Multiple sequence alignment - TraesCS3A01G260000

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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 TraesCS3A01G260000 chr3A 100.000 5338 0 0 1 5338 482407664 482402327 0.000000e+00 9858.0
1 TraesCS3A01G260000 chr3A 91.626 203 16 1 1668 1870 17310870 17311071 4.070000e-71 279.0
2 TraesCS3A01G260000 chr3A 89.904 208 20 1 1668 1875 258745208 258745002 3.170000e-67 267.0
3 TraesCS3A01G260000 chr3B 92.640 5394 258 53 4 5319 472117080 472111748 0.000000e+00 7633.0
4 TraesCS3A01G260000 chr3B 90.500 200 18 1 1671 1870 651678826 651678628 4.100000e-66 263.0
5 TraesCS3A01G260000 chr3D 94.816 4900 143 47 1 4832 362202841 362197985 0.000000e+00 7539.0
6 TraesCS3A01G260000 chr3D 81.604 424 20 14 4746 5147 362197985 362197598 1.120000e-76 298.0
7 TraesCS3A01G260000 chr7A 82.532 790 93 23 975 1744 19470544 19471308 0.000000e+00 652.0
8 TraesCS3A01G260000 chr7A 89.655 203 20 1 1668 1870 584879354 584879555 1.910000e-64 257.0
9 TraesCS3A01G260000 chr7A 86.747 83 10 1 823 904 19469654 19469736 2.050000e-14 91.6
10 TraesCS3A01G260000 chr7D 87.365 277 30 5 975 1250 343299536 343299808 4.010000e-81 313.0
11 TraesCS3A01G260000 chrUn 89.655 203 19 2 1668 1870 81680663 81680863 1.910000e-64 257.0
12 TraesCS3A01G260000 chr4B 88.670 203 16 4 1668 1870 201717448 201717253 1.920000e-59 241.0
13 TraesCS3A01G260000 chr1A 89.840 187 18 1 1668 1854 521035887 521036072 6.910000e-59 239.0
14 TraesCS3A01G260000 chr1A 87.342 79 10 0 1575 1653 402803169 402803091 2.050000e-14 91.6
15 TraesCS3A01G260000 chr6B 94.318 88 5 0 3108 3195 278674700 278674613 9.330000e-28 135.0
16 TraesCS3A01G260000 chr6B 90.123 81 7 1 3107 3187 565749824 565749903 2.630000e-18 104.0
17 TraesCS3A01G260000 chr6B 87.209 86 10 1 3111 3196 698036001 698036085 4.400000e-16 97.1
18 TraesCS3A01G260000 chr6A 94.318 88 5 0 3108 3195 209391428 209391341 9.330000e-28 135.0
19 TraesCS3A01G260000 chr6D 93.182 88 6 0 3108 3195 155602048 155601961 4.340000e-26 130.0
20 TraesCS3A01G260000 chr5A 86.813 91 12 0 3106 3196 342240428 342240518 9.460000e-18 102.0
21 TraesCS3A01G260000 chr4A 89.873 79 8 0 3107 3185 373806316 373806394 9.460000e-18 102.0
22 TraesCS3A01G260000 chr1D 88.608 79 9 0 1575 1653 320400163 320400241 4.400000e-16 97.1
23 TraesCS3A01G260000 chr1B 90.769 65 6 0 1575 1639 433436059 433436123 2.650000e-13 87.9


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 TraesCS3A01G260000 chr3A 482402327 482407664 5337 True 9858.0 9858 100.0000 1 5338 1 chr3A.!!$R2 5337
1 TraesCS3A01G260000 chr3B 472111748 472117080 5332 True 7633.0 7633 92.6400 4 5319 1 chr3B.!!$R1 5315
2 TraesCS3A01G260000 chr3D 362197598 362202841 5243 True 3918.5 7539 88.2100 1 5147 2 chr3D.!!$R1 5146
3 TraesCS3A01G260000 chr7A 19469654 19471308 1654 False 371.8 652 84.6395 823 1744 2 chr7A.!!$F2 921

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
321 324 0.037975 TTTCCCGTCGTTCTACAGGC 60.038 55.000 0.00 0.0 0.00 4.85 F
576 579 0.113385 TGGGCAAATTTCCCTCCGAA 59.887 50.000 19.93 4.0 44.23 4.30 F
1640 2451 1.338674 TGGGTATGACTTTGACGGCTG 60.339 52.381 0.00 0.0 0.00 4.85 F
2767 3583 2.025898 GAGCCGTAGCCTCTCTTACTT 58.974 52.381 0.00 0.0 41.25 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 3056 3.295093 TGATTTCCAAAGGACAGTGCAA 58.705 40.909 0.0 0.00 0.00 4.08 R
