Multiple sequence alignment - TraesCS2D01G239600

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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 TraesCS2D01G239600 chr2D 100.000 6613 0 0 1 6613 255622894 255616282 0.000000e+00 12213.0
1 TraesCS2D01G239600 chr2D 95.322 171 6 1 5896 6064 396613963 396613793 3.040000e-68 270.0
2 TraesCS2D01G239600 chr2D 92.308 52 3 1 4959 5010 119281357 119281307 9.200000e-09 73.1
3 TraesCS2D01G239600 chr2A 97.032 5087 87 18 836 5916 236834247 236839275 0.000000e+00 8499.0
4 TraesCS2D01G239600 chr2A 97.143 245 6 1 6249 6492 236841202 236841446 4.770000e-111 412.0
5 TraesCS2D01G239600 chr2A 96.759 216 7 0 6038 6253 236839320 236839535 1.750000e-95 361.0
6 TraesCS2D01G239600 chr2A 90.833 120 10 1 6495 6613 236841666 236841785 6.860000e-35 159.0
7 TraesCS2D01G239600 chr2A 95.349 86 4 0 6528 6613 236841806 236841891 3.220000e-28 137.0
8 TraesCS2D01G239600 chr2A 94.737 57 2 1 4961 5017 40430385 40430330 3.290000e-13 87.9
9 TraesCS2D01G239600 chr2B 95.306 2791 77 23 836 3592 280483054 280485824 0.000000e+00 4379.0
10 TraesCS2D01G239600 chr2B 97.004 701 19 1 4056 4756 280493557 280494255 0.000000e+00 1177.0
11 TraesCS2D01G239600 chr2B 91.446 643 24 10 5262 5899 280495794 280496410 0.000000e+00 854.0
12 TraesCS2D01G239600 chr2B 85.041 849 96 19 1 832 616478177 616477343 0.000000e+00 835.0
13 TraesCS2D01G239600 chr2B 93.359 512 17 10 3576 4073 280492692 280493200 0.000000e+00 741.0
14 TraesCS2D01G239600 chr2B 90.811 555 41 7 6057 6605 280496410 280496960 0.000000e+00 734.0
15 TraesCS2D01G239600 chr2B 91.093 494 33 8 6118 6605 280497080 280497568 0.000000e+00 658.0
16 TraesCS2D01G239600 chr2B 96.736 337 11 0 4929 5265 280495377 280495713 4.480000e-156 562.0
17 TraesCS2D01G239600 chr2B 96.708 243 5 2 4739 4981 280495130 280495369 1.030000e-107 401.0
18 TraesCS2D01G239600 chr2B 90.625 288 20 4 6118 6402 280497682 280497965 6.260000e-100 375.0
19 TraesCS2D01G239600 chr2B 95.420 131 5 1 6476 6605 280497967 280498097 2.420000e-49 207.0
20 TraesCS2D01G239600 chr4D 86.068 847 93 17 3 832 296675998 296676836 0.000000e+00 887.0
21 TraesCS2D01G239600 chr4D 83.590 195 28 4 3918 4110 294346465 294346273 5.270000e-41 180.0
22 TraesCS2D01G239600 chr4D 80.882 204 34 4 3912 4110 402546679 402546476 8.880000e-34 156.0
23 TraesCS2D01G239600 chr1D 85.280 856 95 16 1 832 24943611 24942763 0.000000e+00 854.0
24 TraesCS2D01G239600 chr3B 84.870 846 102 18 7 832 419795128 419795967 0.000000e+00 830.0
25 TraesCS2D01G239600 chr3B 75.000 552 90 28 306 829 247501042 247500511 1.870000e-50 211.0
26 TraesCS2D01G239600 chr5B 84.778 854 90 16 2 832 58187653 58186817 0.000000e+00 821.0
27 TraesCS2D01G239600 chr5B 78.721 860 142 29 3 835 254263306 254262461 2.710000e-148 536.0
28 TraesCS2D01G239600 chr5B 94.828 174 7 1 5887 6058 575061331 575061158 3.040000e-68 270.0
29 TraesCS2D01G239600 chr5B 91.753 194 13 2 5894 6085 427931368 427931176 3.930000e-67 267.0
30 TraesCS2D01G239600 chr5B 82.667 225 25 10 3901 4112 485912058 485912281 3.150000e-43 187.0
31 TraesCS2D01G239600 chr5B 80.292 137 25 2 693 829 485627348 485627482 1.170000e-17 102.0
32 TraesCS2D01G239600 chr1B 84.579 843 108 11 6 832 497330138 497329302 0.000000e+00 817.0
33 TraesCS2D01G239600 chr1B 74.552 782 120 49 95 827 346416269 346415518 1.090000e-67 268.0
34 TraesCS2D01G239600 chr1B 90.476 63 4 2 4949 5010 57536881 57536942 1.530000e-11 82.4
35 TraesCS2D01G239600 chr1A 83.867 843 117 13 1 829 34193593 34192756 0.000000e+00 785.0
36 TraesCS2D01G239600 chr1A 95.833 168 5 1 5892 6057 132544054 132544221 3.040000e-68 270.0
