Multiple sequence alignment - TraesCS6D01G084300

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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 TraesCS6D01G084300 chr6D 100.000 4759 0 0 1 4759 49217337 49222095 0.000000e+00 8789.0
1 TraesCS6D01G084300 chr6D 96.663 1918 55 7 1886 3799 48868739 48866827 0.000000e+00 3179.0
2 TraesCS6D01G084300 chr6D 87.558 434 38 13 1084 1512 48869405 48868983 5.540000e-134 488.0
3 TraesCS6D01G084300 chr6D 96.721 183 6 0 1593 1775 48868988 48868806 5.980000e-79 305.0
4 TraesCS6D01G084300 chr6B 92.839 4231 197 48 3 4172 121816269 121812084 0.000000e+00 6037.0
5 TraesCS6D01G084300 chr6B 96.186 1940 65 6 1841 3775 122291286 122293221 0.000000e+00 3164.0
6 TraesCS6D01G084300 chr6B 85.408 466 56 10 1054 1512 122290611 122291071 1.550000e-129 473.0
7 TraesCS6D01G084300 chr6B 94.037 218 8 4 1593 1808 122291066 122291280 4.590000e-85 326.0
8 TraesCS6D01G084300 chr6B 89.340 197 19 2 4339 4535 121811926 121811732 3.680000e-61 246.0
9 TraesCS6D01G084300 chr6A 90.984 4370 214 62 1 4285 65685563 65681289 0.000000e+00 5722.0
10 TraesCS6D01G084300 chr6A 96.019 1884 69 4 1891 3769 65798517 65800399 0.000000e+00 3059.0
11 TraesCS6D01G084300 chr6A 89.356 404 39 3 4358 4759 65681258 65680857 5.500000e-139 505.0
12 TraesCS6D01G084300 chr6A 85.945 434 41 11 1081 1512 65797846 65798261 3.380000e-121 446.0
13 TraesCS6D01G084300 chr6A 96.175 183 7 0 1593 1775 65798256 65798438 2.780000e-77 300.0
14 TraesCS6D01G084300 chr5B 91.892 555 33 5 3294 3843 162833187 162833734 0.000000e+00 765.0
15 TraesCS6D01G084300 chr5B 84.328 134 13 6 976 1101 322748901 322749034 1.800000e-24 124.0
16 TraesCS6D01G084300 chr1D 82.667 75 13 0 4250 4324 60938067 60938141 3.070000e-07 67.6


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 TraesCS6D01G084300 chr6D 49217337 49222095 4758 False 8789.000000 8789 100.000000 1 4759 1 chr6D.!!$F1 4758
1 TraesCS6D01G084300 chr6D 48866827 48869405 2578 True 1324.000000 3179 93.647333 1084 3799 3 chr6D.!!$R1 2715
2 TraesCS6D01G084300 chr6B 121811732 121816269 4537 True 3141.500000 6037 91.089500 3 4535 2 chr6B.!!$R1 4532
3 TraesCS6D01G084300 chr6B 122290611 122293221 2610 False 1321.000000 3164 91.877000 1054 3775 3 chr6B.!!$F1 2721
4 TraesCS6D01G084300 chr6A 65680857 65685563 4706 True 3113.500000 5722 90.170000 1 4759 2 chr6A.!!$R1 4758
5 TraesCS6D01G084300 chr6A 65797846 65800399 2553 False 1268.333333 3059 92.713000 1081 3769 3 chr6A.!!$F1 2688
6 TraesCS6D01G084300 chr5B 162833187 162833734 547 False 765.000000 765 91.892000 3294 3843 1 chr5B.!!$F1 549

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
990 1049 0.038744 ATCCCTGTTCTGTTGCCAGG 59.961 55.000 0.00 0.0 44.39 4.45 F
1505 1598 0.178944 TCCACCTCGTCAGGGAGAAA 60.179 55.000 0.00 0.0 45.53 2.52 F
1564 1659 1.000739 ACCGGAGTATTGGTCGGGA 59.999 57.895 9.46 0.0 45.97 5.14 F
2354 2468 1.379977 CCTCCTCCTGGTCACGCTA 60.380 63.158 0.00 0.0 34.23 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2342 1.741401 CACCTCAATGAAGCCGCGA 60.741 57.895 8.23 0.0 0.00 5.87 R
3198 3312 2.184167 CGTTGTGGCCGGTGTTCTT 61.184 57.895 1.90 0.0 0.00 2.52 R
