Multiple sequence alignment - TraesCS5B01G253700

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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 TraesCS5B01G253700 chr5B 100.000 5049 0 0 1 5049 436255201 436260249 0.000000e+00 9324.0
1 TraesCS5B01G253700 chr5B 100.000 161 0 0 5226 5386 436260426 436260586 1.130000e-76 298.0
2 TraesCS5B01G253700 chr5B 100.000 28 0 0 2053 2080 297106199 297106226 1.000000e-02 52.8
3 TraesCS5B01G253700 chr5D 94.128 5058 194 48 1 4999 368329296 368334309 0.000000e+00 7600.0
4 TraesCS5B01G253700 chr5D 92.308 39 3 0 2042 2080 264795574 264795612 7.540000e-04 56.5
5 TraesCS5B01G253700 chr5A 92.222 5001 236 67 1 4945 470192329 470197232 0.000000e+00 6938.0
6 TraesCS5B01G253700 chr5A 100.000 28 0 0 2053 2080 351474478 351474505 1.000000e-02 52.8
7 TraesCS5B01G253700 chr7A 79.211 3218 553 82 1078 4251 206910818 206913963 0.000000e+00 2130.0
8 TraesCS5B01G253700 chr7A 78.409 176 11 18 5226 5384 161219766 161219601 7.430000e-14 89.8
9 TraesCS5B01G253700 chr7D 79.319 2790 498 55 1078 3835 197610796 197613538 0.000000e+00 1882.0
10 TraesCS5B01G253700 chr7D 80.870 345 52 12 3916 4251 197613795 197614134 5.350000e-65 259.0
11 TraesCS5B01G253700 chr7D 90.909 110 10 0 5273 5382 491802760 491802869 1.210000e-31 148.0
12 TraesCS5B01G253700 chr7D 83.030 165 13 9 5226 5383 28867745 28867589 9.410000e-28 135.0
13 TraesCS5B01G253700 chr7D 100.000 43 0 0 5340 5382 68908623 68908581 4.470000e-11 80.5
14 TraesCS5B01G253700 chr7B 79.401 2704 488 46 1078 3757 161776639 161779297 0.000000e+00 1844.0
15 TraesCS5B01G253700 chr7B 80.580 345 53 12 3916 4251 161779449 161779788 2.490000e-63 254.0
16 TraesCS5B01G253700 chr1A 72.336 535 106 31 3219 3741 117246836 117247340 4.380000e-26 130.0
17 TraesCS5B01G253700 chr1A 100.000 45 0 0 5340 5384 261785504 261785548 3.460000e-12 84.2
18 TraesCS5B01G253700 chr1A 100.000 43 0 0 5340 5382 8133015 8133057 4.470000e-11 80.5
19 TraesCS5B01G253700 chr1A 100.000 43 0 0 5340 5382 369515854 369515896 4.470000e-11 80.5
20 TraesCS5B01G253700 chr1A 100.000 43 0 0 5340 5382 578778408 578778450 4.470000e-11 80.5
21 TraesCS5B01G253700 chr1A 97.500 40 1 0 4122 4161 243607992 243608031 9.680000e-08 69.4
22 TraesCS5B01G253700 chr3D 83.478 115 15 3 3960 4071 609739077 609738964 2.650000e-18 104.0
23 TraesCS5B01G253700 chr3D 79.054 148 22 9 3924 4066 46583410 46583553 5.740000e-15 93.5
24 TraesCS5B01G253700 chr3D 100.000 43 0 0 5340 5382 587475550 587475592 4.470000e-11 80.5
25 TraesCS5B01G253700 chr3A 83.478 115 15 3 3960 4071 743377872 743377759 2.650000e-18 104.0
26 TraesCS5B01G253700 chr3A 80.000 145 21 8 3926 4066 57944790 57944650 3.430000e-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 TraesCS5B01G253700 chr5B 436255201 436260586 5385 False 4811.0 9324 100.0000 1 5386 2 chr5B.!!$F2 5385
1 TraesCS5B01G253700 chr5D 368329296 368334309 5013 False 7600.0 7600 94.1280 1 4999 1 chr5D.!!$F2 4998
2 TraesCS5B01G253700 chr5A 470192329 470197232 4903 False 6938.0 6938 92.2220 1 4945 1 chr5A.!!$F2 4944
3 TraesCS5B01G253700 chr7A 206910818 206913963 3145 False 2130.0 2130 79.2110 1078 4251 1 chr7A.!!$F1 3173
4 TraesCS5B01G253700 chr7D 197610796 197614134 3338 False 1070.5 1882 80.0945 1078 4251 2 chr7D.!!$F2 3173
5 TraesCS5B01G253700 chr7B 161776639 161779788 3149 False 1049.0 1844 79.9905 1078 4251 2 chr7B.!!$F1 3173

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
300 314 0.321653 GCGGTTCAGGGTTCAGACAT 60.322 55.000 0.00 0.00 0.00 3.06 F
