Multiple sequence alignment - TraesCS3B01G419700

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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 TraesCS3B01G419700 chr3B 100.000 9212 0 0 1 9212 656281464 656290675 0.000000e+00 17012.0
1 TraesCS3B01G419700 chr3A 93.949 3900 145 27 1 3835 638019286 638023159 0.000000e+00 5810.0
2 TraesCS3B01G419700 chr3A 96.499 2285 43 12 3907 6155 638023151 638025434 0.000000e+00 3742.0
3 TraesCS3B01G419700 chr3A 92.927 2050 90 21 6153 8181 638025678 638027693 0.000000e+00 2931.0
4 TraesCS3B01G419700 chr3A 90.377 1008 57 13 8208 9210 638027692 638028664 0.000000e+00 1288.0
5 TraesCS3B01G419700 chr3A 91.241 137 9 2 4843 4979 12523916 12523783 5.680000e-42 183.0
6 TraesCS3B01G419700 chr3D 94.761 2596 60 19 846 3401 496776370 496778929 0.000000e+00 3971.0
7 TraesCS3B01G419700 chr3D 94.606 2095 83 13 6153 8222 496783522 496785611 0.000000e+00 3216.0
8 TraesCS3B01G419700 chr3D 97.650 1745 21 1 4431 6155 496781534 496783278 0.000000e+00 2977.0
9 TraesCS3B01G419700 chr3D 96.451 1127 28 7 3368 4483 496780407 496781532 0.000000e+00 1849.0
10 TraesCS3B01G419700 chr3D 87.634 1027 70 24 8205 9212 496785620 496786608 0.000000e+00 1140.0
11 TraesCS3B01G419700 chr3D 90.782 857 72 7 1 855 496770823 496771674 0.000000e+00 1138.0
12 TraesCS3B01G419700 chr1B 91.525 59 5 0 4982 5040 534300219 534300277 2.130000e-11 82.4
13 TraesCS3B01G419700 chr7A 100.000 29 0 0 1189 1217 15049414 15049386 5.000000e-03 54.7
14 TraesCS3B01G419700 chr5B 100.000 29 0 0 1192 1220 696995220 696995248 5.000000e-03 54.7
15 TraesCS3B01G419700 chr5B 100.000 28 0 0 1193 1220 131324561 131324588 1.700000e-02 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 TraesCS3B01G419700 chr3B 656281464 656290675 9211 False 17012.00 17012 100.0000 1 9212 1 chr3B.!!$F1 9211
1 TraesCS3B01G419700 chr3A 638019286 638028664 9378 False 3442.75 5810 93.4380 1 9210 4 chr3A.!!$F1 9209
2 TraesCS3B01G419700 chr3D 496776370 496786608 10238 False 2630.60 3971 94.2204 846 9212 5 chr3D.!!$F2 8366
3 TraesCS3B01G419700 chr3D 496770823 496771674 851 False 1138.00 1138 90.7820 1 855 1 chr3D.!!$F1 854

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
355 358 0.035056 CAAAAGGCTGACGGGGATCT 60.035 55.000 0.00 0.0 0.00 2.75 F
1349 1374 0.459237 CTGCCGTCAGATGGTGAGAC 60.459 60.000 10.58 0.0 42.95 3.36 F
1806 1889 3.101437 TCGTGGAAGCAGGGAATAAGTA 58.899 45.455 0.00 0.0 0.00 2.24 F
2174 2257 1.535896 GCGAGTATCAGGAGCGATACA 59.464 52.381 12.27 0.0 46.81 2.29 F
3212 3300 0.105778 GCCCTATGTGTGGCTCTCTC 59.894 60.000 0.00 0.0 44.46 3.20 F
