Multiple sequence alignment - TraesCS1B01G071400

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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 TraesCS1B01G071400 chr1B 100.000 5537 0 0 640 6176 56310296 56315832 0.000000e+00 10226.0
1 TraesCS1B01G071400 chr1B 100.000 227 0 0 1 227 56309657 56309883 2.660000e-113 420.0
2 TraesCS1B01G071400 chr1B 96.059 203 4 3 4850 5052 56314443 56314641 1.660000e-85 327.0
3 TraesCS1B01G071400 chr1B 96.059 203 4 3 4787 4985 56314506 56314708 1.660000e-85 327.0
4 TraesCS1B01G071400 chr1B 94.286 140 4 2 4913 5052 56314443 56314578 1.740000e-50 211.0
5 TraesCS1B01G071400 chr1B 94.286 140 4 2 4787 4922 56314569 56314708 1.740000e-50 211.0
6 TraesCS1B01G071400 chr1B 92.208 77 2 2 4976 5052 56314443 56314515 8.470000e-19 106.0
7 TraesCS1B01G071400 chr1D 96.114 4375 95 29 666 4982 36533210 36537567 0.000000e+00 7068.0
8 TraesCS1B01G071400 chr1D 97.234 687 18 1 4851 5536 36537370 36538056 0.000000e+00 1162.0
9 TraesCS1B01G071400 chr1D 94.433 503 14 8 5685 6176 36538366 36538865 0.000000e+00 761.0
10 TraesCS1B01G071400 chr1D 94.714 227 11 1 2 227 36532653 36532879 9.850000e-93 351.0
11 TraesCS1B01G071400 chr1D 94.853 136 4 1 4787 4919 36537432 36537567 6.270000e-50 209.0
12 TraesCS1B01G071400 chr1D 92.806 139 6 2 4914 5052 36537370 36537504 1.360000e-46 198.0
13 TraesCS1B01G071400 chr1D 93.333 135 7 2 5530 5662 36538246 36538380 1.360000e-46 198.0
14 TraesCS1B01G071400 chr1D 94.521 73 1 1 4787 4856 36537495 36537567 6.550000e-20 110.0
15 TraesCS1B01G071400 chr1D 90.625 64 6 0 3429 3492 36535957 36536020 1.100000e-12 86.1
16 TraesCS1B01G071400 chr1D 100.000 33 0 0 5656 5688 405368497 405368465 1.860000e-05 62.1
17 TraesCS1B01G071400 chr1A 95.517 4350 116 32 707 4985 35931662 35936003 0.000000e+00 6879.0
18 TraesCS1B01G071400 chr1A 96.825 693 14 4 4851 5536 35935796 35936487 0.000000e+00 1151.0
19 TraesCS1B01G071400 chr1A 94.600 500 13 9 5686 6176 35936796 35937290 0.000000e+00 761.0
20 TraesCS1B01G071400 chr1A 92.952 227 9 6 2 227 35931184 35931404 2.150000e-84 324.0
21 TraesCS1B01G071400 chr1A 95.775 142 2 3 4914 5052 35935796 35935936 6.230000e-55 226.0
22 TraesCS1B01G071400 chr1A 93.706 143 2 3 4787 4922 35935861 35936003 2.260000e-49 207.0
23 TraesCS1B01G071400 chr1A 93.284 134 7 2 5530 5662 35936677 35936809 4.880000e-46 196.0
24 TraesCS1B01G071400 chr1A 97.368 76 1 1 4977 5052 35935796 35935870 1.810000e-25 128.0
25 TraesCS1B01G071400 chr1A 93.506 77 1 2 4787 4859 35935927 35936003 1.820000e-20 111.0
26 TraesCS1B01G071400 chr2D 97.508 321 7 1 5717 6036 90783425 90783105 1.170000e-151 547.0
27 TraesCS1B01G071400 chr2D 96.026 302 11 1 5236 5536 90783997 90783696 2.000000e-134 490.0
28 TraesCS1B01G071400 chr2D 94.737 114 5 1 5530 5642 90783529 90783416 6.360000e-40 176.0
29 TraesCS1B01G071400 chr2D 97.222 36 1 0 5659 5694 430605553 430605588 1.860000e-05 62.1
30 TraesCS1B01G071400 chr7B 94.949 198 5 3 4421 4617 159181692 159181885 7.780000e-79 305.0
31 TraesCS1B01G071400 chr7B 99.020 102 1 0 4280 4381 159181591 159181692 3.800000e-42 183.0
