Multiple sequence alignment - TraesCS1D01G437100

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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 TraesCS1D01G437100 chr1D 100.000 5499 0 0 1 5499 484420613 484415115 0.000000e+00 10155.0
1 TraesCS1D01G437100 chr1D 82.057 418 29 19 769 1174 484444351 484443968 1.150000e-81 315.0
2 TraesCS1D01G437100 chr1D 87.903 248 27 3 1 247 484445178 484444933 6.970000e-74 289.0
3 TraesCS1D01G437100 chr1A 92.674 4846 195 68 702 5461 581833160 581828389 0.000000e+00 6835.0
4 TraesCS1D01G437100 chr1A 86.325 468 37 8 2 467 581852981 581852539 8.280000e-133 484.0
5 TraesCS1D01G437100 chr1A 87.129 303 35 2 1468 1770 581851813 581851515 1.900000e-89 340.0
6 TraesCS1D01G437100 chr1A 81.148 244 22 15 8 251 581833782 581833563 2.040000e-39 174.0
7 TraesCS1D01G437100 chr1B 93.665 4120 177 30 1124 5196 674671549 674667467 0.000000e+00 6085.0
8 TraesCS1D01G437100 chr1B 80.168 716 70 42 516 1194 674794517 674793837 2.320000e-128 470.0
9 TraesCS1D01G437100 chr1B 83.951 486 27 24 517 955 674672359 674671878 8.520000e-113 418.0
10 TraesCS1D01G437100 chr1B 86.496 274 23 7 5204 5466 674667432 674667162 6.970000e-74 289.0
11 TraesCS1D01G437100 chr1B 85.830 247 34 1 1 247 674795520 674795275 1.520000e-65 261.0
12 TraesCS1D01G437100 chr1B 81.498 227 20 8 21 247 674672921 674672717 3.410000e-37 167.0
13 TraesCS1D01G437100 chr4B 87.884 586 46 17 4858 5430 544007423 544006850 0.000000e+00 665.0
14 TraesCS1D01G437100 chr5A 87.307 583 56 16 4858 5430 137852285 137852859 0.000000e+00 651.0
15 TraesCS1D01G437100 chr5A 77.679 112 21 4 348 457 596668442 596668551 1.280000e-06 65.8
16 TraesCS1D01G437100 chr3A 86.542 587 51 19 4858 5430 170520424 170519852 6.050000e-174 621.0
17 TraesCS1D01G437100 chr3A 80.032 631 96 21 1467 2076 413679079 413679700 1.820000e-119 440.0
18 TraesCS1D01G437100 chr5B 86.682 443 34 17 4858 5287 70460759 70461189 8.340000e-128 468.0
19 TraesCS1D01G437100 chr4A 86.425 442 34 18 4860 5287 707415622 707415193 1.400000e-125 460.0
20 TraesCS1D01G437100 chr4A 86.261 444 35 17 4858 5286 686721341 686721773 5.020000e-125 459.0
21 TraesCS1D01G437100 chr4A 85.841 113 13 2 348 459 453675498 453675608 3.480000e-22 117.0
22 TraesCS1D01G437100 chr3D 80.507 631 93 21 1467 2076 316170638 316170017 1.810000e-124 457.0
23 TraesCS1D01G437100 chr7B 86.111 432 43 15 4858 5279 671469856 671470280 3.020000e-122 449.0
24 TraesCS1D01G437100 chr3B 79.556 631 99 19 1467 2076 403905558 403906179 1.830000e-114 424.0
25 TraesCS1D01G437100 chrUn 81.967 122 19 3 348 467 82023096 82023216 3.510000e-17 100.0
26 TraesCS1D01G437100 chr7A 81.967 122 19 3 348 467 33088826 33088706 3.510000e-17 100.0


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 TraesCS1D01G437100 chr1D 484415115 484420613 5498 True 10155.00 10155 100.0000 1 5499 1 chr1D.!!$R1 5498
1 TraesCS1D01G437100 chr1D 484443968 484445178 1210 True 302.00 315 84.9800 1 1174 2 chr1D.!!$R2 1173
2 TraesCS1D01G437100 chr1A 581828389 581833782 5393 True 3504.50 6835 86.9110 8 5461 2 chr1A.!!$R1 5453
3 TraesCS1D01G437100 chr1A 581851515 581852981 1466 True 412.00 484 86.7270 2 1770 2 chr1A.!!$R2 1768
4 TraesCS1D01G437100 chr1B 674667162 674672921 5759 True 1739.75 6085 86.4025 21 5466 4 chr1B.!!$R1 5445
