Multiple sequence alignment - TraesCS5D01G478100

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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 TraesCS5D01G478100 chr5D 100.000 3257 0 0 1 3257 517045171 517048427 0.000000e+00 6015.0
1 TraesCS5D01G478100 chr5D 87.546 811 73 19 1 795 548802023 548802821 0.000000e+00 913.0
2 TraesCS5D01G478100 chr5D 77.651 1311 225 44 921 2205 518755457 518756725 0.000000e+00 736.0
3 TraesCS5D01G478100 chr5D 77.574 1311 225 38 921 2205 517976283 517975016 0.000000e+00 728.0
4 TraesCS5D01G478100 chr5D 76.990 691 126 19 1536 2205 518761883 518762561 6.640000e-97 364.0
5 TraesCS5D01G478100 chr5D 76.486 370 69 12 2752 3115 324705707 324706064 5.550000e-43 185.0
6 TraesCS5D01G478100 chr5B 95.625 1440 51 3 883 2313 649453824 649455260 0.000000e+00 2300.0
7 TraesCS5D01G478100 chr5B 78.125 1280 214 38 953 2205 651211059 651212299 0.000000e+00 752.0
8 TraesCS5D01G478100 chr5B 77.928 1187 198 36 953 2113 650983115 650984263 0.000000e+00 682.0
9 TraesCS5D01G478100 chr5B 88.839 448 25 7 2324 2746 649455242 649455689 8.000000e-146 527.0
10 TraesCS5D01G478100 chr5B 75.039 1282 239 46 954 2205 652388318 652389548 1.340000e-143 520.0
11 TraesCS5D01G478100 chr5B 76.121 959 167 34 1272 2205 652375706 652376627 2.310000e-121 446.0
12 TraesCS5D01G478100 chr5B 85.492 193 25 3 2755 2945 655096061 655096252 7.130000e-47 198.0
13 TraesCS5D01G478100 chr1A 90.827 883 65 13 1 871 238884600 238885478 0.000000e+00 1168.0
14 TraesCS5D01G478100 chr2D 90.460 891 59 16 1 870 188518316 188517431 0.000000e+00 1151.0
15 TraesCS5D01G478100 chr2D 75.285 526 95 16 2619 3111 206258394 206257871 5.470000e-53 219.0
16 TraesCS5D01G478100 chr2D 80.351 285 49 5 2752 3030 30101506 30101223 3.290000e-50 209.0
17 TraesCS5D01G478100 chr2D 80.180 111 21 1 2636 2746 569410730 569410839 7.490000e-12 82.4
18 TraesCS5D01G478100 chr6D 90.292 855 47 15 1 845 90413704 90412876 0.000000e+00 1086.0
19 TraesCS5D01G478100 chr6D 86.020 887 72 26 1 871 40979354 40978504 0.000000e+00 904.0
20 TraesCS5D01G478100 chr6D 86.184 152 21 0 2755 2906 105828036 105828187 7.230000e-37 165.0
21 TraesCS5D01G478100 chr4D 89.089 889 75 15 1 870 490150254 490151139 0.000000e+00 1085.0
22 TraesCS5D01G478100 chr4D 85.156 896 82 24 1 883 344951256 344950399 0.000000e+00 870.0
23 TraesCS5D01G478100 chr4D 75.088 570 103 13 2574 3111 16140419 16139857 2.530000e-56 230.0
24 TraesCS5D01G478100 chr1D 88.076 889 81 19 1 870 411397943 411397061 0.000000e+00 1031.0
25 TraesCS5D01G478100 chr1D 90.476 63 4 2 3195 3257 85919979 85920039 7.490000e-12 82.4
26 TraesCS5D01G478100 chr2A 89.341 835 53 17 8 824 202096527 202095711 0.000000e+00 1016.0
27 TraesCS5D01G478100 chr5A 90.969 753 61 3 906 1652 644176880 644177631 0.000000e+00 1007.0
