Multiple sequence alignment - TraesCS5B01G537600

Loading Multiple Alignment...

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 TraesCS5B01G537600 chr5B 100.000 3332 0 0 1 3332 693449179 693452510 0.000000e+00 6154.0
1 TraesCS5B01G537600 chr5B 94.572 1529 72 5 144 1663 693532026 693533552 0.000000e+00 2353.0
2 TraesCS5B01G537600 chr5B 94.048 1529 79 6 144 1663 712305068 712303543 0.000000e+00 2309.0
3 TraesCS5B01G537600 chr5B 92.955 1235 60 13 1956 3178 693533726 693534945 0.000000e+00 1773.0
4 TraesCS5B01G537600 chr5B 90.630 1302 82 15 1890 3178 712303384 712302110 0.000000e+00 1692.0
5 TraesCS5B01G537600 chr5B 89.256 363 36 2 1304 1663 693585829 693586191 5.070000e-123 451.0
6 TraesCS5B01G537600 chr5B 95.783 166 6 1 3167 3332 712302053 712301889 1.970000e-67 267.0
7 TraesCS5B01G537600 chr5B 95.210 167 6 2 3167 3332 693535002 693535167 2.550000e-66 263.0
8 TraesCS5B01G537600 chr5B 79.825 342 48 16 440 771 693713046 693712716 2.590000e-56 230.0
9 TraesCS5B01G537600 chr5B 90.789 152 13 1 3181 3332 595078373 595078523 5.640000e-48 202.0
10 TraesCS5B01G537600 chr5B 80.162 247 37 11 221 461 693532222 693532462 1.230000e-39 174.0
11 TraesCS5B01G537600 chr5B 79.032 248 38 12 221 461 712304872 712304632 1.240000e-34 158.0
12 TraesCS5B01G537600 chr5D 92.736 1707 91 16 286 1974 559242149 559243840 0.000000e+00 2435.0
13 TraesCS5B01G537600 chr5D 90.909 1188 75 22 2007 3178 559243832 559245002 0.000000e+00 1565.0
14 TraesCS5B01G537600 chr5D 89.532 363 35 2 1304 1663 559466606 559466244 1.090000e-124 457.0
15 TraesCS5B01G537600 chr5D 95.181 166 7 1 3167 3332 559245059 559245223 9.170000e-66 261.0
16 TraesCS5B01G537600 chr5D 91.391 151 12 1 3182 3332 483971626 483971775 4.360000e-49 206.0
17 TraesCS5B01G537600 chr5D 84.507 71 9 2 74 143 194672065 194671996 5.960000e-08 69.4
18 TraesCS5B01G537600 chr3A 89.742 1394 121 14 390 1768 743644905 743643519 0.000000e+00 1762.0
19 TraesCS5B01G537600 chr4A 89.327 1293 84 15 383 1663 612441985 612443235 0.000000e+00 1574.0
20 TraesCS5B01G537600 chr4A 88.500 1287 115 18 1778 3052 612443279 612444544 0.000000e+00 1526.0
21 TraesCS5B01G537600 chr4A 84.590 1207 151 24 123 1303 612999269 612998072 0.000000e+00 1166.0
22 TraesCS5B01G537600 chr4A 87.042 764 80 12 174 920 612975760 612974999 0.000000e+00 845.0
23 TraesCS5B01G537600 chr4A 88.331 617 57 10 1781 2397 612974138 612973537 0.000000e+00 726.0
24 TraesCS5B01G537600 chr4A 84.724 635 64 15 1778 2396 613155357 613154740 3.680000e-169 604.0
25 TraesCS5B01G537600 chr4A 84.083 578 62 16 1778 2339 612391747 612392310 6.330000e-147 531.0
26 TraesCS5B01G537600 chr4A 89.617 366 32 3 1304 1663 612391334 612391699 8.420000e-126 460.0
27 TraesCS5B01G537600 chr4A 90.000 360 30 3 1310 1663 613155764 613155405 8.420000e-126 460.0
28 TraesCS5B01G537600 chr4A 80.671 626 79 25 414 1006 612685029 612684413 6.560000e-122 448.0
29 TraesCS5B01G537600 chr4A 90.506 316 28 2 2017 2332 612998075 612997762 1.850000e-112 416.0
30 TraesCS5B01G537600 chr4A 87.725 334 35 2 1009 1336 612974760 612974427 5.210000e-103 385.0
31 TraesCS5B01G537600 chr4A 91.176 170 8 3 3167 3332 612444700 612444866 1.200000e-54 224.0
32 TraesCS5B01G537600 chr4A 93.939 99 6 0 3080 3178 612444545 612444643 2.070000e-32 150.0
33 TraesCS5B01G537600 chr4A 78.363 171 28 8 295 461 612685031 612684866 5.880000e-18 102.0
34 TraesCS5B01G537600 chr4A 91.837 49 4 0 1163 1211 612372528 612372576 5.960000e-08 69.4
35 TraesCS5B01G537600 chr6D 84.581 1109 87 39 1304 2397 136695851 136694812 0.000000e+00 1024.0
