Multiple sequence alignment - TraesCS2A01G156100

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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 TraesCS2A01G156100 chr2A 100.000 3905 0 0 1 3905 103101908 103098004 0.000000e+00 7212.0
1 TraesCS2A01G156100 chr2A 90.291 618 40 6 1007 1617 251390719 251391323 0.000000e+00 791.0
2 TraesCS2A01G156100 chr2A 95.153 392 17 2 1437 1828 762079178 762079567 5.540000e-173 617.0
3 TraesCS2A01G156100 chr2A 93.939 165 9 1 1674 1838 121688683 121688846 8.380000e-62 248.0
4 TraesCS2A01G156100 chr2A 94.828 58 2 1 418 475 103101460 103101404 5.370000e-14 89.8
5 TraesCS2A01G156100 chr2A 94.828 58 2 1 449 505 103101491 103101434 5.370000e-14 89.8
6 TraesCS2A01G156100 chr2D 91.890 1751 86 27 2178 3905 106626789 106625072 0.000000e+00 2396.0
7 TraesCS2A01G156100 chr2D 90.726 1585 108 24 618 2185 106628382 106626820 0.000000e+00 2076.0
8 TraesCS2A01G156100 chr2D 95.619 388 16 1 1437 1824 622712191 622712577 4.290000e-174 621.0
9 TraesCS2A01G156100 chr2D 87.113 388 37 10 1 388 106629198 106628824 1.000000e-115 427.0
10 TraesCS2A01G156100 chr2D 92.670 191 12 2 1758 1947 106627393 106627204 1.380000e-69 274.0
11 TraesCS2A01G156100 chr2D 91.053 190 17 0 1612 1801 106627247 106627058 1.390000e-64 257.0
12 TraesCS2A01G156100 chr2D 94.737 57 3 0 382 438 106628660 106628604 5.370000e-14 89.8
13 TraesCS2A01G156100 chr4D 94.920 1181 51 3 1005 2185 46139925 46138754 0.000000e+00 1840.0
14 TraesCS2A01G156100 chr4D 93.627 612 36 1 1006 1617 45005469 45004861 0.000000e+00 911.0
15 TraesCS2A01G156100 chr2B 94.812 983 22 5 2178 3159 156591839 156590885 0.000000e+00 1506.0
16 TraesCS2A01G156100 chr2B 92.716 810 49 8 617 1421 156593472 156592668 0.000000e+00 1160.0
17 TraesCS2A01G156100 chr2B 90.168 773 68 3 1419 2185 156592640 156591870 0.000000e+00 1000.0
18 TraesCS2A01G156100 chr2B 89.845 709 40 13 3208 3905 156590659 156589972 0.000000e+00 881.0
19 TraesCS2A01G156100 chr2B 95.153 392 17 2 1437 1828 795318205 795317816 5.540000e-173 617.0
20 TraesCS2A01G156100 chr2B 88.838 439 37 9 1 438 156594121 156593694 2.670000e-146 529.0
21 TraesCS2A01G156100 chr7D 95.060 749 36 1 1437 2185 475097436 475096689 0.000000e+00 1177.0
22 TraesCS2A01G156100 chr5B 92.097 620 45 2 1005 1623 236414536 236415152 0.000000e+00 870.0
23 TraesCS2A01G156100 chr5B 91.613 620 48 2 1005 1623 236737069 236737685 0.000000e+00 854.0
24 TraesCS2A01G156100 chr1A 91.176 612 39 2 1006 1617 570975257 570974661 0.000000e+00 817.0
25 TraesCS2A01G156100 chr1A 89.614 337 26 1 1849 2185 570974433 570974106 1.680000e-113 420.0
26 TraesCS2A01G156100 chr5A 90.645 620 48 5 1005 1623 669523780 669523170 0.000000e+00 815.0


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 TraesCS2A01G156100 chr2A 103098004 103101908 3904 True 2463.866667 7212 96.552000 1 3905 3 chr2A.!!$R1 3904
1 TraesCS2A01G156100 chr2A 251390719 251391323 604 False 791.000000 791 90.291000 1007 1617 1 chr2A.!!$F2 610
2 TraesCS2A01G156100 chr2D 106625072 106629198 4126 True 919.966667 2396 91.364833 1 3905 6 chr2D.!!$R1 3904
3 TraesCS2A01G156100 chr4D 46138754 46139925 1171 True 1840.000000 1840 94.920000 1005 2185 1 chr4D.!!$R2 1180
4 TraesCS2A01G156100 chr4D 45004861 45005469 608 True 911.000000 911 93.627000 1006 1617 1 chr4D.!!$R1 611
5 TraesCS2A01G156100 chr2B 156589972 156594121 4149 True 1015.200000 1506 91.275800 1 3905 5 chr2B.!!$R2 3904
