Multiple sequence alignment - TraesCS6A01G152800

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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 TraesCS6A01G152800 chr6A 100.000 2323 0 0 1 2323 137634217 137631895 0.000000e+00 4290.0
1 TraesCS6A01G152800 chr6A 96.809 94 3 0 1635 1728 31108860 31108953 8.590000e-35 158.0
2 TraesCS6A01G152800 chr6A 96.809 94 3 0 1635 1728 53802958 53802865 8.590000e-35 158.0
3 TraesCS6A01G152800 chr6A 91.089 101 8 1 2076 2176 577836489 577836588 4.030000e-28 135.0
4 TraesCS6A01G152800 chrUn 88.067 1500 103 34 278 1728 341019659 341018187 0.000000e+00 1709.0
5 TraesCS6A01G152800 chrUn 90.930 882 34 16 893 1728 454067539 454066658 0.000000e+00 1144.0
6 TraesCS6A01G152800 chrUn 90.282 885 37 20 893 1728 362350727 362349843 0.000000e+00 1112.0
7 TraesCS6A01G152800 chrUn 90.045 884 40 17 893 1728 355920281 355919398 0.000000e+00 1101.0
8 TraesCS6A01G152800 chrUn 91.667 552 36 6 278 828 362351303 362350761 0.000000e+00 756.0
9 TraesCS6A01G152800 chrUn 94.062 320 11 3 1759 2070 355919308 355918989 1.610000e-131 479.0
10 TraesCS6A01G152800 chrUn 93.750 320 12 3 1759 2070 362349753 362349434 7.510000e-130 473.0
11 TraesCS6A01G152800 chrUn 93.189 323 13 4 1756 2070 331841076 331841397 1.260000e-127 466.0
12 TraesCS6A01G152800 chrUn 94.326 282 11 5 1 278 341020008 341019728 5.930000e-116 427.0
13 TraesCS6A01G152800 chrUn 87.037 108 4 5 181 278 355921044 355920937 1.890000e-21 113.0
14 TraesCS6A01G152800 chr5D 88.067 1500 103 34 278 1728 503254332 503255804 0.000000e+00 1709.0
15 TraesCS6A01G152800 chr5D 90.861 755 54 7 893 1634 424172762 424173514 0.000000e+00 998.0
16 TraesCS6A01G152800 chr5D 94.326 282 11 5 1 278 503253983 503254263 5.930000e-116 427.0
17 TraesCS6A01G152800 chr5D 94.297 263 10 5 1 259 523037361 523037622 4.650000e-107 398.0
18 TraesCS6A01G152800 chr5D 100.000 31 0 0 248 278 523037621 523037651 8.970000e-05 58.4
19 TraesCS6A01G152800 chr5A 90.930 882 33 18 893 1728 482021857 482020977 0.000000e+00 1142.0
20 TraesCS6A01G152800 chr5A 92.791 541 30 4 278 812 482022456 482021919 0.000000e+00 774.0
21 TraesCS6A01G152800 chr5A 95.057 263 8 5 1 259 482022815 482022554 2.150000e-110 409.0
22 TraesCS6A01G152800 chr3B 90.899 879 37 16 893 1728 201553153 201552275 0.000000e+00 1140.0
23 TraesCS6A01G152800 chr3B 94.062 320 11 3 1759 2070 201552185 201551866 1.610000e-131 479.0
24 TraesCS6A01G152800 chr3B 92.553 282 11 7 1 278 702968519 702968244 1.670000e-106 396.0
25 TraesCS6A01G152800 chr3D 90.785 879 38 16 893 1728 158939386 158940264 0.000000e+00 1134.0
26 TraesCS6A01G152800 chr3D 93.284 536 32 3 278 812 158938792 158939324 0.000000e+00 787.0
27 TraesCS6A01G152800 chr3D 93.808 323 12 3 1756 2070 158940351 158940673 1.610000e-131 479.0
28 TraesCS6A01G152800 chr3D 93.498 323 13 3 1756 2070 589251294 589251616 7.510000e-130 473.0
29 TraesCS6A01G152800 chr3D 94.677 263 9 5 1 259 589249413 589249674 1.000000e-108 403.0
30 TraesCS6A01G152800 chr3D 91.409 291 11 7 1 278 158932070 158932359 1.010000e-103 387.0
31 TraesCS6A01G152800 chr3D 96.154 52 2 0 893 944 134008323 134008272 4.110000e-13 86.1
32 TraesCS6A01G152800 chr3D 96.875 32 0 1 2181 2211 416410110 416410141 4.000000e-03 52.8
33 TraesCS6A01G152800 chr7B 90.611 884 35 17 893 1728 622428111 622428994 0.000000e+00 1129.0