3299 3413 2.750350 AGGAACCACCGCTTCCTG 59.250 61.111 3.51 0.0 44.98 3.86 R
3944 4096 0.036306 GCCACTCCCCGAAGAAAAGA 59.964 55.000 0.00 0.0 0.00 2.52 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
55 58 6.536224 CCACCCAATTAAATTGATCTGCTTTC 59.464 38.462 0.00 0.00 42.83 2.62
60 63 7.916977 CCAATTAAATTGATCTGCTTTCGATCA 59.083 33.333 0.00 0.00 43.90 2.92
83 87 3.276846 GAGCACGCCACAACCGTT 61.277 61.111 0.00 0.00 36.69 4.44
90 94 3.656045 CCACAACCGTTGCCGTCC 61.656 66.667 11.29 0.00 0.00 4.79
98 102 2.165301 CGTTGCCGTCCGAAGATCC 61.165 63.158 0.00 0.00 0.00 3.36
106 110 1.826487 TCCGAAGATCCGGCGATCA 60.826 57.895 9.30 0.00 46.42 2.92
129 133 1.586564 GAGTTGTCGCGAGGATCCG 60.587 63.158 10.24 0.00 0.00 4.18
171 175 4.719106 AGCCGTCGGACGAGGAGT 62.719 66.667 30.33 8.01 46.05 3.85
192 196 0.107456 GCCATCCACCATCTCGATGT 59.893 55.000 6.20 0.00 37.11 3.06
193 197 1.475751 GCCATCCACCATCTCGATGTT 60.476 52.381 6.20 0.00 37.11 2.71
196 200 2.890808 TCCACCATCTCGATGTTAGC 57.109 50.000 6.20 0.00 37.11 3.09
225 229 3.687102 CCGTCACCGCTACCACCA 61.687 66.667 0.00 0.00 0.00 4.17
228 232 1.295423 GTCACCGCTACCACCACAT 59.705 57.895 0.00 0.00 0.00 3.21
242 246 3.634448 CCACCACATAGACTTCTCTCGAT 59.366 47.826 0.00 0.00 0.00 3.59
244 248 3.634448 ACCACATAGACTTCTCTCGATGG 59.366 47.826 0.00 0.00 29.93 3.51
254 258 1.490910 TCTCTCGATGGTAGCCTCTGA 59.509 52.381 0.00 0.00 0.00 3.27
271 275 1.153005 GATGGCTGCAAGGAGGAGG 60.153 63.158 0.50 0.00 35.99 4.30
272 276 1.617536 ATGGCTGCAAGGAGGAGGA 60.618 57.895 0.50 0.00 35.99 3.71
273 277 1.633915 ATGGCTGCAAGGAGGAGGAG 61.634 60.000 0.50 0.00 35.99 3.69
274 278 2.297129 GGCTGCAAGGAGGAGGAGT 61.297 63.158 0.50 0.00 35.99 3.85
278 282 0.325671 TGCAAGGAGGAGGAGTAGGG 60.326 60.000 0.00 0.00 0.00 3.53
280 284 2.032151 GCAAGGAGGAGGAGTAGGGAG 61.032 61.905 0.00 0.00 0.00 4.30
313 317 2.663188 GTGCAGATCGGATCGCCC 60.663 66.667 22.57 13.56 0.00 6.13
479 484 6.542370 GCCTAGATTCCATAAAACACAGCTAA 59.458 38.462 0.00 0.00 0.00 3.09
480 485 7.254932 GCCTAGATTCCATAAAACACAGCTAAG 60.255 40.741 0.00 0.00 0.00 2.18
482 487 6.183347 AGATTCCATAAAACACAGCTAAGCT 58.817 36.000 0.00 0.00 40.77 3.74
485 490 6.049955 TCCATAAAACACAGCTAAGCTAGT 57.950 37.500 0.00 0.00 36.40 2.57
486 491 5.874810 TCCATAAAACACAGCTAAGCTAGTG 59.125 40.000 0.00 0.00 40.60 2.74
548 559 5.630121 AGGGTAAACAACACATGATGAGAA 58.370 37.500 0.00 0.00 31.97 2.87
577 591 8.352942 ACCAAAACAAGAAGAACAATGATACTC 58.647 33.333 0.00 0.00 0.00 2.59
642 660 1.901159 CACATGGCATTTTCCCCTCAA 59.099 47.619 0.00 0.00 0.00 3.02
654 672 2.444696 CCTCAATTGGGGCCCACA 59.555 61.111 28.84 17.41 30.78 4.17
657 675 1.055040 CTCAATTGGGGCCCACAAAA 58.945 50.000 28.84 11.84 30.78 2.44
706 736 1.300388 GCCAACAAGCAAGCAGGTG 60.300 57.895 0.00 0.00 0.00 4.00
939 976 1.565759 CCAATCCCATCCTCTTGACCA 59.434 52.381 0.00 0.00 0.00 4.02
972 1031 3.565764 TTGATCGGATCAAGCTCCAAT 57.434 42.857 25.39 0.00 43.84 3.16
974 1033 2.224378 TGATCGGATCAAGCTCCAATCC 60.224 50.000 17.94 10.51 36.11 3.01
988 1047 1.619654 CAATCCCTGTTCTGTTGCCA 58.380 50.000 0.00 0.00 0.00 4.92
990 1049 0.038744 ATCCCTGTTCTGTTGCCAGG 59.961 55.000 0.00 0.00 44.39 4.45
