Multiple sequence alignment - TraesCS4B01G273200

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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 TraesCS4B01G273200 chr4B 100.000 3007 0 0 1 3007 550678281 550675275 0.000000e+00 5553.0
1 TraesCS4B01G273200 chr4B 98.095 840 16 0 1985 2824 16554505 16553666 0.000000e+00 1463.0
2 TraesCS4B01G273200 chr4B 84.034 1165 108 54 873 1983 550592729 550591589 0.000000e+00 1050.0
3 TraesCS4B01G273200 chr4B 88.917 794 62 15 1078 1854 550523776 550522992 0.000000e+00 955.0
4 TraesCS4B01G273200 chr4B 97.516 161 4 0 2847 3007 16553375 16553215 2.950000e-70 276.0
5 TraesCS4B01G273200 chr4B 86.598 97 8 5 486 582 24915064 24915155 5.300000e-18 102.0
6 TraesCS4B01G273200 chr4D 91.754 1431 75 23 590 1983 442444256 442442832 0.000000e+00 1949.0
7 TraesCS4B01G273200 chr4D 83.576 1029 105 38 870 1853 442438652 442437643 0.000000e+00 905.0
8 TraesCS4B01G273200 chr4D 90.141 142 14 0 1 142 442445185 442445044 5.120000e-43 185.0
9 TraesCS4B01G273200 chr4A 90.610 1427 75 28 587 1979 24902715 24904116 0.000000e+00 1838.0
10 TraesCS4B01G273200 chr4A 86.788 931 74 18 2106 3007 11708729 11707819 0.000000e+00 992.0
11 TraesCS4B01G273200 chr4A 84.021 945 79 38 1079 1979 24906793 24907709 0.000000e+00 843.0
12 TraesCS4B01G273200 chr4A 91.566 166 14 0 1 166 24902333 24902498 2.330000e-56 230.0
13 TraesCS4B01G273200 chr4A 79.487 156 19 2 307 462 704149909 704150051 6.860000e-17 99.0
14 TraesCS4B01G273200 chr4A 83.333 102 15 2 486 586 585385119 585385019 3.190000e-15 93.5
15 TraesCS4B01G273200 chr3B 97.481 794 19 1 1985 2777 511028917 511029710 0.000000e+00 1354.0
16 TraesCS4B01G273200 chr3B 96.951 164 5 0 2844 3007 511029826 511029989 2.950000e-70 276.0
17 TraesCS4B01G273200 chr3B 85.000 100 12 3 487 585 145319162 145319259 6.860000e-17 99.0
18 TraesCS4B01G273200 chr3B 79.487 156 17 5 307 462 633379076 633378936 2.470000e-16 97.1
19 TraesCS4B01G273200 chr7D 87.849 930 64 15 2106 3007 66986113 66987021 0.000000e+00 1046.0
20 TraesCS4B01G273200 chr7D 96.154 130 4 1 1985 2114 66985292 66985420 8.450000e-51 211.0
21 TraesCS4B01G273200 chr7D 100.000 32 0 0 307 338 517578299 517578330 3.240000e-05 60.2
22 TraesCS4B01G273200 chr6A 87.097 930 72 14 2106 3007 233815663 233814754 0.000000e+00 1009.0
23 TraesCS4B01G273200 chr6A 94.245 139 5 3 1977 2114 233816494 233816358 3.040000e-50 209.0
24 TraesCS4B01G273200 chr6A 87.770 139 10 4 453 585 550290324 550290461 4.010000e-34 156.0
25 TraesCS4B01G273200 chr6A 85.039 127 16 2 336 462 500513074 500513197 3.150000e-25 126.0
26 TraesCS4B01G273200 chr2B 87.083 929 72 15 2106 3007 621185275 621184368 0.000000e+00 1007.0
27 TraesCS4B01G273200 chr2B 95.200 125 5 1 1990 2114 621187577 621187454 2.360000e-46 196.0
28 TraesCS4B01G273200 chr2B 88.535 157 12 3 306 462 683778487 683778637 5.120000e-43 185.0
29 TraesCS4B01G273200 chr2B 86.420 162 16 2 306 462 683818877 683819037 3.990000e-39 172.0
30 TraesCS4B01G273200 chr2B 100.000 32 0 0 307 338 632254831 632254800 3.240000e-05 60.2
31 TraesCS4B01G273200 chr2A 86.486 925 77 19 2111 3007 642959073 642959977 0.000000e+00 972.0
32 TraesCS4B01G273200 chr2A 94.615 130 6 1 1985 2114 642936859 642936987 1.830000e-47 200.0
