Multiple sequence alignment - TraesCS4A01G211600

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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 TraesCS4A01G211600 chr4A 100.000 6058 0 0 1 6058 505795673 505789616 0.000000e+00 11188.0
1 TraesCS4A01G211600 chr4D 95.138 5738 156 45 368 6057 80140423 80146085 0.000000e+00 8937.0
2 TraesCS4A01G211600 chr4B 94.703 5758 193 35 347 6058 112350849 112356540 0.000000e+00 8841.0
3 TraesCS4A01G211600 chr4B 88.189 127 13 2 73 198 112350241 112350366 3.780000e-32 150.0
4 TraesCS4A01G211600 chr2A 86.284 1254 143 10 1961 3193 779205905 779204660 0.000000e+00 1336.0
5 TraesCS4A01G211600 chr2A 87.324 1136 97 16 3212 4333 779204666 779203564 0.000000e+00 1256.0
6 TraesCS4A01G211600 chr2A 85.022 227 29 1 3770 3996 779203325 779203546 6.110000e-55 226.0
7 TraesCS4A01G211600 chr2A 75.904 249 20 22 4541 4783 779203058 779202844 2.330000e-14 91.6
8 TraesCS4A01G211600 chr2B 85.631 1204 137 16 1961 3140 777334778 777335969 0.000000e+00 1232.0
9 TraesCS4A01G211600 chr2B 84.340 811 80 23 3111 3904 777335979 777336759 0.000000e+00 750.0
10 TraesCS4A01G211600 chr2B 90.544 423 37 2 3913 4333 777336930 777337351 1.910000e-154 556.0
11 TraesCS4A01G211600 chr5A 84.153 183 19 4 1211 1393 563769678 563769850 1.040000e-37 169.0
12 TraesCS4A01G211600 chr3D 85.088 114 16 1 3392 3505 299113842 299113730 1.380000e-21 115.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G211600 chr4A 505789616 505795673 6057 True 11188.000000 11188 100.000000 1 6058 1 chr4A.!!$R1 6057
1 TraesCS4A01G211600 chr4D 80140423 80146085 5662 False 8937.000000 8937 95.138000 368 6057 1 chr4D.!!$F1 5689
2 TraesCS4A01G211600 chr4B 112350241 112356540 6299 False 4495.500000 8841 91.446000 73 6058 2 chr4B.!!$F1 5985
3 TraesCS4A01G211600 chr2A 779202844 779205905 3061 True 894.533333 1336 83.170667 1961 4783 3 chr2A.!!$R1 2822
4 TraesCS4A01G211600 chr2B 777334778 777337351 2573 False 846.000000 1232 86.838333 1961 4333 3 chr2B.!!$F1 2372

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
276 330 0.032403 GAAGGCAGCACATGTTTGCA 59.968 50.0 25.31 0.00 45.62 4.08 F
905 1252 0.168128 CGACGAAAGCCATTTCACCC 59.832 55.0 0.00 0.00 44.27 4.61 F
1596 1946 0.606401 CAGTCGGTCAGTGGGCAATT 60.606 55.0 0.00 0.00 0.00 2.32 F
1801 2151 0.615331 CTGCCCTGTTAGCCTGAAGA 59.385 55.0 0.00 0.00 0.00 2.87 F
2387 2778 0.669625 AGAAGGGCGCTTTGTCGTAC 60.670 55.0 17.99 2.78 0.00 3.67 F
2680 3071 0.320771 CACACCCACTTCCTCTTCCG 60.321 60.0 0.00 0.00 0.00 4.30 F
4088 4743 0.389948 CAGTACGAAGGGGTGAGTGC 60.390 60.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 1949 0.179018 GCTCAACACCACCTCCAACT 60.179 55.000 0.00 0.0 0.00 3.16 R
1765 2115 0.804989 CAGCAGAATCCGGTTCCAAC 59.195 55.000 0.00 0.0 37.56 3.77 R
2567 2958 1.134098 CACAGGTGAGGTTGGACAGTT 60.134 52.381 0.00 0.0 0.00 3.16 R
2638 3029 2.467826 GCTTGAGCTCCGTGCATCC 61.468 63.158 12.15 0.0 45.94 3.51 R
3516 3975 2.501723 AGAAAGGATCTGTGCGGTGTAT 59.498 45.455 0.00 0.0 36.88 2.29 R
4464 5549 4.470334 TCATACATAGCACAAGCACAGA 57.530 40.909 0.00 0.0 45.49 3.41 R
5700 6798 0.249447 TCGAGGTGCATATCGGCAAG 60.249 55.000 19.42 0.0 46.93 4.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.869690 GTTGCTCGAAGGTCAAGGC 59.130 57.895 0.00 0.00 0.00 4.35