1019 1079 1.333636 ATGGAGGAAGACCAGAGCCG 61.334 60.000 0.00 0.00 40.89 5.52
1253 1328 3.738281 CGCTCGATCCATCCTTACAACTT 60.738 47.826 0.00 0.00 0.00 2.66
1267 1342 5.051774 CCTTACAACTTTGTTCGTGCAATTG 60.052 40.000 0.00 0.00 42.35 2.32
1300 1378 1.471119 AGTGAATTGAGCTGCCATGG 58.529 50.000 7.63 7.63 0.00 3.66
1505 1598 0.178944 TCCACCTCGTCAGGGAGAAA 60.179 55.000 0.00 0.00 45.53 2.52
1512 1605 1.897802 TCGTCAGGGAGAAAAGGTACC 59.102 52.381 2.73 2.73 0.00 3.34
1513 1606 1.621814 CGTCAGGGAGAAAAGGTACCA 59.378 52.381 15.94 0.00 0.00 3.25
1515 1608 1.982958 TCAGGGAGAAAAGGTACCACC 59.017 52.381 15.94 7.14 38.99 4.61
1518 1611 1.703513 GGGAGAAAAGGTACCACCAGT 59.296 52.381 15.94 0.00 41.95 4.00
1519 1612 2.908351 GGGAGAAAAGGTACCACCAGTA 59.092 50.000 15.94 0.00 41.95 2.74
1530 1623 5.455056 GTACCACCAGTACCAGATCTATG 57.545 47.826 0.00 0.00 44.85 2.23
1531 1624 3.309296 ACCACCAGTACCAGATCTATGG 58.691 50.000 0.00 0.00 46.47 2.74
1532 1625 2.037772 CCACCAGTACCAGATCTATGGC 59.962 54.545 0.00 0.00 44.80 4.40
1533 1626 2.700371 CACCAGTACCAGATCTATGGCA 59.300 50.000 0.00 0.00 44.80 4.92
1534 1627 3.134623 CACCAGTACCAGATCTATGGCAA 59.865 47.826 0.00 0.00 44.80 4.52
1535 1628 3.976654 ACCAGTACCAGATCTATGGCAAT 59.023 43.478 0.00 0.00 44.80 3.56
1536 1629 4.202398 ACCAGTACCAGATCTATGGCAATG 60.202 45.833 0.00 0.00 44.80 2.82
1537 1630 4.321718 CAGTACCAGATCTATGGCAATGG 58.678 47.826 0.00 0.00 44.80 3.16
1538 1631 2.283145 ACCAGATCTATGGCAATGGC 57.717 50.000 0.00 0.00 44.80 4.40
1564 1659 1.000739 ACCGGAGTATTGGTCGGGA 59.999 57.895 9.46 0.00 45.97 5.14
1585 1680 6.797033 CGGGAAATTAATTATGTTCGATCTGC 59.203 38.462 0.01 0.00 0.00 4.26
1586 1681 7.519809 CGGGAAATTAATTATGTTCGATCTGCA 60.520 37.037 0.01 0.00 0.00 4.41
1587 1682 8.299570 GGGAAATTAATTATGTTCGATCTGCAT 58.700 33.333 0.01 0.00 0.00 3.96
1867 1976 2.094957 ACTACTCGAAGCTGCAAGAGAC 60.095 50.000 20.23 0.00 34.07 3.36
1881 1990 5.499313 TGCAAGAGACACATTAATGGATGA 58.501 37.500 19.37 0.00 0.00 2.92
2240 2354 2.690778 GGTGCTTCGCGGCTTCATT 61.691 57.895 6.13 0.00 0.00 2.57
2354 2468 1.379977 CCTCCTCCTGGTCACGCTA 60.380 63.158 0.00 0.00 34.23 4.26
2681 2795 1.796796 GCGCAACATCTTCTCCACC 59.203 57.895 0.30 0.00 0.00 4.61
3198 3312 3.062466 CCGTCCTCGAGGTGCTGA 61.062 66.667 30.17 8.66 39.71 4.26
3623 3744 1.960417 TCATCGACAACCTTGCACAA 58.040 45.000 0.00 0.00 0.00 3.33
3651 3778 9.742144 TTTGGATTTGATGATGGATTGATTTTT 57.258 25.926 0.00 0.00 0.00 1.94
3811 3941 6.262049 AGCACCATTTTTGTTTTGGGAATTAC 59.738 34.615 0.00 0.00 34.72 1.89
3812 3942 6.262049 GCACCATTTTTGTTTTGGGAATTACT 59.738 34.615 0.00 0.00 34.72 2.24
3813 3943 7.638134 CACCATTTTTGTTTTGGGAATTACTG 58.362 34.615 0.00 0.00 34.72 2.74
3854 4006 2.574006 TCTTGAAGCAAGAGCCACAT 57.426 45.000 5.81 0.00 44.27 3.21
3855 4007 2.156917 TCTTGAAGCAAGAGCCACATG 58.843 47.619 5.81 0.00 44.27 3.21
3856 4008 2.156917 CTTGAAGCAAGAGCCACATGA 58.843 47.619 0.00 0.00 43.42 3.07
3857 4009 2.502142 TGAAGCAAGAGCCACATGAT 57.498 45.000 0.00 0.00 43.56 2.45
3858 4010 2.799017 TGAAGCAAGAGCCACATGATT 58.201 42.857 0.00 0.00 43.56 2.57
3859 4011 2.751259 TGAAGCAAGAGCCACATGATTC 59.249 45.455 0.00 7.45 41.13 2.52
