Multiple sequence alignment - TraesCS4D01G216300

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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 TraesCS4D01G216300 chr4D 100.000 2729 0 0 1 2729 370529579 370532307 0.000000e+00 5040.0
1 TraesCS4D01G216300 chr4B 94.257 2159 65 14 610 2729 455615282 455617420 0.000000e+00 3245.0
2 TraesCS4D01G216300 chr4B 89.730 185 12 3 183 365 455615029 455615208 2.110000e-56 230.0
3 TraesCS4D01G216300 chr4B 97.872 47 1 0 1 47 455614906 455614952 6.260000e-12 82.4
4 TraesCS4D01G216300 chr4A 91.286 2192 102 27 592 2728 93898841 93896684 0.000000e+00 2907.0
5 TraesCS4D01G216300 chr4A 89.700 233 14 4 193 421 93899077 93898851 3.440000e-74 289.0
6 TraesCS4D01G216300 chr4A 88.889 162 13 5 423 580 440189008 440189168 7.710000e-46 195.0
7 TraesCS4D01G216300 chr4A 84.756 164 13 5 416 578 670842524 670842676 1.310000e-33 154.0
8 TraesCS4D01G216300 chr6D 89.444 180 16 3 1132 1309 420004058 420004236 9.830000e-55 224.0
9 TraesCS4D01G216300 chr6D 84.277 159 14 5 424 580 100795806 100795955 7.880000e-31 145.0
10 TraesCS4D01G216300 chr6B 89.773 176 16 2 1132 1306 632954892 632955066 9.830000e-55 224.0
11 TraesCS4D01G216300 chr6B 83.439 157 15 3 423 578 244033295 244033149 4.740000e-28 135.0
12 TraesCS4D01G216300 chr6B 83.439 157 14 4 426 580 645980295 645980441 4.740000e-28 135.0
13 TraesCS4D01G216300 chr6A 89.444 180 16 3 1132 1309 563026354 563026532 9.830000e-55 224.0
14 TraesCS4D01G216300 chr6A 84.906 159 14 2 423 580 483551087 483551236 4.710000e-33 152.0
15 TraesCS4D01G216300 chr5D 88.957 163 15 3 423 583 72223092 72222931 5.960000e-47 198.0
16 TraesCS4D01G216300 chr5D 84.049 163 15 3 423 583 432992818 432992665 2.190000e-31 147.0
17 TraesCS4D01G216300 chr5D 83.125 160 15 7 423 580 448922730 448922879 4.740000e-28 135.0
18 TraesCS4D01G216300 chr7A 87.952 166 18 2 1128 1292 126035209 126035045 7.710000e-46 195.0
19 TraesCS4D01G216300 chr7A 92.857 98 3 4 90 184 66692297 66692201 3.660000e-29 139.0
20 TraesCS4D01G216300 chr7A 91.262 103 7 2 93 194 68186870 68186971 3.660000e-29 139.0
21 TraesCS4D01G216300 chr7A 92.784 97 6 1 92 187 708368958 708368862 3.660000e-29 139.0
22 TraesCS4D01G216300 chr7B 84.946 186 20 5 1128 1306 84220622 84220806 6.000000e-42 182.0
23 TraesCS4D01G216300 chr7B 87.395 119 10 5 73 189 640601 640486 6.130000e-27 132.0
24 TraesCS4D01G216300 chr2D 88.667 150 15 2 423 571 170610294 170610146 6.000000e-42 182.0
25 TraesCS4D01G216300 chr2D 85.625 160 11 7 423 580 549605178 549605327 1.010000e-34 158.0
26 TraesCS4D01G216300 chr2D 85.000 160 12 7 423 580 550066588 550066737 4.710000e-33 152.0
27 TraesCS4D01G216300 chr7D 84.409 186 21 4 1128 1306 123146299 123146483 2.790000e-40 176.0
28 TraesCS4D01G216300 chr7D 91.919 99 6 2 93 189 540714217 540714315 1.320000e-28 137.0
29 TraesCS4D01G216300 chr3A 83.951 162 16 3 423 583 466062929 466062777 2.190000e-31 147.0
30 TraesCS4D01G216300 chr3A 82.390 159 18 3 423 580 163792472 163792621 2.210000e-26 130.0
31 TraesCS4D01G216300 chr1B 94.624 93 3 2 99 190 666073882 666073791 2.830000e-30 143.0
32 TraesCS4D01G216300 chr1A 93.750 96 4 2 96 190 52572277 52572371 2.830000e-30 143.0
33 TraesCS4D01G216300 chr1A 82.822 163 16 4 423 583 257567008 257566856 4.740000e-28 135.0
34 TraesCS4D01G216300 chr3B 87.500 120 10 5 75 192 85623889 85623773 1.700000e-27 134.0
35 TraesCS4D01G216300 chr5A 82.317 164 17 9 422 583 270828326 270828173 6.130000e-27 132.0
