Multiple sequence alignment - TraesCS6D01G370600

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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 TraesCS6D01G370600 chr6D 100.000 3623 0 0 1 3623 456499771 456496149 0.000000e+00 6691
1 TraesCS6D01G370600 chr6D 93.413 167 8 3 282 447 14011559 14011395 1.000000e-60 244
2 TraesCS6D01G370600 chr6B 95.596 1544 55 7 2085 3623 694165691 694164156 0.000000e+00 2462
3 TraesCS6D01G370600 chr6B 88.015 1043 84 20 1025 2036 694166803 694165771 0.000000e+00 1195
4 TraesCS6D01G370600 chr6B 88.802 643 42 11 36 663 694167747 694167120 0.000000e+00 761
5 TraesCS6D01G370600 chr6B 93.711 159 7 3 290 447 25594682 25594526 6.050000e-58 235
6 TraesCS6D01G370600 chr6A 90.497 1610 105 30 2038 3623 603205478 603203893 0.000000e+00 2082
7 TraesCS6D01G370600 chr6A 84.663 802 78 21 1251 2040 603206284 603205516 0.000000e+00 758
8 TraesCS6D01G370600 chr6A 88.376 585 49 12 126 696 603207416 603206837 0.000000e+00 686
9 TraesCS6D01G370600 chr6A 94.375 160 6 3 289 447 14625786 14625629 3.610000e-60 243
10 TraesCS6D01G370600 chr6A 83.012 259 25 13 1003 1252 603206568 603206320 2.190000e-52 217
11 TraesCS6D01G370600 chrUn 79.481 1194 176 45 888 2040 367151656 367150491 0.000000e+00 784
12 TraesCS6D01G370600 chrUn 77.964 658 102 27 888 1513 396108276 396107630 4.420000e-99 372
13 TraesCS6D01G370600 chrUn 77.964 658 102 27 888 1513 396190378 396189732 4.420000e-99 372
14 TraesCS6D01G370600 chrUn 81.602 337 44 13 1707 2040 379137207 379136886 2.770000e-66 263
15 TraesCS6D01G370600 chr1A 79.404 1175 185 34 903 2040 32541652 32542806 0.000000e+00 776
16 TraesCS6D01G370600 chr7A 79.354 1177 182 39 903 2040 576770686 576771840 0.000000e+00 771
17 TraesCS6D01G370600 chr7A 79.234 1175 187 35 903 2040 658282093 658280939 0.000000e+00 765
18 TraesCS6D01G370600 chr7A 79.149 1175 188 35 903 2040 658286138 658284984 0.000000e+00 760
19 TraesCS6D01G370600 chr1B 79.160 1166 193 35 903 2040 684684954 684683811 0.000000e+00 761
20 TraesCS6D01G370600 chr2B 83.900 441 55 8 117 548 64870924 64870491 1.210000e-109 407
21 TraesCS6D01G370600 chr1D 92.994 157 9 2 282 437 405132562 405132717 1.010000e-55 228


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 TraesCS6D01G370600 chr6D 456496149 456499771 3622 True 6691.000000 6691 100.000000 1 3623 1 chr6D.!!$R2 3622
1 TraesCS6D01G370600 chr6B 694164156 694167747 3591 True 1472.666667 2462 90.804333 36 3623 3 chr6B.!!$R2 3587
2 TraesCS6D01G370600 chr6A 603203893 603207416 3523 True 935.750000 2082 86.637000 126 3623 4 chr6A.!!$R2 3497
3 TraesCS6D01G370600 chrUn 367150491 367151656 1165 True 784.000000 784 79.481000 888 2040 1 chrUn.!!$R1 1152
4 TraesCS6D01G370600 chrUn 396107630 396108276 646 True 372.000000 372 77.964000 888 1513 1 chrUn.!!$R3 625
5 TraesCS6D01G370600 chrUn 396189732 396190378 646 True 372.000000 372 77.964000 888 1513 1 chrUn.!!$R4 625
6 TraesCS6D01G370600 chr1A 32541652 32542806 1154 False 776.000000 776 79.404000 903 2040 1 chr1A.!!$F1 1137
7 TraesCS6D01G370600 chr7A 576770686 576771840 1154 False 771.000000 771 79.354000 903 2040 1 chr7A.!!$F1 1137
8 TraesCS6D01G370600 chr7A 658280939 658286138 5199 True 762.500000 765 79.191500 903 2040 2 chr7A.!!$R1 1137