34 TraesCS6A01G152800 chr7B 93.808 323 12 3 1756 2070 622429081 622429403 1.610000e-131 479.0
35 TraesCS6A01G152800 chr2D 90.282 885 37 20 893 1728 591995518 591994634 0.000000e+00 1112.0
36 TraesCS6A01G152800 chr2D 91.667 552 36 6 278 828 591996094 591995552 0.000000e+00 756.0
37 TraesCS6A01G152800 chr2D 93.750 320 12 3 1759 2070 591994544 591994225 7.510000e-130 473.0
38 TraesCS6A01G152800 chr2D 94.681 282 10 5 1 278 591996443 591996163 1.270000e-117 433.0
39 TraesCS6A01G152800 chr6D 93.638 723 27 5 893 1610 431006313 431007021 0.000000e+00 1062.0
40 TraesCS6A01G152800 chr6D 92.793 555 34 5 276 828 431005729 431006279 0.000000e+00 798.0
41 TraesCS6A01G152800 chr6D 90.416 553 23 3 1635 2183 431019210 431019736 0.000000e+00 701.0
42 TraesCS6A01G152800 chr6D 96.078 102 4 0 2075 2176 431062131 431062232 1.430000e-37 167.0
43 TraesCS6A01G152800 chr6D 89.764 127 13 0 2197 2323 18403745 18403619 1.850000e-36 163.0
44 TraesCS6A01G152800 chr5B 93.284 536 32 3 278 812 429065161 429065693 0.000000e+00 787.0
45 TraesCS6A01G152800 chr5B 96.970 33 0 1 2179 2210 590378457 590378489 1.000000e-03 54.7
46 TraesCS6A01G152800 chr1D 91.863 553 34 6 278 828 200552469 200553012 0.000000e+00 761.0
47 TraesCS6A01G152800 chr1D 90.753 292 12 4 1 278 200552111 200552401 2.180000e-100 375.0
48 TraesCS6A01G152800 chr1D 90.909 143 13 0 2181 2323 81377326 81377468 2.360000e-45 193.0
49 TraesCS6A01G152800 chr4A 93.262 282 11 6 1 278 219303452 219303175 2.150000e-110 409.0
50 TraesCS6A01G152800 chr1A 94.297 263 10 3 1 259 371941338 371941599 4.650000e-107 398.0
51 TraesCS6A01G152800 chr1A 90.551 127 12 0 2197 2323 24586100 24585974 3.970000e-38 169.0
52 TraesCS6A01G152800 chr1A 90.551 127 12 0 2197 2323 24650430 24650304 3.970000e-38 169.0
53 TraesCS6A01G152800 chr1A 90.551 127 12 0 2197 2323 24755623 24755497 3.970000e-38 169.0
54 TraesCS6A01G152800 chr1A 89.764 127 13 0 2197 2323 24593975 24593849 1.850000e-36 163.0
55 TraesCS6A01G152800 chr1A 89.764 127 13 0 2197 2323 24601867 24601741 1.850000e-36 163.0
56 TraesCS6A01G152800 chr1A 96.809 94 3 0 1635 1728 402483998 402484091 8.590000e-35 158.0
57 TraesCS6A01G152800 chr7D 90.000 140 13 1 2184 2323 26007372 26007510 1.830000e-41 180.0
58 TraesCS6A01G152800 chr7D 90.000 140 13 1 2184 2323 26061902 26062040 1.830000e-41 180.0


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 TraesCS6A01G152800 chr6A 137631895 137634217 2322 True 4290.000000 4290 100.000000 1 2323 1 chr6A.!!$R2 2322
1 TraesCS6A01G152800 chrUn 454066658 454067539 881 True 1144.000000 1144 90.930000 893 1728 1 chrUn.!!$R1 835
2 TraesCS6A01G152800 chrUn 341018187 341020008 1821 True 1068.000000 1709 91.196500 1 1728 2 chrUn.!!$R2 1727
3 TraesCS6A01G152800 chrUn 362349434 362351303 1869 True 780.333333 1112 91.899667 278 2070 3 chrUn.!!$R4 1792
4 TraesCS6A01G152800 chrUn 355918989 355921044 2055 True 564.333333 1101 90.381333 181 2070 3 chrUn.!!$R3 1889
5 TraesCS6A01G152800 chr5D 503253983 503255804 1821 False 1068.000000 1709 91.196500 1 1728 2 chr5D.!!$F2 1727
6 TraesCS6A01G152800 chr5D 424172762 424173514 752 False 998.000000 998 90.861000 893 1634 1 chr5D.!!$F1 741
7 TraesCS6A01G152800 chr5A 482020977 482022815 1838 True 775.000000 1142 92.926000 1 1728 3 chr5A.!!$R1 1727
8 TraesCS6A01G152800 chr3B 201551866 201553153 1287 True 809.500000 1140 92.480500 893 2070 2 chr3B.!!$R2 1177
