Multiple sequence alignment - TraesCS4D01G064600

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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 TraesCS4D01G064600 chr4D 100.000 3281 0 0 1 3281 39985762 39982482 0.000000e+00 6059.0
1 TraesCS4D01G064600 chr4D 81.402 328 47 8 18 340 16118227 16118545 4.200000e-64 255.0
2 TraesCS4D01G064600 chr4B 91.670 2653 158 30 449 3089 58254986 58252385 0.000000e+00 3616.0
3 TraesCS4D01G064600 chr4B 83.807 457 63 6 2 455 58255498 58255050 1.090000e-114 424.0
4 TraesCS4D01G064600 chr4B 90.732 205 9 6 3076 3280 58252365 58252171 6.980000e-67 265.0
5 TraesCS4D01G064600 chr4A 92.722 2487 146 13 556 3019 560313775 560316249 0.000000e+00 3557.0
6 TraesCS4D01G064600 chr4A 91.304 230 11 4 3052 3281 560316464 560316684 4.110000e-79 305.0
7 TraesCS4D01G064600 chr5D 82.749 371 53 5 12 380 25041502 25041863 1.470000e-83 320.0
8 TraesCS4D01G064600 chr2D 80.045 446 68 10 12 455 423615319 423614893 8.840000e-81 311.0
9 TraesCS4D01G064600 chr2D 82.768 354 50 6 30 380 620533128 620532783 4.110000e-79 305.0
10 TraesCS4D01G064600 chr2D 76.263 396 80 10 65 455 582695902 582695516 7.180000e-47 198.0
11 TraesCS4D01G064600 chr2D 81.034 116 9 7 449 562 598021725 598021829 2.710000e-11 80.5
12 TraesCS4D01G064600 chr2D 97.368 38 1 0 535 572 531496200 531496237 7.600000e-07 65.8
13 TraesCS4D01G064600 chr1D 79.684 443 79 5 16 455 465879545 465879979 3.180000e-80 309.0
14 TraesCS4D01G064600 chr1D 79.254 429 70 14 16 438 62440267 62439852 6.930000e-72 281.0
15 TraesCS4D01G064600 chr1D 81.633 147 23 4 449 592 375372598 375372453 5.750000e-23 119.0
16 TraesCS4D01G064600 chr1D 80.556 144 27 1 312 455 467814337 467814479 3.460000e-20 110.0
17 TraesCS4D01G064600 chr6B 79.372 446 72 11 12 455 200512862 200512435 2.480000e-76 296.0
18 TraesCS4D01G064600 chr6A 78.636 440 83 5 16 452 604873700 604874131 6.930000e-72 281.0
19 TraesCS4D01G064600 chr7B 78.634 454 70 17 12 453 698926502 698926064 3.220000e-70 276.0
20 TraesCS4D01G064600 chr7B 77.435 421 71 14 44 453 693389818 693389411 2.550000e-56 230.0
21 TraesCS4D01G064600 chr7B 77.215 158 33 3 298 454 6890150 6889995 4.510000e-14 89.8
22 TraesCS4D01G064600 chr7B 78.571 140 24 5 459 596 36856851 36856716 1.620000e-13 87.9
23 TraesCS4D01G064600 chr7D 78.873 284 47 7 177 455 72119304 72119029 2.600000e-41 180.0
24 TraesCS4D01G064600 chr2B 74.559 397 82 13 65 455 701752583 701752200 4.380000e-34 156.0
25 TraesCS4D01G064600 chr7A 80.137 146 26 3 312 455 529277347 529277491 4.480000e-19 106.0
26 TraesCS4D01G064600 chr6D 79.861 144 24 4 309 452 330115536 330115674 2.080000e-17 100.0
27 TraesCS4D01G064600 chr6D 83.529 85 12 2 479 562 330115756 330115839 9.760000e-11 78.7
28 TraesCS4D01G064600 chr2A 79.630 108 20 2 490 596 748959187 748959293 3.510000e-10 76.8
29 TraesCS4D01G064600 chr3D 85.294 68 5 4 530 597 537166753 537166691 7.600000e-07 65.8
30 TraesCS4D01G064600 chr3D 92.857 42 3 0 530 571 105144298 105144339 9.830000e-06 62.1


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 TraesCS4D01G064600 chr4D 39982482 39985762 3280 True 6059 6059 100.000000 1 3281 1 chr4D.!!$R1 3280
