Multiple sequence alignment - TraesCS3D01G501800

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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 TraesCS3D01G501800 chr3D 100.000 3035 0 0 1 3035 590441503 590438469 0.000000e+00 5605.0
1 TraesCS3D01G501800 chr3A 93.252 1956 68 29 278 2225 720699025 720697126 0.000000e+00 2822.0
2 TraesCS3D01G501800 chr3A 91.652 551 30 10 1775 2321 720693974 720693436 0.000000e+00 749.0
3 TraesCS3D01G501800 chr3A 85.714 721 56 22 2328 3035 720693396 720692710 0.000000e+00 717.0
4 TraesCS3D01G501800 chr3A 85.174 344 17 15 2341 2682 720696893 720696582 3.770000e-84 322.0
5 TraesCS3D01G501800 chr3A 82.547 212 29 6 2 208 720699273 720699065 2.400000e-41 180.0
6 TraesCS3D01G501800 chr3B 90.857 1914 103 47 677 2547 790371475 790369591 0.000000e+00 2499.0
7 TraesCS3D01G501800 chr3B 82.731 498 41 23 105 580 790371999 790371525 4.710000e-108 401.0
8 TraesCS3D01G501800 chr1D 82.727 110 14 4 1691 1800 104021191 104021295 3.220000e-15 93.5
9 TraesCS3D01G501800 chr1D 94.872 39 1 1 209 246 111818623 111818661 3.270000e-05 60.2
10 TraesCS3D01G501800 chr5B 97.143 35 0 1 211 244 649445053 649445019 1.180000e-04 58.4
11 TraesCS3D01G501800 chr5B 100.000 30 0 0 216 245 185222854 185222883 4.230000e-04 56.5
12 TraesCS3D01G501800 chr4D 97.059 34 1 0 216 249 425163401 425163368 1.180000e-04 58.4


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 TraesCS3D01G501800 chr3D 590438469 590441503 3034 True 5605 5605 100.0000 1 3035 1 chr3D.!!$R1 3034
1 TraesCS3D01G501800 chr3A 720692710 720699273 6563 True 958 2822 87.6678 2 3035 5 chr3A.!!$R1 3033
2 TraesCS3D01G501800 chr3B 790369591 790371999 2408 True 1450 2499 86.7940 105 2547 2 chr3B.!!$R1 2442

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
784 828 0.034337 GCTTCACACGTACTTCCCCA 59.966 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 6171 0.104934 AATCCTACGGCTCTCCCCAT 60.105 55.0 0.0 0.0 0.0 4.0 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
22 23 1.654105 GCAGATCGTACGTGTCTTTGG 59.346 52.381 16.05 9.34 0.00 3.28
23 24 2.670229 GCAGATCGTACGTGTCTTTGGA 60.670 50.000 16.05 0.00 0.00 3.53
27 28 3.646611 TCGTACGTGTCTTTGGAATCA 57.353 42.857 16.05 0.00 0.00 2.57
29 30 4.562082 TCGTACGTGTCTTTGGAATCATT 58.438 39.130 16.05 0.00 0.00 2.57
30 31 4.624024 TCGTACGTGTCTTTGGAATCATTC 59.376 41.667 16.05 0.00 0.00 2.67
31 32 4.490319 CGTACGTGTCTTTGGAATCATTCG 60.490 45.833 7.22 0.00 0.00 3.34
32 33 2.159627 ACGTGTCTTTGGAATCATTCGC 59.840 45.455 0.00 0.00 0.00 4.70
33 34 2.774007 GTGTCTTTGGAATCATTCGCG 58.226 47.619 0.00 0.00 0.00 5.87
34 35 1.737236 TGTCTTTGGAATCATTCGCGG 59.263 47.619 6.13 0.00 0.00 6.46
35 36 1.064060 GTCTTTGGAATCATTCGCGGG 59.936 52.381 6.13 0.00 0.00 6.13
36 37 1.065782 TCTTTGGAATCATTCGCGGGA 60.066 47.619 6.13 0.00 0.00 5.14
51 56 1.566404 CGGGAGCAAACAAAAACCAC 58.434 50.000 0.00 0.00 0.00 4.16
82 87 1.609501 CACCGAGACCCCAAGGAGA 60.610 63.158 0.00 0.00 36.73 3.71
83 88 1.157751 ACCGAGACCCCAAGGAGAA 59.842 57.895 0.00 0.00 36.73 2.87
84 89 0.905337 ACCGAGACCCCAAGGAGAAG 60.905 60.000 0.00 0.00 36.73 2.85
103 108 0.037326 GTGCAACTGGAGACCATCGA 60.037 55.000 0.00 0.00 30.82 3.59
187 192 1.674359 ATCTCTGCTCACGACGATCT 58.326 50.000 0.00 0.00 0.00 2.75
188 193 0.729690 TCTCTGCTCACGACGATCTG 59.270 55.000 0.00 0.00 0.00 2.90
