Multiple sequence alignment - TraesCS5D01G258800

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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 TraesCS5D01G258800 chr5D 100.000 3463 0 0 1 3463 365123329 365119867 0.000000e+00 6396.0
1 TraesCS5D01G258800 chr5D 96.674 962 25 5 2508 3463 432505331 432506291 0.000000e+00 1592.0
2 TraesCS5D01G258800 chr5D 96.358 961 28 5 2509 3463 454208878 454209837 0.000000e+00 1574.0
3 TraesCS5D01G258800 chr5A 91.895 2295 130 20 219 2487 466582366 466580102 0.000000e+00 3157.0
4 TraesCS5D01G258800 chr5A 89.831 177 9 4 2 176 466582539 466582370 5.820000e-53 219.0
5 TraesCS5D01G258800 chr5B 92.063 1197 75 14 1332 2520 431070460 431069276 0.000000e+00 1666.0
6 TraesCS5D01G258800 chr5B 88.908 1145 66 26 219 1337 431071647 431070538 0.000000e+00 1354.0
7 TraesCS5D01G258800 chr5B 84.270 178 11 2 1 176 431071813 431071651 1.290000e-34 158.0
8 TraesCS5D01G258800 chr7D 96.764 958 27 4 2509 3463 464034871 464035827 0.000000e+00 1594.0
9 TraesCS5D01G258800 chr7D 96.462 961 27 5 2509 3463 550271138 550272097 0.000000e+00 1580.0
10 TraesCS5D01G258800 chr7D 96.262 963 28 6 2508 3463 101006001 101006962 0.000000e+00 1572.0
11 TraesCS5D01G258800 chr7D 96.254 961 29 5 2509 3463 460640164 460639205 0.000000e+00 1568.0
12 TraesCS5D01G258800 chr6D 96.466 962 28 4 2507 3463 413388734 413389694 0.000000e+00 1583.0
13 TraesCS5D01G258800 chr2D 96.254 961 28 5 2508 3463 556180326 556181283 0.000000e+00 1568.0
14 TraesCS5D01G258800 chr2D 82.432 74 11 2 1472 1544 587298541 587298469 2.890000e-06 63.9
15 TraesCS5D01G258800 chr3D 95.876 970 32 6 2500 3463 524198112 524199079 0.000000e+00 1563.0
16 TraesCS5D01G258800 chrUn 91.525 177 8 3 2 176 49758265 49758094 1.610000e-58 237.0
17 TraesCS5D01G258800 chrUn 84.545 110 4 3 219 319 49758090 49757985 2.840000e-16 97.1
18 TraesCS5D01G258800 chr3A 91.525 177 8 3 2 176 200211441 200211612 1.610000e-58 237.0
19 TraesCS5D01G258800 chr3A 89.831 177 11 3 2 176 633309129 633309300 1.620000e-53 220.0
20 TraesCS5D01G258800 chr3A 84.404 109 4 4 220 319 633309305 633309409 1.020000e-15 95.3
21 TraesCS5D01G258800 chr7A 90.395 177 10 4 2 176 627325063 627325234 3.480000e-55 226.0
22 TraesCS5D01G258800 chr7A 84.071 113 5 3 216 319 627325235 627325343 2.840000e-16 97.1
23 TraesCS5D01G258800 chr1B 89.831 177 11 3 2 176 561144802 561144973 1.620000e-53 220.0
24 TraesCS5D01G258800 chr1B 84.071 113 5 3 216 319 561144974 561145082 2.840000e-16 97.1
25 TraesCS5D01G258800 chr1B 80.822 73 14 0 1472 1544 631717678 631717750 1.340000e-04 58.4
26 TraesCS5D01G258800 chr1A 89.831 177 11 3 2 176 566960214 566960043 1.620000e-53 220.0
27 TraesCS5D01G258800 chr1A 84.545 110 4 3 219 319 566960039 566959934 2.840000e-16 97.1
28 TraesCS5D01G258800 chr1A 80.822 73 14 0 1472 1544 551532866 551532938 1.340000e-04 58.4
29 TraesCS5D01G258800 chr2B 82.432 74 11 2 1472 1544 709830197 709830125 2.890000e-06 63.9
30 TraesCS5D01G258800 chr2A 82.432 74 11 2 1472 1544 722208789 722208717 2.890000e-06 63.9
31 TraesCS5D01G258800 chr1D 81.818 77 13 1 1469 1544 459625433 459625357 2.890000e-06 63.9
