Multiple sequence alignment - TraesCS2D01G019400

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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 TraesCS2D01G019400 chr2D 100.000 3633 0 0 1 3633 9370494 9374126 0.000000e+00 6709.0
1 TraesCS2D01G019400 chr2D 88.493 1738 175 13 883 2600 9277335 9279067 0.000000e+00 2078.0
2 TraesCS2D01G019400 chr2D 88.789 1552 162 6 1006 2546 9502204 9503754 0.000000e+00 1892.0
3 TraesCS2D01G019400 chr2D 83.237 1551 234 17 1006 2544 8686455 8687991 0.000000e+00 1400.0
4 TraesCS2D01G019400 chr2D 84.392 756 109 9 2881 3633 29066265 29065516 0.000000e+00 734.0
5 TraesCS2D01G019400 chr2D 85.033 608 84 6 3028 3633 318432768 318432166 2.400000e-171 612.0
6 TraesCS2D01G019400 chr2D 85.507 552 48 13 371 915 9501137 9501663 6.860000e-152 547.0
7 TraesCS2D01G019400 chr2D 93.704 270 10 3 2597 2863 9280133 9280398 7.310000e-107 398.0
8 TraesCS2D01G019400 chr2D 84.437 302 34 12 568 864 9276992 9277285 5.940000e-73 285.0
9 TraesCS2D01G019400 chr2D 78.409 176 28 10 2863 3034 318437155 318436986 4.960000e-19 106.0
10 TraesCS2D01G019400 chr2D 80.460 87 13 3 481 563 9501695 9501781 3.030000e-06 63.9
11 TraesCS2D01G019400 chr2B 91.803 2147 135 15 491 2600 11560116 11557974 0.000000e+00 2952.0
12 TraesCS2D01G019400 chr2B 92.607 1772 97 9 861 2600 12914383 12916152 0.000000e+00 2516.0
13 TraesCS2D01G019400 chr2B 93.291 1565 96 4 1013 2568 11573680 11572116 0.000000e+00 2300.0
14 TraesCS2D01G019400 chr2B 91.987 312 21 4 684 993 11574041 11573732 5.570000e-118 435.0
15 TraesCS2D01G019400 chr2B 90.335 269 19 5 2597 2863 12929093 12929356 2.690000e-91 346.0
16 TraesCS2D01G019400 chr2B 87.200 250 26 5 582 827 12914136 12914383 2.760000e-71 279.0
17 TraesCS2D01G019400 chr2B 80.537 149 18 9 548 692 11174712 11174571 1.780000e-18 104.0
18 TraesCS2D01G019400 chr2B 96.875 32 1 0 524 555 11912746 11912715 2.000000e-03 54.7
19 TraesCS2D01G019400 chr2A 94.819 1602 75 5 1006 2600 8627409 8629009 0.000000e+00 2492.0
20 TraesCS2D01G019400 chr2A 79.612 1496 276 18 1019 2508 9111119 9109647 0.000000e+00 1046.0
21 TraesCS2D01G019400 chr2A 81.176 765 69 36 266 1002 8626648 8627365 2.470000e-151 545.0
22 TraesCS2D01G019400 chr2A 95.522 268 7 2 2597 2863 8630631 8630894 1.210000e-114 424.0
23 TraesCS2D01G019400 chr2A 85.209 311 38 4 998 1303 8682702 8683009 2.720000e-81 313.0
24 TraesCS2D01G019400 chr2A 83.165 297 40 6 1012 1303 8152317 8152608 2.780000e-66 263.0
25 TraesCS2D01G019400 chr2A 84.689 209 31 1 2 210 8626419 8626626 1.320000e-49 207.0
26 TraesCS2D01G019400 chr2A 100.000 28 0 0 524 551 8412913 8412940 7.000000e-03 52.8
27 TraesCS2D01G019400 chrUn 84.910 1385 199 9 1166 2544 273231379 273229999 0.000000e+00 1391.0
28 TraesCS2D01G019400 chrUn 84.870 1388 200 9 1163 2544 292878470 292879853 0.000000e+00 1391.0
29 TraesCS2D01G019400 chr6A 84.974 772 113 3 2862 3633 73792031 73791263 0.000000e+00 780.0
30 TraesCS2D01G019400 chr3D 82.990 776 123 9 2862 3633 580986100 580986870 0.000000e+00 693.0
31 TraesCS2D01G019400 chr3D 84.211 114 18 0 2862 2975 152686820 152686707 1.070000e-20 111.0
32 TraesCS2D01G019400 chr7D 81.912 774 125 12 2862 3630 80059167 80059930 1.100000e-179 640.0
33 TraesCS2D01G019400 chr4D 80.824 777 128 14 2861 3633 57684871 57685630 1.120000e-164 590.0
