Multiple sequence alignment - TraesCS3D01G091200

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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 TraesCS3D01G091200 chr3D 100.000 2246 0 0 1 2246 46200051 46197806 0.000000e+00 4148.0
1 TraesCS3D01G091200 chr3B 90.685 934 60 14 828 1745 71802658 71803580 0.000000e+00 1218.0
2 TraesCS3D01G091200 chr3B 91.678 721 43 9 966 1678 72112031 72111320 0.000000e+00 983.0
3 TraesCS3D01G091200 chr3B 91.422 443 21 13 840 1267 71976203 71975763 1.920000e-165 592.0
4 TraesCS3D01G091200 chr3B 90.594 404 31 6 818 1215 71968541 71968139 1.530000e-146 529.0
5 TraesCS3D01G091200 chr3B 84.127 504 50 16 791 1287 72092936 72092456 5.650000e-126 460.0
6 TraesCS3D01G091200 chr3B 80.725 607 52 37 3 589 567391112 567391673 1.610000e-111 412.0
7 TraesCS3D01G091200 chr3B 97.101 138 4 0 663 800 567391993 567392130 1.340000e-57 233.0
8 TraesCS3D01G091200 chr3B 79.710 276 29 13 1255 1520 71975489 71975231 8.250000e-40 174.0
9 TraesCS3D01G091200 chr3B 80.625 160 21 5 1876 2028 71803771 71803927 5.070000e-22 115.0
10 TraesCS3D01G091200 chr3B 78.571 168 16 7 803 963 72114727 72114573 2.380000e-15 93.5
11 TraesCS3D01G091200 chr3B 94.231 52 3 0 1759 1810 71803632 71803683 1.850000e-11 80.5
12 TraesCS3D01G091200 chr3A 88.145 1046 78 20 1025 2049 57814521 57813501 0.000000e+00 1203.0
13 TraesCS3D01G091200 chr3A 83.028 601 52 28 1 589 601619666 601619104 1.200000e-137 499.0
14 TraesCS3D01G091200 chr3A 96.667 150 3 2 655 804 503839196 503839049 4.790000e-62 248.0
15 TraesCS3D01G091200 chr3A 90.909 66 6 0 2075 2140 57813502 57813437 3.070000e-14 89.8
16 TraesCS3D01G091200 chr2B 82.370 675 61 33 1 657 109767087 109767721 3.280000e-148 534.0
17 TraesCS3D01G091200 chr2B 83.500 600 52 24 4 591 109131881 109132445 1.190000e-142 516.0
18 TraesCS3D01G091200 chr2B 90.678 236 15 6 1 232 28342190 28342422 7.790000e-80 307.0
19 TraesCS3D01G091200 chr2B 97.842 139 3 0 663 801 109767989 109768127 8.020000e-60 241.0
20 TraesCS3D01G091200 chr2B 97.122 139 4 0 663 801 109132760 109132898 3.730000e-58 235.0
21 TraesCS3D01G091200 chr2A 82.485 668 62 34 1 653 724037788 724037161 3.280000e-148 534.0
22 TraesCS3D01G091200 chr2A 83.726 467 38 18 366 801 724037236 724036777 7.470000e-110 407.0
23 TraesCS3D01G091200 chr5A 82.047 674 62 35 1 657 273445346 273445977 9.190000e-144 520.0
24 TraesCS3D01G091200 chr5A 83.196 607 54 28 1 596 301367868 301368437 1.540000e-141 512.0
25 TraesCS3D01G091200 chr5A 97.122 139 4 0 663 801 273446242 273446380 3.730000e-58 235.0
26 TraesCS3D01G091200 chr5A 97.744 133 3 0 663 795 301368785 301368917 1.740000e-56 230.0
27 TraesCS3D01G091200 chr7B 84.547 563 42 25 1 554 683033128 683033654 1.190000e-142 516.0
28 TraesCS3D01G091200 chr7B 97.122 139 4 0 663 801 683034025 683034163 3.730000e-58 235.0
29 TraesCS3D01G091200 chr5B 83.389 596 52 24 1 585 710204790 710204231 1.990000e-140 508.0
30 TraesCS3D01G091200 chr5B 98.561 139 2 0 663 801 710203621 710203483 1.720000e-61 246.0


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 TraesCS3D01G091200 chr3D 46197806 46200051 2245 True 4148.000000 4148 100.000000 1 2246 1 chr3D.!!$R1 2245
1 TraesCS3D01G091200 chr3B 72111320 72114727 3407 True 538.250000 983 85.124500 803 1678 2 chr3B.!!$R4 875
2 TraesCS3D01G091200 chr3B 71802658 71803927 1269 False 471.166667 1218 88.513667 828 2028 3 chr3B.!!$F1 1200
3 TraesCS3D01G091200 chr3B 71975231 71976203 972 True 383.000000 592 85.566000 840 1520 2 chr3B.!!$R3 680
4 TraesCS3D01G091200 chr3B 567391112 567392130 1018 False 322.500000 412 88.913000 3 800 2 chr3B.!!$F2 797