36 TraesCS4D01G216300 chr2B 87.395 119 10 5 77 193 764736335 764736450 6.130000e-27 132.0
37 TraesCS4D01G216300 chr2B 79.675 123 20 4 1197 1315 1695352 1695473 1.740000e-12 84.2
38 TraesCS4D01G216300 chr3D 82.911 158 13 6 427 583 85003689 85003545 2.210000e-26 130.0


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 TraesCS4D01G216300 chr4D 370529579 370532307 2728 False 5040.0 5040 100.000 1 2729 1 chr4D.!!$F1 2728
1 TraesCS4D01G216300 chr4B 455614906 455617420 2514 False 1185.8 3245 93.953 1 2729 3 chr4B.!!$F1 2728
2 TraesCS4D01G216300 chr4A 93896684 93899077 2393 True 1598.0 2907 90.493 193 2728 2 chr4A.!!$R1 2535

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
441 506 0.03918 GGGGGTGTTTGGTTCTAGGG 59.961 60.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1875 0.319383 GATCGACTCATGGATGCGCT 60.319 55.0 9.73 0.0 0.0 5.92 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
113 142 9.771140 AATAATAATAGATACTCCCTCCGTTCT 57.229 33.333 0.00 0.00 0.00 3.01
116 145 9.597681 AATAATAGATACTCCCTCCGTTCTAAA 57.402 33.333 0.00 0.00 0.00 1.85
117 146 7.909485 AATAGATACTCCCTCCGTTCTAAAA 57.091 36.000 0.00 0.00 0.00 1.52
118 147 8.493787 AATAGATACTCCCTCCGTTCTAAAAT 57.506 34.615 0.00 0.00 0.00 1.82
119 148 9.597681 AATAGATACTCCCTCCGTTCTAAAATA 57.402 33.333 0.00 0.00 0.00 1.40
120 149 7.527568 AGATACTCCCTCCGTTCTAAAATAG 57.472 40.000 0.00 0.00 0.00 1.73
121 150 7.296098 AGATACTCCCTCCGTTCTAAAATAGA 58.704 38.462 0.00 0.00 0.00 1.98
122 151 7.951245 AGATACTCCCTCCGTTCTAAAATAGAT 59.049 37.037 0.00 0.00 34.22 1.98
123 152 6.163135 ACTCCCTCCGTTCTAAAATAGATG 57.837 41.667 0.00 0.00 34.22 2.90
124 153 5.897824 ACTCCCTCCGTTCTAAAATAGATGA 59.102 40.000 0.00 0.00 34.22 2.92
125 154 6.158023 TCCCTCCGTTCTAAAATAGATGAC 57.842 41.667 0.00 0.00 34.22 3.06
126 155 5.070047 TCCCTCCGTTCTAAAATAGATGACC 59.930 44.000 0.00 0.00 34.22 4.02
127 156 5.298347 CCTCCGTTCTAAAATAGATGACCC 58.702 45.833 0.00 0.00 34.22 4.46
128 157 5.163343 CCTCCGTTCTAAAATAGATGACCCA 60.163 44.000 0.00 0.00 34.22 4.51
129 158 6.302535 TCCGTTCTAAAATAGATGACCCAA 57.697 37.500 0.00 0.00 34.22 4.12
130 159 6.110707 TCCGTTCTAAAATAGATGACCCAAC 58.889 40.000 0.00 0.00 34.22 3.77
131 160 6.070424 TCCGTTCTAAAATAGATGACCCAACT 60.070 38.462 0.00 0.00 34.22 3.16
132 161 6.598064 CCGTTCTAAAATAGATGACCCAACTT 59.402 38.462 0.00 0.00 34.22 2.66
133 162 7.120726 CCGTTCTAAAATAGATGACCCAACTTT 59.879 37.037 0.00 0.00 34.22 2.66
134 163 8.512138 CGTTCTAAAATAGATGACCCAACTTTT 58.488 33.333 0.00 0.00 34.22 2.27
175 204 8.480643 AAGTTGAGTCATCTATTTTAGAACGG 57.519 34.615 4.14 0.00 38.50 4.44
176 205 7.837863 AGTTGAGTCATCTATTTTAGAACGGA 58.162 34.615 1.70 0.00 38.50 4.69
177 206 8.478877 AGTTGAGTCATCTATTTTAGAACGGAT 58.521 33.333 1.70 0.00 38.50 4.18
178 207 8.543774 GTTGAGTCATCTATTTTAGAACGGATG 58.456 37.037 0.00 0.00 38.50 3.51
179 208 8.007405 TGAGTCATCTATTTTAGAACGGATGA 57.993 34.615 0.00 0.00 38.50 2.92
180 209 8.474831 TGAGTCATCTATTTTAGAACGGATGAA 58.525 33.333 11.59 0.00 37.60 2.57
181 210 8.879342 AGTCATCTATTTTAGAACGGATGAAG 57.121 34.615 11.59 0.00 37.60 3.02
270 300 4.932200 AGATCTGGTTTTACAGCTCTTTCG 59.068 41.667 0.00 0.00 40.06 3.46
333 363 1.233019 GCAGCTGCCCATGTATGTAG 58.767 55.000 28.76 0.00 34.31 2.74
335 365 0.109342 AGCTGCCCATGTATGTAGGC 59.891 55.000 0.00 1.80 45.96 3.93
339 369 1.792006 GCCCATGTATGTAGGCGTAC 58.208 55.000 9.63 9.63 35.30 3.67
340 370 1.607251 GCCCATGTATGTAGGCGTACC 60.607 57.143 13.68 0.00 36.51 3.34