3860 4012 2.502142 AGCAAGAGCCACATGATTCA 57.498 45.000 0.00 0.00 43.56 2.57
3861 4013 2.089980 AGCAAGAGCCACATGATTCAC 58.910 47.619 0.00 0.00 43.56 3.18
3862 4014 2.089980 GCAAGAGCCACATGATTCACT 58.910 47.619 0.00 0.00 33.58 3.41
3863 4015 2.490903 GCAAGAGCCACATGATTCACTT 59.509 45.455 0.00 0.00 33.58 3.16
3864 4016 3.672511 GCAAGAGCCACATGATTCACTTG 60.673 47.826 0.00 10.41 37.24 3.16
3865 4017 2.089980 AGAGCCACATGATTCACTTGC 58.910 47.619 0.00 0.00 0.00 4.01
3866 4018 2.089980 GAGCCACATGATTCACTTGCT 58.910 47.619 0.00 0.00 0.00 3.91
3867 4019 1.816835 AGCCACATGATTCACTTGCTG 59.183 47.619 0.00 0.00 0.00 4.41
3868 4020 1.135199 GCCACATGATTCACTTGCTGG 60.135 52.381 0.00 0.00 33.08 4.85
3869 4021 1.135199 CCACATGATTCACTTGCTGGC 60.135 52.381 0.00 0.00 0.00 4.85
3870 4022 0.806868 ACATGATTCACTTGCTGGCG 59.193 50.000 0.00 0.00 0.00 5.69
3871 4023 0.524816 CATGATTCACTTGCTGGCGC 60.525 55.000 0.00 0.00 0.00 6.53
3872 4024 1.660560 ATGATTCACTTGCTGGCGCC 61.661 55.000 22.73 22.73 34.43 6.53
3873 4025 2.282391 ATTCACTTGCTGGCGCCA 60.282 55.556 30.59 30.59 34.43 5.69
3874 4026 2.533391 GATTCACTTGCTGGCGCCAC 62.533 60.000 29.03 22.57 34.43 5.01
3909 4061 9.447157 CTTTTCTTCCTCATTCTTCTCTGTAAT 57.553 33.333 0.00 0.00 0.00 1.89
3994 4146 2.896044 TGCTGCCCATGTAAAATCACAA 59.104 40.909 0.00 0.00 30.84 3.33
4004 4156 5.906113 TGTAAAATCACAAATACGCCCAT 57.094 34.783 0.00 0.00 0.00 4.00
4117 4270 7.924103 TTTTCGTTTCTTCATCTTTTTAGCC 57.076 32.000 0.00 0.00 0.00 3.93
4154 4307 1.896220 TGTCAGCTTTGACATCCACC 58.104 50.000 4.76 0.00 43.09 4.61
4156 4309 2.637382 TGTCAGCTTTGACATCCACCTA 59.363 45.455 4.76 0.00 43.09 3.08
4157 4310 3.264193 TGTCAGCTTTGACATCCACCTAT 59.736 43.478 4.76 0.00 43.09 2.57
4159 4312 5.456621 GTCAGCTTTGACATCCACCTATGG 61.457 50.000 1.41 0.00 41.73 2.74
4197 4374 3.367607 GCACACGCACAATTGTTTAAGA 58.632 40.909 8.77 0.00 38.36 2.10
4201 4378 5.458452 CACACGCACAATTGTTTAAGATGTT 59.542 36.000 8.77 0.00 0.00 2.71
4202 4379 5.458452 ACACGCACAATTGTTTAAGATGTTG 59.542 36.000 8.77 1.10 0.00 3.33
4225 4402 7.377766 TGTATGCTGGAAAGAATAGTCAAAC 57.622 36.000 0.00 0.00 0.00 2.93
4242 4419 6.451393 AGTCAAACACAGTACTCTCTTCATC 58.549 40.000 0.00 0.00 0.00 2.92
4243 4420 6.040955 AGTCAAACACAGTACTCTCTTCATCA 59.959 38.462 0.00 0.00 0.00 3.07
4244 4421 6.870965 GTCAAACACAGTACTCTCTTCATCAT 59.129 38.462 0.00 0.00 0.00 2.45
4245 4422 7.386299 GTCAAACACAGTACTCTCTTCATCATT 59.614 37.037 0.00 0.00 0.00 2.57
4246 4423 7.600375 TCAAACACAGTACTCTCTTCATCATTC 59.400 37.037 0.00 0.00 0.00 2.67
4247 4424 6.596309 ACACAGTACTCTCTTCATCATTCA 57.404 37.500 0.00 0.00 0.00 2.57
4304 4481 8.028354 TGAACTGCATAAATACCAAAATGAGTG 58.972 33.333 0.00 0.00 0.00 3.51
4305 4482 7.701539 ACTGCATAAATACCAAAATGAGTGA 57.298 32.000 0.00 0.00 0.00 3.41
4309 4486 8.363390 TGCATAAATACCAAAATGAGTGAACAA 58.637 29.630 0.00 0.00 0.00 2.83
4310 4487 9.202273 GCATAAATACCAAAATGAGTGAACAAA 57.798 29.630 0.00 0.00 0.00 2.83
4314 4491 9.442047 AAATACCAAAATGAGTGAACAAACAAA 57.558 25.926 0.00 0.00 0.00 2.83
4315 4492 6.720012 ACCAAAATGAGTGAACAAACAAAC 57.280 33.333 0.00 0.00 0.00 2.93
4326 4503 7.571892 AGTGAACAAACAAACAAAAATGTGTC 58.428 30.769 0.00 0.00 0.00 3.67
