Multiple sequence alignment - TraesCS3A01G271700

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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 TraesCS3A01G271700 chr3A 100.000 3052 0 0 1 3052 500980026 500976975 0.000000e+00 5637.0
1 TraesCS3A01G271700 chr3A 82.110 218 33 6 1229 1444 544969639 544969852 6.720000e-42 182.0
2 TraesCS3A01G271700 chr3D 88.883 1808 96 41 305 2104 376170817 376169107 0.000000e+00 2128.0
3 TraesCS3A01G271700 chr3D 91.734 871 44 13 2103 2957 376166156 376165298 0.000000e+00 1184.0
4 TraesCS3A01G271700 chr3D 86.335 161 19 3 1229 1389 406772721 406772564 4.050000e-39 172.0
5 TraesCS3A01G271700 chr3D 95.918 98 4 0 2955 3052 376165252 376165155 3.150000e-35 159.0
6 TraesCS3A01G271700 chr3D 84.404 109 17 0 73 181 376171059 376170951 1.160000e-19 108.0
7 TraesCS3A01G271700 chr3B 89.669 1481 69 37 1501 2957 490599851 490598431 0.000000e+00 1810.0
8 TraesCS3A01G271700 chr3B 94.582 646 8 5 876 1515 490600498 490599874 0.000000e+00 974.0
9 TraesCS3A01G271700 chr3B 83.647 532 42 21 194 714 490601488 490600991 2.770000e-125 459.0
10 TraesCS3A01G271700 chr3B 86.957 161 18 3 1229 1389 532667399 532667242 8.700000e-41 178.0
11 TraesCS3A01G271700 chr7B 90.000 130 13 0 1229 1358 712841459 712841588 5.230000e-38 169.0
12 TraesCS3A01G271700 chr5B 89.231 130 14 0 1229 1358 488559796 488559925 2.430000e-36 163.0
13 TraesCS3A01G271700 chr2B 82.682 179 29 2 3 181 763335741 763335565 1.130000e-34 158.0
14 TraesCS3A01G271700 chr2B 81.707 82 12 3 26 107 25689738 25689660 7.060000e-07 65.8
15 TraesCS3A01G271700 chr1D 82.258 186 25 7 1204 1389 426652242 426652419 1.470000e-33 154.0
16 TraesCS3A01G271700 chr1D 83.168 101 17 0 122 222 398942836 398942736 3.240000e-15 93.5
17 TraesCS3A01G271700 chr1A 82.258 186 25 7 1204 1389 521738967 521739144 1.470000e-33 154.0
18 TraesCS3A01G271700 chr1A 77.830 212 41 5 2 213 495650426 495650221 3.190000e-25 126.0
19 TraesCS3A01G271700 chr2A 81.421 183 30 4 2 183 11046711 11046890 2.450000e-31 147.0
20 TraesCS3A01G271700 chr2A 96.774 31 1 0 26 56 16480041 16480011 5.000000e-03 52.8
21 TraesCS3A01G271700 chr7A 82.143 168 29 1 2 169 29014177 29014011 3.170000e-30 143.0
22 TraesCS3A01G271700 chr7D 78.736 174 36 1 2 175 109561570 109561398 6.910000e-22 115.0
23 TraesCS3A01G271700 chr6B 80.420 143 27 1 14 156 12973040 12973181 1.160000e-19 108.0


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 TraesCS3A01G271700 chr3A 500976975 500980026 3051 True 5637.00 5637 100.000000 1 3052 1 chr3A.!!$R1 3051
1 TraesCS3A01G271700 chr3D 376165155 376171059 5904 True 894.75 2128 90.234750 73 3052 4 chr3D.!!$R2 2979
2 TraesCS3A01G271700 chr3B 490598431 490601488 3057 True 1081.00 1810 89.299333 194 2957 3 chr3B.!!$R2 2763

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
940 1340 0.031817 AAAGCAAGGGGGATGGGATG 60.032 55.000 0.0 0.0 0.00 3.51 F
1601 2046 1.073199 CCGTCCACCTTTTGGCTCT 59.927 57.895 0.0 0.0 46.47 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2369 0.259938 ATTGAATGGTCCCTCCCTGC 59.740 55.000 0.0 0.0 34.77 4.85 R
3012 6491 1.066143 AGTACCTGATGCTGGAAACCG 60.066 52.381 0.0 0.0 0.00 4.44 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
19 20 0.663688 TCGCCTCGAGTCTCATTAGC 59.336 55.000 12.31 3.81 0.00 3.09
20 21 0.318275 CGCCTCGAGTCTCATTAGCC 60.318 60.000 12.31 0.00 0.00 3.93
21 22 0.318275 GCCTCGAGTCTCATTAGCCG 60.318 60.000 12.31 0.00 0.00 5.52
22 23 0.312416 CCTCGAGTCTCATTAGCCGG 59.688 60.000 12.31 0.00 0.00 6.13
