Multiple sequence alignment - TraesCS4B01G223500

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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 TraesCS4B01G223500 chr4B 100.000 5697 0 0 1 5697 467919857 467914161 0.000000e+00 10521.0
1 TraesCS4B01G223500 chr4B 92.308 78 3 1 4485 4559 467915292 467915215 2.170000e-19 108.0
2 TraesCS4B01G223500 chr4B 92.308 78 3 1 4566 4643 467915373 467915299 2.170000e-19 108.0
3 TraesCS4B01G223500 chr4D 93.034 3144 118 30 466 3561 380465119 380462029 0.000000e+00 4499.0
4 TraesCS4B01G223500 chr4D 94.085 1251 47 7 3854 5079 380460843 380459595 0.000000e+00 1875.0
5 TraesCS4B01G223500 chr4D 98.980 98 1 0 3592 3689 380460948 380460851 5.870000e-40 176.0
6 TraesCS4B01G223500 chr4D 92.308 78 3 1 4485 4559 380460109 380460032 2.170000e-19 108.0
7 TraesCS4B01G223500 chr2A 92.994 1884 106 9 3217 5077 14941256 14939376 0.000000e+00 2724.0
8 TraesCS4B01G223500 chr4A 94.197 1775 75 10 3329 5079 83319210 83320980 0.000000e+00 2682.0
9 TraesCS4B01G223500 chr4A 94.432 1724 81 6 1560 3271 83317189 83318909 0.000000e+00 2638.0
10 TraesCS4B01G223500 chr4A 88.480 1658 108 44 1 1620 83315225 83316837 0.000000e+00 1927.0
11 TraesCS4B01G223500 chr4A 92.208 77 3 1 4486 4559 83320468 83320544 7.810000e-19 106.0
12 TraesCS4B01G223500 chr7B 96.217 608 11 2 5097 5697 448655707 448656309 0.000000e+00 985.0
13 TraesCS4B01G223500 chr7B 95.395 608 16 2 5097 5697 508202238 508202840 0.000000e+00 957.0
14 TraesCS4B01G223500 chr6B 96.217 608 11 2 5097 5697 210272924 210273526 0.000000e+00 985.0
15 TraesCS4B01G223500 chr7D 95.559 608 15 2 5097 5697 491879611 491880213 0.000000e+00 963.0
16 TraesCS4B01G223500 chr7D 96.000 50 1 1 2103 2152 568198682 568198634 4.730000e-11 80.5
17 TraesCS4B01G223500 chr5B 95.559 608 15 2 5097 5697 396436231 396435629 0.000000e+00 963.0
18 TraesCS4B01G223500 chr5D 95.395 608 16 2 5097 5697 303831072 303831674 0.000000e+00 957.0
19 TraesCS4B01G223500 chr5D 90.116 172 14 3 1446 1617 258647838 258648006 2.670000e-53 220.0
20 TraesCS4B01G223500 chr5D 89.143 175 18 1 1446 1620 443898151 443898324 3.460000e-52 217.0
21 TraesCS4B01G223500 chr2B 95.395 608 16 2 5097 5697 632591568 632590966 0.000000e+00 957.0
22 TraesCS4B01G223500 chr3D 95.230 608 17 2 5097 5697 607833539 607832937 0.000000e+00 952.0
23 TraesCS4B01G223500 chr1D 95.230 608 17 2 5097 5697 269816673 269816071 0.000000e+00 952.0
24 TraesCS4B01G223500 chr2D 91.716 169 10 4 1446 1613 22200809 22200974 1.230000e-56 231.0
25 TraesCS4B01G223500 chr2D 94.000 50 3 0 2103 2152 107866649 107866698 6.120000e-10 76.8
26 TraesCS4B01G223500 chrUn 91.176 170 12 3 1446 1613 318851405 318851237 1.600000e-55 228.0
27 TraesCS4B01G223500 chrUn 91.018 167 13 2 1446 1612 30689258 30689422 2.070000e-54 224.0
28 TraesCS4B01G223500 chr7A 91.176 170 12 3 1446 1613 15787132 15786964 1.600000e-55 228.0
29 TraesCS4B01G223500 chr7A 91.176 170 12 3 1446 1613 15815015 15814847 1.600000e-55 228.0
30 TraesCS4B01G223500 chr1A 96.000 50 1 1 2103 2152 27398438 27398486 4.730000e-11 80.5


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 TraesCS4B01G223500 chr4B 467914161 467919857 5696 True 10521.00 10521 100.00000 1 5697 1 chr4B.!!$R1 5696
1 TraesCS4B01G223500 chr4D 380459595 380465119 5524 True 1664.50 4499 94.60175 466 5079 4 chr4D.!!$R1 4613
2 TraesCS4B01G223500 chr2A 14939376 14941256 1880 True 2724.00 2724 92.99400 3217 5077 1 chr2A.!!$R1 1860
3 TraesCS4B01G223500 chr4A 83315225 83320980 5755 False 1838.25 2682 92.32925 1 5079 4 chr4A.!!$F1 5078
