Multiple sequence alignment - TraesCS3D01G355000

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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 TraesCS3D01G355000 chr3D 100.000 5726 0 0 1 5726 466279663 466285388 0.000000e+00 10575.0
1 TraesCS3D01G355000 chr3B 93.009 2117 101 12 2220 4300 620201132 620203237 0.000000e+00 3046.0
2 TraesCS3D01G355000 chr3B 95.747 823 24 6 4913 5726 620204730 620205550 0.000000e+00 1315.0
3 TraesCS3D01G355000 chr3B 95.906 635 26 0 739 1373 620182396 620183030 0.000000e+00 1029.0
4 TraesCS3D01G355000 chr3B 92.297 740 34 7 1485 2219 620183203 620183924 0.000000e+00 1029.0
5 TraesCS3D01G355000 chr3B 91.333 750 52 5 1 741 620181528 620182273 0.000000e+00 1013.0
6 TraesCS3D01G355000 chr3B 87.173 382 19 11 4486 4866 620204225 620204577 1.920000e-109 407.0
7 TraesCS3D01G355000 chr3B 82.625 259 37 7 3083 3338 39227436 39227183 7.470000e-54 222.0
8 TraesCS3D01G355000 chr3B 93.103 58 3 1 1373 1429 620183072 620183129 3.680000e-12 84.2
9 TraesCS3D01G355000 chr3A 94.406 1287 41 11 4465 5726 609477173 609478453 0.000000e+00 1949.0
10 TraesCS3D01G355000 chr3A 93.277 1190 60 12 1637 2824 609474425 609475596 0.000000e+00 1736.0
11 TraesCS3D01G355000 chr3A 90.666 1232 74 23 2874 4099 609475596 609476792 0.000000e+00 1600.0
12 TraesCS3D01G355000 chr3A 91.595 809 49 8 1 794 609471874 609472678 0.000000e+00 1099.0
13 TraesCS3D01G355000 chr3A 94.295 596 32 1 780 1373 609473260 609473855 0.000000e+00 911.0
14 TraesCS3D01G355000 chr3A 90.732 205 15 1 1438 1638 609474107 609474311 2.630000e-68 270.0
15 TraesCS3D01G355000 chr3A 91.935 124 9 1 4162 4284 609476801 609476924 7.630000e-39 172.0
16 TraesCS3D01G355000 chr3A 90.769 65 5 1 4308 4371 8867776 8867840 1.020000e-12 86.1
17 TraesCS3D01G355000 chr3A 94.545 55 2 1 1373 1426 609473906 609473960 3.680000e-12 84.2
18 TraesCS3D01G355000 chr1D 80.052 767 105 25 1831 2581 473346786 473346052 5.080000e-145 525.0
19 TraesCS3D01G355000 chr1D 86.184 152 20 1 2895 3045 473343013 473342862 4.590000e-36 163.0
20 TraesCS3D01G355000 chr1D 82.482 137 20 4 1 135 282277424 282277558 3.620000e-22 117.0
21 TraesCS3D01G355000 chr1B 79.021 286 47 7 2833 3105 658191998 658191713 3.520000e-42 183.0
22 TraesCS3D01G355000 chr1B 79.310 203 39 3 2069 2268 288810432 288810230 7.740000e-29 139.0
23 TraesCS3D01G355000 chr5B 83.721 172 26 2 2061 2231 101324236 101324066 1.650000e-35 161.0
24 TraesCS3D01G355000 chr5D 82.558 172 28 2 2061 2231 94027366 94027196 3.570000e-32 150.0
25 TraesCS3D01G355000 chr5A 82.558 172 28 2 2061 2231 87933932 87933762 3.570000e-32 150.0
26 TraesCS3D01G355000 chr4A 81.176 170 30 2 2063 2231 684516813 684516645 1.000000e-27 135.0
27 TraesCS3D01G355000 chr4A 89.796 49 4 1 4324 4371 87402663 87402615 1.720000e-05 62.1
28 TraesCS3D01G355000 chr4B 84.173 139 21 1 2061 2198 602783914 602783776 3.600000e-27 134.0
29 TraesCS3D01G355000 chr1A 84.559 136 20 1 1 135 354290757 354290892 3.600000e-27 134.0
30 TraesCS3D01G355000 chr6D 82.653 98 15 2 3242 3338 163436810 163436906 1.020000e-12 86.1
31 TraesCS3D01G355000 chr6A 89.394 66 6 1 4308 4372 19821577 19821512 1.320000e-11 82.4
32 TraesCS3D01G355000 chr2B 88.136 59 7 0 3162 3220 297140908 297140850 2.860000e-08 71.3
33 TraesCS3D01G355000 chr6B 87.931 58 6 1 4308 4364 554605325 554605268 3.700000e-07 67.6


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 TraesCS3D01G355000 chr3D 466279663 466285388 5725 False 10575.000000 10575 100.000000 1 5726 1 chr3D.!!$F1 5725
