Multiple sequence alignment - TraesCS2B01G148700

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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 TraesCS2B01G148700 chr2B 100.000 3788 0 0 1 3788 114760717 114764504 0.000000e+00 6996
1 TraesCS2B01G148700 chr2A 92.154 1797 83 15 520 2275 74874999 74876778 0.000000e+00 2484
2 TraesCS2B01G148700 chr2A 93.456 978 53 6 2281 3248 74877113 74878089 0.000000e+00 1441
3 TraesCS2B01G148700 chr2A 90.019 521 33 12 1 515 74874447 74874954 0.000000e+00 656
4 TraesCS2B01G148700 chr2A 91.610 441 26 3 3297 3730 74878782 74879218 1.950000e-167 599
5 TraesCS2B01G148700 chr2A 89.412 85 9 0 2813 2897 74877697 74877781 1.440000e-19 108
6 TraesCS2B01G148700 chr2D 91.290 1550 104 16 738 2275 75094674 75096204 0.000000e+00 2085
7 TraesCS2B01G148700 chr2D 91.304 943 55 18 2325 3248 75096549 75097483 0.000000e+00 1262
8 TraesCS2B01G148700 chr2D 92.431 436 23 2 3302 3730 75097860 75098292 6.950000e-172 614
9 TraesCS2B01G148700 chr2D 92.697 178 8 4 1 178 75093744 75093916 6.280000e-63 252
10 TraesCS2B01G148700 chr5B 95.395 152 5 2 17 167 574963978 574964128 1.360000e-59 241
11 TraesCS2B01G148700 chr5B 83.550 231 26 9 2493 2711 641162236 641162006 4.960000e-49 206
12 TraesCS2B01G148700 chr7B 84.649 228 23 11 2493 2708 715812686 715812913 2.290000e-52 217
13 TraesCS2B01G148700 chr3D 79.934 304 40 17 2386 2677 15470694 15470988 1.780000e-48 204
14 TraesCS2B01G148700 chr6D 79.016 305 42 17 2386 2677 46461414 46461119 5.000000e-44 189
15 TraesCS2B01G148700 chr6D 79.016 305 42 17 2386 2677 347710643 347710938 5.000000e-44 189
16 TraesCS2B01G148700 chr5D 78.689 305 43 16 2386 2677 249165770 249165475 2.320000e-42 183
17 TraesCS2B01G148700 chr4A 81.858 226 27 12 2499 2712 651734372 651734149 1.080000e-40 178


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 TraesCS2B01G148700 chr2B 114760717 114764504 3787 False 6996.00 6996 100.0000 1 3788 1 chr2B.!!$F1 3787
1 TraesCS2B01G148700 chr2A 74874447 74879218 4771 False 1057.60 2484 91.3302 1 3730 5 chr2A.!!$F1 3729
2 TraesCS2B01G148700 chr2D 75093744 75098292 4548 False 1053.25 2085 91.9305 1 3730 4 chr2D.!!$F1 3729

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
391 437 0.178992 CTGTGGGCCTCCAACTGAAA 60.179 55.000 4.53 0.00 46.04 2.69 F
392 438 0.482446 TGTGGGCCTCCAACTGAAAT 59.518 50.000 4.53 0.00 46.04 2.17 F
663 754 1.676967 CCAGGAGCAGTGCCCTTTC 60.677 63.158 19.11 7.82 29.31 2.62 F
2601 3342 0.176680 CAAGATCCCAGTCCTGTCCG 59.823 60.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 2988 0.179018 GGCCTGGTATTGCTTCCGAT 60.179 55.000 0.0 0.0 0.00 4.18 R
2285 2990 0.815615 GAGGCCTGGTATTGCTTCCG 60.816 60.000 12.0 0.0 0.00 4.30 R
2634 3375 1.068472 GTGTATATCCAGAGGTCGGCG 60.068 57.143 0.0 0.0 0.00 6.46 R
3579 4967 0.246086 CGAAAGCAGTCTCAGGCTCT 59.754 55.000 0.0 0.0 40.01 4.09 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
