Multiple sequence alignment - TraesCS1D01G379200

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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 TraesCS1D01G379200 chr1D 100.000 4225 0 0 1 4225 455112723 455116947 0.000000e+00 7803.0
1 TraesCS1D01G379200 chr1B 90.658 1809 114 22 2433 4225 625809566 625811335 0.000000e+00 2353.0
2 TraesCS1D01G379200 chr1B 90.530 1584 91 31 109 1675 625808015 625809556 0.000000e+00 2039.0
3 TraesCS1D01G379200 chr1B 89.002 491 36 15 1414 1891 625777242 625777727 3.640000e-165 592.0
4 TraesCS1D01G379200 chr1B 89.139 267 24 4 1 264 625774808 625775072 1.130000e-85 327.0
5 TraesCS1D01G379200 chr1B 92.308 221 15 2 1020 1239 625775078 625775297 3.170000e-81 313.0
6 TraesCS1D01G379200 chr1A 90.480 1187 84 17 833 2003 549047451 549048624 0.000000e+00 1539.0
7 TraesCS1D01G379200 chr1A 90.844 1114 58 19 2686 3763 549054072 549055177 0.000000e+00 1452.0
8 TraesCS1D01G379200 chr1A 88.889 855 73 10 1 840 549045662 549046509 0.000000e+00 1033.0
9 TraesCS1D01G379200 chr1A 81.818 682 89 24 2023 2691 549048611 549049270 1.340000e-149 540.0
10 TraesCS1D01G379200 chr1A 91.667 72 3 2 3807 3876 549055313 549055383 3.480000e-16 97.1
11 TraesCS1D01G379200 chr7D 84.855 964 115 24 2273 3218 74599413 74600363 0.000000e+00 942.0
12 TraesCS1D01G379200 chr7D 77.954 948 153 26 765 1677 74597796 74598722 3.720000e-150 542.0
13 TraesCS1D01G379200 chr7D 80.978 552 60 27 1735 2273 176168802 176169321 3.060000e-106 396.0
14 TraesCS1D01G379200 chr7D 79.012 324 53 7 2989 3311 74867043 74867352 1.540000e-49 207.0
15 TraesCS1D01G379200 chr7A 84.440 964 119 23 2273 3218 78510625 78511575 0.000000e+00 920.0
16 TraesCS1D01G379200 chr7A 77.564 936 160 28 765 1677 78509022 78509930 1.740000e-143 520.0
17 TraesCS1D01G379200 chr7A 81.089 349 58 6 2995 3342 78564794 78565135 5.380000e-69 272.0
18 TraesCS1D01G379200 chr7A 84.651 215 25 5 2061 2273 178293647 178293439 1.540000e-49 207.0
19 TraesCS1D01G379200 chr7A 87.342 79 9 1 3904 3981 112248979 112249057 5.820000e-14 89.8
20 TraesCS1D01G379200 chr7B 84.746 944 114 24 2292 3218 18207509 18208439 0.000000e+00 918.0
21 TraesCS1D01G379200 chr7B 77.297 947 154 33 765 1677 18205889 18206808 6.310000e-138 501.0
22 TraesCS1D01G379200 chr7B 87.719 57 7 0 4039 4095 199291094 199291150 2.730000e-07 67.6
23 TraesCS1D01G379200 chr3D 84.564 149 23 0 3893 4041 63859177 63859325 9.460000e-32 148.0
24 TraesCS1D01G379200 chr2A 85.135 74 9 2 4036 4108 360872635 360872563 1.630000e-09 75.0
25 TraesCS1D01G379200 chr3B 100.000 28 0 0 481 508 188441501 188441528 8.000000e-03 52.8


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 TraesCS1D01G379200 chr1D 455112723 455116947 4224 False 7803.000000 7803 100.000000 1 4225 1 chr1D.!!$F1 4224
1 TraesCS1D01G379200 chr1B 625808015 625811335 3320 False 2196.000000 2353 90.594000 109 4225 2 chr1B.!!$F2 4116
2 TraesCS1D01G379200 chr1B 625774808 625777727 2919 False 410.666667 592 90.149667 1 1891 3 chr1B.!!$F1 1890
3 TraesCS1D01G379200 chr1A 549045662 549049270 3608 False 1037.333333 1539 87.062333 1 2691 3 chr1A.!!$F1 2690