189 194 0.729690 CTCTGCTCACGACGATCTGA 59.270 55.000 0.00 0.00 0.00 3.27
211 220 2.584492 CATGTCGCCATGTCTCTGTA 57.416 50.000 0.00 0.00 42.92 2.74
213 222 1.545841 TGTCGCCATGTCTCTGTACT 58.454 50.000 0.00 0.00 0.00 2.73
215 224 2.094700 TGTCGCCATGTCTCTGTACTTC 60.095 50.000 0.00 0.00 0.00 3.01
217 226 2.423892 TCGCCATGTCTCTGTACTTCTC 59.576 50.000 0.00 0.00 0.00 2.87
218 227 2.480416 CGCCATGTCTCTGTACTTCTCC 60.480 54.545 0.00 0.00 0.00 3.71
219 228 2.497675 GCCATGTCTCTGTACTTCTCCA 59.502 50.000 0.00 0.00 0.00 3.86
221 230 4.739137 GCCATGTCTCTGTACTTCTCCATC 60.739 50.000 0.00 0.00 0.00 3.51
222 231 4.498850 CCATGTCTCTGTACTTCTCCATCG 60.499 50.000 0.00 0.00 0.00 3.84
223 232 2.423892 TGTCTCTGTACTTCTCCATCGC 59.576 50.000 0.00 0.00 0.00 4.58
224 233 2.423892 GTCTCTGTACTTCTCCATCGCA 59.576 50.000 0.00 0.00 0.00 5.10
226 235 3.509967 TCTCTGTACTTCTCCATCGCAAA 59.490 43.478 0.00 0.00 0.00 3.68
228 237 4.832248 TCTGTACTTCTCCATCGCAAAAT 58.168 39.130 0.00 0.00 0.00 1.82
229 238 5.972935 TCTGTACTTCTCCATCGCAAAATA 58.027 37.500 0.00 0.00 0.00 1.40
230 239 6.403049 TCTGTACTTCTCCATCGCAAAATAA 58.597 36.000 0.00 0.00 0.00 1.40
231 240 6.535150 TCTGTACTTCTCCATCGCAAAATAAG 59.465 38.462 0.00 0.00 0.00 1.73
233 242 5.551760 ACTTCTCCATCGCAAAATAAGTG 57.448 39.130 0.00 0.00 0.00 3.16
234 243 5.003804 ACTTCTCCATCGCAAAATAAGTGT 58.996 37.500 0.00 0.00 0.00 3.55
235 244 5.122396 ACTTCTCCATCGCAAAATAAGTGTC 59.878 40.000 0.00 0.00 0.00 3.67
236 245 4.832248 TCTCCATCGCAAAATAAGTGTCT 58.168 39.130 0.00 0.00 0.00 3.41
238 247 4.574892 TCCATCGCAAAATAAGTGTCTCA 58.425 39.130 0.00 0.00 0.00 3.27
239 248 5.000591 TCCATCGCAAAATAAGTGTCTCAA 58.999 37.500 0.00 0.00 0.00 3.02
240 249 5.088739 CCATCGCAAAATAAGTGTCTCAAC 58.911 41.667 0.00 0.00 0.00 3.18
241 250 5.106555 CCATCGCAAAATAAGTGTCTCAACT 60.107 40.000 0.00 0.00 0.00 3.16
244 253 7.485418 TCGCAAAATAAGTGTCTCAACTTTA 57.515 32.000 0.00 0.00 40.77 1.85
245 254 7.921787 TCGCAAAATAAGTGTCTCAACTTTAA 58.078 30.769 0.00 0.00 40.77 1.52
246 255 8.564574 TCGCAAAATAAGTGTCTCAACTTTAAT 58.435 29.630 0.00 0.00 40.77 1.40
247 256 9.820229 CGCAAAATAAGTGTCTCAACTTTAATA 57.180 29.630 0.00 0.00 40.77 0.98
255 264 8.853469 AGTGTCTCAACTTTAATACGTATAGC 57.147 34.615 8.83 0.00 0.00 2.97
256 265 8.684520 AGTGTCTCAACTTTAATACGTATAGCT 58.315 33.333 8.83 0.00 0.00 3.32
257 266 9.298774 GTGTCTCAACTTTAATACGTATAGCTT 57.701 33.333 8.83 0.00 0.00 3.74
258 267 9.865321 TGTCTCAACTTTAATACGTATAGCTTT 57.135 29.630 8.83 0.00 0.00 3.51
260 269 9.309516 TCTCAACTTTAATACGTATAGCTTTGG 57.690 33.333 8.83 0.00 0.00 3.28
261 270 9.309516 CTCAACTTTAATACGTATAGCTTTGGA 57.690 33.333 8.83 2.33 0.00 3.53
262 271 9.090692 TCAACTTTAATACGTATAGCTTTGGAC 57.909 33.333 8.83 0.00 0.00 4.02
263 272 9.095065 CAACTTTAATACGTATAGCTTTGGACT 57.905 33.333 8.83 0.00 0.00 3.85
264 273 9.662947 AACTTTAATACGTATAGCTTTGGACTT 57.337 29.630 8.83 0.00 0.00 3.01
265 274 9.662947 ACTTTAATACGTATAGCTTTGGACTTT 57.337 29.630 8.83 0.00 0.00 2.66
394 403 2.803451 CTTGATCGAGAGGAAGAACCG 58.197 52.381 3.60 0.00 44.74 4.44
560 590 7.402640 CGATTAGAATGGAGCAAAGTAACTTC 58.597 38.462 0.00 0.00 0.00 3.01
584 614 7.445121 TCGATTCTAATTTACATCAGAGGCAT 58.555 34.615 0.00 0.00 0.00 4.40
592 622 5.537300 TTACATCAGAGGCATAGACTTCC 57.463 43.478 0.00 0.00 0.00 3.46