34 TraesCS2D01G019400 chr1B 80.282 781 134 19 2862 3633 684906905 684906136 4.070000e-159 571.0
35 TraesCS2D01G019400 chr4B 79.589 779 142 17 2862 3633 34804247 34803479 3.190000e-150 542.0
36 TraesCS2D01G019400 chr4B 78.333 180 31 8 2862 3039 648562451 648562624 3.840000e-20 110.0
37 TraesCS2D01G019400 chr5B 79.204 779 143 18 2862 3633 401081749 401080983 1.160000e-144 523.0


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 TraesCS2D01G019400 chr2D 9370494 9374126 3632 False 6709.000000 6709 100.000000 1 3633 1 chr2D.!!$F2 3632
1 TraesCS2D01G019400 chr2D 8686455 8687991 1536 False 1400.000000 1400 83.237000 1006 2544 1 chr2D.!!$F1 1538
2 TraesCS2D01G019400 chr2D 9276992 9280398 3406 False 920.333333 2078 88.878000 568 2863 3 chr2D.!!$F3 2295
3 TraesCS2D01G019400 chr2D 9501137 9503754 2617 False 834.300000 1892 84.918667 371 2546 3 chr2D.!!$F4 2175
4 TraesCS2D01G019400 chr2D 29065516 29066265 749 True 734.000000 734 84.392000 2881 3633 1 chr2D.!!$R1 752
5 TraesCS2D01G019400 chr2D 318432166 318432768 602 True 612.000000 612 85.033000 3028 3633 1 chr2D.!!$R2 605
6 TraesCS2D01G019400 chr2B 11557974 11560116 2142 True 2952.000000 2952 91.803000 491 2600 1 chr2B.!!$R2 2109
7 TraesCS2D01G019400 chr2B 12914136 12916152 2016 False 1397.500000 2516 89.903500 582 2600 2 chr2B.!!$F2 2018
8 TraesCS2D01G019400 chr2B 11572116 11574041 1925 True 1367.500000 2300 92.639000 684 2568 2 chr2B.!!$R4 1884
9 TraesCS2D01G019400 chr2A 9109647 9111119 1472 True 1046.000000 1046 79.612000 1019 2508 1 chr2A.!!$R1 1489
10 TraesCS2D01G019400 chr2A 8626419 8630894 4475 False 917.000000 2492 89.051500 2 2863 4 chr2A.!!$F4 2861
11 TraesCS2D01G019400 chrUn 273229999 273231379 1380 True 1391.000000 1391 84.910000 1166 2544 1 chrUn.!!$R1 1378
12 TraesCS2D01G019400 chrUn 292878470 292879853 1383 False 1391.000000 1391 84.870000 1163 2544 1 chrUn.!!$F1 1381
13 TraesCS2D01G019400 chr6A 73791263 73792031 768 True 780.000000 780 84.974000 2862 3633 1 chr6A.!!$R1 771
14 TraesCS2D01G019400 chr3D 580986100 580986870 770 False 693.000000 693 82.990000 2862 3633 1 chr3D.!!$F1 771
15 TraesCS2D01G019400 chr7D 80059167 80059930 763 False 640.000000 640 81.912000 2862 3630 1 chr7D.!!$F1 768
16 TraesCS2D01G019400 chr4D 57684871 57685630 759 False 590.000000 590 80.824000 2861 3633 1 chr4D.!!$F1 772
17 TraesCS2D01G019400 chr1B 684906136 684906905 769 True 571.000000 571 80.282000 2862 3633 1 chr1B.!!$R1 771
18 TraesCS2D01G019400 chr4B 34803479 34804247 768 True 542.000000 542 79.589000 2862 3633 1 chr4B.!!$R1 771
19 TraesCS2D01G019400 chr5B 401080983 401081749 766 True 523.000000 523 79.204000 2862 3633 1 chr5B.!!$R1 771

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
601 637 0.035630 GCATGGAGCTGTGGTTCTCT 60.036 55.0 0.0 0.0 41.15 3.10 F
1692 2238 0.723414 CTCATGTGTGTGGCGATGAC 59.277 55.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 2244 0.809385 TAGAGGAGAAGCGTGAACGG 59.191 55.0 4.84 0.0 40.23 4.44 R
2915 5156 0.240945 CCGACATTGTGCCTGTTTCC 59.759 55.0 0.00 0.0 0.00 3.13 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
91 92 6.210796 CAATGACTTTGAATTGCTTCTGTGA 58.789 36.000 0.00 0.00 37.53 3.58
94 95 7.509141 TGACTTTGAATTGCTTCTGTGATTA 57.491 32.000 0.00 0.00 32.29 1.75
98 99 8.579006 ACTTTGAATTGCTTCTGTGATTATTCA 58.421 29.630 0.00 0.00 32.29 2.57
