Multiple sequence alignment - TraesCS7B01G240800

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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 TraesCS7B01G240800 chr7B 100.000 2516 0 0 1 2516 447993962 447996477 0.000000e+00 4647.0
1 TraesCS7B01G240800 chr7B 88.099 689 61 9 621 1304 207443529 207444201 0.000000e+00 798.0
2 TraesCS7B01G240800 chr7B 91.667 216 13 3 33 246 680778450 680778662 6.810000e-76 294.0
3 TraesCS7B01G240800 chr7B 80.656 305 50 8 1996 2296 695074303 695074602 7.000000e-56 228.0
4 TraesCS7B01G240800 chr7B 87.356 87 9 2 1650 1734 196957973 196957887 5.730000e-17 99.0
5 TraesCS7B01G240800 chr7D 98.240 1250 18 4 370 1618 430481453 430482699 0.000000e+00 2183.0
6 TraesCS7B01G240800 chr7D 97.521 605 14 1 1706 2310 430482698 430483301 0.000000e+00 1033.0
7 TraesCS7B01G240800 chr7D 92.417 211 16 0 2306 2516 430484115 430484325 4.070000e-78 302.0
8 TraesCS7B01G240800 chr7D 87.432 183 20 2 63 243 364744855 364744674 9.120000e-50 207.0
9 TraesCS7B01G240800 chr3A 89.212 1446 110 23 242 1649 284299712 284301149 0.000000e+00 1764.0
10 TraesCS7B01G240800 chr3A 87.704 1041 91 15 623 1649 576911756 576912773 0.000000e+00 1179.0
11 TraesCS7B01G240800 chr3A 79.155 355 71 2 1936 2290 679982434 679982083 2.500000e-60 243.0
12 TraesCS7B01G240800 chr7A 88.866 1446 115 27 242 1649 408895905 408897342 0.000000e+00 1736.0
13 TraesCS7B01G240800 chr7A 88.599 1035 91 12 623 1652 242620999 242619987 0.000000e+00 1232.0
14 TraesCS7B01G240800 chr7A 85.938 1024 104 18 622 1641 199320434 199321421 0.000000e+00 1057.0
15 TraesCS7B01G240800 chr7A 93.818 275 17 0 242 516 470289144 470288870 5.010000e-112 414.0
16 TraesCS7B01G240800 chr7A 93.841 276 15 2 242 516 568902826 568903100 5.010000e-112 414.0
17 TraesCS7B01G240800 chr7A 93.478 276 15 2 242 516 526861076 526860803 8.380000e-110 407.0
18 TraesCS7B01G240800 chr7A 80.503 318 56 6 1983 2297 688816581 688816267 3.230000e-59 239.0
19 TraesCS7B01G240800 chr7A 90.000 170 11 3 45 211 315299900 315299734 5.450000e-52 215.0
20 TraesCS7B01G240800 chr7A 83.889 180 23 6 2119 2296 688796513 688796338 1.550000e-37 167.0
21 TraesCS7B01G240800 chr7A 95.556 45 1 1 1689 1732 9434195 9434151 1.250000e-08 71.3
22 TraesCS7B01G240800 chr2D 90.022 1363 89 31 242 1564 230674750 230673395 0.000000e+00 1720.0
23 TraesCS7B01G240800 chr2D 87.500 248 22 8 1 242 564605110 564605354 6.850000e-71 278.0
24 TraesCS7B01G240800 chr2D 85.714 175 19 5 1559 1729 230672490 230672318 1.990000e-41 180.0
25 TraesCS7B01G240800 chr3D 90.909 1309 73 18 383 1652 146133375 146132074 0.000000e+00 1716.0
26 TraesCS7B01G240800 chr3D 95.425 153 6 1 242 394 146133939 146133788 2.500000e-60 243.0
27 TraesCS7B01G240800 chr4A 88.388 1464 101 30 250 1649 119930649 119932107 0.000000e+00 1698.0
28 TraesCS7B01G240800 chr4A 84.783 184 22 4 63 242 216122329 216122148 1.990000e-41 180.0
29 TraesCS7B01G240800 chr2A 87.172 1029 98 16 622 1646 615120216 615119218 0.000000e+00 1138.0
30 TraesCS7B01G240800 chrUn 89.640 666 52 4 622 1285 411526890 411526240 0.000000e+00 832.0
