Multiple sequence alignment - TraesCS5B01G084500

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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 TraesCS5B01G084500 chr5B 100.000 2699 0 0 1 2699 106959051 106961749 0.000000e+00 4985.0
1 TraesCS5B01G084500 chr5B 94.214 1469 59 13 474 1924 105530594 105529134 0.000000e+00 2218.0
2 TraesCS5B01G084500 chr5B 86.262 313 6 10 1 289 105533698 105533399 3.380000e-79 305.0
3 TraesCS5B01G084500 chr5B 95.833 96 4 0 655 750 105530554 105530459 3.600000e-34 156.0
4 TraesCS5B01G084500 chr5B 91.667 108 5 4 487 593 575518844 575518740 2.170000e-31 147.0
5 TraesCS5B01G084500 chr5B 93.814 97 5 1 648 744 286699830 286699925 7.790000e-31 145.0
6 TraesCS5B01G084500 chr5B 87.059 85 10 1 2009 2092 453269613 453269529 7.960000e-16 95.3
7 TraesCS5B01G084500 chr5D 93.162 1477 60 14 474 1924 97587637 97589098 0.000000e+00 2130.0
8 TraesCS5B01G084500 chr5D 87.763 523 26 18 2208 2699 539692132 539692647 6.480000e-161 577.0
9 TraesCS5B01G084500 chr5D 88.123 261 20 5 79 332 97587322 97587578 1.570000e-77 300.0
10 TraesCS5B01G084500 chr5D 90.517 116 6 5 487 601 468686701 468686590 6.020000e-32 148.0
11 TraesCS5B01G084500 chr5D 93.939 99 4 2 668 766 486160709 486160805 6.020000e-32 148.0
12 TraesCS5B01G084500 chr5D 93.939 99 3 3 505 602 97587816 97587912 2.170000e-31 147.0
13 TraesCS5B01G084500 chr5A 93.964 1375 58 16 554 1918 106145865 106144506 0.000000e+00 2056.0
14 TraesCS5B01G084500 chr5A 87.113 388 34 11 79 462 106146393 106146018 2.480000e-115 425.0
15 TraesCS5B01G084500 chr5A 89.062 192 13 7 474 658 106146062 106145872 5.810000e-57 231.0
16 TraesCS5B01G084500 chr6A 87.678 633 35 14 2094 2699 2788929 2789545 0.000000e+00 697.0
17 TraesCS5B01G084500 chr7B 87.520 633 36 14 2094 2699 686970418 686969802 0.000000e+00 691.0
18 TraesCS5B01G084500 chr7B 82.251 462 48 15 2255 2699 139529293 139528849 4.250000e-98 368.0
19 TraesCS5B01G084500 chr7B 87.059 85 10 1 2009 2092 317757801 317757885 7.960000e-16 95.3
20 TraesCS5B01G084500 chr6D 87.220 626 38 14 2094 2699 90342824 90343427 0.000000e+00 675.0
21 TraesCS5B01G084500 chr1D 85.425 494 45 13 2205 2685 416269705 416269226 3.120000e-134 488.0
22 TraesCS5B01G084500 chr1D 94.565 92 4 1 510 601 427630660 427630750 1.010000e-29 141.0
23 TraesCS5B01G084500 chr1B 82.806 506 55 12 2210 2699 678554384 678553895 8.930000e-115 424.0
24 TraesCS5B01G084500 chr1B 92.857 112 3 4 2094 2204 678554540 678554433 1.000000e-34 158.0
25 TraesCS5B01G084500 chr1B 93.939 99 2 3 643 741 22073887 22073981 2.170000e-31 147.0
26 TraesCS5B01G084500 chr1B 93.939 99 3 3 653 749 653876000 653876097 2.170000e-31 147.0
27 TraesCS5B01G084500 chr1B 84.286 140 14 5 1958 2092 415212997 415213133 2.180000e-26 130.0
28 TraesCS5B01G084500 chr2A 95.902 122 4 1 2565 2685 80596376 80596255 2.120000e-46 196.0
29 TraesCS5B01G084500 chr3B 89.565 115 9 3 488 601 526684685 526684573 2.800000e-30 143.0
30 TraesCS5B01G084500 chr3B 96.875 32 1 0 1451 1482 379343158 379343127 1.000000e-03 54.7
31 TraesCS5B01G084500 chr2D 93.750 96 5 1 660 754 386708907 386708812 2.800000e-30 143.0
32 TraesCS5B01G084500 chr3A 97.561 82 1 1 520 601 520963812 520963732 3.620000e-29 139.0
33 TraesCS5B01G084500 chr7A 87.059 85 10 1 2009 2092 127760024 127759940 7.960000e-16 95.3
34 TraesCS5B01G084500 chr3D 96.875 32 1 0 1451 1482 286721532 286721501 1.000000e-03 54.7


