Multiple sequence alignment - TraesCS6A01G167900

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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 TraesCS6A01G167900 chr6A 100.000 5470 0 0 1 5470 172121402 172115933 0.000000e+00 10102.0
1 TraesCS6A01G167900 chr6A 87.413 286 28 8 4284 4565 100664476 100664757 6.840000e-84 322.0
2 TraesCS6A01G167900 chr6A 100.000 33 0 0 4102 4134 172117219 172117187 1.650000e-05 62.1
3 TraesCS6A01G167900 chr6A 100.000 33 0 0 4184 4216 172117301 172117269 1.650000e-05 62.1
4 TraesCS6A01G167900 chr6B 92.562 2998 128 46 1062 4009 231357061 231354109 0.000000e+00 4213.0
5 TraesCS6A01G167900 chr6B 95.981 1070 25 5 1 1070 231672811 231671760 0.000000e+00 1722.0
6 TraesCS6A01G167900 chr6B 97.354 378 10 0 5049 5426 231352921 231352544 1.280000e-180 643.0
7 TraesCS6A01G167900 chr6B 95.082 305 12 2 4648 4952 231353541 231353240 1.380000e-130 477.0
8 TraesCS6A01G167900 chr6B 86.822 387 41 7 4179 4563 231353999 231353621 1.820000e-114 424.0
9 TraesCS6A01G167900 chr6B 88.732 284 27 4 4285 4565 159133398 159133679 5.250000e-90 342.0
10 TraesCS6A01G167900 chr6B 87.676 284 29 5 4284 4564 166114707 166114987 5.280000e-85 326.0
11 TraesCS6A01G167900 chr6B 86.667 285 32 5 4284 4565 159137928 159138209 1.480000e-80 311.0
12 TraesCS6A01G167900 chr6B 100.000 31 0 0 4649 4679 231353623 231353593 2.130000e-04 58.4
13 TraesCS6A01G167900 chr6D 94.056 2086 88 23 2012 4085 133214398 133212337 0.000000e+00 3133.0
14 TraesCS6A01G167900 chr6D 91.470 1313 62 18 4174 5470 133212282 133211004 0.000000e+00 1759.0
15 TraesCS6A01G167900 chr6D 91.300 1092 57 16 834 1905 133215484 133214411 0.000000e+00 1456.0
16 TraesCS6A01G167900 chr6D 98.573 771 11 0 1 771 133216545 133215775 0.000000e+00 1363.0
17 TraesCS6A01G167900 chr6D 86.689 293 29 8 4278 4565 87465770 87466057 3.180000e-82 316.0
18 TraesCS6A01G167900 chr7D 77.978 722 148 8 6 726 507433157 507433868 5.030000e-120 442.0
19 TraesCS6A01G167900 chr7A 80.143 559 106 4 6 563 577236092 577236646 3.940000e-111 412.0
20 TraesCS6A01G167900 chr7B 80.364 494 92 4 6 498 535835414 535835903 2.410000e-98 370.0
21 TraesCS6A01G167900 chr3B 90.840 262 24 0 4284 4545 495471041 495470780 8.720000e-93 351.0
22 TraesCS6A01G167900 chr4B 85.574 305 33 11 4267 4565 579103350 579103649 5.320000e-80 309.0


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 TraesCS6A01G167900 chr6A 172115933 172121402 5469 True 10102.00 10102 100.00000 1 5470 1 chr6A.!!$R1 5469
1 TraesCS6A01G167900 chr6B 231671760 231672811 1051 True 1722.00 1722 95.98100 1 1070 1 chr6B.!!$R1 1069
2 TraesCS6A01G167900 chr6B 231352544 231357061 4517 True 1163.08 4213 94.36400 1062 5426 5 chr6B.!!$R2 4364
3 TraesCS6A01G167900 chr6D 133211004 133216545 5541 True 1927.75 3133 93.84975 1 5470 4 chr6D.!!$R1 5469
4 TraesCS6A01G167900 chr7D 507433157 507433868 711 False 442.00 442 77.97800 6 726 1 chr7D.!!$F1 720
5 TraesCS6A01G167900 chr7A 577236092 577236646 554 False 412.00 412 80.14300 6 563 1 chr7A.!!$F1 557

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
24 25 1.450312 GTCACTCCCTTCCATGGCG 60.450 63.158 6.96 0.0 0.00 5.69 F
1305 1557 0.460987 GAGGTTGTCTCCATCCAGCG 60.461 60.000 0.00 0.0 36.52 5.18 F
2185 2455 0.823356 TTGCTCCACTTTGAGGGCAC 60.823 55.000 0.00 0.0 33.86 5.01 F
4090 4378 0.032515 TCTCCCCGGCTTATGTCTGA 60.033 55.000 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 1760 0.173255 AACGGCCAAACAGCATATGC 59.827 50.000 20.36 20.36 42.49 3.14 R
2962 3241 2.284995 GGGACACCAGAGAGGCCT 60.285 66.667 3.86 3.86 43.14 5.19 R