4328 4505 8.704234 GTGAACAAACAAACAAAAATGTGTCTA 58.296 29.630 0.00 0.00 0.00 2.59
4329 4506 9.429359 TGAACAAACAAACAAAAATGTGTCTAT 57.571 25.926 0.00 0.00 0.00 1.98
4331 4508 7.683746 ACAAACAAACAAAAATGTGTCTATGC 58.316 30.769 0.00 0.00 0.00 3.14
4343 4520 1.206849 TGTCTATGCACAGCCGATTCA 59.793 47.619 0.00 0.00 0.00 2.57
4344 4521 2.158914 TGTCTATGCACAGCCGATTCAT 60.159 45.455 0.00 0.00 0.00 2.57
4345 4522 3.069443 TGTCTATGCACAGCCGATTCATA 59.931 43.478 0.00 0.00 0.00 2.15
4346 4523 4.058124 GTCTATGCACAGCCGATTCATAA 58.942 43.478 0.00 0.00 0.00 1.90
4347 4524 4.151335 GTCTATGCACAGCCGATTCATAAG 59.849 45.833 0.00 0.00 0.00 1.73
4348 4525 2.689553 TGCACAGCCGATTCATAAGA 57.310 45.000 0.00 0.00 0.00 2.10
4349 4526 2.984562 TGCACAGCCGATTCATAAGAA 58.015 42.857 0.00 0.00 38.31 2.52
4350 4527 2.938451 TGCACAGCCGATTCATAAGAAG 59.062 45.455 0.00 0.00 37.14 2.85
4433 4610 3.216147 CACGGAATGTGGAATTGGTTC 57.784 47.619 0.00 0.00 45.21 3.62
4450 4627 3.096852 GGTTCCACCTAAATTTCCCTGG 58.903 50.000 0.00 0.00 34.73 4.45
4481 4658 5.700832 TGAACACATGTACAGAAACATCTCC 59.299 40.000 0.00 0.00 38.01 3.71
4482 4659 4.245660 ACACATGTACAGAAACATCTCCG 58.754 43.478 0.00 0.00 38.01 4.63
4484 4661 3.055819 ACATGTACAGAAACATCTCCGCT 60.056 43.478 0.00 0.00 38.01 5.52
4495 4672 5.998454 AACATCTCCGCTAGATCATTTTG 57.002 39.130 0.00 0.00 43.42 2.44
4527 4704 4.098807 ACTTGGAAAAGTGTAAATTGCGGT 59.901 37.500 0.00 0.00 0.00 5.68
4535 4712 5.127693 AGTGTAAATTGCGGTGCATAAAA 57.872 34.783 0.00 0.00 38.76 1.52
4541 4718 6.401955 AAATTGCGGTGCATAAAATTGTAC 57.598 33.333 0.00 0.00 38.76 2.90
4546 4723 2.446282 GTGCATAAAATTGTACCGGCG 58.554 47.619 0.00 0.00 0.00 6.46
4547 4724 1.202200 TGCATAAAATTGTACCGGCGC 60.202 47.619 0.00 0.00 0.00 6.53
4552 4729 0.098025 AAATTGTACCGGCGCGATTG 59.902 50.000 12.10 0.00 0.00 2.67
4580 4757 7.663905 TCGTGCCTTGCAATAGGTTATAAATAT 59.336 33.333 0.00 0.00 41.47 1.28
4598 4775 6.483888 AAATATTCTGGTATATTGGCCCCT 57.516 37.500 0.00 0.00 32.46 4.79
4606 4783 4.017126 GGTATATTGGCCCCTGATTTAGC 58.983 47.826 0.00 0.00 0.00 3.09
4626 4803 3.443681 AGCTTCCCAATTTAATGTGGTCG 59.556 43.478 4.67 0.00 32.60 4.79
4629 4806 2.490115 TCCCAATTTAATGTGGTCGTGC 59.510 45.455 4.67 0.00 32.60 5.34
4699 4877 4.524802 AAGGGATGTGATATTTGAGGCA 57.475 40.909 0.00 0.00 0.00 4.75
4720 4898 6.369615 AGGCATTTTTATGAAAACTGTGATGC 59.630 34.615 7.72 7.72 38.19 3.91
4726 4904 8.498054 TTTTATGAAAACTGTGATGCCAAAAA 57.502 26.923 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.202830 ACACCCAAGATGTGCCGTTTA 60.203 47.619 0.00 0.00 37.22 2.01
55 58 1.493950 GGCGTGCTCTCCATTGATCG 61.494 60.000 0.00 0.00 0.00 3.69
60 63 1.073025 TTGTGGCGTGCTCTCCATT 59.927 52.632 0.11 0.00 34.47 3.16
111 115 1.586564 CGGATCCTCGCGACAACTC 60.587 63.158 3.71 0.00 0.00 3.01
120 124 4.315122 CGAGACGGCGGATCCTCG 62.315 72.222 21.29 21.29 41.71 4.63
162 166 2.413765 GGATGGCGACTCCTCGTC 59.586 66.667 0.00 0.00 45.22 4.20
171 175 1.115326 ATCGAGATGGTGGATGGCGA 61.115 55.000 0.00 0.00 0.00 5.54
180 184 2.760650 TCTGTGCTAACATCGAGATGGT 59.239 45.455 16.37 12.80 42.91 3.55
192 196 2.359169 CGGGGCCTCTCTGTGCTAA 61.359 63.158 0.00 0.00 0.00 3.09