9 TraesCS6D01G370600 chr1B 684683811 684684954 1143 True 761.000000 761 79.160000 903 2040 1 chr1B.!!$R1 1137

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
740 777 0.034337 TTCGTTCCTTTAGCAGGCGT 59.966 50.0 0.00 0.00 43.55 5.68 F
743 780 0.036294 GTTCCTTTAGCAGGCGTCCT 60.036 55.0 0.00 0.00 43.55 3.85 F
744 781 0.249398 TTCCTTTAGCAGGCGTCCTC 59.751 55.0 0.00 0.00 43.55 3.71 F
812 851 0.254178 ATCCCCACAGCTTGCTAGTG 59.746 55.0 13.97 13.97 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 6388 1.800805 ACAGAGAAGGTTGTGCATCG 58.199 50.000 0.0 0.0 0.00 3.84 R
2456 6732 4.087907 TCAACATCCCAGCATCAAAATGA 58.912 39.130 0.0 0.0 34.61 2.57 R
2457 6733 4.459390 TCAACATCCCAGCATCAAAATG 57.541 40.909 0.0 0.0 35.87 2.32 R
2639 6915 4.851639 ATCAAAAGACTGCTGGGTAGAT 57.148 40.909 0.0 0.0 0.00 1.98 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
25 26 7.948278 ACTACAGTTCAATTTCACAGTAGAC 57.052 36.000 17.07 0.00 36.80 2.59
26 27 6.929606 ACTACAGTTCAATTTCACAGTAGACC 59.070 38.462 17.07 0.00 36.80 3.85
27 28 5.680619 ACAGTTCAATTTCACAGTAGACCA 58.319 37.500 0.00 0.00 0.00 4.02
28 29 6.299141 ACAGTTCAATTTCACAGTAGACCAT 58.701 36.000 0.00 0.00 0.00 3.55
29 30 7.450074 ACAGTTCAATTTCACAGTAGACCATA 58.550 34.615 0.00 0.00 0.00 2.74
30 31 7.604164 ACAGTTCAATTTCACAGTAGACCATAG 59.396 37.037 0.00 0.00 0.00 2.23
31 32 6.595716 AGTTCAATTTCACAGTAGACCATAGC 59.404 38.462 0.00 0.00 0.00 2.97
32 33 6.048732 TCAATTTCACAGTAGACCATAGCA 57.951 37.500 0.00 0.00 0.00 3.49
33 34 6.653020 TCAATTTCACAGTAGACCATAGCAT 58.347 36.000 0.00 0.00 0.00 3.79
34 35 6.763135 TCAATTTCACAGTAGACCATAGCATC 59.237 38.462 0.00 0.00 0.00 3.91
53 54 5.651139 AGCATCTTCAAACTATCATGCTTGT 59.349 36.000 0.00 0.00 43.45 3.16
55 56 6.403964 GCATCTTCAAACTATCATGCTTGTGA 60.404 38.462 0.00 0.00 34.94 3.58
74 76 4.455533 TGTGATCAAAAGCTACCACATCAC 59.544 41.667 14.40 14.40 39.31 3.06
76 78 5.124457 GTGATCAAAAGCTACCACATCACAT 59.876 40.000 15.60 0.00 38.89 3.21
80 82 5.534278 TCAAAAGCTACCACATCACATCAAA 59.466 36.000 0.00 0.00 0.00 2.69
136 138 1.137675 ACAGAGCTAGCATGCGATTCA 59.862 47.619 18.83 0.00 38.13 2.57
140 142 1.139654 AGCTAGCATGCGATTCAAGGA 59.860 47.619 18.83 0.00 38.13 3.36
145 147 2.557924 AGCATGCGATTCAAGGAAACAA 59.442 40.909 13.01 0.00 0.00 2.83
146 148 3.005684 AGCATGCGATTCAAGGAAACAAA 59.994 39.130 13.01 0.00 0.00 2.83
147 149 3.928375 GCATGCGATTCAAGGAAACAAAT 59.072 39.130 0.00 0.00 0.00 2.32
179 182 4.634443 ACCATAACAGCATCGAAAACCTAC 59.366 41.667 0.00 0.00 0.00 3.18
194 197 1.153647 CTACGCAATCACGGCCTCA 60.154 57.895 0.00 0.00 37.37 3.86
197 200 3.499737 GCAATCACGGCCTCACGG 61.500 66.667 0.00 0.00 38.39 4.94
265 285 0.665670 CGGAGTCGCATATGAGCAGG 60.666 60.000 6.97 0.00 0.00 4.85
267 287 0.948141 GAGTCGCATATGAGCAGGGC 60.948 60.000 6.97 0.00 0.00 5.19
269 289 0.815213 GTCGCATATGAGCAGGGCAA 60.815 55.000 6.97 0.00 0.00 4.52
283 305 2.930935 GGCAACCTAGGGATCTGGA 58.069 57.895 14.81 0.00 0.00 3.86
286 308 1.972207 GCAACCTAGGGATCTGGAGGT 60.972 57.143 14.81 7.03 44.35 3.85
287 309 2.972153 AACCTAGGGATCTGGAGGTT 57.028 50.000 14.81 15.62 45.45 3.50
479 504 3.964031 ACAGTCAGAACCCCAGATCTATC 59.036 47.826 0.00 0.00 0.00 2.08
480 505 3.323403 CAGTCAGAACCCCAGATCTATCC 59.677 52.174 0.00 0.00 0.00 2.59
481 506 3.051803 AGTCAGAACCCCAGATCTATCCA 60.052 47.826 0.00 0.00 0.00 3.41
