Multiple sequence alignment - TraesCS6D01G123500

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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 TraesCS6D01G123500 chr6D 100.000 4064 0 0 1 4064 88700471 88704534 0.000000e+00 7505
1 TraesCS6D01G123500 chr6D 90.604 894 65 7 3189 4063 27117189 27116296 0.000000e+00 1168
2 TraesCS6D01G123500 chr6D 77.204 658 109 28 1372 2001 39488706 39489350 3.010000e-91 346
3 TraesCS6D01G123500 chr6D 77.821 514 86 20 1378 1874 40061637 40061135 3.970000e-75 292
4 TraesCS6D01G123500 chr6D 78.427 445 75 15 1567 2001 39673066 39672633 1.860000e-68 270
5 TraesCS6D01G123500 chr6D 73.351 379 87 13 1165 1536 56211726 56212097 1.190000e-25 128
6 TraesCS6D01G123500 chr6B 89.489 2445 129 65 766 3150 169101295 169103671 0.000000e+00 2974
7 TraesCS6D01G123500 chr6B 77.880 651 105 29 1378 2001 91620850 91620212 6.420000e-98 368
8 TraesCS6D01G123500 chr6B 77.273 660 105 31 1372 2001 91199962 91200606 3.010000e-91 346
9 TraesCS6D01G123500 chr6B 76.155 671 111 34 1362 2000 35378316 35377663 1.420000e-79 307
10 TraesCS6D01G123500 chr6A 92.023 2131 86 34 839 2946 106697963 106700032 0.000000e+00 2916
11 TraesCS6D01G123500 chr6A 86.913 894 76 18 3186 4056 163135545 163136420 0.000000e+00 965
12 TraesCS6D01G123500 chr6A 87.540 626 77 1 1 626 106692151 106692775 0.000000e+00 723
13 TraesCS6D01G123500 chr6A 90.244 492 48 0 135 626 106667024 106667515 0.000000e+00 643
14 TraesCS6D01G123500 chr6A 77.880 651 105 26 1378 2001 51479913 51479275 6.420000e-98 368
15 TraesCS6D01G123500 chr6A 76.627 676 105 34 1362 2000 19829239 19829898 1.410000e-84 324
16 TraesCS6D01G123500 chr6A 92.381 210 12 4 2957 3164 106700080 106700287 3.070000e-76 296
17 TraesCS6D01G123500 chr6A 82.086 374 25 20 814 1157 106694641 106695002 8.600000e-72 281
18 TraesCS6D01G123500 chr6A 93.143 175 9 2 627 801 106667592 106667763 1.870000e-63 254
19 TraesCS6D01G123500 chr6A 84.135 208 16 11 814 1016 106667814 106668009 6.940000e-43 185
20 TraesCS6D01G123500 chr6A 96.842 95 3 0 627 721 106692850 106692944 4.200000e-35 159
21 TraesCS6D01G123500 chr6A 90.816 98 6 2 709 806 106694500 106694594 1.190000e-25 128
22 TraesCS6D01G123500 chr5D 93.158 877 57 3 3190 4064 278142068 278142943 0.000000e+00 1284
23 TraesCS6D01G123500 chr5D 91.480 892 52 12 3192 4064 357054339 357055225 0.000000e+00 1205
24 TraesCS6D01G123500 chr3D 90.547 878 73 5 3189 4057 123303371 123302495 0.000000e+00 1153
25 TraesCS6D01G123500 chr1B 90.279 895 61 14 3191 4064 271889320 271890209 0.000000e+00 1147
26 TraesCS6D01G123500 chr7A 89.089 889 71 12 3189 4057 91940344 91941226 0.000000e+00 1081
27 TraesCS6D01G123500 chr7D 88.851 888 76 11 3189 4056 10090634 10091518 0.000000e+00 1070
28 TraesCS6D01G123500 chr7B 90.818 795 69 4 3272 4064 721096860 721097652 0.000000e+00 1061
29 TraesCS6D01G123500 chr1D 87.401 881 102 6 3191 4064 55775074 55774196 0.000000e+00 1003
30 TraesCS6D01G123500 chr3B 79.412 238 27 12 3191 3409 756082391 756082625 9.100000e-32 148


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 TraesCS6D01G123500 chr6D 88700471 88704534 4063 False 7505.000000 7505 100.000000 1 4064 1 chr6D.!!$F3 4063
1 TraesCS6D01G123500 chr6D 27116296 27117189 893 True 1168.000000 1168 90.604000 3189 4063 1 chr6D.!!$R1 874
2 TraesCS6D01G123500 chr6D 39488706 39489350 644 False 346.000000 346 77.204000 1372 2001 1 chr6D.!!$F1 629
