Multiple sequence alignment - TraesCS2D01G095800

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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 TraesCS2D01G095800 chr2D 100.000 3153 0 0 1 3153 48029338 48026186 0.000000e+00 5823.0
1 TraesCS2D01G095800 chr2D 86.215 1313 134 28 859 2153 44339590 44340873 0.000000e+00 1378.0
2 TraesCS2D01G095800 chr2D 85.301 1347 134 44 851 2160 44470358 44469039 0.000000e+00 1332.0
3 TraesCS2D01G095800 chr2A 89.283 1577 112 34 853 2388 51040695 51042255 0.000000e+00 1923.0
4 TraesCS2D01G095800 chr2A 86.309 1322 133 38 853 2160 48347639 48346352 0.000000e+00 1395.0
5 TraesCS2D01G095800 chr2A 84.284 1368 143 46 833 2160 48249755 48251090 0.000000e+00 1269.0
6 TraesCS2D01G095800 chr2A 93.697 476 30 0 1387 1862 48246378 48246853 0.000000e+00 713.0
7 TraesCS2D01G095800 chr2A 90.467 535 35 9 2537 3068 51042406 51042927 0.000000e+00 691.0
8 TraesCS2D01G095800 chr2A 88.147 464 40 12 873 1332 48224211 48224663 3.580000e-149 538.0
9 TraesCS2D01G095800 chr2A 85.530 387 33 8 13 386 51039837 51040213 1.770000e-102 383.0
10 TraesCS2D01G095800 chr2A 92.754 69 2 2 3067 3133 51042962 51043029 2.590000e-16 97.1
11 TraesCS2D01G095800 chr2B 87.235 1512 103 51 853 2330 75990416 75991871 0.000000e+00 1640.0
12 TraesCS2D01G095800 chr2B 85.891 1375 139 41 809 2160 71244528 71243186 0.000000e+00 1413.0
13 TraesCS2D01G095800 chr2B 86.309 1322 132 33 860 2160 71293858 71292565 0.000000e+00 1393.0
14 TraesCS2D01G095800 chr2B 83.883 1334 149 45 849 2160 520970191 520968902 0.000000e+00 1212.0
15 TraesCS2D01G095800 chr2B 89.518 477 30 12 859 1323 70821669 70822137 1.260000e-163 586.0
16 TraesCS2D01G095800 chr2B 86.867 533 45 10 1 524 75989273 75989789 9.810000e-160 573.0
17 TraesCS2D01G095800 chr2B 79.519 874 73 54 2240 3078 75991872 75992674 2.790000e-145 525.0
18 TraesCS2D01G095800 chr2B 87.302 126 9 5 2946 3068 75992770 75992891 1.530000e-28 137.0
19 TraesCS2D01G095800 chr2B 92.857 84 0 3 3072 3151 75992929 75993010 1.990000e-22 117.0


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 TraesCS2D01G095800 chr2D 48026186 48029338 3152 True 5823.000 5823 100.0000 1 3153 1 chr2D.!!$R2 3152
1 TraesCS2D01G095800 chr2D 44339590 44340873 1283 False 1378.000 1378 86.2150 859 2153 1 chr2D.!!$F1 1294
2 TraesCS2D01G095800 chr2D 44469039 44470358 1319 True 1332.000 1332 85.3010 851 2160 1 chr2D.!!$R1 1309
3 TraesCS2D01G095800 chr2A 48346352 48347639 1287 True 1395.000 1395 86.3090 853 2160 1 chr2A.!!$R1 1307
4 TraesCS2D01G095800 chr2A 48246378 48251090 4712 False 991.000 1269 88.9905 833 2160 2 chr2A.!!$F2 1327
5 TraesCS2D01G095800 chr2A 51039837 51043029 3192 False 773.525 1923 89.5085 13 3133 4 chr2A.!!$F3 3120
6 TraesCS2D01G095800 chr2B 71243186 71244528 1342 True 1413.000 1413 85.8910 809 2160 1 chr2B.!!$R1 1351
7 TraesCS2D01G095800 chr2B 71292565 71293858 1293 True 1393.000 1393 86.3090 860 2160 1 chr2B.!!$R2 1300
8 TraesCS2D01G095800 chr2B 520968902 520970191 1289 True 1212.000 1212 83.8830 849 2160 1 chr2B.!!$R3 1311
9 TraesCS2D01G095800 chr2B 75989273 75993010 3737 False 598.400 1640 86.7560 1 3151 5 chr2B.!!$F2 3150

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
259 265 0.035820 GGCCAAGGTTACGTCCATCA 60.036 55.0 0.00 0.00 0.00 3.07 F
449 467 0.110778 CCGATCGACGACATACCTCG 60.111 60.0 18.66 4.37 45.77 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 3977 1.043116 TCGATCCAAGATGCGGAGGT 61.043 55.0 0.00 0.00 35.56 3.85 R