53 54 2.922387 CACTTTCTGAGCTCTCGTCATG 59.078 50.000 16.19 3.36 0.00 3.07
63 64 2.102252 GCTCTCGTCATGAAATCCCTCT 59.898 50.000 0.00 0.00 0.00 3.69
125 126 4.210331 GGTGGTGGCTTCTTCATCATTAT 58.790 43.478 0.00 0.00 0.00 1.28
128 129 4.883585 TGGTGGCTTCTTCATCATTATCAC 59.116 41.667 0.00 0.00 0.00 3.06
129 130 4.276926 GGTGGCTTCTTCATCATTATCACC 59.723 45.833 0.00 0.00 34.97 4.02
130 131 4.883585 GTGGCTTCTTCATCATTATCACCA 59.116 41.667 0.00 0.00 0.00 4.17
131 132 5.533903 GTGGCTTCTTCATCATTATCACCAT 59.466 40.000 0.00 0.00 0.00 3.55
132 133 6.040166 GTGGCTTCTTCATCATTATCACCATT 59.960 38.462 0.00 0.00 0.00 3.16
133 134 6.040054 TGGCTTCTTCATCATTATCACCATTG 59.960 38.462 0.00 0.00 0.00 2.82
134 135 6.263842 GGCTTCTTCATCATTATCACCATTGA 59.736 38.462 0.00 0.00 35.73 2.57
135 136 7.201848 GGCTTCTTCATCATTATCACCATTGAA 60.202 37.037 0.00 0.00 34.61 2.69
136 137 8.192774 GCTTCTTCATCATTATCACCATTGAAA 58.807 33.333 0.00 0.00 34.61 2.69
191 218 4.335315 TCCACAATATCATTTCGCCAACTC 59.665 41.667 0.00 0.00 0.00 3.01
197 224 1.075542 CATTTCGCCAACTCGCTACA 58.924 50.000 0.00 0.00 0.00 2.74
216 243 4.818534 ACACAATTACGCATCATGGATC 57.181 40.909 0.00 0.00 0.00 3.36
246 289 6.494893 TCATGCTTTGTTTACTATCCACAC 57.505 37.500 0.00 0.00 0.00 3.82
255 301 6.539173 TGTTTACTATCCACACCATCAGTTT 58.461 36.000 0.00 0.00 0.00 2.66
274 320 7.326454 TCAGTTTCTCTGGATGAATTCACTAG 58.674 38.462 11.07 11.78 43.76 2.57
296 342 4.470304 AGTAAGGGTTCCCTACAGCTTTAG 59.530 45.833 11.11 0.00 34.97 1.85
359 405 4.515944 CCATTTTAACACGTGGTGTAGGAA 59.484 41.667 18.38 0.00 46.79 3.36
374 420 2.393271 AGGAATGCTTTCGACTCCTG 57.607 50.000 6.28 0.00 35.16 3.86
390 436 1.455849 CTGTGGGCCTCCAACTGAA 59.544 57.895 4.53 0.00 46.04 3.02
391 437 0.178992 CTGTGGGCCTCCAACTGAAA 60.179 55.000 4.53 0.00 46.04 2.69
392 438 0.482446 TGTGGGCCTCCAACTGAAAT 59.518 50.000 4.53 0.00 46.04 2.17
522 611 4.009370 AGAGACTGCTAACTTTGGTTCC 57.991 45.455 0.00 0.00 36.92 3.62
528 617 4.709886 ACTGCTAACTTTGGTTCCAACTTT 59.290 37.500 3.56 3.47 36.92 2.66
623 713 2.025981 ACTATGGAGAGCAACATGGCAA 60.026 45.455 0.00 0.00 35.83 4.52
661 752 2.856000 ACCAGGAGCAGTGCCCTT 60.856 61.111 19.11 0.00 29.31 3.95
662 753 2.437897 CCAGGAGCAGTGCCCTTT 59.562 61.111 19.11 0.00 29.31 3.11
663 754 1.676967 CCAGGAGCAGTGCCCTTTC 60.677 63.158 19.11 7.82 29.31 2.62
726 819 2.157668 GTGTTAGCACGATCAACCACAG 59.842 50.000 0.00 0.00 35.75 3.66
740 1061 7.172190 CGATCAACCACAGAAATATTCTATGCT 59.828 37.037 0.00 0.00 38.11 3.79
795 1124 3.319405 TGCTGCCTTAATTCGGAAACAAA 59.681 39.130 0.00 0.00 0.00 2.83
813 1142 7.540055 GGAAACAAAACTTGCTATTCTCTGATG 59.460 37.037 0.00 0.00 0.00 3.07
845 1174 4.713792 ATGAAGTTCTGGAGTGGTCTTT 57.286 40.909 4.17 0.00 0.00 2.52
998 1350 9.415544 GTTTGTTTATTCTCTTCTTGCATCAAT 57.584 29.630 0.00 0.00 0.00 2.57
