Multiple sequence alignment - TraesCS3B01G220700

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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 TraesCS3B01G220700 chr3B 100.000 3145 0 0 1 3145 270892990 270889846 0.000000e+00 5808.0
1 TraesCS3B01G220700 chr3B 92.857 42 2 1 137 178 7377512 7377472 3.390000e-05 60.2
2 TraesCS3B01G220700 chr3D 89.336 1716 88 46 427 2107 188360064 188358409 0.000000e+00 2067.0
3 TraesCS3B01G220700 chr3D 92.140 598 16 10 2567 3145 188357943 188357358 0.000000e+00 815.0
4 TraesCS3B01G220700 chr3D 95.000 120 6 0 225 344 188360452 188360333 4.140000e-44 189.0
5 TraesCS3B01G220700 chr3D 91.228 57 5 0 2231 2287 543933652 543933596 9.350000e-11 78.7
6 TraesCS3B01G220700 chr3A 92.595 1364 53 17 774 2104 241922114 241923462 0.000000e+00 1916.0
7 TraesCS3B01G220700 chr3A 88.512 914 38 21 2295 3142 241923536 241924448 0.000000e+00 1044.0
8 TraesCS3B01G220700 chr3A 87.399 373 33 8 429 791 241920848 241921216 1.740000e-112 416.0
9 TraesCS3B01G220700 chr3A 90.650 246 19 3 1 243 241920200 241920444 1.090000e-84 324.0
10 TraesCS3B01G220700 chr3A 91.866 209 16 1 225 432 241920495 241920703 1.100000e-74 291.0
11 TraesCS3B01G220700 chr3A 79.545 88 13 4 2567 2651 12842417 12842332 1.220000e-04 58.4
12 TraesCS3B01G220700 chr5D 96.659 419 12 1 1182 1598 535199391 535199809 0.000000e+00 695.0
13 TraesCS3B01G220700 chr7B 96.107 411 14 1 1186 1594 656880622 656881032 0.000000e+00 669.0
14 TraesCS3B01G220700 chr7B 90.385 52 5 0 131 182 667163773 667163722 5.630000e-08 69.4
15 TraesCS3B01G220700 chr2B 94.033 419 19 2 1182 1598 792711038 792711452 5.720000e-177 630.0
16 TraesCS3B01G220700 chr5A 96.410 195 5 1 1406 1598 43189079 43189273 1.410000e-83 320.0
17 TraesCS3B01G220700 chr5A 87.629 194 13 5 1182 1375 43188899 43189081 6.830000e-52 215.0
18 TraesCS3B01G220700 chr5A 97.826 92 2 0 2104 2195 546827525 546827616 3.250000e-35 159.0
19 TraesCS3B01G220700 chr5B 97.895 95 1 1 2104 2198 13718605 13718698 2.510000e-36 163.0
20 TraesCS3B01G220700 chr5B 97.826 92 1 1 2098 2189 689943986 689944076 1.170000e-34 158.0
21 TraesCS3B01G220700 chr5B 88.636 44 5 0 131 174 72076103 72076060 2.000000e-03 54.7
22 TraesCS3B01G220700 chr7D 94.340 106 4 2 2095 2199 542092258 542092362 9.030000e-36 161.0
23 TraesCS3B01G220700 chr7D 91.379 58 3 2 2231 2287 416240207 416240151 9.350000e-11 78.7
24 TraesCS3B01G220700 chr7D 85.915 71 7 3 2240 2307 220975785 220975715 4.350000e-09 73.1
25 TraesCS3B01G220700 chr2A 96.875 96 2 1 2103 2198 98882730 98882824 3.250000e-35 159.0
26 TraesCS3B01G220700 chr2A 96.739 92 2 1 2098 2189 455340493 455340403 5.430000e-33 152.0
27 TraesCS3B01G220700 chr2A 91.379 58 5 0 2230 2287 596429027 596428970 2.600000e-11 80.5
28 TraesCS3B01G220700 chr2A 88.889 63 5 1 2236 2298 352992043 352991983 3.360000e-10 76.8
29 TraesCS3B01G220700 chr2A 79.439 107 18 2 2567 2671 42481197 42481301 4.350000e-09 73.1
30 TraesCS3B01G220700 chr2A 79.630 108 17 3 2567 2671 735378004 735377899 4.350000e-09 73.1
31 TraesCS3B01G220700 chr4B 95.876 97 3 1 2100 2196 140924552 140924647 4.200000e-34 156.0
32 TraesCS3B01G220700 chr1B 95.000 100 2 2 2097 2196 149606479 149606575 1.510000e-33 154.0
33 TraesCS3B01G220700 chr1B 96.774 93 2 1 2103 2195 272976701 272976792 1.510000e-33 154.0
