Multiple sequence alignment - TraesCS6D01G282500

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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 TraesCS6D01G282500 chr6D 100.000 3012 0 0 1 3012 389918872 389915861 0.000000e+00 5563
1 TraesCS6D01G282500 chr6D 85.993 614 76 6 13 625 115644321 115643717 0.000000e+00 649
2 TraesCS6D01G282500 chr6D 84.150 612 93 4 16 625 421797612 421797003 9.300000e-165 590
3 TraesCS6D01G282500 chr6B 90.817 1383 74 24 645 2016 583510698 583509358 0.000000e+00 1801
4 TraesCS6D01G282500 chr6B 92.661 763 34 7 2250 3012 583507594 583506854 0.000000e+00 1079
5 TraesCS6D01G282500 chr6B 94.857 175 8 1 2082 2255 696483384 696483558 3.830000e-69 272
6 TraesCS6D01G282500 chr6B 96.104 77 3 0 2012 2088 583507669 583507593 3.150000e-25 126
7 TraesCS6D01G282500 chr6A 92.404 1277 53 18 835 2088 536227470 536226215 0.000000e+00 1781
8 TraesCS6D01G282500 chr6A 92.078 770 47 7 2250 3012 536226216 536225454 0.000000e+00 1072
9 TraesCS6D01G282500 chr6A 92.188 128 5 3 639 762 536227613 536227487 3.090000e-40 176
10 TraesCS6D01G282500 chr5D 85.256 624 84 4 14 631 452363219 452362598 1.180000e-178 636
11 TraesCS6D01G282500 chr5D 94.886 176 7 2 2087 2260 322384933 322385108 1.060000e-69 274
12 TraesCS6D01G282500 chr4A 83.307 623 88 11 13 625 633377320 633376704 7.290000e-156 560
13 TraesCS6D01G282500 chr7B 82.736 614 98 7 15 625 336644434 336643826 9.500000e-150 540
14 TraesCS6D01G282500 chr7B 91.489 188 13 3 2082 2268 112000708 112000893 3.850000e-64 255
15 TraesCS6D01G282500 chr3D 82.792 616 86 13 15 625 456777400 456776800 1.590000e-147 532
16 TraesCS6D01G282500 chr7A 82.990 582 94 4 11 589 644452756 644453335 3.440000e-144 521
17 TraesCS6D01G282500 chr2A 81.541 623 112 3 5 625 666841511 666840890 7.450000e-141 510
18 TraesCS6D01G282500 chr2A 93.296 179 11 1 2078 2255 94112377 94112555 2.300000e-66 263
19 TraesCS6D01G282500 chr3B 82.095 592 92 9 44 625 377683678 377684265 7.500000e-136 494
20 TraesCS6D01G282500 chr1D 98.788 165 2 0 2087 2251 77381517 77381681 8.170000e-76 294
21 TraesCS6D01G282500 chr2D 94.767 172 9 0 2088 2259 475088339 475088510 4.950000e-68 268
22 TraesCS6D01G282500 chr2D 94.152 171 10 0 2086 2256 29162554 29162384 8.280000e-66 261
23 TraesCS6D01G282500 chr3A 92.896 183 11 2 2087 2267 744920947 744921129 6.400000e-67 265
24 TraesCS6D01G282500 chr7D 92.818 181 11 2 2087 2265 39001285 39001465 8.280000e-66 261


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 TraesCS6D01G282500 chr6D 389915861 389918872 3011 True 5563.000000 5563 100.000000 1 3012 1 chr6D.!!$R2 3011
1 TraesCS6D01G282500 chr6D 115643717 115644321 604 True 649.000000 649 85.993000 13 625 1 chr6D.!!$R1 612
2 TraesCS6D01G282500 chr6D 421797003 421797612 609 True 590.000000 590 84.150000 16 625 1 chr6D.!!$R3 609
3 TraesCS6D01G282500 chr6B 583506854 583510698 3844 True 1002.000000 1801 93.194000 645 3012 3 chr6B.!!$R1 2367
4 TraesCS6D01G282500 chr6A 536225454 536227613 2159 True 1009.666667 1781 92.223333 639 3012 3 chr6A.!!$R1 2373
5 TraesCS6D01G282500 chr5D 452362598 452363219 621 True 636.000000 636 85.256000 14 631 1 chr5D.!!$R1 617
6 TraesCS6D01G282500 chr4A 633376704 633377320 616 True 560.000000 560 83.307000 13 625 1 chr4A.!!$R1 612
