57 2.24
373 376 7.090953 TGACCCAACTTTGTACAAAAGTTAG 57.909 36.000 20.89 19.33 45.57 2.34
374 377 6.660094 TGACCCAACTTTGTACAAAAGTTAGT 59.340 34.615 20.89 21.46 45.57 2.24
375 378 7.828223 TGACCCAACTTTGTACAAAAGTTAGTA 59.172 33.333 20.89 12.46 45.57 1.82
376 379 8.756486 ACCCAACTTTGTACAAAAGTTAGTAT 57.244 30.769 20.89 10.71 45.57 2.12
377 380 9.850198 ACCCAACTTTGTACAAAAGTTAGTATA 57.150 29.630 20.89 0.00 45.57 1.47
386 389 9.850198 TGTACAAAAGTTAGTATAAAGTTGGGT 57.150 29.630 0.00 0.00 0.00 4.51
388 391 8.983702 ACAAAAGTTAGTATAAAGTTGGGTCA 57.016 30.769 0.00 0.00 0.00 4.02
389 392 9.582648 ACAAAAGTTAGTATAAAGTTGGGTCAT 57.417 29.630 0.00 0.00 0.00 3.06
398 401 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
399 402 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
400 403 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
401 404 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
402 405 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
403 406 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
404 407 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
405 408 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
406 409 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
407 410 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
408 411 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
409 412 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
410 413 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
411 414 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
412 415 4.778958 TCTATTTTGGAACGGAGGGAGTAA 59.221 41.667 0.00 0.00 0.00 2.24
413 416 3.860968 TTTTGGAACGGAGGGAGTAAA 57.139 42.857 0.00 0.00 0.00 2.01
414 417 3.860968 TTTGGAACGGAGGGAGTAAAA 57.139 42.857 0.00 0.00 0.00 1.52
415 418 2.845363 TGGAACGGAGGGAGTAAAAC 57.155 50.000 0.00 0.00 0.00 2.43
416 419 1.348696 TGGAACGGAGGGAGTAAAACC 59.651 52.381 0.00 0.00 0.00 3.27
417 420 1.627329 GGAACGGAGGGAGTAAAACCT 59.373 52.381 0.00 0.00 40.54 3.50
418 421 2.833943 GGAACGGAGGGAGTAAAACCTA 59.166 50.000 0.00 0.00 37.18 3.08
419 422 3.261643 GGAACGGAGGGAGTAAAACCTAA 59.738 47.826 0.00 0.00 37.18 2.69
420 423 3.969287 ACGGAGGGAGTAAAACCTAAC 57.031 47.619 0.00 0.00 37.18 2.34
429 432 9.199645 GAGGGAGTAAAACCTAACTATCTAACT 57.800 37.037 0.00 0.00 37.18 2.24
466 469 3.252400 TGCATGGCAAATCGAATGTTTC 58.748 40.909 0.00 0.00 34.76 2.78
473 476 6.686630 TGGCAAATCGAATGTTTCTTATGTT 58.313 32.000 0.00 0.00 0.00 2.71
