Multiple sequence alignment - TraesCS4D01G089100

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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 TraesCS4D01G089100 chr4D 100.000 3459 0 0 1 3459 64607170 64603712 0.000000e+00 6388.0
1 TraesCS4D01G089100 chr4D 80.552 1522 193 48 1969 3459 64616544 64615095 0.000000e+00 1075.0
2 TraesCS4D01G089100 chr4D 81.117 895 129 21 989 1879 64617411 64616553 0.000000e+00 680.0
3 TraesCS4D01G089100 chr4D 84.878 205 28 1 53 257 82567857 82567656 1.630000e-48 204.0
4 TraesCS4D01G089100 chr4B 94.424 1363 43 15 531 1884 95109942 95108604 0.000000e+00 2065.0
5 TraesCS4D01G089100 chr4B 81.435 1519 201 52 1963 3439 95366434 95367913 0.000000e+00 1168.0
6 TraesCS4D01G089100 chr4B 92.197 692 47 4 1963 2652 95108606 95107920 0.000000e+00 972.0
7 TraesCS4D01G089100 chr4B 81.073 988 142 26 910 1881 95218767 95217809 0.000000e+00 747.0
8 TraesCS4D01G089100 chr4B 79.900 1000 125 41 1966 2950 95217805 95216867 0.000000e+00 664.0
9 TraesCS4D01G089100 chr4B 88.551 428 43 4 3038 3459 95107128 95106701 6.620000e-142 514.0
10 TraesCS4D01G089100 chr4B 84.813 428 50 8 3041 3459 95216857 95216436 1.920000e-112 416.0
11 TraesCS4D01G089100 chr4B 84.887 311 42 2 1571 1881 95318122 95317817 3.350000e-80 309.0
12 TraesCS4D01G089100 chr4B 84.494 316 42 3 1566 1881 95366125 95366433 4.340000e-79 305.0
13 TraesCS4D01G089100 chr4B 90.000 190 18 1 7 195 95111969 95111780 9.590000e-61 244.0
14 TraesCS4D01G089100 chr4B 78.344 314 36 17 640 922 95319189 95318877 1.280000e-39 174.0
15 TraesCS4D01G089100 chr4B 96.667 60 2 0 1883 1942 563018457 563018398 2.200000e-17 100.0
16 TraesCS4D01G089100 chr4B 96.667 60 2 0 1883 1942 651131649 651131590 2.200000e-17 100.0
17 TraesCS4D01G089100 chr4B 95.000 60 3 0 1883 1942 9958774 9958715 1.020000e-15 95.3
18 TraesCS4D01G089100 chr4A 88.970 1514 106 27 1963 3455 531326748 531328221 0.000000e+00 1814.0
19 TraesCS4D01G089100 chr4A 80.881 1543 209 55 1963 3459 531248032 531249534 0.000000e+00 1136.0
20 TraesCS4D01G089100 chr4A 97.760 625 12 1 1257 1881 531326125 531326747 0.000000e+00 1075.0
21 TraesCS4D01G089100 chr4A 94.551 679 20 8 531 1202 531325460 531326128 0.000000e+00 1033.0
22 TraesCS4D01G089100 chr4A 79.909 1533 195 55 1963 3459 531312651 531314106 0.000000e+00 1020.0
23 TraesCS4D01G089100 chr4A 79.289 956 146 33 910 1857 531311715 531312626 3.790000e-174 621.0
24 TraesCS4D01G089100 chr4A 87.426 509 35 4 4 507 531324908 531325392 3.020000e-155 558.0
25 TraesCS4D01G089100 chr4A 83.333 318 46 3 1564 1881 531247721 531248031 1.570000e-73 287.0
26 TraesCS4D01G089100 chr4A 82.427 239 30 9 295 526 724132321 724132088 7.570000e-47 198.0
27 TraesCS4D01G089100 chr6B 88.288 222 18 2 294 507 692449933 692450154 3.420000e-65 259.0
28 TraesCS4D01G089100 chr6B 84.914 232 22 6 308 526 661915461 661915692 4.490000e-54 222.0
29 TraesCS4D01G089100 chr6B 84.977 213 28 4 294 504 27127214 27127424 2.700000e-51 213.0
30 TraesCS4D01G089100 chr6A 84.337 249 29 4 294 533 78477097 78477344 5.770000e-58 235.0
31 TraesCS4D01G089100 chr6A 81.731 104 7 5 4 95 597444419 597444522 3.700000e-10 76.8
32 TraesCS4D01G089100 chr5B 83.835 266 24 9 280 526 608363508 608363243 5.770000e-58 235.0
33 TraesCS4D01G089100 chr5B 84.038 213 31 1 50 262 45027366 45027575 5.850000e-48 202.0