343 373 2.288825 CCATGTATGTAGGCGTACCCTG 60.289 54.545 13.68 2.70 45.91 4.45
344 374 2.148446 TGTATGTAGGCGTACCCTGT 57.852 50.000 13.68 1.05 45.91 4.00
345 375 2.459644 TGTATGTAGGCGTACCCTGTT 58.540 47.619 13.68 0.00 45.91 3.16
346 376 2.833338 TGTATGTAGGCGTACCCTGTTT 59.167 45.455 13.68 1.48 45.91 2.83
347 377 3.261390 TGTATGTAGGCGTACCCTGTTTT 59.739 43.478 13.68 0.11 45.91 2.43
348 378 2.460757 TGTAGGCGTACCCTGTTTTC 57.539 50.000 13.68 1.21 45.91 2.29
349 379 1.337074 TGTAGGCGTACCCTGTTTTCG 60.337 52.381 13.68 0.00 45.91 3.46
350 380 0.968405 TAGGCGTACCCTGTTTTCGT 59.032 50.000 11.85 0.00 45.91 3.85
351 381 0.107268 AGGCGTACCCTGTTTTCGTT 59.893 50.000 2.43 0.00 44.28 3.85
352 382 0.946528 GGCGTACCCTGTTTTCGTTT 59.053 50.000 0.00 0.00 0.00 3.60
353 383 1.069703 GGCGTACCCTGTTTTCGTTTC 60.070 52.381 0.00 0.00 0.00 2.78
359 389 5.220719 CGTACCCTGTTTTCGTTTCTTTTCT 60.221 40.000 0.00 0.00 0.00 2.52
418 483 1.078143 GAAGCGTCCAGGAAGGCAT 60.078 57.895 14.61 4.15 37.29 4.40
421 486 2.270205 CGTCCAGGAAGGCATGCT 59.730 61.111 18.92 0.00 37.29 3.79
422 487 2.110967 CGTCCAGGAAGGCATGCTG 61.111 63.158 18.92 7.30 46.32 4.41
425 490 2.441532 CAGGAAGGCATGCTGGGG 60.442 66.667 18.92 0.00 43.29 4.96
427 492 4.066139 GGAAGGCATGCTGGGGGT 62.066 66.667 18.92 0.00 0.00 4.95
428 493 2.757099 GAAGGCATGCTGGGGGTG 60.757 66.667 18.92 0.00 0.00 4.61
429 494 3.590466 GAAGGCATGCTGGGGGTGT 62.590 63.158 18.92 0.00 0.00 4.16
430 495 3.164610 AAGGCATGCTGGGGGTGTT 62.165 57.895 18.92 0.00 0.00 3.32
431 496 2.604382 GGCATGCTGGGGGTGTTT 60.604 61.111 18.92 0.00 0.00 2.83
432 497 2.658422 GCATGCTGGGGGTGTTTG 59.342 61.111 11.37 0.00 0.00 2.93
433 498 2.946346 GCATGCTGGGGGTGTTTGG 61.946 63.158 11.37 0.00 0.00 3.28
434 499 1.533753 CATGCTGGGGGTGTTTGGT 60.534 57.895 0.00 0.00 0.00 3.67
435 500 1.120795 CATGCTGGGGGTGTTTGGTT 61.121 55.000 0.00 0.00 0.00 3.67
436 501 0.831711 ATGCTGGGGGTGTTTGGTTC 60.832 55.000 0.00 0.00 0.00 3.62
437 502 1.152546 GCTGGGGGTGTTTGGTTCT 60.153 57.895 0.00 0.00 0.00 3.01
438 503 0.111639 GCTGGGGGTGTTTGGTTCTA 59.888 55.000 0.00 0.00 0.00 2.10
439 504 1.886655 GCTGGGGGTGTTTGGTTCTAG 60.887 57.143 0.00 0.00 0.00 2.43
440 505 0.774908 TGGGGGTGTTTGGTTCTAGG 59.225 55.000 0.00 0.00 0.00 3.02
441 506 0.039180 GGGGGTGTTTGGTTCTAGGG 59.961 60.000 0.00 0.00 0.00 3.53
442 507 1.069775 GGGGTGTTTGGTTCTAGGGA 58.930 55.000 0.00 0.00 0.00 4.20
443 508 1.271762 GGGGTGTTTGGTTCTAGGGAC 60.272 57.143 0.00 0.00 0.00 4.46
444 509 1.703513 GGGTGTTTGGTTCTAGGGACT 59.296 52.381 0.00 0.00 46.37 3.85
445 510 2.107726 GGGTGTTTGGTTCTAGGGACTT 59.892 50.000 0.00 0.00 41.75 3.01
446 511 3.436035 GGGTGTTTGGTTCTAGGGACTTT 60.436 47.826 0.00 0.00 41.75 2.66
447 512 4.212716 GGTGTTTGGTTCTAGGGACTTTT 58.787 43.478 0.00 0.00 41.75 2.27
448 513 4.647853 GGTGTTTGGTTCTAGGGACTTTTT 59.352 41.667 0.00 0.00 41.75 1.94
490 555 8.809468 AAAGTCCCTAAAATCTCTATCAAACC 57.191 34.615 0.00 0.00 0.00 3.27
491 556 7.510675 AGTCCCTAAAATCTCTATCAAACCA 57.489 36.000 0.00 0.00 0.00 3.67
492 557 7.928873 AGTCCCTAAAATCTCTATCAAACCAA 58.071 34.615 0.00 0.00 0.00 3.67
493 558 8.390921 AGTCCCTAAAATCTCTATCAAACCAAA 58.609 33.333 0.00 0.00 0.00 3.28
494 559 9.190317 GTCCCTAAAATCTCTATCAAACCAAAT 57.810 33.333 0.00 0.00 0.00 2.32
504 569 9.449719 TCTCTATCAAACCAAATAAGGAAGAAC 57.550 33.333 0.00 0.00 0.00 3.01
505 570 9.454859 CTCTATCAAACCAAATAAGGAAGAACT 57.545 33.333 0.00 0.00 0.00 3.01