4 TraesCS4B01G223500 chr7B 448655707 448656309 602 False 985.00 985 96.21700 5097 5697 1 chr7B.!!$F1 600
5 TraesCS4B01G223500 chr7B 508202238 508202840 602 False 957.00 957 95.39500 5097 5697 1 chr7B.!!$F2 600
6 TraesCS4B01G223500 chr6B 210272924 210273526 602 False 985.00 985 96.21700 5097 5697 1 chr6B.!!$F1 600
7 TraesCS4B01G223500 chr7D 491879611 491880213 602 False 963.00 963 95.55900 5097 5697 1 chr7D.!!$F1 600
8 TraesCS4B01G223500 chr5B 396435629 396436231 602 True 963.00 963 95.55900 5097 5697 1 chr5B.!!$R1 600
9 TraesCS4B01G223500 chr5D 303831072 303831674 602 False 957.00 957 95.39500 5097 5697 1 chr5D.!!$F2 600
10 TraesCS4B01G223500 chr2B 632590966 632591568 602 True 957.00 957 95.39500 5097 5697 1 chr2B.!!$R1 600
11 TraesCS4B01G223500 chr3D 607832937 607833539 602 True 952.00 952 95.23000 5097 5697 1 chr3D.!!$R1 600
12 TraesCS4B01G223500 chr1D 269816071 269816673 602 True 952.00 952 95.23000 5097 5697 1 chr1D.!!$R1 600

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
878 909 0.029267 AGGGCATCCTTCATCCCTCT 60.029 55.000 0.0 0.0 45.63 3.69 F
1132 1164 0.250467 AGGCAAGAAGAAAGCGAGCA 60.250 50.000 0.0 0.0 0.00 4.26 F
2814 3287 0.460987 GACTGGGAACTGAGCCATCG 60.461 60.000 0.0 0.0 0.00 3.84 F
3019 3494 1.132365 ACCCTATCCCCTGATTCCCTC 60.132 57.143 0.0 0.0 32.18 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 3257 1.913419 GTTCCCAGTCTCCCAATACCA 59.087 52.381 0.00 0.00 0.00 3.25 R
3019 3494 0.504384 CTTCAGCGTCGTTGACACAG 59.496 55.000 11.59 3.21 32.09 3.66 R
4611 6428 0.175760 TGTGTCGCTAGATGCCTTCC 59.824 55.000 0.00 0.00 38.78 3.46 R
4866 6694 1.242076 GCAAGCACTGGAAGACATGT 58.758 50.000 0.00 0.00 37.43 3.21 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
29 31 4.241590 TGCAGAACCATAAGTGCAAAAG 57.758 40.909 0.00 0.00 42.79 2.27
31 33 4.340666 TGCAGAACCATAAGTGCAAAAGAA 59.659 37.500 0.00 0.00 42.79 2.52
32 34 5.163468 TGCAGAACCATAAGTGCAAAAGAAA 60.163 36.000 0.00 0.00 42.79 2.52
34 36 5.691754 CAGAACCATAAGTGCAAAAGAAACC 59.308 40.000 0.00 0.00 0.00 3.27
35 37 4.600692 ACCATAAGTGCAAAAGAAACCC 57.399 40.909 0.00 0.00 0.00 4.11
36 38 3.005367 ACCATAAGTGCAAAAGAAACCCG 59.995 43.478 0.00 0.00 0.00 5.28
37 39 3.574614 CATAAGTGCAAAAGAAACCCGG 58.425 45.455 0.00 0.00 0.00 5.73
38 40 1.770294 AAGTGCAAAAGAAACCCGGA 58.230 45.000 0.73 0.00 0.00 5.14
39 41 1.995376 AGTGCAAAAGAAACCCGGAT 58.005 45.000 0.73 0.00 0.00 4.18
40 42 1.613437 AGTGCAAAAGAAACCCGGATG 59.387 47.619 0.73 0.00 0.00 3.51
43 45 2.695666 TGCAAAAGAAACCCGGATGAAA 59.304 40.909 0.73 0.00 0.00 2.69
44 46 3.057019 GCAAAAGAAACCCGGATGAAAC 58.943 45.455 0.73 0.00 0.00 2.78
45 47 3.305110 CAAAAGAAACCCGGATGAAACG 58.695 45.455 0.73 0.00 0.00 3.60
47 49 2.554370 AGAAACCCGGATGAAACGAA 57.446 45.000 0.73 0.00 0.00 3.85
48 50 2.423577 AGAAACCCGGATGAAACGAAG 58.576 47.619 0.73 0.00 0.00 3.79
49 51 2.038033 AGAAACCCGGATGAAACGAAGA 59.962 45.455 0.73 0.00 0.00 2.87
50 52 2.554370 AACCCGGATGAAACGAAGAA 57.446 45.000 0.73 0.00 0.00 2.52
87 89 3.297134 AAACCAGCCTACCATACCATG 57.703 47.619 0.00 0.00 0.00 3.66
100 102 0.111061 TACCATGGCCCATGAGATGC 59.889 55.000 25.42 0.00 43.81 3.91
107 109 0.942962 GCCCATGAGATGCGAAGAAG 59.057 55.000 0.00 0.00 0.00 2.85
109 111 0.942962 CCATGAGATGCGAAGAAGCC 59.057 55.000 0.00 0.00 36.02 4.35
114 116 2.205911 GAGATGCGAAGAAGCCTAACC 58.794 52.381 0.00 0.00 36.02 2.85
115 117 1.555075 AGATGCGAAGAAGCCTAACCA 59.445 47.619 0.00 0.00 36.02 3.67
116 118 1.666189 GATGCGAAGAAGCCTAACCAC 59.334 52.381 0.00 0.00 36.02 4.16
