Multiple sequence alignment - TraesCS2D01G235800

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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 TraesCS2D01G235800 chr2D 100.000 2408 0 0 1 2408 226526588 226528995 0.000000e+00 4447
1 TraesCS2D01G235800 chr2D 91.047 659 51 5 161 816 172246152 172246805 0.000000e+00 883
2 TraesCS2D01G235800 chr2D 90.440 659 60 1 161 816 526841512 526840854 0.000000e+00 865
3 TraesCS2D01G235800 chr2A 93.687 1188 68 3 813 1993 271914874 271913687 0.000000e+00 1772
4 TraesCS2D01G235800 chr2A 82.958 1109 172 8 818 1918 382856493 382855394 0.000000e+00 985
5 TraesCS2D01G235800 chr2A 93.151 365 12 4 2045 2408 271913683 271913331 7.630000e-145 523
6 TraesCS2D01G235800 chr4B 87.965 1130 119 8 813 1933 358896121 358895000 0.000000e+00 1317
7 TraesCS2D01G235800 chr4B 88.000 350 23 2 1937 2286 5708890 5708560 1.730000e-106 396
8 TraesCS2D01G235800 chr4B 81.687 486 63 18 1937 2406 557971291 557971766 4.860000e-102 381
9 TraesCS2D01G235800 chr6B 84.500 1129 159 11 813 1933 330983731 330982611 0.000000e+00 1101
10 TraesCS2D01G235800 chr6B 90.147 477 31 7 1933 2408 155466536 155466997 7.360000e-170 606
11 TraesCS2D01G235800 chr6D 86.259 997 122 9 930 1918 55435567 55434578 0.000000e+00 1068
12 TraesCS2D01G235800 chr6D 83.662 1114 165 8 813 1918 462399600 462398496 0.000000e+00 1033
13 TraesCS2D01G235800 chr6D 86.881 808 75 19 18 816 117352864 117353649 0.000000e+00 876
14 TraesCS2D01G235800 chr6D 94.375 480 20 5 1930 2408 324828672 324828199 0.000000e+00 730
15 TraesCS2D01G235800 chr6D 87.083 480 54 6 1931 2408 97242820 97243293 9.800000e-149 536
16 TraesCS2D01G235800 chr6D 83.815 173 20 5 1929 2096 305270411 305270242 8.910000e-35 158
17 TraesCS2D01G235800 chr1D 83.483 1114 167 9 813 1918 176360296 176361400 0.000000e+00 1022
18 TraesCS2D01G235800 chr1D 83.139 1115 168 11 813 1918 356880742 356881845 0.000000e+00 1000
19 TraesCS2D01G235800 chr1D 86.182 825 77 27 1 816 221855823 221856619 0.000000e+00 857
20 TraesCS2D01G235800 chr7D 83.049 1115 171 13 813 1918 219850125 219849020 0.000000e+00 996
21 TraesCS2D01G235800 chr7D 87.015 824 82 19 1 816 283415145 283415951 0.000000e+00 905
22 TraesCS2D01G235800 chr7D 90.152 660 59 4 161 816 353817465 353818122 0.000000e+00 854
23 TraesCS2D01G235800 chr3D 91.252 663 51 2 161 816 80149653 80150315 0.000000e+00 896
24 TraesCS2D01G235800 chr3D 87.936 746 75 14 79 816 277785294 277786032 0.000000e+00 865
25 TraesCS2D01G235800 chr3D 88.050 477 46 9 1933 2408 338551116 338550650 2.700000e-154 555
26 TraesCS2D01G235800 chr5D 90.615 650 58 2 170 816 333576755 333576106 0.000000e+00 859
27 TraesCS2D01G235800 chr7B 89.792 480 38 8 1932 2408 123735943 123735472 2.650000e-169 604
28 TraesCS2D01G235800 chr7B 85.654 474 52 9 1934 2406 725819710 725820168 3.600000e-133 484
29 TraesCS2D01G235800 chr7B 91.760 267 19 1 1937 2203 24044766 24045029 3.780000e-98 368
30 TraesCS2D01G235800 chr4A 79.863 437 46 24 1977 2396 21244887 21244476 5.070000e-72 281


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 TraesCS2D01G235800 chr2D 226526588 226528995 2407 False 4447.0 4447 100.000 1 2408 1 chr2D.!!$F2 2407
1 TraesCS2D01G235800 chr2D 172246152 172246805 653 False 883.0 883 91.047 161 816 1 chr2D.!!$F1 655