1250 1608 9.514822 CTATTATTTTGTTGTTGTTGAATTGCG 57.485 29.630 0.00 0.00 0.00 4.85
1272 1630 6.602803 TGCGGCCATGATTAACATCATTATAT 59.397 34.615 2.24 0.00 46.45 0.86
1304 1663 2.945440 GCAGGTTTATGCTGATGGGACA 60.945 50.000 0.00 0.00 43.27 4.02
1422 1781 8.006298 TCTTTGACTGGTTTGTTCATTATGTT 57.994 30.769 0.00 0.00 0.00 2.71
1518 1877 2.287608 GGAGGACAGGAAACAAAAAGCG 60.288 50.000 0.00 0.00 0.00 4.68
1735 2094 5.931724 TGTCGAGCAAAATTCAGTATCAGAA 59.068 36.000 0.00 0.00 0.00 3.02
1738 2097 7.965107 GTCGAGCAAAATTCAGTATCAGAAAAT 59.035 33.333 0.00 0.00 0.00 1.82
1751 2110 8.598075 CAGTATCAGAAAATATTTGGCTTTTGC 58.402 33.333 0.39 0.00 46.64 3.68
1771 2130 9.921637 CTTTTGCCCTTGATAATAAAACACTTA 57.078 29.630 0.00 0.00 0.00 2.24
1812 2171 7.878621 AATGATAGGTCCTCAGGATTCATAA 57.121 36.000 0.00 0.00 32.73 1.90
1813 2172 8.460317 AATGATAGGTCCTCAGGATTCATAAT 57.540 34.615 0.00 0.00 32.73 1.28
1818 2177 7.084268 AGGTCCTCAGGATTCATAATTAAGG 57.916 40.000 0.00 0.00 32.73 2.69
1822 2181 5.474876 CCTCAGGATTCATAATTAAGGTGGC 59.525 44.000 0.00 0.00 0.00 5.01
1830 2189 2.678471 AATTAAGGTGGCTGCATTGC 57.322 45.000 0.46 0.46 0.00 3.56
1844 2203 4.377635 GCTGCATTGCCAACTTGTAATTTG 60.378 41.667 6.12 0.00 0.00 2.32
1910 2285 5.823861 ATAATTGGGTCCTTTTGTGCTTT 57.176 34.783 0.00 0.00 0.00 3.51
2032 2408 4.885325 TGTCGTTATCATGCTACTAGGTCA 59.115 41.667 0.00 0.00 0.00 4.02
2072 2448 5.219739 TCTTTGGTCTTCATAGGAGGCTAT 58.780 41.667 0.00 0.00 0.00 2.97
2087 2463 4.006319 GAGGCTATGTGGGCATCTAATTC 58.994 47.826 0.00 0.00 37.49 2.17
2119 2495 4.264217 CCCCACCCTATTTAAAGTCACCTT 60.264 45.833 0.00 0.00 0.00 3.50
2148 2524 9.295825 TGACTGGATATTTGCTTTCTTTAGAAA 57.704 29.630 4.95 4.95 41.29 2.52
2187 2563 1.839994 AGCTGGCTTACATGCTCCTTA 59.160 47.619 0.00 0.00 30.97 2.69
2269 2645 2.307686 ACGGGAATTAAGTGGACATGGT 59.692 45.455 0.00 0.00 0.00 3.55
2275 2651 7.514721 GGGAATTAAGTGGACATGGTATCTTA 58.485 38.462 0.00 0.00 0.00 2.10
2276 2652 7.996644 GGGAATTAAGTGGACATGGTATCTTAA 59.003 37.037 13.48 13.48 33.83 1.85
2278 2983 9.391006 GAATTAAGTGGACATGGTATCTTAACA 57.609 33.333 13.43 0.00 32.72 2.41
2279 2984 9.920946 AATTAAGTGGACATGGTATCTTAACAT 57.079 29.630 13.43 7.02 36.28 2.71
2291 2996 5.179555 GGTATCTTAACATGGAATCGGAAGC 59.820 44.000 0.00 0.00 0.00 3.86
2294 2999 5.192927 TCTTAACATGGAATCGGAAGCAAT 58.807 37.500 0.00 0.00 0.00 3.56
2304 3009 0.815615 CGGAAGCAATACCAGGCCTC 60.816 60.000 0.00 0.00 0.00 4.70
2316 3022 1.821136 CCAGGCCTCAGGATTTCAAAC 59.179 52.381 0.00 0.00 0.00 2.93
2436 3142 6.602406 AGAGTAGCTTGAGCATTCATTGAATT 59.398 34.615 9.19 0.00 45.16 2.17
2437 3143 6.561614 AGTAGCTTGAGCATTCATTGAATTG 58.438 36.000 9.19 6.77 45.16 2.32
2470 3176 9.087424 GAATCAGCTTTAAAAAGAAACACACTT 57.913 29.630 6.64 0.00 38.28 3.16
2483 3217 8.587952 AAGAAACACACTTAATTGTATTTGGC 57.412 30.769 6.91 0.00 0.00 4.52
2522 3256 7.172190 ACAGTCTGACAATCAACTTTCTACATG 59.828 37.037 10.88 0.00 0.00 3.21