508 511 2.420022 CGAGGATGGCAAGTTTAGTTGG 59.580 50.000 0.00 0.00 0.00 3.77
517 520 1.453155 AGTTTAGTTGGCGAGCATGG 58.547 50.000 0.00 0.00 0.00 3.66
525 528 1.249469 TGGCGAGCATGGCAAATTCA 61.249 50.000 1.88 0.00 43.90 2.57
528 531 0.179129 CGAGCATGGCAAATTCACCC 60.179 55.000 0.00 0.00 0.00 4.61
531 534 1.603236 GCATGGCAAATTCACCCCGA 61.603 55.000 0.00 0.00 0.00 5.14
742 754 2.664436 CCCAGGTTCGTTCGTTCGC 61.664 63.158 0.00 0.00 0.00 4.70
745 757 0.663568 CAGGTTCGTTCGTTCGCTCT 60.664 55.000 0.00 0.00 0.00 4.09
854 3036 2.044806 GCGTGTCCCTATCCCTGCAT 62.045 60.000 0.00 0.00 0.00 3.96
914 3125 3.243267 CCTTTTTCAAAGTACACACCCCG 60.243 47.826 0.00 0.00 0.00 5.73
916 3127 0.881159 TTCAAAGTACACACCCCGCG 60.881 55.000 0.00 0.00 0.00 6.46
920 3131 3.419759 GTACACACCCCGCGCAAG 61.420 66.667 8.75 0.00 43.44 4.01
933 3145 2.282180 GCAAGCCCCCAAGAACGA 60.282 61.111 0.00 0.00 0.00 3.85
934 3146 1.678970 GCAAGCCCCCAAGAACGAT 60.679 57.895 0.00 0.00 0.00 3.73
935 3147 1.937546 GCAAGCCCCCAAGAACGATG 61.938 60.000 0.00 0.00 0.00 3.84
936 3148 1.000896 AAGCCCCCAAGAACGATGG 60.001 57.895 0.00 0.00 37.71 3.51
937 3149 1.789576 AAGCCCCCAAGAACGATGGT 61.790 55.000 0.00 0.00 36.14 3.55
938 3150 2.046285 GCCCCCAAGAACGATGGTG 61.046 63.158 0.00 0.00 36.14 4.17
939 3151 1.378514 CCCCCAAGAACGATGGTGG 60.379 63.158 0.00 0.00 36.14 4.61
940 3152 1.682849 CCCCAAGAACGATGGTGGA 59.317 57.895 0.00 0.00 36.14 4.02
997 3210 0.665670 CACGACCAGAGCAGAGTGTG 60.666 60.000 0.00 0.00 0.00 3.82
998 3211 0.823769 ACGACCAGAGCAGAGTGTGA 60.824 55.000 0.00 0.00 0.00 3.58
999 3212 0.387878 CGACCAGAGCAGAGTGTGAC 60.388 60.000 0.00 0.00 0.00 3.67
1000 3213 0.676184 GACCAGAGCAGAGTGTGACA 59.324 55.000 0.00 0.00 0.00 3.58
1011 3228 0.385751 AGTGTGACAGACAGACACGG 59.614 55.000 5.43 0.00 44.25 4.94
1147 3392 5.886609 TGATCAACTTCTTTAACCATGGGA 58.113 37.500 18.09 0.00 0.00 4.37
1785 4073 3.292936 GCACAGCACTGCAAGGCT 61.293 61.111 5.97 5.97 40.38 4.58
1846 4134 2.881441 GCATCGATTGCCATGCTTG 58.119 52.632 0.00 0.00 46.15 4.01
1847 4135 1.213094 GCATCGATTGCCATGCTTGC 61.213 55.000 0.00 0.00 46.15 4.01
1848 4136 0.596600 CATCGATTGCCATGCTTGCC 60.597 55.000 0.00 0.00 0.00 4.52
1849 4137 0.754217 ATCGATTGCCATGCTTGCCT 60.754 50.000 0.00 0.00 0.00 4.75
1850 4138 0.966875 TCGATTGCCATGCTTGCCTT 60.967 50.000 0.00 0.00 0.00 4.35
1886 4174 2.076863 GCTTGCTAGTGGATCAACGTT 58.923 47.619 0.00 0.00 0.00 3.99
1902 4190 2.061773 ACGTTTGATCGAAGTGCTCAG 58.938 47.619 0.00 0.00 34.70 3.35
