Multiple sequence alignment - TraesCS3A01G246400

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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 TraesCS3A01G246400 chr3A 100.000 4538 0 0 1 4538 463113562 463118099 0.000000e+00 8381
1 TraesCS3A01G246400 chr3A 89.720 107 11 0 868 974 610509900 610510006 2.200000e-28 137
2 TraesCS3A01G246400 chr3B 94.639 3600 132 21 971 4538 439466305 439462735 0.000000e+00 5522
3 TraesCS3A01G246400 chr3B 92.402 408 17 4 472 869 439466705 439466302 1.830000e-158 569
4 TraesCS3A01G246400 chr3B 95.122 164 6 2 107 268 439467493 439467330 1.620000e-64 257
5 TraesCS3A01G246400 chr3D 95.820 3421 116 8 972 4381 340721963 340718559 0.000000e+00 5500
6 TraesCS3A01G246400 chr3D 95.408 392 17 1 1 391 340723816 340723425 1.390000e-174 623
7 TraesCS3A01G246400 chr3D 89.787 470 20 15 406 869 340722408 340721961 1.090000e-160 577
8 TraesCS3A01G246400 chr3D 92.517 147 8 3 4394 4538 340718452 340718307 1.650000e-49 207
9 TraesCS3A01G246400 chrUn 99.500 400 2 0 2520 2919 478689330 478689729 0.000000e+00 728
10 TraesCS3A01G246400 chr4A 92.661 109 8 0 868 976 40874221 40874329 1.690000e-34 158
11 TraesCS3A01G246400 chr5A 91.150 113 10 0 863 975 43469097 43468985 2.190000e-33 154
12 TraesCS3A01G246400 chr5A 87.719 114 12 2 864 977 548858277 548858166 1.020000e-26 132
13 TraesCS3A01G246400 chr1D 72.784 485 102 23 1232 1704 443552793 443553259 2.200000e-28 137
14 TraesCS3A01G246400 chr1D 90.000 80 8 0 865 944 150938132 150938053 2.230000e-18 104
15 TraesCS3A01G246400 chr1A 87.963 108 12 1 868 974 565117470 565117577 4.770000e-25 126
16 TraesCS3A01G246400 chr1A 89.286 84 9 0 865 948 102451856 102451773 6.210000e-19 106
17 TraesCS3A01G246400 chr5D 86.275 102 14 0 873 974 245775020 245774919 1.330000e-20 111
18 TraesCS3A01G246400 chr6B 88.889 81 9 0 864 944 228695270 228695190 2.890000e-17 100


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 TraesCS3A01G246400 chr3A 463113562 463118099 4537 False 8381.00 8381 100.000000 1 4538 1 chr3A.!!$F1 4537
1 TraesCS3A01G246400 chr3B 439462735 439467493 4758 True 2116.00 5522 94.054333 107 4538 3 chr3B.!!$R1 4431
2 TraesCS3A01G246400 chr3D 340718307 340723816 5509 True 1726.75 5500 93.383000 1 4538 4 chr3D.!!$R1 4537

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
464 1862 0.332972 ATTCCTTGCCTCCACCTTCC 59.667 55.0 0.00 0.00 0.00 3.46 F
1018 2465 0.035056 GATGGACAGGAACCCCACTG 60.035 60.0 0.00 0.00 40.48 3.66 F
1066 2514 0.324830 GCCTACTCCCCTGTCTGTCT 60.325 60.0 0.00 0.00 0.00 3.41 F
1941 3393 0.462759 GGCAGGGTGTACAGCAGATC 60.463 60.0 25.23 8.95 0.00 2.75 F
2455 3907 0.250467 CCGCATAAGCTGGGCATACT 60.250 55.0 5.51 0.00 39.10 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 3453 0.615331 GAGGACAAGTGCATCTGGGA 59.385 55.000 0.00 0.0 0.00 4.37 R
2188 3640 0.731417 CTCTCCAAGCAAATCCGCTG 59.269 55.000 0.00 0.0 42.89 5.18 R
2425 3877 2.744202 AGCTTATGCGGTCAGAGTTTTG 59.256 45.455 0.00 0.0 45.42 2.44 R
3234 4686 1.227823 TTTGTCTGCTGTCACCCCG 60.228 57.895 0.00 0.0 0.00 5.73 R
3729 5181 1.436983 CGCGCTTCACCTAATTCCCC 61.437 60.000 5.56 0.0 0.00 4.81 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
29 30 5.959583 AGGTGAGACTCCTTTATTTAGGG 57.040 43.478 0.00 0.00 35.90 3.53
38 39 5.132312 ACTCCTTTATTTAGGGAACTAGGCC 59.868 44.000 0.00 0.00 45.45 5.19