5 TraesCS1D01G437100 chr1B 674793837 674795520 1683 True 365.50 470 82.9990 1 1194 2 chr1B.!!$R2 1193
6 TraesCS1D01G437100 chr4B 544006850 544007423 573 True 665.00 665 87.8840 4858 5430 1 chr4B.!!$R1 572
7 TraesCS1D01G437100 chr5A 137852285 137852859 574 False 651.00 651 87.3070 4858 5430 1 chr5A.!!$F1 572
8 TraesCS1D01G437100 chr3A 170519852 170520424 572 True 621.00 621 86.5420 4858 5430 1 chr3A.!!$R1 572
9 TraesCS1D01G437100 chr3A 413679079 413679700 621 False 440.00 440 80.0320 1467 2076 1 chr3A.!!$F1 609
10 TraesCS1D01G437100 chr3D 316170017 316170638 621 True 457.00 457 80.5070 1467 2076 1 chr3D.!!$R1 609
11 TraesCS1D01G437100 chr3B 403905558 403906179 621 False 424.00 424 79.5560 1467 2076 1 chr3B.!!$F1 609

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
964 1794 0.906756 CTCCCAGCTCACTTCTCCCA 60.907 60.000 0.00 0.0 0.00 4.37 F
1056 1923 0.795085 CTCTTGCTTGCTTGGACTCG 59.205 55.000 0.00 0.0 0.00 4.18 F
2409 3441 1.004610 CGAATTCGCATCGCAGAATGT 60.005 47.619 15.93 0.6 43.58 2.71 F
2841 3873 1.004927 GATACACTGTCATTTCGCGGC 60.005 52.381 6.13 0.0 0.00 6.53 F
4229 5304 1.079405 AATGTGCGTGTAGTCCCGG 60.079 57.895 0.00 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2152 3183 0.395586 ACAGTGGCAAGCAAGGTGAA 60.396 50.000 0.0 0.0 0.00 3.18 R
2498 3530 1.204062 CGCACATTGACACGACCAC 59.796 57.895 0.0 0.0 0.00 4.16 R
3946 5012 0.393077 AGTCACCCCTGAAAGTGTCG 59.607 55.000 0.0 0.0 35.45 4.35 R
4294 5369 0.460987 AGTGCCTCACTGAATAGCGC 60.461 55.000 0.0 0.0 43.63 5.92 R
5391 6525 1.039068 TTCATGTGGTTGCTGGTTGG 58.961 50.000 0.0 0.0 0.00 3.77 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
80 81 3.440173 CGACCAACTTCAAATAGTGGCAT 59.560 43.478 0.00 0.00 0.00 4.40
156 158 5.589855 CCATGTGGATAACTTGCAACAGATA 59.410 40.000 0.00 0.00 37.39 1.98
166 168 6.131544 ACTTGCAACAGATACGAAACTTTT 57.868 33.333 0.00 0.00 0.00 2.27
167 169 5.971202 ACTTGCAACAGATACGAAACTTTTG 59.029 36.000 0.00 0.00 0.00 2.44
247 249 2.705658 TCCCACTCGAATTGGATATGCT 59.294 45.455 13.29 0.00 36.02 3.79
251 253 5.482006 CCACTCGAATTGGATATGCTCATA 58.518 41.667 6.87 0.00 36.02 2.15
252 254 6.111382 CCACTCGAATTGGATATGCTCATAT 58.889 40.000 6.87 2.26 36.02 1.78
253 255 6.257411 CCACTCGAATTGGATATGCTCATATC 59.743 42.308 17.35 17.35 45.53 1.63
284 925 4.101856 TGTTTAGGGGGTTTGGACAAAAA 58.898 39.130 0.00 0.00 31.33 1.94
290 931 5.935945 AGGGGGTTTGGACAAAAATAAAAG 58.064 37.500 0.00 0.00 31.33 2.27
333 974 6.414732 ACTGAAATTTTGATAGGATGACCGA 58.585 36.000 0.00 0.00 41.83 4.69
334 975 6.884295 ACTGAAATTTTGATAGGATGACCGAA 59.116 34.615 0.00 0.00 41.83 4.30
335 976 7.393234 ACTGAAATTTTGATAGGATGACCGAAA 59.607 33.333 0.00 0.00 41.83 3.46
336 977 7.761409 TGAAATTTTGATAGGATGACCGAAAG 58.239 34.615 0.00 0.00 41.83 2.62
351 992 2.693069 CGAAAGGATGAGCTGTCTTGT 58.307 47.619 0.00 0.00 0.00 3.16
352 993 2.670414 CGAAAGGATGAGCTGTCTTGTC 59.330 50.000 0.00 0.00 0.00 3.18
353 994 3.668447 GAAAGGATGAGCTGTCTTGTCA 58.332 45.455 0.00 0.00 0.00 3.58
354 995 3.996921 AAGGATGAGCTGTCTTGTCAT 57.003 42.857 0.00 0.00 33.53 3.06
358 999 3.456280 GATGAGCTGTCTTGTCATCCTC 58.544 50.000 0.00 0.00 40.44 3.71
480 1145 6.154203 TCTTGTACACCAAATGCATCAAAA 57.846 33.333 0.00 0.00 31.20 2.44
