Multiple sequence alignment - TraesCS1D01G392100

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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 TraesCS1D01G392100 chr1D 100.000 4905 0 0 1 4905 462333079 462337983 0.000000e+00 9058.0
1 TraesCS1D01G392100 chr1D 85.020 247 32 4 282 527 211862836 211863078 3.790000e-61 246.0
2 TraesCS1D01G392100 chr1D 84.739 249 33 5 282 527 200648920 200648674 1.360000e-60 244.0
3 TraesCS1D01G392100 chr1D 84.898 245 31 5 282 524 231071333 231071573 4.910000e-60 243.0
4 TraesCS1D01G392100 chr1D 88.489 139 13 2 1751 1889 460877627 460877762 1.090000e-36 165.0
5 TraesCS1D01G392100 chr1D 78.423 241 43 6 1108 1345 71608384 71608150 1.100000e-31 148.0
6 TraesCS1D01G392100 chr1B 94.916 3934 131 29 530 4439 637396741 637400629 0.000000e+00 6093.0
7 TraesCS1D01G392100 chr1B 93.928 527 25 6 1 525 637395631 637396152 0.000000e+00 789.0
8 TraesCS1D01G392100 chr1B 95.494 466 12 5 4441 4905 637402482 637402939 0.000000e+00 736.0
9 TraesCS1D01G392100 chr1A 95.978 2312 69 9 1886 4191 554103833 554106126 0.000000e+00 3733.0
10 TraesCS1D01G392100 chr1A 95.207 1085 33 6 530 1608 554102043 554103114 0.000000e+00 1698.0
11 TraesCS1D01G392100 chr1A 86.538 104 8 5 1630 1727 554103737 554103840 5.190000e-20 110.0
12 TraesCS1D01G392100 chr4B 86.667 1290 140 13 2473 3751 619138911 619140179 0.000000e+00 1400.0
13 TraesCS1D01G392100 chr4B 81.926 592 100 5 3175 3761 619364312 619363723 1.230000e-135 494.0
14 TraesCS1D01G392100 chr4B 83.575 414 68 0 2692 3105 619364839 619364426 5.950000e-104 388.0
15 TraesCS1D01G392100 chr4B 80.387 413 77 4 2691 3101 619330116 619329706 1.330000e-80 311.0
16 TraesCS1D01G392100 chr4B 84.358 179 15 10 872 1040 619080516 619080691 3.930000e-36 163.0
17 TraesCS1D01G392100 chr4B 84.615 130 12 4 3748 3876 619140550 619140672 6.670000e-24 122.0
18 TraesCS1D01G392100 chr5A 81.439 1126 182 14 2660 3761 666308804 666307682 0.000000e+00 896.0
19 TraesCS1D01G392100 chr5A 79.966 594 109 9 3178 3766 47460599 47460011 3.510000e-116 429.0
20 TraesCS1D01G392100 chr5A 85.143 175 25 1 3951 4125 641588734 641588907 1.400000e-40 178.0
21 TraesCS1D01G392100 chr5A 82.178 202 36 0 1125 1326 666309869 666309668 1.810000e-39 174.0
22 TraesCS1D01G392100 chr5A 87.129 101 12 1 2681 2780 666307155 666307255 4.010000e-21 113.0
23 TraesCS1D01G392100 chr3D 88.054 745 41 15 4194 4905 570138090 570137361 0.000000e+00 839.0
24 TraesCS1D01G392100 chr3D 87.936 746 41 16 4194 4905 570138979 570138249 0.000000e+00 833.0
25 TraesCS1D01G392100 chr3D 87.517 745 45 16 4194 4905 570128429 570127700 0.000000e+00 817.0
26 TraesCS1D01G392100 chr3D 87.601 742 43 17 4197 4905 570117778 570117053 0.000000e+00 815.0
27 TraesCS1D01G392100 chr3D 87.383 745 44 15 4194 4905 570129315 570128588 0.000000e+00 809.0
28 TraesCS1D01G392100 chr3D 87.248 745 47 16 4194 4905 570126655 570125926 0.000000e+00 806.0
29 TraesCS1D01G392100 chr3D 86.997 746 47 17 4194 4905 570123990 570123261 0.000000e+00 795.0
30 TraesCS1D01G392100 chr3D 86.863 746 49 15 4194 4905 570122213 570121483 0.000000e+00 789.0
