Multiple sequence alignment - TraesCS4B01G241500

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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 TraesCS4B01G241500 chr4B 100.000 4900 0 0 1 4900 500258132 500253233 0.000000e+00 9049.0
1 TraesCS4B01G241500 chr4B 83.920 597 54 25 4165 4731 124595960 124596544 2.600000e-147 532.0
2 TraesCS4B01G241500 chr4D 91.273 3873 144 67 8 3794 403400264 403396500 0.000000e+00 5101.0
3 TraesCS4B01G241500 chr4D 97.714 175 4 0 4726 4900 403396508 403396334 7.970000e-78 302.0
4 TraesCS4B01G241500 chr4D 80.000 135 27 0 4730 4864 301299462 301299328 3.120000e-17 100.0
5 TraesCS4B01G241500 chr4A 91.522 1899 79 38 712 2585 60929234 60927393 0.000000e+00 2540.0
6 TraesCS4B01G241500 chr4A 86.413 1104 59 34 2712 3794 60927293 60926260 0.000000e+00 1123.0
7 TraesCS4B01G241500 chr4A 81.213 676 56 34 1 628 60929883 60929231 3.430000e-131 479.0
8 TraesCS4B01G241500 chr4A 97.076 171 5 0 4730 4900 60926264 60926094 6.210000e-74 289.0
9 TraesCS4B01G241500 chr4A 78.947 133 28 0 4727 4859 180397979 180398111 1.880000e-14 91.6
10 TraesCS4B01G241500 chr4A 85.714 56 8 0 3671 3726 737868611 737868556 5.300000e-05 60.2
11 TraesCS4B01G241500 chr4A 85.714 56 8 0 3671 3726 738053546 738053601 5.300000e-05 60.2
12 TraesCS4B01G241500 chr2D 99.684 948 1 2 3789 4735 542779055 542780001 0.000000e+00 1733.0
13 TraesCS4B01G241500 chr1A 99.893 935 1 0 3795 4729 389872850 389873784 0.000000e+00 1722.0
14 TraesCS4B01G241500 chr1A 99.893 932 1 0 3795 4726 149512080 149511149 0.000000e+00 1716.0
15 TraesCS4B01G241500 chr1A 99.566 922 4 0 3794 4715 520766863 520765942 0.000000e+00 1681.0
16 TraesCS4B01G241500 chr1A 82.271 1004 84 38 3795 4726 575690980 575691961 0.000000e+00 782.0
17 TraesCS4B01G241500 chrUn 97.970 936 15 3 3795 4726 307772982 307772047 0.000000e+00 1620.0
18 TraesCS4B01G241500 chr6B 92.838 754 37 12 3794 4545 4550983 4551721 0.000000e+00 1077.0
19 TraesCS4B01G241500 chr6B 78.559 555 58 34 4175 4717 4817430 4816925 4.760000e-80 309.0
20 TraesCS4B01G241500 chr1B 83.283 999 82 33 3794 4726 657187194 657186215 0.000000e+00 841.0
21 TraesCS4B01G241500 chr1D 84.100 761 68 29 4001 4731 354768450 354769187 0.000000e+00 686.0
22 TraesCS4B01G241500 chr1D 80.505 277 32 10 3795 4053 398943482 398943754 5.010000e-45 193.0
23 TraesCS4B01G241500 chr3A 84.746 590 50 24 4165 4726 46568345 46568922 5.540000e-154 555.0
24 TraesCS4B01G241500 chr3A 84.746 590 50 24 4165 4726 163805021 163805598 5.540000e-154 555.0
25 TraesCS4B01G241500 chr3A 80.139 287 47 9 2117 2398 398884963 398884682 6.430000e-49 206.0
26 TraesCS4B01G241500 chr3A 84.694 98 15 0 4727 4824 131406684 131406781 1.120000e-16 99.0
27 TraesCS4B01G241500 chr3A 78.295 129 23 3 3670 3794 589395278 589395405 1.460000e-10 78.7
28 TraesCS4B01G241500 chr5B 80.351 285 50 6 2117 2398 24115387 24115106 1.380000e-50 211.0
29 TraesCS4B01G241500 chr5B 96.970 33 1 0 4731 4763 354785211 354785243 6.850000e-04 56.5
30 TraesCS4B01G241500 chr5A 80.139 287 47 9 2117 2398 21433394 21433113 6.430000e-49 206.0
31 TraesCS4B01G241500 chr5A 96.970 33 1 0 4731 4763 402907699 402907731 6.850000e-04 56.5
32 TraesCS4B01G241500 chr3B 79.791 287 48 9 2117 2398 395384251 395383970 2.990000e-47 200.0