32 TraesCS1B01G071400 chr6B 97.297 37 1 0 5653 5689 646239179 646239143 5.170000e-06 63.9
33 TraesCS1B01G071400 chr5D 100.000 33 0 0 5656 5688 446472595 446472563 1.860000e-05 62.1
34 TraesCS1B01G071400 chr5B 94.737 38 2 0 5659 5696 13175888 13175925 6.690000e-05 60.2
35 TraesCS1B01G071400 chr4D 94.737 38 2 0 5651 5688 320108440 320108403 6.690000e-05 60.2
36 TraesCS1B01G071400 chr7D 94.737 38 0 2 5652 5689 342410918 342410953 2.400000e-04 58.4
37 TraesCS1B01G071400 chr2A 92.500 40 2 1 5649 5688 438523251 438523289 8.650000e-04 56.5
38 TraesCS1B01G071400 chr2A 90.698 43 2 2 5648 5688 675305800 675305842 8.650000e-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 TraesCS1B01G071400 chr1B 56309657 56315832 6175 False 1689.714286 10226 96.128286 1 6176 7 chr1B.!!$F1 6175
1 TraesCS1B01G071400 chr1D 36532653 36538865 6212 False 1127.011111 7068 94.292556 2 6176 9 chr1D.!!$F1 6174
2 TraesCS1B01G071400 chr1A 35931184 35937290 6106 False 1109.222222 6879 94.837000 2 6176 9 chr1A.!!$F1 6174
3 TraesCS1B01G071400 chr2D 90783105 90783997 892 True 404.333333 547 96.090333 5236 6036 3 chr2D.!!$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
974 1153 0.036010 CTGAGGATTGGTCTTGCGGT 60.036 55.0 0.00 0.00 0.00 5.68 F
975 1154 0.321564 TGAGGATTGGTCTTGCGGTG 60.322 55.0 0.00 0.00 0.00 4.94 F
1742 1951 0.614415 ACTGACTCAGAGAGCAGGGG 60.614 60.0 21.23 5.94 37.77 4.79 F
1887 2096 0.912486 AGTACATTGGAGGGTCTGGC 59.088 55.0 0.00 0.00 0.00 4.85 F
3488 3697 0.178941 ACCGAGGTTACTCCAGTGGT 60.179 55.0 9.54 0.00 40.77 4.16 F
3624 3869 0.035317 AGACCGTGCAGAGCAATTCA 59.965 50.0 0.00 0.00 41.47 2.57 F
4732 4977 0.322008 GCTGGAAGGTGACCTTGAGG 60.322 60.0 23.60 11.63 44.82 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2468 1.531365 CTGGGCAGCTTTTCCACCA 60.531 57.895 0.00 0.00 0.00 4.17 R
2960 3169 2.300152 TCTGGTGACCTCAGTGATTCAC 59.700 50.000 19.85 19.85 38.11 3.18 R
3440 3649 0.101399 CGTAGCTGCCACTGGAGTAG 59.899 60.000 0.00 0.00 0.00 2.57 R
3499 3708 0.835941 CTGTTCTCCTCCCCATCAGG 59.164 60.000 0.00 0.00 0.00 3.86 R
4902 5150 0.111061 TTGCATCAGCTGTCACCCTT 59.889 50.000 14.67 0.00 42.74 3.95 R
4903 5151 0.322277 CTTGCATCAGCTGTCACCCT 60.322 55.000 14.67 0.00 42.74 4.34 R
5991 6446 1.002430 CTGCACAAAGCCACTAGGAGA 59.998 52.381 0.00 0.00 44.83 3.71 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
25 26 2.095008 TGAAGCTAAGCTCACTCACTCG 60.095 50.000 0.00 0.00 38.25 4.18
26 27 0.172352 AGCTAAGCTCACTCACTCGC 59.828 55.000 0.00 0.00 30.62 5.03
100 101 4.278513 CCCCACCGGCCAGAACAA 62.279 66.667 0.00 0.00 0.00 2.83
743 900 4.928140 TATCCGCCTCCCGTCCCC 62.928 72.222 0.00 0.00 34.38 4.81
796 960 1.227176 CGCGCTAGGGTTAGGGTTC 60.227 63.158 5.56 0.00 40.82 3.62
846 1020 3.265791 CTTTCTCCGGTGAGATTTCCTG 58.734 50.000 6.29 0.00 46.75 3.86
848 1022 2.257207 TCTCCGGTGAGATTTCCTGTT 58.743 47.619 0.00 0.00 42.73 3.16
860 1034 2.265589 TTCCTGTTCCCTTTCCGTTC 57.734 50.000 0.00 0.00 0.00 3.95
866 1040 1.392510 GTTCCCTTTCCGTTCGATTCG 59.607 52.381 0.00 0.00 0.00 3.34
