Multiple sequence alignment - TraesCS6D01G312800

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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 TraesCS6D01G312800 chr6D 100.000 5875 0 0 1 5875 421879151 421885025 0.000000e+00 10850
1 TraesCS6D01G312800 chr6A 94.633 2180 108 5 2055 4231 564717273 564719446 0.000000e+00 3369
2 TraesCS6D01G312800 chr6A 87.589 1958 120 58 1 1929 564715186 564717049 0.000000e+00 2156
3 TraesCS6D01G312800 chr6A 89.891 1286 68 24 4262 5507 564719441 564720704 0.000000e+00 1598
4 TraesCS6D01G312800 chr6A 81.975 405 28 17 5499 5875 564720923 564721310 9.570000e-78 302
5 TraesCS6D01G312800 chr6B 91.753 2413 137 26 2055 4452 635169552 635171917 0.000000e+00 3297
6 TraesCS6D01G312800 chr6B 87.992 2082 103 61 11 2024 635167458 635169460 0.000000e+00 2324
7 TraesCS6D01G312800 chr6B 87.689 1389 75 43 4498 5842 635171925 635173261 0.000000e+00 1530
8 TraesCS6D01G312800 chr7A 76.774 465 44 40 1106 1508 126576870 126577332 9.980000e-48 202
9 TraesCS6D01G312800 chr7D 92.188 128 8 2 1106 1232 123653640 123653766 4.680000e-41 180


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 TraesCS6D01G312800 chr6D 421879151 421885025 5874 False 10850.000000 10850 100.000000 1 5875 1 chr6D.!!$F1 5874
1 TraesCS6D01G312800 chr6A 564715186 564721310 6124 False 1856.250000 3369 88.522000 1 5875 4 chr6A.!!$F1 5874
2 TraesCS6D01G312800 chr6B 635167458 635173261 5803 False 2383.666667 3297 89.144667 11 5842 3 chr6B.!!$F1 5831

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
931 974 0.034896 CACCTGTAACGCCCTGACTT 59.965 55.000 0.00 0.00 0.00 3.01 F
933 976 0.034896 CCTGTAACGCCCTGACTTGT 59.965 55.000 0.00 0.00 0.00 3.16 F
986 1029 0.036010 AATTGGCGGGAGTGAGTGAG 60.036 55.000 0.00 0.00 0.00 3.51 F
1958 2038 0.179097 TAGCAGTGACACGTGTTGCA 60.179 50.000 33.41 22.09 37.24 4.08 F
2129 2281 0.718343 GATCTCGATTGCATAGCCGC 59.282 55.000 0.00 0.00 0.00 6.53 F
4007 4170 1.201647 CAGCTTTCACTGCCAGATTGG 59.798 52.381 0.00 0.00 41.55 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2692 2853 0.035317 ATTTCGACAGCTGCCACTGA 59.965 50.000 15.27 1.50 40.25 3.41 R
2834 2995 6.862090 ACGCAGAGTAAAGTTTAGAAGTACTG 59.138 38.462 0.00 0.00 0.00 2.74 R
3065 3226 4.527038 AGTTCCGTCTTCTCTTGAATGGTA 59.473 41.667 0.00 0.00 0.00 3.25 R
3080 3241 0.824759 ATAGGCTGGTCAGTTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79 R
4037 4200 1.542375 ACAATCTGGACCAGCCCCT 60.542 57.895 17.33 0.00 34.97 4.79 R
5522 5970 0.819259 CCCACGTTCAGCCCATATGG 60.819 60.000 15.41 15.41 37.09 2.74 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
22 23 1.675641 CGGGCTCCCACAAAAGAGG 60.676 63.158 5.70 0.00 35.37 3.69
28 29 0.260230 TCCCACAAAAGAGGCAACCA 59.740 50.000 0.00 0.00 37.17 3.67
227 228 3.087065 CCACCCATCCCCGTCTTT 58.913 61.111 0.00 0.00 0.00 2.52
348 353 3.857038 CGTATCCACCCACCCCCG 61.857 72.222 0.00 0.00 0.00 5.73
476 492 3.793144 GCGCGAGGCAAAGAGTGG 61.793 66.667 12.10 0.00 42.87 4.00
619 635 2.757077 CAACACCTGTCCTCCCCC 59.243 66.667 0.00 0.00 0.00 5.40
620 636 2.928396 AACACCTGTCCTCCCCCG 60.928 66.667 0.00 0.00 0.00 5.73
677 693 1.671742 GACCTTCTTCCACCTCGCA 59.328 57.895 0.00 0.00 0.00 5.10
679 695 1.376037 CCTTCTTCCACCTCGCACC 60.376 63.158 0.00 0.00 0.00 5.01
