Multiple sequence alignment - TraesCS3D01G133000

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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 TraesCS3D01G133000 chr3D 100.000 3012 0 0 2880 5891 92384266 92381255 0.000000e+00 5563.0
1 TraesCS3D01G133000 chr3D 100.000 2597 0 0 1 2597 92387145 92384549 0.000000e+00 4796.0
2 TraesCS3D01G133000 chr3D 94.587 739 25 3 5166 5891 26668371 26669107 0.000000e+00 1129.0
3 TraesCS3D01G133000 chr3D 81.915 188 30 4 74 259 227582961 227583146 7.900000e-34 156.0
4 TraesCS3D01G133000 chr3D 81.283 187 32 3 62 247 293591517 293591701 1.320000e-31 148.0
5 TraesCS3D01G133000 chr3A 93.527 2611 145 13 1 2597 545970114 545967514 0.000000e+00 3864.0
6 TraesCS3D01G133000 chr3A 94.425 2296 96 11 2880 5171 545967491 545965224 0.000000e+00 3502.0
7 TraesCS3D01G133000 chr3B 93.333 2265 142 6 2908 5171 141979411 141977155 0.000000e+00 3338.0
8 TraesCS3D01G133000 chr3B 89.474 1805 148 19 796 2582 141981386 141979606 0.000000e+00 2242.0
9 TraesCS3D01G133000 chr3B 87.584 741 79 8 57 794 142165517 142164787 0.000000e+00 846.0
10 TraesCS3D01G133000 chr3B 81.188 202 29 8 71 267 600516251 600516054 2.840000e-33 154.0
11 TraesCS3D01G133000 chr1D 79.933 1784 316 31 338 2107 403094816 403096571 0.000000e+00 1273.0
12 TraesCS3D01G133000 chr1D 92.999 757 24 6 5162 5891 42988108 42988862 0.000000e+00 1077.0
13 TraesCS3D01G133000 chr1D 78.850 1617 301 29 301 1905 403151513 403153100 0.000000e+00 1053.0
14 TraesCS3D01G133000 chr1D 80.302 995 173 17 301 1289 403088939 403089916 0.000000e+00 730.0
15 TraesCS3D01G133000 chr1D 80.577 901 152 15 301 1193 403197628 403198513 0.000000e+00 673.0
16 TraesCS3D01G133000 chr1D 79.285 811 151 12 1304 2108 403091587 403092386 8.630000e-153 551.0
17 TraesCS3D01G133000 chr1D 82.192 511 79 8 1601 2108 403099714 403100215 4.220000e-116 429.0
18 TraesCS3D01G133000 chr1D 81.352 429 70 7 301 725 403147408 403147830 2.030000e-89 340.0
19 TraesCS3D01G133000 chr1D 81.579 418 72 5 301 715 403157198 403157613 2.030000e-89 340.0
20 TraesCS3D01G133000 chr1D 80.451 399 68 6 1713 2108 403180179 403180570 4.460000e-76 296.0
21 TraesCS3D01G133000 chr1D 81.905 210 34 4 61 267 79443425 79443633 2.180000e-39 174.0
22 TraesCS3D01G133000 chr1D 81.250 208 35 4 61 266 275630257 275630052 1.310000e-36 165.0
23 TraesCS3D01G133000 chr1D 83.234 167 24 3 2929 3093 475866446 475866610 3.680000e-32 150.0
24 TraesCS3D01G133000 chr1D 85.345 116 15 2 153 267 161976837 161976723 1.040000e-22 119.0
25 TraesCS3D01G133000 chr1A 79.125 1782 325 29 338 2107 498201557 498203303 0.000000e+00 1186.0
26 TraesCS3D01G133000 chr1A 78.266 1822 342 41 301 2106 498196960 498198743 0.000000e+00 1122.0
27 TraesCS3D01G133000 chr1A 79.795 975 173 15 318 1285 498394731 498395688 0.000000e+00 688.0
28 TraesCS3D01G133000 chr1A 79.873 472 89 3 1407 1873 498352373 498352843 2.030000e-89 340.0
29 TraesCS3D01G133000 chr1A 80.645 403 70 8 316 715 498222528 498222925 7.420000e-79 305.0