3 TraesCS6D01G123500 chr6D 40061135 40061637 502 True 292.000000 292 77.821000 1378 1874 1 chr6D.!!$R3 496
4 TraesCS6D01G123500 chr6B 169101295 169103671 2376 False 2974.000000 2974 89.489000 766 3150 1 chr6B.!!$F2 2384
5 TraesCS6D01G123500 chr6B 91620212 91620850 638 True 368.000000 368 77.880000 1378 2001 1 chr6B.!!$R2 623
6 TraesCS6D01G123500 chr6B 91199962 91200606 644 False 346.000000 346 77.273000 1372 2001 1 chr6B.!!$F1 629
7 TraesCS6D01G123500 chr6B 35377663 35378316 653 True 307.000000 307 76.155000 1362 2000 1 chr6B.!!$R1 638
8 TraesCS6D01G123500 chr6A 163135545 163136420 875 False 965.000000 965 86.913000 3186 4056 1 chr6A.!!$F2 870
9 TraesCS6D01G123500 chr6A 106692151 106700287 8136 False 750.500000 2916 90.281333 1 3164 6 chr6A.!!$F4 3163
10 TraesCS6D01G123500 chr6A 51479275 51479913 638 True 368.000000 368 77.880000 1378 2001 1 chr6A.!!$R1 623
11 TraesCS6D01G123500 chr6A 106667024 106668009 985 False 360.666667 643 89.174000 135 1016 3 chr6A.!!$F3 881
12 TraesCS6D01G123500 chr6A 19829239 19829898 659 False 324.000000 324 76.627000 1362 2000 1 chr6A.!!$F1 638
13 TraesCS6D01G123500 chr5D 278142068 278142943 875 False 1284.000000 1284 93.158000 3190 4064 1 chr5D.!!$F1 874
14 TraesCS6D01G123500 chr5D 357054339 357055225 886 False 1205.000000 1205 91.480000 3192 4064 1 chr5D.!!$F2 872
15 TraesCS6D01G123500 chr3D 123302495 123303371 876 True 1153.000000 1153 90.547000 3189 4057 1 chr3D.!!$R1 868
16 TraesCS6D01G123500 chr1B 271889320 271890209 889 False 1147.000000 1147 90.279000 3191 4064 1 chr1B.!!$F1 873
17 TraesCS6D01G123500 chr7A 91940344 91941226 882 False 1081.000000 1081 89.089000 3189 4057 1 chr7A.!!$F1 868
18 TraesCS6D01G123500 chr7D 10090634 10091518 884 False 1070.000000 1070 88.851000 3189 4056 1 chr7D.!!$F1 867
19 TraesCS6D01G123500 chr7B 721096860 721097652 792 False 1061.000000 1061 90.818000 3272 4064 1 chr7B.!!$F1 792
20 TraesCS6D01G123500 chr1D 55774196 55775074 878 True 1003.000000 1003 87.401000 3191 4064 1 chr1D.!!$R1 873

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
526 527 0.179018 GATCAGCCCCACCACCATAC 60.179 60.0 0.0 0.0 0.0 2.39 F
2254 7320 0.036022 AAGTGAAGACCCTGCTCAGC 59.964 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 7546 0.174617 CGTCCTGCTCTTCCTCTTCC 59.825 60.0 0.00 0.0 0.00 3.46 R
3181 8319 0.568697 GGGAGGGAGGGAGTCCTATT 59.431 60.0 9.58 0.0 46.06 1.73 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
19 20 2.735772 GCGGCCATCCTCCTGAGAA 61.736 63.158 2.24 0.00 0.00 2.87
22 23 0.536915 GGCCATCCTCCTGAGAATGC 60.537 60.000 0.00 0.00 0.00 3.56
23 24 0.182061 GCCATCCTCCTGAGAATGCA 59.818 55.000 0.00 0.00 0.00 3.96
26 27 2.105993 CCATCCTCCTGAGAATGCATCA 59.894 50.000 0.00 0.00 0.00 3.07
42 43 4.808558 TGCATCACATTTAAGGTTCTTGC 58.191 39.130 0.00 2.71 0.00 4.01
49 50 4.278419 ACATTTAAGGTTCTTGCGCTTCTT 59.722 37.500 9.73 5.90 0.00 2.52
124 125 1.291877 GCGATGTTCGAAGTGGTGCT 61.292 55.000 0.00 0.00 43.74 4.40
136 137 0.955428 GTGGTGCTTGCGAGATTGGA 60.955 55.000 4.70 0.00 0.00 3.53
184 185 3.189495 GCCATGATCTTCATCTGATGCAG 59.811 47.826 12.78 11.59 34.28 4.41
196 197 7.230849 TCATCTGATGCAGGTTTTAATGTTT 57.769 32.000 12.78 0.00 31.51 2.83
208 209 6.799925 AGGTTTTAATGTTTAATCAAGCGTCG 59.200 34.615 0.00 0.00 0.00 5.12
227 228 5.388682 GCGTCGCTAATTGTTTAGTGTAACA 60.389 40.000 10.68 0.00 43.43 2.41