34 TraesCS4D01G089100 chr5B 91.549 71 3 2 1869 1936 454290427 454290497 1.020000e-15 95.3
35 TraesCS4D01G089100 chr3D 83.969 262 25 6 281 525 582266375 582266636 5.770000e-58 235.0
36 TraesCS4D01G089100 chr3D 83.004 253 29 8 294 533 356632825 356633076 2.090000e-52 217.0
37 TraesCS4D01G089100 chr5A 85.981 214 22 6 294 506 680105109 680105315 4.490000e-54 222.0
38 TraesCS4D01G089100 chr5A 90.244 82 6 2 1860 1940 572048645 572048725 4.720000e-19 106.0
39 TraesCS4D01G089100 chr5A 96.721 61 2 0 1882 1942 11034632 11034572 6.110000e-18 102.0
40 TraesCS4D01G089100 chr2D 84.034 238 24 8 303 526 589703164 589702927 2.090000e-52 217.0
41 TraesCS4D01G089100 chr2D 84.211 209 30 1 53 261 586856777 586856572 2.110000e-47 200.0
42 TraesCS4D01G089100 chr2D 88.462 78 7 2 1872 1949 439417466 439417391 3.680000e-15 93.5
43 TraesCS4D01G089100 chr7B 82.308 260 31 7 10 257 158013855 158013599 9.730000e-51 211.0
44 TraesCS4D01G089100 chr6D 82.213 253 32 6 294 533 5755840 5756092 4.530000e-49 206.0
45 TraesCS4D01G089100 chr3A 84.615 208 29 1 50 257 21796040 21796244 1.630000e-48 204.0
46 TraesCS4D01G089100 chr3B 83.256 215 31 3 53 265 740867265 740867054 3.520000e-45 193.0
47 TraesCS4D01G089100 chr3B 82.727 220 32 4 50 268 507848957 507849171 1.270000e-44 191.0
48 TraesCS4D01G089100 chr3B 82.432 222 30 3 294 506 810665381 810665602 5.900000e-43 185.0
49 TraesCS4D01G089100 chr7D 80.556 216 36 3 1648 1857 620985576 620985361 9.930000e-36 161.0
50 TraesCS4D01G089100 chr7D 95.238 63 3 0 1876 1938 490348987 490349049 2.200000e-17 100.0
51 TraesCS4D01G089100 chrUn 77.778 216 42 5 1648 1857 93057694 93057479 1.010000e-25 128.0
52 TraesCS4D01G089100 chrUn 77.778 216 42 5 1648 1857 310844792 310845007 1.010000e-25 128.0
53 TraesCS4D01G089100 chr5D 91.429 70 3 2 1869 1935 378889232 378889301 3.680000e-15 93.5
54 TraesCS4D01G089100 chr1D 96.970 33 0 1 1934 1965 15439716 15439684 2.000000e-03 54.7
55 TraesCS4D01G089100 chr1B 96.970 33 0 1 1934 1965 201312764 201312732 2.000000e-03 54.7


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 TraesCS4D01G089100 chr4D 64603712 64607170 3458 True 6388.00 6388 100.000000 1 3459 1 chr4D.!!$R1 3458
1 TraesCS4D01G089100 chr4D 64615095 64617411 2316 True 877.50 1075 80.834500 989 3459 2 chr4D.!!$R3 2470
2 TraesCS4D01G089100 chr4B 95106701 95111969 5268 True 948.75 2065 91.293000 7 3459 4 chr4B.!!$R4 3452
3 TraesCS4D01G089100 chr4B 95366125 95367913 1788 False 736.50 1168 82.964500 1566 3439 2 chr4B.!!$F1 1873
4 TraesCS4D01G089100 chr4B 95216436 95218767 2331 True 609.00 747 81.928667 910 3459 3 chr4B.!!$R5 2549
5 TraesCS4D01G089100 chr4B 95317817 95319189 1372 True 241.50 309 81.615500 640 1881 2 chr4B.!!$R6 1241
6 TraesCS4D01G089100 chr4A 531324908 531328221 3313 False 1120.00 1814 92.176750 4 3455 4 chr4A.!!$F3 3451
7 TraesCS4D01G089100 chr4A 531311715 531314106 2391 False 820.50 1020 79.599000 910 3459 2 chr4A.!!$F2 2549
8 TraesCS4D01G089100 chr4A 531247721 531249534 1813 False 711.50 1136 82.107000 1564 3459 2 chr4A.!!$F1 1895

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
325 2093 0.466124 GGGACAGTGGTATCCTCAGC 59.534 60.0 0.0 0.0 35.15 4.26 F
1897 3898 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.0 0.0 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 4029 0.734253 GGAGCTATGTATCCGCTGCG 60.734 60.0 16.34 16.34 32.65 5.18 R