9 TraesCS6A01G152800 chr3D 158938792 158940673 1881 False 800.000000 1134 92.625667 278 2070 3 chr3D.!!$F3 1792
10 TraesCS6A01G152800 chr3D 589249413 589251616 2203 False 438.000000 473 94.087500 1 2070 2 chr3D.!!$F4 2069
11 TraesCS6A01G152800 chr7B 622428111 622429403 1292 False 804.000000 1129 92.209500 893 2070 2 chr7B.!!$F1 1177
12 TraesCS6A01G152800 chr2D 591994225 591996443 2218 True 693.500000 1112 92.595000 1 2070 4 chr2D.!!$R1 2069
13 TraesCS6A01G152800 chr6D 431005729 431007021 1292 False 930.000000 1062 93.215500 276 1610 2 chr6D.!!$F3 1334
14 TraesCS6A01G152800 chr6D 431019210 431019736 526 False 701.000000 701 90.416000 1635 2183 1 chr6D.!!$F1 548
15 TraesCS6A01G152800 chr5B 429065161 429065693 532 False 787.000000 787 93.284000 278 812 1 chr5B.!!$F1 534
16 TraesCS6A01G152800 chr1D 200552111 200553012 901 False 568.000000 761 91.308000 1 828 2 chr1D.!!$F2 827

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
504 598 5.975693 TGGAACAAGAGAGTTGTTTTGTT 57.024 34.783 4.71 1.51 44.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 2503 0.036875 CCCAGTTCCAGAACCAGGAC 59.963 60.0 16.88 0.0 42.06 3.85 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
68 69 6.320418 AGACATCTATTGCTGCAAATCAATCA 59.680 34.615 20.06 0.00 34.95 2.57
341 435 8.667076 AAAGGAATTCCAATCAAAACAGAAAG 57.333 30.769 26.22 0.00 38.89 2.62
353 447 6.281405 TCAAAACAGAAAGTACTGAGTCTCC 58.719 40.000 0.00 0.00 40.63 3.71
367 461 7.540474 ACTGAGTCTCCTAAACAAGACATTA 57.460 36.000 5.42 0.00 34.06 1.90
477 571 7.528996 TCATTGGAATTCACTCAATCAGTTT 57.471 32.000 7.93 0.00 30.26 2.66
504 598 5.975693 TGGAACAAGAGAGTTGTTTTGTT 57.024 34.783 4.71 1.51 44.00 2.83
855 1017 7.885297 TGTCAAAGAGATAAGAATTGGTTTGG 58.115 34.615 0.00 0.00 0.00 3.28
856 1018 7.505585 TGTCAAAGAGATAAGAATTGGTTTGGT 59.494 33.333 0.00 0.00 0.00 3.67
857 1019 9.010029 GTCAAAGAGATAAGAATTGGTTTGGTA 57.990 33.333 0.00 0.00 0.00 3.25
858 1020 9.581289 TCAAAGAGATAAGAATTGGTTTGGTAA 57.419 29.630 0.00 0.00 0.00 2.85
861 1023 9.807921 AAGAGATAAGAATTGGTTTGGTAAAGA 57.192 29.630 0.00 0.00 0.00 2.52
862 1024 9.454859 AGAGATAAGAATTGGTTTGGTAAAGAG 57.545 33.333 0.00 0.00 0.00 2.85
863 1025 9.449719 GAGATAAGAATTGGTTTGGTAAAGAGA 57.550 33.333 0.00 0.00 0.00 3.10
864 1026 9.981460 AGATAAGAATTGGTTTGGTAAAGAGAT 57.019 29.630 0.00 0.00 0.00 2.75
1208 1390 9.209175 GGTTATATGTCTCACATTGAAGGATAC 57.791 37.037 0.00 0.00 39.88 2.24
1374 1569 3.422217 GCGAGTGCTTGTAAAAAGCTTTC 59.578 43.478 13.10 0.35 43.38 2.62
1395 1590 3.627577 TCGTAACTAATCGTGTAGGGGAC 59.372 47.826 1.28 0.00 0.00 4.46
1463 1662 9.293404 GGTAGTTTAGAGTTTAGGGATTTGTTT 57.707 33.333 0.00 0.00 0.00 2.83
1569 1768 3.569701 AGTTGCGAAATCCACACAATTCT 59.430 39.130 0.00 0.00 0.00 2.40
1665 1892 6.340962 TCGACTTCTTCCTCTTTTCACATA 57.659 37.500 0.00 0.00 0.00 2.29
1767 2053 7.227156 AGCCTATTCTACAATGGGTTCTTATG 58.773 38.462 0.00 0.00 41.70 1.90
1771 2057 9.277783 CTATTCTACAATGGGTTCTTATGAAGG 57.722 37.037 0.00 0.00 32.15 3.46
1822 2115 7.233348 TCAAAAGCTTTATTGTTCTTGGGATCT 59.767 33.333 13.10 0.00 0.00 2.75
1827 2120 6.097412 GCTTTATTGTTCTTGGGATCTGGATT 59.903 38.462 0.00 0.00 0.00 3.01
1880 2173 7.861629 TGGATATTCACCAGATAAAAGTCAGT 58.138 34.615 0.00 0.00 33.22 3.41
2060 2354 5.896073 ATAATAGCCTCCTTTACTGCAGT 57.104 39.130 25.12 25.12 0.00 4.40
