Multiple sequence alignment - TraesCS3D01G404800

Loading Multiple Alignment...

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 TraesCS3D01G404800 chr3D 100.000 5576 0 0 1 5576 519252606 519247031 0.000000e+00 10298.0
1 TraesCS3D01G404800 chr3D 80.765 863 129 27 726 1578 24060920 24061755 1.690000e-179 640.0
2 TraesCS3D01G404800 chr3D 89.744 273 23 5 3083 3352 519315214 519314944 1.490000e-90 344.0
3 TraesCS3D01G404800 chr3D 93.478 138 8 1 2880 3017 519315933 519315797 2.630000e-48 204.0
4 TraesCS3D01G404800 chr3D 93.478 138 8 1 2880 3017 519316369 519316233 2.630000e-48 204.0
5 TraesCS3D01G404800 chr3D 94.366 71 4 0 2807 2877 519316042 519315972 5.910000e-20 110.0
6 TraesCS3D01G404800 chr3D 100.000 36 0 0 59 94 434206419 434206454 3.610000e-07 67.6
7 TraesCS3D01G404800 chr3A 96.896 5445 116 20 149 5576 654321099 654315691 0.000000e+00 9070.0
8 TraesCS3D01G404800 chr3A 100.000 60 0 0 1 60 704053140 704053199 1.640000e-20 111.0
9 TraesCS3D01G404800 chr3B 95.438 1666 68 5 3110 4771 683429456 683427795 0.000000e+00 2649.0
10 TraesCS3D01G404800 chr3B 96.285 1615 42 6 1480 3086 683431149 683429545 0.000000e+00 2634.0
11 TraesCS3D01G404800 chr3B 95.461 1344 45 7 155 1482 683432788 683431445 0.000000e+00 2130.0
12 TraesCS3D01G404800 chr3B 94.263 767 40 2 3110 3875 683513565 683512802 0.000000e+00 1170.0
13 TraesCS3D01G404800 chr3B 93.620 768 45 3 3110 3875 683828683 683827918 0.000000e+00 1144.0
14 TraesCS3D01G404800 chr3B 89.235 706 63 3 3221 3926 683827618 683826926 0.000000e+00 870.0
15 TraesCS3D01G404800 chr3B 88.701 708 63 5 3221 3926 683365988 683365296 0.000000e+00 848.0
16 TraesCS3D01G404800 chr3B 88.669 706 67 2 3221 3926 683512505 683511813 0.000000e+00 848.0
17 TraesCS3D01G404800 chr3B 95.054 465 18 2 5112 5576 683425249 683424790 0.000000e+00 726.0
18 TraesCS3D01G404800 chr3B 93.220 413 27 1 3463 3875 683366698 683366287 1.720000e-169 606.0
19 TraesCS3D01G404800 chr3B 94.879 371 19 0 3110 3480 683367248 683366878 1.040000e-161 580.0
20 TraesCS3D01G404800 chr3B 95.522 134 5 1 2914 3046 683829242 683829109 4.380000e-51 213.0
21 TraesCS3D01G404800 chr3B 89.143 175 11 2 2880 3046 683514095 683513921 1.570000e-50 211.0
22 TraesCS3D01G404800 chr3B 93.458 107 7 0 2940 3046 683367780 683367674 5.780000e-35 159.0
23 TraesCS3D01G404800 chr3B 96.875 32 1 0 3055 3086 683828803 683828772 3.000000e-03 54.7
24 TraesCS3D01G404800 chr7D 92.837 712 46 3 3911 4619 45680383 45679674 0.000000e+00 1027.0
25 TraesCS3D01G404800 chr7D 89.662 532 49 4 3385 3915 45696048 45695522 0.000000e+00 673.0
26 TraesCS3D01G404800 chr5B 82.527 1219 143 33 1010 2186 673460927 673462117 0.000000e+00 1007.0
27 TraesCS3D01G404800 chr5B 96.012 326 11 1 114 439 673592123 673591800 3.830000e-146 529.0
28 TraesCS3D01G404800 chr5B 91.700 253 15 3 114 362 76925985 76926235 4.140000e-91 346.0
29 TraesCS3D01G404800 chr5B 98.230 113 2 0 327 439 95839007 95838895 1.230000e-46 198.0
30 TraesCS3D01G404800 chr7A 93.449 519 26 5 3911 4429 47876315 47875805 0.000000e+00 763.0
