Multiple sequence alignment - TraesCS3D01G077900

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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 TraesCS3D01G077900 chr3D 100.000 2399 0 0 1 2399 38604340 38601942 0.000000e+00 4431.0
1 TraesCS3D01G077900 chr3D 89.321 1002 42 20 691 1668 38626053 38625093 0.000000e+00 1197.0
2 TraesCS3D01G077900 chr3D 90.535 729 48 11 1680 2399 38624675 38623959 0.000000e+00 944.0
3 TraesCS3D01G077900 chr3D 89.263 624 41 7 17 622 446856972 446856357 0.000000e+00 758.0
4 TraesCS3D01G077900 chr3D 90.833 120 6 2 786 900 38610490 38610371 3.190000e-34 156.0
5 TraesCS3D01G077900 chr3D 93.590 78 1 2 621 698 38634994 38634921 1.950000e-21 113.0
6 TraesCS3D01G077900 chr3D 78.378 185 14 12 728 898 38374819 38374647 1.960000e-16 97.1
7 TraesCS3D01G077900 chr3B 90.422 971 61 17 693 1644 61533102 61532145 0.000000e+00 1249.0
8 TraesCS3D01G077900 chr3B 90.153 589 46 6 1669 2248 61532158 61531573 0.000000e+00 756.0
9 TraesCS3D01G077900 chr3B 91.930 285 15 3 228 511 215013354 215013077 2.240000e-105 392.0
10 TraesCS3D01G077900 chr3B 92.887 239 16 1 1 239 215013644 215013407 1.770000e-91 346.0
11 TraesCS3D01G077900 chr3B 92.258 155 11 1 2246 2399 61531480 61531326 4.020000e-53 219.0
12 TraesCS3D01G077900 chr3A 92.969 768 28 13 847 1596 49971703 49970944 0.000000e+00 1096.0
13 TraesCS3D01G077900 chr3A 88.838 654 55 13 1757 2399 49970115 49969469 0.000000e+00 787.0
14 TraesCS3D01G077900 chr3A 75.121 414 50 25 1179 1582 49504101 49503731 6.910000e-31 145.0
15 TraesCS3D01G077900 chr3A 86.517 89 4 1 776 856 49610086 49609998 9.130000e-15 91.6
16 TraesCS3D01G077900 chr5D 91.080 639 32 11 1 622 57217063 57216433 0.000000e+00 841.0
17 TraesCS3D01G077900 chr5D 86.677 623 32 16 17 622 510166933 510166345 0.000000e+00 643.0
18 TraesCS3D01G077900 chr7D 90.752 638 34 10 1 622 517992493 517993121 0.000000e+00 828.0
19 TraesCS3D01G077900 chr7D 88.527 645 40 9 1 622 630680088 630679455 0.000000e+00 750.0
20 TraesCS3D01G077900 chr7D 88.800 625 42 9 17 622 49862574 49861959 0.000000e+00 741.0
21 TraesCS3D01G077900 chr7D 89.568 278 18 5 1442 1712 14796947 14797220 2.280000e-90 342.0
22 TraesCS3D01G077900 chr7D 88.430 242 20 4 1728 1963 14801997 14802236 3.900000e-73 285.0
23 TraesCS3D01G077900 chr7D 83.333 102 12 5 2108 2207 463709383 463709285 3.280000e-14 89.8
24 TraesCS3D01G077900 chr7D 100.000 41 0 0 1672 1712 14801974 14802014 2.560000e-10 76.8
25 TraesCS3D01G077900 chr1D 90.610 639 33 8 1 622 482102588 482101960 0.000000e+00 822.0
26 TraesCS3D01G077900 chr1D 86.538 208 20 3 415 622 349256956 349256757 3.100000e-54 222.0
27 TraesCS3D01G077900 chr1D 92.982 57 3 1 2147 2203 470589724 470589669 5.500000e-12 82.4
28 TraesCS3D01G077900 chr1D 97.297 37 0 1 2364 2399 252512019 252512055 7.160000e-06 62.1
29 TraesCS3D01G077900 chr7B 88.046 527 35 8 115 622 639810274 639810791 1.230000e-167 599.0
30 TraesCS3D01G077900 chr6A 91.709 398 22 7 228 623 22430417 22430029 2.100000e-150 542.0
31 TraesCS3D01G077900 chr6A 93.333 225 13 2 1 225 22430966 22430744 4.940000e-87 331.0
32 TraesCS3D01G077900 chr1A 91.011 267 15 4 354 618 472282052 472282311 3.790000e-93 351.0
33 TraesCS3D01G077900 chr4A 83.333 138 19 3 2146 2282 21201878 21201744 9.000000e-25 124.0