2159 2456 5.997746 TGTTTTCTTCATGTAGAGGGACAAG 59.002 40.000 2.09 0.00 31.83 3.16
2184 2481 9.426534 AGATGATATATATTTGATCGGTCTCCA 57.573 33.333 0.00 0.00 0.00 3.86
2185 2482 9.469807 GATGATATATATTTGATCGGTCTCCAC 57.530 37.037 0.00 0.00 0.00 4.02
2186 2483 8.595362 TGATATATATTTGATCGGTCTCCACT 57.405 34.615 0.00 0.00 0.00 4.00
2187 2484 9.695155 TGATATATATTTGATCGGTCTCCACTA 57.305 33.333 0.00 0.00 0.00 2.74
2189 2486 9.702253 ATATATATTTGATCGGTCTCCACTAGT 57.298 33.333 0.00 0.00 0.00 2.57
2191 2488 5.776173 ATTTGATCGGTCTCCACTAGTAG 57.224 43.478 0.00 0.00 0.00 2.57
2192 2489 4.498894 TTGATCGGTCTCCACTAGTAGA 57.501 45.455 3.59 0.00 0.00 2.59
2193 2490 4.498894 TGATCGGTCTCCACTAGTAGAA 57.501 45.455 3.59 0.00 0.00 2.10
2194 2491 4.851843 TGATCGGTCTCCACTAGTAGAAA 58.148 43.478 3.59 0.00 0.00 2.52
2195 2492 5.258841 TGATCGGTCTCCACTAGTAGAAAA 58.741 41.667 3.59 0.00 0.00 2.29
2196 2493 5.713389 TGATCGGTCTCCACTAGTAGAAAAA 59.287 40.000 3.59 0.00 0.00 1.94
2197 2494 5.640189 TCGGTCTCCACTAGTAGAAAAAG 57.360 43.478 3.59 0.00 0.00 2.27
2198 2495 4.461781 TCGGTCTCCACTAGTAGAAAAAGG 59.538 45.833 3.59 0.00 0.00 3.11
2199 2496 4.505808 GGTCTCCACTAGTAGAAAAAGGC 58.494 47.826 3.59 0.00 0.00 4.35
2200 2497 4.505808 GTCTCCACTAGTAGAAAAAGGCC 58.494 47.826 3.59 0.00 0.00 5.19
2201 2498 3.518303 TCTCCACTAGTAGAAAAAGGCCC 59.482 47.826 3.59 0.00 0.00 5.80
2202 2499 3.253220 TCCACTAGTAGAAAAAGGCCCA 58.747 45.455 3.59 0.00 0.00 5.36
2203 2500 3.850173 TCCACTAGTAGAAAAAGGCCCAT 59.150 43.478 3.59 0.00 0.00 4.00
2204 2501 4.291249 TCCACTAGTAGAAAAAGGCCCATT 59.709 41.667 3.59 0.00 0.00 3.16
2205 2502 5.016831 CCACTAGTAGAAAAAGGCCCATTT 58.983 41.667 3.59 0.00 0.00 2.32
2206 2503 5.105756 CCACTAGTAGAAAAAGGCCCATTTG 60.106 44.000 8.01 0.00 0.00 2.32
2207 2504 5.476945 CACTAGTAGAAAAAGGCCCATTTGT 59.523 40.000 8.01 6.88 0.00 2.83
2208 2505 5.710567 ACTAGTAGAAAAAGGCCCATTTGTC 59.289 40.000 8.01 4.02 0.00 3.18
2209 2506 3.832490 AGTAGAAAAAGGCCCATTTGTCC 59.168 43.478 8.01 0.00 28.13 4.02
2210 2507 2.976440 AGAAAAAGGCCCATTTGTCCT 58.024 42.857 8.01 2.84 28.13 3.85
2211 2508 2.634453 AGAAAAAGGCCCATTTGTCCTG 59.366 45.455 8.01 0.00 28.13 3.86
2212 2509 1.351076 AAAAGGCCCATTTGTCCTGG 58.649 50.000 0.00 0.00 0.00 4.45
2213 2510 0.190815 AAAGGCCCATTTGTCCTGGT 59.809 50.000 0.00 0.00 31.44 4.00
2214 2511 0.190815 AAGGCCCATTTGTCCTGGTT 59.809 50.000 0.00 0.00 31.44 3.67
2215 2512 0.251787 AGGCCCATTTGTCCTGGTTC 60.252 55.000 0.00 0.00 31.44 3.62
2216 2513 0.251787 GGCCCATTTGTCCTGGTTCT 60.252 55.000 0.00 0.00 31.44 3.01
2217 2514 0.890683 GCCCATTTGTCCTGGTTCTG 59.109 55.000 0.00 0.00 31.44 3.02
2218 2515 1.549203 CCCATTTGTCCTGGTTCTGG 58.451 55.000 0.00 0.00 31.44 3.86
2219 2516 1.075374 CCCATTTGTCCTGGTTCTGGA 59.925 52.381 0.00 0.00 31.44 3.86
2220 2517 2.490718 CCCATTTGTCCTGGTTCTGGAA 60.491 50.000 0.00 0.00 33.44 3.53
2221 2518 2.558359 CCATTTGTCCTGGTTCTGGAAC 59.442 50.000 5.02 5.02 40.45 3.62
2222 2519 3.490348 CATTTGTCCTGGTTCTGGAACT 58.510 45.455 12.34 0.00 40.94 3.01
2223 2520 2.638480 TTGTCCTGGTTCTGGAACTG 57.362 50.000 12.34 6.70 40.94 3.16
2224 2521 0.764890 TGTCCTGGTTCTGGAACTGG 59.235 55.000 12.34 13.65 40.94 4.00
2225 2522 0.036875 GTCCTGGTTCTGGAACTGGG 59.963 60.000 12.34 13.33 40.94 4.45
2226 2523 0.104672 TCCTGGTTCTGGAACTGGGA 60.105 55.000 16.75 16.75 40.94 4.37