41 42 5.377478 CTTTATTTAGGGAACTAGGCCAGG 58.623 45.833 5.01 0.00 45.45 4.45
48 49 2.854187 GAACTAGGCCAGGCACGGAC 62.854 65.000 15.19 0.00 0.00 4.79
55 56 4.415332 CAGGCACGGACGTAGCGT 62.415 66.667 0.00 3.16 45.10 5.07
86 87 3.058160 CCCACGAGCCAGCCAAAG 61.058 66.667 0.00 0.00 0.00 2.77
249 252 6.016527 GCCATGTATGAACAGATGACAATGAT 60.017 38.462 0.00 0.00 39.49 2.45
277 670 6.624423 ACCATTGTAGAAGACATTCAATTGC 58.376 36.000 0.00 0.00 38.07 3.56
332 726 5.122869 ACAGTTATTGAGCAGCACTGTAATG 59.877 40.000 11.27 0.00 44.91 1.90
344 738 1.066143 ACTGTAATGGCAACGAGAGGG 60.066 52.381 0.00 0.00 42.51 4.30
352 746 1.450312 CAACGAGAGGGACATGGCC 60.450 63.158 10.00 10.00 0.00 5.36
373 767 2.557056 CGAGTCAGTGGTCACCTAGAAA 59.443 50.000 0.00 0.00 0.00 2.52
385 779 4.093998 GTCACCTAGAAACAGCACATGATG 59.906 45.833 0.00 0.00 37.48 3.07
448 1846 8.856490 ATGAAAGCGATATTTGGTGTAAATTC 57.144 30.769 0.00 0.00 39.61 2.17
459 1857 2.492088 GGTGTAAATTCCTTGCCTCCAC 59.508 50.000 0.00 0.00 0.00 4.02
464 1862 0.332972 ATTCCTTGCCTCCACCTTCC 59.667 55.000 0.00 0.00 0.00 3.46
521 1950 2.987125 GGTAGACCGTGGCACCAT 59.013 61.111 12.86 0.00 0.00 3.55
524 1953 3.657448 TAGACCGTGGCACCATGCG 62.657 63.158 12.86 0.00 46.21 4.73
629 2058 4.010349 AGCCAAGAAAATACCGAAGAAGG 58.990 43.478 0.00 0.00 37.30 3.46
795 2238 6.582636 ACTACTCAAGATCACACACTGAAAA 58.417 36.000 0.00 0.00 30.60 2.29
818 2261 7.742556 AACAGTATACGTAGATTCCTAGACC 57.257 40.000 0.08 0.00 0.00 3.85
865 2308 7.309177 CGTGGTCATAAACAAACAAATGGATA 58.691 34.615 0.00 0.00 0.00 2.59
866 2309 7.484641 CGTGGTCATAAACAAACAAATGGATAG 59.515 37.037 0.00 0.00 0.00 2.08
867 2310 8.303876 GTGGTCATAAACAAACAAATGGATAGT 58.696 33.333 0.00 0.00 0.00 2.12
868 2311 9.521841 TGGTCATAAACAAACAAATGGATAGTA 57.478 29.630 0.00 0.00 0.00 1.82
869 2312 9.783256 GGTCATAAACAAACAAATGGATAGTAC 57.217 33.333 0.00 0.00 0.00 2.73
874 2317 8.706322 AAACAAACAAATGGATAGTACTTCCT 57.294 30.769 18.78 7.46 34.17 3.36
875 2318 7.923414 ACAAACAAATGGATAGTACTTCCTC 57.077 36.000 18.78 7.95 34.17 3.71
876 2319 6.884836 ACAAACAAATGGATAGTACTTCCTCC 59.115 38.462 18.78 14.86 34.17 4.30
877 2320 5.277857 ACAAATGGATAGTACTTCCTCCG 57.722 43.478 18.78 10.85 34.17 4.63
878 2321 4.715297 ACAAATGGATAGTACTTCCTCCGT 59.285 41.667 18.78 13.45 34.17 4.69
879 2322 5.189145 ACAAATGGATAGTACTTCCTCCGTT 59.811 40.000 18.78 17.08 38.37 4.44
880 2323 5.952347 AATGGATAGTACTTCCTCCGTTT 57.048 39.130 18.78 10.81 34.14 3.60
881 2324 4.730949 TGGATAGTACTTCCTCCGTTTG 57.269 45.455 18.78 0.00 34.17 2.93
882 2325 3.449737 TGGATAGTACTTCCTCCGTTTGG 59.550 47.826 18.78 0.00 34.17 3.28
883 2326 3.703052 GGATAGTACTTCCTCCGTTTGGA 59.297 47.826 0.00 0.00 43.88 3.53
884 2327 4.161001 GGATAGTACTTCCTCCGTTTGGAA 59.839 45.833 0.00 0.00 45.87 3.53
885 2328 5.337813 GGATAGTACTTCCTCCGTTTGGAAA 60.338 44.000 0.00 0.00 45.87 3.13
886 2329 4.635699 AGTACTTCCTCCGTTTGGAAAT 57.364 40.909 0.00 0.00 45.87 2.17
887 2330 5.750352 AGTACTTCCTCCGTTTGGAAATA 57.250 39.130 0.00 0.00 45.87 1.40
888 2331 5.485620 AGTACTTCCTCCGTTTGGAAATAC 58.514 41.667 10.09 10.09 45.87 1.89
889 2332 4.635699 ACTTCCTCCGTTTGGAAATACT 57.364 40.909 0.00 0.00 45.87 2.12
890 2333 4.981812 ACTTCCTCCGTTTGGAAATACTT 58.018 39.130 0.00 0.00 45.87 2.24
891 2334 4.760204 ACTTCCTCCGTTTGGAAATACTTG 59.240 41.667 0.00 0.00 45.87 3.16
