Multiple sequence alignment - TraesCS7B01G408000

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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 TraesCS7B01G408000 chr7B 100.000 2624 0 0 1 2624 677345159 677347782 0.000000e+00 4846.0
1 TraesCS7B01G408000 chr7B 81.136 880 99 32 1793 2622 677401055 677401917 0.000000e+00 643.0
2 TraesCS7B01G408000 chr7B 83.881 639 76 11 1001 1621 677400178 677400807 3.760000e-163 584.0
3 TraesCS7B01G408000 chr7B 83.750 480 48 8 426 879 677218297 677217822 6.710000e-116 427.0
4 TraesCS7B01G408000 chr7B 86.162 383 46 6 3 379 677239148 677239529 8.740000e-110 407.0
5 TraesCS7B01G408000 chr7B 85.838 346 36 6 426 762 677239627 677239968 3.210000e-94 355.0
6 TraesCS7B01G408000 chr7B 81.169 462 54 13 426 875 677405817 677406257 8.990000e-90 340.0
7 TraesCS7B01G408000 chr7B 79.924 523 55 25 395 875 677355907 677356421 3.230000e-89 339.0
8 TraesCS7B01G408000 chr7B 86.364 198 21 3 946 1143 677242231 677242422 7.360000e-51 211.0
9 TraesCS7B01G408000 chr7B 86.387 191 25 1 163 353 677354737 677354926 9.520000e-50 207.0
10 TraesCS7B01G408000 chr7B 93.277 119 7 1 759 877 677241181 677241298 9.650000e-40 174.0
11 TraesCS7B01G408000 chr7B 96.667 60 2 0 343 402 677355821 677355880 1.660000e-17 100.0
12 TraesCS7B01G408000 chr7B 81.818 77 8 4 881 954 677242132 677242205 2.820000e-05 60.2
13 TraesCS7B01G408000 chr7A 89.375 640 40 10 2011 2624 690707660 690708297 0.000000e+00 780.0
14 TraesCS7B01G408000 chr7A 80.000 885 82 33 1793 2621 690794073 690794918 1.360000e-157 566.0
15 TraesCS7B01G408000 chr7A 88.432 389 29 6 490 875 690838908 690839283 3.080000e-124 455.0
16 TraesCS7B01G408000 chr7A 86.310 168 22 1 212 379 690823220 690823386 5.770000e-42 182.0
17 TraesCS7B01G408000 chr7A 82.915 199 28 3 1001 1196 690707114 690707309 9.650000e-40 174.0
18 TraesCS7B01G408000 chr7D 83.796 648 79 16 992 1621 598308343 598308982 2.250000e-165 592.0
19 TraesCS7B01G408000 chr7D 84.468 470 43 14 1793 2246 598309230 598309685 1.120000e-118 436.0
20 TraesCS7B01G408000 chr7D 82.846 513 52 11 395 875 598334849 598335357 6.710000e-116 427.0
21 TraesCS7B01G408000 chr7D 81.235 405 39 18 2239 2620 598310751 598311141 2.550000e-75 292.0
22 TraesCS7B01G408000 chr7D 85.345 232 30 3 171 398 598334587 598334818 1.210000e-58 237.0


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 TraesCS7B01G408000 chr7B 677345159 677347782 2623 False 4846.000000 4846 100.000000 1 2624 1 chr7B.!!$F1 2623
1 TraesCS7B01G408000 chr7B 677400178 677406257 6079 False 522.333333 643 82.062000 426 2622 3 chr7B.!!$F4 2196
2 TraesCS7B01G408000 chr7B 677239148 677242422 3274 False 241.440000 407 86.691800 3 1143 5 chr7B.!!$F2 1140
3 TraesCS7B01G408000 chr7B 677354737 677356421 1684 False 215.333333 339 87.659333 163 875 3 chr7B.!!$F3 712
4 TraesCS7B01G408000 chr7A 690794073 690794918 845 False 566.000000 566 80.000000 1793 2621 1 chr7A.!!$F1 828
5 TraesCS7B01G408000 chr7A 690707114 690708297 1183 False 477.000000 780 86.145000 1001 2624 2 chr7A.!!$F4 1623
6 TraesCS7B01G408000 chr7D 598308343 598311141 2798 False 440.000000 592 83.166333 992 2620 3 chr7D.!!$F1 1628
7 TraesCS7B01G408000 chr7D 598334587 598335357 770 False 332.000000 427 84.095500 171 875 2 chr7D.!!$F2 704

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
