Multiple sequence alignment - TraesCS5D01G042900

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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 TraesCS5D01G042900 chr5D 100.000 5399 0 0 1 5399 42554291 42559689 0.000000e+00 9971.0
1 TraesCS5D01G042900 chr5D 91.920 3651 225 20 336 3932 52617996 52614362 0.000000e+00 5044.0
2 TraesCS5D01G042900 chr5D 100.000 1890 0 0 5820 7709 42560110 42561999 0.000000e+00 3491.0
3 TraesCS5D01G042900 chr5D 89.412 2720 215 34 835 3520 15352551 15355231 0.000000e+00 3360.0
4 TraesCS5D01G042900 chr5D 91.397 988 68 9 2556 3527 15128904 15129890 0.000000e+00 1338.0
5 TraesCS5D01G042900 chr5D 87.280 1022 124 3 1026 2044 15103070 15104088 0.000000e+00 1162.0
6 TraesCS5D01G042900 chr5D 91.789 682 35 9 3993 4664 52614187 52613517 0.000000e+00 929.0
7 TraesCS5D01G042900 chr5D 92.607 514 38 0 2049 2562 15126696 15127209 0.000000e+00 739.0
8 TraesCS5D01G042900 chr5D 94.000 450 21 2 4684 5130 52605600 52605154 0.000000e+00 676.0
9 TraesCS5D01G042900 chr5D 84.270 356 29 15 1 342 52618362 52618020 9.650000e-84 322.0
10 TraesCS5D01G042900 chr5D 85.551 263 22 11 4879 5130 15216397 15216654 2.130000e-65 261.0
11 TraesCS5D01G042900 chr5D 85.714 161 16 5 3599 3754 52614841 52614683 6.190000e-36 163.0
12 TraesCS5D01G042900 chr5D 100.000 45 0 0 3867 3911 52614233 52614189 4.960000e-12 84.2
13 TraesCS5D01G042900 chr5B 97.423 3104 75 3 831 3932 37059965 37056865 0.000000e+00 5284.0
14 TraesCS5D01G042900 chr5B 92.705 3153 206 8 800 3932 55625416 55622268 0.000000e+00 4527.0
15 TraesCS5D01G042900 chr5B 92.388 1143 58 14 3993 5130 55622181 55621063 0.000000e+00 1602.0
16 TraesCS5D01G042900 chr5B 95.827 647 18 2 4476 5113 37056260 37055614 0.000000e+00 1037.0
17 TraesCS5D01G042900 chr5B 94.797 615 22 6 3837 4445 37056862 37056252 0.000000e+00 950.0
18 TraesCS5D01G042900 chr5B 93.482 583 14 4 1 576 37060555 37059990 0.000000e+00 845.0
19 TraesCS5D01G042900 chr5B 86.168 441 17 15 336 742 55625847 55625417 3.300000e-118 436.0
20 TraesCS5D01G042900 chr5B 91.960 199 9 3 147 342 55626065 55625871 9.860000e-69 272.0
21 TraesCS5D01G042900 chr5B 85.093 161 17 5 3599 3754 55622747 55622589 2.880000e-34 158.0
22 TraesCS5D01G042900 chr1D 97.882 1889 25 3 5820 7706 226953494 226955369 0.000000e+00 3253.0
23 TraesCS5D01G042900 chr1D 97.249 1890 39 4 5820 7706 57213307 57215186 0.000000e+00 3190.0
24 TraesCS5D01G042900 chr1D 96.962 1119 25 2 5820 6938 318649767 318650876 0.000000e+00 1869.0
25 TraesCS5D01G042900 chr1D 97.668 772 16 1 6934 7703 318661343 318662114 0.000000e+00 1325.0
26 TraesCS5D01G042900 chr1D 72.776 1484 333 51 1008 2448 312973483 312972028 3.300000e-118 436.0
27 TraesCS5D01G042900 chr1D 94.245 278 9 2 5128 5399 57212955 57213231 1.200000e-112 418.0
28 TraesCS5D01G042900 chr1D 91.935 248 14 3 5126 5367 318648923 318649170 7.410000e-90 342.0
