Multiple sequence alignment - TraesCS4A01G390800

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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 TraesCS4A01G390800 chr4A 100.000 4262 0 0 1 4262 667851919 667856180 0.000000e+00 7871
1 TraesCS4A01G390800 chr7D 92.481 2447 108 27 1865 4262 52838466 52836047 0.000000e+00 3430
2 TraesCS4A01G390800 chr7D 89.453 1005 47 26 713 1697 52839701 52838736 0.000000e+00 1214
3 TraesCS4A01G390800 chr7D 89.627 617 43 15 117 724 52840453 52839849 0.000000e+00 765
4 TraesCS4A01G390800 chr7D 94.615 130 7 0 1691 1820 52838609 52838480 7.230000e-48 202
5 TraesCS4A01G390800 chr7D 94.068 118 7 0 3 120 52840650 52840533 3.390000e-41 180
6 TraesCS4A01G390800 chr7D 82.386 176 11 12 4092 4247 53410379 53410554 7.430000e-28 135
7 TraesCS4A01G390800 chr7A 90.494 1641 104 18 2648 4259 55363765 55365382 0.000000e+00 2119
8 TraesCS4A01G390800 chr7A 91.174 1371 64 38 187 1537 55361199 55362532 0.000000e+00 1808
9 TraesCS4A01G390800 chr7A 85.000 440 46 13 1857 2291 55362969 55363393 3.040000e-116 429
10 TraesCS4A01G390800 chr7A 90.355 197 7 5 1 197 55359039 55359223 9.150000e-62 248
11 TraesCS4A01G390800 chr7A 92.982 114 8 0 2465 2578 55363651 55363764 2.640000e-37 167
12 TraesCS4A01G390800 chr7A 95.890 73 2 1 2333 2404 55363392 55363464 2.690000e-22 117


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 TraesCS4A01G390800 chr4A 667851919 667856180 4261 False 7871.000000 7871 100.0000 1 4262 1 chr4A.!!$F1 4261
1 TraesCS4A01G390800 chr7D 52836047 52840650 4603 True 1158.200000 3430 92.0488 3 4262 5 chr7D.!!$R1 4259
2 TraesCS4A01G390800 chr7A 55359039 55365382 6343 False 814.666667 2119 90.9825 1 4259 6 chr7A.!!$F1 4258

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
469 2539 0.035056 GGAGAACATCAGGTGGGTGG 60.035 60.0 0.00 0.00 0.0 4.61 F
645 2728 0.249322 CCATCGTACATCCCGGTCAC 60.249 60.0 0.00 0.00 0.0 3.67 F
646 2729 0.249322 CATCGTACATCCCGGTCACC 60.249 60.0 0.00 0.00 0.0 4.02 F
1401 3673 0.878416 TCATTTTCCTTGCCGGTTCG 59.122 50.0 1.90 0.00 0.0 3.95 F
1602 3900 0.960861 GTGTGGTCCTTAGGCTTGCC 60.961 60.0 2.97 2.97 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 3796 0.027979 AATCGCGCACGGATCAAATG 59.972 50.000 8.75 0.00 40.63 2.32 R
2499 5093 1.340889 GGGTCATTGCAGCAAACAAGA 59.659 47.619 12.97 5.43 0.00 3.02 R
2534 5128 1.558167 TAGGCCGGGCAAATCAGTGA 61.558 55.000 31.59 0.00 0.00 3.41 R
3222 5816 1.194280 CGTCGTCATCATGTCCGTCG 61.194 60.000 0.00 5.25 0.00 5.12 R
3571 6172 0.749454 GGAGCCATCCACGCAAAGAT 60.749 55.000 0.00 0.00 45.87 2.40 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
39 40 2.934553 TCGTATATATGGTCGAGCGGAG 59.065 50.000 10.46 0.00 0.00 4.63
46 47 7.818997 ATATATGGTCGAGCGGAGAATATTA 57.181 36.000 10.46 0.00 0.00 0.98
48 49 2.953648 TGGTCGAGCGGAGAATATTACA 59.046 45.455 10.46 0.00 0.00 2.41
57 58 3.493503 CGGAGAATATTACAGGCGGTTTC 59.506 47.826 0.00 0.00 0.00 2.78
106 107 5.482163 TTGTATCCACACATGTTCTCAGA 57.518 39.130 0.00 0.00 33.30 3.27
107 108 4.820897 TGTATCCACACATGTTCTCAGAC 58.179 43.478 0.00 0.00 0.00 3.51
238 2308 2.320781 CTCCCGGAGTATGTGATTCCT 58.679 52.381 0.73 0.00 31.61 3.36
269 2339 2.895242 AGGCTGCAGAGAAAAGGAAT 57.105 45.000 20.43 0.00 0.00 3.01