34 TraesCS3B01G220700 chr1B 91.837 49 4 0 131 179 562454252 562454300 5.630000e-08 69.4
35 TraesCS3B01G220700 chr6A 90.164 61 4 1 2241 2299 614385559 614385619 9.350000e-11 78.7
36 TraesCS3B01G220700 chr6A 100.000 31 0 0 2567 2597 81122074 81122104 1.220000e-04 58.4
37 TraesCS3B01G220700 chr6D 89.831 59 6 0 2229 2287 372879543 372879485 3.360000e-10 76.8
38 TraesCS3B01G220700 chr6D 88.889 63 5 2 2225 2287 377870919 377870859 3.360000e-10 76.8
39 TraesCS3B01G220700 chr6B 84.416 77 10 2 2213 2287 609097655 609097579 1.210000e-09 75.0
40 TraesCS3B01G220700 chr4A 82.222 90 9 5 2567 2652 151317855 151317941 1.560000e-08 71.3
41 TraesCS3B01G220700 chr7A 100.000 31 0 0 2567 2597 115794880 115794910 1.220000e-04 58.4
42 TraesCS3B01G220700 chr7A 100.000 31 0 0 2567 2597 487261774 487261804 1.220000e-04 58.4
43 TraesCS3B01G220700 chr7A 96.774 31 1 0 147 177 566211020 566211050 6.000000e-03 52.8
44 TraesCS3B01G220700 chr2D 100.000 31 0 0 2567 2597 560858911 560858941 1.220000e-04 58.4


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 TraesCS3B01G220700 chr3B 270889846 270892990 3144 True 5808.000000 5808 100.000000 1 3145 1 chr3B.!!$R2 3144
1 TraesCS3B01G220700 chr3D 188357358 188360452 3094 True 1023.666667 2067 92.158667 225 3145 3 chr3D.!!$R2 2920
2 TraesCS3B01G220700 chr3A 241920200 241924448 4248 False 798.200000 1916 90.204400 1 3142 5 chr3A.!!$F1 3141

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
994 2309 0.371645 GAGGTTTTCGCGAGCTCATG 59.628 55.0 15.4 5.11 40.43 3.07 F
1480 2814 0.390492 TGTCCAGTGAGTCAGCAGTG 59.610 55.0 0.0 0.00 38.61 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 3354 1.214062 CACCACTGAGAGCTCGGTC 59.786 63.158 8.37 1.63 45.45 4.79 R
2826 4311 1.668826 AGGACTGATGGGTGCCTTAA 58.331 50.000 0.00 0.00 0.00 1.85 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
96 99 4.434545 AACCTATAGTGAGCGAGTCCTA 57.565 45.455 0.00 0.00 0.00 2.94
98 101 2.737783 CCTATAGTGAGCGAGTCCTACG 59.262 54.545 0.00 0.00 0.00 3.51
111 114 2.308039 CCTACGCTAATTCGCCGGC 61.308 63.158 19.07 19.07 0.00 6.13
148 151 2.106477 AAGGCAAGAGCAGCTTCTAC 57.894 50.000 0.00 0.00 44.61 2.59
160 163 3.570559 CAGCTTCTACCTCGCTATAAGC 58.429 50.000 0.00 0.00 39.62 3.09
214 217 4.955925 ACTATGAGAAGTCACGACTCAG 57.044 45.455 11.42 3.67 42.55 3.35
229 232 2.076622 CTCAGGAGGGATACGCCACG 62.077 65.000 0.00 0.00 38.95 4.94
282 355 9.631452 CAGAAAAGAAGAGAACAAAAAGTTTCT 57.369 29.630 0.00 0.00 41.51 2.52
359 432 1.787057 GATCCAGCCTCGTCGTCGAT 61.787 60.000 5.00 0.00 45.21 3.59
371 444 2.887568 GTCGATGCTGCTCACCCG 60.888 66.667 0.00 0.00 0.00 5.28
379 452 3.669036 CTGCTCACCCGTCTCGTCG 62.669 68.421 0.00 0.00 0.00 5.12
387 460 2.176055 CGTCTCGTCGTCACTGGG 59.824 66.667 0.00 0.00 0.00 4.45
391 464 2.022129 CTCGTCGTCACTGGGTTGC 61.022 63.158 0.00 0.00 0.00 4.17
397 470 1.968540 GTCACTGGGTTGCAGCTCC 60.969 63.158 0.00 0.00 0.00 4.70
419 492 3.712881 GCTCGTGGTCGCAACACC 61.713 66.667 0.00 0.00 35.46 4.16
438 511 4.612412 GGTCGCCGTGTCCCAACA 62.612 66.667 0.00 0.00 0.00 3.33
443 810 0.593773 CGCCGTGTCCCAACAAAAAG 60.594 55.000 0.00 0.00 37.08 2.27
479 846 4.487714 AGAAAATCTCCAATAGTCGCCA 57.512 40.909 0.00 0.00 0.00 5.69
494 861 1.658409 GCCAGTCGCTGCACAAAAC 60.658 57.895 0.00 0.00 0.00 2.43
