Multiple sequence alignment - TraesCS5B01G194000

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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 TraesCS5B01G194000 chr5B 100.000 4923 0 0 1 4923 350409989 350414911 0.000000e+00 9092.0
1 TraesCS5B01G194000 chr5B 90.584 531 46 2 4358 4884 350411305 350411835 0.000000e+00 701.0
2 TraesCS5B01G194000 chr5B 90.584 531 46 2 1317 1847 350414346 350414872 0.000000e+00 701.0
3 TraesCS5B01G194000 chr5B 88.095 168 19 1 1861 2028 490757409 490757575 1.080000e-46 198.0
4 TraesCS5B01G194000 chr5D 95.707 1747 70 3 2849 4590 305731278 305733024 0.000000e+00 2806.0
5 TraesCS5B01G194000 chr5D 92.978 1125 70 5 942 2060 305727102 305728223 0.000000e+00 1631.0
6 TraesCS5B01G194000 chr5D 94.672 807 29 4 2059 2852 305728693 305729498 0.000000e+00 1240.0
7 TraesCS5B01G194000 chr5D 87.813 919 105 4 954 1866 322987987 322987070 0.000000e+00 1070.0
8 TraesCS5B01G194000 chr5D 92.727 605 40 2 3300 3901 322977155 322976552 0.000000e+00 870.0
9 TraesCS5B01G194000 chr5D 90.875 537 38 5 4358 4884 305727477 305728012 0.000000e+00 710.0
10 TraesCS5B01G194000 chr5D 87.682 617 44 15 2025 2620 322987071 322986466 0.000000e+00 689.0
11 TraesCS5B01G194000 chr5D 88.312 539 51 9 4358 4887 322987621 322987086 1.930000e-178 636.0
12 TraesCS5B01G194000 chr5D 85.956 591 62 13 2616 3194 322986409 322985828 3.260000e-171 612.0
13 TraesCS5B01G194000 chr5D 91.909 309 20 2 4577 4884 305734567 305734871 1.270000e-115 427.0
14 TraesCS5B01G194000 chr5D 88.146 329 33 3 1539 1866 305734567 305734890 2.150000e-103 387.0
15 TraesCS5B01G194000 chr5D 92.157 153 7 5 802 950 305722027 305722178 1.390000e-50 211.0
16 TraesCS5B01G194000 chr5D 88.344 163 19 0 1864 2026 391992736 391992574 3.890000e-46 196.0
17 TraesCS5B01G194000 chr5D 100.000 38 0 0 764 801 305719023 305719060 2.460000e-08 71.3
18 TraesCS5B01G194000 chr2B 96.512 774 19 1 1 766 7582578 7581805 0.000000e+00 1273.0
19 TraesCS5B01G194000 chr2B 95.984 772 23 1 1 764 705367044 705367815 0.000000e+00 1247.0
20 TraesCS5B01G194000 chr2B 87.861 173 17 4 1864 2033 744854767 744854596 3.010000e-47 200.0
21 TraesCS5B01G194000 chr5A 94.194 620 34 2 1249 1866 391992634 391992015 0.000000e+00 944.0
22 TraesCS5B01G194000 chr5A 90.467 535 46 2 4358 4887 391992565 391992031 0.000000e+00 701.0
23 TraesCS5B01G194000 chr5A 89.796 392 31 5 840 1223 391993088 391992698 1.230000e-135 494.0
24 TraesCS5B01G194000 chr5A 95.455 44 2 0 764 807 391994457 391994414 2.460000e-08 71.3
25 TraesCS5B01G194000 chr4B 88.846 771 78 1 1 763 581945359 581944589 0.000000e+00 941.0
26 TraesCS5B01G194000 chr6B 88.613 764 81 1 1 764 659669974 659670731 0.000000e+00 924.0
27 TraesCS5B01G194000 chr6B 84.426 732 101 6 44 765 94007172 94006444 0.000000e+00 708.0
28 TraesCS5B01G194000 chr7B 88.114 774 82 3 1 765 732590019 732590791 0.000000e+00 911.0
29 TraesCS5B01G194000 chr7B 74.194 589 133 16 3326 3902 479493138 479493719 1.380000e-55 228.0
30 TraesCS5B01G194000 chr7B 90.741 162 15 0 1865 2026 102234478 102234317 2.980000e-52 217.0
31 TraesCS5B01G194000 chr7B 88.415 164 17 1 1865 2026 12186615 12186452 3.890000e-46 196.0
