Multiple sequence alignment - TraesCS7A01G105200

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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 TraesCS7A01G105200 chr7A 100.000 3175 0 0 1 3175 63792382 63795556 0.000000e+00 5864
1 TraesCS7A01G105200 chr7A 87.664 989 81 15 1294 2273 597553976 597553020 0.000000e+00 1112
2 TraesCS7A01G105200 chr7A 99.504 605 3 0 2501 3105 224323623 224324227 0.000000e+00 1101
3 TraesCS7A01G105200 chr7D 94.370 1190 36 4 891 2059 59712551 59713730 0.000000e+00 1797
4 TraesCS7A01G105200 chr7D 96.418 670 24 0 1349 2018 59863419 59862750 0.000000e+00 1105
5 TraesCS7A01G105200 chr7D 86.687 661 62 16 1 645 59711760 59712410 0.000000e+00 710
6 TraesCS7A01G105200 chr7D 91.875 480 24 7 856 1322 59864267 59863790 0.000000e+00 656
7 TraesCS7A01G105200 chr7D 81.711 678 93 13 101 763 59865282 59864621 1.300000e-148 536
8 TraesCS7A01G105200 chr7D 86.969 353 44 2 14 365 59867189 59866838 2.300000e-106 396
9 TraesCS7A01G105200 chr7D 97.101 69 2 0 3107 3175 59714110 59714178 2.000000e-22 117
10 TraesCS7A01G105200 chr7D 84.259 108 10 2 723 830 59712451 59712551 7.250000e-17 99
11 TraesCS7A01G105200 chrUn 89.515 1011 67 25 1500 2500 84031103 84030122 0.000000e+00 1243
12 TraesCS7A01G105200 chrUn 91.793 463 22 4 928 1378 84033658 84033200 5.780000e-177 630
13 TraesCS7A01G105200 chrUn 91.793 463 22 4 928 1378 310625896 310626354 5.780000e-177 630
14 TraesCS7A01G105200 chrUn 95.652 69 3 0 3107 3175 84030128 84030060 9.310000e-21 111
15 TraesCS7A01G105200 chr3D 88.750 1040 86 20 1301 2329 593933717 593934736 0.000000e+00 1243
16 TraesCS7A01G105200 chr3D 88.686 1043 77 15 1300 2329 365842126 365841112 0.000000e+00 1234
17 TraesCS7A01G105200 chr3D 88.654 1040 77 14 1303 2329 134599414 134598403 0.000000e+00 1229
18 TraesCS7A01G105200 chr3D 90.391 895 70 14 1449 2329 535654960 535655852 0.000000e+00 1162
19 TraesCS7A01G105200 chr2D 88.134 1045 82 14 1299 2329 472192491 472191475 0.000000e+00 1205
20 TraesCS7A01G105200 chr6D 90.604 894 70 12 1449 2329 466182402 466183294 0.000000e+00 1173
21 TraesCS7A01G105200 chr6D 91.220 820 61 9 1520 2329 47793110 47793928 0.000000e+00 1105
22 TraesCS7A01G105200 chr5D 90.679 869 67 12 1474 2329 100988722 100989589 0.000000e+00 1144
23 TraesCS7A01G105200 chr5D 86.273 1049 84 27 1294 2329 498267711 498268712 0.000000e+00 1085
24 TraesCS7A01G105200 chr4A 98.262 633 7 3 2485 3114 104117844 104118475 0.000000e+00 1105
25 TraesCS7A01G105200 chr4A 99.175 606 5 0 2500 3105 352510620 352511225 0.000000e+00 1092
26 TraesCS7A01G105200 chr4A 99.175 606 4 1 2500 3105 575697141 575697745 0.000000e+00 1090
27 TraesCS7A01G105200 chr5B 99.340 606 4 0 2500 3105 419480286 419480891 0.000000e+00 1098
28 TraesCS7A01G105200 chr5B 99.339 605 4 0 2501 3105 499083126 499083730 0.000000e+00 1096
29 TraesCS7A01G105200 chr2B 99.339 605 4 0 2501 3105 126737044 126737648 0.000000e+00 1096
30 TraesCS7A01G105200 chr1B 99.010 606 6 0 2500 3105 322111367 322110762 0.000000e+00 1086
31 TraesCS7A01G105200 chr1B 84.420 276 39 4 36 310 662911202 662910930 5.220000e-68 268