30 TraesCS3D01G133000 chr1A 81.786 280 48 3 301 578 498263221 498263499 1.280000e-56 231.0
31 TraesCS3D01G133000 chr1A 85.792 183 24 2 2911 3093 252276308 252276488 6.020000e-45 193.0
32 TraesCS3D01G133000 chr1A 79.621 211 36 6 63 271 176442317 176442522 1.710000e-30 145.0
33 TraesCS3D01G133000 chr1A 80.214 187 33 4 83 267 248252283 248252467 2.860000e-28 137.0
34 TraesCS3D01G133000 chr1A 79.188 197 36 4 74 267 348590081 348590275 1.330000e-26 132.0
35 TraesCS3D01G133000 chr1A 78.947 114 22 2 2993 3105 542762334 542762222 6.330000e-10 76.8
36 TraesCS3D01G133000 chr4D 94.952 733 24 3 5168 5889 508428889 508428159 0.000000e+00 1136.0
37 TraesCS3D01G133000 chr4D 82.775 209 32 4 61 267 374106462 374106668 3.630000e-42 183.0
38 TraesCS3D01G133000 chr4D 78.636 220 39 7 2882 3097 221299984 221299769 7.960000e-29 139.0
39 TraesCS3D01G133000 chr4D 83.186 113 15 4 159 269 164577279 164577169 3.760000e-17 100.0
40 TraesCS3D01G133000 chr5D 94.016 752 29 6 5153 5891 277478137 277478885 0.000000e+00 1125.0
41 TraesCS3D01G133000 chr5D 94.452 739 24 6 5166 5891 344411278 344410544 0.000000e+00 1122.0
42 TraesCS3D01G133000 chr2D 94.207 725 36 3 5170 5891 618545887 618545166 0.000000e+00 1101.0
43 TraesCS3D01G133000 chr1B 77.936 1831 343 43 301 2108 541376389 541378181 0.000000e+00 1086.0
44 TraesCS3D01G133000 chr1B 76.551 951 159 35 301 1242 541321374 541322269 4.160000e-126 462.0
45 TraesCS3D01G133000 chr1B 81.095 402 72 4 316 715 541364061 541364460 9.530000e-83 318.0
46 TraesCS3D01G133000 chr1B 81.579 190 33 2 2913 3100 262529670 262529859 7.900000e-34 156.0
47 TraesCS3D01G133000 chr1B 85.385 130 16 3 2966 3092 525378883 525378754 1.330000e-26 132.0
48 TraesCS3D01G133000 chr7D 93.741 735 27 7 5170 5891 81871924 81872652 0.000000e+00 1085.0
49 TraesCS3D01G133000 chr7D 81.429 210 26 8 61 267 270696685 270696884 6.110000e-35 159.0
50 TraesCS3D01G133000 chr7D 81.768 181 33 0 2920 3100 620696991 620696811 1.020000e-32 152.0
51 TraesCS3D01G133000 chrUn 94.217 709 24 5 5198 5891 33082256 33081550 0.000000e+00 1066.0
52 TraesCS3D01G133000 chrUn 90.733 723 56 9 5170 5888 91671785 91672500 0.000000e+00 953.0
53 TraesCS3D01G133000 chrUn 83.735 166 25 2 2929 3092 37814898 37815063 7.900000e-34 156.0
54 TraesCS3D01G133000 chr6D 90.759 725 60 6 5170 5891 383769637 383768917 0.000000e+00 961.0
55 TraesCS3D01G133000 chr6D 87.092 736 54 17 5170 5888 308902575 308903286 0.000000e+00 795.0
56 TraesCS3D01G133000 chr6D 82.028 217 33 6 55 267 298615200 298615414 4.690000e-41 180.0
57 TraesCS3D01G133000 chr6D 85.294 136 19 1 126 260 210465228 210465093 7.960000e-29 139.0
58 TraesCS3D01G133000 chr6D 87.629 97 9 3 166 260 367553282 367553377 6.240000e-20 110.0
59 TraesCS3D01G133000 chr6D 84.906 106 13 3 164 267 367549294 367549398 2.900000e-18 104.0
60 TraesCS3D01G133000 chr6D 80.952 105 18 2 164 267 191414882 191414779 1.360000e-11 82.4
61 TraesCS3D01G133000 chr6D 81.443 97 16 2 164 259 191400965 191400870 1.760000e-10 78.7
62 TraesCS3D01G133000 chr5B 88.235 731 76 7 5168 5891 556157948 556157221 0.000000e+00 865.0