2 TraesCS2D01G235800 chr2D 526840854 526841512 658 True 865.0 865 90.440 161 816 1 chr2D.!!$R1 655
3 TraesCS2D01G235800 chr2A 271913331 271914874 1543 True 1147.5 1772 93.419 813 2408 2 chr2A.!!$R2 1595
4 TraesCS2D01G235800 chr2A 382855394 382856493 1099 True 985.0 985 82.958 818 1918 1 chr2A.!!$R1 1100
5 TraesCS2D01G235800 chr4B 358895000 358896121 1121 True 1317.0 1317 87.965 813 1933 1 chr4B.!!$R2 1120
6 TraesCS2D01G235800 chr6B 330982611 330983731 1120 True 1101.0 1101 84.500 813 1933 1 chr6B.!!$R1 1120
7 TraesCS2D01G235800 chr6D 55434578 55435567 989 True 1068.0 1068 86.259 930 1918 1 chr6D.!!$R1 988
8 TraesCS2D01G235800 chr6D 462398496 462399600 1104 True 1033.0 1033 83.662 813 1918 1 chr6D.!!$R4 1105
9 TraesCS2D01G235800 chr6D 117352864 117353649 785 False 876.0 876 86.881 18 816 1 chr6D.!!$F2 798
10 TraesCS2D01G235800 chr1D 176360296 176361400 1104 False 1022.0 1022 83.483 813 1918 1 chr1D.!!$F1 1105
11 TraesCS2D01G235800 chr1D 356880742 356881845 1103 False 1000.0 1000 83.139 813 1918 1 chr1D.!!$F3 1105
12 TraesCS2D01G235800 chr1D 221855823 221856619 796 False 857.0 857 86.182 1 816 1 chr1D.!!$F2 815
13 TraesCS2D01G235800 chr7D 219849020 219850125 1105 True 996.0 996 83.049 813 1918 1 chr7D.!!$R1 1105
14 TraesCS2D01G235800 chr7D 283415145 283415951 806 False 905.0 905 87.015 1 816 1 chr7D.!!$F1 815
15 TraesCS2D01G235800 chr7D 353817465 353818122 657 False 854.0 854 90.152 161 816 1 chr7D.!!$F2 655
16 TraesCS2D01G235800 chr3D 80149653 80150315 662 False 896.0 896 91.252 161 816 1 chr3D.!!$F1 655
17 TraesCS2D01G235800 chr3D 277785294 277786032 738 False 865.0 865 87.936 79 816 1 chr3D.!!$F2 737
18 TraesCS2D01G235800 chr5D 333576106 333576755 649 True 859.0 859 90.615 170 816 1 chr5D.!!$R1 646

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
673 782 0.035317 CACAACAGAGCAGTGCCCTA 59.965 55.0 12.58 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2279 0.243907 GAGAGTGCGTTGACCTAGCA 59.756 55.0 0.0 0.0 38.71 3.49 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 2.673523 AGCCGGATCTGCTGCTTT 59.326 55.556 5.05 0.00 37.76 3.51
38 39 3.182312 GCTTTTGCTCCGGCTCTC 58.818 61.111 0.00 0.00 43.35 3.20
39 40 2.744768 GCTTTTGCTCCGGCTCTCG 61.745 63.158 0.00 0.00 43.35 4.04
40 41 2.742372 TTTTGCTCCGGCTCTCGC 60.742 61.111 0.00 0.00 39.59 5.03
41 42 3.240134 TTTTGCTCCGGCTCTCGCT 62.240 57.895 0.00 0.00 39.59 4.93
42 43 3.649277 TTTGCTCCGGCTCTCGCTC 62.649 63.158 0.00 0.00 39.59 5.03
48 49 4.186433 CGGCTCTCGCTCGCTCTT 62.186 66.667 0.00 0.00 36.09 2.85
49 50 2.278531 GGCTCTCGCTCGCTCTTC 60.279 66.667 0.00 0.00 36.09 2.87
50 51 2.770589 GGCTCTCGCTCGCTCTTCT 61.771 63.158 0.00 0.00 36.09 2.85
51 52 1.586042 GCTCTCGCTCGCTCTTCTG 60.586 63.158 0.00 0.00 0.00 3.02
52 53 1.586042 CTCTCGCTCGCTCTTCTGC 60.586 63.158 0.00 0.00 0.00 4.26
53 54 1.992233 CTCTCGCTCGCTCTTCTGCT 61.992 60.000 0.00 0.00 0.00 4.24
54 55 1.586042 CTCGCTCGCTCTTCTGCTC 60.586 63.158 0.00 0.00 0.00 4.26
55 56 1.992233 CTCGCTCGCTCTTCTGCTCT 61.992 60.000 0.00 0.00 0.00 4.09
56 57 1.873125 CGCTCGCTCTTCTGCTCTG 60.873 63.158 0.00 0.00 0.00 3.35
57 58 2.166579 GCTCGCTCTTCTGCTCTGC 61.167 63.158 0.00 0.00 0.00 4.26
58 59 1.512230 CTCGCTCTTCTGCTCTGCT 59.488 57.895 0.00 0.00 0.00 4.24