32 TraesCS7A01G105200 chr1B 89.209 139 10 3 1294 1432 595498687 595498554 5.450000e-38 169
33 TraesCS7A01G105200 chr6A 98.226 620 10 1 2491 3109 367147960 367147341 0.000000e+00 1083
34 TraesCS7A01G105200 chr5A 90.036 833 71 9 1449 2273 606329389 606330217 0.000000e+00 1068
35 TraesCS7A01G105200 chr3B 91.139 632 43 11 1709 2329 104283024 104283653 0.000000e+00 845
36 TraesCS7A01G105200 chr1D 84.031 382 31 5 1294 1675 59891 59540 1.090000e-89 340
37 TraesCS7A01G105200 chr1A 83.394 277 40 5 36 310 572352449 572352177 5.260000e-63 252
38 TraesCS7A01G105200 chr4B 90.647 139 8 3 1294 1432 24341873 24341740 2.520000e-41 180
39 TraesCS7A01G105200 chr7B 89.928 139 9 3 1294 1432 699546837 699546704 1.170000e-39 174


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 TraesCS7A01G105200 chr7A 63792382 63795556 3174 False 5864.000000 5864 100.00000 1 3175 1 chr7A.!!$F1 3174
1 TraesCS7A01G105200 chr7A 597553020 597553976 956 True 1112.000000 1112 87.66400 1294 2273 1 chr7A.!!$R1 979
2 TraesCS7A01G105200 chr7A 224323623 224324227 604 False 1101.000000 1101 99.50400 2501 3105 1 chr7A.!!$F2 604
3 TraesCS7A01G105200 chr7D 59711760 59714178 2418 False 680.750000 1797 90.60425 1 3175 4 chr7D.!!$F1 3174
4 TraesCS7A01G105200 chr7D 59862750 59867189 4439 True 673.250000 1105 89.24325 14 2018 4 chr7D.!!$R1 2004
5 TraesCS7A01G105200 chrUn 84030060 84033658 3598 True 661.333333 1243 92.32000 928 3175 3 chrUn.!!$R1 2247
6 TraesCS7A01G105200 chr3D 593933717 593934736 1019 False 1243.000000 1243 88.75000 1301 2329 1 chr3D.!!$F2 1028
7 TraesCS7A01G105200 chr3D 365841112 365842126 1014 True 1234.000000 1234 88.68600 1300 2329 1 chr3D.!!$R2 1029
8 TraesCS7A01G105200 chr3D 134598403 134599414 1011 True 1229.000000 1229 88.65400 1303 2329 1 chr3D.!!$R1 1026
9 TraesCS7A01G105200 chr3D 535654960 535655852 892 False 1162.000000 1162 90.39100 1449 2329 1 chr3D.!!$F1 880
10 TraesCS7A01G105200 chr2D 472191475 472192491 1016 True 1205.000000 1205 88.13400 1299 2329 1 chr2D.!!$R1 1030
11 TraesCS7A01G105200 chr6D 466182402 466183294 892 False 1173.000000 1173 90.60400 1449 2329 1 chr6D.!!$F2 880
12 TraesCS7A01G105200 chr6D 47793110 47793928 818 False 1105.000000 1105 91.22000 1520 2329 1 chr6D.!!$F1 809
13 TraesCS7A01G105200 chr5D 100988722 100989589 867 False 1144.000000 1144 90.67900 1474 2329 1 chr5D.!!$F1 855
14 TraesCS7A01G105200 chr5D 498267711 498268712 1001 False 1085.000000 1085 86.27300 1294 2329 1 chr5D.!!$F2 1035
15 TraesCS7A01G105200 chr4A 104117844 104118475 631 False 1105.000000 1105 98.26200 2485 3114 1 chr4A.!!$F1 629
16 TraesCS7A01G105200 chr4A 352510620 352511225 605 False 1092.000000 1092 99.17500 2500 3105 1 chr4A.!!$F2 605
17 TraesCS7A01G105200 chr4A 575697141 575697745 604 False 1090.000000 1090 99.17500 2500 3105 1 chr4A.!!$F3 605
18 TraesCS7A01G105200 chr5B 419480286 419480891 605 False 1098.000000 1098 99.34000 2500 3105 1 chr5B.!!$F1 605
19 TraesCS7A01G105200 chr5B 499083126 499083730 604 False 1096.000000 1096 99.33900 2501 3105 1 chr5B.!!$F2 604
20 TraesCS7A01G105200 chr2B 126737044 126737648 604 False 1096.000000 1096 99.33900 2501 3105 1 chr2B.!!$F1 604