2490 3303 4.385358 AACAAGAACAAACCACACATCC 57.615 40.909 0.0 0.00 0.00 3.51 R
3306 4122 1.136147 GCCAGCTCTGCATGTTTCG 59.864 57.895 0.0 0.00 0.00 3.46 R
4759 5595 0.391661 CCTCGGACACCAGTGGAATG 60.392 60.000 18.4 7.26 34.19 2.67 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
53 56 6.356190 CACCGTGAACGAATTTTACTCTTTTC 59.644 38.462 4.03 0.00 43.02 2.29
207 210 5.009631 TCGGAACATTTGTCCATCTTGATT 58.990 37.500 0.00 0.00 0.00 2.57
208 211 5.097529 CGGAACATTTGTCCATCTTGATTG 58.902 41.667 0.00 0.00 0.00 2.67
209 212 5.106197 CGGAACATTTGTCCATCTTGATTGA 60.106 40.000 0.00 0.00 0.00 2.57
210 213 6.405065 CGGAACATTTGTCCATCTTGATTGAT 60.405 38.462 0.00 0.00 0.00 2.57
231 234 1.207089 TGATTTCTTCGATCGCCACCT 59.793 47.619 11.09 0.00 0.00 4.00
232 235 1.594862 GATTTCTTCGATCGCCACCTG 59.405 52.381 11.09 0.00 0.00 4.00
321 324 0.037975 TTTCCCGTCGTTCTACAGGC 60.038 55.000 0.00 0.00 0.00 4.85
331 334 1.764571 TTCTACAGGCGGTGGCAAGT 61.765 55.000 0.00 0.00 42.47 3.16
332 335 1.302511 CTACAGGCGGTGGCAAGTT 60.303 57.895 0.00 0.00 42.47 2.66
378 381 0.900647 CGTCCTCCTTCCACCTCTGT 60.901 60.000 0.00 0.00 0.00 3.41
390 393 1.283793 CCTCTGTTTTGTGCCGCAG 59.716 57.895 0.00 0.00 0.00 5.18
406 409 3.181397 CCGCAGGCACAGATAAAATTTG 58.819 45.455 0.00 0.00 46.14 2.32
408 411 3.587923 GCAGGCACAGATAAAATTTGCA 58.412 40.909 0.00 0.00 34.76 4.08
414 417 5.469760 GGCACAGATAAAATTTGCACCTTTT 59.530 36.000 9.61 9.61 34.76 2.27
428 431 2.422597 ACCTTTTGTGAATCGCGATGA 58.577 42.857 24.47 9.85 0.00 2.92
465 468 2.221981 CAGCGTTTCTGTTCTGGAGTTC 59.778 50.000 0.00 0.00 38.02 3.01
468 471 2.864343 CGTTTCTGTTCTGGAGTTCGTT 59.136 45.455 0.00 0.00 0.00 3.85
482 485 2.930040 AGTTCGTTTCATCTACGCCATG 59.070 45.455 0.00 0.00 38.81 3.66
485 488 1.860950 CGTTTCATCTACGCCATGGAG 59.139 52.381 18.40 16.40 31.73 3.86
544 547 2.450609 AACCTTGGTAGTGCGTAGTG 57.549 50.000 0.00 0.00 0.00 2.74
549 552 1.080298 GGTAGTGCGTAGTGGCGTT 60.080 57.895 0.00 0.00 35.06 4.84
574 577 1.136891 GATTGGGCAAATTTCCCTCCG 59.863 52.381 19.93 0.00 44.23 4.63
576 579 0.113385 TGGGCAAATTTCCCTCCGAA 59.887 50.000 19.93 4.00 44.23 4.30
625 628 4.202080 CCTTTTGGGTATCATGCTCATGTG 60.202 45.833 9.41 0.00 36.70 3.21
632 635 5.048921 GGGTATCATGCTCATGTGAGATTTG 60.049 44.000 13.94 7.39 44.74 2.32
634 637 4.224991 TCATGCTCATGTGAGATTTGGA 57.775 40.909 13.94 1.23 44.74 3.53
641 644 5.591877 GCTCATGTGAGATTTGGATTAGGTT 59.408 40.000 13.94 0.00 44.74 3.50
642 645 6.096001 GCTCATGTGAGATTTGGATTAGGTTT 59.904 38.462 13.94 0.00 44.74 3.27
645 648 9.527157 TCATGTGAGATTTGGATTAGGTTTTAA 57.473 29.630 0.00 0.00 0.00 1.52
646 649 9.573133 CATGTGAGATTTGGATTAGGTTTTAAC 57.427 33.333 0.00 0.00 0.00 2.01
659 663 5.830000 AGGTTTTAACAAGGTGTTCTGTC 57.170 39.130 0.00 0.00 40.22 3.51
677 681 1.689273 GTCCAACTGTCCAGAGTCTGT 59.311 52.381 18.74 0.00 0.00 3.41
954 1707 5.765677 TCTGCACCATTCTAGCTAGTAGTAG 59.234 44.000 20.10 12.51 0.00 2.57
955 1708 5.446860 TGCACCATTCTAGCTAGTAGTAGT 58.553 41.667 20.10 9.87 0.00 2.73
956 1709 6.598503 TGCACCATTCTAGCTAGTAGTAGTA 58.401 40.000 20.10 4.91 0.00 1.82
1006 1779 6.942163 ATTCATGTATAGGCTGTATGACCT 57.058 37.500 0.00 0.00 40.24 3.85
1007 1780 6.747414 TTCATGTATAGGCTGTATGACCTT 57.253 37.500 0.00 0.00 37.50 3.50
1008 1781 6.747414 TCATGTATAGGCTGTATGACCTTT 57.253 37.500 0.00 0.00 37.50 3.11