2403 5220 0.458260 TCAGCCATGCATACGTACGT 59.542 50.0 25.98 25.98 0.00 3.57 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
25 26 2.427232 ACACACTTACACGTACGCAT 57.573 45.000 16.72 6.10 0.00 4.73
26 27 2.322161 ACACACTTACACGTACGCATC 58.678 47.619 16.72 0.00 0.00 3.91
27 28 2.287728 ACACACTTACACGTACGCATCA 60.288 45.455 16.72 0.00 0.00 3.07
52 53 5.237344 CCAGTACCACTATACGTGTACTACC 59.763 48.000 12.21 0.00 42.20 3.18
65 66 4.278669 CGTGTACTACCTTGCTCTGGATAT 59.721 45.833 0.00 0.00 0.00 1.63
66 67 5.472478 CGTGTACTACCTTGCTCTGGATATA 59.528 44.000 0.00 0.00 0.00 0.86
67 68 6.151312 CGTGTACTACCTTGCTCTGGATATAT 59.849 42.308 0.00 0.00 0.00 0.86
68 69 7.336176 CGTGTACTACCTTGCTCTGGATATATA 59.664 40.741 0.00 0.00 0.00 0.86
73 74 7.730784 ACTACCTTGCTCTGGATATATAACAGT 59.269 37.037 13.61 1.22 34.02 3.55
78 79 7.423844 TGCTCTGGATATATAACAGTATGGG 57.576 40.000 13.61 5.34 43.62 4.00
150 155 0.109781 CTTGGTTCATTTGACCGCGG 60.110 55.000 26.86 26.86 0.00 6.46
219 225 0.883833 GTTTCCTGTGCATGGACCAG 59.116 55.000 15.34 11.58 32.65 4.00
259 265 0.035820 GGCCAAGGTTACGTCCATCA 60.036 55.000 0.00 0.00 0.00 3.07
297 311 4.338964 AGACATTTTATTGCGATGGATGCA 59.661 37.500 0.00 0.00 41.38 3.96
327 341 2.360350 AGCACATGAAGGCGTGGG 60.360 61.111 0.00 0.00 37.50 4.61
328 342 2.359850 GCACATGAAGGCGTGGGA 60.360 61.111 0.00 0.00 36.51 4.37
329 343 1.971167 GCACATGAAGGCGTGGGAA 60.971 57.895 0.00 0.00 36.51 3.97
330 344 1.926511 GCACATGAAGGCGTGGGAAG 61.927 60.000 0.00 0.00 36.51 3.46
334 348 2.094675 CATGAAGGCGTGGGAAGAAAT 58.905 47.619 0.00 0.00 0.00 2.17
347 361 6.019318 CGTGGGAAGAAATAAATACGGTGTAG 60.019 42.308 0.00 0.00 0.00 2.74
387 405 4.052229 CGCGAGGTCGGTTGGAGT 62.052 66.667 0.00 0.00 40.23 3.85
400 418 2.417515 GGTTGGAGTAGCTAGACTGCAC 60.418 54.545 10.07 6.34 46.07 4.57
404 422 2.370349 GAGTAGCTAGACTGCACTCCA 58.630 52.381 0.00 0.00 36.29 3.86
405 423 2.096248 AGTAGCTAGACTGCACTCCAC 58.904 52.381 0.00 0.00 32.54 4.02
406 424 1.135333 GTAGCTAGACTGCACTCCACC 59.865 57.143 0.00 0.00 34.99 4.61
407 425 0.542938 AGCTAGACTGCACTCCACCA 60.543 55.000 0.00 0.00 34.99 4.17
421 439 1.786441 TCCACCAGGAAATTTCACCCT 59.214 47.619 19.49 5.83 42.23 4.34
434 452 1.358152 TCACCCTTCCTGAAACCGAT 58.642 50.000 0.00 0.00 0.00 4.18
435 453 1.278127 TCACCCTTCCTGAAACCGATC 59.722 52.381 0.00 0.00 0.00 3.69
436 454 0.249398 ACCCTTCCTGAAACCGATCG 59.751 55.000 8.51 8.51 0.00 3.69
437 455 0.535335 CCCTTCCTGAAACCGATCGA 59.465 55.000 18.66 0.00 0.00 3.59
439 457 1.269166 CTTCCTGAAACCGATCGACG 58.731 55.000 18.66 2.80 42.18 5.12
449 467 0.110778 CCGATCGACGACATACCTCG 60.111 60.000 18.66 4.37 45.77 4.63
479 497 4.442472 CCTGCTCCAATTGGAATGGAAATC 60.442 45.833 26.87 9.76 45.96 2.17
499 517 0.250553 TGGAATGGGTCGGTGAACAC 60.251 55.000 0.00 0.00 0.00 3.32
531 822 8.880750 GGATTGGATAATAGTATAAACCGCTTC 58.119 37.037 0.00 0.00 0.00 3.86
545 836 2.092968 ACCGCTTCATTATCTCTTGCCA 60.093 45.455 0.00 0.00 0.00 4.92
546 837 2.289002 CCGCTTCATTATCTCTTGCCAC 59.711 50.000 0.00 0.00 0.00 5.01
562 871 8.053963 TCTCTTGCCACTTAATAGACTAGTAGT 58.946 37.037 1.37 1.37 0.00 2.73
563 872 9.339850 CTCTTGCCACTTAATAGACTAGTAGTA 57.660 37.037 1.88 0.00 0.00 1.82
565 874 9.122779 CTTGCCACTTAATAGACTAGTAGTAGT 57.877 37.037 10.09 10.09 42.59 2.73
567 876 9.775854 TGCCACTTAATAGACTAGTAGTAGTAG 57.224 37.037 10.28 10.04 39.78 2.57