496 1164 4.186856 TCAAAATTTCCGGAATCCTTGC 57.813 40.909 19.62 0.00 0.00 4.01
505 1173 2.632996 CCGGAATCCTTGCTCCTATGTA 59.367 50.000 0.00 0.00 0.00 2.29
507 1175 4.499183 CGGAATCCTTGCTCCTATGTATC 58.501 47.826 0.00 0.00 0.00 2.24
508 1176 4.621747 CGGAATCCTTGCTCCTATGTATCC 60.622 50.000 0.00 0.00 0.00 2.59
509 1177 4.287067 GGAATCCTTGCTCCTATGTATCCA 59.713 45.833 0.00 0.00 0.00 3.41
510 1178 5.221925 GGAATCCTTGCTCCTATGTATCCAA 60.222 44.000 0.00 0.00 0.00 3.53
511 1179 5.912149 ATCCTTGCTCCTATGTATCCAAA 57.088 39.130 0.00 0.00 0.00 3.28
514 1212 4.818546 CCTTGCTCCTATGTATCCAAACTG 59.181 45.833 0.00 0.00 0.00 3.16
534 1232 1.488527 GATGACGCATTCGGTAGGAC 58.511 55.000 0.00 0.00 40.69 3.85
620 1321 2.623878 TGACAACCGAACCTAGCAAA 57.376 45.000 0.00 0.00 0.00 3.68
640 1344 7.318893 AGCAAAGATCCTCTTTTTAATTGAGC 58.681 34.615 0.00 0.00 43.62 4.26
661 1366 9.770097 TTGAGCATATAAACAAAATCAAACCAA 57.230 25.926 0.00 0.00 0.00 3.67
778 1489 7.638134 TGAAAATCAAAATGTAAAAGGCAAGC 58.362 30.769 0.00 0.00 0.00 4.01
921 1725 4.410400 GCCACCCACCCTCCTTCG 62.410 72.222 0.00 0.00 0.00 3.79
964 1794 0.906756 CTCCCAGCTCACTTCTCCCA 60.907 60.000 0.00 0.00 0.00 4.37
965 1795 1.194781 TCCCAGCTCACTTCTCCCAC 61.195 60.000 0.00 0.00 0.00 4.61
966 1796 1.298014 CCAGCTCACTTCTCCCACC 59.702 63.158 0.00 0.00 0.00 4.61
967 1797 1.298014 CAGCTCACTTCTCCCACCC 59.702 63.158 0.00 0.00 0.00 4.61
968 1798 1.920835 AGCTCACTTCTCCCACCCC 60.921 63.158 0.00 0.00 0.00 4.95
969 1799 2.224159 GCTCACTTCTCCCACCCCA 61.224 63.158 0.00 0.00 0.00 4.96
970 1800 1.679898 CTCACTTCTCCCACCCCAC 59.320 63.158 0.00 0.00 0.00 4.61
971 1801 1.842381 CTCACTTCTCCCACCCCACC 61.842 65.000 0.00 0.00 0.00 4.61
972 1802 2.531942 ACTTCTCCCACCCCACCC 60.532 66.667 0.00 0.00 0.00 4.61
973 1803 3.339093 CTTCTCCCACCCCACCCC 61.339 72.222 0.00 0.00 0.00 4.95
974 1804 4.209620 TTCTCCCACCCCACCCCA 62.210 66.667 0.00 0.00 0.00 4.96
975 1805 4.995058 TCTCCCACCCCACCCCAC 62.995 72.222 0.00 0.00 0.00 4.61
1055 1922 1.803555 GACTCTTGCTTGCTTGGACTC 59.196 52.381 0.00 0.00 0.00 3.36
1056 1923 0.795085 CTCTTGCTTGCTTGGACTCG 59.205 55.000 0.00 0.00 0.00 4.18
1057 1924 1.208614 CTTGCTTGCTTGGACTCGC 59.791 57.895 0.00 0.00 0.00 5.03
1058 1925 2.504461 CTTGCTTGCTTGGACTCGCG 62.504 60.000 0.00 0.00 0.00 5.87
1059 1926 3.044305 GCTTGCTTGGACTCGCGT 61.044 61.111 5.77 0.00 0.00 6.01
1060 1927 2.856032 CTTGCTTGGACTCGCGTG 59.144 61.111 5.77 6.24 0.00 5.34
1061 1928 1.956170 CTTGCTTGGACTCGCGTGT 60.956 57.895 14.46 14.46 0.00 4.49
1062 1929 2.162921 CTTGCTTGGACTCGCGTGTG 62.163 60.000 19.71 5.27 0.00 3.82
1063 1930 4.077188 GCTTGGACTCGCGTGTGC 62.077 66.667 23.33 23.33 37.91 4.57
1531 2527 1.449601 GCTGATTTTCTCCGGCGGA 60.450 57.895 29.14 29.14 0.00 5.54
1796 2807 3.610669 CCGGCAGATCCTCGAGGG 61.611 72.222 30.80 15.92 35.41 4.30
2212 3243 3.296854 TCCTTGCAGATAGTACATCGGT 58.703 45.455 0.00 0.00 0.00 4.69
2282 3313 3.467374 GCTAGCCAGCTACAAGAGAAT 57.533 47.619 2.29 0.00 44.93 2.40
2310 3342 9.236691 TCATTTGAATTCTCTAATTAATTGCGC 57.763 29.630 11.05 0.00 35.41 6.09
2345 3377 7.843490 ATGGAAAAGAAAGATTGCATCATTG 57.157 32.000 0.00 0.00 33.01 2.82
2348 3380 6.652062 GGAAAAGAAAGATTGCATCATTGGTT 59.348 34.615 0.00 0.00 0.00 3.67
2362 3394 6.531240 GCATCATTGGTTGGTTTATTGTAGTG 59.469 38.462 0.00 0.00 0.00 2.74