36 TraesCS5B01G537600 chr6A 84.629 1106 83 39 1310 2396 178438303 178437266 0.000000e+00 1020.0
37 TraesCS5B01G537600 chr6A 88.623 167 16 3 3167 3332 481621041 481620877 2.030000e-47 200.0
38 TraesCS5B01G537600 chr6B 84.324 1110 89 34 1304 2397 234846291 234845251 0.000000e+00 1007.0
39 TraesCS5B01G537600 chr6B 97.619 84 2 0 1 84 403316780 403316697 9.630000e-31 145.0
40 TraesCS5B01G537600 chrUn 89.916 357 33 2 1310 1663 290197609 290197253 1.090000e-124 457.0
41 TraesCS5B01G537600 chr1D 89.542 153 16 0 3180 3332 412456540 412456388 9.430000e-46 195.0
42 TraesCS5B01G537600 chr1D 91.525 59 5 0 3120 3178 491438573 491438515 7.660000e-12 82.4
43 TraesCS5B01G537600 chr5A 89.474 152 16 0 3181 3332 605741970 605742121 3.390000e-45 193.0
44 TraesCS5B01G537600 chr1B 87.162 148 11 4 1 143 503453691 503453547 9.570000e-36 161.0
45 TraesCS5B01G537600 chr1B 97.619 84 2 0 1 84 224492354 224492437 9.630000e-31 145.0
46 TraesCS5B01G537600 chr3B 86.806 144 17 2 1 143 81069697 81069555 3.440000e-35 159.0
47 TraesCS5B01G537600 chr3B 82.781 151 19 7 1 148 491402758 491402612 9.700000e-26 128.0
48 TraesCS5B01G537600 chr4B 85.906 149 14 5 1 143 227626676 227626823 5.760000e-33 152.0
49 TraesCS5B01G537600 chr4B 85.811 148 14 5 3 143 633664243 633664096 2.070000e-32 150.0
50 TraesCS5B01G537600 chr4B 97.619 84 2 0 1 84 290185584 290185667 9.630000e-31 145.0
51 TraesCS5B01G537600 chr7B 97.619 84 2 0 1 84 202547513 202547430 9.630000e-31 145.0
52 TraesCS5B01G537600 chr7A 77.193 171 34 4 2731 2896 106824395 106824565 9.840000e-16 95.3
53 TraesCS5B01G537600 chr3D 98.000 50 1 0 3129 3178 583478985 583479034 1.650000e-13 87.9
54 TraesCS5B01G537600 chr1A 86.792 53 7 0 2651 2703 15465227 15465175 3.590000e-05 60.2


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 TraesCS5B01G537600 chr5B 693449179 693452510 3331 False 6154.000000 6154 100.000000 1 3332 1 chr5B.!!$F2 3331
1 TraesCS5B01G537600 chr5B 693532026 693535167 3141 False 1140.750000 2353 90.724750 144 3332 4 chr5B.!!$F4 3188
2 TraesCS5B01G537600 chr5B 712301889 712305068 3179 True 1106.500000 2309 89.873250 144 3332 4 chr5B.!!$R2 3188
3 TraesCS5B01G537600 chr5D 559242149 559245223 3074 False 1420.333333 2435 92.942000 286 3332 3 chr5D.!!$F2 3046
4 TraesCS5B01G537600 chr3A 743643519 743644905 1386 True 1762.000000 1762 89.742000 390 1768 1 chr3A.!!$R1 1378
5 TraesCS5B01G537600 chr4A 612441985 612444866 2881 False 868.500000 1574 90.735500 383 3332 4 chr4A.!!$F3 2949
6 TraesCS5B01G537600 chr4A 612997762 612999269 1507 True 791.000000 1166 87.548000 123 2332 2 chr4A.!!$R3 2209
7 TraesCS5B01G537600 chr4A 612973537 612975760 2223 True 652.000000 845 87.699333 174 2397 3 chr4A.!!$R2 2223
8 TraesCS5B01G537600 chr4A 613154740 613155764 1024 True 532.000000 604 87.362000 1310 2396 2 chr4A.!!$R4 1086
9 TraesCS5B01G537600 chr4A 612391334 612392310 976 False 495.500000 531 86.850000 1304 2339 2 chr4A.!!$F2 1035
10 TraesCS5B01G537600 chr4A 612684413 612685031 618 True 275.000000 448 79.517000 295 1006 2 chr4A.!!$R1 711
11 TraesCS5B01G537600 chr6D 136694812 136695851 1039 True 1024.000000 1024 84.581000 1304 2397 1 chr6D.!!$R1 1093
12 TraesCS5B01G537600 chr6A 178437266 178438303 1037 True 1020.000000 1020 84.629000 1310 2396 1 chr6A.!!$R1 1086
13 TraesCS5B01G537600 chr6B 234845251 234846291 1040 True 1007.000000 1007 84.324000 1304 2397 1 chr6B.!!$R1 1093

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