4 TraesCS1D01G379200 chr1A 549054072 549055383 1311 False 774.550000 1452 91.255500 2686 3876 2 chr1A.!!$F2 1190
5 TraesCS1D01G379200 chr7D 74597796 74600363 2567 False 742.000000 942 81.404500 765 3218 2 chr7D.!!$F3 2453
6 TraesCS1D01G379200 chr7D 176168802 176169321 519 False 396.000000 396 80.978000 1735 2273 1 chr7D.!!$F2 538
7 TraesCS1D01G379200 chr7A 78509022 78511575 2553 False 720.000000 920 81.002000 765 3218 2 chr7A.!!$F3 2453
8 TraesCS1D01G379200 chr7B 18205889 18208439 2550 False 709.500000 918 81.021500 765 3218 2 chr7B.!!$F2 2453

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
231 233 0.108520 GTCAGGGGCGACGATGTTAA 60.109 55.0 0.0 0.0 0.0 2.01 F
985 1981 0.393132 GCTAGCTTCTGAACACCCCC 60.393 60.0 7.7 0.0 0.0 5.40 F
2576 5930 0.037790 GGGCAGAGATAGCTAAGCGG 60.038 60.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 4777 0.459934 GCACCACTAGAGCAGCTCAG 60.460 60.0 24.64 19.67 32.06 3.35 R
2711 6065 1.583556 TGCTAGAGCCAATCCCAAGA 58.416 50.0 0.00 0.00 41.18 3.02 R
3688 7087 0.390866 CGTCTGGAAGCATGAGCACT 60.391 55.0 0.00 0.00 45.49 4.40 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
23 24 1.211949 AGCGGCCCAGTACATATGTTT 59.788 47.619 14.77 0.00 0.00 2.83
60 61 5.078411 AGCTGTCAATCTGATACTCGTTT 57.922 39.130 0.00 0.00 0.00 3.60
69 70 9.678941 TCAATCTGATACTCGTTTGTCATATAC 57.321 33.333 0.00 0.00 0.00 1.47
70 71 8.630840 CAATCTGATACTCGTTTGTCATATACG 58.369 37.037 0.00 0.00 36.67 3.06
71 72 7.255491 TCTGATACTCGTTTGTCATATACGT 57.745 36.000 0.00 0.00 36.70 3.57
73 74 8.996271 TCTGATACTCGTTTGTCATATACGTAT 58.004 33.333 13.54 13.54 36.70 3.06
91 92 6.642683 ACGTATACAAGAAAAATCCTGTCG 57.357 37.500 3.32 0.00 0.00 4.35
94 95 8.192774 ACGTATACAAGAAAAATCCTGTCGATA 58.807 33.333 3.32 0.00 0.00 2.92
231 233 0.108520 GTCAGGGGCGACGATGTTAA 60.109 55.000 0.00 0.00 0.00 2.01
363 365 2.815211 GCCGCTGACGCTGATGAA 60.815 61.111 0.00 0.00 38.22 2.57
404 413 1.192146 AAGTTCGCTGGGCAGGAGTA 61.192 55.000 0.00 0.00 0.00 2.59
437 446 1.624865 GAGCTGCTTGCAGACACTCG 61.625 60.000 24.67 0.00 45.94 4.18
477 486 5.649395 TGCTTCTCTTCCCAGTTGAATAATG 59.351 40.000 0.00 0.00 0.00 1.90
512 521 8.303156 TGTAGTTGATTGTTGGTATTTGATTGG 58.697 33.333 0.00 0.00 0.00 3.16
519 528 6.656632 TGTTGGTATTTGATTGGCTTACAA 57.343 33.333 0.00 0.00 44.54 2.41
592 601 9.632807 ATTTAATATGTACAACACGTGCAAATT 57.367 25.926 17.22 0.00 43.90 1.82
675 684 8.939929 ACGAAACCATTAATAGCATCATATGAG 58.060 33.333 11.78 4.86 0.00 2.90
732 741 0.516877 CGCAATGGGTAGTGTGTGTG 59.483 55.000 0.00 0.00 0.00 3.82
745 754 2.110213 GTGTGCCACGTCTGGGAA 59.890 61.111 0.00 0.00 40.12 3.97
904 1871 1.929806 AATGTGACATGCTGCGCCAG 61.930 55.000 4.18 3.40 34.12 4.85
982 1978 2.159028 CCCTAGCTAGCTTCTGAACACC 60.159 54.545 24.88 0.00 0.00 4.16
984 1980 0.615850 AGCTAGCTTCTGAACACCCC 59.384 55.000 12.68 0.00 0.00 4.95
985 1981 0.393132 GCTAGCTTCTGAACACCCCC 60.393 60.000 7.70 0.00 0.00 5.40
986 1982 1.280457 CTAGCTTCTGAACACCCCCT 58.720 55.000 0.00 0.00 0.00 4.79
987 1983 1.208293 CTAGCTTCTGAACACCCCCTC 59.792 57.143 0.00 0.00 0.00 4.30
988 1984 1.002011 GCTTCTGAACACCCCCTCC 60.002 63.158 0.00 0.00 0.00 4.30
989 1985 1.685820 CTTCTGAACACCCCCTCCC 59.314 63.158 0.00 0.00 0.00 4.30