496 863 0.381801 CCAGTCGCTGCACAAAACTT 59.618 50.000 0.00 0.00 0.00 2.66
497 864 1.601903 CCAGTCGCTGCACAAAACTTA 59.398 47.619 0.00 0.00 0.00 2.24
499 866 1.260561 AGTCGCTGCACAAAACTTACG 59.739 47.619 0.00 0.00 0.00 3.18
507 874 1.605232 CACAAAACTTACGGGTCCCAC 59.395 52.381 9.12 0.00 0.00 4.61
513 880 4.645863 AACTTACGGGTCCCACTAAAAT 57.354 40.909 9.12 0.00 0.00 1.82
519 886 5.182169 ACGGGTCCCACTAAAATTTATCA 57.818 39.130 9.12 0.00 0.00 2.15
666 1034 7.697691 AGAACATTAGCCAGATAACATTTTCG 58.302 34.615 0.00 0.00 0.00 3.46
667 1041 6.377327 ACATTAGCCAGATAACATTTTCGG 57.623 37.500 0.00 0.00 0.00 4.30
895 2202 0.911769 CCTAGCCACAACCTCCATCA 59.088 55.000 0.00 0.00 0.00 3.07
992 2307 0.667487 CAGAGGTTTTCGCGAGCTCA 60.667 55.000 22.38 1.21 42.53 4.26
994 2309 0.371645 GAGGTTTTCGCGAGCTCATG 59.628 55.000 15.40 5.11 40.43 3.07
1036 2351 3.160047 CCTCCGATCCTGCCTGCT 61.160 66.667 0.00 0.00 0.00 4.24
1120 2446 3.719883 CTCTCTGCTGCAGGCCTCG 62.720 68.421 27.79 12.28 40.92 4.63
1184 2510 3.141488 CGCCTACTGCCTCGTCCT 61.141 66.667 0.00 0.00 36.24 3.85
1231 2557 0.666577 GTTGGTTGTCCTCGACTCGG 60.667 60.000 0.00 0.00 33.15 4.63
1339 2671 3.066190 CTCGCCTACACCGTCCCA 61.066 66.667 0.00 0.00 0.00 4.37
1448 2782 4.577283 CCAACGACCAAGGTAAGAAAGAAA 59.423 41.667 0.00 0.00 0.00 2.52
1449 2783 5.277828 CCAACGACCAAGGTAAGAAAGAAAG 60.278 44.000 0.00 0.00 0.00 2.62
1473 2807 1.971357 TCCTTCCTTGTCCAGTGAGTC 59.029 52.381 0.00 0.00 0.00 3.36
1476 2810 0.681733 TCCTTGTCCAGTGAGTCAGC 59.318 55.000 0.00 0.00 0.00 4.26
1477 2811 0.394192 CCTTGTCCAGTGAGTCAGCA 59.606 55.000 0.00 0.00 0.00 4.41
1478 2812 1.607509 CCTTGTCCAGTGAGTCAGCAG 60.608 57.143 0.00 0.00 0.00 4.24
1479 2813 1.069823 CTTGTCCAGTGAGTCAGCAGT 59.930 52.381 0.00 0.00 0.00 4.40
1480 2814 0.390492 TGTCCAGTGAGTCAGCAGTG 59.610 55.000 0.00 0.00 38.61 3.66
1491 2825 1.004080 CAGCAGTGACCTGACCTGG 60.004 63.158 0.00 0.00 41.50 4.45
1513 2847 0.762082 TGGGTTTCAAATGCCTGCCA 60.762 50.000 0.00 0.00 0.00 4.92
1514 2848 0.614812 GGGTTTCAAATGCCTGCCAT 59.385 50.000 0.00 0.00 35.06 4.40
1684 3024 1.452801 GGACGTTCTTGGGGTGGAA 59.547 57.895 0.00 0.00 0.00 3.53
1749 3089 0.465460 TGCGCCTTCTCCAACAAAGT 60.465 50.000 4.18 0.00 0.00 2.66
1784 3124 1.679311 GCTCCTCATCACACCCACA 59.321 57.895 0.00 0.00 0.00 4.17
1786 3126 0.979665 CTCCTCATCACACCCACACT 59.020 55.000 0.00 0.00 0.00 3.55
1862 3206 1.112950 TCGTGTGTGTAGGTTCACCA 58.887 50.000 0.00 0.00 38.89 4.17
1863 3207 1.202440 TCGTGTGTGTAGGTTCACCAC 60.202 52.381 0.00 0.00 38.89 4.16
1864 3208 1.471851 CGTGTGTGTAGGTTCACCACA 60.472 52.381 0.00 0.00 38.32 4.17
1976 3321 0.391130 CCGACATGGTGGTCAACGAT 60.391 55.000 0.00 0.00 37.66 3.73
2005 3350 2.047274 CTGCGGTTCCGACACCAT 60.047 61.111 15.69 0.00 36.49 3.55
2081 3426 4.465512 GCATTGGGCGCAGACGTG 62.466 66.667 10.83 1.90 42.83 4.49
2104 3449 4.998051 AGGAAATCCTTGGTTGAAAGCTA 58.002 39.130 0.00 0.00 46.09 3.32
2107 3452 5.106118 GGAAATCCTTGGTTGAAAGCTACTC 60.106 44.000 0.00 0.00 0.00 2.59
2108 3453 3.418684 TCCTTGGTTGAAAGCTACTCC 57.581 47.619 0.00 0.00 0.00 3.85
2109 3454 2.039879 TCCTTGGTTGAAAGCTACTCCC 59.960 50.000 0.00 0.00 0.00 4.30
2110 3455 2.040412 CCTTGGTTGAAAGCTACTCCCT 59.960 50.000 0.00 0.00 0.00 4.20
2111 3456 3.339141 CTTGGTTGAAAGCTACTCCCTC 58.661 50.000 0.00 0.00 0.00 4.30