4104 4392 0.185901 TGGCTTCTCCACCTTTTGCT 59.814 50.000 0.00 0.00 40.72 3.91 R
5435 5966 0.178967 TTGGTCCAGCAGGCAATGAA 60.179 50.000 0.00 0.00 33.74 2.57 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
24 25 1.450312 GTCACTCCCTTCCATGGCG 60.450 63.158 6.96 0.00 0.00 5.69
684 685 1.895051 CGTTTTTGATGATGCGGTCC 58.105 50.000 0.00 0.00 0.00 4.46
689 690 2.106938 GATGATGCGGTCCAGCGA 59.893 61.111 1.59 0.00 40.67 4.93
690 691 1.521457 GATGATGCGGTCCAGCGAA 60.521 57.895 1.59 0.00 40.67 4.70
1012 1243 1.856265 GCCACTGCGGAACTTTCCTG 61.856 60.000 0.00 1.71 45.33 3.86
1042 1273 1.705256 TACCGAACTAGTGCGCTTTG 58.295 50.000 18.39 6.72 0.00 2.77
1085 1316 2.440796 TATTCTCGTCGCCCCGGT 60.441 61.111 0.00 0.00 0.00 5.28
1109 1340 2.434359 CTTCCGAGTCAACCCCGC 60.434 66.667 0.00 0.00 0.00 6.13
1213 1465 4.530857 CCCACCGCCATCTCCGTC 62.531 72.222 0.00 0.00 0.00 4.79
1224 1476 3.839432 CTCCGTCCTTCCTCGCCC 61.839 72.222 0.00 0.00 0.00 6.13
1305 1557 0.460987 GAGGTTGTCTCCATCCAGCG 60.461 60.000 0.00 0.00 36.52 5.18
1407 1659 1.341531 CATCATCGAGACCCAGGTACC 59.658 57.143 2.73 2.73 0.00 3.34
1474 1727 1.882623 GCTATCCATTGCTGTTAGGGC 59.117 52.381 0.00 0.00 0.00 5.19
1559 1813 3.754965 AGCTTGTCAAGGATGCTGTAAA 58.245 40.909 14.40 0.00 32.32 2.01
1622 1877 5.819379 TCAAAACATAGGCTGAGTGATGATC 59.181 40.000 0.00 0.00 0.00 2.92
1624 1879 4.870123 ACATAGGCTGAGTGATGATCTC 57.130 45.455 0.00 0.00 0.00 2.75
1625 1880 3.577848 ACATAGGCTGAGTGATGATCTCC 59.422 47.826 0.00 0.00 0.00 3.71
1672 1929 1.869767 GTAGGATGGCGCATCTTTCTG 59.130 52.381 10.83 0.00 40.39 3.02
1697 1954 2.362120 GCCTCTTGCCATGCACCT 60.362 61.111 0.00 0.00 38.71 4.00
1729 1986 3.165071 TCAGACATGACCTTCTGTGCTA 58.835 45.455 0.00 0.00 40.25 3.49
1826 2096 2.624838 CCTTTGTTGGAGTTGTCAGCAT 59.375 45.455 0.00 0.00 0.00 3.79
1849 2119 8.893727 GCATAACTATCTCCACACACTAATTTT 58.106 33.333 0.00 0.00 0.00 1.82
1928 2198 2.304761 CCAGCTCAACCCTGGTTAACTA 59.695 50.000 5.42 0.00 43.86 2.24
1939 2209 7.604657 ACCCTGGTTAACTATCTCTAATCTG 57.395 40.000 5.42 0.00 0.00 2.90
2031 2301 9.962783 AAATAATGCTAGAGCTTTTCATTGATC 57.037 29.630 7.83 0.00 42.66 2.92
2105 2375 8.975410 TCAGAATGAATCAAAATCAACATGAC 57.025 30.769 0.00 0.00 45.97 3.06
2106 2376 8.799367 TCAGAATGAATCAAAATCAACATGACT 58.201 29.630 0.00 0.00 45.97 3.41
2107 2377 9.419297 CAGAATGAATCAAAATCAACATGACTT 57.581 29.630 0.00 0.00 39.69 3.01
2152 2422 5.858381 TGATATTTAGATCCTGCTGACCAC 58.142 41.667 0.00 0.00 0.00 4.16
2185 2455 0.823356 TTGCTCCACTTTGAGGGCAC 60.823 55.000 0.00 0.00 33.86 5.01
2191 2461 2.441750 TCCACTTTGAGGGCACTACTTT 59.558 45.455 0.00 0.00 0.00 2.66
2298 2571 5.245531 TCAGTCCCACATATTTGACTTCAC 58.754 41.667 0.00 0.00 35.97 3.18
2401 2677 6.600388 TGGCTGTAAGATTTATGCTATTCCA 58.400 36.000 0.00 0.00 34.07 3.53
2441 2717 2.889512 TCTATGCTATCCATGGGTCGT 58.110 47.619 13.02 0.00 35.34 4.34
2442 2718 2.562738 TCTATGCTATCCATGGGTCGTG 59.437 50.000 13.02 0.00 35.34 4.35
2459 2735 3.357079 GCAGCCACCTCGTGTTGG 61.357 66.667 0.00 0.00 0.00 3.77
2586 2862 9.591792 TGAAGTGATATCTGAGTCTTATGTTTG 57.408 33.333 3.98 0.00 0.00 2.93
2670 2946 6.403636 GGACACTTAGCATGAATTTCGAACAT 60.404 38.462 0.00 0.00 0.00 2.71
2671 2947 6.913170 ACACTTAGCATGAATTTCGAACATT 58.087 32.000 0.00 1.18 0.00 2.71
2763 3039 5.077564 TCTCCACTTTGAGAGCACTACTTA 58.922 41.667 0.00 0.00 36.48 2.24
2869 3146 3.197766 TCTCCACATTCATTTAGACCGCT 59.802 43.478 0.00 0.00 0.00 5.52
3129 3411 4.156190 TCTGCTAACCTCTTTCAGTCGTAG 59.844 45.833 0.00 0.00 0.00 3.51
3220 3503 8.140628 TGATTGTGTTAAGCTGCTGAAATTTAA 58.859 29.630 1.35 0.00 0.00 1.52