19 20 1.302511 TTGCTCGAAGGTCAAGGCC 60.303 57.895 0.00 0.00 0.00 5.19
20 21 2.815647 GCTCGAAGGTCAAGGCCG 60.816 66.667 0.00 0.00 0.00 6.13
21 22 2.815647 CTCGAAGGTCAAGGCCGC 60.816 66.667 0.00 0.00 0.00 6.53
22 23 4.388499 TCGAAGGTCAAGGCCGCC 62.388 66.667 0.00 0.00 0.00 6.13
23 24 4.697756 CGAAGGTCAAGGCCGCCA 62.698 66.667 13.15 0.00 0.00 5.69
24 25 3.056328 GAAGGTCAAGGCCGCCAC 61.056 66.667 13.15 0.38 0.00 5.01
25 26 3.842925 GAAGGTCAAGGCCGCCACA 62.843 63.158 13.15 0.00 0.00 4.17
26 27 4.643387 AGGTCAAGGCCGCCACAC 62.643 66.667 13.15 4.51 0.00 3.82
28 29 4.947147 GTCAAGGCCGCCACACCA 62.947 66.667 13.15 0.00 0.00 4.17
29 30 3.965258 TCAAGGCCGCCACACCAT 61.965 61.111 13.15 0.00 0.00 3.55
30 31 3.443045 CAAGGCCGCCACACCATC 61.443 66.667 13.15 0.00 0.00 3.51
31 32 3.965258 AAGGCCGCCACACCATCA 61.965 61.111 13.15 0.00 0.00 3.07
32 33 4.722700 AGGCCGCCACACCATCAC 62.723 66.667 13.15 0.00 0.00 3.06
35 36 4.697756 CCGCCACACCATCACCGT 62.698 66.667 0.00 0.00 0.00 4.83
36 37 3.118454 CGCCACACCATCACCGTC 61.118 66.667 0.00 0.00 0.00 4.79
37 38 3.118454 GCCACACCATCACCGTCG 61.118 66.667 0.00 0.00 0.00 5.12
38 39 2.654289 CCACACCATCACCGTCGA 59.346 61.111 0.00 0.00 0.00 4.20
39 40 1.446099 CCACACCATCACCGTCGAG 60.446 63.158 0.00 0.00 0.00 4.04
40 41 1.584495 CACACCATCACCGTCGAGA 59.416 57.895 0.00 0.00 0.00 4.04
41 42 0.732880 CACACCATCACCGTCGAGAC 60.733 60.000 0.00 0.00 0.00 3.36
51 52 3.681835 GTCGAGACGTGCCCCAGT 61.682 66.667 0.00 0.00 0.00 4.00
52 53 3.680786 TCGAGACGTGCCCCAGTG 61.681 66.667 0.00 0.00 0.00 3.66
53 54 4.742201 CGAGACGTGCCCCAGTGG 62.742 72.222 0.63 0.63 37.09 4.00
54 55 3.311110 GAGACGTGCCCCAGTGGA 61.311 66.667 11.95 0.00 35.39 4.02
55 56 3.591254 GAGACGTGCCCCAGTGGAC 62.591 68.421 11.95 2.57 35.39 4.02
58 59 3.687102 CGTGCCCCAGTGGACGTA 61.687 66.667 11.95 0.00 34.78 3.57
59 60 2.987125 GTGCCCCAGTGGACGTAT 59.013 61.111 11.95 0.00 35.39 3.06
60 61 1.669049 CGTGCCCCAGTGGACGTATA 61.669 60.000 11.95 0.00 34.78 1.47
61 62 0.538118 GTGCCCCAGTGGACGTATAA 59.462 55.000 11.95 0.00 35.39 0.98
62 63 1.065998 GTGCCCCAGTGGACGTATAAA 60.066 52.381 11.95 0.00 35.39 1.40
63 64 1.065998 TGCCCCAGTGGACGTATAAAC 60.066 52.381 11.95 0.00 35.39 2.01
64 65 1.208776 GCCCCAGTGGACGTATAAACT 59.791 52.381 11.95 0.00 35.39 2.66
65 66 2.740904 GCCCCAGTGGACGTATAAACTC 60.741 54.545 11.95 0.00 35.39 3.01
66 67 2.480759 CCCCAGTGGACGTATAAACTCG 60.481 54.545 11.95 0.00 35.39 4.18
67 68 2.165030 CCCAGTGGACGTATAAACTCGT 59.835 50.000 11.95 0.00 43.00 4.18
68 69 3.367703 CCCAGTGGACGTATAAACTCGTT 60.368 47.826 11.95 0.00 40.39 3.85
69 70 4.240096 CCAGTGGACGTATAAACTCGTTT 58.760 43.478 1.68 0.35 40.39 3.60
70 71 4.687483 CCAGTGGACGTATAAACTCGTTTT 59.313 41.667 1.68 0.00 40.39 2.43
71 72 5.389098 CCAGTGGACGTATAAACTCGTTTTG 60.389 44.000 1.68 0.00 40.39 2.44
78 79 7.112009 GGACGTATAAACTCGTTTTGTTTTTCC 59.888 37.037 0.00 0.00 40.39 3.13
80 81 8.130469 ACGTATAAACTCGTTTTGTTTTTCCAT 58.870 29.630 0.00 0.00 38.41 3.41
91 92 7.467947 CGTTTTGTTTTTCCATAATTGGCCTTT 60.468 33.333 3.32 0.00 43.29 3.11
141 142 8.650143 ACTTATTCATGGTTTGGTTAGACAAT 57.350 30.769 0.00 0.00 0.00 2.71
142 143 8.739972 ACTTATTCATGGTTTGGTTAGACAATC 58.260 33.333 0.00 0.00 0.00 2.67