2853 5000 0.100325 CAGACTGCGGTTGTTTTGCA 59.900 50.0 0.00 0.00 37.07 4.08 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
20 21 2.724708 CTGCAGTCGCGTTGAGCTC 61.725 63.158 6.82 6.82 45.59 4.09
82 83 1.870055 GAGGCAGGTGACGGACGTTA 61.870 60.000 0.00 0.00 39.28 3.18
142 144 5.612725 TTTTCCTTCTTGGCTGATGTTTT 57.387 34.783 0.00 0.00 35.26 2.43
180 182 3.804873 ACGTTCTGCTCTCTTTTCAGTTC 59.195 43.478 0.00 0.00 0.00 3.01
184 186 5.028549 TCTGCTCTCTTTTCAGTTCTGTT 57.971 39.130 0.00 0.00 0.00 3.16
212 1848 5.063438 TCGGTGTATACGTGACTTGTAGTAC 59.937 44.000 0.00 0.00 0.00 2.73
292 2055 1.366679 GCTACCTAAGCGAACCAACC 58.633 55.000 0.00 0.00 42.53 3.77
309 2077 2.661176 ACCTTGGATGGTTAGAGGGA 57.339 50.000 0.00 0.00 36.89 4.20
321 2089 3.630311 GGTTAGAGGGACAGTGGTATCCT 60.630 52.174 0.00 0.00 35.15 3.24
324 2092 2.035632 GAGGGACAGTGGTATCCTCAG 58.964 57.143 14.38 0.00 42.50 3.35
325 2093 0.466124 GGGACAGTGGTATCCTCAGC 59.534 60.000 0.00 0.00 35.15 4.26
327 2095 0.466124 GACAGTGGTATCCTCAGCCC 59.534 60.000 0.00 0.00 0.00 5.19
330 2098 0.983378 AGTGGTATCCTCAGCCCACC 60.983 60.000 4.15 0.00 46.84 4.61
343 2111 4.821935 CCACCAGGGTTCAAGTCC 57.178 61.111 0.00 0.00 0.00 3.85
356 2124 0.877071 CAAGTCCTGTTGCTCGCATT 59.123 50.000 0.00 0.00 0.00 3.56
357 2125 2.076100 CAAGTCCTGTTGCTCGCATTA 58.924 47.619 0.00 0.00 0.00 1.90
358 2126 2.679837 CAAGTCCTGTTGCTCGCATTAT 59.320 45.455 0.00 0.00 0.00 1.28
359 2127 2.991250 AGTCCTGTTGCTCGCATTATT 58.009 42.857 0.00 0.00 0.00 1.40
360 2128 2.939103 AGTCCTGTTGCTCGCATTATTC 59.061 45.455 0.00 0.00 0.00 1.75
361 2129 2.032178 GTCCTGTTGCTCGCATTATTCC 59.968 50.000 0.00 0.00 0.00 3.01
362 2130 2.092968 TCCTGTTGCTCGCATTATTCCT 60.093 45.455 0.00 0.00 0.00 3.36
363 2131 2.032550 CCTGTTGCTCGCATTATTCCTG 59.967 50.000 0.00 0.00 0.00 3.86
364 2132 2.016318 TGTTGCTCGCATTATTCCTGG 58.984 47.619 0.00 0.00 0.00 4.45
365 2133 2.288666 GTTGCTCGCATTATTCCTGGA 58.711 47.619 0.00 0.00 0.00 3.86
366 2134 2.880890 GTTGCTCGCATTATTCCTGGAT 59.119 45.455 0.00 0.00 0.00 3.41
367 2135 3.213206 TGCTCGCATTATTCCTGGATT 57.787 42.857 0.00 0.00 0.00 3.01
368 2136 3.554934 TGCTCGCATTATTCCTGGATTT 58.445 40.909 0.00 0.00 0.00 2.17
369 2137 4.713553 TGCTCGCATTATTCCTGGATTTA 58.286 39.130 0.00 0.00 0.00 1.40
370 2138 5.316167 TGCTCGCATTATTCCTGGATTTAT 58.684 37.500 0.00 0.00 0.00 1.40
371 2139 5.769662 TGCTCGCATTATTCCTGGATTTATT 59.230 36.000 0.00 0.00 0.00 1.40
372 2140 6.265196 TGCTCGCATTATTCCTGGATTTATTT 59.735 34.615 0.00 0.00 0.00 1.40
373 2141 7.147976 GCTCGCATTATTCCTGGATTTATTTT 58.852 34.615 0.00 0.00 0.00 1.82
374 2142 8.296713 GCTCGCATTATTCCTGGATTTATTTTA 58.703 33.333 0.00 0.00 0.00 1.52
375 2143 9.831737 CTCGCATTATTCCTGGATTTATTTTAG 57.168 33.333 0.00 0.00 0.00 1.85
376 2144 9.567776 TCGCATTATTCCTGGATTTATTTTAGA 57.432 29.630 0.00 0.00 0.00 2.10
402 2170 1.444895 GCAATGCGCTTTCAGTGGG 60.445 57.895 9.73 0.00 37.77 4.61
438 2206 1.014044 ACGACGAGACGCTTACGGTA 61.014 55.000 0.00 0.00 46.04 4.02
450 2218 5.473039 ACGCTTACGGTAACTTTGTAAGAT 58.527 37.500 13.78 0.66 44.90 2.40
457 2225 7.478520 ACGGTAACTTTGTAAGATGATATGC 57.521 36.000 0.00 0.00 0.00 3.14
460 2228 6.073222 GGTAACTTTGTAAGATGATATGCCGG 60.073 42.308 0.00 0.00 0.00 6.13
465 2233 4.820897 TGTAAGATGATATGCCGGCTTAG 58.179 43.478 29.70 0.00 0.00 2.18
471 2239 2.558795 TGATATGCCGGCTTAGTCTCTC 59.441 50.000 29.70 18.59 0.00 3.20