32 TraesCS5B01G194000 chr3A 83.333 750 114 4 26 765 23297298 23296550 0.000000e+00 682.0
33 TraesCS5B01G194000 chr7D 80.804 771 139 4 1 763 123413001 123413770 3.280000e-166 595.0
34 TraesCS5B01G194000 chr7D 74.695 573 128 15 3340 3902 201194748 201194183 6.370000e-59 239.0
35 TraesCS5B01G194000 chr7D 74.237 590 131 17 3326 3902 457186094 457186675 1.380000e-55 228.0
36 TraesCS5B01G194000 chr4D 80.694 461 85 4 306 764 55069217 55068759 6.060000e-94 355.0
37 TraesCS5B01G194000 chr7A 75.128 587 125 17 3329 3902 543065763 543065185 6.320000e-64 255.0
38 TraesCS5B01G194000 chr3D 88.757 169 19 0 1865 2033 128214007 128214175 1.800000e-49 207.0
39 TraesCS5B01G194000 chr1B 88.166 169 17 2 1865 2031 171034290 171034457 1.080000e-46 198.0
40 TraesCS5B01G194000 chr1A 88.344 163 19 0 1864 2026 441240752 441240914 3.890000e-46 196.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G194000 chr5B 350409989 350414911 4922 False 3498.000000 9092 93.722667 1 4923 3 chr5B.!!$F2 4922
1 TraesCS5B01G194000 chr5D 305727102 305734890 7788 False 1200.166667 2806 92.381167 942 4884 6 chr5D.!!$F2 3942
2 TraesCS5B01G194000 chr5D 322976552 322977155 603 True 870.000000 870 92.727000 3300 3901 1 chr5D.!!$R1 601
3 TraesCS5B01G194000 chr5D 322985828 322987987 2159 True 751.750000 1070 87.440750 954 4887 4 chr5D.!!$R3 3933
4 TraesCS5B01G194000 chr2B 7581805 7582578 773 True 1273.000000 1273 96.512000 1 766 1 chr2B.!!$R1 765
5 TraesCS5B01G194000 chr2B 705367044 705367815 771 False 1247.000000 1247 95.984000 1 764 1 chr2B.!!$F1 763
6 TraesCS5B01G194000 chr5A 391992015 391994457 2442 True 552.575000 944 92.478000 764 4887 4 chr5A.!!$R1 4123
7 TraesCS5B01G194000 chr4B 581944589 581945359 770 True 941.000000 941 88.846000 1 763 1 chr4B.!!$R1 762
8 TraesCS5B01G194000 chr6B 659669974 659670731 757 False 924.000000 924 88.613000 1 764 1 chr6B.!!$F1 763
9 TraesCS5B01G194000 chr6B 94006444 94007172 728 True 708.000000 708 84.426000 44 765 1 chr6B.!!$R1 721
10 TraesCS5B01G194000 chr7B 732590019 732590791 772 False 911.000000 911 88.114000 1 765 1 chr7B.!!$F2 764
11 TraesCS5B01G194000 chr7B 479493138 479493719 581 False 228.000000 228 74.194000 3326 3902 1 chr7B.!!$F1 576
12 TraesCS5B01G194000 chr3A 23296550 23297298 748 True 682.000000 682 83.333000 26 765 1 chr3A.!!$R1 739
13 TraesCS5B01G194000 chr7D 123413001 123413770 769 False 595.000000 595 80.804000 1 763 1 chr7D.!!$F1 762
14 TraesCS5B01G194000 chr7D 201194183 201194748 565 True 239.000000 239 74.695000 3340 3902 1 chr7D.!!$R1 562
15 TraesCS5B01G194000 chr7D 457186094 457186675 581 False 228.000000 228 74.237000 3326 3902 1 chr7D.!!$F2 576
16 TraesCS5B01G194000 chr7A 543065185 543065763 578 True 255.000000 255 75.128000 3329 3902 1 chr7A.!!$R1 573

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
938 2265 0.674895 GGCTTGATGTGAGCGTTCCT 60.675 55.000 0.00 0.00 41.03 3.36 F
1225 2568 0.106569 TGCCCCATTGATCTTCGCAT 60.107 50.000 0.00 0.00 0.00 4.73 F
1707 3086 0.179045 AGACTGCTTGAACCTGCGTT 60.179 50.000 0.00 0.00 33.88 4.84 F