482 507 3.906846 GTCAGAACCCCAGATCTATCCAT 59.093 47.826 0.00 0.00 0.00 3.41
501 530 1.010574 CTAGACGAGAAGGAGCGCG 60.011 63.158 0.00 0.00 37.11 6.86
558 587 0.326264 AGCTCACCATTTCGCCTTCT 59.674 50.000 0.00 0.00 0.00 2.85
570 599 3.764466 CCTTCTCCTGTCGCCGCT 61.764 66.667 0.00 0.00 0.00 5.52
707 736 3.523668 GGCCCGGCCCGTTTTATG 61.524 66.667 18.83 0.00 44.06 1.90
709 738 2.272797 CCCGGCCCGTTTTATGGA 59.727 61.111 0.85 0.00 0.00 3.41
710 739 2.116533 CCCGGCCCGTTTTATGGAC 61.117 63.158 0.85 0.00 0.00 4.02
711 740 1.377463 CCGGCCCGTTTTATGGACA 60.377 57.895 0.85 0.00 0.00 4.02
730 767 1.129058 AGTGGACCTGTTCGTTCCTT 58.871 50.000 0.00 0.00 0.00 3.36
733 770 3.064931 GTGGACCTGTTCGTTCCTTTAG 58.935 50.000 0.00 0.00 0.00 1.85
734 771 2.074576 GGACCTGTTCGTTCCTTTAGC 58.925 52.381 0.00 0.00 0.00 3.09
736 773 2.737252 GACCTGTTCGTTCCTTTAGCAG 59.263 50.000 0.00 0.00 0.00 4.24
737 774 2.076863 CCTGTTCGTTCCTTTAGCAGG 58.923 52.381 0.00 0.00 45.64 4.85
739 776 0.442699 GTTCGTTCCTTTAGCAGGCG 59.557 55.000 0.00 0.00 43.55 5.52
740 777 0.034337 TTCGTTCCTTTAGCAGGCGT 59.966 50.000 0.00 0.00 43.55 5.68
741 778 0.389426 TCGTTCCTTTAGCAGGCGTC 60.389 55.000 0.00 0.00 43.55 5.19
743 780 0.036294 GTTCCTTTAGCAGGCGTCCT 60.036 55.000 0.00 0.00 43.55 3.85
744 781 0.249398 TTCCTTTAGCAGGCGTCCTC 59.751 55.000 0.00 0.00 43.55 3.71
745 782 1.153349 CCTTTAGCAGGCGTCCTCC 60.153 63.158 0.00 0.00 35.13 4.30
756 793 3.637273 GTCCTCCGCCCAGTTGGT 61.637 66.667 0.00 0.00 36.04 3.67
757 794 2.852075 TCCTCCGCCCAGTTGGTT 60.852 61.111 0.00 0.00 36.04 3.67
758 795 2.359975 CCTCCGCCCAGTTGGTTC 60.360 66.667 0.00 0.00 36.04 3.62
759 796 2.359975 CTCCGCCCAGTTGGTTCC 60.360 66.667 0.00 0.00 36.04 3.62
760 797 2.852075 TCCGCCCAGTTGGTTCCT 60.852 61.111 0.00 0.00 36.04 3.36
761 798 2.115266 CCGCCCAGTTGGTTCCTT 59.885 61.111 0.00 0.00 36.04 3.36
765 802 1.271163 CGCCCAGTTGGTTCCTTTAGA 60.271 52.381 0.00 0.00 36.04 2.10
766 803 2.618045 CGCCCAGTTGGTTCCTTTAGAT 60.618 50.000 0.00 0.00 36.04 1.98
767 804 2.755103 GCCCAGTTGGTTCCTTTAGATG 59.245 50.000 0.00 0.00 36.04 2.90
768 805 3.561313 GCCCAGTTGGTTCCTTTAGATGA 60.561 47.826 0.00 0.00 36.04 2.92
769 806 4.662278 CCCAGTTGGTTCCTTTAGATGAA 58.338 43.478 0.00 0.00 0.00 2.57
770 807 5.264395 CCCAGTTGGTTCCTTTAGATGAAT 58.736 41.667 0.00 0.00 0.00 2.57
771 808 5.126061 CCCAGTTGGTTCCTTTAGATGAATG 59.874 44.000 0.00 0.00 0.00 2.67
772 809 5.126061 CCAGTTGGTTCCTTTAGATGAATGG 59.874 44.000 0.00 0.00 34.31 3.16
773 810 4.706962 AGTTGGTTCCTTTAGATGAATGGC 59.293 41.667 0.00 0.00 33.27 4.40
774 811 3.631250 TGGTTCCTTTAGATGAATGGCC 58.369 45.455 0.00 0.00 33.27 5.36
775 812 3.269381 TGGTTCCTTTAGATGAATGGCCT 59.731 43.478 3.32 0.00 33.27 5.19
778 815 5.299531 GGTTCCTTTAGATGAATGGCCTAAC 59.700 44.000 3.32 0.00 33.27 2.34
779 816 4.703897 TCCTTTAGATGAATGGCCTAACG 58.296 43.478 3.32 0.00 33.27 3.18
802 841 1.811266 CAGTTCGCGATCCCCACAG 60.811 63.158 10.88 0.00 0.00 3.66
803 842 3.195698 GTTCGCGATCCCCACAGC 61.196 66.667 10.88 0.00 0.00 4.40
804 843 3.390521 TTCGCGATCCCCACAGCT 61.391 61.111 10.88 0.00 0.00 4.24
805 844 2.954684 TTCGCGATCCCCACAGCTT 61.955 57.895 10.88 0.00 0.00 3.74
807 846 3.512516 GCGATCCCCACAGCTTGC 61.513 66.667 0.00 0.00 0.00 4.01