29 TraesCS5D01G042900 chr1D 92.735 234 10 2 5128 5354 226953177 226953410 1.600000e-86 331.0
30 TraesCS5D01G042900 chr7D 97.671 1889 33 2 5820 7706 266876510 266878389 0.000000e+00 3234.0
31 TraesCS5D01G042900 chr7D 96.718 1889 31 6 5820 7706 169474074 169475933 0.000000e+00 3116.0
32 TraesCS5D01G042900 chr7D 94.964 278 8 1 5128 5399 266876155 266876432 1.540000e-116 431.0
33 TraesCS5D01G042900 chr7D 94.624 279 9 1 5127 5399 169473551 169473829 1.990000e-115 427.0
34 TraesCS5D01G042900 chr7D 93.907 279 11 1 5127 5399 602024971 602024693 4.300000e-112 416.0
35 TraesCS5D01G042900 chr7D 87.889 289 16 5 5128 5397 21760734 21761022 9.650000e-84 322.0
36 TraesCS5D01G042900 chr7D 92.553 94 7 0 3904 3997 167548415 167548508 1.350000e-27 135.0
37 TraesCS5D01G042900 chr7D 90.816 98 7 2 3903 3999 632404591 632404687 6.280000e-26 130.0
38 TraesCS5D01G042900 chr7D 90.722 97 8 1 6462 6558 76916845 76916750 2.260000e-25 128.0
39 TraesCS5D01G042900 chr2B 96.787 1805 55 2 5904 7706 442921008 442922811 0.000000e+00 3009.0
40 TraesCS5D01G042900 chr2B 97.826 46 1 0 7364 7409 442923269 442923314 6.410000e-11 80.5
41 TraesCS5D01G042900 chr3B 97.099 1103 32 0 5904 7006 806123760 806124862 0.000000e+00 1860.0
42 TraesCS5D01G042900 chr3B 75.506 445 105 4 2003 2445 564319144 564319586 1.680000e-51 215.0
43 TraesCS5D01G042900 chr3B 85.714 98 12 2 2493 2589 564319607 564319703 1.370000e-17 102.0
44 TraesCS5D01G042900 chr6A 96.745 1106 36 0 5904 7009 162425722 162424617 0.000000e+00 1844.0
45 TraesCS5D01G042900 chrUn 98.455 906 10 3 6804 7706 108981446 108982350 0.000000e+00 1592.0
46 TraesCS5D01G042900 chrUn 88.182 110 8 4 3916 4024 101630877 101630772 8.120000e-25 126.0
47 TraesCS5D01G042900 chr5A 90.242 1035 59 20 337 1347 41709205 41708189 0.000000e+00 1314.0
48 TraesCS5D01G042900 chr5A 95.556 90 4 0 253 342 41709322 41709233 2.240000e-30 145.0
49 TraesCS5D01G042900 chr5A 92.553 94 7 0 3904 3997 472310936 472311029 1.350000e-27 135.0
50 TraesCS5D01G042900 chr2A 91.732 508 40 2 6646 7153 17787012 17786507 0.000000e+00 704.0
51 TraesCS5D01G042900 chr2A 91.667 96 7 1 3900 3995 722077296 722077202 1.750000e-26 132.0
52 TraesCS5D01G042900 chr1B 72.911 1484 331 51 1008 2448 423209932 423208477 1.530000e-121 448.0
53 TraesCS5D01G042900 chr1B 86.139 404 36 7 7157 7542 181101336 181100935 1.200000e-112 418.0
54 TraesCS5D01G042900 chr1B 91.089 101 6 3 3907 4005 154165149 154165050 4.850000e-27 134.0
55 TraesCS5D01G042900 chr1A 72.862 1485 330 53 1008 2448 392529817 392528362 7.100000e-120 442.0
56 TraesCS5D01G042900 chr1A 93.478 92 6 0 3903 3994 530756665 530756574 3.750000e-28 137.0
57 TraesCS5D01G042900 chr4D 93.165 278 12 2 5128 5399 51342419 51342695 1.200000e-107 401.0