230 231 7.178074 GTCGCTAATTGTTTAGTGTAACATCC 58.822 38.462 6.28 0.00 43.43 3.51
234 235 6.870971 AATTGTTTAGTGTAACATCCGTGT 57.129 33.333 0.00 0.00 41.43 4.49
305 306 2.902705 TCTTGTGGCTCGTAGTTTGT 57.097 45.000 0.00 0.00 0.00 2.83
310 311 1.218875 TGGCTCGTAGTTTGTGTGCG 61.219 55.000 0.00 0.00 0.00 5.34
318 319 2.292103 AGTTTGTGTGCGTTGCATTT 57.708 40.000 0.00 0.00 41.91 2.32
321 322 0.649475 TTGTGTGCGTTGCATTTTGC 59.351 45.000 0.00 0.00 41.91 3.68
347 348 4.274602 TCTTAACGAAACTGCCATACCA 57.725 40.909 0.00 0.00 0.00 3.25
351 352 6.879993 TCTTAACGAAACTGCCATACCAAATA 59.120 34.615 0.00 0.00 0.00 1.40
355 356 4.201910 CGAAACTGCCATACCAAATACCAG 60.202 45.833 0.00 0.00 0.00 4.00
370 371 6.147656 CCAAATACCAGTGCCATTTCTTTTTC 59.852 38.462 0.00 0.00 0.00 2.29
423 424 9.750783 ACCCGTATGAATAGTATAGTTCTGTAT 57.249 33.333 0.00 0.00 0.00 2.29
425 426 9.917872 CCGTATGAATAGTATAGTTCTGTATCG 57.082 37.037 0.00 0.00 0.00 2.92
429 430 7.306213 TGAATAGTATAGTTCTGTATCGCTGC 58.694 38.462 0.00 0.00 0.00 5.25
448 449 5.502382 CGCTGCGTTTATCATTGATGTTAGT 60.502 40.000 14.93 0.00 0.00 2.24
473 474 4.447290 TGTTTCCGACATTCACTGAAAGA 58.553 39.130 1.05 0.00 32.76 2.52
483 484 7.095649 CGACATTCACTGAAAGATCTTGTTGTA 60.096 37.037 9.17 0.00 37.43 2.41
526 527 0.179018 GATCAGCCCCACCACCATAC 60.179 60.000 0.00 0.00 0.00 2.39
545 546 3.961480 ACGTCCATGTTCTTCTCATCA 57.039 42.857 0.00 0.00 0.00 3.07
551 552 6.703165 CGTCCATGTTCTTCTCATCATTATGA 59.297 38.462 0.00 0.00 39.87 2.15
595 596 4.439305 TTGCAACCATGTTTAGAGCATC 57.561 40.909 0.00 0.00 0.00 3.91
616 617 2.202295 TCAGCTCGGCAAACAAAAAC 57.798 45.000 0.00 0.00 0.00 2.43
632 709 4.339814 ACAAAAACGACATGGCTCCTTTTA 59.660 37.500 0.00 0.00 0.00 1.52
658 735 3.273434 TCTACCATCAAAGTGCAGCATC 58.727 45.455 0.00 0.00 0.00 3.91
739 2384 7.937394 GGCACATGATTAGTTTAGTTACCCTAT 59.063 37.037 0.00 0.00 0.00 2.57
740 2385 9.991906 GCACATGATTAGTTTAGTTACCCTATA 57.008 33.333 0.00 0.00 0.00 1.31
806 2454 5.224888 AGTCAAACTCGCACGATTACTTTA 58.775 37.500 0.00 0.00 0.00 1.85
810 2458 6.201425 TCAAACTCGCACGATTACTTTAGTTT 59.799 34.615 0.00 0.00 36.61 2.66
811 2459 7.381948 TCAAACTCGCACGATTACTTTAGTTTA 59.618 33.333 0.00 0.00 34.97 2.01
812 2460 7.642071 AACTCGCACGATTACTTTAGTTTAA 57.358 32.000 0.00 0.00 0.00 1.52
813 2461 7.823149 ACTCGCACGATTACTTTAGTTTAAT 57.177 32.000 0.00 0.00 0.00 1.40
814 2462 8.915871 ACTCGCACGATTACTTTAGTTTAATA 57.084 30.769 0.00 0.00 0.00 0.98
815 2463 9.357652 ACTCGCACGATTACTTTAGTTTAATAA 57.642 29.630 0.00 0.00 0.00 1.40
816 2464 9.615779 CTCGCACGATTACTTTAGTTTAATAAC 57.384 33.333 0.00 0.00 34.36 1.89
817 2465 9.357652 TCGCACGATTACTTTAGTTTAATAACT 57.642 29.630 0.00 0.00 46.18 2.24
818 2466 9.615779 CGCACGATTACTTTAGTTTAATAACTC 57.384 33.333 0.00 0.00 43.45 3.01
848 2536 4.687215 GTGCACGCAGGGAGCAGA 62.687 66.667 9.90 0.00 46.13 4.26
874 5857 3.495670 AATCGAACCAGACGAGAAGAG 57.504 47.619 0.00 0.00 42.81 2.85
887 5870 6.586463 CAGACGAGAAGAGCATTAAAACACTA 59.414 38.462 0.00 0.00 0.00 2.74
1007 5996 1.979693 ACTCCCCTCTCGACACTGC 60.980 63.158 0.00 0.00 0.00 4.40
1019 6008 3.790437 CACTGCTCGGCCCTCCAT 61.790 66.667 0.00 0.00 0.00 3.41
1361 6380 3.812019 TTCGACTCGAGCGCCCTC 61.812 66.667 13.61 0.60 37.14 4.30
1892 6941 0.674581 TCCTGCAGAGCATTGGAACG 60.675 55.000 17.39 0.00 38.13 3.95
1894 6943 1.376543 CTGCAGAGCATTGGAACGAT 58.623 50.000 8.42 0.00 38.13 3.73
1897 6946 2.279741 GCAGAGCATTGGAACGATACA 58.720 47.619 0.00 0.00 0.00 2.29