6 TraesCS2A01G156100 chr7D 475096689 475097436 747 True 1177.000000 1177 95.060000 1437 2185 1 chr7D.!!$R1 748
7 TraesCS2A01G156100 chr5B 236414536 236415152 616 False 870.000000 870 92.097000 1005 1623 1 chr5B.!!$F1 618
8 TraesCS2A01G156100 chr5B 236737069 236737685 616 False 854.000000 854 91.613000 1005 1623 1 chr5B.!!$F2 618
9 TraesCS2A01G156100 chr1A 570974106 570975257 1151 True 618.500000 817 90.395000 1006 2185 2 chr1A.!!$R1 1179
10 TraesCS2A01G156100 chr5A 669523170 669523780 610 True 815.000000 815 90.645000 1005 1623 1 chr5A.!!$R1 618

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
444 616 0.193321 TGGGAGCCTGGGATGCTATA 59.807 55.0 0.0 0.0 39.69 1.31 F
497 669 0.324091 ATTTTGAGCTGGGAGCCTGG 60.324 55.0 0.0 0.0 43.77 4.45 F
945 1223 0.767060 ACTCACCCCTTTCCCTTCGT 60.767 55.0 0.0 0.0 0.00 3.85 F
2549 2987 0.043637 TCGGAAACCTATCCTGGGGT 59.956 55.0 0.0 0.0 37.34 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1814 0.537371 CCCTTGGACAACCTGACACC 60.537 60.000 0.00 0.0 37.04 4.16 R
1517 1848 3.997021 CCTGAAGGACACAATCTACACAC 59.003 47.826 0.00 0.0 37.39 3.82 R
2552 2990 0.666374 TCTCGAGCGTTGAGTTGTCA 59.334 50.000 7.81 0.0 34.99 3.58 R
3429 4048 0.447801 CTGGCTTCCGGTTCGAATTG 59.552 55.000 0.00 0.0 0.00 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
113 114 1.003233 GGAGCGCTTGAAAGACCCT 60.003 57.895 13.26 0.00 0.00 4.34
161 162 4.198530 TGAGCAGACACATGTTTTCAGAA 58.801 39.130 0.00 0.00 0.00 3.02
162 163 4.035558 TGAGCAGACACATGTTTTCAGAAC 59.964 41.667 0.00 0.00 0.00 3.01
164 165 3.066621 GCAGACACATGTTTTCAGAACCA 59.933 43.478 0.00 0.00 0.00 3.67
199 200 5.755861 CCTTAGCTGTAGAAATTCTGTAGGC 59.244 44.000 5.64 5.09 0.00 3.93
204 205 4.843728 TGTAGAAATTCTGTAGGCAAGGG 58.156 43.478 5.64 0.00 0.00 3.95
208 209 0.548510 ATTCTGTAGGCAAGGGAGGC 59.451 55.000 0.00 0.00 0.00 4.70
234 235 2.619849 CCTGATGTTTGGAGGAGCACAT 60.620 50.000 0.00 0.00 32.41 3.21
245 246 2.099756 GAGGAGCACATTTTACATGGCC 59.900 50.000 0.00 0.00 0.00 5.36
283 284 4.879104 TTGGCAAAAGAGCAAATTGTTG 57.121 36.364 0.00 0.00 37.83 3.33
284 285 3.871485 TGGCAAAAGAGCAAATTGTTGT 58.129 36.364 0.00 0.00 37.06 3.32
285 286 4.260170 TGGCAAAAGAGCAAATTGTTGTT 58.740 34.783 0.00 0.00 37.06 2.83
286 287 5.423015 TGGCAAAAGAGCAAATTGTTGTTA 58.577 33.333 0.00 0.00 37.06 2.41
287 288 5.877012 TGGCAAAAGAGCAAATTGTTGTTAA 59.123 32.000 0.00 0.00 37.06 2.01
288 289 6.036953 TGGCAAAAGAGCAAATTGTTGTTAAG 59.963 34.615 0.00 0.00 37.06 1.85
289 290 6.421405 GCAAAAGAGCAAATTGTTGTTAAGG 58.579 36.000 0.00 0.00 37.06 2.69
290 291 6.421405 CAAAAGAGCAAATTGTTGTTAAGGC 58.579 36.000 0.00 0.00 37.06 4.35
291 292 4.935352 AGAGCAAATTGTTGTTAAGGCA 57.065 36.364 0.00 0.00 37.06 4.75
292 293 5.275067 AGAGCAAATTGTTGTTAAGGCAA 57.725 34.783 0.00 0.00 37.06 4.52
297 298 5.752955 GCAAATTGTTGTTAAGGCAAGAGAA 59.247 36.000 0.00 0.00 37.06 2.87
300 301 7.770801 AATTGTTGTTAAGGCAAGAGAAAAC 57.229 32.000 0.00 0.00 0.00 2.43
301 302 4.915704 TGTTGTTAAGGCAAGAGAAAACG 58.084 39.130 0.00 0.00 0.00 3.60
302 303 3.619233 TGTTAAGGCAAGAGAAAACGC 57.381 42.857 0.00 0.00 0.00 4.84
303 304 3.211045 TGTTAAGGCAAGAGAAAACGCT 58.789 40.909 0.00 0.00 0.00 5.07
305 306 4.219802 GTTAAGGCAAGAGAAAACGCTTC 58.780 43.478 0.00 0.00 0.00 3.86
306 307 1.239347 AGGCAAGAGAAAACGCTTCC 58.761 50.000 0.00 0.00 0.00 3.46
312 313 4.065789 CAAGAGAAAACGCTTCCTAGGTT 58.934 43.478 9.08 0.00 0.00 3.50
314 315 5.479124 AGAGAAAACGCTTCCTAGGTTTA 57.521 39.130 9.08 0.00 33.80 2.01
