Multiple sequence alignment - TraesCS3D01G062800

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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 TraesCS3D01G062800 chr3D 100.000 2465 0 0 1 2465 27682282 27679818 0.000000e+00 4553
1 TraesCS3D01G062800 chr3D 91.094 786 68 1 1682 2465 475126104 475125319 0.000000e+00 1062
2 TraesCS3D01G062800 chr3D 77.914 163 32 4 288 448 27663218 27663378 5.610000e-17 99
3 TraesCS3D01G062800 chr3B 93.494 830 48 1 752 1575 47193165 47193994 0.000000e+00 1229
4 TraesCS3D01G062800 chr3B 87.263 581 62 7 155 732 47192604 47193175 0.000000e+00 652
5 TraesCS3D01G062800 chr3B 76.407 835 156 22 752 1575 47121798 47122602 1.760000e-111 412
6 TraesCS3D01G062800 chr3B 75.783 830 160 20 752 1570 46365496 46364697 4.970000e-102 381
7 TraesCS3D01G062800 chr3B 96.774 62 2 0 1 62 168191010 168190949 1.210000e-18 104
8 TraesCS3D01G062800 chr3B 100.000 55 0 0 72 126 47192549 47192603 4.340000e-18 102
9 TraesCS3D01G062800 chr1D 90.868 876 74 5 1593 2465 194181579 194182451 0.000000e+00 1170
10 TraesCS3D01G062800 chr1D 78.261 230 35 12 288 506 381005055 381005280 1.540000e-27 134
11 TraesCS3D01G062800 chr2D 90.230 870 82 2 1596 2465 649551626 649550760 0.000000e+00 1133
12 TraesCS3D01G062800 chr2D 89.954 876 80 5 1592 2465 25658305 25657436 0.000000e+00 1123
13 TraesCS3D01G062800 chr2D 96.774 62 2 0 1 62 204713355 204713294 1.210000e-18 104
14 TraesCS3D01G062800 chr3A 88.776 882 97 2 1586 2465 371621281 371622162 0.000000e+00 1079
15 TraesCS3D01G062800 chr3A 76.562 832 160 15 752 1575 37823391 37822587 8.150000e-115 424
16 TraesCS3D01G062800 chr6A 89.257 875 75 15 1594 2462 54485979 54486840 0.000000e+00 1077
17 TraesCS3D01G062800 chr7B 87.685 877 106 2 1591 2465 510761819 510760943 0.000000e+00 1020
18 TraesCS3D01G062800 chr7B 96.774 62 2 0 1 62 336603333 336603394 1.210000e-18 104
19 TraesCS3D01G062800 chr7B 96.774 62 2 0 1 62 702684943 702685004 1.210000e-18 104
20 TraesCS3D01G062800 chr7B 93.846 65 4 0 1 65 128881454 128881390 5.610000e-17 99
21 TraesCS3D01G062800 chr7A 87.673 868 102 3 1601 2465 434752784 434753649 0.000000e+00 1005
22 TraesCS3D01G062800 chr7A 96.774 62 2 0 1 62 718242661 718242600 1.210000e-18 104
23 TraesCS3D01G062800 chr4A 87.200 875 109 3 1591 2465 722426836 722427707 0.000000e+00 992
24 TraesCS3D01G062800 chr4A 93.939 66 4 0 1 66 520991033 520991098 1.560000e-17 100
25 TraesCS3D01G062800 chr1B 76.829 246 42 12 288 522 510790898 510791139 9.260000e-25 124
26 TraesCS3D01G062800 chr1A 76.518 247 41 14 288 522 481628133 481628374 4.310000e-23 119
27 TraesCS3D01G062800 chr2B 80.142 141 26 2 1113 1252 787034294 787034155 1.210000e-18 104
28 TraesCS3D01G062800 chrUn 95.161 62 3 0 1 62 364697099 364697160 5.610000e-17 99
29 TraesCS3D01G062800 chr6D 95.161 62 3 0 1 62 23102028 23102089 5.610000e-17 99


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 TraesCS3D01G062800 chr3D 27679818 27682282 2464 True 4553 4553 100.000000 1 2465 1 chr3D.!!$R1 2464
1 TraesCS3D01G062800 chr3D 475125319 475126104 785 True 1062 1062 91.094000 1682 2465 1 chr3D.!!$R2 783
2 TraesCS3D01G062800 chr3B 47192549 47193994 1445 False 661 1229 93.585667 72 1575 3 chr3B.!!$F2 1503
3 TraesCS3D01G062800 chr3B 47121798 47122602 804 False 412 412 76.407000 752 1575 1 chr3B.!!$F1 823
4 TraesCS3D01G062800 chr3B 46364697 46365496 799 True 381 381 75.783000 752 1570 1 chr3B.!!$R1 818
