Multiple sequence alignment - TraesCS4D01G052800

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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 TraesCS4D01G052800 chr4D 100.000 3884 0 0 1 3884 29023046 29019163 0.000000e+00 7173
1 TraesCS4D01G052800 chr4D 91.160 905 77 3 2981 3884 458018523 458017621 0.000000e+00 1225
2 TraesCS4D01G052800 chr4B 92.941 2309 96 25 631 2907 41553554 41551281 0.000000e+00 3299
3 TraesCS4D01G052800 chr4B 87.160 514 40 17 1 493 41554264 41553756 9.420000e-156 560
4 TraesCS4D01G052800 chr4A 92.777 2312 102 21 633 2907 574524576 574526859 0.000000e+00 3284
5 TraesCS4D01G052800 chr4A 90.217 460 28 6 5 449 574523691 574524148 5.590000e-163 584
6 TraesCS4D01G052800 chr4A 90.840 262 23 1 2141 2402 731942253 731942513 2.220000e-92 350
7 TraesCS4D01G052800 chr4A 92.814 167 12 0 2578 2744 731942680 731942846 3.880000e-60 243
8 TraesCS4D01G052800 chr4A 90.230 174 16 1 2340 2512 731942513 731942686 3.900000e-55 226
9 TraesCS4D01G052800 chr2D 92.486 905 66 2 2981 3884 477931678 477930775 0.000000e+00 1293
10 TraesCS4D01G052800 chr2D 92.053 906 69 3 2980 3884 303873282 303874185 0.000000e+00 1271
11 TraesCS4D01G052800 chr2D 91.943 906 70 3 2980 3884 303991696 303992599 0.000000e+00 1266
12 TraesCS4D01G052800 chr2D 91.611 906 73 3 2980 3884 303940401 303941304 0.000000e+00 1249
13 TraesCS4D01G052800 chr2D 91.271 905 77 2 2981 3884 477972020 477971117 0.000000e+00 1232
14 TraesCS4D01G052800 chrUn 91.170 906 78 2 2980 3884 111877015 111877919 0.000000e+00 1229
15 TraesCS4D01G052800 chrUn 91.060 906 79 2 2980 3884 111857790 111858694 0.000000e+00 1223
16 TraesCS4D01G052800 chr3D 90.800 913 68 14 2981 3884 142899293 142900198 0.000000e+00 1206
17 TraesCS4D01G052800 chr6B 86.275 357 46 2 1228 1584 640356529 640356176 6.090000e-103 385
18 TraesCS4D01G052800 chr6B 93.846 130 7 1 1626 1755 640356169 640356041 1.100000e-45 195
19 TraesCS4D01G052800 chr7A 88.636 88 1 6 1668 1755 729889718 729889796 8.880000e-17 99


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 TraesCS4D01G052800 chr4D 29019163 29023046 3883 True 7173.0 7173 100.000000 1 3884 1 chr4D.!!$R1 3883
1 TraesCS4D01G052800 chr4D 458017621 458018523 902 True 1225.0 1225 91.160000 2981 3884 1 chr4D.!!$R2 903
2 TraesCS4D01G052800 chr4B 41551281 41554264 2983 True 1929.5 3299 90.050500 1 2907 2 chr4B.!!$R1 2906
3 TraesCS4D01G052800 chr4A 574523691 574526859 3168 False 1934.0 3284 91.497000 5 2907 2 chr4A.!!$F1 2902
4 TraesCS4D01G052800 chr4A 731942253 731942846 593 False 273.0 350 91.294667 2141 2744 3 chr4A.!!$F2 603
5 TraesCS4D01G052800 chr2D 477930775 477931678 903 True 1293.0 1293 92.486000 2981 3884 1 chr2D.!!$R1 903
6 TraesCS4D01G052800 chr2D 303873282 303874185 903 False 1271.0 1271 92.053000 2980 3884 1 chr2D.!!$F1 904
7 TraesCS4D01G052800 chr2D 303991696 303992599 903 False 1266.0 1266 91.943000 2980 3884 1 chr2D.!!$F3 904
8 TraesCS4D01G052800 chr2D 303940401 303941304 903 False 1249.0 1249 91.611000 2980 3884 1 chr2D.!!$F2 904
9 TraesCS4D01G052800 chr2D 477971117 477972020 903 True 1232.0 1232 91.271000 2981 3884 1 chr2D.!!$R2 903
10 TraesCS4D01G052800 chrUn 111877015 111877919 904 False 1229.0 1229 91.170000 2980 3884 1 chrUn.!!$F2 904
11 TraesCS4D01G052800 chrUn 111857790 111858694 904 False 1223.0 1223 91.060000 2980 3884 1 chrUn.!!$F1 904
12 TraesCS4D01G052800 chr3D 142899293 142900198 905 False 1206.0 1206 90.800000 2981 3884 1 chr3D.!!$F1 903

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
