Multiple sequence alignment - TraesCS1A01G243000

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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 TraesCS1A01G243000 chr1A 100.000 4596 0 0 1 4596 431012811 431017406 0.000000e+00 8488.0
1 TraesCS1A01G243000 chr1A 89.280 597 60 3 3 596 548587042 548586447 0.000000e+00 745.0
2 TraesCS1A01G243000 chr1A 100.000 29 0 0 4126 4154 534930318 534930290 2.000000e-03 54.7
3 TraesCS1A01G243000 chr1D 93.335 3856 145 46 601 4418 333218594 333222375 0.000000e+00 5594.0
4 TraesCS1A01G243000 chr1D 100.000 29 0 0 4126 4154 438225917 438225889 2.000000e-03 54.7
5 TraesCS1A01G243000 chr1B 91.147 1909 113 28 2266 4158 448741459 448743327 0.000000e+00 2538.0
6 TraesCS1A01G243000 chr1B 88.186 1786 131 39 451 2213 448739633 448741361 0.000000e+00 2056.0
7 TraesCS1A01G243000 chr1B 91.358 405 14 7 4202 4596 448743327 448743720 6.770000e-148 534.0
8 TraesCS1A01G243000 chr1B 85.500 400 38 8 1 400 448739253 448739632 2.580000e-107 399.0
9 TraesCS1A01G243000 chr1B 88.571 70 8 0 102 171 428620088 428620019 8.190000e-13 86.1
10 TraesCS1A01G243000 chr2B 86.978 599 60 5 3 596 54273857 54273272 0.000000e+00 658.0
11 TraesCS1A01G243000 chr6B 86.889 389 46 3 213 597 33597442 33597055 9.130000e-117 431.0
12 TraesCS1A01G243000 chr5D 78.117 393 81 4 154 543 95061262 95060872 1.280000e-60 244.0
13 TraesCS1A01G243000 chr5D 100.000 37 0 0 4126 4162 80453323 80453287 8.250000e-08 69.4
14 TraesCS1A01G243000 chr5A 100.000 37 0 0 4126 4162 368557912 368557876 8.250000e-08 69.4
15 TraesCS1A01G243000 chr3A 100.000 30 0 0 4133 4162 430531940 430531911 6.420000e-04 56.5


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 TraesCS1A01G243000 chr1A 431012811 431017406 4595 False 8488.00 8488 100.00000 1 4596 1 chr1A.!!$F1 4595
1 TraesCS1A01G243000 chr1A 548586447 548587042 595 True 745.00 745 89.28000 3 596 1 chr1A.!!$R2 593
2 TraesCS1A01G243000 chr1D 333218594 333222375 3781 False 5594.00 5594 93.33500 601 4418 1 chr1D.!!$F1 3817
3 TraesCS1A01G243000 chr1B 448739253 448743720 4467 False 1381.75 2538 89.04775 1 4596 4 chr1B.!!$F1 4595
4 TraesCS1A01G243000 chr2B 54273272 54273857 585 True 658.00 658 86.97800 3 596 1 chr2B.!!$R1 593

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
816 827 0.238553 GCTTCTCAGTTCGGCCAAAC 59.761 55.0 2.24 0.0 0.00 2.93 F
1927 1959 0.036294 GCGGAGTAGCCTTTTGGAGT 60.036 55.0 0.00 0.0 44.07 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 2380 0.315251 GAAAGCACTTGGTTGGGCTC 59.685 55.0 0.0 0.0 35.11 4.70 R
3630 3710 1.382522 CTCGCAGGCACCAATACAAT 58.617 50.0 0.0 0.0 0.00 2.71 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
45 46 4.975147 TGGTAGTCCAAGATGTATGGGAAT 59.025 41.667 0.00 0.00 41.25 3.01
80 81 5.308497 TCATTGTTCTCCCCAAGTACTACAA 59.692 40.000 0.00 0.57 0.00 2.41
84 85 2.504175 TCTCCCCAAGTACTACAATGGC 59.496 50.000 5.88 0.00 0.00 4.40
87 88 1.208535 CCCAAGTACTACAATGGCCGA 59.791 52.381 5.88 0.00 0.00 5.54
98 99 2.119484 AATGGCCGACACCTCCGAAA 62.119 55.000 0.00 0.00 0.00 3.46
120 121 7.480760 AAAAATATGTTGGCCTTGTCTGTAT 57.519 32.000 3.32 0.00 0.00 2.29
175 176 0.837272 GTGGGGATGATCCTTCGGAA 59.163 55.000 11.87 0.00 36.57 4.30