31 TraesCS7B01G240800 chrUn 90.909 44 1 3 1689 1732 85063860 85063820 3.500000e-04 56.5
32 TraesCS7B01G240800 chr1D 88.722 665 60 2 622 1285 70104936 70105586 0.000000e+00 798.0
33 TraesCS7B01G240800 chr1D 91.770 243 8 6 1 242 209978801 209979032 6.710000e-86 327.0
34 TraesCS7B01G240800 chr1D 80.161 373 66 8 1929 2297 408708634 408708266 3.190000e-69 272.0
35 TraesCS7B01G240800 chr1D 82.508 303 47 6 1997 2296 5692663 5692962 6.900000e-66 261.0
36 TraesCS7B01G240800 chr1D 87.640 89 9 2 1649 1735 70131961 70132049 4.430000e-18 102.0
37 TraesCS7B01G240800 chr2B 91.026 234 16 5 5 237 279518974 279519203 6.760000e-81 311.0
38 TraesCS7B01G240800 chr2B 86.441 59 8 0 1689 1747 70836211 70836269 5.810000e-07 65.8
39 TraesCS7B01G240800 chr5B 86.842 190 19 6 63 249 320636414 320636228 9.120000e-50 207.0
40 TraesCS7B01G240800 chr5B 95.918 49 1 1 1689 1736 323107781 323107829 7.460000e-11 78.7
41 TraesCS7B01G240800 chr5D 85.792 183 20 5 63 242 17474078 17473899 3.300000e-44 189.0
42 TraesCS7B01G240800 chr4B 81.609 174 27 5 2120 2291 596668777 596668607 3.370000e-29 139.0
43 TraesCS7B01G240800 chr4B 77.095 179 35 6 2120 2296 3622557 3622731 5.730000e-17 99.0
44 TraesCS7B01G240800 chr5A 93.878 49 2 1 1688 1735 679618361 679618313 3.470000e-09 73.1


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 TraesCS7B01G240800 chr7B 447993962 447996477 2515 False 4647.000000 4647 100.000000 1 2516 1 chr7B.!!$F2 2515
1 TraesCS7B01G240800 chr7B 207443529 207444201 672 False 798.000000 798 88.099000 621 1304 1 chr7B.!!$F1 683
2 TraesCS7B01G240800 chr7D 430481453 430484325 2872 False 1172.666667 2183 96.059333 370 2516 3 chr7D.!!$F1 2146
3 TraesCS7B01G240800 chr3A 284299712 284301149 1437 False 1764.000000 1764 89.212000 242 1649 1 chr3A.!!$F1 1407
4 TraesCS7B01G240800 chr3A 576911756 576912773 1017 False 1179.000000 1179 87.704000 623 1649 1 chr3A.!!$F2 1026
5 TraesCS7B01G240800 chr7A 408895905 408897342 1437 False 1736.000000 1736 88.866000 242 1649 1 chr7A.!!$F2 1407
6 TraesCS7B01G240800 chr7A 242619987 242620999 1012 True 1232.000000 1232 88.599000 623 1652 1 chr7A.!!$R2 1029
7 TraesCS7B01G240800 chr7A 199320434 199321421 987 False 1057.000000 1057 85.938000 622 1641 1 chr7A.!!$F1 1019
8 TraesCS7B01G240800 chr2D 230672318 230674750 2432 True 950.000000 1720 87.868000 242 1729 2 chr2D.!!$R1 1487
9 TraesCS7B01G240800 chr3D 146132074 146133939 1865 True 979.500000 1716 93.167000 242 1652 2 chr3D.!!$R1 1410
10 TraesCS7B01G240800 chr4A 119930649 119932107 1458 False 1698.000000 1698 88.388000 250 1649 1 chr4A.!!$F1 1399
11 TraesCS7B01G240800 chr2A 615119218 615120216 998 True 1138.000000 1138 87.172000 622 1646 1 chr2A.!!$R1 1024
12 TraesCS7B01G240800 chrUn 411526240 411526890 650 True 832.000000 832 89.640000 622 1285 1 chrUn.!!$R2 663
13 TraesCS7B01G240800 chr1D 70104936 70105586 650 False 798.000000 798 88.722000 622 1285 1 chr1D.!!$F2 663

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
40 41 0.033504 CTACTCAGCGGGTGTGTGTT 59.966 55.0 21.15 1.53 34.66 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 3449 1.27055 CGCCACCTTTTTGCAGAATCT 59.729 47.619 0.0 0.0 0.0 2.4 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