5 TraesCS3D01G062800 chr1D 194181579 194182451 872 False 1170 1170 90.868000 1593 2465 1 chr1D.!!$F1 872
6 TraesCS3D01G062800 chr2D 649550760 649551626 866 True 1133 1133 90.230000 1596 2465 1 chr2D.!!$R3 869
7 TraesCS3D01G062800 chr2D 25657436 25658305 869 True 1123 1123 89.954000 1592 2465 1 chr2D.!!$R1 873
8 TraesCS3D01G062800 chr3A 371621281 371622162 881 False 1079 1079 88.776000 1586 2465 1 chr3A.!!$F1 879
9 TraesCS3D01G062800 chr3A 37822587 37823391 804 True 424 424 76.562000 752 1575 1 chr3A.!!$R1 823
10 TraesCS3D01G062800 chr6A 54485979 54486840 861 False 1077 1077 89.257000 1594 2462 1 chr6A.!!$F1 868
11 TraesCS3D01G062800 chr7B 510760943 510761819 876 True 1020 1020 87.685000 1591 2465 1 chr7B.!!$R2 874
12 TraesCS3D01G062800 chr7A 434752784 434753649 865 False 1005 1005 87.673000 1601 2465 1 chr7A.!!$F1 864
13 TraesCS3D01G062800 chr4A 722426836 722427707 871 False 992 992 87.200000 1591 2465 1 chr4A.!!$F2 874

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
422 423 0.032952 TGACTTCTACACGCACCACC 59.967 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1576 1592 0.035739 GAGGGTTACGCCTCCAAACA 59.964 55.0 8.17 0.0 37.43 2.83 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
22 23 5.692115 TGGATAGGTTGCATGTTAAGAGA 57.308 39.130 0.00 0.00 0.00 3.10
23 24 6.061022 TGGATAGGTTGCATGTTAAGAGAA 57.939 37.500 0.00 0.00 0.00 2.87
24 25 6.480763 TGGATAGGTTGCATGTTAAGAGAAA 58.519 36.000 0.00 0.00 0.00 2.52
25 26 7.118723 TGGATAGGTTGCATGTTAAGAGAAAT 58.881 34.615 0.00 0.00 0.00 2.17
26 27 8.271458 TGGATAGGTTGCATGTTAAGAGAAATA 58.729 33.333 0.00 0.00 0.00 1.40
27 28 9.120538 GGATAGGTTGCATGTTAAGAGAAATAA 57.879 33.333 0.00 0.00 0.00 1.40
29 30 9.905713 ATAGGTTGCATGTTAAGAGAAATAAGA 57.094 29.630 0.00 0.00 0.00 2.10
30 31 8.814038 AGGTTGCATGTTAAGAGAAATAAGAT 57.186 30.769 0.00 0.00 0.00 2.40
31 32 9.905713 AGGTTGCATGTTAAGAGAAATAAGATA 57.094 29.630 0.00 0.00 0.00 1.98
43 44 9.579932 AAGAGAAATAAGATAATGGGGATCAAC 57.420 33.333 0.00 0.00 0.00 3.18
44 45 8.953665 AGAGAAATAAGATAATGGGGATCAACT 58.046 33.333 0.00 0.00 0.00 3.16
52 53 8.525729 AGATAATGGGGATCAACTATTTAGGT 57.474 34.615 0.00 0.00 0.00 3.08
53 54 9.629649 AGATAATGGGGATCAACTATTTAGGTA 57.370 33.333 0.00 0.00 0.00 3.08
70 71 8.660295 ATTTAGGTATTATAGATCCACGTCCA 57.340 34.615 0.00 0.00 0.00 4.02
126 127 2.963101 TCCTACGGCACAGCTATACAAT 59.037 45.455 0.00 0.00 0.00 2.71
129 130 1.209504 ACGGCACAGCTATACAATGGT 59.790 47.619 0.00 0.00 0.00 3.55
130 131 1.867233 CGGCACAGCTATACAATGGTC 59.133 52.381 0.00 0.00 0.00 4.02
131 132 2.483714 CGGCACAGCTATACAATGGTCT 60.484 50.000 0.00 0.00 0.00 3.85
132 133 3.134458 GGCACAGCTATACAATGGTCTC 58.866 50.000 0.00 0.00 0.00 3.36
133 134 3.134458 GCACAGCTATACAATGGTCTCC 58.866 50.000 0.00 0.00 0.00 3.71
134 135 3.384668 CACAGCTATACAATGGTCTCCG 58.615 50.000 0.00 0.00 0.00 4.63
135 136 3.068165 CACAGCTATACAATGGTCTCCGA 59.932 47.826 0.00 0.00 0.00 4.55
136 137 3.898123 ACAGCTATACAATGGTCTCCGAT 59.102 43.478 0.00 0.00 0.00 4.18
137 138 5.048013 CACAGCTATACAATGGTCTCCGATA 60.048 44.000 0.00 0.00 0.00 2.92
161 162 6.982899 AGGAACTACTACTTTCTAGGATCCA 58.017 40.000 15.82 0.00 36.02 3.41
162 163 7.597327 AGGAACTACTACTTTCTAGGATCCAT 58.403 38.462 15.82 1.47 36.02 3.41
163 164 7.726738 AGGAACTACTACTTTCTAGGATCCATC 59.273 40.741 15.82 0.00 36.02 3.51
164 165 7.308710 GGAACTACTACTTTCTAGGATCCATCG 60.309 44.444 15.82 1.27 0.00 3.84