5 TraesCS3D01G091200 chr3A 57813437 57814521 1084 True 646.400000 1203 89.527000 1025 2140 2 chr3A.!!$R3 1115
6 TraesCS3D01G091200 chr3A 601619104 601619666 562 True 499.000000 499 83.028000 1 589 1 chr3A.!!$R2 588
7 TraesCS3D01G091200 chr2B 109767087 109768127 1040 False 387.500000 534 90.106000 1 801 2 chr2B.!!$F3 800
8 TraesCS3D01G091200 chr2B 109131881 109132898 1017 False 375.500000 516 90.311000 4 801 2 chr2B.!!$F2 797
9 TraesCS3D01G091200 chr2A 724036777 724037788 1011 True 470.500000 534 83.105500 1 801 2 chr2A.!!$R1 800
10 TraesCS3D01G091200 chr5A 273445346 273446380 1034 False 377.500000 520 89.584500 1 801 2 chr5A.!!$F1 800
11 TraesCS3D01G091200 chr5A 301367868 301368917 1049 False 371.000000 512 90.470000 1 795 2 chr5A.!!$F2 794
12 TraesCS3D01G091200 chr7B 683033128 683034163 1035 False 375.500000 516 90.834500 1 801 2 chr7B.!!$F1 800
13 TraesCS3D01G091200 chr5B 710203483 710204790 1307 True 377.000000 508 90.975000 1 801 2 chr5B.!!$R1 800

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
84 86 0.597637 CGCAGGTGACACTCGAACTT 60.598 55.0 5.39 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 5294 0.107361 CACTGGCCATGATCAGCTGA 60.107 55.0 20.79 20.79 34.57 4.26 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
84 86 0.597637 CGCAGGTGACACTCGAACTT 60.598 55.000 5.39 0.00 0.00 2.66
85 87 1.140816 GCAGGTGACACTCGAACTTC 58.859 55.000 5.39 0.00 0.00 3.01
89 91 1.006571 TGACACTCGAACTTCCGCC 60.007 57.895 0.00 0.00 0.00 6.13
133 135 1.654105 CTAGCCAACTTCGCAACTACG 59.346 52.381 0.00 0.00 0.00 3.51
225 229 7.576861 TCCACGTTTTCTTTTTCTTATTCCT 57.423 32.000 0.00 0.00 0.00 3.36
226 230 8.002984 TCCACGTTTTCTTTTTCTTATTCCTT 57.997 30.769 0.00 0.00 0.00 3.36
227 231 9.122779 TCCACGTTTTCTTTTTCTTATTCCTTA 57.877 29.630 0.00 0.00 0.00 2.69
228 232 9.908152 CCACGTTTTCTTTTTCTTATTCCTTAT 57.092 29.630 0.00 0.00 0.00 1.73
243 248 8.873186 TTATTCCTTATTCCTTTCGTTTTCCT 57.127 30.769 0.00 0.00 0.00 3.36
251 256 5.116069 TCCTTTCGTTTTCCTAAATGCAC 57.884 39.130 0.00 0.00 31.62 4.57
724 1377 2.201921 AGCGAGGGAGCGATCTTATA 57.798 50.000 0.00 0.00 43.00 0.98
801 1454 2.995872 GCGCTGTCGAGGAGGTCTT 61.996 63.158 0.00 0.00 38.10 3.01
806 1459 0.959553 TGTCGAGGAGGTCTTGTGAC 59.040 55.000 0.00 0.00 42.22 3.67
812 1465 4.681978 AGGTCTTGTGACGGCGCC 62.682 66.667 19.07 19.07 43.79 6.53
830 1484 3.793144 GCTTGGGAGAGCGCAACG 61.793 66.667 11.47 0.00 41.37 4.10
925 1582 2.261671 GCGCTCGGTTCCTCTTCA 59.738 61.111 0.00 0.00 0.00 3.02
947 1608 6.466812 TCATCAAAAGCATCTTACTCTGACA 58.533 36.000 0.00 0.00 0.00 3.58
955 1616 4.092675 GCATCTTACTCTGACACTTTGCTC 59.907 45.833 0.00 0.00 0.00 4.26
1218 4428 1.211969 CAGGATCACCGTCGTCGTT 59.788 57.895 0.71 0.00 41.83 3.85
1290 4793 5.599242 ACCTACTAGGAGAGGTATTTTCAGC 59.401 44.000 2.52 0.00 44.51 4.26
1318 4828 2.103373 TCCACAGATCAGTAGGACAGC 58.897 52.381 0.00 0.00 0.00 4.40
1329 4844 4.043200 GGACAGCAGCGGTTTGGC 62.043 66.667 0.00 0.00 0.00 4.52
1455 4981 3.454375 TGCCGATCGAAGAGAATAAACC 58.546 45.455 18.66 0.00 43.63 3.27
1498 5026 2.349886 GAGGCTGCAGAATTAGTGTTCG 59.650 50.000 20.43 0.00 33.36 3.95
1584 5112 2.359975 CACTTTCGGCAGGGGGTC 60.360 66.667 0.00 0.00 0.00 4.46
1668 5196 1.641577 GGTCTTCGGATGTTTCCTCG 58.358 55.000 0.00 0.00 40.17 4.63
1669 5197 1.000145 GTCTTCGGATGTTTCCTCGC 59.000 55.000 0.00 0.00 40.17 5.03
1703 5231 4.467735 GCTTTCATTCCGTTTCTTCTCAC 58.532 43.478 0.00 0.00 0.00 3.51
1736 5269 4.164843 ACAGCAGAAAGGGAAACACTTA 57.835 40.909 0.00 0.00 0.00 2.24
1737 5270 4.137543 ACAGCAGAAAGGGAAACACTTAG 58.862 43.478 0.00 0.00 0.00 2.18