31 TraesCS1D01G392100 chr3D 86.729 746 50 16 4194 4905 570123102 570122372 0.000000e+00 784.0
32 TraesCS1D01G392100 chr3D 85.695 748 43 25 4194 4905 570118659 570117940 0.000000e+00 730.0
33 TraesCS1D01G392100 chr3D 87.059 680 39 16 4260 4905 570130138 570129474 0.000000e+00 723.0
34 TraesCS1D01G392100 chr3D 85.830 247 33 2 282 527 95398241 95398486 1.350000e-65 261.0
35 TraesCS1D01G392100 chr3D 85.057 174 19 6 3950 4118 581366155 581366326 2.350000e-38 171.0
36 TraesCS1D01G392100 chrUn 87.601 742 43 17 4197 4905 287063132 287062407 0.000000e+00 815.0
37 TraesCS1D01G392100 chrUn 86.898 748 44 20 4194 4905 287064023 287063294 0.000000e+00 789.0
38 TraesCS1D01G392100 chr4D 83.590 585 92 4 3175 3757 485538795 485539377 3.340000e-151 545.0
39 TraesCS1D01G392100 chr4D 85.401 411 60 0 2691 3101 485538195 485538605 1.260000e-115 427.0
40 TraesCS1D01G392100 chr4D 85.670 321 21 12 530 842 485526050 485526353 1.020000e-81 315.0
41 TraesCS1D01G392100 chr4D 87.045 247 28 4 282 527 399526307 399526064 4.840000e-70 276.0
42 TraesCS1D01G392100 chr4D 93.714 175 11 0 1125 1299 485526542 485526716 3.770000e-66 263.0
43 TraesCS1D01G392100 chr4D 83.051 236 34 2 1097 1326 485537030 485537265 4.980000e-50 209.0
44 TraesCS1D01G392100 chr4D 79.755 163 26 6 111 272 22584039 22583883 1.440000e-20 111.0
45 TraesCS1D01G392100 chr4D 90.196 51 5 0 1640 1690 306303416 306303466 3.170000e-07 67.6
46 TraesCS1D01G392100 chr7D 81.918 636 97 12 3149 3768 45432978 45432345 5.630000e-144 521.0
47 TraesCS1D01G392100 chr7D 76.630 184 35 6 22 202 422336748 422336570 1.450000e-15 95.3
48 TraesCS1D01G392100 chr7D 85.714 70 10 0 1887 1956 6961025 6961094 1.890000e-09 75.0
49 TraesCS1D01G392100 chr2B 79.346 673 113 18 3110 3761 41377420 41378087 2.690000e-122 449.0
50 TraesCS1D01G392100 chr2B 84.836 244 35 2 282 524 556181483 556181725 1.360000e-60 244.0
51 TraesCS1D01G392100 chr2B 81.893 243 33 7 1107 1345 41375288 41375523 1.390000e-45 195.0
52 TraesCS1D01G392100 chr2B 83.704 135 13 2 1751 1885 26445986 26446111 8.620000e-23 119.0
53 TraesCS1D01G392100 chr2B 87.719 57 7 0 1632 1688 677045573 677045517 3.170000e-07 67.6
54 TraesCS1D01G392100 chr2B 91.489 47 4 0 1642 1688 265432008 265432054 1.140000e-06 65.8
55 TraesCS1D01G392100 chr2B 82.667 75 12 1 1883 1956 546830249 546830323 1.140000e-06 65.8
56 TraesCS1D01G392100 chr3B 79.739 612 104 13 3170 3763 176322047 176322656 4.540000e-115 425.0
57 TraesCS1D01G392100 chr3B 81.651 109 14 5 122 229 734494433 734494536 8.750000e-13 86.1
58 TraesCS1D01G392100 chr5D 85.081 248 32 4 282 527 396784704 396784460 1.050000e-61 248.0
59 TraesCS1D01G392100 chr5D 76.604 265 58 4 2788 3050 58229115 58229377 5.120000e-30 143.0
60 TraesCS1D01G392100 chr5D 88.793 116 11 2 1771 1886 299397915 299398028 1.840000e-29 141.0
61 TraesCS1D01G392100 chr2D 85.246 244 31 4 282 524 143326569 143326808 3.790000e-61 246.0
62 TraesCS1D01G392100 chr2D 82.158 241 34 5 1108 1345 607810610 607810844 1.080000e-46 198.0
63 TraesCS1D01G392100 chr2D 87.586 145 11 5 1742 1884 45122794 45122655 1.410000e-35 161.0
64 TraesCS1D01G392100 chr2D 82.143 112 17 3 156 266 202072907 202072798 5.230000e-15 93.5