2227 2524 0.036875 CCTGGTTCTGGAACTGGGAC 59.963 60.000 12.34 0.00 40.94 4.46
2228 2525 1.059913 CTGGTTCTGGAACTGGGACT 58.940 55.000 12.34 0.00 40.94 3.85
2229 2526 2.257207 CTGGTTCTGGAACTGGGACTA 58.743 52.381 12.34 0.00 40.94 2.59
2230 2527 2.637872 CTGGTTCTGGAACTGGGACTAA 59.362 50.000 12.34 0.00 40.94 2.24
2231 2528 3.050089 TGGTTCTGGAACTGGGACTAAA 58.950 45.455 12.34 0.00 40.94 1.85
2232 2529 3.072476 TGGTTCTGGAACTGGGACTAAAG 59.928 47.826 12.34 0.00 40.94 1.85
2233 2530 3.075148 GTTCTGGAACTGGGACTAAAGC 58.925 50.000 6.26 0.00 38.25 3.51
2234 2531 1.628846 TCTGGAACTGGGACTAAAGCC 59.371 52.381 0.00 0.00 0.00 4.35
2235 2532 0.696501 TGGAACTGGGACTAAAGCCC 59.303 55.000 0.00 0.00 46.22 5.19
2242 2539 2.304221 GGGACTAAAGCCCAAAACCT 57.696 50.000 0.00 0.00 45.31 3.50
2243 2540 2.605257 GGGACTAAAGCCCAAAACCTT 58.395 47.619 0.00 0.00 45.31 3.50
2244 2541 2.969950 GGGACTAAAGCCCAAAACCTTT 59.030 45.455 0.00 0.00 45.31 3.11
2245 2542 4.154176 GGGACTAAAGCCCAAAACCTTTA 58.846 43.478 0.00 0.00 45.31 1.85
2250 2547 6.255596 CTAAAGCCCAAAACCTTTAGTCTC 57.744 41.667 10.46 0.00 42.49 3.36
2251 2548 2.779506 AGCCCAAAACCTTTAGTCTCG 58.220 47.619 0.00 0.00 0.00 4.04
2252 2549 1.810755 GCCCAAAACCTTTAGTCTCGG 59.189 52.381 0.00 0.00 0.00 4.63
2253 2550 2.812983 GCCCAAAACCTTTAGTCTCGGT 60.813 50.000 0.00 0.00 0.00 4.69
2254 2551 3.483421 CCCAAAACCTTTAGTCTCGGTT 58.517 45.455 0.00 0.00 42.52 4.44
2255 2552 3.501062 CCCAAAACCTTTAGTCTCGGTTC 59.499 47.826 0.00 0.00 39.97 3.62
2256 2553 3.185797 CCAAAACCTTTAGTCTCGGTTCG 59.814 47.826 0.00 0.00 39.97 3.95
2257 2554 2.075979 AACCTTTAGTCTCGGTTCGC 57.924 50.000 0.00 0.00 36.32 4.70
2258 2555 1.254954 ACCTTTAGTCTCGGTTCGCT 58.745 50.000 0.00 0.00 0.00 4.93
2259 2556 1.617357 ACCTTTAGTCTCGGTTCGCTT 59.383 47.619 0.00 0.00 0.00 4.68
2260 2557 2.821969 ACCTTTAGTCTCGGTTCGCTTA 59.178 45.455 0.00 0.00 0.00 3.09
2261 2558 3.177487 CCTTTAGTCTCGGTTCGCTTAC 58.823 50.000 0.00 0.00 0.00 2.34
2262 2559 2.532531 TTAGTCTCGGTTCGCTTACG 57.467 50.000 0.00 0.00 42.01 3.18
2272 2569 4.979204 CGCTTACGAACTGGGACA 57.021 55.556 0.00 0.00 43.93 4.02
2283 2580 3.483587 TGGGACAGAAGGTGCTCC 58.516 61.111 0.00 0.00 38.05 4.70
2284 2581 1.461268 TGGGACAGAAGGTGCTCCA 60.461 57.895 7.70 0.00 38.05 3.86
2285 2582 0.842030 TGGGACAGAAGGTGCTCCAT 60.842 55.000 7.70 0.00 38.05 3.41
2286 2583 0.393537 GGGACAGAAGGTGCTCCATG 60.394 60.000 7.70 5.46 38.05 3.66
2287 2584 0.326264 GGACAGAAGGTGCTCCATGT 59.674 55.000 7.70 8.64 34.56 3.21
2288 2585 1.446907 GACAGAAGGTGCTCCATGTG 58.553 55.000 13.07 9.72 35.89 3.21
2289 2586 0.037303 ACAGAAGGTGCTCCATGTGG 59.963 55.000 11.26 0.00 31.33 4.17
2290 2587 1.001641 AGAAGGTGCTCCATGTGGC 60.002 57.895 7.70 0.00 35.89 5.01
2291 2588 1.001641 GAAGGTGCTCCATGTGGCT 60.002 57.895 7.70 0.00 35.89 4.75
2292 2589 1.303888 AAGGTGCTCCATGTGGCTG 60.304 57.895 7.70 0.00 35.89 4.85
2293 2590 3.446570 GGTGCTCCATGTGGCTGC 61.447 66.667 0.00 9.02 35.83 5.25
2294 2591 2.360852 GTGCTCCATGTGGCTGCT 60.361 61.111 14.50 0.00 36.10 4.24
2295 2592 1.078214 GTGCTCCATGTGGCTGCTA 60.078 57.895 14.50 0.00 36.10 3.49
2296 2593 1.078214 TGCTCCATGTGGCTGCTAC 60.078 57.895 9.40 9.40 36.10 3.58
2297 2594 2.176273 GCTCCATGTGGCTGCTACG 61.176 63.158 11.58 0.00 33.71 3.51
2298 2595 1.522355 CTCCATGTGGCTGCTACGG 60.522 63.158 11.58 7.61 34.44 4.02
2299 2596 2.514592 CCATGTGGCTGCTACGGG 60.515 66.667 11.58 11.35 0.00 5.28