593 623 3.652055 ACATCAGAGGCATAGACTTCCT 58.348 45.455 0.00 0.00 0.00 3.36
634 664 1.559831 CGTGAACGCATGAGCATAGA 58.440 50.000 0.00 0.00 42.27 1.98
635 665 2.130395 CGTGAACGCATGAGCATAGAT 58.870 47.619 0.00 0.00 42.27 1.98
636 666 2.541346 CGTGAACGCATGAGCATAGATT 59.459 45.455 0.00 0.00 42.27 2.40
637 667 3.603173 CGTGAACGCATGAGCATAGATTG 60.603 47.826 0.00 0.00 42.27 2.67
638 668 3.557185 GTGAACGCATGAGCATAGATTGA 59.443 43.478 0.00 0.00 42.27 2.57
639 669 3.805971 TGAACGCATGAGCATAGATTGAG 59.194 43.478 0.00 0.00 42.27 3.02
640 670 3.740631 ACGCATGAGCATAGATTGAGA 57.259 42.857 0.00 0.00 42.27 3.27
641 671 4.268797 ACGCATGAGCATAGATTGAGAT 57.731 40.909 0.00 0.00 42.27 2.75
642 672 3.995048 ACGCATGAGCATAGATTGAGATG 59.005 43.478 0.00 0.00 42.27 2.90
643 673 3.371285 CGCATGAGCATAGATTGAGATGG 59.629 47.826 0.00 0.00 42.27 3.51
644 674 4.576879 GCATGAGCATAGATTGAGATGGA 58.423 43.478 0.00 0.00 41.58 3.41
645 675 5.186942 GCATGAGCATAGATTGAGATGGAT 58.813 41.667 0.00 0.00 41.58 3.41
646 676 5.648526 GCATGAGCATAGATTGAGATGGATT 59.351 40.000 0.00 0.00 41.58 3.01
647 677 6.151312 GCATGAGCATAGATTGAGATGGATTT 59.849 38.462 0.00 0.00 41.58 2.17
648 678 7.626664 GCATGAGCATAGATTGAGATGGATTTC 60.627 40.741 0.00 0.00 41.58 2.17
649 679 6.236409 TGAGCATAGATTGAGATGGATTTCC 58.764 40.000 0.00 0.00 0.00 3.13
658 688 4.421365 TGGATTTCCAGCCAGCAC 57.579 55.556 0.00 0.00 42.01 4.40
659 689 1.459812 TGGATTTCCAGCCAGCACA 59.540 52.632 0.00 0.00 42.01 4.57
660 690 0.895100 TGGATTTCCAGCCAGCACAC 60.895 55.000 0.00 0.00 42.01 3.82
661 691 0.895100 GGATTTCCAGCCAGCACACA 60.895 55.000 0.00 0.00 35.64 3.72
662 692 0.524862 GATTTCCAGCCAGCACACAG 59.475 55.000 0.00 0.00 0.00 3.66
663 693 1.530013 ATTTCCAGCCAGCACACAGC 61.530 55.000 0.00 0.00 46.19 4.40
695 730 4.370364 AGCAGCGAAAAGAAGTTTGAAA 57.630 36.364 0.00 0.00 0.00 2.69
697 732 3.061863 GCAGCGAAAAGAAGTTTGAAACG 60.062 43.478 1.97 0.00 36.23 3.60
698 733 4.095610 CAGCGAAAAGAAGTTTGAAACGT 58.904 39.130 1.97 0.00 36.23 3.99
699 734 4.028509 CAGCGAAAAGAAGTTTGAAACGTG 60.029 41.667 0.32 0.00 36.23 4.49
700 735 4.092816 GCGAAAAGAAGTTTGAAACGTGA 58.907 39.130 0.32 0.00 36.23 4.35
701 736 4.733405 GCGAAAAGAAGTTTGAAACGTGAT 59.267 37.500 0.32 0.00 36.23 3.06
702 737 5.108742 GCGAAAAGAAGTTTGAAACGTGATC 60.109 40.000 0.32 0.30 36.23 2.92
703 738 5.112052 CGAAAAGAAGTTTGAAACGTGATCG 59.888 40.000 0.32 5.61 43.34 3.69
752 789 3.242936 CGTTCAACAACACCCCACTAAAG 60.243 47.826 0.00 0.00 32.14 1.85
784 828 0.034337 GCTTCACACGTACTTCCCCA 59.966 55.000 0.00 0.00 0.00 4.96
787 831 2.536761 TCACACGTACTTCCCCAAAG 57.463 50.000 0.00 0.00 41.08 2.77
789 833 2.635915 TCACACGTACTTCCCCAAAGAT 59.364 45.455 0.00 0.00 38.44 2.40
843 898 5.130519 CGTAAAGAAATCACACGTCAACTG 58.869 41.667 0.00 0.00 0.00 3.16
1013 1079 1.016130 ACAGCGATGGAAGTGAAGCG 61.016 55.000 5.32 0.00 0.00 4.68
1329 1395 3.902086 GAGGACTACGAGGCGGCC 61.902 72.222 12.11 12.11 0.00 6.13
1575 1641 2.579787 CTCGTGATGACGGACGGC 60.580 66.667 4.51 0.00 46.11 5.68
2085 2151 1.544724 ATTTGCACGCTGGTGGTATT 58.455 45.000 0.00 0.00 44.54 1.89
2086 2152 2.186532 TTTGCACGCTGGTGGTATTA 57.813 45.000 0.00 0.00 44.54 0.98
2131 5792 8.191446 CAGCTGATGTAAATACTACAGTACTGT 58.809 37.037 30.13 30.13 46.87 3.55
2162 5827 7.604927 GTGTGTACACTAATGGTTATTTGAGGA 59.395 37.037 25.60 0.00 43.25 3.71