174 175 6.672147 AGCAATGACTCTGAATTGTTTGTAC 58.328 36.000 3.34 0.00 36.39 2.90
185 186 7.931407 TCTGAATTGTTTGTACATATATCCGCT 59.069 33.333 0.00 0.00 33.44 5.52
196 197 2.638480 ATATCCGCTAAGCAAAGGCA 57.362 45.000 0.00 0.00 44.61 4.75
199 200 1.094785 TCCGCTAAGCAAAGGCAATC 58.905 50.000 0.00 0.00 44.61 2.67
205 206 4.176271 GCTAAGCAAAGGCAATCGAAAAT 58.824 39.130 0.00 0.00 44.61 1.82
210 211 5.240121 AGCAAAGGCAATCGAAAATTCAAT 58.760 33.333 0.00 0.00 44.61 2.57
211 212 5.121142 AGCAAAGGCAATCGAAAATTCAATG 59.879 36.000 0.00 0.00 44.61 2.82
212 213 5.318349 CAAAGGCAATCGAAAATTCAATGC 58.682 37.500 0.00 6.36 0.00 3.56
213 214 4.191033 AGGCAATCGAAAATTCAATGCA 57.809 36.364 13.34 0.00 33.80 3.96
214 215 4.761975 AGGCAATCGAAAATTCAATGCAT 58.238 34.783 0.00 0.00 33.80 3.96
215 216 4.569162 AGGCAATCGAAAATTCAATGCATG 59.431 37.500 0.00 0.00 33.80 4.06
216 217 4.268522 GCAATCGAAAATTCAATGCATGC 58.731 39.130 11.82 11.82 32.96 4.06
217 218 4.201734 GCAATCGAAAATTCAATGCATGCA 60.202 37.500 25.04 25.04 32.96 3.96
218 219 5.252583 CAATCGAAAATTCAATGCATGCAC 58.747 37.500 25.37 5.76 0.00 4.57
219 220 3.252400 TCGAAAATTCAATGCATGCACC 58.748 40.909 25.37 2.99 0.00 5.01
220 221 3.056678 TCGAAAATTCAATGCATGCACCT 60.057 39.130 25.37 10.76 0.00 4.00
221 222 4.157472 TCGAAAATTCAATGCATGCACCTA 59.843 37.500 25.37 8.16 0.00 3.08
222 223 5.045215 CGAAAATTCAATGCATGCACCTAT 58.955 37.500 25.37 11.35 0.00 2.57
223 224 6.039159 TCGAAAATTCAATGCATGCACCTATA 59.961 34.615 25.37 8.18 0.00 1.31
239 240 7.053498 TGCACCTATAATAGATGCAGACAAAA 58.947 34.615 2.57 0.00 41.18 2.44
240 241 7.720957 TGCACCTATAATAGATGCAGACAAAAT 59.279 33.333 2.57 0.00 41.18 1.82
241 242 8.019669 GCACCTATAATAGATGCAGACAAAATG 58.980 37.037 0.00 0.00 36.30 2.32
243 244 9.851686 ACCTATAATAGATGCAGACAAAATGAA 57.148 29.630 0.00 0.00 0.00 2.57
247 248 4.627611 AGATGCAGACAAAATGAATCGG 57.372 40.909 0.00 0.00 37.72 4.18
248 249 4.012374 AGATGCAGACAAAATGAATCGGT 58.988 39.130 0.00 0.00 37.72 4.69
249 250 5.185454 AGATGCAGACAAAATGAATCGGTA 58.815 37.500 0.00 0.00 37.72 4.02
250 251 5.647658 AGATGCAGACAAAATGAATCGGTAA 59.352 36.000 0.00 0.00 37.72 2.85
251 252 5.697473 TGCAGACAAAATGAATCGGTAAA 57.303 34.783 0.00 0.00 0.00 2.01
252 253 6.266168 TGCAGACAAAATGAATCGGTAAAT 57.734 33.333 0.00 0.00 0.00 1.40
253 254 7.384439 TGCAGACAAAATGAATCGGTAAATA 57.616 32.000 0.00 0.00 0.00 1.40
254 255 7.821652 TGCAGACAAAATGAATCGGTAAATAA 58.178 30.769 0.00 0.00 0.00 1.40
255 256 8.465999 TGCAGACAAAATGAATCGGTAAATAAT 58.534 29.630 0.00 0.00 0.00 1.28
256 257 8.958043 GCAGACAAAATGAATCGGTAAATAATC 58.042 33.333 0.00 0.00 0.00 1.75
268 269 7.359262 TCGGTAAATAATCAATAAGATGGCG 57.641 36.000 0.00 0.00 36.96 5.69
286 287 2.607180 GGCGCAACAAACTGTTCAAAAT 59.393 40.909 10.83 0.00 38.77 1.82
287 288 3.799420 GGCGCAACAAACTGTTCAAAATA 59.201 39.130 10.83 0.00 38.77 1.40
288 289 4.085107 GGCGCAACAAACTGTTCAAAATAG 60.085 41.667 10.83 0.00 38.77 1.73
289 290 4.737765 GCGCAACAAACTGTTCAAAATAGA 59.262 37.500 0.30 0.00 38.77 1.98
290 291 5.402270 GCGCAACAAACTGTTCAAAATAGAT 59.598 36.000 0.30 0.00 38.77 1.98
309 310 8.804912 AATAGATGATGAGATTCATAAAGGCC 57.195 34.615 0.00 0.00 37.20 5.19
310 311 6.196918 AGATGATGAGATTCATAAAGGCCA 57.803 37.500 5.01 0.00 37.20 5.36
343 344 2.104963 ACCTCACCTCTCTGTTTGTTCC 59.895 50.000 0.00 0.00 0.00 3.62
347 348 1.344763 ACCTCTCTGTTTGTTCCGGAG 59.655 52.381 3.34 0.00 36.79 4.63