1933 4221 1.647346 AATATTCGACGGCGCAGAAA 58.353 45.000 16.26 5.90 37.46 2.52
1987 4275 9.045223 AGTAAAAAGTTTTGCTGGATCAATTTC 57.955 29.630 0.61 0.00 40.73 2.17
1989 4277 5.813513 AAGTTTTGCTGGATCAATTTCCT 57.186 34.783 0.00 0.00 36.68 3.36
2413 4716 0.107410 TGGCGTTCAGTTCAACCACT 60.107 50.000 0.00 0.00 0.00 4.00
2422 4729 3.072330 TCAGTTCAACCACTTGGATGCTA 59.928 43.478 1.14 0.00 37.82 3.49
2446 4753 2.864343 CGGGTTAGCTGAATAAGTTCCG 59.136 50.000 0.00 0.00 33.26 4.30
2467 4774 2.135581 TCAGTTTCACCCGTCCCGT 61.136 57.895 0.00 0.00 0.00 5.28
2507 4821 6.037098 CCGACTAAAACTATCTCAGGAGTTG 58.963 44.000 0.00 0.00 36.05 3.16
2531 4845 2.434359 CCGTGGCGAAAGGAGGAC 60.434 66.667 0.00 0.00 0.00 3.85
2577 4892 5.462068 ACATATGCACATGTACATACGTGAC 59.538 40.000 23.51 16.59 44.02 3.67
2617 4932 3.149005 TCTAACCACCCAACCATGAAC 57.851 47.619 0.00 0.00 0.00 3.18
2628 4943 3.065233 CCAACCATGAACCATCACGTATG 59.935 47.826 0.00 0.00 38.69 2.39
2629 4944 3.627395 ACCATGAACCATCACGTATGT 57.373 42.857 0.00 0.00 38.69 2.29
2633 4948 5.056480 CCATGAACCATCACGTATGTATGT 58.944 41.667 0.00 0.00 38.69 2.29
2640 4955 5.580691 ACCATCACGTATGTATGTTGTTGAG 59.419 40.000 0.00 0.00 33.34 3.02
2660 4975 0.107361 TGGACGGTCTAGCTCGATCA 60.107 55.000 8.23 6.20 0.00 2.92
2668 4983 3.500680 GGTCTAGCTCGATCAGGTAAGAG 59.499 52.174 0.00 0.00 34.59 2.85
2711 5026 2.766828 GTGGCACCATCTAGGAGTTACT 59.233 50.000 6.29 0.00 41.22 2.24
2712 5027 3.958798 GTGGCACCATCTAGGAGTTACTA 59.041 47.826 6.29 0.00 41.22 1.82
2713 5028 4.038162 GTGGCACCATCTAGGAGTTACTAG 59.962 50.000 6.29 0.00 41.22 2.57
2716 5031 4.135306 CACCATCTAGGAGTTACTAGCGA 58.865 47.826 0.00 0.00 40.18 4.93
2721 5036 6.485984 CCATCTAGGAGTTACTAGCGAGTTAA 59.514 42.308 4.33 0.00 40.18 2.01
2735 5050 4.153117 AGCGAGTTAAGACAAGCAAATGAG 59.847 41.667 0.00 0.00 34.34 2.90
2746 5061 3.166560 AGCAAATGAGGGAGCTCTTTT 57.833 42.857 14.64 3.83 33.03 2.27
2749 5064 3.338249 CAAATGAGGGAGCTCTTTTCGA 58.662 45.455 14.64 1.50 31.25 3.71
2752 5067 5.359194 AATGAGGGAGCTCTTTTCGATTA 57.641 39.130 14.64 0.00 0.00 1.75
2753 5068 4.124851 TGAGGGAGCTCTTTTCGATTAC 57.875 45.455 14.64 0.00 0.00 1.89
2756 5071 3.118592 AGGGAGCTCTTTTCGATTACCAG 60.119 47.826 14.64 0.00 0.00 4.00
2757 5072 2.609916 GGAGCTCTTTTCGATTACCAGC 59.390 50.000 14.64 0.00 0.00 4.85
2758 5073 3.262420 GAGCTCTTTTCGATTACCAGCA 58.738 45.455 6.43 0.00 0.00 4.41
2759 5074 3.265791 AGCTCTTTTCGATTACCAGCAG 58.734 45.455 6.65 0.00 0.00 4.24
