Multiple sequence alignment - TraesCS2D01G568900

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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 TraesCS2D01G568900 chr2D 100.000 3023 0 0 1 3023 636794397 636791375 0.000000e+00 5583.0
1 TraesCS2D01G568900 chr2D 96.418 698 21 3 2328 3023 413349516 413350211 0.000000e+00 1147.0
2 TraesCS2D01G568900 chr2D 84.777 1143 167 6 4 1141 637340272 637339132 0.000000e+00 1140.0
3 TraesCS2D01G568900 chr2D 75.867 663 138 17 1376 2029 636735570 636734921 4.860000e-83 318.0
4 TraesCS2D01G568900 chr2D 77.551 245 48 6 1376 1619 637330860 637330622 1.130000e-29 141.0
5 TraesCS2D01G568900 chr2B 93.108 2191 112 12 1 2167 794671144 794668969 0.000000e+00 3173.0
6 TraesCS2D01G568900 chr2B 96.423 699 22 2 2327 3023 733080676 733079979 0.000000e+00 1149.0
7 TraesCS2D01G568900 chr2B 81.025 1249 220 11 2 1244 794629466 794628229 0.000000e+00 977.0
8 TraesCS2D01G568900 chr2B 80.969 1156 196 21 5 1148 794564446 794563303 0.000000e+00 894.0
9 TraesCS2D01G568900 chr2B 80.919 1132 182 19 2 1125 794485299 794486404 0.000000e+00 863.0
10 TraesCS2D01G568900 chr2B 74.655 580 105 22 1641 2185 794426209 794425637 5.070000e-53 219.0
11 TraesCS2D01G568900 chr2B 74.549 554 99 21 1655 2172 794595404 794595951 1.420000e-48 204.0
12 TraesCS2D01G568900 chr2B 77.551 245 33 6 1952 2174 794795331 794795087 8.800000e-26 128.0
13 TraesCS2D01G568900 chr4D 96.275 698 24 1 2328 3023 450708126 450708823 0.000000e+00 1144.0
14 TraesCS2D01G568900 chr4D 87.963 108 11 2 2187 2293 89536110 89536004 3.160000e-25 126.0
15 TraesCS2D01G568900 chr6D 96.143 700 24 2 2326 3023 218127523 218126825 0.000000e+00 1140.0
16 TraesCS2D01G568900 chr6D 89.720 107 9 2 2184 2289 140221649 140221754 5.260000e-28 135.0
17 TraesCS2D01G568900 chr6D 89.091 110 10 2 2184 2293 434181678 434181785 5.260000e-28 135.0
18 TraesCS2D01G568900 chr7D 96.132 698 25 1 2328 3023 634567470 634568167 0.000000e+00 1138.0
19 TraesCS2D01G568900 chr7D 95.869 702 27 1 2324 3023 231336278 231336979 0.000000e+00 1134.0
20 TraesCS2D01G568900 chr5D 96.132 698 25 1 2328 3023 555438640 555439337 0.000000e+00 1138.0
21 TraesCS2D01G568900 chr5D 96.121 696 23 3 2331 3023 267658898 267658204 0.000000e+00 1133.0
22 TraesCS2D01G568900 chr5D 81.757 148 24 2 2042 2186 45478373 45478226 1.470000e-23 121.0
23 TraesCS2D01G568900 chr5D 88.172 93 9 2 2191 2282 448446180 448446089 3.190000e-20 110.0
24 TraesCS2D01G568900 chr5D 86.517 89 11 1 2205 2293 556379028 556378941 2.480000e-16 97.1
25 TraesCS2D01G568900 chr3B 95.634 710 26 4 2317 3023 165351505 165352212 0.000000e+00 1134.0
26 TraesCS2D01G568900 chr7B 80.465 1377 242 19 2 1363 746156255 746154891 0.000000e+00 1027.0
27 TraesCS2D01G568900 chr7B 76.533 848 150 20 1372 2178 746154720 746153881 4.660000e-113 418.0
28 TraesCS2D01G568900 chr6B 80.306 1371 249 17 2 1363 130302903 130304261 0.000000e+00 1016.0
29 TraesCS2D01G568900 chr6B 74.257 505 93 12 1651 2123 130304744 130305243 8.610000e-41 178.0
30 TraesCS2D01G568900 chr2A 80.499 1323 211 32 2 1313 762892028 762893314 0.000000e+00 970.0
31 TraesCS2D01G568900 chr2A 83.102 935 155 1 2 936 762730193 762731124 0.000000e+00 848.0
32 TraesCS2D01G568900 chr2A 74.656 655 142 19 1376 2020 762773373 762774013 4.970000e-68 268.0
33 TraesCS2D01G568900 chr2A 75.089 562 99 23 1651 2178 762738873 762739427 1.090000e-54 224.0
34 TraesCS2D01G568900 chr2A 84.211 133 18 2 2039 2168 762761865 762761997 3.160000e-25 126.0
35 TraesCS2D01G568900 chr1B 78.803 1387 256 29 2 1362 626092188 626093562 0.000000e+00 898.0
36 TraesCS2D01G568900 chr1D 80.469 1152 212 12 2 1148 455754035 455755178 0.000000e+00 869.0
