Multiple sequence alignment - TraesCS3B01G462500

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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 TraesCS3B01G462500 chr3B 100.000 4299 0 0 1 4299 705545170 705549468 0.000000e+00 7939.0
1 TraesCS3B01G462500 chr3B 90.608 905 75 7 2211 3110 705564240 705565139 0.000000e+00 1192.0
2 TraesCS3B01G462500 chr3B 81.711 935 145 16 1560 2478 705566540 705567464 0.000000e+00 756.0
3 TraesCS3B01G462500 chr3B 82.258 620 94 10 1560 2167 705563625 705564240 4.930000e-144 521.0
4 TraesCS3B01G462500 chr3B 79.245 477 80 13 2649 3110 705154490 705154962 8.970000e-82 315.0
5 TraesCS3B01G462500 chr3B 78.664 464 81 13 2642 3092 705005447 705005905 4.200000e-75 292.0
6 TraesCS3B01G462500 chr3B 87.879 231 27 1 2587 2817 705567519 705567748 1.970000e-68 270.0
7 TraesCS3B01G462500 chr3B 93.750 48 3 0 3358 3405 74456325 74456278 5.960000e-09 73.1
8 TraesCS3B01G462500 chr3B 88.333 60 4 2 2483 2542 399974488 399974544 7.710000e-08 69.4
9 TraesCS3B01G462500 chr3A 94.031 3535 182 17 776 4299 669523662 669527178 0.000000e+00 5332.0
10 TraesCS3B01G462500 chr3A 81.537 937 144 19 1560 2478 669566315 669567240 0.000000e+00 745.0
11 TraesCS3B01G462500 chr3A 86.067 689 72 7 1 685 669522852 669523520 0.000000e+00 719.0
12 TraesCS3B01G462500 chr3A 89.180 573 57 4 2541 3110 669564339 669564909 0.000000e+00 710.0
13 TraesCS3B01G462500 chr3A 83.110 746 103 10 1553 2282 669563485 669564223 0.000000e+00 658.0
14 TraesCS3B01G462500 chr3A 86.580 231 30 1 2587 2817 669567295 669567524 1.980000e-63 254.0
15 TraesCS3B01G462500 chr3D 94.333 1394 60 9 776 2156 533668255 533669642 0.000000e+00 2119.0
16 TraesCS3B01G462500 chr3D 93.913 1150 59 8 2217 3362 533669641 533670783 0.000000e+00 1725.0
17 TraesCS3B01G462500 chr3D 94.463 596 20 4 3394 3988 533671046 533671629 0.000000e+00 905.0
18 TraesCS3B01G462500 chr3D 82.963 945 123 23 1560 2478 533673609 533674541 0.000000e+00 819.0
19 TraesCS3B01G462500 chr3D 90.925 573 46 3 2541 3110 533674538 533675107 0.000000e+00 765.0
20 TraesCS3B01G462500 chr3D 81.838 936 140 21 1560 2478 533676509 533677431 0.000000e+00 760.0
21 TraesCS3B01G462500 chr3D 90.717 474 35 6 1 467 533667432 533667903 1.310000e-174 623.0
22 TraesCS3B01G462500 chr3D 92.661 327 21 3 3975 4299 533671644 533671969 6.510000e-128 468.0
23 TraesCS3B01G462500 chr3D 79.192 495 83 14 2632 3110 532956683 532957173 4.150000e-85 326.0
24 TraesCS3B01G462500 chr3D 78.119 521 91 16 2586 3092 532776989 532777500 4.180000e-80 309.0
25 TraesCS3B01G462500 chr3D 75.929 565 102 28 1652 2201 532955830 532956375 4.260000e-65 259.0
26 TraesCS3B01G462500 chr2A 87.379 206 22 3 486 688 42185562 42185358 2.580000e-57 233.0
27 TraesCS3B01G462500 chr2D 86.772 189 22 2 479 665 384256062 384256249 1.570000e-49 207.0
28 TraesCS3B01G462500 chr7D 85.149 202 28 1 486 685 191547124 191547325 5.640000e-49 206.0
29 TraesCS3B01G462500 chr7D 92.308 52 1 2 3196 3247 351576980 351577028 2.140000e-08 71.3
30 TraesCS3B01G462500 chr6A 85.149 202 27 2 486 685 262056494 262056694 2.030000e-48 204.0
31 TraesCS3B01G462500 chr6A 84.080 201 31 1 488 687 462228071 462227871 4.390000e-45 193.0
32 TraesCS3B01G462500 chr6A 77.812 320 52 15 3198 3510 535177667 535177360 3.420000e-41 180.0
