Multiple sequence alignment - TraesCS3B01G522400

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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 TraesCS3B01G522400 chr3B 100.000 4894 0 0 1 4894 765546922 765551815 0.000000e+00 9038.0
1 TraesCS3B01G522400 chr3B 83.802 2099 304 29 2160 4242 765623478 765625556 0.000000e+00 1960.0
2 TraesCS3B01G522400 chr3B 82.258 2046 321 33 2250 4270 765928465 765930493 0.000000e+00 1729.0
3 TraesCS3B01G522400 chr3B 86.716 1227 144 12 699 1913 765667905 765669124 0.000000e+00 1345.0
4 TraesCS3B01G522400 chr3B 88.439 1038 114 5 873 1906 765621832 765622867 0.000000e+00 1247.0
5 TraesCS3B01G522400 chr3B 88.506 957 106 4 889 1843 765656634 765657588 0.000000e+00 1155.0
6 TraesCS3B01G522400 chr3B 84.541 207 23 2 1904 2101 765669983 765670189 3.860000e-46 196.0
7 TraesCS3B01G522400 chr3B 81.448 221 30 4 1904 2115 765623269 765623487 2.340000e-38 171.0
8 TraesCS3B01G522400 chr3B 80.556 216 29 6 4685 4894 765599820 765600028 2.360000e-33 154.0
9 TraesCS3B01G522400 chr3B 78.241 216 32 7 4684 4893 765678123 765678329 1.850000e-24 124.0
10 TraesCS3B01G522400 chr3A 92.715 2471 139 17 2159 4605 710838126 710840579 0.000000e+00 3528.0
11 TraesCS3B01G522400 chr3A 95.145 1730 72 4 385 2103 710836396 710838124 0.000000e+00 2719.0
12 TraesCS3B01G522400 chr3A 84.070 2128 309 23 2160 4270 710937416 710939530 0.000000e+00 2025.0
13 TraesCS3B01G522400 chr3A 83.651 2098 314 21 2160 4241 711057832 711059916 0.000000e+00 1947.0
14 TraesCS3B01G522400 chr3A 84.871 1474 186 28 2299 3741 710948367 710949834 0.000000e+00 1452.0
15 TraesCS3B01G522400 chr3A 86.525 1128 130 14 1001 2115 711056723 711057841 0.000000e+00 1221.0
16 TraesCS3B01G522400 chr3A 84.502 1226 170 16 699 1912 710935303 710936520 0.000000e+00 1194.0
17 TraesCS3B01G522400 chr3A 94.872 390 15 5 1 387 710835983 710836370 5.420000e-169 604.0
18 TraesCS3B01G522400 chr3A 86.709 316 29 8 1 308 532848984 532849294 6.070000e-89 339.0
19 TraesCS3B01G522400 chr3A 83.088 408 33 18 1 387 644630324 644629932 6.070000e-89 339.0
20 TraesCS3B01G522400 chr3A 90.114 263 12 5 4638 4894 710840576 710840830 3.650000e-86 329.0
21 TraesCS3B01G522400 chr3A 81.343 402 47 18 7 389 521574006 521573614 7.960000e-78 302.0
22 TraesCS3B01G522400 chr3A 97.368 38 1 0 4595 4632 466806942 466806979 1.140000e-06 65.8
23 TraesCS3B01G522400 chr3A 97.368 38 0 1 4595 4632 57262244 57262208 4.090000e-06 63.9
24 TraesCS3B01G522400 chr3A 88.462 52 3 3 4583 4632 720370542 720370592 5.290000e-05 60.2
25 TraesCS3B01G522400 chr3D 92.787 2440 128 16 2162 4570 574781744 574779322 0.000000e+00 3487.0
26 TraesCS3B01G522400 chr3D 89.036 1815 188 10 2271 4075 575479921 575481734 0.000000e+00 2239.0
27 TraesCS3B01G522400 chr3D 95.004 1381 61 3 740 2115 574783114 574781737 0.000000e+00 2161.0
28 TraesCS3B01G522400 chr3D 84.236 1846 264 22 2252 4075 575527368 575529208 0.000000e+00 1772.0
29 TraesCS3B01G522400 chr3D 81.478 2165 347 38 2118 4256 575546458 575548594 0.000000e+00 1727.0
30 TraesCS3B01G522400 chr3D 82.265 2013 320 30 2250 4239 574770149 574768151 0.000000e+00 1705.0
31 TraesCS3B01G522400 chr3D 82.265 2013 320 30 2250 4239 575488028 575490026 0.000000e+00 1705.0
32 TraesCS3B01G522400 chr3D 81.660 1265 204 22 699 1944 574771540 574770285 0.000000e+00 1026.0