37 TraesCS2D01G239600 chr7B 83.937 828 107 10 1 803 229213927 229214753 0.000000e+00 769.0
38 TraesCS2D01G239600 chr5D 83.429 869 97 24 2 831 447102249 447101389 0.000000e+00 763.0
39 TraesCS2D01G239600 chr4B 83.294 850 117 14 1 832 418758655 418757813 0.000000e+00 760.0
40 TraesCS2D01G239600 chr4B 92.973 185 9 3 5896 6078 113961281 113961099 3.930000e-67 267.0
41 TraesCS2D01G239600 chr4B 84.153 183 26 3 3929 4110 362144214 362144034 2.450000e-39 174.0
42 TraesCS2D01G239600 chr4B 80.769 208 33 6 3912 4114 565735392 565735187 8.880000e-34 156.0
43 TraesCS2D01G239600 chr4B 94.737 57 2 1 4961 5017 104337366 104337421 3.290000e-13 87.9
44 TraesCS2D01G239600 chr7A 82.331 815 109 15 29 822 114090412 114089612 0.000000e+00 675.0
45 TraesCS2D01G239600 chr7A 76.712 511 84 26 346 827 260263787 260264291 1.100000e-62 252.0
46 TraesCS2D01G239600 chr6D 95.906 171 5 1 5896 6064 406391359 406391529 6.530000e-70 276.0
47 TraesCS2D01G239600 chr6D 93.820 178 8 2 5896 6070 392896975 392897152 1.410000e-66 265.0
48 TraesCS2D01G239600 chr6D 91.228 57 3 2 4954 5010 262513949 262513895 7.110000e-10 76.8
49 TraesCS2D01G239600 chr7D 94.857 175 7 1 5893 6065 500255330 500255156 8.450000e-69 272.0
50 TraesCS2D01G239600 chr7D 80.882 204 35 3 3911 4110 71339574 71339777 2.470000e-34 158.0
51 TraesCS2D01G239600 chr7D 94.737 57 2 1 4961 5017 553426331 553426386 3.290000e-13 87.9
52 TraesCS2D01G239600 chr3A 94.798 173 6 2 5895 6065 585605803 585605632 3.930000e-67 267.0
53 TraesCS2D01G239600 chr3A 94.737 57 2 1 4961 5017 113364102 113364047 3.290000e-13 87.9
54 TraesCS2D01G239600 chr3A 94.737 57 2 1 4961 5017 714035475 714035420 3.290000e-13 87.9
55 TraesCS2D01G239600 chr4A 81.159 207 33 5 3910 4110 179057200 179057406 1.910000e-35 161.0
56 TraesCS2D01G239600 chr4A 94.737 57 2 1 4961 5017 211051169 211051114 3.290000e-13 87.9
57 TraesCS2D01G239600 chr4A 90.476 63 4 2 4949 5010 617962610 617962671 1.530000e-11 82.4
58 TraesCS2D01G239600 chr6A 94.737 57 2 1 4961 5017 588944625 588944570 3.290000e-13 87.9


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 TraesCS2D01G239600 chr2D 255616282 255622894 6612 True 12213.000000 12213 100.000000 1 6613 1 chr2D.!!$R2 6612
1 TraesCS2D01G239600 chr2A 236834247 236841891 7644 False 1913.600000 8499 95.423200 836 6613 5 chr2A.!!$F1 5777
2 TraesCS2D01G239600 chr2B 280483054 280485824 2770 False 4379.000000 4379 95.306000 836 3592 1 chr2B.!!$F1 2756
3 TraesCS2D01G239600 chr2B 616477343 616478177 834 True 835.000000 835 85.041000 1 832 1 chr2B.!!$R1 831
4 TraesCS2D01G239600 chr2B 280492692 280498097 5405 False 634.333333 1177 93.689111 3576 6605 9 chr2B.!!$F2 3029
5 TraesCS2D01G239600 chr4D 296675998 296676836 838 False 887.000000 887 86.068000 3 832 1 chr4D.!!$F1 829
6 TraesCS2D01G239600 chr1D 24942763 24943611 848 True 854.000000 854 85.280000 1 832 1 chr1D.!!$R1 831
7 TraesCS2D01G239600 chr3B 419795128 419795967 839 False 830.000000 830 84.870000 7 832 1 chr3B.!!$F1 825
8 TraesCS2D01G239600 chr3B 247500511 247501042 531 True 211.000000 211 75.000000 306 829 1 chr3B.!!$R1 523
9 TraesCS2D01G239600 chr5B 58186817 58187653 836 True 821.000000 821 84.778000 2 832 1 chr5B.!!$R1 830
10 TraesCS2D01G239600 chr5B 254262461 254263306 845 True 536.000000 536 78.721000 3 835 1 chr5B.!!$R2 832
11 TraesCS2D01G239600 chr1B 497329302 497330138 836 True 817.000000 817 84.579000 6 832 1 chr1B.!!$R2 826
12 TraesCS2D01G239600 chr1B 346415518 346416269 751 True 268.000000 268 74.552000 95 827 1 chr1B.!!$R1 732
13 TraesCS2D01G239600 chr1A 34192756 34193593 837 True 785.000000 785 83.867000 1 829 1 chr1A.!!$R1 828