33 TraesCS3B01G462500 chr6A 82.812 64 8 3 713 773 162441764 162441827 2.000000e-03 54.7
34 TraesCS3B01G462500 chr4A 83.902 205 32 1 485 688 110088263 110088059 1.220000e-45 195.0
35 TraesCS3B01G462500 chr4A 83.495 206 32 2 485 688 110087735 110087530 1.580000e-44 191.0
36 TraesCS3B01G462500 chr2B 83.654 208 28 4 485 688 672525572 672525777 1.580000e-44 191.0
37 TraesCS3B01G462500 chr5A 83.415 205 32 1 486 688 484562458 484562662 5.680000e-44 189.0
38 TraesCS3B01G462500 chr6B 76.418 335 65 11 3198 3527 581287953 581287628 7.390000e-38 169.0
39 TraesCS3B01G462500 chr5B 76.214 206 33 9 3202 3403 489507248 489507441 1.270000e-15 95.3


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 TraesCS3B01G462500 chr3B 705545170 705549468 4298 False 7939.00 7939 100.000000 1 4299 1 chr3B.!!$F4 4298
1 TraesCS3B01G462500 chr3B 705563625 705567748 4123 False 684.75 1192 85.614000 1560 3110 4 chr3B.!!$F5 1550
2 TraesCS3B01G462500 chr3A 669522852 669527178 4326 False 3025.50 5332 90.049000 1 4299 2 chr3A.!!$F1 4298
3 TraesCS3B01G462500 chr3A 669563485 669567524 4039 False 591.75 745 85.101750 1553 3110 4 chr3A.!!$F2 1557
4 TraesCS3B01G462500 chr3D 533667432 533677431 9999 False 1023.00 2119 90.226625 1 4299 8 chr3D.!!$F3 4298
5 TraesCS3B01G462500 chr3D 532776989 532777500 511 False 309.00 309 78.119000 2586 3092 1 chr3D.!!$F1 506
6 TraesCS3B01G462500 chr3D 532955830 532957173 1343 False 292.50 326 77.560500 1652 3110 2 chr3D.!!$F2 1458

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
145 147 0.032403 CATTGTATGCCATTGCCGGG 59.968 55.000 2.18 0.0 36.33 5.73 F
509 517 0.890683 GCATGGCCAATGTATAGCCC 59.109 55.000 10.96 0.0 46.55 5.19 F
803 939 1.067071 ACGCTTCCCTCGTCTAAAAGG 60.067 52.381 0.00 0.0 34.84 3.11 F
2666 7424 0.620556 CTTTCCAGGGCAAGCTCCTA 59.379 55.000 0.00 0.0 32.49 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1985 0.318955 GCAAGTGCGGCTCAATTTGT 60.319 50.000 0.00 0.0 29.43 2.83 R
2413 2595 3.444703 ACTGAGACTCAACAGTGTGAC 57.555 47.619 6.61 0.0 44.18 3.67 R
2705 7463 0.464036 GGGCGATCATGGTGTGTAGA 59.536 55.000 0.00 0.0 0.00 2.59 R
3979 8802 0.240945 CCATCCGCAGTTTCCACAAC 59.759 55.000 0.00 0.0 0.00 3.32 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
126 128 4.409187 ACTATATTCTCCGTCCTCCTTCC 58.591 47.826 0.00 0.00 0.00 3.46
133 135 2.700897 CTCCGTCCTCCTTCCATTGTAT 59.299 50.000 0.00 0.00 0.00 2.29
139 141 3.205056 TCCTCCTTCCATTGTATGCCATT 59.795 43.478 0.00 0.00 0.00 3.16
145 147 0.032403 CATTGTATGCCATTGCCGGG 59.968 55.000 2.18 0.00 36.33 5.73
157 159 2.758736 TTGCCGGGGATTGAAAAATG 57.241 45.000 2.18 0.00 0.00 2.32
162 164 2.462889 CGGGGATTGAAAAATGCATCG 58.537 47.619 0.00 0.00 0.00 3.84
165 167 4.696455 GGGGATTGAAAAATGCATCGAAT 58.304 39.130 0.00 0.00 0.00 3.34
168 170 5.461078 GGGATTGAAAAATGCATCGAATCAG 59.539 40.000 0.00 0.00 0.00 2.90
172 174 4.622313 TGAAAAATGCATCGAATCAGCAAC 59.378 37.500 0.00 1.90 42.15 4.17
194 196 2.514458 AGGAAATGGCCACCTACAAG 57.486 50.000 8.16 0.00 31.78 3.16
207 209 1.679944 CCTACAAGTGCCCTCACCATG 60.680 57.143 0.00 0.00 44.16 3.66
230 232 5.935206 TGTCAGTCTTTGAATACCGCAATAA 59.065 36.000 0.00 0.00 37.61 1.40
238 240 6.603237 TTGAATACCGCAATAATCACTCAG 57.397 37.500 0.00 0.00 0.00 3.35
263 269 3.710326 TGAGACGAGATCCATAAACCG 57.290 47.619 0.00 0.00 0.00 4.44