1740 3120 1.133792 CCCGGGGTGATAAGAATGCTT 60.134 52.381 14.71 0.00 38.15 3.91 F
1860 3240 1.271163 CCACGAGTAAGGGCCTTTCAA 60.271 52.381 26.29 3.02 0.00 2.69 F
3821 7559 1.207488 AGATGGGGTGGCTGCAACTA 61.207 55.000 7.18 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2642 4578 0.383949 TGAACAGCACGGGAAAAAGC 59.616 50.000 0.00 0.0 0.00 3.51 R
3137 6867 2.224018 GCTGGTAGCAAGAGATGGAGAG 60.224 54.545 0.00 0.0 41.89 3.20 R
3538 7276 0.820891 CCAAGCTGCAACTGTCACCT 60.821 55.000 1.02 0.0 0.00 4.00 R
3816 7554 6.033619 CGAGTCGTTTGGAGAACTAATAGTTG 59.966 42.308 10.76 0.0 38.80 3.16 R
3910 7648 3.132824 TGAACGATCATCAGTAGCCATGT 59.867 43.478 0.00 0.0 0.00 3.21 R
4887 10183 0.031314 AGCTGGCGACGTATCAGATG 59.969 55.000 14.06 0.0 0.00 2.90 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
24 25 6.211515 GTCTTTGCAAATTGTGATGACTTCT 58.788 36.000 13.23 0.00 0.00 2.85
81 82 2.942376 TGGTCGCTTCGCAATGATTTAT 59.058 40.909 0.00 0.00 0.00 1.40
115 124 1.004595 GTGCCTCCGATTCCGTTTAC 58.995 55.000 0.00 0.00 0.00 2.01
483 492 3.069300 CCATCATCGTCCAGTCTGATTCT 59.931 47.826 0.00 0.00 0.00 2.40
499 508 6.981559 GTCTGATTCTTCGTTAGCTATTTCCT 59.018 38.462 0.00 0.00 0.00 3.36
606 615 8.911918 TTATTCCTATGAAAATTAGCCGCTTA 57.088 30.769 0.00 0.00 33.32 3.09
654 663 4.056740 CCTCTTACAGTCGTATAGAGCGA 58.943 47.826 0.00 0.00 34.69 4.93
796 805 7.068839 TGGAGAACAAATTTACTAACCTTTGCA 59.931 33.333 0.00 0.00 33.03 4.08
825 2149 7.560368 TGACCATTTGGAAGTGTAAACAAAAT 58.440 30.769 3.01 0.00 36.53 1.82
826 2150 8.043710 TGACCATTTGGAAGTGTAAACAAAATT 58.956 29.630 3.01 0.00 36.53 1.82
827 2151 8.800370 ACCATTTGGAAGTGTAAACAAAATTT 57.200 26.923 3.01 0.00 36.53 1.82
828 2152 9.892130 ACCATTTGGAAGTGTAAACAAAATTTA 57.108 25.926 3.01 0.00 36.53 1.40
938 2265 0.674895 GGCTTGATGTGAGCGTTCCT 60.675 55.000 0.00 0.00 41.03 3.36
939 2266 1.405526 GGCTTGATGTGAGCGTTCCTA 60.406 52.381 0.00 0.00 41.03 2.94
940 2267 1.661112 GCTTGATGTGAGCGTTCCTAC 59.339 52.381 0.00 0.00 0.00 3.18
950 2279 2.556534 GCGTTCCTACTCTCGCTAAA 57.443 50.000 0.00 0.00 44.28 1.85
998 2327 2.207924 AGAGAAACCCTCGCGTGGT 61.208 57.895 24.30 19.86 46.49 4.16
1022 2351 2.269241 GCCTCCTCCAACGGAAGG 59.731 66.667 0.00 0.00 31.44 3.46
1047 2376 0.472543 TCCGGCATGGATCAGAGGAT 60.473 55.000 0.00 0.00 43.74 3.24
1077 2406 0.756294 TCTGCCTTTCTGTTCACGGA 59.244 50.000 0.00 0.00 0.00 4.69
1080 2409 1.140052 TGCCTTTCTGTTCACGGAGAA 59.860 47.619 0.00 0.00 32.05 2.87
1161 2493 0.253044 CAGAACCCCGTGATGACCAT 59.747 55.000 0.00 0.00 0.00 3.55
1225 2568 0.106569 TGCCCCATTGATCTTCGCAT 60.107 50.000 0.00 0.00 0.00 4.73
1234 2577 5.240183 CCATTGATCTTCGCATATCCTTTGT 59.760 40.000 0.00 0.00 0.00 2.83
1247 2620 2.243810 TCCTTTGTGCCAACCCAATAC 58.756 47.619 0.00 0.00 0.00 1.89
1397 2771 1.871080 CGATGACAAGGATGGTAGCC 58.129 55.000 0.00 0.00 0.00 3.93
1456 2830 2.417924 GGCAGACGAGAACAGTGATGAT 60.418 50.000 0.00 0.00 0.00 2.45
1688 3067 3.304391 GCAGTTTCAACAAAGCGTATGGA 60.304 43.478 0.00 0.00 0.00 3.41
1707 3086 0.179045 AGACTGCTTGAACCTGCGTT 60.179 50.000 0.00 0.00 33.88 4.84
1740 3120 1.133792 CCCGGGGTGATAAGAATGCTT 60.134 52.381 14.71 0.00 38.15 3.91
