Multiple sequence alignment - TraesCS1A01G083000

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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 TraesCS1A01G083000 chr1A 100.000 3972 0 0 1 3972 66174277 66178248 0.000000e+00 7336
1 TraesCS1A01G083000 chr1A 96.535 606 21 0 3355 3960 300564438 300565043 0.000000e+00 1003
2 TraesCS1A01G083000 chr1A 95.098 612 28 1 3351 3960 392499300 392498689 0.000000e+00 963
3 TraesCS1A01G083000 chr1A 94.079 608 34 2 3353 3960 469308490 469307885 0.000000e+00 922
4 TraesCS1A01G083000 chr1D 91.724 3323 157 48 68 3349 67860665 67863910 0.000000e+00 4505
5 TraesCS1A01G083000 chr1B 92.481 2926 133 34 474 3355 109210835 109213717 0.000000e+00 4104
6 TraesCS1A01G083000 chr1B 87.500 232 24 2 211 440 109197985 109198213 3.040000e-66 263
7 TraesCS1A01G083000 chr7A 94.910 609 30 1 3352 3960 404469710 404470317 0.000000e+00 952
8 TraesCS1A01G083000 chr7A 95.804 572 23 1 3390 3960 47043487 47044058 0.000000e+00 922
9 TraesCS1A01G083000 chr3A 94.281 612 32 2 3351 3960 508532567 508533177 0.000000e+00 933
10 TraesCS1A01G083000 chr5A 94.079 608 33 2 3355 3960 576588292 576587686 0.000000e+00 920
11 TraesCS1A01G083000 chr5A 92.739 606 39 2 3355 3960 573303724 573304324 0.000000e+00 870
12 TraesCS1A01G083000 chr5D 91.598 607 50 1 3355 3960 79107037 79107643 0.000000e+00 837


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 TraesCS1A01G083000 chr1A 66174277 66178248 3971 False 7336 7336 100.000 1 3972 1 chr1A.!!$F1 3971
1 TraesCS1A01G083000 chr1A 300564438 300565043 605 False 1003 1003 96.535 3355 3960 1 chr1A.!!$F2 605
2 TraesCS1A01G083000 chr1A 392498689 392499300 611 True 963 963 95.098 3351 3960 1 chr1A.!!$R1 609
3 TraesCS1A01G083000 chr1A 469307885 469308490 605 True 922 922 94.079 3353 3960 1 chr1A.!!$R2 607
4 TraesCS1A01G083000 chr1D 67860665 67863910 3245 False 4505 4505 91.724 68 3349 1 chr1D.!!$F1 3281
5 TraesCS1A01G083000 chr1B 109210835 109213717 2882 False 4104 4104 92.481 474 3355 1 chr1B.!!$F2 2881
6 TraesCS1A01G083000 chr7A 404469710 404470317 607 False 952 952 94.910 3352 3960 1 chr7A.!!$F2 608
7 TraesCS1A01G083000 chr7A 47043487 47044058 571 False 922 922 95.804 3390 3960 1 chr7A.!!$F1 570
8 TraesCS1A01G083000 chr3A 508532567 508533177 610 False 933 933 94.281 3351 3960 1 chr3A.!!$F1 609
9 TraesCS1A01G083000 chr5A 576587686 576588292 606 True 920 920 94.079 3355 3960 1 chr5A.!!$R1 605
10 TraesCS1A01G083000 chr5A 573303724 573304324 600 False 870 870 92.739 3355 3960 1 chr5A.!!$F1 605
11 TraesCS1A01G083000 chr5D 79107037 79107643 606 False 837 837 91.598 3355 3960 1 chr5D.!!$F1 605

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
991 998 0.174845 TATATATCCACGCCTGCCGC 59.825 55.0 0.00 0.0 41.76 6.53 F
2099 2128 0.037697 GTGAGCACCGGACACATACA 60.038 55.0 9.46 0.0 35.06 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2330 0.942410 CCACTTCGGTGTACGGTGTG 60.942 60.0 0.00 0.0 43.91 3.82 R
3218 3268 0.039527 CACCGGGCACAGCTTTAAAC 60.040 55.0 6.32 0.0 0.00 2.01 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
29 30 2.233271 CACATATTGGGTGGGAGATGC 58.767 52.381 0.00 0.00 32.65 3.91
30 31 1.145738 ACATATTGGGTGGGAGATGCC 59.854 52.381 0.00 0.00 0.00 4.40
31 32 1.145531 CATATTGGGTGGGAGATGCCA 59.854 52.381 0.00 0.00 38.95 4.92
32 33 0.846015 TATTGGGTGGGAGATGCCAG 59.154 55.000 0.00 0.00 38.95 4.85
33 34 2.578586 ATTGGGTGGGAGATGCCAGC 62.579 60.000 13.52 13.52 38.95 4.85