1 TraesCS4D01G064600 chr4B 58252171 58255498 3327 True 1435 3616 88.736333 2 3280 3 chr4B.!!$R1 3278
2 TraesCS4D01G064600 chr4A 560313775 560316684 2909 False 1931 3557 92.013000 556 3281 2 chr4A.!!$F1 2725

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
426 428 0.039617 TTTGGTTCGGCAAGCGAATG 60.040 50.0 0.00 0.0 29.87 2.67 F
537 611 0.243907 TTCGCTACTGCTCAGTGACC 59.756 55.0 12.43 0.7 42.52 4.02 F
1319 1397 0.606401 CTGTTCAGGGCCATGTTCGT 60.606 55.0 18.43 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1770 0.536460 GCCCGTCTTCAACCTTTCCA 60.536 55.000 0.00 0.00 0.00 3.53 R
1923 2001 1.153469 CTTCTCGAGCTCCTTGGCC 60.153 63.158 7.81 0.00 0.00 5.36 R
3139 3476 1.398390 AGAATTTGGTTCGCTGATCGC 59.602 47.619 0.23 0.23 41.84 4.58 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
59 60 4.966787 GCCAACGGAGGGGTTGCA 62.967 66.667 0.09 0.00 44.58 4.08
70 71 2.668550 GGTTGCACGTCCTCCACC 60.669 66.667 0.00 0.00 0.00 4.61
71 72 3.041940 GTTGCACGTCCTCCACCG 61.042 66.667 0.00 0.00 0.00 4.94
97 98 1.626654 GACATCAGTTGGACCGCACG 61.627 60.000 0.00 0.00 0.00 5.34
119 120 4.742201 CCGGTGAGGCAGTGACGG 62.742 72.222 0.00 0.00 35.01 4.79
142 143 1.945394 CAACTAGTGCCAGATCCATGC 59.055 52.381 0.00 0.00 0.00 4.06
152 153 1.411246 CAGATCCATGCACCATTTGGG 59.589 52.381 3.50 0.00 44.81 4.12
168 169 0.679640 TGGGTGGACGCAATGGATTC 60.680 55.000 0.00 0.00 35.80 2.52
170 171 0.394352 GGTGGACGCAATGGATTCCT 60.394 55.000 3.95 0.00 0.00 3.36
200 201 4.827087 CCGAGCGCTGCCTCACAT 62.827 66.667 18.48 0.00 0.00 3.21
201 202 2.104928 CGAGCGCTGCCTCACATA 59.895 61.111 18.48 0.00 0.00 2.29
203 204 2.202987 AGCGCTGCCTCACATAGC 60.203 61.111 10.39 0.00 0.00 2.97
204 205 2.512286 GCGCTGCCTCACATAGCA 60.512 61.111 0.00 0.00 37.29 3.49
205 206 1.890979 GCGCTGCCTCACATAGCAT 60.891 57.895 0.00 0.00 38.56 3.79
206 207 1.839598 GCGCTGCCTCACATAGCATC 61.840 60.000 0.00 0.00 38.56 3.91
207 208 1.226686 CGCTGCCTCACATAGCATCC 61.227 60.000 0.00 0.00 38.56 3.51
273 275 4.147449 CCGCGTGGGATGAGCTCA 62.147 66.667 20.79 20.79 38.47 4.26
275 277 2.202987 GCGTGGGATGAGCTCAGG 60.203 66.667 22.96 5.13 35.96 3.86
280 282 2.107953 GGATGAGCTCAGGGTCGC 59.892 66.667 22.96 6.73 42.30 5.19
282 284 2.364842 ATGAGCTCAGGGTCGCCT 60.365 61.111 22.96 0.00 42.30 5.52
288 290 1.109920 GCTCAGGGTCGCCTGATCTA 61.110 60.000 11.61 0.00 44.48 1.98
289 291 1.403814 CTCAGGGTCGCCTGATCTAA 58.596 55.000 11.61 0.00 44.48 2.10
290 292 1.757118 CTCAGGGTCGCCTGATCTAAA 59.243 52.381 11.61 0.00 44.48 1.85
291 293 2.168521 CTCAGGGTCGCCTGATCTAAAA 59.831 50.000 11.61 0.00 44.48 1.52
292 294 2.569853 TCAGGGTCGCCTGATCTAAAAA 59.430 45.455 7.61 0.00 41.27 1.94
314 316 0.382515 GAGGTGGAGGACTCGAATCG 59.617 60.000 0.00 0.00 0.00 3.34
367 369 2.741092 GGACGGGAGCTTGTGTGA 59.259 61.111 0.00 0.00 0.00 3.58
369 371 2.022129 GACGGGAGCTTGTGTGACG 61.022 63.158 0.00 0.00 0.00 4.35
373 375 1.666011 GGAGCTTGTGTGACGGAGA 59.334 57.895 0.00 0.00 0.00 3.71
381 383 1.202842 TGTGTGACGGAGAGGAGTGTA 60.203 52.381 0.00 0.00 0.00 2.90
382 384 1.884579 GTGTGACGGAGAGGAGTGTAA 59.115 52.381 0.00 0.00 0.00 2.41