808 847 2.270205 CGATCCCCACAGCTTGCT 59.730 61.111 0.00 0.00 0.00 3.91
810 849 0.531532 CGATCCCCACAGCTTGCTAG 60.532 60.000 0.00 0.00 0.00 3.42
811 850 0.543749 GATCCCCACAGCTTGCTAGT 59.456 55.000 0.00 0.00 0.00 2.57
812 851 0.254178 ATCCCCACAGCTTGCTAGTG 59.746 55.000 13.97 13.97 0.00 2.74
855 904 1.761784 CTGCTAGTGGAATCTGCTCCT 59.238 52.381 0.00 0.00 36.35 3.69
857 906 1.809651 GCTAGTGGAATCTGCTCCTGC 60.810 57.143 0.00 0.00 36.35 4.85
863 912 3.258228 AATCTGCTCCTGCCGCACA 62.258 57.895 0.00 0.00 38.71 4.57
885 934 2.126031 GGACGAACTGCCGACCTC 60.126 66.667 0.00 0.00 40.29 3.85
886 935 2.637383 GGACGAACTGCCGACCTCT 61.637 63.158 0.00 0.00 40.29 3.69
887 936 1.153997 GACGAACTGCCGACCTCTC 60.154 63.158 0.00 0.00 0.00 3.20
888 937 2.202492 CGAACTGCCGACCTCTCG 60.202 66.667 0.00 0.00 39.83 4.04
889 938 2.507324 GAACTGCCGACCTCTCGC 60.507 66.667 0.00 0.00 38.70 5.03
890 939 3.991536 GAACTGCCGACCTCTCGCC 62.992 68.421 0.00 0.00 38.70 5.54
943 992 0.912006 ACCCCAGGAAGAGAGAAGCC 60.912 60.000 0.00 0.00 0.00 4.35
952 5046 5.476254 CAGGAAGAGAGAAGCCAAGATTTTT 59.524 40.000 0.00 0.00 0.00 1.94
1020 5114 2.750657 GGCCATGGAGGAGGTGGAG 61.751 68.421 18.40 0.00 41.22 3.86
1023 5117 1.630126 CCATGGAGGAGGTGGAGGTG 61.630 65.000 5.56 0.00 41.22 4.00
1072 5172 4.157656 TGGATCCAAATCGGTAAGCAAAAG 59.842 41.667 13.46 0.00 35.57 2.27
1082 5182 5.313712 TCGGTAAGCAAAAGGAAGAGAATT 58.686 37.500 0.00 0.00 0.00 2.17
1099 5200 7.536159 AGAGAATTTGCTCTTGGATTTCTTT 57.464 32.000 0.00 0.00 42.41 2.52
1101 5202 7.232127 AGAGAATTTGCTCTTGGATTTCTTTGA 59.768 33.333 0.00 0.00 42.41 2.69
1122 5225 6.490566 TGATTGCTTGATTCATATCCATCG 57.509 37.500 0.00 0.00 0.00 3.84
1135 5238 6.778821 TCATATCCATCGTAATCCACCATTT 58.221 36.000 0.00 0.00 0.00 2.32
1153 5256 7.372714 CACCATTTGTTTCTTGATTCATCTGA 58.627 34.615 0.00 0.00 0.00 3.27
1264 5404 4.056050 GTTCGGTAAGTGATTCAGTGTGT 58.944 43.478 0.00 0.00 0.00 3.72
1291 5451 6.085555 TGTGTTCAGTAGTAAGTCTCAAGG 57.914 41.667 0.00 0.00 0.00 3.61
1292 5452 5.010719 TGTGTTCAGTAGTAAGTCTCAAGGG 59.989 44.000 0.00 0.00 0.00 3.95
1320 5480 2.097825 AGAATGGGATCAGCAAAGTGC 58.902 47.619 0.00 0.00 45.46 4.40
1338 5498 3.584848 AGTGCAAAGATGACCTCTTACCT 59.415 43.478 0.00 0.00 43.60 3.08
1535 5720 2.185533 AATTTGGGGCTGGCCAGGAT 62.186 55.000 33.46 8.93 37.98 3.24
1585 5770 1.153862 GCGAATTGGCATGCGGAAA 60.154 52.632 12.44 6.58 31.11 3.13
1641 5863 9.449719 AGGTAACCTGATTTTTCATGTTAGTAG 57.550 33.333 4.71 0.00 33.59 2.57
1645 5867 9.520515 AACCTGATTTTTCATGTTAGTAGATGT 57.479 29.630 0.00 0.00 29.11 3.06
1648 5870 9.764870 CTGATTTTTCATGTTAGTAGATGTGTG 57.235 33.333 0.00 0.00 0.00 3.82
1661 5883 4.196626 AGATGTGTGCCATTGGATTTTG 57.803 40.909 6.95 0.00 32.56 2.44
1662 5884 3.579586 AGATGTGTGCCATTGGATTTTGT 59.420 39.130 6.95 0.00 32.56 2.83
1670 5892 5.700373 GTGCCATTGGATTTTGTGTTGTAAT 59.300 36.000 6.95 0.00 0.00 1.89
1671 5893 5.699915 TGCCATTGGATTTTGTGTTGTAATG 59.300 36.000 6.95 0.00 0.00 1.90
1678 5900 9.689976 TTGGATTTTGTGTTGTAATGTAAGATG 57.310 29.630 0.00 0.00 0.00 2.90
1680 5902 9.341899 GGATTTTGTGTTGTAATGTAAGATGTC 57.658 33.333 0.00 0.00 0.00 3.06
1697 5919 9.937175 GTAAGATGTCTTTAGTTTGGATAATGC 57.063 33.333 0.00 0.00 37.40 3.56
1705 5929 9.616156 TCTTTAGTTTGGATAATGCGGTATTTA 57.384 29.630 0.00 0.00 0.00 1.40
