Multiple sequence alignment - TraesCS2D01G499100

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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 TraesCS2D01G499100 chr2D 100.000 5882 0 0 1 5882 594187713 594193594 0.000000e+00 10863.0
1 TraesCS2D01G499100 chr2D 94.244 886 43 4 4968 5848 634587845 634586963 0.000000e+00 1347.0
2 TraesCS2D01G499100 chr2D 91.760 267 14 3 377 638 594147198 594147461 1.200000e-96 364.0
3 TraesCS2D01G499100 chr2D 86.207 261 33 3 85 342 594146937 594147197 4.490000e-71 279.0
4 TraesCS2D01G499100 chr2D 92.414 145 9 2 5737 5881 594383435 594383577 7.730000e-49 206.0
5 TraesCS2D01G499100 chr2D 79.621 211 30 11 4657 4857 595489639 595489432 7.950000e-29 139.0
6 TraesCS2D01G499100 chr2D 97.436 39 0 1 5844 5882 634586458 634586421 1.370000e-06 65.8
7 TraesCS2D01G499100 chr2B 94.009 3889 178 31 782 4640 721276646 721280509 0.000000e+00 5840.0
8 TraesCS2D01G499100 chr2B 96.364 715 18 4 4649 5360 721280553 721281262 0.000000e+00 1170.0
9 TraesCS2D01G499100 chr2B 94.398 357 10 4 405 755 721276089 721276441 1.860000e-149 540.0
10 TraesCS2D01G499100 chr2B 86.029 136 13 3 5583 5712 721285077 721285212 2.210000e-29 141.0
11 TraesCS2D01G499100 chr2A 93.546 3068 137 29 1452 4501 728773005 728776029 0.000000e+00 4512.0
12 TraesCS2D01G499100 chr2A 93.347 1007 52 7 4649 5642 728776404 728777408 0.000000e+00 1474.0
13 TraesCS2D01G499100 chr2A 90.344 1046 59 15 406 1446 728772048 728773056 0.000000e+00 1334.0
14 TraesCS2D01G499100 chr2A 80.409 342 35 19 93 421 728771700 728772022 1.270000e-56 231.0
15 TraesCS2D01G499100 chr2A 88.095 168 10 4 4482 4640 728776195 728776361 2.160000e-44 191.0
16 TraesCS2D01G499100 chr2A 84.138 145 21 2 5737 5881 728778282 728778424 7.950000e-29 139.0
17 TraesCS2D01G499100 chrUn 91.959 2450 143 22 692 3123 331036555 331038968 0.000000e+00 3384.0
18 TraesCS2D01G499100 chr6B 94.183 2080 109 6 725 2798 197736207 197738280 0.000000e+00 3160.0
19 TraesCS2D01G499100 chr6B 88.728 346 22 11 2787 3123 197738946 197739283 1.970000e-109 407.0
20 TraesCS2D01G499100 chr1D 94.130 920 45 5 4968 5882 415209929 415210844 0.000000e+00 1391.0
21 TraesCS2D01G499100 chr6D 94.022 920 46 5 4968 5882 110743124 110742209 0.000000e+00 1386.0
22 TraesCS2D01G499100 chr3D 93.890 802 42 3 5052 5848 405374724 405375523 0.000000e+00 1203.0
23 TraesCS2D01G499100 chr3D 97.436 39 0 1 5844 5882 405376028 405376065 1.370000e-06 65.8


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 TraesCS2D01G499100 chr2D 594187713 594193594 5881 False 10863.00 10863 100.000000 1 5882 1 chr2D.!!$F1 5881
1 TraesCS2D01G499100 chr2D 634586421 634587845 1424 True 706.40 1347 95.840000 4968 5882 2 chr2D.!!$R2 914
2 TraesCS2D01G499100 chr2D 594146937 594147461 524 False 321.50 364 88.983500 85 638 2 chr2D.!!$F3 553
3 TraesCS2D01G499100 chr2B 721276089 721285212 9123 False 1922.75 5840 92.700000 405 5712 4 chr2B.!!$F1 5307
4 TraesCS2D01G499100 chr2A 728771700 728778424 6724 False 1313.50 4512 88.313167 93 5881 6 chr2A.!!$F1 5788
5 TraesCS2D01G499100 chrUn 331036555 331038968 2413 False 3384.00 3384 91.959000 692 3123 1 chrUn.!!$F1 2431
6 TraesCS2D01G499100 chr6B 197736207 197739283 3076 False 1783.50 3160 91.455500 725 3123 2 chr6B.!!$F1 2398
7 TraesCS2D01G499100 chr1D 415209929 415210844 915 False 1391.00 1391 94.130000 4968 5882 1 chr1D.!!$F1 914