639 908 0.109723 AGAAACTTGGGGCAGCGTTA 59.890 50.0 0.0 0.0 0.00 3.18 F
647 916 0.451783 GGGGCAGCGTTAATTCAGTG 59.548 55.0 0.0 0.0 0.00 3.66 F
893 1190 0.460987 CGTCTCCAACAGATCCCAGC 60.461 60.0 0.0 0.0 32.08 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2337 0.608640 ACGGCAGGTAGACCTCTTTG 59.391 55.0 0.0 0.0 46.65 2.77 R
2796 3185 0.179215 GCTCGTTCGGCATCTTGTTG 60.179 55.0 0.0 0.0 0.00 3.33 R
2972 3361 0.179029 CCAACCCCGACAAGTTCTGT 60.179 55.0 0.0 0.0 42.61 3.41 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
33 34 4.326009 CGGGCACATAACTTTATTTGCAAC 59.674 41.667 17.59 10.96 44.50 4.17
43 44 6.819397 ACTTTATTTGCAACTCTCTAACCC 57.181 37.500 0.00 0.00 0.00 4.11
107 112 2.643995 TACATGTGATGCCCCTGATG 57.356 50.000 9.11 0.00 0.00 3.07
109 114 1.315690 CATGTGATGCCCCTGATGTC 58.684 55.000 0.00 0.00 0.00 3.06
149 155 2.050144 TCTCCCAGAAAGAGTTGCTGT 58.950 47.619 0.00 0.00 32.93 4.40
193 199 1.134220 ACCTAGTCGCTCAGAGGAGAG 60.134 57.143 0.00 0.00 44.26 3.20
194 200 1.140052 CCTAGTCGCTCAGAGGAGAGA 59.860 57.143 0.00 0.00 45.96 3.10
296 306 6.965500 GCTGTATCATGAACATTCTTGAGTTG 59.035 38.462 13.62 7.04 42.31 3.16
297 307 7.381766 TGTATCATGAACATTCTTGAGTTGG 57.618 36.000 13.62 0.00 42.31 3.77
350 361 9.737427 CGTAGAGTTGTATTTTATCATCAGTCT 57.263 33.333 0.00 0.00 0.00 3.24
441 464 0.529773 TCGTTGTCTGTCACCTGTGC 60.530 55.000 0.00 0.00 0.00 4.57
442 465 1.821241 CGTTGTCTGTCACCTGTGCG 61.821 60.000 0.00 0.00 0.00 5.34
452 510 3.663176 CCTGTGCGGTGCCAGTTG 61.663 66.667 6.55 0.00 0.00 3.16
472 530 3.626472 GCGCCGGCTTGTCTATAC 58.374 61.111 26.68 0.00 35.83 1.47
474 532 0.600255 GCGCCGGCTTGTCTATACAT 60.600 55.000 26.68 0.00 34.97 2.29
478 536 3.467803 GCCGGCTTGTCTATACATCTTT 58.532 45.455 22.15 0.00 34.97 2.52
485 543 6.270815 GCTTGTCTATACATCTTTCACGGTA 58.729 40.000 0.00 0.00 34.97 4.02
489 547 8.913487 TGTCTATACATCTTTCACGGTAGATA 57.087 34.615 0.00 0.00 30.20 1.98
493 551 4.547532 ACATCTTTCACGGTAGATATCGC 58.452 43.478 0.00 0.00 31.88 4.58
495 553 4.485024 TCTTTCACGGTAGATATCGCTC 57.515 45.455 0.00 0.00 31.88 5.03
497 555 3.898517 TTCACGGTAGATATCGCTCTG 57.101 47.619 0.00 0.26 31.88 3.35
498 556 1.535896 TCACGGTAGATATCGCTCTGC 59.464 52.381 0.00 0.00 31.88 4.26
499 557 1.537638 CACGGTAGATATCGCTCTGCT 59.462 52.381 0.00 0.00 31.88 4.24
501 559 1.131504 CGGTAGATATCGCTCTGCTCC 59.868 57.143 0.00 0.00 0.00 4.70
502 560 1.131504 GGTAGATATCGCTCTGCTCCG 59.868 57.143 0.00 0.00 0.00 4.63
503 561 0.805614 TAGATATCGCTCTGCTCCGC 59.194 55.000 0.00 0.00 0.00 5.54
504 562 1.175347 AGATATCGCTCTGCTCCGCA 61.175 55.000 0.00 0.00 36.92 5.69
507 565 1.944234 TATCGCTCTGCTCCGCACAA 61.944 55.000 0.00 0.00 33.79 3.33
510 568 2.345244 CTCTGCTCCGCACAACCT 59.655 61.111 0.00 0.00 33.79 3.50
511 569 2.031012 TCTGCTCCGCACAACCTG 59.969 61.111 0.00 0.00 33.79 4.00
513 571 1.893808 CTGCTCCGCACAACCTGTT 60.894 57.895 0.00 0.00 33.79 3.16
514 572 2.121564 CTGCTCCGCACAACCTGTTG 62.122 60.000 8.42 8.42 45.58 3.33
515 573 1.891919 GCTCCGCACAACCTGTTGA 60.892 57.895 16.41 0.00 42.93 3.18
518 576 0.531974 TCCGCACAACCTGTTGAGTC 60.532 55.000 16.41 4.85 42.93 3.36
519 577 1.507141 CCGCACAACCTGTTGAGTCC 61.507 60.000 16.41 1.63 42.93 3.85
520 578 1.507141 CGCACAACCTGTTGAGTCCC 61.507 60.000 16.41 0.00 42.93 4.46
521 579 0.179018 GCACAACCTGTTGAGTCCCT 60.179 55.000 16.41 0.00 42.93 4.20
522 580 1.884235 CACAACCTGTTGAGTCCCTC 58.116 55.000 16.41 0.00 42.93 4.30
523 581 0.393077 ACAACCTGTTGAGTCCCTCG 59.607 55.000 16.41 0.00 42.93 4.63
524 582 0.393077 CAACCTGTTGAGTCCCTCGT 59.607 55.000 3.96 0.00 42.93 4.18