2760 5075 3.055819 AGCTCTTTTCGATTACCAGCAGA 60.056 43.478 6.65 0.00 0.00 4.26
2763 5078 5.163713 GCTCTTTTCGATTACCAGCAGAATT 60.164 40.000 0.00 0.00 0.00 2.17
2768 5088 7.441890 TTTCGATTACCAGCAGAATTTACAA 57.558 32.000 0.00 0.00 0.00 2.41
2778 5098 7.933033 ACCAGCAGAATTTACAAATCAAACAAT 59.067 29.630 0.00 0.00 0.00 2.71
2779 5099 8.437742 CCAGCAGAATTTACAAATCAAACAATC 58.562 33.333 0.00 0.00 0.00 2.67
2787 5107 5.880054 ACAAATCAAACAATCTCCCTACG 57.120 39.130 0.00 0.00 0.00 3.51
2791 5114 4.188247 TCAAACAATCTCCCTACGACAG 57.812 45.455 0.00 0.00 0.00 3.51
2843 5166 4.081420 ACATTCAGAAGCAGAACGGAGTAT 60.081 41.667 0.00 0.00 45.00 2.12
2844 5167 5.127194 ACATTCAGAAGCAGAACGGAGTATA 59.873 40.000 0.00 0.00 45.00 1.47
2845 5168 5.854010 TTCAGAAGCAGAACGGAGTATAT 57.146 39.130 0.00 0.00 45.00 0.86
2847 5170 6.561737 TCAGAAGCAGAACGGAGTATATAG 57.438 41.667 0.00 0.00 45.00 1.31
2883 5206 2.862541 AGGTAGTCAAGCAATTGCACA 58.137 42.857 30.89 12.17 45.16 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.453868 TGTGGATGAAGAAGGAGATGGA 58.546 45.455 0.00 0.00 0.00 3.41
1 2 3.920231 TGTGGATGAAGAAGGAGATGG 57.080 47.619 0.00 0.00 0.00 3.51
13 14 1.144691 TGGAGGGTTGTTGTGGATGA 58.855 50.000 0.00 0.00 0.00 2.92
63 64 2.269241 GGGAGGCTCGGTTCAAGG 59.731 66.667 8.69 0.00 0.00 3.61
106 107 1.781555 GTCGTCAAGGCACGTCATG 59.218 57.895 0.00 0.00 40.79 3.07
107 108 1.733041 CGTCGTCAAGGCACGTCAT 60.733 57.895 0.00 0.00 40.79 3.06
108 109 2.354188 CGTCGTCAAGGCACGTCA 60.354 61.111 0.00 0.00 40.79 4.35
117 118 0.319555 CCTTCTCTTGCCGTCGTCAA 60.320 55.000 0.00 0.00 0.00 3.18
161 162 4.964593 AGTAACTTTGCGAGGGAACTAAA 58.035 39.130 0.00 0.00 44.43 1.85
166 167 2.370849 AGGAAGTAACTTTGCGAGGGAA 59.629 45.455 0.00 0.00 0.00 3.97
167 168 1.975680 AGGAAGTAACTTTGCGAGGGA 59.024 47.619 0.00 0.00 0.00 4.20
170 171 5.674933 AAAGAAGGAAGTAACTTTGCGAG 57.325 39.130 0.00 0.00 32.49 5.03
172 173 6.017357 ACCTAAAAGAAGGAAGTAACTTTGCG 60.017 38.462 0.00 0.00 39.15 4.85
173 174 7.228906 AGACCTAAAAGAAGGAAGTAACTTTGC 59.771 37.037 0.00 0.00 39.15 3.68
174 175 8.678593 AGACCTAAAAGAAGGAAGTAACTTTG 57.321 34.615 0.00 0.00 39.15 2.77
177 178 7.234988 TGCTAGACCTAAAAGAAGGAAGTAACT 59.765 37.037 0.00 0.00 39.15 2.24
194 196 2.896039 ACTGAACTCCTTGCTAGACCT 58.104 47.619 0.00 0.00 0.00 3.85
195 197 3.764972 ACTACTGAACTCCTTGCTAGACC 59.235 47.826 0.00 0.00 0.00 3.85
236 238 2.724174 GGAGCGCACACAATAAAACAAC 59.276 45.455 11.47 0.00 0.00 3.32