506 571 9.807921 TCTATCAAACCAAATAAGGAAGAACTT 57.192 29.630 0.00 0.00 34.52 2.66
532 597 8.785329 TTTTGTGACTTTTTGCTAAAAATCCT 57.215 26.923 11.27 0.00 39.43 3.24
533 598 8.785329 TTTGTGACTTTTTGCTAAAAATCCTT 57.215 26.923 11.27 0.00 39.43 3.36
534 599 9.877178 TTTGTGACTTTTTGCTAAAAATCCTTA 57.123 25.926 11.27 0.00 39.43 2.69
535 600 9.528018 TTGTGACTTTTTGCTAAAAATCCTTAG 57.472 29.630 11.27 0.00 39.43 2.18
536 601 8.908903 TGTGACTTTTTGCTAAAAATCCTTAGA 58.091 29.630 11.27 0.00 39.43 2.10
537 602 9.744468 GTGACTTTTTGCTAAAAATCCTTAGAA 57.256 29.630 11.27 0.00 39.43 2.10
538 603 9.965824 TGACTTTTTGCTAAAAATCCTTAGAAG 57.034 29.630 11.27 0.00 39.43 2.85
539 604 8.818141 ACTTTTTGCTAAAAATCCTTAGAAGC 57.182 30.769 7.45 0.00 39.43 3.86
540 605 8.421002 ACTTTTTGCTAAAAATCCTTAGAAGCA 58.579 29.630 7.45 0.00 39.43 3.91
541 606 8.587952 TTTTTGCTAAAAATCCTTAGAAGCAC 57.412 30.769 3.49 0.00 38.15 4.40
542 607 5.897377 TGCTAAAAATCCTTAGAAGCACC 57.103 39.130 0.00 0.00 33.84 5.01
543 608 5.570320 TGCTAAAAATCCTTAGAAGCACCT 58.430 37.500 0.00 0.00 33.84 4.00
544 609 5.648092 TGCTAAAAATCCTTAGAAGCACCTC 59.352 40.000 0.00 0.00 33.84 3.85
545 610 5.883115 GCTAAAAATCCTTAGAAGCACCTCT 59.117 40.000 0.00 0.00 31.59 3.69
546 611 6.375736 GCTAAAAATCCTTAGAAGCACCTCTT 59.624 38.462 0.00 0.00 37.83 2.85
547 612 7.094162 GCTAAAAATCCTTAGAAGCACCTCTTT 60.094 37.037 0.00 0.00 34.56 2.52
548 613 9.449719 CTAAAAATCCTTAGAAGCACCTCTTTA 57.550 33.333 0.00 0.00 34.56 1.85
549 614 8.706322 AAAAATCCTTAGAAGCACCTCTTTAA 57.294 30.769 0.00 0.00 34.56 1.52
550 615 7.929941 AAATCCTTAGAAGCACCTCTTTAAG 57.070 36.000 0.00 0.00 34.56 1.85
551 616 6.875972 ATCCTTAGAAGCACCTCTTTAAGA 57.124 37.500 0.00 0.00 34.56 2.10
552 617 6.287589 TCCTTAGAAGCACCTCTTTAAGAG 57.712 41.667 14.57 14.57 41.96 2.85
553 618 5.780793 TCCTTAGAAGCACCTCTTTAAGAGT 59.219 40.000 19.16 6.30 40.72 3.24
554 619 6.071278 TCCTTAGAAGCACCTCTTTAAGAGTC 60.071 42.308 19.16 10.50 40.72 3.36
555 620 6.071051 CCTTAGAAGCACCTCTTTAAGAGTCT 60.071 42.308 19.16 16.20 40.72 3.24
556 621 5.816955 AGAAGCACCTCTTTAAGAGTCTT 57.183 39.130 19.16 17.21 40.72 3.01
557 622 6.181206 AGAAGCACCTCTTTAAGAGTCTTT 57.819 37.500 19.16 8.96 40.72 2.52
558 623 6.596621 AGAAGCACCTCTTTAAGAGTCTTTT 58.403 36.000 19.16 11.69 40.72 2.27
559 624 7.057264 AGAAGCACCTCTTTAAGAGTCTTTTT 58.943 34.615 19.16 8.06 40.72 1.94
560 625 8.211629 AGAAGCACCTCTTTAAGAGTCTTTTTA 58.788 33.333 19.16 0.00 40.72 1.52
561 626 8.747538 AAGCACCTCTTTAAGAGTCTTTTTAA 57.252 30.769 19.16 0.00 40.72 1.52
562 627 8.747538 AGCACCTCTTTAAGAGTCTTTTTAAA 57.252 30.769 19.16 5.00 40.72 1.52
563 628 9.185680 AGCACCTCTTTAAGAGTCTTTTTAAAA 57.814 29.630 19.16 4.64 40.72 1.52
564 629 9.797556 GCACCTCTTTAAGAGTCTTTTTAAAAA 57.202 29.630 19.16 12.62 40.72 1.94
574 639 9.916360 AAGAGTCTTTTTAAAAAGTCCTAAGGA 57.084 29.630 30.32 13.45 44.37 3.36
588 653 5.997384 TCCTAAGGACTAGAGAACCAAAC 57.003 43.478 0.00 0.00 0.00 2.93
589 654 5.399991 TCCTAAGGACTAGAGAACCAAACA 58.600 41.667 0.00 0.00 0.00 2.83
590 655 5.245526 TCCTAAGGACTAGAGAACCAAACAC 59.754 44.000 0.00 0.00 0.00 3.32
591 656 4.353383 AAGGACTAGAGAACCAAACACC 57.647 45.455 0.00 0.00 0.00 4.16
592 657 3.314693 AGGACTAGAGAACCAAACACCA 58.685 45.455 0.00 0.00 0.00 4.17
593 658 3.071167 AGGACTAGAGAACCAAACACCAC 59.929 47.826 0.00 0.00 0.00 4.16
594 659 3.400255 GACTAGAGAACCAAACACCACC 58.600 50.000 0.00 0.00 0.00 4.61
605 670 3.081804 CAAACACCACCTACATTCTCCC 58.918 50.000 0.00 0.00 0.00 4.30
