Multiple sequence alignment - TraesCS7D01G267300

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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 TraesCS7D01G267300 chr7D 100.000 6572 0 0 1 6572 250667839 250674410 0.000000e+00 12137.0
1 TraesCS7D01G267300 chr7A 98.217 3253 30 5 1958 5182 270764643 270761391 0.000000e+00 5661.0
2 TraesCS7D01G267300 chr7A 97.553 1226 21 1 748 1973 270773789 270772573 0.000000e+00 2089.0
3 TraesCS7D01G267300 chr7A 92.924 749 39 6 5456 6203 270761019 270760284 0.000000e+00 1077.0
4 TraesCS7D01G267300 chr7A 83.269 777 60 31 1 751 270774794 270774062 0.000000e+00 651.0
5 TraesCS7D01G267300 chr7A 93.767 369 21 2 6204 6572 270760355 270759989 2.680000e-153 553.0
6 TraesCS7D01G267300 chr7A 99.087 219 1 1 5181 5399 270761230 270761013 6.180000e-105 392.0
7 TraesCS7D01G267300 chr7A 89.256 121 9 3 1852 1969 12720898 12721017 1.480000e-31 148.0
8 TraesCS7D01G267300 chr7B 94.786 1496 55 9 1964 3448 227281085 227282568 0.000000e+00 2309.0
9 TraesCS7D01G267300 chr7B 89.276 1893 106 42 4132 5962 227283353 227285210 0.000000e+00 2281.0
10 TraesCS7D01G267300 chr7B 89.566 1428 74 36 349 1719 227279584 227280993 0.000000e+00 1742.0
11 TraesCS7D01G267300 chr7B 93.027 631 25 5 3445 4057 227282707 227283336 0.000000e+00 904.0
12 TraesCS7D01G267300 chr7B 88.410 371 21 8 1 350 227278954 227279323 1.690000e-115 427.0
13 TraesCS7D01G267300 chr7B 100.000 43 0 0 1750 1792 227280992 227281034 5.460000e-11 80.5
14 TraesCS7D01G267300 chr7B 93.478 46 2 1 634 679 619415235 619415191 4.250000e-07 67.6
15 TraesCS7D01G267300 chr7B 94.595 37 1 1 1807 1843 227281034 227281069 1.000000e-03 56.5
16 TraesCS7D01G267300 chr5D 86.063 287 40 0 3055 3341 399947620 399947906 6.400000e-80 309.0
17 TraesCS7D01G267300 chr5D 87.931 58 6 1 616 673 547797115 547797059 4.250000e-07 67.6
18 TraesCS7D01G267300 chr5A 86.063 287 40 0 3055 3341 505504383 505504669 6.400000e-80 309.0
19 TraesCS7D01G267300 chr5A 88.525 122 10 3 1852 1971 440988308 440988427 1.910000e-30 145.0
20 TraesCS7D01G267300 chr5A 93.333 45 2 1 632 676 389199788 389199745 1.530000e-06 65.8
21 TraesCS7D01G267300 chr5B 85.714 287 41 0 3055 3341 479827923 479828209 2.980000e-78 303.0
22 TraesCS7D01G267300 chr5B 95.122 41 1 1 634 674 612069895 612069856 5.500000e-06 63.9
23 TraesCS7D01G267300 chr2D 91.525 118 8 1 1852 1967 607675743 607675860 1.900000e-35 161.0
24 TraesCS7D01G267300 chr2D 88.525 122 11 2 1852 1971 484361939 484362059 1.910000e-30 145.0
25 TraesCS7D01G267300 chr2D 79.762 168 24 5 6259 6419 485605150 485604986 5.390000e-21 113.0
26 TraesCS7D01G267300 chr2D 79.882 169 22 5 6259 6419 485648363 485648199 5.390000e-21 113.0
27 TraesCS7D01G267300 chr6D 89.600 125 8 2 1852 1974 87598597 87598718 3.170000e-33 154.0
28 TraesCS7D01G267300 chr1D 88.462 130 12 2 1852 1979 465887145 465887273 3.170000e-33 154.0
29 TraesCS7D01G267300 chr1B 87.903 124 12 3 1852 1973 620130564 620130442 6.870000e-30 143.0
30 TraesCS7D01G267300 chr4A 85.507 138 15 4 1832 1966 619189951 619190086 8.890000e-29 139.0
31 TraesCS7D01G267300 chr6B 90.625 64 4 2 617 679 691617256 691617194 4.220000e-12 84.2
32 TraesCS7D01G267300 chr3D 90.741 54 4 1 616 669 336665376 336665324 3.290000e-08 71.3