316 317 4.964593 AGAAAACGCTTCCTAGGTTTACA 58.035 39.130 9.08 0.00 33.80 2.41
317 318 5.557866 AGAAAACGCTTCCTAGGTTTACAT 58.442 37.500 9.08 0.00 33.80 2.29
325 326 3.884895 TCCTAGGTTTACATGCCATGTG 58.115 45.455 20.36 1.45 44.60 3.21
326 327 2.358898 CCTAGGTTTACATGCCATGTGC 59.641 50.000 20.36 9.91 44.60 4.57
332 333 3.625649 TTACATGCCATGTGCTGTAGA 57.374 42.857 20.36 0.00 44.60 2.59
333 334 2.034104 ACATGCCATGTGCTGTAGAG 57.966 50.000 10.06 0.00 43.01 2.43
334 335 1.280133 ACATGCCATGTGCTGTAGAGT 59.720 47.619 10.06 0.00 43.01 3.24
335 336 2.501316 ACATGCCATGTGCTGTAGAGTA 59.499 45.455 10.06 0.00 43.01 2.59
336 337 2.672961 TGCCATGTGCTGTAGAGTAC 57.327 50.000 0.86 0.86 42.00 2.73
341 342 4.038042 GCCATGTGCTGTAGAGTACTATGA 59.962 45.833 15.99 0.00 35.90 2.15
375 377 6.204882 CCTGAGACTTTTCGGAACTTTGTATT 59.795 38.462 0.00 0.00 0.00 1.89
380 382 8.727910 AGACTTTTCGGAACTTTGTATTATTCC 58.272 33.333 0.00 0.00 37.79 3.01
414 586 4.502105 TGATGTCAAAGCTATTGCCCTA 57.498 40.909 0.00 0.00 40.80 3.53
440 612 4.891037 GCTGGGAGCCTGGGATGC 62.891 72.222 0.00 0.00 34.48 3.91
441 613 3.095163 CTGGGAGCCTGGGATGCT 61.095 66.667 0.00 0.00 43.03 3.79
442 614 1.767672 CTGGGAGCCTGGGATGCTA 60.768 63.158 0.00 0.00 39.69 3.49
443 615 1.073474 TGGGAGCCTGGGATGCTAT 60.073 57.895 0.00 0.00 39.69 2.97
444 616 0.193321 TGGGAGCCTGGGATGCTATA 59.807 55.000 0.00 0.00 39.69 1.31
445 617 1.362224 GGGAGCCTGGGATGCTATAA 58.638 55.000 0.00 0.00 39.69 0.98
446 618 1.705186 GGGAGCCTGGGATGCTATAAA 59.295 52.381 0.00 0.00 39.69 1.40
447 619 2.310052 GGGAGCCTGGGATGCTATAAAT 59.690 50.000 0.00 0.00 39.69 1.40
448 620 3.245407 GGGAGCCTGGGATGCTATAAATT 60.245 47.826 0.00 0.00 39.69 1.82
449 621 4.411013 GGAGCCTGGGATGCTATAAATTT 58.589 43.478 0.00 0.00 39.69 1.82
450 622 4.835056 GGAGCCTGGGATGCTATAAATTTT 59.165 41.667 0.00 0.00 39.69 1.82
451 623 5.305386 GGAGCCTGGGATGCTATAAATTTTT 59.695 40.000 0.00 0.00 39.69 1.94
452 624 6.165700 AGCCTGGGATGCTATAAATTTTTG 57.834 37.500 0.00 0.00 37.28 2.44
453 625 5.070847 AGCCTGGGATGCTATAAATTTTTGG 59.929 40.000 0.00 0.00 37.28 3.28
454 626 5.742838 GCCTGGGATGCTATAAATTTTTGGG 60.743 44.000 0.00 0.00 0.00 4.12
455 627 5.289083 TGGGATGCTATAAATTTTTGGGC 57.711 39.130 0.00 0.00 0.00 5.36
456 628 4.968080 TGGGATGCTATAAATTTTTGGGCT 59.032 37.500 0.00 0.00 0.00 5.19
457 629 5.163322 TGGGATGCTATAAATTTTTGGGCTG 60.163 40.000 0.00 0.00 0.00 4.85
458 630 5.299949 GGATGCTATAAATTTTTGGGCTGG 58.700 41.667 0.00 0.00 0.00 4.85
459 631 4.751767 TGCTATAAATTTTTGGGCTGGG 57.248 40.909 0.00 0.00 0.00 4.45
460 632 4.357325 TGCTATAAATTTTTGGGCTGGGA 58.643 39.130 0.00 0.00 0.00 4.37
461 633 4.405358 TGCTATAAATTTTTGGGCTGGGAG 59.595 41.667 0.00 0.00 0.00 4.30
462 634 3.912496 ATAAATTTTTGGGCTGGGAGC 57.088 42.857 0.00 0.00 41.46 4.70
484 656 5.898972 AGCCTGGGATGCTATAAAATTTTGA 59.101 36.000 13.76 0.78 37.28 2.69
489 661 6.183360 TGGGATGCTATAAAATTTTGAGCTGG 60.183 38.462 26.75 10.41 33.89 4.85
490 662 6.218746 GGATGCTATAAAATTTTGAGCTGGG 58.781 40.000 26.75 9.66 33.89 4.45
491 663 6.040842 GGATGCTATAAAATTTTGAGCTGGGA 59.959 38.462 26.75 15.23 33.89 4.37
492 664 6.455360 TGCTATAAAATTTTGAGCTGGGAG 57.545 37.500 26.75 10.95 33.89 4.30
493 665 5.163519 TGCTATAAAATTTTGAGCTGGGAGC 60.164 40.000 26.75 17.28 42.84 4.70
494 666 4.743057 ATAAAATTTTGAGCTGGGAGCC 57.257 40.909 13.76 0.00 43.77 4.70
497 669 0.324091 ATTTTGAGCTGGGAGCCTGG 60.324 55.000 0.00 0.00 43.77 4.45