34 TraesCS3D01G077900 chr4D 84.677 124 16 2 2160 2282 446174401 446174522 1.160000e-23 121.0
35 TraesCS3D01G077900 chr4D 84.211 76 8 3 2128 2203 38590271 38590342 1.190000e-08 71.3
36 TraesCS3D01G077900 chr6D 82.796 93 11 5 2119 2208 445157320 445157410 7.110000e-11 78.7
37 TraesCS3D01G077900 chr5A 94.000 50 3 0 2346 2395 35989660 35989709 2.560000e-10 76.8
38 TraesCS3D01G077900 chr2B 88.889 54 6 0 2346 2399 246374576 246374629 1.540000e-07 67.6


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 TraesCS3D01G077900 chr3D 38601942 38604340 2398 True 4431.000000 4431 100.000000 1 2399 1 chr3D.!!$R2 2398
1 TraesCS3D01G077900 chr3D 38623959 38626053 2094 True 1070.500000 1197 89.928000 691 2399 2 chr3D.!!$R6 1708
2 TraesCS3D01G077900 chr3D 446856357 446856972 615 True 758.000000 758 89.263000 17 622 1 chr3D.!!$R5 605
3 TraesCS3D01G077900 chr3B 61531326 61533102 1776 True 741.333333 1249 90.944333 693 2399 3 chr3B.!!$R1 1706
4 TraesCS3D01G077900 chr3B 215013077 215013644 567 True 369.000000 392 92.408500 1 511 2 chr3B.!!$R2 510
5 TraesCS3D01G077900 chr3A 49969469 49971703 2234 True 941.500000 1096 90.903500 847 2399 2 chr3A.!!$R3 1552
6 TraesCS3D01G077900 chr5D 57216433 57217063 630 True 841.000000 841 91.080000 1 622 1 chr5D.!!$R1 621
7 TraesCS3D01G077900 chr5D 510166345 510166933 588 True 643.000000 643 86.677000 17 622 1 chr5D.!!$R2 605
8 TraesCS3D01G077900 chr7D 517992493 517993121 628 False 828.000000 828 90.752000 1 622 1 chr7D.!!$F2 621
9 TraesCS3D01G077900 chr7D 630679455 630680088 633 True 750.000000 750 88.527000 1 622 1 chr7D.!!$R3 621
10 TraesCS3D01G077900 chr7D 49861959 49862574 615 True 741.000000 741 88.800000 17 622 1 chr7D.!!$R1 605
11 TraesCS3D01G077900 chr1D 482101960 482102588 628 True 822.000000 822 90.610000 1 622 1 chr1D.!!$R3 621
12 TraesCS3D01G077900 chr7B 639810274 639810791 517 False 599.000000 599 88.046000 115 622 1 chr7B.!!$F1 507
13 TraesCS3D01G077900 chr6A 22430029 22430966 937 True 436.500000 542 92.521000 1 623 2 chr6A.!!$R1 622

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
672 1057 0.039618 TGTGCCCATTCCTTCCTTCC 59.96 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 3340 0.254462 TCATGCCCGCTGTGGAAATA 59.746 50.0 9.25 0.0 42.0 1.4 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
76 77 4.389890 TCAAATGCCAATGCCACTAATC 57.610 40.909 0.00 0.00 36.33 1.75
347 723 7.520614 GCATAAATTCCACTCCTACATGCTTAC 60.521 40.741 0.00 0.00 34.78 2.34
359 735 7.053498 TCCTACATGCTTACTTTTGCATATCA 58.947 34.615 0.00 0.00 46.65 2.15
471 856 1.367346 TGGGCCCATGAAGTCTTGTA 58.633 50.000 24.45 0.00 0.00 2.41
472 857 1.707989 TGGGCCCATGAAGTCTTGTAA 59.292 47.619 24.45 0.00 0.00 2.41
473 858 2.092323 GGGCCCATGAAGTCTTGTAAC 58.908 52.381 19.95 0.00 0.00 2.50
474 859 2.290960 GGGCCCATGAAGTCTTGTAACT 60.291 50.000 19.95 0.00 0.00 2.24
475 860 3.421844 GGCCCATGAAGTCTTGTAACTT 58.578 45.455 0.00 0.00 42.10 2.66
476 861 3.191371 GGCCCATGAAGTCTTGTAACTTG 59.809 47.826 0.00 0.00 39.55 3.16
477 862 3.821033 GCCCATGAAGTCTTGTAACTTGT 59.179 43.478 0.00 0.00 39.55 3.16
478 863 5.001232 GCCCATGAAGTCTTGTAACTTGTA 58.999 41.667 0.00 0.00 39.55 2.41