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 TraesCS5B01G084500 chr5B 106959051 106961749 2698 False 4985 4985 100.000000 1 2699 1 chr5B.!!$F1 2698
1 TraesCS5B01G084500 chr5B 105529134 105533698 4564 True 893 2218 92.103000 1 1924 3 chr5B.!!$R3 1923
2 TraesCS5B01G084500 chr5D 97587322 97589098 1776 False 859 2130 91.741333 79 1924 3 chr5D.!!$F3 1845
3 TraesCS5B01G084500 chr5D 539692132 539692647 515 False 577 577 87.763000 2208 2699 1 chr5D.!!$F2 491
4 TraesCS5B01G084500 chr5A 106144506 106146393 1887 True 904 2056 90.046333 79 1918 3 chr5A.!!$R1 1839
5 TraesCS5B01G084500 chr6A 2788929 2789545 616 False 697 697 87.678000 2094 2699 1 chr6A.!!$F1 605
6 TraesCS5B01G084500 chr7B 686969802 686970418 616 True 691 691 87.520000 2094 2699 1 chr7B.!!$R2 605
7 TraesCS5B01G084500 chr6D 90342824 90343427 603 False 675 675 87.220000 2094 2699 1 chr6D.!!$F1 605
8 TraesCS5B01G084500 chr1B 678553895 678554540 645 True 291 424 87.831500 2094 2699 2 chr1B.!!$R1 605

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
914 3695 0.250727 TCCACCGAAGCAAAAGGGAG 60.251 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 5009 1.430707 GCGGCGGCGGAGTTTTAATA 61.431 55.0 33.02 0.0 0.0 0.98 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
51 52 2.032681 AGGCAGCAAACCGGACTC 59.967 61.111 9.46 0.00 0.00 3.36
122 147 2.223618 ACTAGATCGAAGCGAGAAAGGC 60.224 50.000 0.00 0.00 39.91 4.35
205 239 0.807667 CCTCATCTTCTCCAACGCCG 60.808 60.000 0.00 0.00 0.00 6.46
206 240 1.424493 CTCATCTTCTCCAACGCCGC 61.424 60.000 0.00 0.00 0.00 6.53
207 241 2.125106 ATCTTCTCCAACGCCGCC 60.125 61.111 0.00 0.00 0.00 6.13
208 242 2.660064 ATCTTCTCCAACGCCGCCT 61.660 57.895 0.00 0.00 0.00 5.52
209 243 2.185310 ATCTTCTCCAACGCCGCCTT 62.185 55.000 0.00 0.00 0.00 4.35
210 244 2.358247 TTCTCCAACGCCGCCTTC 60.358 61.111 0.00 0.00 0.00 3.46
211 245 4.735132 TCTCCAACGCCGCCTTCG 62.735 66.667 0.00 0.00 0.00 3.79
254 294 2.956077 ATCTCCTCCCGCTCCTTCCC 62.956 65.000 0.00 0.00 0.00 3.97
278 318 5.521544 GCGAGTTCTATCTGGTTAGTTAGG 58.478 45.833 0.00 0.00 30.49 2.69
279 319 5.507650 GCGAGTTCTATCTGGTTAGTTAGGG 60.508 48.000 0.00 0.00 30.49 3.53
280 320 5.507650 CGAGTTCTATCTGGTTAGTTAGGGC 60.508 48.000 0.00 0.00 30.49 5.19
357 2634 4.362677 TCTCTATATGGGTCTATTGGGCC 58.637 47.826 0.00 0.00 0.00 5.80
360 2638 5.170198 TCTATATGGGTCTATTGGGCCTTT 58.830 41.667 4.53 0.00 0.00 3.11
361 2639 4.832560 ATATGGGTCTATTGGGCCTTTT 57.167 40.909 4.53 0.00 0.00 2.27
362 2640 2.230130 TGGGTCTATTGGGCCTTTTG 57.770 50.000 4.53 0.00 0.00 2.44
364 2642 1.555967 GGTCTATTGGGCCTTTTGCA 58.444 50.000 4.53 0.00 43.89 4.08
366 2644 2.171003 GTCTATTGGGCCTTTTGCACT 58.829 47.619 4.53 0.00 46.54 4.40
367 2645 2.164422 GTCTATTGGGCCTTTTGCACTC 59.836 50.000 4.53 0.00 46.54 3.51
462 2742 7.594351 AAGAGAAGAGAGGAAAAGCAAAAAT 57.406 32.000 0.00 0.00 0.00 1.82
464 2744 8.334263 AGAGAAGAGAGGAAAAGCAAAAATAG 57.666 34.615 0.00 0.00 0.00 1.73
465 2745 6.918626 AGAAGAGAGGAAAAGCAAAAATAGC 58.081 36.000 0.00 0.00 0.00 2.97
466 2746 5.651387 AGAGAGGAAAAGCAAAAATAGCC 57.349 39.130 0.00 0.00 0.00 3.93
467 2747 4.464244 AGAGAGGAAAAGCAAAAATAGCCC 59.536 41.667 0.00 0.00 0.00 5.19
468 2748 3.193479 AGAGGAAAAGCAAAAATAGCCCG 59.807 43.478 0.00 0.00 0.00 6.13
469 2749 3.161866 AGGAAAAGCAAAAATAGCCCGA 58.838 40.909 0.00 0.00 0.00 5.14
470 2750 3.056821 AGGAAAAGCAAAAATAGCCCGAC 60.057 43.478 0.00 0.00 0.00 4.79