165 166 4.857509 ACTACTTTCTAGGATCCATCGC 57.142 45.455 15.82 0.00 0.00 4.58
166 167 4.215908 ACTACTTTCTAGGATCCATCGCA 58.784 43.478 15.82 0.00 0.00 5.10
167 168 3.460857 ACTTTCTAGGATCCATCGCAC 57.539 47.619 15.82 0.00 0.00 5.34
168 169 2.103263 ACTTTCTAGGATCCATCGCACC 59.897 50.000 15.82 0.00 0.00 5.01
169 170 1.788229 TTCTAGGATCCATCGCACCA 58.212 50.000 15.82 0.00 0.00 4.17
173 174 0.327924 AGGATCCATCGCACCAAACA 59.672 50.000 15.82 0.00 0.00 2.83
197 198 1.114722 CAACCTTGCCTTTGCCCTCA 61.115 55.000 0.00 0.00 36.33 3.86
199 200 1.075482 CCTTGCCTTTGCCCTCAGA 59.925 57.895 0.00 0.00 36.33 3.27
208 209 0.603569 TTGCCCTCAGAGTCTTCGAC 59.396 55.000 0.00 0.00 0.00 4.20
212 213 1.324005 CCTCAGAGTCTTCGACCCCC 61.324 65.000 0.00 0.00 32.18 5.40
214 215 2.362632 AGAGTCTTCGACCCCCGG 60.363 66.667 0.00 0.00 39.14 5.73
228 229 3.512516 CCGGTCCCTCGTACGTCC 61.513 72.222 16.05 9.97 0.00 4.79
242 243 4.408821 GTCCCGCCACCATGAGCA 62.409 66.667 0.00 0.00 0.00 4.26
246 247 1.606885 CCCGCCACCATGAGCAAAAT 61.607 55.000 0.00 0.00 0.00 1.82
270 271 2.741985 CGCCGACATGACCTGCAA 60.742 61.111 0.00 0.00 0.00 4.08
275 276 1.021390 CGACATGACCTGCAACTCCC 61.021 60.000 0.00 0.00 0.00 4.30
302 303 3.192799 GGTGACGATCTCCTCTGGA 57.807 57.895 0.00 0.00 0.00 3.86
321 322 1.955458 AAGATCCTCCTCCGCCTCCT 61.955 60.000 0.00 0.00 0.00 3.69
390 391 4.736896 GCGTCTCACCACCGACCC 62.737 72.222 0.00 0.00 0.00 4.46
401 402 1.229529 ACCGACCCCATGTTCCTCT 60.230 57.895 0.00 0.00 0.00 3.69
403 404 1.553690 CCGACCCCATGTTCCTCTGT 61.554 60.000 0.00 0.00 0.00 3.41
404 405 0.391661 CGACCCCATGTTCCTCTGTG 60.392 60.000 0.00 0.00 0.00 3.66
413 414 4.021104 CCATGTTCCTCTGTGACTTCTACA 60.021 45.833 0.00 0.00 0.00 2.74
422 423 0.032952 TGACTTCTACACGCACCACC 59.967 55.000 0.00 0.00 0.00 4.61
453 454 0.809385 CTCCTCGGCGTCTTTGAGTA 59.191 55.000 6.85 0.00 0.00 2.59
457 458 1.080974 CGGCGTCTTTGAGTACCGT 60.081 57.895 0.00 0.00 35.99 4.83
460 461 1.403780 GGCGTCTTTGAGTACCGTGAT 60.404 52.381 0.00 0.00 0.00 3.06
479 480 4.342378 GTGATAGCATGGTCTTCACCTCTA 59.658 45.833 21.52 1.92 44.17 2.43
488 489 2.288458 GTCTTCACCTCTATCCTCGACG 59.712 54.545 0.00 0.00 0.00 5.12
506 508 2.687200 CCCGGACCACATCCCTCA 60.687 66.667 0.73 0.00 46.04 3.86
507 509 2.584608 CCGGACCACATCCCTCAC 59.415 66.667 0.00 0.00 46.04 3.51
517 519 2.351244 ATCCCTCACGAGCGCTTCA 61.351 57.895 13.26 0.00 0.00 3.02
531 533 1.739067 GCTTCAACCTCCAACGCTAT 58.261 50.000 0.00 0.00 0.00 2.97
534 536 3.679083 GCTTCAACCTCCAACGCTATAGT 60.679 47.826 0.84 0.00 0.00 2.12
550 552 0.246910 TAGTTGCCGCCACGAATACA 59.753 50.000 0.00 0.00 0.00 2.29
562 564 0.673333 CGAATACAGCACACCCAGCA 60.673 55.000 0.00 0.00 0.00 4.41
588 590 0.320374 CCCACAGGAACGAAGTGCTA 59.680 55.000 0.00 0.00 45.00 3.49
600 602 3.880846 GTGCTATGCTGCCGCCAC 61.881 66.667 0.00 0.00 34.43 5.01
617 619 2.129146 ACGGTCGTGTCCTCACCAA 61.129 57.895 0.00 0.00 41.09 3.67
621 623 1.429463 GTCGTGTCCTCACCAATGAC 58.571 55.000 0.00 0.00 41.09 3.06
647 649 1.195448 GTGCAAGGAACTCATCGTGTG 59.805 52.381 0.00 0.00 38.49 3.82
654 656 2.436646 CTCATCGTGTGCACCCCC 60.437 66.667 15.69 0.98 0.00 5.40
660 662 4.555709 GTGTGCACCCCCGTCACA 62.556 66.667 15.69 0.00 38.27 3.58
661 663 3.565214 TGTGCACCCCCGTCACAT 61.565 61.111 15.69 0.00 35.99 3.21
667 669 4.082523 CCCCCGTCACATGCGAGT 62.083 66.667 0.00 0.00 0.00 4.18
670 672 1.511305 CCCGTCACATGCGAGTAGT 59.489 57.895 0.00 0.00 0.00 2.73
674 676 1.260206 GTCACATGCGAGTAGTGTCG 58.740 55.000 0.00 0.00 43.08 4.35