63 TraesCS3D01G133000 chr6A 84.438 739 88 18 5168 5888 531301705 531302434 0.000000e+00 702.0
64 TraesCS3D01G133000 chr6A 78.307 189 39 2 82 269 72612192 72612005 2.880000e-23 121.0
65 TraesCS3D01G133000 chr7A 82.464 211 27 8 2888 3093 252945954 252946159 6.070000e-40 176.0
66 TraesCS3D01G133000 chr4B 80.383 209 36 5 61 267 460326868 460327073 2.840000e-33 154.0
67 TraesCS3D01G133000 chr4B 79.798 198 32 7 74 267 528380341 528380534 2.860000e-28 137.0
68 TraesCS3D01G133000 chr5A 80.711 197 32 6 74 267 118163447 118163254 1.320000e-31 148.0


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 TraesCS3D01G133000 chr3D 92381255 92387145 5890 True 5179.50 5563 100.0000 1 5891 2 chr3D.!!$R1 5890
1 TraesCS3D01G133000 chr3D 26668371 26669107 736 False 1129.00 1129 94.5870 5166 5891 1 chr3D.!!$F1 725
2 TraesCS3D01G133000 chr3A 545965224 545970114 4890 True 3683.00 3864 93.9760 1 5171 2 chr3A.!!$R1 5170
3 TraesCS3D01G133000 chr3B 141977155 141981386 4231 True 2790.00 3338 91.4035 796 5171 2 chr3B.!!$R3 4375
4 TraesCS3D01G133000 chr3B 142164787 142165517 730 True 846.00 846 87.5840 57 794 1 chr3B.!!$R1 737
5 TraesCS3D01G133000 chr1D 42988108 42988862 754 False 1077.00 1077 92.9990 5162 5891 1 chr1D.!!$F1 729
6 TraesCS3D01G133000 chr1D 403088939 403100215 11276 False 745.75 1273 80.4280 301 2108 4 chr1D.!!$F7 1807
7 TraesCS3D01G133000 chr1D 403147408 403153100 5692 False 696.50 1053 80.1010 301 1905 2 chr1D.!!$F8 1604
8 TraesCS3D01G133000 chr1D 403197628 403198513 885 False 673.00 673 80.5770 301 1193 1 chr1D.!!$F5 892
9 TraesCS3D01G133000 chr1A 498196960 498203303 6343 False 1154.00 1186 78.6955 301 2107 2 chr1A.!!$F9 1806
10 TraesCS3D01G133000 chr1A 498394731 498395688 957 False 688.00 688 79.7950 318 1285 1 chr1A.!!$F8 967
11 TraesCS3D01G133000 chr4D 508428159 508428889 730 True 1136.00 1136 94.9520 5168 5889 1 chr4D.!!$R3 721
12 TraesCS3D01G133000 chr5D 277478137 277478885 748 False 1125.00 1125 94.0160 5153 5891 1 chr5D.!!$F1 738
13 TraesCS3D01G133000 chr5D 344410544 344411278 734 True 1122.00 1122 94.4520 5166 5891 1 chr5D.!!$R1 725
14 TraesCS3D01G133000 chr2D 618545166 618545887 721 True 1101.00 1101 94.2070 5170 5891 1 chr2D.!!$R1 721
15 TraesCS3D01G133000 chr1B 541376389 541378181 1792 False 1086.00 1086 77.9360 301 2108 1 chr1B.!!$F4 1807
16 TraesCS3D01G133000 chr1B 541321374 541322269 895 False 462.00 462 76.5510 301 1242 1 chr1B.!!$F2 941
17 TraesCS3D01G133000 chr7D 81871924 81872652 728 False 1085.00 1085 93.7410 5170 5891 1 chr7D.!!$F1 721
18 TraesCS3D01G133000 chrUn 33081550 33082256 706 True 1066.00 1066 94.2170 5198 5891 1 chrUn.!!$R1 693
19 TraesCS3D01G133000 chrUn 91671785 91672500 715 False 953.00 953 90.7330 5170 5888 1 chrUn.!!$F2 718
20 TraesCS3D01G133000 chr6D 383768917 383769637 720 True 961.00 961 90.7590 5170 5891 1 chr6D.!!$R4 721
21 TraesCS3D01G133000 chr6D 308902575 308903286 711 False 795.00 795 87.0920 5170 5888 1 chr6D.!!$F2 718
22 TraesCS3D01G133000 chr5B 556157221 556157948 727 True 865.00 865 88.2350 5168 5891 1 chr5B.!!$R1 723