589 898 8.414778 AGTAGTAGCATATACCAGAGTCAAAAC 58.585 37.037 0.00 0.00 0.00 2.43
618 930 3.376859 TGCCATCCGTTGACAAATCATAC 59.623 43.478 0.00 0.00 33.85 2.39
623 935 5.351233 TCCGTTGACAAATCATACAACAC 57.649 39.130 0.00 0.00 41.44 3.32
661 979 5.449314 CGGTGATTTAATATCACGCCCAAAA 60.449 40.000 17.16 0.00 46.85 2.44
667 985 4.637483 AATATCACGCCCAAAATCACTG 57.363 40.909 0.00 0.00 0.00 3.66
710 1028 5.142061 TCGTGAGTTACCATACAACATGT 57.858 39.130 0.00 0.00 0.00 3.21
711 1029 6.270156 TCGTGAGTTACCATACAACATGTA 57.730 37.500 0.00 0.00 37.24 2.29
712 1030 6.094719 TCGTGAGTTACCATACAACATGTAC 58.905 40.000 0.00 0.00 35.42 2.90
714 1032 5.865552 GTGAGTTACCATACAACATGTACGT 59.134 40.000 0.00 2.03 35.42 3.57
715 1033 6.034256 GTGAGTTACCATACAACATGTACGTC 59.966 42.308 0.00 0.00 35.42 4.34
716 1034 5.413499 AGTTACCATACAACATGTACGTCC 58.587 41.667 0.00 0.00 35.42 4.79
717 1035 3.255969 ACCATACAACATGTACGTCCC 57.744 47.619 0.00 0.00 35.42 4.46
719 1037 3.194861 CCATACAACATGTACGTCCCAG 58.805 50.000 0.00 0.00 35.42 4.45
720 1038 3.118920 CCATACAACATGTACGTCCCAGA 60.119 47.826 0.00 0.00 35.42 3.86
722 1040 5.221362 CCATACAACATGTACGTCCCAGATA 60.221 44.000 0.00 0.00 35.42 1.98
724 1042 5.155278 ACAACATGTACGTCCCAGATAAA 57.845 39.130 0.00 0.00 0.00 1.40
725 1043 5.175859 ACAACATGTACGTCCCAGATAAAG 58.824 41.667 0.00 0.00 0.00 1.85
728 1046 4.141711 ACATGTACGTCCCAGATAAAGCAT 60.142 41.667 0.00 0.00 0.00 3.79
731 1049 3.845781 ACGTCCCAGATAAAGCATGAT 57.154 42.857 0.00 0.00 0.00 2.45
733 1051 5.489792 ACGTCCCAGATAAAGCATGATAT 57.510 39.130 0.00 0.00 0.00 1.63
735 1053 6.634805 ACGTCCCAGATAAAGCATGATATAG 58.365 40.000 0.00 0.00 0.00 1.31
736 1054 6.211584 ACGTCCCAGATAAAGCATGATATAGT 59.788 38.462 0.00 0.00 0.00 2.12
737 1055 7.396339 ACGTCCCAGATAAAGCATGATATAGTA 59.604 37.037 0.00 0.00 0.00 1.82
738 1056 8.417106 CGTCCCAGATAAAGCATGATATAGTAT 58.583 37.037 0.00 0.00 0.00 2.12
739 1057 9.757227 GTCCCAGATAAAGCATGATATAGTATC 57.243 37.037 0.00 0.00 0.00 2.24
740 1058 9.720874 TCCCAGATAAAGCATGATATAGTATCT 57.279 33.333 0.00 0.00 0.00 1.98
760 1080 9.308000 AGTATCTACAATTAGGGAGATCTTCTG 57.692 37.037 0.00 0.00 31.25 3.02
765 1085 9.672673 CTACAATTAGGGAGATCTTCTGAAAAA 57.327 33.333 0.00 0.00 0.00 1.94
807 1148 4.390909 ACGAAATGAACGGGTGATAAAGTC 59.609 41.667 0.00 0.00 34.93 3.01
820 1161 4.806247 GTGATAAAGTCCTCAGACATTCCG 59.194 45.833 0.00 0.00 46.15 4.30
824 1165 1.678627 AGTCCTCAGACATTCCGATCG 59.321 52.381 8.51 8.51 46.15 3.69
829 1170 0.387202 CAGACATTCCGATCGAGGCT 59.613 55.000 18.66 8.03 0.00 4.58
830 1171 0.671251 AGACATTCCGATCGAGGCTC 59.329 55.000 18.66 3.87 0.00 4.70
832 1173 0.757188 ACATTCCGATCGAGGCTCCT 60.757 55.000 18.66 0.00 0.00 3.69
833 1174 0.390860 CATTCCGATCGAGGCTCCTT 59.609 55.000 18.66 0.00 0.00 3.36
834 1175 1.123928 ATTCCGATCGAGGCTCCTTT 58.876 50.000 18.66 0.00 0.00 3.11
835 1176 0.902531 TTCCGATCGAGGCTCCTTTT 59.097 50.000 18.66 0.00 0.00 2.27
922 3532 2.256174 CAAGCATCCATCAAACAAGCG 58.744 47.619 0.00 0.00 0.00 4.68
933 3543 0.381801 AAACAAGCGCAAGTCCACAG 59.618 50.000 11.47 0.00 41.68 3.66
954 3580 2.223548 GCACACAGCAAACACATCTCAA 60.224 45.455 0.00 0.00 44.79 3.02
955 3581 3.551454 GCACACAGCAAACACATCTCAAT 60.551 43.478 0.00 0.00 44.79 2.57
956 3582 4.613944 CACACAGCAAACACATCTCAATT 58.386 39.130 0.00 0.00 0.00 2.32
957 3583 4.678287 CACACAGCAAACACATCTCAATTC 59.322 41.667 0.00 0.00 0.00 2.17
