Multiple sequence alignment - TraesCS1D01G353000

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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 TraesCS1D01G353000 chr1D 100.000 2333 0 0 1 2333 438328991 438326659 0.000000e+00 4309
1 TraesCS1D01G353000 chr1D 97.143 140 3 1 299 438 349468537 349468399 3.880000e-58 235
2 TraesCS1D01G353000 chr1A 89.760 1670 136 19 681 2333 535037370 535035719 0.000000e+00 2104
3 TraesCS1D01G353000 chr1A 95.000 140 6 1 292 431 491146232 491146370 3.900000e-53 219
4 TraesCS1D01G353000 chr1B 91.880 1133 75 6 429 1555 594010535 594009414 0.000000e+00 1567
5 TraesCS1D01G353000 chr1B 96.000 300 12 0 1 300 594012221 594011922 2.690000e-134 488
6 TraesCS1D01G353000 chr1B 83.095 349 47 10 1652 1993 594009377 594009034 8.100000e-80 307
7 TraesCS1D01G353000 chr1B 95.139 144 5 2 301 443 626892872 626892730 2.330000e-55 226
8 TraesCS1D01G353000 chr7B 74.776 670 133 27 697 1342 92908453 92909110 3.820000e-68 268
9 TraesCS1D01G353000 chr7B 93.333 150 8 2 299 447 663839864 663839716 1.090000e-53 220
10 TraesCS1D01G353000 chr2A 98.571 140 2 0 296 435 162455765 162455904 4.980000e-62 248
11 TraesCS1D01G353000 chr5B 97.857 140 3 0 296 435 671039664 671039803 2.320000e-60 243
12 TraesCS1D01G353000 chr5B 95.000 140 6 1 292 431 13909993 13910131 3.900000e-53 219
13 TraesCS1D01G353000 chr5B 94.326 141 6 2 290 430 544951075 544951213 5.050000e-52 215
14 TraesCS1D01G353000 chr5B 93.269 104 5 2 460 561 373680145 373680042 4.020000e-33 152
15 TraesCS1D01G353000 chr5B 93.137 102 7 0 460 561 158782673 158782572 1.440000e-32 150
16 TraesCS1D01G353000 chr4D 97.222 144 2 2 296 439 454807927 454808068 2.320000e-60 243
17 TraesCS1D01G353000 chr4D 97.842 139 3 0 296 434 124601484 124601622 8.330000e-60 241
18 TraesCS1D01G353000 chr6B 96.479 142 4 1 292 433 65064821 65064681 1.390000e-57 233
19 TraesCS1D01G353000 chr6B 95.270 148 5 2 296 442 149443236 149443382 1.390000e-57 233
20 TraesCS1D01G353000 chr3D 96.479 142 4 1 296 437 499956176 499956316 1.390000e-57 233
21 TraesCS1D01G353000 chr3D 96.212 132 4 1 300 431 454197252 454197122 5.050000e-52 215
22 TraesCS1D01G353000 chr7D 97.059 136 4 0 296 431 585392336 585392471 1.800000e-56 230
23 TraesCS1D01G353000 chr7D 93.137 102 7 0 460 561 175941713 175941814 1.440000e-32 150
24 TraesCS1D01G353000 chr3B 92.593 162 8 4 292 450 94663624 94663464 1.800000e-56 230
25 TraesCS1D01G353000 chr3B 95.139 144 5 2 299 442 564341028 564340887 2.330000e-55 226
26 TraesCS1D01G353000 chr4B 95.683 139 6 0 291 429 490320401 490320539 8.390000e-55 224
27 TraesCS1D01G353000 chr2B 96.241 133 5 0 299 431 644511719 644511587 3.900000e-53 219
28 TraesCS1D01G353000 chr4A 91.772 158 9 4 291 445 690617440 690617596 1.400000e-52 217
29 TraesCS1D01G353000 chr6D 93.939 99 6 0 460 558 249987114 249987212 1.440000e-32 150
30 TraesCS1D01G353000 chr6D 93.137 102 7 0 460 561 267532913 267532812 1.440000e-32 150
31 TraesCS1D01G353000 chr6A 93.137 102 7 0 460 561 381088806 381088705 1.440000e-32 150
32 TraesCS1D01G353000 chr5D 93.137 102 7 0 460 561 184081088 184081189 1.440000e-32 150