28 TraesCS5D01G478100 chr5A 91.568 676 43 4 1650 2313 644208727 644209400 0.000000e+00 920.0
29 TraesCS5D01G478100 chr5A 77.168 1257 224 36 975 2205 645393115 645394334 0.000000e+00 673.0
30 TraesCS5D01G478100 chr5A 82.979 564 67 15 2317 2870 644209375 644209919 1.760000e-132 483.0
31 TraesCS5D01G478100 chr5A 79.658 526 84 13 1530 2039 644330000 644330518 1.110000e-94 357.0
32 TraesCS5D01G478100 chr5A 78.261 414 66 13 2866 3256 644211473 644211885 9.030000e-61 244.0
33 TraesCS5D01G478100 chr6A 88.041 878 63 14 1 870 615583137 615583980 0.000000e+00 1002.0
34 TraesCS5D01G478100 chr1B 87.717 863 76 18 1 850 688404735 688403890 0.000000e+00 979.0
35 TraesCS5D01G478100 chr7B 92.401 579 36 5 1 574 440190248 440190823 0.000000e+00 819.0
36 TraesCS5D01G478100 chr7B 81.090 312 52 6 2755 3059 728071486 728071797 3.250000e-60 243.0
37 TraesCS5D01G478100 chr2B 92.606 568 33 7 12 574 147620818 147620255 0.000000e+00 808.0
38 TraesCS5D01G478100 chr3B 84.353 850 87 16 1 816 764503532 764504369 0.000000e+00 791.0
39 TraesCS5D01G478100 chr3B 80.450 844 74 28 1 830 50243398 50244164 7.890000e-156 560.0
40 TraesCS5D01G478100 chr3D 77.582 852 144 28 1465 2286 597867947 597868781 3.800000e-129 472.0
41 TraesCS5D01G478100 chr3D 81.967 549 54 23 331 870 554134541 554134029 1.080000e-114 424.0
42 TraesCS5D01G478100 chr3D 76.487 353 70 11 2755 3099 429297481 429297134 2.580000e-41 180.0
43 TraesCS5D01G478100 chr4B 76.884 584 87 24 2570 3111 12238416 12237839 1.480000e-73 287.0
44 TraesCS5D01G478100 chr7A 75.087 578 89 23 2564 3114 562174027 562174576 5.470000e-53 219.0
45 TraesCS5D01G478100 chr7A 75.397 252 56 5 2782 3028 165932499 165932749 2.050000e-22 117.0
46 TraesCS5D01G478100 chr3A 76.567 367 65 14 2752 3111 533628824 533629176 7.180000e-42 182.0
47 TraesCS5D01G478100 chr3A 84.043 94 15 0 2652 2745 702152007 702152100 1.240000e-14 91.6
48 TraesCS5D01G478100 chr3A 83.696 92 12 3 2656 2746 106445899 106445988 2.080000e-12 84.2
49 TraesCS5D01G478100 chr3A 97.059 34 0 1 2713 2746 725161723 725161691 4.540000e-04 56.5
50 TraesCS5D01G478100 chr6B 80.693 202 34 4 2903 3099 664196385 664196184 5.630000e-33 152.0
51 TraesCS5D01G478100 chr4A 76.250 320 48 20 2752 3059 82395672 82395975 9.420000e-31 145.0
52 TraesCS5D01G478100 chr7D 81.333 75 13 1 2673 2746 379056821 379056747 3.510000e-05 60.2
53 TraesCS5D01G478100 chrUn 97.059 34 0 1 2713 2746 455756910 455756878 4.540000e-04 56.5


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 TraesCS5D01G478100 chr5D 517045171 517048427 3256 False 6015.0 6015 100.000000 1 3257 1 chr5D.!!$F2 3256
1 TraesCS5D01G478100 chr5D 548802023 548802821 798 False 913.0 913 87.546000 1 795 1 chr5D.!!$F5 794
2 TraesCS5D01G478100 chr5D 518755457 518756725 1268 False 736.0 736 77.651000 921 2205 1 chr5D.!!$F3 1284