1 TraesCS3D01G355000 chr3B 620201132 620205550 4418 False 1589.333333 3046 91.976333 2220 5726 3 chr3B.!!$F2 3506
2 TraesCS3D01G355000 chr3B 620181528 620183924 2396 False 788.800000 1029 93.159750 1 2219 4 chr3B.!!$F1 2218
3 TraesCS3D01G355000 chr3A 609471874 609478453 6579 False 977.650000 1949 92.681375 1 5726 8 chr3A.!!$F2 5725
4 TraesCS3D01G355000 chr1D 473342862 473346786 3924 True 344.000000 525 83.118000 1831 3045 2 chr1D.!!$R1 1214

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
453 458 0.899019 ACTCGCTCTCTTCCCTTTCC 59.101 55.000 0.00 0.00 0.00 3.13 F
1333 2077 1.551964 AAGGGGAGGAGTAGGGGGA 60.552 63.158 0.00 0.00 0.00 4.81 F
2562 3633 1.082496 GCAAGACACGCAGTTCTGC 60.082 57.895 13.97 13.97 41.61 4.26 F
4213 8024 0.519077 CTTTCTTGCCGTGCTTCTCC 59.481 55.000 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 3068 1.131638 AAGGCTCAACTGTCCACTCA 58.868 50.000 0.00 0.0 0.00 3.41 R
3103 6901 1.295423 GGAGAGTAGCCGCACCAAA 59.705 57.895 0.00 0.0 0.00 3.28 R
4417 8404 0.034616 GACAGCAGAGCAAGTCACCT 59.965 55.000 8.91 0.0 36.42 4.00 R
5240 10060 1.825191 CAGGAACCATGGGGCATCG 60.825 63.158 18.09 0.0 37.90 3.84 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
69 70 2.596904 AGTAAATCGGGTCATGACGG 57.403 50.000 19.33 13.63 0.00 4.79
215 216 1.403814 CAGGCTCCTTATCACCGAGA 58.596 55.000 0.00 0.00 0.00 4.04
222 223 3.497332 TCCTTATCACCGAGACCTATGG 58.503 50.000 0.00 0.00 0.00 2.74
272 273 5.299949 CCTTGCTTTATGTTTCCTTGCTTT 58.700 37.500 0.00 0.00 0.00 3.51
289 290 2.483714 GCTTTCATGCGGAGGTCTGATA 60.484 50.000 0.00 0.00 0.00 2.15
344 349 5.831702 GAGACCTGGTTCTTCTCGTATTA 57.168 43.478 0.00 0.00 0.00 0.98
453 458 0.899019 ACTCGCTCTCTTCCCTTTCC 59.101 55.000 0.00 0.00 0.00 3.13
462 470 2.849318 CTCTTCCCTTTCCCATCTCCTT 59.151 50.000 0.00 0.00 0.00 3.36
463 471 2.846827 TCTTCCCTTTCCCATCTCCTTC 59.153 50.000 0.00 0.00 0.00 3.46
465 473 3.795755 TCCCTTTCCCATCTCCTTCTA 57.204 47.619 0.00 0.00 0.00 2.10
466 474 3.658725 TCCCTTTCCCATCTCCTTCTAG 58.341 50.000 0.00 0.00 0.00 2.43
467 475 3.014110 TCCCTTTCCCATCTCCTTCTAGT 59.986 47.826 0.00 0.00 0.00 2.57
468 476 3.783082 CCCTTTCCCATCTCCTTCTAGTT 59.217 47.826 0.00 0.00 0.00 2.24
480 490 9.219603 CATCTCCTTCTAGTTTGTGATTGTTTA 57.780 33.333 0.00 0.00 0.00 2.01
538 548 2.224695 TGGAACGAGGTGTGAGTCTAGA 60.225 50.000 0.00 0.00 0.00 2.43
541 551 4.639310 GGAACGAGGTGTGAGTCTAGATTA 59.361 45.833 0.00 0.00 0.00 1.75
546 556 7.091443 ACGAGGTGTGAGTCTAGATTAAAAAG 58.909 38.462 0.00 0.00 0.00 2.27
547 557 7.039923 ACGAGGTGTGAGTCTAGATTAAAAAGA 60.040 37.037 0.00 0.00 0.00 2.52
581 591 8.301720 CGCCACTACATTTGAGGTATATAGTTA 58.698 37.037 0.00 0.00 0.00 2.24
644 657 2.367567 ACGGTCCACAAACAGATAGTGT 59.632 45.455 0.00 0.00 43.24 3.55
645 658 2.736721 CGGTCCACAAACAGATAGTGTG 59.263 50.000 0.00 0.00 40.26 3.82
682 695 2.164827 TGTACACCGAAGATACGCACAT 59.835 45.455 0.00 0.00 0.00 3.21
692 705 4.033990 AGATACGCACATATATCTGCCG 57.966 45.455 7.31 5.60 36.89 5.69
741 887 2.220653 ACTAGTACCCTGTGCCGTAA 57.779 50.000 0.00 0.00 0.00 3.18
922 1666 2.041762 TGCTCTGCTCCTCCCCAT 59.958 61.111 0.00 0.00 0.00 4.00
1003 1747 3.335729 ACCGACCCAATCCACCCC 61.336 66.667 0.00 0.00 0.00 4.95
1266 2010 1.593787 CTGCGAGGGTGATGACTGT 59.406 57.895 0.00 0.00 0.00 3.55
1278 2022 2.037641 TGATGACTGTGTGGTTCTGGAG 59.962 50.000 0.00 0.00 0.00 3.86
1296 2040 2.908015 GGCGACCCTGATAAGCCA 59.092 61.111 0.00 0.00 46.48 4.75
1333 2077 1.551964 AAGGGGAGGAGTAGGGGGA 60.552 63.158 0.00 0.00 0.00 4.81