65 TraesCS1D01G392100 chr2D 85.135 74 10 1 1884 1956 352876633 352876560 1.890000e-09 75.0
66 TraesCS1D01G392100 chr2D 91.111 45 4 0 1644 1688 81326899 81326943 1.470000e-05 62.1
67 TraesCS1D01G392100 chr7A 87.425 167 18 2 3953 4119 680684337 680684500 6.480000e-44 189.0
68 TraesCS1D01G392100 chr7A 78.924 223 30 8 1123 1345 47517495 47517290 8.560000e-28 135.0
69 TraesCS1D01G392100 chr7A 85.106 94 12 2 154 246 511408236 511408328 1.450000e-15 95.3
70 TraesCS1D01G392100 chr7A 78.333 120 21 5 155 271 218267420 218267537 6.810000e-09 73.1
71 TraesCS1D01G392100 chr7A 93.023 43 2 1 1883 1924 408758652 408758610 1.470000e-05 62.1
72 TraesCS1D01G392100 chr2A 86.826 167 19 3 3953 4118 735788789 735788953 3.020000e-42 183.0
73 TraesCS1D01G392100 chr2A 74.138 232 50 10 20 246 74793887 74793661 2.430000e-13 87.9
74 TraesCS1D01G392100 chr2A 76.224 143 24 7 1200 1340 761541927 761541793 3.170000e-07 67.6
75 TraesCS1D01G392100 chr4A 86.310 168 21 2 3953 4119 615058664 615058498 1.080000e-41 182.0
76 TraesCS1D01G392100 chr4A 85.629 167 22 2 3953 4118 614962857 614962692 1.810000e-39 174.0
77 TraesCS1D01G392100 chr4A 86.869 99 8 2 1742 1840 58870402 58870495 6.710000e-19 106.0
78 TraesCS1D01G392100 chr4A 93.478 46 3 0 1643 1688 4010018 4010063 8.810000e-08 69.4
79 TraesCS1D01G392100 chr4A 90.196 51 4 1 1638 1688 742318730 742318779 1.140000e-06 65.8
80 TraesCS1D01G392100 chr5B 86.145 166 22 1 3953 4118 549671907 549671743 1.400000e-40 178.0
81 TraesCS1D01G392100 chr5B 75.379 264 63 2 2788 3050 63296960 63297222 5.150000e-25 126.0
82 TraesCS1D01G392100 chr5B 83.908 87 13 1 1883 1968 341533813 341533727 1.130000e-11 82.4
83 TraesCS1D01G392100 chr6D 88.811 143 12 3 1743 1885 307532493 307532355 6.530000e-39 172.0
84 TraesCS1D01G392100 chr6D 87.692 65 7 1 1883 1946 464983791 464983855 1.890000e-09 75.0
85 TraesCS1D01G392100 chr6A 87.075 147 10 7 1742 1887 596073417 596073555 1.830000e-34 158.0
86 TraesCS1D01G392100 chr6A 89.231 65 6 1 1883 1946 169514001 169514065 4.070000e-11 80.5
87 TraesCS1D01G392100 chr6A 93.333 45 3 0 1643 1687 616974707 616974751 3.170000e-07 67.6
88 TraesCS1D01G392100 chr3A 84.000 125 13 5 122 246 695049811 695049928 4.010000e-21 113.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G392100 chr1D 462333079 462337983 4904 False 9058.000000 9058 100.000000 1 4905 1 chr1D.!!$F4 4904
1 TraesCS1D01G392100 chr1B 637395631 637402939 7308 False 2539.333333 6093 94.779333 1 4905 3 chr1B.!!$F1 4904
2 TraesCS1D01G392100 chr1A 554102043 554106126 4083 False 1847.000000 3733 92.574333 530 4191 3 chr1A.!!$F1 3661
3 TraesCS1D01G392100 chr4B 619138911 619140672 1761 False 761.000000 1400 85.641000 2473 3876 2 chr4B.!!$F2 1403
4 TraesCS1D01G392100 chr4B 619363723 619364839 1116 True 441.000000 494 82.750500 2692 3761 2 chr4B.!!$R2 1069
5 TraesCS1D01G392100 chr5A 666307682 666309869 2187 True 535.000000 896 81.808500 1125 3761 2 chr5A.!!$R2 2636
6 TraesCS1D01G392100 chr5A 47460011 47460599 588 True 429.000000 429 79.966000 3178 3766 1 chr5A.!!$R1 588
7 TraesCS1D01G392100 chr3D 570137361 570138979 1618 True 836.000000 839 87.995000 4194 4905 2 chr3D.!!$R2 711
