Multiple sequence alignment - TraesCS5A01G418100

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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 TraesCS5A01G418100 chr5A 100.000 3015 0 0 1 3015 606162950 606159936 0.000000e+00 5568.0
1 TraesCS5A01G418100 chr5A 84.257 343 37 15 2679 3015 430246306 430246637 4.850000e-83 318.0
2 TraesCS5A01G418100 chr5D 87.193 2077 131 45 2 1986 484578467 484576434 0.000000e+00 2237.0
3 TraesCS5A01G418100 chr5D 95.804 858 25 9 2165 3015 484575553 484574700 0.000000e+00 1375.0
4 TraesCS5A01G418100 chr5D 82.405 341 42 14 2682 3015 326370201 326369872 6.360000e-72 281.0
5 TraesCS5A01G418100 chr5D 89.333 75 8 0 2093 2167 484575929 484575855 8.900000e-16 95.3
6 TraesCS5A01G418100 chr5B 85.569 1677 141 42 4 1613 595662516 595660874 0.000000e+00 1663.0
7 TraesCS5A01G418100 chr5B 94.125 783 38 6 2240 3015 595660016 595659235 0.000000e+00 1184.0
8 TraesCS5A01G418100 chr5B 86.268 284 24 6 1609 1886 595660917 595660643 8.170000e-76 294.0
9 TraesCS5A01G418100 chr5B 86.090 266 31 5 2750 3015 378816531 378816272 6.360000e-72 281.0
10 TraesCS5A01G418100 chr2B 79.514 288 40 14 2733 3015 40280107 40280380 1.430000e-43 187.0
11 TraesCS5A01G418100 chr2B 84.286 70 7 2 2096 2162 143807484 143807552 6.980000e-07 65.8
12 TraesCS5A01G418100 chr2A 90.909 66 6 0 2099 2164 141506381 141506316 4.140000e-14 89.8
13 TraesCS5A01G418100 chr6B 91.667 60 4 1 2108 2167 184636269 184636327 6.930000e-12 82.4
14 TraesCS5A01G418100 chr4D 90.909 55 5 0 2108 2162 481578814 481578760 1.160000e-09 75.0
15 TraesCS5A01G418100 chr2D 90.909 55 5 0 2108 2162 28425307 28425361 1.160000e-09 75.0
16 TraesCS5A01G418100 chr2D 91.304 46 4 0 2116 2161 14800325 14800370 2.510000e-06 63.9
17 TraesCS5A01G418100 chr1D 100.000 31 0 0 2133 2163 42514862 42514892 1.170000e-04 58.4
18 TraesCS5A01G418100 chr1D 100.000 31 0 0 2133 2163 459948297 459948327 1.170000e-04 58.4


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 TraesCS5A01G418100 chr5A 606159936 606162950 3014 True 5568.000000 5568 100.000000 1 3015 1 chr5A.!!$R1 3014
1 TraesCS5A01G418100 chr5D 484574700 484578467 3767 True 1235.766667 2237 90.776667 2 3015 3 chr5D.!!$R2 3013
2 TraesCS5A01G418100 chr5B 595659235 595662516 3281 True 1047.000000 1663 88.654000 4 3015 3 chr5B.!!$R2 3011

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
723 801 0.029300 ATCCAAATTTGCGATCGCGG 59.971 50.0 32.64 25.65 45.51 6.46 F
814 894 0.038744 ATCTGGTCAAAGGGTGCAGG 59.961 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2051 0.392729 GCTGCTTCTGTCTGGAGCAT 60.393 55.0 12.69 0.0 45.03 3.79 R
2090 2683 0.749049 CATCCGGACTGAGATGAGCA 59.251 55.0 6.12 0.0 42.04 4.26 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
23 24 2.424601 CCTGCATGTGGAAATACTGTGG 59.575 50.000 0.00 0.00 0.00 4.17
58 59 1.882198 CGATGTTTTGATGTCACGCC 58.118 50.000 0.00 0.00 0.00 5.68
81 82 6.402442 GCCATGTTTTATTTCAGGCAATTGTC 60.402 38.462 0.50 0.50 40.29 3.18
102 103 0.524862 GATTGTGGGCTGCTTCTGTG 59.475 55.000 0.00 0.00 0.00 3.66
163 164 4.081406 TGGTAAGACCGTAAGAAGCTGTA 58.919 43.478 0.00 0.00 42.58 2.74
182 183 4.348486 TGTAGCCTCTCATTTCTCTGACT 58.652 43.478 0.00 0.00 0.00 3.41
183 184 4.774726 TGTAGCCTCTCATTTCTCTGACTT 59.225 41.667 0.00 0.00 0.00 3.01
222 224 8.504005 CGAGAAATAACATACTGTTCCTGTTTT 58.496 33.333 7.92 0.42 40.22 2.43
247 253 7.962934 GCGAATGCATGTATTAACTTGTAAA 57.037 32.000 9.16 0.00 42.15 2.01
281 297 2.523440 TGGAACAGGGTTCGTCTGT 58.477 52.632 3.30 0.00 46.22 3.41
431 447 3.393800 CAAGAGGAACAAGAAGAGCGAA 58.606 45.455 0.00 0.00 0.00 4.70