2300 2597 2.514592 CATGTGGCTGCTACGGGG 60.515 66.667 11.58 0.00 0.00 5.73
2301 2598 4.489771 ATGTGGCTGCTACGGGGC 62.490 66.667 11.58 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
337 431 7.595875 GTCTTGTTTAGGAGACTCAGTACTTTC 59.404 40.741 4.53 0.00 43.67 2.62
341 435 6.328641 TGTCTTGTTTAGGAGACTCAGTAC 57.671 41.667 4.53 0.00 42.13 2.73
477 571 9.349713 ACAAAACAACTCTCTTGTTCCATAATA 57.650 29.630 0.00 0.00 41.30 0.98
631 744 7.501844 TGGGTTTAGTTGGGTAAATTCAAAAG 58.498 34.615 0.00 0.00 0.00 2.27
750 864 8.673711 CGATTTACCAAACCAATTCTTATCTCA 58.326 33.333 0.00 0.00 0.00 3.27
829 991 8.526147 CCAAACCAATTCTTATCTCTTTGACAT 58.474 33.333 0.00 0.00 0.00 3.06
830 992 7.505585 ACCAAACCAATTCTTATCTCTTTGACA 59.494 33.333 0.00 0.00 0.00 3.58
831 993 7.886338 ACCAAACCAATTCTTATCTCTTTGAC 58.114 34.615 0.00 0.00 0.00 3.18
832 994 9.581289 TTACCAAACCAATTCTTATCTCTTTGA 57.419 29.630 0.00 0.00 0.00 2.69
836 998 9.454859 CTCTTTACCAAACCAATTCTTATCTCT 57.545 33.333 0.00 0.00 0.00 3.10
837 999 9.449719 TCTCTTTACCAAACCAATTCTTATCTC 57.550 33.333 0.00 0.00 0.00 2.75
838 1000 9.981460 ATCTCTTTACCAAACCAATTCTTATCT 57.019 29.630 0.00 0.00 0.00 1.98
864 1026 9.781834 CCGTGCATATCTTTACTTCAATTTTTA 57.218 29.630 0.00 0.00 0.00 1.52
865 1027 7.759433 CCCGTGCATATCTTTACTTCAATTTTT 59.241 33.333 0.00 0.00 0.00 1.94
866 1028 7.093945 ACCCGTGCATATCTTTACTTCAATTTT 60.094 33.333 0.00 0.00 0.00 1.82
867 1029 6.377146 ACCCGTGCATATCTTTACTTCAATTT 59.623 34.615 0.00 0.00 0.00 1.82
868 1030 5.885912 ACCCGTGCATATCTTTACTTCAATT 59.114 36.000 0.00 0.00 0.00 2.32
869 1031 5.437060 ACCCGTGCATATCTTTACTTCAAT 58.563 37.500 0.00 0.00 0.00 2.57
870 1032 4.839121 ACCCGTGCATATCTTTACTTCAA 58.161 39.130 0.00 0.00 0.00 2.69
871 1033 4.161565 AGACCCGTGCATATCTTTACTTCA 59.838 41.667 0.00 0.00 0.00 3.02
872 1034 4.694339 AGACCCGTGCATATCTTTACTTC 58.306 43.478 0.00 0.00 0.00 3.01
873 1035 4.755266 AGACCCGTGCATATCTTTACTT 57.245 40.909 0.00 0.00 0.00 2.24
874 1036 4.406003 AGAAGACCCGTGCATATCTTTACT 59.594 41.667 0.00 0.00 31.58 2.24
875 1037 4.694339 AGAAGACCCGTGCATATCTTTAC 58.306 43.478 0.00 0.00 31.58 2.01
876 1038 4.202223 GGAGAAGACCCGTGCATATCTTTA 60.202 45.833 0.00 0.00 31.58 1.85
877 1039 3.432326 GGAGAAGACCCGTGCATATCTTT 60.432 47.826 0.00 0.00 31.58 2.52
878 1040 2.103263 GGAGAAGACCCGTGCATATCTT 59.897 50.000 0.00 0.00 34.11 2.40
879 1041 1.689273 GGAGAAGACCCGTGCATATCT 59.311 52.381 0.00 0.00 0.00 1.98
880 1042 1.270358 GGGAGAAGACCCGTGCATATC 60.270 57.143 0.00 0.00 40.49 1.63
905 1074 7.981225 GCCAAATTCCATTGACATAATAACTGT 59.019 33.333 0.00 0.00 31.84 3.55
1046 1225 8.883302 TCCAAGACCATTGATATTGATAGATCA 58.117 33.333 0.00 0.00 30.44 2.92
1228 1410 7.095523 CCAACATGGAAGTATTGAAAAAGCTTG 60.096 37.037 0.00 0.00 40.96 4.01
1232 1414 6.991938 TCCCAACATGGAAGTATTGAAAAAG 58.008 36.000 0.00 0.00 40.96 2.27
1374 1569 3.629398 AGTCCCCTACACGATTAGTTACG 59.371 47.826 0.00 0.00 0.00 3.18
1735 1985 6.329197 ACCCATTGTAGAATAGGCTAAGCTTA 59.671 38.462 5.94 5.94 0.00 3.09
1767 2053 5.979517 GCATCCAATGTAATAAAGCACCTTC 59.020 40.000 0.00 0.00 0.00 3.46
1771 2057 9.185192 GAATAAGCATCCAATGTAATAAAGCAC 57.815 33.333 0.00 0.00 0.00 4.40
1822 2115 7.416213 GGTTCCATTGAATGAATAACGAATCCA 60.416 37.037 6.76 0.00 31.98 3.41
1827 2120 6.414732 AGAGGTTCCATTGAATGAATAACGA 58.585 36.000 6.76 0.00 31.98 3.85