33 TraesCS4B01G273200 chr1A 88.113 816 69 7 2218 3007 121878739 121879552 0.000000e+00 944.0
34 TraesCS4B01G273200 chr1A 94.656 131 6 1 1984 2114 121877671 121877800 5.080000e-48 202.0
35 TraesCS4B01G273200 chr7B 84.724 923 85 26 2114 3007 725792184 725791289 0.000000e+00 872.0
36 TraesCS4B01G273200 chr7B 93.846 130 7 1 1985 2114 725793014 725792886 8.510000e-46 195.0
37 TraesCS4B01G273200 chr7A 92.564 511 26 5 2107 2608 228662462 228662969 0.000000e+00 723.0
38 TraesCS4B01G273200 chr7A 95.833 408 15 2 2600 3007 228675385 228675790 0.000000e+00 658.0
39 TraesCS4B01G273200 chr7A 97.692 130 3 0 1985 2114 228540448 228540577 1.080000e-54 224.0
40 TraesCS4B01G273200 chr5D 78.707 263 20 11 347 585 437356240 437356490 3.120000e-30 143.0
41 TraesCS4B01G273200 chr6B 76.096 251 45 12 347 585 498851061 498850814 1.890000e-22 117.0
42 TraesCS4B01G273200 chr6B 88.372 43 5 0 109 151 41911807 41911765 5.000000e-03 52.8
43 TraesCS4B01G273200 chr2D 86.364 110 9 4 353 462 118470191 118470088 6.810000e-22 115.0
44 TraesCS4B01G273200 chr2D 91.667 48 3 1 355 402 64154997 64155043 6.960000e-07 65.8
45 TraesCS4B01G273200 chr2D 100.000 32 0 0 307 338 24574826 24574795 3.240000e-05 60.2
46 TraesCS4B01G273200 chr5B 89.773 88 8 1 307 394 575609710 575609624 8.810000e-21 111.0
47 TraesCS4B01G273200 chr1B 85.294 102 13 2 485 585 166478167 166478267 1.470000e-18 104.0
48 TraesCS4B01G273200 chr1B 76.812 138 25 4 11 146 491703583 491703715 1.500000e-08 71.3
49 TraesCS4B01G273200 chr1D 85.149 101 13 2 486 585 249558790 249558691 5.300000e-18 102.0
50 TraesCS4B01G273200 chr3D 83.000 100 17 0 486 585 607818864 607818765 1.150000e-14 91.6


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 TraesCS4B01G273200 chr4B 550675275 550678281 3006 True 5553.000000 5553 100.000000 1 3007 1 chr4B.!!$R3 3006
1 TraesCS4B01G273200 chr4B 550591589 550592729 1140 True 1050.000000 1050 84.034000 873 1983 1 chr4B.!!$R2 1110
2 TraesCS4B01G273200 chr4B 550522992 550523776 784 True 955.000000 955 88.917000 1078 1854 1 chr4B.!!$R1 776
3 TraesCS4B01G273200 chr4B 16553215 16554505 1290 True 869.500000 1463 97.805500 1985 3007 2 chr4B.!!$R4 1022
4 TraesCS4B01G273200 chr4D 442442832 442445185 2353 True 1067.000000 1949 90.947500 1 1983 2 chr4D.!!$R2 1982
5 TraesCS4B01G273200 chr4D 442437643 442438652 1009 True 905.000000 905 83.576000 870 1853 1 chr4D.!!$R1 983
6 TraesCS4B01G273200 chr4A 11707819 11708729 910 True 992.000000 992 86.788000 2106 3007 1 chr4A.!!$R1 901
7 TraesCS4B01G273200 chr4A 24902333 24907709 5376 False 970.333333 1838 88.732333 1 1979 3 chr4A.!!$F2 1978
8 TraesCS4B01G273200 chr3B 511028917 511029989 1072 False 815.000000 1354 97.216000 1985 3007 2 chr3B.!!$F2 1022
9 TraesCS4B01G273200 chr7D 66985292 66987021 1729 False 628.500000 1046 92.001500 1985 3007 2 chr7D.!!$F2 1022
10 TraesCS4B01G273200 chr6A 233814754 233816494 1740 True 609.000000 1009 90.671000 1977 3007 2 chr6A.!!$R1 1030
11 TraesCS4B01G273200 chr2B 621184368 621187577 3209 True 601.500000 1007 91.141500 1990 3007 2 chr2B.!!$R2 1017
12 TraesCS4B01G273200 chr2A 642959073 642959977 904 False 972.000000 972 86.486000 2111 3007 1 chr2A.!!$F2 896