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 TraesCS7D01G267300 chr7D 250667839 250674410 6571 False 12137.000000 12137 100.000000 1 6572 1 chr7D.!!$F1 6571
1 TraesCS7D01G267300 chr7A 270759989 270764643 4654 True 1920.750000 5661 95.998750 1958 6572 4 chr7A.!!$R1 4614
2 TraesCS7D01G267300 chr7A 270772573 270774794 2221 True 1370.000000 2089 90.411000 1 1973 2 chr7A.!!$R2 1972
3 TraesCS7D01G267300 chr7B 227278954 227285210 6256 False 1114.285714 2309 92.808571 1 5962 7 chr7B.!!$F1 5961

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
175 198 0.398696 TCCCGTGTTTAGCACCACAT 59.601 50.000 0.00 0.0 44.97 3.21 F
879 1451 0.809385 CTGGCCAAGTGCAGAATCAG 59.191 55.000 7.01 0.0 43.89 2.90 F
1876 2496 0.108041 TCCGCCCCGAATTACTTGTC 60.108 55.000 0.00 0.0 0.00 3.18 F
3435 4068 1.045911 TGCTGGGGGTTTCACCAAAC 61.046 55.000 0.00 0.0 41.02 2.93 F
3824 4606 1.065410 TGGTGTTGTCCTGATGGGGT 61.065 55.000 0.00 0.0 35.33 4.95 F
5439 6444 1.656441 GGCATTGAATAGGCCTGCG 59.344 57.895 17.99 0.0 44.32 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 2295 0.252197 GGTGAATTACGGGCAGTCCT 59.748 55.000 0.00 0.0 0.00 3.85 R
2219 2839 1.063616 CAGCTGATCAATGCCGTTCAG 59.936 52.381 8.42 0.0 38.86 3.02 R
3598 4380 2.499214 TTTTTGCGTCAGTTGGCCT 58.501 47.368 3.32 0.0 0.00 5.19 R
5424 6429 1.202855 AGATGCGCAGGCCTATTCAAT 60.203 47.619 18.32 0.0 38.85 2.57 R
5442 6447 0.107410 AAACAACACCAGCCGTGAGA 60.107 50.000 8.44 0.0 46.20 3.27 R
6514 7550 0.031178 GCATGGTGGCGGATTTGATC 59.969 55.000 0.00 0.0 0.00 2.92 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
46 47 1.448922 GGTCCTCTAGAGCGACGCAT 61.449 60.000 23.70 12.71 32.80 4.73
48 49 0.748367 TCCTCTAGAGCGACGCATGT 60.748 55.000 23.70 8.23 0.00 3.21
74 77 6.648879 TGTTATGTGATGAGATGGACGATA 57.351 37.500 0.00 0.00 0.00 2.92
75 78 6.447162 TGTTATGTGATGAGATGGACGATAC 58.553 40.000 0.00 0.00 0.00 2.24
76 79 3.626028 TGTGATGAGATGGACGATACG 57.374 47.619 0.00 0.00 0.00 3.06
122 125 4.245251 ACCCCTATAAAATCAAAGCGGT 57.755 40.909 0.00 0.00 0.00 5.68
150 173 0.912487 TCCACCCTACCCATGTCCAC 60.912 60.000 0.00 0.00 0.00 4.02
173 196 1.574702 GCTCCCGTGTTTAGCACCAC 61.575 60.000 0.00 0.00 44.97 4.16
175 198 0.398696 TCCCGTGTTTAGCACCACAT 59.601 50.000 0.00 0.00 44.97 3.21
225 251 4.468868 TGATCTCAGCCATCATATACCCTG 59.531 45.833 0.00 0.00 0.00 4.45
324 350 7.846107 CCGTCAAAATATGTCAATCTAAAGACG 59.154 37.037 0.00 0.00 41.32 4.18
328 354 7.715265 AAATATGTCAATCTAAAGACGCGAT 57.285 32.000 15.93 0.00 37.58 4.58
351 639 9.515020 CGATGTTTAACATGGCAAGTAATTATT 57.485 29.630 15.83 0.00 39.27 1.40
412 700 7.469343 TCTTCCTCAATCTATCTGCTCTCTAT 58.531 38.462 0.00 0.00 0.00 1.98
428 716 5.392767 TCTCTATGCAGAACGAGACTTTT 57.607 39.130 0.00 0.00 0.00 2.27
635 926 5.657474 TGAATACTCGCTCCGTTCTAAAAT 58.343 37.500 0.00 0.00 0.00 1.82
636 927 6.103997 TGAATACTCGCTCCGTTCTAAAATT 58.896 36.000 0.00 0.00 0.00 1.82
638 929 7.221452 TGAATACTCGCTCCGTTCTAAAATTAC 59.779 37.037 0.00 0.00 0.00 1.89
640 931 5.476614 ACTCGCTCCGTTCTAAAATTACTT 58.523 37.500 0.00 0.00 0.00 2.24
641 932 5.347907 ACTCGCTCCGTTCTAAAATTACTTG 59.652 40.000 0.00 0.00 0.00 3.16
642 933 5.232463 TCGCTCCGTTCTAAAATTACTTGT 58.768 37.500 0.00 0.00 0.00 3.16
643 934 5.119588 TCGCTCCGTTCTAAAATTACTTGTG 59.880 40.000 0.00 0.00 0.00 3.33