2530 3264 8.680903 ACAATCAACTTTCTACATGATCCATTC 58.319 33.333 0.00 0.00 31.58 2.67
2541 3275 6.683974 ACATGATCCATTCGGTTTCTTTAG 57.316 37.500 0.00 0.00 0.00 1.85
2574 3315 1.536662 GTGTGGTCTCCCTCCCTGT 60.537 63.158 0.00 0.00 0.00 4.00
2601 3342 0.176680 CAAGATCCCAGTCCTGTCCG 59.823 60.000 0.00 0.00 0.00 4.79
2670 3411 2.981859 ACACGGATAACAGGGACATC 57.018 50.000 0.00 0.00 0.00 3.06
2689 3430 4.124351 TCGACATGGCGACGGTCC 62.124 66.667 22.34 0.00 35.01 4.46
2866 3607 5.447279 GCTGTAGACATTACCAATTGTTCGG 60.447 44.000 4.43 0.00 0.00 4.30
2925 3666 2.044555 CATCAGTGGGGTGCTGCTG 61.045 63.158 0.00 0.00 34.21 4.41
2988 3729 0.528684 GCTTATGAACGCTCCGAGCT 60.529 55.000 18.14 0.00 39.60 4.09
3025 3766 6.384305 AGGCTCTTTATGTATGTGAGGTACTT 59.616 38.462 0.00 0.00 41.55 2.24
3117 3858 4.895297 CCTTGGGCATGTAAGTAATGGATT 59.105 41.667 0.00 0.00 0.00 3.01
3118 3859 5.363580 CCTTGGGCATGTAAGTAATGGATTT 59.636 40.000 0.00 0.00 0.00 2.17
3152 3895 8.131100 GTGGACATGTAAGTAATGAATCATTGG 58.869 37.037 17.93 1.31 35.54 3.16
3219 3962 6.265422 TCTGGAAGAATATGCTCTGTTCGATA 59.735 38.462 0.00 0.00 42.31 2.92
3224 3967 7.126726 AGAATATGCTCTGTTCGATATTTGC 57.873 36.000 0.00 0.00 30.78 3.68
3233 3976 4.033019 TGTTCGATATTTGCGTCGACTAG 58.967 43.478 14.70 0.00 45.43 2.57
3254 4021 0.111266 GCAGTGTGTACTTTGACGCG 60.111 55.000 3.53 3.53 34.07 6.01
3274 4042 3.549625 GCGAATTCTGCAGGAATCCATTC 60.550 47.826 15.13 4.49 43.17 2.67
3282 4050 3.209410 GCAGGAATCCATTCGATTGAGT 58.791 45.455 8.84 0.00 41.47 3.41
3286 4060 3.249559 GGAATCCATTCGATTGAGTCTGC 59.750 47.826 8.84 0.00 41.47 4.26
3287 4061 3.548745 ATCCATTCGATTGAGTCTGCA 57.451 42.857 8.84 0.00 0.00 4.41
3288 4062 3.333029 TCCATTCGATTGAGTCTGCAA 57.667 42.857 8.84 0.00 0.00 4.08
3289 4063 3.673902 TCCATTCGATTGAGTCTGCAAA 58.326 40.909 8.84 0.00 0.00 3.68
3290 4064 3.686241 TCCATTCGATTGAGTCTGCAAAG 59.314 43.478 8.84 0.00 0.00 2.77
3292 4066 4.436584 CCATTCGATTGAGTCTGCAAAGTC 60.437 45.833 8.84 0.00 0.00 3.01
3293 4067 3.667497 TCGATTGAGTCTGCAAAGTCT 57.333 42.857 0.00 0.00 0.00 3.24
3297 4071 4.212004 CGATTGAGTCTGCAAAGTCTGAAA 59.788 41.667 0.00 0.00 0.00 2.69
3298 4072 5.277490 CGATTGAGTCTGCAAAGTCTGAAAA 60.277 40.000 0.00 0.00 0.00 2.29
3318 4706 0.530744 TCTTTCTGCGCCATAGACGT 59.469 50.000 4.18 0.00 0.00 4.34
3432 4820 3.865164 TGATGAATGGAATCAGTCGAACG 59.135 43.478 0.00 0.00 40.50 3.95
3495 4883 2.360138 CTGGAGTGTCAGCTCTGGT 58.640 57.895 0.00 0.00 35.89 4.00
3516 4904 1.539869 AGTGGCCTGAGGTGGATGT 60.540 57.895 3.32 0.00 0.00 3.06
3574 4962 3.124560 TCTTGTCATGTTTTACACGCGA 58.875 40.909 15.93 0.00 0.00 5.87
3623 5018 1.303309 GAAATCATCCACCAGCCTCG 58.697 55.000 0.00 0.00 0.00 4.63
3720 5115 4.712873 CCGCGGTTCGAAACGTGC 62.713 66.667 36.62 21.06 41.67 5.34
3730 5125 0.835120 CGAAACGTGCGTTTGGTTTC 59.165 50.000 24.40 10.82 46.80 2.78