33 TraesCS4B01G241500 chr3B 89.286 56 6 0 3671 3726 76433068 76433013 2.450000e-08 71.3
34 TraesCS4B01G241500 chr3D 80.576 278 32 10 3794 4053 19290068 19289795 1.390000e-45 195.0
35 TraesCS4B01G241500 chr3D 79.443 287 49 9 2117 2398 323693510 323693791 1.390000e-45 195.0
36 TraesCS4B01G241500 chr5D 79.021 286 52 8 2117 2398 33025526 33025245 6.470000e-44 189.0
37 TraesCS4B01G241500 chr7B 92.727 55 3 1 3672 3726 57633393 57633340 1.460000e-10 78.7
38 TraesCS4B01G241500 chr7B 97.059 34 1 0 2203 2236 577205266 577205233 1.910000e-04 58.4
39 TraesCS4B01G241500 chr6D 95.556 45 2 0 3679 3723 470961823 470961779 6.800000e-09 73.1
40 TraesCS4B01G241500 chr7A 80.952 84 10 6 2156 2236 618241763 618241843 1.470000e-05 62.1
41 TraesCS4B01G241500 chr7A 83.871 62 10 0 3665 3726 5600386 5600447 5.300000e-05 60.2
42 TraesCS4B01G241500 chr7D 85.714 56 8 0 3671 3726 5018167 5018222 5.300000e-05 60.2
43 TraesCS4B01G241500 chr2B 100.000 28 0 0 1519 1546 775127303 775127330 9.000000e-03 52.8


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 TraesCS4B01G241500 chr4B 500253233 500258132 4899 True 9049.00 9049 100.0000 1 4900 1 chr4B.!!$R1 4899
1 TraesCS4B01G241500 chr4B 124595960 124596544 584 False 532.00 532 83.9200 4165 4731 1 chr4B.!!$F1 566
2 TraesCS4B01G241500 chr4D 403396334 403400264 3930 True 2701.50 5101 94.4935 8 4900 2 chr4D.!!$R2 4892
3 TraesCS4B01G241500 chr4A 60926094 60929883 3789 True 1107.75 2540 89.0560 1 4900 4 chr4A.!!$R2 4899
4 TraesCS4B01G241500 chr2D 542779055 542780001 946 False 1733.00 1733 99.6840 3789 4735 1 chr2D.!!$F1 946
5 TraesCS4B01G241500 chr1A 389872850 389873784 934 False 1722.00 1722 99.8930 3795 4729 1 chr1A.!!$F1 934
6 TraesCS4B01G241500 chr1A 149511149 149512080 931 True 1716.00 1716 99.8930 3795 4726 1 chr1A.!!$R1 931
7 TraesCS4B01G241500 chr1A 520765942 520766863 921 True 1681.00 1681 99.5660 3794 4715 1 chr1A.!!$R2 921
8 TraesCS4B01G241500 chr1A 575690980 575691961 981 False 782.00 782 82.2710 3795 4726 1 chr1A.!!$F2 931
9 TraesCS4B01G241500 chrUn 307772047 307772982 935 True 1620.00 1620 97.9700 3795 4726 1 chrUn.!!$R1 931
10 TraesCS4B01G241500 chr6B 4550983 4551721 738 False 1077.00 1077 92.8380 3794 4545 1 chr6B.!!$F1 751
11 TraesCS4B01G241500 chr6B 4816925 4817430 505 True 309.00 309 78.5590 4175 4717 1 chr6B.!!$R1 542
12 TraesCS4B01G241500 chr1B 657186215 657187194 979 True 841.00 841 83.2830 3794 4726 1 chr1B.!!$R1 932
13 TraesCS4B01G241500 chr1D 354768450 354769187 737 False 686.00 686 84.1000 4001 4731 1 chr1D.!!$F1 730
14 TraesCS4B01G241500 chr3A 46568345 46568922 577 False 555.00 555 84.7460 4165 4726 1 chr3A.!!$F1 561
15 TraesCS4B01G241500 chr3A 163805021 163805598 577 False 555.00 555 84.7460 4165 4726 1 chr3A.!!$F3 561

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
396 434 0.179020 TCACTCAACCCCAAGCACAG 60.179 55.0 0.00 0.00 0.00 3.66 F
407 445 0.315886 CAAGCACAGCAGCATTCCAA 59.684 50.0 0.00 0.00 36.85 3.53 F
408 446 0.316204 AAGCACAGCAGCATTCCAAC 59.684 50.0 0.00 0.00 36.85 3.77 F
1461 1533 0.319555 TCGGGCAGAACAAGTTCTCG 60.320 55.0 12.27 12.83 46.13 4.04 F