1373 2117 1.671850 GGAGATCGTTGCGGTGAAAGA 60.672 52.381 0.00 0.00 0.00 2.52
1448 2386 7.976734 ACTTTGTCAAATCCGTTCAAATAACAA 59.023 29.630 0.00 0.00 0.00 2.83
1449 2387 8.879342 TTTGTCAAATCCGTTCAAATAACAAT 57.121 26.923 0.00 0.00 0.00 2.71
1450 2388 8.879342 TTGTCAAATCCGTTCAAATAACAATT 57.121 26.923 0.00 0.00 0.00 2.32
1513 2451 5.479306 TGGTTTACAGCTGAGAACATACTC 58.521 41.667 23.35 10.92 37.42 2.59
1552 2490 5.203358 TCTGATTCGTTAAAGTTGCATCG 57.797 39.130 0.00 0.00 0.00 3.84
1672 2729 7.439157 TGTCTTATCAAGCACATAATATGGC 57.561 36.000 5.16 5.55 33.60 4.40
1711 2768 8.695456 TGTTCTTACTGTCTATGAATATCTGCA 58.305 33.333 0.00 0.00 0.00 4.41
1730 2787 5.007626 TCTGCAGTTTCAGTTCATGTTGTAC 59.992 40.000 14.67 0.00 35.63 2.90
1757 2815 5.669477 ACAGACATGAGGATTAGAGCTTTC 58.331 41.667 0.00 0.00 0.00 2.62
1803 2861 1.559682 TCCCTGTGGTAGCATTCCTTC 59.440 52.381 0.00 0.00 0.00 3.46
1863 2921 2.295885 GCAGATAGCATGCAAGGACTT 58.704 47.619 21.98 0.00 43.31 3.01
1864 2922 2.290093 GCAGATAGCATGCAAGGACTTC 59.710 50.000 21.98 5.52 43.31 3.01
1865 2923 2.877168 CAGATAGCATGCAAGGACTTCC 59.123 50.000 21.98 0.00 0.00 3.46
1907 2965 1.980765 TGTTCTGAGATGCCCTTCAGT 59.019 47.619 7.91 0.00 0.00 3.41
1919 2977 2.237392 GCCCTTCAGTACCACTTCTCAT 59.763 50.000 0.00 0.00 0.00 2.90
1949 3007 2.083774 TGCAGCATGGTAAGTAGCAAC 58.916 47.619 4.56 0.00 37.24 4.17
1980 3039 5.972107 ACTCCCTGTCATTGATTCTTTTG 57.028 39.130 0.00 0.00 0.00 2.44
1984 3043 4.240096 CCTGTCATTGATTCTTTTGGCAC 58.760 43.478 0.00 0.00 0.00 5.01
2009 3068 8.639761 ACTATGGTTACAAAGATTATCGTAGCT 58.360 33.333 0.00 0.00 0.00 3.32
2014 3073 7.043325 GGTTACAAAGATTATCGTAGCTGAGTG 60.043 40.741 0.00 0.00 0.00 3.51
2043 3102 4.334552 TGAGCCTTTCTAATGTGATTGCA 58.665 39.130 0.00 0.00 0.00 4.08
2044 3103 4.951715 TGAGCCTTTCTAATGTGATTGCAT 59.048 37.500 0.00 0.00 0.00 3.96
2045 3104 5.419788 TGAGCCTTTCTAATGTGATTGCATT 59.580 36.000 0.00 0.00 41.42 3.56
2046 3105 6.602803 TGAGCCTTTCTAATGTGATTGCATTA 59.397 34.615 0.00 0.00 39.50 1.90
2047 3106 7.122501 TGAGCCTTTCTAATGTGATTGCATTAA 59.877 33.333 0.00 0.00 39.80 1.40
2048 3107 7.486647 AGCCTTTCTAATGTGATTGCATTAAG 58.513 34.615 0.00 0.00 39.80 1.85
2049 3108 6.199719 GCCTTTCTAATGTGATTGCATTAAGC 59.800 38.462 0.00 0.00 39.80 3.09
2050 3109 7.486647 CCTTTCTAATGTGATTGCATTAAGCT 58.513 34.615 0.00 0.00 45.94 3.74
2051 3110 8.623903 CCTTTCTAATGTGATTGCATTAAGCTA 58.376 33.333 0.00 0.00 45.94 3.32
2181 3240 5.105756 ACTGACAAGGAAACAAAGTGGAAAG 60.106 40.000 0.00 0.00 0.00 2.62
2193 3252 3.857157 AGTGGAAAGTACTGAGGCAAA 57.143 42.857 0.00 0.00 0.00 3.68
2562 3633 1.082496 GCAAGACACGCAGTTCTGC 60.082 57.895 13.97 13.97 41.61 4.26
2723 5153 1.333308 CGATGTTTGTGCTGTGTGGAA 59.667 47.619 0.00 0.00 0.00 3.53
2775 5206 4.469657 TCATTTCTAGCCACTTGGTTTGT 58.530 39.130 0.00 0.00 37.57 2.83
2776 5207 5.626142 TCATTTCTAGCCACTTGGTTTGTA 58.374 37.500 0.00 0.00 37.57 2.41
2841 5273 9.739786 CAAATAATTTAAACATGTTTCTTCGCC 57.260 29.630 26.46 0.00 34.23 5.54
2842 5274 9.705290 AAATAATTTAAACATGTTTCTTCGCCT 57.295 25.926 26.46 3.73 34.23 5.52
2843 5275 9.705290 AATAATTTAAACATGTTTCTTCGCCTT 57.295 25.926 26.46 13.48 34.23 4.35
2844 5276 7.637709 AATTTAAACATGTTTCTTCGCCTTC 57.362 32.000 26.46 0.00 34.23 3.46
2845 5277 6.385649 TTTAAACATGTTTCTTCGCCTTCT 57.614 33.333 26.46 1.68 34.23 2.85
2846 5278 4.489679 AAACATGTTTCTTCGCCTTCTC 57.510 40.909 18.13 0.00 0.00 2.87
2847 5279 3.409026 ACATGTTTCTTCGCCTTCTCT 57.591 42.857 0.00 0.00 0.00 3.10
2849 5281 4.499183 ACATGTTTCTTCGCCTTCTCTAG 58.501 43.478 0.00 0.00 0.00 2.43