33 TraesCS3B01G522400 chr3D 81.660 1265 204 22 699 1944 575486637 575487892 0.000000e+00 1026.0
34 TraesCS3B01G522400 chr3D 92.573 377 16 3 385 755 574785228 574784858 9.330000e-147 531.0
35 TraesCS3B01G522400 chr3D 89.950 398 18 12 1 387 574785640 574785254 1.220000e-135 494.0
36 TraesCS3B01G522400 chr3D 89.200 250 19 5 4646 4894 574779083 574778841 6.150000e-79 305.0
37 TraesCS3B01G522400 chr3D 88.213 263 18 7 4638 4894 575481901 575482156 7.960000e-78 302.0
38 TraesCS3B01G522400 chr3D 90.055 181 13 2 4430 4605 575481724 575481904 3.810000e-56 230.0
39 TraesCS3B01G522400 chr3D 95.327 107 5 0 4643 4749 574779283 574779177 2.340000e-38 171.0
40 TraesCS3B01G522400 chr1B 87.382 317 31 7 1 311 263981664 263981351 6.030000e-94 355.0
41 TraesCS3B01G522400 chr6A 82.872 397 51 12 1 387 59902847 59902458 1.690000e-89 340.0
42 TraesCS3B01G522400 chr6A 94.737 38 2 0 4594 4631 122681291 122681254 5.290000e-05 60.2
43 TraesCS3B01G522400 chr1D 83.844 359 38 8 1 344 58567710 58568063 1.700000e-84 324.0
44 TraesCS3B01G522400 chr1D 97.297 37 1 0 4596 4632 12039448 12039412 4.090000e-06 63.9
45 TraesCS3B01G522400 chr4A 81.108 397 61 11 1 387 596787406 596787798 6.150000e-79 305.0
46 TraesCS3B01G522400 chr2D 83.333 342 35 17 1 335 37826643 37826317 3.700000e-76 296.0
47 TraesCS3B01G522400 chr2D 93.023 43 0 2 4589 4630 7150952 7150912 5.290000e-05 60.2
48 TraesCS3B01G522400 chr2D 91.304 46 1 2 4587 4632 274856312 274856354 5.290000e-05 60.2
49 TraesCS3B01G522400 chr5A 80.952 399 44 19 3 387 616353058 616353438 2.230000e-73 287.0
50 TraesCS3B01G522400 chr5A 93.182 44 3 0 4587 4630 472311042 472310999 1.140000e-06 65.8
51 TraesCS3B01G522400 chr2B 93.023 43 0 2 4589 4630 2111250 2111290 5.290000e-05 60.2
52 TraesCS3B01G522400 chr2A 93.023 43 0 2 4589 4630 62700673 62700713 5.290000e-05 60.2
53 TraesCS3B01G522400 chr2A 91.304 46 1 2 4587 4632 332027690 332027732 5.290000e-05 60.2


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 TraesCS3B01G522400 chr3B 765546922 765551815 4893 False 9038.000000 9038 100.000000 1 4894 1 chr3B.!!$F1 4893
1 TraesCS3B01G522400 chr3B 765928465 765930493 2028 False 1729.000000 1729 82.258000 2250 4270 1 chr3B.!!$F5 2020
2 TraesCS3B01G522400 chr3B 765656634 765657588 954 False 1155.000000 1155 88.506000 889 1843 1 chr3B.!!$F3 954
3 TraesCS3B01G522400 chr3B 765621832 765625556 3724 False 1126.000000 1960 84.563000 873 4242 3 chr3B.!!$F6 3369
4 TraesCS3B01G522400 chr3B 765667905 765670189 2284 False 770.500000 1345 85.628500 699 2101 2 chr3B.!!$F7 1402
5 TraesCS3B01G522400 chr3A 710835983 710840830 4847 False 1795.000000 3528 93.211500 1 4894 4 chr3A.!!$F5 4893
6 TraesCS3B01G522400 chr3A 710935303 710939530 4227 False 1609.500000 2025 84.286000 699 4270 2 chr3A.!!$F6 3571
7 TraesCS3B01G522400 chr3A 711056723 711059916 3193 False 1584.000000 1947 85.088000 1001 4241 2 chr3A.!!$F7 3240
8 TraesCS3B01G522400 chr3A 710948367 710949834 1467 False 1452.000000 1452 84.871000 2299 3741 1 chr3A.!!$F3 1442
9 TraesCS3B01G522400 chr3D 575527368 575529208 1840 False 1772.000000 1772 84.236000 2252 4075 1 chr3D.!!$F1 1823
10 TraesCS3B01G522400 chr3D 575546458 575548594 2136 False 1727.000000 1727 81.478000 2118 4256 1 chr3D.!!$F2 2138
11 TraesCS3B01G522400 chr3D 574768151 574771540 3389 True 1365.500000 1705 81.962500 699 4239 2 chr3D.!!$R1 3540
