Multiple sequence alignment - TraesCS2B01G295400

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 TraesCS2B01G295400 chr2B 100.000 7916 0 0 1 7916 412409315 412401400 0.000000e+00 14619
1 TraesCS2B01G295400 chr2B 99.137 695 3 1 4882 5573 348401065 348400371 0.000000e+00 1247
2 TraesCS2B01G295400 chr2A 94.550 4917 159 43 39 4892 460909080 460904210 0.000000e+00 7494
3 TraesCS2B01G295400 chr2A 91.993 1074 37 24 6870 7916 460902478 460901427 0.000000e+00 1461
4 TraesCS2B01G295400 chr2A 94.917 905 22 4 5708 6590 460903785 460902883 0.000000e+00 1395
5 TraesCS2B01G295400 chr2A 92.746 193 10 4 5703 5893 460903998 460903808 7.820000e-70 276
6 TraesCS2B01G295400 chr2D 95.994 3844 104 23 39 3851 346585340 346581516 0.000000e+00 6200
7 TraesCS2B01G295400 chr2D 92.390 1209 47 14 3720 4898 346581534 346580341 0.000000e+00 1681
8 TraesCS2B01G295400 chr2D 93.045 1064 40 17 6870 7916 346577651 346576605 0.000000e+00 1524
9 TraesCS2B01G295400 chr2D 93.768 1027 32 9 5653 6649 346579291 346578267 0.000000e+00 1513
10 TraesCS2B01G295400 chr6A 99.144 818 7 0 4882 5699 124140392 124141209 0.000000e+00 1472
11 TraesCS2B01G295400 chr3A 99.144 818 7 0 4882 5699 732491044 732490227 0.000000e+00 1472
12 TraesCS2B01G295400 chr3A 97.333 750 9 1 4911 5660 732491793 732491055 0.000000e+00 1264
13 TraesCS2B01G295400 chr3A 94.133 784 40 4 4918 5699 39602976 39602197 0.000000e+00 1188
14 TraesCS2B01G295400 chr3A 98.294 586 7 1 5088 5670 39603572 39602987 0.000000e+00 1024
15 TraesCS2B01G295400 chr3A 99.658 292 1 0 5387 5678 37812533 37812242 1.170000e-147 534
16 TraesCS2B01G295400 chr3A 91.905 210 12 5 4882 5091 39603916 39603712 1.010000e-73 289
17 TraesCS2B01G295400 chrUn 98.765 648 8 0 4930 5577 471241550 471240903 0.000000e+00 1153
18 TraesCS2B01G295400 chr7D 90.956 774 56 5 7147 7916 91678514 91679277 0.000000e+00 1029
19 TraesCS2B01G295400 chr7A 90.360 778 57 13 7145 7915 93251287 93252053 0.000000e+00 1005
20 TraesCS2B01G295400 chr7B 89.793 774 65 7 7147 7916 43250146 43249383 0.000000e+00 979
21 TraesCS2B01G295400 chr5D 86.344 681 81 4 7248 7916 543586060 543586740 0.000000e+00 732
22 TraesCS2B01G295400 chr5A 92.188 384 30 0 7533 7916 9593204 9593587 1.940000e-150 544
23 TraesCS2B01G295400 chr5A 88.660 388 35 7 7147 7529 9589856 9590239 1.560000e-126 464


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 TraesCS2B01G295400 chr2B 412401400 412409315 7915 True 14619.000000 14619 100.000000 1 7916 1 chr2B.!!$R2 7915
1 TraesCS2B01G295400 chr2B 348400371 348401065 694 True 1247.000000 1247 99.137000 4882 5573 1 chr2B.!!$R1 691
2 TraesCS2B01G295400 chr2A 460901427 460909080 7653 True 2656.500000 7494 93.551500 39 7916 4 chr2A.!!$R1 7877
3 TraesCS2B01G295400 chr2D 346576605 346585340 8735 True 2729.500000 6200 93.799250 39 7916 4 chr2D.!!$R1 7877
4 TraesCS2B01G295400 chr6A 124140392 124141209 817 False 1472.000000 1472 99.144000 4882 5699 1 chr6A.!!$F1 817
5 TraesCS2B01G295400 chr3A 732490227 732491793 1566 True 1368.000000 1472 98.238500 4882 5699 2 chr3A.!!$R3 817
6 TraesCS2B01G295400 chr3A 39602197 39603916 1719 True 833.666667 1188 94.777333 4882 5699 3 chr3A.!!$R2 817
7 TraesCS2B01G295400 chrUn 471240903 471241550 647 True 1153.000000 1153 98.765000 4930 5577 1 chrUn.!!$R1 647
8 TraesCS2B01G295400 chr7D 91678514 91679277 763 False 1029.000000 1029 90.956000 7147 7916 1 chr7D.!!$F1 769