300 2370 2.486203 GGTCCATGAACACGCAAATGTA 59.514 45.455 0.00 0.00 30.75 2.29
307 2377 1.519408 ACACGCAAATGTACAGGACC 58.481 50.000 0.33 0.00 0.00 4.46
336 2406 4.340617 TGCGGGAGAATAATTCAAACCTT 58.659 39.130 0.00 0.00 0.00 3.50
343 2413 2.715737 TAATTCAAACCTTGCGGTGC 57.284 45.000 0.00 0.00 44.73 5.01
380 2450 6.932947 AGCGTTAGTATCTGGTTAAACTCTT 58.067 36.000 0.00 0.00 0.00 2.85
413 2483 9.953697 ATGAAATGTTTGAAAAACATGGAAATG 57.046 25.926 16.70 0.00 40.43 2.32
450 2520 1.752753 TTTGCAAAATGACGCACTCG 58.247 45.000 10.02 0.00 38.00 4.18
469 2539 0.035056 GGAGAACATCAGGTGGGTGG 60.035 60.000 0.00 0.00 0.00 4.61
485 2555 2.033675 GGGTGGTTTTGAAACAGGTACG 59.966 50.000 8.68 0.00 40.63 3.67
640 2723 2.355837 CGGCCATCGTACATCCCG 60.356 66.667 2.24 0.00 0.00 5.14
641 2724 2.030562 GGCCATCGTACATCCCGG 59.969 66.667 0.00 0.00 0.00 5.73
643 2726 1.300697 GCCATCGTACATCCCGGTC 60.301 63.158 0.00 0.00 0.00 4.79
644 2727 2.023414 GCCATCGTACATCCCGGTCA 62.023 60.000 0.00 0.00 0.00 4.02
645 2728 0.249322 CCATCGTACATCCCGGTCAC 60.249 60.000 0.00 0.00 0.00 3.67
646 2729 0.249322 CATCGTACATCCCGGTCACC 60.249 60.000 0.00 0.00 0.00 4.02
686 2769 6.812879 ATCATATGCATCATGTGTAGTTGG 57.187 37.500 0.19 0.00 35.12 3.77
801 3053 5.586243 TGCCAACAAAAATCGAAATGGAAAA 59.414 32.000 0.00 0.00 0.00 2.29
810 3062 5.683876 ATCGAAATGGAAAAGAGAGAGGA 57.316 39.130 0.00 0.00 0.00 3.71
831 3083 7.279758 AGAGGAGAGATTTTTCATCATTTCGAC 59.720 37.037 0.00 0.00 0.00 4.20
897 3149 1.244019 CCAAGTGGAAAAGGCCTCCG 61.244 60.000 5.23 0.00 35.55 4.63
905 3157 2.619590 GGAAAAGGCCTCCGTTCCATAA 60.620 50.000 26.70 0.00 40.19 1.90
966 3227 2.041819 GACCCGTCTCCTCCCCAT 60.042 66.667 0.00 0.00 0.00 4.00
968 3229 3.227276 CCCGTCTCCTCCCCATCG 61.227 72.222 0.00 0.00 0.00 3.84
969 3230 3.917760 CCGTCTCCTCCCCATCGC 61.918 72.222 0.00 0.00 0.00 4.58
971 3232 3.551407 GTCTCCTCCCCATCGCCC 61.551 72.222 0.00 0.00 0.00 6.13
1202 3471 3.118454 CGATTTGACAGCGGCGGT 61.118 61.111 5.44 5.44 0.00 5.68
1372 3644 1.931635 AGGCCTCGTCTCTTCTTCTT 58.068 50.000 0.00 0.00 0.00 2.52
1373 3645 1.822371 AGGCCTCGTCTCTTCTTCTTC 59.178 52.381 0.00 0.00 0.00 2.87
1374 3646 1.822371 GGCCTCGTCTCTTCTTCTTCT 59.178 52.381 0.00 0.00 0.00 2.85
1385 3657 5.011125 TCTCTTCTTCTTCTCACGGTTTCAT 59.989 40.000 0.00 0.00 0.00 2.57
1400 3672 3.057019 GTTTCATTTTCCTTGCCGGTTC 58.943 45.455 1.90 0.00 0.00 3.62
1401 3673 0.878416 TCATTTTCCTTGCCGGTTCG 59.122 50.000 1.90 0.00 0.00 3.95
1498 3772 1.150536 AAGGTCAGCGCTTTCCCAA 59.849 52.632 19.93 0.00 0.00 4.12
1516 3790 2.550423 CCAATTTTTGGTGCCATCTGCA 60.550 45.455 0.00 0.00 45.00 4.41
1550 3833 1.695893 CGTGCGCGATTGGATTGTCT 61.696 55.000 16.08 0.00 41.33 3.41
1556 3839 3.123621 GCGCGATTGGATTGTCTAATAGG 59.876 47.826 12.10 0.00 27.21 2.57
1560 3843 5.527582 GCGATTGGATTGTCTAATAGGTTGT 59.472 40.000 0.00 0.00 27.21 3.32
1602 3900 0.960861 GTGTGGTCCTTAGGCTTGCC 60.961 60.000 2.97 2.97 0.00 4.52
1617 3915 2.796032 GCTTGCCGTTATTGCCTTGATC 60.796 50.000 0.00 0.00 0.00 2.92
1703 4148 2.003301 GCTCTAGTTGTAAGGCAGCAC 58.997 52.381 0.00 0.00 0.00 4.40
1709 4154 1.323534 GTTGTAAGGCAGCACGATACG 59.676 52.381 0.00 0.00 0.00 3.06
1737 4182 4.541779 CTGATAGATTCAGTCCAGCGTAC 58.458 47.826 0.00 0.00 45.79 3.67