526 584 2.233305 ACCTGTTGAGTCCCTCGTAT 57.767 50.000 0.00 0.00 32.35 3.06
532 590 4.084287 TGTTGAGTCCCTCGTATAGTTGT 58.916 43.478 0.00 0.00 32.35 3.32
533 591 5.255687 TGTTGAGTCCCTCGTATAGTTGTA 58.744 41.667 0.00 0.00 32.35 2.41
534 592 5.889853 TGTTGAGTCCCTCGTATAGTTGTAT 59.110 40.000 0.00 0.00 32.35 2.29
535 593 6.379133 TGTTGAGTCCCTCGTATAGTTGTATT 59.621 38.462 0.00 0.00 32.35 1.89
537 595 7.414222 TGAGTCCCTCGTATAGTTGTATTTT 57.586 36.000 0.00 0.00 32.35 1.82
538 596 7.844009 TGAGTCCCTCGTATAGTTGTATTTTT 58.156 34.615 0.00 0.00 32.35 1.94
539 597 8.970020 TGAGTCCCTCGTATAGTTGTATTTTTA 58.030 33.333 0.00 0.00 32.35 1.52
541 599 9.978044 AGTCCCTCGTATAGTTGTATTTTTATC 57.022 33.333 0.00 0.00 0.00 1.75
551 617 3.142951 TGTATTTTTATCATCCGGCCGG 58.857 45.455 39.13 39.13 0.00 6.13
554 620 2.596553 TTTTATCATCCGGCCGGCGT 62.597 55.000 39.89 26.81 34.68 5.68
573 639 2.253154 CGTCGTGTACCGCACTCA 59.747 61.111 0.00 0.00 45.57 3.41
588 654 1.164041 ACTCACCGACGGGCAAAAAG 61.164 55.000 20.00 8.18 36.48 2.27
589 655 2.050442 CACCGACGGGCAAAAAGC 60.050 61.111 20.00 0.00 44.65 3.51
600 666 1.215014 GCAAAAAGCACGGACAAGGC 61.215 55.000 0.00 0.00 44.79 4.35
601 667 0.597377 CAAAAAGCACGGACAAGGCC 60.597 55.000 0.00 0.00 0.00 5.19
639 908 0.109723 AGAAACTTGGGGCAGCGTTA 59.890 50.000 0.00 0.00 0.00 3.18
647 916 0.451783 GGGGCAGCGTTAATTCAGTG 59.548 55.000 0.00 0.00 0.00 3.66
648 917 1.165270 GGGCAGCGTTAATTCAGTGT 58.835 50.000 0.00 0.00 0.00 3.55
649 918 2.352388 GGGCAGCGTTAATTCAGTGTA 58.648 47.619 0.00 0.00 0.00 2.90
651 920 3.189702 GGGCAGCGTTAATTCAGTGTAAA 59.810 43.478 0.00 0.00 0.00 2.01
652 921 4.403453 GGCAGCGTTAATTCAGTGTAAAG 58.597 43.478 0.00 0.00 0.00 1.85
653 922 4.083484 GGCAGCGTTAATTCAGTGTAAAGT 60.083 41.667 0.00 0.00 0.00 2.66
658 927 7.898309 CAGCGTTAATTCAGTGTAAAGTGTATC 59.102 37.037 0.00 0.00 0.00 2.24
677 947 2.198304 CTCACCAACCCAGGGTAGGC 62.198 65.000 13.17 0.00 36.72 3.93
750 1028 2.281761 GCCCCGGCATCATACCTG 60.282 66.667 0.00 0.00 41.49 4.00
765 1043 1.194781 ACCTGTCTTGGCATCGGAGT 61.195 55.000 0.00 0.00 0.00 3.85
768 1046 2.167861 GTCTTGGCATCGGAGTCGC 61.168 63.158 0.00 0.00 36.13 5.19
772 1050 4.819761 GGCATCGGAGTCGCAGCA 62.820 66.667 0.00 0.00 37.52 4.41
777 1055 2.449031 ATCGGAGTCGCAGCAAACCA 62.449 55.000 0.00 0.00 36.13 3.67
796 1075 2.556622 CCAAATCCAAAACCTAGCGTGT 59.443 45.455 0.00 0.00 0.00 4.49
847 1136 2.121645 ATGGCTTTGGCATAGCTGC 58.878 52.632 25.43 13.09 46.84 5.25
882 1179 3.695060 GGTCTAGATCTTGTCGTCTCCAA 59.305 47.826 0.00 0.00 0.00 3.53
893 1190 0.460987 CGTCTCCAACAGATCCCAGC 60.461 60.000 0.00 0.00 32.08 4.85
895 1192 0.907486 TCTCCAACAGATCCCAGCTG 59.093 55.000 6.78 6.78 39.26 4.24
902 1199 2.672098 ACAGATCCCAGCTGTAGTAGG 58.328 52.381 13.81 6.28 44.27 3.18
903 1200 2.245028 ACAGATCCCAGCTGTAGTAGGA 59.755 50.000 13.81 11.99 44.27 2.94
905 1202 2.516277 AGATCCCAGCTGTAGTAGGAGT 59.484 50.000 13.81 0.73 0.00 3.85
906 1203 3.722627 AGATCCCAGCTGTAGTAGGAGTA 59.277 47.826 13.81 0.00 0.00 2.59
931 1228 2.265467 TTAGCTGATCCGGGTTGGGC 62.265 60.000 0.00 0.00 38.76 5.36
955 1252 3.077556 TTCTGCTCTCCCGCTCCC 61.078 66.667 0.00 0.00 0.00 4.30
1005 1302 2.625314 CCCAATCGAGACAGAGATGCTA 59.375 50.000 0.00 0.00 0.00 3.49
1007 1304 4.047822 CCAATCGAGACAGAGATGCTAAC 58.952 47.826 0.00 0.00 0.00 2.34
1013 1310 0.905357 ACAGAGATGCTAACCCGCTT 59.095 50.000 0.00 0.00 0.00 4.68
1018 1315 3.451178 AGAGATGCTAACCCGCTTCTTTA 59.549 43.478 0.00 0.00 42.36 1.85
1176 1481 6.425417 GCATTATTGGTTTCTAGTAGGCTCTC 59.575 42.308 0.00 0.00 0.00 3.20
1179 1484 3.015327 TGGTTTCTAGTAGGCTCTCGTC 58.985 50.000 0.00 0.00 0.00 4.20