8 TraesCS1D01G392100 chr3D 570117053 570130138 13085 True 785.333333 817 87.010222 4194 4905 9 chr3D.!!$R1 711
9 TraesCS1D01G392100 chrUn 287062407 287064023 1616 True 802.000000 815 87.249500 4194 4905 2 chrUn.!!$R1 711
10 TraesCS1D01G392100 chr4D 485537030 485539377 2347 False 393.666667 545 84.014000 1097 3757 3 chr4D.!!$F3 2660
11 TraesCS1D01G392100 chr4D 485526050 485526716 666 False 289.000000 315 89.692000 530 1299 2 chr4D.!!$F2 769
12 TraesCS1D01G392100 chr7D 45432345 45432978 633 True 521.000000 521 81.918000 3149 3768 1 chr7D.!!$R1 619
13 TraesCS1D01G392100 chr2B 41375288 41378087 2799 False 322.000000 449 80.619500 1107 3761 2 chr2B.!!$F5 2654
14 TraesCS1D01G392100 chr3B 176322047 176322656 609 False 425.000000 425 79.739000 3170 3763 1 chr3B.!!$F1 593

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
266 269 0.595588 CGCTATCTGAGAGGCACGAT 59.404 55.000 10.02 0.0 0.00 3.73 F
339 342 1.989165 CGCTTCACTGTTCAGAGCTAC 59.011 52.381 6.83 0.0 0.00 3.58 F
348 351 2.085320 GTTCAGAGCTACTCGTCTCCA 58.915 52.381 0.00 0.0 35.36 3.86 F
944 1546 2.620115 CCAGCCCATGTGCAAACTATAG 59.380 50.000 2.19 0.0 0.00 1.31 F
2417 3929 0.388907 CCAAATGCAAAGACGGCCAG 60.389 55.000 2.24 0.0 0.00 4.85 F
2545 4090 0.460284 TTTCTCGCAGAATCTCCGCC 60.460 55.000 0.00 0.0 33.67 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 3057 1.066143 AGATGTGTCCTAAACAGGCCG 60.066 52.381 0.00 0.0 38.97 6.13 R
1751 3081 4.164843 ACAAACATAGTGGACACAAGGT 57.835 40.909 5.14 0.0 0.00 3.50 R
1752 3082 5.305585 ACTACAAACATAGTGGACACAAGG 58.694 41.667 5.14 0.0 34.02 3.61 R
2539 4084 0.036875 AGTTTTTGGAGGAGGCGGAG 59.963 55.000 0.00 0.0 0.00 4.63 R
3487 5464 0.032615 CCTCCTCCTGAGCTACCACT 60.033 60.000 0.00 0.0 39.98 4.00 R
3958 6325 1.060622 CTGTAGCCGTCTCGTCGTC 59.939 63.158 0.00 0.0 0.00 4.20 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
86 87 5.183530 CATATCTATGCCCCCATGAGAAA 57.816 43.478 0.00 0.00 32.85 2.52
94 95 5.661503 TGCCCCCATGAGAAATAAATCTA 57.338 39.130 0.00 0.00 0.00 1.98
109 110 4.592485 AAATCTATGTCTCTCGCGGAAT 57.408 40.909 6.13 0.00 0.00 3.01
128 129 7.062371 CGCGGAATAAACAAAATGGAAAACATA 59.938 33.333 0.00 0.00 39.40 2.29
153 155 0.753867 TTTCCTTTTTCCGGGTTGCC 59.246 50.000 0.00 0.00 0.00 4.52
159 161 3.835790 TTTCCGGGTTGCCAGACCG 62.836 63.158 0.00 2.55 46.79 4.79
207 209 2.333926 TCCGCGAGAAGTAAATGTGTG 58.666 47.619 8.23 0.00 0.00 3.82
208 210 1.201921 CCGCGAGAAGTAAATGTGTGC 60.202 52.381 8.23 0.00 0.00 4.57
222 224 0.954452 GTGTGCCTCTTGTGAAAGGG 59.046 55.000 0.00 0.00 32.98 3.95
266 269 0.595588 CGCTATCTGAGAGGCACGAT 59.404 55.000 10.02 0.00 0.00 3.73
339 342 1.989165 CGCTTCACTGTTCAGAGCTAC 59.011 52.381 6.83 0.00 0.00 3.58
348 351 2.085320 GTTCAGAGCTACTCGTCTCCA 58.915 52.381 0.00 0.00 35.36 3.86
400 403 6.259608 CACACAAGGCTTCTAATTATGAGGAG 59.740 42.308 0.00 0.00 0.00 3.69
416 419 9.830186 ATTATGAGGAGAAGAGTATTAGCCTAA 57.170 33.333 0.00 0.00 0.00 2.69
417 420 9.830186 TTATGAGGAGAAGAGTATTAGCCTAAT 57.170 33.333 2.01 2.01 0.00 1.73
496 499 7.375053 GCTCCAAAACTTGTGTATCCAAATAA 58.625 34.615 0.00 0.00 0.00 1.40
709 1300 3.394836 GGCGGCAGGACCTCTCTT 61.395 66.667 3.07 0.00 35.61 2.85