37 TraesCS2D01G568900 chrUn 75.066 381 77 14 1659 2029 359504873 359504501 8.670000e-36 161.0
38 TraesCS2D01G568900 chr4B 87.500 112 10 4 2184 2293 518140209 518140318 3.160000e-25 126.0
39 TraesCS2D01G568900 chr4B 85.217 115 14 3 2181 2293 1866176 1866063 6.850000e-22 115.0
40 TraesCS2D01G568900 chr6A 84.545 110 17 0 2032 2141 13970025 13970134 3.190000e-20 110.0
41 TraesCS2D01G568900 chr5B 91.358 81 5 2 2212 2291 54826495 54826416 3.190000e-20 110.0
42 TraesCS2D01G568900 chr1A 86.000 100 10 2 2187 2282 337681687 337681786 1.480000e-18 104.0


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 TraesCS2D01G568900 chr2D 636791375 636794397 3022 True 5583.0 5583 100.0000 1 3023 1 chr2D.!!$R2 3022
1 TraesCS2D01G568900 chr2D 413349516 413350211 695 False 1147.0 1147 96.4180 2328 3023 1 chr2D.!!$F1 695
2 TraesCS2D01G568900 chr2D 637339132 637340272 1140 True 1140.0 1140 84.7770 4 1141 1 chr2D.!!$R4 1137
3 TraesCS2D01G568900 chr2D 636734921 636735570 649 True 318.0 318 75.8670 1376 2029 1 chr2D.!!$R1 653
4 TraesCS2D01G568900 chr2B 794668969 794671144 2175 True 3173.0 3173 93.1080 1 2167 1 chr2B.!!$R5 2166
5 TraesCS2D01G568900 chr2B 733079979 733080676 697 True 1149.0 1149 96.4230 2327 3023 1 chr2B.!!$R1 696
6 TraesCS2D01G568900 chr2B 794628229 794629466 1237 True 977.0 977 81.0250 2 1244 1 chr2B.!!$R4 1242
7 TraesCS2D01G568900 chr2B 794563303 794564446 1143 True 894.0 894 80.9690 5 1148 1 chr2B.!!$R3 1143
8 TraesCS2D01G568900 chr2B 794485299 794486404 1105 False 863.0 863 80.9190 2 1125 1 chr2B.!!$F1 1123
9 TraesCS2D01G568900 chr2B 794425637 794426209 572 True 219.0 219 74.6550 1641 2185 1 chr2B.!!$R2 544
10 TraesCS2D01G568900 chr2B 794595404 794595951 547 False 204.0 204 74.5490 1655 2172 1 chr2B.!!$F2 517
11 TraesCS2D01G568900 chr4D 450708126 450708823 697 False 1144.0 1144 96.2750 2328 3023 1 chr4D.!!$F1 695
12 TraesCS2D01G568900 chr6D 218126825 218127523 698 True 1140.0 1140 96.1430 2326 3023 1 chr6D.!!$R1 697
13 TraesCS2D01G568900 chr7D 634567470 634568167 697 False 1138.0 1138 96.1320 2328 3023 1 chr7D.!!$F2 695
14 TraesCS2D01G568900 chr7D 231336278 231336979 701 False 1134.0 1134 95.8690 2324 3023 1 chr7D.!!$F1 699
15 TraesCS2D01G568900 chr5D 555438640 555439337 697 False 1138.0 1138 96.1320 2328 3023 1 chr5D.!!$F1 695
16 TraesCS2D01G568900 chr5D 267658204 267658898 694 True 1133.0 1133 96.1210 2331 3023 1 chr5D.!!$R2 692
17 TraesCS2D01G568900 chr3B 165351505 165352212 707 False 1134.0 1134 95.6340 2317 3023 1 chr3B.!!$F1 706
18 TraesCS2D01G568900 chr7B 746153881 746156255 2374 True 722.5 1027 78.4990 2 2178 2 chr7B.!!$R1 2176
19 TraesCS2D01G568900 chr6B 130302903 130305243 2340 False 597.0 1016 77.2815 2 2123 2 chr6B.!!$F1 2121
20 TraesCS2D01G568900 chr2A 762892028 762893314 1286 False 970.0 970 80.4990 2 1313 1 chr2A.!!$F5 1311
21 TraesCS2D01G568900 chr2A 762730193 762731124 931 False 848.0 848 83.1020 2 936 1 chr2A.!!$F1 934
22 TraesCS2D01G568900 chr2A 762773373 762774013 640 False 268.0 268 74.6560 1376 2020 1 chr2A.!!$F4 644
23 TraesCS2D01G568900 chr2A 762738873 762739427 554 False 224.0 224 75.0890 1651 2178 1 chr2A.!!$F2 527
24 TraesCS2D01G568900 chr1B 626092188 626093562 1374 False 898.0 898 78.8030 2 1362 1 chr1B.!!$F1 1360
25 TraesCS2D01G568900 chr1D 455754035 455755178 1143 False 869.0 869 80.4690 2 1148 1 chr1D.!!$F1 1146

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
384 386 1.032114 CGGAAGGCTTTGTGGATCCC 61.032 60.0 9.9 0.85 0.0 3.85 F