2824 2957 0.035820 GTTGCGTGGGGTCTAATCCA 60.036 55.0 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1695 0.915364 AGGAGTCCTTGGGCATCTTC 59.085 55.000 5.62 0.00 0.00 2.87 R
2065 2149 1.608717 ATCAGCTTCTTCGAGCCCGT 61.609 55.000 0.00 0.00 43.74 5.28 R
2307 2391 3.812544 TAGTAGGCGCGGAGGGGA 61.813 66.667 8.83 0.00 42.39 4.81 R
3274 3436 0.039256 ACGTTTCATGTGCATGTGCC 60.039 50.000 11.38 0.00 41.18 5.01 R
4773 5104 0.531200 CCTCCACGTTCTGGTACCTC 59.469 60.000 14.36 0.45 41.52 3.85 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
57 58 0.179054 AGCGTGATGATGCAGCTCAT 60.179 50.000 2.53 2.46 38.57 2.90
91 93 1.106944 ACCGGAACCAAAAGCCTGTG 61.107 55.000 9.46 0.00 0.00 3.66
109 111 0.737367 TGAAGCGTGCGATCCTGAAG 60.737 55.000 0.00 0.00 0.00 3.02
137 139 5.997129 CCCAGTTAAATTTGCCTTTTCACAT 59.003 36.000 0.00 0.00 0.00 3.21
162 168 1.534163 GTGAACCTGCCGAGTTTTACC 59.466 52.381 0.00 0.00 0.00 2.85
170 176 1.414897 CGAGTTTTACCGCTGCGTC 59.585 57.895 21.59 8.80 0.00 5.19
171 177 1.007336 CGAGTTTTACCGCTGCGTCT 61.007 55.000 21.59 7.98 0.00 4.18
179 185 3.782244 CGCTGCGTCTTCAGGCAC 61.782 66.667 14.93 0.00 38.50 5.01
180 186 3.426568 GCTGCGTCTTCAGGCACC 61.427 66.667 0.00 0.00 38.50 5.01
181 187 3.114616 CTGCGTCTTCAGGCACCG 61.115 66.667 0.00 0.00 38.50 4.94
182 188 4.680237 TGCGTCTTCAGGCACCGG 62.680 66.667 0.00 0.00 38.50 5.28
312 330 1.400737 GATGCTCGGGTACTACCACT 58.599 55.000 7.57 0.00 41.02 4.00
326 344 2.558286 CCACTGGCACTTGCACTGG 61.558 63.158 3.15 0.47 44.36 4.00
391 429 2.875296 TGGAATTCACTCAACCCCAAG 58.125 47.619 7.93 0.00 0.00 3.61
394 432 1.620822 ATTCACTCAACCCCAAGCAC 58.379 50.000 0.00 0.00 0.00 4.40
395 433 0.257328 TTCACTCAACCCCAAGCACA 59.743 50.000 0.00 0.00 0.00 4.57
396 434 0.179020 TCACTCAACCCCAAGCACAG 60.179 55.000 0.00 0.00 0.00 3.66
397 435 1.529244 ACTCAACCCCAAGCACAGC 60.529 57.895 0.00 0.00 0.00 4.40
398 436 1.529010 CTCAACCCCAAGCACAGCA 60.529 57.895 0.00 0.00 0.00 4.41
399 437 1.521450 CTCAACCCCAAGCACAGCAG 61.521 60.000 0.00 0.00 0.00 4.24
400 438 2.914097 AACCCCAAGCACAGCAGC 60.914 61.111 0.00 0.00 0.00 5.25
401 439 3.736996 AACCCCAAGCACAGCAGCA 62.737 57.895 0.00 0.00 36.85 4.41
402 440 2.678934 CCCCAAGCACAGCAGCAT 60.679 61.111 0.00 0.00 36.85 3.79
403 441 2.280552 CCCCAAGCACAGCAGCATT 61.281 57.895 0.00 0.00 36.85 3.56
404 442 1.214589 CCCAAGCACAGCAGCATTC 59.785 57.895 0.00 0.00 36.85 2.67
405 443 1.214589 CCAAGCACAGCAGCATTCC 59.785 57.895 0.00 0.00 36.85 3.01
406 444 1.529152 CCAAGCACAGCAGCATTCCA 61.529 55.000 0.00 0.00 36.85 3.53
407 445 0.315886 CAAGCACAGCAGCATTCCAA 59.684 50.000 0.00 0.00 36.85 3.53
408 446 0.316204 AAGCACAGCAGCATTCCAAC 59.684 50.000 0.00 0.00 36.85 3.77
496 534 1.139095 GGTTCACCCGTCTAGCTCG 59.861 63.158 0.00 0.00 0.00 5.03
497 535 1.593296 GGTTCACCCGTCTAGCTCGT 61.593 60.000 0.00 0.00 0.00 4.18
650 707 2.092158 GCTAATCTGCCTTTTCCCCTCT 60.092 50.000 0.00 0.00 0.00 3.69
873 945 0.682852 GCCAGTACTACCACCACACA 59.317 55.000 0.00 0.00 0.00 3.72
874 946 1.337823 GCCAGTACTACCACCACACAG 60.338 57.143 0.00 0.00 0.00 3.66
879 951 2.383442 ACTACCACCACACAGAGAGT 57.617 50.000 0.00 0.00 0.00 3.24
896 968 3.873952 GAGAGTGTGTCTGTGCTTTTCTT 59.126 43.478 0.00 0.00 34.71 2.52
920 992 2.758327 CATGGCCATGGCAGTGCT 60.758 61.111 36.56 13.88 42.43 4.40
1164 1236 4.030452 GCGTGGAACAGCAGCACC 62.030 66.667 0.00 0.00 41.80 5.01