3731 5126 1.530236 CGAAACGTGCGTTTGGTTTCT 60.530 47.619 24.40 1.62 46.80 2.52
3732 5127 2.285718 CGAAACGTGCGTTTGGTTTCTA 60.286 45.455 24.40 0.00 46.80 2.10
3733 5128 3.605231 CGAAACGTGCGTTTGGTTTCTAT 60.605 43.478 24.40 0.20 46.80 1.98
3734 5129 4.376210 CGAAACGTGCGTTTGGTTTCTATA 60.376 41.667 24.40 0.00 46.80 1.31
3735 5130 5.616488 AAACGTGCGTTTGGTTTCTATAT 57.384 34.783 19.83 0.00 45.34 0.86
3736 5131 4.852609 ACGTGCGTTTGGTTTCTATATC 57.147 40.909 0.00 0.00 0.00 1.63
3737 5132 4.501071 ACGTGCGTTTGGTTTCTATATCT 58.499 39.130 0.00 0.00 0.00 1.98
3738 5133 4.933400 ACGTGCGTTTGGTTTCTATATCTT 59.067 37.500 0.00 0.00 0.00 2.40
3739 5134 5.063060 ACGTGCGTTTGGTTTCTATATCTTC 59.937 40.000 0.00 0.00 0.00 2.87
3740 5135 5.291128 CGTGCGTTTGGTTTCTATATCTTCT 59.709 40.000 0.00 0.00 0.00 2.85
3741 5136 6.508088 CGTGCGTTTGGTTTCTATATCTTCTC 60.508 42.308 0.00 0.00 0.00 2.87
3742 5137 5.815740 TGCGTTTGGTTTCTATATCTTCTCC 59.184 40.000 0.00 0.00 0.00 3.71
3743 5138 5.050972 GCGTTTGGTTTCTATATCTTCTCCG 60.051 44.000 0.00 0.00 0.00 4.63
3744 5139 5.462398 CGTTTGGTTTCTATATCTTCTCCGG 59.538 44.000 0.00 0.00 0.00 5.14
3745 5140 4.602340 TGGTTTCTATATCTTCTCCGGC 57.398 45.455 0.00 0.00 0.00 6.13
3746 5141 3.964688 TGGTTTCTATATCTTCTCCGGCA 59.035 43.478 0.00 0.00 0.00 5.69
3747 5142 4.407621 TGGTTTCTATATCTTCTCCGGCAA 59.592 41.667 0.00 0.00 0.00 4.52
3748 5143 5.104693 TGGTTTCTATATCTTCTCCGGCAAA 60.105 40.000 0.00 0.00 0.00 3.68
3749 5144 5.467063 GGTTTCTATATCTTCTCCGGCAAAG 59.533 44.000 0.00 2.54 0.00 2.77
3750 5145 6.281405 GTTTCTATATCTTCTCCGGCAAAGA 58.719 40.000 17.33 17.33 36.05 2.52
3751 5146 5.455056 TCTATATCTTCTCCGGCAAAGAC 57.545 43.478 17.36 0.00 34.52 3.01
3752 5147 2.981859 TATCTTCTCCGGCAAAGACC 57.018 50.000 17.36 0.00 34.52 3.85
3753 5148 1.280457 ATCTTCTCCGGCAAAGACCT 58.720 50.000 17.36 3.92 34.52 3.85
3754 5149 0.608640 TCTTCTCCGGCAAAGACCTC 59.391 55.000 12.68 0.00 0.00 3.85
3755 5150 0.610687 CTTCTCCGGCAAAGACCTCT 59.389 55.000 9.37 0.00 0.00 3.69
3756 5151 1.002544 CTTCTCCGGCAAAGACCTCTT 59.997 52.381 9.37 0.00 37.91 2.85
3757 5152 1.056660 TCTCCGGCAAAGACCTCTTT 58.943 50.000 0.00 0.00 46.23 2.52
3758 5153 1.420138 TCTCCGGCAAAGACCTCTTTT 59.580 47.619 0.00 0.00 43.07 2.27
3759 5154 2.158667 TCTCCGGCAAAGACCTCTTTTT 60.159 45.455 0.00 0.00 43.07 1.94
3778 5173 3.982576 TTTTTCTCCGGCAAAGAACTC 57.017 42.857 3.66 0.00 32.64 3.01
3779 5174 2.930826 TTTCTCCGGCAAAGAACTCT 57.069 45.000 3.66 0.00 32.64 3.24
3780 5175 2.457366 TTCTCCGGCAAAGAACTCTC 57.543 50.000 0.00 0.00 0.00 3.20
3781 5176 1.633774 TCTCCGGCAAAGAACTCTCT 58.366 50.000 0.00 0.00 0.00 3.10
3782 5177 1.971357 TCTCCGGCAAAGAACTCTCTT 59.029 47.619 0.00 0.00 44.11 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.055667 TCCTATATTCCACTAGTGCTTCAAG 57.944 40.000 17.86 9.34 0.00 3.02
53 54 4.083484 CGTACACCAACAAAGAGGGATTTC 60.083 45.833 0.00 0.00 0.00 2.17