12 TraesCS3B01G522400 chr3D 575486637 575490026 3389 False 1365.500000 1705 81.962500 699 4239 2 chr3D.!!$F4 3540
13 TraesCS3B01G522400 chr3D 574778841 574785640 6799 True 1191.500000 3487 92.473500 1 4894 6 chr3D.!!$R2 4893
14 TraesCS3B01G522400 chr3D 575479921 575482156 2235 False 923.666667 2239 89.101333 2271 4894 3 chr3D.!!$F3 2623


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
934 2755 0.463295 CGATCATTGCCCAGAGTGCT 60.463 55.000 0.00 0.00 0.00 4.40 F
1138 2962 0.459899 CACATTGATGCATGCTGCCT 59.540 50.000 20.33 0.46 44.23 4.75 F
1428 3252 1.026182 TGCCGCAAAGGTATGAGCAG 61.026 55.000 0.00 0.00 43.70 4.24 F
2733 5777 1.880027 ACGGTTTGGAGCAGATGAAAC 59.120 47.619 0.00 0.00 0.00 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 5130 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.00 0.00 3.72 R
3085 6135 0.036732 TCTGCGGACCTTGCTTTCAT 59.963 50.0 0.00 0.00 0.00 2.57 R
3320 6373 0.320771 CAGTGGGAAGGTCCTCAACG 60.321 60.0 0.00 0.00 36.57 4.10 R
4332 7416 0.102120 CAGCAGAGGTTAGCTCGAGG 59.898 60.0 15.58 1.62 39.50 4.63 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
297 309 4.530553 ACACACATACACCTCACATCCTTA 59.469 41.667 0.00 0.00 0.00 2.69
308 320 8.548877 ACACCTCACATCCTTATTTACTTGTAT 58.451 33.333 0.00 0.00 0.00 2.29
370 383 3.193267 TCTCAAAAATTCGGCCTTCATGG 59.807 43.478 0.00 0.00 39.35 3.66
393 434 1.334419 GCCGAGATCCAAAATGATGCG 60.334 52.381 0.00 0.00 0.00 4.73
394 435 1.265095 CCGAGATCCAAAATGATGCGG 59.735 52.381 0.00 0.00 34.81 5.69
413 454 3.425404 CGGCAATTCATGGAGTTAAACG 58.575 45.455 0.00 0.00 0.00 3.60
517 558 3.070018 AGTAACTGTCATGCTTGTCTGC 58.930 45.455 0.00 0.00 0.00 4.26
644 691 3.426191 GTCACATGAAAACTACGCGTACA 59.574 43.478 16.41 11.96 0.00 2.90
654 701 2.159599 ACTACGCGTACACTAAGTCAGC 60.160 50.000 16.41 0.00 0.00 4.26
688 735 3.189285 GTGGTGCGGTGTATAATTACGT 58.811 45.455 0.00 0.00 0.00 3.57
744 2550 6.008331 TCTAAGCCTTGTCAGAGTAACACTA 58.992 40.000 0.00 0.00 0.00 2.74
934 2755 0.463295 CGATCATTGCCCAGAGTGCT 60.463 55.000 0.00 0.00 0.00 4.40
968 2790 0.470080 ATAGCGCTTCCAGCCCTCTA 60.470 55.000 18.68 0.00 38.18 2.43
1138 2962 0.459899 CACATTGATGCATGCTGCCT 59.540 50.000 20.33 0.46 44.23 4.75
1160 2984 2.972713 TGAGTAAGGTGGCAGAAGTTCT 59.027 45.455 0.00 0.00 0.00 3.01
1396 3220 5.234466 AGAAGTGGTTCATCAAGCTAAGT 57.766 39.130 0.00 0.00 34.82 2.24
1428 3252 1.026182 TGCCGCAAAGGTATGAGCAG 61.026 55.000 0.00 0.00 43.70 4.24
1454 3278 1.950909 GCGAGATCCTAGCACTAGTGT 59.049 52.381 23.44 12.90 32.52 3.55
1457 3281 4.216687 GCGAGATCCTAGCACTAGTGTTAT 59.783 45.833 23.44 8.81 32.52 1.89
1548 3372 7.295952 AGACGAGTTGATAAACATGTTGATC 57.704 36.000 24.09 24.09 32.23 2.92
1791 3615 8.331740 AGTGAAGAATGGGAAGAAAATCATCTA 58.668 33.333 0.00 0.00 0.00 1.98
1970 4981 9.507280 CTTTTGGCATAAATGATGTAGTTAGTG 57.493 33.333 0.00 0.00 37.90 2.74
2064 5087 5.281693 TGATCTCAACTGTTAATGCAACG 57.718 39.130 0.00 0.00 40.26 4.10
2115 5138 7.132694 CACATAAGTTATCATGTGTGTGTGT 57.867 36.000 8.50 0.00 44.50 3.72
2116 5139 7.017055 CACATAAGTTATCATGTGTGTGTGTG 58.983 38.462 8.50 1.25 44.50 3.82
2365 5401 2.717639 ATGGGATACAGAAGTGTGGC 57.282 50.000 0.00 0.00 37.52 5.01
2496 5535 8.746052 TCTACAAAATGAAACCTCTTTCTGAA 57.254 30.769 0.00 0.00 37.30 3.02
2570 5613 2.416547 CCAAGAGTTGGTGCAAGTATCG 59.583 50.000 0.00 0.00 45.93 2.92