174 175 9.744468 AAGTTTTTAGGTGATTACAACATGAAC 57.256 29.630 0.00 0.00 35.97 3.18
176 177 6.489127 TTTAGGTGATTACAACATGAACCG 57.511 37.500 0.00 0.00 35.97 4.44
190 191 3.980646 TGAACCGTGTTTCAGGAAATG 57.019 42.857 0.00 0.00 31.68 2.32
192 193 3.066064 TGAACCGTGTTTCAGGAAATGTG 59.934 43.478 0.00 0.00 31.68 3.21
193 194 2.650322 ACCGTGTTTCAGGAAATGTGT 58.350 42.857 0.00 0.00 32.36 3.72
221 275 8.974060 TTTGATTCTAGGTATTAGGCGATTTT 57.026 30.769 0.00 0.00 0.00 1.82
226 280 7.364149 TCTAGGTATTAGGCGATTTTAACCA 57.636 36.000 0.00 0.00 0.00 3.67
233 287 4.174411 AGGCGATTTTAACCAGCTTTTC 57.826 40.909 0.00 0.00 0.00 2.29
237 291 4.612939 GCGATTTTAACCAGCTTTTCGAGT 60.613 41.667 0.00 0.00 0.00 4.18
240 294 7.073265 CGATTTTAACCAGCTTTTCGAGTTTA 58.927 34.615 0.00 0.00 0.00 2.01
245 299 4.204799 ACCAGCTTTTCGAGTTTAGGTTT 58.795 39.130 0.00 0.00 0.00 3.27
264 318 4.209080 GGTTTCGAACAAATTTGAAGGCAG 59.791 41.667 24.64 9.24 39.04 4.85
266 320 2.360483 TCGAACAAATTTGAAGGCAGCA 59.640 40.909 24.64 0.00 0.00 4.41
276 330 0.032403 GAAGGCAGCACATGTTTGCA 59.968 50.000 25.31 0.00 45.62 4.08
306 360 2.957402 AAAAGAGGCATGGTGAGTGA 57.043 45.000 0.00 0.00 0.00 3.41
310 364 1.841302 GAGGCATGGTGAGTGACCCA 61.841 60.000 0.00 0.00 45.45 4.51
312 366 1.376466 GCATGGTGAGTGACCCAGT 59.624 57.895 0.00 0.00 45.45 4.00
334 388 2.262915 GGCACCCTCTCGTGTCAG 59.737 66.667 0.00 0.00 38.28 3.51
341 395 1.478510 CCCTCTCGTGTCAGCACTAAT 59.521 52.381 0.00 0.00 43.16 1.73
342 396 2.534298 CCTCTCGTGTCAGCACTAATG 58.466 52.381 0.00 0.00 43.16 1.90
344 398 2.164422 CTCTCGTGTCAGCACTAATGGA 59.836 50.000 0.00 0.00 43.16 3.41
345 399 2.164422 TCTCGTGTCAGCACTAATGGAG 59.836 50.000 0.00 0.00 43.16 3.86
354 691 4.466015 TCAGCACTAATGGAGTACATCACA 59.534 41.667 0.00 0.00 39.40 3.58
374 711 3.879892 ACAAGTGCTCTTCTTTTGGACTC 59.120 43.478 0.00 0.00 31.37 3.36
402 739 4.619973 CATCAGTGCTCACTAATCTCTCC 58.380 47.826 1.79 0.00 40.20 3.71
428 765 1.277273 CAGCCAGTGAGTGATCAAGGA 59.723 52.381 0.00 0.00 0.00 3.36
436 773 4.823989 AGTGAGTGATCAAGGAAAACAAGG 59.176 41.667 0.00 0.00 0.00 3.61
470 807 2.743928 GCAACCACTCCGCTCTGG 60.744 66.667 0.00 0.00 40.09 3.86
577 914 2.351276 GACGCAACATGGTCCCCT 59.649 61.111 0.00 0.00 0.00 4.79
578 915 1.745489 GACGCAACATGGTCCCCTC 60.745 63.158 0.00 0.00 0.00 4.30
630 967 2.742053 CACCTACCGGTCACAAAAGATG 59.258 50.000 12.40 0.00 43.24 2.90
825 1166 3.213402 CCCTCTCGCTCCTCGTCC 61.213 72.222 0.00 0.00 39.67 4.79
905 1252 0.168128 CGACGAAAGCCATTTCACCC 59.832 55.000 0.00 0.00 44.27 4.61
920 1267 0.926293 CACCCCTCTCTCTCTCTCCT 59.074 60.000 0.00 0.00 0.00 3.69
936 1283 3.885297 CTCTCCTCCACATCTCTTCTCTC 59.115 52.174 0.00 0.00 0.00 3.20
943 1290 4.108699 CACATCTCTTCTCTCTGTGGAC 57.891 50.000 0.00 0.00 34.88 4.02
953 1300 1.555533 TCTCTGTGGACTAGCTCTCGA 59.444 52.381 0.00 0.00 0.00 4.04
959 1306 2.517402 ACTAGCTCTCGAGGCCGG 60.517 66.667 13.56 12.05 36.24 6.13
960 1307 2.203224 CTAGCTCTCGAGGCCGGA 60.203 66.667 13.56 0.00 36.24 5.14
1045 1392 3.808656 GGAGCAAGAGCAAGGCGC 61.809 66.667 0.00 0.00 45.49 6.53
1121 1468 1.801178 CAGGAAGAACAAGAAGGCGAC 59.199 52.381 0.00 0.00 0.00 5.19
1341 1688 2.280628 GGAATTTACAGGTGAGAGGCG 58.719 52.381 0.00 0.00 0.00 5.52