9 TraesCS2B01G295400 chr7A 93251287 93252053 766 False 1005.000000 1005 90.360000 7145 7915 1 chr7A.!!$F1 770
10 TraesCS2B01G295400 chr7B 43249383 43250146 763 True 979.000000 979 89.793000 7147 7916 1 chr7B.!!$R1 769
11 TraesCS2B01G295400 chr5D 543586060 543586740 680 False 732.000000 732 86.344000 7248 7916 1 chr5D.!!$F1 668
12 TraesCS2B01G295400 chr5A 9589856 9593587 3731 False 504.000000 544 90.424000 7147 7916 2 chr5A.!!$F1 769

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
112 113 0.326927 CGCCCTTTTTAGACCCTCCA 59.673 55.000 0.0 0.0 0.00 3.86 F
719 757 1.051556 GGGCAAAAACCACTGGGGAA 61.052 55.000 1.1 0.0 41.15 3.97 F
1150 1205 0.179119 CCTGACCCGATTCGTGTACC 60.179 60.000 5.2 0.0 0.00 3.34 F
1339 1394 1.007038 CCGTCCGTTGTTTCCTCGA 60.007 57.895 0.0 0.0 0.00 4.04 F
1746 1801 1.302832 CTGTTGCCCCTGTGGAGAC 60.303 63.158 0.0 0.0 35.39 3.36 F
1979 2034 1.750682 GCCTGTTGTGGAGGAAACACT 60.751 52.381 0.0 0.0 39.52 3.55 F
2758 2820 1.881973 GAGCAGCAACATTCAAGACCA 59.118 47.619 0.0 0.0 0.00 4.02 F
4215 4418 0.613260 AGGACGCCTGCATGAACTTA 59.387 50.000 0.0 0.0 29.57 2.24 F
4324 4527 0.396974 TGCAGGTCTTGGGTTGCTTT 60.397 50.000 0.0 0.0 37.45 3.51 F
4767 4982 1.280982 CTGTGACGATTGATGACCGG 58.719 55.000 0.0 0.0 0.00 5.28 F
6370 8314 1.668151 GTGTCGTGAGCTGGGTTCC 60.668 63.158 0.0 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1150 1205 0.388649 CCACCTGGAAGACGAAGACG 60.389 60.000 0.0 0.0 40.81 4.18 R
2695 2757 0.399454 AGCATCAACAGCCACAGACT 59.601 50.000 0.0 0.0 0.00 3.24 R
2972 3034 5.356426 TCATCACGTTGAGAGAAGAAAACA 58.644 37.500 0.0 0.0 0.00 2.83 R
3209 3274 4.889409 AGGCATTCCCATTAACTACACATG 59.111 41.667 0.0 0.0 35.39 3.21 R
3404 3480 2.037901 TCAAAGGCAGCACCAATCAAA 58.962 42.857 0.0 0.0 43.14 2.69 R
3691 3770 2.355132 ACAGGTAGTCAGATAGCGAACG 59.645 50.000 0.0 0.0 0.00 3.95 R
4263 4466 0.677731 TACAGCAATGCCAGCTCCAC 60.678 55.000 0.0 0.0 41.14 4.02 R
6020 7964 2.159028 GCTACTACCTGAAGCCAGAAGG 60.159 54.545 0.0 0.0 43.02 3.46 R
6370 8314 2.943345 GCTGACAACGACCGCACAG 61.943 63.158 0.0 0.0 0.00 3.66 R
6736 8746 0.320374 CTTGTACTCCGCCTTGTCCA 59.680 55.000 0.0 0.0 0.00 4.02 R
7328 9711 0.673644 CCAAGTTCCCGTTGAGCGAT 60.674 55.000 0.0 0.0 44.77 4.58 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
19 20 2.385013 CACCGTCATCCACTTCATGA 57.615 50.000 0.00 0.00 0.00 3.07
20 21 2.002586 CACCGTCATCCACTTCATGAC 58.997 52.381 0.00 3.19 44.62 3.06
24 25 3.729526 GTCATCCACTTCATGACGTTG 57.270 47.619 1.38 0.00 40.53 4.10
25 26 3.325870 GTCATCCACTTCATGACGTTGA 58.674 45.455 8.33 8.33 40.53 3.18
26 27 3.935203 GTCATCCACTTCATGACGTTGAT 59.065 43.478 11.75 11.75 40.53 2.57
27 28 4.393062 GTCATCCACTTCATGACGTTGATT 59.607 41.667 14.14 1.12 40.53 2.57
29 30 5.122239 TCATCCACTTCATGACGTTGATTTC 59.878 40.000 14.14 0.00 0.00 2.17
31 32 5.003160 TCCACTTCATGACGTTGATTTCAT 58.997 37.500 1.38 0.00 32.44 2.57
33 34 5.327091 CACTTCATGACGTTGATTTCATCC 58.673 41.667 1.38 0.00 29.64 3.51
34 35 5.122869 CACTTCATGACGTTGATTTCATCCT 59.877 40.000 1.38 0.00 29.64 3.24
35 36 5.352569 ACTTCATGACGTTGATTTCATCCTC 59.647 40.000 0.00 0.00 29.64 3.71
102 103 2.162681 CACATTCTCCTCGCCCTTTTT 58.837 47.619 0.00 0.00 0.00 1.94
106 107 3.329929 TTCTCCTCGCCCTTTTTAGAC 57.670 47.619 0.00 0.00 0.00 2.59
112 113 0.326927 CGCCCTTTTTAGACCCTCCA 59.673 55.000 0.00 0.00 0.00 3.86
197 199 4.574599 AGATGAGAAAACTGTGGTTTGC 57.425 40.909 0.00 0.00 43.90 3.68
311 313 5.136828 AGATCTAGATGACGGTGAACTCAT 58.863 41.667 10.74 0.00 0.00 2.90