3269 3552 8.752005 ATCTGCAGTTGGTAATATTTGTATGT 57.248 30.769 14.67 0.00 0.00 2.29
3270 3553 9.845740 ATCTGCAGTTGGTAATATTTGTATGTA 57.154 29.630 14.67 0.00 0.00 2.29
3499 3782 2.037901 TCTGCCAACAAGATGCCAAAA 58.962 42.857 0.00 0.00 0.00 2.44
3502 3785 2.137523 GCCAACAAGATGCCAAAACTG 58.862 47.619 0.00 0.00 0.00 3.16
3610 3893 2.288666 GTTGTTTCAGCTGTCACCTCA 58.711 47.619 14.67 3.46 0.00 3.86
3641 3924 1.103398 TCTAGCGCCGTAAGTACCCC 61.103 60.000 2.29 0.00 0.00 4.95
3667 3950 8.792633 CCAACCTGAATTTTGATACTTCAGTTA 58.207 33.333 9.81 0.00 42.69 2.24
3669 3952 9.793259 AACCTGAATTTTGATACTTCAGTTAGA 57.207 29.630 9.81 0.00 42.69 2.10
3670 3953 9.965902 ACCTGAATTTTGATACTTCAGTTAGAT 57.034 29.630 9.81 0.00 42.69 1.98
3700 3983 7.627340 TCTTCACGTGTCTTCTTTTGAATAAC 58.373 34.615 16.51 0.00 37.85 1.89
3780 4066 0.246635 CAACTGGAATCGTCCCGACT 59.753 55.000 0.00 0.00 44.23 4.18
3922 4208 8.783833 ATGCATGAATAACACTATGATACCTC 57.216 34.615 0.00 0.00 0.00 3.85
3974 4261 4.982295 GGCACTGTGTTGGAAAAAGTATTC 59.018 41.667 9.86 0.00 0.00 1.75
3986 4273 3.806949 AAAGTATTCTTGGCACTGGGA 57.193 42.857 0.00 0.00 33.79 4.37
4009 4297 9.444600 GGGATTTGTAACTTGTATAAGAGTTGA 57.555 33.333 6.19 0.00 36.79 3.18
4013 4301 9.826574 TTTGTAACTTGTATAAGAGTTGACAGT 57.173 29.630 6.19 0.00 36.79 3.55
4014 4302 9.472361 TTGTAACTTGTATAAGAGTTGACAGTC 57.528 33.333 6.19 0.00 36.79 3.51
4015 4303 8.635328 TGTAACTTGTATAAGAGTTGACAGTCA 58.365 33.333 6.19 0.00 36.79 3.41
4016 4304 9.130312 GTAACTTGTATAAGAGTTGACAGTCAG 57.870 37.037 6.19 0.00 36.79 3.51
4017 4305 6.159988 ACTTGTATAAGAGTTGACAGTCAGC 58.840 40.000 9.32 9.32 37.36 4.26
4019 4307 5.714047 TGTATAAGAGTTGACAGTCAGCAG 58.286 41.667 18.61 0.00 29.40 4.24
4020 4308 1.876322 AAGAGTTGACAGTCAGCAGC 58.124 50.000 18.61 10.40 29.40 5.25
4021 4309 0.034616 AGAGTTGACAGTCAGCAGCC 59.965 55.000 18.61 7.96 29.40 4.85
4022 4310 0.034616 GAGTTGACAGTCAGCAGCCT 59.965 55.000 18.61 4.68 29.40 4.58
4047 4335 4.006319 GCATCTCTGCTTAGTTGGAACTT 58.994 43.478 0.00 0.00 45.32 2.66
4048 4336 5.178797 GCATCTCTGCTTAGTTGGAACTTA 58.821 41.667 0.00 0.00 45.32 2.24
4049 4337 5.819901 GCATCTCTGCTTAGTTGGAACTTAT 59.180 40.000 0.00 0.00 45.32 1.73
4050 4338 6.018343 GCATCTCTGCTTAGTTGGAACTTATC 60.018 42.308 0.00 0.00 45.32 1.75
4051 4339 6.859112 TCTCTGCTTAGTTGGAACTTATCT 57.141 37.500 0.00 0.00 40.37 1.98
4052 4340 6.868622 TCTCTGCTTAGTTGGAACTTATCTC 58.131 40.000 0.00 0.00 40.37 2.75
4053 4341 5.651530 TCTGCTTAGTTGGAACTTATCTCG 58.348 41.667 0.00 0.00 40.37 4.04
4054 4342 5.417894 TCTGCTTAGTTGGAACTTATCTCGA 59.582 40.000 0.00 0.00 40.37 4.04
4055 4343 6.032956 TGCTTAGTTGGAACTTATCTCGAA 57.967 37.500 0.00 0.00 40.37 3.71
4056 4344 6.100004 TGCTTAGTTGGAACTTATCTCGAAG 58.900 40.000 0.00 0.00 40.37 3.79
4057 4345 6.100668 GCTTAGTTGGAACTTATCTCGAAGT 58.899 40.000 0.00 0.00 41.50 3.01
4062 4350 7.760437 AGTTGGAACTTATCTCGAAGTAGTAC 58.240 38.462 0.00 0.00 38.75 2.73
4085 4373 1.002087 GGTACATCTCCCCGGCTTATG 59.998 57.143 0.00 0.00 0.00 1.90
4087 4375 0.759346 ACATCTCCCCGGCTTATGTC 59.241 55.000 0.00 0.00 0.00 3.06
4089 4377 1.051812 ATCTCCCCGGCTTATGTCTG 58.948 55.000 0.00 0.00 0.00 3.51
4090 4378 0.032515 TCTCCCCGGCTTATGTCTGA 60.033 55.000 0.00 0.00 0.00 3.27
4091 4379 0.105039 CTCCCCGGCTTATGTCTGAC 59.895 60.000 0.00 0.00 0.00 3.51
4094 4382 1.541233 CCCCGGCTTATGTCTGACATC 60.541 57.143 25.35 12.23 39.88 3.06
4096 4384 2.205074 CCGGCTTATGTCTGACATCAC 58.795 52.381 25.35 15.67 39.88 3.06
4101 4389 5.580691 CGGCTTATGTCTGACATCACTTTTA 59.419 40.000 25.35 4.88 39.88 1.52