681 697 2.111999 CTTCTTCCACCTCGCACCCA 62.112 60.000 0.00 0.00 0.00 4.51
682 698 2.358737 CTTCCACCTCGCACCCAC 60.359 66.667 0.00 0.00 0.00 4.61
692 708 2.501610 GCACCCACCCGATCTCTC 59.498 66.667 0.00 0.00 0.00 3.20
695 719 0.396417 CACCCACCCGATCTCTCTCT 60.396 60.000 0.00 0.00 0.00 3.10
706 730 4.767409 CCGATCTCTCTCTCTCTCTCTCTA 59.233 50.000 0.00 0.00 0.00 2.43
707 731 5.336055 CCGATCTCTCTCTCTCTCTCTCTAC 60.336 52.000 0.00 0.00 0.00 2.59
708 732 5.617973 CGATCTCTCTCTCTCTCTCTCTACG 60.618 52.000 0.00 0.00 0.00 3.51
710 734 4.338400 TCTCTCTCTCTCTCTCTCTACGTG 59.662 50.000 0.00 0.00 0.00 4.49
711 735 3.123804 CTCTCTCTCTCTCTCTACGTGC 58.876 54.545 0.00 0.00 0.00 5.34
735 759 3.512516 GCACCAATCGCTCCTGGC 61.513 66.667 0.00 0.00 36.03 4.85
741 765 2.964310 AATCGCTCCTGGCAGCAGT 61.964 57.895 9.56 0.00 39.62 4.40
744 768 2.985456 GCTCCTGGCAGCAGTAGT 59.015 61.111 9.56 0.00 39.43 2.73
747 771 1.479709 CTCCTGGCAGCAGTAGTAGT 58.520 55.000 9.56 0.00 0.00 2.73
749 773 3.024547 CTCCTGGCAGCAGTAGTAGTAA 58.975 50.000 9.56 0.00 0.00 2.24
751 775 2.761208 CCTGGCAGCAGTAGTAGTAACT 59.239 50.000 9.56 0.00 39.91 2.24
760 784 5.502153 CAGTAGTAGTAACTGCTCGGATT 57.498 43.478 0.00 0.00 44.38 3.01
776 800 5.235305 TCGGATTTGCTCTTGCTAAATTC 57.765 39.130 0.00 0.00 37.45 2.17
800 824 1.148310 CTGCCGCCCATACTTAATCG 58.852 55.000 0.00 0.00 0.00 3.34
826 852 4.154347 CGCCTCCTGTCCTCCTGC 62.154 72.222 0.00 0.00 0.00 4.85
874 915 2.512515 GCTGCTCCCCATCACGAC 60.513 66.667 0.00 0.00 0.00 4.34
895 938 4.969196 CACGGCCGCTGTGTCTGT 62.969 66.667 28.58 0.00 36.14 3.41
896 939 4.664677 ACGGCCGCTGTGTCTGTC 62.665 66.667 28.58 0.00 0.00 3.51
897 940 4.662961 CGGCCGCTGTGTCTGTCA 62.663 66.667 14.67 0.00 0.00 3.58
898 941 2.740055 GGCCGCTGTGTCTGTCAG 60.740 66.667 0.00 0.00 36.18 3.51
910 953 2.283173 TGTCAGGCTGGAGCTCGA 60.283 61.111 15.73 2.19 41.70 4.04
919 962 0.888619 CTGGAGCTCGAACACCTGTA 59.111 55.000 7.83 0.00 0.00 2.74
921 964 1.000506 TGGAGCTCGAACACCTGTAAC 59.999 52.381 7.83 0.00 0.00 2.50
924 967 1.623973 GCTCGAACACCTGTAACGCC 61.624 60.000 0.00 0.00 0.00 5.68
931 974 0.034896 CACCTGTAACGCCCTGACTT 59.965 55.000 0.00 0.00 0.00 3.01
933 976 0.034896 CCTGTAACGCCCTGACTTGT 59.965 55.000 0.00 0.00 0.00 3.16
935 978 0.882927 TGTAACGCCCTGACTTGTGC 60.883 55.000 0.00 0.00 0.00 4.57
937 980 1.764571 TAACGCCCTGACTTGTGCCT 61.765 55.000 0.00 0.00 0.00 4.75
938 981 3.052082 CGCCCTGACTTGTGCCTG 61.052 66.667 0.00 0.00 0.00 4.85
939 982 3.368571 GCCCTGACTTGTGCCTGC 61.369 66.667 0.00 0.00 0.00 4.85
940 983 2.674380 CCCTGACTTGTGCCTGCC 60.674 66.667 0.00 0.00 0.00 4.85
941 984 2.433446 CCTGACTTGTGCCTGCCT 59.567 61.111 0.00 0.00 0.00 4.75
942 985 1.970114 CCTGACTTGTGCCTGCCTG 60.970 63.158 0.00 0.00 0.00 4.85
943 986 1.228063 CTGACTTGTGCCTGCCTGT 60.228 57.895 0.00 0.00 0.00 4.00
944 987 1.512996 CTGACTTGTGCCTGCCTGTG 61.513 60.000 0.00 0.00 0.00 3.66
945 988 1.526917 GACTTGTGCCTGCCTGTGT 60.527 57.895 0.00 0.00 0.00 3.72
962 1005 3.443037 TGTGTGCTTTTTGATTCGGTTG 58.557 40.909 0.00 0.00 0.00 3.77
964 1007 2.690497 TGTGCTTTTTGATTCGGTTGGA 59.310 40.909 0.00 0.00 0.00 3.53
965 1008 3.320541 TGTGCTTTTTGATTCGGTTGGAT 59.679 39.130 0.00 0.00 0.00 3.41