443 459 7.081349 ACAAGAAGAGCGAATAGATTAGATCG 58.919 38.462 0.00 0.00 33.89 3.69
446 462 5.811399 AGAGCGAATAGATTAGATCGGAG 57.189 43.478 0.00 0.00 33.89 4.63
447 463 4.638421 AGAGCGAATAGATTAGATCGGAGG 59.362 45.833 0.00 0.00 33.89 4.30
448 464 3.697045 AGCGAATAGATTAGATCGGAGGG 59.303 47.826 0.00 0.00 35.91 4.30
498 532 1.207593 GCCTAGTTTGTGTGCTGCG 59.792 57.895 0.00 0.00 0.00 5.18
583 628 3.481839 GTTTAAATTTAACCGCGACGCT 58.518 40.909 19.02 1.24 0.00 5.07
600 645 1.294659 GCTTGCGTCTGTTCTCCCAG 61.295 60.000 0.00 0.00 0.00 4.45
622 670 2.154567 ATTTGTGGGATGCTGCTCAT 57.845 45.000 0.00 0.00 38.32 2.90
623 671 2.804986 TTTGTGGGATGCTGCTCATA 57.195 45.000 0.00 0.00 35.05 2.15
624 672 3.301794 TTTGTGGGATGCTGCTCATAT 57.698 42.857 0.00 0.00 35.05 1.78
626 674 4.645863 TTGTGGGATGCTGCTCATATAT 57.354 40.909 0.00 0.00 35.05 0.86
627 675 4.645863 TGTGGGATGCTGCTCATATATT 57.354 40.909 0.00 0.00 35.05 1.28
628 676 4.329392 TGTGGGATGCTGCTCATATATTG 58.671 43.478 0.00 0.00 35.05 1.90
662 721 5.761726 TGCATATATTGGAAGTTGAGCTCAG 59.238 40.000 17.43 0.90 0.00 3.35
684 743 4.516698 AGATTCGTTGTGCTTTGTCAGAAT 59.483 37.500 0.00 0.00 0.00 2.40
685 744 3.607422 TCGTTGTGCTTTGTCAGAATG 57.393 42.857 0.00 0.00 37.54 2.67
704 782 2.725637 TGAGAATTGCTTGCTGCCATA 58.274 42.857 0.00 0.00 42.00 2.74
715 793 3.182341 TGCTGCCATATCCAAATTTGC 57.818 42.857 12.92 0.03 0.00 3.68
723 801 0.029300 ATCCAAATTTGCGATCGCGG 59.971 50.000 32.64 25.65 45.51 6.46
724 802 1.136565 CCAAATTTGCGATCGCGGT 59.863 52.632 32.64 19.21 45.51 5.68
725 803 1.133363 CCAAATTTGCGATCGCGGTG 61.133 55.000 32.64 23.44 45.51 4.94
732 811 0.927537 TGCGATCGCGGTGATTTTAG 59.072 50.000 32.64 0.11 45.51 1.85
739 818 1.789054 CGCGGTGATTTTAGTTTCGGC 60.789 52.381 0.00 0.00 0.00 5.54
749 828 0.927537 TAGTTTCGGCGATTGCGATG 59.072 50.000 11.76 0.00 44.10 3.84
750 829 0.739462 AGTTTCGGCGATTGCGATGA 60.739 50.000 11.76 0.00 44.10 2.92
754 833 1.296867 CGGCGATTGCGATGAACAC 60.297 57.895 0.00 0.00 44.10 3.32
762 841 1.362768 TGCGATGAACACTCATGCTC 58.637 50.000 0.00 0.00 42.60 4.26
814 894 0.038744 ATCTGGTCAAAGGGTGCAGG 59.961 55.000 0.00 0.00 0.00 4.85
832 912 1.828979 GGTTAAGCACCGGATTTGGA 58.171 50.000 9.46 0.00 35.12 3.53
842 922 2.290323 ACCGGATTTGGAAGTCAGAAGG 60.290 50.000 9.46 0.00 0.00 3.46
876 956 2.143876 AGTTTTCAGGTGGTGTTGCT 57.856 45.000 0.00 0.00 0.00 3.91
911 991 3.640257 ATGCACCTGGAGCTGCTGG 62.640 63.158 26.28 26.28 34.29 4.85
917 997 0.600057 CCTGGAGCTGCTGGAAAAAC 59.400 55.000 24.30 0.00 0.00 2.43
931 1011 5.337813 GCTGGAAAAACCCATGAGATGATTT 60.338 40.000 0.00 0.00 38.00 2.17
933 1013 7.169158 TGGAAAAACCCATGAGATGATTTAC 57.831 36.000 0.00 0.00 38.00 2.01
985 1067 1.616628 CCTACCCCCAGCTCCAAGT 60.617 63.158 0.00 0.00 0.00 3.16
989 1071 1.303282 CCCCCAGCTCCAAGTTACC 59.697 63.158 0.00 0.00 0.00 2.85
992 1074 0.693049 CCCAGCTCCAAGTTACCAGT 59.307 55.000 0.00 0.00 0.00 4.00
993 1075 1.339151 CCCAGCTCCAAGTTACCAGTC 60.339 57.143 0.00 0.00 0.00 3.51
997 1080 1.071699 GCTCCAAGTTACCAGTCACCA 59.928 52.381 0.00 0.00 0.00 4.17
1015 1098 1.400494 CCACGCTATAAAACCTGCACC 59.600 52.381 0.00 0.00 0.00 5.01
1018 1101 1.379527 GCTATAAAACCTGCACCGCT 58.620 50.000 0.00 0.00 0.00 5.52
1022 1105 1.225376 TAAAACCTGCACCGCTCACG 61.225 55.000 0.00 0.00 39.67 4.35
1058 1141 4.617520 TCGCCGGCAAGAACAGCA 62.618 61.111 28.98 0.00 0.00 4.41
1059 1142 4.389576 CGCCGGCAAGAACAGCAC 62.390 66.667 28.98 0.00 0.00 4.40
1060 1143 4.043200 GCCGGCAAGAACAGCACC 62.043 66.667 24.80 0.00 0.00 5.01
1061 1144 3.365265 CCGGCAAGAACAGCACCC 61.365 66.667 0.00 0.00 0.00 4.61