990 1986 1.850755 TTCTGAACACCCCCTCCCC 60.851 63.158 0.00 0.00 0.00 4.81
991 1987 3.339093 CTGAACACCCCCTCCCCC 61.339 72.222 0.00 0.00 0.00 5.40
1137 2133 0.459899 CTGGTGGATCGATCGTTCCA 59.540 55.000 33.72 33.72 40.50 3.53
1363 4110 3.154710 TCGAGTAAGGCTGTCAAGAAGA 58.845 45.455 0.00 0.00 0.00 2.87
1412 4161 6.113411 CACCGGAAGAAGACAGGTAAATTAT 58.887 40.000 9.46 0.00 34.42 1.28
1622 4467 2.289694 GCTGCCTGTGAGAGTAGGAAAA 60.290 50.000 0.00 0.00 36.11 2.29
1677 4522 4.652822 ACCTAACATCAAGGTTTGTCTCC 58.347 43.478 0.00 0.00 45.26 3.71
1708 4559 2.373169 ACTGAGGAGTCCAATGCTTCAA 59.627 45.455 12.86 0.00 0.00 2.69
1732 4583 2.685106 TTGTAGGCCCAAATGGTTCA 57.315 45.000 0.00 0.00 36.04 3.18
1779 4631 5.659440 TCAGTTTTGGAAGAAGCAAAAGT 57.341 34.783 0.00 0.00 33.34 2.66
1842 4715 4.595781 TGTACCTGTTGATTGGTAGGAAGT 59.404 41.667 0.00 0.00 39.22 3.01
1853 4727 3.774734 TGGTAGGAAGTGCTCTGTTAGA 58.225 45.455 0.00 0.00 0.00 2.10
1878 4755 3.366883 CCTGTCTGAAGTTCCTCTCTTCG 60.367 52.174 0.00 0.00 42.68 3.79
1900 4777 3.065925 GGAGTCATTAGTTGCTGCCAATC 59.934 47.826 0.00 0.00 32.75 2.67
1928 4805 2.226674 GCTCTAGTGGTGCCAAAACTTC 59.773 50.000 0.00 0.00 0.00 3.01
1937 4815 0.835971 GCCAAAACTTCCCCCACCAT 60.836 55.000 0.00 0.00 0.00 3.55
1942 4820 1.455822 AACTTCCCCCACCATTCTGA 58.544 50.000 0.00 0.00 0.00 3.27
1960 4838 3.909995 TCTGAATTCACTCTTCCCTGGAA 59.090 43.478 3.38 0.00 0.00 3.53
1962 4840 5.014544 TCTGAATTCACTCTTCCCTGGAAAT 59.985 40.000 3.38 0.00 33.34 2.17
1994 4872 5.068198 CCATTGCAAGCAATACCTGTAGAAT 59.932 40.000 18.81 0.00 43.92 2.40
2003 4881 8.839310 AGCAATACCTGTAGAATATGATTGTC 57.161 34.615 0.00 0.00 0.00 3.18
2004 4882 8.654997 AGCAATACCTGTAGAATATGATTGTCT 58.345 33.333 0.00 0.00 0.00 3.41
2005 4883 9.277783 GCAATACCTGTAGAATATGATTGTCTT 57.722 33.333 0.00 0.00 0.00 3.01
2010 4888 9.965902 ACCTGTAGAATATGATTGTCTTTCTTT 57.034 29.630 0.00 0.00 0.00 2.52
2031 4909 5.843673 TTTTTGCAAGGTGTAGAACATGA 57.156 34.783 0.00 0.00 0.00 3.07
2032 4910 6.403866 TTTTTGCAAGGTGTAGAACATGAT 57.596 33.333 0.00 0.00 0.00 2.45
2033 4911 6.403866 TTTTGCAAGGTGTAGAACATGATT 57.596 33.333 0.00 0.00 0.00 2.57
2034 4912 6.403866 TTTGCAAGGTGTAGAACATGATTT 57.596 33.333 0.00 0.00 0.00 2.17
2035 4913 6.403866 TTGCAAGGTGTAGAACATGATTTT 57.596 33.333 0.00 0.00 0.00 1.82
2044 4922 9.535878 GGTGTAGAACATGATTTTTAAAACCAA 57.464 29.630 0.00 0.00 0.00 3.67
2046 4924 9.535878 TGTAGAACATGATTTTTAAAACCAACC 57.464 29.630 0.00 0.00 0.00 3.77
2059 4944 8.485976 TTTAAAACCAACCTTTGAAGAATGTG 57.514 30.769 0.00 0.00 0.00 3.21
2106 4999 3.985127 TCAAGTTACGGAAGGGATCCTA 58.015 45.455 12.58 0.00 46.98 2.94
2187 5081 1.322442 GCCTTAGCCCATAAGCCAAG 58.678 55.000 0.00 0.00 39.76 3.61
2188 5082 1.133792 GCCTTAGCCCATAAGCCAAGA 60.134 52.381 0.00 0.00 39.76 3.02
2251 5594 6.418057 AGGCATCTGTAGAAGATCCTTTAG 57.582 41.667 0.00 0.00 44.24 1.85
2252 5595 4.994217 GGCATCTGTAGAAGATCCTTTAGC 59.006 45.833 0.00 0.00 44.24 3.09
2275 5618 5.041287 CAGAAATTAATCGAGCGAGTACCA 58.959 41.667 0.00 0.00 0.00 3.25
2285 5628 1.376609 GCGAGTACCATTTGCCCCTG 61.377 60.000 0.00 0.00 0.00 4.45
2356 5702 5.047802 AGGTAAATTTCATGGCAGAACACAG 60.048 40.000 0.00 0.00 0.00 3.66