3 TraesCS5D01G478100 chr5D 517975016 517976283 1267 True 728.0 728 77.574000 921 2205 1 chr5D.!!$R1 1284
4 TraesCS5D01G478100 chr5D 518761883 518762561 678 False 364.0 364 76.990000 1536 2205 1 chr5D.!!$F4 669
5 TraesCS5D01G478100 chr5B 649453824 649455689 1865 False 1413.5 2300 92.232000 883 2746 2 chr5B.!!$F6 1863
6 TraesCS5D01G478100 chr5B 651211059 651212299 1240 False 752.0 752 78.125000 953 2205 1 chr5B.!!$F2 1252
7 TraesCS5D01G478100 chr5B 650983115 650984263 1148 False 682.0 682 77.928000 953 2113 1 chr5B.!!$F1 1160
8 TraesCS5D01G478100 chr5B 652388318 652389548 1230 False 520.0 520 75.039000 954 2205 1 chr5B.!!$F4 1251
9 TraesCS5D01G478100 chr5B 652375706 652376627 921 False 446.0 446 76.121000 1272 2205 1 chr5B.!!$F3 933
10 TraesCS5D01G478100 chr1A 238884600 238885478 878 False 1168.0 1168 90.827000 1 871 1 chr1A.!!$F1 870
11 TraesCS5D01G478100 chr2D 188517431 188518316 885 True 1151.0 1151 90.460000 1 870 1 chr2D.!!$R2 869
12 TraesCS5D01G478100 chr2D 206257871 206258394 523 True 219.0 219 75.285000 2619 3111 1 chr2D.!!$R3 492
13 TraesCS5D01G478100 chr6D 90412876 90413704 828 True 1086.0 1086 90.292000 1 845 1 chr6D.!!$R2 844
14 TraesCS5D01G478100 chr6D 40978504 40979354 850 True 904.0 904 86.020000 1 871 1 chr6D.!!$R1 870
15 TraesCS5D01G478100 chr4D 490150254 490151139 885 False 1085.0 1085 89.089000 1 870 1 chr4D.!!$F1 869
16 TraesCS5D01G478100 chr4D 344950399 344951256 857 True 870.0 870 85.156000 1 883 1 chr4D.!!$R2 882
17 TraesCS5D01G478100 chr4D 16139857 16140419 562 True 230.0 230 75.088000 2574 3111 1 chr4D.!!$R1 537
18 TraesCS5D01G478100 chr1D 411397061 411397943 882 True 1031.0 1031 88.076000 1 870 1 chr1D.!!$R1 869
19 TraesCS5D01G478100 chr2A 202095711 202096527 816 True 1016.0 1016 89.341000 8 824 1 chr2A.!!$R1 816
20 TraesCS5D01G478100 chr5A 644176880 644177631 751 False 1007.0 1007 90.969000 906 1652 1 chr5A.!!$F1 746
21 TraesCS5D01G478100 chr5A 645393115 645394334 1219 False 673.0 673 77.168000 975 2205 1 chr5A.!!$F3 1230
22 TraesCS5D01G478100 chr5A 644208727 644211885 3158 False 549.0 920 84.269333 1650 3256 3 chr5A.!!$F4 1606
23 TraesCS5D01G478100 chr5A 644330000 644330518 518 False 357.0 357 79.658000 1530 2039 1 chr5A.!!$F2 509
24 TraesCS5D01G478100 chr6A 615583137 615583980 843 False 1002.0 1002 88.041000 1 870 1 chr6A.!!$F1 869
25 TraesCS5D01G478100 chr1B 688403890 688404735 845 True 979.0 979 87.717000 1 850 1 chr1B.!!$R1 849
26 TraesCS5D01G478100 chr7B 440190248 440190823 575 False 819.0 819 92.401000 1 574 1 chr7B.!!$F1 573
27 TraesCS5D01G478100 chr2B 147620255 147620818 563 True 808.0 808 92.606000 12 574 1 chr2B.!!$R1 562
28 TraesCS5D01G478100 chr3B 764503532 764504369 837 False 791.0 791 84.353000 1 816 1 chr3B.!!$F2 815
29 TraesCS5D01G478100 chr3B 50243398 50244164 766 False 560.0 560 80.450000 1 830 1 chr3B.!!$F1 829