2167 5832 8.738645 ACACTAATGGTTATTTGAGGAGATTC 57.261 34.615 0.00 0.00 0.00 2.52
2199 5864 5.947228 TTCACAAGAAATGTTAGAGGCTG 57.053 39.130 0.00 0.00 41.46 4.85
2204 5869 6.805271 CACAAGAAATGTTAGAGGCTGATTTG 59.195 38.462 0.00 0.00 41.46 2.32
2241 5906 9.495572 TTTTGTACAAGTTTCAAATTCTTTGGT 57.504 25.926 8.56 0.00 40.98 3.67
2262 5927 4.550422 GTTGGCAAATTTCAGGAGAACTC 58.450 43.478 0.00 0.00 32.39 3.01
2264 5929 3.074412 GGCAAATTTCAGGAGAACTCGA 58.926 45.455 0.00 0.00 32.39 4.04
2268 5933 5.570589 GCAAATTTCAGGAGAACTCGATTTG 59.429 40.000 0.00 0.00 39.23 2.32
2269 5934 5.886960 AATTTCAGGAGAACTCGATTTGG 57.113 39.130 0.00 0.00 32.39 3.28
2272 5937 4.617253 TCAGGAGAACTCGATTTGGAAA 57.383 40.909 0.00 0.00 0.00 3.13
2274 5939 3.437049 CAGGAGAACTCGATTTGGAAACC 59.563 47.826 0.00 0.00 0.00 3.27
2275 5940 2.415512 GGAGAACTCGATTTGGAAACCG 59.584 50.000 0.00 0.00 0.00 4.44
2278 5943 1.439679 ACTCGATTTGGAAACCGAGC 58.560 50.000 14.53 0.00 46.56 5.03
2281 5946 2.420022 CTCGATTTGGAAACCGAGCAAT 59.580 45.455 3.01 0.00 40.56 3.56
2295 5960 3.974401 CCGAGCAATTGTTTTGTGTGTAG 59.026 43.478 7.40 0.00 0.00 2.74
2296 5961 3.974401 CGAGCAATTGTTTTGTGTGTAGG 59.026 43.478 7.40 0.00 0.00 3.18
2321 5986 5.424895 AGAGGAGCAACTCTCATATTGACTT 59.575 40.000 4.53 0.00 44.23 3.01
2322 5987 6.609212 AGAGGAGCAACTCTCATATTGACTTA 59.391 38.462 4.53 0.00 44.23 2.24
2323 5988 6.815089 AGGAGCAACTCTCATATTGACTTAG 58.185 40.000 0.00 0.00 43.70 2.18
2324 5989 6.382570 AGGAGCAACTCTCATATTGACTTAGT 59.617 38.462 0.00 0.00 43.70 2.24
2325 5990 7.561722 AGGAGCAACTCTCATATTGACTTAGTA 59.438 37.037 0.00 0.00 43.70 1.82
2327 5992 8.299990 AGCAACTCTCATATTGACTTAGTAGT 57.700 34.615 0.00 0.00 37.31 2.73
2328 5993 8.754080 AGCAACTCTCATATTGACTTAGTAGTT 58.246 33.333 0.00 0.00 33.84 2.24
2329 5994 9.372369 GCAACTCTCATATTGACTTAGTAGTTT 57.628 33.333 0.00 0.00 33.84 2.66
2343 6041 8.502105 ACTTAGTAGTTTGTTTTGCAGTAGTT 57.498 30.769 0.00 0.00 0.00 2.24
2371 6069 3.423749 TGTTGACTCGTGGGTGTATCTA 58.576 45.455 0.00 0.00 0.00 1.98
2372 6070 3.442625 TGTTGACTCGTGGGTGTATCTAG 59.557 47.826 0.00 0.00 0.00 2.43
2375 6073 2.358267 GACTCGTGGGTGTATCTAGGTG 59.642 54.545 0.00 0.00 0.00 4.00
2376 6074 2.025605 ACTCGTGGGTGTATCTAGGTGA 60.026 50.000 0.00 0.00 0.00 4.02
2377 6075 3.223435 CTCGTGGGTGTATCTAGGTGAT 58.777 50.000 0.00 0.00 39.11 3.06
2378 6076 2.956333 TCGTGGGTGTATCTAGGTGATG 59.044 50.000 0.00 0.00 36.65 3.07
2421 6120 0.384725 CTTGGAAACGACGCAAGCTG 60.385 55.000 0.00 0.00 45.62 4.24
2436 6139 0.247736 AGCTGAAGTGGACGGTGATC 59.752 55.000 0.00 0.00 0.00 2.92
2437 6140 0.037326 GCTGAAGTGGACGGTGATCA 60.037 55.000 0.00 0.00 0.00 2.92
2450 6153 3.181454 ACGGTGATCATAGGATTTGACCC 60.181 47.826 0.00 0.00 32.67 4.46
2451 6154 3.403038 GGTGATCATAGGATTTGACCCG 58.597 50.000 0.00 0.00 32.67 5.28
2468 6171 4.077184 GGCCGACCATCACGACCA 62.077 66.667 0.00 0.00 33.74 4.02
2470 6173 2.173669 GCCGACCATCACGACCATG 61.174 63.158 0.00 0.00 0.00 3.66
2558 6262 3.129113 GTCAGCATGCACATCCAAATGTA 59.871 43.478 21.98 0.00 39.38 2.29
2559 6263 3.762823 TCAGCATGCACATCCAAATGTAA 59.237 39.130 21.98 0.00 39.38 2.41
2581 6286 1.392168 CGATTGTACATCGCGTTTGGT 59.608 47.619 5.77 2.89 34.66 3.67
2587 6292 0.108804 ACATCGCGTTTGGTCGATCT 60.109 50.000 5.77 0.00 42.73 2.75