64 65 0.458543 ATTCCGCTGCTAGTGTGTCG 60.459 55.0 0.0 0.0 0.00 4.35 F
69 70 0.946221 GCTGCTAGTGTGTCGTTGCT 60.946 55.0 0.0 0.0 0.00 3.91 F
1109 1327 1.049289 CCCTGGAGTAGTGGGGTAGC 61.049 65.0 0.0 0.0 37.37 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1865 0.317770 CACAAAAGCACGCCGTGAAT 60.318 50.0 23.33 5.38 35.23 2.57 R
1888 2217 0.744874 TGGTCGCTACTACCATCTGC 59.255 55.0 0.00 0.00 42.10 4.26 R
2935 3317 0.744874 TCATCCGCTTTACCTCTCGG 59.255 55.0 0.00 0.00 42.96 4.63 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.898320 TGATGACTATGTTGTTGCTCTGT 58.102 39.130 0.00 0.00 0.00 3.41
24 25 5.308014 TGATGACTATGTTGTTGCTCTGTT 58.692 37.500 0.00 0.00 0.00 3.16
25 26 6.463360 TGATGACTATGTTGTTGCTCTGTTA 58.537 36.000 0.00 0.00 0.00 2.41
26 27 7.105588 TGATGACTATGTTGTTGCTCTGTTAT 58.894 34.615 0.00 0.00 0.00 1.89
27 28 6.726258 TGACTATGTTGTTGCTCTGTTATG 57.274 37.500 0.00 0.00 0.00 1.90
28 29 5.122239 TGACTATGTTGTTGCTCTGTTATGC 59.878 40.000 0.00 0.00 0.00 3.14
29 30 5.248640 ACTATGTTGTTGCTCTGTTATGCT 58.751 37.500 0.00 0.00 0.00 3.79
30 31 5.707298 ACTATGTTGTTGCTCTGTTATGCTT 59.293 36.000 0.00 0.00 0.00 3.91
31 32 6.878923 ACTATGTTGTTGCTCTGTTATGCTTA 59.121 34.615 0.00 0.00 0.00 3.09
32 33 6.764308 ATGTTGTTGCTCTGTTATGCTTAT 57.236 33.333 0.00 0.00 0.00 1.73
33 34 7.864108 ATGTTGTTGCTCTGTTATGCTTATA 57.136 32.000 0.00 0.00 0.00 0.98
34 35 7.072177 TGTTGTTGCTCTGTTATGCTTATAC 57.928 36.000 0.00 0.00 0.00 1.47
35 36 6.093495 TGTTGTTGCTCTGTTATGCTTATACC 59.907 38.462 0.00 0.00 0.00 2.73
36 37 5.989477 TGTTGCTCTGTTATGCTTATACCT 58.011 37.500 0.00 0.00 0.00 3.08
37 38 5.817296 TGTTGCTCTGTTATGCTTATACCTG 59.183 40.000 0.00 0.00 0.00 4.00
38 39 5.869649 TGCTCTGTTATGCTTATACCTGA 57.130 39.130 0.00 0.00 0.00 3.86
39 40 5.847304 TGCTCTGTTATGCTTATACCTGAG 58.153 41.667 0.00 0.00 0.00 3.35
40 41 5.363868 TGCTCTGTTATGCTTATACCTGAGT 59.636 40.000 0.00 0.00 0.00 3.41
41 42 6.549736 TGCTCTGTTATGCTTATACCTGAGTA 59.450 38.462 0.00 0.00 0.00 2.59
42 43 6.864165 GCTCTGTTATGCTTATACCTGAGTAC 59.136 42.308 0.00 0.00 0.00 2.73
43 44 7.255660 GCTCTGTTATGCTTATACCTGAGTACT 60.256 40.741 0.00 0.00 0.00 2.73
44 45 8.534954 TCTGTTATGCTTATACCTGAGTACTT 57.465 34.615 0.00 0.00 0.00 2.24
45 46 9.636789 TCTGTTATGCTTATACCTGAGTACTTA 57.363 33.333 0.00 0.00 0.00 2.24
50 51 6.978338 TGCTTATACCTGAGTACTTATTCCG 58.022 40.000 0.00 0.00 0.00 4.30
51 52 5.862860 GCTTATACCTGAGTACTTATTCCGC 59.137 44.000 0.00 0.00 0.00 5.54
52 53 6.294620 GCTTATACCTGAGTACTTATTCCGCT 60.295 42.308 0.00 0.00 0.00 5.52
53 54 3.802948 ACCTGAGTACTTATTCCGCTG 57.197 47.619 0.00 0.00 0.00 5.18
54 55 2.159085 ACCTGAGTACTTATTCCGCTGC 60.159 50.000 0.00 0.00 0.00 5.25
55 56 2.101582 CCTGAGTACTTATTCCGCTGCT 59.898 50.000 0.00 0.00 0.00 4.24
56 57 3.318275 CCTGAGTACTTATTCCGCTGCTA 59.682 47.826 0.00 0.00 0.00 3.49
57 58 4.541779 CTGAGTACTTATTCCGCTGCTAG 58.458 47.826 0.00 0.00 0.00 3.42
58 59 3.952323 TGAGTACTTATTCCGCTGCTAGT 59.048 43.478 0.00 0.00 0.00 2.57
59 60 4.202020 TGAGTACTTATTCCGCTGCTAGTG 60.202 45.833 0.00 0.00 0.00 2.74
60 61 3.700038 AGTACTTATTCCGCTGCTAGTGT 59.300 43.478 0.00 0.00 0.00 3.55
61 62 2.893637 ACTTATTCCGCTGCTAGTGTG 58.106 47.619 0.00 0.00 0.00 3.82
62 63 2.233922 ACTTATTCCGCTGCTAGTGTGT 59.766 45.455 0.00 0.00 0.00 3.72
63 64 2.579207 TATTCCGCTGCTAGTGTGTC 57.421 50.000 0.00 0.00 0.00 3.67
64 65 0.458543 ATTCCGCTGCTAGTGTGTCG 60.459 55.000 0.00 0.00 0.00 4.35
65 66 1.802337 TTCCGCTGCTAGTGTGTCGT 61.802 55.000 0.00 0.00 0.00 4.34
66 67 1.372997 CCGCTGCTAGTGTGTCGTT 60.373 57.895 0.00 0.00 0.00 3.85
