Multiple sequence alignment - TraesCS5A01G337700

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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 TraesCS5A01G337700 chr5A 100.000 3305 0 0 1 3305 545983620 545986924 0.000000e+00 6104.0
1 TraesCS5A01G337700 chr5A 92.346 1790 91 25 998 2750 546146219 546147999 0.000000e+00 2505.0
2 TraesCS5A01G337700 chr5A 95.192 1331 64 0 992 2322 546154208 546155538 0.000000e+00 2104.0
3 TraesCS5A01G337700 chr5A 90.978 1441 116 7 997 2432 545870668 545872099 0.000000e+00 1929.0
4 TraesCS5A01G337700 chr5A 87.791 516 38 5 2813 3305 589021808 589022321 6.150000e-162 580.0
5 TraesCS5A01G337700 chr5A 84.746 531 36 18 2814 3305 473113995 473114519 1.070000e-134 490.0
6 TraesCS5A01G337700 chr5A 83.495 515 41 10 2814 3305 426387532 426388025 1.090000e-119 440.0
7 TraesCS5A01G337700 chr5A 85.577 104 9 5 760 859 546145838 546145939 1.620000e-18 104.0
8 TraesCS5A01G337700 chr5B 90.820 1928 134 24 918 2815 520036714 520038628 0.000000e+00 2540.0
9 TraesCS5A01G337700 chr5B 92.707 1522 99 8 911 2426 519660960 519662475 0.000000e+00 2185.0
10 TraesCS5A01G337700 chr5B 94.515 1331 73 0 992 2322 520046514 520047844 0.000000e+00 2054.0
11 TraesCS5A01G337700 chr5B 86.189 1325 157 15 997 2305 488561072 488562386 0.000000e+00 1410.0
12 TraesCS5A01G337700 chr5B 83.969 393 44 9 519 905 519660476 519660855 3.140000e-95 359.0
13 TraesCS5A01G337700 chr5B 79.302 401 42 15 1 364 519644666 519645062 3.290000e-60 243.0
14 TraesCS5A01G337700 chr5B 90.071 141 14 0 344 484 519645926 519646066 2.030000e-42 183.0
15 TraesCS5A01G337700 chr5B 97.436 39 1 0 867 905 520036592 520036630 2.130000e-07 67.6
16 TraesCS5A01G337700 chr5D 89.580 1881 144 26 914 2753 430445461 430447330 0.000000e+00 2340.0
17 TraesCS5A01G337700 chr5D 94.816 1331 69 0 992 2322 430511639 430512969 0.000000e+00 2076.0
18 TraesCS5A01G337700 chr5D 90.770 1441 119 7 997 2432 430164059 430165490 0.000000e+00 1912.0
19 TraesCS5A01G337700 chr5D 86.717 1325 150 14 997 2305 407517489 407518803 0.000000e+00 1448.0
20 TraesCS5A01G337700 chr5D 76.559 1331 273 27 1001 2301 430968654 430969975 0.000000e+00 693.0
21 TraesCS5A01G337700 chr5D 84.522 659 93 7 1657 2310 430986205 430986859 0.000000e+00 643.0
22 TraesCS5A01G337700 chr5D 79.868 606 63 21 1 557 430444465 430445060 4.000000e-104 388.0
23 TraesCS5A01G337700 chr5D 93.007 143 4 3 763 905 430445236 430445372 1.550000e-48 204.0
24 TraesCS5A01G337700 chr5D 88.235 119 8 4 304 422 430445122 430445234 1.600000e-28 137.0
25 TraesCS5A01G337700 chr6A 87.819 509 36 13 2814 3299 430499798 430500303 1.030000e-159 573.0
26 TraesCS5A01G337700 chr6A 87.273 495 37 8 2834 3305 54775342 54775833 2.900000e-150 542.0
27 TraesCS5A01G337700 chr6A 85.409 514 40 12 2813 3305 275291752 275291253 4.920000e-138 501.0
28 TraesCS5A01G337700 chr6A 84.825 514 43 11 2813 3305 275360535 275360036 4.960000e-133 484.0
29 TraesCS5A01G337700 chr1A 87.598 508 40 13 2814 3301 406141207 406140703 4.790000e-158 568.0
30 TraesCS5A01G337700 chr1A 86.355 513 33 11 2814 3305 578325322 578325818 2.920000e-145 525.0
31 TraesCS5A01G337700 chr1A 92.330 352 22 2 2950 3300 561682283 561682630 2.290000e-136 496.0