23 24 1.025812 CTCGAGTCTCATTAGCCGGT 58.974 55.000 3.62 0.00 0.00 5.28
24 25 0.738975 TCGAGTCTCATTAGCCGGTG 59.261 55.000 1.90 0.00 0.00 4.94
25 26 0.872021 CGAGTCTCATTAGCCGGTGC 60.872 60.000 1.90 0.00 37.95 5.01
26 27 0.872021 GAGTCTCATTAGCCGGTGCG 60.872 60.000 1.90 0.00 44.33 5.34
27 28 1.153628 GTCTCATTAGCCGGTGCGT 60.154 57.895 1.90 0.00 44.33 5.24
28 29 1.153647 TCTCATTAGCCGGTGCGTG 60.154 57.895 1.90 0.00 44.33 5.34
29 30 1.447838 CTCATTAGCCGGTGCGTGT 60.448 57.895 1.90 0.00 44.33 4.49
30 31 1.421410 CTCATTAGCCGGTGCGTGTC 61.421 60.000 1.90 0.00 44.33 3.67
31 32 1.739929 CATTAGCCGGTGCGTGTCA 60.740 57.895 1.90 0.00 44.33 3.58
32 33 1.740296 ATTAGCCGGTGCGTGTCAC 60.740 57.895 1.90 0.00 44.33 3.67
39 40 4.361253 GTGCGTGTCACATGTCCT 57.639 55.556 3.42 0.00 44.98 3.85
40 41 3.507597 GTGCGTGTCACATGTCCTA 57.492 52.632 3.42 0.00 44.98 2.94
41 42 1.068474 GTGCGTGTCACATGTCCTAC 58.932 55.000 3.42 0.00 44.98 3.18
42 43 0.966179 TGCGTGTCACATGTCCTACT 59.034 50.000 3.42 0.00 0.00 2.57
43 44 1.067846 TGCGTGTCACATGTCCTACTC 60.068 52.381 3.42 0.00 0.00 2.59
44 45 1.202582 GCGTGTCACATGTCCTACTCT 59.797 52.381 3.42 0.00 0.00 3.24
45 46 2.422479 GCGTGTCACATGTCCTACTCTA 59.578 50.000 3.42 0.00 0.00 2.43
46 47 3.731264 GCGTGTCACATGTCCTACTCTAC 60.731 52.174 3.42 0.00 0.00 2.59
47 48 3.181499 CGTGTCACATGTCCTACTCTACC 60.181 52.174 3.42 0.00 0.00 3.18
48 49 4.017808 GTGTCACATGTCCTACTCTACCT 58.982 47.826 0.00 0.00 0.00 3.08
49 50 4.096682 GTGTCACATGTCCTACTCTACCTC 59.903 50.000 0.00 0.00 0.00 3.85
50 51 3.312973 GTCACATGTCCTACTCTACCTCG 59.687 52.174 0.00 0.00 0.00 4.63
51 52 2.033550 CACATGTCCTACTCTACCTCGC 59.966 54.545 0.00 0.00 0.00 5.03
52 53 1.609555 CATGTCCTACTCTACCTCGCC 59.390 57.143 0.00 0.00 0.00 5.54
53 54 0.622136 TGTCCTACTCTACCTCGCCA 59.378 55.000 0.00 0.00 0.00 5.69
54 55 1.310904 GTCCTACTCTACCTCGCCAG 58.689 60.000 0.00 0.00 0.00 4.85
55 56 0.465824 TCCTACTCTACCTCGCCAGC 60.466 60.000 0.00 0.00 0.00 4.85
56 57 0.752009 CCTACTCTACCTCGCCAGCA 60.752 60.000 0.00 0.00 0.00 4.41
57 58 1.103803 CTACTCTACCTCGCCAGCAA 58.896 55.000 0.00 0.00 0.00 3.91
58 59 0.815734 TACTCTACCTCGCCAGCAAC 59.184 55.000 0.00 0.00 0.00 4.17
59 60 1.153549 CTCTACCTCGCCAGCAACC 60.154 63.158 0.00 0.00 0.00 3.77
60 61 2.509336 CTACCTCGCCAGCAACCG 60.509 66.667 0.00 0.00 0.00 4.44
61 62 4.077184 TACCTCGCCAGCAACCGG 62.077 66.667 0.00 0.00 0.00 5.28
67 68 3.670377 GCCAGCAACCGGACCAAC 61.670 66.667 9.46 0.00 0.00 3.77
68 69 2.203280 CCAGCAACCGGACCAACA 60.203 61.111 9.46 0.00 0.00 3.33
69 70 2.551912 CCAGCAACCGGACCAACAC 61.552 63.158 9.46 0.00 0.00 3.32
70 71 1.525995 CAGCAACCGGACCAACACT 60.526 57.895 9.46 0.00 0.00 3.55
71 72 1.101049 CAGCAACCGGACCAACACTT 61.101 55.000 9.46 0.00 0.00 3.16
108 109 3.788766 GCCGCACATGGACACGAC 61.789 66.667 0.00 0.00 0.00 4.34
109 110 3.478394 CCGCACATGGACACGACG 61.478 66.667 0.00 0.00 0.00 5.12
113 114 1.584495 CACATGGACACGACGGAGA 59.416 57.895 0.00 0.00 0.00 3.71
127 128 2.026879 GAGATGGACGAGCTCCGC 59.973 66.667 8.47 0.00 43.03 5.54
146 147 4.152759 TCCGCTTAAATTAGGTTTCACGTG 59.847 41.667 9.94 9.94 0.00 4.49
147 148 4.399978 CGCTTAAATTAGGTTTCACGTGG 58.600 43.478 17.00 0.00 0.00 4.94
150 151 5.621329 GCTTAAATTAGGTTTCACGTGGCAT 60.621 40.000 17.00 6.88 0.00 4.40
151 152 3.848272 AATTAGGTTTCACGTGGCATG 57.152 42.857 17.00 4.87 0.00 4.06
162 163 4.508662 TCACGTGGCATGTAATTGTATGA 58.491 39.130 17.00 0.00 0.00 2.15
170 171 7.436080 GTGGCATGTAATTGTATGAATTTGAGG 59.564 37.037 7.65 0.00 0.00 3.86