896 1494 4.927782 TGCAGTCTTGGGCGCGTT 62.928 61.111 8.43 0.00 0.00 4.84
944 1546 2.620115 CCAGCCCATGTGCAAACTATAG 59.380 50.000 2.19 0.00 0.00 1.31
1354 1969 6.577103 AGACTGCCGGTATGAATATGATATG 58.423 40.000 1.90 0.00 0.00 1.78
1574 2293 4.957759 TTCCGTCTATTTTTGCTTAGCC 57.042 40.909 0.29 0.00 0.00 3.93
1598 2317 4.023193 CGCACTTGATTTCTACCCAACTTT 60.023 41.667 0.00 0.00 0.00 2.66
1735 3065 7.395206 ACTTTAGGTAAATTTATTCGGCCTGTT 59.605 33.333 12.39 0.00 0.00 3.16
1754 3084 6.287589 CTGTTTAGGACACATCTAGAACCT 57.712 41.667 0.00 4.03 33.82 3.50
1755 3085 6.681729 TGTTTAGGACACATCTAGAACCTT 57.318 37.500 0.00 0.00 32.00 3.50
1756 3086 6.464222 TGTTTAGGACACATCTAGAACCTTG 58.536 40.000 0.00 0.00 32.00 3.61
1757 3087 6.042781 TGTTTAGGACACATCTAGAACCTTGT 59.957 38.462 0.00 0.00 32.00 3.16
1758 3088 4.543590 AGGACACATCTAGAACCTTGTG 57.456 45.455 18.41 18.41 43.88 3.33
1773 3103 5.298989 ACCTTGTGTCCACTATGTTTGTA 57.701 39.130 0.00 0.00 0.00 2.41
1834 3164 6.019779 TGTTGTTGTGTTATTTATGGGAGC 57.980 37.500 0.00 0.00 0.00 4.70
1845 3175 8.439971 TGTTATTTATGGGAGCTTAGATGTGAT 58.560 33.333 0.00 0.00 0.00 3.06
1846 3176 8.725148 GTTATTTATGGGAGCTTAGATGTGATG 58.275 37.037 0.00 0.00 0.00 3.07
1848 3178 3.827008 TGGGAGCTTAGATGTGATGTC 57.173 47.619 0.00 0.00 0.00 3.06
1857 3187 7.271511 AGCTTAGATGTGATGTCCTTAGAAAG 58.728 38.462 0.00 0.00 0.00 2.62
1858 3188 6.018343 GCTTAGATGTGATGTCCTTAGAAAGC 60.018 42.308 0.00 0.00 0.00 3.51
1866 3196 7.093333 TGTGATGTCCTTAGAAAGCATCTAGAA 60.093 37.037 0.00 0.00 41.59 2.10
1918 3267 9.602568 TTATTTTGCTTCGTATGTAGTCCATAA 57.397 29.630 0.00 0.00 37.77 1.90
1925 3274 8.223769 GCTTCGTATGTAGTCCATAATGAAATG 58.776 37.037 0.00 0.00 37.77 2.32
1933 3284 8.902806 TGTAGTCCATAATGAAATGCCTAAAAG 58.097 33.333 0.00 0.00 0.00 2.27
1958 3467 8.847196 AGGACTTATTTTTACAAACAGAGGAAC 58.153 33.333 0.00 0.00 0.00 3.62
2417 3929 0.388907 CCAAATGCAAAGACGGCCAG 60.389 55.000 2.24 0.00 0.00 4.85
2539 4084 6.595772 ACACTGATAATTTCTCGCAGAATC 57.404 37.500 0.00 0.00 33.67 2.52
2540 4085 6.344500 ACACTGATAATTTCTCGCAGAATCT 58.656 36.000 0.00 0.00 33.67 2.40
2541 4086 6.478344 ACACTGATAATTTCTCGCAGAATCTC 59.522 38.462 0.00 0.00 33.67 2.75
2542 4087 5.988561 ACTGATAATTTCTCGCAGAATCTCC 59.011 40.000 0.00 0.00 33.67 3.71
2543 4088 4.984785 TGATAATTTCTCGCAGAATCTCCG 59.015 41.667 0.00 0.00 33.67 4.63
2544 4089 1.576356 ATTTCTCGCAGAATCTCCGC 58.424 50.000 0.00 0.00 33.67 5.54
2545 4090 0.460284 TTTCTCGCAGAATCTCCGCC 60.460 55.000 0.00 0.00 33.67 6.13
2546 4091 1.323271 TTCTCGCAGAATCTCCGCCT 61.323 55.000 0.00 0.00 34.09 5.52
2547 4092 1.299773 CTCGCAGAATCTCCGCCTC 60.300 63.158 0.00 0.00 34.09 4.70
2567 4124 1.889170 CCTCCAAAAACTGGGCTTCTC 59.111 52.381 0.00 0.00 46.44 2.87
3078 4659 2.997986 CTCTACGGTGCCAATAACGTTT 59.002 45.455 5.91 0.00 40.38 3.60
3202 5179 2.223735 GCATGAGATTGTGCTGGGATTG 60.224 50.000 0.00 0.00 38.30 2.67
3487 5464 3.707025 ATGCGGTAGGGGGCCTGTA 62.707 63.158 0.84 0.00 34.61 2.74
3500 5477 0.461961 GCCTGTAGTGGTAGCTCAGG 59.538 60.000 10.30 10.30 45.68 3.86
3938 6305 4.520111 CACAGGAACATTCAACCATTCAGA 59.480 41.667 0.00 0.00 0.00 3.27