32 TraesCS5A01G337700 chr4A 86.460 517 42 8 2814 3305 163822539 163823052 2.900000e-150 542.0
33 TraesCS5A01G337700 chr4A 91.436 362 25 3 2950 3305 202222526 202222887 2.960000e-135 492.0
34 TraesCS5A01G337700 chr7A 87.657 478 36 10 2850 3305 544208536 544209012 4.850000e-148 534.0
35 TraesCS5A01G337700 chr7A 87.333 150 15 2 2814 2960 646136098 646135950 5.670000e-38 169.0
36 TraesCS5A01G337700 chr2A 86.694 481 35 12 2849 3305 734514863 734514388 1.060000e-139 507.0
37 TraesCS5A01G337700 chr3A 85.249 522 41 11 2814 3305 737793192 737793707 3.810000e-139 505.0
38 TraesCS5A01G337700 chr3A 83.456 544 32 21 2813 3305 568965845 568966381 1.400000e-123 453.0
39 TraesCS5A01G337700 chr7D 93.277 119 7 1 2814 2932 17126295 17126412 1.220000e-39 174.0
40 TraesCS5A01G337700 chr4D 93.023 43 1 2 1882 1923 469073050 469073009 9.900000e-06 62.1
41 TraesCS5A01G337700 chr4B 93.023 43 1 2 1882 1923 588787673 588787632 9.900000e-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 TraesCS5A01G337700 chr5A 545983620 545986924 3304 False 6104.00 6104 100.0000 1 3305 1 chr5A.!!$F4 3304
1 TraesCS5A01G337700 chr5A 546154208 546155538 1330 False 2104.00 2104 95.1920 992 2322 1 chr5A.!!$F5 1330
2 TraesCS5A01G337700 chr5A 545870668 545872099 1431 False 1929.00 1929 90.9780 997 2432 1 chr5A.!!$F3 1435
3 TraesCS5A01G337700 chr5A 546145838 546147999 2161 False 1304.50 2505 88.9615 760 2750 2 chr5A.!!$F7 1990
4 TraesCS5A01G337700 chr5A 589021808 589022321 513 False 580.00 580 87.7910 2813 3305 1 chr5A.!!$F6 492
5 TraesCS5A01G337700 chr5A 473113995 473114519 524 False 490.00 490 84.7460 2814 3305 1 chr5A.!!$F2 491
6 TraesCS5A01G337700 chr5B 520046514 520047844 1330 False 2054.00 2054 94.5150 992 2322 1 chr5B.!!$F2 1330
7 TraesCS5A01G337700 chr5B 488561072 488562386 1314 False 1410.00 1410 86.1890 997 2305 1 chr5B.!!$F1 1308
8 TraesCS5A01G337700 chr5B 520036592 520038628 2036 False 1303.80 2540 94.1280 867 2815 2 chr5B.!!$F5 1948
9 TraesCS5A01G337700 chr5B 519660476 519662475 1999 False 1272.00 2185 88.3380 519 2426 2 chr5B.!!$F4 1907
10 TraesCS5A01G337700 chr5B 519644666 519646066 1400 False 213.00 243 84.6865 1 484 2 chr5B.!!$F3 483
11 TraesCS5A01G337700 chr5D 430511639 430512969 1330 False 2076.00 2076 94.8160 992 2322 1 chr5D.!!$F3 1330
12 TraesCS5A01G337700 chr5D 430164059 430165490 1431 False 1912.00 1912 90.7700 997 2432 1 chr5D.!!$F2 1435
13 TraesCS5A01G337700 chr5D 407517489 407518803 1314 False 1448.00 1448 86.7170 997 2305 1 chr5D.!!$F1 1308
14 TraesCS5A01G337700 chr5D 430444465 430447330 2865 False 767.25 2340 87.6725 1 2753 4 chr5D.!!$F6 2752
15 TraesCS5A01G337700 chr5D 430968654 430969975 1321 False 693.00 693 76.5590 1001 2301 1 chr5D.!!$F4 1300
16 TraesCS5A01G337700 chr5D 430986205 430986859 654 False 643.00 643 84.5220 1657 2310 1 chr5D.!!$F5 653
17 TraesCS5A01G337700 chr6A 430499798 430500303 505 False 573.00 573 87.8190 2814 3299 1 chr6A.!!$F2 485
18 TraesCS5A01G337700 chr1A 406140703 406141207 504 True 568.00 568 87.5980 2814 3301 1 chr1A.!!$R1 487
19 TraesCS5A01G337700 chr4A 163822539 163823052 513 False 542.00 542 86.4600 2814 3305 1 chr4A.!!$F1 491
