Multiple sequence alignment - TraesCS5A01G162200

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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 TraesCS5A01G162200 chr5A 100.000 3043 0 0 1 3043 346130446 346133488 0.000000e+00 5620
1 TraesCS5A01G162200 chr5A 99.371 159 1 0 878 1036 400418190 400418348 3.840000e-74 289
2 TraesCS5A01G162200 chr5D 94.196 2016 95 10 1036 3042 260107633 260105631 0.000000e+00 3055
3 TraesCS5A01G162200 chr5D 87.332 892 75 21 1 882 260108487 260107624 0.000000e+00 987
4 TraesCS5A01G162200 chr5D 100.000 157 0 0 880 1036 457999431 457999587 1.070000e-74 291
5 TraesCS5A01G162200 chr5B 95.026 1548 54 7 1036 2570 294123422 294124959 0.000000e+00 2410
6 TraesCS5A01G162200 chr5B 84.336 715 102 10 2329 3041 412283533 412284239 0.000000e+00 691
7 TraesCS5A01G162200 chr5B 87.090 457 40 8 430 882 294122990 294123431 1.630000e-137 499
8 TraesCS5A01G162200 chr5B 85.990 414 48 8 1 407 294121880 294122290 4.660000e-118 435
9 TraesCS5A01G162200 chr3D 85.345 696 99 3 2347 3041 380179909 380180602 0.000000e+00 717
10 TraesCS5A01G162200 chr3D 83.477 696 112 3 2347 3041 414778345 414777652 0.000000e+00 645
11 TraesCS5A01G162200 chr3D 83.214 697 112 4 2347 3041 433443330 433444023 4.280000e-178 634
12 TraesCS5A01G162200 chr3D 100.000 157 0 0 880 1036 170655859 170655703 1.070000e-74 291
13 TraesCS5A01G162200 chr2D 83.741 695 105 7 2347 3041 23303651 23302965 0.000000e+00 651
14 TraesCS5A01G162200 chr2D 99.379 161 1 0 876 1036 62112052 62111892 2.970000e-75 292
15 TraesCS5A01G162200 chr2B 83.548 699 105 9 2347 3041 100027004 100027696 0.000000e+00 645
16 TraesCS5A01G162200 chr2B 100.000 157 0 0 880 1036 644555150 644554994 1.070000e-74 291
17 TraesCS5A01G162200 chr1B 83.405 699 106 9 2347 3041 8705260 8705952 9.200000e-180 640
18 TraesCS5A01G162200 chr6D 83.119 699 104 10 2347 3041 336996723 336996035 2.580000e-175 625
19 TraesCS5A01G162200 chr4A 100.000 158 0 0 879 1036 153778250 153778407 2.970000e-75 292
20 TraesCS5A01G162200 chr7A 99.375 160 1 0 882 1041 87010295 87010454 1.070000e-74 291
21 TraesCS5A01G162200 chr7A 99.371 159 1 0 878 1036 144657769 144657927 3.840000e-74 289
22 TraesCS5A01G162200 chr1A 100.000 157 0 0 880 1036 490890782 490890938 1.070000e-74 291


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 TraesCS5A01G162200 chr5A 346130446 346133488 3042 False 5620.000000 5620 100.000000 1 3043 1 chr5A.!!$F1 3042
1 TraesCS5A01G162200 chr5D 260105631 260108487 2856 True 2021.000000 3055 90.764000 1 3042 2 chr5D.!!$R1 3041
2 TraesCS5A01G162200 chr5B 294121880 294124959 3079 False 1114.666667 2410 89.368667 1 2570 3 chr5B.!!$F2 2569
3 TraesCS5A01G162200 chr5B 412283533 412284239 706 False 691.000000 691 84.336000 2329 3041 1 chr5B.!!$F1 712
4 TraesCS5A01G162200 chr3D 380179909 380180602 693 False 717.000000 717 85.345000 2347 3041 1 chr3D.!!$F1 694
5 TraesCS5A01G162200 chr3D 414777652 414778345 693 True 645.000000 645 83.477000 2347 3041 1 chr3D.!!$R2 694
6 TraesCS5A01G162200 chr3D 433443330 433444023 693 False 634.000000 634 83.214000 2347 3041 1 chr3D.!!$F2 694
7 TraesCS5A01G162200 chr2D 23302965 23303651 686 True 651.000000 651 83.741000 2347 3041 1 chr2D.!!$R1 694
8 TraesCS5A01G162200 chr2B 100027004 100027696 692 False 645.000000 645 83.548000 2347 3041 1 chr2B.!!$F1 694
9 TraesCS5A01G162200 chr1B 8705260 8705952 692 False 640.000000 640 83.405000 2347 3041 1 chr1B.!!$F1 694