33 TraesCS1D01G353000 chr5D 93.137 102 7 0 460 561 322379339 322379238 1.440000e-32 150


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 TraesCS1D01G353000 chr1D 438326659 438328991 2332 True 4309.000000 4309 100.000 1 2333 1 chr1D.!!$R2 2332
1 TraesCS1D01G353000 chr1A 535035719 535037370 1651 True 2104.000000 2104 89.760 681 2333 1 chr1A.!!$R1 1652
2 TraesCS1D01G353000 chr1B 594009034 594012221 3187 True 787.333333 1567 90.325 1 1993 3 chr1B.!!$R2 1992
3 TraesCS1D01G353000 chr7B 92908453 92909110 657 False 268.000000 268 74.776 697 1342 1 chr7B.!!$F1 645

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
427 728 1.037493 GTCCCTGGAAACAAACACCC 58.963 55.0 0.0 0.0 42.06 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 2997 0.039256 TCGCAAATGGCAACTTGAGC 60.039 50.0 14.77 3.43 45.17 4.26 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
93 94 8.034804 GGAAATGTGTATGGAAGCAATAAACTT 58.965 33.333 0.00 0.00 0.00 2.66
100 101 4.527816 ATGGAAGCAATAAACTTGCAAGGA 59.472 37.500 29.18 14.99 46.49 3.36
106 107 5.384787 GCAATAAACTTGCAAGGATTTTGC 58.615 37.500 28.11 28.11 44.34 3.68
107 108 5.179929 GCAATAAACTTGCAAGGATTTTGCT 59.820 36.000 31.04 16.39 45.13 3.91
209 210 6.778069 TCCCTCAAATCTAGTTATCTCGACAT 59.222 38.462 0.00 0.00 0.00 3.06
218 219 3.195610 AGTTATCTCGACATGTGGCTTCA 59.804 43.478 1.15 0.00 0.00 3.02
219 220 2.768253 ATCTCGACATGTGGCTTCAA 57.232 45.000 1.15 0.00 0.00 2.69
221 222 2.143122 TCTCGACATGTGGCTTCAAAC 58.857 47.619 1.15 0.00 0.00 2.93
229 230 2.649190 TGTGGCTTCAAACTGCAGTTA 58.351 42.857 31.31 15.19 37.25 2.24
266 267 1.349688 AGTCATACTTTTGGTGCCGGA 59.650 47.619 5.05 0.00 0.00 5.14
300 301 3.973206 ACGTATCACAACTTCCCATGA 57.027 42.857 0.00 0.00 0.00 3.07
301 302 3.861840 ACGTATCACAACTTCCCATGAG 58.138 45.455 0.00 0.00 0.00 2.90
302 303 3.513912 ACGTATCACAACTTCCCATGAGA 59.486 43.478 0.00 0.00 0.00 3.27
303 304 4.115516 CGTATCACAACTTCCCATGAGAG 58.884 47.826 0.00 0.00 0.00 3.20
304 305 4.382040 CGTATCACAACTTCCCATGAGAGT 60.382 45.833 0.00 0.00 0.00 3.24
305 306 3.685139 TCACAACTTCCCATGAGAGTC 57.315 47.619 0.00 0.00 0.00 3.36
308 309 4.838423 TCACAACTTCCCATGAGAGTCTTA 59.162 41.667 0.00 0.00 0.00 2.10
309 310 5.485353 TCACAACTTCCCATGAGAGTCTTAT 59.515 40.000 0.00 0.00 0.00 1.73
311 312 6.656693 CACAACTTCCCATGAGAGTCTTATTT 59.343 38.462 0.00 0.00 0.00 1.40
314 315 7.205515 ACTTCCCATGAGAGTCTTATTTCAT 57.794 36.000 0.00 0.00 0.00 2.57
315 316 8.324191 ACTTCCCATGAGAGTCTTATTTCATA 57.676 34.615 0.00 0.00 0.00 2.15
316 317 8.772250 ACTTCCCATGAGAGTCTTATTTCATAA 58.228 33.333 0.00 0.00 0.00 1.90
318 319 8.324191 TCCCATGAGAGTCTTATTTCATAAGT 57.676 34.615 0.00 0.00 42.21 2.24
319 320 8.424918 TCCCATGAGAGTCTTATTTCATAAGTC 58.575 37.037 0.00 0.00 42.21 3.01
320 321 7.659390 CCCATGAGAGTCTTATTTCATAAGTCC 59.341 40.741 0.00 0.00 42.21 3.85
321 322 7.659390 CCATGAGAGTCTTATTTCATAAGTCCC 59.341 40.741 0.00 0.00 42.21 4.46
322 323 7.733773 TGAGAGTCTTATTTCATAAGTCCCA 57.266 36.000 0.00 0.00 42.21 4.37
323 324 8.146053 TGAGAGTCTTATTTCATAAGTCCCAA 57.854 34.615 0.00 0.00 42.21 4.12
325 326 9.620259 GAGAGTCTTATTTCATAAGTCCCAAAT 57.380 33.333 0.00 0.00 42.21 2.32