471 2751 3.056821 GGAAAAGCAAAAATAGCCCGACT 60.057 43.478 0.00 0.00 0.00 4.18
472 2752 3.850122 AAAGCAAAAATAGCCCGACTC 57.150 42.857 0.00 0.00 0.00 3.36
485 3144 1.339151 CCCGACTCAAAAGAGAAGGGG 60.339 57.143 16.42 11.48 38.10 4.79
515 3174 7.594351 AAGAGAAGAGAGGAAAAGCAAAAAT 57.406 32.000 0.00 0.00 0.00 1.82
517 3176 8.334263 AGAGAAGAGAGGAAAAGCAAAAATAG 57.666 34.615 0.00 0.00 0.00 1.73
616 3394 6.482973 TCAATTGATGAAACTTTTGGGCTTTC 59.517 34.615 3.38 0.00 34.30 2.62
628 3406 7.433680 ACTTTTGGGCTTTCTAACTACAATTG 58.566 34.615 3.24 3.24 0.00 2.32
629 3407 6.969993 TTTGGGCTTTCTAACTACAATTGT 57.030 33.333 16.68 16.68 0.00 2.71
634 3412 6.016610 GGGCTTTCTAACTACAATTGTGTTGA 60.017 38.462 21.42 16.67 39.30 3.18
639 3417 1.535462 ACTACAATTGTGTTGAGCCGC 59.465 47.619 21.42 0.00 39.30 6.53
658 3438 4.265320 GCCGCACATAATAAAGAGCAAAAC 59.735 41.667 0.00 0.00 0.00 2.43
906 3687 1.116536 TACACCACTCCACCGAAGCA 61.117 55.000 0.00 0.00 0.00 3.91
914 3695 0.250727 TCCACCGAAGCAAAAGGGAG 60.251 55.000 0.00 0.00 0.00 4.30
938 3720 1.815840 TTTGCACGTCGCCAAGTCA 60.816 52.632 7.38 0.00 41.33 3.41
939 3721 2.042520 TTTGCACGTCGCCAAGTCAC 62.043 55.000 7.38 0.00 41.33 3.67
940 3722 4.059459 GCACGTCGCCAAGTCACG 62.059 66.667 0.00 0.00 39.48 4.35
941 3723 3.403057 CACGTCGCCAAGTCACGG 61.403 66.667 0.00 0.00 37.86 4.94
955 3737 0.687920 TCACGGCTGAACCATTACCA 59.312 50.000 0.00 0.00 39.03 3.25
960 3742 1.892474 GGCTGAACCATTACCAAGCAA 59.108 47.619 0.00 0.00 38.86 3.91
986 3768 1.298116 GATCCATCGACGACGCGAA 60.298 57.895 15.93 3.51 44.22 4.70
1022 3809 2.876645 GTCGCTTCTGTCGCCGAG 60.877 66.667 0.00 0.00 0.00 4.63
1192 3989 4.787563 GCGCTGTCAATCTATTTCCATGTG 60.788 45.833 0.00 0.00 0.00 3.21
1237 4046 4.947077 CAACAACTTGCAATTTACCGAC 57.053 40.909 0.00 0.00 0.00 4.79
1238 4047 3.262135 ACAACTTGCAATTTACCGACG 57.738 42.857 0.00 0.00 0.00 5.12
1833 4647 1.221466 ATACGATGCGCCATTCGGTG 61.221 55.000 22.68 0.00 46.34 4.94
1861 4675 9.691362 CAATACTGCAGGTTTTTGTATTAAAGT 57.309 29.630 19.93 0.00 33.67 2.66
1877 4691 5.883503 TTAAAGTGGTGTTGTCGAACTTT 57.116 34.783 12.34 12.34 42.21 2.66
1881 4695 3.126343 AGTGGTGTTGTCGAACTTTTGAC 59.874 43.478 2.76 2.76 41.10 3.18
1882 4696 3.075148 TGGTGTTGTCGAACTTTTGACA 58.925 40.909 7.81 7.81 46.88 3.58
1924 4739 6.450545 AGCTTTTCTGCATCTTTAAAAGGAC 58.549 36.000 14.66 5.19 38.67 3.85
1925 4740 6.266330 AGCTTTTCTGCATCTTTAAAAGGACT 59.734 34.615 14.66 6.60 38.67 3.85
1926 4741 7.448469 AGCTTTTCTGCATCTTTAAAAGGACTA 59.552 33.333 14.66 0.00 38.67 2.59
1927 4742 7.752686 GCTTTTCTGCATCTTTAAAAGGACTAG 59.247 37.037 14.66 0.00 38.67 2.57
1928 4743 8.691661 TTTTCTGCATCTTTAAAAGGACTAGT 57.308 30.769 0.00 0.00 0.00 2.57
1929 4744 9.787435 TTTTCTGCATCTTTAAAAGGACTAGTA 57.213 29.630 0.00 0.00 0.00 1.82
1930 4745 9.436957 TTTCTGCATCTTTAAAAGGACTAGTAG 57.563 33.333 0.00 0.00 0.00 2.57
1931 4746 8.362464 TCTGCATCTTTAAAAGGACTAGTAGA 57.638 34.615 3.59 0.00 0.00 2.59
1932 4747 8.812972 TCTGCATCTTTAAAAGGACTAGTAGAA 58.187 33.333 3.59 0.00 0.00 2.10
1933 4748 9.606631 CTGCATCTTTAAAAGGACTAGTAGAAT 57.393 33.333 3.59 0.00 0.00 2.40
1934 4749 9.383519 TGCATCTTTAAAAGGACTAGTAGAATG 57.616 33.333 3.59 0.00 0.00 2.67
1935 4750 8.338986 GCATCTTTAAAAGGACTAGTAGAATGC 58.661 37.037 3.59 1.86 0.00 3.56
1936 4751 9.383519 CATCTTTAAAAGGACTAGTAGAATGCA 57.616 33.333 3.59 0.00 0.00 3.96
1937 4752 8.773404 TCTTTAAAAGGACTAGTAGAATGCAC 57.227 34.615 3.59 0.00 0.00 4.57