21 TraesCS7A01G105200 chr1B 322110762 322111367 605 True 1086.000000 1086 99.01000 2500 3105 1 chr1B.!!$R1 605
22 TraesCS7A01G105200 chr6A 367147341 367147960 619 True 1083.000000 1083 98.22600 2491 3109 1 chr6A.!!$R1 618
23 TraesCS7A01G105200 chr5A 606329389 606330217 828 False 1068.000000 1068 90.03600 1449 2273 1 chr5A.!!$F1 824
24 TraesCS7A01G105200 chr3B 104283024 104283653 629 False 845.000000 845 91.13900 1709 2329 1 chr3B.!!$F1 620

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
721 788 0.30776 GCAAGTTGAAGGTGTCCACG 59.692 55.0 7.16 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2417 7054 0.462937 CGGTGTGGTGTGGTGAGAAA 60.463 55.0 0.0 0.0 0.0 2.52 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
39 42 1.521681 GATGGTCGGTGCACTAGGC 60.522 63.158 17.98 12.62 45.13 3.93
47 50 1.134818 CGGTGCACTAGGCTGTTGATA 60.135 52.381 17.98 0.00 45.15 2.15
53 56 3.133003 GCACTAGGCTGTTGATAGAAGGA 59.867 47.826 0.00 0.00 40.25 3.36
58 61 3.010420 GGCTGTTGATAGAAGGACAACC 58.990 50.000 0.00 0.00 41.82 3.77
74 77 3.293311 CAACCAATGTTGCTCTTGGAG 57.707 47.619 8.23 0.00 44.86 3.86
78 81 1.542915 CAATGTTGCTCTTGGAGGGTG 59.457 52.381 0.00 0.00 0.00 4.61
137 140 6.635755 ACTCTAGAACAAGGAATACAAGAGC 58.364 40.000 0.00 0.00 32.97 4.09
182 185 6.655003 GTGAACCTATTTTCCTCTTCATGACA 59.345 38.462 0.00 0.00 0.00 3.58
223 226 5.744666 TTTTGCACTGTAACTAACCAGTC 57.255 39.130 0.00 0.00 39.83 3.51
230 233 4.894114 ACTGTAACTAACCAGTCTGTGTCT 59.106 41.667 0.00 0.00 37.34 3.41
245 248 5.531287 GTCTGTGTCTAGGAATTTTGTTGGT 59.469 40.000 0.00 0.00 0.00 3.67
278 281 2.083774 CATTGCGGAGGCTCTGTTTAA 58.916 47.619 23.61 16.30 40.82 1.52
297 300 7.500992 TGTTTAAGAGATACATAGAGCAAGGG 58.499 38.462 0.00 0.00 0.00 3.95
306 309 3.072184 ACATAGAGCAAGGGATGGATGAC 59.928 47.826 0.00 0.00 0.00 3.06
312 315 2.941415 GCAAGGGATGGATGACGAGTTT 60.941 50.000 0.00 0.00 0.00 2.66
317 320 3.313526 GGGATGGATGACGAGTTTGATTG 59.686 47.826 0.00 0.00 0.00 2.67
354 357 1.334869 CAAAGAAGGTATGCCGCCATC 59.665 52.381 0.00 0.00 40.50 3.51
359 362 2.949177 AGGTATGCCGCCATCAATTA 57.051 45.000 0.00 0.00 40.50 1.40
365 395 5.590259 GGTATGCCGCCATCAATTATTATCT 59.410 40.000 0.00 0.00 32.85 1.98
366 396 6.095440 GGTATGCCGCCATCAATTATTATCTT 59.905 38.462 0.00 0.00 32.85 2.40
367 397 6.594788 ATGCCGCCATCAATTATTATCTTT 57.405 33.333 0.00 0.00 0.00 2.52
368 398 6.403866 TGCCGCCATCAATTATTATCTTTT 57.596 33.333 0.00 0.00 0.00 2.27
369 399 6.815089 TGCCGCCATCAATTATTATCTTTTT 58.185 32.000 0.00 0.00 0.00 1.94
370 400 6.700960 TGCCGCCATCAATTATTATCTTTTTG 59.299 34.615 0.00 0.00 0.00 2.44
371 401 6.346838 GCCGCCATCAATTATTATCTTTTTGC 60.347 38.462 0.00 0.00 0.00 3.68
372 402 6.700960 CCGCCATCAATTATTATCTTTTTGCA 59.299 34.615 0.00 0.00 0.00 4.08
373 403 7.095940 CCGCCATCAATTATTATCTTTTTGCAG 60.096 37.037 0.00 0.00 0.00 4.41
374 404 7.648908 CGCCATCAATTATTATCTTTTTGCAGA 59.351 33.333 0.00 0.00 0.00 4.26
375 405 8.758715 GCCATCAATTATTATCTTTTTGCAGAC 58.241 33.333 0.00 0.00 0.00 3.51
376 406 9.806203 CCATCAATTATTATCTTTTTGCAGACA 57.194 29.630 0.00 0.00 0.00 3.41
385 415 9.798994 ATTATCTTTTTGCAGACATCTTTCATC 57.201 29.630 0.00 0.00 0.00 2.92