892 2335 4.360951 TCCTCCGTTTGGAAATACTTGT 57.639 40.909 0.00 0.00 45.87 3.16
893 2336 4.320870 TCCTCCGTTTGGAAATACTTGTC 58.679 43.478 0.00 0.00 45.87 3.18
894 2337 3.439129 CCTCCGTTTGGAAATACTTGTCC 59.561 47.826 0.00 0.00 45.87 4.02
895 2338 4.324267 CTCCGTTTGGAAATACTTGTCCT 58.676 43.478 0.00 0.00 45.87 3.85
896 2339 5.484715 CTCCGTTTGGAAATACTTGTCCTA 58.515 41.667 0.00 0.00 45.87 2.94
897 2340 5.867330 TCCGTTTGGAAATACTTGTCCTAA 58.133 37.500 0.00 0.00 42.85 2.69
898 2341 6.297582 TCCGTTTGGAAATACTTGTCCTAAA 58.702 36.000 0.00 0.00 42.85 1.85
899 2342 6.771749 TCCGTTTGGAAATACTTGTCCTAAAA 59.228 34.615 0.00 0.00 42.85 1.52
900 2343 7.284944 TCCGTTTGGAAATACTTGTCCTAAAAA 59.715 33.333 0.00 0.00 42.85 1.94
901 2344 8.085909 CCGTTTGGAAATACTTGTCCTAAAAAT 58.914 33.333 0.00 0.00 37.49 1.82
902 2345 8.911662 CGTTTGGAAATACTTGTCCTAAAAATG 58.088 33.333 0.00 0.00 31.78 2.32
903 2346 9.203421 GTTTGGAAATACTTGTCCTAAAAATGG 57.797 33.333 0.00 0.00 31.78 3.16
904 2347 8.485578 TTGGAAATACTTGTCCTAAAAATGGT 57.514 30.769 0.00 0.00 34.77 3.55
905 2348 8.485578 TGGAAATACTTGTCCTAAAAATGGTT 57.514 30.769 0.00 0.00 34.77 3.67
906 2349 8.364142 TGGAAATACTTGTCCTAAAAATGGTTG 58.636 33.333 0.00 0.00 34.77 3.77
907 2350 8.364894 GGAAATACTTGTCCTAAAAATGGTTGT 58.635 33.333 0.00 0.00 0.00 3.32
911 2354 9.975218 ATACTTGTCCTAAAAATGGTTGTATCT 57.025 29.630 0.00 0.00 0.00 1.98
913 2356 9.449719 ACTTGTCCTAAAAATGGTTGTATCTAG 57.550 33.333 0.00 0.00 0.00 2.43
914 2357 9.667107 CTTGTCCTAAAAATGGTTGTATCTAGA 57.333 33.333 0.00 0.00 0.00 2.43
959 2402 9.320352 ACAACCATTTTTAACACAAGTATTTCC 57.680 29.630 0.00 0.00 0.00 3.13
960 2403 8.484008 CAACCATTTTTAACACAAGTATTTCCG 58.516 33.333 0.00 0.00 0.00 4.30
961 2404 7.942990 ACCATTTTTAACACAAGTATTTCCGA 58.057 30.769 0.00 0.00 0.00 4.55
962 2405 8.414778 ACCATTTTTAACACAAGTATTTCCGAA 58.585 29.630 0.00 0.00 0.00 4.30
963 2406 9.418045 CCATTTTTAACACAAGTATTTCCGAAT 57.582 29.630 0.00 0.00 0.00 3.34
965 2408 8.804688 TTTTTAACACAAGTATTTCCGAATGG 57.195 30.769 0.00 0.00 0.00 3.16
966 2409 7.747155 TTTAACACAAGTATTTCCGAATGGA 57.253 32.000 0.00 0.00 44.61 3.41
988 2431 3.449018 AGGGAGTAGCTCAGTACACAATG 59.551 47.826 0.00 0.00 31.08 2.82
1018 2465 0.035056 GATGGACAGGAACCCCACTG 60.035 60.000 0.00 0.00 40.48 3.66
1066 2514 0.324830 GCCTACTCCCCTGTCTGTCT 60.325 60.000 0.00 0.00 0.00 3.41
1067 2515 1.479709 CCTACTCCCCTGTCTGTCTG 58.520 60.000 0.00 0.00 0.00 3.51
1068 2516 1.272760 CCTACTCCCCTGTCTGTCTGT 60.273 57.143 0.00 0.00 0.00 3.41
1069 2517 2.096248 CTACTCCCCTGTCTGTCTGTC 58.904 57.143 0.00 0.00 0.00 3.51
1133 2585 2.315155 TCTACCCAGTAGCCCTTCTTCT 59.685 50.000 0.00 0.00 36.22 2.85
1134 2586 2.046280 ACCCAGTAGCCCTTCTTCTT 57.954 50.000 0.00 0.00 0.00 2.52
1135 2587 1.909986 ACCCAGTAGCCCTTCTTCTTC 59.090 52.381 0.00 0.00 0.00 2.87
1166 2618 0.831288 ACTCTGCTCTGCTCCTGTGT 60.831 55.000 0.00 0.00 0.00 3.72
1185 2637 3.731728 TCCCCATGGCAGAGCACC 61.732 66.667 6.09 0.00 0.00 5.01
1239 2691 0.523966 AGAAAGTCCTGCTCGTCTCG 59.476 55.000 0.00 0.00 0.00 4.04
1339 2791 2.732016 CCACCGACAAGACCGTCA 59.268 61.111 0.40 0.00 35.54 4.35
1433 2885 0.736325 GTCCTCACCGACGTCAATGG 60.736 60.000 17.16 11.35 0.00 3.16
1440 2892 2.444624 CGACGTCAATGGCTCCACG 61.445 63.158 17.16 0.00 38.24 4.94