1772 3152 5.382616 TCTTTTCCTTTGAAAGTACTCCCC 58.617 41.667 4.02 0.00 41.31 4.81
1860 3240 1.271163 CCACGAGTAAGGGCCTTTCAA 60.271 52.381 26.29 3.02 0.00 2.69
1885 3265 9.467030 AATCTTACTCCCTCCTTTCCTAAATAT 57.533 33.333 0.00 0.00 0.00 1.28
1969 3349 2.693069 AGATTCACTCAGTTTGCTCCG 58.307 47.619 0.00 0.00 0.00 4.63
1986 3366 6.510879 TGCTCCGTATGTAGTCTATATTGG 57.489 41.667 0.00 0.00 0.00 3.16
1992 3372 9.175312 TCCGTATGTAGTCTATATTGGAATCTC 57.825 37.037 7.43 0.00 0.00 2.75
2017 3397 6.812879 AAAAGGACTTGTATTTAGGAACGG 57.187 37.500 0.00 0.00 0.00 4.44
2134 3985 1.479323 CCCAATCCAAGAACCATGCTG 59.521 52.381 0.00 0.00 0.00 4.41
2244 4095 4.124238 CGGCGGAATCTTATCTTTAACCA 58.876 43.478 0.00 0.00 0.00 3.67
2369 4240 3.495331 TGTCAATTAGCTTCTTTGCCCA 58.505 40.909 0.00 0.00 0.00 5.36
2560 4435 4.216257 TCTTCTGCTTTCATTTTCGGAAGG 59.784 41.667 9.07 0.00 40.50 3.46
2642 4578 5.440610 AGTAAATAAGCTTGGATCACTGGG 58.559 41.667 9.86 0.00 0.00 4.45
2673 4619 4.629634 CCGTGCTGTTCATTTACACATCTA 59.370 41.667 0.00 0.00 0.00 1.98
2807 4754 1.409521 CCGGGTGCATTGATCCCTTTA 60.410 52.381 7.67 0.00 39.10 1.85
2818 4765 4.733077 TGATCCCTTTAGAACCCAACAA 57.267 40.909 0.00 0.00 0.00 2.83
3006 6736 5.248020 TGGAGATTGGGCATGTGTTAAAAAT 59.752 36.000 0.00 0.00 0.00 1.82
3137 6867 4.928661 ACACATACACGAGAGCATTTTC 57.071 40.909 0.00 0.00 0.00 2.29
3166 6896 2.914777 CTTGCTACCAGCCTCTCCGC 62.915 65.000 0.00 0.00 41.51 5.54
3203 6933 8.064222 GGACAACATCAAATTCGTCTGTATATG 58.936 37.037 0.00 0.00 0.00 1.78
3204 6934 8.492673 ACAACATCAAATTCGTCTGTATATGT 57.507 30.769 0.00 0.00 0.00 2.29
3790 7528 5.186797 ACAAGTGGAGAAAATGGTGTTTCAA 59.813 36.000 0.97 0.00 39.52 2.69
3816 7554 2.757099 CCAAGATGGGGTGGCTGC 60.757 66.667 0.00 0.00 32.67 5.25
3821 7559 1.207488 AGATGGGGTGGCTGCAACTA 61.207 55.000 7.18 0.00 0.00 2.24
3910 7648 2.547218 GGACTTGCAACCAGTTAGACGA 60.547 50.000 0.00 0.00 0.00 4.20
3960 7698 9.062524 CCGATGTGGATGTTAGGAATAAATTAA 57.937 33.333 0.00 0.00 42.00 1.40
4025 7763 3.414269 CGTTATTGGTAAGGGGTGTGTT 58.586 45.455 0.00 0.00 0.00 3.32
4063 7801 6.536941 GTCATGTCCCTTCTCTCTTTATTGTC 59.463 42.308 0.00 0.00 0.00 3.18
4108 7846 3.454812 TGCCCCTGAATAAGTACCTCTTC 59.545 47.826 0.00 0.00 37.56 2.87
4124 7862 8.502738 AGTACCTCTTCTTCTCATCTCTTCTAT 58.497 37.037 0.00 0.00 0.00 1.98
4182 7920 6.611613 ATCAACAGAAATCAGGACTAGTCA 57.388 37.500 23.91 4.49 0.00 3.41
4274 8012 0.461870 CTAGGCAGCGGTTATGCACA 60.462 55.000 0.00 0.00 45.68 4.57
4276 8014 2.331893 GGCAGCGGTTATGCACACA 61.332 57.895 0.00 0.00 45.68 3.72
4282 8020 2.095263 AGCGGTTATGCACACATGAAAC 60.095 45.455 0.00 0.00 37.04 2.78
4343 8082 2.507102 CGATCAACAGCGGCGAGT 60.507 61.111 12.98 5.09 0.00 4.18
4379 8118 0.463654 GTGAGCACACAGGTGGACAA 60.464 55.000 9.58 0.00 45.38 3.18
4389 8128 1.052124 AGGTGGACAAGGACGACCAA 61.052 55.000 6.71 0.00 38.33 3.67
4408 8147 2.672996 GCCGTGCCCAAGTGATGT 60.673 61.111 0.00 0.00 0.00 3.06
4444 8183 1.202417 ACAAGGATGGTAGCGATCACG 60.202 52.381 0.00 0.00 42.93 4.35
4457 8196 0.109504 GATCACGAGGAGGATAGCGC 60.110 60.000 0.00 0.00 0.00 5.92
4490 8229 3.629398 GCCCAAATGGTAGATGAGAACAG 59.371 47.826 0.00 0.00 36.04 3.16