2596 6301 4.142988 GCGTTTGGTCGATCTTCAAACATA 60.143 41.667 23.15 0.01 46.01 2.29
2597 6302 5.550981 CGTTTGGTCGATCTTCAAACATAG 58.449 41.667 23.15 12.16 46.01 2.23
2608 6313 4.759693 TCTTCAAACATAGAAATGCACGGT 59.240 37.500 0.00 0.00 36.50 4.83
2655 6361 3.933332 AGCAAGTCGTTCATAAACTAGCC 59.067 43.478 0.00 0.00 32.95 3.93
2670 6376 1.966901 TAGCCGATGTCCCGCACATT 61.967 55.000 0.27 0.00 46.53 2.71
2680 6386 2.174592 CGCACATTTACGCGCCAA 59.825 55.556 5.73 0.00 45.57 4.52
2746 6456 8.739972 AGAATGTTACTATTAGTTTTTGCCCTG 58.260 33.333 0.85 0.00 0.00 4.45
2752 6462 7.017319 ACTATTAGTTTTTGCCCTGACTAGT 57.983 36.000 0.00 0.00 0.00 2.57
2766 6476 1.355916 CTAGTAGGGTCACTCGCGC 59.644 63.158 0.00 0.00 0.00 6.86
2771 6481 0.818938 TAGGGTCACTCGCGCATTTA 59.181 50.000 8.75 0.00 0.00 1.40
2772 6482 0.178068 AGGGTCACTCGCGCATTTAT 59.822 50.000 8.75 0.00 0.00 1.40
2774 6484 1.006832 GGTCACTCGCGCATTTATGT 58.993 50.000 8.75 0.00 0.00 2.29
2775 6485 1.267532 GGTCACTCGCGCATTTATGTG 60.268 52.381 8.75 6.65 41.07 3.21
2786 6496 3.367292 CGCATTTATGTGCCCAGACTTTT 60.367 43.478 0.00 0.00 42.06 2.27
2797 6509 7.217200 TGTGCCCAGACTTTTGATATATCTAC 58.783 38.462 13.79 0.00 0.00 2.59
2835 6547 7.010160 ACATTTTAAGAGGGTCTCCAAATCAA 58.990 34.615 0.00 0.00 34.83 2.57
2842 6554 6.794534 AGAGGGTCTCCAAATCAATAGTTTT 58.205 36.000 0.00 0.00 34.83 2.43
2947 6663 9.712305 CACCTGGACAATCTAAGTATTATTAGG 57.288 37.037 0.00 0.00 34.20 2.69
2948 6664 9.448587 ACCTGGACAATCTAAGTATTATTAGGT 57.551 33.333 0.00 0.00 34.20 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.987149 CAAAGACACGTACGATCTGCTT 59.013 45.455 24.41 13.65 0.00 3.91
9 10 4.724036 GCGAATGATTCCAAAGACACGTAC 60.724 45.833 0.00 0.00 0.00 3.67
22 23 0.732571 TTTGCTCCCGCGAATGATTC 59.267 50.000 8.23 0.00 39.65 2.52
23 24 0.451783 GTTTGCTCCCGCGAATGATT 59.548 50.000 8.23 0.00 41.37 2.57
27 28 0.671251 TTTTGTTTGCTCCCGCGAAT 59.329 45.000 8.23 0.00 41.37 3.34
29 30 0.248702 GTTTTTGTTTGCTCCCGCGA 60.249 50.000 8.23 0.00 39.65 5.87
30 31 1.212455 GGTTTTTGTTTGCTCCCGCG 61.212 55.000 0.00 0.00 39.65 6.46
31 32 0.179097 TGGTTTTTGTTTGCTCCCGC 60.179 50.000 0.00 0.00 0.00 6.13
32 33 1.566404 GTGGTTTTTGTTTGCTCCCG 58.434 50.000 0.00 0.00 0.00 5.14
33 34 1.474320 GGGTGGTTTTTGTTTGCTCCC 60.474 52.381 0.00 0.00 0.00 4.30
34 35 1.208293 TGGGTGGTTTTTGTTTGCTCC 59.792 47.619 0.00 0.00 0.00 4.70
35 36 2.682155 TGGGTGGTTTTTGTTTGCTC 57.318 45.000 0.00 0.00 0.00 4.26
36 37 2.771372 AGATGGGTGGTTTTTGTTTGCT 59.229 40.909 0.00 0.00 0.00 3.91
38 39 4.126437 GGAAGATGGGTGGTTTTTGTTTG 58.874 43.478 0.00 0.00 0.00 2.93
51 56 0.176680 CTCGGTGTCAGGAAGATGGG 59.823 60.000 0.00 0.00 0.00 4.00
82 87 1.609061 CGATGGTCTCCAGTTGCACTT 60.609 52.381 0.00 0.00 36.75 3.16
83 88 0.036952 CGATGGTCTCCAGTTGCACT 60.037 55.000 0.00 0.00 36.75 4.40
84 89 0.037326 TCGATGGTCTCCAGTTGCAC 60.037 55.000 0.00 0.00 36.75 4.57
103 108 3.685139 TCTGATTTCTGAACCGAAGCT 57.315 42.857 0.00 0.00 0.00 3.74
175 180 0.383590 ATGCCTCAGATCGTCGTGAG 59.616 55.000 4.74 4.74 40.03 3.51
179 184 0.932123 CGACATGCCTCAGATCGTCG 60.932 60.000 0.00 0.00 40.04 5.12
200 209 4.605968 CGATGGAGAAGTACAGAGACATG 58.394 47.826 0.00 0.00 0.00 3.21
208 217 6.092122 CACTTATTTTGCGATGGAGAAGTACA 59.908 38.462 0.00 0.00 0.00 2.90
209 218 6.092259 ACACTTATTTTGCGATGGAGAAGTAC 59.908 38.462 0.00 0.00 0.00 2.73
