Multiple sequence alignment - TraesCS4B01G098000

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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 TraesCS4B01G098000 chr4B 100.000 4925 0 0 1 4925 103002662 103007586 0.000000e+00 9095.0
1 TraesCS4B01G098000 chr4D 92.390 4967 229 65 1 4925 69644915 69649774 0.000000e+00 6940.0
2 TraesCS4B01G098000 chr4A 93.004 3116 130 36 1839 4925 521813159 521816215 0.000000e+00 4466.0
3 TraesCS4B01G098000 chr4A 90.978 1840 107 33 1 1802 521811344 521813162 0.000000e+00 2423.0
4 TraesCS4B01G098000 chr3D 95.692 1764 48 13 2107 3863 567166156 567164414 0.000000e+00 2811.0
5 TraesCS4B01G098000 chr3D 83.932 473 59 8 3379 3838 554382163 554382631 2.110000e-118 436.0
6 TraesCS4B01G098000 chr3D 84.014 294 28 13 1314 1605 504065829 504066105 1.050000e-66 265.0
7 TraesCS4B01G098000 chr1D 93.130 1703 63 23 2168 3863 26569462 26567807 0.000000e+00 2447.0
8 TraesCS4B01G098000 chr7B 80.284 776 138 11 3149 3913 732087197 732087968 5.530000e-159 571.0
9 TraesCS4B01G098000 chr7B 80.180 777 136 13 3149 3913 731961441 731962211 2.570000e-157 566.0
10 TraesCS4B01G098000 chrUn 80.155 776 139 11 3149 3913 88429641 88430412 2.570000e-157 566.0
11 TraesCS4B01G098000 chrUn 80.155 776 139 11 3149 3913 160383506 160384277 2.570000e-157 566.0
12 TraesCS4B01G098000 chrUn 82.877 438 71 4 3149 3584 435951464 435951899 1.660000e-104 390.0
13 TraesCS4B01G098000 chr5A 84.755 387 44 7 1008 1392 546811536 546811909 1.670000e-99 374.0
14 TraesCS4B01G098000 chr5A 87.097 93 8 3 4835 4925 698349750 698349660 8.720000e-18 102.0
15 TraesCS4B01G098000 chr5A 88.462 78 8 1 4848 4925 698334977 698334901 5.250000e-15 93.5
16 TraesCS4B01G098000 chr5A 100.000 29 0 0 691 719 640722727 640722755 2.000000e-03 54.7
17 TraesCS4B01G098000 chr6B 81.138 334 41 15 1274 1605 695072978 695072665 1.060000e-61 248.0
18 TraesCS4B01G098000 chr2D 86.842 76 10 0 632 707 344302766 344302841 8.780000e-13 86.1
19 TraesCS4B01G098000 chr2A 91.489 47 4 0 679 725 744446373 744446327 1.140000e-06 65.8
20 TraesCS4B01G098000 chr5D 100.000 28 0 0 692 719 477022113 477022140 9.000000e-03 52.8


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 TraesCS4B01G098000 chr4B 103002662 103007586 4924 False 9095.0 9095 100.000 1 4925 1 chr4B.!!$F1 4924
1 TraesCS4B01G098000 chr4D 69644915 69649774 4859 False 6940.0 6940 92.390 1 4925 1 chr4D.!!$F1 4924
2 TraesCS4B01G098000 chr4A 521811344 521816215 4871 False 3444.5 4466 91.991 1 4925 2 chr4A.!!$F1 4924
3 TraesCS4B01G098000 chr3D 567164414 567166156 1742 True 2811.0 2811 95.692 2107 3863 1 chr3D.!!$R1 1756
4 TraesCS4B01G098000 chr1D 26567807 26569462 1655 True 2447.0 2447 93.130 2168 3863 1 chr1D.!!$R1 1695
5 TraesCS4B01G098000 chr7B 732087197 732087968 771 False 571.0 571 80.284 3149 3913 1 chr7B.!!$F2 764
6 TraesCS4B01G098000 chr7B 731961441 731962211 770 False 566.0 566 80.180 3149 3913 1 chr7B.!!$F1 764
7 TraesCS4B01G098000 chrUn 88429641 88430412 771 False 566.0 566 80.155 3149 3913 1 chrUn.!!$F1 764
8 TraesCS4B01G098000 chrUn 160383506 160384277 771 False 566.0 566 80.155 3149 3913 1 chrUn.!!$F2 764

