Multiple sequence alignment - TraesCS3D01G248500

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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 TraesCS3D01G248500 chr3D 100.000 4316 0 0 1 4316 347453839 347458154 0.000000e+00 7971
1 TraesCS3D01G248500 chr3D 99.655 290 1 0 4027 4316 116222562 116222273 8.220000e-147 531
2 TraesCS3D01G248500 chr3B 95.499 1844 75 6 1604 3443 447262874 447264713 0.000000e+00 2939
3 TraesCS3D01G248500 chr3B 91.001 1189 45 28 428 1593 447261742 447262891 0.000000e+00 1546
4 TraesCS3D01G248500 chr3B 94.068 236 12 2 84 318 447259795 447260029 1.480000e-94 357
5 TraesCS3D01G248500 chr3B 92.500 120 9 0 315 434 447260063 447260182 5.740000e-39 172
6 TraesCS3D01G248500 chr3A 93.424 1399 66 6 2045 3443 466645621 466646993 0.000000e+00 2050
7 TraesCS3D01G248500 chr3A 86.211 1813 110 49 288 2037 466643836 466645571 0.000000e+00 1834
8 TraesCS3D01G248500 chr3A 93.033 732 48 3 3442 4171 165024656 165023926 0.000000e+00 1066
9 TraesCS3D01G248500 chr3A 88.983 118 10 2 127 241 466643719 466643836 4.500000e-30 143
10 TraesCS3D01G248500 chr5D 93.166 878 56 4 3443 4316 408106272 408107149 0.000000e+00 1286
11 TraesCS3D01G248500 chr7D 93.037 876 59 2 3443 4316 368427177 368426302 0.000000e+00 1279
12 TraesCS3D01G248500 chr7D 91.628 872 68 4 3443 4313 263387338 263388205 0.000000e+00 1201
13 TraesCS3D01G248500 chr2D 89.468 883 84 8 3440 4315 292063974 292064854 0.000000e+00 1107
14 TraesCS3D01G248500 chr2D 89.588 874 81 8 3443 4315 72856208 72855344 0.000000e+00 1101
15 TraesCS3D01G248500 chr2D 98.646 591 7 1 3441 4030 114076199 114075609 0.000000e+00 1046
16 TraesCS3D01G248500 chr2D 88.973 789 77 6 3531 4316 514282638 514281857 0.000000e+00 966
17 TraesCS3D01G248500 chr7A 91.598 726 60 1 3443 4167 190830770 190830045 0.000000e+00 1002
18 TraesCS3D01G248500 chr6B 94.619 446 24 0 3871 4316 167799354 167798909 0.000000e+00 691
19 TraesCS3D01G248500 chr7B 93.878 49 3 0 499 547 689942333 689942381 1.660000e-09 75


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 TraesCS3D01G248500 chr3D 347453839 347458154 4315 False 7971.000000 7971 100.000000 1 4316 1 chr3D.!!$F1 4315
1 TraesCS3D01G248500 chr3B 447259795 447264713 4918 False 1253.500000 2939 93.267000 84 3443 4 chr3B.!!$F1 3359
2 TraesCS3D01G248500 chr3A 466643719 466646993 3274 False 1342.333333 2050 89.539333 127 3443 3 chr3A.!!$F1 3316
3 TraesCS3D01G248500 chr3A 165023926 165024656 730 True 1066.000000 1066 93.033000 3442 4171 1 chr3A.!!$R1 729
4 TraesCS3D01G248500 chr5D 408106272 408107149 877 False 1286.000000 1286 93.166000 3443 4316 1 chr5D.!!$F1 873
5 TraesCS3D01G248500 chr7D 368426302 368427177 875 True 1279.000000 1279 93.037000 3443 4316 1 chr7D.!!$R1 873
6 TraesCS3D01G248500 chr7D 263387338 263388205 867 False 1201.000000 1201 91.628000 3443 4313 1 chr7D.!!$F1 870
7 TraesCS3D01G248500 chr2D 292063974 292064854 880 False 1107.000000 1107 89.468000 3440 4315 1 chr2D.!!$F1 875
8 TraesCS3D01G248500 chr2D 72855344 72856208 864 True 1101.000000 1101 89.588000 3443 4315 1 chr2D.!!$R1 872
9 TraesCS3D01G248500 chr2D 114075609 114076199 590 True 1046.000000 1046 98.646000 3441 4030 1 chr2D.!!$R2 589