313 315 2.680312 AGATGACGGTGAACTCATGG 57.320 50.000 0.00 0.00 0.00 3.66
320 322 2.009774 CGGTGAACTCATGGTGGAATC 58.990 52.381 0.00 0.00 0.00 2.52
358 360 6.381250 AGGAGAGAAATACTAGATGGAAGCT 58.619 40.000 0.00 0.00 35.48 3.74
361 363 7.039082 GGAGAGAAATACTAGATGGAAGCTGAT 60.039 40.741 0.00 0.00 30.71 2.90
427 430 4.096732 GTGGACCTCACATTTTACATGC 57.903 45.455 0.00 0.00 45.39 4.06
473 482 5.465390 TCAAGAACTACCAAACGAATCACAG 59.535 40.000 0.00 0.00 0.00 3.66
719 757 1.051556 GGGCAAAAACCACTGGGGAA 61.052 55.000 1.10 0.00 41.15 3.97
987 1030 4.150454 CTCGCCCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
988 1031 4.144727 TCGCCCCTCCTCCTCCTC 62.145 72.222 0.00 0.00 0.00 3.71
990 1033 3.773154 GCCCCTCCTCCTCCTCCT 61.773 72.222 0.00 0.00 0.00 3.69
991 1034 2.612251 CCCCTCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
1150 1205 0.179119 CCTGACCCGATTCGTGTACC 60.179 60.000 5.20 0.00 0.00 3.34
1213 1268 1.434188 ACAACATCCTCCACCAGTCA 58.566 50.000 0.00 0.00 0.00 3.41
1339 1394 1.007038 CCGTCCGTTGTTTCCTCGA 60.007 57.895 0.00 0.00 0.00 4.04
1746 1801 1.302832 CTGTTGCCCCTGTGGAGAC 60.303 63.158 0.00 0.00 35.39 3.36
1979 2034 1.750682 GCCTGTTGTGGAGGAAACACT 60.751 52.381 0.00 0.00 39.52 3.55
2329 2385 9.162764 GGAGAGTAAATGTTTACATGAAGCTTA 57.837 33.333 15.67 0.00 44.14 3.09
2489 2551 5.185828 ACATCACTGTTGTCTATCTAGTGCA 59.814 40.000 0.00 0.00 38.81 4.57
2499 2561 6.472016 TGTCTATCTAGTGCATTTGGTTGAA 58.528 36.000 0.00 0.00 0.00 2.69
2524 2586 6.698766 AGAATTGTTTGAAGCTTGTTGATGTC 59.301 34.615 2.10 0.00 0.00 3.06
2637 2699 1.962807 CAGTTCTGCCACCAAATTCCA 59.037 47.619 0.00 0.00 0.00 3.53
2669 2731 2.430610 GCCTGCACCACCAAAACCA 61.431 57.895 0.00 0.00 0.00 3.67
2758 2820 1.881973 GAGCAGCAACATTCAAGACCA 59.118 47.619 0.00 0.00 0.00 4.02
2972 3034 4.288626 TCCAAGTTAGAAGCCACAAGGTAT 59.711 41.667 0.00 0.00 37.19 2.73
2989 3051 6.202954 ACAAGGTATGTTTTCTTCTCTCAACG 59.797 38.462 0.00 0.00 40.06 4.10
3244 3309 3.585289 TGGGAATGCCTGTAGTGAGTTTA 59.415 43.478 0.00 0.00 0.00 2.01
3404 3480 9.195411 CAAAGCAAGTTCATTGTGTTTATGTAT 57.805 29.630 0.00 0.00 41.29 2.29
3661 3740 3.895041 TGAGTTGGAGATTTTCAAACCCC 59.105 43.478 0.00 0.00 40.11 4.95
3662 3741 3.895041 GAGTTGGAGATTTTCAAACCCCA 59.105 43.478 0.00 0.00 40.11 4.96
3691 3770 2.092968 TCCCCTAACACATGCATGAGTC 60.093 50.000 32.75 0.00 31.23 3.36
3708 3787 3.309138 TGAGTCGTTCGCTATCTGACTAC 59.691 47.826 0.00 0.00 39.83 2.73
3723 3802 6.761099 TCTGACTACCTGTAGAGAATGTTC 57.239 41.667 11.14 0.00 36.97 3.18
3774 3970 7.918076 ACAAGGTTCTTGAGGAATGTATCTTA 58.082 34.615 13.74 0.00 36.24 2.10
3853 4051 1.940613 GTTGCTTCCACTTGTTCTCGT 59.059 47.619 0.00 0.00 0.00 4.18
3862 4060 4.215827 TCCACTTGTTCTCGTACTCTCTTC 59.784 45.833 0.00 0.00 0.00 2.87
3884 4082 6.373005 TCATCCTAGATCTTGTTTGGTTCA 57.627 37.500 0.00 0.00 0.00 3.18
3894 4092 8.352942 AGATCTTGTTTGGTTCATAGTTTTGAC 58.647 33.333 0.00 0.00 0.00 3.18
3905 4103 5.227908 TCATAGTTTTGACGACTTGAGTCC 58.772 41.667 5.61 0.00 41.86 3.85
3913 4111 2.915463 GACGACTTGAGTCCGTTACATG 59.085 50.000 5.61 0.00 41.86 3.21
3937 4135 6.266558 TGTGTTTGTTCAGTTGGGCTATAAAT 59.733 34.615 0.00 0.00 0.00 1.40
3998 4198 3.593442 ACACCCACCTCATTCTGAAAA 57.407 42.857 0.00 0.00 0.00 2.29
4015 4215 4.946445 TGAAAACAGAAAATGCTGCATCA 58.054 34.783 16.55 3.32 39.51 3.07
4158 4361 3.202818 TCCATATGAGAAGCACCACCATT 59.797 43.478 3.65 0.00 0.00 3.16
4170 4373 2.624838 CACCACCATTGAAAGAGCAGTT 59.375 45.455 0.00 0.00 0.00 3.16
