Multiple sequence alignment - TraesCS3D01G252400

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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 TraesCS3D01G252400 chr3D 100.000 7199 0 0 1 7199 352958544 352951346 0.000000e+00 13295.0
1 TraesCS3D01G252400 chr3D 81.375 349 51 10 6623 6966 64836203 64835864 9.200000e-69 272.0
2 TraesCS3D01G252400 chr3A 95.687 6539 198 36 1 6504 471826846 471820357 0.000000e+00 10436.0
3 TraesCS3D01G252400 chr3A 84.992 613 54 15 6555 7165 471820358 471819782 8.050000e-164 588.0
4 TraesCS3D01G252400 chr3A 95.082 61 2 1 7140 7199 471819778 471819718 2.140000e-15 95.3
5 TraesCS3D01G252400 chr3B 92.770 3707 182 35 747 4419 452113559 452109905 0.000000e+00 5282.0
6 TraesCS3D01G252400 chr3B 94.313 1143 47 3 4436 5578 452109298 452108174 0.000000e+00 1735.0
7 TraesCS3D01G252400 chr3B 94.953 951 27 10 5575 6512 452108138 452107196 0.000000e+00 1471.0
8 TraesCS3D01G252400 chr3B 86.356 623 65 13 6546 7165 452107072 452106467 0.000000e+00 662.0
9 TraesCS3D01G252400 chr3B 86.111 360 41 6 411 761 452114427 452114068 5.270000e-101 379.0
10 TraesCS3D01G252400 chr3B 96.721 61 1 1 7140 7199 452106434 452106374 4.600000e-17 100.0
11 TraesCS3D01G252400 chr5D 83.152 368 52 10 6625 6987 379088251 379087889 1.940000e-85 327.0
12 TraesCS3D01G252400 chr2A 81.875 320 49 7 6676 6991 755278405 755278719 1.990000e-65 261.0
13 TraesCS3D01G252400 chr7B 79.467 375 65 12 6624 6990 611713778 611713408 9.270000e-64 255.0
14 TraesCS3D01G252400 chr7B 79.775 356 63 9 6640 6990 611717921 611717570 4.310000e-62 250.0
15 TraesCS3D01G252400 chr7B 79.539 347 60 10 6624 6963 733423751 733423409 3.360000e-58 237.0
16 TraesCS3D01G252400 chr7A 81.046 306 47 11 6694 6995 571257747 571258045 4.340000e-57 233.0


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 TraesCS3D01G252400 chr3D 352951346 352958544 7198 True 13295.000000 13295 100.000000 1 7199 1 chr3D.!!$R2 7198
1 TraesCS3D01G252400 chr3A 471819718 471826846 7128 True 3706.433333 10436 91.920333 1 7199 3 chr3A.!!$R1 7198
2 TraesCS3D01G252400 chr3B 452106374 452114427 8053 True 1604.833333 5282 91.870667 411 7199 6 chr3B.!!$R1 6788
3 TraesCS3D01G252400 chr7B 611713408 611717921 4513 True 252.500000 255 79.621000 6624 6990 2 chr7B.!!$R2 366

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
28 33 0.176680 CCTCCCCTCATCACAAGACG 59.823 60.000 0.00 0.0 0.00 4.18 F
235 241 0.457851 CGTGAGCACTCTTCCCCTAG 59.542 60.000 0.00 0.0 0.00 3.02 F
404 411 0.514691 CAAGAGCTTCAACGTGCCTC 59.485 55.000 0.00 0.0 0.00 4.70 F
2000 2564 0.390340 GTGATGCCTGCAGAGACGAA 60.390 55.000 17.39 0.0 0.00 3.85 F
2468 3034 0.741915 GTTTTCCAAACGCTGGTCCA 59.258 50.000 4.19 0.0 46.51 4.02 F
2470 3036 1.028905 TTTCCAAACGCTGGTCCAAG 58.971 50.000 4.19 0.0 46.51 3.61 F
2661 3235 1.117150 GTGCCCGTCCTTATGGTCTA 58.883 55.000 0.00 0.0 34.23 2.59 F
2708 3282 2.650322 TGTTTCCTTCACTGGAACCAC 58.350 47.619 0.00 0.0 44.83 4.16 F
3317 3893 4.722220 CCATTTGAGGAGCATGAGGATAA 58.278 43.478 0.00 0.0 0.00 1.75 F
5147 6320 1.153745 CTGGTCGACTACTGCTGGC 60.154 63.158 16.46 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 2303 0.039180 CTCCTACACCCCCAAAACCC 59.961 60.000 0.00 0.00 0.00 4.11 R
1835 2399 1.351012 GCAGCAAGCTAGCATCACG 59.649 57.895 18.83 3.22 41.15 4.35 R
2189 2753 1.902508 CTGAAGGGTGCCTAACAGAGA 59.097 52.381 0.00 0.00 39.03 3.10 R
2990 3564 0.958822 AGAAACAATTGGACCACCGC 59.041 50.000 10.83 0.00 39.42 5.68 R