1743 5970 3.825585 TGTTCTTGATACAGGCAATGCAA 59.174 39.130 7.79 0.00 0.00 4.08
1767 5994 1.676014 GGTTATCAGCGCACCTTGACT 60.676 52.381 11.47 0.00 0.00 3.41
1780 6007 4.618460 GCACCTTGACTGTTCTATCTCGAA 60.618 45.833 0.00 0.00 0.00 3.71
1963 6191 4.437682 TTTTCTCTCAGGTGGTGTCAAT 57.562 40.909 0.00 0.00 0.00 2.57
2054 6325 6.549364 TCAGGTATAAATTTATGCACCCCTTG 59.451 38.462 22.61 15.43 0.00 3.61
2067 6338 4.156922 TGCACCCCTTGTTTATAAATCACG 59.843 41.667 0.31 0.38 0.00 4.35
2117 6388 5.416947 TGCCCTTATCGAAGAAGTAACTTC 58.583 41.667 9.00 0.00 43.58 3.01
2131 6402 3.746492 AGTAACTTCGATGCACAACCTTC 59.254 43.478 0.00 0.00 0.00 3.46
2253 6524 3.844577 CAAGAATGCAGGGTGAGAAAG 57.155 47.619 0.00 0.00 0.00 2.62
2303 6574 5.120363 CGATGGACTATGATGATTTGCTCAG 59.880 44.000 0.00 0.00 37.28 3.35
2404 6679 7.275183 TCCAGAGTAAGGTACATCATTTCATG 58.725 38.462 0.00 0.00 0.00 3.07
2659 6935 3.327757 ACATCTACCCAGCAGTCTTTTGA 59.672 43.478 0.00 0.00 0.00 2.69
2667 6943 5.774690 ACCCAGCAGTCTTTTGATATTTTCA 59.225 36.000 0.00 0.00 0.00 2.69
2726 7004 3.077359 CACAGTGAGAATCCTTGGTTCC 58.923 50.000 0.00 0.00 0.00 3.62
2743 7022 7.719193 CCTTGGTTCCAAAACTTCCATTTTATT 59.281 33.333 5.76 0.00 35.61 1.40
2771 7050 1.748493 AGTTGCAAGCCTTTCGAAACA 59.252 42.857 6.47 0.00 0.00 2.83
2958 7249 6.166982 AGAAGGTTCTTGAATCTTCCTTACG 58.833 40.000 24.44 0.00 37.05 3.18
3045 7336 6.205464 ACATGAAACTCTTGGTCACAGTAATG 59.795 38.462 0.00 0.00 0.00 1.90
3148 7439 5.045578 ACACTCTGTAATCCTAGCCAACAAT 60.046 40.000 0.00 0.00 0.00 2.71
3178 7469 2.295909 CTGCTCCTAGCTGTCTACCATC 59.704 54.545 0.00 0.00 42.97 3.51
3179 7470 2.311463 GCTCCTAGCTGTCTACCATCA 58.689 52.381 0.00 0.00 38.45 3.07
3180 7471 2.295909 GCTCCTAGCTGTCTACCATCAG 59.704 54.545 0.00 0.00 38.45 2.90
3371 7665 1.365633 GGGCAGCTGGTAGATCTCG 59.634 63.158 17.12 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.441458 GGTCTACTGTGAAATTGAACTGTAGTT 59.559 37.037 22.98 0.00 43.63 2.24
1 2 6.929606 GGTCTACTGTGAAATTGAACTGTAGT 59.070 38.462 22.98 10.26 43.63 2.73
2 3 6.929049 TGGTCTACTGTGAAATTGAACTGTAG 59.071 38.462 20.52 20.52 44.12 2.74
3 4 6.822442 TGGTCTACTGTGAAATTGAACTGTA 58.178 36.000 8.99 8.99 31.82 2.74
4 5 5.680619 TGGTCTACTGTGAAATTGAACTGT 58.319 37.500 7.95 7.95 33.66 3.55
5 6 6.808008 ATGGTCTACTGTGAAATTGAACTG 57.192 37.500 0.00 0.00 0.00 3.16
6 7 6.595716 GCTATGGTCTACTGTGAAATTGAACT 59.404 38.462 0.00 0.00 0.00 3.01
7 8 6.371548 TGCTATGGTCTACTGTGAAATTGAAC 59.628 38.462 0.00 0.00 0.00 3.18
8 9 6.472016 TGCTATGGTCTACTGTGAAATTGAA 58.528 36.000 0.00 0.00 0.00 2.69
9 10 6.048732 TGCTATGGTCTACTGTGAAATTGA 57.951 37.500 0.00 0.00 0.00 2.57
10 11 6.765036 AGATGCTATGGTCTACTGTGAAATTG 59.235 38.462 0.00 0.00 0.00 2.32
11 12 6.893583 AGATGCTATGGTCTACTGTGAAATT 58.106 36.000 0.00 0.00 0.00 1.82
12 13 6.491714 AGATGCTATGGTCTACTGTGAAAT 57.508 37.500 0.00 0.00 0.00 2.17
13 14 5.939764 AGATGCTATGGTCTACTGTGAAA 57.060 39.130 0.00 0.00 0.00 2.69
14 15 5.422012 TGAAGATGCTATGGTCTACTGTGAA 59.578 40.000 0.00 0.00 0.00 3.18
15 16 4.956075 TGAAGATGCTATGGTCTACTGTGA 59.044 41.667 0.00 0.00 0.00 3.58
16 17 5.268118 TGAAGATGCTATGGTCTACTGTG 57.732 43.478 0.00 0.00 0.00 3.66
17 18 5.939764 TTGAAGATGCTATGGTCTACTGT 57.060 39.130 0.00 0.00 0.00 3.55
18 19 6.344500 AGTTTGAAGATGCTATGGTCTACTG 58.656 40.000 0.00 0.00 0.00 2.74