7 TraesCS6D01G282500 chr7B 336643826 336644434 608 True 540.000000 540 82.736000 15 625 1 chr7B.!!$R1 610
8 TraesCS6D01G282500 chr3D 456776800 456777400 600 True 532.000000 532 82.792000 15 625 1 chr3D.!!$R1 610
9 TraesCS6D01G282500 chr7A 644452756 644453335 579 False 521.000000 521 82.990000 11 589 1 chr7A.!!$F1 578
10 TraesCS6D01G282500 chr2A 666840890 666841511 621 True 510.000000 510 81.541000 5 625 1 chr2A.!!$R1 620
11 TraesCS6D01G282500 chr3B 377683678 377684265 587 False 494.000000 494 82.095000 44 625 1 chr3B.!!$F1 581

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
809 834 0.034896 AGTGAACTAACTGGGGTGCG 59.965 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 4364 0.340208 GAGAGAGAGGGGGAAGGGAA 59.66 60.0 0.0 0.0 0.0 3.97 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
36 37 2.288025 GGGCACTAGAACCCACCGA 61.288 63.158 16.90 0.00 46.22 4.69
104 105 3.079478 AGCAGATCGAGCAGGCCA 61.079 61.111 5.01 0.00 0.00 5.36
261 262 1.077644 CTCCTCCTCGTCTCCGGAA 60.078 63.158 5.23 0.00 33.95 4.30
305 306 4.451150 GGACATGCTCGCCGGTGA 62.451 66.667 18.43 18.43 0.00 4.02
380 391 0.251742 TAGGGTTTCTTCCGGACGGA 60.252 55.000 1.83 9.76 43.52 4.69
391 405 0.321298 CCGGACGGAGGATTTTGTGT 60.321 55.000 4.40 0.00 37.50 3.72
486 501 2.213499 GCCCTACATTTGAGACGGATG 58.787 52.381 0.00 0.00 0.00 3.51
504 519 2.997315 TGAGAGGTGCCGGTCAGG 60.997 66.667 1.90 0.00 44.97 3.86
515 530 1.290955 CGGTCAGGCTGGACGTTTA 59.709 57.895 15.73 0.00 38.70 2.01
526 541 4.004982 GCTGGACGTTTAAGACCCATTTA 58.995 43.478 0.00 0.00 0.00 1.40
539 554 1.209504 CCCATTTAAGAGCTCCGGTCA 59.790 52.381 10.93 0.00 31.89 4.02
576 593 1.810030 GTCAGTGATCGAACGGCCC 60.810 63.158 0.00 0.00 0.00 5.80
610 630 0.526662 GACGGATATAGAGCACCCGG 59.473 60.000 0.00 0.00 43.98 5.73
626 646 0.531532 CCGGGCTGTAGATGCTCTTG 60.532 60.000 0.00 0.00 0.00 3.02
631 651 1.850377 CTGTAGATGCTCTTGCTCCG 58.150 55.000 0.00 0.00 40.48 4.63
632 652 1.135915 CTGTAGATGCTCTTGCTCCGT 59.864 52.381 0.00 0.00 40.48 4.69
633 653 2.359214 CTGTAGATGCTCTTGCTCCGTA 59.641 50.000 0.00 0.00 40.48 4.02
634 654 2.959030 TGTAGATGCTCTTGCTCCGTAT 59.041 45.455 0.00 0.00 40.48 3.06
635 655 2.810439 AGATGCTCTTGCTCCGTATC 57.190 50.000 0.00 0.00 40.48 2.24
636 656 2.034878 AGATGCTCTTGCTCCGTATCA 58.965 47.619 0.00 0.00 40.48 2.15
637 657 2.035704 AGATGCTCTTGCTCCGTATCAG 59.964 50.000 0.00 0.00 40.48 2.90
643 663 0.758734 TTGCTCCGTATCAGGGGATG 59.241 55.000 0.00 0.00 34.89 3.51
769 792 0.611062 TGATCGGTCGGGTGAGTCTT 60.611 55.000 0.00 0.00 0.00 3.01
808 833 1.523758 CAGTGAACTAACTGGGGTGC 58.476 55.000 0.00 0.00 43.22 5.01
809 834 0.034896 AGTGAACTAACTGGGGTGCG 59.965 55.000 0.00 0.00 0.00 5.34
810 835 1.302192 TGAACTAACTGGGGTGCGC 60.302 57.895 0.00 0.00 0.00 6.09
811 836 2.358247 AACTAACTGGGGTGCGCG 60.358 61.111 0.00 0.00 0.00 6.86
812 837 2.775032 GAACTAACTGGGGTGCGCGA 62.775 60.000 12.10 0.00 0.00 5.87
813 838 2.509336 CTAACTGGGGTGCGCGAG 60.509 66.667 12.10 0.00 0.00 5.03
814 839 4.077184 TAACTGGGGTGCGCGAGG 62.077 66.667 12.10 0.00 0.00 4.63
821 846 3.670377 GGTGCGCGAGGCCTTTTT 61.670 61.111 12.10 0.00 42.61 1.94
858 883 3.763671 GCCTATTGATTGGCCGGG 58.236 61.111 2.18 0.00 41.84 5.73
925 958 2.511600 GGTTCCCGTGCCAGATCG 60.512 66.667 0.00 0.00 0.00 3.69