1339 1411 3.138798 CCATCCCCGACGACGTCT 61.139 66.667 24.36 3.62 37.88 4.18
1461 1533 0.319555 TCGGGCAGAACAAGTTCTCG 60.320 55.000 12.27 12.83 46.13 4.04
1854 1929 1.451028 GCTGCTCGCCCTGATCTTT 60.451 57.895 0.00 0.00 0.00 2.52
2065 2149 2.037367 CAGGAGGAGGGTCGACCA 59.963 66.667 34.40 0.00 43.89 4.02
2407 2491 4.566070 CCCTCCTCCACGGTAACAAAAATA 60.566 45.833 0.00 0.00 0.00 1.40
2412 2496 7.201835 TCCTCCACGGTAACAAAAATAAAAAC 58.798 34.615 0.00 0.00 0.00 2.43
2430 2515 4.411256 AAACCTTCTCTTTCACCGTACA 57.589 40.909 0.00 0.00 0.00 2.90
2431 2516 3.662247 ACCTTCTCTTTCACCGTACAG 57.338 47.619 0.00 0.00 0.00 2.74
2432 2517 2.963782 ACCTTCTCTTTCACCGTACAGT 59.036 45.455 0.00 0.00 0.00 3.55
2433 2518 3.005578 ACCTTCTCTTTCACCGTACAGTC 59.994 47.826 0.00 0.00 0.00 3.51
2434 2519 3.576648 CTTCTCTTTCACCGTACAGTCC 58.423 50.000 0.00 0.00 0.00 3.85
2435 2520 1.538512 TCTCTTTCACCGTACAGTCCG 59.461 52.381 0.00 0.00 0.00 4.79
2436 2521 1.538512 CTCTTTCACCGTACAGTCCGA 59.461 52.381 0.00 0.00 0.00 4.55
2452 2537 5.163374 ACAGTCCGAGTAACTTTTTACAGGT 60.163 40.000 8.14 0.00 40.25 4.00
2477 2562 2.737376 GGGCCGGATCGTTATCGC 60.737 66.667 5.05 0.00 36.96 4.58
2596 2695 3.320826 CCATTCCGTTTGAGACCCTTTTT 59.679 43.478 0.00 0.00 0.00 1.94
2613 2712 0.543410 TTTACCAGTGCTCCCTCGGA 60.543 55.000 0.00 0.00 0.00 4.55
2617 2716 2.997897 AGTGCTCCCTCGGACACC 60.998 66.667 8.73 0.00 35.73 4.16
2630 2729 2.832672 GGACACCGATCAATTTGCTC 57.167 50.000 0.00 0.00 0.00 4.26
2635 2734 1.009078 CCGATCAATTTGCTCGCTCA 58.991 50.000 15.27 0.00 34.99 4.26
2692 2795 0.683179 GGCCCGGTTTCTTTATGGCT 60.683 55.000 0.00 0.00 38.89 4.75
2725 2851 4.201812 CCAAGGTGTACATTTCATACGCTG 60.202 45.833 0.00 0.00 34.22 5.18
2747 2873 3.417185 GAACTGCAATTTGTACGCTAGC 58.583 45.455 4.06 4.06 0.00 3.42
2749 2875 3.009723 ACTGCAATTTGTACGCTAGCAT 58.990 40.909 16.45 0.65 0.00 3.79
2750 2876 3.181507 ACTGCAATTTGTACGCTAGCATG 60.182 43.478 16.45 1.28 0.00 4.06
2752 2878 3.935828 TGCAATTTGTACGCTAGCATGTA 59.064 39.130 16.45 6.96 0.00 2.29
2753 2879 4.033932 TGCAATTTGTACGCTAGCATGTAG 59.966 41.667 16.45 0.00 0.00 2.74
2754 2880 4.552767 GCAATTTGTACGCTAGCATGTAGG 60.553 45.833 16.45 0.00 0.00 3.18
2755 2881 4.665833 ATTTGTACGCTAGCATGTAGGA 57.334 40.909 16.45 0.00 0.00 2.94
2787 2919 3.151912 ACAGTAGTAGACTTGTCGGGT 57.848 47.619 0.00 0.00 35.64 5.28
2819 2952 2.642254 CCGAGTTGCGTGGGGTCTA 61.642 63.158 0.00 0.00 38.67 2.59
2820 2953 1.290955 CGAGTTGCGTGGGGTCTAA 59.709 57.895 0.00 0.00 34.64 2.10
2821 2954 0.108329 CGAGTTGCGTGGGGTCTAAT 60.108 55.000 0.00 0.00 34.64 1.73
2822 2955 1.653151 GAGTTGCGTGGGGTCTAATC 58.347 55.000 0.00 0.00 0.00 1.75
2823 2956 0.252197 AGTTGCGTGGGGTCTAATCC 59.748 55.000 0.00 0.00 0.00 3.01
2824 2957 0.035820 GTTGCGTGGGGTCTAATCCA 60.036 55.000 0.00 0.00 0.00 3.41
2908 3041 1.539388 CATTTGCGACCAACTTGCCTA 59.461 47.619 0.00 0.00 0.00 3.93
2951 3087 2.814336 AGGCTCTCGTTTTGAAATCCAC 59.186 45.455 0.00 0.00 0.00 4.02
2954 3090 4.093556 GGCTCTCGTTTTGAAATCCACTAG 59.906 45.833 0.00 0.00 0.00 2.57
2955 3091 4.691216 GCTCTCGTTTTGAAATCCACTAGT 59.309 41.667 0.00 0.00 0.00 2.57
2968 3124 3.461061 TCCACTAGTACTGTCCGATACG 58.539 50.000 5.39 0.00 0.00 3.06