3392 3969 2.370281 TGTCCTGAAAGTCGCAGATC 57.630 50.000 0.00 0.00 40.67 2.75 R
4325 4906 4.427312 AGCAAATCAAGCGATGGAAAATC 58.573 39.130 0.00 0.00 37.01 2.17 R
4476 5647 7.053316 TCACATCTTTTTCACCATGTCAAAT 57.947 32.000 0.00 0.00 0.00 2.32 R
4513 5684 9.213799 TGCAAAATTCATAAATAAAACAGGTCC 57.786 29.630 0.00 0.00 0.00 4.46 R
5179 6352 0.182537 TCGTGGCCTAATGGAATGGG 59.817 55.000 3.32 0.00 34.57 4.00 R
6536 7762 0.092351 GACATTGTGTAACCGCGTCG 59.908 55.000 4.92 0.00 34.36 5.12 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
22 27 1.768077 CTCCCCCTCCCCTCATCAC 60.768 68.421 0.00 0.00 0.00 3.06
28 33 0.176680 CCTCCCCTCATCACAAGACG 59.823 60.000 0.00 0.00 0.00 4.18
35 40 3.056536 CCCTCATCACAAGACGAAAGAGA 60.057 47.826 0.00 0.00 0.00 3.10
52 58 2.158667 AGAGAAGACGAGAGGGAGATCC 60.159 54.545 0.00 0.00 0.00 3.36
95 101 2.203126 CATGGCGCCTCTCTTCCC 60.203 66.667 29.70 0.00 0.00 3.97
103 109 1.986413 CCTCTCTTCCCCACACCAG 59.014 63.158 0.00 0.00 0.00 4.00
165 171 1.527844 GCTGGGCCTCATGGATGTC 60.528 63.158 4.53 0.00 34.57 3.06
167 173 2.111878 GGGCCTCATGGATGTCGG 59.888 66.667 0.84 0.00 34.57 4.79
178 184 2.435418 GATGTCGGCTCCATCCTCT 58.565 57.895 0.00 0.00 34.02 3.69
207 213 2.158740 GGGAGAGGAAGCCCTATGTTTC 60.159 54.545 0.00 0.00 44.53 2.78
212 218 2.092699 AGGAAGCCCTATGTTTCTGCTC 60.093 50.000 0.00 0.00 42.15 4.26
214 220 2.706339 AGCCCTATGTTTCTGCTCAG 57.294 50.000 0.00 0.00 0.00 3.35
234 240 0.970937 CCGTGAGCACTCTTCCCCTA 60.971 60.000 0.00 0.00 0.00 3.53
235 241 0.457851 CGTGAGCACTCTTCCCCTAG 59.542 60.000 0.00 0.00 0.00 3.02
241 248 1.903183 GCACTCTTCCCCTAGTGACTT 59.097 52.381 6.65 0.00 44.79 3.01
246 253 2.183679 CTTCCCCTAGTGACTTCTGCT 58.816 52.381 0.00 0.00 0.00 4.24
258 265 1.209019 ACTTCTGCTGCTACCCATCAG 59.791 52.381 0.00 0.00 38.68 2.90
271 278 2.500910 ACCCATCAGCAAGAGAGAAGAG 59.499 50.000 0.00 0.00 0.00 2.85
278 285 3.099141 AGCAAGAGAGAAGAGAAGAGGG 58.901 50.000 0.00 0.00 0.00 4.30
286 293 3.835395 GAGAAGAGAAGAGGGGAGAACAA 59.165 47.826 0.00 0.00 0.00 2.83
316 323 1.123928 GGAGATCGATCAGGTTGGGT 58.876 55.000 26.47 3.64 0.00 4.51
317 324 1.202580 GGAGATCGATCAGGTTGGGTG 60.203 57.143 26.47 0.00 0.00 4.61
322 329 2.034066 ATCAGGTTGGGTGCCACG 59.966 61.111 0.00 0.00 30.78 4.94
329 336 1.378646 TTGGGTGCCACGACAACAA 60.379 52.632 0.00 0.00 30.78 2.83
363 370 0.617820 TCCCCTCCAGCTTCCTACAC 60.618 60.000 0.00 0.00 0.00 2.90
379 386 1.227999 ACACGCCTTTGTCCATGACG 61.228 55.000 0.00 0.00 34.95 4.35
404 411 0.514691 CAAGAGCTTCAACGTGCCTC 59.485 55.000 0.00 0.00 0.00 4.70
526 535 3.239253 GAGGTGGGTGGTGGACGT 61.239 66.667 0.00 0.00 0.00 4.34
544 553 4.891727 GGTGACGATGGGCGCGAT 62.892 66.667 12.10 0.00 46.04 4.58
731 747 0.667993 AGCATGGACGGTGTGTTTTG 59.332 50.000 0.00 0.00 0.00 2.44
800 1342 0.827368 ACGAATCTCAAGGAGAGGGC 59.173 55.000 2.13 0.00 42.26 5.19
851 1409 8.431910 AGTACTTATCCCTTTTGAGTTCTGTA 57.568 34.615 0.00 0.00 0.00 2.74
852 1410 9.047947 AGTACTTATCCCTTTTGAGTTCTGTAT 57.952 33.333 0.00 0.00 0.00 2.29
1261 1821 0.519519 TATGGCCAAACGCTTGTTCG 59.480 50.000 10.96 0.00 37.74 3.95
1266 1826 1.064946 CAAACGCTTGTTCGGCCAA 59.935 52.632 2.24 0.00 33.81 4.52
1394 1955 2.974285 TGGGGGTAGATTTAGGGTCA 57.026 50.000 0.00 0.00 0.00 4.02
1397 1958 1.420514 GGGGTAGATTTAGGGTCAGGC 59.579 57.143 0.00 0.00 0.00 4.85
1430 1991 2.771943 TGATCCCGATACCTCAAGCTTT 59.228 45.455 0.00 0.00 0.00 3.51
1454 2015 3.244805 GGGGACTTGGTGTAGCTTAGTTT 60.245 47.826 0.00 0.00 0.00 2.66
1459 2020 3.308438 TGGTGTAGCTTAGTTTCCGTC 57.692 47.619 0.00 0.00 0.00 4.79