688 690 4.256090 GTCGCATGGCCATTCCGC 62.256 66.667 23.97 19.83 37.80 5.54
696 698 4.193334 GCCATTCCGCCCGCTTTC 62.193 66.667 0.00 0.00 0.00 2.62
697 699 2.749839 CCATTCCGCCCGCTTTCA 60.750 61.111 0.00 0.00 0.00 2.69
698 700 2.764314 CCATTCCGCCCGCTTTCAG 61.764 63.158 0.00 0.00 0.00 3.02
706 708 1.770957 GCCCGCTTTCAGTTTCAAAG 58.229 50.000 0.00 0.00 34.47 2.77
725 727 4.574674 AAGCATTCCTCTACCACATCAA 57.425 40.909 0.00 0.00 0.00 2.57
734 736 3.213264 CCACATCAATGGGGCAGC 58.787 61.111 0.00 0.00 45.73 5.25
735 737 2.428925 CCACATCAATGGGGCAGCC 61.429 63.158 1.26 1.26 45.73 4.85
736 738 1.380785 CACATCAATGGGGCAGCCT 60.381 57.895 12.43 0.00 0.00 4.58
737 739 0.974010 CACATCAATGGGGCAGCCTT 60.974 55.000 12.43 0.00 0.00 4.35
738 740 0.252375 ACATCAATGGGGCAGCCTTT 60.252 50.000 12.43 0.00 0.00 3.11
739 741 0.906775 CATCAATGGGGCAGCCTTTT 59.093 50.000 12.43 0.00 0.00 2.27
740 742 1.134610 CATCAATGGGGCAGCCTTTTC 60.135 52.381 12.43 0.00 0.00 2.29
741 743 1.216178 CAATGGGGCAGCCTTTTCG 59.784 57.895 12.43 0.00 0.00 3.46
742 744 1.984026 AATGGGGCAGCCTTTTCGG 60.984 57.895 12.43 0.00 0.00 4.30
743 745 2.439553 AATGGGGCAGCCTTTTCGGA 62.440 55.000 12.43 0.00 33.16 4.55
744 746 2.282887 GGGGCAGCCTTTTCGGAA 60.283 61.111 12.43 0.00 33.16 4.30
745 747 1.906333 GGGGCAGCCTTTTCGGAAA 60.906 57.895 12.43 0.00 33.16 3.13
746 748 1.468506 GGGGCAGCCTTTTCGGAAAA 61.469 55.000 12.43 14.64 33.16 2.29
747 749 0.391228 GGGCAGCCTTTTCGGAAAAA 59.609 50.000 12.43 2.14 33.42 1.94
771 773 0.469705 TCAATGGGGCAGTGCTTTGT 60.470 50.000 16.11 0.00 29.02 2.83
819 821 2.050269 CGGTTGTCACTCCAGTCCT 58.950 57.895 0.00 0.00 0.00 3.85
829 831 2.104792 CACTCCAGTCCTTTCAAGGTGA 59.895 50.000 5.48 0.00 46.54 4.02
855 857 4.468713 TGGTGATCATGAACCAACAAGAA 58.531 39.130 15.51 0.00 43.46 2.52
888 890 2.560981 TCTCGCATGTGTTTACTCCTCA 59.439 45.455 6.09 0.00 0.00 3.86
979 981 1.603678 GGTCACTTGTTGGCAATGCAG 60.604 52.381 7.79 2.41 33.65 4.41
1007 1009 5.477984 ACTGGTTGGTTACTACGATGAGTTA 59.522 40.000 0.00 0.00 0.00 2.24
1009 1011 4.795278 GGTTGGTTACTACGATGAGTTACG 59.205 45.833 0.00 0.00 31.26 3.18
1088 1090 1.324740 CCGGTTACAGATCGTCCCCA 61.325 60.000 0.00 0.00 0.00 4.96
1093 1095 1.182667 TACAGATCGTCCCCACTGTG 58.817 55.000 0.00 0.00 42.37 3.66
1111 1113 1.065199 GTGGTCAGATCATCCAAGCCA 60.065 52.381 0.00 0.00 32.82 4.75
1141 1143 1.561643 TGGTGCTGTTGGTTTTTCCA 58.438 45.000 0.00 0.00 45.60 3.53
1172 1174 1.863012 CGCGCTTACAAATGTGGCG 60.863 57.895 22.04 22.04 46.13 5.69
1261 1269 0.918799 TGGGCTCCCTATTCAGGCAA 60.919 55.000 6.50 0.00 41.08 4.52
1296 1304 4.878439 TCGAAACCATACTGGGATATTCG 58.122 43.478 14.16 14.16 43.37 3.34
1297 1305 4.585581 TCGAAACCATACTGGGATATTCGA 59.414 41.667 16.83 16.83 43.28 3.71
1440 1448 5.652452 AGGTTTCTATTCACCAGGTATTTGC 59.348 40.000 0.00 0.00 35.25 3.68
1485 1501 4.382291 AGCAAGGACGTTATGTTGTGTAA 58.618 39.130 0.00 0.00 0.00 2.41
1559 1575 7.562454 TCTTAATCAACAAGTTTCCTTTCGT 57.438 32.000 0.00 0.00 0.00 3.85
1575 1591 6.618811 TCCTTTCGTTAGATAGACACACTTC 58.381 40.000 0.00 0.00 0.00 3.01
1576 1592 6.433404 TCCTTTCGTTAGATAGACACACTTCT 59.567 38.462 0.00 0.00 0.00 2.85
1577 1593 6.528423 CCTTTCGTTAGATAGACACACTTCTG 59.472 42.308 0.00 0.00 0.00 3.02
1578 1594 6.570672 TTCGTTAGATAGACACACTTCTGT 57.429 37.500 0.00 0.00 0.00 3.41
1579 1595 6.570672 TCGTTAGATAGACACACTTCTGTT 57.429 37.500 0.00 0.00 0.00 3.16
1580 1596 6.978338 TCGTTAGATAGACACACTTCTGTTT 58.022 36.000 0.00 0.00 0.00 2.83