10 TraesCS5A01G162200 chr6D 336996035 336996723 688 True 625.000000 625 83.119000 2347 3041 1 chr6D.!!$R1 694

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
793 1493 0.035458 CACCTTCAAACTCGCCTCCT 59.965 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 3344 0.180171 CATGCGGGGGATGTCAGTTA 59.82 55.0 0.0 0.0 0.0 2.24 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
23 24 5.132502 ACAACATCAAGACAAATCCAGTCA 58.867 37.500 0.00 0.00 38.46 3.41
29 30 4.338118 TCAAGACAAATCCAGTCAAACCAC 59.662 41.667 0.00 0.00 38.46 4.16
43 44 3.006110 TCAAACCACGAAGTACCTACCTG 59.994 47.826 0.00 0.00 41.61 4.00
46 47 1.274167 CCACGAAGTACCTACCTGCAA 59.726 52.381 0.00 0.00 41.61 4.08
51 52 5.066893 CACGAAGTACCTACCTGCAACTATA 59.933 44.000 0.00 0.00 41.61 1.31
58 59 4.896482 ACCTACCTGCAACTATAGAGGAAG 59.104 45.833 6.78 1.75 0.00 3.46
66 67 7.418368 CCTGCAACTATAGAGGAAGAAATCTCA 60.418 40.741 6.78 0.00 32.76 3.27
67 68 7.851228 TGCAACTATAGAGGAAGAAATCTCAA 58.149 34.615 6.78 0.00 32.76 3.02
88 89 9.856488 TCTCAACAAATCATAACAGTAGTAGAC 57.144 33.333 0.00 0.00 0.00 2.59
118 121 2.746277 GGAGGTTGGCAATCGCGT 60.746 61.111 5.77 0.00 39.92 6.01
141 144 3.941188 ATACCAGCGATGGGGCCG 61.941 66.667 25.79 0.00 0.00 6.13
158 161 1.401905 GCCGCCAAACCAAGAAGATAG 59.598 52.381 0.00 0.00 0.00 2.08
163 166 4.693566 CGCCAAACCAAGAAGATAGTGTTA 59.306 41.667 0.00 0.00 0.00 2.41
171 174 7.280356 ACCAAGAAGATAGTGTTACAGTTGTT 58.720 34.615 0.00 0.00 0.00 2.83
191 194 0.976963 GATGCACATGAAAACACGCG 59.023 50.000 3.53 3.53 0.00 6.01
199 204 0.878523 TGAAAACACGCGACCTGGAG 60.879 55.000 15.93 0.00 0.00 3.86
217 222 5.048294 CCTGGAGTACAAATAACCAACCAAC 60.048 44.000 0.00 0.00 0.00 3.77
230 236 9.981114 AATAACCAACCAACTTTTCATAAAGAG 57.019 29.630 4.77 0.00 42.78 2.85
235 241 7.865889 CCAACCAACTTTTCATAAAGAGTAACC 59.134 37.037 4.77 0.00 42.78 2.85
241 247 5.486735 TTTCATAAAGAGTAACCGGGACA 57.513 39.130 6.32 0.00 0.00 4.02
278 285 0.311790 CTCAGCAACGCAACACCAAT 59.688 50.000 0.00 0.00 0.00 3.16
338 345 6.114767 TGACATTGATAGCATTGTTAGAGCA 58.885 36.000 9.63 1.12 38.37 4.26
347 354 5.491070 AGCATTGTTAGAGCAACATCACTA 58.509 37.500 0.00 0.00 46.38 2.74
348 355 5.939883 AGCATTGTTAGAGCAACATCACTAA 59.060 36.000 0.00 0.00 46.38 2.24
350 357 6.092670 GCATTGTTAGAGCAACATCACTAAGA 59.907 38.462 0.00 0.00 46.38 2.10
351 358 7.459486 CATTGTTAGAGCAACATCACTAAGAC 58.541 38.462 0.00 0.00 46.38 3.01
352 359 6.096673 TGTTAGAGCAACATCACTAAGACA 57.903 37.500 0.00 0.00 42.29 3.41
353 360 5.926542 TGTTAGAGCAACATCACTAAGACAC 59.073 40.000 0.00 0.00 42.29 3.67
354 361 4.607293 AGAGCAACATCACTAAGACACA 57.393 40.909 0.00 0.00 0.00 3.72
355 362 4.960938 AGAGCAACATCACTAAGACACAA 58.039 39.130 0.00 0.00 0.00 3.33
356 363 5.368145 AGAGCAACATCACTAAGACACAAA 58.632 37.500 0.00 0.00 0.00 2.83
357 364 5.822519 AGAGCAACATCACTAAGACACAAAA 59.177 36.000 0.00 0.00 0.00 2.44
358 365 5.821204 AGCAACATCACTAAGACACAAAAC 58.179 37.500 0.00 0.00 0.00 2.43
359 366 5.590259 AGCAACATCACTAAGACACAAAACT 59.410 36.000 0.00 0.00 0.00 2.66
360 367 6.095440 AGCAACATCACTAAGACACAAAACTT 59.905 34.615 0.00 0.00 0.00 2.66
361 368 6.197096 GCAACATCACTAAGACACAAAACTTG 59.803 38.462 0.00 0.00 0.00 3.16
362 369 5.821204 ACATCACTAAGACACAAAACTTGC 58.179 37.500 0.00 0.00 0.00 4.01
363 370 5.590259 ACATCACTAAGACACAAAACTTGCT 59.410 36.000 0.00 0.00 0.00 3.91
373 394 4.111916 CACAAAACTTGCTACACAAAGGG 58.888 43.478 0.00 0.00 37.96 3.95