390 392 2.104170 GAGAGGAGTGTAAGGGAGTGG 58.896 57.143 0.00 0.00 0.00 4.00
406 408 1.978580 AGTGGAGTGAAGTGGTTAGGG 59.021 52.381 0.00 0.00 0.00 3.53
413 415 3.053170 AGTGAAGTGGTTAGGGTTTGGTT 60.053 43.478 0.00 0.00 0.00 3.67
421 423 0.891904 TAGGGTTTGGTTCGGCAAGC 60.892 55.000 0.00 0.00 0.00 4.01
423 425 2.548295 GGTTTGGTTCGGCAAGCGA 61.548 57.895 0.00 0.00 32.20 4.93
426 428 0.039617 TTTGGTTCGGCAAGCGAATG 60.040 50.000 0.00 0.00 29.87 2.67
429 431 2.038269 GTTCGGCAAGCGAATGGGA 61.038 57.895 0.00 0.00 0.00 4.37
432 434 1.745115 CGGCAAGCGAATGGGAAGA 60.745 57.895 0.00 0.00 0.00 2.87
440 442 6.374333 GGCAAGCGAATGGGAAGAAATATATA 59.626 38.462 0.00 0.00 0.00 0.86
467 540 2.595655 GTGGGTATGAGGGGTGCC 59.404 66.667 0.00 0.00 0.00 5.01
469 542 3.873812 GGGTATGAGGGGTGCCGG 61.874 72.222 0.00 0.00 0.00 6.13
473 546 2.063979 TATGAGGGGTGCCGGTCAG 61.064 63.158 1.90 0.00 0.00 3.51
487 561 3.532896 GTCAGCCCGACATTTGAGA 57.467 52.632 0.00 0.00 44.69 3.27
495 569 3.581755 CCCGACATTTGAGACTCGTTTA 58.418 45.455 0.00 0.00 0.00 2.01
505 579 0.387750 GACTCGTTTAAGGCGTCCGT 60.388 55.000 0.00 0.00 0.00 4.69
510 584 1.017701 GTTTAAGGCGTCCGTCTGGG 61.018 60.000 0.00 0.00 35.24 4.45
516 590 2.315386 GCGTCCGTCTGGGTCAAAC 61.315 63.158 0.00 0.00 37.00 2.93
523 597 1.594331 GTCTGGGTCAAACTTTCGCT 58.406 50.000 0.00 0.00 0.00 4.93
524 598 2.762745 GTCTGGGTCAAACTTTCGCTA 58.237 47.619 0.00 0.00 0.00 4.26
526 600 2.367567 TCTGGGTCAAACTTTCGCTACT 59.632 45.455 0.00 0.00 0.00 2.57
528 602 1.197036 GGGTCAAACTTTCGCTACTGC 59.803 52.381 0.00 0.00 0.00 4.40
532 606 3.059884 TCAAACTTTCGCTACTGCTCAG 58.940 45.455 0.00 0.00 36.97 3.35
534 608 2.071688 ACTTTCGCTACTGCTCAGTG 57.928 50.000 12.43 4.40 42.52 3.66
535 609 1.613925 ACTTTCGCTACTGCTCAGTGA 59.386 47.619 12.43 0.00 42.52 3.41
536 610 1.989165 CTTTCGCTACTGCTCAGTGAC 59.011 52.381 12.43 3.87 42.52 3.67
537 611 0.243907 TTCGCTACTGCTCAGTGACC 59.756 55.000 12.43 0.70 42.52 4.02
538 612 1.515088 CGCTACTGCTCAGTGACCG 60.515 63.158 12.43 8.18 42.52 4.79
539 613 1.153745 GCTACTGCTCAGTGACCGG 60.154 63.158 12.43 0.00 42.52 5.28
540 614 1.513158 CTACTGCTCAGTGACCGGG 59.487 63.158 6.32 0.00 42.52 5.73
541 615 2.564553 CTACTGCTCAGTGACCGGGC 62.565 65.000 6.32 1.57 42.52 6.13
562 636 4.367023 CCGCCCGGACGTTTGAGA 62.367 66.667 9.94 0.00 37.50 3.27
576 650 3.454375 GTTTGAGACAGGTTTGAGACGA 58.546 45.455 0.00 0.00 0.00 4.20
577 651 2.795175 TGAGACAGGTTTGAGACGAC 57.205 50.000 0.00 0.00 0.00 4.34
578 652 1.001706 TGAGACAGGTTTGAGACGACG 60.002 52.381 0.00 0.00 0.00 5.12
586 660 1.804396 TTTGAGACGACGGGCGGTAA 61.804 55.000 8.66 0.00 46.49 2.85
627 704 4.174762 GCACCGTTTGACTTAAACCAAAA 58.825 39.130 4.18 0.00 44.62 2.44
651 728 9.599866 AAATTACAAGGTTCTCTTTTTCAAAGG 57.400 29.630 0.00 0.00 32.41 3.11
661 738 2.292828 TTTTCAAAGGCAGAGAGGGG 57.707 50.000 0.00 0.00 0.00 4.79
689 766 1.743252 CAGCAACTCGGCCCTCTTC 60.743 63.158 0.00 0.00 0.00 2.87
1319 1397 0.606401 CTGTTCAGGGCCATGTTCGT 60.606 55.000 18.43 0.00 0.00 3.85
1488 1566 2.080693 CTGGTAAGCATGTACGCCAAA 58.919 47.619 0.00 0.00 0.00 3.28