328 329 7.068716 AGTCTTATTTCATAAGTCCCAAATGCC 59.931 37.037 3.93 0.00 42.21 4.40
330 331 3.464720 TTCATAAGTCCCAAATGCCCA 57.535 42.857 0.00 0.00 0.00 5.36
331 332 2.733956 TCATAAGTCCCAAATGCCCAC 58.266 47.619 0.00 0.00 0.00 4.61
334 335 2.101640 AAGTCCCAAATGCCCACTTT 57.898 45.000 0.00 0.00 0.00 2.66
336 337 3.252554 AGTCCCAAATGCCCACTTTAA 57.747 42.857 0.00 0.00 0.00 1.52
337 338 3.165071 AGTCCCAAATGCCCACTTTAAG 58.835 45.455 0.00 0.00 0.00 1.85
338 339 2.897326 GTCCCAAATGCCCACTTTAAGT 59.103 45.455 0.00 0.00 0.00 2.24
339 340 3.056821 GTCCCAAATGCCCACTTTAAGTC 60.057 47.826 0.00 0.00 0.00 3.01
341 342 2.233676 CCAAATGCCCACTTTAAGTCCC 59.766 50.000 0.00 0.00 0.00 4.46
342 343 3.165071 CAAATGCCCACTTTAAGTCCCT 58.835 45.455 0.00 0.00 0.00 4.20
343 344 4.340617 CAAATGCCCACTTTAAGTCCCTA 58.659 43.478 0.00 0.00 0.00 3.53
344 345 4.881157 AATGCCCACTTTAAGTCCCTAT 57.119 40.909 0.00 0.00 0.00 2.57
345 346 5.987019 AATGCCCACTTTAAGTCCCTATA 57.013 39.130 0.00 0.00 0.00 1.31
346 347 5.987019 ATGCCCACTTTAAGTCCCTATAA 57.013 39.130 0.00 0.00 0.00 0.98
347 348 5.367945 TGCCCACTTTAAGTCCCTATAAG 57.632 43.478 0.00 0.00 0.00 1.73
348 349 4.786454 TGCCCACTTTAAGTCCCTATAAGT 59.214 41.667 0.00 0.00 0.00 2.24
349 350 5.104652 TGCCCACTTTAAGTCCCTATAAGTC 60.105 44.000 0.00 0.00 0.00 3.01
354 355 5.904169 ACTTTAAGTCCCTATAAGTCCCTCC 59.096 44.000 0.00 0.00 0.00 4.30
358 359 3.275228 AGTCCCTATAAGTCCCTCCTGTT 59.725 47.826 0.00 0.00 0.00 3.16
359 360 4.038633 GTCCCTATAAGTCCCTCCTGTTT 58.961 47.826 0.00 0.00 0.00 2.83
360 361 4.037927 TCCCTATAAGTCCCTCCTGTTTG 58.962 47.826 0.00 0.00 0.00 2.93
361 362 3.136626 CCCTATAAGTCCCTCCTGTTTGG 59.863 52.174 0.00 0.00 37.10 3.28
365 584 5.853572 ATAAGTCCCTCCTGTTTGGTTTA 57.146 39.130 0.00 0.00 37.07 2.01
372 591 3.010138 CCTCCTGTTTGGTTTAGATGGGA 59.990 47.826 0.00 0.00 37.07 4.37
375 594 4.105697 TCCTGTTTGGTTTAGATGGGACTT 59.894 41.667 0.00 0.00 37.07 3.01
376 595 5.311121 TCCTGTTTGGTTTAGATGGGACTTA 59.689 40.000 0.00 0.00 37.07 2.24
381 600 6.509523 TTGGTTTAGATGGGACTTATAGGG 57.490 41.667 0.00 0.00 0.00 3.53
383 602 5.605488 TGGTTTAGATGGGACTTATAGGGAC 59.395 44.000 0.00 0.00 0.00 4.46
384 603 5.845065 GGTTTAGATGGGACTTATAGGGACT 59.155 44.000 0.00 0.00 46.37 3.85
386 605 7.147355 GGTTTAGATGGGACTTATAGGGACTTT 60.147 40.741 0.00 0.00 41.75 2.66
388 607 6.910259 AGATGGGACTTATAGGGACTTTTT 57.090 37.500 0.00 0.00 41.75 1.94
422 723 7.610580 AAATCAATAAGTCCCTGGAAACAAA 57.389 32.000 0.00 0.00 42.06 2.83
423 724 6.590234 ATCAATAAGTCCCTGGAAACAAAC 57.410 37.500 0.00 0.00 42.06 2.93
424 725 5.450453 TCAATAAGTCCCTGGAAACAAACA 58.550 37.500 0.00 0.00 42.06 2.83
425 726 5.300792 TCAATAAGTCCCTGGAAACAAACAC 59.699 40.000 0.00 0.00 42.06 3.32
426 727 2.067365 AGTCCCTGGAAACAAACACC 57.933 50.000 0.00 0.00 42.06 4.16
427 728 1.037493 GTCCCTGGAAACAAACACCC 58.963 55.000 0.00 0.00 42.06 4.61
496 1755 2.158986 CCATGAGCTGGTTTCGAGATCT 60.159 50.000 0.00 0.00 40.49 2.75
511 1770 4.054671 CGAGATCTTATGGGTTTCAGCTC 58.945 47.826 0.00 0.00 0.00 4.09
516 1775 3.134804 TCTTATGGGTTTCAGCTCTAGCC 59.865 47.826 0.00 0.00 43.38 3.93
532 1791 2.287977 AGCCTACCCCAACTTGTTTC 57.712 50.000 0.00 0.00 0.00 2.78