588 973 3.721087 AGGAATCGACTGACCCATTTT 57.279 42.857 0.00 0.00 0.00 1.82
591 976 3.375299 GGAATCGACTGACCCATTTTCTG 59.625 47.826 0.00 0.00 0.00 3.02
623 1008 4.326227 ACCAGTAGCCGGTCCCCA 62.326 66.667 1.90 0.00 27.30 4.96
624 1009 3.470888 CCAGTAGCCGGTCCCCAG 61.471 72.222 1.90 0.00 0.00 4.45
625 1010 4.162690 CAGTAGCCGGTCCCCAGC 62.163 72.222 1.90 0.00 0.00 4.85
626 1011 4.400251 AGTAGCCGGTCCCCAGCT 62.400 66.667 1.90 0.00 40.66 4.24
627 1012 3.851128 GTAGCCGGTCCCCAGCTC 61.851 72.222 1.90 0.00 38.06 4.09
632 1017 4.135153 CGGTCCCCAGCTCGAGTG 62.135 72.222 15.13 10.78 0.00 3.51
633 1018 2.997897 GGTCCCCAGCTCGAGTGT 60.998 66.667 15.13 0.00 0.00 3.55
634 1019 2.574399 GTCCCCAGCTCGAGTGTC 59.426 66.667 15.13 0.00 0.00 3.67
635 1020 1.979693 GTCCCCAGCTCGAGTGTCT 60.980 63.158 15.13 0.00 0.00 3.41
636 1021 1.679305 TCCCCAGCTCGAGTGTCTC 60.679 63.158 15.13 0.00 0.00 3.36
637 1022 1.680651 CCCCAGCTCGAGTGTCTCT 60.681 63.158 15.13 0.00 0.00 3.10
638 1023 1.510383 CCCAGCTCGAGTGTCTCTG 59.490 63.158 15.13 11.75 0.00 3.35
639 1024 1.510383 CCAGCTCGAGTGTCTCTGG 59.490 63.158 17.96 17.96 38.41 3.86
640 1025 0.962855 CCAGCTCGAGTGTCTCTGGA 60.963 60.000 23.98 0.00 45.31 3.86
641 1026 1.102154 CAGCTCGAGTGTCTCTGGAT 58.898 55.000 15.13 0.00 30.92 3.41
642 1027 1.102154 AGCTCGAGTGTCTCTGGATG 58.898 55.000 15.13 0.00 30.92 3.51
643 1028 0.527385 GCTCGAGTGTCTCTGGATGC 60.527 60.000 15.13 0.00 30.92 3.91
644 1029 0.813821 CTCGAGTGTCTCTGGATGCA 59.186 55.000 3.62 0.00 30.92 3.96
645 1030 0.528017 TCGAGTGTCTCTGGATGCAC 59.472 55.000 0.00 0.00 0.00 4.57
646 1031 0.529833 CGAGTGTCTCTGGATGCACT 59.470 55.000 0.00 0.00 43.85 4.40
647 1032 1.745653 CGAGTGTCTCTGGATGCACTA 59.254 52.381 0.00 0.00 41.59 2.74
648 1033 2.223456 CGAGTGTCTCTGGATGCACTAG 60.223 54.545 0.00 0.00 41.59 2.57
649 1034 2.100584 GAGTGTCTCTGGATGCACTAGG 59.899 54.545 0.00 0.00 41.59 3.02
650 1035 0.826715 TGTCTCTGGATGCACTAGGC 59.173 55.000 0.00 0.00 45.13 3.93
651 1036 1.118838 GTCTCTGGATGCACTAGGCT 58.881 55.000 0.00 0.00 45.15 4.58
652 1037 2.311463 GTCTCTGGATGCACTAGGCTA 58.689 52.381 0.00 0.00 45.15 3.93
653 1038 2.896685 GTCTCTGGATGCACTAGGCTAT 59.103 50.000 0.00 0.00 45.15 2.97
654 1039 2.896044 TCTCTGGATGCACTAGGCTATG 59.104 50.000 0.00 0.00 45.15 2.23
655 1040 2.632028 CTCTGGATGCACTAGGCTATGT 59.368 50.000 0.00 0.00 45.15 2.29
656 1041 2.366590 TCTGGATGCACTAGGCTATGTG 59.633 50.000 15.44 15.44 45.15 3.21
668 1053 1.322442 GCTATGTGCCCATTCCTTCC 58.678 55.000 0.00 0.00 35.15 3.46
669 1054 1.133668 GCTATGTGCCCATTCCTTCCT 60.134 52.381 0.00 0.00 35.15 3.36
670 1055 2.687914 GCTATGTGCCCATTCCTTCCTT 60.688 50.000 0.00 0.00 35.15 3.36
671 1056 2.149973 ATGTGCCCATTCCTTCCTTC 57.850 50.000 0.00 0.00 0.00 3.46
672 1057 0.039618 TGTGCCCATTCCTTCCTTCC 59.960 55.000 0.00 0.00 0.00 3.46
673 1058 0.684479 GTGCCCATTCCTTCCTTCCC 60.684 60.000 0.00 0.00 0.00 3.97
674 1059 0.850883 TGCCCATTCCTTCCTTCCCT 60.851 55.000 0.00 0.00 0.00 4.20
675 1060 0.106469 GCCCATTCCTTCCTTCCCTC 60.106 60.000 0.00 0.00 0.00 4.30
676 1061 0.553333 CCCATTCCTTCCTTCCCTCC 59.447 60.000 0.00 0.00 0.00 4.30
677 1062 1.601248 CCATTCCTTCCTTCCCTCCT 58.399 55.000 0.00 0.00 0.00 3.69
678 1063 1.925959 CCATTCCTTCCTTCCCTCCTT 59.074 52.381 0.00 0.00 0.00 3.36