183 184 9.774742 GTATGAATTTGAGGTTTCATAGTTGAC 57.225 33.333 5.79 0.00 42.46 3.18
186 187 5.666969 TTTGAGGTTTCATAGTTGACGTG 57.333 39.130 0.00 0.00 32.27 4.49
188 189 4.699637 TGAGGTTTCATAGTTGACGTGTT 58.300 39.130 0.00 0.00 0.00 3.32
190 191 4.699637 AGGTTTCATAGTTGACGTGTTCA 58.300 39.130 0.00 0.00 0.00 3.18
191 192 5.120399 AGGTTTCATAGTTGACGTGTTCAA 58.880 37.500 0.00 0.00 42.26 2.69
261 290 0.608130 TGCAGACATACAGAAGGCGT 59.392 50.000 0.00 0.00 0.00 5.68
267 296 5.696724 GCAGACATACAGAAGGCGTATTTAT 59.303 40.000 0.00 0.00 0.00 1.40
279 309 4.039488 AGGCGTATTTATCATGTCCGGTTA 59.961 41.667 0.00 0.00 0.00 2.85
348 379 2.586635 ACGAAACGTCAGGCGCAA 60.587 55.556 10.83 0.00 46.11 4.85
351 382 1.259544 CGAAACGTCAGGCGCAAAAC 61.260 55.000 10.83 2.04 46.11 2.43
356 388 1.272781 CGTCAGGCGCAAAACAAAAA 58.727 45.000 10.83 0.00 0.00 1.94
383 415 1.228894 TGGCTCAACGACTCCCTCT 60.229 57.895 0.00 0.00 0.00 3.69
413 446 1.444933 AGGGGATCAACCAAGACACA 58.555 50.000 8.23 0.00 41.20 3.72
414 447 1.780309 AGGGGATCAACCAAGACACAA 59.220 47.619 8.23 0.00 41.20 3.33
513 546 9.798885 GTCAAACGACAAGAAGAATATATATGC 57.201 33.333 0.00 0.00 33.34 3.14
533 567 4.428209 TGCTAGAGAAAAAGAGATCGCTG 58.572 43.478 0.00 0.00 0.00 5.18
627 661 2.361104 GCCAAATCCTGGGCGTCA 60.361 61.111 0.00 0.00 46.54 4.35
628 662 2.700773 GCCAAATCCTGGGCGTCAC 61.701 63.158 0.00 0.00 46.54 3.67
676 720 5.357878 TGGATTTTTCTAGTGACCATGCATC 59.642 40.000 0.00 0.00 0.00 3.91
714 758 4.040461 TCATATCCTCCCGTCCAAGATTTC 59.960 45.833 0.00 0.00 0.00 2.17
716 760 3.110293 TCCTCCCGTCCAAGATTTCTA 57.890 47.619 0.00 0.00 0.00 2.10
717 761 2.764572 TCCTCCCGTCCAAGATTTCTAC 59.235 50.000 0.00 0.00 0.00 2.59
718 762 2.766828 CCTCCCGTCCAAGATTTCTACT 59.233 50.000 0.00 0.00 0.00 2.57
723 767 4.441634 CCCGTCCAAGATTTCTACTACTGG 60.442 50.000 0.00 0.00 0.00 4.00
827 881 7.176690 GGTAGAAAATATCCAGAGAGAGAGAGG 59.823 44.444 0.00 0.00 0.00 3.69
829 883 4.402616 AATATCCAGAGAGAGAGAGGGG 57.597 50.000 0.00 0.00 0.00 4.79
940 1340 0.031817 AAAGCAAGGGGGATGGGATG 60.032 55.000 0.00 0.00 0.00 3.51
941 1341 1.953100 AAGCAAGGGGGATGGGATGG 61.953 60.000 0.00 0.00 0.00 3.51
942 1342 2.937650 CAAGGGGGATGGGATGGG 59.062 66.667 0.00 0.00 0.00 4.00
1012 1413 2.040043 CCTCCATCTCCCCTGCCT 60.040 66.667 0.00 0.00 0.00 4.75
1013 1414 2.146061 CCTCCATCTCCCCTGCCTC 61.146 68.421 0.00 0.00 0.00 4.70
1015 1416 2.040043 CCATCTCCCCTGCCTCCT 60.040 66.667 0.00 0.00 0.00 3.69
1016 1417 2.146061 CCATCTCCCCTGCCTCCTC 61.146 68.421 0.00 0.00 0.00 3.71
1601 2046 1.073199 CCGTCCACCTTTTGGCTCT 59.927 57.895 0.00 0.00 46.47 4.09
1741 2189 3.944087 ACGAATGGAAGAGAGGAAAAGG 58.056 45.455 0.00 0.00 0.00 3.11
1742 2190 3.583086 ACGAATGGAAGAGAGGAAAAGGA 59.417 43.478 0.00 0.00 0.00 3.36
1743 2191 4.041691 ACGAATGGAAGAGAGGAAAAGGAA 59.958 41.667 0.00 0.00 0.00 3.36
1744 2192 5.003804 CGAATGGAAGAGAGGAAAAGGAAA 58.996 41.667 0.00 0.00 0.00 3.13
1745 2193 5.106515 CGAATGGAAGAGAGGAAAAGGAAAC 60.107 44.000 0.00 0.00 0.00 2.78
1782 2230 9.953825 CGTACTTAGTTGAAATGAATGTACTTC 57.046 33.333 0.00 0.00 0.00 3.01
1820 2268 5.402398 GTGGCAATGATGATGATGATGATG 58.598 41.667 0.00 0.00 0.00 3.07
1821 2269 5.183140 GTGGCAATGATGATGATGATGATGA 59.817 40.000 0.00 0.00 0.00 2.92
1822 2270 5.951747 TGGCAATGATGATGATGATGATGAT 59.048 36.000 0.00 0.00 0.00 2.45
1823 2271 6.127647 TGGCAATGATGATGATGATGATGATG 60.128 38.462 0.00 0.00 0.00 3.07
1824 2272 6.095440 GGCAATGATGATGATGATGATGATGA 59.905 38.462 0.00 0.00 0.00 2.92
1825 2273 7.201857 GGCAATGATGATGATGATGATGATGAT 60.202 37.037 0.00 0.00 0.00 2.45