2007 7062 2.288457 ACCATCATCAAGGTATCGCTCG 60.288 50.000 0.00 0.00 36.07 5.03
2031 7088 3.211000 ACTCCCCATCCTATTTCTCCTCT 59.789 47.826 0.00 0.00 0.00 3.69
2046 7103 6.591750 TTCTCCTCTTAGTGGTTAGACAAG 57.408 41.667 0.00 0.00 0.00 3.16
2078 7139 2.124570 GGATGCGATGGTGTGGCT 60.125 61.111 0.00 0.00 32.08 4.75
2079 7140 1.750399 GGATGCGATGGTGTGGCTT 60.750 57.895 0.00 0.00 32.08 4.35
2080 7141 1.315257 GGATGCGATGGTGTGGCTTT 61.315 55.000 0.00 0.00 32.08 3.51
2081 7142 1.378531 GATGCGATGGTGTGGCTTTA 58.621 50.000 0.00 0.00 32.08 1.85
2082 7143 1.064060 GATGCGATGGTGTGGCTTTAC 59.936 52.381 0.00 0.00 32.08 2.01
2083 7144 0.250510 TGCGATGGTGTGGCTTTACA 60.251 50.000 0.00 0.00 32.08 2.41
2084 7145 0.878416 GCGATGGTGTGGCTTTACAA 59.122 50.000 0.00 0.00 31.36 2.41
2254 7320 0.036022 AAGTGAAGACCCTGCTCAGC 59.964 55.000 0.00 0.00 0.00 4.26
2329 7395 3.707793 ACCTTCATCTCGCTCGATTTAC 58.292 45.455 0.00 0.00 0.00 2.01
2330 7396 3.130516 ACCTTCATCTCGCTCGATTTACA 59.869 43.478 0.00 0.00 0.00 2.41
2331 7397 4.112634 CCTTCATCTCGCTCGATTTACAA 58.887 43.478 0.00 0.00 0.00 2.41
2332 7398 4.747108 CCTTCATCTCGCTCGATTTACAAT 59.253 41.667 0.00 0.00 0.00 2.71
2333 7399 5.235186 CCTTCATCTCGCTCGATTTACAATT 59.765 40.000 0.00 0.00 0.00 2.32
2334 7400 6.238211 CCTTCATCTCGCTCGATTTACAATTT 60.238 38.462 0.00 0.00 0.00 1.82
2335 7401 6.662414 TCATCTCGCTCGATTTACAATTTT 57.338 33.333 0.00 0.00 0.00 1.82
2336 7402 6.477742 TCATCTCGCTCGATTTACAATTTTG 58.522 36.000 0.00 0.00 0.00 2.44
2337 7403 5.856126 TCTCGCTCGATTTACAATTTTGT 57.144 34.783 1.08 1.08 44.86 2.83
2338 7404 6.954616 TCTCGCTCGATTTACAATTTTGTA 57.045 33.333 0.00 0.00 42.35 2.41
2339 7405 6.758149 TCTCGCTCGATTTACAATTTTGTAC 58.242 36.000 2.71 0.00 42.84 2.90
2340 7406 6.366604 TCTCGCTCGATTTACAATTTTGTACA 59.633 34.615 2.71 0.00 42.84 2.90
2341 7407 6.530567 TCGCTCGATTTACAATTTTGTACAG 58.469 36.000 2.71 0.00 42.84 2.74
2342 7408 6.146510 TCGCTCGATTTACAATTTTGTACAGT 59.853 34.615 2.71 0.00 42.84 3.55
2343 7409 6.461698 CGCTCGATTTACAATTTTGTACAGTC 59.538 38.462 2.71 2.07 42.84 3.51
2344 7410 7.295201 GCTCGATTTACAATTTTGTACAGTCA 58.705 34.615 2.71 0.00 42.84 3.41
2465 7545 3.768878 AGAACGAAGAGGAAGAGGAAGA 58.231 45.455 0.00 0.00 0.00 2.87
2466 7546 3.761752 AGAACGAAGAGGAAGAGGAAGAG 59.238 47.826 0.00 0.00 0.00 2.85
2467 7547 2.452505 ACGAAGAGGAAGAGGAAGAGG 58.547 52.381 0.00 0.00 0.00 3.69
2468 7548 2.041891 ACGAAGAGGAAGAGGAAGAGGA 59.958 50.000 0.00 0.00 0.00 3.71
2469 7549 3.093057 CGAAGAGGAAGAGGAAGAGGAA 58.907 50.000 0.00 0.00 0.00 3.36
2470 7550 3.130340 CGAAGAGGAAGAGGAAGAGGAAG 59.870 52.174 0.00 0.00 0.00 3.46
2475 7555 3.078305 AGGAAGAGGAAGAGGAAGAGGAA 59.922 47.826 0.00 0.00 0.00 3.36
2486 7566 0.174617 GAAGAGGAAGAGCAGGACGG 59.825 60.000 0.00 0.00 0.00 4.79
2487 7567 1.893919 AAGAGGAAGAGCAGGACGGC 61.894 60.000 0.00 0.00 0.00 5.68
2504 7584 3.039202 GCAAAGACGCGGGTGATGG 62.039 63.158 10.96 0.00 0.00 3.51
2592 7672 2.301346 CAAGTGAAGAAGGTGGTGCTT 58.699 47.619 0.00 0.00 0.00 3.91
2595 7675 2.107204 AGTGAAGAAGGTGGTGCTTGAT 59.893 45.455 0.00 0.00 0.00 2.57
2596 7676 3.327757 AGTGAAGAAGGTGGTGCTTGATA 59.672 43.478 0.00 0.00 0.00 2.15
2643 7723 2.939103 GGGATTCCTCAAGTTCGTGATG 59.061 50.000 2.01 0.00 0.00 3.07
2841 7921 2.288666 GCGTCTGATCTCTCTCTGAGT 58.711 52.381 4.32 0.00 43.13 3.41
2891 7971 3.807538 GGAGCGTCCGTGAGCGTA 61.808 66.667 0.00 0.00 38.61 4.42