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
861 878 0.247736 ATGGAGCGCGTTCTTCTTCT 59.752 50.0 22.36 0.00 0.00 2.85 F
1323 1353 0.573987 CGTAGATCGTCGTCTGCGTA 59.426 55.0 19.13 0.00 45.34 4.42 F
1609 1643 0.608640 AGCCTTACTTCCTGGACGTG 59.391 55.0 15.43 2.88 0.00 4.49 F
3033 3085 0.972134 TGCTGGGAACTCAGACTCTG 59.028 55.0 5.83 0.00 36.93 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2070 1.746220 TGTGGCACCTACAACAACAAC 59.254 47.619 16.26 0.0 0.0 3.32 R
3037 3089 0.773644 AGGCATTCAGTTCAGGTGGT 59.226 50.000 0.00 0.0 0.0 4.16 R
3038 3090 1.171308 CAGGCATTCAGTTCAGGTGG 58.829 55.000 0.00 0.0 0.0 4.61 R
4289 4359 0.253894 CTCCCATGACCATGAGTGCA 59.746 55.000 11.28 0.0 41.2 4.57 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
30 31 5.807520 TCGATAAAAGAGAAGTCAGATGTGC 59.192 40.000 0.00 0.00 0.00 4.57
83 84 8.715191 AAAATGTTGTGCAAAATTTAGACAGA 57.285 26.923 11.98 0.00 0.00 3.41
141 142 4.310769 AGAGAAGTGAAAACGACATCAGG 58.689 43.478 0.00 0.00 0.00 3.86
160 161 3.891049 AGGCCATCAATAGGACTGAAAC 58.109 45.455 5.01 0.00 44.84 2.78
214 215 0.798771 GCGTCTCTCCGTGCTAGTTG 60.799 60.000 0.00 0.00 0.00 3.16
220 221 0.732880 CTCCGTGCTAGTTGACGTGG 60.733 60.000 0.00 0.00 33.66 4.94
276 277 2.178912 TGGTCGTTGGTCTCCATTTC 57.821 50.000 0.00 0.00 31.53 2.17
309 310 7.105588 AGAAAATGCAAGGAAAATTATCCACC 58.894 34.615 0.00 0.00 42.27 4.61
390 400 5.173664 TGCACACAATTTTCATGTTTGACA 58.826 33.333 0.00 0.00 31.69 3.58
391 401 5.640783 TGCACACAATTTTCATGTTTGACAA 59.359 32.000 0.00 0.00 31.69 3.18
479 494 2.113139 AACACAGGGTTCGCCTGG 59.887 61.111 11.61 0.00 39.38 4.45
486 501 0.323451 AGGGTTCGCCTGGATTTTCC 60.323 55.000 0.00 0.00 37.45 3.13
510 525 3.065233 GCACATTGAATATCCAGCGAACA 59.935 43.478 0.00 0.00 0.00 3.18
513 528 4.212004 ACATTGAATATCCAGCGAACATCG 59.788 41.667 0.00 0.00 43.89 3.84
521 536 1.267532 CCAGCGAACATCGGATTTTCG 60.268 52.381 26.51 26.51 43.92 3.46
588 604 8.827832 ATGAGGATGGAAATTTAGTTGATGAA 57.172 30.769 0.00 0.00 0.00 2.57
602 618 8.565896 TTAGTTGATGAACATAGCAAATCTGT 57.434 30.769 0.00 0.00 34.17 3.41
662 679 3.059188 CCGTGCTCGTCAACTAAATTTGT 60.059 43.478 7.47 0.00 35.01 2.83
666 683 6.400621 CGTGCTCGTCAACTAAATTTGTCATA 60.401 38.462 0.00 0.00 0.00 2.15
668 685 7.962918 GTGCTCGTCAACTAAATTTGTCATATT 59.037 33.333 0.00 0.00 0.00 1.28
670 687 8.175069 GCTCGTCAACTAAATTTGTCATATTCA 58.825 33.333 0.00 0.00 0.00 2.57
687 704 9.040543 GTCATATTCACGTCAATATAAATTGCG 57.959 33.333 4.24 10.92 41.96 4.85
726 743 3.018856 TGCCATGCCTAAAACTCTGATG 58.981 45.455 0.00 0.00 0.00 3.07
727 744 3.282021 GCCATGCCTAAAACTCTGATGA 58.718 45.455 0.00 0.00 0.00 2.92
778 795 9.158097 AGAATCTCTCTCTTTCTAGCCAATAAT 57.842 33.333 0.00 0.00 0.00 1.28
861 878 0.247736 ATGGAGCGCGTTCTTCTTCT 59.752 50.000 22.36 0.00 0.00 2.85
884 902 2.027469 CCCACTATAAATACCCCTCGCC 60.027 54.545 0.00 0.00 0.00 5.54
987 1006 4.697756 CGCCGCCACCTTCCTTCA 62.698 66.667 0.00 0.00 0.00 3.02
1173 1195 3.885521 GGGTACGCGGTCTCCTCG 61.886 72.222 12.47 0.00 0.00 4.63
1198 1220 1.064463 TGCCCTGATCAGATTGGGTTC 60.064 52.381 24.62 6.39 41.59 3.62