1018 1055 3.454573 AACCGATAGCCCACGCGA 61.455 61.111 15.93 0.00 41.18 5.87
1164 1205 1.528542 CTATCCGTCTCCCGCTCCA 60.529 63.158 0.00 0.00 34.38 3.86
1313 1354 3.873883 GACGGCGTCGACGAGGAT 61.874 66.667 39.74 21.55 43.02 3.24
1764 1808 5.759059 TGCTAAGGATGGTTCATTGAGATT 58.241 37.500 0.00 0.00 0.00 2.40
1831 1875 1.140852 CATTGGGATCGCCTAGGTGAA 59.859 52.381 28.12 12.44 38.20 3.18
1950 1997 5.987347 CCCATGAATCAAGTATGAAATTGCC 59.013 40.000 0.00 0.00 39.49 4.52
2018 3769 2.683768 ACCCAATTGCCAACCTTACAA 58.316 42.857 0.00 0.00 0.00 2.41
2019 3770 3.041946 ACCCAATTGCCAACCTTACAAA 58.958 40.909 0.00 0.00 0.00 2.83
2020 3771 3.070878 ACCCAATTGCCAACCTTACAAAG 59.929 43.478 0.00 0.00 0.00 2.77
2021 3772 3.066380 CCAATTGCCAACCTTACAAAGC 58.934 45.455 0.00 0.00 0.00 3.51
2022 3773 3.494048 CCAATTGCCAACCTTACAAAGCA 60.494 43.478 0.00 0.00 0.00 3.91
2023 3774 4.125703 CAATTGCCAACCTTACAAAGCAA 58.874 39.130 0.00 0.00 43.59 3.91
2024 3775 4.622260 ATTGCCAACCTTACAAAGCAAT 57.378 36.364 2.37 2.37 43.92 3.56
2025 3776 3.383620 TGCCAACCTTACAAAGCAATG 57.616 42.857 0.00 0.00 0.00 2.82
2026 3777 2.961741 TGCCAACCTTACAAAGCAATGA 59.038 40.909 0.00 0.00 0.00 2.57
2085 3836 2.605837 TCAAACGCTGAAGTACCACA 57.394 45.000 0.00 0.00 0.00 4.17
2086 3837 3.120321 TCAAACGCTGAAGTACCACAT 57.880 42.857 0.00 0.00 0.00 3.21
2087 3838 4.260139 TCAAACGCTGAAGTACCACATA 57.740 40.909 0.00 0.00 0.00 2.29
2088 3839 3.991773 TCAAACGCTGAAGTACCACATAC 59.008 43.478 0.00 0.00 0.00 2.39
2089 3840 3.955650 AACGCTGAAGTACCACATACT 57.044 42.857 0.00 0.00 46.75 2.12
2090 3841 3.505464 ACGCTGAAGTACCACATACTC 57.495 47.619 0.00 0.00 43.79 2.59
2091 3842 2.165845 ACGCTGAAGTACCACATACTCC 59.834 50.000 0.00 0.00 43.79 3.85
2092 3843 2.481449 CGCTGAAGTACCACATACTCCC 60.481 54.545 0.00 0.00 43.79 4.30
2093 3844 2.766828 GCTGAAGTACCACATACTCCCT 59.233 50.000 0.00 0.00 43.79 4.20
2094 3845 3.181474 GCTGAAGTACCACATACTCCCTC 60.181 52.174 0.00 0.00 43.79 4.30
2095 3846 3.371965 TGAAGTACCACATACTCCCTCC 58.628 50.000 0.00 0.00 43.79 4.30
2096 3847 2.068834 AGTACCACATACTCCCTCCG 57.931 55.000 0.00 0.00 40.31 4.63
2097 3848 1.287146 AGTACCACATACTCCCTCCGT 59.713 52.381 0.00 0.00 40.31 4.69
2098 3849 2.105766 GTACCACATACTCCCTCCGTT 58.894 52.381 0.00 0.00 0.00 4.44
2099 3850 1.192428 ACCACATACTCCCTCCGTTC 58.808 55.000 0.00 0.00 0.00 3.95
2100 3851 0.464452 CCACATACTCCCTCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
2101 3852 1.486211 CACATACTCCCTCCGTTCCT 58.514 55.000 0.00 0.00 0.00 3.36
2102 3853 2.662866 CACATACTCCCTCCGTTCCTA 58.337 52.381 0.00 0.00 0.00 2.94
2103 3854 3.028850 CACATACTCCCTCCGTTCCTAA 58.971 50.000 0.00 0.00 0.00 2.69
2104 3855 3.449737 CACATACTCCCTCCGTTCCTAAA 59.550 47.826 0.00 0.00 0.00 1.85
2105 3856 4.101119 CACATACTCCCTCCGTTCCTAAAT 59.899 45.833 0.00 0.00 0.00 1.40
2106 3857 4.720273 ACATACTCCCTCCGTTCCTAAATT 59.280 41.667 0.00 0.00 0.00 1.82
2107 3858 5.191124 ACATACTCCCTCCGTTCCTAAATTT 59.809 40.000 0.00 0.00 0.00 1.82
2108 3859 4.652679 ACTCCCTCCGTTCCTAAATTTT 57.347 40.909 0.00 0.00 0.00 1.82
2109 3860 4.994282 ACTCCCTCCGTTCCTAAATTTTT 58.006 39.130 0.00 0.00 0.00 1.94
2110 3861 4.765339 ACTCCCTCCGTTCCTAAATTTTTG 59.235 41.667 0.00 0.00 0.00 2.44
2111 3862 4.732065 TCCCTCCGTTCCTAAATTTTTGT 58.268 39.130 0.00 0.00 0.00 2.83