14 TraesCS2D01G239600 chr7B 229213927 229214753 826 False 769.000000 769 83.937000 1 803 1 chr7B.!!$F1 802
15 TraesCS2D01G239600 chr5D 447101389 447102249 860 True 763.000000 763 83.429000 2 831 1 chr5D.!!$R1 829
16 TraesCS2D01G239600 chr4B 418757813 418758655 842 True 760.000000 760 83.294000 1 832 1 chr4B.!!$R3 831
17 TraesCS2D01G239600 chr7A 114089612 114090412 800 True 675.000000 675 82.331000 29 822 1 chr7A.!!$R1 793
18 TraesCS2D01G239600 chr7A 260263787 260264291 504 False 252.000000 252 76.712000 346 827 1 chr7A.!!$F1 481

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
483 509 0.529833 CTCTGCTTCCTCTGCTTCGA 59.470 55.000 0.00 0.0 0.0 3.71 F
1248 1424 0.323302 TATTGTTGCGCTCAGGTGGA 59.677 50.000 9.73 0.0 0.0 4.02 F
1628 1806 3.296322 TGGAAGGCTTTTATTGCAACG 57.704 42.857 0.00 0.0 0.0 4.10 F
3431 3627 3.211045 GCTTTCTTTGTCCACCAGTGTA 58.789 45.455 0.00 0.0 0.0 2.90 F
4681 5269 0.908198 GATCCAGCCTCTCTTGTGGT 59.092 55.000 0.00 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 1962 0.109132 GCCTTTGTAGCATGTGTGGC 60.109 55.000 0.00 0.00 0.00 5.01 R
2883 3079 5.238432 ACTTCAATTAGACGCAAATGACACA 59.762 36.000 0.00 0.00 0.00 3.72 R
3598 3795 6.183360 ACACTTTCCAAGTTTGACTAATGTGG 60.183 38.462 15.87 0.00 40.46 4.17 R
5325 6948 2.232452 CCCTCCGAGTATATCTTGCCAG 59.768 54.545 0.00 0.00 0.00 4.85 R
5779 7408 0.105964 TCCTAGCTAGAGGCAGGTGG 60.106 60.000 22.70 2.85 44.79 4.61 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
18 19 3.775065 CGTCGAGGATGATGCGTAT 57.225 52.632 0.00 0.00 0.00 3.06
63 64 1.138247 GTACTGGACGCCGACGAAT 59.862 57.895 0.00 0.00 43.93 3.34
157 158 4.430765 CCGTCGGCGTTGCTAGGT 62.431 66.667 9.28 0.00 36.15 3.08
282 284 1.323271 ATCATCCCTGTGCGAGACGT 61.323 55.000 0.00 0.00 0.00 4.34
362 388 2.528127 TGTCCCGGGCCTTCTTGA 60.528 61.111 18.49 0.00 0.00 3.02
483 509 0.529833 CTCTGCTTCCTCTGCTTCGA 59.470 55.000 0.00 0.00 0.00 3.71
673 793 3.733960 GACCCACGCGCCTTTTCC 61.734 66.667 5.73 0.00 0.00 3.13
758 893 3.437741 ACCGGCGAAAAACGAGATTTTAT 59.562 39.130 9.30 0.00 45.77 1.40
771 906 3.537580 AGATTTTATGGGCGCGACTAAA 58.462 40.909 13.91 7.17 0.00 1.85
782 917 2.411806 GCGCGACTAAACCGATTTTCAA 60.412 45.455 12.10 0.00 0.00 2.69
879 1025 2.124570 GCATGTCGGTGGCCAGAT 60.125 61.111 5.11 0.00 0.00 2.90
955 1101 2.564553 GATTCTCCTCACGCACCGCT 62.565 60.000 0.00 0.00 0.00 5.52
956 1102 2.172483 ATTCTCCTCACGCACCGCTT 62.172 55.000 0.00 0.00 0.00 4.68
958 1104 3.288308 CTCCTCACGCACCGCTTCT 62.288 63.158 0.00 0.00 0.00 2.85
1120 1284 2.437359 CCTTCTCCAAGGCCGCTG 60.437 66.667 0.00 0.00 43.14 5.18
1121 1285 3.130160 CTTCTCCAAGGCCGCTGC 61.130 66.667 0.00 0.00 0.00 5.25
1248 1424 0.323302 TATTGTTGCGCTCAGGTGGA 59.677 50.000 9.73 0.00 0.00 4.02
1383 1559 6.852853 CGTAGATTTGCAACATGGAATATGTC 59.147 38.462 0.00 0.00 0.00 3.06
1494 1672 7.648510 CCTACAGTATTTTCGTTCATAGGACTC 59.351 40.741 0.00 0.00 30.23 3.36
1628 1806 3.296322 TGGAAGGCTTTTATTGCAACG 57.704 42.857 0.00 0.00 0.00 4.10
1667 1854 5.287674 AGATGTGTGGATGTATGGAGAAG 57.712 43.478 0.00 0.00 0.00 2.85
1691 1878 7.349598 AGTGGAAGGATTATATTGCAAAGTCT 58.650 34.615 1.71 0.00 0.00 3.24
1692 1879 7.284034 AGTGGAAGGATTATATTGCAAAGTCTG 59.716 37.037 1.71 0.00 0.00 3.51
1767 1954 5.231265 TCATCGCTACTTAGTGTGTACTG 57.769 43.478 0.00 0.00 37.78 2.74
1775 1962 5.584253 ACTTAGTGTGTACTGCCTATCTG 57.416 43.478 0.00 0.00 37.78 2.90
2143 2336 4.409570 CACTTTCAGCATTTCCTTGATCG 58.590 43.478 0.00 0.00 0.00 3.69
2438 2631 6.599244 CAGATAGGAGGAACATGTTTTTGCTA 59.401 38.462 13.36 17.22 0.00 3.49
2637 2830 4.776837 AGTTGCATCATGTTCCCCAAATTA 59.223 37.500 0.00 0.00 0.00 1.40