967 1010 5.010112 TGTGCTTTTTGATTCGGTTGGATTA 59.990 36.000 0.00 0.00 0.00 1.75
978 1021 1.681264 GGTTGGATTAATTGGCGGGAG 59.319 52.381 0.00 0.00 0.00 4.30
979 1022 2.375146 GTTGGATTAATTGGCGGGAGT 58.625 47.619 0.00 0.00 0.00 3.85
981 1024 1.562008 TGGATTAATTGGCGGGAGTGA 59.438 47.619 0.00 0.00 0.00 3.41
983 1026 2.421529 GGATTAATTGGCGGGAGTGAGT 60.422 50.000 0.00 0.00 0.00 3.41
984 1027 2.107950 TTAATTGGCGGGAGTGAGTG 57.892 50.000 0.00 0.00 0.00 3.51
985 1028 1.271856 TAATTGGCGGGAGTGAGTGA 58.728 50.000 0.00 0.00 0.00 3.41
986 1029 0.036010 AATTGGCGGGAGTGAGTGAG 60.036 55.000 0.00 0.00 0.00 3.51
987 1030 1.903877 ATTGGCGGGAGTGAGTGAGG 61.904 60.000 0.00 0.00 0.00 3.86
988 1031 3.775654 GGCGGGAGTGAGTGAGGG 61.776 72.222 0.00 0.00 0.00 4.30
989 1032 3.775654 GCGGGAGTGAGTGAGGGG 61.776 72.222 0.00 0.00 0.00 4.79
990 1033 2.037367 CGGGAGTGAGTGAGGGGA 59.963 66.667 0.00 0.00 0.00 4.81
991 1034 1.381872 CGGGAGTGAGTGAGGGGAT 60.382 63.158 0.00 0.00 0.00 3.85
992 1035 1.395826 CGGGAGTGAGTGAGGGGATC 61.396 65.000 0.00 0.00 0.00 3.36
993 1036 1.395826 GGGAGTGAGTGAGGGGATCG 61.396 65.000 0.00 0.00 0.00 3.69
994 1037 1.395826 GGAGTGAGTGAGGGGATCGG 61.396 65.000 0.00 0.00 0.00 4.18
995 1038 0.395862 GAGTGAGTGAGGGGATCGGA 60.396 60.000 0.00 0.00 0.00 4.55
996 1039 0.263172 AGTGAGTGAGGGGATCGGAT 59.737 55.000 0.00 0.00 0.00 4.18
997 1040 0.676736 GTGAGTGAGGGGATCGGATC 59.323 60.000 9.54 9.54 0.00 3.36
1170 1213 3.702048 CCGGGCAAGGACTTCGGA 61.702 66.667 0.00 0.00 42.94 4.55
1317 1360 4.154347 CAGGGCTCCCTCACGCTC 62.154 72.222 4.06 0.00 46.28 5.03
1615 1658 2.370189 CCTATGGTGAATCCTCTGTCCC 59.630 54.545 0.00 0.00 37.07 4.46
1620 1663 1.144936 GAATCCTCTGTCCCTGGCG 59.855 63.158 0.00 0.00 0.00 5.69
1659 1702 1.457831 ATACGGACAGGGAGGAGGC 60.458 63.158 0.00 0.00 0.00 4.70
1788 1834 0.315869 CGCCGATGCCGTATGTTTTC 60.316 55.000 0.00 0.00 0.00 2.29
1912 1958 4.202253 GCCAGAGGAAACAGGTGAAAATTT 60.202 41.667 0.00 0.00 0.00 1.82
1958 2038 0.179097 TAGCAGTGACACGTGTTGCA 60.179 50.000 33.41 22.09 37.24 4.08
1970 2055 6.048073 ACACGTGTTGCACAATCATATATC 57.952 37.500 17.22 0.00 33.40 1.63
1974 2059 7.164662 CACGTGTTGCACAATCATATATCTTTG 59.835 37.037 7.58 3.62 33.40 2.77
2096 2248 3.450457 TGGGCATGCTAAATTACAAAGGG 59.550 43.478 18.92 0.00 0.00 3.95
2114 2266 6.721208 ACAAAGGGTACAAACATGAATGATCT 59.279 34.615 0.00 0.00 0.00 2.75
2115 2267 7.094205 ACAAAGGGTACAAACATGAATGATCTC 60.094 37.037 0.00 0.00 0.00 2.75
2117 2269 5.104941 AGGGTACAAACATGAATGATCTCGA 60.105 40.000 0.00 0.00 0.00 4.04
2122 2274 5.124297 ACAAACATGAATGATCTCGATTGCA 59.876 36.000 0.00 0.00 0.00 4.08
2123 2275 6.183360 ACAAACATGAATGATCTCGATTGCAT 60.183 34.615 0.00 0.00 0.00 3.96
2129 2281 0.718343 GATCTCGATTGCATAGCCGC 59.282 55.000 0.00 0.00 0.00 6.53
2144 2296 1.908066 GCCGCCGTCTTCGAAAATGT 61.908 55.000 0.00 0.00 39.71 2.71
2154 2306 7.295201 CCGTCTTCGAAAATGTTTGAATCTTA 58.705 34.615 0.00 0.00 36.69 2.10
2195 2347 2.618045 CCAATAGGTTCTCCTTGCCGTT 60.618 50.000 0.00 0.00 42.12 4.44
2208 2360 2.248280 TGCCGTTGAGCTTCTGTAAA 57.752 45.000 0.00 0.00 0.00 2.01
2212 2364 3.062774 GCCGTTGAGCTTCTGTAAATCTC 59.937 47.826 0.00 0.00 0.00 2.75
2235 2387 8.258007 TCTCGGATAATCGATATTGGCTAAATT 58.742 33.333 0.00 0.00 38.55 1.82