178 179 2.158623 TGGGGATGATCCTTCGGAAATG 60.159 50.000 11.87 0.00 36.57 2.32
254 255 5.774184 AGCTCTAGAGATTGAGATACATGCA 59.226 40.000 24.24 0.00 32.44 3.96
255 256 6.438108 AGCTCTAGAGATTGAGATACATGCAT 59.562 38.462 24.24 0.00 32.44 3.96
284 285 1.083489 GTATGGCGCTTGCTACACAA 58.917 50.000 7.64 0.00 39.13 3.33
315 316 0.542333 TCCGGTGTTGGTTCAGTCAA 59.458 50.000 0.00 0.00 0.00 3.18
322 323 5.660460 GGTGTTGGTTCAGTCAAATTCTTT 58.340 37.500 0.00 0.00 0.00 2.52
339 340 7.530426 AATTCTTTGACTGCCTTATCTTGTT 57.470 32.000 0.00 0.00 0.00 2.83
445 446 2.345641 CGCAGAAACTTCATAGGTCACG 59.654 50.000 0.00 0.00 0.00 4.35
446 447 3.326747 GCAGAAACTTCATAGGTCACGT 58.673 45.455 0.00 0.00 0.00 4.49
447 448 3.123621 GCAGAAACTTCATAGGTCACGTG 59.876 47.826 9.94 9.94 0.00 4.49
472 473 2.295909 GTGTTGCAGATTGCCTGGTAAA 59.704 45.455 0.16 0.00 44.23 2.01
473 474 2.961741 TGTTGCAGATTGCCTGGTAAAA 59.038 40.909 0.16 0.00 44.23 1.52
516 517 1.312371 GGCTATGTGGCTCGGCAAAA 61.312 55.000 0.00 0.00 38.32 2.44
540 543 4.446889 GCCCCATGTATTGAGGATCTCTTT 60.447 45.833 0.00 0.00 34.92 2.52
551 554 6.891306 TGAGGATCTCTTTCCCAAAGATTA 57.109 37.500 0.00 0.00 45.75 1.75
581 588 5.937975 ACCATGATGGAATAAAACCCTTG 57.062 39.130 20.11 0.00 40.96 3.61
588 595 7.638444 TGATGGAATAAAACCCTTGTGATCTA 58.362 34.615 0.00 0.00 0.00 1.98
589 596 8.112822 TGATGGAATAAAACCCTTGTGATCTAA 58.887 33.333 0.00 0.00 0.00 2.10
617 627 8.715191 AAAAGTCTAATCTGATGAAGCTACAG 57.285 34.615 0.00 0.00 0.00 2.74
619 629 7.038154 AGTCTAATCTGATGAAGCTACAGAC 57.962 40.000 12.59 0.00 42.18 3.51
621 631 7.341769 AGTCTAATCTGATGAAGCTACAGACTT 59.658 37.037 12.59 10.94 42.18 3.01
625 635 7.608308 ATCTGATGAAGCTACAGACTTTTTC 57.392 36.000 12.59 0.00 42.18 2.29
626 636 6.524734 TCTGATGAAGCTACAGACTTTTTCA 58.475 36.000 8.17 0.00 36.04 2.69
627 637 6.648310 TCTGATGAAGCTACAGACTTTTTCAG 59.352 38.462 8.17 0.00 37.55 3.02
628 638 5.702670 TGATGAAGCTACAGACTTTTTCAGG 59.297 40.000 0.00 0.00 0.00 3.86
630 640 5.680619 TGAAGCTACAGACTTTTTCAGGAA 58.319 37.500 0.00 0.00 0.00 3.36
631 641 6.119536 TGAAGCTACAGACTTTTTCAGGAAA 58.880 36.000 0.00 0.00 0.00 3.13
717 728 0.618458 ACATGGCGATTGGTACTGGT 59.382 50.000 0.00 0.00 0.00 4.00
785 796 1.076549 GTGCCAACCATTCCCCTGA 59.923 57.895 0.00 0.00 0.00 3.86
797 808 1.971481 TCCCCTGAAATGCATCATCG 58.029 50.000 0.00 0.00 0.00 3.84
816 827 0.238553 GCTTCTCAGTTCGGCCAAAC 59.761 55.000 2.24 0.00 0.00 2.93
818 829 1.264288 CTTCTCAGTTCGGCCAAACAC 59.736 52.381 9.72 0.00 0.00 3.32
834 845 1.387737 CACCACCCAACCATCCCAT 59.612 57.895 0.00 0.00 0.00 4.00
892 903 2.047844 CACCACGAGCTCCCAGTG 60.048 66.667 8.47 10.55 35.79 3.66
905 916 1.079490 TCCCAGTGTCTCCTCATTCCT 59.921 52.381 0.00 0.00 0.00 3.36
931 942 2.420890 GATCGGGAGCAGAGCAGG 59.579 66.667 0.00 0.00 0.00 4.85
933 944 1.680522 GATCGGGAGCAGAGCAGGAA 61.681 60.000 0.00 0.00 0.00 3.36
934 945 1.965754 ATCGGGAGCAGAGCAGGAAC 61.966 60.000 0.00 0.00 0.00 3.62
935 946 2.947532 CGGGAGCAGAGCAGGAACA 61.948 63.158 0.00 0.00 0.00 3.18
936 947 1.078567 GGGAGCAGAGCAGGAACAG 60.079 63.158 0.00 0.00 0.00 3.16
937 948 1.548357 GGGAGCAGAGCAGGAACAGA 61.548 60.000 0.00 0.00 0.00 3.41
988 1001 4.771684 CGTACCGTCGGATTTCGT 57.228 55.556 20.51 0.00 40.32 3.85
