Multiple sequence alignment - TraesCS2A01G097400

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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 TraesCS2A01G097400 chr2A 100.000 3166 0 0 1 3166 51039846 51043011 0.000000e+00 5847.0
1 TraesCS2A01G097400 chr2A 84.222 1407 157 45 778 2173 48347704 48346352 0.000000e+00 1308.0
2 TraesCS2A01G097400 chr2A 84.586 1304 133 47 893 2173 48249832 48251090 0.000000e+00 1232.0
3 TraesCS2A01G097400 chr2A 92.017 476 38 0 1409 1884 48246383 48246858 0.000000e+00 669.0
4 TraesCS2A01G097400 chr2A 88.367 447 42 7 871 1314 48224211 48224650 2.160000e-146 529.0
5 TraesCS2A01G097400 chr2B 89.545 1693 91 38 686 2350 75990235 75991869 0.000000e+00 2067.0
6 TraesCS2A01G097400 chr2B 85.169 1335 139 40 857 2173 71293858 71292565 0.000000e+00 1314.0
7 TraesCS2A01G097400 chr2B 83.832 1404 159 40 778 2173 71244529 71243186 0.000000e+00 1273.0
8 TraesCS2A01G097400 chr2B 82.166 1413 169 53 778 2173 520970248 520968902 0.000000e+00 1136.0
9 TraesCS2A01G097400 chr2B 83.137 848 109 21 1327 2166 70837221 70838042 0.000000e+00 743.0
10 TraesCS2A01G097400 chr2B 80.920 870 66 39 2252 3090 75991872 75992672 2.100000e-166 595.0
11 TraesCS2A01G097400 chr2B 85.358 601 52 23 732 1323 70821564 70822137 9.780000e-165 590.0
12 TraesCS2A01G097400 chr2B 85.600 375 36 9 1 368 75989294 75989657 8.290000e-101 377.0
13 TraesCS2A01G097400 chr2B 87.204 211 16 9 2961 3166 75992770 75992974 2.460000e-56 230.0
14 TraesCS2A01G097400 chr2D 89.297 1579 108 38 850 2410 48028486 48026951 0.000000e+00 1923.0
15 TraesCS2A01G097400 chr2D 85.225 1401 146 38 777 2166 44339523 44340873 0.000000e+00 1384.0
16 TraesCS2A01G097400 chr2D 84.327 1359 142 47 848 2173 44470359 44469039 0.000000e+00 1264.0
17 TraesCS2A01G097400 chr2D 90.335 538 36 9 2561 3085 48026802 48026268 0.000000e+00 691.0
18 TraesCS2A01G097400 chr2D 85.791 373 33 7 3 368 48029312 48028953 8.290000e-101 377.0
19 TraesCS2A01G097400 chr2D 98.039 51 0 1 3117 3166 48026272 48026222 1.560000e-13 87.9


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 TraesCS2A01G097400 chr2A 51039846 51043011 3165 False 5847.000 5847 100.00000 1 3166 1 chr2A.!!$F2 3165
1 TraesCS2A01G097400 chr2A 48346352 48347704 1352 True 1308.000 1308 84.22200 778 2173 1 chr2A.!!$R1 1395
2 TraesCS2A01G097400 chr2A 48246383 48251090 4707 False 950.500 1232 88.30150 893 2173 2 chr2A.!!$F3 1280
3 TraesCS2A01G097400 chr2B 71292565 71293858 1293 True 1314.000 1314 85.16900 857 2173 1 chr2B.!!$R2 1316
4 TraesCS2A01G097400 chr2B 71243186 71244529 1343 True 1273.000 1273 83.83200 778 2173 1 chr2B.!!$R1 1395
5 TraesCS2A01G097400 chr2B 520968902 520970248 1346 True 1136.000 1136 82.16600 778 2173 1 chr2B.!!$R3 1395
6 TraesCS2A01G097400 chr2B 75989294 75992974 3680 False 817.250 2067 85.81725 1 3166 4 chr2B.!!$F3 3165
7 TraesCS2A01G097400 chr2B 70837221 70838042 821 False 743.000 743 83.13700 1327 2166 1 chr2B.!!$F2 839
8 TraesCS2A01G097400 chr2B 70821564 70822137 573 False 590.000 590 85.35800 732 1323 1 chr2B.!!$F1 591
9 TraesCS2A01G097400 chr2D 44339523 44340873 1350 False 1384.000 1384 85.22500 777 2166 1 chr2D.!!$F1 1389
10 TraesCS2A01G097400 chr2D 44469039 44470359 1320 True 1264.000 1264 84.32700 848 2173 1 chr2D.!!$R1 1325
11 TraesCS2A01G097400 chr2D 48026222 48029312 3090 True 769.725 1923 90.86550 3 3166 4 chr2D.!!$R2 3163

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
911 3514 0.034186 TCCACCACCAAGCATCCATC 60.034 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2537 5379 0.038892 AACAAGGCAGCAGCGAAATG 60.039 50.0 0.0 0.0 43.41 2.32 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