19 20 6.552445 AGTTTGAAGATGCTATGGTCTACT 57.448 37.500 0.00 0.00 0.00 2.57
20 21 8.144478 TGATAGTTTGAAGATGCTATGGTCTAC 58.856 37.037 0.00 0.00 0.00 2.59
21 22 8.250143 TGATAGTTTGAAGATGCTATGGTCTA 57.750 34.615 0.00 0.00 0.00 2.59
22 23 7.129457 TGATAGTTTGAAGATGCTATGGTCT 57.871 36.000 0.00 0.00 0.00 3.85
23 24 7.572724 GCATGATAGTTTGAAGATGCTATGGTC 60.573 40.741 0.00 0.00 34.64 4.02
24 25 6.206243 GCATGATAGTTTGAAGATGCTATGGT 59.794 38.462 0.00 0.00 34.64 3.55
25 26 6.430308 AGCATGATAGTTTGAAGATGCTATGG 59.570 38.462 0.00 0.00 43.55 2.74
26 27 7.436430 AGCATGATAGTTTGAAGATGCTATG 57.564 36.000 0.00 0.00 43.55 2.23
27 28 7.501559 ACAAGCATGATAGTTTGAAGATGCTAT 59.498 33.333 0.00 0.00 44.37 2.97
28 29 6.825213 ACAAGCATGATAGTTTGAAGATGCTA 59.175 34.615 0.00 0.00 44.37 3.49
29 30 5.651139 ACAAGCATGATAGTTTGAAGATGCT 59.349 36.000 0.00 0.00 46.48 3.79
30 31 5.742453 CACAAGCATGATAGTTTGAAGATGC 59.258 40.000 0.00 0.00 37.14 3.91
31 32 7.080353 TCACAAGCATGATAGTTTGAAGATG 57.920 36.000 0.00 0.00 34.36 2.90
32 33 7.555195 TGATCACAAGCATGATAGTTTGAAGAT 59.445 33.333 0.00 0.00 39.48 2.40
33 34 6.880529 TGATCACAAGCATGATAGTTTGAAGA 59.119 34.615 0.00 0.00 39.48 2.87
34 35 7.080353 TGATCACAAGCATGATAGTTTGAAG 57.920 36.000 0.00 0.00 39.48 3.02
53 54 4.650734 TGTGATGTGGTAGCTTTTGATCA 58.349 39.130 0.00 0.00 0.00 2.92
55 56 5.255687 TGATGTGATGTGGTAGCTTTTGAT 58.744 37.500 0.00 0.00 0.00 2.57
66 67 3.442625 AGCTCATGTTTGATGTGATGTGG 59.557 43.478 0.00 0.00 0.00 4.17
74 76 6.732531 TCTTTGAGTAGCTCATGTTTGATG 57.267 37.500 0.00 0.00 40.39 3.07
76 78 6.466812 TGATCTTTGAGTAGCTCATGTTTGA 58.533 36.000 0.00 0.00 40.39 2.69
80 82 5.104610 ACCATGATCTTTGAGTAGCTCATGT 60.105 40.000 13.31 3.40 42.78 3.21
104 106 1.279496 AGCTCTGTTGCCCTGATGTA 58.721 50.000 0.00 0.00 0.00 2.29
111 113 1.722636 GCATGCTAGCTCTGTTGCCC 61.723 60.000 17.23 0.00 0.00 5.36
136 138 4.264623 TGGTAGCCCCATATTTGTTTCCTT 60.265 41.667 0.00 0.00 38.72 3.36
160 162 2.669434 GCGTAGGTTTTCGATGCTGTTA 59.331 45.455 0.00 0.00 0.00 2.41
179 182 3.853330 CGTGAGGCCGTGATTGCG 61.853 66.667 0.00 0.00 0.00 4.85
194 197 2.436646 CGCTTCATTCTGGCCCGT 60.437 61.111 0.00 0.00 0.00 5.28
197 200 3.880846 CGGCGCTTCATTCTGGCC 61.881 66.667 7.64 0.00 40.36 5.36
205 219 2.586079 GCTAGATGCGGCGCTTCA 60.586 61.111 37.72 25.90 35.57 3.02
265 285 0.761802 CTCCAGATCCCTAGGTTGCC 59.238 60.000 8.29 0.00 0.00 4.52
267 287 2.182516 ACCTCCAGATCCCTAGGTTG 57.817 55.000 8.29 0.61 39.32 3.77
269 289 1.344496 CCAACCTCCAGATCCCTAGGT 60.344 57.143 8.29 4.96 44.24 3.08
272 294 1.023719 TCCCAACCTCCAGATCCCTA 58.976 55.000 0.00 0.00 0.00 3.53
283 305 1.542547 CGCAAGTGTAAGTCCCAACCT 60.543 52.381 0.00 0.00 0.00 3.50
286 308 0.759959 TCCGCAAGTGTAAGTCCCAA 59.240 50.000 0.00 0.00 0.00 4.12
287 309 0.981183 ATCCGCAAGTGTAAGTCCCA 59.019 50.000 0.00 0.00 0.00 4.37
479 504 1.265635 CGCTCCTTCTCGTCTAGATGG 59.734 57.143 12.06 3.44 46.42 3.51
480 505 1.334599 GCGCTCCTTCTCGTCTAGATG 60.335 57.143 5.53 5.53 33.05 2.90
481 506 0.948678 GCGCTCCTTCTCGTCTAGAT 59.051 55.000 0.00 0.00 33.05 1.98
482 507 1.429927 CGCGCTCCTTCTCGTCTAGA 61.430 60.000 5.56 0.00 0.00 2.43
595 624 4.045334 TCTCTTCTTCCTCCTCTCCTCTTT 59.955 45.833 0.00 0.00 0.00 2.52
692 721 2.116533 GTCCATAAAACGGGCCGGG 61.117 63.158 31.78 20.21 0.00 5.73