1739 5272 4.214332 CAGCAGAAAGGGAAACACTTAGAC 59.786 45.833 0.00 0.00 0.00 2.59
1740 5273 4.103311 AGCAGAAAGGGAAACACTTAGACT 59.897 41.667 0.00 0.00 0.00 3.24
1745 5284 7.171678 CAGAAAGGGAAACACTTAGACTAACTG 59.828 40.741 0.00 0.00 0.00 3.16
1755 5294 6.127423 ACACTTAGACTAACTGTTGTGTCACT 60.127 38.462 21.56 10.83 34.97 3.41
1756 5295 6.418226 CACTTAGACTAACTGTTGTGTCACTC 59.582 42.308 21.56 0.00 32.41 3.51
1790 5363 4.095483 GGCCAGTGTGATCTTGATTTACAG 59.905 45.833 0.00 0.00 0.00 2.74
1791 5364 4.437930 GCCAGTGTGATCTTGATTTACAGC 60.438 45.833 0.00 0.00 0.00 4.40
1811 5384 4.268884 CAGCTCGATTAGTTTGTTCCTAGC 59.731 45.833 0.00 0.00 0.00 3.42
1823 5396 8.307582 AGTTTGTTCCTAGCATGTACTACTAT 57.692 34.615 0.00 0.00 0.00 2.12
1826 5399 7.891498 TGTTCCTAGCATGTACTACTATTGA 57.109 36.000 0.00 0.00 0.00 2.57
1836 5409 7.308408 GCATGTACTACTATTGAGGTATCGTGA 60.308 40.741 0.00 0.00 0.00 4.35
1842 5415 8.475639 ACTACTATTGAGGTATCGTGAAATTGT 58.524 33.333 0.00 0.00 0.00 2.71
1853 5426 9.659830 GGTATCGTGAAATTGTTTATGGTAATC 57.340 33.333 0.00 0.00 0.00 1.75
1854 5427 9.365311 GTATCGTGAAATTGTTTATGGTAATCG 57.635 33.333 0.00 0.00 0.00 3.34
1863 5470 7.718272 TTGTTTATGGTAATCGTATACAGGC 57.282 36.000 3.32 0.00 32.91 4.85
1871 5478 6.720748 TGGTAATCGTATACAGGCTTATGGTA 59.279 38.462 3.32 0.00 0.00 3.25
1897 5504 6.621596 GCGTGCTCATTTTATGAAGAGAAACT 60.622 38.462 0.00 0.00 39.11 2.66
1925 5532 2.772568 TGATTTGTTCCTTGCACACG 57.227 45.000 0.00 0.00 0.00 4.49
1927 5534 2.884012 TGATTTGTTCCTTGCACACGAT 59.116 40.909 0.00 0.00 0.00 3.73
1970 5587 1.069204 GGAATCGATGGCTGAGCAGTA 59.931 52.381 6.82 0.00 0.00 2.74
1976 5593 0.471617 ATGGCTGAGCAGTACCCATC 59.528 55.000 6.82 0.00 30.81 3.51
1996 5613 4.330944 TCGTGAGAGTAGAGAGGAGATC 57.669 50.000 0.00 0.00 34.84 2.75
1997 5614 3.057019 CGTGAGAGTAGAGAGGAGATCG 58.943 54.545 0.00 0.00 0.00 3.69
1998 5615 3.243602 CGTGAGAGTAGAGAGGAGATCGA 60.244 52.174 0.00 0.00 0.00 3.59
2004 5624 1.961793 AGAGAGGAGATCGAACTCGG 58.038 55.000 15.53 0.00 40.29 4.63
2010 5630 2.944349 AGGAGATCGAACTCGGTTAGTC 59.056 50.000 15.53 1.35 37.50 2.59
2040 5660 6.455360 AATGAGCACTTCTTGTTTGAAGAA 57.545 33.333 10.68 0.00 44.40 2.52
2042 5662 4.699735 TGAGCACTTCTTGTTTGAAGAACA 59.300 37.500 10.68 0.00 44.40 3.18
2054 5674 8.731275 TTGTTTGAAGAACAAGAGAATACAGA 57.269 30.769 0.55 0.00 39.77 3.41
2055 5675 8.370493 TGTTTGAAGAACAAGAGAATACAGAG 57.630 34.615 0.00 0.00 39.77 3.35
2056 5676 7.987458 TGTTTGAAGAACAAGAGAATACAGAGT 59.013 33.333 0.00 0.00 39.77 3.24
2057 5677 8.831550 GTTTGAAGAACAAGAGAATACAGAGTT 58.168 33.333 0.00 0.00 39.77 3.01
2058 5678 8.594881 TTGAAGAACAAGAGAATACAGAGTTC 57.405 34.615 0.00 0.00 35.40 3.01
2059 5679 7.957002 TGAAGAACAAGAGAATACAGAGTTCT 58.043 34.615 0.00 0.00 44.11 3.01
2107 5727 5.571658 GCTCCTTGTAGGAAATGAGAAGGAA 60.572 44.000 0.00 0.00 45.28 3.36
2117 5737 5.795441 GGAAATGAGAAGGAAATTTTCGACG 59.205 40.000 3.17 0.00 0.00 5.12
2127 5747 2.457366 ATTTTCGACGGCTTCAGAGT 57.543 45.000 0.00 0.00 0.00 3.24
2134 5754 1.222115 ACGGCTTCAGAGTTGCGAAC 61.222 55.000 0.00 0.00 0.00 3.95
2135 5755 1.221466 CGGCTTCAGAGTTGCGAACA 61.221 55.000 0.00 0.00 0.00 3.18
2140 5760 0.944386 TCAGAGTTGCGAACAAAGGC 59.056 50.000 0.00 0.00 37.58 4.35
2141 5761 0.662619 CAGAGTTGCGAACAAAGGCA 59.337 50.000 0.00 0.00 37.58 4.75
2142 5762 0.947244 AGAGTTGCGAACAAAGGCAG 59.053 50.000 0.00 0.00 40.75 4.85
2143 5763 0.040067 GAGTTGCGAACAAAGGCAGG 60.040 55.000 0.00 0.00 40.75 4.85
2144 5764 0.465460 AGTTGCGAACAAAGGCAGGA 60.465 50.000 0.00 0.00 40.75 3.86
2145 5765 0.383949 GTTGCGAACAAAGGCAGGAA 59.616 50.000 0.00 0.00 40.75 3.36
2146 5766 0.383949 TTGCGAACAAAGGCAGGAAC 59.616 50.000 0.00 0.00 40.75 3.62
