Multiple sequence alignment - TraesCS3D01G151800

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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 TraesCS3D01G151800 chr3D 100.000 2264 0 0 1 2264 116061515 116063778 0.000000e+00 4181
1 TraesCS3D01G151800 chr3D 90.853 2099 134 21 1 2054 310406073 310408158 0.000000e+00 2760
2 TraesCS3D01G151800 chr3D 97.516 161 3 1 2105 2264 1004885 1004725 7.970000e-70 274
3 TraesCS3D01G151800 chr1D 93.917 2055 85 22 1 2022 198508582 198510629 0.000000e+00 3066
4 TraesCS3D01G151800 chr1D 89.320 103 11 0 2011 2113 481985811 481985709 1.820000e-26 130
5 TraesCS3D01G151800 chr5D 91.327 2110 105 27 1 2039 358006708 358004606 0.000000e+00 2811
6 TraesCS3D01G151800 chr5D 91.870 1968 103 25 1 1923 520878578 520880533 0.000000e+00 2695
7 TraesCS3D01G151800 chr5D 98.089 157 3 0 2108 2264 467138769 467138925 7.970000e-70 274
8 TraesCS3D01G151800 chr5D 98.089 157 2 1 2108 2264 374985989 374985834 2.870000e-69 272
9 TraesCS3D01G151800 chr5D 96.894 161 4 1 2105 2264 553078693 553078853 3.710000e-68 268
10 TraesCS3D01G151800 chrUn 90.379 2162 146 24 1 2112 10399152 10401301 0.000000e+00 2784
11 TraesCS3D01G151800 chr7D 90.191 2151 151 22 1 2103 131689373 131691511 0.000000e+00 2748
12 TraesCS3D01G151800 chr7D 98.089 157 2 1 2108 2264 227327176 227327331 2.870000e-69 272
13 TraesCS3D01G151800 chr7D 98.089 157 2 1 2108 2264 228682363 228682208 2.870000e-69 272
14 TraesCS3D01G151800 chr2B 91.289 2009 119 20 1 1963 215847148 215849146 0.000000e+00 2689
15 TraesCS3D01G151800 chr2B 92.004 1926 106 23 3 1892 430232481 430230568 0.000000e+00 2660
16 TraesCS3D01G151800 chr1B 90.073 2065 121 26 1 2039 449940900 449942906 0.000000e+00 2601
17 TraesCS3D01G151800 chr3B 88.315 2131 149 40 1 2078 809559723 809557640 0.000000e+00 2464
18 TraesCS3D01G151800 chr3B 91.088 1268 70 21 726 1968 548879796 548881045 0.000000e+00 1676
19 TraesCS3D01G151800 chr3B 87.904 1298 116 16 826 2105 103209615 103210889 0.000000e+00 1489
20 TraesCS3D01G151800 chr3B 91.722 604 27 5 1533 2113 169643848 169644451 0.000000e+00 817
21 TraesCS3D01G151800 chr2D 93.690 1553 64 7 1 1543 476789265 476790793 0.000000e+00 2294
22 TraesCS3D01G151800 chr2D 92.970 1138 53 5 995 2112 78320039 78318909 0.000000e+00 1633
23 TraesCS3D01G151800 chr2D 94.334 1006 44 5 1 997 78327682 78326681 0.000000e+00 1530
24 TraesCS3D01G151800 chr6A 91.818 1210 72 14 771 1964 607999748 607998550 0.000000e+00 1661
25 TraesCS3D01G151800 chr6A 89.758 908 63 12 1226 2113 466347387 466348284 0.000000e+00 1134
26 TraesCS3D01G151800 chr6A 89.648 908 61 14 1226 2113 466149456 466150350 0.000000e+00 1125
27 TraesCS3D01G151800 chr6A 89.426 889 79 7 1226 2113 466411476 466412350 0.000000e+00 1107
28 TraesCS3D01G151800 chr6A 88.087 831 64 11 1305 2113 466355830 466356647 0.000000e+00 953
29 TraesCS3D01G151800 chr6A 89.320 103 10 1 2011 2113 466412512 466412411 6.560000e-26 128
30 TraesCS3D01G151800 chr6B 91.326 1222 76 19 761 1964 702946740 702945531 0.000000e+00 1642