59 60 0.526096 CTCGCTCTTCTGCTCTGCTC 60.526 60.000 0.00 0.00 0.00 4.26
60 61 0.964860 TCGCTCTTCTGCTCTGCTCT 60.965 55.000 0.00 0.00 0.00 4.09
61 62 0.526096 CGCTCTTCTGCTCTGCTCTC 60.526 60.000 0.00 0.00 0.00 3.20
62 63 0.179103 GCTCTTCTGCTCTGCTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
63 64 0.461135 CTCTTCTGCTCTGCTCTCCC 59.539 60.000 0.00 0.00 0.00 4.30
64 65 0.975040 TCTTCTGCTCTGCTCTCCCC 60.975 60.000 0.00 0.00 0.00 4.81
65 66 1.970352 CTTCTGCTCTGCTCTCCCCC 61.970 65.000 0.00 0.00 0.00 5.40
66 67 2.365370 CTGCTCTGCTCTCCCCCT 60.365 66.667 0.00 0.00 0.00 4.79
67 68 2.364842 TGCTCTGCTCTCCCCCTC 60.365 66.667 0.00 0.00 0.00 4.30
68 69 3.535962 GCTCTGCTCTCCCCCTCG 61.536 72.222 0.00 0.00 0.00 4.63
69 70 3.535962 CTCTGCTCTCCCCCTCGC 61.536 72.222 0.00 0.00 0.00 5.03
70 71 4.067512 TCTGCTCTCCCCCTCGCT 62.068 66.667 0.00 0.00 0.00 4.93
71 72 3.535962 CTGCTCTCCCCCTCGCTC 61.536 72.222 0.00 0.00 0.00 5.03
74 75 3.522731 CTCTCCCCCTCGCTCGTG 61.523 72.222 0.00 0.00 0.00 4.35
85 86 3.488978 GCTCGTGCTGCTGCTCTG 61.489 66.667 17.00 9.52 40.48 3.35
86 87 3.488978 CTCGTGCTGCTGCTCTGC 61.489 66.667 17.00 3.60 40.48 4.26
87 88 3.936204 CTCGTGCTGCTGCTCTGCT 62.936 63.158 17.00 0.00 39.95 4.24
90 91 1.671704 GTGCTGCTGCTCTGCTCTT 60.672 57.895 17.00 0.00 39.95 2.85
91 92 1.671379 TGCTGCTGCTCTGCTCTTG 60.671 57.895 17.00 0.00 39.95 3.02
93 94 1.376166 CTGCTGCTCTGCTCTTGCT 60.376 57.895 0.00 0.00 40.48 3.91
115 116 2.279054 CTCGCGCTGCTGATGCTA 60.279 61.111 5.56 0.00 40.48 3.49
116 117 2.279054 TCGCGCTGCTGATGCTAG 60.279 61.111 5.56 0.00 40.48 3.42
118 119 1.299392 CGCGCTGCTGATGCTAGTA 60.299 57.895 5.56 0.00 40.48 1.82
120 121 0.528466 GCGCTGCTGATGCTAGTACA 60.528 55.000 0.00 0.00 40.48 2.90
121 122 1.871408 GCGCTGCTGATGCTAGTACAT 60.871 52.381 0.00 0.00 40.48 2.29
122 123 1.791204 CGCTGCTGATGCTAGTACATG 59.209 52.381 0.00 0.00 40.48 3.21
123 124 2.141517 GCTGCTGATGCTAGTACATGG 58.858 52.381 0.00 0.00 40.48 3.66
124 125 2.763933 CTGCTGATGCTAGTACATGGG 58.236 52.381 0.00 0.00 40.48 4.00
125 126 1.202687 TGCTGATGCTAGTACATGGGC 60.203 52.381 0.00 0.00 40.48 5.36
142 178 2.816958 CTGCTGCAGCTACACGGG 60.817 66.667 36.61 15.13 42.66 5.28
149 220 2.187946 AGCTACACGGGCTGATGC 59.812 61.111 0.00 0.00 38.73 3.91
150 221 2.125147 GCTACACGGGCTGATGCA 60.125 61.111 0.00 0.00 41.91 3.96
167 267 2.048409 AGCTCACGTGCTGCTCTG 60.048 61.111 23.54 5.53 42.33 3.35
173 273 1.979155 ACGTGCTGCTCTGGCTCTA 60.979 57.895 0.00 0.00 39.59 2.43
175 275 1.896694 GTGCTGCTCTGGCTCTAGT 59.103 57.895 0.00 0.00 39.59 2.57
259 362 1.302033 CTGCTCCTCCAAGCGTTGT 60.302 57.895 0.00 0.00 45.54 3.32
268 371 2.978010 AAGCGTTGTTGCTCCGGG 60.978 61.111 0.00 0.00 46.60 5.73
270 373 3.284449 GCGTTGTTGCTCCGGGTT 61.284 61.111 0.00 0.00 0.00 4.11
271 374 1.962306 GCGTTGTTGCTCCGGGTTA 60.962 57.895 0.00 0.00 0.00 2.85
311 414 1.009829 GTCGATCGCCTGCTGATTTT 58.990 50.000 11.09 0.00 0.00 1.82
318 421 1.202222 CGCCTGCTGATTTTGATCACC 60.202 52.381 0.00 0.00 0.00 4.02
379 482 1.190643 GAAGTGCCTCTCTGCTACCT 58.809 55.000 0.00 0.00 0.00 3.08
408 511 6.964370 CGTTCAGTTTCAACAGTAACATTCAA 59.036 34.615 0.00 0.00 0.00 2.69
412 515 9.868277 TCAGTTTCAACAGTAACATTCAAATTT 57.132 25.926 0.00 0.00 0.00 1.82