211 220 5.003804 ACACTTATTTTGCGATGGAGAAGT 58.996 37.500 0.00 0.00 0.00 3.01
213 222 5.245531 AGACACTTATTTTGCGATGGAGAA 58.754 37.500 0.00 0.00 0.00 2.87
215 224 4.631377 TGAGACACTTATTTTGCGATGGAG 59.369 41.667 0.00 0.00 0.00 3.86
217 226 4.944962 TGAGACACTTATTTTGCGATGG 57.055 40.909 0.00 0.00 0.00 3.51
218 227 5.931532 AGTTGAGACACTTATTTTGCGATG 58.068 37.500 0.00 0.00 0.00 3.84
219 228 6.560253 AAGTTGAGACACTTATTTTGCGAT 57.440 33.333 0.00 0.00 35.10 4.58
221 230 8.728088 ATTAAAGTTGAGACACTTATTTTGCG 57.272 30.769 0.00 0.00 35.87 4.85
229 238 9.298774 GCTATACGTATTAAAGTTGAGACACTT 57.701 33.333 14.33 0.00 38.74 3.16
230 239 8.684520 AGCTATACGTATTAAAGTTGAGACACT 58.315 33.333 14.33 0.00 0.00 3.55
231 240 8.853469 AGCTATACGTATTAAAGTTGAGACAC 57.147 34.615 14.33 0.00 0.00 3.67
234 243 9.309516 CCAAAGCTATACGTATTAAAGTTGAGA 57.690 33.333 14.33 0.00 0.00 3.27
235 244 9.309516 TCCAAAGCTATACGTATTAAAGTTGAG 57.690 33.333 14.33 3.42 0.00 3.02
236 245 9.090692 GTCCAAAGCTATACGTATTAAAGTTGA 57.909 33.333 14.33 1.54 0.00 3.18
238 247 9.662947 AAGTCCAAAGCTATACGTATTAAAGTT 57.337 29.630 14.33 0.16 0.00 2.66
239 248 9.662947 AAAGTCCAAAGCTATACGTATTAAAGT 57.337 29.630 14.33 0.00 0.00 2.66
247 256 9.741647 GTACTATAAAAGTCCAAAGCTATACGT 57.258 33.333 0.00 0.00 39.80 3.57
248 257 9.740239 TGTACTATAAAAGTCCAAAGCTATACG 57.260 33.333 0.00 0.00 39.80 3.06
251 260 9.057089 GCATGTACTATAAAAGTCCAAAGCTAT 57.943 33.333 0.00 0.00 39.80 2.97
252 261 7.223971 CGCATGTACTATAAAAGTCCAAAGCTA 59.776 37.037 0.00 0.00 39.80 3.32
253 262 6.037172 CGCATGTACTATAAAAGTCCAAAGCT 59.963 38.462 0.00 0.00 39.80 3.74
254 263 6.036735 TCGCATGTACTATAAAAGTCCAAAGC 59.963 38.462 0.00 0.00 39.80 3.51
255 264 7.534085 TCGCATGTACTATAAAAGTCCAAAG 57.466 36.000 0.00 0.00 39.80 2.77
256 265 7.412129 CGTTCGCATGTACTATAAAAGTCCAAA 60.412 37.037 0.00 0.00 39.80 3.28
257 266 6.035220 CGTTCGCATGTACTATAAAAGTCCAA 59.965 38.462 0.00 0.00 39.80 3.53
258 267 5.517411 CGTTCGCATGTACTATAAAAGTCCA 59.483 40.000 0.00 0.00 39.80 4.02
259 268 5.555818 GCGTTCGCATGTACTATAAAAGTCC 60.556 44.000 12.33 0.00 39.80 3.85
260 269 5.421203 GCGTTCGCATGTACTATAAAAGTC 58.579 41.667 12.33 0.00 39.80 3.01
261 270 4.027132 CGCGTTCGCATGTACTATAAAAGT 60.027 41.667 16.98 0.00 42.62 2.66
262 271 4.027132 ACGCGTTCGCATGTACTATAAAAG 60.027 41.667 5.58 0.00 39.84 2.27
263 272 3.858812 ACGCGTTCGCATGTACTATAAAA 59.141 39.130 5.58 0.00 39.84 1.52
264 273 3.437428 ACGCGTTCGCATGTACTATAAA 58.563 40.909 5.58 0.00 39.84 1.40
265 274 3.069074 ACGCGTTCGCATGTACTATAA 57.931 42.857 5.58 0.00 39.84 0.98
266 275 2.761392 ACGCGTTCGCATGTACTATA 57.239 45.000 5.58 0.00 39.84 1.31
267 276 1.586578 CAACGCGTTCGCATGTACTAT 59.413 47.619 23.92 0.00 39.84 2.12
268 277 0.986270 CAACGCGTTCGCATGTACTA 59.014 50.000 23.92 0.00 39.84 1.82
269 278 1.779061 CAACGCGTTCGCATGTACT 59.221 52.632 23.92 0.00 39.84 2.73
270 279 1.857426 GCAACGCGTTCGCATGTAC 60.857 57.895 28.88 9.28 39.84 2.90
394 403 2.979130 GCTGTGAGCGATAAGGGTC 58.021 57.895 0.00 0.00 35.07 4.46
491 521 3.259902 GGGTAGTTGGCGAGTAAAGAAG 58.740 50.000 0.00 0.00 0.00 2.85
492 522 2.353011 CGGGTAGTTGGCGAGTAAAGAA 60.353 50.000 0.00 0.00 0.00 2.52
560 590 7.664082 ATGCCTCTGATGTAAATTAGAATCG 57.336 36.000 0.00 0.00 0.00 3.34
576 606 3.740764 GCTGAAGGAAGTCTATGCCTCTG 60.741 52.174 0.00 0.00 0.00 3.35