30 TraesCS5D01G478100 chr3D 597867947 597868781 834 False 472.0 472 77.582000 1465 2286 1 chr3D.!!$F1 821
31 TraesCS5D01G478100 chr3D 554134029 554134541 512 True 424.0 424 81.967000 331 870 1 chr3D.!!$R2 539
32 TraesCS5D01G478100 chr4B 12237839 12238416 577 True 287.0 287 76.884000 2570 3111 1 chr4B.!!$R1 541
33 TraesCS5D01G478100 chr7A 562174027 562174576 549 False 219.0 219 75.087000 2564 3114 1 chr7A.!!$F2 550

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
896 1122 0.674581 TTGCTCCGCATCTGACCTTG 60.675 55.0 0.00 0.00 38.76 3.61 F
1396 1631 0.106868 CTTCATGGCCTGCCTCATGA 60.107 55.0 9.97 8.28 45.31 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2512 0.034756 ATTTTTCCTTTGGGCGGTGC 59.965 50.0 0.00 0.0 0.0 5.01 R
2962 4895 0.179048 CCATAGGATCAGCGCACCAA 60.179 55.0 11.47 0.0 0.0 3.67 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
20 21 3.757745 AAATCGGACGCAAATTTCGAT 57.242 38.095 14.21 10.33 41.49 3.59
163 168 8.803397 AACATTTTCTTAGTATAGGGTGAACC 57.197 34.615 0.00 0.00 40.67 3.62
221 230 3.423206 CGCTGAACTTTTTCTGAATGCAC 59.577 43.478 0.00 0.00 33.56 4.57
288 298 9.077885 ACACTGAACATATTTCAATGTAAGGTT 57.922 29.630 10.77 0.00 37.15 3.50
289 299 9.912634 CACTGAACATATTTCAATGTAAGGTTT 57.087 29.630 0.00 0.00 39.16 3.27
557 759 6.636850 AGTCAAACGAATTTCGAAAAATCTGG 59.363 34.615 24.50 7.38 43.74 3.86
707 929 6.902224 ATGAAGAAAACCGAAAAACCTTTG 57.098 33.333 0.00 0.00 0.00 2.77
710 932 6.588373 TGAAGAAAACCGAAAAACCTTTGAAG 59.412 34.615 0.00 0.00 0.00 3.02
754 980 3.181443 GGTTCAGGGAAACTTCTGGAAGA 60.181 47.826 16.06 0.00 44.68 2.87
762 988 5.048434 GGGAAACTTCTGGAAGATTCACAAG 60.048 44.000 24.20 0.00 46.46 3.16
871 1097 1.402456 GCGTCATATAGGAATCGCCGT 60.402 52.381 10.28 0.00 43.43 5.68
872 1098 2.516923 CGTCATATAGGAATCGCCGTC 58.483 52.381 0.00 0.00 43.43 4.79
873 1099 2.731341 CGTCATATAGGAATCGCCGTCC 60.731 54.545 0.00 0.00 43.43 4.79
874 1100 2.230508 GTCATATAGGAATCGCCGTCCA 59.769 50.000 0.00 0.00 43.43 4.02
875 1101 2.492088 TCATATAGGAATCGCCGTCCAG 59.508 50.000 0.00 0.00 43.43 3.86
876 1102 1.254026 TATAGGAATCGCCGTCCAGG 58.746 55.000 0.00 0.00 43.43 4.45
877 1103 0.759436 ATAGGAATCGCCGTCCAGGT 60.759 55.000 0.00 0.00 43.43 4.00
878 1104 0.974010 TAGGAATCGCCGTCCAGGTT 60.974 55.000 0.00 0.00 43.43 3.50
879 1105 2.106683 GGAATCGCCGTCCAGGTTG 61.107 63.158 0.00 0.00 43.70 3.77
880 1106 2.746277 AATCGCCGTCCAGGTTGC 60.746 61.111 0.00 0.00 43.70 4.17
881 1107 3.254024 AATCGCCGTCCAGGTTGCT 62.254 57.895 0.00 0.00 43.70 3.91
896 1122 0.674581 TTGCTCCGCATCTGACCTTG 60.675 55.000 0.00 0.00 38.76 3.61
1059 1291 1.065928 GCACGTCCCGATCTTCGAT 59.934 57.895 0.00 0.00 43.74 3.59
1305 1540 0.916086 TGTTGGGCGACAGGGATTAT 59.084 50.000 0.00 0.00 0.00 1.28