34 35 3.731728 GGGTGGGAGATGCCAGCA 61.732 66.667 21.69 0.00 38.95 4.41
35 36 2.356278 GGTGGGAGATGCCAGCAA 59.644 61.111 16.50 0.00 38.95 3.91
36 37 1.304381 GGTGGGAGATGCCAGCAAA 60.304 57.895 16.50 0.00 38.95 3.68
37 38 0.685458 GGTGGGAGATGCCAGCAAAT 60.685 55.000 16.50 0.00 38.95 2.32
38 39 0.743097 GTGGGAGATGCCAGCAAATC 59.257 55.000 0.00 0.00 38.95 2.17
39 40 0.396139 TGGGAGATGCCAGCAAATCC 60.396 55.000 14.87 14.87 38.95 3.01
40 41 0.396139 GGGAGATGCCAGCAAATCCA 60.396 55.000 21.31 0.00 36.76 3.41
41 42 1.477553 GGAGATGCCAGCAAATCCAA 58.522 50.000 17.19 0.00 35.77 3.53
42 43 2.037144 GGAGATGCCAGCAAATCCAAT 58.963 47.619 17.19 0.00 35.77 3.16
43 44 3.225104 GGAGATGCCAGCAAATCCAATA 58.775 45.455 17.19 0.00 35.77 1.90
44 45 3.255149 GGAGATGCCAGCAAATCCAATAG 59.745 47.826 17.19 0.00 35.77 1.73
45 46 3.228453 AGATGCCAGCAAATCCAATAGG 58.772 45.455 0.00 0.00 0.00 2.57
46 47 2.530460 TGCCAGCAAATCCAATAGGT 57.470 45.000 0.00 0.00 35.89 3.08
47 48 2.818921 TGCCAGCAAATCCAATAGGTT 58.181 42.857 0.00 0.00 35.89 3.50
48 49 2.496871 TGCCAGCAAATCCAATAGGTTG 59.503 45.455 0.00 0.00 35.89 3.77
57 58 4.675063 ATCCAATAGGTTGGGTTGACTT 57.325 40.909 7.30 0.00 46.88 3.01
58 59 5.010708 ATCCAATAGGTTGGGTTGACTTT 57.989 39.130 7.30 0.00 46.88 2.66
59 60 5.016831 ATCCAATAGGTTGGGTTGACTTTC 58.983 41.667 7.30 0.00 46.88 2.62
60 61 5.222337 ATCCAATAGGTTGGGTTGACTTTCT 60.222 40.000 7.30 0.00 46.88 2.52
61 62 6.011981 ATCCAATAGGTTGGGTTGACTTTCTA 60.012 38.462 7.30 0.00 46.88 2.10
62 63 6.743575 CAATAGGTTGGGTTGACTTTCTAG 57.256 41.667 0.00 0.00 0.00 2.43
63 64 3.790089 AGGTTGGGTTGACTTTCTAGG 57.210 47.619 0.00 0.00 0.00 3.02
64 65 3.053826 AGGTTGGGTTGACTTTCTAGGT 58.946 45.455 0.00 0.00 0.00 3.08
65 66 3.462205 AGGTTGGGTTGACTTTCTAGGTT 59.538 43.478 0.00 0.00 0.00 3.50
66 67 3.568430 GGTTGGGTTGACTTTCTAGGTTG 59.432 47.826 0.00 0.00 0.00 3.77
79 80 2.781174 TCTAGGTTGGTTTGGGTTGACT 59.219 45.455 0.00 0.00 0.00 3.41
92 93 3.072476 TGGGTTGACTTTTCTAGGTCCAG 59.928 47.826 0.00 0.00 0.00 3.86
97 98 1.348036 ACTTTTCTAGGTCCAGCGCTT 59.652 47.619 7.50 0.00 0.00 4.68
111 112 2.388232 CGCTTACTGGGTTGTCCGC 61.388 63.158 0.00 0.00 38.76 5.54
112 113 1.003718 GCTTACTGGGTTGTCCGCT 60.004 57.895 0.00 0.00 38.76 5.52
113 114 0.605589 GCTTACTGGGTTGTCCGCTT 60.606 55.000 0.00 0.00 38.76 4.68
114 115 1.338389 GCTTACTGGGTTGTCCGCTTA 60.338 52.381 0.00 0.00 38.76 3.09
124 125 4.226761 GGTTGTCCGCTTAAACATTTGAG 58.773 43.478 0.00 0.00 0.00 3.02
133 134 6.294286 CCGCTTAAACATTTGAGAAGGGTTTA 60.294 38.462 0.62 0.00 34.00 2.01
135 136 7.812669 CGCTTAAACATTTGAGAAGGGTTTAAT 59.187 33.333 0.00 0.00 40.80 1.40
140 141 7.360113 ACATTTGAGAAGGGTTTAATGTGTT 57.640 32.000 0.00 0.00 35.55 3.32
142 143 5.682943 TTGAGAAGGGTTTAATGTGTTCG 57.317 39.130 0.00 0.00 0.00 3.95
144 145 4.070009 GAGAAGGGTTTAATGTGTTCGGT 58.930 43.478 0.00 0.00 0.00 4.69
146 147 2.786777 AGGGTTTAATGTGTTCGGTCC 58.213 47.619 0.00 0.00 0.00 4.46
149 150 3.686241 GGGTTTAATGTGTTCGGTCCTAC 59.314 47.826 0.00 0.00 0.00 3.18
166 167 0.601558 TACCGGACTTCTCACTGCAC 59.398 55.000 9.46 0.00 0.00 4.57
170 171 1.810031 CGGACTTCTCACTGCACCAAA 60.810 52.381 0.00 0.00 0.00 3.28
175 176 0.836606 TCTCACTGCACCAAAGGACA 59.163 50.000 0.00 0.00 0.00 4.02
194 195 0.796312 AACGAATCGTGCACCATCAC 59.204 50.000 9.74 1.58 39.99 3.06
195 196 1.019278 ACGAATCGTGCACCATCACC 61.019 55.000 7.77 0.00 39.18 4.02
196 197 1.715585 GAATCGTGCACCATCACCG 59.284 57.895 12.15 0.00 33.57 4.94