1062 1145 2.594303 CGGCAAGAACAGCACCCA 60.594 61.111 0.00 0.00 0.00 4.51
1063 1146 2.908073 CGGCAAGAACAGCACCCAC 61.908 63.158 0.00 0.00 0.00 4.61
1065 1148 2.908073 GCAAGAACAGCACCCACGG 61.908 63.158 0.00 0.00 0.00 4.94
1066 1149 1.227823 CAAGAACAGCACCCACGGA 60.228 57.895 0.00 0.00 0.00 4.69
1067 1150 1.071471 AAGAACAGCACCCACGGAG 59.929 57.895 0.00 0.00 0.00 4.63
1068 1151 3.050275 GAACAGCACCCACGGAGC 61.050 66.667 0.00 0.00 39.54 4.70
1074 1157 1.295423 GCACCCACGGAGCTAAGAA 59.705 57.895 0.00 0.00 36.40 2.52
1099 1182 1.148723 GAGCCATGGAGCAGAGCAT 59.851 57.895 18.40 0.00 34.23 3.79
1119 1202 4.831307 CGTCCGTCTTCCTCGGCG 62.831 72.222 0.00 0.00 46.49 6.46
1127 1210 3.398353 CTTCCTCGGCGTCCTCGTC 62.398 68.421 6.85 0.00 39.49 4.20
1183 1266 2.188829 TCCTCCACGACAACGACGT 61.189 57.895 0.00 0.00 44.83 4.34
1391 1486 4.530857 GCGGGGAGGGACGATGTG 62.531 72.222 0.00 0.00 0.00 3.21
1392 1487 2.758327 CGGGGAGGGACGATGTGA 60.758 66.667 0.00 0.00 0.00 3.58
1393 1488 2.786495 CGGGGAGGGACGATGTGAG 61.786 68.421 0.00 0.00 0.00 3.51
1394 1489 1.686110 GGGGAGGGACGATGTGAGT 60.686 63.158 0.00 0.00 0.00 3.41
1395 1490 1.265454 GGGGAGGGACGATGTGAGTT 61.265 60.000 0.00 0.00 0.00 3.01
1397 1492 0.175989 GGAGGGACGATGTGAGTTCC 59.824 60.000 0.00 0.00 37.53 3.62
1664 1765 0.039256 GCATGCCGTTCAGCTTCAAA 60.039 50.000 6.36 0.00 0.00 2.69
1822 1929 3.071602 CACTGACAAGGAAGGAAGGAGAA 59.928 47.826 0.00 0.00 0.00 2.87
1823 1930 3.716872 ACTGACAAGGAAGGAAGGAGAAA 59.283 43.478 0.00 0.00 0.00 2.52
1826 1933 5.705400 TGACAAGGAAGGAAGGAGAAAAAT 58.295 37.500 0.00 0.00 0.00 1.82
1857 1964 2.532715 ACCTGACCTGGGTGCCAT 60.533 61.111 0.00 0.00 35.51 4.40
1886 1993 7.012799 CCAAGAGTATAAGCCCAGAATCTTTTC 59.987 40.741 0.00 0.00 0.00 2.29
1889 1996 6.122964 AGTATAAGCCCAGAATCTTTTCACC 58.877 40.000 0.00 0.00 34.08 4.02
1899 2006 7.093465 CCCAGAATCTTTTCACCAGTAGTAGTA 60.093 40.741 0.00 0.00 34.08 1.82
1901 2008 7.489757 CAGAATCTTTTCACCAGTAGTAGTAGC 59.510 40.741 0.00 0.00 34.08 3.58
1912 2019 5.455040 CCAGTAGTAGTAGCTACTAGCACCT 60.455 48.000 29.74 24.09 46.18 4.00
1924 2031 0.247460 TAGCACCTGCACTGCTACAG 59.753 55.000 14.71 0.00 43.37 2.74
1936 2043 1.131883 CTGCTACAGTGCCATTTGCTC 59.868 52.381 0.00 0.00 42.00 4.26
1937 2044 1.271543 TGCTACAGTGCCATTTGCTCT 60.272 47.619 0.00 0.00 44.35 4.09
1951 2059 3.928727 TTGCTCTGAAAAATGCTCCAG 57.071 42.857 0.00 0.00 0.00 3.86
1987 2107 8.833264 GCAAAATTCAAAATGATGAACAATTCG 58.167 29.630 0.00 0.00 41.78 3.34
1992 2112 9.859427 ATTCAAAATGATGAACAATTCGTATGT 57.141 25.926 0.00 0.00 41.78 2.29
2000 2120 9.767684 TGATGAACAATTCGTATGTATTTTGAC 57.232 29.630 0.00 0.00 0.00 3.18
2001 2121 9.767684 GATGAACAATTCGTATGTATTTTGACA 57.232 29.630 0.00 0.00 0.00 3.58
2002 2122 8.942669 TGAACAATTCGTATGTATTTTGACAC 57.057 30.769 0.00 0.00 30.52 3.67
2003 2123 7.742525 TGAACAATTCGTATGTATTTTGACACG 59.257 33.333 0.00 0.00 30.52 4.49
2005 2125 7.012943 ACAATTCGTATGTATTTTGACACGTG 58.987 34.615 15.48 15.48 30.52 4.49
2006 2126 6.954616 ATTCGTATGTATTTTGACACGTGA 57.045 33.333 25.01 0.00 30.52 4.35
2007 2127 6.384178 TTCGTATGTATTTTGACACGTGAG 57.616 37.500 25.01 0.00 30.52 3.51
2008 2128 4.325204 TCGTATGTATTTTGACACGTGAGC 59.675 41.667 25.01 14.17 30.52 4.26
2011 2131 5.779806 ATGTATTTTGACACGTGAGCTAC 57.220 39.130 25.01 13.86 30.52 3.58
2012 2132 4.623002 TGTATTTTGACACGTGAGCTACA 58.377 39.130 25.01 16.03 0.00 2.74
2013 2133 4.446385 TGTATTTTGACACGTGAGCTACAC 59.554 41.667 25.01 11.56 45.11 2.90
2046 2639 9.651913 ATGAAAAGTTTTAGTGTGTTTGTTCAT 57.348 25.926 0.00 0.00 0.00 2.57