13 TraesCS4B01G273200 chr1A 121877671 121879552 1881 False 573.000000 944 91.384500 1984 3007 2 chr1A.!!$F1 1023
14 TraesCS4B01G273200 chr7B 725791289 725793014 1725 True 533.500000 872 89.285000 1985 3007 2 chr7B.!!$R1 1022
15 TraesCS4B01G273200 chr7A 228662462 228662969 507 False 723.000000 723 92.564000 2107 2608 1 chr7A.!!$F2 501

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
369 785 0.033228 CAACCAAAGCCCGATGCAAA 59.967 50.0 0.0 0.0 44.83 3.68 F
382 798 0.108396 ATGCAAAAACACCCAAGCCC 59.892 50.0 0.0 0.0 0.00 5.19 F
487 903 0.108851 AAATGGCGAAAACGATGGGC 60.109 50.0 0.0 0.0 0.00 5.36 F
1033 1479 0.760567 CCACCGATCCTCCTGATCCA 60.761 60.0 0.0 0.0 46.06 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 6074 0.243907 TTCAGGCAGCTCGTGTAGTC 59.756 55.000 0.0 0.0 32.68 2.59 R
1923 6075 0.679505 TTTCAGGCAGCTCGTGTAGT 59.320 50.000 0.0 0.0 32.68 2.73 R
1929 6081 2.120232 CGTAGTATTTCAGGCAGCTCG 58.880 52.381 0.0 0.0 0.00 5.03 R
2845 9372 1.826385 AAACACATGACTAGCAGGGC 58.174 50.000 0.0 0.0 31.20 5.19 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
48 49 1.144969 GATGTTTGAGCGTCGTTCCA 58.855 50.000 6.63 0.00 0.00 3.53
60 61 2.546368 CGTCGTTCCATTCCTGAAAACA 59.454 45.455 0.00 0.00 0.00 2.83
61 62 3.363970 CGTCGTTCCATTCCTGAAAACAG 60.364 47.826 0.00 0.00 0.00 3.16
70 71 5.394005 CCATTCCTGAAAACAGTGTTGTTGA 60.394 40.000 9.79 0.00 46.54 3.18
109 110 5.186021 TGTTGTTGTGATGTAAAAGGTGGTT 59.814 36.000 0.00 0.00 0.00 3.67
114 115 3.634910 GTGATGTAAAAGGTGGTTGGTGT 59.365 43.478 0.00 0.00 0.00 4.16
122 123 1.284785 AGGTGGTTGGTGTGGATATGG 59.715 52.381 0.00 0.00 0.00 2.74
129 130 3.517296 TGGTGTGGATATGGTTGTTGT 57.483 42.857 0.00 0.00 0.00 3.32
148 149 8.678510 GTTGTTGTTGTAGTTTATTGATCGTTG 58.321 33.333 0.00 0.00 0.00 4.10
161 162 5.697473 TTGATCGTTGTTTTGATGGCTTA 57.303 34.783 0.00 0.00 0.00 3.09
166 167 4.764823 TCGTTGTTTTGATGGCTTAGGATT 59.235 37.500 0.00 0.00 0.00 3.01
174 589 4.556697 TGATGGCTTAGGATTCCACTCTA 58.443 43.478 5.29 0.00 31.94 2.43
195 610 9.080097 ACTCTATGTATCCCAGAAGTTATACAC 57.920 37.037 0.00 0.00 37.57 2.90
199 614 7.348080 TGTATCCCAGAAGTTATACACAGAG 57.652 40.000 0.00 0.00 31.60 3.35
225 640 5.221185 GGATGTATGCTCATTGTCATGCTTT 60.221 40.000 0.00 1.52 0.00 3.51
322 738 2.496679 AGGTATACCTGGCCATCTGT 57.503 50.000 24.01 6.94 46.55 3.41
323 739 2.330216 AGGTATACCTGGCCATCTGTC 58.670 52.381 24.01 0.00 46.55 3.51
325 741 1.000955 GTATACCTGGCCATCTGTCGG 59.999 57.143 5.51 5.16 0.00 4.79
345 761 4.419921 CGGGCCGGGCTTTAGGTT 62.420 66.667 28.80 0.00 0.00 3.50
346 762 2.754254 GGGCCGGGCTTTAGGTTG 60.754 66.667 28.80 0.00 0.00 3.77
348 764 2.754254 GCCGGGCTTTAGGTTGGG 60.754 66.667 12.87 0.00 0.00 4.12
349 765 2.754254 CCGGGCTTTAGGTTGGGC 60.754 66.667 0.00 0.00 0.00 5.36
353 769 1.541310 GGGCTTTAGGTTGGGCCAAC 61.541 60.000 35.93 35.93 45.68 3.77
364 780 2.679996 GGCCAACCAAAGCCCGAT 60.680 61.111 0.00 0.00 43.76 4.18
365 781 2.573340 GCCAACCAAAGCCCGATG 59.427 61.111 0.00 0.00 0.00 3.84
366 782 2.573340 CCAACCAAAGCCCGATGC 59.427 61.111 0.00 0.00 41.71 3.91
369 785 0.033228 CAACCAAAGCCCGATGCAAA 59.967 50.000 0.00 0.00 44.83 3.68
371 787 0.755686 ACCAAAGCCCGATGCAAAAA 59.244 45.000 0.00 0.00 44.83 1.94