400 417 1.202770 GGTAACAGCCACTGTCAACCT 60.203 52.381 18.17 1.07 44.62 3.50 F
930 975 1.601759 CCACATCCCCATCGCCATC 60.602 63.158 0.00 0.00 0.00 3.51 F
1465 1527 1.611673 CGCTCAACTCCAATTCCCTGT 60.612 52.381 0.00 0.00 0.00 4.00 F
2613 2675 0.606604 ACGTGTCCGATAACCAGCTT 59.393 50.000 0.00 0.00 37.88 3.74 F
3890 4102 2.463653 CACAAGCACATTTTGAACGTCG 59.536 45.455 0.00 0.00 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1574 0.385098 CGTTGTCGTAGAGCGTGACA 60.385 55.000 0.00 0.0 40.62 3.58 R
1626 1688 2.187946 CAGCCGCCGATCTCCTTT 59.812 61.111 0.00 0.0 0.00 3.11 R
2613 2675 2.596851 GGACCTCAGCTGCCCAGAA 61.597 63.158 9.47 0.0 0.00 3.02 R
3090 3152 0.100682 TGGCTATCTTGAGCGTCGTC 59.899 55.000 0.00 0.0 43.83 4.20 R
3909 4129 0.104120 GCACACCCCAAGAACCAAAC 59.896 55.000 0.00 0.0 0.00 2.93 R
4916 5239 0.032130 CTCGATCCATACACCCCGTG 59.968 60.000 0.00 0.0 39.75 4.94 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
32 35 2.707791 ACATACCACCTGATGATGGGAG 59.292 50.000 0.00 0.00 40.59 4.30
44 47 1.325355 GATGGGAGCATGAATGGGTG 58.675 55.000 0.00 0.00 0.00 4.61
85 88 4.582701 AAATCGTTGAATTGACCAGCAA 57.417 36.364 0.00 0.00 41.53 3.91
106 109 6.041979 AGCAAAAGGAATTATGTTTCACCTGT 59.958 34.615 0.00 0.00 0.00 4.00
116 119 5.917541 ATGTTTCACCTGTAAACAGTACG 57.082 39.130 9.17 0.00 46.66 3.67
137 148 4.641094 ACGTTTGTACTGTTGGGAAAATGA 59.359 37.500 0.00 0.00 0.00 2.57
152 163 6.214615 TGGGAAAATGAGAGGTACAGTAATCA 59.785 38.462 0.00 0.00 0.00 2.57
154 165 7.364762 GGGAAAATGAGAGGTACAGTAATCAGA 60.365 40.741 0.00 0.00 0.00 3.27
163 174 6.331061 AGGTACAGTAATCAGACACGAAATC 58.669 40.000 0.00 0.00 0.00 2.17
175 186 4.881850 AGACACGAAATCCAGTTCAAGTTT 59.118 37.500 0.00 0.00 0.00 2.66
299 313 1.070786 GCGGTTCAGGGTTCAGACA 59.929 57.895 0.00 0.00 0.00 3.41
300 314 0.321653 GCGGTTCAGGGTTCAGACAT 60.322 55.000 0.00 0.00 0.00 3.06
311 325 5.006386 AGGGTTCAGACATTCAGAAACATC 58.994 41.667 0.00 0.00 32.07 3.06
314 328 6.092807 GGGTTCAGACATTCAGAAACATCTAC 59.907 42.308 0.00 0.00 32.07 2.59
318 332 7.670364 TCAGACATTCAGAAACATCTACAAGA 58.330 34.615 0.00 0.00 0.00 3.02
319 333 8.150296 TCAGACATTCAGAAACATCTACAAGAA 58.850 33.333 0.00 0.00 0.00 2.52
320 334 8.441608 CAGACATTCAGAAACATCTACAAGAAG 58.558 37.037 0.00 0.00 0.00 2.85
321 335 7.605691 AGACATTCAGAAACATCTACAAGAAGG 59.394 37.037 0.00 0.00 0.00 3.46
322 336 7.227156 ACATTCAGAAACATCTACAAGAAGGT 58.773 34.615 0.00 0.00 0.00 3.50
323 337 7.721399 ACATTCAGAAACATCTACAAGAAGGTT 59.279 33.333 0.00 0.00 30.38 3.50
324 338 9.219603 CATTCAGAAACATCTACAAGAAGGTTA 57.780 33.333 0.00 0.00 29.47 2.85
325 339 9.793259 ATTCAGAAACATCTACAAGAAGGTTAA 57.207 29.630 0.00 0.00 29.47 2.01
326 340 8.603242 TCAGAAACATCTACAAGAAGGTTAAC 57.397 34.615 0.00 0.00 29.47 2.01
327 341 7.660208 TCAGAAACATCTACAAGAAGGTTAACC 59.340 37.037 17.41 17.41 29.47 2.85
329 343 4.828829 ACATCTACAAGAAGGTTAACCCG 58.171 43.478 21.30 7.45 38.74 5.28
371 388 4.022935 TCCTGCACATGCTAAAAAGAACAG 60.023 41.667 5.31 0.00 42.66 3.16
372 389 4.261741 CCTGCACATGCTAAAAAGAACAGT 60.262 41.667 5.31 0.00 42.66 3.55
373 390 5.048782 CCTGCACATGCTAAAAAGAACAGTA 60.049 40.000 5.31 0.00 42.66 2.74
374 391 6.384258 TGCACATGCTAAAAAGAACAGTAA 57.616 33.333 5.31 0.00 42.66 2.24
375 392 6.800543 TGCACATGCTAAAAAGAACAGTAAA 58.199 32.000 5.31 0.00 42.66 2.01
376 393 6.695278 TGCACATGCTAAAAAGAACAGTAAAC 59.305 34.615 5.31 0.00 42.66 2.01
377 394 6.695278 GCACATGCTAAAAAGAACAGTAAACA 59.305 34.615 0.00 0.00 38.21 2.83
378 395 7.221838 GCACATGCTAAAAAGAACAGTAAACAA 59.778 33.333 0.00 0.00 38.21 2.83