1500 1578 4.440127 GCCAAATGCGGGTGCCTG 62.440 66.667 0.00 0.00 41.78 4.85
1560 1638 0.902984 ATGAGTACGTCTGGGGCACA 60.903 55.000 0.00 0.00 0.00 4.57
1566 1644 1.603455 CGTCTGGGGCACAATGGTT 60.603 57.895 0.00 0.00 0.00 3.67
1569 1647 1.228831 CTGGGGCACAATGGTTGGA 60.229 57.895 0.00 0.00 34.12 3.53
1734 1812 1.480137 AGACTTCTCAAGGAGATGCGG 59.520 52.381 8.53 0.00 38.56 5.69
1797 1875 2.432456 GTCGACATGCTGTGCCGA 60.432 61.111 11.55 0.00 0.00 5.54
1854 1932 3.344137 AATGCCGATGACCCCGCTT 62.344 57.895 0.00 0.00 0.00 4.68
1869 1947 3.443045 CTTGCATCGGTGTGGGGC 61.443 66.667 0.00 0.00 0.00 5.80
1923 2001 2.281761 AAGTTGGCTGAGGTGGCG 60.282 61.111 0.00 0.00 35.06 5.69
1995 2073 4.702131 GTCCAGCTGTCCAACATTTATCTT 59.298 41.667 13.81 0.00 0.00 2.40
2064 2142 2.757077 CGGGGGCTCAAGAAGGTT 59.243 61.111 0.00 0.00 0.00 3.50
2067 2145 1.767692 GGGGCTCAAGAAGGTTCCA 59.232 57.895 0.00 0.00 0.00 3.53
2200 2278 4.900154 GGCTGAAGTCAGACGAGG 57.100 61.111 12.54 0.00 46.59 4.63
2201 2279 2.268022 GGCTGAAGTCAGACGAGGA 58.732 57.895 12.54 0.00 46.59 3.71
2202 2280 0.172352 GGCTGAAGTCAGACGAGGAG 59.828 60.000 12.54 0.00 46.59 3.69
2205 2283 1.470890 CTGAAGTCAGACGAGGAGGAC 59.529 57.143 1.88 0.00 46.59 3.85
2235 2316 1.254313 GAAACAACCTTTTCGTTGCGC 59.746 47.619 0.00 0.00 45.75 6.09
2243 2326 0.589223 TTTTCGTTGCGCCCTTGTAG 59.411 50.000 4.18 0.00 0.00 2.74
2247 2330 4.413928 TTGCGCCCTTGTAGCAAT 57.586 50.000 4.18 0.00 44.66 3.56
2252 2335 2.163412 TGCGCCCTTGTAGCAATAAAAG 59.837 45.455 4.18 0.00 38.01 2.27
2253 2336 2.479560 GCGCCCTTGTAGCAATAAAAGG 60.480 50.000 0.00 0.00 39.15 3.11
2322 2412 5.975410 GGAGCAGCAACCGATATATATTC 57.025 43.478 0.00 0.00 0.00 1.75
2325 2415 6.540189 GGAGCAGCAACCGATATATATTCATT 59.460 38.462 0.00 0.00 0.00 2.57
2326 2416 7.066284 GGAGCAGCAACCGATATATATTCATTT 59.934 37.037 0.00 0.00 0.00 2.32
2327 2417 9.098355 GAGCAGCAACCGATATATATTCATTTA 57.902 33.333 0.00 0.00 0.00 1.40
2362 2452 6.986817 AGGAATATGATACTCAGGAAACAACG 59.013 38.462 0.00 0.00 0.00 4.10
2364 2454 3.328382 TGATACTCAGGAAACAACGGG 57.672 47.619 0.00 0.00 0.00 5.28
2370 2460 2.036733 CTCAGGAAACAACGGGACAGTA 59.963 50.000 0.00 0.00 0.00 2.74
2393 2483 6.892658 ATTCAGCACCAAACACAAAGTATA 57.107 33.333 0.00 0.00 0.00 1.47
2396 2486 7.283625 TCAGCACCAAACACAAAGTATATTT 57.716 32.000 0.00 0.00 0.00 1.40
2398 2488 7.651304 TCAGCACCAAACACAAAGTATATTTTG 59.349 33.333 16.64 16.64 42.38 2.44
2400 2490 7.984617 AGCACCAAACACAAAGTATATTTTGTT 59.015 29.630 20.18 11.29 46.18 2.83
2401 2491 8.608317 GCACCAAACACAAAGTATATTTTGTTT 58.392 29.630 20.18 13.46 46.18 2.83
2420 2510 7.899178 TTGTTTCTGAGTTTTTCCTTTTTCC 57.101 32.000 0.00 0.00 0.00 3.13
2426 2516 6.439058 TCTGAGTTTTTCCTTTTTCCTTCCAA 59.561 34.615 0.00 0.00 0.00 3.53
2431 2521 8.956426 AGTTTTTCCTTTTTCCTTCCAATTTTC 58.044 29.630 0.00 0.00 0.00 2.29
2443 2533 9.678260 TTCCTTCCAATTTTCTTCAAATTTTGA 57.322 25.926 7.74 7.74 41.57 2.69
2444 2534 9.328845 TCCTTCCAATTTTCTTCAAATTTTGAG 57.671 29.630 11.41 6.99 41.57 3.02
2445 2535 9.112725 CCTTCCAATTTTCTTCAAATTTTGAGT 57.887 29.630 11.41 0.00 41.57 3.41
2447 2537 7.918643 TCCAATTTTCTTCAAATTTTGAGTGC 58.081 30.769 11.41 0.00 41.57 4.40