32 TraesCS5D01G258800 chr1D 80.822 73 14 0 1472 1544 459522644 459522716 1.340000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G258800 chr5D 365119867 365123329 3462 True 6396.000000 6396 100.000000 1 3463 1 chr5D.!!$R1 3462
1 TraesCS5D01G258800 chr5D 432505331 432506291 960 False 1592.000000 1592 96.674000 2508 3463 1 chr5D.!!$F1 955
2 TraesCS5D01G258800 chr5D 454208878 454209837 959 False 1574.000000 1574 96.358000 2509 3463 1 chr5D.!!$F2 954
3 TraesCS5D01G258800 chr5A 466580102 466582539 2437 True 1688.000000 3157 90.863000 2 2487 2 chr5A.!!$R1 2485
4 TraesCS5D01G258800 chr5B 431069276 431071813 2537 True 1059.333333 1666 88.413667 1 2520 3 chr5B.!!$R1 2519
5 TraesCS5D01G258800 chr7D 464034871 464035827 956 False 1594.000000 1594 96.764000 2509 3463 1 chr7D.!!$F2 954
6 TraesCS5D01G258800 chr7D 550271138 550272097 959 False 1580.000000 1580 96.462000 2509 3463 1 chr7D.!!$F3 954
7 TraesCS5D01G258800 chr7D 101006001 101006962 961 False 1572.000000 1572 96.262000 2508 3463 1 chr7D.!!$F1 955
8 TraesCS5D01G258800 chr7D 460639205 460640164 959 True 1568.000000 1568 96.254000 2509 3463 1 chr7D.!!$R1 954
9 TraesCS5D01G258800 chr6D 413388734 413389694 960 False 1583.000000 1583 96.466000 2507 3463 1 chr6D.!!$F1 956
10 TraesCS5D01G258800 chr2D 556180326 556181283 957 False 1568.000000 1568 96.254000 2508 3463 1 chr2D.!!$F1 955
11 TraesCS5D01G258800 chr3D 524198112 524199079 967 False 1563.000000 1563 95.876000 2500 3463 1 chr3D.!!$F1 963

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
921 949 0.248990 GAGGCATCTGCGACTCTCTG 60.249 60.0 0.00 0.00 43.26 3.35 F
1189 1217 0.179029 ACCCGGTGTTGAAGTCCTTG 60.179 55.0 0.00 0.00 0.00 3.61 F
1255 1285 1.147473 CGGCAATTCCTTGGTTTTGC 58.853 50.0 15.56 15.56 42.81 3.68 F
2123 2274 1.276145 GCTACGGTCGGATTCATCGC 61.276 60.0 0.00 0.00 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2352 0.945813 GCTCAATCATGCTCTCAGCC 59.054 55.000 0.00 0.0 41.51 4.85 R
2334 2485 1.878522 CCTGTAGGACATCACGCGC 60.879 63.158 5.73 0.0 37.39 6.86 R
2351 2502 2.125106 ACGAGCGATTTCTGGGCC 60.125 61.111 0.00 0.0 0.00 5.80 R
3330 3493 1.210234 AGATCATGGCGGTGTCAATGA 59.790 47.619 0.00 0.0 0.00 2.57 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
40 41 1.676006 GGTGCCAAATATTCAGACGGG 59.324 52.381 0.00 0.00 0.00 5.28
55 56 0.320771 ACGGGTGTCAAGCTTGCTAG 60.321 55.000 21.99 11.22 0.00 3.42
56 57 0.320771 CGGGTGTCAAGCTTGCTAGT 60.321 55.000 21.99 0.00 0.00 2.57
57 58 1.067142 CGGGTGTCAAGCTTGCTAGTA 60.067 52.381 21.99 0.56 0.00 1.82
58 59 2.347731 GGGTGTCAAGCTTGCTAGTAC 58.652 52.381 21.99 14.24 0.00 2.73
59 60 2.289444 GGGTGTCAAGCTTGCTAGTACA 60.289 50.000 21.99 16.67 0.00 2.90
60 61 3.600388 GGTGTCAAGCTTGCTAGTACAT 58.400 45.455 21.99 0.00 0.00 2.29
89 90 7.142680 ACATGTTTATTTCAGTTGGTTAACCG 58.857 34.615 19.65 5.57 37.52 4.44
91 92 2.981400 ATTTCAGTTGGTTAACCGCG 57.019 45.000 19.65 0.00 37.52 6.46
164 167 6.246420 TCGTCCTACTGTAGAAGTAAACAC 57.754 41.667 16.22 0.00 40.92 3.32
169 172 4.049546 ACTGTAGAAGTAAACACGCACA 57.950 40.909 0.00 0.00 37.36 4.57
176 179 4.686554 AGAAGTAAACACGCACAATCTCTC 59.313 41.667 0.00 0.00 0.00 3.20