2147 5767 0.749818 TGCGAACAAAGGCAGGAACA 60.750 50.000 0.00 0.00 33.52 3.18
2148 5768 0.383949 GCGAACAAAGGCAGGAACAA 59.616 50.000 0.00 0.00 0.00 2.83
2149 5769 1.000274 GCGAACAAAGGCAGGAACAAT 60.000 47.619 0.00 0.00 0.00 2.71
2150 5770 2.545742 GCGAACAAAGGCAGGAACAATT 60.546 45.455 0.00 0.00 0.00 2.32
2151 5771 3.308530 CGAACAAAGGCAGGAACAATTC 58.691 45.455 0.00 0.00 0.00 2.17
2152 5772 3.243367 CGAACAAAGGCAGGAACAATTCA 60.243 43.478 0.00 0.00 0.00 2.57
2153 5773 4.559300 CGAACAAAGGCAGGAACAATTCAT 60.559 41.667 0.00 0.00 0.00 2.57
2154 5774 4.961438 ACAAAGGCAGGAACAATTCATT 57.039 36.364 0.00 0.00 0.00 2.57
2155 5775 4.886579 ACAAAGGCAGGAACAATTCATTC 58.113 39.130 0.00 0.00 0.00 2.67
2156 5776 4.344679 ACAAAGGCAGGAACAATTCATTCA 59.655 37.500 2.28 0.00 0.00 2.57
2157 5777 4.796038 AAGGCAGGAACAATTCATTCAG 57.204 40.909 2.28 0.00 0.00 3.02
2158 5778 3.094572 AGGCAGGAACAATTCATTCAGG 58.905 45.455 2.28 0.00 0.00 3.86
2159 5779 2.417787 GGCAGGAACAATTCATTCAGGC 60.418 50.000 2.28 4.32 0.00 4.85
2160 5780 2.231964 GCAGGAACAATTCATTCAGGCA 59.768 45.455 2.28 0.00 31.03 4.75
2161 5781 3.841643 CAGGAACAATTCATTCAGGCAC 58.158 45.455 2.28 0.00 0.00 5.01
2162 5782 2.827921 AGGAACAATTCATTCAGGCACC 59.172 45.455 2.28 0.00 0.00 5.01
2163 5783 2.562298 GGAACAATTCATTCAGGCACCA 59.438 45.455 2.28 0.00 0.00 4.17
2164 5784 3.006752 GGAACAATTCATTCAGGCACCAA 59.993 43.478 2.28 0.00 0.00 3.67
2165 5785 4.322953 GGAACAATTCATTCAGGCACCAAT 60.323 41.667 2.28 0.00 0.00 3.16
2166 5786 5.105392 GGAACAATTCATTCAGGCACCAATA 60.105 40.000 2.28 0.00 0.00 1.90
2167 5787 5.329035 ACAATTCATTCAGGCACCAATAC 57.671 39.130 0.00 0.00 0.00 1.89
2168 5788 4.142403 ACAATTCATTCAGGCACCAATACG 60.142 41.667 0.00 0.00 0.00 3.06
2169 5789 2.036958 TCATTCAGGCACCAATACGG 57.963 50.000 0.00 0.00 42.50 4.02
2181 5801 3.611766 CCAATACGGTCTCCTGAACTT 57.388 47.619 0.00 0.00 0.00 2.66
2182 5802 4.730949 CCAATACGGTCTCCTGAACTTA 57.269 45.455 0.00 0.00 0.00 2.24
2183 5803 5.080969 CCAATACGGTCTCCTGAACTTAA 57.919 43.478 0.00 0.00 0.00 1.85
2184 5804 4.868734 CCAATACGGTCTCCTGAACTTAAC 59.131 45.833 0.00 0.00 0.00 2.01
2185 5805 5.475719 CAATACGGTCTCCTGAACTTAACA 58.524 41.667 0.00 0.00 0.00 2.41
2186 5806 3.662247 ACGGTCTCCTGAACTTAACAG 57.338 47.619 0.00 0.00 35.43 3.16
2187 5807 3.228453 ACGGTCTCCTGAACTTAACAGA 58.772 45.455 0.00 0.00 37.54 3.41
2188 5808 3.005578 ACGGTCTCCTGAACTTAACAGAC 59.994 47.826 0.00 0.00 37.54 3.51
2189 5809 3.576648 GGTCTCCTGAACTTAACAGACG 58.423 50.000 0.00 0.00 37.54 4.18
2190 5810 3.255149 GGTCTCCTGAACTTAACAGACGA 59.745 47.826 0.00 0.00 37.54 4.20
2191 5811 4.082136 GGTCTCCTGAACTTAACAGACGAT 60.082 45.833 0.00 0.00 37.54 3.73
2192 5812 5.125097 GGTCTCCTGAACTTAACAGACGATA 59.875 44.000 0.00 0.00 37.54 2.92
2193 5813 6.349944 GGTCTCCTGAACTTAACAGACGATAA 60.350 42.308 0.00 0.00 37.54 1.75
2194 5814 6.748198 GTCTCCTGAACTTAACAGACGATAAG 59.252 42.308 0.00 0.00 37.54 1.73
2195 5815 6.433404 TCTCCTGAACTTAACAGACGATAAGT 59.567 38.462 0.00 0.00 41.12 2.24
2206 5826 3.369835 GACGATAAGTCTTTTGTGCGG 57.630 47.619 0.00 0.00 46.13 5.69
2207 5827 2.735134 GACGATAAGTCTTTTGTGCGGT 59.265 45.455 0.00 0.00 46.13 5.68
2208 5828 3.916761 ACGATAAGTCTTTTGTGCGGTA 58.083 40.909 0.00 0.00 0.00 4.02
2209 5829 4.501071 ACGATAAGTCTTTTGTGCGGTAT 58.499 39.130 0.00 0.00 0.00 2.73
2210 5830 4.328983 ACGATAAGTCTTTTGTGCGGTATG 59.671 41.667 0.00 0.00 0.00 2.39
2211 5831 4.328983 CGATAAGTCTTTTGTGCGGTATGT 59.671 41.667 0.00 0.00 0.00 2.29
2212 5832 5.517411 CGATAAGTCTTTTGTGCGGTATGTA 59.483 40.000 0.00 0.00 0.00 2.29
2213 5833 6.507456 CGATAAGTCTTTTGTGCGGTATGTAC 60.507 42.308 0.00 0.00 0.00 2.90