361 362 2.276869 CGGAGGATGAGGTGTGTCA 58.723 57.895 0.00 0.00 0.00 3.58
362 363 0.826715 CGGAGGATGAGGTGTGTCAT 59.173 55.000 0.00 0.00 40.00 3.06
363 364 2.031870 CGGAGGATGAGGTGTGTCATA 58.968 52.381 0.00 0.00 37.29 2.15
365 366 3.553715 CGGAGGATGAGGTGTGTCATATG 60.554 52.174 0.00 0.00 37.29 1.78
367 368 4.588951 GGAGGATGAGGTGTGTCATATGTA 59.411 45.833 1.90 0.00 37.29 2.29
368 369 5.070446 GGAGGATGAGGTGTGTCATATGTAA 59.930 44.000 1.90 0.00 37.29 2.41
388 422 7.403312 TGTAAAATATGGGAAATGAGGTGTG 57.597 36.000 0.00 0.00 0.00 3.82
506 541 3.074412 CGGTTAAAGACTGAACTGGCAT 58.926 45.455 0.00 0.00 36.72 4.40
510 545 6.612306 GGTTAAAGACTGAACTGGCATAAAG 58.388 40.000 0.00 0.00 0.00 1.85
519 554 1.086696 CTGGCATAAAGTGGACCACG 58.913 55.000 18.93 5.56 39.64 4.94
521 556 1.654023 GGCATAAAGTGGACCACGGC 61.654 60.000 18.93 16.76 39.64 5.68
556 591 4.339530 GGTTCTGAAGAAACCAAAAGAGCT 59.660 41.667 0.00 0.00 35.78 4.09
558 593 6.431278 GTTCTGAAGAAACCAAAAGAGCTAC 58.569 40.000 0.00 0.00 35.58 3.58
562 597 6.588204 TGAAGAAACCAAAAGAGCTACTGTA 58.412 36.000 0.00 0.00 0.00 2.74
563 598 6.706270 TGAAGAAACCAAAAGAGCTACTGTAG 59.294 38.462 10.48 10.48 0.00 2.74
601 637 0.035630 GCATGGAGCTGTGGTTCTCT 60.036 55.000 0.00 0.00 41.15 3.10
661 698 5.350365 TCATTTACTTACGATGACTTGTGCC 59.650 40.000 0.00 0.00 0.00 5.01
719 759 3.153919 AGCAAATTCCCACGTGTGTAAT 58.846 40.909 15.65 8.01 0.00 1.89
727 767 8.514330 AATTCCCACGTGTGTAATATGTAAAT 57.486 30.769 15.65 0.00 0.00 1.40
779 826 9.429359 GATGATTAGATATCATTTCTGAACGGT 57.571 33.333 5.32 0.00 38.73 4.83
1027 1554 1.692395 TCAATCCCGGCCATGGAGA 60.692 57.895 18.40 6.28 34.80 3.71
1124 1654 1.202639 TGCGCAGTCAGAGGAAAAGAA 60.203 47.619 5.66 0.00 0.00 2.52
1337 1867 2.941064 GCAGCAATGACTCATCTAGCAA 59.059 45.455 11.44 0.00 0.00 3.91
1379 1918 2.476619 CAGTCAAGCGTTCTCGAACAAT 59.523 45.455 10.10 0.00 41.20 2.71
1380 1919 2.476619 AGTCAAGCGTTCTCGAACAATG 59.523 45.455 10.10 5.64 41.20 2.82
1500 2039 1.810853 TGGATGTGAGCGCATGTCG 60.811 57.895 11.47 5.35 42.12 4.35
1692 2238 0.723414 CTCATGTGTGTGGCGATGAC 59.277 55.000 0.00 0.00 0.00 3.06
1698 2244 1.741770 GTGTGGCGATGACAGGGTC 60.742 63.158 0.00 0.00 0.00 4.46
1778 2324 0.479815 GATGGGAGGGCCATGATTGA 59.520 55.000 6.18 0.00 35.15 2.57
1834 2380 5.089970 TGTAGGTGATGATGACTGGAAAG 57.910 43.478 0.00 0.00 0.00 2.62
1876 2422 0.324091 AATGGGCAGAGGAAGCAAGG 60.324 55.000 0.00 0.00 0.00 3.61
1965 2511 4.040217 GGGCTATCTCATGATGAGTTGACT 59.960 45.833 20.82 6.04 44.58 3.41
1996 2542 1.214589 GCACTCGCCTTCGGAAGTA 59.785 57.895 16.07 1.45 36.13 2.24
2055 2603 4.682320 GCAGATGAATTTGCCATGGTGATT 60.682 41.667 14.67 10.96 34.28 2.57
2058 2606 5.365605 AGATGAATTTGCCATGGTGATTCAT 59.634 36.000 30.80 30.80 45.22 2.57
2106 2655 7.301789 CAACAAATATGTTCACGGATGTGTTA 58.698 34.615 0.00 0.00 46.78 2.41
2121 2670 3.128349 TGTGTTAAGAAGCAACCTCGAC 58.872 45.455 0.00 0.00 0.00 4.20
2153 2702 3.275999 GGCGTTGTATATTGGACAAGGT 58.724 45.455 9.91 0.00 42.10 3.50
2680 4919 5.945144 TCAATTTGGACCTACCTACCTAC 57.055 43.478 0.00 0.00 39.86 3.18
2681 4920 4.718276 TCAATTTGGACCTACCTACCTACC 59.282 45.833 0.00 0.00 39.86 3.18
2682 4921 4.639019 ATTTGGACCTACCTACCTACCT 57.361 45.455 0.00 0.00 39.86 3.08
2683 4922 5.756314 ATTTGGACCTACCTACCTACCTA 57.244 43.478 0.00 0.00 39.86 3.08