67 68 1.617755 CCGCTGCTAGTGTGTCGTTG 61.618 60.000 0.00 0.00 0.00 4.10
68 69 1.493311 GCTGCTAGTGTGTCGTTGC 59.507 57.895 0.00 0.00 0.00 4.17
69 70 0.946221 GCTGCTAGTGTGTCGTTGCT 60.946 55.000 0.00 0.00 0.00 3.91
70 71 1.502231 CTGCTAGTGTGTCGTTGCTT 58.498 50.000 0.00 0.00 0.00 3.91
71 72 1.867233 CTGCTAGTGTGTCGTTGCTTT 59.133 47.619 0.00 0.00 0.00 3.51
72 73 1.597195 TGCTAGTGTGTCGTTGCTTTG 59.403 47.619 0.00 0.00 0.00 2.77
73 74 1.069906 GCTAGTGTGTCGTTGCTTTGG 60.070 52.381 0.00 0.00 0.00 3.28
74 75 2.479837 CTAGTGTGTCGTTGCTTTGGA 58.520 47.619 0.00 0.00 0.00 3.53
75 76 1.745232 AGTGTGTCGTTGCTTTGGAA 58.255 45.000 0.00 0.00 0.00 3.53
76 77 2.297701 AGTGTGTCGTTGCTTTGGAAT 58.702 42.857 0.00 0.00 0.00 3.01
77 78 2.687935 AGTGTGTCGTTGCTTTGGAATT 59.312 40.909 0.00 0.00 0.00 2.17
78 79 3.130340 AGTGTGTCGTTGCTTTGGAATTT 59.870 39.130 0.00 0.00 0.00 1.82
79 80 3.485743 GTGTGTCGTTGCTTTGGAATTTC 59.514 43.478 0.00 0.00 0.00 2.17
80 81 3.129462 TGTGTCGTTGCTTTGGAATTTCA 59.871 39.130 0.00 0.00 0.00 2.69
81 82 4.202101 TGTGTCGTTGCTTTGGAATTTCAT 60.202 37.500 0.00 0.00 0.00 2.57
82 83 4.382754 GTGTCGTTGCTTTGGAATTTCATC 59.617 41.667 0.00 0.00 0.00 2.92
83 84 4.037327 TGTCGTTGCTTTGGAATTTCATCA 59.963 37.500 0.00 0.00 0.00 3.07
84 85 4.618489 GTCGTTGCTTTGGAATTTCATCAG 59.382 41.667 0.00 0.00 0.00 2.90
85 86 4.278170 TCGTTGCTTTGGAATTTCATCAGT 59.722 37.500 0.00 0.00 0.00 3.41
86 87 4.383649 CGTTGCTTTGGAATTTCATCAGTG 59.616 41.667 0.00 0.00 0.00 3.66
87 88 5.531634 GTTGCTTTGGAATTTCATCAGTGA 58.468 37.500 0.00 0.00 0.00 3.41
88 89 5.125100 TGCTTTGGAATTTCATCAGTGAC 57.875 39.130 0.00 0.00 33.11 3.67
89 90 4.161333 GCTTTGGAATTTCATCAGTGACG 58.839 43.478 0.00 0.00 33.11 4.35
90 91 4.083324 GCTTTGGAATTTCATCAGTGACGA 60.083 41.667 0.00 0.00 33.11 4.20
91 92 5.562696 GCTTTGGAATTTCATCAGTGACGAA 60.563 40.000 0.00 0.00 33.11 3.85
92 93 6.573664 TTTGGAATTTCATCAGTGACGAAT 57.426 33.333 1.94 0.00 33.11 3.34
93 94 6.573664 TTGGAATTTCATCAGTGACGAATT 57.426 33.333 1.94 6.24 33.11 2.17
94 95 6.573664 TGGAATTTCATCAGTGACGAATTT 57.426 33.333 1.94 5.68 33.11 1.82
95 96 6.380995 TGGAATTTCATCAGTGACGAATTTG 58.619 36.000 12.33 0.00 33.11 2.32
96 97 6.016360 TGGAATTTCATCAGTGACGAATTTGT 60.016 34.615 12.33 0.00 33.11 2.83
97 98 7.174080 TGGAATTTCATCAGTGACGAATTTGTA 59.826 33.333 12.33 0.00 33.11 2.41
98 99 8.020819 GGAATTTCATCAGTGACGAATTTGTAA 58.979 33.333 12.33 0.00 33.11 2.41
99 100 9.393249 GAATTTCATCAGTGACGAATTTGTAAA 57.607 29.630 12.33 2.96 33.11 2.01
100 101 9.743057 AATTTCATCAGTGACGAATTTGTAAAA 57.257 25.926 1.94 0.00 33.11 1.52
101 102 9.743057 ATTTCATCAGTGACGAATTTGTAAAAA 57.257 25.926 1.94 0.00 33.11 1.94
102 103 9.743057 TTTCATCAGTGACGAATTTGTAAAAAT 57.257 25.926 1.94 0.00 33.11 1.82
103 104 8.948853 TCATCAGTGACGAATTTGTAAAAATC 57.051 30.769 0.00 0.00 0.00 2.17
104 105 7.744276 TCATCAGTGACGAATTTGTAAAAATCG 59.256 33.333 8.26 8.26 37.34 3.34
105 106 6.367421 TCAGTGACGAATTTGTAAAAATCGG 58.633 36.000 13.05 2.64 36.35 4.18
106 107 6.203145 TCAGTGACGAATTTGTAAAAATCGGA 59.797 34.615 13.05 0.51 36.35 4.55
107 108 7.021196 CAGTGACGAATTTGTAAAAATCGGAT 58.979 34.615 13.05 0.00 36.35 4.18
108 109 8.172484 CAGTGACGAATTTGTAAAAATCGGATA 58.828 33.333 13.05 0.00 36.35 2.59
109 110 8.889717 AGTGACGAATTTGTAAAAATCGGATAT 58.110 29.630 13.05 0.00 36.35 1.63
110 111 9.155053 GTGACGAATTTGTAAAAATCGGATATC 57.845 33.333 13.05 0.00 36.35 1.63
111 112 8.339714 TGACGAATTTGTAAAAATCGGATATCC 58.660 33.333 12.14 12.14 36.35 2.59
112 113 7.645402 ACGAATTTGTAAAAATCGGATATCCC 58.355 34.615 16.36 0.00 36.35 3.85