374 395 3.767131 ACAAAACTTGCTACACAAAGGGT 59.233 39.130 0.00 0.00 37.96 4.34
386 407 1.421646 ACAAAGGGTGAGAGACAAGGG 59.578 52.381 0.00 0.00 0.00 3.95
475 1172 0.324943 TGTGGCAGCTAGGGTTTCTC 59.675 55.000 0.00 0.00 0.00 2.87
501 1198 6.417635 CACAATGAAGGTTTTATGTCACACAC 59.582 38.462 0.00 0.00 0.00 3.82
502 1199 6.096141 ACAATGAAGGTTTTATGTCACACACA 59.904 34.615 0.00 0.00 40.18 3.72
503 1200 6.707440 ATGAAGGTTTTATGTCACACACAA 57.293 33.333 0.00 0.00 38.97 3.33
504 1201 6.707440 TGAAGGTTTTATGTCACACACAAT 57.293 33.333 0.00 0.00 38.97 2.71
505 1202 6.734137 TGAAGGTTTTATGTCACACACAATC 58.266 36.000 0.00 0.00 38.97 2.67
506 1203 6.319911 TGAAGGTTTTATGTCACACACAATCA 59.680 34.615 0.00 0.00 38.97 2.57
507 1204 6.317789 AGGTTTTATGTCACACACAATCAG 57.682 37.500 0.00 0.00 38.97 2.90
508 1205 5.827797 AGGTTTTATGTCACACACAATCAGT 59.172 36.000 0.00 0.00 38.97 3.41
532 1229 6.595716 GTCAATCACTTAGCCTTTCACAGTAT 59.404 38.462 0.00 0.00 0.00 2.12
534 1231 4.832248 TCACTTAGCCTTTCACAGTATGG 58.168 43.478 0.00 0.00 43.62 2.74
583 1280 7.933577 TGAACCGCAGAAATCTATGAATCTATT 59.066 33.333 0.00 0.00 0.00 1.73
620 1317 1.203052 TCGTATCCGGTCACAAGTTCC 59.797 52.381 0.00 0.00 33.95 3.62
623 1320 1.056660 ATCCGGTCACAAGTTCCTGT 58.943 50.000 0.00 0.00 0.00 4.00
637 1334 5.857822 AGTTCCTGTTCAGTAAAATACGC 57.142 39.130 0.00 0.00 0.00 4.42
650 1347 5.703592 AGTAAAATACGCAGTGGAACATCAA 59.296 36.000 0.00 0.00 45.73 2.57
652 1349 4.882671 AATACGCAGTGGAACATCAATC 57.117 40.909 0.00 0.00 45.73 2.67
657 1354 2.681848 GCAGTGGAACATCAATCCTCAG 59.318 50.000 0.00 0.00 44.52 3.35
665 1362 3.607741 ACATCAATCCTCAGCTCTGTTG 58.392 45.455 0.00 0.00 0.00 3.33
673 1370 2.233186 CCTCAGCTCTGTTGATCTGTGA 59.767 50.000 0.00 0.00 37.61 3.58
793 1493 0.035458 CACCTTCAAACTCGCCTCCT 59.965 55.000 0.00 0.00 0.00 3.69
794 1494 0.321996 ACCTTCAAACTCGCCTCCTC 59.678 55.000 0.00 0.00 0.00 3.71
795 1495 0.391793 CCTTCAAACTCGCCTCCTCC 60.392 60.000 0.00 0.00 0.00 4.30
815 1515 2.620112 CCAGCGCACCCAACAGAAG 61.620 63.158 11.47 0.00 0.00 2.85
833 1533 3.661648 CCACCTTCCCACCCCCAG 61.662 72.222 0.00 0.00 0.00 4.45
877 1577 3.434319 CGCTGCAATGCCGTTCCT 61.434 61.111 1.53 0.00 0.00 3.36
878 1578 2.180017 GCTGCAATGCCGTTCCTG 59.820 61.111 1.53 0.00 0.00 3.86
879 1579 2.334946 GCTGCAATGCCGTTCCTGA 61.335 57.895 1.53 0.00 0.00 3.86
880 1580 1.798735 CTGCAATGCCGTTCCTGAG 59.201 57.895 1.53 0.00 0.00 3.35
881 1581 2.262471 CTGCAATGCCGTTCCTGAGC 62.262 60.000 1.53 0.00 0.00 4.26
882 1582 2.334946 GCAATGCCGTTCCTGAGCA 61.335 57.895 0.00 0.00 41.50 4.26
883 1583 1.798735 CAATGCCGTTCCTGAGCAG 59.201 57.895 0.00 0.00 40.40 4.24
884 1584 0.957395 CAATGCCGTTCCTGAGCAGT 60.957 55.000 0.00 0.00 40.40 4.40
885 1585 0.957395 AATGCCGTTCCTGAGCAGTG 60.957 55.000 0.00 0.00 40.40 3.66
886 1586 2.743928 GCCGTTCCTGAGCAGTGG 60.744 66.667 0.00 0.00 0.00 4.00
887 1587 2.743928 CCGTTCCTGAGCAGTGGC 60.744 66.667 0.00 0.00 41.61 5.01
905 1605 3.780624 CGTAGCCAGCCCAATAAGT 57.219 52.632 0.00 0.00 0.00 2.24
906 1606 1.583054 CGTAGCCAGCCCAATAAGTC 58.417 55.000 0.00 0.00 0.00 3.01
907 1607 1.134521 CGTAGCCAGCCCAATAAGTCA 60.135 52.381 0.00 0.00 0.00 3.41
908 1608 2.565841 GTAGCCAGCCCAATAAGTCAG 58.434 52.381 0.00 0.00 0.00 3.51
909 1609 0.257039 AGCCAGCCCAATAAGTCAGG 59.743 55.000 0.00 0.00 0.00 3.86
910 1610 0.753111 GCCAGCCCAATAAGTCAGGG 60.753 60.000 0.00 0.00 45.68 4.45