4184 4387 0.645868 GCAGTTTCGACCGCTGATAC 59.354 55.000 12.50 0.00 32.39 2.24
4192 4395 1.596464 CGACCGCTGATACTCGTTACC 60.596 57.143 0.00 0.00 0.00 2.85
4215 4418 0.613260 AGGACGCCTGCATGAACTTA 59.387 50.000 0.00 0.00 29.57 2.24
4260 4463 2.603473 CGTGGTGGTGGGAGGAGA 60.603 66.667 0.00 0.00 0.00 3.71
4263 4466 3.391382 GGTGGTGGGAGGAGACCG 61.391 72.222 0.00 0.00 34.69 4.79
4300 4503 1.048160 TAGATGCGGTGGATCAGCCA 61.048 55.000 0.00 0.00 46.96 4.75
4324 4527 0.396974 TGCAGGTCTTGGGTTGCTTT 60.397 50.000 0.00 0.00 37.45 3.51
4378 4581 8.915654 GGTCAATTTGTTGTTATTTGTGAGATC 58.084 33.333 0.00 0.00 0.00 2.75
4416 4619 6.862209 TCGGATTTCTTTTATTGATTGGGTG 58.138 36.000 0.00 0.00 0.00 4.61
4418 4621 6.350949 CGGATTTCTTTTATTGATTGGGTGGT 60.351 38.462 0.00 0.00 0.00 4.16
4423 4626 9.771534 TTTCTTTTATTGATTGGGTGGTTTAAG 57.228 29.630 0.00 0.00 0.00 1.85
4438 4641 5.183904 GTGGTTTAAGTCAATGCCAGATCTT 59.816 40.000 0.00 0.00 0.00 2.40
4485 4700 6.155221 ACAGAGCATACCAGAGACAAGATAAA 59.845 38.462 0.00 0.00 0.00 1.40
4551 4766 2.690173 TTTTGGTCATGCCGTTTACG 57.310 45.000 0.00 0.00 41.21 3.18
4579 4794 6.370718 GCCGTAGTAATCCGATTCCAATTAAT 59.629 38.462 0.00 0.00 0.00 1.40
4622 4837 3.321682 CCACACATGTTCCTGGATTGTTT 59.678 43.478 0.00 0.00 0.00 2.83
4630 4845 4.586421 TGTTCCTGGATTGTTTGTTATGCA 59.414 37.500 0.00 0.00 0.00 3.96
4705 4920 8.757982 ATCAATTTCATAAGCTCCATACTTGT 57.242 30.769 0.00 0.00 0.00 3.16
4767 4982 1.280982 CTGTGACGATTGATGACCGG 58.719 55.000 0.00 0.00 0.00 5.28
4770 4985 2.202878 ACGATTGATGACCGGCCG 60.203 61.111 21.04 21.04 0.00 6.13
5223 5817 4.159879 ACGGTTACTAAATCTGCTAGCACT 59.840 41.667 14.93 0.58 0.00 4.40
5864 7786 8.319143 TGAGATGAACATGAAGCACATATATG 57.681 34.615 11.29 11.29 37.46 1.78
6248 8192 3.941188 CACTCTGGCACCGGTGGT 61.941 66.667 34.58 20.93 35.62 4.16
6370 8314 1.668151 GTGTCGTGAGCTGGGTTCC 60.668 63.158 0.00 0.00 0.00 3.62
6408 8352 5.527214 TCAGCGTATTCAGGTCATAAATTGG 59.473 40.000 0.00 0.00 0.00 3.16
6439 8383 2.204237 GTTTTGTGGCAAGGAAAGCAG 58.796 47.619 0.00 0.00 0.00 4.24
6574 8518 8.816640 ATGTTACAAATCCAACATCAGTTTTC 57.183 30.769 0.00 0.00 40.47 2.29
6591 8535 5.927689 CAGTTTTCTTTAGCATGGCAAATCA 59.072 36.000 0.00 0.00 0.00 2.57
6600 8544 2.690786 CATGGCAAATCAAACACCTGG 58.309 47.619 0.00 0.00 0.00 4.45
6619 8563 4.441913 CCTGGGATGGCAAATTATGTTGTC 60.442 45.833 0.00 0.00 33.59 3.18
6621 8565 3.115554 GGATGGCAAATTATGTTGTCGC 58.884 45.455 0.00 0.00 35.83 5.19
6625 8569 2.413502 GGCAAATTATGTTGTCGCGTGA 60.414 45.455 5.77 0.00 0.00 4.35
6688 8696 7.854557 TCCACAATCTAAAATCTGATGTCAG 57.145 36.000 3.61 3.61 45.08 3.51
6744 8754 4.500499 AGATCTCCTGATTTGGACAAGG 57.500 45.455 0.00 0.00 32.19 3.61
6756 8766 0.391263 GGACAAGGCGGAGTACAAGG 60.391 60.000 0.00 0.00 0.00 3.61
6761 8832 2.820037 GCGGAGTACAAGGCTGGC 60.820 66.667 0.00 0.00 0.00 4.85
6776 8848 3.031013 GGCTGGCTGGGTAATTGTTTAT 58.969 45.455 0.00 0.00 0.00 1.40
6784 8856 6.265577 GCTGGGTAATTGTTTATAGTTGCTG 58.734 40.000 0.00 0.00 0.00 4.41
6804 9114 6.228995 TGCTGAAAATTAATGCATCAAACCA 58.771 32.000 0.00 0.00 0.00 3.67
6836 9148 4.439057 GGAACGACTAAATGGCATCAGTA 58.561 43.478 13.01 1.12 0.00 2.74
6859 9171 6.076981 ACCTGTGCTTTAGAATTGAACTTG 57.923 37.500 0.00 0.00 0.00 3.16
6877 9226 6.264292 TGAACTTGCTAATTTGGTCTGCTTTA 59.736 34.615 0.00 0.00 0.00 1.85
6880 9229 4.016444 TGCTAATTTGGTCTGCTTTAGGG 58.984 43.478 0.00 0.00 0.00 3.53
6886 9235 2.334977 TGGTCTGCTTTAGGGTCTCAA 58.665 47.619 0.00 0.00 0.00 3.02