2263 2415 5.007136 GCCTTCTGATATGCAACAGAGTTAC 59.993 44.000 16.74 8.50 42.72 2.50
2411 2571 2.754552 TGCGCATTCTAGCATTCCTTTT 59.245 40.909 5.66 0.00 38.59 2.27
2421 2581 9.860898 ATTCTAGCATTCCTTTTTATTTGTGAC 57.139 29.630 0.00 0.00 0.00 3.67
2567 2727 7.716560 TCAATCAAAGAGAGAACAAATCACAGA 59.283 33.333 0.00 0.00 0.00 3.41
2692 2853 8.240267 TGGTAGCAGTTAACAAAAATAGGTTT 57.760 30.769 8.61 0.00 0.00 3.27
3080 3241 9.912634 TTTGCTTATTTTACCATTCAAGAGAAG 57.087 29.630 0.00 0.00 37.14 2.85
3083 3244 7.905493 GCTTATTTTACCATTCAAGAGAAGACG 59.095 37.037 0.00 0.00 37.14 4.18
3116 3277 3.119990 GCCTATGTGCGCTCTTTTGTTTA 60.120 43.478 9.73 0.00 0.00 2.01
3328 3491 9.912634 ACACTTGTTTGAATAGGAAATGTTATG 57.087 29.630 0.00 0.00 0.00 1.90
3391 3554 9.715121 TGGTTTTCTTATCGTATACTTGACTTT 57.285 29.630 0.56 0.00 0.00 2.66
3429 3592 3.971032 AAGTAAAGCTGTGTGAACTGC 57.029 42.857 0.00 0.02 35.25 4.40
3430 3593 2.222027 AGTAAAGCTGTGTGAACTGCC 58.778 47.619 4.39 0.00 35.55 4.85
3533 3696 7.657354 AGTGGCTTCAAATGATTTAAGAAAACC 59.343 33.333 9.66 6.88 0.00 3.27
3677 3840 7.490962 TTGGTGTTACTTTGTTCATCTGTAG 57.509 36.000 0.00 0.00 0.00 2.74
3873 4036 5.147032 TCCCATGAGAAATGGTGTTTCTTT 58.853 37.500 0.00 0.00 38.73 2.52
3955 4118 4.080413 TCAGCCACTTTCATCATGATACCA 60.080 41.667 8.15 0.00 0.00 3.25
3996 4159 2.552315 TCCATCGTTTTCCAGCTTTCAC 59.448 45.455 0.00 0.00 0.00 3.18
4007 4170 1.201647 CAGCTTTCACTGCCAGATTGG 59.798 52.381 0.00 0.00 41.55 3.16
4018 4181 2.352503 CCAGATTGGCCAAGTTTTCG 57.647 50.000 24.94 11.85 0.00 3.46
4127 4290 1.302752 TACTGTGCCTGGCTTGCTG 60.303 57.895 21.03 15.06 0.00 4.41
4130 4293 1.741327 CTGTGCCTGGCTTGCTGTTT 61.741 55.000 21.03 0.00 0.00 2.83
4308 4477 7.062322 TGATATTATGAGAAATGTGTGGGCTT 58.938 34.615 0.00 0.00 0.00 4.35
4320 4489 2.755103 GTGTGGGCTTTCTGATTTAGGG 59.245 50.000 0.00 0.00 0.00 3.53
4440 4611 2.359848 GGGGCGTAGTTTTCTTTTGTGT 59.640 45.455 0.00 0.00 0.00 3.72
4456 4627 6.485313 TCTTTTGTGTATGTTGACCCACTTAG 59.515 38.462 0.00 0.00 0.00 2.18
4481 4652 4.038883 AGTCGTACAAAGCCTTAGACTGTT 59.961 41.667 0.00 0.00 36.31 3.16
4492 4663 4.924462 GCCTTAGACTGTTAGACACTTGAC 59.076 45.833 0.00 0.00 0.00 3.18
4552 4723 2.452600 AAAGGGTGAAACTTCTGCCA 57.547 45.000 6.16 0.00 36.74 4.92
4610 4792 6.346678 GCTGTTCCTAGTTAAAAGAAGTGACG 60.347 42.308 0.00 0.00 0.00 4.35
4620 4802 0.616111 AGAAGTGACGGCTCCTCCAT 60.616 55.000 0.00 0.00 34.01 3.41
4644 4826 5.744171 TGTTCTGTAGGCATTGTCATATGT 58.256 37.500 1.90 0.00 0.00 2.29
4646 4828 5.612725 TCTGTAGGCATTGTCATATGTCA 57.387 39.130 1.90 0.00 32.56 3.58
4669 4851 4.471904 TTCTGAGATTGCCTCGTTACAT 57.528 40.909 0.00 0.00 44.92 2.29
4677 4859 3.410631 TGCCTCGTTACATTTCAGGAA 57.589 42.857 0.00 0.00 0.00 3.36
4736 4918 4.386867 TGCAGGTATTCGAGAAGGTTAG 57.613 45.455 0.00 0.00 0.00 2.34
4738 4920 3.430374 GCAGGTATTCGAGAAGGTTAGCA 60.430 47.826 0.00 0.00 0.00 3.49
4752 4934 1.492133 TTAGCAGGCAAGCTGGACCT 61.492 55.000 13.76 0.00 46.11 3.85
4755 4937 1.078143 CAGGCAAGCTGGACCTACC 60.078 63.158 4.02 0.00 39.54 3.18
4758 4940 1.553690 GGCAAGCTGGACCTACCTCA 61.554 60.000 0.00 0.00 39.86 3.86
4835 5017 7.046292 TGTAAACTAGAGCACACTACTTTCA 57.954 36.000 0.00 0.00 0.00 2.69
4844 5026 1.136690 CACTACTTTCAACGCTGCGA 58.863 50.000 30.47 2.82 0.00 5.10