379 396 8.531530 CACATGCTAAAAAGAACAGTAAACAAC 58.468 33.333 0.00 0.00 0.00 3.32
380 397 7.431084 ACATGCTAAAAAGAACAGTAAACAACG 59.569 33.333 0.00 0.00 0.00 4.10
400 417 1.202770 GGTAACAGCCACTGTCAACCT 60.203 52.381 18.17 1.07 44.62 3.50
409 426 3.005554 CCACTGTCAACCTCTGCATAAG 58.994 50.000 0.00 0.00 0.00 1.73
431 448 2.304761 TGCAGGGGTAGTACAAAGGAAG 59.695 50.000 2.06 0.00 0.00 3.46
481 498 2.045524 ACAAATGCCCCACAAATCACA 58.954 42.857 0.00 0.00 0.00 3.58
562 579 3.070018 CACGAGAAGGAGCAGATGTTTT 58.930 45.455 0.00 0.00 0.00 2.43
621 638 2.705220 CACTGTCATGGCATCGCG 59.295 61.111 0.00 0.00 0.00 5.87
756 800 4.446719 CACTGCAGAAGCCAAAATCTTTTC 59.553 41.667 23.35 0.00 41.13 2.29
873 918 4.741239 ACCATGGGGCGGTCTCCT 62.741 66.667 18.09 0.00 37.90 3.69
928 973 4.504596 GCCACATCCCCATCGCCA 62.505 66.667 0.00 0.00 0.00 5.69
929 974 2.517414 CCACATCCCCATCGCCAT 59.483 61.111 0.00 0.00 0.00 4.40
930 975 1.601759 CCACATCCCCATCGCCATC 60.602 63.158 0.00 0.00 0.00 3.51
1095 1148 3.512516 GTCAATGAGCAGGGCCGC 61.513 66.667 11.60 11.60 0.00 6.53
1465 1527 1.611673 CGCTCAACTCCAATTCCCTGT 60.612 52.381 0.00 0.00 0.00 4.00
1512 1574 4.827087 CTCGCCAGCCTCACGCAT 62.827 66.667 0.00 0.00 41.38 4.73
1902 1964 2.031012 TGGCAGAACCAGCTCGTG 59.969 61.111 0.00 0.00 46.36 4.35
2091 2153 3.362399 CTGCACCTCGCTGACGGAT 62.362 63.158 0.00 0.00 41.88 4.18
2382 2444 1.677552 CACCAACCTCTACCGGCTT 59.322 57.895 0.00 0.00 0.00 4.35
2598 2660 1.734477 CCTCCAGCTCGTTGACGTG 60.734 63.158 0.00 2.37 40.80 4.49
2613 2675 0.606604 ACGTGTCCGATAACCAGCTT 59.393 50.000 0.00 0.00 37.88 3.74
2616 2678 2.674177 CGTGTCCGATAACCAGCTTTCT 60.674 50.000 0.00 0.00 35.63 2.52
2745 2807 4.463879 CAGCTGCTGGACCTCGGG 62.464 72.222 21.71 0.00 0.00 5.14
2976 3038 3.449018 ACATCTCATACAACGCCTTCTCT 59.551 43.478 0.00 0.00 0.00 3.10
3052 3114 2.632544 AATCGCCACCTCGTCGTCA 61.633 57.895 0.00 0.00 0.00 4.35
3312 3386 3.382803 GATCGGCACAGGCAGCTCT 62.383 63.158 0.00 0.00 43.71 4.09
3525 3599 2.928396 AGCTACCTGCCCAACGGT 60.928 61.111 0.00 0.00 44.23 4.83
3766 3840 2.705487 ATCCTCTCCTCCGGGCAGA 61.705 63.158 0.00 0.00 0.00 4.26
3838 3927 2.930385 CTACATGGCGCCAGGTCCAG 62.930 65.000 45.89 34.55 40.28 3.86
3841 3930 2.683465 ATGGCGCCAGGTCCAGAAT 61.683 57.895 35.36 11.90 35.57 2.40
3868 4075 3.747099 GCACTTGCAAGATCGTACAAT 57.253 42.857 32.50 3.89 41.59 2.71
3871 4078 4.641954 CACTTGCAAGATCGTACAATCAC 58.358 43.478 32.50 0.00 0.00 3.06
3872 4079 4.152223 CACTTGCAAGATCGTACAATCACA 59.848 41.667 32.50 0.00 0.00 3.58
3887 4099 4.503734 ACAATCACAAGCACATTTTGAACG 59.496 37.500 0.00 0.00 0.00 3.95
3889 4101 3.690422 TCACAAGCACATTTTGAACGTC 58.310 40.909 0.00 0.00 0.00 4.34
3890 4102 2.463653 CACAAGCACATTTTGAACGTCG 59.536 45.455 0.00 0.00 0.00 5.12
3909 4129 4.206200 CGTCGTTTTTCCTGACATTTTTGG 59.794 41.667 0.00 0.00 32.91 3.28
3910 4130 5.106442 GTCGTTTTTCCTGACATTTTTGGT 58.894 37.500 0.00 0.00 32.91 3.67
3912 4132 6.091577 GTCGTTTTTCCTGACATTTTTGGTTT 59.908 34.615 0.00 0.00 32.91 3.27
3914 4134 6.550843 GTTTTTCCTGACATTTTTGGTTTGG 58.449 36.000 0.00 0.00 0.00 3.28
4217 4511 2.885644 CCCGCGATGAAGGACGTG 60.886 66.667 8.23 0.00 39.27 4.49
4406 4703 4.282449 TGAGACCGATCTTCAGTTTTGGTA 59.718 41.667 0.00 0.00 34.34 3.25
4413 4710 4.610605 TCTTCAGTTTTGGTACCGATCA 57.389 40.909 7.57 0.00 0.00 2.92
4414 4711 4.566004 TCTTCAGTTTTGGTACCGATCAG 58.434 43.478 7.57 0.00 0.00 2.90
4458 4756 1.330521 GCTCGATCGGCAAATTTAGCA 59.669 47.619 16.41 0.00 0.00 3.49
4540 4840 1.290203 GTGTGTAGATCATGGCGTGG 58.710 55.000 6.90 0.00 0.00 4.94
