Multiple sequence alignment - TraesCS3B01G342900

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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 TraesCS3B01G342900 chr3B 100.000 4863 0 0 1 4863 550728817 550733679 0.000000e+00 8981.0
1 TraesCS3B01G342900 chr3B 95.065 851 36 3 1 850 460338442 460339287 0.000000e+00 1334.0
2 TraesCS3B01G342900 chr3B 94.947 851 37 3 1 850 460325745 460326590 0.000000e+00 1328.0
3 TraesCS3B01G342900 chr3B 94.947 851 37 3 1 850 460331545 460332390 0.000000e+00 1328.0
4 TraesCS3B01G342900 chr3B 94.947 851 37 3 1 850 460344428 460345273 0.000000e+00 1328.0
5 TraesCS3B01G342900 chr3B 87.500 640 69 8 4199 4834 639434142 639434774 0.000000e+00 728.0
6 TraesCS3B01G342900 chr3A 91.743 2931 154 34 1287 4152 566327637 566324730 0.000000e+00 3991.0
7 TraesCS3B01G342900 chr3A 99.049 841 8 0 1 841 723143346 723142506 0.000000e+00 1509.0
8 TraesCS3B01G342900 chr3A 96.269 402 14 1 840 1241 566328038 566327638 0.000000e+00 658.0
9 TraesCS3B01G342900 chr3D 92.693 2258 85 33 1996 4198 422648396 422650628 0.000000e+00 3182.0
10 TraesCS3B01G342900 chr3D 97.506 401 8 2 841 1241 422647187 422647585 0.000000e+00 684.0
11 TraesCS3B01G342900 chr3D 89.358 545 41 8 1287 1821 422647586 422648123 0.000000e+00 669.0
12 TraesCS3B01G342900 chr3D 94.771 153 8 0 1815 1967 422648146 422648298 6.290000e-59 239.0
13 TraesCS3B01G342900 chr4A 95.193 853 39 2 1 852 271087203 271088054 0.000000e+00 1347.0
14 TraesCS3B01G342900 chr2D 94.656 842 41 3 1 840 295576574 295575735 0.000000e+00 1303.0
15 TraesCS3B01G342900 chr2D 86.917 665 78 9 4198 4858 313845875 313845216 0.000000e+00 737.0
16 TraesCS3B01G342900 chrUn 96.311 759 24 2 1 756 96416066 96415309 0.000000e+00 1243.0
17 TraesCS3B01G342900 chrUn 100.000 179 0 0 1 179 479358356 479358534 1.010000e-86 331.0
18 TraesCS3B01G342900 chrUn 92.857 98 7 0 746 843 96414581 96414484 5.070000e-30 143.0
19 TraesCS3B01G342900 chr6B 91.445 678 42 6 4201 4863 292823713 292824389 0.000000e+00 917.0
20 TraesCS3B01G342900 chr6B 91.189 681 46 3 4197 4863 537721430 537720750 0.000000e+00 913.0
21 TraesCS3B01G342900 chr6B 91.176 680 46 3 4198 4863 382921713 382921034 0.000000e+00 911.0
22 TraesCS3B01G342900 chr6B 90.105 667 62 4 4199 4863 199044003 199043339 0.000000e+00 863.0
23 TraesCS3B01G342900 chr4D 91.228 684 45 4 4195 4863 15122132 15122815 0.000000e+00 917.0
24 TraesCS3B01G342900 chr4D 86.826 668 77 9 4199 4863 403547638 403546979 0.000000e+00 736.0
25 TraesCS3B01G342900 chr2B 91.189 681 43 6 4198 4863 195951382 195950704 0.000000e+00 909.0
26 TraesCS3B01G342900 chr2B 91.029 680 47 4 4198 4863 595364267 595363588 0.000000e+00 905.0
27 TraesCS3B01G342900 chr2B 85.859 99 11 3 744 840 601390163 601390260 8.610000e-18 102.0
28 TraesCS3B01G342900 chr5B 94.128 596 35 0 4268 4863 499007793 499007198 0.000000e+00 907.0
29 TraesCS3B01G342900 chr5B 87.779 671 65 12 4199 4863 121938587 121939246 0.000000e+00 769.0