1010 1029 2.761465 GGGAGGCCATGGAGAAGGG 61.761 68.421 18.40 0.00 0.00 3.95
1074 1093 4.082523 CAGCGGTGGGTGATCGGT 62.083 66.667 6.74 0.00 44.37 4.69
1077 1096 2.125673 CGGTGGGTGATCGGTGTC 60.126 66.667 0.00 0.00 0.00 3.67
1306 1329 3.711782 CCCCTCCCTCCCTCCCTT 61.712 72.222 0.00 0.00 0.00 3.95
1307 1330 2.461637 CCCTCCCTCCCTCCCTTT 59.538 66.667 0.00 0.00 0.00 3.11
1308 1331 1.716689 CCCTCCCTCCCTCCCTTTA 59.283 63.158 0.00 0.00 0.00 1.85
1309 1332 0.272235 CCCTCCCTCCCTCCCTTTAT 59.728 60.000 0.00 0.00 0.00 1.40
1359 1382 1.621317 TCAGATCTACCAACAACGCCA 59.379 47.619 0.00 0.00 0.00 5.69
1360 1383 1.732259 CAGATCTACCAACAACGCCAC 59.268 52.381 0.00 0.00 0.00 5.01
1361 1384 1.084289 GATCTACCAACAACGCCACC 58.916 55.000 0.00 0.00 0.00 4.61
1410 1433 2.296190 TCCTCATCGTGATTCCATACCG 59.704 50.000 0.00 0.00 0.00 4.02
1414 1437 1.046472 TCGTGATTCCATACCGCCCT 61.046 55.000 0.00 0.00 0.00 5.19
1468 1491 1.310933 ACCACGCTCGATTCCGTACT 61.311 55.000 5.75 0.00 35.69 2.73
1469 1492 0.591741 CCACGCTCGATTCCGTACTC 60.592 60.000 5.75 0.00 35.69 2.59
1470 1493 0.098200 CACGCTCGATTCCGTACTCA 59.902 55.000 5.75 0.00 35.69 3.41
1479 1502 3.736126 CGATTCCGTACTCACCTTTACCC 60.736 52.174 0.00 0.00 0.00 3.69
1551 1576 2.290323 CCGAGATTTTCACCTTCCCTGT 60.290 50.000 0.00 0.00 0.00 4.00
1556 1581 2.561478 TTTCACCTTCCCTGTACTGC 57.439 50.000 0.00 0.00 0.00 4.40
1617 1646 3.741805 TCACTGATTAGACGAGTCGTG 57.258 47.619 25.31 9.20 41.37 4.35
1682 1711 1.229428 TTTGCGCTGTCTTTGGAGAG 58.771 50.000 9.73 0.00 36.13 3.20
1684 1713 0.392706 TGCGCTGTCTTTGGAGAGAA 59.607 50.000 9.73 0.00 35.17 2.87
1685 1714 1.202639 TGCGCTGTCTTTGGAGAGAAA 60.203 47.619 9.73 0.00 35.17 2.52
1686 1715 1.873591 GCGCTGTCTTTGGAGAGAAAA 59.126 47.619 0.00 0.00 35.17 2.29
1687 1716 2.290641 GCGCTGTCTTTGGAGAGAAAAA 59.709 45.455 0.00 0.00 35.17 1.94
1713 1745 8.587952 AAGAAAAAGAAAAATGATAACCACGG 57.412 30.769 0.00 0.00 0.00 4.94
1779 1811 1.153568 ATCGGTGTCATGTGGCGAG 60.154 57.895 0.00 0.00 0.00 5.03
1780 1812 3.490759 CGGTGTCATGTGGCGAGC 61.491 66.667 0.00 0.00 0.00 5.03
1809 1841 4.957967 CGCTGCAAAGAATATACTTGAACG 59.042 41.667 0.00 0.00 0.00 3.95
1927 1959 0.036294 GCGGAGTAGCCTTTTGGAGT 60.036 55.000 0.00 0.00 44.07 3.85
1941 1973 1.299976 GGAGTAGCAACCAGGGTGG 59.700 63.158 6.63 0.00 45.02 4.61
2007 2039 6.308766 GTGCACAAGTGTTATGATGAAATTCC 59.691 38.462 13.17 0.00 0.00 3.01
2065 2097 5.730568 GCATTACAGAACTTAAGATTGCCCG 60.731 44.000 10.09 0.00 0.00 6.13
2078 2110 0.250234 TTGCCCGTCCTCAGATTCTG 59.750 55.000 7.38 7.38 0.00 3.02
2108 2140 8.584157 TGAAGTCTTAATTTGTGCAATACCATT 58.416 29.630 0.00 0.00 0.00 3.16
2149 2181 6.581171 AATCACTTTGGTCTTTGATTCTCC 57.419 37.500 0.00 0.00 34.30 3.71
2154 2186 6.920210 CACTTTGGTCTTTGATTCTCCTTTTC 59.080 38.462 0.00 0.00 0.00 2.29
2157 2189 4.520492 TGGTCTTTGATTCTCCTTTTCAGC 59.480 41.667 0.00 0.00 0.00 4.26
2166 2198 2.093288 TCTCCTTTTCAGCTCGCATCAT 60.093 45.455 0.00 0.00 0.00 2.45
2210 2243 5.843019 TGATCCCCTTGGTTTAGATATCC 57.157 43.478 0.00 0.00 0.00 2.59
2303 2380 7.274904 CACTTCATGAACAGATTGGCATAAAAG 59.725 37.037 3.38 0.00 0.00 2.27
2318 2396 0.752658 AAAAGAGCCCAACCAAGTGC 59.247 50.000 0.00 0.00 0.00 4.40