10 TraesCS3D01G248500 chr2D 514281857 514282638 781 True 966.000000 966 88.973000 3531 4316 1 chr2D.!!$R3 785
11 TraesCS3D01G248500 chr7A 190830045 190830770 725 True 1002.000000 1002 91.598000 3443 4167 1 chr7A.!!$R1 724

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
109 110 0.179000 ATCTTGACCCTTAGCGCAGG 59.821 55.0 11.47 8.78 0.00 4.85 F
771 2398 0.472471 ACAATAGGGCCATACGTGGG 59.528 55.0 6.18 0.00 46.14 4.61 F
1323 2970 0.249826 TGACTCAGTTCGTGCATGCA 60.250 50.0 18.46 18.46 0.00 3.96 F
1392 3041 0.378257 ACAAACACAAGAGCGTGCAG 59.622 50.0 0.00 0.00 40.73 4.41 F
3048 4776 0.697658 TCATTGTCCATGGCCTCACA 59.302 50.0 6.96 2.95 33.07 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 2971 0.178995 TGTGCATCTTGGTCTTGGCA 60.179 50.000 0.00 0.00 0.00 4.92 R
1800 3463 2.159028 GCTGACCTAGAAACTAGGCCAG 60.159 54.545 25.75 25.75 44.72 4.85 R
3026 4754 0.257039 GAGGCCATGGACAATGAGGT 59.743 55.000 22.78 0.00 38.72 3.85 R
3276 5004 1.197036 GTCCCAGTAACAAAGAAGCGC 59.803 52.381 0.00 0.00 0.00 5.92 R
3872 5602 0.329596 GGAATGAGCCTCTGTTGGGT 59.670 55.000 0.00 0.00 40.97 4.51 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
23 24 5.674525 ACTTCTCACTCAAAACAGTCATCA 58.325 37.500 0.00 0.00 0.00 3.07
24 25 6.294473 ACTTCTCACTCAAAACAGTCATCAT 58.706 36.000 0.00 0.00 0.00 2.45
25 26 6.204301 ACTTCTCACTCAAAACAGTCATCATG 59.796 38.462 0.00 0.00 0.00 3.07
26 27 5.857268 TCTCACTCAAAACAGTCATCATGA 58.143 37.500 0.00 0.00 0.00 3.07
27 28 5.930569 TCTCACTCAAAACAGTCATCATGAG 59.069 40.000 0.09 0.00 40.01 2.90
28 29 5.857268 TCACTCAAAACAGTCATCATGAGA 58.143 37.500 0.09 0.00 38.10 3.27
29 30 5.930569 TCACTCAAAACAGTCATCATGAGAG 59.069 40.000 0.09 0.70 38.10 3.20
30 31 5.930569 CACTCAAAACAGTCATCATGAGAGA 59.069 40.000 0.09 0.00 38.10 3.10
31 32 6.426025 CACTCAAAACAGTCATCATGAGAGAA 59.574 38.462 0.09 0.00 38.10 2.87
32 33 6.994496 ACTCAAAACAGTCATCATGAGAGAAA 59.006 34.615 0.09 0.00 38.10 2.52
33 34 7.500227 ACTCAAAACAGTCATCATGAGAGAAAA 59.500 33.333 0.09 0.00 38.10 2.29
34 35 8.400184 TCAAAACAGTCATCATGAGAGAAAAT 57.600 30.769 0.09 0.00 0.00 1.82
35 36 8.294577 TCAAAACAGTCATCATGAGAGAAAATG 58.705 33.333 0.09 4.90 0.00 2.32
36 37 7.756395 AAACAGTCATCATGAGAGAAAATGT 57.244 32.000 0.09 5.46 0.00 2.71
37 38 8.853077 AAACAGTCATCATGAGAGAAAATGTA 57.147 30.769 0.09 0.00 0.00 2.29
38 39 8.489990 AACAGTCATCATGAGAGAAAATGTAG 57.510 34.615 0.09 0.00 0.00 2.74
39 40 7.046652 ACAGTCATCATGAGAGAAAATGTAGG 58.953 38.462 0.09 0.00 0.00 3.18
40 41 7.093156 ACAGTCATCATGAGAGAAAATGTAGGA 60.093 37.037 0.09 0.00 0.00 2.94
41 42 7.767659 CAGTCATCATGAGAGAAAATGTAGGAA 59.232 37.037 0.09 0.00 0.00 3.36
42 43 8.492782 AGTCATCATGAGAGAAAATGTAGGAAT 58.507 33.333 0.09 0.00 0.00 3.01
43 44 8.772705 GTCATCATGAGAGAAAATGTAGGAATC 58.227 37.037 0.09 0.00 0.00 2.52
44 45 7.654923 TCATCATGAGAGAAAATGTAGGAATCG 59.345 37.037 0.09 0.00 0.00 3.34
45 46 7.112452 TCATGAGAGAAAATGTAGGAATCGA 57.888 36.000 0.00 0.00 0.00 3.59
46 47 7.555965 TCATGAGAGAAAATGTAGGAATCGAA 58.444 34.615 0.00 0.00 0.00 3.71
47 48 8.040727 TCATGAGAGAAAATGTAGGAATCGAAA 58.959 33.333 0.00 0.00 0.00 3.46