8 TraesCS2D01G499100 chr6D 110742209 110743124 915 True 1386.00 1386 94.022000 4968 5882 1 chr6D.!!$R1 914
9 TraesCS2D01G499100 chr3D 405374724 405376065 1341 False 634.40 1203 95.663000 5052 5882 2 chr3D.!!$F1 830

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
79 80 0.108520 TCCGTAACTCGTCAATGGCC 60.109 55.0 0.00 0.0 37.94 5.36 F
193 194 0.179004 TCAATCCAACACCCAACGCT 60.179 50.0 0.00 0.0 0.00 5.07 F
1277 1537 0.179020 TTGCACCAGGGAGTTCACAG 60.179 55.0 0.00 0.0 0.00 3.66 F
1308 1568 0.456221 CCTCTTACATGCTCGGACGT 59.544 55.0 0.00 0.0 0.00 4.34 F
2836 3776 0.370273 GCAGTGCAACGTTATCTCGG 59.630 55.0 11.09 0.0 45.86 4.63 F
3467 4418 2.223805 CCTTTTGAAGTCAAGGCCACAC 60.224 50.0 5.01 0.0 37.15 3.82 F
3899 4858 1.079503 GCTAACAGGAAGTTGAGCGG 58.920 55.0 0.00 0.0 41.50 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1728 0.107410 ACAGCAGAACCCGTTGACAA 60.107 50.000 0.00 0.0 0.00 3.18 R
1578 1838 1.071605 GCAACAACTCTCCAGCTACG 58.928 55.000 0.00 0.0 0.00 3.51 R
2718 2980 0.466189 ATAAGAGGGGCAATGCGGTG 60.466 55.000 0.00 0.0 0.00 4.94 R
3126 4077 1.125384 CGGTTCCGTGTTACATCAACG 59.875 52.381 2.82 0.0 40.26 4.10 R
3663 4614 0.036732 GCATCTCCAGTGTCCACCAA 59.963 55.000 0.00 0.0 0.00 3.67 R
4586 5741 1.072266 ACAAGGTAGGGCACAATCCA 58.928 50.000 0.00 0.0 0.00 3.41 R
5479 6688 0.608640 CTACCCACCAGTCCAGTGAC 59.391 60.000 0.00 0.0 42.09 3.67 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 3.931578 CCCATCCGATCCTGAAATCTAC 58.068 50.000 0.00 0.00 0.00 2.59
22 23 3.324846 CCCATCCGATCCTGAAATCTACA 59.675 47.826 0.00 0.00 0.00 2.74
23 24 4.202357 CCCATCCGATCCTGAAATCTACAA 60.202 45.833 0.00 0.00 0.00 2.41
24 25 4.993584 CCATCCGATCCTGAAATCTACAAG 59.006 45.833 0.00 0.00 0.00 3.16
25 26 4.060038 TCCGATCCTGAAATCTACAAGC 57.940 45.455 0.00 0.00 0.00 4.01
26 27 2.797156 CCGATCCTGAAATCTACAAGCG 59.203 50.000 0.00 0.00 0.00 4.68
27 28 3.448686 CGATCCTGAAATCTACAAGCGT 58.551 45.455 0.00 0.00 0.00 5.07
28 29 3.487574 CGATCCTGAAATCTACAAGCGTC 59.512 47.826 0.00 0.00 0.00 5.19
29 30 3.953712 TCCTGAAATCTACAAGCGTCA 57.046 42.857 0.00 0.00 0.00 4.35
30 31 4.265904 TCCTGAAATCTACAAGCGTCAA 57.734 40.909 0.00 0.00 0.00 3.18
31 32 4.245660 TCCTGAAATCTACAAGCGTCAAG 58.754 43.478 0.00 0.00 0.00 3.02
43 44 2.759783 CGTCAAGCATCCAGTGGAG 58.240 57.895 18.69 10.76 34.05 3.86
44 45 0.247460 CGTCAAGCATCCAGTGGAGA 59.753 55.000 18.69 5.97 34.05 3.71
45 46 1.134580 CGTCAAGCATCCAGTGGAGAT 60.135 52.381 18.69 5.80 34.05 2.75
46 47 2.559440 GTCAAGCATCCAGTGGAGATC 58.441 52.381 18.69 8.84 34.05 2.75
47 48 2.170187 GTCAAGCATCCAGTGGAGATCT 59.830 50.000 18.69 11.00 34.05 2.75
48 49 2.433604 TCAAGCATCCAGTGGAGATCTC 59.566 50.000 18.69 14.75 34.05 2.75
49 50 2.435069 CAAGCATCCAGTGGAGATCTCT 59.565 50.000 21.81 6.79 34.05 3.10
50 51 2.040939 AGCATCCAGTGGAGATCTCTG 58.959 52.381 21.81 10.77 34.05 3.35
51 52 1.070445 GCATCCAGTGGAGATCTCTGG 59.930 57.143 21.81 20.25 46.94 3.86
52 53 1.070445 CATCCAGTGGAGATCTCTGGC 59.930 57.143 21.81 12.06 45.67 4.85
53 54 1.039785 TCCAGTGGAGATCTCTGGCG 61.040 60.000 21.81 8.84 45.67 5.69
54 55 1.440893 CAGTGGAGATCTCTGGCGG 59.559 63.158 21.81 9.44 0.00 6.13
55 56 1.039785 CAGTGGAGATCTCTGGCGGA 61.040 60.000 21.81 0.00 0.00 5.54
56 57 0.754957 AGTGGAGATCTCTGGCGGAG 60.755 60.000 21.81 17.47 43.12 4.63
71 72 3.735181 GGAGCATTCCGTAACTCGT 57.265 52.632 0.00 0.00 37.94 4.18
72 73 1.557651 GGAGCATTCCGTAACTCGTC 58.442 55.000 0.00 0.00 37.94 4.20