3022 3183 5.023533 TGCAGATTGATTCCTGGTAGTAC 57.976 43.478 0.00 0.00 0.00 2.73
3023 3184 4.051922 GCAGATTGATTCCTGGTAGTACG 58.948 47.826 0.00 0.00 0.00 3.67
3024 3185 4.202121 GCAGATTGATTCCTGGTAGTACGA 60.202 45.833 0.00 0.00 0.00 3.43
3025 3186 5.524284 CAGATTGATTCCTGGTAGTACGAG 58.476 45.833 5.38 5.38 0.00 4.18
3026 3187 5.067936 CAGATTGATTCCTGGTAGTACGAGT 59.932 44.000 10.93 0.00 0.00 4.18
3027 3188 6.262496 CAGATTGATTCCTGGTAGTACGAGTA 59.738 42.308 10.93 0.24 0.00 2.59
3028 3189 6.487331 AGATTGATTCCTGGTAGTACGAGTAG 59.513 42.308 10.93 0.00 0.00 2.57
3029 3190 5.108187 TGATTCCTGGTAGTACGAGTAGT 57.892 43.478 10.93 0.00 0.00 2.73
3030 3191 6.239217 TGATTCCTGGTAGTACGAGTAGTA 57.761 41.667 10.93 0.00 0.00 1.82
3200 3362 1.804326 GGCTGGCGTACGTACACAG 60.804 63.158 29.10 29.10 35.32 3.66
3202 3364 0.797249 GCTGGCGTACGTACACAGAG 60.797 60.000 33.82 21.75 34.62 3.35
3204 3366 0.800631 TGGCGTACGTACACAGAGAG 59.199 55.000 24.50 8.18 0.00 3.20
3205 3367 1.081892 GGCGTACGTACACAGAGAGA 58.918 55.000 24.50 0.00 0.00 3.10
3206 3368 1.466167 GGCGTACGTACACAGAGAGAA 59.534 52.381 24.50 0.00 0.00 2.87
3260 3422 3.134081 ACGGGGTAGATAAGAACACATGG 59.866 47.826 0.00 0.00 0.00 3.66
3261 3423 3.494398 CGGGGTAGATAAGAACACATGGG 60.494 52.174 0.00 0.00 0.00 4.00
3262 3424 3.458487 GGGGTAGATAAGAACACATGGGT 59.542 47.826 0.00 0.00 0.00 4.51
3271 3433 3.520862 CACATGGGTGGCATCCGC 61.521 66.667 13.09 0.00 41.45 5.54
3272 3434 4.045781 ACATGGGTGGCATCCGCA 62.046 61.111 13.09 4.71 41.24 5.69
3273 3435 2.520020 CATGGGTGGCATCCGCAT 60.520 61.111 13.09 7.07 41.24 4.73
3274 3436 2.520020 ATGGGTGGCATCCGCATG 60.520 61.111 13.09 0.00 41.24 4.06
3341 3514 3.206246 AACCGTGTTGCACCGTGG 61.206 61.111 0.00 0.00 0.00 4.94
3391 3590 9.507280 GTGTTAATAATCTTCATGTGATTGTGG 57.493 33.333 19.36 0.00 35.90 4.17
3392 3591 9.241919 TGTTAATAATCTTCATGTGATTGTGGT 57.758 29.630 19.36 7.89 35.90 4.16
3539 3739 2.457366 ACATCAAGTCCTCCAACGTC 57.543 50.000 0.00 0.00 0.00 4.34
3719 3919 2.436292 CTGCTGGAGCTGCTCACC 60.436 66.667 28.95 15.49 42.66 4.02
3790 3990 3.991051 CTGGGTGCAGTCCGTCGT 61.991 66.667 0.00 0.00 0.00 4.34
3791 3991 3.916392 CTGGGTGCAGTCCGTCGTC 62.916 68.421 0.00 0.00 0.00 4.20
3792 3992 4.736896 GGGTGCAGTCCGTCGTCC 62.737 72.222 0.00 0.00 0.00 4.79
4773 5104 0.318441 TGTTCGACCAAGAGCTCCTG 59.682 55.000 10.93 7.89 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.082679 CGAGACTCGGCTACTCGTCA 61.083 60.000 17.27 0.00 45.23 4.35
57 58 3.379445 GGTCAAGGACTCGCGGGA 61.379 66.667 15.95 0.92 32.47 5.14
60 61 3.277211 TTCCGGTCAAGGACTCGCG 62.277 63.158 0.00 0.00 40.56 5.87
91 93 2.002127 CTTCAGGATCGCACGCTTC 58.998 57.895 0.00 0.00 0.00 3.86
109 111 1.276138 AGGCAAATTTAACTGGGCAGC 59.724 47.619 0.00 0.00 0.00 5.25
137 139 1.290955 CTCGGCAGGTTCACGGTTA 59.709 57.895 0.00 0.00 0.00 2.85
162 168 3.782244 GTGCCTGAAGACGCAGCG 61.782 66.667 14.82 14.82 35.20 5.18
170 176 1.597797 TACGTACCCGGTGCCTGAAG 61.598 60.000 0.00 0.00 38.78 3.02
171 177 1.606025 TACGTACCCGGTGCCTGAA 60.606 57.895 0.00 0.00 38.78 3.02
179 185 2.088178 GCAACACGTACGTACCCGG 61.088 63.158 22.34 10.93 38.78 5.73
180 186 2.088178 GGCAACACGTACGTACCCG 61.088 63.158 22.34 11.34 40.83 5.28
181 187 1.006337 TGGCAACACGTACGTACCC 60.006 57.895 22.34 17.73 46.17 3.69