911 1611 0.625849 CCAGCCCAATAAGTCAGGGT 59.374 55.000 0.00 0.00 44.69 4.34
912 1612 1.683011 CCAGCCCAATAAGTCAGGGTG 60.683 57.143 0.00 0.00 44.69 4.61
913 1613 0.625849 AGCCCAATAAGTCAGGGTGG 59.374 55.000 0.00 0.00 44.69 4.61
914 1614 0.331616 GCCCAATAAGTCAGGGTGGT 59.668 55.000 0.00 0.00 44.69 4.16
915 1615 1.682087 GCCCAATAAGTCAGGGTGGTC 60.682 57.143 0.00 0.00 44.69 4.02
916 1616 1.064685 CCCAATAAGTCAGGGTGGTCC 60.065 57.143 0.00 0.00 37.81 4.46
917 1617 1.633432 CCAATAAGTCAGGGTGGTCCA 59.367 52.381 0.00 0.00 38.24 4.02
918 1618 2.618045 CCAATAAGTCAGGGTGGTCCAC 60.618 54.545 14.13 14.13 38.24 4.02
990 1690 9.548631 TTTTTAATACACTATGGGGAAATTCCA 57.451 29.630 14.68 0.00 38.64 3.53
991 1691 8.760980 TTTAATACACTATGGGGAAATTCCAG 57.239 34.615 14.68 4.99 38.64 3.86
992 1692 3.669939 ACACTATGGGGAAATTCCAGG 57.330 47.619 14.68 1.46 38.64 4.45
993 1693 2.244769 ACACTATGGGGAAATTCCAGGG 59.755 50.000 14.68 6.09 38.64 4.45
994 1694 2.244769 CACTATGGGGAAATTCCAGGGT 59.755 50.000 14.68 2.40 38.64 4.34
995 1695 2.244769 ACTATGGGGAAATTCCAGGGTG 59.755 50.000 14.68 3.49 38.64 4.61
996 1696 0.339510 ATGGGGAAATTCCAGGGTGG 59.660 55.000 14.68 0.00 38.64 4.61
997 1697 1.077298 TGGGGAAATTCCAGGGTGGT 61.077 55.000 14.68 0.00 38.64 4.16
998 1698 0.324368 GGGGAAATTCCAGGGTGGTC 60.324 60.000 14.68 0.00 38.64 4.02
999 1699 0.324368 GGGAAATTCCAGGGTGGTCC 60.324 60.000 14.68 0.00 38.64 4.46
1000 1700 0.407918 GGAAATTCCAGGGTGGTCCA 59.592 55.000 7.23 0.00 39.03 4.02
1001 1701 1.007118 GGAAATTCCAGGGTGGTCCAT 59.993 52.381 7.23 0.00 39.03 3.41
1002 1702 2.102578 GAAATTCCAGGGTGGTCCATG 58.897 52.381 0.00 0.00 44.12 3.66
1014 1714 3.338250 TCCATGGACCACCCTGGC 61.338 66.667 11.44 0.00 46.80 4.85
1015 1715 4.447342 CCATGGACCACCCTGGCC 62.447 72.222 5.56 0.00 43.04 5.36
1016 1716 3.660571 CATGGACCACCCTGGCCA 61.661 66.667 4.71 4.71 43.97 5.36
1017 1717 3.661648 ATGGACCACCCTGGCCAC 61.662 66.667 0.00 0.00 43.14 5.01
1024 1724 4.760220 ACCCTGGCCACCCCCTAG 62.760 72.222 0.00 0.00 0.00 3.02
1027 1727 2.040884 CTGGCCACCCCCTAGCTA 60.041 66.667 0.00 0.00 0.00 3.32
1028 1728 2.366435 TGGCCACCCCCTAGCTAC 60.366 66.667 0.00 0.00 0.00 3.58
1029 1729 3.547513 GGCCACCCCCTAGCTACG 61.548 72.222 0.00 0.00 0.00 3.51
1030 1730 4.237207 GCCACCCCCTAGCTACGC 62.237 72.222 0.00 0.00 0.00 4.42
1031 1731 3.547513 CCACCCCCTAGCTACGCC 61.548 72.222 0.00 0.00 0.00 5.68
1032 1732 2.762459 CACCCCCTAGCTACGCCA 60.762 66.667 0.00 0.00 0.00 5.69
1033 1733 2.762875 ACCCCCTAGCTACGCCAC 60.763 66.667 0.00 0.00 0.00 5.01
1034 1734 2.444140 CCCCCTAGCTACGCCACT 60.444 66.667 0.00 0.00 0.00 4.00
1198 1898 2.291605 ACCCCCTTCTGTAATTGCTTCC 60.292 50.000 0.00 0.00 0.00 3.46
1285 1985 2.513893 GCTTTCTTGCTTCGCTGATTC 58.486 47.619 0.00 0.00 0.00 2.52
1298 1998 1.663135 GCTGATTCGTGCCTCTTTCTC 59.337 52.381 0.00 0.00 0.00 2.87
1306 2006 2.544267 CGTGCCTCTTTCTCGTTTCTTT 59.456 45.455 0.00 0.00 0.00 2.52
1661 2361 2.202716 CAGTCGCATGCGCTCTCT 60.203 61.111 34.45 23.85 39.59 3.10
1879 2579 2.210013 TGAAGGAGGTGCTCACGCT 61.210 57.895 0.00 0.00 36.97 5.07
2072 2774 0.529378 CCATGGCCTGCTTCTTTGAC 59.471 55.000 3.32 0.00 0.00 3.18
2214 2921 3.961480 ATCTGAATCTGTGAACCGACA 57.039 42.857 0.00 0.00 0.00 4.35
2249 2956 5.464965 ACCATCGTGAAATCGTGTTAATC 57.535 39.130 0.00 0.00 0.00 1.75
2252 2959 4.811158 TCGTGAAATCGTGTTAATCGAC 57.189 40.909 7.63 0.00 40.07 4.20
2254 2961 3.058520 CGTGAAATCGTGTTAATCGACGT 59.941 43.478 7.63 0.00 40.07 4.34