31 TraesCS3D01G404800 chr7A 91.525 531 45 0 3385 3915 47897871 47897341 0.000000e+00 732.0
32 TraesCS3D01G404800 chr7A 95.833 192 8 0 145 336 114077788 114077979 1.510000e-80 311.0
33 TraesCS3D01G404800 chr7A 98.333 60 1 0 1 60 434761132 434761073 7.640000e-19 106.0
34 TraesCS3D01G404800 chr4A 89.118 533 53 4 3385 3915 658894973 658894444 0.000000e+00 658.0
35 TraesCS3D01G404800 chr4A 92.551 443 31 2 3921 4362 658881730 658881289 7.880000e-178 634.0
36 TraesCS3D01G404800 chr4A 92.691 301 12 6 114 412 92967936 92967644 5.160000e-115 425.0
37 TraesCS3D01G404800 chr4A 92.647 204 15 0 3911 4114 658882118 658881915 1.520000e-75 294.0
38 TraesCS3D01G404800 chr4A 92.268 194 15 0 3921 4114 658881919 658881726 5.500000e-70 276.0
39 TraesCS3D01G404800 chr4A 100.000 60 0 0 1 60 92967992 92967933 1.640000e-20 111.0
40 TraesCS3D01G404800 chr4A 98.333 60 1 0 1 60 393373251 393373192 7.640000e-19 106.0
41 TraesCS3D01G404800 chr4A 89.362 47 4 1 1798 1844 637320086 637320041 2.170000e-04 58.4
42 TraesCS3D01G404800 chr4A 89.362 47 4 1 1798 1844 637456701 637456656 2.170000e-04 58.4
43 TraesCS3D01G404800 chr4B 95.137 329 13 2 114 439 670735403 670735075 2.980000e-142 516.0
44 TraesCS3D01G404800 chr4B 98.305 118 1 1 327 443 613852198 613852315 7.320000e-49 206.0
45 TraesCS3D01G404800 chr4B 98.333 60 1 0 1 60 670735459 670735400 7.640000e-19 106.0
46 TraesCS3D01G404800 chr4B 100.000 28 0 0 94 121 591904840 591904813 1.000000e-02 52.8
47 TraesCS3D01G404800 chr7B 95.092 326 12 2 114 439 676733701 676733380 1.390000e-140 510.0
48 TraesCS3D01G404800 chr7B 100.000 60 0 0 1 60 676733757 676733698 1.640000e-20 111.0
49 TraesCS3D01G404800 chr7B 100.000 36 0 0 59 94 439589901 439589936 3.610000e-07 67.6
50 TraesCS3D01G404800 chr7B 89.091 55 4 2 41 94 743365519 743365572 3.610000e-07 67.6
51 TraesCS3D01G404800 chr7B 89.091 55 4 2 41 94 743378982 743379035 3.610000e-07 67.6
52 TraesCS3D01G404800 chr7B 89.091 55 4 2 41 94 743380660 743380713 3.610000e-07 67.6
53 TraesCS3D01G404800 chr7B 88.889 54 4 2 41 93 743371816 743371868 1.300000e-06 65.8
54 TraesCS3D01G404800 chr2A 95.222 293 8 3 114 406 76049539 76049825 5.090000e-125 459.0
55 TraesCS3D01G404800 chr2A 78.977 176 21 9 1612 1773 49325093 49324920 7.640000e-19 106.0
56 TraesCS3D01G404800 chr5A 81.796 412 45 12 1374 1765 495585263 495585664 9.010000e-83 318.0
57 TraesCS3D01G404800 chr5A 98.333 60 1 0 1 60 676251083 676251142 7.640000e-19 106.0
58 TraesCS3D01G404800 chr5A 77.895 190 24 11 1609 1784 444552859 444553044 9.880000e-18 102.0
59 TraesCS3D01G404800 chr2D 80.456 307 47 13 812 1110 561957664 561957363 7.270000e-54 222.0
60 TraesCS3D01G404800 chr5D 88.806 134 13 2 2437 2569 563593871 563594003 4.470000e-36 163.0
61 TraesCS3D01G404800 chr6A 100.000 60 0 0 1 60 26251148 26251207 1.640000e-20 111.0
62 TraesCS3D01G404800 chr1A 100.000 60 0 0 1 60 53433360 53433301 1.640000e-20 111.0
63 TraesCS3D01G404800 chrUn 100.000 37 0 0 58 94 266834831 266834795 1.000000e-07 69.4
64 TraesCS3D01G404800 chr6B 100.000 36 0 0 59 94 719865972 719866007 3.610000e-07 67.6