478 583 7.773690 ACAGTTTTTACCTCATCTGTTGTAGTT 59.226 33.333 0.00 0.00 33.26 2.24
489 594 8.149973 TCATCTGTTGTAGTTAGGTGTTTTTC 57.850 34.615 0.00 0.00 0.00 2.29
491 596 5.006941 TCTGTTGTAGTTAGGTGTTTTTCGC 59.993 40.000 0.00 0.00 0.00 4.70
576 681 8.964476 TGTTATTAGAATCCCACTTGAGATTC 57.036 34.615 5.55 5.55 45.72 2.52
596 701 7.619050 AGATTCATGATGTCTGTCTTGTACTT 58.381 34.615 9.61 0.00 0.00 2.24
673 782 0.035317 CACAACAGAGCAGTGCCCTA 59.965 55.000 12.58 0.00 0.00 3.53
741 850 3.802675 GCCACCTCTGTCGTAACTTCTTT 60.803 47.826 0.00 0.00 0.00 2.52
746 855 4.474113 CTCTGTCGTAACTTCTTTAGCGT 58.526 43.478 0.00 0.00 0.00 5.07
781 890 2.359107 AGGTCGACACGGCTACGA 60.359 61.111 18.91 0.00 44.60 3.43
809 918 4.144297 AGGTTGTACACTTGTTGCATCAT 58.856 39.130 0.00 0.00 0.00 2.45
847 956 0.100503 GGCCCATTGATGTACAACGC 59.899 55.000 0.00 0.00 41.52 4.84
849 958 1.201181 GCCCATTGATGTACAACGCAA 59.799 47.619 0.00 5.65 41.52 4.85
873 982 8.869897 CAATCTTTCAATTCCAATCTCACAATG 58.130 33.333 0.00 0.00 0.00 2.82
1156 1267 1.134280 AGATCTCGCCCATTTGTCCTG 60.134 52.381 0.00 0.00 0.00 3.86
1363 1474 3.126000 TCACAATGTGCGCGAAATGATTA 59.874 39.130 12.10 0.00 32.98 1.75
1376 1487 6.346838 CGCGAAATGATTATTGTCTCAGCATA 60.347 38.462 0.00 0.00 0.00 3.14
1416 1533 7.704472 ACGAAAAATTGTGCATAAGAAGACAAA 59.296 29.630 1.43 0.00 32.34 2.83
1598 1719 1.342174 GGGAACGATGAGGCGGTATTA 59.658 52.381 0.00 0.00 35.12 0.98
1918 2039 5.071923 AGCCCGGTAGATTAGCTAGATTTTT 59.928 40.000 0.00 0.00 30.46 1.94
1950 2071 7.141100 TCGGATTTTCTTTTCAAGGATACAC 57.859 36.000 0.00 0.00 41.41 2.90
2003 2124 2.853159 CCAAGCGGCTGATACAACA 58.147 52.632 1.81 0.00 0.00 3.33
2004 2125 0.447801 CCAAGCGGCTGATACAACAC 59.552 55.000 1.81 0.00 0.00 3.32
2005 2126 0.447801 CAAGCGGCTGATACAACACC 59.552 55.000 1.81 0.00 0.00 4.16
2006 2127 0.324943 AAGCGGCTGATACAACACCT 59.675 50.000 1.81 0.00 0.00 4.00
2007 2128 0.324943 AGCGGCTGATACAACACCTT 59.675 50.000 0.00 0.00 0.00 3.50
2008 2129 1.165270 GCGGCTGATACAACACCTTT 58.835 50.000 0.00 0.00 0.00 3.11
2009 2130 1.130561 GCGGCTGATACAACACCTTTC 59.869 52.381 0.00 0.00 0.00 2.62
2010 2131 1.393539 CGGCTGATACAACACCTTTCG 59.606 52.381 0.00 0.00 0.00 3.46
2011 2132 1.737793 GGCTGATACAACACCTTTCGG 59.262 52.381 0.00 0.00 0.00 4.30
2012 2133 1.130561 GCTGATACAACACCTTTCGGC 59.869 52.381 0.00 0.00 0.00 5.54
2013 2134 2.422597 CTGATACAACACCTTTCGGCA 58.577 47.619 0.00 0.00 0.00 5.69
2014 2135 2.147958 TGATACAACACCTTTCGGCAC 58.852 47.619 0.00 0.00 0.00 5.01
2015 2136 2.147958 GATACAACACCTTTCGGCACA 58.852 47.619 0.00 0.00 0.00 4.57
2016 2137 1.301423 TACAACACCTTTCGGCACAC 58.699 50.000 0.00 0.00 0.00 3.82
2017 2138 0.678366 ACAACACCTTTCGGCACACA 60.678 50.000 0.00 0.00 0.00 3.72
2018 2139 0.029300 CAACACCTTTCGGCACACAG 59.971 55.000 0.00 0.00 0.00 3.66
2019 2140 1.101049 AACACCTTTCGGCACACAGG 61.101 55.000 0.00 0.00 0.00 4.00
2020 2141 1.227823 CACCTTTCGGCACACAGGA 60.228 57.895 0.00 0.00 0.00 3.86
2021 2142 1.227853 ACCTTTCGGCACACAGGAC 60.228 57.895 0.00 0.00 0.00 3.85
2022 2143 1.227823 CCTTTCGGCACACAGGACA 60.228 57.895 0.00 0.00 0.00 4.02
2023 2144 1.507141 CCTTTCGGCACACAGGACAC 61.507 60.000 0.00 0.00 0.00 3.67
2024 2145 0.813610 CTTTCGGCACACAGGACACA 60.814 55.000 0.00 0.00 0.00 3.72
2025 2146 1.092921 TTTCGGCACACAGGACACAC 61.093 55.000 0.00 0.00 0.00 3.82