485 2253 6.567701 GCTTAGTCTCTCGAAGGTGATCATAG 60.568 46.154 0.00 0.00 31.09 2.23
488 2256 2.560542 CTCTCGAAGGTGATCATAGGGG 59.439 54.545 0.00 0.00 0.00 4.79
491 2259 3.497332 TCGAAGGTGATCATAGGGGTAG 58.503 50.000 0.00 0.00 0.00 3.18
507 2275 1.202533 GGTAGGATATGCGTGTGTGCT 60.203 52.381 0.00 0.00 35.36 4.40
512 2285 1.737236 GATATGCGTGTGTGCTTTGGA 59.263 47.619 0.00 0.00 35.36 3.53
522 2295 5.277011 CGTGTGTGCTTTGGATGAGTATATG 60.277 44.000 0.00 0.00 0.00 1.78
523 2296 4.576053 TGTGTGCTTTGGATGAGTATATGC 59.424 41.667 0.00 0.00 0.00 3.14
524 2297 3.809279 TGTGCTTTGGATGAGTATATGCG 59.191 43.478 0.00 0.00 0.00 4.73
527 2300 3.364366 GCTTTGGATGAGTATATGCGCAC 60.364 47.826 14.90 0.00 0.00 5.34
533 2345 4.327357 GGATGAGTATATGCGCACATGTAC 59.673 45.833 14.90 11.23 45.99 2.90
665 2486 4.971125 GCGCTACAGATCCCCCGC 62.971 72.222 0.00 0.00 34.50 6.13
717 2553 3.077359 CAAGTCAACTCAACCCAGATCC 58.923 50.000 0.00 0.00 0.00 3.36
788 2625 3.139025 TCAGAATCCTCATCCCCATTTCC 59.861 47.826 0.00 0.00 0.00 3.13
813 2655 1.276421 TCTGTTCCCAGCTTCTAGCAC 59.724 52.381 1.09 0.00 45.56 4.40
1267 3187 2.590821 ACATTGCTGTGAAGAGGCTTT 58.409 42.857 0.00 0.00 33.22 3.51
1829 3828 0.590481 GAACAAACACGGGCGAACAC 60.590 55.000 0.00 0.00 0.00 3.32
1830 3829 2.052590 CAAACACGGGCGAACACG 60.053 61.111 0.00 0.00 0.00 4.49
1881 3882 7.642586 GCCGGTTACAACTGTGATAATATTTTC 59.357 37.037 1.90 0.00 33.38 2.29
1882 3883 8.889717 CCGGTTACAACTGTGATAATATTTTCT 58.110 33.333 7.32 0.00 33.38 2.52
1888 3889 9.614792 ACAACTGTGATAATATTTTCTACTCCC 57.385 33.333 7.32 0.00 0.00 4.30
1889 3890 9.838339 CAACTGTGATAATATTTTCTACTCCCT 57.162 33.333 7.32 0.00 0.00 4.20
1891 3892 8.652290 ACTGTGATAATATTTTCTACTCCCTCC 58.348 37.037 7.32 0.00 0.00 4.30
1892 3893 7.667557 TGTGATAATATTTTCTACTCCCTCCG 58.332 38.462 7.32 0.00 0.00 4.63
1893 3894 7.289317 TGTGATAATATTTTCTACTCCCTCCGT 59.711 37.037 7.32 0.00 0.00 4.69
1894 3895 7.813627 GTGATAATATTTTCTACTCCCTCCGTC 59.186 40.741 7.32 0.00 0.00 4.79
1895 3896 5.548181 AATATTTTCTACTCCCTCCGTCC 57.452 43.478 0.00 0.00 0.00 4.79
1896 3897 1.565067 TTTTCTACTCCCTCCGTCCC 58.435 55.000 0.00 0.00 0.00 4.46
1897 3898 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
1898 3899 0.410663 TTCTACTCCCTCCGTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
1899 3900 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
1900 3901 1.203212 TCTACTCCCTCCGTCCCAAAA 60.203 52.381 0.00 0.00 0.00 2.44
1901 3902 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
1902 3903 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1903 3904 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1904 3905 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1905 3906 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1906 3907 2.914278 TCCCTCCGTCCCAAAATTCTTA 59.086 45.455 0.00 0.00 0.00 2.10
1907 3908 3.526019 TCCCTCCGTCCCAAAATTCTTAT 59.474 43.478 0.00 0.00 0.00 1.73
1908 3909 3.883489 CCCTCCGTCCCAAAATTCTTATC 59.117 47.826 0.00 0.00 0.00 1.75
1909 3910 4.385310 CCCTCCGTCCCAAAATTCTTATCT 60.385 45.833 0.00 0.00 0.00 1.98
1910 3911 5.193679 CCTCCGTCCCAAAATTCTTATCTT 58.806 41.667 0.00 0.00 0.00 2.40
1911 3912 6.354130 CCTCCGTCCCAAAATTCTTATCTTA 58.646 40.000 0.00 0.00 0.00 2.10
1912 3913 6.483640 CCTCCGTCCCAAAATTCTTATCTTAG 59.516 42.308 0.00 0.00 0.00 2.18
1913 3914 7.190335 TCCGTCCCAAAATTCTTATCTTAGA 57.810 36.000 0.00 0.00 0.00 2.10