2112 3863 5.878627 TCCCTCCGTTCCTAAATTTTTGTA 58.121 37.500 0.00 0.00 0.00 2.41
2113 3864 6.486941 TCCCTCCGTTCCTAAATTTTTGTAT 58.513 36.000 0.00 0.00 0.00 2.29
2114 3865 6.949463 TCCCTCCGTTCCTAAATTTTTGTATT 59.051 34.615 0.00 0.00 0.00 1.89
2115 3866 7.452189 TCCCTCCGTTCCTAAATTTTTGTATTT 59.548 33.333 0.00 0.00 0.00 1.40
2116 3867 8.092068 CCCTCCGTTCCTAAATTTTTGTATTTT 58.908 33.333 0.00 0.00 0.00 1.82
2117 3868 9.483916 CCTCCGTTCCTAAATTTTTGTATTTTT 57.516 29.630 0.00 0.00 0.00 1.94
2147 3898 4.789899 TGGGCTACCACATACGGA 57.210 55.556 0.00 0.00 43.37 4.69
2148 3899 3.233953 TGGGCTACCACATACGGAT 57.766 52.632 0.00 0.00 43.37 4.18
2149 3900 0.756294 TGGGCTACCACATACGGATG 59.244 55.000 5.94 5.94 43.37 3.51
2151 3902 1.965643 GGGCTACCACATACGGATGTA 59.034 52.381 14.23 0.00 44.82 2.29
2152 3903 2.565834 GGGCTACCACATACGGATGTAT 59.434 50.000 14.23 7.46 44.82 2.29
2153 3904 3.765511 GGGCTACCACATACGGATGTATA 59.234 47.826 14.23 8.27 44.82 1.47
2154 3905 4.404715 GGGCTACCACATACGGATGTATAT 59.595 45.833 14.23 4.37 44.82 0.86
2155 3906 5.595542 GGGCTACCACATACGGATGTATATA 59.404 44.000 14.23 5.36 44.82 0.86
2156 3907 6.238953 GGGCTACCACATACGGATGTATATAG 60.239 46.154 14.23 15.27 44.82 1.31
2157 3908 6.544931 GGCTACCACATACGGATGTATATAGA 59.455 42.308 14.23 0.00 44.82 1.98
2158 3909 7.230913 GGCTACCACATACGGATGTATATAGAT 59.769 40.741 14.23 0.00 44.82 1.98
2159 3910 9.281371 GCTACCACATACGGATGTATATAGATA 57.719 37.037 14.23 0.00 44.82 1.98
2192 3943 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
2193 3944 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
2194 3945 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
2195 3946 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
2196 3947 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2197 3948 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
2198 3949 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
2199 3950 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
2200 3951 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2201 3952 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2202 3953 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
2203 3954 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
2204 3955 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
2205 3956 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
2206 3957 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
2207 3958 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
2208 3959 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
2209 3960 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
2210 3961 6.016213 TGCTTCGTATGTAGTCACTTGTTA 57.984 37.500 0.00 0.00 0.00 2.41
2211 3962 6.448852 TGCTTCGTATGTAGTCACTTGTTAA 58.551 36.000 0.00 0.00 0.00 2.01
2212 3963 6.924612 TGCTTCGTATGTAGTCACTTGTTAAA 59.075 34.615 0.00 0.00 0.00 1.52
2213 3964 7.438757 TGCTTCGTATGTAGTCACTTGTTAAAA 59.561 33.333 0.00 0.00 0.00 1.52
2214 3965 8.440833 GCTTCGTATGTAGTCACTTGTTAAAAT 58.559 33.333 0.00 0.00 0.00 1.82