177 180 3.990092 AGTAAACACGCACAATCTCTCA 58.010 40.909 0.00 0.00 0.00 3.27
178 181 4.569943 AGTAAACACGCACAATCTCTCAT 58.430 39.130 0.00 0.00 0.00 2.90
179 182 3.818961 AAACACGCACAATCTCTCATG 57.181 42.857 0.00 0.00 0.00 3.07
180 183 1.081892 ACACGCACAATCTCTCATGC 58.918 50.000 0.00 0.00 34.66 4.06
181 184 1.081094 CACGCACAATCTCTCATGCA 58.919 50.000 0.00 0.00 37.97 3.96
182 185 1.669265 CACGCACAATCTCTCATGCAT 59.331 47.619 0.00 0.00 37.97 3.96
183 186 1.938577 ACGCACAATCTCTCATGCATC 59.061 47.619 0.00 0.00 37.97 3.91
184 187 1.263484 CGCACAATCTCTCATGCATCC 59.737 52.381 0.00 0.00 37.97 3.51
185 188 1.607628 GCACAATCTCTCATGCATCCC 59.392 52.381 0.00 0.00 38.00 3.85
186 189 1.871676 CACAATCTCTCATGCATCCCG 59.128 52.381 0.00 0.00 0.00 5.14
187 190 1.202734 ACAATCTCTCATGCATCCCGG 60.203 52.381 0.00 0.00 0.00 5.73
188 191 1.135094 AATCTCTCATGCATCCCGGT 58.865 50.000 0.00 0.00 0.00 5.28
189 192 1.135094 ATCTCTCATGCATCCCGGTT 58.865 50.000 0.00 0.00 0.00 4.44
190 193 1.788229 TCTCTCATGCATCCCGGTTA 58.212 50.000 0.00 0.00 0.00 2.85
191 194 2.115427 TCTCTCATGCATCCCGGTTAA 58.885 47.619 0.00 0.00 0.00 2.01
192 195 2.705658 TCTCTCATGCATCCCGGTTAAT 59.294 45.455 0.00 0.00 0.00 1.40
193 196 3.901222 TCTCTCATGCATCCCGGTTAATA 59.099 43.478 0.00 0.00 0.00 0.98
194 197 4.346709 TCTCTCATGCATCCCGGTTAATAA 59.653 41.667 0.00 0.00 0.00 1.40
195 198 5.013079 TCTCTCATGCATCCCGGTTAATAAT 59.987 40.000 0.00 0.00 0.00 1.28
196 199 5.003160 TCTCATGCATCCCGGTTAATAATG 58.997 41.667 0.00 0.00 0.00 1.90
197 200 4.979335 TCATGCATCCCGGTTAATAATGA 58.021 39.130 0.00 0.00 0.00 2.57
198 201 4.759693 TCATGCATCCCGGTTAATAATGAC 59.240 41.667 0.00 0.00 0.00 3.06
199 202 3.135225 TGCATCCCGGTTAATAATGACG 58.865 45.455 0.00 0.00 0.00 4.35
200 203 3.181464 TGCATCCCGGTTAATAATGACGA 60.181 43.478 0.00 0.00 0.00 4.20
201 204 3.185797 GCATCCCGGTTAATAATGACGAC 59.814 47.826 0.00 0.00 0.00 4.34
202 205 4.373527 CATCCCGGTTAATAATGACGACA 58.626 43.478 0.00 0.00 0.00 4.35
203 206 4.468765 TCCCGGTTAATAATGACGACAA 57.531 40.909 0.00 0.00 0.00 3.18
204 207 5.026038 TCCCGGTTAATAATGACGACAAT 57.974 39.130 0.00 0.00 0.00 2.71
205 208 4.812091 TCCCGGTTAATAATGACGACAATG 59.188 41.667 0.00 0.00 0.00 2.82
206 209 4.523813 CCGGTTAATAATGACGACAATGC 58.476 43.478 0.00 0.00 0.00 3.56
207 210 4.523813 CGGTTAATAATGACGACAATGCC 58.476 43.478 0.00 0.00 0.00 4.40
208 211 4.034626 CGGTTAATAATGACGACAATGCCA 59.965 41.667 0.00 0.00 0.00 4.92
209 212 5.277779 CGGTTAATAATGACGACAATGCCAT 60.278 40.000 0.00 0.00 0.00 4.40
210 213 6.073494 CGGTTAATAATGACGACAATGCCATA 60.073 38.462 0.00 0.00 0.00 2.74
211 214 7.360861 CGGTTAATAATGACGACAATGCCATAT 60.361 37.037 0.00 0.00 0.00 1.78
212 215 7.750458 GGTTAATAATGACGACAATGCCATATG 59.250 37.037 0.00 0.00 0.00 1.78
213 216 6.882610 AATAATGACGACAATGCCATATGT 57.117 33.333 1.24 0.00 0.00 2.29
214 217 7.977789 AATAATGACGACAATGCCATATGTA 57.022 32.000 1.24 0.00 0.00 2.29
217 220 5.733226 TGACGACAATGCCATATGTAAAG 57.267 39.130 1.24 0.00 0.00 1.85
231 234 3.319137 TGTAAAGCAGCTACTGACCAG 57.681 47.619 0.00 0.00 32.44 4.00
257 260 8.140112 AGTCATGTTCTAGTCCACTTTCTTAT 57.860 34.615 0.00 0.00 0.00 1.73