1200 1505 5.501413 CGTCTCCATTGATTCGTTGATTGAG 60.501 44.000 0.00 0.00 0.00 3.02
1217 1526 2.663852 GGTGTGGGTTCGACGTGG 60.664 66.667 0.00 0.00 0.00 4.94
1219 1528 3.851128 TGTGGGTTCGACGTGGCA 61.851 61.111 0.00 0.00 0.00 4.92
1317 1632 1.808411 TCGACAAAATCTGCACCCTC 58.192 50.000 0.00 0.00 0.00 4.30
2010 2337 1.218316 CACGCTCTACTTCCACCCC 59.782 63.158 0.00 0.00 0.00 4.95
2331 2658 2.202932 CTCGGCCCGATCAACCTG 60.203 66.667 6.16 0.00 34.61 4.00
2652 3041 4.509737 GTGGCGGCGGAGTACCTC 62.510 72.222 9.78 0.00 0.00 3.85
2796 3185 2.892425 CCGGCGGAGAACATGCTC 60.892 66.667 24.41 0.00 0.00 4.26
2823 3212 1.807573 GCCGAACGAGCTCTCCAAG 60.808 63.158 12.85 0.00 0.00 3.61
2835 3224 2.614013 TCCAAGGAGGAAGGGCCC 60.614 66.667 16.46 16.46 45.65 5.80
2902 3291 1.000163 AGGCGTAGAGTGAAGTGTGTG 60.000 52.381 0.00 0.00 0.00 3.82
2904 3293 1.419374 CGTAGAGTGAAGTGTGTGGC 58.581 55.000 0.00 0.00 0.00 5.01
2905 3294 1.000163 CGTAGAGTGAAGTGTGTGGCT 60.000 52.381 0.00 0.00 0.00 4.75
2908 3297 3.004752 AGAGTGAAGTGTGTGGCTTTT 57.995 42.857 0.00 0.00 0.00 2.27
2909 3298 2.945668 AGAGTGAAGTGTGTGGCTTTTC 59.054 45.455 0.00 0.00 0.00 2.29
2910 3299 2.682856 GAGTGAAGTGTGTGGCTTTTCA 59.317 45.455 0.00 0.00 0.00 2.69
2911 3300 3.290710 AGTGAAGTGTGTGGCTTTTCAT 58.709 40.909 0.00 0.00 31.28 2.57
2912 3301 3.701040 AGTGAAGTGTGTGGCTTTTCATT 59.299 39.130 0.00 0.00 31.28 2.57
2913 3302 4.160252 AGTGAAGTGTGTGGCTTTTCATTT 59.840 37.500 0.00 0.00 31.28 2.32
2914 3303 4.869861 GTGAAGTGTGTGGCTTTTCATTTT 59.130 37.500 0.00 0.00 31.28 1.82
2915 3304 5.351189 GTGAAGTGTGTGGCTTTTCATTTTT 59.649 36.000 0.00 0.00 31.28 1.94
2939 3328 8.810652 TTTTAAAAAGTGTGTGGCTTGATATC 57.189 30.769 0.00 0.00 0.00 1.63
2940 3329 5.391312 AAAAAGTGTGTGGCTTGATATCC 57.609 39.130 0.00 0.00 0.00 2.59
2941 3330 4.307032 AAAGTGTGTGGCTTGATATCCT 57.693 40.909 0.00 0.00 0.00 3.24
2942 3331 3.272574 AGTGTGTGGCTTGATATCCTG 57.727 47.619 0.00 0.00 0.00 3.86
2943 3332 2.840038 AGTGTGTGGCTTGATATCCTGA 59.160 45.455 0.00 0.00 0.00 3.86
2944 3333 3.457380 AGTGTGTGGCTTGATATCCTGAT 59.543 43.478 0.00 0.00 0.00 2.90
2945 3334 3.812053 GTGTGTGGCTTGATATCCTGATC 59.188 47.826 0.00 0.00 0.00 2.92
2946 3335 3.062763 GTGTGGCTTGATATCCTGATCG 58.937 50.000 0.00 0.00 0.00 3.69
2947 3336 2.700371 TGTGGCTTGATATCCTGATCGT 59.300 45.455 0.00 0.00 0.00 3.73
2948 3337 3.134623 TGTGGCTTGATATCCTGATCGTT 59.865 43.478 0.00 0.00 0.00 3.85
2949 3338 3.496130 GTGGCTTGATATCCTGATCGTTG 59.504 47.826 0.00 0.00 0.00 4.10
2950 3339 3.070018 GGCTTGATATCCTGATCGTTGG 58.930 50.000 0.00 0.00 0.00 3.77
2951 3340 3.070018 GCTTGATATCCTGATCGTTGGG 58.930 50.000 0.00 0.00 0.00 4.12
2952 3341 3.244215 GCTTGATATCCTGATCGTTGGGA 60.244 47.826 0.00 0.00 0.00 4.37
2953 3342 4.310769 CTTGATATCCTGATCGTTGGGAC 58.689 47.826 0.00 0.00 31.48 4.46
2967 3356 4.916099 GTTGGGACGAGTGTATTGTAAC 57.084 45.455 0.00 0.00 0.00 2.50
2968 3357 4.309099 GTTGGGACGAGTGTATTGTAACA 58.691 43.478 0.00 0.00 0.00 2.41
2969 3358 4.811969 TGGGACGAGTGTATTGTAACAT 57.188 40.909 0.00 0.00 0.00 2.71
2970 3359 4.500127 TGGGACGAGTGTATTGTAACATG 58.500 43.478 0.00 0.00 0.00 3.21
2971 3360 4.221041 TGGGACGAGTGTATTGTAACATGA 59.779 41.667 0.00 0.00 0.00 3.07
2972 3361 5.172934 GGGACGAGTGTATTGTAACATGAA 58.827 41.667 0.00 0.00 0.00 2.57
2973 3362 5.063060 GGGACGAGTGTATTGTAACATGAAC 59.937 44.000 0.00 0.00 0.00 3.18
2974 3363 5.636121 GGACGAGTGTATTGTAACATGAACA 59.364 40.000 0.00 0.00 0.00 3.18
2975 3364 6.183360 GGACGAGTGTATTGTAACATGAACAG 60.183 42.308 0.00 0.00 0.00 3.16