73 74 1.135199 GGAGCATTCCGTAACTCGTCA 60.135 52.381 0.00 0.00 37.94 4.35
74 75 2.602878 GAGCATTCCGTAACTCGTCAA 58.397 47.619 0.00 0.00 37.94 3.18
75 76 3.187700 GAGCATTCCGTAACTCGTCAAT 58.812 45.455 0.00 0.00 37.94 2.57
76 77 2.930040 AGCATTCCGTAACTCGTCAATG 59.070 45.455 0.00 0.00 39.16 2.82
77 78 2.030457 GCATTCCGTAACTCGTCAATGG 59.970 50.000 0.00 0.00 37.87 3.16
78 79 1.717194 TTCCGTAACTCGTCAATGGC 58.283 50.000 0.00 0.00 37.94 4.40
79 80 0.108520 TCCGTAACTCGTCAATGGCC 60.109 55.000 0.00 0.00 37.94 5.36
80 81 0.390603 CCGTAACTCGTCAATGGCCA 60.391 55.000 8.56 8.56 37.94 5.36
81 82 0.999406 CGTAACTCGTCAATGGCCAG 59.001 55.000 13.05 0.00 34.52 4.85
82 83 1.403647 CGTAACTCGTCAATGGCCAGA 60.404 52.381 13.05 0.00 34.52 3.86
83 84 2.738643 CGTAACTCGTCAATGGCCAGAT 60.739 50.000 13.05 0.00 34.52 2.90
89 90 1.386533 GTCAATGGCCAGATCCACAG 58.613 55.000 13.05 0.00 39.25 3.66
118 119 7.857456 TCTAAATGACCCTAGAGCATACAAAA 58.143 34.615 0.00 0.00 0.00 2.44
138 139 5.622346 AAAAATAACTTCCAAGGCCACAA 57.378 34.783 5.01 0.00 0.00 3.33
160 161 1.900245 TTTTCAGCGTAAAGGGGTCC 58.100 50.000 0.00 0.00 0.00 4.46
182 183 4.335416 CAGGGTTTCTAAGCTCAATCCAA 58.665 43.478 0.00 0.00 0.00 3.53
186 187 4.082733 GGTTTCTAAGCTCAATCCAACACC 60.083 45.833 0.00 0.00 0.00 4.16
189 190 2.380064 AAGCTCAATCCAACACCCAA 57.620 45.000 0.00 0.00 0.00 4.12
190 191 1.620822 AGCTCAATCCAACACCCAAC 58.379 50.000 0.00 0.00 0.00 3.77
193 194 0.179004 TCAATCCAACACCCAACGCT 60.179 50.000 0.00 0.00 0.00 5.07
200 201 1.503818 AACACCCAACGCTAAGCACG 61.504 55.000 0.00 0.00 0.00 5.34
203 204 1.666553 CCCAACGCTAAGCACGACA 60.667 57.895 0.00 0.00 0.00 4.35
204 205 1.225376 CCCAACGCTAAGCACGACAA 61.225 55.000 0.00 0.00 0.00 3.18
268 270 1.900981 CCCGTGGGATGTTTGTGCA 60.901 57.895 0.00 0.00 37.50 4.57
271 273 0.179192 CGTGGGATGTTTGTGCATCG 60.179 55.000 0.00 0.00 44.47 3.84
360 364 1.684049 CCCAATTTTAGGGGCCGCA 60.684 57.895 23.39 5.16 42.90 5.69
375 420 1.919918 GCCGCATCAAAATTCGGAAAG 59.080 47.619 5.28 0.00 43.40 2.62
381 426 4.678840 GCATCAAAATTCGGAAAGGAGCAT 60.679 41.667 0.00 0.00 0.00 3.79
385 430 5.710099 TCAAAATTCGGAAAGGAGCATAACT 59.290 36.000 0.00 0.00 0.00 2.24
388 433 5.567138 ATTCGGAAAGGAGCATAACTTTG 57.433 39.130 0.00 0.00 37.07 2.77
513 565 4.318021 CACGCCTGCTGCACACAC 62.318 66.667 0.00 0.00 41.33 3.82
680 743 2.761160 CCCCGCCAAACCCTAACT 59.239 61.111 0.00 0.00 0.00 2.24
789 1035 2.390599 CCTCGCCATGGTGAACGTG 61.391 63.158 27.33 16.03 33.98 4.49
1190 1449 3.119096 GGTCAACTCGAAGCCCGC 61.119 66.667 0.00 0.00 38.37 6.13
1202 1462 4.643387 GCCCGCCAGTTCAGGTGT 62.643 66.667 0.00 0.00 37.47 4.16
1277 1537 0.179020 TTGCACCAGGGAGTTCACAG 60.179 55.000 0.00 0.00 0.00 3.66
1282 1542 0.764890 CCAGGGAGTTCACAGTGGAA 59.235 55.000 0.00 0.00 0.00 3.53
1308 1568 0.456221 CCTCTTACATGCTCGGACGT 59.544 55.000 0.00 0.00 0.00 4.34
1317 1577 2.668280 GCTCGGACGTGCAAAGGAC 61.668 63.158 8.11 0.00 35.06 3.85
1321 1581 1.598130 GGACGTGCAAAGGACAGCT 60.598 57.895 0.63 0.00 0.00 4.24
1432 1692 1.072489 TGGCAATGGGTTCTCGTGTAA 59.928 47.619 0.00 0.00 0.00 2.41
1458 1718 1.997606 GCATCTCCACAATTTGCTTGC 59.002 47.619 0.00 0.00 38.50 4.01
1548 1808 1.541310 TTACCCTGACTGCCACTCGG 61.541 60.000 0.00 0.00 0.00 4.63
1566 1826 7.471120 GCCACTCGGTATAAGTTAGTTCCTTAT 60.471 40.741 0.00 0.00 38.38 1.73
1569 1829 9.418839 ACTCGGTATAAGTTAGTTCCTTATCTT 57.581 33.333 0.00 0.00 36.68 2.40