4541 4841 0.461870 TGTGTAGATCATGGCGTGGC 60.462 55.000 6.90 0.00 0.00 5.01
4542 4842 0.461870 GTGTAGATCATGGCGTGGCA 60.462 55.000 6.90 0.00 0.00 4.92
4543 4843 0.251634 TGTAGATCATGGCGTGGCAA 59.748 50.000 6.90 0.00 0.00 4.52
4548 4848 1.949525 GATCATGGCGTGGCAAGTAAT 59.050 47.619 6.90 0.00 0.00 1.89
4553 4853 4.036262 TCATGGCGTGGCAAGTAATTAATC 59.964 41.667 6.90 0.00 0.00 1.75
4558 4858 4.670621 GCGTGGCAAGTAATTAATCAATCG 59.329 41.667 1.69 0.00 0.00 3.34
4591 4895 6.806751 TGTACTTAGGTGTAATCATCTCTGC 58.193 40.000 0.00 0.00 36.35 4.26
4639 4943 0.253610 TGGTTCTTTGGTCGTGTGGT 59.746 50.000 0.00 0.00 0.00 4.16
4748 5062 0.036732 TTTGGACTTGCTCGCTGGAT 59.963 50.000 0.00 0.00 0.00 3.41
4749 5063 0.674581 TTGGACTTGCTCGCTGGATG 60.675 55.000 0.00 0.00 0.00 3.51
4836 5159 1.376812 GCCGTCGAGGGTTTTGGAT 60.377 57.895 24.11 0.00 41.48 3.41
4879 5202 2.034221 GCAGTGGGGTGGGTTCTC 59.966 66.667 0.00 0.00 0.00 2.87
4880 5203 2.529744 GCAGTGGGGTGGGTTCTCT 61.530 63.158 0.00 0.00 0.00 3.10
4881 5204 1.376466 CAGTGGGGTGGGTTCTCTG 59.624 63.158 0.00 0.00 0.00 3.35
4906 5229 4.351938 CTCCGGTTCGCACGTCCA 62.352 66.667 0.00 0.00 0.00 4.02
4932 5255 0.106149 GTCCACGGGGTGTATGGATC 59.894 60.000 2.12 0.00 44.21 3.36
4941 5264 4.065789 GGGGTGTATGGATCGAGATTTTC 58.934 47.826 0.00 0.00 0.00 2.29
4944 5267 5.467063 GGGTGTATGGATCGAGATTTTCTTC 59.533 44.000 0.00 0.00 0.00 2.87
4947 5270 6.916387 GTGTATGGATCGAGATTTTCTTCGTA 59.084 38.462 0.00 0.00 0.00 3.43
4948 5271 7.113684 GTGTATGGATCGAGATTTTCTTCGTAG 59.886 40.741 0.00 0.00 0.00 3.51
4949 5272 4.360563 TGGATCGAGATTTTCTTCGTAGC 58.639 43.478 0.00 0.00 0.00 3.58
4950 5273 4.098044 TGGATCGAGATTTTCTTCGTAGCT 59.902 41.667 0.00 0.00 0.00 3.32
4951 5274 5.044558 GGATCGAGATTTTCTTCGTAGCTT 58.955 41.667 0.00 0.00 0.00 3.74
4953 5276 6.696148 GGATCGAGATTTTCTTCGTAGCTTTA 59.304 38.462 0.00 0.00 0.00 1.85
4954 5277 7.382759 GGATCGAGATTTTCTTCGTAGCTTTAT 59.617 37.037 0.00 0.00 0.00 1.40
4955 5278 9.395707 GATCGAGATTTTCTTCGTAGCTTTATA 57.604 33.333 0.00 0.00 0.00 0.98
4956 5279 9.915629 ATCGAGATTTTCTTCGTAGCTTTATAT 57.084 29.630 0.00 0.00 0.00 0.86
4972 5295 8.997621 AGCTTTATATAGAAGTCAAAACGTCA 57.002 30.769 0.00 0.00 36.48 4.35
4981 5304 6.725246 AGAAGTCAAAACGTCAATTACAAGG 58.275 36.000 0.00 0.00 36.48 3.61
4988 5311 8.339714 TCAAAACGTCAATTACAAGGAAACTAG 58.660 33.333 0.00 0.00 42.68 2.57
5029 5352 5.921962 AAAAATCCAAGAATAGAGTGCCC 57.078 39.130 0.00 0.00 0.00 5.36
5030 5353 3.584733 AATCCAAGAATAGAGTGCCCC 57.415 47.619 0.00 0.00 0.00 5.80
5031 5354 1.213296 TCCAAGAATAGAGTGCCCCC 58.787 55.000 0.00 0.00 0.00 5.40
5032 5355 0.179045 CCAAGAATAGAGTGCCCCCG 60.179 60.000 0.00 0.00 0.00 5.73
5033 5356 0.541863 CAAGAATAGAGTGCCCCCGT 59.458 55.000 0.00 0.00 0.00 5.28
5034 5357 0.541863 AAGAATAGAGTGCCCCCGTG 59.458 55.000 0.00 0.00 0.00 4.94
5035 5358 1.523938 GAATAGAGTGCCCCCGTGC 60.524 63.158 0.00 0.00 0.00 5.34
5036 5359 2.942648 GAATAGAGTGCCCCCGTGCC 62.943 65.000 0.00 0.00 0.00 5.01
5306 5629 4.838152 CCGATCTGGGCGGTGTGG 62.838 72.222 0.00 0.00 43.66 4.17
5308 5631 4.101448 GATCTGGGCGGTGTGGCT 62.101 66.667 0.00 0.00 44.11 4.75
5309 5632 4.101448 ATCTGGGCGGTGTGGCTC 62.101 66.667 0.00 0.00 44.11 4.70
5317 5640 3.009115 GGTGTGGCTCCCCTGCTA 61.009 66.667 0.00 0.00 0.00 3.49
5318 5641 2.586792 GTGTGGCTCCCCTGCTAG 59.413 66.667 0.00 0.00 0.00 3.42
5319 5642 2.688666 TGTGGCTCCCCTGCTAGG 60.689 66.667 0.00 0.00 34.30 3.02
5320 5643 2.689034 GTGGCTCCCCTGCTAGGT 60.689 66.667 0.00 0.00 31.93 3.08
5321 5644 2.688666 TGGCTCCCCTGCTAGGTG 60.689 66.667 0.00 0.00 31.93 4.00