2786 2982 4.558178 TCCATTTGAATGTCATGTTGTGC 58.442 39.130 3.30 0.00 34.60 4.57
2850 3046 6.712095 ACATGAAGTGCTTTGTGAATTCTAGA 59.288 34.615 7.05 0.00 0.00 2.43
2883 3079 8.837099 TGTTAATGAAATTGGACTGGGATATT 57.163 30.769 0.00 0.00 36.99 1.28
3091 3287 4.552355 GAAAGGACGGTGTTAAATTTGGG 58.448 43.478 0.00 0.00 0.00 4.12
3431 3627 3.211045 GCTTTCTTTGTCCACCAGTGTA 58.789 45.455 0.00 0.00 0.00 2.90
3672 3872 6.677781 GCAAGAAGCATAACCTACATGTTA 57.322 37.500 2.30 0.00 44.79 2.41
3673 3873 7.083875 GCAAGAAGCATAACCTACATGTTAA 57.916 36.000 2.30 0.00 44.79 2.01
3674 3874 7.189512 GCAAGAAGCATAACCTACATGTTAAG 58.810 38.462 2.30 0.00 44.79 1.85
3707 3907 7.911130 TTCCCATTGGAATATATCAGCAAAA 57.089 32.000 3.62 0.00 45.88 2.44
3763 3963 8.836413 TGCTCTTCTTGGTTATTTATATTTCCG 58.164 33.333 0.00 0.00 0.00 4.30
3880 4094 6.926272 GTCATTTTTGCACAGGGTTGTTTATA 59.074 34.615 0.00 0.00 34.62 0.98
4421 5009 6.942886 TTTTGTTGTGAAAGTTCATGTGAC 57.057 33.333 0.00 0.00 39.73 3.67
4433 5021 5.171476 AGTTCATGTGACACATACTAGTGC 58.829 41.667 20.42 7.36 43.23 4.40
4681 5269 0.908198 GATCCAGCCTCTCTTGTGGT 59.092 55.000 0.00 0.00 0.00 4.16
4846 6325 6.146347 GCACCTATCGACCAGAAGATAAAATC 59.854 42.308 0.00 0.00 0.00 2.17
4981 6520 6.537660 AGTTCACTACACCTAGTGTCAAAAAC 59.462 38.462 3.18 5.97 43.92 2.43
4982 6521 5.979993 TCACTACACCTAGTGTCAAAAACA 58.020 37.500 3.18 0.00 43.92 2.83
5001 6540 7.492352 AAAACACTCTTATATTATGGGACGC 57.508 36.000 0.00 0.00 0.00 5.19
5027 6566 5.509332 GGGAGTATTAGTTAGTACTGCAGCC 60.509 48.000 15.27 4.53 38.16 4.85
5089 6628 7.604164 ACCATAGTAATTATGTGATGTAGCTGC 59.396 37.037 0.00 0.00 37.96 5.25
5325 6948 3.141398 TGTTCTGTTGAATCTCAGGCAC 58.859 45.455 6.29 5.07 34.40 5.01
5532 7160 8.470002 ACTTTTCAACAACAGATAAAGAAGCTT 58.530 29.630 0.00 0.00 0.00 3.74
5565 7193 4.268522 CAACTTCAAGTTTACGACCGTTG 58.731 43.478 0.00 0.00 36.03 4.10
5581 7209 3.783362 TTGTGCCAACCGTCCCCAG 62.783 63.158 0.00 0.00 0.00 4.45
5586 7214 4.722700 CAACCGTCCCCAGCCCAG 62.723 72.222 0.00 0.00 0.00 4.45
5590 7218 3.636231 CGTCCCCAGCCCAGTGAA 61.636 66.667 0.00 0.00 0.00 3.18
5591 7219 2.352805 GTCCCCAGCCCAGTGAAG 59.647 66.667 0.00 0.00 0.00 3.02
5592 7220 3.650950 TCCCCAGCCCAGTGAAGC 61.651 66.667 0.00 0.00 0.00 3.86
5593 7221 3.970410 CCCCAGCCCAGTGAAGCA 61.970 66.667 7.70 0.00 0.00 3.91
5594 7222 2.115910 CCCAGCCCAGTGAAGCAA 59.884 61.111 7.70 0.00 0.00 3.91
5595 7223 2.270986 CCCAGCCCAGTGAAGCAAC 61.271 63.158 7.70 0.00 0.00 4.17
5596 7224 2.270986 CCAGCCCAGTGAAGCAACC 61.271 63.158 7.70 0.00 0.00 3.77
5597 7225 2.281761 AGCCCAGTGAAGCAACCG 60.282 61.111 7.70 0.00 0.00 4.44
5598 7226 2.594592 GCCCAGTGAAGCAACCGT 60.595 61.111 0.00 0.00 0.00 4.83
5599 7227 2.617274 GCCCAGTGAAGCAACCGTC 61.617 63.158 0.00 0.00 0.00 4.79
5600 7228 1.966451 CCCAGTGAAGCAACCGTCC 60.966 63.158 0.00 0.00 0.00 4.79
5601 7229 1.966451 CCAGTGAAGCAACCGTCCC 60.966 63.158 0.00 0.00 0.00 4.46
5602 7230 1.966451 CAGTGAAGCAACCGTCCCC 60.966 63.158 0.00 0.00 0.00 4.81
5603 7231 2.112297 GTGAAGCAACCGTCCCCA 59.888 61.111 0.00 0.00 0.00 4.96
5619 7247 2.031012 CAGCCCAGTGAAGCGACA 59.969 61.111 0.00 0.00 0.00 4.35
5760 7389 5.565592 TTTATGCACGAATCTCAGCATTT 57.434 34.783 3.97 0.00 44.63 2.32
5761 7390 5.565592 TTATGCACGAATCTCAGCATTTT 57.434 34.783 3.97 0.00 44.63 1.82
5906 7535 0.107654 AATGCTTGTACTCCCTCCGC 60.108 55.000 0.00 0.00 0.00 5.54
5910 7539 0.684805 CTTGTACTCCCTCCGCTCCT 60.685 60.000 0.00 0.00 0.00 3.69
5916 7545 3.261818 ACTCCCTCCGCTCCTAAATAT 57.738 47.619 0.00 0.00 0.00 1.28
5917 7546 3.588569 ACTCCCTCCGCTCCTAAATATT 58.411 45.455 0.00 0.00 0.00 1.28
5919 7548 4.040584 ACTCCCTCCGCTCCTAAATATTTC 59.959 45.833 3.39 0.00 0.00 2.17