2513 2603 8.311836 TCGACCTCTTGATCATACTAAAGTTTT 58.688 33.333 0.00 0.00 0.00 2.43
2516 2606 9.220767 ACCTCTTGATCATACTAAAGTTTTCAC 57.779 33.333 0.00 0.00 0.00 3.18
2523 2613 7.979444 TCATACTAAAGTTTTCACTTCCCTG 57.021 36.000 0.00 0.00 42.89 4.45
2584 2676 5.302568 TGGCCTTAAAATCTTCAGCCATATG 59.697 40.000 3.32 0.00 43.65 1.78
2602 2694 6.231951 CCATATGGCCATAATCAAATGCAAA 58.768 36.000 28.75 3.84 0.00 3.68
2608 2700 5.054477 GCCATAATCAAATGCAAAGCTCAT 58.946 37.500 0.00 0.00 0.00 2.90
2613 2705 9.256477 CATAATCAAATGCAAAGCTCATTGTAT 57.744 29.630 0.00 0.00 37.24 2.29
2614 2706 9.826574 ATAATCAAATGCAAAGCTCATTGTATT 57.173 25.926 8.21 8.21 44.18 1.89
2865 2977 2.496899 CCTACAGGTTGCTTGGATGT 57.503 50.000 0.00 0.00 0.00 3.06
2870 2982 4.098914 ACAGGTTGCTTGGATGTTTAGA 57.901 40.909 0.00 0.00 0.00 2.10
2913 3025 6.615264 ATGCTAGAATATGTTGCAGACTTG 57.385 37.500 0.00 0.00 37.07 3.16
2947 3059 7.418254 GCAATCCATACCATCAAGAGGAAAAAT 60.418 37.037 0.00 0.00 0.00 1.82
2958 3070 7.749377 TCAAGAGGAAAAATATACCAGGAGA 57.251 36.000 0.00 0.00 0.00 3.71
2984 3097 3.441222 TCTGTTTGCAAGCATATGTGGAG 59.559 43.478 16.74 2.68 0.00 3.86
3006 3119 6.541278 GGAGGTTGAAATGGTTAGTATGGTAC 59.459 42.308 0.00 0.00 0.00 3.34
3024 3137 6.290294 TGGTACGAACCTTTTAGATTAGCT 57.710 37.500 0.00 0.00 46.91 3.32
3139 3476 6.430451 GTTGAGACAAACACTTTGATACCAG 58.570 40.000 1.75 0.00 43.26 4.00
3140 3477 4.515191 TGAGACAAACACTTTGATACCAGC 59.485 41.667 1.75 0.00 43.26 4.85
3141 3478 3.498397 AGACAAACACTTTGATACCAGCG 59.502 43.478 1.75 0.00 43.26 5.18
3142 3479 3.472652 ACAAACACTTTGATACCAGCGA 58.527 40.909 1.75 0.00 43.26 4.93
3143 3480 4.072131 ACAAACACTTTGATACCAGCGAT 58.928 39.130 1.75 0.00 43.26 4.58
3144 3481 4.154195 ACAAACACTTTGATACCAGCGATC 59.846 41.667 1.75 0.00 43.26 3.69
3145 3482 3.610040 ACACTTTGATACCAGCGATCA 57.390 42.857 0.00 0.00 0.00 2.92
3146 3483 3.525537 ACACTTTGATACCAGCGATCAG 58.474 45.455 0.00 0.00 34.85 2.90
3271 3608 2.290577 GGGATTCTACCCTCATCCATGC 60.291 54.545 0.00 0.00 45.90 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.622060 AACCCCTCCGTTGGCGATG 62.622 63.158 0.00 0.00 41.33 3.84
40 41 4.323477 CAACCCCTCCGTTGGCGA 62.323 66.667 0.00 0.00 39.58 5.54
59 60 2.264794 GAATGCGGTGGAGGACGT 59.735 61.111 0.00 0.00 0.00 4.34
70 71 0.374758 CCAACTGATGTCCGAATGCG 59.625 55.000 0.00 0.00 37.24 4.73
71 72 1.398390 GTCCAACTGATGTCCGAATGC 59.602 52.381 0.00 0.00 0.00 3.56
73 74 1.405526 CGGTCCAACTGATGTCCGAAT 60.406 52.381 11.21 0.00 42.96 3.34
81 82 2.047274 CCGTGCGGTCCAACTGAT 60.047 61.111 1.93 0.00 0.00 2.90
82 83 4.980805 GCCGTGCGGTCCAACTGA 62.981 66.667 12.46 0.00 37.65 3.41
124 125 1.206878 TGCATGGATCTGGCACTAGT 58.793 50.000 0.00 0.00 31.58 2.57
131 132 1.411246 CCAAATGGTGCATGGATCTGG 59.589 52.381 0.00 0.00 36.27 3.86
133 134 1.784358 CCCAAATGGTGCATGGATCT 58.216 50.000 4.81 0.00 36.27 2.75
152 153 2.325583 TAGGAATCCATTGCGTCCAC 57.674 50.000 0.61 0.00 32.98 4.02
153 154 3.213506 CATTAGGAATCCATTGCGTCCA 58.786 45.455 0.61 0.00 32.98 4.02
168 169 1.069358 GCTCGGACTCCTTCCATTAGG 59.931 57.143 0.00 0.00 46.29 2.69