679 1064 2.092158 CCATTCCTTCCTTCCCTCCTTC 60.092 54.545 0.00 0.00 0.00 3.46
680 1065 2.433444 TTCCTTCCTTCCCTCCTTCA 57.567 50.000 0.00 0.00 0.00 3.02
681 1066 2.668850 TCCTTCCTTCCCTCCTTCAT 57.331 50.000 0.00 0.00 0.00 2.57
682 1067 3.795755 TCCTTCCTTCCCTCCTTCATA 57.204 47.619 0.00 0.00 0.00 2.15
683 1068 3.658725 TCCTTCCTTCCCTCCTTCATAG 58.341 50.000 0.00 0.00 0.00 2.23
684 1069 3.014110 TCCTTCCTTCCCTCCTTCATAGT 59.986 47.826 0.00 0.00 0.00 2.12
685 1070 3.135530 CCTTCCTTCCCTCCTTCATAGTG 59.864 52.174 0.00 0.00 0.00 2.74
686 1071 2.764269 TCCTTCCCTCCTTCATAGTGG 58.236 52.381 0.00 0.00 0.00 4.00
687 1072 2.317900 TCCTTCCCTCCTTCATAGTGGA 59.682 50.000 0.00 0.00 0.00 4.02
688 1073 3.051032 TCCTTCCCTCCTTCATAGTGGAT 60.051 47.826 0.00 0.00 0.00 3.41
689 1074 3.326297 CCTTCCCTCCTTCATAGTGGATC 59.674 52.174 0.00 0.00 0.00 3.36
710 1095 1.316651 GGGGCATGCAAAAGCAAAAA 58.683 45.000 21.36 0.00 0.00 1.94
755 1140 1.131883 GTAGCTCTTGTGCCTGCATTG 59.868 52.381 0.00 0.00 0.00 2.82
771 1156 2.294233 GCATTGCAGTTCCTCTGTTTGA 59.706 45.455 3.15 0.00 45.23 2.69
772 1157 3.854784 GCATTGCAGTTCCTCTGTTTGAC 60.855 47.826 3.15 0.00 45.23 3.18
773 1158 3.281727 TTGCAGTTCCTCTGTTTGACT 57.718 42.857 0.00 0.00 45.23 3.41
776 1161 2.945668 GCAGTTCCTCTGTTTGACTGTT 59.054 45.455 0.00 0.00 45.23 3.16
777 1162 3.378427 GCAGTTCCTCTGTTTGACTGTTT 59.622 43.478 0.00 0.00 45.23 2.83
778 1163 4.731773 GCAGTTCCTCTGTTTGACTGTTTG 60.732 45.833 0.00 0.00 45.23 2.93
779 1164 3.947834 AGTTCCTCTGTTTGACTGTTTGG 59.052 43.478 0.00 0.00 0.00 3.28
782 1167 4.199310 TCCTCTGTTTGACTGTTTGGAAG 58.801 43.478 0.00 0.00 0.00 3.46
814 1207 3.768922 GGAGCAGCTGAGCGGAGT 61.769 66.667 20.43 0.00 40.15 3.85
904 1307 1.001181 CAAACCCCAGACAATTGCAGG 59.999 52.381 5.05 4.91 0.00 4.85
909 1312 0.896940 CCAGACAATTGCAGGGTGCT 60.897 55.000 5.05 0.00 45.31 4.40
946 1351 4.518970 TGCTGTGTATATACATCTCGCTCA 59.481 41.667 18.27 8.94 38.63 4.26
1407 1834 3.888583 AGGACAGGTGTAGTAGACTAGC 58.111 50.000 0.00 0.00 0.00 3.42
1425 1862 1.403493 GCATGACGCTAGATCACTCG 58.597 55.000 0.00 0.00 37.77 4.18
1426 1863 1.002359 GCATGACGCTAGATCACTCGA 60.002 52.381 0.00 0.00 37.77 4.04
1427 1864 2.914861 CATGACGCTAGATCACTCGAG 58.085 52.381 11.84 11.84 0.00 4.04
1428 1865 2.311124 TGACGCTAGATCACTCGAGA 57.689 50.000 21.68 0.00 0.00 4.04
1429 1866 2.629051 TGACGCTAGATCACTCGAGAA 58.371 47.619 21.68 7.11 0.00 2.87
1452 1889 4.695396 TCGAGATGTACTACTCTCCAGTC 58.305 47.826 14.37 0.00 35.52 3.51
1472 1910 0.881118 TCTGAAATTTGTCAGCGGCC 59.119 50.000 0.00 0.00 44.01 6.13
1510 1949 3.253432 GTCTTTCTGAACTTTCCGGCAAT 59.747 43.478 0.00 0.00 0.00 3.56
1513 1952 2.582052 TCTGAACTTTCCGGCAATTGT 58.418 42.857 7.40 0.00 0.00 2.71
1514 1953 2.552315 TCTGAACTTTCCGGCAATTGTC 59.448 45.455 7.40 3.05 0.00 3.18
1515 1954 2.554032 CTGAACTTTCCGGCAATTGTCT 59.446 45.455 8.67 0.00 0.00 3.41
1516 1955 2.293122 TGAACTTTCCGGCAATTGTCTG 59.707 45.455 8.67 1.20 0.00 3.51
1517 1956 1.981256 ACTTTCCGGCAATTGTCTGT 58.019 45.000 8.67 0.00 0.00 3.41
1518 1957 1.880027 ACTTTCCGGCAATTGTCTGTC 59.120 47.619 8.67 0.00 0.00 3.51
1522 1961 1.081892 CCGGCAATTGTCTGTCTCTG 58.918 55.000 8.67 0.00 0.00 3.35
1537 1983 7.072647 GTCTGTCTCTGTATATATGTGACACG 58.927 42.308 14.20 11.90 32.94 4.49