22 23 4.789807 TGCGTTAGGACTCTATAGAACCT 58.210 43.478 23.09 23.09 37.08 3.50
23 24 5.933617 TGCGTTAGGACTCTATAGAACCTA 58.066 41.667 21.63 21.63 35.72 3.08
24 25 5.762218 TGCGTTAGGACTCTATAGAACCTAC 59.238 44.000 23.68 19.06 36.16 3.18
25 26 5.997129 GCGTTAGGACTCTATAGAACCTACT 59.003 44.000 23.68 11.20 36.16 2.57
26 27 6.147656 GCGTTAGGACTCTATAGAACCTACTC 59.852 46.154 23.68 19.57 36.16 2.59
27 28 7.215789 CGTTAGGACTCTATAGAACCTACTCA 58.784 42.308 23.68 13.67 36.16 3.41
28 29 7.385752 CGTTAGGACTCTATAGAACCTACTCAG 59.614 44.444 23.68 15.70 36.16 3.35
29 30 5.627135 AGGACTCTATAGAACCTACTCAGC 58.373 45.833 20.12 0.00 33.68 4.26
30 31 4.453136 GGACTCTATAGAACCTACTCAGCG 59.547 50.000 14.69 0.00 0.00 5.18
31 32 4.391155 ACTCTATAGAACCTACTCAGCGG 58.609 47.826 3.57 0.00 0.00 5.52
32 33 3.752665 TCTATAGAACCTACTCAGCGGG 58.247 50.000 0.00 0.00 0.00 6.13
33 34 2.456073 ATAGAACCTACTCAGCGGGT 57.544 50.000 0.00 0.00 34.47 5.28
34 35 1.471119 TAGAACCTACTCAGCGGGTG 58.529 55.000 0.00 0.00 33.20 4.61
35 36 0.542232 AGAACCTACTCAGCGGGTGT 60.542 55.000 7.12 0.00 33.20 4.16
36 37 0.389948 GAACCTACTCAGCGGGTGTG 60.390 60.000 7.12 7.39 33.20 3.82
37 38 1.119574 AACCTACTCAGCGGGTGTGT 61.120 55.000 17.47 17.47 36.79 3.72
38 39 1.079819 CCTACTCAGCGGGTGTGTG 60.080 63.158 21.15 12.56 34.66 3.82
39 40 1.666011 CTACTCAGCGGGTGTGTGT 59.334 57.895 21.15 14.03 34.66 3.72
40 41 0.033504 CTACTCAGCGGGTGTGTGTT 59.966 55.000 21.15 1.53 34.66 3.32
41 42 0.249699 TACTCAGCGGGTGTGTGTTG 60.250 55.000 21.15 4.13 34.66 3.33
42 43 1.523711 CTCAGCGGGTGTGTGTTGT 60.524 57.895 7.12 0.00 0.00 3.32
43 44 1.775039 CTCAGCGGGTGTGTGTTGTG 61.775 60.000 7.12 0.00 0.00 3.33
44 45 2.112198 CAGCGGGTGTGTGTTGTGT 61.112 57.895 0.00 0.00 0.00 3.72
45 46 2.112198 AGCGGGTGTGTGTTGTGTG 61.112 57.895 0.00 0.00 0.00 3.82
46 47 2.403378 GCGGGTGTGTGTTGTGTGT 61.403 57.895 0.00 0.00 0.00 3.72
47 48 1.427419 CGGGTGTGTGTTGTGTGTG 59.573 57.895 0.00 0.00 0.00 3.82
48 49 1.302383 CGGGTGTGTGTTGTGTGTGT 61.302 55.000 0.00 0.00 0.00 3.72
49 50 0.170116 GGGTGTGTGTTGTGTGTGTG 59.830 55.000 0.00 0.00 0.00 3.82
50 51 0.878416 GGTGTGTGTTGTGTGTGTGT 59.122 50.000 0.00 0.00 0.00 3.72
51 52 1.400888 GGTGTGTGTTGTGTGTGTGTG 60.401 52.381 0.00 0.00 0.00 3.82
52 53 1.265635 GTGTGTGTTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
53 54 1.265365 TGTGTGTTGTGTGTGTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
54 55 1.265635 GTGTGTTGTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
55 56 1.265365 TGTGTTGTGTGTGTGTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
56 57 1.265635 GTGTTGTGTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
57 58 1.950216 TGTTGTGTGTGTGTGTGTGTT 59.050 42.857 0.00 0.00 0.00 3.32
58 59 2.359214 TGTTGTGTGTGTGTGTGTGTTT 59.641 40.909 0.00 0.00 0.00 2.83
59 60 2.695613 TGTGTGTGTGTGTGTGTTTG 57.304 45.000 0.00 0.00 0.00 2.93
60 61 1.950216 TGTGTGTGTGTGTGTGTTTGT 59.050 42.857 0.00 0.00 0.00 2.83
61 62 2.359214 TGTGTGTGTGTGTGTGTTTGTT 59.641 40.909 0.00 0.00 0.00 2.83