170 171 0.744874 CGCTCGGACTCCTTCCATTA 59.255 55.000 0.00 0.00 46.29 1.90
190 191 1.270732 GGAGGATGCTATGTGAGGCAG 60.271 57.143 0.00 0.00 41.88 4.85
221 223 4.520846 CCATTCGGCTTGCGCGTC 62.521 66.667 8.43 0.00 36.88 5.19
236 238 2.444706 CCGAGGAGGAGATGGCCA 60.445 66.667 8.56 8.56 45.00 5.36
237 239 3.237741 CCCGAGGAGGAGATGGCC 61.238 72.222 0.00 0.00 45.00 5.36
289 291 2.637872 TCGAGTCCTCCACCTCATTTTT 59.362 45.455 0.00 0.00 0.00 1.94
290 292 2.257207 TCGAGTCCTCCACCTCATTTT 58.743 47.619 0.00 0.00 0.00 1.82
291 293 1.938585 TCGAGTCCTCCACCTCATTT 58.061 50.000 0.00 0.00 0.00 2.32
292 294 1.938585 TTCGAGTCCTCCACCTCATT 58.061 50.000 0.00 0.00 0.00 2.57
293 295 2.035632 GATTCGAGTCCTCCACCTCAT 58.964 52.381 0.00 0.00 0.00 2.90
294 296 1.475403 GATTCGAGTCCTCCACCTCA 58.525 55.000 0.00 0.00 0.00 3.86
302 304 2.496817 GCAGCCGATTCGAGTCCT 59.503 61.111 7.83 0.00 0.00 3.85
306 308 4.514577 ACGGGCAGCCGATTCGAG 62.515 66.667 14.01 0.00 36.94 4.04
307 309 4.508128 GACGGGCAGCCGATTCGA 62.508 66.667 14.01 0.00 36.94 3.71
308 310 4.812476 TGACGGGCAGCCGATTCG 62.812 66.667 5.00 5.75 36.94 3.34
352 354 2.029073 CGTCACACAAGCTCCCGT 59.971 61.111 0.00 0.00 0.00 5.28
354 356 1.374758 CTCCGTCACACAAGCTCCC 60.375 63.158 0.00 0.00 0.00 4.30
363 365 2.160205 CTTACACTCCTCTCCGTCACA 58.840 52.381 0.00 0.00 0.00 3.58
367 369 0.702902 TCCCTTACACTCCTCTCCGT 59.297 55.000 0.00 0.00 0.00 4.69
369 371 2.104170 CACTCCCTTACACTCCTCTCC 58.896 57.143 0.00 0.00 0.00 3.71
373 375 1.433592 ACTCCACTCCCTTACACTCCT 59.566 52.381 0.00 0.00 0.00 3.69
381 383 1.059913 CCACTTCACTCCACTCCCTT 58.940 55.000 0.00 0.00 0.00 3.95
382 384 0.104934 ACCACTTCACTCCACTCCCT 60.105 55.000 0.00 0.00 0.00 4.20
390 392 3.146847 CCAAACCCTAACCACTTCACTC 58.853 50.000 0.00 0.00 0.00 3.51
406 408 3.027292 TCGCTTGCCGAACCAAAC 58.973 55.556 0.00 0.00 44.21 2.93
413 415 1.745115 CTTCCCATTCGCTTGCCGA 60.745 57.895 0.00 0.00 45.77 5.54
421 423 7.346471 ACCCCATATATATTTCTTCCCATTCG 58.654 38.462 0.00 0.00 0.00 3.34
423 425 7.346471 CGACCCCATATATATTTCTTCCCATT 58.654 38.462 0.00 0.00 0.00 3.16
426 428 5.397559 CCCGACCCCATATATATTTCTTCCC 60.398 48.000 0.00 0.00 0.00 3.97
429 431 5.045140 CCACCCGACCCCATATATATTTCTT 60.045 44.000 0.00 0.00 0.00 2.52
432 434 3.526019 CCCACCCGACCCCATATATATTT 59.474 47.826 0.00 0.00 0.00 1.40
440 442 2.076184 CATACCCACCCGACCCCAT 61.076 63.158 0.00 0.00 0.00 4.00
473 546 0.389948 ACGAGTCTCAAATGTCGGGC 60.390 55.000 0.00 0.00 36.74 6.13
476 549 4.434330 GCCTTAAACGAGTCTCAAATGTCG 60.434 45.833 0.00 0.00 38.40 4.35
478 551 3.432252 CGCCTTAAACGAGTCTCAAATGT 59.568 43.478 0.00 0.00 0.00 2.71
479 552 3.432252 ACGCCTTAAACGAGTCTCAAATG 59.568 43.478 0.00 0.00 0.00 2.32
480 553 3.660865 ACGCCTTAAACGAGTCTCAAAT 58.339 40.909 0.00 0.00 0.00 2.32
486 560 0.387750 ACGGACGCCTTAAACGAGTC 60.388 55.000 4.70 1.82 0.00 3.36
487 561 0.387750 GACGGACGCCTTAAACGAGT 60.388 55.000 4.70 2.37 0.00 4.18
495 569 3.692406 GACCCAGACGGACGCCTT 61.692 66.667 0.00 0.00 34.64 4.35
505 579 2.367567 AGTAGCGAAAGTTTGACCCAGA 59.632 45.455 0.00 0.00 0.00 3.86
523 597 2.646175 GCCCGGTCACTGAGCAGTA 61.646 63.158 8.89 0.00 40.20 2.74