193 197 2.759973 CGGGGCCTCTCTGTGCTA 60.760 66.667 0.00 0.00 0.00 3.49
196 200 2.997315 TGACGGGGCCTCTCTGTG 60.997 66.667 0.00 0.00 0.00 3.66
218 222 3.945921 CGAGAGAAGTCTATGTGGTGGTA 59.054 47.826 0.00 0.00 30.97 3.25
254 258 1.617536 TCCTCCTCCTTGCAGCCAT 60.618 57.895 0.00 0.00 0.00 4.40
287 291 1.421485 CGATCTGCACAAACTCCGC 59.579 57.895 0.00 0.00 0.00 5.54
356 361 2.025605 AGACACATGAGCCACCATTCAT 60.026 45.455 0.00 0.00 34.48 2.57
365 370 0.037326 TCAACCGAGACACATGAGCC 60.037 55.000 0.00 0.00 0.00 4.70
390 395 6.165577 AGGAATGAACATTTTGGTGTTATGC 58.834 36.000 1.56 0.00 42.08 3.14
479 484 4.506271 CCATGGAATCTAATGGCACTAGCT 60.506 45.833 5.56 0.00 41.70 3.32
480 485 3.755378 CCATGGAATCTAATGGCACTAGC 59.245 47.826 5.56 0.00 37.15 3.42
482 487 4.202461 GGTCCATGGAATCTAATGGCACTA 60.202 45.833 18.20 0.00 42.67 2.74
485 490 2.513317 TGGTCCATGGAATCTAATGGCA 59.487 45.455 18.20 0.00 42.67 4.92
486 491 3.228188 TGGTCCATGGAATCTAATGGC 57.772 47.619 18.20 0.00 42.67 4.40
548 559 4.799564 TTGTTCTTCTTGTTTTGGTGCT 57.200 36.364 0.00 0.00 0.00 4.40
642 660 3.848975 TGATTAATTTTGTGGGCCCCAAT 59.151 39.130 22.27 9.59 34.18 3.16
654 672 7.500629 AGAAGGAAGGGCAATGATTAATTTT 57.499 32.000 0.00 0.00 0.00 1.82
657 675 8.230306 AGATAAGAAGGAAGGGCAATGATTAAT 58.770 33.333 0.00 0.00 0.00 1.40
706 736 1.789506 AGCTTGAAGACAGCGAAGTC 58.210 50.000 0.00 0.00 38.81 3.01
881 917 4.868171 CGTATATAAATGGGATCACGTGGG 59.132 45.833 17.00 0.00 0.00 4.61
939 976 3.636679 TCCGATCAAGATCTCAAGGTCT 58.363 45.455 8.30 0.00 35.72 3.85
988 1047 1.692042 CCTCCATGCCTGTCCTCCT 60.692 63.158 0.00 0.00 0.00 3.69
990 1049 0.179936 CTTCCTCCATGCCTGTCCTC 59.820 60.000 0.00 0.00 0.00 3.71
1191 1254 1.587613 GAGGCTCTCGATGTGCGAC 60.588 63.158 7.40 0.00 45.59 5.19
1228 1291 0.959553 TAAGGATGGATCGAGCGGTC 59.040 55.000 4.06 4.06 0.00 4.79
1253 1328 1.202463 CCAACCCAATTGCACGAACAA 60.202 47.619 0.00 0.00 36.93 2.83
1267 1342 1.616159 TTCACTAAGCAAGCCAACCC 58.384 50.000 0.00 0.00 0.00 4.11
1300 1378 1.216122 GTTCTCGATGATCCTGCAGC 58.784 55.000 8.66 0.00 0.00 5.25
1430 1523 1.880340 GGCGAGGTTGATGAGCGAG 60.880 63.158 0.00 0.00 0.00 5.03
1512 1605 2.700371 TGCCATAGATCTGGTACTGGTG 59.300 50.000 5.18 0.00 38.63 4.17
1513 1606 3.046283 TGCCATAGATCTGGTACTGGT 57.954 47.619 5.18 0.00 38.63 4.00
1515 1608 4.321718 CCATTGCCATAGATCTGGTACTG 58.678 47.826 5.18 4.13 38.63 2.74
1518 1611 3.423539 GCCATTGCCATAGATCTGGTA 57.576 47.619 5.18 0.00 38.63 3.25
1519 1612 2.283145 GCCATTGCCATAGATCTGGT 57.717 50.000 5.18 0.00 38.63 4.00
1549 1642 6.954487 AATTAATTTCCCGACCAATACTCC 57.046 37.500 0.00 0.00 0.00 3.85
1554 1647 7.283580 TCGAACATAATTAATTTCCCGACCAAT 59.716 33.333 5.91 0.00 0.00 3.16
1585 1680 1.270839 CCGGCCCAGTACCTGAATATG 60.271 57.143 0.00 0.00 32.44 1.78
1586 1681 1.056660 CCGGCCCAGTACCTGAATAT 58.943 55.000 0.00 0.00 32.44 1.28
1587 1682 1.692173 GCCGGCCCAGTACCTGAATA 61.692 60.000 18.11 0.00 32.44 1.75
2228 2342 1.741401 CACCTCAATGAAGCCGCGA 60.741 57.895 8.23 0.00 0.00 5.87
3198 3312 2.184167 CGTTGTGGCCGGTGTTCTT 61.184 57.895 1.90 0.00 0.00 2.52
3299 3413 2.750350 AGGAACCACCGCTTCCTG 59.250 61.111 3.51 0.00 44.98 3.86