1938 4753 7.544566 TCTTTAAAAGGACTAGTAGAATGCACG 59.455 37.037 3.59 0.00 0.00 5.34
1939 4754 4.803098 AAAGGACTAGTAGAATGCACGT 57.197 40.909 3.59 0.00 0.00 4.49
1940 4755 3.784701 AGGACTAGTAGAATGCACGTG 57.215 47.619 12.28 12.28 0.00 4.49
1941 4756 2.159226 AGGACTAGTAGAATGCACGTGC 60.159 50.000 33.11 33.11 42.50 5.34
1957 4772 2.704725 GTGCATTGTCACGGACATTT 57.295 45.000 7.43 0.00 42.40 2.32
1958 4773 3.011949 GTGCATTGTCACGGACATTTT 57.988 42.857 7.43 0.00 42.40 1.82
1959 4774 4.153958 GTGCATTGTCACGGACATTTTA 57.846 40.909 7.43 0.00 42.40 1.52
1960 4775 4.541779 GTGCATTGTCACGGACATTTTAA 58.458 39.130 7.43 0.00 42.40 1.52
1961 4776 4.979197 GTGCATTGTCACGGACATTTTAAA 59.021 37.500 7.43 0.00 42.40 1.52
1962 4777 5.460419 GTGCATTGTCACGGACATTTTAAAA 59.540 36.000 2.51 2.51 42.40 1.52
1963 4778 6.019479 GTGCATTGTCACGGACATTTTAAAAA 60.019 34.615 4.44 0.00 42.40 1.94
1964 4779 6.703607 TGCATTGTCACGGACATTTTAAAAAT 59.296 30.769 4.44 0.00 42.40 1.82
1965 4780 7.095857 TGCATTGTCACGGACATTTTAAAAATC 60.096 33.333 4.44 5.94 42.40 2.17
1966 4781 7.116233 GCATTGTCACGGACATTTTAAAAATCT 59.884 33.333 4.44 0.00 42.40 2.40
1967 4782 8.977505 CATTGTCACGGACATTTTAAAAATCTT 58.022 29.630 4.44 0.00 42.40 2.40
1968 4783 8.934507 TTGTCACGGACATTTTAAAAATCTTT 57.065 26.923 4.44 0.00 42.40 2.52
1969 4784 8.568732 TGTCACGGACATTTTAAAAATCTTTC 57.431 30.769 4.44 0.00 37.67 2.62
1970 4785 8.410141 TGTCACGGACATTTTAAAAATCTTTCT 58.590 29.630 4.44 0.00 37.67 2.52
1971 4786 8.690840 GTCACGGACATTTTAAAAATCTTTCTG 58.309 33.333 4.44 5.15 32.09 3.02
1972 4787 7.381139 TCACGGACATTTTAAAAATCTTTCTGC 59.619 33.333 4.44 0.00 0.00 4.26
1973 4788 7.382218 CACGGACATTTTAAAAATCTTTCTGCT 59.618 33.333 4.44 0.00 0.00 4.24
1974 4789 7.926018 ACGGACATTTTAAAAATCTTTCTGCTT 59.074 29.630 4.44 0.00 0.00 3.91
1975 4790 8.427774 CGGACATTTTAAAAATCTTTCTGCTTC 58.572 33.333 4.44 0.00 0.00 3.86
1976 4791 9.260002 GGACATTTTAAAAATCTTTCTGCTTCA 57.740 29.630 4.44 0.00 0.00 3.02
1984 4799 8.928270 AAAAATCTTTCTGCTTCATCATGATC 57.072 30.769 4.86 0.00 0.00 2.92
1985 4800 7.640597 AAATCTTTCTGCTTCATCATGATCA 57.359 32.000 4.86 0.00 0.00 2.92
1986 4801 7.825331 AATCTTTCTGCTTCATCATGATCAT 57.175 32.000 4.86 1.18 0.00 2.45
1987 4802 6.619801 TCTTTCTGCTTCATCATGATCATG 57.380 37.500 26.79 26.79 40.09 3.07
1988 4803 6.120220 TCTTTCTGCTTCATCATGATCATGT 58.880 36.000 30.01 17.46 39.72 3.21
1989 4804 6.602009 TCTTTCTGCTTCATCATGATCATGTT 59.398 34.615 30.01 21.64 39.72 2.71
1990 4805 6.769134 TTCTGCTTCATCATGATCATGTTT 57.231 33.333 30.01 18.55 39.72 2.83
1991 4806 6.769134 TCTGCTTCATCATGATCATGTTTT 57.231 33.333 30.01 16.38 39.72 2.43
1992 4807 7.868906 TCTGCTTCATCATGATCATGTTTTA 57.131 32.000 30.01 15.10 39.72 1.52
1993 4808 7.700505 TCTGCTTCATCATGATCATGTTTTAC 58.299 34.615 30.01 18.40 39.72 2.01
1994 4809 7.555195 TCTGCTTCATCATGATCATGTTTTACT 59.445 33.333 30.01 10.50 39.72 2.24
1995 4810 7.477494 TGCTTCATCATGATCATGTTTTACTG 58.523 34.615 30.01 19.13 39.72 2.74
1996 4811 7.121611 TGCTTCATCATGATCATGTTTTACTGT 59.878 33.333 30.01 8.91 39.72 3.55
1997 4812 7.642978 GCTTCATCATGATCATGTTTTACTGTC 59.357 37.037 30.01 12.11 39.72 3.51
1998 4813 8.564509 TTCATCATGATCATGTTTTACTGTCA 57.435 30.769 30.01 11.40 39.72 3.58
1999 4814 8.564509 TCATCATGATCATGTTTTACTGTCAA 57.435 30.769 30.01 10.93 39.72 3.18
2000 4815 9.012161 TCATCATGATCATGTTTTACTGTCAAA 57.988 29.630 30.01 10.74 39.72 2.69
2001 4816 9.628746 CATCATGATCATGTTTTACTGTCAAAA 57.371 29.630 30.01 10.34 39.72 2.44