197 198 2.309764 GAATCGTGCACCATCACCGC 62.310 60.000 12.15 0.00 33.57 5.68
290 293 4.559229 GCCGCCCGTCGTAGGTAC 62.559 72.222 0.00 0.00 36.19 3.34
314 317 4.148825 GGACGCAGGCCTCGACAT 62.149 66.667 25.01 8.31 0.00 3.06
346 349 0.826715 ATGCCACGAGAGCACATACT 59.173 50.000 0.00 0.00 44.40 2.12
347 350 1.470051 TGCCACGAGAGCACATACTA 58.530 50.000 0.00 0.00 34.69 1.82
348 351 1.134367 TGCCACGAGAGCACATACTAC 59.866 52.381 0.00 0.00 34.69 2.73
354 357 2.791560 CGAGAGCACATACTACATGCAC 59.208 50.000 0.00 0.00 41.97 4.57
368 371 1.078759 ATGCACGTCGAGCAACTAGC 61.079 55.000 20.90 1.87 46.27 3.42
381 386 1.164041 AACTAGCGTGTGTTGGTGGC 61.164 55.000 0.00 0.00 0.00 5.01
424 429 1.467342 GAGTGTCCGCAAATGTTACCC 59.533 52.381 0.00 0.00 0.00 3.69
426 431 1.135939 GTCCGCAAATGTTACCCGC 59.864 57.895 0.00 0.00 0.00 6.13
449 454 4.139420 CGTGAAAGCTGCGGCGAG 62.139 66.667 12.98 6.53 44.37 5.03
450 455 2.738521 GTGAAAGCTGCGGCGAGA 60.739 61.111 12.98 0.00 44.37 4.04
451 456 2.738521 TGAAAGCTGCGGCGAGAC 60.739 61.111 12.98 6.01 44.37 3.36
460 465 4.436998 CGGCGAGACCCTGGACAC 62.437 72.222 0.00 0.00 33.26 3.67
461 466 3.311110 GGCGAGACCCTGGACACA 61.311 66.667 0.00 0.00 0.00 3.72
462 467 2.741092 GCGAGACCCTGGACACAA 59.259 61.111 0.00 0.00 0.00 3.33
544 550 1.455773 AGCCACCGGATCGAGATCA 60.456 57.895 9.46 0.00 39.54 2.92
547 553 0.312416 CCACCGGATCGAGATCACTC 59.688 60.000 9.46 0.00 39.54 3.51
764 771 1.740718 GCTCTTCCTTAACTGCTCCCG 60.741 57.143 0.00 0.00 0.00 5.14
799 806 2.811317 GGTTCAGACGGCTCTGCG 60.811 66.667 0.00 0.00 43.45 5.18
813 820 4.578898 TGCGTCGAGTTGGTGCGT 62.579 61.111 0.00 0.00 0.00 5.24
814 821 4.059459 GCGTCGAGTTGGTGCGTG 62.059 66.667 0.00 0.00 0.00 5.34
815 822 4.059459 CGTCGAGTTGGTGCGTGC 62.059 66.667 0.00 0.00 0.00 5.34
816 823 4.059459 GTCGAGTTGGTGCGTGCG 62.059 66.667 0.00 0.00 0.00 5.34
819 826 2.736995 GAGTTGGTGCGTGCGCTA 60.737 61.111 17.49 0.00 42.51 4.26
852 859 2.932194 TCCTTCCCTGCAGCTGCT 60.932 61.111 36.61 0.00 42.66 4.24
853 860 2.750637 CCTTCCCTGCAGCTGCTG 60.751 66.667 36.61 34.20 42.66 4.41
902 909 7.403671 GGGAAGAGGGGAGATAAAATAATACC 58.596 42.308 0.00 0.00 0.00 2.73
983 990 4.083110 ACCTCCGTCGTTTATATATCCACG 60.083 45.833 9.38 9.38 0.00 4.94
991 998 0.174845 TATATATCCACGCCTGCCGC 59.825 55.000 0.00 0.00 41.76 6.53
1042 1049 1.876664 GCCGTGCTCTTCCTTTTCC 59.123 57.895 0.00 0.00 0.00 3.13
1683 1702 0.733223 GAAGCAAGTCCGTCGAGTCC 60.733 60.000 0.00 0.00 0.00 3.85
1824 1843 3.446570 GTGCCTGTCCAGCATGCC 61.447 66.667 15.66 0.00 43.29 4.40
1855 1874 1.115930 AGCGGCGTTATCCCAGAGAT 61.116 55.000 9.37 0.00 39.15 2.75
1906 1925 0.953960 ACCGAGATTGCAACCGGAAC 60.954 55.000 30.84 9.71 44.29 3.62
1907 1926 1.644786 CCGAGATTGCAACCGGAACC 61.645 60.000 24.12 0.00 44.29 3.62
2004 2023 1.302383 CGACCTCGTCTGTCTGCTCT 61.302 60.000 0.00 0.00 34.11 4.09
2013 2032 1.287730 CTGTCTGCTCTGACAACGGC 61.288 60.000 10.12 0.00 44.98 5.68
2096 2125 2.347490 GGTGAGCACCGGACACAT 59.653 61.111 9.46 0.00 42.29 3.21
2097 2126 1.594833 GGTGAGCACCGGACACATA 59.405 57.895 9.46 0.00 42.29 2.29
2098 2127 0.739813 GGTGAGCACCGGACACATAC 60.740 60.000 9.46 0.00 42.29 2.39
2099 2128 0.037697 GTGAGCACCGGACACATACA 60.038 55.000 9.46 0.00 35.06 2.29
2100 2129 0.901827 TGAGCACCGGACACATACAT 59.098 50.000 9.46 0.00 0.00 2.29
2101 2130 1.290203 GAGCACCGGACACATACATG 58.710 55.000 9.46 0.00 0.00 3.21
2102 2131 0.107703 AGCACCGGACACATACATGG 60.108 55.000 9.46 0.00 0.00 3.66