30 32 5.718130 AGTACCACCATACTGCACTACTTTA 59.282 40.000 0.00 0.00 34.02 1.85
41 43 5.428783 ACTGCACTACTTTACCCTGGATAAT 59.571 40.000 0.00 0.00 0.00 1.28
44 46 6.614087 TGCACTACTTTACCCTGGATAATAGT 59.386 38.462 0.00 0.00 0.00 2.12
45 47 6.929606 GCACTACTTTACCCTGGATAATAGTG 59.070 42.308 13.78 13.78 39.84 2.74
46 48 7.418712 GCACTACTTTACCCTGGATAATAGTGT 60.419 40.741 17.20 7.40 39.32 3.55
47 49 9.139734 CACTACTTTACCCTGGATAATAGTGTA 57.860 37.037 11.24 0.88 34.77 2.90
50 52 6.835488 ACTTTACCCTGGATAATAGTGTACGA 59.165 38.462 0.00 0.00 0.00 3.43
52 54 4.801164 ACCCTGGATAATAGTGTACGAGT 58.199 43.478 0.00 0.00 0.00 4.18
53 55 5.206587 ACCCTGGATAATAGTGTACGAGTT 58.793 41.667 0.00 0.00 0.00 3.01
54 56 5.301298 ACCCTGGATAATAGTGTACGAGTTC 59.699 44.000 0.00 0.00 0.00 3.01
80 84 7.941238 CCTCTGATCATGGTTACATTATCCTTT 59.059 37.037 0.00 0.00 37.06 3.11
81 85 8.681486 TCTGATCATGGTTACATTATCCTTTG 57.319 34.615 0.00 0.00 37.06 2.77
83 91 8.224389 TGATCATGGTTACATTATCCTTTGTG 57.776 34.615 0.00 0.00 37.06 3.33
85 93 8.821686 ATCATGGTTACATTATCCTTTGTGAA 57.178 30.769 0.00 0.00 34.35 3.18
88 96 8.522830 CATGGTTACATTATCCTTTGTGAACTT 58.477 33.333 0.00 0.00 34.35 2.66
104 112 6.292150 TGTGAACTTATAACACACCATGTCA 58.708 36.000 3.87 0.00 42.31 3.58
136 144 2.179547 CCGCGCCATGTGCTGATTA 61.180 57.895 0.00 0.00 36.86 1.75
141 149 2.536803 GCGCCATGTGCTGATTAAATTG 59.463 45.455 0.00 0.00 38.05 2.32
193 201 1.549203 GTTTCCTGTGCATGGACCAT 58.451 50.000 15.34 0.00 32.65 3.55
279 287 3.981211 ACATTTTATTGCGATGGATGCC 58.019 40.909 0.00 0.00 0.00 4.40
282 290 0.179032 TTATTGCGATGGATGCCGGT 60.179 50.000 1.90 0.00 0.00 5.28
298 306 1.336440 CCGGTTGATTTGACAGCACAA 59.664 47.619 0.00 0.00 0.00 3.33
309 321 2.281761 AGCACAAGAAGGCGTGGG 60.282 61.111 0.00 0.00 33.62 4.61
321 333 1.093496 GGCGTGGGAAGAAATACGGG 61.093 60.000 0.00 0.00 0.00 5.28
340 352 1.689352 GGTACATTTCACCGGACGCG 61.689 60.000 9.46 3.53 0.00 6.01
393 430 0.542702 ACCCCTCCTAAAACCGACGA 60.543 55.000 0.00 0.00 0.00 4.20
394 431 0.108472 CCCCTCCTAAAACCGACGAC 60.108 60.000 0.00 0.00 0.00 4.34
395 432 0.604578 CCCTCCTAAAACCGACGACA 59.395 55.000 0.00 0.00 0.00 4.35
396 433 1.206371 CCCTCCTAAAACCGACGACAT 59.794 52.381 0.00 0.00 0.00 3.06
403 452 0.533951 AAACCGACGACATACCTCCC 59.466 55.000 0.00 0.00 0.00 4.30
443 492 0.604243 TTGGAATGGGTCGGTGAACG 60.604 55.000 0.00 0.00 46.11 3.95
445 494 1.296056 GGAATGGGTCGGTGAACGTG 61.296 60.000 0.00 0.00 44.69 4.49
495 813 2.287915 CCGCTTGATTATCTGTTTCCCG 59.712 50.000 0.00 0.00 0.00 5.14
501 819 6.540438 TTGATTATCTGTTTCCCGTCTAGT 57.460 37.500 0.00 0.00 0.00 2.57
502 820 5.902681 TGATTATCTGTTTCCCGTCTAGTG 58.097 41.667 0.00 0.00 0.00 2.74
503 821 4.730949 TTATCTGTTTCCCGTCTAGTGG 57.269 45.455 0.00 0.00 0.00 4.00
504 822 2.005370 TCTGTTTCCCGTCTAGTGGT 57.995 50.000 3.63 0.00 0.00 4.16
511 829 0.104304 CCCGTCTAGTGGTACATGGC 59.896 60.000 0.00 0.00 44.52 4.40
520 838 7.095774 CGTCTAGTGGTACATGGCATTTAATAC 60.096 40.741 0.00 0.00 44.52 1.89
524 842 6.318648 AGTGGTACATGGCATTTAATACAGTG 59.681 38.462 0.00 0.00 44.52 3.66
525 843 5.067153 TGGTACATGGCATTTAATACAGTGC 59.933 40.000 0.00 0.00 36.88 4.40
559 886 7.547227 ACCAAAGTCAAAATAGAATATGCCAC 58.453 34.615 0.00 0.00 0.00 5.01
560 887 6.980397 CCAAAGTCAAAATAGAATATGCCACC 59.020 38.462 0.00 0.00 0.00 4.61
561 888 7.363705 CCAAAGTCAAAATAGAATATGCCACCA 60.364 37.037 0.00 0.00 0.00 4.17
581 908 4.876107 ACCATCCGTTGACAAATCATAGAC 59.124 41.667 0.00 0.00 33.85 2.59
584 911 5.097742 TCCGTTGACAAATCATAGACCAT 57.902 39.130 0.00 0.00 33.85 3.55