117 119 0.394938 TGCGAAGAAGCCTAACCACA 59.605 50.000 0.00 0.00 36.02 4.17
118 120 1.202710 TGCGAAGAAGCCTAACCACAA 60.203 47.619 0.00 0.00 36.02 3.33
119 121 1.197036 GCGAAGAAGCCTAACCACAAC 59.803 52.381 0.00 0.00 0.00 3.32
120 122 1.804748 CGAAGAAGCCTAACCACAACC 59.195 52.381 0.00 0.00 0.00 3.77
132 134 0.463833 CCACAACCGAGCTATTCCCC 60.464 60.000 0.00 0.00 0.00 4.81
135 137 0.830648 CAACCGAGCTATTCCCCTCA 59.169 55.000 0.00 0.00 0.00 3.86
142 146 3.323403 CGAGCTATTCCCCTCATTCTTCT 59.677 47.826 0.00 0.00 0.00 2.85
144 148 3.323403 AGCTATTCCCCTCATTCTTCTCG 59.677 47.826 0.00 0.00 0.00 4.04
145 149 2.629336 ATTCCCCTCATTCTTCTCGC 57.371 50.000 0.00 0.00 0.00 5.03
160 164 0.030908 CTCGCGACCTCCTATTCCAC 59.969 60.000 3.71 0.00 0.00 4.02
163 167 2.017559 GCGACCTCCTATTCCACGCT 62.018 60.000 0.00 0.00 41.07 5.07
189 193 0.107017 AAGCGTGGAATGATGGAGGG 60.107 55.000 0.00 0.00 0.00 4.30
204 208 2.308570 TGGAGGGAACACATGTGCTTAT 59.691 45.455 25.68 9.62 0.00 1.73
205 209 2.684881 GGAGGGAACACATGTGCTTATG 59.315 50.000 25.68 1.07 0.00 1.90
215 219 5.275067 ACATGTGCTTATGTGGTTTGTTT 57.725 34.783 0.00 0.00 39.68 2.83
216 220 6.398234 ACATGTGCTTATGTGGTTTGTTTA 57.602 33.333 0.00 0.00 39.68 2.01
219 223 7.930865 ACATGTGCTTATGTGGTTTGTTTATTT 59.069 29.630 0.00 0.00 39.68 1.40
220 224 8.772705 CATGTGCTTATGTGGTTTGTTTATTTT 58.227 29.630 0.00 0.00 0.00 1.82
221 225 8.723942 TGTGCTTATGTGGTTTGTTTATTTTT 57.276 26.923 0.00 0.00 0.00 1.94
222 226 8.607459 TGTGCTTATGTGGTTTGTTTATTTTTG 58.393 29.630 0.00 0.00 0.00 2.44
224 228 9.383519 TGCTTATGTGGTTTGTTTATTTTTGAA 57.616 25.926 0.00 0.00 0.00 2.69
334 338 4.216257 GGGAAATGTGCATGCTCGTATATT 59.784 41.667 20.33 8.09 0.00 1.28
336 340 6.072728 GGGAAATGTGCATGCTCGTATATTTA 60.073 38.462 20.33 0.00 0.00 1.40
340 344 8.560576 AATGTGCATGCTCGTATATTTAAAAC 57.439 30.769 20.33 3.64 0.00 2.43
356 360 9.885934 ATATTTAAAACATGTTAATCGCGCATA 57.114 25.926 12.39 0.00 0.00 3.14
397 402 7.703298 ATTGAAAATGGTCATCGCATATTTG 57.297 32.000 0.00 0.00 0.00 2.32
398 403 6.448207 TGAAAATGGTCATCGCATATTTGA 57.552 33.333 0.00 0.00 0.00 2.69
399 404 6.861144 TGAAAATGGTCATCGCATATTTGAA 58.139 32.000 0.00 0.00 0.00 2.69
498 512 7.645058 AAGAAAGAAACCATCAGAAAACTCA 57.355 32.000 0.00 0.00 0.00 3.41
528 542 4.455917 AACGAAAAACGAAATACGCAGA 57.544 36.364 0.00 0.00 46.94 4.26
611 626 3.518068 CCGCGGGGATTTGCCTTC 61.518 66.667 20.10 0.00 36.66 3.46
683 712 2.622436 GGGGAATCAGACTGTTTCTCG 58.378 52.381 20.42 0.00 29.50 4.04
738 767 0.253327 GATTGAACCCCTTCCGCTCT 59.747 55.000 0.00 0.00 0.00 4.09
745 775 1.685820 CCCTTCCGCTCTTTCCCTT 59.314 57.895 0.00 0.00 0.00 3.95
746 776 0.393132 CCCTTCCGCTCTTTCCCTTC 60.393 60.000 0.00 0.00 0.00 3.46
768 798 2.047179 GTCCGGACCACAGAAGGC 60.047 66.667 24.75 0.00 0.00 4.35
769 799 2.525629 TCCGGACCACAGAAGGCA 60.526 61.111 0.00 0.00 0.00 4.75
770 800 2.358737 CCGGACCACAGAAGGCAC 60.359 66.667 0.00 0.00 0.00 5.01
771 801 2.358737 CGGACCACAGAAGGCACC 60.359 66.667 0.00 0.00 0.00 5.01
772 802 2.836154 GGACCACAGAAGGCACCA 59.164 61.111 0.00 0.00 0.00 4.17
773 803 1.600916 GGACCACAGAAGGCACCAC 60.601 63.158 0.00 0.00 0.00 4.16
774 804 1.148273 GACCACAGAAGGCACCACA 59.852 57.895 0.00 0.00 0.00 4.17
775 805 0.886490 GACCACAGAAGGCACCACAG 60.886 60.000 0.00 0.00 0.00 3.66
776 806 1.601759 CCACAGAAGGCACCACAGG 60.602 63.158 0.00 0.00 0.00 4.00
777 807 1.601759 CACAGAAGGCACCACAGGG 60.602 63.158 0.00 0.00 41.29 4.45
807 838 0.030705 CCTCTCCCTCTTCCCCATCA 60.031 60.000 0.00 0.00 0.00 3.07