2112 3457 1.628846 TGGTTGAAAGCTACTCCCTCC 59.371 52.381 0.00 0.00 0.00 4.30
2113 3458 1.405661 GGTTGAAAGCTACTCCCTCCG 60.406 57.143 0.00 0.00 0.00 4.63
2114 3459 1.275573 GTTGAAAGCTACTCCCTCCGT 59.724 52.381 0.00 0.00 0.00 4.69
2115 3460 1.640917 TGAAAGCTACTCCCTCCGTT 58.359 50.000 0.00 0.00 0.00 4.44
2116 3461 1.975680 TGAAAGCTACTCCCTCCGTTT 59.024 47.619 0.00 0.00 0.00 3.60
2117 3462 2.028385 TGAAAGCTACTCCCTCCGTTTC 60.028 50.000 0.00 0.00 0.00 2.78
2118 3463 1.640917 AAGCTACTCCCTCCGTTTCA 58.359 50.000 0.00 0.00 0.00 2.69
2119 3464 1.640917 AGCTACTCCCTCCGTTTCAA 58.359 50.000 0.00 0.00 0.00 2.69
2120 3465 1.975680 AGCTACTCCCTCCGTTTCAAA 59.024 47.619 0.00 0.00 0.00 2.69
2121 3466 2.370849 AGCTACTCCCTCCGTTTCAAAA 59.629 45.455 0.00 0.00 0.00 2.44
2122 3467 3.009143 AGCTACTCCCTCCGTTTCAAAAT 59.991 43.478 0.00 0.00 0.00 1.82
2123 3468 4.224370 AGCTACTCCCTCCGTTTCAAAATA 59.776 41.667 0.00 0.00 0.00 1.40
2124 3469 4.571176 GCTACTCCCTCCGTTTCAAAATAG 59.429 45.833 0.00 0.00 0.00 1.73
2125 3470 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
2126 3471 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
2127 3472 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
2128 3473 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
2129 3474 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
2130 3475 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
2131 3476 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
2132 3477 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
2133 3478 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
2134 3479 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
2135 3480 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
2136 3481 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
2137 3482 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
2138 3483 8.895845 CGTTTCAAAATAGATGACTCAACTTTG 58.104 33.333 0.00 0.00 0.00 2.77
2139 3484 9.736023 GTTTCAAAATAGATGACTCAACTTTGT 57.264 29.630 0.00 0.00 0.00 2.83
2142 3487 9.778741 TCAAAATAGATGACTCAACTTTGTACT 57.221 29.630 0.00 0.00 0.00 2.73
2175 3520 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2176 3521 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2177 3522 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2178 3523 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2179 3524 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2180 3525 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2181 3526 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2182 3527 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2183 3528 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2184 3529 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2185 3530 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2186 3531 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2187 3532 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2188 3533 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2189 3534 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2192 3537 2.019807 TGGAACGGAGGGAGTACTTT 57.980 50.000 0.00 0.00 0.00 2.66
2213 3558 4.632327 TTTTAGGGGAATTTTGCCTTGG 57.368 40.909 0.69 0.00 38.90 3.61
2221 3588 2.407340 ATTTTGCCTTGGGGGTGTTA 57.593 45.000 0.00 0.00 37.43 2.41