2334 2412 1.069204 AGTGCTTTCGAGCTTGACAGA 59.931 47.619 19.46 3.78 35.49 3.41
2454 2533 4.096833 TGTCAAATGCCATAACTGATGCTC 59.903 41.667 0.00 0.00 33.79 4.26
2879 2959 6.183360 CCAGTTCTTCACTACTGTGGCTATAT 60.183 42.308 0.00 0.00 43.94 0.86
2923 3003 4.680110 CCAAAGGCGACTACTAATACATCG 59.320 45.833 0.00 0.00 42.68 3.84
2962 3042 3.801114 AAACAAACCAAAGAGCTGTCC 57.199 42.857 0.00 0.00 0.00 4.02
3211 3291 0.720027 CTCTGCAGTTCATCACAGCG 59.280 55.000 14.67 0.00 40.80 5.18
3280 3360 3.713764 AGGTGGGAATATCAGACTCCTTG 59.286 47.826 0.00 0.00 0.00 3.61
3530 3610 0.100682 GATTGAGGCTGCATGCACAG 59.899 55.000 18.46 9.68 45.15 3.66
3592 3672 3.875571 AGGGAAGGAGAAGAAGGAAGAA 58.124 45.455 0.00 0.00 0.00 2.52
3612 3692 8.257306 GGAAGAATAGAATCCATCTGTAGGATC 58.743 40.741 0.00 0.00 44.94 3.36
3613 3693 7.732222 AGAATAGAATCCATCTGTAGGATCC 57.268 40.000 2.48 2.48 44.94 3.36
3614 3694 6.671779 AGAATAGAATCCATCTGTAGGATCCC 59.328 42.308 8.55 0.00 44.94 3.85
3615 3695 4.500389 AGAATCCATCTGTAGGATCCCT 57.500 45.455 8.55 0.00 44.94 4.20
3616 3696 5.623551 AGAATCCATCTGTAGGATCCCTA 57.376 43.478 8.55 0.00 44.94 3.53
3617 3697 5.588845 AGAATCCATCTGTAGGATCCCTAG 58.411 45.833 8.55 4.60 44.94 3.02
3618 3698 3.835478 TCCATCTGTAGGATCCCTAGG 57.165 52.381 8.55 0.06 36.71 3.02
3619 3699 3.346028 TCCATCTGTAGGATCCCTAGGA 58.654 50.000 11.48 3.90 36.71 2.94
3620 3700 3.932562 TCCATCTGTAGGATCCCTAGGAT 59.067 47.826 11.48 5.15 46.28 3.24
3660 3740 1.003355 CCTGCGAGGCTTTCCTTCA 60.003 57.895 0.00 0.00 44.46 3.02
3755 3835 3.314541 TTAGGTTCTTCAGTTCCGAGC 57.685 47.619 0.00 0.00 0.00 5.03
3804 3884 6.780031 TCTTAAGAGGCAAGAGCAGATATACT 59.220 38.462 0.00 0.00 44.61 2.12
3837 3917 4.452455 TCATTCTTTTCGTCTTTCAGGAGC 59.548 41.667 0.00 0.00 0.00 4.70
3838 3918 3.753294 TCTTTTCGTCTTTCAGGAGCT 57.247 42.857 0.00 0.00 0.00 4.09
3839 3919 4.866508 TCTTTTCGTCTTTCAGGAGCTA 57.133 40.909 0.00 0.00 0.00 3.32
3840 3920 5.407407 TCTTTTCGTCTTTCAGGAGCTAT 57.593 39.130 0.00 0.00 0.00 2.97
3841 3921 6.525578 TCTTTTCGTCTTTCAGGAGCTATA 57.474 37.500 0.00 0.00 0.00 1.31
3842 3922 7.113658 TCTTTTCGTCTTTCAGGAGCTATAT 57.886 36.000 0.00 0.00 0.00 0.86
3843 3923 6.980978 TCTTTTCGTCTTTCAGGAGCTATATG 59.019 38.462 0.00 0.00 0.00 1.78
3844 3924 6.465439 TTTCGTCTTTCAGGAGCTATATGA 57.535 37.500 0.00 0.00 0.00 2.15
3845 3925 6.656632 TTCGTCTTTCAGGAGCTATATGAT 57.343 37.500 0.00 0.00 0.00 2.45
3847 3927 7.761038 TCGTCTTTCAGGAGCTATATGATAA 57.239 36.000 0.00 0.00 0.00 1.75
3848 3928 8.178313 TCGTCTTTCAGGAGCTATATGATAAA 57.822 34.615 0.00 0.00 0.00 1.40
3872 3955 2.983898 TGGGGGTGTAAGTAGCTTTTCT 59.016 45.455 0.00 0.00 0.00 2.52
3933 4016 6.722590 TGAGATGTGTAACTAGTTGAACCCTA 59.277 38.462 18.56 1.68 38.04 3.53
3976 4062 1.211703 TGTCTTTGGTCTGCCAGTTCA 59.788 47.619 0.00 0.00 46.91 3.18
3977 4063 1.876156 GTCTTTGGTCTGCCAGTTCAG 59.124 52.381 0.00 0.00 46.91 3.02
3978 4064 1.490490 TCTTTGGTCTGCCAGTTCAGT 59.510 47.619 0.00 0.00 46.91 3.41
3979 4065 2.092429 TCTTTGGTCTGCCAGTTCAGTT 60.092 45.455 0.00 0.00 46.91 3.16
4021 4107 4.385825 TGTGTGTGGAAAAGTCTATGTCC 58.614 43.478 0.00 0.00 0.00 4.02
4027 4119 6.016276 GTGTGGAAAAGTCTATGTCCAATTGT 60.016 38.462 4.43 0.00 41.72 2.71