4845 5027 1.525197 CACTACTTTCAACGCTGCGAA 59.475 47.619 30.47 10.02 0.00 4.70
4930 5114 2.171003 TCCGATGCTTCAGAGTTCAGA 58.829 47.619 0.08 0.00 0.00 3.27
4962 5146 2.060004 TAGACTGCCGGCGATCTTCG 62.060 60.000 30.53 12.54 43.89 3.79
5061 5245 6.150976 CCATGTGTTGGTGTGATACTACATTT 59.849 38.462 0.00 0.00 40.99 2.32
5062 5246 7.309133 CCATGTGTTGGTGTGATACTACATTTT 60.309 37.037 0.00 0.00 40.99 1.82
5063 5247 7.197071 TGTGTTGGTGTGATACTACATTTTC 57.803 36.000 0.00 0.00 32.43 2.29
5064 5248 6.995686 TGTGTTGGTGTGATACTACATTTTCT 59.004 34.615 0.00 0.00 32.43 2.52
5065 5249 8.151596 TGTGTTGGTGTGATACTACATTTTCTA 58.848 33.333 0.00 0.00 32.43 2.10
5067 5251 9.733556 TGTTGGTGTGATACTACATTTTCTATT 57.266 29.630 0.00 0.00 32.43 1.73
5210 5402 1.089112 CTCCATTGTGCGCATCTTCA 58.911 50.000 15.91 3.18 0.00 3.02
5268 5461 0.986527 AGATGTGTGTCTGATGGGCA 59.013 50.000 0.00 0.00 0.00 5.36
5491 5713 5.840243 TTACGAGAACTTCCGGATCAATA 57.160 39.130 4.15 0.00 0.00 1.90
5503 5725 9.621629 ACTTCCGGATCAATAATGTAAATTACA 57.378 29.630 4.15 8.40 43.80 2.41
5522 5970 8.794335 AATTACAACTATCTTTTCTGGAGGTC 57.206 34.615 0.00 0.00 0.00 3.85
5584 6032 2.106511 GGGAGCATATTCCACCTGCTTA 59.893 50.000 0.00 0.00 45.79 3.09
5585 6033 3.435026 GGGAGCATATTCCACCTGCTTAA 60.435 47.826 0.00 0.00 45.79 1.85
5586 6034 3.817647 GGAGCATATTCCACCTGCTTAAG 59.182 47.826 0.00 0.00 45.79 1.85
5595 6043 1.003839 CCTGCTTAAGGTCCGTGCA 60.004 57.895 4.29 0.00 41.74 4.57
5684 6148 0.179084 CGTGGCCATCCTAATCACGT 60.179 55.000 9.72 0.00 43.92 4.49
5697 6161 9.261180 CATCCTAATCACGTGAATATACAAACT 57.739 33.333 24.13 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.315251 GTTGCCTCTTTTGTGGGAGC 59.685 55.000 0.00 0.00 34.97 4.70
13 14 2.158871 TCGTACTGGTTGCCTCTTTTGT 60.159 45.455 0.00 0.00 0.00 2.83
15 16 2.490991 GTCGTACTGGTTGCCTCTTTT 58.509 47.619 0.00 0.00 0.00 2.27
22 23 2.713894 GCGTCGTCGTACTGGTTGC 61.714 63.158 3.66 0.00 39.49 4.17
28 29 4.456253 CGGCTGCGTCGTCGTACT 62.456 66.667 3.66 0.00 39.49 2.73
158 159 4.408821 GTGGGTGCATCTGGGCGA 62.409 66.667 0.00 0.00 36.28 5.54
326 330 4.185286 GTGGGTGGATACGGGGGC 62.185 72.222 0.00 0.00 42.51 5.80
620 636 3.902086 GACGGCGAGAGGGGTAGC 61.902 72.222 16.62 0.00 0.00 3.58
663 679 2.144078 TGGGTGCGAGGTGGAAGAA 61.144 57.895 0.00 0.00 0.00 2.52
664 680 2.525629 TGGGTGCGAGGTGGAAGA 60.526 61.111 0.00 0.00 0.00 2.87
677 693 0.106419 GAGAGAGAGATCGGGTGGGT 60.106 60.000 0.00 0.00 0.00 4.51
679 695 1.142870 AGAGAGAGAGAGATCGGGTGG 59.857 57.143 0.00 0.00 0.00 4.61
681 697 2.368875 GAGAGAGAGAGAGAGATCGGGT 59.631 54.545 0.00 0.00 0.00 5.28
682 698 2.634940 AGAGAGAGAGAGAGAGATCGGG 59.365 54.545 0.00 0.00 0.00 5.14
692 708 1.858458 CGCACGTAGAGAGAGAGAGAG 59.142 57.143 0.00 0.00 0.00 3.20
695 719 1.422179 CGCGCACGTAGAGAGAGAGA 61.422 60.000 8.75 0.00 33.53 3.10
741 765 4.401519 AGCAAATCCGAGCAGTTACTACTA 59.598 41.667 0.00 0.00 31.96 1.82
744 768 3.447586 AGAGCAAATCCGAGCAGTTACTA 59.552 43.478 0.00 0.00 0.00 1.82
747 771 3.002791 CAAGAGCAAATCCGAGCAGTTA 58.997 45.455 0.00 0.00 0.00 2.24
749 773 1.446907 CAAGAGCAAATCCGAGCAGT 58.553 50.000 0.00 0.00 0.00 4.40
751 775 0.321919 AGCAAGAGCAAATCCGAGCA 60.322 50.000 0.00 0.00 45.49 4.26
753 777 4.889832 ATTTAGCAAGAGCAAATCCGAG 57.110 40.909 0.00 0.00 45.49 4.63