3941 6308 4.763793 AGGAACATTCAACCATTCAGAGTG 59.236 41.667 0.00 0.00 0.00 3.51
3942 6309 4.520492 GGAACATTCAACCATTCAGAGTGT 59.480 41.667 0.00 0.00 34.30 3.55
3943 6310 5.335191 GGAACATTCAACCATTCAGAGTGTC 60.335 44.000 0.00 0.00 32.11 3.67
3944 6311 4.717877 ACATTCAACCATTCAGAGTGTCA 58.282 39.130 0.00 0.00 27.73 3.58
3945 6312 5.319453 ACATTCAACCATTCAGAGTGTCAT 58.681 37.500 0.00 0.00 27.73 3.06
3946 6313 5.771666 ACATTCAACCATTCAGAGTGTCATT 59.228 36.000 0.00 0.00 27.73 2.57
3948 6315 7.448161 ACATTCAACCATTCAGAGTGTCATTTA 59.552 33.333 0.00 0.00 27.73 1.40
3950 6317 8.408043 TTCAACCATTCAGAGTGTCATTTATT 57.592 30.769 0.00 0.00 0.00 1.40
3951 6318 8.044060 TCAACCATTCAGAGTGTCATTTATTC 57.956 34.615 0.00 0.00 0.00 1.75
3958 6325 2.864343 GAGTGTCATTTATTCCCCGTCG 59.136 50.000 0.00 0.00 0.00 5.12
3975 6342 2.733671 CGACGACGAGACGGCTACA 61.734 63.158 0.00 0.00 42.66 2.74
3992 6359 5.169295 GGCTACAGTGACTTCGTAAATCTT 58.831 41.667 0.00 0.00 0.00 2.40
4006 6373 9.208022 CTTCGTAAATCTTAAGATGATATGCCA 57.792 33.333 18.61 9.32 34.49 4.92
4189 6559 8.578308 TTTTCTCATTTGTAGCATCAAAACTG 57.422 30.769 9.63 5.91 40.05 3.16
4190 6560 6.882610 TCTCATTTGTAGCATCAAAACTGT 57.117 33.333 9.63 0.00 40.05 3.55
4191 6561 6.902341 TCTCATTTGTAGCATCAAAACTGTC 58.098 36.000 9.63 0.00 40.05 3.51
4192 6562 6.712095 TCTCATTTGTAGCATCAAAACTGTCT 59.288 34.615 9.63 0.00 40.05 3.41
4272 6643 1.134946 GGCTTTGGTGCATGTGGATAC 59.865 52.381 0.00 0.00 34.04 2.24
4394 6769 0.038166 TCAGACAAGCCCCACATTCC 59.962 55.000 0.00 0.00 0.00 3.01
4401 6776 0.779997 AGCCCCACATTCCTTTGTCT 59.220 50.000 0.00 0.00 0.00 3.41
4459 8160 7.931015 TTTATCCCTACCATGAAGACTATGT 57.069 36.000 0.00 0.00 0.00 2.29
4587 13637 8.996651 ATTTGAGGAGGGAACGAATTTATATT 57.003 30.769 0.00 0.00 0.00 1.28
4588 13638 8.817092 TTTGAGGAGGGAACGAATTTATATTT 57.183 30.769 0.00 0.00 0.00 1.40
4722 19100 0.598562 TCACACAACGCCTCTCTCTC 59.401 55.000 0.00 0.00 0.00 3.20
4723 19101 0.600557 CACACAACGCCTCTCTCTCT 59.399 55.000 0.00 0.00 0.00 3.10
4724 19102 0.885196 ACACAACGCCTCTCTCTCTC 59.115 55.000 0.00 0.00 0.00 3.20
4725 19103 1.173043 CACAACGCCTCTCTCTCTCT 58.827 55.000 0.00 0.00 0.00 3.10
4739 19117 0.316841 CTCTCTCTATTCCCTGCGCC 59.683 60.000 4.18 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.064207 TGGTCGTGATTCTCGAAAAAGG 58.936 45.455 11.95 0.00 39.01 3.11
74 75 7.465116 AGACATAGATTTATTTCTCATGGGGG 58.535 38.462 0.00 0.00 0.00 5.40
86 87 5.707242 TTCCGCGAGAGACATAGATTTAT 57.293 39.130 8.23 0.00 0.00 1.40
94 95 3.520290 TGTTTATTCCGCGAGAGACAT 57.480 42.857 8.23 0.00 0.00 3.06
159 161 1.841663 TTTGCTTTCGCGAGAGGCAC 61.842 55.000 25.84 11.56 45.26 5.01
170 172 1.135575 CGGAGGCACAGATTTGCTTTC 60.136 52.381 0.00 0.00 42.56 2.62
180 182 1.934220 TACTTCTCGCGGAGGCACAG 61.934 60.000 6.13 0.00 39.92 3.66
245 248 1.448119 CGTGCCTCTCAGATAGCGGA 61.448 60.000 0.00 0.00 31.02 5.54
247 250 0.595588 ATCGTGCCTCTCAGATAGCG 59.404 55.000 0.00 0.00 0.00 4.26
248 251 1.400888 CGATCGTGCCTCTCAGATAGC 60.401 57.143 7.03 0.00 0.00 2.97
249 252 1.876799 ACGATCGTGCCTCTCAGATAG 59.123 52.381 22.06 0.00 0.00 2.08
250 253 1.604278 CACGATCGTGCCTCTCAGATA 59.396 52.381 32.93 0.00 39.39 1.98