2242 3993 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2243 3994 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2244 3995 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2245 3996 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2246 3997 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2247 3998 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2248 3999 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2256 4007 7.530426 TTTAGGAACGGAGGGAGTAATATAC 57.470 40.000 0.00 0.00 0.00 1.47
2259 4010 4.831710 GGAACGGAGGGAGTAATATACTGT 59.168 45.833 0.00 0.00 39.59 3.55
2267 4018 7.178628 GGAGGGAGTAATATACTGTGCATTAGA 59.821 40.741 7.80 0.00 39.59 2.10
2400 4151 1.181098 AAGCCACACCACCTTGCATC 61.181 55.000 0.00 0.00 0.00 3.91
2489 4245 1.386155 CTGGTTTGGGGGTATGGCA 59.614 57.895 0.00 0.00 0.00 4.92
2600 4356 2.426738 CGATGGCAGTCTCTCTCTTTCT 59.573 50.000 0.00 0.00 0.00 2.52
2601 4357 3.489059 CGATGGCAGTCTCTCTCTTTCTC 60.489 52.174 0.00 0.00 0.00 2.87
2603 4359 3.088532 TGGCAGTCTCTCTCTTTCTCTC 58.911 50.000 0.00 0.00 0.00 3.20
2604 4360 3.245229 TGGCAGTCTCTCTCTTTCTCTCT 60.245 47.826 0.00 0.00 0.00 3.10
2605 4361 3.378427 GGCAGTCTCTCTCTTTCTCTCTC 59.622 52.174 0.00 0.00 0.00 3.20
2608 4364 3.852578 AGTCTCTCTCTTTCTCTCTCCCT 59.147 47.826 0.00 0.00 0.00 4.20
2609 4365 4.292306 AGTCTCTCTCTTTCTCTCTCCCTT 59.708 45.833 0.00 0.00 0.00 3.95
2613 4369 2.657459 TCTCTTTCTCTCTCCCTTCCCT 59.343 50.000 0.00 0.00 0.00 4.20
2614 4370 3.078305 TCTCTTTCTCTCTCCCTTCCCTT 59.922 47.826 0.00 0.00 0.00 3.95
2616 4372 2.255770 TTCTCTCTCCCTTCCCTTCC 57.744 55.000 0.00 0.00 0.00 3.46
2644 4400 1.719378 TCTCTTCTCCCTGTCTCCCTT 59.281 52.381 0.00 0.00 0.00 3.95
2717 4473 1.523154 GCCGTGGGCTTCAACAATGA 61.523 55.000 0.00 0.00 46.69 2.57
2858 4614 1.777878 TGTTAGGTTGGGATGGTGTGT 59.222 47.619 0.00 0.00 0.00 3.72
2877 4633 2.035442 GGCTTCTCAGGCCGTTGTC 61.035 63.158 0.00 0.00 40.19 3.18
2933 4689 1.632920 TCACCCATGACAACCATAGCA 59.367 47.619 0.00 0.00 33.31 3.49
2937 4693 3.459598 ACCCATGACAACCATAGCAGTAT 59.540 43.478 0.00 0.00 33.31 2.12
2938 4694 4.067896 CCCATGACAACCATAGCAGTATC 58.932 47.826 0.00 0.00 33.31 2.24
3008 4764 3.234353 TGAGCTATGGTAGATCACCTGG 58.766 50.000 13.32 0.00 45.33 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.420890 CCTGCTCGATCTGCTCCC 59.579 66.667 8.62 0.00 0.00 4.30
235 236 3.972276 CGAGGAGGAGCTAGCGCC 61.972 72.222 28.28 28.28 36.60 6.53
305 306 3.053077 TCCCAATCCGTCAAATCCCTAT 58.947 45.455 0.00 0.00 0.00 2.57
380 391 0.251165 CCCCGACCACACAAAATCCT 60.251 55.000 0.00 0.00 0.00 3.24
486 501 2.262915 CTGACCGGCACCTCTCAC 59.737 66.667 0.00 0.00 0.00 3.51
504 519 2.109425 ATGGGTCTTAAACGTCCAGC 57.891 50.000 0.00 0.00 0.00 4.85
506 521 5.867330 TCTTAAATGGGTCTTAAACGTCCA 58.133 37.500 0.00 0.00 0.00 4.02
515 530 2.092914 CCGGAGCTCTTAAATGGGTCTT 60.093 50.000 14.64 0.00 0.00 3.01
526 541 2.344203 CGACCTGACCGGAGCTCTT 61.344 63.158 9.46 0.00 36.31 2.85
576 593 2.802667 CGTCTCAAATGCTCGGGCG 61.803 63.158 1.14 0.00 42.25 6.13
582 602 4.281941 TGCTCTATATCCGTCTCAAATGCT 59.718 41.667 0.00 0.00 0.00 3.79
585 605 4.021016 GGGTGCTCTATATCCGTCTCAAAT 60.021 45.833 0.00 0.00 0.00 2.32
626 646 0.832135 TCCATCCCCTGATACGGAGC 60.832 60.000 0.00 0.00 0.00 4.70
631 651 2.303311 GTTAGGCTCCATCCCCTGATAC 59.697 54.545 0.00 0.00 32.65 2.24
632 652 2.182312 AGTTAGGCTCCATCCCCTGATA 59.818 50.000 0.00 0.00 32.65 2.15
633 653 1.061033 AGTTAGGCTCCATCCCCTGAT 60.061 52.381 0.00 0.00 32.65 2.90