2214 5834 2.991190 AGTCTTTTGTGCGGTATGTACG 59.009 45.455 0.00 0.00 35.72 3.67
2215 5835 2.093152 GTCTTTTGTGCGGTATGTACGG 59.907 50.000 0.00 0.00 35.72 4.02
2216 5836 1.395608 CTTTTGTGCGGTATGTACGGG 59.604 52.381 0.00 0.00 35.72 5.28
2217 5837 0.607112 TTTGTGCGGTATGTACGGGA 59.393 50.000 0.00 0.00 35.72 5.14
2218 5838 0.607112 TTGTGCGGTATGTACGGGAA 59.393 50.000 0.00 0.00 35.72 3.97
2219 5839 0.607112 TGTGCGGTATGTACGGGAAA 59.393 50.000 0.00 0.00 35.72 3.13
2220 5840 1.001624 GTGCGGTATGTACGGGAAAC 58.998 55.000 0.00 0.00 0.00 2.78
2221 5841 0.607112 TGCGGTATGTACGGGAAACA 59.393 50.000 0.00 0.00 0.00 2.83
2222 5842 1.207570 TGCGGTATGTACGGGAAACAT 59.792 47.619 0.00 0.00 40.57 2.71
2223 5843 1.595794 GCGGTATGTACGGGAAACATG 59.404 52.381 0.00 0.00 38.05 3.21
2224 5844 1.595794 CGGTATGTACGGGAAACATGC 59.404 52.381 0.00 0.00 38.05 4.06
2225 5845 2.634600 GGTATGTACGGGAAACATGCA 58.365 47.619 6.62 0.00 40.46 3.96
2226 5846 3.011119 GGTATGTACGGGAAACATGCAA 58.989 45.455 0.00 0.00 40.46 4.08
2227 5847 3.064820 GGTATGTACGGGAAACATGCAAG 59.935 47.826 0.00 0.00 40.46 4.01
2228 5848 0.878416 TGTACGGGAAACATGCAAGC 59.122 50.000 0.00 0.00 0.00 4.01
2229 5849 1.165270 GTACGGGAAACATGCAAGCT 58.835 50.000 0.00 0.00 0.00 3.74
2230 5850 1.135689 GTACGGGAAACATGCAAGCTG 60.136 52.381 0.00 0.00 0.00 4.24
2231 5851 0.537143 ACGGGAAACATGCAAGCTGA 60.537 50.000 0.00 0.00 0.00 4.26
2232 5852 0.597568 CGGGAAACATGCAAGCTGAA 59.402 50.000 0.00 0.00 0.00 3.02
2233 5853 1.401931 CGGGAAACATGCAAGCTGAAG 60.402 52.381 0.00 0.00 0.00 3.02
2234 5854 1.888512 GGGAAACATGCAAGCTGAAGA 59.111 47.619 0.00 0.00 0.00 2.87
2235 5855 2.297033 GGGAAACATGCAAGCTGAAGAA 59.703 45.455 0.00 0.00 0.00 2.52
2236 5856 3.056322 GGGAAACATGCAAGCTGAAGAAT 60.056 43.478 0.00 0.00 0.00 2.40
2237 5857 4.171754 GGAAACATGCAAGCTGAAGAATC 58.828 43.478 0.00 0.00 0.00 2.52
2238 5858 3.482722 AACATGCAAGCTGAAGAATCG 57.517 42.857 0.00 0.00 0.00 3.34
2239 5859 2.703416 ACATGCAAGCTGAAGAATCGA 58.297 42.857 0.00 0.00 0.00 3.59
2240 5860 3.276857 ACATGCAAGCTGAAGAATCGAT 58.723 40.909 0.00 0.00 0.00 3.59
2241 5861 4.445453 ACATGCAAGCTGAAGAATCGATA 58.555 39.130 0.00 0.00 0.00 2.92
2242 5862 4.272018 ACATGCAAGCTGAAGAATCGATAC 59.728 41.667 0.00 0.00 0.00 2.24
2243 5863 2.860136 TGCAAGCTGAAGAATCGATACG 59.140 45.455 0.00 0.00 0.00 3.06
2244 5864 2.860735 GCAAGCTGAAGAATCGATACGT 59.139 45.455 0.00 0.00 0.00 3.57
2245 5865 4.042398 GCAAGCTGAAGAATCGATACGTA 58.958 43.478 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 0.314302 CGGAAGTTCGAGTGTCACCT 59.686 55.000 0.00 0.00 0.00 4.00
84 86 1.602237 CTAAAAGGCAGAGGGCGGA 59.398 57.895 0.00 0.00 46.16 5.54
85 87 2.115291 GCTAAAAGGCAGAGGGCGG 61.115 63.158 0.00 0.00 46.16 6.13
89 91 2.941720 CAGCTAAGCTAAAAGGCAGAGG 59.058 50.000 0.00 0.00 36.40 3.69
133 135 3.686726 AGGATCTCACGAATCAAAGCAAC 59.313 43.478 0.00 0.00 0.00 4.17
139 141 7.510549 AAAGAAAAAGGATCTCACGAATCAA 57.489 32.000 0.00 0.00 0.00 2.57
225 229 7.810759 GTGCATTTAGGAAAACGAAAGGAATAA 59.189 33.333 0.00 0.00 28.73 1.40
226 230 7.309920 GTGCATTTAGGAAAACGAAAGGAATA 58.690 34.615 0.00 0.00 28.73 1.75
227 231 6.156519 GTGCATTTAGGAAAACGAAAGGAAT 58.843 36.000 0.00 0.00 28.73 3.01
228 232 5.525199 GTGCATTTAGGAAAACGAAAGGAA 58.475 37.500 0.00 0.00 28.73 3.36
229 233 4.319911 CGTGCATTTAGGAAAACGAAAGGA 60.320 41.667 0.00 0.00 28.73 3.36
230 234 3.911964 CGTGCATTTAGGAAAACGAAAGG 59.088 43.478 0.00 0.00 0.00 3.11
231 235 4.778904 TCGTGCATTTAGGAAAACGAAAG 58.221 39.130 0.00 0.00 0.00 2.62
232 236 4.815040 TCGTGCATTTAGGAAAACGAAA 57.185 36.364 0.00 0.00 0.00 3.46