878 909 0.029267 AGGGCATCCTTCATCCCTCT 60.029 55.000 0.00 0.00 45.63 3.69
990 1022 2.113243 GAAACCCTCGCCTCACCACT 62.113 60.000 0.00 0.00 0.00 4.00
1095 1127 2.582687 GAAGACGATGAAGACGACGTT 58.417 47.619 0.13 0.00 39.04 3.99
1132 1164 0.250467 AGGCAAGAAGAAAGCGAGCA 60.250 50.000 0.00 0.00 0.00 4.26
1140 1172 4.664677 AAAGCGAGCACGGCGAGT 62.665 61.111 16.62 0.00 40.15 4.18
1235 1276 0.545071 AATGGGGGTGCAAAGAAGGG 60.545 55.000 0.00 0.00 0.00 3.95
1362 1406 5.593679 AGAAGGTTCGATTCGGATCTTTA 57.406 39.130 13.92 0.00 0.00 1.85
1401 1445 0.587768 TTTGTGTGAGCAGCATGTCG 59.412 50.000 0.00 0.00 39.31 4.35
1484 1534 5.640783 TCTTGCACATCTAAGTGACTCAATG 59.359 40.000 0.00 0.00 42.05 2.82
1629 2092 9.790389 AAAACTGTAATTTTTATTGACACACGA 57.210 25.926 0.00 0.00 0.00 4.35
1644 2107 3.255149 ACACACGAGGATTTCTTACGAGT 59.745 43.478 0.00 0.00 0.00 4.18
1657 2120 5.505165 TCTTACGAGTGTTTTGCGATTAC 57.495 39.130 0.00 0.00 0.00 1.89
1747 2210 7.066781 TCAGTTAGAGAAAAATTGGAGGGTTT 58.933 34.615 0.00 0.00 0.00 3.27
1921 2384 4.708909 GGGAAATGAGAAGGAGAAAAGCAT 59.291 41.667 0.00 0.00 0.00 3.79
1995 2458 3.692593 TGATGATGAATGCAAGGTCACAG 59.307 43.478 0.00 0.00 0.00 3.66
2291 2763 4.431524 CTGGGGTGGAGGGGGCTA 62.432 72.222 0.00 0.00 0.00 3.93
2292 2764 3.717564 TGGGGTGGAGGGGGCTAT 61.718 66.667 0.00 0.00 0.00 2.97
2295 2767 2.006991 GGGTGGAGGGGGCTATTGT 61.007 63.158 0.00 0.00 0.00 2.71
2315 2787 3.711704 TGTGGTGAAGAAGGAGAGAAAGT 59.288 43.478 0.00 0.00 0.00 2.66
2363 2835 6.846505 ACATGATCCTCCTCCTGAAGTATAAA 59.153 38.462 0.00 0.00 0.00 1.40
2405 2877 7.959689 ATCTGATATGTTCTGATTCCTTTCG 57.040 36.000 0.00 0.00 39.28 3.46
2412 2884 3.498927 TCTGATTCCTTTCGTACGGAC 57.501 47.619 16.52 0.00 0.00 4.79
2426 2898 4.928615 TCGTACGGACCAATAATCGTTTTT 59.071 37.500 16.52 0.00 37.10 1.94
2488 2960 2.215191 CTCTATGAGCAGGTGCCCA 58.785 57.895 0.00 0.00 43.38 5.36
2517 2989 0.961019 TGGCTGCATTTTGGTGAGAC 59.039 50.000 0.50 0.00 0.00 3.36
2537 3009 6.210584 TGAGACACCACATCTATGAAACACTA 59.789 38.462 0.00 0.00 0.00 2.74
2706 3179 9.075678 GAATTCTCCACCTCATAATTTCATGAT 57.924 33.333 0.00 0.00 34.50 2.45
2765 3238 1.067974 CGAAAACCCAGTCCCAAAACC 59.932 52.381 0.00 0.00 0.00 3.27
2769 3242 3.915346 AACCCAGTCCCAAAACCTAAT 57.085 42.857 0.00 0.00 0.00 1.73
2784 3257 9.958180 CCAAAACCTAATTCCCAATAATTTCTT 57.042 29.630 0.00 0.00 31.63 2.52
2814 3287 0.460987 GACTGGGAACTGAGCCATCG 60.461 60.000 0.00 0.00 0.00 3.84
2967 3442 4.722700 AAAGCTCGCCATGGCCGT 62.723 61.111 30.79 12.51 37.98 5.68
3019 3494 1.132365 ACCCTATCCCCTGATTCCCTC 60.132 57.143 0.00 0.00 32.18 4.30
3020 3495 1.153132 CCCTATCCCCTGATTCCCTCT 59.847 57.143 0.00 0.00 32.18 3.69
3021 3496 2.264455 CCTATCCCCTGATTCCCTCTG 58.736 57.143 0.00 0.00 32.18 3.35
3022 3497 2.428484 CCTATCCCCTGATTCCCTCTGT 60.428 54.545 0.00 0.00 32.18 3.41
3023 3498 1.516110 ATCCCCTGATTCCCTCTGTG 58.484 55.000 0.00 0.00 0.00 3.66
3026 3501 1.279496 CCCTGATTCCCTCTGTGTCA 58.721 55.000 0.00 0.00 0.00 3.58
3049 3524 2.046892 GCTGAAGGCCGCTTCTCA 60.047 61.111 0.00 0.00 34.64 3.27
3195 3673 2.638154 CGATCGGAGGAGGCGTAC 59.362 66.667 7.38 0.00 0.00 3.67
3718 5508 8.438513 CCGAACTAACATGAAGCTATTATGATG 58.561 37.037 0.00 0.00 0.00 3.07
3719 5509 9.196552 CGAACTAACATGAAGCTATTATGATGA 57.803 33.333 0.00 0.00 0.00 2.92
3879 5669 4.062991 ACGACGATAATAAAATCCTGGCC 58.937 43.478 0.00 0.00 0.00 5.36
4080 5873 3.682696 GAGGTCCGTTTTTCTTGGGTAT 58.317 45.455 0.00 0.00 0.00 2.73
4107 5903 1.211457 GGGCCATGAGTCAGAGATGTT 59.789 52.381 4.39 0.00 0.00 2.71