63 64 4.277174 AGAATTGCATCGTACACCAACAAA 59.723 37.500 0.00 0.00 0.00 2.83
143 144 4.718961 ACAATTTCCCTGAAGATATCCGG 58.281 43.478 0.00 0.00 32.48 5.14
144 145 5.590259 ACAACAATTTCCCTGAAGATATCCG 59.410 40.000 0.00 0.00 0.00 4.18
145 146 6.039829 GGACAACAATTTCCCTGAAGATATCC 59.960 42.308 0.00 0.00 0.00 2.59
152 155 3.636679 TGTGGACAACAATTTCCCTGAA 58.363 40.909 0.00 0.00 35.24 3.02
191 218 3.534889 CATGATGCGTAATTGTGTAGCG 58.465 45.455 0.00 0.00 0.00 4.26
197 224 5.858381 ACTAGATCCATGATGCGTAATTGT 58.142 37.500 0.00 0.00 0.00 2.71
255 301 6.325028 CCCTTACTAGTGAATTCATCCAGAGA 59.675 42.308 12.12 1.42 0.00 3.10
333 379 4.816786 ACACCACGTGTTAAAATGGTAC 57.183 40.909 15.65 0.00 45.08 3.34
334 380 4.996122 CCTACACCACGTGTTAAAATGGTA 59.004 41.667 15.65 4.19 45.08 3.25
337 383 5.676532 TTCCTACACCACGTGTTAAAATG 57.323 39.130 15.65 5.34 45.08 2.32
338 384 5.335348 GCATTCCTACACCACGTGTTAAAAT 60.335 40.000 15.65 2.29 45.08 1.82
359 405 0.036010 CCCACAGGAGTCGAAAGCAT 60.036 55.000 0.00 0.00 33.47 3.79
374 420 2.369394 CTATTTCAGTTGGAGGCCCAC 58.631 52.381 0.00 0.00 43.41 4.61
517 566 4.587262 AGGAACATGGTTAAAGTTGGAACC 59.413 41.667 11.43 11.43 44.60 3.62
522 611 7.827236 TGAGGTATAGGAACATGGTTAAAGTTG 59.173 37.037 0.00 0.00 0.00 3.16
528 617 8.966155 TCATATGAGGTATAGGAACATGGTTA 57.034 34.615 0.00 0.00 29.73 2.85
623 713 5.774690 TGGTGATTTCCTCAAATAAACTGCT 59.225 36.000 0.00 0.00 35.07 4.24
711 804 4.882671 ATATTTCTGTGGTTGATCGTGC 57.117 40.909 0.00 0.00 0.00 5.34
714 807 7.293745 GCATAGAATATTTCTGTGGTTGATCG 58.706 38.462 13.57 0.00 45.61 3.69
740 1061 1.630223 TGGCCAGCAATGACATCAAA 58.370 45.000 0.00 0.00 0.00 2.69
795 1124 6.373774 CCAACTTCATCAGAGAATAGCAAGTT 59.626 38.462 0.00 0.00 34.03 2.66
813 1142 4.821805 TCCAGAACTTCATTGACCAACTTC 59.178 41.667 0.00 0.00 0.00 3.01
971 1323 8.169977 TGATGCAAGAAGAGAATAAACAAACT 57.830 30.769 0.00 0.00 0.00 2.66
1272 1630 6.658816 TCAGCATAAACCTGCAGATTTAAGAA 59.341 34.615 17.19 0.00 44.77 2.52
1304 1663 1.704628 TCATGAGTGGACATGGTGGTT 59.295 47.619 0.00 0.00 45.10 3.67
1368 1727 2.111756 GCGTGAAACAGTTGCAGAAAG 58.888 47.619 0.00 0.00 35.74 2.62
1735 2094 5.240013 TCAAGGGCAAAAGCCAAATATTT 57.760 34.783 8.94 0.00 0.00 1.40
1738 2097 6.558488 ATTATCAAGGGCAAAAGCCAAATA 57.442 33.333 8.94 0.00 0.00 1.40
1751 2110 9.467258 CATGCATAAGTGTTTTATTATCAAGGG 57.533 33.333 0.00 0.00 0.00 3.95
1771 2130 7.670140 ACCTATCATTTCATCTTGATCATGCAT 59.330 33.333 0.00 0.00 34.52 3.96
1822 2181 4.989797 TCAAATTACAAGTTGGCAATGCAG 59.010 37.500 7.79 0.00 34.95 4.41
1830 2189 8.918658 CAGATTGATTGTCAAATTACAAGTTGG 58.081 33.333 7.96 0.00 42.33 3.77
1871 2230 6.129179 CCAATTATTTCCTAGGTGACCATGT 58.871 40.000 9.08 0.00 0.00 3.21
2011 2387 6.004574 AGATGACCTAGTAGCATGATAACGA 58.995 40.000 0.00 0.00 0.00 3.85
2032 2408 5.713861 ACCAAAGAGCAAGCTCATAAAAGAT 59.286 36.000 22.68 0.00 44.99 2.40