31 TraesCS3D01G151800 chr6B 88.989 1335 111 17 729 2039 702991738 702990416 0.000000e+00 1618
32 TraesCS3D01G151800 chr6B 89.140 1326 92 23 729 2035 703008265 703006973 0.000000e+00 1604
33 TraesCS3D01G151800 chr6B 89.083 1319 91 23 730 2029 703064166 703062882 0.000000e+00 1589
34 TraesCS3D01G151800 chr6B 83.824 272 39 5 1844 2113 126306368 126306636 1.040000e-63 254
35 TraesCS3D01G151800 chr6D 98.089 157 2 1 2108 2264 200839830 200839985 2.870000e-69 272
36 TraesCS3D01G151800 chr6D 96.914 162 3 1 2105 2264 437868535 437868696 1.030000e-68 270
37 TraesCS3D01G151800 chr6D 96.875 160 5 0 2105 2264 27864179 27864338 3.710000e-68 268


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 TraesCS3D01G151800 chr3D 116061515 116063778 2263 False 4181 4181 100.000 1 2264 1 chr3D.!!$F1 2263
1 TraesCS3D01G151800 chr3D 310406073 310408158 2085 False 2760 2760 90.853 1 2054 1 chr3D.!!$F2 2053
2 TraesCS3D01G151800 chr1D 198508582 198510629 2047 False 3066 3066 93.917 1 2022 1 chr1D.!!$F1 2021
3 TraesCS3D01G151800 chr5D 358004606 358006708 2102 True 2811 2811 91.327 1 2039 1 chr5D.!!$R1 2038
4 TraesCS3D01G151800 chr5D 520878578 520880533 1955 False 2695 2695 91.870 1 1923 1 chr5D.!!$F2 1922
5 TraesCS3D01G151800 chrUn 10399152 10401301 2149 False 2784 2784 90.379 1 2112 1 chrUn.!!$F1 2111
6 TraesCS3D01G151800 chr7D 131689373 131691511 2138 False 2748 2748 90.191 1 2103 1 chr7D.!!$F1 2102
7 TraesCS3D01G151800 chr2B 215847148 215849146 1998 False 2689 2689 91.289 1 1963 1 chr2B.!!$F1 1962
8 TraesCS3D01G151800 chr2B 430230568 430232481 1913 True 2660 2660 92.004 3 1892 1 chr2B.!!$R1 1889
9 TraesCS3D01G151800 chr1B 449940900 449942906 2006 False 2601 2601 90.073 1 2039 1 chr1B.!!$F1 2038
10 TraesCS3D01G151800 chr3B 809557640 809559723 2083 True 2464 2464 88.315 1 2078 1 chr3B.!!$R1 2077
11 TraesCS3D01G151800 chr3B 548879796 548881045 1249 False 1676 1676 91.088 726 1968 1 chr3B.!!$F3 1242
12 TraesCS3D01G151800 chr3B 103209615 103210889 1274 False 1489 1489 87.904 826 2105 1 chr3B.!!$F1 1279
13 TraesCS3D01G151800 chr3B 169643848 169644451 603 False 817 817 91.722 1533 2113 1 chr3B.!!$F2 580
14 TraesCS3D01G151800 chr2D 476789265 476790793 1528 False 2294 2294 93.690 1 1543 1 chr2D.!!$F1 1542
15 TraesCS3D01G151800 chr2D 78318909 78320039 1130 True 1633 1633 92.970 995 2112 1 chr2D.!!$R1 1117
16 TraesCS3D01G151800 chr2D 78326681 78327682 1001 True 1530 1530 94.334 1 997 1 chr2D.!!$R2 996
17 TraesCS3D01G151800 chr6A 607998550 607999748 1198 True 1661 1661 91.818 771 1964 1 chr6A.!!$R2 1193
18 TraesCS3D01G151800 chr6A 466347387 466348284 897 False 1134 1134 89.758 1226 2113 1 chr6A.!!$F2 887
19 TraesCS3D01G151800 chr6A 466149456 466150350 894 False 1125 1125 89.648 1226 2113 1 chr6A.!!$F1 887
20 TraesCS3D01G151800 chr6A 466411476 466412350 874 False 1107 1107 89.426 1226 2113 1 chr6A.!!$F4 887
21 TraesCS3D01G151800 chr6A 466355830 466356647 817 False 953 953 88.087 1305 2113 1 chr6A.!!$F3 808
22 TraesCS3D01G151800 chr6B 702945531 702946740 1209 True 1642 1642 91.326 761 1964 1 chr6B.!!$R1 1203