4155 5951 6.720012 ACAAACCTTGCTTGTTTTTAGTTG 57.280 33.333 0.00 0.00 33.16 3.16
4194 5990 2.748605 GCTCCTGACCGATTCATACAG 58.251 52.381 0.00 0.00 32.17 2.74
4255 6051 7.491682 AGCTTGTGTGTTGAAATTGTTATTCT 58.508 30.769 0.00 0.00 0.00 2.40
4270 6066 6.642707 TGTTATTCTTTCATGTCCGGTTTT 57.357 33.333 0.00 0.00 0.00 2.43
4319 6115 4.530553 TCCTCTGATGTAAGCAAGTAACCA 59.469 41.667 0.00 0.00 0.00 3.67
4392 6188 3.134458 CAGAGGTCTTTGCGAAGAAACT 58.866 45.455 18.16 17.88 43.21 2.66
4598 6415 2.158827 GCCACAAAGGGAAAAACCACAT 60.159 45.455 0.00 0.00 41.20 3.21
4608 6425 5.188751 AGGGAAAAACCACATCACAAAAGAA 59.811 36.000 0.00 0.00 41.20 2.52
4609 6426 5.523552 GGGAAAAACCACATCACAAAAGAAG 59.476 40.000 0.00 0.00 41.20 2.85
4611 6428 6.476706 GGAAAAACCACATCACAAAAGAAGAG 59.523 38.462 0.00 0.00 38.79 2.85
4670 6490 4.973168 TGACTTTGTCATGCCTAAGAAGT 58.027 39.130 4.97 1.61 37.67 3.01
4727 6548 2.095263 CCTTAAACAAGGCATGTGTCCG 60.095 50.000 0.00 0.00 42.99 4.79
4866 6694 2.672874 GTGTGAAGCGATGCAATGACTA 59.327 45.455 0.00 0.00 0.00 2.59
4920 6748 3.887621 TCCATCGTGAACCTTAGGAAG 57.112 47.619 4.77 0.00 0.00 3.46
4978 6806 5.204833 TCATGTTTTTCTTTTCGCTTCGAG 58.795 37.500 0.00 0.00 37.14 4.04
4992 6820 3.126514 CGCTTCGAGTTCTACTGAGGTTA 59.873 47.826 0.00 0.00 0.00 2.85
5021 6849 4.272489 TGGAGCATCATTTTCTACCCAAG 58.728 43.478 0.00 0.00 36.25 3.61
5079 6907 3.683802 AGCTGAATGTTTCTTCTCCCAG 58.316 45.455 0.00 0.00 0.00 4.45
5080 6908 3.073650 AGCTGAATGTTTCTTCTCCCAGT 59.926 43.478 0.00 0.00 0.00 4.00
5081 6909 4.287067 AGCTGAATGTTTCTTCTCCCAGTA 59.713 41.667 0.00 0.00 0.00 2.74
5082 6910 5.045286 AGCTGAATGTTTCTTCTCCCAGTAT 60.045 40.000 0.00 0.00 0.00 2.12
5083 6911 5.295540 GCTGAATGTTTCTTCTCCCAGTATC 59.704 44.000 0.00 0.00 0.00 2.24
5084 6912 6.627087 TGAATGTTTCTTCTCCCAGTATCT 57.373 37.500 0.00 0.00 0.00 1.98
5085 6913 6.409704 TGAATGTTTCTTCTCCCAGTATCTG 58.590 40.000 0.00 0.00 0.00 2.90
5086 6914 6.213397 TGAATGTTTCTTCTCCCAGTATCTGA 59.787 38.462 0.00 0.00 32.44 3.27
5087 6915 6.821616 ATGTTTCTTCTCCCAGTATCTGAT 57.178 37.500 0.00 0.00 32.44 2.90
5088 6916 6.227298 TGTTTCTTCTCCCAGTATCTGATC 57.773 41.667 0.00 0.00 32.44 2.92
5089 6917 5.129485 TGTTTCTTCTCCCAGTATCTGATCC 59.871 44.000 0.00 0.00 32.44 3.36
5090 6918 4.823364 TCTTCTCCCAGTATCTGATCCT 57.177 45.455 0.00 0.00 32.44 3.24
5091 6919 4.478203 TCTTCTCCCAGTATCTGATCCTG 58.522 47.826 3.45 3.45 32.44 3.86
5092 6920 4.168871 TCTTCTCCCAGTATCTGATCCTGA 59.831 45.833 11.36 0.00 32.44 3.86
5093 6921 4.756203 TCTCCCAGTATCTGATCCTGAT 57.244 45.455 11.36 0.00 32.44 2.90
5094 6922 5.085275 TCTCCCAGTATCTGATCCTGATT 57.915 43.478 11.36 0.00 32.44 2.57
5095 6923 6.219537 TCTCCCAGTATCTGATCCTGATTA 57.780 41.667 11.36 0.00 32.44 1.75
5190 7025 1.519719 GAGTGGATTGCGGCTCTCT 59.480 57.895 0.00 0.00 0.00 3.10
5382 7217 1.685765 CGTGGGAGAGGGGTCATCA 60.686 63.158 0.00 0.00 0.00 3.07
5457 7292 1.003839 GATGTGGACAACCTGGCGA 60.004 57.895 0.00 0.00 37.04 5.54
5458 7293 0.605319 GATGTGGACAACCTGGCGAA 60.605 55.000 0.00 0.00 37.04 4.70
5571 7406 2.195567 CGCATAACCCATGGGCTGG 61.196 63.158 31.73 18.32 45.51 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.439305 TTGCACTTATGGTTCTGCATTC 57.561 40.909 0.00 0.00 32.14 2.67
11 13 5.221441 GGGTTTCTTTTGCACTTATGGTTCT 60.221 40.000 0.00 0.00 0.00 3.01
12 14 4.988540 GGGTTTCTTTTGCACTTATGGTTC 59.011 41.667 0.00 0.00 0.00 3.62
21 23 1.611491 TCATCCGGGTTTCTTTTGCAC 59.389 47.619 0.00 0.00 0.00 4.57
29 31 2.419667 TCTTCGTTTCATCCGGGTTTC 58.580 47.619 0.00 0.00 0.00 2.78