65 TraesCS3D01G404800 chr6B 100.000 33 0 0 62 94 570198020 570197988 1.680000e-05 62.1
66 TraesCS3D01G404800 chr6D 100.000 28 0 0 95 122 433724321 433724294 1.000000e-02 52.8


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 TraesCS3D01G404800 chr3D 519247031 519252606 5575 True 10298.000000 10298 100.000000 1 5576 1 chr3D.!!$R1 5575
1 TraesCS3D01G404800 chr3D 24060920 24061755 835 False 640.000000 640 80.765000 726 1578 1 chr3D.!!$F1 852
2 TraesCS3D01G404800 chr3D 519314944 519316369 1425 True 215.500000 344 92.766500 2807 3352 4 chr3D.!!$R2 545
3 TraesCS3D01G404800 chr3A 654315691 654321099 5408 True 9070.000000 9070 96.896000 149 5576 1 chr3A.!!$R1 5427
4 TraesCS3D01G404800 chr3B 683424790 683432788 7998 True 2034.750000 2649 95.559500 155 5576 4 chr3B.!!$R2 5421
5 TraesCS3D01G404800 chr3B 683511813 683514095 2282 True 743.000000 1170 90.691667 2880 3926 3 chr3B.!!$R3 1046
6 TraesCS3D01G404800 chr3B 683826926 683829242 2316 True 570.425000 1144 93.813000 2914 3926 4 chr3B.!!$R4 1012
7 TraesCS3D01G404800 chr3B 683365296 683367780 2484 True 548.250000 848 92.564500 2940 3926 4 chr3B.!!$R1 986
8 TraesCS3D01G404800 chr7D 45679674 45680383 709 True 1027.000000 1027 92.837000 3911 4619 1 chr7D.!!$R1 708
9 TraesCS3D01G404800 chr7D 45695522 45696048 526 True 673.000000 673 89.662000 3385 3915 1 chr7D.!!$R2 530
10 TraesCS3D01G404800 chr5B 673460927 673462117 1190 False 1007.000000 1007 82.527000 1010 2186 1 chr5B.!!$F2 1176
11 TraesCS3D01G404800 chr7A 47875805 47876315 510 True 763.000000 763 93.449000 3911 4429 1 chr7A.!!$R1 518
12 TraesCS3D01G404800 chr7A 47897341 47897871 530 True 732.000000 732 91.525000 3385 3915 1 chr7A.!!$R2 530
13 TraesCS3D01G404800 chr4A 658894444 658894973 529 True 658.000000 658 89.118000 3385 3915 1 chr4A.!!$R4 530
14 TraesCS3D01G404800 chr4A 658881289 658882118 829 True 401.333333 634 92.488667 3911 4362 3 chr4A.!!$R6 451

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
873 886 1.070601 GAACCTTTTGTGCCCAGCAAT 59.929 47.619 0.00 0.00 41.47 3.56 F
879 892 2.706339 TTGTGCCCAGCAATTTTGTT 57.294 40.000 0.00 0.00 41.47 2.83 F
1854 2207 2.607635 CGTGTGCAACTCACTGTAAGTT 59.392 45.455 4.63 0.00 41.86 2.66 F
3777 6177 0.580104 GCGCGTTTTACAGTGACACT 59.420 50.000 8.43 1.07 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2207 2.423290 TACGCTGTAACTGCCGTGCA 62.423 55.000 0.00 0.0 36.92 4.57 R
2773 3170 4.588951 ACAATCTCTGGTCTTACACAGTCA 59.411 41.667 0.00 0.0 36.17 3.41 R
3789 6189 0.040058 AGCCACATGAGCATTTGGGA 59.960 50.000 15.31 0.0 38.69 4.37 R
5391 10404 0.603707 CTGTCCAACCACGATGCACT 60.604 55.000 0.00 0.0 0.00 4.40 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
21 22 2.742589 GAGTGCAGGTAGTGTTTTAGCC 59.257 50.000 0.00 0.00 0.00 3.93
23 24 2.882137 GTGCAGGTAGTGTTTTAGCCAA 59.118 45.455 0.00 0.00 0.00 4.52
24 25 3.316868 GTGCAGGTAGTGTTTTAGCCAAA 59.683 43.478 0.00 0.00 0.00 3.28
26 27 3.305131 GCAGGTAGTGTTTTAGCCAAACC 60.305 47.826 6.65 0.00 43.87 3.27
27 28 4.142038 CAGGTAGTGTTTTAGCCAAACCT 58.858 43.478 6.65 6.18 43.87 3.50
29 30 3.504906 GGTAGTGTTTTAGCCAAACCTCC 59.495 47.826 6.65 1.84 43.87 4.30