2047 2640 9.134734 TGAAAAGTTTTAGTGTGTTTGTTCATC 57.865 29.630 0.00 0.00 0.00 2.92
2048 2641 9.134734 GAAAAGTTTTAGTGTGTTTGTTCATCA 57.865 29.630 0.00 0.00 0.00 3.07
2050 2643 8.460831 AAGTTTTAGTGTGTTTGTTCATCAAC 57.539 30.769 0.00 0.00 35.61 3.18
2051 2644 7.826690 AGTTTTAGTGTGTTTGTTCATCAACT 58.173 30.769 0.00 0.00 35.61 3.16
2052 2645 8.303876 AGTTTTAGTGTGTTTGTTCATCAACTT 58.696 29.630 0.00 0.00 35.61 2.66
2053 2646 8.583765 GTTTTAGTGTGTTTGTTCATCAACTTC 58.416 33.333 0.00 0.00 35.61 3.01
2054 2647 7.624360 TTAGTGTGTTTGTTCATCAACTTCT 57.376 32.000 0.00 0.00 35.61 2.85
2055 2648 8.725405 TTAGTGTGTTTGTTCATCAACTTCTA 57.275 30.769 0.00 0.00 35.61 2.10
2056 2649 7.624360 AGTGTGTTTGTTCATCAACTTCTAA 57.376 32.000 0.00 0.00 35.61 2.10
2057 2650 8.050778 AGTGTGTTTGTTCATCAACTTCTAAA 57.949 30.769 0.00 0.00 35.61 1.85
2058 2651 8.519526 AGTGTGTTTGTTCATCAACTTCTAAAA 58.480 29.630 0.00 0.00 35.61 1.52
2059 2652 9.134734 GTGTGTTTGTTCATCAACTTCTAAAAA 57.865 29.630 0.00 0.00 35.61 1.94
2060 2653 9.134734 TGTGTTTGTTCATCAACTTCTAAAAAC 57.865 29.630 0.00 0.00 35.61 2.43
2061 2654 8.592155 GTGTTTGTTCATCAACTTCTAAAAACC 58.408 33.333 0.00 0.00 35.61 3.27
2062 2655 7.762159 TGTTTGTTCATCAACTTCTAAAAACCC 59.238 33.333 0.00 0.00 35.61 4.11
2063 2656 7.654022 TTGTTCATCAACTTCTAAAAACCCT 57.346 32.000 0.00 0.00 33.17 4.34
2064 2657 8.754991 TTGTTCATCAACTTCTAAAAACCCTA 57.245 30.769 0.00 0.00 33.17 3.53
2065 2658 8.161699 TGTTCATCAACTTCTAAAAACCCTAC 57.838 34.615 0.00 0.00 33.17 3.18
2066 2659 7.776030 TGTTCATCAACTTCTAAAAACCCTACA 59.224 33.333 0.00 0.00 33.17 2.74
2067 2660 8.626526 GTTCATCAACTTCTAAAAACCCTACAA 58.373 33.333 0.00 0.00 0.00 2.41
2068 2661 8.391075 TCATCAACTTCTAAAAACCCTACAAG 57.609 34.615 0.00 0.00 0.00 3.16
2069 2662 7.447238 TCATCAACTTCTAAAAACCCTACAAGG 59.553 37.037 0.00 0.00 34.30 3.61
2070 2663 6.665695 TCAACTTCTAAAAACCCTACAAGGT 58.334 36.000 0.00 0.00 44.00 3.50
2071 2664 6.769341 TCAACTTCTAAAAACCCTACAAGGTC 59.231 38.462 0.00 0.00 40.05 3.85
2072 2665 6.256643 ACTTCTAAAAACCCTACAAGGTCA 57.743 37.500 0.00 0.00 40.05 4.02
2073 2666 6.665695 ACTTCTAAAAACCCTACAAGGTCAA 58.334 36.000 0.00 0.00 40.05 3.18
2074 2667 6.544931 ACTTCTAAAAACCCTACAAGGTCAAC 59.455 38.462 0.00 0.00 40.05 3.18
2075 2668 6.256643 TCTAAAAACCCTACAAGGTCAACT 57.743 37.500 0.00 0.00 40.05 3.16
2076 2669 6.293698 TCTAAAAACCCTACAAGGTCAACTC 58.706 40.000 0.00 0.00 40.05 3.01
2077 2670 3.503800 AAACCCTACAAGGTCAACTCC 57.496 47.619 0.00 0.00 40.05 3.85
2078 2671 1.359168 ACCCTACAAGGTCAACTCCC 58.641 55.000 0.00 0.00 33.81 4.30
2079 2672 1.132495 ACCCTACAAGGTCAACTCCCT 60.132 52.381 0.00 0.00 33.81 4.20
2080 2673 2.113052 ACCCTACAAGGTCAACTCCCTA 59.887 50.000 0.00 0.00 33.81 3.53
2081 2674 2.500504 CCCTACAAGGTCAACTCCCTAC 59.499 54.545 0.00 0.00 31.93 3.18
2082 2675 3.170717 CCTACAAGGTCAACTCCCTACA 58.829 50.000 0.00 0.00 0.00 2.74
2083 2676 3.775316 CCTACAAGGTCAACTCCCTACAT 59.225 47.826 0.00 0.00 0.00 2.29
2084 2677 4.225267 CCTACAAGGTCAACTCCCTACATT 59.775 45.833 0.00 0.00 0.00 2.71
2085 2678 4.021102 ACAAGGTCAACTCCCTACATTG 57.979 45.455 0.00 0.00 39.92 2.82
2086 2679 2.749621 CAAGGTCAACTCCCTACATTGC 59.250 50.000 0.00 0.00 29.59 3.56
2087 2680 1.282157 AGGTCAACTCCCTACATTGCC 59.718 52.381 0.00 0.00 0.00 4.52
2088 2681 1.004277 GGTCAACTCCCTACATTGCCA 59.996 52.381 0.00 0.00 0.00 4.92
2089 2682 2.357154 GGTCAACTCCCTACATTGCCAT 60.357 50.000 0.00 0.00 0.00 4.40
2090 2683 3.356290 GTCAACTCCCTACATTGCCATT 58.644 45.455 0.00 0.00 0.00 3.16
2091 2684 3.129287 GTCAACTCCCTACATTGCCATTG 59.871 47.826 0.00 0.00 0.00 2.82