1184 1204 0.460311 CCAGGCACCTTAGAGTACCG 59.540 60.0 0.0 0.00 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2200 0.037303 CAAGTGATGTGAGGCCCAGT 59.963 55.0 0.0 0.0 0.0 4.00 R
2968 3254 0.107410 ACCAAAGACAACCTCGCACA 60.107 50.0 0.0 0.0 0.0 4.57 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
129 130 4.216411 TCCTAAATTGAAGGGTTCTCCG 57.784 45.455 7.15 0.00 41.52 4.63
337 339 8.919145 TGTACCCAAAAGATTACAAATTTGAGT 58.081 29.630 24.64 9.48 35.34 3.41
338 340 9.758651 GTACCCAAAAGATTACAAATTTGAGTT 57.241 29.630 24.64 8.05 35.34 3.01
352 354 5.966742 ATTTGAGTTGGTTTCCTTAGCTC 57.033 39.130 0.00 0.00 0.00 4.09
353 355 3.040147 TGAGTTGGTTTCCTTAGCTCG 57.960 47.619 0.00 0.00 0.00 5.03
384 386 1.032114 CGGAAGGCTTTGTGGATCCC 61.032 60.000 9.90 0.85 0.00 3.85
385 387 1.032114 GGAAGGCTTTGTGGATCCCG 61.032 60.000 9.90 0.00 0.00 5.14
418 420 7.549488 GTGCTACAATTCTATCTACAAGTTGGT 59.451 37.037 7.96 0.00 0.00 3.67
601 603 4.993584 GTCATCTGCACATACTCCCTAATG 59.006 45.833 0.00 0.00 0.00 1.90
639 641 5.129634 TCCAACTTGTTGAGTCTATGCAAA 58.870 37.500 14.30 0.00 37.72 3.68
949 954 8.084684 AGTTGATCAATTTAGAGAGTTTTTGGC 58.915 33.333 12.12 0.00 0.00 4.52
983 988 1.335132 TATTCTGCCGGGGGTGAGAC 61.335 60.000 2.18 0.00 0.00 3.36
1148 1165 7.624360 AGTATCTAGAAGAGTTGTCACTGAG 57.376 40.000 0.00 0.00 31.22 3.35
1182 1202 0.902531 TGCCAGGCACCTTAGAGTAC 59.097 55.000 11.22 0.00 31.71 2.73
1184 1204 0.460311 CCAGGCACCTTAGAGTACCG 59.540 60.000 0.00 0.00 0.00 4.02
1262 1297 7.537596 AGTCTCTGTATCTTGAGGATTATGG 57.462 40.000 0.00 0.00 35.98 2.74
1325 1360 6.987386 TGCCAAGCTTAAAATTGCTTACTTA 58.013 32.000 0.00 0.00 46.29 2.24
1374 1571 2.473760 ATCTCCCTCGACGTCAGCG 61.474 63.158 17.16 2.08 44.93 5.18
1438 1635 8.463930 TGAAGAACTGAAAATGGATTACAGTT 57.536 30.769 17.20 17.20 43.30 3.16
1647 1880 6.484643 GCTGTTCTCTTGCATATATTGAAGGA 59.515 38.462 0.00 0.00 0.00 3.36
1677 1910 2.999331 ACATTCCCGTCCCTTAATGTG 58.001 47.619 0.00 0.00 40.18 3.21
1736 1969 2.016318 TGGCATCCTAACGCAAGAATG 58.984 47.619 0.00 0.00 43.62 2.67
1799 2032 1.661341 CTACTGTCTCTGCCCATTGC 58.339 55.000 0.00 0.00 41.77 3.56
1857 2108 1.239968 GCCCAAGTCTCAACTGGCAG 61.240 60.000 14.16 14.16 41.84 4.85
1858 2109 0.607489 CCCAAGTCTCAACTGGCAGG 60.607 60.000 20.34 1.44 35.36 4.85
1911 2162 2.422597 CTCGGCTTAACACAATGTGGA 58.577 47.619 18.37 2.09 37.94 4.02
1929 2180 6.596309 TGTGGAGATATCTCACCATATGTC 57.404 41.667 29.33 12.49 42.97 3.06
1933 2184 4.026744 AGATATCTCACCATATGTCCCCG 58.973 47.826 0.00 0.00 0.00 5.73
1960 2215 0.618680 AGCTACTGGGCCTCACATCA 60.619 55.000 4.53 0.00 0.00 3.07
2029 2287 4.083802 GGCGACATTTGGCATAGTAATCTC 60.084 45.833 0.00 0.00 0.00 2.75
2031 2289 4.982295 CGACATTTGGCATAGTAATCTCGA 59.018 41.667 2.41 0.00 0.00 4.04
2081 2358 0.823356 GGTGGAGCAAAGGCAGTTGA 60.823 55.000 5.24 0.00 44.61 3.18
2099 2376 7.425606 GCAGTTGAGAAAATAAAGAAGGTGAA 58.574 34.615 0.00 0.00 0.00 3.18
2125 2402 8.383175 AGATATCCAACTGTCCAAACTTAAAGA 58.617 33.333 0.00 0.00 0.00 2.52
2133 2410 4.641094 TGTCCAAACTTAAAGAAAGCGGAA 59.359 37.500 0.00 0.00 38.93 4.30
2185 2466 5.388408 GTGCTTACACTAGTTACCTGTCT 57.612 43.478 0.00 0.00 43.85 3.41
2186 2467 5.162075 GTGCTTACACTAGTTACCTGTCTG 58.838 45.833 0.00 0.00 43.85 3.51
2187 2468 4.831155 TGCTTACACTAGTTACCTGTCTGT 59.169 41.667 0.00 0.00 0.00 3.41
2188 2469 5.303589 TGCTTACACTAGTTACCTGTCTGTT 59.696 40.000 0.00 0.00 0.00 3.16
2189 2470 6.183360 TGCTTACACTAGTTACCTGTCTGTTT 60.183 38.462 0.00 0.00 0.00 2.83
2190 2471 7.014518 TGCTTACACTAGTTACCTGTCTGTTTA 59.985 37.037 0.00 0.00 0.00 2.01
2191 2472 8.033626 GCTTACACTAGTTACCTGTCTGTTTAT 58.966 37.037 0.00 0.00 0.00 1.40
2192 2473 9.355215 CTTACACTAGTTACCTGTCTGTTTATG 57.645 37.037 0.00 0.00 0.00 1.90