58 TraesCS5D01G042900 chr3D 93.443 244 9 2 5120 5357 562384098 562383856 9.510000e-94 355.0
59 TraesCS5D01G042900 chr3D 76.009 446 101 6 2003 2445 432135149 432135591 7.780000e-55 226.0
60 TraesCS5D01G042900 chr3D 71.612 937 213 38 2493 3398 432135612 432136526 2.820000e-49 207.0
61 TraesCS5D01G042900 chr7A 79.848 263 30 16 7449 7691 688960900 688961159 3.700000e-38 171.0
62 TraesCS5D01G042900 chr4A 86.400 125 16 1 6212 6335 196611068 196610944 1.350000e-27 135.0
63 TraesCS5D01G042900 chr4A 94.231 52 3 0 5985 6036 521864083 521864134 6.410000e-11 80.5
64 TraesCS5D01G042900 chr2D 92.473 93 7 0 3903 3995 643235914 643235822 4.850000e-27 134.0


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 TraesCS5D01G042900 chr5D 42554291 42561999 7708 False 6731.00 9971 100.00000 1 7709 2 chr5D.!!$F5 7708
1 TraesCS5D01G042900 chr5D 15352551 15355231 2680 False 3360.00 3360 89.41200 835 3520 1 chr5D.!!$F3 2685
2 TraesCS5D01G042900 chr5D 52613517 52618362 4845 True 1308.44 5044 90.73860 1 4664 5 chr5D.!!$R2 4663
3 TraesCS5D01G042900 chr5D 15103070 15104088 1018 False 1162.00 1162 87.28000 1026 2044 1 chr5D.!!$F1 1018
4 TraesCS5D01G042900 chr5D 15126696 15129890 3194 False 1038.50 1338 92.00200 2049 3527 2 chr5D.!!$F4 1478
5 TraesCS5D01G042900 chr5B 37055614 37060555 4941 True 2029.00 5284 95.38225 1 5113 4 chr5B.!!$R1 5112
6 TraesCS5D01G042900 chr5B 55621063 55626065 5002 True 1399.00 4527 89.66280 147 5130 5 chr5B.!!$R2 4983
7 TraesCS5D01G042900 chr1D 57212955 57215186 2231 False 1804.00 3190 95.74700 5128 7706 2 chr1D.!!$F2 2578
8 TraesCS5D01G042900 chr1D 226953177 226955369 2192 False 1792.00 3253 95.30850 5128 7706 2 chr1D.!!$F3 2578
9 TraesCS5D01G042900 chr1D 318661343 318662114 771 False 1325.00 1325 97.66800 6934 7703 1 chr1D.!!$F1 769
10 TraesCS5D01G042900 chr1D 318648923 318650876 1953 False 1105.50 1869 94.44850 5126 6938 2 chr1D.!!$F4 1812
11 TraesCS5D01G042900 chr1D 312972028 312973483 1455 True 436.00 436 72.77600 1008 2448 1 chr1D.!!$R1 1440
12 TraesCS5D01G042900 chr7D 266876155 266878389 2234 False 1832.50 3234 96.31750 5128 7706 2 chr7D.!!$F5 2578
13 TraesCS5D01G042900 chr7D 169473551 169475933 2382 False 1771.50 3116 95.67100 5127 7706 2 chr7D.!!$F4 2579
14 TraesCS5D01G042900 chr2B 442921008 442923314 2306 False 1544.75 3009 97.30650 5904 7706 2 chr2B.!!$F1 1802
15 TraesCS5D01G042900 chr3B 806123760 806124862 1102 False 1860.00 1860 97.09900 5904 7006 1 chr3B.!!$F1 1102
16 TraesCS5D01G042900 chr6A 162424617 162425722 1105 True 1844.00 1844 96.74500 5904 7009 1 chr6A.!!$R1 1105
17 TraesCS5D01G042900 chrUn 108981446 108982350 904 False 1592.00 1592 98.45500 6804 7706 1 chrUn.!!$F1 902
18 TraesCS5D01G042900 chr5A 41708189 41709322 1133 True 729.50 1314 92.89900 253 1347 2 chr5A.!!$R1 1094
19 TraesCS5D01G042900 chr2A 17786507 17787012 505 True 704.00 704 91.73200 6646 7153 1 chr2A.!!$R1 507