2097 2690 2.295349 CCCTACATTGCCATTGCTCATC 59.705 50.000 0.00 0.00 38.71 2.92
2104 2697 1.307097 GCCATTGCTCATCTCAGTCC 58.693 55.000 0.00 0.00 33.53 3.85
2106 2699 1.579698 CATTGCTCATCTCAGTCCGG 58.420 55.000 0.00 0.00 0.00 5.14
2110 2703 0.749649 GCTCATCTCAGTCCGGATGT 59.250 55.000 7.81 0.00 39.93 3.06
2122 2715 6.124340 TCAGTCCGGATGTAGTTCATACTAA 58.876 40.000 7.81 0.00 38.55 2.24
2125 2718 7.926555 CAGTCCGGATGTAGTTCATACTAAAAT 59.073 37.037 7.81 0.00 38.55 1.82
2127 2720 6.704493 TCCGGATGTAGTTCATACTAAAATGC 59.296 38.462 0.00 0.00 38.55 3.56
2128 2721 6.073222 CCGGATGTAGTTCATACTAAAATGCC 60.073 42.308 0.00 0.00 38.55 4.40
2174 3071 4.421948 GAAGGGAGTACTACATTGACACG 58.578 47.826 10.30 0.00 0.00 4.49
2337 3299 5.380043 CATATTCACAGGGCTACAGGATTT 58.620 41.667 0.00 0.00 0.00 2.17
2398 3363 8.618702 ATGCAGGATATACAGATTCAGAAAAG 57.381 34.615 0.00 0.00 0.00 2.27
2450 3417 5.820947 CCATGTCATCTCAACAATCATCTCA 59.179 40.000 0.00 0.00 0.00 3.27
2452 3419 6.290294 TGTCATCTCAACAATCATCTCAGA 57.710 37.500 0.00 0.00 0.00 3.27
2558 3526 4.987912 GTCTGATAGATAAGCTGCCTCAAC 59.012 45.833 0.00 0.00 0.00 3.18
2574 3542 2.740981 CTCAACACAGATGCAGAAGTCC 59.259 50.000 0.00 0.00 0.00 3.85
2579 3547 2.164422 CACAGATGCAGAAGTCCGTAGA 59.836 50.000 0.00 0.00 0.00 2.59
2642 3610 3.136626 AGCTCAACCTAACAAGTTGGTCT 59.863 43.478 7.96 0.00 43.83 3.85
2699 3667 6.486320 CAGGTGCACCAAAAATCCTTAAAAAT 59.514 34.615 36.39 7.60 38.89 1.82
2766 3734 3.066203 GGTTGACCTTTTGCTTCTTCGAA 59.934 43.478 0.00 0.00 0.00 3.71
2768 3736 5.281727 GTTGACCTTTTGCTTCTTCGAATT 58.718 37.500 0.00 0.00 0.00 2.17
2838 3806 4.854399 TGTCGCTTGTTAAGGTCAATTTG 58.146 39.130 0.00 0.00 0.00 2.32
2890 3858 5.104859 TCGGATTAGTGTGGCAAATAGGTTA 60.105 40.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.949754 CACAGTATTTCCACATGCAGGAT 59.050 43.478 4.84 0.00 34.56 3.24
23 24 1.590932 ATCGCCTGATGATGAACAGC 58.409 50.000 0.00 0.00 32.21 4.40
39 40 1.196581 TGGCGTGACATCAAAACATCG 59.803 47.619 0.00 0.00 0.00 3.84
58 59 6.183360 CCGACAATTGCCTGAAATAAAACATG 60.183 38.462 5.05 0.00 0.00 3.21
81 82 1.377725 AGAAGCAGCCCACAATCCG 60.378 57.895 0.00 0.00 0.00 4.18
102 103 1.973812 GTTGAACCAGCTCCCAGCC 60.974 63.158 0.00 0.00 43.77 4.85
163 164 4.906747 AAAGTCAGAGAAATGAGAGGCT 57.093 40.909 0.00 0.00 0.00 4.58
246 252 5.139727 TGTTCCAGGTGATCAGAAAATGTT 58.860 37.500 0.00 0.00 0.00 2.71
247 253 4.728772 TGTTCCAGGTGATCAGAAAATGT 58.271 39.130 0.00 0.00 0.00 2.71
404 420 0.110486 TCTTGTTCCTCTTGGTGGGC 59.890 55.000 0.00 0.00 34.23 5.36
431 447 4.020543 GAGTGCCCTCCGATCTAATCTAT 58.979 47.826 0.00 0.00 0.00 1.98
443 459 3.070018 CGATAAATCATGAGTGCCCTCC 58.930 50.000 0.09 0.00 36.86 4.30
446 462 3.733337 ACTCGATAAATCATGAGTGCCC 58.267 45.455 0.09 0.00 40.03 5.36
498 532 2.826128 TCTCACATGACACTACAGGTCC 59.174 50.000 0.00 0.00 32.49 4.46
583 628 0.468226 AACTGGGAGAACAGACGCAA 59.532 50.000 0.00 0.00 40.97 4.85
600 645 2.754552 TGAGCAGCATCCCACAAATAAC 59.245 45.455 0.00 0.00 0.00 1.89
623 671 9.017509 CCAATATATGCAGACAACTTCCAATAT 57.982 33.333 0.00 0.00 0.00 1.28
624 672 8.217111 TCCAATATATGCAGACAACTTCCAATA 58.783 33.333 0.00 0.00 0.00 1.90
626 674 6.422333 TCCAATATATGCAGACAACTTCCAA 58.578 36.000 0.00 0.00 0.00 3.53
627 675 6.000246 TCCAATATATGCAGACAACTTCCA 58.000 37.500 0.00 0.00 0.00 3.53
628 676 6.543831 ACTTCCAATATATGCAGACAACTTCC 59.456 38.462 0.00 0.00 0.00 3.46
662 721 3.878086 TCTGACAAAGCACAACGAATC 57.122 42.857 0.00 0.00 0.00 2.52
695 773 2.481622 CGCAAATTTGGATATGGCAGCA 60.482 45.455 19.47 0.00 0.00 4.41