1009 1782 7.849322 TCATGTATAGGCTGTATGACCTTTA 57.151 36.000 0.00 0.00 37.50 1.85
1010 1783 8.435931 TCATGTATAGGCTGTATGACCTTTAT 57.564 34.615 0.00 0.00 37.50 1.40
1282 2067 8.368668 AGGAAACTAGTATGATATAGGTTGCAC 58.631 37.037 0.00 0.00 38.93 4.57
1360 2145 5.868454 TGTGTATCATTATGCAGTATGGCT 58.132 37.500 10.04 2.93 35.86 4.75
1449 2253 3.713003 TCTGTCATGGTCATGTAGAGGT 58.287 45.455 10.32 0.00 39.72 3.85
1478 2283 6.523840 ACTCAGAATTCATGATAGAAGCCTC 58.476 40.000 8.44 0.00 0.00 4.70
1640 2451 1.338674 TGGGTATGACTTTGACGGCTG 60.339 52.381 0.00 0.00 0.00 4.85
1720 2532 3.781079 TTCTTGTGCCTGTTGTTTGAG 57.219 42.857 0.00 0.00 0.00 3.02
1991 2803 2.884012 CAAGGTACAGGAATTGTGCACA 59.116 45.455 17.42 17.42 43.39 4.57
2018 2830 9.965824 ACTTCTGTTTATACATTTTGAGTTTGG 57.034 29.630 0.00 0.00 32.86 3.28
2038 2850 2.955660 GGTGTCCATTGAGTTTGGTTGA 59.044 45.455 0.00 0.00 35.64 3.18
2100 2913 3.403038 ACTTATTCAGGACCATATGCGC 58.597 45.455 0.00 0.00 0.00 6.09
2243 3056 2.686915 GCTCAGCTGCCTGAATTGTAAT 59.313 45.455 9.47 0.00 46.84 1.89
2767 3583 2.025898 GAGCCGTAGCCTCTCTTACTT 58.974 52.381 0.00 0.00 41.25 2.24
2841 3657 5.885912 ACACCAAGTTTCATGACAAGTACTT 59.114 36.000 1.12 1.12 0.00 2.24
2987 3803 6.868339 CGCTTTTGGAAGAAATAGGAACAAAT 59.132 34.615 0.00 0.00 34.71 2.32
3179 3995 8.459521 TGAAATGCCAAAACGACTTATATTTG 57.540 30.769 0.00 0.00 33.62 2.32
3306 4122 8.020819 TCGTTTTTCTATGTTCCAATGAATGAC 58.979 33.333 0.00 0.00 31.98 3.06
3428 4244 3.837213 AATTGGATGCGTTGAGTTCAG 57.163 42.857 0.00 0.00 0.00 3.02
3686 4503 6.458210 AGATGAATGGGAAATGTTGTTTGTC 58.542 36.000 0.00 0.00 0.00 3.18
3896 4722 8.469309 TCATATTCAGTAGTCACATCTGATGA 57.531 34.615 23.59 0.35 37.91 2.92
3960 4786 6.406093 TCGCTCTCGTATAATCTACTTAGC 57.594 41.667 0.00 0.00 36.96 3.09
4025 4851 8.265055 TGGTTTTGGTGTTAATTTTGGATTACA 58.735 29.630 0.00 0.00 0.00 2.41
4075 4901 3.953612 TCTGAAACATTTTGCAGGTCACT 59.046 39.130 0.00 0.00 38.79 3.41
4108 4934 3.553508 CGGTCTCCTGTTTCTTCGGTAAA 60.554 47.826 0.00 0.00 0.00 2.01
4120 4946 5.578005 TCTTCGGTAAATCTCGACAATCT 57.422 39.130 0.00 0.00 34.99 2.40
4157 4983 0.671796 TCGAGCCACTTGTTCGAAGA 59.328 50.000 0.00 0.00 40.05 2.87
4272 5099 0.530288 GCACTCTCTCGCCTCTTTCT 59.470 55.000 0.00 0.00 0.00 2.52
4273 5100 1.735369 GCACTCTCTCGCCTCTTTCTG 60.735 57.143 0.00 0.00 0.00 3.02
4292 5119 9.254133 TCTTTCTGAGAAATCGCTTATGATTAG 57.746 33.333 8.23 0.00 37.59 1.73
4385 5214 2.826128 TGACTACTTCAGGATCGCAGTT 59.174 45.455 0.00 0.00 0.00 3.16
4387 5216 3.589988 ACTACTTCAGGATCGCAGTTTG 58.410 45.455 0.00 0.00 0.00 2.93
4474 5303 0.109873 GCGCTTATCATGATGCCTGC 60.110 55.000 18.72 12.75 0.00 4.85
4495 5324 4.221924 TGCCTGTCTACTTGTTATGTGCTA 59.778 41.667 0.00 0.00 0.00 3.49
4607 5442 0.972134 TCAGAGGAGACCTGCACTTG 59.028 55.000 0.00 0.00 31.76 3.16
4608 5443 0.683973 CAGAGGAGACCTGCACTTGT 59.316 55.000 0.00 0.00 31.76 3.16
4609 5444 0.683973 AGAGGAGACCTGCACTTGTG 59.316 55.000 0.00 0.00 31.76 3.33
4611 5446 1.968540 GGAGACCTGCACTTGTGGC 60.969 63.158 2.81 0.00 0.00 5.01
4651 5487 8.287503 GTCACATTATGTTTTTCCGTAACTCTT 58.712 33.333 0.00 0.00 0.00 2.85
4713 5549 3.762616 AACCCCAGGTGGTTGTCA 58.237 55.556 10.70 0.00 46.76 3.58
4715 5551 0.112412 AACCCCAGGTGGTTGTCATC 59.888 55.000 10.70 0.00 46.76 2.92
4718 5554 0.391661 CCCAGGTGGTTGTCATCGAG 60.392 60.000 0.00 0.00 0.00 4.04