20 TraesCS5D01G042900 chr1B 423208477 423209932 1455 True 448.00 448 72.91100 1008 2448 1 chr1B.!!$R3 1440
21 TraesCS5D01G042900 chr1A 392528362 392529817 1455 True 442.00 442 72.86200 1008 2448 1 chr1A.!!$R1 1440
22 TraesCS5D01G042900 chr3D 432135149 432136526 1377 False 216.50 226 73.81050 2003 3398 2 chr3D.!!$F1 1395

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
809 890 0.249868 CTGTCCTTGCGTGGTTCTCA 60.250 55.000 0.00 0.0 0.00 3.27 F
817 898 0.310543 GCGTGGTTCTCATTGCACAA 59.689 50.000 0.00 0.0 32.23 3.33 F
2760 4591 0.035317 ACAAGCACGATCTTCAGGCA 59.965 50.000 0.00 0.0 0.00 4.75 F
2816 4647 0.523072 CTGGGCAATTCACTTCACGG 59.477 55.000 0.00 0.0 0.00 4.94 F
4277 6437 1.696063 AAGCACCTTGAAGCACACAT 58.304 45.000 0.00 0.0 0.00 3.21 F
4982 7154 1.079127 ACGGCGGAGTCATGGAAAG 60.079 57.895 13.24 0.0 0.00 2.62 F
5194 7366 3.625764 GCCATGTCGCCTTTAAATACTCA 59.374 43.478 0.00 0.0 0.00 3.41 F
6125 8793 0.038159 GTAGAGCAGTCCGCAGTGTT 60.038 55.000 0.00 0.0 46.13 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2760 4591 1.000843 TGCAGTACGTCACAGAGCAAT 59.999 47.619 0.00 0.00 31.51 3.56 R
2816 4647 1.555533 CAGACTCCCTAACCTTGTCCC 59.444 57.143 0.00 0.00 0.00 4.46 R
4251 6411 1.464997 GCTTCAAGGTGCTTTAGACGG 59.535 52.381 0.00 0.00 0.00 4.79 R
4465 6627 2.642807 TGGGAAGGAAAGACTACCCAAG 59.357 50.000 0.00 0.00 43.34 3.61 R
5866 8534 0.615850 GGAGTTGGAGGAGTTGGAGG 59.384 60.000 0.00 0.00 0.00 4.30 R
5867 8535 0.615850 GGGAGTTGGAGGAGTTGGAG 59.384 60.000 0.00 0.00 0.00 3.86 R
6131 8799 1.446272 CTCGAAGGCAAGGACGACC 60.446 63.158 0.00 0.00 0.00 4.79 R
7497 10172 2.273449 CTGGGCCCCTACAGCAAG 59.727 66.667 22.27 2.57 0.00 4.01 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
286 302 6.180567 GTGTTTTCGTACGCTGGTATTATTC 58.819 40.000 11.24 0.00 0.00 1.75
452 500 6.428083 TCAGTAAGTTCTTGGGTTACATCA 57.572 37.500 0.00 0.00 0.00 3.07
504 569 4.097418 CCAGAAACTCCCTCCTCTCTTTA 58.903 47.826 0.00 0.00 0.00 1.85
651 730 1.814248 GCTAAATCCCTACTTGCCGGG 60.814 57.143 2.18 0.00 42.05 5.73
653 732 1.587066 AAATCCCTACTTGCCGGGTA 58.413 50.000 2.18 0.00 41.40 3.69
654 733 1.815757 AATCCCTACTTGCCGGGTAT 58.184 50.000 2.18 0.00 41.40 2.73
655 734 2.708037 ATCCCTACTTGCCGGGTATA 57.292 50.000 2.18 0.00 41.40 1.47
656 735 2.005370 TCCCTACTTGCCGGGTATAG 57.995 55.000 2.18 0.00 41.40 1.31
657 736 1.500303 TCCCTACTTGCCGGGTATAGA 59.500 52.381 2.18 0.00 41.40 1.98
702 781 2.200373 GTGGTCTATTGGTGCCACTT 57.800 50.000 5.42 0.00 45.64 3.16
715 794 1.654954 GCCACTTGATCCTGCTGCTG 61.655 60.000 0.00 0.00 0.00 4.41
720 799 3.192844 CACTTGATCCTGCTGCTGATTTT 59.807 43.478 8.20 0.00 0.00 1.82
752 833 7.011994 ACATCCATCCATCCTTATAATTTGCA 58.988 34.615 0.00 0.00 0.00 4.08
754 835 7.528996 TCCATCCATCCTTATAATTTGCAAG 57.471 36.000 0.00 0.00 0.00 4.01