5920 7549 4.232091 TCCCTCCGCTCCTAAATATTTCT 58.768 43.478 3.39 0.00 0.00 2.52
5921 7550 4.658901 TCCCTCCGCTCCTAAATATTTCTT 59.341 41.667 3.39 0.00 0.00 2.52
5924 7553 6.292150 CCTCCGCTCCTAAATATTTCTTTCT 58.708 40.000 3.39 0.00 0.00 2.52
5926 7555 7.600752 CCTCCGCTCCTAAATATTTCTTTCTAG 59.399 40.741 3.39 0.00 0.00 2.43
5927 7556 8.246430 TCCGCTCCTAAATATTTCTTTCTAGA 57.754 34.615 3.39 0.00 0.00 2.43
5928 7557 8.361139 TCCGCTCCTAAATATTTCTTTCTAGAG 58.639 37.037 3.39 3.48 0.00 2.43
5929 7558 8.361139 CCGCTCCTAAATATTTCTTTCTAGAGA 58.639 37.037 3.39 0.00 0.00 3.10
5930 7559 9.921637 CGCTCCTAAATATTTCTTTCTAGAGAT 57.078 33.333 3.39 0.00 0.00 2.75
5955 7584 7.884816 TTTAACAAGTGACTACATACAGAGC 57.115 36.000 0.00 0.00 0.00 4.09
5956 7585 5.468540 AACAAGTGACTACATACAGAGCA 57.531 39.130 0.00 0.00 0.00 4.26
5958 7587 5.853936 ACAAGTGACTACATACAGAGCAAA 58.146 37.500 0.00 0.00 0.00 3.68
5959 7588 6.288294 ACAAGTGACTACATACAGAGCAAAA 58.712 36.000 0.00 0.00 0.00 2.44
5960 7589 6.936900 ACAAGTGACTACATACAGAGCAAAAT 59.063 34.615 0.00 0.00 0.00 1.82
5961 7590 6.974932 AGTGACTACATACAGAGCAAAATG 57.025 37.500 0.00 0.00 0.00 2.32
5962 7591 6.701340 AGTGACTACATACAGAGCAAAATGA 58.299 36.000 0.00 0.00 0.00 2.57
5963 7592 6.815641 AGTGACTACATACAGAGCAAAATGAG 59.184 38.462 0.00 0.00 0.00 2.90
5964 7593 6.591834 GTGACTACATACAGAGCAAAATGAGT 59.408 38.462 0.00 0.00 0.00 3.41
5965 7594 6.591448 TGACTACATACAGAGCAAAATGAGTG 59.409 38.462 0.00 0.00 0.00 3.51
5966 7595 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
5967 7596 7.161404 ACTACATACAGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.00 0.00 3.18
5968 7597 7.826252 ACTACATACAGAGCAAAATGAGTGAAT 59.174 33.333 0.00 0.00 0.00 2.57
5969 7598 7.081526 ACATACAGAGCAAAATGAGTGAATC 57.918 36.000 0.00 0.00 0.00 2.52
5970 7599 6.883217 ACATACAGAGCAAAATGAGTGAATCT 59.117 34.615 0.00 0.00 0.00 2.40
5971 7600 8.043113 ACATACAGAGCAAAATGAGTGAATCTA 58.957 33.333 0.00 0.00 0.00 1.98
5972 7601 6.734104 ACAGAGCAAAATGAGTGAATCTAC 57.266 37.500 0.00 0.00 0.00 2.59
5973 7602 6.233434 ACAGAGCAAAATGAGTGAATCTACA 58.767 36.000 0.00 0.00 0.00 2.74
5974 7603 6.148480 ACAGAGCAAAATGAGTGAATCTACAC 59.852 38.462 0.00 0.00 40.60 2.90
6007 7636 7.997773 ATGTCTATATACGTCTGTATGTGGT 57.002 36.000 0.00 0.00 41.37 4.16
6009 7638 8.315391 TGTCTATATACGTCTGTATGTGGTAC 57.685 38.462 0.00 0.00 41.37 3.34
6010 7639 8.152898 TGTCTATATACGTCTGTATGTGGTACT 58.847 37.037 0.00 0.00 41.37 2.73
6011 7640 8.655092 GTCTATATACGTCTGTATGTGGTACTC 58.345 40.741 0.00 0.00 41.37 2.59
6012 7641 6.814506 ATATACGTCTGTATGTGGTACTCC 57.185 41.667 0.00 0.00 41.37 3.85
6013 7642 2.799017 ACGTCTGTATGTGGTACTCCA 58.201 47.619 0.00 0.00 42.05 3.86
6014 7643 3.362706 ACGTCTGTATGTGGTACTCCAT 58.637 45.455 0.00 0.00 46.20 3.41
6015 7644 3.767673 ACGTCTGTATGTGGTACTCCATT 59.232 43.478 3.69 0.00 46.20 3.16
6016 7645 4.222145 ACGTCTGTATGTGGTACTCCATTT 59.778 41.667 3.69 0.00 46.20 2.32
6017 7646 4.566759 CGTCTGTATGTGGTACTCCATTTG 59.433 45.833 3.69 0.00 46.20 2.32
6018 7647 5.623596 CGTCTGTATGTGGTACTCCATTTGA 60.624 44.000 3.69 0.00 46.20 2.69
6019 7648 6.170506 GTCTGTATGTGGTACTCCATTTGAA 58.829 40.000 3.69 0.00 46.20 2.69
6020 7649 6.653320 GTCTGTATGTGGTACTCCATTTGAAA 59.347 38.462 3.69 0.00 46.20 2.69
6021 7650 7.336931 GTCTGTATGTGGTACTCCATTTGAAAT 59.663 37.037 3.69 0.00 46.20 2.17
6022 7651 7.552687 TCTGTATGTGGTACTCCATTTGAAATC 59.447 37.037 3.69 0.00 46.20 2.17
6023 7652 7.402054 TGTATGTGGTACTCCATTTGAAATCT 58.598 34.615 3.69 0.00 46.20 2.40
6024 7653 7.552687 TGTATGTGGTACTCCATTTGAAATCTC 59.447 37.037 3.69 0.00 46.20 2.75