2372 3404 9.341899 GTTGGTTTATTGTAGTGAATCAATGTC 57.658 33.333 0.00 0.00 36.06 3.06
2382 3414 9.725019 TGTAGTGAATCAATGTCTTCTTAATGT 57.275 29.630 0.00 0.00 0.00 2.71
2409 3441 1.004610 CGAATTCGCATCGCAGAATGT 60.005 47.619 15.93 0.60 43.58 2.71
2503 3535 3.846754 CCGACGTTAACGGTGGTC 58.153 61.111 29.81 17.63 44.57 4.02
2553 3585 5.231702 TGAATTGTGACTGAAATGGCATTG 58.768 37.500 14.47 3.90 0.00 2.82
2554 3586 3.663995 TTGTGACTGAAATGGCATTGG 57.336 42.857 14.47 9.67 0.00 3.16
2621 3653 3.599285 CTTACGCTGGCCGGGAACA 62.599 63.158 15.02 0.00 42.52 3.18
2692 3724 2.605257 CATCTGGGGAAATGCATGGAT 58.395 47.619 0.00 0.00 0.00 3.41
2702 3734 2.281345 GCATGGATGCGAGGAGGG 60.281 66.667 0.00 0.00 44.67 4.30
2707 3739 3.917760 GATGCGAGGAGGGTCGGG 61.918 72.222 0.00 0.00 40.44 5.14
2802 3834 3.969976 TCTCTGGCCTTATAGCTTGTGAT 59.030 43.478 3.32 0.00 0.00 3.06
2804 3836 5.782331 TCTCTGGCCTTATAGCTTGTGATAT 59.218 40.000 3.32 0.00 0.00 1.63
2841 3873 1.004927 GATACACTGTCATTTCGCGGC 60.005 52.381 6.13 0.00 0.00 6.53
2925 3957 2.888051 GAAGCGCTTCTCCGGCTC 60.888 66.667 36.70 13.99 35.64 4.70
2943 3975 2.027653 GCTCAACAAACTAGAGGAGGCT 60.028 50.000 0.00 0.00 0.00 4.58
3036 4068 4.394300 GGCATGGTAGCTGATTCATATGTC 59.606 45.833 1.90 0.00 34.17 3.06
3045 4077 5.530171 AGCTGATTCATATGTCCATGTTGTC 59.470 40.000 1.90 0.00 0.00 3.18
3088 4120 6.431234 GGCATTTGGGAGGTACAATTCTATAG 59.569 42.308 0.00 0.00 0.00 1.31
3094 4126 5.070580 GGGAGGTACAATTCTATAGCACACT 59.929 44.000 0.00 0.00 0.00 3.55
3097 4129 6.810911 AGGTACAATTCTATAGCACACTGAG 58.189 40.000 0.00 0.00 0.00 3.35
3101 4133 5.367937 ACAATTCTATAGCACACTGAGGGAT 59.632 40.000 0.00 0.00 0.00 3.85
3104 4136 7.805083 ATTCTATAGCACACTGAGGGATTAT 57.195 36.000 0.00 0.00 0.00 1.28
3110 4142 4.063689 GCACACTGAGGGATTATGATCAG 58.936 47.826 0.09 0.00 43.81 2.90
3116 4148 5.933617 CTGAGGGATTATGATCAGTTTCCA 58.066 41.667 17.57 2.60 35.52 3.53
3121 4153 7.589993 AGGGATTATGATCAGTTTCCATTTCT 58.410 34.615 17.57 6.94 33.77 2.52
3281 4313 4.526650 GCTCAGGGGAATGACCTTTTTAAA 59.473 41.667 0.00 0.00 35.78 1.52
3284 4316 4.283212 CAGGGGAATGACCTTTTTAAAGCA 59.717 41.667 0.00 0.00 35.78 3.91
3351 4383 2.479566 TGAGTCCTCAAATCCAGTGC 57.520 50.000 0.00 0.00 36.53 4.40
3546 4587 6.999950 TCACCTAGTAGTATGCTTTTGACAA 58.000 36.000 0.00 0.00 29.76 3.18
3646 4687 2.029964 GACACGGAGGTTGCGGAA 59.970 61.111 0.00 0.00 34.75 4.30
3772 4813 1.336332 CGAGCTGCTATACATTCGCCT 60.336 52.381 0.15 0.00 31.36 5.52
3803 4844 8.812972 AGTTTTTCCTTTACAAGTTTTTCCTCT 58.187 29.630 0.00 0.00 0.00 3.69
3853 4919 8.840321 CCTTAATTATGCTAGTACATGCTTTGT 58.160 33.333 10.62 0.00 42.62 2.83
3940 5006 2.433604 TCTCAAGATGGCCTGACTGATC 59.566 50.000 3.32 0.00 0.00 2.92
3946 5012 4.205587 AGATGGCCTGACTGATCAAAATC 58.794 43.478 3.32 0.00 33.30 2.17
4229 5304 1.079405 AATGTGCGTGTAGTCCCGG 60.079 57.895 0.00 0.00 0.00 5.73
4294 5369 2.147958 TGCCCTAGCTTACACGTTTTG 58.852 47.619 0.00 0.00 40.80 2.44
4325 5400 0.105778 GAGGCACTATGCTGTCTCCC 59.894 60.000 0.13 0.00 44.28 4.30
4513 5599 4.510038 ACATCAAAGAGTTTGCCATCAC 57.490 40.909 0.00 0.00 40.43 3.06
4514 5600 3.256631 ACATCAAAGAGTTTGCCATCACC 59.743 43.478 0.00 0.00 40.43 4.02
4515 5601 2.238521 TCAAAGAGTTTGCCATCACCC 58.761 47.619 0.00 0.00 40.43 4.61