62 63 2.977169 GTGTGTGTGTGTGTGTTTGTTC 59.023 45.455 0.00 0.00 0.00 3.18
63 64 2.618709 TGTGTGTGTGTGTGTTTGTTCA 59.381 40.909 0.00 0.00 0.00 3.18
64 65 3.233578 GTGTGTGTGTGTGTTTGTTCAG 58.766 45.455 0.00 0.00 0.00 3.02
65 66 3.058570 GTGTGTGTGTGTGTTTGTTCAGA 60.059 43.478 0.00 0.00 0.00 3.27
66 67 3.058570 TGTGTGTGTGTGTTTGTTCAGAC 60.059 43.478 0.00 0.00 33.17 3.51
67 68 3.058570 GTGTGTGTGTGTTTGTTCAGACA 60.059 43.478 0.00 0.00 38.84 3.41
68 69 3.755905 TGTGTGTGTGTTTGTTCAGACAT 59.244 39.130 0.00 0.00 42.03 3.06
69 70 4.938226 TGTGTGTGTGTTTGTTCAGACATA 59.062 37.500 0.00 0.00 42.03 2.29
70 71 5.588246 TGTGTGTGTGTTTGTTCAGACATAT 59.412 36.000 0.00 0.00 42.03 1.78
71 72 6.763610 TGTGTGTGTGTTTGTTCAGACATATA 59.236 34.615 0.00 0.00 42.03 0.86
72 73 7.443879 TGTGTGTGTGTTTGTTCAGACATATAT 59.556 33.333 0.00 0.00 42.03 0.86
73 74 8.289618 GTGTGTGTGTTTGTTCAGACATATATT 58.710 33.333 0.00 0.00 42.03 1.28
74 75 8.845227 TGTGTGTGTTTGTTCAGACATATATTT 58.155 29.630 0.00 0.00 42.03 1.40
197 198 2.739885 TTTTTCCATTGCGGACATGG 57.260 45.000 10.45 10.45 46.36 3.66
198 199 0.246086 TTTTCCATTGCGGACATGGC 59.754 50.000 11.45 0.00 46.36 4.40
199 200 0.611618 TTTCCATTGCGGACATGGCT 60.612 50.000 0.00 0.00 46.36 4.75
200 201 0.611618 TTCCATTGCGGACATGGCTT 60.612 50.000 0.00 0.00 46.36 4.35
201 202 0.611618 TCCATTGCGGACATGGCTTT 60.612 50.000 0.00 0.00 39.64 3.51
202 203 1.102154 CCATTGCGGACATGGCTTTA 58.898 50.000 0.00 0.00 36.56 1.85
203 204 1.066002 CCATTGCGGACATGGCTTTAG 59.934 52.381 0.00 0.00 36.56 1.85
204 205 0.740737 ATTGCGGACATGGCTTTAGC 59.259 50.000 0.00 0.00 41.14 3.09
205 206 1.643868 TTGCGGACATGGCTTTAGCG 61.644 55.000 0.00 0.00 43.26 4.26
206 207 2.106683 GCGGACATGGCTTTAGCGT 61.107 57.895 0.00 0.00 43.26 5.07
207 208 1.715585 CGGACATGGCTTTAGCGTG 59.284 57.895 0.00 0.49 43.26 5.34
208 209 1.429423 GGACATGGCTTTAGCGTGC 59.571 57.895 0.00 0.00 43.26 5.34
213 214 3.490890 GGCTTTAGCGTGCCTCTG 58.509 61.111 0.00 0.00 45.26 3.35
214 215 2.754995 GGCTTTAGCGTGCCTCTGC 61.755 63.158 0.00 0.00 45.26 4.26
215 216 3.084579 CTTTAGCGTGCCTCTGCG 58.915 61.111 0.00 0.00 41.78 5.18
221 222 3.434319 CGTGCCTCTGCGCCATTT 61.434 61.111 4.18 0.00 45.29 2.32
222 223 2.180017 GTGCCTCTGCGCCATTTG 59.820 61.111 4.18 0.00 42.25 2.32
223 224 3.063704 TGCCTCTGCGCCATTTGG 61.064 61.111 4.18 0.87 41.78 3.28
233 234 3.679738 CCATTTGGCGCAACGGGT 61.680 61.111 10.83 0.00 0.00 5.28
234 235 2.126502 CATTTGGCGCAACGGGTC 60.127 61.111 10.83 0.00 0.00 4.46
235 236 3.370231 ATTTGGCGCAACGGGTCC 61.370 61.111 10.83 0.00 0.00 4.46
236 237 4.877619 TTTGGCGCAACGGGTCCA 62.878 61.111 10.83 0.00 0.00 4.02
237 238 4.652131 TTGGCGCAACGGGTCCAT 62.652 61.111 10.83 0.00 0.00 3.41
238 239 4.652131 TGGCGCAACGGGTCCATT 62.652 61.111 10.83 0.00 0.00 3.16
239 240 2.437002 GGCGCAACGGGTCCATTA 60.437 61.111 10.83 0.00 0.00 1.90
240 241 2.469516 GGCGCAACGGGTCCATTAG 61.470 63.158 10.83 0.00 0.00 1.73
266 267 6.228258 AGCTATTAAAAACTCTTCACGGTCA 58.772 36.000 0.00 0.00 0.00 4.02
286 287 6.017934 CGGTCATACATGCTATATAATTGGCC 60.018 42.308 0.00 0.00 0.00 5.36
291 292 8.905850 CATACATGCTATATAATTGGCCAATCA 58.094 33.333 30.74 18.63 0.00 2.57