2733 5777 1.880027 ACGGTTTGGAGCAGATGAAAC 59.120 47.619 0.00 0.00 0.00 2.78
2786 5830 5.826208 ACCTTCGTATCTGAAACCTTGTTTT 59.174 36.000 0.00 0.00 0.00 2.43
3026 6076 4.815308 GTGCTTGATCTCATATGCTCACTT 59.185 41.667 0.00 0.00 0.00 3.16
3069 6119 1.881973 CAATATTGGATGGCACCGGAG 59.118 52.381 9.46 0.00 0.00 4.63
3122 6172 4.576053 CGCAGATTGTCCATCCAAAATAGA 59.424 41.667 0.00 0.00 31.20 1.98
3128 6178 9.484806 AGATTGTCCATCCAAAATAGAAAGATT 57.515 29.630 0.00 0.00 31.20 2.40
3198 6248 4.827835 TCACCAATAATGTTGTCGGGAAAA 59.172 37.500 0.00 0.00 0.00 2.29
3200 6250 6.015010 TCACCAATAATGTTGTCGGGAAAATT 60.015 34.615 0.00 0.00 0.00 1.82
3440 6494 3.617284 TCTAAGACGTCTGATGTGCCTA 58.383 45.455 20.85 3.95 0.00 3.93
3676 6739 6.448006 ACAGTCTAGATATTTATGTCCGTGC 58.552 40.000 0.00 0.00 0.00 5.34
3807 6870 2.458951 CTTCATCGCTTTCTCTCCTCG 58.541 52.381 0.00 0.00 0.00 4.63
4076 7146 2.428890 ACCTTCTCAGCTAAGTGGATCG 59.571 50.000 5.83 0.00 0.00 3.69
4127 7197 1.219393 CTCCCTTCCTTGGAGCGAC 59.781 63.158 0.00 0.00 42.75 5.19
4172 7242 1.032657 AGCTAGTGATCGCGAGGTGT 61.033 55.000 18.44 0.00 0.00 4.16
4173 7243 0.179134 GCTAGTGATCGCGAGGTGTT 60.179 55.000 16.66 0.00 0.00 3.32
4174 7244 1.065102 GCTAGTGATCGCGAGGTGTTA 59.935 52.381 16.66 2.57 0.00 2.41
4244 7314 1.374252 CCGTCCCGTCCTTGACTTG 60.374 63.158 0.00 0.00 0.00 3.16
4270 7340 2.738846 GACGCATGCATAGGAATAGGTG 59.261 50.000 19.57 0.00 0.00 4.00
4281 7351 1.134788 GGAATAGGTGCGCACACTAGT 60.135 52.381 38.60 32.04 46.57 2.57
4282 7352 1.927174 GAATAGGTGCGCACACTAGTG 59.073 52.381 38.60 21.44 46.57 2.74
4320 7404 8.055279 TCTTTGTTTCTTTCTCAGTTTCATGT 57.945 30.769 0.00 0.00 0.00 3.21
4332 7416 2.093235 AGTTTCATGTGGAGGCTAGCTC 60.093 50.000 15.72 9.94 0.00 4.09
4333 7417 0.833287 TTCATGTGGAGGCTAGCTCC 59.167 55.000 15.72 18.51 41.21 4.70
4334 7418 0.031716 TCATGTGGAGGCTAGCTCCT 60.032 55.000 24.53 12.60 41.39 3.69
4349 7447 0.383949 CTCCTCGAGCTAACCTCTGC 59.616 60.000 6.99 0.00 38.49 4.26
4373 7471 6.358822 GCTGTACGTGTATTCTTTTGTTTTCC 59.641 38.462 0.00 0.00 0.00 3.13
4374 7472 6.420588 TGTACGTGTATTCTTTTGTTTTCCG 58.579 36.000 0.00 0.00 0.00 4.30
4382 7480 5.394224 TTCTTTTGTTTTCCGACCAAGTT 57.606 34.783 0.00 0.00 0.00 2.66
4397 7495 5.705905 CGACCAAGTTTTTAATTCCTCTCCT 59.294 40.000 0.00 0.00 0.00 3.69
4403 7501 8.510505 CAAGTTTTTAATTCCTCTCCTCTTCTG 58.489 37.037 0.00 0.00 0.00 3.02
4454 7552 2.351726 GGTCGATTCACCAAATCTTCCG 59.648 50.000 0.00 0.00 41.46 4.30
4577 7686 7.962964 TGTAATATGAACTGCTTATGCTACC 57.037 36.000 1.96 0.00 40.48 3.18
4599 7708 9.832445 CTACCAAGGTACAAGATTACATATGTT 57.168 33.333 14.77 0.00 0.00 2.71
4612 7721 9.091220 AGATTACATATGTTAAGTACTCCCTCC 57.909 37.037 14.77 0.00 0.00 4.30
4613 7722 5.786264 ACATATGTTAAGTACTCCCTCCG 57.214 43.478 1.41 0.00 0.00 4.63
4614 7723 5.206587 ACATATGTTAAGTACTCCCTCCGT 58.793 41.667 1.41 0.00 0.00 4.69
4615 7724 6.367983 ACATATGTTAAGTACTCCCTCCGTA 58.632 40.000 1.41 0.00 0.00 4.02
4616 7725 6.835488 ACATATGTTAAGTACTCCCTCCGTAA 59.165 38.462 1.41 0.00 0.00 3.18
4617 7726 7.342799 ACATATGTTAAGTACTCCCTCCGTAAA 59.657 37.037 1.41 0.00 0.00 2.01
4618 7727 5.649782 TGTTAAGTACTCCCTCCGTAAAG 57.350 43.478 0.00 0.00 0.00 1.85
4619 7728 5.324409 TGTTAAGTACTCCCTCCGTAAAGA 58.676 41.667 0.00 0.00 0.00 2.52
4620 7729 5.774690 TGTTAAGTACTCCCTCCGTAAAGAA 59.225 40.000 0.00 0.00 0.00 2.52