4498 8237 4.403752 TGGTAGATGAGAACAGTGATGAGG 59.596 45.833 0.00 0.00 0.00 3.86
4519 8259 8.757307 TGAGGAGGTTAGGGATGAATATTATT 57.243 34.615 0.00 0.00 0.00 1.40
4561 8301 1.247567 CGAGACAAATTGCCCAGGTT 58.752 50.000 0.00 0.00 0.00 3.50
4635 9931 8.061857 TGAAAATAATTAACTGACGATCGATGC 58.938 33.333 24.34 11.07 0.00 3.91
4637 9933 8.812147 AAATAATTAACTGACGATCGATGCTA 57.188 30.769 24.34 4.14 0.00 3.49
4649 9945 4.325741 CGATCGATGCTACATTGATTCCTC 59.674 45.833 10.26 0.49 0.00 3.71
4651 9947 5.219343 TCGATGCTACATTGATTCCTCAT 57.781 39.130 0.00 0.00 0.00 2.90
4685 9981 2.616510 CCAAGGAAGAAGCGGATGAAGT 60.617 50.000 0.00 0.00 0.00 3.01
4692 9988 3.093057 AGAAGCGGATGAAGTAGTGTCT 58.907 45.455 0.00 0.00 0.00 3.41
4705 10001 3.762288 AGTAGTGTCTAGATGGTTTCGCA 59.238 43.478 0.00 0.00 0.00 5.10
4741 10037 2.418368 TGTTGACTGCTTGAACCTGT 57.582 45.000 0.00 0.00 0.00 4.00
4757 10053 2.763448 ACCTGTGTGAGGAGATTCTAGC 59.237 50.000 0.00 0.00 46.33 3.42
4762 10058 0.470080 TGAGGAGATTCTAGCCCGGG 60.470 60.000 19.09 19.09 0.00 5.73
4778 10074 1.140852 CCGGGGTGATAAGAATGCTCA 59.859 52.381 0.00 0.00 0.00 4.26
4798 10094 5.474876 GCTCATCTTCCTTCTTTTCCTTTGA 59.525 40.000 0.00 0.00 0.00 2.69
4807 10103 6.771267 TCCTTCTTTTCCTTTGAAAGTACTCC 59.229 38.462 4.02 0.00 41.31 3.85
4812 10108 4.351874 TCCTTTGAAAGTACTCCCTGTG 57.648 45.455 4.02 0.00 0.00 3.66
4814 10110 3.181443 CCTTTGAAAGTACTCCCTGTGGT 60.181 47.826 4.02 0.00 0.00 4.16
4865 10161 2.864343 GCTACCACCGTGAATACATGAC 59.136 50.000 0.00 0.00 35.25 3.06
4884 10180 1.021390 CCCATGACACTTCCACGAGC 61.021 60.000 0.00 0.00 0.00 5.03
4887 10183 1.195448 CATGACACTTCCACGAGCAAC 59.805 52.381 0.00 0.00 0.00 4.17
4888 10184 0.176910 TGACACTTCCACGAGCAACA 59.823 50.000 0.00 0.00 0.00 3.33
4889 10185 1.202639 TGACACTTCCACGAGCAACAT 60.203 47.619 0.00 0.00 0.00 2.71
4891 10187 1.070758 ACACTTCCACGAGCAACATCT 59.929 47.619 0.00 0.00 0.00 2.90
4892 10188 1.462283 CACTTCCACGAGCAACATCTG 59.538 52.381 0.00 0.00 0.00 2.90
4893 10189 1.344438 ACTTCCACGAGCAACATCTGA 59.656 47.619 0.00 0.00 0.00 3.27
4895 10191 3.195610 ACTTCCACGAGCAACATCTGATA 59.804 43.478 0.00 0.00 0.00 2.15
4896 10192 3.165058 TCCACGAGCAACATCTGATAC 57.835 47.619 0.00 0.00 0.00 2.24
4897 10193 1.854743 CCACGAGCAACATCTGATACG 59.145 52.381 0.00 0.00 0.00 3.06
4900 10196 1.775770 CGAGCAACATCTGATACGTCG 59.224 52.381 0.00 0.00 0.00 5.12
4901 10197 1.518929 GAGCAACATCTGATACGTCGC 59.481 52.381 0.00 0.00 0.00 5.19
4902 10198 0.577269 GCAACATCTGATACGTCGCC 59.423 55.000 0.00 0.00 0.00 5.54
4903 10199 1.921243 CAACATCTGATACGTCGCCA 58.079 50.000 0.00 0.00 0.00 5.69
4904 10200 1.854743 CAACATCTGATACGTCGCCAG 59.145 52.381 0.00 0.00 0.00 4.85
4905 10201 0.249073 ACATCTGATACGTCGCCAGC 60.249 55.000 0.00 0.00 0.00 4.85
4906 10202 0.031314 CATCTGATACGTCGCCAGCT 59.969 55.000 0.00 0.00 0.00 4.24
4907 10203 0.747255 ATCTGATACGTCGCCAGCTT 59.253 50.000 0.00 0.00 0.00 3.74
4908 10204 0.530744 TCTGATACGTCGCCAGCTTT 59.469 50.000 0.00 0.00 0.00 3.51
4909 10205 1.746787 TCTGATACGTCGCCAGCTTTA 59.253 47.619 0.00 0.00 0.00 1.85
4910 10206 2.361119 TCTGATACGTCGCCAGCTTTAT 59.639 45.455 0.00 0.00 0.00 1.40