1759 4206 8.227119 CGTACACAATCATGTTTGTCTTCATAA 58.773 33.333 17.33 0.00 37.73 1.90
1760 4207 9.329913 GTACACAATCATGTTTGTCTTCATAAC 57.670 33.333 17.33 6.50 37.73 1.89
1803 4250 4.870123 AAAATGAGGCTGTATGTTGCAA 57.130 36.364 0.00 0.00 0.00 4.08
1804 4251 4.445452 AAATGAGGCTGTATGTTGCAAG 57.555 40.909 0.00 0.00 0.00 4.01
1820 4267 5.291614 TGTTGCAAGCAAATTTGTCTTCTTC 59.708 36.000 19.03 12.84 37.70 2.87
1821 4268 5.266733 TGCAAGCAAATTTGTCTTCTTCT 57.733 34.783 19.03 3.48 0.00 2.85
1822 4269 5.045215 TGCAAGCAAATTTGTCTTCTTCTG 58.955 37.500 19.03 11.62 0.00 3.02
1823 4270 4.446719 GCAAGCAAATTTGTCTTCTTCTGG 59.553 41.667 19.03 10.39 0.00 3.86
1824 4271 4.861102 AGCAAATTTGTCTTCTTCTGGG 57.139 40.909 19.03 0.00 0.00 4.45
1825 4272 4.218312 AGCAAATTTGTCTTCTTCTGGGT 58.782 39.130 19.03 0.00 0.00 4.51
1826 4273 4.651045 AGCAAATTTGTCTTCTTCTGGGTT 59.349 37.500 19.03 0.00 0.00 4.11
1827 4274 4.746611 GCAAATTTGTCTTCTTCTGGGTTG 59.253 41.667 19.03 0.00 0.00 3.77
1829 4276 5.520376 AATTTGTCTTCTTCTGGGTTGTG 57.480 39.130 0.00 0.00 0.00 3.33
1830 4277 3.924114 TTGTCTTCTTCTGGGTTGTGA 57.076 42.857 0.00 0.00 0.00 3.58
1831 4278 4.437682 TTGTCTTCTTCTGGGTTGTGAT 57.562 40.909 0.00 0.00 0.00 3.06
1832 4279 5.560722 TTGTCTTCTTCTGGGTTGTGATA 57.439 39.130 0.00 0.00 0.00 2.15
1833 4280 5.560722 TGTCTTCTTCTGGGTTGTGATAA 57.439 39.130 0.00 0.00 0.00 1.75
1834 4281 6.126863 TGTCTTCTTCTGGGTTGTGATAAT 57.873 37.500 0.00 0.00 0.00 1.28
1835 4282 7.252612 TGTCTTCTTCTGGGTTGTGATAATA 57.747 36.000 0.00 0.00 0.00 0.98
1836 4283 7.331026 TGTCTTCTTCTGGGTTGTGATAATAG 58.669 38.462 0.00 0.00 0.00 1.73
1837 4284 7.038302 TGTCTTCTTCTGGGTTGTGATAATAGT 60.038 37.037 0.00 0.00 0.00 2.12
1838 4285 7.492994 GTCTTCTTCTGGGTTGTGATAATAGTC 59.507 40.741 0.00 0.00 0.00 2.59
1839 4286 6.867519 TCTTCTGGGTTGTGATAATAGTCA 57.132 37.500 0.00 0.00 0.00 3.41
1840 4287 7.437713 TCTTCTGGGTTGTGATAATAGTCAT 57.562 36.000 0.00 0.00 0.00 3.06
1841 4288 7.861629 TCTTCTGGGTTGTGATAATAGTCATT 58.138 34.615 0.00 0.00 0.00 2.57
1842 4289 7.770433 TCTTCTGGGTTGTGATAATAGTCATTG 59.230 37.037 0.00 0.00 0.00 2.82
1843 4290 5.822519 TCTGGGTTGTGATAATAGTCATTGC 59.177 40.000 0.00 0.00 0.00 3.56
1844 4291 5.504853 TGGGTTGTGATAATAGTCATTGCA 58.495 37.500 0.00 0.00 0.00 4.08
1845 4292 5.948758 TGGGTTGTGATAATAGTCATTGCAA 59.051 36.000 0.00 0.00 0.00 4.08
1846 4293 6.435591 TGGGTTGTGATAATAGTCATTGCAAA 59.564 34.615 1.71 0.00 0.00 3.68
1847 4294 7.039434 TGGGTTGTGATAATAGTCATTGCAAAA 60.039 33.333 1.71 0.00 0.00 2.44
1848 4295 7.816995 GGGTTGTGATAATAGTCATTGCAAAAA 59.183 33.333 1.71 0.00 0.00 1.94
1849 4296 9.369904 GGTTGTGATAATAGTCATTGCAAAAAT 57.630 29.630 1.71 0.00 0.00 1.82
1852 4299 9.791820 TGTGATAATAGTCATTGCAAAAATGAG 57.208 29.630 1.71 0.00 37.34 2.90
1853 4300 9.241317 GTGATAATAGTCATTGCAAAAATGAGG 57.759 33.333 1.71 0.00 37.34 3.86
1854 4301 7.922278 TGATAATAGTCATTGCAAAAATGAGGC 59.078 33.333 1.71 0.00 37.34 4.70
1855 4302 5.927281 ATAGTCATTGCAAAAATGAGGCT 57.073 34.783 1.71 0.22 37.34 4.58
1872 4319 9.860898 AAATGAGGCTGATTTTAACATTCTTAC 57.139 29.630 6.08 0.00 0.00 2.34
1876 4323 6.653320 AGGCTGATTTTAACATTCTTACGACA 59.347 34.615 0.00 0.00 0.00 4.35
1985 4432 9.836864 TTGTGATAATATGTATCAGCTGTCTTT 57.163 29.630 14.67 0.09 34.93 2.52