719 1015 4.767928 ACAAGTAATTTGGGGCGTTGATAA 59.232 37.500 0.00 0.00 41.25 1.75
720 1016 5.420739 ACAAGTAATTTGGGGCGTTGATAAT 59.579 36.000 0.00 0.00 41.25 1.28
721 1017 6.603997 ACAAGTAATTTGGGGCGTTGATAATA 59.396 34.615 0.00 0.00 41.25 0.98
848 1420 2.238084 TGTCTGGGAGCTGACTGTAT 57.762 50.000 0.00 0.00 34.57 2.29
851 1423 2.362717 GTCTGGGAGCTGACTGTATACC 59.637 54.545 0.00 0.00 0.00 2.73
879 1451 0.809385 CTGGCCAAGTGCAGAATCAG 59.191 55.000 7.01 0.00 43.89 2.90
1130 1702 1.071228 CTCCCTTGCCATCATCATCGA 59.929 52.381 0.00 0.00 0.00 3.59
1221 1798 1.959985 GACAGGCAGATAGCTCAGCTA 59.040 52.381 9.36 9.36 45.55 3.32
1317 1897 2.270527 GCTGAGGTGAGGCTTCCC 59.729 66.667 6.14 1.19 0.00 3.97
1876 2496 0.108041 TCCGCCCCGAATTACTTGTC 60.108 55.000 0.00 0.00 0.00 3.18
2669 3299 3.173151 TGATACTTCAGCTGACCCTGAA 58.827 45.455 18.03 0.00 46.48 3.02
2866 3499 3.242867 ACTGTCTGGAAGGAGATCAACA 58.757 45.455 0.00 0.00 0.00 3.33
3435 4068 1.045911 TGCTGGGGGTTTCACCAAAC 61.046 55.000 0.00 0.00 41.02 2.93
3727 4509 8.638873 CAGAGTCTTGTTACATGGGTATGTATA 58.361 37.037 0.00 0.00 46.22 1.47
3824 4606 1.065410 TGGTGTTGTCCTGATGGGGT 61.065 55.000 0.00 0.00 35.33 4.95
4057 4850 6.074356 GCACGTCAGTAAAGATTTTTGCAATT 60.074 34.615 0.00 0.00 32.09 2.32
4474 5285 8.565896 TTCTCAGCTTTGCTCAAATATTCTTA 57.434 30.769 0.00 0.00 36.40 2.10
4599 5418 7.124750 AGTTGCTATGAATTGCTAGGGAAAATT 59.875 33.333 0.00 0.00 0.00 1.82
4670 5489 5.902613 TTTATTTGCTATCTGTGCAGCTT 57.097 34.783 0.00 0.00 41.71 3.74
5223 6219 4.852134 TGCTAATGCATGTTTGTTGAGT 57.148 36.364 0.00 0.00 45.31 3.41
5391 6390 9.736023 GTGAGAATTTGGTAAATTATTAGCAGG 57.264 33.333 0.00 0.00 46.73 4.85
5424 6429 2.047061 ACACTGTACTTCCTTCAGGCA 58.953 47.619 0.00 0.00 34.02 4.75
5439 6444 1.656441 GGCATTGAATAGGCCTGCG 59.344 57.895 17.99 0.00 44.32 5.18
5441 6446 1.727511 GCATTGAATAGGCCTGCGCA 61.728 55.000 17.99 10.98 36.38 6.09
5442 6447 0.956633 CATTGAATAGGCCTGCGCAT 59.043 50.000 17.99 0.00 36.38 4.73
5518 6548 7.479291 CACAGTTCTTTTTGCATGTTCTTTTTG 59.521 33.333 0.00 0.00 0.00 2.44
5649 6683 0.510790 TACTTCACGCACATGCAACG 59.489 50.000 4.49 0.00 42.21 4.10
5685 6719 3.244215 GCTAACATATACTCTGCCTGGCA 60.244 47.826 21.96 21.96 36.92 4.92
5691 6725 0.538584 TACTCTGCCTGGCACATCAG 59.461 55.000 19.30 13.22 39.21 2.90
5746 6780 0.678684 ATAAAAACGCGAGGGTGGGG 60.679 55.000 15.93 0.00 0.00 4.96
5910 6944 1.227704 TTCGTGCACGGGACAATGT 60.228 52.632 36.41 0.00 40.29 2.71
5923 6957 1.870458 CAATGTGCAAGATGCCGCG 60.870 57.895 0.00 0.00 44.23 6.46
5924 6958 2.334946 AATGTGCAAGATGCCGCGT 61.335 52.632 4.92 0.00 44.23 6.01
5980 7015 2.357517 CTGAGCACACGGTCCACC 60.358 66.667 0.00 0.00 38.96 4.61
5995 7030 0.322816 CCACCTGTCATGGACCCTTG 60.323 60.000 0.00 0.00 39.87 3.61
6024 7059 4.789075 CGGGTGCGTACTGTCCGG 62.789 72.222 11.00 0.00 37.35 5.14
6025 7060 3.688159 GGGTGCGTACTGTCCGGT 61.688 66.667 0.00 0.00 0.00 5.28
6028 7063 1.138247 GTGCGTACTGTCCGGTAGG 59.862 63.158 0.00 2.39 39.46 3.18
6039 7074 1.080974 CCGGTAGGTCACACGACAC 60.081 63.158 0.00 0.00 44.54 3.67
6097 7133 1.304134 AATGGACGGGGCAAAGGAC 60.304 57.895 0.00 0.00 0.00 3.85
6106 7142 2.035442 GGCAAAGGACAGTCTCGCC 61.035 63.158 0.00 4.13 0.00 5.54