339 342 5.568685 TCTTCTAATTCACTGGAGACGAG 57.431 43.478 0.00 0.00 0.00 4.18
348 351 8.421002 GCTCTAATCTCCTTCTTCTAATTCACT 58.579 37.037 0.00 0.00 0.00 3.41
444 447 8.068892 TCCTCTAATTCTTCTAGTTCCAGTTC 57.931 38.462 0.00 0.00 0.00 3.01
647 1235 5.178438 GCCTTCACAAGTTCACTCTAGAAAG 59.822 44.000 0.00 0.00 0.00 2.62
648 1236 5.057149 GCCTTCACAAGTTCACTCTAGAAA 58.943 41.667 0.00 0.00 0.00 2.52
649 1237 4.100963 TGCCTTCACAAGTTCACTCTAGAA 59.899 41.667 0.00 0.00 0.00 2.10
654 1242 1.604278 GGTGCCTTCACAAGTTCACTC 59.396 52.381 0.00 0.00 44.87 3.51
692 1280 3.378399 GAAGAGAGGTCCTGCCGCC 62.378 68.421 0.00 0.00 43.70 6.13
695 1283 2.153034 AGTAGAAGAGAGGTCCTGCC 57.847 55.000 0.00 0.00 37.58 4.85
709 1300 3.105283 GGAGCCCTTGGTAAGAAGTAGA 58.895 50.000 0.00 0.00 0.00 2.59
743 1334 5.784625 GTGAACGCAATGCAATTATTTGTTG 59.215 36.000 5.91 0.00 32.46 3.33
775 1366 1.529309 GAGCCCTGATGTTCCCTCC 59.471 63.158 0.00 0.00 0.00 4.30
896 1494 0.748450 AGACCCGTGAACTCGTCAAA 59.252 50.000 0.00 0.00 38.23 2.69
1520 2239 5.644977 TGGAGTACGATATCATCACCATC 57.355 43.478 3.12 0.00 0.00 3.51
1523 2242 6.151312 ACACTATGGAGTACGATATCATCACC 59.849 42.308 3.12 1.65 33.32 4.02
1524 2243 7.147143 ACACTATGGAGTACGATATCATCAC 57.853 40.000 3.12 0.00 33.32 3.06
1574 2293 2.107950 TGGGTAGAAATCAAGTGCGG 57.892 50.000 0.00 0.00 0.00 5.69
1598 2317 7.556275 ACAATTAATTTGAATCGAAGGAGGCTA 59.444 33.333 0.00 0.00 38.76 3.93
1727 3057 1.066143 AGATGTGTCCTAAACAGGCCG 60.066 52.381 0.00 0.00 38.97 6.13
1730 3060 5.187967 AGGTTCTAGATGTGTCCTAAACAGG 59.812 44.000 0.00 0.00 38.97 4.00
1735 3065 6.037786 CACAAGGTTCTAGATGTGTCCTAA 57.962 41.667 13.72 0.00 38.62 2.69
1748 3078 4.706842 AACATAGTGGACACAAGGTTCT 57.293 40.909 5.14 0.00 0.00 3.01
1751 3081 4.164843 ACAAACATAGTGGACACAAGGT 57.835 40.909 5.14 0.00 0.00 3.50
1752 3082 5.305585 ACTACAAACATAGTGGACACAAGG 58.694 41.667 5.14 0.00 34.02 3.61
1753 3083 6.223852 AGACTACAAACATAGTGGACACAAG 58.776 40.000 5.14 0.00 35.48 3.16
1754 3084 6.169557 AGACTACAAACATAGTGGACACAA 57.830 37.500 5.14 0.00 35.48 3.33
1755 3085 5.801531 AGACTACAAACATAGTGGACACA 57.198 39.130 5.14 0.00 35.48 3.72
1756 3086 8.656849 CAAATAGACTACAAACATAGTGGACAC 58.343 37.037 0.00 0.00 35.48 3.67
1757 3087 8.372459 ACAAATAGACTACAAACATAGTGGACA 58.628 33.333 0.00 0.00 35.48 4.02
1758 3088 8.773404 ACAAATAGACTACAAACATAGTGGAC 57.227 34.615 0.00 0.00 35.48 4.02
1759 3089 9.787435 AAACAAATAGACTACAAACATAGTGGA 57.213 29.630 0.00 0.00 35.48 4.02
1773 3103 5.454966 ACCTGGGACAAAAACAAATAGACT 58.545 37.500 0.00 0.00 38.70 3.24
1816 3146 8.052748 ACATCTAAGCTCCCATAAATAACACAA 58.947 33.333 0.00 0.00 0.00 3.33
1817 3147 7.498900 CACATCTAAGCTCCCATAAATAACACA 59.501 37.037 0.00 0.00 0.00 3.72
1834 3164 7.044181 TGCTTTCTAAGGACATCACATCTAAG 58.956 38.462 0.00 0.00 0.00 2.18
1845 3175 6.437477 TCACTTCTAGATGCTTTCTAAGGACA 59.563 38.462 5.57 0.00 36.50 4.02
1846 3176 6.868622 TCACTTCTAGATGCTTTCTAAGGAC 58.131 40.000 5.57 0.00 36.50 3.85
1848 3178 8.729805 AATTCACTTCTAGATGCTTTCTAAGG 57.270 34.615 5.57 0.00 36.50 2.69
1857 3187 8.386606 CAGTTTGTCTAATTCACTTCTAGATGC 58.613 37.037 5.57 0.00 0.00 3.91