634 654 0.343372 AGTTAGGCTCCATCCCCTGA 59.657 55.000 0.00 0.00 32.65 3.86
635 655 0.761802 GAGTTAGGCTCCATCCCCTG 59.238 60.000 0.00 0.00 38.27 4.45
636 656 0.760945 CGAGTTAGGCTCCATCCCCT 60.761 60.000 0.00 0.00 41.10 4.79
637 657 0.759436 TCGAGTTAGGCTCCATCCCC 60.759 60.000 0.00 0.00 41.10 4.81
643 663 1.093159 TCGAGTTCGAGTTAGGCTCC 58.907 55.000 0.00 0.00 44.22 4.70
743 766 3.640000 CCGACCGATCAATGGCGC 61.640 66.667 0.00 0.00 0.00 6.53
769 792 1.160870 TTTCCCAGGCCTCTCTCCA 59.839 57.895 0.00 0.00 0.00 3.86
821 846 3.728636 CGCGCGCCACCCTAAAAA 61.729 61.111 27.72 0.00 0.00 1.94
822 847 4.683721 TCGCGCGCCACCCTAAAA 62.684 61.111 27.95 0.00 0.00 1.52
833 858 1.956170 AATCAATAGGCCTCGCGCG 60.956 57.895 26.76 26.76 38.94 6.86
858 883 3.814049 CGATGGATCGCTTTCTTGC 57.186 52.632 0.00 0.00 43.84 4.01
891 924 2.404186 CCCCGTGACGATCGACTCA 61.404 63.158 24.34 13.46 0.00 3.41
920 953 2.066999 GGGAAGTGGGAGCCGATCT 61.067 63.158 0.00 0.00 0.00 2.75
1030 1067 1.376466 GGATGGGATGGGATCGGTG 59.624 63.158 0.00 0.00 0.00 4.94
1298 1339 3.791928 CTCATCCTCGTCGACGCCG 62.792 68.421 32.19 23.49 39.60 6.46
1313 1354 3.005539 GAGACCCAGCAGCCCTCA 61.006 66.667 0.00 0.00 0.00 3.86
1588 1632 1.516603 GTAGCTTCGTCTGCCCGAC 60.517 63.158 0.00 0.00 36.42 4.79
1595 1639 3.060615 ACCGCCGTAGCTTCGTCT 61.061 61.111 11.94 0.00 36.60 4.18
1764 1808 2.214376 AATTCCACCTTTGGCGATCA 57.786 45.000 0.00 0.00 43.56 2.92
1848 1895 7.457852 TGGAGGCATATTGACCACTATTAGTAT 59.542 37.037 0.00 0.00 0.00 2.12
1913 1960 7.178983 ACTTGATTCATGGGCTGATTCTTTTTA 59.821 33.333 4.75 0.00 35.95 1.52
1919 1966 5.766670 TCATACTTGATTCATGGGCTGATTC 59.233 40.000 4.75 0.00 35.65 2.52
1920 1967 5.698104 TCATACTTGATTCATGGGCTGATT 58.302 37.500 4.75 0.00 32.72 2.57
1950 1997 5.902681 TGTAGTGTCAAGAAATAGATCGGG 58.097 41.667 0.00 0.00 0.00 5.14
2018 3769 3.091545 ACCACGAATTCCATCATTGCTT 58.908 40.909 0.00 0.00 0.00 3.91
2019 3770 2.424601 CACCACGAATTCCATCATTGCT 59.575 45.455 0.00 0.00 0.00 3.91
2020 3771 2.164219 ACACCACGAATTCCATCATTGC 59.836 45.455 0.00 0.00 0.00 3.56
2021 3772 3.439825 TCACACCACGAATTCCATCATTG 59.560 43.478 0.00 0.00 0.00 2.82
2022 3773 3.684908 TCACACCACGAATTCCATCATT 58.315 40.909 0.00 0.00 0.00 2.57
2023 3774 3.348647 TCACACCACGAATTCCATCAT 57.651 42.857 0.00 0.00 0.00 2.45
2024 3775 2.849294 TCACACCACGAATTCCATCA 57.151 45.000 0.00 0.00 0.00 3.07
2025 3776 3.270027 TCATCACACCACGAATTCCATC 58.730 45.455 0.00 0.00 0.00 3.51
2026 3777 3.348647 TCATCACACCACGAATTCCAT 57.651 42.857 0.00 0.00 0.00 3.41
2085 3836 5.970501 AAATTTAGGAACGGAGGGAGTAT 57.029 39.130 0.00 0.00 0.00 2.12
2086 3837 5.767277 AAAATTTAGGAACGGAGGGAGTA 57.233 39.130 0.00 0.00 0.00 2.59
2087 3838 4.652679 AAAATTTAGGAACGGAGGGAGT 57.347 40.909 0.00 0.00 0.00 3.85
2088 3839 4.765339 ACAAAAATTTAGGAACGGAGGGAG 59.235 41.667 0.00 0.00 0.00 4.30
2089 3840 4.732065 ACAAAAATTTAGGAACGGAGGGA 58.268 39.130 0.00 0.00 0.00 4.20
2090 3841 6.769134 ATACAAAAATTTAGGAACGGAGGG 57.231 37.500 0.00 0.00 0.00 4.30
2091 3842 9.483916 AAAAATACAAAAATTTAGGAACGGAGG 57.516 29.630 0.00 0.00 0.00 4.30
2113 3864 9.315363 TGGTAGCCCATTTAAAATCTCTAAAAA 57.685 29.630 0.00 0.00 35.17 1.94
2114 3865 8.745590 GTGGTAGCCCATTTAAAATCTCTAAAA 58.254 33.333 0.00 0.00 44.35 1.52