2103 2132 0.392461 GCACCGGACACATACATGGT 60.392 55.000 9.46 0.00 0.00 3.55
2104 2133 1.948611 GCACCGGACACATACATGGTT 60.949 52.381 9.46 0.00 0.00 3.67
2105 2134 2.678479 GCACCGGACACATACATGGTTA 60.678 50.000 9.46 0.00 0.00 2.85
2106 2135 3.601435 CACCGGACACATACATGGTTAA 58.399 45.455 9.46 0.00 0.00 2.01
2127 2156 2.019951 CCGCGAACGCAGTACTGTT 61.020 57.895 23.44 11.35 45.00 3.16
2135 2164 2.755650 ACGCAGTACTGTTCTTCTTGG 58.244 47.619 23.44 5.41 41.94 3.61
2168 2200 2.758089 CGCAATCTGCCTGCAGGAC 61.758 63.158 37.21 25.98 41.12 3.85
2171 2203 0.323178 CAATCTGCCTGCAGGACCTT 60.323 55.000 37.21 19.12 43.75 3.50
2298 2330 6.359617 CGATCCCGAATGCACAAAATAAATAC 59.640 38.462 0.00 0.00 38.22 1.89
2343 2379 4.004982 TCTTCCGGTTGCTAAATTGGTAC 58.995 43.478 0.00 0.00 0.00 3.34
2348 2384 3.621715 CGGTTGCTAAATTGGTACTCCTC 59.378 47.826 0.00 0.00 34.23 3.71
2369 2405 5.240403 CCTCCTTGGAAGATAGCTAAATTGC 59.760 44.000 0.00 1.59 38.35 3.56
2465 2501 2.543777 ACTGCAACAAGGTACACGAT 57.456 45.000 0.00 0.00 0.00 3.73
2466 2502 2.413837 ACTGCAACAAGGTACACGATC 58.586 47.619 0.00 0.00 0.00 3.69
2475 2512 2.467880 AGGTACACGATCCATCAACCT 58.532 47.619 0.00 0.00 0.00 3.50
2477 2514 2.936498 GGTACACGATCCATCAACCTTG 59.064 50.000 0.00 0.00 0.00 3.61
2486 2523 2.892852 TCCATCAACCTTGGCAAGAAAG 59.107 45.455 28.18 16.01 34.06 2.62
2490 2527 1.682854 CAACCTTGGCAAGAAAGCTCA 59.317 47.619 28.18 0.00 34.17 4.26
2495 2532 4.141642 ACCTTGGCAAGAAAGCTCAAAAAT 60.142 37.500 28.18 0.00 34.17 1.82
2496 2533 5.070313 ACCTTGGCAAGAAAGCTCAAAAATA 59.930 36.000 28.18 0.00 34.17 1.40
2787 2826 2.047655 CGCGCAGTTCCCTTACCA 60.048 61.111 8.75 0.00 0.00 3.25
2938 2977 2.433318 GAGCACGAGCAGACACCC 60.433 66.667 7.77 0.00 45.49 4.61
2981 3020 0.390860 AGCAATGTAGCCTAGCTCCG 59.609 55.000 0.00 0.00 40.44 4.63
3092 3142 5.689383 TCTTTGTGAGACTGTAAAATGGC 57.311 39.130 0.00 0.00 0.00 4.40
3194 3244 2.989639 TGCTTCCCGCTGCAGTAT 59.010 55.556 16.64 0.00 40.11 2.12
3216 3266 2.771943 TCAATCCTGACATGTCCTACCC 59.228 50.000 22.85 0.00 0.00 3.69
3217 3267 2.774234 CAATCCTGACATGTCCTACCCT 59.226 50.000 22.85 0.74 0.00 4.34
3218 3268 1.866015 TCCTGACATGTCCTACCCTG 58.134 55.000 22.85 1.91 0.00 4.45
3219 3269 1.078823 TCCTGACATGTCCTACCCTGT 59.921 52.381 22.85 0.00 0.00 4.00
3222 3272 3.517901 CCTGACATGTCCTACCCTGTTTA 59.482 47.826 22.85 0.00 0.00 2.01
3223 3273 4.019681 CCTGACATGTCCTACCCTGTTTAA 60.020 45.833 22.85 0.00 0.00 1.52
3224 3274 5.514136 CCTGACATGTCCTACCCTGTTTAAA 60.514 44.000 22.85 0.00 0.00 1.52
3225 3275 5.556915 TGACATGTCCTACCCTGTTTAAAG 58.443 41.667 22.85 0.00 0.00 1.85
3226 3276 4.332828 ACATGTCCTACCCTGTTTAAAGC 58.667 43.478 0.00 0.00 0.00 3.51
3227 3277 4.042934 ACATGTCCTACCCTGTTTAAAGCT 59.957 41.667 0.00 0.00 0.00 3.74
3229 3279 3.393278 TGTCCTACCCTGTTTAAAGCTGT 59.607 43.478 0.00 0.00 0.00 4.40
3230 3280 3.751698 GTCCTACCCTGTTTAAAGCTGTG 59.248 47.826 0.00 0.00 0.00 3.66
3233 3283 0.603065 CCCTGTTTAAAGCTGTGCCC 59.397 55.000 0.00 0.00 0.00 5.36
3234 3284 0.240945 CCTGTTTAAAGCTGTGCCCG 59.759 55.000 0.00 0.00 0.00 6.13
3235 3285 0.240945 CTGTTTAAAGCTGTGCCCGG 59.759 55.000 0.00 0.00 0.00 5.73
3238 3288 1.801309 TTTAAAGCTGTGCCCGGTGC 61.801 55.000 0.00 4.04 41.77 5.01
3289 3353 6.703607 ACAAGAGTCAATCTGAAGTACTGTTG 59.296 38.462 17.26 17.26 43.33 3.33
3291 3355 4.319177 AGTCAATCTGAAGTACTGTTGGC 58.681 43.478 0.00 0.00 0.00 4.52
3312 3376 3.281395 CATGCATCATGGCGCCGA 61.281 61.111 23.90 14.82 38.11 5.54