1518 2079 4.167307 GGGAGGGAGGGTGAATGTTTTATA 59.833 45.833 0.00 0.00 0.00 0.98
1525 2086 6.265422 GGAGGGTGAATGTTTTATAATCTGGG 59.735 42.308 0.00 0.00 0.00 4.45
1526 2087 6.136155 AGGGTGAATGTTTTATAATCTGGGG 58.864 40.000 0.00 0.00 0.00 4.96
1581 2142 3.659786 TGTGAACTATTGGTGGTCGAAG 58.340 45.455 0.00 0.00 0.00 3.79
1742 2303 2.034879 GGGTGTGCTCGTGTCATGG 61.035 63.158 0.00 0.00 0.00 3.66
1835 2399 6.811665 GCTGGTAAAATAGTTGGATTTGGTTC 59.188 38.462 0.00 0.00 0.00 3.62
1904 2468 9.651913 TTGCAAAAGAACTAAAGAAGTGATTTT 57.348 25.926 0.00 0.00 38.88 1.82
2000 2564 0.390340 GTGATGCCTGCAGAGACGAA 60.390 55.000 17.39 0.00 0.00 3.85
2054 2618 1.805945 CTCGAGTAAGGCGCCACAC 60.806 63.158 31.54 24.74 0.00 3.82
2189 2753 6.211785 TGGTTTTAGTTGGGAGTTTGTTCTTT 59.788 34.615 0.00 0.00 0.00 2.52
2207 2771 3.008049 TCTTTCTCTGTTAGGCACCCTTC 59.992 47.826 0.00 0.00 34.61 3.46
2372 2936 5.586155 TCCAGTCCCAACCAGTTTAATTA 57.414 39.130 0.00 0.00 0.00 1.40
2468 3034 0.741915 GTTTTCCAAACGCTGGTCCA 59.258 50.000 4.19 0.00 46.51 4.02
2470 3036 1.028905 TTTCCAAACGCTGGTCCAAG 58.971 50.000 4.19 0.00 46.51 3.61
2621 3195 8.429493 TTGAATGATGAATACACTCTTAGCAG 57.571 34.615 0.00 0.00 0.00 4.24
2656 3230 4.196193 TCTAAATTGTGCCCGTCCTTATG 58.804 43.478 0.00 0.00 0.00 1.90
2661 3235 1.117150 GTGCCCGTCCTTATGGTCTA 58.883 55.000 0.00 0.00 34.23 2.59
2687 3261 6.665992 TCTGTAGTTTTACTGGTGTGATCT 57.334 37.500 0.00 0.00 31.68 2.75
2708 3282 2.650322 TGTTTCCTTCACTGGAACCAC 58.350 47.619 0.00 0.00 44.83 4.16
2733 3307 6.747414 AGTTCCTGGCATGACAATATACTA 57.253 37.500 1.11 0.00 0.00 1.82
2734 3308 6.763355 AGTTCCTGGCATGACAATATACTAG 58.237 40.000 1.11 0.00 0.00 2.57
2735 3309 6.327626 AGTTCCTGGCATGACAATATACTAGT 59.672 38.462 1.11 0.00 0.00 2.57
2911 3485 8.871629 AGTACATGACCTTACTCCTAGATATG 57.128 38.462 0.00 0.00 0.00 1.78
2912 3486 8.670490 AGTACATGACCTTACTCCTAGATATGA 58.330 37.037 0.00 0.00 0.00 2.15
2992 3566 7.017645 GTGAGGAATTATATATTGCTGTTGCG 58.982 38.462 0.00 0.00 43.34 4.85
3317 3893 4.722220 CCATTTGAGGAGCATGAGGATAA 58.278 43.478 0.00 0.00 0.00 1.75
3392 3969 6.317140 TGCTCTAGCTTACCTGATTGAAATTG 59.683 38.462 3.26 0.00 42.66 2.32
4325 4906 7.167635 ACATCGTACAAGTGAGAATTATAAGCG 59.832 37.037 0.00 0.00 0.00 4.68
4513 5684 2.719739 AGATGTGAGCCCATGTTTCAG 58.280 47.619 0.00 0.00 0.00 3.02
4651 5822 2.092646 TGCTTGTGTCCTGGTTTGTACT 60.093 45.455 0.00 0.00 0.00 2.73
4711 5883 5.653255 AGGATAATGGTAGGTTGCTGATT 57.347 39.130 0.00 0.00 0.00 2.57
4875 6047 8.682936 ACTACCAGAATTATGAAAGCTTATGG 57.317 34.615 0.00 0.00 36.34 2.74
4878 6050 7.582719 ACCAGAATTATGAAAGCTTATGGGTA 58.417 34.615 0.00 0.00 34.94 3.69
5147 6320 1.153745 CTGGTCGACTACTGCTGGC 60.154 63.158 16.46 0.00 0.00 4.85
5179 6352 4.291540 TGTGTCTCATGCTTGTTTGAAC 57.708 40.909 0.00 0.00 0.00 3.18
5183 6356 3.256631 GTCTCATGCTTGTTTGAACCCAT 59.743 43.478 0.00 0.00 0.00 4.00
5197 6370 0.106719 ACCCATTCCATTAGGCCACG 60.107 55.000 5.01 0.00 33.74 4.94
5198 6371 0.182537 CCCATTCCATTAGGCCACGA 59.817 55.000 5.01 0.00 33.74 4.35
5267 6440 7.630082 GCTTACTATTCTCCCTTCAAACTACGA 60.630 40.741 0.00 0.00 0.00 3.43
5342 6515 3.288092 GGATCCCACATTCCTTACCAAC 58.712 50.000 0.00 0.00 0.00 3.77
5347 6520 2.446435 CACATTCCTTACCAACCCCAG 58.554 52.381 0.00 0.00 0.00 4.45
5364 6537 7.257016 CCAACCCCAGACCAGAATATTCATATA 60.257 40.741 17.56 0.00 0.00 0.86
5393 6566 5.131475 GGGTAGAGTATTGGTGGGAATACAA 59.869 44.000 0.00 0.00 40.07 2.41