1572 1832 9.813446 CGGTATAAGTTAGTTCCTTATCTTGTT 57.187 33.333 0.00 0.00 36.68 2.83
1578 1838 8.100508 AGTTAGTTCCTTATCTTGTTGCTTTC 57.899 34.615 0.00 0.00 0.00 2.62
1594 1854 2.610727 GCTTTCGTAGCTGGAGAGTTGT 60.611 50.000 0.00 0.00 46.77 3.32
1612 1872 1.623811 TGTTGCTAGGTGAGAAGACCC 59.376 52.381 0.00 0.00 36.56 4.46
1656 1916 8.473358 TCCCAATACGAGAGAATATTTACTCA 57.527 34.615 17.01 5.23 35.83 3.41
1734 1994 8.088463 AGATGGTTATCATAATCCTCAGATCC 57.912 38.462 0.00 0.00 35.97 3.36
1824 2084 2.348411 ATAGGAAAACATGGCTCCGG 57.652 50.000 0.00 0.00 34.22 5.14
1921 2181 2.490328 ATTTGCAAACGACCTGTGTG 57.510 45.000 15.41 0.00 38.97 3.82
1929 2189 2.831685 ACGACCTGTGTGCTGAATTA 57.168 45.000 0.00 0.00 0.00 1.40
2148 2408 4.743644 ACAGTCGCAGTTAAAGTAAGACAC 59.256 41.667 0.00 0.00 0.00 3.67
2549 2809 6.966534 ACATTCAACCATCTCTTTGTCTTT 57.033 33.333 0.00 0.00 0.00 2.52
2550 2810 6.974965 ACATTCAACCATCTCTTTGTCTTTC 58.025 36.000 0.00 0.00 0.00 2.62
2607 2869 8.736244 GGGAGTACATGCTTTCTGTATTAAAAA 58.264 33.333 0.00 0.00 32.13 1.94
2718 2980 1.732259 CGCACCAACCAAGATACAGAC 59.268 52.381 0.00 0.00 0.00 3.51
2776 3038 1.069978 TGAACAGCGTGGAACAGATGA 59.930 47.619 0.00 0.00 41.80 2.92
2836 3776 0.370273 GCAGTGCAACGTTATCTCGG 59.630 55.000 11.09 0.00 45.86 4.63
3026 3966 5.642491 CCTGCACATATTGATATGGACTCTG 59.358 44.000 13.83 5.46 43.38 3.35
3038 3985 9.679661 TTGATATGGACTCTGCAATTACTTAAA 57.320 29.630 0.00 0.00 0.00 1.52
3236 4187 6.919721 ACTTTGTTCTTCAAAAAGTACTGCA 58.080 32.000 0.00 0.00 44.08 4.41
3242 4193 5.868257 TCTTCAAAAAGTACTGCATATGCG 58.132 37.500 22.21 18.20 37.55 4.73
3260 4211 7.063426 GCATATGCGAGCTCACAGTATTAATAA 59.937 37.037 12.82 0.00 0.00 1.40
3268 4219 8.654230 AGCTCACAGTATTAATAACATCACTG 57.346 34.615 10.79 10.79 39.38 3.66
3308 4259 5.658634 TGATAAGCCTCAGTATGTCTGTCTT 59.341 40.000 0.00 0.00 43.97 3.01
3467 4418 2.223805 CCTTTTGAAGTCAAGGCCACAC 60.224 50.000 5.01 0.00 37.15 3.82
3730 4681 8.328014 AGGTGATTTTATTGGCATTTTGGTATT 58.672 29.630 0.00 0.00 0.00 1.89
3747 4706 9.579932 TTTTGGTATTGAAAAATTGGGCTATTT 57.420 25.926 0.00 0.00 0.00 1.40
3760 4719 3.630312 TGGGCTATTTTATTGAACGGCTC 59.370 43.478 0.00 0.00 0.00 4.70
3768 4727 2.717639 ATTGAACGGCTCCTGCTTAT 57.282 45.000 0.00 0.00 39.59 1.73
3812 4771 9.318041 CGCAGTAAATATTGTATTTAGATGCAC 57.682 33.333 22.87 9.49 37.30 4.57
3826 4785 1.315257 ATGCACGCCTTGGATTGTCC 61.315 55.000 0.00 0.00 30.65 4.02
3899 4858 1.079503 GCTAACAGGAAGTTGAGCGG 58.920 55.000 0.00 0.00 41.50 5.52
4079 5038 5.178797 ACCTGTGTGCTTATGATGTACTTC 58.821 41.667 1.85 1.85 0.00 3.01
4173 5132 2.084546 GTAGAGCACCATGACCCAAAC 58.915 52.381 0.00 0.00 0.00 2.93
4179 5138 2.102252 GCACCATGACCCAAACTTCAAA 59.898 45.455 0.00 0.00 0.00 2.69
4188 5147 7.941431 TGACCCAAACTTCAAAACTACTTAA 57.059 32.000 0.00 0.00 0.00 1.85
4238 5197 5.288015 CAGAAACTGTATCGCTCATGAGAT 58.712 41.667 27.04 14.18 36.67 2.75
4256 5215 5.595885 TGAGATAAGTATGCAGTGAGCTTC 58.404 41.667 0.00 0.00 45.94 3.86
4257 5216 5.362143 TGAGATAAGTATGCAGTGAGCTTCT 59.638 40.000 0.00 0.00 45.94 2.85
4286 5245 4.464008 AGCATTTGGTCTTGAAGTTCTCA 58.536 39.130 4.17 0.00 0.00 3.27
4287 5246 4.889409 AGCATTTGGTCTTGAAGTTCTCAA 59.111 37.500 4.17 0.00 41.93 3.02
4311 5270 8.338259 CAAATACTATTGATCTTGTGTAGTGCC 58.662 37.037 0.00 0.00 31.84 5.01
4329 5288 6.212888 AGTGCCCAGTTTGAATTTGATATC 57.787 37.500 0.00 0.00 0.00 1.63
4352 5314 4.399303 CAGGCATAAAGGGGTTCTTAGTTG 59.601 45.833 0.00 0.00 34.78 3.16