754 778 4.201812 CGAATTTAGCAAGAGCAAATCCGA 60.202 41.667 0.00 0.00 45.49 4.55
760 784 2.095263 GTGCCGAATTTAGCAAGAGCAA 60.095 45.455 5.05 0.00 45.49 3.91
786 810 1.809684 GGGCTCGATTAAGTATGGGC 58.190 55.000 0.00 0.00 0.00 5.36
812 836 2.679349 GCTTTAAGCAGGAGGACAGGAG 60.679 54.545 12.54 0.00 41.89 3.69
813 837 1.279271 GCTTTAAGCAGGAGGACAGGA 59.721 52.381 12.54 0.00 41.89 3.86
874 915 4.373116 ACACAGCGGCCGTGGTAG 62.373 66.667 28.70 19.37 38.74 3.18
895 938 1.908299 TGTTCGAGCTCCAGCCTGA 60.908 57.895 8.47 0.00 43.38 3.86
896 939 1.739562 GTGTTCGAGCTCCAGCCTG 60.740 63.158 8.47 0.00 43.38 4.85
897 940 2.659610 GTGTTCGAGCTCCAGCCT 59.340 61.111 8.47 0.00 43.38 4.58
898 941 2.435059 GGTGTTCGAGCTCCAGCC 60.435 66.667 14.57 0.00 43.38 4.85
910 953 0.250166 GTCAGGGCGTTACAGGTGTT 60.250 55.000 0.00 0.00 0.00 3.32
919 962 2.594592 GGCACAAGTCAGGGCGTT 60.595 61.111 0.00 0.00 0.00 4.84
921 964 3.052082 CAGGCACAAGTCAGGGCG 61.052 66.667 0.00 0.00 0.00 6.13
924 967 1.970114 CAGGCAGGCACAAGTCAGG 60.970 63.158 0.00 0.00 0.00 3.86
931 974 3.719646 AAGCACACAGGCAGGCACA 62.720 57.895 0.00 0.00 35.83 4.57
933 976 1.329171 AAAAAGCACACAGGCAGGCA 61.329 50.000 0.00 0.00 35.83 4.75
935 978 0.746063 TCAAAAAGCACACAGGCAGG 59.254 50.000 0.00 0.00 35.83 4.85
937 980 2.543445 CGAATCAAAAAGCACACAGGCA 60.543 45.455 0.00 0.00 35.83 4.75
938 981 2.053627 CGAATCAAAAAGCACACAGGC 58.946 47.619 0.00 0.00 0.00 4.85
939 982 2.034558 ACCGAATCAAAAAGCACACAGG 59.965 45.455 0.00 0.00 0.00 4.00
940 983 3.354089 ACCGAATCAAAAAGCACACAG 57.646 42.857 0.00 0.00 0.00 3.66
941 984 3.443037 CAACCGAATCAAAAAGCACACA 58.557 40.909 0.00 0.00 0.00 3.72
942 985 2.794350 CCAACCGAATCAAAAAGCACAC 59.206 45.455 0.00 0.00 0.00 3.82
943 986 2.690497 TCCAACCGAATCAAAAAGCACA 59.310 40.909 0.00 0.00 0.00 4.57
944 987 3.363341 TCCAACCGAATCAAAAAGCAC 57.637 42.857 0.00 0.00 0.00 4.40
945 988 4.599047 AATCCAACCGAATCAAAAAGCA 57.401 36.364 0.00 0.00 0.00 3.91
962 1005 2.222027 CTCACTCCCGCCAATTAATCC 58.778 52.381 0.00 0.00 0.00 3.01
964 1007 2.238646 TCACTCACTCCCGCCAATTAAT 59.761 45.455 0.00 0.00 0.00 1.40
965 1008 1.626321 TCACTCACTCCCGCCAATTAA 59.374 47.619 0.00 0.00 0.00 1.40
967 1010 0.036010 CTCACTCACTCCCGCCAATT 60.036 55.000 0.00 0.00 0.00 2.32
978 1021 0.676736 GATCCGATCCCCTCACTCAC 59.323 60.000 0.00 0.00 0.00 3.51
979 1022 0.470080 GGATCCGATCCCCTCACTCA 60.470 60.000 15.75 0.00 43.88 3.41
981 1024 4.629442 GGATCCGATCCCCTCACT 57.371 61.111 15.75 0.00 43.88 3.41
992 1035 0.597637 CGGAAAGTCCATCGGATCCG 60.598 60.000 28.62 28.62 43.08 4.18
993 1036 0.249911 CCGGAAAGTCCATCGGATCC 60.250 60.000 0.00 0.00 44.69 3.36
994 1037 0.249911 CCCGGAAAGTCCATCGGATC 60.250 60.000 0.73 0.00 44.69 3.36
995 1038 0.689745 TCCCGGAAAGTCCATCGGAT 60.690 55.000 0.73 0.00 44.69 4.18
996 1039 1.305465 TCCCGGAAAGTCCATCGGA 60.305 57.895 0.73 0.00 44.69 4.55
997 1040 1.144057 CTCCCGGAAAGTCCATCGG 59.856 63.158 0.73 0.00 41.90 4.18
998 1041 1.144057 CCTCCCGGAAAGTCCATCG 59.856 63.158 0.73 0.00 35.91 3.84
999 1042 0.981277 TCCCTCCCGGAAAGTCCATC 60.981 60.000 0.73 0.00 37.88 3.51
1596 1639 3.041211 CAGGGACAGAGGATTCACCATA 58.959 50.000 0.00 0.00 42.04 2.74
1615 1658 0.734889 GTCATCAACCCATTCGCCAG 59.265 55.000 0.00 0.00 0.00 4.85