309 316 4.724399 TCACCCACACATAACAATCTTGT 58.276 39.130 0.00 0.00 44.72 3.16
321 328 7.491372 ACATAACAATCTTGTAGTACATCACCG 59.509 37.037 3.28 0.00 41.31 4.94
333 340 2.729479 ATCACCGCCAGCTCAGAGG 61.729 63.158 0.00 1.86 0.00 3.69
373 381 3.428725 GCCACACAACACTGTTGAAATCA 60.429 43.478 25.50 0.00 31.64 2.57
395 403 3.255831 TCATACCAATAGCCAGCCCATA 58.744 45.455 0.00 0.00 0.00 2.74
418 426 5.048846 ACTCTCTTTAAAAGACTTGCCCA 57.951 39.130 0.00 0.00 33.12 5.36
457 465 9.191479 TCTTTAAAAGACATACCAGGAAACAAA 57.809 29.630 0.00 0.00 31.20 2.83
462 470 7.418337 AAGACATACCAGGAAACAAACTTTT 57.582 32.000 0.00 0.00 0.00 2.27
463 471 8.528044 AAGACATACCAGGAAACAAACTTTTA 57.472 30.769 0.00 0.00 0.00 1.52
466 474 6.041182 ACATACCAGGAAACAAACTTTTACCC 59.959 38.462 0.00 0.00 0.00 3.69
467 475 4.616553 ACCAGGAAACAAACTTTTACCCT 58.383 39.130 0.00 0.00 0.00 4.34
468 476 5.027460 ACCAGGAAACAAACTTTTACCCTT 58.973 37.500 0.00 0.00 0.00 3.95
469 477 6.196434 ACCAGGAAACAAACTTTTACCCTTA 58.804 36.000 0.00 0.00 0.00 2.69
470 478 6.842280 ACCAGGAAACAAACTTTTACCCTTAT 59.158 34.615 0.00 0.00 0.00 1.73
471 479 7.346175 ACCAGGAAACAAACTTTTACCCTTATT 59.654 33.333 0.00 0.00 0.00 1.40
472 480 8.862085 CCAGGAAACAAACTTTTACCCTTATTA 58.138 33.333 0.00 0.00 0.00 0.98
477 485 9.917129 AAACAAACTTTTACCCTTATTAATCGG 57.083 29.630 0.00 0.00 0.00 4.18
478 486 8.058667 ACAAACTTTTACCCTTATTAATCGGG 57.941 34.615 17.18 17.18 43.79 5.14
479 487 7.889600 ACAAACTTTTACCCTTATTAATCGGGA 59.110 33.333 22.98 3.85 40.55 5.14
480 488 7.870509 AACTTTTACCCTTATTAATCGGGAC 57.129 36.000 22.98 0.00 40.55 4.46
509 517 0.890683 GCATGGCCAATGTATAGCCC 59.109 55.000 10.96 0.00 46.55 5.19
510 518 1.548582 GCATGGCCAATGTATAGCCCT 60.549 52.381 10.96 0.00 46.55 5.19
530 538 1.450134 GGGTGATGTCTCGCATGCA 60.450 57.895 19.57 4.02 38.06 3.96
559 567 5.422331 AGGATCGGATGTCAGAAAAAGTAGA 59.578 40.000 0.00 0.00 0.00 2.59
564 572 6.813649 TCGGATGTCAGAAAAAGTAGATTCAG 59.186 38.462 0.00 0.00 0.00 3.02
575 583 3.387962 AGTAGATTCAGATGGGGAAGCA 58.612 45.455 0.00 0.00 33.30 3.91
584 592 1.414061 ATGGGGAAGCAGGATCCTCG 61.414 60.000 12.69 9.05 40.58 4.63
673 683 6.379988 TGGAGTAAAGATGCATGTGTACTAGA 59.620 38.462 23.00 12.04 0.00 2.43
674 684 6.920758 GGAGTAAAGATGCATGTGTACTAGAG 59.079 42.308 23.00 0.00 0.00 2.43
676 686 7.484975 AGTAAAGATGCATGTGTACTAGAGTC 58.515 38.462 21.96 0.00 0.00 3.36
678 688 6.537453 AAGATGCATGTGTACTAGAGTCTT 57.463 37.500 2.46 0.00 0.00 3.01
679 689 6.537453 AGATGCATGTGTACTAGAGTCTTT 57.463 37.500 2.46 0.00 0.00 2.52
680 690 7.646548 AGATGCATGTGTACTAGAGTCTTTA 57.353 36.000 2.46 0.00 0.00 1.85
681 691 8.243961 AGATGCATGTGTACTAGAGTCTTTAT 57.756 34.615 2.46 0.00 0.00 1.40
682 692 8.700051 AGATGCATGTGTACTAGAGTCTTTATT 58.300 33.333 2.46 0.00 0.00 1.40
683 693 9.319143 GATGCATGTGTACTAGAGTCTTTATTT 57.681 33.333 2.46 0.00 0.00 1.40
684 694 9.672673 ATGCATGTGTACTAGAGTCTTTATTTT 57.327 29.630 0.00 0.00 0.00 1.82
685 695 9.151471 TGCATGTGTACTAGAGTCTTTATTTTC 57.849 33.333 0.00 0.00 0.00 2.29
686 696 9.372369 GCATGTGTACTAGAGTCTTTATTTTCT 57.628 33.333 0.00 0.00 0.00 2.52
749 763 5.955488 TGAGACTCACTAGTGATAACTTGC 58.045 41.667 25.35 13.34 39.13 4.01
755 769 6.815641 ACTCACTAGTGATAACTTGCATTGAG 59.184 38.462 25.35 11.08 39.13 3.02
803 939 1.067071 ACGCTTCCCTCGTCTAAAAGG 60.067 52.381 0.00 0.00 34.84 3.11