30 31 2.594131 AGTGTTTTAGCCAAACCTCCC 58.406 47.619 6.65 0.00 43.87 4.30
52 53 6.107901 CCCCCTCTGAACTCATCTATTTAG 57.892 45.833 0.00 0.00 0.00 1.85
56 57 7.016072 CCCCTCTGAACTCATCTATTTAGTCAT 59.984 40.741 0.00 0.00 0.00 3.06
67 68 9.702253 TCATCTATTTAGTCATATACTCCCTCC 57.298 37.037 0.00 0.00 39.80 4.30
68 69 8.625651 CATCTATTTAGTCATATACTCCCTCCG 58.374 40.741 0.00 0.00 39.80 4.63
70 71 8.168725 TCTATTTAGTCATATACTCCCTCCGTT 58.831 37.037 0.00 0.00 39.80 4.44
72 73 7.427989 TTTAGTCATATACTCCCTCCGTTTT 57.572 36.000 0.00 0.00 39.80 2.43
73 74 5.277857 AGTCATATACTCCCTCCGTTTTG 57.722 43.478 0.00 0.00 30.33 2.44
74 75 4.960469 AGTCATATACTCCCTCCGTTTTGA 59.040 41.667 0.00 0.00 30.33 2.69
75 76 5.602978 AGTCATATACTCCCTCCGTTTTGAT 59.397 40.000 0.00 0.00 30.33 2.57
76 77 6.099845 AGTCATATACTCCCTCCGTTTTGATT 59.900 38.462 0.00 0.00 30.33 2.57
77 78 6.766467 GTCATATACTCCCTCCGTTTTGATTT 59.234 38.462 0.00 0.00 0.00 2.17
78 79 7.929785 GTCATATACTCCCTCCGTTTTGATTTA 59.070 37.037 0.00 0.00 0.00 1.40
79 80 7.929785 TCATATACTCCCTCCGTTTTGATTTAC 59.070 37.037 0.00 0.00 0.00 2.01
80 81 4.635699 ACTCCCTCCGTTTTGATTTACT 57.364 40.909 0.00 0.00 0.00 2.24
81 82 4.576879 ACTCCCTCCGTTTTGATTTACTC 58.423 43.478 0.00 0.00 0.00 2.59
84 85 3.370061 CCCTCCGTTTTGATTTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
85 86 3.060363 CCTCCGTTTTGATTTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
86 87 3.641648 TCCGTTTTGATTTACTCGTCGT 58.358 40.909 0.00 0.00 0.00 4.34
87 88 3.426191 TCCGTTTTGATTTACTCGTCGTG 59.574 43.478 0.00 0.00 0.00 4.35
89 90 3.182972 CGTTTTGATTTACTCGTCGTGGT 59.817 43.478 0.00 0.00 0.00 4.16
91 92 5.504392 GTTTTGATTTACTCGTCGTGGTTT 58.496 37.500 0.00 0.00 0.00 3.27
92 93 5.738118 TTTGATTTACTCGTCGTGGTTTT 57.262 34.783 0.00 0.00 0.00 2.43
93 94 6.841443 TTTGATTTACTCGTCGTGGTTTTA 57.159 33.333 0.00 0.00 0.00 1.52
96 97 8.531622 TTGATTTACTCGTCGTGGTTTTATAA 57.468 30.769 0.00 0.00 0.00 0.98
97 98 8.531622 TGATTTACTCGTCGTGGTTTTATAAA 57.468 30.769 0.00 0.00 0.00 1.40
99 100 9.628983 GATTTACTCGTCGTGGTTTTATAAATC 57.371 33.333 0.00 0.00 32.48 2.17
101 102 4.563976 ACTCGTCGTGGTTTTATAAATCGG 59.436 41.667 0.00 0.00 0.00 4.18
104 105 5.062058 TCGTCGTGGTTTTATAAATCGGAAC 59.938 40.000 0.00 0.00 0.00 3.62
123 124 6.210287 GGAACGGAGGGAGTATATATGAAG 57.790 45.833 0.00 0.00 0.00 3.02
124 125 5.394333 GGAACGGAGGGAGTATATATGAAGC 60.394 48.000 0.00 0.00 0.00 3.86
126 127 5.084519 ACGGAGGGAGTATATATGAAGCAA 58.915 41.667 0.00 0.00 0.00 3.91
127 128 5.047235 ACGGAGGGAGTATATATGAAGCAAC 60.047 44.000 0.00 0.00 0.00 4.17
128 129 5.624738 CGGAGGGAGTATATATGAAGCAACC 60.625 48.000 0.00 0.00 0.00 3.77
129 130 5.248477 GGAGGGAGTATATATGAAGCAACCA 59.752 44.000 0.00 0.00 0.00 3.67
134 135 7.885399 GGGAGTATATATGAAGCAACCAAATCT 59.115 37.037 0.00 0.00 0.00 2.40
135 136 8.725148 GGAGTATATATGAAGCAACCAAATCTG 58.275 37.037 0.00 0.00 0.00 2.90
254 260 3.793801 GCACAAATAGTTGTTGCAACGGA 60.794 43.478 23.79 12.77 46.01 4.69
289 295 5.060662 TCGATGCTCACACTATATTAGGC 57.939 43.478 0.00 0.00 0.00 3.93