6160 7196 8.127327 CCAGCATCTTTTACAAGAGTAATGATG 58.873 37.037 17.62 17.62 42.53 3.07
6163 7199 7.420800 CATCTTTTACAAGAGTAATGATGCCC 58.579 38.462 13.53 0.00 42.53 5.36
6164 7200 5.885912 TCTTTTACAAGAGTAATGATGCCCC 59.114 40.000 0.00 0.00 39.78 5.80
6165 7201 4.853468 TTACAAGAGTAATGATGCCCCA 57.147 40.909 0.00 0.00 35.37 4.96
6166 7202 3.737559 ACAAGAGTAATGATGCCCCAA 57.262 42.857 0.00 0.00 0.00 4.12
6167 7203 3.356290 ACAAGAGTAATGATGCCCCAAC 58.644 45.455 0.00 0.00 0.00 3.77
6168 7204 2.332063 AGAGTAATGATGCCCCAACG 57.668 50.000 0.00 0.00 0.00 4.10
6169 7205 1.559682 AGAGTAATGATGCCCCAACGT 59.440 47.619 0.00 0.00 0.00 3.99
6170 7206 1.940613 GAGTAATGATGCCCCAACGTC 59.059 52.381 0.00 0.00 0.00 4.34
6171 7207 1.559682 AGTAATGATGCCCCAACGTCT 59.440 47.619 0.00 0.00 0.00 4.18
6172 7208 1.940613 GTAATGATGCCCCAACGTCTC 59.059 52.381 0.00 0.00 0.00 3.36
6173 7209 0.394352 AATGATGCCCCAACGTCTCC 60.394 55.000 0.00 0.00 0.00 3.71
6174 7210 1.561769 ATGATGCCCCAACGTCTCCA 61.562 55.000 0.00 0.00 0.00 3.86
6175 7211 1.002624 GATGCCCCAACGTCTCCAA 60.003 57.895 0.00 0.00 0.00 3.53
6176 7212 0.394352 GATGCCCCAACGTCTCCAAT 60.394 55.000 0.00 0.00 0.00 3.16
6177 7213 0.916086 ATGCCCCAACGTCTCCAATA 59.084 50.000 0.00 0.00 0.00 1.90
6178 7214 0.251916 TGCCCCAACGTCTCCAATAG 59.748 55.000 0.00 0.00 0.00 1.73
6179 7215 0.463833 GCCCCAACGTCTCCAATAGG 60.464 60.000 0.00 0.00 0.00 2.57
6180 7216 0.909623 CCCCAACGTCTCCAATAGGT 59.090 55.000 0.00 0.00 35.89 3.08
6181 7217 2.112998 CCCCAACGTCTCCAATAGGTA 58.887 52.381 0.00 0.00 35.89 3.08
6182 7218 2.159000 CCCCAACGTCTCCAATAGGTAC 60.159 54.545 0.00 0.00 35.89 3.34
6183 7219 2.159000 CCCAACGTCTCCAATAGGTACC 60.159 54.545 2.73 2.73 35.89 3.34
6184 7220 2.159000 CCAACGTCTCCAATAGGTACCC 60.159 54.545 8.74 0.00 35.89 3.69
6185 7221 2.498481 CAACGTCTCCAATAGGTACCCA 59.502 50.000 8.74 0.00 35.89 4.51
6186 7222 2.823959 ACGTCTCCAATAGGTACCCAA 58.176 47.619 8.74 0.00 35.89 4.12
6187 7223 3.381335 ACGTCTCCAATAGGTACCCAAT 58.619 45.455 8.74 0.00 35.89 3.16
6188 7224 4.549668 ACGTCTCCAATAGGTACCCAATA 58.450 43.478 8.74 0.00 35.89 1.90
6189 7225 4.964262 ACGTCTCCAATAGGTACCCAATAA 59.036 41.667 8.74 0.00 35.89 1.40
6190 7226 5.605488 ACGTCTCCAATAGGTACCCAATAAT 59.395 40.000 8.74 0.00 35.89 1.28
6191 7227 6.783977 ACGTCTCCAATAGGTACCCAATAATA 59.216 38.462 8.74 0.00 35.89 0.98
6192 7228 7.290714 ACGTCTCCAATAGGTACCCAATAATAA 59.709 37.037 8.74 0.00 35.89 1.40
6193 7229 7.817962 CGTCTCCAATAGGTACCCAATAATAAG 59.182 40.741 8.74 0.00 35.89 1.73
6194 7230 8.101419 GTCTCCAATAGGTACCCAATAATAAGG 58.899 40.741 8.74 0.73 35.89 2.69
6195 7231 6.786122 TCCAATAGGTACCCAATAATAAGGC 58.214 40.000 8.74 0.00 35.89 4.35
6196 7232 6.333168 TCCAATAGGTACCCAATAATAAGGCA 59.667 38.462 8.74 0.00 35.89 4.75
6197 7233 6.433093 CCAATAGGTACCCAATAATAAGGCAC 59.567 42.308 8.74 0.00 0.00 5.01
6198 7234 6.773583 ATAGGTACCCAATAATAAGGCACA 57.226 37.500 8.74 0.00 0.00 4.57
6199 7235 5.459982 AGGTACCCAATAATAAGGCACAA 57.540 39.130 8.74 0.00 0.00 3.33
6200 7236 5.198207 AGGTACCCAATAATAAGGCACAAC 58.802 41.667 8.74 0.00 0.00 3.32
6201 7237 4.340097 GGTACCCAATAATAAGGCACAACC 59.660 45.833 0.00 0.00 39.61 3.77
6202 7238 4.054359 ACCCAATAATAAGGCACAACCA 57.946 40.909 0.00 0.00 43.14 3.67
6203 7239 4.421131 ACCCAATAATAAGGCACAACCAA 58.579 39.130 0.00 0.00 43.14 3.67