20 TraesCS5A01G337700 chr3A 737793192 737793707 515 False 505.00 505 85.2490 2814 3305 1 chr3A.!!$F2 491
21 TraesCS5A01G337700 chr3A 568965845 568966381 536 False 453.00 453 83.4560 2813 3305 1 chr3A.!!$F1 492

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
626 683 0.172803 GAGGCCTTCATGCAAAGCTG 59.827 55.0 6.77 0.0 0.0 4.24 F
714 776 0.174162 ACGCCACGGTACATCCTAAC 59.826 55.0 0.00 0.0 0.0 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 2045 2.456119 GCAGACCGGCGATGAAGTG 61.456 63.158 9.3 0.0 0.0 3.16 R
2572 3181 3.988976 TCTGCTCCATCTTAAACAGCT 57.011 42.857 0.0 0.0 0.0 4.24 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
34 35 7.792374 TGCTTATCTAATGCCAAAACTCTAG 57.208 36.000 0.00 0.00 0.00 2.43
43 44 4.072131 TGCCAAAACTCTAGTGATCAACC 58.928 43.478 0.00 0.00 0.00 3.77
51 52 2.232941 TCTAGTGATCAACCCCAACGTC 59.767 50.000 0.00 0.00 0.00 4.34
59 70 4.620589 TCAACCCCAACGTCAGTAATTA 57.379 40.909 0.00 0.00 0.00 1.40
66 77 5.151389 CCCAACGTCAGTAATTACAAAAGC 58.849 41.667 17.65 2.74 0.00 3.51
75 86 6.426937 TCAGTAATTACAAAAGCACTCCTCAC 59.573 38.462 17.65 0.00 0.00 3.51
77 88 3.569194 TTACAAAAGCACTCCTCACCA 57.431 42.857 0.00 0.00 0.00 4.17
79 90 2.949447 ACAAAAGCACTCCTCACCAAT 58.051 42.857 0.00 0.00 0.00 3.16
81 92 3.319122 ACAAAAGCACTCCTCACCAATTC 59.681 43.478 0.00 0.00 0.00 2.17
132 147 1.949525 CATCCATAGTTTTCCCCGCTG 59.050 52.381 0.00 0.00 0.00 5.18
135 150 2.167662 CCATAGTTTTCCCCGCTGTTT 58.832 47.619 0.00 0.00 0.00 2.83
163 178 2.992124 TCGTCCTTTCTTGGTGAACA 57.008 45.000 0.00 0.00 33.88 3.18
167 182 3.315191 CGTCCTTTCTTGGTGAACACATT 59.685 43.478 7.25 0.00 33.88 2.71
185 211 1.522668 TTGTTTCCGACAGAGCCATG 58.477 50.000 0.00 0.00 39.94 3.66
195 224 4.899239 GAGCCATGCCCGTCGGAG 62.899 72.222 14.39 3.94 0.00 4.63
212 251 4.092091 GTCGGAGAAAAACATAGCTCACTG 59.908 45.833 0.00 0.00 39.69 3.66
231 270 6.413892 TCACTGCTGGTTCATCAAATATGTA 58.586 36.000 0.00 0.00 0.00 2.29
233 272 7.066163 TCACTGCTGGTTCATCAAATATGTAAG 59.934 37.037 0.00 0.00 0.00 2.34
234 273 7.066163 CACTGCTGGTTCATCAAATATGTAAGA 59.934 37.037 0.00 0.00 0.00 2.10
235 274 7.281774 ACTGCTGGTTCATCAAATATGTAAGAG 59.718 37.037 0.00 0.00 0.00 2.85
236 275 7.112122 TGCTGGTTCATCAAATATGTAAGAGT 58.888 34.615 0.00 0.00 0.00 3.24
237 276 7.066163 TGCTGGTTCATCAAATATGTAAGAGTG 59.934 37.037 0.00 0.00 0.00 3.51
238 277 7.280876 GCTGGTTCATCAAATATGTAAGAGTGA 59.719 37.037 0.00 0.00 0.00 3.41
239 278 9.334947 CTGGTTCATCAAATATGTAAGAGTGAT 57.665 33.333 0.00 0.00 0.00 3.06
271 310 9.723601 AAATTGTACATTGAGCCATATGTTTTT 57.276 25.926 0.00 0.00 36.46 1.94
309 348 8.515414 AGTTTTGTTATTTCTCAGACTATTGCC 58.485 33.333 0.00 0.00 0.00 4.52
313 352 8.402798 TGTTATTTCTCAGACTATTGCCAAAA 57.597 30.769 0.00 0.00 0.00 2.44
316 355 6.560253 TTTCTCAGACTATTGCCAAAAGAC 57.440 37.500 0.00 0.00 0.00 3.01
328 367 4.827692 TGCCAAAAGACTATTTCTAGCGA 58.172 39.130 0.00 0.00 32.51 4.93
330 369 6.578944 TGCCAAAAGACTATTTCTAGCGATA 58.421 36.000 0.00 0.00 32.51 2.92
331 370 7.045416 TGCCAAAAGACTATTTCTAGCGATAA 58.955 34.615 0.00 0.00 32.51 1.75
332 371 7.011109 TGCCAAAAGACTATTTCTAGCGATAAC 59.989 37.037 0.00 0.00 32.51 1.89
333 372 7.224949 GCCAAAAGACTATTTCTAGCGATAACT 59.775 37.037 0.00 0.00 32.51 2.24