3462 3530 5.358298 AAGTTTTTCAGCGGATTGTCTAC 57.642 39.130 0.00 0.00 0.00 2.59
3612 3683 1.134367 GGAGAAAATAAACCAGCCGCC 59.866 52.381 0.00 0.00 0.00 6.13
3624 3695 5.351948 AACCAGCCGCCAAATTATTTTAT 57.648 34.783 0.00 0.00 0.00 1.40
3819 3890 4.616953 AGCCAACATTTTTGGTTTAGACG 58.383 39.130 3.64 0.00 41.53 4.18
3863 3934 2.017049 GGACGACGGGTAGCTAGTTTA 58.983 52.381 0.00 0.00 0.00 2.01
3908 3979 3.485394 TGCAATAGACAAGCCACTGAAA 58.515 40.909 0.00 0.00 0.00 2.69
3917 3988 3.924073 ACAAGCCACTGAAAACGTTTTTC 59.076 39.130 25.86 18.49 0.00 2.29
3960 4032 8.891671 ATTTGATATAAACCATCATTTGCACC 57.108 30.769 0.00 0.00 32.63 5.01
3961 4033 7.658525 TTGATATAAACCATCATTTGCACCT 57.341 32.000 0.00 0.00 32.63 4.00
3962 4034 8.759481 TTGATATAAACCATCATTTGCACCTA 57.241 30.769 0.00 0.00 32.63 3.08
3963 4035 8.938801 TGATATAAACCATCATTTGCACCTAT 57.061 30.769 0.00 0.00 0.00 2.57
3968 4040 6.889301 AACCATCATTTGCACCTATAGATG 57.111 37.500 0.00 0.00 33.15 2.90
3969 4041 4.763793 ACCATCATTTGCACCTATAGATGC 59.236 41.667 12.58 12.58 42.40 3.91
3970 4042 5.008331 CCATCATTTGCACCTATAGATGCT 58.992 41.667 19.94 0.00 42.55 3.79
3971 4043 5.123502 CCATCATTTGCACCTATAGATGCTC 59.876 44.000 19.94 0.00 42.55 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.233271 GCATCTCCCACCCAATATGTG 58.767 52.381 0.00 0.00 0.00 3.21
10 11 1.145738 GGCATCTCCCACCCAATATGT 59.854 52.381 0.00 0.00 0.00 2.29
11 12 1.145531 TGGCATCTCCCACCCAATATG 59.854 52.381 0.00 0.00 0.00 1.78
12 13 1.426598 CTGGCATCTCCCACCCAATAT 59.573 52.381 0.00 0.00 0.00 1.28
13 14 0.846015 CTGGCATCTCCCACCCAATA 59.154 55.000 0.00 0.00 0.00 1.90
14 15 1.616921 CTGGCATCTCCCACCCAAT 59.383 57.895 0.00 0.00 0.00 3.16
15 16 3.089838 CTGGCATCTCCCACCCAA 58.910 61.111 0.00 0.00 0.00 4.12
16 17 3.731728 GCTGGCATCTCCCACCCA 61.732 66.667 0.00 0.00 0.00 4.51
17 18 2.786512 TTTGCTGGCATCTCCCACCC 62.787 60.000 0.00 0.00 0.00 4.61
18 19 0.685458 ATTTGCTGGCATCTCCCACC 60.685 55.000 0.00 0.00 0.00 4.61
19 20 0.743097 GATTTGCTGGCATCTCCCAC 59.257 55.000 0.00 0.00 0.00 4.61
20 21 0.396139 GGATTTGCTGGCATCTCCCA 60.396 55.000 10.81 0.00 0.00 4.37
21 22 0.396139 TGGATTTGCTGGCATCTCCC 60.396 55.000 16.15 8.34 0.00 4.30
22 23 1.477553 TTGGATTTGCTGGCATCTCC 58.522 50.000 13.55 13.55 0.00 3.71
23 24 3.255149 CCTATTGGATTTGCTGGCATCTC 59.745 47.826 0.00 0.00 34.57 2.75
24 25 3.228453 CCTATTGGATTTGCTGGCATCT 58.772 45.455 0.00 0.00 34.57 2.90
25 26 2.961062 ACCTATTGGATTTGCTGGCATC 59.039 45.455 0.00 0.00 37.04 3.91
26 27 3.036452 ACCTATTGGATTTGCTGGCAT 57.964 42.857 0.00 0.00 37.04 4.40
27 28 2.496871 CAACCTATTGGATTTGCTGGCA 59.503 45.455 0.00 0.00 37.04 4.92
28 29 3.169355 CAACCTATTGGATTTGCTGGC 57.831 47.619 0.00 0.00 37.04 4.85
39 40 5.648092 CCTAGAAAGTCAACCCAACCTATTG 59.352 44.000 0.00 0.00 35.40 1.90
40 41 5.312443 ACCTAGAAAGTCAACCCAACCTATT 59.688 40.000 0.00 0.00 0.00 1.73
41 42 4.850386 ACCTAGAAAGTCAACCCAACCTAT 59.150 41.667 0.00 0.00 0.00 2.57
42 43 4.237018 ACCTAGAAAGTCAACCCAACCTA 58.763 43.478 0.00 0.00 0.00 3.08
43 44 3.053826 ACCTAGAAAGTCAACCCAACCT 58.946 45.455 0.00 0.00 0.00 3.50
44 45 3.503800 ACCTAGAAAGTCAACCCAACC 57.496 47.619 0.00 0.00 0.00 3.77
45 46 3.568430 CCAACCTAGAAAGTCAACCCAAC 59.432 47.826 0.00 0.00 0.00 3.77
46 47 3.203487 ACCAACCTAGAAAGTCAACCCAA 59.797 43.478 0.00 0.00 0.00 4.12
47 48 2.781174 ACCAACCTAGAAAGTCAACCCA 59.219 45.455 0.00 0.00 0.00 4.51
48 49 3.503800 ACCAACCTAGAAAGTCAACCC 57.496 47.619 0.00 0.00 0.00 4.11