4722 5558 1.296715 GTGGTTGTCATCGAGGCCT 59.703 57.895 3.86 3.86 0.00 5.19
4723 5559 1.021390 GTGGTTGTCATCGAGGCCTG 61.021 60.000 12.00 2.19 0.00 4.85
4724 5560 1.450312 GGTTGTCATCGAGGCCTGG 60.450 63.158 12.00 10.16 0.00 4.45
4726 5562 2.669133 TTGTCATCGAGGCCTGGGG 61.669 63.158 12.00 5.37 0.00 4.96
4743 5579 2.409651 GCCGATCTCGAGCTCGTT 59.590 61.111 33.33 20.25 43.02 3.85
4751 5587 3.869272 CGAGCTCGTTGCCATGCC 61.869 66.667 27.79 0.00 44.23 4.40
4762 5598 3.069946 CCATGCCGTGCACCCATT 61.070 61.111 12.15 0.00 43.04 3.16
4783 5619 2.047844 CTGGTGTCCGAGGTGCTG 60.048 66.667 0.00 0.00 0.00 4.41
4784 5620 4.314440 TGGTGTCCGAGGTGCTGC 62.314 66.667 0.00 0.00 0.00 5.25
4789 5723 1.227380 GTCCGAGGTGCTGCTATGG 60.227 63.158 0.00 0.00 0.00 2.74
4791 5725 1.227380 CCGAGGTGCTGCTATGGTC 60.227 63.158 0.00 0.00 0.00 4.02
4822 5756 2.890474 GCCGAGTGCCCACATACG 60.890 66.667 0.82 3.96 0.00 3.06
4854 5788 1.402984 GGTTGTCTCTTCGTGCGATCT 60.403 52.381 0.00 0.00 0.00 2.75
4858 5792 0.098905 TCTCTTCGTGCGATCTTCGG 59.901 55.000 0.00 0.00 40.84 4.30
4859 5793 0.179161 CTCTTCGTGCGATCTTCGGT 60.179 55.000 0.00 0.00 40.84 4.69
4860 5794 0.456142 TCTTCGTGCGATCTTCGGTG 60.456 55.000 0.00 0.00 40.84 4.94
4861 5795 1.413767 CTTCGTGCGATCTTCGGTGG 61.414 60.000 0.00 0.00 40.84 4.61
4862 5796 2.829043 TTCGTGCGATCTTCGGTGGG 62.829 60.000 0.00 0.00 40.84 4.61
4863 5797 2.577059 GTGCGATCTTCGGTGGGA 59.423 61.111 0.00 0.00 40.84 4.37
4864 5798 1.144057 GTGCGATCTTCGGTGGGAT 59.856 57.895 0.00 0.00 40.84 3.85
4865 5799 1.143838 TGCGATCTTCGGTGGGATG 59.856 57.895 0.00 0.00 40.84 3.51
4866 5800 1.595382 GCGATCTTCGGTGGGATGG 60.595 63.158 0.00 0.00 40.84 3.51
4867 5801 1.069765 CGATCTTCGGTGGGATGGG 59.930 63.158 0.00 0.00 36.00 4.00
4868 5802 1.227973 GATCTTCGGTGGGATGGGC 60.228 63.158 0.00 0.00 0.00 5.36
4869 5803 1.694169 ATCTTCGGTGGGATGGGCT 60.694 57.895 0.00 0.00 0.00 5.19
4870 5804 1.700042 ATCTTCGGTGGGATGGGCTC 61.700 60.000 0.00 0.00 0.00 4.70
4871 5805 2.285368 TTCGGTGGGATGGGCTCT 60.285 61.111 0.00 0.00 0.00 4.09
4872 5806 1.915078 CTTCGGTGGGATGGGCTCTT 61.915 60.000 0.00 0.00 0.00 2.85
4873 5807 2.124570 CGGTGGGATGGGCTCTTG 60.125 66.667 0.00 0.00 0.00 3.02
4874 5808 2.971598 CGGTGGGATGGGCTCTTGT 61.972 63.158 0.00 0.00 0.00 3.16
4878 5812 1.384191 GGGATGGGCTCTTGTTGGT 59.616 57.895 0.00 0.00 0.00 3.67
4906 5840 2.930826 TTTGACTGACCAACTCCCTC 57.069 50.000 0.00 0.00 0.00 4.30
4954 5888 7.023575 CGTATTTCAGCTAAGAGCACAAATTT 58.976 34.615 10.92 0.00 45.56 1.82
4955 5889 7.538678 CGTATTTCAGCTAAGAGCACAAATTTT 59.461 33.333 10.92 0.00 45.56 1.82
4956 5890 9.196552 GTATTTCAGCTAAGAGCACAAATTTTT 57.803 29.630 10.92 0.00 45.56 1.94
4990 5927 1.973515 TCCTGAGCCATAGCCATACAG 59.026 52.381 0.00 0.00 41.25 2.74
5029 5966 1.412710 TGAAAGCTAGCCTATGTCCCG 59.587 52.381 12.13 0.00 0.00 5.14
5052 5989 5.845953 CGATTATTACATCGTTGACATTGCC 59.154 40.000 0.00 0.00 41.03 4.52
5152 6105 4.794648 CGCGGGCTGGGATTGGAA 62.795 66.667 3.99 0.00 0.00 3.53
5157 6110 1.512694 GGCTGGGATTGGAAAAGCG 59.487 57.895 0.00 0.00 34.66 4.68
5164 6117 2.233676 GGGATTGGAAAAGCGGTTGAAT 59.766 45.455 0.00 0.00 0.00 2.57
5166 6119 3.056891 GGATTGGAAAAGCGGTTGAATGA 60.057 43.478 0.00 0.00 0.00 2.57
5169 6122 2.690497 TGGAAAAGCGGTTGAATGACAA 59.310 40.909 0.00 0.00 36.02 3.18