588 915 5.815222 CGTTGACAAATCATAGACCATGGTA 59.185 40.000 19.80 2.89 33.85 3.25
589 916 6.315144 CGTTGACAAATCATAGACCATGGTAA 59.685 38.462 19.80 9.86 33.85 2.85
654 986 7.859598 TCTTACCGTCTCTAATTAAGATCGTC 58.140 38.462 0.00 0.00 32.41 4.20
672 1004 3.930229 TCGTCAGTTACCATACAACATGC 59.070 43.478 0.00 0.00 0.00 4.06
673 1005 3.932710 CGTCAGTTACCATACAACATGCT 59.067 43.478 0.00 0.00 0.00 3.79
674 1006 4.391830 CGTCAGTTACCATACAACATGCTT 59.608 41.667 0.00 0.00 0.00 3.91
675 1007 5.579119 CGTCAGTTACCATACAACATGCTTA 59.421 40.000 0.00 0.00 0.00 3.09
676 1008 6.455113 CGTCAGTTACCATACAACATGCTTAC 60.455 42.308 0.00 0.00 0.00 2.34
678 1010 7.065803 GTCAGTTACCATACAACATGCTTACAT 59.934 37.037 0.00 0.00 36.79 2.29
681 1013 9.627123 AGTTACCATACAACATGCTTACATTAT 57.373 29.630 0.00 0.00 32.87 1.28
684 1016 8.383318 ACCATACAACATGCTTACATTATCTC 57.617 34.615 0.00 0.00 32.87 2.75
713 1060 4.591072 AGAGATAGGGGGATCTTCGAAAAG 59.409 45.833 0.00 0.00 36.27 2.27
743 1090 6.636850 CACCCAAGAGTAAAAACGAAATGAAG 59.363 38.462 0.00 0.00 0.00 3.02
747 1094 4.217767 AGAGTAAAAACGAAATGAAGGGGC 59.782 41.667 0.00 0.00 0.00 5.80
756 1103 2.891191 AATGAAGGGGCGGTAAAGAA 57.109 45.000 0.00 0.00 0.00 2.52
758 1105 1.354101 TGAAGGGGCGGTAAAGAAGA 58.646 50.000 0.00 0.00 0.00 2.87
760 1107 1.002773 GAAGGGGCGGTAAAGAAGACA 59.997 52.381 0.00 0.00 0.00 3.41
837 1190 3.483954 CCATTTCGTGGCCTGATCT 57.516 52.632 3.32 0.00 42.12 2.75
838 1191 1.019673 CCATTTCGTGGCCTGATCTG 58.980 55.000 3.32 2.95 42.12 2.90
841 1194 0.391661 TTTCGTGGCCTGATCTGCTC 60.392 55.000 3.32 0.38 0.00 4.26
842 1195 2.563050 TTCGTGGCCTGATCTGCTCG 62.563 60.000 3.32 11.39 0.00 5.03
843 1196 2.895680 GTGGCCTGATCTGCTCGA 59.104 61.111 3.32 0.00 0.00 4.04
845 1198 2.279120 GGCCTGATCTGCTCGACG 60.279 66.667 0.00 0.00 0.00 5.12
846 1199 2.959071 GCCTGATCTGCTCGACGC 60.959 66.667 0.00 0.58 39.77 5.19
850 1203 2.352915 GATCTGCTCGACGCCTCG 60.353 66.667 0.00 0.00 41.65 4.63
874 1227 4.122149 CCACGCCCCCATTGCCTA 62.122 66.667 0.00 0.00 0.00 3.93
875 1228 2.195683 CACGCCCCCATTGCCTAT 59.804 61.111 0.00 0.00 0.00 2.57
876 1229 1.454104 CACGCCCCCATTGCCTATA 59.546 57.895 0.00 0.00 0.00 1.31
877 1230 0.038166 CACGCCCCCATTGCCTATAT 59.962 55.000 0.00 0.00 0.00 0.86
878 1231 1.280710 CACGCCCCCATTGCCTATATA 59.719 52.381 0.00 0.00 0.00 0.86
879 1232 1.989586 ACGCCCCCATTGCCTATATAA 59.010 47.619 0.00 0.00 0.00 0.98
880 1233 2.377193 ACGCCCCCATTGCCTATATAAA 59.623 45.455 0.00 0.00 0.00 1.40
881 1234 2.752903 CGCCCCCATTGCCTATATAAAC 59.247 50.000 0.00 0.00 0.00 2.01
882 1235 3.773560 GCCCCCATTGCCTATATAAACA 58.226 45.455 0.00 0.00 0.00 2.83
883 1236 3.509967 GCCCCCATTGCCTATATAAACAC 59.490 47.826 0.00 0.00 0.00 3.32
884 1237 4.086457 CCCCCATTGCCTATATAAACACC 58.914 47.826 0.00 0.00 0.00 4.16
886 1239 3.756434 CCCATTGCCTATATAAACACCGG 59.244 47.826 0.00 0.00 0.00 5.28
887 1240 3.190535 CCATTGCCTATATAAACACCGGC 59.809 47.826 0.00 2.27 38.01 6.13
888 1241 2.554370 TGCCTATATAAACACCGGCC 57.446 50.000 0.00 0.00 36.74 6.13
889 1242 1.769465 TGCCTATATAAACACCGGCCA 59.231 47.619 0.00 0.00 36.74 5.36
890 1243 2.224426 TGCCTATATAAACACCGGCCAG 60.224 50.000 0.00 0.00 36.74 4.85
891 1244 2.423577 CCTATATAAACACCGGCCAGC 58.576 52.381 0.00 0.00 0.00 4.85
892 1245 2.038557 CCTATATAAACACCGGCCAGCT 59.961 50.000 0.00 0.00 0.00 4.24
893 1246 2.256117 ATATAAACACCGGCCAGCTC 57.744 50.000 0.00 0.00 0.00 4.09
894 1247 0.179468 TATAAACACCGGCCAGCTCC 59.821 55.000 0.00 0.00 0.00 4.70
895 1248 1.847798 ATAAACACCGGCCAGCTCCA 61.848 55.000 0.00 0.00 0.00 3.86
911 3514 0.034186 TCCACCACCAAGCATCCATC 60.034 55.000 0.00 0.00 0.00 3.51