663 669 8.856490 ACAATGTGATTCAAACTGTAAAACTC 57.144 30.769 0.00 0.00 0.00 3.01
690 701 9.605275 TGATCTTCTACTGTAATTGAAGAATGG 57.395 33.333 16.88 0.00 45.01 3.16
873 886 1.070601 GAACCTTTTGTGCCCAGCAAT 59.929 47.619 0.00 0.00 41.47 3.56
879 892 2.706339 TTGTGCCCAGCAATTTTGTT 57.294 40.000 0.00 0.00 41.47 2.83
905 922 9.161629 TGTTTATGATTCATATGAGTTGTCGTT 57.838 29.630 5.39 0.00 0.00 3.85
1033 1051 7.989826 ACTATTTGTAGATGATGGCAACTTTC 58.010 34.615 0.00 0.00 37.61 2.62
1096 1116 6.770785 TGCTATTTGTTTACTTGAGTCCTTGT 59.229 34.615 0.00 0.00 0.00 3.16
1150 1174 4.461198 CACCTTCCTTTGGTTTACAGTCT 58.539 43.478 0.00 0.00 35.28 3.24
1854 2207 2.607635 CGTGTGCAACTCACTGTAAGTT 59.392 45.455 4.63 0.00 41.86 2.66
1895 2248 8.714179 GCGTACTTTTTAGGGCAATTTTATTTT 58.286 29.630 0.00 0.00 0.00 1.82
2764 3158 5.104485 ACCTCTGTAAGACCAGAACTGTTTT 60.104 40.000 0.00 0.00 38.67 2.43
2765 3159 5.823045 CCTCTGTAAGACCAGAACTGTTTTT 59.177 40.000 0.00 0.00 38.67 1.94
2851 3248 8.974060 ACCAAGTTAACATTTTTACTCAGAGA 57.026 30.769 8.61 0.00 0.00 3.10
3086 4276 2.413112 CAGGCATGAGACTGTACGTTTG 59.587 50.000 0.00 0.00 46.28 2.93
3087 4277 2.037251 AGGCATGAGACTGTACGTTTGT 59.963 45.455 0.00 0.00 0.00 2.83
3089 4279 6.853398 CAGGCATGAGACTGTACGTTTGTAC 61.853 48.000 0.00 0.00 46.28 2.90
3161 4418 4.946157 CAGGCTGAGGTTTCACTATTCAAT 59.054 41.667 9.42 0.00 0.00 2.57
3191 4448 2.672651 CGCCACATTCAGCCACCA 60.673 61.111 0.00 0.00 0.00 4.17
3245 4505 3.389329 AGGAGGTAATCTGGTATGTGCAG 59.611 47.826 0.00 0.00 0.00 4.41
3581 5038 3.904339 AGTTCACTACACCAGATGGAAGT 59.096 43.478 5.72 6.43 38.94 3.01
3722 6122 5.597182 TGACTTGTACCTACTCACAGTTTCT 59.403 40.000 0.00 0.00 0.00 2.52
3726 6126 1.961394 ACCTACTCACAGTTTCTCGCA 59.039 47.619 0.00 0.00 0.00 5.10
3777 6177 0.580104 GCGCGTTTTACAGTGACACT 59.420 50.000 8.43 1.07 0.00 3.55
3785 6185 6.193959 GCGTTTTACAGTGACACTTTTGTTAG 59.806 38.462 5.04 0.00 35.47 2.34
3789 6189 4.261801 ACAGTGACACTTTTGTTAGCTGT 58.738 39.130 5.04 0.00 37.39 4.40
3847 6248 3.618690 AACCAGGAATCTGTGTAGAGC 57.381 47.619 0.00 0.00 39.31 4.09
3930 6331 5.365025 AGTTATCTGACAGTGGATGCTACAT 59.635 40.000 1.59 0.00 0.00 2.29
4251 7030 5.732331 TCCCTGGACAATTGATATTCCTT 57.268 39.130 13.59 0.00 0.00 3.36
4252 7031 5.448654 TCCCTGGACAATTGATATTCCTTG 58.551 41.667 13.59 6.04 0.00 3.61
4522 7304 0.801872 CGCATCCACGAAATCAACCA 59.198 50.000 0.00 0.00 34.06 3.67
4608 7393 6.780457 AGGTGCATTATTAAGACATGCTTT 57.220 33.333 14.20 0.00 43.22 3.51
4778 7564 0.736325 CCGTCGTAGGCCTGAAGTTG 60.736 60.000 17.99 0.14 0.00 3.16
5031 7817 2.742348 TGGCGATAACTCACTTAGGGA 58.258 47.619 0.00 0.00 0.00 4.20
5105 7891 5.069119 AGCTAAGGTTTTTGAAGAAGGTTGG 59.931 40.000 0.00 0.00 0.00 3.77
5174 10183 0.109272 GGGCCGAGCTTAAAACTTGC 60.109 55.000 0.00 0.00 0.00 4.01
5186 10195 5.691754 GCTTAAAACTTGCTGTGCTAATGTT 59.308 36.000 0.00 0.00 0.00 2.71
5419 10432 1.072331 GTGGTTGGACAGGTGATGAGT 59.928 52.381 0.00 0.00 0.00 3.41
5496 10509 4.700213 AGTGTAGCCAAATATGTGTGGAAC 59.300 41.667 2.15 0.54 37.03 3.62
5543 10556 7.116075 TGTAATGTGATGCCTGGTAAAATAGT 58.884 34.615 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.742589 GGCTAAAACACTACCTGCACTC 59.257 50.000 0.00 0.00 0.00 3.51