2045 4860 9.669353 ATGATATTTCTCGTTGCAATTAATGTC 57.331 29.630 0.59 6.99 0.00 3.06
2046 4861 8.672815 TGATATTTCTCGTTGCAATTAATGTCA 58.327 29.630 0.59 9.23 0.00 3.58
2047 4862 9.669353 GATATTTCTCGTTGCAATTAATGTCAT 57.331 29.630 0.59 0.00 0.00 3.06
2050 4865 9.853555 ATTTCTCGTTGCAATTAATGTCATTAA 57.146 25.926 18.09 18.09 38.90 1.40
2051 4866 9.684448 TTTCTCGTTGCAATTAATGTCATTAAA 57.316 25.926 19.35 3.28 38.15 1.52
2052 4867 9.853555 TTCTCGTTGCAATTAATGTCATTAAAT 57.146 25.926 19.35 10.44 38.15 1.40
2053 4868 9.853555 TCTCGTTGCAATTAATGTCATTAAATT 57.146 25.926 19.35 12.26 38.15 1.82
2081 4896 6.445267 GATCTATCGAAGCATGTGTAAGTG 57.555 41.667 0.00 0.00 0.00 3.16
2082 4897 4.112634 TCTATCGAAGCATGTGTAAGTGC 58.887 43.478 0.00 0.00 41.57 4.40
2083 4898 2.162319 TCGAAGCATGTGTAAGTGCA 57.838 45.000 0.00 0.00 43.63 4.57
2084 4899 2.488952 TCGAAGCATGTGTAAGTGCAA 58.511 42.857 0.00 0.00 43.63 4.08
2085 4900 2.875317 TCGAAGCATGTGTAAGTGCAAA 59.125 40.909 0.00 0.00 43.63 3.68
2086 4901 3.313803 TCGAAGCATGTGTAAGTGCAAAA 59.686 39.130 0.00 0.00 43.63 2.44
2087 4902 3.665409 CGAAGCATGTGTAAGTGCAAAAG 59.335 43.478 0.00 0.00 43.63 2.27
2088 4903 4.610945 GAAGCATGTGTAAGTGCAAAAGT 58.389 39.130 0.00 0.00 43.63 2.66
2089 4904 5.559991 CGAAGCATGTGTAAGTGCAAAAGTA 60.560 40.000 0.00 0.00 43.63 2.24
2090 4905 5.766150 AGCATGTGTAAGTGCAAAAGTAA 57.234 34.783 0.00 0.00 43.63 2.24
2091 4906 6.142818 AGCATGTGTAAGTGCAAAAGTAAA 57.857 33.333 0.00 0.00 43.63 2.01
2092 4907 5.977129 AGCATGTGTAAGTGCAAAAGTAAAC 59.023 36.000 0.00 0.00 43.63 2.01
2101 4916 9.078753 GTAAGTGCAAAAGTAAACAGCTTTTTA 57.921 29.630 0.85 0.85 42.25 1.52
2102 4917 8.716646 AAGTGCAAAAGTAAACAGCTTTTTAT 57.283 26.923 8.24 0.00 42.25 1.40
2103 4918 8.130307 AGTGCAAAAGTAAACAGCTTTTTATG 57.870 30.769 8.24 4.29 42.25 1.90
2105 4920 7.011016 GTGCAAAAGTAAACAGCTTTTTATGGT 59.989 33.333 8.24 0.00 42.25 3.55
2106 4921 8.198109 TGCAAAAGTAAACAGCTTTTTATGGTA 58.802 29.630 8.24 0.00 42.25 3.25
2132 4947 3.181416 CCCTATACTGCTAGGAGAAGGGT 60.181 52.174 27.32 9.63 40.76 4.34
2148 4963 8.499406 AGGAGAAGGGTAGCAGTATATATCTAG 58.501 40.741 0.00 0.00 0.00 2.43
2424 5298 2.268920 GCAGGCCTCGAACATCCA 59.731 61.111 0.00 0.00 0.00 3.41
2446 5320 6.069673 TCCACTGCCTTCTTATGGATTAGAAA 60.070 38.462 0.00 0.00 34.50 2.52
2449 5323 8.689972 CACTGCCTTCTTATGGATTAGAAATTT 58.310 33.333 0.00 0.00 30.55 1.82
2494 5376 9.817809 ATATCCGTATATGTGGTATGATTTCAC 57.182 33.333 0.00 0.00 0.00 3.18
2505 5387 6.370718 GTGGTATGATTTCACCGTAGAAACTT 59.629 38.462 2.16 0.21 40.03 2.66
2507 5389 7.546667 TGGTATGATTTCACCGTAGAAACTTAC 59.453 37.037 2.16 8.25 40.03 2.34
2511 5393 4.942761 TTCACCGTAGAAACTTACTGGT 57.057 40.909 0.00 0.00 33.68 4.00
2532 5414 7.113658 TGGTGTTAAAAATTTCTTGCAGGTA 57.886 32.000 0.00 0.00 0.00 3.08
2548 5430 4.035278 CAGGTACTACTGCTAACTGCTC 57.965 50.000 0.00 0.00 39.17 4.26
2668 5572 5.847111 ATACTAAACTATCCGTGAGCACA 57.153 39.130 1.20 0.00 0.00 4.57
2685 5593 0.458260 ACATGTCGCCTACGTATGCA 59.542 50.000 20.51 7.14 41.18 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.029470 CCTGCCTACGGATGAGAGATTC 60.029 54.545 0.00 0.00 0.00 2.52
32 33 4.043200 GTCCGGTTTGCTGCCTGC 62.043 66.667 0.00 0.00 43.25 4.85
51 52 9.113838 GCTGATGTGGAATTACTATATTATGGG 57.886 37.037 0.00 0.00 0.00 4.00
122 147 3.430098 GGTCAACTATGTCAGCCTCTCTG 60.430 52.174 0.00 0.00 44.21 3.35
207 241 3.869272 GACATGGCGGCAGCGAAG 61.869 66.667 19.29 7.18 46.35 3.79