6025 7654 6.126863 TGTGGTACTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
6026 7655 7.252612 TGTGGTACTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
6027 7656 7.685481 TGTGGTACTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
6028 7657 8.160765 TGTGGTACTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
6029 7658 9.010029 GTGGTACTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
6030 7659 9.581289 TGGTACTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
6034 7663 9.354673 ACTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
6074 7703 8.272889 GGAGGGAGTAGTATTTTACCATTTTCT 58.727 37.037 0.00 0.00 0.00 2.52
6081 7710 9.353999 GTAGTATTTTACCATTTTCTTTGCTGG 57.646 33.333 0.00 0.00 34.84 4.85
6203 8441 5.425196 ACAAAGCATATTGGAGCCAATTT 57.575 34.783 18.94 9.42 43.32 1.82
6333 10242 2.054453 GGGCTTGCATGGTCCCTTC 61.054 63.158 7.73 0.00 35.87 3.46
6337 10247 1.620323 GCTTGCATGGTCCCTTCTTTT 59.380 47.619 1.34 0.00 0.00 2.27
6383 10293 1.205055 AGAGATCCTTTTCCCCGTCC 58.795 55.000 0.00 0.00 0.00 4.79
6405 10315 4.798387 CCTTTTTGCCAGTTATTATCGTGC 59.202 41.667 0.00 0.00 0.00 5.34
6433 10343 1.152756 AAGAAACCTGGGTGCGCTT 60.153 52.632 9.73 0.00 0.00 4.68
6555 11221 1.421268 TGGGCCCTATGTGAATGCTAG 59.579 52.381 25.70 0.00 0.00 3.42
6565 11231 7.551974 CCCTATGTGAATGCTAGGAGAAATATG 59.448 40.741 0.00 0.00 35.07 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 1.535202 TTTTCACATGGCCACCCCC 60.535 57.895 8.16 0.00 0.00 5.40
102 103 3.039252 TCAACCCCAACATCACCTTTT 57.961 42.857 0.00 0.00 0.00 2.27
282 284 2.048222 CGGCGGAACAAGCAGAGA 60.048 61.111 0.00 0.00 36.08 3.10
362 388 2.665185 GCGGAACAGGCTCAACGT 60.665 61.111 0.00 0.00 0.00 3.99
483 509 4.284550 ATGCCAACGCCACCCAGT 62.285 61.111 0.00 0.00 0.00 4.00
686 806 2.045045 CGAATGCAAGCCCTGGGA 60.045 61.111 19.27 0.00 0.00 4.37
698 832 3.564027 GCGAACCCGAGCCGAATG 61.564 66.667 0.00 0.00 38.22 2.67
758 893 2.510064 AATCGGTTTAGTCGCGCCCA 62.510 55.000 0.00 0.00 0.00 5.36
771 906 2.686816 CCGGCGCTTGAAAATCGGT 61.687 57.895 7.64 0.00 35.73 4.69
806 949 3.579302 CCCCAACAGGCACCCTCA 61.579 66.667 0.00 0.00 0.00 3.86
832 978 2.740440 CCGCGTGTGTGTATGCCA 60.740 61.111 4.92 0.00 0.00 4.92
834 980 4.160635 GCCCGCGTGTGTGTATGC 62.161 66.667 4.92 0.00 0.00 3.14
879 1025 0.042581 TCCAGCCACAGAGATACCCA 59.957 55.000 0.00 0.00 0.00 4.51
1248 1424 1.410517 CCGCCAGATCACACTATGAGT 59.589 52.381 0.00 0.00 41.91 3.41
1383 1559 3.748083 AGCACACATATCAAGCCTATGG 58.252 45.455 0.00 0.00 32.06 2.74
1494 1672 3.628032 TCGAGTGTTGCTAGGTAGATCAG 59.372 47.826 0.00 0.00 0.00 2.90
1561 1739 6.488006 AGTGCACATCTTTGTAGATCAAAAGT 59.512 34.615 21.04 0.00 44.08 2.66
1628 1806 5.527582 ACACATCTTTACAGACTTGTTGGAC 59.472 40.000 0.00 0.00 38.76 4.02
1667 1854 7.283127 TCAGACTTTGCAATATAATCCTTCCAC 59.717 37.037 0.00 0.00 0.00 4.02
1691 1878 6.540551 TGTATAAGTCAGCAACAAACTTGTCA 59.459 34.615 0.00 0.00 41.31 3.58
1692 1879 6.954944 TGTATAAGTCAGCAACAAACTTGTC 58.045 36.000 0.00 0.00 41.31 3.18
1730 1917 7.896811 AGTAGCGATGAATATCACTAAATGGA 58.103 34.615 0.00 0.00 31.66 3.41
1767 1954 0.465097 AGCATGTGTGGCAGATAGGC 60.465 55.000 9.92 9.92 44.50 3.93
1775 1962 0.109132 GCCTTTGTAGCATGTGTGGC 60.109 55.000 0.00 0.00 0.00 5.01
2163 2356 8.575589 TCTTATTGCAGCAGAAATACAGAAAAA 58.424 29.630 0.00 0.00 0.00 1.94
2438 2631 7.255730 GCAGAAAATATAACTCCTCAATGGCAT 60.256 37.037 0.00 0.00 35.26 4.40
2667 2862 9.116067 GCAAATGTAATGTACCTCTATAAACCA 57.884 33.333 0.00 0.00 0.00 3.67
2704 2900 6.852664 AGCATTTCTTTACCTTCCATAAACG 58.147 36.000 0.00 0.00 0.00 3.60
2786 2982 6.577427 GTGTTTATTGACAGAAAGCCTTAACG 59.423 38.462 0.00 0.00 0.00 3.18