373 789 1.539929 CCAAAGCCCGATGCAAAAACA 60.540 47.619 0.00 0.00 44.83 2.83
376 792 1.374125 GCCCGATGCAAAAACACCC 60.374 57.895 0.00 0.00 40.77 4.61
377 793 2.045280 CCCGATGCAAAAACACCCA 58.955 52.632 0.00 0.00 0.00 4.51
379 795 1.605202 CCCGATGCAAAAACACCCAAG 60.605 52.381 0.00 0.00 0.00 3.61
380 796 1.139163 CGATGCAAAAACACCCAAGC 58.861 50.000 0.00 0.00 0.00 4.01
381 797 1.511850 GATGCAAAAACACCCAAGCC 58.488 50.000 0.00 0.00 0.00 4.35
382 798 0.108396 ATGCAAAAACACCCAAGCCC 59.892 50.000 0.00 0.00 0.00 5.19
383 799 1.594021 GCAAAAACACCCAAGCCCG 60.594 57.895 0.00 0.00 0.00 6.13
384 800 2.022240 GCAAAAACACCCAAGCCCGA 62.022 55.000 0.00 0.00 0.00 5.14
386 802 1.744320 AAAAACACCCAAGCCCGAGC 61.744 55.000 0.00 0.00 40.32 5.03
387 803 4.660938 AACACCCAAGCCCGAGCC 62.661 66.667 0.00 0.00 41.25 4.70
412 828 3.161450 GCCCGGTCATCAGGCCTA 61.161 66.667 3.98 0.00 41.00 3.93
413 829 2.742116 GCCCGGTCATCAGGCCTAA 61.742 63.158 3.98 0.00 41.00 2.69
414 830 1.912220 CCCGGTCATCAGGCCTAAA 59.088 57.895 3.98 0.00 0.00 1.85
416 832 1.133792 CCCGGTCATCAGGCCTAAAAT 60.134 52.381 3.98 0.00 0.00 1.82
417 833 2.654863 CCGGTCATCAGGCCTAAAATT 58.345 47.619 3.98 0.00 0.00 1.82
418 834 2.618709 CCGGTCATCAGGCCTAAAATTC 59.381 50.000 3.98 0.00 0.00 2.17
419 835 3.278574 CGGTCATCAGGCCTAAAATTCA 58.721 45.455 3.98 0.00 0.00 2.57
420 836 3.313526 CGGTCATCAGGCCTAAAATTCAG 59.686 47.826 3.98 0.00 0.00 3.02
421 837 3.633986 GGTCATCAGGCCTAAAATTCAGG 59.366 47.826 3.98 2.32 36.16 3.86
428 844 1.025041 CCTAAAATTCAGGCCCGAGC 58.975 55.000 0.00 0.00 38.76 5.03
441 857 2.669569 CGAGCCCGGCCCATTATG 60.670 66.667 5.55 0.00 0.00 1.90
442 858 2.985847 GAGCCCGGCCCATTATGC 60.986 66.667 5.55 0.00 0.00 3.14
443 859 3.497884 GAGCCCGGCCCATTATGCT 62.498 63.158 5.55 0.00 0.00 3.79
444 860 2.124507 GAGCCCGGCCCATTATGCTA 62.125 60.000 5.55 0.00 0.00 3.49
445 861 1.228429 GCCCGGCCCATTATGCTAA 60.228 57.895 0.00 0.00 0.00 3.09
446 862 0.825840 GCCCGGCCCATTATGCTAAA 60.826 55.000 0.00 0.00 0.00 1.85
449 865 1.000274 CCGGCCCATTATGCTAAAAGC 60.000 52.381 0.00 0.00 42.82 3.51
450 866 1.000274 CGGCCCATTATGCTAAAAGCC 60.000 52.381 0.00 0.00 41.51 4.35
451 867 2.319844 GGCCCATTATGCTAAAAGCCT 58.680 47.619 0.00 0.00 41.51 4.58
452 868 2.036346 GGCCCATTATGCTAAAAGCCTG 59.964 50.000 0.00 0.00 41.51 4.85
453 869 2.546584 GCCCATTATGCTAAAAGCCTGC 60.547 50.000 0.00 0.00 41.51 4.85
454 870 2.036346 CCCATTATGCTAAAAGCCTGCC 59.964 50.000 0.00 0.00 41.51 4.85
455 871 2.287788 CCATTATGCTAAAAGCCTGCCG 60.288 50.000 0.00 0.00 41.51 5.69
456 872 1.388547 TTATGCTAAAAGCCTGCCGG 58.611 50.000 0.00 0.00 41.51 6.13
467 883 3.721706 CTGCCGGGCCTCTTCCTT 61.722 66.667 17.97 0.00 0.00 3.36
469 885 1.910580 CTGCCGGGCCTCTTCCTTAA 61.911 60.000 17.97 0.00 0.00 1.85
470 886 1.301954 GCCGGGCCTCTTCCTTAAA 59.698 57.895 8.12 0.00 0.00 1.52
472 888 1.680338 CCGGGCCTCTTCCTTAAATG 58.320 55.000 0.84 0.00 0.00 2.32
474 890 1.403814 GGGCCTCTTCCTTAAATGGC 58.596 55.000 0.84 0.00 36.32 4.40
475 891 1.025041 GGCCTCTTCCTTAAATGGCG 58.975 55.000 0.00 0.00 37.30 5.69
476 892 1.408266 GGCCTCTTCCTTAAATGGCGA 60.408 52.381 0.00 0.00 37.30 5.54
477 893 2.365582 GCCTCTTCCTTAAATGGCGAA 58.634 47.619 0.00 0.00 30.28 4.70