969 8316 0.106335 CATCTGGCCTCTGCTACAGG 59.894 60.0 3.32 0.0 37.74 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 9353 1.495584 AACTACACACGCAAGCACGG 61.496 55.0 0.0 0.0 45.62 4.94 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
35 36 3.181474 CGGGATGTCTTCTAAAGTCCTCC 60.181 52.174 0.00 1.62 33.16 4.30
39 40 3.511477 TGTCTTCTAAAGTCCTCCAGCT 58.489 45.455 0.00 0.00 0.00 4.24
40 41 3.259374 TGTCTTCTAAAGTCCTCCAGCTG 59.741 47.826 6.78 6.78 0.00 4.24
42 43 3.511934 TCTTCTAAAGTCCTCCAGCTGTC 59.488 47.826 13.81 0.00 0.00 3.51
72 73 1.611491 TGATCATATGCGTCTACGGCA 59.389 47.619 4.49 3.62 40.23 5.69
75 76 0.597377 CATATGCGTCTACGGCAGCA 60.597 55.000 4.49 0.00 44.13 4.41
105 106 0.380024 CACATGCACGTGGTCAACAA 59.620 50.000 18.88 0.00 33.05 2.83
109 110 3.505680 ACATGCACGTGGTCAACAAATAT 59.494 39.130 18.88 0.00 0.00 1.28
116 117 5.123820 CACGTGGTCAACAAATATCCATCTT 59.876 40.000 7.95 0.00 0.00 2.40
129 131 2.509336 ATCTTGTTCGCGCTCCCG 60.509 61.111 5.56 0.00 37.57 5.14
141 143 2.281761 CTCCCGCTGCCAAGTGTT 60.282 61.111 0.00 0.00 31.58 3.32
142 144 1.003839 CTCCCGCTGCCAAGTGTTA 60.004 57.895 0.00 0.00 31.58 2.41
152 154 1.865865 CCAAGTGTTAGTGTCACGCT 58.134 50.000 0.00 0.00 40.28 5.07
178 180 1.679641 CATGTGAGGGCCATGTGCA 60.680 57.895 6.18 0.00 43.89 4.57
189 191 1.439201 CATGTGCACGCGTCTTGTG 60.439 57.895 9.86 0.00 40.32 3.33
263 265 0.908910 TCCGGTGCTGGTGAACATAT 59.091 50.000 0.00 0.00 0.00 1.78
264 266 1.280710 TCCGGTGCTGGTGAACATATT 59.719 47.619 0.00 0.00 0.00 1.28
292 299 3.944015 AGCCAGCTCAGTGATTATGTTTC 59.056 43.478 0.00 0.00 0.00 2.78
300 307 9.624373 AGCTCAGTGATTATGTTTCTTATCATT 57.376 29.630 0.00 0.00 30.51 2.57
332 339 5.504830 GCTTGAGACTTTGAAAGACCTTGTC 60.505 44.000 12.53 0.00 0.00 3.18
353 360 3.509967 TCGGCATCTCGTATCATAATGGT 59.490 43.478 0.00 0.00 0.00 3.55
354 1266 4.703093 TCGGCATCTCGTATCATAATGGTA 59.297 41.667 0.00 0.00 0.00 3.25
395 1310 5.403166 CCAGCAAAAATGACAACACACTATG 59.597 40.000 0.00 0.00 0.00 2.23
397 1312 6.864685 CAGCAAAAATGACAACACACTATGAT 59.135 34.615 0.00 0.00 0.00 2.45
398 1313 6.864685 AGCAAAAATGACAACACACTATGATG 59.135 34.615 0.00 0.00 37.14 3.07
399 1314 6.862608 GCAAAAATGACAACACACTATGATGA 59.137 34.615 0.00 0.00 34.77 2.92
400 1315 7.543172 GCAAAAATGACAACACACTATGATGAT 59.457 33.333 0.00 0.00 34.77 2.45
401 1316 8.856247 CAAAAATGACAACACACTATGATGATG 58.144 33.333 0.00 0.00 34.77 3.07
402 1317 7.926674 AAATGACAACACACTATGATGATGA 57.073 32.000 0.00 0.00 34.77 2.92
403 1318 7.549615 AATGACAACACACTATGATGATGAG 57.450 36.000 0.00 0.00 34.77 2.90
405 1320 6.881570 TGACAACACACTATGATGATGAGAT 58.118 36.000 0.00 0.00 34.77 2.75
406 1321 7.333323 TGACAACACACTATGATGATGAGATT 58.667 34.615 0.00 0.00 34.77 2.40
407 1322 7.825761 TGACAACACACTATGATGATGAGATTT 59.174 33.333 0.00 0.00 34.77 2.17
408 1323 7.982224 ACAACACACTATGATGATGAGATTTG 58.018 34.615 0.00 0.00 34.77 2.32
409 1324 7.825761 ACAACACACTATGATGATGAGATTTGA 59.174 33.333 0.00 0.00 34.77 2.69
410 1325 8.336080 CAACACACTATGATGATGAGATTTGAG 58.664 37.037 0.00 0.00 32.93 3.02
411 1326 7.789026 ACACACTATGATGATGAGATTTGAGA 58.211 34.615 0.00 0.00 0.00 3.27
415 1330 8.713271 CACTATGATGATGAGATTTGAGATGTG 58.287 37.037 0.00 0.00 0.00 3.21
419 1334 4.117685 TGATGAGATTTGAGATGTGAGCG 58.882 43.478 0.00 0.00 0.00 5.03