872 1331 6.037098 AGAATCTAACATCTCAACTACGCAC 58.963 40.000 0.00 0.00 0.00 5.34
1133 1595 3.616076 CGAAGAAGCAATCTGTGTCTCCT 60.616 47.826 0.00 0.00 38.79 3.69
1180 1645 0.906066 TCACCTTAGTTATGGCCGCA 59.094 50.000 0.00 0.00 0.00 5.69
1356 1836 6.480763 TCTCTATAAACATTTGTGGCAAGGA 58.519 36.000 0.00 0.00 0.00 3.36
1364 1844 0.817634 TTGTGGCAAGGAACGTGGAG 60.818 55.000 0.00 0.00 38.52 3.86
1626 3037 1.067142 TGCGTGACTGTATTGGACTCC 60.067 52.381 0.00 0.00 0.00 3.85
1641 3052 2.410730 GGACTCCAAACAATACGTGTCG 59.589 50.000 0.00 0.00 40.60 4.35
1649 3060 5.119588 CCAAACAATACGTGTCGATGTAGTT 59.880 40.000 0.00 0.00 40.60 2.24
1652 3063 6.426980 ACAATACGTGTCGATGTAGTTCTA 57.573 37.500 0.00 0.00 34.38 2.10
1653 3064 6.845302 ACAATACGTGTCGATGTAGTTCTAA 58.155 36.000 0.00 0.00 34.38 2.10
1654 3065 7.478322 ACAATACGTGTCGATGTAGTTCTAAT 58.522 34.615 0.00 0.00 34.38 1.73
1656 3067 5.556355 ACGTGTCGATGTAGTTCTAATCA 57.444 39.130 0.00 0.00 0.00 2.57
1657 3068 5.946298 ACGTGTCGATGTAGTTCTAATCAA 58.054 37.500 0.00 0.00 0.00 2.57
1658 3069 6.384224 ACGTGTCGATGTAGTTCTAATCAAA 58.616 36.000 0.00 0.00 0.00 2.69
1661 3072 5.803461 TGTCGATGTAGTTCTAATCAAACGG 59.197 40.000 0.00 0.00 0.00 4.44
1662 3073 4.802039 TCGATGTAGTTCTAATCAAACGGC 59.198 41.667 0.00 0.00 0.00 5.68
1663 3074 4.317139 CGATGTAGTTCTAATCAAACGGCG 60.317 45.833 4.80 4.80 0.00 6.46
1701 3116 1.671845 GTGAACAAACGTGGTGGCTTA 59.328 47.619 0.00 0.00 0.00 3.09
1808 3223 7.173218 TCACTTTACAAAGATTCATGTCCACTC 59.827 37.037 8.65 0.00 39.31 3.51
1901 3316 4.627058 ACCTTTTTATGCAAACCTTTCGG 58.373 39.130 0.00 0.00 0.00 4.30
1993 3408 2.218603 ACCCAGTTTTTACACGAGCAG 58.781 47.619 0.00 0.00 0.00 4.24
1998 3413 4.510340 CCAGTTTTTACACGAGCAGTAACT 59.490 41.667 0.00 0.00 31.67 2.24
2012 3427 8.033038 ACGAGCAGTAACTAAGATAATTTGACA 58.967 33.333 0.00 0.00 0.00 3.58
2081 3496 3.681897 CCAGCAGGATAGCATTTATCGAC 59.318 47.826 0.00 0.00 36.89 4.20
2147 3562 1.906574 CCTGTTCCAGGCCTAGTACAA 59.093 52.381 3.98 0.00 45.13 2.41
2170 3585 5.479306 ACACTGTTCGTCTGCTGTATATTT 58.521 37.500 0.00 0.00 0.00 1.40
2196 3611 3.297134 TTCCAACTCTGCCTTCAAACT 57.703 42.857 0.00 0.00 0.00 2.66
2231 3646 3.797256 ACGCTACTTTATCTGTCAATCGC 59.203 43.478 0.00 0.00 0.00 4.58
2294 3709 1.659098 CATAGACCAAACGTTCGCCTC 59.341 52.381 0.00 0.00 0.00 4.70
2310 3725 1.118838 CCTCCGCTTCTCTCTTCCAT 58.881 55.000 0.00 0.00 0.00 3.41
2311 3726 1.202510 CCTCCGCTTCTCTCTTCCATG 60.203 57.143 0.00 0.00 0.00 3.66
2312 3727 0.826715 TCCGCTTCTCTCTTCCATGG 59.173 55.000 4.97 4.97 0.00 3.66
2313 3728 0.539051 CCGCTTCTCTCTTCCATGGT 59.461 55.000 12.58 0.00 0.00 3.55
2314 3729 1.649664 CGCTTCTCTCTTCCATGGTG 58.350 55.000 12.58 6.40 0.00 4.17
2315 3730 1.066573 CGCTTCTCTCTTCCATGGTGT 60.067 52.381 12.58 0.00 0.00 4.16
2320 4553 1.273606 CTCTCTTCCATGGTGTCACGT 59.726 52.381 12.58 0.00 0.00 4.49
2356 4589 4.521062 CTCGCCCTCCCGAGCTTG 62.521 72.222 0.00 0.00 46.69 4.01
2375 4608 1.076705 GCCCCATCTTCTTCCACCC 60.077 63.158 0.00 0.00 0.00 4.61
2391 4624 2.737180 CCAGACAGCCACAGACGT 59.263 61.111 0.00 0.00 0.00 4.34
2449 4682 2.269241 GCCTCTTCTTGGGGGACG 59.731 66.667 0.00 0.00 0.00 4.79