1988 4435 8.650490 TGATAATATGTATCAGCTGTCTTTGGA 58.350 33.333 14.67 0.00 31.09 3.53
2066 4516 1.867233 CCAACCACTTGTTCTGACTCG 59.133 52.381 0.00 0.00 34.00 4.18
2089 4539 4.470304 GGACCCACCTCTTGAACTTATACT 59.530 45.833 0.00 0.00 35.41 2.12
2418 4870 3.044156 TCTTCCAGCCTAATGCATCTCT 58.956 45.455 0.00 0.00 44.83 3.10
2419 4871 4.226384 TCTTCCAGCCTAATGCATCTCTA 58.774 43.478 0.00 0.00 44.83 2.43
2468 5062 8.637196 TCAAGAACAGACTATTCTCAGTTAGA 57.363 34.615 0.00 0.00 35.31 2.10
2481 5075 4.631377 TCTCAGTTAGAATGGTGAATTGCG 59.369 41.667 0.00 0.00 0.00 4.85
2499 5093 2.961526 CGTAGCTGTCCCTGTGTATT 57.038 50.000 0.00 0.00 0.00 1.89
2534 5128 4.741928 ATGACCCCTTTCTGTTTTACCT 57.258 40.909 0.00 0.00 0.00 3.08
2547 5141 3.572255 TGTTTTACCTCACTGATTTGCCC 59.428 43.478 0.00 0.00 0.00 5.36
2595 5189 3.902261 TGACTTGCAACAGCTGTTATG 57.098 42.857 30.67 21.55 36.32 1.90
2597 5191 4.384940 TGACTTGCAACAGCTGTTATGTA 58.615 39.130 30.67 17.73 36.32 2.29
2627 5221 4.361451 GTGAGTTCACAAATAGGCATGG 57.639 45.455 7.37 0.00 45.75 3.66
2692 5286 2.092646 TGTTGGCTCAACTGTACCTTGT 60.093 45.455 15.91 0.00 43.85 3.16
2703 5297 6.426633 TCAACTGTACCTTGTGTATCATTGTG 59.573 38.462 0.00 0.00 0.00 3.33
2743 5337 7.876936 TTCTACTCGTATGGTCTAACTGAAT 57.123 36.000 0.00 0.00 0.00 2.57
2777 5371 5.306419 TCCACATCCTCATTCATAGGAAGAG 59.694 44.000 0.00 3.29 46.06 2.85
2796 5390 3.129871 GAGCCAGCTATCATTCAGTCAC 58.870 50.000 0.00 0.00 0.00 3.67
2873 5467 6.566079 TGAATCCATAATTCTGTCTCCACT 57.434 37.500 0.08 0.00 43.61 4.00
2925 5519 8.878211 TCTCCTGCATCTTATCTAGAAATGATT 58.122 33.333 0.00 0.00 36.22 2.57
3034 5628 1.497722 GTTGAAGAAAGGCGAGCCG 59.502 57.895 8.63 0.00 41.95 5.52
3164 5758 2.886523 TGTTGCCTCCATGTTTTCTGAG 59.113 45.455 0.00 0.00 0.00 3.35
3222 5816 2.071636 TTGGGAACGGAGGAAACCCC 62.072 60.000 0.00 0.00 39.78 4.95
3522 6123 6.671614 TTCATTAAACAAACAGTGACGTCT 57.328 33.333 17.92 0.00 0.00 4.18
3528 6129 2.858344 ACAAACAGTGACGTCTCTTTCG 59.142 45.455 17.08 9.27 0.00 3.46
3549 6150 3.565516 GTTTTCGACTTGCCTTTCATCC 58.434 45.455 0.00 0.00 0.00 3.51
3571 6172 7.531857 TCCAGTCAATAAGGTTTTAATTGCA 57.468 32.000 0.00 0.00 0.00 4.08
3591 6192 2.745884 TTTGCGTGGATGGCTCCG 60.746 61.111 0.00 0.00 45.37 4.63
3592 6193 3.545124 TTTGCGTGGATGGCTCCGT 62.545 57.895 0.00 0.00 45.37 4.69
3593 6194 4.758251 TGCGTGGATGGCTCCGTG 62.758 66.667 0.00 0.00 45.37 4.94
3596 6197 2.100631 CGTGGATGGCTCCGTGTTC 61.101 63.158 0.00 0.00 45.37 3.18
3627 6228 0.823460 CAACTGTTTTGCTGGTGGGT 59.177 50.000 0.00 0.00 31.12 4.51
3638 6239 5.398603 TTGCTGGTGGGTAATTTGTTATG 57.601 39.130 0.00 0.00 0.00 1.90
3639 6240 3.766591 TGCTGGTGGGTAATTTGTTATGG 59.233 43.478 0.00 0.00 0.00 2.74
3682 6283 3.481951 CGATCTTGATCCGTTGTTTGTCG 60.482 47.826 5.18 0.00 0.00 4.35
3686 6291 1.269154 TGATCCGTTGTTTGTCGTCGA 60.269 47.619 0.00 0.00 0.00 4.20
3704 6309 5.526010 GTCGAGTTTTGATGACGGTAAAT 57.474 39.130 0.00 0.00 0.00 1.40
3708 6313 6.529125 TCGAGTTTTGATGACGGTAAATAGAC 59.471 38.462 0.00 0.00 0.00 2.59
3742 6347 6.529220 ACTGTCAATCAAGCTCTAGTTTCTT 58.471 36.000 0.00 0.00 0.00 2.52
3745 6350 6.767902 TGTCAATCAAGCTCTAGTTTCTTTGT 59.232 34.615 0.00 0.00 0.00 2.83
3746 6351 7.931407 TGTCAATCAAGCTCTAGTTTCTTTGTA 59.069 33.333 0.00 0.00 0.00 2.41