5170 6123 3.243367 TGGAAAAGCGGTTGAATGACAAG 60.243 43.478 0.00 0.00 39.30 3.16
5172 6125 3.626028 AAAGCGGTTGAATGACAAGAC 57.374 42.857 0.00 0.00 39.30 3.01
5173 6126 2.254546 AGCGGTTGAATGACAAGACA 57.745 45.000 0.00 0.00 39.30 3.41
5174 6127 2.146342 AGCGGTTGAATGACAAGACAG 58.854 47.619 0.00 0.00 39.30 3.51
5177 6131 3.130633 CGGTTGAATGACAAGACAGACA 58.869 45.455 0.00 0.00 39.30 3.41
5182 6136 1.059098 ATGACAAGACAGACAGCCCA 58.941 50.000 0.00 0.00 0.00 5.36
5186 6140 0.946221 CAAGACAGACAGCCCACGAC 60.946 60.000 0.00 0.00 0.00 4.34
5187 6141 2.421877 AAGACAGACAGCCCACGACG 62.422 60.000 0.00 0.00 0.00 5.12
5233 6193 6.466308 TCATCATAAAATAACGCTGATCGG 57.534 37.500 0.00 0.00 43.86 4.18
5256 6216 7.221838 TCGGAAGAAATTTTAAAACAACTGCAG 59.778 33.333 13.48 13.48 37.03 4.41
5269 6229 4.610945 ACAACTGCAGATGTTTTAGCAAC 58.389 39.130 22.61 0.00 36.44 4.17
5270 6230 4.097741 ACAACTGCAGATGTTTTAGCAACA 59.902 37.500 22.61 0.00 36.44 3.33
5275 6235 3.304391 GCAGATGTTTTAGCAACACCGAA 60.304 43.478 0.00 0.00 32.37 4.30
5276 6236 4.791411 GCAGATGTTTTAGCAACACCGAAA 60.791 41.667 0.00 0.00 32.37 3.46
5277 6237 5.277825 CAGATGTTTTAGCAACACCGAAAA 58.722 37.500 0.00 0.00 32.37 2.29
5278 6238 5.746245 CAGATGTTTTAGCAACACCGAAAAA 59.254 36.000 0.00 0.00 32.37 1.94
5289 6249 7.598278 AGCAACACCGAAAAATAATGTTATCA 58.402 30.769 0.00 0.00 32.39 2.15
5290 6250 7.754924 AGCAACACCGAAAAATAATGTTATCAG 59.245 33.333 0.00 0.00 32.39 2.90
5291 6251 7.462724 GCAACACCGAAAAATAATGTTATCAGC 60.463 37.037 0.00 0.00 32.39 4.26
5313 6274 0.520404 GTCTAGACAGAACACGCGGA 59.480 55.000 18.20 0.00 30.85 5.54
5314 6275 1.132643 GTCTAGACAGAACACGCGGAT 59.867 52.381 18.20 0.00 30.85 4.18
5315 6276 1.132453 TCTAGACAGAACACGCGGATG 59.868 52.381 12.47 2.37 0.00 3.51
5316 6277 0.885879 TAGACAGAACACGCGGATGT 59.114 50.000 12.47 3.18 0.00 3.06
5317 6278 0.667487 AGACAGAACACGCGGATGTG 60.667 55.000 12.47 7.37 45.41 3.21
5318 6279 2.227968 GACAGAACACGCGGATGTGC 62.228 60.000 12.47 5.21 43.74 4.57
5319 6280 2.742372 AGAACACGCGGATGTGCC 60.742 61.111 12.47 2.83 43.74 5.01
5328 6289 3.434319 GGATGTGCCGTGCCTGTG 61.434 66.667 0.00 0.00 0.00 3.66
5329 6290 2.358615 GATGTGCCGTGCCTGTGA 60.359 61.111 0.00 0.00 0.00 3.58
5330 6291 1.746615 GATGTGCCGTGCCTGTGAT 60.747 57.895 0.00 0.00 0.00 3.06
5331 6292 1.985447 GATGTGCCGTGCCTGTGATG 61.985 60.000 0.00 0.00 0.00 3.07
5332 6293 3.434319 GTGCCGTGCCTGTGATGG 61.434 66.667 0.00 0.00 0.00 3.51
5333 6294 4.720902 TGCCGTGCCTGTGATGGG 62.721 66.667 0.00 0.00 0.00 4.00
5334 6295 4.722700 GCCGTGCCTGTGATGGGT 62.723 66.667 0.00 0.00 0.00 4.51
5335 6296 2.034066 CCGTGCCTGTGATGGGTT 59.966 61.111 0.00 0.00 0.00 4.11
5336 6297 2.334946 CCGTGCCTGTGATGGGTTG 61.335 63.158 0.00 0.00 0.00 3.77
5337 6298 1.600636 CGTGCCTGTGATGGGTTGT 60.601 57.895 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 30 4.985044 AGAGTAAAATTCGTTCACGGTG 57.015 40.909 0.56 0.56 40.29 4.94
53 56 5.816919 ACGTATTGGTTTTCTCAACAACAG 58.183 37.500 0.00 0.00 0.00 3.16
93 96 4.811761 GACGCCGCGTGGAAATGC 62.812 66.667 25.60 2.56 41.37 3.56
147 150 2.284331 TGCGGGGCAGAGAGGTAA 60.284 61.111 0.00 0.00 33.32 2.85
166 169 1.993370 CGAGGTTTTCGGCTGAAGTAG 59.007 52.381 8.23 0.00 45.54 2.57
195 198 7.642978 CGAAGAAATCAATCAATCAAGATGGAC 59.357 37.037 0.00 0.00 31.00 4.02
207 210 3.309682 GTGGCGATCGAAGAAATCAATCA 59.690 43.478 21.57 0.00 43.58 2.57