4102 4390 6.092122 CGGCTTATGTCTGACATCACTTTTAA 59.908 38.462 25.35 12.10 39.88 1.52
4104 4392 9.109393 GGCTTATGTCTGACATCACTTTTAATA 57.891 33.333 25.35 2.69 39.88 0.98
4107 4395 9.665719 TTATGTCTGACATCACTTTTAATAGCA 57.334 29.630 25.35 1.55 39.88 3.49
4108 4396 7.977789 TGTCTGACATCACTTTTAATAGCAA 57.022 32.000 6.36 0.00 0.00 3.91
4109 4397 8.389779 TGTCTGACATCACTTTTAATAGCAAA 57.610 30.769 6.36 0.00 0.00 3.68
4111 4399 9.334693 GTCTGACATCACTTTTAATAGCAAAAG 57.665 33.333 2.24 6.75 46.41 2.27
4114 4402 8.081633 TGACATCACTTTTAATAGCAAAAGGTG 58.918 33.333 11.72 9.61 45.65 4.00
4115 4403 7.378181 ACATCACTTTTAATAGCAAAAGGTGG 58.622 34.615 11.72 3.22 45.65 4.61
4119 4407 7.504238 TCACTTTTAATAGCAAAAGGTGGAGAA 59.496 33.333 11.72 0.00 45.65 2.87
4120 4408 7.809806 CACTTTTAATAGCAAAAGGTGGAGAAG 59.190 37.037 11.72 0.00 45.65 2.85
4122 4410 2.200373 TAGCAAAAGGTGGAGAAGCC 57.800 50.000 0.00 0.00 37.10 4.35
4139 4427 8.415553 TGGAGAAGCCAAATAATAACATCATTG 58.584 33.333 0.00 0.00 45.87 2.82
4140 4428 8.416329 GGAGAAGCCAAATAATAACATCATTGT 58.584 33.333 0.00 0.00 35.24 2.71
4169 4457 9.844790 TTTGAGAATAGCAAAACATCTTGTATG 57.155 29.630 0.00 0.00 32.75 2.39
4170 4458 7.475015 TGAGAATAGCAAAACATCTTGTATGC 58.525 34.615 9.19 9.19 41.07 3.14
4171 4459 6.489675 AGAATAGCAAAACATCTTGTATGCG 58.510 36.000 10.68 0.00 43.64 4.73
4172 4460 6.316140 AGAATAGCAAAACATCTTGTATGCGA 59.684 34.615 10.68 7.66 43.64 5.10
4219 4513 7.859325 TGGAGAAGCCAAATAATAACACTAC 57.141 36.000 0.00 0.00 45.87 2.73
4220 4514 7.630082 TGGAGAAGCCAAATAATAACACTACT 58.370 34.615 0.00 0.00 45.87 2.57
4221 4515 8.764558 TGGAGAAGCCAAATAATAACACTACTA 58.235 33.333 0.00 0.00 45.87 1.82
4222 4516 9.609346 GGAGAAGCCAAATAATAACACTACTAA 57.391 33.333 0.00 0.00 36.34 2.24
4274 4568 5.750067 CCTGTTTTCCTGACTGACAAAATTG 59.250 40.000 0.00 0.00 0.00 2.32
4280 4574 6.317789 TCCTGACTGACAAAATTGTGATTC 57.682 37.500 1.62 0.04 42.43 2.52
4491 4789 3.449632 GCCGAGAAAGGTATGAGTTCTC 58.550 50.000 3.14 3.14 42.47 2.87
4536 4834 4.150454 CCTCTCCCGGCTCCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
4574 4872 3.412386 GTGGGACTAAACTTGCATCACT 58.588 45.455 0.00 0.00 0.00 3.41
4576 4874 3.010420 GGGACTAAACTTGCATCACTCC 58.990 50.000 0.00 0.00 0.00 3.85
4597 4906 0.249238 GAGCGCTCTGTGTGGGATAG 60.249 60.000 29.88 0.00 0.00 2.08
4624 4933 2.803133 GCTGGGCTCTTTTTGACCAAAC 60.803 50.000 0.00 0.00 0.00 2.93
4628 4937 2.959030 GGCTCTTTTTGACCAAACCTCT 59.041 45.455 0.00 0.00 0.00 3.69
4630 4939 3.243535 GCTCTTTTTGACCAAACCTCTGG 60.244 47.826 0.00 0.00 42.68 3.86
4642 4951 2.045926 CTCTGGAGGCCCAAACCG 60.046 66.667 0.00 0.00 42.98 4.44
4696 5005 0.889186 AGGCCCAAACTACACGCTTG 60.889 55.000 0.00 0.00 0.00 4.01
4697 5006 1.081442 GCCCAAACTACACGCTTGC 60.081 57.895 0.00 0.00 0.00 4.01
4698 5007 1.791103 GCCCAAACTACACGCTTGCA 61.791 55.000 0.00 0.00 0.00 4.08
4699 5008 0.238289 CCCAAACTACACGCTTGCAG 59.762 55.000 0.00 0.00 0.00 4.41
4700 5009 0.385974 CCAAACTACACGCTTGCAGC 60.386 55.000 0.00 0.00 38.02 5.25
4710 5019 4.749310 CTTGCAGCGCCGGAGACT 62.749 66.667 10.31 2.40 0.00 3.24
4711 5020 3.356639 CTTGCAGCGCCGGAGACTA 62.357 63.158 10.31 0.00 0.00 2.59
4838 5147 3.047877 GTCACCGTTCAAGGCCCG 61.048 66.667 0.00 0.00 33.69 6.13
4857 5166 4.767892 CCCTTCTCCCAGCCCCCT 62.768 72.222 0.00 0.00 0.00 4.79
4974 5283 1.516386 ATCGCACGTCATCACCGTC 60.516 57.895 0.00 0.00 36.17 4.79
4984 5293 0.311165 CATCACCGTCCCTAGCTACG 59.689 60.000 7.82 7.82 38.80 3.51
4992 5301 0.752009 TCCCTAGCTACGCAGGTGAG 60.752 60.000 0.00 0.00 33.61 3.51
4993 5302 1.038130 CCCTAGCTACGCAGGTGAGT 61.038 60.000 0.00 0.00 33.61 3.41