48 49 8.668353 CATGAGAGAAAATGTAGGAATCGAAAA 58.332 33.333 0.00 0.00 0.00 2.29
49 50 8.615878 TGAGAGAAAATGTAGGAATCGAAAAA 57.384 30.769 0.00 0.00 0.00 1.94
50 51 9.231297 TGAGAGAAAATGTAGGAATCGAAAAAT 57.769 29.630 0.00 0.00 0.00 1.82
59 60 7.693952 TGTAGGAATCGAAAAATATCAGTTGC 58.306 34.615 0.00 0.00 0.00 4.17
60 61 6.757897 AGGAATCGAAAAATATCAGTTGCA 57.242 33.333 0.00 0.00 0.00 4.08
61 62 7.338800 AGGAATCGAAAAATATCAGTTGCAT 57.661 32.000 0.00 0.00 0.00 3.96
62 63 7.198390 AGGAATCGAAAAATATCAGTTGCATG 58.802 34.615 0.00 0.00 0.00 4.06
63 64 7.067372 AGGAATCGAAAAATATCAGTTGCATGA 59.933 33.333 0.00 0.00 0.00 3.07
64 65 7.377928 GGAATCGAAAAATATCAGTTGCATGAG 59.622 37.037 0.00 0.00 31.44 2.90
65 66 6.122850 TCGAAAAATATCAGTTGCATGAGG 57.877 37.500 0.00 0.00 31.44 3.86
66 67 5.879777 TCGAAAAATATCAGTTGCATGAGGA 59.120 36.000 0.00 0.00 31.44 3.71
67 68 6.543465 TCGAAAAATATCAGTTGCATGAGGAT 59.457 34.615 0.00 0.00 31.44 3.24
68 69 7.714813 TCGAAAAATATCAGTTGCATGAGGATA 59.285 33.333 0.00 0.00 31.44 2.59
69 70 8.344831 CGAAAAATATCAGTTGCATGAGGATAA 58.655 33.333 0.00 0.00 31.44 1.75
70 71 9.674824 GAAAAATATCAGTTGCATGAGGATAAG 57.325 33.333 0.00 0.00 31.44 1.73
71 72 6.814506 AATATCAGTTGCATGAGGATAAGC 57.185 37.500 0.00 0.00 31.44 3.09
72 73 3.632643 TCAGTTGCATGAGGATAAGCA 57.367 42.857 0.00 0.00 34.79 3.91
73 74 3.954200 TCAGTTGCATGAGGATAAGCAA 58.046 40.909 0.00 0.00 43.90 3.91
77 78 4.454728 TTGCATGAGGATAAGCAAAACC 57.545 40.909 0.00 0.00 43.24 3.27
78 79 2.760092 TGCATGAGGATAAGCAAAACCC 59.240 45.455 0.00 0.00 33.48 4.11
79 80 2.101415 GCATGAGGATAAGCAAAACCCC 59.899 50.000 0.00 0.00 0.00 4.95
80 81 2.525105 TGAGGATAAGCAAAACCCCC 57.475 50.000 0.00 0.00 0.00 5.40
81 82 1.713647 TGAGGATAAGCAAAACCCCCA 59.286 47.619 0.00 0.00 0.00 4.96
82 83 2.110899 TGAGGATAAGCAAAACCCCCAA 59.889 45.455 0.00 0.00 0.00 4.12
109 110 0.179000 ATCTTGACCCTTAGCGCAGG 59.821 55.000 11.47 8.78 0.00 4.85
123 124 1.470890 GCGCAGGCATTTGGTAGTTAA 59.529 47.619 0.30 0.00 39.62 2.01
159 160 6.401047 TTTTCTCGGTGTATATACAGGAGG 57.599 41.667 27.49 16.01 37.98 4.30
227 228 3.459232 ACCTGTCGGTGACATATGATG 57.541 47.619 10.38 0.00 43.51 3.07
302 303 1.875420 TTGTTGCATGTGGCCATCGG 61.875 55.000 9.72 1.79 43.89 4.18
326 364 9.046296 CGGAAAAGAATGCAAGTAGTATAGATT 57.954 33.333 0.00 0.00 0.00 2.40
388 428 4.443978 AGGAGGTGGGAATACATTCATG 57.556 45.455 4.45 0.00 38.53 3.07
477 2101 5.582665 GGATACAACAAGAGCAAACTAGAGG 59.417 44.000 0.00 0.00 0.00 3.69
569 2193 4.564769 GCAGTCTCTGTTGCTTACTCATAC 59.435 45.833 0.00 0.00 37.35 2.39
570 2194 5.623368 GCAGTCTCTGTTGCTTACTCATACT 60.623 44.000 0.00 0.00 37.35 2.12
571 2195 6.404844 GCAGTCTCTGTTGCTTACTCATACTA 60.405 42.308 0.00 0.00 37.35 1.82
573 2197 8.841300 CAGTCTCTGTTGCTTACTCATACTATA 58.159 37.037 0.00 0.00 0.00 1.31
574 2198 9.581289 AGTCTCTGTTGCTTACTCATACTATAT 57.419 33.333 0.00 0.00 0.00 0.86
580 2204 7.801783 TGTTGCTTACTCATACTATATTCGTCG 59.198 37.037 0.00 0.00 0.00 5.12
587 2211 4.758165 TCATACTATATTCGTCGAGGCACA 59.242 41.667 0.00 0.00 0.00 4.57
726 2353 4.074526 TCAGAGCTGAGCCGTGCC 62.075 66.667 0.00 0.00 34.14 5.01
747 2374 0.950836 CCCATGCACAAACAACGAGA 59.049 50.000 0.00 0.00 0.00 4.04