2850 5282 8.270489 TAAACATGTTTCTTCGCCTTCTCTAGG 61.270 40.741 26.46 0.00 39.23 3.02
2851 5283 2.897969 TGTTTCTTCGCCTTCTCTAGGT 59.102 45.455 0.00 0.00 46.61 3.08
2852 5284 3.323979 TGTTTCTTCGCCTTCTCTAGGTT 59.676 43.478 0.00 0.00 46.61 3.50
2853 5285 4.525487 TGTTTCTTCGCCTTCTCTAGGTTA 59.475 41.667 0.00 0.00 46.61 2.85
2854 5286 5.187186 TGTTTCTTCGCCTTCTCTAGGTTAT 59.813 40.000 0.00 0.00 46.61 1.89
2856 5288 5.517322 TCTTCGCCTTCTCTAGGTTATTC 57.483 43.478 0.00 0.00 46.61 1.75
2858 5290 5.598830 TCTTCGCCTTCTCTAGGTTATTCAT 59.401 40.000 0.00 0.00 46.61 2.57
2859 5291 5.871396 TCGCCTTCTCTAGGTTATTCATT 57.129 39.130 0.00 0.00 46.61 2.57
2860 5292 5.844004 TCGCCTTCTCTAGGTTATTCATTC 58.156 41.667 0.00 0.00 46.61 2.67
2862 5294 4.449405 GCCTTCTCTAGGTTATTCATTCGC 59.551 45.833 0.00 0.00 46.61 4.70
2864 5296 6.516860 GCCTTCTCTAGGTTATTCATTCGCTA 60.517 42.308 0.00 0.00 46.61 4.26
2865 5297 7.607250 CCTTCTCTAGGTTATTCATTCGCTAT 58.393 38.462 0.00 0.00 39.39 2.97
2866 5298 7.543868 CCTTCTCTAGGTTATTCATTCGCTATG 59.456 40.741 0.00 0.00 39.39 2.23
2867 5299 6.925211 TCTCTAGGTTATTCATTCGCTATGG 58.075 40.000 0.00 0.00 34.85 2.74
2868 5300 6.719829 TCTCTAGGTTATTCATTCGCTATGGA 59.280 38.462 0.00 0.00 34.85 3.41
2870 5302 8.589701 TCTAGGTTATTCATTCGCTATGGATA 57.410 34.615 0.00 0.00 34.21 2.59
2871 5303 9.201989 TCTAGGTTATTCATTCGCTATGGATAT 57.798 33.333 0.00 0.00 35.16 1.63
2872 5304 9.469807 CTAGGTTATTCATTCGCTATGGATATC 57.530 37.037 0.00 0.00 35.16 1.63
3021 6819 1.141053 AGAGCCGTGGATATGGGTTTC 59.859 52.381 0.00 0.00 43.54 2.78
3098 6896 6.413818 GCCGTGTGAGTATGTTTTATAAATGC 59.586 38.462 0.00 0.00 0.00 3.56
3215 7014 3.118629 TGCAGTATGGATGGAGTGTCTTC 60.119 47.826 0.00 0.00 35.86 2.87
3363 7163 4.385754 GGAACTCCTTAATCTGAAGCCCAT 60.386 45.833 0.00 0.00 0.00 4.00
3397 7197 5.138125 TCCTCATTCTGCCAATTTGTTTC 57.862 39.130 0.00 0.00 0.00 2.78
3425 7225 1.368641 TGCAATGACACGCCATCTAC 58.631 50.000 0.00 0.00 0.00 2.59
3428 7228 2.032549 GCAATGACACGCCATCTACATC 60.033 50.000 0.00 0.00 0.00 3.06
3453 7253 5.764686 AGACTGTTCTGTGACATAATTTGCA 59.235 36.000 0.00 0.00 0.00 4.08
3499 7299 1.076332 GCCAGTGTCACGTGTAATCC 58.924 55.000 16.51 0.59 0.00 3.01
3555 7361 9.528018 CTTTGCTGACTTACCTTTAATTTGAAA 57.472 29.630 0.00 0.00 0.00 2.69
3573 7379 0.620556 AAATGCAGGAGATGGACGGT 59.379 50.000 0.00 0.00 28.84 4.83
3666 7472 2.034685 CAGTCGACCAGTGTCTTCTTCA 59.965 50.000 13.01 0.00 39.47 3.02
3773 7579 2.166664 GTGCCAAAGTTGTTTACCACCA 59.833 45.455 0.00 0.00 0.00 4.17
3783 7589 2.635915 TGTTTACCACCACGGAAGAGAT 59.364 45.455 0.00 0.00 38.63 2.75
3814 7620 0.947180 CCCGTTTGGATTCGTCACGT 60.947 55.000 0.00 0.00 37.49 4.49
3840 7646 2.174319 GCGGCAGGAATCGGAGAAC 61.174 63.158 0.00 0.00 43.58 3.01
3872 7678 1.143305 CTCAACAAGCAGGTCAGTCG 58.857 55.000 0.00 0.00 0.00 4.18
3881 7687 4.295119 GGTCAGTCGGTGCGTGGT 62.295 66.667 0.00 0.00 0.00 4.16
3882 7688 2.733593 GTCAGTCGGTGCGTGGTC 60.734 66.667 0.00 0.00 0.00 4.02
3883 7689 2.910479 TCAGTCGGTGCGTGGTCT 60.910 61.111 0.00 0.00 0.00 3.85
3884 7690 2.734723 CAGTCGGTGCGTGGTCTG 60.735 66.667 0.00 0.00 0.00 3.51
3885 7691 3.991051 AGTCGGTGCGTGGTCTGG 61.991 66.667 0.00 0.00 0.00 3.86
3886 7692 3.986006 GTCGGTGCGTGGTCTGGA 61.986 66.667 0.00 0.00 0.00 3.86
3887 7693 3.986006 TCGGTGCGTGGTCTGGAC 61.986 66.667 0.00 0.00 0.00 4.02
3993 7799 6.646240 TGAAGCTAATTTTCAAGCACCATTTC 59.354 34.615 1.03 0.00 41.32 2.17
4213 8024 0.519077 CTTTCTTGCCGTGCTTCTCC 59.481 55.000 0.00 0.00 0.00 3.71
4264 8075 8.953313 TGTAACAGACGAGTAGAAATCATAAGA 58.047 33.333 0.00 0.00 0.00 2.10