1581 1597 6.861572 TCGTTAGATAGACACACTTCTGTTTG 59.138 38.462 0.00 0.00 0.00 2.93
1582 1598 6.089551 CGTTAGATAGACACACTTCTGTTTGG 59.910 42.308 0.00 0.00 0.00 3.28
1583 1599 5.808366 AGATAGACACACTTCTGTTTGGA 57.192 39.130 0.00 0.00 0.00 3.53
1584 1600 5.788450 AGATAGACACACTTCTGTTTGGAG 58.212 41.667 0.00 0.00 0.00 3.86
1606 1622 2.338015 TAACCCTCTCGCGTCGCTT 61.338 57.895 16.36 3.22 0.00 4.68
1768 1787 4.704833 GCGAGGGCTTGGTGCTGA 62.705 66.667 0.00 0.00 42.39 4.26
1858 1879 1.662608 CTGCTGTGTCTCGTCCTGT 59.337 57.895 0.00 0.00 0.00 4.00
1896 1918 3.882326 CTGGGGCTGCGGGATCAT 61.882 66.667 0.00 0.00 0.00 2.45
2164 2191 1.021202 CAACGGCTTTGGTCTTCACA 58.979 50.000 0.00 0.00 0.00 3.58
2249 2277 2.795973 CGACTACGGTCATGGCGA 59.204 61.111 0.00 0.00 42.21 5.54
2263 2291 2.577644 GCGAACGATGTCGGCGTA 60.578 61.111 6.85 0.00 41.75 4.42
2288 2316 5.604892 ATGACGTCATTCCCTTCTTGAGGA 61.605 45.833 25.18 0.00 39.79 3.71
2325 2353 4.760047 GCGCCCCACTCGTGATGT 62.760 66.667 0.00 0.00 0.00 3.06
2338 2366 0.250989 GTGATGTTCCGGGGGAAACA 60.251 55.000 8.70 8.70 43.86 2.83
2419 2449 1.244019 GGGCATCGTTTTGGAGCACT 61.244 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.692115 TCTCTTAACATGCAACCTATCCA 57.308 39.130 0.00 0.00 0.00 3.41
1 2 7.573968 ATTTCTCTTAACATGCAACCTATCC 57.426 36.000 0.00 0.00 0.00 2.59
3 4 9.905713 TCTTATTTCTCTTAACATGCAACCTAT 57.094 29.630 0.00 0.00 0.00 2.57
4 5 9.905713 ATCTTATTTCTCTTAACATGCAACCTA 57.094 29.630 0.00 0.00 0.00 3.08
5 6 8.814038 ATCTTATTTCTCTTAACATGCAACCT 57.186 30.769 0.00 0.00 0.00 3.50
17 18 9.579932 GTTGATCCCCATTATCTTATTTCTCTT 57.420 33.333 0.00 0.00 0.00 2.85
18 19 8.953665 AGTTGATCCCCATTATCTTATTTCTCT 58.046 33.333 0.00 0.00 0.00 3.10
26 27 8.960064 ACCTAAATAGTTGATCCCCATTATCTT 58.040 33.333 0.00 0.00 0.00 2.40
27 28 8.525729 ACCTAAATAGTTGATCCCCATTATCT 57.474 34.615 0.00 0.00 0.00 1.98
44 45 9.758021 TGGACGTGGATCTATAATACCTAAATA 57.242 33.333 0.00 0.00 0.00 1.40
45 46 8.529476 GTGGACGTGGATCTATAATACCTAAAT 58.471 37.037 0.00 0.00 0.00 1.40
46 47 7.039504 GGTGGACGTGGATCTATAATACCTAAA 60.040 40.741 0.00 0.00 0.00 1.85
47 48 6.435277 GGTGGACGTGGATCTATAATACCTAA 59.565 42.308 0.00 0.00 0.00 2.69
48 49 5.948162 GGTGGACGTGGATCTATAATACCTA 59.052 44.000 0.00 0.00 0.00 3.08
49 50 4.771054 GGTGGACGTGGATCTATAATACCT 59.229 45.833 0.00 0.00 0.00 3.08
50 51 4.525487 TGGTGGACGTGGATCTATAATACC 59.475 45.833 0.00 0.00 0.00 2.73
51 52 5.467705 GTGGTGGACGTGGATCTATAATAC 58.532 45.833 0.00 0.00 0.00 1.89
52 53 4.216902 CGTGGTGGACGTGGATCTATAATA 59.783 45.833 0.00 0.00 43.50 0.98
53 54 3.005472 CGTGGTGGACGTGGATCTATAAT 59.995 47.826 0.00 0.00 43.50 1.28
54 55 2.359848 CGTGGTGGACGTGGATCTATAA 59.640 50.000 0.00 0.00 43.50 0.98
55 56 1.951602 CGTGGTGGACGTGGATCTATA 59.048 52.381 0.00 0.00 43.50 1.31
56 57 0.744874 CGTGGTGGACGTGGATCTAT 59.255 55.000 0.00 0.00 43.50 1.98
57 58 2.186155 CGTGGTGGACGTGGATCTA 58.814 57.895 0.00 0.00 43.50 1.98
58 59 2.970639 CGTGGTGGACGTGGATCT 59.029 61.111 0.00 0.00 43.50 2.75
66 67 0.454196 AGCAAACAAACGTGGTGGAC 59.546 50.000 0.00 0.00 0.00 4.02
67 68 0.736053 GAGCAAACAAACGTGGTGGA 59.264 50.000 0.00 0.00 0.00 4.02
68 69 0.591236 CGAGCAAACAAACGTGGTGG 60.591 55.000 0.00 0.00 0.00 4.61
69 70 0.591236 CCGAGCAAACAAACGTGGTG 60.591 55.000 0.00 0.00 0.00 4.17
70 71 1.725066 CCGAGCAAACAAACGTGGT 59.275 52.632 0.00 0.00 0.00 4.16
126 127 3.947612 AGTAGTTCCTATCGGAGACCA 57.052 47.619 0.00 0.00 42.51 4.02