478 894 2.752903 GCCTCTTCCTTAAATGGCGAAA 59.247 45.455 0.00 0.00 30.28 3.46
479 895 3.192633 GCCTCTTCCTTAAATGGCGAAAA 59.807 43.478 0.00 0.00 30.28 2.29
481 897 4.403453 CTCTTCCTTAAATGGCGAAAACG 58.597 43.478 0.00 0.00 0.00 3.60
482 898 4.066490 TCTTCCTTAAATGGCGAAAACGA 58.934 39.130 0.00 0.00 0.00 3.85
484 900 4.349663 TCCTTAAATGGCGAAAACGATG 57.650 40.909 0.00 0.00 0.00 3.84
486 902 3.434637 CTTAAATGGCGAAAACGATGGG 58.565 45.455 0.00 0.00 0.00 4.00
487 903 0.108851 AAATGGCGAAAACGATGGGC 60.109 50.000 0.00 0.00 0.00 5.36
490 906 4.174129 GCGAAAACGATGGGCCCG 62.174 66.667 19.37 7.98 0.00 6.13
492 908 3.822192 GAAAACGATGGGCCCGGC 61.822 66.667 19.37 10.78 0.00 6.13
517 933 2.648059 CCACCAGGCTCAAAATCTAGG 58.352 52.381 0.00 0.00 0.00 3.02
519 935 1.064389 ACCAGGCTCAAAATCTAGGCC 60.064 52.381 0.00 0.00 42.74 5.19
523 939 3.133141 GGCTCAAAATCTAGGCCTAGG 57.867 52.381 34.43 20.53 39.68 3.02
524 940 2.499197 GCTCAAAATCTAGGCCTAGGC 58.501 52.381 34.43 26.55 41.06 3.93
546 962 3.636231 CCTGTGGGCAAGGTCGGA 61.636 66.667 0.00 0.00 0.00 4.55
547 963 2.671070 CTGTGGGCAAGGTCGGAT 59.329 61.111 0.00 0.00 0.00 4.18
548 964 1.450312 CTGTGGGCAAGGTCGGATC 60.450 63.158 0.00 0.00 0.00 3.36
549 965 2.511600 GTGGGCAAGGTCGGATCG 60.512 66.667 0.00 0.00 0.00 3.69
550 966 3.781307 TGGGCAAGGTCGGATCGG 61.781 66.667 0.00 0.00 0.00 4.18
551 967 4.547367 GGGCAAGGTCGGATCGGG 62.547 72.222 0.00 0.00 0.00 5.14
721 1138 1.797211 GAAGAGGGGCGACGATCGAT 61.797 60.000 24.34 5.96 43.74 3.59
981 1427 2.006169 CCGGCACATATATATTGCGCA 58.994 47.619 5.66 5.66 37.11 6.09
1017 1463 1.747709 ACATCATCAGCTTGAGCCAC 58.252 50.000 0.00 0.00 43.38 5.01
1028 1474 1.617018 TTGAGCCACCGATCCTCCTG 61.617 60.000 0.00 0.00 0.00 3.86
1033 1479 0.760567 CCACCGATCCTCCTGATCCA 60.761 60.000 0.00 0.00 46.06 3.41
1035 1481 0.760945 ACCGATCCTCCTGATCCACC 60.761 60.000 0.00 0.00 46.06 4.61
1228 1732 2.159824 GCTTCTGTTCTTAACGCCCTTC 59.840 50.000 0.00 0.00 0.00 3.46
1239 1746 2.003672 CGCCCTTCGTGTATTTCCG 58.996 57.895 0.00 0.00 0.00 4.30
1583 2131 1.456705 GGAGATGGAGGAGGACGCT 60.457 63.158 0.00 0.00 0.00 5.07
1628 2185 2.576317 GACTACGCCAGCGACGAC 60.576 66.667 20.32 5.64 42.83 4.34
1700 5844 3.999285 AGGGACCGGAGCAGGAGT 61.999 66.667 9.46 0.00 34.73 3.85
1710 5854 1.229625 AGCAGGAGTGGGATGGTGA 60.230 57.895 0.00 0.00 0.00 4.02
1891 6043 4.302455 CGCTGAAGATAAGATCATTCGGT 58.698 43.478 0.00 0.00 31.38 4.69
1892 6044 5.461526 CGCTGAAGATAAGATCATTCGGTA 58.538 41.667 0.00 0.00 31.38 4.02
1893 6045 5.920840 CGCTGAAGATAAGATCATTCGGTAA 59.079 40.000 0.00 0.00 31.38 2.85
1907 6059 5.823570 TCATTCGGTAAAGAAAAACAGTGGA 59.176 36.000 0.00 0.00 33.43 4.02
1922 6074 1.825474 AGTGGACAAGATACGGGACTG 59.175 52.381 0.00 0.00 0.00 3.51
1923 6075 1.822990 GTGGACAAGATACGGGACTGA 59.177 52.381 0.00 0.00 0.00 3.41
1929 6081 3.442977 ACAAGATACGGGACTGACTACAC 59.557 47.826 0.00 0.00 0.00 2.90
2169 8668 8.347771 CAGTTGTAGCACGGTTCTATAGTATAA 58.652 37.037 0.00 0.00 0.00 0.98
2499 9007 9.674068 GACTACTCTGAAAGGGAAAGATAAAAT 57.326 33.333 0.00 0.00 35.24 1.82
2541 9049 7.598278 ACCTGCGAACAAAACAATATCATAAA 58.402 30.769 0.00 0.00 0.00 1.40
2832 9357 3.636282 ACAAATCCGTAGTTTTGTGGC 57.364 42.857 0.62 0.00 41.91 5.01