867 1041 0.738412 TCCCTTTCCGTTCGATTCGC 60.738 55.000 0.00 0.00 0.00 4.70
868 1042 1.343821 CCTTTCCGTTCGATTCGCG 59.656 57.895 0.00 0.00 42.69 5.87
869 1043 1.343821 CTTTCCGTTCGATTCGCGG 59.656 57.895 16.05 16.05 46.12 6.46
870 1044 2.020836 CTTTCCGTTCGATTCGCGGG 62.021 60.000 20.10 12.45 44.97 6.13
907 1081 2.442272 CGGAGGAGTGGGGTCGAT 60.442 66.667 0.00 0.00 0.00 3.59
961 1140 0.380378 GCGTGTGTTTTTGCTGAGGA 59.620 50.000 0.00 0.00 0.00 3.71
967 1146 3.068024 TGTGTTTTTGCTGAGGATTGGTC 59.932 43.478 0.00 0.00 0.00 4.02
969 1148 3.960102 TGTTTTTGCTGAGGATTGGTCTT 59.040 39.130 0.00 0.00 0.00 3.01
971 1150 1.538047 TTGCTGAGGATTGGTCTTGC 58.462 50.000 0.00 0.00 0.00 4.01
972 1151 0.674581 TGCTGAGGATTGGTCTTGCG 60.675 55.000 0.00 0.00 0.00 4.85
973 1152 1.372087 GCTGAGGATTGGTCTTGCGG 61.372 60.000 0.00 0.00 0.00 5.69
974 1153 0.036010 CTGAGGATTGGTCTTGCGGT 60.036 55.000 0.00 0.00 0.00 5.68
975 1154 0.321564 TGAGGATTGGTCTTGCGGTG 60.322 55.000 0.00 0.00 0.00 4.94
976 1155 1.002134 AGGATTGGTCTTGCGGTGG 60.002 57.895 0.00 0.00 0.00 4.61
977 1156 1.303317 GGATTGGTCTTGCGGTGGT 60.303 57.895 0.00 0.00 0.00 4.16
1086 1268 3.894947 GAGGACGAGGAGGAGCGC 61.895 72.222 0.00 0.00 0.00 5.92
1203 1412 1.617947 GGATGGGGTCTGACGAGCTT 61.618 60.000 1.07 0.00 37.77 3.74
1293 1502 1.227946 GGAGCTCTACGACCTCCCT 59.772 63.158 14.64 0.00 39.36 4.20
1353 1562 2.436292 CTCTCCGAGGACGACCGT 60.436 66.667 0.00 0.00 42.66 4.83
1518 1727 2.753043 ATCGTCCTGTACCGCCGT 60.753 61.111 0.00 0.00 0.00 5.68
1576 1785 3.134623 CCATCTGCAGAGGTACCACAATA 59.865 47.826 25.35 0.00 0.00 1.90
1742 1951 0.614415 ACTGACTCAGAGAGCAGGGG 60.614 60.000 21.23 5.94 37.77 4.79
1887 2096 0.912486 AGTACATTGGAGGGTCTGGC 59.088 55.000 0.00 0.00 0.00 4.85
2300 2509 4.657814 ATAAAGCTCCCAAAGTGGAAGA 57.342 40.909 0.00 0.00 40.96 2.87
2386 2595 1.134670 GCGATTACAGGAGCAGGAAGT 60.135 52.381 0.00 0.00 0.00 3.01
2960 3169 2.621338 TGATAGCAACGAGAAAGCCAG 58.379 47.619 0.00 0.00 0.00 4.85
3087 3296 2.960170 GCAAGTTGCAGCTCTGGG 59.040 61.111 22.90 0.00 44.26 4.45
3122 3331 7.544217 GCAAAAAGGAAGAGTTGAACTTACAAA 59.456 33.333 0.00 0.00 31.27 2.83
3129 3338 5.123936 AGAGTTGAACTTACAAACCTGGAC 58.876 41.667 0.00 0.00 0.00 4.02
3171 3380 2.257207 TCTGGTCCAAAGGTGGTAGAG 58.743 52.381 0.00 0.00 46.11 2.43
3327 3536 7.686434 AGAAGTATGTACCAATTACACCAACT 58.314 34.615 0.00 0.00 43.71 3.16
3372 3581 2.857592 TCGTACATCTTCTAACCGCC 57.142 50.000 0.00 0.00 0.00 6.13
3420 3629 1.147153 GGATACTCCAGTGGCAGCC 59.853 63.158 3.66 3.66 36.28 4.85
3433 3642 2.646175 GCAGCCACGGTCACTCCTA 61.646 63.158 0.00 0.00 0.00 2.94
3440 3649 0.966370 ACGGTCACTCCTACTGAGGC 60.966 60.000 0.00 0.00 46.01 4.70
3471 3680 0.739561 CAGCTACGGTCACTCCTACC 59.260 60.000 0.00 0.00 0.00 3.18
3488 3697 0.178941 ACCGAGGTTACTCCAGTGGT 60.179 55.000 9.54 0.00 40.77 4.16
3624 3869 0.035317 AGACCGTGCAGAGCAATTCA 59.965 50.000 0.00 0.00 41.47 2.57
3631 3876 1.660560 GCAGAGCAATTCACCGGCAT 61.661 55.000 0.00 0.00 0.00 4.40
3652 3897 6.803807 GGCATTAACTGTTCAAGATCTTGTTC 59.196 38.462 29.80 23.36 41.16 3.18