766 847 9.499585 CTTATAATTTGCAAGACACATCTCTTG 57.500 33.333 0.00 4.82 46.89 3.02
769 850 5.929697 TTTGCAAGACACATCTCTTGTAG 57.070 39.130 0.00 0.00 46.18 2.74
773 854 5.171476 GCAAGACACATCTCTTGTAGCTTA 58.829 41.667 9.95 0.00 46.18 3.09
809 890 0.249868 CTGTCCTTGCGTGGTTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
817 898 0.310543 GCGTGGTTCTCATTGCACAA 59.689 50.000 0.00 0.00 32.23 3.33
824 905 3.550842 GGTTCTCATTGCACAAGTCCAAC 60.551 47.826 0.00 0.00 0.00 3.77
1102 1192 1.641577 GCTCCAAGAGCGTAATCGTT 58.358 50.000 0.06 0.00 45.85 3.85
1495 1588 3.199946 TGTGTTTGAGGAGGAGAACTTGT 59.800 43.478 0.00 0.00 0.00 3.16
1617 1716 5.401531 AAGCTCTACGGAATGTTCTTACA 57.598 39.130 0.00 0.00 38.95 2.41
1924 2033 2.111041 GCGTTTTGCTCATGCTATCC 57.889 50.000 0.00 0.00 41.73 2.59
1964 2073 1.439543 ACTGAGAAGCCCCTCTGTTT 58.560 50.000 8.88 0.00 40.80 2.83
2702 4533 6.475727 CGTATCATGAGAAGATTAAACACCGT 59.524 38.462 0.09 0.00 0.00 4.83
2760 4591 0.035317 ACAAGCACGATCTTCAGGCA 59.965 50.000 0.00 0.00 0.00 4.75
2766 4597 1.329906 CACGATCTTCAGGCATTGCTC 59.670 52.381 8.82 0.00 0.00 4.26
2816 4647 0.523072 CTGGGCAATTCACTTCACGG 59.477 55.000 0.00 0.00 0.00 4.94
2994 4831 3.996363 TGCAGTATTACAGTGTGAAGCTG 59.004 43.478 5.88 11.21 39.67 4.24
3586 5440 3.216800 TGGCTGCTCCACATGATTATTC 58.783 45.455 0.00 0.00 40.72 1.75
3614 5468 2.602217 GCCGCCATTCTAATTAGTTGCG 60.602 50.000 21.88 21.88 0.00 4.85
3840 5895 5.408909 GCCCTTCTACAACAAGTTAGACTTC 59.591 44.000 0.00 0.00 36.03 3.01
3912 6061 4.010349 GCAGACCAGGCAATTTAGTACTT 58.990 43.478 0.00 0.00 0.00 2.24
3913 6062 4.142600 GCAGACCAGGCAATTTAGTACTTG 60.143 45.833 0.00 0.00 0.00 3.16
3914 6063 5.003804 CAGACCAGGCAATTTAGTACTTGT 58.996 41.667 0.00 0.00 0.00 3.16
3943 6092 9.817809 TGTGAAGAAATATAAGAGCGTTTAGAT 57.182 29.630 0.00 0.00 0.00 1.98
3986 6135 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
3988 6137 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
3989 6138 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
3990 6139 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
4057 6211 7.565768 TCCCAAATAGACTTTTAAAAGGTTGGT 59.434 33.333 27.23 10.57 40.31 3.67
4065 6219 4.202212 CTTTTAAAAGGTTGGTGGACCAGG 60.202 45.833 18.51 0.00 42.35 4.45
4277 6437 1.696063 AAGCACCTTGAAGCACACAT 58.304 45.000 0.00 0.00 0.00 3.21
4317 6477 4.079787 TCCTCTAGCCAGGTGCATTTTTAT 60.080 41.667 0.00 0.00 44.83 1.40
4347 6507 5.592282 TGTTGTGTTTTCTGGAGCATTCTTA 59.408 36.000 0.00 0.00 0.00 2.10
4447 6609 3.323403 CCTGTGAGGAACTTTCACTCTCT 59.677 47.826 6.89 0.00 44.08 3.10
4448 6610 4.202305 CCTGTGAGGAACTTTCACTCTCTT 60.202 45.833 6.89 0.00 44.08 2.85
4450 6612 6.463049 CCTGTGAGGAACTTTCACTCTCTTAA 60.463 42.308 6.89 0.00 44.08 1.85
4451 6613 6.516718 TGTGAGGAACTTTCACTCTCTTAAG 58.483 40.000 0.00 0.00 44.08 1.85