182 188 4.651585 TGGCAACACGTACGTACC 57.348 55.556 22.34 19.23 46.17 3.34
391 429 0.109412 GAGTTGGAATGCTGCTGTGC 60.109 55.000 0.00 0.00 0.00 4.57
394 432 1.250328 TTGGAGTTGGAATGCTGCTG 58.750 50.000 0.00 0.00 0.00 4.41
395 433 1.999648 TTTGGAGTTGGAATGCTGCT 58.000 45.000 0.00 0.00 0.00 4.24
396 434 2.297033 TCTTTTGGAGTTGGAATGCTGC 59.703 45.455 0.00 0.00 0.00 5.25
397 435 4.589216 TTCTTTTGGAGTTGGAATGCTG 57.411 40.909 0.00 0.00 0.00 4.41
398 436 5.082425 AGATTCTTTTGGAGTTGGAATGCT 58.918 37.500 0.00 0.00 0.00 3.79
399 437 5.397142 AGATTCTTTTGGAGTTGGAATGC 57.603 39.130 0.00 0.00 0.00 3.56
400 438 5.477984 TGGAGATTCTTTTGGAGTTGGAATG 59.522 40.000 0.00 0.00 0.00 2.67
401 439 5.644188 TGGAGATTCTTTTGGAGTTGGAAT 58.356 37.500 0.00 0.00 0.00 3.01
402 440 5.060427 TGGAGATTCTTTTGGAGTTGGAA 57.940 39.130 0.00 0.00 0.00 3.53
403 441 4.655963 CTGGAGATTCTTTTGGAGTTGGA 58.344 43.478 0.00 0.00 0.00 3.53
404 442 3.192212 GCTGGAGATTCTTTTGGAGTTGG 59.808 47.826 0.00 0.00 0.00 3.77
405 443 3.120060 CGCTGGAGATTCTTTTGGAGTTG 60.120 47.826 0.00 0.00 0.00 3.16
406 444 3.077359 CGCTGGAGATTCTTTTGGAGTT 58.923 45.455 0.00 0.00 0.00 3.01
407 445 2.704572 CGCTGGAGATTCTTTTGGAGT 58.295 47.619 0.00 0.00 0.00 3.85
408 446 1.399791 GCGCTGGAGATTCTTTTGGAG 59.600 52.381 0.00 0.00 0.00 3.86
484 522 1.536284 GGAAATCACGAGCTAGACGGG 60.536 57.143 0.00 9.50 35.35 5.28
486 524 2.853731 AGGAAATCACGAGCTAGACG 57.146 50.000 0.00 0.55 0.00 4.18
496 534 7.068593 TCCATGATGGATTGTTTAGGAAATCAC 59.931 37.037 10.75 0.00 42.67 3.06
497 535 7.124721 TCCATGATGGATTGTTTAGGAAATCA 58.875 34.615 10.75 0.00 42.67 2.57
530 572 8.627208 AATAATACTGCTGCAGTGCTAATAAT 57.373 30.769 37.89 22.26 45.01 1.28
531 573 8.450578 AAATAATACTGCTGCAGTGCTAATAA 57.549 30.769 37.89 21.10 45.01 1.40
532 574 8.450578 AAAATAATACTGCTGCAGTGCTAATA 57.549 30.769 37.89 24.01 45.01 0.98
533 575 6.949352 AAATAATACTGCTGCAGTGCTAAT 57.051 33.333 37.89 23.91 45.01 1.73
534 576 6.757897 AAAATAATACTGCTGCAGTGCTAA 57.242 33.333 37.89 22.82 45.01 3.09
536 578 5.416952 AGAAAAATAATACTGCTGCAGTGCT 59.583 36.000 37.89 27.46 45.01 4.40
537 579 5.644644 AGAAAAATAATACTGCTGCAGTGC 58.355 37.500 37.89 18.19 45.01 4.40
538 580 5.961843 CGAGAAAAATAATACTGCTGCAGTG 59.038 40.000 37.89 17.30 45.01 3.66
540 582 5.961843 CACGAGAAAAATAATACTGCTGCAG 59.038 40.000 27.02 27.02 37.52 4.41
541 583 5.411361 ACACGAGAAAAATAATACTGCTGCA 59.589 36.000 0.88 0.88 0.00 4.41
546 592 8.840867 GCAAAAGACACGAGAAAAATAATACTG 58.159 33.333 0.00 0.00 0.00 2.74
589 641 1.406539 CCGATGAAATGAAAGGCTGGG 59.593 52.381 0.00 0.00 0.00 4.45
650 707 3.610040 TTCTAATCCAAAGCTCGCTCA 57.390 42.857 0.00 0.00 0.00 4.26
831 896 4.579340 CAGTAGTAGAAATAGAGTGGGCGA 59.421 45.833 0.00 0.00 0.00 5.54
873 945 3.133721 AGAAAAGCACAGACACACTCTCT 59.866 43.478 0.00 0.00 0.00 3.10
874 946 3.462021 AGAAAAGCACAGACACACTCTC 58.538 45.455 0.00 0.00 0.00 3.20
879 951 4.517285 AGAAGAAGAAAAGCACAGACACA 58.483 39.130 0.00 0.00 0.00 3.72
886 958 3.366781 GCCATGGAGAAGAAGAAAAGCAC 60.367 47.826 18.40 0.00 0.00 4.40
920 992 0.894141 GCTCTGTCAGCTCAAGGAGA 59.106 55.000 0.00 0.00 45.83 3.71
942 1014 1.517475 GGCGGCGAGAGTCTTCTTC 60.517 63.158 12.98 0.00 32.53 2.87
943 1015 2.574399 GGCGGCGAGAGTCTTCTT 59.426 61.111 12.98 0.00 32.53 2.52