2234 3601 3.573967 GGGGGTGTTAGCCATGAATATTG 59.426 47.826 0.00 0.00 37.54 1.90
2240 3607 7.417797 GGGTGTTAGCCATGAATATTGTGAAAT 60.418 37.037 0.00 0.00 35.40 2.17
2241 3608 8.629158 GGTGTTAGCCATGAATATTGTGAAATA 58.371 33.333 0.00 0.00 0.00 1.40
2242 3609 9.450807 GTGTTAGCCATGAATATTGTGAAATAC 57.549 33.333 0.00 0.00 0.00 1.89
2243 3610 9.407380 TGTTAGCCATGAATATTGTGAAATACT 57.593 29.630 0.00 0.00 0.00 2.12
2246 3613 8.757982 AGCCATGAATATTGTGAAATACTTCT 57.242 30.769 0.00 0.00 32.33 2.85
2250 3617 9.655769 CATGAATATTGTGAAATACTTCTTCCG 57.344 33.333 0.00 0.00 32.33 4.30
2251 3618 7.693952 TGAATATTGTGAAATACTTCTTCCGC 58.306 34.615 0.00 0.00 32.33 5.54
2252 3619 7.552687 TGAATATTGTGAAATACTTCTTCCGCT 59.447 33.333 0.00 0.00 32.33 5.52
2253 3620 7.865706 ATATTGTGAAATACTTCTTCCGCTT 57.134 32.000 0.00 0.00 32.33 4.68
2254 3621 5.607119 TTGTGAAATACTTCTTCCGCTTC 57.393 39.130 0.00 0.00 32.33 3.86
2255 3622 4.637276 TGTGAAATACTTCTTCCGCTTCA 58.363 39.130 0.00 0.00 32.33 3.02
2259 3626 7.084486 GTGAAATACTTCTTCCGCTTCAAAAT 58.916 34.615 0.00 0.00 32.33 1.82
2261 3628 8.450964 TGAAATACTTCTTCCGCTTCAAAATAG 58.549 33.333 0.00 0.00 32.33 1.73
2263 3630 8.738645 AATACTTCTTCCGCTTCAAAATAGAT 57.261 30.769 0.00 0.00 0.00 1.98
2264 3631 6.428385 ACTTCTTCCGCTTCAAAATAGATG 57.572 37.500 0.00 0.00 0.00 2.90
2266 3633 6.092807 ACTTCTTCCGCTTCAAAATAGATGAC 59.907 38.462 0.00 0.00 0.00 3.06
2268 3635 5.812642 TCTTCCGCTTCAAAATAGATGACTC 59.187 40.000 0.00 0.00 0.00 3.36
2270 3637 5.487433 TCCGCTTCAAAATAGATGACTCAA 58.513 37.500 0.00 0.00 0.00 3.02
2271 3638 5.351465 TCCGCTTCAAAATAGATGACTCAAC 59.649 40.000 0.00 0.00 0.00 3.18
2273 3640 6.128172 CCGCTTCAAAATAGATGACTCAACTT 60.128 38.462 0.00 0.00 0.00 2.66
2274 3641 7.301054 CGCTTCAAAATAGATGACTCAACTTT 58.699 34.615 0.00 0.00 0.00 2.66
2275 3642 7.269937 CGCTTCAAAATAGATGACTCAACTTTG 59.730 37.037 0.00 0.00 0.00 2.77
2276 3643 8.078596 GCTTCAAAATAGATGACTCAACTTTGT 58.921 33.333 0.00 0.00 0.00 2.83
2337 3737 6.874134 GTGATAAGACTTTCAAGTAGCAAGGA 59.126 38.462 0.00 0.00 39.88 3.36
2354 3754 4.348168 GCAAGGATGGAGGGTTTATCTCTA 59.652 45.833 0.00 0.00 0.00 2.43
2389 3789 2.908688 AACAAAAATGAGGGGCACAC 57.091 45.000 0.00 0.00 0.00 3.82
2422 3831 3.746045 TTTGCGAGTCCTACAGTTCTT 57.254 42.857 0.00 0.00 0.00 2.52
2529 4009 9.855361 GTCACTTGATTCATAAGATACGAAATG 57.145 33.333 0.00 0.00 0.00 2.32
2541 4021 6.910536 AGATACGAAATGTGAAGGATTGAC 57.089 37.500 0.00 0.00 30.83 3.18
2557 4037 5.141182 GGATTGACTCCTATCCTACACAGA 58.859 45.833 0.00 0.00 40.21 3.41
2563 4043 7.583625 TGACTCCTATCCTACACAGAAATAGA 58.416 38.462 0.00 0.00 0.00 1.98
2615 4096 6.162777 ACAAACTTAGTGCTGCAAAGAAAAA 58.837 32.000 18.21 1.47 0.00 1.94
2616 4097 6.311200 ACAAACTTAGTGCTGCAAAGAAAAAG 59.689 34.615 18.21 11.40 0.00 2.27
2619 4100 6.398095 ACTTAGTGCTGCAAAGAAAAAGTTT 58.602 32.000 18.21 0.00 0.00 2.66
2804 4289 4.505313 TCCATCATACGAGCATCAGTAC 57.495 45.455 0.00 0.00 33.17 2.73
2826 4311 5.683681 ACAGAATTCCCACAAAAAGCAATT 58.316 33.333 0.65 0.00 0.00 2.32
2880 4369 9.702253 TGCTGGTAAAATAGGGAATATTTACAA 57.298 29.630 8.85 0.00 42.14 2.41
2966 4455 6.419484 TCGATATCTATTCCTGGCAGAAAA 57.581 37.500 17.94 10.40 0.00 2.29
3066 4555 5.607477 TCATATACTTTAGCAGAAACCCGG 58.393 41.667 0.00 0.00 0.00 5.73