912 3515 1.378882 CCACCACCAAGCATCCATCG 61.379 60.000 0.00 0.00 0.00 3.84
953 3557 4.043750 CACAACACACATCAAACACATCC 58.956 43.478 0.00 0.00 0.00 3.51
1353 3989 3.387374 AGCTTGATCCATCGTCTCTTCAT 59.613 43.478 0.00 0.00 0.00 2.57
1389 4044 0.101399 ATGCTGACGACGATGAGGTC 59.899 55.000 0.00 0.00 0.00 3.85
1498 4159 2.833582 TCGACCTCGAGATGGGCC 60.834 66.667 15.71 0.00 44.22 5.80
1746 4407 2.097038 CGCCGAGCAGGACTTTCTG 61.097 63.158 2.12 0.00 45.00 3.02
1759 4420 5.049129 CAGGACTTTCTGAACATGTTCTTCC 60.049 44.000 32.57 25.43 40.14 3.46
1907 4579 6.024049 GCTTCACAGCTTTGTCATATAACAC 58.976 40.000 0.00 0.00 43.51 3.32
1908 4580 5.778161 TCACAGCTTTGTCATATAACACG 57.222 39.130 0.00 0.00 0.00 4.49
1931 4610 7.165647 CACGATATTATGATTCTCATCTCGCTC 59.834 40.741 0.00 0.00 38.26 5.03
1935 4622 3.279853 TGATTCTCATCTCGCTCGATG 57.720 47.619 5.92 5.92 41.64 3.84
1936 4623 1.984990 GATTCTCATCTCGCTCGATGC 59.015 52.381 7.10 0.00 40.41 3.91
2057 4755 1.740285 GTGGGCCATCTACGACGAT 59.260 57.895 10.70 0.00 0.00 3.73
2081 4788 0.606401 GCCTCAACTACAAGCCTGCA 60.606 55.000 0.00 0.00 0.00 4.41
2147 4854 2.943978 CGCCGTCAAGTCCTTCCCT 61.944 63.158 0.00 0.00 0.00 4.20
2168 4875 2.494445 CCATCGGCTGCGTAGTCA 59.506 61.111 5.82 0.00 0.00 3.41
2294 5008 8.956533 TTTGGTATTGTAGATCATCAATCGAA 57.043 30.769 15.28 8.41 39.55 3.71
2328 5042 5.218139 CAGTGTTCTTTTCTTGATTGAGGC 58.782 41.667 0.00 0.00 0.00 4.70
2334 5048 2.270352 TTCTTGATTGAGGCACGGTT 57.730 45.000 0.00 0.00 0.00 4.44
2349 5155 5.123344 AGGCACGGTTATCATAGTGTTTTTC 59.877 40.000 0.00 0.00 36.99 2.29
2409 5215 1.134907 CGCGGTTGGTCCAACTACTAT 60.135 52.381 29.41 0.00 43.14 2.12
2432 5238 4.577693 TGTTTATAGATCGACCTGCTACGT 59.422 41.667 0.00 0.00 0.00 3.57
2433 5239 5.759763 TGTTTATAGATCGACCTGCTACGTA 59.240 40.000 0.00 0.00 0.00 3.57
2434 5240 6.429078 TGTTTATAGATCGACCTGCTACGTAT 59.571 38.462 0.00 0.00 0.00 3.06
2435 5241 7.603784 TGTTTATAGATCGACCTGCTACGTATA 59.396 37.037 0.00 0.00 0.00 1.47
2436 5242 7.531280 TTATAGATCGACCTGCTACGTATAC 57.469 40.000 0.00 0.00 0.00 1.47
2437 5243 4.005487 AGATCGACCTGCTACGTATACT 57.995 45.455 0.00 0.00 0.00 2.12
2453 5259 2.519377 TACTACACGTATGCATGGCC 57.481 50.000 10.16 0.00 0.00 5.36
2454 5260 0.179056 ACTACACGTATGCATGGCCC 60.179 55.000 10.16 0.00 0.00 5.80
2467 5273 0.678950 ATGGCCCAAACGTTTTGGAG 59.321 50.000 29.73 18.50 42.06 3.86
2470 5276 2.164338 GGCCCAAACGTTTTGGAGATA 58.836 47.619 29.73 0.00 42.06 1.98
2471 5277 2.758423 GGCCCAAACGTTTTGGAGATAT 59.242 45.455 29.73 0.00 42.06 1.63
2472 5278 3.194755 GGCCCAAACGTTTTGGAGATATT 59.805 43.478 29.73 0.00 42.06 1.28
2473 5279 4.322424 GGCCCAAACGTTTTGGAGATATTT 60.322 41.667 29.73 0.00 42.06 1.40
2474 5280 5.234752 GCCCAAACGTTTTGGAGATATTTT 58.765 37.500 29.73 0.00 42.06 1.82
2475 5281 5.347635 GCCCAAACGTTTTGGAGATATTTTC 59.652 40.000 29.73 9.05 42.06 2.29
2476 5282 5.867174 CCCAAACGTTTTGGAGATATTTTCC 59.133 40.000 23.25 1.28 42.06 3.13
2477 5283 5.867174 CCAAACGTTTTGGAGATATTTTCCC 59.133 40.000 11.66 0.00 42.06 3.97
2478 5284 6.451393 CAAACGTTTTGGAGATATTTTCCCA 58.549 36.000 11.66 0.00 33.62 4.37
2479 5285 6.658188 AACGTTTTGGAGATATTTTCCCAA 57.342 33.333 0.00 0.00 34.67 4.12
2480 5286 6.020971 ACGTTTTGGAGATATTTTCCCAAC 57.979 37.500 0.00 6.89 35.61 3.77
2481 5287 5.773176 ACGTTTTGGAGATATTTTCCCAACT 59.227 36.000 0.00 0.00 35.61 3.16
2534 5376 9.231297 CGTATCCCTTTGTATATTCATTGGATT 57.769 33.333 10.80 0.55 0.00 3.01
2537 5379 8.924511 TCCCTTTGTATATTCATTGGATTCTC 57.075 34.615 3.72 0.00 0.00 2.87
2538 5380 8.501904 TCCCTTTGTATATTCATTGGATTCTCA 58.498 33.333 3.72 0.00 0.00 3.27