2266 2973 6.420008 GTGTTAATCGACGTAATATGCTCCTT 59.580 38.462 0.00 0.00 0.00 3.36
2283 2990 2.958355 TCCTTTTGCCACTTTGAAGGAG 59.042 45.455 0.00 0.00 40.55 3.69
2325 3032 5.120674 TGTGAATTGCAGTGTTTCTATCTCG 59.879 40.000 0.00 0.00 0.00 4.04
2405 3113 0.040425 GCCACACAAACACCGACATC 60.040 55.000 0.00 0.00 0.00 3.06
2465 3183 0.107508 ATGCATGTCCCTCTTCACCG 60.108 55.000 0.00 0.00 0.00 4.94
2466 3184 1.450312 GCATGTCCCTCTTCACCGG 60.450 63.158 0.00 0.00 0.00 5.28
2480 3198 3.284793 TCACCGGGAAAAAGAAGACAA 57.715 42.857 6.32 0.00 0.00 3.18
2556 3274 3.595190 ACCTCCAAAGTAGTTTGCCTT 57.405 42.857 16.26 0.00 41.64 4.35
2606 3324 4.263572 CAGGGCAACGTGTCCCCA 62.264 66.667 18.69 0.00 45.08 4.96
2626 3344 3.244009 CCAGACATGCTATCGAACTCCAT 60.244 47.826 0.00 0.00 0.00 3.41
2635 3353 5.069119 TGCTATCGAACTCCATAACTGACAT 59.931 40.000 0.00 0.00 0.00 3.06
2677 3395 1.270826 GGAGAAGGAAGCCAAAACTGC 59.729 52.381 0.00 0.00 0.00 4.40
2680 3398 1.620323 GAAGGAAGCCAAAACTGCCAT 59.380 47.619 0.00 0.00 37.92 4.40
2699 3417 1.153539 TCCTCCAATCACCAACCCAA 58.846 50.000 0.00 0.00 0.00 4.12
2727 3445 1.134699 TGCACCTTCTTCCAGCTATCG 60.135 52.381 0.00 0.00 0.00 2.92
2733 3451 1.144716 CTTCCAGCTATCGCCTGCA 59.855 57.895 0.00 0.00 36.60 4.41
2825 3543 3.306989 CCACAGTAAGATGGACAGAGCAA 60.307 47.826 0.00 0.00 38.34 3.91
2840 3558 0.550914 AGCAAAAGGGGAGACACACA 59.449 50.000 0.00 0.00 34.58 3.72
2889 3610 4.706476 CCAACACCATCCATGAACACTAAT 59.294 41.667 0.00 0.00 0.00 1.73
2918 3639 4.803613 TGATATGAAGGATCGACAAACACG 59.196 41.667 0.00 0.00 0.00 4.49
2974 3695 4.742201 CGCCGGTGTGAGAGTGGG 62.742 72.222 6.91 0.00 0.00 4.61
3042 3763 1.529865 GCTCACCACGACCTACAAAAC 59.470 52.381 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.338118 GTGGTTTGACTGGATTTGTCTTGA 59.662 41.667 0.00 0.00 35.63 3.02
20 21 3.006217 AGGTAGGTACTTCGTGGTTTGAC 59.994 47.826 0.00 0.00 41.75 3.18
23 24 2.289257 GCAGGTAGGTACTTCGTGGTTT 60.289 50.000 0.00 0.00 40.93 3.27
29 30 4.650754 ATAGTTGCAGGTAGGTACTTCG 57.349 45.455 0.00 0.00 41.75 3.79
43 44 7.766278 TGTTGAGATTTCTTCCTCTATAGTTGC 59.234 37.037 0.00 0.00 0.00 4.17
51 52 9.745018 TTATGATTTGTTGAGATTTCTTCCTCT 57.255 29.630 0.00 0.00 0.00 3.69
66 67 7.609056 ACGGTCTACTACTGTTATGATTTGTT 58.391 34.615 0.00 0.00 45.88 2.83
67 68 7.166691 ACGGTCTACTACTGTTATGATTTGT 57.833 36.000 0.00 0.00 45.88 2.83
88 89 2.278596 CCTCCATGTACGCGACGG 60.279 66.667 15.93 5.33 0.00 4.79
118 121 0.179048 CCCATCGCTGGTATGCTTGA 60.179 55.000 4.31 0.00 41.37 3.02
141 144 5.472137 TGTAACACTATCTTCTTGGTTTGGC 59.528 40.000 0.00 0.00 0.00 4.52
142 145 6.710744 ACTGTAACACTATCTTCTTGGTTTGG 59.289 38.462 0.00 0.00 0.00 3.28
145 148 7.280356 ACAACTGTAACACTATCTTCTTGGTT 58.720 34.615 0.00 0.00 0.00 3.67
151 154 7.095229 TGCATCAACAACTGTAACACTATCTTC 60.095 37.037 0.00 0.00 0.00 2.87
158 161 4.285807 TGTGCATCAACAACTGTAACAC 57.714 40.909 0.00 0.00 0.00 3.32
163 166 4.652421 TTTCATGTGCATCAACAACTGT 57.348 36.364 0.00 0.00 32.81 3.55
171 174 1.662592 CGCGTGTTTTCATGTGCATCA 60.663 47.619 0.00 0.00 39.85 3.07
191 194 4.698780 GGTTGGTTATTTGTACTCCAGGTC 59.301 45.833 0.00 0.00 0.00 3.85
199 204 8.880878 ATGAAAAGTTGGTTGGTTATTTGTAC 57.119 30.769 0.00 0.00 0.00 2.90
217 222 5.935789 TGTCCCGGTTACTCTTTATGAAAAG 59.064 40.000 0.00 0.00 42.99 2.27
228 233 3.208594 AGTTTTTGTGTCCCGGTTACTC 58.791 45.455 0.00 0.00 0.00 2.59
230 236 3.002965 CAGAGTTTTTGTGTCCCGGTTAC 59.997 47.826 0.00 0.00 0.00 2.50