3654 3899 8.025445 GCATTAACTGTTCAAGATCTTGTTCAT 58.975 33.333 29.80 18.59 41.16 2.57
3819 4064 3.192633 ACAAGTCGAACAAAAGCTGGTTT 59.807 39.130 0.00 0.00 0.00 3.27
3843 4088 2.360475 GGTCCACTGCCTTCTGCC 60.360 66.667 0.00 0.00 40.16 4.85
4266 4511 2.203070 GATCGCCCTCCGCATGTT 60.203 61.111 0.00 0.00 37.30 2.71
4710 4955 4.080863 GGTGTTCAGGATCCATCTAACAGT 60.081 45.833 15.82 0.00 30.59 3.55
4732 4977 0.322008 GCTGGAAGGTGACCTTGAGG 60.322 60.000 23.60 11.63 44.82 3.86
4786 5031 2.877043 AACCAGCAAGCTTGTTTCTG 57.123 45.000 26.55 22.72 29.16 3.02
4899 5147 2.093816 CAGACCTTCAGTAGATGCAGCA 60.094 50.000 4.07 0.00 0.00 4.41
4900 5148 2.168106 AGACCTTCAGTAGATGCAGCAG 59.832 50.000 4.07 0.00 0.00 4.24
4901 5149 1.297664 CCTTCAGTAGATGCAGCAGC 58.702 55.000 4.07 1.15 42.57 5.25
4911 5159 2.595463 GCAGCAGCAAGGGTGACA 60.595 61.111 0.00 0.00 41.58 3.58
4912 5160 2.623915 GCAGCAGCAAGGGTGACAG 61.624 63.158 0.00 0.00 41.58 3.51
4913 5161 2.282040 AGCAGCAAGGGTGACAGC 60.282 61.111 0.00 0.00 32.22 4.40
4914 5162 2.282040 GCAGCAAGGGTGACAGCT 60.282 61.111 4.38 0.00 37.95 4.24
4915 5163 3.664495 CAGCAAGGGTGACAGCTG 58.336 61.111 13.48 13.48 46.98 4.24
4916 5164 3.567308 AGCAAGGGTGACAGCTGA 58.433 55.556 23.35 0.00 35.72 4.26
4917 5165 2.073232 AGCAAGGGTGACAGCTGAT 58.927 52.632 23.35 4.35 35.72 2.90
4918 5166 0.322277 AGCAAGGGTGACAGCTGATG 60.322 55.000 23.35 8.24 35.72 3.07
4919 5167 1.930908 GCAAGGGTGACAGCTGATGC 61.931 60.000 23.35 13.94 40.05 3.91
4920 5168 0.607217 CAAGGGTGACAGCTGATGCA 60.607 55.000 23.35 12.50 42.74 3.96
4921 5169 0.111061 AAGGGTGACAGCTGATGCAA 59.889 50.000 23.35 0.00 42.74 4.08
4922 5170 0.322277 AGGGTGACAGCTGATGCAAG 60.322 55.000 23.35 0.00 42.74 4.01
4923 5171 1.310933 GGGTGACAGCTGATGCAAGG 61.311 60.000 23.35 0.00 42.74 3.61
4924 5172 1.505353 GTGACAGCTGATGCAAGGC 59.495 57.895 23.35 0.00 42.74 4.35
4925 5173 1.676635 TGACAGCTGATGCAAGGCC 60.677 57.895 23.35 0.00 42.74 5.19
4926 5174 1.676635 GACAGCTGATGCAAGGCCA 60.677 57.895 23.35 0.00 42.74 5.36
4927 5175 1.654954 GACAGCTGATGCAAGGCCAG 61.655 60.000 23.35 0.00 42.74 4.85
4928 5176 1.378119 CAGCTGATGCAAGGCCAGA 60.378 57.895 8.42 0.00 42.74 3.86
4929 5177 0.752009 CAGCTGATGCAAGGCCAGAT 60.752 55.000 8.42 3.98 42.74 2.90
4930 5178 0.841961 AGCTGATGCAAGGCCAGATA 59.158 50.000 5.01 0.00 42.74 1.98
4931 5179 1.424302 AGCTGATGCAAGGCCAGATAT 59.576 47.619 5.01 0.00 42.74 1.63
4932 5180 2.158505 AGCTGATGCAAGGCCAGATATT 60.159 45.455 5.01 0.00 42.74 1.28
4933 5181 2.030185 GCTGATGCAAGGCCAGATATTG 60.030 50.000 5.01 0.45 39.41 1.90
4934 5182 5.167448 GCTGATGCAAGGCCAGATATTGG 62.167 52.174 5.01 0.94 43.82 3.16
5039 5287 3.345028 AGCAGCAGCAAGGGGGAT 61.345 61.111 3.17 0.00 45.49 3.85
5133 5381 5.710099 CAGGGAGTTTAATAAAGGTGCAGAA 59.290 40.000 0.00 0.00 0.00 3.02
5150 5398 3.416156 CAGAAAGAGAGGGGTCAAAAGG 58.584 50.000 0.00 0.00 0.00 3.11
5183 5431 2.687425 CAACCCCGTCATGAATAATGCA 59.313 45.455 0.00 0.00 36.11 3.96
5540 5988 1.294857 GCTAGTAGCTTTCCTGCAGC 58.705 55.000 15.16 0.00 38.45 5.25
5662 6111 2.034053 GCGTGGGAAGTGATTTGAACAA 59.966 45.455 0.00 0.00 0.00 2.83