4994 5303 0.382515 CCTAGCTACGCAGGTGAGTC 59.617 60.000 0.00 0.00 33.61 3.36
5001 5310 2.716017 CGCAGGTGAGTCCCTCTCC 61.716 68.421 4.55 4.55 42.47 3.71
5004 5313 2.365768 GGTGAGTCCCTCTCCCCC 60.366 72.222 1.72 0.00 42.12 5.40
5005 5314 2.760385 GTGAGTCCCTCTCCCCCG 60.760 72.222 0.00 0.00 42.12 5.73
5111 5642 2.328099 GCTTGCAGGGTGGTTCTCG 61.328 63.158 0.00 0.00 0.00 4.04
5249 5780 1.125093 TCAAGAGGTTCCGGGCAAGA 61.125 55.000 0.00 0.00 0.00 3.02
5426 5957 1.198178 GCGACGACTTCTCAGTCTTCT 59.802 52.381 0.00 0.00 46.67 2.85
5427 5958 2.350964 GCGACGACTTCTCAGTCTTCTT 60.351 50.000 0.00 0.00 46.67 2.52
5428 5959 3.484683 CGACGACTTCTCAGTCTTCTTC 58.515 50.000 7.14 0.00 46.67 2.87
5429 5960 3.187637 CGACGACTTCTCAGTCTTCTTCT 59.812 47.826 7.14 0.00 46.67 2.85
5430 5961 4.668177 CGACGACTTCTCAGTCTTCTTCTC 60.668 50.000 7.14 0.00 46.67 2.87
5431 5962 4.138290 ACGACTTCTCAGTCTTCTTCTCA 58.862 43.478 0.00 0.00 46.67 3.27
5432 5963 4.215399 ACGACTTCTCAGTCTTCTTCTCAG 59.785 45.833 0.00 0.00 46.67 3.35
5433 5964 4.215399 CGACTTCTCAGTCTTCTTCTCAGT 59.785 45.833 1.12 0.00 46.67 3.41
5434 5965 5.616866 CGACTTCTCAGTCTTCTTCTCAGTC 60.617 48.000 1.12 0.00 46.67 3.51
5435 5966 5.385198 ACTTCTCAGTCTTCTTCTCAGTCT 58.615 41.667 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.020543 TGGCACAGGGGTTTATAAATGAC 58.979 43.478 0.31 0.00 0.00 3.06
62 63 1.810030 GATCACCGCCTCAACGACC 60.810 63.158 0.00 0.00 34.06 4.79
772 773 2.710826 GCCTCTCTCCCCCTCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
778 779 4.541648 TAGCGGCCTCTCTCCCCC 62.542 72.222 0.00 0.00 0.00 5.40
779 780 3.228017 GTAGCGGCCTCTCTCCCC 61.228 72.222 0.00 0.00 0.00 4.81
780 781 3.597728 CGTAGCGGCCTCTCTCCC 61.598 72.222 0.00 0.00 0.00 4.30
1042 1273 3.741476 CGCAGGGAGCAAAGTGGC 61.741 66.667 0.00 0.00 46.13 5.01
1085 1316 1.346722 GGTTGACTCGGAAGGGAGAAA 59.653 52.381 0.00 0.00 37.49 2.52
1109 1340 1.153429 GGTGTTAGCTAGGGCACGG 60.153 63.158 14.62 0.00 41.70 4.94
1159 1411 2.237965 TTGGTGGTGGGGATGGGAG 61.238 63.158 0.00 0.00 0.00 4.30
1165 1417 2.369015 AGGTGTTGGTGGTGGGGA 60.369 61.111 0.00 0.00 0.00 4.81
1167 1419 2.115266 GGAGGTGTTGGTGGTGGG 59.885 66.667 0.00 0.00 0.00 4.61
1168 1420 2.281484 CGGAGGTGTTGGTGGTGG 60.281 66.667 0.00 0.00 0.00 4.61
1169 1421 2.978010 GCGGAGGTGTTGGTGGTG 60.978 66.667 0.00 0.00 0.00 4.17
1170 1422 4.265056 GGCGGAGGTGTTGGTGGT 62.265 66.667 0.00 0.00 0.00 4.16
1171 1423 3.901797 GAGGCGGAGGTGTTGGTGG 62.902 68.421 0.00 0.00 0.00 4.61
1172 1424 2.358737 GAGGCGGAGGTGTTGGTG 60.359 66.667 0.00 0.00 0.00 4.17
1213 1465 3.447025 GATGTCGGGGCGAGGAAGG 62.447 68.421 0.00 0.00 36.23 3.46
1305 1557 3.515901 AGGTCAGTGGGATTTCACTACTC 59.484 47.826 0.00 0.00 45.24 2.59
1407 1659 1.299541 AAGACACACAAAGAGGCACG 58.700 50.000 0.00 0.00 0.00 5.34
1474 1727 2.440539 AGTAGAGTTCACTTGCACCG 57.559 50.000 0.00 0.00 0.00 4.94
1506 1760 0.173255 AACGGCCAAACAGCATATGC 59.827 50.000 20.36 20.36 42.49 3.14
1559 1813 4.619863 GCCATTGTTCAAATCAGTCATGCT 60.620 41.667 0.00 0.00 0.00 3.79
1611 1866 8.529476 CATGAATACTATGGAGATCATCACTCA 58.471 37.037 0.00 0.00 37.30 3.41
1697 1954 6.114187 AGGTCATGTCTGATCAACAAAGTA 57.886 37.500 12.60 0.62 34.74 2.24
1786 2043 9.713684 AACAAAGGGAAATCAATATCCAAGATA 57.286 29.630 0.00 0.00 37.46 1.98
1787 2044 8.480501 CAACAAAGGGAAATCAATATCCAAGAT 58.519 33.333 0.00 0.00 37.46 2.40
1788 2045 7.093377 CCAACAAAGGGAAATCAATATCCAAGA 60.093 37.037 0.00 0.00 37.46 3.02
1928 2198 7.432869 CATCTTCTTCCGAACAGATTAGAGAT 58.567 38.462 0.00 0.00 0.00 2.75
1939 2209 5.469084 ACAAGTTAACCATCTTCTTCCGAAC 59.531 40.000 0.88 0.00 0.00 3.95