266 269 8.470805 TCTAGTCCACTTTCTTATCACAAGATC 58.529 37.037 0.00 0.00 35.67 2.75
285 297 8.956426 ACAAGATCATACATATGGTTCGTTTTT 58.044 29.630 7.80 0.00 34.50 1.94
490 505 3.321111 TCCTAATCTCACCTTCGGTATGC 59.679 47.826 0.00 0.00 32.11 3.14
508 523 2.591923 TGCAACAACTGGGCTTGATTA 58.408 42.857 0.00 0.00 0.00 1.75
568 583 6.479990 TCTTGTAAGCAGAATTGACCATATCG 59.520 38.462 0.00 0.00 0.00 2.92
587 602 2.487762 TCGTTGGAAATCATTCAGGCAC 59.512 45.455 0.00 0.00 37.29 5.01
609 624 1.195674 GGAGTGAAAACGCTTGAGCTC 59.804 52.381 6.82 6.82 39.32 4.09
612 627 1.333619 GTGAAAACGCTTGAGCTCCAA 59.666 47.619 12.15 4.89 39.32 3.53
678 693 2.488355 CTCAAGGCTGCCATTGCG 59.512 61.111 22.65 12.94 41.78 4.85
699 714 1.831736 CCCGGTATCCAAGAACTCACT 59.168 52.381 0.00 0.00 0.00 3.41
707 722 1.808945 CCAAGAACTCACTGTGATGCC 59.191 52.381 11.45 3.43 0.00 4.40
717 732 1.488812 ACTGTGATGCCGCCCTTATTA 59.511 47.619 0.00 0.00 0.00 0.98
719 734 1.210722 TGTGATGCCGCCCTTATTACA 59.789 47.619 0.00 0.00 0.00 2.41
723 738 1.523032 GCCGCCCTTATTACAGCGT 60.523 57.895 2.40 0.00 46.85 5.07
830 858 1.227823 CGGACTTGGTTGCCTGACA 60.228 57.895 0.00 0.00 0.00 3.58
877 905 2.430244 CGACGACGAGTTGGGGTG 60.430 66.667 0.00 0.00 42.66 4.61
886 914 1.271163 CGAGTTGGGGTGCTTCCTTTA 60.271 52.381 0.00 0.00 36.25 1.85
890 918 2.755103 GTTGGGGTGCTTCCTTTATGAG 59.245 50.000 0.00 0.00 36.25 2.90
921 949 0.248990 GAGGCATCTGCGACTCTCTG 60.249 60.000 0.00 0.00 43.26 3.35
922 950 0.682532 AGGCATCTGCGACTCTCTGA 60.683 55.000 0.00 0.00 43.26 3.27
1040 1068 3.262915 AGCAATGCCCCAGATATCTCTAC 59.737 47.826 1.03 0.00 0.00 2.59
1052 1080 5.760743 CAGATATCTCTACTGTCGACCTTGA 59.239 44.000 14.12 5.38 0.00 3.02
1123 1151 3.002791 CAAGTGAAGCAGCTCCGAATAA 58.997 45.455 0.00 0.00 0.00 1.40
1143 1171 1.271926 ACACCTGCATCCCCAAGTTAC 60.272 52.381 0.00 0.00 0.00 2.50
1189 1217 0.179029 ACCCGGTGTTGAAGTCCTTG 60.179 55.000 0.00 0.00 0.00 3.61
1196 1224 4.695455 CGGTGTTGAAGTCCTTGACATATT 59.305 41.667 0.00 0.00 34.60 1.28
1238 1268 3.190874 GCAATCTGAGACTTTAGACCGG 58.809 50.000 0.00 0.00 0.00 5.28
1255 1285 1.147473 CGGCAATTCCTTGGTTTTGC 58.853 50.000 15.56 15.56 42.81 3.68
1260 1290 3.402110 CAATTCCTTGGTTTTGCCTTCC 58.598 45.455 0.00 0.00 38.35 3.46
1261 1291 2.166907 TTCCTTGGTTTTGCCTTCCA 57.833 45.000 0.00 0.00 38.35 3.53
1262 1292 2.397044 TCCTTGGTTTTGCCTTCCAT 57.603 45.000 0.00 0.00 38.35 3.41
1263 1293 3.534357 TCCTTGGTTTTGCCTTCCATA 57.466 42.857 0.00 0.00 38.35 2.74
1264 1294 3.850752 TCCTTGGTTTTGCCTTCCATAA 58.149 40.909 0.00 0.00 38.35 1.90
1265 1295 4.424842 TCCTTGGTTTTGCCTTCCATAAT 58.575 39.130 0.00 0.00 38.35 1.28
1266 1296 5.584913 TCCTTGGTTTTGCCTTCCATAATA 58.415 37.500 0.00 0.00 38.35 0.98
1267 1297 6.019748 TCCTTGGTTTTGCCTTCCATAATAA 58.980 36.000 0.00 0.00 38.35 1.40
1268 1298 6.154363 TCCTTGGTTTTGCCTTCCATAATAAG 59.846 38.462 0.00 0.00 38.35 1.73
1269 1299 6.154363 CCTTGGTTTTGCCTTCCATAATAAGA 59.846 38.462 0.00 0.00 38.35 2.10
1270 1300 6.773976 TGGTTTTGCCTTCCATAATAAGAG 57.226 37.500 0.00 0.00 38.35 2.85
1315 1458 7.448748 AACTTAAATTACTTGGTTCTGCGAT 57.551 32.000 0.00 0.00 0.00 4.58