129 130 6.897986 AGAAAGTAGTAGTTCCTATCGGAGA 58.102 40.000 0.00 0.00 41.25 3.71
130 131 7.388500 CCTAGAAAGTAGTAGTTCCTATCGGAG 59.612 44.444 0.00 0.00 41.25 4.63
131 132 7.071698 TCCTAGAAAGTAGTAGTTCCTATCGGA 59.928 40.741 0.00 0.00 37.60 4.55
132 133 7.222872 TCCTAGAAAGTAGTAGTTCCTATCGG 58.777 42.308 0.00 0.00 0.00 4.18
133 134 8.851541 ATCCTAGAAAGTAGTAGTTCCTATCG 57.148 38.462 0.00 0.00 0.00 2.92
134 135 9.234827 GGATCCTAGAAAGTAGTAGTTCCTATC 57.765 40.741 3.84 0.00 0.00 2.08
135 136 8.734763 TGGATCCTAGAAAGTAGTAGTTCCTAT 58.265 37.037 14.23 0.00 0.00 2.57
136 137 8.110743 TGGATCCTAGAAAGTAGTAGTTCCTA 57.889 38.462 14.23 0.00 0.00 2.94
137 138 6.982899 TGGATCCTAGAAAGTAGTAGTTCCT 58.017 40.000 14.23 0.00 0.00 3.36
139 140 7.586747 CGATGGATCCTAGAAAGTAGTAGTTC 58.413 42.308 14.23 0.00 0.00 3.01
140 141 6.016108 GCGATGGATCCTAGAAAGTAGTAGTT 60.016 42.308 14.23 0.00 0.00 2.24
141 142 5.474189 GCGATGGATCCTAGAAAGTAGTAGT 59.526 44.000 14.23 0.00 0.00 2.73
142 143 5.473846 TGCGATGGATCCTAGAAAGTAGTAG 59.526 44.000 14.23 0.00 0.00 2.57
143 144 5.241064 GTGCGATGGATCCTAGAAAGTAGTA 59.759 44.000 14.23 0.00 0.00 1.82
144 145 4.038162 GTGCGATGGATCCTAGAAAGTAGT 59.962 45.833 14.23 0.00 0.00 2.73
145 146 4.551388 GTGCGATGGATCCTAGAAAGTAG 58.449 47.826 14.23 0.00 0.00 2.57
146 147 3.321111 GGTGCGATGGATCCTAGAAAGTA 59.679 47.826 14.23 0.00 0.00 2.24
147 148 2.103263 GGTGCGATGGATCCTAGAAAGT 59.897 50.000 14.23 0.00 0.00 2.66
148 149 2.103094 TGGTGCGATGGATCCTAGAAAG 59.897 50.000 14.23 0.00 0.00 2.62
149 150 2.115427 TGGTGCGATGGATCCTAGAAA 58.885 47.619 14.23 0.00 0.00 2.52
150 151 1.788229 TGGTGCGATGGATCCTAGAA 58.212 50.000 14.23 0.00 0.00 2.10
151 152 1.788229 TTGGTGCGATGGATCCTAGA 58.212 50.000 14.23 0.00 0.00 2.43
152 153 2.213499 GTTTGGTGCGATGGATCCTAG 58.787 52.381 14.23 5.33 0.00 3.02
153 154 1.557371 TGTTTGGTGCGATGGATCCTA 59.443 47.619 14.23 0.00 0.00 2.94
154 155 0.327924 TGTTTGGTGCGATGGATCCT 59.672 50.000 14.23 0.00 0.00 3.24
155 156 1.173043 TTGTTTGGTGCGATGGATCC 58.827 50.000 4.20 4.20 0.00 3.36
156 157 3.438360 GATTTGTTTGGTGCGATGGATC 58.562 45.455 0.00 0.00 0.00 3.36
157 158 2.166254 GGATTTGTTTGGTGCGATGGAT 59.834 45.455 0.00 0.00 0.00 3.41
158 159 1.543802 GGATTTGTTTGGTGCGATGGA 59.456 47.619 0.00 0.00 0.00 3.41
159 160 1.271934 TGGATTTGTTTGGTGCGATGG 59.728 47.619 0.00 0.00 0.00 3.51
160 161 2.721274 TGGATTTGTTTGGTGCGATG 57.279 45.000 0.00 0.00 0.00 3.84
161 162 2.288763 GGTTGGATTTGTTTGGTGCGAT 60.289 45.455 0.00 0.00 0.00 4.58
162 163 1.067821 GGTTGGATTTGTTTGGTGCGA 59.932 47.619 0.00 0.00 0.00 5.10
163 164 1.068434 AGGTTGGATTTGTTTGGTGCG 59.932 47.619 0.00 0.00 0.00 5.34
164 165 2.871633 CAAGGTTGGATTTGTTTGGTGC 59.128 45.455 0.00 0.00 0.00 5.01
165 166 2.871633 GCAAGGTTGGATTTGTTTGGTG 59.128 45.455 0.00 0.00 0.00 4.17
166 167 2.158827 GGCAAGGTTGGATTTGTTTGGT 60.159 45.455 0.00 0.00 0.00 3.67
167 168 2.104622 AGGCAAGGTTGGATTTGTTTGG 59.895 45.455 0.00 0.00 0.00 3.28
168 169 3.473923 AGGCAAGGTTGGATTTGTTTG 57.526 42.857 0.00 0.00 0.00 2.93
169 170 4.198530 CAAAGGCAAGGTTGGATTTGTTT 58.801 39.130 0.00 0.00 0.00 2.83
173 174 1.072173 GGCAAAGGCAAGGTTGGATTT 59.928 47.619 0.00 0.00 43.71 2.17
212 213 3.512516 GGGACGTACGAGGGACCG 61.513 72.222 24.41 0.00 0.00 4.79
226 227 2.705312 TTTTGCTCATGGTGGCGGGA 62.705 55.000 0.00 0.00 0.00 5.14
228 229 0.179129 GATTTTGCTCATGGTGGCGG 60.179 55.000 0.00 0.00 0.00 6.13