1216 1238 3.007723 GGTTCGTTCTTAGGATATCCCCC 59.992 52.174 18.56 0.00 36.42 5.40
1232 1254 1.227823 CCCGGTTCTGTTCTGTGCA 60.228 57.895 0.00 0.00 0.00 4.57
1233 1255 0.817634 CCCGGTTCTGTTCTGTGCAA 60.818 55.000 0.00 0.00 0.00 4.08
1241 1268 4.212143 TCTGTTCTGTGCAAGCAGATAT 57.788 40.909 7.76 0.00 43.99 1.63
1262 1289 5.859205 ATGCAGATCTTTGGGGTTTATTC 57.141 39.130 0.00 0.00 0.00 1.75
1271 1298 2.243810 TGGGGTTTATTCGCAGCTTTT 58.756 42.857 0.00 0.00 0.00 2.27
1279 1306 1.919918 TTCGCAGCTTTTGTTGGTTG 58.080 45.000 0.00 0.00 0.00 3.77
1323 1353 0.573987 CGTAGATCGTCGTCTGCGTA 59.426 55.000 19.13 0.00 45.34 4.42
1425 1456 1.679032 GCCTTTTGTCCGTCTGCCTAT 60.679 52.381 0.00 0.00 0.00 2.57
1426 1457 2.711542 CCTTTTGTCCGTCTGCCTATT 58.288 47.619 0.00 0.00 0.00 1.73
1427 1458 3.081804 CCTTTTGTCCGTCTGCCTATTT 58.918 45.455 0.00 0.00 0.00 1.40
1428 1459 4.258543 CCTTTTGTCCGTCTGCCTATTTA 58.741 43.478 0.00 0.00 0.00 1.40
1581 1615 1.185315 GTCACCATGAACATTGGGGG 58.815 55.000 0.00 0.00 0.00 5.40
1609 1643 0.608640 AGCCTTACTTCCTGGACGTG 59.391 55.000 15.43 2.88 0.00 4.49
1624 1658 4.760047 GTGGACACCGGCAGCGAT 62.760 66.667 0.00 0.00 0.00 4.58
1660 1694 4.660938 GACGCCCCCTGCCAAAGT 62.661 66.667 0.00 0.00 36.24 2.66
1699 1733 5.298989 ACGCCCCAATGTTATATCTTACA 57.701 39.130 0.00 0.00 0.00 2.41
1821 1863 7.801783 GTGTTAAAAGTAGCATGTACCAACTTC 59.198 37.037 0.00 0.00 30.37 3.01
1868 1910 6.869315 TGTGATCTTTTCCGTCAAAACATA 57.131 33.333 0.00 0.00 30.42 2.29
1912 1954 3.096489 TCTTGCTTGGTTTGCATCAAC 57.904 42.857 0.00 0.00 40.34 3.18
1953 1995 6.869206 TCCACTACTGGCTTAATTCTAGTT 57.131 37.500 0.00 0.00 37.49 2.24
1968 2010 5.560722 TTCTAGTTCCAGATTTGGTGTGA 57.439 39.130 1.59 0.00 45.26 3.58
2007 2051 2.879208 TTCCTTTCCCCAGGGTTTTT 57.121 45.000 4.22 0.00 34.24 1.94
2244 2288 2.699954 GAATTCATCCACTGTCCGTGT 58.300 47.619 0.00 0.00 42.20 4.49
2263 2307 2.158726 TGTCAACCTCACCTTTGGGTAC 60.159 50.000 0.00 0.00 45.41 3.34
2275 2319 5.944007 CACCTTTGGGTACTAATATATGCCC 59.056 44.000 0.00 0.00 45.41 5.36
2345 2389 9.598517 TTGATGTTTAATTGCTTCTCTTTTTGT 57.401 25.926 0.00 0.00 0.00 2.83
2346 2390 9.033481 TGATGTTTAATTGCTTCTCTTTTTGTG 57.967 29.630 0.00 0.00 0.00 3.33
2527 2572 1.187087 GAGGCTTCCTCTTCTTCGGA 58.813 55.000 5.65 0.00 46.41 4.55
2743 2789 5.374154 TGGACCTAATGAAATGGCCCTATTA 59.626 40.000 0.00 0.00 0.00 0.98
2808 2855 1.466167 TCTCATCTTCTTGCGCTTTGC 59.534 47.619 9.73 0.00 46.70 3.68
2922 2972 6.141560 TCAGTCTATCATCAAGCAGTGTAG 57.858 41.667 0.00 0.00 0.00 2.74
2934 2984 9.874215 CATCAAGCAGTGTAGTTCATATTAATG 57.126 33.333 0.00 0.00 0.00 1.90
2981 3031 8.068892 TCAGAAAAAGGGTAAAAACTTTAGCA 57.931 30.769 9.74 0.00 35.99 3.49
3030 3082 3.297134 TTTTTGCTGGGAACTCAGACT 57.703 42.857 5.83 0.00 36.93 3.24
3031 3083 2.550830 TTTGCTGGGAACTCAGACTC 57.449 50.000 5.83 0.00 36.93 3.36
3032 3084 1.722034 TTGCTGGGAACTCAGACTCT 58.278 50.000 5.83 0.00 36.93 3.24
3033 3085 0.972134 TGCTGGGAACTCAGACTCTG 59.028 55.000 5.83 0.00 36.93 3.35
3034 3086 0.972883 GCTGGGAACTCAGACTCTGT 59.027 55.000 5.83 0.00 36.93 3.41
3035 3087 1.346068 GCTGGGAACTCAGACTCTGTT 59.654 52.381 5.83 0.00 36.93 3.16