498 670 2.430704 TTTTGAGCTGGGAGCCTGGG 62.431 60.000 0.00 0.00 43.77 4.45
499 671 3.870607 TTGAGCTGGGAGCCTGGGA 62.871 63.158 0.00 0.00 43.77 4.37
501 673 3.095163 AGCTGGGAGCCTGGGATG 61.095 66.667 0.00 0.00 43.77 3.51
512 687 1.871080 CCTGGGATGTATCTCGTTGC 58.129 55.000 0.00 0.00 0.00 4.17
596 872 8.138074 GCAAGAGTTCCTCTAAAAGAAACATTT 58.862 33.333 0.00 0.00 40.28 2.32
641 917 9.706846 GGAAAAGAAACATTTTCAACAAGAATG 57.293 29.630 12.46 0.00 46.41 2.67
664 940 2.164827 TGGTGCTAAATGATGCTTGCTG 59.835 45.455 0.00 0.00 0.00 4.41
668 944 2.424601 GCTAAATGATGCTTGCTGGTGA 59.575 45.455 0.00 0.00 0.00 4.02
681 957 4.906065 TGCTGGTGAATTATCATGAAGC 57.094 40.909 0.00 0.96 38.01 3.86
689 965 5.750067 GTGAATTATCATGAAGCCGCAAAAT 59.250 36.000 0.00 0.00 38.01 1.82
690 966 6.917477 GTGAATTATCATGAAGCCGCAAAATA 59.083 34.615 0.00 0.00 38.01 1.40
691 967 7.113965 GTGAATTATCATGAAGCCGCAAAATAG 59.886 37.037 0.00 0.00 38.01 1.73
694 970 4.621068 TCATGAAGCCGCAAAATAGAAG 57.379 40.909 0.00 0.00 0.00 2.85
731 1007 4.967442 TGCATTATCCCATCCAATTCCAAA 59.033 37.500 0.00 0.00 0.00 3.28
733 1009 6.101442 TGCATTATCCCATCCAATTCCAAAAT 59.899 34.615 0.00 0.00 0.00 1.82
735 1011 8.323567 GCATTATCCCATCCAATTCCAAAATAT 58.676 33.333 0.00 0.00 0.00 1.28
748 1024 9.480053 CAATTCCAAAATATTAATACAGCCAGG 57.520 33.333 0.00 0.00 0.00 4.45
765 1041 3.006859 GCCAGGTTCCAGCTAAACATTTT 59.993 43.478 11.90 0.00 0.00 1.82
797 1074 1.598962 CACTGCCAGTGGGTCACAG 60.599 63.158 17.22 11.88 42.35 3.66
820 1097 1.771255 CCTCTTATCCCAACCCCAGAG 59.229 57.143 0.00 0.00 0.00 3.35
916 1194 3.920841 ACTATAAAACCCCCTCCACAGTT 59.079 43.478 0.00 0.00 0.00 3.16
945 1223 0.767060 ACTCACCCCTTTCCCTTCGT 60.767 55.000 0.00 0.00 0.00 3.85
1290 1571 1.302511 CAACCTCCCCTTCACCGTG 60.303 63.158 0.00 0.00 0.00 4.94
1368 1649 5.460419 CGAGGTATAAATTCACACTCTCTGC 59.540 44.000 0.00 0.00 0.00 4.26
1376 1657 3.103447 TCACACTCTCTGCTCTTGTTG 57.897 47.619 0.00 0.00 0.00 3.33
1389 1676 6.040504 TCTGCTCTTGTTGACTAACAGTTAGA 59.959 38.462 24.59 2.66 46.63 2.10
1415 1702 4.657075 CGCGAATTATAACGGGCTAAAT 57.343 40.909 0.00 0.00 35.93 1.40
1424 1741 9.758651 AATTATAACGGGCTAAATTGAAATTCC 57.241 29.630 0.00 0.00 0.00 3.01
1483 1814 2.792749 GGGACGTTTTGTTTCAGTGTG 58.207 47.619 0.00 0.00 0.00 3.82
1517 1848 3.577848 TCCAAGGGATGTTGAATTGTTGG 59.422 43.478 0.00 0.00 35.52 3.77
1745 2082 7.897575 AATAGTCTCAGCTTGAACTAAGTTG 57.102 36.000 3.66 0.00 45.70 3.16
1831 2226 9.007901 GGTCGTGGAGTTGTTATACTAGTATAT 57.992 37.037 20.67 7.85 0.00 0.86
1913 2308 8.579863 AGCTTGAATTGCTTCAGTAAATTACTT 58.420 29.630 2.41 0.00 42.19 2.24
2088 2483 3.660111 GAAGTTGCTGCCGCCGTT 61.660 61.111 0.00 0.00 34.43 4.44
2158 2553 7.279615 CACCTTATCTTGGTACATTACATGGA 58.720 38.462 0.00 0.00 39.30 3.41
2312 2745 2.358898 AGTGCGAACTTTGCTGATTGTT 59.641 40.909 0.00 0.00 0.00 2.83
2549 2987 0.043637 TCGGAAACCTATCCTGGGGT 59.956 55.000 0.00 0.00 37.34 4.95
2552 2990 1.639108 GGAAACCTATCCTGGGGTGTT 59.361 52.381 0.00 0.00 36.50 3.32
2606 3044 2.299326 AAGGAAAGGTGCTTGATGCT 57.701 45.000 0.00 0.00 43.37 3.79
2630 3068 1.389555 TCATCTATGACCGCGACAGT 58.610 50.000 8.23 0.00 0.00 3.55
2841 3279 4.513406 TGGTTTTGTTCTGTAGGACCTT 57.487 40.909 0.00 0.00 0.00 3.50
3175 3614 3.018423 TGCTGTGTATGGCTCTCTCTA 57.982 47.619 0.00 0.00 0.00 2.43
3176 3615 2.690497 TGCTGTGTATGGCTCTCTCTAC 59.310 50.000 0.00 0.00 0.00 2.59
3177 3616 2.035321 GCTGTGTATGGCTCTCTCTACC 59.965 54.545 0.00 0.00 0.00 3.18