6891 9240 6.385759 TGGTCTGCTTTAGGGTCTCAATATAA 59.614 38.462 0.00 0.00 0.00 0.98
6952 9302 4.390297 GGATCGAGAAAAACTGAAGGTGAG 59.610 45.833 0.00 0.00 0.00 3.51
6963 9313 6.672266 AACTGAAGGTGAGTCTGAATTCTA 57.328 37.500 7.05 0.00 0.00 2.10
6969 9319 4.081198 AGGTGAGTCTGAATTCTAGCCAAG 60.081 45.833 7.05 0.00 0.00 3.61
6970 9320 4.081420 GGTGAGTCTGAATTCTAGCCAAGA 60.081 45.833 7.05 0.00 0.00 3.02
6971 9321 5.396213 GGTGAGTCTGAATTCTAGCCAAGAT 60.396 44.000 7.05 0.00 33.05 2.40
6972 9322 5.752955 GTGAGTCTGAATTCTAGCCAAGATC 59.247 44.000 7.05 0.00 33.05 2.75
6973 9323 5.423290 TGAGTCTGAATTCTAGCCAAGATCA 59.577 40.000 7.05 3.92 33.05 2.92
6974 9324 5.669477 AGTCTGAATTCTAGCCAAGATCAC 58.331 41.667 7.05 0.00 33.05 3.06
6975 9325 5.424895 AGTCTGAATTCTAGCCAAGATCACT 59.575 40.000 7.05 0.00 33.05 3.41
6976 9326 6.070309 AGTCTGAATTCTAGCCAAGATCACTT 60.070 38.462 7.05 0.00 33.05 3.16
6977 9327 7.124901 AGTCTGAATTCTAGCCAAGATCACTTA 59.875 37.037 7.05 0.00 34.70 2.24
6994 9344 2.634940 ACTTACAGATGACCACTGCAGT 59.365 45.455 15.25 15.25 38.74 4.40
6999 9349 2.998670 CAGATGACCACTGCAGTACTTG 59.001 50.000 21.20 10.93 0.00 3.16
7002 9352 2.321719 TGACCACTGCAGTACTTGGTA 58.678 47.619 22.71 11.25 42.60 3.25
7013 9363 2.148768 GTACTTGGTAGTGGTTGCACC 58.851 52.381 0.00 0.00 39.22 5.01
7051 9401 3.669557 GCGAACCGTATTTTTGACAGCAT 60.670 43.478 0.00 0.00 0.00 3.79
7107 9457 6.560253 TTTTTGCAACTTATCTCTCTGTCC 57.440 37.500 0.00 0.00 0.00 4.02
7109 9459 4.890158 TGCAACTTATCTCTCTGTCCAA 57.110 40.909 0.00 0.00 0.00 3.53
7110 9460 5.426689 TGCAACTTATCTCTCTGTCCAAT 57.573 39.130 0.00 0.00 0.00 3.16
7111 9461 6.544928 TGCAACTTATCTCTCTGTCCAATA 57.455 37.500 0.00 0.00 0.00 1.90
7114 9490 7.334421 TGCAACTTATCTCTCTGTCCAATAAAC 59.666 37.037 0.00 0.00 0.00 2.01
7218 9601 3.557898 CCTCCACTGTCTGTATGCAAGTT 60.558 47.826 0.00 0.00 0.00 2.66
7234 9617 9.379791 GTATGCAAGTTCTTTGGTAATACTAGT 57.620 33.333 0.00 0.00 37.26 2.57
7236 9619 8.997621 TGCAAGTTCTTTGGTAATACTAGTAG 57.002 34.615 8.85 0.00 37.26 2.57
7237 9620 8.591072 TGCAAGTTCTTTGGTAATACTAGTAGT 58.409 33.333 8.85 8.47 37.26 2.73
7346 9729 0.443869 CATCGCTCAACGGGAACTTG 59.556 55.000 0.00 0.00 43.89 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.325870 TCAACGTCATGAAGTGGATGAC 58.674 45.455 15.21 0.00 44.24 3.06
5 6 3.676291 TCAACGTCATGAAGTGGATGA 57.324 42.857 15.21 12.04 0.00 2.92
6 7 4.952262 AATCAACGTCATGAAGTGGATG 57.048 40.909 26.23 16.26 34.44 3.51
8 9 4.384940 TGAAATCAACGTCATGAAGTGGA 58.615 39.130 19.37 19.37 32.06 4.02
9 10 4.747540 TGAAATCAACGTCATGAAGTGG 57.252 40.909 15.21 12.36 32.06 4.00
24 25 7.040132 AGGAAAGTGAGTTTTGAGGATGAAATC 60.040 37.037 0.00 0.00 44.55 2.17
25 26 6.779539 AGGAAAGTGAGTTTTGAGGATGAAAT 59.220 34.615 0.00 0.00 0.00 2.17
26 27 6.129179 AGGAAAGTGAGTTTTGAGGATGAAA 58.871 36.000 0.00 0.00 0.00 2.69
27 28 5.694995 AGGAAAGTGAGTTTTGAGGATGAA 58.305 37.500 0.00 0.00 0.00 2.57
29 30 4.457257 GGAGGAAAGTGAGTTTTGAGGATG 59.543 45.833 0.00 0.00 0.00 3.51
31 32 3.458118 TGGAGGAAAGTGAGTTTTGAGGA 59.542 43.478 0.00 0.00 0.00 3.71
33 34 4.036852 GGTTGGAGGAAAGTGAGTTTTGAG 59.963 45.833 0.00 0.00 0.00 3.02
34 35 3.951680 GGTTGGAGGAAAGTGAGTTTTGA 59.048 43.478 0.00 0.00 0.00 2.69
35 36 3.068165 GGGTTGGAGGAAAGTGAGTTTTG 59.932 47.826 0.00 0.00 0.00 2.44
102 103 1.273098 GGAGAAGTGGTGGAGGGTCTA 60.273 57.143 0.00 0.00 0.00 2.59
106 107 2.982130 CGGAGAAGTGGTGGAGGG 59.018 66.667 0.00 0.00 0.00 4.30