4911 10207 2.726760 CTGATACGTCGCCAGCTTTATC 59.273 50.000 0.00 0.00 0.00 1.75
4912 10208 2.361119 TGATACGTCGCCAGCTTTATCT 59.639 45.455 0.00 0.00 0.00 1.98
4913 10209 3.566742 TGATACGTCGCCAGCTTTATCTA 59.433 43.478 0.00 0.00 0.00 1.98
4914 10210 2.953466 ACGTCGCCAGCTTTATCTAA 57.047 45.000 0.00 0.00 0.00 2.10
4915 10211 3.241067 ACGTCGCCAGCTTTATCTAAA 57.759 42.857 0.00 0.00 0.00 1.85
4916 10212 3.793559 ACGTCGCCAGCTTTATCTAAAT 58.206 40.909 0.00 0.00 0.00 1.40
4917 10213 4.189231 ACGTCGCCAGCTTTATCTAAATT 58.811 39.130 0.00 0.00 0.00 1.82
4918 10214 4.270325 ACGTCGCCAGCTTTATCTAAATTC 59.730 41.667 0.00 0.00 0.00 2.17
4919 10215 4.508124 CGTCGCCAGCTTTATCTAAATTCT 59.492 41.667 0.00 0.00 0.00 2.40
4920 10216 5.006746 CGTCGCCAGCTTTATCTAAATTCTT 59.993 40.000 0.00 0.00 0.00 2.52
4921 10217 6.195165 GTCGCCAGCTTTATCTAAATTCTTG 58.805 40.000 0.00 0.00 0.00 3.02
4922 10218 6.037172 GTCGCCAGCTTTATCTAAATTCTTGA 59.963 38.462 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.571605 TCAAGAAGTCATCACAATTTGCAAA 58.428 32.000 15.44 15.44 0.00 3.68
24 25 4.356405 ACATGATCACACAGTCCTTCAA 57.644 40.909 0.00 0.00 0.00 2.69
81 82 1.003839 GCACTTCCGTCCCATGTGA 60.004 57.895 0.00 0.00 0.00 3.58
115 124 4.385146 CGATTGCATGTAGCTCTGTAGATG 59.615 45.833 0.00 0.00 45.94 2.90
483 492 7.926555 CCAGATAAAGAGGAAATAGCTAACGAA 59.073 37.037 0.00 0.00 0.00 3.85
606 615 4.406003 AGACGATCTGCTACCCTATTTTGT 59.594 41.667 0.00 0.00 0.00 2.83
654 663 1.538047 CCAGCCATACAGCAGTTGTT 58.462 50.000 0.00 0.00 41.29 2.83
796 805 6.549364 TGTTTACACTTCCAAATGGTCAGATT 59.451 34.615 0.00 0.00 36.34 2.40
901 2225 3.499737 GAGCGCAACATGGACCGG 61.500 66.667 11.47 0.00 0.00 5.28
902 2226 3.853330 CGAGCGCAACATGGACCG 61.853 66.667 11.47 0.00 0.00 4.79
904 2228 4.166011 GCCGAGCGCAACATGGAC 62.166 66.667 11.47 0.00 37.47 4.02
905 2229 3.899981 AAGCCGAGCGCAACATGGA 62.900 57.895 11.47 0.00 41.38 3.41
950 2279 3.284449 GCTTTGTGGTTCGGGCGT 61.284 61.111 0.00 0.00 0.00 5.68
998 2327 1.223487 GTTGGAGGAGGCGCCATTA 59.777 57.895 31.54 5.40 40.02 1.90
1034 2363 5.271598 GGATCTCAGTATCCTCTGATCCAT 58.728 45.833 13.08 0.00 41.57 3.41
1054 2383 2.613977 CGTGAACAGAAAGGCAGAGGAT 60.614 50.000 0.00 0.00 0.00 3.24
1060 2389 0.756294 TCTCCGTGAACAGAAAGGCA 59.244 50.000 0.00 0.00 0.00 4.75
1080 2409 4.974721 CAAACGCTGGGGTGGCCT 62.975 66.667 3.32 0.00 0.00 5.19
1137 2466 3.606687 GTCATCACGGGGTTCTGTAATT 58.393 45.455 0.00 0.00 0.00 1.40
1161 2493 4.662961 CCTGTGGACACGAGCGCA 62.663 66.667 11.47 0.00 0.00 6.09
1234 2577 1.003696 TGATGTCGTATTGGGTTGGCA 59.996 47.619 0.00 0.00 0.00 4.92
1247 2620 7.571089 AACAAACAATTGATCAATGATGTCG 57.429 32.000 21.39 17.29 38.94 4.35
1325 2699 2.939022 GTCGCTGTCCAACTGTGC 59.061 61.111 0.00 0.00 0.00 4.57
1397 2771 1.226802 CGCTGTCCTCCTCGTCATG 60.227 63.158 0.00 0.00 0.00 3.07
1456 2830 5.157770 AGTATTCATCCCTAACCTCCTCA 57.842 43.478 0.00 0.00 0.00 3.86
1593 2970 4.165565 TCCTGAGGAATCAATTCAGCATCT 59.834 41.667 0.00 0.00 37.58 2.90
1688 3067 0.179045 AACGCAGGTTCAAGCAGTCT 60.179 50.000 0.00 0.00 0.00 3.24
1707 3086 1.054406 CCCCGGGCTAGAATCTCCAA 61.054 60.000 17.73 0.00 0.00 3.53