233 237 5.365403 AATCGTGCATTTAGGAAAACGAA 57.635 34.783 0.00 0.00 32.18 3.85
234 238 5.365403 AAATCGTGCATTTAGGAAAACGA 57.635 34.783 0.00 0.00 32.48 3.85
235 239 7.555639 TTTAAATCGTGCATTTAGGAAAACG 57.444 32.000 0.00 0.00 38.06 3.60
275 282 9.587772 TGAATAAAAAGTTCACGAATTGGAAAA 57.412 25.926 0.00 0.00 31.07 2.29
276 283 9.587772 TTGAATAAAAAGTTCACGAATTGGAAA 57.412 25.926 0.00 0.00 35.47 3.13
277 284 9.587772 TTTGAATAAAAAGTTCACGAATTGGAA 57.412 25.926 0.00 0.00 35.47 3.53
278 285 9.587772 TTTTGAATAAAAAGTTCACGAATTGGA 57.412 25.926 0.00 0.00 35.47 3.53
282 289 9.672086 TCGATTTTGAATAAAAAGTTCACGAAT 57.328 25.926 0.00 0.00 41.00 3.34
283 290 9.672086 ATCGATTTTGAATAAAAAGTTCACGAA 57.328 25.926 0.00 0.00 41.00 3.85
284 291 9.112789 CATCGATTTTGAATAAAAAGTTCACGA 57.887 29.630 0.00 0.00 41.00 4.35
285 292 9.112789 TCATCGATTTTGAATAAAAAGTTCACG 57.887 29.630 0.00 0.00 41.00 4.35
639 1245 4.518970 CCTCCGGTTCTTGAATTCAGAAAA 59.481 41.667 16.73 8.00 0.00 2.29
908 1562 1.148759 GATGAAGAGGAACCGAGCGC 61.149 60.000 0.00 0.00 0.00 5.92
920 1575 7.332926 GTCAGAGTAAGATGCTTTTGATGAAGA 59.667 37.037 0.00 0.00 0.00 2.87
925 1582 6.471146 AGTGTCAGAGTAAGATGCTTTTGAT 58.529 36.000 0.00 0.00 0.00 2.57
971 4181 1.394618 CACCTACCTCCCTCTTCTCG 58.605 60.000 0.00 0.00 0.00 4.04
1242 4452 3.117663 GGTGAAACTATGGATGGGGCTAA 60.118 47.826 0.00 0.00 36.74 3.09
1290 4793 0.742281 CTGATCTGTGGAAGCACGGG 60.742 60.000 0.00 0.00 32.55 5.28
1318 4828 0.929615 CAAAACAAGCCAAACCGCTG 59.070 50.000 0.00 0.00 39.64 5.18
1365 4885 4.099573 AGAGTGACACGAGGAAGAAAAGAA 59.900 41.667 0.00 0.00 0.00 2.52
1366 4886 3.637229 AGAGTGACACGAGGAAGAAAAGA 59.363 43.478 0.00 0.00 0.00 2.52
1367 4887 3.738282 CAGAGTGACACGAGGAAGAAAAG 59.262 47.826 0.00 0.00 0.00 2.27
1368 4888 3.132289 ACAGAGTGACACGAGGAAGAAAA 59.868 43.478 0.00 0.00 0.00 2.29
1369 4889 2.693591 ACAGAGTGACACGAGGAAGAAA 59.306 45.455 0.00 0.00 0.00 2.52
1455 4981 1.929169 ACTGATGAATGACACGCATCG 59.071 47.619 12.25 10.13 40.89 3.84
1584 5112 3.046390 GTCTTAGAATCAGCCATCGTCG 58.954 50.000 0.00 0.00 0.00 5.12
1585 5113 3.799420 GTGTCTTAGAATCAGCCATCGTC 59.201 47.826 0.00 0.00 0.00 4.20
1586 5114 3.430929 GGTGTCTTAGAATCAGCCATCGT 60.431 47.826 0.00 0.00 0.00 3.73
1587 5115 3.126831 GGTGTCTTAGAATCAGCCATCG 58.873 50.000 0.00 0.00 0.00 3.84
1668 5196 5.467705 GGAATGAAAGCCAATGATATCAGC 58.532 41.667 11.78 9.27 0.00 4.26
1669 5197 5.240183 ACGGAATGAAAGCCAATGATATCAG 59.760 40.000 11.78 0.00 0.00 2.90
1703 5231 2.245159 TCTGCTGTTGTCTCTTGTGG 57.755 50.000 0.00 0.00 0.00 4.17
1736 5269 4.737946 GCTGAGTGACACAACAGTTAGTCT 60.738 45.833 23.61 1.39 32.05 3.24
1737 5270 3.491267 GCTGAGTGACACAACAGTTAGTC 59.509 47.826 23.61 9.93 32.05 2.59
1739 5272 3.492383 CAGCTGAGTGACACAACAGTTAG 59.508 47.826 23.61 14.89 33.57 2.34
1740 5273 3.132111 TCAGCTGAGTGACACAACAGTTA 59.868 43.478 23.61 12.99 33.57 2.24
1745 5284 2.759191 TGATCAGCTGAGTGACACAAC 58.241 47.619 22.96 2.19 0.00 3.32
1755 5294 0.107361 CACTGGCCATGATCAGCTGA 60.107 55.000 20.79 20.79 34.57 4.26
1756 5295 0.393944 ACACTGGCCATGATCAGCTG 60.394 55.000 5.51 7.63 34.57 4.24
1790 5363 4.181578 TGCTAGGAACAAACTAATCGAGC 58.818 43.478 0.00 0.00 0.00 5.03
1791 5364 5.812642 ACATGCTAGGAACAAACTAATCGAG 59.187 40.000 0.00 0.00 0.00 4.04
1811 5384 8.095937 TCACGATACCTCAATAGTAGTACATG 57.904 38.462 2.52 0.00 0.00 3.21
1823 5396 7.392113 ACCATAAACAATTTCACGATACCTCAA 59.608 33.333 0.00 0.00 0.00 3.02
1826 5399 8.795842 TTACCATAAACAATTTCACGATACCT 57.204 30.769 0.00 0.00 0.00 3.08
1842 5415 9.647797 CATAAGCCTGTATACGATTACCATAAA 57.352 33.333 0.00 0.00 0.00 1.40
1853 5426 3.057736 ACGCTACCATAAGCCTGTATACG 60.058 47.826 0.00 0.00 39.43 3.06