1880 2173 4.986054 AACCGCCCATAAGAACCATATA 57.014 40.909 0.00 0.00 0.00 0.86
2142 2439 7.862274 ATATCATCTTGTCCCTCTACATGAA 57.138 36.000 0.00 0.00 37.17 2.57
2159 2456 9.469807 GTGGAGACCGATCAAATATATATCATC 57.530 37.037 0.00 0.00 0.00 2.92
2173 2470 5.831702 TTTTCTACTAGTGGAGACCGATC 57.168 43.478 9.07 0.00 0.00 3.69
2183 2480 5.476945 ACAAATGGGCCTTTTTCTACTAGTG 59.523 40.000 14.22 4.27 0.00 2.74
2184 2481 5.641155 ACAAATGGGCCTTTTTCTACTAGT 58.359 37.500 14.22 0.00 0.00 2.57
2185 2482 5.125578 GGACAAATGGGCCTTTTTCTACTAG 59.874 44.000 14.22 4.93 0.00 2.57
2186 2483 5.014202 GGACAAATGGGCCTTTTTCTACTA 58.986 41.667 14.22 0.00 0.00 1.82
2187 2484 3.832490 GGACAAATGGGCCTTTTTCTACT 59.168 43.478 14.22 0.00 0.00 2.57
2188 2485 3.832490 AGGACAAATGGGCCTTTTTCTAC 59.168 43.478 14.22 4.42 0.00 2.59
2189 2486 3.831911 CAGGACAAATGGGCCTTTTTCTA 59.168 43.478 14.22 0.00 0.00 2.10
2190 2487 2.634453 CAGGACAAATGGGCCTTTTTCT 59.366 45.455 14.22 9.66 0.00 2.52
2191 2488 2.289631 CCAGGACAAATGGGCCTTTTTC 60.290 50.000 14.22 13.86 33.94 2.29
2192 2489 1.699083 CCAGGACAAATGGGCCTTTTT 59.301 47.619 14.22 6.91 33.94 1.94
2193 2490 1.351076 CCAGGACAAATGGGCCTTTT 58.649 50.000 11.35 11.35 33.94 2.27
2194 2491 0.190815 ACCAGGACAAATGGGCCTTT 59.809 50.000 4.53 0.76 42.48 3.11
2195 2492 0.190815 AACCAGGACAAATGGGCCTT 59.809 50.000 4.53 0.00 42.48 4.35
2196 2493 0.251787 GAACCAGGACAAATGGGCCT 60.252 55.000 4.53 0.00 42.48 5.19
2197 2494 0.251787 AGAACCAGGACAAATGGGCC 60.252 55.000 0.00 0.00 42.48 5.80
2198 2495 0.890683 CAGAACCAGGACAAATGGGC 59.109 55.000 0.00 0.00 42.48 5.36
2199 2496 1.075374 TCCAGAACCAGGACAAATGGG 59.925 52.381 0.00 0.00 42.48 4.00
2200 2497 2.558359 GTTCCAGAACCAGGACAAATGG 59.442 50.000 0.00 0.00 43.87 3.16
2201 2498 3.254166 CAGTTCCAGAACCAGGACAAATG 59.746 47.826 6.91 0.00 42.06 2.32
2202 2499 3.490348 CAGTTCCAGAACCAGGACAAAT 58.510 45.455 6.91 0.00 42.06 2.32
2203 2500 2.422803 CCAGTTCCAGAACCAGGACAAA 60.423 50.000 12.07 0.00 42.06 2.83
2204 2501 1.142870 CCAGTTCCAGAACCAGGACAA 59.857 52.381 12.07 0.00 42.06 3.18
2205 2502 0.764890 CCAGTTCCAGAACCAGGACA 59.235 55.000 12.07 0.00 42.06 4.02
2206 2503 0.036875 CCCAGTTCCAGAACCAGGAC 59.963 60.000 16.88 0.00 42.06 3.85
2207 2504 0.104672 TCCCAGTTCCAGAACCAGGA 60.105 55.000 16.88 14.83 42.06 3.86
2208 2505 0.036875 GTCCCAGTTCCAGAACCAGG 59.963 60.000 6.91 9.25 42.06 4.45
2209 2506 1.059913 AGTCCCAGTTCCAGAACCAG 58.940 55.000 6.91 0.90 42.06 4.00
2210 2507 2.409064 TAGTCCCAGTTCCAGAACCA 57.591 50.000 6.91 0.00 42.06 3.67
2211 2508 3.676093 CTTTAGTCCCAGTTCCAGAACC 58.324 50.000 6.91 0.00 42.06 3.62
2212 2509 3.075148 GCTTTAGTCCCAGTTCCAGAAC 58.925 50.000 2.19 2.19 41.45 3.01
2213 2510 2.039879 GGCTTTAGTCCCAGTTCCAGAA 59.960 50.000 0.00 0.00 0.00 3.02
2214 2511 1.628846 GGCTTTAGTCCCAGTTCCAGA 59.371 52.381 0.00 0.00 0.00 3.86
2215 2512 1.340114 GGGCTTTAGTCCCAGTTCCAG 60.340 57.143 4.89 0.00 43.37 3.86
2216 2513 0.696501 GGGCTTTAGTCCCAGTTCCA 59.303 55.000 4.89 0.00 43.37 3.53
2217 2514 3.571748 GGGCTTTAGTCCCAGTTCC 57.428 57.895 4.89 0.00 43.37 3.62
2223 2520 2.304221 AGGTTTTGGGCTTTAGTCCC 57.696 50.000 0.00 0.54 39.61 4.46
2224 2521 4.831155 ACTAAAGGTTTTGGGCTTTAGTCC 59.169 41.667 2.77 0.00 44.39 3.85
2227 2524 5.106673 CGAGACTAAAGGTTTTGGGCTTTAG 60.107 44.000 1.97 1.97 42.08 1.85
2228 2525 4.758165 CGAGACTAAAGGTTTTGGGCTTTA 59.242 41.667 0.00 0.00 0.00 1.85