751 2378 2.823196 TGCACAAACAACGAGACAAG 57.177 45.000 0.00 0.00 0.00 3.16
753 2380 2.095213 TGCACAAACAACGAGACAAGAC 59.905 45.455 0.00 0.00 0.00 3.01
754 2381 2.095213 GCACAAACAACGAGACAAGACA 59.905 45.455 0.00 0.00 0.00 3.41
755 2382 3.425625 GCACAAACAACGAGACAAGACAA 60.426 43.478 0.00 0.00 0.00 3.18
756 2383 4.730613 GCACAAACAACGAGACAAGACAAT 60.731 41.667 0.00 0.00 0.00 2.71
757 2384 5.503357 GCACAAACAACGAGACAAGACAATA 60.503 40.000 0.00 0.00 0.00 1.90
758 2385 6.129393 CACAAACAACGAGACAAGACAATAG 58.871 40.000 0.00 0.00 0.00 1.73
761 2388 2.673368 CAACGAGACAAGACAATAGGGC 59.327 50.000 0.00 0.00 0.00 5.19
762 2389 1.207329 ACGAGACAAGACAATAGGGCC 59.793 52.381 0.00 0.00 0.00 5.80
763 2390 1.207089 CGAGACAAGACAATAGGGCCA 59.793 52.381 6.18 0.00 0.00 5.36
764 2391 2.158900 CGAGACAAGACAATAGGGCCAT 60.159 50.000 6.18 0.00 0.00 4.40
765 2392 3.069586 CGAGACAAGACAATAGGGCCATA 59.930 47.826 6.18 0.43 0.00 2.74
766 2393 4.381411 GAGACAAGACAATAGGGCCATAC 58.619 47.826 6.18 0.00 0.00 2.39
767 2394 3.131396 GACAAGACAATAGGGCCATACG 58.869 50.000 6.18 0.00 0.00 3.06
768 2395 2.504175 ACAAGACAATAGGGCCATACGT 59.496 45.455 6.18 2.46 0.00 3.57
769 2396 2.872245 CAAGACAATAGGGCCATACGTG 59.128 50.000 6.18 6.74 0.00 4.49
771 2398 0.472471 ACAATAGGGCCATACGTGGG 59.528 55.000 6.18 0.00 46.14 4.61
803 2430 0.724453 CAATTCGAAACGTGCGGGTG 60.724 55.000 0.00 4.01 0.00 4.61
965 2612 4.124351 CCTCGCCCGCTTGTCGTA 62.124 66.667 0.00 0.00 36.19 3.43
968 2615 1.985447 CTCGCCCGCTTGTCGTACTA 61.985 60.000 0.00 0.00 36.19 1.82
969 2616 1.585521 CGCCCGCTTGTCGTACTAG 60.586 63.158 0.00 0.00 36.19 2.57
1016 2663 2.903357 CATGGCGGTAGCTGGAGT 59.097 61.111 0.00 0.00 44.37 3.85
1021 2668 2.439701 CGGTAGCTGGAGTCGGGA 60.440 66.667 0.00 0.00 0.00 5.14
1047 2694 2.463589 ATCGCTTTCGCTTCCACCCA 62.464 55.000 0.00 0.00 35.26 4.51
1307 2954 8.297426 TGATCATACGAGGTGAGTTTATATGAC 58.703 37.037 0.00 0.00 32.12 3.06
1323 2970 0.249826 TGACTCAGTTCGTGCATGCA 60.250 50.000 18.46 18.46 0.00 3.96
1324 2971 1.081892 GACTCAGTTCGTGCATGCAT 58.918 50.000 25.64 3.87 0.00 3.96
1325 2972 0.800631 ACTCAGTTCGTGCATGCATG 59.199 50.000 30.20 30.20 0.00 4.06
1339 2987 1.179152 TGCATGCCAAGACCAAGATG 58.821 50.000 16.68 0.00 0.00 2.90
1371 3019 7.095523 TGTGATGTGAATCAAGTCGCATATATG 60.096 37.037 8.45 8.45 46.23 1.78
1392 3041 0.378257 ACAAACACAAGAGCGTGCAG 59.622 50.000 0.00 0.00 40.73 4.41
1447 3096 2.949644 GGCATAAATTTCAGTAGGGCGT 59.050 45.455 0.00 0.00 0.00 5.68
1588 3237 5.939296 CCAAGGTACCCAAAACTAACGAATA 59.061 40.000 8.74 0.00 0.00 1.75
1589 3238 6.430616 CCAAGGTACCCAAAACTAACGAATAA 59.569 38.462 8.74 0.00 0.00 1.40
1593 3242 9.737844 AGGTACCCAAAACTAACGAATAAATTA 57.262 29.630 8.74 0.00 0.00 1.40
1594 3243 9.773328 GGTACCCAAAACTAACGAATAAATTAC 57.227 33.333 0.00 0.00 0.00 1.89
1709 3366 2.027745 AGCTCTACCCAAGTGTGTGATG 60.028 50.000 0.00 0.00 0.00 3.07
1800 3463 4.072131 TGATTTCCAGCCAGTAGTTTCAC 58.928 43.478 0.00 0.00 0.00 3.18
1831 3495 2.667470 TCTAGGTCAGCTGGTATGGAC 58.333 52.381 15.13 2.87 0.00 4.02
1856 3520 0.829990 TGATGCGGTAGCTGATGGAA 59.170 50.000 0.00 0.00 45.42 3.53
1941 3605 1.559682 TCCTAGCTTGTTGATGGACCC 59.440 52.381 0.00 0.00 0.00 4.46