4516 5602 1.273327 CAAAGAGTTTGCCATCACCCC 59.727 52.381 0.00 0.00 33.36 4.95
4517 5603 0.251787 AAGAGTTTGCCATCACCCCC 60.252 55.000 0.00 0.00 0.00 5.40
4532 5618 1.152881 CCCCCATCCTGTTGCTAGC 60.153 63.158 8.10 8.10 0.00 3.42
4670 5756 0.462225 CTGCTCTCTGCCACCTCATG 60.462 60.000 0.00 0.00 42.00 3.07
4673 5759 0.743701 CTCTCTGCCACCTCATGCAC 60.744 60.000 0.00 0.00 33.17 4.57
4674 5760 1.748122 CTCTGCCACCTCATGCACC 60.748 63.158 0.00 0.00 33.17 5.01
4675 5761 2.034532 CTGCCACCTCATGCACCA 59.965 61.111 0.00 0.00 33.17 4.17
4676 5762 1.379443 CTGCCACCTCATGCACCAT 60.379 57.895 0.00 0.00 33.17 3.55
4696 5782 4.885907 CCATTTCCATACATTCTGCTCTGT 59.114 41.667 0.00 0.00 0.00 3.41
4894 5996 2.065906 AACGGTCGCGCCATTTTTGT 62.066 50.000 17.57 5.37 36.97 2.83
4899 6001 1.206578 CGCGCCATTTTTGTCGTCT 59.793 52.632 0.00 0.00 0.00 4.18
4943 6045 6.950842 TGAGAAGGATGTTGATGTAATCTGT 58.049 36.000 0.00 0.00 45.81 3.41
4944 6046 6.820152 TGAGAAGGATGTTGATGTAATCTGTG 59.180 38.462 0.00 0.00 45.81 3.66
5109 6211 1.372683 ACTCATGCTGCGGTTGAGT 59.627 52.632 20.87 20.87 43.91 3.41
5112 6214 0.534877 TCATGCTGCGGTTGAGTGTT 60.535 50.000 0.00 0.00 0.00 3.32
5113 6215 0.311790 CATGCTGCGGTTGAGTGTTT 59.688 50.000 0.00 0.00 0.00 2.83
5114 6216 1.032014 ATGCTGCGGTTGAGTGTTTT 58.968 45.000 0.00 0.00 0.00 2.43
5115 6217 0.814457 TGCTGCGGTTGAGTGTTTTT 59.186 45.000 0.00 0.00 0.00 1.94
5291 6425 4.083110 ACTTACTGAACTGCATTGCACATC 60.083 41.667 7.38 9.35 33.79 3.06
5365 6499 0.440758 CGGTTTGCTACGCGAATCAA 59.559 50.000 15.93 10.38 32.96 2.57
5391 6525 3.863142 ATGCCTGCTGAAACTGAATTC 57.137 42.857 0.00 0.00 0.00 2.17
5404 6546 1.962807 CTGAATTCCAACCAGCAACCA 59.037 47.619 2.27 0.00 0.00 3.67
5405 6547 1.686052 TGAATTCCAACCAGCAACCAC 59.314 47.619 2.27 0.00 0.00 4.16
5445 6587 5.520288 TCGAAAATGGCGAATTTTGTTTTGA 59.480 32.000 12.05 0.00 46.29 2.69
5491 6633 9.167311 AGGTATTACTAGATTTGTTTTGCTCAG 57.833 33.333 0.00 0.00 0.00 3.35
5492 6634 8.398665 GGTATTACTAGATTTGTTTTGCTCAGG 58.601 37.037 0.00 0.00 0.00 3.86
5493 6635 8.947115 GTATTACTAGATTTGTTTTGCTCAGGT 58.053 33.333 0.00 0.00 0.00 4.00
5494 6636 7.817418 TTACTAGATTTGTTTTGCTCAGGTT 57.183 32.000 0.00 0.00 0.00 3.50
5495 6637 6.715347 ACTAGATTTGTTTTGCTCAGGTTT 57.285 33.333 0.00 0.00 0.00 3.27
5496 6638 7.112452 ACTAGATTTGTTTTGCTCAGGTTTT 57.888 32.000 0.00 0.00 0.00 2.43
5497 6639 6.980397 ACTAGATTTGTTTTGCTCAGGTTTTG 59.020 34.615 0.00 0.00 0.00 2.44
5498 6640 5.118286 AGATTTGTTTTGCTCAGGTTTTGG 58.882 37.500 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 181 8.882415 ATCTGAAATTGTCCAAATGATATTGC 57.118 30.769 0.00 0.00 0.00 3.56
213 215 4.023980 TCGAGTGGGAGTGTCAATCTTAT 58.976 43.478 0.00 0.00 0.00 1.73
247 249 7.147033 ACCCCCTAAACAAACATATGGATATGA 60.147 37.037 12.61 0.00 42.05 2.15
251 253 5.481615 ACCCCCTAAACAAACATATGGAT 57.518 39.130 7.80 0.00 0.00 3.41
252 254 4.957606 ACCCCCTAAACAAACATATGGA 57.042 40.909 7.80 0.00 0.00 3.41
253 255 5.337975 CCAAACCCCCTAAACAAACATATGG 60.338 44.000 7.80 0.00 0.00 2.74
254 256 5.482175 TCCAAACCCCCTAAACAAACATATG 59.518 40.000 0.00 0.00 0.00 1.78
255 257 5.482526 GTCCAAACCCCCTAAACAAACATAT 59.517 40.000 0.00 0.00 0.00 1.78
256 258 4.833938 GTCCAAACCCCCTAAACAAACATA 59.166 41.667 0.00 0.00 0.00 2.29