1566 2012 5.836347 AGTTTCAGGCAACAAAAATCTCTC 58.164 37.500 0.00 0.00 41.41 3.20
1631 2123 3.733883 ATCAAGGATGCATATGAGGGG 57.266 47.619 6.97 0.00 0.00 4.79
1632 2124 2.421725 TCAAGGATGCATATGAGGGGT 58.578 47.619 6.97 0.00 0.00 4.95
1633 2125 2.785269 TCAAGGATGCATATGAGGGGTT 59.215 45.455 6.97 0.00 0.00 4.11
1634 2126 2.889045 CAAGGATGCATATGAGGGGTTG 59.111 50.000 6.97 0.30 0.00 3.77
1635 2127 2.138542 AGGATGCATATGAGGGGTTGT 58.861 47.619 6.97 0.00 0.00 3.32
1636 2128 3.326521 AGGATGCATATGAGGGGTTGTA 58.673 45.455 6.97 0.00 0.00 2.41
1637 2129 3.073062 AGGATGCATATGAGGGGTTGTAC 59.927 47.826 6.97 0.00 0.00 2.90
1638 2130 2.613026 TGCATATGAGGGGTTGTACG 57.387 50.000 6.97 0.00 0.00 3.67
1639 2131 1.834896 TGCATATGAGGGGTTGTACGT 59.165 47.619 6.97 0.00 0.00 3.57
1640 2132 2.210116 GCATATGAGGGGTTGTACGTG 58.790 52.381 6.97 0.00 0.00 4.49
1641 2133 2.833794 CATATGAGGGGTTGTACGTGG 58.166 52.381 0.00 0.00 0.00 4.94
1642 2134 0.538118 TATGAGGGGTTGTACGTGGC 59.462 55.000 0.00 0.00 0.00 5.01
1643 2135 1.198759 ATGAGGGGTTGTACGTGGCT 61.199 55.000 0.00 0.00 0.00 4.75
1644 2136 1.375523 GAGGGGTTGTACGTGGCTG 60.376 63.158 0.00 0.00 0.00 4.85
1645 2137 1.823169 GAGGGGTTGTACGTGGCTGA 61.823 60.000 0.00 0.00 0.00 4.26
1646 2138 1.670083 GGGGTTGTACGTGGCTGAC 60.670 63.158 0.00 0.00 0.00 3.51
1647 2139 1.370064 GGGTTGTACGTGGCTGACT 59.630 57.895 0.00 0.00 0.00 3.41
1648 2140 0.250166 GGGTTGTACGTGGCTGACTT 60.250 55.000 0.00 0.00 0.00 3.01
1649 2141 1.145803 GGTTGTACGTGGCTGACTTC 58.854 55.000 0.00 0.00 0.00 3.01
1650 2142 1.270147 GGTTGTACGTGGCTGACTTCT 60.270 52.381 0.00 0.00 0.00 2.85
1651 2143 2.029649 GGTTGTACGTGGCTGACTTCTA 60.030 50.000 0.00 0.00 0.00 2.10
1652 2144 2.985139 GTTGTACGTGGCTGACTTCTAC 59.015 50.000 0.00 0.00 0.00 2.59
1653 2145 2.511659 TGTACGTGGCTGACTTCTACT 58.488 47.619 0.00 0.00 0.00 2.57
1654 2146 2.889045 TGTACGTGGCTGACTTCTACTT 59.111 45.455 0.00 0.00 0.00 2.24
1655 2147 4.074259 TGTACGTGGCTGACTTCTACTTA 58.926 43.478 0.00 0.00 0.00 2.24
1656 2148 3.572604 ACGTGGCTGACTTCTACTTAC 57.427 47.619 0.00 0.00 0.00 2.34
1657 2149 3.155501 ACGTGGCTGACTTCTACTTACT 58.844 45.455 0.00 0.00 0.00 2.24
1658 2150 3.573110 ACGTGGCTGACTTCTACTTACTT 59.427 43.478 0.00 0.00 0.00 2.24
1659 2151 4.038883 ACGTGGCTGACTTCTACTTACTTT 59.961 41.667 0.00 0.00 0.00 2.66
1660 2152 4.989168 CGTGGCTGACTTCTACTTACTTTT 59.011 41.667 0.00 0.00 0.00 2.27
1661 2153 5.465724 CGTGGCTGACTTCTACTTACTTTTT 59.534 40.000 0.00 0.00 0.00 1.94
1733 2964 3.341857 TTTTCTTGCGCGTAATTGTGT 57.658 38.095 10.79 0.00 0.00 3.72
1840 3263 4.897924 CACGCATAAAACATAGTACGCATG 59.102 41.667 8.46 8.46 0.00 4.06
1844 3267 6.590357 GCATAAAACATAGTACGCATGGTAG 58.410 40.000 13.09 2.48 0.00 3.18
1846 3269 7.383029 GCATAAAACATAGTACGCATGGTAGTA 59.617 37.037 13.09 9.80 40.41 1.82
1847 3270 8.697067 CATAAAACATAGTACGCATGGTAGTAC 58.303 37.037 13.09 0.00 39.28 2.73
1931 3354 1.540267 TTGGTTATTTCCACAGCGGG 58.460 50.000 0.00 0.00 37.20 6.13
2103 3531 5.515534 GCATGGATCAGGGAATGGTATTACT 60.516 44.000 0.00 0.00 0.00 2.24
2335 3863 9.776158 TTGCGTATATATTTACACACAAAAAGG 57.224 29.630 4.52 0.00 0.00 3.11
2345 3873 5.771602 ACACACAAAAAGGTTAAAAAGCG 57.228 34.783 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.093495 TCCGGATCAAAATAATGAATATCGGC 59.907 38.462 0.00 0.00 34.53 5.54