232 233 2.675889 GCCCTTGATTTTGCTCATGGTG 60.676 50.000 0.00 0.00 38.28 4.17
233 234 1.551883 GCCCTTGATTTTGCTCATGGT 59.448 47.619 0.00 0.00 38.28 3.55
242 243 0.965363 ATGTCGGCGCCCTTGATTTT 60.965 50.000 23.46 0.00 0.00 1.82
246 247 3.700970 TCATGTCGGCGCCCTTGA 61.701 61.111 23.46 18.01 0.00 3.02
275 276 4.129737 ATCGTCACCGTCCGGCAG 62.130 66.667 5.47 0.00 39.32 4.85
286 287 2.808906 TCTTCCAGAGGAGATCGTCA 57.191 50.000 5.43 0.00 31.21 4.35
302 303 1.458588 GGAGGCGGAGGAGGATCTT 60.459 63.158 0.00 0.00 33.73 2.40
324 325 3.775654 GGAGGGAGGACGGCTGTG 61.776 72.222 0.80 0.00 0.00 3.66
372 373 3.681835 GGTCGGTGGTGAGACGCT 61.682 66.667 0.00 0.00 38.20 5.07
375 376 2.291043 ATGGGGTCGGTGGTGAGAC 61.291 63.158 0.00 0.00 36.70 3.36
376 377 2.121832 ATGGGGTCGGTGGTGAGA 59.878 61.111 0.00 0.00 0.00 3.27
377 378 2.124507 AACATGGGGTCGGTGGTGAG 62.125 60.000 0.00 0.00 0.00 3.51
380 381 2.754375 GAACATGGGGTCGGTGGT 59.246 61.111 0.00 0.00 0.00 4.16
382 383 1.078426 GAGGAACATGGGGTCGGTG 60.078 63.158 0.00 0.00 0.00 4.94
390 391 3.692257 AGAAGTCACAGAGGAACATGG 57.308 47.619 0.00 0.00 0.00 3.66
401 402 0.747852 TGGTGCGTGTAGAAGTCACA 59.252 50.000 0.00 0.00 35.79 3.58
403 404 0.032952 GGTGGTGCGTGTAGAAGTCA 59.967 55.000 0.00 0.00 0.00 3.41
404 405 1.007336 CGGTGGTGCGTGTAGAAGTC 61.007 60.000 0.00 0.00 0.00 3.01
453 454 1.831106 TGAAGACCATGCTATCACGGT 59.169 47.619 0.00 0.00 42.21 4.83
457 458 3.378512 AGAGGTGAAGACCATGCTATCA 58.621 45.455 0.00 0.00 45.98 2.15
460 461 3.898123 GGATAGAGGTGAAGACCATGCTA 59.102 47.826 0.00 0.00 45.98 3.49
506 508 2.048127 GGAGGTTGAAGCGCTCGT 60.048 61.111 12.06 0.00 0.00 4.18
507 509 1.667830 TTGGAGGTTGAAGCGCTCG 60.668 57.895 12.06 0.00 0.00 5.03
517 519 2.629051 GCAACTATAGCGTTGGAGGTT 58.371 47.619 0.00 0.00 43.37 3.50
531 533 0.246910 TGTATTCGTGGCGGCAACTA 59.753 50.000 15.50 1.28 0.00 2.24
534 536 2.395360 GCTGTATTCGTGGCGGCAA 61.395 57.895 15.50 0.00 34.85 4.52
550 552 2.851102 AGGACTGCTGGGTGTGCT 60.851 61.111 0.00 0.00 0.00 4.40
562 564 1.913762 CGTTCCTGTGGGGAGGACT 60.914 63.158 0.00 0.00 46.01 3.85
600 602 1.014044 CATTGGTGAGGACACGACCG 61.014 60.000 0.00 0.00 46.77 4.79
617 619 1.888512 GTTCCTTGCACACATGGTCAT 59.111 47.619 0.00 0.00 40.99 3.06
621 623 1.608055 TGAGTTCCTTGCACACATGG 58.392 50.000 0.00 0.00 41.44 3.66
654 656 1.260206 GACACTACTCGCATGTGACG 58.740 55.000 4.45 4.63 35.83 4.35
667 669 0.463654 GGAATGGCCATGCGACACTA 60.464 55.000 21.63 0.00 36.34 2.74
670 672 2.823593 CGGAATGGCCATGCGACA 60.824 61.111 21.63 0.00 35.94 4.35
688 690 1.770957 GCTTTGAAACTGAAAGCGGG 58.229 50.000 0.00 0.00 44.23 6.13
692 694 6.081872 AGAGGAATGCTTTGAAACTGAAAG 57.918 37.500 0.00 0.00 42.29 2.62
693 695 6.016276 GGTAGAGGAATGCTTTGAAACTGAAA 60.016 38.462 0.00 0.00 0.00 2.69
694 696 5.473504 GGTAGAGGAATGCTTTGAAACTGAA 59.526 40.000 0.00 0.00 0.00 3.02
695 697 5.003804 GGTAGAGGAATGCTTTGAAACTGA 58.996 41.667 0.00 0.00 0.00 3.41
696 698 4.761739 TGGTAGAGGAATGCTTTGAAACTG 59.238 41.667 0.00 0.00 0.00 3.16
697 699 4.762251 GTGGTAGAGGAATGCTTTGAAACT 59.238 41.667 0.00 0.00 0.00 2.66
698 700 4.518970 TGTGGTAGAGGAATGCTTTGAAAC 59.481 41.667 0.00 0.00 0.00 2.78
706 708 3.567164 CCATTGATGTGGTAGAGGAATGC 59.433 47.826 0.00 0.00 34.46 3.56
712 714 1.212688 TGCCCCATTGATGTGGTAGAG 59.787 52.381 0.00 0.00 37.57 2.43
725 727 2.362889 CCGAAAAGGCTGCCCCAT 60.363 61.111 16.57 0.46 35.39 4.00
747 749 1.980036 AGCACTGCCCCATTGATTTTT 59.020 42.857 0.00 0.00 0.00 1.94