257 259 3.644265 GTCCAAACCCCCTAAACAAACAT 59.356 43.478 0.00 0.00 0.00 2.71
258 260 3.032459 GTCCAAACCCCCTAAACAAACA 58.968 45.455 0.00 0.00 0.00 2.83
266 268 6.043358 CCTTTTATTTTTGTCCAAACCCCCTA 59.957 38.462 0.00 0.00 0.00 3.53
290 931 8.530804 TTTCAGTACTACTCCTAATTCCTACC 57.469 38.462 0.00 0.00 0.00 3.18
311 952 7.148086 CCTTTCGGTCATCCTATCAAAATTTCA 60.148 37.037 0.00 0.00 0.00 2.69
333 974 3.777106 TGACAAGACAGCTCATCCTTT 57.223 42.857 0.00 0.00 0.00 3.11
334 975 3.871485 GATGACAAGACAGCTCATCCTT 58.129 45.455 0.00 0.00 36.01 3.36
335 976 3.540314 GATGACAAGACAGCTCATCCT 57.460 47.619 0.00 0.00 36.01 3.24
337 978 3.118847 TGAGGATGACAAGACAGCTCATC 60.119 47.826 2.15 2.15 39.68 2.92
338 979 2.836372 TGAGGATGACAAGACAGCTCAT 59.164 45.455 0.00 0.00 0.00 2.90
340 981 2.495270 TCTGAGGATGACAAGACAGCTC 59.505 50.000 0.00 0.00 0.00 4.09
341 982 2.533916 TCTGAGGATGACAAGACAGCT 58.466 47.619 0.00 0.00 0.00 4.24
342 983 3.325293 TTCTGAGGATGACAAGACAGC 57.675 47.619 0.00 0.00 0.00 4.40
343 984 5.243981 ACAATTCTGAGGATGACAAGACAG 58.756 41.667 0.00 0.00 0.00 3.51
344 985 5.012458 AGACAATTCTGAGGATGACAAGACA 59.988 40.000 0.00 0.00 0.00 3.41
345 986 5.486526 AGACAATTCTGAGGATGACAAGAC 58.513 41.667 0.00 0.00 0.00 3.01
346 987 5.752036 AGACAATTCTGAGGATGACAAGA 57.248 39.130 0.00 0.00 0.00 3.02
347 988 5.704515 ACAAGACAATTCTGAGGATGACAAG 59.295 40.000 0.00 0.00 29.98 3.16
348 989 5.624159 ACAAGACAATTCTGAGGATGACAA 58.376 37.500 0.00 0.00 29.98 3.18
349 990 5.012458 AGACAAGACAATTCTGAGGATGACA 59.988 40.000 0.00 0.00 29.98 3.58
350 991 5.486526 AGACAAGACAATTCTGAGGATGAC 58.513 41.667 0.00 0.00 29.98 3.06
351 992 5.752036 AGACAAGACAATTCTGAGGATGA 57.248 39.130 0.00 0.00 29.98 2.92
352 993 6.638610 ACTAGACAAGACAATTCTGAGGATG 58.361 40.000 0.00 0.00 29.98 3.51
353 994 6.865834 ACTAGACAAGACAATTCTGAGGAT 57.134 37.500 0.00 0.00 29.98 3.24
354 995 6.295349 GGAACTAGACAAGACAATTCTGAGGA 60.295 42.308 0.00 0.00 29.98 3.71
358 999 7.378966 TGTAGGAACTAGACAAGACAATTCTG 58.621 38.462 0.00 0.00 44.14 3.02
480 1145 1.566231 AGGAGCAAGGATTCCGGAAAT 59.434 47.619 23.08 9.95 38.54 2.17
507 1175 1.202065 CGAATGCGTCATCCAGTTTGG 60.202 52.381 0.00 0.00 39.43 3.28
508 1176 1.202065 CCGAATGCGTCATCCAGTTTG 60.202 52.381 0.00 0.00 35.23 2.93
509 1177 1.086696 CCGAATGCGTCATCCAGTTT 58.913 50.000 0.00 0.00 35.23 2.66
510 1178 0.036388 ACCGAATGCGTCATCCAGTT 60.036 50.000 0.00 0.00 35.23 3.16
511 1179 0.821517 TACCGAATGCGTCATCCAGT 59.178 50.000 0.00 0.00 35.23 4.00
514 1212 0.387929 TCCTACCGAATGCGTCATCC 59.612 55.000 0.00 0.00 35.23 3.51
534 1232 8.341903 TGCACTTTCATCAACCGTTATATATTG 58.658 33.333 0.00 0.00 0.00 1.90
661 1366 8.574251 AAATGTTTTTAGTTCCTTGCCTTTTT 57.426 26.923 0.00 0.00 0.00 1.94
695 1405 6.149308 CCTTTTCTATTTTGATTTTGTGGGGC 59.851 38.462 0.00 0.00 0.00 5.80
753 1464 7.281774 TGCTTGCCTTTTACATTTTGATTTTCA 59.718 29.630 0.00 0.00 0.00 2.69
754 1465 7.638134 TGCTTGCCTTTTACATTTTGATTTTC 58.362 30.769 0.00 0.00 0.00 2.29
921 1725 8.856153 AGGAAAGGAATAGAAGAAGAAAGAAC 57.144 34.615 0.00 0.00 0.00 3.01
999 1852 4.716977 GGTGGGTCGGAGGGGTCT 62.717 72.222 0.00 0.00 0.00 3.85
1056 1923 3.038417 AGAGAAGCACGCACACGC 61.038 61.111 0.00 0.00 45.53 5.34
1058 1925 1.287730 CTCCAGAGAAGCACGCACAC 61.288 60.000 0.00 0.00 0.00 3.82