1454 2906 2.513204 CACGGCATGGGAGAGCAG 60.513 66.667 0.00 0.00 0.00 4.24
1458 2910 2.202987 GCATGGGAGAGCAGGACG 60.203 66.667 0.00 0.00 0.00 4.79
1459 2911 2.725312 GCATGGGAGAGCAGGACGA 61.725 63.158 0.00 0.00 0.00 4.20
1617 3069 0.765510 ACAAGTTGGTCTCCCAGTCC 59.234 55.000 7.96 0.00 43.15 3.85
1674 3126 1.135170 GTCCTACGCCTCCTGTACAAC 60.135 57.143 0.00 0.00 0.00 3.32
1794 3246 1.901650 GCGAGGGCAAGTTCTTGTCG 61.902 60.000 13.04 14.13 39.62 4.35
1797 3249 0.603975 AGGGCAAGTTCTTGTCGAGC 60.604 55.000 13.04 0.34 0.00 5.03
1824 3276 3.385577 GTTCAAGATGATAGCCTCGGAC 58.614 50.000 0.00 0.00 0.00 4.79
1827 3279 1.529226 AGATGATAGCCTCGGACTCG 58.471 55.000 0.00 0.00 37.82 4.18
1863 3315 3.886505 AGAGAAGGATCACCATCGACTAC 59.113 47.826 0.00 0.00 38.71 2.73
1932 3384 1.200519 GTATCACAGGGCAGGGTGTA 58.799 55.000 0.00 0.00 36.43 2.90
1941 3393 0.462759 GGCAGGGTGTACAGCAGATC 60.463 60.000 25.23 8.95 0.00 2.75
2001 3453 2.603473 TACTCACCAGCAGGCCGT 60.603 61.111 0.00 0.00 39.06 5.68
2142 3594 4.652822 AGGTTCCTCATGGTGACTTTTAC 58.347 43.478 0.00 0.00 34.23 2.01
2148 3600 3.482436 TCATGGTGACTTTTACGGCTTT 58.518 40.909 0.00 0.00 0.00 3.51
2188 3640 2.158900 TCAATCTCCCTCGAAGAATGCC 60.159 50.000 0.00 0.00 34.09 4.40
2189 3641 1.500474 ATCTCCCTCGAAGAATGCCA 58.500 50.000 0.00 0.00 34.09 4.92
2295 3747 1.339097 ACGGCCAGGTCTATCCATAC 58.661 55.000 2.24 0.00 39.02 2.39
2300 3752 2.303311 GCCAGGTCTATCCATACTTCCC 59.697 54.545 0.00 0.00 39.02 3.97
2301 3753 3.587498 CCAGGTCTATCCATACTTCCCA 58.413 50.000 0.00 0.00 39.02 4.37
2438 3890 4.629634 TGCATACATACAAAACTCTGACCG 59.370 41.667 0.00 0.00 0.00 4.79
2455 3907 0.250467 CCGCATAAGCTGGGCATACT 60.250 55.000 5.51 0.00 39.10 2.12
2494 3946 5.335976 GCTATATTAGGGGCAGTTGAATTGC 60.336 44.000 3.89 3.89 40.80 3.56
2518 3970 6.543831 GCTTTTTATCATGACAGGATGGTACT 59.456 38.462 12.74 0.00 43.62 2.73
2703 4155 0.868406 GAGACAAGAAGGTTGTGGCG 59.132 55.000 0.00 0.00 31.96 5.69
2823 4275 0.600057 GGTTTTGCTCAGAAGGCCAG 59.400 55.000 5.01 0.00 0.00 4.85
3015 4467 6.211184 TCCATTGTGATGTAAAGCCAGAAAAT 59.789 34.615 0.00 0.00 0.00 1.82
3234 4686 0.253327 CTGGGAGTAGGGTTTCCAGC 59.747 60.000 0.00 0.00 38.55 4.85
3250 4702 4.314440 GCGGGGTGACAGCAGACA 62.314 66.667 7.01 0.00 35.87 3.41
3263 4715 3.262660 ACAGCAGACAAAGATGAGATGGA 59.737 43.478 0.00 0.00 0.00 3.41
3336 4788 1.610363 TGCAATTTGTTCAGGCGGTA 58.390 45.000 0.00 0.00 0.00 4.02
3516 4968 1.640428 TGGAATGCGACGATGAAGAC 58.360 50.000 0.00 0.00 0.00 3.01
3544 4996 3.633525 TCCTGCATACTTTTGATGGCATC 59.366 43.478 20.52 20.52 0.00 3.91
3565 5017 4.005650 TCTTACCAGAAGCATGAAAGCAG 58.994 43.478 0.00 0.00 36.85 4.24
3589 5041 4.321718 CTGAACAAGGCATCAGAAGAGAA 58.678 43.478 0.00 0.00 44.64 2.87
3645 5097 7.939039 AGTGTATACCTTATGTCATGAATTGGG 59.061 37.037 0.00 0.00 0.00 4.12
3676 5128 4.305539 TCCATTCTCCAGATTTTCTGCA 57.694 40.909 0.00 0.00 42.98 4.41
3729 5181 2.439156 GCTGCAAGGCTGGTAGGG 60.439 66.667 9.17 0.00 0.00 3.53
3748 5201 1.436983 GGGGAATTAGGTGAAGCGCG 61.437 60.000 0.00 0.00 0.00 6.86
3829 5283 3.491342 TGGTCGGTTCAAATTGGATCAA 58.509 40.909 0.00 0.00 0.00 2.57
3831 5285 4.526262 TGGTCGGTTCAAATTGGATCAATT 59.474 37.500 0.00 0.54 44.62 2.32
3851 5305 4.930463 TTAGTTTGATAATGCGTTGCGA 57.070 36.364 0.08 0.00 0.00 5.10
3855 5309 6.779115 AGTTTGATAATGCGTTGCGATATA 57.221 33.333 0.08 0.00 0.00 0.86