4452 6614 5.407084 GTGAGGAACTTTCACTCTCTTAAGC 59.593 44.000 0.00 0.00 41.55 3.09
4453 6615 5.305644 TGAGGAACTTTCACTCTCTTAAGCT 59.694 40.000 0.00 0.00 41.55 3.74
4454 6616 6.493802 TGAGGAACTTTCACTCTCTTAAGCTA 59.506 38.462 0.00 0.00 41.55 3.32
4455 6617 7.179338 TGAGGAACTTTCACTCTCTTAAGCTAT 59.821 37.037 0.00 0.00 41.55 2.97
4456 6618 8.596781 AGGAACTTTCACTCTCTTAAGCTATA 57.403 34.615 0.00 0.00 27.25 1.31
4457 6619 9.207868 AGGAACTTTCACTCTCTTAAGCTATAT 57.792 33.333 0.00 0.00 27.25 0.86
4462 6624 9.868277 CTTTCACTCTCTTAAGCTATATATGGG 57.132 37.037 0.00 0.00 0.00 4.00
4463 6625 8.958060 TTCACTCTCTTAAGCTATATATGGGT 57.042 34.615 0.00 0.00 0.00 4.51
4465 6627 9.463902 TCACTCTCTTAAGCTATATATGGGTAC 57.536 37.037 0.83 0.00 0.00 3.34
4466 6628 9.469097 CACTCTCTTAAGCTATATATGGGTACT 57.531 37.037 0.83 0.00 0.00 2.73
4921 7093 1.265905 CGTTGTTTCAGGGGTACAAGC 59.734 52.381 0.00 0.00 32.89 4.01
4982 7154 1.079127 ACGGCGGAGTCATGGAAAG 60.079 57.895 13.24 0.00 0.00 2.62
5194 7366 3.625764 GCCATGTCGCCTTTAAATACTCA 59.374 43.478 0.00 0.00 0.00 3.41
5213 7391 4.460382 ACTCATGCCAGTAAATTCCTTGTG 59.540 41.667 0.00 0.00 0.00 3.33
5864 8532 4.729918 CTGCTGCACCCACTCCCC 62.730 72.222 0.00 0.00 0.00 4.81
5866 8534 4.416738 GCTGCACCCACTCCCCTC 62.417 72.222 0.00 0.00 0.00 4.30
5867 8535 3.721706 CTGCACCCACTCCCCTCC 61.722 72.222 0.00 0.00 0.00 4.30
5868 8536 4.270153 TGCACCCACTCCCCTCCT 62.270 66.667 0.00 0.00 0.00 3.69
5869 8537 3.403558 GCACCCACTCCCCTCCTC 61.404 72.222 0.00 0.00 0.00 3.71
5870 8538 2.689034 CACCCACTCCCCTCCTCC 60.689 72.222 0.00 0.00 0.00 4.30
5871 8539 3.208592 ACCCACTCCCCTCCTCCA 61.209 66.667 0.00 0.00 0.00 3.86
5872 8540 2.124996 CCCACTCCCCTCCTCCAA 59.875 66.667 0.00 0.00 0.00 3.53
5929 8597 2.395360 GCGTCGTGCCTATTGCCAA 61.395 57.895 0.00 0.00 40.16 4.52
5939 8607 1.339631 CCTATTGCCAAGACGGGACAA 60.340 52.381 0.00 0.00 32.85 3.18
6065 8733 3.254654 CGCGGTGTATGAGGTGCG 61.255 66.667 0.00 0.00 39.57 5.34
6096 8764 1.375523 CCGCGGCAGGTTAAACTCT 60.376 57.895 14.67 0.00 0.00 3.24
6125 8793 0.038159 GTAGAGCAGTCCGCAGTGTT 60.038 55.000 0.00 0.00 46.13 3.32
6595 9264 4.051661 TCTTCAGATTTCCCTGGCAATT 57.948 40.909 0.00 0.00 34.99 2.32
7613 10289 3.605664 GCATATTGGTGCGCCCCC 61.606 66.667 15.15 6.33 35.10 5.40
7706 10382 2.112898 GAGTCCCTGCGGAATCGTA 58.887 57.895 0.00 0.00 42.97 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.272504 GTGAAGTAGTACAAGCAAGCAACA 59.727 41.667 2.52 0.00 0.00 3.33
107 116 5.055265 TCAACCAATGAGGACAAAACCTA 57.945 39.130 0.00 0.00 40.73 3.08
114 123 3.805066 TGGATTCAACCAATGAGGACA 57.195 42.857 0.00 0.00 39.77 4.02
286 302 1.527311 GCGAAAAATCCTAGCTAGCGG 59.473 52.381 15.74 5.63 0.00 5.52
452 500 5.570439 GCTGCATGGTCCTAATATAAGCTCT 60.570 44.000 0.00 0.00 0.00 4.09
504 569 1.069823 CTGCTGACACCAGAACAGAGT 59.930 52.381 0.00 0.00 43.02 3.24