4032 4124 7.093771 GGAAAAGTCTATGTCCAATTGTCCATT 60.094 37.037 11.08 0.00 0.00 3.16
4100 4192 3.503748 AGCAATTTAGGTGAGCACAAGTC 59.496 43.478 2.75 0.00 0.00 3.01
4104 4196 6.349280 GCAATTTAGGTGAGCACAAGTCATAA 60.349 38.462 2.75 0.00 0.00 1.90
4105 4197 6.743575 ATTTAGGTGAGCACAAGTCATAAC 57.256 37.500 2.75 0.00 0.00 1.89
4107 4199 2.299013 AGGTGAGCACAAGTCATAACGA 59.701 45.455 2.75 0.00 0.00 3.85
4108 4200 3.064207 GGTGAGCACAAGTCATAACGAA 58.936 45.455 2.75 0.00 0.00 3.85
4111 4203 3.987868 TGAGCACAAGTCATAACGAACTC 59.012 43.478 0.00 0.00 0.00 3.01
4112 4204 4.238514 GAGCACAAGTCATAACGAACTCT 58.761 43.478 0.00 0.00 0.00 3.24
4113 4205 5.048294 TGAGCACAAGTCATAACGAACTCTA 60.048 40.000 0.00 0.00 0.00 2.43
4165 4282 9.982291 GTAGAATCTACATTTTTACGATTTGCA 57.018 29.630 15.01 0.00 0.00 4.08
4186 4304 4.494855 GCAATCCTACATTTTCAGACGCTC 60.495 45.833 0.00 0.00 0.00 5.03
4263 4382 2.411160 GCGACCTTCTAAAGTTTGACGC 60.411 50.000 0.00 0.00 36.06 5.19
4277 4396 4.883006 AGTTTGACGCTTTACTTTTGGGTA 59.117 37.500 0.00 0.00 0.00 3.69
4305 4424 5.188359 ACGGTTACTTGTAGGGAACACATAT 59.812 40.000 0.00 0.00 38.00 1.78
4306 4425 6.380846 ACGGTTACTTGTAGGGAACACATATA 59.619 38.462 0.00 0.00 38.00 0.86
4369 4488 6.054860 ACACATACTCTCCAAAAGCTGTAT 57.945 37.500 0.00 0.00 0.00 2.29
4416 4535 4.025040 AGGTCAATTTCATGCTGTGAGA 57.975 40.909 0.00 0.00 38.29 3.27
4428 4547 1.404181 GCTGTGAGACTAATGGTGCGA 60.404 52.381 0.00 0.00 0.00 5.10
4432 4551 3.508402 TGTGAGACTAATGGTGCGACTTA 59.492 43.478 0.00 0.00 0.00 2.24
4498 4617 2.300437 CTCCCTCCCTCCGTTTCATATC 59.700 54.545 0.00 0.00 0.00 1.63
4503 4622 4.344102 CCTCCCTCCGTTTCATATCAGTTA 59.656 45.833 0.00 0.00 0.00 2.24
4504 4623 5.509840 CCTCCCTCCGTTTCATATCAGTTAG 60.510 48.000 0.00 0.00 0.00 2.34
4505 4624 4.960469 TCCCTCCGTTTCATATCAGTTAGT 59.040 41.667 0.00 0.00 0.00 2.24
4519 4647 6.893958 ATCAGTTAGTTGTCGCTGATTTAG 57.106 37.500 0.00 0.00 43.64 1.85
4525 4653 3.918591 AGTTGTCGCTGATTTAGTACACG 59.081 43.478 0.00 0.00 0.00 4.49
4526 4654 3.564235 TGTCGCTGATTTAGTACACGT 57.436 42.857 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 2.119484 TTTTCGGAGGTGTCGGCCAT 62.119 55.000 2.24 0.00 0.00 4.40
84 85 3.267483 ACATATTTTTCGGAGGTGTCGG 58.733 45.455 0.00 0.00 0.00 4.79
87 88 3.192633 GCCAACATATTTTTCGGAGGTGT 59.807 43.478 0.00 0.00 0.00 4.16
98 99 7.231317 CCATATACAGACAAGGCCAACATATTT 59.769 37.037 5.01 0.00 0.00 1.40
175 176 3.928005 AGATGACTGAGCCATCACATT 57.072 42.857 11.31 0.00 42.03 2.71
178 179 2.097142 GCAAAGATGACTGAGCCATCAC 59.903 50.000 11.31 0.00 42.03 3.06
227 228 6.552859 TGTATCTCAATCTCTAGAGCTTCG 57.447 41.667 15.35 7.07 0.00 3.79
254 255 2.867624 AGCGCCATACCAATCATCAAT 58.132 42.857 2.29 0.00 0.00 2.57
255 256 2.346766 AGCGCCATACCAATCATCAA 57.653 45.000 2.29 0.00 0.00 2.57
284 285 1.267121 ACACCGGAAGCTCTGTATGT 58.733 50.000 9.46 0.00 0.00 2.29
315 316 7.530426 AACAAGATAAGGCAGTCAAAGAATT 57.470 32.000 0.00 0.00 0.00 2.17
322 323 5.592282 TGTGAAAAACAAGATAAGGCAGTCA 59.408 36.000 0.00 0.00 35.24 3.41
361 362 5.651530 CCACTAACTGACGATACACTGAAT 58.348 41.667 0.00 0.00 0.00 2.57
365 366 3.090037 AGCCACTAACTGACGATACACT 58.910 45.455 0.00 0.00 0.00 3.55