4372 5334 4.668138 TGGGTTAGCTTTCCAACCTTAT 57.332 40.909 14.34 0.00 43.17 1.73
4437 5402 3.503363 TGCAGCCATGTCTAGTTTTTCTG 59.497 43.478 0.00 0.00 0.00 3.02
4556 5711 2.264794 GGATGGTCGCCGAAGTGT 59.735 61.111 0.00 0.00 0.00 3.55
4631 5789 4.161189 TGGAAGATTGTAGCTCCTTCTGAG 59.839 45.833 0.00 0.00 44.47 3.35
4640 5798 2.024464 AGCTCCTTCTGAGGCTCTTCTA 60.024 50.000 16.72 0.00 43.21 2.10
4641 5799 2.763448 GCTCCTTCTGAGGCTCTTCTAA 59.237 50.000 16.72 3.93 43.21 2.10
4642 5800 3.196685 GCTCCTTCTGAGGCTCTTCTAAA 59.803 47.826 16.72 2.25 43.21 1.85
4643 5801 4.680440 GCTCCTTCTGAGGCTCTTCTAAAG 60.680 50.000 16.72 10.98 43.21 1.85
4646 5804 5.723887 TCCTTCTGAGGCTCTTCTAAAGATT 59.276 40.000 16.72 0.00 43.21 2.40
4647 5805 5.816777 CCTTCTGAGGCTCTTCTAAAGATTG 59.183 44.000 16.72 5.25 35.94 2.67
4845 6044 1.002011 GGAAGACTGGGCCAAGTCC 60.002 63.158 32.96 20.21 46.51 3.85
5289 6490 7.846644 TTGTTTCAAAGAAACCTACGTCTTA 57.153 32.000 17.14 0.00 32.90 2.10
5304 6505 9.886132 ACCTACGTCTTATCTGACATAATTTTT 57.114 29.630 0.00 0.00 36.82 1.94
5395 6601 1.709147 GCAGGCACCTCAATACAGCG 61.709 60.000 0.00 0.00 0.00 5.18
5404 6610 2.939103 CCTCAATACAGCGGGAAGAAAG 59.061 50.000 0.00 0.00 0.00 2.62
5429 6635 0.035739 GGTTACAAAGGAGGACGCCA 59.964 55.000 0.00 0.00 0.00 5.69
5446 6652 1.063174 GCCAAGCACTAGCAAGAATCG 59.937 52.381 0.00 0.00 45.49 3.34
5521 8931 1.676967 CCTCAAGAACCCTGCTGCC 60.677 63.158 0.00 0.00 0.00 4.85
5592 10450 4.043435 AGAAACTTGATCTTAGGCCCTTGT 59.957 41.667 0.00 0.00 0.00 3.16
5593 10451 3.356529 ACTTGATCTTAGGCCCTTGTG 57.643 47.619 0.00 0.00 0.00 3.33
5713 10577 4.261238 GCCTTGATCAGCTTGATGATTCAG 60.261 45.833 2.83 2.90 40.02 3.02
5760 11437 3.987863 CTTGCGATTTTGGGCGGCC 62.988 63.158 23.42 23.42 0.00 6.13
5777 11454 2.464157 GCCTACATGCCTCCAGATAC 57.536 55.000 0.00 0.00 0.00 2.24
5848 11525 7.470289 AAGATCTTCGTACTATGTTGATTGC 57.530 36.000 0.88 0.00 0.00 3.56
5849 11526 6.810911 AGATCTTCGTACTATGTTGATTGCT 58.189 36.000 0.00 0.00 0.00 3.91
5853 11530 6.871492 TCTTCGTACTATGTTGATTGCTTTGA 59.129 34.615 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.607293 TGTAGATTTCAGGATCGGATGG 57.393 45.455 0.00 0.00 0.00 3.51
3 4 4.636249 GCTTGTAGATTTCAGGATCGGAT 58.364 43.478 0.00 0.00 0.00 4.18
4 5 3.490933 CGCTTGTAGATTTCAGGATCGGA 60.491 47.826 0.00 0.00 0.00 4.55
6 7 3.448686 ACGCTTGTAGATTTCAGGATCG 58.551 45.455 0.00 0.00 0.00 3.69
7 8 4.433615 TGACGCTTGTAGATTTCAGGATC 58.566 43.478 0.00 0.00 0.00 3.36
8 9 4.471904 TGACGCTTGTAGATTTCAGGAT 57.528 40.909 0.00 0.00 0.00 3.24
9 10 3.953712 TGACGCTTGTAGATTTCAGGA 57.046 42.857 0.00 0.00 0.00 3.86
10 11 3.181516 GCTTGACGCTTGTAGATTTCAGG 60.182 47.826 0.00 0.00 35.14 3.86
11 12 3.433274 TGCTTGACGCTTGTAGATTTCAG 59.567 43.478 0.00 0.00 40.11 3.02
12 13 3.398406 TGCTTGACGCTTGTAGATTTCA 58.602 40.909 0.00 0.00 40.11 2.69
13 14 4.494855 GGATGCTTGACGCTTGTAGATTTC 60.495 45.833 0.00 0.00 40.11 2.17
14 15 3.375299 GGATGCTTGACGCTTGTAGATTT 59.625 43.478 0.00 0.00 40.11 2.17
15 16 2.939103 GGATGCTTGACGCTTGTAGATT 59.061 45.455 0.00 0.00 40.11 2.40
16 17 2.093500 TGGATGCTTGACGCTTGTAGAT 60.093 45.455 0.00 0.00 40.11 1.98
17 18 1.275010 TGGATGCTTGACGCTTGTAGA 59.725 47.619 0.00 0.00 40.11 2.59
18 19 1.662629 CTGGATGCTTGACGCTTGTAG 59.337 52.381 0.00 0.00 40.11 2.74
19 20 1.001974 ACTGGATGCTTGACGCTTGTA 59.998 47.619 0.00 0.00 40.11 2.41
20 21 0.250467 ACTGGATGCTTGACGCTTGT 60.250 50.000 0.00 0.00 40.11 3.16