6204 7240 4.221924 ACCCAATAATAAGGCACAACCAAC 59.778 41.667 0.00 0.00 43.14 3.77
6205 7241 4.466015 CCCAATAATAAGGCACAACCAACT 59.534 41.667 0.00 0.00 43.14 3.16
6206 7242 5.394115 CCCAATAATAAGGCACAACCAACTC 60.394 44.000 0.00 0.00 43.14 3.01
6207 7243 5.394115 CCAATAATAAGGCACAACCAACTCC 60.394 44.000 0.00 0.00 43.14 3.85
6208 7244 2.969821 ATAAGGCACAACCAACTCCA 57.030 45.000 0.00 0.00 43.14 3.86
6209 7245 2.270352 TAAGGCACAACCAACTCCAG 57.730 50.000 0.00 0.00 43.14 3.86
6210 7246 1.109323 AAGGCACAACCAACTCCAGC 61.109 55.000 0.00 0.00 43.14 4.85
6211 7247 1.827789 GGCACAACCAACTCCAGCA 60.828 57.895 0.00 0.00 38.86 4.41
6212 7248 1.181098 GGCACAACCAACTCCAGCAT 61.181 55.000 0.00 0.00 38.86 3.79
6213 7249 0.242017 GCACAACCAACTCCAGCATC 59.758 55.000 0.00 0.00 0.00 3.91
6214 7250 1.901591 CACAACCAACTCCAGCATCT 58.098 50.000 0.00 0.00 0.00 2.90
6215 7251 2.233271 CACAACCAACTCCAGCATCTT 58.767 47.619 0.00 0.00 0.00 2.40
6216 7252 2.624838 CACAACCAACTCCAGCATCTTT 59.375 45.455 0.00 0.00 0.00 2.52
6217 7253 3.068590 CACAACCAACTCCAGCATCTTTT 59.931 43.478 0.00 0.00 0.00 2.27
6218 7254 4.278170 CACAACCAACTCCAGCATCTTTTA 59.722 41.667 0.00 0.00 0.00 1.52
6219 7255 5.047802 CACAACCAACTCCAGCATCTTTTAT 60.048 40.000 0.00 0.00 0.00 1.40
6220 7256 6.150976 CACAACCAACTCCAGCATCTTTTATA 59.849 38.462 0.00 0.00 0.00 0.98
6221 7257 6.719370 ACAACCAACTCCAGCATCTTTTATAA 59.281 34.615 0.00 0.00 0.00 0.98
6222 7258 7.094205 ACAACCAACTCCAGCATCTTTTATAAG 60.094 37.037 0.00 0.00 0.00 1.73
6223 7259 6.721318 ACCAACTCCAGCATCTTTTATAAGA 58.279 36.000 0.00 0.00 44.16 2.10
6224 7260 6.825721 ACCAACTCCAGCATCTTTTATAAGAG 59.174 38.462 2.08 0.00 43.33 2.85
6225 7261 6.825721 CCAACTCCAGCATCTTTTATAAGAGT 59.174 38.462 3.17 0.00 43.33 3.24
6226 7262 7.987458 CCAACTCCAGCATCTTTTATAAGAGTA 59.013 37.037 3.17 0.00 43.33 2.59
6227 7263 9.383519 CAACTCCAGCATCTTTTATAAGAGTAA 57.616 33.333 3.17 0.00 43.33 2.24
6229 7265 9.553064 ACTCCAGCATCTTTTATAAGAGTAATG 57.447 33.333 3.17 2.57 43.33 1.90
6230 7266 9.770097 CTCCAGCATCTTTTATAAGAGTAATGA 57.230 33.333 8.20 0.00 43.33 2.57
6256 7292 2.975489 CCAGCATCTCCAATAGGTACCT 59.025 50.000 20.57 20.57 35.89 3.08
6272 7308 9.788889 AATAGGTACCTAATAATAAGGCACAAC 57.211 33.333 25.25 0.00 37.67 3.32
6309 7345 2.730550 AAGTGCTTTGCCTTGTATGC 57.269 45.000 0.00 0.00 0.00 3.14
6320 7356 3.995705 TGCCTTGTATGCAAAAAGATTGC 59.004 39.130 6.23 6.23 45.11 3.56
6321 7357 4.248058 GCCTTGTATGCAAAAAGATTGCT 58.752 39.130 13.59 3.33 45.13 3.91
6340 7376 2.155539 GCTTTTAATTTGCAGCACCACG 59.844 45.455 0.00 0.00 32.17 4.94
6448 7484 1.949525 CCACCCAATCGGCTAAATCTG 59.050 52.381 0.00 0.00 33.26 2.90
6459 7495 3.690685 TAAATCTGCACCCCGCCGG 62.691 63.158 0.00 0.00 41.33 6.13
6486 7522 2.125673 CCGTCGCGGGATCTGTTT 60.126 61.111 6.13 0.00 44.15 2.83
6498 7534 3.804873 GGGATCTGTTTAGCATCTTCGTC 59.195 47.826 0.00 0.00 0.00 4.20
6533 7569 0.031178 GATCAAATCCGCCACCATGC 59.969 55.000 0.00 0.00 0.00 4.06
6539 7575 3.443045 CCGCCACCATGCAACCTC 61.443 66.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 6.051074 GTCCATCTCATCACATAACATCACA 58.949 40.000 0.00 0.00 0.00 3.58
48 49 5.068987 TCGTCCATCTCATCACATAACATCA 59.931 40.000 0.00 0.00 0.00 3.07