386 416 6.889301 TCTTTTTGCAGACATCTTTCATCT 57.111 33.333 0.00 0.00 0.00 2.90
387 417 7.281040 TCTTTTTGCAGACATCTTTCATCTT 57.719 32.000 0.00 0.00 0.00 2.40
388 418 7.719483 TCTTTTTGCAGACATCTTTCATCTTT 58.281 30.769 0.00 0.00 0.00 2.52
389 419 8.849168 TCTTTTTGCAGACATCTTTCATCTTTA 58.151 29.630 0.00 0.00 0.00 1.85
390 420 8.801715 TTTTTGCAGACATCTTTCATCTTTAC 57.198 30.769 0.00 0.00 0.00 2.01
391 421 7.750229 TTTGCAGACATCTTTCATCTTTACT 57.250 32.000 0.00 0.00 0.00 2.24
403 433 6.916360 TTCATCTTTACTTGCAATTTCCCT 57.084 33.333 0.00 0.00 0.00 4.20
429 459 1.142688 ACCAGGGGGATGCTTGAAGT 61.143 55.000 0.00 0.00 38.05 3.01
439 469 4.083271 GGGATGCTTGAAGTGAACAAGTAC 60.083 45.833 0.00 0.00 44.25 2.73
445 475 5.294552 GCTTGAAGTGAACAAGTACTTGAGT 59.705 40.000 36.14 24.56 44.25 3.41
471 508 3.418684 AAGGAGTTCAACAAGGCGTAT 57.581 42.857 0.00 0.00 0.00 3.06
472 509 3.418684 AGGAGTTCAACAAGGCGTATT 57.581 42.857 0.00 0.00 0.00 1.89
473 510 3.074412 AGGAGTTCAACAAGGCGTATTG 58.926 45.455 0.00 0.89 36.22 1.90
486 528 5.772825 AGGCGTATTGTGCATCATTTTAT 57.227 34.783 0.00 0.00 0.00 1.40
491 533 6.373779 CGTATTGTGCATCATTTTATCCCTC 58.626 40.000 0.00 0.00 0.00 4.30
493 535 4.149511 TGTGCATCATTTTATCCCTCGA 57.850 40.909 0.00 0.00 0.00 4.04
505 547 5.468540 TTATCCCTCGAATGGACATACTG 57.531 43.478 5.53 0.00 33.94 2.74
513 555 6.293790 CCTCGAATGGACATACTGTACGAATA 60.294 42.308 0.00 0.00 32.63 1.75
514 556 7.210718 TCGAATGGACATACTGTACGAATAT 57.789 36.000 0.00 0.00 32.63 1.28
561 603 2.276732 ATCAGGAGTGTTGTGTTGGG 57.723 50.000 0.00 0.00 0.00 4.12
565 607 1.733526 GAGTGTTGTGTTGGGTGGC 59.266 57.895 0.00 0.00 0.00 5.01
582 624 3.054655 GGTGGCCAGAGGTTTTATGTAGA 60.055 47.826 5.11 0.00 0.00 2.59
584 626 4.816925 GTGGCCAGAGGTTTTATGTAGATC 59.183 45.833 5.11 0.00 0.00 2.75
586 628 5.191722 TGGCCAGAGGTTTTATGTAGATCTT 59.808 40.000 0.00 0.00 0.00 2.40
588 630 6.603599 GGCCAGAGGTTTTATGTAGATCTTTT 59.396 38.462 0.00 0.00 0.00 2.27
590 632 7.970614 GCCAGAGGTTTTATGTAGATCTTTTTG 59.029 37.037 0.00 0.00 0.00 2.44
618 660 6.633500 TGAAACTACAACTTTTCATCCTGG 57.367 37.500 0.00 0.00 36.92 4.45
646 713 4.516698 GTCCATGATTAAGTTGGATGCGAT 59.483 41.667 0.00 0.00 41.37 4.58
647 714 5.009010 GTCCATGATTAAGTTGGATGCGATT 59.991 40.000 0.00 0.00 41.37 3.34
679 746 2.853159 CACTGCCCGTGCTGAAATA 58.147 52.632 3.41 0.00 39.51 1.40
694 761 6.417930 GTGCTGAAATAGTTGACCAAAAGTTC 59.582 38.462 0.00 0.00 0.00 3.01
695 762 5.625311 GCTGAAATAGTTGACCAAAAGTTCG 59.375 40.000 0.00 0.00 0.00 3.95
721 788 0.307760 GCAAGTTGAAGGTGTCCACG 59.692 55.000 7.16 0.00 0.00 4.94
775 873 2.596346 TGACCCATGTTGCAATTGTCT 58.404 42.857 0.59 0.00 0.00 3.41
776 874 3.760738 TGACCCATGTTGCAATTGTCTA 58.239 40.909 0.59 0.00 0.00 2.59
825 923 5.304686 ACAATAGAGGGGATTTATTGCGA 57.695 39.130 0.00 0.00 37.98 5.10
829 927 4.647564 AGAGGGGATTTATTGCGATCAT 57.352 40.909 0.00 0.00 0.00 2.45
832 957 5.940470 AGAGGGGATTTATTGCGATCATAAC 59.060 40.000 0.00 0.00 0.00 1.89
835 960 7.633789 AGGGGATTTATTGCGATCATAACTAT 58.366 34.615 0.00 0.00 0.00 2.12
836 961 7.554118 AGGGGATTTATTGCGATCATAACTATG 59.446 37.037 0.00 0.00 35.04 2.23