2940 8023 8.173542 AGAACTTATTAGGAGTAGCTAGCTTC 57.826 38.462 24.88 18.51 0.00 3.86
2957 8040 6.292061 GCTAGCTTCAAGAACTTATCATGACG 60.292 42.308 7.70 0.00 35.61 4.35
3025 8161 0.253044 GTGACCTGGCTTGGCTGATA 59.747 55.000 0.00 0.00 0.00 2.15
3026 8162 0.991146 TGACCTGGCTTGGCTGATAA 59.009 50.000 0.00 0.00 0.00 1.75
3060 8196 6.260714 TGCGACATTTATCTATGCTTGATTGT 59.739 34.615 0.00 0.00 0.00 2.71
3073 8209 0.392336 TGATTGTTGCTGTTTGGGGC 59.608 50.000 0.00 0.00 0.00 5.80
3082 8219 0.593128 CTGTTTGGGGCGTGAAAGAG 59.407 55.000 0.00 0.00 0.00 2.85
3093 8230 1.443802 GTGAAAGAGTAGTGCTGGCC 58.556 55.000 0.00 0.00 0.00 5.36
3164 8302 6.698380 AGTCTATGTATTTATAAGCCCGGTG 58.302 40.000 0.00 0.00 0.00 4.94
3165 8303 5.873164 GTCTATGTATTTATAAGCCCGGTGG 59.127 44.000 0.00 0.00 0.00 4.61
3166 8304 4.986054 ATGTATTTATAAGCCCGGTGGA 57.014 40.909 0.00 0.00 0.00 4.02
3167 8305 4.345859 TGTATTTATAAGCCCGGTGGAG 57.654 45.455 0.00 0.00 0.00 3.86
3168 8306 3.712733 TGTATTTATAAGCCCGGTGGAGT 59.287 43.478 0.00 0.00 0.00 3.85
3169 8307 3.945640 ATTTATAAGCCCGGTGGAGTT 57.054 42.857 0.00 0.00 0.00 3.01
3170 8308 2.702592 TTATAAGCCCGGTGGAGTTG 57.297 50.000 0.00 0.00 0.00 3.16
3171 8309 0.834612 TATAAGCCCGGTGGAGTTGG 59.165 55.000 0.00 0.00 0.00 3.77
3172 8310 0.912487 ATAAGCCCGGTGGAGTTGGA 60.912 55.000 0.00 0.00 0.00 3.53
3173 8311 0.912487 TAAGCCCGGTGGAGTTGGAT 60.912 55.000 0.00 0.00 0.00 3.41
3174 8312 0.912487 AAGCCCGGTGGAGTTGGATA 60.912 55.000 0.00 0.00 0.00 2.59
3175 8313 1.146263 GCCCGGTGGAGTTGGATAG 59.854 63.158 0.00 0.00 0.00 2.08
3176 8314 1.146263 CCCGGTGGAGTTGGATAGC 59.854 63.158 0.00 0.00 0.00 2.97
3177 8315 1.622607 CCCGGTGGAGTTGGATAGCA 61.623 60.000 0.00 0.00 0.00 3.49
3178 8316 0.179073 CCGGTGGAGTTGGATAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
3179 8317 0.824109 CGGTGGAGTTGGATAGCAGA 59.176 55.000 0.00 0.00 0.00 4.26
3180 8318 1.471676 CGGTGGAGTTGGATAGCAGAC 60.472 57.143 0.00 0.00 0.00 3.51
3181 8319 1.555075 GGTGGAGTTGGATAGCAGACA 59.445 52.381 0.00 0.00 0.00 3.41
3182 8320 2.027192 GGTGGAGTTGGATAGCAGACAA 60.027 50.000 0.00 0.00 0.00 3.18
3183 8321 3.370953 GGTGGAGTTGGATAGCAGACAAT 60.371 47.826 0.00 0.00 0.00 2.71
3184 8322 4.141711 GGTGGAGTTGGATAGCAGACAATA 60.142 45.833 0.00 0.00 0.00 1.90
3185 8323 5.053145 GTGGAGTTGGATAGCAGACAATAG 58.947 45.833 0.00 0.00 0.00 1.73
3186 8324 4.101585 TGGAGTTGGATAGCAGACAATAGG 59.898 45.833 0.00 0.00 0.00 2.57
3187 8325 4.345257 GGAGTTGGATAGCAGACAATAGGA 59.655 45.833 0.00 0.00 0.00 2.94
3413 8599 2.365370 CTGCCTCAGCTCCCTCCT 60.365 66.667 0.00 0.00 40.80 3.69
3421 8607 2.366972 GCTCCCTCCTTGCCCCTA 60.367 66.667 0.00 0.00 0.00 3.53
3502 8690 1.638679 CCCCTGGATCATGCTGGTGA 61.639 60.000 1.30 0.00 0.00 4.02
3536 8725 2.511600 CCCAGATTCGGACGGTGC 60.512 66.667 0.00 0.00 0.00 5.01
3538 8727 2.180769 CAGATTCGGACGGTGCGA 59.819 61.111 20.85 20.85 38.78 5.10
3694 8889 1.745864 TGGTGCGTGTCCGTTTTGT 60.746 52.632 0.00 0.00 36.15 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.093322 AGAACCTTAAATGTGATGCATTCTC 57.907 36.000 0.00 0.00 46.29 2.87
19 20 5.413499 GCAAGAACCTTAAATGTGATGCAT 58.587 37.500 0.00 0.00 40.03 3.96
22 23 3.853671 GCGCAAGAACCTTAAATGTGATG 59.146 43.478 0.30 0.00 43.02 3.07
23 24 3.758554 AGCGCAAGAACCTTAAATGTGAT 59.241 39.130 11.47 0.00 43.02 3.06
26 27 3.821033 AGAAGCGCAAGAACCTTAAATGT 59.179 39.130 11.47 0.00 43.02 2.71