1316 1459 7.073342 ACTTAAATTACTTGGTTCTGCGATC 57.927 36.000 0.00 0.00 0.00 3.69
1317 1460 6.653320 ACTTAAATTACTTGGTTCTGCGATCA 59.347 34.615 0.00 0.00 0.00 2.92
1318 1461 5.551760 AAATTACTTGGTTCTGCGATCAG 57.448 39.130 0.00 0.00 41.67 2.90
1367 1510 7.969690 ATATCAGGGGACATACTAATCTGAG 57.030 40.000 0.00 0.00 34.01 3.35
1369 1512 4.170053 TCAGGGGACATACTAATCTGAGGA 59.830 45.833 0.00 0.00 0.00 3.71
1371 1514 5.545723 CAGGGGACATACTAATCTGAGGAAT 59.454 44.000 0.00 0.00 0.00 3.01
1419 1562 2.578714 GGTGCCCGGCAAATTCCAA 61.579 57.895 15.39 0.00 41.47 3.53
1449 1592 8.380742 TCAAGTACTTGAATATTTCTCTCCCT 57.619 34.615 31.26 0.00 45.56 4.20
1603 1746 4.547406 ACCGTTTCTTTACAAAGTCTGC 57.453 40.909 1.86 0.00 37.31 4.26
1803 1946 2.140717 GGTCAGGTTACAGTTGTTCCG 58.859 52.381 0.00 0.00 0.00 4.30
1904 2052 7.112565 GCATATTTGAGATTGTAACAATGCTCG 59.887 37.037 0.00 0.00 29.95 5.03
2005 2156 6.799926 TTGAGCCCATTTTTATTTTTCAGC 57.200 33.333 0.00 0.00 0.00 4.26
2006 2157 6.112927 TGAGCCCATTTTTATTTTTCAGCT 57.887 33.333 0.00 0.00 0.00 4.24
2052 2203 8.559536 TCATTTTTGTGAGAAGTAGTTGACATC 58.440 33.333 0.00 0.00 0.00 3.06
2112 2263 2.029649 TGTGTTAACAGAGGCTACGGTC 60.030 50.000 8.98 0.00 0.00 4.79
2123 2274 1.276145 GCTACGGTCGGATTCATCGC 61.276 60.000 0.00 0.00 0.00 4.58
2146 2297 3.565910 TTTCACATTTGGCGCGGGC 62.566 57.895 17.31 17.31 38.90 6.13
2177 2328 1.941999 GCCATGGCAGCCTCAAGAAC 61.942 60.000 32.08 0.00 41.49 3.01
2186 2337 1.816835 AGCCTCAAGAACGTGACGATA 59.183 47.619 13.70 0.00 0.00 2.92
2201 2352 8.705239 ACGTGACGATATATAGTTTTTACTCG 57.295 34.615 13.70 3.15 0.00 4.18
2268 2419 2.356313 CGCTTGAGTGCCTGACGT 60.356 61.111 0.00 0.00 0.00 4.34
2280 2431 1.597027 CTGACGTTGGACACCACCC 60.597 63.158 0.00 0.00 30.78 4.61
2334 2485 2.438434 GGTGCTTCCCCATGGACG 60.438 66.667 15.22 2.40 41.57 4.79
2351 2502 2.224217 CGCGCGTGATGTCCTACAG 61.224 63.158 24.19 0.00 0.00 2.74
2361 2512 1.668826 TGTCCTACAGGCCCAGAAAT 58.331 50.000 0.00 0.00 34.44 2.17
2426 2577 7.202526 CCTGTAATGTCAACTTGATTGTTGTT 58.797 34.615 7.17 0.00 45.26 2.83
2449 2600 0.524862 CCTTGCAGTTCCTGTCATGC 59.475 55.000 0.00 0.00 39.14 4.06
2455 2606 2.815211 TTCCTGTCATGCGAGCGC 60.815 61.111 8.08 8.08 42.35 5.92
2475 2626 6.166982 AGCGCTAACTGATTCTAGACTTTTT 58.833 36.000 8.99 0.00 0.00 1.94
2546 2697 2.136878 TTGCAACGGGGCCACATTT 61.137 52.632 5.46 0.00 0.00 2.32
2549 2700 0.108851 GCAACGGGGCCACATTTAAG 60.109 55.000 5.46 0.00 0.00 1.85
2562 2713 7.170828 GGGCCACATTTAAGTTTAAAAGTTCAG 59.829 37.037 4.39 0.00 33.74 3.02
2622 2773 9.249457 CATACATATTAAGTGACATTGACGACT 57.751 33.333 0.00 0.00 0.00 4.18
2751 2907 5.652891 GGAGACTACCAACTGAGACATTAGA 59.347 44.000 0.00 0.00 0.00 2.10
2850 3006 6.702716 AAACCAAAAGGACGATGTAAAAGA 57.297 33.333 0.00 0.00 0.00 2.52
2904 3062 3.386237 GCTCAGCGGTCCAGTCCT 61.386 66.667 0.00 0.00 0.00 3.85
3139 3302 2.037687 ACCGACCCCGTCCACATA 59.962 61.111 0.00 0.00 0.00 2.29
3187 3350 1.874345 TTGTCGAGGAGCTCCGAACC 61.874 60.000 26.95 16.41 42.08 3.62
3330 3493 1.003051 ATGTCTTCCCCTAGGGCGT 59.997 57.895 23.84 6.79 43.94 5.68