2031 3695 5.120208 CCGTGACTTTAGTTCGATGATGTTT 59.880 40.000 8.99 0.00 0.00 2.83
2399 4125 9.672086 TCTTACTAAACAACAAATTTTCATCCG 57.328 29.630 0.00 0.00 0.00 4.18
2400 4126 9.458374 CTTACTAAACAACAAATTTTCATCCGT 57.542 29.630 0.00 0.00 0.00 4.69
2401 4127 9.804758 TTACTAAACAACAAATTTTCATCCGTT 57.195 25.926 0.00 0.00 0.00 4.44
2402 4128 8.710835 ACTAAACAACAAATTTTCATCCGTTT 57.289 26.923 0.00 0.00 0.00 3.60
2403 4129 8.813282 ACTAAACAACAAATTTTCATCCGTTTC 58.187 29.630 0.00 0.00 0.00 2.78
2404 4130 5.881637 ACAACAAATTTTCATCCGTTTCG 57.118 34.783 0.00 0.00 0.00 3.46
2405 4131 5.583495 ACAACAAATTTTCATCCGTTTCGA 58.417 33.333 0.00 0.00 0.00 3.71
2406 4132 6.037098 ACAACAAATTTTCATCCGTTTCGAA 58.963 32.000 0.00 0.00 0.00 3.71
2407 4133 6.531948 ACAACAAATTTTCATCCGTTTCGAAA 59.468 30.769 6.47 6.47 0.00 3.46
2408 4134 7.063544 ACAACAAATTTTCATCCGTTTCGAAAA 59.936 29.630 13.10 0.00 41.43 2.29
2409 4135 7.527084 ACAAATTTTCATCCGTTTCGAAAAA 57.473 28.000 13.10 0.79 40.78 1.94
2540 4266 3.492102 GGCATAGCCTTTGGACATCTA 57.508 47.619 0.00 0.00 46.69 1.98
2598 4324 6.691818 GTCTAACATATGTGTCTAGTTCCACG 59.308 42.308 9.63 0.00 37.67 4.94
2654 4382 8.565896 TCTACATTGTAATGAGACAAATTGCT 57.434 30.769 11.29 0.00 42.39 3.91
2692 4420 8.979574 TGTGAAATTTTCGTAAAACTTTTGTGT 58.020 25.926 4.76 0.00 30.16 3.72
2704 4432 4.568152 ACTTTTGTGTAGCACATGGTTC 57.432 40.909 2.65 0.00 44.16 3.62
2916 4644 5.125578 CCCCTATTAGTTCTTTGCCAGAAAC 59.874 44.000 0.00 0.00 43.52 2.78
2919 4647 7.255801 CCCTATTAGTTCTTTGCCAGAAACAAA 60.256 37.037 0.00 0.00 43.52 2.83
3026 4754 0.983378 GCTTCTTAGGCCCCTCAGGA 60.983 60.000 0.00 0.00 38.24 3.86
3047 4775 1.386533 CTCATTGTCCATGGCCTCAC 58.613 55.000 6.96 0.00 33.07 3.51
3048 4776 0.697658 TCATTGTCCATGGCCTCACA 59.302 50.000 6.96 2.95 33.07 3.58
3054 4782 1.270550 GTCCATGGCCTCACAACAAAG 59.729 52.381 6.96 0.00 0.00 2.77
3068 4796 2.165319 ACAAAGTCTTAGGTGCGTCC 57.835 50.000 0.00 0.00 0.00 4.79
3151 4879 2.430367 GTTCAACGGAGGGGTGCT 59.570 61.111 0.00 0.00 0.00 4.40
3152 4880 1.122632 TGTTCAACGGAGGGGTGCTA 61.123 55.000 0.00 0.00 0.00 3.49
3177 4905 5.445964 GTGAAGAAGAGGGTAGAGAGAGAT 58.554 45.833 0.00 0.00 0.00 2.75
3276 5004 0.179062 CTCAAGATCCTGCTTCGGGG 60.179 60.000 0.00 0.00 0.00 5.73
3725 5455 1.747745 GGTCGGGTTTTGGATCCGG 60.748 63.158 7.39 0.00 43.54 5.14
3793 5523 1.402968 CATCATTGGCTGGAGGAAACG 59.597 52.381 0.00 0.00 0.00 3.60
3885 5617 2.743718 CACGACCCAACAGAGGCT 59.256 61.111 0.00 0.00 0.00 4.58
3909 5641 4.211330 TGTGAAAAGGCCGGCCCA 62.211 61.111 41.72 28.92 36.58 5.36
4051 5802 1.540267 TTTAACTTCCGGCCCATGTG 58.460 50.000 0.00 0.00 0.00 3.21
4063 5814 1.000521 CCATGTGTGGCCCATGACT 60.001 57.895 18.83 0.00 41.78 3.41
4083 5834 1.801242 TCTTTCGGCCCATATGAGGA 58.199 50.000 3.65 0.00 0.00 3.71
4227 5979 1.755783 GCCTTCTCAGGGCCCATTG 60.756 63.158 27.56 15.49 43.49 2.82
4244 5996 4.439057 CCATTGATTCTTGGGCTCATTTG 58.561 43.478 0.00 0.00 0.00 2.32
4259 6011 2.816672 TCATTTGCAGCATTCGGTTACA 59.183 40.909 0.00 0.00 0.00 2.41
4262 6014 5.299028 TCATTTGCAGCATTCGGTTACATAT 59.701 36.000 0.00 0.00 0.00 1.78
4288 6040 4.693566 CCCGTTACTGTCATTTTCTGCTTA 59.306 41.667 0.00 0.00 0.00 3.09