606 671 2.038863 ACACCACCTACATTCTCCCA 57.961 50.000 0.00 0.00 0.00 4.37
616 681 1.137872 ACATTCTCCCACGAGATCTGC 59.862 52.381 0.00 0.00 44.68 4.26
829 899 1.133598 CACGCACGTACATCCTCCTAA 59.866 52.381 0.00 0.00 0.00 2.69
890 963 0.180406 CCCCTTTCCCACGATCGAAT 59.820 55.000 24.34 0.00 0.00 3.34
1194 1289 4.615815 GAGATCAGGGCGCCGCAT 62.616 66.667 22.54 12.02 0.00 4.73
1531 1638 3.680786 CCGACGTCCAGGAGCACA 61.681 66.667 10.58 0.00 0.00 4.57
1737 1844 2.306341 GCTTCTGCTAGAGTGATGCA 57.694 50.000 0.00 0.00 36.03 3.96
1739 1846 2.544686 GCTTCTGCTAGAGTGATGCATG 59.455 50.000 2.46 0.00 36.07 4.06
1740 1847 3.794717 CTTCTGCTAGAGTGATGCATGT 58.205 45.455 2.46 0.00 36.07 3.21
1741 1848 3.449528 TCTGCTAGAGTGATGCATGTC 57.550 47.619 2.46 0.00 36.07 3.06
1759 1866 2.537560 CCCGTCTGCAATGGATCGC 61.538 63.158 8.26 0.00 35.91 4.58
2023 2134 4.450976 TGTATGTCTGTATGGGTTGATGC 58.549 43.478 0.00 0.00 0.00 3.91
2232 2345 1.347707 TGTAAGTCTGCAACTCTGGGG 59.652 52.381 2.65 0.00 37.17 4.96
2237 2350 1.609072 GTCTGCAACTCTGGGGTTTTC 59.391 52.381 0.00 0.00 0.00 2.29
2285 2398 6.398234 TGCTTTCGATCTAGCTAAGATTCT 57.602 37.500 13.60 0.00 45.35 2.40
2377 2509 4.160439 CACTTACTCCAGCTAGTCATCCAA 59.840 45.833 0.00 0.00 0.00 3.53
2494 2627 2.223377 CCTAGTTCGTTGCAGGTGTTTC 59.777 50.000 0.00 0.00 0.00 2.78
2644 2777 5.230942 AGAAACAGCTGTATGACTGTACAC 58.769 41.667 22.01 0.00 46.17 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.339141 AGCAAGAGTTTAGCTGCCTAAC 58.661 45.455 0.00 0.92 37.20 2.34
91 120 9.597681 TTTTAGAACGGAGGGAGTATCTATTAT 57.402 33.333 0.00 0.00 33.73 1.28
92 121 9.597681 ATTTTAGAACGGAGGGAGTATCTATTA 57.402 33.333 0.00 0.00 33.73 0.98
93 122 7.909485 TTTTAGAACGGAGGGAGTATCTATT 57.091 36.000 0.00 0.00 33.73 1.73
95 124 8.443176 TCTATTTTAGAACGGAGGGAGTATCTA 58.557 37.037 0.00 0.00 33.73 1.98
96 125 7.296098 TCTATTTTAGAACGGAGGGAGTATCT 58.704 38.462 0.00 0.00 33.73 1.98
97 126 7.521871 TCTATTTTAGAACGGAGGGAGTATC 57.478 40.000 0.00 0.00 0.00 2.24
98 127 7.728981 TCATCTATTTTAGAACGGAGGGAGTAT 59.271 37.037 0.00 0.00 38.50 2.12
99 128 7.014038 GTCATCTATTTTAGAACGGAGGGAGTA 59.986 40.741 0.00 0.00 38.50 2.59
100 129 5.897824 TCATCTATTTTAGAACGGAGGGAGT 59.102 40.000 0.00 0.00 38.50 3.85
101 130 6.217294 GTCATCTATTTTAGAACGGAGGGAG 58.783 44.000 0.00 0.00 38.50 4.30
102 131 5.070047 GGTCATCTATTTTAGAACGGAGGGA 59.930 44.000 0.00 0.00 38.50 4.20
103 132 5.298347 GGTCATCTATTTTAGAACGGAGGG 58.702 45.833 0.00 0.00 38.50 4.30
104 133 5.163343 TGGGTCATCTATTTTAGAACGGAGG 60.163 44.000 0.00 0.00 38.50 4.30
105 134 5.914033 TGGGTCATCTATTTTAGAACGGAG 58.086 41.667 0.00 0.00 38.50 4.63
106 135 5.943349 TGGGTCATCTATTTTAGAACGGA 57.057 39.130 0.00 0.00 38.50 4.69
107 136 6.113411 AGTTGGGTCATCTATTTTAGAACGG 58.887 40.000 0.00 0.00 38.50 4.44
108 137 7.611213 AAGTTGGGTCATCTATTTTAGAACG 57.389 36.000 0.00 0.00 38.50 3.95
149 178 8.936864 CCGTTCTAAAATAGATGACTCAACTTT 58.063 33.333 0.00 0.00 34.22 2.66
150 179 8.311836 TCCGTTCTAAAATAGATGACTCAACTT 58.688 33.333 0.00 0.00 34.22 2.66
151 180 7.837863 TCCGTTCTAAAATAGATGACTCAACT 58.162 34.615 0.00 0.00 34.22 3.16
152 181 8.543774 CATCCGTTCTAAAATAGATGACTCAAC 58.456 37.037 0.00 0.00 34.22 3.18
153 182 8.474831 TCATCCGTTCTAAAATAGATGACTCAA 58.525 33.333 0.00 0.00 33.94 3.02
154 183 8.007405 TCATCCGTTCTAAAATAGATGACTCA 57.993 34.615 0.00 0.00 33.94 3.41
155 184 8.873215 TTCATCCGTTCTAAAATAGATGACTC 57.127 34.615 0.00 0.00 36.40 3.36
156 185 8.478877 ACTTCATCCGTTCTAAAATAGATGACT 58.521 33.333 0.00 0.00 36.40 3.41