21 22 0.167470 CACTGGATGCTTGACGCTTG 59.833 55.000 0.00 0.00 40.11 4.01
22 23 0.957395 CCACTGGATGCTTGACGCTT 60.957 55.000 0.00 0.00 40.11 4.68
23 24 1.376424 CCACTGGATGCTTGACGCT 60.376 57.895 0.00 0.00 40.11 5.07
24 25 1.364626 CTCCACTGGATGCTTGACGC 61.365 60.000 0.00 0.00 39.77 5.19
25 26 0.247460 TCTCCACTGGATGCTTGACG 59.753 55.000 0.00 0.00 0.00 4.35
26 27 2.170187 AGATCTCCACTGGATGCTTGAC 59.830 50.000 0.00 0.00 0.00 3.18
27 28 2.433604 GAGATCTCCACTGGATGCTTGA 59.566 50.000 12.00 0.00 0.00 3.02
28 29 2.435069 AGAGATCTCCACTGGATGCTTG 59.565 50.000 19.30 0.00 0.00 4.01
29 30 2.435069 CAGAGATCTCCACTGGATGCTT 59.565 50.000 19.30 0.00 0.00 3.91
30 31 2.040939 CAGAGATCTCCACTGGATGCT 58.959 52.381 19.30 0.00 0.00 3.79
31 32 2.529780 CAGAGATCTCCACTGGATGC 57.470 55.000 19.30 0.00 0.00 3.91
36 37 1.039785 TCCGCCAGAGATCTCCACTG 61.040 60.000 19.30 10.95 0.00 3.66
37 38 0.754957 CTCCGCCAGAGATCTCCACT 60.755 60.000 19.30 0.00 46.50 4.00
38 39 1.739049 CTCCGCCAGAGATCTCCAC 59.261 63.158 19.30 8.03 46.50 4.02
39 40 2.130426 GCTCCGCCAGAGATCTCCA 61.130 63.158 19.30 0.00 46.50 3.86
40 41 1.470996 ATGCTCCGCCAGAGATCTCC 61.471 60.000 19.30 3.28 46.50 3.71
41 42 0.392336 AATGCTCCGCCAGAGATCTC 59.608 55.000 15.29 15.29 46.50 2.75
42 43 0.392336 GAATGCTCCGCCAGAGATCT 59.608 55.000 0.00 0.00 46.50 2.75
43 44 0.602372 GGAATGCTCCGCCAGAGATC 60.602 60.000 2.62 0.00 46.50 2.75
44 45 1.449353 GGAATGCTCCGCCAGAGAT 59.551 57.895 2.62 0.00 46.50 2.75
45 46 2.903357 GGAATGCTCCGCCAGAGA 59.097 61.111 2.62 0.00 46.50 3.10
63 64 2.380084 TCTGGCCATTGACGAGTTAC 57.620 50.000 5.51 0.00 0.00 2.50
64 65 2.158957 GGATCTGGCCATTGACGAGTTA 60.159 50.000 5.51 0.00 0.00 2.24
65 66 1.407437 GGATCTGGCCATTGACGAGTT 60.407 52.381 5.51 0.00 0.00 3.01
66 67 0.179000 GGATCTGGCCATTGACGAGT 59.821 55.000 5.51 0.00 0.00 4.18
67 68 0.178767 TGGATCTGGCCATTGACGAG 59.821 55.000 5.51 0.00 31.66 4.18
68 69 0.107703 GTGGATCTGGCCATTGACGA 60.108 55.000 5.51 0.00 40.68 4.20
69 70 0.392863 TGTGGATCTGGCCATTGACG 60.393 55.000 5.51 0.00 40.68 4.35
70 71 1.340405 ACTGTGGATCTGGCCATTGAC 60.340 52.381 5.51 0.00 40.68 3.18
71 72 0.994247 ACTGTGGATCTGGCCATTGA 59.006 50.000 5.51 0.00 40.68 2.57
72 73 1.100510 CACTGTGGATCTGGCCATTG 58.899 55.000 5.51 0.00 40.68 2.82
73 74 0.994247 TCACTGTGGATCTGGCCATT 59.006 50.000 5.51 0.00 40.68 3.16
74 75 1.142465 GATCACTGTGGATCTGGCCAT 59.858 52.381 5.51 0.00 40.68 4.40
75 76 0.543277 GATCACTGTGGATCTGGCCA 59.457 55.000 4.71 4.71 40.41 5.36
76 77 3.393472 GATCACTGTGGATCTGGCC 57.607 57.895 8.11 0.00 40.41 5.36
81 82 5.059833 GGGTCATTTAGATCACTGTGGATC 58.940 45.833 8.11 9.51 43.21 3.36
82 83 4.723789 AGGGTCATTTAGATCACTGTGGAT 59.276 41.667 8.11 0.32 0.00 3.41
83 84 4.104086 AGGGTCATTTAGATCACTGTGGA 58.896 43.478 8.11 0.00 0.00 4.02
89 90 5.537300 TGCTCTAGGGTCATTTAGATCAC 57.463 43.478 0.00 0.00 0.00 3.06
118 119 4.223144 AGTTGTGGCCTTGGAAGTTATTT 58.777 39.130 3.32 0.00 0.00 1.40
121 122 3.306472 AAGTTGTGGCCTTGGAAGTTA 57.694 42.857 3.32 0.00 0.00 2.24
127 128 2.825205 CTGAAAAAGTTGTGGCCTTGG 58.175 47.619 3.32 0.00 0.00 3.61
138 139 2.882761 GACCCCTTTACGCTGAAAAAGT 59.117 45.455 0.00 0.00 32.02 2.66
160 161 3.955471 TGGATTGAGCTTAGAAACCCTG 58.045 45.455 0.00 0.00 0.00 4.45
182 183 1.959226 CGTGCTTAGCGTTGGGTGT 60.959 57.895 0.00 0.00 0.00 4.16
186 187 0.110823 GTTGTCGTGCTTAGCGTTGG 60.111 55.000 0.00 0.00 0.00 3.77