4144 5748 0.035056 GTCCCCTGCTACAACTGCAT 60.035 55.000 0.00 0.0 39.86 3.96 F
5084 6783 2.068519 GCTGCCTGCAAATAAAACACC 58.931 47.619 0.00 0.0 42.31 4.16 F
6032 7731 0.537653 GAGGACCTTACACCTGCCTC 59.462 60.000 0.00 0.0 36.57 4.70 F
6552 8514 0.317160 TGTCAGAGCTGTTACACCGG 59.683 55.000 0.00 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1701 2.191908 GTGTCCAGTGCCACCACA 59.808 61.111 0.00 0.00 44.53 4.17 R
2174 2257 2.875094 ATCTTCTTGACTTGCTGCCT 57.125 45.000 0.00 0.00 0.00 4.75 R
3052 3140 4.559153 AGTAAATGAAACAAGCATGCCAC 58.441 39.130 15.66 0.34 0.00 5.01 R
3933 5537 1.337703 TGTCAATGCTTGCCTGTCAAC 59.662 47.619 0.00 0.00 0.00 3.18 R
5117 6816 0.322816 AACATTCACCGCTGCCTCAT 60.323 50.000 0.00 0.00 0.00 2.90 R
5862 7561 1.985473 ACAGTTCCAGCATCTGCAAA 58.015 45.000 4.79 0.00 45.16 3.68 R
6433 8378 0.534203 TGACACTTCCAAACGGCTCC 60.534 55.000 0.00 0.00 0.00 4.70 R
7768 9733 1.146358 GACCGGTATGCTGCGAGAAC 61.146 60.000 7.34 0.00 0.00 3.01 R
8381 10380 0.316442 CACGCCTATGCTGCATTTCG 60.316 55.000 21.56 21.10 34.43 3.46 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
29 30 6.923199 ATGGAATTCAAAATGACCTTCAGT 57.077 33.333 7.93 0.00 0.00 3.41
40 41 3.184628 TGACCTTCAGTGATCATTCCCT 58.815 45.455 0.00 0.00 0.00 4.20
59 60 2.035449 CCTCACGACCTACAACTTCACA 59.965 50.000 0.00 0.00 0.00 3.58
60 61 3.491964 CCTCACGACCTACAACTTCACAA 60.492 47.826 0.00 0.00 0.00 3.33
97 98 4.683400 CGTATAGGCCAAGGTTGTGAGAAT 60.683 45.833 5.01 0.00 0.00 2.40
159 160 4.380867 GCGGAGTTGAATGTTTGGAATGAT 60.381 41.667 0.00 0.00 0.00 2.45
203 204 7.118723 AGGAAGATGCATTTTAGTGGAACATA 58.881 34.615 0.00 0.00 44.52 2.29
205 206 7.148086 GGAAGATGCATTTTAGTGGAACATACA 60.148 37.037 0.00 0.00 44.52 2.29
209 210 7.459795 TGCATTTTAGTGGAACATACATTCA 57.540 32.000 0.00 0.00 44.52 2.57
218 219 8.579850 AGTGGAACATACATTCAAACATGTAT 57.420 30.769 0.00 1.26 46.84 2.29
250 251 7.558444 TCCTTGTGTGGTTGTTCTTATTTAACT 59.442 33.333 0.00 0.00 0.00 2.24
251 252 7.647715 CCTTGTGTGGTTGTTCTTATTTAACTG 59.352 37.037 0.00 0.00 0.00 3.16
284 286 7.632721 TGAATACTTCTTTAACCGTTCAACAC 58.367 34.615 0.00 0.00 0.00 3.32
321 323 0.834612 ATTGCATTGGCCAAGATGGG 59.165 50.000 24.94 11.38 38.19 4.00
347 349 0.890683 CCCCACATCAAAAGGCTGAC 59.109 55.000 0.00 0.00 0.00 3.51
348 350 0.523072 CCCACATCAAAAGGCTGACG 59.477 55.000 0.00 0.00 0.00 4.35
355 358 0.035056 CAAAAGGCTGACGGGGATCT 60.035 55.000 0.00 0.00 0.00 2.75
359 362 0.909610 AGGCTGACGGGGATCTTCAA 60.910 55.000 0.00 0.00 0.00 2.69
403 406 1.455217 GGCAAGCTGGATGGCATCT 60.455 57.895 25.48 4.25 42.45 2.90
405 408 0.750546 GCAAGCTGGATGGCATCTCA 60.751 55.000 25.48 19.58 34.17 3.27