1396 1631 0.106868 CTTCATGGCCTGCCTCATGA 60.107 55.000 9.97 8.28 45.31 3.07
1440 1675 4.475135 GAACTCCTGGAGCGGCCC 62.475 72.222 23.43 4.82 34.97 5.80
1522 1757 1.305802 TACGATGGAGGGTGGCAGT 60.306 57.895 0.00 0.00 0.00 4.40
1586 1830 2.651361 CGAGTGGACGAAGCAGGT 59.349 61.111 0.00 0.00 35.09 4.00
2013 2292 1.221840 GCTGCTCCTGGAATCGGAA 59.778 57.895 0.00 0.00 0.00 4.30
2023 2302 1.906574 TGGAATCGGAAGCCTACAAGT 59.093 47.619 1.93 0.00 0.00 3.16
2217 2508 1.475280 CACAGCCACATCAAAGATGGG 59.525 52.381 11.29 7.08 33.81 4.00
2221 2512 1.133025 GCCACATCAAAGATGGGTTCG 59.867 52.381 11.29 0.00 33.81 3.95
2348 2649 8.712363 ACTGCTATATGATGTTATTTAAGCACG 58.288 33.333 0.00 0.00 0.00 5.34
2351 2652 7.893236 GCTATATGATGTTATTTAAGCACGTCG 59.107 37.037 0.00 0.00 30.26 5.12
2448 2749 7.531857 TTTGGCAACCAAGTGATAATTCTAA 57.468 32.000 0.00 0.00 44.84 2.10
2483 2784 3.454042 TTGTCAAGATGCAAACGATCG 57.546 42.857 14.88 14.88 0.00 3.69
2485 2786 1.732259 GTCAAGATGCAAACGATCGGT 59.268 47.619 20.98 10.86 0.00 4.69
2497 2798 4.127744 ATCGGTGGCCCATGGGTG 62.128 66.667 31.58 16.18 37.65 4.61
2514 2832 2.421529 GGGTGGAGACATAACATGGTCC 60.422 54.545 0.00 3.87 46.14 4.46
2528 2846 9.613428 CATAACATGGTCCAAGACTTAATCTTA 57.387 33.333 0.00 0.00 46.52 2.10
2537 2855 5.946377 CCAAGACTTAATCTTAAGGGCTTGT 59.054 40.000 25.53 7.10 46.52 3.16
2611 2929 3.340928 GAAAAGGCGGCTAGGTTTTCTA 58.659 45.455 20.54 0.00 36.43 2.10
2697 3023 2.515996 GATTCCGGCCCTTGTCGACA 62.516 60.000 15.76 15.76 43.95 4.35
2711 3037 0.038526 TCGACAAGAGGGCTCGTTTC 60.039 55.000 0.00 0.00 34.09 2.78
2746 3074 4.515361 TCGAGTTTTGTTAGGGTTTGTGA 58.485 39.130 0.00 0.00 0.00 3.58
2747 3075 4.942483 TCGAGTTTTGTTAGGGTTTGTGAA 59.058 37.500 0.00 0.00 0.00 3.18
2749 3077 4.989044 AGTTTTGTTAGGGTTTGTGAACG 58.011 39.130 0.00 0.00 36.61 3.95
2777 3131 6.044171 CCTGAAGATGGAATAAGATTCTCCCT 59.956 42.308 0.00 0.00 0.00 4.20
2778 3132 7.236432 CCTGAAGATGGAATAAGATTCTCCCTA 59.764 40.741 0.00 0.00 0.00 3.53
2845 3205 3.302347 GAGGTGTGTCTCCAGCGGG 62.302 68.421 0.00 0.00 37.88 6.13
2854 3214 1.377725 CTCCAGCGGGTCTTGCAAT 60.378 57.895 0.00 0.00 34.93 3.56
2922 4850 4.188462 TCGTTCATGTGTCTTCAAGTTGT 58.812 39.130 2.11 0.00 0.00 3.32
2937 4866 8.816894 TCTTCAAGTTGTATCCTTTGATCTACT 58.183 33.333 2.11 0.00 32.18 2.57
2991 4924 0.250513 GATCCTATGGGGCCTTAGCG 59.749 60.000 0.84 0.61 41.24 4.26
3005 4938 1.940883 TTAGCGCGATGACTTCCCGT 61.941 55.000 12.10 0.00 0.00 5.28
3012 4945 1.726791 CGATGACTTCCCGTTTGTCTG 59.273 52.381 0.00 0.00 0.00 3.51
3031 4964 1.410882 TGCTACAACAAGTTTTGCCCC 59.589 47.619 0.00 0.00 0.00 5.80
3032 4965 1.686587 GCTACAACAAGTTTTGCCCCT 59.313 47.619 0.00 0.00 0.00 4.79
3043 4976 1.075601 TTTGCCCCTCTCCAATGAGT 58.924 50.000 0.00 0.00 39.75 3.41
3051 4984 0.547471 TCTCCAATGAGTGAGGGGCA 60.547 55.000 0.00 0.00 39.75 5.36