113 114 7.081976 CGAATTTGTAAAAATCGGATATCCCC 58.918 38.462 16.36 0.00 31.69 4.81
114 115 6.911250 ATTTGTAAAAATCGGATATCCCCC 57.089 37.500 16.36 0.00 0.00 5.40
135 136 5.338137 CCCCCTCCCTTAATCGATATAACAC 60.338 48.000 0.00 0.00 0.00 3.32
136 137 5.247564 CCCCTCCCTTAATCGATATAACACA 59.752 44.000 0.00 0.00 0.00 3.72
137 138 6.164176 CCCTCCCTTAATCGATATAACACAC 58.836 44.000 0.00 0.00 0.00 3.82
139 140 7.442656 CCTCCCTTAATCGATATAACACACTT 58.557 38.462 0.00 0.00 0.00 3.16
141 142 8.882415 TCCCTTAATCGATATAACACACTTTC 57.118 34.615 0.00 0.00 0.00 2.62
404 434 8.561738 TTTCTTACAGGAAGACATTAATGACC 57.438 34.615 22.16 16.79 44.12 4.02
410 441 6.264518 ACAGGAAGACATTAATGACCGTTTTT 59.735 34.615 22.16 5.84 0.00 1.94
695 734 8.154649 GCTTTTGCATACATTACCACTACTAT 57.845 34.615 0.00 0.00 46.58 2.12
721 761 7.152645 ACTGAACGTATTTTGTCTCTGTGTAT 58.847 34.615 0.00 0.00 0.00 2.29
733 778 5.884232 TGTCTCTGTGTATAACCGACAGTAT 59.116 40.000 0.00 0.00 38.60 2.12
855 915 2.765807 CCCTGGCCTCTCGTCCAT 60.766 66.667 3.32 0.00 0.00 3.41
979 1050 2.147958 CTCGATCTCTAACCTCCTCCG 58.852 57.143 0.00 0.00 0.00 4.63
1109 1327 1.049289 CCCTGGAGTAGTGGGGTAGC 61.049 65.000 0.00 0.00 37.37 3.58
1219 1437 1.068417 CGTCCACGTCTTTGGTCCA 59.932 57.895 0.00 0.00 37.93 4.02
1292 1516 3.066190 CTCCGGTAGCGGTGACCA 61.066 66.667 30.74 12.13 36.72 4.02
1325 1570 2.368548 GGCAAGAGGGGTCAAATTTTGT 59.631 45.455 8.89 0.00 0.00 2.83
1384 1632 3.703556 TGTGTCAAAATCAAAGGAGCCAA 59.296 39.130 0.00 0.00 0.00 4.52
1613 1865 6.545666 TCAAAGTCTCAACAAATAAGAAGGCA 59.454 34.615 0.00 0.00 0.00 4.75
1772 2071 5.384063 TCTGTGCTGATTATCTAGCTAGC 57.616 43.478 16.35 6.62 40.52 3.42
1844 2173 6.146184 GCTTGAGAGCGCTGATGTTTATTATA 59.854 38.462 18.48 0.00 39.48 0.98
1873 2202 9.710900 TTGCACTGATTGATTAATCGTATCTAT 57.289 29.630 21.46 12.47 44.55 1.98
1874 2203 9.710900 TGCACTGATTGATTAATCGTATCTATT 57.289 29.630 21.46 10.10 44.55 1.73
1888 2217 8.994429 ATCGTATCTATTTTCTATGCCTCTTG 57.006 34.615 0.00 0.00 0.00 3.02
1912 2241 1.171308 TGGTAGTAGCGACCAGTGTC 58.829 55.000 0.00 0.00 42.15 3.67
2003 2332 4.080919 CCATGAAGACCTCAACTGTATCCA 60.081 45.833 0.00 0.00 37.67 3.41
2106 2444 0.252742 AACAAGGGGAGGACGAGGAT 60.253 55.000 0.00 0.00 0.00 3.24
2162 2500 5.171476 CGCTTGATCTATTGTATACCCCAG 58.829 45.833 0.00 0.00 0.00 4.45
2280 2639 5.045578 AGACTTTAGGGCTAGCTTTGATTCA 60.046 40.000 15.72 0.00 0.00 2.57
2325 2684 9.104965 CAACCTTGACCGTTCATATTAATAAGA 57.895 33.333 0.00 0.00 0.00 2.10
2482 2841 1.077787 GGTCCATGGCCATGTCGAA 60.078 57.895 37.30 20.68 37.11 3.71
2546 2911 0.618458 GGGTGTGAGGGCACTAATCA 59.382 55.000 0.00 0.00 45.36 2.57
2688 3055 1.050988 GCTCATCTGGGTAGGAGGCA 61.051 60.000 0.00 0.00 0.00 4.75
2757 3132 0.733150 GTATTGTTCTCGGCCAAGGC 59.267 55.000 2.24 1.52 41.06 4.35
2817 3193 0.680061 GAACAGAACACGGGGACTCT 59.320 55.000 0.00 0.00 0.00 3.24
2987 3369 5.732647 CGTCAGCACAATTATTTAGTTTCCG 59.267 40.000 0.00 0.00 0.00 4.30
3001 3383 8.726870 ATTTAGTTTCCGGAAATAAATCTCGA 57.273 30.769 31.13 15.05 32.36 4.04
3021 3403 4.023963 TCGACAAACGATGTAATTGCCAAA 60.024 37.500 0.00 0.00 46.45 3.28
3063 3446 0.822532 CTAGGCGATACGGACCCAGT 60.823 60.000 0.00 0.00 0.00 4.00
3100 3483 2.636830 CTGTTTGCCGAGATCCTTGAT 58.363 47.619 0.00 0.00 0.00 2.57
3178 3561 1.528586 CTGAGTTGTGTTCTCGGCAAG 59.471 52.381 0.00 0.00 34.99 4.01
3206 3656 6.432783 CCCTGGAACAAAAGACATATACACAA 59.567 38.462 0.00 0.00 38.70 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.898320 ACAGAGCAACAACATAGTCATCA 58.102 39.130 0.00 0.00 0.00 3.07