30 31 2.031157 GCAAGAAGCGCAAGAACCTTAA 60.031 45.455 11.47 0.00 43.02 1.85
96 97 3.554692 GAACATCGCGAGGCACCG 61.555 66.667 22.18 3.83 0.00 4.94
102 103 0.732880 ACCACTTCGAACATCGCGAG 60.733 55.000 16.66 9.51 40.21 5.03
105 106 1.132640 GCACCACTTCGAACATCGC 59.867 57.895 0.00 0.00 40.21 4.58
124 125 0.391130 CGGGAAGTCCAATCTCGCAA 60.391 55.000 0.00 0.00 33.51 4.85
136 137 4.394712 CTTGGCGCCTCGGGAAGT 62.395 66.667 29.70 0.00 0.00 3.01
184 185 6.451960 GCGACGCTTGATTAAACATTAAAACC 60.452 38.462 13.73 0.00 0.00 3.27
196 197 5.539582 AAACAATTAGCGACGCTTGATTA 57.460 34.783 29.54 6.38 40.44 1.75
208 209 6.959311 CACGGATGTTACACTAAACAATTAGC 59.041 38.462 0.00 0.00 42.33 3.09
227 228 3.263425 AGAACAATAGACCCAACACGGAT 59.737 43.478 0.00 0.00 36.56 4.18
230 231 3.617263 GCTAGAACAATAGACCCAACACG 59.383 47.826 0.00 0.00 0.00 4.49
305 306 1.948138 CCGCAAAATGCAACGCACA 60.948 52.632 2.99 0.00 45.36 4.57
310 311 4.605135 CGTTAAGAAACCGCAAAATGCAAC 60.605 41.667 2.99 0.00 45.36 4.17
330 331 4.157105 GGTATTTGGTATGGCAGTTTCGTT 59.843 41.667 0.00 0.00 0.00 3.85
331 332 3.692593 GGTATTTGGTATGGCAGTTTCGT 59.307 43.478 0.00 0.00 0.00 3.85
347 348 5.925969 CGAAAAAGAAATGGCACTGGTATTT 59.074 36.000 0.00 0.00 0.00 1.40
351 352 2.693074 ACGAAAAAGAAATGGCACTGGT 59.307 40.909 0.00 0.00 0.00 4.00
355 356 4.981674 TGATGAACGAAAAAGAAATGGCAC 59.018 37.500 0.00 0.00 0.00 5.01
370 371 7.545362 AGATCAGAAACCTAATTGATGAACG 57.455 36.000 0.00 0.00 30.85 3.95
399 400 9.917872 CGATACAGAACTATACTATTCATACGG 57.082 37.037 0.00 0.00 0.00 4.02
400 401 9.423427 GCGATACAGAACTATACTATTCATACG 57.577 37.037 0.00 0.00 0.00 3.06
418 419 4.209080 TCAATGATAAACGCAGCGATACAG 59.791 41.667 24.65 2.04 0.00 2.74
423 424 2.935849 ACATCAATGATAAACGCAGCGA 59.064 40.909 24.65 0.00 0.00 4.93
425 426 5.810525 ACTAACATCAATGATAAACGCAGC 58.189 37.500 0.00 0.00 0.00 5.25
448 449 5.568685 TTCAGTGAATGTCGGAAACAAAA 57.431 34.783 0.08 0.00 42.37 2.44
455 456 4.808414 AGATCTTTCAGTGAATGTCGGA 57.192 40.909 16.01 6.94 0.00 4.55
457 458 5.852738 ACAAGATCTTTCAGTGAATGTCG 57.147 39.130 16.01 3.04 0.00 4.35
473 474 6.118170 CCAGACTTCATCCATACAACAAGAT 58.882 40.000 0.00 0.00 0.00 2.40
483 484 4.723789 ACCTGAATACCAGACTTCATCCAT 59.276 41.667 0.00 0.00 45.78 3.41
526 527 6.703165 TCATAATGATGAGAAGAACATGGACG 59.297 38.462 0.00 0.00 37.15 4.79
545 546 4.178339 TGATAGGCCTCCACCATCATAAT 58.822 43.478 9.68 0.00 0.00 1.28
551 552 0.695462 TGCTGATAGGCCTCCACCAT 60.695 55.000 9.68 0.00 0.00 3.55
595 596 2.420628 TTTTGTTTGCCGAGCTGATG 57.579 45.000 0.00 0.00 0.00 3.07
603 604 1.520590 CCATGTCGTTTTTGTTTGCCG 59.479 47.619 0.00 0.00 0.00 5.69
616 617 4.455877 AGAACTTTAAAAGGAGCCATGTCG 59.544 41.667 0.00 0.00 0.00 4.35
632 709 4.022849 GCTGCACTTTGATGGTAGAACTTT 60.023 41.667 0.00 0.00 0.00 2.66
658 735 2.749621 GCAGGTCATAAACTTGGGACAG 59.250 50.000 0.00 0.00 42.39 3.51
773 2418 5.613795 CGTGCGAGTTTGACTTAATTAAGCA 60.614 40.000 22.45 17.97 36.79 3.91
806 2454 9.877542 ACGGCAGGATTCGTGAGTTATTAAACT 62.878 40.741 10.43 0.00 39.21 2.66
810 2458 3.131577 ACGGCAGGATTCGTGAGTTATTA 59.868 43.478 10.43 0.00 38.25 0.98
811 2459 2.093658 ACGGCAGGATTCGTGAGTTATT 60.094 45.455 10.43 0.00 38.25 1.40
812 2460 1.480954 ACGGCAGGATTCGTGAGTTAT 59.519 47.619 10.43 0.00 38.25 1.89
813 2461 0.892755 ACGGCAGGATTCGTGAGTTA 59.107 50.000 10.43 0.00 38.25 2.24
814 2462 1.671742 ACGGCAGGATTCGTGAGTT 59.328 52.632 10.43 0.00 38.25 3.01