1858 3188 9.429359 ACAGTTTGTCTAATTCACTTCTAGATG 57.571 33.333 4.14 4.14 0.00 2.90
1925 3274 9.752961 TGTTTGTAAAAATAAGTCCTTTTAGGC 57.247 29.630 0.00 0.00 34.61 3.93
1933 3284 8.847196 AGTTCCTCTGTTTGTAAAAATAAGTCC 58.153 33.333 0.00 0.00 0.00 3.85
2437 3949 2.262423 ACTGACCTTCCAGAGTTTGC 57.738 50.000 0.00 0.00 37.59 3.68
2539 4084 0.036875 AGTTTTTGGAGGAGGCGGAG 59.963 55.000 0.00 0.00 0.00 4.63
2540 4085 0.250727 CAGTTTTTGGAGGAGGCGGA 60.251 55.000 0.00 0.00 0.00 5.54
2541 4086 2.257353 CAGTTTTTGGAGGAGGCGG 58.743 57.895 0.00 0.00 0.00 6.13
2567 4124 1.062587 GAACCGACAGAAATGCCGATG 59.937 52.381 0.00 0.00 0.00 3.84
2649 4218 2.275318 CTGACGGATTTTCTCCTGCTC 58.725 52.381 0.00 0.00 42.47 4.26
2697 4278 5.152623 TGATCATCTTCGAGGAAGTTGTT 57.847 39.130 0.00 7.60 39.20 2.83
3078 4659 2.375174 ACCTAACAGACCATGGAAGCAA 59.625 45.455 21.47 0.00 0.00 3.91
3487 5464 0.032615 CCTCCTCCTGAGCTACCACT 60.033 60.000 0.00 0.00 39.98 4.00
3500 5477 2.725008 CATCGCGTCCTCCTCCTC 59.275 66.667 5.77 0.00 0.00 3.71
3905 6271 2.971660 TGTTCCTGTGAAACGAGACA 57.028 45.000 0.00 0.00 42.39 3.41
3906 6272 3.807622 TGAATGTTCCTGTGAAACGAGAC 59.192 43.478 0.00 0.00 42.39 3.36
3910 6277 3.066064 TGGTTGAATGTTCCTGTGAAACG 59.934 43.478 0.00 0.00 42.39 3.60
3938 6305 2.498481 TCGACGGGGAATAAATGACACT 59.502 45.455 0.00 0.00 0.00 3.55
3941 6308 1.856597 CGTCGACGGGGAATAAATGAC 59.143 52.381 29.70 0.00 35.37 3.06
3942 6309 1.750206 TCGTCGACGGGGAATAAATGA 59.250 47.619 35.05 10.71 40.29 2.57
3943 6310 1.856597 GTCGTCGACGGGGAATAAATG 59.143 52.381 35.05 5.23 40.29 2.32
3944 6311 2.214387 GTCGTCGACGGGGAATAAAT 57.786 50.000 35.05 0.00 40.29 1.40
3945 6312 3.719699 GTCGTCGACGGGGAATAAA 57.280 52.632 35.05 12.79 40.29 1.40
3958 6325 1.060622 CTGTAGCCGTCTCGTCGTC 59.939 63.158 0.00 0.00 0.00 4.20
3970 6337 7.754027 TCTTAAGATTTACGAAGTCACTGTAGC 59.246 37.037 0.00 0.00 43.93 3.58
3992 6359 5.557576 AACTGAGCTGGCATATCATCTTA 57.442 39.130 0.00 0.00 0.00 2.10
4006 6373 3.484407 AGCATCTTCAACAAACTGAGCT 58.516 40.909 0.00 0.00 0.00 4.09
4212 6583 2.503920 ATGGATACCGCGTAGTTCAC 57.496 50.000 4.92 0.00 0.00 3.18
4216 6587 2.816087 ACGATAATGGATACCGCGTAGT 59.184 45.455 4.92 0.00 0.00 2.73
4227 6598 1.694844 TGGACGCCTACGATAATGGA 58.305 50.000 0.00 0.00 43.93 3.41
4394 6769 2.289072 ACAGGTCGATGGTGAGACAAAG 60.289 50.000 0.00 0.00 39.01 2.77
4401 6776 2.092323 CTAGTCACAGGTCGATGGTGA 58.908 52.381 11.26 11.26 39.09 4.02
4443 8143 4.954202 ACGAGGAACATAGTCTTCATGGTA 59.046 41.667 0.00 0.00 0.00 3.25
4456 8157 1.202758 TGTGCTCCAAACGAGGAACAT 60.203 47.619 0.00 0.00 41.13 2.71
4459 8160 2.045561 TTTGTGCTCCAAACGAGGAA 57.954 45.000 0.00 0.00 41.13 3.36
4700 19078 0.464036 AGAGAGGCGTTGTGTGACAA 59.536 50.000 0.00 0.00 35.42 3.18
4722 19100 0.316841 GAGGCGCAGGGAATAGAGAG 59.683 60.000 10.83 0.00 0.00 3.20
4723 19101 0.105964 AGAGGCGCAGGGAATAGAGA 60.106 55.000 10.83 0.00 0.00 3.10
4724 19102 0.316841 GAGAGGCGCAGGGAATAGAG 59.683 60.000 10.83 0.00 0.00 2.43
4725 19103 0.105964 AGAGAGGCGCAGGGAATAGA 60.106 55.000 10.83 0.00 0.00 1.98
4739 19117 3.889815 AGAGAGAGGTGATGTGAGAGAG 58.110 50.000 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.