1914 3915 7.802117 TCCGTCCCAAAATTCTTATCTTAGAT 58.198 34.615 0.00 0.00 0.00 1.98
1915 3916 8.272173 TCCGTCCCAAAATTCTTATCTTAGATT 58.728 33.333 0.00 0.00 0.00 2.40
1916 3917 8.903820 CCGTCCCAAAATTCTTATCTTAGATTT 58.096 33.333 0.00 0.00 0.00 2.17
1917 3918 9.722056 CGTCCCAAAATTCTTATCTTAGATTTG 57.278 33.333 0.00 0.00 29.84 2.32
1941 3942 9.734984 TTGTCTAGATACGGATATATCAAGACA 57.265 33.333 14.60 14.91 34.50 3.41
1942 3943 9.734984 TGTCTAGATACGGATATATCAAGACAA 57.265 33.333 14.60 1.23 34.50 3.18
1951 3952 8.840321 ACGGATATATCAAGACAAGAATTTTGG 58.160 33.333 14.60 0.00 0.00 3.28
1952 3953 8.292448 CGGATATATCAAGACAAGAATTTTGGG 58.708 37.037 14.60 0.00 0.00 4.12
1953 3954 9.354673 GGATATATCAAGACAAGAATTTTGGGA 57.645 33.333 14.60 0.00 0.00 4.37
1955 3956 9.699410 ATATATCAAGACAAGAATTTTGGGACA 57.301 29.630 5.68 0.00 0.00 4.02
1956 3957 5.772825 TCAAGACAAGAATTTTGGGACAG 57.227 39.130 5.68 0.00 42.39 3.51
1957 3958 5.445069 TCAAGACAAGAATTTTGGGACAGA 58.555 37.500 5.68 0.00 42.39 3.41
1958 3959 5.532406 TCAAGACAAGAATTTTGGGACAGAG 59.468 40.000 5.68 0.00 42.39 3.35
1959 3960 4.401925 AGACAAGAATTTTGGGACAGAGG 58.598 43.478 5.68 0.00 42.39 3.69
1960 3961 4.141158 AGACAAGAATTTTGGGACAGAGGT 60.141 41.667 5.68 0.00 42.39 3.85
1961 3962 5.073144 AGACAAGAATTTTGGGACAGAGGTA 59.927 40.000 5.68 0.00 42.39 3.08
2142 4148 1.468914 GGCGAGAAGAATCAACCCAAC 59.531 52.381 0.00 0.00 0.00 3.77
2184 4190 8.882736 GCAAGGGATTTTATTGAAAATGTAAGG 58.117 33.333 0.56 0.00 43.76 2.69
2223 4242 6.009589 TGAAATCTGGAAGCTTATGTTGGAA 58.990 36.000 0.00 0.00 0.00 3.53
2224 4243 6.493115 TGAAATCTGGAAGCTTATGTTGGAAA 59.507 34.615 0.00 0.00 0.00 3.13
2227 4246 6.916360 TCTGGAAGCTTATGTTGGAAATTT 57.084 33.333 0.00 0.00 0.00 1.82
2233 4252 9.489084 GGAAGCTTATGTTGGAAATTTACTTTT 57.511 29.630 0.00 0.00 0.00 2.27
2332 4352 7.798596 AGCATCCAGATACTCAATGTTAAAG 57.201 36.000 0.00 0.00 0.00 1.85
2429 4449 9.753674 AGAGACCTTCCATTGAAAATATTGTTA 57.246 29.630 0.00 0.00 0.00 2.41
2440 4460 7.915293 TGAAAATATTGTTAAGAGGCTCGAA 57.085 32.000 9.22 4.80 0.00 3.71
2505 4537 3.092511 GGCTGGATCAGGGGCTCA 61.093 66.667 0.00 0.00 31.21 4.26
2512 4544 1.771255 GGATCAGGGGCTCAGTATTGT 59.229 52.381 0.00 0.00 0.00 2.71
2603 4649 4.521639 GGAAACCTACCTCCGAAATTGTTT 59.478 41.667 0.00 0.00 0.00 2.83
2609 4655 2.693074 ACCTCCGAAATTGTTTGCTTGT 59.307 40.909 0.00 0.00 0.00 3.16
2623 4671 7.667043 TGTTTGCTTGTTTCCTATACACTAG 57.333 36.000 0.00 0.00 0.00 2.57
2636 4684 6.495872 TCCTATACACTAGTGTTTCAAGTGGT 59.504 38.462 32.15 7.16 43.91 4.16
2745 4892 9.699410 TGTTCAAATTAGACTATGAATGGGATT 57.301 29.630 1.39 0.00 34.62 3.01
2841 4988 6.757010 CACATCGGCTAGTTTTTGTAGAGTAT 59.243 38.462 0.00 0.00 0.00 2.12
2888 5037 5.291858 CGCAGTCTGTGTATTCATATGTTGT 59.708 40.000 5.17 0.00 0.00 3.32
2912 5062 5.399604 AACTTTTTCTCGTGAAGTTACCG 57.600 39.130 0.00 0.00 40.67 4.02
3003 5165 2.352388 CAGCCCAAAATGCTTGGATTG 58.648 47.619 4.82 0.00 42.06 2.67
3007 5169 3.853475 CCCAAAATGCTTGGATTGAGAC 58.147 45.455 4.82 0.00 42.06 3.36
3032 5196 9.569122 ACATTAGCAACCTACTTTTCTAAAAGA 57.431 29.630 19.33 5.14 46.39 2.52
3074 5564 3.056821 GCATACTTGGTTTCCTTTGGTCC 60.057 47.826 0.00 0.00 0.00 4.46
3180 5675 3.598019 ATGTTGCATTTAAGCTGGTGG 57.402 42.857 0.00 0.00 34.99 4.61
3187 5685 3.674138 GCATTTAAGCTGGTGGTGACATG 60.674 47.826 0.00 0.00 46.14 3.21