2026 2147 2.203001 CGGCACACAGGACACACA 60.203 61.111 0.00 0.00 0.00 3.72
2027 2148 2.534019 CGGCACACAGGACACACAC 61.534 63.158 0.00 0.00 0.00 3.82
2028 2149 2.186826 GGCACACAGGACACACACC 61.187 63.158 0.00 0.00 0.00 4.16
2029 2150 1.451207 GCACACAGGACACACACCA 60.451 57.895 0.00 0.00 0.00 4.17
2030 2151 1.714899 GCACACAGGACACACACCAC 61.715 60.000 0.00 0.00 0.00 4.16
2031 2152 1.153449 ACACAGGACACACACCACG 60.153 57.895 0.00 0.00 0.00 4.94
2032 2153 1.142965 CACAGGACACACACCACGA 59.857 57.895 0.00 0.00 0.00 4.35
2033 2154 1.143183 ACAGGACACACACCACGAC 59.857 57.895 0.00 0.00 0.00 4.34
2034 2155 1.327690 ACAGGACACACACCACGACT 61.328 55.000 0.00 0.00 0.00 4.18
2035 2156 0.671796 CAGGACACACACCACGACTA 59.328 55.000 0.00 0.00 0.00 2.59
2036 2157 0.672342 AGGACACACACCACGACTAC 59.328 55.000 0.00 0.00 0.00 2.73
2037 2158 0.386476 GGACACACACCACGACTACA 59.614 55.000 0.00 0.00 0.00 2.74
2038 2159 1.202440 GGACACACACCACGACTACAA 60.202 52.381 0.00 0.00 0.00 2.41
2039 2160 1.856597 GACACACACCACGACTACAAC 59.143 52.381 0.00 0.00 0.00 3.32
2040 2161 0.850217 CACACACCACGACTACAACG 59.150 55.000 0.00 0.00 0.00 4.10
2041 2162 0.740149 ACACACCACGACTACAACGA 59.260 50.000 0.00 0.00 34.70 3.85
2042 2163 1.126079 CACACCACGACTACAACGAC 58.874 55.000 0.00 0.00 34.70 4.34
2043 2164 1.027357 ACACCACGACTACAACGACT 58.973 50.000 0.00 0.00 34.70 4.18
2065 2186 1.629043 ACTCGCCTAGTTGAACCTCA 58.371 50.000 0.00 0.00 33.35 3.86
2085 2206 3.291611 CCACAATGGCAAGGAGGC 58.708 61.111 0.00 0.00 44.50 4.70
2113 2234 2.125106 GATCAAGGGCCGCGTCTT 60.125 61.111 4.92 2.88 0.00 3.01
2123 2244 2.544359 CGCGTCTTGACCAACACG 59.456 61.111 0.00 6.25 36.12 4.49
2149 2270 2.172717 ACCTAGAAGCACAACACCAACT 59.827 45.455 0.00 0.00 0.00 3.16
2158 2279 3.253188 GCACAACACCAACTACATCACAT 59.747 43.478 0.00 0.00 0.00 3.21
2243 2364 1.780309 TGGTTCCCAAGAAGGTGTCAT 59.220 47.619 0.00 0.00 34.66 3.06
2244 2365 2.224769 TGGTTCCCAAGAAGGTGTCATC 60.225 50.000 0.00 0.00 34.66 2.92
2245 2366 2.437413 GTTCCCAAGAAGGTGTCATCC 58.563 52.381 0.00 0.00 34.66 3.51
2246 2367 1.741028 TCCCAAGAAGGTGTCATCCA 58.259 50.000 0.00 0.00 34.66 3.41
2247 2368 2.061848 TCCCAAGAAGGTGTCATCCAA 58.938 47.619 0.00 0.00 34.66 3.53
2248 2369 2.040278 TCCCAAGAAGGTGTCATCCAAG 59.960 50.000 0.00 0.00 34.66 3.61
2249 2370 2.440409 CCAAGAAGGTGTCATCCAAGG 58.560 52.381 0.00 0.00 0.00 3.61
2250 2371 2.440409 CAAGAAGGTGTCATCCAAGGG 58.560 52.381 0.00 0.00 0.00 3.95
2256 2377 1.559682 GGTGTCATCCAAGGGAAGCTA 59.440 52.381 0.00 0.00 34.34 3.32
2260 2381 2.237392 GTCATCCAAGGGAAGCTAGTGT 59.763 50.000 0.00 0.00 34.34 3.55
2271 2392 2.762535 AGCTAGTGTTGGCGTACATT 57.237 45.000 0.00 0.00 35.69 2.71
2272 2393 3.880047 AGCTAGTGTTGGCGTACATTA 57.120 42.857 0.00 0.00 35.69 1.90
2273 2394 4.402056 AGCTAGTGTTGGCGTACATTAT 57.598 40.909 0.00 0.00 35.69 1.28
2314 2435 2.034532 CAGCAGCCACCATCACCA 59.965 61.111 0.00 0.00 0.00 4.17
2377 2499 0.890683 CCACCTCCAGCAACAATTCC 59.109 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.586042 GCAGAAGAGCGAGCGAGAG 60.586 63.158 0.00 0.00 0.00 3.20
35 36 1.987704 GAGCAGAAGAGCGAGCGAGA 61.988 60.000 0.00 0.00 40.15 4.04
36 37 1.586042 GAGCAGAAGAGCGAGCGAG 60.586 63.158 0.00 0.00 40.15 5.03
37 38 2.043405 AGAGCAGAAGAGCGAGCGA 61.043 57.895 0.00 0.00 40.15 4.93