916 1053 1.675007 CCCTTCCTTTCTCCCCTCTT 58.325 55.000 0.00 0.00 0.00 2.85
1069 1206 1.215382 CGACTGGCACCGAAGATGA 59.785 57.895 0.00 0.00 0.00 2.92
1159 1296 3.379445 AGGACGCGTGGGTCGATT 61.379 61.111 20.70 0.00 42.86 3.34
1184 1321 3.863543 CGTGATGATGCGCGGCAA 61.864 61.111 8.83 0.00 43.62 4.52
1229 1366 2.833943 TCAGTGCTCTTATCTGCTCCAA 59.166 45.455 0.00 0.00 0.00 3.53
1233 1370 3.944015 GTGCTCTTATCTGCTCCAATTGT 59.056 43.478 4.43 0.00 0.00 2.71
1321 1460 2.158755 AGGCATCATGCTTACTGGTACC 60.159 50.000 10.11 4.43 44.28 3.34
1466 1607 4.865365 CGTTTAGATCCTCTGTTCAGTTCC 59.135 45.833 0.00 0.00 0.00 3.62
1608 1752 5.477291 TCGAGTATATAGGAAGGAAGCCAAG 59.523 44.000 0.00 0.00 0.00 3.61
1639 1783 2.183555 CGGAGGAGGTTACCGCAC 59.816 66.667 7.54 0.47 40.19 5.34
1669 1813 3.441922 GGAGGCTTGAGGAAATCTTGTTC 59.558 47.826 0.00 0.00 0.00 3.18
1821 1985 6.497259 GGGAGTACTACAATATGATGAAGGGA 59.503 42.308 7.57 0.00 0.00 4.20
1886 2050 1.661617 TCAGAACCAACAACGACAACG 59.338 47.619 0.00 0.00 45.75 4.10
2122 2292 1.122632 TTCCTTCAGGCCGTGTACCA 61.123 55.000 0.00 0.00 34.44 3.25
2447 2631 7.373617 TGAGTCTCAGTATTTGCCCATATTA 57.626 36.000 0.00 0.00 0.00 0.98
2478 2662 8.510243 TGACATTTCTGAACATGCATATACTT 57.490 30.769 0.00 0.00 0.00 2.24
2517 2701 1.741145 AGACGGCTTTTGACAAACGTT 59.259 42.857 14.02 0.00 34.43 3.99
2531 2715 8.918961 TTGACAAACGTTTTACATTTTGAGAT 57.081 26.923 11.66 0.00 33.90 2.75
2638 7396 6.981559 TGTTTCCATTTACTAACTTGGTTTGC 59.018 34.615 0.00 0.00 0.00 3.68
2639 7397 6.716934 TTCCATTTACTAACTTGGTTTGCA 57.283 33.333 0.00 0.00 0.00 4.08
2657 7415 1.673923 GCATTGCTTTCTTTCCAGGGC 60.674 52.381 0.16 0.00 0.00 5.19
2666 7424 0.620556 CTTTCCAGGGCAAGCTCCTA 59.379 55.000 0.00 0.00 32.49 2.94
2677 7435 3.470709 GCAAGCTCCTAATCAGCATGTA 58.529 45.455 0.00 0.00 37.78 2.29
2705 7463 1.988107 TGCTTTCTCTGGGGATGAACT 59.012 47.619 0.00 0.00 0.00 3.01
2811 7570 5.825679 TGGTAAGAATTGTGCACTGTACTTT 59.174 36.000 19.41 8.14 0.00 2.66
2866 7637 2.031120 AGGCTTGCTTACAAACTGCAA 58.969 42.857 0.00 0.00 43.25 4.08
2889 7660 0.928505 ATGGTGATGCAGGAATCCCA 59.071 50.000 0.00 0.00 33.90 4.37
3037 7808 1.123861 AGGCTCAGAGCAAGTGTCCA 61.124 55.000 24.09 0.00 44.75 4.02
3121 7943 4.200092 GACCTGATCCACCCTGTTTTATC 58.800 47.826 0.00 0.00 0.00 1.75
3135 7957 6.377429 CCCTGTTTTATCTTCTCTTTTACCCC 59.623 42.308 0.00 0.00 0.00 4.95
3136 7958 6.377429 CCTGTTTTATCTTCTCTTTTACCCCC 59.623 42.308 0.00 0.00 0.00 5.40
3189 8011 5.591877 CAGAAGGAGGTTTGATTAAGGATGG 59.408 44.000 0.00 0.00 0.00 3.51
3208 8030 4.098914 TGGCATTAACAGGGATATGGAC 57.901 45.455 0.00 0.00 0.00 4.02
3300 8122 2.668457 CGCTGTGAGTTGTATCTTGGTC 59.332 50.000 0.00 0.00 0.00 4.02
3367 8189 8.962884 TCAGAGTTGTTGCATATATATGTTGT 57.037 30.769 21.10 3.03 36.11 3.32
3410 8232 4.183865 GTGTTGTGATATCTACTGCTGCA 58.816 43.478 0.88 0.88 0.00 4.41
3432 8254 2.553536 CACGTCGTGTGTATGTTGTG 57.446 50.000 17.30 0.00 43.88 3.33
3510 8332 2.428890 AGGTGCTAGATCTGTACAGTGC 59.571 50.000 21.99 17.75 0.00 4.40
3511 8333 2.455032 GTGCTAGATCTGTACAGTGCG 58.545 52.381 21.99 8.90 0.00 5.34
3517 8339 1.257750 ATCTGTACAGTGCGGCTCCA 61.258 55.000 21.99 0.05 0.00 3.86
3533 8355 1.886542 CTCCAAGGGCGCTAAACTTTT 59.113 47.619 7.64 0.00 0.00 2.27
3534 8356 1.611491 TCCAAGGGCGCTAAACTTTTG 59.389 47.619 7.64 0.00 0.00 2.44