1740 3120 6.663523 ACTTTCAAAGGAAAAGAAGGAAGACA 59.336 34.615 1.31 0.00 42.18 3.41
1772 3152 2.054687 TGCGTAGACTTGTTACCACG 57.945 50.000 0.00 0.00 0.00 4.94
1947 3327 3.614616 CGGAGCAAACTGAGTGAATCTAC 59.385 47.826 0.00 0.00 0.00 2.59
1992 3372 7.820872 TCCGTTCCTAAATACAAGTCCTTTTAG 59.179 37.037 0.00 0.00 33.47 1.85
1998 3378 4.439968 CCTCCGTTCCTAAATACAAGTCC 58.560 47.826 0.00 0.00 0.00 3.85
2002 3382 4.098894 ACTCCCTCCGTTCCTAAATACAA 58.901 43.478 0.00 0.00 0.00 2.41
2003 3383 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
2004 3384 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
2017 3397 4.688021 CAACTGCAGATTACTACTCCCTC 58.312 47.826 23.35 0.00 0.00 4.30
2060 3440 3.469739 AGGACAAAAAGGCAAAATGCTG 58.530 40.909 2.00 0.00 44.28 4.41
2134 3985 0.952984 AGCGCAAAGAGAAGACCTGC 60.953 55.000 11.47 0.00 0.00 4.85
2244 4095 1.327303 GACAGCATCCTCTCTCCGAT 58.673 55.000 0.00 0.00 0.00 4.18
2610 4485 4.455606 CAAGCTTATTTACTCTCCCCCTG 58.544 47.826 0.00 0.00 0.00 4.45
2642 4578 0.383949 TGAACAGCACGGGAAAAAGC 59.616 50.000 0.00 0.00 0.00 3.51
2673 4619 5.163311 GCCCAATGACCATTTAATTAAGCCT 60.163 40.000 0.00 0.00 0.00 4.58
2807 4754 6.012333 TGTTATACATAGGGTTGTTGGGTTCT 60.012 38.462 0.00 0.00 0.00 3.01
2818 4765 7.571025 CCCAGTTTAACTGTTATACATAGGGT 58.429 38.462 21.63 5.80 44.50 4.34
3006 6736 6.472016 TGAAACTGTAACAAGATAGCCATGA 58.528 36.000 0.00 0.00 0.00 3.07
3137 6867 2.224018 GCTGGTAGCAAGAGATGGAGAG 60.224 54.545 0.00 0.00 41.89 3.20
3166 6896 3.326109 GTTGTCCACAACGACCGG 58.674 61.111 0.00 0.00 45.44 5.28
3203 6933 7.224753 TCAGTCACTCTGTTTCAGAATACAAAC 59.775 37.037 1.22 0.00 40.18 2.93
3204 6934 7.272244 TCAGTCACTCTGTTTCAGAATACAAA 58.728 34.615 1.22 0.00 40.18 2.83
3214 6944 3.809905 ACCCTTTCAGTCACTCTGTTTC 58.190 45.455 0.00 0.00 43.97 2.78
3538 7276 0.820891 CCAAGCTGCAACTGTCACCT 60.821 55.000 1.02 0.00 0.00 4.00
3816 7554 6.033619 CGAGTCGTTTGGAGAACTAATAGTTG 59.966 42.308 10.76 0.00 38.80 3.16
3821 7559 4.778534 TCGAGTCGTTTGGAGAACTAAT 57.221 40.909 13.12 0.00 0.00 1.73
3910 7648 3.132824 TGAACGATCATCAGTAGCCATGT 59.867 43.478 0.00 0.00 0.00 3.21
3999 7737 3.441222 CACCCCTTACCAATAACGGTTTC 59.559 47.826 0.00 0.00 40.67 2.78
4025 7763 2.224769 GGACATGACTCTTTGGGGTTGA 60.225 50.000 0.00 0.00 0.00 3.18
4030 7768 2.307098 AGAAGGGACATGACTCTTTGGG 59.693 50.000 11.64 0.00 30.06 4.12
4033 7771 4.424842 AGAGAGAAGGGACATGACTCTTT 58.575 43.478 11.64 2.54 37.93 2.52
4063 7801 5.818136 TCCTTCAAAATAGATGCCTTTCG 57.182 39.130 0.00 0.00 0.00 3.46
4072 7810 3.527253 TCAGGGGCATCCTTCAAAATAGA 59.473 43.478 0.00 0.00 45.47 1.98
4150 7888 6.822170 TCCTGATTTCTGTTGATTCTCATCTG 59.178 38.462 0.00 0.00 0.00 2.90
4164 7902 5.604758 TGGATGACTAGTCCTGATTTCTG 57.395 43.478 20.11 0.00 36.68 3.02
4214 7952 4.217118 GGAGAGCGAAGGGATAATAACGTA 59.783 45.833 0.00 0.00 0.00 3.57
4274 8012 3.722295 CGTGCGGGCGTTTCATGT 61.722 61.111 0.00 0.00 0.00 3.21
4294 8032 3.876255 TAGGGGAGGCACCGGGTTT 62.876 63.158 6.32 0.00 40.11 3.27
4311 8049 3.369410 ATCGAGGGAGGGCGTGGTA 62.369 63.158 0.00 0.00 0.00 3.25
4360 8099 0.463654 TTGTCCACCTGTGTGCTCAC 60.464 55.000 11.94 11.94 41.35 3.51