122 125 1.356398 GGGTAGGGTGGATTTGGTTCA 59.644 52.381 0.00 0.00 0.00 3.18
150 173 3.186047 CTAAACACGGGAGCGGCG 61.186 66.667 0.51 0.51 0.00 6.46
225 251 3.650139 TCTCCACTCTTCGTGCTTTTAC 58.350 45.455 0.00 0.00 42.42 2.01
324 350 3.216147 ACTTGCCATGTTAAACATCGC 57.784 42.857 0.00 0.00 41.99 4.58
377 665 7.736691 AGATAGATTGAGGAAGATAACCATGGA 59.263 37.037 21.47 0.00 0.00 3.41
435 723 2.159037 TGTAGTCTTGTGCGTACTCTCG 59.841 50.000 4.97 0.00 0.00 4.04
436 724 3.188873 AGTGTAGTCTTGTGCGTACTCTC 59.811 47.826 4.97 0.00 0.00 3.20
437 725 3.147629 AGTGTAGTCTTGTGCGTACTCT 58.852 45.455 4.97 1.43 0.00 3.24
438 726 3.555917 AGTGTAGTCTTGTGCGTACTC 57.444 47.619 4.97 0.00 0.00 2.59
439 727 5.443185 TTAAGTGTAGTCTTGTGCGTACT 57.557 39.130 4.97 0.00 0.00 2.73
440 728 6.701432 ATTTAAGTGTAGTCTTGTGCGTAC 57.299 37.500 0.00 0.00 0.00 3.67
441 729 8.815141 TTAATTTAAGTGTAGTCTTGTGCGTA 57.185 30.769 0.00 0.00 0.00 4.42
443 731 8.996988 TTTTAATTTAAGTGTAGTCTTGTGCG 57.003 30.769 0.00 0.00 0.00 5.34
570 861 9.956720 CAATTTATGATCACAAGATTTAGACCC 57.043 33.333 0.00 0.00 33.72 4.46
638 929 9.146984 TCCGTATCTAGACAAATTTAACACAAG 57.853 33.333 0.00 0.00 0.00 3.16
685 976 8.352942 GCCCCAAATTACTTGTCATTTATCTAG 58.647 37.037 0.00 0.00 32.65 2.43
686 977 7.012894 CGCCCCAAATTACTTGTCATTTATCTA 59.987 37.037 0.00 0.00 32.65 1.98
688 979 5.977129 CGCCCCAAATTACTTGTCATTTATC 59.023 40.000 0.00 0.00 32.65 1.75
690 981 4.767928 ACGCCCCAAATTACTTGTCATTTA 59.232 37.500 0.00 0.00 32.65 1.40
692 983 3.161866 ACGCCCCAAATTACTTGTCATT 58.838 40.909 0.00 0.00 32.65 2.57
693 984 2.802719 ACGCCCCAAATTACTTGTCAT 58.197 42.857 0.00 0.00 32.65 3.06
851 1423 1.742761 CACTTGGCCAGATACCACTG 58.257 55.000 5.11 0.00 36.76 3.66
961 1533 2.147958 TGCCTAACGTGTTTGGTGATC 58.852 47.619 13.38 0.00 37.69 2.92
1106 1678 1.490490 TGATGATGGCAAGGGAGTACC 59.510 52.381 0.00 0.00 40.67 3.34
1221 1798 1.307430 GGGAGAGGAAGAGCCCCTT 60.307 63.158 0.00 0.00 37.37 3.95
1317 1897 4.185413 CACGAATGACGGGGTCAG 57.815 61.111 4.65 0.00 46.04 3.51
1677 2295 0.252197 GGTGAATTACGGGCAGTCCT 59.748 55.000 0.00 0.00 0.00 3.85
1876 2496 4.898829 TCCATTTCTATCCATTTGTGCG 57.101 40.909 0.00 0.00 0.00 5.34
1919 2539 5.927030 TGTCGCAGAAATGAATGTCTAAAC 58.073 37.500 0.00 0.00 39.69 2.01
2219 2839 1.063616 CAGCTGATCAATGCCGTTCAG 59.936 52.381 8.42 0.00 38.86 3.02
2669 3299 4.699735 TGTGCGATAAATTCATTGTCAGGT 59.300 37.500 0.00 0.00 0.00 4.00
2866 3499 3.007635 GCAAATTCGTAGGCCAGTAAGT 58.992 45.455 5.01 0.00 0.00 2.24
3435 4068 4.446371 AGAATCCTTTCTTACTGCGATGG 58.554 43.478 0.00 0.00 39.18 3.51
3598 4380 2.499214 TTTTTGCGTCAGTTGGCCT 58.501 47.368 3.32 0.00 0.00 5.19
3727 4509 4.956075 AGGGTGAACAAAAGAAGTGAATGT 59.044 37.500 0.00 0.00 0.00 2.71
4474 5285 5.442391 TCCCTAGCAACACAAAGTAACTTT 58.558 37.500 0.00 0.00 33.58 2.66
4599 5418 5.921976 CACAAATCTAGTTCAAGCAATGCAA 59.078 36.000 8.35 0.00 0.00 4.08
4935 5759 4.443978 ACAGGGTGATCCATAAGATTGG 57.556 45.455 0.00 0.00 34.42 3.16
5424 6429 1.202855 AGATGCGCAGGCCTATTCAAT 60.203 47.619 18.32 0.00 38.85 2.57
5439 6444 1.672356 AACACCAGCCGTGAGATGC 60.672 57.895 8.44 0.00 46.20 3.91
5441 6446 0.108585 AACAACACCAGCCGTGAGAT 59.891 50.000 8.44 0.00 46.20 2.75
5442 6447 0.107410 AAACAACACCAGCCGTGAGA 60.107 50.000 8.44 0.00 46.20 3.27