5427 6600 0.594796 CTCGTTGTGCCAACTTTGCC 60.595 55.000 13.76 0.00 0.00 4.52
5668 6880 2.646798 GCAATATCCTGGAATCCCCTCT 59.353 50.000 0.00 0.00 35.38 3.69
5670 6882 4.289672 GCAATATCCTGGAATCCCCTCTAA 59.710 45.833 0.00 0.00 35.38 2.10
5671 6883 5.044550 GCAATATCCTGGAATCCCCTCTAAT 60.045 44.000 0.00 0.00 35.38 1.73
5688 6900 6.421801 CCCTCTAATTTTTGAGCTTGTTTGTG 59.578 38.462 0.00 0.00 0.00 3.33
5718 6930 7.587037 TGAATTGAAGATGTGAAAAGACCTT 57.413 32.000 0.00 0.00 0.00 3.50
5719 6931 8.010733 TGAATTGAAGATGTGAAAAGACCTTT 57.989 30.769 0.00 0.00 0.00 3.11
5720 6932 9.130661 TGAATTGAAGATGTGAAAAGACCTTTA 57.869 29.630 0.00 0.00 31.63 1.85
5721 6933 9.617975 GAATTGAAGATGTGAAAAGACCTTTAG 57.382 33.333 0.00 0.00 31.63 1.85
5722 6934 8.924511 ATTGAAGATGTGAAAAGACCTTTAGA 57.075 30.769 0.00 0.00 31.63 2.10
5937 7158 0.299895 CTGCAGCGATGAAAGTAGCG 59.700 55.000 4.02 0.00 34.34 4.26
6063 7284 0.237498 TCTACGAGCGATGTATGCCG 59.763 55.000 0.00 0.00 33.96 5.69
6126 7348 9.557061 CCATAGTATCTTTCCCATCATCATATG 57.443 37.037 0.00 0.00 0.00 1.78
6289 7513 1.477558 CCCAGCCTGTTGTCTTCTTGT 60.478 52.381 0.00 0.00 0.00 3.16
6353 7579 1.407437 GGTTGTACCTGAGAGGGCATG 60.407 57.143 0.00 0.00 40.58 4.06
6379 7605 6.759827 CCTTTCATTGCCTAGGAATGATTTTG 59.240 38.462 24.85 17.90 39.11 2.44
6512 7738 5.640783 CCTCCTTGGCAAAATCAAAATCTTC 59.359 40.000 0.00 0.00 0.00 2.87
6513 7739 6.423776 TCCTTGGCAAAATCAAAATCTTCT 57.576 33.333 0.00 0.00 0.00 2.85
6514 7740 6.458210 TCCTTGGCAAAATCAAAATCTTCTC 58.542 36.000 0.00 0.00 0.00 2.87
6516 7742 5.151297 TGGCAAAATCAAAATCTTCTCCC 57.849 39.130 0.00 0.00 0.00 4.30
6517 7743 4.840115 TGGCAAAATCAAAATCTTCTCCCT 59.160 37.500 0.00 0.00 0.00 4.20
6518 7744 5.173664 GGCAAAATCAAAATCTTCTCCCTG 58.826 41.667 0.00 0.00 0.00 4.45
6519 7745 5.173664 GCAAAATCAAAATCTTCTCCCTGG 58.826 41.667 0.00 0.00 0.00 4.45
6521 7747 6.393171 CAAAATCAAAATCTTCTCCCTGGTC 58.607 40.000 0.00 0.00 0.00 4.02
6522 7748 3.721087 TCAAAATCTTCTCCCTGGTCC 57.279 47.619 0.00 0.00 0.00 4.46
6524 7750 4.435137 TCAAAATCTTCTCCCTGGTCCTA 58.565 43.478 0.00 0.00 0.00 2.94
6526 7752 4.354208 AAATCTTCTCCCTGGTCCTAGA 57.646 45.455 0.00 0.00 0.00 2.43
6527 7753 4.567987 AATCTTCTCCCTGGTCCTAGAT 57.432 45.455 0.00 0.00 0.00 1.98
6529 7755 3.647636 TCTTCTCCCTGGTCCTAGATTG 58.352 50.000 0.00 0.00 0.00 2.67
6533 7759 1.651770 TCCCTGGTCCTAGATTGGTCT 59.348 52.381 0.00 0.00 38.52 3.85
6534 7760 2.043227 CCCTGGTCCTAGATTGGTCTC 58.957 57.143 0.00 0.00 35.87 3.36
6535 7761 2.626950 CCCTGGTCCTAGATTGGTCTCA 60.627 54.545 0.00 0.00 35.87 3.27
6536 7762 2.432510 CCTGGTCCTAGATTGGTCTCAC 59.567 54.545 0.00 0.00 35.87 3.51
6537 7763 2.099921 CTGGTCCTAGATTGGTCTCACG 59.900 54.545 0.00 0.00 35.87 4.35
6538 7764 2.291346 TGGTCCTAGATTGGTCTCACGA 60.291 50.000 0.00 0.00 35.87 4.35
6539 7765 2.099427 GGTCCTAGATTGGTCTCACGAC 59.901 54.545 0.00 0.00 39.49 4.34
6540 7766 2.014857 TCCTAGATTGGTCTCACGACG 58.985 52.381 0.00 0.00 41.16 5.12
6541 7767 1.534175 CCTAGATTGGTCTCACGACGC 60.534 57.143 0.00 0.00 41.16 5.19
6542 7768 0.098200 TAGATTGGTCTCACGACGCG 59.902 55.000 3.53 3.53 41.16 6.01
6543 7769 2.126071 ATTGGTCTCACGACGCGG 60.126 61.111 12.47 0.00 41.16 6.46
6544 7770 2.814183 GATTGGTCTCACGACGCGGT 62.814 60.000 12.47 0.00 41.16 5.68
6619 7935 3.565905 CAAGCAACTTGTCTCCCATTC 57.434 47.619 0.00 0.00 36.79 2.67
6620 7936 2.206576 AGCAACTTGTCTCCCATTCC 57.793 50.000 0.00 0.00 0.00 3.01
6621 7937 1.177401 GCAACTTGTCTCCCATTCCC 58.823 55.000 0.00 0.00 0.00 3.97