545 1804 3.400255 ACTTGTTTCGGACTAAAGGCTC 58.600 45.455 0.00 0.00 0.00 4.70
546 1805 3.071167 ACTTGTTTCGGACTAAAGGCTCT 59.929 43.478 0.00 0.00 0.00 4.09
547 1806 3.040147 TGTTTCGGACTAAAGGCTCTG 57.960 47.619 0.00 0.00 0.00 3.35
548 1807 2.367567 TGTTTCGGACTAAAGGCTCTGT 59.632 45.455 0.00 0.00 0.00 3.41
549 1808 3.181458 TGTTTCGGACTAAAGGCTCTGTT 60.181 43.478 0.00 0.00 0.00 3.16
550 1809 2.743636 TCGGACTAAAGGCTCTGTTG 57.256 50.000 0.00 0.00 0.00 3.33
561 1820 2.423538 AGGCTCTGTTGTTGTTGTTGTC 59.576 45.455 0.00 0.00 0.00 3.18
593 1852 4.660303 AGGGGCTAGTGATCATTAATGACA 59.340 41.667 20.19 16.14 40.03 3.58
630 1889 8.424133 TCATATAGCAGTAGTTATATGCCATGG 58.576 37.037 7.63 7.63 44.74 3.66
891 2154 2.880890 CCTCTAGCTTGCAACAACAACT 59.119 45.455 0.00 0.00 0.00 3.16
930 2203 1.734163 AACTATAGGGTGCACGTTGC 58.266 50.000 11.45 0.00 45.29 4.17
948 2223 1.204704 TGCTCCTTCACACAGGTATCG 59.795 52.381 0.00 0.00 35.15 2.92
979 2257 8.029522 GGAACGTAGAGCATGAATTGATATCTA 58.970 37.037 3.98 0.00 0.00 1.98
987 2265 9.486497 GAGCATGAATTGATATCTAAAGACTCA 57.514 33.333 3.98 0.00 0.00 3.41
1051 2329 3.406764 GATGTGACCATCATAGGCTTCC 58.593 50.000 0.00 0.00 45.68 3.46
1056 2334 0.179048 CCATCATAGGCTTCCGTGCA 60.179 55.000 0.00 0.00 34.04 4.57
1199 2480 1.059913 AGTTACAAGTGCAGCCCTCT 58.940 50.000 0.00 0.00 0.00 3.69
1263 2544 2.694628 GGCCATTGGAAGATATGTTGCA 59.305 45.455 6.95 2.48 0.00 4.08
1296 2577 3.818773 CCTCCACCGTCAAGTTAAATGTT 59.181 43.478 0.00 0.00 0.00 2.71
1322 2603 1.568612 CTCTGCGAACGTTGCCATGT 61.569 55.000 5.00 0.00 0.00 3.21
1366 2647 5.460646 TGTTTCTCCGCTTCAATGAATTTC 58.539 37.500 0.00 0.00 0.00 2.17
1383 2664 9.661563 AATGAATTTCATGTTGCATAGATTGTT 57.338 25.926 12.50 0.00 37.15 2.83
1396 2677 5.904080 GCATAGATTGTTGCTTCGTATTGTC 59.096 40.000 0.00 0.00 35.95 3.18
1427 2708 3.818210 ACTACAATGCGAATCACCAAACA 59.182 39.130 0.00 0.00 0.00 2.83
1430 2711 3.236816 CAATGCGAATCACCAAACAGAC 58.763 45.455 0.00 0.00 0.00 3.51
1464 2745 2.668457 CTGTGGATACGTCTGAACTTGC 59.332 50.000 0.00 0.00 42.51 4.01
1465 2746 2.000447 GTGGATACGTCTGAACTTGCC 59.000 52.381 0.00 0.00 42.51 4.52
1468 2749 2.611971 GGATACGTCTGAACTTGCCACA 60.612 50.000 0.00 0.00 0.00 4.17
1482 2765 2.370445 CCACAGGTGGGGCTCTAGG 61.370 68.421 10.67 0.00 46.81 3.02
1491 2774 1.348775 GGGGCTCTAGGCATCCAACT 61.349 60.000 5.85 0.00 44.01 3.16
1538 2823 1.803334 ACGGAGCGAGCATAAAAACA 58.197 45.000 0.00 0.00 0.00 2.83
1592 2877 9.843334 TTATAAACACACGGATGAAATTTAACC 57.157 29.630 0.00 0.00 0.00 2.85
1650 2936 7.448777 TGTGAGATACTGGATAGATACAAGACC 59.551 40.741 0.00 0.00 0.00 3.85
1668 2954 3.447586 AGACCGTGAGCTTGTATACATGT 59.552 43.478 17.33 2.69 0.00 3.21
1686 2972 1.340889 TGTCACTTTTGAGGCCATTGC 59.659 47.619 5.01 0.00 30.10 3.56
1711 2997 1.284297 TGTCATCGTCTGCGCTGTTG 61.284 55.000 9.73 5.56 35.90 3.33
1730 3016 0.039256 GCTCAAGTTGCCATTTGCGA 60.039 50.000 0.00 0.00 45.60 5.10
1884 3187 2.431683 GAGCTGGTGGTTGAGGCA 59.568 61.111 0.00 0.00 0.00 4.75
1966 3269 1.078759 CGACTTGGCTCTTCGCGAAT 61.079 55.000 23.67 4.23 40.44 3.34
1970 3273 2.819595 GGCTCTTCGCGAATGCCA 60.820 61.111 38.10 19.63 38.67 4.92