2883 3079 5.238432 ACTTCAATTAGACGCAAATGACACA 59.762 36.000 0.00 0.00 0.00 3.72
3091 3287 9.098355 TGATTGTAAGTTTCATAGATGTACTGC 57.902 33.333 0.00 0.00 0.00 4.40
3598 3795 6.183360 ACACTTTCCAAGTTTGACTAATGTGG 60.183 38.462 15.87 0.00 40.46 4.17
3707 3907 7.309377 CCACTCACATCATAAAACATCCAAACT 60.309 37.037 0.00 0.00 0.00 2.66
3763 3963 7.589574 AAAAATGACAGTACAACAACAAACC 57.410 32.000 0.00 0.00 0.00 3.27
3880 4094 1.211457 GTGATTCCATCTCCCTGTGCT 59.789 52.381 0.00 0.00 0.00 4.40
3910 4124 8.602424 TCAAATATTCTGAAAAGAGGGAGTACA 58.398 33.333 0.00 0.00 0.00 2.90
4097 4685 7.357951 TCAAAACATTTGAAGTTTGACCAAC 57.642 32.000 3.18 0.00 39.02 3.77
4215 4803 4.812626 CAGCTTTTTCCTCACAAGCAAAAT 59.187 37.500 5.95 0.00 44.57 1.82
4420 5008 3.377485 CCTGTAGACGCACTAGTATGTGT 59.623 47.826 0.00 0.00 45.84 3.72
4421 5009 3.377485 ACCTGTAGACGCACTAGTATGTG 59.623 47.826 0.00 0.00 40.62 3.21
4433 5021 2.440539 AGCAAGTTGACCTGTAGACG 57.559 50.000 7.16 0.00 0.00 4.18
4704 5292 5.248477 AGACCATGTGACCTGTTTGTAGTAT 59.752 40.000 0.00 0.00 0.00 2.12
4846 6325 7.061673 GCTGATCGCTAAGATAAGATAACACAG 59.938 40.741 2.84 0.00 39.77 3.66
4865 6344 4.212847 CCTCATAAGAACAATGGCTGATCG 59.787 45.833 0.00 0.00 32.24 3.69
4981 6520 5.171476 CCTGCGTCCCATAATATAAGAGTG 58.829 45.833 0.00 0.00 0.00 3.51
4982 6521 4.223032 CCCTGCGTCCCATAATATAAGAGT 59.777 45.833 0.00 0.00 0.00 3.24
5001 6540 6.710597 TGCAGTACTAACTAATACTCCCTG 57.289 41.667 0.00 0.00 33.48 4.45
5027 6566 3.189287 AGTTGCCGCTTTGATGTTAGAAG 59.811 43.478 0.00 0.00 0.00 2.85
5089 6628 5.560966 AGAAATACAGCCCACAATTTACG 57.439 39.130 0.00 0.00 0.00 3.18
5325 6948 2.232452 CCCTCCGAGTATATCTTGCCAG 59.768 54.545 0.00 0.00 0.00 4.85
5532 7160 3.620488 ACTTGAAGTTGCCAGAGAACAA 58.380 40.909 0.00 0.00 0.00 2.83
5581 7209 2.594592 ACGGTTGCTTCACTGGGC 60.595 61.111 0.00 0.00 0.00 5.36
5582 7210 1.966451 GGACGGTTGCTTCACTGGG 60.966 63.158 0.00 0.00 0.00 4.45
5583 7211 1.966451 GGGACGGTTGCTTCACTGG 60.966 63.158 0.00 0.00 0.00 4.00
5584 7212 1.966451 GGGGACGGTTGCTTCACTG 60.966 63.158 0.00 0.00 0.00 3.66
5585 7213 2.397413 CTGGGGACGGTTGCTTCACT 62.397 60.000 0.00 0.00 0.00 3.41
5586 7214 1.966451 CTGGGGACGGTTGCTTCAC 60.966 63.158 0.00 0.00 0.00 3.18
5587 7215 2.429930 CTGGGGACGGTTGCTTCA 59.570 61.111 0.00 0.00 0.00 3.02
5588 7216 3.056328 GCTGGGGACGGTTGCTTC 61.056 66.667 0.00 0.00 39.64 3.86
5589 7217 4.660938 GGCTGGGGACGGTTGCTT 62.661 66.667 0.00 0.00 39.64 3.91
5592 7220 4.722700 CTGGGCTGGGGACGGTTG 62.723 72.222 0.00 0.00 39.64 3.77
5596 7224 3.612247 CTTCACTGGGCTGGGGACG 62.612 68.421 0.00 0.00 0.00 4.79
5597 7225 2.352805 CTTCACTGGGCTGGGGAC 59.647 66.667 0.00 0.00 0.00 4.46
5598 7226 3.650950 GCTTCACTGGGCTGGGGA 61.651 66.667 0.00 0.00 0.00 4.81
5600 7228 4.020617 TCGCTTCACTGGGCTGGG 62.021 66.667 0.00 0.00 0.00 4.45
5601 7229 2.743928 GTCGCTTCACTGGGCTGG 60.744 66.667 0.00 0.00 0.00 4.85
5602 7230 1.364626 GATGTCGCTTCACTGGGCTG 61.365 60.000 0.00 0.00 0.00 4.85
5603 7231 1.078848 GATGTCGCTTCACTGGGCT 60.079 57.895 0.00 0.00 0.00 5.19
5619 7247 0.659427 CAATGCCAACGCTCATCGAT 59.341 50.000 0.00 0.00 41.67 3.59
5779 7408 0.105964 TCCTAGCTAGAGGCAGGTGG 60.106 60.000 22.70 2.85 44.79 4.61
5929 7558 8.936864 GCTCTGTATGTAGTCACTTGTTAAAAT 58.063 33.333 0.00 0.00 0.00 1.82
5930 7559 7.929245 TGCTCTGTATGTAGTCACTTGTTAAAA 59.071 33.333 0.00 0.00 0.00 1.52
5932 7561 6.988522 TGCTCTGTATGTAGTCACTTGTTAA 58.011 36.000 0.00 0.00 0.00 2.01
5933 7562 6.584185 TGCTCTGTATGTAGTCACTTGTTA 57.416 37.500 0.00 0.00 0.00 2.41
5934 7563 5.468540 TGCTCTGTATGTAGTCACTTGTT 57.531 39.130 0.00 0.00 0.00 2.83