5322 5645 3.483869 GGCTCCCCTGCTAGGTGG 61.484 72.222 0.00 0.00 31.93 4.61
5323 5646 4.182433 GCTCCCCTGCTAGGTGGC 62.182 72.222 0.00 0.00 31.93 5.01
5324 5647 3.854669 CTCCCCTGCTAGGTGGCG 61.855 72.222 0.00 0.00 31.93 5.69
5327 5650 3.154473 CCCTGCTAGGTGGCGCTA 61.154 66.667 7.64 0.00 31.93 4.26
5328 5651 2.107141 CCTGCTAGGTGGCGCTAC 59.893 66.667 16.51 16.51 34.52 3.58
5329 5652 2.278857 CTGCTAGGTGGCGCTACG 60.279 66.667 18.14 5.35 34.52 3.51
5330 5653 3.774959 CTGCTAGGTGGCGCTACGG 62.775 68.421 18.14 11.24 34.52 4.02
5331 5654 3.834799 GCTAGGTGGCGCTACGGT 61.835 66.667 18.14 10.09 0.00 4.83
5332 5655 2.104331 CTAGGTGGCGCTACGGTG 59.896 66.667 18.14 6.07 0.00 4.94
5335 5658 4.137872 GGTGGCGCTACGGTGCTA 62.138 66.667 18.14 0.00 46.94 3.49
5336 5659 2.582498 GTGGCGCTACGGTGCTAG 60.582 66.667 8.55 0.00 46.94 3.42
5337 5660 4.508128 TGGCGCTACGGTGCTAGC 62.508 66.667 8.10 8.10 46.94 3.42
5338 5661 4.508128 GGCGCTACGGTGCTAGCA 62.508 66.667 14.93 14.93 46.94 3.49
5339 5662 2.956964 GCGCTACGGTGCTAGCAG 60.957 66.667 20.03 10.30 44.66 4.24
5340 5663 2.956964 CGCTACGGTGCTAGCAGC 60.957 66.667 32.12 32.12 39.40 5.25
5369 5692 4.144727 GGCTCCTCCTCCTCCCGA 62.145 72.222 0.00 0.00 0.00 5.14
5370 5693 2.200092 GCTCCTCCTCCTCCCGAT 59.800 66.667 0.00 0.00 0.00 4.18
5371 5694 1.906333 GCTCCTCCTCCTCCCGATC 60.906 68.421 0.00 0.00 0.00 3.69
5372 5695 1.850549 CTCCTCCTCCTCCCGATCT 59.149 63.158 0.00 0.00 0.00 2.75
5373 5696 0.539438 CTCCTCCTCCTCCCGATCTG 60.539 65.000 0.00 0.00 0.00 2.90
5374 5697 0.994050 TCCTCCTCCTCCCGATCTGA 60.994 60.000 0.00 0.00 0.00 3.27
5375 5698 0.114168 CCTCCTCCTCCCGATCTGAT 59.886 60.000 0.00 0.00 0.00 2.90
5376 5699 1.255882 CTCCTCCTCCCGATCTGATG 58.744 60.000 0.00 0.00 0.00 3.07
5377 5700 0.178950 TCCTCCTCCCGATCTGATGG 60.179 60.000 0.00 0.00 0.00 3.51
5378 5701 1.670590 CTCCTCCCGATCTGATGGC 59.329 63.158 0.00 0.00 0.00 4.40
5379 5702 2.152297 CTCCTCCCGATCTGATGGCG 62.152 65.000 0.00 0.00 0.00 5.69
5380 5703 2.356793 CTCCCGATCTGATGGCGC 60.357 66.667 0.00 0.00 0.00 6.53
5381 5704 3.873026 CTCCCGATCTGATGGCGCC 62.873 68.421 22.73 22.73 0.00 6.53
5382 5705 4.240103 CCCGATCTGATGGCGCCA 62.240 66.667 34.80 34.80 0.00 5.69
5383 5706 2.969238 CCGATCTGATGGCGCCAC 60.969 66.667 35.50 25.23 0.00 5.01
5384 5707 2.202919 CGATCTGATGGCGCCACA 60.203 61.111 35.50 28.28 0.00 4.17
5385 5708 2.242572 CGATCTGATGGCGCCACAG 61.243 63.158 34.39 34.39 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.470709 CCATCATCAGGTGGTATGTGTC 58.529 50.000 0.00 0.00 0.00 3.67
32 35 1.404391 CTCTGAAGCACCCATTCATGC 59.596 52.381 0.00 0.00 42.39 4.06
44 47 6.401581 CGATTTTAGTTCTGAACCTCTGAAGC 60.402 42.308 16.48 7.24 35.48 3.86
85 88 8.919145 TGTTTACAGGTGAAACATAATTCCTTT 58.081 29.630 0.00 0.00 40.85 3.11
116 119 6.385649 TCTCATTTTCCCAACAGTACAAAC 57.614 37.500 0.00 0.00 0.00 2.93
137 148 4.586884 TCGTGTCTGATTACTGTACCTCT 58.413 43.478 0.00 0.00 0.00 3.69
152 163 4.073293 ACTTGAACTGGATTTCGTGTCT 57.927 40.909 0.00 0.00 0.00 3.41
154 165 6.687081 TTAAACTTGAACTGGATTTCGTGT 57.313 33.333 0.00 0.00 0.00 4.49
299 313 9.793259 TTAACCTTCTTGTAGATGTTTCTGAAT 57.207 29.630 0.00 0.00 33.17 2.57
300 314 9.052759 GTTAACCTTCTTGTAGATGTTTCTGAA 57.947 33.333 0.00 0.00 33.17 3.02
311 325 3.048337 TGCGGGTTAACCTTCTTGTAG 57.952 47.619 23.69 6.98 36.97 2.74
314 328 2.882137 TCTTTGCGGGTTAACCTTCTTG 59.118 45.455 23.69 10.11 36.97 3.02
318 332 2.626266 CCTTTCTTTGCGGGTTAACCTT 59.374 45.455 23.69 0.00 36.97 3.50
319 333 2.235891 CCTTTCTTTGCGGGTTAACCT 58.764 47.619 23.69 0.00 36.97 3.50