23 TraesCS3D01G133000 chr6A 531301705 531302434 729 False 702.00 702 84.4380 5168 5888 1 chr6A.!!$F1 720

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
110 113 0.032952 CGAAGACAACGGGGAGAACA 59.967 55.000 0.00 0.00 0.00 3.18 F
717 728 0.108585 GTGTGGACCAAAGCCTCTCA 59.891 55.000 0.00 0.00 0.00 3.27 F
1720 16383 0.524862 GCTGGACAAATCACCTGCAG 59.475 55.000 6.78 6.78 45.76 4.41 F
1724 16387 0.895100 GACAAATCACCTGCAGCCCA 60.895 55.000 8.66 0.00 0.00 5.36 F
1914 16582 0.949397 CACATGCCATATGCGCTCTT 59.051 50.000 9.73 0.00 45.60 2.85 F
2163 20480 1.304464 GCCCCCTCCAAGTTTGAGG 60.304 63.158 14.79 14.79 35.94 3.86 F
2458 20778 2.700371 CAGAAAAACCCCTGCCTTTTCT 59.300 45.455 3.76 3.76 45.66 2.52 F
4135 22459 1.227556 CGGGGCCTAACATCGAAGG 60.228 63.158 0.84 0.00 35.86 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 16630 0.179156 TTCGCAACCTCGATCGGTAC 60.179 55.000 16.41 1.76 38.37 3.34 R
1957 16631 0.742505 ATTCGCAACCTCGATCGGTA 59.257 50.000 16.41 0.00 38.37 4.02 R
3112 21433 1.204146 CCCACCTATCCCCATATCCG 58.796 60.000 0.00 0.00 0.00 4.18 R
3440 21761 7.040478 TGTCATCTCAAACAATAAAGGTCAAGG 60.040 37.037 0.00 0.00 0.00 3.61 R
3834 22157 0.704076 TTGGACAGGCTAGCCCAAAT 59.296 50.000 30.42 13.22 35.91 2.32 R
4135 22459 1.737008 GACGCTTCCTGAACCGACC 60.737 63.158 1.91 0.00 0.00 4.79 R
4176 22500 2.817834 GCGGTTGTGCTGCGGATA 60.818 61.111 0.00 0.00 39.99 2.59 R
5125 23449 0.109597 CAAAAGGGTGCATGTCGAGC 60.110 55.000 0.00 0.00 0.00 5.03 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
30 31 1.164041 AGTTTTCGGGCGAGGTTGTG 61.164 55.000 0.00 0.00 0.00 3.33
53 54 3.368571 GGGTCTTGCTGTGCAGGC 61.369 66.667 4.80 4.80 40.61 4.85
55 56 2.595463 GTCTTGCTGTGCAGGCCA 60.595 61.111 5.01 0.00 40.61 5.36
84 86 0.765510 AAGGGTGGTGGTCTCAGAAC 59.234 55.000 0.00 0.00 0.00 3.01
110 113 0.032952 CGAAGACAACGGGGAGAACA 59.967 55.000 0.00 0.00 0.00 3.18
195 198 6.255950 CGGATGATATGATGATGAATGCAAC 58.744 40.000 0.00 0.00 0.00 4.17
269 272 2.824936 TCGGTCTCGGGTTGTTACATTA 59.175 45.455 0.00 0.00 36.95 1.90
294 297 4.141846 GCCACATCTTAGGAGAGTCAATGA 60.142 45.833 0.00 0.00 34.85 2.57
299 302 6.265196 ACATCTTAGGAGAGTCAATGAGCTAG 59.735 42.308 0.00 0.00 34.85 3.42
324 327 3.094572 CCAGGCTTGAGTTGGATTTCAT 58.905 45.455 0.00 0.00 33.76 2.57
414 420 1.078426 CCTCCACTAAGGTTGGCCG 60.078 63.158 0.00 0.00 40.50 6.13
424 432 1.220749 GGTTGGCCGCTACATCTCA 59.779 57.895 0.00 0.00 0.00 3.27
429 437 1.270465 TGGCCGCTACATCTCATCATG 60.270 52.381 0.00 0.00 0.00 3.07
504 513 6.628919 AACGGAAGCAGTTACTAAAAACAT 57.371 33.333 0.00 0.00 0.00 2.71
526 537 4.584874 TGTGGTCAAGAAGAAAACTGACA 58.415 39.130 3.72 0.00 0.00 3.58
717 728 0.108585 GTGTGGACCAAAGCCTCTCA 59.891 55.000 0.00 0.00 0.00 3.27
775 789 3.128764 TGCTCTAGTGAGTTGTACCGATG 59.871 47.826 0.00 0.00 42.13 3.84
812 826 1.340017 TGTGCAATAGTTGGCCTCCTC 60.340 52.381 3.32 0.00 0.00 3.71
813 827 1.065126 GTGCAATAGTTGGCCTCCTCT 60.065 52.381 3.32 0.00 0.00 3.69
825 839 1.406205 GCCTCCTCTAAGACAACTGGC 60.406 57.143 0.00 0.00 0.00 4.85