841 966 8.492673 TTTATTGCGATCATAACTATGGGATC 57.507 34.615 0.00 0.00 34.50 3.36
848 973 6.294731 CGATCATAACTATGGGATCACACTCA 60.295 42.308 0.00 0.00 34.50 3.41
850 975 6.762333 TCATAACTATGGGATCACACTCATG 58.238 40.000 0.00 0.13 34.50 3.07
851 976 6.327365 TCATAACTATGGGATCACACTCATGT 59.673 38.462 0.00 0.00 35.33 3.21
852 977 4.679373 ACTATGGGATCACACTCATGTC 57.321 45.455 0.00 0.00 36.72 3.06
854 979 3.555527 ATGGGATCACACTCATGTCAG 57.444 47.619 0.00 0.00 36.72 3.51
886 1011 9.990868 AAAAAGTATAGGATCACACCCTAATTT 57.009 29.630 0.00 0.00 39.50 1.82
897 1022 4.664150 CACCCTAATTTGTGTGGTGTTT 57.336 40.909 0.00 0.00 41.20 2.83
1081 3275 0.322975 CCATCCAGATCCATCCGTCC 59.677 60.000 0.00 0.00 0.00 4.79
1820 6376 1.729838 GCTCGACGAGACGCACTTT 60.730 57.895 28.43 0.00 0.00 2.66
2020 6576 8.520835 TTTAGCATGTCTCGTATGATGATTAC 57.479 34.615 0.00 0.00 0.00 1.89
2024 6580 5.845391 TGTCTCGTATGATGATTACACCA 57.155 39.130 0.00 0.00 0.00 4.17
2083 6639 2.095768 TGCGACAATAAGCTTGTTCTGC 60.096 45.455 9.86 12.13 31.96 4.26
2104 6660 2.932614 CGGCGAGTGATTTCAAATCTCT 59.067 45.455 13.39 13.39 0.00 3.10
2137 6693 6.428083 TGTTTAGGTCTGTTACATTCTGGA 57.572 37.500 0.00 0.00 0.00 3.86
2138 6694 6.464222 TGTTTAGGTCTGTTACATTCTGGAG 58.536 40.000 0.00 0.00 0.00 3.86
2144 6705 5.409826 GGTCTGTTACATTCTGGAGTTTCTG 59.590 44.000 0.00 0.00 0.00 3.02
2146 6707 5.071788 TCTGTTACATTCTGGAGTTTCTGGT 59.928 40.000 0.00 0.00 0.00 4.00
2259 6826 2.687566 CTGGGTAGAAGGCGGGGT 60.688 66.667 0.00 0.00 0.00 4.95
2260 6827 3.006728 TGGGTAGAAGGCGGGGTG 61.007 66.667 0.00 0.00 0.00 4.61
2261 6828 3.007323 GGGTAGAAGGCGGGGTGT 61.007 66.667 0.00 0.00 0.00 4.16
2262 6829 1.686800 GGGTAGAAGGCGGGGTGTA 60.687 63.158 0.00 0.00 0.00 2.90
2277 6845 0.970427 GTGTAATGGCTGGTTGGGGG 60.970 60.000 0.00 0.00 0.00 5.40
2298 6866 4.450053 GGGAGGACTGAATTTCATCTCTG 58.550 47.826 16.76 3.87 0.00 3.35
2299 6867 4.080638 GGGAGGACTGAATTTCATCTCTGT 60.081 45.833 16.76 6.33 0.00 3.41
2357 6994 7.772332 AGGAACAAACTGAATGTCGTATATC 57.228 36.000 0.00 0.00 0.00 1.63
2359 6996 7.492669 AGGAACAAACTGAATGTCGTATATCTG 59.507 37.037 0.00 0.00 0.00 2.90
2391 7028 5.930837 AGACAGAGTTCCTTCTCTTATGG 57.069 43.478 0.00 0.00 42.10 2.74
2417 7054 1.610522 GGCAATGAGTCTGTTGTTGCT 59.389 47.619 8.10 0.00 43.36 3.91
2418 7055 2.035066 GGCAATGAGTCTGTTGTTGCTT 59.965 45.455 8.10 0.00 43.36 3.91
2422 7059 5.210715 CAATGAGTCTGTTGTTGCTTTCTC 58.789 41.667 0.00 0.00 0.00 2.87
2423 7060 3.872696 TGAGTCTGTTGTTGCTTTCTCA 58.127 40.909 0.00 0.00 0.00 3.27
2424 7061 3.623060 TGAGTCTGTTGTTGCTTTCTCAC 59.377 43.478 0.00 0.00 0.00 3.51
2425 7062 2.945668 AGTCTGTTGTTGCTTTCTCACC 59.054 45.455 0.00 0.00 0.00 4.02
2426 7063 2.682856 GTCTGTTGTTGCTTTCTCACCA 59.317 45.455 0.00 0.00 0.00 4.17
2482 7119 2.097825 GCTCTCTGGATTGCAAATGGT 58.902 47.619 1.71 0.00 0.00 3.55
2761 7400 1.153349 AAATCGAGCTTCTCCGGCC 60.153 57.895 0.00 0.00 0.00 6.13
3121 7760 5.779241 ACTTTGATTTCATCACCTCCCTA 57.221 39.130 0.00 0.00 39.39 3.53
3124 7763 7.872138 ACTTTGATTTCATCACCTCCCTAATA 58.128 34.615 0.00 0.00 39.39 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.738314 GACCATCCAAAAGCAAATGCAC 59.262 45.455 8.28 0.00 45.16 4.57