3953 5411 9.935241 GTTTCTAGATATGGATCTGCAATAGAA 57.065 33.333 0.00 0.00 42.66 2.10
4078 5536 3.929610 GCAGTGCCAAACTTTGTTTTGTA 59.070 39.130 2.85 0.00 36.83 2.41
4101 5559 2.035632 GCTGTCTATCACTAGTGGGCT 58.964 52.381 22.48 10.33 0.00 5.19
4126 5584 6.428771 TGCCAGGTTTATACAAACTGACTTAC 59.571 38.462 11.83 0.00 43.06 2.34
4162 5621 7.197017 CGATCCTGCACTCTATATATAACACC 58.803 42.308 0.00 0.00 0.00 4.16
4166 5625 7.673926 TCCTGCACTCTATATATAACACCATGA 59.326 37.037 0.00 0.00 0.00 3.07
4258 5719 0.743097 GGCAAGGGATGTCATGAAGC 59.257 55.000 0.00 0.00 32.41 3.86
4293 5754 7.387948 AGAATGTTGTAATGTGTGAGACCTAAC 59.612 37.037 0.00 0.00 0.00 2.34
4348 5809 7.815840 TTGGTCTTTTGAACATATGAAGTGA 57.184 32.000 10.38 0.00 46.73 3.41
4377 5838 8.974060 ACAAAATTCTTGACCTAAGTGACTTA 57.026 30.769 4.81 4.81 37.65 2.24
4432 5991 8.922931 AAAAATGAAAGTGCCCAGAATTATTT 57.077 26.923 0.00 0.00 0.00 1.40
4433 5992 8.922931 AAAATGAAAGTGCCCAGAATTATTTT 57.077 26.923 0.00 0.00 0.00 1.82
4434 5993 8.922931 AAATGAAAGTGCCCAGAATTATTTTT 57.077 26.923 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.125106 CCGTGCCTGGCCTAGTTC 60.125 66.667 17.53 0.00 0.00 3.01
38 39 3.909258 AACGCTACGTCCGTGCCTG 62.909 63.158 13.81 0.00 39.99 4.85
41 42 1.129209 GAAAACGCTACGTCCGTGC 59.871 57.895 13.81 4.18 39.99 5.34
86 87 1.801178 GCATCCGTATTTGGAGCTAGC 59.199 52.381 6.62 6.62 42.45 3.42
249 252 7.815840 TTGAATGTCTTCTACAATGGTTGAA 57.184 32.000 0.00 0.00 42.70 2.69
332 726 1.450312 CCATGTCCCTCTCGTTGCC 60.450 63.158 0.00 0.00 0.00 4.52
344 738 1.448540 CCACTGACTCGGCCATGTC 60.449 63.158 15.78 15.78 0.00 3.06
352 746 1.822506 TCTAGGTGACCACTGACTCG 58.177 55.000 3.63 0.00 0.00 4.18
373 767 5.959618 CATGAATATCCATCATGTGCTGT 57.040 39.130 8.06 0.00 45.79 4.40
448 1846 1.793820 AAGGGAAGGTGGAGGCAAGG 61.794 60.000 0.00 0.00 0.00 3.61
459 1857 1.836802 CCCAGAGAGAGAAAGGGAAGG 59.163 57.143 0.00 0.00 42.25 3.46
464 1862 0.987294 TTGCCCCAGAGAGAGAAAGG 59.013 55.000 0.00 0.00 0.00 3.11
517 1946 2.824041 GTGGATTCGCCGCATGGT 60.824 61.111 0.00 0.00 46.72 3.55
524 1953 1.644786 CCTTGTTCGGTGGATTCGCC 61.645 60.000 0.00 0.00 40.08 5.54
608 2037 3.427638 GCCTTCTTCGGTATTTTCTTGGC 60.428 47.826 0.00 0.00 0.00 4.52
613 2042 2.608090 CTCGGCCTTCTTCGGTATTTTC 59.392 50.000 0.00 0.00 0.00 2.29
795 2238 6.835174 TGGTCTAGGAATCTACGTATACTGT 58.165 40.000 0.00 3.71 0.00 3.55
818 2261 1.357258 GGTGATGAGTGCGTCTGCTG 61.357 60.000 0.00 0.00 43.34 4.41
865 2308 4.635699 ATTTCCAAACGGAGGAAGTACT 57.364 40.909 5.77 0.00 45.25 2.73
866 2309 5.791367 GTATTTCCAAACGGAGGAAGTAC 57.209 43.478 16.56 16.56 45.10 2.73
867 2310 5.750352 AGTATTTCCAAACGGAGGAAGTA 57.250 39.130 5.77 5.17 45.25 2.24
868 2311 4.635699 AGTATTTCCAAACGGAGGAAGT 57.364 40.909 5.77 5.99 45.25 3.01
869 2312 4.760204 ACAAGTATTTCCAAACGGAGGAAG 59.240 41.667 5.77 0.00 45.25 3.46
870 2313 4.721132 ACAAGTATTTCCAAACGGAGGAA 58.279 39.130 1.90 1.90 43.13 3.36
871 2314 4.320870 GACAAGTATTTCCAAACGGAGGA 58.679 43.478 0.00 0.00 32.88 3.71
872 2315 3.439129 GGACAAGTATTTCCAAACGGAGG 59.561 47.826 0.00 0.00 32.88 4.30
873 2316 4.324267 AGGACAAGTATTTCCAAACGGAG 58.676 43.478 0.00 0.00 33.92 4.63
874 2317 4.360951 AGGACAAGTATTTCCAAACGGA 57.639 40.909 0.00 0.00 33.92 4.69
875 2318 6.563222 TTTAGGACAAGTATTTCCAAACGG 57.437 37.500 0.00 0.00 33.92 4.44