208 242 4.393155 AGACATGGCGGCAGCGAA 62.393 61.111 19.29 0.00 46.35 4.70
212 246 3.200593 GAGCAGACATGGCGGCAG 61.201 66.667 25.96 12.11 36.08 4.85
213 247 2.753009 AAAGAGCAGACATGGCGGCA 62.753 55.000 25.96 16.34 36.08 5.69
254 294 3.694535 ACTAACCAGATAGAACTCGCG 57.305 47.619 0.00 0.00 0.00 5.87
255 295 5.507650 CCCTAACTAACCAGATAGAACTCGC 60.508 48.000 0.00 0.00 30.60 5.03
298 2575 1.205417 ACATAACACGTAACCCTCCGG 59.795 52.381 0.00 0.00 0.00 5.14
357 2634 3.063861 GCAACCCAAAAAGAGTGCAAAAG 59.936 43.478 0.00 0.00 0.00 2.27
360 2638 1.470632 CGCAACCCAAAAAGAGTGCAA 60.471 47.619 0.00 0.00 0.00 4.08
361 2639 0.102120 CGCAACCCAAAAAGAGTGCA 59.898 50.000 0.00 0.00 0.00 4.57
362 2640 0.383949 TCGCAACCCAAAAAGAGTGC 59.616 50.000 0.00 0.00 0.00 4.40
364 2642 1.947456 GAGTCGCAACCCAAAAAGAGT 59.053 47.619 0.00 0.00 0.00 3.24
366 2644 1.314730 GGAGTCGCAACCCAAAAAGA 58.685 50.000 0.00 0.00 0.00 2.52
367 2645 0.040425 CGGAGTCGCAACCCAAAAAG 60.040 55.000 0.00 0.00 0.00 2.27
439 2719 7.094420 GCTATTTTTGCTTTTCCTCTCTTCTCT 60.094 37.037 0.00 0.00 0.00 3.10
462 2742 2.233922 CCTTCTCTTTTGAGTCGGGCTA 59.766 50.000 0.00 0.00 46.30 3.93
464 2744 1.443802 CCTTCTCTTTTGAGTCGGGC 58.556 55.000 0.00 0.00 46.30 6.13
465 2745 1.339151 CCCCTTCTCTTTTGAGTCGGG 60.339 57.143 12.14 12.14 46.56 5.14
466 2746 1.623811 TCCCCTTCTCTTTTGAGTCGG 59.376 52.381 0.00 0.00 46.30 4.79
467 2747 3.402628 TTCCCCTTCTCTTTTGAGTCG 57.597 47.619 0.00 0.00 46.30 4.18
492 3151 7.094420 GCTATTTTTGCTTTTCCTCTCTTCTCT 60.094 37.037 0.00 0.00 0.00 3.10
616 3394 4.669197 GCGGCTCAACACAATTGTAGTTAG 60.669 45.833 11.53 14.48 33.55 2.34
628 3406 4.094294 TCTTTATTATGTGCGGCTCAACAC 59.906 41.667 8.95 0.00 37.31 3.32
629 3407 4.257731 TCTTTATTATGTGCGGCTCAACA 58.742 39.130 8.95 1.19 0.00 3.33
634 3412 2.917933 TGCTCTTTATTATGTGCGGCT 58.082 42.857 0.00 0.00 0.00 5.52
639 3417 8.087750 TCCCTTTGTTTTGCTCTTTATTATGTG 58.912 33.333 0.00 0.00 0.00 3.21
658 3438 0.460311 AGCGGAGTCGTATCCCTTTG 59.540 55.000 3.57 0.00 35.82 2.77
906 3687 2.039418 GTGCAAACCTTCCTCCCTTTT 58.961 47.619 0.00 0.00 0.00 2.27
914 3695 2.251371 GCGACGTGCAAACCTTCC 59.749 61.111 0.00 0.00 45.45 3.46
938 3720 1.821216 CTTGGTAATGGTTCAGCCGT 58.179 50.000 0.00 0.00 41.21 5.68
939 3721 0.451783 GCTTGGTAATGGTTCAGCCG 59.548 55.000 0.00 0.00 41.21 5.52
940 3722 1.544724 TGCTTGGTAATGGTTCAGCC 58.455 50.000 0.00 0.00 37.90 4.85
941 3723 3.578688 CTTTGCTTGGTAATGGTTCAGC 58.421 45.455 0.00 0.00 0.00 4.26
955 3737 0.337428 ATGGATCCCCTGCTTTGCTT 59.663 50.000 9.90 0.00 0.00 3.91
960 3742 1.832912 GTCGATGGATCCCCTGCTT 59.167 57.895 9.90 0.00 0.00 3.91
986 3768 1.606531 GCCATTGCCACCTCTCTCT 59.393 57.895 0.00 0.00 0.00 3.10
1192 3989 3.490759 CACGCACGCATGGAGTCC 61.491 66.667 0.73 0.73 0.00 3.85
1219 4028 1.976045 GCGTCGGTAAATTGCAAGTTG 59.024 47.619 21.57 5.79 0.00 3.16
1861 4675 3.075148 TGTCAAAAGTTCGACAACACCA 58.925 40.909 5.78 0.00 39.14 4.17
1882 4696 5.476091 AAGCTAAGTACAGAAGTGCTTCT 57.524 39.130 8.51 8.51 45.86 2.85
1902 4717 8.787852 ACTAGTCCTTTTAAAGATGCAGAAAAG 58.212 33.333 6.24 3.39 38.20 2.27
1938 4753 2.704725 AAATGTCCGTGACAATGCAC 57.295 45.000 10.17 0.00 45.96 4.57
1939 4754 4.837896 TTAAAATGTCCGTGACAATGCA 57.162 36.364 10.17 0.00 45.96 3.96
1940 4755 6.517914 TTTTTAAAATGTCCGTGACAATGC 57.482 33.333 10.17 0.00 45.96 3.56
1941 4756 8.519492 AGATTTTTAAAATGTCCGTGACAATG 57.481 30.769 7.72 0.00 45.96 2.82