2115 3866 7.891183 TGTGGTAGCCCATTTAAAATCTCTAAA 59.109 33.333 0.00 0.00 44.35 1.85
2116 3867 7.406916 TGTGGTAGCCCATTTAAAATCTCTAA 58.593 34.615 0.00 0.00 44.35 2.10
2117 3868 6.964464 TGTGGTAGCCCATTTAAAATCTCTA 58.036 36.000 0.00 0.00 44.35 2.43
2118 3869 5.826643 TGTGGTAGCCCATTTAAAATCTCT 58.173 37.500 0.00 0.00 44.35 3.10
2119 3870 6.715347 ATGTGGTAGCCCATTTAAAATCTC 57.285 37.500 0.00 0.00 44.35 2.75
2120 3871 6.262273 CGTATGTGGTAGCCCATTTAAAATCT 59.738 38.462 0.00 0.00 44.35 2.40
2121 3872 6.435428 CGTATGTGGTAGCCCATTTAAAATC 58.565 40.000 0.00 0.00 44.35 2.17
2122 3873 5.300792 CCGTATGTGGTAGCCCATTTAAAAT 59.699 40.000 0.00 0.00 44.35 1.82
2123 3874 4.641094 CCGTATGTGGTAGCCCATTTAAAA 59.359 41.667 0.00 0.00 44.35 1.52
2124 3875 4.080469 TCCGTATGTGGTAGCCCATTTAAA 60.080 41.667 0.00 0.00 44.35 1.52
2125 3876 3.455177 TCCGTATGTGGTAGCCCATTTAA 59.545 43.478 0.00 0.00 44.35 1.52
2126 3877 3.039743 TCCGTATGTGGTAGCCCATTTA 58.960 45.455 0.00 0.00 44.35 1.40
2127 3878 1.841277 TCCGTATGTGGTAGCCCATTT 59.159 47.619 0.00 0.00 44.35 2.32
2128 3879 1.502690 TCCGTATGTGGTAGCCCATT 58.497 50.000 0.00 0.00 44.35 3.16
2129 3880 1.347707 CATCCGTATGTGGTAGCCCAT 59.652 52.381 0.00 0.00 44.35 4.00
2130 3881 0.756294 CATCCGTATGTGGTAGCCCA 59.244 55.000 0.00 0.00 38.87 5.36
2131 3882 0.756903 ACATCCGTATGTGGTAGCCC 59.243 55.000 0.00 0.00 44.79 5.19
2132 3883 3.955650 ATACATCCGTATGTGGTAGCC 57.044 47.619 3.56 0.00 45.99 3.93
2133 3884 7.563888 TCTATATACATCCGTATGTGGTAGC 57.436 40.000 3.56 0.00 45.99 3.58
2169 3920 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
2170 3921 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
2171 3922 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2172 3923 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
2173 3924 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
2174 3925 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
2175 3926 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
2176 3927 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
2177 3928 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2178 3929 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
2179 3930 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
2180 3931 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
2181 3932 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
2182 3933 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
2183 3934 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
2184 3935 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
2185 3936 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
2186 3937 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
2187 3938 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
2188 3939 6.939551 TTAACAAGTGACTACATACGAAGC 57.060 37.500 0.00 0.00 0.00 3.86
2216 3967 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2217 3968 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2218 3969 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2219 3970 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2220 3971 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2221 3972 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2222 3973 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2223 3974 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2224 3975 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2225 3976 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2226 3977 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2227 3978 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2228 3979 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