3623 3744 9.914834 AAATCAATCCATCATCAAATCCAAATT 57.085 25.926 0.00 0.00 0.00 1.82
3651 3778 1.114627 AGCGGAGATATCTGCACACA 58.885 50.000 22.51 0.00 44.04 3.72
3776 3903 0.971386 AAATGGTGCTGGCTTTCAGG 59.029 50.000 0.00 0.00 43.54 3.86
3777 3904 2.803956 CAAAAATGGTGCTGGCTTTCAG 59.196 45.455 0.00 0.00 46.03 3.02
3778 3905 2.170187 ACAAAAATGGTGCTGGCTTTCA 59.830 40.909 0.00 0.00 0.00 2.69
3779 3906 2.837498 ACAAAAATGGTGCTGGCTTTC 58.163 42.857 0.00 0.00 0.00 2.62
3811 3941 2.470257 GGAAACACGTCGACAGTAACAG 59.530 50.000 17.16 5.41 0.00 3.16
3812 3942 2.099592 AGGAAACACGTCGACAGTAACA 59.900 45.455 17.16 0.00 0.00 2.41
3813 3943 2.470257 CAGGAAACACGTCGACAGTAAC 59.530 50.000 17.16 10.26 0.00 2.50
3853 4005 1.805254 GCGCCAGCAAGTGAATCAT 59.195 52.632 0.00 0.00 44.35 2.45
3854 4006 3.266964 GCGCCAGCAAGTGAATCA 58.733 55.556 0.00 0.00 44.35 2.57
3864 4016 2.583685 GAAAGAATCGTGGCGCCAGC 62.584 60.000 33.73 23.13 44.18 4.85
3865 4017 1.021390 AGAAAGAATCGTGGCGCCAG 61.021 55.000 33.73 23.58 0.00 4.85
3866 4018 0.605319 AAGAAAGAATCGTGGCGCCA 60.605 50.000 29.03 29.03 0.00 5.69
3867 4019 0.521735 AAAGAAAGAATCGTGGCGCC 59.478 50.000 22.73 22.73 0.00 6.53
3868 4020 2.095718 AGAAAAGAAAGAATCGTGGCGC 60.096 45.455 0.00 0.00 0.00 6.53
3869 4021 3.813529 AGAAAAGAAAGAATCGTGGCG 57.186 42.857 0.00 0.00 0.00 5.69
3870 4022 4.216472 AGGAAGAAAAGAAAGAATCGTGGC 59.784 41.667 0.00 0.00 0.00 5.01
3871 4023 5.470098 TGAGGAAGAAAAGAAAGAATCGTGG 59.530 40.000 0.00 0.00 0.00 4.94
3872 4024 6.545504 TGAGGAAGAAAAGAAAGAATCGTG 57.454 37.500 0.00 0.00 0.00 4.35
3873 4025 7.663493 AGAATGAGGAAGAAAAGAAAGAATCGT 59.337 33.333 0.00 0.00 0.00 3.73
3874 4026 8.038492 AGAATGAGGAAGAAAAGAAAGAATCG 57.962 34.615 0.00 0.00 0.00 3.34
3909 4061 2.487762 CGCAAGCAAATCCTGAACCTAA 59.512 45.455 0.00 0.00 0.00 2.69
3941 4093 3.219281 CCACTCCCCGAAGAAAAGAAAA 58.781 45.455 0.00 0.00 0.00 2.29
3942 4094 2.858745 CCACTCCCCGAAGAAAAGAAA 58.141 47.619 0.00 0.00 0.00 2.52
3943 4095 1.544759 GCCACTCCCCGAAGAAAAGAA 60.545 52.381 0.00 0.00 0.00 2.52
3944 4096 0.036306 GCCACTCCCCGAAGAAAAGA 59.964 55.000 0.00 0.00 0.00 2.52
3959 4111 2.543641 GGCAGCAAATTATTCAGCCAC 58.456 47.619 0.00 0.00 40.29 5.01
3994 4146 3.057315 GCTTATTGCATCATGGGCGTATT 60.057 43.478 0.00 0.00 42.31 1.89
4093 4246 6.921307 GGGCTAAAAAGATGAAGAAACGAAAA 59.079 34.615 0.00 0.00 0.00 2.29
4097 4250 5.629079 AGGGCTAAAAAGATGAAGAAACG 57.371 39.130 0.00 0.00 0.00 3.60
4102 4255 6.385033 CAACAGAAGGGCTAAAAAGATGAAG 58.615 40.000 0.00 0.00 0.00 3.02
4114 4267 1.073923 ACGAAATCCAACAGAAGGGCT 59.926 47.619 0.00 0.00 0.00 5.19
4117 4270 3.563808 TGACAACGAAATCCAACAGAAGG 59.436 43.478 0.00 0.00 0.00 3.46
4182 4335 7.329226 AGCATACAACATCTTAAACAATTGTGC 59.671 33.333 12.82 5.19 32.76 4.57
4185 4338 8.028354 TCCAGCATACAACATCTTAAACAATTG 58.972 33.333 3.24 3.24 0.00 2.32
4197 4374 7.112122 TGACTATTCTTTCCAGCATACAACAT 58.888 34.615 0.00 0.00 0.00 2.71
4201 4378 6.939730 TGTTTGACTATTCTTTCCAGCATACA 59.060 34.615 0.00 0.00 0.00 2.29
4202 4379 7.094805 TGTGTTTGACTATTCTTTCCAGCATAC 60.095 37.037 0.00 0.00 0.00 2.39
4225 4402 9.591792 TTTATGAATGATGAAGAGAGTACTGTG 57.408 33.333 0.00 0.00 0.00 3.66