4308 6060 2.885113 GGCCAAATTCAGCCCGTC 59.115 61.111 0.00 0.00 43.76 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.426025 TCATGATGACTGTTTTGAGTGAGAAG 59.574 38.462 0.00 0.00 0.00 2.85
2 3 6.290605 TCATGATGACTGTTTTGAGTGAGAA 58.709 36.000 0.00 0.00 0.00 2.87
3 4 5.857268 TCATGATGACTGTTTTGAGTGAGA 58.143 37.500 0.00 0.00 0.00 3.27
6 7 5.930569 TCTCTCATGATGACTGTTTTGAGTG 59.069 40.000 0.00 0.00 33.88 3.51
10 11 8.080417 ACATTTTCTCTCATGATGACTGTTTTG 58.920 33.333 0.00 0.00 0.00 2.44
11 12 8.174733 ACATTTTCTCTCATGATGACTGTTTT 57.825 30.769 0.00 0.00 0.00 2.43
12 13 7.756395 ACATTTTCTCTCATGATGACTGTTT 57.244 32.000 0.00 0.00 0.00 2.83
13 14 7.551974 CCTACATTTTCTCTCATGATGACTGTT 59.448 37.037 0.00 0.00 0.00 3.16
14 15 7.046652 CCTACATTTTCTCTCATGATGACTGT 58.953 38.462 0.00 4.92 0.00 3.55
15 16 7.270779 TCCTACATTTTCTCTCATGATGACTG 58.729 38.462 0.00 0.00 0.00 3.51
16 17 7.429374 TCCTACATTTTCTCTCATGATGACT 57.571 36.000 0.00 0.00 0.00 3.41
17 18 8.674263 ATTCCTACATTTTCTCTCATGATGAC 57.326 34.615 0.00 0.00 0.00 3.06
18 19 7.654923 CGATTCCTACATTTTCTCTCATGATGA 59.345 37.037 0.00 0.00 0.00 2.92
19 20 7.654923 TCGATTCCTACATTTTCTCTCATGATG 59.345 37.037 0.00 0.00 0.00 3.07
20 21 7.730084 TCGATTCCTACATTTTCTCTCATGAT 58.270 34.615 0.00 0.00 0.00 2.45
21 22 7.112452 TCGATTCCTACATTTTCTCTCATGA 57.888 36.000 0.00 0.00 0.00 3.07
22 23 7.776933 TTCGATTCCTACATTTTCTCTCATG 57.223 36.000 0.00 0.00 0.00 3.07
23 24 8.792830 TTTTCGATTCCTACATTTTCTCTCAT 57.207 30.769 0.00 0.00 0.00 2.90
24 25 8.615878 TTTTTCGATTCCTACATTTTCTCTCA 57.384 30.769 0.00 0.00 0.00 3.27
33 34 8.345565 GCAACTGATATTTTTCGATTCCTACAT 58.654 33.333 0.00 0.00 0.00 2.29
34 35 7.335673 TGCAACTGATATTTTTCGATTCCTACA 59.664 33.333 0.00 0.00 0.00 2.74
35 36 7.693952 TGCAACTGATATTTTTCGATTCCTAC 58.306 34.615 0.00 0.00 0.00 3.18
36 37 7.857734 TGCAACTGATATTTTTCGATTCCTA 57.142 32.000 0.00 0.00 0.00 2.94
37 38 6.757897 TGCAACTGATATTTTTCGATTCCT 57.242 33.333 0.00 0.00 0.00 3.36
38 39 7.195646 TCATGCAACTGATATTTTTCGATTCC 58.804 34.615 0.00 0.00 0.00 3.01
39 40 7.377928 CCTCATGCAACTGATATTTTTCGATTC 59.622 37.037 0.00 0.00 0.00 2.52
40 41 7.067372 TCCTCATGCAACTGATATTTTTCGATT 59.933 33.333 0.00 0.00 0.00 3.34
41 42 6.543465 TCCTCATGCAACTGATATTTTTCGAT 59.457 34.615 0.00 0.00 0.00 3.59
42 43 5.879777 TCCTCATGCAACTGATATTTTTCGA 59.120 36.000 0.00 0.00 0.00 3.71
43 44 6.122850 TCCTCATGCAACTGATATTTTTCG 57.877 37.500 0.00 0.00 0.00 3.46
44 45 9.674824 CTTATCCTCATGCAACTGATATTTTTC 57.325 33.333 0.00 0.00 0.00 2.29
45 46 8.139989 GCTTATCCTCATGCAACTGATATTTTT 58.860 33.333 0.00 0.00 0.00 1.94
46 47 7.286087 TGCTTATCCTCATGCAACTGATATTTT 59.714 33.333 0.00 0.00 32.12 1.82
47 48 6.774170 TGCTTATCCTCATGCAACTGATATTT 59.226 34.615 0.00 0.00 32.12 1.40
48 49 6.301486 TGCTTATCCTCATGCAACTGATATT 58.699 36.000 0.00 0.00 32.12 1.28
49 50 5.872963 TGCTTATCCTCATGCAACTGATAT 58.127 37.500 0.00 0.00 32.12 1.63
50 51 5.294734 TGCTTATCCTCATGCAACTGATA 57.705 39.130 0.00 0.00 32.12 2.15
51 52 4.160642 TGCTTATCCTCATGCAACTGAT 57.839 40.909 0.00 0.00 32.12 2.90
52 53 3.632643 TGCTTATCCTCATGCAACTGA 57.367 42.857 0.00 0.00 32.12 3.41
53 54 4.707030 TTTGCTTATCCTCATGCAACTG 57.293 40.909 0.00 0.00 43.74 3.16