2765 5006 5.598005 TCCTTGTCACATCTTTGGACATTTT 59.402 36.000 0.00 0.00 40.84 1.82
2836 5077 5.412594 TCAAATCATCCCTTGAGACTTTTCG 59.587 40.000 0.00 0.00 37.89 3.46
2850 5091 5.402398 AGACTTTTCGATTTTGCCAATAGC 58.598 37.500 0.00 0.00 44.14 2.97
2851 5092 5.183904 AGACTTTTCGATTTTGCCAATAGCT 59.816 36.000 0.00 0.00 44.23 3.32
2852 5093 5.783111 ACTTTTCGATTTTGCCAATAGCTT 58.217 33.333 0.00 0.00 44.23 3.74
2853 5094 6.223120 ACTTTTCGATTTTGCCAATAGCTTT 58.777 32.000 0.00 0.00 44.23 3.51
2854 5095 6.146021 ACTTTTCGATTTTGCCAATAGCTTTG 59.854 34.615 0.00 0.00 44.23 2.77
2855 5096 3.510719 TCGATTTTGCCAATAGCTTTGC 58.489 40.909 0.00 0.00 44.23 3.68
2856 5097 2.604462 CGATTTTGCCAATAGCTTTGCC 59.396 45.455 0.00 0.00 44.23 4.52
2857 5098 3.598299 GATTTTGCCAATAGCTTTGCCA 58.402 40.909 0.00 0.00 44.23 4.92
2858 5099 2.747396 TTTGCCAATAGCTTTGCCAG 57.253 45.000 0.00 0.00 44.23 4.85
2859 5100 1.921982 TTGCCAATAGCTTTGCCAGA 58.078 45.000 0.00 0.00 44.23 3.86
2926 5167 2.041153 CCCACAAGGAAACAGGCAC 58.959 57.895 0.00 0.00 38.24 5.01
2928 5169 1.110442 CCACAAGGAAACAGGCACAA 58.890 50.000 0.00 0.00 36.89 3.33
2934 5175 0.240945 GGAAACAGGCACAATGTCGG 59.759 55.000 0.00 0.00 0.00 4.79
2938 5179 3.281727 AACAGGCACAATGTCGGATAT 57.718 42.857 0.00 0.00 0.00 1.63
2951 5192 4.866921 TGTCGGATATTCGGACATTACAG 58.133 43.478 12.22 0.00 46.93 2.74
2959 5200 3.226346 TCGGACATTACAGAACGAAGG 57.774 47.619 0.00 0.00 0.00 3.46
2994 5240 6.267070 GGCTACACACTAATACAGAAGTCTC 58.733 44.000 0.00 0.00 0.00 3.36
3034 5281 2.534903 GCGAGCGGAATACAAGGCC 61.535 63.158 0.00 0.00 0.00 5.19
3196 5445 0.609151 TTCGCCAACGGACTCCATTA 59.391 50.000 0.00 0.00 40.63 1.90
3200 5449 1.338769 GCCAACGGACTCCATTACTGT 60.339 52.381 0.00 0.00 0.00 3.55
3220 5469 4.447054 CTGTAAGAGGATAGAGCATTTGCG 59.553 45.833 0.00 0.00 41.39 4.85
3265 5514 3.522553 GGAACAGTCCTTCGATGGTAAG 58.477 50.000 16.29 9.82 41.24 2.34
3274 5523 3.252215 CCTTCGATGGTAAGTTTGTTGCA 59.748 43.478 9.17 0.00 0.00 4.08
3276 5525 4.902443 TCGATGGTAAGTTTGTTGCAAA 57.098 36.364 0.00 0.00 0.00 3.68
3317 5566 3.162666 CATCGCCCCTATACTAGTCCAA 58.837 50.000 0.00 0.00 0.00 3.53
3346 5595 1.978455 TTGTGCTGACCCTGAACCGT 61.978 55.000 0.00 0.00 0.00 4.83
3475 5724 0.693622 TGGTTTGCATTCTCGGGGTA 59.306 50.000 0.00 0.00 0.00 3.69
3524 5773 4.121317 CCGTACCATTCCGTTTAGCAATA 58.879 43.478 0.00 0.00 0.00 1.90
3533 5782 8.356657 CCATTCCGTTTAGCAATATTAATGGAA 58.643 33.333 18.33 18.33 44.98 3.53
3556 5805 1.595357 GAAGACGGTCCCGGAACAT 59.405 57.895 0.73 0.00 44.69 2.71
3625 5874 4.340617 AGACCTTTGACCTCTCTCTGTAG 58.659 47.826 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.860930 TTTCCCAAGTGGAGCCGCC 62.861 63.158 0.00 0.00 46.24 6.13
24 25 2.727103 TTTTTCCCAAGTGGAGCCG 58.273 52.632 0.00 0.00 46.24 5.52
74 75 9.361315 CATGAATAATCACAGAAGCAATTCAAA 57.639 29.630 0.00 0.00 38.69 2.69
83 84 9.529325 AAATCAATGCATGAATAATCACAGAAG 57.471 29.630 0.00 0.00 42.54 2.85
129 130 4.321008 GCTTATGATCCATGATGCCACAAG 60.321 45.833 0.00 0.00 0.00 3.16
133 134 3.512219 TGCTTATGATCCATGATGCCA 57.488 42.857 0.00 0.00 0.00 4.92
134 135 4.461431 TCATTGCTTATGATCCATGATGCC 59.539 41.667 0.00 0.00 38.35 4.40
159 160 7.931407 AGCGGATATATGTACAAACAATTCAGA 59.069 33.333 0.00 0.00 39.58 3.27
160 161 8.087982 AGCGGATATATGTACAAACAATTCAG 57.912 34.615 0.00 0.00 39.58 3.02
174 175 4.002982 TGCCTTTGCTTAGCGGATATATG 58.997 43.478 0.00 0.00 38.71 1.78