2833 9358 2.031508 ACAAATCCGTAGTTTTGTGGCG 60.032 45.455 0.62 0.00 41.91 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.200092 GAGGAAGGTTCTTCAACAACACT 58.800 43.478 9.48 0.00 33.89 3.55
61 62 3.945285 TGAGGAAGGTTCTTCAACAACAC 59.055 43.478 9.48 0.00 39.86 3.32
70 71 4.956075 ACAACAACAATGAGGAAGGTTCTT 59.044 37.500 0.00 0.00 0.00 2.52
109 110 3.517296 ACAACAACCATATCCACACCA 57.483 42.857 0.00 0.00 0.00 4.17
114 115 8.871629 ATAAACTACAACAACAACCATATCCA 57.128 30.769 0.00 0.00 0.00 3.41
122 123 8.678510 CAACGATCAATAAACTACAACAACAAC 58.321 33.333 0.00 0.00 0.00 3.32
148 149 4.706962 AGTGGAATCCTAAGCCATCAAAAC 59.293 41.667 0.00 0.00 33.66 2.43
161 162 5.090139 CTGGGATACATAGAGTGGAATCCT 58.910 45.833 0.00 0.00 41.10 3.24
166 167 5.144159 ACTTCTGGGATACATAGAGTGGA 57.856 43.478 0.00 0.00 33.62 4.02
174 589 7.472100 GCTCTGTGTATAACTTCTGGGATACAT 60.472 40.741 0.00 0.00 37.18 2.29
199 614 2.212652 TGACAATGAGCATACATCCGC 58.787 47.619 0.00 0.00 0.00 5.54
272 688 2.432874 CCATCCACTAACGTATCCCACA 59.567 50.000 0.00 0.00 0.00 4.17
301 717 2.090494 ACAGATGGCCAGGTATACCTCT 60.090 50.000 22.09 11.98 46.65 3.69
306 722 1.338107 CCGACAGATGGCCAGGTATA 58.662 55.000 13.05 0.00 0.00 1.47
307 723 1.410850 CCCGACAGATGGCCAGGTAT 61.411 60.000 13.05 0.00 0.00 2.73
309 725 3.402681 CCCGACAGATGGCCAGGT 61.403 66.667 13.05 9.65 0.00 4.00
328 744 4.419921 AACCTAAAGCCCGGCCCG 62.420 66.667 5.55 0.00 0.00 6.13
329 745 2.754254 CAACCTAAAGCCCGGCCC 60.754 66.667 5.55 0.00 0.00 5.80
330 746 2.754254 CCAACCTAAAGCCCGGCC 60.754 66.667 5.55 0.00 0.00 6.13
332 748 2.754254 GCCCAACCTAAAGCCCGG 60.754 66.667 0.00 0.00 0.00 5.73
333 749 2.754254 GGCCCAACCTAAAGCCCG 60.754 66.667 0.00 0.00 39.60 6.13
335 751 1.972198 GTTGGCCCAACCTAAAGCC 59.028 57.895 16.01 0.00 45.96 4.35
348 764 2.573340 CATCGGGCTTTGGTTGGC 59.427 61.111 0.00 0.00 0.00 4.52
349 765 1.814772 TTGCATCGGGCTTTGGTTGG 61.815 55.000 0.00 0.00 45.15 3.77
353 769 1.147473 GTTTTTGCATCGGGCTTTGG 58.853 50.000 0.00 0.00 45.15 3.28
354 770 1.526464 GTGTTTTTGCATCGGGCTTTG 59.474 47.619 0.00 0.00 45.15 2.77
355 771 1.540146 GGTGTTTTTGCATCGGGCTTT 60.540 47.619 0.00 0.00 45.15 3.51
356 772 0.033366 GGTGTTTTTGCATCGGGCTT 59.967 50.000 0.00 0.00 45.15 4.35
357 773 1.665442 GGTGTTTTTGCATCGGGCT 59.335 52.632 0.00 0.00 45.15 5.19
358 774 1.374125 GGGTGTTTTTGCATCGGGC 60.374 57.895 0.00 0.00 45.13 6.13
359 775 0.390860 TTGGGTGTTTTTGCATCGGG 59.609 50.000 0.00 0.00 0.00 5.14
360 776 1.782044 CTTGGGTGTTTTTGCATCGG 58.218 50.000 0.00 0.00 0.00 4.18
361 777 1.139163 GCTTGGGTGTTTTTGCATCG 58.861 50.000 0.00 0.00 0.00 3.84
362 778 1.511850 GGCTTGGGTGTTTTTGCATC 58.488 50.000 0.00 0.00 0.00 3.91
364 780 1.524482 GGGCTTGGGTGTTTTTGCA 59.476 52.632 0.00 0.00 0.00 4.08
365 781 1.594021 CGGGCTTGGGTGTTTTTGC 60.594 57.895 0.00 0.00 0.00 3.68
366 782 0.031994 CTCGGGCTTGGGTGTTTTTG 59.968 55.000 0.00 0.00 0.00 2.44
369 785 2.597510 GCTCGGGCTTGGGTGTTT 60.598 61.111 0.00 0.00 35.22 2.83
396 812 0.254747 TTTTAGGCCTGATGACCGGG 59.745 55.000 17.99 0.00 44.49 5.73
398 814 3.278574 TGAATTTTAGGCCTGATGACCG 58.721 45.455 17.99 0.00 0.00 4.79
400 816 4.907879 CCTGAATTTTAGGCCTGATGAC 57.092 45.455 17.99 3.07 0.00 3.06
409 825 1.025041 GCTCGGGCCTGAATTTTAGG 58.975 55.000 16.91 2.81 38.39 2.69