38 39 1.873125 CAGAGCAGAAGAGCGAGCG 60.873 63.158 0.00 0.00 40.15 5.03
39 40 2.166579 GCAGAGCAGAAGAGCGAGC 61.167 63.158 0.00 0.00 40.15 5.03
40 41 0.526096 GAGCAGAGCAGAAGAGCGAG 60.526 60.000 0.00 0.00 40.15 5.03
41 42 0.964860 AGAGCAGAGCAGAAGAGCGA 60.965 55.000 0.00 0.00 40.15 4.93
42 43 0.526096 GAGAGCAGAGCAGAAGAGCG 60.526 60.000 0.00 0.00 40.15 5.03
43 44 0.179103 GGAGAGCAGAGCAGAAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
44 45 0.461135 GGGAGAGCAGAGCAGAAGAG 59.539 60.000 0.00 0.00 0.00 2.85
45 46 0.975040 GGGGAGAGCAGAGCAGAAGA 60.975 60.000 0.00 0.00 0.00 2.87
46 47 1.521616 GGGGAGAGCAGAGCAGAAG 59.478 63.158 0.00 0.00 0.00 2.85
47 48 1.992277 GGGGGAGAGCAGAGCAGAA 60.992 63.158 0.00 0.00 0.00 3.02
48 49 2.364842 GGGGGAGAGCAGAGCAGA 60.365 66.667 0.00 0.00 0.00 4.26
49 50 2.365370 AGGGGGAGAGCAGAGCAG 60.365 66.667 0.00 0.00 0.00 4.24
50 51 2.364842 GAGGGGGAGAGCAGAGCA 60.365 66.667 0.00 0.00 0.00 4.26
51 52 3.535962 CGAGGGGGAGAGCAGAGC 61.536 72.222 0.00 0.00 0.00 4.09
52 53 3.535962 GCGAGGGGGAGAGCAGAG 61.536 72.222 0.00 0.00 0.00 3.35
53 54 4.067512 AGCGAGGGGGAGAGCAGA 62.068 66.667 0.00 0.00 0.00 4.26
54 55 3.535962 GAGCGAGGGGGAGAGCAG 61.536 72.222 0.00 0.00 0.00 4.24
57 58 3.522731 CACGAGCGAGGGGGAGAG 61.523 72.222 0.00 0.00 0.00 3.20
68 69 3.488978 CAGAGCAGCAGCACGAGC 61.489 66.667 3.17 0.00 45.49 5.03
69 70 3.488978 GCAGAGCAGCAGCACGAG 61.489 66.667 3.17 0.00 45.49 4.18
70 71 3.928966 GAGCAGAGCAGCAGCACGA 62.929 63.158 3.17 0.00 45.49 4.35
71 72 3.488978 GAGCAGAGCAGCAGCACG 61.489 66.667 3.17 0.00 45.49 5.34
72 73 1.671704 AAGAGCAGAGCAGCAGCAC 60.672 57.895 3.17 0.00 45.49 4.40
73 74 1.671379 CAAGAGCAGAGCAGCAGCA 60.671 57.895 3.17 0.00 45.49 4.41
74 75 3.041627 GCAAGAGCAGAGCAGCAGC 62.042 63.158 0.00 0.00 41.58 5.25
75 76 1.363145 GAGCAAGAGCAGAGCAGCAG 61.363 60.000 0.00 0.00 45.49 4.24
76 77 1.375652 GAGCAAGAGCAGAGCAGCA 60.376 57.895 0.00 0.00 45.49 4.41
77 78 1.078988 AGAGCAAGAGCAGAGCAGC 60.079 57.895 0.00 0.00 45.49 5.25
78 79 0.802994 CGAGAGCAAGAGCAGAGCAG 60.803 60.000 0.00 0.00 45.49 4.24
79 80 1.214853 CGAGAGCAAGAGCAGAGCA 59.785 57.895 0.00 0.00 45.49 4.26
80 81 4.091548 CGAGAGCAAGAGCAGAGC 57.908 61.111 0.00 0.00 45.49 4.09
110 111 1.135094 AGCAGCCCATGTACTAGCAT 58.865 50.000 0.00 0.00 0.00 3.79
115 116 1.077930 CTGCAGCAGCCCATGTACT 60.078 57.895 10.14 0.00 41.13 2.73
116 117 3.506108 CTGCAGCAGCCCATGTAC 58.494 61.111 10.14 0.00 41.13 2.90
125 126 2.816958 CCCGTGTAGCTGCAGCAG 60.817 66.667 38.24 18.93 45.16 4.24
154 225 2.218037 TAGAGCCAGAGCAGCACGTG 62.218 60.000 12.28 12.28 43.56 4.49
155 226 1.943116 CTAGAGCCAGAGCAGCACGT 61.943 60.000 0.00 0.00 43.56 4.49
156 227 1.226916 CTAGAGCCAGAGCAGCACG 60.227 63.158 0.00 0.00 43.56 5.34
158 258 0.534412 GAACTAGAGCCAGAGCAGCA 59.466 55.000 0.00 0.00 43.56 4.41
159 259 0.527385 CGAACTAGAGCCAGAGCAGC 60.527 60.000 0.00 0.00 43.56 5.25
167 267 1.079819 TGCAGCACGAACTAGAGCC 60.080 57.895 0.00 0.00 0.00 4.70
173 273 1.004080 AGCATCTGCAGCACGAACT 60.004 52.632 9.47 0.00 45.16 3.01
175 275 2.036571 CCAGCATCTGCAGCACGAA 61.037 57.895 9.47 0.00 45.16 3.85
259 362 2.047061 AGCAGATATAACCCGGAGCAA 58.953 47.619 0.73 0.00 0.00 3.91
268 371 5.298347 GGGGAACACAGTAGCAGATATAAC 58.702 45.833 0.00 0.00 0.00 1.89