2976 3365 6.452242 ACGAGTGTATTGTAACATGAACAGA 58.548 36.000 0.00 0.00 0.00 3.41
2977 3366 6.926826 ACGAGTGTATTGTAACATGAACAGAA 59.073 34.615 0.00 0.00 0.00 3.02
2978 3367 7.095774 ACGAGTGTATTGTAACATGAACAGAAC 60.096 37.037 0.00 6.32 0.00 3.01
2979 3368 7.116376 CGAGTGTATTGTAACATGAACAGAACT 59.884 37.037 0.00 5.84 0.00 3.01
2980 3369 8.677148 AGTGTATTGTAACATGAACAGAACTT 57.323 30.769 0.00 0.00 0.00 2.66
2981 3370 8.559536 AGTGTATTGTAACATGAACAGAACTTG 58.440 33.333 0.00 0.00 0.00 3.16
2982 3371 8.342634 GTGTATTGTAACATGAACAGAACTTGT 58.657 33.333 0.00 0.00 43.45 3.16
2983 3372 8.556194 TGTATTGTAACATGAACAGAACTTGTC 58.444 33.333 0.00 0.00 39.73 3.18
2984 3373 5.651172 TGTAACATGAACAGAACTTGTCG 57.349 39.130 0.00 0.00 39.73 4.35
2999 3388 4.939368 TCGGGGTTGGGTGCAACG 62.939 66.667 0.00 0.00 38.12 4.10
3028 3417 5.953548 CCAATGGATGGCTTATTATGATGGA 59.046 40.000 0.00 0.00 43.80 3.41
3044 3433 0.167470 TGGAAGCGAGTAGAACGTCG 59.833 55.000 0.00 0.00 39.25 5.12
3144 3533 0.616111 CACCCCTAGTCCTGCTCTGT 60.616 60.000 0.00 0.00 0.00 3.41
3173 3562 1.596260 CGCATGATCACTAAGGCACTG 59.404 52.381 0.00 0.00 40.86 3.66
3240 3629 3.953006 CAAGGCTTGCTCTCCTCTT 57.047 52.632 15.25 0.00 0.00 2.85
3241 3630 2.197283 CAAGGCTTGCTCTCCTCTTT 57.803 50.000 15.25 0.00 0.00 2.52
3320 3713 2.502947 GGTTTATATAGGCCTACCCCCG 59.497 54.545 16.61 0.00 36.11 5.73
3349 3742 0.986019 ATGGTAATCTGGCCGGGTGA 60.986 55.000 12.87 0.00 0.00 4.02
3382 3775 3.063084 GTCTCTCTGGTCGCCGGT 61.063 66.667 1.90 0.00 0.00 5.28
3399 3792 1.588082 GTTTCTCCGCCGTCTGGTA 59.412 57.895 0.00 0.00 37.67 3.25
3407 3800 2.754658 CCGTCTGGTAGGCCTCGT 60.755 66.667 9.68 0.00 35.27 4.18
3422 3815 1.380524 CTCGTCGACTGGTCTGGTAT 58.619 55.000 14.70 0.00 0.00 2.73
3435 3828 1.305802 TGGTATGGAGCCGACAGGT 60.306 57.895 0.00 0.00 40.50 4.00
3675 4070 4.675404 CGTCTTTCGGGCTCTTGT 57.325 55.556 0.00 0.00 35.71 3.16
3748 4143 3.706373 GGCTCCGCCTGACAGGAA 61.706 66.667 26.25 8.48 46.69 3.36
3824 4219 4.996434 GAGCACTGTGGCCACGCT 62.996 66.667 29.71 29.71 35.14 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.297736 AGGGAATGTACGGGTTAGAGAG 58.702 50.000 0.00 0.00 0.00 3.20
43 44 2.678336 GCAAAAGGAGAGGGAATGTACG 59.322 50.000 0.00 0.00 0.00 3.67
107 112 3.441572 ACCAACTCATATGCTTGCTTGAC 59.558 43.478 0.00 0.00 0.00 3.18
109 114 3.693085 AGACCAACTCATATGCTTGCTTG 59.307 43.478 0.00 0.00 0.00 4.01
149 155 8.491958 GGTAGGTTATTTATCTTCCTTTCAGGA 58.508 37.037 0.00 0.00 44.10 3.86
296 306 0.244721 GACAACAGATTGCTTGGGCC 59.755 55.000 0.00 0.00 39.66 5.80
297 307 0.109597 CGACAACAGATTGCTTGGGC 60.110 55.000 0.00 0.00 39.66 5.36
350 361 7.043722 GCAACGACACAATAGAAACAATTTTGA 60.044 33.333 0.00 0.00 0.00 2.69
384 407 2.650608 CAAACTAGCAACGGCAACTTC 58.349 47.619 0.00 0.00 44.61 3.01
386 409 0.310854 GCAAACTAGCAACGGCAACT 59.689 50.000 0.00 0.00 44.61 3.16
423 446 1.821241 CGCACAGGTGACAGACAACG 61.821 60.000 3.10 0.00 41.74 4.10
441 464 4.389576 GCGCTTCAACTGGCACCG 62.390 66.667 0.00 0.00 0.00 4.94
442 465 4.043200 GGCGCTTCAACTGGCACC 62.043 66.667 7.64 0.00 0.00 5.01
471 529 4.278669 AGCGATATCTACCGTGAAAGATGT 59.721 41.667 0.34 0.00 34.36 3.06
472 530 4.799678 AGCGATATCTACCGTGAAAGATG 58.200 43.478 0.34 0.00 34.36 2.90
474 532 4.023963 CAGAGCGATATCTACCGTGAAAGA 60.024 45.833 0.34 0.00 0.00 2.52
478 536 1.535896 GCAGAGCGATATCTACCGTGA 59.464 52.381 0.34 0.00 0.00 4.35
497 555 1.845809 CTCAACAGGTTGTGCGGAGC 61.846 60.000 11.55 0.00 46.92 4.70
498 556 0.532862 ACTCAACAGGTTGTGCGGAG 60.533 55.000 11.55 4.54 41.16 4.63
499 557 0.531974 GACTCAACAGGTTGTGCGGA 60.532 55.000 11.55 0.00 41.16 5.54