3178 3617 2.625790 CTGTGTATGGCTCTCTCTACCC 59.374 54.545 0.00 0.00 0.00 3.69
3230 3846 9.784531 TCTGAATGTCTTTTTCTAGATGAAGTT 57.215 29.630 12.66 3.85 35.89 2.66
3277 3896 4.154015 TCGTAAATCCACTGAATTGCTGTG 59.846 41.667 0.00 0.00 43.66 3.66
3400 4019 3.318557 CGATGGTCTAACCCTCTTCCTAC 59.681 52.174 0.00 0.00 37.50 3.18
3429 4048 1.301479 AACGCTTCTTCCCCACGTC 60.301 57.895 0.00 0.00 35.64 4.34
3495 4114 4.581493 CCTATATATGGCGTGTACGTACG 58.419 47.826 20.18 15.01 46.28 3.67
3562 4181 3.088532 CTGCTAGTCTAGGGCATAGAGG 58.911 54.545 9.47 4.49 41.28 3.69
3563 4182 2.447429 TGCTAGTCTAGGGCATAGAGGT 59.553 50.000 9.47 2.77 41.28 3.85
3564 4183 3.656264 TGCTAGTCTAGGGCATAGAGGTA 59.344 47.826 9.47 3.83 41.28 3.08
3565 4184 4.263550 TGCTAGTCTAGGGCATAGAGGTAG 60.264 50.000 9.47 13.63 41.28 3.18
3566 4185 4.263594 GCTAGTCTAGGGCATAGAGGTAGT 60.264 50.000 9.47 0.00 41.28 2.73
3567 4186 4.107127 AGTCTAGGGCATAGAGGTAGTG 57.893 50.000 9.47 0.00 41.28 2.74
3568 4187 3.722627 AGTCTAGGGCATAGAGGTAGTGA 59.277 47.826 9.47 0.00 41.28 3.41
3569 4188 4.076394 GTCTAGGGCATAGAGGTAGTGAG 58.924 52.174 9.47 0.00 41.28 3.51
3575 4194 4.153411 GGCATAGAGGTAGTGAGGTACAT 58.847 47.826 0.00 0.00 0.00 2.29
3585 4204 2.421424 AGTGAGGTACATCGACGTAACC 59.579 50.000 2.53 2.90 28.63 2.85
3803 4431 2.203509 CGTCTCCGGCCTATCCCT 60.204 66.667 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 4.471386 ACAGCTAAGGATATCTGTTGTGGT 59.529 41.667 2.05 0.00 35.50 4.16
162 163 5.028549 ACAGCTAAGGATATCTGTTGTGG 57.971 43.478 2.05 0.00 35.50 4.17
164 165 7.661536 TTCTACAGCTAAGGATATCTGTTGT 57.338 36.000 2.05 7.68 38.87 3.32
188 189 1.064389 GCCTCCCTTGCCTACAGAATT 60.064 52.381 0.00 0.00 0.00 2.17
189 190 0.548510 GCCTCCCTTGCCTACAGAAT 59.451 55.000 0.00 0.00 0.00 2.40
192 193 2.592308 GGCCTCCCTTGCCTACAG 59.408 66.667 0.00 0.00 45.70 2.74
208 209 0.682209 CCTCCAAACATCAGGCCTGG 60.682 60.000 32.23 19.57 0.00 4.45
213 214 1.271543 TGTGCTCCTCCAAACATCAGG 60.272 52.381 0.00 0.00 0.00 3.86
234 235 2.208132 ATCACCACGGCCATGTAAAA 57.792 45.000 2.24 0.00 0.00 1.52
245 246 2.794350 GCCAAAAGAAACAATCACCACG 59.206 45.455 0.00 0.00 0.00 4.94
275 276 7.010091 CGTTTTCTCTTGCCTTAACAACAATTT 59.990 33.333 0.00 0.00 0.00 1.82
283 284 3.898517 AGCGTTTTCTCTTGCCTTAAC 57.101 42.857 0.00 0.00 0.00 2.01
284 285 3.252458 GGAAGCGTTTTCTCTTGCCTTAA 59.748 43.478 0.00 0.00 28.95 1.85
285 286 2.812011 GGAAGCGTTTTCTCTTGCCTTA 59.188 45.455 0.00 0.00 28.95 2.69
286 287 1.609072 GGAAGCGTTTTCTCTTGCCTT 59.391 47.619 0.00 0.00 28.95 4.35
287 288 1.202818 AGGAAGCGTTTTCTCTTGCCT 60.203 47.619 0.00 0.00 34.33 4.75
288 289 1.239347 AGGAAGCGTTTTCTCTTGCC 58.761 50.000 0.00 0.00 34.33 4.52
289 290 2.416893 CCTAGGAAGCGTTTTCTCTTGC 59.583 50.000 1.05 0.00 34.08 4.01
290 291 3.665190 ACCTAGGAAGCGTTTTCTCTTG 58.335 45.455 17.98 0.00 0.00 3.02
291 292 4.353383 AACCTAGGAAGCGTTTTCTCTT 57.647 40.909 17.98 0.00 0.00 2.85
292 293 4.353383 AAACCTAGGAAGCGTTTTCTCT 57.647 40.909 17.98 0.00 0.00 3.10
297 298 3.439129 GCATGTAAACCTAGGAAGCGTTT 59.561 43.478 17.98 7.68 33.48 3.60
300 301 1.940613 GGCATGTAAACCTAGGAAGCG 59.059 52.381 17.98 0.00 0.00 4.68
301 302 2.999331 TGGCATGTAAACCTAGGAAGC 58.001 47.619 17.98 7.89 0.00 3.86
302 303 4.336433 CACATGGCATGTAAACCTAGGAAG 59.664 45.833 30.96 11.71 42.70 3.46
303 304 4.269183 CACATGGCATGTAAACCTAGGAA 58.731 43.478 30.96 0.00 42.70 3.36
305 306 2.358898 GCACATGGCATGTAAACCTAGG 59.641 50.000 30.96 17.56 42.70 3.02