958 3584 4.581824 ACACAGCAAACACATCTCAATTCT 59.418 37.500 0.00 0.00 0.00 2.40
959 3585 5.152097 CACAGCAAACACATCTCAATTCTC 58.848 41.667 0.00 0.00 0.00 2.87
960 3586 4.823442 ACAGCAAACACATCTCAATTCTCA 59.177 37.500 0.00 0.00 0.00 3.27
961 3587 5.152097 CAGCAAACACATCTCAATTCTCAC 58.848 41.667 0.00 0.00 0.00 3.51
1312 3943 1.226974 CGCATCTGGGAGGTACGTG 60.227 63.158 0.00 0.00 0.00 4.49
1315 3955 0.249120 CATCTGGGAGGTACGTGCAA 59.751 55.000 5.86 0.00 0.00 4.08
1325 3973 2.892852 AGGTACGTGCAACACCTACTAA 59.107 45.455 12.26 0.00 41.03 2.24
1329 3977 4.589216 ACGTGCAACACCTACTAACTAA 57.411 40.909 0.00 0.00 35.74 2.24
1331 3979 3.676646 CGTGCAACACCTACTAACTAACC 59.323 47.826 0.00 0.00 35.74 2.85
1439 4103 2.994995 TGGACGCGGACATCCAGT 60.995 61.111 12.47 0.00 40.17 4.00
1471 4135 3.261897 ACATAGACCACCTCTTTGACCTG 59.738 47.826 0.00 0.00 33.39 4.00
1489 4153 1.698532 CTGGAGATGGGCAGCTTCTAT 59.301 52.381 0.00 0.00 0.00 1.98
1729 4396 1.374758 CGCCGAGCAGGACTTTCTT 60.375 57.895 2.12 0.00 45.00 2.52
1883 4552 2.548057 TGCTTTGGTCTTTGTCATCGTC 59.452 45.455 0.00 0.00 0.00 4.20
1892 4579 4.929808 GTCTTTGTCATCGTCCTTACACAT 59.070 41.667 0.00 0.00 0.00 3.21
1893 4580 4.929211 TCTTTGTCATCGTCCTTACACATG 59.071 41.667 0.00 0.00 0.00 3.21
1894 4581 2.616960 TGTCATCGTCCTTACACATGC 58.383 47.619 0.00 0.00 0.00 4.06
1895 4582 2.028567 TGTCATCGTCCTTACACATGCA 60.029 45.455 0.00 0.00 0.00 3.96
1907 4595 8.026607 GTCCTTACACATGCAAAGCTTAATTTA 58.973 33.333 0.00 0.00 0.00 1.40
1908 4596 8.580720 TCCTTACACATGCAAAGCTTAATTTAA 58.419 29.630 0.00 0.00 0.00 1.52
1909 4597 9.202273 CCTTACACATGCAAAGCTTAATTTAAA 57.798 29.630 0.00 0.00 0.00 1.52
1913 4601 8.711457 ACACATGCAAAGCTTAATTTAAATGTC 58.289 29.630 0.00 0.00 30.72 3.06
1914 4602 8.928733 CACATGCAAAGCTTAATTTAAATGTCT 58.071 29.630 0.00 0.00 30.72 3.41
1915 4603 9.143631 ACATGCAAAGCTTAATTTAAATGTCTC 57.856 29.630 0.00 0.00 28.67 3.36
1916 4604 7.795431 TGCAAAGCTTAATTTAAATGTCTCG 57.205 32.000 0.00 0.00 0.00 4.04
1917 4605 6.307800 TGCAAAGCTTAATTTAAATGTCTCGC 59.692 34.615 0.00 1.43 0.00 5.03
1918 4606 6.237569 GCAAAGCTTAATTTAAATGTCTCGCC 60.238 38.462 0.00 0.00 0.00 5.54
1919 4607 6.759497 AAGCTTAATTTAAATGTCTCGCCT 57.241 33.333 0.00 0.00 0.00 5.52
1920 4608 6.124088 AGCTTAATTTAAATGTCTCGCCTG 57.876 37.500 0.39 0.00 0.00 4.85
1921 4609 5.880332 AGCTTAATTTAAATGTCTCGCCTGA 59.120 36.000 0.39 0.00 0.00 3.86
1922 4610 6.543831 AGCTTAATTTAAATGTCTCGCCTGAT 59.456 34.615 0.39 0.00 0.00 2.90
1923 4611 6.853362 GCTTAATTTAAATGTCTCGCCTGATC 59.147 38.462 0.39 0.00 0.00 2.92
1954 4657 2.054453 GCTTCCATGGCAGGGTTCC 61.054 63.158 18.88 3.61 0.00 3.62
2023 4726 4.008330 ACATCAAGATGCTGGTCAAGAAG 58.992 43.478 9.85 0.00 42.39 2.85
2155 4858 2.233654 GCCATCAGCTGCGTAGTCG 61.234 63.158 9.47 0.00 38.99 4.18
2230 4939 7.928103 TCAGAGATTTCCTCAGTACGTAATAC 58.072 38.462 0.00 0.00 44.40 1.89
2294 5010 8.179148 GATCAATCGATCATATACAGTGTTCC 57.821 38.462 0.00 0.00 46.33 3.62
2298 5014 8.830580 CAATCGATCATATACAGTGTTCCTTTT 58.169 33.333 0.00 0.00 0.00 2.27
2318 5034 1.452110 TTGATTGAGGTGCGGTCATG 58.548 50.000 0.00 0.00 0.00 3.07
2330 5046 2.428890 TGCGGTCATGGTGTTTTTCTTT 59.571 40.909 0.00 0.00 0.00 2.52
2369 5179 9.332502 AGGATTTTGTAAATACGTATATGCACA 57.667 29.630 8.83 7.76 0.00 4.57
2402 5219 9.111613 GTGTAACTATATAGATCGACCTGCTAT 57.888 37.037 16.79 0.00 0.00 2.97
2405 5227 7.949903 ACTATATAGATCGACCTGCTATACG 57.050 40.000 16.79 0.00 31.90 3.06