3207 5705 7.094805 TGACATGTACTCTACAAAATTTCAGGC 60.095 37.037 0.00 0.00 42.76 4.85
3211 5709 5.248380 ACTCTACAAAATTTCAGGCCTCT 57.752 39.130 0.00 0.00 0.00 3.69
3260 5758 7.821846 ACTAGGATCTTCTCTTGATGAAACAAC 59.178 37.037 0.00 0.00 31.52 3.32
3285 5783 4.984785 GCACCATGGAAAGAAAAGAACTTC 59.015 41.667 21.47 0.00 0.00 3.01
3439 5941 5.721876 ATGCAATGTTGTTGTTTCTGTTG 57.278 34.783 0.00 0.00 0.00 3.33
3440 5942 3.931468 TGCAATGTTGTTGTTTCTGTTGG 59.069 39.130 0.00 0.00 0.00 3.77
3442 5944 2.663826 TGTTGTTGTTTCTGTTGGGC 57.336 45.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.736236 CTCAACGCGACTGCAGCT 60.736 61.111 15.93 0.23 42.97 4.24
1 2 4.436448 GCTCAACGCGACTGCAGC 62.436 66.667 15.93 15.44 42.97 5.25
2 3 2.724708 GAGCTCAACGCGACTGCAG 61.725 63.158 15.93 13.48 45.59 4.41
20 21 0.175760 ACGAATCACCTCATCACCCG 59.824 55.000 0.00 0.00 0.00 5.28
82 83 3.515602 AAATCCCTTGAGCTTGACACT 57.484 42.857 0.00 0.00 0.00 3.55
142 144 5.328691 CAGAACGTTAGTCTTTGCACAAAA 58.671 37.500 0.00 0.00 0.00 2.44
158 160 3.460857 ACTGAAAAGAGAGCAGAACGT 57.539 42.857 0.00 0.00 33.94 3.99
180 182 5.007430 AGTCACGTATACACCGATCTAACAG 59.993 44.000 3.32 0.00 0.00 3.16
184 186 4.877823 ACAAGTCACGTATACACCGATCTA 59.122 41.667 3.32 0.00 0.00 1.98
247 2007 9.831737 CACTACTTGACTATTTCTTTTTCATGG 57.168 33.333 0.00 0.00 0.00 3.66
292 2055 2.840651 ACTGTCCCTCTAACCATCCAAG 59.159 50.000 0.00 0.00 0.00 3.61
309 2077 0.252696 TGGGCTGAGGATACCACTGT 60.253 55.000 0.00 0.00 37.17 3.55
327 2095 3.329300 CAGGACTTGAACCCTGGTG 57.671 57.895 0.00 0.00 44.68 4.17
343 2111 2.032550 CCAGGAATAATGCGAGCAACAG 59.967 50.000 0.57 0.00 0.00 3.16
360 2128 9.874205 TGCTGAAAATTCTAAAATAAATCCAGG 57.126 29.630 0.00 0.00 0.00 4.45
366 2134 8.167985 GCGCATTGCTGAAAATTCTAAAATAAA 58.832 29.630 0.30 0.00 41.73 1.40
367 2135 7.674564 GCGCATTGCTGAAAATTCTAAAATAA 58.325 30.769 0.30 0.00 41.73 1.40
368 2136 7.220599 GCGCATTGCTGAAAATTCTAAAATA 57.779 32.000 0.30 0.00 41.73 1.40
369 2137 6.098367 GCGCATTGCTGAAAATTCTAAAAT 57.902 33.333 0.30 0.00 41.73 1.82
370 2138 5.514059 GCGCATTGCTGAAAATTCTAAAA 57.486 34.783 0.30 0.00 41.73 1.52
432 2200 7.654520 GGCATATCATCTTACAAAGTTACCGTA 59.345 37.037 0.00 0.00 0.00 4.02
438 2206 4.275936 GCCGGCATATCATCTTACAAAGTT 59.724 41.667 24.80 0.00 0.00 2.66
450 2218 2.558795 GAGAGACTAAGCCGGCATATCA 59.441 50.000 31.54 7.27 0.00 2.15
457 2225 0.382515 CCTTCGAGAGACTAAGCCGG 59.617 60.000 0.00 0.00 41.84 6.13
460 2228 3.378742 TGATCACCTTCGAGAGACTAAGC 59.621 47.826 0.00 0.00 41.84 3.09
465 2233 3.254657 CCCTATGATCACCTTCGAGAGAC 59.745 52.174 0.00 0.00 41.84 3.36
471 2239 2.563179 CCTACCCCTATGATCACCTTCG 59.437 54.545 0.00 0.00 0.00 3.79
485 2253 0.756903 ACACACGCATATCCTACCCC 59.243 55.000 0.00 0.00 0.00 4.95
488 2256 2.225068 AGCACACACGCATATCCTAC 57.775 50.000 0.00 0.00 0.00 3.18
491 2259 1.202177 CCAAAGCACACACGCATATCC 60.202 52.381 0.00 0.00 0.00 2.59
507 2275 3.802866 TGTGCGCATATACTCATCCAAA 58.197 40.909 15.91 0.00 0.00 3.28
512 2285 5.139435 AGTACATGTGCGCATATACTCAT 57.861 39.130 22.38 11.14 40.23 2.90
522 2295 5.479716 AATTTTAGGTAGTACATGTGCGC 57.520 39.130 9.11 0.00 0.00 6.09
523 2296 6.837992 ACAAATTTTAGGTAGTACATGTGCG 58.162 36.000 9.11 0.00 0.00 5.34
524 2297 8.943002 AGTACAAATTTTAGGTAGTACATGTGC 58.057 33.333 9.11 7.34 35.51 4.57
561 2377 1.502231 CGCGCTGGATTATACTGCTT 58.498 50.000 5.56 0.00 0.00 3.91