306 307 3.698029 GCACATGGCATGTAAACCTAG 57.302 47.619 30.96 18.25 42.70 3.02
325 326 6.315091 TCCGAATTCATAGTACTCTACAGC 57.685 41.667 0.00 0.00 0.00 4.40
326 327 7.013464 AGGTTCCGAATTCATAGTACTCTACAG 59.987 40.741 0.00 0.00 0.00 2.74
332 333 5.892119 TCTCAGGTTCCGAATTCATAGTACT 59.108 40.000 6.22 0.00 0.00 2.73
333 334 5.978322 GTCTCAGGTTCCGAATTCATAGTAC 59.022 44.000 6.22 0.00 0.00 2.73
334 335 5.892119 AGTCTCAGGTTCCGAATTCATAGTA 59.108 40.000 6.22 0.00 0.00 1.82
335 336 4.712337 AGTCTCAGGTTCCGAATTCATAGT 59.288 41.667 6.22 0.00 0.00 2.12
336 337 5.269505 AGTCTCAGGTTCCGAATTCATAG 57.730 43.478 6.22 0.00 0.00 2.23
341 342 3.746492 CGAAAAGTCTCAGGTTCCGAATT 59.254 43.478 0.00 0.00 0.00 2.17
375 377 8.993404 TGACATCATAAACAATCCATGGAATA 57.007 30.769 20.67 7.69 0.00 1.75
380 382 7.262772 AGCTTTGACATCATAAACAATCCATG 58.737 34.615 0.00 0.00 0.00 3.66
427 599 3.728385 ATTTATAGCATCCCAGGCTCC 57.272 47.619 0.00 0.00 42.62 4.70
428 600 6.218746 CAAAAATTTATAGCATCCCAGGCTC 58.781 40.000 0.00 0.00 42.62 4.70
438 610 4.357325 TCCCAGCCCAAAAATTTATAGCA 58.643 39.130 0.00 0.00 0.00 3.49
439 611 4.740634 GCTCCCAGCCCAAAAATTTATAGC 60.741 45.833 0.00 0.00 34.48 2.97
440 612 4.948847 GCTCCCAGCCCAAAAATTTATAG 58.051 43.478 0.00 0.00 34.48 1.31
442 614 3.912496 GCTCCCAGCCCAAAAATTTAT 57.088 42.857 0.00 0.00 34.48 1.40
454 626 4.891037 GCATCCCAGGCTCCCAGC 62.891 72.222 0.00 0.00 41.46 4.85
455 627 1.132554 ATAGCATCCCAGGCTCCCAG 61.133 60.000 0.00 0.00 42.62 4.45
456 628 0.193321 TATAGCATCCCAGGCTCCCA 59.807 55.000 0.00 0.00 42.62 4.37
457 629 1.362224 TTATAGCATCCCAGGCTCCC 58.638 55.000 0.00 0.00 42.62 4.30
458 630 3.508845 TTTTATAGCATCCCAGGCTCC 57.491 47.619 0.00 0.00 42.62 4.70
459 631 6.040842 TCAAAATTTTATAGCATCCCAGGCTC 59.959 38.462 2.44 0.00 42.62 4.70
460 632 5.898972 TCAAAATTTTATAGCATCCCAGGCT 59.101 36.000 2.44 0.00 45.18 4.58
461 633 6.160576 TCAAAATTTTATAGCATCCCAGGC 57.839 37.500 2.44 0.00 0.00 4.85
462 634 6.041296 AGCTCAAAATTTTATAGCATCCCAGG 59.959 38.462 26.70 5.38 33.30 4.45
484 656 2.551856 TACATCCCAGGCTCCCAGCT 62.552 60.000 0.00 0.00 41.99 4.24
489 661 0.605589 CGAGATACATCCCAGGCTCC 59.394 60.000 0.00 0.00 0.00 4.70
490 662 1.333177 ACGAGATACATCCCAGGCTC 58.667 55.000 0.00 0.00 0.00 4.70
491 663 1.414181 CAACGAGATACATCCCAGGCT 59.586 52.381 0.00 0.00 0.00 4.58
492 664 1.871080 CAACGAGATACATCCCAGGC 58.129 55.000 0.00 0.00 0.00 4.85
493 665 1.414181 AGCAACGAGATACATCCCAGG 59.586 52.381 0.00 0.00 0.00 4.45
494 666 2.159043 ACAGCAACGAGATACATCCCAG 60.159 50.000 0.00 0.00 0.00 4.45
497 669 2.535984 CGAACAGCAACGAGATACATCC 59.464 50.000 0.00 0.00 0.00 3.51
498 670 2.535984 CCGAACAGCAACGAGATACATC 59.464 50.000 0.00 0.00 0.00 3.06
499 671 2.540515 CCGAACAGCAACGAGATACAT 58.459 47.619 0.00 0.00 0.00 2.29
501 673 0.645868 GCCGAACAGCAACGAGATAC 59.354 55.000 0.00 0.00 0.00 2.24
512 687 1.805945 GCTCGTACCAGCCGAACAG 60.806 63.158 0.27 0.00 33.34 3.16
538 714 4.724279 ACTGGAAGGTGAAGTGGTAAAT 57.276 40.909 0.00 0.00 39.30 1.40
612 888 9.500785 TCTTGTTGAAAATGTTTCTTTTCCTTT 57.499 25.926 6.78 0.00 42.06 3.11
613 889 9.500785 TTCTTGTTGAAAATGTTTCTTTTCCTT 57.499 25.926 6.78 0.00 42.06 3.36
614 890 9.671279 ATTCTTGTTGAAAATGTTTCTTTTCCT 57.329 25.926 6.78 0.00 42.06 3.36
615 891 9.706846 CATTCTTGTTGAAAATGTTTCTTTTCC 57.293 29.630 6.78 0.00 42.06 3.13
641 917 2.925563 GCAAGCATCATTTAGCACCAAC 59.074 45.455 0.00 0.00 0.00 3.77
643 919 2.164827 CAGCAAGCATCATTTAGCACCA 59.835 45.455 0.00 0.00 0.00 4.17