2229 2526 3.568430 CGAGACTAAAGGTTTTGGGCTTT 59.432 43.478 0.00 0.00 0.00 3.51
2230 2527 3.146847 CGAGACTAAAGGTTTTGGGCTT 58.853 45.455 0.00 0.00 0.00 4.35
2231 2528 2.552373 CCGAGACTAAAGGTTTTGGGCT 60.552 50.000 0.00 0.00 31.80 5.19
2232 2529 1.810755 CCGAGACTAAAGGTTTTGGGC 59.189 52.381 0.00 0.00 31.80 5.36
2233 2530 3.136009 ACCGAGACTAAAGGTTTTGGG 57.864 47.619 0.00 0.00 37.77 4.12
2239 2536 1.254954 AGCGAACCGAGACTAAAGGT 58.745 50.000 0.00 0.00 40.50 3.50
2240 2537 2.365408 AAGCGAACCGAGACTAAAGG 57.635 50.000 0.00 0.00 0.00 3.11
2241 2538 2.844804 CGTAAGCGAACCGAGACTAAAG 59.155 50.000 0.00 0.00 41.33 1.85
2242 2539 2.483877 TCGTAAGCGAACCGAGACTAAA 59.516 45.455 0.00 0.00 44.92 1.85
2243 2540 2.076100 TCGTAAGCGAACCGAGACTAA 58.924 47.619 0.00 0.00 44.92 2.24
2244 2541 1.725641 TCGTAAGCGAACCGAGACTA 58.274 50.000 0.00 0.00 44.92 2.59
2245 2542 2.548178 TCGTAAGCGAACCGAGACT 58.452 52.632 0.00 0.00 44.92 3.24
2254 2551 0.242825 CTGTCCCAGTTCGTAAGCGA 59.757 55.000 0.00 0.00 46.36 4.93
2255 2552 0.242825 TCTGTCCCAGTTCGTAAGCG 59.757 55.000 0.00 0.00 34.53 4.68
2256 2553 2.338500 CTTCTGTCCCAGTTCGTAAGC 58.662 52.381 0.00 0.00 32.61 3.09
2257 2554 2.299297 ACCTTCTGTCCCAGTTCGTAAG 59.701 50.000 0.00 0.00 32.61 2.34
2258 2555 2.036733 CACCTTCTGTCCCAGTTCGTAA 59.963 50.000 0.00 0.00 32.61 3.18
2259 2556 1.616865 CACCTTCTGTCCCAGTTCGTA 59.383 52.381 0.00 0.00 32.61 3.43
2260 2557 0.393077 CACCTTCTGTCCCAGTTCGT 59.607 55.000 0.00 0.00 32.61 3.85
2261 2558 0.951040 GCACCTTCTGTCCCAGTTCG 60.951 60.000 0.00 0.00 32.61 3.95
2262 2559 0.398318 AGCACCTTCTGTCCCAGTTC 59.602 55.000 0.00 0.00 32.61 3.01
2263 2560 0.398318 GAGCACCTTCTGTCCCAGTT 59.602 55.000 0.00 0.00 32.61 3.16
2264 2561 1.484444 GGAGCACCTTCTGTCCCAGT 61.484 60.000 0.00 0.00 32.61 4.00
2265 2562 1.298014 GGAGCACCTTCTGTCCCAG 59.702 63.158 0.00 0.00 0.00 4.45
2266 2563 0.842030 ATGGAGCACCTTCTGTCCCA 60.842 55.000 0.71 0.00 37.04 4.37
2267 2564 0.393537 CATGGAGCACCTTCTGTCCC 60.394 60.000 0.71 0.00 37.04 4.46
2268 2565 0.326264 ACATGGAGCACCTTCTGTCC 59.674 55.000 0.71 0.00 37.04 4.02
2269 2566 1.446907 CACATGGAGCACCTTCTGTC 58.553 55.000 0.71 0.00 37.04 3.51
2270 2567 0.037303 CCACATGGAGCACCTTCTGT 59.963 55.000 0.71 0.00 37.39 3.41
2271 2568 1.310933 GCCACATGGAGCACCTTCTG 61.311 60.000 0.87 0.00 37.39 3.02
2272 2569 1.001641 GCCACATGGAGCACCTTCT 60.002 57.895 0.87 0.00 37.39 2.85
2273 2570 1.001641 AGCCACATGGAGCACCTTC 60.002 57.895 11.28 0.00 37.39 3.46
2274 2571 1.303888 CAGCCACATGGAGCACCTT 60.304 57.895 11.28 0.00 37.39 3.50
2275 2572 2.353958 CAGCCACATGGAGCACCT 59.646 61.111 11.28 0.00 37.39 4.00
2276 2573 2.541547 TAGCAGCCACATGGAGCACC 62.542 60.000 15.41 0.00 39.31 5.01
2277 2574 1.078214 TAGCAGCCACATGGAGCAC 60.078 57.895 15.41 3.69 39.31 4.40
2278 2575 1.078214 GTAGCAGCCACATGGAGCA 60.078 57.895 15.41 2.65 39.31 4.26
2279 2576 2.176273 CGTAGCAGCCACATGGAGC 61.176 63.158 0.87 4.89 37.82 4.70
2280 2577 1.522355 CCGTAGCAGCCACATGGAG 60.522 63.158 0.87 0.00 37.39 3.86
2281 2578 2.584064 CCGTAGCAGCCACATGGA 59.416 61.111 0.87 0.00 37.39 3.41
2282 2579 2.514592 CCCGTAGCAGCCACATGG 60.515 66.667 0.00 0.00 38.53 3.66
2283 2580 2.514592 CCCCGTAGCAGCCACATG 60.515 66.667 0.00 0.00 0.00 3.21
2284 2581 4.489771 GCCCCGTAGCAGCCACAT 62.490 66.667 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.