157 186 8.649973 ACTTCATCCGTTCTAAAATAGATGAC 57.350 34.615 0.00 0.00 36.40 3.06
167 196 9.976511 CCTTACATAATACTTCATCCGTTCTAA 57.023 33.333 0.00 0.00 0.00 2.10
168 197 8.086522 GCCTTACATAATACTTCATCCGTTCTA 58.913 37.037 0.00 0.00 0.00 2.10
169 198 6.929606 GCCTTACATAATACTTCATCCGTTCT 59.070 38.462 0.00 0.00 0.00 3.01
170 199 6.929606 AGCCTTACATAATACTTCATCCGTTC 59.070 38.462 0.00 0.00 0.00 3.95
171 200 6.827727 AGCCTTACATAATACTTCATCCGTT 58.172 36.000 0.00 0.00 0.00 4.44
172 201 6.420913 AGCCTTACATAATACTTCATCCGT 57.579 37.500 0.00 0.00 0.00 4.69
173 202 7.730364 AAAGCCTTACATAATACTTCATCCG 57.270 36.000 0.00 0.00 0.00 4.18
174 203 8.568794 GGAAAAGCCTTACATAATACTTCATCC 58.431 37.037 0.00 0.00 0.00 3.51
175 204 8.568794 GGGAAAAGCCTTACATAATACTTCATC 58.431 37.037 0.00 0.00 36.66 2.92
176 205 7.228706 CGGGAAAAGCCTTACATAATACTTCAT 59.771 37.037 0.00 0.00 36.66 2.57
177 206 6.540914 CGGGAAAAGCCTTACATAATACTTCA 59.459 38.462 0.00 0.00 36.66 3.02
178 207 6.541278 ACGGGAAAAGCCTTACATAATACTTC 59.459 38.462 0.00 0.00 36.66 3.01
179 208 6.420638 ACGGGAAAAGCCTTACATAATACTT 58.579 36.000 0.00 0.00 36.66 2.24
180 209 5.997843 ACGGGAAAAGCCTTACATAATACT 58.002 37.500 0.00 0.00 36.66 2.12
181 210 6.316890 TGAACGGGAAAAGCCTTACATAATAC 59.683 38.462 0.00 0.00 36.66 1.89
188 217 3.254903 ACAATGAACGGGAAAAGCCTTAC 59.745 43.478 0.00 0.00 36.66 2.34
191 220 1.995376 ACAATGAACGGGAAAAGCCT 58.005 45.000 0.00 0.00 36.66 4.58
270 300 6.319405 TCGGAAAACCTATAATTAAAGCCACC 59.681 38.462 0.00 0.00 0.00 4.61
327 357 3.429272 CGAAAACAGGGTACGCCTACATA 60.429 47.826 6.27 0.00 34.45 2.29
328 358 2.675889 CGAAAACAGGGTACGCCTACAT 60.676 50.000 6.27 0.00 34.45 2.29
333 363 0.946528 AAACGAAAACAGGGTACGCC 59.053 50.000 6.27 0.00 0.00 5.68
335 365 4.541085 AAAGAAACGAAAACAGGGTACG 57.459 40.909 0.00 0.00 0.00 3.67
336 366 6.127810 AGAAAAGAAACGAAAACAGGGTAC 57.872 37.500 0.00 0.00 0.00 3.34
337 367 6.762702 AAGAAAAGAAACGAAAACAGGGTA 57.237 33.333 0.00 0.00 0.00 3.69
338 368 5.654603 AAGAAAAGAAACGAAAACAGGGT 57.345 34.783 0.00 0.00 0.00 4.34
339 369 6.811665 AGAAAAGAAAAGAAACGAAAACAGGG 59.188 34.615 0.00 0.00 0.00 4.45
340 370 7.812309 AGAAAAGAAAAGAAACGAAAACAGG 57.188 32.000 0.00 0.00 0.00 4.00
351 381 8.860128 GCGAGAAAAGAAAAGAAAAGAAAAGAA 58.140 29.630 0.00 0.00 0.00 2.52
352 382 7.488150 GGCGAGAAAAGAAAAGAAAAGAAAAGA 59.512 33.333 0.00 0.00 0.00 2.52
353 383 7.275560 TGGCGAGAAAAGAAAAGAAAAGAAAAG 59.724 33.333 0.00 0.00 0.00 2.27
359 389 5.317733 TGTGGCGAGAAAAGAAAAGAAAA 57.682 34.783 0.00 0.00 0.00 2.29
418 483 1.456705 GAACCAAACACCCCCAGCA 60.457 57.895 0.00 0.00 0.00 4.41
421 486 0.774908 CCTAGAACCAAACACCCCCA 59.225 55.000 0.00 0.00 0.00 4.96
422 487 0.039180 CCCTAGAACCAAACACCCCC 59.961 60.000 0.00 0.00 0.00 5.40
423 488 1.069775 TCCCTAGAACCAAACACCCC 58.930 55.000 0.00 0.00 0.00 4.95
424 489 1.703513 AGTCCCTAGAACCAAACACCC 59.296 52.381 0.00 0.00 0.00 4.61
425 490 3.503800 AAGTCCCTAGAACCAAACACC 57.496 47.619 0.00 0.00 0.00 4.16
464 529 9.244292 GGTTTGATAGAGATTTTAGGGACTTTT 57.756 33.333 0.00 0.00 41.75 2.27
465 530 8.390921 TGGTTTGATAGAGATTTTAGGGACTTT 58.609 33.333 0.00 0.00 41.75 2.66
466 531 7.928873 TGGTTTGATAGAGATTTTAGGGACTT 58.071 34.615 0.00 0.00 41.75 3.01
467 532 7.510675 TGGTTTGATAGAGATTTTAGGGACT 57.489 36.000 0.00 0.00 46.37 3.85
468 533 8.575649 TTTGGTTTGATAGAGATTTTAGGGAC 57.424 34.615 0.00 0.00 0.00 4.46
478 543 9.449719 GTTCTTCCTTATTTGGTTTGATAGAGA 57.550 33.333 0.00 0.00 0.00 3.10