4268 8080 9.522804 ACAGACGAGTAGAAATCATAAGAATTC 57.477 33.333 0.00 0.00 34.54 2.17
4300 8112 4.110072 TCAGACCTACAGTACTACCTCCT 58.890 47.826 0.00 0.00 0.00 3.69
4301 8113 4.163839 TCAGACCTACAGTACTACCTCCTC 59.836 50.000 0.00 0.00 0.00 3.71
4302 8114 4.164604 CAGACCTACAGTACTACCTCCTCT 59.835 50.000 0.00 0.00 0.00 3.69
4303 8115 4.164604 AGACCTACAGTACTACCTCCTCTG 59.835 50.000 0.00 0.00 0.00 3.35
4304 8116 3.851374 ACCTACAGTACTACCTCCTCTGT 59.149 47.826 0.00 0.00 41.32 3.41
4305 8117 4.080413 ACCTACAGTACTACCTCCTCTGTC 60.080 50.000 0.00 0.00 39.54 3.51
4364 8351 8.302515 TCTAAGACAACTAATTTAGGACGGAT 57.697 34.615 8.26 0.00 0.00 4.18
4365 8352 8.195436 TCTAAGACAACTAATTTAGGACGGATG 58.805 37.037 8.26 0.90 0.00 3.51
4417 8404 3.517500 TCATGTTGCCTACTGTATCCACA 59.482 43.478 0.00 0.00 0.00 4.17
4427 8414 2.472695 TGTATCCACAGGTGACTTGC 57.527 50.000 0.00 0.00 40.21 4.01
4428 8415 1.977854 TGTATCCACAGGTGACTTGCT 59.022 47.619 0.00 0.00 40.21 3.91
4435 8488 0.250209 CAGGTGACTTGCTCTGCTGT 60.250 55.000 0.00 0.00 40.21 4.40
4442 8495 3.169155 TTGCTCTGCTGTCACCGCT 62.169 57.895 0.00 0.00 0.00 5.52
4462 8595 1.956170 GTGGTGCCACTGTCTCGTG 60.956 63.158 13.68 0.00 43.12 4.35
4463 8596 2.131067 TGGTGCCACTGTCTCGTGA 61.131 57.895 0.00 0.00 37.06 4.35
4474 8607 1.979155 TCTCGTGACAGCCTCCAGG 60.979 63.158 0.00 0.00 38.53 4.45
4494 8627 1.168714 CAACTAGGCAAACAGCTCCC 58.831 55.000 0.00 0.00 44.79 4.30
4584 9278 3.912899 AAAAATGGCCTGCTTTCCG 57.087 47.368 3.32 0.00 0.00 4.30
4588 9282 3.976701 ATGGCCTGCTTTCCGGTCG 62.977 63.158 3.32 0.00 0.00 4.79
4649 9343 2.535984 GCAGCACGTATAGACACACATC 59.464 50.000 0.00 0.00 0.00 3.06
4701 9395 9.750125 CATCTATAACACAACAGCTCTATACAA 57.250 33.333 0.00 0.00 0.00 2.41
5036 9856 0.521867 CACTTGCGGCATGATTCACG 60.522 55.000 21.01 0.00 0.00 4.35
5240 10060 3.833732 AGGGGAAAGAGTTGAGAAAACC 58.166 45.455 0.00 0.00 0.00 3.27
5261 10081 0.116940 ATGCCCCATGGTTCCTGTTT 59.883 50.000 11.73 0.00 0.00 2.83
5346 10173 7.404671 AAAACCGAGTGCATATTTTAGGAAT 57.595 32.000 0.00 0.00 0.00 3.01
5569 10421 3.960102 AGTGGTCTGAATTTTTCTTGCCA 59.040 39.130 0.00 0.00 0.00 4.92
5675 10529 0.396435 AGAAAGCACGGTCATGGACA 59.604 50.000 0.00 0.00 33.68 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 2.700773 GCGATCCACCAAGGGCAAC 61.701 63.158 0.00 0.00 38.24 4.17
174 175 2.808315 GAGAAGCCGAGCGATCCA 59.192 61.111 0.00 0.00 0.00 3.41
215 216 1.141019 CGCGCTACACACCATAGGT 59.859 57.895 5.56 0.00 35.62 3.08
222 223 0.806102 ACATCATCCGCGCTACACAC 60.806 55.000 5.56 0.00 0.00 3.82
272 273 1.040646 GGTATCAGACCTCCGCATGA 58.959 55.000 0.00 0.00 45.89 3.07
344 349 7.686434 ACCTACTAACACCACTCAACATTTAT 58.314 34.615 0.00 0.00 0.00 1.40
453 458 6.176183 ACAATCACAAACTAGAAGGAGATGG 58.824 40.000 0.00 0.00 0.00 3.51
462 470 8.651391 TTCGAACTAAACAATCACAAACTAGA 57.349 30.769 0.00 0.00 0.00 2.43
463 471 9.318041 CATTCGAACTAAACAATCACAAACTAG 57.682 33.333 0.00 0.00 0.00 2.57
465 473 7.703328 ACATTCGAACTAAACAATCACAAACT 58.297 30.769 0.00 0.00 0.00 2.66
466 474 7.908193 ACATTCGAACTAAACAATCACAAAC 57.092 32.000 0.00 0.00 0.00 2.93
467 475 8.832521 AGTACATTCGAACTAAACAATCACAAA 58.167 29.630 0.00 0.00 0.00 2.83
468 476 8.279800 CAGTACATTCGAACTAAACAATCACAA 58.720 33.333 0.00 0.00 0.00 3.33
480 490 9.436957 AACAGAAATATTCAGTACATTCGAACT 57.563 29.630 0.00 0.00 0.00 3.01
503 513 5.116180 CCTCGTTCCATCAATAGCTTAACA 58.884 41.667 0.00 0.00 0.00 2.41
538 548 6.156748 AGTGGCGGAGTTTTTCTTTTTAAT 57.843 33.333 0.00 0.00 0.00 1.40