3747 6352 8.439286 GTCAATCAAGCTCTAGTTTCTTTGTAG 58.561 37.037 0.00 0.00 0.00 2.74
3748 6353 8.150945 TCAATCAAGCTCTAGTTTCTTTGTAGT 58.849 33.333 0.00 0.00 0.00 2.73
3792 6397 6.484364 AACATTCAAACCTTGGATTTGTCT 57.516 33.333 11.48 2.84 38.08 3.41
3871 6497 6.814954 TCCCTCTTTGCTCATCTACTTAAT 57.185 37.500 0.00 0.00 0.00 1.40
3898 6524 6.734137 ACTTAACAATTGAAAGTGCGAATGA 58.266 32.000 21.81 0.00 32.38 2.57
3939 6565 2.179018 GCGCGATGCCATTTGTGT 59.821 55.556 12.10 0.00 37.76 3.72
3940 6566 1.869132 GCGCGATGCCATTTGTGTC 60.869 57.895 12.10 0.00 37.76 3.67
3941 6567 1.580893 CGCGATGCCATTTGTGTCG 60.581 57.895 0.00 0.00 35.56 4.35
3942 6568 4.365287 CGATGCCATTTGTGTCGC 57.635 55.556 0.00 0.00 0.00 5.19
3943 6569 1.796151 CGATGCCATTTGTGTCGCT 59.204 52.632 0.00 0.00 0.00 4.93
4001 6627 2.438021 TCGCCTGTTGCCTATCCTATTT 59.562 45.455 0.00 0.00 36.24 1.40
4019 6650 8.263940 TCCTATTTGAAATTTACGACTCAAGG 57.736 34.615 0.00 0.00 0.00 3.61
4067 6706 4.438148 TCAAGTTGAGAATGTCGTTGTCA 58.562 39.130 0.08 0.59 38.23 3.58
4068 6707 5.056480 TCAAGTTGAGAATGTCGTTGTCAT 58.944 37.500 0.08 0.00 39.54 3.06
4069 6708 5.177511 TCAAGTTGAGAATGTCGTTGTCATC 59.822 40.000 0.08 5.41 39.54 2.92
4070 6709 4.887748 AGTTGAGAATGTCGTTGTCATCT 58.112 39.130 5.53 7.41 39.54 2.90
4124 6763 2.561419 TCAAAACTGGGAGTAGGACGAG 59.439 50.000 0.00 0.00 0.00 4.18
4129 6769 2.042162 ACTGGGAGTAGGACGAGGTAAA 59.958 50.000 0.00 0.00 0.00 2.01
4147 6787 4.161377 GGTAAAGAGCTCAGAAGATGGTCT 59.839 45.833 17.77 0.00 39.79 3.85
4150 6790 1.830477 GAGCTCAGAAGATGGTCTGGT 59.170 52.381 9.40 0.00 44.40 4.00
4175 6818 1.304282 GATGGGGAGCAGAAAGGCA 59.696 57.895 0.00 0.00 35.83 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 6.963049 ATATCGAAACCGCCTGTAATATTC 57.037 37.500 0.00 0.00 0.00 1.75
46 47 2.980568 TCAAATATCGAAACCGCCTGT 58.019 42.857 0.00 0.00 0.00 4.00
48 49 4.957296 AGTATCAAATATCGAAACCGCCT 58.043 39.130 0.00 0.00 0.00 5.52
57 58 8.744008 ATTCCGTACAAGAGTATCAAATATCG 57.256 34.615 0.00 0.00 37.82 2.92
132 216 9.444600 AGCAAATTAACCTCGAAAGTTCTATAA 57.555 29.630 3.90 0.00 0.00 0.98
133 217 9.444600 AAGCAAATTAACCTCGAAAGTTCTATA 57.555 29.630 3.90 0.00 0.00 1.31
238 2308 8.574251 TTTCTCTGCAGCCTAATAAATTGTTA 57.426 30.769 9.47 0.00 0.00 2.41
269 2339 1.617850 GTTCATGGACCAAACATGCCA 59.382 47.619 0.00 0.00 44.07 4.92
300 2370 4.609995 CGCAAATACGGGTCCTGT 57.390 55.556 8.79 8.79 0.00 4.00
336 2406 1.904287 AGGTTCTTAATTGCACCGCA 58.096 45.000 0.00 0.00 36.47 5.69
343 2413 8.969267 CAGATACTAACGCTAGGTTCTTAATTG 58.031 37.037 0.00 0.00 40.09 2.32
350 2420 4.915158 ACCAGATACTAACGCTAGGTTC 57.085 45.455 0.00 0.00 40.09 3.62
380 2450 9.635520 ATGTTTTTCAAACATTTCATGCAAAAA 57.364 22.222 8.71 0.00 37.58 1.94
436 2506 1.798813 GTTCTCCGAGTGCGTCATTTT 59.201 47.619 0.00 0.00 35.23 1.82
442 2512 0.109086 CTGATGTTCTCCGAGTGCGT 60.109 55.000 0.00 0.00 35.23 5.24
450 2520 0.035056 CCACCCACCTGATGTTCTCC 60.035 60.000 0.00 0.00 0.00 3.71
469 2539 5.292589 TCAACTCTCGTACCTGTTTCAAAAC 59.707 40.000 0.00 0.00 39.33 2.43
485 2555 5.759963 TCGAGACAAGTTTACTCAACTCTC 58.240 41.667 0.00 0.00 45.77 3.20
629 2712 2.409055 CGGTGACCGGGATGTACGA 61.409 63.158 17.80 0.00 44.15 3.43
640 2723 6.630444 TTATAATAGAGTGTCTCGGTGACC 57.370 41.667 7.65 0.00 44.75 4.02