1942 4757 9.541143 AAAGATTTTTAAAATGTCCGTGACAAT 57.459 25.926 7.72 0.60 45.96 2.71
1943 4758 8.934507 AAAGATTTTTAAAATGTCCGTGACAA 57.065 26.923 7.72 0.00 45.96 3.18
1944 4759 8.410141 AGAAAGATTTTTAAAATGTCCGTGACA 58.590 29.630 7.72 8.81 46.90 3.58
1945 4760 8.690840 CAGAAAGATTTTTAAAATGTCCGTGAC 58.309 33.333 7.72 0.00 0.00 3.67
1946 4761 7.381139 GCAGAAAGATTTTTAAAATGTCCGTGA 59.619 33.333 7.72 0.00 0.00 4.35
1947 4762 7.382218 AGCAGAAAGATTTTTAAAATGTCCGTG 59.618 33.333 7.72 3.80 0.00 4.94
1948 4763 7.433680 AGCAGAAAGATTTTTAAAATGTCCGT 58.566 30.769 7.72 0.00 0.00 4.69
1949 4764 7.873739 AGCAGAAAGATTTTTAAAATGTCCG 57.126 32.000 7.72 0.00 0.00 4.79
1950 4765 9.260002 TGAAGCAGAAAGATTTTTAAAATGTCC 57.740 29.630 7.72 0.65 0.00 4.02
1959 4774 8.528643 TGATCATGATGAAGCAGAAAGATTTTT 58.471 29.630 14.30 0.00 0.00 1.94
1960 4775 8.063200 TGATCATGATGAAGCAGAAAGATTTT 57.937 30.769 14.30 0.00 0.00 1.82
1961 4776 7.640597 TGATCATGATGAAGCAGAAAGATTT 57.359 32.000 14.30 0.00 0.00 2.17
1962 4777 7.285629 ACATGATCATGATGAAGCAGAAAGATT 59.714 33.333 36.37 9.76 41.20 2.40
1963 4778 6.773200 ACATGATCATGATGAAGCAGAAAGAT 59.227 34.615 36.37 10.12 41.20 2.40
1964 4779 6.120220 ACATGATCATGATGAAGCAGAAAGA 58.880 36.000 36.37 0.00 41.20 2.52
1965 4780 6.378710 ACATGATCATGATGAAGCAGAAAG 57.621 37.500 36.37 10.06 41.20 2.62
1966 4781 6.769134 AACATGATCATGATGAAGCAGAAA 57.231 33.333 36.37 0.00 41.20 2.52
1967 4782 6.769134 AAACATGATCATGATGAAGCAGAA 57.231 33.333 36.37 0.00 41.20 3.02
1968 4783 6.769134 AAAACATGATCATGATGAAGCAGA 57.231 33.333 36.37 0.00 41.20 4.26
1969 4784 7.644157 CAGTAAAACATGATCATGATGAAGCAG 59.356 37.037 36.37 17.89 41.20 4.24
1970 4785 7.121611 ACAGTAAAACATGATCATGATGAAGCA 59.878 33.333 36.37 14.87 41.20 3.91
1971 4786 7.478322 ACAGTAAAACATGATCATGATGAAGC 58.522 34.615 36.37 21.65 41.20 3.86
1972 4787 8.671028 TGACAGTAAAACATGATCATGATGAAG 58.329 33.333 36.37 21.85 41.20 3.02
1973 4788 8.564509 TGACAGTAAAACATGATCATGATGAA 57.435 30.769 36.37 18.65 41.20 2.57
1974 4789 8.564509 TTGACAGTAAAACATGATCATGATGA 57.435 30.769 36.37 18.16 41.20 2.92
1975 4790 9.628746 TTTTGACAGTAAAACATGATCATGATG 57.371 29.630 36.37 24.49 41.20 3.07
2019 4834 9.669353 GACATTAATTGCAACGAGAAATATCAT 57.331 29.630 0.00 0.00 0.00 2.45
2020 4835 8.672815 TGACATTAATTGCAACGAGAAATATCA 58.327 29.630 0.00 0.00 0.00 2.15
2021 4836 9.669353 ATGACATTAATTGCAACGAGAAATATC 57.331 29.630 0.00 0.00 0.00 1.63
2024 4839 9.853555 TTAATGACATTAATTGCAACGAGAAAT 57.146 25.926 15.20 0.00 30.25 2.17
2025 4840 9.684448 TTTAATGACATTAATTGCAACGAGAAA 57.316 25.926 18.88 1.60 34.92 2.52
2026 4841 9.853555 ATTTAATGACATTAATTGCAACGAGAA 57.146 25.926 18.88 3.02 34.92 2.87
2027 4842 9.853555 AATTTAATGACATTAATTGCAACGAGA 57.146 25.926 18.88 3.46 34.92 4.04
2057 4872 8.227689 GCACTTACACATGCTTCGATAGATCG 62.228 46.154 5.55 5.55 43.67 3.69
2058 4873 5.107683 GCACTTACACATGCTTCGATAGATC 60.108 44.000 0.00 0.00 38.49 2.75
2059 4874 4.747108 GCACTTACACATGCTTCGATAGAT 59.253 41.667 0.00 0.00 38.49 1.98
2060 4875 4.112634 GCACTTACACATGCTTCGATAGA 58.887 43.478 0.00 0.00 40.17 1.98
2061 4876 3.865164 TGCACTTACACATGCTTCGATAG 59.135 43.478 0.00 0.00 42.55 2.08
2062 4877 3.855858 TGCACTTACACATGCTTCGATA 58.144 40.909 0.00 0.00 42.55 2.92
2063 4878 2.698803 TGCACTTACACATGCTTCGAT 58.301 42.857 0.00 0.00 42.55 3.59
2064 4879 2.162319 TGCACTTACACATGCTTCGA 57.838 45.000 0.00 0.00 42.55 3.71