3036 3088 2.224402 GCTGGGAACTCAGACTCTGTTT 60.224 50.000 5.83 1.28 36.93 2.83
3037 3089 3.006967 GCTGGGAACTCAGACTCTGTTTA 59.993 47.826 5.83 0.00 36.93 2.01
3038 3090 4.561105 CTGGGAACTCAGACTCTGTTTAC 58.439 47.826 5.94 2.15 36.93 2.01
3212 3269 2.862347 CTTCGACCGACGCCCACTAC 62.862 65.000 0.00 0.00 42.26 2.73
3384 3441 4.096532 TCGGATACTTGTCTTGTAGCTCAG 59.903 45.833 0.00 0.00 0.00 3.35
3535 3592 4.643784 GGCAAGAATTCTGTCATGGAGATT 59.356 41.667 9.17 0.00 0.00 2.40
4051 4121 2.097825 ACATGAGCCTGAGGAAAATGC 58.902 47.619 0.65 0.00 0.00 3.56
4112 4182 9.935241 AGGCAGATAAAGTTACTGATATGTATG 57.065 33.333 0.00 0.48 34.07 2.39
4160 4230 8.651389 TGGAGTCTATATTTTACCATCTCCTTG 58.349 37.037 0.00 0.00 39.44 3.61
4234 4304 0.592637 TGGTTGCAGAACTGAATGCG 59.407 50.000 5.97 0.00 45.54 4.73
4254 4324 2.597305 CGGCACATACTGAACGACTTAC 59.403 50.000 0.00 0.00 0.00 2.34
4255 4325 3.672511 CGGCACATACTGAACGACTTACT 60.673 47.826 0.00 0.00 0.00 2.24
4256 4326 3.612860 GGCACATACTGAACGACTTACTG 59.387 47.826 0.00 0.00 0.00 2.74
4258 4328 5.103000 GCACATACTGAACGACTTACTGAT 58.897 41.667 0.00 0.00 0.00 2.90
4259 4329 5.577164 GCACATACTGAACGACTTACTGATT 59.423 40.000 0.00 0.00 0.00 2.57
4260 4330 6.454318 GCACATACTGAACGACTTACTGATTG 60.454 42.308 0.00 0.00 0.00 2.67
4262 4332 4.258702 ACTGAACGACTTACTGATTGCT 57.741 40.909 0.00 0.00 0.00 3.91
4263 4333 3.990469 ACTGAACGACTTACTGATTGCTG 59.010 43.478 0.00 0.00 0.00 4.41
4267 4337 3.579709 ACGACTTACTGATTGCTGACTG 58.420 45.455 0.00 0.00 0.00 3.51
4268 4338 3.255888 ACGACTTACTGATTGCTGACTGA 59.744 43.478 0.00 0.00 0.00 3.41
4269 4339 4.081972 ACGACTTACTGATTGCTGACTGAT 60.082 41.667 0.00 0.00 0.00 2.90
4270 4340 4.267214 CGACTTACTGATTGCTGACTGATG 59.733 45.833 0.00 0.00 0.00 3.07
4271 4341 5.157940 ACTTACTGATTGCTGACTGATGT 57.842 39.130 0.00 0.00 0.00 3.06
4272 4342 4.934001 ACTTACTGATTGCTGACTGATGTG 59.066 41.667 0.00 0.00 0.00 3.21
4274 4344 4.217836 ACTGATTGCTGACTGATGTGAT 57.782 40.909 0.00 0.00 0.00 3.06
4278 4348 7.503549 ACTGATTGCTGACTGATGTGATATAA 58.496 34.615 0.00 0.00 0.00 0.98
4280 4350 9.649167 CTGATTGCTGACTGATGTGATATAATA 57.351 33.333 0.00 0.00 0.00 0.98
4284 4354 8.260270 TGCTGACTGATGTGATATAATAATGC 57.740 34.615 0.00 0.00 0.00 3.56
4285 4355 8.098912 TGCTGACTGATGTGATATAATAATGCT 58.901 33.333 0.00 0.00 0.00 3.79
4286 4356 9.591792 GCTGACTGATGTGATATAATAATGCTA 57.408 33.333 0.00 0.00 0.00 3.49
4304 4374 4.941325 GCTATATGCACTCATGGTCATG 57.059 45.455 4.67 4.67 42.31 3.07
4305 4375 3.688185 GCTATATGCACTCATGGTCATGG 59.312 47.826 10.61 4.91 42.31 3.66
4306 4376 2.643995 TATGCACTCATGGTCATGGG 57.356 50.000 9.11 9.11 44.73 4.00
4307 4377 0.921166 ATGCACTCATGGTCATGGGA 59.079 50.000 16.79 0.80 41.81 4.37
4308 4378 0.253894 TGCACTCATGGTCATGGGAG 59.746 55.000 16.79 10.36 41.81 4.30
4309 4379 0.254178 GCACTCATGGTCATGGGAGT 59.746 55.000 16.79 8.32 41.81 3.85
4310 4380 1.745141 GCACTCATGGTCATGGGAGTC 60.745 57.143 16.79 3.19 41.81 3.36
4311 4381 1.556451 CACTCATGGTCATGGGAGTCA 59.444 52.381 16.79 0.00 41.81 3.41
4312 4382 1.556911 ACTCATGGTCATGGGAGTCAC 59.443 52.381 16.79 0.00 41.81 3.67