584 614 3.677148 CGCATTCTGCTGAAGGAAGTCTA 60.677 47.826 20.25 0.00 42.25 2.59
592 622 1.376543 ATGGTCGCATTCTGCTGAAG 58.623 50.000 11.86 5.53 42.25 3.02
593 623 1.739466 GAATGGTCGCATTCTGCTGAA 59.261 47.619 8.59 8.59 42.25 3.02
634 664 3.563223 CTGGCTGGAAATCCATCTCAAT 58.437 45.455 1.93 0.00 46.46 2.57
635 665 2.947243 GCTGGCTGGAAATCCATCTCAA 60.947 50.000 1.93 0.00 46.46 3.02
636 666 1.409241 GCTGGCTGGAAATCCATCTCA 60.409 52.381 1.93 1.66 46.46 3.27
637 667 1.316651 GCTGGCTGGAAATCCATCTC 58.683 55.000 1.93 0.00 46.46 2.75
638 668 0.627451 TGCTGGCTGGAAATCCATCT 59.373 50.000 1.93 0.00 46.46 2.90
639 669 0.743097 GTGCTGGCTGGAAATCCATC 59.257 55.000 1.93 0.00 46.46 3.51
640 670 0.040058 TGTGCTGGCTGGAAATCCAT 59.960 50.000 1.93 0.00 46.46 3.41
641 671 0.895100 GTGTGCTGGCTGGAAATCCA 60.895 55.000 1.53 1.53 45.30 3.41
642 672 0.895100 TGTGTGCTGGCTGGAAATCC 60.895 55.000 0.00 0.00 0.00 3.01
643 673 0.524862 CTGTGTGCTGGCTGGAAATC 59.475 55.000 0.00 0.00 0.00 2.17
644 674 1.530013 GCTGTGTGCTGGCTGGAAAT 61.530 55.000 0.00 0.00 38.95 2.17
645 675 2.195567 GCTGTGTGCTGGCTGGAAA 61.196 57.895 0.00 0.00 38.95 3.13
646 676 2.595463 GCTGTGTGCTGGCTGGAA 60.595 61.111 0.00 0.00 38.95 3.53
647 677 2.702040 AATGCTGTGTGCTGGCTGGA 62.702 55.000 0.00 0.00 43.37 3.86
648 678 1.812686 AAATGCTGTGTGCTGGCTGG 61.813 55.000 0.00 0.00 43.37 4.85
649 679 0.666274 CAAATGCTGTGTGCTGGCTG 60.666 55.000 0.00 0.00 43.37 4.85
650 680 1.663739 CAAATGCTGTGTGCTGGCT 59.336 52.632 0.00 0.00 43.37 4.75
651 681 2.025418 GCAAATGCTGTGTGCTGGC 61.025 57.895 0.00 0.00 43.37 4.85
652 682 1.373748 GGCAAATGCTGTGTGCTGG 60.374 57.895 5.25 0.00 43.37 4.85
653 683 0.666274 CTGGCAAATGCTGTGTGCTG 60.666 55.000 5.25 0.00 43.37 4.41
654 684 0.824595 TCTGGCAAATGCTGTGTGCT 60.825 50.000 5.25 0.00 43.37 4.40
655 685 0.032403 TTCTGGCAAATGCTGTGTGC 59.968 50.000 5.25 0.00 41.70 4.57
656 686 1.933500 GCTTCTGGCAAATGCTGTGTG 60.934 52.381 5.25 0.00 41.70 3.82
657 687 0.316204 GCTTCTGGCAAATGCTGTGT 59.684 50.000 5.25 0.00 41.70 3.72
658 688 3.117589 GCTTCTGGCAAATGCTGTG 57.882 52.632 5.25 0.00 41.70 3.66
695 730 1.669049 TACCATTCCCGCGATCACGT 61.669 55.000 8.23 0.00 41.98 4.49
697 732 1.658994 TTTACCATTCCCGCGATCAC 58.341 50.000 8.23 0.00 0.00 3.06
698 733 2.285083 CTTTTACCATTCCCGCGATCA 58.715 47.619 8.23 0.00 0.00 2.92
699 734 1.002792 GCTTTTACCATTCCCGCGATC 60.003 52.381 8.23 0.00 0.00 3.69
700 735 1.021968 GCTTTTACCATTCCCGCGAT 58.978 50.000 8.23 0.00 0.00 4.58
701 736 1.363145 CGCTTTTACCATTCCCGCGA 61.363 55.000 8.23 0.00 41.39 5.87
702 737 1.061887 CGCTTTTACCATTCCCGCG 59.938 57.895 0.00 0.00 0.00 6.46
703 738 1.226575 GCGCTTTTACCATTCCCGC 60.227 57.895 0.00 0.00 0.00 6.13
752 789 4.686554 ACGTGTGAAGCTTCTTGATCTTAC 59.313 41.667 26.09 14.00 0.00 2.34
784 828 6.098266 AGGTTGAAGCCACTTTGTTAATCTTT 59.902 34.615 0.00 0.00 0.00 2.52
787 831 5.453567 AGGTTGAAGCCACTTTGTTAATC 57.546 39.130 0.00 0.00 0.00 1.75
789 833 5.220892 CGTAAGGTTGAAGCCACTTTGTTAA 60.221 40.000 0.00 0.00 0.00 2.01
2155 5820 4.630644 AGCACAGAAGAATCTCCTCAAA 57.369 40.909 0.00 0.00 32.03 2.69
2189 5854 8.470002 ACAAATAATTCCAAATCAGCCTCTAAC 58.530 33.333 0.00 0.00 0.00 2.34
2190 5855 8.593945 ACAAATAATTCCAAATCAGCCTCTAA 57.406 30.769 0.00 0.00 0.00 2.10
2241 5906 3.253188 CGAGTTCTCCTGAAATTTGCCAA 59.747 43.478 0.00 0.00 33.52 4.52