2019 2289 8.910944 AGTTGGAGATAATGGATCAATGAAAAG 58.089 33.333 0.00 0.00 36.98 2.27
2031 2301 3.395607 TCATGGGGAGTTGGAGATAATGG 59.604 47.826 0.00 0.00 0.00 3.16
2152 2422 4.816385 AGTGGAGCAATGGTTAACATATCG 59.184 41.667 8.10 0.00 39.40 2.92
2298 2571 6.986817 ACAACGAAATCAATACCCTAGATGAG 59.013 38.462 0.00 0.00 0.00 2.90
2441 2717 2.591429 CAACACGAGGTGGCTGCA 60.591 61.111 0.50 0.00 37.94 4.41
2442 2718 3.357079 CCAACACGAGGTGGCTGC 61.357 66.667 3.30 0.00 37.94 5.25
2681 2957 7.715266 TGATCAACCCATCATTTTTGTGATA 57.285 32.000 0.00 0.00 36.72 2.15
2700 2976 5.572066 CCATATATGGTGGTCAGCATGATCA 60.572 44.000 21.85 0.00 46.66 2.92
2792 3068 8.884124 AACATATAATTATGTGATTCCCCCAG 57.116 34.615 24.11 0.00 46.10 4.45
2962 3241 2.284995 GGGACACCAGAGAGGCCT 60.285 66.667 3.86 3.86 43.14 5.19
3112 3394 2.826725 CTCCCTACGACTGAAAGAGGTT 59.173 50.000 0.00 0.00 37.43 3.50
3220 3503 9.099454 GATCAGTGTAAAAATTACGAGGAAGAT 57.901 33.333 0.00 0.00 0.00 2.40
3243 3526 8.840321 ACATACAAATATTACCAACTGCAGATC 58.160 33.333 23.35 0.00 0.00 2.75
3269 3552 6.183361 CCACCAACATGTCTTATGGTCCTATA 60.183 42.308 15.56 0.00 44.12 1.31
3270 3553 5.397899 CCACCAACATGTCTTATGGTCCTAT 60.398 44.000 15.56 0.00 44.12 2.57
3376 3659 1.202222 CCGATGCCGTAGAAGTAACGT 60.202 52.381 0.00 0.00 38.67 3.99
3499 3782 3.567478 TTCGTCGGTCGCATGCAGT 62.567 57.895 19.57 0.00 39.67 4.40
3502 3785 4.210304 GCTTCGTCGGTCGCATGC 62.210 66.667 7.91 7.91 39.67 4.06
3610 3893 3.005897 ACGGCGCTAGATATTCACAGAAT 59.994 43.478 6.90 0.00 0.00 2.40
3641 3924 7.661040 AACTGAAGTATCAAAATTCAGGTTGG 58.339 34.615 16.61 0.00 46.20 3.77
3667 3950 9.877178 AAAAGAAGACACGTGAAGATTATATCT 57.123 29.630 25.01 8.19 42.61 1.98
3669 3952 9.653287 TCAAAAGAAGACACGTGAAGATTATAT 57.347 29.630 25.01 0.00 0.00 0.86
3670 3953 9.483916 TTCAAAAGAAGACACGTGAAGATTATA 57.516 29.630 25.01 0.00 0.00 0.98
3678 3961 5.050634 CGGTTATTCAAAAGAAGACACGTGA 60.051 40.000 25.01 0.00 0.00 4.35
3839 4125 3.675225 CGCCTGAAGGATTACATATGACG 59.325 47.826 10.38 0.00 37.39 4.35
3974 4261 3.157087 AGTTACAAATCCCAGTGCCAAG 58.843 45.455 0.00 0.00 0.00 3.61
4009 4297 1.270414 ATGCCTAGGCTGCTGACTGT 61.270 55.000 33.07 6.38 42.51 3.55
4011 4299 0.690411 AGATGCCTAGGCTGCTGACT 60.690 55.000 33.07 18.83 42.51 3.41
4013 4301 0.398239 AGAGATGCCTAGGCTGCTGA 60.398 55.000 33.07 14.38 42.51 4.26
4014 4302 0.249953 CAGAGATGCCTAGGCTGCTG 60.250 60.000 33.07 26.50 42.51 4.41
4015 4303 2.042404 GCAGAGATGCCTAGGCTGCT 62.042 60.000 33.07 27.71 46.17 4.24
4016 4304 1.597578 GCAGAGATGCCTAGGCTGC 60.598 63.158 33.07 28.22 44.11 5.25
4017 4305 0.469070 AAGCAGAGATGCCTAGGCTG 59.531 55.000 33.07 23.14 42.51 4.85
4019 4307 1.691434 ACTAAGCAGAGATGCCTAGGC 59.309 52.381 27.71 27.71 42.35 3.93
4020 4308 3.494048 CCAACTAAGCAGAGATGCCTAGG 60.494 52.174 3.67 3.67 34.17 3.02
4021 4309 3.386078 TCCAACTAAGCAGAGATGCCTAG 59.614 47.826 4.69 4.69 35.55 3.02
4022 4310 3.374764 TCCAACTAAGCAGAGATGCCTA 58.625 45.455 0.00 0.00 34.90 3.93
4042 4330 4.897362 CGCGTACTACTTCGAGATAAGTTC 59.103 45.833 0.00 0.00 40.20 3.01
4045 4333 3.247173 ACCGCGTACTACTTCGAGATAAG 59.753 47.826 4.92 0.00 0.00 1.73
4047 4335 2.826428 ACCGCGTACTACTTCGAGATA 58.174 47.619 4.92 0.00 0.00 1.98
4048 4336 1.661341 ACCGCGTACTACTTCGAGAT 58.339 50.000 4.92 0.00 0.00 2.75
4049 4337 1.927174 GTACCGCGTACTACTTCGAGA 59.073 52.381 4.92 0.00 36.25 4.04
4050 4338 1.660607 TGTACCGCGTACTACTTCGAG 59.339 52.381 4.92 0.00 39.49 4.04
4051 4339 1.720805 TGTACCGCGTACTACTTCGA 58.279 50.000 4.92 0.00 39.49 3.71
4052 4340 2.286294 AGATGTACCGCGTACTACTTCG 59.714 50.000 4.92 0.00 39.49 3.79