739 820 8.218338 AGAGATGTGTCTTGCAAATTATAAGG 57.782 34.615 0.00 0.00 33.97 2.69
769 850 8.182227 GGACAGGACTGTTACAAATTATTAAGC 58.818 37.037 6.40 0.00 45.05 3.09
773 854 7.309194 GCAAGGACAGGACTGTTACAAATTATT 60.309 37.037 6.40 0.00 45.05 1.40
809 890 3.490348 AGCTTAGTTGGACTTGTGCAAT 58.510 40.909 10.62 3.85 0.00 3.56
1017 1107 5.762218 CGGATCCTGAGCATCTTTTAGAATT 59.238 40.000 10.75 0.00 34.92 2.17
1102 1192 2.118403 AAGGACAGGAGGAAGTTGGA 57.882 50.000 0.00 0.00 0.00 3.53
1495 1588 2.631160 ATTGTGTCCTTGTCGAACCA 57.369 45.000 0.00 0.00 0.00 3.67
1924 2033 1.800805 AAGTGACAATCTGCACTCGG 58.199 50.000 0.00 0.00 44.06 4.63
1964 2073 2.158827 TGTAGCAGAAGTGGAACAAGCA 60.159 45.455 0.00 0.00 44.16 3.91
2293 2423 1.012841 GGAGAATGCCGAAGCTCAAG 58.987 55.000 0.00 0.00 40.80 3.02
2486 2616 4.768583 AGGTGAAAGCTCAGATGAGATTC 58.231 43.478 13.25 14.91 44.61 2.52
2760 4591 1.000843 TGCAGTACGTCACAGAGCAAT 59.999 47.619 0.00 0.00 31.51 3.56
2816 4647 1.555533 CAGACTCCCTAACCTTGTCCC 59.444 57.143 0.00 0.00 0.00 4.46
2994 4831 5.309638 GCCTCTAAATAGATTGGGGAGAAC 58.690 45.833 0.00 0.00 0.00 3.01
3576 5430 2.577450 CGGCATGTGCGAATAATCATG 58.423 47.619 0.00 0.00 43.26 3.07
3586 5440 1.713937 TTAGAATGGCGGCATGTGCG 61.714 55.000 26.50 0.00 43.26 5.34
3912 6061 7.097192 ACGCTCTTATATTTCTTCACAGAACA 58.903 34.615 0.00 0.00 38.86 3.18
3913 6062 7.527084 ACGCTCTTATATTTCTTCACAGAAC 57.473 36.000 0.00 0.00 38.86 3.01
3914 6063 8.547967 AAACGCTCTTATATTTCTTCACAGAA 57.452 30.769 0.00 0.00 37.24 3.02
3986 6135 9.549078 CTTTCTTTCCAGATTATTAGTACTCCC 57.451 37.037 0.00 0.00 0.00 4.30
4057 6211 3.838565 TGACATTTAAAAGCCTGGTCCA 58.161 40.909 0.00 0.00 0.00 4.02
4065 6219 9.304731 TGATATCAGCAAATGACATTTAAAAGC 57.695 29.630 12.98 11.96 41.91 3.51
4251 6411 1.464997 GCTTCAAGGTGCTTTAGACGG 59.535 52.381 0.00 0.00 0.00 4.79
4277 6437 3.953612 AGAGGACACATTTCAAAGTGCAA 59.046 39.130 0.00 0.00 39.30 4.08
4317 6477 2.828520 TCCAGAAAACACAACAGCCAAA 59.171 40.909 0.00 0.00 0.00 3.28
4347 6507 6.725364 ACATTCCTTGTTGTAATCCTGAGAT 58.275 36.000 0.00 0.00 33.74 2.75
4447 6609 9.263446 CTACCCAAGTACCCATATATAGCTTAA 57.737 37.037 0.00 0.00 0.00 1.85
4448 6610 8.404265 ACTACCCAAGTACCCATATATAGCTTA 58.596 37.037 0.00 0.00 36.36 3.09
4450 6612 6.812649 ACTACCCAAGTACCCATATATAGCT 58.187 40.000 0.00 0.00 36.36 3.32
4451 6613 6.896307 AGACTACCCAAGTACCCATATATAGC 59.104 42.308 0.00 0.00 39.07 2.97
4452 6614 8.896722 AAGACTACCCAAGTACCCATATATAG 57.103 38.462 0.00 0.00 39.07 1.31
4453 6615 9.317827 GAAAGACTACCCAAGTACCCATATATA 57.682 37.037 0.00 0.00 39.07 0.86
4454 6616 7.237055 GGAAAGACTACCCAAGTACCCATATAT 59.763 40.741 0.00 0.00 39.07 0.86
4455 6617 6.556116 GGAAAGACTACCCAAGTACCCATATA 59.444 42.308 0.00 0.00 39.07 0.86
4456 6618 5.368816 GGAAAGACTACCCAAGTACCCATAT 59.631 44.000 0.00 0.00 39.07 1.78
4457 6619 4.718276 GGAAAGACTACCCAAGTACCCATA 59.282 45.833 0.00 0.00 39.07 2.74