5936 7565 6.785488 TTTTGCTCTGTATGTAGTCACTTG 57.215 37.500 0.00 0.00 0.00 3.16
5937 7566 7.161404 TCATTTTGCTCTGTATGTAGTCACTT 58.839 34.615 0.00 0.00 0.00 3.16
5938 7567 6.701340 TCATTTTGCTCTGTATGTAGTCACT 58.299 36.000 0.00 0.00 0.00 3.41
5939 7568 6.591834 ACTCATTTTGCTCTGTATGTAGTCAC 59.408 38.462 0.00 0.00 0.00 3.67
5941 7570 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
5942 7571 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
5943 7572 7.601073 TTCACTCATTTTGCTCTGTATGTAG 57.399 36.000 0.00 0.00 0.00 2.74
5944 7573 8.043113 AGATTCACTCATTTTGCTCTGTATGTA 58.957 33.333 0.00 0.00 0.00 2.29
5945 7574 6.883217 AGATTCACTCATTTTGCTCTGTATGT 59.117 34.615 0.00 0.00 0.00 2.29
5946 7575 7.317842 AGATTCACTCATTTTGCTCTGTATG 57.682 36.000 0.00 0.00 0.00 2.39
5948 7577 7.331934 GTGTAGATTCACTCATTTTGCTCTGTA 59.668 37.037 0.00 0.00 35.68 2.74
5949 7578 6.148480 GTGTAGATTCACTCATTTTGCTCTGT 59.852 38.462 0.00 0.00 35.68 3.41
5950 7579 6.370994 AGTGTAGATTCACTCATTTTGCTCTG 59.629 38.462 0.00 0.00 44.07 3.35
5951 7580 6.471146 AGTGTAGATTCACTCATTTTGCTCT 58.529 36.000 0.00 0.00 44.07 4.09
5981 7610 9.682465 ACCACATACAGACGTATATAGACATAT 57.318 33.333 0.00 0.00 36.11 1.78
5983 7612 7.997773 ACCACATACAGACGTATATAGACAT 57.002 36.000 0.00 0.00 36.11 3.06
5984 7613 8.152898 AGTACCACATACAGACGTATATAGACA 58.847 37.037 0.00 0.00 36.11 3.41
5985 7614 8.545229 AGTACCACATACAGACGTATATAGAC 57.455 38.462 0.00 0.00 36.11 2.59
5986 7615 7.821359 GGAGTACCACATACAGACGTATATAGA 59.179 40.741 0.00 0.00 36.09 1.98
5987 7616 7.605309 TGGAGTACCACATACAGACGTATATAG 59.395 40.741 0.00 0.00 41.77 1.31
5988 7617 7.452562 TGGAGTACCACATACAGACGTATATA 58.547 38.462 0.00 0.00 41.77 0.86
5989 7618 6.301486 TGGAGTACCACATACAGACGTATAT 58.699 40.000 0.00 0.00 41.77 0.86
5990 7619 5.683681 TGGAGTACCACATACAGACGTATA 58.316 41.667 0.00 0.00 41.77 1.47
5991 7620 4.529897 TGGAGTACCACATACAGACGTAT 58.470 43.478 0.00 0.00 41.77 3.06
5992 7621 3.954200 TGGAGTACCACATACAGACGTA 58.046 45.455 0.00 0.00 41.77 3.57
5993 7622 2.799017 TGGAGTACCACATACAGACGT 58.201 47.619 0.00 0.00 41.77 4.34
6008 7637 9.354673 TGTCTTTTTAGAGATTTCAAATGGAGT 57.645 29.630 0.00 0.00 0.00 3.85
6026 7655 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
6027 7656 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
6028 7657 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
6029 7658 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
6030 7659 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
6031 7660 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
6032 7661 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
6033 7662 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
6034 7663 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
6035 7664 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
6036 7665 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
6042 7671 3.684408 AATACTACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
6074 7703 3.011566 TCTCAAGTCCAAACCAGCAAA 57.988 42.857 0.00 0.00 0.00 3.68
6081 7710 5.947228 TGTGAATGATCTCAAGTCCAAAC 57.053 39.130 0.00 0.00 0.00 2.93
6203 8441 9.577110 GATGATGAAATTTTCTCAGCAATTACA 57.423 29.630 10.33 0.00 42.06 2.41
6333 10242 3.133691 GCTGGAAAAAGGGCTGAAAAAG 58.866 45.455 0.00 0.00 0.00 2.27
6337 10247 1.133513 TCTGCTGGAAAAAGGGCTGAA 60.134 47.619 0.00 0.00 31.69 3.02
6383 10293 5.512788 CAGCACGATAATAACTGGCAAAAAG 59.487 40.000 0.00 0.00 0.00 2.27
6433 10343 4.095185 CCGCGTTTCTAAATAAATGGTCCA 59.905 41.667 4.92 0.00 0.00 4.02
6555 11221 0.308993 GCAGCACCGCATATTTCTCC 59.691 55.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.