39 42 5.707298 ACATTGGTTGTCCTTCTATCAACAG 59.293 40.000 8.98 0.44 41.87 3.16
58 61 1.542915 CACCCTCCAAGAGCAACATTG 59.457 52.381 0.00 0.00 0.00 2.82
137 140 4.130118 CACCTCTTTCCCCAAAGATATCG 58.870 47.826 0.00 0.00 45.70 2.92
182 185 8.960591 GTGCAAAATATAATAGGCACCATAGAT 58.039 33.333 0.00 0.00 44.20 1.98
223 226 5.334105 CGACCAACAAAATTCCTAGACACAG 60.334 44.000 0.00 0.00 0.00 3.66
230 233 3.482436 ACAGCGACCAACAAAATTCCTA 58.518 40.909 0.00 0.00 0.00 2.94
245 248 2.409055 GCAATGCCATGGACAGCGA 61.409 57.895 18.40 0.00 0.00 4.93
278 281 4.776837 CCATCCCTTGCTCTATGTATCTCT 59.223 45.833 0.00 0.00 0.00 3.10
297 300 5.352569 AGAACAATCAAACTCGTCATCCATC 59.647 40.000 0.00 0.00 0.00 3.51
306 309 4.222114 GCCTTTGAGAACAATCAAACTCG 58.778 43.478 0.00 0.00 42.68 4.18
312 315 4.012374 GAGATGGCCTTTGAGAACAATCA 58.988 43.478 3.32 0.00 35.85 2.57
317 320 4.074970 TCTTTGAGATGGCCTTTGAGAAC 58.925 43.478 3.32 0.00 0.00 3.01
359 362 9.798994 GATGAAAGATGTCTGCAAAAAGATAAT 57.201 29.630 0.00 0.00 0.00 1.28
365 395 8.632679 AGTAAAGATGAAAGATGTCTGCAAAAA 58.367 29.630 0.00 0.00 0.00 1.94
366 396 8.169977 AGTAAAGATGAAAGATGTCTGCAAAA 57.830 30.769 0.00 0.00 0.00 2.44
367 397 7.750229 AGTAAAGATGAAAGATGTCTGCAAA 57.250 32.000 0.00 0.00 0.00 3.68
368 398 7.587629 CAAGTAAAGATGAAAGATGTCTGCAA 58.412 34.615 0.00 0.00 0.00 4.08
369 399 6.348786 GCAAGTAAAGATGAAAGATGTCTGCA 60.349 38.462 0.00 0.00 0.00 4.41
370 400 6.026513 GCAAGTAAAGATGAAAGATGTCTGC 58.973 40.000 0.00 0.00 0.00 4.26
371 401 7.137490 TGCAAGTAAAGATGAAAGATGTCTG 57.863 36.000 0.00 0.00 0.00 3.51
372 402 7.750229 TTGCAAGTAAAGATGAAAGATGTCT 57.250 32.000 0.00 0.00 0.00 3.41
373 403 8.976986 AATTGCAAGTAAAGATGAAAGATGTC 57.023 30.769 4.94 0.00 0.00 3.06
374 404 9.415544 GAAATTGCAAGTAAAGATGAAAGATGT 57.584 29.630 4.94 0.00 0.00 3.06
375 405 8.866956 GGAAATTGCAAGTAAAGATGAAAGATG 58.133 33.333 4.94 0.00 0.00 2.90
376 406 8.037166 GGGAAATTGCAAGTAAAGATGAAAGAT 58.963 33.333 4.94 0.00 0.00 2.40
377 407 7.233348 AGGGAAATTGCAAGTAAAGATGAAAGA 59.767 33.333 4.94 0.00 0.00 2.52
378 408 7.381323 AGGGAAATTGCAAGTAAAGATGAAAG 58.619 34.615 4.94 0.00 0.00 2.62
379 409 7.233348 AGAGGGAAATTGCAAGTAAAGATGAAA 59.767 33.333 4.94 0.00 0.00 2.69
380 410 6.721208 AGAGGGAAATTGCAAGTAAAGATGAA 59.279 34.615 4.94 0.00 0.00 2.57
381 411 6.248433 AGAGGGAAATTGCAAGTAAAGATGA 58.752 36.000 4.94 0.00 0.00 2.92
382 412 6.521151 AGAGGGAAATTGCAAGTAAAGATG 57.479 37.500 4.94 0.00 0.00 2.90
383 413 7.544804 AAAGAGGGAAATTGCAAGTAAAGAT 57.455 32.000 4.94 0.00 0.00 2.40
384 414 6.976934 AAAGAGGGAAATTGCAAGTAAAGA 57.023 33.333 4.94 0.00 0.00 2.52
385 415 8.978539 GTAAAAAGAGGGAAATTGCAAGTAAAG 58.021 33.333 4.94 0.00 0.00 1.85
386 416 7.929245 GGTAAAAAGAGGGAAATTGCAAGTAAA 59.071 33.333 4.94 0.00 0.00 2.01
387 417 7.070074 TGGTAAAAAGAGGGAAATTGCAAGTAA 59.930 33.333 4.94 0.00 0.00 2.24
388 418 6.551601 TGGTAAAAAGAGGGAAATTGCAAGTA 59.448 34.615 4.94 0.00 0.00 2.24
389 419 5.365314 TGGTAAAAAGAGGGAAATTGCAAGT 59.635 36.000 4.94 0.00 0.00 3.16
390 420 5.852827 TGGTAAAAAGAGGGAAATTGCAAG 58.147 37.500 4.94 0.00 0.00 4.01