2229 3980 8.912614 ATATTACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
2230 3981 9.247861 GTATATTACTCCCTCCGTTCCTAAATA 57.752 37.037 0.00 0.00 0.00 1.40
2231 3982 7.954620 AGTATATTACTCCCTCCGTTCCTAAAT 59.045 37.037 0.00 0.00 32.47 1.40
2232 3983 7.232127 CAGTATATTACTCCCTCCGTTCCTAAA 59.768 40.741 0.00 0.00 36.76 1.85
2233 3984 6.718454 CAGTATATTACTCCCTCCGTTCCTAA 59.282 42.308 0.00 0.00 36.76 2.69
2234 3985 6.183361 ACAGTATATTACTCCCTCCGTTCCTA 60.183 42.308 0.00 0.00 36.76 2.94
2235 3986 5.078256 CAGTATATTACTCCCTCCGTTCCT 58.922 45.833 0.00 0.00 36.76 3.36
2236 3987 4.831710 ACAGTATATTACTCCCTCCGTTCC 59.168 45.833 0.00 0.00 36.76 3.62
2237 3988 5.770417 CACAGTATATTACTCCCTCCGTTC 58.230 45.833 0.00 0.00 36.76 3.95
2238 3989 4.038883 GCACAGTATATTACTCCCTCCGTT 59.961 45.833 0.00 0.00 36.76 4.44
2239 3990 3.573110 GCACAGTATATTACTCCCTCCGT 59.427 47.826 0.00 0.00 36.76 4.69
2240 3991 3.572682 TGCACAGTATATTACTCCCTCCG 59.427 47.826 0.00 0.00 36.76 4.63
2241 3992 5.746990 ATGCACAGTATATTACTCCCTCC 57.253 43.478 0.00 0.00 36.76 4.30
2242 3993 8.123639 TCTAATGCACAGTATATTACTCCCTC 57.876 38.462 0.00 0.00 36.76 4.30
2243 3994 8.492415 TTCTAATGCACAGTATATTACTCCCT 57.508 34.615 0.00 0.00 36.76 4.20
2244 3995 9.372369 GATTCTAATGCACAGTATATTACTCCC 57.628 37.037 0.00 0.00 36.76 4.30
2245 3996 9.929180 TGATTCTAATGCACAGTATATTACTCC 57.071 33.333 0.00 0.00 36.76 3.85
2267 4018 6.645827 CGTCTCTTCTATCTTGATGCATGATT 59.354 38.462 2.46 0.00 32.04 2.57
2400 4151 4.351054 GTGGCTGGTGGTGAGGGG 62.351 72.222 0.00 0.00 0.00 4.79
2489 4245 4.761058 TCTCCCCGCCTTCGAGCT 62.761 66.667 0.00 0.00 38.10 4.09
2600 4356 1.396594 GGGGAAGGGAAGGGAGAGA 59.603 63.158 0.00 0.00 0.00 3.10
2601 4357 1.694525 GGGGGAAGGGAAGGGAGAG 60.695 68.421 0.00 0.00 0.00 3.20
2603 4359 1.694525 GAGGGGGAAGGGAAGGGAG 60.695 68.421 0.00 0.00 0.00 4.30
2604 4360 2.191846 AGAGGGGGAAGGGAAGGGA 61.192 63.158 0.00 0.00 0.00 4.20
2605 4361 1.694525 GAGAGGGGGAAGGGAAGGG 60.695 68.421 0.00 0.00 0.00 3.95
2608 4364 0.340208 GAGAGAGAGGGGGAAGGGAA 59.660 60.000 0.00 0.00 0.00 3.97
2609 4365 0.556380 AGAGAGAGAGGGGGAAGGGA 60.556 60.000 0.00 0.00 0.00 4.20
2613 4369 1.289530 GGAGAAGAGAGAGAGGGGGAA 59.710 57.143 0.00 0.00 0.00 3.97
2614 4370 0.930726 GGAGAAGAGAGAGAGGGGGA 59.069 60.000 0.00 0.00 0.00 4.81
2616 4372 0.933700 AGGGAGAAGAGAGAGAGGGG 59.066 60.000 0.00 0.00 0.00 4.79
2644 4400 3.407424 CACAGATGTGTTGGGAGAGAA 57.593 47.619 4.77 0.00 40.96 2.87
2717 4473 3.011821 TGGACCTCCTAGATCTTCTGTGT 59.988 47.826 0.00 0.00 36.82 3.72
2877 4633 0.588252 CAACCTCCTCGTTGCACTTG 59.412 55.000 0.00 0.00 36.96 3.16
2933 4689 0.673644 GGCGGCACAACACAGATACT 60.674 55.000 3.07 0.00 0.00 2.12
2937 4693 2.449031 CTAGGGCGGCACAACACAGA 62.449 60.000 12.47 0.00 0.00 3.41
2938 4694 2.031919 TAGGGCGGCACAACACAG 59.968 61.111 12.47 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.