665 2486 5.240403 CCTCAAGTCTTCCTTTCAAAGAAGG 59.760 44.000 0.00 0.00 46.17 3.46
717 2553 4.909696 TGCATATAAATGAACCCAACGG 57.090 40.909 0.00 0.00 34.84 4.44
1267 3187 1.607612 GGAGGGGAGCATTTTCGGA 59.392 57.895 0.00 0.00 0.00 4.55
1829 3828 1.452110 TGATCCCACAACATTCTGCG 58.548 50.000 0.00 0.00 0.00 5.18
1830 3829 4.202441 ACTATGATCCCACAACATTCTGC 58.798 43.478 0.00 0.00 0.00 4.26
1881 3882 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
1882 3883 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1883 3884 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
1884 3885 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1885 3886 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
1886 3887 2.215942 AAGAATTTTGGGACGGAGGG 57.784 50.000 0.00 0.00 0.00 4.30
1887 3888 4.781934 AGATAAGAATTTTGGGACGGAGG 58.218 43.478 0.00 0.00 0.00 4.30
1888 3889 7.272978 TCTAAGATAAGAATTTTGGGACGGAG 58.727 38.462 0.00 0.00 0.00 4.63
1889 3890 7.190335 TCTAAGATAAGAATTTTGGGACGGA 57.810 36.000 0.00 0.00 0.00 4.69
1890 3891 8.451908 AATCTAAGATAAGAATTTTGGGACGG 57.548 34.615 0.00 0.00 0.00 4.79
1891 3892 9.722056 CAAATCTAAGATAAGAATTTTGGGACG 57.278 33.333 0.00 0.00 28.49 4.79
1925 3926 8.840321 CCAAAATTCTTGTCTTGATATATCCGT 58.160 33.333 10.25 0.00 0.00 4.69
1926 3927 8.292448 CCCAAAATTCTTGTCTTGATATATCCG 58.708 37.037 10.25 1.95 0.00 4.18
1927 3928 9.354673 TCCCAAAATTCTTGTCTTGATATATCC 57.645 33.333 10.25 0.00 0.00 2.59
1929 3930 9.699410 TGTCCCAAAATTCTTGTCTTGATATAT 57.301 29.630 0.00 0.00 0.00 0.86
1930 3931 9.177608 CTGTCCCAAAATTCTTGTCTTGATATA 57.822 33.333 0.00 0.00 0.00 0.86
1931 3932 7.890127 TCTGTCCCAAAATTCTTGTCTTGATAT 59.110 33.333 0.00 0.00 0.00 1.63
1932 3933 7.230747 TCTGTCCCAAAATTCTTGTCTTGATA 58.769 34.615 0.00 0.00 0.00 2.15
1933 3934 6.070656 TCTGTCCCAAAATTCTTGTCTTGAT 58.929 36.000 0.00 0.00 0.00 2.57
1934 3935 5.445069 TCTGTCCCAAAATTCTTGTCTTGA 58.555 37.500 0.00 0.00 0.00 3.02
1935 3936 5.278660 CCTCTGTCCCAAAATTCTTGTCTTG 60.279 44.000 0.00 0.00 0.00 3.02
1936 3937 4.829492 CCTCTGTCCCAAAATTCTTGTCTT 59.171 41.667 0.00 0.00 0.00 3.01
1937 3938 4.141158 ACCTCTGTCCCAAAATTCTTGTCT 60.141 41.667 0.00 0.00 0.00 3.41
1938 3939 4.145052 ACCTCTGTCCCAAAATTCTTGTC 58.855 43.478 0.00 0.00 0.00 3.18
1939 3940 4.184649 ACCTCTGTCCCAAAATTCTTGT 57.815 40.909 0.00 0.00 0.00 3.16
1940 3941 5.316987 ACTACCTCTGTCCCAAAATTCTTG 58.683 41.667 0.00 0.00 0.00 3.02
1941 3942 5.584551 ACTACCTCTGTCCCAAAATTCTT 57.415 39.130 0.00 0.00 0.00 2.52
1942 3943 5.785940 ACTACTACCTCTGTCCCAAAATTCT 59.214 40.000 0.00 0.00 0.00 2.40
1943 3944 6.051179 ACTACTACCTCTGTCCCAAAATTC 57.949 41.667 0.00 0.00 0.00 2.17
1944 3945 7.563724 TTACTACTACCTCTGTCCCAAAATT 57.436 36.000 0.00 0.00 0.00 1.82
1945 3946 7.563724 TTTACTACTACCTCTGTCCCAAAAT 57.436 36.000 0.00 0.00 0.00 1.82
1946 3947 6.999705 TTTACTACTACCTCTGTCCCAAAA 57.000 37.500 0.00 0.00 0.00 2.44
1947 3948 7.391620 CAATTTACTACTACCTCTGTCCCAAA 58.608 38.462 0.00 0.00 0.00 3.28
1948 3949 6.575649 GCAATTTACTACTACCTCTGTCCCAA 60.576 42.308 0.00 0.00 0.00 4.12
1949 3950 5.105064 GCAATTTACTACTACCTCTGTCCCA 60.105 44.000 0.00 0.00 0.00 4.37
1950 3951 5.105064 TGCAATTTACTACTACCTCTGTCCC 60.105 44.000 0.00 0.00 0.00 4.46
1951 3952 5.974108 TGCAATTTACTACTACCTCTGTCC 58.026 41.667 0.00 0.00 0.00 4.02
1952 3953 8.494016 AAATGCAATTTACTACTACCTCTGTC 57.506 34.615 0.00 0.00 46.47 3.51