652 928 4.891168 TGATAATTCACCAGCAAGCATCAT 59.109 37.500 0.00 0.00 0.00 2.45
653 929 4.271661 TGATAATTCACCAGCAAGCATCA 58.728 39.130 0.00 0.00 0.00 3.07
664 940 2.618241 TGCGGCTTCATGATAATTCACC 59.382 45.455 0.00 0.00 33.85 4.02
668 944 7.275888 TCTATTTTGCGGCTTCATGATAATT 57.724 32.000 0.00 0.00 0.00 1.40
681 957 6.481313 TCTCATCAAGATCTTCTATTTTGCGG 59.519 38.462 4.57 0.00 0.00 5.69
689 965 6.728089 ATGCACTCTCATCAAGATCTTCTA 57.272 37.500 4.57 0.00 32.19 2.10
690 966 5.617528 ATGCACTCTCATCAAGATCTTCT 57.382 39.130 4.57 0.00 32.19 2.85
691 967 7.118101 GGATAATGCACTCTCATCAAGATCTTC 59.882 40.741 4.57 0.00 32.19 2.87
694 970 5.642919 GGGATAATGCACTCTCATCAAGATC 59.357 44.000 0.00 0.00 32.19 2.75
731 1007 5.770162 GCTGGAACCTGGCTGTATTAATATT 59.230 40.000 0.00 0.00 0.00 1.28
733 1009 4.412199 AGCTGGAACCTGGCTGTATTAATA 59.588 41.667 9.90 0.00 34.82 0.98
735 1011 2.576191 AGCTGGAACCTGGCTGTATTAA 59.424 45.455 9.90 0.00 34.82 1.40
739 1015 1.651737 TTAGCTGGAACCTGGCTGTA 58.348 50.000 16.74 6.89 37.50 2.74
745 1021 4.559153 CCAAAATGTTTAGCTGGAACCTG 58.441 43.478 0.00 0.00 0.00 4.00
748 1024 3.989817 CAGCCAAAATGTTTAGCTGGAAC 59.010 43.478 16.62 1.82 40.85 3.62
765 1041 2.527624 AGTGTGAGAGGCCAGCCA 60.528 61.111 12.03 0.00 38.92 4.75
792 1069 0.044092 TGGGATAAGAGGGGCTGTGA 59.956 55.000 0.00 0.00 0.00 3.58
797 1074 1.537172 GGGTTGGGATAAGAGGGGC 59.463 63.158 0.00 0.00 0.00 5.80
805 1082 5.486332 AGATATTTCTCTGGGGTTGGGATA 58.514 41.667 0.00 0.00 0.00 2.59
820 1097 7.922382 TGGATATTTCTCTGGGGAGATATTTC 58.078 38.462 4.80 6.41 46.51 2.17
916 1194 1.841556 GGGGTGAGTGTGGGAGTGA 60.842 63.158 0.00 0.00 0.00 3.41
945 1223 4.344865 GCCGCTGGGGTTTGGAGA 62.345 66.667 12.70 0.00 38.44 3.71
1368 1649 7.360438 GCCAATCTAACTGTTAGTCAACAAGAG 60.360 40.741 22.95 1.10 43.92 2.85
1376 1657 2.281762 CGCGCCAATCTAACTGTTAGTC 59.718 50.000 22.95 10.30 34.81 2.59
1389 1676 1.533731 CCCGTTATAATTCGCGCCAAT 59.466 47.619 0.00 0.00 0.00 3.16
1415 1702 1.067000 CAATGCCCAGCGGAATTTCAA 60.067 47.619 0.00 0.00 34.81 2.69
1424 1741 1.665264 TAACCATGCAATGCCCAGCG 61.665 55.000 1.53 0.00 44.97 5.18
1483 1814 0.537371 CCCTTGGACAACCTGACACC 60.537 60.000 0.00 0.00 37.04 4.16
1517 1848 3.997021 CCTGAAGGACACAATCTACACAC 59.003 47.826 0.00 0.00 37.39 3.82
1730 2067 5.140454 ACCAATTCCAACTTAGTTCAAGCT 58.860 37.500 0.00 0.00 37.83 3.74
1745 2082 7.626452 GCTGTAGTGATTTACTGAACCAATTCC 60.626 40.741 0.00 0.00 40.65 3.01
1807 2202 9.565090 ACATATACTAGTATAACAACTCCACGA 57.435 33.333 23.14 1.75 32.39 4.35
1863 2258 5.712152 AGTTCAAGCCAAGACCATTTTAG 57.288 39.130 0.00 0.00 0.00 1.85
1891 2286 8.023128 GCAGAAGTAATTTACTGAAGCAATTCA 58.977 33.333 9.78 0.00 39.39 2.57
1913 2308 5.142061 ACAATTGAGCATTGATTTGCAGA 57.858 34.783 13.59 0.00 44.78 4.26
1915 2310 4.865925 GCTACAATTGAGCATTGATTTGCA 59.134 37.500 13.59 0.00 44.78 4.08
1987 2382 9.109393 GTATACAACCTGCAAGAAATGAGATAA 57.891 33.333 0.00 0.00 34.07 1.75
2088 2483 5.221106 GCTTACATAGCCATTGAATTGCTCA 60.221 40.000 7.05 0.00 44.48 4.26
2172 2567 5.699097 AACACCCAACAATGTATACACAC 57.301 39.130 7.96 0.00 37.54 3.82
2516 2954 3.568538 GTTTCCGACGTAGAGCTTGTTA 58.431 45.455 0.00 0.00 0.00 2.41
2552 2990 0.666374 TCTCGAGCGTTGAGTTGTCA 59.334 50.000 7.81 0.00 34.99 3.58
2630 3068 2.852075 AAACCCCTCGACCTGCCA 60.852 61.111 0.00 0.00 0.00 4.92
2672 3110 1.006825 TCGCATTGTTGACCTCGTCG 61.007 55.000 0.00 0.00 34.95 5.12
2841 3279 4.147449 CGGATCTGCCTGCCGTCA 62.147 66.667 0.00 0.00 40.17 4.35