2193 2474 7.534723 ACACTAGTTACCTGTCTGTTTATGA 57.465 36.000 0.00 0.00 0.00 2.15
2194 2475 7.603651 ACACTAGTTACCTGTCTGTTTATGAG 58.396 38.462 0.00 0.00 0.00 2.90
2195 2476 6.531948 CACTAGTTACCTGTCTGTTTATGAGC 59.468 42.308 0.00 0.00 0.00 4.26
2196 2477 4.833390 AGTTACCTGTCTGTTTATGAGCC 58.167 43.478 0.00 0.00 0.00 4.70
2197 2478 4.532521 AGTTACCTGTCTGTTTATGAGCCT 59.467 41.667 0.00 0.00 0.00 4.58
2198 2479 5.720041 AGTTACCTGTCTGTTTATGAGCCTA 59.280 40.000 0.00 0.00 0.00 3.93
2199 2480 4.473477 ACCTGTCTGTTTATGAGCCTAC 57.527 45.455 0.00 0.00 0.00 3.18
2200 2481 4.097418 ACCTGTCTGTTTATGAGCCTACT 58.903 43.478 0.00 0.00 0.00 2.57
2201 2482 4.532521 ACCTGTCTGTTTATGAGCCTACTT 59.467 41.667 0.00 0.00 0.00 2.24
2202 2483 4.872691 CCTGTCTGTTTATGAGCCTACTTG 59.127 45.833 0.00 0.00 0.00 3.16
2203 2484 4.832248 TGTCTGTTTATGAGCCTACTTGG 58.168 43.478 0.00 0.00 39.35 3.61
2204 2485 4.530553 TGTCTGTTTATGAGCCTACTTGGA 59.469 41.667 0.00 0.00 38.35 3.53
2205 2486 5.012664 TGTCTGTTTATGAGCCTACTTGGAA 59.987 40.000 0.00 0.00 38.35 3.53
2206 2487 5.351740 GTCTGTTTATGAGCCTACTTGGAAC 59.648 44.000 0.00 0.00 38.35 3.62
2207 2488 5.248477 TCTGTTTATGAGCCTACTTGGAACT 59.752 40.000 0.00 0.00 38.35 3.01
2208 2489 5.876357 TGTTTATGAGCCTACTTGGAACTT 58.124 37.500 0.00 0.00 38.35 2.66
2209 2490 7.011499 TGTTTATGAGCCTACTTGGAACTTA 57.989 36.000 0.00 0.00 38.35 2.24
2210 2491 7.630082 TGTTTATGAGCCTACTTGGAACTTAT 58.370 34.615 0.00 0.00 38.35 1.73
2211 2492 7.552687 TGTTTATGAGCCTACTTGGAACTTATG 59.447 37.037 0.00 0.00 38.35 1.90
2212 2493 5.957771 ATGAGCCTACTTGGAACTTATGA 57.042 39.130 0.00 0.00 38.35 2.15
2213 2494 5.086104 TGAGCCTACTTGGAACTTATGAC 57.914 43.478 0.00 0.00 38.35 3.06
2214 2495 4.777896 TGAGCCTACTTGGAACTTATGACT 59.222 41.667 0.00 0.00 38.35 3.41
2215 2496 5.248477 TGAGCCTACTTGGAACTTATGACTT 59.752 40.000 0.00 0.00 38.35 3.01
2216 2497 6.128138 AGCCTACTTGGAACTTATGACTTT 57.872 37.500 0.00 0.00 38.35 2.66
2217 2498 5.940470 AGCCTACTTGGAACTTATGACTTTG 59.060 40.000 0.00 0.00 38.35 2.77
2218 2499 5.938125 GCCTACTTGGAACTTATGACTTTGA 59.062 40.000 0.00 0.00 38.35 2.69
2219 2500 6.599638 GCCTACTTGGAACTTATGACTTTGAT 59.400 38.462 0.00 0.00 38.35 2.57
2220 2501 7.769044 GCCTACTTGGAACTTATGACTTTGATA 59.231 37.037 0.00 0.00 38.35 2.15
2221 2502 9.099454 CCTACTTGGAACTTATGACTTTGATAC 57.901 37.037 0.00 0.00 38.35 2.24
2222 2503 7.596749 ACTTGGAACTTATGACTTTGATACG 57.403 36.000 0.00 0.00 0.00 3.06
2223 2504 7.159372 ACTTGGAACTTATGACTTTGATACGT 58.841 34.615 0.00 0.00 0.00 3.57
2224 2505 7.660208 ACTTGGAACTTATGACTTTGATACGTT 59.340 33.333 0.00 0.00 0.00 3.99
2225 2506 7.972832 TGGAACTTATGACTTTGATACGTTT 57.027 32.000 0.00 0.00 0.00 3.60
2226 2507 8.385898 TGGAACTTATGACTTTGATACGTTTT 57.614 30.769 0.00 0.00 0.00 2.43
2227 2508 8.842280 TGGAACTTATGACTTTGATACGTTTTT 58.158 29.630 0.00 0.00 0.00 1.94
2240 2521 9.666626 TTTGATACGTTTTTAATAATATGGCCG 57.333 29.630 0.00 0.00 0.00 6.13
2241 2522 7.299586 TGATACGTTTTTAATAATATGGCCGC 58.700 34.615 0.00 0.00 0.00 6.53
2242 2523 5.502153 ACGTTTTTAATAATATGGCCGCA 57.498 34.783 0.00 0.00 0.00 5.69
2243 2524 6.079424 ACGTTTTTAATAATATGGCCGCAT 57.921 33.333 0.00 0.00 0.00 4.73
2244 2525 5.918011 ACGTTTTTAATAATATGGCCGCATG 59.082 36.000 0.00 0.00 0.00 4.06
2245 2526 5.164100 CGTTTTTAATAATATGGCCGCATGC 60.164 40.000 7.91 7.91 40.16 4.06
2246 2527 5.459536 TTTTAATAATATGGCCGCATGCA 57.540 34.783 19.57 0.00 43.89 3.96
2247 2528 5.657826 TTTAATAATATGGCCGCATGCAT 57.342 34.783 19.57 5.96 43.89 3.96
2248 2529 3.788333 AATAATATGGCCGCATGCATC 57.212 42.857 19.57 8.10 43.89 3.91
2249 2530 1.085893 TAATATGGCCGCATGCATCG 58.914 50.000 19.57 5.23 43.89 3.84