30 TraesCS3B01G342900 chr7B 90.776 683 49 4 4195 4863 389227824 389228506 0.000000e+00 900.0
31 TraesCS3B01G342900 chr4B 87.592 677 74 8 4195 4863 602048253 602048927 0.000000e+00 776.0
32 TraesCS3B01G342900 chr4B 88.346 635 63 9 4234 4863 548566071 548566699 0.000000e+00 752.0
33 TraesCS3B01G342900 chr5D 87.500 664 72 11 4199 4858 112941165 112940509 0.000000e+00 756.0
34 TraesCS3B01G342900 chr7A 86.154 650 78 10 4199 4846 217884178 217883539 0.000000e+00 691.0
35 TraesCS3B01G342900 chr7A 85.562 658 67 14 1094 1738 95652068 95652710 0.000000e+00 664.0
36 TraesCS3B01G342900 chr7A 87.261 157 17 3 944 1098 95644837 95644992 5.000000e-40 176.0
37 TraesCS3B01G342900 chr1A 84.211 133 20 1 3344 3476 516786899 516786768 1.420000e-25 128.0
38 TraesCS3B01G342900 chr1A 73.789 351 68 20 2893 3231 516787546 516787208 3.080000e-22 117.0
39 TraesCS3B01G342900 chr1A 78.899 109 23 0 2893 3001 516850148 516850040 1.880000e-09 75.0
40 TraesCS3B01G342900 chr1B 83.459 133 21 1 3344 3476 568569130 568568999 6.610000e-24 122.0
41 TraesCS3B01G342900 chr1B 73.219 351 73 18 2893 3231 568569750 568569409 1.850000e-19 108.0
42 TraesCS3B01G342900 chr1B 79.817 109 22 0 2893 3001 568644106 568643998 4.030000e-11 80.5
43 TraesCS3B01G342900 chr1D 82.707 133 22 1 3344 3476 420554311 420554180 3.080000e-22 117.0
44 TraesCS3B01G342900 chr1D 85.714 91 11 2 2893 2982 420555042 420554953 1.440000e-15 95.3
45 TraesCS3B01G342900 chr1D 79.245 106 22 0 2893 2998 420565690 420565585 1.880000e-09 75.0


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 TraesCS3B01G342900 chr3B 550728817 550733679 4862 False 8981.0 8981 100.000 1 4863 1 chr3B.!!$F5 4862
1 TraesCS3B01G342900 chr3B 460338442 460339287 845 False 1334.0 1334 95.065 1 850 1 chr3B.!!$F3 849
2 TraesCS3B01G342900 chr3B 460325745 460326590 845 False 1328.0 1328 94.947 1 850 1 chr3B.!!$F1 849
3 TraesCS3B01G342900 chr3B 460331545 460332390 845 False 1328.0 1328 94.947 1 850 1 chr3B.!!$F2 849
4 TraesCS3B01G342900 chr3B 460344428 460345273 845 False 1328.0 1328 94.947 1 850 1 chr3B.!!$F4 849
5 TraesCS3B01G342900 chr3B 639434142 639434774 632 False 728.0 728 87.500 4199 4834 1 chr3B.!!$F6 635
6 TraesCS3B01G342900 chr3A 566324730 566328038 3308 True 2324.5 3991 94.006 840 4152 2 chr3A.!!$R2 3312
7 TraesCS3B01G342900 chr3A 723142506 723143346 840 True 1509.0 1509 99.049 1 841 1 chr3A.!!$R1 840
8 TraesCS3B01G342900 chr3D 422647187 422650628 3441 False 1193.5 3182 93.582 841 4198 4 chr3D.!!$F1 3357
9 TraesCS3B01G342900 chr4A 271087203 271088054 851 False 1347.0 1347 95.193 1 852 1 chr4A.!!$F1 851
10 TraesCS3B01G342900 chr2D 295575735 295576574 839 True 1303.0 1303 94.656 1 840 1 chr2D.!!$R1 839
11 TraesCS3B01G342900 chr2D 313845216 313845875 659 True 737.0 737 86.917 4198 4858 1 chr2D.!!$R2 660
12 TraesCS3B01G342900 chrUn 96414484 96416066 1582 True 693.0 1243 94.584 1 843 2 chrUn.!!$R1 842
13 TraesCS3B01G342900 chr6B 292823713 292824389 676 False 917.0 917 91.445 4201 4863 1 chr6B.!!$F1 662