112 113 1.968493 TCTACAAAGCGGAGAAGTGGT 59.032 47.619 0.00 0.00 0.00 4.16
197 199 0.249073 CGACGGATTAGGGCAGAGTG 60.249 60.000 0.00 0.00 0.00 3.51
320 322 1.227089 CTCCTCACCGCGGAATCTG 60.227 63.158 35.90 20.40 0.00 2.90
332 334 6.266558 GCTTCCATCTAGTATTTCTCTCCTCA 59.733 42.308 0.00 0.00 0.00 3.86
473 482 0.784778 GTGTACTTGTGTCGCTCTGC 59.215 55.000 0.00 0.00 0.00 4.26
522 539 3.569200 GACCAGCCCCAACTCCACC 62.569 68.421 0.00 0.00 0.00 4.61
561 578 0.313043 ACCGGTGTAACGTGTCAGAG 59.687 55.000 6.12 0.00 38.12 3.35
719 757 2.594592 GCGGGAGTGCCTGTGTTT 60.595 61.111 0.00 0.00 42.93 2.83
956 999 2.115266 CGAGGGTTTTGGCAGGGT 59.885 61.111 0.00 0.00 0.00 4.34
986 1029 1.182385 GGCCATCGTAGGAGGAGGAG 61.182 65.000 0.00 0.00 0.00 3.69
987 1030 1.152525 GGCCATCGTAGGAGGAGGA 60.153 63.158 0.00 0.00 0.00 3.71
988 1031 2.565645 CGGCCATCGTAGGAGGAGG 61.566 68.421 2.24 0.00 0.00 4.30
989 1032 3.043419 CGGCCATCGTAGGAGGAG 58.957 66.667 2.24 0.00 0.00 3.69
990 1033 3.224324 GCGGCCATCGTAGGAGGA 61.224 66.667 2.24 0.00 41.72 3.71
991 1034 4.647615 CGCGGCCATCGTAGGAGG 62.648 72.222 2.24 0.00 41.72 4.30
1150 1205 0.388649 CCACCTGGAAGACGAAGACG 60.389 60.000 0.00 0.00 40.81 4.18
1715 1770 2.810439 GCAACAGTACCATTTGCCAA 57.190 45.000 11.01 0.00 39.82 4.52
1874 1929 3.011144 AGGAACAGACTCAGAGAGATCCA 59.989 47.826 3.79 0.00 33.32 3.41
1979 2034 3.994317 TCATCTATGACCTCAGGAACCA 58.006 45.455 0.00 0.00 0.00 3.67
2211 2267 9.679661 TTTCAATATATGCAGAACCTGTAAAGA 57.320 29.630 0.00 0.00 33.43 2.52
2329 2385 9.975218 ACAATAACCTTAAAAGTGAGACCATAT 57.025 29.630 0.00 0.00 0.00 1.78
2421 2480 3.436243 TGTTCCCCGGCAAAAGATAAAT 58.564 40.909 0.00 0.00 0.00 1.40
2489 2551 7.049754 AGCTTCAAACAATTCTTCAACCAAAT 58.950 30.769 0.00 0.00 0.00 2.32
2499 2561 6.576185 ACATCAACAAGCTTCAAACAATTCT 58.424 32.000 0.00 0.00 0.00 2.40
2524 2586 1.719246 CCAACGTACATATCATCCGCG 59.281 52.381 0.00 0.00 0.00 6.46
2695 2757 0.399454 AGCATCAACAGCCACAGACT 59.601 50.000 0.00 0.00 0.00 3.24
2773 2835 9.598517 GAAGGTTTTCAATGCAATATTGGATTA 57.401 29.630 28.13 15.53 45.61 1.75
2972 3034 5.356426 TCATCACGTTGAGAGAAGAAAACA 58.644 37.500 0.00 0.00 0.00 2.83
3042 3107 6.985645 CCCTTGAATCTGTGTTTTCAATTGAA 59.014 34.615 16.91 16.91 40.13 2.69
3209 3274 4.889409 AGGCATTCCCATTAACTACACATG 59.111 41.667 0.00 0.00 35.39 3.21
3210 3275 4.889409 CAGGCATTCCCATTAACTACACAT 59.111 41.667 0.00 0.00 35.39 3.21
3264 3329 7.395190 TGCTCATGCTTGTATTGTTAAGAAT 57.605 32.000 3.09 3.09 40.48 2.40
3266 3331 7.254898 GCTATGCTCATGCTTGTATTGTTAAGA 60.255 37.037 0.00 0.00 40.48 2.10
3267 3332 6.854892 GCTATGCTCATGCTTGTATTGTTAAG 59.145 38.462 0.00 0.00 40.48 1.85
3273 3346 5.768662 AGAATGCTATGCTCATGCTTGTATT 59.231 36.000 0.00 0.00 40.48 1.89
3404 3480 2.037901 TCAAAGGCAGCACCAATCAAA 58.962 42.857 0.00 0.00 43.14 2.69
3661 3740 4.037208 GCATGTGTTAGGGGATTGAGAATG 59.963 45.833 0.00 0.00 0.00 2.67
3662 3741 4.210331 GCATGTGTTAGGGGATTGAGAAT 58.790 43.478 0.00 0.00 0.00 2.40
3691 3770 2.355132 ACAGGTAGTCAGATAGCGAACG 59.645 50.000 0.00 0.00 0.00 3.95
3708 3787 4.574013 GCATGGAAGAACATTCTCTACAGG 59.426 45.833 0.00 0.00 36.28 4.00
3723 3802 2.886523 TGAACACCAAAGAGCATGGAAG 59.113 45.455 0.00 0.00 40.56 3.46
3853 4051 8.690884 CAAACAAGATCTAGGATGAAGAGAGTA 58.309 37.037 0.00 0.00 0.00 2.59
3862 4060 7.989741 ACTATGAACCAAACAAGATCTAGGATG 59.010 37.037 0.00 0.00 0.00 3.51
3884 4082 4.235360 CGGACTCAAGTCGTCAAAACTAT 58.765 43.478 4.17 0.00 45.65 2.12
3894 4092 2.661675 CACATGTAACGGACTCAAGTCG 59.338 50.000 0.00 2.98 45.65 4.18