3535 8357 1.336795 CCAAGGGCGCTAAACTTTTGG 60.337 52.381 7.64 1.97 0.00 3.28
3536 8358 1.611491 CAAGGGCGCTAAACTTTTGGA 59.389 47.619 7.64 0.00 0.00 3.53
3537 8359 1.534729 AGGGCGCTAAACTTTTGGAG 58.465 50.000 7.64 0.00 0.00 3.86
3538 8360 1.073284 AGGGCGCTAAACTTTTGGAGA 59.927 47.619 7.64 0.00 0.00 3.71
3614 8436 0.105039 GGTCATTGCCTAGTCCCTCG 59.895 60.000 0.00 0.00 0.00 4.63
3630 8452 0.871722 CTCGCTGATAGGAGGAGACG 59.128 60.000 0.00 0.00 0.00 4.18
3663 8486 3.926821 TTTTCTTTTACGGCCATGACC 57.073 42.857 2.24 0.00 0.00 4.02
3665 8488 2.107950 TCTTTTACGGCCATGACCTG 57.892 50.000 2.24 0.00 0.00 4.00
3685 8508 2.231380 GCCCTTTGGACCTCCTGGA 61.231 63.158 0.00 0.00 36.82 3.86
3770 8593 1.559368 TTTATGCTGCAATGGTGGCT 58.441 45.000 6.36 0.00 0.00 4.75
3802 8625 0.038801 TGAGATGCTCGATGATCGGC 60.039 55.000 15.48 16.60 40.88 5.54
3831 8654 1.659098 GGTTCCAACAAGATAGCGTCG 59.341 52.381 0.00 0.00 0.00 5.12
3852 8675 1.134907 GTGGCCTCTTTGCATCCATTG 60.135 52.381 3.32 0.00 0.00 2.82
3853 8676 1.188863 GGCCTCTTTGCATCCATTGT 58.811 50.000 0.00 0.00 0.00 2.71
3858 8681 4.152938 GCCTCTTTGCATCCATTGTTTTTC 59.847 41.667 0.00 0.00 0.00 2.29
3889 8712 1.398958 TTCTTTGGTTGTGCCCCTGC 61.399 55.000 0.00 0.00 36.04 4.85
3921 8744 9.561069 ACTTTGTACTAGTTGTTCAGATTGATT 57.439 29.630 0.00 0.00 0.00 2.57
3979 8802 2.089980 CTTGAAGATGGCACCAAGAGG 58.910 52.381 12.51 0.00 38.52 3.69
4014 8837 2.355310 GGATGGGTCGAACATGGTGTAA 60.355 50.000 1.31 0.00 0.00 2.41
4057 8880 1.844687 AGCCTCAAGCCTTGGATTTC 58.155 50.000 4.30 0.00 45.47 2.17
4083 8907 5.180810 AGGAAATGAAAGGTAGGAGGTTC 57.819 43.478 0.00 0.00 0.00 3.62
4117 8941 3.637911 TGCCAATATACTTCGGTGGTT 57.362 42.857 0.00 0.00 0.00 3.67
4133 8957 6.050432 TCGGTGGTTGTTTATATACATGGTC 58.950 40.000 0.00 0.00 0.00 4.02
4138 8962 7.226720 GTGGTTGTTTATATACATGGTCCTCAG 59.773 40.741 0.00 0.00 0.00 3.35
4142 8966 6.765989 TGTTTATATACATGGTCCTCAGTTGC 59.234 38.462 0.00 0.00 0.00 4.17
4235 9059 8.395633 AGTTATGTTGTAGAAGTTGTGTTTCAC 58.604 33.333 0.00 0.00 34.56 3.18
4242 9159 5.866335 AGAAGTTGTGTTTCACGTGTTTA 57.134 34.783 16.51 0.00 37.14 2.01
4255 9172 2.356695 ACGTGTTTAGGAAAGTGGCAAC 59.643 45.455 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.648142 TCTGTTTCCAGTTGTCAATTCATTAC 58.352 34.615 0.00 0.00 39.82 1.89
117 119 2.204463 TGGCATACAATGGAAGGAGGA 58.796 47.619 0.00 0.00 0.00 3.71
126 128 0.032403 CCCGGCAATGGCATACAATG 59.968 55.000 7.75 0.00 43.71 2.82
133 135 2.759149 CAATCCCCGGCAATGGCA 60.759 61.111 7.75 0.00 43.71 4.92
139 141 0.248843 GCATTTTTCAATCCCCGGCA 59.751 50.000 0.00 0.00 0.00 5.69
145 147 5.051240 GCTGATTCGATGCATTTTTCAATCC 60.051 40.000 0.00 0.00 0.00 3.01
157 159 2.162208 TCCTTTGTTGCTGATTCGATGC 59.838 45.455 0.00 0.00 0.00 3.91
162 164 3.681417 GCCATTTCCTTTGTTGCTGATTC 59.319 43.478 0.00 0.00 0.00 2.52
165 167 1.344114 GGCCATTTCCTTTGTTGCTGA 59.656 47.619 0.00 0.00 0.00 4.26
168 170 1.511850 GTGGCCATTTCCTTTGTTGC 58.488 50.000 9.72 0.00 0.00 4.17
172 174 2.524306 TGTAGGTGGCCATTTCCTTTG 58.476 47.619 17.93 0.00 33.34 2.77
194 196 0.674895 GACTGACATGGTGAGGGCAC 60.675 60.000 0.00 0.00 44.39 5.01
207 209 4.946784 ATTGCGGTATTCAAAGACTGAC 57.053 40.909 0.65 0.00 32.21 3.51
238 240 0.755686 ATGGATCTCGTCTCAAGGGC 59.244 55.000 0.00 0.00 0.00 5.19
263 269 8.988934 TGATACTTTAACCGATAATGCTTCATC 58.011 33.333 0.00 0.00 0.00 2.92