704 782 0.029300 CCGCGATCGCAAATTTGGAT 59.971 50.000 36.45 18.06 42.06 3.41
715 793 3.594312 GAAACTAAAATCACCGCGATCG 58.406 45.455 11.69 11.69 31.11 3.69
723 801 3.542310 GCAATCGCCGAAACTAAAATCAC 59.458 43.478 0.00 0.00 0.00 3.06
724 802 3.726486 CGCAATCGCCGAAACTAAAATCA 60.726 43.478 0.00 0.00 33.11 2.57
725 803 2.776225 CGCAATCGCCGAAACTAAAATC 59.224 45.455 0.00 0.00 33.11 2.17
732 811 0.096281 TTCATCGCAATCGCCGAAAC 59.904 50.000 0.00 0.00 38.31 2.78
739 818 2.848376 GCATGAGTGTTCATCGCAATCG 60.848 50.000 0.00 0.00 42.12 3.34
749 828 1.669779 GCATGGAGAGCATGAGTGTTC 59.330 52.381 0.00 0.00 35.98 3.18
750 829 1.747709 GCATGGAGAGCATGAGTGTT 58.252 50.000 0.00 0.00 32.09 3.32
754 833 3.331319 GCGCATGGAGAGCATGAG 58.669 61.111 0.30 0.00 43.16 2.90
762 841 1.657094 GCAAGAAATTTGCGCATGGAG 59.343 47.619 12.75 0.00 35.58 3.86
770 849 1.453148 GACAGCACGCAAGAAATTTGC 59.547 47.619 0.00 1.93 41.71 3.68
783 862 2.143122 TGACCAGATTTTCGACAGCAC 58.857 47.619 0.00 0.00 0.00 4.40
785 864 3.365364 CCTTTGACCAGATTTTCGACAGC 60.365 47.826 0.00 0.00 0.00 4.40
814 894 2.817844 ACTTCCAAATCCGGTGCTTAAC 59.182 45.455 0.00 0.00 0.00 2.01
824 904 3.753797 GTCACCTTCTGACTTCCAAATCC 59.246 47.826 0.00 0.00 45.38 3.01
842 922 5.449999 CCTGAAAACTAACAACTTGGGTCAC 60.450 44.000 0.00 0.00 0.00 3.67
901 981 0.827507 TGGGTTTTTCCAGCAGCTCC 60.828 55.000 0.00 0.00 38.11 4.70
911 991 9.657419 ATTTGTAAATCATCTCATGGGTTTTTC 57.343 29.630 0.00 0.00 0.00 2.29
917 997 5.764686 TCCGATTTGTAAATCATCTCATGGG 59.235 40.000 15.36 7.41 43.85 4.00
931 1011 0.323302 TGCCTGCACTCCGATTTGTA 59.677 50.000 0.00 0.00 0.00 2.41
933 1013 1.798735 CTGCCTGCACTCCGATTTG 59.201 57.895 0.00 0.00 0.00 2.32
985 1067 4.804868 TTTATAGCGTGGTGACTGGTAA 57.195 40.909 0.00 0.00 0.00 2.85
989 1071 3.370978 CAGGTTTTATAGCGTGGTGACTG 59.629 47.826 0.00 0.00 0.00 3.51
992 1074 2.289756 TGCAGGTTTTATAGCGTGGTGA 60.290 45.455 0.00 0.00 0.00 4.02
993 1075 2.080693 TGCAGGTTTTATAGCGTGGTG 58.919 47.619 0.00 0.00 0.00 4.17
997 1080 1.365699 CGGTGCAGGTTTTATAGCGT 58.634 50.000 0.00 0.00 0.00 5.07
1018 1101 2.596338 TGAGTGGGAGACGCGTGA 60.596 61.111 20.70 0.00 33.90 4.35
1022 1105 2.048127 GTGGTGAGTGGGAGACGC 60.048 66.667 0.00 0.00 0.00 5.19
1058 1141 0.608640 CTGTTCTTAGCTCCGTGGGT 59.391 55.000 0.00 0.00 0.00 4.51
1059 1142 0.895530 TCTGTTCTTAGCTCCGTGGG 59.104 55.000 0.00 0.00 0.00 4.61
1060 1143 1.737363 GCTCTGTTCTTAGCTCCGTGG 60.737 57.143 0.00 0.00 35.80 4.94
1061 1144 1.634702 GCTCTGTTCTTAGCTCCGTG 58.365 55.000 0.00 0.00 35.80 4.94
1062 1145 0.171455 CGCTCTGTTCTTAGCTCCGT 59.829 55.000 0.00 0.00 36.56 4.69
1063 1146 0.452184 TCGCTCTGTTCTTAGCTCCG 59.548 55.000 0.00 0.00 36.56 4.63
1065 1148 1.555477 GCTCGCTCTGTTCTTAGCTC 58.445 55.000 0.00 0.00 36.56 4.09
1066 1149 0.174617 GGCTCGCTCTGTTCTTAGCT 59.825 55.000 0.00 0.00 36.56 3.32
1067 1150 0.108615 TGGCTCGCTCTGTTCTTAGC 60.109 55.000 0.00 0.00 35.33 3.09
1068 1151 2.200067 CATGGCTCGCTCTGTTCTTAG 58.800 52.381 0.00 0.00 0.00 2.18
1069 1152 1.134699 CCATGGCTCGCTCTGTTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
1070 1153 0.392193 CCATGGCTCGCTCTGTTCTT 60.392 55.000 0.00 0.00 0.00 2.52
1074 1157 2.898738 CTCCATGGCTCGCTCTGT 59.101 61.111 6.96 0.00 0.00 3.41
1099 1182 3.744719 CGAGGAAGACGGACGGCA 61.745 66.667 0.00 0.00 0.00 5.69
1119 1202 3.462678 GGCCAGGAGGACGAGGAC 61.463 72.222 0.00 0.00 36.89 3.85
1163 1246 1.361271 GTCGTTGTCGTGGAGGACA 59.639 57.895 0.00 0.00 44.74 4.02
1164 1247 1.728426 CGTCGTTGTCGTGGAGGAC 60.728 63.158 0.00 0.00 38.33 3.85
1195 1278 2.183555 CGAACTCCTGGGCGTACC 59.816 66.667 0.00 0.00 40.81 3.34