2250 2531 0.606130 AATATGGCCGCATGCATCGA 60.606 50.000 19.57 5.91 43.89 3.59
2251 2532 0.393402 ATATGGCCGCATGCATCGAT 60.393 50.000 19.57 12.90 43.89 3.59
2252 2533 0.606130 TATGGCCGCATGCATCGATT 60.606 50.000 19.57 0.00 43.89 3.34
2253 2534 2.050714 GGCCGCATGCATCGATTG 60.051 61.111 19.57 0.00 43.89 2.67
2254 2535 2.545596 GGCCGCATGCATCGATTGA 61.546 57.895 19.57 0.00 43.89 2.57
2255 2536 1.577922 GCCGCATGCATCGATTGAT 59.422 52.632 19.57 0.00 40.77 2.57
2264 2545 0.873054 CATCGATTGATGCAGAGGCC 59.127 55.000 10.05 0.00 45.06 5.19
2265 2546 0.602106 ATCGATTGATGCAGAGGCCG 60.602 55.000 0.00 0.00 40.13 6.13
2266 2547 2.249535 CGATTGATGCAGAGGCCGG 61.250 63.158 0.00 0.00 40.13 6.13
2267 2548 1.146930 GATTGATGCAGAGGCCGGA 59.853 57.895 5.05 0.00 40.13 5.14
2268 2549 0.883814 GATTGATGCAGAGGCCGGAG 60.884 60.000 5.05 0.00 40.13 4.63
2289 2570 5.397553 AGGTCACCCTCCTTTTTCTAAAA 57.602 39.130 0.00 0.00 35.62 1.52
2290 2571 5.773091 AGGTCACCCTCCTTTTTCTAAAAA 58.227 37.500 0.00 1.05 35.62 1.94
2313 2594 8.515473 AAAAACTTGTTACTTGTCTGTTGTTC 57.485 30.769 0.00 0.00 0.00 3.18
2314 2595 5.464965 ACTTGTTACTTGTCTGTTGTTCG 57.535 39.130 0.00 0.00 0.00 3.95
2315 2596 5.172934 ACTTGTTACTTGTCTGTTGTTCGA 58.827 37.500 0.00 0.00 0.00 3.71
2316 2597 5.640357 ACTTGTTACTTGTCTGTTGTTCGAA 59.360 36.000 0.00 0.00 0.00 3.71
2317 2598 6.148150 ACTTGTTACTTGTCTGTTGTTCGAAA 59.852 34.615 0.00 0.00 0.00 3.46
2318 2599 6.671614 TGTTACTTGTCTGTTGTTCGAAAT 57.328 33.333 0.00 0.00 0.00 2.17
2319 2600 7.079182 TGTTACTTGTCTGTTGTTCGAAATT 57.921 32.000 0.00 0.00 0.00 1.82
2320 2601 7.184106 TGTTACTTGTCTGTTGTTCGAAATTC 58.816 34.615 0.00 0.00 0.00 2.17
2321 2602 5.169836 ACTTGTCTGTTGTTCGAAATTCC 57.830 39.130 0.00 0.00 0.00 3.01
2322 2603 4.036380 ACTTGTCTGTTGTTCGAAATTCCC 59.964 41.667 0.00 0.00 0.00 3.97
2323 2604 3.815809 TGTCTGTTGTTCGAAATTCCCT 58.184 40.909 0.00 0.00 0.00 4.20
2324 2605 4.963373 TGTCTGTTGTTCGAAATTCCCTA 58.037 39.130 0.00 0.00 0.00 3.53
2325 2606 5.556915 TGTCTGTTGTTCGAAATTCCCTAT 58.443 37.500 0.00 0.00 0.00 2.57
2326 2607 6.703319 TGTCTGTTGTTCGAAATTCCCTATA 58.297 36.000 0.00 0.00 0.00 1.31
2327 2608 7.335627 TGTCTGTTGTTCGAAATTCCCTATAT 58.664 34.615 0.00 0.00 0.00 0.86
2328 2609 7.827236 TGTCTGTTGTTCGAAATTCCCTATATT 59.173 33.333 0.00 0.00 0.00 1.28
2329 2610 9.321562 GTCTGTTGTTCGAAATTCCCTATATTA 57.678 33.333 0.00 0.00 0.00 0.98
2333 2614 9.807386 GTTGTTCGAAATTCCCTATATTATTCG 57.193 33.333 0.00 0.00 39.43 3.34
2334 2615 9.767228 TTGTTCGAAATTCCCTATATTATTCGA 57.233 29.630 0.00 3.86 43.48 3.71
2354 2635 6.870971 TCGATAAAGGGCGCTTTTATTATT 57.129 33.333 30.56 10.15 32.42 1.40
2390 2671 6.441274 CATCAAGCGGATACAAAGCATTATT 58.559 36.000 0.00 0.00 33.95 1.40
2401 2682 9.116067 GATACAAAGCATTATTAGTAACACCCA 57.884 33.333 0.00 0.00 0.00 4.51
2649 2935 1.881973 ACTCGTTGTAGCGTAGACCAA 59.118 47.619 0.00 0.00 0.00 3.67
2776 3062 0.978667 TGCTCCCACCCGTATTAGCA 60.979 55.000 0.00 0.00 37.62 3.49
2789 3075 8.230486 CACCCGTATTAGCATTTTGAATCTATC 58.770 37.037 0.00 0.00 0.00 2.08
2792 3078 9.208022 CCGTATTAGCATTTTGAATCTATCTGA 57.792 33.333 0.00 0.00 0.00 3.27
2818 3104 2.288152 CCGTCCAACCAATGACCAAAAG 60.288 50.000 0.00 0.00 0.00 2.27
2968 3254 3.850098 CTCCCTGGCCAGTTGCGTT 62.850 63.158 30.63 0.00 42.61 4.84
3014 3300 1.978454 ACTCCCCTACGAAGATACCG 58.022 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 1.206831 GAGAGTTTTCGCGGCCAAC 59.793 57.895 6.13 7.07 0.00 3.77
138 139 1.429463 ACATGCGACCGAGAGTTTTC 58.571 50.000 0.00 0.00 0.00 2.29
337 339 3.713826 AATCCGAGCTAAGGAAACCAA 57.286 42.857 13.63 0.00 41.69 3.67
338 340 3.343617 CAAATCCGAGCTAAGGAAACCA 58.656 45.455 13.63 0.00 41.69 3.67