244 246 1.221840 CCTAGGGAGCGCACACAAT 59.778 57.895 11.47 0.00 0.00 2.71
255 257 0.710588 TTCACCAGAGAGCCTAGGGA 59.289 55.000 11.72 0.00 0.00 4.20
270 273 1.944676 CGGTCGGCTATCGCTTCAC 60.945 63.158 0.00 0.00 39.05 3.18
296 299 1.541379 ATGGGCTTTGAACCGGTAAC 58.459 50.000 8.00 6.09 0.00 2.50
302 305 9.146984 GTAGTTTTAAATAATGGGCTTTGAACC 57.853 33.333 0.00 0.00 0.00 3.62
328 331 7.201565 GGGTCATCTATTTTGAAACGAAGAGAG 60.202 40.741 0.00 0.00 0.00 3.20
329 332 6.594159 GGGTCATCTATTTTGAAACGAAGAGA 59.406 38.462 0.00 0.00 0.00 3.10
330 333 6.371548 TGGGTCATCTATTTTGAAACGAAGAG 59.628 38.462 0.00 0.00 0.00 2.85
331 334 6.234920 TGGGTCATCTATTTTGAAACGAAGA 58.765 36.000 0.00 0.00 0.00 2.87
334 337 6.001460 AGTTGGGTCATCTATTTTGAAACGA 58.999 36.000 0.00 0.00 0.00 3.85
335 338 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
336 339 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
337 340 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
338 341 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
339 342 7.721842 TGTACAAAGTTGGGTCATCTATTTTGA 59.278 33.333 0.00 0.00 0.00 2.69
340 343 7.881142 TGTACAAAGTTGGGTCATCTATTTTG 58.119 34.615 0.00 0.00 0.00 2.44
341 344 8.472007 TTGTACAAAGTTGGGTCATCTATTTT 57.528 30.769 5.64 0.00 0.00 1.82
342 345 8.472007 TTTGTACAAAGTTGGGTCATCTATTT 57.528 30.769 17.01 0.00 0.00 1.40
343 346 8.472007 TTTTGTACAAAGTTGGGTCATCTATT 57.528 30.769 19.72 0.00 0.00 1.73
344 347 7.724061 ACTTTTGTACAAAGTTGGGTCATCTAT 59.276 33.333 19.72 0.00 37.18 1.98
345 348 7.057894 ACTTTTGTACAAAGTTGGGTCATCTA 58.942 34.615 19.72 1.33 37.18 1.98
346 349 5.891551 ACTTTTGTACAAAGTTGGGTCATCT 59.108 36.000 19.72 0.00 37.18 2.90
347 350 6.144078 ACTTTTGTACAAAGTTGGGTCATC 57.856 37.500 19.72 0.00 37.18 2.92
348 351 6.538945 AACTTTTGTACAAAGTTGGGTCAT 57.461 33.333 23.48 8.30 45.58 3.06
349 352 5.986501 AACTTTTGTACAAAGTTGGGTCA 57.013 34.783 23.48 9.13 45.58 4.02
350 353 7.092137 ACTAACTTTTGTACAAAGTTGGGTC 57.908 36.000 28.62 0.00 46.38 4.46
351 354 8.756486 ATACTAACTTTTGTACAAAGTTGGGT 57.244 30.769 28.62 26.41 46.38 4.51
360 363 9.850198 ACCCAACTTTATACTAACTTTTGTACA 57.150 29.630 0.00 0.00 0.00 2.90
363 366 8.983702 TGACCCAACTTTATACTAACTTTTGT 57.016 30.769 0.00 0.00 0.00 2.83
372 375 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
373 376 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
374 377 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
375 378 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