424 840 2.669569 CATAATGGGCCGGGCTCG 60.670 66.667 28.80 0.00 0.00 5.03
425 841 2.124507 TAGCATAATGGGCCGGGCTC 62.125 60.000 28.80 16.93 33.10 4.70
426 842 1.715019 TTAGCATAATGGGCCGGGCT 61.715 55.000 28.80 15.17 35.50 5.19
428 844 1.613437 CTTTTAGCATAATGGGCCGGG 59.387 52.381 2.18 0.00 0.00 5.73
429 845 1.000274 GCTTTTAGCATAATGGGCCGG 60.000 52.381 0.00 0.00 41.89 6.13
430 846 1.000274 GGCTTTTAGCATAATGGGCCG 60.000 52.381 0.00 0.00 44.75 6.13
431 847 2.036346 CAGGCTTTTAGCATAATGGGCC 59.964 50.000 0.00 0.00 44.75 5.80
432 848 2.546584 GCAGGCTTTTAGCATAATGGGC 60.547 50.000 0.67 0.00 44.75 5.36
433 849 2.036346 GGCAGGCTTTTAGCATAATGGG 59.964 50.000 0.67 0.00 44.75 4.00
434 850 2.287788 CGGCAGGCTTTTAGCATAATGG 60.288 50.000 0.67 0.00 44.75 3.16
435 851 2.287788 CCGGCAGGCTTTTAGCATAATG 60.288 50.000 0.00 0.00 44.75 1.90
436 852 1.956477 CCGGCAGGCTTTTAGCATAAT 59.044 47.619 0.00 0.00 44.75 1.28
437 853 1.388547 CCGGCAGGCTTTTAGCATAA 58.611 50.000 0.00 0.00 44.75 1.90
438 854 0.465460 CCCGGCAGGCTTTTAGCATA 60.465 55.000 0.00 0.00 44.75 3.14
440 856 2.361104 CCCGGCAGGCTTTTAGCA 60.361 61.111 0.00 0.00 44.75 3.49
450 866 1.910580 TTAAGGAAGAGGCCCGGCAG 61.911 60.000 12.58 0.00 0.00 4.85
451 867 1.493854 TTTAAGGAAGAGGCCCGGCA 61.494 55.000 12.58 0.00 0.00 5.69
452 868 0.106669 ATTTAAGGAAGAGGCCCGGC 60.107 55.000 0.00 0.00 0.00 6.13
453 869 1.680338 CATTTAAGGAAGAGGCCCGG 58.320 55.000 0.00 0.00 0.00 5.73
454 870 1.680338 CCATTTAAGGAAGAGGCCCG 58.320 55.000 0.00 0.00 0.00 6.13
455 871 1.403814 GCCATTTAAGGAAGAGGCCC 58.596 55.000 0.00 0.00 36.75 5.80
456 872 1.025041 CGCCATTTAAGGAAGAGGCC 58.975 55.000 0.00 0.00 38.48 5.19
458 874 4.671766 CGTTTTCGCCATTTAAGGAAGAGG 60.672 45.833 0.00 0.00 36.22 3.69
459 875 4.153475 TCGTTTTCGCCATTTAAGGAAGAG 59.847 41.667 0.00 0.00 43.73 2.85
460 876 4.066490 TCGTTTTCGCCATTTAAGGAAGA 58.934 39.130 0.00 0.00 43.73 2.87
462 878 4.380023 CCATCGTTTTCGCCATTTAAGGAA 60.380 41.667 0.00 0.00 43.73 3.36
463 879 3.127895 CCATCGTTTTCGCCATTTAAGGA 59.872 43.478 0.00 0.00 43.73 3.36
465 881 3.434637 CCCATCGTTTTCGCCATTTAAG 58.565 45.455 0.00 0.00 43.73 1.85
466 882 2.416162 GCCCATCGTTTTCGCCATTTAA 60.416 45.455 0.00 0.00 43.73 1.52
467 883 1.133407 GCCCATCGTTTTCGCCATTTA 59.867 47.619 0.00 0.00 43.73 1.40
469 885 1.510844 GCCCATCGTTTTCGCCATT 59.489 52.632 0.00 0.00 43.73 3.16
470 886 2.414785 GGCCCATCGTTTTCGCCAT 61.415 57.895 0.00 0.00 43.73 4.40
472 888 3.822192 GGGCCCATCGTTTTCGCC 61.822 66.667 19.95 0.00 43.73 5.54
474 890 3.505184 CCGGGCCCATCGTTTTCG 61.505 66.667 24.92 3.62 45.64 3.46
475 891 3.822192 GCCGGGCCCATCGTTTTC 61.822 66.667 24.92 0.00 0.00 2.29
497 913 2.648059 CCTAGATTTTGAGCCTGGTGG 58.352 52.381 0.00 0.00 0.00 4.61
499 915 1.064389 GGCCTAGATTTTGAGCCTGGT 60.064 52.381 0.00 0.00 40.57 4.00
503 919 2.812243 GCCTAGGCCTAGATTTTGAGCC 60.812 54.545 36.80 13.08 44.20 4.70
529 945 2.876368 GATCCGACCTTGCCCACAGG 62.876 65.000 0.00 0.00 0.00 4.00
530 946 1.450312 GATCCGACCTTGCCCACAG 60.450 63.158 0.00 0.00 0.00 3.66
531 947 2.668632 GATCCGACCTTGCCCACA 59.331 61.111 0.00 0.00 0.00 4.17
532 948 2.511600 CGATCCGACCTTGCCCAC 60.512 66.667 0.00 0.00 0.00 4.61
533 949 3.781307 CCGATCCGACCTTGCCCA 61.781 66.667 0.00 0.00 0.00 5.36