1389 1738 4.347607 ACATACTAGTTGGTCCGGTAGTT 58.652 43.478 0.00 0.00 0.00 2.24
1390 1739 5.509498 ACATACTAGTTGGTCCGGTAGTTA 58.491 41.667 0.00 0.00 0.00 2.24
1391 1740 5.951747 ACATACTAGTTGGTCCGGTAGTTAA 59.048 40.000 0.00 0.00 0.00 2.01
1429 1778 1.205893 GTGGTTGGTTGGTTGCTTCAA 59.794 47.619 0.00 0.00 0.00 2.69
1495 1844 5.098218 TGAATTCGGTGTAAAGTTTTCGG 57.902 39.130 0.04 0.00 0.00 4.30
1581 1931 7.652300 TTGTTGAATATATATGCCGTCAGTC 57.348 36.000 0.00 0.00 0.00 3.51
1591 1941 2.258591 CGTCAGTCGGTCAGTGGG 59.741 66.667 0.00 0.00 35.71 4.61
1592 1942 2.048127 GTCAGTCGGTCAGTGGGC 60.048 66.667 0.00 0.00 0.00 5.36
1593 1943 2.523168 TCAGTCGGTCAGTGGGCA 60.523 61.111 0.00 0.00 0.00 5.36
1594 1944 2.137528 TCAGTCGGTCAGTGGGCAA 61.138 57.895 0.00 0.00 0.00 4.52
1595 1945 1.003355 CAGTCGGTCAGTGGGCAAT 60.003 57.895 0.00 0.00 0.00 3.56
1596 1946 0.606401 CAGTCGGTCAGTGGGCAATT 60.606 55.000 0.00 0.00 0.00 2.32
1597 1947 0.606401 AGTCGGTCAGTGGGCAATTG 60.606 55.000 0.00 0.00 0.00 2.32
1598 1948 1.303236 TCGGTCAGTGGGCAATTGG 60.303 57.895 7.72 0.00 0.00 3.16
1599 1949 1.303236 CGGTCAGTGGGCAATTGGA 60.303 57.895 7.72 0.00 0.00 3.53
1600 1950 1.308069 CGGTCAGTGGGCAATTGGAG 61.308 60.000 7.72 0.00 0.00 3.86
1637 1987 5.610398 TGAGCTGTTCTTGACATCTGTTTA 58.390 37.500 0.00 0.00 34.99 2.01
1649 1999 7.439157 TGACATCTGTTTAGGTTTCAGATTG 57.561 36.000 4.47 4.18 43.53 2.67
1735 2085 6.239217 AGTTATGTGTCCATGCTCTGATTA 57.761 37.500 0.00 0.00 32.29 1.75
1754 2104 8.686334 TCTGATTAATTCTTTGATTAGTTGGCC 58.314 33.333 0.00 0.00 0.00 5.36
1765 2115 2.620251 TAGTTGGCCGATGAATCCAG 57.380 50.000 0.00 0.00 0.00 3.86
1801 2151 0.615331 CTGCCCTGTTAGCCTGAAGA 59.385 55.000 0.00 0.00 0.00 2.87
1854 2231 2.379005 CTATTCCCTGGGCTTTGTTCC 58.621 52.381 8.22 0.00 0.00 3.62
1966 2344 6.222038 TGGTACTGGATTAGTGATGTCTTC 57.778 41.667 0.00 0.00 40.65 2.87
2162 2545 9.511144 GTTGACCTTTTCTTCTTTCGAATAAAA 57.489 29.630 0.00 1.38 34.69 1.52
2280 2671 5.316770 GTTCATAGATGTGCGTTTCAACTC 58.683 41.667 0.00 0.00 0.00 3.01
2362 2753 5.236478 TGATTCTCGGAAACAAAGTCTTGTC 59.764 40.000 0.00 0.00 45.25 3.18
2387 2778 0.669625 AGAAGGGCGCTTTGTCGTAC 60.670 55.000 17.99 2.78 0.00 3.67
2539 2930 0.958382 TGTTTGCTACACGGATGCCC 60.958 55.000 0.00 0.00 0.00 5.36
2548 2939 3.160047 CGGATGCCCAGCTCTCCT 61.160 66.667 0.00 0.00 31.98 3.69
2567 2958 3.650942 TCCTCCTAGTTCAAGAGGCAAAA 59.349 43.478 7.02 0.00 45.73 2.44
2602 2993 2.490903 ACCTGTGCATTCAAGAGCATTC 59.509 45.455 0.00 0.00 43.44 2.67
2638 3029 1.448540 CCCTACTGCGTGGCAAGAG 60.449 63.158 4.11 1.67 38.41 2.85
2680 3071 0.320771 CACACCCACTTCCTCTTCCG 60.321 60.000 0.00 0.00 0.00 4.30
2689 3092 4.521062 CCTCTTCCGCCAGGCTCG 62.521 72.222 10.54 0.00 37.47 5.03
2707 3110 2.819595 CCGTGCACATCTTCCCGG 60.820 66.667 18.64 5.62 0.00 5.73
2834 3237 7.170965 TCTATTTTCTCCTGTTCTTCAGCAAT 58.829 34.615 0.00 0.00 42.38 3.56
2943 3346 9.807649 GTTAAGGTTATTGCTGATGATTCAAAT 57.192 29.630 0.00 0.00 0.00 2.32
2987 3390 6.206243 CAGCTAAATCAGGTATCATCTTTGGG 59.794 42.308 0.00 0.00 32.37 4.12
2993 3396 4.074970 CAGGTATCATCTTTGGGGCATAC 58.925 47.826 0.00 0.00 0.00 2.39
3157 3599 6.422776 ACAAAACATATGACGATCTTCCAC 57.577 37.500 10.38 0.00 0.00 4.02
3276 3735 3.508845 AGTTAGGTGGTTCTGCAATGT 57.491 42.857 0.00 0.00 0.00 2.71