49 50 4.037565 CCAAACCAACCTAGAAAGTCAACC 59.962 45.833 0.00 0.00 0.00 3.77
50 51 4.037565 CCCAAACCAACCTAGAAAGTCAAC 59.962 45.833 0.00 0.00 0.00 3.18
51 52 4.211920 CCCAAACCAACCTAGAAAGTCAA 58.788 43.478 0.00 0.00 0.00 3.18
52 53 3.203487 ACCCAAACCAACCTAGAAAGTCA 59.797 43.478 0.00 0.00 0.00 3.41
53 54 3.828921 ACCCAAACCAACCTAGAAAGTC 58.171 45.455 0.00 0.00 0.00 3.01
54 55 3.958147 CAACCCAAACCAACCTAGAAAGT 59.042 43.478 0.00 0.00 0.00 2.66
55 56 4.037565 GTCAACCCAAACCAACCTAGAAAG 59.962 45.833 0.00 0.00 0.00 2.62
56 57 3.955551 GTCAACCCAAACCAACCTAGAAA 59.044 43.478 0.00 0.00 0.00 2.52
57 58 3.203487 AGTCAACCCAAACCAACCTAGAA 59.797 43.478 0.00 0.00 0.00 2.10
58 59 2.781174 AGTCAACCCAAACCAACCTAGA 59.219 45.455 0.00 0.00 0.00 2.43
59 60 3.223674 AGTCAACCCAAACCAACCTAG 57.776 47.619 0.00 0.00 0.00 3.02
60 61 3.673543 AAGTCAACCCAAACCAACCTA 57.326 42.857 0.00 0.00 0.00 3.08
61 62 2.543037 AAGTCAACCCAAACCAACCT 57.457 45.000 0.00 0.00 0.00 3.50
62 63 3.196901 AGAAAAGTCAACCCAAACCAACC 59.803 43.478 0.00 0.00 0.00 3.77
63 64 4.465632 AGAAAAGTCAACCCAAACCAAC 57.534 40.909 0.00 0.00 0.00 3.77
64 65 4.647399 CCTAGAAAAGTCAACCCAAACCAA 59.353 41.667 0.00 0.00 0.00 3.67
65 66 4.211920 CCTAGAAAAGTCAACCCAAACCA 58.788 43.478 0.00 0.00 0.00 3.67
66 67 4.212716 ACCTAGAAAAGTCAACCCAAACC 58.787 43.478 0.00 0.00 0.00 3.27
79 80 2.565834 AGTAAGCGCTGGACCTAGAAAA 59.434 45.455 12.58 0.00 0.00 2.29
92 93 2.388232 CGGACAACCCAGTAAGCGC 61.388 63.158 0.00 0.00 34.14 5.92
97 98 2.104451 TGTTTAAGCGGACAACCCAGTA 59.896 45.455 0.00 0.00 34.14 2.74
111 112 9.981114 ACATTAAACCCTTCTCAAATGTTTAAG 57.019 29.630 10.45 6.58 41.75 1.85
112 113 9.757227 CACATTAAACCCTTCTCAAATGTTTAA 57.243 29.630 7.94 7.94 42.29 1.52
113 114 8.919145 ACACATTAAACCCTTCTCAAATGTTTA 58.081 29.630 0.00 0.00 35.87 2.01
114 115 7.791029 ACACATTAAACCCTTCTCAAATGTTT 58.209 30.769 0.00 0.00 35.87 2.83
124 125 3.189910 GGACCGAACACATTAAACCCTTC 59.810 47.826 0.00 0.00 0.00 3.46
144 145 1.835494 CAGTGAGAAGTCCGGTAGGA 58.165 55.000 0.00 0.00 46.11 2.94
146 147 0.888619 TGCAGTGAGAAGTCCGGTAG 59.111 55.000 0.00 0.00 0.00 3.18
149 150 1.374758 GGTGCAGTGAGAAGTCCGG 60.375 63.158 0.00 0.00 0.00 5.14
166 167 1.399727 GCACGATTCGTTGTCCTTTGG 60.400 52.381 9.40 0.00 38.32 3.28
170 171 0.949105 GGTGCACGATTCGTTGTCCT 60.949 55.000 9.40 0.00 38.32 3.85
175 176 0.796312 GTGATGGTGCACGATTCGTT 59.204 50.000 15.94 0.00 38.32 3.85
198 199 3.642778 CTGTAGTCCGGTGGCCACG 62.643 68.421 29.08 22.59 0.00 4.94
199 200 2.264794 CTGTAGTCCGGTGGCCAC 59.735 66.667 28.57 28.57 0.00 5.01
200 201 3.702048 GCTGTAGTCCGGTGGCCA 61.702 66.667 0.00 0.00 0.00 5.36
201 202 4.468689 GGCTGTAGTCCGGTGGCC 62.469 72.222 0.00 0.00 0.00 5.36
202 203 4.814294 CGGCTGTAGTCCGGTGGC 62.814 72.222 0.00 0.00 42.99 5.01
309 312 0.811219 ATGCATGTGTCCGGATGTCG 60.811 55.000 7.81 0.00 38.88 4.35
314 317 2.438254 GGCATGCATGTGTCCGGA 60.438 61.111 26.79 0.00 0.00 5.14
346 349 0.038618 AGTTGCTCGACGTGCATGTA 60.039 50.000 23.45 7.94 40.34 2.29
347 350 0.038618 TAGTTGCTCGACGTGCATGT 60.039 50.000 23.45 12.38 40.34 3.21
348 351 0.642291 CTAGTTGCTCGACGTGCATG 59.358 55.000 23.45 3.82 40.34 4.06
354 357 1.442184 ACACGCTAGTTGCTCGACG 60.442 57.895 0.00 0.00 40.11 5.12
362 365 1.164041 GCCACCAACACACGCTAGTT 61.164 55.000 0.00 0.00 0.00 2.24
368 371 3.645975 GTCCGCCACCAACACACG 61.646 66.667 0.00 0.00 0.00 4.49
381 386 3.315949 TTTCCTCCCACCGGTCCG 61.316 66.667 2.59 3.60 0.00 4.79