541 551 4.399934 TGTAGTGGCGGAGTTTTTCTTTTT 59.600 37.500 0.00 0.00 0.00 1.94
546 556 4.023536 TCAAATGTAGTGGCGGAGTTTTTC 60.024 41.667 0.00 0.00 0.00 2.29
547 557 3.886505 TCAAATGTAGTGGCGGAGTTTTT 59.113 39.130 0.00 0.00 0.00 1.94
581 591 2.897969 ACGATACGGGAGCCTATCATTT 59.102 45.455 0.00 0.00 0.00 2.32
644 657 2.116533 CATGCATCTCCAAGGCGCA 61.117 57.895 10.83 0.00 36.95 6.09
645 658 0.815213 TACATGCATCTCCAAGGCGC 60.815 55.000 0.00 0.00 0.00 6.53
682 695 1.877576 CGGGCAGAGCGGCAGATATA 61.878 60.000 1.45 0.00 43.60 0.86
692 705 0.460311 ATGTACTACACGGGCAGAGC 59.540 55.000 0.00 0.00 0.00 4.09
781 1523 3.291383 CGGGGCCGTTTGCTTTCA 61.291 61.111 0.00 0.00 40.92 2.69
1026 1770 3.001406 AAACCCCGACCCGAGGAG 61.001 66.667 0.00 0.00 0.00 3.69
1128 1872 4.516195 GGCGAGCGGGAAGACCTC 62.516 72.222 0.00 0.00 36.97 3.85
1247 1991 1.812922 CAGTCATCACCCTCGCAGC 60.813 63.158 0.00 0.00 0.00 5.25
1266 2010 2.525629 TCGCCCTCCAGAACCACA 60.526 61.111 0.00 0.00 0.00 4.17
1278 2022 2.111251 GGCTTATCAGGGTCGCCC 59.889 66.667 6.80 6.80 45.90 6.13
1373 2117 2.839228 AGGAGATGCTCTTGTAAGGGT 58.161 47.619 0.00 0.00 0.00 4.34
1450 2388 7.036220 TCTAAAGCCACAAATTTCACGAAAAA 58.964 30.769 0.00 0.00 33.56 1.94
1513 2451 8.824781 ACGAATCAGATATTGTTTGAATCAGAG 58.175 33.333 0.00 0.00 0.00 3.35
1580 2518 6.434302 ACCCAATGATGAACCTTTGATGATA 58.566 36.000 0.00 0.00 0.00 2.15
1583 2521 5.410355 AACCCAATGATGAACCTTTGATG 57.590 39.130 0.00 0.00 0.00 3.07
1584 2522 6.438186 AAAACCCAATGATGAACCTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
1653 2710 6.378661 AGGAGCCATATTATGTGCTTGATA 57.621 37.500 16.03 0.00 37.07 2.15
1672 2729 5.244178 ACAGTAAGAACAGGTAGTCAAGGAG 59.756 44.000 0.00 0.00 0.00 3.69
1711 2768 5.462398 GTCGAGTACAACATGAACTGAAACT 59.538 40.000 0.00 3.68 0.00 2.66
1730 2787 4.556501 GCTCTAATCCTCATGTCTGTCGAG 60.557 50.000 0.00 0.00 0.00 4.04
1757 2815 7.125792 ACTGGTGTAGTATAATTCCTTCAGG 57.874 40.000 0.00 0.00 38.04 3.86
1803 2861 9.988350 GTAAATGTAACTGTAATTGGACTGATG 57.012 33.333 0.00 0.00 0.00 3.07
1863 2921 3.760035 GCGCGAGTGAGGGAAGGA 61.760 66.667 12.10 0.00 0.00 3.36
1864 2922 4.821589 GGCGCGAGTGAGGGAAGG 62.822 72.222 12.10 0.00 0.00 3.46
1865 2923 2.859273 AATGGCGCGAGTGAGGGAAG 62.859 60.000 12.10 0.00 0.00 3.46
1866 2924 2.852495 GAATGGCGCGAGTGAGGGAA 62.852 60.000 12.10 0.00 0.00 3.97
1907 2965 1.275010 TGCTTCGCATGAGAAGTGGTA 59.725 47.619 31.37 17.57 46.82 3.25
1919 2977 1.153920 CATGCTGCAATGCTTCGCA 60.154 52.632 16.47 16.47 44.86 5.10
1968 3027 6.610075 AACCATAGTGCCAAAAGAATCAAT 57.390 33.333 0.00 0.00 0.00 2.57
1977 3036 6.909550 AATCTTTGTAACCATAGTGCCAAA 57.090 33.333 0.00 0.00 0.00 3.28
1980 3039 6.482308 ACGATAATCTTTGTAACCATAGTGCC 59.518 38.462 0.00 0.00 0.00 5.01
1984 3043 8.916654 CAGCTACGATAATCTTTGTAACCATAG 58.083 37.037 0.00 0.00 0.00 2.23
2009 3068 1.131638 AAGGCTCAACTGTCCACTCA 58.868 50.000 0.00 0.00 0.00 3.41
2014 3073 4.154918 CACATTAGAAAGGCTCAACTGTCC 59.845 45.833 0.00 0.00 0.00 4.02
2047 3106 9.586435 GCATTTGGAAAACAGTAATTAATAGCT 57.414 29.630 0.00 0.00 0.00 3.32
2048 3107 9.364989 TGCATTTGGAAAACAGTAATTAATAGC 57.635 29.630 0.00 0.00 0.00 2.97
2051 3110 9.206870 CACTGCATTTGGAAAACAGTAATTAAT 57.793 29.630 9.55 0.00 37.31 1.40
2052 3111 7.170658 GCACTGCATTTGGAAAACAGTAATTAA 59.829 33.333 9.55 0.00 37.31 1.40
2053 3112 6.644592 GCACTGCATTTGGAAAACAGTAATTA 59.355 34.615 9.55 0.00 37.31 1.40
2181 3240 5.154222 GCACTTAAATGTTTGCCTCAGTAC 58.846 41.667 0.00 0.00 0.00 2.73
2193 3252 4.119136 GGCACACTTTTGCACTTAAATGT 58.881 39.130 0.00 0.00 44.94 2.71