320 334 1.271379 CCCTTTCTTTGCGGGTTAACC 59.729 52.381 16.85 16.85 33.16 2.85
321 335 2.717580 CCCTTTCTTTGCGGGTTAAC 57.282 50.000 0.00 0.00 33.16 2.01
326 340 0.527565 CATGACCCTTTCTTTGCGGG 59.472 55.000 0.00 0.00 43.79 6.13
327 341 0.109132 GCATGACCCTTTCTTTGCGG 60.109 55.000 0.00 0.00 0.00 5.69
329 343 0.598065 ACGCATGACCCTTTCTTTGC 59.402 50.000 0.00 0.00 33.27 3.68
371 388 2.874086 AGTGGCTGTTACCGTTGTTTAC 59.126 45.455 0.00 0.00 0.00 2.01
372 389 2.873472 CAGTGGCTGTTACCGTTGTTTA 59.127 45.455 0.00 0.00 0.00 2.01
373 390 1.673920 CAGTGGCTGTTACCGTTGTTT 59.326 47.619 0.00 0.00 0.00 2.83
374 391 1.305201 CAGTGGCTGTTACCGTTGTT 58.695 50.000 0.00 0.00 0.00 2.83
375 392 0.179468 ACAGTGGCTGTTACCGTTGT 59.821 50.000 0.00 0.00 42.59 3.32
376 393 0.865769 GACAGTGGCTGTTACCGTTG 59.134 55.000 3.16 0.00 45.44 4.10
377 394 0.466543 TGACAGTGGCTGTTACCGTT 59.533 50.000 0.00 0.00 45.44 4.44
378 395 0.466543 TTGACAGTGGCTGTTACCGT 59.533 50.000 0.00 0.00 45.44 4.83
379 396 0.865769 GTTGACAGTGGCTGTTACCG 59.134 55.000 0.00 0.00 45.44 4.02
380 397 1.202770 AGGTTGACAGTGGCTGTTACC 60.203 52.381 18.48 18.48 45.44 2.85
409 426 1.626825 TCCTTTGTACTACCCCTGCAC 59.373 52.381 0.00 0.00 0.00 4.57
481 498 5.740290 TCCAACTCTTCTTCTATCCGTTT 57.260 39.130 0.00 0.00 0.00 3.60
562 579 1.281419 TAATGGCTCCCGAGGTGAAA 58.719 50.000 0.00 0.00 0.00 2.69
621 638 8.395633 CAACTTGGTGTACTTATTATTACTGCC 58.604 37.037 0.00 0.00 0.00 4.85
756 800 5.986135 TCCCGTTTGTTTTTATCACCAAATG 59.014 36.000 0.00 0.00 34.91 2.32
762 807 6.617879 AGCTAATCCCGTTTGTTTTTATCAC 58.382 36.000 0.00 0.00 0.00 3.06
856 901 4.741239 AGGAGACCGCCCCATGGT 62.741 66.667 11.73 0.00 44.10 3.55
857 902 3.866582 GAGGAGACCGCCCCATGG 61.867 72.222 4.14 4.14 0.00 3.66
873 918 2.496070 CTGTCGTTGGGATTGTAGAGGA 59.504 50.000 0.00 0.00 0.00 3.71
927 972 0.751643 GGACGGATGGTTTGGGGATG 60.752 60.000 0.00 0.00 0.00 3.51
928 973 1.613061 GGACGGATGGTTTGGGGAT 59.387 57.895 0.00 0.00 0.00 3.85
929 974 2.961893 CGGACGGATGGTTTGGGGA 61.962 63.158 0.00 0.00 0.00 4.81
930 975 2.437716 CGGACGGATGGTTTGGGG 60.438 66.667 0.00 0.00 0.00 4.96
973 1023 4.477975 GTGACCGACGAGGCGAGG 62.478 72.222 0.00 0.00 46.52 4.63
1362 1424 2.202362 CTGAGGTCGAGCGTGACG 60.202 66.667 9.28 0.00 39.83 4.35
1512 1574 0.385098 CGTTGTCGTAGAGCGTGACA 60.385 55.000 0.00 0.00 40.62 3.58
1626 1688 2.187946 CAGCCGCCGATCTCCTTT 59.812 61.111 0.00 0.00 0.00 3.11
1710 1772 2.419851 GGTCTGGATCTTCTTGAGCTGG 60.420 54.545 0.00 0.00 0.00 4.85
2613 2675 2.596851 GGACCTCAGCTGCCCAGAA 61.597 63.158 9.47 0.00 0.00 3.02
2616 2678 3.324930 CTGGACCTCAGCTGCCCA 61.325 66.667 9.47 12.15 36.60 5.36
2745 2807 2.668280 GCCAGAGAACGCGTTGTCC 61.668 63.158 36.40 22.43 33.82 4.02
2976 3038 4.373116 GTGTTCGGGAGCTCGCCA 62.373 66.667 23.61 13.75 0.00 5.69
3090 3152 0.100682 TGGCTATCTTGAGCGTCGTC 59.899 55.000 0.00 0.00 43.83 4.20
3312 3386 2.845317 ACCCTGTACACCACGCCA 60.845 61.111 0.00 0.00 0.00 5.69
3525 3599 2.038975 AGGAGGCCGCTCAGGTTA 59.961 61.111 6.40 0.00 43.70 2.85
3766 3840 1.928706 GAGGAGTCGTCGAGCTTGCT 61.929 60.000 0.00 0.00 0.00 3.91
3866 4073 4.681744 ACGTTCAAAATGTGCTTGTGATT 58.318 34.783 0.00 0.00 0.00 2.57
3867 4074 4.290155 GACGTTCAAAATGTGCTTGTGAT 58.710 39.130 0.00 0.00 0.00 3.06
3868 4075 3.690422 GACGTTCAAAATGTGCTTGTGA 58.310 40.909 0.00 0.00 0.00 3.58
3871 4078 2.715268 ACGACGTTCAAAATGTGCTTG 58.285 42.857 0.00 0.00 0.00 4.01
3872 4079 3.414549 AACGACGTTCAAAATGTGCTT 57.585 38.095 7.57 0.00 0.00 3.91
3887 4099 5.106442 ACCAAAAATGTCAGGAAAAACGAC 58.894 37.500 0.00 0.00 0.00 4.34