3060 4993 1.077716 GTGAGGGGCAATAACGGCT 60.078 57.895 0.00 0.00 0.00 5.52
3061 4994 0.179468 GTGAGGGGCAATAACGGCTA 59.821 55.000 0.00 0.00 0.00 3.93
3063 4996 0.179468 GAGGGGCAATAACGGCTACA 59.821 55.000 0.00 0.00 0.00 2.74
3082 5015 3.433343 ACATGCCATTGGATCACTTCAA 58.567 40.909 6.95 0.00 0.00 2.69
3099 5032 1.000052 TCAATGGTTGTAGTCGTCGCA 60.000 47.619 0.00 0.00 0.00 5.10
3117 5050 3.009723 CGCAAAATGGTCTACTGATGGT 58.990 45.455 0.00 0.00 0.00 3.55
3122 5055 2.238084 TGGTCTACTGATGGTCTGCT 57.762 50.000 0.00 0.00 0.00 4.24
3123 5056 3.382083 TGGTCTACTGATGGTCTGCTA 57.618 47.619 0.00 0.00 0.00 3.49
3124 5057 3.916035 TGGTCTACTGATGGTCTGCTAT 58.084 45.455 0.00 0.00 0.00 2.97
3128 5061 3.963374 TCTACTGATGGTCTGCTATTGCT 59.037 43.478 0.00 0.00 40.48 3.91
3129 5062 5.010112 GTCTACTGATGGTCTGCTATTGCTA 59.990 44.000 0.00 0.00 40.48 3.49
3130 5063 4.333913 ACTGATGGTCTGCTATTGCTAG 57.666 45.455 0.00 0.00 40.48 3.42
3138 5072 4.141688 GGTCTGCTATTGCTAGGGTTTACT 60.142 45.833 0.00 0.00 40.48 2.24
3149 5083 5.704053 TGCTAGGGTTTACTTGTAGCTTTTC 59.296 40.000 0.00 0.00 37.57 2.29
3151 5085 4.070009 AGGGTTTACTTGTAGCTTTTCCG 58.930 43.478 0.00 0.00 0.00 4.30
3163 5097 6.385033 TGTAGCTTTTCCGAAGTAAGAGTAC 58.615 40.000 0.00 0.00 0.00 2.73
3169 5103 3.209410 TCCGAAGTAAGAGTACCGATCC 58.791 50.000 0.00 0.00 0.00 3.36
3172 5106 3.568853 CGAAGTAAGAGTACCGATCCCAT 59.431 47.826 0.00 0.00 0.00 4.00
3176 5110 2.606751 AGAGTACCGATCCCATAGGG 57.393 55.000 0.00 0.00 46.11 3.53
3193 5127 2.551270 AGGGAGTACAAGAATCAGCCA 58.449 47.619 0.00 0.00 0.00 4.75
3196 5130 3.879892 GGGAGTACAAGAATCAGCCATTC 59.120 47.826 0.00 0.00 41.37 2.67
3197 5131 4.517285 GGAGTACAAGAATCAGCCATTCA 58.483 43.478 8.35 0.00 43.27 2.57
3198 5132 4.943705 GGAGTACAAGAATCAGCCATTCAA 59.056 41.667 8.35 0.00 43.27 2.69
3256 5206 5.527582 GCAATAGTAGTATGGGTGAAAGTGG 59.472 44.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 103 6.726035 TTCGCTTTCTAAAAATTGTTCACG 57.274 33.333 0.00 0.00 0.00 4.35
194 201 6.363357 GCATTCAGAAAAAGTTCAGCGTATTT 59.637 34.615 0.00 0.00 36.09 1.40
221 230 6.602179 TCATGTAGAGAAATTTTGTTCAGCG 58.398 36.000 0.00 0.00 0.00 5.18
322 335 7.118101 GCATTCAAAAGGAGTTCATTGCATTTA 59.882 33.333 0.00 0.00 0.00 1.40
326 339 4.202233 TGCATTCAAAAGGAGTTCATTGCA 60.202 37.500 0.00 0.00 34.33 4.08
327 340 4.309099 TGCATTCAAAAGGAGTTCATTGC 58.691 39.130 0.00 0.00 0.00 3.56
328 341 5.163893 GCATGCATTCAAAAGGAGTTCATTG 60.164 40.000 14.21 0.00 0.00 2.82
329 342 4.933400 GCATGCATTCAAAAGGAGTTCATT 59.067 37.500 14.21 0.00 0.00 2.57
406 574 9.829507 AAGAAAAATGTTCACCATACATTGAAA 57.170 25.926 0.00 0.00 43.44 2.69
515 715 8.643752 TCGTTTGACTTTTCAGAAAATGTTTTC 58.356 29.630 8.81 9.61 45.22 2.29
683 904 7.773149 TCAAAGGTTTTTCGGTTTTCTTCATA 58.227 30.769 0.00 0.00 0.00 2.15
743 969 4.103153 TGGTCTTGTGAATCTTCCAGAAGT 59.897 41.667 7.26 0.00 39.38 3.01