944 1016 3.453679 GGGCGGCGAGAGTCTTCT 61.454 66.667 12.98 0.00 36.01 2.85
965 1037 1.077357 TGAGAGAGAGCGGGAGGAC 60.077 63.158 0.00 0.00 0.00 3.85
1068 1140 2.821688 GAGGTCGTCGGAGCGGTAG 61.822 68.421 0.00 0.00 45.26 3.18
1339 1411 3.838271 GAGCTCGGTCATGCGGGA 61.838 66.667 0.00 0.00 0.00 5.14
1414 1486 2.970974 GCACCAGGTTCTTCAGCGC 61.971 63.158 0.00 0.00 0.00 5.92
1419 1491 2.032681 AGCCGCACCAGGTTCTTC 59.967 61.111 0.00 0.00 0.00 2.87
1623 1695 0.915364 AGGAGTCCTTGGGCATCTTC 59.085 55.000 5.62 0.00 0.00 2.87
1849 1924 2.879103 TTCCGGCAGAGGAAAAAGAT 57.121 45.000 0.00 0.00 46.36 2.40
2065 2149 1.608717 ATCAGCTTCTTCGAGCCCGT 61.609 55.000 0.00 0.00 43.74 5.28
2175 2259 4.729856 ACCGCCTTGTACGCCGTC 62.730 66.667 0.00 0.00 0.00 4.79
2307 2391 3.812544 TAGTAGGCGCGGAGGGGA 61.813 66.667 8.83 0.00 42.39 4.81
2407 2491 5.187687 TGTACGGTGAAAGAGAAGGTTTTT 58.812 37.500 0.00 0.00 0.00 1.94
2412 2496 3.576648 GACTGTACGGTGAAAGAGAAGG 58.423 50.000 13.27 0.00 0.00 3.46
2430 2515 5.541953 ACCTGTAAAAAGTTACTCGGACT 57.458 39.130 10.44 0.00 40.35 3.85
2431 2516 5.107722 CGAACCTGTAAAAAGTTACTCGGAC 60.108 44.000 10.44 0.00 40.35 4.79
2432 2517 4.984161 CGAACCTGTAAAAAGTTACTCGGA 59.016 41.667 10.44 0.00 40.35 4.55
2433 2518 4.376717 GCGAACCTGTAAAAAGTTACTCGG 60.377 45.833 0.00 6.24 40.35 4.63
2434 2519 4.662394 CGCGAACCTGTAAAAAGTTACTCG 60.662 45.833 0.00 1.33 40.35 4.18
2435 2520 4.695200 CGCGAACCTGTAAAAAGTTACTC 58.305 43.478 0.00 0.00 40.35 2.59
2436 2521 3.059393 GCGCGAACCTGTAAAAAGTTACT 60.059 43.478 12.10 0.00 40.35 2.24
2467 2552 2.661866 GGCAGCGGCGATAACGAT 60.662 61.111 12.98 0.00 42.47 3.73
2486 2571 0.323629 GTTTGGATCCACCGACAGGA 59.676 55.000 15.91 0.00 42.61 3.86
2536 2629 1.731093 CCACCGCGTTGGACTTTTT 59.269 52.632 19.17 0.00 42.00 1.94
2596 2695 1.681327 GTCCGAGGGAGCACTGGTA 60.681 63.158 0.00 0.00 29.39 3.25
2626 2725 2.125952 CCGTGATGTGAGCGAGCA 60.126 61.111 0.00 0.00 0.00 4.26
2630 2729 3.490759 GTGGCCGTGATGTGAGCG 61.491 66.667 0.00 0.00 0.00 5.03
2671 2774 1.102978 CCATAAAGAAACCGGGCCAG 58.897 55.000 6.32 0.00 0.00 4.85
2692 2795 0.403655 TACACCTTGGCAATGGCAGA 59.596 50.000 9.96 0.79 43.71 4.26
2725 2851 2.989422 AGCGTACAAATTGCAGTTCC 57.011 45.000 0.00 0.00 0.00 3.62
2747 2873 6.047870 ACTGTAGTCGTAGTACTCCTACATG 58.952 44.000 20.33 17.32 45.40 3.21
2749 2875 5.667539 ACTGTAGTCGTAGTACTCCTACA 57.332 43.478 19.51 19.51 45.40 2.74
2750 2876 6.801575 ACTACTGTAGTCGTAGTACTCCTAC 58.198 44.000 14.53 14.62 44.10 3.18
2752 2878 5.930837 ACTACTGTAGTCGTAGTACTCCT 57.069 43.478 14.53 0.00 44.10 3.69
2753 2879 6.915843 GTCTACTACTGTAGTCGTAGTACTCC 59.084 46.154 22.79 0.00 44.10 3.85
2754 2880 7.703328 AGTCTACTACTGTAGTCGTAGTACTC 58.297 42.308 22.79 8.66 44.10 2.59
2755 2881 7.639113 AGTCTACTACTGTAGTCGTAGTACT 57.361 40.000 22.79 15.55 44.10 2.73
2778 2904 1.569493 CAACGCTGAACCCGACAAG 59.431 57.895 0.00 0.00 0.00 3.16
2787 2919 4.617520 TCGGCTGGCAACGCTGAA 62.618 61.111 7.71 0.00 44.48 3.02
2819 2952 7.054751 GCCTTAAACTAGTGGATTAGTGGATT 58.945 38.462 0.00 0.00 34.24 3.01
2820 2953 6.157994 TGCCTTAAACTAGTGGATTAGTGGAT 59.842 38.462 0.00 0.00 34.24 3.41
2821 2954 5.486063 TGCCTTAAACTAGTGGATTAGTGGA 59.514 40.000 0.00 0.00 34.24 4.02