6622 7938 1.547675 GCAACTTGTCTCCCATTCCCA 60.548 52.381 0.00 0.00 0.00 4.37
6623 7939 2.885554 GCAACTTGTCTCCCATTCCCAT 60.886 50.000 0.00 0.00 0.00 4.00
6703 8439 9.513727 GTGGTAAAATTTAAGGAACGTTTGTAA 57.486 29.630 0.46 0.00 0.00 2.41
6736 8801 3.763097 TCATCACGAAATCACATTGGC 57.237 42.857 0.00 0.00 0.00 4.52
6744 8809 2.226962 AATCACATTGGCAGAAGGCT 57.773 45.000 0.00 0.00 44.01 4.58
6751 8816 1.909700 TTGGCAGAAGGCTTGGTAAG 58.090 50.000 3.46 0.00 44.01 2.34
6753 8818 1.423541 TGGCAGAAGGCTTGGTAAGAA 59.576 47.619 3.46 0.00 44.01 2.52
6754 8819 2.158534 TGGCAGAAGGCTTGGTAAGAAA 60.159 45.455 3.46 0.00 44.01 2.52
6755 8820 2.890945 GGCAGAAGGCTTGGTAAGAAAA 59.109 45.455 3.46 0.00 44.01 2.29
6756 8821 3.320826 GGCAGAAGGCTTGGTAAGAAAAA 59.679 43.478 3.46 0.00 44.01 1.94
6805 9293 5.370679 ACTTTCAAATGCATTTTGGAGCTT 58.629 33.333 21.95 0.00 44.07 3.74
6834 9324 4.527509 TCTTTTTGCCACAACTTTCACA 57.472 36.364 0.00 0.00 0.00 3.58
6878 9368 9.852091 AAATTTTGTATGCACAACAAACATTTT 57.148 22.222 22.32 18.74 44.26 1.82
6880 9370 8.886816 TTTTGTATGCACAACAAACATTTTTC 57.113 26.923 22.32 0.00 44.26 2.29
6898 9388 8.397148 ACATTTTTCAAAGTATGCCACAAAAAG 58.603 29.630 0.00 0.00 29.76 2.27
6904 9394 7.495901 TCAAAGTATGCCACAAAAAGATTCAA 58.504 30.769 0.00 0.00 0.00 2.69
6967 12461 1.250328 CACCAGAAGCATTTGAGCCA 58.750 50.000 0.00 0.00 34.23 4.75
6970 12464 1.615116 CCAGAAGCATTTGAGCCAGGA 60.615 52.381 0.00 0.00 34.23 3.86
6976 12470 0.744874 CATTTGAGCCAGGATGCAGG 59.255 55.000 0.00 0.00 31.97 4.85
7004 12498 3.502191 TTTTGCTTGTTTGCTTCGTCT 57.498 38.095 0.00 0.00 0.00 4.18
7010 12504 3.612423 GCTTGTTTGCTTCGTCTTTTGTT 59.388 39.130 0.00 0.00 0.00 2.83
7012 12506 5.458779 GCTTGTTTGCTTCGTCTTTTGTTAT 59.541 36.000 0.00 0.00 0.00 1.89
7014 12508 7.166804 GCTTGTTTGCTTCGTCTTTTGTTATTA 59.833 33.333 0.00 0.00 0.00 0.98
7032 12526 9.688091 TTGTTATTATTGTTATTAGTGCCTCCA 57.312 29.630 0.00 0.00 0.00 3.86
7051 12545 6.314784 CCTCCATTTTGTAATTCTTGTCGTC 58.685 40.000 0.00 0.00 0.00 4.20
7068 12562 8.602328 TCTTGTCGTCGTTTTAGTTTAAATTGA 58.398 29.630 0.00 0.00 0.00 2.57
7071 12565 9.719279 TGTCGTCGTTTTAGTTTAAATTGAAAT 57.281 25.926 4.38 0.00 0.00 2.17
7073 12567 9.932699 TCGTCGTTTTAGTTTAAATTGAAATGA 57.067 25.926 14.78 14.78 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 15 1.186200 TCGTCTTGTGATGAGGGGAG 58.814 55.000 0.00 0.00 33.66 4.30
22 27 4.148563 TCTCGTCTTCTCTTTCGTCTTG 57.851 45.455 0.00 0.00 0.00 3.02
28 33 3.349022 TCTCCCTCTCGTCTTCTCTTTC 58.651 50.000 0.00 0.00 0.00 2.62
35 40 1.286553 ACTGGATCTCCCTCTCGTCTT 59.713 52.381 0.00 0.00 35.38 3.01
52 58 2.047844 CGGCTGACCTGGTCACTG 60.048 66.667 25.12 20.64 37.67 3.66
73 79 4.899239 GAGAGGCGCCATGGTCGG 62.899 72.222 31.54 11.68 0.00 4.79
83 89 2.266055 GTGTGGGGAAGAGAGGCG 59.734 66.667 0.00 0.00 0.00 5.52
95 101 1.577328 GCGTGTTGGATCTGGTGTGG 61.577 60.000 0.00 0.00 0.00 4.17
103 109 0.179097 GAGAGGGAGCGTGTTGGATC 60.179 60.000 0.00 0.00 0.00 3.36
148 154 1.227764 CGACATCCATGAGGCCCAG 60.228 63.158 0.00 0.00 33.74 4.45
162 168 0.614697 TTGAGAGGATGGAGCCGACA 60.615 55.000 0.00 0.00 0.00 4.35
165 171 1.227497 GCTTGAGAGGATGGAGCCG 60.227 63.158 0.00 0.00 0.00 5.52
167 173 1.595466 CATGCTTGAGAGGATGGAGC 58.405 55.000 0.00 0.00 45.07 4.70
178 184 0.254178 GCTTCCTCTCCCATGCTTGA 59.746 55.000 0.22 0.00 0.00 3.02
212 218 1.739562 GGAAGAGTGCTCACGGCTG 60.740 63.158 1.82 0.00 42.39 4.85
214 220 2.435059 GGGAAGAGTGCTCACGGC 60.435 66.667 1.82 0.00 42.22 5.68
223 229 3.436243 CAGAAGTCACTAGGGGAAGAGT 58.564 50.000 0.00 0.00 0.00 3.24