1620 1663 1.668419 CTCCGGTCATCAACCCATTC 58.332 55.000 0.00 0.00 46.27 2.67
1673 1716 3.937062 GCGAAACCATAGCGGGCG 61.937 66.667 0.00 0.00 40.22 6.13
1674 1717 3.583086 GGCGAAACCATAGCGGGC 61.583 66.667 0.00 0.00 40.22 6.13
1675 1718 3.269347 CGGCGAAACCATAGCGGG 61.269 66.667 0.00 0.00 40.22 6.13
1770 1816 0.730265 TGAAAACATACGGCATCGGC 59.270 50.000 0.00 0.00 41.39 5.54
1912 1958 8.397906 GCAAGCAAACACATCAGATAGTAATAA 58.602 33.333 0.00 0.00 0.00 1.40
1917 1963 4.330250 AGCAAGCAAACACATCAGATAGT 58.670 39.130 0.00 0.00 0.00 2.12
1937 2017 0.508641 CAACACGTGTCACTGCTAGC 59.491 55.000 23.61 8.10 0.00 3.42
1996 2081 0.449388 GAGCTGCTGTTGTGCCATAC 59.551 55.000 7.01 0.00 0.00 2.39
2057 2209 6.201425 GCATGCCCATGTCAATTTAACATAAG 59.799 38.462 6.36 0.90 40.80 1.73
2073 2225 4.101430 CCCTTTGTAATTTAGCATGCCCAT 59.899 41.667 15.66 0.46 0.00 4.00
2075 2227 3.450817 ACCCTTTGTAATTTAGCATGCCC 59.549 43.478 15.66 0.00 0.00 5.36
2096 2248 6.630443 GCAATCGAGATCATTCATGTTTGTAC 59.370 38.462 0.00 0.00 0.00 2.90
2114 2266 2.661537 CGGCGGCTATGCAATCGA 60.662 61.111 7.61 0.00 36.28 3.59
2115 2267 2.943345 GACGGCGGCTATGCAATCG 61.943 63.158 13.24 0.00 36.28 3.34
2117 2269 1.153168 AAGACGGCGGCTATGCAAT 60.153 52.632 19.29 0.00 36.28 3.56
2122 2274 0.108520 TTTTCGAAGACGGCGGCTAT 60.109 50.000 19.29 6.38 40.21 2.97
2123 2275 0.108520 ATTTTCGAAGACGGCGGCTA 60.109 50.000 19.29 0.00 40.21 3.93
2129 2281 5.689819 AGATTCAAACATTTTCGAAGACGG 58.310 37.500 0.00 0.00 40.21 4.79
2154 2306 9.823647 CTATTGGTGTTAGATATTGTTCTCACT 57.176 33.333 0.00 0.00 0.00 3.41
2195 2347 6.465439 TTATCCGAGATTTACAGAAGCTCA 57.535 37.500 5.11 0.00 0.00 4.26
2208 2360 5.860941 AGCCAATATCGATTATCCGAGAT 57.139 39.130 1.71 0.00 41.53 2.75
2212 2364 8.450964 ACAAATTTAGCCAATATCGATTATCCG 58.549 33.333 1.71 0.00 0.00 4.18
2235 2387 3.419943 TGTTGCATATCAGAAGGCACAA 58.580 40.909 0.00 0.00 35.74 3.33
2263 2415 4.135306 CCTCAGTCTCCAATTCCATCATG 58.865 47.826 0.00 0.00 0.00 3.07
2644 2804 7.926018 ACCATGAGTTTTAGTTTTGTGGAAATC 59.074 33.333 0.00 0.00 0.00 2.17
2692 2853 0.035317 ATTTCGACAGCTGCCACTGA 59.965 50.000 15.27 1.50 40.25 3.41
2834 2995 6.862090 ACGCAGAGTAAAGTTTAGAAGTACTG 59.138 38.462 0.00 0.00 0.00 2.74
3056 3217 8.730680 GTCTTCTCTTGAATGGTAAAATAAGCA 58.269 33.333 0.00 0.00 0.00 3.91
3065 3226 4.527038 AGTTCCGTCTTCTCTTGAATGGTA 59.473 41.667 0.00 0.00 0.00 3.25
3080 3241 0.824759 ATAGGCTGGTCAGTTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
3083 3244 2.014068 GCACATAGGCTGGTCAGTTCC 61.014 57.143 0.00 0.00 0.00 3.62
3327 3490 9.239310 CTACATCAGTAGCTGTCAATCAGACCA 62.239 44.444 0.00 0.00 42.55 4.02
3328 3491 6.954455 CTACATCAGTAGCTGTCAATCAGACC 60.954 46.154 0.00 0.00 42.55 3.85
3391 3554 7.436430 TTTACTTTGTCAATACGGCATTGTA 57.564 32.000 10.63 1.61 43.88 2.41
3422 3585 2.682856 GCCTTATCATTTCGGCAGTTCA 59.317 45.455 0.00 0.00 42.06 3.18
3429 3592 2.526304 TCCTCGCCTTATCATTTCGG 57.474 50.000 0.00 0.00 0.00 4.30
3430 3593 4.058124 TCAATCCTCGCCTTATCATTTCG 58.942 43.478 0.00 0.00 0.00 3.46
3533 3696 2.733227 GCAGTTGGCCGATCAATTCAAG 60.733 50.000 0.00 0.00 36.11 3.02
3677 3840 9.341899 CAACATTTTATCTTGTTAAGCTGGTAC 57.658 33.333 0.00 0.00 34.42 3.34
3719 3882 4.335315 TCTGGTCTAAAAACTGCACTTGTG 59.665 41.667 0.00 0.00 0.00 3.33