4053 4341 3.303659 GGAGATGTACCGCGTACTACTTC 60.304 52.174 4.92 9.07 39.49 3.01
4054 4342 2.615912 GGAGATGTACCGCGTACTACTT 59.384 50.000 4.92 0.00 39.49 2.24
4055 4343 2.216898 GGAGATGTACCGCGTACTACT 58.783 52.381 4.92 10.66 39.49 2.57
4056 4344 1.265365 GGGAGATGTACCGCGTACTAC 59.735 57.143 4.92 2.00 39.49 2.73
4057 4345 1.597742 GGGAGATGTACCGCGTACTA 58.402 55.000 4.92 0.22 39.49 1.82
4085 4373 9.334693 CTTTTGCTATTAAAAGTGATGTCAGAC 57.665 33.333 0.00 0.00 40.85 3.51
4087 4375 8.299570 ACCTTTTGCTATTAAAAGTGATGTCAG 58.700 33.333 9.35 0.00 43.02 3.51
4089 4377 7.542130 CCACCTTTTGCTATTAAAAGTGATGTC 59.458 37.037 9.35 0.00 43.02 3.06
4090 4378 7.232534 TCCACCTTTTGCTATTAAAAGTGATGT 59.767 33.333 9.35 0.00 43.02 3.06
4091 4379 7.601856 TCCACCTTTTGCTATTAAAAGTGATG 58.398 34.615 9.35 5.65 43.02 3.07
4094 4382 7.214467 TCTCCACCTTTTGCTATTAAAAGTG 57.786 36.000 9.35 7.79 43.02 3.16
4096 4384 6.808704 GCTTCTCCACCTTTTGCTATTAAAAG 59.191 38.462 0.00 0.00 43.76 2.27
4101 4389 3.092301 GGCTTCTCCACCTTTTGCTATT 58.908 45.455 0.00 0.00 34.01 1.73
4102 4390 2.041620 TGGCTTCTCCACCTTTTGCTAT 59.958 45.455 0.00 0.00 40.72 2.97
4104 4392 0.185901 TGGCTTCTCCACCTTTTGCT 59.814 50.000 0.00 0.00 40.72 3.91
4106 4394 5.467035 TTATTTGGCTTCTCCACCTTTTG 57.533 39.130 0.00 0.00 46.55 2.44
4107 4395 7.234577 TGTTATTATTTGGCTTCTCCACCTTTT 59.765 33.333 0.00 0.00 46.55 2.27
4108 4396 6.723977 TGTTATTATTTGGCTTCTCCACCTTT 59.276 34.615 0.00 0.00 46.55 3.11
4109 4397 6.252995 TGTTATTATTTGGCTTCTCCACCTT 58.747 36.000 0.00 0.00 46.55 3.50
4111 4399 6.321181 TGATGTTATTATTTGGCTTCTCCACC 59.679 38.462 0.00 0.00 46.55 4.61
4114 4402 8.416329 ACAATGATGTTATTATTTGGCTTCTCC 58.584 33.333 0.00 0.00 35.91 3.71
4144 4432 7.970061 GCATACAAGATGTTTTGCTATTCTCAA 59.030 33.333 9.50 0.00 36.20 3.02
4146 4434 6.630443 CGCATACAAGATGTTTTGCTATTCTC 59.370 38.462 12.94 0.00 36.65 2.87
4147 4435 6.316140 TCGCATACAAGATGTTTTGCTATTCT 59.684 34.615 12.94 0.00 36.65 2.40
4149 4437 6.435430 TCGCATACAAGATGTTTTGCTATT 57.565 33.333 12.94 0.00 36.65 1.73
4150 4438 6.624352 ATCGCATACAAGATGTTTTGCTAT 57.376 33.333 12.94 7.46 36.65 2.97
4153 4441 6.258160 ACTAATCGCATACAAGATGTTTTGC 58.742 36.000 7.60 7.60 35.95 3.68
4156 4444 8.039603 TCAAACTAATCGCATACAAGATGTTT 57.960 30.769 0.00 0.00 0.00 2.83
4157 4445 7.549134 TCTCAAACTAATCGCATACAAGATGTT 59.451 33.333 0.00 0.00 0.00 2.71
4158 4446 7.041721 TCTCAAACTAATCGCATACAAGATGT 58.958 34.615 0.00 0.00 0.00 3.06
4159 4447 7.468922 TCTCAAACTAATCGCATACAAGATG 57.531 36.000 0.00 0.00 0.00 2.90
4160 4448 8.668510 ATTCTCAAACTAATCGCATACAAGAT 57.331 30.769 0.00 0.00 0.00 2.40
4161 4449 9.249457 CTATTCTCAAACTAATCGCATACAAGA 57.751 33.333 0.00 0.00 0.00 3.02
4162 4450 8.006590 GCTATTCTCAAACTAATCGCATACAAG 58.993 37.037 0.00 0.00 0.00 3.16
4163 4451 7.494298 TGCTATTCTCAAACTAATCGCATACAA 59.506 33.333 0.00 0.00 31.27 2.41
4164 4452 6.983890 TGCTATTCTCAAACTAATCGCATACA 59.016 34.615 0.00 0.00 31.27 2.29
4165 4453 7.408132 TGCTATTCTCAAACTAATCGCATAC 57.592 36.000 0.00 0.00 31.27 2.39
4166 4454 8.432110 TTTGCTATTCTCAAACTAATCGCATA 57.568 30.769 0.00 0.00 34.83 3.14
4167 4455 6.925610 TTGCTATTCTCAAACTAATCGCAT 57.074 33.333 0.00 0.00 34.83 4.73
4168 4456 6.735678 TTTGCTATTCTCAAACTAATCGCA 57.264 33.333 0.00 0.00 33.51 5.10
4169 4457 6.688813 CCTTTTGCTATTCTCAAACTAATCGC 59.311 38.462 0.00 0.00 33.66 4.58
4170 4458 7.693951 CACCTTTTGCTATTCTCAAACTAATCG 59.306 37.037 0.00 0.00 33.66 3.34
4171 4459 7.970614 CCACCTTTTGCTATTCTCAAACTAATC 59.029 37.037 0.00 0.00 33.66 1.75