420 1335 3.599730 TGAGATTTGAGATGTGAGCGT 57.400 42.857 0.00 0.00 0.00 5.07
421 1336 4.718940 TGAGATTTGAGATGTGAGCGTA 57.281 40.909 0.00 0.00 0.00 4.42
422 1337 4.424626 TGAGATTTGAGATGTGAGCGTAC 58.575 43.478 0.00 0.00 0.00 3.67
423 1338 3.786635 AGATTTGAGATGTGAGCGTACC 58.213 45.455 0.00 0.00 0.00 3.34
424 1339 3.195610 AGATTTGAGATGTGAGCGTACCA 59.804 43.478 0.00 0.00 0.00 3.25
425 1340 2.654749 TTGAGATGTGAGCGTACCAG 57.345 50.000 0.00 0.00 0.00 4.00
426 1341 0.817654 TGAGATGTGAGCGTACCAGG 59.182 55.000 0.00 0.00 0.00 4.45
427 1342 0.528684 GAGATGTGAGCGTACCAGGC 60.529 60.000 0.00 0.00 0.00 4.85
429 1344 0.179073 GATGTGAGCGTACCAGGCAT 60.179 55.000 0.00 0.00 0.00 4.40
451 5670 2.819608 GTGTTGTGCTGTATTCCCACAT 59.180 45.455 0.00 0.00 39.03 3.21
499 5719 6.922957 TCAACTTTTCAAGCCATTTATGTGTC 59.077 34.615 0.00 0.00 0.00 3.67
526 5754 0.180642 CATGGAGCCAGCTGATCACT 59.819 55.000 17.39 6.76 0.00 3.41
556 5784 1.816224 GTTACCATCATGCGTTTGGGT 59.184 47.619 9.03 4.01 34.72 4.51
557 5785 3.011119 GTTACCATCATGCGTTTGGGTA 58.989 45.455 9.03 3.15 34.72 3.69
558 5786 1.459450 ACCATCATGCGTTTGGGTAC 58.541 50.000 9.03 0.00 34.72 3.34
559 5787 1.271652 ACCATCATGCGTTTGGGTACA 60.272 47.619 9.03 0.00 34.72 2.90
560 5788 2.023673 CCATCATGCGTTTGGGTACAT 58.976 47.619 0.00 0.00 0.00 2.29
562 5790 3.629855 CCATCATGCGTTTGGGTACATTA 59.370 43.478 0.00 0.00 0.00 1.90
563 5791 4.097135 CCATCATGCGTTTGGGTACATTAA 59.903 41.667 0.00 0.00 0.00 1.40
564 5792 4.955925 TCATGCGTTTGGGTACATTAAG 57.044 40.909 0.00 0.00 0.00 1.85
565 5793 3.127895 TCATGCGTTTGGGTACATTAAGC 59.872 43.478 0.00 0.00 0.00 3.09
601 5829 2.150837 GCGTCGTACTTGTCGGCTC 61.151 63.158 0.00 0.00 0.00 4.70
605 5833 1.089920 TCGTACTTGTCGGCTCTACC 58.910 55.000 0.00 0.00 0.00 3.18
635 5869 5.718649 GTAGCATACGACAACACATCATT 57.281 39.130 0.00 0.00 0.00 2.57
695 5946 0.307760 GCCCAATTAAGGCGATCACG 59.692 55.000 3.09 0.00 41.41 4.35
707 5958 1.991264 GCGATCACGATCATCATGGAG 59.009 52.381 7.75 0.00 42.66 3.86
716 5967 6.014327 TCACGATCATCATGGAGGAATATGAA 60.014 38.462 0.00 0.00 30.90 2.57
719 5970 6.822170 CGATCATCATGGAGGAATATGAACAT 59.178 38.462 0.00 0.00 30.90 2.71
730 5981 4.453819 GGAATATGAACATGTCTAGCTGCC 59.546 45.833 0.00 0.00 0.00 4.85
767 7236 7.967890 TCGCAATTAATGTCATGAGTATGAT 57.032 32.000 0.00 0.00 44.62 2.45
781 7250 5.831997 TGAGTATGATTGTATGAGGTCGTG 58.168 41.667 0.00 0.00 0.00 4.35
800 7275 5.922544 GTCGTGTACTTTTAGGCTTCAAGTA 59.077 40.000 12.03 12.03 32.88 2.24
818 7293 5.301551 TCAAGTAACCAACATGCAGATTTGT 59.698 36.000 0.00 0.00 0.00 2.83
861 7336 4.297510 TCGGCAACAATGACAAAAATCAG 58.702 39.130 0.00 0.00 32.33 2.90
877 7352 2.359107 AGGCGTGCATGTGTGAGG 60.359 61.111 7.93 0.00 0.00 3.86
878 7353 4.107051 GGCGTGCATGTGTGAGGC 62.107 66.667 7.93 0.00 0.00 4.70
879 7354 3.052082 GCGTGCATGTGTGAGGCT 61.052 61.111 7.93 0.00 30.62 4.58
920 8233 5.453480 GGATGCCGGAGACTAGTCTTATTTT 60.453 44.000 25.86 10.28 40.61 1.82
922 8235 6.534475 TGCCGGAGACTAGTCTTATTTTAA 57.466 37.500 25.86 7.11 40.61 1.52
923 8236 6.570692 TGCCGGAGACTAGTCTTATTTTAAG 58.429 40.000 25.86 10.53 40.61 1.85
924 8237 5.462729 GCCGGAGACTAGTCTTATTTTAAGC 59.537 44.000 25.86 15.60 40.61 3.09
925 8238 6.570692 CCGGAGACTAGTCTTATTTTAAGCA 58.429 40.000 25.86 0.00 40.61 3.91
926 8239 6.476053 CCGGAGACTAGTCTTATTTTAAGCAC 59.524 42.308 25.86 8.79 40.61 4.40