208 211 3.303395 GGTGGCGATCGAAGAAATCAATC 60.303 47.826 21.57 0.00 43.58 2.67
209 212 2.614057 GGTGGCGATCGAAGAAATCAAT 59.386 45.455 21.57 0.00 43.58 2.57
210 213 2.006888 GGTGGCGATCGAAGAAATCAA 58.993 47.619 21.57 0.00 43.58 2.57
231 234 0.033504 GACGGAGAACTCAACTGGCA 59.966 55.000 4.23 0.00 0.00 4.92
232 235 0.033504 TGACGGAGAACTCAACTGGC 59.966 55.000 4.23 0.00 0.00 4.85
299 302 1.725164 CTGTAGAACGACGGGAAAAGC 59.275 52.381 0.00 0.00 0.00 3.51
343 346 1.632422 GACGAACCGCGGATTTCTAA 58.368 50.000 35.90 0.00 46.49 2.10
351 354 3.984200 GAAGGAGGACGAACCGCGG 62.984 68.421 26.86 26.86 46.49 6.46
390 393 4.192429 AGGTGCAAATTTTATCTGTGCC 57.808 40.909 0.00 0.00 34.25 5.01
408 411 2.416547 CTCATCGCGATTCACAAAAGGT 59.583 45.455 21.14 0.00 0.00 3.50
414 417 1.143838 CCCCTCATCGCGATTCACA 59.856 57.895 21.14 2.65 0.00 3.58
465 468 1.860950 CTCCATGGCGTAGATGAAACG 59.139 52.381 6.96 0.00 43.12 3.60
468 471 3.686622 GCTCCATGGCGTAGATGAA 57.313 52.632 6.96 0.00 0.00 2.57
482 485 1.402968 TCACGGTATCTGTAACGCTCC 59.597 52.381 0.00 0.00 44.77 4.70
485 488 4.110482 AGATTTCACGGTATCTGTAACGC 58.890 43.478 0.00 0.00 44.77 4.84
568 571 1.915228 ATGGTCACCATTCGGAGGG 59.085 57.895 2.35 0.00 42.23 4.30
625 628 8.803235 ACCTTGTTAAAACCTAATCCAAATCTC 58.197 33.333 0.00 0.00 0.00 2.75
632 635 7.013942 ACAGAACACCTTGTTAAAACCTAATCC 59.986 37.037 0.00 0.00 41.28 3.01
634 637 7.013942 GGACAGAACACCTTGTTAAAACCTAAT 59.986 37.037 0.00 0.00 41.28 1.73
641 644 5.124776 CAGTTGGACAGAACACCTTGTTAAA 59.875 40.000 0.00 0.00 41.28 1.52
642 645 4.638421 CAGTTGGACAGAACACCTTGTTAA 59.362 41.667 0.00 0.00 41.28 2.01
645 648 2.026262 ACAGTTGGACAGAACACCTTGT 60.026 45.455 0.00 0.00 0.00 3.16
646 649 2.614057 GACAGTTGGACAGAACACCTTG 59.386 50.000 0.00 0.00 0.00 3.61
659 663 2.103094 TCAACAGACTCTGGACAGTTGG 59.897 50.000 10.86 0.00 36.17 3.77
677 681 9.730420 GCTAGTAAAAACTTCAGAATTGTTCAA 57.270 29.630 0.00 0.00 0.00 2.69
926 957 6.095432 ACTAGCTAGAATGGTGCAGATAAG 57.905 41.667 27.45 0.00 0.00 1.73
1019 1797 4.040217 TGCCCATTGTTTCTGCAGTTAAAT 59.960 37.500 14.67 7.17 0.00 1.40
1282 2067 4.212004 CCTTACAATGCGATGTACATGAGG 59.788 45.833 14.43 3.46 35.60 3.86
1338 2123 6.174451 CAGCCATACTGCATAATGATACAC 57.826 41.667 9.41 0.00 40.19 2.90
1360 2145 9.599866 AATCTTCAAGTCAATATCGACAATACA 57.400 29.630 0.00 0.00 38.43 2.29
1720 2532 4.543590 TTCCACCTGAGAGATGAACTTC 57.456 45.455 0.00 0.00 0.00 3.01
2018 2830 3.548014 CGTCAACCAAACTCAATGGACAC 60.548 47.826 0.00 0.00 40.56 3.67
2038 2850 9.490379 AAGTAAATAAAGAAGAACAGACATCGT 57.510 29.630 0.00 0.00 0.00 3.73
2243 3056 3.295093 TGATTTCCAAAGGACAGTGCAA 58.705 40.909 0.00 0.00 0.00 4.08
2490 3303 4.385358 AACAAGAACAAACCACACATCC 57.615 40.909 0.00 0.00 0.00 3.51
2767 3583 3.004839 CCTGCTATAGCTGCGACTTCTTA 59.995 47.826 24.61 0.00 42.66 2.10
2807 3623 8.234546 GTCATGAAACTTGGTGTAAATACGAAT 58.765 33.333 0.00 0.00 0.00 3.34
2841 3657 9.851686 ATCTAAGGAACAATGCACTCAAATATA 57.148 29.630 0.00 0.00 0.00 0.86
2987 3803 9.810545 TGTATCACGTTGTATATCAAGATCAAA 57.189 29.630 0.00 0.00 36.66 2.69
3306 4122 1.136147 GCCAGCTCTGCATGTTTCG 59.864 57.895 0.00 0.00 0.00 3.46
3428 4244 3.953612 TCCATAGTTCCAAACCATCATGC 59.046 43.478 0.00 0.00 0.00 4.06
3686 4503 3.967332 ACTTGCCCCAGAAAATGATTG 57.033 42.857 0.00 0.00 0.00 2.67