14 TraesCS3B01G342900 chr6B 537720750 537721430 680 True 913.0 913 91.189 4197 4863 1 chr6B.!!$R3 666
15 TraesCS3B01G342900 chr6B 382921034 382921713 679 True 911.0 911 91.176 4198 4863 1 chr6B.!!$R2 665
16 TraesCS3B01G342900 chr6B 199043339 199044003 664 True 863.0 863 90.105 4199 4863 1 chr6B.!!$R1 664
17 TraesCS3B01G342900 chr4D 15122132 15122815 683 False 917.0 917 91.228 4195 4863 1 chr4D.!!$F1 668
18 TraesCS3B01G342900 chr4D 403546979 403547638 659 True 736.0 736 86.826 4199 4863 1 chr4D.!!$R1 664
19 TraesCS3B01G342900 chr2B 195950704 195951382 678 True 909.0 909 91.189 4198 4863 1 chr2B.!!$R1 665
20 TraesCS3B01G342900 chr2B 595363588 595364267 679 True 905.0 905 91.029 4198 4863 1 chr2B.!!$R2 665
21 TraesCS3B01G342900 chr5B 499007198 499007793 595 True 907.0 907 94.128 4268 4863 1 chr5B.!!$R1 595
22 TraesCS3B01G342900 chr5B 121938587 121939246 659 False 769.0 769 87.779 4199 4863 1 chr5B.!!$F1 664
23 TraesCS3B01G342900 chr7B 389227824 389228506 682 False 900.0 900 90.776 4195 4863 1 chr7B.!!$F1 668
24 TraesCS3B01G342900 chr4B 602048253 602048927 674 False 776.0 776 87.592 4195 4863 1 chr4B.!!$F2 668
25 TraesCS3B01G342900 chr4B 548566071 548566699 628 False 752.0 752 88.346 4234 4863 1 chr4B.!!$F1 629
26 TraesCS3B01G342900 chr5D 112940509 112941165 656 True 756.0 756 87.500 4199 4858 1 chr5D.!!$R1 659
27 TraesCS3B01G342900 chr7A 217883539 217884178 639 True 691.0 691 86.154 4199 4846 1 chr7A.!!$R1 647
28 TraesCS3B01G342900 chr7A 95652068 95652710 642 False 664.0 664 85.562 1094 1738 1 chr7A.!!$F2 644

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
608 613 0.761187 GACATAGCTGATGGGGAGCA 59.239 55.0 0.00 0.0 40.18 4.26 F
1566 2313 0.178533 AATTGCATCCGCCCAAATGG 59.821 50.0 0.00 0.0 37.32 3.16 F
2626 3524 0.677731 GTAGCATTGGTCAGGCTGCA 60.678 55.0 10.34 0.0 39.60 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 3503 0.035152 CAGCCTGACCAATGCTACCA 60.035 55.0 0.00 0.0 33.16 3.25 R
3466 4384 0.553819 ACCAACCCAACTTACCTGCA 59.446 50.0 0.00 0.0 0.00 4.41 R
4624 5573 0.974010 AACCGGCAGATCTCGGGTAA 60.974 55.0 22.66 0.0 45.54 2.85 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
513 518 6.350906 TGGGGAGTACAAAGGTAATTATTCG 58.649 40.000 0.00 0.00 0.00 3.34
605 610 4.907269 TCTTTATGACATAGCTGATGGGGA 59.093 41.667 0.00 0.00 40.18 4.81
608 613 0.761187 GACATAGCTGATGGGGAGCA 59.239 55.000 0.00 0.00 40.18 4.26
805 1549 5.277058 GCTCGCATAGAGGAAAAAGTACATG 60.277 44.000 0.00 0.00 46.91 3.21
843 1587 1.032794 CGGGCACTCAGCTAGTCATA 58.967 55.000 0.00 0.00 44.79 2.15
844 1588 1.269309 CGGGCACTCAGCTAGTCATAC 60.269 57.143 0.00 0.00 44.79 2.39
845 1589 1.757118 GGGCACTCAGCTAGTCATACA 59.243 52.381 0.00 0.00 44.79 2.29
855 1599 6.249192 TCAGCTAGTCATACATACATAGCCT 58.751 40.000 0.00 0.00 37.03 4.58
864 1608 2.162608 ACATACATAGCCTCGCGATCTC 59.837 50.000 10.36 1.23 0.00 2.75
933 1677 4.016706 CCCCGGTTCAGTTCGCCT 62.017 66.667 0.00 0.00 0.00 5.52