4621 7730 6.267471 TGTTAAGTACTCCCTCCGTAAAGAAA 59.733 38.462 0.00 0.00 0.00 2.52
4622 7731 7.038799 TGTTAAGTACTCCCTCCGTAAAGAAAT 60.039 37.037 0.00 0.00 0.00 2.17
4623 7732 8.470002 GTTAAGTACTCCCTCCGTAAAGAAATA 58.530 37.037 0.00 0.00 0.00 1.40
4624 7733 7.672122 AAGTACTCCCTCCGTAAAGAAATAT 57.328 36.000 0.00 0.00 0.00 1.28
4625 7734 8.773033 AAGTACTCCCTCCGTAAAGAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
4626 7735 8.773033 AGTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
4627 7736 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
4628 7737 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
4629 7738 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
4630 7739 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
4631 7740 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
4632 7741 5.118817 CCTCCGTAAAGAAATATAAGAGCGC 59.881 44.000 0.00 0.00 0.00 5.92
4633 7742 5.593968 TCCGTAAAGAAATATAAGAGCGCA 58.406 37.500 11.47 0.00 0.00 6.09
4634 7743 5.690409 TCCGTAAAGAAATATAAGAGCGCAG 59.310 40.000 11.47 0.00 0.00 5.18
4635 7744 5.107453 CCGTAAAGAAATATAAGAGCGCAGG 60.107 44.000 11.47 0.00 0.00 4.85
4636 7745 5.107453 CGTAAAGAAATATAAGAGCGCAGGG 60.107 44.000 11.47 0.00 0.00 4.45
4637 7746 4.689612 AAGAAATATAAGAGCGCAGGGA 57.310 40.909 11.47 0.00 0.00 4.20
4638 7747 4.264460 AGAAATATAAGAGCGCAGGGAG 57.736 45.455 11.47 0.00 0.00 4.30
4639 7748 2.464157 AATATAAGAGCGCAGGGAGC 57.536 50.000 11.47 0.00 40.87 4.70
4677 7983 8.660373 GTGAGCAATCCACTAAGTAATATATGC 58.340 37.037 0.00 0.00 0.00 3.14
4699 8005 5.125900 TGCTTCTATTGGATGAAACATGTGG 59.874 40.000 0.00 0.00 0.00 4.17
4701 8007 6.678900 GCTTCTATTGGATGAAACATGTGGTC 60.679 42.308 0.00 0.39 0.00 4.02
4704 8011 6.947733 TCTATTGGATGAAACATGTGGTCTTT 59.052 34.615 0.00 0.00 0.00 2.52
4705 8012 4.852134 TGGATGAAACATGTGGTCTTTG 57.148 40.909 0.00 0.00 0.00 2.77
4737 8044 4.023279 TCGGAACATTTGACTGAACCATTG 60.023 41.667 0.00 0.00 0.00 2.82
4745 8052 2.308570 TGACTGAACCATTGGTATGCCT 59.691 45.455 9.20 0.00 33.12 4.75
4746 8053 2.684881 GACTGAACCATTGGTATGCCTG 59.315 50.000 9.20 5.92 33.12 4.85
4747 8054 2.041620 ACTGAACCATTGGTATGCCTGT 59.958 45.455 9.20 6.49 33.12 4.00
4748 8055 2.424601 CTGAACCATTGGTATGCCTGTG 59.575 50.000 9.20 0.00 33.12 3.66
4749 8056 2.040947 TGAACCATTGGTATGCCTGTGA 59.959 45.455 9.20 0.00 33.12 3.58
4750 8057 3.290710 GAACCATTGGTATGCCTGTGAT 58.709 45.455 9.20 0.00 33.12 3.06
4751 8058 2.658285 ACCATTGGTATGCCTGTGATG 58.342 47.619 6.54 0.88 32.11 3.07
4759 8066 2.495155 ATGCCTGTGATGTGTGCTTA 57.505 45.000 0.00 0.00 0.00 3.09
4762 8069 2.086869 GCCTGTGATGTGTGCTTACAT 58.913 47.619 6.17 6.17 43.61 2.29
4766 8073 5.118286 CCTGTGATGTGTGCTTACATGATA 58.882 41.667 10.45 1.54 41.15 2.15
4775 8082 5.582269 GTGTGCTTACATGATACACATCTGT 59.418 40.000 14.97 0.00 42.63 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.598894 CTCCATGGAGCTCGGCCG 62.599 72.222 28.45 22.12 35.31 6.13
339 351 6.700081 AGGCCGAATTTTTGAGAAACTAAAAC 59.300 34.615 0.00 0.00 36.45 2.43
340 352 6.811954 AGGCCGAATTTTTGAGAAACTAAAA 58.188 32.000 0.00 0.00 37.53 1.52
344 356 4.340950 TGAAGGCCGAATTTTTGAGAAACT 59.659 37.500 0.00 0.00 0.00 2.66
345 357 4.616953 TGAAGGCCGAATTTTTGAGAAAC 58.383 39.130 0.00 0.00 0.00 2.78
349 362 3.193267 TCCATGAAGGCCGAATTTTTGAG 59.807 43.478 0.00 0.00 37.29 3.02