3361 3820 1.336440 TGCAAACAATGAAGTGTCCCG 59.664 47.619 0.00 0.00 0.00 5.14
3522 3981 1.814248 GCCATCCTCCGGAAATACACC 60.814 57.143 5.23 0.00 34.34 4.16
3604 4063 7.763528 ACTGAGCAGTCATCAAAGTAAATAGAG 59.236 37.037 0.00 0.00 36.92 2.43
4088 4743 0.389948 CAGTACGAAGGGGTGAGTGC 60.390 60.000 0.00 0.00 0.00 4.40
4602 5687 2.349886 CAGGTAAAGACAAGCATCGAGC 59.650 50.000 0.00 0.00 46.19 5.03
4688 5773 3.200605 TGCCAGCATCTTCTATTCCTTCA 59.799 43.478 0.00 0.00 0.00 3.02
4703 5788 4.736126 TCCTTCAATATCAACTCGCAGA 57.264 40.909 0.00 0.00 0.00 4.26
4734 5819 5.523916 GCCATGTATGTTCTCGTTCACTAAT 59.476 40.000 0.00 0.00 0.00 1.73
4762 5853 8.764524 TTGCTAAAAATATGGTAAATTGCGTT 57.235 26.923 0.00 0.00 0.00 4.84
4865 5956 2.764314 GCCATGCACTAGCCCGTTG 61.764 63.158 0.00 0.00 41.13 4.10
4972 6063 4.568072 TCAACAATGTGCTGTACCCTAT 57.432 40.909 0.00 0.00 0.00 2.57
5123 6214 7.312415 ACTCCATAAGTTAAGGTGTTACTGT 57.688 36.000 6.14 0.00 33.03 3.55
5124 6215 8.426569 ACTCCATAAGTTAAGGTGTTACTGTA 57.573 34.615 6.14 0.00 33.03 2.74
5229 6320 7.308589 CCTCGTCCTTTGTACAAATTCAGAAAT 60.309 37.037 20.83 0.00 0.00 2.17
5318 6416 6.946340 ACCTGTATCTGTTGTGTATGATCAA 58.054 36.000 0.00 0.00 0.00 2.57
5384 6482 4.634004 TGATTTACAGATAAGGTGTTGCGG 59.366 41.667 0.00 0.00 0.00 5.69
5592 6690 0.514691 CAAAGCTGAAGACACGGAGC 59.485 55.000 0.00 0.00 0.00 4.70
5620 6718 2.823147 GCTGCTTGATGCCGCTCT 60.823 61.111 0.00 0.00 46.27 4.09
5693 6791 2.282462 CTTGCCTTCCTTGCCGGT 60.282 61.111 1.90 0.00 0.00 5.28
5987 7085 1.740025 GTCCAGTACTTCTTGCCATGC 59.260 52.381 0.00 0.00 0.00 4.06
5997 7095 4.992740 TGCCATGCCTTTGCCGGT 62.993 61.111 1.90 0.00 36.33 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.578206 GGCCTTGACCTTCGAGCAAC 61.578 60.000 0.00 0.00 0.00 4.17
2 3 2.347490 GGCCTTGACCTTCGAGCA 59.653 61.111 0.00 0.00 0.00 4.26
5 6 4.388499 GGCGGCCTTGACCTTCGA 62.388 66.667 12.87 0.00 0.00 3.71
6 7 4.697756 TGGCGGCCTTGACCTTCG 62.698 66.667 21.46 0.00 0.00 3.79
7 8 3.056328 GTGGCGGCCTTGACCTTC 61.056 66.667 21.46 0.00 0.00 3.46
8 9 3.884774 TGTGGCGGCCTTGACCTT 61.885 61.111 21.46 0.00 0.00 3.50
9 10 4.643387 GTGTGGCGGCCTTGACCT 62.643 66.667 21.46 0.00 0.00 3.85
11 12 4.947147 TGGTGTGGCGGCCTTGAC 62.947 66.667 21.46 10.84 0.00 3.18
12 13 3.918253 GATGGTGTGGCGGCCTTGA 62.918 63.158 21.46 0.00 0.00 3.02
13 14 3.443045 GATGGTGTGGCGGCCTTG 61.443 66.667 21.46 0.00 0.00 3.61
14 15 3.965258 TGATGGTGTGGCGGCCTT 61.965 61.111 21.46 0.00 0.00 4.35
15 16 4.722700 GTGATGGTGTGGCGGCCT 62.723 66.667 21.46 0.00 0.00 5.19
18 19 4.697756 ACGGTGATGGTGTGGCGG 62.698 66.667 0.00 0.00 0.00 6.13
19 20 3.118454 GACGGTGATGGTGTGGCG 61.118 66.667 0.00 0.00 0.00 5.69
20 21 3.118454 CGACGGTGATGGTGTGGC 61.118 66.667 0.00 0.00 0.00 5.01
21 22 1.446099 CTCGACGGTGATGGTGTGG 60.446 63.158 0.00 0.00 0.00 4.17
22 23 0.732880 GTCTCGACGGTGATGGTGTG 60.733 60.000 0.00 0.00 0.00 3.82
23 24 1.585006 GTCTCGACGGTGATGGTGT 59.415 57.895 0.00 0.00 0.00 4.16
24 25 4.478195 GTCTCGACGGTGATGGTG 57.522 61.111 0.00 0.00 0.00 4.17
34 35 3.681835 ACTGGGGCACGTCTCGAC 61.682 66.667 0.00 0.00 0.00 4.20
35 36 3.680786 CACTGGGGCACGTCTCGA 61.681 66.667 0.00 0.00 0.00 4.04
36 37 4.742201 CCACTGGGGCACGTCTCG 62.742 72.222 0.00 0.00 0.00 4.04