2406 5228 7.499292 ACTATATAGATCGACCTGCTATACGT 58.501 38.462 16.79 0.00 31.90 3.57
2423 5245 1.068588 ACGTACGTATGCATGGCTGAT 59.931 47.619 21.41 0.00 0.00 2.90
2426 5248 2.169832 ACGTATGCATGGCTGATACC 57.830 50.000 10.16 0.00 0.00 2.73
2431 5253 4.036734 CGTATGCATGGCTGATACCTTTTT 59.963 41.667 10.16 0.00 0.00 1.94
2433 5255 2.496871 TGCATGGCTGATACCTTTTTGG 59.503 45.455 0.00 0.00 42.93 3.28
2437 5259 5.353938 CATGGCTGATACCTTTTTGGAATG 58.646 41.667 0.00 0.00 39.71 2.67
2438 5260 3.768757 TGGCTGATACCTTTTTGGAATGG 59.231 43.478 0.00 0.00 39.71 3.16
2439 5261 4.023291 GGCTGATACCTTTTTGGAATGGA 58.977 43.478 0.00 0.00 39.71 3.41
2440 5262 4.466015 GGCTGATACCTTTTTGGAATGGAA 59.534 41.667 0.00 0.00 39.71 3.53
2441 5263 5.410924 GCTGATACCTTTTTGGAATGGAAC 58.589 41.667 0.00 0.00 39.71 3.62
2442 5264 5.185828 GCTGATACCTTTTTGGAATGGAACT 59.814 40.000 0.00 0.00 39.71 3.01
2443 5265 6.377146 GCTGATACCTTTTTGGAATGGAACTA 59.623 38.462 0.00 0.00 39.71 2.24
2444 5266 7.068716 GCTGATACCTTTTTGGAATGGAACTAT 59.931 37.037 0.00 0.00 39.71 2.12
2445 5267 8.292444 TGATACCTTTTTGGAATGGAACTATG 57.708 34.615 0.00 0.00 39.71 2.23
2446 5268 7.893302 TGATACCTTTTTGGAATGGAACTATGT 59.107 33.333 0.00 0.00 39.71 2.29
2447 5269 9.403583 GATACCTTTTTGGAATGGAACTATGTA 57.596 33.333 0.00 0.00 39.71 2.29
2448 5270 9.762381 ATACCTTTTTGGAATGGAACTATGTAA 57.238 29.630 0.00 0.00 39.71 2.41
2449 5271 8.122472 ACCTTTTTGGAATGGAACTATGTAAG 57.878 34.615 0.00 0.00 39.71 2.34
2521 5344 1.202486 TGTGATCGCCGTATCCCTTTC 60.202 52.381 3.31 0.00 0.00 2.62
2551 5400 1.257750 GGATTGGTGTTCCCCTTGCC 61.258 60.000 0.00 0.00 0.00 4.52
2590 5439 1.414919 TGTCCTACTTTGCGACCAACT 59.585 47.619 0.00 0.00 0.00 3.16
2599 5448 1.334160 TGCGACCAACTCCAACTAGA 58.666 50.000 0.00 0.00 0.00 2.43
2600 5449 1.272490 TGCGACCAACTCCAACTAGAG 59.728 52.381 0.00 0.00 39.91 2.43
2603 5452 3.672781 GCGACCAACTCCAACTAGAGTAC 60.673 52.174 0.00 0.00 46.44 2.73
2606 5455 5.163774 CGACCAACTCCAACTAGAGTACTAC 60.164 48.000 0.00 0.00 46.44 2.73
2607 5456 4.699257 ACCAACTCCAACTAGAGTACTACG 59.301 45.833 0.00 0.00 46.44 3.51
2608 5457 4.699257 CCAACTCCAACTAGAGTACTACGT 59.301 45.833 0.00 0.00 46.44 3.57
2609 5458 5.877012 CCAACTCCAACTAGAGTACTACGTA 59.123 44.000 0.00 0.00 46.44 3.57
2610 5459 6.036953 CCAACTCCAACTAGAGTACTACGTAG 59.963 46.154 20.97 20.97 46.44 3.51
2611 5460 6.293004 ACTCCAACTAGAGTACTACGTAGT 57.707 41.667 29.62 29.62 45.31 2.73
2612 5461 7.411486 ACTCCAACTAGAGTACTACGTAGTA 57.589 40.000 27.51 27.51 45.31 1.82
2630 5479 8.367943 ACGTAGTAGAGTAGTATCATCTGTTG 57.632 38.462 0.00 0.00 41.94 3.33
2702 5551 1.393883 GAGATGGTCCGTTTCTTTCGC 59.606 52.381 0.00 0.00 0.00 4.70
2719 5568 2.809601 CTTGGACTTAGCGCGCGT 60.810 61.111 32.35 18.35 0.00 6.01
2720 5569 2.789203 CTTGGACTTAGCGCGCGTC 61.789 63.158 32.35 25.30 0.00 5.19
2721 5570 4.789075 TGGACTTAGCGCGCGTCC 62.789 66.667 35.28 35.28 45.76 4.79
2959 6035 0.666577 CAACGACTGGTTCCTCGTCC 60.667 60.000 6.60 0.00 42.21 4.79
2961 6037 1.111116 ACGACTGGTTCCTCGTCCAA 61.111 55.000 0.00 0.00 38.80 3.53
2973 6049 2.404215 CTCGTCCAATTCGTCAACACT 58.596 47.619 0.00 0.00 0.00 3.55
3016 6092 4.181010 CCATGGCACGGGGAGGAG 62.181 72.222 0.00 0.00 0.00 3.69
3017 6093 3.083349 CATGGCACGGGGAGGAGA 61.083 66.667 0.00 0.00 0.00 3.71
3151 6270 1.838568 CGTGATCGGGATGCATGCAG 61.839 60.000 26.69 16.27 0.00 4.41