1229 1973 4.210304 GCGCCGCGTCATCAAGAC 62.210 66.667 15.34 0.00 44.02 3.01
1241 1985 2.169769 TCATCAAGACGGTAATGTCCCC 59.830 50.000 0.00 0.00 39.77 4.81
1247 1991 2.913501 GGTAATGTCCCCGACCCC 59.086 66.667 0.00 0.00 0.00 4.95
1248 1992 2.502577 GTAATGTCCCCGACCCCG 59.497 66.667 0.00 0.00 0.00 5.73
1316 2060 2.433436 CGATTTCGGGGAGAGGTTTTT 58.567 47.619 0.00 0.00 35.37 1.94
1357 2101 2.240612 GAATCGCCTTCCGTGTGTGC 62.241 60.000 0.00 0.00 38.35 4.57
1407 2152 2.112928 TGCAACATGGTGGACGCT 59.887 55.556 13.78 0.00 0.00 5.07
1465 2210 1.599419 GCGTGGTCATGTTTGTTGGTC 60.599 52.381 0.00 0.00 0.00 4.02
1478 2223 1.765904 TGTTGGTCTGCAAGGTCAGTA 59.234 47.619 0.00 0.00 35.63 2.74
1486 2231 0.253044 GCAAGGTCAGTATGCCCTGA 59.747 55.000 0.00 0.00 39.11 3.86
1499 2244 1.153745 CCCTGACTGCTGCTACGTC 60.154 63.158 0.00 5.84 0.00 4.34
1529 2274 7.653647 TGTCCAAATTCTGTTTTGTGGTATAC 58.346 34.615 0.00 0.00 35.30 1.47
1566 2313 0.178533 AATTGCATCCGCCCAAATGG 59.821 50.000 0.00 0.00 37.32 3.16
1632 2383 5.013236 CGGTTAAATTCGATGAGAACAACG 58.987 41.667 0.00 0.00 42.39 4.10
1638 2389 6.961359 AATTCGATGAGAACAACGTTATCA 57.039 33.333 0.00 6.64 42.39 2.15
1639 2390 6.961359 ATTCGATGAGAACAACGTTATCAA 57.039 33.333 0.00 0.00 42.39 2.57
1640 2391 5.756950 TCGATGAGAACAACGTTATCAAC 57.243 39.130 0.00 5.23 41.70 3.18
1726 2485 8.067189 GGCAAACGATTGAAACAAATTAACATT 58.933 29.630 9.88 0.00 38.94 2.71
1766 2525 8.410141 TCACCTTCAATGTTACTTTTACTTTGG 58.590 33.333 0.00 0.00 33.74 3.28
1775 2540 3.735591 ACTTTTACTTTGGCGAGCTACA 58.264 40.909 0.00 0.00 0.00 2.74
1792 2557 4.837298 AGCTACAGGCATATGATTCTCTCA 59.163 41.667 6.97 0.00 44.79 3.27
1834 2627 3.375299 ACAAGAAGCGATGTAATTGGAGC 59.625 43.478 0.00 0.00 0.00 4.70
1842 2635 3.804325 CGATGTAATTGGAGCTGTAGTGG 59.196 47.826 0.00 0.00 0.00 4.00
1957 2750 8.153221 TCTTGGATGGGTAGTTTGTAATTAGA 57.847 34.615 0.00 0.00 0.00 2.10
1991 2856 7.216494 TCGGTGATTAGATTGCATTCTTATCA 58.784 34.615 25.22 25.22 38.67 2.15
2055 2922 1.107114 CTGGCTCACTACTGATCGGT 58.893 55.000 12.79 12.79 0.00 4.69
2068 2935 9.000486 CACTACTGATCGGTTATATGTCTTCTA 58.000 37.037 13.53 0.00 0.00 2.10
2086 2953 4.764679 TCTACATGTTGGTTGCATTGAC 57.235 40.909 2.30 0.00 0.00 3.18
2304 3195 6.671190 TCACTTCAACTGCTTATGATTTGTG 58.329 36.000 0.00 0.00 0.00 3.33
2312 3203 7.934855 ACTGCTTATGATTTGTGATCTCTTT 57.065 32.000 0.00 0.00 0.00 2.52
2343 3234 2.549064 TGTTGTGTCACTGCAGCTAT 57.451 45.000 15.27 0.00 0.00 2.97
2406 3297 8.414003 GTGGAGAGGTTTAGAAAAGAAAATTGT 58.586 33.333 0.00 0.00 0.00 2.71
2605 3503 7.000472 CAGACCTGGTAATATTTGTGATGGAT 59.000 38.462 0.00 0.00 0.00 3.41
2606 3504 7.000472 AGACCTGGTAATATTTGTGATGGATG 59.000 38.462 0.00 0.00 0.00 3.51
2626 3524 0.677731 GTAGCATTGGTCAGGCTGCA 60.678 55.000 10.34 0.00 39.60 4.41
2641 3539 1.945354 CTGCATTTGCTCAGGCCCAG 61.945 60.000 0.00 0.00 42.66 4.45
2662 3560 1.340889 GCATTCAGGCAAAGTGTTCCA 59.659 47.619 0.00 0.00 0.00 3.53