1382 1477 1.810030 GCCGGAACTCACATCGTCC 60.810 63.158 5.05 0.00 0.00 4.79
1387 1482 1.003355 CTGGTGCCGGAACTCACAT 60.003 57.895 13.69 0.00 35.04 3.21
1388 1483 2.425592 CTGGTGCCGGAACTCACA 59.574 61.111 13.69 0.55 35.04 3.58
1390 1485 3.535629 CTGCTGGTGCCGGAACTCA 62.536 63.158 13.69 8.06 38.71 3.41
1391 1486 2.743928 CTGCTGGTGCCGGAACTC 60.744 66.667 13.69 3.06 38.71 3.01
1394 1489 4.349503 ATGCTGCTGGTGCCGGAA 62.350 61.111 5.05 0.00 38.71 4.30
1397 1492 3.047718 CTTCATGCTGCTGGTGCCG 62.048 63.158 0.00 0.00 38.71 5.69
1445 1546 2.031465 TTCGGGAACAGCGGGAAC 59.969 61.111 0.00 0.00 0.00 3.62
1822 1929 5.126061 GTCAGGTGATTGATGCCACTATTTT 59.874 40.000 0.00 0.00 33.99 1.82
1823 1930 4.641989 GTCAGGTGATTGATGCCACTATTT 59.358 41.667 0.00 0.00 33.99 1.40
1826 1933 2.092968 GGTCAGGTGATTGATGCCACTA 60.093 50.000 0.00 0.00 33.99 2.74
1899 2006 0.534412 CAGTGCAGGTGCTAGTAGCT 59.466 55.000 22.34 6.73 42.97 3.32
1901 2008 3.056628 GCAGTGCAGGTGCTAGTAG 57.943 57.895 11.09 0.00 42.66 2.57
1932 2039 2.816087 GTCTGGAGCATTTTTCAGAGCA 59.184 45.455 0.00 0.00 37.00 4.26
1933 2040 2.816087 TGTCTGGAGCATTTTTCAGAGC 59.184 45.455 0.00 0.00 37.00 4.09
1936 2043 4.615452 GCTTCTGTCTGGAGCATTTTTCAG 60.615 45.833 5.16 0.00 0.00 3.02
1937 2044 3.254166 GCTTCTGTCTGGAGCATTTTTCA 59.746 43.478 5.16 0.00 0.00 2.69
1943 2051 0.392729 GCTGCTTCTGTCTGGAGCAT 60.393 55.000 12.69 0.00 45.03 3.79
1951 2059 5.971895 TTTTGAATTTTGCTGCTTCTGTC 57.028 34.783 0.00 0.00 0.00 3.51
1987 2107 5.779806 AGCTCACGTGTCAAAATACATAC 57.220 39.130 16.51 0.00 0.00 2.39
1989 2109 5.120208 GTGTAGCTCACGTGTCAAAATACAT 59.880 40.000 16.51 0.00 37.31 2.29
1991 2111 4.942765 GTGTAGCTCACGTGTCAAAATAC 58.057 43.478 16.51 11.21 37.31 1.89
2019 2139 9.482627 TGAACAAACACACTAAAACTTTTCATT 57.517 25.926 0.00 0.00 0.00 2.57
2020 2140 9.651913 ATGAACAAACACACTAAAACTTTTCAT 57.348 25.926 0.00 0.00 0.00 2.57
2021 2141 9.134734 GATGAACAAACACACTAAAACTTTTCA 57.865 29.630 0.00 0.00 0.00 2.69
2022 2142 9.134734 TGATGAACAAACACACTAAAACTTTTC 57.865 29.630 0.00 0.00 0.00 2.29
2032 2625 7.624360 TTAGAAGTTGATGAACAAACACACT 57.376 32.000 0.00 0.00 40.36 3.55
2046 2639 6.665695 ACCTTGTAGGGTTTTTAGAAGTTGA 58.334 36.000 0.00 0.00 40.58 3.18
2047 2640 6.544564 TGACCTTGTAGGGTTTTTAGAAGTTG 59.455 38.462 0.00 0.00 40.58 3.16
2048 2641 6.665695 TGACCTTGTAGGGTTTTTAGAAGTT 58.334 36.000 0.00 0.00 40.58 2.66
2050 2643 6.771267 AGTTGACCTTGTAGGGTTTTTAGAAG 59.229 38.462 0.00 0.00 40.58 2.85
2051 2644 6.665695 AGTTGACCTTGTAGGGTTTTTAGAA 58.334 36.000 0.00 0.00 40.58 2.10
2052 2645 6.256643 AGTTGACCTTGTAGGGTTTTTAGA 57.743 37.500 0.00 0.00 40.58 2.10
2053 2646 5.472478 GGAGTTGACCTTGTAGGGTTTTTAG 59.528 44.000 0.00 0.00 40.58 1.85
2054 2647 5.379187 GGAGTTGACCTTGTAGGGTTTTTA 58.621 41.667 0.00 0.00 40.58 1.52
2055 2648 4.212716 GGAGTTGACCTTGTAGGGTTTTT 58.787 43.478 0.00 0.00 40.58 1.94
2056 2649 3.436035 GGGAGTTGACCTTGTAGGGTTTT 60.436 47.826 0.00 0.00 40.58 2.43
2057 2650 2.107726 GGGAGTTGACCTTGTAGGGTTT 59.892 50.000 0.00 0.00 40.58 3.27
2058 2651 1.703513 GGGAGTTGACCTTGTAGGGTT 59.296 52.381 0.00 0.00 40.58 4.11
2059 2652 1.132495 AGGGAGTTGACCTTGTAGGGT 60.132 52.381 0.00 0.00 40.58 4.34
2060 2653 1.657804 AGGGAGTTGACCTTGTAGGG 58.342 55.000 0.00 0.00 40.58 3.53
2061 2654 3.170717 TGTAGGGAGTTGACCTTGTAGG 58.829 50.000 0.00 0.00 42.49 3.18
2062 2655 5.178797 CAATGTAGGGAGTTGACCTTGTAG 58.821 45.833 0.00 0.00 39.54 2.74
2063 2656 4.564821 GCAATGTAGGGAGTTGACCTTGTA 60.565 45.833 0.00 0.00 39.54 2.41
2064 2657 3.810743 GCAATGTAGGGAGTTGACCTTGT 60.811 47.826 0.00 0.00 39.54 3.16