309 316 0.744874 GAGCTGGCGGTGATGTACTA 59.255 55.000 0.00 0.00 0.00 1.82
321 328 0.829333 TCTTCATCCTCTGAGCTGGC 59.171 55.000 0.00 0.00 34.68 4.85
333 340 2.557924 TGGCATGGTGTGTTTCTTCATC 59.442 45.455 0.00 0.00 0.00 2.92
373 381 2.065007 TGGGCTGGCTATTGGTATGAT 58.935 47.619 0.00 0.00 0.00 2.45
395 403 5.445964 TGGGCAAGTCTTTTAAAGAGAGTT 58.554 37.500 7.74 11.51 38.41 3.01
444 452 5.768752 AGGGTAAAAGTTTGTTTCCTGGTA 58.231 37.500 0.00 0.00 0.00 3.25
457 465 6.051074 CGTCCCGATTAATAAGGGTAAAAGT 58.949 40.000 21.44 0.00 45.27 2.66
462 470 3.253188 CGACGTCCCGATTAATAAGGGTA 59.747 47.826 21.44 10.53 45.27 3.69
463 471 2.035066 CGACGTCCCGATTAATAAGGGT 59.965 50.000 21.44 8.43 45.27 4.34
466 474 4.913924 CCTTACGACGTCCCGATTAATAAG 59.086 45.833 10.58 3.91 0.00 1.73
467 475 4.261572 CCCTTACGACGTCCCGATTAATAA 60.262 45.833 10.58 0.00 0.00 1.40
468 476 3.253188 CCCTTACGACGTCCCGATTAATA 59.747 47.826 10.58 0.00 0.00 0.98
469 477 2.035066 CCCTTACGACGTCCCGATTAAT 59.965 50.000 10.58 0.00 0.00 1.40
470 478 1.405105 CCCTTACGACGTCCCGATTAA 59.595 52.381 10.58 0.00 0.00 1.40
471 479 1.024271 CCCTTACGACGTCCCGATTA 58.976 55.000 10.58 0.00 0.00 1.75
472 480 1.811860 CCCTTACGACGTCCCGATT 59.188 57.895 10.58 0.00 0.00 3.34
473 481 2.779033 GCCCTTACGACGTCCCGAT 61.779 63.158 10.58 0.00 0.00 4.18
474 482 3.443045 GCCCTTACGACGTCCCGA 61.443 66.667 10.58 0.00 0.00 5.14
475 483 3.072486 ATGCCCTTACGACGTCCCG 62.072 63.158 10.58 1.95 0.00 5.14
476 484 1.520787 CATGCCCTTACGACGTCCC 60.521 63.158 10.58 0.00 0.00 4.46
477 485 1.520787 CCATGCCCTTACGACGTCC 60.521 63.158 10.58 0.00 0.00 4.79
478 486 2.171725 GCCATGCCCTTACGACGTC 61.172 63.158 2.43 5.18 0.00 4.34
479 487 2.125269 GCCATGCCCTTACGACGT 60.125 61.111 5.52 5.52 0.00 4.34
480 488 2.895372 GGCCATGCCCTTACGACG 60.895 66.667 0.00 0.00 44.06 5.12
502 510 3.561528 CGAGACATCACCCTAGGGCTATA 60.562 52.174 28.88 11.06 39.32 1.31
509 517 1.871408 GCATGCGAGACATCACCCTAG 60.871 57.143 0.00 0.00 36.64 3.02
510 518 0.104855 GCATGCGAGACATCACCCTA 59.895 55.000 0.00 0.00 36.64 3.53
530 538 5.614324 TTTCTGACATCCGATCCTACATT 57.386 39.130 0.00 0.00 0.00 2.71
559 567 1.600058 TCCTGCTTCCCCATCTGAAT 58.400 50.000 0.00 0.00 0.00 2.57
564 572 0.399833 GAGGATCCTGCTTCCCCATC 59.600 60.000 22.02 0.00 33.45 3.51
632 640 8.966868 TCTTTACTCCATTTCAACTTTTTCAGT 58.033 29.630 0.00 0.00 37.30 3.41
640 648 6.435277 ACATGCATCTTTACTCCATTTCAACT 59.565 34.615 0.00 0.00 0.00 3.16
647 655 5.994250 AGTACACATGCATCTTTACTCCAT 58.006 37.500 0.00 0.00 0.00 3.41
655 665 6.537453 AAGACTCTAGTACACATGCATCTT 57.463 37.500 0.00 0.00 0.00 2.40
732 746 6.935167 TCTCAATGCAAGTTATCACTAGTGA 58.065 36.000 27.07 27.07 44.59 3.41
762 776 3.002042 GTCCGTCTCGAAATCTACATCGA 59.998 47.826 0.00 0.00 45.01 3.59
763 777 3.289911 GTCCGTCTCGAAATCTACATCG 58.710 50.000 0.00 0.00 40.31 3.84
764 778 3.289911 CGTCCGTCTCGAAATCTACATC 58.710 50.000 0.00 0.00 0.00 3.06
765 779 2.541178 GCGTCCGTCTCGAAATCTACAT 60.541 50.000 0.00 0.00 0.00 2.29
766 780 1.202110 GCGTCCGTCTCGAAATCTACA 60.202 52.381 0.00 0.00 0.00 2.74
767 781 1.063764 AGCGTCCGTCTCGAAATCTAC 59.936 52.381 0.00 0.00 0.00 2.59
769 783 0.526662 AAGCGTCCGTCTCGAAATCT 59.473 50.000 0.00 0.00 0.00 2.40
770 784 0.915227 GAAGCGTCCGTCTCGAAATC 59.085 55.000 0.00 0.00 0.00 2.17