3458 3621 3.075005 GGGTAGCCACCGAGCTCA 61.075 66.667 15.40 0.00 46.86 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.428171 CTGAATATTTGGCACCCCACTG 59.572 50.000 0.00 0.00 41.97 3.66
40 41 5.411781 ACTATGTACTAGCAAGCTTGACAC 58.588 41.667 30.39 17.41 0.00 3.67
57 58 9.515226 ACCAACTGAAATAAACATGTACTATGT 57.485 29.630 0.00 5.45 0.00 2.29
89 90 0.383949 TTCTGGAACAAACTTGGCGC 59.616 50.000 0.00 0.00 38.70 6.53
91 92 4.385358 TCTTTTCTGGAACAAACTTGGC 57.615 40.909 0.00 0.00 38.70 4.52
164 167 1.263484 GGATGCATGAGAGATTGTGCG 59.737 52.381 2.46 0.00 40.34 5.34
169 172 1.135094 ACCGGGATGCATGAGAGATT 58.865 50.000 2.46 0.00 0.00 2.40
176 179 4.378356 CGTCATTATTAACCGGGATGCATG 60.378 45.833 2.46 0.65 0.00 4.06
177 180 3.751175 CGTCATTATTAACCGGGATGCAT 59.249 43.478 6.32 0.00 0.00 3.96
178 181 3.135225 CGTCATTATTAACCGGGATGCA 58.865 45.455 6.32 0.00 0.00 3.96
179 182 3.185797 GTCGTCATTATTAACCGGGATGC 59.814 47.826 6.32 0.00 0.00 3.91
180 183 4.373527 TGTCGTCATTATTAACCGGGATG 58.626 43.478 6.32 0.13 0.00 3.51
181 184 4.675976 TGTCGTCATTATTAACCGGGAT 57.324 40.909 6.32 0.00 0.00 3.85
182 185 4.468765 TTGTCGTCATTATTAACCGGGA 57.531 40.909 6.32 0.00 0.00 5.14
183 186 4.553938 GCATTGTCGTCATTATTAACCGGG 60.554 45.833 6.32 0.00 0.00 5.73
184 187 4.523813 GCATTGTCGTCATTATTAACCGG 58.476 43.478 0.00 0.00 0.00 5.28
185 188 4.034626 TGGCATTGTCGTCATTATTAACCG 59.965 41.667 0.00 0.00 0.00 4.44
186 189 5.493133 TGGCATTGTCGTCATTATTAACC 57.507 39.130 0.00 0.00 0.00 2.85
187 190 8.289618 ACATATGGCATTGTCGTCATTATTAAC 58.710 33.333 4.78 0.00 0.00 2.01
188 191 8.389779 ACATATGGCATTGTCGTCATTATTAA 57.610 30.769 4.78 0.00 0.00 1.40
189 192 7.977789 ACATATGGCATTGTCGTCATTATTA 57.022 32.000 4.78 0.00 0.00 0.98
190 193 6.882610 ACATATGGCATTGTCGTCATTATT 57.117 33.333 4.78 0.00 0.00 1.40
191 194 7.977789 TTACATATGGCATTGTCGTCATTAT 57.022 32.000 4.78 0.00 0.00 1.28
192 195 7.519809 GCTTTACATATGGCATTGTCGTCATTA 60.520 37.037 4.78 0.00 0.00 1.90
193 196 6.691754 TTTACATATGGCATTGTCGTCATT 57.308 33.333 4.78 0.00 0.00 2.57
194 197 5.277974 GCTTTACATATGGCATTGTCGTCAT 60.278 40.000 4.78 0.00 0.00 3.06
195 198 4.035091 GCTTTACATATGGCATTGTCGTCA 59.965 41.667 4.78 0.00 0.00 4.35
196 199 4.035091 TGCTTTACATATGGCATTGTCGTC 59.965 41.667 4.78 2.41 0.00 4.20
197 200 3.944650 TGCTTTACATATGGCATTGTCGT 59.055 39.130 4.78 0.59 0.00 4.34
198 201 4.530388 CTGCTTTACATATGGCATTGTCG 58.470 43.478 4.78 4.35 34.12 4.35
199 202 4.037208 AGCTGCTTTACATATGGCATTGTC 59.963 41.667 4.78 0.00 34.12 3.18
200 203 3.956199 AGCTGCTTTACATATGGCATTGT 59.044 39.130 4.78 12.32 34.12 2.71
201 204 4.579454 AGCTGCTTTACATATGGCATTG 57.421 40.909 4.78 6.70 34.12 2.82
202 205 5.240183 CAGTAGCTGCTTTACATATGGCATT 59.760 40.000 7.79 0.00 34.12 3.56
203 206 4.758674 CAGTAGCTGCTTTACATATGGCAT 59.241 41.667 7.79 4.88 34.12 4.40
204 207 4.129380 CAGTAGCTGCTTTACATATGGCA 58.871 43.478 7.79 5.96 0.00 4.92
205 208 4.212214 GTCAGTAGCTGCTTTACATATGGC 59.788 45.833 7.79 1.08 0.00 4.40
206 209 4.752101 GGTCAGTAGCTGCTTTACATATGG 59.248 45.833 7.79 0.00 0.00 2.74
207 210 5.359756 TGGTCAGTAGCTGCTTTACATATG 58.640 41.667 7.79 0.00 0.00 1.78
208 211 5.363868 TCTGGTCAGTAGCTGCTTTACATAT 59.636 40.000 7.79 0.00 0.00 1.78