189 190 0.320421 ATGGTTGTCGTGCTTAGCGT 60.320 50.000 0.00 0.00 0.00 5.07
190 191 0.370273 GATGGTTGTCGTGCTTAGCG 59.630 55.000 0.00 0.00 0.00 4.26
193 194 3.368013 CCACTAGATGGTTGTCGTGCTTA 60.368 47.826 0.00 0.00 44.46 3.09
271 273 3.611792 GATCTCTCGTGCGCGTGC 61.612 66.667 20.50 15.48 43.20 5.34
280 282 9.884465 GGATAAAAATAACAATTGGATCTCTCG 57.116 33.333 10.83 0.00 0.00 4.04
329 332 4.519540 AAAATTGGGACCGTGAAATGAG 57.480 40.909 0.00 0.00 0.00 2.90
360 364 6.378280 AGTTATGCTCCTTTCCGAATTTTGAT 59.622 34.615 0.00 0.00 0.00 2.57
532 584 2.379459 GGAAGAAGGGAGGAGGGGC 61.379 68.421 0.00 0.00 0.00 5.80
1190 1449 0.947244 GTTCTGCACACCTGAACTGG 59.053 55.000 8.17 0.00 44.40 4.00
1202 1462 0.955428 GCTCGACCCAATGTTCTGCA 60.955 55.000 0.00 0.00 0.00 4.41
1282 1542 0.987294 AGCATGTAAGAGGTGGCTGT 59.013 50.000 0.00 0.00 0.00 4.40
1284 1544 0.176680 CGAGCATGTAAGAGGTGGCT 59.823 55.000 0.00 0.00 0.00 4.75
1286 1546 0.824109 TCCGAGCATGTAAGAGGTGG 59.176 55.000 0.00 0.00 0.00 4.61
1293 1553 0.319986 TTGCACGTCCGAGCATGTAA 60.320 50.000 12.28 0.00 40.97 2.41
1294 1554 0.319986 TTTGCACGTCCGAGCATGTA 60.320 50.000 12.28 0.00 40.97 2.29
1308 1568 3.263170 TCCAGTATAAGCTGTCCTTTGCA 59.737 43.478 0.00 0.00 34.95 4.08
1317 1577 1.071385 CCAGGGCTCCAGTATAAGCTG 59.929 57.143 0.00 0.00 38.58 4.24
1321 1581 0.837272 GCACCAGGGCTCCAGTATAA 59.163 55.000 0.00 0.00 0.00 0.98
1362 1622 1.888215 ATGCATTCCGGCTACATGAG 58.112 50.000 0.00 0.00 34.04 2.90
1432 1692 4.060205 GCAAATTGTGGAGATGCTTTTGT 58.940 39.130 0.00 0.00 34.29 2.83
1468 1728 0.107410 ACAGCAGAACCCGTTGACAA 60.107 50.000 0.00 0.00 0.00 3.18
1578 1838 1.071605 GCAACAACTCTCCAGCTACG 58.928 55.000 0.00 0.00 0.00 3.51
1594 1854 2.024176 TGGGTCTTCTCACCTAGCAA 57.976 50.000 0.00 0.00 36.57 3.91
1656 1916 3.753434 CGGCTGTCCTGAGCTCGT 61.753 66.667 9.64 0.00 39.11 4.18
1698 1958 6.737720 ATGATAACCATCTCTACTGCTGAA 57.262 37.500 0.00 0.00 31.93 3.02
1744 2004 8.311836 CAGTATACTGGGAGTAAACAAGAAAGA 58.688 37.037 22.95 0.00 40.20 2.52
1800 2060 4.273480 CGGAGCCATGTTTTCCTATACTTG 59.727 45.833 0.00 0.00 0.00 3.16
1824 2084 4.174009 TCTCTAAAGTACGATGCACAAGC 58.826 43.478 0.00 0.00 42.57 4.01
1921 2181 6.182039 TGTGTGTAGCTTTGATAATTCAGC 57.818 37.500 0.00 0.00 32.27 4.26
1923 2183 7.594758 GCTTTTGTGTGTAGCTTTGATAATTCA 59.405 33.333 0.00 0.00 32.26 2.57
1929 2189 4.499696 GGTGCTTTTGTGTGTAGCTTTGAT 60.500 41.667 0.00 0.00 35.93 2.57
2148 2408 1.938585 TTGAGTCTCCTACACCAGGG 58.061 55.000 0.00 0.00 45.58 4.45
2549 2809 6.916360 AGGCAAAACAGAAATAAGAATGGA 57.084 33.333 0.00 0.00 0.00 3.41
2550 2810 7.656948 TCAAAGGCAAAACAGAAATAAGAATGG 59.343 33.333 0.00 0.00 0.00 3.16
2607 2869 5.369110 AGGGAAATCTCTATCATTCTGCTGT 59.631 40.000 0.00 0.00 0.00 4.40
2718 2980 0.466189 ATAAGAGGGGCAATGCGGTG 60.466 55.000 0.00 0.00 0.00 4.94
2798 3738 6.712547 GCACTGCTTATTCCTTTACATATCCT 59.287 38.462 0.00 0.00 0.00 3.24
2878 3818 2.287427 GCAGCAAGATACATGTCATGCC 60.287 50.000 12.91 2.88 42.17 4.40
3035 3982 8.474831 TGCTAACTGATAGTGCTATGTTCTTTA 58.525 33.333 0.00 0.00 33.87 1.85
3038 3985 6.322456 TCTGCTAACTGATAGTGCTATGTTCT 59.678 38.462 0.00 0.00 33.87 3.01
3126 4077 1.125384 CGGTTCCGTGTTACATCAACG 59.875 52.381 2.82 0.00 40.26 4.10
3236 4187 8.088365 TGTTATTAATACTGTGAGCTCGCATAT 58.912 33.333 29.02 22.61 35.63 1.78
3242 4193 8.759641 CAGTGATGTTATTAATACTGTGAGCTC 58.240 37.037 6.82 6.82 32.92 4.09