641 2724 7.872881 TGATTATAATAGAGTGTCTCGGTGAC 58.127 38.462 0.00 3.34 45.54 3.67
645 2728 9.457110 GCATATGATTATAATAGAGTGTCTCGG 57.543 37.037 6.97 0.00 35.36 4.63
665 2748 7.227314 AGTTACCAACTACACATGATGCATATG 59.773 37.037 0.00 6.88 40.69 1.78
801 3053 7.679732 ATGATGAAAAATCTCTCCTCTCTCT 57.320 36.000 0.00 0.00 0.00 3.10
810 3062 5.874810 TCCGTCGAAATGATGAAAAATCTCT 59.125 36.000 0.00 0.00 35.48 3.10
850 3102 3.536956 TTTCTAGGCAACCGATAGTGG 57.463 47.619 0.00 0.00 37.17 4.00
857 3109 3.304458 GGTGTTTCTTTTCTAGGCAACCG 60.304 47.826 0.00 0.00 37.17 4.44
897 3149 1.134220 TGCCGATGGGTCTTATGGAAC 60.134 52.381 0.00 0.00 34.97 3.62
905 3157 2.430610 GCTCTCTGCCGATGGGTCT 61.431 63.158 0.00 0.00 35.15 3.85
1245 3517 1.300233 GATCGGCATCACGTCCTCC 60.300 63.158 0.00 0.00 34.94 4.30
1327 3599 3.141488 CACGACGGAGGAGGGAGG 61.141 72.222 0.00 0.00 0.00 4.30
1328 3600 3.141488 CCACGACGGAGGAGGGAG 61.141 72.222 0.00 0.00 36.56 4.30
1372 3644 3.004315 GCAAGGAAAATGAAACCGTGAGA 59.996 43.478 0.00 0.00 35.77 3.27
1373 3645 3.308530 GCAAGGAAAATGAAACCGTGAG 58.691 45.455 0.00 0.00 35.77 3.51
1374 3646 2.035321 GGCAAGGAAAATGAAACCGTGA 59.965 45.455 0.00 0.00 35.77 4.35
1385 3657 0.664224 GAACGAACCGGCAAGGAAAA 59.336 50.000 0.00 0.00 45.00 2.29
1400 3672 0.032952 TCCAACGAGGGTCAAGAACG 59.967 55.000 0.00 0.00 38.24 3.95
1401 3673 2.474410 ATCCAACGAGGGTCAAGAAC 57.526 50.000 0.00 0.00 38.24 3.01
1516 3790 1.401552 CGCACGGATCAAATGACCATT 59.598 47.619 0.00 0.00 0.00 3.16
1522 3796 0.027979 AATCGCGCACGGATCAAATG 59.972 50.000 8.75 0.00 40.63 2.32
1550 3833 5.616270 TCAGTGCAGACAAACAACCTATTA 58.384 37.500 0.00 0.00 0.00 0.98
1556 3839 3.798337 CCATTTCAGTGCAGACAAACAAC 59.202 43.478 0.00 0.00 0.00 3.32
1560 3843 3.286353 TCACCATTTCAGTGCAGACAAA 58.714 40.909 0.00 0.00 35.14 2.83
1617 3915 8.967664 AACCACTCTCTGACTATTACTAGTAG 57.032 38.462 2.23 0.00 38.33 2.57
1637 3949 5.240844 ACCTAACTTATGTTCAGCAAACCAC 59.759 40.000 0.00 0.00 37.03 4.16
1678 3990 3.009723 TGCCTTACAACTAGAGCAATGC 58.990 45.455 0.00 0.00 0.00 3.56
1737 4182 9.467258 AAAGTTATGAAGACAAACATGATTGTG 57.533 29.630 24.12 7.05 43.31 3.33
1760 4207 4.886247 TTACCAACACGACTTCCAAAAG 57.114 40.909 0.00 0.00 38.54 2.27
1803 4250 4.218312 ACCCAGAAGAAGACAAATTTGCT 58.782 39.130 18.12 12.78 0.00 3.91
1804 4251 4.590850 ACCCAGAAGAAGACAAATTTGC 57.409 40.909 18.12 10.76 0.00 3.68
1820 4267 5.589855 TGCAATGACTATTATCACAACCCAG 59.410 40.000 0.00 0.00 0.00 4.45
1821 4268 5.504853 TGCAATGACTATTATCACAACCCA 58.495 37.500 0.00 0.00 0.00 4.51
1822 4269 6.449635 TTGCAATGACTATTATCACAACCC 57.550 37.500 0.00 0.00 0.00 4.11
1823 4270 8.755696 TTTTTGCAATGACTATTATCACAACC 57.244 30.769 0.00 0.00 0.00 3.77
1826 4273 9.791820 CTCATTTTTGCAATGACTATTATCACA 57.208 29.630 0.00 0.00 33.51 3.58
1827 4274 9.241317 CCTCATTTTTGCAATGACTATTATCAC 57.759 33.333 0.00 0.00 33.51 3.06
1829 4276 8.139989 AGCCTCATTTTTGCAATGACTATTATC 58.860 33.333 0.00 0.00 33.51 1.75
1830 4277 7.924412 CAGCCTCATTTTTGCAATGACTATTAT 59.076 33.333 0.00 0.00 33.51 1.28
1831 4278 7.122501 TCAGCCTCATTTTTGCAATGACTATTA 59.877 33.333 0.00 0.00 33.51 0.98
1832 4279 6.071221 TCAGCCTCATTTTTGCAATGACTATT 60.071 34.615 0.00 0.00 33.51 1.73
1833 4280 5.419788 TCAGCCTCATTTTTGCAATGACTAT 59.580 36.000 0.00 0.00 33.51 2.12