1 2 2.105821 TGGCTAAAACACTACCTGCACT 59.894 45.455 0.00 0.00 0.00 4.40
2 3 2.500229 TGGCTAAAACACTACCTGCAC 58.500 47.619 0.00 0.00 0.00 4.57
3 4 2.940994 TGGCTAAAACACTACCTGCA 57.059 45.000 0.00 0.00 0.00 4.41
4 5 3.897325 GTTTGGCTAAAACACTACCTGC 58.103 45.455 0.00 0.00 46.30 4.85
13 14 1.263356 GGGGGAGGTTTGGCTAAAAC 58.737 55.000 1.70 1.70 46.32 2.43
29 30 5.604650 ACTAAATAGATGAGTTCAGAGGGGG 59.395 44.000 0.00 0.00 0.00 5.40
30 31 6.325028 TGACTAAATAGATGAGTTCAGAGGGG 59.675 42.308 0.00 0.00 0.00 4.79
41 42 9.702253 GGAGGGAGTATATGACTAAATAGATGA 57.298 37.037 0.00 0.00 39.06 2.92
42 43 8.625651 CGGAGGGAGTATATGACTAAATAGATG 58.374 40.741 0.00 0.00 39.06 2.90
45 46 7.941431 ACGGAGGGAGTATATGACTAAATAG 57.059 40.000 0.00 0.00 39.06 1.73
46 47 8.716674 AAACGGAGGGAGTATATGACTAAATA 57.283 34.615 0.00 0.00 39.06 1.40
47 48 7.613551 AAACGGAGGGAGTATATGACTAAAT 57.386 36.000 0.00 0.00 39.06 1.40
48 49 7.124599 TCAAAACGGAGGGAGTATATGACTAAA 59.875 37.037 0.00 0.00 39.06 1.85
49 50 6.608405 TCAAAACGGAGGGAGTATATGACTAA 59.392 38.462 0.00 0.00 39.06 2.24
50 51 6.131264 TCAAAACGGAGGGAGTATATGACTA 58.869 40.000 0.00 0.00 39.06 2.59
51 52 4.960469 TCAAAACGGAGGGAGTATATGACT 59.040 41.667 0.00 0.00 42.90 3.41
52 53 5.272283 TCAAAACGGAGGGAGTATATGAC 57.728 43.478 0.00 0.00 0.00 3.06
56 57 7.427989 AGTAAATCAAAACGGAGGGAGTATA 57.572 36.000 0.00 0.00 0.00 1.47
58 59 5.622914 CGAGTAAATCAAAACGGAGGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
59 60 4.576879 GAGTAAATCAAAACGGAGGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
61 62 3.007182 ACGAGTAAATCAAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
62 63 3.332034 ACGAGTAAATCAAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
63 64 3.060363 CGACGAGTAAATCAAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
64 65 3.671928 ACGACGAGTAAATCAAAACGGAG 59.328 43.478 0.00 0.00 0.00 4.63
65 66 3.426191 CACGACGAGTAAATCAAAACGGA 59.574 43.478 0.00 0.00 0.00 4.69
66 67 3.422603 CCACGACGAGTAAATCAAAACGG 60.423 47.826 0.00 0.00 0.00 4.44
67 68 3.182972 ACCACGACGAGTAAATCAAAACG 59.817 43.478 0.00 0.00 0.00 3.60
68 69 4.720530 ACCACGACGAGTAAATCAAAAC 57.279 40.909 0.00 0.00 0.00 2.43
70 71 5.738118 AAAACCACGACGAGTAAATCAAA 57.262 34.783 0.00 0.00 0.00 2.69
72 73 8.531622 TTTATAAAACCACGACGAGTAAATCA 57.468 30.769 0.00 0.00 0.00 2.57
73 74 9.628983 GATTTATAAAACCACGACGAGTAAATC 57.371 33.333 0.00 5.16 32.39 2.17
74 75 8.323140 CGATTTATAAAACCACGACGAGTAAAT 58.677 33.333 0.00 0.00 0.00 1.40
75 76 7.201427 CCGATTTATAAAACCACGACGAGTAAA 60.201 37.037 0.00 0.00 0.00 2.01
76 77 6.253298 CCGATTTATAAAACCACGACGAGTAA 59.747 38.462 0.00 0.00 0.00 2.24
77 78 5.743398 CCGATTTATAAAACCACGACGAGTA 59.257 40.000 0.00 0.00 0.00 2.59
78 79 4.563976 CCGATTTATAAAACCACGACGAGT 59.436 41.667 0.00 0.00 0.00 4.18
79 80 4.799949 TCCGATTTATAAAACCACGACGAG 59.200 41.667 0.00 0.00 0.00 4.18
80 81 4.742417 TCCGATTTATAAAACCACGACGA 58.258 39.130 0.00 0.00 0.00 4.20
81 82 5.250332 GTTCCGATTTATAAAACCACGACG 58.750 41.667 1.21 0.00 0.00 5.12