234 240 0.610687 GGGTAGCAGCAGAAGTCACT 59.389 55.000 0.00 0.00 0.00 3.41
235 241 0.321671 TGGGTAGCAGCAGAAGTCAC 59.678 55.000 0.00 0.00 0.00 3.67
258 265 2.168313 CCCCTCTTCTCTTCTCTCTTGC 59.832 54.545 0.00 0.00 0.00 4.01
286 293 3.459598 TGATCGATCTCCCTCCCATTTTT 59.540 43.478 25.02 0.00 0.00 1.94
294 301 1.342819 CCAACCTGATCGATCTCCCTC 59.657 57.143 25.02 0.39 0.00 4.30
306 313 3.164977 TCGTGGCACCCAACCTGA 61.165 61.111 12.86 0.00 34.18 3.86
316 323 2.897846 CCGGTTGTTGTCGTGGCA 60.898 61.111 0.00 0.00 0.00 4.92
317 324 2.898343 ACCGGTTGTTGTCGTGGC 60.898 61.111 0.00 0.00 0.00 5.01
322 329 0.883370 GGAGGTCACCGGTTGTTGTC 60.883 60.000 2.97 0.00 0.00 3.18
329 336 4.716977 GGAGGGGAGGTCACCGGT 62.717 72.222 0.00 0.00 46.41 5.28
363 370 1.361668 CTCCGTCATGGACAAAGGCG 61.362 60.000 0.00 0.00 43.74 5.52
379 386 1.270358 ACGTTGAAGCTCTTGACCTCC 60.270 52.381 0.00 0.00 0.00 4.30
603 612 6.976925 GTCCGATTTAAATCCTCGACTTCTTA 59.023 38.462 20.01 0.00 34.41 2.10
664 676 6.648879 ACATAAATTGTAACTGGCACACTT 57.351 33.333 0.00 0.00 36.57 3.16
731 747 2.478370 CGAATTCATCATGGGCACACAC 60.478 50.000 6.22 0.00 0.00 3.82
800 1342 2.101582 CCAAGACTATCTCCACCCTTCG 59.898 54.545 0.00 0.00 0.00 3.79
1233 1793 1.330521 CGTTTGGCCATACCGAATCTG 59.669 52.381 19.18 1.26 44.05 2.90
1394 1955 1.686052 GGATCAGATTCTCGTCTGCCT 59.314 52.381 0.00 0.00 44.15 4.75
1397 1958 1.950216 TCGGGATCAGATTCTCGTCTG 59.050 52.381 0.00 0.00 45.51 3.51
1430 1991 2.337359 AAGCTACACCAAGTCCCCTA 57.663 50.000 0.00 0.00 0.00 3.53
1454 2015 1.173043 GGGCAAAATCACATGACGGA 58.827 50.000 0.00 0.00 0.00 4.69
1459 2020 3.337694 ACCATTGGGCAAAATCACATG 57.662 42.857 7.78 0.00 37.90 3.21
1518 2079 4.352893 ACCTTTTACTGTACACCCCAGATT 59.647 41.667 0.00 0.00 34.04 2.40
1581 2142 8.349983 ACCAGTGACAACATAAAATTCAACTAC 58.650 33.333 0.00 0.00 0.00 2.73
1742 2303 0.039180 CTCCTACACCCCCAAAACCC 59.961 60.000 0.00 0.00 0.00 4.11
1782 2344 6.469782 TTCACAAAGAAGAAAATGCCTCTT 57.530 33.333 0.00 0.00 35.82 2.85
1783 2345 6.462067 CCTTTCACAAAGAAGAAAATGCCTCT 60.462 38.462 0.00 0.00 41.02 3.69
1835 2399 1.351012 GCAGCAAGCTAGCATCACG 59.649 57.895 18.83 3.22 41.15 4.35
1856 2420 4.192429 AGCAAATAAGCAATTGTCCCAC 57.808 40.909 7.40 0.00 36.85 4.61
1904 2468 4.217510 CCATCAAGCAAGGGATCCATAAA 58.782 43.478 15.23 0.00 0.00 1.40
2000 2564 7.884877 TGTCCATCAAAACTTACTCAATCTGAT 59.115 33.333 0.00 0.00 0.00 2.90
2054 2618 3.577805 ATTCAGTTATTCCCTTCCCCG 57.422 47.619 0.00 0.00 0.00 5.73
2102 2666 7.651704 GTGAAGTAATTTGCTGGTTAAATGTGT 59.348 33.333 0.00 0.00 0.00 3.72
2189 2753 1.902508 CTGAAGGGTGCCTAACAGAGA 59.097 52.381 0.00 0.00 39.03 3.10
2207 2771 7.817641 TGAGTACAACTCTACAACATAGTCTG 58.182 38.462 8.42 0.00 45.27 3.51
2621 3195 9.476202 GGGCACAATTTAGAATAATATTTCCAC 57.524 33.333 0.00 0.00 0.00 4.02
2623 3197 8.357402 ACGGGCACAATTTAGAATAATATTTCC 58.643 33.333 0.00 0.00 0.00 3.13
2656 3230 8.693625 ACACCAGTAAAACTACAGATATAGACC 58.306 37.037 0.00 0.00 0.00 3.85
2661 3235 8.982723 AGATCACACCAGTAAAACTACAGATAT 58.017 33.333 0.00 0.00 0.00 1.63
2708 3282 5.824624 AGTATATTGTCATGCCAGGAACTTG 59.175 40.000 0.00 0.00 34.60 3.16
2733 3307 8.807948 TTAATTCAAGATTTAGCTTGCCTACT 57.192 30.769 2.96 0.00 43.78 2.57
2734 3308 9.508567 CTTTAATTCAAGATTTAGCTTGCCTAC 57.491 33.333 2.96 0.00 43.78 3.18
2735 3309 9.243105 ACTTTAATTCAAGATTTAGCTTGCCTA 57.757 29.630 6.38 0.00 43.78 3.93
2966 3540 7.307930 CGCAACAGCAATATATAATTCCTCACA 60.308 37.037 0.00 0.00 0.00 3.58