372 373 5.163854 CCTTAATTTCAGCCACTAACTGACG 60.164 44.000 0.00 0.00 43.64 4.35
413 414 5.465935 TGAAGTTTCTGCGAAACAAAAACT 58.534 33.333 25.21 10.96 32.81 2.66
423 424 3.585862 GTGACCTATGAAGTTTCTGCGA 58.414 45.455 0.00 0.00 0.00 5.10
496 497 2.476852 TTTGCCGAGCCACATAGCCA 62.477 55.000 0.00 0.00 0.00 4.75
540 543 6.787458 TCATGGTAGAGCTATAATCTTTGGGA 59.213 38.462 0.00 0.00 0.00 4.37
551 554 7.885399 GGTTTTATTCCATCATGGTAGAGCTAT 59.115 37.037 2.79 0.00 39.03 2.97
649 659 2.179018 CGGCATGCCTTTTCGGTG 59.821 61.111 33.07 12.26 34.25 4.94
785 796 3.276857 ACTGAGAAGCGATGATGCATTT 58.723 40.909 0.00 0.00 37.31 2.32
797 808 0.238553 GTTTGGCCGAACTGAGAAGC 59.761 55.000 26.19 0.00 0.00 3.86
816 827 0.971959 CATGGGATGGTTGGGTGGTG 60.972 60.000 0.00 0.00 0.00 4.17
818 829 0.971959 CACATGGGATGGTTGGGTGG 60.972 60.000 0.00 0.00 33.60 4.61
834 845 3.246112 CGGGGGTGGAAGGACACA 61.246 66.667 0.00 0.00 43.08 3.72
887 898 3.604582 GAAAGGAATGAGGAGACACTGG 58.395 50.000 0.00 0.00 0.00 4.00
892 903 3.615155 CAAGGGAAAGGAATGAGGAGAC 58.385 50.000 0.00 0.00 0.00 3.36
931 942 1.005394 TCGCCGGACCTTTCTGTTC 60.005 57.895 5.05 0.00 0.00 3.18
933 944 2.342648 GTCGCCGGACCTTTCTGT 59.657 61.111 5.05 0.00 37.19 3.41
934 945 2.809601 CGTCGCCGGACCTTTCTG 60.810 66.667 5.05 0.00 40.17 3.02
935 946 4.736896 GCGTCGCCGGACCTTTCT 62.737 66.667 5.05 0.00 40.17 2.52
988 1001 2.367377 CTCCATGGCCTCCCTCCA 60.367 66.667 6.96 0.00 38.09 3.86
1010 1029 4.785453 CGCCCTCCACCTTCTGCC 62.785 72.222 0.00 0.00 0.00 4.85
1074 1093 3.164977 TGCACCCAGAACCCGACA 61.165 61.111 0.00 0.00 0.00 4.35
1077 1096 4.722700 CCCTGCACCCAGAACCCG 62.723 72.222 0.00 0.00 41.77 5.28
1155 1174 1.680522 GGATCTGCAGCGAGGAGGAA 61.681 60.000 9.47 0.00 36.17 3.36
1359 1382 0.175073 GGTCGCAGATTACGGAAGGT 59.825 55.000 0.00 0.00 40.67 3.50
1360 1383 0.870307 CGGTCGCAGATTACGGAAGG 60.870 60.000 0.00 0.00 40.67 3.46
1361 1384 0.099968 TCGGTCGCAGATTACGGAAG 59.900 55.000 0.00 0.00 40.67 3.46
1410 1433 7.011389 ACGTTATTATCCGTTAAAGTAAAGGGC 59.989 37.037 1.01 0.00 37.80 5.19
1414 1437 8.994429 TCCACGTTATTATCCGTTAAAGTAAA 57.006 30.769 0.00 0.00 34.59 2.01
1468 1491 2.038820 CCAGGTTAACGGGTAAAGGTGA 59.961 50.000 0.00 0.00 0.00 4.02
1469 1492 2.038820 TCCAGGTTAACGGGTAAAGGTG 59.961 50.000 12.93 0.00 35.71 4.00
1470 1493 2.337849 TCCAGGTTAACGGGTAAAGGT 58.662 47.619 12.93 0.00 35.71 3.50
1479 1502 3.173668 TCCGATCATTCCAGGTTAACG 57.826 47.619 0.00 0.00 0.00 3.18
1556 1581 3.629883 ATTGTGCGCGCAACATGGG 62.630 57.895 38.24 0.00 0.00 4.00
1617 1646 2.501723 TCCTACACTGCTCAGAATTCCC 59.498 50.000 0.65 0.00 0.00 3.97
1687 1716 9.040939 CCGTGGTTATCATTTTTCTTTTTCTTT 57.959 29.630 0.00 0.00 0.00 2.52
1688 1717 8.201464 ACCGTGGTTATCATTTTTCTTTTTCTT 58.799 29.630 0.00 0.00 0.00 2.52
1689 1718 7.722363 ACCGTGGTTATCATTTTTCTTTTTCT 58.278 30.769 0.00 0.00 0.00 2.52
1690 1719 7.940178 ACCGTGGTTATCATTTTTCTTTTTC 57.060 32.000 0.00 0.00 0.00 2.29
1691 1720 8.852135 TCTACCGTGGTTATCATTTTTCTTTTT 58.148 29.630 0.00 0.00 0.00 1.94
1692 1721 8.398878 TCTACCGTGGTTATCATTTTTCTTTT 57.601 30.769 0.00 0.00 0.00 2.27
1713 1745 5.249420 AGAAAGGAATGTGGAAAGCTCTAC 58.751 41.667 0.00 0.00 33.77 2.59
1780 1812 2.873170 TATTCTTTGCAGCGTTGTCG 57.127 45.000 0.00 0.00 40.37 4.35