235 241 1.873591 CTCCAGAGTTTTTGTGTCCCG 59.126 52.381 0.00 0.00 0.00 5.14
241 247 2.439507 TGAGGAGCTCCAGAGTTTTTGT 59.560 45.455 33.90 9.66 38.89 2.83
278 285 6.059484 AGTCCTTCAACTCCAATCGTTTTTA 58.941 36.000 0.00 0.00 0.00 1.52
333 340 4.607293 TGTGTCTTAGTGATGTTGCTCT 57.393 40.909 0.00 0.00 0.00 4.09
338 345 6.095440 AGCAAGTTTTGTGTCTTAGTGATGTT 59.905 34.615 0.00 0.00 0.00 2.71
347 354 5.637006 TTGTGTAGCAAGTTTTGTGTCTT 57.363 34.783 0.00 0.00 32.52 3.01
348 355 5.393027 CCTTTGTGTAGCAAGTTTTGTGTCT 60.393 40.000 0.00 0.00 38.47 3.41
350 357 4.381505 CCCTTTGTGTAGCAAGTTTTGTGT 60.382 41.667 0.00 0.00 38.47 3.72
351 358 4.111916 CCCTTTGTGTAGCAAGTTTTGTG 58.888 43.478 0.00 0.00 38.47 3.33
352 359 3.767131 ACCCTTTGTGTAGCAAGTTTTGT 59.233 39.130 0.00 0.00 38.47 2.83
353 360 4.111916 CACCCTTTGTGTAGCAAGTTTTG 58.888 43.478 0.00 0.00 40.26 2.44
354 361 4.020543 TCACCCTTTGTGTAGCAAGTTTT 58.979 39.130 0.00 0.00 45.61 2.43
355 362 3.626930 TCACCCTTTGTGTAGCAAGTTT 58.373 40.909 0.00 0.00 45.61 2.66
356 363 3.118038 TCTCACCCTTTGTGTAGCAAGTT 60.118 43.478 0.00 0.00 45.61 2.66
357 364 2.438021 TCTCACCCTTTGTGTAGCAAGT 59.562 45.455 0.00 0.00 45.61 3.16
358 365 3.070018 CTCTCACCCTTTGTGTAGCAAG 58.930 50.000 0.00 0.00 45.61 4.01
359 366 2.703536 TCTCTCACCCTTTGTGTAGCAA 59.296 45.455 0.00 0.00 45.61 3.91
360 367 2.037251 GTCTCTCACCCTTTGTGTAGCA 59.963 50.000 0.00 0.00 45.61 3.49
361 368 2.037251 TGTCTCTCACCCTTTGTGTAGC 59.963 50.000 0.00 0.00 45.61 3.58
362 369 4.310769 CTTGTCTCTCACCCTTTGTGTAG 58.689 47.826 0.00 0.00 45.61 2.74
363 370 3.071023 CCTTGTCTCTCACCCTTTGTGTA 59.929 47.826 0.00 0.00 45.61 2.90
373 394 2.700722 GGATTCCCCTTGTCTCTCAC 57.299 55.000 0.00 0.00 0.00 3.51
475 1172 5.920273 GTGTGACATAAAACCTTCATTGTGG 59.080 40.000 0.00 0.00 0.00 4.17
501 1198 6.149973 TGAAAGGCTAAGTGATTGACTGATTG 59.850 38.462 0.00 0.00 34.02 2.67
502 1199 6.150140 GTGAAAGGCTAAGTGATTGACTGATT 59.850 38.462 0.00 0.00 34.02 2.57
503 1200 5.645497 GTGAAAGGCTAAGTGATTGACTGAT 59.355 40.000 0.00 0.00 34.02 2.90
504 1201 4.997395 GTGAAAGGCTAAGTGATTGACTGA 59.003 41.667 0.00 0.00 34.02 3.41
505 1202 4.756642 TGTGAAAGGCTAAGTGATTGACTG 59.243 41.667 0.00 0.00 34.02 3.51
506 1203 4.973168 TGTGAAAGGCTAAGTGATTGACT 58.027 39.130 0.00 0.00 35.94 3.41
507 1204 4.757149 ACTGTGAAAGGCTAAGTGATTGAC 59.243 41.667 0.00 0.00 0.00 3.18
508 1205 4.973168 ACTGTGAAAGGCTAAGTGATTGA 58.027 39.130 0.00 0.00 0.00 2.57
583 1280 5.642063 GGATACGAAAAGAGGAACATGAACA 59.358 40.000 0.00 0.00 0.00 3.18
620 1317 4.688879 TCCACTGCGTATTTTACTGAACAG 59.311 41.667 0.00 0.00 0.00 3.16
623 1320 5.057819 TGTTCCACTGCGTATTTTACTGAA 58.942 37.500 0.00 0.00 0.00 3.02
637 1334 2.681848 GCTGAGGATTGATGTTCCACTG 59.318 50.000 0.00 0.00 35.59 3.66
650 1347 3.106054 ACAGATCAACAGAGCTGAGGAT 58.894 45.455 16.53 6.45 46.06 3.24
652 1349 2.233186 TCACAGATCAACAGAGCTGAGG 59.767 50.000 16.53 8.73 46.06 3.86
657 1354 3.037431 ACAGTCACAGATCAACAGAGC 57.963 47.619 0.00 0.00 0.00 4.09
665 1362 4.462508 TGAGATCCAACAGTCACAGATC 57.537 45.455 0.00 0.00 34.79 2.75
673 1370 4.223032 ACCGTTAGATTGAGATCCAACAGT 59.777 41.667 0.00 0.00 34.73 3.55
707 1404 2.202797 TCGATCAGCGCTTCAGGC 60.203 61.111 7.50 0.00 40.61 4.85
793 1493 4.947147 GTTGGGTGCGCTGGTGGA 62.947 66.667 9.73 0.00 0.00 4.02
795 1495 3.663176 CTGTTGGGTGCGCTGGTG 61.663 66.667 9.73 0.00 0.00 4.17
833 1533 2.430921 CGTGTGACCTGCGGAGAC 60.431 66.667 5.10 0.00 0.00 3.36