426 431 3.793144 GCAGCTTTCACGCGAGGG 61.793 66.667 15.93 1.17 34.40 4.30
446 451 1.004918 GGTTGTGTCCAGGGTCTCG 60.005 63.158 0.00 0.00 0.00 4.04
447 452 1.004918 CGGTTGTGTCCAGGGTCTC 60.005 63.158 0.00 0.00 0.00 3.36
448 453 1.764854 ACGGTTGTGTCCAGGGTCT 60.765 57.895 0.00 0.00 0.00 3.85
449 454 1.597027 CACGGTTGTGTCCAGGGTC 60.597 63.158 0.00 0.00 41.34 4.46
450 455 2.508928 CACGGTTGTGTCCAGGGT 59.491 61.111 0.00 0.00 41.34 4.34
459 464 2.038387 ACTTTCTCTTGCACGGTTGT 57.962 45.000 0.00 0.00 0.00 3.32
460 465 3.108144 CAAACTTTCTCTTGCACGGTTG 58.892 45.455 0.00 0.00 0.00 3.77
461 466 2.099098 CCAAACTTTCTCTTGCACGGTT 59.901 45.455 0.00 0.00 0.00 4.44
462 467 1.676006 CCAAACTTTCTCTTGCACGGT 59.324 47.619 0.00 0.00 0.00 4.83
498 504 4.647615 CGCCTATCCTCGTGGCCG 62.648 72.222 0.00 0.00 43.42 6.13
525 531 1.006805 GATCTCGATCCGGTGGCTG 60.007 63.158 0.00 0.00 31.76 4.85
544 550 2.284625 TCTGCCCATCACCCGAGT 60.285 61.111 0.00 0.00 0.00 4.18
547 553 2.124983 CTGTCTGCCCATCACCCG 60.125 66.667 0.00 0.00 0.00 5.28
572 578 1.939838 GCTAGACCACGACCTGTTTGG 60.940 57.143 0.00 0.00 42.93 3.28
606 612 4.593864 GCGATCGAGAGGGGTGGC 62.594 72.222 21.57 0.00 0.00 5.01
607 613 3.917760 GGCGATCGAGAGGGGTGG 61.918 72.222 21.57 0.00 0.00 4.61
608 614 4.271816 CGGCGATCGAGAGGGGTG 62.272 72.222 21.57 0.00 42.43 4.61
609 615 4.816984 ACGGCGATCGAGAGGGGT 62.817 66.667 21.57 3.35 42.43 4.95
702 708 1.727511 CGCCATTGATGCCAACGGAT 61.728 55.000 0.00 0.00 37.82 4.18
764 771 4.489795 CGATGCGCGTGTGTGAGC 62.490 66.667 6.97 0.00 34.64 4.26
799 806 4.059459 CGCACGCACCAACTCGAC 62.059 66.667 0.00 0.00 0.00 4.20
813 820 2.052690 GTGGAGGAGGAGTAGCGCA 61.053 63.158 11.47 0.00 0.00 6.09
814 821 2.787567 GGTGGAGGAGGAGTAGCGC 61.788 68.421 0.00 0.00 0.00 5.92
815 822 2.128507 GGGTGGAGGAGGAGTAGCG 61.129 68.421 0.00 0.00 0.00 4.26
816 823 1.762858 GGGGTGGAGGAGGAGTAGC 60.763 68.421 0.00 0.00 0.00 3.58
817 824 0.105913 GAGGGGTGGAGGAGGAGTAG 60.106 65.000 0.00 0.00 0.00 2.57
818 825 1.591280 GGAGGGGTGGAGGAGGAGTA 61.591 65.000 0.00 0.00 0.00 2.59
819 826 2.781406 GAGGGGTGGAGGAGGAGT 59.219 66.667 0.00 0.00 0.00 3.85
864 871 0.820482 TCTTCCCGTCACGAGTCACA 60.820 55.000 0.00 0.00 0.00 3.58
930 937 4.436998 GCGGCGACAGGTGTAGCT 62.437 66.667 12.98 0.00 44.42 3.32
961 968 4.409570 CGTGGATATATAAACGACGGAGG 58.590 47.826 12.20 0.00 38.27 4.30
991 998 1.002134 AAACTCACATCCCCGGCAG 60.002 57.895 0.00 0.00 0.00 4.85
1042 1049 2.159653 CGGCGAATCAAGAACCAAGAAG 60.160 50.000 0.00 0.00 0.00 2.85
1085 1092 2.730672 GCGCGCACACCAGACTAAG 61.731 63.158 29.10 0.00 0.00 2.18
1086 1093 2.736995 GCGCGCACACCAGACTAA 60.737 61.111 29.10 0.00 0.00 2.24
1170 1186 0.596083 CGTTATCCCAGAGCAGCTCG 60.596 60.000 16.99 11.45 35.36 5.03
1240 1256 2.588877 CTTCATAGTGCCGGCGGG 60.589 66.667 29.48 9.91 0.00 6.13
1665 1684 1.289380 GGACTCGACGGACTTGCTT 59.711 57.895 0.00 0.00 0.00 3.91
1683 1702 2.974148 TTGGTCTGCAGCAGCGTG 60.974 61.111 18.43 0.00 46.23 5.34
1786 1805 4.135153 CGGTGCCAGAGGACGAGG 62.135 72.222 0.00 0.00 0.00 4.63
1836 1855 1.115930 ATCTCTGGGATAACGCCGCT 61.116 55.000 0.00 0.00 32.04 5.52
1846 1865 1.198094 TCCGGTTGCAATCTCTGGGA 61.198 55.000 8.32 3.99 0.00 4.37
1855 1874 2.668212 CCTCGCTTCCGGTTGCAA 60.668 61.111 18.20 0.00 34.56 4.08
2004 2023 4.717629 CTCCGCTCGCCGTTGTCA 62.718 66.667 0.00 0.00 34.38 3.58
2013 2032 4.441695 TTCAGCTGGCTCCGCTCG 62.442 66.667 15.13 0.00 35.07 5.03