815 2463 3.377656 ACGGCAGGATTCGTGAGT 58.622 55.556 10.43 6.36 38.25 3.41
864 5847 5.847670 AGTGTTTTAATGCTCTTCTCGTC 57.152 39.130 0.00 0.00 0.00 4.20
874 5857 1.202256 GGCCCGCTAGTGTTTTAATGC 60.202 52.381 1.99 0.00 0.00 3.56
1149 6165 4.324991 GTCCTCCCCGCCGTTGTT 62.325 66.667 0.00 0.00 0.00 2.83
1329 6348 4.011517 GAACTCGAACCCGCCCCA 62.012 66.667 0.00 0.00 35.37 4.96
1331 6350 4.060038 TCGAACTCGAACCCGCCC 62.060 66.667 0.00 0.00 46.30 6.13
1498 6526 2.126031 GGTTGACGAGGACGAGGC 60.126 66.667 0.00 0.00 42.66 4.70
2007 7062 2.640332 GGAGAAATAGGATGGGGAGTCC 59.360 54.545 0.00 0.00 35.94 3.85
2046 7103 7.094634 ACCATCGCATCCATGAAGATTAATAAC 60.095 37.037 0.00 0.00 0.00 1.89
2058 7119 2.027325 CCACACCATCGCATCCATG 58.973 57.895 0.00 0.00 0.00 3.66
2080 7141 8.486383 CGAAGTTGAAATCAATGCAAAATTGTA 58.514 29.630 0.00 0.00 38.24 2.41
2081 7142 7.224362 TCGAAGTTGAAATCAATGCAAAATTGT 59.776 29.630 0.00 0.00 38.24 2.71
2082 7143 7.565848 TCGAAGTTGAAATCAATGCAAAATTG 58.434 30.769 0.00 0.00 38.24 2.32
2083 7144 7.712264 TCGAAGTTGAAATCAATGCAAAATT 57.288 28.000 0.00 0.00 38.24 1.82
2084 7145 7.201376 CGATCGAAGTTGAAATCAATGCAAAAT 60.201 33.333 10.26 0.00 38.24 1.82
2132 7196 1.001181 AGCCTGCAAATCAAACGCAAT 59.999 42.857 0.00 0.00 34.75 3.56
2135 7199 1.010419 CCAGCCTGCAAATCAAACGC 61.010 55.000 0.00 0.00 0.00 4.84
2254 7320 3.077484 TGGGGAAAGCATCTCAAGAAG 57.923 47.619 0.00 0.00 0.00 2.85
2329 7395 8.207252 CGCAAATTAGTTGACTGTACAAAATTG 58.793 33.333 0.00 0.00 39.87 2.32
2330 7396 7.918562 ACGCAAATTAGTTGACTGTACAAAATT 59.081 29.630 0.00 0.00 39.87 1.82
2331 7397 7.422399 ACGCAAATTAGTTGACTGTACAAAAT 58.578 30.769 0.00 0.00 39.87 1.82
2332 7398 6.787225 ACGCAAATTAGTTGACTGTACAAAA 58.213 32.000 0.00 0.00 39.87 2.44
2333 7399 6.037281 TGACGCAAATTAGTTGACTGTACAAA 59.963 34.615 0.00 0.00 39.87 2.83
2334 7400 5.524281 TGACGCAAATTAGTTGACTGTACAA 59.476 36.000 0.00 0.00 39.87 2.41
2335 7401 5.051153 TGACGCAAATTAGTTGACTGTACA 58.949 37.500 0.00 0.00 39.87 2.90
2336 7402 5.585500 TGACGCAAATTAGTTGACTGTAC 57.415 39.130 0.00 0.00 39.87 2.90
2337 7403 5.929415 TGATGACGCAAATTAGTTGACTGTA 59.071 36.000 0.00 0.00 39.87 2.74
2338 7404 4.754618 TGATGACGCAAATTAGTTGACTGT 59.245 37.500 0.00 0.00 39.87 3.55
2339 7405 5.281693 TGATGACGCAAATTAGTTGACTG 57.718 39.130 0.00 0.00 39.87 3.51
2340 7406 4.393062 CCTGATGACGCAAATTAGTTGACT 59.607 41.667 0.00 0.00 39.87 3.41
2341 7407 4.391830 TCCTGATGACGCAAATTAGTTGAC 59.608 41.667 0.00 0.00 39.87 3.18
2342 7408 4.574892 TCCTGATGACGCAAATTAGTTGA 58.425 39.130 0.00 0.00 39.87 3.18
2343 7409 4.728882 GCTCCTGATGACGCAAATTAGTTG 60.729 45.833 0.00 0.00 40.50 3.16
2344 7410 3.375299 GCTCCTGATGACGCAAATTAGTT 59.625 43.478 0.00 0.00 0.00 2.24
2465 7545 1.567357 GTCCTGCTCTTCCTCTTCCT 58.433 55.000 0.00 0.00 0.00 3.36
2466 7546 0.174617 CGTCCTGCTCTTCCTCTTCC 59.825 60.000 0.00 0.00 0.00 3.46
2467 7547 0.174617 CCGTCCTGCTCTTCCTCTTC 59.825 60.000 0.00 0.00 0.00 2.87
2468 7548 1.893919 GCCGTCCTGCTCTTCCTCTT 61.894 60.000 0.00 0.00 0.00 2.85
2469 7549 2.355193 GCCGTCCTGCTCTTCCTCT 61.355 63.158 0.00 0.00 0.00 3.69
2470 7550 2.172483 TTGCCGTCCTGCTCTTCCTC 62.172 60.000 0.00 0.00 0.00 3.71
2475 7555 1.004440 GTCTTTGCCGTCCTGCTCT 60.004 57.895 0.00 0.00 0.00 4.09
2486 7566 2.480555 CATCACCCGCGTCTTTGC 59.519 61.111 4.92 0.00 0.00 3.68
2487 7567 3.039202 GCCATCACCCGCGTCTTTG 62.039 63.158 4.92 0.00 0.00 2.77
2531 7611 2.294078 CCGGCCTCCTTCCAGAACT 61.294 63.158 0.00 0.00 0.00 3.01