2453 4686 1.152204 TCTTCTTGGGGGACGTCCA 60.152 57.895 34.40 13.91 37.91 4.02
2458 4691 0.037590 CTTGGGGGACGTCCATTCAA 59.962 55.000 34.40 28.58 37.91 2.69
2497 4730 4.003788 CCGACGGGCTCCACAACT 62.004 66.667 5.81 0.00 0.00 3.16
2506 4739 1.525995 CTCCACAACTGCACCGGTT 60.526 57.895 2.97 0.00 32.65 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.997129 AGTAGGTTCTATAGAGTCCTAACGC 59.003 44.000 24.62 17.36 35.72 4.84
2 3 7.215789 TGAGTAGGTTCTATAGAGTCCTAACG 58.784 42.308 24.62 0.00 35.72 3.18
3 4 7.173735 GCTGAGTAGGTTCTATAGAGTCCTAAC 59.826 44.444 24.62 21.74 35.72 2.34
4 5 7.225725 GCTGAGTAGGTTCTATAGAGTCCTAA 58.774 42.308 24.62 15.25 35.72 2.69
5 6 6.518706 CGCTGAGTAGGTTCTATAGAGTCCTA 60.519 46.154 21.62 21.62 34.14 2.94
6 7 5.627135 GCTGAGTAGGTTCTATAGAGTCCT 58.373 45.833 23.06 23.06 35.53 3.85
7 8 4.453136 CGCTGAGTAGGTTCTATAGAGTCC 59.547 50.000 14.46 14.46 0.00 3.85
8 9 4.453136 CCGCTGAGTAGGTTCTATAGAGTC 59.547 50.000 2.02 0.97 0.00 3.36
9 10 4.391155 CCGCTGAGTAGGTTCTATAGAGT 58.609 47.826 2.02 0.00 0.00 3.24
10 11 3.754323 CCCGCTGAGTAGGTTCTATAGAG 59.246 52.174 2.02 0.00 0.00 2.43
11 12 3.137913 ACCCGCTGAGTAGGTTCTATAGA 59.862 47.826 0.00 0.00 0.00 1.98
12 13 3.253677 CACCCGCTGAGTAGGTTCTATAG 59.746 52.174 0.00 0.00 0.00 1.31
13 14 3.220110 CACCCGCTGAGTAGGTTCTATA 58.780 50.000 0.00 0.00 0.00 1.31
14 15 2.032620 CACCCGCTGAGTAGGTTCTAT 58.967 52.381 0.00 0.00 0.00 1.98
15 16 1.272313 ACACCCGCTGAGTAGGTTCTA 60.272 52.381 0.00 0.00 0.00 2.10
16 17 0.542232 ACACCCGCTGAGTAGGTTCT 60.542 55.000 0.00 0.00 0.00 3.01
17 18 0.389948 CACACCCGCTGAGTAGGTTC 60.390 60.000 0.00 0.00 0.00 3.62
18 19 1.119574 ACACACCCGCTGAGTAGGTT 61.120 55.000 0.00 0.00 0.00 3.50
19 20 1.533273 ACACACCCGCTGAGTAGGT 60.533 57.895 0.00 0.00 0.00 3.08
20 21 1.079819 CACACACCCGCTGAGTAGG 60.080 63.158 0.00 0.00 0.00 3.18
21 22 0.033504 AACACACACCCGCTGAGTAG 59.966 55.000 0.00 0.00 0.00 2.57
22 23 0.249699 CAACACACACCCGCTGAGTA 60.250 55.000 0.00 0.00 0.00 2.59
23 24 1.523711 CAACACACACCCGCTGAGT 60.524 57.895 0.00 0.00 0.00 3.41
24 25 1.523711 ACAACACACACCCGCTGAG 60.524 57.895 0.00 0.00 0.00 3.35
25 26 1.817520 CACAACACACACCCGCTGA 60.818 57.895 0.00 0.00 0.00 4.26
26 27 2.112198 ACACAACACACACCCGCTG 61.112 57.895 0.00 0.00 0.00 5.18
27 28 2.112198 CACACAACACACACCCGCT 61.112 57.895 0.00 0.00 0.00 5.52
28 29 2.403378 ACACACAACACACACCCGC 61.403 57.895 0.00 0.00 0.00 6.13
29 30 1.302383 ACACACACAACACACACCCG 61.302 55.000 0.00 0.00 0.00 5.28
30 31 0.170116 CACACACACAACACACACCC 59.830 55.000 0.00 0.00 0.00 4.61
31 32 0.878416 ACACACACACAACACACACC 59.122 50.000 0.00 0.00 0.00 4.16
32 33 1.265635 ACACACACACACAACACACAC 59.734 47.619 0.00 0.00 0.00 3.82
33 34 1.265365 CACACACACACACAACACACA 59.735 47.619 0.00 0.00 0.00 3.72
34 35 1.265635 ACACACACACACACAACACAC 59.734 47.619 0.00 0.00 0.00 3.82
35 36 1.265365 CACACACACACACACAACACA 59.735 47.619 0.00 0.00 0.00 3.72
36 37 1.265635 ACACACACACACACACAACAC 59.734 47.619 0.00 0.00 0.00 3.32
37 38 1.598882 ACACACACACACACACAACA 58.401 45.000 0.00 0.00 0.00 3.33
38 39 2.697431 AACACACACACACACACAAC 57.303 45.000 0.00 0.00 0.00 3.32