334 373 8.543774 CCAAAAGACTATTTCTAGCGATAACTG 58.456 37.037 0.00 0.00 32.51 3.16
335 374 7.701809 AAAGACTATTTCTAGCGATAACTGC 57.298 36.000 0.00 0.00 32.51 4.40
357 402 4.492570 GCAAGTGAAATATTGAGTCGGACG 60.493 45.833 1.89 0.00 0.00 4.79
376 421 6.072838 TCGGACGGCTATTAATACTTGACTAG 60.073 42.308 0.00 0.00 0.00 2.57
429 479 7.899178 TTCAAAAGGAAGAAAAACTGAAACC 57.101 32.000 0.00 0.00 0.00 3.27
450 506 3.379372 CCAAGACATATGTGGCAAGGAAG 59.621 47.826 14.43 0.00 35.06 3.46
453 509 4.666512 AGACATATGTGGCAAGGAAGTTT 58.333 39.130 14.43 0.00 35.06 2.66
455 511 4.406456 ACATATGTGGCAAGGAAGTTTGA 58.594 39.130 7.78 0.00 0.00 2.69
459 515 4.751767 TGTGGCAAGGAAGTTTGATTTT 57.248 36.364 0.00 0.00 0.00 1.82
461 517 6.418057 TGTGGCAAGGAAGTTTGATTTTAT 57.582 33.333 0.00 0.00 0.00 1.40
464 520 6.928492 GTGGCAAGGAAGTTTGATTTTATTCA 59.072 34.615 0.00 0.00 0.00 2.57
467 523 9.002600 GGCAAGGAAGTTTGATTTTATTCATTT 57.997 29.630 0.00 0.00 0.00 2.32
476 532 9.432077 GTTTGATTTTATTCATTTTTGTGCGTT 57.568 25.926 0.00 0.00 0.00 4.84
485 541 6.746104 TCATTTTTGTGCGTTAATTGAGTG 57.254 33.333 0.00 0.00 0.00 3.51
488 544 3.889196 TTGTGCGTTAATTGAGTGGAC 57.111 42.857 0.00 0.00 0.00 4.02
491 547 4.570930 TGTGCGTTAATTGAGTGGACATA 58.429 39.130 0.00 0.00 0.00 2.29
515 571 3.409026 GTGGAACTCATTGTCCACTCT 57.591 47.619 14.20 0.00 46.53 3.24
524 580 4.717877 TCATTGTCCACTCTTCAACATGT 58.282 39.130 0.00 0.00 0.00 3.21
553 609 1.322442 AGGCAAACTCTTGGAACAGC 58.678 50.000 0.00 0.00 42.39 4.40
559 615 3.297134 AACTCTTGGAACAGCCTTTCA 57.703 42.857 0.00 0.00 42.39 2.69
611 668 0.543749 ATACAAGGCAGTGAGGAGGC 59.456 55.000 0.00 0.00 0.00 4.70
616 673 2.596851 GGCAGTGAGGAGGCCTTCA 61.597 63.158 15.31 8.66 44.32 3.02
618 675 0.747283 GCAGTGAGGAGGCCTTCATG 60.747 60.000 15.31 11.99 31.76 3.07
625 682 0.969409 GGAGGCCTTCATGCAAAGCT 60.969 55.000 6.77 0.00 0.00 3.74
626 683 0.172803 GAGGCCTTCATGCAAAGCTG 59.827 55.000 6.77 0.00 0.00 4.24
631 688 2.094390 GCCTTCATGCAAAGCTGATTCA 60.094 45.455 0.00 0.00 0.00 2.57
633 690 3.428999 CCTTCATGCAAAGCTGATTCAGG 60.429 47.826 15.28 0.00 31.21 3.86
640 697 3.242870 GCAAAGCTGATTCAGGATAACCG 60.243 47.826 15.28 0.00 41.83 4.44
646 703 4.513442 CTGATTCAGGATAACCGGACAAA 58.487 43.478 9.46 0.00 39.86 2.83
647 704 4.258543 TGATTCAGGATAACCGGACAAAC 58.741 43.478 9.46 0.00 39.86 2.93
653 715 2.137523 GATAACCGGACAAACACACGT 58.862 47.619 9.46 0.00 0.00 4.49
656 718 0.808453 ACCGGACAAACACACGTGAG 60.808 55.000 25.01 18.00 0.00 3.51
686 748 7.445900 TGTCGAGAAATAATACAAGTAAGCG 57.554 36.000 0.00 0.00 0.00 4.68
688 750 8.183536 TGTCGAGAAATAATACAAGTAAGCGTA 58.816 33.333 0.00 0.00 0.00 4.42
706 768 1.985684 GTAAGTACAACGCCACGGTAC 59.014 52.381 0.00 0.00 38.08 3.34
707 769 0.388659 AAGTACAACGCCACGGTACA 59.611 50.000 0.00 0.00 39.78 2.90
708 770 0.604578 AGTACAACGCCACGGTACAT 59.395 50.000 0.00 0.00 39.78 2.29
709 771 0.994263 GTACAACGCCACGGTACATC 59.006 55.000 0.00 0.00 37.81 3.06
714 776 0.174162 ACGCCACGGTACATCCTAAC 59.826 55.000 0.00 0.00 0.00 2.34
723 785 5.575606 CACGGTACATCCTAACACACTTAAG 59.424 44.000 0.00 0.00 0.00 1.85
727 789 6.592994 GGTACATCCTAACACACTTAAGTTCC 59.407 42.308 5.07 0.00 0.00 3.62
730 792 4.964593 TCCTAACACACTTAAGTTCCACC 58.035 43.478 5.07 0.00 0.00 4.61