4313 4383 1.556451 CTCATGGTCATGGGAGTCACA 59.444 52.381 4.91 0.00 41.81 3.58
4314 4384 1.984424 TCATGGTCATGGGAGTCACAA 59.016 47.619 0.00 0.00 39.24 3.33
4315 4385 2.086869 CATGGTCATGGGAGTCACAAC 58.913 52.381 0.00 0.00 35.24 3.32
4346 4416 1.237285 ACTGAGGAATTGCACGTGCC 61.237 55.000 35.72 20.83 41.18 5.01
4355 4425 0.462375 TTGCACGTGCCGACCTATAT 59.538 50.000 35.72 0.00 41.18 0.86
4358 4428 2.297880 TGCACGTGCCGACCTATATTAT 59.702 45.455 35.72 0.00 41.18 1.28
4384 4454 7.716768 TCTAACATTGAACACAAATCGTACA 57.283 32.000 0.00 0.00 0.00 2.90
4389 4459 7.648142 ACATTGAACACAAATCGTACAAAGAT 58.352 30.769 0.00 0.00 0.00 2.40
4407 4477 3.402110 AGATTTGTGTTCTGATCACGCA 58.598 40.909 12.70 3.47 38.48 5.24
4421 4491 4.158579 TGATCACGCAGTCTCTTACAAGAT 59.841 41.667 0.00 0.00 41.61 2.40
4429 4499 6.606768 GCAGTCTCTTACAAGATGAAAAAGG 58.393 40.000 0.00 0.00 33.93 3.11
4430 4500 6.348868 GCAGTCTCTTACAAGATGAAAAAGGG 60.349 42.308 0.00 0.00 33.93 3.95
4432 4502 6.712547 AGTCTCTTACAAGATGAAAAAGGGTG 59.287 38.462 0.00 0.00 33.93 4.61
4440 4510 4.410099 AGATGAAAAAGGGTGAGATGCAA 58.590 39.130 0.00 0.00 0.00 4.08
4465 4536 4.517075 TCAAATTTGCACAGATCACGGTTA 59.483 37.500 13.54 0.00 0.00 2.85
4475 4546 3.997021 CAGATCACGGTTAAGCTGTTTCT 59.003 43.478 2.76 5.05 33.66 2.52
4476 4547 4.452455 CAGATCACGGTTAAGCTGTTTCTT 59.548 41.667 2.76 0.00 33.66 2.52
4485 4556 6.631636 CGGTTAAGCTGTTTCTTAGTTTGAAC 59.368 38.462 2.76 0.00 31.01 3.18
4528 4599 4.141321 ACCAATCTATCTGATGGCATGTGT 60.141 41.667 3.81 0.00 35.21 3.72
4530 4601 5.048921 CCAATCTATCTGATGGCATGTGTTC 60.049 44.000 3.81 0.00 35.21 3.18
4547 4618 5.353111 TGTGTTCAACATTCTAGACGTTCA 58.647 37.500 0.00 0.00 32.36 3.18
4566 4637 5.569059 CGTTCAAACTGCTGGTATGAAAATC 59.431 40.000 8.69 0.08 32.36 2.17
4617 4688 9.685828 GGTTGTAACCGTATACCGTAATAATAA 57.314 33.333 0.00 0.00 39.66 1.40
4798 4882 6.241645 AGTAGAAAATGACAGAAAAGGGAGG 58.758 40.000 0.00 0.00 0.00 4.30
4846 4930 6.037786 TCGAGGTGAGATACAAATCAAAGT 57.962 37.500 0.00 0.00 34.28 2.66
4853 4937 7.041098 GGTGAGATACAAATCAAAGTCAGTTGT 60.041 37.037 0.00 0.00 36.45 3.32
4884 4968 2.283298 CTGAATGCCGCTACTGTCATT 58.717 47.619 0.00 0.00 32.44 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.006165 CCGCACATCTGACTTCTCTTTTATC 59.994 44.000 0.00 0.00 0.00 1.75
10 11 4.245660 CCGCACATCTGACTTCTCTTTTA 58.754 43.478 0.00 0.00 0.00 1.52
15 16 1.354040 CACCGCACATCTGACTTCTC 58.646 55.000 0.00 0.00 0.00 2.87
16 17 0.671781 GCACCGCACATCTGACTTCT 60.672 55.000 0.00 0.00 0.00 2.85
17 18 1.790387 GCACCGCACATCTGACTTC 59.210 57.895 0.00 0.00 0.00 3.01
30 31 0.179137 TAAGATGTCTCTGCGCACCG 60.179 55.000 5.66 0.00 0.00 4.94
44 45 7.178274 TGCACAACATTTTTCAGGGTATAAGAT 59.822 33.333 0.00 0.00 0.00 2.40
83 84 1.617357 GTGGGACTAAGACGGACAAGT 59.383 52.381 0.00 0.00 0.00 3.16
141 142 3.891049 AGGTTTCAGTCCTATTGATGGC 58.109 45.455 0.00 0.00 33.04 4.40
160 161 3.005554 CAGACCATCACTTGCTTGTAGG 58.994 50.000 0.00 0.00 0.00 3.18
208 209 4.045104 GCTATCATGTCCACGTCAACTAG 58.955 47.826 0.00 0.00 0.00 2.57
214 215 2.860735 GAGTTGCTATCATGTCCACGTC 59.139 50.000 0.00 0.00 0.00 4.34
220 221 4.502282 CGAGACTTGAGTTGCTATCATGTC 59.498 45.833 17.04 17.04 45.33 3.06