754 980 2.887152 GCAAGGAACTGGTCTTGTGAAT 59.113 45.455 0.00 0.00 40.86 2.57
762 988 1.202818 ACTTGGAGCAAGGAACTGGTC 60.203 52.381 0.00 0.00 44.81 4.02
880 1106 0.809241 GCTCAAGGTCAGATGCGGAG 60.809 60.000 0.00 0.00 0.00 4.63
881 1107 1.219124 GCTCAAGGTCAGATGCGGA 59.781 57.895 0.00 0.00 0.00 5.54
896 1122 2.656560 TTAGCTTCTCTCCGTTGCTC 57.343 50.000 0.00 0.00 35.47 4.26
1059 1291 1.202758 TCCTGCTCTTTTTCTTCGGCA 60.203 47.619 0.00 0.00 0.00 5.69
1396 1631 3.239253 AGGAAAGACCGTGGGCGT 61.239 61.111 0.00 0.00 44.74 5.68
1803 2075 3.589542 TCCTTGGGGTTGGGGCAG 61.590 66.667 0.00 0.00 0.00 4.85
2013 2292 2.606587 CCCCTGGCACTTGTAGGCT 61.607 63.158 0.00 0.00 0.00 4.58
2195 2480 2.439409 CATCTTTGATGTGGCTGTGGA 58.561 47.619 0.00 0.00 0.00 4.02
2217 2508 4.038080 CCTTTGGGCGGTGCGAAC 62.038 66.667 0.00 0.00 0.00 3.95
2221 2512 0.034756 ATTTTTCCTTTGGGCGGTGC 59.965 50.000 0.00 0.00 0.00 5.01
2314 2615 6.435430 AACATCATATAGCAGTCGCAAAAA 57.565 33.333 0.00 0.00 42.27 1.94
2315 2616 7.728847 ATAACATCATATAGCAGTCGCAAAA 57.271 32.000 0.00 0.00 42.27 2.44
2316 2617 7.728847 AATAACATCATATAGCAGTCGCAAA 57.271 32.000 0.00 0.00 42.27 3.68
2319 2620 7.900352 GCTTAAATAACATCATATAGCAGTCGC 59.100 37.037 0.00 0.00 38.99 5.19
2325 2626 7.893236 CGACGTGCTTAAATAACATCATATAGC 59.107 37.037 0.00 0.00 0.00 2.97
2348 2649 5.352016 TGGTTGCCAAATACACTAATACGAC 59.648 40.000 0.00 0.00 0.00 4.34
2351 2652 7.027161 CACTTGGTTGCCAAATACACTAATAC 58.973 38.462 2.07 0.00 43.44 1.89
2403 2704 8.125448 GCCAAATACTTAAAAGATGAGCTACAG 58.875 37.037 0.00 0.00 0.00 2.74
2448 2749 7.226325 GCATCTTGACAATTCTGCTAACTAGAT 59.774 37.037 0.00 0.00 0.00 1.98
2497 2798 4.080863 AGTCTTGGACCATGTTATGTCTCC 60.081 45.833 7.22 0.00 32.18 3.71
2502 2803 8.511604 AAGATTAAGTCTTGGACCATGTTATG 57.488 34.615 7.22 0.00 45.38 1.90
2505 2806 7.611855 CCTTAAGATTAAGTCTTGGACCATGTT 59.388 37.037 3.36 0.00 46.50 2.71
2514 2832 6.127897 CCACAAGCCCTTAAGATTAAGTCTTG 60.128 42.308 24.48 24.48 46.50 3.02
2528 2846 1.152546 GTGTTCCCCACAAGCCCTT 60.153 57.895 0.00 0.00 43.92 3.95
2537 2855 4.047166 AGGATATGATCTTGTGTTCCCCA 58.953 43.478 0.00 0.00 0.00 4.96
2555 2873 1.344496 ACGAAGGGGAGGATGAAGGAT 60.344 52.381 0.00 0.00 0.00 3.24
2697 3023 3.515901 ACATCTAAGAAACGAGCCCTCTT 59.484 43.478 0.00 0.00 33.97 2.85
2746 3074 4.469945 TCTTATTCCATCTTCAGGGTCGTT 59.530 41.667 0.00 0.00 0.00 3.85
2747 3075 4.030913 TCTTATTCCATCTTCAGGGTCGT 58.969 43.478 0.00 0.00 0.00 4.34
2749 3077 6.836242 AGAATCTTATTCCATCTTCAGGGTC 58.164 40.000 0.00 0.00 0.00 4.46
2777 3131 2.194056 CGAGACGGGGGCTAGGTA 59.806 66.667 0.00 0.00 0.00 3.08
2778 3132 4.835891 CCGAGACGGGGGCTAGGT 62.836 72.222 2.00 0.00 44.15 3.08
2818 3172 3.454587 GACACACCTCCACACGCCA 62.455 63.158 0.00 0.00 0.00 5.69
2845 3205 3.063997 CCACCGACTGAATATTGCAAGAC 59.936 47.826 4.94 0.00 0.00 3.01