2262 5927 2.916716 CAATTGCTCGGTTTCCAAATCG 59.083 45.455 0.00 0.00 43.53 3.34
2264 5929 4.335400 AACAATTGCTCGGTTTCCAAAT 57.665 36.364 5.05 0.00 0.00 2.32
2268 5933 3.245048 CACAAAACAATTGCTCGGTTTCC 59.755 43.478 5.05 0.00 33.91 3.13
2269 5934 3.862845 ACACAAAACAATTGCTCGGTTTC 59.137 39.130 5.05 0.00 33.91 2.78
2272 5937 2.165437 ACACACAAAACAATTGCTCGGT 59.835 40.909 5.05 0.00 0.00 4.69
2274 5939 3.974401 CCTACACACAAAACAATTGCTCG 59.026 43.478 5.05 0.00 0.00 5.03
2275 5940 5.008613 TCTCCTACACACAAAACAATTGCTC 59.991 40.000 5.05 0.00 0.00 4.26
2277 5942 5.181690 TCTCCTACACACAAAACAATTGC 57.818 39.130 5.05 0.00 0.00 3.56
2278 5943 5.530915 TCCTCTCCTACACACAAAACAATTG 59.469 40.000 3.24 3.24 0.00 2.32
2281 5946 4.703897 CTCCTCTCCTACACACAAAACAA 58.296 43.478 0.00 0.00 0.00 2.83
2311 5976 9.891828 TGCAAAACAAACTACTAAGTCAATATG 57.108 29.630 0.00 0.00 33.75 1.78
2343 6041 2.290008 ACCCACGAGTCAACATAATGCA 60.290 45.455 0.00 0.00 0.00 3.96
2346 6044 3.695830 ACACCCACGAGTCAACATAAT 57.304 42.857 0.00 0.00 0.00 1.28
2394 6093 2.669434 GCGTCGTTTCCAAGCTGTAATA 59.331 45.455 0.00 0.00 0.00 0.98
2421 6120 2.693591 TCCTATGATCACCGTCCACTTC 59.306 50.000 0.00 0.00 0.00 3.01
2436 6139 0.884704 CGGCCGGGTCAAATCCTATG 60.885 60.000 20.10 0.00 0.00 2.23
2437 6140 1.052124 TCGGCCGGGTCAAATCCTAT 61.052 55.000 27.83 0.00 0.00 2.57
2467 6170 0.833834 ATCCTACGGCTCTCCCCATG 60.834 60.000 0.00 0.00 0.00 3.66
2468 6171 0.104934 AATCCTACGGCTCTCCCCAT 60.105 55.000 0.00 0.00 0.00 4.00
2470 6173 0.393448 GAAATCCTACGGCTCTCCCC 59.607 60.000 0.00 0.00 0.00 4.81
2558 6262 1.717194 AACGCGATGTACAATCGGTT 58.283 45.000 15.93 19.24 41.42 4.44
2559 6263 1.392168 CAAACGCGATGTACAATCGGT 59.608 47.619 15.93 12.49 41.42 4.69
2581 6286 6.455513 CGTGCATTTCTATGTTTGAAGATCGA 60.456 38.462 0.00 0.00 34.12 3.59
2587 6292 5.446143 AACCGTGCATTTCTATGTTTGAA 57.554 34.783 0.00 0.00 34.12 2.69
2627 6332 0.235665 ATGAACGACTTGCTTGTGCG 59.764 50.000 0.00 0.00 43.34 5.34
2655 6361 0.300491 CGTAAATGTGCGGGACATCG 59.700 55.000 15.67 11.14 45.12 3.84
2670 6376 7.478044 GCGTATATAATAAAAATTGGCGCGTAA 59.522 33.333 8.43 3.91 0.00 3.18
2746 6456 0.656785 CGCGAGTGACCCTACTAGTC 59.343 60.000 0.00 0.00 34.72 2.59
2752 6462 0.818938 TAAATGCGCGAGTGACCCTA 59.181 50.000 12.10 0.00 0.00 3.53
2761 6471 3.106552 GGGCACATAAATGCGCGA 58.893 55.556 12.10 0.00 46.81 5.87
2766 6476 5.389859 TCAAAAGTCTGGGCACATAAATG 57.610 39.130 0.00 0.00 0.00 2.32
2771 6481 6.845908 AGATATATCAAAAGTCTGGGCACAT 58.154 36.000 15.08 0.00 0.00 3.21
2772 6482 6.252599 AGATATATCAAAAGTCTGGGCACA 57.747 37.500 15.08 0.00 0.00 4.57
2774 6484 7.147567 TGTGTAGATATATCAAAAGTCTGGGCA 60.148 37.037 15.08 0.00 0.00 5.36
2775 6485 7.217200 TGTGTAGATATATCAAAAGTCTGGGC 58.783 38.462 15.08 0.00 0.00 5.36
2776 6486 9.212641 CATGTGTAGATATATCAAAAGTCTGGG 57.787 37.037 15.08 0.00 0.00 4.45
2797 6509 9.357652 CCCTCTTAAAATGTAAAACATCATGTG 57.642 33.333 0.00 0.00 37.97 3.21
2804 6516 7.291566 TGGAGACCCTCTTAAAATGTAAAACA 58.708 34.615 0.00 0.00 0.00 2.83
2811 6523 7.466746 TTGATTTGGAGACCCTCTTAAAATG 57.533 36.000 0.00 0.00 0.00 2.32
3008 6724 2.772077 TTGCCAACCGATAAGCTACA 57.228 45.000 0.00 0.00 0.00 2.74
3009 6725 3.186613 GCTATTGCCAACCGATAAGCTAC 59.813 47.826 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.