3152 6271 1.228033 TGATCGGGATGCATGCAGG 60.228 57.895 26.69 14.60 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 7.984050 CCCATACTGTTATATATCCAGAGCAAG 59.016 40.741 15.62 4.46 0.00 4.01
66 67 8.853126 CATGATCAAATTGACCCATACTGTTAT 58.147 33.333 0.00 0.00 0.00 1.89
67 68 7.285172 CCATGATCAAATTGACCCATACTGTTA 59.715 37.037 0.00 0.00 0.00 2.41
68 69 6.097270 CCATGATCAAATTGACCCATACTGTT 59.903 38.462 0.00 0.00 0.00 3.16
73 74 7.122048 TGTAACCATGATCAAATTGACCCATA 58.878 34.615 0.00 0.00 0.00 2.74
78 79 9.683069 GGATAATGTAACCATGATCAAATTGAC 57.317 33.333 0.00 0.00 39.78 3.18
150 155 5.084722 GCGAGATAATTAATCAGCACATGC 58.915 41.667 0.00 0.00 39.13 4.06
329 343 9.106070 GGTGAAATCTACACCGTATTTATTTCT 57.894 33.333 0.00 0.00 46.15 2.52
347 361 1.411493 GAGACGCGTCCGGTGAAATC 61.411 60.000 34.08 19.05 39.22 2.17
387 405 1.272480 TGGTGGAGTGCAGTCTAGCTA 60.272 52.381 29.60 17.56 34.99 3.32
400 418 2.171003 GGGTGAAATTTCCTGGTGGAG 58.829 52.381 15.48 0.00 44.24 3.86
404 422 2.450886 AGGAAGGGTGAAATTTCCTGGT 59.549 45.455 15.48 0.00 46.70 4.00
405 423 3.175438 AGGAAGGGTGAAATTTCCTGG 57.825 47.619 15.48 0.00 46.70 4.45
421 439 0.883153 TCGTCGATCGGTTTCAGGAA 59.117 50.000 16.41 0.00 40.32 3.36
449 467 4.496336 ATTGGAGCAGGAGCCCGC 62.496 66.667 0.00 0.00 43.56 6.13
479 497 0.036164 TGTTCACCGACCCATTCCAG 59.964 55.000 0.00 0.00 0.00 3.86
562 871 9.636789 TTTTGACTCTGGTATATGCTACTACTA 57.363 33.333 0.00 0.00 0.00 1.82
563 872 8.414778 GTTTTGACTCTGGTATATGCTACTACT 58.585 37.037 0.00 0.00 0.00 2.57
565 874 8.301252 TGTTTTGACTCTGGTATATGCTACTA 57.699 34.615 0.00 0.00 0.00 1.82
567 876 7.265673 TCTGTTTTGACTCTGGTATATGCTAC 58.734 38.462 0.00 0.00 0.00 3.58
580 889 5.504665 CGGATGGCATATTCTGTTTTGACTC 60.505 44.000 0.00 0.00 0.00 3.36
589 898 3.205338 TGTCAACGGATGGCATATTCTG 58.795 45.455 0.00 0.00 39.16 3.02
661 979 7.565398 TCTTAATTAGAGAGGGTAAGCAGTGAT 59.435 37.037 0.00 0.00 0.00 3.06
667 985 6.864165 CACGATCTTAATTAGAGAGGGTAAGC 59.136 42.308 0.00 0.00 36.02 3.09
710 1028 4.955811 ATCATGCTTTATCTGGGACGTA 57.044 40.909 0.00 0.00 0.00 3.57
711 1029 3.845781 ATCATGCTTTATCTGGGACGT 57.154 42.857 0.00 0.00 0.00 4.34
712 1030 6.634805 ACTATATCATGCTTTATCTGGGACG 58.365 40.000 0.00 0.00 0.00 4.79
714 1032 9.720874 AGATACTATATCATGCTTTATCTGGGA 57.279 33.333 0.00 0.00 0.00 4.37
735 1053 9.303116 TCAGAAGATCTCCCTAATTGTAGATAC 57.697 37.037 0.00 0.00 0.00 2.24
736 1054 9.883293 TTCAGAAGATCTCCCTAATTGTAGATA 57.117 33.333 0.00 0.00 0.00 1.98
737 1055 8.789767 TTCAGAAGATCTCCCTAATTGTAGAT 57.210 34.615 0.00 0.00 0.00 1.98
738 1056 8.609617 TTTCAGAAGATCTCCCTAATTGTAGA 57.390 34.615 0.00 0.00 0.00 2.59
739 1057 9.672673 TTTTTCAGAAGATCTCCCTAATTGTAG 57.327 33.333 0.00 0.00 0.00 2.74
775 1095 3.567530 CCGTTCATTTCGTTTTTACCCC 58.432 45.455 0.00 0.00 0.00 4.95
777 1097 3.976306 CACCCGTTCATTTCGTTTTTACC 59.024 43.478 0.00 0.00 0.00 2.85
807 1148 1.000827 CCTCGATCGGAATGTCTGAGG 60.001 57.143 16.41 7.29 34.87 3.86
834 1175 3.058085 GGTCGGAATGGAAAGCGTAAAAA 60.058 43.478 0.00 0.00 0.00 1.94
835 1176 2.485038 GGTCGGAATGGAAAGCGTAAAA 59.515 45.455 0.00 0.00 0.00 1.52
922 3532 1.650912 CTGTGTGCTGTGGACTTGC 59.349 57.895 0.00 0.00 0.00 4.01
933 3543 1.334556 TGAGATGTGTTTGCTGTGTGC 59.665 47.619 0.00 0.00 43.25 4.57
954 3580 2.420687 GCTTCGAAGGATGGGTGAGAAT 60.421 50.000 25.77 0.00 0.00 2.40
955 3581 1.066143 GCTTCGAAGGATGGGTGAGAA 60.066 52.381 25.77 0.00 0.00 2.87
956 3582 0.537188 GCTTCGAAGGATGGGTGAGA 59.463 55.000 25.77 0.00 0.00 3.27