695 724 0.808755 CACTGTCCATAAAACGGGCC 59.191 55.000 0.00 0.00 0.00 5.80
697 726 2.081462 GTCCACTGTCCATAAAACGGG 58.919 52.381 0.00 0.00 0.00 5.28
698 727 2.081462 GGTCCACTGTCCATAAAACGG 58.919 52.381 0.00 0.00 0.00 4.44
699 728 2.742053 CAGGTCCACTGTCCATAAAACG 59.258 50.000 0.00 0.00 42.42 3.60
739 776 3.192103 AACCAACTGGGCGGAGGAC 62.192 63.158 0.00 0.00 42.05 3.85
740 777 2.852075 AACCAACTGGGCGGAGGA 60.852 61.111 0.00 0.00 42.05 3.71
741 778 2.359975 GAACCAACTGGGCGGAGG 60.360 66.667 0.00 0.00 42.05 4.30
743 780 2.002018 AAAGGAACCAACTGGGCGGA 62.002 55.000 0.00 0.00 42.05 5.54
744 781 0.250989 TAAAGGAACCAACTGGGCGG 60.251 55.000 0.00 0.00 42.05 6.13
745 782 1.165270 CTAAAGGAACCAACTGGGCG 58.835 55.000 0.00 0.00 42.05 6.13
749 786 5.393461 GCCATTCATCTAAAGGAACCAACTG 60.393 44.000 0.00 0.00 0.00 3.16
750 787 4.706962 GCCATTCATCTAAAGGAACCAACT 59.293 41.667 0.00 0.00 0.00 3.16
751 788 4.142160 GGCCATTCATCTAAAGGAACCAAC 60.142 45.833 0.00 0.00 0.00 3.77
753 790 3.269381 AGGCCATTCATCTAAAGGAACCA 59.731 43.478 5.01 0.00 0.00 3.67
756 793 5.123227 CGTTAGGCCATTCATCTAAAGGAA 58.877 41.667 5.01 0.00 0.00 3.36
757 794 4.444306 CCGTTAGGCCATTCATCTAAAGGA 60.444 45.833 5.01 0.00 41.69 3.36
758 795 3.815401 CCGTTAGGCCATTCATCTAAAGG 59.185 47.826 5.01 0.51 36.71 3.11
759 796 3.815401 CCCGTTAGGCCATTCATCTAAAG 59.185 47.826 5.01 0.00 35.76 1.85
760 797 3.815809 CCCGTTAGGCCATTCATCTAAA 58.184 45.455 5.01 0.00 35.76 1.85
761 798 3.485463 CCCGTTAGGCCATTCATCTAA 57.515 47.619 5.01 0.00 35.76 2.10
773 810 2.125269 CGAACTGGGCCCGTTAGG 60.125 66.667 25.44 18.33 39.47 2.69
774 811 2.818274 GCGAACTGGGCCCGTTAG 60.818 66.667 25.44 24.95 0.00 2.34
775 812 4.745751 CGCGAACTGGGCCCGTTA 62.746 66.667 25.44 6.07 0.00 3.18
786 823 3.195698 GCTGTGGGGATCGCGAAC 61.196 66.667 15.24 11.28 0.00 3.95
795 832 1.377725 CCACTAGCAAGCTGTGGGG 60.378 63.158 23.91 15.67 45.29 4.96
802 841 2.418060 GGAGAGAGTTCCACTAGCAAGC 60.418 54.545 0.00 0.00 37.20 4.01
803 842 2.167487 GGGAGAGAGTTCCACTAGCAAG 59.833 54.545 0.00 0.00 39.09 4.01
804 843 2.180276 GGGAGAGAGTTCCACTAGCAA 58.820 52.381 0.00 0.00 39.09 3.91
805 844 1.077169 TGGGAGAGAGTTCCACTAGCA 59.923 52.381 0.00 0.00 39.09 3.49
807 846 4.891992 TTTTGGGAGAGAGTTCCACTAG 57.108 45.455 0.00 0.00 39.09 2.57
837 884 1.809651 GCAGGAGCAGATTCCACTAGC 60.810 57.143 0.00 0.00 39.84 3.42
841 888 1.817099 CGGCAGGAGCAGATTCCAC 60.817 63.158 0.00 0.00 44.61 4.02
867 916 3.966026 GAGGTCGGCAGTTCGTCCG 62.966 68.421 0.00 0.00 46.52 4.79
868 917 2.126031 GAGGTCGGCAGTTCGTCC 60.126 66.667 0.00 0.00 38.32 4.79
869 918 1.153997 GAGAGGTCGGCAGTTCGTC 60.154 63.158 0.00 0.00 0.00 4.20
870 919 2.963371 GAGAGGTCGGCAGTTCGT 59.037 61.111 0.00 0.00 0.00 3.85
871 920 2.202492 CGAGAGGTCGGCAGTTCG 60.202 66.667 0.00 0.00 42.87 3.95
872 921 2.507324 GCGAGAGGTCGGCAGTTC 60.507 66.667 0.00 0.00 46.91 3.01
920 969 0.787084 TCTCTCTTCCTGGGGTCACT 59.213 55.000 0.00 0.00 0.00 3.41
921 970 1.552792 CTTCTCTCTTCCTGGGGTCAC 59.447 57.143 0.00 0.00 0.00 3.67
922 971 1.944177 CTTCTCTCTTCCTGGGGTCA 58.056 55.000 0.00 0.00 0.00 4.02
978 5072 1.738099 CACGGCCGTCCTCTTCAAG 60.738 63.158 31.80 10.34 0.00 3.02
1006 5100 1.997874 GCACCTCCACCTCCTCCAT 60.998 63.158 0.00 0.00 0.00 3.41