3124 4623 3.790089 TCCAGATCCTACTCGAGCATA 57.210 47.619 13.61 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 132 1.339535 GGTAGAAGCTGCTCTTGCCTT 60.340 52.381 0.00 0.00 38.71 4.35
131 134 0.251634 AGGTAGAAGCTGCTCTTGCC 59.748 55.000 0.00 7.48 38.71 4.52
139 142 3.570559 GCTTATAGCGAGGTAGAAGCTG 58.429 50.000 25.12 3.29 41.83 4.24
160 163 3.560902 TTCCGCAAGAGCTATATCTCG 57.439 47.619 0.00 0.00 43.02 4.04
203 206 1.677052 GTATCCCTCCTGAGTCGTGAC 59.323 57.143 0.00 0.00 0.00 3.67
207 210 1.655329 GCGTATCCCTCCTGAGTCG 59.345 63.158 0.00 0.00 0.00 4.18
214 217 1.797211 CTCTCGTGGCGTATCCCTCC 61.797 65.000 0.00 0.00 0.00 4.30
229 232 1.142748 CACCATGTCGGCCTCTCTC 59.857 63.158 0.00 0.00 39.03 3.20
359 432 4.056125 CGAGACGGGTGAGCAGCA 62.056 66.667 0.00 0.00 0.00 4.41
371 444 0.663568 CAACCCAGTGACGACGAGAC 60.664 60.000 0.00 0.00 0.00 3.36
379 452 1.968540 GGAGCTGCAACCCAGTGAC 60.969 63.158 0.00 0.00 43.71 3.67
432 505 6.112058 TCCTGAAATTTGTCTTTTTGTTGGG 58.888 36.000 0.00 0.00 0.00 4.12
433 506 7.608308 TTCCTGAAATTTGTCTTTTTGTTGG 57.392 32.000 0.00 0.00 0.00 3.77
434 507 8.934825 TCTTTCCTGAAATTTGTCTTTTTGTTG 58.065 29.630 0.00 0.00 0.00 3.33
435 508 9.500785 TTCTTTCCTGAAATTTGTCTTTTTGTT 57.499 25.926 0.00 0.00 0.00 2.83
443 810 8.143835 TGGAGATTTTCTTTCCTGAAATTTGTC 58.856 33.333 0.00 0.00 36.07 3.18
479 846 1.260561 CGTAAGTTTTGTGCAGCGACT 59.739 47.619 0.00 0.00 0.00 4.18
494 861 6.824704 TGATAAATTTTAGTGGGACCCGTAAG 59.175 38.462 5.91 0.00 0.00 2.34
496 863 6.310764 TGATAAATTTTAGTGGGACCCGTA 57.689 37.500 5.91 0.00 0.00 4.02
497 864 5.182169 TGATAAATTTTAGTGGGACCCGT 57.818 39.130 5.91 0.00 0.00 5.28
499 866 4.036380 CGCTGATAAATTTTAGTGGGACCC 59.964 45.833 2.45 2.45 0.00 4.46
507 874 7.246674 TGCTAGAACCGCTGATAAATTTTAG 57.753 36.000 0.00 0.00 0.00 1.85
513 880 5.950758 TTTTTGCTAGAACCGCTGATAAA 57.049 34.783 0.00 0.00 0.00 1.40
646 1014 7.339466 AGAAACCGAAAATGTTATCTGGCTAAT 59.661 33.333 0.00 0.00 0.00 1.73
648 1016 6.177610 AGAAACCGAAAATGTTATCTGGCTA 58.822 36.000 0.00 0.00 0.00 3.93
666 1034 1.066454 CCCGTGGTGACAAAAGAAACC 59.934 52.381 0.00 0.00 46.06 3.27
667 1041 1.066454 CCCCGTGGTGACAAAAGAAAC 59.934 52.381 0.00 0.00 46.06 2.78
720 1109 4.441695 TTCTCTCGCGCTGCCAGG 62.442 66.667 5.56 0.00 0.00 4.45
843 2150 3.057019 CCTCTTATAATACGCAGCGCAA 58.943 45.455 16.61 3.30 0.00 4.85
848 2155 5.921408 GGTGAACTCCTCTTATAATACGCAG 59.079 44.000 0.00 0.00 0.00 5.18
895 2202 1.420138 AGTTGGTCAAGATGTTCCGGT 59.580 47.619 0.00 0.00 0.00 5.28
940 2255 1.556373 GGGTAGGGTTTACTGGGCGT 61.556 60.000 0.00 0.00 0.00 5.68
946 2261 2.382882 GCGAGTAGGGTAGGGTTTACT 58.617 52.381 0.00 0.00 0.00 2.24
947 2262 1.410517 GGCGAGTAGGGTAGGGTTTAC 59.589 57.143 0.00 0.00 0.00 2.01
1064 2380 8.196802 AGCATCATCACATTGATCAATTTTTG 57.803 30.769 18.41 14.82 34.28 2.44
1138 2464 4.675029 CGCGAACACCCCGACCTT 62.675 66.667 0.00 0.00 0.00 3.50
1231 2557 2.281762 GTCGCGATTAACCATGACAGAC 59.718 50.000 14.06 0.00 0.00 3.51
1263 2595 6.459573 CGAGAGGACCAATTAGAAGAGAAGAG 60.460 46.154 0.00 0.00 0.00 2.85
1339 2671 0.107508 CGATGGATGCCTTGACCACT 60.108 55.000 0.00 0.00 36.49 4.00
1402 2734 0.320374 TGTGTGGTAGAAGAAGGCCG 59.680 55.000 0.00 0.00 0.00 6.13
1473 2807 1.004080 CCAGGTCAGGTCACTGCTG 60.004 63.158 0.00 0.00 44.54 4.41
1476 2810 0.675837 CATGCCAGGTCAGGTCACTG 60.676 60.000 0.00 0.00 46.30 3.66