501 559 1.507141 GGGACTCAACAGGTTGTGCG 61.507 60.000 11.55 5.09 41.16 5.34
502 560 0.179018 AGGGACTCAACAGGTTGTGC 60.179 55.000 11.55 6.20 41.16 4.57
521 579 9.414295 CCGGATGATAAAAATACAACTATACGA 57.586 33.333 0.00 0.00 0.00 3.43
522 580 8.166706 GCCGGATGATAAAAATACAACTATACG 58.833 37.037 5.05 0.00 0.00 3.06
523 581 8.448615 GGCCGGATGATAAAAATACAACTATAC 58.551 37.037 5.05 0.00 0.00 1.47
524 582 7.332430 CGGCCGGATGATAAAAATACAACTATA 59.668 37.037 20.10 0.00 0.00 1.31
526 584 5.467399 CGGCCGGATGATAAAAATACAACTA 59.533 40.000 20.10 0.00 0.00 2.24
573 639 2.517402 TGCTTTTTGCCCGTCGGT 60.517 55.556 11.06 0.00 42.00 4.69
592 658 4.048470 GAGGTGGGGGCCTTGTCC 62.048 72.222 0.84 0.70 39.34 4.02
593 659 2.936032 AGAGGTGGGGGCCTTGTC 60.936 66.667 0.84 0.00 39.34 3.18
594 660 2.936032 GAGAGGTGGGGGCCTTGT 60.936 66.667 0.84 0.00 39.34 3.16
595 661 3.732849 GGAGAGGTGGGGGCCTTG 61.733 72.222 0.84 0.00 39.34 3.61
600 666 4.499116 ATCGGGGAGAGGTGGGGG 62.499 72.222 0.00 0.00 0.00 5.40
601 667 3.164269 CATCGGGGAGAGGTGGGG 61.164 72.222 0.00 0.00 0.00 4.96
604 670 1.617018 TTCTGCATCGGGGAGAGGTG 61.617 60.000 0.00 0.00 45.34 4.00
605 671 0.909610 TTTCTGCATCGGGGAGAGGT 60.910 55.000 0.00 0.00 45.34 3.85
651 920 5.958096 ACCCTGGGTTGGTGAGATACACT 62.958 52.174 14.05 0.00 40.29 3.55
652 921 3.687463 ACCCTGGGTTGGTGAGATACAC 61.687 54.545 14.05 0.00 39.93 2.90
653 922 1.285280 CCCTGGGTTGGTGAGATACA 58.715 55.000 3.97 0.00 0.00 2.29
658 927 1.991230 CCTACCCTGGGTTGGTGAG 59.009 63.158 30.99 19.23 42.22 3.51
750 1028 2.167861 GCGACTCCGATGCCAAGAC 61.168 63.158 0.00 0.00 38.22 3.01
765 1043 1.035923 TTGGATTTGGTTTGCTGCGA 58.964 45.000 0.00 0.00 0.00 5.10
768 1046 3.807553 AGGTTTTGGATTTGGTTTGCTG 58.192 40.909 0.00 0.00 0.00 4.41
772 1050 3.639561 ACGCTAGGTTTTGGATTTGGTTT 59.360 39.130 0.00 0.00 0.00 3.27
777 1055 3.482436 TCACACGCTAGGTTTTGGATTT 58.518 40.909 0.00 0.00 0.00 2.17
796 1075 5.310409 ACTTGAGAAGTGAAAGGGATTCA 57.690 39.130 0.00 0.00 45.71 2.57
849 1138 0.760945 ATCTAGACCCGGCTTGGAGG 60.761 60.000 0.00 0.00 42.00 4.30
850 1139 0.676736 GATCTAGACCCGGCTTGGAG 59.323 60.000 0.00 0.00 42.00 3.86
854 1143 1.757699 GACAAGATCTAGACCCGGCTT 59.242 52.381 0.00 0.00 0.00 4.35
882 1179 2.245028 TCCTACTACAGCTGGGATCTGT 59.755 50.000 19.93 9.32 45.71 3.41
893 1190 5.887035 AGCTAACCAACTACTCCTACTACAG 59.113 44.000 0.00 0.00 0.00 2.74
895 1192 5.884792 TCAGCTAACCAACTACTCCTACTAC 59.115 44.000 0.00 0.00 0.00 2.73
896 1193 6.070951 TCAGCTAACCAACTACTCCTACTA 57.929 41.667 0.00 0.00 0.00 1.82
902 1199 3.491104 CCGGATCAGCTAACCAACTACTC 60.491 52.174 0.00 0.00 0.00 2.59
903 1200 2.431057 CCGGATCAGCTAACCAACTACT 59.569 50.000 0.00 0.00 0.00 2.57
905 1202 1.760613 CCCGGATCAGCTAACCAACTA 59.239 52.381 0.73 0.00 0.00 2.24
906 1203 0.541863 CCCGGATCAGCTAACCAACT 59.458 55.000 0.73 0.00 0.00 3.16
931 1228 1.444553 GGGAGAGCAGAACGTGTCG 60.445 63.158 0.00 0.00 0.00 4.35
957 1254 1.966451 GTGGTGTTTGGAGCGGGAG 60.966 63.158 0.00 0.00 0.00 4.30
958 1255 2.112297 GTGGTGTTTGGAGCGGGA 59.888 61.111 0.00 0.00 0.00 5.14
959 1256 2.983592 GGTGGTGTTTGGAGCGGG 60.984 66.667 0.00 0.00 0.00 6.13
960 1257 3.353836 CGGTGGTGTTTGGAGCGG 61.354 66.667 0.00 0.00 0.00 5.52
1176 1481 4.329801 TCAATCAACGAATCAATGGAGACG 59.670 41.667 0.00 0.00 0.00 4.18
1179 1484 4.637534 ACCTCAATCAACGAATCAATGGAG 59.362 41.667 0.00 0.00 0.00 3.86
1200 1505 2.663852 CCACGTCGAACCCACACC 60.664 66.667 0.00 0.00 0.00 4.16
1217 1526 2.809601 CGCCACCTACACGAGTGC 60.810 66.667 2.76 0.00 32.48 4.40
1219 1528 3.379445 CCCGCCACCTACACGAGT 61.379 66.667 0.00 0.00 0.00 4.18