2032 3335 1.126846 GAGAGGCATTTGTTCGTGTCG 59.873 52.381 0.00 0.00 0.00 4.35
2048 3351 1.754803 TGTCGAGGAAGACACACAGTT 59.245 47.619 0.00 0.00 45.18 3.16
2066 3369 4.463186 ACAGTTAGCTTGGAGGTAGTACTG 59.537 45.833 5.39 13.37 40.31 2.74
2073 3376 4.159879 GCTTGGAGGTAGTACTGTACACAT 59.840 45.833 19.27 12.56 0.00 3.21
2095 3398 2.119484 TTGTGGCTAGGACGGTTGGG 62.119 60.000 0.00 0.00 0.00 4.12
2096 3399 3.006728 TGGCTAGGACGGTTGGGG 61.007 66.667 0.00 0.00 0.00 4.96
2097 3400 3.793888 GGCTAGGACGGTTGGGGG 61.794 72.222 0.00 0.00 0.00 5.40
2120 3423 0.252284 GGACTCCTCCTCCTCCACAA 60.252 60.000 0.00 0.00 33.07 3.33
2125 3428 1.153289 CTCCTCCTCCACAATGGCG 60.153 63.158 0.00 0.00 37.47 5.69
2130 3433 0.394216 TCCTCCACAATGGCGAATGG 60.394 55.000 0.00 0.00 37.47 3.16
2133 3436 0.327924 TCCACAATGGCGAATGGACT 59.672 50.000 0.00 0.00 36.30 3.85
2135 3438 1.679944 CCACAATGGCGAATGGACTCT 60.680 52.381 0.00 0.00 33.80 3.24
2139 3442 2.732412 ATGGCGAATGGACTCTATCG 57.268 50.000 0.00 0.00 38.28 2.92
2140 3443 0.673985 TGGCGAATGGACTCTATCGG 59.326 55.000 0.00 0.00 35.91 4.18
2180 3483 1.396301 GTCTGCTTCTCTTTCATGCGG 59.604 52.381 0.00 0.00 0.00 5.69
2188 3491 4.118093 TCTCTTTCATGCGGTATTCGAA 57.882 40.909 0.00 0.00 42.43 3.71
2221 3524 1.686325 CTACATGGTGGGGAGGTCGG 61.686 65.000 0.00 0.00 0.00 4.79
2237 3540 1.153628 CGGCTCCTCCTTTACACGG 60.154 63.158 0.00 0.00 0.00 4.94
2253 3556 3.686016 ACACGGCATCTAATTTGGAAGT 58.314 40.909 0.00 0.00 0.00 3.01
2265 3568 1.433053 TTGGAAGTCGCGGTTGTGTG 61.433 55.000 6.13 0.00 0.00 3.82
2266 3569 2.604174 GGAAGTCGCGGTTGTGTGG 61.604 63.158 6.13 0.00 0.00 4.17
2275 3578 1.000896 GGTTGTGTGGAGGGGATGG 60.001 63.158 0.00 0.00 0.00 3.51
2282 3585 0.324645 GTGGAGGGGATGGCATTGTT 60.325 55.000 0.00 0.00 0.00 2.83
2290 3593 1.331756 GGATGGCATTGTTAGACTGCG 59.668 52.381 0.00 0.00 36.76 5.18
2297 3600 2.736144 TTGTTAGACTGCGGTCGATT 57.264 45.000 19.79 5.59 46.29 3.34
2320 3623 0.818296 AACCACTAGAGCGCGATCTT 59.182 50.000 33.44 13.15 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 3.499918 CGGTCAACTCTCTTGAGCAAAAT 59.500 43.478 11.59 0.00 44.53 1.82
106 107 2.266554 GATGCGGTCAACTCTCTTGAG 58.733 52.381 0.00 0.00 45.43 3.02
107 108 1.618343 TGATGCGGTCAACTCTCTTGA 59.382 47.619 0.00 0.00 32.78 3.02
209 210 1.473258 AACTGCAGTTTGAAGCCACA 58.527 45.000 26.36 0.00 33.93 4.17
218 219 2.054799 TCCCTGGAGTAACTGCAGTTT 58.945 47.619 35.20 20.08 46.18 2.66
219 220 1.729586 TCCCTGGAGTAACTGCAGTT 58.270 50.000 32.97 32.97 46.18 3.16
221 222 1.202463 CGATCCCTGGAGTAACTGCAG 60.202 57.143 13.48 13.48 46.96 4.41
229 230 2.104170 GACTTCTTCGATCCCTGGAGT 58.896 52.381 0.00 0.00 0.00 3.85
266 267 3.002553 GTGATACGTTTCGTTGGGTTGTT 59.997 43.478 0.00 0.00 41.54 2.83
308 309 4.162131 GTGGGCATTTGGGACTTATGAAAT 59.838 41.667 0.00 0.00 0.00 2.17
309 310 3.513515 GTGGGCATTTGGGACTTATGAAA 59.486 43.478 0.00 0.00 0.00 2.69
311 312 2.311542 AGTGGGCATTTGGGACTTATGA 59.688 45.455 0.00 0.00 0.00 2.15
314 315 2.990740 AAGTGGGCATTTGGGACTTA 57.009 45.000 0.00 0.00 0.00 2.24
315 316 2.101640 AAAGTGGGCATTTGGGACTT 57.898 45.000 0.00 0.00 0.00 3.01