2968 3542 6.149308 CCGCAACAGCAATATATAATTCCTCA 59.851 38.462 0.00 0.00 0.00 3.86
2990 3564 0.958822 AGAAACAATTGGACCACCGC 59.041 50.000 10.83 0.00 39.42 5.68
2992 3566 4.099419 ACTTGAAGAAACAATTGGACCACC 59.901 41.667 10.83 0.00 0.00 4.61
3317 3893 8.812972 TCTGAAGGTACAACTGAACTTACATAT 58.187 33.333 0.00 0.00 0.00 1.78
3366 3943 5.620738 TTCAATCAGGTAAGCTAGAGCAT 57.379 39.130 4.01 0.00 45.16 3.79
3392 3969 2.370281 TGTCCTGAAAGTCGCAGATC 57.630 50.000 0.00 0.00 40.67 2.75
4325 4906 4.427312 AGCAAATCAAGCGATGGAAAATC 58.573 39.130 0.00 0.00 37.01 2.17
4396 4977 9.891828 CTAACATAGTTCACTAGCTCTCATTAG 57.108 37.037 0.00 0.00 0.00 1.73
4476 5647 7.053316 TCACATCTTTTTCACCATGTCAAAT 57.947 32.000 0.00 0.00 0.00 2.32
4513 5684 9.213799 TGCAAAATTCATAAATAAAACAGGTCC 57.786 29.630 0.00 0.00 0.00 4.46
5091 6264 8.097662 GGAAGAGAAAGAAATGAGTTAGGAAGA 58.902 37.037 0.00 0.00 0.00 2.87
5147 6320 1.977188 TGAGACACATAACAGTCGCG 58.023 50.000 0.00 0.00 39.67 5.87
5179 6352 0.182537 TCGTGGCCTAATGGAATGGG 59.817 55.000 3.32 0.00 34.57 4.00
5183 6356 1.837439 AGATGTCGTGGCCTAATGGAA 59.163 47.619 3.32 0.00 34.57 3.53
5197 6370 8.837788 AAATGAAAAGGAAAATTGGAGATGTC 57.162 30.769 0.00 0.00 0.00 3.06
5198 6371 9.631257 AAAAATGAAAAGGAAAATTGGAGATGT 57.369 25.926 0.00 0.00 0.00 3.06
5227 6400 8.263940 AGAATAGTAAGCAAGATACGCAAAAA 57.736 30.769 0.00 0.00 0.00 1.94
5228 6401 7.011109 GGAGAATAGTAAGCAAGATACGCAAAA 59.989 37.037 0.00 0.00 0.00 2.44
5229 6402 6.479001 GGAGAATAGTAAGCAAGATACGCAAA 59.521 38.462 0.00 0.00 0.00 3.68
5230 6403 5.983720 GGAGAATAGTAAGCAAGATACGCAA 59.016 40.000 0.00 0.00 0.00 4.85
5231 6404 5.509163 GGGAGAATAGTAAGCAAGATACGCA 60.509 44.000 0.00 0.00 0.00 5.24
5267 6440 3.650942 TGTGGATTTGGTAAGAGTCCTGT 59.349 43.478 0.00 0.00 0.00 4.00
5342 6515 6.769822 GCATATATGAATATTCTGGTCTGGGG 59.230 42.308 17.10 0.43 0.00 4.96
5364 6537 2.439507 CCACCAATACTCTACCCAGCAT 59.560 50.000 0.00 0.00 0.00 3.79
5393 6566 3.297736 CAACGAGACTTCCTATACCCCT 58.702 50.000 0.00 0.00 0.00 4.79
5427 6600 1.980844 GTGCAAATCACAACATCTGCG 59.019 47.619 0.00 0.00 44.98 5.18
5590 6802 5.010282 AGCCACCAAAGTATTCCTACAAAG 58.990 41.667 0.00 0.00 0.00 2.77
5668 6880 5.105752 ACGCACAAACAAGCTCAAAAATTA 58.894 33.333 0.00 0.00 0.00 1.40
5670 6882 3.520569 ACGCACAAACAAGCTCAAAAAT 58.479 36.364 0.00 0.00 0.00 1.82
5671 6883 2.953020 ACGCACAAACAAGCTCAAAAA 58.047 38.095 0.00 0.00 0.00 1.94
5688 6900 6.509317 TTTCACATCTTCAATTCAAAACGC 57.491 33.333 0.00 0.00 0.00 4.84
5937 7158 3.202706 GATTTGGCCTCCGCGTCC 61.203 66.667 3.32 0.79 35.02 4.79
6063 7284 5.904362 AAAAATTGCTGGAGGATGAGTAC 57.096 39.130 0.00 0.00 0.00 2.73
6126 7348 2.357881 GAAACGTCACCGGGGGTC 60.358 66.667 2.42 0.00 38.78 4.46
6289 7513 0.874175 CAACAGAGACAACACGCGGA 60.874 55.000 12.47 0.00 0.00 5.54
6353 7579 3.290710 TCATTCCTAGGCAATGAAAGGC 58.709 45.455 23.35 0.00 37.33 4.35
6379 7605 4.218417 ACAGTATCCAAAATGCACCAACTC 59.782 41.667 0.00 0.00 0.00 3.01
6414 7640 5.844004 ACGAGATACACATTATTCCCTGAC 58.156 41.667 0.00 0.00 0.00 3.51
6512 7738 2.043227 GACCAATCTAGGACCAGGGAG 58.957 57.143 0.00 0.00 0.00 4.30
6513 7739 1.651770 AGACCAATCTAGGACCAGGGA 59.348 52.381 0.00 0.00 31.46 4.20
6514 7740 2.043227 GAGACCAATCTAGGACCAGGG 58.957 57.143 0.00 0.00 34.34 4.45
6516 7742 2.099921 CGTGAGACCAATCTAGGACCAG 59.900 54.545 0.00 0.00 34.34 4.00
6517 7743 2.100197 CGTGAGACCAATCTAGGACCA 58.900 52.381 0.00 0.00 34.34 4.02
6518 7744 2.376109 TCGTGAGACCAATCTAGGACC 58.624 52.381 0.00 0.00 34.34 4.46