2360 5706 4.998671 TTTCATGGCAGAACACAGAAAA 57.001 36.364 0.00 0.00 30.00 2.29
2364 5710 2.942804 TGGCAGAACACAGAAAATGGA 58.057 42.857 0.00 0.00 0.00 3.41
2367 5713 3.550842 GGCAGAACACAGAAAATGGACAC 60.551 47.826 0.00 0.00 0.00 3.67
2368 5714 3.316308 GCAGAACACAGAAAATGGACACT 59.684 43.478 0.00 0.00 0.00 3.55
2380 5726 9.793252 CAGAAAATGGACACTAATATTTTCCAG 57.207 33.333 14.23 7.07 44.52 3.86
2437 5787 7.504574 TCTCCCGAAAATACATCATAGTCTGTA 59.495 37.037 0.00 0.00 32.75 2.74
2454 5804 7.721286 AGTCTGTATACTATTCATGCTTTGC 57.279 36.000 4.17 0.00 0.00 3.68
2576 5930 0.037790 GGGCAGAGATAGCTAAGCGG 60.038 60.000 0.00 0.00 0.00 5.52
2650 6004 2.650196 GCAATTTGCACGGAGGCA 59.350 55.556 16.35 0.00 44.26 4.75
2662 6016 2.656069 GGAGGCAGACCGGCACTAA 61.656 63.158 0.00 0.00 44.47 2.24
2711 6065 7.162082 CCCTTCTACAGAACTACATCAAAAGT 58.838 38.462 0.00 0.00 0.00 2.66
2776 6133 3.446442 AGAACCTCCATTGTCAGCATT 57.554 42.857 0.00 0.00 0.00 3.56
2792 6149 1.606313 ATTTTCACCAGCACCCCCG 60.606 57.895 0.00 0.00 0.00 5.73
3122 6512 7.047271 TCGTAAACATTGAATCTGGATGATCA 58.953 34.615 0.00 0.00 33.57 2.92
3237 6630 3.141398 TGCAGCTAGTGGACAAGAAAAG 58.859 45.455 0.00 0.00 0.00 2.27
3373 6766 4.019174 ACAGGCAATAGAATGACCTTTGG 58.981 43.478 0.00 0.00 0.00 3.28
3378 6771 5.827797 GGCAATAGAATGACCTTTGGATGTA 59.172 40.000 0.00 0.00 0.00 2.29
3446 6839 7.468922 CATGTTGTATGTAGTACATGGACTG 57.531 40.000 21.47 14.01 42.63 3.51
3603 7002 9.692325 ATCAAAAGATAAAGAGAACCTAAGCAT 57.308 29.630 0.00 0.00 0.00 3.79
3688 7087 3.701040 GCAGAGGATATGCCCAAAAGAAA 59.299 43.478 0.00 0.00 37.73 2.52
3689 7088 4.202090 GCAGAGGATATGCCCAAAAGAAAG 60.202 45.833 0.00 0.00 37.73 2.62
3698 7097 2.680577 CCCAAAAGAAAGTGCTCATGC 58.319 47.619 0.00 0.00 40.20 4.06
3737 7136 1.262417 TTCAGACGACAGGCCACATA 58.738 50.000 5.01 0.00 0.00 2.29
3738 7137 0.817654 TCAGACGACAGGCCACATAG 59.182 55.000 5.01 0.00 0.00 2.23
3739 7138 0.532573 CAGACGACAGGCCACATAGT 59.467 55.000 5.01 0.00 0.00 2.12
3745 7145 2.479730 CGACAGGCCACATAGTACTCAC 60.480 54.545 5.01 0.00 0.00 3.51
3755 7155 1.541379 TAGTACTCACGCTTCCTGCA 58.459 50.000 0.00 0.00 43.06 4.41
3756 7156 0.244994 AGTACTCACGCTTCCTGCAG 59.755 55.000 6.78 6.78 43.06 4.41
3774 7174 5.182950 CCTGCAGTTTCATTACACACCAATA 59.817 40.000 13.81 0.00 0.00 1.90
3784 7184 5.957842 TTACACACCAATAGCTTCCAAAG 57.042 39.130 0.00 0.00 0.00 2.77
3882 7377 2.029380 GCAAAATAAAGGCGACCAACCT 60.029 45.455 0.00 0.00 40.02 3.50
3908 7403 1.156645 GGATGACACTGATGCTCGCC 61.157 60.000 0.00 0.00 0.00 5.54
3917 7412 2.079158 CTGATGCTCGCCTTTTTCTGA 58.921 47.619 0.00 0.00 0.00 3.27
3923 7418 5.643379 TGCTCGCCTTTTTCTGAATTTAT 57.357 34.783 0.00 0.00 0.00 1.40
3958 7453 1.463693 CGACGTACGTTCAGTGAGAGG 60.464 57.143 23.70 0.00 37.22 3.69
3963 7458 1.982660 ACGTTCAGTGAGAGGAGACA 58.017 50.000 0.00 0.00 0.00 3.41
3967 7462 4.202264 ACGTTCAGTGAGAGGAGACATTTT 60.202 41.667 0.00 0.00 0.00 1.82
3972 7467 2.917971 GTGAGAGGAGACATTTTCGTCG 59.082 50.000 0.00 0.00 40.98 5.12
4001 7496 6.907533 CGAATGCGTTTATGGTAATTTTGTC 58.092 36.000 0.00 0.00 0.00 3.18
4022 7517 7.381766 TGTCAATCTCAAAATGATGTACTGG 57.618 36.000 0.00 0.00 0.00 4.00