772 786 1.080974 GGAAGCGTCCGTCTCGAAA 60.081 57.895 1.94 0.00 33.05 3.46
773 787 2.564975 GGAAGCGTCCGTCTCGAA 59.435 61.111 1.94 0.00 33.05 3.71
797 928 6.041637 GCTTCCCTTTTCTTTCTTCCCTTTTA 59.958 38.462 0.00 0.00 0.00 1.52
803 939 2.351835 GCGCTTCCCTTTTCTTTCTTCC 60.352 50.000 0.00 0.00 0.00 3.46
806 942 0.875059 CGCGCTTCCCTTTTCTTTCT 59.125 50.000 5.56 0.00 0.00 2.52
807 943 0.591659 ACGCGCTTCCCTTTTCTTTC 59.408 50.000 5.73 0.00 0.00 2.62
808 944 0.591659 GACGCGCTTCCCTTTTCTTT 59.408 50.000 5.73 0.00 0.00 2.52
809 945 1.566018 CGACGCGCTTCCCTTTTCTT 61.566 55.000 5.73 0.00 0.00 2.52
810 946 2.027625 CGACGCGCTTCCCTTTTCT 61.028 57.895 5.73 0.00 0.00 2.52
1053 1190 0.670546 CGTTCATCTTCGGTGCCAGT 60.671 55.000 0.00 0.00 0.00 4.00
1059 1196 3.179265 CGCGCGTTCATCTTCGGT 61.179 61.111 24.19 0.00 0.00 4.69
1060 1197 3.126722 GACGCGCGTTCATCTTCGG 62.127 63.158 38.03 2.39 0.00 4.30
1159 1296 0.460109 CGCATCATCACGAACTGGGA 60.460 55.000 0.00 0.00 0.00 4.37
1184 1321 2.618053 CTTACATCTTTTCTCGGGCGT 58.382 47.619 0.00 0.00 0.00 5.68
1186 1323 1.327764 CGCTTACATCTTTTCTCGGGC 59.672 52.381 0.00 0.00 0.00 6.13
1194 1331 3.403038 AGCACTGAACGCTTACATCTTT 58.597 40.909 0.00 0.00 35.82 2.52
1251 1388 0.402861 TCCAACCCCTTTCCTGGAGT 60.403 55.000 0.00 0.00 32.97 3.85
1258 1395 5.481824 AGAGAATTCAATTCCAACCCCTTTC 59.518 40.000 8.44 0.00 40.13 2.62
1262 1399 6.210584 TGTTTAGAGAATTCAATTCCAACCCC 59.789 38.462 8.44 0.00 40.13 4.95
1292 1429 1.688772 AGCATGATGCCTGATGGAAC 58.311 50.000 14.72 0.00 46.52 3.62
1354 1493 5.968261 CGAACAGCACTATATCTATGATCGG 59.032 44.000 0.00 0.00 31.81 4.18
1410 1551 4.057432 GTTGCCAAATGTGTATGCAAAGT 58.943 39.130 0.00 0.00 42.86 2.66
1466 1607 5.046520 AGCCTTATAGCCTAAATAACCCTCG 60.047 44.000 0.00 0.00 0.00 4.63
1608 1752 4.838152 TCCGCCAATCAGCCGAGC 62.838 66.667 0.00 0.00 0.00 5.03
1669 1813 3.573967 ACACCTTGCTTGGGTATTTTCTG 59.426 43.478 1.00 0.00 35.00 3.02
1796 1960 6.497259 TCCCTTCATCATATTGTAGTACTCCC 59.503 42.308 0.00 0.00 0.00 4.30
1821 1985 0.318955 GCAAGTGCGGCTCAATTTGT 60.319 50.000 0.00 0.00 29.43 2.83
1886 2050 4.338118 TCTGTCTTGACAATTGTTGGTTCC 59.662 41.667 13.36 0.00 34.12 3.62
2413 2595 3.444703 ACTGAGACTCAACAGTGTGAC 57.555 47.619 6.61 0.00 44.18 3.67
2461 2645 6.286758 ACAGAGGAAGTATATGCATGTTCAG 58.713 40.000 10.16 0.00 0.00 3.02
2469 2653 7.497249 ACATTTTGAGACAGAGGAAGTATATGC 59.503 37.037 0.00 0.00 0.00 3.14
2478 2662 5.470368 CGTCTTACATTTTGAGACAGAGGA 58.530 41.667 0.00 0.00 39.74 3.71
2531 2715 5.941058 CCAAGACTGAACAGTACTCTCTCTA 59.059 44.000 7.46 0.00 42.66 2.43
2536 2720 3.257127 GCTCCAAGACTGAACAGTACTCT 59.743 47.826 7.46 0.00 42.66 3.24
2544 2728 2.675348 GCATACAGCTCCAAGACTGAAC 59.325 50.000 0.00 0.00 41.15 3.18
2638 7396 1.619827 TGCCCTGGAAAGAAAGCAATG 59.380 47.619 0.00 0.00 0.00 2.82
2639 7397 2.014010 TGCCCTGGAAAGAAAGCAAT 57.986 45.000 0.00 0.00 0.00 3.56
2657 7415 5.355071 TGTTTACATGCTGATTAGGAGCTTG 59.645 40.000 0.00 0.00 43.68 4.01
2666 7424 3.822735 AGCAGTGTGTTTACATGCTGATT 59.177 39.130 15.78 5.31 43.49 2.57
2677 7435 2.301346 CCCAGAGAAAGCAGTGTGTTT 58.699 47.619 0.00 0.00 0.00 2.83
2705 7463 0.464036 GGGCGATCATGGTGTGTAGA 59.536 55.000 0.00 0.00 0.00 2.59
2835 7594 1.002868 GCAAGCCTTGGAGAGCTGA 60.003 57.895 6.57 0.00 39.87 4.26
2866 7637 2.422519 GGATTCCTGCATCACCATGAGT 60.423 50.000 0.00 0.00 30.57 3.41