1477 2811 1.681666 CATGCCAGGTCAGGTCACT 59.318 57.895 0.00 0.00 0.00 3.41
1478 2812 1.377725 CCATGCCAGGTCAGGTCAC 60.378 63.158 0.00 0.00 0.00 3.67
1479 2813 2.605607 CCCATGCCAGGTCAGGTCA 61.606 63.158 0.00 0.00 0.00 4.02
1480 2814 2.142292 AACCCATGCCAGGTCAGGTC 62.142 60.000 0.00 0.00 36.27 3.85
1482 2816 0.967380 GAAACCCATGCCAGGTCAGG 60.967 60.000 0.00 0.00 36.27 3.86
1483 2817 0.251297 TGAAACCCATGCCAGGTCAG 60.251 55.000 0.00 0.00 36.27 3.51
1491 2825 1.729284 CAGGCATTTGAAACCCATGC 58.271 50.000 0.00 0.00 42.26 4.06
1684 3024 0.036952 CGATGGTCTGCCTGAACACT 60.037 55.000 0.00 0.00 46.28 3.55
1784 3124 4.534797 AGGTTGAATCGTAGGTAGCTAGT 58.465 43.478 0.86 0.00 0.00 2.57
1786 3126 4.337555 GTGAGGTTGAATCGTAGGTAGCTA 59.662 45.833 0.00 0.00 0.00 3.32
1862 3206 2.520020 TCCTCCACCGACGTGTGT 60.520 61.111 13.14 0.00 38.41 3.72
1863 3207 2.049433 GTCCTCCACCGACGTGTG 60.049 66.667 0.00 0.00 38.41 3.82
1864 3208 3.300765 GGTCCTCCACCGACGTGT 61.301 66.667 0.00 0.00 38.41 4.49
1960 3305 1.533625 CCAATCGTTGACCACCATGT 58.466 50.000 0.00 0.00 0.00 3.21
2005 3350 3.443925 CTGAGAGCTCGGTCGCCA 61.444 66.667 8.37 0.44 0.00 5.69
2009 3354 1.214062 CACCACTGAGAGCTCGGTC 59.786 63.158 8.37 1.63 45.45 4.79
2104 3449 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
2107 3452 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
2108 3453 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
2109 3454 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
2110 3455 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
2111 3456 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
2112 3457 8.895845 CAAAGTTGAGTCATCTATTTTGAAACG 58.104 33.333 4.14 0.00 38.91 3.60
2113 3458 9.736023 ACAAAGTTGAGTCATCTATTTTGAAAC 57.264 29.630 15.99 0.00 38.91 2.78
2116 3461 9.778741 AGTACAAAGTTGAGTCATCTATTTTGA 57.221 29.630 15.99 3.46 38.91 2.69
2149 3494 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2150 3495 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2151 3496 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2152 3497 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2153 3498 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2154 3499 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2155 3500 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2156 3501 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2157 3502 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2158 3503 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2159 3504 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2160 3505 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2161 3506 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2162 3507 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2163 3508 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2164 3509 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2165 3510 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2166 3511 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2167 3512 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2168 3513 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2169 3514 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2170 3515 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