5663 6112 3.628017 CGTGGGAAGTGATTTGAACAAC 58.372 45.455 0.00 0.00 0.00 3.32
5664 6113 3.066064 CGTGGGAAGTGATTTGAACAACA 59.934 43.478 0.00 0.00 0.00 3.33
5665 6114 4.439426 CGTGGGAAGTGATTTGAACAACAA 60.439 41.667 0.00 0.00 36.65 2.83
5666 6115 4.803613 GTGGGAAGTGATTTGAACAACAAC 59.196 41.667 0.00 0.00 38.29 3.32
5667 6116 4.464244 TGGGAAGTGATTTGAACAACAACA 59.536 37.500 0.00 0.00 38.29 3.33
5668 6117 5.047021 TGGGAAGTGATTTGAACAACAACAA 60.047 36.000 0.00 0.00 38.29 2.83
5669 6118 5.290885 GGGAAGTGATTTGAACAACAACAAC 59.709 40.000 0.00 0.00 38.29 3.32
5670 6119 5.866633 GGAAGTGATTTGAACAACAACAACA 59.133 36.000 0.00 0.00 38.29 3.33
5671 6120 6.367422 GGAAGTGATTTGAACAACAACAACAA 59.633 34.615 0.00 0.00 38.29 2.83
5672 6121 7.095439 GGAAGTGATTTGAACAACAACAACAAA 60.095 33.333 0.00 0.00 38.29 2.83
5673 6122 7.350110 AGTGATTTGAACAACAACAACAAAG 57.650 32.000 0.00 0.00 38.29 2.77
5674 6123 6.014898 GTGATTTGAACAACAACAACAAAGC 58.985 36.000 0.00 0.00 38.29 3.51
5675 6124 4.999751 TTTGAACAACAACAACAAAGCC 57.000 36.364 0.00 0.00 38.29 4.35
5676 6125 3.951775 TGAACAACAACAACAAAGCCT 57.048 38.095 0.00 0.00 0.00 4.58
5677 6126 4.264460 TGAACAACAACAACAAAGCCTT 57.736 36.364 0.00 0.00 0.00 4.35
5678 6127 4.636249 TGAACAACAACAACAAAGCCTTT 58.364 34.783 0.00 0.00 0.00 3.11
5679 6128 5.784177 TGAACAACAACAACAAAGCCTTTA 58.216 33.333 0.00 0.00 0.00 1.85
5680 6129 5.866633 TGAACAACAACAACAAAGCCTTTAG 59.133 36.000 0.00 0.00 0.00 1.85
5681 6130 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
5682 6131 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
5683 6132 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
5684 6133 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
5685 6134 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
5686 6135 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
5687 6136 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
5688 6137 4.653801 ACAACAAAGCCTTTAGTCCCAAAT 59.346 37.500 0.00 0.00 0.00 2.32
5689 6138 4.871933 ACAAAGCCTTTAGTCCCAAATG 57.128 40.909 0.00 0.00 0.00 2.32
5690 6139 4.479158 ACAAAGCCTTTAGTCCCAAATGA 58.521 39.130 0.00 0.00 0.00 2.57
5691 6140 5.086621 ACAAAGCCTTTAGTCCCAAATGAT 58.913 37.500 0.00 0.00 0.00 2.45
5692 6141 5.543790 ACAAAGCCTTTAGTCCCAAATGATT 59.456 36.000 0.00 0.00 0.00 2.57
5693 6142 6.043127 ACAAAGCCTTTAGTCCCAAATGATTT 59.957 34.615 0.00 0.00 0.00 2.17
5694 6143 6.686484 AAGCCTTTAGTCCCAAATGATTTT 57.314 33.333 0.00 0.00 0.00 1.82
5695 6144 7.790782 AAGCCTTTAGTCCCAAATGATTTTA 57.209 32.000 0.00 0.00 0.00 1.52
5696 6145 7.790782 AGCCTTTAGTCCCAAATGATTTTAA 57.209 32.000 0.00 0.00 0.00 1.52
5697 6146 7.611770 AGCCTTTAGTCCCAAATGATTTTAAC 58.388 34.615 0.00 0.00 0.00 2.01
5698 6147 7.234577 AGCCTTTAGTCCCAAATGATTTTAACA 59.765 33.333 0.00 0.00 0.00 2.41
5699 6148 7.545615 GCCTTTAGTCCCAAATGATTTTAACAG 59.454 37.037 0.00 0.00 0.00 3.16
5700 6149 8.802267 CCTTTAGTCCCAAATGATTTTAACAGA 58.198 33.333 0.00 0.00 0.00 3.41
5836 6289 5.623551 ATCCCCATACTGAGGATCTCTTA 57.376 43.478 0.00 0.00 35.41 2.10