2 3 5.869753 AACAGAGCAACAACATAGTCATC 57.130 39.130 0.00 0.00 0.00 2.92
5 6 5.352569 AGCATAACAGAGCAACAACATAGTC 59.647 40.000 0.00 0.00 0.00 2.59
6 7 5.248640 AGCATAACAGAGCAACAACATAGT 58.751 37.500 0.00 0.00 0.00 2.12
7 8 5.808042 AGCATAACAGAGCAACAACATAG 57.192 39.130 0.00 0.00 0.00 2.23
8 9 7.864108 ATAAGCATAACAGAGCAACAACATA 57.136 32.000 0.00 0.00 0.00 2.29
9 10 6.764308 ATAAGCATAACAGAGCAACAACAT 57.236 33.333 0.00 0.00 0.00 2.71
10 11 6.093495 GGTATAAGCATAACAGAGCAACAACA 59.907 38.462 0.00 0.00 0.00 3.33
11 12 6.316390 AGGTATAAGCATAACAGAGCAACAAC 59.684 38.462 0.00 0.00 0.00 3.32
12 13 6.316140 CAGGTATAAGCATAACAGAGCAACAA 59.684 38.462 0.00 0.00 0.00 2.83
13 14 5.817296 CAGGTATAAGCATAACAGAGCAACA 59.183 40.000 0.00 0.00 0.00 3.33
14 15 6.049149 TCAGGTATAAGCATAACAGAGCAAC 58.951 40.000 0.00 0.00 0.00 4.17
15 16 6.127054 ACTCAGGTATAAGCATAACAGAGCAA 60.127 38.462 2.53 0.00 40.09 3.91
16 17 5.363868 ACTCAGGTATAAGCATAACAGAGCA 59.636 40.000 2.53 0.00 40.09 4.26
17 18 5.848406 ACTCAGGTATAAGCATAACAGAGC 58.152 41.667 2.53 0.00 40.09 4.09
18 19 8.172352 AGTACTCAGGTATAAGCATAACAGAG 57.828 38.462 0.00 1.38 41.45 3.35
19 20 8.534954 AAGTACTCAGGTATAAGCATAACAGA 57.465 34.615 0.00 0.00 0.00 3.41
24 25 8.737175 CGGAATAAGTACTCAGGTATAAGCATA 58.263 37.037 0.00 0.00 0.00 3.14
25 26 7.603651 CGGAATAAGTACTCAGGTATAAGCAT 58.396 38.462 0.00 0.00 0.00 3.79
26 27 6.516194 GCGGAATAAGTACTCAGGTATAAGCA 60.516 42.308 0.00 0.00 0.00 3.91
27 28 5.862860 GCGGAATAAGTACTCAGGTATAAGC 59.137 44.000 0.00 0.00 0.00 3.09
28 29 7.085116 CAGCGGAATAAGTACTCAGGTATAAG 58.915 42.308 0.00 0.00 0.00 1.73
29 30 6.516194 GCAGCGGAATAAGTACTCAGGTATAA 60.516 42.308 0.00 0.00 0.00 0.98
30 31 5.048224 GCAGCGGAATAAGTACTCAGGTATA 60.048 44.000 0.00 0.00 0.00 1.47
31 32 4.262079 GCAGCGGAATAAGTACTCAGGTAT 60.262 45.833 0.00 0.00 0.00 2.73
32 33 3.067742 GCAGCGGAATAAGTACTCAGGTA 59.932 47.826 0.00 0.00 0.00 3.08
33 34 2.159085 GCAGCGGAATAAGTACTCAGGT 60.159 50.000 0.00 0.00 0.00 4.00
34 35 2.101582 AGCAGCGGAATAAGTACTCAGG 59.898 50.000 0.00 0.00 0.00 3.86
35 36 3.444703 AGCAGCGGAATAAGTACTCAG 57.555 47.619 0.00 0.00 0.00 3.35
36 37 3.952323 ACTAGCAGCGGAATAAGTACTCA 59.048 43.478 0.00 0.00 0.00 3.41
37 38 4.202030 ACACTAGCAGCGGAATAAGTACTC 60.202 45.833 0.00 0.00 0.00 2.59
38 39 3.700038 ACACTAGCAGCGGAATAAGTACT 59.300 43.478 0.00 0.00 0.00 2.73
39 40 3.797256 CACACTAGCAGCGGAATAAGTAC 59.203 47.826 0.00 0.00 0.00 2.73
40 41 3.446161 ACACACTAGCAGCGGAATAAGTA 59.554 43.478 0.00 0.00 0.00 2.24
41 42 2.233922 ACACACTAGCAGCGGAATAAGT 59.766 45.455 0.00 0.00 0.00 2.24
42 43 2.860735 GACACACTAGCAGCGGAATAAG 59.139 50.000 0.00 0.00 0.00 1.73
43 44 2.734175 CGACACACTAGCAGCGGAATAA 60.734 50.000 0.00 0.00 0.00 1.40
44 45 1.202256 CGACACACTAGCAGCGGAATA 60.202 52.381 0.00 0.00 0.00 1.75
45 46 0.458543 CGACACACTAGCAGCGGAAT 60.459 55.000 0.00 0.00 0.00 3.01
46 47 1.080772 CGACACACTAGCAGCGGAA 60.081 57.895 0.00 0.00 0.00 4.30
47 48 1.802337 AACGACACACTAGCAGCGGA 61.802 55.000 0.00 0.00 0.00 5.54
48 49 1.372997 AACGACACACTAGCAGCGG 60.373 57.895 0.00 0.00 0.00 5.52
49 50 1.775344 CAACGACACACTAGCAGCG 59.225 57.895 0.00 0.00 0.00 5.18
50 51 0.946221 AGCAACGACACACTAGCAGC 60.946 55.000 0.00 0.00 0.00 5.25
51 52 1.502231 AAGCAACGACACACTAGCAG 58.498 50.000 0.00 0.00 0.00 4.24
52 53 1.597195 CAAAGCAACGACACACTAGCA 59.403 47.619 0.00 0.00 0.00 3.49
53 54 1.069906 CCAAAGCAACGACACACTAGC 60.070 52.381 0.00 0.00 0.00 3.42
54 55 2.479837 TCCAAAGCAACGACACACTAG 58.520 47.619 0.00 0.00 0.00 2.57