3905 4103 4.732923 CCAACTGAACAAACACATGTAACG 59.267 41.667 0.00 0.00 32.02 3.18
3913 4111 5.699097 TTATAGCCCAACTGAACAAACAC 57.301 39.130 0.00 0.00 0.00 3.32
3937 4135 8.278639 AGGTGTTATCCAATTACATGGTATTCA 58.721 33.333 0.00 0.00 41.46 2.57
3998 4198 2.161012 CGAGTGATGCAGCATTTTCTGT 59.839 45.455 8.41 0.00 36.49 3.41
4015 4215 0.885196 GTGCAGGAAGAGAGACGAGT 59.115 55.000 0.00 0.00 0.00 4.18
4158 4361 1.497991 CGGTCGAAACTGCTCTTTCA 58.502 50.000 0.00 0.00 31.46 2.69
4170 4373 0.806868 AACGAGTATCAGCGGTCGAA 59.193 50.000 1.89 0.00 36.30 3.71
4215 4418 2.478894 CACAGTTCGTTCGTAGCCATTT 59.521 45.455 0.00 0.00 0.00 2.32
4260 4463 2.360350 CAATGCCAGCTCCACGGT 60.360 61.111 0.00 0.00 0.00 4.83
4263 4466 0.677731 TACAGCAATGCCAGCTCCAC 60.678 55.000 0.00 0.00 41.14 4.02
4300 4503 1.655114 AACCCAAGACCTGCACCCTT 61.655 55.000 0.00 0.00 0.00 3.95
4324 4527 2.416747 CAGCACAGAAGAACGGAATCA 58.583 47.619 0.00 0.00 0.00 2.57
4378 4581 2.090400 ATCCGATTGATCCAGCATCG 57.910 50.000 6.68 6.68 33.61 3.84
4416 4619 5.904362 AAGATCTGGCATTGACTTAAACC 57.096 39.130 0.00 0.00 0.00 3.27
4485 4700 6.404293 GCCACGGACTGTAACATAATCAATTT 60.404 38.462 0.00 0.00 0.00 1.82
4551 4766 2.798847 GGAATCGGATTACTACGGCAAC 59.201 50.000 5.67 0.00 0.00 4.17
4579 4794 6.096987 TGTGGTCCAAAATAAGCAGTGTAAAA 59.903 34.615 0.00 0.00 0.00 1.52
4651 4866 6.459298 GGCAGTCATGGAAGTTGATTCATTAG 60.459 42.308 0.00 0.00 39.91 1.73
5355 6104 8.651389 AGATAGGAATAGGTTCATTTCGAATCA 58.349 33.333 0.00 0.00 37.18 2.57
5699 7414 5.499139 AATAATACATGTGAGCCAAACGG 57.501 39.130 9.11 0.00 0.00 4.44
5700 7415 9.811655 CTAATAATAATACATGTGAGCCAAACG 57.188 33.333 9.11 0.00 0.00 3.60
5701 7416 9.612620 GCTAATAATAATACATGTGAGCCAAAC 57.387 33.333 9.11 0.00 0.00 2.93
5864 7786 8.871862 TGTGCATCAAAATAATTCAGCAATTAC 58.128 29.630 0.00 0.00 37.31 1.89
5996 7918 8.970020 AGGAAATAGCACATGTATCAATCAAAA 58.030 29.630 0.00 0.00 0.00 2.44
5997 7919 8.523915 AGGAAATAGCACATGTATCAATCAAA 57.476 30.769 0.00 0.00 0.00 2.69
6020 7964 2.159028 GCTACTACCTGAAGCCAGAAGG 60.159 54.545 0.00 0.00 43.02 3.46
6370 8314 2.943345 GCTGACAACGACCGCACAG 61.943 63.158 0.00 0.00 0.00 3.66
6408 8352 1.269257 GCCACAAAACAAGGAGAGCAC 60.269 52.381 0.00 0.00 0.00 4.40
6439 8383 9.826574 TCTACAATTAGTAACCAATATCACCAC 57.173 33.333 0.00 0.00 30.92 4.16
6558 8502 6.899393 TGCTAAAGAAAACTGATGTTGGAT 57.101 33.333 0.00 0.00 36.39 3.41
6561 8505 5.346822 GCCATGCTAAAGAAAACTGATGTTG 59.653 40.000 0.00 0.00 36.39 3.33
6574 8518 4.389687 GGTGTTTGATTTGCCATGCTAAAG 59.610 41.667 0.00 0.00 0.00 1.85
6591 8535 2.028561 ATTTGCCATCCCAGGTGTTT 57.971 45.000 0.00 0.00 0.00 2.83
6600 8544 3.115554 GCGACAACATAATTTGCCATCC 58.884 45.455 0.00 0.00 0.00 3.51
6662 8662 8.044060 TGACATCAGATTTTAGATTGTGGAAC 57.956 34.615 0.00 0.00 37.35 3.62
6663 8663 8.272545 CTGACATCAGATTTTAGATTGTGGAA 57.727 34.615 2.51 0.00 46.59 3.53
6713 8721 9.759473 TCCAAATCAGGAGATCTTTCTTAAATT 57.241 29.630 0.00 0.00 31.90 1.82
6714 8722 9.183368 GTCCAAATCAGGAGATCTTTCTTAAAT 57.817 33.333 0.00 0.00 38.64 1.40
6715 8723 8.163408 TGTCCAAATCAGGAGATCTTTCTTAAA 58.837 33.333 0.00 0.00 38.64 1.52
6720 8730 5.356470 CCTTGTCCAAATCAGGAGATCTTTC 59.644 44.000 0.00 0.00 38.64 2.62
6721 8731 5.259632 CCTTGTCCAAATCAGGAGATCTTT 58.740 41.667 0.00 0.00 38.64 2.52
6722 8732 4.853007 CCTTGTCCAAATCAGGAGATCTT 58.147 43.478 0.00 0.00 38.64 2.40
6725 8735 2.681976 CGCCTTGTCCAAATCAGGAGAT 60.682 50.000 0.00 0.00 38.64 2.75