276 277 5.964958 TTCCTTGCATTTTCTTCACCTAG 57.035 39.130 0.00 0.00 0.00 3.02
368 377 5.715429 TGTCAAACATGAAAATTGTGTGC 57.285 34.783 0.00 0.00 33.21 4.57
479 494 5.221224 TGGATATTCAATGTGCCGGAAAATC 60.221 40.000 5.05 0.00 0.00 2.17
486 501 1.069703 CGCTGGATATTCAATGTGCCG 60.070 52.381 0.00 0.00 0.00 5.69
491 506 4.377738 CCGATGTTCGCTGGATATTCAATG 60.378 45.833 0.00 0.00 38.82 2.82
510 525 6.072508 CCATTTGTCATATCCGAAAATCCGAT 60.073 38.462 0.00 0.00 0.00 4.18
513 528 6.633500 TCCATTTGTCATATCCGAAAATCC 57.367 37.500 0.00 0.00 0.00 3.01
545 560 9.212641 CATCCTCATCTAACATAGTTTACCATG 57.787 37.037 0.00 0.00 0.00 3.66
563 578 8.689972 GTTCATCAACTAAATTTCCATCCTCAT 58.310 33.333 0.00 0.00 0.00 2.90
588 604 8.743085 AATGAACTGATACAGATTTGCTATGT 57.257 30.769 5.76 0.00 35.18 2.29
616 632 8.711457 CGGCAATTTTCTGACAAAAGAATAATT 58.289 29.630 0.00 0.00 36.12 1.40
617 633 7.872483 ACGGCAATTTTCTGACAAAAGAATAAT 59.128 29.630 0.00 0.00 36.12 1.28
620 636 5.463061 CACGGCAATTTTCTGACAAAAGAAT 59.537 36.000 0.00 0.00 36.12 2.40
622 638 4.358851 CACGGCAATTTTCTGACAAAAGA 58.641 39.130 0.00 0.00 0.00 2.52
629 646 0.516877 CGAGCACGGCAATTTTCTGA 59.483 50.000 0.00 0.00 35.72 3.27
640 657 3.059188 ACAAATTTAGTTGACGAGCACGG 60.059 43.478 8.74 0.00 36.57 4.94
662 679 8.983724 TCGCAATTTATATTGACGTGAATATGA 58.016 29.630 24.80 16.81 43.12 2.15
666 683 6.481976 TCCTCGCAATTTATATTGACGTGAAT 59.518 34.615 5.38 5.38 43.12 2.57
668 685 5.353111 TCCTCGCAATTTATATTGACGTGA 58.647 37.500 9.76 10.00 43.12 4.35
670 687 6.671614 TTTCCTCGCAATTTATATTGACGT 57.328 33.333 9.76 0.00 43.12 4.34
687 704 4.116238 TGGCAAATTGAACGTTTTTCCTC 58.884 39.130 0.46 0.00 0.00 3.71
802 819 3.181458 TGCCCGGTTACTCATTTATCTCC 60.181 47.826 0.00 0.00 0.00 3.71
856 873 4.349930 GGGGTATTTATAGTGGGCAGAAGA 59.650 45.833 0.00 0.00 0.00 2.87
861 878 2.635915 CGAGGGGTATTTATAGTGGGCA 59.364 50.000 0.00 0.00 0.00 5.36
1173 1195 2.004408 AATCTGATCAGGGCAGGGGC 62.004 60.000 22.42 0.00 40.13 5.80
1198 1220 1.549170 CCGGGGGATATCCTAAGAACG 59.451 57.143 21.18 14.93 35.95 3.95
1216 1238 0.040958 GCTTGCACAGAACAGAACCG 60.041 55.000 0.00 0.00 0.00 4.44
1241 1268 3.694072 CGAATAAACCCCAAAGATCTGCA 59.306 43.478 0.00 0.00 0.00 4.41
1262 1289 0.179113 ACCAACCAACAAAAGCTGCG 60.179 50.000 0.00 0.00 0.00 5.18
1271 1298 2.494073 GTCAGAAACCAACCAACCAACA 59.506 45.455 0.00 0.00 0.00 3.33
1279 1306 1.606668 TGCATTCGTCAGAAACCAACC 59.393 47.619 0.00 0.00 40.15 3.77
1307 1337 1.090625 AGCTACGCAGACGACGATCT 61.091 55.000 0.00 0.00 43.93 2.75
1323 1353 4.087892 ATCAACGCCCGCAGAGCT 62.088 61.111 0.00 0.00 0.00 4.09
1536 1570 4.043200 GCCTGCAGAAACGGCACC 62.043 66.667 17.39 0.00 43.25 5.01
1609 1643 4.148825 AGATCGCTGCCGGTGTCC 62.149 66.667 1.90 0.00 34.56 4.02
1624 1658 2.346365 CACTGCAGCCAGCTGAGA 59.654 61.111 23.40 7.64 46.30 3.27
1675 1709 6.828788 TGTAAGATATAACATTGGGGCGTAA 58.171 36.000 0.00 0.00 0.00 3.18
1699 1733 6.325919 TCTCCGTGCAATTCAAGTAATTTT 57.674 33.333 0.00 0.00 35.54 1.82
1705 1743 3.820467 TGAATTCTCCGTGCAATTCAAGT 59.180 39.130 7.05 0.00 43.06 3.16