5518 6548 5.050091 CGTCTATGTTTACAATCCATCAGGC 60.050 44.000 0.00 0.00 33.74 4.85
5685 6719 0.456824 CACTAGTGCGCGACTGATGT 60.457 55.000 12.10 8.76 35.96 3.06
5691 6725 0.914551 CACATACACTAGTGCGCGAC 59.085 55.000 22.90 5.29 0.00 5.19
5816 6850 4.101448 ACAGGAGGGGCATGCGTC 62.101 66.667 12.44 8.16 0.00 5.19
5923 6957 0.961019 TGATTTTGGCTGCCTCACAC 59.039 50.000 21.03 9.21 0.00 3.82
5924 6958 0.961019 GTGATTTTGGCTGCCTCACA 59.039 50.000 25.28 14.21 36.94 3.58
5932 6967 2.112998 CATCATGGGGTGATTTTGGCT 58.887 47.619 0.00 0.00 45.25 4.75
5980 7015 2.421107 CCATCTCAAGGGTCCATGACAG 60.421 54.545 0.00 0.00 33.68 3.51
6024 7059 1.265095 TCTTCGTGTCGTGTGACCTAC 59.735 52.381 0.00 0.00 44.86 3.18
6025 7060 1.534163 CTCTTCGTGTCGTGTGACCTA 59.466 52.381 0.00 0.00 44.86 3.08
6028 7063 1.276145 GGCTCTTCGTGTCGTGTGAC 61.276 60.000 0.00 0.00 45.71 3.67
6039 7074 3.532155 CCTCTCGGGGGCTCTTCG 61.532 72.222 0.00 0.00 0.00 3.79
6077 7113 2.573340 CTTTGCCCCGTCCATTGC 59.427 61.111 0.00 0.00 0.00 3.56
6097 7133 4.135153 CCTCCACGGGCGAGACTG 62.135 72.222 4.89 0.00 0.00 3.51
6139 7175 6.547510 GGGGCATCATTACTCTTGTAAAAGAT 59.452 38.462 0.00 0.00 41.36 2.40
6160 7196 0.463833 CCTATTGGAGACGTTGGGGC 60.464 60.000 0.00 0.00 34.57 5.80
6161 7197 0.909623 ACCTATTGGAGACGTTGGGG 59.090 55.000 0.00 0.00 37.04 4.96
6162 7198 2.159000 GGTACCTATTGGAGACGTTGGG 60.159 54.545 4.06 0.00 37.04 4.12
6163 7199 3.175109 GGTACCTATTGGAGACGTTGG 57.825 52.381 4.06 0.00 37.04 3.77
6176 7212 8.961353 TGGTTGTGCCTTATTATTGGGTACCTA 61.961 40.741 12.72 1.71 44.58 3.08
6177 7213 8.236749 TGGTTGTGCCTTATTATTGGGTACCT 62.237 42.308 12.72 0.00 44.58 3.08
6178 7214 6.099539 TGGTTGTGCCTTATTATTGGGTACC 61.100 44.000 2.17 2.17 44.55 3.34
6179 7215 4.951094 TGGTTGTGCCTTATTATTGGGTAC 59.049 41.667 0.00 0.00 38.35 3.34
6180 7216 5.194473 TGGTTGTGCCTTATTATTGGGTA 57.806 39.130 0.00 0.00 38.35 3.69
6181 7217 4.054359 TGGTTGTGCCTTATTATTGGGT 57.946 40.909 0.00 0.00 38.35 4.51
6182 7218 4.466015 AGTTGGTTGTGCCTTATTATTGGG 59.534 41.667 0.00 0.00 38.35 4.12
6183 7219 5.394115 GGAGTTGGTTGTGCCTTATTATTGG 60.394 44.000 0.00 0.00 38.35 3.16
6184 7220 5.184864 TGGAGTTGGTTGTGCCTTATTATTG 59.815 40.000 0.00 0.00 38.35 1.90
6185 7221 5.329399 TGGAGTTGGTTGTGCCTTATTATT 58.671 37.500 0.00 0.00 38.35 1.40
6186 7222 4.929479 TGGAGTTGGTTGTGCCTTATTAT 58.071 39.130 0.00 0.00 38.35 1.28
6187 7223 4.331968 CTGGAGTTGGTTGTGCCTTATTA 58.668 43.478 0.00 0.00 38.35 0.98
6188 7224 3.157087 CTGGAGTTGGTTGTGCCTTATT 58.843 45.455 0.00 0.00 38.35 1.40
6189 7225 2.795329 CTGGAGTTGGTTGTGCCTTAT 58.205 47.619 0.00 0.00 38.35 1.73
6190 7226 1.817740 GCTGGAGTTGGTTGTGCCTTA 60.818 52.381 0.00 0.00 38.35 2.69
6191 7227 1.109323 GCTGGAGTTGGTTGTGCCTT 61.109 55.000 0.00 0.00 38.35 4.35
6192 7228 1.529244 GCTGGAGTTGGTTGTGCCT 60.529 57.895 0.00 0.00 38.35 4.75
6193 7229 1.181098 ATGCTGGAGTTGGTTGTGCC 61.181 55.000 0.00 0.00 37.90 5.01
6194 7230 0.242017 GATGCTGGAGTTGGTTGTGC 59.758 55.000 0.00 0.00 0.00 4.57
6195 7231 1.901591 AGATGCTGGAGTTGGTTGTG 58.098 50.000 0.00 0.00 0.00 3.33
6196 7232 2.664402 AAGATGCTGGAGTTGGTTGT 57.336 45.000 0.00 0.00 0.00 3.32
6197 7233 5.649782 ATAAAAGATGCTGGAGTTGGTTG 57.350 39.130 0.00 0.00 0.00 3.77
6198 7234 7.175104 TCTTATAAAAGATGCTGGAGTTGGTT 58.825 34.615 0.00 0.00 36.80 3.67