479 544 9.454859 AGTTCTTCCTTATTTGGTTTGATAGAG 57.545 33.333 0.00 0.00 0.00 2.43
480 545 9.807921 AAGTTCTTCCTTATTTGGTTTGATAGA 57.192 29.630 0.00 0.00 0.00 1.98
506 571 9.225436 AGGATTTTTAGCAAAAAGTCACAAAAA 57.775 25.926 10.88 0.00 42.97 1.94
507 572 8.785329 AGGATTTTTAGCAAAAAGTCACAAAA 57.215 26.923 10.88 0.00 42.97 2.44
508 573 8.785329 AAGGATTTTTAGCAAAAAGTCACAAA 57.215 26.923 10.88 0.00 42.97 2.83
509 574 9.528018 CTAAGGATTTTTAGCAAAAAGTCACAA 57.472 29.630 10.88 0.00 42.97 3.33
510 575 8.908903 TCTAAGGATTTTTAGCAAAAAGTCACA 58.091 29.630 10.88 0.25 42.97 3.58
511 576 9.744468 TTCTAAGGATTTTTAGCAAAAAGTCAC 57.256 29.630 10.88 0.26 42.97 3.67
512 577 9.965824 CTTCTAAGGATTTTTAGCAAAAAGTCA 57.034 29.630 10.88 0.00 42.97 3.41
513 578 8.916654 GCTTCTAAGGATTTTTAGCAAAAAGTC 58.083 33.333 10.88 0.42 42.97 3.01
514 579 8.421002 TGCTTCTAAGGATTTTTAGCAAAAAGT 58.579 29.630 10.88 0.00 42.97 2.66
515 580 8.703336 GTGCTTCTAAGGATTTTTAGCAAAAAG 58.297 33.333 0.00 0.00 42.97 2.27
516 581 7.655732 GGTGCTTCTAAGGATTTTTAGCAAAAA 59.344 33.333 0.00 8.54 43.76 1.94
517 582 7.015195 AGGTGCTTCTAAGGATTTTTAGCAAAA 59.985 33.333 0.00 0.00 38.69 2.44
518 583 6.493458 AGGTGCTTCTAAGGATTTTTAGCAAA 59.507 34.615 0.00 0.00 38.69 3.68
519 584 6.010219 AGGTGCTTCTAAGGATTTTTAGCAA 58.990 36.000 0.00 0.00 38.69 3.91
520 585 5.570320 AGGTGCTTCTAAGGATTTTTAGCA 58.430 37.500 0.00 0.00 35.05 3.49
521 586 5.883115 AGAGGTGCTTCTAAGGATTTTTAGC 59.117 40.000 0.00 0.00 32.01 3.09
522 587 7.929941 AAGAGGTGCTTCTAAGGATTTTTAG 57.070 36.000 0.00 0.00 28.17 1.85
523 588 9.802039 TTAAAGAGGTGCTTCTAAGGATTTTTA 57.198 29.630 0.00 0.00 35.24 1.52
524 589 8.706322 TTAAAGAGGTGCTTCTAAGGATTTTT 57.294 30.769 0.00 0.00 35.24 1.94
525 590 8.164070 TCTTAAAGAGGTGCTTCTAAGGATTTT 58.836 33.333 0.00 0.00 35.24 1.82
526 591 7.690256 TCTTAAAGAGGTGCTTCTAAGGATTT 58.310 34.615 0.00 0.00 35.24 2.17
527 592 7.037945 ACTCTTAAAGAGGTGCTTCTAAGGATT 60.038 37.037 0.00 0.00 46.45 3.01
528 593 6.442244 ACTCTTAAAGAGGTGCTTCTAAGGAT 59.558 38.462 0.00 0.00 46.45 3.24
529 594 5.780793 ACTCTTAAAGAGGTGCTTCTAAGGA 59.219 40.000 0.00 0.00 46.45 3.36
530 595 6.043854 ACTCTTAAAGAGGTGCTTCTAAGG 57.956 41.667 0.00 0.00 46.45 2.69
531 596 6.930731 AGACTCTTAAAGAGGTGCTTCTAAG 58.069 40.000 0.00 0.00 46.45 2.18
532 597 6.919775 AGACTCTTAAAGAGGTGCTTCTAA 57.080 37.500 0.00 0.00 46.45 2.10
533 598 6.919775 AAGACTCTTAAAGAGGTGCTTCTA 57.080 37.500 0.00 0.00 46.45 2.10
534 599 5.816955 AAGACTCTTAAAGAGGTGCTTCT 57.183 39.130 0.00 0.00 46.45 2.85
535 600 6.869315 AAAAGACTCTTAAAGAGGTGCTTC 57.131 37.500 0.00 0.00 46.45 3.86
536 601 8.747538 TTAAAAAGACTCTTAAAGAGGTGCTT 57.252 30.769 0.00 0.00 46.45 3.91
537 602 8.747538 TTTAAAAAGACTCTTAAAGAGGTGCT 57.252 30.769 0.00 0.00 46.45 4.40
538 603 9.797556 TTTTTAAAAAGACTCTTAAAGAGGTGC 57.202 29.630 9.31 0.00 46.45 5.01
548 613 9.916360 TCCTTAGGACTTTTTAAAAAGACTCTT 57.084 29.630 35.81 24.95 46.39 2.85
566 631 5.245526 GTGTTTGGTTCTCTAGTCCTTAGGA 59.754 44.000 0.00 0.00 0.00 2.94
567 632 5.480205 GTGTTTGGTTCTCTAGTCCTTAGG 58.520 45.833 0.00 0.00 0.00 2.69
568 633 5.011738 TGGTGTTTGGTTCTCTAGTCCTTAG 59.988 44.000 0.00 0.00 0.00 2.18
569 634 4.903049 TGGTGTTTGGTTCTCTAGTCCTTA 59.097 41.667 0.00 0.00 0.00 2.69
570 635 3.714798 TGGTGTTTGGTTCTCTAGTCCTT 59.285 43.478 0.00 0.00 0.00 3.36
571 636 3.071167 GTGGTGTTTGGTTCTCTAGTCCT 59.929 47.826 0.00 0.00 0.00 3.85
572 637 3.400255 GTGGTGTTTGGTTCTCTAGTCC 58.600 50.000 0.00 0.00 0.00 3.85