4458 6620 3.522343 GGAAAGACTACCCAAGTACCCAT 59.478 47.826 0.00 0.00 39.07 4.00
4459 6621 2.908351 GGAAAGACTACCCAAGTACCCA 59.092 50.000 0.00 0.00 39.07 4.51
4460 6622 3.179685 AGGAAAGACTACCCAAGTACCC 58.820 50.000 0.00 0.00 39.07 3.69
4461 6623 4.323333 GGAAGGAAAGACTACCCAAGTACC 60.323 50.000 0.00 0.00 39.07 3.34
4462 6624 4.323333 GGGAAGGAAAGACTACCCAAGTAC 60.323 50.000 0.00 0.00 39.07 2.73
4463 6625 3.842436 GGGAAGGAAAGACTACCCAAGTA 59.158 47.826 0.00 0.00 39.07 2.24
4464 6626 2.643304 GGGAAGGAAAGACTACCCAAGT 59.357 50.000 0.00 0.00 42.80 3.16
4465 6627 2.642807 TGGGAAGGAAAGACTACCCAAG 59.357 50.000 0.00 0.00 43.34 3.61
4466 6628 2.708759 TGGGAAGGAAAGACTACCCAA 58.291 47.619 0.00 0.00 43.34 4.12
4759 6922 7.422399 TGTTTCACAAAGTAAATAGTTCCTGC 58.578 34.615 0.00 0.00 0.00 4.85
4840 7003 7.596995 CAGCAGCAAGAGGAAACTATATACTAC 59.403 40.741 0.00 0.00 44.43 2.73
4982 7154 4.757149 CCATAATTCCGAAATCAGTCCCTC 59.243 45.833 0.00 0.00 0.00 4.30
5060 7232 2.420547 GCTGTCCTTCCATGCATCTGTA 60.421 50.000 0.00 0.00 0.00 2.74
5140 7312 0.744771 GCCTAGCGGTTCTTCAAGGG 60.745 60.000 0.00 0.00 0.00 3.95
5176 7348 3.625764 GGCATGAGTATTTAAAGGCGACA 59.374 43.478 0.00 0.00 0.00 4.35
5194 7366 2.497273 GGCACAAGGAATTTACTGGCAT 59.503 45.455 0.00 0.00 0.00 4.40
5256 7434 3.258228 ATTGCACGGGAGCTGCTGA 62.258 57.895 22.20 0.00 37.62 4.26
5864 8532 1.552792 GAGTTGGAGGAGTTGGAGGAG 59.447 57.143 0.00 0.00 0.00 3.69
5865 8533 1.645710 GAGTTGGAGGAGTTGGAGGA 58.354 55.000 0.00 0.00 0.00 3.71
5866 8534 0.615850 GGAGTTGGAGGAGTTGGAGG 59.384 60.000 0.00 0.00 0.00 4.30
5867 8535 0.615850 GGGAGTTGGAGGAGTTGGAG 59.384 60.000 0.00 0.00 0.00 3.86
5868 8536 0.840722 GGGGAGTTGGAGGAGTTGGA 60.841 60.000 0.00 0.00 0.00 3.53
5869 8537 1.685820 GGGGAGTTGGAGGAGTTGG 59.314 63.158 0.00 0.00 0.00 3.77
5870 8538 1.133809 TGGGGGAGTTGGAGGAGTTG 61.134 60.000 0.00 0.00 0.00 3.16
5871 8539 1.134438 GTGGGGGAGTTGGAGGAGTT 61.134 60.000 0.00 0.00 0.00 3.01
5872 8540 1.539124 GTGGGGGAGTTGGAGGAGT 60.539 63.158 0.00 0.00 0.00 3.85
5929 8597 2.928396 CACCCCCTTGTCCCGTCT 60.928 66.667 0.00 0.00 0.00 4.18
5953 8621 3.382832 AACACCCGCTCTCTCCCG 61.383 66.667 0.00 0.00 0.00 5.14
6065 8733 2.336809 CGCGGCATCCTCCTCTAC 59.663 66.667 0.00 0.00 0.00 2.59
6096 8764 1.544691 GACTGCTCTACAACGGGAGAA 59.455 52.381 0.00 0.00 0.00 2.87
6125 8793 2.028484 GCAAGGACGACCGTGACA 59.972 61.111 22.06 0.00 45.94 3.58
6131 8799 1.446272 CTCGAAGGCAAGGACGACC 60.446 63.158 0.00 0.00 0.00 4.79
6435 9103 6.959671 AAATGAGATTGAGTCGAGAGAAAC 57.040 37.500 0.00 0.00 45.01 2.78
6595 9264 3.207265 TGCCTGAAGCTAAACTGACAA 57.793 42.857 0.00 0.00 44.23 3.18
7497 10172 2.273449 CTGGGCCCCTACAGCAAG 59.727 66.667 22.27 2.57 0.00 4.01


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

AutoCloner maintained by Alex Coulton.