3873 4036 6.393990 AGCTGAAATTGTTGTTGTTACACAA 58.606 32.000 0.00 0.00 35.42 3.33
3918 4081 3.070015 AGTGGCTGAAATTTTCCCACAAG 59.930 43.478 26.11 12.15 41.58 3.16
3955 4118 7.471539 CGATGGAGTTGTTAACCAGTCCTATAT 60.472 40.741 25.92 15.82 37.12 0.86
4018 4181 9.366216 CAGCCCCTAACTAAAATTTTAATTGAC 57.634 33.333 13.45 1.09 0.00 3.18
4037 4200 1.542375 ACAATCTGGACCAGCCCCT 60.542 57.895 17.33 0.00 34.97 4.79
4159 4322 7.563270 CGCATTCTATTAGAAGAAAAGAGAGC 58.437 38.462 11.56 4.35 37.69 4.09
4252 4417 9.844790 GATAATGATGTGTGAACTTCAAAATGA 57.155 29.630 0.00 0.00 0.00 2.57
4258 4423 6.710278 TGGAGATAATGATGTGTGAACTTCA 58.290 36.000 0.00 0.00 0.00 3.02
4308 4477 1.564348 GGTCCCTGCCCTAAATCAGAA 59.436 52.381 0.00 0.00 32.26 3.02
4440 4611 3.368013 CGACTGCTAAGTGGGTCAACATA 60.368 47.826 0.00 0.00 36.52 2.29
4456 4627 2.666994 GTCTAAGGCTTTGTACGACTGC 59.333 50.000 4.45 0.00 0.00 4.40
4481 4652 1.975680 GGAACCTGGGTCAAGTGTCTA 59.024 52.381 14.79 0.00 0.00 2.59
4492 4663 4.408921 TGATTGTATAGAGTGGAACCTGGG 59.591 45.833 0.00 0.00 37.80 4.45
4569 4751 7.713764 AGGAACAGCAAAACAAAATGTAATC 57.286 32.000 0.00 0.00 0.00 1.75
4610 4792 2.911484 CTACAGAACAATGGAGGAGCC 58.089 52.381 0.00 0.00 37.10 4.70
4620 4802 6.179756 ACATATGACAATGCCTACAGAACAA 58.820 36.000 10.38 0.00 0.00 2.83
4644 4826 3.616956 ACGAGGCAATCTCAGAAATGA 57.383 42.857 0.00 0.00 42.55 2.57
4646 4828 4.832248 TGTAACGAGGCAATCTCAGAAAT 58.168 39.130 0.00 0.00 42.55 2.17
4687 4869 5.723887 ACCATTTCCAAATTATGTTAGGGCA 59.276 36.000 0.00 0.00 0.00 5.36
4696 4878 8.725606 ACCTGCATATACCATTTCCAAATTAT 57.274 30.769 0.00 0.00 0.00 1.28
4703 4885 6.170506 TCGAATACCTGCATATACCATTTCC 58.829 40.000 0.00 0.00 0.00 3.13
4704 4886 7.097192 TCTCGAATACCTGCATATACCATTTC 58.903 38.462 0.00 0.00 0.00 2.17
4705 4887 7.004555 TCTCGAATACCTGCATATACCATTT 57.995 36.000 0.00 0.00 0.00 2.32
4708 4890 5.047306 CCTTCTCGAATACCTGCATATACCA 60.047 44.000 0.00 0.00 0.00 3.25
4736 4918 1.746991 GTAGGTCCAGCTTGCCTGC 60.747 63.158 9.95 5.73 40.36 4.85
4738 4920 1.229658 AGGTAGGTCCAGCTTGCCT 60.230 57.895 5.87 5.87 39.02 4.75
4755 4937 1.666054 GCAGGCAGATCCTCTTTGAG 58.334 55.000 0.00 0.00 45.52 3.02
4758 4940 1.222936 CCGCAGGCAGATCCTCTTT 59.777 57.895 0.00 0.00 45.52 2.52
4791 4973 1.298667 GCCTTCGGCTTACCAAGGA 59.701 57.895 13.92 0.00 46.69 3.36
4835 5017 4.865925 TGTATGTATAAACTTCGCAGCGTT 59.134 37.500 15.93 3.98 0.00 4.84
4930 5114 1.820090 GCAGTCTATCGGCCTAGGAGT 60.820 57.143 14.75 0.00 0.00 3.85
4962 5146 2.538861 GACGGCTAAAAACCTATCGAGC 59.461 50.000 0.00 0.00 0.00 5.03
5210 5402 3.230134 AGCTCAGTTCAGTTCACTCTCT 58.770 45.455 0.00 0.00 0.00 3.10
5268 5461 3.887716 AGAAGCTTTGCTGTGTCTGATTT 59.112 39.130 0.00 0.00 39.62 2.17
5278 5471 3.755378 ACCAGATACAAGAAGCTTTGCTG 59.245 43.478 0.00 0.92 39.62 4.41
5520 5968 1.299541 CACGTTCAGCCCATATGGAC 58.700 55.000 24.00 12.24 37.39 4.02
5522 5970 0.819259 CCCACGTTCAGCCCATATGG 60.819 60.000 15.41 15.41 37.09 2.74
5622 6086 3.991051 CCTGCGTGTCACGTCCCT 61.991 66.667 25.18 0.00 44.73 4.20
5684 6148 6.092122 CAGCGAGTTTCCAGTTTGTATATTCA 59.908 38.462 0.00 0.00 0.00 2.57
5697 6161 2.204461 TCCGGACAGCGAGTTTCCA 61.204 57.895 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.