734 796 3.958018 ACACACTTAAGTTCCACCACAA 58.042 40.909 5.07 0.00 0.00 3.33
735 797 3.692593 ACACACTTAAGTTCCACCACAAC 59.307 43.478 5.07 0.00 0.00 3.32
756 818 1.066143 ACGCCATGAGGGAAACAGTAG 60.066 52.381 0.00 0.00 40.01 2.57
761 823 3.009033 CCATGAGGGAAACAGTAGGAACA 59.991 47.826 0.00 0.00 40.01 3.18
798 860 4.804806 GGGTAACAGCCCGTTCAA 57.195 55.556 0.00 0.00 39.17 2.69
823 885 5.772521 AGTCAAAACACAAGCATGGATTAC 58.227 37.500 0.00 0.00 0.00 1.89
826 888 5.301551 TCAAAACACAAGCATGGATTACAGT 59.698 36.000 0.00 0.00 0.00 3.55
827 889 6.488344 TCAAAACACAAGCATGGATTACAGTA 59.512 34.615 0.00 0.00 0.00 2.74
828 890 5.880054 AACACAAGCATGGATTACAGTAC 57.120 39.130 0.00 0.00 0.00 2.73
905 994 4.781959 CCGTTTCCCGCGAGCGTA 62.782 66.667 8.23 1.20 37.81 4.42
947 1177 3.609807 GCAAACTTTTGATCATTCTCGCC 59.390 43.478 5.87 0.00 40.55 5.54
948 1178 3.747099 AACTTTTGATCATTCTCGCCG 57.253 42.857 0.00 0.00 0.00 6.46
949 1179 2.009774 ACTTTTGATCATTCTCGCCGG 58.990 47.619 0.00 0.00 0.00 6.13
950 1180 0.732571 TTTTGATCATTCTCGCCGGC 59.267 50.000 19.07 19.07 0.00 6.13
1696 2045 2.555547 AAGGCGCACTTCACCAAGC 61.556 57.895 10.83 0.00 32.85 4.01
2262 2798 3.646637 CCTTCGTACCCCTATTCCAAGAT 59.353 47.826 0.00 0.00 0.00 2.40
2341 2927 5.405571 TGAATTAGTCGAAGAAACAGTGAGC 59.594 40.000 0.00 0.00 39.69 4.26
2342 2928 2.890808 AGTCGAAGAAACAGTGAGCA 57.109 45.000 0.00 0.00 39.69 4.26
2357 2943 4.577693 CAGTGAGCAAGGCACATACATTAT 59.422 41.667 0.00 0.00 38.70 1.28
2382 2970 5.385198 TCATTTATTATTGAGAGGGTGGCC 58.615 41.667 0.00 0.00 0.00 5.36
2389 2983 3.534357 TTGAGAGGGTGGCCAAAAATA 57.466 42.857 7.24 0.00 0.00 1.40
2396 2990 5.073008 AGAGGGTGGCCAAAAATATGTTTTT 59.927 36.000 7.24 7.06 45.78 1.94
2426 3020 5.348986 TCTCGTTGAGAATTGTATAGTGCC 58.651 41.667 0.00 0.00 35.59 5.01
2432 3026 5.804639 TGAGAATTGTATAGTGCCACTGTT 58.195 37.500 7.83 0.00 0.00 3.16
2433 3027 6.941857 TGAGAATTGTATAGTGCCACTGTTA 58.058 36.000 7.83 0.00 0.00 2.41
2434 3028 7.564793 TGAGAATTGTATAGTGCCACTGTTAT 58.435 34.615 7.83 0.00 0.00 1.89
2435 3029 7.710907 TGAGAATTGTATAGTGCCACTGTTATC 59.289 37.037 7.83 1.12 0.00 1.75
2437 3031 8.213679 AGAATTGTATAGTGCCACTGTTATCAT 58.786 33.333 7.83 0.00 0.00 2.45
2438 3032 7.734924 ATTGTATAGTGCCACTGTTATCATG 57.265 36.000 7.83 0.00 0.00 3.07
2439 3033 6.233905 TGTATAGTGCCACTGTTATCATGT 57.766 37.500 7.83 0.00 0.00 3.21
2444 3050 6.485830 AGTGCCACTGTTATCATGTATACT 57.514 37.500 0.00 0.00 0.00 2.12
2483 3089 8.568676 TTCGGATCAAACAAGTTCCATTATAA 57.431 30.769 0.00 0.00 0.00 0.98
2486 3092 8.240682 CGGATCAAACAAGTTCCATTATAAACA 58.759 33.333 0.00 0.00 0.00 2.83
2517 3123 8.611051 ACCTTATCTTACCTACTGTTTGATCT 57.389 34.615 0.00 0.00 0.00 2.75
2536 3142 8.818141 TTGATCTGACTTGAACACTAAACTAG 57.182 34.615 0.00 0.00 0.00 2.57
2588 3197 7.687941 TCCTAAAAAGCTGTTTAAGATGGAG 57.312 36.000 10.31 0.00 0.00 3.86
2590 3199 5.789643 AAAAAGCTGTTTAAGATGGAGCA 57.210 34.783 0.00 0.00 31.80 4.26
2592 3201 3.988976 AGCTGTTTAAGATGGAGCAGA 57.011 42.857 0.00 0.00 31.80 4.26
2604 3213 7.707624 AAGATGGAGCAGATTACAAAAATGA 57.292 32.000 0.00 0.00 0.00 2.57
2633 3242 7.332182 GTGTATTTTGTTTTCTGTGGGAAACAA 59.668 33.333 10.22 10.22 42.80 2.83