1854 5427 4.235360 CACGCTACCATAAGCCTGTATAC 58.765 47.826 0.00 0.00 39.43 1.47
1863 5470 4.882671 AAAATGAGCACGCTACCATAAG 57.117 40.909 0.00 0.00 0.00 1.73
1871 5478 4.507710 TCTCTTCATAAAATGAGCACGCT 58.492 39.130 0.00 0.00 40.94 5.07
1897 5504 6.202570 GTGCAAGGAACAAATCAATTGCTTTA 59.797 34.615 6.93 0.00 45.43 1.85
1903 5510 4.050553 CGTGTGCAAGGAACAAATCAATT 58.949 39.130 0.00 0.00 0.00 2.32
1907 5514 3.559238 ATCGTGTGCAAGGAACAAATC 57.441 42.857 0.00 0.00 0.00 2.17
1925 5532 3.666902 GCATTGTCACACCACACGTTATC 60.667 47.826 0.00 0.00 0.00 1.75
1927 5534 1.600013 GCATTGTCACACCACACGTTA 59.400 47.619 0.00 0.00 0.00 3.18
1970 5587 2.422235 CCTCTCTACTCTCACGATGGGT 60.422 54.545 0.00 0.00 0.00 4.51
1976 5593 3.057019 CGATCTCCTCTCTACTCTCACG 58.943 54.545 0.00 0.00 0.00 4.35
1995 5612 1.133253 CGCGACTAACCGAGTTCGA 59.867 57.895 0.00 0.00 39.06 3.71
1996 5613 0.856490 CTCGCGACTAACCGAGTTCG 60.856 60.000 3.71 0.00 44.25 3.95
1997 5614 2.927437 CTCGCGACTAACCGAGTTC 58.073 57.895 3.71 0.00 44.25 3.01
2004 5624 2.028165 GTGCTCATTTCTCGCGACTAAC 59.972 50.000 3.71 0.00 0.00 2.34
2010 5630 1.354040 AGAAGTGCTCATTTCTCGCG 58.646 50.000 0.00 0.00 32.86 5.87
2040 5660 6.426646 AACCAGAACTCTGTATTCTCTTGT 57.573 37.500 6.01 0.00 42.27 3.16
2066 5686 2.948315 GGAGCCAAAATGTTGCCAAAAA 59.052 40.909 0.00 0.00 33.01 1.94
2067 5687 2.172293 AGGAGCCAAAATGTTGCCAAAA 59.828 40.909 0.00 0.00 33.01 2.44
2068 5688 1.767681 AGGAGCCAAAATGTTGCCAAA 59.232 42.857 0.00 0.00 33.01 3.28
2069 5689 1.422531 AGGAGCCAAAATGTTGCCAA 58.577 45.000 0.00 0.00 33.01 4.52
2070 5690 1.070445 CAAGGAGCCAAAATGTTGCCA 59.930 47.619 0.00 0.00 33.01 4.92
2071 5691 1.070601 ACAAGGAGCCAAAATGTTGCC 59.929 47.619 0.00 0.00 33.01 4.52
2072 5692 2.531522 ACAAGGAGCCAAAATGTTGC 57.468 45.000 0.00 0.00 33.01 4.17
2073 5693 3.826157 TCCTACAAGGAGCCAAAATGTTG 59.174 43.478 0.00 0.00 40.06 3.33
2078 5698 4.735369 TCATTTCCTACAAGGAGCCAAAA 58.265 39.130 0.00 0.00 46.73 2.44
2107 5727 2.767505 ACTCTGAAGCCGTCGAAAATT 58.232 42.857 0.00 0.00 0.00 1.82
2117 5737 0.944386 TTGTTCGCAACTCTGAAGCC 59.056 50.000 1.68 0.00 31.15 4.35
2127 5747 0.383949 GTTCCTGCCTTTGTTCGCAA 59.616 50.000 0.00 0.00 33.87 4.85
2134 5754 4.885413 TGAATGAATTGTTCCTGCCTTTG 58.115 39.130 0.00 0.00 0.00 2.77
2135 5755 4.020839 CCTGAATGAATTGTTCCTGCCTTT 60.021 41.667 0.00 0.00 0.00 3.11
2140 5760 3.367703 GGTGCCTGAATGAATTGTTCCTG 60.368 47.826 0.00 0.00 0.00 3.86
2141 5761 2.827921 GGTGCCTGAATGAATTGTTCCT 59.172 45.455 0.00 0.00 0.00 3.36
2142 5762 2.562298 TGGTGCCTGAATGAATTGTTCC 59.438 45.455 0.00 0.00 0.00 3.62
2143 5763 3.940209 TGGTGCCTGAATGAATTGTTC 57.060 42.857 0.00 0.00 0.00 3.18
2144 5764 4.895668 ATTGGTGCCTGAATGAATTGTT 57.104 36.364 0.00 0.00 0.00 2.83
2145 5765 4.142403 CGTATTGGTGCCTGAATGAATTGT 60.142 41.667 0.00 0.00 0.00 2.71
2146 5766 4.353737 CGTATTGGTGCCTGAATGAATTG 58.646 43.478 0.00 0.00 0.00 2.32
2147 5767 3.381272 CCGTATTGGTGCCTGAATGAATT 59.619 43.478 0.00 0.00 0.00 2.17
2148 5768 2.951642 CCGTATTGGTGCCTGAATGAAT 59.048 45.455 0.00 0.00 0.00 2.57
2149 5769 2.364632 CCGTATTGGTGCCTGAATGAA 58.635 47.619 0.00 0.00 0.00 2.57
2150 5770 2.036958 CCGTATTGGTGCCTGAATGA 57.963 50.000 0.00 0.00 0.00 2.57
2161 5781 3.611766 AAGTTCAGGAGACCGTATTGG 57.388 47.619 0.00 0.00 46.41 3.16
2162 5782 5.475719 TGTTAAGTTCAGGAGACCGTATTG 58.524 41.667 0.00 0.00 0.00 1.90
2163 5783 5.479375 TCTGTTAAGTTCAGGAGACCGTATT 59.521 40.000 0.00 0.00 34.15 1.89
2164 5784 5.014858 TCTGTTAAGTTCAGGAGACCGTAT 58.985 41.667 0.00 0.00 34.15 3.06
2165 5785 4.217118 GTCTGTTAAGTTCAGGAGACCGTA 59.783 45.833 0.00 0.00 34.15 4.02