352 354 0.811616 CCTTCCGCTCTCCAAATCCG 60.812 60.000 0.00 0.00 0.00 4.18
353 355 1.098129 GCCTTCCGCTCTCCAAATCC 61.098 60.000 0.00 0.00 0.00 3.01
384 386 2.699954 AGAATTGTAGCACCACCTTCG 58.300 47.619 0.00 0.00 0.00 3.79
385 387 5.675538 AGATAGAATTGTAGCACCACCTTC 58.324 41.667 0.40 0.00 0.00 3.46
418 420 5.472137 GTGCCACAAGGTCTTCAAAATACTA 59.528 40.000 0.00 0.00 37.19 1.82
601 603 6.924111 ACAAGTTGGAATAATCAATGTCACC 58.076 36.000 7.96 0.00 0.00 4.02
607 609 8.641498 AGACTCAACAAGTTGGAATAATCAAT 57.359 30.769 12.54 0.00 38.74 2.57
639 641 0.739813 GGGTACGCAGCTTCGTGAAT 60.740 55.000 21.75 0.00 43.21 2.57
949 954 5.124457 CGGCAGAATATGAAAATCCCTATGG 59.876 44.000 0.00 0.00 0.00 2.74
1148 1165 0.179020 TGGCATCGATGAACCCATCC 60.179 55.000 29.20 17.74 44.87 3.51
1182 1202 2.710377 TGTTTGTTCTGGATGATCCGG 58.290 47.619 14.26 14.26 44.41 5.14
1184 1204 4.156739 GGACTTGTTTGTTCTGGATGATCC 59.843 45.833 4.05 4.05 36.96 3.36
1262 1297 4.704833 TTGGGAGCGAGGCACTGC 62.705 66.667 0.00 0.00 41.55 4.40
1325 1360 3.002791 CCAAGTCGAACACAGCATACAT 58.997 45.455 0.00 0.00 0.00 2.29
1438 1635 1.071542 TCTTCGGGTGCTGATGTTTGA 59.928 47.619 0.00 0.00 0.00 2.69
1495 1692 8.462016 GTCAATACTGCAAAAGATACCAGAATT 58.538 33.333 0.00 0.00 0.00 2.17
1596 1793 1.174783 TGCTCAACCTCCGTAGAGAC 58.825 55.000 0.00 0.00 43.39 3.36
1624 1821 8.677300 GTTTCCTTCAATATATGCAAGAGAACA 58.323 33.333 0.00 0.00 0.00 3.18
1647 1880 3.558533 GGGACGGGAATGTTCTAGTGTTT 60.559 47.826 0.00 0.00 0.00 2.83
1677 1910 3.125316 CACGACAGGATGAAACCTTTAGC 59.875 47.826 0.00 0.00 39.69 3.09
1736 1969 3.814005 TTTCCTCAATAGCGGGTAGAC 57.186 47.619 0.00 0.00 0.00 2.59
1799 2032 9.309516 CCAGATGTTTCAGATTTGGAAAATATG 57.690 33.333 0.00 0.00 36.14 1.78
1911 2162 4.026744 CGGGGACATATGGTGAGATATCT 58.973 47.826 4.47 4.47 0.00 1.98
1943 2198 1.198713 AGTGATGTGAGGCCCAGTAG 58.801 55.000 0.00 0.00 0.00 2.57
1944 2199 1.278985 CAAGTGATGTGAGGCCCAGTA 59.721 52.381 0.00 0.00 0.00 2.74
1945 2200 0.037303 CAAGTGATGTGAGGCCCAGT 59.963 55.000 0.00 0.00 0.00 4.00
1946 2201 0.037303 ACAAGTGATGTGAGGCCCAG 59.963 55.000 0.00 0.00 41.93 4.45
1960 2215 2.105477 ACCAATGCTCAGTGAGACAAGT 59.895 45.455 24.55 15.27 0.00 3.16
2029 2287 1.803334 TCTGGACAACCCGAAATTCG 58.197 50.000 8.62 8.62 40.07 3.34
2031 2289 3.721087 AGATCTGGACAACCCGAAATT 57.279 42.857 0.00 0.00 37.93 1.82
2099 2376 8.383175 TCTTTAAGTTTGGACAGTTGGATATCT 58.617 33.333 2.05 0.00 0.00 1.98
2125 2402 3.685139 TCTTCTGATCTGTTCCGCTTT 57.315 42.857 0.00 0.00 0.00 3.51
2133 2410 0.250513 GGCGGGTTCTTCTGATCTGT 59.749 55.000 0.00 0.00 0.00 3.41
2178 2459 4.097418 AGTAGGCTCATAAACAGACAGGT 58.903 43.478 0.00 0.00 0.00 4.00
2185 2466 5.499004 AGTTCCAAGTAGGCTCATAAACA 57.501 39.130 0.00 0.00 37.29 2.83
2186 2467 7.769044 TCATAAGTTCCAAGTAGGCTCATAAAC 59.231 37.037 0.00 0.00 37.29 2.01
2187 2468 7.769044 GTCATAAGTTCCAAGTAGGCTCATAAA 59.231 37.037 0.00 0.00 37.29 1.40
2188 2469 7.125811 AGTCATAAGTTCCAAGTAGGCTCATAA 59.874 37.037 0.00 0.00 37.29 1.90
2189 2470 6.611642 AGTCATAAGTTCCAAGTAGGCTCATA 59.388 38.462 0.00 0.00 37.29 2.15
2190 2471 5.426833 AGTCATAAGTTCCAAGTAGGCTCAT 59.573 40.000 0.00 0.00 37.29 2.90
2191 2472 4.777896 AGTCATAAGTTCCAAGTAGGCTCA 59.222 41.667 0.00 0.00 37.29 4.26
2192 2473 5.346181 AGTCATAAGTTCCAAGTAGGCTC 57.654 43.478 0.00 0.00 37.29 4.70
2193 2474 5.763876 AAGTCATAAGTTCCAAGTAGGCT 57.236 39.130 0.00 0.00 37.29 4.58
2194 2475 5.938125 TCAAAGTCATAAGTTCCAAGTAGGC 59.062 40.000 0.00 0.00 37.29 3.93
2195 2476 9.099454 GTATCAAAGTCATAAGTTCCAAGTAGG 57.901 37.037 0.00 0.00 39.47 3.18