876 2319 8.911662 CATTTTTAGGACAAGTATTTCCAAACG 58.088 33.333 0.00 0.00 33.92 3.60
877 2320 9.203421 CCATTTTTAGGACAAGTATTTCCAAAC 57.797 33.333 0.00 0.00 33.92 2.93
878 2321 8.929487 ACCATTTTTAGGACAAGTATTTCCAAA 58.071 29.630 0.00 0.00 33.92 3.28
879 2322 8.485578 ACCATTTTTAGGACAAGTATTTCCAA 57.514 30.769 0.00 0.00 33.92 3.53
880 2323 8.364142 CAACCATTTTTAGGACAAGTATTTCCA 58.636 33.333 0.00 0.00 33.92 3.53
881 2324 8.364894 ACAACCATTTTTAGGACAAGTATTTCC 58.635 33.333 0.00 0.00 0.00 3.13
885 2328 9.975218 AGATACAACCATTTTTAGGACAAGTAT 57.025 29.630 0.00 0.00 0.00 2.12
887 2330 9.449719 CTAGATACAACCATTTTTAGGACAAGT 57.550 33.333 0.00 0.00 0.00 3.16
888 2331 9.667107 TCTAGATACAACCATTTTTAGGACAAG 57.333 33.333 0.00 0.00 0.00 3.16
933 2376 9.320352 GGAAATACTTGTGTTAAAAATGGTTGT 57.680 29.630 0.00 0.00 0.00 3.32
934 2377 8.484008 CGGAAATACTTGTGTTAAAAATGGTTG 58.516 33.333 0.00 0.00 0.00 3.77
935 2378 8.414778 TCGGAAATACTTGTGTTAAAAATGGTT 58.585 29.630 0.00 0.00 0.00 3.67
936 2379 7.942990 TCGGAAATACTTGTGTTAAAAATGGT 58.057 30.769 0.00 0.00 0.00 3.55
937 2380 8.804688 TTCGGAAATACTTGTGTTAAAAATGG 57.195 30.769 0.00 0.00 0.00 3.16
939 2382 9.418045 CCATTCGGAAATACTTGTGTTAAAAAT 57.582 29.630 0.00 0.00 0.00 1.82
940 2383 8.630917 TCCATTCGGAAATACTTGTGTTAAAAA 58.369 29.630 0.00 0.00 38.83 1.94
941 2384 8.167605 TCCATTCGGAAATACTTGTGTTAAAA 57.832 30.769 0.00 0.00 38.83 1.52
942 2385 7.094549 CCTCCATTCGGAAATACTTGTGTTAAA 60.095 37.037 0.00 0.00 42.21 1.52
943 2386 6.373216 CCTCCATTCGGAAATACTTGTGTTAA 59.627 38.462 0.00 0.00 42.21 2.01
944 2387 5.878116 CCTCCATTCGGAAATACTTGTGTTA 59.122 40.000 0.00 0.00 42.21 2.41
945 2388 4.700213 CCTCCATTCGGAAATACTTGTGTT 59.300 41.667 0.00 0.00 42.21 3.32
946 2389 4.261801 CCTCCATTCGGAAATACTTGTGT 58.738 43.478 0.00 0.00 42.21 3.72
947 2390 3.627577 CCCTCCATTCGGAAATACTTGTG 59.372 47.826 0.00 0.00 42.21 3.33
948 2391 3.521937 TCCCTCCATTCGGAAATACTTGT 59.478 43.478 0.00 0.00 42.21 3.16
949 2392 4.130118 CTCCCTCCATTCGGAAATACTTG 58.870 47.826 0.00 0.00 42.21 3.16
950 2393 3.780850 ACTCCCTCCATTCGGAAATACTT 59.219 43.478 0.00 0.00 42.21 2.24
951 2394 3.385115 ACTCCCTCCATTCGGAAATACT 58.615 45.455 0.00 0.00 42.21 2.12
952 2395 3.840124 ACTCCCTCCATTCGGAAATAC 57.160 47.619 0.00 0.00 42.21 1.89
953 2396 3.323979 GCTACTCCCTCCATTCGGAAATA 59.676 47.826 0.00 0.00 42.21 1.40
954 2397 2.104963 GCTACTCCCTCCATTCGGAAAT 59.895 50.000 0.00 0.00 42.21 2.17
955 2398 1.485066 GCTACTCCCTCCATTCGGAAA 59.515 52.381 0.00 0.00 42.21 3.13
956 2399 1.120530 GCTACTCCCTCCATTCGGAA 58.879 55.000 0.00 0.00 42.21 4.30
957 2400 0.261991 AGCTACTCCCTCCATTCGGA 59.738 55.000 0.00 0.00 39.79 4.55
958 2401 0.676736 GAGCTACTCCCTCCATTCGG 59.323 60.000 0.00 0.00 0.00 4.30
959 2402 1.339610 CTGAGCTACTCCCTCCATTCG 59.660 57.143 0.00 0.00 0.00 3.34
960 2403 2.393646 ACTGAGCTACTCCCTCCATTC 58.606 52.381 0.00 0.00 0.00 2.67
961 2404 2.559381 ACTGAGCTACTCCCTCCATT 57.441 50.000 0.00 0.00 0.00 3.16
962 2405 2.245028 TGTACTGAGCTACTCCCTCCAT 59.755 50.000 0.00 0.00 0.00 3.41
963 2406 1.639108 TGTACTGAGCTACTCCCTCCA 59.361 52.381 0.00 0.00 0.00 3.86
964 2407 2.025898 GTGTACTGAGCTACTCCCTCC 58.974 57.143 0.00 0.00 0.00 4.30
965 2408 2.724454 TGTGTACTGAGCTACTCCCTC 58.276 52.381 0.00 0.00 0.00 4.30
966 2409 2.901338 TGTGTACTGAGCTACTCCCT 57.099 50.000 0.00 0.00 0.00 4.20