39 40 2.359214 ACAAACACACACACACACACAA 59.641 40.909 0.00 0.00 0.00 3.33
40 41 1.950216 ACAAACACACACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
41 42 2.697431 ACAAACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
42 43 2.618709 TGAACAAACACACACACACACA 59.381 40.909 0.00 0.00 0.00 3.72
43 44 3.058570 TCTGAACAAACACACACACACAC 60.059 43.478 0.00 0.00 0.00 3.82
44 45 3.058570 GTCTGAACAAACACACACACACA 60.059 43.478 0.00 0.00 0.00 3.72
45 46 3.058570 TGTCTGAACAAACACACACACAC 60.059 43.478 0.00 0.00 30.70 3.82
46 47 3.142174 TGTCTGAACAAACACACACACA 58.858 40.909 0.00 0.00 30.70 3.72
47 48 3.822594 TGTCTGAACAAACACACACAC 57.177 42.857 0.00 0.00 30.70 3.82
48 49 7.977789 ATATATGTCTGAACAAACACACACA 57.022 32.000 0.00 0.00 39.30 3.72
183 184 1.066002 CTAAAGCCATGTCCGCAATGG 59.934 52.381 5.20 5.20 38.45 3.16
184 185 1.534595 GCTAAAGCCATGTCCGCAATG 60.535 52.381 0.00 0.00 34.31 2.82
185 186 0.740737 GCTAAAGCCATGTCCGCAAT 59.259 50.000 0.00 0.00 34.31 3.56
186 187 1.643868 CGCTAAAGCCATGTCCGCAA 61.644 55.000 0.00 0.00 37.91 4.85
187 188 2.106074 CGCTAAAGCCATGTCCGCA 61.106 57.895 0.00 0.00 37.91 5.69
188 189 2.106683 ACGCTAAAGCCATGTCCGC 61.107 57.895 0.00 0.00 37.91 5.54
189 190 1.715585 CACGCTAAAGCCATGTCCG 59.284 57.895 0.00 0.00 37.91 4.79
190 191 1.429423 GCACGCTAAAGCCATGTCC 59.571 57.895 0.00 0.00 37.91 4.02
197 198 2.787915 GCAGAGGCACGCTAAAGC 59.212 61.111 0.00 0.00 35.27 3.51
198 199 3.084579 CGCAGAGGCACGCTAAAG 58.915 61.111 0.00 0.00 35.27 1.85
216 217 3.625082 GACCCGTTGCGCCAAATGG 62.625 63.158 4.18 8.46 36.18 3.16
217 218 2.126502 GACCCGTTGCGCCAAATG 60.127 61.111 4.18 0.00 0.00 2.32
218 219 3.370231 GGACCCGTTGCGCCAAAT 61.370 61.111 4.18 0.00 0.00 2.32
219 220 4.877619 TGGACCCGTTGCGCCAAA 62.878 61.111 4.18 0.00 0.00 3.28
220 221 2.749706 TAATGGACCCGTTGCGCCAA 62.750 55.000 4.18 0.00 33.51 4.52
221 222 3.255423 TAATGGACCCGTTGCGCCA 62.255 57.895 4.18 0.00 34.45 5.69
222 223 2.437002 TAATGGACCCGTTGCGCC 60.437 61.111 4.18 0.00 0.00 6.53
223 224 0.460635 TACTAATGGACCCGTTGCGC 60.461 55.000 0.00 0.00 0.00 6.09
224 225 1.567504 CTACTAATGGACCCGTTGCG 58.432 55.000 3.85 0.00 0.00 4.85
225 226 1.134491 AGCTACTAATGGACCCGTTGC 60.134 52.381 3.85 0.00 0.00 4.17
226 227 2.981859 AGCTACTAATGGACCCGTTG 57.018 50.000 3.85 0.00 0.00 4.10
227 228 6.736110 TTAATAGCTACTAATGGACCCGTT 57.264 37.500 0.00 0.00 0.00 4.44
228 229 6.736110 TTTAATAGCTACTAATGGACCCGT 57.264 37.500 0.00 0.00 0.00 5.28
229 230 7.713942 AGTTTTTAATAGCTACTAATGGACCCG 59.286 37.037 0.00 0.00 0.00 5.28
230 231 8.975663 AGTTTTTAATAGCTACTAATGGACCC 57.024 34.615 0.00 0.00 0.00 4.46
231 232 9.833917 AGAGTTTTTAATAGCTACTAATGGACC 57.166 33.333 0.00 0.00 0.00 4.46
237 238 9.362539 CCGTGAAGAGTTTTTAATAGCTACTAA 57.637 33.333 0.00 0.00 0.00 2.24
238 239 8.526147 ACCGTGAAGAGTTTTTAATAGCTACTA 58.474 33.333 0.00 0.00 0.00 1.82
239 240 7.384477 ACCGTGAAGAGTTTTTAATAGCTACT 58.616 34.615 0.00 0.00 0.00 2.57
240 241 7.330208 TGACCGTGAAGAGTTTTTAATAGCTAC 59.670 37.037 0.00 0.00 0.00 3.58
266 267 9.478238 TTGATTGGCCAATTATATAGCATGTAT 57.522 29.630 31.13 4.47 0.00 2.29