1826 2274 7.646922 GCAATGATGATGATGATGATGATGATG 59.353 37.037 0.00 0.00 0.00 3.07
1827 2275 8.896744 CAATGATGATGATGATGATGATGATGA 58.103 33.333 0.00 0.00 0.00 2.92
1828 2276 9.638176 AATGATGATGATGATGATGATGATGAT 57.362 29.630 0.00 0.00 0.00 2.45
1829 2277 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
1830 2278 8.267183 TGATGATGATGATGATGATGATGATGA 58.733 33.333 0.00 0.00 0.00 2.92
1831 2279 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
1846 2294 9.590451 GATGATGATGATAATCTTCTCTCTTCC 57.410 37.037 7.33 0.00 0.00 3.46
1857 2305 1.630878 TCTCTCTTCCTCCCTTTTGCC 59.369 52.381 0.00 0.00 0.00 4.52
1864 2312 4.986708 TCCCTTTTGCCGCCCCAC 62.987 66.667 0.00 0.00 0.00 4.61
1905 2363 3.873361 TCAGTTATTAGATGCAGTGCAGC 59.127 43.478 25.49 25.49 45.98 5.25
1972 2430 3.925453 TGACACACACACACACACT 57.075 47.368 0.00 0.00 0.00 3.55
1973 2431 1.720805 TGACACACACACACACACTC 58.279 50.000 0.00 0.00 0.00 3.51
1974 2432 0.645355 GACACACACACACACACTCG 59.355 55.000 0.00 0.00 0.00 4.18
2075 2533 2.564062 ACCACTTGAAGAATGCCAATGG 59.436 45.455 0.00 0.00 0.00 3.16
2086 2544 4.798288 CCAATGGCATCAACGCAG 57.202 55.556 0.00 0.00 0.00 5.18
2089 2547 2.053865 AATGGCATCAACGCAGGGG 61.054 57.895 0.00 0.00 0.00 4.79
2105 2565 2.930935 GGGGGCAGAGGAATCTACA 58.069 57.895 0.00 0.00 0.00 2.74
2106 2566 0.470341 GGGGGCAGAGGAATCTACAC 59.530 60.000 0.00 0.00 0.00 2.90
2108 2568 1.204146 GGGCAGAGGAATCTACACCA 58.796 55.000 0.00 0.00 0.00 4.17
2110 2570 2.224402 GGGCAGAGGAATCTACACCATC 60.224 54.545 0.00 0.00 0.00 3.51
2112 2572 3.898123 GGCAGAGGAATCTACACCATCTA 59.102 47.826 0.00 0.00 0.00 1.98
2113 2573 4.021544 GGCAGAGGAATCTACACCATCTAG 60.022 50.000 0.00 0.00 0.00 2.43
2116 2576 4.832266 AGAGGAATCTACACCATCTAGCAG 59.168 45.833 0.00 0.00 0.00 4.24
2121 5537 3.300388 TCTACACCATCTAGCAGGAAGG 58.700 50.000 7.22 0.00 0.00 3.46
2148 5567 2.036604 GGCATCTACTACCTGAGAAGGC 59.963 54.545 0.00 0.00 0.00 4.35
2150 5569 3.243704 GCATCTACTACCTGAGAAGGCTG 60.244 52.174 0.00 0.00 0.00 4.85
2225 5644 3.798878 CGTTAGTGATGGCATAGTGTCAG 59.201 47.826 0.00 0.00 34.38 3.51
2249 5668 8.058915 CAGTTTCTTTACTTGTTCTTCTTCTCG 58.941 37.037 0.00 0.00 0.00 4.04
2283 5702 3.005791 AGGCATCGTATTCATGTCATCGA 59.994 43.478 0.00 0.00 0.00 3.59
2297 5716 5.873179 TGTCATCGATAAACAAAAGTCCC 57.127 39.130 9.65 0.00 0.00 4.46
2328 5747 3.633525 GGTGCATTATCATCACATGGTGT 59.366 43.478 0.00 0.00 34.79 4.16
2356 5778 4.688511 TTAAACTCACCACACAACACAC 57.311 40.909 0.00 0.00 0.00 3.82
2375 5797 3.414700 CAGACCGCGTTCCAGTGC 61.415 66.667 4.92 0.00 0.00 4.40
2396 5818 2.029110 CGGCATTTGAACAGGGTCAATT 60.029 45.455 0.00 0.00 37.36 2.32
2461 5883 3.508012 CCCGAGCTAGTATATTGACAGCT 59.492 47.826 0.00 0.00 44.95 4.24
2465 5887 2.911723 GCTAGTATATTGACAGCTCGCG 59.088 50.000 0.00 0.00 0.00 5.87
2523 5945 6.292168 CGACCTCCTTGCGTAAATAATGTTAG 60.292 42.308 0.00 0.00 0.00 2.34
2544 5966 0.543277 TGCCAGCTCAACCATAGGAG 59.457 55.000 0.00 0.00 0.00 3.69
2604 6026 4.420168 ACACGGAACTTGAATTTGTGTTG 58.580 39.130 0.00 0.00 35.74 3.33
2612 6034 3.451141 TGAATTTGTGTTGGCCAACTC 57.549 42.857 40.40 36.92 41.67 3.01
2615 6037 0.032615 TTTGTGTTGGCCAACTCCCT 60.033 50.000 40.40 0.00 41.67 4.20
2626 6048 2.552743 GCCAACTCCCTTTTGTACAGTC 59.447 50.000 0.00 0.00 0.00 3.51
2627 6049 3.815809 CCAACTCCCTTTTGTACAGTCA 58.184 45.455 0.00 0.00 0.00 3.41
2628 6050 4.204012 CCAACTCCCTTTTGTACAGTCAA 58.796 43.478 0.00 0.00 0.00 3.18
2654 6076 1.892209 AAACTTTCTCCGCGGAATGT 58.108 45.000 30.53 19.79 35.88 2.71