2041 2417 2.498167 TGAAGACCAAAGAGCAAGCTC 58.502 47.619 14.00 14.00 43.03 4.09
2072 2448 5.645056 TCCATTAGAATTAGATGCCCACA 57.355 39.130 0.00 0.00 0.00 4.17
2087 2463 4.536295 AAATAGGGTGGGGTTCCATTAG 57.464 45.455 0.00 0.00 46.09 1.73
2119 2495 6.899393 AAGAAAGCAAATATCCAGTCAACA 57.101 33.333 0.00 0.00 0.00 3.33
2148 2524 7.668886 AGCCAGCTCAAAGCAAATATATATTCT 59.331 33.333 8.42 0.18 45.56 2.40
2154 2530 5.885352 TGTAAGCCAGCTCAAAGCAAATATA 59.115 36.000 1.29 0.00 45.56 0.86
2250 2626 5.941788 AGATACCATGTCCACTTAATTCCC 58.058 41.667 0.00 0.00 0.00 3.97
2259 2635 5.680619 TCCATGTTAAGATACCATGTCCAC 58.319 41.667 0.00 0.00 35.34 4.02
2269 2645 5.924356 TGCTTCCGATTCCATGTTAAGATA 58.076 37.500 0.00 0.00 0.00 1.98
2275 2651 3.632145 GGTATTGCTTCCGATTCCATGTT 59.368 43.478 0.00 0.00 0.00 2.71
2276 2652 3.214328 GGTATTGCTTCCGATTCCATGT 58.786 45.455 0.00 0.00 0.00 3.21
2278 2983 3.480470 CTGGTATTGCTTCCGATTCCAT 58.520 45.455 0.00 0.00 33.38 3.41
2279 2984 2.421388 CCTGGTATTGCTTCCGATTCCA 60.421 50.000 0.00 0.00 32.97 3.53
2283 2988 0.179018 GGCCTGGTATTGCTTCCGAT 60.179 55.000 0.00 0.00 0.00 4.18
2285 2990 0.815615 GAGGCCTGGTATTGCTTCCG 60.816 60.000 12.00 0.00 0.00 4.30
2291 2996 3.217626 GAAATCCTGAGGCCTGGTATTG 58.782 50.000 12.00 0.00 33.58 1.90
2294 2999 1.965414 TGAAATCCTGAGGCCTGGTA 58.035 50.000 12.00 0.00 33.58 3.25
2304 3009 1.336440 TGCACACCGTTTGAAATCCTG 59.664 47.619 0.00 0.00 0.00 3.86
2316 3022 2.078849 TCTAGTCATTGTGCACACCG 57.921 50.000 21.56 13.81 0.00 4.94
2470 3176 7.392953 TGACATGTTCAGAGCCAAATACAATTA 59.607 33.333 0.00 0.00 0.00 1.40
2522 3256 5.429130 AGGTCTAAAGAAACCGAATGGATC 58.571 41.667 0.00 0.00 40.63 3.36
2530 3264 8.767478 TTAGAACAATAGGTCTAAAGAAACCG 57.233 34.615 0.77 0.00 40.63 4.44
2541 3275 6.038997 AGACCACACTTAGAACAATAGGTC 57.961 41.667 0.00 0.00 42.43 3.85
2574 3315 3.469006 AGGACTGGGATCTTGATCTCCTA 59.531 47.826 13.91 0.00 0.00 2.94
2634 3375 1.068472 GTGTATATCCAGAGGTCGGCG 60.068 57.143 0.00 0.00 0.00 6.46
2689 3430 0.179150 CGCCTCAGGTTCTCTCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
2925 3666 3.265791 CTCCAGAAATGTCTACAGCACC 58.734 50.000 0.00 0.00 30.85 5.01
3130 3873 7.776969 AGAGCCAATGATTCATTACTTACATGT 59.223 33.333 11.44 2.69 32.35 3.21
3174 3917 0.413037 ATGGCATTCCCCCAAACAGA 59.587 50.000 0.00 0.00 35.67 3.41
3219 3962 1.202582 ACTGCTCTAGTCGACGCAAAT 59.797 47.619 15.18 5.77 33.17 2.32
3224 3967 0.517755 ACACACTGCTCTAGTCGACG 59.482 55.000 10.46 0.00 37.60 5.12
3233 3976 1.192534 GCGTCAAAGTACACACTGCTC 59.807 52.381 0.00 0.00 34.36 4.26
3254 4021 3.879295 TCGAATGGATTCCTGCAGAATTC 59.121 43.478 17.39 12.14 45.52 2.17
3274 4042 3.320626 TCAGACTTTGCAGACTCAATCG 58.679 45.455 0.00 0.00 0.00 3.34
3282 4050 6.732154 CAGAAAGATTTTCAGACTTTGCAGA 58.268 36.000 0.00 0.00 34.63 4.26
3286 4060 4.380974 GCGCAGAAAGATTTTCAGACTTTG 59.619 41.667 0.30 0.00 34.63 2.77