125 127 6.718522 TGGATTAGTGACATCGGTATTACA 57.281 37.500 0.00 0.00 0.00 2.41
161 163 6.049263 AGATTTCCGCGAAAAATAGTGATC 57.951 37.500 8.23 1.54 35.11 2.92
163 165 4.932799 TGAGATTTCCGCGAAAAATAGTGA 59.067 37.500 8.23 0.00 35.11 3.41
347 723 7.758613 TGCACATTTGTATGATATGCAAAAG 57.241 32.000 8.67 7.37 45.48 2.27
359 735 9.323985 ACTTACACAAAAATTGCACATTTGTAT 57.676 25.926 18.10 12.70 43.36 2.29
425 810 5.238214 GCAAAACAATGGCCTGTTGATAAAA 59.762 36.000 22.77 0.00 39.47 1.52
435 820 1.271488 CCCAATGCAAAACAATGGCCT 60.271 47.619 3.32 0.00 46.54 5.19
471 856 5.914898 AAACCAACAGAAGCTTACAAGTT 57.085 34.783 0.00 0.00 0.00 2.66
472 857 5.185056 ACAAAACCAACAGAAGCTTACAAGT 59.815 36.000 0.00 0.00 0.00 3.16
473 858 5.650543 ACAAAACCAACAGAAGCTTACAAG 58.349 37.500 0.00 0.00 0.00 3.16
474 859 5.652994 ACAAAACCAACAGAAGCTTACAA 57.347 34.783 0.00 0.00 0.00 2.41
475 860 6.734137 CATACAAAACCAACAGAAGCTTACA 58.266 36.000 0.00 0.00 0.00 2.41
476 861 5.629435 GCATACAAAACCAACAGAAGCTTAC 59.371 40.000 0.00 0.00 0.00 2.34
477 862 5.300539 TGCATACAAAACCAACAGAAGCTTA 59.699 36.000 0.00 0.00 0.00 3.09
478 863 4.099266 TGCATACAAAACCAACAGAAGCTT 59.901 37.500 0.00 0.00 0.00 3.74
516 901 5.887598 TCAGCCAATTTCAGTGTTATAGCAT 59.112 36.000 0.00 0.00 0.00 3.79
623 1008 1.102154 CATCCAGAGACACTCGAGCT 58.898 55.000 13.61 0.73 35.36 4.09
624 1009 0.527385 GCATCCAGAGACACTCGAGC 60.527 60.000 13.61 0.00 35.36 5.03
625 1010 0.813821 TGCATCCAGAGACACTCGAG 59.186 55.000 11.84 11.84 35.36 4.04
626 1011 0.528017 GTGCATCCAGAGACACTCGA 59.472 55.000 0.00 0.00 35.36 4.04
627 1012 0.529833 AGTGCATCCAGAGACACTCG 59.470 55.000 0.00 0.00 39.04 4.18
628 1013 2.100584 CCTAGTGCATCCAGAGACACTC 59.899 54.545 8.22 0.00 42.19 3.51
629 1014 2.106566 CCTAGTGCATCCAGAGACACT 58.893 52.381 9.50 9.50 45.02 3.55
630 1015 1.472376 GCCTAGTGCATCCAGAGACAC 60.472 57.143 0.00 0.00 40.77 3.67
631 1016 0.826715 GCCTAGTGCATCCAGAGACA 59.173 55.000 0.00 0.00 40.77 3.41
632 1017 1.118838 AGCCTAGTGCATCCAGAGAC 58.881 55.000 0.00 0.00 44.83 3.36
633 1018 2.755952 TAGCCTAGTGCATCCAGAGA 57.244 50.000 0.00 0.00 44.83 3.10
634 1019 2.632028 ACATAGCCTAGTGCATCCAGAG 59.368 50.000 0.00 0.00 44.83 3.35
635 1020 2.366590 CACATAGCCTAGTGCATCCAGA 59.633 50.000 0.00 0.00 44.83 3.86
636 1021 2.763933 CACATAGCCTAGTGCATCCAG 58.236 52.381 0.00 0.00 44.83 3.86
637 1022 2.916702 CACATAGCCTAGTGCATCCA 57.083 50.000 0.00 0.00 44.83 3.41
649 1034 1.133668 AGGAAGGAATGGGCACATAGC 60.134 52.381 0.00 0.00 44.65 2.97
650 1035 3.217626 GAAGGAAGGAATGGGCACATAG 58.782 50.000 0.00 0.00 35.94 2.23
651 1036 2.091885 GGAAGGAAGGAATGGGCACATA 60.092 50.000 0.00 0.00 35.94 2.29
652 1037 1.342374 GGAAGGAAGGAATGGGCACAT 60.342 52.381 0.00 0.00 39.54 3.21
653 1038 0.039618 GGAAGGAAGGAATGGGCACA 59.960 55.000 0.00 0.00 0.00 4.57
654 1039 0.684479 GGGAAGGAAGGAATGGGCAC 60.684 60.000 0.00 0.00 0.00 5.01
655 1040 0.850883 AGGGAAGGAAGGAATGGGCA 60.851 55.000 0.00 0.00 0.00 5.36
656 1041 0.106469 GAGGGAAGGAAGGAATGGGC 60.106 60.000 0.00 0.00 0.00 5.36
657 1042 0.553333 GGAGGGAAGGAAGGAATGGG 59.447 60.000 0.00 0.00 0.00 4.00
658 1043 1.601248 AGGAGGGAAGGAAGGAATGG 58.399 55.000 0.00 0.00 0.00 3.16