1223 1532 2.433664 CGAACCCGCCACCTACAC 60.434 66.667 0.00 0.00 0.00 2.90
1293 1608 1.266718 GTGCAGATTTTGTCGAAGGCA 59.733 47.619 0.00 0.00 45.30 4.75
1345 1660 2.508663 GTAGAAGGTGGCGCCGTC 60.509 66.667 23.90 23.06 44.60 4.79
1506 1821 0.687757 AGGCCCAGACGAGCTCATAA 60.688 55.000 15.40 0.00 0.00 1.90
1815 2142 3.757248 CTTCTCCCGCATTCCCCGG 62.757 68.421 0.00 0.00 45.17 5.73
1816 2143 2.203070 CTTCTCCCGCATTCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
1818 2145 2.193248 CCCTTCTCCCGCATTCCC 59.807 66.667 0.00 0.00 0.00 3.97
1821 2148 1.152881 GATGCCCTTCTCCCGCATT 60.153 57.895 0.00 0.00 43.09 3.56
1904 2231 2.867855 TTCTTGAGGCACGCGAGGT 61.868 57.895 15.93 0.00 40.21 3.85
2010 2337 0.608640 ACGGCAGGTAGACCTCTTTG 59.391 55.000 0.00 0.00 46.65 2.77
2796 3185 0.179215 GCTCGTTCGGCATCTTGTTG 60.179 55.000 0.00 0.00 0.00 3.33
2835 3224 3.628646 CTTCTCCTTGGGCCCGGTG 62.629 68.421 19.37 14.25 0.00 4.94
2913 3302 9.255304 GATATCAAGCCACACACTTTTTAAAAA 57.745 29.630 12.62 12.62 0.00 1.94
2914 3303 7.870445 GGATATCAAGCCACACACTTTTTAAAA 59.130 33.333 4.83 0.00 0.00 1.52
2915 3304 7.232534 AGGATATCAAGCCACACACTTTTTAAA 59.767 33.333 4.83 0.00 31.71 1.52
2916 3305 6.719370 AGGATATCAAGCCACACACTTTTTAA 59.281 34.615 4.83 0.00 31.71 1.52
2917 3306 6.150976 CAGGATATCAAGCCACACACTTTTTA 59.849 38.462 4.83 0.00 31.71 1.52
2918 3307 5.047802 CAGGATATCAAGCCACACACTTTTT 60.048 40.000 4.83 0.00 31.71 1.94
2919 3308 4.460382 CAGGATATCAAGCCACACACTTTT 59.540 41.667 4.83 0.00 31.71 2.27
2920 3309 4.012374 CAGGATATCAAGCCACACACTTT 58.988 43.478 4.83 0.00 31.71 2.66
2921 3310 3.264193 TCAGGATATCAAGCCACACACTT 59.736 43.478 4.83 0.00 31.71 3.16
2922 3311 2.840038 TCAGGATATCAAGCCACACACT 59.160 45.455 4.83 0.00 31.71 3.55
2923 3312 3.266510 TCAGGATATCAAGCCACACAC 57.733 47.619 4.83 0.00 31.71 3.82
2924 3313 3.493176 CGATCAGGATATCAAGCCACACA 60.493 47.826 4.83 0.00 31.71 3.72
2925 3314 3.062763 CGATCAGGATATCAAGCCACAC 58.937 50.000 4.83 0.00 31.71 3.82
2926 3315 2.700371 ACGATCAGGATATCAAGCCACA 59.300 45.455 4.83 0.00 31.71 4.17
2927 3316 3.393089 ACGATCAGGATATCAAGCCAC 57.607 47.619 4.83 0.00 31.71 5.01
2928 3317 3.494924 CCAACGATCAGGATATCAAGCCA 60.495 47.826 4.83 0.00 31.71 4.75
2929 3318 3.070018 CCAACGATCAGGATATCAAGCC 58.930 50.000 4.83 0.00 0.00 4.35
2930 3319 3.070018 CCCAACGATCAGGATATCAAGC 58.930 50.000 4.83 0.00 0.00 4.01
2931 3320 4.310769 GTCCCAACGATCAGGATATCAAG 58.689 47.826 4.83 0.00 30.92 3.02
2932 3321 4.336889 GTCCCAACGATCAGGATATCAA 57.663 45.455 4.83 0.00 30.92 2.57
2946 3335 4.309099 TGTTACAATACACTCGTCCCAAC 58.691 43.478 0.00 0.00 0.00 3.77
2947 3336 4.603989 TGTTACAATACACTCGTCCCAA 57.396 40.909 0.00 0.00 0.00 4.12
2948 3337 4.221041 TCATGTTACAATACACTCGTCCCA 59.779 41.667 0.00 0.00 0.00 4.37
2949 3338 4.751060 TCATGTTACAATACACTCGTCCC 58.249 43.478 0.00 0.00 0.00 4.46
2950 3339 5.636121 TGTTCATGTTACAATACACTCGTCC 59.364 40.000 0.00 0.00 0.00 4.79
2951 3340 6.584942 TCTGTTCATGTTACAATACACTCGTC 59.415 38.462 0.00 0.00 0.00 4.20
2952 3341 6.452242 TCTGTTCATGTTACAATACACTCGT 58.548 36.000 0.00 0.00 0.00 4.18
2953 3342 6.944557 TCTGTTCATGTTACAATACACTCG 57.055 37.500 0.00 0.00 0.00 4.18
2954 3343 8.311650 AGTTCTGTTCATGTTACAATACACTC 57.688 34.615 0.00 0.00 0.00 3.51
2955 3344 8.559536 CAAGTTCTGTTCATGTTACAATACACT 58.440 33.333 0.00 0.00 0.00 3.55
2956 3345 8.342634 ACAAGTTCTGTTCATGTTACAATACAC 58.657 33.333 0.00 0.00 32.99 2.90
2957 3346 8.445275 ACAAGTTCTGTTCATGTTACAATACA 57.555 30.769 0.00 0.00 32.99 2.29