458 461 6.670464 TCCCTTACACAGATTAGGTCACATTA 59.330 38.462 0.00 0.00 0.00 1.90
463 466 9.952030 TTACACAGATTAGGTCACATTATTTGA 57.048 29.630 0.00 0.00 0.00 2.69
467 470 9.739276 ACAGATTAGGTCACATTATTTGAAAGA 57.261 29.630 0.00 0.00 0.00 2.52
485 488 9.528018 TTTGAAAGAGTGGTGTTATTTTTCATC 57.472 29.630 0.00 0.00 34.31 2.92
524 527 4.343814 TGTATTCGGTGGATGCTAATCTCA 59.656 41.667 0.00 0.00 32.95 3.27
525 528 3.904800 TTCGGTGGATGCTAATCTCAA 57.095 42.857 0.00 0.00 32.95 3.02
530 533 2.115427 TGGATGCTAATCTCAACGGGA 58.885 47.619 0.00 0.00 32.95 5.14
538 541 4.394920 GCTAATCTCAACGGGAATGTTTGA 59.605 41.667 0.00 0.00 0.00 2.69
602 605 2.159198 GCAACTTTTCATCCCGCATCAT 60.159 45.455 0.00 0.00 0.00 2.45
606 609 4.019174 ACTTTTCATCCCGCATCATCTTT 58.981 39.130 0.00 0.00 0.00 2.52
611 614 3.763360 TCATCCCGCATCATCTTTGTTTT 59.237 39.130 0.00 0.00 0.00 2.43
625 628 2.027003 TGTTTTCGACCAACTTCGGT 57.973 45.000 7.90 0.00 43.91 4.69
651 654 4.063967 CACCGCGGTCTGGCACTA 62.064 66.667 31.80 0.00 0.00 2.74
663 666 2.342279 GCACTAGACACCACCGCA 59.658 61.111 0.00 0.00 0.00 5.69
716 719 1.059369 CTTGTAGCACGCACATCGC 59.941 57.895 0.00 0.00 43.23 4.58
725 728 2.410469 GCACATCGCCATCTTGCC 59.590 61.111 0.00 0.00 32.94 4.52
744 747 2.586425 CCTGACACCCTTCATTGTTGT 58.414 47.619 0.00 0.00 0.00 3.32
773 776 0.878961 GTTCACCGTCGACTTGCCTT 60.879 55.000 14.70 0.00 0.00 4.35
787 790 0.534203 TGCCTTCAACTCCGTTCACC 60.534 55.000 0.00 0.00 0.00 4.02
805 821 1.211969 CGTCTCCTTTTCTCGCCGA 59.788 57.895 0.00 0.00 0.00 5.54
872 888 7.394641 CCTACCTTTTCTTGCTAAAATTCTCCT 59.605 37.037 0.00 0.00 0.00 3.69
904 920 6.479660 TCAACAAAGCTCATTGATTTTTGACC 59.520 34.615 20.73 0.00 32.23 4.02
983 1003 2.394632 TCGCTATTAGCTCTTTCCCCA 58.605 47.619 13.55 0.00 39.60 4.96
984 1004 2.972713 TCGCTATTAGCTCTTTCCCCAT 59.027 45.455 13.55 0.00 39.60 4.00
985 1005 3.006967 TCGCTATTAGCTCTTTCCCCATC 59.993 47.826 13.55 0.00 39.60 3.51
986 1006 3.244215 CGCTATTAGCTCTTTCCCCATCA 60.244 47.826 13.55 0.00 39.60 3.07
987 1007 4.068599 GCTATTAGCTCTTTCCCCATCAC 58.931 47.826 8.47 0.00 38.45 3.06
988 1008 4.202409 GCTATTAGCTCTTTCCCCATCACT 60.202 45.833 8.47 0.00 38.45 3.41
1349 1374 0.459237 CTGCCGTCAGATGGTGAGAC 60.459 60.000 10.58 0.00 42.95 3.36
1622 1701 5.677319 TCTGATAGGTGAAATCGGAGTTT 57.323 39.130 0.00 0.00 34.53 2.66
1773 1856 7.552687 TGAATACAGTTCATTAAGCTGTTAGGG 59.447 37.037 1.72 0.00 42.60 3.53
1806 1889 3.101437 TCGTGGAAGCAGGGAATAAGTA 58.899 45.455 0.00 0.00 0.00 2.24
2174 2257 1.535896 GCGAGTATCAGGAGCGATACA 59.464 52.381 12.27 0.00 46.81 2.29
2212 2295 7.371043 AGAAGATAGGGGAACTTGAGGTATAA 58.629 38.462 0.00 0.00 0.00 0.98