967 2410 3.786635 CATTGTGTACTGAGCTACTCCC 58.213 50.000 0.00 0.00 0.00 4.30
968 2411 3.118956 AGCATTGTGTACTGAGCTACTCC 60.119 47.826 0.00 0.00 0.00 3.85
969 2412 3.862267 CAGCATTGTGTACTGAGCTACTC 59.138 47.826 0.00 0.00 33.10 2.59
988 2431 0.459237 CTGTCCATCTCGTGACCAGC 60.459 60.000 0.00 0.00 0.00 4.85
1018 2465 2.994671 GCCTTTGCGGGGCTCTTTC 61.995 63.158 7.08 0.00 45.57 2.62
1066 2514 2.046292 TGTTGGAGGTGATGACAGACA 58.954 47.619 0.00 0.00 0.00 3.41
1067 2515 2.808543 GTTGTTGGAGGTGATGACAGAC 59.191 50.000 0.00 0.00 0.00 3.51
1068 2516 2.224523 GGTTGTTGGAGGTGATGACAGA 60.225 50.000 0.00 0.00 0.00 3.41
1069 2517 2.154462 GGTTGTTGGAGGTGATGACAG 58.846 52.381 0.00 0.00 0.00 3.51
1133 2585 0.979665 CAGAGTGGAGAGCAAGGGAA 59.020 55.000 0.00 0.00 0.00 3.97
1134 2586 1.548357 GCAGAGTGGAGAGCAAGGGA 61.548 60.000 0.00 0.00 0.00 4.20
1135 2587 1.078567 GCAGAGTGGAGAGCAAGGG 60.079 63.158 0.00 0.00 0.00 3.95
1185 2637 2.612672 CAGAGATGTGCCTGTGCTTATG 59.387 50.000 0.00 0.00 38.71 1.90
1239 2691 1.003233 GGAGAAGGTGGTGTCTGGC 60.003 63.158 0.00 0.00 0.00 4.85
1339 2791 1.742768 GAGGATTCGCCGTCCAGAT 59.257 57.895 0.00 0.00 43.43 2.90
1440 2892 2.191641 GTCCTGCTCTCCCATGCC 59.808 66.667 0.00 0.00 0.00 4.40
1458 2910 3.368571 GTGTGCTTGCCCCAGCTC 61.369 66.667 1.78 0.00 40.79 4.09
1459 2911 3.736996 TTGTGTGCTTGCCCCAGCT 62.737 57.895 1.78 0.00 40.79 4.24
1509 2961 1.597797 TACCGGCCGAGTCGTTGATT 61.598 55.000 30.73 0.46 0.00 2.57
1583 3035 2.474816 ACTTGTTTGCTCTCGTCAGAC 58.525 47.619 0.00 0.00 0.00 3.51
1617 3069 6.802348 CGAAATAGAGGACATGGTAACTATCG 59.198 42.308 0.00 0.39 37.61 2.92
1674 3126 2.100631 GCTTGTGATGTCCGGTCCG 61.101 63.158 3.60 3.60 0.00 4.79
1740 3192 1.165907 TCTTGCTGCTGTTGAACCGG 61.166 55.000 0.00 0.00 0.00 5.28
1741 3193 0.877071 ATCTTGCTGCTGTTGAACCG 59.123 50.000 0.00 0.00 0.00 4.44
1794 3246 2.315925 TCATCTTGAACCCATCGCTC 57.684 50.000 0.00 0.00 0.00 5.03
1797 3249 3.070018 GGCTATCATCTTGAACCCATCG 58.930 50.000 0.00 0.00 0.00 3.84
1824 3276 1.224592 CTGGATCCCCAAACCCGAG 59.775 63.158 9.90 0.00 42.98 4.63
1827 3279 0.999712 TTCTCTGGATCCCCAAACCC 59.000 55.000 9.90 0.00 42.98 4.11
1863 3315 2.080286 ACATTCTGAAGTTCCCGTCG 57.920 50.000 0.00 0.00 0.00 5.12
1866 3318 3.926616 ACTGTACATTCTGAAGTTCCCG 58.073 45.455 0.00 0.00 0.00 5.14
1941 3393 4.417506 CACACAATCCATGCACATAACAG 58.582 43.478 0.00 0.00 0.00 3.16
2001 3453 0.615331 GAGGACAAGTGCATCTGGGA 59.385 55.000 0.00 0.00 0.00 4.37
2066 3518 1.851021 TTGGATGCTGAACGTTGGCG 61.851 55.000 5.00 0.00 44.93 5.69
2098 3550 5.183904 CCTTGACGAATTGAAAATCCTCCTT 59.816 40.000 0.00 0.00 0.00 3.36
2142 3594 2.099141 TGGAAGTGAGATCAAAGCCG 57.901 50.000 0.00 0.00 0.00 5.52
2148 3600 4.687901 TGACTTGTTGGAAGTGAGATCA 57.312 40.909 0.00 0.00 0.00 2.92
2188 3640 0.731417 CTCTCCAAGCAAATCCGCTG 59.269 55.000 0.00 0.00 42.89 5.18
2189 3641 3.165606 CTCTCCAAGCAAATCCGCT 57.834 52.632 0.00 0.00 46.67 5.52
2212 3664 6.690098 GCTTTGTATGTGAAAGATATGCACAG 59.310 38.462 0.00 0.00 44.66 3.66
2295 3747 3.578716 TGAAGTAGTTGTCTCCTGGGAAG 59.421 47.826 0.00 0.00 0.00 3.46
2300 3752 5.467063 GGAAGTTTGAAGTAGTTGTCTCCTG 59.533 44.000 0.00 0.00 0.00 3.86
2301 3753 5.367060 AGGAAGTTTGAAGTAGTTGTCTCCT 59.633 40.000 0.00 0.00 0.00 3.69
2425 3877 2.744202 AGCTTATGCGGTCAGAGTTTTG 59.256 45.455 0.00 0.00 45.42 2.44