23 TraesCS3D01G151800 chr6B 702990416 702991738 1322 True 1618 1618 88.989 729 2039 1 chr6B.!!$R2 1310
24 TraesCS3D01G151800 chr6B 703006973 703008265 1292 True 1604 1604 89.140 729 2035 1 chr6B.!!$R3 1306
25 TraesCS3D01G151800 chr6B 703062882 703064166 1284 True 1589 1589 89.083 730 2029 1 chr6B.!!$R4 1299

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
345 346 0.373716 GCGAGAAACTTGCCGGTATG 59.626 55.0 1.9 3.01 35.0 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2785 0.100682 GCTTCCACTCGCGATCTACA 59.899 55.0 10.36 0.0 0.0 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
66 67 3.462483 TTCTGAAAGCACGACCAAGTA 57.538 42.857 0.00 0.00 0.00 2.24
345 346 0.373716 GCGAGAAACTTGCCGGTATG 59.626 55.000 1.90 3.01 35.00 2.39
346 347 1.006832 CGAGAAACTTGCCGGTATGG 58.993 55.000 1.90 0.00 42.50 2.74
641 645 1.651987 CAACGACACAGGACACAACT 58.348 50.000 0.00 0.00 0.00 3.16
654 658 3.758554 GGACACAACTTTAGGACATGCAT 59.241 43.478 0.00 0.00 0.00 3.96
678 682 3.421844 AGAAACCTAGAACCAACATGGC 58.578 45.455 0.00 0.00 42.67 4.40
694 698 0.882927 TGGCCACTAGTCAAACACGC 60.883 55.000 0.00 0.00 0.00 5.34
769 815 1.229951 AGTGGGCCATGGAGGAAGA 60.230 57.895 18.40 0.00 41.22 2.87
851 1002 2.430694 TCTAGGACATGTCGGGTTGATG 59.569 50.000 19.33 4.27 0.00 3.07
1121 1311 2.513753 TGTGAAGATTCCGCCATGTTT 58.486 42.857 0.00 0.00 0.00 2.83
1153 1343 0.817634 TTGCAAGGTGAAGGTGTCCG 60.818 55.000 0.00 0.00 0.00 4.79
1238 1432 1.495951 GTGCGCTTCCAACTAACGG 59.504 57.895 9.73 0.00 0.00 4.44
1361 1555 5.450688 GCAAGTACTTCACGTGGATAGATCT 60.451 44.000 17.00 0.00 37.15 2.75
1369 1563 4.705023 TCACGTGGATAGATCTTGAAGTGA 59.295 41.667 17.00 7.37 33.28 3.41
1417 1611 0.905357 AGATTGTCTTAGGCGCCAGT 59.095 50.000 31.54 12.06 0.00 4.00
1512 1707 3.151022 GAGGAGGAGAGGGCACGG 61.151 72.222 0.00 0.00 0.00 4.94
1760 1984 4.922692 TGTCGTGAATGAATTTGCCATTTC 59.077 37.500 0.00 0.00 34.67 2.17
1807 2047 3.105937 GCAAGGTGTCGTGAAAACTTTC 58.894 45.455 0.00 0.00 37.69 2.62
1829 2069 3.725740 CGTTTGTCAGCAATTTCTGTGAC 59.274 43.478 4.99 2.78 36.97 3.67
1830 2070 3.607422 TTGTCAGCAATTTCTGTGACG 57.393 42.857 4.99 0.00 38.16 4.35
1831 2071 2.832563 TGTCAGCAATTTCTGTGACGA 58.167 42.857 4.99 0.00 38.16 4.20
1832 2072 3.402110 TGTCAGCAATTTCTGTGACGAT 58.598 40.909 4.99 0.00 38.16 3.73
1833 2073 3.814842 TGTCAGCAATTTCTGTGACGATT 59.185 39.130 4.99 0.00 38.16 3.34
1834 2074 4.275689 TGTCAGCAATTTCTGTGACGATTT 59.724 37.500 4.99 0.00 38.16 2.17
1835 2075 5.215160 GTCAGCAATTTCTGTGACGATTTT 58.785 37.500 4.99 0.00 35.63 1.82
1836 2076 5.687285 GTCAGCAATTTCTGTGACGATTTTT 59.313 36.000 4.99 0.00 35.63 1.94
1837 2077 6.855914 GTCAGCAATTTCTGTGACGATTTTTA 59.144 34.615 4.99 0.00 35.63 1.52
1838 2078 7.538678 GTCAGCAATTTCTGTGACGATTTTTAT 59.461 33.333 4.99 0.00 35.63 1.40
2002 2572 3.749284 AAGCAACCCCTTGGCGGTT 62.749 57.895 6.70 6.70 44.60 4.44
2113 2684 1.602377 GACGAGAAAAACCACCACCTG 59.398 52.381 0.00 0.00 0.00 4.00
2114 2685 1.064979 ACGAGAAAAACCACCACCTGT 60.065 47.619 0.00 0.00 0.00 4.00
2115 2686 2.021457 CGAGAAAAACCACCACCTGTT 58.979 47.619 0.00 0.00 0.00 3.16