3037 7808 1.252904 TTAGCGTCCTACGGCAGGTT 61.253 55.000 5.36 0.00 45.71 3.50
3121 7943 3.875865 CCCGGGGGTAAAAGAGAAG 57.124 57.895 14.71 0.00 0.00 2.85
3135 7957 1.033746 ATCTGATTTGCAGCACCCGG 61.034 55.000 0.00 0.00 44.52 5.73
3136 7958 0.099968 CATCTGATTTGCAGCACCCG 59.900 55.000 0.00 0.00 44.52 5.28
3143 7965 6.433716 TCTGAAATGTTACCATCTGATTTGCA 59.566 34.615 0.00 0.00 0.00 4.08
3171 7993 5.859205 AATGCCATCCTTAATCAAACCTC 57.141 39.130 0.00 0.00 0.00 3.85
3189 8011 3.740115 ACGTCCATATCCCTGTTAATGC 58.260 45.455 0.00 0.00 0.00 3.56
3300 8122 1.588674 TACAACACAAGGGTCTTGCG 58.411 50.000 7.48 1.36 0.00 4.85
3367 8189 6.009589 ACACAATTCCATAACAGATCCACAA 58.990 36.000 0.00 0.00 0.00 3.33
3449 8271 1.488705 TTGACCCGAAGATGCCACCT 61.489 55.000 0.00 0.00 0.00 4.00
3517 8339 1.886542 CTCCAAAAGTTTAGCGCCCTT 59.113 47.619 2.29 0.00 0.00 3.95
3527 8349 2.288395 CGCAAAGGCATCTCCAAAAGTT 60.288 45.455 0.00 0.00 41.24 2.66
3533 8355 1.078214 CCTCGCAAAGGCATCTCCA 60.078 57.895 0.00 0.00 38.67 3.86
3534 8356 3.819188 CCTCGCAAAGGCATCTCC 58.181 61.111 0.00 0.00 38.67 3.71
3604 8426 2.432444 CTCCTATCAGCGAGGGACTAG 58.568 57.143 0.00 0.00 41.55 2.57
3614 8436 0.825840 AGGCGTCTCCTCCTATCAGC 60.826 60.000 0.00 0.00 43.20 4.26
3663 8486 1.204113 AGGAGGTCCAAAGGGCTCAG 61.204 60.000 0.00 0.00 38.89 3.35
3665 8488 1.301293 CAGGAGGTCCAAAGGGCTC 59.699 63.158 0.00 0.00 38.89 4.70
3685 8508 2.287188 CGTGAGCAATCACAAGCTTGTT 60.287 45.455 29.23 14.14 42.04 2.83
3709 8532 0.249031 TCAGGCGCATGTCATAGACG 60.249 55.000 22.69 0.00 34.95 4.18
3757 8580 1.134367 CATGAGAAGCCACCATTGCAG 59.866 52.381 0.00 0.00 0.00 4.41
3831 8654 0.685458 ATGGATGCAAAGAGGCCACC 60.685 55.000 5.01 0.00 0.00 4.61
3852 8675 3.527533 AGAAAGCCCCAAAACGAAAAAC 58.472 40.909 0.00 0.00 0.00 2.43
3853 8676 3.897141 AGAAAGCCCCAAAACGAAAAA 57.103 38.095 0.00 0.00 0.00 1.94
3858 8681 1.138069 ACCAAAGAAAGCCCCAAAACG 59.862 47.619 0.00 0.00 0.00 3.60
3889 8712 5.693104 TGAACAACTAGTACAAAGTAAGCCG 59.307 40.000 0.00 0.00 0.00 5.52
3919 8742 5.473504 CCGCCTTTATAGATAAAGCACCAAT 59.526 40.000 14.15 0.00 44.85 3.16
3921 8744 4.385825 CCGCCTTTATAGATAAAGCACCA 58.614 43.478 14.15 0.00 44.85 4.17
3979 8802 0.240945 CCATCCGCAGTTTCCACAAC 59.759 55.000 0.00 0.00 0.00 3.32
3980 8803 0.893270 CCCATCCGCAGTTTCCACAA 60.893 55.000 0.00 0.00 0.00 3.33
3986 8809 0.953960 GTTCGACCCATCCGCAGTTT 60.954 55.000 0.00 0.00 0.00 2.66
4014 8837 5.975693 TCTTTTCGCCCAAATGTATTCTT 57.024 34.783 0.00 0.00 0.00 2.52
4057 8880 4.384647 CCTCCTACCTTTCATTTCCTCCTG 60.385 50.000 0.00 0.00 0.00 3.86
4073 8896 2.187163 GCCTGCCGAACCTCCTAC 59.813 66.667 0.00 0.00 0.00 3.18
4117 8941 6.765989 GCAACTGAGGACCATGTATATAAACA 59.234 38.462 0.00 0.00 0.00 2.83
4133 8957 2.949106 CTTGCACGGCAACTGAGG 59.051 61.111 7.15 0.00 43.99 3.86
4186 9010 8.485578 ACTCTTAAAACCCAAATGAATAACCA 57.514 30.769 0.00 0.00 0.00 3.67
4235 9059 2.601266 CGTTGCCACTTTCCTAAACACG 60.601 50.000 0.00 0.00 0.00 4.49
4242 9159 2.414750 CAACCGTTGCCACTTTCCT 58.585 52.632 0.00 0.00 0.00 3.36
4255 9172 0.605319 TAACCTTGGAGCAGCAACCG 60.605 55.000 0.00 0.00 0.00 4.44
4262 9179 5.710646 AGATCTAGATCTAACCTTGGAGCA 58.289 41.667 29.92 0.00 45.69 4.26


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

AutoCloner maintained by Alex Coulton.