316 317 2.990740 TAAAGTGGGCATTTGGGACT 57.009 45.000 0.00 0.00 0.00 3.85
318 319 3.161866 GACTTAAAGTGGGCATTTGGGA 58.838 45.455 0.00 0.00 0.00 4.37
319 320 2.233676 GGACTTAAAGTGGGCATTTGGG 59.766 50.000 0.00 0.00 0.00 4.12
320 321 2.233676 GGGACTTAAAGTGGGCATTTGG 59.766 50.000 0.00 0.00 0.00 3.28
321 322 3.165071 AGGGACTTAAAGTGGGCATTTG 58.835 45.455 0.00 0.00 27.25 2.32
322 323 3.542969 AGGGACTTAAAGTGGGCATTT 57.457 42.857 0.00 0.00 27.25 2.32
323 324 4.881157 ATAGGGACTTAAAGTGGGCATT 57.119 40.909 0.00 0.00 41.75 3.56
325 326 4.786454 ACTTATAGGGACTTAAAGTGGGCA 59.214 41.667 0.00 0.00 39.58 5.36
328 329 5.666265 AGGGACTTATAGGGACTTAAAGTGG 59.334 44.000 0.00 0.00 40.60 4.00
330 331 5.904169 GGAGGGACTTATAGGGACTTAAAGT 59.096 44.000 0.00 0.00 42.31 2.66
331 332 6.042208 CAGGAGGGACTTATAGGGACTTAAAG 59.958 46.154 0.00 0.00 41.55 1.85
334 335 4.485021 ACAGGAGGGACTTATAGGGACTTA 59.515 45.833 0.00 0.00 41.55 2.24
336 337 2.866454 ACAGGAGGGACTTATAGGGACT 59.134 50.000 0.00 0.00 41.55 3.85
337 338 3.331718 ACAGGAGGGACTTATAGGGAC 57.668 52.381 0.00 0.00 41.55 4.46
338 339 4.037927 CAAACAGGAGGGACTTATAGGGA 58.962 47.826 0.00 0.00 41.55 4.20
339 340 3.136626 CCAAACAGGAGGGACTTATAGGG 59.863 52.174 0.00 0.00 41.55 3.53
341 342 5.437191 AACCAAACAGGAGGGACTTATAG 57.563 43.478 0.00 0.00 41.55 1.31
342 343 5.853572 AAACCAAACAGGAGGGACTTATA 57.146 39.130 0.00 0.00 41.55 0.98
343 344 4.741928 AAACCAAACAGGAGGGACTTAT 57.258 40.909 0.00 0.00 41.55 1.73
344 345 4.909088 TCTAAACCAAACAGGAGGGACTTA 59.091 41.667 0.00 0.00 41.55 2.24
345 346 3.720002 TCTAAACCAAACAGGAGGGACTT 59.280 43.478 0.00 0.00 41.55 3.01
347 348 3.782656 TCTAAACCAAACAGGAGGGAC 57.217 47.619 0.00 0.00 41.22 4.46
348 349 3.010138 CCATCTAAACCAAACAGGAGGGA 59.990 47.826 0.00 0.00 41.22 4.20
349 350 3.356290 CCATCTAAACCAAACAGGAGGG 58.644 50.000 0.00 0.00 41.22 4.30
354 355 7.499232 CCTATAAGTCCCATCTAAACCAAACAG 59.501 40.741 0.00 0.00 0.00 3.16
358 359 6.100714 GTCCCTATAAGTCCCATCTAAACCAA 59.899 42.308 0.00 0.00 0.00 3.67
359 360 5.605488 GTCCCTATAAGTCCCATCTAAACCA 59.395 44.000 0.00 0.00 0.00 3.67
360 361 5.845065 AGTCCCTATAAGTCCCATCTAAACC 59.155 44.000 0.00 0.00 0.00 3.27
361 362 6.997942 AGTCCCTATAAGTCCCATCTAAAC 57.002 41.667 0.00 0.00 0.00 2.01
365 584 6.910259 AAAAAGTCCCTATAAGTCCCATCT 57.090 37.500 0.00 0.00 0.00 2.90
386 605 9.470399 GGGACTTATTGATTTAGGGACTTAAAA 57.530 33.333 0.00 0.00 41.75 1.52
388 607 8.272173 CAGGGACTTATTGATTTAGGGACTTAA 58.728 37.037 0.00 0.00 36.39 1.85
389 608 7.147373 CCAGGGACTTATTGATTTAGGGACTTA 60.147 40.741 0.00 0.00 36.39 2.24
391 610 5.132816 CCAGGGACTTATTGATTTAGGGACT 59.867 44.000 0.00 0.00 39.39 3.85
393 612 5.293643 TCCAGGGACTTATTGATTTAGGGA 58.706 41.667 0.00 0.00 34.60 4.20
395 614 6.889722 TGTTTCCAGGGACTTATTGATTTAGG 59.110 38.462 0.00 0.00 34.60 2.69
396 615 7.938140 TGTTTCCAGGGACTTATTGATTTAG 57.062 36.000 0.00 0.00 34.60 1.85
397 616 8.581578 GTTTGTTTCCAGGGACTTATTGATTTA 58.418 33.333 0.00 0.00 34.60 1.40
399 618 6.553100 TGTTTGTTTCCAGGGACTTATTGATT 59.447 34.615 0.00 0.00 34.60 2.57
400 619 6.015434 GTGTTTGTTTCCAGGGACTTATTGAT 60.015 38.462 0.00 0.00 34.60 2.57