1809 1841 6.855836 TGTGAATAATCAAGAGGACAATTGC 58.144 36.000 5.05 0.00 37.30 3.56
1927 1959 1.302949 GATGCCACCCTGGTTGCTA 59.697 57.895 12.93 1.47 40.46 3.49
1941 1973 3.001736 GGCTGAGAAAAGATACACGATGC 59.998 47.826 0.00 0.00 0.00 3.91
2007 2039 1.739466 CACACCATCCGTCCATCTTTG 59.261 52.381 0.00 0.00 0.00 2.77
2045 2077 4.501071 GACGGGCAATCTTAAGTTCTGTA 58.499 43.478 1.63 0.00 0.00 2.74
2049 2081 2.937149 GAGGACGGGCAATCTTAAGTTC 59.063 50.000 1.63 0.00 0.00 3.01
2065 2097 3.260740 CTTCAGCACAGAATCTGAGGAC 58.739 50.000 18.20 3.11 40.07 3.85
2078 2110 4.858935 TGCACAAATTAAGACTTCAGCAC 58.141 39.130 0.00 0.00 0.00 4.40
2149 2181 5.475273 TCTAAATGATGCGAGCTGAAAAG 57.525 39.130 0.00 0.00 0.00 2.27
2154 2186 4.871993 AACTTCTAAATGATGCGAGCTG 57.128 40.909 0.00 0.00 0.00 4.24
2157 2189 5.750547 TGAGCTAACTTCTAAATGATGCGAG 59.249 40.000 0.00 0.00 0.00 5.03
2210 2243 6.677781 TCCCTGAATTTATTTAACTGCTCG 57.322 37.500 0.00 0.00 0.00 5.03
2226 2259 1.131638 AATCGCCATAGCTCCCTGAA 58.868 50.000 0.00 0.00 36.60 3.02
2303 2380 0.315251 GAAAGCACTTGGTTGGGCTC 59.685 55.000 0.00 0.00 35.11 4.70
2318 2396 2.154854 TGGTCTGTCAAGCTCGAAAG 57.845 50.000 0.00 0.00 0.00 2.62
2434 2512 3.635373 AGGAGCATCAGTTATGGCATTTG 59.365 43.478 4.78 2.57 36.25 2.32
2438 2516 1.839354 TCAGGAGCATCAGTTATGGCA 59.161 47.619 0.00 0.00 36.25 4.92
2454 2533 0.952497 ACACAGTGCGCATCTTCAGG 60.952 55.000 15.91 2.38 0.00 3.86
2526 2605 6.970484 ACCACAGCAAAAGAAGTTATGTTAG 58.030 36.000 0.00 0.00 0.00 2.34
2879 2959 2.175202 GAGTTTGAGGGAGCTCTCAGA 58.825 52.381 17.82 4.15 43.64 3.27
2923 3003 2.325583 TACGGATGCTGGAAATCACC 57.674 50.000 0.00 0.00 0.00 4.02
2962 3042 2.011349 CGGCATACAGAGCGCGTAG 61.011 63.158 8.43 0.00 0.00 3.51
3182 3262 4.750021 TGAACTGCAGAGCTGATAAGAT 57.250 40.909 23.35 0.00 0.00 2.40
3211 3291 2.407361 CACGTCTGACAACATTACGACC 59.593 50.000 8.73 0.00 38.10 4.79
3592 3672 6.177663 AGGGATCCTACAGATGGATTCTAT 57.822 41.667 12.58 0.00 43.68 1.98
3612 3692 3.718956 ACAATCTCTTTGGGATCCTAGGG 59.281 47.826 12.58 7.13 39.80 3.53
3613 3693 6.694445 ATACAATCTCTTTGGGATCCTAGG 57.306 41.667 12.58 0.82 39.80 3.02
3614 3694 6.939163 CCAATACAATCTCTTTGGGATCCTAG 59.061 42.308 12.58 7.19 39.80 3.02
3615 3695 6.389869 ACCAATACAATCTCTTTGGGATCCTA 59.610 38.462 12.58 1.47 42.34 2.94
3616 3696 5.194537 ACCAATACAATCTCTTTGGGATCCT 59.805 40.000 12.58 0.00 42.34 3.24
3617 3697 5.300286 CACCAATACAATCTCTTTGGGATCC 59.700 44.000 1.92 1.92 42.34 3.36
3618 3698 5.221126 GCACCAATACAATCTCTTTGGGATC 60.221 44.000 5.61 0.00 42.34 3.36
3619 3699 4.646492 GCACCAATACAATCTCTTTGGGAT 59.354 41.667 5.61 0.00 42.34 3.85
3620 3700 4.016444 GCACCAATACAATCTCTTTGGGA 58.984 43.478 5.61 0.00 42.34 4.37
3621 3701 3.131046 GGCACCAATACAATCTCTTTGGG 59.869 47.826 5.61 0.00 42.34 4.12
3630 3710 1.382522 CTCGCAGGCACCAATACAAT 58.617 50.000 0.00 0.00 0.00 2.71
3660 3740 1.676006 CTCAGGCACCGACAAAAGTTT 59.324 47.619 0.00 0.00 0.00 2.66
3755 3835 3.571119 CTGAAAGGCCACAGAGCG 58.429 61.111 16.15 0.00 36.38 5.03
3837 3917 9.807921 ACTTACACCCCCAAATTTATCATATAG 57.192 33.333 0.00 0.00 0.00 1.31
3839 3919 9.807921 CTACTTACACCCCCAAATTTATCATAT 57.192 33.333 0.00 0.00 0.00 1.78