370 383 2.332063 TCATTTTGGATCTCGGCCTC 57.668 50.000 0.00 0.00 0.00 4.70
393 434 3.428862 CCCGTTTAACTCCATGAATTGCC 60.429 47.826 0.00 0.00 0.00 4.52
394 435 3.192633 ACCCGTTTAACTCCATGAATTGC 59.807 43.478 0.00 0.00 0.00 3.56
413 454 4.937201 AACAAAGGACAGATTTGAACCC 57.063 40.909 5.50 0.00 39.50 4.11
517 558 3.044986 CAACTCGGTTTTGCATTGACTG 58.955 45.455 0.00 0.00 0.00 3.51
530 571 1.696097 AAGCACCAGGACAACTCGGT 61.696 55.000 0.00 0.00 32.90 4.69
531 572 0.320374 TAAGCACCAGGACAACTCGG 59.680 55.000 0.00 0.00 0.00 4.63
532 573 2.163818 TTAAGCACCAGGACAACTCG 57.836 50.000 0.00 0.00 0.00 4.18
644 691 0.679505 TCACAAGGCGCTGACTTAGT 59.320 50.000 7.64 1.16 0.00 2.24
654 701 1.580942 CACCACCAATCACAAGGCG 59.419 57.895 0.00 0.00 0.00 5.52
688 735 8.274322 TCTTGAGATGGAAGAAATAAATAGCCA 58.726 33.333 0.00 0.00 0.00 4.75
717 764 3.902881 ACTCTGACAAGGCTTAGATGG 57.097 47.619 0.00 0.00 0.00 3.51
744 2550 5.832060 AGCGGTTGTGGTAGTAATAGTAGAT 59.168 40.000 0.00 0.00 0.00 1.98
968 2790 0.106217 CTGGGAGTGGTTTGGGTGTT 60.106 55.000 0.00 0.00 0.00 3.32
1138 2962 3.391296 AGAACTTCTGCCACCTTACTCAA 59.609 43.478 0.00 0.00 0.00 3.02
1160 2984 0.249868 CTTGTGAAGCTGGTCCACGA 60.250 55.000 0.00 0.00 33.78 4.35
1412 3236 1.097547 CCCCTGCTCATACCTTTGCG 61.098 60.000 0.00 0.00 0.00 4.85
1413 3237 0.255890 TCCCCTGCTCATACCTTTGC 59.744 55.000 0.00 0.00 0.00 3.68
1428 3252 1.188219 TGCTAGGATCTCGCATCCCC 61.188 60.000 9.07 1.19 38.98 4.81
1454 3278 3.342377 TCATGCGAGGGTCAACAATAA 57.658 42.857 0.00 0.00 0.00 1.40
1457 3281 1.452110 CATCATGCGAGGGTCAACAA 58.548 50.000 0.00 0.00 0.00 2.83
1548 3372 3.426695 GCTTCAACCAATCATCACCTTCG 60.427 47.826 0.00 0.00 0.00 3.79
1970 4981 7.917505 CCCTAATTGTTGAAAGATGAGTTATGC 59.082 37.037 0.00 0.00 0.00 3.14
1977 4988 5.415701 GCACTCCCTAATTGTTGAAAGATGA 59.584 40.000 0.00 0.00 0.00 2.92
2029 5044 3.827008 TGAGATCATCCACTTAGGCAC 57.173 47.619 0.00 0.00 37.29 5.01
2103 5126 1.468127 ACACACACACACACACACATG 59.532 47.619 0.00 0.00 0.00 3.21
2104 5127 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
2106 5129 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2107 5130 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2108 5131 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2109 5132 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2110 5133 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2111 5134 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2112 5135 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2113 5136 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2114 5137 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2115 5138 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2116 5139 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2365 5401 6.680810 TGGAGAAAGCACACTTGATTAATTG 58.319 36.000 0.00 0.00 35.85 2.32
2496 5535 9.784531 TTTAAGAAGAGAATTCTTGACACATCT 57.215 29.630 9.87 1.44 43.63 2.90
2570 5613 7.042523 CCACCACATTTCTTCAAAATGTCTTTC 60.043 37.037 11.99 0.00 45.87 2.62
2656 5700 4.747810 CAAAGCATACCATTGGTCCTTTC 58.252 43.478 12.68 0.00 37.09 2.62
2786 5830 4.349636 TCCGGGAAGATGCCAAGATATAAA 59.650 41.667 0.00 0.00 0.00 1.40
2988 6038 2.813172 CAAGCACCATGTCATGTACACA 59.187 45.455 11.84 0.00 42.09 3.72
3026 6076 6.976088 TGTGACAAAGTTTTCTTCACTTGAA 58.024 32.000 16.90 0.00 39.48 2.69