2657 6079 0.447801 CTTTCTCCGCGGAATGTTGG 59.552 55.000 30.53 16.53 0.00 3.77
2658 6080 0.250553 TTTCTCCGCGGAATGTTGGT 60.251 50.000 30.53 0.00 0.00 3.67
2702 6132 0.104487 CCTCAGCGTGCATCTCATCT 59.896 55.000 0.00 0.00 0.00 2.90
2703 6133 1.339291 CCTCAGCGTGCATCTCATCTA 59.661 52.381 0.00 0.00 0.00 1.98
2704 6134 2.392821 CTCAGCGTGCATCTCATCTAC 58.607 52.381 0.00 0.00 0.00 2.59
2705 6135 1.126890 CAGCGTGCATCTCATCTACG 58.873 55.000 0.00 0.00 37.77 3.51
2746 6176 3.967987 GGCCCCAGATTAGACTCTTCTAA 59.032 47.826 0.00 0.00 46.26 2.10
2749 6179 5.818336 GCCCCAGATTAGACTCTTCTAAAAC 59.182 44.000 0.00 0.00 45.52 2.43
2751 6181 6.157123 CCCCAGATTAGACTCTTCTAAAACCT 59.843 42.308 0.00 0.00 45.52 3.50
2820 6250 9.956720 AAACAGAATCAAGTTACTTCATTTCAG 57.043 29.630 0.00 0.29 0.00 3.02
2876 6306 3.317430 GCTTAAAGGGAAGGATGAGCATG 59.683 47.826 0.00 0.00 0.00 4.06
2986 6465 8.749354 ACAACAACCTTCTCTTTGTTTTTCTAT 58.251 29.630 0.00 0.00 42.04 1.98
2987 6466 9.586435 CAACAACCTTCTCTTTGTTTTTCTATT 57.414 29.630 0.00 0.00 42.04 1.73
3012 6491 3.303229 CCAAAACAGTGTTCAAACTTCGC 59.697 43.478 9.40 0.00 0.00 4.70
3021 6500 0.941542 TCAAACTTCGCGGTTTCCAG 59.058 50.000 6.13 0.00 37.32 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.318275 GGCTAATGAGACTCGAGGCG 60.318 60.000 18.41 0.13 0.00 5.52
2 3 0.318275 CGGCTAATGAGACTCGAGGC 60.318 60.000 18.41 15.26 0.00 4.70
3 4 0.312416 CCGGCTAATGAGACTCGAGG 59.688 60.000 18.41 0.00 0.00 4.63
4 5 1.025812 ACCGGCTAATGAGACTCGAG 58.974 55.000 11.84 11.84 0.00 4.04
5 6 0.738975 CACCGGCTAATGAGACTCGA 59.261 55.000 0.00 0.00 0.00 4.04
6 7 0.872021 GCACCGGCTAATGAGACTCG 60.872 60.000 0.00 0.00 36.96 4.18
7 8 0.872021 CGCACCGGCTAATGAGACTC 60.872 60.000 0.00 0.00 38.10 3.36
8 9 1.141881 CGCACCGGCTAATGAGACT 59.858 57.895 0.00 0.00 38.10 3.24
9 10 1.153628 ACGCACCGGCTAATGAGAC 60.154 57.895 0.00 0.00 38.10 3.36
10 11 1.153647 CACGCACCGGCTAATGAGA 60.154 57.895 0.00 0.00 38.10 3.27
11 12 1.421410 GACACGCACCGGCTAATGAG 61.421 60.000 0.00 0.00 38.10 2.90
12 13 1.447140 GACACGCACCGGCTAATGA 60.447 57.895 0.00 0.00 38.10 2.57
13 14 1.739929 TGACACGCACCGGCTAATG 60.740 57.895 0.00 0.00 38.10 1.90
14 15 1.740296 GTGACACGCACCGGCTAAT 60.740 57.895 0.00 0.00 41.78 1.73
15 16 2.356553 GTGACACGCACCGGCTAA 60.357 61.111 0.00 0.00 41.78 3.09
23 24 0.966179 AGTAGGACATGTGACACGCA 59.034 50.000 1.15 0.00 0.00 5.24
24 25 1.202582 AGAGTAGGACATGTGACACGC 59.797 52.381 1.15 0.00 0.00 5.34
25 26 3.181499 GGTAGAGTAGGACATGTGACACG 60.181 52.174 1.15 0.00 0.00 4.49
26 27 4.017808 AGGTAGAGTAGGACATGTGACAC 58.982 47.826 1.15 0.00 0.00 3.67
27 28 4.270834 GAGGTAGAGTAGGACATGTGACA 58.729 47.826 1.15 0.00 0.00 3.58
28 29 3.312973 CGAGGTAGAGTAGGACATGTGAC 59.687 52.174 1.15 0.00 0.00 3.67
29 30 3.542648 CGAGGTAGAGTAGGACATGTGA 58.457 50.000 1.15 0.00 0.00 3.58
30 31 2.033550 GCGAGGTAGAGTAGGACATGTG 59.966 54.545 1.15 0.00 0.00 3.21
31 32 2.299521 GCGAGGTAGAGTAGGACATGT 58.700 52.381 0.00 0.00 0.00 3.21
32 33 1.609555 GGCGAGGTAGAGTAGGACATG 59.390 57.143 0.00 0.00 0.00 3.21
33 34 1.214673 TGGCGAGGTAGAGTAGGACAT 59.785 52.381 0.00 0.00 0.00 3.06
34 35 0.622136 TGGCGAGGTAGAGTAGGACA 59.378 55.000 0.00 0.00 0.00 4.02
35 36 1.310904 CTGGCGAGGTAGAGTAGGAC 58.689 60.000 0.00 0.00 0.00 3.85
36 37 0.465824 GCTGGCGAGGTAGAGTAGGA 60.466 60.000 0.00 0.00 0.00 2.94
37 38 0.752009 TGCTGGCGAGGTAGAGTAGG 60.752 60.000 0.00 0.00 0.00 3.18
38 39 1.103803 TTGCTGGCGAGGTAGAGTAG 58.896 55.000 0.00 0.00 0.00 2.57
39 40 0.815734 GTTGCTGGCGAGGTAGAGTA 59.184 55.000 0.00 0.00 0.00 2.59