37 38 3.311110 TCCACTGGGGCACGTCTC 61.311 66.667 0.00 0.00 36.21 3.36
38 39 3.626924 GTCCACTGGGGCACGTCT 61.627 66.667 0.00 0.00 39.19 4.18
41 42 1.669049 TATACGTCCACTGGGGCACG 61.669 60.000 15.96 15.96 39.40 5.34
42 43 0.538118 TTATACGTCCACTGGGGCAC 59.462 55.000 0.00 0.00 39.40 5.01
43 44 1.065998 GTTTATACGTCCACTGGGGCA 60.066 52.381 0.00 0.00 39.40 5.36
44 45 1.208776 AGTTTATACGTCCACTGGGGC 59.791 52.381 0.00 0.00 36.21 5.80
45 46 2.480759 CGAGTTTATACGTCCACTGGGG 60.481 54.545 0.00 0.00 38.37 4.96
46 47 2.165030 ACGAGTTTATACGTCCACTGGG 59.835 50.000 0.00 0.00 38.34 4.45
47 48 3.498927 ACGAGTTTATACGTCCACTGG 57.501 47.619 0.00 0.00 38.34 4.00
48 49 5.176223 ACAAAACGAGTTTATACGTCCACTG 59.824 40.000 0.00 0.00 41.87 3.66
49 50 5.291971 ACAAAACGAGTTTATACGTCCACT 58.708 37.500 0.00 0.00 41.87 4.00
50 51 5.580911 ACAAAACGAGTTTATACGTCCAC 57.419 39.130 0.00 0.00 41.87 4.02
51 52 6.601741 AAACAAAACGAGTTTATACGTCCA 57.398 33.333 0.00 0.00 41.87 4.02
52 53 7.112009 GGAAAAACAAAACGAGTTTATACGTCC 59.888 37.037 0.00 2.56 41.87 4.79
53 54 7.639461 TGGAAAAACAAAACGAGTTTATACGTC 59.361 33.333 0.00 0.00 41.87 4.34
54 55 7.470900 TGGAAAAACAAAACGAGTTTATACGT 58.529 30.769 1.32 0.00 44.57 3.57
55 56 7.895582 TGGAAAAACAAAACGAGTTTATACG 57.104 32.000 1.32 0.00 38.17 3.06
122 123 4.991776 TGGATTGTCTAACCAAACCATGA 58.008 39.130 0.00 0.00 40.91 3.07
138 139 8.661352 AATCACCTAAAAACTTGTTTGGATTG 57.339 30.769 7.72 0.76 0.00 2.67
141 142 8.294954 TGTAATCACCTAAAAACTTGTTTGGA 57.705 30.769 7.72 0.00 0.00 3.53
142 143 8.813282 GTTGTAATCACCTAAAAACTTGTTTGG 58.187 33.333 0.00 0.32 0.00 3.28
174 175 3.708563 AACACATTTCCTGAAACACGG 57.291 42.857 0.00 0.00 32.51 4.94
207 259 6.373186 AAGCTGGTTAAAATCGCCTAATAC 57.627 37.500 0.00 0.00 0.00 1.89
215 267 5.030874 ACTCGAAAAGCTGGTTAAAATCG 57.969 39.130 0.00 2.12 0.00 3.34
221 275 4.964593 ACCTAAACTCGAAAAGCTGGTTA 58.035 39.130 0.00 0.00 0.00 2.85
226 280 4.374399 TCGAAACCTAAACTCGAAAAGCT 58.626 39.130 0.00 0.00 38.56 3.74
233 287 6.908284 TCAAATTTGTTCGAAACCTAAACTCG 59.092 34.615 17.47 0.00 0.00 4.18
237 291 6.477360 GCCTTCAAATTTGTTCGAAACCTAAA 59.523 34.615 17.47 0.02 0.00 1.85
240 294 4.142049 TGCCTTCAAATTTGTTCGAAACCT 60.142 37.500 17.47 0.00 0.00 3.50
245 299 2.360483 TGCTGCCTTCAAATTTGTTCGA 59.640 40.909 17.47 0.00 0.00 3.71
264 318 3.631145 TTCTCTCTTGCAAACATGTGC 57.369 42.857 0.00 0.00 45.15 4.57
289 343 0.326264 GGTCACTCACCATGCCTCTT 59.674 55.000 0.00 0.00 45.98 2.85
298 352 1.674057 CCAGACTGGGTCACTCACC 59.326 63.158 14.26 0.00 45.97 4.02
334 388 5.063944 CACTTGTGATGTACTCCATTAGTGC 59.936 44.000 13.57 0.00 39.39 4.40
341 395 2.899900 AGAGCACTTGTGATGTACTCCA 59.100 45.455 4.79 0.00 30.32 3.86
342 396 3.601443 AGAGCACTTGTGATGTACTCC 57.399 47.619 4.79 0.00 30.32 3.85
344 398 4.881019 AGAAGAGCACTTGTGATGTACT 57.119 40.909 0.00 0.00 36.39 2.73
345 399 5.931441 AAAGAAGAGCACTTGTGATGTAC 57.069 39.130 0.00 0.00 36.39 2.90
354 691 4.156455 TGAGTCCAAAAGAAGAGCACTT 57.844 40.909 0.00 0.00 39.24 3.16
436 773 2.125350 CCGGCTGCAGGAAGAGTC 60.125 66.667 17.12 0.00 0.00 3.36
507 844 3.118454 GGATGTGGCGTGACGTGG 61.118 66.667 6.91 0.00 0.00 4.94
630 967 2.504519 GGTAGCGATGGGGTCACC 59.495 66.667 0.00 0.00 40.81 4.02
825 1166 1.150536 CGAGAGGAGAGGAGAGGGG 59.849 68.421 0.00 0.00 0.00 4.79