2166 5786 3.005578 GTCTGTTAAGTTCAGGAGACCGT 59.994 47.826 0.00 0.00 34.15 4.83
2167 5787 3.576648 GTCTGTTAAGTTCAGGAGACCG 58.423 50.000 0.00 0.00 34.15 4.79
2168 5788 3.255149 TCGTCTGTTAAGTTCAGGAGACC 59.745 47.826 0.00 0.00 34.15 3.85
2169 5789 4.500603 TCGTCTGTTAAGTTCAGGAGAC 57.499 45.455 0.00 0.00 34.15 3.36
2170 5790 6.433404 ACTTATCGTCTGTTAAGTTCAGGAGA 59.567 38.462 0.00 0.00 37.33 3.71
2171 5791 6.622549 ACTTATCGTCTGTTAAGTTCAGGAG 58.377 40.000 0.00 0.00 37.33 3.69
2172 5792 6.585695 ACTTATCGTCTGTTAAGTTCAGGA 57.414 37.500 0.00 0.00 37.33 3.86
2173 5793 6.872670 GACTTATCGTCTGTTAAGTTCAGG 57.127 41.667 0.00 0.00 39.53 3.86
2186 5806 2.735134 ACCGCACAAAAGACTTATCGTC 59.265 45.455 0.00 0.00 43.17 4.20
2187 5807 2.762745 ACCGCACAAAAGACTTATCGT 58.237 42.857 0.00 0.00 0.00 3.73
2188 5808 4.328983 ACATACCGCACAAAAGACTTATCG 59.671 41.667 0.00 0.00 0.00 2.92
2189 5809 5.796350 ACATACCGCACAAAAGACTTATC 57.204 39.130 0.00 0.00 0.00 1.75
2190 5810 5.290158 CGTACATACCGCACAAAAGACTTAT 59.710 40.000 0.00 0.00 0.00 1.73
2191 5811 4.622313 CGTACATACCGCACAAAAGACTTA 59.378 41.667 0.00 0.00 0.00 2.24
2192 5812 3.430895 CGTACATACCGCACAAAAGACTT 59.569 43.478 0.00 0.00 0.00 3.01
2193 5813 2.991190 CGTACATACCGCACAAAAGACT 59.009 45.455 0.00 0.00 0.00 3.24
2194 5814 2.093152 CCGTACATACCGCACAAAAGAC 59.907 50.000 0.00 0.00 0.00 3.01
2195 5815 2.339418 CCGTACATACCGCACAAAAGA 58.661 47.619 0.00 0.00 0.00 2.52
2196 5816 1.395608 CCCGTACATACCGCACAAAAG 59.604 52.381 0.00 0.00 0.00 2.27
2197 5817 1.001746 TCCCGTACATACCGCACAAAA 59.998 47.619 0.00 0.00 0.00 2.44
2198 5818 0.607112 TCCCGTACATACCGCACAAA 59.393 50.000 0.00 0.00 0.00 2.83
2199 5819 0.607112 TTCCCGTACATACCGCACAA 59.393 50.000 0.00 0.00 0.00 3.33
2200 5820 0.607112 TTTCCCGTACATACCGCACA 59.393 50.000 0.00 0.00 0.00 4.57
2201 5821 1.001624 GTTTCCCGTACATACCGCAC 58.998 55.000 0.00 0.00 0.00 5.34
2202 5822 0.607112 TGTTTCCCGTACATACCGCA 59.393 50.000 0.00 0.00 0.00 5.69
2203 5823 1.595794 CATGTTTCCCGTACATACCGC 59.404 52.381 0.00 0.00 34.59 5.68
2204 5824 1.595794 GCATGTTTCCCGTACATACCG 59.404 52.381 0.00 0.00 34.59 4.02
2205 5825 2.634600 TGCATGTTTCCCGTACATACC 58.365 47.619 0.00 0.00 34.59 2.73
2206 5826 3.486875 GCTTGCATGTTTCCCGTACATAC 60.487 47.826 1.14 0.00 34.59 2.39
2207 5827 2.680841 GCTTGCATGTTTCCCGTACATA 59.319 45.455 1.14 0.00 34.59 2.29
2208 5828 1.472480 GCTTGCATGTTTCCCGTACAT 59.528 47.619 1.14 0.00 36.70 2.29
2209 5829 0.878416 GCTTGCATGTTTCCCGTACA 59.122 50.000 1.14 0.00 0.00 2.90
2210 5830 1.135689 CAGCTTGCATGTTTCCCGTAC 60.136 52.381 1.14 0.00 0.00 3.67
2211 5831 1.164411 CAGCTTGCATGTTTCCCGTA 58.836 50.000 1.14 0.00 0.00 4.02
2212 5832 0.537143 TCAGCTTGCATGTTTCCCGT 60.537 50.000 1.14 0.00 0.00 5.28
2213 5833 0.597568 TTCAGCTTGCATGTTTCCCG 59.402 50.000 1.14 0.00 0.00 5.14
2214 5834 1.888512 TCTTCAGCTTGCATGTTTCCC 59.111 47.619 1.14 0.00 0.00 3.97
2215 5835 3.648339 TTCTTCAGCTTGCATGTTTCC 57.352 42.857 1.14 0.00 0.00 3.13
2216 5836 3.850273 CGATTCTTCAGCTTGCATGTTTC 59.150 43.478 1.14 0.00 0.00 2.78
2217 5837 3.503363 TCGATTCTTCAGCTTGCATGTTT 59.497 39.130 1.14 0.00 0.00 2.83
2218 5838 3.076621 TCGATTCTTCAGCTTGCATGTT 58.923 40.909 1.14 0.00 0.00 2.71
2219 5839 2.703416 TCGATTCTTCAGCTTGCATGT 58.297 42.857 1.14 0.00 0.00 3.21
2220 5840 3.965292 ATCGATTCTTCAGCTTGCATG 57.035 42.857 0.00 0.00 0.00 4.06
2221 5841 3.492383 CGTATCGATTCTTCAGCTTGCAT 59.508 43.478 1.71 0.00 0.00 3.96
2222 5842 2.860136 CGTATCGATTCTTCAGCTTGCA 59.140 45.455 1.71 0.00 0.00 4.08
2223 5843 2.860735 ACGTATCGATTCTTCAGCTTGC 59.139 45.455 1.71 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.