1059 1926 1.005748 CTCCAGAGAAGCACGCACA 60.006 57.895 0.00 0.00 0.00 4.57
1060 1927 2.386660 GCTCCAGAGAAGCACGCAC 61.387 63.158 0.00 0.00 0.00 5.34
1061 1928 2.047844 GCTCCAGAGAAGCACGCA 60.048 61.111 0.00 0.00 0.00 5.24
1062 1929 1.809209 GAGCTCCAGAGAAGCACGC 60.809 63.158 0.87 0.00 0.00 5.34
1063 1930 1.515952 CGAGCTCCAGAGAAGCACG 60.516 63.158 8.47 0.95 36.49 5.34
1064 1931 0.457681 GACGAGCTCCAGAGAAGCAC 60.458 60.000 8.47 0.00 0.00 4.40
1065 1932 0.610509 AGACGAGCTCCAGAGAAGCA 60.611 55.000 8.47 0.00 0.00 3.91
1066 1933 0.530288 AAGACGAGCTCCAGAGAAGC 59.470 55.000 8.47 0.00 0.00 3.86
1067 1934 1.735369 GCAAGACGAGCTCCAGAGAAG 60.735 57.143 8.47 0.00 0.00 2.85
1068 1935 0.244994 GCAAGACGAGCTCCAGAGAA 59.755 55.000 8.47 0.00 0.00 2.87
1133 2123 4.715130 AGCGCCACCCCCTCACTA 62.715 66.667 2.29 0.00 0.00 2.74
1507 2503 2.472909 GGAGAAAATCAGCGGCCCG 61.473 63.158 0.00 0.00 0.00 6.13
2152 3183 0.395586 ACAGTGGCAAGCAAGGTGAA 60.396 50.000 0.00 0.00 0.00 3.18
2309 3341 1.587946 CTTTTCCATTATTTGCGGCGC 59.412 47.619 27.44 27.44 0.00 6.53
2310 3342 3.143807 TCTTTTCCATTATTTGCGGCG 57.856 42.857 0.51 0.51 0.00 6.46
2316 3348 9.947433 TGATGCAATCTTTCTTTTCCATTATTT 57.053 25.926 0.00 0.00 45.81 1.40
2319 3351 9.373603 CAATGATGCAATCTTTCTTTTCCATTA 57.626 29.630 0.00 0.00 45.81 1.90
2345 3377 8.303876 ACATTGATTCACTACAATAAACCAACC 58.696 33.333 0.00 0.00 35.39 3.77
2348 3380 8.862325 AGACATTGATTCACTACAATAAACCA 57.138 30.769 0.00 0.00 35.39 3.67
2362 3394 7.427606 CGAAGCACATTAAGAAGACATTGATTC 59.572 37.037 0.00 0.00 0.00 2.52
2409 3441 4.701651 CAGATAAGCACTCCATTTGAACCA 59.298 41.667 0.00 0.00 0.00 3.67
2477 3509 1.978097 CGTTAACGTCGGATCGAAACA 59.022 47.619 19.75 0.00 37.72 2.83
2498 3530 1.204062 CGCACATTGACACGACCAC 59.796 57.895 0.00 0.00 0.00 4.16
2499 3531 1.958715 CCGCACATTGACACGACCA 60.959 57.895 0.00 0.00 0.00 4.02
2503 3535 1.266842 CGATTACCGCACATTGACACG 60.267 52.381 0.00 0.00 0.00 4.49
2553 3585 1.514087 CTGCAATGTGGCCATCACC 59.486 57.895 9.72 0.00 45.48 4.02
2554 3586 1.252904 ACCTGCAATGTGGCCATCAC 61.253 55.000 9.72 0.00 46.23 3.06
2621 3653 2.050269 CAGGGTCAGACTGGTTCGT 58.950 57.895 1.81 0.00 32.38 3.85
2702 3734 2.579738 GCTCTTCCAGTCCCCGAC 59.420 66.667 0.00 0.00 0.00 4.79
2707 3739 4.443266 AGCGCGCTCTTCCAGTCC 62.443 66.667 31.32 0.00 0.00 3.85
2841 3873 3.070018 AGAAACTGAATTCTGACGCTGG 58.930 45.455 18.13 0.00 38.22 4.85
2925 3957 3.685139 TCAGCCTCCTCTAGTTTGTTG 57.315 47.619 0.00 0.00 0.00 3.33
2943 3975 6.871492 TCAGCAAACTTGTAATAGTCGAATCA 59.129 34.615 0.00 0.00 0.00 2.57
3036 4068 1.252904 CCTGGGCTTGGACAACATGG 61.253 60.000 0.00 0.00 0.00 3.66
3045 4077 1.252904 CCATGTTGACCTGGGCTTGG 61.253 60.000 0.00 0.00 0.00 3.61
3088 4120 4.063689 CTGATCATAATCCCTCAGTGTGC 58.936 47.826 0.00 0.00 32.35 4.57
3094 4126 5.974156 TGGAAACTGATCATAATCCCTCA 57.026 39.130 14.70 0.00 0.00 3.86
3097 4129 7.255730 CCAGAAATGGAAACTGATCATAATCCC 60.256 40.741 14.70 6.41 34.07 3.85
3101 4133 8.106462 TGTACCAGAAATGGAAACTGATCATAA 58.894 33.333 0.00 0.00 34.07 1.90
3104 4136 5.875224 TGTACCAGAAATGGAAACTGATCA 58.125 37.500 0.31 0.00 34.07 2.92
3110 4142 4.846779 TGCTTGTACCAGAAATGGAAAC 57.153 40.909 0.31 0.00 0.00 2.78
3116 4148 6.568462 CGACTTTCAATGCTTGTACCAGAAAT 60.568 38.462 0.00 0.00 0.00 2.17