391 421 5.221621 CCTGGTAAAAAGAGGGAAATTGCAA 60.222 40.000 0.00 0.00 0.00 4.08
403 433 2.000048 AGCATCCCCCTGGTAAAAAGA 59.000 47.619 0.00 0.00 0.00 2.52
418 448 5.931441 AGTACTTGTTCACTTCAAGCATC 57.069 39.130 5.72 0.00 43.97 3.91
429 459 5.888691 TTTTGCACTCAAGTACTTGTTCA 57.111 34.783 29.83 20.60 41.16 3.18
439 469 4.637483 TGAACTCCTTTTTGCACTCAAG 57.363 40.909 0.00 0.00 33.12 3.02
445 475 3.678529 GCCTTGTTGAACTCCTTTTTGCA 60.679 43.478 0.00 0.00 0.00 4.08
471 508 4.522114 TCGAGGGATAAAATGATGCACAA 58.478 39.130 0.00 0.00 0.00 3.33
472 509 4.149511 TCGAGGGATAAAATGATGCACA 57.850 40.909 0.00 0.00 0.00 4.57
473 510 5.455392 CATTCGAGGGATAAAATGATGCAC 58.545 41.667 0.00 0.00 32.14 4.57
514 556 9.907229 TCACTTCTAGAGACACTATCTTCATAA 57.093 33.333 0.00 0.00 38.00 1.90
524 566 6.013379 TCCTGATTTCACTTCTAGAGACACT 58.987 40.000 0.00 0.00 0.00 3.55
525 567 6.071616 ACTCCTGATTTCACTTCTAGAGACAC 60.072 42.308 0.00 0.00 0.00 3.67
528 570 6.013379 ACACTCCTGATTTCACTTCTAGAGA 58.987 40.000 0.00 0.00 0.00 3.10
534 576 4.576463 ACACAACACTCCTGATTTCACTTC 59.424 41.667 0.00 0.00 0.00 3.01
561 603 4.216411 TCTACATAAAACCTCTGGCCAC 57.784 45.455 0.00 0.00 0.00 5.01
565 607 7.970614 GCAAAAAGATCTACATAAAACCTCTGG 59.029 37.037 0.00 0.00 0.00 3.86
586 628 9.862371 TGAAAAGTTGTAGTTTCAATAGCAAAA 57.138 25.926 0.00 0.00 40.00 2.44
588 630 9.677567 GATGAAAAGTTGTAGTTTCAATAGCAA 57.322 29.630 3.22 0.00 44.52 3.91
590 632 8.515414 AGGATGAAAAGTTGTAGTTTCAATAGC 58.485 33.333 3.22 0.00 44.52 2.97
596 638 6.635030 ACCAGGATGAAAAGTTGTAGTTTC 57.365 37.500 0.00 0.00 39.69 2.78
602 644 4.536765 ACAGAACCAGGATGAAAAGTTGT 58.463 39.130 0.00 0.00 39.69 3.32
603 645 4.022849 GGACAGAACCAGGATGAAAAGTTG 60.023 45.833 0.00 0.00 39.69 3.16
618 660 6.678900 GCATCCAACTTAATCATGGACAGAAC 60.679 42.308 6.25 0.00 45.47 3.01
664 731 1.164411 CAACTATTTCAGCACGGGCA 58.836 50.000 14.57 0.00 44.61 5.36
669 736 5.831997 ACTTTTGGTCAACTATTTCAGCAC 58.168 37.500 0.00 0.00 0.00 4.40
671 738 5.625311 CGAACTTTTGGTCAACTATTTCAGC 59.375 40.000 0.00 0.00 35.43 4.26
674 741 6.492254 ACACGAACTTTTGGTCAACTATTTC 58.508 36.000 0.00 0.00 35.43 2.17
679 746 3.340034 TGACACGAACTTTTGGTCAACT 58.660 40.909 0.00 0.00 35.72 3.16
694 761 0.588252 CCTTCAACTTGCCTGACACG 59.412 55.000 0.00 0.00 0.00 4.49
695 762 1.334869 CACCTTCAACTTGCCTGACAC 59.665 52.381 0.00 0.00 0.00 3.67
739 837 3.069946 CATGTTGCGCCCACCCAT 61.070 61.111 4.18 0.00 0.00 4.00
746 844 2.491152 CATGGGTCATGTTGCGCC 59.509 61.111 4.18 0.00 37.12 6.53
825 923 7.016957 ACATGAGTGTGATCCCATAGTTATGAT 59.983 37.037 0.00 0.00 35.69 2.45
829 927 5.660864 TGACATGAGTGTGATCCCATAGTTA 59.339 40.000 0.00 0.00 39.09 2.24
832 957 4.343239 TCTGACATGAGTGTGATCCCATAG 59.657 45.833 0.00 0.00 39.09 2.23
835 960 2.539302 TCTGACATGAGTGTGATCCCA 58.461 47.619 0.00 0.00 39.09 4.37
836 961 3.616956 TTCTGACATGAGTGTGATCCC 57.383 47.619 0.00 0.00 39.09 3.85
860 985 9.990868 AAATTAGGGTGTGATCCTATACTTTTT 57.009 29.630 0.00 0.00 36.81 1.94
862 987 8.557450 ACAAATTAGGGTGTGATCCTATACTTT 58.443 33.333 0.00 0.00 36.81 2.66
863 988 7.993183 CACAAATTAGGGTGTGATCCTATACTT 59.007 37.037 2.40 0.00 46.56 2.24