2260 3319 2.349100 CTGATGTCTGGGGGATGGCC 62.349 65.000 0.00 0.00 0.00 5.36
2478 3543 6.135819 TCATGAATCAGGAATATGAGGCAT 57.864 37.500 0.00 0.00 31.44 4.40
2511 3576 3.449377 TGCAGGACCATATTTAGTCGTGA 59.551 43.478 17.69 6.30 46.62 4.35
2562 3633 2.225017 ACCAATAACAACAGGGGGAGTG 60.225 50.000 0.00 0.00 0.00 3.51
2652 5082 4.188462 TGCAACGTAAAGATATCACCCAG 58.812 43.478 5.32 0.00 0.00 4.45
2655 5085 5.107837 CGATCTGCAACGTAAAGATATCACC 60.108 44.000 5.32 0.00 30.83 4.02
2723 5153 6.500684 AACGATCTTGTAATCAACAGCATT 57.499 33.333 0.00 0.00 39.87 3.56
2823 5255 5.763204 AGAGAAGGCGAAGAAACATGTTTAA 59.237 36.000 23.33 0.00 32.11 1.52
2826 5258 3.744660 AGAGAAGGCGAAGAAACATGTT 58.255 40.909 4.92 4.92 0.00 2.71
2827 5259 3.409026 AGAGAAGGCGAAGAAACATGT 57.591 42.857 0.00 0.00 0.00 3.21
2828 5260 3.868077 CCTAGAGAAGGCGAAGAAACATG 59.132 47.826 0.00 0.00 38.97 3.21
2829 5261 4.130286 CCTAGAGAAGGCGAAGAAACAT 57.870 45.455 0.00 0.00 38.97 2.71
2830 5262 3.594603 CCTAGAGAAGGCGAAGAAACA 57.405 47.619 0.00 0.00 38.97 2.83
2840 5272 7.543868 CATAGCGAATGAATAACCTAGAGAAGG 59.456 40.741 0.00 0.00 44.07 3.46
2841 5273 7.543868 CCATAGCGAATGAATAACCTAGAGAAG 59.456 40.741 3.89 0.00 37.86 2.85
2842 5274 7.232737 TCCATAGCGAATGAATAACCTAGAGAA 59.767 37.037 3.89 0.00 37.86 2.87
2843 5275 6.719829 TCCATAGCGAATGAATAACCTAGAGA 59.280 38.462 3.89 0.00 37.86 3.10
2844 5276 6.925211 TCCATAGCGAATGAATAACCTAGAG 58.075 40.000 3.89 0.00 37.86 2.43
2845 5277 6.911250 TCCATAGCGAATGAATAACCTAGA 57.089 37.500 3.89 0.00 37.86 2.43
2846 5278 9.469807 GATATCCATAGCGAATGAATAACCTAG 57.530 37.037 3.89 0.00 37.86 3.02
2847 5279 9.201989 AGATATCCATAGCGAATGAATAACCTA 57.798 33.333 0.00 0.00 37.86 3.08
2849 5281 7.766278 ACAGATATCCATAGCGAATGAATAACC 59.234 37.037 0.00 0.00 37.86 2.85
2850 5282 8.709386 ACAGATATCCATAGCGAATGAATAAC 57.291 34.615 0.00 0.00 37.86 1.89
2851 5283 9.725019 AAACAGATATCCATAGCGAATGAATAA 57.275 29.630 0.00 0.00 37.86 1.40
2852 5284 9.371136 GAAACAGATATCCATAGCGAATGAATA 57.629 33.333 0.00 0.00 37.86 1.75
2853 5285 7.879677 TGAAACAGATATCCATAGCGAATGAAT 59.120 33.333 0.00 0.00 37.86 2.57
2854 5286 7.216494 TGAAACAGATATCCATAGCGAATGAA 58.784 34.615 0.00 0.00 37.86 2.57
2856 5288 7.332678 TGATGAAACAGATATCCATAGCGAATG 59.667 37.037 0.00 0.00 35.15 2.67
2858 5290 6.758254 TGATGAAACAGATATCCATAGCGAA 58.242 36.000 0.00 0.00 0.00 4.70
2859 5291 6.015095 ACTGATGAAACAGATATCCATAGCGA 60.015 38.462 0.00 0.00 40.63 4.93
2860 5292 6.090493 CACTGATGAAACAGATATCCATAGCG 59.910 42.308 0.00 0.00 40.63 4.26
2862 5294 8.899427 AACACTGATGAAACAGATATCCATAG 57.101 34.615 0.00 0.00 40.63 2.23
2864 5296 9.857656 AATAACACTGATGAAACAGATATCCAT 57.142 29.630 0.00 0.00 40.63 3.41
2865 5297 9.112725 CAATAACACTGATGAAACAGATATCCA 57.887 33.333 0.00 0.00 40.63 3.41
2866 5298 9.330063 TCAATAACACTGATGAAACAGATATCC 57.670 33.333 0.00 0.00 40.63 2.59
2870 5302 9.334947 CCTATCAATAACACTGATGAAACAGAT 57.665 33.333 0.00 0.00 40.63 2.90
2871 5303 7.280876 GCCTATCAATAACACTGATGAAACAGA 59.719 37.037 0.00 0.00 40.63 3.41
2872 5304 7.066163 TGCCTATCAATAACACTGATGAAACAG 59.934 37.037 0.00 0.00 42.78 3.16
3098 6896 2.000447 GAGTAGCCGCACCAAAGTTAG 59.000 52.381 0.00 0.00 0.00 2.34
3103 6901 1.295423 GGAGAGTAGCCGCACCAAA 59.705 57.895 0.00 0.00 0.00 3.28
3215 7014 2.047370 GCAAATGCAAACCGGGGG 60.047 61.111 6.32 0.00 41.59 5.40
3363 7163 6.730507 TGGCAGAATGAGGATATGTATTAGGA 59.269 38.462 0.00 0.00 39.69 2.94
3397 7197 2.222678 GCGTGTCATTGCATGATCTAGG 59.777 50.000 0.00 0.00 42.04 3.02