2539 5381 9.305555 CCCTTTGTATATTCATTGGATTCTCAT 57.694 33.333 3.72 0.00 0.00 2.90
2544 5386 8.506437 TGTATATTCATTGGATTCTCATTTCGC 58.494 33.333 0.00 0.00 0.00 4.70
2545 5387 7.756395 ATATTCATTGGATTCTCATTTCGCT 57.244 32.000 0.00 0.00 0.00 4.93
2546 5388 4.888038 TCATTGGATTCTCATTTCGCTG 57.112 40.909 0.00 0.00 0.00 5.18
2547 5389 3.065786 TCATTGGATTCTCATTTCGCTGC 59.934 43.478 0.00 0.00 0.00 5.25
2557 5399 0.038892 ATTTCGCTGCTGCCTTGTTG 60.039 50.000 10.24 0.00 35.36 3.33
2585 5427 0.541063 TCCCCTTGCTGTCTACGTGA 60.541 55.000 0.00 0.00 0.00 4.35
2586 5428 0.108615 CCCCTTGCTGTCTACGTGAG 60.109 60.000 0.00 0.00 0.00 3.51
2618 5460 1.531149 CTACTTTGCGACCAACACCAG 59.469 52.381 0.00 0.00 0.00 4.00
2634 5487 6.183360 CCAACACCAGCTAGTAGAAGTAGTAG 60.183 46.154 0.00 0.00 35.84 2.57
2635 5488 6.064735 ACACCAGCTAGTAGAAGTAGTAGT 57.935 41.667 0.00 0.00 35.37 2.73
2637 5490 7.274447 ACACCAGCTAGTAGAAGTAGTAGTAG 58.726 42.308 0.00 0.00 35.37 2.57
2638 5491 7.125507 ACACCAGCTAGTAGAAGTAGTAGTAGA 59.874 40.741 0.00 0.00 35.37 2.59
2649 5502 8.671384 AGAAGTAGTAGTAGATGTTAGCTCAG 57.329 38.462 0.00 0.00 0.00 3.35
2661 5514 4.676546 TGTTAGCTCAGTCGATCAAGATG 58.323 43.478 0.00 0.00 0.00 2.90
2675 5528 1.857217 CAAGATGAAGCGATGGAGACG 59.143 52.381 0.00 0.00 0.00 4.18
2878 5732 2.051804 CTCGGCATGTCCAAATCGCC 62.052 60.000 6.92 0.00 39.45 5.54
2962 6040 4.053067 GTCGCTCCTACAACGACG 57.947 61.111 0.00 0.00 45.52 5.12
2988 6066 2.921754 CCTCGTCTATTTCGTCAACACC 59.078 50.000 0.00 0.00 0.00 4.16
2989 6067 2.587956 TCGTCTATTTCGTCAACACCG 58.412 47.619 0.00 0.00 0.00 4.94
3059 6141 1.674817 GGAAACGTAGCTAGCTTGCCA 60.675 52.381 24.88 0.61 0.00 4.92
3066 6148 2.982130 CTAGCTTGCCACCGGACT 59.018 61.111 9.46 0.00 0.00 3.85
3086 6168 2.494530 GGGCGAGATCGAGCTCCTT 61.495 63.158 24.00 0.00 43.02 3.36
3087 6169 1.007849 GGCGAGATCGAGCTCCTTC 60.008 63.158 24.00 13.29 43.02 3.46
3088 6170 1.369930 GCGAGATCGAGCTCCTTCG 60.370 63.158 24.00 14.71 43.02 3.79
3090 6172 1.218763 CGAGATCGAGCTCCTTCGTA 58.781 55.000 24.00 0.00 43.02 3.43
3097 6179 2.879462 GCTCCTTCGTACGGTGCG 60.879 66.667 16.52 12.54 32.23 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 23 8.019656 ACACTATTATCCAGGGTAAAGTAGTG 57.980 38.462 21.97 21.97 41.17 2.74
30 32 4.801164 ACTCGTACACTATTATCCAGGGT 58.199 43.478 0.00 0.00 33.25 4.34
50 52 8.153550 GATAATGTAACCATGATCAGAGGAACT 58.846 37.037 20.48 9.12 39.02 3.01
52 54 7.293299 AGGATAATGTAACCATGATCAGAGGAA 59.707 37.037 20.48 7.93 39.78 3.36
53 55 6.789457 AGGATAATGTAACCATGATCAGAGGA 59.211 38.462 20.48 2.10 39.78 3.71
54 56 7.013823 AGGATAATGTAACCATGATCAGAGG 57.986 40.000 13.85 13.85 39.78 3.69
80 84 6.292150 TGACATGGTGTGTTATAAGTTCACA 58.708 36.000 0.00 9.11 42.36 3.58
81 85 6.795098 TGACATGGTGTGTTATAAGTTCAC 57.205 37.500 0.00 6.23 42.36 3.18
83 91 7.250569 CCAATGACATGGTGTGTTATAAGTTC 58.749 38.462 0.00 0.00 42.36 3.01
85 93 5.125417 GCCAATGACATGGTGTGTTATAAGT 59.875 40.000 0.00 0.00 42.36 2.24
88 96 4.854173 AGCCAATGACATGGTGTGTTATA 58.146 39.130 0.00 0.00 42.36 0.98
94 102 2.519771 ATGAGCCAATGACATGGTGT 57.480 45.000 0.00 0.00 42.75 4.16
104 112 1.802636 CGCGGTCAAATGAGCCAAT 59.197 52.632 0.00 0.00 39.23 3.16
136 144 1.005394 ACGGACGGCGAGACAATTT 60.005 52.632 16.62 0.00 0.00 1.82
246 254 2.981859 TAAAATGTCTCCGGCTCTCC 57.018 50.000 0.00 0.00 0.00 3.71
247 255 3.002759 GCAATAAAATGTCTCCGGCTCTC 59.997 47.826 0.00 0.00 0.00 3.20
248 256 2.945668 GCAATAAAATGTCTCCGGCTCT 59.054 45.455 0.00 0.00 0.00 4.09
249 257 2.286418 CGCAATAAAATGTCTCCGGCTC 60.286 50.000 0.00 0.00 0.00 4.70