209 212 4.709886 TCTGGTCAGTAGCTGCTTTACATA 59.290 41.667 7.79 0.00 0.00 2.29
210 213 3.515502 TCTGGTCAGTAGCTGCTTTACAT 59.484 43.478 7.79 0.00 0.00 2.29
211 214 2.897326 TCTGGTCAGTAGCTGCTTTACA 59.103 45.455 7.79 0.20 0.00 2.41
212 215 3.056465 ACTCTGGTCAGTAGCTGCTTTAC 60.056 47.826 7.79 3.48 0.00 2.01
213 216 3.165875 ACTCTGGTCAGTAGCTGCTTTA 58.834 45.455 7.79 0.00 0.00 1.85
214 217 1.974236 ACTCTGGTCAGTAGCTGCTTT 59.026 47.619 7.79 0.00 0.00 3.51
217 220 0.891373 TGACTCTGGTCAGTAGCTGC 59.109 55.000 0.00 0.00 46.19 5.25
231 234 6.031751 AGAAAGTGGACTAGAACATGACTC 57.968 41.667 0.00 0.00 0.00 3.36
257 260 6.816136 ACGAACCATATGTATGATCTTGTGA 58.184 36.000 1.24 0.00 35.75 3.58
277 289 5.024785 AGTGGGGCAAAAATAAAAACGAA 57.975 34.783 0.00 0.00 0.00 3.85
490 505 5.452078 TTTCTAATCAAGCCCAGTTGTTG 57.548 39.130 0.00 0.00 0.00 3.33
508 523 2.576615 GTCCACTGTTCCTGCTTTTCT 58.423 47.619 0.00 0.00 0.00 2.52
518 533 2.433868 TGCTACTTCGTCCACTGTTC 57.566 50.000 0.00 0.00 0.00 3.18
519 534 2.902705 TTGCTACTTCGTCCACTGTT 57.097 45.000 0.00 0.00 0.00 3.16
533 548 5.357742 TCTGCTTACAAGATCCATTGCTA 57.642 39.130 0.00 0.00 33.28 3.49
547 562 6.422223 CAACGATATGGTCAATTCTGCTTAC 58.578 40.000 0.00 0.00 0.00 2.34
568 583 2.415893 CGGTGCCTGAATGATTTCCAAC 60.416 50.000 0.00 0.00 0.00 3.77
587 602 0.512952 CTCAAGCGTTTTCACTCCGG 59.487 55.000 0.00 0.00 0.00 5.14
609 624 1.133809 TCCAGTTCCAGGGGAGTTGG 61.134 60.000 9.58 9.58 37.95 3.77
612 627 0.401395 TGTTCCAGTTCCAGGGGAGT 60.401 55.000 0.00 0.00 31.21 3.85
678 693 0.539986 TGAGTTCTTGGATACCGGGC 59.460 55.000 6.32 0.00 0.00 6.13
699 714 1.210722 TGTAATAAGGGCGGCATCACA 59.789 47.619 12.47 3.76 0.00 3.58
717 732 0.105408 ACGGGAAGTTGTAACGCTGT 59.895 50.000 0.00 0.00 0.00 4.40
719 734 1.226030 GCACGGGAAGTTGTAACGCT 61.226 55.000 0.00 0.00 0.00 5.07
722 737 0.788391 CGAGCACGGGAAGTTGTAAC 59.212 55.000 0.00 0.00 35.72 2.50
723 738 0.947180 GCGAGCACGGGAAGTTGTAA 60.947 55.000 5.52 0.00 40.15 2.41
854 882 1.061411 CAACTCGTCGTCGCCGATA 59.939 57.895 0.00 0.00 46.30 2.92
877 905 4.013050 AGCCAAAGACTCATAAAGGAAGC 58.987 43.478 0.00 0.00 0.00 3.86
886 914 2.165998 GCCTCAAAGCCAAAGACTCAT 58.834 47.619 0.00 0.00 0.00 2.90
890 918 2.094854 CAGATGCCTCAAAGCCAAAGAC 60.095 50.000 0.00 0.00 0.00 3.01
921 949 3.806380 AGCAGATGATCTCACCACAATC 58.194 45.455 0.00 0.00 0.00 2.67
922 950 3.928005 AGCAGATGATCTCACCACAAT 57.072 42.857 0.00 0.00 0.00 2.71
1040 1068 0.868406 GCCAAGTTCAAGGTCGACAG 59.132 55.000 18.91 6.72 0.00 3.51
1123 1151 1.072266 TAACTTGGGGATGCAGGTGT 58.928 50.000 0.00 0.00 0.00 4.16
1238 1268 2.549064 AGGCAAAACCAAGGAATTGC 57.451 45.000 18.51 18.51 45.59 3.56
1255 1285 6.119240 TGGAGATGCTCTTATTATGGAAGG 57.881 41.667 0.00 0.00 0.00 3.46
1256 1286 7.392418 TGATGGAGATGCTCTTATTATGGAAG 58.608 38.462 0.00 0.00 0.00 3.46
1260 1290 7.711772 GGATCTGATGGAGATGCTCTTATTATG 59.288 40.741 0.00 0.00 44.26 1.90
1261 1291 7.794041 GGATCTGATGGAGATGCTCTTATTAT 58.206 38.462 0.00 0.00 44.26 1.28
1262 1292 7.180322 GGATCTGATGGAGATGCTCTTATTA 57.820 40.000 0.00 0.00 44.26 0.98
1263 1293 6.052405 GGATCTGATGGAGATGCTCTTATT 57.948 41.667 0.00 0.00 44.26 1.40