40 41 1.592223 GTTGCTGGCGAGGTAGAGT 59.408 57.895 0.00 0.00 0.00 3.24
41 42 1.153549 GGTTGCTGGCGAGGTAGAG 60.154 63.158 0.00 0.00 0.00 2.43
42 43 2.978824 GGTTGCTGGCGAGGTAGA 59.021 61.111 0.00 0.00 0.00 2.59
43 44 2.509336 CGGTTGCTGGCGAGGTAG 60.509 66.667 0.00 0.00 0.00 3.18
44 45 4.077184 CCGGTTGCTGGCGAGGTA 62.077 66.667 0.00 0.00 0.00 3.08
50 51 3.670377 GTTGGTCCGGTTGCTGGC 61.670 66.667 0.00 0.00 0.00 4.85
51 52 2.203280 TGTTGGTCCGGTTGCTGG 60.203 61.111 0.00 0.00 0.00 4.85
52 53 1.101049 AAGTGTTGGTCCGGTTGCTG 61.101 55.000 0.00 0.00 0.00 4.41
53 54 0.818040 GAAGTGTTGGTCCGGTTGCT 60.818 55.000 0.00 0.00 0.00 3.91
54 55 1.652563 GAAGTGTTGGTCCGGTTGC 59.347 57.895 0.00 0.00 0.00 4.17
55 56 2.327228 GGAAGTGTTGGTCCGGTTG 58.673 57.895 0.00 0.00 0.00 3.77
56 57 4.892002 GGAAGTGTTGGTCCGGTT 57.108 55.556 0.00 0.00 0.00 4.44
60 61 1.003718 CCCTCGGAAGTGTTGGTCC 60.004 63.158 0.00 0.00 0.00 4.46
61 62 1.003718 CCCCTCGGAAGTGTTGGTC 60.004 63.158 0.00 0.00 0.00 4.02
62 63 3.157680 CCCCTCGGAAGTGTTGGT 58.842 61.111 0.00 0.00 0.00 3.67
63 64 2.359975 GCCCCTCGGAAGTGTTGG 60.360 66.667 0.00 0.00 0.00 3.77
64 65 2.742372 CGCCCCTCGGAAGTGTTG 60.742 66.667 0.00 0.00 33.78 3.33
65 66 4.699522 GCGCCCCTCGGAAGTGTT 62.700 66.667 0.00 0.00 38.94 3.32
94 95 2.048597 TCCGTCGTGTCCATGTGC 60.049 61.111 0.00 0.00 0.00 4.57
95 96 0.173481 ATCTCCGTCGTGTCCATGTG 59.827 55.000 0.00 0.00 0.00 3.21
100 101 1.139095 GTCCATCTCCGTCGTGTCC 59.861 63.158 0.00 0.00 0.00 4.02
102 103 1.645704 CTCGTCCATCTCCGTCGTGT 61.646 60.000 0.00 0.00 0.00 4.49
108 109 2.725008 GGAGCTCGTCCATCTCCG 59.275 66.667 7.83 0.00 46.10 4.63
127 128 5.365403 TGCCACGTGAAACCTAATTTAAG 57.635 39.130 19.30 0.00 0.00 1.85
146 147 7.491682 ACCTCAAATTCATACAATTACATGCC 58.508 34.615 0.00 0.00 0.00 4.40
147 148 8.931385 AACCTCAAATTCATACAATTACATGC 57.069 30.769 0.00 0.00 0.00 4.06
162 163 6.262273 ACACGTCAACTATGAAACCTCAAATT 59.738 34.615 0.00 0.00 37.30 1.82
181 182 7.908193 AATAATTTTCACAGTTGAACACGTC 57.092 32.000 0.00 0.00 41.64 4.34
228 249 0.039798 TCTGCAACACGTCTACGGAC 60.040 55.000 7.50 0.00 44.95 4.79
232 253 3.571571 TGTATGTCTGCAACACGTCTAC 58.428 45.455 4.23 4.54 41.75 2.59
241 262 1.001974 ACGCCTTCTGTATGTCTGCAA 59.998 47.619 0.00 0.00 0.00 4.08
261 290 8.758829 AGCATCTATAACCGGACATGATAAATA 58.241 33.333 9.46 0.00 0.00 1.40
267 296 6.398095 CAATAGCATCTATAACCGGACATGA 58.602 40.000 9.46 0.00 0.00 3.07
279 309 6.239402 GGATTTGTTTGGGCAATAGCATCTAT 60.239 38.462 0.00 0.00 44.61 1.98
356 388 2.564947 AGTCGTTGAGCCAGATTCTCTT 59.435 45.455 0.00 0.00 0.00 2.85
367 399 0.968393 AGGAGAGGGAGTCGTTGAGC 60.968 60.000 0.00 0.00 0.00 4.26
368 400 0.814457 CAGGAGAGGGAGTCGTTGAG 59.186 60.000 0.00 0.00 0.00 3.02
383 415 0.616395 TGATCCCCTACGCAACAGGA 60.616 55.000 0.00 0.00 34.91 3.86
425 458 4.261155 CGGACTCAACTGATGAAGCAAAAA 60.261 41.667 0.00 0.00 37.67 1.94
426 459 3.250762 CGGACTCAACTGATGAAGCAAAA 59.749 43.478 0.00 0.00 37.67 2.44
427 460 2.807967 CGGACTCAACTGATGAAGCAAA 59.192 45.455 0.00 0.00 37.67 3.68
428 461 2.224281 ACGGACTCAACTGATGAAGCAA 60.224 45.455 0.00 0.00 37.67 3.91
429 462 1.344438 ACGGACTCAACTGATGAAGCA 59.656 47.619 0.00 0.00 37.67 3.91
512 545 4.677584 TCAGCGATCTCTTTTTCTCTAGC 58.322 43.478 0.00 0.00 0.00 3.42
513 546 6.811170 ACTTTCAGCGATCTCTTTTTCTCTAG 59.189 38.462 0.00 0.00 0.00 2.43
518 551 5.597813 TGACTTTCAGCGATCTCTTTTTC 57.402 39.130 0.00 0.00 0.00 2.29
530 564 1.126846 CCGATCGTGTTGACTTTCAGC 59.873 52.381 15.09 0.00 0.00 4.26