376 379 7.094549 CGTTCCAAAATAGATGACCCAACTTTA 60.095 37.037 0.00 0.00 0.00 1.85
377 380 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
378 381 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
379 382 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
380 383 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
381 384 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
382 385 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
383 386 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
384 387 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
385 388 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
386 389 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
387 390 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
388 391 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
389 392 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
390 393 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
391 394 5.502089 TTTACTCCCTCCGTTCCAAAATA 57.498 39.130 0.00 0.00 0.00 1.40
392 395 4.376225 TTTACTCCCTCCGTTCCAAAAT 57.624 40.909 0.00 0.00 0.00 1.82
393 396 3.860968 TTTACTCCCTCCGTTCCAAAA 57.139 42.857 0.00 0.00 0.00 2.44
394 397 3.479489 GTTTTACTCCCTCCGTTCCAAA 58.521 45.455 0.00 0.00 0.00 3.28
395 398 2.224597 GGTTTTACTCCCTCCGTTCCAA 60.225 50.000 0.00 0.00 0.00 3.53
396 399 1.348696 GGTTTTACTCCCTCCGTTCCA 59.651 52.381 0.00 0.00 0.00 3.53
397 400 1.627329 AGGTTTTACTCCCTCCGTTCC 59.373 52.381 0.00 0.00 0.00 3.62
398 401 4.020751 AGTTAGGTTTTACTCCCTCCGTTC 60.021 45.833 0.00 0.00 32.08 3.95
399 402 3.906218 AGTTAGGTTTTACTCCCTCCGTT 59.094 43.478 0.00 0.00 32.08 4.44
400 403 3.514539 AGTTAGGTTTTACTCCCTCCGT 58.485 45.455 0.00 0.00 32.08 4.69
401 404 5.597594 AGATAGTTAGGTTTTACTCCCTCCG 59.402 44.000 0.00 0.00 32.08 4.63
402 405 8.420222 GTTAGATAGTTAGGTTTTACTCCCTCC 58.580 40.741 0.00 0.00 32.08 4.30
403 406 9.199645 AGTTAGATAGTTAGGTTTTACTCCCTC 57.800 37.037 0.00 0.00 32.08 4.30
429 432 5.593502 TGCCATGCATACAAATCTGATGTTA 59.406 36.000 0.00 0.00 31.71 2.41
473 476 5.883115 TGCCATCCTCGACAAACATAATTTA 59.117 36.000 0.00 0.00 0.00 1.40
486 489 3.334691 CAACTAAACTTGCCATCCTCGA 58.665 45.455 0.00 0.00 0.00 4.04
508 511 0.803380 GGTGAATTTGCCATGCTCGC 60.803 55.000 0.00 0.00 0.00 5.03
517 520 3.525268 AATGAATCGGGGTGAATTTGC 57.475 42.857 0.00 0.00 0.00 3.68
541 544 8.719560 TTGCAAGTACGATAATTGTATGGTAA 57.280 30.769 0.00 0.00 34.05 2.85
611 614 4.095355 GTTCGTCGCTTTGAACGC 57.905 55.556 0.00 0.00 35.61 4.84