3287 4061 4.540824 GCGCAGAAAGATTTTCAGACTTT 58.459 39.130 0.30 0.00 36.71 2.66
3288 4062 3.057946 GGCGCAGAAAGATTTTCAGACTT 60.058 43.478 10.83 0.00 0.00 3.01
3289 4063 2.485814 GGCGCAGAAAGATTTTCAGACT 59.514 45.455 10.83 0.00 0.00 3.24
3290 4064 2.226437 TGGCGCAGAAAGATTTTCAGAC 59.774 45.455 10.83 0.00 0.00 3.51
3292 4066 2.995466 TGGCGCAGAAAGATTTTCAG 57.005 45.000 10.83 0.00 0.00 3.02
3293 4067 4.094887 GTCTATGGCGCAGAAAGATTTTCA 59.905 41.667 10.83 0.00 0.00 2.69
3297 4071 2.205074 CGTCTATGGCGCAGAAAGATT 58.795 47.619 10.83 0.00 0.00 2.40
3298 4072 1.137086 ACGTCTATGGCGCAGAAAGAT 59.863 47.619 10.83 0.00 0.00 2.40
3318 4706 4.264253 CAATCCATACAGCTTGTCTCCAA 58.736 43.478 0.00 0.00 0.00 3.53
3432 4820 3.423154 CCTCTTGCAACGACGGCC 61.423 66.667 0.00 0.00 0.00 6.13
3495 4883 0.252696 ATCCACCTCAGGCCACTGTA 60.253 55.000 5.01 0.00 45.14 2.74
3503 4891 3.276857 CAAATGAGACATCCACCTCAGG 58.723 50.000 0.00 0.00 42.00 3.86
3508 4896 3.420893 TGGAACAAATGAGACATCCACC 58.579 45.455 0.00 0.00 32.28 4.61
3516 4904 0.953471 CGGGCGTGGAACAAATGAGA 60.953 55.000 0.00 0.00 44.16 3.27
3574 4962 2.582272 CAGTCTCAGGCTCTGCTCT 58.418 57.895 0.00 0.00 0.00 4.09
3579 4967 0.246086 CGAAAGCAGTCTCAGGCTCT 59.754 55.000 0.00 0.00 40.01 4.09
3581 4969 1.294780 CCGAAAGCAGTCTCAGGCT 59.705 57.895 0.00 0.00 43.46 4.58
3703 5098 4.712873 GCACGTTTCGAACCGCGG 62.713 66.667 26.86 26.86 41.33 6.46
3720 5115 5.462398 CCGGAGAAGATATAGAAACCAAACG 59.538 44.000 0.00 0.00 0.00 3.60
3730 5125 4.282195 AGGTCTTTGCCGGAGAAGATATAG 59.718 45.833 18.98 0.94 34.68 1.31
3731 5126 4.223953 AGGTCTTTGCCGGAGAAGATATA 58.776 43.478 18.98 0.00 34.68 0.86
3732 5127 3.041946 AGGTCTTTGCCGGAGAAGATAT 58.958 45.455 18.98 10.60 34.68 1.63
3733 5128 2.431057 GAGGTCTTTGCCGGAGAAGATA 59.569 50.000 18.98 0.27 34.68 1.98
3734 5129 1.208293 GAGGTCTTTGCCGGAGAAGAT 59.792 52.381 18.98 7.79 34.68 2.40
3735 5130 0.608640 GAGGTCTTTGCCGGAGAAGA 59.391 55.000 5.05 10.99 0.00 2.87
3736 5131 0.610687 AGAGGTCTTTGCCGGAGAAG 59.389 55.000 5.05 8.42 0.00 2.85
3737 5132 1.056660 AAGAGGTCTTTGCCGGAGAA 58.943 50.000 5.05 0.00 30.82 2.87
3738 5133 1.056660 AAAGAGGTCTTTGCCGGAGA 58.943 50.000 5.05 0.00 43.87 3.71
3739 5134 1.897560 AAAAGAGGTCTTTGCCGGAG 58.102 50.000 5.05 0.00 44.69 4.63
3740 5135 2.358322 AAAAAGAGGTCTTTGCCGGA 57.642 45.000 5.05 0.00 44.69 5.14
3758 5153 3.551846 AGAGTTCTTTGCCGGAGAAAAA 58.448 40.909 5.05 0.00 35.11 1.94
3759 5154 3.139077 GAGAGTTCTTTGCCGGAGAAAA 58.861 45.455 5.05 0.83 35.11 2.29
3760 5155 2.368875 AGAGAGTTCTTTGCCGGAGAAA 59.631 45.455 5.05 1.65 35.11 2.52
3761 5156 1.971357 AGAGAGTTCTTTGCCGGAGAA 59.029 47.619 5.05 1.96 0.00 2.87
3762 5157 1.633774 AGAGAGTTCTTTGCCGGAGA 58.366 50.000 5.05 0.00 0.00 3.71
3763 5158 2.464157 AAGAGAGTTCTTTGCCGGAG 57.536 50.000 5.05 0.00 40.79 4.63


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

AutoCloner maintained by Alex Coulton.