927 8240 6.476053 CGGAGACTAGTCTTATTTTAAGCACC 59.524 42.308 25.86 15.86 40.61 5.01
928 8241 7.328737 GGAGACTAGTCTTATTTTAAGCACCA 58.671 38.462 25.86 0.00 40.61 4.17
929 8242 7.492994 GGAGACTAGTCTTATTTTAAGCACCAG 59.507 40.741 25.86 0.00 40.61 4.00
954 8267 1.282157 GCCCCTGTTTCTGGTACATCT 59.718 52.381 0.00 0.00 38.20 2.90
955 8268 2.941415 GCCCCTGTTTCTGGTACATCTG 60.941 54.545 0.00 0.00 38.20 2.90
957 8270 2.359900 CCTGTTTCTGGTACATCTGGC 58.640 52.381 0.00 0.00 38.20 4.85
963 8310 0.179062 CTGGTACATCTGGCCTCTGC 60.179 60.000 3.32 0.00 38.20 4.26
969 8316 0.106335 CATCTGGCCTCTGCTACAGG 59.894 60.000 3.32 0.00 37.74 4.00
975 8322 1.271926 GGCCTCTGCTACAGGGAAAAA 60.272 52.381 0.00 0.00 32.95 1.94
976 8323 2.087646 GCCTCTGCTACAGGGAAAAAG 58.912 52.381 0.00 0.00 32.95 2.27
977 8324 2.716217 CCTCTGCTACAGGGAAAAAGG 58.284 52.381 0.00 0.00 32.95 3.11
987 8334 4.979335 ACAGGGAAAAAGGAAGAGAAGAG 58.021 43.478 0.00 0.00 0.00 2.85
988 8335 4.202514 ACAGGGAAAAAGGAAGAGAAGAGG 60.203 45.833 0.00 0.00 0.00 3.69
989 8336 4.042187 CAGGGAAAAAGGAAGAGAAGAGGA 59.958 45.833 0.00 0.00 0.00 3.71
1053 8400 0.773644 AGCAGGCCTTCCTCAAGAAA 59.226 50.000 0.00 0.00 41.93 2.52
1057 8404 2.057922 AGGCCTTCCTCAAGAAACTCA 58.942 47.619 0.00 0.00 38.72 3.41
1085 8432 4.479993 GCAGCTCCAGGGACGCAT 62.480 66.667 10.82 0.00 0.00 4.73
1089 8436 2.725312 GCTCCAGGGACGCATGAGA 61.725 63.158 2.50 0.00 0.00 3.27
1092 8439 0.904865 TCCAGGGACGCATGAGAACT 60.905 55.000 2.50 0.00 0.00 3.01
1157 8504 3.423154 CAAGTCCTCCGCCAACGC 61.423 66.667 0.00 0.00 38.22 4.84
1246 8596 1.522092 GCCGTCTCACCATCATCCA 59.478 57.895 0.00 0.00 0.00 3.41
1258 8608 4.170062 CATCCAGCGCGTGCAAGG 62.170 66.667 24.79 23.20 46.23 3.61
1278 8628 2.513204 CAGAGGTGCAGGCGGATG 60.513 66.667 0.00 0.00 0.00 3.51
1287 8637 2.685017 AGGCGGATGGTGAGCAGA 60.685 61.111 0.00 0.00 0.00 4.26
1304 8654 4.845580 ATGCTGCCGCCGGAAGAG 62.846 66.667 17.47 3.91 26.79 2.85
1326 8676 1.342819 AGCTGGATTAGATCAGGTCGC 59.657 52.381 0.00 0.00 37.15 5.19
1330 8680 1.540267 GGATTAGATCAGGTCGCGCTA 59.460 52.381 5.56 0.00 0.00 4.26
1334 8684 1.299468 GATCAGGTCGCGCTAGTGG 60.299 63.158 5.56 0.00 0.00 4.00
1354 8704 4.415332 GCGACGTTGCGAGGAGGA 62.415 66.667 12.96 0.00 0.00 3.71
1356 8706 1.725665 CGACGTTGCGAGGAGGATA 59.274 57.895 0.00 0.00 0.00 2.59
1361 8726 1.202533 CGTTGCGAGGAGGATAATGGT 60.203 52.381 0.00 0.00 0.00 3.55
1371 8736 2.038295 GAGGATAATGGTGCTGAGGGAG 59.962 54.545 0.00 0.00 0.00 4.30
1416 8781 2.642254 CGTCAACGAGGCCACCCTA 61.642 63.158 5.01 0.00 43.12 3.53
1440 8805 2.900273 GAGGCCATGGACTACGCA 59.100 61.111 23.66 0.00 30.74 5.24
1475 8840 4.148825 GGTCGACATGCTCCGCCT 62.149 66.667 18.91 0.00 0.00 5.52
1476 8841 2.887568 GTCGACATGCTCCGCCTG 60.888 66.667 11.55 0.00 0.00 4.85
1477 8842 4.819761 TCGACATGCTCCGCCTGC 62.820 66.667 0.00 0.00 0.00 4.85
1507 8872 0.392193 CGTGCAAAGATCCAGCTCCT 60.392 55.000 0.00 0.00 0.00 3.69
1508 8873 1.093159 GTGCAAAGATCCAGCTCCTG 58.907 55.000 0.00 0.00 0.00 3.86
1509 8874 0.679002 TGCAAAGATCCAGCTCCTGC 60.679 55.000 0.00 0.00 40.05 4.85
1520 8885 4.527583 CTCCTGCTCGGCTGCTCC 62.528 72.222 0.00 0.00 0.00 4.70
1541 8906 1.142314 GCGGGTACGTGGCAATCTA 59.858 57.895 0.00 0.00 43.45 1.98
1542 8907 0.460635 GCGGGTACGTGGCAATCTAA 60.461 55.000 0.00 0.00 43.45 2.10