3416 7216 2.879002 ACAGTCTGATGTAGATGGCG 57.121 50.000 6.91 0.00 37.83 5.69
3453 7253 7.383687 TCGAGAAGTAATAACAACCACAAGAT 58.616 34.615 0.00 0.00 0.00 2.40
3555 7361 1.414181 CTACCGTCCATCTCCTGCATT 59.586 52.381 0.00 0.00 0.00 3.56
3573 7379 0.115547 TGTACACAGTCAGGGGCCTA 59.884 55.000 0.84 0.00 0.00 3.93
3666 7472 7.718753 GGAAGATTGTCCACATAGATCTTGAAT 59.281 37.037 0.00 0.00 37.24 2.57
3773 7579 4.162690 GCCCGGCATCTCTTCCGT 62.163 66.667 3.91 0.00 43.87 4.69
3793 7599 1.003112 TGACGAATCCAAACGGGGG 60.003 57.895 0.00 0.00 37.22 5.40
3801 7607 2.024868 CGCCAACGTGACGAATCCA 61.025 57.895 13.70 0.00 33.53 3.41
3804 7610 3.545911 GTCGCCAACGTGACGAAT 58.454 55.556 13.70 0.00 39.58 3.34
3872 7678 4.295119 ACGTCCAGACCACGCACC 62.295 66.667 0.00 0.00 41.10 5.01
3881 7687 0.105964 CAACCAACCAGACGTCCAGA 59.894 55.000 13.01 0.00 0.00 3.86
3882 7688 1.507141 GCAACCAACCAGACGTCCAG 61.507 60.000 13.01 6.40 0.00 3.86
3883 7689 1.525077 GCAACCAACCAGACGTCCA 60.525 57.895 13.01 0.00 0.00 4.02
3884 7690 2.258726 GGCAACCAACCAGACGTCC 61.259 63.158 13.01 0.00 0.00 4.79
3885 7691 1.227853 AGGCAACCAACCAGACGTC 60.228 57.895 7.70 7.70 37.17 4.34
3886 7692 1.525995 CAGGCAACCAACCAGACGT 60.526 57.895 0.00 0.00 37.17 4.34
3887 7693 1.507141 GACAGGCAACCAACCAGACG 61.507 60.000 0.00 0.00 37.17 4.18
3888 7694 0.465460 TGACAGGCAACCAACCAGAC 60.465 55.000 0.00 0.00 37.17 3.51
3947 7753 1.127397 CATCCGCGATTCCAATCATCG 59.873 52.381 8.23 0.00 45.26 3.84
4159 7970 4.822350 TCTGAATCTAGACCAGTATCACGG 59.178 45.833 18.25 0.00 0.00 4.94
4213 8024 6.433093 AGGGGTAGTAACACTAAATGCAAAAG 59.567 38.462 0.00 0.00 31.62 2.27
4285 8097 5.775813 AAGACAGAGGAGGTAGTACTGTA 57.224 43.478 5.39 0.00 41.01 2.74
4287 8099 5.986501 AAAAGACAGAGGAGGTAGTACTG 57.013 43.478 5.39 0.00 35.14 2.74
4356 8343 9.106070 GTTTTTATGAAATACTACATCCGTCCT 57.894 33.333 0.00 0.00 0.00 3.85
4413 8400 1.233285 GCAGAGCAAGTCACCTGTGG 61.233 60.000 0.00 0.00 0.00 4.17
4417 8404 0.034616 GACAGCAGAGCAAGTCACCT 59.965 55.000 8.91 0.00 36.42 4.00
4419 8406 3.295734 TGACAGCAGAGCAAGTCAC 57.704 52.632 11.47 0.00 39.53 3.67
4421 8408 1.287730 CGGTGACAGCAGAGCAAGTC 61.288 60.000 5.35 7.40 36.74 3.01
4423 8410 2.675056 GCGGTGACAGCAGAGCAAG 61.675 63.158 2.09 0.00 34.19 4.01
4424 8411 2.666190 GCGGTGACAGCAGAGCAA 60.666 61.111 2.09 0.00 34.19 3.91
4425 8412 3.619767 AGCGGTGACAGCAGAGCA 61.620 61.111 10.82 0.00 37.01 4.26
4427 8414 2.433838 CCAGCGGTGACAGCAGAG 60.434 66.667 17.83 0.00 37.01 3.35
4428 8415 3.233980 ACCAGCGGTGACAGCAGA 61.234 61.111 17.83 0.00 32.98 4.26
4470 8603 0.883833 CTGTTTGCCTAGTTGCCTGG 59.116 55.000 0.00 0.00 0.00 4.45
4474 8607 0.523519 GGAGCTGTTTGCCTAGTTGC 59.476 55.000 0.00 0.00 44.23 4.17
4479 8612 2.562298 CAATTTGGGAGCTGTTTGCCTA 59.438 45.455 0.00 0.00 44.23 3.93
4584 9278 0.892358 GGGTTTTTCCTGGTCCGACC 60.892 60.000 10.96 10.96 39.22 4.79
4609 9303 1.372582 CTACGCATGCTTGTGACCAT 58.627 50.000 17.13 0.22 36.82 3.55
4649 9343 6.898041 TGAATCCGTGAAATCTGTTTACAAG 58.102 36.000 0.00 0.00 0.00 3.16
4834 9529 0.744874 GGCTCGCCTGTACTCATACA 59.255 55.000 0.00 0.00 39.06 2.29
5000 9820 3.022557 AGTGTAAGGTACATAGCGGGA 57.977 47.619 0.00 0.00 41.34 5.14
5002 9822 2.864343 GCAAGTGTAAGGTACATAGCGG 59.136 50.000 0.00 0.00 41.34 5.52
5240 10060 1.825191 CAGGAACCATGGGGCATCG 60.825 63.158 18.09 0.00 37.90 3.84
5621 10475 6.146216 TCAAACGGTGTAAAATGCAGTATTG 58.854 36.000 0.00 0.00 0.00 1.90
5634 10488 2.105134 ACCTGTCCATTCAAACGGTGTA 59.895 45.455 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.