872 1572 0.737715 CTACGCCACTGCTCAGGAAC 60.738 60.000 1.66 0.00 34.43 3.62
873 1573 1.591703 CTACGCCACTGCTCAGGAA 59.408 57.895 1.66 0.00 34.43 3.36
874 1574 3.006756 GCTACGCCACTGCTCAGGA 62.007 63.158 1.66 0.00 34.43 3.86
875 1575 2.510238 GCTACGCCACTGCTCAGG 60.510 66.667 1.66 0.00 34.43 3.86
886 1586 0.463833 ACTTATTGGGCTGGCTACGC 60.464 55.000 0.00 0.00 0.00 4.42
887 1587 1.134521 TGACTTATTGGGCTGGCTACG 60.135 52.381 0.00 0.00 0.00 3.51
888 1588 2.565841 CTGACTTATTGGGCTGGCTAC 58.434 52.381 0.00 0.00 0.00 3.58
889 1589 1.490490 CCTGACTTATTGGGCTGGCTA 59.510 52.381 0.00 0.00 0.00 3.93
890 1590 0.257039 CCTGACTTATTGGGCTGGCT 59.743 55.000 0.00 0.00 0.00 4.75
891 1591 0.753111 CCCTGACTTATTGGGCTGGC 60.753 60.000 0.00 0.00 33.88 4.85
892 1592 0.625849 ACCCTGACTTATTGGGCTGG 59.374 55.000 0.00 0.00 44.56 4.85
893 1593 1.683011 CCACCCTGACTTATTGGGCTG 60.683 57.143 0.00 0.00 44.56 4.85
894 1594 0.625849 CCACCCTGACTTATTGGGCT 59.374 55.000 0.00 0.00 44.56 5.19
895 1595 0.331616 ACCACCCTGACTTATTGGGC 59.668 55.000 0.00 0.00 44.56 5.36
896 1596 1.064685 GGACCACCCTGACTTATTGGG 60.065 57.143 0.00 0.00 46.07 4.12
897 1597 1.633432 TGGACCACCCTGACTTATTGG 59.367 52.381 0.00 0.00 35.38 3.16
898 1598 2.711542 GTGGACCACCCTGACTTATTG 58.288 52.381 14.16 0.00 35.38 1.90
964 1664 9.548631 TGGAATTTCCCCATAGTGTATTAAAAA 57.451 29.630 12.90 0.00 35.03 1.94
965 1665 9.196139 CTGGAATTTCCCCATAGTGTATTAAAA 57.804 33.333 12.90 0.00 35.03 1.52
966 1666 7.782644 CCTGGAATTTCCCCATAGTGTATTAAA 59.217 37.037 12.90 0.00 35.03 1.52
967 1667 7.294584 CCTGGAATTTCCCCATAGTGTATTAA 58.705 38.462 12.90 0.00 35.03 1.40
968 1668 6.183361 CCCTGGAATTTCCCCATAGTGTATTA 60.183 42.308 12.90 0.00 35.03 0.98
969 1669 5.400189 CCCTGGAATTTCCCCATAGTGTATT 60.400 44.000 12.90 0.00 35.03 1.89
970 1670 4.106341 CCCTGGAATTTCCCCATAGTGTAT 59.894 45.833 12.90 0.00 35.03 2.29
971 1671 3.461831 CCCTGGAATTTCCCCATAGTGTA 59.538 47.826 12.90 0.00 35.03 2.90
972 1672 2.244769 CCCTGGAATTTCCCCATAGTGT 59.755 50.000 12.90 0.00 35.03 3.55
973 1673 2.244769 ACCCTGGAATTTCCCCATAGTG 59.755 50.000 12.90 0.00 35.03 2.74
974 1674 2.244769 CACCCTGGAATTTCCCCATAGT 59.755 50.000 12.90 1.12 35.03 2.12
975 1675 2.424812 CCACCCTGGAATTTCCCCATAG 60.425 54.545 12.90 3.52 40.96 2.23
976 1676 1.573376 CCACCCTGGAATTTCCCCATA 59.427 52.381 12.90 0.00 40.96 2.74
977 1677 0.339510 CCACCCTGGAATTTCCCCAT 59.660 55.000 12.90 0.00 40.96 4.00
978 1678 1.077298 ACCACCCTGGAATTTCCCCA 61.077 55.000 12.90 0.00 40.96 4.96
979 1679 0.324368 GACCACCCTGGAATTTCCCC 60.324 60.000 12.90 0.00 40.96 4.81
980 1680 0.324368 GGACCACCCTGGAATTTCCC 60.324 60.000 12.90 0.00 40.96 3.97
981 1681 0.407918 TGGACCACCCTGGAATTTCC 59.592 55.000 8.59 8.59 40.96 3.13
982 1682 2.102578 CATGGACCACCCTGGAATTTC 58.897 52.381 0.00 0.00 40.96 2.17
983 1683 2.236489 CATGGACCACCCTGGAATTT 57.764 50.000 0.00 0.00 40.96 1.82
999 1699 3.660571 TGGCCAGGGTGGTCCATG 61.661 66.667 0.00 0.00 42.76 3.66
1000 1700 3.661648 GTGGCCAGGGTGGTCCAT 61.662 66.667 5.11 0.00 42.76 3.41
1007 1707 4.760220 CTAGGGGGTGGCCAGGGT 62.760 72.222 5.11 0.00 0.00 4.34
1009 1709 3.714078 TAGCTAGGGGGTGGCCAGG 62.714 68.421 5.11 0.00 31.44 4.45
1010 1710 2.040884 TAGCTAGGGGGTGGCCAG 60.041 66.667 5.11 0.00 31.44 4.85
1011 1711 2.366435 GTAGCTAGGGGGTGGCCA 60.366 66.667 0.00 0.00 31.44 5.36
1012 1712 3.547513 CGTAGCTAGGGGGTGGCC 61.548 72.222 5.50 0.00 31.44 5.36