84 85 4.329528 TCCGTTCCGATTTATAAAACCACG 59.670 41.667 1.21 7.13 0.00 4.94
85 86 5.220719 CCTCCGTTCCGATTTATAAAACCAC 60.221 44.000 1.21 0.00 0.00 4.16
86 87 4.877251 CCTCCGTTCCGATTTATAAAACCA 59.123 41.667 1.21 0.00 0.00 3.67
87 88 4.274214 CCCTCCGTTCCGATTTATAAAACC 59.726 45.833 1.21 0.00 0.00 3.27
89 90 5.104817 ACTCCCTCCGTTCCGATTTATAAAA 60.105 40.000 1.21 0.00 0.00 1.52
91 92 3.962718 ACTCCCTCCGTTCCGATTTATAA 59.037 43.478 0.00 0.00 0.00 0.98
92 93 3.569491 ACTCCCTCCGTTCCGATTTATA 58.431 45.455 0.00 0.00 0.00 0.98
93 94 2.395619 ACTCCCTCCGTTCCGATTTAT 58.604 47.619 0.00 0.00 0.00 1.40
96 97 2.083628 ATACTCCCTCCGTTCCGATT 57.916 50.000 0.00 0.00 0.00 3.34
97 98 2.965671 TATACTCCCTCCGTTCCGAT 57.034 50.000 0.00 0.00 0.00 4.18
99 100 4.267536 TCATATATACTCCCTCCGTTCCG 58.732 47.826 0.00 0.00 0.00 4.30
101 102 5.185249 TGCTTCATATATACTCCCTCCGTTC 59.815 44.000 0.00 0.00 0.00 3.95
104 105 5.411781 GTTGCTTCATATATACTCCCTCCG 58.588 45.833 0.00 0.00 0.00 4.63
106 107 6.360370 TGGTTGCTTCATATATACTCCCTC 57.640 41.667 0.00 0.00 0.00 4.30
107 108 6.763715 TTGGTTGCTTCATATATACTCCCT 57.236 37.500 0.00 0.00 0.00 4.20
109 110 8.725148 CAGATTTGGTTGCTTCATATATACTCC 58.275 37.037 0.00 0.00 0.00 3.85
110 111 9.277783 ACAGATTTGGTTGCTTCATATATACTC 57.722 33.333 0.00 0.00 0.00 2.59
111 112 9.632638 AACAGATTTGGTTGCTTCATATATACT 57.367 29.630 0.00 0.00 0.00 2.12
128 129 2.038659 ACCCACACCCAAACAGATTTG 58.961 47.619 0.00 0.00 44.19 2.32
129 130 2.038659 CACCCACACCCAAACAGATTT 58.961 47.619 0.00 0.00 0.00 2.17
134 135 0.967887 CACACACCCACACCCAAACA 60.968 55.000 0.00 0.00 0.00 2.83
135 136 0.968393 ACACACACCCACACCCAAAC 60.968 55.000 0.00 0.00 0.00 2.93
140 141 1.377987 ACACACACACACCCACACC 60.378 57.895 0.00 0.00 0.00 4.16
141 142 0.958382 ACACACACACACACCCACAC 60.958 55.000 0.00 0.00 0.00 3.82
142 143 0.957888 CACACACACACACACCCACA 60.958 55.000 0.00 0.00 0.00 4.17
143 144 0.958382 ACACACACACACACACCCAC 60.958 55.000 0.00 0.00 0.00 4.61
145 146 0.885196 AAACACACACACACACACCC 59.115 50.000 0.00 0.00 0.00 4.61
146 147 1.975837 CAAACACACACACACACACC 58.024 50.000 0.00 0.00 0.00 4.16
254 260 4.631813 GTGAGCATCGAAAGTTCCAATAGT 59.368 41.667 0.00 0.00 38.61 2.12
289 295 9.128107 CATAACACCAAGCTAAACATTAAACAG 57.872 33.333 0.00 0.00 0.00 3.16
478 484 9.027129 TGTAATTTATAGTAGCTTTACAGTGCG 57.973 33.333 0.00 0.00 0.00 5.34
810 822 8.617809 GTTTCAAAAGTTGATACTACAGGAACA 58.382 33.333 4.84 0.00 39.84 3.18
879 892 8.716646 ACGACAACTCATATGAATCATAAACA 57.283 30.769 7.07 0.00 29.74 2.83
1033 1051 9.462174 CATATAGAACTTCAGTAGAGCTTTCTG 57.538 37.037 2.51 5.00 0.00 3.02
1854 2207 2.423290 TACGCTGTAACTGCCGTGCA 62.423 55.000 0.00 0.00 36.92 4.57
1895 2248 4.608948 ACCAACCAAACAAAGACAAACA 57.391 36.364 0.00 0.00 0.00 2.83
2081 2471 8.671384 TGTAAATTAGTGTAAGTTTGTCAGCT 57.329 30.769 0.00 0.00 0.00 4.24
2401 2795 5.701290 ACACTACAAGTCCACTAAGATTTGC 59.299 40.000 0.00 0.00 37.07 3.68
2402 2796 8.827177 TTACACTACAAGTCCACTAAGATTTG 57.173 34.615 0.00 0.00 38.89 2.32
2773 3170 4.588951 ACAATCTCTGGTCTTACACAGTCA 59.411 41.667 0.00 0.00 36.17 3.41