2907 3345 2.025155 TCTCTAACCAGCGTCAGGATC 58.975 52.381 0.00 0.00 0.00 3.36
2908 3346 2.145397 TCTCTAACCAGCGTCAGGAT 57.855 50.000 0.00 0.00 0.00 3.24
3177 3616 1.065418 GTGGGCATTATATCGAGGGGG 60.065 57.143 0.00 0.00 0.00 5.40
3178 3617 1.909302 AGTGGGCATTATATCGAGGGG 59.091 52.381 0.00 0.00 0.00 4.79
3182 3621 5.070446 AGAGAAACAGTGGGCATTATATCGA 59.930 40.000 0.00 0.00 0.00 3.59
3184 3623 6.291377 TCAGAGAAACAGTGGGCATTATATC 58.709 40.000 0.00 0.00 0.00 1.63
3185 3624 6.252599 TCAGAGAAACAGTGGGCATTATAT 57.747 37.500 0.00 0.00 0.00 0.86
3186 3625 5.692115 TCAGAGAAACAGTGGGCATTATA 57.308 39.130 0.00 0.00 0.00 0.98
3187 3626 4.574674 TCAGAGAAACAGTGGGCATTAT 57.425 40.909 0.00 0.00 0.00 1.28
3188 3627 4.365514 TTCAGAGAAACAGTGGGCATTA 57.634 40.909 0.00 0.00 0.00 1.90
3195 3640 7.701445 AGAAAAAGACATTCAGAGAAACAGTG 58.299 34.615 0.00 0.00 0.00 3.66
3242 3858 5.179555 AGTGGATTTACGAGTCTTTCTTTGC 59.820 40.000 0.00 0.00 0.00 3.68
3243 3859 6.423905 TCAGTGGATTTACGAGTCTTTCTTTG 59.576 38.462 0.00 0.00 0.00 2.77
3247 3863 6.969828 ATTCAGTGGATTTACGAGTCTTTC 57.030 37.500 0.00 0.00 0.00 2.62
3251 3868 4.631813 AGCAATTCAGTGGATTTACGAGTC 59.368 41.667 0.00 0.00 0.00 3.36
3301 3920 6.263168 GGGATCGATGACAATTTAGTGGATTT 59.737 38.462 0.54 0.00 0.00 2.17
3302 3921 5.765182 GGGATCGATGACAATTTAGTGGATT 59.235 40.000 0.54 0.00 0.00 3.01
3304 3923 4.444306 GGGGATCGATGACAATTTAGTGGA 60.444 45.833 0.54 0.00 0.00 4.02
3305 3924 3.815401 GGGGATCGATGACAATTTAGTGG 59.185 47.826 0.54 0.00 0.00 4.00
3355 3974 1.361271 GACTCGACCGTGTCACCAA 59.639 57.895 16.54 0.00 38.19 3.67
3358 3977 1.919956 ATCCGACTCGACCGTGTCAC 61.920 60.000 19.84 0.00 38.19 3.67
3362 3981 2.022902 CGATCCGACTCGACCGTG 59.977 66.667 0.00 0.00 41.12 4.94
3400 4019 2.215907 AGAAGCGTTGATGATCGGAG 57.784 50.000 0.00 0.00 0.00 4.63
3429 4048 0.447801 CTGGCTTCCGGTTCGAATTG 59.552 55.000 0.00 0.00 0.00 2.32
3495 4114 2.879826 GCTAATTGCACCCAATGTCAC 58.120 47.619 0.00 0.00 40.69 3.67
3521 4140 2.908940 CCTGGATTCCCATGGCGC 60.909 66.667 6.09 0.00 42.59 6.53
3562 4181 4.494855 GGTTACGTCGATGTACCTCACTAC 60.495 50.000 16.97 10.37 0.00 2.73
3563 4182 3.623060 GGTTACGTCGATGTACCTCACTA 59.377 47.826 16.97 0.00 0.00 2.74
3564 4183 2.421424 GGTTACGTCGATGTACCTCACT 59.579 50.000 16.97 0.00 0.00 3.41
3565 4184 2.162208 TGGTTACGTCGATGTACCTCAC 59.838 50.000 24.34 17.51 0.00 3.51
3566 4185 2.162208 GTGGTTACGTCGATGTACCTCA 59.838 50.000 24.34 17.32 0.00 3.86
3567 4186 2.421424 AGTGGTTACGTCGATGTACCTC 59.579 50.000 24.34 21.97 0.00 3.85
3568 4187 2.421424 GAGTGGTTACGTCGATGTACCT 59.579 50.000 24.34 16.04 0.00 3.08
3569 4188 2.421424 AGAGTGGTTACGTCGATGTACC 59.579 50.000 16.97 19.18 0.00 3.34
3575 4194 1.741706 GATGGAGAGTGGTTACGTCGA 59.258 52.381 0.00 0.00 0.00 4.20
3585 4204 2.614520 ACTACACGATCGATGGAGAGTG 59.385 50.000 26.38 14.32 38.60 3.51
3645 4273 3.576356 CCATGTCGATGGCGTGGC 61.576 66.667 0.00 0.00 43.00 5.01
3702 4330 2.280052 GAGAGGCGAGCTGATGGC 60.280 66.667 0.00 0.00 42.19 4.40
3787 4415 2.873525 GCAGGGATAGGCCGGAGAC 61.874 68.421 5.05 0.00 37.63 3.36
3788 4416 2.524394 GCAGGGATAGGCCGGAGA 60.524 66.667 5.05 0.00 37.63 3.71
3797 4425 2.767445 CGTCGACGTGGCAGGGATA 61.767 63.158 29.08 0.00 34.11 2.59
3824 4461 2.894387 GCACTCTGATGGCTCGGC 60.894 66.667 0.00 0.00 0.00 5.54
3835 4472 3.640407 ATGCACACCCCGCACTCT 61.640 61.111 0.00 0.00 43.35 3.24


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

AutoCloner maintained by Alex Coulton.