878 892 0.541392 TTGGACAGTGATGGGATCCG 59.459 55.000 5.45 0.00 31.65 4.18
940 963 9.615295 AAAATGTGTGTATTTGGAACGTTATAC 57.385 29.630 0.00 6.39 31.05 1.47
1112 15775 1.137594 TCAAATCCCACCCCCTTCGT 61.138 55.000 0.00 0.00 0.00 3.85
1180 15843 2.102252 GGTGGACATGCTTTTCAACCAA 59.898 45.455 7.31 0.00 31.86 3.67
1185 15848 2.036346 ACATGCTTTTCAACCAAGAGCC 59.964 45.455 0.00 0.00 32.53 4.70
1232 15895 3.077907 CGGAAGGGAGGGCTGAAA 58.922 61.111 0.00 0.00 0.00 2.69
1455 16118 2.301870 AGCATTCCACGGAGAACAGTAA 59.698 45.455 0.00 0.00 0.00 2.24
1464 16127 1.270678 GGAGAACAGTAAAGCGGTGGT 60.271 52.381 0.00 0.00 0.00 4.16
1504 16167 1.432657 GCCGGAAGAGGACGAGTAC 59.567 63.158 5.05 0.00 0.00 2.73
1552 16215 4.783764 TTTGAGTAGCTTGATCTCACGA 57.216 40.909 0.00 0.00 37.84 4.35
1616 16279 1.888215 TGCTTGCAGACTTCTCAAGG 58.112 50.000 14.76 3.95 38.05 3.61
1690 16353 0.745845 CAGGACGGATTGGGAAGCAG 60.746 60.000 0.00 0.00 0.00 4.24
1720 16383 0.524862 GCTGGACAAATCACCTGCAG 59.475 55.000 6.78 6.78 45.76 4.41
1724 16387 0.895100 GACAAATCACCTGCAGCCCA 60.895 55.000 8.66 0.00 0.00 5.36
1914 16582 0.949397 CACATGCCATATGCGCTCTT 59.051 50.000 9.73 0.00 45.60 2.85
2056 20373 3.033184 TCCCCCGTCGTTTATAGATGTT 58.967 45.455 0.00 0.00 0.00 2.71
2163 20480 1.304464 GCCCCCTCCAAGTTTGAGG 60.304 63.158 14.79 14.79 35.94 3.86
2324 20643 7.192913 TCTAGTAAATATTTGCCACAATTGCG 58.807 34.615 11.05 0.00 0.00 4.85
2343 20663 8.918658 CAATTGCGTACTAGTCAAGTTTTAGTA 58.081 33.333 0.00 0.00 39.80 1.82
2458 20778 2.700371 CAGAAAAACCCCTGCCTTTTCT 59.300 45.455 3.76 3.76 45.66 2.52
2470 20790 6.424032 CCCTGCCTTTTCTAGTAATAAACCT 58.576 40.000 0.00 0.00 0.00 3.50
2492 20812 4.130857 TGCGGTTCATCTTTAAGTCACAA 58.869 39.130 0.00 0.00 0.00 3.33
2562 20883 7.983484 CCTTTCTGCTAATTAAATTGCAATCCT 59.017 33.333 13.38 5.81 34.90 3.24
2906 21227 3.769536 GTTAATCAACCCGCAATCCTTG 58.230 45.455 0.00 0.00 0.00 3.61
3097 21418 9.132923 AGCACATGATTCATCTTTCTTTCATAT 57.867 29.630 0.00 0.00 0.00 1.78
3098 21419 9.395707 GCACATGATTCATCTTTCTTTCATATC 57.604 33.333 0.00 0.00 0.00 1.63
3112 21433 8.874745 TTCTTTCATATCGACGTCAAATTTTC 57.125 30.769 17.16 0.00 0.00 2.29
4135 22459 1.227556 CGGGGCCTAACATCGAAGG 60.228 63.158 0.84 0.00 35.86 3.46
4190 22514 2.135933 GGAGTATATCCGCAGCACAAC 58.864 52.381 0.00 0.00 38.67 3.32
4192 22516 0.859232 GTATATCCGCAGCACAACCG 59.141 55.000 0.00 0.00 0.00 4.44
4539 22863 3.028130 CAGGATGCATGCGCGAAT 58.972 55.556 12.10 0.00 42.97 3.34
4540 22864 1.370051 CAGGATGCATGCGCGAATG 60.370 57.895 23.27 23.27 42.97 2.67
4552 22876 0.670546 CGCGAATGTGAACCTGTCCT 60.671 55.000 0.00 0.00 0.00 3.85
4634 22958 1.368950 CCGGTGGCATCGATGATCT 59.631 57.895 29.20 0.00 0.00 2.75
4639 22963 1.122227 TGGCATCGATGATCTGGACA 58.878 50.000 29.20 6.06 0.00 4.02
4648 22972 3.934579 CGATGATCTGGACAACATCAACA 59.065 43.478 0.00 0.00 38.99 3.33
4684 23008 1.153429 GGGGATTTCCTGACGTCCG 60.153 63.158 14.12 6.54 35.95 4.79
4859 23183 1.520564 TGCGACGTGGCATGTATCC 60.521 57.895 21.95 4.73 38.17 2.59