1082 5182 5.011329 AGCAATCAAAGAAATCCAAGAGCAA 59.989 36.000 0.00 0.00 0.00 3.91
1099 5200 5.999600 ACGATGGATATGAATCAAGCAATCA 59.000 36.000 0.00 0.00 33.41 2.57
1101 5202 7.984422 TTACGATGGATATGAATCAAGCAAT 57.016 32.000 0.00 0.00 33.41 3.56
1122 5225 8.087750 TGAATCAAGAAACAAATGGTGGATTAC 58.912 33.333 0.00 0.00 0.00 1.89
1135 5238 6.128200 CCGTCATTCAGATGAATCAAGAAACA 60.128 38.462 5.09 0.00 43.58 2.83
1153 5256 2.597340 CCCATCCCTGCCGTCATT 59.403 61.111 0.00 0.00 0.00 2.57
1174 5277 1.741770 GCACCACACCACCTCGATC 60.742 63.158 0.00 0.00 0.00 3.69
1264 5404 7.812690 TGAGACTTACTACTGAACACAGTAA 57.187 36.000 10.53 0.00 43.53 2.24
1274 5414 3.677424 GCTGCCCTTGAGACTTACTACTG 60.677 52.174 0.00 0.00 0.00 2.74
1291 5451 1.143684 TGATCCCATTCTTAGGCTGCC 59.856 52.381 11.65 11.65 0.00 4.85
1292 5452 2.502295 CTGATCCCATTCTTAGGCTGC 58.498 52.381 0.00 0.00 0.00 5.25
1338 5498 9.012161 TGTATGAATGAAACACATCAAAGATGA 57.988 29.630 13.46 0.00 38.38 2.92
1443 5620 4.098196 AGTTCCGCATAGTACCTTCTTCTC 59.902 45.833 0.00 0.00 0.00 2.87
1585 5770 2.035449 TCAACCATCACGAAAGACGAGT 59.965 45.455 0.00 0.00 45.77 4.18
1648 5870 5.700373 ACATTACAACACAAAATCCAATGGC 59.300 36.000 0.00 0.00 0.00 4.40
1671 5893 9.937175 GCATTATCCAAACTAAAGACATCTTAC 57.063 33.333 0.00 0.00 34.61 2.34
1678 5900 5.813080 ACCGCATTATCCAAACTAAAGAC 57.187 39.130 0.00 0.00 0.00 3.01
1683 5905 8.788806 CCATTAAATACCGCATTATCCAAACTA 58.211 33.333 0.00 0.00 0.00 2.24
1697 5919 6.526325 CACAAACATGTGTCCATTAAATACCG 59.474 38.462 0.00 0.00 35.25 4.02
1743 5970 2.200373 AGGTGCGCTGATAACCTTTT 57.800 45.000 9.73 0.00 41.65 2.27
1767 5994 9.179909 AGAGAGTTCTTAATTCGAGATAGAACA 57.820 33.333 22.41 0.00 44.35 3.18
1780 6007 6.276847 CGTCCTTGCATAGAGAGTTCTTAAT 58.723 40.000 0.00 0.00 34.79 1.40
1856 6084 3.498774 ACAGTGTGAGAGAAGGCATTT 57.501 42.857 0.00 0.00 0.00 2.32
1963 6191 4.642437 TCAGAACCACACAAAAGCATTACA 59.358 37.500 0.00 0.00 0.00 2.41
2067 6338 9.705290 ATTCAAACAACAATTAAATAGGACACC 57.295 29.630 0.00 0.00 0.00 4.16
2117 6388 1.800805 ACAGAGAAGGTTGTGCATCG 58.199 50.000 0.00 0.00 0.00 3.84
2273 6544 6.419484 AATCATCATAGTCCATCGGTGTAA 57.581 37.500 0.00 0.00 0.00 2.41
2404 6679 6.270815 TCTAATCATACAGAAACCAGCGTAC 58.729 40.000 0.00 0.00 0.00 3.67
2447 6723 5.935789 CCCAGCATCAAAATGAAAGTGAAAT 59.064 36.000 0.00 0.00 34.61 2.17
2451 6727 4.524316 TCCCAGCATCAAAATGAAAGTG 57.476 40.909 0.00 0.00 34.61 3.16
2452 6728 4.529377 ACATCCCAGCATCAAAATGAAAGT 59.471 37.500 0.00 0.00 34.61 2.66
2453 6729 5.080969 ACATCCCAGCATCAAAATGAAAG 57.919 39.130 0.00 0.00 34.61 2.62
2456 6732 4.087907 TCAACATCCCAGCATCAAAATGA 58.912 39.130 0.00 0.00 34.61 2.57
2457 6733 4.459390 TCAACATCCCAGCATCAAAATG 57.541 40.909 0.00 0.00 35.87 2.32
2639 6915 4.851639 ATCAAAAGACTGCTGGGTAGAT 57.148 40.909 0.00 0.00 0.00 1.98
2833 7112 2.577449 TGATAATCGCAGCTTGTCGA 57.423 45.000 5.16 5.16 39.17 4.20
2958 7249 5.607119 AAGACCGATACATTGACAACAAC 57.393 39.130 0.00 0.00 38.90 3.32
3045 7336 4.886579 AGGATGAAACAAAATGGCAGAAC 58.113 39.130 0.00 0.00 0.00 3.01
3170 7461 0.177373 CTGCTGCTGCTGATGGTAGA 59.823 55.000 17.00 0.00 40.01 2.59
3351 7645 2.280457 GATCTACCAGCTGCCCGC 60.280 66.667 8.66 0.00 39.57 6.13


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

AutoCloner maintained by Alex Coulton.