4024 7519 5.945191 TCAATCTCAAAATGATGTACTGGCA 59.055 36.000 0.00 0.00 0.00 4.92
4025 7520 6.604396 TCAATCTCAAAATGATGTACTGGCAT 59.396 34.615 0.00 0.00 0.00 4.40
4027 7522 7.741027 ATCTCAAAATGATGTACTGGCATAG 57.259 36.000 0.00 0.00 0.00 2.23
4031 7526 6.763135 TCAAAATGATGTACTGGCATAGTCTC 59.237 38.462 0.00 0.00 40.89 3.36
4061 7556 4.267928 GTGTGCGTTCATAAGGATGAGTAC 59.732 45.833 0.00 0.00 43.03 2.73
4083 7578 9.104965 AGTACATGTGCGTATGTATAAACATTT 57.895 29.630 9.11 0.00 44.07 2.32
4086 7581 8.059502 ACATGTGCGTATGTATAAACATTTACG 58.940 33.333 0.00 8.66 44.07 3.18
4087 7582 7.522901 TGTGCGTATGTATAAACATTTACGT 57.477 32.000 12.66 0.00 44.07 3.57
4102 7598 7.633361 ACATTTACGTCTGTACTGTGTTTAG 57.367 36.000 0.00 0.00 29.84 1.85
4107 7603 8.700722 TTACGTCTGTACTGTGTTTAGAAAAA 57.299 30.769 0.00 0.00 0.00 1.94
4126 7622 6.591448 AGAAAAATAGCAAAATACAGCAAGCC 59.409 34.615 0.00 0.00 0.00 4.35
4127 7623 4.391405 AATAGCAAAATACAGCAAGCCC 57.609 40.909 0.00 0.00 0.00 5.19
4128 7624 1.631405 AGCAAAATACAGCAAGCCCA 58.369 45.000 0.00 0.00 0.00 5.36
4129 7625 1.273327 AGCAAAATACAGCAAGCCCAC 59.727 47.619 0.00 0.00 0.00 4.61
4130 7626 1.981254 CAAAATACAGCAAGCCCACG 58.019 50.000 0.00 0.00 0.00 4.94
4131 7627 0.887933 AAAATACAGCAAGCCCACGG 59.112 50.000 0.00 0.00 0.00 4.94
4132 7628 0.251165 AAATACAGCAAGCCCACGGT 60.251 50.000 0.00 0.00 0.00 4.83
4151 7647 3.504134 CGGTACAGGGAGATCATACAGAG 59.496 52.174 0.00 0.00 0.00 3.35
4152 7648 4.730966 GGTACAGGGAGATCATACAGAGA 58.269 47.826 0.00 0.00 0.00 3.10
4154 7650 5.777732 GGTACAGGGAGATCATACAGAGATT 59.222 44.000 0.00 0.00 0.00 2.40
4193 7690 2.087646 GAATCACAGGGAAAGAGCCAC 58.912 52.381 0.00 0.00 0.00 5.01
4196 7693 0.178992 CACAGGGAAAGAGCCACCAA 60.179 55.000 0.00 0.00 0.00 3.67
4204 7701 0.679960 AAGAGCCACCAAATACGGGC 60.680 55.000 0.00 0.00 46.77 6.13
4217 7714 4.424711 CGGGCCCCAAGCTAGCAA 62.425 66.667 18.66 0.00 43.05 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.153513 GCACAACACAAACATATGTACTGG 58.846 41.667 9.21 6.75 30.84 4.00
42 43 6.893958 ATGACAAACGAGTATCAGATTGAC 57.106 37.500 0.00 0.00 33.17 3.18
69 70 6.880822 TCGACAGGATTTTTCTTGTATACG 57.119 37.500 0.00 0.00 29.85 3.06
73 74 9.582431 CTACTTATCGACAGGATTTTTCTTGTA 57.418 33.333 0.00 0.00 36.55 2.41
74 75 8.095169 ACTACTTATCGACAGGATTTTTCTTGT 58.905 33.333 0.00 0.00 36.55 3.16
75 76 8.480643 ACTACTTATCGACAGGATTTTTCTTG 57.519 34.615 0.00 0.00 36.55 3.02
94 95 9.593134 CTCTCTGCACTTGATTATAAACTACTT 57.407 33.333 0.00 0.00 0.00 2.24
106 107 3.974719 TCTAGACCTCTCTGCACTTGAT 58.025 45.455 0.00 0.00 0.00 2.57
231 233 0.251033 TCTTGCTTGCAGCCATGAGT 60.251 50.000 0.00 0.00 41.51 3.41
300 302 2.751436 TCTGGCGGGCATGAAAGC 60.751 61.111 4.16 0.00 0.00 3.51
360 362 0.874175 CGACCTCACTGTGCGTTTCA 60.874 55.000 2.12 0.00 0.00 2.69
363 365 1.143183 AACGACCTCACTGTGCGTT 59.857 52.632 15.01 15.01 39.95 4.84
404 413 1.506493 CAGCTCGAAGCAAACAGAGT 58.494 50.000 9.09 0.00 45.56 3.24
437 446 3.068873 AGAAGCAGGAAGACGATCATACC 59.931 47.826 0.00 0.00 0.00 2.73
477 486 6.430000 ACCAACAATCAACTACATAGGTTCAC 59.570 38.462 0.00 0.00 0.00 3.18
562 571 8.937884 TGCACGTGTTGTACATATTAAATAAGT 58.062 29.630 18.38 0.00 0.00 2.24