1025 1725 0.737715 GCTCAGGAACAGTGGCGTAG 60.738 60.000 0.00 0.00 0.00 3.51
1026 1726 1.292223 GCTCAGGAACAGTGGCGTA 59.708 57.895 0.00 0.00 0.00 4.42
1027 1727 2.031163 GCTCAGGAACAGTGGCGT 59.969 61.111 0.00 0.00 0.00 5.68
1028 1728 2.743928 GGCTCAGGAACAGTGGCG 60.744 66.667 0.00 0.00 0.00 5.69
1029 1729 2.360475 GGGCTCAGGAACAGTGGC 60.360 66.667 0.00 0.00 33.54 5.01
1030 1730 2.352805 GGGGCTCAGGAACAGTGG 59.647 66.667 0.00 0.00 0.00 4.00
1031 1731 2.190488 GAGGGGGCTCAGGAACAGTG 62.190 65.000 0.00 0.00 0.00 3.66
1032 1732 1.920835 GAGGGGGCTCAGGAACAGT 60.921 63.158 0.00 0.00 0.00 3.55
1033 1733 2.674220 GGAGGGGGCTCAGGAACAG 61.674 68.421 0.00 0.00 0.00 3.16
1034 1734 2.610859 GGAGGGGGCTCAGGAACA 60.611 66.667 0.00 0.00 0.00 3.18
1198 1898 1.705186 TCTTGGACAAGAAAGGGAGGG 59.295 52.381 12.04 0.00 43.79 4.30
1285 1985 1.784525 AGAAACGAGAAAGAGGCACG 58.215 50.000 0.00 0.00 0.00 5.34
1298 1998 1.491563 CGCTGGTCGGAAAGAAACG 59.508 57.895 0.00 0.00 33.78 3.60
2000 2700 0.659427 CTCTGGCATTGGTACGCATG 59.341 55.000 0.00 0.00 0.00 4.06
2072 2774 1.081892 CCAACAGGCTTCAGTCATCG 58.918 55.000 0.00 0.00 0.00 3.84
2150 2857 1.911357 ACCATCTGAAGCTCACCATGA 59.089 47.619 0.00 0.00 0.00 3.07
2214 2921 1.229428 CGATGGTTCACACAACTGCT 58.771 50.000 0.00 0.00 0.00 4.24
2249 2956 3.303132 GGCAAAAGGAGCATATTACGTCG 60.303 47.826 0.00 0.00 0.00 5.12
2252 2959 3.627577 AGTGGCAAAAGGAGCATATTACG 59.372 43.478 0.00 0.00 0.00 3.18
2254 2961 5.714333 TCAAAGTGGCAAAAGGAGCATATTA 59.286 36.000 0.00 0.00 0.00 0.98
2266 2973 3.255642 GCATACTCCTTCAAAGTGGCAAA 59.744 43.478 0.00 0.00 32.15 3.68
2283 2990 9.708222 CAATTCACAAAACTACTATGAGCATAC 57.292 33.333 0.00 0.00 0.00 2.39
2374 3082 5.177696 GTGTTTGTGTGGCTTGTAACAAAAA 59.822 36.000 1.73 0.00 42.37 1.94
2377 3085 3.367498 GGTGTTTGTGTGGCTTGTAACAA 60.367 43.478 0.00 0.00 0.00 2.83
2405 3113 3.887621 TCCTATCTTTTCGGTCCTGTG 57.112 47.619 0.00 0.00 0.00 3.66
2445 3155 1.673168 GGTGAAGAGGGACATGCATC 58.327 55.000 0.00 0.00 0.00 3.91
2465 3183 5.536538 AGAGGTGATTTGTCTTCTTTTTCCC 59.463 40.000 0.00 0.00 0.00 3.97
2466 3184 6.641169 AGAGGTGATTTGTCTTCTTTTTCC 57.359 37.500 0.00 0.00 0.00 3.13
2480 3198 3.369892 CCAGTTCGGATGAAGAGGTGATT 60.370 47.826 0.00 0.00 36.56 2.57
2556 3274 2.362397 TCAACGGCAATGGTTTTGCTTA 59.638 40.909 9.86 0.00 44.36 3.09
2606 3324 5.303078 AGTTATGGAGTTCGATAGCATGTCT 59.697 40.000 0.00 0.00 0.00 3.41
2626 3344 0.180171 CATGCGGGGGATGTCAGTTA 59.820 55.000 0.00 0.00 0.00 2.24
2635 3353 2.043752 TCGTAGTCATGCGGGGGA 60.044 61.111 0.00 0.00 35.00 4.81
2677 3395 1.686115 GGGTTGGTGATTGGAGGATGG 60.686 57.143 0.00 0.00 0.00 3.51
2680 3398 1.153539 TTGGGTTGGTGATTGGAGGA 58.846 50.000 0.00 0.00 0.00 3.71
2727 3445 2.384203 GACGGTTGTCTATGCAGGC 58.616 57.895 0.00 0.00 42.08 4.85
2825 3543 3.490348 CTTTCATGTGTGTCTCCCCTTT 58.510 45.455 0.00 0.00 0.00 3.11
2840 3558 1.741770 GCGACAGCGACCCTTTCAT 60.742 57.895 0.00 0.00 40.82 2.57
2889 3610 2.629617 TCGATCCTTCATATCAGCAGCA 59.370 45.455 0.00 0.00 0.00 4.41
2918 3639 2.349886 GTCTCGAAGTTGATGGCATCAC 59.650 50.000 28.83 21.91 39.39 3.06
2974 3695 1.265365 GCGAATAAATCTGCCTCAGCC 59.735 52.381 0.00 0.00 38.69 4.85
3005 3726 2.897762 GCCGTTGGGGTAGTGGGAA 61.898 63.158 0.00 0.00 38.44 3.97
3012 3733 2.527123 TGGTGAGCCGTTGGGGTA 60.527 61.111 0.00 0.00 46.15 3.69


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

AutoCloner maintained by Alex Coulton.