31 33 2.554370 TTCTTCGTTTCATCCGGGTT 57.446 45.000 0.00 0.00 0.00 4.11
32 34 2.554370 TTTCTTCGTTTCATCCGGGT 57.446 45.000 0.00 0.00 0.00 5.28
80 82 1.272313 GCATCTCATGGGCCATGGTAT 60.272 52.381 38.66 29.41 41.66 2.73
81 83 0.111061 GCATCTCATGGGCCATGGTA 59.889 55.000 38.66 28.68 41.66 3.25
82 84 1.152610 GCATCTCATGGGCCATGGT 60.153 57.895 38.66 25.00 41.66 3.55
84 86 0.820482 TTCGCATCTCATGGGCCATG 60.820 55.000 35.67 35.67 42.60 3.66
87 89 0.464373 TTCTTCGCATCTCATGGGCC 60.464 55.000 0.00 0.00 42.34 5.80
88 90 0.942962 CTTCTTCGCATCTCATGGGC 59.057 55.000 0.00 0.00 42.34 5.36
91 93 1.950828 AGGCTTCTTCGCATCTCATG 58.049 50.000 0.00 0.00 0.00 3.07
92 94 3.462021 GTTAGGCTTCTTCGCATCTCAT 58.538 45.455 0.00 0.00 0.00 2.90
93 95 2.418746 GGTTAGGCTTCTTCGCATCTCA 60.419 50.000 0.00 0.00 0.00 3.27
100 102 1.804748 GGTTGTGGTTAGGCTTCTTCG 59.195 52.381 0.00 0.00 0.00 3.79
107 109 0.248289 TAGCTCGGTTGTGGTTAGGC 59.752 55.000 0.00 0.00 0.00 3.93
109 111 3.195661 GGAATAGCTCGGTTGTGGTTAG 58.804 50.000 0.00 0.00 0.00 2.34
114 116 0.541863 AGGGGAATAGCTCGGTTGTG 59.458 55.000 0.00 0.00 0.00 3.33
115 117 0.831307 GAGGGGAATAGCTCGGTTGT 59.169 55.000 0.00 0.00 0.00 3.32
116 118 0.830648 TGAGGGGAATAGCTCGGTTG 59.169 55.000 0.00 0.00 0.00 3.77
117 119 1.807814 ATGAGGGGAATAGCTCGGTT 58.192 50.000 0.00 0.00 0.00 4.44
118 120 1.694696 GAATGAGGGGAATAGCTCGGT 59.305 52.381 0.00 0.00 0.00 4.69
119 121 1.974236 AGAATGAGGGGAATAGCTCGG 59.026 52.381 0.00 0.00 0.00 4.63
120 122 3.323403 AGAAGAATGAGGGGAATAGCTCG 59.677 47.826 0.00 0.00 0.00 5.03
132 134 1.535015 GGAGGTCGCGAGAAGAATGAG 60.535 57.143 10.24 0.00 45.01 2.90
135 137 2.054232 TAGGAGGTCGCGAGAAGAAT 57.946 50.000 10.24 0.00 45.01 2.40
142 146 1.721664 CGTGGAATAGGAGGTCGCGA 61.722 60.000 3.71 3.71 33.85 5.87
144 148 1.591863 GCGTGGAATAGGAGGTCGC 60.592 63.158 0.00 0.00 35.86 5.19
145 149 0.460311 AAGCGTGGAATAGGAGGTCG 59.540 55.000 0.00 0.00 0.00 4.79
163 167 6.039270 CCTCCATCATTCCACGCTTAATTAAA 59.961 38.462 0.00 0.00 0.00 1.52
181 185 1.098050 GCACATGTGTTCCCTCCATC 58.902 55.000 26.01 2.50 0.00 3.51
184 188 2.489938 TAAGCACATGTGTTCCCTCC 57.510 50.000 26.01 8.36 0.00 4.30
304 308 5.362105 AGCATGCACATTTCCCATTTTAT 57.638 34.783 21.98 0.00 0.00 1.40
310 314 0.608856 ACGAGCATGCACATTTCCCA 60.609 50.000 21.98 0.00 0.00 4.37
318 322 7.643764 ACATGTTTTAAATATACGAGCATGCAC 59.356 33.333 21.98 13.43 35.85 4.57
334 338 8.449085 TTTTATGCGCGATTAACATGTTTTAA 57.551 26.923 17.78 6.31 0.00 1.52
336 340 6.936222 TTTTATGCGCGATTAACATGTTTT 57.064 29.167 17.78 4.84 0.00 2.43
340 344 8.900762 TGAATATTTTTATGCGCGATTAACATG 58.099 29.630 12.10 0.00 0.00 3.21
371 376 9.414295 CAAATATGCGATGACCATTTTCAATAT 57.586 29.630 0.00 0.00 0.00 1.28
376 381 7.754069 TTTCAAATATGCGATGACCATTTTC 57.246 32.000 0.00 0.00 0.00 2.29
462 467 9.833182 GATGGTTTCTTTCTTTCTGTCTTTATC 57.167 33.333 0.00 0.00 0.00 1.75
470 484 8.193438 AGTTTTCTGATGGTTTCTTTCTTTCTG 58.807 33.333 0.00 0.00 0.00 3.02
548 562 1.577922 GGCCGTTTTTCTTCCGTCC 59.422 57.895 0.00 0.00 0.00 4.79
611 626 1.672356 CAGGCTTCGTTGGACTGGG 60.672 63.158 0.00 0.00 36.27 4.45
664 693 2.622436 CCGAGAAACAGTCTGATTCCC 58.378 52.381 16.77 6.74 36.41 3.97
683 712 1.166531 CGGTATTAAGCTGGGCTGCC 61.167 60.000 11.05 11.05 39.62 4.85
738 767 0.832983 TCCGGACGAAGGAAGGGAAA 60.833 55.000 0.00 0.00 34.33 3.13
745 775 2.203523 TGTGGTCCGGACGAAGGA 60.204 61.111 27.68 9.16 34.99 3.36
746 776 1.812686 TTCTGTGGTCCGGACGAAGG 61.813 60.000 27.68 18.73 0.00 3.46
793 824 2.922234 GGCTGATGGGGAAGAGGG 59.078 66.667 0.00 0.00 0.00 4.30