250 258 1.670811 CGCAATAAAATGTCTCCGGCT 59.329 47.619 0.00 0.00 0.00 5.52
251 259 1.668751 TCGCAATAAAATGTCTCCGGC 59.331 47.619 0.00 0.00 0.00 6.13
279 287 2.290367 TCTTGTGCTGTCAAATCAACCG 59.710 45.455 0.00 0.00 0.00 4.44
282 290 3.243501 GCCTTCTTGTGCTGTCAAATCAA 60.244 43.478 0.00 0.00 0.00 2.57
298 306 2.677037 CGTATTTCTTCCCACGCCTTCT 60.677 50.000 0.00 0.00 0.00 2.85
309 321 5.065602 GGTGAAATGTACCCCGTATTTCTTC 59.934 44.000 13.61 8.67 40.01 2.87
321 333 1.689352 CGCGTCCGGTGAAATGTACC 61.689 60.000 0.00 0.00 34.81 3.34
393 430 1.134098 CAATTGGAGCGGGAGGTATGT 60.134 52.381 0.00 0.00 43.00 2.29
394 431 1.597742 CAATTGGAGCGGGAGGTATG 58.402 55.000 0.00 0.00 43.00 2.39
395 432 0.474184 CCAATTGGAGCGGGAGGTAT 59.526 55.000 20.50 0.00 43.00 2.73
396 433 0.619255 TCCAATTGGAGCGGGAGGTA 60.619 55.000 23.63 0.00 43.00 3.08
403 452 3.806625 AATTCCATTCCAATTGGAGCG 57.193 42.857 25.69 19.83 46.36 5.03
464 513 9.477484 AACAGATAATCAAGCGGTTTATACTAG 57.523 33.333 0.00 0.00 0.00 2.57
495 813 7.713507 TGTATTAAATGCCATGTACCACTAGAC 59.286 37.037 0.00 0.00 0.00 2.59
501 819 5.067153 GCACTGTATTAAATGCCATGTACCA 59.933 40.000 0.00 0.00 31.71 3.25
502 820 5.299279 AGCACTGTATTAAATGCCATGTACC 59.701 40.000 0.00 0.00 38.92 3.34
503 821 6.377327 AGCACTGTATTAAATGCCATGTAC 57.623 37.500 0.00 0.00 38.92 2.90
504 822 6.204688 GCTAGCACTGTATTAAATGCCATGTA 59.795 38.462 10.63 0.00 38.92 2.29
511 829 9.435688 TGGTATATGCTAGCACTGTATTAAATG 57.564 33.333 22.07 0.00 0.00 2.32
520 838 5.359756 TGACTTTGGTATATGCTAGCACTG 58.640 41.667 22.07 5.03 0.00 3.66
524 842 9.273016 TCTATTTTGACTTTGGTATATGCTAGC 57.727 33.333 8.10 8.10 0.00 3.42
559 886 4.273480 GGTCTATGATTTGTCAACGGATGG 59.727 45.833 0.00 0.00 0.00 3.51
560 887 4.875536 TGGTCTATGATTTGTCAACGGATG 59.124 41.667 0.00 0.00 0.00 3.51
561 888 5.097742 TGGTCTATGATTTGTCAACGGAT 57.902 39.130 0.00 0.00 0.00 4.18
617 948 3.326880 AGACGGTAAGAAGTGATTTGGGT 59.673 43.478 0.00 0.00 0.00 4.51
654 986 6.735678 TGTAAGCATGTTGTATGGTAACTG 57.264 37.500 0.00 0.00 37.61 3.16
681 1013 5.800646 AGATCCCCCTATCTCTTATCTGAGA 59.199 44.000 0.00 0.00 45.71 3.27
684 1016 5.359576 CGAAGATCCCCCTATCTCTTATCTG 59.640 48.000 0.00 0.00 35.10 2.90
700 1045 4.127907 GGGTGGATACTTTTCGAAGATCC 58.872 47.826 17.18 17.18 37.23 3.36
713 1060 5.240121 TCGTTTTTACTCTTGGGTGGATAC 58.760 41.667 0.00 0.00 0.00 2.24
743 1090 2.835027 CTATGTCTTCTTTACCGCCCC 58.165 52.381 0.00 0.00 0.00 5.80
747 1094 5.769484 TCCTAGCTATGTCTTCTTTACCG 57.231 43.478 0.00 0.00 0.00 4.02
810 1163 1.444836 CCACGAAATGGGAAGCGTAA 58.555 50.000 0.00 0.00 45.95 3.18
812 1165 3.981308 CCACGAAATGGGAAGCGT 58.019 55.556 0.00 0.00 45.95 5.07
820 1173 0.379669 GCAGATCAGGCCACGAAATG 59.620 55.000 5.01 5.63 0.00 2.32
823 1176 1.219124 GAGCAGATCAGGCCACGAA 59.781 57.895 5.01 0.00 0.00 3.85
824 1177 2.895680 GAGCAGATCAGGCCACGA 59.104 61.111 5.01 0.06 0.00 4.35
825 1178 2.584418 CGAGCAGATCAGGCCACG 60.584 66.667 5.01 8.42 0.00 4.94
826 1179 1.520342 GTCGAGCAGATCAGGCCAC 60.520 63.158 5.01 0.00 0.00 5.01
863 1216 3.756434 CGGTGTTTATATAGGCAATGGGG 59.244 47.826 0.00 0.00 0.00 4.96
865 1218 3.190535 GCCGGTGTTTATATAGGCAATGG 59.809 47.826 1.90 4.29 43.65 3.16
866 1219 3.190535 GGCCGGTGTTTATATAGGCAATG 59.809 47.826 1.90 0.00 45.79 2.82
867 1220 3.181438 TGGCCGGTGTTTATATAGGCAAT 60.181 43.478 1.90 0.00 45.79 3.56
868 1221 2.172930 TGGCCGGTGTTTATATAGGCAA 59.827 45.455 1.90 0.00 45.79 4.52
869 1222 1.769465 TGGCCGGTGTTTATATAGGCA 59.231 47.619 1.90 0.59 45.79 4.75
870 1223 2.423577 CTGGCCGGTGTTTATATAGGC 58.576 52.381 2.29 0.80 43.47 3.93
871 1224 2.038557 AGCTGGCCGGTGTTTATATAGG 59.961 50.000 14.55 0.00 0.00 2.57