1834 4281 4.766373 TCAGCCTCATTTTTGCAATGACTA 59.234 37.500 0.00 0.00 33.51 2.59
1835 4282 3.575256 TCAGCCTCATTTTTGCAATGACT 59.425 39.130 0.00 0.00 33.51 3.41
1836 4283 3.916761 TCAGCCTCATTTTTGCAATGAC 58.083 40.909 0.00 0.00 33.51 3.06
1837 4284 4.811969 ATCAGCCTCATTTTTGCAATGA 57.188 36.364 0.00 0.00 35.56 2.57
1838 4285 5.873179 AAATCAGCCTCATTTTTGCAATG 57.127 34.783 0.00 0.00 0.00 2.82
1839 4286 7.444792 TGTTAAAATCAGCCTCATTTTTGCAAT 59.555 29.630 0.00 0.00 35.52 3.56
1840 4287 6.765036 TGTTAAAATCAGCCTCATTTTTGCAA 59.235 30.769 0.00 0.00 35.52 4.08
1841 4288 6.286758 TGTTAAAATCAGCCTCATTTTTGCA 58.713 32.000 0.00 0.00 35.52 4.08
1842 4289 6.783892 TGTTAAAATCAGCCTCATTTTTGC 57.216 33.333 0.00 0.00 35.52 3.68
1843 4290 9.211485 AGAATGTTAAAATCAGCCTCATTTTTG 57.789 29.630 0.00 0.00 35.52 2.44
1844 4291 9.783081 AAGAATGTTAAAATCAGCCTCATTTTT 57.217 25.926 0.00 0.00 35.52 1.94
1846 4293 9.860898 GTAAGAATGTTAAAATCAGCCTCATTT 57.139 29.630 0.00 0.00 0.00 2.32
1847 4294 8.184192 CGTAAGAATGTTAAAATCAGCCTCATT 58.816 33.333 0.00 0.00 43.02 2.57
1848 4295 7.697691 CGTAAGAATGTTAAAATCAGCCTCAT 58.302 34.615 0.00 0.00 43.02 2.90
1849 4296 7.072177 CGTAAGAATGTTAAAATCAGCCTCA 57.928 36.000 0.00 0.00 43.02 3.86
1872 4319 4.926860 TGTTCAAGCAATGACTATGTCG 57.073 40.909 0.00 0.00 37.92 4.35
1876 4323 6.366877 GCACAAAATGTTCAAGCAATGACTAT 59.633 34.615 0.00 0.00 37.92 2.12
1985 4432 9.995003 AATTGTCTTTTAACATGCTAAAATCCA 57.005 25.926 13.04 10.25 31.94 3.41
2066 4516 4.470304 AGTATAAGTTCAAGAGGTGGGTCC 59.530 45.833 0.00 0.00 0.00 4.46
2089 4539 5.163622 GCAAATTCTAGATGCCTGCAAGTAA 60.164 40.000 5.63 0.00 34.03 2.24
2388 4839 5.277538 GCATTAGGCTGGAAGATAAGAAACG 60.278 44.000 0.00 0.00 40.25 3.60
2468 5062 2.420022 GACAGCTACGCAATTCACCATT 59.580 45.455 0.00 0.00 0.00 3.16
2481 5075 4.184629 CAAGAATACACAGGGACAGCTAC 58.815 47.826 0.00 0.00 0.00 3.58
2485 5079 4.320494 GCAAACAAGAATACACAGGGACAG 60.320 45.833 0.00 0.00 0.00 3.51
2499 5093 1.340889 GGGTCATTGCAGCAAACAAGA 59.659 47.619 12.97 5.43 0.00 3.02
2534 5128 1.558167 TAGGCCGGGCAAATCAGTGA 61.558 55.000 31.59 0.00 0.00 3.41
2547 5141 6.934645 TGGATAAGTTATGAGAAAATAGGCCG 59.065 38.462 0.00 0.00 0.00 6.13
2622 5216 3.656559 AGAACAAAACAGAATGCCATGC 58.343 40.909 0.00 0.00 42.53 4.06
2626 5220 5.580297 TGTCAAAAGAACAAAACAGAATGCC 59.420 36.000 0.00 0.00 42.53 4.40
2627 5221 6.645700 TGTCAAAAGAACAAAACAGAATGC 57.354 33.333 0.00 0.00 42.53 3.56
2692 5286 6.875948 ACAACTAAAGTGCACAATGATACA 57.124 33.333 21.04 0.00 0.00 2.29
2729 5323 7.716998 GGACACATATTCATTCAGTTAGACCAT 59.283 37.037 0.00 0.00 0.00 3.55
2777 5371 2.611292 GTGTGACTGAATGATAGCTGGC 59.389 50.000 0.00 0.00 0.00 4.85
2796 5390 4.339247 ACCAACAATCCTCTTGTCAAAGTG 59.661 41.667 0.00 0.00 34.78 3.16
2873 5467 2.224185 TGAAGTTTCGCAGCCTCTGTTA 60.224 45.455 0.00 0.00 33.43 2.41
2966 5560 5.105997 CCTCTGAAAAGGAGCAAAATAGTGG 60.106 44.000 0.00 0.00 38.87 4.00
3164 5758 7.455447 CGGAAATAAAGTTGGAATTTCAATGC 58.545 34.615 1.62 0.00 40.02 3.56
3222 5816 1.194280 CGTCGTCATCATGTCCGTCG 61.194 60.000 0.00 5.25 0.00 5.12
3357 5956 2.309528 TAAACTCTATGGGCACGCAG 57.690 50.000 0.00 0.00 0.00 5.18
3522 6123 2.557317 AGGCAAGTCGAAAACGAAAGA 58.443 42.857 0.00 0.00 0.00 2.52