2755 3653 9.498176 GTATTCACTTCCCTTTTCTTACACTAA 57.502 33.333 0.00 0.00 0.00 2.24
2880 3793 8.842280 TCATTAACATTTCAAGACCTAACGTTT 58.158 29.630 5.91 0.00 0.00 3.60
3022 3935 4.873827 AGTGTAAATATTAGGTGTGGCGTG 59.126 41.667 0.00 0.00 0.00 5.34
3043 3956 5.933463 CGTGTTACCTGTGTATTCCCTTTAA 59.067 40.000 0.00 0.00 0.00 1.52
3045 3958 6.149973 GTGTTACCTGTGTATTCCCTTTAACC 59.850 42.308 0.00 0.00 0.00 2.85
3046 3959 6.044637 TGTTACCTGTGTATTCCCTTTAACCT 59.955 38.462 0.00 0.00 0.00 3.50
3047 3960 5.175388 ACCTGTGTATTCCCTTTAACCTC 57.825 43.478 0.00 0.00 0.00 3.85
3049 3962 4.227527 CCTGTGTATTCCCTTTAACCTCCT 59.772 45.833 0.00 0.00 0.00 3.69
3051 3964 5.566469 TGTGTATTCCCTTTAACCTCCTTG 58.434 41.667 0.00 0.00 0.00 3.61
3084 3999 5.139727 CAATTGGCAGGTATGGGAGATTTA 58.860 41.667 0.00 0.00 0.00 1.40
3118 4033 3.402628 ACAAGGCTCGTCAAGTTGTAT 57.597 42.857 2.11 0.00 29.63 2.29
3123 4038 2.000447 GCTCGTCAAGTTGTATCCACC 59.000 52.381 2.11 0.00 0.00 4.61
3251 4166 6.017109 CAGGTAAGCTTGCTTTAGTCTTTCAA 60.017 38.462 14.47 0.00 0.00 2.69
3319 4234 4.153117 GGCTCGATTGCTGTTTGATATAGG 59.847 45.833 0.00 0.00 0.00 2.57
3387 4305 3.420893 TGTTGCCTGGATTTAGTTCTGG 58.579 45.455 0.00 0.00 0.00 3.86
3433 4351 3.523564 AGCAGGGTGAGGCTAAGATAAAA 59.476 43.478 0.00 0.00 38.90 1.52
3466 4384 4.041321 ACGATGATGGATTCCATGACAGAT 59.959 41.667 22.89 6.67 45.26 2.90
3504 4422 1.965930 GAGTCAACCCATGCGTGCA 60.966 57.895 0.00 0.00 0.00 4.57
3515 4433 5.123227 ACCCATGCGTGCATATATATTACC 58.877 41.667 7.07 0.00 34.91 2.85
3604 4522 4.305539 TCCAAAGCTGATGAAGGAATCA 57.694 40.909 1.45 0.00 43.67 2.57
3645 4563 3.746949 GATCTGGCCGGCCTGTCAG 62.747 68.421 43.34 32.20 36.57 3.51
3772 4690 2.685380 AGCAAGTCCCTCCCTCCG 60.685 66.667 0.00 0.00 0.00 4.63
3793 4711 3.746114 CGGAGCTACTGACTCAGATAGGT 60.746 52.174 13.25 14.23 35.79 3.08
3801 4719 3.106827 TGACTCAGATAGGTGGCATTGA 58.893 45.455 0.00 0.00 0.00 2.57
3804 4722 3.713248 ACTCAGATAGGTGGCATTGATGA 59.287 43.478 0.00 0.00 0.00 2.92
3815 4733 4.096382 GTGGCATTGATGAATTACGGTCTT 59.904 41.667 0.00 0.00 0.00 3.01
3885 4805 5.861727 ACTTGAACGGATTAAGTAGGTTGT 58.138 37.500 0.00 0.00 33.22 3.32
3888 4808 8.098912 ACTTGAACGGATTAAGTAGGTTGTAAT 58.901 33.333 0.00 0.00 33.22 1.89
3903 4824 2.821546 TGTAATCGGCAATCTTCGAGG 58.178 47.619 0.00 0.00 38.83 4.63
3968 4889 7.414540 GCCAAATTGTAAATTGGTTTGTTCACA 60.415 33.333 11.83 0.00 46.29 3.58
3975 4896 8.470805 TGTAAATTGGTTTGTTCACAGTAACAT 58.529 29.630 0.00 0.00 39.04 2.71
3977 4898 8.785329 AAATTGGTTTGTTCACAGTAACATTT 57.215 26.923 0.00 0.00 39.04 2.32
3999 4922 5.941146 TTAGCCCCCAATGGTTCTTATAT 57.059 39.130 0.00 0.00 0.00 0.86
4030 4953 7.581213 TGAATGAATTGTCTGTTGGTAAAGT 57.419 32.000 0.00 0.00 0.00 2.66
4035 4958 7.254852 TGAATTGTCTGTTGGTAAAGTCAAAC 58.745 34.615 0.00 0.00 0.00 2.93
4152 5077 9.209048 AGGACTACATATGTAATTGTTCTACCA 57.791 33.333 16.17 0.00 0.00 3.25
4191 5116 9.238368 TGGAAATAACTACACAGAAAAATAGGG 57.762 33.333 0.00 0.00 0.00 3.53