4865 23189 1.280710 ACGTGGCATGTATCCTTTCCA 59.719 47.619 11.37 0.00 0.00 3.53
4870 23194 4.037208 GTGGCATGTATCCTTTCCAGATTG 59.963 45.833 0.00 0.00 0.00 2.67
4921 23245 7.804614 TGAACAATTTGTTGTACTTGTGTTC 57.195 32.000 19.03 0.00 41.28 3.18
4924 23248 8.825667 AACAATTTGTTGTACTTGTGTTCTTT 57.174 26.923 13.80 0.00 39.45 2.52
4925 23249 8.825667 ACAATTTGTTGTACTTGTGTTCTTTT 57.174 26.923 0.00 0.00 32.60 2.27
4977 23301 6.434302 TCCATTTCCATCATTACAATCCAGT 58.566 36.000 0.00 0.00 0.00 4.00
4986 23310 7.445096 CCATCATTACAATCCAGTGCTATTGTA 59.555 37.037 18.25 18.25 42.87 2.41
5031 23355 5.178623 CAGAAAAATGCACGGAGTACTACAA 59.821 40.000 5.80 0.00 41.61 2.41
5048 23372 5.451908 ACTACAAGAAACATGACATTTGCG 58.548 37.500 0.00 0.00 0.00 4.85
5101 23425 1.055040 AGCAGAGCAAAGGAGTCACT 58.945 50.000 0.00 0.00 0.00 3.41
5125 23449 3.309682 AGTGTCACACTCGACAAACATTG 59.690 43.478 3.98 0.00 46.99 2.82
5143 23467 0.537143 TGCTCGACATGCACCCTTTT 60.537 50.000 0.00 0.00 35.31 2.27
5248 23575 2.598985 AAAAATGGCCCGGTCGCA 60.599 55.556 0.00 0.00 0.00 5.10
5272 23599 1.525077 AGGACGACAAAAAGCGCCA 60.525 52.632 2.29 0.00 0.00 5.69
5648 24022 3.282745 GACGAGGAAGTGCTCGCCA 62.283 63.158 20.29 0.00 45.79 5.69
5745 24120 0.524862 CTGGCGAGCAATGAAAAGCT 59.475 50.000 0.00 0.00 45.25 3.74
5860 24235 3.414700 CCACTTCACGGCGACAGC 61.415 66.667 16.62 0.00 44.18 4.40
5877 24252 2.202298 CACATTTCGGCGCCGTTC 60.202 61.111 44.16 10.35 40.74 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.031465 TCGCCCGAAAACTGTCCC 59.969 61.111 0.00 0.00 0.00 4.46
9 10 1.147600 AACCTCGCCCGAAAACTGT 59.852 52.632 0.00 0.00 0.00 3.55
18 19 2.359975 CCCTTCACAACCTCGCCC 60.360 66.667 0.00 0.00 0.00 6.13
19 20 2.359975 CCCCTTCACAACCTCGCC 60.360 66.667 0.00 0.00 0.00 5.54
46 47 3.349006 CACGTGACTGGCCTGCAC 61.349 66.667 10.90 19.87 0.00 4.57
53 54 2.111043 ACCCTTGCACGTGACTGG 59.889 61.111 22.23 16.13 0.00 4.00
55 56 2.111043 CCACCCTTGCACGTGACT 59.889 61.111 22.23 0.00 31.36 3.41
84 86 1.554042 CCCGTTGTCTTCGTTGACCG 61.554 60.000 7.76 5.59 36.21 4.79
100 102 1.616865 TGTAGTTGTCTGTTCTCCCCG 59.383 52.381 0.00 0.00 0.00 5.73
110 113 5.126067 ACTTGCATCTGTTTGTAGTTGTCT 58.874 37.500 0.00 0.00 0.00 3.41
173 176 8.912658 GTTTGTTGCATTCATCATCATATCATC 58.087 33.333 0.00 0.00 0.00 2.92
195 198 6.862944 ATCGCCGTGTTAATTATTTGTTTG 57.137 33.333 0.00 0.00 0.00 2.93
269 272 3.378512 TGACTCTCCTAAGATGTGGCAT 58.621 45.455 0.00 0.00 0.00 4.40
294 297 0.901124 CTCAAGCCTGGTGTCTAGCT 59.099 55.000 0.00 0.00 37.10 3.32
299 302 0.108585 TCCAACTCAAGCCTGGTGTC 59.891 55.000 0.00 0.00 0.00 3.67
324 327 8.674173 TCCTAAGTAAATGGCCCATATAATCAA 58.326 33.333 0.00 0.00 0.00 2.57
414 420 4.063998 TCCACACATGATGAGATGTAGC 57.936 45.455 0.00 0.00 34.69 3.58
424 432 6.484288 TCCTAAAATCACTTCCACACATGAT 58.516 36.000 0.00 0.00 33.18 2.45
429 437 6.385649 TGTTTCCTAAAATCACTTCCACAC 57.614 37.500 0.00 0.00 0.00 3.82
504 513 4.584874 TGTCAGTTTTCTTCTTGACCACA 58.415 39.130 1.53 0.00 0.00 4.17
717 728 5.221048 GGTGACAAATTTGTTACAGCTGACT 60.221 40.000 33.85 8.50 46.01 3.41