402 621 5.508994 GGTGTTTGTTTCCAGGGACTTATTG 60.509 44.000 0.00 0.00 34.60 1.90
403 622 4.587262 GGTGTTTGTTTCCAGGGACTTATT 59.413 41.667 0.00 0.00 34.60 1.40
404 623 4.149598 GGTGTTTGTTTCCAGGGACTTAT 58.850 43.478 0.00 0.00 34.60 1.73
405 624 3.558033 GGTGTTTGTTTCCAGGGACTTA 58.442 45.455 0.00 0.00 34.60 2.24
406 625 2.384828 GGTGTTTGTTTCCAGGGACTT 58.615 47.619 0.00 0.00 34.60 3.01
407 626 1.411074 GGGTGTTTGTTTCCAGGGACT 60.411 52.381 0.00 0.00 43.88 3.85
408 627 1.037493 GGGTGTTTGTTTCCAGGGAC 58.963 55.000 0.00 0.00 0.00 4.46
409 628 0.930726 AGGGTGTTTGTTTCCAGGGA 59.069 50.000 0.00 0.00 0.00 4.20
410 629 1.133482 AGAGGGTGTTTGTTTCCAGGG 60.133 52.381 0.00 0.00 0.00 4.45
422 723 6.436218 ACAAAAACTTTAGTTTGAGAGGGTGT 59.564 34.615 8.51 3.27 46.47 4.16
423 724 6.863275 ACAAAAACTTTAGTTTGAGAGGGTG 58.137 36.000 8.51 2.78 46.47 4.61
424 725 7.476540 AACAAAAACTTTAGTTTGAGAGGGT 57.523 32.000 8.51 0.16 46.47 4.34
425 726 8.771920 AAAACAAAAACTTTAGTTTGAGAGGG 57.228 30.769 8.51 0.00 46.47 4.30
426 727 8.583765 CGAAAACAAAAACTTTAGTTTGAGAGG 58.416 33.333 8.51 1.09 46.47 3.69
427 728 9.124807 ACGAAAACAAAAACTTTAGTTTGAGAG 57.875 29.630 8.51 2.89 46.47 3.20
490 1749 5.289083 AGAGCTGAAACCCATAAGATCTC 57.711 43.478 0.00 0.00 29.78 2.75
496 1755 3.115390 AGGCTAGAGCTGAAACCCATAA 58.885 45.455 0.00 0.00 41.70 1.90
511 1770 3.344515 GAAACAAGTTGGGGTAGGCTAG 58.655 50.000 7.96 0.00 0.00 3.42
516 1775 2.148768 GTCCGAAACAAGTTGGGGTAG 58.851 52.381 7.96 0.00 35.83 3.18
532 1791 2.457366 ACAACAGAGCCTTTAGTCCG 57.543 50.000 0.00 0.00 0.00 4.79
622 1881 6.454223 AGGTTACACTATATTCCATGGCAT 57.546 37.500 6.96 4.02 0.00 4.40
623 1882 5.904984 AGGTTACACTATATTCCATGGCA 57.095 39.130 6.96 0.00 0.00 4.92
679 1942 8.517878 GGCGTACTGAAGTCCTACATATAATAA 58.482 37.037 0.00 0.00 0.00 1.40
689 1952 2.029623 GATGGGCGTACTGAAGTCCTA 58.970 52.381 0.00 0.00 0.00 2.94
891 2154 8.885693 ATAGTTACATGCAGAGATAGGATACA 57.114 34.615 0.00 0.00 41.41 2.29
930 2203 1.204704 TGCGATACCTGTGTGAAGGAG 59.795 52.381 0.00 0.00 40.02 3.69
948 2223 1.135139 TCATGCTCTACGTTCCTCTGC 59.865 52.381 0.00 0.00 0.00 4.26
987 2265 0.036952 CTGGCATCCGTCTCAACACT 60.037 55.000 0.00 0.00 0.00 3.55
1051 2329 1.154093 CCATGCTCTTTGCTGCACG 60.154 57.895 0.00 0.00 42.26 5.34
1056 2334 1.160137 GTTCGACCATGCTCTTTGCT 58.840 50.000 0.00 0.00 43.37 3.91
1199 2480 1.406180 CAATCATCCGCTTGCCAATCA 59.594 47.619 0.00 0.00 0.00 2.57
1263 2544 0.396811 CGGTGGAGGGAACTTTGTCT 59.603 55.000 0.00 0.00 44.43 3.41
1296 2577 2.058798 CAACGTTCGCAGAGCTTCTTA 58.941 47.619 0.00 0.00 38.43 2.10
1322 2603 5.202765 ACATCAGGCACAATCATTCCATTA 58.797 37.500 0.00 0.00 0.00 1.90
1366 2647 4.497966 CGAAGCAACAATCTATGCAACATG 59.502 41.667 0.00 0.00 44.95 3.21
1383 2664 3.932822 TGCCTTAAGACAATACGAAGCA 58.067 40.909 3.36 0.00 0.00 3.91
1396 2677 4.678509 TTCGCATTGTAGTTGCCTTAAG 57.321 40.909 0.00 0.00 36.75 1.85
1408 2689 2.884012 TCTGTTTGGTGATTCGCATTGT 59.116 40.909 0.00 0.00 0.00 2.71
1416 2697 2.218603 GGTGTCGTCTGTTTGGTGATT 58.781 47.619 0.00 0.00 0.00 2.57
1427 2708 3.513912 TCCACAGATATTTGGTGTCGTCT 59.486 43.478 0.00 0.00 34.19 4.18
1430 2711 4.444388 CGTATCCACAGATATTTGGTGTCG 59.556 45.833 0.00 0.00 37.32 4.35