3840 3920 7.722285 GCTACTTACACCCCCAAATTTATCATA 59.278 37.037 0.00 0.00 0.00 2.15
3841 3921 6.549736 GCTACTTACACCCCCAAATTTATCAT 59.450 38.462 0.00 0.00 0.00 2.45
3842 3922 5.889289 GCTACTTACACCCCCAAATTTATCA 59.111 40.000 0.00 0.00 0.00 2.15
3843 3923 6.127101 AGCTACTTACACCCCCAAATTTATC 58.873 40.000 0.00 0.00 0.00 1.75
3844 3924 6.087276 AGCTACTTACACCCCCAAATTTAT 57.913 37.500 0.00 0.00 0.00 1.40
3845 3925 5.523883 AGCTACTTACACCCCCAAATTTA 57.476 39.130 0.00 0.00 0.00 1.40
3847 3927 4.397919 AAGCTACTTACACCCCCAAATT 57.602 40.909 0.00 0.00 0.00 1.82
3848 3928 4.397919 AAAGCTACTTACACCCCCAAAT 57.602 40.909 0.00 0.00 0.00 2.32
3912 3995 6.675413 TGTAGGGTTCAACTAGTTACACAT 57.325 37.500 8.04 3.72 0.00 3.21
3976 4062 8.392612 CACAAAGAATGAAAAGAAATGCAAACT 58.607 29.630 0.00 0.00 0.00 2.66
3977 4063 8.177013 ACACAAAGAATGAAAAGAAATGCAAAC 58.823 29.630 0.00 0.00 0.00 2.93
3978 4064 8.176365 CACACAAAGAATGAAAAGAAATGCAAA 58.824 29.630 0.00 0.00 0.00 3.68
3979 4065 7.333921 ACACACAAAGAATGAAAAGAAATGCAA 59.666 29.630 0.00 0.00 0.00 4.08
4021 4107 7.865875 TCGTTACATGAAAAATGGACAATTG 57.134 32.000 3.24 3.24 0.00 2.32
4027 4119 6.869315 TCAGTTCGTTACATGAAAAATGGA 57.131 33.333 0.00 0.00 0.00 3.41
4032 4124 7.442969 AGGTACAATCAGTTCGTTACATGAAAA 59.557 33.333 0.00 0.00 0.00 2.29
4107 4199 8.480133 AAATCGTATCCTAGAACCATAGAGTT 57.520 34.615 0.00 0.00 0.00 3.01
4108 4200 8.361139 CAAAATCGTATCCTAGAACCATAGAGT 58.639 37.037 0.00 0.00 0.00 3.24
4111 4203 7.442656 ACCAAAATCGTATCCTAGAACCATAG 58.557 38.462 0.00 0.00 0.00 2.23
4112 4204 7.369551 ACCAAAATCGTATCCTAGAACCATA 57.630 36.000 0.00 0.00 0.00 2.74
4113 4205 6.248569 ACCAAAATCGTATCCTAGAACCAT 57.751 37.500 0.00 0.00 0.00 3.55
4154 4271 7.821652 TGAAAATGTAGGATTGCAAATCGTAA 58.178 30.769 1.71 1.11 0.00 3.18
4165 4282 4.192317 GGAGCGTCTGAAAATGTAGGATT 58.808 43.478 0.00 0.00 0.00 3.01
4186 4304 3.355378 TGCATAGAGAAACATTGGGTGG 58.645 45.455 0.00 0.00 0.00 4.61
4263 4382 8.190122 AGTAACCGTTTTTACCCAAAAGTAAAG 58.810 33.333 0.00 0.00 41.78 1.85
4277 4396 5.066375 GTGTTCCCTACAAGTAACCGTTTTT 59.934 40.000 0.00 0.00 38.80 1.94
4305 4424 9.959721 AAGATTTATGTGTTCTTTAGCTCCTTA 57.040 29.630 0.00 0.00 0.00 2.69
4306 4425 8.870075 AAGATTTATGTGTTCTTTAGCTCCTT 57.130 30.769 0.00 0.00 0.00 3.36
4350 4469 7.549488 GTGTGTTATACAGCTTTTGGAGAGTAT 59.451 37.037 0.00 0.00 40.69 2.12
4357 4476 9.638239 AATTTATGTGTGTTATACAGCTTTTGG 57.362 29.630 0.00 0.00 40.69 3.28
4369 4488 9.521841 TTCCCTATTGACAATTTATGTGTGTTA 57.478 29.630 5.89 0.00 44.12 2.41
4416 4535 3.133003 AGCTCATAAGTCGCACCATTAGT 59.867 43.478 0.00 0.00 0.00 2.24
4428 4547 8.588290 ACTATGCTTATAGCTAGCTCATAAGT 57.412 34.615 29.86 22.19 42.97 2.24
4432 4551 8.592809 AGAAAACTATGCTTATAGCTAGCTCAT 58.407 33.333 23.26 19.46 42.97 2.90
4498 4617 6.584942 TGTACTAAATCAGCGACAACTAACTG 59.415 38.462 0.00 0.00 0.00 3.16
4503 4622 3.918591 CGTGTACTAAATCAGCGACAACT 59.081 43.478 0.00 0.00 0.00 3.16
4504 4623 3.671928 ACGTGTACTAAATCAGCGACAAC 59.328 43.478 0.00 0.00 0.00 3.32
4505 4624 3.904571 ACGTGTACTAAATCAGCGACAA 58.095 40.909 0.00 0.00 0.00 3.18
4539 4667 6.041069 ACATCCCTCTGTTCTATAGTAGTTGC 59.959 42.308 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.