3069 6119 8.491331 TTGCTTTCATAATTAGGCATTTTTCC 57.509 30.769 0.00 0.00 0.00 3.13
3085 6135 0.036732 TCTGCGGACCTTGCTTTCAT 59.963 50.000 0.00 0.00 0.00 2.57
3086 6136 0.036732 ATCTGCGGACCTTGCTTTCA 59.963 50.000 0.00 0.00 0.00 2.69
3128 6178 5.310331 TGCCATCCTAGAAATATCCACATCA 59.690 40.000 0.00 0.00 0.00 3.07
3158 6208 5.223449 TGGTGAAAACGGTAAGAGATCTT 57.777 39.130 0.00 0.07 39.85 2.40
3320 6373 0.320771 CAGTGGGAAGGTCCTCAACG 60.321 60.000 0.00 0.00 36.57 4.10
3440 6494 7.551974 GGCAGCTTCATATGATAGTCAACATAT 59.448 37.037 6.17 0.00 39.36 1.78
3686 6749 5.253330 ACCCAATCTTCGCTCAAGAAATTA 58.747 37.500 0.00 0.00 44.66 1.40
3693 6756 1.351017 AGGAACCCAATCTTCGCTCAA 59.649 47.619 0.00 0.00 0.00 3.02
3807 6870 9.569122 TTTAACCACCTTTATATGAAGATAGGC 57.431 33.333 8.74 0.00 0.00 3.93
3907 6971 3.325870 CACCACACGCTCTTCATAGAAA 58.674 45.455 0.00 0.00 0.00 2.52
4076 7146 2.250188 CAAATCGATGTTTTCACGGGC 58.750 47.619 0.00 0.00 0.00 6.13
4127 7197 9.734984 TTCCTCCTTAATAACTTTAACCTCAAG 57.265 33.333 0.00 0.00 0.00 3.02
4172 7242 4.009675 CTGCCTTTGCTTCATACACCTAA 58.990 43.478 0.00 0.00 38.71 2.69
4173 7243 3.609853 CTGCCTTTGCTTCATACACCTA 58.390 45.455 0.00 0.00 38.71 3.08
4174 7244 2.440409 CTGCCTTTGCTTCATACACCT 58.560 47.619 0.00 0.00 38.71 4.00
4281 7351 5.923684 AGAAACAAAGAAAAAGCAACGAACA 59.076 32.000 0.00 0.00 0.00 3.18
4282 7352 6.389622 AGAAACAAAGAAAAAGCAACGAAC 57.610 33.333 0.00 0.00 0.00 3.95
4283 7353 7.383843 AGAAAGAAACAAAGAAAAAGCAACGAA 59.616 29.630 0.00 0.00 0.00 3.85
4286 7370 8.017587 TGAGAAAGAAACAAAGAAAAAGCAAC 57.982 30.769 0.00 0.00 0.00 4.17
4292 7376 9.927668 ATGAAACTGAGAAAGAAACAAAGAAAA 57.072 25.926 0.00 0.00 0.00 2.29
4332 7416 0.102120 CAGCAGAGGTTAGCTCGAGG 59.898 60.000 15.58 1.62 39.50 4.63
4333 7417 0.814457 ACAGCAGAGGTTAGCTCGAG 59.186 55.000 8.45 8.45 39.50 4.04
4334 7418 1.743958 GTACAGCAGAGGTTAGCTCGA 59.256 52.381 5.75 0.00 39.50 4.04
4349 7447 6.572254 CGGAAAACAAAAGAATACACGTACAG 59.428 38.462 0.00 0.00 0.00 2.74
4373 7471 5.705905 AGGAGAGGAATTAAAAACTTGGTCG 59.294 40.000 0.00 0.00 0.00 4.79
4374 7472 6.943146 AGAGGAGAGGAATTAAAAACTTGGTC 59.057 38.462 0.00 0.00 0.00 4.02
4382 7480 7.518188 ACAACAGAAGAGGAGAGGAATTAAAA 58.482 34.615 0.00 0.00 0.00 1.52
4403 7501 0.317854 GCCGCCTGAAACTGAACAAC 60.318 55.000 0.00 0.00 0.00 3.32
4507 7605 3.388024 TCAATCGACCTAGCTAGCCAAAT 59.612 43.478 15.74 3.46 0.00 2.32
4566 7675 4.766375 TCTTGTACCTTGGTAGCATAAGC 58.234 43.478 0.00 0.00 42.56 3.09
4599 7708 8.773033 ATATTTCTTTACGGAGGGAGTACTTA 57.227 34.615 0.00 0.00 0.00 2.24
4604 7713 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
4605 7714 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
4606 7715 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
4607 7716 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
4608 7717 5.118817 GCGCTCTTATATTTCTTTACGGAGG 59.881 44.000 0.00 0.00 0.00 4.30
4609 7718 5.690409 TGCGCTCTTATATTTCTTTACGGAG 59.310 40.000 9.73 0.00 0.00 4.63
4610 7719 5.593968 TGCGCTCTTATATTTCTTTACGGA 58.406 37.500 9.73 0.00 0.00 4.69
4611 7720 5.107453 CCTGCGCTCTTATATTTCTTTACGG 60.107 44.000 9.73 0.00 0.00 4.02
4612 7721 5.107453 CCCTGCGCTCTTATATTTCTTTACG 60.107 44.000 9.73 0.00 0.00 3.18
4613 7722 5.989777 TCCCTGCGCTCTTATATTTCTTTAC 59.010 40.000 9.73 0.00 0.00 2.01