563 572 9.762062 TTGCACGTGTTGTACATATTAAATAAG 57.238 29.630 18.38 0.00 0.00 1.73
566 575 9.632807 AATTTGCACGTGTTGTACATATTAAAT 57.367 25.926 18.38 0.00 27.73 1.40
571 580 9.710979 GTATTAATTTGCACGTGTTGTACATAT 57.289 29.630 18.38 3.99 0.00 1.78
572 581 8.718734 TGTATTAATTTGCACGTGTTGTACATA 58.281 29.630 18.38 1.61 0.00 2.29
575 584 9.544314 TTATGTATTAATTTGCACGTGTTGTAC 57.456 29.630 18.38 10.93 0.00 2.90
623 632 6.647212 TCTATGTGATCAAAAGTAAGCACG 57.353 37.500 0.00 0.00 0.00 5.34
732 741 0.663153 GCATTATTCCCAGACGTGGC 59.337 55.000 0.00 0.00 43.44 5.01
739 748 7.889469 ACTAATAAAGCATGCATTATTCCCAG 58.111 34.615 32.69 27.27 33.62 4.45
925 1892 4.384647 GGATGATGCTTCCTCTTTACCTGT 60.385 45.833 5.16 0.00 0.00 4.00
958 1943 0.760945 TCAGAAGCTAGCTAGGGGGC 60.761 60.000 19.70 8.70 0.00 5.80
994 1990 2.373169 AGCAACTGAAACCCATGAGAGA 59.627 45.455 0.00 0.00 0.00 3.10
998 1994 2.238521 GGAAGCAACTGAAACCCATGA 58.761 47.619 0.00 0.00 0.00 3.07
1137 2133 6.182627 TGACTCATGATAGAAGGTTGCAAAT 58.817 36.000 0.00 0.00 0.00 2.32
1363 4110 4.021192 CCATTGCCCTTTGACAACATTAGT 60.021 41.667 0.00 0.00 0.00 2.24
1412 4161 9.703892 ATTTAACAAAGCATGCATAAACAGTTA 57.296 25.926 21.98 14.38 30.80 2.24
1609 4454 5.012046 TCTCTGCATTGTTTTCCTACTCTCA 59.988 40.000 0.00 0.00 0.00 3.27
1610 4455 5.482908 TCTCTGCATTGTTTTCCTACTCTC 58.517 41.667 0.00 0.00 0.00 3.20
1622 4467 2.490903 GTGCCATCTTTCTCTGCATTGT 59.509 45.455 0.00 0.00 34.04 2.71
1677 4522 3.134458 GGACTCCTCAGTTCAAACAGTG 58.866 50.000 0.00 0.00 30.63 3.66
1708 4559 5.723887 TGAACCATTTGGGCCTACAATTTAT 59.276 36.000 4.53 0.00 42.05 1.40
1760 4612 7.770801 ATAACACTTTTGCTTCTTCCAAAAC 57.229 32.000 0.00 0.00 37.28 2.43
1794 4656 5.440234 CGTACAGCAGATACAGGATTAGT 57.560 43.478 0.00 0.00 0.00 2.24
1842 4715 2.762887 CAGACAGGGATCTAACAGAGCA 59.237 50.000 0.00 0.00 30.96 4.26
1853 4727 3.103742 GAGAGGAACTTCAGACAGGGAT 58.896 50.000 0.00 0.00 41.55 3.85
1878 4755 2.113860 TGGCAGCAACTAATGACTCC 57.886 50.000 0.00 0.00 0.00 3.85
1900 4777 0.459934 GCACCACTAGAGCAGCTCAG 60.460 60.000 24.64 19.67 32.06 3.35
1928 4805 2.102578 GTGAATTCAGAATGGTGGGGG 58.897 52.381 8.80 0.00 36.16 5.40
1937 4815 3.909995 TCCAGGGAAGAGTGAATTCAGAA 59.090 43.478 8.80 0.00 0.00 3.02
1942 4820 6.210185 CAGAAATTTCCAGGGAAGAGTGAATT 59.790 38.462 14.61 0.00 35.38 2.17
2009 4887 5.843673 TCATGTTCTACACCTTGCAAAAA 57.156 34.783 0.00 0.00 0.00 1.94
2010 4888 6.403866 AATCATGTTCTACACCTTGCAAAA 57.596 33.333 0.00 0.00 0.00 2.44
2011 4889 6.403866 AAATCATGTTCTACACCTTGCAAA 57.596 33.333 0.00 0.00 0.00 3.68
2012 4890 6.403866 AAAATCATGTTCTACACCTTGCAA 57.596 33.333 0.00 0.00 0.00 4.08
2013 4891 6.403866 AAAAATCATGTTCTACACCTTGCA 57.596 33.333 0.00 0.00 0.00 4.08
2014 4892 8.810652 TTTAAAAATCATGTTCTACACCTTGC 57.189 30.769 0.00 0.00 0.00 4.01
2016 4894 9.758651 GGTTTTAAAAATCATGTTCTACACCTT 57.241 29.630 1.31 0.00 0.00 3.50
2017 4895 8.919145 TGGTTTTAAAAATCATGTTCTACACCT 58.081 29.630 1.31 0.00 0.00 4.00
2018 4896 9.535878 TTGGTTTTAAAAATCATGTTCTACACC 57.464 29.630 1.31 0.00 0.00 4.16
2020 4898 9.535878 GGTTGGTTTTAAAAATCATGTTCTACA 57.464 29.630 1.31 0.00 0.00 2.74
2021 4899 9.758651 AGGTTGGTTTTAAAAATCATGTTCTAC 57.241 29.630 1.31 0.00 0.00 2.59