2171 3516 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2172 3517 2.019807 AAGTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2173 3518 2.019807 AAAGTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
2174 3519 3.413846 AAAAAGTACTCCCTCCGTTCC 57.586 47.619 0.00 0.00 0.00 3.62
2192 3537 3.329225 CCCAAGGCAAAATTCCCCTAAAA 59.671 43.478 0.00 0.00 0.00 1.52
2213 3558 4.037923 CACAATATTCATGGCTAACACCCC 59.962 45.833 0.00 0.00 0.00 4.95
2221 3588 8.757982 AGAAGTATTTCACAATATTCATGGCT 57.242 30.769 0.44 0.00 35.70 4.75
2234 3601 5.607119 TTGAAGCGGAAGAAGTATTTCAC 57.393 39.130 0.44 0.00 35.70 3.18
2240 3607 7.277981 GTCATCTATTTTGAAGCGGAAGAAGTA 59.722 37.037 0.00 0.00 0.00 2.24
2241 3608 6.092807 GTCATCTATTTTGAAGCGGAAGAAGT 59.907 38.462 0.00 0.00 0.00 3.01
2242 3609 6.314896 AGTCATCTATTTTGAAGCGGAAGAAG 59.685 38.462 0.00 0.00 0.00 2.85
2243 3610 6.173339 AGTCATCTATTTTGAAGCGGAAGAA 58.827 36.000 0.00 0.00 0.00 2.52
2245 3612 5.582269 TGAGTCATCTATTTTGAAGCGGAAG 59.418 40.000 0.00 0.00 0.00 3.46
2246 3613 5.487433 TGAGTCATCTATTTTGAAGCGGAA 58.513 37.500 0.00 0.00 0.00 4.30
2250 3617 8.078596 ACAAAGTTGAGTCATCTATTTTGAAGC 58.921 33.333 15.99 0.00 38.91 3.86
2253 3620 9.778741 AGTACAAAGTTGAGTCATCTATTTTGA 57.221 29.630 15.99 3.46 38.91 2.69
2263 3630 7.436080 CCGTAAAGTTAGTACAAAGTTGAGTCA 59.564 37.037 0.00 0.00 0.00 3.41
2264 3631 7.649306 TCCGTAAAGTTAGTACAAAGTTGAGTC 59.351 37.037 0.00 0.00 0.00 3.36
2266 3633 7.115947 CCTCCGTAAAGTTAGTACAAAGTTGAG 59.884 40.741 0.00 0.00 0.00 3.02
2268 3635 6.146673 CCCTCCGTAAAGTTAGTACAAAGTTG 59.853 42.308 0.00 0.00 0.00 3.16
2270 3637 5.539955 TCCCTCCGTAAAGTTAGTACAAAGT 59.460 40.000 0.00 0.00 0.00 2.66
2271 3638 6.029346 TCCCTCCGTAAAGTTAGTACAAAG 57.971 41.667 0.00 0.00 0.00 2.77
2273 3640 5.079643 ACTCCCTCCGTAAAGTTAGTACAA 58.920 41.667 0.00 0.00 0.00 2.41
2274 3641 4.666512 ACTCCCTCCGTAAAGTTAGTACA 58.333 43.478 0.00 0.00 0.00 2.90
2275 3642 5.883115 ACTACTCCCTCCGTAAAGTTAGTAC 59.117 44.000 0.00 0.00 0.00 2.73
2276 3643 6.067217 ACTACTCCCTCCGTAAAGTTAGTA 57.933 41.667 0.00 0.00 0.00 1.82
2277 3644 4.928263 ACTACTCCCTCCGTAAAGTTAGT 58.072 43.478 0.00 0.00 0.00 2.24
2280 3647 4.928263 AGTACTACTCCCTCCGTAAAGTT 58.072 43.478 0.00 0.00 0.00 2.66
2281 3648 4.582973 AGTACTACTCCCTCCGTAAAGT 57.417 45.455 0.00 0.00 0.00 2.66
2282 3649 5.911378 AAAGTACTACTCCCTCCGTAAAG 57.089 43.478 0.00 0.00 0.00 1.85
2337 3737 6.100424 CAGGTCTTTAGAGATAAACCCTCCAT 59.900 42.308 0.00 0.00 33.70 3.41
2389 3789 3.247442 ACTCGCAAATTGCATTGTCATG 58.753 40.909 18.65 0.00 45.36 3.07
2576 4056 9.667107 CACTAAGTTTGTAGGAATGGATTCTTA 57.333 33.333 0.00 0.00 37.00 2.10
2577 4057 7.121315 GCACTAAGTTTGTAGGAATGGATTCTT 59.879 37.037 0.00 0.00 37.00 2.52
2578 4058 6.599638 GCACTAAGTTTGTAGGAATGGATTCT 59.400 38.462 0.00 0.00 37.00 2.40
2615 4096 7.544804 AAAGGATAGGAATTTTGCAGAAACT 57.455 32.000 0.00 0.00 0.00 2.66
2616 4097 8.739972 TCTAAAGGATAGGAATTTTGCAGAAAC 58.260 33.333 0.00 0.00 0.00 2.78
2619 4100 9.125026 GATTCTAAAGGATAGGAATTTTGCAGA 57.875 33.333 0.00 0.00 0.00 4.26
2804 4289 6.622833 AAATTGCTTTTTGTGGGAATTCTG 57.377 33.333 5.23 0.00 33.58 3.02
2826 4311 1.668826 AGGACTGATGGGTGCCTTAA 58.331 50.000 0.00 0.00 0.00 1.85
2910 4399 9.732130 GCCCTAGATTCTTATTTATGTTGATCT 57.268 33.333 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.