6102 6557 4.516698 CACTCATATTTGGATACCAGCCAC 59.483 45.833 0.00 0.00 34.56 5.01
6135 6590 1.002087 CCAGTGACACTTGACCTACCC 59.998 57.143 5.04 0.00 0.00 3.69
6155 6610 0.381801 ACAGTTGAGGCTTGTTTGCG 59.618 50.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.887337 GAGTGAGCTTAGCTTCACTCC 58.113 52.381 32.25 22.87 45.91 3.85
9 10 0.528017 TGGCGAGTGAGTGAGCTTAG 59.472 55.000 0.00 0.00 0.00 2.18
13 14 1.086634 GGATTGGCGAGTGAGTGAGC 61.087 60.000 0.00 0.00 0.00 4.26
17 18 1.194781 ACTGGGATTGGCGAGTGAGT 61.195 55.000 0.00 0.00 0.00 3.41
25 26 1.763968 GGGAACTAACTGGGATTGGC 58.236 55.000 0.00 0.00 0.00 4.52
26 27 2.017113 GCGGGAACTAACTGGGATTGG 61.017 57.143 0.00 0.00 0.00 3.16
752 910 4.777854 GGGTTGTGGGGATGGGGC 62.778 72.222 0.00 0.00 0.00 5.80
846 1020 1.392510 CGAATCGAACGGAAAGGGAAC 59.607 52.381 0.00 0.00 0.00 3.62
848 1022 0.738412 GCGAATCGAACGGAAAGGGA 60.738 55.000 6.91 0.00 0.00 4.20
893 1067 1.995626 CCCAATCGACCCCACTCCT 60.996 63.158 0.00 0.00 0.00 3.69
896 1070 1.378762 CAACCCAATCGACCCCACT 59.621 57.895 0.00 0.00 0.00 4.00
903 1077 0.107410 CCCGAATCCAACCCAATCGA 60.107 55.000 0.00 0.00 35.65 3.59
904 1078 1.101049 CCCCGAATCCAACCCAATCG 61.101 60.000 0.00 0.00 0.00 3.34
906 1080 1.309688 CCCCCGAATCCAACCCAAT 59.690 57.895 0.00 0.00 0.00 3.16
907 1081 2.767352 CCCCCGAATCCAACCCAA 59.233 61.111 0.00 0.00 0.00 4.12
961 1140 0.673437 CAAACCACCGCAAGACCAAT 59.327 50.000 0.00 0.00 43.02 3.16
967 1146 4.999939 GCGCCAAACCACCGCAAG 63.000 66.667 0.00 0.00 46.32 4.01
972 1151 3.977244 CACCTGCGCCAAACCACC 61.977 66.667 4.18 0.00 0.00 4.61
973 1152 3.977244 CCACCTGCGCCAAACCAC 61.977 66.667 4.18 0.00 0.00 4.16
974 1153 4.514585 ACCACCTGCGCCAAACCA 62.515 61.111 4.18 0.00 0.00 3.67
975 1154 3.977244 CACCACCTGCGCCAAACC 61.977 66.667 4.18 0.00 0.00 3.27
976 1155 4.645921 GCACCACCTGCGCCAAAC 62.646 66.667 4.18 0.00 35.72 2.93
1156 1338 2.445654 CTCCTCCTCCTCCTGGCC 60.446 72.222 0.00 0.00 0.00 5.36
1157 1339 2.445654 CCTCCTCCTCCTCCTGGC 60.446 72.222 0.00 0.00 0.00 4.85
1158 1340 1.075600 GTCCTCCTCCTCCTCCTGG 60.076 68.421 0.00 0.00 0.00 4.45
1159 1341 1.454847 CGTCCTCCTCCTCCTCCTG 60.455 68.421 0.00 0.00 0.00 3.86
1203 1412 2.491621 CCGAGCTGCGTGATCTCA 59.508 61.111 0.00 0.00 38.67 3.27
1536 1745 1.087771 GGTAGTAATGCTTGCGCCGT 61.088 55.000 4.18 0.00 34.43 5.68
1548 1757 3.958798 GGTACCTCTGCAGATGGTAGTAA 59.041 47.826 29.83 17.41 37.06 2.24
1576 1785 4.415150 CAGCCCCAGCACCATCGT 62.415 66.667 0.00 0.00 43.56 3.73
1650 1859 1.977056 TCATTGCATCCATGGCTCTC 58.023 50.000 6.96 0.00 0.00 3.20
1656 1865 1.478916 TGTGCCTTCATTGCATCCATG 59.521 47.619 0.00 0.00 41.46 3.66
1901 2110 2.223711 CGAGAAAGCTTAGAGAGAGCCC 60.224 54.545 0.00 0.00 41.03 5.19
2259 2468 1.531365 CTGGGCAGCTTTTCCACCA 60.531 57.895 0.00 0.00 0.00 4.17
2300 2509 2.687610 CCAGCTGGCCAATCCCTCT 61.688 63.158 22.33 0.00 0.00 3.69
2386 2595 2.437651 TCACACCATGACCAACTTGAGA 59.562 45.455 0.00 0.00 29.99 3.27
2690 2899 7.487829 TGACTGATTTGCTAAGTTTGTTTGAAC 59.512 33.333 0.00 0.00 0.00 3.18
2691 2900 7.542890 TGACTGATTTGCTAAGTTTGTTTGAA 58.457 30.769 0.00 0.00 0.00 2.69