2023 4901 9.679661 AAAGGTTGGTTTTAAAAATCATGTTCT 57.320 25.926 1.31 0.00 0.00 3.01
2024 4902 9.715123 CAAAGGTTGGTTTTAAAAATCATGTTC 57.285 29.630 1.31 0.00 0.00 3.18
2025 4903 9.454859 TCAAAGGTTGGTTTTAAAAATCATGTT 57.545 25.926 1.31 0.00 0.00 2.71
2026 4904 9.454859 TTCAAAGGTTGGTTTTAAAAATCATGT 57.545 25.926 1.31 0.00 0.00 3.21
2027 4905 9.934190 CTTCAAAGGTTGGTTTTAAAAATCATG 57.066 29.630 1.31 0.72 0.00 3.07
2028 4906 9.898152 TCTTCAAAGGTTGGTTTTAAAAATCAT 57.102 25.926 1.31 0.00 0.00 2.45
2029 4907 9.726438 TTCTTCAAAGGTTGGTTTTAAAAATCA 57.274 25.926 1.31 1.90 0.00 2.57
2032 4910 9.508642 ACATTCTTCAAAGGTTGGTTTTAAAAA 57.491 25.926 1.31 0.00 0.00 1.94
2033 4911 8.940952 CACATTCTTCAAAGGTTGGTTTTAAAA 58.059 29.630 0.00 0.00 0.00 1.52
2034 4912 7.065204 GCACATTCTTCAAAGGTTGGTTTTAAA 59.935 33.333 0.00 0.00 0.00 1.52
2035 4913 6.536941 GCACATTCTTCAAAGGTTGGTTTTAA 59.463 34.615 0.00 0.00 0.00 1.52
2044 4922 5.072741 ACTACATGCACATTCTTCAAAGGT 58.927 37.500 0.00 0.00 0.00 3.50
2046 4924 7.132694 TGTACTACATGCACATTCTTCAAAG 57.867 36.000 0.00 0.00 0.00 2.77
2142 5035 9.793259 CCCAAGCCAAAAGATATCTTACTAATA 57.207 33.333 18.23 0.00 34.61 0.98
2222 5116 6.529220 GGATCTTCTACAGATGCCTAACAAT 58.471 40.000 0.00 0.00 43.12 2.71
2251 5594 4.085004 GGTACTCGCTCGATTAATTTCTGC 60.085 45.833 0.00 0.00 0.00 4.26
2252 5595 5.041287 TGGTACTCGCTCGATTAATTTCTG 58.959 41.667 0.00 0.00 0.00 3.02
2275 5618 7.070696 AGACTTTTTAAGTTAACAGGGGCAAAT 59.929 33.333 8.61 0.00 43.03 2.32
2332 5676 4.832266 TGTGTTCTGCCATGAAATTTACCT 59.168 37.500 0.00 0.00 0.00 3.08
2410 5758 6.865726 CAGACTATGATGTATTTTCGGGAGAG 59.134 42.308 0.00 0.00 41.75 3.20
2412 5760 6.516718 ACAGACTATGATGTATTTTCGGGAG 58.483 40.000 0.00 0.00 0.00 4.30
2662 6016 3.102204 CCTGATTTGGGATTCTTGGCTT 58.898 45.455 0.00 0.00 0.00 4.35
2711 6065 1.583556 TGCTAGAGCCAATCCCAAGA 58.416 50.000 0.00 0.00 41.18 3.02
2776 6133 3.172106 TCGGGGGTGCTGGTGAAA 61.172 61.111 0.00 0.00 0.00 2.69
2792 6149 3.376859 TCATATGTGCCCGATTTTGTGTC 59.623 43.478 1.90 0.00 0.00 3.67
3052 6442 9.893975 TCATATCCATATCTATCTCATGGTCAT 57.106 33.333 0.00 0.00 40.18 3.06
3122 6512 0.968901 CTGCCAGCATCACCAATGGT 60.969 55.000 0.00 0.00 46.92 3.55
3146 6536 3.096489 TGCACAGTTTTGATTTCTGGC 57.904 42.857 0.00 0.00 34.02 4.85
3313 6706 8.237949 AGAAGGTCGTCATATCATCTATAAACG 58.762 37.037 0.00 0.00 35.88 3.60
3314 6707 9.347934 CAGAAGGTCGTCATATCATCTATAAAC 57.652 37.037 0.00 0.00 0.00 2.01
3455 6848 8.579006 ACACTGATTCAACATGTAATCAAACAT 58.421 29.630 19.61 7.79 40.56 2.71
3587 6982 9.490379 CGGTAATATTATGCTTAGGTTCTCTTT 57.510 33.333 0.00 0.00 0.00 2.52
3660 7059 1.349026 GGGCATATCCTCTGCTTGCTA 59.651 52.381 0.00 0.00 39.60 3.49
3688 7087 0.390866 CGTCTGGAAGCATGAGCACT 60.391 55.000 0.00 0.00 45.49 4.40
3689 7088 0.671781 ACGTCTGGAAGCATGAGCAC 60.672 55.000 0.00 0.00 45.49 4.40
3698 7097 4.862574 TGAATATGTCGAAACGTCTGGAAG 59.137 41.667 0.00 0.00 0.00 3.46
3755 7155 6.151144 GGAAGCTATTGGTGTGTAATGAAACT 59.849 38.462 0.00 0.00 0.00 2.66
3756 7156 6.072175 TGGAAGCTATTGGTGTGTAATGAAAC 60.072 38.462 0.00 0.00 0.00 2.78
3774 7174 8.302438 CAAAAACTGATATTCTCTTTGGAAGCT 58.698 33.333 0.00 0.00 0.00 3.74