2854 3214 5.046159 ACCAAAGATAACCACCGACTGAATA 60.046 40.000 0.00 0.00 0.00 1.75
2922 4850 7.230510 GCTGAGAGAAGAGTAGATCAAAGGATA 59.769 40.741 0.00 0.00 32.67 2.59
2937 4866 0.179127 CAATCGCCGCTGAGAGAAGA 60.179 55.000 0.00 0.00 0.00 2.87
2962 4895 0.179048 CCATAGGATCAGCGCACCAA 60.179 55.000 11.47 0.00 0.00 3.67
2991 4924 0.442699 GACAAACGGGAAGTCATCGC 59.557 55.000 0.00 0.00 37.62 4.58
3012 4945 1.686587 AGGGGCAAAACTTGTTGTAGC 59.313 47.619 0.00 0.00 0.00 3.58
3031 4964 0.179936 GCCCCTCACTCATTGGAGAG 59.820 60.000 0.00 0.00 44.26 3.20
3032 4965 0.547471 TGCCCCTCACTCATTGGAGA 60.547 55.000 0.00 0.00 44.26 3.71
3043 4976 0.179468 GTAGCCGTTATTGCCCCTCA 59.821 55.000 0.00 0.00 0.00 3.86
3060 4993 4.233632 TGAAGTGATCCAATGGCATGTA 57.766 40.909 0.00 0.00 0.00 2.29
3061 4994 3.090210 TGAAGTGATCCAATGGCATGT 57.910 42.857 0.00 0.00 0.00 3.21
3063 4996 4.665833 CATTGAAGTGATCCAATGGCAT 57.334 40.909 12.19 0.00 43.40 4.40
3068 5001 6.248433 ACTACAACCATTGAAGTGATCCAAT 58.752 36.000 0.00 0.00 33.66 3.16
3070 5003 5.241403 ACTACAACCATTGAAGTGATCCA 57.759 39.130 0.00 0.00 0.00 3.41
3073 5006 4.894784 ACGACTACAACCATTGAAGTGAT 58.105 39.130 0.00 0.00 0.00 3.06
3076 5009 3.314553 CGACGACTACAACCATTGAAGT 58.685 45.455 0.00 0.00 0.00 3.01
3082 5015 2.157834 TTTGCGACGACTACAACCAT 57.842 45.000 0.00 0.00 0.00 3.55
3099 5032 4.018960 AGCAGACCATCAGTAGACCATTTT 60.019 41.667 0.00 0.00 0.00 1.82
3117 5050 5.045869 ACAAGTAAACCCTAGCAATAGCAGA 60.046 40.000 0.00 0.00 45.49 4.26
3122 5055 6.555463 AGCTACAAGTAAACCCTAGCAATA 57.445 37.500 0.00 0.00 33.61 1.90
3123 5056 5.437191 AGCTACAAGTAAACCCTAGCAAT 57.563 39.130 0.00 0.00 33.61 3.56
3124 5057 4.903045 AGCTACAAGTAAACCCTAGCAA 57.097 40.909 0.00 0.00 33.61 3.91
3128 5061 5.011943 TCGGAAAAGCTACAAGTAAACCCTA 59.988 40.000 0.00 0.00 0.00 3.53
3129 5062 4.070009 CGGAAAAGCTACAAGTAAACCCT 58.930 43.478 0.00 0.00 0.00 4.34
3130 5063 4.067192 TCGGAAAAGCTACAAGTAAACCC 58.933 43.478 0.00 0.00 0.00 4.11
3138 5072 5.850614 ACTCTTACTTCGGAAAAGCTACAA 58.149 37.500 0.00 0.00 0.00 2.41
3149 5083 2.292845 GGGATCGGTACTCTTACTTCGG 59.707 54.545 0.00 0.00 0.00 4.30
3151 5085 5.183522 CCTATGGGATCGGTACTCTTACTTC 59.816 48.000 0.00 0.00 33.58 3.01
3169 5103 4.503991 GGCTGATTCTTGTACTCCCTATGG 60.504 50.000 0.00 0.00 0.00 2.74
3172 5106 3.719871 TGGCTGATTCTTGTACTCCCTA 58.280 45.455 0.00 0.00 0.00 3.53
3176 5110 5.645497 AGTTGAATGGCTGATTCTTGTACTC 59.355 40.000 9.48 0.00 41.16 2.59
3179 5113 5.586243 GCTAGTTGAATGGCTGATTCTTGTA 59.414 40.000 9.48 0.66 41.16 2.41
3183 5117 4.226427 TGCTAGTTGAATGGCTGATTCT 57.774 40.909 9.48 0.00 41.16 2.40
3190 5124 2.214387 GGCATTGCTAGTTGAATGGC 57.786 50.000 8.82 16.41 44.72 4.40
3220 5170 9.071276 CCATACTACTATTGCTTTGGATTTCAT 57.929 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.