697 704 1.534175 GGTATCTCTGGACAGCGAACG 60.534 57.143 0.00 0.00 0.00 3.95
742 754 1.063174 GCTTTCCTTGCGTGCATAGAG 59.937 52.381 0.00 0.00 0.00 2.43
745 757 1.312371 GGGCTTTCCTTGCGTGCATA 61.312 55.000 0.00 0.00 0.00 3.14
914 3125 4.056125 GTTCTTGGGGGCTTGCGC 62.056 66.667 0.00 0.00 0.00 6.09
916 3127 1.678970 ATCGTTCTTGGGGGCTTGC 60.679 57.895 0.00 0.00 0.00 4.01
920 3131 2.046285 CACCATCGTTCTTGGGGGC 61.046 63.158 0.00 0.00 38.64 5.80
921 3132 4.319133 CACCATCGTTCTTGGGGG 57.681 61.111 0.00 0.00 38.64 5.40
933 3145 3.952508 TGCGCACCACTCCACCAT 61.953 61.111 5.66 0.00 0.00 3.55
934 3146 4.927782 GTGCGCACCACTCCACCA 62.928 66.667 30.12 0.00 41.35 4.17
997 3210 1.472878 TGCTATCCGTGTCTGTCTGTC 59.527 52.381 0.00 0.00 0.00 3.51
998 3211 1.474478 CTGCTATCCGTGTCTGTCTGT 59.526 52.381 0.00 0.00 0.00 3.41
999 3212 1.800655 GCTGCTATCCGTGTCTGTCTG 60.801 57.143 0.00 0.00 0.00 3.51
1000 3213 0.457851 GCTGCTATCCGTGTCTGTCT 59.542 55.000 0.00 0.00 0.00 3.41
1011 3228 1.043816 TGCCTGAGGTAGCTGCTATC 58.956 55.000 13.20 12.58 0.00 2.08
1147 3392 3.063084 GCCTCCGAGTCAGGACGT 61.063 66.667 0.64 0.00 36.14 4.34
1193 3438 1.666011 GGTCGTGGAGAGCAGACAA 59.334 57.895 0.00 0.00 46.08 3.18
1434 3709 4.101790 CGCGCCTTTTGATGCCGT 62.102 61.111 0.00 0.00 0.00 5.68
1444 3719 4.749310 CTCCTGAGCACGCGCCTT 62.749 66.667 5.73 0.00 39.83 4.35
1697 3978 2.173669 CGATCATTTCGCTGCCCGT 61.174 57.895 0.00 0.00 41.69 5.28
1789 4077 0.329261 AGCTTGGGCATGCAGAAGTA 59.671 50.000 21.36 0.00 41.70 2.24
1791 4079 0.680280 AGAGCTTGGGCATGCAGAAG 60.680 55.000 21.36 19.87 41.70 2.85
1886 4174 1.718396 CAGCTGAGCACTTCGATCAA 58.282 50.000 8.42 0.00 0.00 2.57
1902 4190 4.203828 CGTCGAATATTTACATGTGCAGC 58.796 43.478 9.11 0.00 0.00 5.25
1933 4221 3.324846 TCTGTCAGATTGCCAGTACAGTT 59.675 43.478 0.00 0.00 36.56 3.16
1987 4275 2.933834 AAAGGGGGACACGGGAGG 60.934 66.667 0.00 0.00 0.00 4.30
1989 4277 2.931649 GGAAAGGGGGACACGGGA 60.932 66.667 0.00 0.00 0.00 5.14
2107 4407 4.974721 AGCAGTTTGGCCCACGGG 62.975 66.667 0.00 0.00 38.57 5.28
2113 4413 3.056313 GCGGATCAGCAGTTTGGCC 62.056 63.158 13.30 0.00 37.05 5.36
2117 4417 3.490759 CGCGCGGATCAGCAGTTT 61.491 61.111 24.84 0.00 36.85 2.66
2396 4699 1.268539 CCAAGTGGTTGAACTGAACGC 60.269 52.381 0.00 0.00 35.46 4.84
2422 4729 1.206371 ACTTATTCAGCTAACCCGCGT 59.794 47.619 4.92 0.00 34.40 6.01
2446 4753 2.315386 GGACGGGTGAAACTGACGC 61.315 63.158 0.00 0.00 36.74 5.19