54 55 4.082026 GGTTTTGCTTATCCTCATGCAACT 60.082 41.667 0.00 0.00 43.74 3.16
55 56 4.176271 GGTTTTGCTTATCCTCATGCAAC 58.824 43.478 0.00 0.00 43.74 4.17
56 57 3.195396 GGGTTTTGCTTATCCTCATGCAA 59.805 43.478 0.00 0.00 42.60 4.08
57 58 2.760092 GGGTTTTGCTTATCCTCATGCA 59.240 45.455 0.00 0.00 0.00 3.96
58 59 2.101415 GGGGTTTTGCTTATCCTCATGC 59.899 50.000 0.00 0.00 0.00 4.06
59 60 2.695147 GGGGGTTTTGCTTATCCTCATG 59.305 50.000 0.00 0.00 0.00 3.07
60 61 2.314549 TGGGGGTTTTGCTTATCCTCAT 59.685 45.455 0.00 0.00 0.00 2.90
61 62 1.713647 TGGGGGTTTTGCTTATCCTCA 59.286 47.619 0.00 0.00 0.00 3.86
62 63 2.525105 TGGGGGTTTTGCTTATCCTC 57.475 50.000 0.00 0.00 0.00 3.71
63 64 3.268034 TTTGGGGGTTTTGCTTATCCT 57.732 42.857 0.00 0.00 0.00 3.24
64 65 4.359434 TTTTTGGGGGTTTTGCTTATCC 57.641 40.909 0.00 0.00 0.00 2.59
82 83 5.528870 CGCTAAGGGTCAAGATTTGTTTTT 58.471 37.500 0.00 0.00 0.00 1.94
159 160 7.928167 TGAGGAGTGACATGTCATTTATCATAC 59.072 37.037 30.10 14.45 42.18 2.39
227 228 6.878317 AGCAAAGCTTTAGATAAAATTCCCC 58.122 36.000 12.25 0.00 33.89 4.81
326 364 3.749226 TGCCAGATGTTGACATGTTGTA 58.251 40.909 0.00 0.00 36.57 2.41
388 428 3.574354 ATCTCTCTCCATTTCTTGCCC 57.426 47.619 0.00 0.00 0.00 5.36
477 2101 3.876320 TCATTTTCCTTTTGGCAGCAAAC 59.124 39.130 0.00 0.00 40.12 2.93
560 2184 6.652062 TGCCTCGACGAATATAGTATGAGTAA 59.348 38.462 0.00 0.00 0.00 2.24
569 2193 2.320367 GCTGTGCCTCGACGAATATAG 58.680 52.381 0.00 0.00 0.00 1.31
570 2194 1.334689 CGCTGTGCCTCGACGAATATA 60.335 52.381 0.00 0.00 0.00 0.86
571 2195 0.595053 CGCTGTGCCTCGACGAATAT 60.595 55.000 0.00 0.00 0.00 1.28
573 2197 2.507102 CGCTGTGCCTCGACGAAT 60.507 61.111 0.00 0.00 0.00 3.34
726 2353 1.006337 CGTTGTTTGTGCATGGGGG 60.006 57.895 0.00 0.00 0.00 5.40
727 2354 0.039256 CTCGTTGTTTGTGCATGGGG 60.039 55.000 0.00 0.00 0.00 4.96
740 2367 2.673368 GCCCTATTGTCTTGTCTCGTTG 59.327 50.000 0.00 0.00 0.00 4.10
747 2374 2.504175 ACGTATGGCCCTATTGTCTTGT 59.496 45.455 0.00 0.00 0.00 3.16
751 2378 1.542547 CCCACGTATGGCCCTATTGTC 60.543 57.143 0.00 0.00 45.76 3.18
753 2380 0.889186 GCCCACGTATGGCCCTATTG 60.889 60.000 15.58 0.00 45.76 1.90
754 2381 1.454539 GCCCACGTATGGCCCTATT 59.545 57.895 15.58 0.00 45.76 1.73
755 2382 2.879233 CGCCCACGTATGGCCCTAT 61.879 63.158 19.38 0.00 46.48 2.57
756 2383 3.542676 CGCCCACGTATGGCCCTA 61.543 66.667 19.38 0.00 46.48 3.53
767 2394 3.431725 GTTGCCTGCTACGCCCAC 61.432 66.667 0.00 0.00 0.00 4.61
768 2395 2.762969 ATTGTTGCCTGCTACGCCCA 62.763 55.000 0.00 0.00 0.00 5.36
769 2396 1.595093 AATTGTTGCCTGCTACGCCC 61.595 55.000 0.00 0.00 0.00 6.13
770 2397 0.179163 GAATTGTTGCCTGCTACGCC 60.179 55.000 0.00 0.00 0.00 5.68
771 2398 0.521242 CGAATTGTTGCCTGCTACGC 60.521 55.000 0.00 0.00 0.00 4.42
772 2399 1.075542 TCGAATTGTTGCCTGCTACG 58.924 50.000 0.00 0.00 0.00 3.51
773 2400 3.234386 GTTTCGAATTGTTGCCTGCTAC 58.766 45.455 0.00 0.00 0.00 3.58
774 2401 2.095969 CGTTTCGAATTGTTGCCTGCTA 60.096 45.455 0.00 0.00 0.00 3.49
775 2402 1.334960 CGTTTCGAATTGTTGCCTGCT 60.335 47.619 0.00 0.00 0.00 4.24
965 2612 0.618680 TCAGTGCATGGGGAGCTAGT 60.619 55.000 0.00 0.00 0.00 2.57
968 2615 1.530771 GATCAGTGCATGGGGAGCT 59.469 57.895 0.00 0.00 0.00 4.09