270 373 3.572682 CGGGGAACACAGTAGCAGATATA 59.427 47.826 0.00 0.00 0.00 0.86
271 374 2.365617 CGGGGAACACAGTAGCAGATAT 59.634 50.000 0.00 0.00 0.00 1.63
311 414 6.315642 CACTAGTAGTAGAGAAACGGTGATCA 59.684 42.308 11.68 0.00 0.00 2.92
318 421 4.565962 TCGAGCACTAGTAGTAGAGAAACG 59.434 45.833 11.68 9.62 0.00 3.60
379 482 2.080693 ACTGTTGAAACTGAACGCACA 58.919 42.857 7.02 0.00 0.00 4.57
478 583 6.811253 ATTTACATCAGCGAAAAACACCTA 57.189 33.333 0.00 0.00 0.00 3.08
553 658 9.565090 CATGAATCTCAAGTGGGATTCTAATAA 57.435 33.333 26.46 12.37 44.56 1.40
576 681 7.664082 AAAGAAGTACAAGACAGACATCATG 57.336 36.000 0.00 0.00 0.00 3.07
596 701 2.094894 CGTAAGACGTCGAGGCTAAAGA 59.905 50.000 10.46 0.00 37.06 2.52
673 782 0.739561 GGAATCTGTAGACGGCGTCT 59.260 55.000 39.98 39.98 45.54 4.18
729 838 3.921119 TGGACGCTAAAGAAGTTACGA 57.079 42.857 0.00 0.00 0.00 3.43
732 841 3.071312 TGGGTTGGACGCTAAAGAAGTTA 59.929 43.478 0.00 0.00 31.67 2.24
741 850 2.016604 GCATCATTGGGTTGGACGCTA 61.017 52.381 0.00 0.00 31.67 4.26
746 855 1.341285 CCTCAGCATCATTGGGTTGGA 60.341 52.381 0.00 0.00 0.00 3.53
809 918 6.486056 TGGGCCACATAGTTTGTCTAATAAA 58.514 36.000 0.00 0.00 36.00 1.40
847 956 8.869897 CATTGTGAGATTGGAATTGAAAGATTG 58.130 33.333 0.00 0.00 0.00 2.67
849 958 8.130671 ACATTGTGAGATTGGAATTGAAAGAT 57.869 30.769 0.00 0.00 0.00 2.40
999 1109 4.383335 GGGTTTACTGTGATTCGTCCCATA 60.383 45.833 0.00 0.00 33.33 2.74
1156 1267 3.527775 CTAGGCCCTCCGAGCATGC 62.528 68.421 10.51 10.51 37.47 4.06
1363 1474 4.598807 TCCCACCATATATGCTGAGACAAT 59.401 41.667 7.24 0.00 0.00 2.71
1376 1487 6.210584 ACAATTTTTCGTCTTTCCCACCATAT 59.789 34.615 0.00 0.00 0.00 1.78
1416 1533 5.401531 AGAAATTTGATGTGCATTCTGCT 57.598 34.783 0.00 0.00 45.31 4.24
1581 1700 3.635373 TCTCTTAATACCGCCTCATCGTT 59.365 43.478 0.00 0.00 0.00 3.85
1588 1707 5.353394 TTTGTCATCTCTTAATACCGCCT 57.647 39.130 0.00 0.00 0.00 5.52
1598 1719 7.121315 GCAATAAACCTACCTTTGTCATCTCTT 59.879 37.037 0.00 0.00 0.00 2.85
1682 1803 4.096984 GCCAGTGATAGACCAAATTTGAGG 59.903 45.833 19.86 6.38 0.00 3.86
1890 2011 3.170991 AGCTAATCTACCGGGCTCATA 57.829 47.619 6.32 0.00 0.00 2.15
1918 2039 4.884744 TGAAAAGAAAATCCGAGGTCACAA 59.115 37.500 0.00 0.00 0.00 3.33
1950 2071 2.359981 ATTGATGCACCTCTCCATGG 57.640 50.000 4.97 4.97 0.00 3.66
2005 2126 0.813610 TGTGTCCTGTGTGCCGAAAG 60.814 55.000 0.00 0.00 0.00 2.62
2006 2127 1.092921 GTGTGTCCTGTGTGCCGAAA 61.093 55.000 0.00 0.00 0.00 3.46
2007 2128 1.522806 GTGTGTCCTGTGTGCCGAA 60.523 57.895 0.00 0.00 0.00 4.30
2008 2129 2.108157 GTGTGTCCTGTGTGCCGA 59.892 61.111 0.00 0.00 0.00 5.54
2009 2130 2.203001 TGTGTGTCCTGTGTGCCG 60.203 61.111 0.00 0.00 0.00 5.69
2010 2131 2.186826 GGTGTGTGTCCTGTGTGCC 61.187 63.158 0.00 0.00 0.00 5.01
2011 2132 1.451207 TGGTGTGTGTCCTGTGTGC 60.451 57.895 0.00 0.00 0.00 4.57
2012 2133 1.428370 CGTGGTGTGTGTCCTGTGTG 61.428 60.000 0.00 0.00 0.00 3.82
2013 2134 1.153449 CGTGGTGTGTGTCCTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
2014 2135 1.142965 TCGTGGTGTGTGTCCTGTG 59.857 57.895 0.00 0.00 0.00 3.66
2015 2136 1.143183 GTCGTGGTGTGTGTCCTGT 59.857 57.895 0.00 0.00 0.00 4.00
2016 2137 0.671796 TAGTCGTGGTGTGTGTCCTG 59.328 55.000 0.00 0.00 0.00 3.86
2017 2138 0.672342 GTAGTCGTGGTGTGTGTCCT 59.328 55.000 0.00 0.00 0.00 3.85