2761 3389 8.746751 GCAAAAAGAAACTAAGAATGAGACAAC 58.253 33.333 0.00 0.00 0.00 3.32
2772 3400 7.721286 AAGAATGAGACAACAACAGTAAGAG 57.279 36.000 0.00 0.00 0.00 2.85
2774 3402 7.500992 AGAATGAGACAACAACAGTAAGAGAA 58.499 34.615 0.00 0.00 0.00 2.87
2791 3419 1.228245 AAACACCATGGCAGCGTCT 60.228 52.632 13.04 0.00 0.00 4.18
2811 3439 0.991920 GGGGAGATCCTGGTTGAACA 59.008 55.000 0.00 0.00 35.95 3.18
2955 3605 1.758319 AACGACACAAACACGGCGAG 61.758 55.000 16.62 8.85 0.00 5.03
3138 3802 0.166814 GTAGAACCGCGTGTAGTCGT 59.833 55.000 4.92 0.00 0.00 4.34
3208 3926 1.616930 TGCAACCCTCCCCCGATTA 60.617 57.895 0.00 0.00 0.00 1.75
3271 3990 0.383590 CTGTCGAGGATCATGACGCT 59.616 55.000 0.00 0.00 35.40 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.156736 CTGACGTTGGGGTTGATCAC 58.843 55.000 0.00 0.00 0.00 3.06
43 44 5.151389 GCTTTTGTAATTACTGACGTTGGG 58.849 41.667 16.33 0.06 0.00 4.12
51 52 6.348540 GGTGAGGAGTGCTTTTGTAATTACTG 60.349 42.308 16.33 5.83 0.00 2.74
59 70 2.435372 TTGGTGAGGAGTGCTTTTGT 57.565 45.000 0.00 0.00 0.00 2.83
66 77 7.636150 ATTAAGAATGAATTGGTGAGGAGTG 57.364 36.000 0.00 0.00 0.00 3.51
100 112 9.444600 GGAAAACTATGGATGTTTGAGTTAGTA 57.555 33.333 0.00 0.00 37.64 1.82
132 147 2.750301 AAGGACGAAAGACGCAAAAC 57.250 45.000 0.00 0.00 46.94 2.43
135 150 2.234300 AGAAAGGACGAAAGACGCAA 57.766 45.000 0.00 0.00 46.94 4.85
141 156 3.625764 TGTTCACCAAGAAAGGACGAAAG 59.374 43.478 0.00 0.00 38.13 2.62
163 178 1.202758 TGGCTCTGTCGGAAACAATGT 60.203 47.619 0.00 0.00 37.45 2.71
167 182 0.955428 GCATGGCTCTGTCGGAAACA 60.955 55.000 0.00 0.00 36.18 2.83
185 211 1.664151 CTATGTTTTTCTCCGACGGGC 59.336 52.381 15.25 0.00 0.00 6.13
189 215 4.092091 CAGTGAGCTATGTTTTTCTCCGAC 59.908 45.833 0.00 0.00 0.00 4.79
212 251 7.280876 TCACTCTTACATATTTGATGAACCAGC 59.719 37.037 0.00 0.00 0.00 4.85
283 322 8.515414 GGCAATAGTCTGAGAAATAACAAAACT 58.485 33.333 0.00 0.00 0.00 2.66
299 338 9.606631 CTAGAAATAGTCTTTTGGCAATAGTCT 57.393 33.333 17.76 17.76 37.84 3.24
300 339 8.338986 GCTAGAAATAGTCTTTTGGCAATAGTC 58.661 37.037 15.73 11.20 37.84 2.59
301 340 7.011482 CGCTAGAAATAGTCTTTTGGCAATAGT 59.989 37.037 15.73 4.41 37.84 2.12
309 348 8.058915 GCAGTTATCGCTAGAAATAGTCTTTTG 58.941 37.037 0.00 0.00 37.84 2.44
313 352 6.392625 TGCAGTTATCGCTAGAAATAGTCT 57.607 37.500 0.00 0.00 40.71 3.24
316 355 6.697455 TCACTTGCAGTTATCGCTAGAAATAG 59.303 38.462 0.00 0.00 36.03 1.73
328 367 7.201644 CCGACTCAATATTTCACTTGCAGTTAT 60.202 37.037 0.00 0.00 0.00 1.89
330 369 5.106555 CCGACTCAATATTTCACTTGCAGTT 60.107 40.000 0.00 0.00 0.00 3.16
331 370 4.393062 CCGACTCAATATTTCACTTGCAGT 59.607 41.667 0.00 0.00 0.00 4.40
332 371 4.631377 TCCGACTCAATATTTCACTTGCAG 59.369 41.667 0.00 0.00 0.00 4.41
333 372 4.391830 GTCCGACTCAATATTTCACTTGCA 59.608 41.667 0.00 0.00 0.00 4.08
334 373 4.492570 CGTCCGACTCAATATTTCACTTGC 60.493 45.833 0.00 0.00 0.00 4.01
335 374 4.032900 CCGTCCGACTCAATATTTCACTTG 59.967 45.833 0.00 0.00 0.00 3.16
408 456 7.602644 GTCTTGGTTTCAGTTTTTCTTCCTTTT 59.397 33.333 0.00 0.00 0.00 2.27
414 462 8.695456 ACATATGTCTTGGTTTCAGTTTTTCTT 58.305 29.630 1.41 0.00 0.00 2.52
416 464 7.382218 CCACATATGTCTTGGTTTCAGTTTTTC 59.618 37.037 5.07 0.00 0.00 2.29
419 467 5.278957 GCCACATATGTCTTGGTTTCAGTTT 60.279 40.000 5.07 0.00 32.50 2.66