878 909 6.380274 AGGAATAACGACAGAGGATTTAGACA 59.620 38.462 0.00 0.00 0.00 3.41
1095 1127 4.116328 CGAGAGAACGCCAGCGGA 62.116 66.667 17.33 0.00 44.69 5.54
1140 1172 0.401738 CCTTCTTGACCTTGGAGGCA 59.598 55.000 0.00 0.00 39.63 4.75
1144 1176 2.260822 CTCCTCCTTCTTGACCTTGGA 58.739 52.381 0.00 0.00 0.00 3.53
1235 1276 2.830321 TCCTCGTACTCCTCCTTTTTCC 59.170 50.000 0.00 0.00 0.00 3.13
1362 1406 2.818751 TTGGCACCGAAAATATCCCT 57.181 45.000 0.00 0.00 0.00 4.20
1427 1471 7.094549 GCACATCTAACCTAGACAGACCTATAG 60.095 44.444 0.00 0.00 37.69 1.31
1444 1488 3.263170 TGCAAGAACTAGGGCACATCTAA 59.737 43.478 0.00 0.00 0.00 2.10
1445 1489 2.837591 TGCAAGAACTAGGGCACATCTA 59.162 45.455 0.00 0.00 0.00 1.98
1447 1491 2.113860 TGCAAGAACTAGGGCACATC 57.886 50.000 0.00 0.00 0.00 3.06
1567 1619 6.772605 TCTAGATGTGCCATAAGTATTGCAT 58.227 36.000 0.92 0.00 36.83 3.96
1644 2107 5.640357 ACGAATCCTTAGTAATCGCAAAACA 59.360 36.000 4.03 0.00 37.03 2.83
1657 2120 6.093495 TGGCAAATGAGTTTACGAATCCTTAG 59.907 38.462 0.00 0.00 0.00 2.18
1802 2265 6.006449 ACATCTCAGCTGAAGGTAATTTTGT 58.994 36.000 18.85 7.83 0.00 2.83
1811 2274 4.412796 TCCAATACATCTCAGCTGAAGG 57.587 45.455 18.85 12.62 0.00 3.46
1921 2384 2.825532 GCCTTCACCTTGCTATTGGAAA 59.174 45.455 0.00 0.00 0.00 3.13
1995 2458 7.503521 AAATCTGGAACAAGAGAAGAAGAAC 57.496 36.000 0.00 0.00 38.70 3.01
2291 2763 4.982241 TTCTCTCCTTCTTCACCACAAT 57.018 40.909 0.00 0.00 0.00 2.71
2292 2764 4.164221 ACTTTCTCTCCTTCTTCACCACAA 59.836 41.667 0.00 0.00 0.00 3.33
2295 2767 4.164221 ACAACTTTCTCTCCTTCTTCACCA 59.836 41.667 0.00 0.00 0.00 4.17
2405 2877 6.413018 AGAAAAACGATTATTGGTCCGTAC 57.587 37.500 0.00 0.00 34.60 3.67
2412 2884 9.672086 TGTAACAAGAAGAAAAACGATTATTGG 57.328 29.630 0.00 0.00 0.00 3.16
2426 2898 4.425772 TGGATCCCTCTGTAACAAGAAGA 58.574 43.478 9.90 0.00 0.00 2.87
2517 2989 7.439356 CAGGTATAGTGTTTCATAGATGTGGTG 59.561 40.741 0.00 0.00 0.00 4.17
2583 3056 9.804758 CAAGTTTGTTTAAATACCCTGTACAAA 57.195 29.630 0.00 0.00 33.22 2.83
2617 3090 3.256704 TCAGGGGGTTCTACTGTGATTT 58.743 45.455 0.00 0.00 34.02 2.17
2706 3179 6.374417 AGATGGGTTAGAGTTGCTTTAAGA 57.626 37.500 0.00 0.00 0.00 2.10
2784 3257 1.913419 GTTCCCAGTCTCCCAATACCA 59.087 52.381 0.00 0.00 0.00 3.25
2814 3287 5.468540 AAAAATGGGAGTCAAGTTTAGGC 57.531 39.130 0.00 0.00 0.00 3.93
3019 3494 0.504384 CTTCAGCGTCGTTGACACAG 59.496 55.000 11.59 3.21 32.09 3.66
3020 3495 0.874175 CCTTCAGCGTCGTTGACACA 60.874 55.000 11.59 0.00 32.09 3.72
3021 3496 1.853319 CCTTCAGCGTCGTTGACAC 59.147 57.895 11.59 0.00 32.09 3.67
3022 3497 1.954146 GCCTTCAGCGTCGTTGACA 60.954 57.895 11.59 3.02 32.09 3.58
3023 3498 2.668280 GGCCTTCAGCGTCGTTGAC 61.668 63.158 11.59 0.59 45.17 3.18
3181 3659 0.536687 CCTATGTACGCCTCCTCCGA 60.537 60.000 0.00 0.00 0.00 4.55
3182 3660 1.957562 CCTATGTACGCCTCCTCCG 59.042 63.158 0.00 0.00 0.00 4.63
3215 3693 2.743718 CAAGTCACCGGCTCTGGT 59.256 61.111 0.00 0.00 45.21 4.00
3250 3728 3.039134 CCACCGTCAAAGTTGCCC 58.961 61.111 0.00 0.00 0.00 5.36
3279 3757 4.762251 AGGAGAAATTTTCCTTCCTCAACG 59.238 41.667 12.08 0.00 42.40 4.10
3284 3762 3.181418 TGGCAGGAGAAATTTTCCTTCCT 60.181 43.478 24.18 17.17 45.19 3.36
3554 4277 5.786264 ACGCTGGCTATATTGTAGTAAGT 57.214 39.130 0.00 0.00 0.00 2.24
3555 4278 7.368833 AGTAACGCTGGCTATATTGTAGTAAG 58.631 38.462 0.00 0.00 0.00 2.34
3556 4279 7.281040 AGTAACGCTGGCTATATTGTAGTAA 57.719 36.000 0.00 0.00 0.00 2.24
3557 4280 6.889301 AGTAACGCTGGCTATATTGTAGTA 57.111 37.500 0.00 0.00 0.00 1.82
3718 5508 3.470709 TGCATTAATCTACCAGCAGCTC 58.529 45.455 0.00 0.00 0.00 4.09