957 3583 0.250234 TGCTTCGAAGGATGGGTGAG 59.750 55.000 25.77 0.00 0.00 3.51
958 3584 0.690192 TTGCTTCGAAGGATGGGTGA 59.310 50.000 25.77 4.83 0.00 4.02
959 3585 1.089920 CTTGCTTCGAAGGATGGGTG 58.910 55.000 25.77 8.20 0.00 4.61
960 3586 0.984230 TCTTGCTTCGAAGGATGGGT 59.016 50.000 25.77 0.00 0.00 4.51
961 3587 1.339055 TGTCTTGCTTCGAAGGATGGG 60.339 52.381 25.77 15.70 0.00 4.00
1312 3943 4.502016 GGAGGTTAGTTAGTAGGTGTTGC 58.498 47.826 0.00 0.00 0.00 4.17
1315 3955 2.757314 GCGGAGGTTAGTTAGTAGGTGT 59.243 50.000 0.00 0.00 0.00 4.16
1325 3973 1.568504 TCCAAGATGCGGAGGTTAGT 58.431 50.000 0.00 0.00 0.00 2.24
1329 3977 1.043116 TCGATCCAAGATGCGGAGGT 61.043 55.000 0.00 0.00 35.56 3.85
1331 3979 1.797046 CAATCGATCCAAGATGCGGAG 59.203 52.381 0.00 0.00 35.56 4.63
1439 4103 3.575256 AGGTGGTCTATGTTGTCGTACAA 59.425 43.478 0.00 0.00 35.42 2.41
1471 4135 1.881498 GCATAGAAGCTGCCCATCTCC 60.881 57.143 0.00 0.00 33.44 3.71
1729 4396 3.070446 ACACGTCCCTGAAGAACATGTTA 59.930 43.478 11.95 0.00 0.00 2.41
1862 4531 2.548057 GACGATGACAAAGACCAAAGCA 59.452 45.455 0.00 0.00 0.00 3.91
1863 4532 2.095718 GGACGATGACAAAGACCAAAGC 60.096 50.000 0.00 0.00 0.00 3.51
1864 4533 3.403038 AGGACGATGACAAAGACCAAAG 58.597 45.455 0.00 0.00 0.00 2.77
1865 4534 3.485463 AGGACGATGACAAAGACCAAA 57.515 42.857 0.00 0.00 0.00 3.28
1866 4535 3.485463 AAGGACGATGACAAAGACCAA 57.515 42.857 0.00 0.00 0.00 3.67
1867 4536 3.322541 TGTAAGGACGATGACAAAGACCA 59.677 43.478 0.00 0.00 0.00 4.02
1868 4537 3.678548 GTGTAAGGACGATGACAAAGACC 59.321 47.826 0.00 0.00 0.00 3.85
1869 4538 4.304110 TGTGTAAGGACGATGACAAAGAC 58.696 43.478 0.00 0.00 0.00 3.01
1870 4539 4.594123 TGTGTAAGGACGATGACAAAGA 57.406 40.909 0.00 0.00 0.00 2.52
1883 4552 8.755696 TTAAATTAAGCTTTGCATGTGTAAGG 57.244 30.769 3.20 0.00 0.00 2.69
1892 4579 6.307800 GCGAGACATTTAAATTAAGCTTTGCA 59.692 34.615 3.20 0.00 0.00 4.08
1893 4580 6.237569 GGCGAGACATTTAAATTAAGCTTTGC 60.238 38.462 3.20 3.07 0.00 3.68
1894 4581 7.008628 CAGGCGAGACATTTAAATTAAGCTTTG 59.991 37.037 3.20 0.00 0.00 2.77
1895 4582 7.029563 CAGGCGAGACATTTAAATTAAGCTTT 58.970 34.615 3.20 0.00 0.00 3.51
1907 4595 3.548745 TGATGATCAGGCGAGACATTT 57.451 42.857 0.09 0.00 0.00 2.32
1908 4596 3.070590 TCATGATGATCAGGCGAGACATT 59.929 43.478 1.61 0.00 0.00 2.71
1909 4597 2.631545 TCATGATGATCAGGCGAGACAT 59.368 45.455 1.61 0.00 0.00 3.06
1920 4608 4.251268 TGGAAGCATCGATCATGATGATC 58.749 43.478 22.32 22.32 43.70 2.92
1921 4609 4.281898 TGGAAGCATCGATCATGATGAT 57.718 40.909 14.30 7.81 46.23 2.45
1922 4610 3.756933 TGGAAGCATCGATCATGATGA 57.243 42.857 14.30 11.23 46.98 2.92
1923 4611 3.127030 CCATGGAAGCATCGATCATGATG 59.873 47.826 14.30 5.89 46.78 3.07
1954 4657 1.375523 GGTGTACCTCCACGGCTTG 60.376 63.158 0.00 0.00 36.16 4.01
2163 4866 8.603242 ATTTATTAGAACATACGCCTAACTGG 57.397 34.615 0.00 0.00 39.35 4.00
2298 5014 1.811965 CATGACCGCACCTCAATCAAA 59.188 47.619 0.00 0.00 0.00 2.69
2310 5026 2.793278 AAGAAAAACACCATGACCGC 57.207 45.000 0.00 0.00 0.00 5.68
2356 5166 2.166050 ACCAACCGTGTGCATATACGTA 59.834 45.455 16.30 0.00 39.43 3.57
2369 5179 6.712095 TCGATCTATATAGTTACACCAACCGT 59.288 38.462 9.58 0.00 37.93 4.83
2379 5189 9.473640 CGTATAGCAGGTCGATCTATATAGTTA 57.526 37.037 9.58 0.00 30.70 2.24
2402 5219 1.677052 TCAGCCATGCATACGTACGTA 59.323 47.619 28.62 28.62 34.87 3.57
2403 5220 0.458260 TCAGCCATGCATACGTACGT 59.542 50.000 25.98 25.98 0.00 3.57