3751 4577 6.156949 TCCTTCTCTATCCAGTTGTTAATGCT 59.843 38.462 0.00 0.00 0.00 3.79
3896 4722 9.586732 TTTATGCATTTGGCTCTTTATACCTAT 57.413 29.630 3.54 0.00 45.15 2.57
4025 4851 6.260936 CCAAGTTCATTACTCAGAAGTGTTGT 59.739 38.462 0.00 0.00 35.54 3.32
4075 4901 2.095461 CAGGAGACCGAGATCTTGACA 58.905 52.381 11.89 0.00 0.00 3.58
4108 4934 2.768253 TGCCAACAGATTGTCGAGAT 57.232 45.000 0.00 0.00 33.60 2.75
4120 4946 4.245660 CTCGAGTAAAGATTCTGCCAACA 58.754 43.478 3.62 0.00 0.00 3.33
4157 4983 4.219288 CCTGCAAAAGAGTTCCATTAGCTT 59.781 41.667 0.00 0.00 0.00 3.74
4272 5099 6.763135 ACAAGCTAATCATAAGCGATTTCTCA 59.237 34.615 0.00 0.00 44.87 3.27
4273 5100 7.068341 CACAAGCTAATCATAAGCGATTTCTC 58.932 38.462 0.00 0.00 44.87 2.87
4292 5119 3.941483 ACAGACACCATATTAGCACAAGC 59.059 43.478 0.00 0.00 42.56 4.01
4360 5187 2.423892 GCGATCCTGAAGTAGTCACTCA 59.576 50.000 0.00 0.00 32.29 3.41
4385 5214 1.957186 GCAACCACCTACGACGCAA 60.957 57.895 0.00 0.00 0.00 4.85
4387 5216 0.458889 TATGCAACCACCTACGACGC 60.459 55.000 0.00 0.00 0.00 5.19
4474 5303 6.341316 ACATAGCACATAACAAGTAGACAGG 58.659 40.000 0.00 0.00 0.00 4.00
4607 5442 3.980775 GTGACAACATAACACATTGCCAC 59.019 43.478 0.00 0.00 31.14 5.01
4608 5443 3.633986 TGTGACAACATAACACATTGCCA 59.366 39.130 0.00 0.00 39.17 4.92
4609 5444 4.235939 TGTGACAACATAACACATTGCC 57.764 40.909 0.00 0.00 39.17 4.52
4651 5487 4.334203 CCAGCCGTGCTTATTACAAACATA 59.666 41.667 0.00 0.00 36.40 2.29
4682 5518 4.252878 CCTGGGGTTGAAAAACATAATGC 58.747 43.478 0.00 0.00 32.77 3.56
4722 5558 4.841617 AGCTCGAGATCGGCCCCA 62.842 66.667 18.75 0.00 40.29 4.96
4723 5559 3.984749 GAGCTCGAGATCGGCCCC 61.985 72.222 18.75 0.00 40.29 5.80
4759 5595 0.391661 CCTCGGACACCAGTGGAATG 60.392 60.000 18.40 7.26 34.19 2.67
4762 5598 2.200370 ACCTCGGACACCAGTGGA 59.800 61.111 18.40 0.00 34.19 4.02
4822 5756 0.739561 AGACAACCTCGATCGCCTAC 59.260 55.000 11.09 0.00 0.00 3.18
4854 5788 1.923395 AAGAGCCCATCCCACCGAA 60.923 57.895 0.00 0.00 0.00 4.30
4858 5792 0.967380 CCAACAAGAGCCCATCCCAC 60.967 60.000 0.00 0.00 0.00 4.61
4859 5793 1.383799 CCAACAAGAGCCCATCCCA 59.616 57.895 0.00 0.00 0.00 4.37
4860 5794 0.967380 CACCAACAAGAGCCCATCCC 60.967 60.000 0.00 0.00 0.00 3.85
4861 5795 1.598701 GCACCAACAAGAGCCCATCC 61.599 60.000 0.00 0.00 0.00 3.51
4862 5796 0.895100 TGCACCAACAAGAGCCCATC 60.895 55.000 0.00 0.00 0.00 3.51
4863 5797 0.251922 ATGCACCAACAAGAGCCCAT 60.252 50.000 0.00 0.00 0.00 4.00
4864 5798 0.469705 AATGCACCAACAAGAGCCCA 60.470 50.000 0.00 0.00 0.00 5.36
4865 5799 0.037975 CAATGCACCAACAAGAGCCC 60.038 55.000 0.00 0.00 0.00 5.19
4866 5800 0.675633 ACAATGCACCAACAAGAGCC 59.324 50.000 0.00 0.00 0.00 4.70
4867 5801 2.514205 AACAATGCACCAACAAGAGC 57.486 45.000 0.00 0.00 0.00 4.09
4868 5802 4.869297 TCAAAAACAATGCACCAACAAGAG 59.131 37.500 0.00 0.00 0.00 2.85
4869 5803 4.629200 GTCAAAAACAATGCACCAACAAGA 59.371 37.500 0.00 0.00 0.00 3.02
4870 5804 4.630940 AGTCAAAAACAATGCACCAACAAG 59.369 37.500 0.00 0.00 0.00 3.16
4871 5805 4.391216 CAGTCAAAAACAATGCACCAACAA 59.609 37.500 0.00 0.00 0.00 2.83
4872 5806 3.931468 CAGTCAAAAACAATGCACCAACA 59.069 39.130 0.00 0.00 0.00 3.33
4873 5807 4.032786 GTCAGTCAAAAACAATGCACCAAC 59.967 41.667 0.00 0.00 0.00 3.77
4874 5808 4.180057 GTCAGTCAAAAACAATGCACCAA 58.820 39.130 0.00 0.00 0.00 3.67
4878 5812 4.081752 AGTTGGTCAGTCAAAAACAATGCA 60.082 37.500 0.00 0.00 0.00 3.96