2018 2139 0.386476 TGTAGTCGTGGTGTGTGTCC 59.614 55.000 0.00 0.00 0.00 4.02
2019 2140 1.856597 GTTGTAGTCGTGGTGTGTGTC 59.143 52.381 0.00 0.00 0.00 3.67
2020 2141 1.799917 CGTTGTAGTCGTGGTGTGTGT 60.800 52.381 0.00 0.00 0.00 3.72
2021 2142 0.850217 CGTTGTAGTCGTGGTGTGTG 59.150 55.000 0.00 0.00 0.00 3.82
2022 2143 0.740149 TCGTTGTAGTCGTGGTGTGT 59.260 50.000 0.00 0.00 0.00 3.72
2023 2144 1.126079 GTCGTTGTAGTCGTGGTGTG 58.874 55.000 0.00 0.00 0.00 3.82
2024 2145 1.002033 GAGTCGTTGTAGTCGTGGTGT 60.002 52.381 0.00 0.00 0.00 4.16
2025 2146 1.002142 TGAGTCGTTGTAGTCGTGGTG 60.002 52.381 0.00 0.00 0.00 4.17
2026 2147 1.311859 TGAGTCGTTGTAGTCGTGGT 58.688 50.000 0.00 0.00 0.00 4.16
2027 2148 2.049228 GTTGAGTCGTTGTAGTCGTGG 58.951 52.381 0.00 0.00 0.00 4.94
2028 2149 2.971915 GAGTTGAGTCGTTGTAGTCGTG 59.028 50.000 0.00 0.00 0.00 4.35
2029 2150 2.349249 CGAGTTGAGTCGTTGTAGTCGT 60.349 50.000 0.19 0.00 35.14 4.34
2030 2151 2.231693 CGAGTTGAGTCGTTGTAGTCG 58.768 52.381 0.19 0.00 35.14 4.18
2031 2152 1.977412 GCGAGTTGAGTCGTTGTAGTC 59.023 52.381 9.67 0.00 42.17 2.59
2032 2153 1.335689 GGCGAGTTGAGTCGTTGTAGT 60.336 52.381 9.67 0.00 42.17 2.73
2033 2154 1.068472 AGGCGAGTTGAGTCGTTGTAG 60.068 52.381 9.67 0.00 42.17 2.74
2034 2155 0.956633 AGGCGAGTTGAGTCGTTGTA 59.043 50.000 9.67 0.00 42.17 2.41
2035 2156 0.956633 TAGGCGAGTTGAGTCGTTGT 59.043 50.000 9.67 0.00 42.17 3.32
2036 2157 1.068472 ACTAGGCGAGTTGAGTCGTTG 60.068 52.381 9.67 1.73 42.17 4.10
2037 2158 1.245732 ACTAGGCGAGTTGAGTCGTT 58.754 50.000 9.67 2.36 42.17 3.85
2038 2159 2.944075 ACTAGGCGAGTTGAGTCGT 58.056 52.632 9.67 0.00 42.17 4.34
2057 2178 1.619654 CCATTGTGGCTTGAGGTTCA 58.380 50.000 0.00 0.00 0.00 3.18
2085 2206 2.354259 GCCCTTGATCTGTGAGTCTTG 58.646 52.381 0.00 0.00 0.00 3.02
2113 2234 2.960384 TCTAGGTTTCTCGTGTTGGTCA 59.040 45.455 0.00 0.00 0.00 4.02
2123 2244 3.498777 GGTGTTGTGCTTCTAGGTTTCTC 59.501 47.826 0.00 0.00 0.00 2.87
2149 2270 3.780902 CGTTGACCTAGCATGTGATGTA 58.219 45.455 0.00 0.00 0.00 2.29
2158 2279 0.243907 GAGAGTGCGTTGACCTAGCA 59.756 55.000 0.00 0.00 38.71 3.49
2230 2351 2.040278 TCCCTTGGATGACACCTTCTTG 59.960 50.000 0.00 0.00 0.00 3.02
2243 2364 1.351017 CCAACACTAGCTTCCCTTGGA 59.649 52.381 0.00 0.00 31.49 3.53
2244 2365 1.826385 CCAACACTAGCTTCCCTTGG 58.174 55.000 0.00 0.00 0.00 3.61
2245 2366 1.168714 GCCAACACTAGCTTCCCTTG 58.831 55.000 0.00 0.00 0.00 3.61
2246 2367 0.321653 CGCCAACACTAGCTTCCCTT 60.322 55.000 0.00 0.00 0.00 3.95
2247 2368 1.296715 CGCCAACACTAGCTTCCCT 59.703 57.895 0.00 0.00 0.00 4.20
2248 2369 0.248289 TACGCCAACACTAGCTTCCC 59.752 55.000 0.00 0.00 0.00 3.97
2249 2370 1.337447 TGTACGCCAACACTAGCTTCC 60.337 52.381 0.00 0.00 0.00 3.46
2250 2371 2.074547 TGTACGCCAACACTAGCTTC 57.925 50.000 0.00 0.00 0.00 3.86
2256 2377 2.095213 CGCAATAATGTACGCCAACACT 59.905 45.455 0.00 0.00 30.75 3.55
2260 2381 3.907927 GCGCAATAATGTACGCCAA 57.092 47.368 0.30 0.00 45.35 4.52
2271 2392 1.379309 GGGTTCTTGGGGCGCAATA 60.379 57.895 17.78 7.90 0.00 1.90
2272 2393 2.679996 GGGTTCTTGGGGCGCAAT 60.680 61.111 17.78 0.00 0.00 3.56
2273 2394 3.521765 ATGGGTTCTTGGGGCGCAA 62.522 57.895 16.55 16.55 0.00 4.85


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

AutoCloner maintained by Alex Coulton.