775 789 1.134670 CACAGTGGGTTCTAGCTAGCC 60.135 57.143 16.35 12.00 0.00 3.93
812 826 1.160137 GGTGCAGCCAGTTGTCTTAG 58.840 55.000 4.03 0.00 37.17 2.18
813 827 0.764890 AGGTGCAGCCAGTTGTCTTA 59.235 50.000 13.29 0.00 40.61 2.10
825 839 0.246360 TCCGTGTACATGAGGTGCAG 59.754 55.000 16.87 0.00 43.04 4.41
878 892 3.644399 GAGGTGAAGGTCGGCCGTC 62.644 68.421 27.15 20.62 42.50 4.79
940 963 0.387202 TGGCACAAAACCGTCCAATG 59.613 50.000 0.00 0.00 31.92 2.82
1112 15775 1.064003 TGGAAGCAAGCCAGGAACTA 58.936 50.000 0.00 0.00 36.02 2.24
1202 15865 0.460987 CCTTCCGCCTCAGTCATCAC 60.461 60.000 0.00 0.00 0.00 3.06
1227 15890 1.550976 AGCTCGGGAAGTACCTTTCAG 59.449 52.381 0.00 0.00 38.98 3.02
1232 15895 0.684805 CTGGAGCTCGGGAAGTACCT 60.685 60.000 7.83 0.00 38.98 3.08
1288 15951 1.320344 TGTCAGGAACTCCGATCGGG 61.320 60.000 32.79 24.50 42.08 5.14
1339 16002 1.026718 GCATGTCGAAGGTGAAGGGG 61.027 60.000 0.00 0.00 0.00 4.79
1370 16033 1.271102 GCCATAACCAGCAACCGAAAA 59.729 47.619 0.00 0.00 0.00 2.29
1373 16036 0.958382 GTGCCATAACCAGCAACCGA 60.958 55.000 0.00 0.00 41.48 4.69
1445 16108 1.798813 CACCACCGCTTTACTGTTCTC 59.201 52.381 0.00 0.00 0.00 2.87
1455 16118 2.920076 TTTGGAAGGCACCACCGCTT 62.920 55.000 3.02 0.00 46.52 4.68
1479 16142 4.796231 CCTCTTCCGGCGTCCACG 62.796 72.222 6.01 0.00 43.27 4.94
1504 16167 8.728088 AACAAAACAGATTTAGCTATTTCACG 57.272 30.769 0.00 0.00 0.00 4.35
1533 16196 3.081804 TGTCGTGAGATCAAGCTACTCA 58.918 45.455 0.00 8.17 45.19 3.41
1534 16197 3.766676 TGTCGTGAGATCAAGCTACTC 57.233 47.619 0.00 0.00 45.19 2.59
1552 16215 7.359431 CGAAATTAAGCAGAAAAACATGCATGT 60.359 33.333 26.61 26.61 45.01 3.21
1616 16279 2.158475 TCCCATAATGAGCCACCAATCC 60.158 50.000 0.00 0.00 0.00 3.01
1771 16439 9.048446 CATGCAAGATTTCCCCTAATTAAAATG 57.952 33.333 0.00 0.00 0.00 2.32
1905 16573 9.801873 ATAATATAACAAAAACAAAGAGCGCAT 57.198 25.926 11.47 0.00 0.00 4.73
1946 16620 7.359014 GCAACCTCGATCGGTACTTAATTATTC 60.359 40.741 16.41 0.00 35.89 1.75
1956 16630 0.179156 TTCGCAACCTCGATCGGTAC 60.179 55.000 16.41 1.76 38.37 3.34
1957 16631 0.742505 ATTCGCAACCTCGATCGGTA 59.257 50.000 16.41 0.00 38.37 4.02
2027 20344 2.793288 AACGACGGGGGACATTAATT 57.207 45.000 0.00 0.00 0.00 1.40
2088 20405 2.317040 ACCGAAGACTCCAGAAACTCA 58.683 47.619 0.00 0.00 0.00 3.41
2232 20551 8.922931 TCCAACAATTCACATGCTATATATGT 57.077 30.769 0.00 0.00 39.23 2.29
2241 20560 2.331194 GTGCTCCAACAATTCACATGC 58.669 47.619 0.00 0.00 0.00 4.06
2254 20573 1.001764 CAGATGGCAAGGTGCTCCA 60.002 57.895 7.70 0.00 44.28 3.86
2324 20643 7.381323 TGGCCTTACTAAAACTTGACTAGTAC 58.619 38.462 3.32 0.00 35.54 2.73
2343 20663 7.776618 AACTTAGCTAAACTAAAATGGCCTT 57.223 32.000 7.74 0.00 40.36 4.35
2470 20790 3.734463 TGTGACTTAAAGATGAACCGCA 58.266 40.909 0.00 0.00 0.00 5.69
2476 20796 7.981142 ACGTTTTTCTTGTGACTTAAAGATGA 58.019 30.769 0.00 0.00 32.65 2.92
2530 20851 7.201947 GCAATTTAATTAGCAGAAAGGAGGGAT 60.202 37.037 7.05 0.00 0.00 3.85
2896 21217 9.046296 AGAAGTATTTATTCTACAAGGATTGCG 57.954 33.333 0.00 0.00 38.46 4.85