573 638 3.071167 AGGTGGTGTTTGGTTCTCTAGTC 59.929 47.826 0.00 0.00 0.00 2.59
574 639 3.046374 AGGTGGTGTTTGGTTCTCTAGT 58.954 45.455 0.00 0.00 0.00 2.57
575 640 3.771577 AGGTGGTGTTTGGTTCTCTAG 57.228 47.619 0.00 0.00 0.00 2.43
576 641 3.968649 TGTAGGTGGTGTTTGGTTCTCTA 59.031 43.478 0.00 0.00 0.00 2.43
577 642 2.775384 TGTAGGTGGTGTTTGGTTCTCT 59.225 45.455 0.00 0.00 0.00 3.10
578 643 3.202829 TGTAGGTGGTGTTTGGTTCTC 57.797 47.619 0.00 0.00 0.00 2.87
579 644 3.876309 ATGTAGGTGGTGTTTGGTTCT 57.124 42.857 0.00 0.00 0.00 3.01
580 645 4.142038 AGAATGTAGGTGGTGTTTGGTTC 58.858 43.478 0.00 0.00 0.00 3.62
581 646 4.142038 GAGAATGTAGGTGGTGTTTGGTT 58.858 43.478 0.00 0.00 0.00 3.67
582 647 3.497942 GGAGAATGTAGGTGGTGTTTGGT 60.498 47.826 0.00 0.00 0.00 3.67
583 648 3.081804 GGAGAATGTAGGTGGTGTTTGG 58.918 50.000 0.00 0.00 0.00 3.28
584 649 3.081804 GGGAGAATGTAGGTGGTGTTTG 58.918 50.000 0.00 0.00 0.00 2.93
585 650 2.714250 TGGGAGAATGTAGGTGGTGTTT 59.286 45.455 0.00 0.00 0.00 2.83
586 651 2.039879 GTGGGAGAATGTAGGTGGTGTT 59.960 50.000 0.00 0.00 0.00 3.32
587 652 1.628846 GTGGGAGAATGTAGGTGGTGT 59.371 52.381 0.00 0.00 0.00 4.16
588 653 1.405526 CGTGGGAGAATGTAGGTGGTG 60.406 57.143 0.00 0.00 0.00 4.17
589 654 0.902531 CGTGGGAGAATGTAGGTGGT 59.097 55.000 0.00 0.00 0.00 4.16
590 655 1.137086 CTCGTGGGAGAATGTAGGTGG 59.863 57.143 0.00 0.00 43.27 4.61
591 656 2.100197 TCTCGTGGGAGAATGTAGGTG 58.900 52.381 0.00 0.00 46.11 4.00
592 657 2.526888 TCTCGTGGGAGAATGTAGGT 57.473 50.000 0.00 0.00 46.11 3.08
605 670 1.537638 AGCGTATAGGCAGATCTCGTG 59.462 52.381 18.89 0.00 34.64 4.35
606 671 1.807742 GAGCGTATAGGCAGATCTCGT 59.192 52.381 18.89 0.00 34.64 4.18
616 681 4.386867 TGTTTGAGAAGGAGCGTATAGG 57.613 45.455 0.00 0.00 0.00 2.57
829 899 2.859806 GCAAAGTCACCACGTACGTACT 60.860 50.000 22.34 17.70 0.00 2.73
890 963 2.223947 TGAACTGAACGCTGCTAGTGAA 60.224 45.455 0.00 0.00 0.00 3.18
1047 1142 3.136750 CTCTCTGCCATAGCCGCT 58.863 61.111 0.00 0.00 38.69 5.52
1194 1289 2.496341 CAGATCCGGCGCTTCTGA 59.504 61.111 24.28 8.17 39.36 3.27
1363 1470 1.993391 GGATGGACCTCGGGGACAA 60.993 63.158 9.33 0.00 36.25 3.18
1531 1638 1.211969 CGGACATCGAAGACGTGGT 59.788 57.895 0.00 0.00 42.51 4.16
1574 1681 2.024871 GCTCGTCGTGATCTCCCG 59.975 66.667 0.00 0.00 0.00 5.14
1734 1841 1.002257 ATTGCAGACGGGACATGCA 60.002 52.632 0.00 0.00 0.00 3.96
1737 1844 0.548031 ATCCATTGCAGACGGGACAT 59.452 50.000 0.59 0.00 31.04 3.06
1739 1846 1.154205 CGATCCATTGCAGACGGGAC 61.154 60.000 0.59 0.00 31.04 4.46
1740 1847 1.143838 CGATCCATTGCAGACGGGA 59.856 57.895 1.03 1.03 0.00 5.14
1741 1848 2.537560 GCGATCCATTGCAGACGGG 61.538 63.158 0.00 0.00 37.15 5.28
1759 1866 2.815503 TCATGGATGCGCTTATCAATGG 59.184 45.455 19.62 6.69 38.49 3.16
1768 1875 0.319383 GATCGACTCATGGATGCGCT 60.319 55.000 9.73 0.00 0.00 5.92
2023 2134 1.642037 CCAATGCAGCCAGTCTCACG 61.642 60.000 0.00 0.00 0.00 4.35
2133 2246 1.204312 GAGACACAAAGCGCGTTCC 59.796 57.895 8.43 0.00 0.00 3.62
2290 2403 8.738106 AGCTAGATCATCCTCAAAAAGAAAAAG 58.262 33.333 0.00 0.00 0.00 2.27
2377 2509 6.037172 GTGTGAACACTGAACAGACTTAACAT 59.963 38.462 8.87 0.00 43.25 2.71
2634 2767 1.467342 CACCGAGATCGTGTACAGTCA 59.533 52.381 0.00 0.00 37.74 3.41
2640 2773 3.865446 TCTTAGACACCGAGATCGTGTA 58.135 45.455 5.04 0.00 35.16 2.90
2644 2777 4.822036 AGATTCTTAGACACCGAGATCG 57.178 45.455 0.00 0.00 39.44 3.69


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

AutoCloner maintained by Alex Coulton.