2116 2687 2.223479 CGAGAAAAACCACCACCTGTTG 60.223 50.000 0.00 0.00 0.00 3.33
2124 2695 3.077907 CCACCTGTTGGGGATCGT 58.922 61.111 0.00 0.00 42.54 3.73
2125 2696 2.292866 CCACCTGTTGGGGATCGTA 58.707 57.895 0.00 0.00 42.54 3.43
2126 2697 0.178068 CCACCTGTTGGGGATCGTAG 59.822 60.000 0.00 0.00 42.54 3.51
2127 2698 0.462047 CACCTGTTGGGGATCGTAGC 60.462 60.000 0.00 0.00 39.76 3.58
2128 2699 0.907704 ACCTGTTGGGGATCGTAGCA 60.908 55.000 0.00 0.00 40.03 3.49
2129 2700 0.179073 CCTGTTGGGGATCGTAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
2130 2701 0.824109 CTGTTGGGGATCGTAGCAGA 59.176 55.000 0.00 0.00 0.00 4.26
2131 2702 1.207089 CTGTTGGGGATCGTAGCAGAA 59.793 52.381 0.00 0.00 0.00 3.02
2132 2703 1.837439 TGTTGGGGATCGTAGCAGAAT 59.163 47.619 0.00 0.00 0.00 2.40
2133 2704 2.238646 TGTTGGGGATCGTAGCAGAATT 59.761 45.455 0.00 0.00 0.00 2.17
2134 2705 3.279434 GTTGGGGATCGTAGCAGAATTT 58.721 45.455 0.00 0.00 0.00 1.82
2135 2706 4.080807 TGTTGGGGATCGTAGCAGAATTTA 60.081 41.667 0.00 0.00 0.00 1.40
2136 2707 4.764050 TGGGGATCGTAGCAGAATTTAA 57.236 40.909 0.00 0.00 0.00 1.52
2137 2708 5.105567 TGGGGATCGTAGCAGAATTTAAA 57.894 39.130 0.00 0.00 0.00 1.52
2138 2709 5.502079 TGGGGATCGTAGCAGAATTTAAAA 58.498 37.500 0.00 0.00 0.00 1.52
2139 2710 5.946972 TGGGGATCGTAGCAGAATTTAAAAA 59.053 36.000 0.00 0.00 0.00 1.94
2140 2711 6.605594 TGGGGATCGTAGCAGAATTTAAAAAT 59.394 34.615 0.00 0.00 0.00 1.82
2141 2712 7.123547 TGGGGATCGTAGCAGAATTTAAAAATT 59.876 33.333 0.37 0.37 41.06 1.82
2142 2713 7.979537 GGGGATCGTAGCAGAATTTAAAAATTT 59.020 33.333 2.41 0.00 38.64 1.82
2143 2714 9.020813 GGGATCGTAGCAGAATTTAAAAATTTC 57.979 33.333 2.41 0.00 38.64 2.17
2144 2715 9.020813 GGATCGTAGCAGAATTTAAAAATTTCC 57.979 33.333 2.41 0.00 38.64 3.13
2145 2716 9.788960 GATCGTAGCAGAATTTAAAAATTTCCT 57.211 29.630 2.41 3.02 38.64 3.36
2148 2719 9.834628 CGTAGCAGAATTTAAAAATTTCCTACA 57.165 29.630 19.68 0.00 38.64 2.74
2158 2729 9.757227 TTTAAAAATTTCCTACACATCACCAAG 57.243 29.630 0.00 0.00 0.00 3.61
2159 2730 7.595819 AAAAATTTCCTACACATCACCAAGA 57.404 32.000 0.00 0.00 0.00 3.02
2160 2731 7.781324 AAAATTTCCTACACATCACCAAGAT 57.219 32.000 0.00 0.00 37.48 2.40
2161 2732 7.396540 AAATTTCCTACACATCACCAAGATC 57.603 36.000 0.00 0.00 33.72 2.75
2162 2733 4.487714 TTCCTACACATCACCAAGATCC 57.512 45.455 0.00 0.00 33.72 3.36
2163 2734 3.449918 TCCTACACATCACCAAGATCCA 58.550 45.455 0.00 0.00 33.72 3.41
2164 2735 4.040047 TCCTACACATCACCAAGATCCAT 58.960 43.478 0.00 0.00 33.72 3.41
2165 2736 4.101585 TCCTACACATCACCAAGATCCATC 59.898 45.833 0.00 0.00 33.72 3.51
2166 2737 4.102210 CCTACACATCACCAAGATCCATCT 59.898 45.833 0.00 0.00 39.22 2.90
2167 2738 5.305386 CCTACACATCACCAAGATCCATCTA 59.695 44.000 0.00 0.00 35.76 1.98
2168 2739 5.901413 ACACATCACCAAGATCCATCTAT 57.099 39.130 0.00 0.00 35.76 1.98
2169 2740 5.618236 ACACATCACCAAGATCCATCTATG 58.382 41.667 0.00 0.00 35.76 2.23
2186 2757 7.379098 CATCTATGGAGTATACTAGCAACGA 57.621 40.000 5.09 0.00 0.00 3.85
2187 2758 7.468441 CATCTATGGAGTATACTAGCAACGAG 58.532 42.308 5.09 0.00 0.00 4.18