2196 2477 8.808529 CGTATCAAAGTCATAAGTTCCAAGTAG 58.191 37.037 0.00 0.00 0.00 2.57
2197 2478 8.308931 ACGTATCAAAGTCATAAGTTCCAAGTA 58.691 33.333 0.00 0.00 0.00 2.24
2198 2479 7.159372 ACGTATCAAAGTCATAAGTTCCAAGT 58.841 34.615 0.00 0.00 0.00 3.16
2199 2480 7.596749 ACGTATCAAAGTCATAAGTTCCAAG 57.403 36.000 0.00 0.00 0.00 3.61
2200 2481 7.972832 AACGTATCAAAGTCATAAGTTCCAA 57.027 32.000 0.00 0.00 0.00 3.53
2201 2482 7.972832 AAACGTATCAAAGTCATAAGTTCCA 57.027 32.000 0.00 0.00 30.19 3.53
2214 2495 9.666626 CGGCCATATTATTAAAAACGTATCAAA 57.333 29.630 2.24 0.00 0.00 2.69
2215 2496 7.804129 GCGGCCATATTATTAAAAACGTATCAA 59.196 33.333 2.24 0.00 0.00 2.57
2216 2497 7.041303 TGCGGCCATATTATTAAAAACGTATCA 60.041 33.333 2.24 0.00 0.00 2.15
2217 2498 7.299586 TGCGGCCATATTATTAAAAACGTATC 58.700 34.615 2.24 0.00 0.00 2.24
2218 2499 7.204496 TGCGGCCATATTATTAAAAACGTAT 57.796 32.000 2.24 0.00 0.00 3.06
2219 2500 6.615264 TGCGGCCATATTATTAAAAACGTA 57.385 33.333 2.24 0.00 0.00 3.57
2220 2501 5.502153 TGCGGCCATATTATTAAAAACGT 57.498 34.783 2.24 0.00 0.00 3.99
2221 2502 5.164100 GCATGCGGCCATATTATTAAAAACG 60.164 40.000 0.00 0.00 36.11 3.60
2222 2503 5.694006 TGCATGCGGCCATATTATTAAAAAC 59.306 36.000 14.09 0.00 43.89 2.43
2223 2504 5.847304 TGCATGCGGCCATATTATTAAAAA 58.153 33.333 14.09 0.00 43.89 1.94
2224 2505 5.459536 TGCATGCGGCCATATTATTAAAA 57.540 34.783 14.09 0.00 43.89 1.52
2225 2506 5.649557 GATGCATGCGGCCATATTATTAAA 58.350 37.500 14.09 0.00 43.89 1.52
2226 2507 4.201901 CGATGCATGCGGCCATATTATTAA 60.202 41.667 14.09 0.00 43.89 1.40
2227 2508 3.312146 CGATGCATGCGGCCATATTATTA 59.688 43.478 14.09 0.00 43.89 0.98
2228 2509 2.097954 CGATGCATGCGGCCATATTATT 59.902 45.455 14.09 0.00 43.89 1.40
2229 2510 1.672363 CGATGCATGCGGCCATATTAT 59.328 47.619 14.09 0.00 43.89 1.28
2230 2511 1.085893 CGATGCATGCGGCCATATTA 58.914 50.000 14.09 0.00 43.89 0.98
2231 2512 0.606130 TCGATGCATGCGGCCATATT 60.606 50.000 14.09 0.00 43.89 1.28
2232 2513 0.393402 ATCGATGCATGCGGCCATAT 60.393 50.000 14.09 0.00 43.89 1.78
2233 2514 0.606130 AATCGATGCATGCGGCCATA 60.606 50.000 14.09 0.00 43.89 2.74
2234 2515 1.900016 AATCGATGCATGCGGCCAT 60.900 52.632 14.09 0.00 43.89 4.40
2235 2516 2.516695 AATCGATGCATGCGGCCA 60.517 55.556 14.09 0.00 43.89 5.36
2236 2517 1.859427 ATCAATCGATGCATGCGGCC 61.859 55.000 14.09 3.42 43.89 6.13
2237 2518 0.728129 CATCAATCGATGCATGCGGC 60.728 55.000 14.09 6.36 42.54 6.53
2238 2519 3.378013 CATCAATCGATGCATGCGG 57.622 52.632 14.09 4.98 42.54 5.69
2246 2527 0.602106 CGGCCTCTGCATCAATCGAT 60.602 55.000 0.00 0.00 40.13 3.59
2247 2528 1.227350 CGGCCTCTGCATCAATCGA 60.227 57.895 0.00 0.00 40.13 3.59
2248 2529 2.249535 CCGGCCTCTGCATCAATCG 61.250 63.158 0.00 0.00 40.13 3.34
2249 2530 0.883814 CTCCGGCCTCTGCATCAATC 60.884 60.000 0.00 0.00 40.13 2.67
2250 2531 1.147824 CTCCGGCCTCTGCATCAAT 59.852 57.895 0.00 0.00 40.13 2.57
2251 2532 2.586245 CTCCGGCCTCTGCATCAA 59.414 61.111 0.00 0.00 40.13 2.57
2252 2533 3.473647 CCTCCGGCCTCTGCATCA 61.474 66.667 0.00 0.00 40.13 3.07
2253 2534 3.453070 GACCTCCGGCCTCTGCATC 62.453 68.421 0.00 0.00 40.13 3.91
2254 2535 3.474570 GACCTCCGGCCTCTGCAT 61.475 66.667 0.00 0.00 40.13 3.96
2256 2537 4.459089 GTGACCTCCGGCCTCTGC 62.459 72.222 0.00 0.00 0.00 4.26
2257 2538 3.775654 GGTGACCTCCGGCCTCTG 61.776 72.222 0.00 0.00 0.00 3.35
2288 2569 7.325097 CGAACAACAGACAAGTAACAAGTTTTT 59.675 33.333 0.00 0.00 0.00 1.94
2289 2570 6.799925 CGAACAACAGACAAGTAACAAGTTTT 59.200 34.615 0.00 0.00 0.00 2.43
2290 2571 6.148150 TCGAACAACAGACAAGTAACAAGTTT 59.852 34.615 0.00 0.00 0.00 2.66
2291 2572 5.640357 TCGAACAACAGACAAGTAACAAGTT 59.360 36.000 0.00 0.00 0.00 2.66