4192 5117 8.683615 GGAAATAACTACACAGAAAAATAGGGG 58.316 37.037 0.00 0.00 0.00 4.79
4227 5153 1.132500 CTGGATTAGGGGGTCCTCAC 58.868 60.000 0.00 0.00 43.66 3.51
4374 5316 4.420522 AACCGACTTTGTGTAACCCTAA 57.579 40.909 0.00 0.00 34.36 2.69
4470 5418 3.487120 AGGGTTTAGCCATTACGATCC 57.513 47.619 0.26 0.00 39.65 3.36
4547 5496 7.015064 GGAAGTAGGGTATTACCTCCATAGAA 58.985 42.308 12.54 0.00 42.09 2.10
4619 5568 0.736325 CTTAGACGCACAGTTCGGGG 60.736 60.000 0.00 0.00 0.00 5.73
4785 5735 2.046700 CCGACTGGGCGGCTTTAA 60.047 61.111 9.56 0.00 45.38 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 183 0.248417 CGACTGAGAGGATGTCTGCG 60.248 60.000 0.00 0.00 34.71 5.18
513 518 8.209869 CGACAATTTGAATTTTCTTCACATGTC 58.790 33.333 2.79 12.39 35.02 3.06
605 610 4.037803 TGACACAACTACAAAATGCATGCT 59.962 37.500 20.33 1.07 0.00 3.79
608 613 4.925054 GCATGACACAACTACAAAATGCAT 59.075 37.500 0.00 0.00 39.13 3.96
843 1587 2.162608 GAGATCGCGAGGCTATGTATGT 59.837 50.000 16.66 0.00 0.00 2.29
844 1588 2.478709 GGAGATCGCGAGGCTATGTATG 60.479 54.545 16.66 0.00 0.00 2.39
845 1589 1.746220 GGAGATCGCGAGGCTATGTAT 59.254 52.381 16.66 0.00 0.00 2.29
855 1599 3.709348 TTCGAGGGGGAGATCGCGA 62.709 63.158 13.09 13.09 38.79 5.87
864 1608 4.043100 GGGTGGGTTTCGAGGGGG 62.043 72.222 0.00 0.00 0.00 5.40
933 1677 3.458163 CGGTTGGCTAGGGCTCGA 61.458 66.667 0.00 0.00 38.73 4.04
1259 2003 2.813908 GGCTAGGGCGTGTTCGTG 60.814 66.667 0.00 0.00 39.81 4.35
1260 2004 2.995574 AGGCTAGGGCGTGTTCGT 60.996 61.111 0.00 0.00 39.81 3.85
1261 2005 2.509336 CAGGCTAGGGCGTGTTCG 60.509 66.667 0.00 0.00 45.72 3.95
1283 2027 2.348666 CCGAAATCGCACGAGAGAATTT 59.651 45.455 0.00 0.00 38.18 1.82
1357 2101 2.677003 CGGCCTACAGCAACAACGG 61.677 63.158 0.00 0.00 46.50 4.44
1428 2173 0.672401 CGCACGGCTTCCCTTTCTTA 60.672 55.000 0.00 0.00 0.00 2.10
1452 2197 2.101249 ACCTTGCAGACCAACAAACATG 59.899 45.455 0.00 0.00 0.00 3.21
1465 2210 2.785868 GGGCATACTGACCTTGCAG 58.214 57.895 0.00 0.00 44.12 4.41
1478 2223 1.222936 GTAGCAGCAGTCAGGGCAT 59.777 57.895 0.00 0.00 0.00 4.40
1486 2231 1.273606 ACAGAATGACGTAGCAGCAGT 59.726 47.619 0.00 0.00 39.69 4.40
1499 2244 6.201425 CCACAAAACAGAATTTGGACAGAATG 59.799 38.462 4.96 0.00 43.10 2.67
1529 2274 6.331845 TGCAATTGCTAAAACATCAGGTATG 58.668 36.000 29.37 0.00 42.66 2.39
1566 2313 4.142816 GGAATAACAGATGCCGCATATGTC 60.143 45.833 28.71 18.04 44.05 3.06
1638 2389 9.429359 CAGAACTAATCAAGTCACTATGAAGTT 57.571 33.333 6.71 6.71 37.50 2.66
1639 2390 8.807118 TCAGAACTAATCAAGTCACTATGAAGT 58.193 33.333 0.00 0.00 37.50 3.01
1640 2391 9.814899 ATCAGAACTAATCAAGTCACTATGAAG 57.185 33.333 0.00 0.00 37.50 3.02
1705 2464 7.923344 TGACCAATGTTAATTTGTTTCAATCGT 59.077 29.630 0.00 0.00 0.00 3.73
1710 2469 6.481644 GGCTTGACCAATGTTAATTTGTTTCA 59.518 34.615 0.00 1.70 38.86 2.69
1726 2485 1.729586 AGGTGACTAAGGCTTGACCA 58.270 50.000 10.69 1.58 39.65 4.02
1766 2525 2.376808 ATCATATGCCTGTAGCTCGC 57.623 50.000 0.00 0.00 44.23 5.03