421 469 3.758554 GCCACATATGTCTTGGTTTCAGT 59.241 43.478 5.07 0.00 32.50 3.41
429 479 4.012374 ACTTCCTTGCCACATATGTCTTG 58.988 43.478 5.07 0.00 0.00 3.02
450 506 8.986039 ACGCACAAAAATGAATAAAATCAAAC 57.014 26.923 0.00 0.00 32.06 2.93
459 515 8.910666 CACTCAATTAACGCACAAAAATGAATA 58.089 29.630 0.00 0.00 0.00 1.75
461 517 6.199908 CCACTCAATTAACGCACAAAAATGAA 59.800 34.615 0.00 0.00 0.00 2.57
464 520 5.689961 GTCCACTCAATTAACGCACAAAAAT 59.310 36.000 0.00 0.00 0.00 1.82
467 523 3.628032 TGTCCACTCAATTAACGCACAAA 59.372 39.130 0.00 0.00 0.00 2.83
469 525 2.839975 TGTCCACTCAATTAACGCACA 58.160 42.857 0.00 0.00 0.00 4.57
476 532 7.888021 AGTTCCACAATTATGTCCACTCAATTA 59.112 33.333 0.00 0.00 37.82 1.40
485 541 6.404734 GGACAATGAGTTCCACAATTATGTCC 60.405 42.308 0.00 0.00 44.18 4.02
488 544 6.151648 AGTGGACAATGAGTTCCACAATTATG 59.848 38.462 19.40 0.00 44.22 1.90
491 547 4.473444 AGTGGACAATGAGTTCCACAATT 58.527 39.130 19.40 1.43 44.22 2.32
515 571 8.394121 GTTTGCCTTCAATAAAAACATGTTGAA 58.606 29.630 12.82 9.83 38.01 2.69
524 580 7.118496 TCCAAGAGTTTGCCTTCAATAAAAA 57.882 32.000 0.00 0.00 32.79 1.94
584 640 7.227512 CCTCCTCACTGCCTTGTATTATTAAAG 59.772 40.741 0.00 0.00 0.00 1.85
585 641 7.054124 CCTCCTCACTGCCTTGTATTATTAAA 58.946 38.462 0.00 0.00 0.00 1.52
586 642 6.591935 CCTCCTCACTGCCTTGTATTATTAA 58.408 40.000 0.00 0.00 0.00 1.40
588 644 4.687219 GCCTCCTCACTGCCTTGTATTATT 60.687 45.833 0.00 0.00 0.00 1.40
590 646 2.170607 GCCTCCTCACTGCCTTGTATTA 59.829 50.000 0.00 0.00 0.00 0.98
591 647 1.065126 GCCTCCTCACTGCCTTGTATT 60.065 52.381 0.00 0.00 0.00 1.89
595 652 2.045536 GGCCTCCTCACTGCCTTG 60.046 66.667 0.00 0.00 42.01 3.61
600 657 0.747283 GCATGAAGGCCTCCTCACTG 60.747 60.000 5.23 8.84 30.89 3.66
611 668 3.428999 CCTGAATCAGCTTTGCATGAAGG 60.429 47.826 4.40 0.00 0.00 3.46
616 673 4.340381 GGTTATCCTGAATCAGCTTTGCAT 59.660 41.667 4.40 0.00 0.00 3.96
618 675 3.242870 CGGTTATCCTGAATCAGCTTTGC 60.243 47.826 4.40 0.00 0.00 3.68
625 682 4.258543 GTTTGTCCGGTTATCCTGAATCA 58.741 43.478 0.00 0.00 0.00 2.57
626 683 4.094442 GTGTTTGTCCGGTTATCCTGAATC 59.906 45.833 0.00 0.00 0.00 2.52
631 688 2.774687 GTGTGTTTGTCCGGTTATCCT 58.225 47.619 0.00 0.00 0.00 3.24
633 690 2.096614 CACGTGTGTTTGTCCGGTTATC 60.097 50.000 7.58 0.00 0.00 1.75
640 697 1.519758 CGTACTCACGTGTGTTTGTCC 59.480 52.381 26.26 10.19 43.31 4.02
653 715 7.529158 TGTATTATTTCTCGACAACGTACTCA 58.471 34.615 0.00 0.00 40.69 3.41
656 718 8.166367 ACTTGTATTATTTCTCGACAACGTAC 57.834 34.615 0.00 0.00 40.69 3.67
686 748 1.985684 GTACCGTGGCGTTGTACTTAC 59.014 52.381 0.00 0.00 33.68 2.34
688 750 0.388659 TGTACCGTGGCGTTGTACTT 59.611 50.000 10.31 0.00 36.63 2.24
700 762 5.244626 ACTTAAGTGTGTTAGGATGTACCGT 59.755 40.000 7.48 0.00 44.74 4.83
706 768 5.411669 GGTGGAACTTAAGTGTGTTAGGATG 59.588 44.000 9.34 0.00 36.74 3.51
707 769 5.072600 TGGTGGAACTTAAGTGTGTTAGGAT 59.927 40.000 9.34 0.00 36.74 3.24
708 770 4.409574 TGGTGGAACTTAAGTGTGTTAGGA 59.590 41.667 9.34 0.00 36.74 2.94
709 771 4.514066 GTGGTGGAACTTAAGTGTGTTAGG 59.486 45.833 9.34 0.00 36.74 2.69
714 776 3.692101 TGTTGTGGTGGAACTTAAGTGTG 59.308 43.478 9.34 0.00 36.74 3.82
723 785 1.452145 ATGGCGTGTTGTGGTGGAAC 61.452 55.000 0.00 0.00 0.00 3.62