1565 8930 7.494922 AATTGCTTAGTCCCATTTATTGGTT 57.505 32.000 0.00 0.00 44.83 3.67
1575 8940 9.762381 AGTCCCATTTATTGGTTATTTTCAGTA 57.238 29.630 0.00 0.00 44.83 2.74
1578 8943 9.762933 CCCATTTATTGGTTATTTTCAGTATGG 57.237 33.333 0.00 0.00 44.83 2.74
1602 8967 3.627577 AGTAATACCTTGCTCATTTGGCG 59.372 43.478 0.00 0.00 0.00 5.69
1608 8973 1.454572 TTGCTCATTTGGCGTGCAGT 61.455 50.000 0.00 0.00 35.02 4.40
1628 9031 5.220548 GCAGTGTCAGCAGTGATTAAGTATG 60.221 44.000 6.61 0.00 46.27 2.39
1631 9034 4.631377 TGTCAGCAGTGATTAAGTATGTGC 59.369 41.667 0.00 0.00 34.36 4.57
1667 9070 3.156293 TGCCTCTGCAATAAGAAAAGCA 58.844 40.909 0.00 0.00 46.66 3.91
1676 9079 4.795278 GCAATAAGAAAAGCATTGTCTCCG 59.205 41.667 0.00 0.00 33.22 4.63
1686 9089 3.136763 GCATTGTCTCCGTGATGATCAT 58.863 45.455 8.25 8.25 0.00 2.45
1705 9108 5.643379 TCATGAAAGAAATAGGCACAACC 57.357 39.130 0.00 0.00 39.61 3.77
1824 9266 2.275134 TCAGCAGAGAAAATGGTGCA 57.725 45.000 0.47 0.00 43.97 4.57
1892 9353 5.239525 AGAGAGTGTGGAAAGTTGCATAAAC 59.760 40.000 0.00 0.00 39.24 2.01
1898 9359 2.030274 GGAAAGTTGCATAAACCGTGCT 60.030 45.455 0.00 0.00 42.92 4.40
1907 9368 1.090625 TAAACCGTGCTTGCGTGTGT 61.091 50.000 0.00 0.00 0.00 3.72
1914 9375 1.329292 GTGCTTGCGTGTGTAGTTTGA 59.671 47.619 0.00 0.00 0.00 2.69
1937 9399 4.621068 ATTCAAGGTATGTTCGTGCATG 57.379 40.909 0.00 0.00 0.00 4.06
1982 9444 3.196901 TGATGCCAGGAATTACGTACTGT 59.803 43.478 9.33 0.00 0.00 3.55
1983 9445 2.967362 TGCCAGGAATTACGTACTGTG 58.033 47.619 9.33 3.76 0.00 3.66
1989 9451 5.106830 CCAGGAATTACGTACTGTGGAAAAC 60.107 44.000 9.33 0.00 0.00 2.43
2167 9643 3.402186 CTGGAACTGCAGGTTGTGA 57.598 52.632 19.93 0.00 38.41 3.58
2174 9650 3.788227 ACTGCAGGTTGTGAAATAGGA 57.212 42.857 19.93 0.00 0.00 2.94
2218 9694 0.684153 GCTGCAAATTCCCCAGGCTA 60.684 55.000 0.00 0.00 0.00 3.93
2223 9699 2.158914 GCAAATTCCCCAGGCTATTTGG 60.159 50.000 17.06 3.15 36.21 3.28
2287 10836 9.810545 TTGTGTAAAGATAAACCAAGGAAAAAG 57.189 29.630 0.00 0.00 0.00 2.27
2288 10837 8.973182 TGTGTAAAGATAAACCAAGGAAAAAGT 58.027 29.630 0.00 0.00 0.00 2.66
2340 10900 7.824672 TCTAGTGAACTTACTAAGGTAGCAAC 58.175 38.462 0.88 0.00 33.09 4.17
2431 10992 8.861086 TGGTTTTATTTTTCCACATAGCTTACA 58.139 29.630 0.00 0.00 0.00 2.41
2518 11091 0.535335 TCCAGTTTCCCGGATCGAAG 59.465 55.000 0.73 0.00 0.00 3.79
2552 11125 9.788960 GTTTATAAGAAGAAACAATAGCAAGGG 57.211 33.333 0.00 0.00 36.91 3.95
2558 11131 8.829373 AGAAGAAACAATAGCAAGGGAAATAT 57.171 30.769 0.00 0.00 0.00 1.28
2573 11146 3.246226 GGAAATATGACACACTGCTAGCG 59.754 47.826 10.77 7.61 0.00 4.26
2585 11165 2.956439 CTAGCGCGCTTCGATGCA 60.956 61.111 41.04 18.75 41.67 3.96
2596 11176 0.324614 TTCGATGCATGTGGTGGTCT 59.675 50.000 2.46 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.161377 AGCTGGAGGACTTTAGAAGACATC 59.839 45.833 0.00 0.00 34.21 3.06
26 27 0.832135 TCGGACAGCTGGAGGACTTT 60.832 55.000 19.93 0.00 0.00 2.66
39 40 1.697284 ATGATCAGCTAGCTCGGACA 58.303 50.000 16.15 12.95 0.00 4.02
40 41 3.768406 CATATGATCAGCTAGCTCGGAC 58.232 50.000 16.15 7.48 0.00 4.79
42 43 2.538437 GCATATGATCAGCTAGCTCGG 58.462 52.381 16.15 4.79 0.00 4.63
105 106 2.802816 GAGCGCGAACAAGATGGATATT 59.197 45.455 12.10 0.00 0.00 1.28
109 110 1.447838 GGAGCGCGAACAAGATGGA 60.448 57.895 12.10 0.00 0.00 3.41
129 131 1.264288 GTGACACTAACACTTGGCAGC 59.736 52.381 0.00 0.00 28.87 5.25