4906 5840 3.119291 GCATATCAGTCTGTCGGTTCAG 58.881 50.000 0.00 0.00 36.85 3.02
4971 5905 1.973515 TCTGTATGGCTATGGCTCAGG 59.026 52.381 0.00 0.00 38.73 3.86
4974 5908 1.345741 TGCTCTGTATGGCTATGGCTC 59.654 52.381 0.00 0.00 38.73 4.70
4990 5927 0.319405 ACCTTGCCATTTGCTTGCTC 59.681 50.000 0.00 0.00 42.00 4.26
5029 5966 6.724263 TGGCAATGTCAACGATGTAATAATC 58.276 36.000 0.00 0.00 0.00 1.75
5052 5989 2.032054 CCCGTGCAAGCAATGTAGTATG 59.968 50.000 0.00 0.00 0.00 2.39
5152 6105 2.948979 TGTCTTGTCATTCAACCGCTTT 59.051 40.909 0.00 0.00 32.18 3.51
5157 6110 3.058639 GCTGTCTGTCTTGTCATTCAACC 60.059 47.826 0.00 0.00 32.18 3.77
5164 6117 0.106708 GTGGGCTGTCTGTCTTGTCA 59.893 55.000 0.00 0.00 0.00 3.58
5166 6119 1.069765 CGTGGGCTGTCTGTCTTGT 59.930 57.895 0.00 0.00 0.00 3.16
5169 6122 2.920645 CGTCGTGGGCTGTCTGTCT 61.921 63.158 0.00 0.00 0.00 3.41
5170 6123 2.430921 CGTCGTGGGCTGTCTGTC 60.431 66.667 0.00 0.00 0.00 3.51
5187 6141 4.994756 CCTTGGTGGGGTGGTGCC 62.995 72.222 0.00 0.00 0.00 5.01
5210 6164 6.220201 TCCGATCAGCGTTATTTTATGATGA 58.780 36.000 0.00 0.00 38.67 2.92
5211 6165 6.466308 TCCGATCAGCGTTATTTTATGATG 57.534 37.500 0.00 0.00 38.67 3.07
5212 6166 6.929049 TCTTCCGATCAGCGTTATTTTATGAT 59.071 34.615 0.00 0.00 38.67 2.45
5213 6167 6.277605 TCTTCCGATCAGCGTTATTTTATGA 58.722 36.000 0.00 0.00 38.67 2.15
5214 6168 6.525121 TCTTCCGATCAGCGTTATTTTATG 57.475 37.500 0.00 0.00 38.67 1.90
5215 6169 7.548196 TTTCTTCCGATCAGCGTTATTTTAT 57.452 32.000 0.00 0.00 38.67 1.40
5216 6170 6.971527 TTTCTTCCGATCAGCGTTATTTTA 57.028 33.333 0.00 0.00 38.67 1.52
5218 6172 6.436843 AATTTCTTCCGATCAGCGTTATTT 57.563 33.333 0.00 0.00 38.67 1.40
5233 6193 9.853921 CATCTGCAGTTGTTTTAAAATTTCTTC 57.146 29.630 14.67 0.00 0.00 2.87
5251 6211 3.568538 GGTGTTGCTAAAACATCTGCAG 58.431 45.455 7.63 7.63 36.75 4.41
5253 6213 2.225491 TCGGTGTTGCTAAAACATCTGC 59.775 45.455 0.51 0.00 32.23 4.26
5256 6216 6.763303 ATTTTTCGGTGTTGCTAAAACATC 57.237 33.333 0.00 0.00 32.23 3.06
5269 6229 5.171337 GCGCTGATAACATTATTTTTCGGTG 59.829 40.000 0.00 0.00 0.00 4.94
5270 6230 5.270853 GCGCTGATAACATTATTTTTCGGT 58.729 37.500 0.00 0.00 0.00 4.69
5275 6235 5.734855 AGACGCGCTGATAACATTATTTT 57.265 34.783 5.73 0.00 0.00 1.82
5276 6236 6.144080 GTCTAGACGCGCTGATAACATTATTT 59.856 38.462 5.73 0.00 0.00 1.40
5277 6237 5.629849 GTCTAGACGCGCTGATAACATTATT 59.370 40.000 5.73 0.00 0.00 1.40
5278 6238 5.154932 GTCTAGACGCGCTGATAACATTAT 58.845 41.667 5.73 0.00 0.00 1.28
5289 6249 0.109689 GTGTTCTGTCTAGACGCGCT 60.110 55.000 17.85 7.21 31.21 5.92
5290 6250 1.396543 CGTGTTCTGTCTAGACGCGC 61.397 60.000 17.85 12.57 34.15 6.86
5291 6251 1.396543 GCGTGTTCTGTCTAGACGCG 61.397 60.000 17.85 13.26 36.61 6.01
5313 6274 2.042259 CATCACAGGCACGGCACAT 61.042 57.895 0.00 0.00 0.00 3.21
5314 6275 2.669229 CATCACAGGCACGGCACA 60.669 61.111 0.00 0.00 0.00 4.57
5315 6276 3.434319 CCATCACAGGCACGGCAC 61.434 66.667 0.00 0.00 0.00 5.01
5316 6277 4.720902 CCCATCACAGGCACGGCA 62.721 66.667 0.00 0.00 0.00 5.69
5317 6278 4.722700 ACCCATCACAGGCACGGC 62.723 66.667 0.00 0.00 0.00 5.68
5318 6279 2.034066 AACCCATCACAGGCACGG 59.966 61.111 0.00 0.00 0.00 4.94
5319 6280 1.600636 ACAACCCATCACAGGCACG 60.601 57.895 0.00 0.00 0.00 5.34
5320 6281 4.500265 ACAACCCATCACAGGCAC 57.500 55.556 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.