2851 3248 8.920509 AGTAAAAAGTAAAAATGCTTTCGTGT 57.079 26.923 0.00 0.00 34.26 4.49
2884 3317 1.297456 GCTCCTGCAGAGAACAGCAC 61.297 60.000 17.39 0.00 46.50 4.40
3082 4272 7.892609 AGGATAAACAATGGAAAGGTACAAAC 58.107 34.615 0.00 0.00 0.00 2.93
3086 4276 7.067129 GGAAGAGGATAAACAATGGAAAGGTAC 59.933 40.741 0.00 0.00 0.00 3.34
3087 4277 7.116736 GGAAGAGGATAAACAATGGAAAGGTA 58.883 38.462 0.00 0.00 0.00 3.08
3089 4279 5.951747 TGGAAGAGGATAAACAATGGAAAGG 59.048 40.000 0.00 0.00 0.00 3.11
3090 4280 7.466746 TTGGAAGAGGATAAACAATGGAAAG 57.533 36.000 0.00 0.00 0.00 2.62
3091 4281 7.847711 TTTGGAAGAGGATAAACAATGGAAA 57.152 32.000 0.00 0.00 0.00 3.13
3094 4284 6.044682 GCATTTGGAAGAGGATAAACAATGG 58.955 40.000 0.00 0.00 0.00 3.16
3095 4285 6.755141 CAGCATTTGGAAGAGGATAAACAATG 59.245 38.462 0.00 0.00 0.00 2.82
3097 4287 6.009589 TCAGCATTTGGAAGAGGATAAACAA 58.990 36.000 0.00 0.00 0.00 2.83
3161 4418 0.899019 TGTGGCGGTACTGCTGATAA 59.101 50.000 25.32 5.44 34.52 1.75
3191 4448 2.370445 CCACCCGAGCTTCCATCCT 61.370 63.158 0.00 0.00 0.00 3.24
3245 4505 1.901085 CTCTGTAGCCTGTCCACCC 59.099 63.158 0.00 0.00 0.00 4.61
3581 5038 2.912956 ACTGTGGGCTTGAGATTTCCTA 59.087 45.455 0.00 0.00 0.00 2.94
3777 6177 3.640967 AGCATTTGGGACAGCTAACAAAA 59.359 39.130 7.91 0.00 42.39 2.44
3785 6185 1.135199 CACATGAGCATTTGGGACAGC 60.135 52.381 0.00 0.00 42.39 4.40
3789 6189 0.040058 AGCCACATGAGCATTTGGGA 59.960 50.000 15.31 0.00 38.69 4.37
3997 6587 2.497675 GAGTAGTGCATTGGACCAGAGA 59.502 50.000 4.52 0.00 0.00 3.10
4274 7056 3.706698 TCTGCGATAAGAGGATTTGTCG 58.293 45.455 0.00 1.36 42.32 4.35
4522 7304 5.825593 ACCAATGGGACGATAACTGATAT 57.174 39.130 3.55 0.00 38.05 1.63
4608 7393 6.585695 AGTCGACCATGAAAACTAGACTAA 57.414 37.500 13.01 0.00 36.15 2.24
4657 7442 1.333169 CGATGAAATGATTCCGGTGCG 60.333 52.381 0.00 0.00 34.49 5.34
4778 7564 6.887376 TGTTATCTCAAGCGTCATAGTTTC 57.113 37.500 0.00 0.00 0.00 2.78
5105 7891 6.922407 GGACTCTACGAAATCTAATACAACCC 59.078 42.308 0.00 0.00 0.00 4.11
5208 10217 5.938125 TCTTAGTCAAAAGCCATCTACAACC 59.062 40.000 0.00 0.00 0.00 3.77
5342 10351 7.195374 ACTGTCCATAAAAGTAAGCCATAGA 57.805 36.000 0.00 0.00 0.00 1.98
5343 10352 9.561069 AATACTGTCCATAAAAGTAAGCCATAG 57.439 33.333 0.00 0.00 30.61 2.23
5344 10353 9.555727 GAATACTGTCCATAAAAGTAAGCCATA 57.444 33.333 0.00 0.00 30.61 2.74
5345 10354 8.275040 AGAATACTGTCCATAAAAGTAAGCCAT 58.725 33.333 0.00 0.00 30.61 4.40
5346 10355 7.630082 AGAATACTGTCCATAAAAGTAAGCCA 58.370 34.615 0.00 0.00 30.61 4.75
5389 10402 1.337728 TGTCCAACCACGATGCACTAG 60.338 52.381 0.00 0.00 0.00 2.57
5390 10403 0.682292 TGTCCAACCACGATGCACTA 59.318 50.000 0.00 0.00 0.00 2.74
5391 10404 0.603707 CTGTCCAACCACGATGCACT 60.604 55.000 0.00 0.00 0.00 4.40
5392 10405 1.577328 CCTGTCCAACCACGATGCAC 61.577 60.000 0.00 0.00 0.00 4.57
5419 10432 8.338072 TCTTTACAAGAACAAAACCTACAACA 57.662 30.769 0.00 0.00 33.83 3.33
5496 10509 6.831769 ACAATCTAATGCACAAGAACTTACG 58.168 36.000 4.08 0.00 0.00 3.18
5543 10556 7.148086 ACGGCAAAATTCAATCATAAAGCTCTA 60.148 33.333 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.