152 154 2.046988 CCCTCACATGCAGCGTCA 60.047 61.111 0.00 0.00 0.00 4.35
178 180 1.068127 AGAGGTAAACACAAGACGCGT 59.932 47.619 13.85 13.85 0.00 6.01
189 191 3.154589 CGGGAGGCAAGAGGTAAAC 57.845 57.895 0.00 0.00 0.00 2.01
252 254 2.158871 GGCTCCCGTAATATGTTCACCA 60.159 50.000 0.00 0.00 0.00 4.17
263 265 1.609501 ACTGAGCTGGCTCCCGTAA 60.610 57.895 18.30 0.45 42.09 3.18
264 266 2.037367 ACTGAGCTGGCTCCCGTA 59.963 61.111 18.30 0.79 42.09 4.02
292 299 6.368243 AGTCTCAAGCGCATGATAATGATAAG 59.632 38.462 16.57 1.09 0.00 1.73
300 307 3.860641 TCAAAGTCTCAAGCGCATGATA 58.139 40.909 16.57 6.16 0.00 2.15
332 339 3.849911 ACCATTATGATACGAGATGCCG 58.150 45.455 0.00 0.00 0.00 5.69
395 1310 5.107414 CGCTCACATCTCAAATCTCATCATC 60.107 44.000 0.00 0.00 0.00 2.92
397 1312 4.117685 CGCTCACATCTCAAATCTCATCA 58.882 43.478 0.00 0.00 0.00 3.07
398 1313 4.118410 ACGCTCACATCTCAAATCTCATC 58.882 43.478 0.00 0.00 0.00 2.92
399 1314 4.134379 ACGCTCACATCTCAAATCTCAT 57.866 40.909 0.00 0.00 0.00 2.90
400 1315 3.599730 ACGCTCACATCTCAAATCTCA 57.400 42.857 0.00 0.00 0.00 3.27
401 1316 3.799420 GGTACGCTCACATCTCAAATCTC 59.201 47.826 0.00 0.00 0.00 2.75
402 1317 3.195610 TGGTACGCTCACATCTCAAATCT 59.804 43.478 0.00 0.00 0.00 2.40
403 1318 3.521560 TGGTACGCTCACATCTCAAATC 58.478 45.455 0.00 0.00 0.00 2.17
405 1320 2.353704 CCTGGTACGCTCACATCTCAAA 60.354 50.000 0.00 0.00 0.00 2.69
406 1321 1.204704 CCTGGTACGCTCACATCTCAA 59.795 52.381 0.00 0.00 0.00 3.02
407 1322 0.817654 CCTGGTACGCTCACATCTCA 59.182 55.000 0.00 0.00 0.00 3.27
408 1323 0.528684 GCCTGGTACGCTCACATCTC 60.529 60.000 0.00 0.00 0.00 2.75
409 1324 1.257750 TGCCTGGTACGCTCACATCT 61.258 55.000 0.00 0.00 0.00 2.90
410 1325 0.179073 ATGCCTGGTACGCTCACATC 60.179 55.000 0.00 0.00 0.00 3.06
411 1326 0.462581 CATGCCTGGTACGCTCACAT 60.463 55.000 0.00 0.00 0.00 3.21
415 1330 0.673644 AACACATGCCTGGTACGCTC 60.674 55.000 0.00 0.00 0.00 5.03
419 1334 0.240945 GCACAACACATGCCTGGTAC 59.759 55.000 0.00 0.00 37.08 3.34
420 1335 0.110295 AGCACAACACATGCCTGGTA 59.890 50.000 0.00 0.00 44.53 3.25
421 1336 1.152694 AGCACAACACATGCCTGGT 60.153 52.632 0.00 0.00 44.53 4.00
422 1337 1.287815 CAGCACAACACATGCCTGG 59.712 57.895 0.00 0.00 44.53 4.45
423 1338 1.237533 TACAGCACAACACATGCCTG 58.762 50.000 0.00 0.00 44.53 4.85
424 1339 2.205022 ATACAGCACAACACATGCCT 57.795 45.000 0.00 0.00 44.53 4.75
425 1340 2.415893 GGAATACAGCACAACACATGCC 60.416 50.000 0.00 0.00 44.53 4.40
426 1341 2.415893 GGGAATACAGCACAACACATGC 60.416 50.000 0.00 0.00 43.74 4.06
427 1342 2.819019 TGGGAATACAGCACAACACATG 59.181 45.455 0.00 0.00 0.00 3.21
429 1344 2.226330 GTGGGAATACAGCACAACACA 58.774 47.619 0.00 0.00 0.00 3.72
451 5670 7.039270 TGAAAGAGAGTTTTGCTATATACGCA 58.961 34.615 3.61 3.61 35.22 5.24
499 5719 0.952280 GCTGGCTCCATGTCATGATG 59.048 55.000 14.67 7.41 0.00 3.07
526 5754 6.506147 ACGCATGATGGTAACGTAATTACTA 58.494 36.000 13.56 0.00 42.58 1.82
556 5784 4.393834 TGTCCACAAGCTTGCTTAATGTA 58.606 39.130 26.27 0.55 0.00 2.29
557 5785 3.221771 TGTCCACAAGCTTGCTTAATGT 58.778 40.909 26.27 2.31 0.00 2.71
558 5786 3.921119 TGTCCACAAGCTTGCTTAATG 57.079 42.857 26.27 15.76 0.00 1.90
559 5787 4.157289 CAGATGTCCACAAGCTTGCTTAAT 59.843 41.667 26.27 13.31 0.00 1.40
560 5788 3.503363 CAGATGTCCACAAGCTTGCTTAA 59.497 43.478 26.27 8.98 0.00 1.85