2592 7672 0.390603 CGCCCACGGTGAACTTATCA 60.391 55.000 10.28 0.00 34.74 2.15
2595 7675 2.357760 GCGCCCACGGTGAACTTA 60.358 61.111 10.28 0.00 40.57 2.24
2891 7971 5.684704 TCAGAGAAACATCCAAAGTGTTCT 58.315 37.500 0.00 0.00 38.76 3.01
2940 8023 5.292834 AGACATGCGTCATGATAAGTTCTTG 59.707 40.000 21.37 0.00 43.81 3.02
2957 8040 3.732721 GTCACAGCAAAAAGAAGACATGC 59.267 43.478 0.00 0.00 37.28 4.06
3002 8138 2.674380 CCAAGCCAGGTCACAGCC 60.674 66.667 0.00 0.00 0.00 4.85
3025 8161 8.886719 CATAGATAAATGTCGCATGATGGTATT 58.113 33.333 0.00 0.00 0.00 1.89
3026 8162 7.011763 GCATAGATAAATGTCGCATGATGGTAT 59.988 37.037 0.00 0.00 0.00 2.73
3060 8196 1.323271 TTTCACGCCCCAAACAGCAA 61.323 50.000 0.00 0.00 0.00 3.91
3073 8209 1.071605 GCCAGCACTACTCTTTCACG 58.928 55.000 0.00 0.00 0.00 4.35
3082 8219 4.136796 TGATTTATCATGGCCAGCACTAC 58.863 43.478 13.05 0.00 0.00 2.73
3093 8230 5.994054 ACGGACCAATCTCTGATTTATCATG 59.006 40.000 0.00 0.00 36.02 3.07
3164 8302 4.345257 TCCTATTGTCTGCTATCCAACTCC 59.655 45.833 0.00 0.00 0.00 3.85
3165 8303 5.069781 AGTCCTATTGTCTGCTATCCAACTC 59.930 44.000 0.00 0.00 0.00 3.01
3166 8304 4.965532 AGTCCTATTGTCTGCTATCCAACT 59.034 41.667 0.00 0.00 0.00 3.16
3167 8305 5.283457 AGTCCTATTGTCTGCTATCCAAC 57.717 43.478 0.00 0.00 0.00 3.77
3168 8306 4.345257 GGAGTCCTATTGTCTGCTATCCAA 59.655 45.833 0.41 0.00 0.00 3.53
3169 8307 3.898123 GGAGTCCTATTGTCTGCTATCCA 59.102 47.826 0.41 0.00 0.00 3.41
3170 8308 3.259625 GGGAGTCCTATTGTCTGCTATCC 59.740 52.174 9.58 0.00 0.00 2.59
3171 8309 4.156477 AGGGAGTCCTATTGTCTGCTATC 58.844 47.826 9.58 0.00 42.75 2.08
3172 8310 4.156477 GAGGGAGTCCTATTGTCTGCTAT 58.844 47.826 9.58 0.00 45.05 2.97
3173 8311 3.567397 GAGGGAGTCCTATTGTCTGCTA 58.433 50.000 9.58 0.00 45.05 3.49
3174 8312 2.393646 GAGGGAGTCCTATTGTCTGCT 58.606 52.381 9.58 0.00 45.05 4.24
3175 8313 1.414550 GGAGGGAGTCCTATTGTCTGC 59.585 57.143 9.58 0.00 45.05 4.26
3176 8314 2.043227 GGGAGGGAGTCCTATTGTCTG 58.957 57.143 9.58 0.00 46.06 3.51
3177 8315 1.940957 AGGGAGGGAGTCCTATTGTCT 59.059 52.381 9.58 0.00 46.06 3.41
3178 8316 2.321719 GAGGGAGGGAGTCCTATTGTC 58.678 57.143 9.58 0.00 46.06 3.18
3179 8317 1.062044 GGAGGGAGGGAGTCCTATTGT 60.062 57.143 9.58 0.00 46.06 2.71
3180 8318 1.723288 GGAGGGAGGGAGTCCTATTG 58.277 60.000 9.58 0.00 46.06 1.90
3181 8319 0.568697 GGGAGGGAGGGAGTCCTATT 59.431 60.000 9.58 0.00 46.06 1.73
3182 8320 1.381089 GGGGAGGGAGGGAGTCCTAT 61.381 65.000 9.58 0.00 46.06 2.57
3183 8321 2.019272 GGGGAGGGAGGGAGTCCTA 61.019 68.421 9.58 0.00 46.06 2.94
3184 8322 3.369388 GGGGAGGGAGGGAGTCCT 61.369 72.222 9.58 0.00 46.06 3.85
3185 8323 4.862823 CGGGGAGGGAGGGAGTCC 62.863 77.778 0.00 0.00 46.10 3.85
3186 8324 3.742248 CTCGGGGAGGGAGGGAGTC 62.742 73.684 0.00 0.00 0.00 3.36
3187 8325 3.756783 CTCGGGGAGGGAGGGAGT 61.757 72.222 0.00 0.00 0.00 3.85
3413 8599 2.221299 ACCAGAACGCTAGGGGCAA 61.221 57.895 11.95 0.00 41.91 4.52
3421 8607 3.560251 ACCAGCCACCAGAACGCT 61.560 61.111 0.00 0.00 0.00 5.07
3538 8727 4.284550 ACTGCCACCGCCAACCAT 62.285 61.111 0.00 0.00 0.00 3.55
3570 8759 1.149627 AGCGCCACCACCTAAACAA 59.850 52.632 2.29 0.00 0.00 2.83
3657 8852 1.077068 CCACCACCACAACACCAGT 60.077 57.895 0.00 0.00 0.00 4.00
3694 8889 3.829044 CCGCCCACCATACGTCGA 61.829 66.667 0.00 0.00 0.00 4.20
3736 8933 2.904866 GGAGCAACAACCACGCCA 60.905 61.111 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.