3812 7304 4.699522 GCTCGCCCCGGTGTTTCT 62.700 66.667 0.00 0.00 0.00 2.52
3869 7363 2.113139 CCACAGGTTGGTCGCCTT 59.887 61.111 0.00 0.00 41.10 4.35
3882 7377 2.781923 CATCAGTGTCATCCAACCACA 58.218 47.619 0.00 0.00 0.00 4.17
3934 7429 2.872925 CTGAACGTACGTCGCCGG 60.873 66.667 23.05 14.56 44.19 6.13
3941 7436 2.074576 TCTCCTCTCACTGAACGTACG 58.925 52.381 15.01 15.01 0.00 3.67
3943 7438 3.136009 TGTCTCCTCTCACTGAACGTA 57.864 47.619 0.00 0.00 0.00 3.57
3944 7439 1.982660 TGTCTCCTCTCACTGAACGT 58.017 50.000 0.00 0.00 0.00 3.99
3978 7473 7.804614 TGACAAAATTACCATAAACGCATTC 57.195 32.000 0.00 0.00 0.00 2.67
3981 7476 7.598278 AGATTGACAAAATTACCATAAACGCA 58.402 30.769 0.00 0.00 0.00 5.24
3997 7492 7.575532 GCCAGTACATCATTTTGAGATTGACAA 60.576 37.037 0.00 0.00 0.00 3.18
3998 7493 6.127925 GCCAGTACATCATTTTGAGATTGACA 60.128 38.462 0.00 0.00 0.00 3.58
3999 7494 6.127925 TGCCAGTACATCATTTTGAGATTGAC 60.128 38.462 0.00 0.00 0.00 3.18
4001 7496 6.198650 TGCCAGTACATCATTTTGAGATTG 57.801 37.500 0.00 0.00 0.00 2.67
4017 7512 5.720041 ACACCTTTAAGAGACTATGCCAGTA 59.280 40.000 0.00 0.00 37.72 2.74
4020 7515 4.832248 CACACCTTTAAGAGACTATGCCA 58.168 43.478 0.00 0.00 0.00 4.92
4022 7517 3.307242 CGCACACCTTTAAGAGACTATGC 59.693 47.826 0.00 0.00 0.00 3.14
4024 7519 4.803098 ACGCACACCTTTAAGAGACTAT 57.197 40.909 0.00 0.00 0.00 2.12
4025 7520 4.038282 TGAACGCACACCTTTAAGAGACTA 59.962 41.667 0.00 0.00 0.00 2.59
4027 7522 3.128349 TGAACGCACACCTTTAAGAGAC 58.872 45.455 0.00 0.00 0.00 3.36
4031 7526 4.693566 TCCTTATGAACGCACACCTTTAAG 59.306 41.667 0.00 0.00 0.00 1.85
4061 7556 8.059502 ACGTAAATGTTTATACATACGCACATG 58.940 33.333 16.57 0.00 44.63 3.21
4083 7578 8.876275 ATTTTTCTAAACACAGTACAGACGTA 57.124 30.769 0.00 0.00 0.00 3.57
4084 7579 7.781548 ATTTTTCTAAACACAGTACAGACGT 57.218 32.000 0.00 0.00 0.00 4.34
4085 7580 7.950496 GCTATTTTTCTAAACACAGTACAGACG 59.050 37.037 0.00 0.00 0.00 4.18
4086 7581 8.770828 TGCTATTTTTCTAAACACAGTACAGAC 58.229 33.333 0.00 0.00 0.00 3.51
4087 7582 8.896320 TGCTATTTTTCTAAACACAGTACAGA 57.104 30.769 0.00 0.00 0.00 3.41
4102 7598 6.183360 GGGCTTGCTGTATTTTGCTATTTTTC 60.183 38.462 0.00 0.00 0.00 2.29
4107 7603 3.131046 GTGGGCTTGCTGTATTTTGCTAT 59.869 43.478 0.00 0.00 0.00 2.97
4126 7622 1.414158 ATGATCTCCCTGTACCGTGG 58.586 55.000 0.00 0.00 0.00 4.94
4127 7623 2.956333 TGTATGATCTCCCTGTACCGTG 59.044 50.000 0.00 0.00 0.00 4.94
4128 7624 3.117625 TCTGTATGATCTCCCTGTACCGT 60.118 47.826 0.00 0.00 0.00 4.83
4129 7625 3.487372 TCTGTATGATCTCCCTGTACCG 58.513 50.000 0.00 0.00 0.00 4.02
4130 7626 4.730966 TCTCTGTATGATCTCCCTGTACC 58.269 47.826 0.00 0.00 0.00 3.34
4131 7627 6.295011 CCAATCTCTGTATGATCTCCCTGTAC 60.295 46.154 0.00 0.00 0.00 2.90
4132 7628 5.777223 CCAATCTCTGTATGATCTCCCTGTA 59.223 44.000 0.00 0.00 0.00 2.74
4151 7647 3.268023 CCTGTAACAGGTCCTCCAATC 57.732 52.381 0.00 0.00 45.82 2.67
4193 7690 2.423064 GCTTGGGGCCCGTATTTGG 61.423 63.158 19.83 2.37 34.27 3.28
4196 7693 1.837090 CTAGCTTGGGGCCCGTATT 59.163 57.895 19.83 6.38 43.05 1.89
4204 7701 2.825836 CGCCTTGCTAGCTTGGGG 60.826 66.667 21.69 21.69 0.00 4.96


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

AutoCloner maintained by Alex Coulton.