562 5790 1.884579 CAGATGTCCACAAGCTTGCTT 59.115 47.619 26.27 4.91 0.00 3.91
563 5791 1.531423 CAGATGTCCACAAGCTTGCT 58.469 50.000 26.27 10.34 0.00 3.91
564 5792 0.524862 CCAGATGTCCACAAGCTTGC 59.475 55.000 26.27 10.47 0.00 4.01
565 5793 0.524862 GCCAGATGTCCACAAGCTTG 59.475 55.000 24.84 24.84 0.00 4.01
635 5869 5.070446 AGGCGTGTCATATTCTTCCTTGATA 59.930 40.000 0.00 0.00 0.00 2.15
695 5946 7.610692 ACATGTTCATATTCCTCCATGATGATC 59.389 37.037 0.00 0.00 35.04 2.92
707 5958 4.453819 GGCAGCTAGACATGTTCATATTCC 59.546 45.833 0.00 0.00 0.00 3.01
719 5970 3.758755 CCTTCATATGGCAGCTAGACA 57.241 47.619 2.13 0.00 41.62 3.41
730 5981 6.864685 ACATTAATTGCGATTGCCTTCATATG 59.135 34.615 9.60 0.00 41.78 1.78
767 7236 6.392354 CCTAAAAGTACACGACCTCATACAA 58.608 40.000 0.00 0.00 0.00 2.41
781 7250 7.012610 TGTTGGTTACTTGAAGCCTAAAAGTAC 59.987 37.037 0.00 0.00 36.42 2.73
800 7275 3.638160 AGTGACAAATCTGCATGTTGGTT 59.362 39.130 8.49 0.00 0.00 3.67
818 7293 2.999507 AACAACGTTTTGTGCAGTGA 57.000 40.000 0.00 0.00 45.69 3.41
861 7336 4.107051 GCCTCACACATGCACGCC 62.107 66.667 0.00 0.00 0.00 5.68
877 7352 4.128925 TCCATGTGATGTCACTAAGAGC 57.871 45.455 13.71 0.00 46.55 4.09
920 8233 1.995626 GGGGCTCTCCTGGTGCTTA 60.996 63.158 0.00 0.00 35.10 3.09
922 8235 4.345286 AGGGGCTCTCCTGGTGCT 62.345 66.667 0.00 0.00 35.47 4.40
928 8241 1.204113 CCAGAAACAGGGGCTCTCCT 61.204 60.000 0.00 0.00 37.71 3.69
929 8242 1.301293 CCAGAAACAGGGGCTCTCC 59.699 63.158 0.00 0.00 0.00 3.71
954 8267 0.840288 TTTCCCTGTAGCAGAGGCCA 60.840 55.000 5.01 0.00 42.56 5.36
955 8268 0.328258 TTTTCCCTGTAGCAGAGGCC 59.672 55.000 0.00 0.00 42.56 5.19
957 8270 2.305927 TCCTTTTTCCCTGTAGCAGAGG 59.694 50.000 0.00 0.00 32.44 3.69
963 8310 6.115448 TCTTCTCTTCCTTTTTCCCTGTAG 57.885 41.667 0.00 0.00 0.00 2.74
969 8316 8.929487 TCTATATCCTCTTCTCTTCCTTTTTCC 58.071 37.037 0.00 0.00 0.00 3.13
975 8322 6.016555 GGCTTCTATATCCTCTTCTCTTCCT 58.983 44.000 0.00 0.00 0.00 3.36
976 8323 5.777732 TGGCTTCTATATCCTCTTCTCTTCC 59.222 44.000 0.00 0.00 0.00 3.46
977 8324 6.909550 TGGCTTCTATATCCTCTTCTCTTC 57.090 41.667 0.00 0.00 0.00 2.87
987 8334 4.006319 GACCTTGCATGGCTTCTATATCC 58.994 47.826 18.17 0.00 0.00 2.59
988 8335 4.006319 GGACCTTGCATGGCTTCTATATC 58.994 47.826 18.17 5.90 0.00 1.63
989 8336 3.654806 AGGACCTTGCATGGCTTCTATAT 59.345 43.478 18.17 0.00 0.00 0.86
1053 8400 2.685017 TGCAGGCCGAGGATGAGT 60.685 61.111 0.00 0.00 0.00 3.41
1057 8404 3.859414 GAGCTGCAGGCCGAGGAT 61.859 66.667 17.12 0.00 43.05 3.24
1079 8426 1.656095 CGAAGGAAGTTCTCATGCGTC 59.344 52.381 2.25 0.00 31.97 5.19
1138 8485 1.079127 CGTTGGCGGAGGACTTGAT 60.079 57.895 0.00 0.00 0.00 2.57
1226 8573 1.592669 GATGATGGTGAGACGGCCG 60.593 63.158 26.86 26.86 0.00 6.13
1227 8574 1.227674 GGATGATGGTGAGACGGCC 60.228 63.158 0.00 0.00 0.00 6.13
1232 8579 1.144716 GCGCTGGATGATGGTGAGA 59.855 57.895 0.00 0.00 0.00 3.27
1273 8623 3.728474 GCATCTGCTCACCATCCG 58.272 61.111 0.00 0.00 38.21 4.18
1296 8646 1.342819 CTAATCCAGCTCCTCTTCCGG 59.657 57.143 0.00 0.00 0.00 5.14
1304 8654 2.029470 CGACCTGATCTAATCCAGCTCC 60.029 54.545 0.00 0.00 0.00 4.70
1340 8690 1.202533 CCATTATCCTCCTCGCAACGT 60.203 52.381 0.00 0.00 0.00 3.99
1341 8691 1.202533 ACCATTATCCTCCTCGCAACG 60.203 52.381 0.00 0.00 0.00 4.10
1354 8704 1.492176 CACCTCCCTCAGCACCATTAT 59.508 52.381 0.00 0.00 0.00 1.28