2065 4880 2.967459 TTGCACTTACACATGCTTCG 57.033 45.000 0.00 0.00 42.55 3.79
2066 4881 4.610945 ACTTTTGCACTTACACATGCTTC 58.389 39.130 0.00 0.00 42.55 3.86
2067 4882 4.654091 ACTTTTGCACTTACACATGCTT 57.346 36.364 0.00 0.00 42.55 3.91
2068 4883 5.766150 TTACTTTTGCACTTACACATGCT 57.234 34.783 0.00 0.00 42.55 3.79
2069 4884 5.746245 TGTTTACTTTTGCACTTACACATGC 59.254 36.000 0.00 0.00 42.40 4.06
2070 4885 6.074888 GCTGTTTACTTTTGCACTTACACATG 60.075 38.462 0.00 0.00 0.00 3.21
2071 4886 5.977129 GCTGTTTACTTTTGCACTTACACAT 59.023 36.000 0.00 0.00 0.00 3.21
2072 4887 5.124776 AGCTGTTTACTTTTGCACTTACACA 59.875 36.000 0.00 0.00 0.00 3.72
2073 4888 5.578776 AGCTGTTTACTTTTGCACTTACAC 58.421 37.500 0.00 0.00 0.00 2.90
2074 4889 5.828299 AGCTGTTTACTTTTGCACTTACA 57.172 34.783 0.00 0.00 0.00 2.41
2075 4890 7.520119 AAAAGCTGTTTACTTTTGCACTTAC 57.480 32.000 0.97 0.00 43.76 2.34
2076 4891 9.810545 ATAAAAAGCTGTTTACTTTTGCACTTA 57.189 25.926 11.34 0.00 44.44 2.24
2077 4892 8.603181 CATAAAAAGCTGTTTACTTTTGCACTT 58.397 29.630 11.34 0.00 44.44 3.16
2078 4893 7.224557 CCATAAAAAGCTGTTTACTTTTGCACT 59.775 33.333 11.34 0.00 44.44 4.40
2079 4894 7.011016 ACCATAAAAAGCTGTTTACTTTTGCAC 59.989 33.333 11.34 0.00 44.44 4.57
2080 4895 7.044798 ACCATAAAAAGCTGTTTACTTTTGCA 58.955 30.769 11.34 0.00 44.44 4.08
2081 4896 7.477144 ACCATAAAAAGCTGTTTACTTTTGC 57.523 32.000 11.34 0.00 44.44 3.68
2082 4897 9.744468 ACTACCATAAAAAGCTGTTTACTTTTG 57.256 29.630 11.34 6.06 44.44 2.44
2085 4900 9.006839 GGTACTACCATAAAAAGCTGTTTACTT 57.993 33.333 11.34 1.95 38.42 2.24
2086 4901 7.609146 GGGTACTACCATAAAAAGCTGTTTACT 59.391 37.037 11.34 0.52 41.02 2.24
2087 4902 7.609146 AGGGTACTACCATAAAAAGCTGTTTAC 59.391 37.037 11.34 0.00 41.02 2.01
2088 4903 7.692172 AGGGTACTACCATAAAAAGCTGTTTA 58.308 34.615 11.50 11.50 41.02 2.01
2089 4904 6.549242 AGGGTACTACCATAAAAAGCTGTTT 58.451 36.000 7.15 7.15 41.02 2.83
2090 4905 6.135819 AGGGTACTACCATAAAAAGCTGTT 57.864 37.500 7.57 0.00 41.02 3.16
2091 4906 5.774102 AGGGTACTACCATAAAAAGCTGT 57.226 39.130 7.57 0.00 41.02 4.40
2092 4907 8.648693 AGTATAGGGTACTACCATAAAAAGCTG 58.351 37.037 7.57 0.00 38.11 4.24
2101 4916 5.554747 TCCTAGCAGTATAGGGTACTACCAT 59.445 44.000 7.57 2.47 42.36 3.55
2102 4917 4.915809 TCCTAGCAGTATAGGGTACTACCA 59.084 45.833 7.57 0.00 42.36 3.25
2103 4918 5.250313 TCTCCTAGCAGTATAGGGTACTACC 59.750 48.000 0.00 0.00 42.36 3.18
2105 4920 6.012683 CCTTCTCCTAGCAGTATAGGGTACTA 60.013 46.154 0.16 0.00 42.36 1.82
2106 4921 5.222171 CCTTCTCCTAGCAGTATAGGGTACT 60.222 48.000 0.16 0.00 42.36 2.73
2132 4947 7.849160 ACGGTGAGACTAGATATATACTGCTA 58.151 38.462 0.00 0.00 0.00 3.49
2148 4963 2.917971 CTCGAGAAATCAACGGTGAGAC 59.082 50.000 9.97 2.63 37.14 3.36
2193 5009 1.430707 GCGGCGGCGGAGTTTTAATA 61.431 55.000 33.02 0.00 0.00 0.98
2424 5298 8.829373 AAATTTCTAATCCATAAGAAGGCAGT 57.171 30.769 0.00 0.00 33.49 4.40
2494 5376 7.481275 TTTTAACACCAGTAAGTTTCTACGG 57.519 36.000 0.00 0.00 0.00 4.02
2505 5387 7.147811 ACCTGCAAGAAATTTTTAACACCAGTA 60.148 33.333 0.00 0.00 34.07 2.74
2507 5389 6.048509 ACCTGCAAGAAATTTTTAACACCAG 58.951 36.000 0.00 0.00 34.07 4.00
2511 5393 9.127277 AGTAGTACCTGCAAGAAATTTTTAACA 57.873 29.630 0.00 0.00 34.07 2.41
2548 5430 3.066760 GCAATCGGTTATTTCCAAGGAGG 59.933 47.826 0.00 0.00 39.47 4.30
2668 5572 1.605457 CCATGCATACGTAGGCGACAT 60.605 52.381 25.15 12.10 42.00 3.06


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

AutoCloner maintained by Alex Coulton.