3528 6129 3.004315 TGGATGAAAGGCAAGTCGAAAAC 59.996 43.478 0.00 0.00 0.00 2.43
3538 6139 4.263905 ACCTTATTGACTGGATGAAAGGCA 60.264 41.667 0.00 0.00 36.33 4.75
3549 6150 9.643693 AAGATGCAATTAAAACCTTATTGACTG 57.356 29.630 0.00 0.00 0.00 3.51
3571 6172 0.749454 GGAGCCATCCACGCAAAGAT 60.749 55.000 0.00 0.00 45.87 2.40
3584 6185 2.425592 CCACTGAACACGGAGCCA 59.574 61.111 0.00 0.00 0.00 4.75
3591 6192 1.001378 GTTGATGTGGCCACTGAACAC 60.001 52.381 34.75 20.63 35.75 3.32
3592 6193 1.133823 AGTTGATGTGGCCACTGAACA 60.134 47.619 34.75 24.17 0.00 3.18
3593 6194 1.267806 CAGTTGATGTGGCCACTGAAC 59.732 52.381 34.75 29.25 0.00 3.18
3596 6197 1.321474 AACAGTTGATGTGGCCACTG 58.679 50.000 34.75 25.14 43.00 3.66
3627 6228 6.767524 AAACGATGCTCCCATAACAAATTA 57.232 33.333 0.00 0.00 0.00 1.40
3638 6239 0.521735 AAAGCGAAAACGATGCTCCC 59.478 50.000 0.00 0.00 38.17 4.30
3639 6240 1.196808 TCAAAGCGAAAACGATGCTCC 59.803 47.619 0.00 0.00 38.17 4.70
3682 6283 4.977741 TTTACCGTCATCAAAACTCGAC 57.022 40.909 0.00 0.00 0.00 4.20
3686 6291 6.708285 AGGTCTATTTACCGTCATCAAAACT 58.292 36.000 0.00 0.00 44.77 2.66
3699 6304 7.159372 TGACAGTTTCCTCAAGGTCTATTTAC 58.841 38.462 0.00 0.00 36.34 2.01
3704 6309 5.306937 TGATTGACAGTTTCCTCAAGGTCTA 59.693 40.000 0.00 0.00 36.34 2.59
3708 6313 4.320788 GCTTGATTGACAGTTTCCTCAAGG 60.321 45.833 15.19 0.00 40.31 3.61
3742 6347 8.894731 TCAGCAAACAACTAAATGTTACTACAA 58.105 29.630 0.00 0.00 42.49 2.41
3745 6350 9.724839 GTTTCAGCAAACAACTAAATGTTACTA 57.275 29.630 0.00 0.00 42.49 1.82
3746 6351 8.628882 GTTTCAGCAAACAACTAAATGTTACT 57.371 30.769 0.00 0.00 42.49 2.24
3763 6368 3.703556 TCCAAGGTTTGAATGTTTCAGCA 59.296 39.130 0.00 0.00 41.38 4.41
3792 6397 1.953686 GTTGGTGAAGCCTGCACTTTA 59.046 47.619 2.13 0.00 38.35 1.85
3871 6497 6.125327 TCGCACTTTCAATTGTTAAGTTGA 57.875 33.333 19.19 17.21 30.08 3.18
3898 6524 4.096382 CACGGGGAATTTCATCGAGAATTT 59.904 41.667 14.52 0.00 35.83 1.82
3908 6534 3.059386 GCGCCACGGGGAATTTCA 61.059 61.111 8.67 0.00 35.59 2.69
3941 6567 2.574212 CGATTTGGCGCGACAAGC 60.574 61.111 28.46 21.82 43.95 4.01
3942 6568 2.098298 CCGATTTGGCGCGACAAG 59.902 61.111 28.46 16.50 0.00 3.16
3943 6569 2.177654 GAACCGATTTGGCGCGACAA 62.178 55.000 26.47 26.47 43.94 3.18
4001 6627 5.235516 GTCTCCCTTGAGTCGTAAATTTCA 58.764 41.667 0.00 0.00 39.75 2.69
4019 6650 1.270907 TGAGCTTTCCTCTGGTCTCC 58.729 55.000 0.00 0.00 41.35 3.71
4067 6706 8.533657 TGTTGATCCTTGCAAATCATAAAAGAT 58.466 29.630 13.25 0.11 32.24 2.40
4068 6707 7.894708 TGTTGATCCTTGCAAATCATAAAAGA 58.105 30.769 13.25 0.00 32.24 2.52
4069 6708 8.712285 ATGTTGATCCTTGCAAATCATAAAAG 57.288 30.769 13.25 0.00 32.24 2.27
4070 6709 9.153721 GAATGTTGATCCTTGCAAATCATAAAA 57.846 29.630 13.25 0.00 32.24 1.52
4124 6763 4.161377 AGACCATCTTCTGAGCTCTTTACC 59.839 45.833 16.19 0.00 0.00 2.85
4129 6769 2.109774 CCAGACCATCTTCTGAGCTCT 58.890 52.381 16.19 0.00 45.19 4.09
4147 6787 1.687840 CTCCCCATCCGTGGTACCA 60.688 63.158 11.60 11.60 44.48 3.25
4150 6790 2.039787 TGCTCCCCATCCGTGGTA 59.960 61.111 0.00 0.00 44.48 3.25
4162 6805 0.884514 GACCTTTGCCTTTCTGCTCC 59.115 55.000 0.00 0.00 0.00 4.70
4175 6818 4.736896 GCGACGGCGAGGACCTTT 62.737 66.667 18.90 0.00 40.82 3.11


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

AutoCloner maintained by Alex Coulton.