55 56 2.605837 TCCAAAGCAACGACACACTA 57.394 45.000 0.00 0.00 0.00 2.74
56 57 1.745232 TTCCAAAGCAACGACACACT 58.255 45.000 0.00 0.00 0.00 3.55
57 58 2.774439 ATTCCAAAGCAACGACACAC 57.226 45.000 0.00 0.00 0.00 3.82
58 59 3.129462 TGAAATTCCAAAGCAACGACACA 59.871 39.130 0.00 0.00 0.00 3.72
59 60 3.701241 TGAAATTCCAAAGCAACGACAC 58.299 40.909 0.00 0.00 0.00 3.67
60 61 4.037327 TGATGAAATTCCAAAGCAACGACA 59.963 37.500 0.00 0.00 0.00 4.35
61 62 4.545610 TGATGAAATTCCAAAGCAACGAC 58.454 39.130 0.00 0.00 0.00 4.34
62 63 4.278170 ACTGATGAAATTCCAAAGCAACGA 59.722 37.500 0.00 0.00 0.00 3.85
63 64 4.383649 CACTGATGAAATTCCAAAGCAACG 59.616 41.667 0.00 0.00 0.00 4.10
64 65 5.403466 GTCACTGATGAAATTCCAAAGCAAC 59.597 40.000 0.00 0.00 36.31 4.17
65 66 5.531634 GTCACTGATGAAATTCCAAAGCAA 58.468 37.500 0.00 0.00 36.31 3.91
66 67 4.320421 CGTCACTGATGAAATTCCAAAGCA 60.320 41.667 0.00 0.00 36.31 3.91
67 68 4.083324 TCGTCACTGATGAAATTCCAAAGC 60.083 41.667 0.00 0.00 36.31 3.51
68 69 5.611796 TCGTCACTGATGAAATTCCAAAG 57.388 39.130 0.00 0.00 36.31 2.77
69 70 6.573664 ATTCGTCACTGATGAAATTCCAAA 57.426 33.333 16.02 0.00 40.33 3.28
70 71 6.573664 AATTCGTCACTGATGAAATTCCAA 57.426 33.333 16.02 0.00 40.33 3.53
71 72 6.016360 ACAAATTCGTCACTGATGAAATTCCA 60.016 34.615 16.02 0.00 40.33 3.53
72 73 6.381801 ACAAATTCGTCACTGATGAAATTCC 58.618 36.000 16.02 0.00 40.33 3.01
73 74 8.948853 TTACAAATTCGTCACTGATGAAATTC 57.051 30.769 16.02 0.00 40.33 2.17
74 75 9.743057 TTTTACAAATTCGTCACTGATGAAATT 57.257 25.926 16.02 11.88 40.33 1.82
75 76 9.743057 TTTTTACAAATTCGTCACTGATGAAAT 57.257 25.926 16.02 6.74 40.33 2.17
76 77 9.743057 ATTTTTACAAATTCGTCACTGATGAAA 57.257 25.926 16.02 0.00 40.33 2.69
77 78 9.393249 GATTTTTACAAATTCGTCACTGATGAA 57.607 29.630 14.71 14.71 41.04 2.57
78 79 7.744276 CGATTTTTACAAATTCGTCACTGATGA 59.256 33.333 0.00 0.00 32.35 2.92
79 80 7.007367 CCGATTTTTACAAATTCGTCACTGATG 59.993 37.037 10.79 0.00 32.35 3.07
80 81 7.021196 CCGATTTTTACAAATTCGTCACTGAT 58.979 34.615 10.79 0.00 32.35 2.90
81 82 6.203145 TCCGATTTTTACAAATTCGTCACTGA 59.797 34.615 10.79 1.50 32.35 3.41
82 83 6.367421 TCCGATTTTTACAAATTCGTCACTG 58.633 36.000 10.79 0.00 32.35 3.66
83 84 6.548441 TCCGATTTTTACAAATTCGTCACT 57.452 33.333 10.79 0.00 32.35 3.41
84 85 9.155053 GATATCCGATTTTTACAAATTCGTCAC 57.845 33.333 10.79 0.00 32.35 3.67
85 86 8.339714 GGATATCCGATTTTTACAAATTCGTCA 58.660 33.333 5.86 1.26 32.35 4.35
86 87 7.801783 GGGATATCCGATTTTTACAAATTCGTC 59.198 37.037 15.69 4.27 32.35 4.20
87 88 7.255346 GGGGATATCCGATTTTTACAAATTCGT 60.255 37.037 15.69 0.00 32.35 3.85
88 89 7.081976 GGGGATATCCGATTTTTACAAATTCG 58.918 38.462 15.69 6.56 32.35 3.34
89 90 7.375834 GGGGGATATCCGATTTTTACAAATTC 58.624 38.462 15.69 0.00 32.35 2.17
90 91 7.297936 GGGGGATATCCGATTTTTACAAATT 57.702 36.000 15.69 0.00 32.35 1.82
91 92 6.911250 GGGGGATATCCGATTTTTACAAAT 57.089 37.500 15.69 0.00 35.12 2.32
111 112 4.781087 TGTTATATCGATTAAGGGAGGGGG 59.219 45.833 1.71 0.00 0.00 5.40
112 113 5.247564 TGTGTTATATCGATTAAGGGAGGGG 59.752 44.000 1.71 0.00 0.00 4.79
113 114 6.014499 AGTGTGTTATATCGATTAAGGGAGGG 60.014 42.308 1.71 0.00 0.00 4.30
114 115 6.994221 AGTGTGTTATATCGATTAAGGGAGG 58.006 40.000 1.71 0.00 0.00 4.30
115 116 8.888579 AAAGTGTGTTATATCGATTAAGGGAG 57.111 34.615 1.71 0.00 0.00 4.30
116 117 8.479689 TGAAAGTGTGTTATATCGATTAAGGGA 58.520 33.333 1.71 0.00 0.00 4.20
117 118 8.657074 TGAAAGTGTGTTATATCGATTAAGGG 57.343 34.615 1.71 0.00 0.00 3.95
293 299 7.421530 TTTGCTGAACACAAGAAGTATACTC 57.578 36.000 5.70 0.20 0.00 2.59