1775 2540 4.347292 TCAGCTTGAGAGAATCATATGCCT 59.653 41.667 0.00 0.00 37.89 4.75
1806 2571 7.335673 TCCAATTACATCGCTTCTTGTATCAAA 59.664 33.333 0.00 0.00 0.00 2.69
1812 2577 3.375299 GCTCCAATTACATCGCTTCTTGT 59.625 43.478 0.00 0.00 0.00 3.16
1821 2614 4.770795 ACCACTACAGCTCCAATTACATC 58.229 43.478 0.00 0.00 0.00 3.06
1834 2627 7.672983 ACATAAGAATGTTTGACCACTACAG 57.327 36.000 0.00 0.00 44.07 2.74
1957 2750 5.525378 GCAATCTAATCACCGAAATGTCTCT 59.475 40.000 0.00 0.00 0.00 3.10
1967 2760 7.425577 TGATAAGAATGCAATCTAATCACCG 57.574 36.000 4.33 0.00 0.00 4.94
1991 2856 5.357257 CACACCGAAGCCAAATAGTAGTAT 58.643 41.667 0.00 0.00 0.00 2.12
1996 2861 1.613255 CCCACACCGAAGCCAAATAGT 60.613 52.381 0.00 0.00 0.00 2.12
1997 2862 1.094785 CCCACACCGAAGCCAAATAG 58.905 55.000 0.00 0.00 0.00 1.73
1998 2863 0.322997 CCCCACACCGAAGCCAAATA 60.323 55.000 0.00 0.00 0.00 1.40
2068 2935 3.888323 TGTAGTCAATGCAACCAACATGT 59.112 39.130 0.00 0.00 0.00 3.21
2071 2938 4.300189 GTTGTAGTCAATGCAACCAACA 57.700 40.909 0.00 0.00 45.66 3.33
2086 2953 4.456911 ACCTGCATGAACAAGATGTTGTAG 59.543 41.667 8.88 1.53 46.68 2.74
2343 3234 8.632679 GCAATTTTTACTGGATCAGATTCCATA 58.367 33.333 1.59 0.00 44.66 2.74
2406 3297 9.987272 CCACTTGTATCTACAATTATGAGATCA 57.013 33.333 3.40 0.00 44.34 2.92
2436 3327 2.887152 GAGGGATGCTTCTTGTTTGTGT 59.113 45.455 0.00 0.00 0.00 3.72
2549 3447 4.664150 TGATATCGTCACAATGCAGGTA 57.336 40.909 0.00 0.00 0.00 3.08
2605 3503 0.035152 CAGCCTGACCAATGCTACCA 60.035 55.000 0.00 0.00 33.16 3.25
2606 3504 1.379642 GCAGCCTGACCAATGCTACC 61.380 60.000 0.00 0.00 35.78 3.18
2626 3524 2.363406 GCCTGGGCCTGAGCAAAT 60.363 61.111 12.58 0.00 42.56 2.32
2641 3539 1.337167 GGAACACTTTGCCTGAATGCC 60.337 52.381 0.00 0.00 0.00 4.40
2662 3560 6.458232 TTTGTAACAATTACAGCACCAACT 57.542 33.333 1.99 0.00 45.92 3.16
2807 3713 9.793259 TCTCAGGTTCTTTAATGTTAATGTTCT 57.207 29.630 0.00 0.00 0.00 3.01
2809 3715 8.515414 GCTCTCAGGTTCTTTAATGTTAATGTT 58.485 33.333 0.00 0.00 0.00 2.71
2810 3716 7.665559 TGCTCTCAGGTTCTTTAATGTTAATGT 59.334 33.333 0.00 0.00 0.00 2.71
2821 3727 4.006319 GCTACATTGCTCTCAGGTTCTTT 58.994 43.478 0.00 0.00 0.00 2.52
2822 3728 3.008375 TGCTACATTGCTCTCAGGTTCTT 59.992 43.478 0.00 0.00 0.00 2.52
2868 3774 6.596497 TGAAGAGAAACAAAAACGTTAGGTCT 59.404 34.615 0.00 2.74 0.00 3.85
2869 3775 6.778108 TGAAGAGAAACAAAAACGTTAGGTC 58.222 36.000 0.00 0.00 0.00 3.85
2880 3793 3.266636 TGCGACACTGAAGAGAAACAAA 58.733 40.909 0.00 0.00 0.00 2.83
3022 3935 6.479006 AGGTTAAAGGGAATACACAGGTAAC 58.521 40.000 0.00 0.00 32.19 2.50
3043 3956 2.949177 TGCACAATGTACAAGGAGGT 57.051 45.000 0.00 0.00 0.00 3.85
3045 3958 4.487948 CCAATTGCACAATGTACAAGGAG 58.512 43.478 0.00 0.00 0.00 3.69
3046 3959 3.305950 GCCAATTGCACAATGTACAAGGA 60.306 43.478 0.00 0.00 40.77 3.36
3047 3960 2.995258 GCCAATTGCACAATGTACAAGG 59.005 45.455 0.00 3.20 40.77 3.61
3084 3999 1.898574 CTTGTTCAGCAAGCCCGGT 60.899 57.895 0.00 0.00 46.68 5.28
3118 4033 1.052617 TCAGGTTGTTGATCGGTGGA 58.947 50.000 0.00 0.00 0.00 4.02