4389 8128 2.048023 CATCACTTGGGCACGGCAT 61.048 57.895 0.00 0.00 0.00 4.40
4408 8147 2.959030 CCTTGTCATCGATGTCCTCCTA 59.041 50.000 24.09 0.73 0.00 2.94
4424 8163 1.202417 CGTGATCGCTACCATCCTTGT 60.202 52.381 4.48 0.00 0.00 3.16
4444 8183 3.445450 TCATATTCAGCGCTATCCTCCTC 59.555 47.826 10.99 0.00 0.00 3.71
4457 8196 6.005823 TCTACCATTTGGGCATCATATTCAG 58.994 40.000 0.96 0.00 42.05 3.02
4490 8229 3.309296 TCATCCCTAACCTCCTCATCAC 58.691 50.000 0.00 0.00 0.00 3.06
4618 9914 4.625972 TGTAGCATCGATCGTCAGTTAA 57.374 40.909 15.94 0.00 0.00 2.01
4623 9919 3.708563 TCAATGTAGCATCGATCGTCA 57.291 42.857 15.94 0.00 0.00 4.35
4660 9956 1.933021 TCCGCTTCTTCCTTGGAGTA 58.067 50.000 0.00 0.00 0.00 2.59
4661 9957 1.065854 CATCCGCTTCTTCCTTGGAGT 60.066 52.381 0.00 0.00 31.10 3.85
4662 9958 1.208052 TCATCCGCTTCTTCCTTGGAG 59.792 52.381 0.00 0.00 31.10 3.86
4663 9959 1.275666 TCATCCGCTTCTTCCTTGGA 58.724 50.000 0.00 0.00 0.00 3.53
4664 9960 2.012673 CTTCATCCGCTTCTTCCTTGG 58.987 52.381 0.00 0.00 0.00 3.61
4666 9962 3.515901 ACTACTTCATCCGCTTCTTCCTT 59.484 43.478 0.00 0.00 0.00 3.36
4667 9963 3.100671 ACTACTTCATCCGCTTCTTCCT 58.899 45.455 0.00 0.00 0.00 3.36
4668 9964 3.190874 CACTACTTCATCCGCTTCTTCC 58.809 50.000 0.00 0.00 0.00 3.46
4669 9965 3.851098 ACACTACTTCATCCGCTTCTTC 58.149 45.455 0.00 0.00 0.00 2.87
4685 9981 3.762288 ACTGCGAAACCATCTAGACACTA 59.238 43.478 0.00 0.00 0.00 2.74
4692 9988 4.130857 TGTTGAAACTGCGAAACCATCTA 58.869 39.130 0.00 0.00 0.00 1.98
4705 10001 2.869233 ACATGCGCTTTGTTGAAACT 57.131 40.000 9.73 0.00 0.00 2.66
4741 10037 1.403814 CGGGCTAGAATCTCCTCACA 58.596 55.000 0.00 0.00 0.00 3.58
4757 10053 0.474184 AGCATTCTTATCACCCCGGG 59.526 55.000 15.80 15.80 0.00 5.73
4762 10058 5.619220 AGGAAGATGAGCATTCTTATCACC 58.381 41.667 0.32 3.45 37.68 4.02
4778 10074 7.904558 ACTTTCAAAGGAAAAGAAGGAAGAT 57.095 32.000 1.31 0.00 42.18 2.40
4798 10094 4.657039 TCTTGTTACCACAGGGAGTACTTT 59.343 41.667 0.00 0.00 38.05 2.66
4807 10103 3.937814 TGCATAGTCTTGTTACCACAGG 58.062 45.455 0.00 0.00 33.22 4.00
4812 10108 7.535139 TGCTTTTAATGCATAGTCTTGTTACC 58.465 34.615 0.00 0.00 35.31 2.85
4814 10110 8.572185 TGTTGCTTTTAATGCATAGTCTTGTTA 58.428 29.630 0.00 0.00 40.34 2.41
4865 10161 1.021390 GCTCGTGGAAGTGTCATGGG 61.021 60.000 0.00 0.00 0.00 4.00
4884 10180 1.854743 CTGGCGACGTATCAGATGTTG 59.145 52.381 6.46 0.00 0.00 3.33
4887 10183 0.031314 AGCTGGCGACGTATCAGATG 59.969 55.000 14.06 0.00 0.00 2.90
4888 10184 0.747255 AAGCTGGCGACGTATCAGAT 59.253 50.000 14.06 6.79 0.00 2.90
4889 10185 0.530744 AAAGCTGGCGACGTATCAGA 59.469 50.000 14.06 0.00 0.00 3.27
4891 10187 2.361119 AGATAAAGCTGGCGACGTATCA 59.639 45.455 0.00 0.00 0.00 2.15
4892 10188 3.014604 AGATAAAGCTGGCGACGTATC 57.985 47.619 0.00 0.00 0.00 2.24
4893 10189 4.579454 TTAGATAAAGCTGGCGACGTAT 57.421 40.909 0.00 0.00 0.00 3.06
4895 10191 2.953466 TTAGATAAAGCTGGCGACGT 57.047 45.000 0.00 0.00 0.00 4.34
4896 10192 4.508124 AGAATTTAGATAAAGCTGGCGACG 59.492 41.667 0.00 0.00 0.00 5.12
4897 10193 5.993106 AGAATTTAGATAAAGCTGGCGAC 57.007 39.130 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.