2023 4029 0.734253 GGAGCTATGTATCCGCTGCG 60.734 60.000 16.34 16.34 32.65 5.18
2142 4148 0.878523 TTGCTGACGGTTCGTTCTGG 60.879 55.000 0.00 0.00 41.37 3.86
2332 4352 1.923356 TTTCCTGGAGGTCATTTGCC 58.077 50.000 0.00 0.00 36.34 4.52
2429 4449 1.979693 AGCGTCCTTCGAGCCTCTT 60.980 57.895 0.00 0.00 42.86 2.85
2440 4460 0.463654 TTCAGTTTGCACAGCGTCCT 60.464 50.000 0.00 0.00 0.00 3.85
2505 4537 8.046708 TGCATGGAACTAAGTGATTACAATACT 58.953 33.333 0.00 0.00 0.00 2.12
2591 4637 4.116238 GGAAACAAGCAAACAATTTCGGA 58.884 39.130 0.00 0.00 31.42 4.55
2593 4639 7.593273 TGTATAGGAAACAAGCAAACAATTTCG 59.407 33.333 0.00 0.00 31.42 3.46
2603 4649 6.354794 ACACTAGTGTATAGGAAACAAGCA 57.645 37.500 26.91 0.00 42.90 3.91
2609 4655 7.876068 CCACTTGAAACACTAGTGTATAGGAAA 59.124 37.037 28.13 15.11 45.74 3.13
2623 4671 2.357952 GGAACTCCACCACTTGAAACAC 59.642 50.000 0.00 0.00 35.64 3.32
2676 4823 4.022242 GGGTACATCATGCGTATCTACAGT 60.022 45.833 0.00 0.00 0.00 3.55
2677 4824 4.218635 AGGGTACATCATGCGTATCTACAG 59.781 45.833 0.00 0.00 0.00 2.74
2678 4825 4.149598 AGGGTACATCATGCGTATCTACA 58.850 43.478 0.00 0.00 0.00 2.74
2681 4828 2.563179 GGAGGGTACATCATGCGTATCT 59.437 50.000 0.00 4.10 0.00 1.98
2682 4829 2.299013 TGGAGGGTACATCATGCGTATC 59.701 50.000 0.00 0.00 0.00 2.24
2683 4830 2.325484 TGGAGGGTACATCATGCGTAT 58.675 47.619 0.00 0.00 0.00 3.06
2684 4831 1.783071 TGGAGGGTACATCATGCGTA 58.217 50.000 0.00 0.00 0.00 4.42
2685 4832 0.908910 TTGGAGGGTACATCATGCGT 59.091 50.000 0.00 0.00 0.00 5.24
2686 4833 2.036958 TTTGGAGGGTACATCATGCG 57.963 50.000 0.00 0.00 0.00 4.73
2687 4834 4.646492 AGAATTTTGGAGGGTACATCATGC 59.354 41.667 0.00 0.00 0.00 4.06
2688 4835 9.745018 ATATAGAATTTTGGAGGGTACATCATG 57.255 33.333 0.00 0.00 0.00 3.07
2737 4884 1.846439 ACGATCCACCTCAATCCCATT 59.154 47.619 0.00 0.00 0.00 3.16
2745 4892 6.419484 AATGTATTATCACGATCCACCTCA 57.581 37.500 0.00 0.00 0.00 3.86
2841 4988 5.053145 GGTTGTTTTGCATTGTGGTGAATA 58.947 37.500 0.00 0.00 0.00 1.75
2853 5000 0.100325 CAGACTGCGGTTGTTTTGCA 59.900 50.000 0.00 0.00 37.07 4.08
2854 5001 0.100503 ACAGACTGCGGTTGTTTTGC 59.899 50.000 0.00 0.00 0.00 3.68
2888 5037 6.018832 CCGGTAACTTCACGAGAAAAAGTTTA 60.019 38.462 5.19 0.00 41.89 2.01
2912 5062 3.065925 GGCAGATAGTTTGAGTGCAATCC 59.934 47.826 12.27 0.00 35.78 3.01
3003 5165 8.773404 TTAGAAAAGTAGGTTGCTAATGTCTC 57.227 34.615 0.00 0.00 0.00 3.36
3102 5592 8.484641 ACATGATAACAGTGACAAATCTACAG 57.515 34.615 0.00 0.00 0.00 2.74
3112 5602 8.349983 ACAAGGTAAAAACATGATAACAGTGAC 58.650 33.333 0.00 0.00 0.00 3.67
3180 5675 8.230486 CCTGAAATTTTGTAGAGTACATGTCAC 58.770 37.037 0.00 0.00 38.68 3.67
3187 5685 6.174049 AGAGGCCTGAAATTTTGTAGAGTAC 58.826 40.000 12.00 0.00 0.00 2.73
3207 5705 0.107703 TTGCATGGGAGCGTTAGAGG 60.108 55.000 0.00 0.00 37.31 3.69
3211 5709 0.394216 ATGCTTGCATGGGAGCGTTA 60.394 50.000 7.35 0.00 41.75 3.18
3260 5758 1.885887 TCTTTTCTTTCCATGGTGCCG 59.114 47.619 12.58 0.00 0.00 5.69
3336 5834 6.922247 TTTAACAAGTTCCACAATGACGTA 57.078 33.333 0.00 0.00 0.00 3.57
3376 5874 7.727578 TGGACTACAACAGATAATGGAGTAA 57.272 36.000 0.00 0.00 40.80 2.24
3379 5877 5.994054 CCATGGACTACAACAGATAATGGAG 59.006 44.000 5.56 0.00 35.01 3.86
3390 5888 7.107542 TGGAGTATAAAACCATGGACTACAAC 58.892 38.462 21.47 9.63 0.00 3.32


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

AutoCloner maintained by Alex Coulton.