2188 2759 5.938710 TCTATGGAGTATACTAGCAACGAGG 59.061 44.000 5.09 0.00 0.00 4.63
2189 2760 3.220110 TGGAGTATACTAGCAACGAGGG 58.780 50.000 5.09 0.00 0.00 4.30
2190 2761 2.557490 GGAGTATACTAGCAACGAGGGG 59.443 54.545 5.09 0.00 0.00 4.79
2191 2762 3.484407 GAGTATACTAGCAACGAGGGGA 58.516 50.000 5.09 0.00 0.00 4.81
2192 2763 3.887716 GAGTATACTAGCAACGAGGGGAA 59.112 47.826 5.09 0.00 0.00 3.97
2193 2764 4.284178 AGTATACTAGCAACGAGGGGAAA 58.716 43.478 2.75 0.00 0.00 3.13
2194 2765 3.821421 ATACTAGCAACGAGGGGAAAG 57.179 47.619 0.00 0.00 0.00 2.62
2195 2766 0.613777 ACTAGCAACGAGGGGAAAGG 59.386 55.000 0.00 0.00 0.00 3.11
2196 2767 0.902531 CTAGCAACGAGGGGAAAGGA 59.097 55.000 0.00 0.00 0.00 3.36
2197 2768 0.902531 TAGCAACGAGGGGAAAGGAG 59.097 55.000 0.00 0.00 0.00 3.69
2198 2769 1.128188 AGCAACGAGGGGAAAGGAGT 61.128 55.000 0.00 0.00 0.00 3.85
2199 2770 0.955919 GCAACGAGGGGAAAGGAGTG 60.956 60.000 0.00 0.00 0.00 3.51
2200 2771 0.955919 CAACGAGGGGAAAGGAGTGC 60.956 60.000 0.00 0.00 0.00 4.40
2201 2772 1.415672 AACGAGGGGAAAGGAGTGCA 61.416 55.000 0.00 0.00 0.00 4.57
2202 2773 1.201429 ACGAGGGGAAAGGAGTGCAT 61.201 55.000 0.00 0.00 0.00 3.96
2203 2774 0.462759 CGAGGGGAAAGGAGTGCATC 60.463 60.000 0.00 0.00 0.00 3.91
2204 2775 0.915364 GAGGGGAAAGGAGTGCATCT 59.085 55.000 0.00 0.00 0.00 2.90
2205 2776 2.119495 GAGGGGAAAGGAGTGCATCTA 58.881 52.381 0.00 0.00 0.00 1.98
2206 2777 1.840635 AGGGGAAAGGAGTGCATCTAC 59.159 52.381 0.00 0.00 0.00 2.59
2207 2778 1.559682 GGGGAAAGGAGTGCATCTACA 59.440 52.381 0.00 0.00 0.00 2.74
2208 2779 2.173569 GGGGAAAGGAGTGCATCTACAT 59.826 50.000 0.00 0.00 0.00 2.29
2209 2780 3.391296 GGGGAAAGGAGTGCATCTACATA 59.609 47.826 0.00 0.00 0.00 2.29
2210 2781 4.381411 GGGAAAGGAGTGCATCTACATAC 58.619 47.826 0.00 0.00 0.00 2.39
2211 2782 4.381411 GGAAAGGAGTGCATCTACATACC 58.619 47.826 0.00 0.00 0.00 2.73
2212 2783 4.381411 GAAAGGAGTGCATCTACATACCC 58.619 47.826 0.00 0.00 0.00 3.69
2213 2784 3.336509 AGGAGTGCATCTACATACCCT 57.663 47.619 0.00 0.00 0.00 4.34
2214 2785 3.658725 AGGAGTGCATCTACATACCCTT 58.341 45.455 0.00 0.00 0.00 3.95
2215 2786 3.389329 AGGAGTGCATCTACATACCCTTG 59.611 47.826 0.00 0.00 0.00 3.61
2216 2787 3.134804 GGAGTGCATCTACATACCCTTGT 59.865 47.826 0.00 0.00 0.00 3.16
2217 2788 4.344102 GGAGTGCATCTACATACCCTTGTA 59.656 45.833 0.00 0.00 0.00 2.41
2218 2789 5.509840 GGAGTGCATCTACATACCCTTGTAG 60.510 48.000 5.47 5.47 46.85 2.74
2224 2795 2.795175 ACATACCCTTGTAGATCGCG 57.205 50.000 0.00 0.00 0.00 5.87
2225 2796 2.304092 ACATACCCTTGTAGATCGCGA 58.696 47.619 13.09 13.09 0.00 5.87
2226 2797 2.293677 ACATACCCTTGTAGATCGCGAG 59.706 50.000 16.66 0.00 0.00 5.03
2227 2798 2.048444 TACCCTTGTAGATCGCGAGT 57.952 50.000 16.66 7.01 0.00 4.18
2228 2799 0.456221 ACCCTTGTAGATCGCGAGTG 59.544 55.000 16.66 0.00 0.00 3.51
2229 2800 0.249073 CCCTTGTAGATCGCGAGTGG 60.249 60.000 16.66 8.22 0.00 4.00
2230 2801 0.738975 CCTTGTAGATCGCGAGTGGA 59.261 55.000 16.66 0.00 0.00 4.02
2231 2802 1.134367 CCTTGTAGATCGCGAGTGGAA 59.866 52.381 16.66 2.59 0.00 3.53
2232 2803 2.455032 CTTGTAGATCGCGAGTGGAAG 58.545 52.381 16.66 8.95 0.00 3.46