3097 21418 4.269123 CCATATCCGAAAATTTGACGTCGA 59.731 41.667 11.62 6.16 35.54 4.20
3098 21419 4.514506 CCATATCCGAAAATTTGACGTCG 58.485 43.478 11.62 9.32 0.00 5.12
3112 21433 1.204146 CCCACCTATCCCCATATCCG 58.796 60.000 0.00 0.00 0.00 4.18
3436 21757 9.927081 ATCTCAAACAATAAAGGTCAAGGATAT 57.073 29.630 0.00 0.00 0.00 1.63
3437 21758 9.177608 CATCTCAAACAATAAAGGTCAAGGATA 57.822 33.333 0.00 0.00 0.00 2.59
3439 21760 7.174946 GTCATCTCAAACAATAAAGGTCAAGGA 59.825 37.037 0.00 0.00 0.00 3.36
3440 21761 7.040478 TGTCATCTCAAACAATAAAGGTCAAGG 60.040 37.037 0.00 0.00 0.00 3.61
3821 22144 3.172339 AGCCCAAATTTGCCATCTAACA 58.828 40.909 12.92 0.00 0.00 2.41
3834 22157 0.704076 TTGGACAGGCTAGCCCAAAT 59.296 50.000 30.42 13.22 35.91 2.32
4135 22459 1.737008 GACGCTTCCTGAACCGACC 60.737 63.158 1.91 0.00 0.00 4.79
4176 22500 2.817834 GCGGTTGTGCTGCGGATA 60.818 61.111 0.00 0.00 39.99 2.59
4192 22516 3.414700 CACGCTCTTGTCACCCGC 61.415 66.667 0.00 0.00 0.00 6.13
4490 22814 2.730090 CGCTGGCTAAACATTTGCTGAG 60.730 50.000 0.00 0.00 0.00 3.35
4539 22863 2.295349 GAGTAACGAGGACAGGTTCACA 59.705 50.000 0.00 0.00 0.00 3.58
4540 22864 2.295349 TGAGTAACGAGGACAGGTTCAC 59.705 50.000 0.00 0.00 0.00 3.18
4552 22876 2.740981 GACCGAGACTCTTGAGTAACGA 59.259 50.000 21.13 0.00 0.00 3.85
4616 22940 0.947660 CAGATCATCGATGCCACCGG 60.948 60.000 20.81 0.00 0.00 5.28
4634 22958 3.401033 AGACGATGTTGATGTTGTCCA 57.599 42.857 0.00 0.00 0.00 4.02
4639 22963 4.122776 GCCATCTAGACGATGTTGATGTT 58.877 43.478 0.00 0.00 46.56 2.71
4648 22972 1.626686 CCAGAGGCCATCTAGACGAT 58.373 55.000 5.01 0.00 36.10 3.73
4665 22989 1.895020 CGGACGTCAGGAAATCCCCA 61.895 60.000 18.91 0.00 36.42 4.96
4691 23015 3.259374 TCTCAGTTGAATCCAGTGAGGTC 59.741 47.826 16.20 0.00 36.56 3.85
4696 23020 2.289072 ACCGTCTCAGTTGAATCCAGTG 60.289 50.000 0.00 0.00 0.00 3.66
4783 23107 3.559238 ACATCAGCGAATTGAACAACC 57.441 42.857 0.00 0.00 0.00 3.77
4845 23169 1.280710 TGGAAAGGATACATGCCACGT 59.719 47.619 0.00 0.00 41.41 4.49
4859 23183 5.712152 AAAAGTACTGGCAATCTGGAAAG 57.288 39.130 0.00 0.00 0.00 2.62
4924 23248 9.913310 TCCACATACTAAATCATTGTCCATAAA 57.087 29.630 0.00 0.00 0.00 1.40
4963 23287 7.992608 ACATACAATAGCACTGGATTGTAATGA 59.007 33.333 10.52 0.00 46.30 2.57
4977 23301 5.869649 TCCTAGCTCAACATACAATAGCA 57.130 39.130 0.00 0.00 35.63 3.49
4986 23310 5.543020 TCTGATCATCATCCTAGCTCAACAT 59.457 40.000 0.00 0.00 0.00 2.71
5031 23355 6.675486 GCATACTACGCAAATGTCATGTTTCT 60.675 38.462 0.00 0.00 0.00 2.52
5066 23390 3.807553 TCTGCTGATTTCGCCATTCATA 58.192 40.909 0.00 0.00 0.00 2.15
5121 23445 1.028330 AGGGTGCATGTCGAGCAATG 61.028 55.000 0.00 0.00 44.64 2.82
5125 23449 0.109597 CAAAAGGGTGCATGTCGAGC 60.110 55.000 0.00 0.00 0.00 5.03
5143 23467 5.012664 ACACTCAACATATACCACCTTGTCA 59.987 40.000 0.00 0.00 0.00 3.58
5248 23575 0.179001 CTTTTTGTCGTCCTGGGGGT 60.179 55.000 0.00 0.00 0.00 4.95
5585 23959 1.169661 AAATCGCCGAACACCTTGCA 61.170 50.000 0.00 0.00 0.00 4.08
5648 24022 2.604686 TTCCTCCTCCAGCAGCGT 60.605 61.111 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.