620 655 7.968405 TGATATGAGATATACACCGAAATCACG 59.032 37.037 0.00 0.00 0.00 4.35
695 734 6.509656 ACACAGAGACAAAATACGTTCAGTA 58.490 36.000 0.00 0.00 40.03 2.74
721 761 2.696187 TGGCTGCATATACTGTCGGTTA 59.304 45.455 0.50 0.00 0.00 2.85
733 778 1.240641 CGGTTGGTGTTGGCTGCATA 61.241 55.000 0.50 0.00 0.00 3.14
855 915 4.973055 CGGGGCGAACGGAACACA 62.973 66.667 0.00 0.00 0.00 3.72
946 1011 5.759506 AGAGATCGAGAAAGCTAAATCGA 57.240 39.130 16.36 16.36 46.90 3.59
954 1019 3.634910 AGGAGGTTAGAGATCGAGAAAGC 59.365 47.826 0.00 0.00 0.00 3.51
979 1050 2.851588 GATGGAGGGAGGGAGGGC 60.852 72.222 0.00 0.00 0.00 5.19
991 1062 3.346315 CAATTATGGGCATAGCGATGGA 58.654 45.455 8.97 0.00 33.26 3.41
1107 1325 4.699522 GGCGTGGGTTCTTCCGCT 62.700 66.667 0.00 0.00 45.11 5.52
1148 1366 2.781158 AAATAATGGTGGCCCGCGC 61.781 57.895 0.00 0.00 0.00 6.86
1219 1437 2.190578 GGAGGCTGGCGCATAAGT 59.809 61.111 10.83 0.00 38.10 2.24
1292 1516 0.622665 CTCTTGCCCATCCAGTCCTT 59.377 55.000 0.00 0.00 0.00 3.36
1325 1570 7.362834 CCATACTACCTGCATCACAATTTTGAA 60.363 37.037 0.00 0.00 0.00 2.69
1384 1632 5.136392 AGGAAGTAGTATCAGTATCAGGGGT 59.864 44.000 0.00 0.00 0.00 4.95
1419 1667 3.364764 GCTTGACTGCTGTTGAAGATGAC 60.365 47.826 16.03 0.00 0.00 3.06
1613 1865 0.317770 CACAAAAGCACGCCGTGAAT 60.318 50.000 23.33 5.38 35.23 2.57
1772 2071 7.371159 TGATATTAGACAGCTCTTAATGGACG 58.629 38.462 0.00 0.00 0.00 4.79
1844 2173 6.441093 ACGATTAATCAATCAGTGCAATGT 57.559 33.333 14.62 0.00 40.61 2.71
1888 2217 0.744874 TGGTCGCTACTACCATCTGC 59.255 55.000 0.00 0.00 42.10 4.26
1912 2241 9.829507 AACTCAGATTTTATCATACTCTCCAAG 57.170 33.333 0.00 0.00 0.00 3.61
1942 2271 6.012858 AGGACCAGTACCAACAATCATTCTTA 60.013 38.462 0.00 0.00 0.00 2.10
2003 2332 1.885887 GTAGATCCTGAGAGCGAGCAT 59.114 52.381 0.00 0.00 32.16 3.79
2106 2444 2.232941 GACACCGATGGTTCTGGTTCTA 59.767 50.000 0.00 0.00 31.02 2.10
2162 2500 4.248859 TGCTCTGCAGAACATCTTAAGTC 58.751 43.478 18.85 0.44 33.32 3.01
2280 2639 2.649831 CAGCATTGCAGGAACACCT 58.350 52.632 11.91 0.00 33.85 4.00
2294 2653 1.444119 GAACGGTCAAGGTTGCAGCA 61.444 55.000 2.05 0.00 0.00 4.41
2325 2684 8.988934 CGCACAACTATATTCTGGTAAATATGT 58.011 33.333 0.00 0.00 34.47 2.29
2339 2698 6.522054 ACATAAGTAAGGCGCACAACTATAT 58.478 36.000 10.83 6.87 0.00 0.86
2546 2911 2.521547 ACCTAGGCCTACTTACACGT 57.478 50.000 8.91 0.00 0.00 4.49
2674 3041 1.384502 CCCATGCCTCCTACCCAGA 60.385 63.158 0.00 0.00 0.00 3.86
2757 3132 1.614413 GGTAGGATTCGGGCTGAGTAG 59.386 57.143 0.00 0.00 0.00 2.57
2861 3243 4.675029 CGTCCGGCCCGTGAAGTT 62.675 66.667 0.85 0.00 0.00 2.66
2935 3317 0.744874 TCATCCGCTTTACCTCTCGG 59.255 55.000 0.00 0.00 42.96 4.63
2937 3319 2.427453 TCACTCATCCGCTTTACCTCTC 59.573 50.000 0.00 0.00 0.00 3.20
2939 3321 2.427453 TCTCACTCATCCGCTTTACCTC 59.573 50.000 0.00 0.00 0.00 3.85
2940 3322 2.166664 GTCTCACTCATCCGCTTTACCT 59.833 50.000 0.00 0.00 0.00 3.08
2941 3323 2.094182 TGTCTCACTCATCCGCTTTACC 60.094 50.000 0.00 0.00 0.00 2.85
2942 3324 2.924290 GTGTCTCACTCATCCGCTTTAC 59.076 50.000 0.00 0.00 0.00 2.01
2943 3325 2.415491 CGTGTCTCACTCATCCGCTTTA 60.415 50.000 0.00 0.00 31.34 1.85
2950 3332 1.068264 TGCTGACGTGTCTCACTCATC 60.068 52.381 0.00 0.00 31.34 2.92
3001 3383 6.481644 ACAAATTTGGCAATTACATCGTTTGT 59.518 30.769 21.74 6.29 42.62 2.83
3021 3403 0.958822 GCCACTCGGGAAACACAAAT 59.041 50.000 0.00 0.00 40.01 2.32
3100 3483 8.307483 TGGTTCATTTCTTTGACAAGTGTAAAA 58.693 29.630 0.00 0.00 0.00 1.52
3178 3561 1.398692 TGTCTTTTGTTCCAGGGCAC 58.601 50.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.