4614 7723 6.169557 TCCCTGCGCTCTTATATTTCTTTA 57.830 37.500 9.73 0.00 0.00 1.85
4615 7724 5.036117 TCCCTGCGCTCTTATATTTCTTT 57.964 39.130 9.73 0.00 0.00 2.52
4616 7725 4.636249 CTCCCTGCGCTCTTATATTTCTT 58.364 43.478 9.73 0.00 0.00 2.52
4617 7726 3.556004 GCTCCCTGCGCTCTTATATTTCT 60.556 47.826 9.73 0.00 0.00 2.52
4618 7727 2.739379 GCTCCCTGCGCTCTTATATTTC 59.261 50.000 9.73 0.00 0.00 2.17
4619 7728 2.104792 TGCTCCCTGCGCTCTTATATTT 59.895 45.455 9.73 0.00 46.63 1.40
4620 7729 1.694150 TGCTCCCTGCGCTCTTATATT 59.306 47.619 9.73 0.00 46.63 1.28
4621 7730 1.342074 TGCTCCCTGCGCTCTTATAT 58.658 50.000 9.73 0.00 46.63 0.86
4622 7731 1.119684 TTGCTCCCTGCGCTCTTATA 58.880 50.000 9.73 0.00 46.63 0.98
4623 7732 0.471617 ATTGCTCCCTGCGCTCTTAT 59.528 50.000 9.73 0.00 46.63 1.73
4624 7733 0.253044 AATTGCTCCCTGCGCTCTTA 59.747 50.000 9.73 0.00 46.63 2.10
4625 7734 1.001641 AATTGCTCCCTGCGCTCTT 60.002 52.632 9.73 0.00 46.63 2.85
4626 7735 1.451028 GAATTGCTCCCTGCGCTCT 60.451 57.895 9.73 0.00 46.63 4.09
4627 7736 1.712977 CTGAATTGCTCCCTGCGCTC 61.713 60.000 9.73 0.00 46.63 5.03
4628 7737 1.748122 CTGAATTGCTCCCTGCGCT 60.748 57.895 9.73 0.00 46.63 5.92
4629 7738 1.099879 ATCTGAATTGCTCCCTGCGC 61.100 55.000 0.00 0.00 46.63 6.09
4630 7739 1.386533 AATCTGAATTGCTCCCTGCG 58.613 50.000 0.00 0.00 46.63 5.18
4631 7740 3.314635 CACTAATCTGAATTGCTCCCTGC 59.685 47.826 0.00 0.00 43.25 4.85
4632 7741 4.774124 TCACTAATCTGAATTGCTCCCTG 58.226 43.478 0.00 0.00 0.00 4.45
4633 7742 4.685575 GCTCACTAATCTGAATTGCTCCCT 60.686 45.833 0.00 0.00 0.00 4.20
4634 7743 3.563390 GCTCACTAATCTGAATTGCTCCC 59.437 47.826 0.00 0.00 0.00 4.30
4635 7744 4.194640 TGCTCACTAATCTGAATTGCTCC 58.805 43.478 0.00 0.00 0.00 4.70
4636 7745 5.808042 TTGCTCACTAATCTGAATTGCTC 57.192 39.130 0.00 0.00 0.00 4.26
4637 7746 5.298777 GGATTGCTCACTAATCTGAATTGCT 59.701 40.000 0.00 0.00 35.42 3.91
4638 7747 5.066893 TGGATTGCTCACTAATCTGAATTGC 59.933 40.000 0.00 0.00 35.42 3.56
4639 7748 6.318144 AGTGGATTGCTCACTAATCTGAATTG 59.682 38.462 0.00 0.00 42.91 2.32
4674 7980 6.183360 CCACATGTTTCATCCAATAGAAGCAT 60.183 38.462 0.00 0.00 43.44 3.79
4677 7983 6.600822 AGACCACATGTTTCATCCAATAGAAG 59.399 38.462 0.00 0.00 0.00 2.85
4694 8000 4.202010 CCGAACAGAAAACAAAGACCACAT 60.202 41.667 0.00 0.00 0.00 3.21
4699 8005 4.976987 TGTTCCGAACAGAAAACAAAGAC 58.023 39.130 9.99 0.00 36.25 3.01
4701 8007 6.529829 TCAAATGTTCCGAACAGAAAACAAAG 59.470 34.615 18.46 2.86 45.95 2.77
4704 8011 5.124776 AGTCAAATGTTCCGAACAGAAAACA 59.875 36.000 18.46 0.00 45.95 2.83
4705 8012 5.455525 CAGTCAAATGTTCCGAACAGAAAAC 59.544 40.000 18.46 13.46 45.95 2.43
4737 8044 0.734889 GCACACATCACAGGCATACC 59.265 55.000 0.00 0.00 0.00 2.73
4745 8052 5.351189 GTGTATCATGTAAGCACACATCACA 59.649 40.000 11.86 8.85 37.02 3.58
4746 8053 5.351189 TGTGTATCATGTAAGCACACATCAC 59.649 40.000 12.96 10.68 43.22 3.06
4747 8054 5.486526 TGTGTATCATGTAAGCACACATCA 58.513 37.500 12.96 0.00 43.22 3.07
4751 8058 5.582269 ACAGATGTGTATCATGTAAGCACAC 59.418 40.000 13.80 11.60 41.88 3.82
4759 8066 8.777413 GCAAATACATACAGATGTGTATCATGT 58.223 33.333 12.35 12.61 45.20 3.21
4762 8069 9.696917 CTAGCAAATACATACAGATGTGTATCA 57.303 33.333 12.35 4.68 45.20 2.15
4766 8073 6.348498 TGCTAGCAAATACATACAGATGTGT 58.652 36.000 16.84 0.00 46.11 3.72



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

AutoCloner maintained by Alex Coulton.