4279 4456 8.243426 TCACTCATTTTGGTATTTATGCAGTTC 58.757 33.333 0.00 0.00 0.00 3.01
4289 4466 8.878769 GTTTGTTTGTTCACTCATTTTGGTATT 58.121 29.630 0.00 0.00 0.00 1.89
4291 4468 7.378966 TGTTTGTTTGTTCACTCATTTTGGTA 58.621 30.769 0.00 0.00 0.00 3.25
4294 4471 9.443283 TTTTTGTTTGTTTGTTCACTCATTTTG 57.557 25.926 0.00 0.00 0.00 2.44
4297 4474 8.782144 ACATTTTTGTTTGTTTGTTCACTCATT 58.218 25.926 0.00 0.00 0.00 2.57
4301 4478 7.440856 AGACACATTTTTGTTTGTTTGTTCACT 59.559 29.630 0.00 0.00 0.00 3.41
4304 4481 9.687717 CATAGACACATTTTTGTTTGTTTGTTC 57.312 29.630 0.00 0.00 0.00 3.18
4305 4482 8.174422 GCATAGACACATTTTTGTTTGTTTGTT 58.826 29.630 0.00 0.00 0.00 2.83
4309 4486 6.815641 TGTGCATAGACACATTTTTGTTTGTT 59.184 30.769 0.00 0.00 45.36 2.83
4310 4487 6.336566 TGTGCATAGACACATTTTTGTTTGT 58.663 32.000 0.00 0.00 45.36 2.83
4311 4488 6.825284 TGTGCATAGACACATTTTTGTTTG 57.175 33.333 0.00 0.00 45.36 2.93
4326 4503 4.309933 TCTTATGAATCGGCTGTGCATAG 58.690 43.478 6.03 6.03 0.00 2.23
4328 4505 3.198409 TCTTATGAATCGGCTGTGCAT 57.802 42.857 0.00 0.00 0.00 3.96
4329 4506 2.689553 TCTTATGAATCGGCTGTGCA 57.310 45.000 0.00 0.00 0.00 4.57
4331 4508 5.801350 TTTCTTCTTATGAATCGGCTGTG 57.199 39.130 0.00 0.00 0.00 3.66
4433 4610 7.782644 TCATAATTACCAGGGAAATTTAGGTGG 59.217 37.037 12.00 10.82 33.91 4.61
4481 4658 6.313905 AGTTCAGTAACCAAAATGATCTAGCG 59.686 38.462 0.00 0.00 36.15 4.26
4482 4659 7.617041 AGTTCAGTAACCAAAATGATCTAGC 57.383 36.000 0.00 0.00 36.15 3.42
4484 4661 8.160765 TCCAAGTTCAGTAACCAAAATGATCTA 58.839 33.333 0.00 0.00 36.15 1.98
4495 4672 5.830000 ACACTTTTCCAAGTTCAGTAACC 57.170 39.130 0.00 0.00 40.66 2.85
4527 4704 1.202200 GCGCCGGTACAATTTTATGCA 60.202 47.619 1.90 0.00 0.00 3.96
4535 4712 1.022451 AACAATCGCGCCGGTACAAT 61.022 50.000 1.90 0.00 0.00 2.71
4552 4729 1.165270 ACCTATTGCAAGGCACGAAC 58.835 50.000 4.94 0.00 40.62 3.95
4556 4733 9.626045 GAATATTTATAACCTATTGCAAGGCAC 57.374 33.333 4.94 0.00 40.62 5.01
4580 4757 2.782922 TCAGGGGCCAATATACCAGAA 58.217 47.619 4.39 0.00 0.00 3.02
4595 4772 6.790232 TTAAATTGGGAAGCTAAATCAGGG 57.210 37.500 0.00 0.00 0.00 4.45
4598 4775 7.180051 ACCACATTAAATTGGGAAGCTAAATCA 59.820 33.333 9.82 0.00 37.18 2.57
4606 4783 4.732784 CACGACCACATTAAATTGGGAAG 58.267 43.478 9.82 4.17 37.18 3.46
4660 4837 4.357399 TCCCTTATTGACCTACCCCAAAAA 59.643 41.667 0.00 0.00 0.00 1.94
4665 4842 3.053826 ACATCCCTTATTGACCTACCCC 58.946 50.000 0.00 0.00 0.00 4.95
4666 4843 3.714798 TCACATCCCTTATTGACCTACCC 59.285 47.826 0.00 0.00 0.00 3.69
4669 4846 8.944138 TCAAATATCACATCCCTTATTGACCTA 58.056 33.333 0.00 0.00 0.00 3.08
4670 4847 7.815383 TCAAATATCACATCCCTTATTGACCT 58.185 34.615 0.00 0.00 0.00 3.85
4671 4848 7.175641 CCTCAAATATCACATCCCTTATTGACC 59.824 40.741 0.00 0.00 0.00 4.02
4672 4849 7.308830 GCCTCAAATATCACATCCCTTATTGAC 60.309 40.741 0.00 0.00 0.00 3.18
4673 4850 6.716628 GCCTCAAATATCACATCCCTTATTGA 59.283 38.462 0.00 0.00 0.00 2.57
4681 4859 9.199982 CATAAAAATGCCTCAAATATCACATCC 57.800 33.333 0.00 0.00 0.00 3.51
4699 4877 8.674263 TTTGGCATCACAGTTTTCATAAAAAT 57.326 26.923 0.00 0.00 36.77 1.82
4726 4904 6.658555 TTTTCCCTCTCCCTTCTCATATTT 57.341 37.500 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.