533 567 3.725010 GCATTCCGATCGTGTTGACTTTC 60.725 47.826 15.09 0.00 0.00 2.62
625 659 1.020861 GTGCGGCATCATGTGAGTGA 61.021 55.000 5.72 0.00 0.00 3.41
626 660 1.022982 AGTGCGGCATCATGTGAGTG 61.023 55.000 5.72 0.00 0.00 3.51
627 661 0.321919 AAGTGCGGCATCATGTGAGT 60.322 50.000 5.72 0.00 0.00 3.41
628 662 0.376152 GAAGTGCGGCATCATGTGAG 59.624 55.000 5.72 0.00 0.00 3.51
676 720 2.549064 TATGAATGGAGTCATGGGCG 57.451 50.000 0.00 0.00 38.69 6.13
803 857 7.237982 CCCTCTCTCTCTCTGGATATTTTCTA 58.762 42.308 0.00 0.00 0.00 2.10
843 897 3.505773 ATGCATGGCCCTCTCCCC 61.506 66.667 0.00 0.00 0.00 4.81
980 1381 1.603739 GAGGTGGGTGGGAAAGTGC 60.604 63.158 0.00 0.00 0.00 4.40
989 1390 2.378634 GGGGAGATGGAGGTGGGTG 61.379 68.421 0.00 0.00 0.00 4.61
1012 1413 2.040442 TTCGCCATGGAGGGAGGA 59.960 61.111 18.40 0.00 38.09 3.71
1013 1414 2.190578 GTTCGCCATGGAGGGAGG 59.809 66.667 18.40 0.00 38.09 4.30
1015 1416 2.285368 AGGTTCGCCATGGAGGGA 60.285 61.111 18.40 6.18 40.60 4.20
1016 1417 2.190578 GAGGTTCGCCATGGAGGG 59.809 66.667 18.40 3.45 40.60 4.30
1173 1574 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
1174 1575 2.015726 GGGAGGAGGAGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1175 1576 2.612251 GGGAGGAGGAGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1176 1577 2.612251 GGGGAGGAGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
1177 1578 3.036959 GGGGGAGGAGGAGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
1459 1866 4.742201 TCAACGCTCTCCGCTGCC 62.742 66.667 0.00 0.00 41.76 4.85
1695 2143 2.895372 GCCGTGGCCGTATCCTTG 60.895 66.667 0.00 0.00 34.56 3.61
1721 2169 4.207891 TCCTTTTCCTCTCTTCCATTCG 57.792 45.455 0.00 0.00 0.00 3.34
1759 2207 9.574516 AAGGAAGTACATTCATTTCAACTAAGT 57.425 29.630 0.00 0.00 38.74 2.24
1782 2230 1.672356 CCACGGCTCACAAGGAAGG 60.672 63.158 0.00 0.00 0.00 3.46
1820 2268 9.590451 GGAAGAGAGAAGATTATCATCATCATC 57.410 37.037 0.28 1.25 30.69 2.92
1821 2269 9.328975 AGGAAGAGAGAAGATTATCATCATCAT 57.671 33.333 0.28 0.00 30.69 2.45
1822 2270 8.724113 AGGAAGAGAGAAGATTATCATCATCA 57.276 34.615 0.28 0.00 30.69 3.07
1823 2271 8.253113 GGAGGAAGAGAGAAGATTATCATCATC 58.747 40.741 0.28 0.00 0.00 2.92
1824 2272 7.180766 GGGAGGAAGAGAGAAGATTATCATCAT 59.819 40.741 0.28 0.00 0.00 2.45
1825 2273 6.496565 GGGAGGAAGAGAGAAGATTATCATCA 59.503 42.308 0.28 0.00 0.00 3.07
1826 2274 6.725834 AGGGAGGAAGAGAGAAGATTATCATC 59.274 42.308 0.00 0.00 0.00 2.92
1827 2275 6.633062 AGGGAGGAAGAGAGAAGATTATCAT 58.367 40.000 0.00 0.00 0.00 2.45
1828 2276 6.036926 AGGGAGGAAGAGAGAAGATTATCA 57.963 41.667 0.00 0.00 0.00 2.15
1829 2277 6.994421 AAGGGAGGAAGAGAGAAGATTATC 57.006 41.667 0.00 0.00 0.00 1.75
1830 2278 7.572814 CAAAAGGGAGGAAGAGAGAAGATTAT 58.427 38.462 0.00 0.00 0.00 1.28
1831 2279 6.577239 GCAAAAGGGAGGAAGAGAGAAGATTA 60.577 42.308 0.00 0.00 0.00 1.75
1832 2280 5.806079 GCAAAAGGGAGGAAGAGAGAAGATT 60.806 44.000 0.00 0.00 0.00 2.40
1833 2281 4.324176 GCAAAAGGGAGGAAGAGAGAAGAT 60.324 45.833 0.00 0.00 0.00 2.40
1834 2282 3.008485 GCAAAAGGGAGGAAGAGAGAAGA 59.992 47.826 0.00 0.00 0.00 2.87
1835 2283 3.342719 GCAAAAGGGAGGAAGAGAGAAG 58.657 50.000 0.00 0.00 0.00 2.85
1838 2286 1.677217 CGGCAAAAGGGAGGAAGAGAG 60.677 57.143 0.00 0.00 0.00 3.20
1840 2288 1.308783 GCGGCAAAAGGGAGGAAGAG 61.309 60.000 0.00 0.00 0.00 2.85
1846 2294 4.676951 TGGGGCGGCAAAAGGGAG 62.677 66.667 12.47 0.00 0.00 4.30
1864 2312 1.396301 GAATGCTGCAGAGGAGAAACG 59.604 52.381 20.43 0.00 0.00 3.60
1909 2367 4.115199 AATGGTCCCTCCCTGCGC 62.115 66.667 0.00 0.00 34.77 6.09