182 183 0.726827 TCGATTGCCTTTGCTTAGCG 59.273 50.000 0.00 0.00 38.71 4.26
185 186 5.777802 TGAATTTTCGATTGCCTTTGCTTA 58.222 33.333 0.00 0.00 38.71 3.09
196 197 4.330620 GGTGCATGCATTGAATTTTCGATT 59.669 37.500 25.64 0.00 0.00 3.34
199 200 3.255725 AGGTGCATGCATTGAATTTTCG 58.744 40.909 25.64 0.00 0.00 3.46
205 206 8.047413 CATCTATTATAGGTGCATGCATTGAA 57.953 34.615 25.64 13.91 28.88 2.69
216 217 9.276590 TCATTTTGTCTGCATCTATTATAGGTG 57.723 33.333 8.07 8.07 39.92 4.00
217 218 9.851686 TTCATTTTGTCTGCATCTATTATAGGT 57.148 29.630 0.00 0.00 0.00 3.08
221 222 8.509690 CCGATTCATTTTGTCTGCATCTATTAT 58.490 33.333 0.00 0.00 0.00 1.28
222 223 7.498900 ACCGATTCATTTTGTCTGCATCTATTA 59.501 33.333 0.00 0.00 0.00 0.98
223 224 6.319658 ACCGATTCATTTTGTCTGCATCTATT 59.680 34.615 0.00 0.00 0.00 1.73
241 242 9.774742 GCCATCTTATTGATTATTTACCGATTC 57.225 33.333 0.00 0.00 32.05 2.52
243 244 7.414098 GCGCCATCTTATTGATTATTTACCGAT 60.414 37.037 0.00 0.00 32.05 4.18
244 245 6.128391 GCGCCATCTTATTGATTATTTACCGA 60.128 38.462 0.00 0.00 32.05 4.69
245 246 6.021596 GCGCCATCTTATTGATTATTTACCG 58.978 40.000 0.00 0.00 32.05 4.02
246 247 6.908825 TGCGCCATCTTATTGATTATTTACC 58.091 36.000 4.18 0.00 32.05 2.85
247 248 7.860373 TGTTGCGCCATCTTATTGATTATTTAC 59.140 33.333 4.18 0.00 32.05 2.01
248 249 7.935520 TGTTGCGCCATCTTATTGATTATTTA 58.064 30.769 4.18 0.00 32.05 1.40
249 250 6.804677 TGTTGCGCCATCTTATTGATTATTT 58.195 32.000 4.18 0.00 32.05 1.40
250 251 6.389830 TGTTGCGCCATCTTATTGATTATT 57.610 33.333 4.18 0.00 32.05 1.40
251 252 6.389830 TTGTTGCGCCATCTTATTGATTAT 57.610 33.333 4.18 0.00 32.05 1.28
252 253 5.826601 TTGTTGCGCCATCTTATTGATTA 57.173 34.783 4.18 0.00 32.05 1.75
253 254 4.717233 TTGTTGCGCCATCTTATTGATT 57.283 36.364 4.18 0.00 32.05 2.57
254 255 4.158394 AGTTTGTTGCGCCATCTTATTGAT 59.842 37.500 4.18 0.00 35.40 2.57
255 256 3.505680 AGTTTGTTGCGCCATCTTATTGA 59.494 39.130 4.18 0.00 0.00 2.57
256 257 3.609373 CAGTTTGTTGCGCCATCTTATTG 59.391 43.478 4.18 0.00 0.00 1.90
257 258 3.255642 ACAGTTTGTTGCGCCATCTTATT 59.744 39.130 4.18 0.00 0.00 1.40
258 259 2.819608 ACAGTTTGTTGCGCCATCTTAT 59.180 40.909 4.18 0.00 0.00 1.73
259 260 2.226330 ACAGTTTGTTGCGCCATCTTA 58.774 42.857 4.18 0.00 0.00 2.10
260 261 1.032014 ACAGTTTGTTGCGCCATCTT 58.968 45.000 4.18 0.00 0.00 2.40
261 262 1.001378 GAACAGTTTGTTGCGCCATCT 60.001 47.619 4.18 0.00 41.28 2.90
262 263 1.268999 TGAACAGTTTGTTGCGCCATC 60.269 47.619 4.18 0.00 41.28 3.51
263 264 0.743688 TGAACAGTTTGTTGCGCCAT 59.256 45.000 4.18 0.00 41.28 4.40
264 265 0.528017 TTGAACAGTTTGTTGCGCCA 59.472 45.000 4.18 0.00 41.28 5.69
268 269 7.928908 TCATCTATTTTGAACAGTTTGTTGC 57.071 32.000 0.00 0.00 41.28 4.17
286 287 7.320384 TGGCCTTTATGAATCTCATCATCTA 57.680 36.000 3.32 0.00 40.44 1.98
287 288 6.196918 TGGCCTTTATGAATCTCATCATCT 57.803 37.500 3.32 0.00 40.44 2.90
288 289 6.889301 TTGGCCTTTATGAATCTCATCATC 57.111 37.500 3.32 0.00 40.44 2.92
289 290 7.664552 TTTTGGCCTTTATGAATCTCATCAT 57.335 32.000 3.32 0.00 42.52 2.45
290 291 7.664552 ATTTTGGCCTTTATGAATCTCATCA 57.335 32.000 3.32 0.00 38.26 3.07
320 321 4.202326 GGAACAAACAGAGAGGTGAGGTAA 60.202 45.833 0.00 0.00 0.00 2.85
321 322 3.323979 GGAACAAACAGAGAGGTGAGGTA 59.676 47.826 0.00 0.00 0.00 3.08
323 324 2.772287 GGAACAAACAGAGAGGTGAGG 58.228 52.381 0.00 0.00 0.00 3.86
335 336 1.003233 ACCTCATCCTCCGGAACAAAC 59.997 52.381 5.23 0.00 34.34 2.93