6199 7235 6.721318 TCTTATAAAAGATGCTGGAGTTGGT 58.279 36.000 0.00 0.00 36.80 3.67
6200 7236 6.825721 ACTCTTATAAAAGATGCTGGAGTTGG 59.174 38.462 0.00 0.00 40.92 3.77
6201 7237 7.856145 ACTCTTATAAAAGATGCTGGAGTTG 57.144 36.000 0.00 0.00 40.92 3.16
6203 7239 9.553064 CATTACTCTTATAAAAGATGCTGGAGT 57.447 33.333 0.00 0.00 40.92 3.85
6204 7240 9.770097 TCATTACTCTTATAAAAGATGCTGGAG 57.230 33.333 0.00 0.00 40.92 3.86
6207 7243 9.823098 GCATCATTACTCTTATAAAAGATGCTG 57.177 33.333 18.87 3.46 43.92 4.41
6208 7244 9.007901 GGCATCATTACTCTTATAAAAGATGCT 57.992 33.333 22.03 0.00 45.03 3.79
6209 7245 8.239998 GGGCATCATTACTCTTATAAAAGATGC 58.760 37.037 18.39 18.39 45.00 3.91
6210 7246 8.734386 GGGGCATCATTACTCTTATAAAAGATG 58.266 37.037 0.00 0.00 40.92 2.90
6211 7247 8.448008 TGGGGCATCATTACTCTTATAAAAGAT 58.552 33.333 0.00 0.00 40.92 2.40
6212 7248 7.811282 TGGGGCATCATTACTCTTATAAAAGA 58.189 34.615 0.00 0.00 39.47 2.52
6213 7249 7.308830 GCTGGGGCATCATTACTCTTATAAAAG 60.309 40.741 0.00 0.00 38.54 2.27
6214 7250 6.490040 GCTGGGGCATCATTACTCTTATAAAA 59.510 38.462 0.00 0.00 38.54 1.52
6215 7251 6.003950 GCTGGGGCATCATTACTCTTATAAA 58.996 40.000 0.00 0.00 38.54 1.40
6216 7252 5.073008 TGCTGGGGCATCATTACTCTTATAA 59.927 40.000 0.00 0.00 44.28 0.98
6217 7253 4.597075 TGCTGGGGCATCATTACTCTTATA 59.403 41.667 0.00 0.00 44.28 0.98
6218 7254 3.395607 TGCTGGGGCATCATTACTCTTAT 59.604 43.478 0.00 0.00 44.28 1.73
6219 7255 2.777114 TGCTGGGGCATCATTACTCTTA 59.223 45.455 0.00 0.00 44.28 2.10
6220 7256 1.565759 TGCTGGGGCATCATTACTCTT 59.434 47.619 0.00 0.00 44.28 2.85
6221 7257 1.216064 TGCTGGGGCATCATTACTCT 58.784 50.000 0.00 0.00 44.28 3.24
6222 7258 3.806941 TGCTGGGGCATCATTACTC 57.193 52.632 0.00 0.00 44.28 2.59
6231 7267 2.942893 CCTATTGGAGATGCTGGGGCA 61.943 57.143 0.00 0.00 44.10 5.36
6232 7268 0.251077 CCTATTGGAGATGCTGGGGC 60.251 60.000 0.00 0.00 35.51 5.80
6247 7283 8.380867 GGTTGTGCCTTATTATTAGGTACCTAT 58.619 37.037 22.36 11.09 44.78 2.57
6256 7292 7.600752 GCAAAAAGTGGTTGTGCCTTATTATTA 59.399 33.333 0.00 0.00 38.35 0.98
6314 7350 4.692155 GGTGCTGCAAATTAAAAGCAATCT 59.308 37.500 2.77 0.00 46.48 2.40
6315 7351 4.451774 TGGTGCTGCAAATTAAAAGCAATC 59.548 37.500 2.77 6.96 46.48 2.67
6316 7352 4.213906 GTGGTGCTGCAAATTAAAAGCAAT 59.786 37.500 2.77 0.00 46.48 3.56
6318 7354 3.129871 GTGGTGCTGCAAATTAAAAGCA 58.870 40.909 2.77 5.10 43.10 3.91
6319 7355 2.155539 CGTGGTGCTGCAAATTAAAAGC 59.844 45.455 2.77 0.00 36.18 3.51
6320 7356 3.637432 TCGTGGTGCTGCAAATTAAAAG 58.363 40.909 2.77 0.00 0.00 2.27
6321 7357 3.717400 TCGTGGTGCTGCAAATTAAAA 57.283 38.095 2.77 0.00 0.00 1.52
6340 7376 4.521256 TGTAACACTTGGTGCCCTATTTTC 59.479 41.667 0.00 0.00 36.98 2.29
6420 7456 1.573829 CCGATTGGGTGGTGTTGACG 61.574 60.000 0.00 0.00 0.00 4.35
6472 7508 0.464036 ATGCTAAACAGATCCCGCGA 59.536 50.000 8.23 0.00 0.00 5.87
6473 7509 0.861837 GATGCTAAACAGATCCCGCG 59.138 55.000 0.00 0.00 0.00 6.46
6514 7550 0.031178 GCATGGTGGCGGATTTGATC 59.969 55.000 0.00 0.00 0.00 2.92
6517 7553 0.737019 GTTGCATGGTGGCGGATTTG 60.737 55.000 0.00 0.00 36.28 2.32
6533 7569 1.613437 GGTGTGGTGAAATGGAGGTTG 59.387 52.381 0.00 0.00 0.00 3.77
6539 7575 1.247567 GAGGTGGTGTGGTGAAATGG 58.752 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.