892 1237 1.283321 GAGAGAGGGGTGAAATGGCTT 59.717 52.381 0.00 0.00 0.00 4.35
905 1252 1.563879 TGTGGAGGAGAGAGAGAGAGG 59.436 57.143 0.00 0.00 0.00 3.69
936 1283 1.021202 CCTCGAGAGCTAGTCCACAG 58.979 60.000 15.71 0.00 0.00 3.66
943 1290 2.203224 TCCGGCCTCGAGAGCTAG 60.203 66.667 15.71 12.95 39.00 3.42
1082 1429 2.038975 CCTTCTCCCCGTCCCTCA 59.961 66.667 0.00 0.00 0.00 3.86
1158 1505 4.274008 TGCTGCAGCTGCTTCCCA 62.274 61.111 36.61 24.15 42.66 4.37
1341 1688 1.146041 TGGTGATCAGTATGGCGCC 59.854 57.895 22.73 22.73 40.31 6.53
1389 1738 5.192927 CCACCCAAACTCAGCAGATTATTA 58.807 41.667 0.00 0.00 0.00 0.98
1390 1739 4.019174 CCACCCAAACTCAGCAGATTATT 58.981 43.478 0.00 0.00 0.00 1.40
1391 1740 3.010584 ACCACCCAAACTCAGCAGATTAT 59.989 43.478 0.00 0.00 0.00 1.28
1429 1778 4.058817 CTCTCGAACTTTTAGCCTGTGTT 58.941 43.478 0.00 0.00 0.00 3.32
1462 1811 0.366871 CCGAATTCAACACGAGAGCG 59.633 55.000 6.22 0.00 44.79 5.03
1516 1866 4.179926 TCAGCAGAACAGCAACTAGTAG 57.820 45.455 0.00 0.00 36.85 2.57
1581 1931 1.303236 TCCAATTGCCCACTGACCG 60.303 57.895 0.00 0.00 0.00 4.79
1584 1934 1.619654 CAACTCCAATTGCCCACTGA 58.380 50.000 0.00 0.00 0.00 3.41
1585 1935 0.604578 CCAACTCCAATTGCCCACTG 59.395 55.000 0.00 0.00 0.00 3.66
1587 1937 0.890683 CTCCAACTCCAATTGCCCAC 59.109 55.000 0.00 0.00 0.00 4.61
1588 1938 0.251742 CCTCCAACTCCAATTGCCCA 60.252 55.000 0.00 0.00 0.00 5.36
1589 1939 0.251787 ACCTCCAACTCCAATTGCCC 60.252 55.000 0.00 0.00 0.00 5.36
1590 1940 0.890683 CACCTCCAACTCCAATTGCC 59.109 55.000 0.00 0.00 0.00 4.52
1591 1941 0.890683 CCACCTCCAACTCCAATTGC 59.109 55.000 0.00 0.00 0.00 3.56
1592 1942 1.888512 CACCACCTCCAACTCCAATTG 59.111 52.381 0.00 0.00 0.00 2.32
1593 1943 1.499007 ACACCACCTCCAACTCCAATT 59.501 47.619 0.00 0.00 0.00 2.32
1594 1944 1.149101 ACACCACCTCCAACTCCAAT 58.851 50.000 0.00 0.00 0.00 3.16
1595 1945 0.923358 AACACCACCTCCAACTCCAA 59.077 50.000 0.00 0.00 0.00 3.53
1596 1946 0.182537 CAACACCACCTCCAACTCCA 59.817 55.000 0.00 0.00 0.00 3.86
1597 1947 0.472471 TCAACACCACCTCCAACTCC 59.528 55.000 0.00 0.00 0.00 3.85
1598 1948 1.884235 CTCAACACCACCTCCAACTC 58.116 55.000 0.00 0.00 0.00 3.01
1599 1949 0.179018 GCTCAACACCACCTCCAACT 60.179 55.000 0.00 0.00 0.00 3.16
1600 1950 0.179018 AGCTCAACACCACCTCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
1637 1987 4.141733 CCACAAAAACCCAATCTGAAACCT 60.142 41.667 0.00 0.00 0.00 3.50
1649 1999 1.298602 CAAAGCAGCCACAAAAACCC 58.701 50.000 0.00 0.00 0.00 4.11
1735 2085 5.652014 TCATCGGCCAACTAATCAAAGAATT 59.348 36.000 2.24 0.00 0.00 2.17
1754 2104 1.665679 CGGTTCCAACTGGATTCATCG 59.334 52.381 0.00 0.00 44.98 3.84
1765 2115 0.804989 CAGCAGAATCCGGTTCCAAC 59.195 55.000 0.00 0.00 37.56 3.77
1807 2157 9.880157 CCTGAATTTTGTAAAAAGATGATCCAT 57.120 29.630 0.00 0.00 0.00 3.41
1808 2158 7.818930 GCCTGAATTTTGTAAAAAGATGATCCA 59.181 33.333 0.00 0.00 0.00 3.41
1810 2160 8.992835 AGCCTGAATTTTGTAAAAAGATGATC 57.007 30.769 0.00 0.00 0.00 2.92
1814 2164 9.875691 GGAATAGCCTGAATTTTGTAAAAAGAT 57.124 29.630 0.00 0.00 0.00 2.40
1815 2165 8.311109 GGGAATAGCCTGAATTTTGTAAAAAGA 58.689 33.333 0.00 0.00 36.66 2.52
1816 2166 8.314021 AGGGAATAGCCTGAATTTTGTAAAAAG 58.686 33.333 0.00 0.00 36.66 2.27