969 2616 1.527844 GGATCAGTGCATGGGGAGC 60.528 63.158 0.00 0.00 0.00 4.70
1035 2682 4.308458 CCGTGTGGGTGGAAGCGA 62.308 66.667 0.00 0.00 33.03 4.93
1307 2954 3.598678 CATGCATGCACGAACTGAG 57.401 52.632 25.37 1.78 0.00 3.35
1323 2970 1.180029 GTGCATCTTGGTCTTGGCAT 58.820 50.000 0.00 0.00 33.43 4.40
1324 2971 0.178995 TGTGCATCTTGGTCTTGGCA 60.179 50.000 0.00 0.00 0.00 4.92
1325 2972 1.180029 ATGTGCATCTTGGTCTTGGC 58.820 50.000 0.00 0.00 0.00 4.52
1326 2973 2.559668 ACAATGTGCATCTTGGTCTTGG 59.440 45.455 13.68 0.00 0.00 3.61
1327 2974 3.253921 TCACAATGTGCATCTTGGTCTTG 59.746 43.478 8.78 5.22 32.98 3.02
1330 2977 3.192001 ACATCACAATGTGCATCTTGGTC 59.808 43.478 8.78 0.00 44.51 4.02
1331 2978 3.159472 ACATCACAATGTGCATCTTGGT 58.841 40.909 8.78 0.00 44.51 3.67
1371 3019 1.202348 GCACGCTCTTGTGTTTGTGC 61.202 55.000 0.00 0.00 44.72 4.57
1392 3041 3.181510 CCAAACCGATCCGATCAAAACTC 60.182 47.826 9.07 0.00 0.00 3.01
1709 3366 4.201881 GCTATTTCACCCAAACGTATGGTC 60.202 45.833 0.00 0.00 38.91 4.02
1800 3463 2.159028 GCTGACCTAGAAACTAGGCCAG 60.159 54.545 25.75 25.75 44.72 4.85
1831 3495 2.590007 GCTACCGCATCAGGCTGG 60.590 66.667 15.73 0.00 41.67 4.85
2086 3792 8.097038 AGCTACTTCAAACACTAAATCTCATCA 58.903 33.333 0.00 0.00 0.00 3.07
2095 3801 8.967664 TTTTTCCTAGCTACTTCAAACACTAA 57.032 30.769 0.00 0.00 0.00 2.24
2320 4026 2.906389 AGTCACACATTTCCTAGCCTGA 59.094 45.455 0.00 0.00 0.00 3.86
2328 4034 4.232221 CAATTGAGCAGTCACACATTTCC 58.768 43.478 0.00 0.00 30.10 3.13
2540 4266 6.839124 TTGCACCAATTGAGATTTCTATGT 57.161 33.333 7.12 0.00 0.00 2.29
2598 4324 9.952341 GACACTTCCGCAAAATAAAATAAAATC 57.048 29.630 0.00 0.00 0.00 2.17
2986 4714 3.619929 GCAAGAAATTTGCTAGCCCATTG 59.380 43.478 13.29 8.59 41.87 2.82
3026 4754 0.257039 GAGGCCATGGACAATGAGGT 59.743 55.000 22.78 0.00 38.72 3.85
3047 4775 2.223377 GGACGCACCTAAGACTTTGTTG 59.777 50.000 0.00 0.00 35.41 3.33
3048 4776 2.490991 GGACGCACCTAAGACTTTGTT 58.509 47.619 0.00 0.00 35.41 2.83
3151 4879 4.224594 TCTCTCTACCCTCTTCTTCACGTA 59.775 45.833 0.00 0.00 0.00 3.57
3152 4880 3.009253 TCTCTCTACCCTCTTCTTCACGT 59.991 47.826 0.00 0.00 0.00 4.49
3177 4905 5.570206 CACTACATAGTTTGCGTCGTCTTTA 59.430 40.000 0.00 0.00 33.46 1.85
3276 5004 1.197036 GTCCCAGTAACAAAGAAGCGC 59.803 52.381 0.00 0.00 0.00 5.92
3725 5455 1.020861 CGGGGCTGTTAACGGGTTAC 61.021 60.000 16.13 0.00 0.00 2.50
3872 5602 0.329596 GGAATGAGCCTCTGTTGGGT 59.670 55.000 0.00 0.00 40.97 4.51
3885 5617 1.533625 CGGCCTTTTCACAGGAATGA 58.466 50.000 0.00 0.00 35.71 2.57
4051 5802 0.804989 CGAAAGAAGTCATGGGCCAC 59.195 55.000 9.28 0.00 0.00 5.01
4063 5814 2.123589 TCCTCATATGGGCCGAAAGAA 58.876 47.619 2.13 0.00 0.00 2.52
4083 5834 1.497286 TGGGCCAAGAGTTACAAAGGT 59.503 47.619 2.13 0.00 0.00 3.50
4197 5949 3.118592 CCTGAGAAGGCCGAAAGATAACT 60.119 47.826 0.00 0.00 0.00 2.24
4227 5979 2.737679 GCTGCAAATGAGCCCAAGAATC 60.738 50.000 0.00 0.00 0.00 2.52
4244 5996 2.350772 GCCATATGTAACCGAATGCTGC 60.351 50.000 1.24 0.00 0.00 5.25
4259 6011 3.857157 AATGACAGTAACGGGCCATAT 57.143 42.857 4.39 0.00 0.00 1.78
4262 6014 2.156098 GAAAATGACAGTAACGGGCCA 58.844 47.619 4.39 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.