2467 4774 1.968017 CGGCAAAGGCAGAGCAGAA 60.968 57.895 0.00 0.00 43.71 3.02
2577 4892 3.823873 AGATAGAGTAATCGAGCCACCAG 59.176 47.826 0.00 0.00 0.00 4.00
2617 4932 5.580691 ACTCAACAACATACATACGTGATGG 59.419 40.000 0.00 0.00 40.18 3.51
2628 4943 2.735134 GACCGTCCACTCAACAACATAC 59.265 50.000 0.00 0.00 0.00 2.39
2629 4944 2.631062 AGACCGTCCACTCAACAACATA 59.369 45.455 0.00 0.00 0.00 2.29
2633 4948 1.000506 GCTAGACCGTCCACTCAACAA 59.999 52.381 0.00 0.00 0.00 2.83
2640 4955 0.308376 GATCGAGCTAGACCGTCCAC 59.692 60.000 0.00 0.00 0.00 4.02
2660 4975 2.691011 GCGTGAGGATCTTCTCTTACCT 59.309 50.000 6.38 0.00 34.92 3.08
2668 4983 1.139734 TGCTCGCGTGAGGATCTTC 59.860 57.895 26.24 9.79 42.79 2.87
2711 5026 5.234752 TCATTTGCTTGTCTTAACTCGCTA 58.765 37.500 0.00 0.00 0.00 4.26
2712 5027 4.065088 TCATTTGCTTGTCTTAACTCGCT 58.935 39.130 0.00 0.00 0.00 4.93
2713 5028 4.398247 CTCATTTGCTTGTCTTAACTCGC 58.602 43.478 0.00 0.00 0.00 5.03
2716 5031 4.985538 TCCCTCATTTGCTTGTCTTAACT 58.014 39.130 0.00 0.00 0.00 2.24
2721 5036 1.353694 AGCTCCCTCATTTGCTTGTCT 59.646 47.619 0.00 0.00 30.96 3.41
2735 5050 3.198872 CTGGTAATCGAAAAGAGCTCCC 58.801 50.000 10.93 0.38 0.00 4.30
2746 5061 7.335673 TGATTTGTAAATTCTGCTGGTAATCGA 59.664 33.333 0.00 0.00 0.00 3.59
2749 5064 9.423061 GTTTGATTTGTAAATTCTGCTGGTAAT 57.577 29.630 0.00 0.00 0.00 1.89
2752 5067 6.815089 TGTTTGATTTGTAAATTCTGCTGGT 58.185 32.000 0.00 0.00 0.00 4.00
2753 5068 7.712264 TTGTTTGATTTGTAAATTCTGCTGG 57.288 32.000 0.00 0.00 0.00 4.85
2756 5071 8.650714 GGAGATTGTTTGATTTGTAAATTCTGC 58.349 33.333 0.00 0.00 0.00 4.26
2757 5072 9.143631 GGGAGATTGTTTGATTTGTAAATTCTG 57.856 33.333 0.00 0.00 0.00 3.02
2758 5073 9.093458 AGGGAGATTGTTTGATTTGTAAATTCT 57.907 29.630 0.00 0.00 0.00 2.40
2763 5078 7.118680 GTCGTAGGGAGATTGTTTGATTTGTAA 59.881 37.037 0.00 0.00 0.00 2.41
2768 5088 5.160607 TGTCGTAGGGAGATTGTTTGATT 57.839 39.130 0.00 0.00 0.00 2.57
2778 5098 0.607217 TCGTTGCTGTCGTAGGGAGA 60.607 55.000 0.00 0.00 0.00 3.71
2779 5099 0.456312 GTCGTTGCTGTCGTAGGGAG 60.456 60.000 0.00 0.00 0.00 4.30
2785 5105 2.598907 CGATTTTTGTCGTTGCTGTCGT 60.599 45.455 0.00 0.00 36.88 4.34
2787 5107 1.708680 GCGATTTTTGTCGTTGCTGTC 59.291 47.619 0.00 0.00 43.27 3.51
2791 5114 0.425656 CGTGCGATTTTTGTCGTTGC 59.574 50.000 0.00 0.00 43.27 4.17
2845 5168 9.246670 TGACTACCTATGTTAAGTTAGTTGCTA 57.753 33.333 0.00 0.00 0.00 3.49
2847 5170 8.767478 TTGACTACCTATGTTAAGTTAGTTGC 57.233 34.615 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.