4172 4460 7.669722 TCCACCTTTTGCTATTCTCAAACTAAT 59.330 33.333 0.00 0.00 33.66 1.73
4213 4507 9.403583 TGTTCTTTCCTTTCAATTTAGTAGTGT 57.596 29.630 0.00 0.00 0.00 3.55
4214 4508 9.884465 CTGTTCTTTCCTTTCAATTTAGTAGTG 57.116 33.333 0.00 0.00 0.00 2.74
4215 4509 9.067986 CCTGTTCTTTCCTTTCAATTTAGTAGT 57.932 33.333 0.00 0.00 0.00 2.73
4216 4510 9.067986 ACCTGTTCTTTCCTTTCAATTTAGTAG 57.932 33.333 0.00 0.00 0.00 2.57
4218 4512 7.898014 ACCTGTTCTTTCCTTTCAATTTAGT 57.102 32.000 0.00 0.00 0.00 2.24
4219 4513 8.197439 ACAACCTGTTCTTTCCTTTCAATTTAG 58.803 33.333 0.00 0.00 0.00 1.85
4220 4514 8.073467 ACAACCTGTTCTTTCCTTTCAATTTA 57.927 30.769 0.00 0.00 0.00 1.40
4221 4515 6.946340 ACAACCTGTTCTTTCCTTTCAATTT 58.054 32.000 0.00 0.00 0.00 1.82
4222 4516 6.544928 ACAACCTGTTCTTTCCTTTCAATT 57.455 33.333 0.00 0.00 0.00 2.32
4250 4544 4.981806 TTTTGTCAGTCAGGAAAACAGG 57.018 40.909 0.00 0.00 0.00 4.00
4274 4568 0.243636 CCCCAACCAAAGCGAATCAC 59.756 55.000 0.00 0.00 0.00 3.06
4280 4574 4.341502 CGCACCCCAACCAAAGCG 62.342 66.667 0.00 0.00 39.17 4.68
4346 4640 2.093447 GTCCACCACAGTAGCTTGCTAT 60.093 50.000 5.59 0.00 0.00 2.97
4403 4701 1.845791 TCTGATATGTGGGCCATGTGT 59.154 47.619 10.70 0.00 34.86 3.72
4491 4789 4.527583 GAGAGGCAGGGCAGCGAG 62.528 72.222 0.00 0.00 34.64 5.03
4574 4872 4.056125 CACACAGAGCGCTCGGGA 62.056 66.667 35.06 0.00 34.09 5.14
4597 4906 0.960861 AAAAAGAGCCCAGCTACGCC 60.961 55.000 0.72 0.00 39.88 5.68
4611 4920 3.319122 CCTCCAGAGGTTTGGTCAAAAAG 59.681 47.826 5.47 0.00 43.61 2.27
4628 4937 1.073548 GTTACGGTTTGGGCCTCCA 59.926 57.895 4.53 0.00 42.25 3.86
4630 4939 0.037419 TACGTTACGGTTTGGGCCTC 60.037 55.000 10.20 0.00 0.00 4.70
4696 5005 3.477224 CTCTAGTCTCCGGCGCTGC 62.477 68.421 11.81 0.00 0.00 5.25
4697 5006 2.718731 CTCTAGTCTCCGGCGCTG 59.281 66.667 9.96 9.96 0.00 5.18
4698 5007 2.517402 CCTCTAGTCTCCGGCGCT 60.517 66.667 7.64 0.00 0.00 5.92
4699 5008 1.664321 TTTCCTCTAGTCTCCGGCGC 61.664 60.000 0.00 0.00 0.00 6.53
4700 5009 0.100861 GTTTCCTCTAGTCTCCGGCG 59.899 60.000 0.00 0.00 0.00 6.46
4701 5010 0.100861 CGTTTCCTCTAGTCTCCGGC 59.899 60.000 0.00 0.00 0.00 6.13
4702 5011 0.739561 CCGTTTCCTCTAGTCTCCGG 59.260 60.000 0.00 0.00 0.00 5.14
4703 5012 1.401199 GTCCGTTTCCTCTAGTCTCCG 59.599 57.143 0.00 0.00 0.00 4.63
4704 5013 1.750206 GGTCCGTTTCCTCTAGTCTCC 59.250 57.143 0.00 0.00 0.00 3.71
4706 5015 1.004044 TCGGTCCGTTTCCTCTAGTCT 59.996 52.381 11.88 0.00 0.00 3.24
4707 5016 1.401199 CTCGGTCCGTTTCCTCTAGTC 59.599 57.143 11.88 0.00 0.00 2.59
4708 5017 1.004044 TCTCGGTCCGTTTCCTCTAGT 59.996 52.381 11.88 0.00 0.00 2.57
4709 5018 1.671845 CTCTCGGTCCGTTTCCTCTAG 59.328 57.143 11.88 0.00 0.00 2.43
4710 5019 1.280133 TCTCTCGGTCCGTTTCCTCTA 59.720 52.381 11.88 0.00 0.00 2.43
4711 5020 0.037877 TCTCTCGGTCCGTTTCCTCT 59.962 55.000 11.88 0.00 0.00 3.69
4838 5147 3.412408 GGGGCTGGGAGAAGGGTC 61.412 72.222 0.00 0.00 0.00 4.46
5045 5354 2.183636 GTCTTCGCGTTTACTAGAGGC 58.816 52.381 5.77 0.00 0.00 4.70
5089 5620 3.429372 AACCACCCTGCAAGCGGAA 62.429 57.895 1.69 0.00 0.00 4.30
5111 5642 0.456142 TGTCGCTGATGCTGTCGTAC 60.456 55.000 0.00 0.00 36.97 3.67
5431 5962 0.694771 TCCAGCAGGCAATGAAGACT 59.305 50.000 0.00 0.00 33.74 3.24
5432 5963 0.807496 GTCCAGCAGGCAATGAAGAC 59.193 55.000 0.00 0.00 33.74 3.01
5433 5964 0.322816 GGTCCAGCAGGCAATGAAGA 60.323 55.000 0.00 0.00 33.74 2.87
5434 5965 0.609957 TGGTCCAGCAGGCAATGAAG 60.610 55.000 0.00 0.00 33.74 3.02
5435 5966 0.178967 TTGGTCCAGCAGGCAATGAA 60.179 50.000 0.00 0.00 33.74 2.57


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

AutoCloner maintained by Alex Coulton.