343 344 0.826715 ATGACACACCTCATCCTCCG 59.173 55.000 0.00 0.00 0.00 4.63
347 348 7.807977 ATTTTACATATGACACACCTCATCC 57.192 36.000 10.38 0.00 32.86 3.51
361 362 9.881773 ACACCTCATTTCCCATATTTTACATAT 57.118 29.630 0.00 0.00 0.00 1.78
362 363 9.130661 CACACCTCATTTCCCATATTTTACATA 57.869 33.333 0.00 0.00 0.00 2.29
363 364 7.619302 ACACACCTCATTTCCCATATTTTACAT 59.381 33.333 0.00 0.00 0.00 2.29
365 366 7.122055 TGACACACCTCATTTCCCATATTTTAC 59.878 37.037 0.00 0.00 0.00 2.01
367 368 6.015918 TGACACACCTCATTTCCCATATTTT 58.984 36.000 0.00 0.00 0.00 1.82
368 369 5.579047 TGACACACCTCATTTCCCATATTT 58.421 37.500 0.00 0.00 0.00 1.40
431 465 5.413213 CGGTTGTTCCATGTGGTTCTTAATA 59.587 40.000 0.00 0.00 36.34 0.98
506 541 1.180456 TCTCGCCGTGGTCCACTTTA 61.180 55.000 19.82 2.18 31.34 1.85
510 545 3.681835 AGTCTCGCCGTGGTCCAC 61.682 66.667 12.40 12.40 0.00 4.02
519 554 0.250513 AGAACCCAATCAGTCTCGCC 59.749 55.000 0.00 0.00 0.00 5.54
521 556 3.056536 TCTTCAGAACCCAATCAGTCTCG 60.057 47.826 0.00 0.00 0.00 4.04
556 591 7.939784 TCAGTAATCTTTCAGAGCTACAGTA 57.060 36.000 0.00 0.00 0.00 2.74
558 593 6.255453 GCTTCAGTAATCTTTCAGAGCTACAG 59.745 42.308 0.00 0.00 0.00 2.74
562 597 5.157940 TGCTTCAGTAATCTTTCAGAGCT 57.842 39.130 0.00 0.00 0.00 4.09
563 598 5.220815 CCATGCTTCAGTAATCTTTCAGAGC 60.221 44.000 0.00 0.00 0.00 4.09
627 663 7.598869 TCATCGTAAGTAAATGATATGTGCCTC 59.401 37.037 0.00 0.00 39.48 4.70
643 679 1.623811 AGGGCACAAGTCATCGTAAGT 59.376 47.619 0.00 0.00 39.48 2.24
661 698 2.421619 GAACTTCAGTGGAGAAGCAGG 58.578 52.381 5.11 0.00 46.97 4.85
719 759 7.721842 TGTCTTTTGTTGGACTCCATTTACATA 59.278 33.333 0.00 0.00 31.53 2.29
727 767 3.278574 CACTGTCTTTTGTTGGACTCCA 58.721 45.455 0.00 0.00 34.01 3.86
779 826 7.214460 TGGTAGGTCCAAATCCATTATTGTA 57.786 36.000 0.00 0.00 44.12 2.41
1027 1554 2.380941 TGCAACTGCTGATATGGCAAT 58.619 42.857 2.95 0.00 42.66 3.56
1124 1654 0.178953 ATGCTGCAACCTTTCCACCT 60.179 50.000 6.36 0.00 0.00 4.00
1161 1691 1.721664 CCGCCTCCTCGACGATTGTA 61.722 60.000 0.00 0.00 0.00 2.41
1164 1694 2.439701 TCCGCCTCCTCGACGATT 60.440 61.111 0.00 0.00 0.00 3.34
1299 1829 0.321298 TGCTAACCTTGTCGAAGCCC 60.321 55.000 0.86 0.00 32.14 5.19
1309 1839 3.423539 TGAGTCATTGCTGCTAACCTT 57.576 42.857 0.00 0.00 0.00 3.50
1337 1867 7.936847 TGACTGGAATGACTAAATACAAACTGT 59.063 33.333 0.00 0.00 0.00 3.55
1379 1918 1.321474 CTTGTTGCCTTTCTCTGCCA 58.679 50.000 0.00 0.00 0.00 4.92
1380 1919 0.600057 CCTTGTTGCCTTTCTCTGCC 59.400 55.000 0.00 0.00 0.00 4.85
1500 2039 5.178797 AGATAAACATCATATGGCCTACGC 58.821 41.667 3.32 0.00 33.60 4.42
1692 2238 2.027625 GAAGCGTGAACGGACCCTG 61.028 63.158 4.84 0.00 40.23 4.45
1698 2244 0.809385 TAGAGGAGAAGCGTGAACGG 59.191 55.000 4.84 0.00 40.23 4.44
1800 2346 6.358974 TCATCACCTACATCAGAAGTGAAA 57.641 37.500 0.00 0.00 40.56 2.69
1996 2542 1.069823 CGGATGTTCTGCTGGCTCTAT 59.930 52.381 0.00 0.00 0.00 1.98
2079 2628 3.840890 TCCGTGAACATATTTGTTGCC 57.159 42.857 6.25 0.00 46.01 4.52
2106 2655 1.202486 TGAACGTCGAGGTTGCTTCTT 60.202 47.619 26.63 1.97 0.00 2.52
2121 2670 1.493772 TACAACGCCAGAACTGAACG 58.506 50.000 3.19 9.04 36.49 3.95
2153 2702 5.606505 GGTTTCTTTTAACCATTCTTGCCA 58.393 37.500 0.00 0.00 45.59 4.92
2191 2744 2.208132 ATACGCATGGTTGGGTTCAA 57.792 45.000 0.91 0.00 45.88 2.69
2342 2895 1.630878 AGTCTCCTTTGGGCCTAACAG 59.369 52.381 0.00 2.60 0.00 3.16