748 750 1.648116 AGCACTGCCCCATTGATTTT 58.352 45.000 0.00 0.00 0.00 1.82
749 751 1.648116 AAGCACTGCCCCATTGATTT 58.352 45.000 0.00 0.00 0.00 2.17
750 752 1.276989 CAAAGCACTGCCCCATTGATT 59.723 47.619 0.00 0.00 0.00 2.57
756 758 3.225798 GCACAAAGCACTGCCCCA 61.226 61.111 0.00 0.00 44.79 4.96
888 890 0.842030 TGCCCCATGAACCAGTCTCT 60.842 55.000 0.00 0.00 0.00 3.10
979 981 5.124457 TCATCGTAGTAACCAACCAGTAGAC 59.876 44.000 0.00 0.00 0.00 2.59
1007 1009 3.350219 ACTTAAGCATGTCATTCCCGT 57.650 42.857 1.29 0.00 0.00 5.28
1009 1011 5.643379 TCAAACTTAAGCATGTCATTCCC 57.357 39.130 1.29 0.00 0.00 3.97
1088 1090 2.355513 GCTTGGATGATCTGACCACAGT 60.356 50.000 5.79 0.00 43.81 3.55
1093 1095 2.295885 CTTGGCTTGGATGATCTGACC 58.704 52.381 0.00 0.00 0.00 4.02
1111 1113 0.403271 ACAGCACCATCTTCAGCCTT 59.597 50.000 0.00 0.00 0.00 4.35
1141 1143 4.444536 TGTAAGCGCGGGTAAGATAAAAT 58.555 39.130 8.83 0.00 0.00 1.82
1230 1232 4.337264 AGGGAGCCCAAGAATATTGTTT 57.663 40.909 8.53 0.00 38.92 2.83
1261 1269 0.685660 GTTTCGAACCCTCTCCACCT 59.314 55.000 0.00 0.00 0.00 4.00
1324 1332 6.894654 TGAACCATGTATAAATTGGTGTCCAT 59.105 34.615 3.88 0.00 42.85 3.41
1338 1346 8.530311 TGCATTGATTTAAGTTGAACCATGTAT 58.470 29.630 0.00 0.00 0.00 2.29
1467 1475 5.310451 ACCATTTACACAACATAACGTCCT 58.690 37.500 0.00 0.00 0.00 3.85
1468 1476 5.616488 ACCATTTACACAACATAACGTCC 57.384 39.130 0.00 0.00 0.00 4.79
1485 1501 7.267128 CACAATATAGATGTTTGGCAACCATT 58.733 34.615 11.73 5.00 31.53 3.16
1557 1573 6.089551 CCAAACAGAAGTGTGTCTATCTAACG 59.910 42.308 0.00 0.00 36.84 3.18
1559 1575 7.297936 TCCAAACAGAAGTGTGTCTATCTAA 57.702 36.000 0.00 0.00 36.84 2.10
1575 1591 0.036306 AGGGTTACGCCTCCAAACAG 59.964 55.000 0.00 0.00 37.43 3.16
1576 1592 0.035739 GAGGGTTACGCCTCCAAACA 59.964 55.000 8.17 0.00 37.43 2.83
1577 1593 0.323957 AGAGGGTTACGCCTCCAAAC 59.676 55.000 13.66 0.00 37.43 2.93
1578 1594 0.611714 GAGAGGGTTACGCCTCCAAA 59.388 55.000 13.66 0.00 37.43 3.28
1579 1595 1.601419 CGAGAGGGTTACGCCTCCAA 61.601 60.000 13.66 0.00 37.43 3.53
1580 1596 2.050350 CGAGAGGGTTACGCCTCCA 61.050 63.158 13.66 0.00 37.43 3.86
1581 1597 2.806237 CGAGAGGGTTACGCCTCC 59.194 66.667 13.66 7.06 37.43 4.30
1582 1598 2.104530 GCGAGAGGGTTACGCCTC 59.895 66.667 10.56 10.56 45.35 4.70
1628 1644 4.796495 GCCGGTGGCTAGGGTTGG 62.796 72.222 1.90 0.00 46.69 3.77
1640 1656 3.459063 GAGACCTAAGGCGCCGGT 61.459 66.667 22.64 22.64 0.00 5.28
1844 1865 2.335011 CGCACAGGACGAGACACA 59.665 61.111 0.00 0.00 0.00 3.72
1848 1869 2.596338 TCCACGCACAGGACGAGA 60.596 61.111 0.00 0.00 0.00 4.04
2057 2084 3.234730 GGCGGATCTGGACGGGAT 61.235 66.667 3.14 0.00 0.00 3.85
2097 2124 2.365635 CCCTCACCGGTCCTCCAT 60.366 66.667 2.59 0.00 0.00 3.41
2146 2173 1.308998 CTGTGAAGACCAAAGCCGTT 58.691 50.000 0.00 0.00 0.00 4.44
2164 2191 2.710724 AAACCGAACGGAGCTTCGCT 62.711 55.000 16.11 0.41 43.88 4.93
2208 2236 4.556501 GCACGATTTTCACTGGAAATCACA 60.557 41.667 18.94 0.00 42.31 3.58
2249 2277 2.658285 GTCATATACGCCGACATCGTT 58.342 47.619 0.00 0.00 40.89 3.85
2263 2291 5.453903 CCTCAAGAAGGGAATGACGTCATAT 60.454 44.000 30.16 19.74 42.03 1.78
2288 2316 2.747446 GCCATGACCTACAACAACGATT 59.253 45.455 0.00 0.00 0.00 3.34
2325 2353 1.835531 GATCTAGTGTTTCCCCCGGAA 59.164 52.381 0.73 0.00 40.27 4.30
2338 2366 2.133520 TCCGGTAGACCCAGATCTAGT 58.866 52.381 0.00 0.00 31.75 2.57
2419 2449 3.650950 GTCCCCTCCAGCCAGCAA 61.651 66.667 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.