1356 8706 0.842030 TCACCTCCCTCAGCACCATT 60.842 55.000 0.00 0.00 0.00 3.16
1361 8726 0.691078 GGGTATCACCTCCCTCAGCA 60.691 60.000 0.00 0.00 40.48 4.41
1371 8736 3.925090 CGGCCTCCGGGTATCACC 61.925 72.222 0.00 0.00 44.15 4.02
1401 8766 0.175073 GTAGTAGGGTGGCCTCGTTG 59.825 60.000 3.32 0.00 0.00 4.10
1402 8767 1.318158 CGTAGTAGGGTGGCCTCGTT 61.318 60.000 3.32 0.00 0.00 3.85
1405 8770 2.813200 GCGTAGTAGGGTGGCCTC 59.187 66.667 3.32 0.00 0.00 4.70
1416 8781 2.758327 TCCATGGCCTCGCGTAGT 60.758 61.111 6.96 0.00 0.00 2.73
1525 8890 3.963383 CAATTAGATTGCCACGTACCC 57.037 47.619 0.00 0.00 32.92 3.69
1575 8940 6.322201 CCAAATGAGCAAGGTATTACTTCCAT 59.678 38.462 0.00 0.00 0.00 3.41
1578 8943 5.582550 GCCAAATGAGCAAGGTATTACTTC 58.417 41.667 0.00 0.00 0.00 3.01
1587 8952 1.444895 GCACGCCAAATGAGCAAGG 60.445 57.895 0.00 0.00 0.00 3.61
1602 8967 1.233019 AATCACTGCTGACACTGCAC 58.767 50.000 0.00 0.00 34.77 4.57
1608 8973 4.631377 GCACATACTTAATCACTGCTGACA 59.369 41.667 0.00 0.00 0.00 3.58
1628 9031 0.588252 CACTGGCACAACACTAGCAC 59.412 55.000 0.00 0.00 38.70 4.40
1631 9034 0.250467 AGGCACTGGCACAACACTAG 60.250 55.000 5.25 0.00 43.71 2.57
1656 9059 5.245531 TCACGGAGACAATGCTTTTCTTAT 58.754 37.500 0.00 0.00 0.00 1.73
1665 9068 2.554142 TGATCATCACGGAGACAATGC 58.446 47.619 0.00 0.00 0.00 3.56
1667 9070 4.677673 TCATGATCATCACGGAGACAAT 57.322 40.909 4.86 0.00 0.00 2.71
1676 9079 7.137426 GTGCCTATTTCTTTCATGATCATCAC 58.863 38.462 4.86 2.58 0.00 3.06
1711 9114 2.851263 TTCTTTACCGGTCTGCACAT 57.149 45.000 12.40 0.00 0.00 3.21
1714 9117 5.468746 GCATATATTTCTTTACCGGTCTGCA 59.531 40.000 12.40 0.00 0.00 4.41
1720 9123 6.878923 TCCTGATGCATATATTTCTTTACCGG 59.121 38.462 0.00 0.00 0.00 5.28
1824 9266 8.267894 AGATACAACTGCAGTACATAATTCCTT 58.732 33.333 22.01 0.00 0.00 3.36
1858 9319 8.431910 ACTTTCCACACTCTCTAATACCTTTA 57.568 34.615 0.00 0.00 0.00 1.85
1892 9353 1.495584 AACTACACACGCAAGCACGG 61.496 55.000 0.00 0.00 45.62 4.94
1898 9359 5.236655 TGAATTTCAAACTACACACGCAA 57.763 34.783 0.00 0.00 0.00 4.85
1907 9368 8.286800 CACGAACATACCTTGAATTTCAAACTA 58.713 33.333 12.62 5.79 35.73 2.24
1914 9375 5.401550 CATGCACGAACATACCTTGAATTT 58.598 37.500 0.00 0.00 0.00 1.82
1955 9417 5.248870 ACGTAATTCCTGGCATCATTTTC 57.751 39.130 0.00 0.00 0.00 2.29
1962 9424 3.531538 CACAGTACGTAATTCCTGGCAT 58.468 45.455 13.56 0.00 0.00 4.40
1982 9444 7.051623 ACAGTGACTGTTATACAAGTTTTCCA 58.948 34.615 13.33 0.00 42.59 3.53
1983 9445 7.492352 ACAGTGACTGTTATACAAGTTTTCC 57.508 36.000 13.33 0.00 42.59 3.13
1989 9451 8.019669 AGTACGTTACAGTGACTGTTATACAAG 58.980 37.037 24.54 10.71 42.59 3.16
2062 9535 5.010314 TCAGAGACTGCTTTTGAAAATGCAT 59.990 36.000 14.44 0.00 44.59 3.96
2167 9643 6.318648 TGAAGATTTTATGCGTGCTCCTATTT 59.681 34.615 0.00 0.00 0.00 1.40
2174 9650 6.283694 TCTAGATGAAGATTTTATGCGTGCT 58.716 36.000 0.00 0.00 0.00 4.40
2431 10992 7.556275 ACATATCCTTGGTTTCGATAACATTGT 59.444 33.333 0.00 0.00 0.00 2.71
2552 11125 3.302740 GCGCTAGCAGTGTGTCATATTTC 60.303 47.826 16.45 0.00 44.35 2.17
2558 11131 2.430751 CGCGCTAGCAGTGTGTCA 60.431 61.111 16.45 0.00 45.49 3.58
2573 11146 2.023741 CCACATGCATCGAAGCGC 59.976 61.111 8.26 0.00 37.31 5.92
2585 11165 1.845627 CTGAGGCCAGACCACCACAT 61.846 60.000 5.01 0.00 43.02 3.21


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

AutoCloner maintained by Alex Coulton.