1910 2368 2.190578 GAATGGTCCCTCCCTGCG 59.809 66.667 0.00 0.00 34.77 5.18
1911 2369 0.259938 ATTGAATGGTCCCTCCCTGC 59.740 55.000 0.00 0.00 34.77 4.85
1912 2370 2.834638 AATTGAATGGTCCCTCCCTG 57.165 50.000 0.00 0.00 34.77 4.45
1913 2371 2.654385 TGAAATTGAATGGTCCCTCCCT 59.346 45.455 0.00 0.00 34.77 4.20
1914 2372 3.100207 TGAAATTGAATGGTCCCTCCC 57.900 47.619 0.00 0.00 34.77 4.30
1966 2424 3.005897 ACTCAACTCAATAGCGAGTGTGT 59.994 43.478 0.00 0.00 45.56 3.72
1968 2426 3.944055 ACTCAACTCAATAGCGAGTGT 57.056 42.857 0.00 0.00 45.56 3.55
1969 2427 3.181526 GCAACTCAACTCAATAGCGAGTG 60.182 47.826 0.00 0.00 45.56 3.51
1971 2429 3.061831 CAGCAACTCAACTCAATAGCGAG 59.938 47.826 0.00 0.00 39.05 5.03
1972 2430 2.995939 CAGCAACTCAACTCAATAGCGA 59.004 45.455 0.00 0.00 0.00 4.93
1973 2431 2.738846 ACAGCAACTCAACTCAATAGCG 59.261 45.455 0.00 0.00 0.00 4.26
1974 2432 5.171476 TCTACAGCAACTCAACTCAATAGC 58.829 41.667 0.00 0.00 0.00 2.97
2010 2468 1.132262 CCAACCACGTATGCATTCCAC 59.868 52.381 3.54 0.00 0.00 4.02
2089 2547 1.204146 TGGTGTAGATTCCTCTGCCC 58.796 55.000 0.00 0.00 33.54 5.36
2105 2565 2.122768 CCTTCCTTCCTGCTAGATGGT 58.877 52.381 0.00 0.00 33.75 3.55
2106 2566 2.368221 CTCCTTCCTTCCTGCTAGATGG 59.632 54.545 0.00 0.00 33.40 3.51
2108 2568 2.688477 CCTCCTTCCTTCCTGCTAGAT 58.312 52.381 0.00 0.00 0.00 1.98
2110 2570 0.467804 GCCTCCTTCCTTCCTGCTAG 59.532 60.000 0.00 0.00 0.00 3.42
2112 2572 0.918310 ATGCCTCCTTCCTTCCTGCT 60.918 55.000 0.00 0.00 0.00 4.24
2113 2573 0.465278 GATGCCTCCTTCCTTCCTGC 60.465 60.000 0.00 0.00 0.00 4.85
2116 2576 2.403561 AGTAGATGCCTCCTTCCTTCC 58.596 52.381 0.00 0.00 0.00 3.46
2121 5537 3.567397 TCAGGTAGTAGATGCCTCCTTC 58.433 50.000 0.00 0.00 43.12 3.46
2148 5567 3.119029 CCTGTTTGTTGGGATAATGCCAG 60.119 47.826 0.00 0.00 39.66 4.85
2150 5569 2.418609 GCCTGTTTGTTGGGATAATGCC 60.419 50.000 0.00 0.00 0.00 4.40
2225 5644 7.907194 ACGAGAAGAAGAACAAGTAAAGAAAC 58.093 34.615 0.00 0.00 0.00 2.78
2283 5702 3.236047 GTGGTGGGGGACTTTTGTTTAT 58.764 45.455 0.00 0.00 0.00 1.40
2375 5797 0.958091 TTGACCCTGTTCAAATGCCG 59.042 50.000 0.00 0.00 32.42 5.69
2523 5945 1.141657 TCCTATGGTTGAGCTGGCATC 59.858 52.381 0.00 0.00 0.00 3.91
2544 5966 2.951475 TTTGGTGCACTGACCCCGAC 62.951 60.000 17.98 0.00 34.79 4.79
2604 6026 1.886542 CTGTACAAAAGGGAGTTGGCC 59.113 52.381 0.00 0.00 0.00 5.36
2612 6034 5.576447 ACTTTGTTGACTGTACAAAAGGG 57.424 39.130 16.07 0.00 42.87 3.95
2615 6037 9.968870 AAAGTTTACTTTGTTGACTGTACAAAA 57.031 25.926 7.05 0.00 43.87 2.44
2626 6048 3.966218 CGCGGAGAAAGTTTACTTTGTTG 59.034 43.478 12.27 6.89 45.37 3.33
2627 6049 3.002965 CCGCGGAGAAAGTTTACTTTGTT 59.997 43.478 24.07 1.37 45.37 2.83
2628 6050 2.546789 CCGCGGAGAAAGTTTACTTTGT 59.453 45.455 24.07 8.52 45.37 2.83
2702 6132 1.731433 GAGATGCCGCCAGGTACGTA 61.731 60.000 0.00 0.00 40.50 3.57
2703 6133 3.075005 AGATGCCGCCAGGTACGT 61.075 61.111 0.00 0.00 40.50 3.57
2704 6134 2.279517 GAGATGCCGCCAGGTACG 60.280 66.667 0.00 0.00 40.50 3.67
2705 6135 2.109181 GGAGATGCCGCCAGGTAC 59.891 66.667 0.00 0.00 40.50 3.34
2727 6157 7.189079 AGGTTTTAGAAGAGTCTAATCTGGG 57.811 40.000 4.83 0.00 44.12 4.45
2777 6207 3.625853 TGTTTAATGCCGATCCCATTCA 58.374 40.909 8.94 1.33 34.87 2.57
2820 6250 2.476185 GGCATGCATGAGTTTACACGTC 60.476 50.000 30.64 7.39 0.00 4.34
2986 6465 5.652994 AGTTTGAACACTGTTTTGGCTAA 57.347 34.783 0.00 0.00 0.00 3.09
2987 6466 5.646606 GAAGTTTGAACACTGTTTTGGCTA 58.353 37.500 0.00 0.00 0.00 3.93
3012 6491 1.066143 AGTACCTGATGCTGGAAACCG 60.066 52.381 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.