2438 3890 2.856222 AGAAGTATGCCCAGCTTATGC 58.144 47.619 0.00 0.00 40.05 3.14
2455 3907 8.097038 CCCTAATATAGCAGCAAAGATGTAGAA 58.903 37.037 0.00 0.00 0.00 2.10
2494 3946 8.511604 AAGTACCATCCTGTCATGATAAAAAG 57.488 34.615 0.00 0.00 0.00 2.27
2518 3970 6.481644 GGTATGTTGTGCATTTTGAAAAGGAA 59.518 34.615 6.49 0.00 38.94 3.36
2703 4155 8.773404 TTCTAACATCTGTAAGCTTCTTTACC 57.227 34.615 0.00 0.00 33.56 2.85
2823 4275 5.246145 ACTCGTAGACTAATAACCTGTGC 57.754 43.478 0.00 0.00 0.00 4.57
3015 4467 4.334481 TCGAATTCTCGTGTCAGCAGTATA 59.666 41.667 3.52 0.00 45.62 1.47
3102 4554 2.164422 CGTTGTGCCTCTCATCTGAGTA 59.836 50.000 7.07 0.00 42.60 2.59
3108 4560 2.109126 GCCCGTTGTGCCTCTCATC 61.109 63.158 0.00 0.00 0.00 2.92
3171 4623 3.766151 TCCGAAGCTGTAAACATCTACG 58.234 45.455 0.00 0.00 0.00 3.51
3234 4686 1.227823 TTTGTCTGCTGTCACCCCG 60.228 57.895 0.00 0.00 0.00 5.73
3250 4702 4.851843 TGCATCAAGTCCATCTCATCTTT 58.148 39.130 0.00 0.00 0.00 2.52
3263 4715 2.564062 CCACTGGGAATTTGCATCAAGT 59.436 45.455 0.00 0.00 35.59 3.16
3336 4788 2.684881 CCCATTAGCGAGCATCTGTTTT 59.315 45.455 0.00 0.00 0.00 2.43
3486 4938 4.051237 CGTCGCATTCCATGAGATTTCTA 58.949 43.478 0.00 0.00 41.07 2.10
3516 4968 6.349115 GCCATCAAAAGTATGCAGGATGATAG 60.349 42.308 0.00 0.00 39.69 2.08
3544 4996 3.128242 CCTGCTTTCATGCTTCTGGTAAG 59.872 47.826 0.00 0.00 0.00 2.34
3565 5017 1.471684 CTTCTGATGCCTTGTTCAGCC 59.528 52.381 0.00 0.00 39.36 4.85
3611 5063 8.422577 TGACATAAGGTATACACTGCATAGAT 57.577 34.615 5.01 0.00 0.00 1.98
3645 5097 9.571816 AAAATCTGGAGAATGGATCTAATCTTC 57.428 33.333 0.00 0.00 38.96 2.87
3676 5128 5.939296 CCAACCACAATTTGAATAAGGCAAT 59.061 36.000 2.79 0.00 0.00 3.56
3729 5181 1.436983 CGCGCTTCACCTAATTCCCC 61.437 60.000 5.56 0.00 0.00 4.81
3733 5185 2.614829 ATACCGCGCTTCACCTAATT 57.385 45.000 5.56 0.00 0.00 1.40
3742 5195 5.305139 ACATAAAAGAAAATACCGCGCTT 57.695 34.783 5.56 0.00 0.00 4.68
3790 5244 8.974060 ACCGACCATTATCAAAACAGTTATAT 57.026 30.769 0.00 0.00 0.00 0.86
3829 5283 5.478233 TCGCAACGCATTATCAAACTAAT 57.522 34.783 0.00 0.00 0.00 1.73
3831 5285 6.779115 ATATCGCAACGCATTATCAAACTA 57.221 33.333 0.00 0.00 0.00 2.24
3898 5356 1.674221 GCAGAGCTCAATGAACCGACT 60.674 52.381 17.77 0.00 0.00 4.18
3953 5411 6.650807 CGGTATGGAAGAACATAATGCACTAT 59.349 38.462 0.00 0.00 35.29 2.12
3954 5412 5.989168 CGGTATGGAAGAACATAATGCACTA 59.011 40.000 0.00 0.00 35.29 2.74
3957 5415 4.133820 CCGGTATGGAAGAACATAATGCA 58.866 43.478 0.00 0.00 42.00 3.96
4078 5536 3.181461 GCCCACTAGTGATAGACAGCATT 60.181 47.826 24.68 0.00 0.00 3.56
4101 5559 4.980573 AGTCAGTTTGTATAAACCTGGCA 58.019 39.130 11.06 0.00 45.77 4.92
4162 5621 9.507280 CAAAATTACAACAGCCTATACTTCATG 57.493 33.333 0.00 0.00 0.00 3.07
4166 5625 6.404293 CCGCAAAATTACAACAGCCTATACTT 60.404 38.462 0.00 0.00 0.00 2.24
4215 5674 4.382470 CCATCTGGTAGCCTATACTGCATC 60.382 50.000 0.00 0.00 0.00 3.91
4258 5719 7.959109 CACACATTACAACATTCTCACACATAG 59.041 37.037 0.00 0.00 0.00 2.23
4293 5754 8.236586 TCCGAAAATGACACATAATTCAAGAAG 58.763 33.333 0.00 0.00 0.00 2.85
4348 5809 8.837389 GTCACTTAGGTCAAGAATTTTGTAAGT 58.163 33.333 0.00 0.00 37.71 2.24
4377 5838 8.426569 AGCATTTAGCCATCAAAATATGGTAT 57.573 30.769 4.89 0.00 46.93 2.73


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

AutoCloner maintained by Alex Coulton.