300 301 9.975218 AACCATGGTATAAGTTTCTAAATCAGT 57.025 29.630 20.12 0.00 0.00 3.41
322 323 7.062749 AGTACATGAGTAACTCAAAGAACCA 57.937 36.000 0.00 0.00 44.04 3.67
323 324 7.441458 ACAAGTACATGAGTAACTCAAAGAACC 59.559 37.037 4.87 0.00 44.04 3.62
475 905 7.806409 TGATTGACCAACTTATATGACATGG 57.194 36.000 0.00 0.00 0.00 3.66
607 1065 5.321959 TGTGTCATTCTGCTTCAAACAAA 57.678 34.783 0.00 0.00 0.00 2.83
872 1331 2.886523 TGGCTTCTGGAACAAACAGATG 59.113 45.455 0.00 0.00 43.82 2.90
1133 1595 1.550524 AGAAGCAGGACACAGCGATAA 59.449 47.619 0.00 0.00 33.86 1.75
1180 1645 8.566260 GTTTAAATCAGCAGCATGAGAGATAAT 58.434 33.333 0.00 0.00 39.69 1.28
1356 1836 1.302033 CTGAAGCAGGCTCCACGTT 60.302 57.895 0.00 0.00 0.00 3.99
1626 3037 5.756950 ACTACATCGACACGTATTGTTTG 57.243 39.130 0.00 0.00 39.17 2.93
1641 3052 4.565564 ACGCCGTTTGATTAGAACTACATC 59.434 41.667 0.00 0.00 0.00 3.06
1680 3095 1.298041 GCCACCACGTTTGTTCACG 60.298 57.895 0.00 0.00 46.04 4.35
1684 3099 4.394439 AAAATAAGCCACCACGTTTGTT 57.606 36.364 0.00 0.00 0.00 2.83
1726 3141 3.306364 CCTCGAGGGGTGCAATCTATTAG 60.306 52.174 24.62 0.00 0.00 1.73
1808 3223 7.092079 TGCAGGAATGAAAGTTATGTCAATTG 58.908 34.615 0.00 0.00 0.00 2.32
1901 3316 9.764870 GGAAAGGAATTGAGTAATACGTAAAAC 57.235 33.333 0.00 0.58 0.00 2.43
1993 3408 8.788325 ACCTGGTGTCAAATTATCTTAGTTAC 57.212 34.615 0.00 0.00 0.00 2.50
2012 3427 1.343069 GTCCTTGTGAGAGACCTGGT 58.657 55.000 0.00 0.00 0.00 4.00
2023 3438 3.616956 TGCAGAATCTAGGTCCTTGTG 57.383 47.619 0.00 0.00 0.00 3.33
2034 3449 1.270550 CGCCACCTTTTTGCAGAATCT 59.729 47.619 0.00 0.00 0.00 2.40
2081 3496 2.274834 GACGCGTTTTCCATCGTCGG 62.275 60.000 15.53 0.00 41.16 4.79
2147 3562 4.720649 ATATACAGCAGACGAACAGTGT 57.279 40.909 0.00 0.00 0.00 3.55
2170 3585 3.214328 GAAGGCAGAGTTGGAAAAGTGA 58.786 45.455 0.00 0.00 0.00 3.41
2196 3611 8.141909 AGATAAAGTAGCGTTTGAGCATATACA 58.858 33.333 0.00 0.00 40.15 2.29
2231 3646 1.686566 ATGCGTCAATCAGTGCGTCG 61.687 55.000 0.00 0.00 0.00 5.12
2294 3709 0.539051 ACCATGGAAGAGAGAAGCGG 59.461 55.000 21.47 0.00 0.00 5.52
2310 3725 1.369692 GTGGATGGACGTGACACCA 59.630 57.895 0.00 0.00 40.57 4.17
2311 3726 1.736645 CGTGGATGGACGTGACACC 60.737 63.158 0.00 0.00 34.56 4.16
2312 3727 1.736645 CCGTGGATGGACGTGACAC 60.737 63.158 0.00 0.00 37.66 3.67
2313 3728 2.654289 CCGTGGATGGACGTGACA 59.346 61.111 0.00 0.00 37.66 3.58
2314 3729 2.813908 GCCGTGGATGGACGTGAC 60.814 66.667 0.00 0.00 37.66 3.67
2315 3730 4.077184 GGCCGTGGATGGACGTGA 62.077 66.667 0.00 0.00 37.66 4.35
2356 4589 1.076705 GGTGGAAGAAGATGGGGCC 60.077 63.158 0.00 0.00 0.00 5.80
2375 4608 0.037882 ATCACGTCTGTGGCTGTCTG 60.038 55.000 0.00 0.00 46.42 3.51
2429 4662 2.044551 CCCCCAAGAAGAGGCTGC 60.045 66.667 0.00 0.00 0.00 5.25
2453 4686 3.009723 CACCGTAGTGCTCCATTTGAAT 58.990 45.455 0.00 0.00 37.14 2.57
2483 4716 3.872603 TGCAGTTGTGGAGCCCGT 61.873 61.111 0.00 0.00 0.00 5.28
2494 4727 1.528309 CCTCCAAACCGGTGCAGTT 60.528 57.895 8.52 0.00 35.57 3.16
2497 4730 2.112297 GTCCTCCAAACCGGTGCA 59.888 61.111 8.52 0.00 35.57 4.57


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

AutoCloner maintained by Alex Coulton.