659 1044 2.578021 TGAAGGAGGGAAGGAAGGAATG 59.422 50.000 0.00 0.00 0.00 2.67
660 1045 2.934722 TGAAGGAGGGAAGGAAGGAAT 58.065 47.619 0.00 0.00 0.00 3.01
661 1046 2.433444 TGAAGGAGGGAAGGAAGGAA 57.567 50.000 0.00 0.00 0.00 3.36
662 1047 2.668850 ATGAAGGAGGGAAGGAAGGA 57.331 50.000 0.00 0.00 0.00 3.36
663 1048 3.135530 CACTATGAAGGAGGGAAGGAAGG 59.864 52.174 0.00 0.00 0.00 3.46
664 1049 3.135530 CCACTATGAAGGAGGGAAGGAAG 59.864 52.174 0.00 0.00 0.00 3.46
665 1050 3.115390 CCACTATGAAGGAGGGAAGGAA 58.885 50.000 0.00 0.00 0.00 3.36
666 1051 2.317900 TCCACTATGAAGGAGGGAAGGA 59.682 50.000 0.00 0.00 0.00 3.36
667 1052 2.764269 TCCACTATGAAGGAGGGAAGG 58.236 52.381 0.00 0.00 0.00 3.46
668 1053 3.326297 GGATCCACTATGAAGGAGGGAAG 59.674 52.174 6.95 0.00 37.34 3.46
669 1054 3.318313 GGATCCACTATGAAGGAGGGAA 58.682 50.000 6.95 0.00 37.34 3.97
670 1055 2.756576 CGGATCCACTATGAAGGAGGGA 60.757 54.545 13.41 0.00 37.34 4.20
671 1056 1.620819 CGGATCCACTATGAAGGAGGG 59.379 57.143 13.41 0.00 37.34 4.30
672 1057 1.620819 CCGGATCCACTATGAAGGAGG 59.379 57.143 13.41 0.00 37.34 4.30
673 1058 1.620819 CCCGGATCCACTATGAAGGAG 59.379 57.143 13.41 0.00 37.34 3.69
674 1059 1.717032 CCCGGATCCACTATGAAGGA 58.283 55.000 13.41 0.00 38.50 3.36
675 1060 0.687354 CCCCGGATCCACTATGAAGG 59.313 60.000 13.41 1.57 0.00 3.46
676 1061 0.035458 GCCCCGGATCCACTATGAAG 59.965 60.000 13.41 0.00 0.00 3.02
677 1062 0.692756 TGCCCCGGATCCACTATGAA 60.693 55.000 13.41 0.00 0.00 2.57
678 1063 0.473694 ATGCCCCGGATCCACTATGA 60.474 55.000 13.41 0.00 0.00 2.15
679 1064 0.321919 CATGCCCCGGATCCACTATG 60.322 60.000 13.41 4.96 0.00 2.23
680 1065 2.069776 CATGCCCCGGATCCACTAT 58.930 57.895 13.41 0.00 0.00 2.12
681 1066 2.818169 GCATGCCCCGGATCCACTA 61.818 63.158 13.41 0.00 0.00 2.74
682 1067 4.195334 GCATGCCCCGGATCCACT 62.195 66.667 13.41 0.00 0.00 4.00
683 1068 4.504596 TGCATGCCCCGGATCCAC 62.505 66.667 16.68 0.00 0.00 4.02
684 1069 2.795024 TTTTGCATGCCCCGGATCCA 62.795 55.000 16.68 0.00 0.00 3.41
685 1070 2.019897 CTTTTGCATGCCCCGGATCC 62.020 60.000 16.68 0.00 0.00 3.36
686 1071 1.438814 CTTTTGCATGCCCCGGATC 59.561 57.895 16.68 0.00 0.00 3.36
687 1072 2.724273 GCTTTTGCATGCCCCGGAT 61.724 57.895 16.68 0.00 46.58 4.18
688 1073 3.381136 GCTTTTGCATGCCCCGGA 61.381 61.111 16.68 0.00 46.58 5.14
710 1095 3.392285 TCTGCCAATCTGCCTATGTATGT 59.608 43.478 0.00 0.00 0.00 2.29
771 1156 2.689983 CAGTTTCCAGCTTCCAAACAGT 59.310 45.455 12.31 0.00 33.26 3.55
772 1157 2.544486 GCAGTTTCCAGCTTCCAAACAG 60.544 50.000 12.31 7.12 33.26 3.16
773 1158 1.408702 GCAGTTTCCAGCTTCCAAACA 59.591 47.619 12.31 0.00 33.26 2.83
776 1161 1.133823 TCTGCAGTTTCCAGCTTCCAA 60.134 47.619 14.67 0.00 0.00 3.53
777 1162 0.473755 TCTGCAGTTTCCAGCTTCCA 59.526 50.000 14.67 0.00 0.00 3.53
778 1163 1.163554 CTCTGCAGTTTCCAGCTTCC 58.836 55.000 14.67 0.00 0.00 3.46
779 1164 1.163554 CCTCTGCAGTTTCCAGCTTC 58.836 55.000 14.67 0.00 0.00 3.86
782 1167 1.304509 GCTCCTCTGCAGTTTCCAGC 61.305 60.000 14.67 11.24 0.00 4.85
814 1207 5.478407 TCTGCAATTGTCAAGTTCGATCTA 58.522 37.500 7.40 0.00 0.00 1.98
954 1359 1.004394 GGTTTTCTTCGTCCTGGGGAT 59.996 52.381 0.00 0.00 32.73 3.85
1407 1834 2.545946 TCTCGAGTGATCTAGCGTCATG 59.454 50.000 13.13 0.00 0.00 3.07
1424 1861 5.119588 GGAGAGTAGTACATCTCGATTCTCG 59.880 48.000 16.73 0.00 42.40 4.04