727 789 1.575922 CTCATGGCGTGTTGTGGTG 59.424 57.895 6.60 0.00 0.00 4.17
730 792 0.888736 TTCCCTCATGGCGTGTTGTG 60.889 55.000 6.60 0.00 0.00 3.33
734 796 0.606401 CTGTTTCCCTCATGGCGTGT 60.606 55.000 6.60 0.00 0.00 4.49
735 797 0.606401 ACTGTTTCCCTCATGGCGTG 60.606 55.000 0.00 0.00 0.00 5.34
756 818 2.287547 ACGTGCAAATGTCACATGTTCC 60.288 45.455 0.00 0.00 34.27 3.62
761 823 2.030893 CCAGAACGTGCAAATGTCACAT 60.031 45.455 0.00 0.00 34.27 3.21
798 860 6.594788 AATCCATGCTTGTGTTTTGACTAT 57.405 33.333 0.00 0.00 0.00 2.12
823 885 4.473520 CCTGGCCCGCCTGTACTG 62.474 72.222 7.35 0.00 36.94 2.74
905 994 2.028567 GCAACAGAGAGCTTGTAGGAGT 60.029 50.000 0.00 0.00 0.00 3.85
947 1177 2.286418 GCTAATCAAGTTTGATCGGCCG 60.286 50.000 22.12 22.12 46.60 6.13
948 1178 2.286418 CGCTAATCAAGTTTGATCGGCC 60.286 50.000 17.84 0.00 46.60 6.13
949 1179 2.607635 TCGCTAATCAAGTTTGATCGGC 59.392 45.455 7.74 12.58 46.60 5.54
950 1180 3.616821 TGTCGCTAATCAAGTTTGATCGG 59.383 43.478 7.74 5.54 46.60 4.18
1347 1622 0.251354 GGTCAGGATGCAGCTTCAGA 59.749 55.000 0.22 4.90 34.76 3.27
1696 2045 2.456119 GCAGACCGGCGATGAAGTG 61.456 63.158 9.30 0.00 0.00 3.16
2262 2798 5.757886 CATTCTTTGAACGCTTGAAGGTTA 58.242 37.500 0.00 0.00 0.00 2.85
2357 2943 6.323739 GGCCACCCTCTCAATAATAAATGAAA 59.676 38.462 0.00 0.00 0.00 2.69
2407 3001 5.643777 ACAGTGGCACTATACAATTCTCAAC 59.356 40.000 21.59 0.00 0.00 3.18
2503 3109 5.991606 TGTTCAAGTCAGATCAAACAGTAGG 59.008 40.000 0.00 0.00 0.00 3.18
2517 3123 9.607988 TGATTTTCTAGTTTAGTGTTCAAGTCA 57.392 29.630 0.00 0.00 0.00 3.41
2572 3181 3.988976 TCTGCTCCATCTTAAACAGCT 57.011 42.857 0.00 0.00 0.00 4.24
2573 3182 5.586243 TGTAATCTGCTCCATCTTAAACAGC 59.414 40.000 0.00 0.00 0.00 4.40
2604 3213 7.176589 TCCCACAGAAAACAAAATACACTTT 57.823 32.000 0.00 0.00 0.00 2.66
2673 3291 5.127693 TGTAAAACCATTGCATGTACCAC 57.872 39.130 0.00 0.00 0.00 4.16
2676 3294 7.359181 GCTCTTTTGTAAAACCATTGCATGTAC 60.359 37.037 0.00 0.00 0.00 2.90
2686 3304 8.608844 TTTCTTTTTGCTCTTTTGTAAAACCA 57.391 26.923 0.00 0.00 0.00 3.67
2755 3383 5.585047 GGTGTTTCTCTTACTGTTGTTGTCT 59.415 40.000 0.00 0.00 0.00 3.41
2756 3384 5.353123 TGGTGTTTCTCTTACTGTTGTTGTC 59.647 40.000 0.00 0.00 0.00 3.18
2761 3389 4.320494 GCCATGGTGTTTCTCTTACTGTTG 60.320 45.833 14.67 0.00 0.00 3.33
2772 3400 1.210155 GACGCTGCCATGGTGTTTC 59.790 57.895 14.67 0.18 0.00 2.78
2774 3402 1.968017 CAGACGCTGCCATGGTGTT 60.968 57.895 14.67 0.00 0.00 3.32
2791 3419 0.991920 GTTCAACCAGGATCTCCCCA 59.008 55.000 0.00 0.00 36.42 4.96
2795 3423 3.438434 GCTCTTTGTTCAACCAGGATCTC 59.562 47.826 0.00 0.00 0.00 2.75
2811 3439 0.326264 AACGGCTGGAGATGCTCTTT 59.674 50.000 0.00 0.00 0.00 2.52
2847 3475 2.555670 CGTCCCCAGGGGTGATTTTTAA 60.556 50.000 25.52 0.00 44.74 1.52
2899 3528 4.980805 GCCGCGACTGGGTGACAA 62.981 66.667 8.23 0.00 0.00 3.18
2934 3564 1.367195 GCCGTGTTTGTGTCGTTCG 60.367 57.895 0.00 0.00 0.00 3.95
2940 3570 0.741574 TGAACTCGCCGTGTTTGTGT 60.742 50.000 5.98 0.00 0.00 3.72
2955 3605 6.310960 GTGTTTGGTTGAATTTGGTTTGAAC 58.689 36.000 0.00 0.00 0.00 3.18
3242 3960 2.276120 CTCGACAGCGACGACGAG 60.276 66.667 12.29 15.19 42.51 4.18


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

AutoCloner maintained by Alex Coulton.