6728 8738 0.322456 CCGCCTTGTCCAAATCAGGA 60.322 55.000 0.00 0.00 34.64 3.86
6736 8746 0.320374 CTTGTACTCCGCCTTGTCCA 59.680 55.000 0.00 0.00 0.00 4.02
6738 8748 1.019805 GCCTTGTACTCCGCCTTGTC 61.020 60.000 0.00 0.00 0.00 3.18
6744 8754 2.820037 GCCAGCCTTGTACTCCGC 60.820 66.667 0.00 0.00 0.00 5.54
6756 8766 4.887655 ACTATAAACAATTACCCAGCCAGC 59.112 41.667 0.00 0.00 0.00 4.85
6761 8832 7.624360 TCAGCAACTATAAACAATTACCCAG 57.376 36.000 0.00 0.00 0.00 4.45
6776 8848 8.924691 GTTTGATGCATTAATTTTCAGCAACTA 58.075 29.630 4.56 0.77 38.85 2.24
6784 8856 9.949174 AAAAAGTGGTTTGATGCATTAATTTTC 57.051 25.926 4.56 0.00 0.00 2.29
6792 9102 4.503643 CCCAGAAAAAGTGGTTTGATGCAT 60.504 41.667 0.00 0.00 32.62 3.96
6797 9107 3.129638 CGTTCCCAGAAAAAGTGGTTTGA 59.870 43.478 0.00 0.00 32.62 2.69
6804 9114 5.240844 CCATTTAGTCGTTCCCAGAAAAAGT 59.759 40.000 0.00 0.00 0.00 2.66
6836 9148 5.507985 GCAAGTTCAATTCTAAAGCACAGGT 60.508 40.000 0.00 0.00 0.00 4.00
6859 9171 4.017126 ACCCTAAAGCAGACCAAATTAGC 58.983 43.478 0.00 0.00 0.00 3.09
6891 9240 4.363991 ACCTCTGCAGAAGAACAAATCT 57.636 40.909 19.22 0.00 41.32 2.40
6952 9302 5.669477 AGTGATCTTGGCTAGAATTCAGAC 58.331 41.667 8.44 6.05 36.22 3.51
6963 9313 4.383552 GGTCATCTGTAAGTGATCTTGGCT 60.384 45.833 0.00 0.00 35.36 4.75
6969 9319 3.868077 GCAGTGGTCATCTGTAAGTGATC 59.132 47.826 0.00 0.00 35.60 2.92
6970 9320 3.261643 TGCAGTGGTCATCTGTAAGTGAT 59.738 43.478 0.00 0.00 35.60 3.06
6971 9321 2.632512 TGCAGTGGTCATCTGTAAGTGA 59.367 45.455 0.00 0.00 35.60 3.41
6972 9322 2.998670 CTGCAGTGGTCATCTGTAAGTG 59.001 50.000 5.25 0.00 35.60 3.16
6973 9323 2.634940 ACTGCAGTGGTCATCTGTAAGT 59.365 45.455 20.97 0.00 35.60 2.24
6974 9324 3.325293 ACTGCAGTGGTCATCTGTAAG 57.675 47.619 20.97 0.00 35.60 2.34
6975 9325 3.832490 AGTACTGCAGTGGTCATCTGTAA 59.168 43.478 29.57 1.01 35.60 2.41
6976 9326 3.431415 AGTACTGCAGTGGTCATCTGTA 58.569 45.455 29.57 1.60 35.60 2.74
6977 9327 2.251818 AGTACTGCAGTGGTCATCTGT 58.748 47.619 29.57 0.97 35.60 3.41
7013 9363 0.800631 TCGCTCTTTGCTGATGCTTG 59.199 50.000 0.00 0.00 40.48 4.01
7098 9448 8.200792 AGCTTAGTATGTTTATTGGACAGAGAG 58.799 37.037 0.00 0.00 0.00 3.20
7111 9461 8.995220 TGTTCGTTTATTCAGCTTAGTATGTTT 58.005 29.630 0.00 0.00 0.00 2.83
7114 9490 8.817100 TGATGTTCGTTTATTCAGCTTAGTATG 58.183 33.333 0.00 0.00 0.00 2.39
7118 9494 6.456988 GGGTGATGTTCGTTTATTCAGCTTAG 60.457 42.308 0.00 0.00 0.00 2.18
7195 9575 3.071580 GCATACAGACAGTGGAGGC 57.928 57.895 0.00 0.00 40.26 4.70
7234 9617 7.166970 GCTGATCGTCGTCAATGTTTATTACTA 59.833 37.037 0.00 0.00 0.00 1.82
7236 9619 6.019801 AGCTGATCGTCGTCAATGTTTATTAC 60.020 38.462 0.00 0.00 0.00 1.89
7237 9620 6.040247 AGCTGATCGTCGTCAATGTTTATTA 58.960 36.000 0.00 0.00 0.00 0.98
7238 9621 4.870426 AGCTGATCGTCGTCAATGTTTATT 59.130 37.500 0.00 0.00 0.00 1.40
7239 9622 4.433615 AGCTGATCGTCGTCAATGTTTAT 58.566 39.130 0.00 0.00 0.00 1.40
7240 9623 3.845178 AGCTGATCGTCGTCAATGTTTA 58.155 40.909 0.00 0.00 0.00 2.01
7241 9624 2.668457 GAGCTGATCGTCGTCAATGTTT 59.332 45.455 0.00 0.00 0.00 2.83
7242 9625 2.094494 AGAGCTGATCGTCGTCAATGTT 60.094 45.455 0.00 0.00 0.00 2.71
7243 9626 1.474478 AGAGCTGATCGTCGTCAATGT 59.526 47.619 0.00 0.00 0.00 2.71
7328 9711 0.673644 CCAAGTTCCCGTTGAGCGAT 60.674 55.000 0.00 0.00 44.77 4.58
7346 9729 0.809385 TGAAGACGGTGATCGACTCC 59.191 55.000 0.00 0.00 42.45 3.85
7545 12892 2.029073 CGGTGTCAGCTGGTCGTT 59.971 61.111 15.13 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.