1711 1749 2.749621 GGAGTTGAATTCTCCGTGCAAT 59.250 45.455 7.05 0.00 41.36 3.56
1784 1824 7.671302 TGCTACTTTTAACACAGAAGAGAGAT 58.329 34.615 0.00 0.00 0.00 2.75
1821 1863 8.504005 ACAATCTTAAACTGGAAATGTAAGTCG 58.496 33.333 0.00 0.00 0.00 4.18
1912 1954 6.090483 AGTGGATTAGGATAATCAGTGACG 57.910 41.667 10.73 0.00 0.00 4.35
1953 1995 3.229293 TGCATTTCACACCAAATCTGGA 58.771 40.909 0.00 0.00 46.92 3.86
2007 2051 6.729690 ACAACCAGGAAGAAAATCAATCAA 57.270 33.333 0.00 0.00 0.00 2.57
2026 2070 1.746220 TGTGGCACCTACAACAACAAC 59.254 47.619 16.26 0.00 0.00 3.32
2275 2319 7.701924 CACTACCAAGGCAATGTAACATAAATG 59.298 37.037 0.00 0.00 0.00 2.32
2343 2387 2.171027 TGATCATATCCACAGCTGCACA 59.829 45.455 15.27 0.00 0.00 4.57
2344 2388 2.806818 CTGATCATATCCACAGCTGCAC 59.193 50.000 15.27 0.00 0.00 4.57
2345 2389 3.121738 CTGATCATATCCACAGCTGCA 57.878 47.619 15.27 0.00 0.00 4.41
2527 2572 3.082548 CGAGGTGGGTACGATATCATCT 58.917 50.000 3.12 0.00 0.00 2.90
2743 2789 8.467402 TTTTTACGTTGTCATGTTGTTTCAAT 57.533 26.923 0.00 0.00 0.00 2.57
3030 3082 4.764050 TTCAGTTCAGGTGGTAAACAGA 57.236 40.909 0.00 0.00 0.00 3.41
3031 3083 4.320494 GCATTCAGTTCAGGTGGTAAACAG 60.320 45.833 0.00 0.00 0.00 3.16
3032 3084 3.568007 GCATTCAGTTCAGGTGGTAAACA 59.432 43.478 0.00 0.00 0.00 2.83
3033 3085 3.057526 GGCATTCAGTTCAGGTGGTAAAC 60.058 47.826 0.00 0.00 0.00 2.01
3034 3086 3.153919 GGCATTCAGTTCAGGTGGTAAA 58.846 45.455 0.00 0.00 0.00 2.01
3035 3087 2.375174 AGGCATTCAGTTCAGGTGGTAA 59.625 45.455 0.00 0.00 0.00 2.85
3036 3088 1.985159 AGGCATTCAGTTCAGGTGGTA 59.015 47.619 0.00 0.00 0.00 3.25
3037 3089 0.773644 AGGCATTCAGTTCAGGTGGT 59.226 50.000 0.00 0.00 0.00 4.16
3038 3090 1.171308 CAGGCATTCAGTTCAGGTGG 58.829 55.000 0.00 0.00 0.00 4.61
3212 3269 1.750399 CCTCCATTGGCTTCACCCG 60.750 63.158 0.00 0.00 37.83 5.28
3720 3781 6.984474 ACTGTGTGTATGAATTTATACCTCCG 59.016 38.462 15.55 8.39 33.56 4.63
4051 4121 0.898320 TTCTCCTCTCCTTTCTGCCG 59.102 55.000 0.00 0.00 0.00 5.69
4112 4182 5.009410 CCATTTCATTATGAACAGGAGGAGC 59.991 44.000 15.64 0.00 35.89 4.70
4160 4230 9.352784 CATATAGAAAGATAGAGCTGCAAGTAC 57.647 37.037 1.02 0.00 35.30 2.73
4234 4304 3.612860 CAGTAAGTCGTTCAGTATGTGCC 59.387 47.826 0.00 0.00 37.40 5.01
4254 4324 7.958053 TTATATCACATCAGTCAGCAATCAG 57.042 36.000 0.00 0.00 0.00 2.90
4258 4328 8.724229 GCATTATTATATCACATCAGTCAGCAA 58.276 33.333 0.00 0.00 0.00 3.91
4259 4329 8.098912 AGCATTATTATATCACATCAGTCAGCA 58.901 33.333 0.00 0.00 0.00 4.41
4260 4330 8.489990 AGCATTATTATATCACATCAGTCAGC 57.510 34.615 0.00 0.00 0.00 4.26
4282 4352 4.320870 CATGACCATGAGTGCATATAGCA 58.679 43.478 4.03 0.00 45.79 3.49
4283 4353 3.688185 CCATGACCATGAGTGCATATAGC 59.312 47.826 11.28 0.00 41.20 2.97
4284 4354 4.019950 TCCCATGACCATGAGTGCATATAG 60.020 45.833 11.28 0.00 41.20 1.31
4285 4355 3.909364 TCCCATGACCATGAGTGCATATA 59.091 43.478 11.28 0.00 41.20 0.86
4286 4356 2.712627 TCCCATGACCATGAGTGCATAT 59.287 45.455 11.28 0.00 41.20 1.78
4287 4357 2.105306 CTCCCATGACCATGAGTGCATA 59.895 50.000 11.28 0.00 41.20 3.14
4288 4358 0.921166 TCCCATGACCATGAGTGCAT 59.079 50.000 11.28 0.00 41.20 3.96
4289 4359 0.253894 CTCCCATGACCATGAGTGCA 59.746 55.000 11.28 0.00 41.20 4.57