2233 2804 0.100682 TGTAGATCGCGAGTGGAAGC 59.899 55.000 16.66 1.43 0.00 3.86
2253 2824 1.611519 GTTCCAATGAACGGGGTTGA 58.388 50.000 0.00 0.00 41.35 3.18
2254 2825 2.167662 GTTCCAATGAACGGGGTTGAT 58.832 47.619 0.00 0.00 41.35 2.57
2255 2826 1.832883 TCCAATGAACGGGGTTGATG 58.167 50.000 0.00 0.00 0.00 3.07
2256 2827 0.817013 CCAATGAACGGGGTTGATGG 59.183 55.000 0.00 0.00 0.00 3.51
2257 2828 1.615651 CCAATGAACGGGGTTGATGGA 60.616 52.381 0.00 0.00 0.00 3.41
2258 2829 1.745087 CAATGAACGGGGTTGATGGAG 59.255 52.381 0.00 0.00 0.00 3.86
2259 2830 0.991920 ATGAACGGGGTTGATGGAGT 59.008 50.000 0.00 0.00 0.00 3.85
2260 2831 0.323629 TGAACGGGGTTGATGGAGTC 59.676 55.000 0.00 0.00 0.00 3.36
2261 2832 0.739813 GAACGGGGTTGATGGAGTCG 60.740 60.000 0.00 0.00 0.00 4.18
2262 2833 1.477685 AACGGGGTTGATGGAGTCGT 61.478 55.000 0.00 0.00 0.00 4.34
2263 2834 0.612732 ACGGGGTTGATGGAGTCGTA 60.613 55.000 0.00 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 3.356529 AGTCCATCTTTTCGCCAATCT 57.643 42.857 0.00 0.00 0.00 2.40
257 258 1.278985 CCTCTCACACTGGCACCAATA 59.721 52.381 0.00 0.00 0.00 1.90
258 259 0.037303 CCTCTCACACTGGCACCAAT 59.963 55.000 0.00 0.00 0.00 3.16
340 341 1.101049 CCGTTGTGCCATCCCATACC 61.101 60.000 0.00 0.00 0.00 2.73
457 458 1.065199 GGATCTGGCACAATGTCTGGA 60.065 52.381 0.00 0.00 38.70 3.86
484 488 1.072965 CTTCCCCTCATAGGCACCATC 59.927 57.143 0.00 0.00 32.73 3.51
561 565 3.153919 TGACCACTACCAAATTGCTTCC 58.846 45.455 0.00 0.00 0.00 3.46
641 645 5.324409 AGGTTTCTTCATGCATGTCCTAAA 58.676 37.500 25.43 17.49 0.00 1.85
654 658 5.070001 CCATGTTGGTTCTAGGTTTCTTCA 58.930 41.667 0.00 0.00 31.35 3.02
678 682 0.319211 TCCGCGTGTTTGACTAGTGG 60.319 55.000 4.92 0.00 0.00 4.00
694 698 2.943978 AAGGCTTGTCCTCCGTCCG 61.944 63.158 0.00 0.00 46.94 4.79
769 815 2.309504 GCCCCCTCCAAGGCTAGTT 61.310 63.158 0.00 0.00 46.14 2.24
851 1002 1.148498 CGTTGATAGGCCTTCCCCC 59.852 63.158 12.58 0.00 0.00 5.40
991 1181 3.018856 CAGATGAAGCCATGCCTACAAA 58.981 45.455 0.00 0.00 32.09 2.83
1121 1311 1.955778 CCTTGCAAACATCTCCACACA 59.044 47.619 0.00 0.00 0.00 3.72
1153 1343 0.721718 CATGACTTCTTTCGGTCGGC 59.278 55.000 0.00 0.00 35.45 5.54
1238 1432 1.117150 TACCGGTGGAAGGTCATAGC 58.883 55.000 19.93 0.00 42.81 2.97
1417 1611 2.341846 AACCTTTCTTCGAACAGCCA 57.658 45.000 0.00 0.00 0.00 4.75
1760 1984 6.764308 ACATCTCCACACCAAATTCAATAG 57.236 37.500 0.00 0.00 0.00 1.73
1807 2047 3.725740 GTCACAGAAATTGCTGACAAACG 59.274 43.478 20.85 1.59 39.77 3.60
1836 2076 9.665719 TCATCTGAGCACAACAGTTTATAAATA 57.334 29.630 0.31 0.00 36.81 1.40
1837 2077 8.565896 TCATCTGAGCACAACAGTTTATAAAT 57.434 30.769 0.31 0.00 36.81 1.40
1838 2078 7.119699 CCTCATCTGAGCACAACAGTTTATAAA 59.880 37.037 1.51 0.00 40.75 1.40
2002 2572 2.349755 GCGGTAGGGTTTGAGCCA 59.650 61.111 0.00 0.00 38.48 4.75
2035 2605 0.179073 CGGTAGGATCCAGCAACCTG 60.179 60.000 15.82 8.35 38.85 4.00
2079 2650 4.521130 TTCTCGTCACAGAAACTATGCT 57.479 40.909 0.00 0.00 29.01 3.79
2113 2684 2.622064 ATTCTGCTACGATCCCCAAC 57.378 50.000 0.00 0.00 0.00 3.77
2114 2685 3.644966 AAATTCTGCTACGATCCCCAA 57.355 42.857 0.00 0.00 0.00 4.12