2960 3169 2.300152 TCTGGTGACCTCAGTGATTCAC 59.700 50.000 19.85 19.85 38.11 3.18
3087 3296 4.141937 ACTCTTCCTTTTTGCCTTTTGGAC 60.142 41.667 0.00 0.00 44.07 4.02
3122 3331 4.457496 CGCCATGCTCGTCCAGGT 62.457 66.667 0.00 0.00 0.00 4.00
3129 3338 3.238260 GCATACTCGCCATGCTCG 58.762 61.111 8.03 0.00 44.35 5.03
3171 3380 0.174389 TCTTCGAGCTGCCACTGATC 59.826 55.000 0.00 0.00 0.00 2.92
3372 3581 1.859080 GCGACCATAGCCTTCTTAACG 59.141 52.381 0.00 0.00 0.00 3.18
3390 3599 2.136196 GAGTATCCTCAGCCGGAGCG 62.136 65.000 5.05 0.00 46.67 5.03
3433 3642 1.261238 GCCACTGGAGTAGCCTCAGT 61.261 60.000 0.00 0.00 39.64 3.41
3440 3649 0.101399 CGTAGCTGCCACTGGAGTAG 59.899 60.000 0.00 0.00 0.00 2.57
3471 3680 1.134560 GCTACCACTGGAGTAACCTCG 59.865 57.143 0.71 0.00 38.70 4.63
3488 3697 1.144716 CCATCAGGCTGCTTCGCTA 59.855 57.895 10.34 0.00 0.00 4.26
3499 3708 0.835941 CTGTTCTCCTCCCCATCAGG 59.164 60.000 0.00 0.00 0.00 3.86
3611 3856 2.334946 GCCGGTGAATTGCTCTGCA 61.335 57.895 1.90 0.00 36.47 4.41
3612 3857 1.660560 ATGCCGGTGAATTGCTCTGC 61.661 55.000 1.90 0.00 0.00 4.26
3624 3869 3.134574 TCTTGAACAGTTAATGCCGGT 57.865 42.857 1.90 0.00 0.00 5.28
3631 3876 7.095229 CCGATGAACAAGATCTTGAACAGTTAA 60.095 37.037 36.15 16.72 42.93 2.01
3819 4064 1.943730 AAGGCAGTGGACCAACCCAA 61.944 55.000 0.00 0.00 38.06 4.12
3843 4088 9.029368 TCTTCATTAGGATCACTATATGAGGTG 57.971 37.037 0.00 0.00 41.91 4.00
4266 4511 8.625651 GCATCTCTTACAAGACAGAGAATAGTA 58.374 37.037 3.10 0.00 46.78 1.82
4710 4955 1.774217 AAGGTCACCTTCCAGCCCA 60.774 57.895 2.03 0.00 40.17 5.36
4786 5031 1.906990 ATATCTGGCCTTGCATCAGC 58.093 50.000 3.32 0.00 42.57 4.26
4844 5092 1.676635 GGCCTTGCATCAGCTGTCA 60.677 57.895 14.67 7.74 42.74 3.58
4899 5147 0.322277 CATCAGCTGTCACCCTTGCT 60.322 55.000 14.67 0.00 36.04 3.91
4900 5148 1.930908 GCATCAGCTGTCACCCTTGC 61.931 60.000 14.67 8.87 37.91 4.01
4901 5149 0.607217 TGCATCAGCTGTCACCCTTG 60.607 55.000 14.67 2.97 42.74 3.61
4902 5150 0.111061 TTGCATCAGCTGTCACCCTT 59.889 50.000 14.67 0.00 42.74 3.95
4903 5151 0.322277 CTTGCATCAGCTGTCACCCT 60.322 55.000 14.67 0.00 42.74 4.34
4904 5152 1.310933 CCTTGCATCAGCTGTCACCC 61.311 60.000 14.67 0.00 42.74 4.61
4905 5153 1.930908 GCCTTGCATCAGCTGTCACC 61.931 60.000 14.67 1.69 42.74 4.02
4906 5154 1.505353 GCCTTGCATCAGCTGTCAC 59.495 57.895 14.67 4.66 42.74 3.67
4907 5155 1.676635 GGCCTTGCATCAGCTGTCA 60.677 57.895 14.67 7.74 42.74 3.58
4908 5156 1.654954 CTGGCCTTGCATCAGCTGTC 61.655 60.000 14.67 5.07 42.74 3.51
4909 5157 1.677966 CTGGCCTTGCATCAGCTGT 60.678 57.895 14.67 0.00 42.74 4.40
4910 5158 0.752009 ATCTGGCCTTGCATCAGCTG 60.752 55.000 7.63 7.63 42.74 4.24
4911 5159 0.841961 TATCTGGCCTTGCATCAGCT 59.158 50.000 3.32 0.00 42.74 4.24
4912 5160 1.906990 ATATCTGGCCTTGCATCAGC 58.093 50.000 3.32 0.00 42.57 4.26
4913 5161 2.557056 CCAATATCTGGCCTTGCATCAG 59.443 50.000 3.32 0.00 38.76 2.90
4914 5162 2.589720 CCAATATCTGGCCTTGCATCA 58.410 47.619 3.32 0.00 38.76 3.07
4933 5181 1.562783 ACTGAAGGTCTGGAGCTACC 58.437 55.000 2.66 0.00 38.35 3.18