524 598 4.008933 GCCCGGTCACTGAGCAGT 62.009 66.667 8.89 0.00 43.61 4.40
528 602 4.436998 GACGGCCCGGTCACTGAG 62.437 72.222 8.57 0.00 36.91 3.35
552 626 3.245519 GTCTCAAACCTGTCTCAAACGTC 59.754 47.826 0.00 0.00 0.00 4.34
553 627 3.195661 GTCTCAAACCTGTCTCAAACGT 58.804 45.455 0.00 0.00 0.00 3.99
562 636 1.366366 CCCGTCGTCTCAAACCTGT 59.634 57.895 0.00 0.00 0.00 4.00
576 650 0.538118 TTAGAGCATTTACCGCCCGT 59.462 50.000 0.00 0.00 0.00 5.28
577 651 1.878953 ATTAGAGCATTTACCGCCCG 58.121 50.000 0.00 0.00 0.00 6.13
578 652 5.298527 AGTTTAATTAGAGCATTTACCGCCC 59.701 40.000 0.00 0.00 0.00 6.13
582 656 8.860128 GTGCAAAGTTTAATTAGAGCATTTACC 58.140 33.333 0.00 0.00 32.98 2.85
586 660 6.092748 CGGTGCAAAGTTTAATTAGAGCATT 58.907 36.000 0.00 0.00 32.98 3.56
627 704 7.147742 TGCCTTTGAAAAAGAGAACCTTGTAAT 60.148 33.333 1.31 0.00 34.79 1.89
651 728 2.066999 CCCTGTACCCCCTCTCTGC 61.067 68.421 0.00 0.00 0.00 4.26
661 738 1.377333 GAGTTGCTGGCCCTGTACC 60.377 63.158 0.00 0.00 0.00 3.34
732 809 1.607467 ATGCTGGTTTGGTCTGGCC 60.607 57.895 0.00 0.00 37.90 5.36
1473 1551 3.719699 GCATTTGGCGTACATGCTT 57.280 47.368 7.64 0.00 40.23 3.91
1509 1587 1.812686 TTCCCTCGAACACCCTCACG 61.813 60.000 0.00 0.00 0.00 4.35
1512 1590 0.744771 GCATTCCCTCGAACACCCTC 60.745 60.000 0.00 0.00 0.00 4.30
1560 1638 2.677003 CGCGAACGCTCCAACCATT 61.677 57.895 16.66 0.00 39.32 3.16
1692 1770 0.536460 GCCCGTCTTCAACCTTTCCA 60.536 55.000 0.00 0.00 0.00 3.53
1854 1932 4.408821 GAGCCCCACACCGATGCA 62.409 66.667 0.00 0.00 0.00 3.96
1869 1947 1.741525 GCAGCCTGCTAGGAGAGAG 59.258 63.158 13.63 2.79 40.96 3.20
1906 1984 2.281761 CGCCACCTCAGCCAACTT 60.282 61.111 0.00 0.00 0.00 2.66
1923 2001 1.153469 CTTCTCGAGCTCCTTGGCC 60.153 63.158 7.81 0.00 0.00 5.36
2139 2217 3.460857 AGCAAGTCCCATATCTCGAAC 57.539 47.619 0.00 0.00 0.00 3.95
2197 2275 4.239304 GTTTCTTCTTCTTCGTCCTCCTC 58.761 47.826 0.00 0.00 0.00 3.71
2198 2276 3.641906 TGTTTCTTCTTCTTCGTCCTCCT 59.358 43.478 0.00 0.00 0.00 3.69
2199 2277 3.991367 TGTTTCTTCTTCTTCGTCCTCC 58.009 45.455 0.00 0.00 0.00 4.30
2200 2278 4.211584 GGTTGTTTCTTCTTCTTCGTCCTC 59.788 45.833 0.00 0.00 0.00 3.71
2201 2279 4.127907 GGTTGTTTCTTCTTCTTCGTCCT 58.872 43.478 0.00 0.00 0.00 3.85
2202 2280 4.127907 AGGTTGTTTCTTCTTCTTCGTCC 58.872 43.478 0.00 0.00 0.00 4.79
2205 2283 5.677178 CGAAAAGGTTGTTTCTTCTTCTTCG 59.323 40.000 0.00 0.00 35.70 3.79
2235 2316 8.093927 TCAAATTTCCTTTTATTGCTACAAGGG 58.906 33.333 0.00 0.00 36.06 3.95
2243 2326 9.396938 CATGGTTTTCAAATTTCCTTTTATTGC 57.603 29.630 0.00 0.00 0.00 3.56
2252 2335 7.926018 AGTCTGTTACATGGTTTTCAAATTTCC 59.074 33.333 0.00 0.00 0.00 3.13
2253 2336 8.871686 AGTCTGTTACATGGTTTTCAAATTTC 57.128 30.769 0.00 0.00 0.00 2.17
2299 2389 2.370281 ATATATCGGTTGCTGCTCCG 57.630 50.000 23.05 23.05 46.93 4.63
2300 2390 5.419542 TGAATATATATCGGTTGCTGCTCC 58.580 41.667 0.00 2.78 0.00 4.70
2301 2391 7.545362 AATGAATATATATCGGTTGCTGCTC 57.455 36.000 0.00 0.00 0.00 4.26
2302 2392 7.928307 AAATGAATATATATCGGTTGCTGCT 57.072 32.000 0.00 0.00 0.00 4.24
2362 2452 2.488153 GTTTGGTGCTGAATACTGTCCC 59.512 50.000 0.00 0.00 0.00 4.46