2115 2686 4.764050 TTAAATTCTGCTACGATCCCCA 57.236 40.909 0.00 0.00 0.00 4.96
2116 2687 6.445357 TTTTTAAATTCTGCTACGATCCCC 57.555 37.500 0.00 0.00 0.00 4.81
2117 2688 8.926715 AAATTTTTAAATTCTGCTACGATCCC 57.073 30.769 1.26 0.00 37.62 3.85
2118 2689 9.020813 GGAAATTTTTAAATTCTGCTACGATCC 57.979 33.333 1.26 0.00 37.62 3.36
2119 2690 9.788960 AGGAAATTTTTAAATTCTGCTACGATC 57.211 29.630 1.26 0.00 37.62 3.69
2122 2693 9.834628 TGTAGGAAATTTTTAAATTCTGCTACG 57.165 29.630 20.27 0.00 37.62 3.51
2132 2703 9.757227 CTTGGTGATGTGTAGGAAATTTTTAAA 57.243 29.630 0.00 0.00 0.00 1.52
2133 2704 9.137459 TCTTGGTGATGTGTAGGAAATTTTTAA 57.863 29.630 0.00 0.00 0.00 1.52
2134 2705 8.698973 TCTTGGTGATGTGTAGGAAATTTTTA 57.301 30.769 0.00 0.00 0.00 1.52
2135 2706 7.595819 TCTTGGTGATGTGTAGGAAATTTTT 57.404 32.000 0.00 0.00 0.00 1.94
2136 2707 7.093771 GGATCTTGGTGATGTGTAGGAAATTTT 60.094 37.037 0.00 0.00 35.14 1.82
2137 2708 6.378280 GGATCTTGGTGATGTGTAGGAAATTT 59.622 38.462 0.00 0.00 35.14 1.82
2138 2709 5.888161 GGATCTTGGTGATGTGTAGGAAATT 59.112 40.000 0.00 0.00 35.14 1.82
2139 2710 5.044919 TGGATCTTGGTGATGTGTAGGAAAT 60.045 40.000 0.00 0.00 35.14 2.17
2140 2711 4.288366 TGGATCTTGGTGATGTGTAGGAAA 59.712 41.667 0.00 0.00 35.14 3.13
2141 2712 3.843619 TGGATCTTGGTGATGTGTAGGAA 59.156 43.478 0.00 0.00 35.14 3.36
2142 2713 3.449918 TGGATCTTGGTGATGTGTAGGA 58.550 45.455 0.00 0.00 35.14 2.94
2143 2714 3.912496 TGGATCTTGGTGATGTGTAGG 57.088 47.619 0.00 0.00 35.14 3.18
2144 2715 5.287674 AGATGGATCTTGGTGATGTGTAG 57.712 43.478 0.00 0.00 35.14 2.74
2145 2716 6.762333 CATAGATGGATCTTGGTGATGTGTA 58.238 40.000 0.00 0.00 38.32 2.90
2146 2717 5.618236 CATAGATGGATCTTGGTGATGTGT 58.382 41.667 0.00 0.00 38.32 3.72
2162 2733 7.379098 TCGTTGCTAGTATACTCCATAGATG 57.621 40.000 9.12 0.15 0.00 2.90
2163 2734 6.600032 CCTCGTTGCTAGTATACTCCATAGAT 59.400 42.308 9.12 0.00 0.00 1.98
2164 2735 5.938710 CCTCGTTGCTAGTATACTCCATAGA 59.061 44.000 9.12 9.14 0.00 1.98
2165 2736 5.124138 CCCTCGTTGCTAGTATACTCCATAG 59.876 48.000 9.12 2.18 0.00 2.23
2166 2737 5.008331 CCCTCGTTGCTAGTATACTCCATA 58.992 45.833 9.12 0.00 0.00 2.74
2167 2738 3.827302 CCCTCGTTGCTAGTATACTCCAT 59.173 47.826 9.12 0.00 0.00 3.41
2168 2739 3.220110 CCCTCGTTGCTAGTATACTCCA 58.780 50.000 9.12 5.38 0.00 3.86
2169 2740 2.557490 CCCCTCGTTGCTAGTATACTCC 59.443 54.545 9.12 2.61 0.00 3.85
2170 2741 3.484407 TCCCCTCGTTGCTAGTATACTC 58.516 50.000 9.12 0.00 0.00 2.59
2171 2742 3.589951 TCCCCTCGTTGCTAGTATACT 57.410 47.619 10.87 10.87 0.00 2.12
2172 2743 4.501058 CCTTTCCCCTCGTTGCTAGTATAC 60.501 50.000 0.00 0.00 0.00 1.47
2173 2744 3.640029 CCTTTCCCCTCGTTGCTAGTATA 59.360 47.826 0.00 0.00 0.00 1.47
2174 2745 2.434702 CCTTTCCCCTCGTTGCTAGTAT 59.565 50.000 0.00 0.00 0.00 2.12
2175 2746 1.829222 CCTTTCCCCTCGTTGCTAGTA 59.171 52.381 0.00 0.00 0.00 1.82
2176 2747 0.613777 CCTTTCCCCTCGTTGCTAGT 59.386 55.000 0.00 0.00 0.00 2.57
2177 2748 0.902531 TCCTTTCCCCTCGTTGCTAG 59.097 55.000 0.00 0.00 0.00 3.42
2178 2749 0.902531 CTCCTTTCCCCTCGTTGCTA 59.097 55.000 0.00 0.00 0.00 3.49