1465 2746 3.036429 GCCTAGAGCCCCACCTGTG 62.036 68.421 0.00 0.00 34.35 3.66
1468 2749 1.768077 GATGCCTAGAGCCCCACCT 60.768 63.158 0.00 0.00 42.71 4.00
1491 2774 9.650539 CAAATATTTGAACATTTGGTGTCCATA 57.349 29.630 21.35 0.00 41.14 2.74
1509 2793 3.006940 TGCTCGCTCCGTTCAAATATTT 58.993 40.909 0.00 0.00 0.00 1.40
1512 2796 2.309528 ATGCTCGCTCCGTTCAAATA 57.690 45.000 0.00 0.00 0.00 1.40
1627 2913 6.655848 ACGGTCTTGTATCTATCCAGTATCTC 59.344 42.308 0.00 0.00 0.00 2.75
1646 2932 3.447586 ACATGTATACAAGCTCACGGTCT 59.552 43.478 10.14 0.00 0.00 3.85
1650 2936 4.424626 AGTGACATGTATACAAGCTCACG 58.575 43.478 22.90 8.27 34.30 4.35
1668 2954 1.340889 GTGCAATGGCCTCAAAAGTGA 59.659 47.619 3.32 0.00 40.13 3.41
1686 2972 0.439985 CGCAGACGATGACAAAGGTG 59.560 55.000 0.00 0.00 43.93 4.00
1711 2997 0.039256 TCGCAAATGGCAACTTGAGC 60.039 50.000 14.77 3.43 45.17 4.26
1730 3016 0.462789 AACCACGACGAGAAAGGTGT 59.537 50.000 0.00 0.00 31.86 4.16
1768 3055 3.650298 GAGCAGGGATGCCTGGCAA 62.650 63.158 31.75 9.47 43.62 4.52
1796 3099 3.243892 CGTCTCAAGAGCGAGCGC 61.244 66.667 6.78 6.78 42.33 5.92
1836 3139 1.675310 CCGATGAAGCCCAAGTGCA 60.675 57.895 0.00 0.00 0.00 4.57
1884 3187 2.045926 GCTCCCGCCATCAGTGTT 60.046 61.111 0.00 0.00 0.00 3.32
2032 3335 3.669251 AGCTAACTGTGTGTCTTCCTC 57.331 47.619 0.00 0.00 0.00 3.71
2046 3349 5.416952 TGTACAGTACTACCTCCAAGCTAAC 59.583 44.000 12.07 0.00 0.00 2.34
2048 3351 4.946157 GTGTACAGTACTACCTCCAAGCTA 59.054 45.833 12.07 0.00 0.00 3.32
2073 3376 0.981183 AACCGTCCTAGCCACAATCA 59.019 50.000 0.00 0.00 0.00 2.57
2098 3401 2.284151 GAGGAGGAGGAGTCCCCC 59.716 72.222 5.25 2.72 45.26 5.40
2104 3407 0.835941 CCATTGTGGAGGAGGAGGAG 59.164 60.000 0.00 0.00 40.96 3.69
2105 3408 1.274703 GCCATTGTGGAGGAGGAGGA 61.275 60.000 0.00 0.00 40.96 3.71
2106 3409 1.225704 GCCATTGTGGAGGAGGAGG 59.774 63.158 0.00 0.00 40.96 4.30
2115 3418 0.734889 GAGTCCATTCGCCATTGTGG 59.265 55.000 0.00 0.00 41.55 4.17
2120 3423 1.273606 CCGATAGAGTCCATTCGCCAT 59.726 52.381 2.38 0.00 39.76 4.40
2125 3428 2.128035 CGCAACCGATAGAGTCCATTC 58.872 52.381 0.00 0.00 36.29 2.67
2130 3433 1.189403 CGTTCGCAACCGATAGAGTC 58.811 55.000 0.00 0.00 43.97 3.36
2133 3436 0.099968 CCTCGTTCGCAACCGATAGA 59.900 55.000 0.00 0.00 43.97 1.98
2135 3438 1.517694 GCCTCGTTCGCAACCGATA 60.518 57.895 0.00 0.00 43.97 2.92
2180 3483 3.303132 GCCACGACATCCAATTCGAATAC 60.303 47.826 11.83 0.00 38.63 1.89
2188 3491 2.564771 CATGTAGCCACGACATCCAAT 58.435 47.619 0.00 0.00 35.31 3.16
2221 3524 0.107654 ATGCCGTGTAAAGGAGGAGC 60.108 55.000 0.00 0.00 37.88 4.70
2237 3540 2.286418 CCGCGACTTCCAAATTAGATGC 60.286 50.000 8.23 0.00 0.00 3.91
2253 3556 4.308458 CCCTCCACACAACCGCGA 62.308 66.667 8.23 0.00 0.00 5.87
2265 3568 1.494721 TCTAACAATGCCATCCCCTCC 59.505 52.381 0.00 0.00 0.00 4.30
2266 3569 2.173569 AGTCTAACAATGCCATCCCCTC 59.826 50.000 0.00 0.00 0.00 4.30
2275 3578 0.370273 CGACCGCAGTCTAACAATGC 59.630 55.000 0.00 0.00 41.16 3.56
2282 3585 3.504863 GTTGTTAATCGACCGCAGTCTA 58.495 45.455 0.00 0.00 41.16 2.59
2297 3600 0.883153 TCGCGCTCTAGTGGTTGTTA 59.117 50.000 5.56 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.