2292 2573 5.172934 TCGAACAACAGACAAGTAACAAGT 58.827 37.500 0.00 0.00 0.00 3.16
2293 2574 5.712217 TCGAACAACAGACAAGTAACAAG 57.288 39.130 0.00 0.00 0.00 3.16
2294 2575 6.483385 TTTCGAACAACAGACAAGTAACAA 57.517 33.333 0.00 0.00 0.00 2.83
2295 2576 6.671614 ATTTCGAACAACAGACAAGTAACA 57.328 33.333 0.00 0.00 0.00 2.41
2296 2577 6.631636 GGAATTTCGAACAACAGACAAGTAAC 59.368 38.462 0.00 0.00 0.00 2.50
2297 2578 6.238538 GGGAATTTCGAACAACAGACAAGTAA 60.239 38.462 0.00 0.00 0.00 2.24
2298 2579 5.237779 GGGAATTTCGAACAACAGACAAGTA 59.762 40.000 0.00 0.00 0.00 2.24
2299 2580 4.036380 GGGAATTTCGAACAACAGACAAGT 59.964 41.667 0.00 0.00 0.00 3.16
2300 2581 4.275936 AGGGAATTTCGAACAACAGACAAG 59.724 41.667 0.00 0.00 0.00 3.16
2301 2582 4.204012 AGGGAATTTCGAACAACAGACAA 58.796 39.130 0.00 0.00 0.00 3.18
2302 2583 3.815809 AGGGAATTTCGAACAACAGACA 58.184 40.909 0.00 0.00 0.00 3.41
2303 2584 7.787725 ATATAGGGAATTTCGAACAACAGAC 57.212 36.000 0.00 0.00 0.00 3.51
2307 2588 9.807386 CGAATAATATAGGGAATTTCGAACAAC 57.193 33.333 0.00 0.00 0.00 3.32
2308 2589 9.767228 TCGAATAATATAGGGAATTTCGAACAA 57.233 29.630 0.00 0.00 0.00 2.83
2309 2590 9.938280 ATCGAATAATATAGGGAATTTCGAACA 57.062 29.630 0.00 0.00 0.00 3.18
2316 2597 9.628500 GCCCTTTATCGAATAATATAGGGAATT 57.372 33.333 18.29 0.00 45.96 2.17
2317 2598 7.931948 CGCCCTTTATCGAATAATATAGGGAAT 59.068 37.037 18.29 0.00 45.96 3.01
2318 2599 7.270047 CGCCCTTTATCGAATAATATAGGGAA 58.730 38.462 18.29 0.00 45.96 3.97
2319 2600 6.684613 GCGCCCTTTATCGAATAATATAGGGA 60.685 42.308 18.29 0.00 45.96 4.20
2320 2601 5.465724 GCGCCCTTTATCGAATAATATAGGG 59.534 44.000 12.51 12.51 45.89 3.53
2321 2602 6.281405 AGCGCCCTTTATCGAATAATATAGG 58.719 40.000 2.29 0.00 32.88 2.57
2322 2603 7.772332 AAGCGCCCTTTATCGAATAATATAG 57.228 36.000 2.29 0.00 0.00 1.31
2323 2604 8.556213 AAAAGCGCCCTTTATCGAATAATATA 57.444 30.769 2.29 0.00 40.30 0.86
2324 2605 7.448748 AAAAGCGCCCTTTATCGAATAATAT 57.551 32.000 2.29 0.00 40.30 1.28
2325 2606 6.870971 AAAAGCGCCCTTTATCGAATAATA 57.129 33.333 2.29 0.00 40.30 0.98
2326 2607 5.767816 AAAAGCGCCCTTTATCGAATAAT 57.232 34.783 2.29 0.00 40.30 1.28
2327 2608 6.870971 ATAAAAGCGCCCTTTATCGAATAA 57.129 33.333 15.73 0.00 40.30 1.40
2328 2609 6.870971 AATAAAAGCGCCCTTTATCGAATA 57.129 33.333 19.70 0.22 40.30 1.75
2329 2610 5.767816 AATAAAAGCGCCCTTTATCGAAT 57.232 34.783 19.70 6.97 40.30 3.34
2330 2611 6.870971 ATAATAAAAGCGCCCTTTATCGAA 57.129 33.333 19.70 12.05 40.30 3.71
2331 2612 6.870971 AATAATAAAAGCGCCCTTTATCGA 57.129 33.333 19.70 13.69 40.30 3.59
2332 2613 6.302313 CGAAATAATAAAAGCGCCCTTTATCG 59.698 38.462 19.70 16.37 40.30 2.92
2333 2614 7.357303 TCGAAATAATAAAAGCGCCCTTTATC 58.643 34.615 19.70 10.76 40.30 1.75
2334 2615 7.266922 TCGAAATAATAAAAGCGCCCTTTAT 57.733 32.000 15.73 15.73 40.30 1.40
2354 2635 2.351418 CCGCTTGATGCTACATTTCGAA 59.649 45.455 0.00 0.00 40.11 3.71
2390 2671 0.902531 GCAGAGGCTGGGTGTTACTA 59.097 55.000 0.00 0.00 36.96 1.82
2467 2749 4.360563 ACTCTACTATCGCCGATTTGTTG 58.639 43.478 4.31 6.49 0.00 3.33
2481 2765 5.611128 AGTGTCGGTCTATGACTCTACTA 57.389 43.478 0.00 0.00 38.14 1.82
2649 2935 2.165380 TACGCACTCGCTTCGTACT 58.835 52.632 0.00 0.00 39.84 2.73
2727 3013 1.532868 CTATGGTCGCTTTGGCTATGC 59.467 52.381 0.00 0.00 36.09 3.14
2776 3062 9.057089 GGACGGTATTTCAGATAGATTCAAAAT 57.943 33.333 0.00 0.00 0.00 1.82
2789 3075 4.006989 TCATTGGTTGGACGGTATTTCAG 58.993 43.478 0.00 0.00 0.00 3.02
2792 3078 3.086282 GGTCATTGGTTGGACGGTATTT 58.914 45.455 0.00 0.00 34.87 1.40
2818 3104 0.802494 CCCACAAGTGTCGCCAATAC 59.198 55.000 0.00 0.00 0.00 1.89
2968 3254 0.107410 ACCAAAGACAACCTCGCACA 60.107 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.