4291 4361 1.556451 TGACTCCCATGACCATGAGTG 59.444 52.381 11.28 2.29 41.20 3.51
4292 4362 1.556911 GTGACTCCCATGACCATGAGT 59.443 52.381 11.28 7.63 41.20 3.41
4295 4365 2.086869 GTTGTGACTCCCATGACCATG 58.913 52.381 0.00 3.11 38.51 3.66
4296 4366 1.988107 AGTTGTGACTCCCATGACCAT 59.012 47.619 0.00 0.00 0.00 3.55
4297 4367 1.434188 AGTTGTGACTCCCATGACCA 58.566 50.000 0.00 0.00 0.00 4.02
4298 4368 3.008049 AGTTAGTTGTGACTCCCATGACC 59.992 47.826 0.00 0.00 37.33 4.02
4299 4369 3.997021 CAGTTAGTTGTGACTCCCATGAC 59.003 47.826 0.00 0.00 37.33 3.06
4300 4370 3.646162 ACAGTTAGTTGTGACTCCCATGA 59.354 43.478 0.00 0.00 37.33 3.07
4304 4374 7.331193 CAGTATAAACAGTTAGTTGTGACTCCC 59.669 40.741 0.00 0.00 41.19 4.30
4305 4375 8.086522 TCAGTATAAACAGTTAGTTGTGACTCC 58.913 37.037 0.00 0.00 41.19 3.85
4306 4376 9.130312 CTCAGTATAAACAGTTAGTTGTGACTC 57.870 37.037 0.00 0.00 41.19 3.36
4307 4377 8.088981 CCTCAGTATAAACAGTTAGTTGTGACT 58.911 37.037 0.00 0.00 41.19 3.41
4308 4378 8.086522 TCCTCAGTATAAACAGTTAGTTGTGAC 58.913 37.037 0.00 0.00 41.19 3.67
4309 4379 8.185506 TCCTCAGTATAAACAGTTAGTTGTGA 57.814 34.615 0.00 0.00 41.19 3.58
4310 4380 8.827177 TTCCTCAGTATAAACAGTTAGTTGTG 57.173 34.615 0.00 0.00 41.19 3.33
4313 4383 8.947115 GCAATTCCTCAGTATAAACAGTTAGTT 58.053 33.333 0.00 0.00 43.89 2.24
4314 4384 8.100791 TGCAATTCCTCAGTATAAACAGTTAGT 58.899 33.333 0.00 0.00 0.00 2.24
4315 4385 8.391106 GTGCAATTCCTCAGTATAAACAGTTAG 58.609 37.037 0.00 0.00 0.00 2.34
4358 4428 8.613482 TGTACGATTTGTGTTCAATGTTAGAAA 58.387 29.630 0.00 0.00 33.32 2.52
4384 4454 4.275689 TGCGTGATCAGAACACAAATCTTT 59.724 37.500 11.10 0.00 38.04 2.52
4389 4459 2.543848 GACTGCGTGATCAGAACACAAA 59.456 45.455 11.10 0.00 38.04 2.83
4407 4477 6.712547 CACCCTTTTTCATCTTGTAAGAGACT 59.287 38.462 0.51 0.00 38.66 3.24
4421 4491 3.565307 ACTTGCATCTCACCCTTTTTCA 58.435 40.909 0.00 0.00 0.00 2.69
4429 4499 3.676646 GCAAATTTGACTTGCATCTCACC 59.323 43.478 22.31 0.00 46.78 4.02
4430 4500 4.898328 GCAAATTTGACTTGCATCTCAC 57.102 40.909 22.31 0.00 46.78 3.51
4440 4510 3.058016 CCGTGATCTGTGCAAATTTGACT 60.058 43.478 22.31 2.28 0.00 3.41
4465 4536 7.702348 GTCATTGTTCAAACTAAGAAACAGCTT 59.298 33.333 0.00 0.00 0.00 3.74
4524 4595 5.353111 TGAACGTCTAGAATGTTGAACACA 58.647 37.500 14.48 5.29 37.22 3.72
4525 4596 5.900339 TGAACGTCTAGAATGTTGAACAC 57.100 39.130 14.48 3.18 37.22 3.32
4528 4599 6.511121 GCAGTTTGAACGTCTAGAATGTTGAA 60.511 38.462 14.48 10.52 37.22 2.69
4530 4601 5.050091 AGCAGTTTGAACGTCTAGAATGTTG 60.050 40.000 14.48 3.63 37.22 3.33
4537 4608 2.755650 ACCAGCAGTTTGAACGTCTAG 58.244 47.619 0.00 0.00 0.00 2.43
4543 4614 5.863935 GGATTTTCATACCAGCAGTTTGAAC 59.136 40.000 10.74 3.07 43.40 3.18
4547 4618 4.220602 GTGGGATTTTCATACCAGCAGTTT 59.779 41.667 0.00 0.00 45.10 2.66
4645 4727 7.792374 TGCTATTAAAAGAGATGTGCTAAGG 57.208 36.000 0.00 0.00 0.00 2.69
4853 4937 5.531122 AGCGGCATTCAGTTAGATAGTTA 57.469 39.130 1.45 0.00 0.00 2.24
4884 4968 9.485206 GTTAAGACAGTACAGACTTTATTTGGA 57.515 33.333 8.13 0.00 31.73 3.53


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

AutoCloner maintained by Alex Coulton.