2958 3347 7.740346 CGACAAGTTCTGTTCATGTTACAATAC 59.260 37.037 0.00 0.78 38.84 1.89
2959 3348 7.095397 CCGACAAGTTCTGTTCATGTTACAATA 60.095 37.037 0.00 0.00 38.84 1.90
2960 3349 6.293407 CCGACAAGTTCTGTTCATGTTACAAT 60.293 38.462 0.00 0.00 38.84 2.71
2961 3350 5.007234 CCGACAAGTTCTGTTCATGTTACAA 59.993 40.000 0.00 0.00 38.84 2.41
2962 3351 4.509970 CCGACAAGTTCTGTTCATGTTACA 59.490 41.667 0.00 0.00 38.84 2.41
2963 3352 4.084013 CCCGACAAGTTCTGTTCATGTTAC 60.084 45.833 0.00 0.00 38.84 2.50
2964 3353 4.062293 CCCGACAAGTTCTGTTCATGTTA 58.938 43.478 0.00 0.00 38.84 2.41
2965 3354 2.878406 CCCGACAAGTTCTGTTCATGTT 59.122 45.455 0.00 0.00 38.84 2.71
2966 3355 2.494059 CCCGACAAGTTCTGTTCATGT 58.506 47.619 0.00 0.00 38.84 3.21
2967 3356 1.806542 CCCCGACAAGTTCTGTTCATG 59.193 52.381 0.00 0.00 38.84 3.07
2968 3357 1.420138 ACCCCGACAAGTTCTGTTCAT 59.580 47.619 0.00 0.00 38.84 2.57
2969 3358 0.834612 ACCCCGACAAGTTCTGTTCA 59.165 50.000 0.00 0.00 38.84 3.18
2970 3359 1.602377 CAACCCCGACAAGTTCTGTTC 59.398 52.381 0.00 0.00 38.84 3.18
2971 3360 1.675552 CAACCCCGACAAGTTCTGTT 58.324 50.000 0.00 0.00 38.84 3.16
2972 3361 0.179029 CCAACCCCGACAAGTTCTGT 60.179 55.000 0.00 0.00 42.61 3.41
2973 3362 0.889186 CCCAACCCCGACAAGTTCTG 60.889 60.000 0.00 0.00 0.00 3.02
2974 3363 1.350310 ACCCAACCCCGACAAGTTCT 61.350 55.000 0.00 0.00 0.00 3.01
2975 3364 1.149854 ACCCAACCCCGACAAGTTC 59.850 57.895 0.00 0.00 0.00 3.01
2976 3365 1.152839 CACCCAACCCCGACAAGTT 60.153 57.895 0.00 0.00 0.00 2.66
2977 3366 2.513895 CACCCAACCCCGACAAGT 59.486 61.111 0.00 0.00 0.00 3.16
2978 3367 2.983592 GCACCCAACCCCGACAAG 60.984 66.667 0.00 0.00 0.00 3.16
2979 3368 3.360423 TTGCACCCAACCCCGACAA 62.360 57.895 0.00 0.00 0.00 3.18
2980 3369 3.810188 TTGCACCCAACCCCGACA 61.810 61.111 0.00 0.00 0.00 4.35
2981 3370 3.292159 GTTGCACCCAACCCCGAC 61.292 66.667 0.00 0.00 44.37 4.79
2982 3371 4.939368 CGTTGCACCCAACCCCGA 62.939 66.667 0.00 0.00 46.76 5.14
2983 3372 3.828694 TACGTTGCACCCAACCCCG 62.829 63.158 0.00 0.00 46.76 5.73
2984 3373 1.303806 ATACGTTGCACCCAACCCC 60.304 57.895 0.00 0.00 46.76 4.95
3020 3409 3.630769 ACGTTCTACTCGCTTCCATCATA 59.369 43.478 0.00 0.00 0.00 2.15
3024 3413 1.202154 CGACGTTCTACTCGCTTCCAT 60.202 52.381 0.00 0.00 0.00 3.41
3097 3486 4.475135 GGAGAGCCCCGAACCTGC 62.475 72.222 0.00 0.00 0.00 4.85
3144 3533 1.688884 TGATCATGCGGAGACCCCA 60.689 57.895 0.00 0.00 34.14 4.96
3173 3562 1.279271 AGGAGCACCATTGTACTCACC 59.721 52.381 2.07 0.00 36.72 4.02
3240 3629 5.590818 AGAATTAGACTCACACCTAGGGAA 58.409 41.667 14.81 0.00 0.00 3.97
3241 3630 5.208294 AGAATTAGACTCACACCTAGGGA 57.792 43.478 14.81 0.00 0.00 4.20
3298 3688 3.811842 GGGGGTAGGCCTATATAAACCT 58.188 50.000 17.38 8.02 36.27 3.50
3320 3713 4.324331 GGCCAGATTACCATTATACCCCTC 60.324 50.000 0.00 0.00 0.00 4.30
3328 3721 1.142060 CACCCGGCCAGATTACCATTA 59.858 52.381 2.24 0.00 0.00 1.90
3349 3742 2.352817 GACTGACAGTCGGGTCCTT 58.647 57.895 19.41 0.00 35.28 3.36
3382 3775 1.601419 CCTACCAGACGGCGGAGAAA 61.601 60.000 13.24 0.00 34.57 2.52
3393 3786 1.748122 GTCGACGAGGCCTACCAGA 60.748 63.158 4.42 0.00 39.06 3.86
3399 3792 3.063084 GACCAGTCGACGAGGCCT 61.063 66.667 24.23 3.86 0.00 5.19
3404 3797 1.092348 CATACCAGACCAGTCGACGA 58.908 55.000 10.46 0.00 34.09 4.20
3407 3800 1.763968 CTCCATACCAGACCAGTCGA 58.236 55.000 0.00 0.00 34.09 4.20
3513 3907 4.814294 CGGGACTGTAGCCACGCC 62.814 72.222 0.00 0.00 0.00 5.68
3540 3934 2.383855 GAGTGGCTACAGTGATCTCCT 58.616 52.381 2.02 0.00 0.00 3.69
3748 4143 3.461773 CTCCGCCCCTGACGTCAT 61.462 66.667 20.40 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.