3121 4153 2.811431 CCGACTTTCAATGCTTGTACCA 59.189 45.455 0.00 0.00 0.00 3.25
3171 4203 0.179086 GCTCTGGCCTTCTCAGCTAC 60.179 60.000 3.32 0.00 32.63 3.58
3546 4587 1.331214 CAACAATGCCAACAGGGAGT 58.669 50.000 0.00 0.00 40.01 3.85
3853 4919 7.554959 AACTCTTTCAAGTATAGAACTGGGA 57.445 36.000 0.00 0.00 38.88 4.37
3940 5006 2.884639 ACCCCTGAAAGTGTCGATTTTG 59.115 45.455 0.00 0.00 0.00 2.44
3946 5012 0.393077 AGTCACCCCTGAAAGTGTCG 59.607 55.000 0.00 0.00 35.45 4.35
4219 5294 1.271856 TCTTGAATGCCGGGACTACA 58.728 50.000 2.18 0.00 0.00 2.74
4229 5304 4.083802 GCCGTCCTTGTATATCTTGAATGC 60.084 45.833 0.00 0.00 0.00 3.56
4294 5369 0.460987 AGTGCCTCACTGAATAGCGC 60.461 55.000 0.00 0.00 43.63 5.92
4325 5400 4.163078 ACTGGTATGACCTCCTCAAGAATG 59.837 45.833 0.00 0.00 39.58 2.67
4514 5600 1.152881 GCTAGCAACAGGATGGGGG 60.153 63.158 10.63 0.00 43.62 5.40
4515 5601 1.152881 GGCTAGCAACAGGATGGGG 60.153 63.158 18.24 0.00 43.62 4.96
4516 5602 1.152881 GGGCTAGCAACAGGATGGG 60.153 63.158 18.24 0.00 43.62 4.00
4517 5603 0.465097 CAGGGCTAGCAACAGGATGG 60.465 60.000 18.24 0.00 43.62 3.51
4518 5604 0.543277 TCAGGGCTAGCAACAGGATG 59.457 55.000 18.24 3.44 46.00 3.51
4519 5605 0.835941 CTCAGGGCTAGCAACAGGAT 59.164 55.000 18.24 0.00 0.00 3.24
4532 5618 0.545309 TGAAGGGTCAGGACTCAGGG 60.545 60.000 1.62 0.00 33.19 4.45
4670 5756 3.382546 AGCAGAATGTATGGAAATGGTGC 59.617 43.478 0.00 0.00 39.31 5.01
4673 5759 4.885907 ACAGAGCAGAATGTATGGAAATGG 59.114 41.667 0.00 0.00 39.31 3.16
4674 5760 5.008415 GGACAGAGCAGAATGTATGGAAATG 59.992 44.000 0.00 0.00 39.31 2.32
4675 5761 5.128919 GGACAGAGCAGAATGTATGGAAAT 58.871 41.667 0.00 0.00 39.31 2.17
4676 5762 4.517285 GGACAGAGCAGAATGTATGGAAA 58.483 43.478 0.00 0.00 39.31 3.13
4894 5996 0.400213 AATGGAAACTGGCCAGACGA 59.600 50.000 39.19 24.05 39.11 4.20
4899 6001 2.364970 CAACTCAAATGGAAACTGGCCA 59.635 45.455 4.71 4.71 40.24 5.36
4943 6045 5.055265 TGAAAATGACAACCTTCCTACCA 57.945 39.130 0.00 0.00 0.00 3.25
4944 6046 5.476945 ACATGAAAATGACAACCTTCCTACC 59.523 40.000 0.00 0.00 0.00 3.18
5291 6425 2.478134 CTGAACCAAAGAGACTTCAGCG 59.522 50.000 0.00 0.00 34.78 5.18
5391 6525 1.039068 TTCATGTGGTTGCTGGTTGG 58.961 50.000 0.00 0.00 0.00 3.77
5404 6546 4.649088 TTCGATCGTGTAGGATTCATGT 57.351 40.909 15.94 0.00 0.00 3.21
5405 6547 5.966636 TTTTCGATCGTGTAGGATTCATG 57.033 39.130 15.94 0.00 0.00 3.07
5466 6608 8.398665 CCTGAGCAAAACAAATCTAGTAATACC 58.601 37.037 0.00 0.00 0.00 2.73
5467 6609 8.947115 ACCTGAGCAAAACAAATCTAGTAATAC 58.053 33.333 0.00 0.00 0.00 1.89
5468 6610 9.515226 AACCTGAGCAAAACAAATCTAGTAATA 57.485 29.630 0.00 0.00 0.00 0.98
5469 6611 8.409358 AACCTGAGCAAAACAAATCTAGTAAT 57.591 30.769 0.00 0.00 0.00 1.89
5470 6612 7.817418 AACCTGAGCAAAACAAATCTAGTAA 57.183 32.000 0.00 0.00 0.00 2.24
5471 6613 7.817418 AAACCTGAGCAAAACAAATCTAGTA 57.183 32.000 0.00 0.00 0.00 1.82
5472 6614 6.715347 AAACCTGAGCAAAACAAATCTAGT 57.285 33.333 0.00 0.00 0.00 2.57
5473 6615 6.421801 CCAAAACCTGAGCAAAACAAATCTAG 59.578 38.462 0.00 0.00 0.00 2.43
5474 6616 6.279882 CCAAAACCTGAGCAAAACAAATCTA 58.720 36.000 0.00 0.00 0.00 1.98
5475 6617 5.118286 CCAAAACCTGAGCAAAACAAATCT 58.882 37.500 0.00 0.00 0.00 2.40
5476 6618 5.408204 CCAAAACCTGAGCAAAACAAATC 57.592 39.130 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.