1264 1294 5.680594 GGATCTGATGGAGATGCTCTTAT 57.319 43.478 0.00 0.00 44.26 1.73
1301 1342 0.322975 AGCTGATCGCAGAACCAAGT 59.677 50.000 11.20 0.00 45.17 3.16
1318 1461 5.908341 ACAACTACTCCTTAGAGCAATAGC 58.092 41.667 0.00 0.00 44.65 2.97
1322 1465 9.197306 TGATATAACAACTACTCCTTAGAGCAA 57.803 33.333 0.00 0.00 44.65 3.91
1323 1466 8.762481 TGATATAACAACTACTCCTTAGAGCA 57.238 34.615 0.00 0.00 44.65 4.26
1324 1467 8.301002 CCTGATATAACAACTACTCCTTAGAGC 58.699 40.741 0.00 0.00 44.65 4.09
1325 1468 8.798402 CCCTGATATAACAACTACTCCTTAGAG 58.202 40.741 0.00 0.00 46.36 2.43
1326 1469 7.728981 CCCCTGATATAACAACTACTCCTTAGA 59.271 40.741 0.00 0.00 0.00 2.10
1327 1470 7.728981 TCCCCTGATATAACAACTACTCCTTAG 59.271 40.741 0.00 0.00 0.00 2.18
1328 1471 7.508296 GTCCCCTGATATAACAACTACTCCTTA 59.492 40.741 0.00 0.00 0.00 2.69
1329 1472 6.326843 GTCCCCTGATATAACAACTACTCCTT 59.673 42.308 0.00 0.00 0.00 3.36
1330 1473 5.839606 GTCCCCTGATATAACAACTACTCCT 59.160 44.000 0.00 0.00 0.00 3.69
1331 1474 5.601313 TGTCCCCTGATATAACAACTACTCC 59.399 44.000 0.00 0.00 0.00 3.85
1332 1475 6.726490 TGTCCCCTGATATAACAACTACTC 57.274 41.667 0.00 0.00 0.00 2.59
1333 1476 8.011290 AGTATGTCCCCTGATATAACAACTACT 58.989 37.037 0.00 0.00 0.00 2.57
1367 1510 3.688673 CACCTGCTGAAGAAAGAGATTCC 59.311 47.826 0.00 0.00 38.94 3.01
1369 1512 4.577875 CTCACCTGCTGAAGAAAGAGATT 58.422 43.478 0.00 0.00 0.00 2.40
1371 1514 2.289320 GCTCACCTGCTGAAGAAAGAGA 60.289 50.000 0.00 0.00 0.00 3.10
1410 1553 6.039270 TCAAGTACTTGAGGTGTTGGAATTTG 59.961 38.462 30.07 3.76 43.90 2.32
1536 1679 7.375834 TCAATGGCTATATAACAGGACTTACG 58.624 38.462 0.00 0.00 0.00 3.18
1614 1757 7.313740 AGACAATAGGCATGATAATCTGAGT 57.686 36.000 0.00 0.00 0.00 3.41
1623 1766 5.933617 TCAGCTAAAGACAATAGGCATGAT 58.066 37.500 0.00 0.00 0.00 2.45
1697 1840 8.665685 GGTGTCGTGTATTTATGAAAAGAGATT 58.334 33.333 0.00 0.00 0.00 2.40
1803 1946 5.245531 TGTGTGATCCCTGACAAATCTAAC 58.754 41.667 0.00 0.00 0.00 2.34
1859 2007 1.580815 CATGTTTGGCCGTTGCTTTT 58.419 45.000 0.00 0.00 37.74 2.27
1864 2012 2.582728 ATATGCATGTTTGGCCGTTG 57.417 45.000 10.16 0.00 0.00 4.10
2112 2263 1.592543 TGAAACATCGCGATGAATCCG 59.407 47.619 45.64 25.01 41.20 4.18
2146 2297 1.135315 CCATGGCGAAACTCTTGCG 59.865 57.895 0.00 0.00 0.00 4.85
2153 2304 3.056313 GAGGCTGCCATGGCGAAAC 62.056 63.158 30.87 20.25 45.51 2.78
2177 2328 7.201215 GCCGAGTAAAAACTATATATCGTCACG 60.201 40.741 0.00 0.00 0.00 4.35
2186 2337 6.183360 TGCTCTCAGCCGAGTAAAAACTATAT 60.183 38.462 0.00 0.00 41.51 0.86
2201 2352 0.945813 GCTCAATCATGCTCTCAGCC 59.054 55.000 0.00 0.00 41.51 4.85
2280 2431 4.466370 TGAGGAACACCTAGAGTAACCATG 59.534 45.833 0.00 0.00 33.73 3.66
2334 2485 1.878522 CCTGTAGGACATCACGCGC 60.879 63.158 5.73 0.00 37.39 6.86
2351 2502 2.125106 ACGAGCGATTTCTGGGCC 60.125 61.111 0.00 0.00 0.00 5.80
2449 2600 3.002862 AGTCTAGAATCAGTTAGCGCTCG 59.997 47.826 16.34 0.55 0.00 5.03
2904 3062 4.456253 GAGAAGACGACCGCGCGA 62.456 66.667 34.63 0.00 42.48 5.87
3163 3326 4.432601 AGCTCCTCGACAAGCTCT 57.567 55.556 10.32 0.00 45.57 4.09
3330 3493 1.210234 AGATCATGGCGGTGTCAATGA 59.790 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.