3889 4101 6.247176 CAAACCAAAAATGTCAGGAAAAACG 58.753 36.000 0.00 0.00 0.00 3.60
3890 4102 6.150307 ACCAAACCAAAAATGTCAGGAAAAAC 59.850 34.615 0.00 0.00 0.00 2.43
3909 4129 0.104120 GCACACCCCAAGAACCAAAC 59.896 55.000 0.00 0.00 0.00 2.93
3910 4130 0.324738 TGCACACCCCAAGAACCAAA 60.325 50.000 0.00 0.00 0.00 3.28
3912 4132 1.152777 CTGCACACCCCAAGAACCA 60.153 57.895 0.00 0.00 0.00 3.67
3914 4134 0.179018 ACTCTGCACACCCCAAGAAC 60.179 55.000 0.00 0.00 0.00 3.01
4342 4636 3.575351 AACGAGTCGCCCACAGAGC 62.575 63.158 13.59 0.00 0.00 4.09
4406 4703 3.240134 AACGCACTGCCTGATCGGT 62.240 57.895 0.00 0.00 34.25 4.69
4413 4710 0.393077 AGTTACTGAACGCACTGCCT 59.607 50.000 0.00 0.00 40.76 4.75
4414 4711 1.993370 CTAGTTACTGAACGCACTGCC 59.007 52.381 0.00 0.00 40.76 4.85
4540 4840 7.215194 GCATCGATCGATTGATTAATTACTTGC 59.785 37.037 27.45 19.22 34.09 4.01
4541 4841 8.438513 AGCATCGATCGATTGATTAATTACTTG 58.561 33.333 27.45 13.69 34.09 3.16
4542 4842 8.438513 CAGCATCGATCGATTGATTAATTACTT 58.561 33.333 27.45 0.00 34.09 2.24
4543 4843 7.600375 ACAGCATCGATCGATTGATTAATTACT 59.400 33.333 27.98 11.95 34.09 2.24
4548 4848 6.447162 AGTACAGCATCGATCGATTGATTAA 58.553 36.000 27.98 12.40 34.09 1.40
4553 4853 4.618912 CCTAAGTACAGCATCGATCGATTG 59.381 45.833 27.45 24.48 31.62 2.67
4558 4858 4.308899 ACACCTAAGTACAGCATCGATC 57.691 45.455 0.00 0.00 0.00 3.69
4591 4895 0.828022 TCGCAGGGTATGTACAAGGG 59.172 55.000 0.00 0.00 0.00 3.95
4748 5062 1.202758 AGCAAGTCACGTCCATTTCCA 60.203 47.619 0.00 0.00 0.00 3.53
4749 5063 1.197721 CAGCAAGTCACGTCCATTTCC 59.802 52.381 0.00 0.00 0.00 3.13
4916 5239 0.032130 CTCGATCCATACACCCCGTG 59.968 60.000 0.00 0.00 39.75 4.94
4922 5245 5.749109 ACGAAGAAAATCTCGATCCATACAC 59.251 40.000 0.00 0.00 0.00 2.90
4944 5267 9.017669 ACGTTTTGACTTCTATATAAAGCTACG 57.982 33.333 0.00 0.00 0.00 3.51
4947 5270 8.997621 TGACGTTTTGACTTCTATATAAAGCT 57.002 30.769 0.00 0.00 0.00 3.74
4955 5278 8.504005 CCTTGTAATTGACGTTTTGACTTCTAT 58.496 33.333 0.00 0.00 0.00 1.98
4956 5279 7.711772 TCCTTGTAATTGACGTTTTGACTTCTA 59.288 33.333 0.00 0.00 0.00 2.10
4957 5280 6.540914 TCCTTGTAATTGACGTTTTGACTTCT 59.459 34.615 0.00 0.00 0.00 2.85
4958 5281 6.721321 TCCTTGTAATTGACGTTTTGACTTC 58.279 36.000 0.00 0.00 0.00 3.01
4959 5282 6.687081 TCCTTGTAATTGACGTTTTGACTT 57.313 33.333 0.00 0.00 0.00 3.01
4962 5285 7.090953 AGTTTCCTTGTAATTGACGTTTTGA 57.909 32.000 0.00 0.00 0.00 2.69
4963 5286 7.112984 GCTAGTTTCCTTGTAATTGACGTTTTG 59.887 37.037 0.00 0.00 0.00 2.44
4964 5287 7.136772 GCTAGTTTCCTTGTAATTGACGTTTT 58.863 34.615 0.00 0.00 0.00 2.43
4965 5288 6.261381 TGCTAGTTTCCTTGTAATTGACGTTT 59.739 34.615 0.00 0.00 0.00 3.60
4966 5289 5.761234 TGCTAGTTTCCTTGTAATTGACGTT 59.239 36.000 0.00 0.00 0.00 3.99
4967 5290 5.178809 GTGCTAGTTTCCTTGTAATTGACGT 59.821 40.000 0.00 0.00 0.00 4.34
4968 5291 5.408604 AGTGCTAGTTTCCTTGTAATTGACG 59.591 40.000 0.00 0.00 0.00 4.35
4972 5295 4.392138 GCGAGTGCTAGTTTCCTTGTAATT 59.608 41.667 0.00 0.00 38.39 1.40
5007 5330 4.711846 GGGGCACTCTATTCTTGGATTTTT 59.288 41.667 0.00 0.00 0.00 1.94
5008 5331 4.281657 GGGGCACTCTATTCTTGGATTTT 58.718 43.478 0.00 0.00 0.00 1.82
5009 5332 3.373110 GGGGGCACTCTATTCTTGGATTT 60.373 47.826 0.00 0.00 0.00 2.17
5010 5333 2.175715 GGGGGCACTCTATTCTTGGATT 59.824 50.000 0.00 0.00 0.00 3.01
5011 5334 1.777272 GGGGGCACTCTATTCTTGGAT 59.223 52.381 0.00 0.00 0.00 3.41
5012 5335 1.213296 GGGGGCACTCTATTCTTGGA 58.787 55.000 0.00 0.00 0.00 3.53
5013 5336 0.179045 CGGGGGCACTCTATTCTTGG 60.179 60.000 0.00 0.00 0.00 3.61