534 950 4.547367 CCCGATCCGACCTTGCCC 62.547 72.222 0.00 0.00 0.00 5.36
578 994 0.622665 ATTTCCTCCTGGCAGTCCTG 59.377 55.000 14.43 0.00 0.00 3.86
579 995 0.915364 GATTTCCTCCTGGCAGTCCT 59.085 55.000 14.43 0.00 0.00 3.85
580 996 0.620556 TGATTTCCTCCTGGCAGTCC 59.379 55.000 14.43 0.00 0.00 3.85
581 997 2.026822 TCTTGATTTCCTCCTGGCAGTC 60.027 50.000 14.43 2.86 0.00 3.51
582 998 1.988107 TCTTGATTTCCTCCTGGCAGT 59.012 47.619 14.43 0.00 0.00 4.40
583 999 2.641305 CTCTTGATTTCCTCCTGGCAG 58.359 52.381 7.75 7.75 0.00 4.85
584 1000 1.283029 CCTCTTGATTTCCTCCTGGCA 59.717 52.381 0.00 0.00 0.00 4.92
585 1001 1.561542 TCCTCTTGATTTCCTCCTGGC 59.438 52.381 0.00 0.00 0.00 4.85
586 1002 3.371380 CCTTCCTCTTGATTTCCTCCTGG 60.371 52.174 0.00 0.00 0.00 4.45
587 1003 3.371380 CCCTTCCTCTTGATTTCCTCCTG 60.371 52.174 0.00 0.00 0.00 3.86
588 1004 2.849318 CCCTTCCTCTTGATTTCCTCCT 59.151 50.000 0.00 0.00 0.00 3.69
760 1177 0.796312 TTCCTCTGTTCGCGCAATTC 59.204 50.000 8.75 0.00 0.00 2.17
761 1178 1.234821 TTTCCTCTGTTCGCGCAATT 58.765 45.000 8.75 0.00 0.00 2.32
762 1179 1.069227 GTTTTCCTCTGTTCGCGCAAT 60.069 47.619 8.75 0.00 0.00 3.56
763 1180 0.306533 GTTTTCCTCTGTTCGCGCAA 59.693 50.000 8.75 0.00 0.00 4.85
764 1181 1.503818 GGTTTTCCTCTGTTCGCGCA 61.504 55.000 8.75 0.00 36.94 6.09
848 1268 2.433664 GGACTGGTACGTTGCGGG 60.434 66.667 0.00 0.00 0.00 6.13
981 1427 4.252878 TGATGTAAATCGATGTGCTGTGT 58.747 39.130 0.00 0.00 0.00 3.72
1028 1474 1.067582 CGTAAGGCGAGGGTGGATC 59.932 63.158 0.00 0.00 44.77 3.36
1162 1661 2.922950 CGGGGAGGTTGACGACGAA 61.923 63.158 0.00 0.00 0.00 3.85
1228 1732 0.638746 GTCGTCAGCGGAAATACACG 59.361 55.000 0.00 0.00 38.89 4.49
1373 1891 0.674895 CCTGGAACTCCTTGCGGAAG 60.675 60.000 10.08 10.08 39.29 3.46
1489 2007 1.004560 TCTGCCGCTGACTTTGAGG 60.005 57.895 0.00 0.00 0.00 3.86
1491 2009 1.301716 GGTCTGCCGCTGACTTTGA 60.302 57.895 24.39 0.00 33.75 2.69
1497 2015 4.056125 CTCGTGGTCTGCCGCTGA 62.056 66.667 0.00 0.00 42.91 4.26
1583 2131 4.124351 CCCGCACGACGCTTCCTA 62.124 66.667 0.00 0.00 41.76 2.94
1700 5844 2.204136 AGTGCCCTCACCATCCCA 60.204 61.111 0.00 0.00 44.16 4.37
1891 6043 7.041644 CCGTATCTTGTCCACTGTTTTTCTTTA 60.042 37.037 0.00 0.00 0.00 1.85
1892 6044 6.238648 CCGTATCTTGTCCACTGTTTTTCTTT 60.239 38.462 0.00 0.00 0.00 2.52
1893 6045 5.238650 CCGTATCTTGTCCACTGTTTTTCTT 59.761 40.000 0.00 0.00 0.00 2.52
1907 6059 3.442977 GTGTAGTCAGTCCCGTATCTTGT 59.557 47.826 0.00 0.00 0.00 3.16
1922 6074 0.243907 TTCAGGCAGCTCGTGTAGTC 59.756 55.000 0.00 0.00 32.68 2.59
1923 6075 0.679505 TTTCAGGCAGCTCGTGTAGT 59.320 50.000 0.00 0.00 32.68 2.73
1929 6081 2.120232 CGTAGTATTTCAGGCAGCTCG 58.880 52.381 0.00 0.00 0.00 5.03
1979 6140 4.387559 CACGTGCAAGCTTATTAGTGTGTA 59.612 41.667 0.82 0.00 0.00 2.90
2499 9007 4.542697 GCAGGTATTTAATCCTTGGGGAA 58.457 43.478 0.00 0.00 45.78 3.97
2548 9056 8.887036 TGTAGTGGTTGTGCATATCTAATAAG 57.113 34.615 0.00 0.00 0.00 1.73
2557 9066 7.569639 TTAAAAGTTGTAGTGGTTGTGCATA 57.430 32.000 0.00 0.00 0.00 3.14
2845 9372 1.826385 AAACACATGACTAGCAGGGC 58.174 50.000 0.00 0.00 31.20 5.19
2935 9730 9.535170 TTTCTATTCCCAATTAAATGTGTACCA 57.465 29.630 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.