2352 2905 5.702670 TGCAATTAGAGTGAAGTCTCCTTTG 59.297 40.000 0.00 0.00 35.28 2.77
2562 3121 7.274468 CACTGTATGTCACTTGAGATCTGTAAC 59.726 40.741 0.00 0.00 30.22 2.50
2568 3127 6.393990 AGTTCACTGTATGTCACTTGAGATC 58.606 40.000 0.00 0.00 30.22 2.75
2653 4892 7.746703 AGGTAGGTAGGTCCAAATTGATTATC 58.253 38.462 0.00 0.00 39.02 1.75
2683 4922 9.860650 TTGGCCAATATTTATAATACTCACAGT 57.139 29.630 16.05 0.00 0.00 3.55
2765 5006 8.030692 ACACACGCATACTTGTCTAGTTTAATA 58.969 33.333 0.00 0.00 38.33 0.98
2850 5091 5.418310 TCGTTCTAAAAAGTCTGGCAAAG 57.582 39.130 0.00 0.00 0.00 2.77
2851 5092 5.587043 TCTTCGTTCTAAAAAGTCTGGCAAA 59.413 36.000 0.00 0.00 0.00 3.68
2852 5093 5.007332 GTCTTCGTTCTAAAAAGTCTGGCAA 59.993 40.000 0.00 0.00 0.00 4.52
2853 5094 4.510340 GTCTTCGTTCTAAAAAGTCTGGCA 59.490 41.667 0.00 0.00 0.00 4.92
2854 5095 4.376109 CGTCTTCGTTCTAAAAAGTCTGGC 60.376 45.833 0.00 0.00 0.00 4.85
2855 5096 4.376109 GCGTCTTCGTTCTAAAAAGTCTGG 60.376 45.833 0.00 0.00 39.49 3.86
2856 5097 4.444720 AGCGTCTTCGTTCTAAAAAGTCTG 59.555 41.667 0.00 0.00 39.49 3.51
2857 5098 4.618965 AGCGTCTTCGTTCTAAAAAGTCT 58.381 39.130 0.00 0.00 39.49 3.24
2858 5099 4.968660 AGCGTCTTCGTTCTAAAAAGTC 57.031 40.909 0.00 0.00 39.49 3.01
2859 5100 4.922103 CCTAGCGTCTTCGTTCTAAAAAGT 59.078 41.667 0.00 0.00 39.49 2.66
2915 5156 0.240945 CCGACATTGTGCCTGTTTCC 59.759 55.000 0.00 0.00 0.00 3.13
2926 5167 5.694458 TGTAATGTCCGAATATCCGACATTG 59.306 40.000 24.38 0.00 43.56 2.82
2928 5169 5.243060 TCTGTAATGTCCGAATATCCGACAT 59.757 40.000 8.03 8.03 38.01 3.06
2934 5175 6.144080 CCTTCGTTCTGTAATGTCCGAATATC 59.856 42.308 0.00 0.00 34.33 1.63
2938 5179 3.581755 CCTTCGTTCTGTAATGTCCGAA 58.418 45.455 0.00 0.00 33.79 4.30
2976 5222 6.350277 CCCTTTCGAGACTTCTGTATTAGTGT 60.350 42.308 0.00 0.00 0.00 3.55
2979 5225 6.210287 ACCCTTTCGAGACTTCTGTATTAG 57.790 41.667 0.00 0.00 0.00 1.73
2981 5227 5.011738 TGAACCCTTTCGAGACTTCTGTATT 59.988 40.000 0.00 0.00 34.04 1.89
2983 5229 3.893200 TGAACCCTTTCGAGACTTCTGTA 59.107 43.478 0.00 0.00 34.04 2.74
2994 5240 0.598065 CCAGGCTTTGAACCCTTTCG 59.402 55.000 0.00 0.00 34.04 3.46
3117 5366 1.696884 TGTGCACCAGGTCTATGTGAA 59.303 47.619 15.69 0.00 31.66 3.18
3118 5367 1.001974 GTGTGCACCAGGTCTATGTGA 59.998 52.381 15.69 0.00 31.66 3.58
3196 5445 5.363939 GCAAATGCTCTATCCTCTTACAGT 58.636 41.667 0.00 0.00 38.21 3.55
3200 5449 4.937201 TCGCAAATGCTCTATCCTCTTA 57.063 40.909 3.63 0.00 39.32 2.10
3220 5469 3.332034 ACGCACCCGGCTAATATTATTC 58.668 45.455 0.00 0.00 41.67 1.75
3241 5490 0.530744 CATCGAAGGACTGTTCCCGA 59.469 55.000 4.09 4.09 44.10 5.14
3249 5498 4.618920 ACAAACTTACCATCGAAGGACT 57.381 40.909 14.76 0.00 0.00 3.85
3274 5523 3.954258 GCTATGGTCCTTGTGGCTTATTT 59.046 43.478 0.00 0.00 0.00 1.40
3276 5525 2.509548 TGCTATGGTCCTTGTGGCTTAT 59.490 45.455 0.00 0.00 0.00 1.73
3346 5595 1.490490 AGCTTGTGGAACTCCTTGACA 59.510 47.619 0.00 0.00 38.04 3.58
3505 5754 8.788806 CCATTAATATTGCTAAACGGAATGGTA 58.211 33.333 10.65 0.00 37.22 3.25
3506 5755 7.504238 TCCATTAATATTGCTAAACGGAATGGT 59.496 33.333 15.48 0.00 40.95 3.55
3524 5773 5.163332 GGACCGTCTTCCTACTTCCATTAAT 60.163 44.000 0.00 0.00 32.24 1.40
3533 5782 1.379576 CCGGGACCGTCTTCCTACT 60.380 63.158 10.17 0.00 35.76 2.57


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

AutoCloner maintained by Alex Coulton.