2405 5227 2.993899 GGTATCAGCCATGCATACGTAC 59.006 50.000 0.00 1.99 0.00 3.67
2406 5228 2.897326 AGGTATCAGCCATGCATACGTA 59.103 45.455 0.00 0.00 0.00 3.57
2423 5245 9.238368 CTTACATAGTTCCATTCCAAAAAGGTA 57.762 33.333 0.00 0.00 39.02 3.08
2426 5248 7.830739 AGCTTACATAGTTCCATTCCAAAAAG 58.169 34.615 0.00 0.00 0.00 2.27
2431 5253 6.808321 ACTAGCTTACATAGTTCCATTCCA 57.192 37.500 0.00 0.00 29.01 3.53
2442 5264 9.043548 GGGGGAAATATCTTACTAGCTTACATA 57.956 37.037 0.00 0.00 0.00 2.29
2443 5265 7.919151 GGGGGAAATATCTTACTAGCTTACAT 58.081 38.462 0.00 0.00 0.00 2.29
2444 5266 7.312415 GGGGGAAATATCTTACTAGCTTACA 57.688 40.000 0.00 0.00 0.00 2.41
2465 5287 1.906574 TCTACAAGCAAGTAGTGGGGG 59.093 52.381 13.24 0.00 41.68 5.40
2469 5291 5.349817 CCACAGAATCTACAAGCAAGTAGTG 59.650 44.000 13.24 8.23 41.68 2.74
2470 5292 5.012148 ACCACAGAATCTACAAGCAAGTAGT 59.988 40.000 13.24 0.00 41.68 2.73
2471 5293 5.349817 CACCACAGAATCTACAAGCAAGTAG 59.650 44.000 8.76 8.76 42.21 2.57
2472 5294 5.221641 ACACCACAGAATCTACAAGCAAGTA 60.222 40.000 0.00 0.00 0.00 2.24
2473 5295 4.067896 CACCACAGAATCTACAAGCAAGT 58.932 43.478 0.00 0.00 0.00 3.16
2474 5296 4.067896 ACACCACAGAATCTACAAGCAAG 58.932 43.478 0.00 0.00 0.00 4.01
2475 5297 4.065088 GACACCACAGAATCTACAAGCAA 58.935 43.478 0.00 0.00 0.00 3.91
2521 5344 6.209391 GGGGAACACCAATCCAATGAATATAG 59.791 42.308 0.00 0.00 42.91 1.31
2551 5400 1.455786 CAAACTCAAGGCACGTAGACG 59.544 52.381 0.00 0.00 46.33 4.18
2590 5439 7.340743 ACTCTACTACGTAGTACTCTAGTTGGA 59.659 40.741 27.51 18.88 45.11 3.53
2603 5452 9.695526 AACAGATGATACTACTCTACTACGTAG 57.304 37.037 20.97 20.97 39.14 3.51
2606 5455 7.571613 GCCAACAGATGATACTACTCTACTACG 60.572 44.444 0.00 0.00 0.00 3.51
2607 5456 7.446013 AGCCAACAGATGATACTACTCTACTAC 59.554 40.741 0.00 0.00 0.00 2.73
2608 5457 7.519057 AGCCAACAGATGATACTACTCTACTA 58.481 38.462 0.00 0.00 0.00 1.82
2609 5458 6.369629 AGCCAACAGATGATACTACTCTACT 58.630 40.000 0.00 0.00 0.00 2.57
2610 5459 6.263392 TGAGCCAACAGATGATACTACTCTAC 59.737 42.308 0.00 0.00 0.00 2.59
2611 5460 6.263392 GTGAGCCAACAGATGATACTACTCTA 59.737 42.308 0.00 0.00 0.00 2.43
2612 5461 5.068460 GTGAGCCAACAGATGATACTACTCT 59.932 44.000 0.00 0.00 0.00 3.24
2613 5462 5.068460 AGTGAGCCAACAGATGATACTACTC 59.932 44.000 0.00 0.00 0.00 2.59
2621 5470 1.256812 TCGAGTGAGCCAACAGATGA 58.743 50.000 0.00 0.00 0.00 2.92
2622 5471 2.200067 GATCGAGTGAGCCAACAGATG 58.800 52.381 0.00 0.00 0.00 2.90
2624 5473 1.256812 TGATCGAGTGAGCCAACAGA 58.743 50.000 0.00 0.00 0.00 3.41
2625 5474 1.998315 CTTGATCGAGTGAGCCAACAG 59.002 52.381 1.30 0.00 0.00 3.16
2630 5479 2.879002 TGATCTTGATCGAGTGAGCC 57.121 50.000 9.87 0.00 0.00 4.70
2702 5551 2.789203 GACGCGCGCTAAGTCCAAG 61.789 63.158 32.58 12.54 0.00 3.61
2719 5568 4.747529 TCGACGGAGAGCGACGGA 62.748 66.667 0.00 0.00 33.84 4.69
2720 5569 4.517703 GTCGACGGAGAGCGACGG 62.518 72.222 0.00 0.00 44.57 4.79
2820 5670 2.105128 CAGGAGCATCGTCGTCCC 59.895 66.667 0.00 0.00 34.37 4.46
2836 5687 0.669318 GACATGCCGAGGACGAAACA 60.669 55.000 0.00 0.00 42.66 2.83
2931 5783 1.153823 CCAGTCGTTGTAGGAGCGG 60.154 63.158 0.00 0.00 0.00 5.52
2959 6035 1.148310 AGCGGAGTGTTGACGAATTG 58.852 50.000 0.00 0.00 0.00 2.32
2961 6037 1.736032 GCTAGCGGAGTGTTGACGAAT 60.736 52.381 0.00 0.00 0.00 3.34
3016 6092 1.025113 GCTACGTTTTCCAGGCCCTC 61.025 60.000 0.00 0.00 0.00 4.30
3017 6093 1.002502 GCTACGTTTTCCAGGCCCT 60.003 57.895 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.