2364 2454 3.563808 TGTGTTTGGTGCTGAATACTGTC 59.436 43.478 0.00 0.00 0.00 3.51
2370 2460 5.789643 ATACTTTGTGTTTGGTGCTGAAT 57.210 34.783 0.00 0.00 0.00 2.57
2396 2486 7.676004 AGGAAAAAGGAAAAACTCAGAAACAA 58.324 30.769 0.00 0.00 0.00 2.83
2398 2488 7.277981 GGAAGGAAAAAGGAAAAACTCAGAAAC 59.722 37.037 0.00 0.00 0.00 2.78
2400 2490 6.439058 TGGAAGGAAAAAGGAAAAACTCAGAA 59.561 34.615 0.00 0.00 0.00 3.02
2401 2491 5.955355 TGGAAGGAAAAAGGAAAAACTCAGA 59.045 36.000 0.00 0.00 0.00 3.27
2402 2492 6.220726 TGGAAGGAAAAAGGAAAAACTCAG 57.779 37.500 0.00 0.00 0.00 3.35
2403 2493 6.613153 TTGGAAGGAAAAAGGAAAAACTCA 57.387 33.333 0.00 0.00 0.00 3.41
2412 2502 8.504812 TTTGAAGAAAATTGGAAGGAAAAAGG 57.495 30.769 0.00 0.00 0.00 3.11
2420 2510 9.925268 CACTCAAAATTTGAAGAAAATTGGAAG 57.075 29.630 9.85 0.00 45.73 3.46
2426 2516 6.200854 GGACGCACTCAAAATTTGAAGAAAAT 59.799 34.615 9.85 0.00 40.32 1.82
2431 2521 4.023707 AGAGGACGCACTCAAAATTTGAAG 60.024 41.667 9.85 6.66 39.58 3.02
2441 2531 4.827284 TCATATATCAAGAGGACGCACTCA 59.173 41.667 9.30 0.00 39.97 3.41
2442 2532 5.378292 TCATATATCAAGAGGACGCACTC 57.622 43.478 0.00 0.00 37.77 3.51
2443 2533 5.337089 CCATCATATATCAAGAGGACGCACT 60.337 44.000 0.00 0.00 0.00 4.40
2444 2534 4.867047 CCATCATATATCAAGAGGACGCAC 59.133 45.833 0.00 0.00 0.00 5.34
2445 2535 4.772100 TCCATCATATATCAAGAGGACGCA 59.228 41.667 0.00 0.00 0.00 5.24
2447 2537 6.760298 CCATTCCATCATATATCAAGAGGACG 59.240 42.308 0.00 0.00 0.00 4.79
2513 2603 3.784178 ACAGAATCTCTCAGGGAAGTGA 58.216 45.455 0.00 0.00 0.00 3.41
2516 2606 6.232581 ACAATACAGAATCTCTCAGGGAAG 57.767 41.667 0.00 0.00 0.00 3.46
2584 2676 3.800531 AGCTTTGCATTTGATTATGGCC 58.199 40.909 0.00 0.00 0.00 5.36
2870 2982 6.839454 AGCATTAGAAATGGATGACTCTGAT 58.161 36.000 2.11 0.00 0.00 2.90
2913 3025 2.722094 TGGTATGGATTGCACACCTTC 58.278 47.619 7.17 1.50 0.00 3.46
2947 3059 5.012664 TGCAAACAGAAGTTCTCCTGGTATA 59.987 40.000 1.26 0.00 36.84 1.47
2958 3070 5.224888 CACATATGCTTGCAAACAGAAGTT 58.775 37.500 8.71 0.00 40.40 2.66
2984 3097 6.108015 TCGTACCATACTAACCATTTCAACC 58.892 40.000 0.00 0.00 0.00 3.77
3006 3119 8.969267 CACTGTATAGCTAATCTAAAAGGTTCG 58.031 37.037 0.00 0.00 0.00 3.95
3024 3137 7.342026 TCTGAATACTTCCTTCTGCACTGTATA 59.658 37.037 0.00 0.00 0.00 1.47
3059 3363 3.425359 GGCTGTTGTTCGAACTCATGATG 60.425 47.826 27.32 15.00 0.00 3.07
3139 3476 1.398390 AGAATTTGGTTCGCTGATCGC 59.602 47.619 0.23 0.23 41.84 4.58
3140 3477 2.672874 TGAGAATTTGGTTCGCTGATCG 59.327 45.455 0.00 0.00 41.84 3.69
3141 3478 4.656041 CTTGAGAATTTGGTTCGCTGATC 58.344 43.478 0.00 0.00 41.84 2.92
3142 3479 3.119708 GCTTGAGAATTTGGTTCGCTGAT 60.120 43.478 0.00 0.00 41.84 2.90
3143 3480 2.226437 GCTTGAGAATTTGGTTCGCTGA 59.774 45.455 0.00 0.00 41.84 4.26
3144 3481 2.030893 TGCTTGAGAATTTGGTTCGCTG 60.031 45.455 0.00 0.00 41.84 5.18
3145 3482 2.229792 TGCTTGAGAATTTGGTTCGCT 58.770 42.857 0.00 0.00 41.84 4.93
3146 3483 2.704725 TGCTTGAGAATTTGGTTCGC 57.295 45.000 0.00 0.00 41.84 4.70
3238 3575 4.451760 GGGTAGAATCCCCCTTATGGTCTA 60.452 50.000 0.00 0.00 41.54 2.59


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

AutoCloner maintained by Alex Coulton.