3719 5509 3.565764 TGCATTAATCTACCAGCAGCT 57.434 42.857 0.00 0.00 0.00 4.24
3773 5563 7.657354 GTGGAGATTAAAAATTCTGGTGCTTTT 59.343 33.333 0.00 0.00 0.00 2.27
4155 5951 3.798202 AGCGACTGATAAGTGGAAATCC 58.202 45.455 0.00 0.00 0.00 3.01
4255 6051 9.197694 CATAAAATGTAAAAACCGGACATGAAA 57.802 29.630 9.46 0.00 34.10 2.69
4319 6115 5.191727 TCCATCAACCTGTACATCCAAAT 57.808 39.130 0.00 0.00 0.00 2.32
4392 6188 1.416401 GTGACCTCAGTTTCTGACCCA 59.584 52.381 0.00 0.00 35.39 4.51
4598 6415 3.576078 TGCCTTCCTCTTCTTTTGTGA 57.424 42.857 0.00 0.00 0.00 3.58
4608 6425 1.036707 GTCGCTAGATGCCTTCCTCT 58.963 55.000 0.00 0.00 38.78 3.69
4609 6426 0.747255 TGTCGCTAGATGCCTTCCTC 59.253 55.000 0.00 0.00 38.78 3.71
4611 6428 0.175760 TGTGTCGCTAGATGCCTTCC 59.824 55.000 0.00 0.00 38.78 3.46
4670 6490 5.046014 AGCTAGAGATCTTTTGCTTCTTGGA 60.046 40.000 14.91 0.00 0.00 3.53
4866 6694 1.242076 GCAAGCACTGGAAGACATGT 58.758 50.000 0.00 0.00 37.43 3.21
4920 6748 4.872691 AGTACTGCAAGACATGTCAATAGC 59.127 41.667 27.02 22.19 37.43 2.97
4978 6806 6.285990 TCCAGTTTGTTAACCTCAGTAGAAC 58.714 40.000 2.48 0.00 34.71 3.01
4992 6820 5.796424 AGAAAATGATGCTCCAGTTTGTT 57.204 34.783 8.55 0.00 34.94 2.83
5079 6907 8.932945 TGCGAATATTAATCAGGATCAGATAC 57.067 34.615 0.00 0.00 0.00 2.24
5080 6908 9.591792 CTTGCGAATATTAATCAGGATCAGATA 57.408 33.333 0.00 0.00 0.00 1.98
5081 6909 7.551974 CCTTGCGAATATTAATCAGGATCAGAT 59.448 37.037 0.00 0.00 0.00 2.90
5082 6910 6.875726 CCTTGCGAATATTAATCAGGATCAGA 59.124 38.462 0.00 0.00 0.00 3.27
5083 6911 6.402983 GCCTTGCGAATATTAATCAGGATCAG 60.403 42.308 0.00 0.00 0.00 2.90
5084 6912 5.412594 GCCTTGCGAATATTAATCAGGATCA 59.587 40.000 0.00 0.00 0.00 2.92
5085 6913 5.163713 GGCCTTGCGAATATTAATCAGGATC 60.164 44.000 0.00 0.00 0.00 3.36
5086 6914 4.702131 GGCCTTGCGAATATTAATCAGGAT 59.298 41.667 0.00 0.00 0.00 3.24
5087 6915 4.072131 GGCCTTGCGAATATTAATCAGGA 58.928 43.478 0.00 0.00 0.00 3.86
5088 6916 4.074970 AGGCCTTGCGAATATTAATCAGG 58.925 43.478 0.00 0.00 0.00 3.86
5089 6917 5.695851 AAGGCCTTGCGAATATTAATCAG 57.304 39.130 19.73 0.00 0.00 2.90
5090 6918 5.592282 TCAAAGGCCTTGCGAATATTAATCA 59.408 36.000 21.33 0.00 34.76 2.57
5091 6919 5.915196 GTCAAAGGCCTTGCGAATATTAATC 59.085 40.000 21.33 0.89 34.76 1.75
5092 6920 5.594317 AGTCAAAGGCCTTGCGAATATTAAT 59.406 36.000 21.33 0.00 34.76 1.40
5093 6921 4.947388 AGTCAAAGGCCTTGCGAATATTAA 59.053 37.500 21.33 0.00 34.76 1.40
5094 6922 4.523083 AGTCAAAGGCCTTGCGAATATTA 58.477 39.130 21.33 0.00 34.76 0.98
5095 6923 3.356290 AGTCAAAGGCCTTGCGAATATT 58.644 40.909 21.33 0.00 34.76 1.28
5271 7106 1.022903 AGGAGAGGAGAGATGGGGTT 58.977 55.000 0.00 0.00 0.00 4.11
5352 7187 1.071542 TCTCCCACGAATCTTGTGCAA 59.928 47.619 0.00 0.00 36.01 4.08
5457 7292 1.212935 CCCGAATCCCCTCAGAATGTT 59.787 52.381 0.00 0.00 37.40 2.71
5458 7293 0.839946 CCCGAATCCCCTCAGAATGT 59.160 55.000 0.00 0.00 37.40 2.71
5490 7325 4.878397 GCTCTTATGGAAGTTAGTGCACAT 59.122 41.667 21.04 6.83 34.03 3.21
5571 7406 2.032681 CCCTAATAGCCGGCAGCC 59.967 66.667 31.54 0.00 45.47 4.85
5572 7407 2.669910 GCCCTAATAGCCGGCAGC 60.670 66.667 31.54 15.07 42.52 5.25
5573 7408 1.302033 CAGCCCTAATAGCCGGCAG 60.302 63.158 31.54 17.33 45.56 4.85
5574 7409 2.828868 CAGCCCTAATAGCCGGCA 59.171 61.111 31.54 15.56 45.56 5.69
5575 7410 2.669910 GCAGCCCTAATAGCCGGC 60.670 66.667 21.89 21.89 43.35 6.13
5582 7417 1.453928 GCGGAAAGGCAGCCCTAAT 60.454 57.895 8.22 0.00 41.90 1.73


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

AutoCloner maintained by Alex Coulton.