2822 2955 5.741011 TGCCTTAAACTAGTGGATTAGTGG 58.259 41.667 0.00 0.17 34.24 4.00
2823 2956 5.294552 GCTGCCTTAAACTAGTGGATTAGTG 59.705 44.000 0.00 0.00 34.24 2.74
2824 2957 5.429130 GCTGCCTTAAACTAGTGGATTAGT 58.571 41.667 0.00 0.00 35.44 2.24
2825 2958 4.816925 GGCTGCCTTAAACTAGTGGATTAG 59.183 45.833 12.43 0.00 0.00 1.73
2826 2959 4.226394 TGGCTGCCTTAAACTAGTGGATTA 59.774 41.667 21.03 0.00 0.00 1.75
2951 3087 5.163972 GCATAGTCGTATCGGACAGTACTAG 60.164 48.000 0.00 0.00 39.42 2.57
2954 3090 3.663754 CGCATAGTCGTATCGGACAGTAC 60.664 52.174 0.00 0.00 39.42 2.73
2955 3091 2.477754 CGCATAGTCGTATCGGACAGTA 59.522 50.000 0.00 0.00 39.42 2.74
2968 3124 1.781429 CATGTACGTGCTCGCATAGTC 59.219 52.381 8.29 0.00 41.18 2.59
3022 3183 5.873179 TGCCAAGGAAATTTTACTACTCG 57.127 39.130 0.00 0.00 0.00 4.18
3023 3184 7.215719 ACTTGCCAAGGAAATTTTACTACTC 57.784 36.000 9.64 0.00 0.00 2.59
3024 3185 7.433680 CAACTTGCCAAGGAAATTTTACTACT 58.566 34.615 9.64 0.00 0.00 2.57
3025 3186 6.145534 GCAACTTGCCAAGGAAATTTTACTAC 59.854 38.462 9.64 0.00 37.42 2.73
3026 3187 6.220201 GCAACTTGCCAAGGAAATTTTACTA 58.780 36.000 9.64 0.00 37.42 1.82
3027 3188 5.056480 GCAACTTGCCAAGGAAATTTTACT 58.944 37.500 9.64 0.00 37.42 2.24
3028 3189 4.084589 CGCAACTTGCCAAGGAAATTTTAC 60.085 41.667 9.64 0.00 41.12 2.01
3029 3190 4.054671 CGCAACTTGCCAAGGAAATTTTA 58.945 39.130 9.64 0.00 41.12 1.52
3030 3191 2.871633 CGCAACTTGCCAAGGAAATTTT 59.128 40.909 9.64 0.00 41.12 1.82
3081 3242 3.590466 ATCAACCACCCTGCCAGCC 62.590 63.158 0.00 0.00 0.00 4.85
3082 3243 2.036256 ATCAACCACCCTGCCAGC 59.964 61.111 0.00 0.00 0.00 4.85
3083 3244 0.251297 TTCATCAACCACCCTGCCAG 60.251 55.000 0.00 0.00 0.00 4.85
3084 3245 0.539438 GTTCATCAACCACCCTGCCA 60.539 55.000 0.00 0.00 0.00 4.92
3261 3423 4.197498 GTGCCATGCGGATGCCAC 62.197 66.667 15.02 15.02 41.78 5.01
3262 3424 4.737177 TGTGCCATGCGGATGCCA 62.737 61.111 11.99 3.39 41.78 4.92
3263 3425 3.221389 ATGTGCCATGCGGATGCC 61.221 61.111 11.99 0.00 41.78 4.40
3264 3426 2.027024 CATGTGCCATGCGGATGC 59.973 61.111 11.99 7.82 43.20 3.91
3265 3427 2.027024 GCATGTGCCATGCGGATG 59.973 61.111 19.75 10.35 35.17 3.51
3270 3432 0.108567 TTCATGTGCATGTGCCATGC 60.109 50.000 24.69 24.69 43.24 4.06
3271 3433 1.996898 GTTTCATGTGCATGTGCCATG 59.003 47.619 20.69 20.69 44.05 3.66
3272 3434 1.403116 CGTTTCATGTGCATGTGCCAT 60.403 47.619 11.38 3.21 41.18 4.40
3273 3435 0.039346 CGTTTCATGTGCATGTGCCA 60.039 50.000 11.38 0.88 41.18 4.92
3274 3436 0.039256 ACGTTTCATGTGCATGTGCC 60.039 50.000 11.38 0.00 41.18 5.01
3341 3514 1.135489 TCTCATCACAGTTACCGCGTC 60.135 52.381 4.92 0.00 0.00 5.19
3346 3519 4.569943 ACACACATCTCATCACAGTTACC 58.430 43.478 0.00 0.00 0.00 2.85
3347 3520 7.652300 TTAACACACATCTCATCACAGTTAC 57.348 36.000 0.00 0.00 0.00 2.50
3391 3590 3.660111 GGTTCCCTGCACGCACAC 61.660 66.667 0.00 0.00 0.00 3.82
3602 3802 3.148279 CGGGTCGGGGAGAAGGAG 61.148 72.222 0.00 0.00 0.00 3.69
3665 3865 4.719369 ACGTCGGCCTTCTGCGAC 62.719 66.667 0.00 0.39 42.61 5.19
4764 5095 1.003646 TCTGGTACCTCAGGAGCTCT 58.996 55.000 14.64 0.00 35.58 4.09
4773 5104 0.531200 CCTCCACGTTCTGGTACCTC 59.469 60.000 14.36 0.45 41.52 3.85


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

AutoCloner maintained by Alex Coulton.