3123 4038 4.503910 TCATAAGGTCAGGTTGTTGATCG 58.496 43.478 0.00 0.00 33.37 3.69
3178 4093 5.220605 GGTTCTGGAATTGCTCGTACATAAC 60.221 44.000 0.00 0.00 0.00 1.89
3387 4305 3.018856 TCATGTCCTTGTGGCATCAATC 58.981 45.455 0.00 0.00 31.15 2.67
3433 4351 5.394224 GGAATCCATCATCGTCATATACCGT 60.394 44.000 0.00 0.00 0.00 4.83
3466 4384 0.553819 ACCAACCCAACTTACCTGCA 59.446 50.000 0.00 0.00 0.00 4.41
3539 4457 5.991328 ATGATATTTGGACGTAAGCACAG 57.009 39.130 0.00 0.00 45.62 3.66
3604 4522 1.369625 GAGCAATCCGAACAATCCGT 58.630 50.000 0.00 0.00 0.00 4.69
3772 4690 3.568007 CACCTATCTGAGTCAGTAGCTCC 59.432 52.174 19.53 0.00 32.61 4.70
3793 4711 3.884895 AGACCGTAATTCATCAATGCCA 58.115 40.909 0.00 0.00 0.00 4.92
3801 4719 5.647658 TGATTCAGCAAAGACCGTAATTCAT 59.352 36.000 0.00 0.00 0.00 2.57
3804 4722 5.122396 GTCTGATTCAGCAAAGACCGTAATT 59.878 40.000 8.89 0.00 34.29 1.40
3815 4733 1.618343 TGAGACCGTCTGATTCAGCAA 59.382 47.619 5.57 0.00 0.00 3.91
3885 4805 1.412710 AGCCTCGAAGATTGCCGATTA 59.587 47.619 0.00 0.00 35.20 1.75
3888 4808 1.141881 GAGCCTCGAAGATTGCCGA 59.858 57.895 0.00 0.00 35.20 5.54
3903 4824 4.453819 AGTTCAAAACTCTGCATGTAGAGC 59.546 41.667 32.95 18.65 46.44 4.09
3968 4889 4.030216 CCATTGGGGGCTAAAATGTTACT 58.970 43.478 0.00 0.00 30.84 2.24
3975 4896 3.268034 AAGAACCATTGGGGGCTAAAA 57.732 42.857 7.78 0.00 42.91 1.52
3977 4898 5.941146 ATATAAGAACCATTGGGGGCTAA 57.059 39.130 7.78 0.00 42.91 3.09
3999 4922 9.295825 ACCAACAGACAATTCATTCAATAACTA 57.704 29.630 0.00 0.00 0.00 2.24
4030 4953 3.893521 GGGAAAATATCTCCCGGTTTGA 58.106 45.455 0.00 0.00 43.27 2.69
4126 5051 9.209048 TGGTAGAACAATTACATATGTAGTCCT 57.791 33.333 14.96 6.69 0.00 3.85
4156 5081 9.470399 TCTGTGTAGTTATTTCCAGTATCAGTA 57.530 33.333 0.00 0.00 0.00 2.74
4158 5083 9.653287 TTTCTGTGTAGTTATTTCCAGTATCAG 57.347 33.333 0.00 0.00 0.00 2.90
4166 5091 8.683615 CCCCTATTTTTCTGTGTAGTTATTTCC 58.316 37.037 0.00 0.00 0.00 3.13
4176 5101 7.027874 TCAAGTATCCCCTATTTTTCTGTGT 57.972 36.000 0.00 0.00 0.00 3.72
4188 5113 1.062044 GGACTCCCTCAAGTATCCCCT 60.062 57.143 0.00 0.00 0.00 4.79
4191 5116 2.043227 CCAGGACTCCCTCAAGTATCC 58.957 57.143 0.00 0.00 42.02 2.59
4192 5117 3.033659 TCCAGGACTCCCTCAAGTATC 57.966 52.381 0.00 0.00 42.02 2.24
4227 5153 2.930040 CAAAGTACATAGTCCGGCTGTG 59.070 50.000 16.89 16.89 41.40 3.66
4292 5233 1.001406 CTTCCACGCAAAGGAGAGTCT 59.999 52.381 0.00 0.00 36.33 3.24
4374 5316 4.845530 TTATATAGACACTGGAGGGGGT 57.154 45.455 0.00 0.00 0.00 4.95
4470 5418 3.594603 ACAAGAGTTGATCTACCACGG 57.405 47.619 3.54 1.04 37.23 4.94
4619 5568 1.749033 CAGATCTCGGGTAAGGGGC 59.251 63.158 0.00 0.00 0.00 5.80
4624 5573 0.974010 AACCGGCAGATCTCGGGTAA 60.974 55.000 22.66 0.00 45.54 2.85
4751 5701 2.231380 GGAGGGTTTGGCCTGAGGA 61.231 63.158 0.65 0.00 37.43 3.71
4834 5784 2.069273 CTGACACGAAGGCGATTTTCT 58.931 47.619 0.00 0.00 41.64 2.52


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

AutoCloner maintained by Alex Coulton.