874 1227 1.202770 GGAGCTGGCCGGTGTTTATAT 60.203 52.381 14.55 0.00 0.00 0.86
875 1228 0.179468 GGAGCTGGCCGGTGTTTATA 59.821 55.000 14.55 0.00 0.00 0.98
876 1229 1.077716 GGAGCTGGCCGGTGTTTAT 60.078 57.895 14.55 0.00 0.00 1.40
877 1230 2.349755 GGAGCTGGCCGGTGTTTA 59.650 61.111 14.55 0.00 0.00 2.01
878 1231 3.884774 TGGAGCTGGCCGGTGTTT 61.885 61.111 14.55 0.00 0.00 2.83
879 1232 4.643387 GTGGAGCTGGCCGGTGTT 62.643 66.667 14.55 0.00 0.00 3.32
886 1239 2.674380 CTTGGTGGTGGAGCTGGC 60.674 66.667 0.00 0.00 0.00 4.85
887 1240 2.674380 GCTTGGTGGTGGAGCTGG 60.674 66.667 0.00 0.00 33.72 4.85
888 1241 1.303888 ATGCTTGGTGGTGGAGCTG 60.304 57.895 0.00 0.00 37.32 4.24
889 1242 1.001641 GATGCTTGGTGGTGGAGCT 60.002 57.895 0.00 0.00 37.32 4.09
890 1243 2.048603 GGATGCTTGGTGGTGGAGC 61.049 63.158 0.00 0.00 36.95 4.70
891 1244 0.033796 ATGGATGCTTGGTGGTGGAG 60.034 55.000 0.00 0.00 0.00 3.86
892 1245 0.034186 GATGGATGCTTGGTGGTGGA 60.034 55.000 0.00 0.00 0.00 4.02
893 1246 1.378882 CGATGGATGCTTGGTGGTGG 61.379 60.000 0.00 0.00 0.00 4.61
894 1247 0.392863 TCGATGGATGCTTGGTGGTG 60.393 55.000 0.00 0.00 0.00 4.17
895 1248 0.327924 TTCGATGGATGCTTGGTGGT 59.672 50.000 0.00 0.00 0.00 4.16
911 3514 0.654472 GACTTGTGCGTGCTTGTTCG 60.654 55.000 0.00 0.00 0.00 3.95
912 3515 0.317020 GGACTTGTGCGTGCTTGTTC 60.317 55.000 0.00 0.00 0.00 3.18
953 3557 4.160814 TGCTTCAAATCAAAGGATGGATGG 59.839 41.667 0.00 0.00 32.92 3.51
1005 3625 2.517875 ATCCGCTTGAGCATGGGC 60.518 61.111 3.65 0.00 42.21 5.36
1353 3989 3.598019 GCATCAAGCCAAGGATGAAAA 57.402 42.857 5.86 0.00 42.73 2.29
1389 4044 5.011090 ACTGCATAGTACATACACCACAG 57.989 43.478 0.00 0.00 34.74 3.66
1446 4101 0.524414 TGTCGTACACCTGGATGTCG 59.476 55.000 0.00 7.58 33.85 4.35
1498 4159 2.158959 CCTTGACGGCGTAGAAGCG 61.159 63.158 14.74 8.64 38.18 4.68
1550 4211 0.040246 GTAGCCGATCTCGTACTGCC 60.040 60.000 0.00 0.00 37.74 4.85
1684 4345 4.633769 CTTCTGAAGCAGGGCCTC 57.366 61.111 0.95 0.00 31.51 4.70
1695 4356 0.803117 CGGTGACTACGAGCTTCTGA 59.197 55.000 0.00 0.00 0.00 3.27
1696 4357 0.803117 TCGGTGACTACGAGCTTCTG 59.197 55.000 0.00 0.00 35.12 3.02
1698 4359 3.309453 GTCGGTGACTACGAGCTTC 57.691 57.895 0.00 0.00 41.50 3.86
1746 4407 1.076332 CGTCCCGGAAGAACATGTTC 58.924 55.000 27.69 27.69 39.78 3.18
1880 4552 2.849880 TGACAAAGCTGTGAAGCAAC 57.150 45.000 11.93 0.00 35.30 4.17
1935 4622 0.873054 CCATGGAAGCATCGATCAGC 59.127 55.000 5.56 0.00 0.00 4.26
1936 4623 0.873054 GCCATGGAAGCATCGATCAG 59.127 55.000 18.40 0.00 0.00 2.90
2057 4755 1.276421 GGCTTGTAGTTGAGGCTCTCA 59.724 52.381 16.72 0.00 38.87 3.27
2328 5042 5.121142 ACCGAAAAACACTATGATAACCGTG 59.879 40.000 0.00 0.00 0.00 4.94
2361 5167 4.096532 TGCACGTGTTTACAAAATCCTTCA 59.903 37.500 18.38 0.00 0.00 3.02
2409 5215 4.577693 ACGTAGCAGGTCGATCTATAAACA 59.422 41.667 0.00 0.00 0.00 2.83
2432 5238 3.056393 GGGCCATGCATACGTGTAGTATA 60.056 47.826 4.39 0.00 43.78 1.47
2433 5239 2.289444 GGGCCATGCATACGTGTAGTAT 60.289 50.000 4.39 0.00 46.37 2.12
2434 5240 1.069513 GGGCCATGCATACGTGTAGTA 59.930 52.381 4.39 0.00 40.03 1.82
2435 5241 0.179056 GGGCCATGCATACGTGTAGT 60.179 55.000 4.39 0.00 0.00 2.73
2436 5242 0.179059 TGGGCCATGCATACGTGTAG 60.179 55.000 0.00 0.00 0.00 2.74
2437 5243 0.253327 TTGGGCCATGCATACGTGTA 59.747 50.000 7.26 0.00 0.00 2.90
2453 5259 5.867174 GGGAAAATATCTCCAAAACGTTTGG 59.133 40.000 15.46 17.06 40.87 3.28
2454 5260 6.451393 TGGGAAAATATCTCCAAAACGTTTG 58.549 36.000 15.46 8.73 34.34 2.93
2467 5273 6.378280 ACCACAGAATCAGTTGGGAAAATATC 59.622 38.462 0.00 0.00 0.00 1.63
2470 5276 4.281688 CACCACAGAATCAGTTGGGAAAAT 59.718 41.667 0.00 0.00 0.00 1.82