3260 4211 3.719268 TGGCAAGAATACCAGTGATGT 57.281 42.857 0.00 0.00 0.00 3.06
3268 4219 5.985530 GGCTTATCAAATTGGCAAGAATACC 59.014 40.000 5.96 0.00 0.00 2.73
3413 4364 4.083003 GGATTTCTTGGTTGTGCAATACGA 60.083 41.667 0.00 0.00 0.00 3.43
3467 4418 2.094390 TCCTACATCGAGGAAAACCACG 60.094 50.000 3.06 0.00 42.90 4.94
3654 4605 5.144100 TCCAGTGTCCACCAATAACAAAAT 58.856 37.500 0.00 0.00 0.00 1.82
3663 4614 0.036732 GCATCTCCAGTGTCCACCAA 59.963 55.000 0.00 0.00 0.00 3.67
3664 4615 0.837691 AGCATCTCCAGTGTCCACCA 60.838 55.000 0.00 0.00 0.00 4.17
3665 4616 0.326264 AAGCATCTCCAGTGTCCACC 59.674 55.000 0.00 0.00 0.00 4.61
3730 4681 8.930760 CGTTCAATAAAATAGCCCAATTTTTCA 58.069 29.630 7.17 0.00 39.27 2.69
3747 4706 2.489938 AAGCAGGAGCCGTTCAATAA 57.510 45.000 0.00 0.00 43.56 1.40
3755 4714 3.476552 TCCATTTAATAAGCAGGAGCCG 58.523 45.455 0.00 0.00 43.56 5.52
3760 4719 5.733620 ATGCCATCCATTTAATAAGCAGG 57.266 39.130 0.00 0.00 31.70 4.85
3768 4727 2.757314 TGCGACAATGCCATCCATTTAA 59.243 40.909 0.00 0.00 42.15 1.52
3806 4765 0.099436 GACAATCCAAGGCGTGCATC 59.901 55.000 0.00 0.00 0.00 3.91
3899 4858 2.100197 GTACCCCAGAAGGAAAATGCC 58.900 52.381 0.00 0.00 38.24 4.40
4188 5147 7.002879 AGGCACTATTAATCATGAGCAATTCT 58.997 34.615 0.09 0.00 36.02 2.40
4286 5245 7.499232 GGGCACTACACAAGATCAATAGTATTT 59.501 37.037 0.00 0.00 0.00 1.40
4287 5246 6.992715 GGGCACTACACAAGATCAATAGTATT 59.007 38.462 0.00 0.00 0.00 1.89
4311 5270 6.211587 TGCCTGATATCAAATTCAAACTGG 57.788 37.500 6.90 1.65 0.00 4.00
4329 5288 4.236527 ACTAAGAACCCCTTTATGCCTG 57.763 45.455 0.00 0.00 36.34 4.85
4391 5353 8.989980 GCAATGACAGTTACTACTTTAGTTTCT 58.010 33.333 0.00 0.00 40.14 2.52
4392 5354 8.770828 TGCAATGACAGTTACTACTTTAGTTTC 58.229 33.333 0.00 0.00 40.14 2.78
4393 5355 8.671384 TGCAATGACAGTTACTACTTTAGTTT 57.329 30.769 0.00 0.00 40.14 2.66
4395 5357 6.369065 GCTGCAATGACAGTTACTACTTTAGT 59.631 38.462 0.00 0.00 40.05 2.24
4396 5358 6.183360 GGCTGCAATGACAGTTACTACTTTAG 60.183 42.308 0.50 0.00 39.96 1.85
4537 5688 1.811266 CACTTCGGCGACCATCCTG 60.811 63.158 10.16 0.00 0.00 3.86
4586 5741 1.072266 ACAAGGTAGGGCACAATCCA 58.928 50.000 0.00 0.00 0.00 3.41
4587 5742 1.463674 CACAAGGTAGGGCACAATCC 58.536 55.000 0.00 0.00 0.00 3.01
4631 5789 9.255304 CAGATAAGTACAATCTTTAGAAGAGCC 57.745 37.037 7.76 0.00 41.61 4.70
4662 5855 9.606631 AGTACAGAAGCAGAAAATATAGGAAAG 57.393 33.333 0.00 0.00 0.00 2.62
5304 6505 3.760738 TCTGCATCCCAAACATACACAA 58.239 40.909 0.00 0.00 0.00 3.33
5395 6601 3.479489 TGTAACCCGTTTCTTTCTTCCC 58.521 45.455 0.00 0.00 0.00 3.97
5404 6610 2.810274 GTCCTCCTTTGTAACCCGTTTC 59.190 50.000 0.00 0.00 0.00 2.78
5429 6635 3.873952 GGAATCGATTCTTGCTAGTGCTT 59.126 43.478 31.32 0.00 37.24 3.91
5446 6652 2.034305 GTCATGGCAGATGCAAGGAATC 59.966 50.000 7.19 0.00 36.45 2.52
5479 6688 0.608640 CTACCCACCAGTCCAGTGAC 59.391 60.000 0.00 0.00 42.09 3.67
5521 8931 3.619419 TGGATCATTGGGTGTGTATGTG 58.381 45.455 0.00 0.00 0.00 3.21
5592 10450 1.376466 GGCAGCTTGGAGAAGACCA 59.624 57.895 0.00 0.00 38.24 4.02
5593 10451 0.957888 GTGGCAGCTTGGAGAAGACC 60.958 60.000 0.00 0.00 0.00 3.85
5713 10577 4.223032 TCAAGGTGGACATTTCCTCTAGAC 59.777 45.833 0.00 0.00 43.31 2.59
5734 10598 1.339610 CCAAAATCGCAAGGTGGTTCA 59.660 47.619 0.00 0.00 38.47 3.18
5760 11437 3.244353 CCTTGGTATCTGGAGGCATGTAG 60.244 52.174 0.00 0.00 0.00 2.74
5761 11438 2.705658 CCTTGGTATCTGGAGGCATGTA 59.294 50.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.