2065 2658 2.749621 GCAATGTAGGGAGTTGACCTTG 59.250 50.000 0.00 0.00 39.54 3.61
2066 2659 2.290960 GGCAATGTAGGGAGTTGACCTT 60.291 50.000 0.00 0.00 39.54 3.50
2067 2660 1.282157 GGCAATGTAGGGAGTTGACCT 59.718 52.381 0.00 0.00 42.15 3.85
2068 2661 1.004277 TGGCAATGTAGGGAGTTGACC 59.996 52.381 0.00 0.00 29.73 4.02
2069 2662 2.489938 TGGCAATGTAGGGAGTTGAC 57.510 50.000 0.00 0.00 0.00 3.18
2070 2663 3.355378 CAATGGCAATGTAGGGAGTTGA 58.645 45.455 0.00 0.00 0.00 3.18
2071 2664 2.159198 GCAATGGCAATGTAGGGAGTTG 60.159 50.000 4.21 0.00 40.72 3.16
2072 2665 2.102578 GCAATGGCAATGTAGGGAGTT 58.897 47.619 4.21 0.00 40.72 3.01
2073 2666 1.285962 AGCAATGGCAATGTAGGGAGT 59.714 47.619 4.21 0.00 44.61 3.85
2074 2667 1.952296 GAGCAATGGCAATGTAGGGAG 59.048 52.381 4.21 0.00 44.61 4.30
2075 2668 1.284491 TGAGCAATGGCAATGTAGGGA 59.716 47.619 4.21 0.00 44.61 4.20
2076 2669 1.766494 TGAGCAATGGCAATGTAGGG 58.234 50.000 4.21 0.00 44.61 3.53
2077 2670 3.220110 AGATGAGCAATGGCAATGTAGG 58.780 45.455 4.21 0.00 44.61 3.18
2078 2671 3.881089 TGAGATGAGCAATGGCAATGTAG 59.119 43.478 4.21 0.00 44.61 2.74
2079 2672 3.881089 CTGAGATGAGCAATGGCAATGTA 59.119 43.478 4.21 0.00 44.61 2.29
2080 2673 2.688446 CTGAGATGAGCAATGGCAATGT 59.312 45.455 4.21 0.00 44.61 2.71
2081 2674 2.688446 ACTGAGATGAGCAATGGCAATG 59.312 45.455 0.00 0.00 44.61 2.82
2082 2675 2.950309 GACTGAGATGAGCAATGGCAAT 59.050 45.455 0.00 0.00 44.61 3.56
2083 2676 2.362736 GACTGAGATGAGCAATGGCAA 58.637 47.619 0.00 0.00 44.61 4.52
2084 2677 1.407851 GGACTGAGATGAGCAATGGCA 60.408 52.381 0.00 0.00 44.61 4.92
2085 2678 1.307097 GGACTGAGATGAGCAATGGC 58.693 55.000 0.00 0.00 41.61 4.40
2086 2679 1.579698 CGGACTGAGATGAGCAATGG 58.420 55.000 0.00 0.00 0.00 3.16
2087 2680 1.137675 TCCGGACTGAGATGAGCAATG 59.862 52.381 0.00 0.00 0.00 2.82
2088 2681 1.489481 TCCGGACTGAGATGAGCAAT 58.511 50.000 0.00 0.00 0.00 3.56
2089 2682 1.137675 CATCCGGACTGAGATGAGCAA 59.862 52.381 6.12 0.00 42.04 3.91
2090 2683 0.749049 CATCCGGACTGAGATGAGCA 59.251 55.000 6.12 0.00 42.04 4.26
2091 2684 0.749649 ACATCCGGACTGAGATGAGC 59.250 55.000 6.12 0.00 42.04 4.26
2097 2690 4.580995 AGTATGAACTACATCCGGACTGAG 59.419 45.833 6.12 6.53 40.07 3.35
2104 2697 6.073222 GGGCATTTTAGTATGAACTACATCCG 60.073 42.308 0.00 0.00 37.94 4.18
2106 2699 7.801716 TGGGCATTTTAGTATGAACTACATC 57.198 36.000 0.00 0.00 37.94 3.06
2110 2703 8.410673 TGTTTTGGGCATTTTAGTATGAACTA 57.589 30.769 0.00 0.00 37.15 2.24
2364 3326 5.007626 TCTGTATATCCTGCATTTTTGTCGC 59.992 40.000 0.00 0.00 0.00 5.19
2398 3363 3.096092 TCTGGTTACCATGGCCATTTTC 58.904 45.455 17.92 5.10 30.82 2.29
2450 3417 8.484214 TGTTAGTCCTTGATATTAGCTGATCT 57.516 34.615 0.00 0.00 0.00 2.75
2452 3419 8.486210 TGTTGTTAGTCCTTGATATTAGCTGAT 58.514 33.333 0.00 0.00 0.00 2.90
2558 3526 2.164422 TCTACGGACTTCTGCATCTGTG 59.836 50.000 9.33 1.43 35.95 3.66
2574 3542 1.067354 AGGCCGTAAAACCTGTCTACG 60.067 52.381 0.00 5.41 38.47 3.51
2579 3547 4.276678 GTCTTTTTAGGCCGTAAAACCTGT 59.723 41.667 15.44 0.00 39.79 4.00
2642 3610 1.604604 GCTGTGTTAAGCCAACTGGA 58.395 50.000 0.00 0.00 38.05 3.86
2672 3640 1.963515 AGGATTTTTGGTGCACCTGAC 59.036 47.619 34.75 19.12 36.82 3.51
2699 3667 4.974645 ACTCATTCTTGGTAACTGGTCA 57.025 40.909 0.00 0.00 37.61 4.02
2766 3734 5.363580 TGAAGCCAAGAAAAACAAGGAGAAT 59.636 36.000 0.00 0.00 0.00 2.40
2768 3736 4.097892 GTGAAGCCAAGAAAAACAAGGAGA 59.902 41.667 0.00 0.00 0.00 3.71
2890 3858 6.825721 ACTAGCAGCTGTGAAGCTTAAATATT 59.174 34.615 16.64 0.00 43.52 1.28


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

AutoCloner maintained by Alex Coulton.