6533 7759 0.318869 ATTGTGTAACCGCGTCGTGA 60.319 50.000 7.51 0.00 34.36 4.35
6534 7760 0.179260 CATTGTGTAACCGCGTCGTG 60.179 55.000 4.92 0.00 34.36 4.35
6535 7761 0.598158 ACATTGTGTAACCGCGTCGT 60.598 50.000 4.92 0.00 34.36 4.34
6536 7762 0.092351 GACATTGTGTAACCGCGTCG 59.908 55.000 4.92 0.00 34.36 5.12
6537 7763 0.441145 GGACATTGTGTAACCGCGTC 59.559 55.000 4.92 0.00 34.36 5.19
6538 7764 1.286354 CGGACATTGTGTAACCGCGT 61.286 55.000 4.92 0.00 32.34 6.01
6539 7765 1.418367 CGGACATTGTGTAACCGCG 59.582 57.895 0.00 0.00 32.34 6.46
6541 7767 0.672401 AGGCGGACATTGTGTAACCG 60.672 55.000 9.60 9.60 39.75 4.44
6542 7768 1.084289 GAGGCGGACATTGTGTAACC 58.916 55.000 0.00 0.00 34.36 2.85
6543 7769 0.719465 CGAGGCGGACATTGTGTAAC 59.281 55.000 0.00 0.00 37.35 2.50
6544 7770 3.131326 CGAGGCGGACATTGTGTAA 57.869 52.632 0.00 0.00 0.00 2.41
6615 7931 5.882000 TGAATCTACTGTTCACATGGGAATG 59.118 40.000 14.71 12.35 31.07 2.67
6616 7932 6.065976 TGAATCTACTGTTCACATGGGAAT 57.934 37.500 14.71 0.00 31.07 3.01
6617 7933 5.497464 TGAATCTACTGTTCACATGGGAA 57.503 39.130 6.21 6.21 31.07 3.97
6618 7934 5.497464 TTGAATCTACTGTTCACATGGGA 57.503 39.130 0.00 0.00 35.47 4.37
6619 7935 6.573664 TTTTGAATCTACTGTTCACATGGG 57.426 37.500 0.00 0.00 35.47 4.00
6695 8431 8.858186 TGATGAATTTTGCATACATTACAAACG 58.142 29.630 0.00 0.00 33.29 3.60
6703 8439 7.975058 TGATTTCGTGATGAATTTTGCATACAT 59.025 29.630 0.00 0.00 36.22 2.29
6753 8818 7.862512 TTTCCAGAGCATTGATTTTGTTTTT 57.137 28.000 0.00 0.00 0.00 1.94
6754 8819 7.499895 ACATTTCCAGAGCATTGATTTTGTTTT 59.500 29.630 0.00 0.00 0.00 2.43
6755 8820 6.993902 ACATTTCCAGAGCATTGATTTTGTTT 59.006 30.769 0.00 0.00 0.00 2.83
6756 8821 6.527423 ACATTTCCAGAGCATTGATTTTGTT 58.473 32.000 0.00 0.00 0.00 2.83
6757 8822 6.105397 ACATTTCCAGAGCATTGATTTTGT 57.895 33.333 0.00 0.00 0.00 2.83
6758 8823 7.816031 AGTAACATTTCCAGAGCATTGATTTTG 59.184 33.333 0.00 0.00 0.00 2.44
6814 9304 5.604010 TTTGTGAAAGTTGTGGCAAAAAG 57.396 34.783 0.00 0.00 0.00 2.27
6815 9305 5.471456 ACATTTGTGAAAGTTGTGGCAAAAA 59.529 32.000 0.00 0.00 31.10 1.94
6816 9306 4.999950 ACATTTGTGAAAGTTGTGGCAAAA 59.000 33.333 0.00 0.00 31.10 2.44
6878 9368 7.495901 TGAATCTTTTTGTGGCATACTTTGAA 58.504 30.769 0.00 0.00 0.00 2.69
6880 9370 7.712264 TTGAATCTTTTTGTGGCATACTTTG 57.288 32.000 0.00 0.00 0.00 2.77
6944 12438 2.095364 GCTCAAATGCTTCTGGTGTGAG 60.095 50.000 0.00 0.00 35.28 3.51
6967 12461 3.385755 GCAAAAATACCATCCTGCATCCT 59.614 43.478 0.00 0.00 0.00 3.24
6970 12464 4.223477 ACAAGCAAAAATACCATCCTGCAT 59.777 37.500 0.00 0.00 32.21 3.96
6976 12470 6.544038 AAGCAAACAAGCAAAAATACCATC 57.456 33.333 0.00 0.00 36.85 3.51
7012 12506 9.030452 ACAAAATGGAGGCACTAATAACAATAA 57.970 29.630 0.00 0.00 41.55 1.40
7014 12508 7.480760 ACAAAATGGAGGCACTAATAACAAT 57.519 32.000 0.00 0.00 41.55 2.71
7031 12525 7.603297 AAACGACGACAAGAATTACAAAATG 57.397 32.000 0.00 0.00 0.00 2.32
7032 12526 9.377383 CTAAAACGACGACAAGAATTACAAAAT 57.623 29.630 0.00 0.00 0.00 1.82
7071 12565 8.306038 CACTTCCACAAAATGATATTTCCTTCA 58.694 33.333 0.00 0.00 0.00 3.02
7073 12567 8.421249 TCACTTCCACAAAATGATATTTCCTT 57.579 30.769 0.00 0.00 0.00 3.36
7079 12573 4.646492 GCCCTCACTTCCACAAAATGATAT 59.354 41.667 0.00 0.00 0.00 1.63
7083 12577 2.029649 CAGCCCTCACTTCCACAAAATG 60.030 50.000 0.00 0.00 0.00 2.32
7084 12578 2.242043 CAGCCCTCACTTCCACAAAAT 58.758 47.619 0.00 0.00 0.00 1.82
7090 12584 0.185901 AAAAGCAGCCCTCACTTCCA 59.814 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.