2101 2130 2.171701 GCGTTCGCGGTGTTAACC 59.828 61.111 6.13 0.00 43.76 2.85
2102 2131 1.154727 CTGCGTTCGCGGTGTTAAC 60.155 57.895 16.47 1.25 41.67 2.01
2103 2132 3.236322 CTGCGTTCGCGGTGTTAA 58.764 55.556 16.47 0.00 41.67 2.01
2111 2140 1.124477 GAAGAACAGTACTGCGTTCGC 59.876 52.381 22.90 10.34 44.94 4.70
2127 2156 6.494842 CGTTTGAGATTTTGAACCAAGAAGA 58.505 36.000 0.00 0.00 0.00 2.87
2135 2164 5.387752 GCAGATTGCGTTTGAGATTTTGAAC 60.388 40.000 0.00 0.00 31.71 3.18
2168 2200 4.796231 CCGGCCTCGTCGTCAAGG 62.796 72.222 0.00 0.00 35.65 3.61
2298 2330 0.942410 CCACTTCGGTGTACGGTGTG 60.942 60.000 0.00 0.00 43.91 3.82
2348 2384 5.591877 ACAGCAATTTAGCTATCTTCCAAGG 59.408 40.000 0.00 0.00 44.54 3.61
2369 2405 5.050644 TCTGCAACAGCAATTTCATACAG 57.949 39.130 0.00 0.00 37.91 2.74
2465 2501 2.673775 TTCTTGCCAAGGTTGATGGA 57.326 45.000 4.30 0.00 40.56 3.41
2466 2502 2.611224 GCTTTCTTGCCAAGGTTGATGG 60.611 50.000 4.30 0.00 41.08 3.51
2475 2512 6.160576 AGTATTTTTGAGCTTTCTTGCCAA 57.839 33.333 0.00 0.00 0.00 4.52
2477 2514 6.701400 TCAAAGTATTTTTGAGCTTTCTTGCC 59.299 34.615 0.00 0.00 35.03 4.52
2486 2523 6.142958 GTGCTCTTGTCAAAGTATTTTTGAGC 59.857 38.462 9.53 9.53 38.88 4.26
2490 2527 8.411318 CTTTGTGCTCTTGTCAAAGTATTTTT 57.589 30.769 8.20 0.00 41.40 1.94
2605 2644 1.135046 CCATCGTCGACATCATCTGC 58.865 55.000 17.16 0.00 0.00 4.26
3017 3067 0.741221 GAGTTACCGAGCCTTGCTGG 60.741 60.000 0.00 0.00 39.88 4.85
3194 3244 3.199946 GGGTAGGACATGTCAGGATTGAA 59.800 47.826 26.47 0.51 34.49 2.69
3216 3266 0.240945 CCGGGCACAGCTTTAAACAG 59.759 55.000 0.00 0.00 0.00 3.16
3217 3267 0.466555 ACCGGGCACAGCTTTAAACA 60.467 50.000 6.32 0.00 0.00 2.83
3218 3268 0.039527 CACCGGGCACAGCTTTAAAC 60.040 55.000 6.32 0.00 0.00 2.01
3219 3269 1.801309 GCACCGGGCACAGCTTTAAA 61.801 55.000 6.32 0.00 43.97 1.52
3255 3305 2.504244 GACTCTTGTCCGTCCGCG 60.504 66.667 0.00 0.00 37.24 6.46
3256 3306 0.389948 ATTGACTCTTGTCCGTCCGC 60.390 55.000 0.00 0.00 42.28 5.54
3257 3307 1.202582 AGATTGACTCTTGTCCGTCCG 59.797 52.381 0.00 0.00 42.28 4.79
3258 3308 2.231478 TCAGATTGACTCTTGTCCGTCC 59.769 50.000 0.00 0.00 42.28 4.79
3259 3309 3.577649 TCAGATTGACTCTTGTCCGTC 57.422 47.619 0.00 0.00 42.28 4.79
3264 3319 6.412362 ACAGTACTTCAGATTGACTCTTGT 57.588 37.500 0.00 0.00 29.16 3.16
3267 3322 5.788450 CCAACAGTACTTCAGATTGACTCT 58.212 41.667 0.00 0.00 33.14 3.24
3289 3353 2.027024 CCATGATGCATGTGCGCC 59.973 61.111 2.46 0.00 45.83 6.53
3291 3355 2.353030 CGCCATGATGCATGTGCG 60.353 61.111 20.18 20.18 46.03 5.34
3447 3515 4.340950 TCATGTATGTAGACAATCCGCTGA 59.659 41.667 0.00 0.00 31.83 4.26
3624 3695 2.092646 AGGGTGTTGCTAGTGTTGAACA 60.093 45.455 0.00 0.00 0.00 3.18
3744 3815 2.367202 GGAGGATGTCGGCAGGGAA 61.367 63.158 0.00 0.00 0.00 3.97
3756 3827 2.954318 CAATTCGGAGCAATTGGAGGAT 59.046 45.455 7.72 0.00 39.26 3.24
3819 3890 2.499214 TGGACAACCAAGCCACAAC 58.501 52.632 0.00 0.00 43.91 3.32
3863 3934 9.341899 GCATCGTTTAAAATTTAGACAATGTCT 57.658 29.630 20.48 20.48 45.54 3.41
3882 3953 2.420022 GTGGCTTGTCTATTGCATCGTT 59.580 45.455 0.00 0.00 0.00 3.85
3887 3958 2.857186 TCAGTGGCTTGTCTATTGCA 57.143 45.000 0.00 0.00 0.00 4.08
3908 3979 0.741915 ACCACATGCCGAAAAACGTT 59.258 45.000 0.00 0.00 40.78 3.99
3917 3988 4.634004 TCAAATTTAGACTACCACATGCCG 59.366 41.667 0.00 0.00 0.00 5.69
3945 4017 5.242393 GCATCTATAGGTGCAAATGATGGTT 59.758 40.000 29.18 0.00 40.94 3.67


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

AutoCloner maintained by Alex Coulton.