1425 1862 5.992829 TGGAGAGTAGTACATCTCGATTCTC 59.007 44.000 16.73 11.15 42.40 2.87
1426 1863 5.931294 TGGAGAGTAGTACATCTCGATTCT 58.069 41.667 16.73 4.62 42.40 2.40
1427 1864 5.761234 ACTGGAGAGTAGTACATCTCGATTC 59.239 44.000 16.73 6.60 42.40 2.52
1428 1865 5.686753 ACTGGAGAGTAGTACATCTCGATT 58.313 41.667 16.73 9.42 42.40 3.34
1429 1866 5.071250 AGACTGGAGAGTAGTACATCTCGAT 59.929 44.000 16.73 9.33 42.40 3.59
1452 1889 1.135575 GGCCGCTGACAAATTTCAGAG 60.136 52.381 10.69 7.45 45.19 3.35
1472 1910 4.574013 AGAAAGACTTGTCTCTGCTTTGTG 59.426 41.667 3.58 0.00 0.00 3.33
1510 1949 8.406297 GTGTCACATATATACAGAGACAGACAA 58.594 37.037 13.75 0.00 34.43 3.18
1513 1952 6.204882 CCGTGTCACATATATACAGAGACAGA 59.795 42.308 13.75 0.00 34.43 3.41
1514 1953 6.204882 TCCGTGTCACATATATACAGAGACAG 59.795 42.308 13.75 9.86 34.43 3.51
1515 1954 6.059484 TCCGTGTCACATATATACAGAGACA 58.941 40.000 3.42 10.96 31.98 3.41
1516 1955 6.555812 TCCGTGTCACATATATACAGAGAC 57.444 41.667 3.42 7.31 0.00 3.36
1517 1956 6.996282 TCTTCCGTGTCACATATATACAGAGA 59.004 38.462 3.42 0.00 0.00 3.10
1518 1957 7.203255 TCTTCCGTGTCACATATATACAGAG 57.797 40.000 3.42 0.00 0.00 3.35
1522 1961 8.644318 AAACTTCTTCCGTGTCACATATATAC 57.356 34.615 3.42 0.00 0.00 1.47
1537 1983 4.385358 TTTGTTGCCTGAAACTTCTTCC 57.615 40.909 0.00 0.00 0.00 3.46
1566 2012 8.095937 TGAAGCTCTATAATCATCATGCTTTG 57.904 34.615 0.00 0.00 39.23 2.77
1631 2123 2.150397 AGAAGTCAGCCACGTACAAC 57.850 50.000 0.00 0.00 0.00 3.32
1632 2124 2.889045 AGTAGAAGTCAGCCACGTACAA 59.111 45.455 0.00 0.00 0.00 2.41
1633 2125 2.511659 AGTAGAAGTCAGCCACGTACA 58.488 47.619 0.00 0.00 0.00 2.90
1634 2126 3.572604 AAGTAGAAGTCAGCCACGTAC 57.427 47.619 0.00 0.00 0.00 3.67
1635 2127 4.330250 AGTAAGTAGAAGTCAGCCACGTA 58.670 43.478 0.00 0.00 0.00 3.57
1636 2128 3.155501 AGTAAGTAGAAGTCAGCCACGT 58.844 45.455 0.00 0.00 0.00 4.49
1637 2129 3.851976 AGTAAGTAGAAGTCAGCCACG 57.148 47.619 0.00 0.00 0.00 4.94
1638 2130 6.862711 AAAAAGTAAGTAGAAGTCAGCCAC 57.137 37.500 0.00 0.00 0.00 5.01
1659 2151 3.612472 GCACGTACAGCCAACTAAAAA 57.388 42.857 0.00 0.00 0.00 1.94
1723 2741 3.896648 AGGTGAAGCAACACAATTACG 57.103 42.857 13.57 0.00 41.88 3.18
1733 2964 6.109156 TCATTACTAGTCAAGGTGAAGCAA 57.891 37.500 0.00 0.00 0.00 3.91
1908 3331 4.439563 CCCGCTGTGGAAATAACCAAATAC 60.440 45.833 9.25 0.00 41.87 1.89
1917 3340 0.254462 TCATGCCCGCTGTGGAAATA 59.746 50.000 9.25 0.00 42.00 1.40
1918 3341 1.001020 TCATGCCCGCTGTGGAAAT 60.001 52.632 9.25 0.00 42.00 2.17
1968 3391 7.404139 GAGACGTGCTCTTCTTTTTACTTTA 57.596 36.000 0.00 0.00 40.61 1.85
1970 3393 5.908916 GAGACGTGCTCTTCTTTTTACTT 57.091 39.130 0.00 0.00 40.61 2.24
2071 3499 4.623932 TCCCTGATCCATGCTTACATAC 57.376 45.455 0.00 0.00 33.67 2.39
2157 3589 7.343241 AGGGTAATACCAATGCCACTAATAT 57.657 36.000 12.03 0.00 41.02 1.28
2158 3590 6.773583 AGGGTAATACCAATGCCACTAATA 57.226 37.500 12.03 0.00 41.02 0.98
2334 3862 6.421405 TCTTAGAAAACGTCGCTTTTTAACC 58.579 36.000 0.00 0.00 0.00 2.85
2335 3863 7.881516 TTCTTAGAAAACGTCGCTTTTTAAC 57.118 32.000 0.00 0.00 0.00 2.01
2365 3893 7.156694 AGGGTAATACCAATGGCACTAATTA 57.843 36.000 12.03 0.00 41.02 1.40


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

AutoCloner maintained by Alex Coulton.