1823 2194 3.385755 CCCAGGGAATAGCCTGAATTTTG 59.614 47.826 0.00 0.00 36.26 2.44
1854 2231 2.158986 TGACAGCAAAACCAAACCCATG 60.159 45.455 0.00 0.00 0.00 3.66
1885 2263 4.450419 TGTTGCAACCAAGAAAACAAGTTG 59.550 37.500 26.14 0.00 40.55 3.16
1996 2375 6.863126 ACTGCCTTGAAAAATTAATCGAACAG 59.137 34.615 0.00 0.00 0.00 3.16
2118 2501 3.539253 CAAGCATTGTCGCCTATGC 57.461 52.632 4.70 4.70 46.15 3.14
2362 2753 1.339151 ACAAAGCGCCCTTCTTCTAGG 60.339 52.381 2.29 0.00 34.92 3.02
2387 2778 5.991606 TGTTATTCTCCGAAGCCAGATTATG 59.008 40.000 0.00 0.00 0.00 1.90
2539 2930 3.360867 TCTTGAACTAGGAGGAGAGCTG 58.639 50.000 0.00 0.00 0.00 4.24
2548 2939 4.821805 CAGTTTTTGCCTCTTGAACTAGGA 59.178 41.667 0.00 0.00 34.58 2.94
2567 2958 1.134098 CACAGGTGAGGTTGGACAGTT 60.134 52.381 0.00 0.00 0.00 3.16
2638 3029 2.467826 GCTTGAGCTCCGTGCATCC 61.468 63.158 12.15 0.00 45.94 3.51
2689 3092 3.499737 CGGGAAGATGTGCACGGC 61.500 66.667 13.13 6.50 0.00 5.68
2834 3237 8.434392 AGTATACTGTACAAAGGAAAGGTTCAA 58.566 33.333 4.10 0.00 0.00 2.69
2943 3346 3.470709 CTGCCTCAGACACTCTTTTGAA 58.529 45.455 0.00 0.00 32.44 2.69
2987 3390 3.475566 TGCTGACTAATCCAGTATGCC 57.524 47.619 0.00 0.00 37.72 4.40
2993 3396 5.608449 TGAGAATGATGCTGACTAATCCAG 58.392 41.667 0.00 0.00 34.88 3.86
3157 3599 8.874745 AATGTTACATGTTCGAGAATAAAACG 57.125 30.769 2.30 0.00 0.00 3.60
3207 3653 9.868277 CTGTGATTGCTTGGGTAATTTATTTAA 57.132 29.630 0.00 0.00 0.00 1.52
3267 3726 7.815549 TGTATCTAACGAAGTAAACATTGCAGA 59.184 33.333 0.00 0.00 45.00 4.26
3361 3820 8.015087 GCAAAAGGGTAAATCTGCAAATAAAAC 58.985 33.333 0.00 0.00 0.00 2.43
3516 3975 2.501723 AGAAAGGATCTGTGCGGTGTAT 59.498 45.455 0.00 0.00 36.88 2.29
3604 4063 8.785329 TTTTCAAAAATAAATGGCCATCCTAC 57.215 30.769 21.08 0.00 0.00 3.18
4464 5549 4.470334 TCATACATAGCACAAGCACAGA 57.530 40.909 0.00 0.00 45.49 3.41
4602 5687 5.982516 GTGATAAGCTTCTGTAGGATGACAG 59.017 44.000 0.00 0.00 46.90 3.51
4688 5773 2.697751 AGAGGCTCTGCGAGTTGATATT 59.302 45.455 17.96 0.00 31.39 1.28
4703 5788 1.842562 AGAACATACATGGCAGAGGCT 59.157 47.619 0.00 0.00 40.87 4.58
4758 5849 4.451096 TCTGTTAGACAATGGAAGAAACGC 59.549 41.667 0.00 0.00 0.00 4.84
4762 5853 6.881065 CCAGATTCTGTTAGACAATGGAAGAA 59.119 38.462 12.54 0.00 0.00 2.52
4865 5956 2.815647 GACTGCCTGTACTGCCGC 60.816 66.667 5.66 0.72 0.00 6.53
4972 6063 0.744414 GAGATAGTTGCTTGGCCGCA 60.744 55.000 0.59 0.59 38.31 5.69
5120 6211 5.246429 ACCTTTGTCCTCCTAAGTTCTACAG 59.754 44.000 0.00 0.00 0.00 2.74
5121 6212 5.011738 CACCTTTGTCCTCCTAAGTTCTACA 59.988 44.000 0.00 0.00 0.00 2.74
5122 6213 5.011840 ACACCTTTGTCCTCCTAAGTTCTAC 59.988 44.000 0.00 0.00 0.00 2.59
5123 6214 5.152934 ACACCTTTGTCCTCCTAAGTTCTA 58.847 41.667 0.00 0.00 0.00 2.10
5124 6215 3.974642 ACACCTTTGTCCTCCTAAGTTCT 59.025 43.478 0.00 0.00 0.00 3.01
5229 6320 8.389779 TGCTATTGTTTTTCACTACATCTCAA 57.610 30.769 0.00 0.00 0.00 3.02
5495 6593 0.253160 TGAGGGTGCCAAGGGAGTAT 60.253 55.000 0.00 0.00 0.00 2.12
5539 6637 4.471386 AGCAAATACTGACACTGGGACTAT 59.529 41.667 0.00 0.00 0.00 2.12
5620 6718 2.180769 CGATGAACTCGCGGTCCA 59.819 61.111 6.13 0.00 41.14 4.02
5700 6798 0.249447 TCGAGGTGCATATCGGCAAG 60.249 55.000 19.42 0.00 46.93 4.01


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

AutoCloner maintained by Alex Coulton.