864 989 7.127339 ACACAAATTAGGGTGTGATCCTATACT 59.873 37.037 13.56 0.00 46.56 2.12
883 1008 2.490115 ACGTGACAAACACCACACAAAT 59.510 40.909 0.00 0.00 45.73 2.32
886 1011 2.381725 TACGTGACAAACACCACACA 57.618 45.000 0.00 0.00 45.73 3.72
897 1022 5.242434 AGTTTTGCATCCTTATACGTGACA 58.758 37.500 0.00 0.00 0.00 3.58
907 1032 5.106555 CGTGACATTCTAGTTTTGCATCCTT 60.107 40.000 0.00 0.00 0.00 3.36
1820 6376 1.001068 TCGTAGTTGGTGCCGAAATCA 59.999 47.619 0.00 0.00 0.00 2.57
2020 6576 6.072508 ACACAAGTTTTATAGCAGTCATGGTG 60.073 38.462 0.00 0.00 37.78 4.17
2083 6639 2.932614 AGAGATTTGAAATCACTCGCCG 59.067 45.455 19.02 0.00 33.53 6.46
2104 6660 9.562408 TGTAACAGACCTAAACATTACATTTGA 57.438 29.630 0.00 0.00 29.87 2.69
2121 6677 5.409826 CCAGAAACTCCAGAATGTAACAGAC 59.590 44.000 0.00 0.00 0.00 3.51
2137 6693 9.440761 AGATAGTATTCTTGGATACCAGAAACT 57.559 33.333 0.00 4.28 33.81 2.66
2144 6705 7.091443 CACCGAAGATAGTATTCTTGGATACC 58.909 42.308 5.93 0.00 36.10 2.73
2146 6707 6.295123 GCCACCGAAGATAGTATTCTTGGATA 60.295 42.308 5.93 0.00 36.10 2.59
2165 6726 2.039974 TGTTGCTATGCTGCCACCG 61.040 57.895 0.00 0.00 0.00 4.94
2259 6826 1.386155 CCCCCAACCAGCCATTACA 59.614 57.895 0.00 0.00 0.00 2.41
2260 6827 4.355151 CCCCCAACCAGCCATTAC 57.645 61.111 0.00 0.00 0.00 1.89
2277 6845 4.874966 CACAGAGATGAAATTCAGTCCTCC 59.125 45.833 14.67 0.00 0.00 4.30
2298 6866 8.500753 TGTTGTTCCTGTATATAAATGGACAC 57.499 34.615 0.00 0.08 0.00 3.67
2299 6867 9.693739 ATTGTTGTTCCTGTATATAAATGGACA 57.306 29.630 0.68 0.00 0.00 4.02
2331 6968 9.309516 GATATACGACATTCAGTTTGTTCCTAA 57.690 33.333 0.00 0.00 0.00 2.69
2357 6994 1.620819 ACTCTGTCTAAGGTGTGGCAG 59.379 52.381 0.00 0.00 0.00 4.85
2359 6996 2.613223 GGAACTCTGTCTAAGGTGTGGC 60.613 54.545 0.00 0.00 0.00 5.01
2391 7028 3.758554 ACAACAGACTCATTGCCCATAAC 59.241 43.478 0.00 0.00 0.00 1.89
2417 7054 0.462937 CGGTGTGGTGTGGTGAGAAA 60.463 55.000 0.00 0.00 0.00 2.52
2418 7055 1.145156 CGGTGTGGTGTGGTGAGAA 59.855 57.895 0.00 0.00 0.00 2.87
2422 7059 2.594303 ATGCGGTGTGGTGTGGTG 60.594 61.111 0.00 0.00 0.00 4.17
2423 7060 2.281484 GATGCGGTGTGGTGTGGT 60.281 61.111 0.00 0.00 0.00 4.16
2424 7061 2.281414 TGATGCGGTGTGGTGTGG 60.281 61.111 0.00 0.00 0.00 4.17
2425 7062 1.236616 ATGTGATGCGGTGTGGTGTG 61.237 55.000 0.00 0.00 0.00 3.82
2426 7063 0.955428 GATGTGATGCGGTGTGGTGT 60.955 55.000 0.00 0.00 0.00 4.16
2482 7119 5.263599 ACAGTGGATGAAATTAAGGATGCA 58.736 37.500 0.00 0.00 0.00 3.96
2494 7131 3.149196 GCCTTCTTGAACAGTGGATGAA 58.851 45.455 0.00 0.00 0.00 2.57
2495 7132 2.783135 GCCTTCTTGAACAGTGGATGA 58.217 47.619 0.00 0.00 0.00 2.92
2496 7133 1.466167 CGCCTTCTTGAACAGTGGATG 59.534 52.381 0.00 0.00 0.00 3.51
2497 7134 1.813513 CGCCTTCTTGAACAGTGGAT 58.186 50.000 0.00 0.00 0.00 3.41
2498 7135 0.884704 GCGCCTTCTTGAACAGTGGA 60.885 55.000 0.00 0.00 0.00 4.02
2761 7400 0.179062 CCGGAGAAGCTCAATCCCTG 60.179 60.000 0.00 0.00 31.08 4.45
3121 7760 4.457257 GGTCAAGACAAGAAGCAGCTTATT 59.543 41.667 7.92 8.68 0.00 1.40
3124 7763 2.225467 GGTCAAGACAAGAAGCAGCTT 58.775 47.619 7.60 7.60 0.00 3.74


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

AutoCloner maintained by Alex Coulton.