2471 5277 3.636300 CACCACAGAATCAGTTGGGAAAA 59.364 43.478 0.00 0.00 0.00 2.29
2472 5278 3.221771 CACCACAGAATCAGTTGGGAAA 58.778 45.455 0.00 0.00 0.00 3.13
2473 5279 2.174639 ACACCACAGAATCAGTTGGGAA 59.825 45.455 0.00 0.00 0.00 3.97
2474 5280 1.774254 ACACCACAGAATCAGTTGGGA 59.226 47.619 0.00 0.00 0.00 4.37
2475 5281 2.154462 GACACCACAGAATCAGTTGGG 58.846 52.381 0.00 0.00 0.00 4.12
2476 5282 2.549754 GTGACACCACAGAATCAGTTGG 59.450 50.000 0.00 0.00 42.72 3.77
2477 5283 2.549754 GGTGACACCACAGAATCAGTTG 59.450 50.000 20.14 0.00 44.93 3.16
2478 5284 2.439507 AGGTGACACCACAGAATCAGTT 59.560 45.455 26.30 0.00 44.93 3.16
2479 5285 2.050144 AGGTGACACCACAGAATCAGT 58.950 47.619 26.30 0.00 44.93 3.41
2480 5286 2.224378 ACAGGTGACACCACAGAATCAG 60.224 50.000 26.30 6.89 44.93 2.90
2481 5287 1.768275 ACAGGTGACACCACAGAATCA 59.232 47.619 26.30 0.00 44.93 2.57
2504 5346 3.604875 ATATACAAAGGGATACGGCGG 57.395 47.619 13.24 0.00 37.60 6.13
2534 5376 0.321919 AAGGCAGCAGCGAAATGAGA 60.322 50.000 0.00 0.00 43.41 3.27
2535 5377 0.179171 CAAGGCAGCAGCGAAATGAG 60.179 55.000 0.00 0.00 43.41 2.90
2536 5378 0.890542 ACAAGGCAGCAGCGAAATGA 60.891 50.000 0.00 0.00 43.41 2.57
2537 5379 0.038892 AACAAGGCAGCAGCGAAATG 60.039 50.000 0.00 0.00 43.41 2.32
2538 5380 0.038892 CAACAAGGCAGCAGCGAAAT 60.039 50.000 0.00 0.00 43.41 2.17
2539 5381 1.359833 CAACAAGGCAGCAGCGAAA 59.640 52.632 0.00 0.00 43.41 3.46
2540 5382 2.554636 CCAACAAGGCAGCAGCGAA 61.555 57.895 0.00 0.00 43.41 4.70
2541 5383 2.979676 CCAACAAGGCAGCAGCGA 60.980 61.111 0.00 0.00 43.41 4.93
2542 5384 4.047059 CCCAACAAGGCAGCAGCG 62.047 66.667 0.00 0.00 43.41 5.18
2543 5385 2.914097 ACCCAACAAGGCAGCAGC 60.914 61.111 0.00 0.00 41.10 5.25
2544 5386 2.567497 CCACCCAACAAGGCAGCAG 61.567 63.158 0.00 0.00 35.39 4.24
2545 5387 2.521465 CCACCCAACAAGGCAGCA 60.521 61.111 0.00 0.00 35.39 4.41
2546 5388 2.521708 ACCACCCAACAAGGCAGC 60.522 61.111 0.00 0.00 35.39 5.25
2547 5389 1.042559 AACACCACCCAACAAGGCAG 61.043 55.000 0.00 0.00 35.39 4.85
2585 5427 3.560068 CGCAAAGTAGGACAAACTCAACT 59.440 43.478 0.00 0.00 0.00 3.16
2586 5428 3.558418 TCGCAAAGTAGGACAAACTCAAC 59.442 43.478 0.00 0.00 0.00 3.18
2634 5487 5.425577 TGATCGACTGAGCTAACATCTAC 57.574 43.478 0.00 0.00 0.00 2.59
2635 5488 5.823045 TCTTGATCGACTGAGCTAACATCTA 59.177 40.000 0.00 0.00 0.00 1.98
2637 5490 4.926244 TCTTGATCGACTGAGCTAACATC 58.074 43.478 0.00 0.00 0.00 3.06
2638 5491 4.991153 TCTTGATCGACTGAGCTAACAT 57.009 40.909 0.00 0.00 0.00 2.71
2649 5502 2.474359 CCATCGCTTCATCTTGATCGAC 59.526 50.000 0.00 0.00 35.64 4.20
2661 5514 1.590259 GCCTCGTCTCCATCGCTTC 60.590 63.158 0.00 0.00 0.00 3.86
2675 5528 1.281656 CGTTTTGGTTGGTCGCCTC 59.718 57.895 0.00 0.00 0.00 4.70
2788 5641 2.430382 TTCACGTCGACAAGGAGGCC 62.430 60.000 17.16 0.00 0.00 5.19
2791 5644 1.419374 CCTTTCACGTCGACAAGGAG 58.581 55.000 21.91 10.25 35.54 3.69
2962 6040 2.165030 TGACGAAATAGACGAGGAACCC 59.835 50.000 0.00 0.00 34.70 4.11
3030 6108 1.019805 GCTACGTTTCCCAGGTCAGC 61.020 60.000 0.00 0.00 0.00 4.26
3035 6113 0.824759 AGCTAGCTACGTTTCCCAGG 59.175 55.000 17.69 0.00 0.00 4.45
3037 6115 1.674817 GCAAGCTAGCTACGTTTCCCA 60.675 52.381 19.70 0.00 0.00 4.37
3039 6117 1.007580 GGCAAGCTAGCTACGTTTCC 58.992 55.000 19.70 1.90 34.17 3.13
3040 6118 1.393883 GTGGCAAGCTAGCTACGTTTC 59.606 52.381 19.70 5.65 36.28 2.78
3059 6141 1.528776 GATCTCGCCCTAGTCCGGT 60.529 63.158 0.00 0.00 0.00 5.28
3066 6148 1.601197 GGAGCTCGATCTCGCCCTA 60.601 63.158 7.83 0.00 39.60 3.53


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

AutoCloner maintained by Alex Coulton.