4934 5182 3.622630 TCTACTGAAGGTCTGGAGCTAC 58.377 50.000 2.66 0.00 38.35 3.58
4935 5183 4.211125 CATCTACTGAAGGTCTGGAGCTA 58.789 47.826 2.66 0.00 38.35 3.32
4936 5184 2.909504 TCTACTGAAGGTCTGGAGCT 57.090 50.000 0.00 0.00 41.53 4.09
4937 5185 2.482839 GCATCTACTGAAGGTCTGGAGC 60.483 54.545 0.00 0.00 0.00 4.70
4938 5186 2.762887 TGCATCTACTGAAGGTCTGGAG 59.237 50.000 0.00 0.00 0.00 3.86
4939 5187 2.762887 CTGCATCTACTGAAGGTCTGGA 59.237 50.000 0.00 0.00 0.00 3.86
4940 5188 2.741228 GCTGCATCTACTGAAGGTCTGG 60.741 54.545 0.00 0.00 30.11 3.86
4941 5189 2.093816 TGCTGCATCTACTGAAGGTCTG 60.094 50.000 0.00 0.00 30.11 3.51
5133 5381 3.657727 TGAATCCTTTTGACCCCTCTCTT 59.342 43.478 0.00 0.00 0.00 2.85
5150 5398 0.670162 CGGGGTTGCATCCATGAATC 59.330 55.000 15.63 0.00 0.00 2.52
5183 5431 5.338708 GGTGCTCCAATATATGTCCTGCTAT 60.339 44.000 0.00 0.00 0.00 2.97
5256 5504 7.008021 ACAATGAAAAGAATGCCTGGTAAAT 57.992 32.000 0.00 0.00 0.00 1.40
5388 5637 6.664428 ACACAGTTTTGGTATAAAGGCAAT 57.336 33.333 0.00 0.00 0.00 3.56
5662 6111 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
5663 6112 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
5664 6113 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
5665 6114 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
5666 6115 4.664150 TTTGGGACTAAAGGCTTTGTTG 57.336 40.909 22.32 13.85 0.00 3.33
5667 6116 4.898861 TCATTTGGGACTAAAGGCTTTGTT 59.101 37.500 22.32 8.73 0.00 2.83
5668 6117 4.479158 TCATTTGGGACTAAAGGCTTTGT 58.521 39.130 22.32 16.86 0.00 2.83
5669 6118 5.665916 ATCATTTGGGACTAAAGGCTTTG 57.334 39.130 22.32 13.97 0.00 2.77
5670 6119 6.686484 AAATCATTTGGGACTAAAGGCTTT 57.314 33.333 17.76 17.76 0.00 3.51
5671 6120 6.686484 AAAATCATTTGGGACTAAAGGCTT 57.314 33.333 0.00 0.00 0.00 4.35
5672 6121 7.234577 TGTTAAAATCATTTGGGACTAAAGGCT 59.765 33.333 0.00 0.00 0.00 4.58
5673 6122 7.382898 TGTTAAAATCATTTGGGACTAAAGGC 58.617 34.615 0.00 0.00 0.00 4.35
5674 6123 8.802267 TCTGTTAAAATCATTTGGGACTAAAGG 58.198 33.333 0.00 0.00 0.00 3.11
5677 6126 9.308000 ACATCTGTTAAAATCATTTGGGACTAA 57.692 29.630 0.00 0.00 0.00 2.24
5678 6127 8.877864 ACATCTGTTAAAATCATTTGGGACTA 57.122 30.769 0.00 0.00 0.00 2.59
5679 6128 7.781324 ACATCTGTTAAAATCATTTGGGACT 57.219 32.000 0.00 0.00 0.00 3.85
5680 6129 8.831715 AAACATCTGTTAAAATCATTTGGGAC 57.168 30.769 0.00 0.00 37.25 4.46
5681 6130 9.844257 AAAAACATCTGTTAAAATCATTTGGGA 57.156 25.926 0.00 0.00 37.25 4.37
5708 6157 7.705752 GTCGGTGAACTAAAAATTAACCCAAAA 59.294 33.333 0.00 0.00 27.45 2.44
5712 6161 6.205270 TCAGTCGGTGAACTAAAAATTAACCC 59.795 38.462 0.00 0.00 27.45 4.11
5713 6162 7.193377 TCAGTCGGTGAACTAAAAATTAACC 57.807 36.000 0.00 0.00 29.64 2.85
5836 6289 4.888326 TCATACCCTGCAAAGCAAAAAT 57.112 36.364 0.00 0.00 38.41 1.82
5989 6444 2.079925 GCACAAAGCCACTAGGAGAAG 58.920 52.381 0.00 0.00 36.89 2.85
5991 6446 1.002430 CTGCACAAAGCCACTAGGAGA 59.998 52.381 0.00 0.00 44.83 3.71
6102 6557 1.270550 GTCACTGGCACTGGAATTTGG 59.729 52.381 0.00 0.00 0.00 3.28
6135 6590 1.843992 GCAAACAAGCCTCAACTGTG 58.156 50.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.