5014 5337 0.541863 ACGGGGGCACTCTATTCTTG 59.458 55.000 0.00 0.00 0.00 3.02
5015 5338 0.541863 CACGGGGGCACTCTATTCTT 59.458 55.000 0.00 0.00 0.00 2.52
5016 5339 1.972660 GCACGGGGGCACTCTATTCT 61.973 60.000 0.00 0.00 0.00 2.40
5017 5340 1.523938 GCACGGGGGCACTCTATTC 60.524 63.158 0.00 0.00 0.00 1.75
5018 5341 2.590092 GCACGGGGGCACTCTATT 59.410 61.111 0.00 0.00 0.00 1.73
5019 5342 3.480133 GGCACGGGGGCACTCTAT 61.480 66.667 0.00 0.00 42.77 1.98
5291 5614 4.101448 AGCCACACCGCCCAGATC 62.101 66.667 0.00 0.00 0.00 2.75
5292 5615 4.101448 GAGCCACACCGCCCAGAT 62.101 66.667 0.00 0.00 0.00 2.90
5300 5623 3.009115 TAGCAGGGGAGCCACACC 61.009 66.667 0.00 0.00 43.70 4.16
5301 5624 2.586792 CTAGCAGGGGAGCCACAC 59.413 66.667 0.00 0.00 34.23 3.82
5302 5625 2.688666 CCTAGCAGGGGAGCCACA 60.689 66.667 0.00 0.00 34.23 4.17
5303 5626 2.689034 ACCTAGCAGGGGAGCCAC 60.689 66.667 7.06 0.00 40.58 5.01
5304 5627 2.688666 CACCTAGCAGGGGAGCCA 60.689 66.667 7.06 0.00 43.10 4.75
5305 5628 3.483869 CCACCTAGCAGGGGAGCC 61.484 72.222 6.07 0.00 43.10 4.70
5306 5629 4.182433 GCCACCTAGCAGGGGAGC 62.182 72.222 6.07 4.61 43.10 4.70
5307 5630 3.854669 CGCCACCTAGCAGGGGAG 61.855 72.222 6.07 3.50 43.10 4.30
5310 5633 3.154473 TAGCGCCACCTAGCAGGG 61.154 66.667 2.29 0.71 40.58 4.45
5311 5634 2.107141 GTAGCGCCACCTAGCAGG 59.893 66.667 2.29 1.16 42.49 4.85
5312 5635 2.278857 CGTAGCGCCACCTAGCAG 60.279 66.667 2.29 0.00 35.48 4.24
5313 5636 3.833645 CCGTAGCGCCACCTAGCA 61.834 66.667 2.29 0.00 35.48 3.49
5314 5637 3.834799 ACCGTAGCGCCACCTAGC 61.835 66.667 2.29 0.00 0.00 3.42
5315 5638 2.104331 CACCGTAGCGCCACCTAG 59.896 66.667 2.29 0.00 0.00 3.02
5316 5639 4.137872 GCACCGTAGCGCCACCTA 62.138 66.667 2.29 0.00 0.00 3.08
5318 5641 4.137872 TAGCACCGTAGCGCCACC 62.138 66.667 2.29 0.00 40.15 4.61
5319 5642 2.582498 CTAGCACCGTAGCGCCAC 60.582 66.667 2.29 0.00 40.15 5.01
5320 5643 4.508128 GCTAGCACCGTAGCGCCA 62.508 66.667 10.63 0.00 36.34 5.69
5324 5647 2.956964 CGCTGCTAGCACCGTAGC 60.957 66.667 21.58 17.83 42.58 3.58
5325 5648 2.278857 CCGCTGCTAGCACCGTAG 60.279 66.667 26.11 13.12 42.58 3.51
5326 5649 4.508128 GCCGCTGCTAGCACCGTA 62.508 66.667 26.11 1.70 42.58 4.02
5352 5675 3.460478 ATCGGGAGGAGGAGGAGCC 62.460 68.421 0.00 0.00 0.00 4.70
5353 5676 1.906333 GATCGGGAGGAGGAGGAGC 60.906 68.421 0.00 0.00 0.00 4.70
5354 5677 0.539438 CAGATCGGGAGGAGGAGGAG 60.539 65.000 0.00 0.00 0.00 3.69
5355 5678 0.994050 TCAGATCGGGAGGAGGAGGA 60.994 60.000 0.00 0.00 0.00 3.71
5356 5679 0.114168 ATCAGATCGGGAGGAGGAGG 59.886 60.000 0.00 0.00 0.00 4.30
5357 5680 1.255882 CATCAGATCGGGAGGAGGAG 58.744 60.000 0.00 0.00 0.00 3.69
5358 5681 0.178950 CCATCAGATCGGGAGGAGGA 60.179 60.000 4.05 0.00 0.00 3.71
5359 5682 1.825281 GCCATCAGATCGGGAGGAGG 61.825 65.000 8.26 5.69 0.00 4.30
5360 5683 1.670590 GCCATCAGATCGGGAGGAG 59.329 63.158 8.26 0.00 0.00 3.69
5361 5684 2.203082 CGCCATCAGATCGGGAGGA 61.203 63.158 8.26 0.00 0.00 3.71
5362 5685 2.341543 CGCCATCAGATCGGGAGG 59.658 66.667 0.00 0.00 0.00 4.30
5363 5686 2.356793 GCGCCATCAGATCGGGAG 60.357 66.667 0.00 0.00 0.00 4.30
5364 5687 3.928779 GGCGCCATCAGATCGGGA 61.929 66.667 24.80 0.00 0.00 5.14
5365 5688 4.240103 TGGCGCCATCAGATCGGG 62.240 66.667 29.03 0.00 0.00 5.14
5366 5689 2.969238 GTGGCGCCATCAGATCGG 60.969 66.667 35.23 0.00 0.00 4.18
5367 5690 2.202919 TGTGGCGCCATCAGATCG 60.203 61.111 35.23 0.00 0.00 3.69
5368 5691 3.728474 CTGTGGCGCCATCAGATC 58.272 61.111 35.73 23.84 31.53 2.75


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

AutoCloner maintained by Alex Coulton.