2179 2750 1.128188 ACTCCTTTCCCCTCGTTGCT 61.128 55.000 0.00 0.00 0.00 3.91
2180 2751 0.955919 CACTCCTTTCCCCTCGTTGC 60.956 60.000 0.00 0.00 0.00 4.17
2181 2752 0.955919 GCACTCCTTTCCCCTCGTTG 60.956 60.000 0.00 0.00 0.00 4.10
2182 2753 1.375326 GCACTCCTTTCCCCTCGTT 59.625 57.895 0.00 0.00 0.00 3.85
2183 2754 1.201429 ATGCACTCCTTTCCCCTCGT 61.201 55.000 0.00 0.00 0.00 4.18
2184 2755 0.462759 GATGCACTCCTTTCCCCTCG 60.463 60.000 0.00 0.00 0.00 4.63
2185 2756 0.915364 AGATGCACTCCTTTCCCCTC 59.085 55.000 0.00 0.00 0.00 4.30
2186 2757 1.840635 GTAGATGCACTCCTTTCCCCT 59.159 52.381 0.00 0.00 0.00 4.79
2187 2758 1.559682 TGTAGATGCACTCCTTTCCCC 59.440 52.381 0.00 0.00 0.00 4.81
2188 2759 3.567478 ATGTAGATGCACTCCTTTCCC 57.433 47.619 0.00 0.00 0.00 3.97
2189 2760 4.381411 GGTATGTAGATGCACTCCTTTCC 58.619 47.826 0.00 0.00 0.00 3.13
2190 2761 4.101741 AGGGTATGTAGATGCACTCCTTTC 59.898 45.833 0.00 0.00 0.00 2.62
2191 2762 4.040755 AGGGTATGTAGATGCACTCCTTT 58.959 43.478 0.00 0.00 0.00 3.11
2192 2763 3.658725 AGGGTATGTAGATGCACTCCTT 58.341 45.455 0.00 0.00 0.00 3.36
2193 2764 3.336509 AGGGTATGTAGATGCACTCCT 57.663 47.619 0.00 0.00 0.00 3.69
2194 2765 3.134804 ACAAGGGTATGTAGATGCACTCC 59.865 47.826 0.00 0.00 25.83 3.85
2195 2766 4.408182 ACAAGGGTATGTAGATGCACTC 57.592 45.455 0.00 0.00 25.83 3.51
2204 2775 3.479489 TCGCGATCTACAAGGGTATGTA 58.521 45.455 3.71 0.00 34.75 2.29
2205 2776 2.293677 CTCGCGATCTACAAGGGTATGT 59.706 50.000 10.36 0.00 37.32 2.29
2206 2777 2.293677 ACTCGCGATCTACAAGGGTATG 59.706 50.000 10.36 0.00 0.00 2.39
2207 2778 2.293677 CACTCGCGATCTACAAGGGTAT 59.706 50.000 10.36 0.00 0.00 2.73
2208 2779 1.674441 CACTCGCGATCTACAAGGGTA 59.326 52.381 10.36 0.00 0.00 3.69
2209 2780 0.456221 CACTCGCGATCTACAAGGGT 59.544 55.000 10.36 0.00 0.00 4.34
2210 2781 0.249073 CCACTCGCGATCTACAAGGG 60.249 60.000 10.36 0.00 0.00 3.95
2211 2782 0.738975 TCCACTCGCGATCTACAAGG 59.261 55.000 10.36 4.27 0.00 3.61
2212 2783 2.455032 CTTCCACTCGCGATCTACAAG 58.545 52.381 10.36 4.93 0.00 3.16
2213 2784 1.469251 GCTTCCACTCGCGATCTACAA 60.469 52.381 10.36 0.00 0.00 2.41
2214 2785 0.100682 GCTTCCACTCGCGATCTACA 59.899 55.000 10.36 0.00 0.00 2.74
2215 2786 2.874709 GCTTCCACTCGCGATCTAC 58.125 57.895 10.36 0.00 0.00 2.59
2235 2806 2.166829 CATCAACCCCGTTCATTGGAA 58.833 47.619 0.00 0.00 0.00 3.53
2236 2807 1.615651 CCATCAACCCCGTTCATTGGA 60.616 52.381 0.00 0.00 0.00 3.53
2237 2808 0.817013 CCATCAACCCCGTTCATTGG 59.183 55.000 0.00 0.00 0.00 3.16
2238 2809 1.745087 CTCCATCAACCCCGTTCATTG 59.255 52.381 0.00 0.00 0.00 2.82
2239 2810 1.354368 ACTCCATCAACCCCGTTCATT 59.646 47.619 0.00 0.00 0.00 2.57
2240 2811 0.991920 ACTCCATCAACCCCGTTCAT 59.008 50.000 0.00 0.00 0.00 2.57
2241 2812 0.323629 GACTCCATCAACCCCGTTCA 59.676 55.000 0.00 0.00 0.00 3.18
2242 2813 0.739813 CGACTCCATCAACCCCGTTC 60.740 60.000 0.00 0.00 0.00 3.95
2243 2814 1.295423 CGACTCCATCAACCCCGTT 59.705 57.895 0.00 0.00 0.00 4.44
2244 2815 0.612732 TACGACTCCATCAACCCCGT 60.613 55.000 0.00 0.00 0.00 5.28
2245 2816 2.195389 TACGACTCCATCAACCCCG 58.805 57.895 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.