2213 2296 8.019652 AGAAGATAGGGGAACTTGAGGTATAAT 58.980 37.037 0.00 0.00 0.00 1.28
3030 3118 3.553715 GCCTTGACGATGATAGCTGATGA 60.554 47.826 0.00 0.00 0.00 2.92
3031 3119 3.986572 CCTTGACGATGATAGCTGATGAC 59.013 47.826 0.00 0.00 0.00 3.06
3032 3120 4.261952 CCTTGACGATGATAGCTGATGACT 60.262 45.833 0.00 0.00 0.00 3.41
3033 3121 4.234530 TGACGATGATAGCTGATGACTG 57.765 45.455 0.00 0.00 0.00 3.51
3034 3122 3.885297 TGACGATGATAGCTGATGACTGA 59.115 43.478 0.00 0.00 0.00 3.41
3035 3123 4.522022 TGACGATGATAGCTGATGACTGAT 59.478 41.667 0.00 0.00 0.00 2.90
3036 3124 4.807443 ACGATGATAGCTGATGACTGATG 58.193 43.478 0.00 0.00 0.00 3.07
3052 3140 9.888878 GATGACTGATGTTATGTGAATATTTGG 57.111 33.333 0.00 0.00 0.00 3.28
3212 3300 0.105778 GCCCTATGTGTGGCTCTCTC 59.894 60.000 0.00 0.00 44.46 3.20
3225 3316 2.224018 GGCTCTCTCAACTGCCATAGAG 60.224 54.545 0.00 0.00 44.34 2.43
3365 3456 7.921786 TGTACCCTTCAATTTTAGACATCTG 57.078 36.000 0.00 0.00 0.00 2.90
3366 3457 7.685481 TGTACCCTTCAATTTTAGACATCTGA 58.315 34.615 0.00 0.00 0.00 3.27
3368 3459 6.784031 ACCCTTCAATTTTAGACATCTGAGT 58.216 36.000 0.00 0.00 0.00 3.41
3479 5083 7.118723 TGTATATCCAGGAAAAAGAAGTGCAT 58.881 34.615 0.00 0.00 0.00 3.96
3576 5180 1.804748 GGAAACGAGCCGAAACAGAAT 59.195 47.619 1.50 0.00 0.00 2.40
3885 5489 2.746904 TGATATTGTTGGCAAGGACGTG 59.253 45.455 0.00 0.00 38.10 4.49
4143 5747 1.374947 GTCCCCTGCTACAACTGCA 59.625 57.895 0.00 0.00 38.81 4.41
4144 5748 0.035056 GTCCCCTGCTACAACTGCAT 60.035 55.000 0.00 0.00 39.86 3.96
4205 5809 7.054124 ACCATAAATACACTTGTAGTCCCATG 58.946 38.462 0.00 0.00 33.52 3.66
4425 6044 8.464404 TGGTTAAATTATCGATCTAGGGATACG 58.536 37.037 0.00 0.00 37.60 3.06
4448 6067 5.450412 CGCATAGGCATTACAAACTGGAAAT 60.450 40.000 0.00 0.00 41.24 2.17
4544 6217 6.283544 TGTCAATAATTCACATTGGCATGT 57.716 33.333 3.19 0.00 41.69 3.21
4688 6361 3.181434 TGTCATCCAAGGTTAGCAGGTTT 60.181 43.478 0.00 0.00 0.00 3.27
4787 6466 8.369424 CAGAAAATGGAGTCAGATCTATCTCAT 58.631 37.037 20.51 12.81 34.22 2.90
5084 6783 2.068519 GCTGCCTGCAAATAAAACACC 58.931 47.619 0.00 0.00 42.31 4.16
5266 6965 5.399013 GTTGTGGGTGCAACTATGAATTAC 58.601 41.667 0.00 0.00 43.74 1.89
5406 7105 6.360329 CACAAAAGTACTTCGTATGGTGAAC 58.640 40.000 8.95 0.00 0.00 3.18
6032 7731 0.537653 GAGGACCTTACACCTGCCTC 59.462 60.000 0.00 0.00 36.57 4.70
6140 7839 8.911247 ATGCGTTCAACTCTATTAATTTTTCC 57.089 30.769 0.00 0.00 0.00 3.13
6188 8133 1.428912 GGCATCCCCCAATTATCTGGA 59.571 52.381 0.00 0.00 38.96 3.86
6255 8200 1.522258 CAAATTTGTCAACGTGGCTGC 59.478 47.619 10.15 0.00 0.00 5.25
6331 8276 2.353803 GGTACAGGACGAGCATTCAGTT 60.354 50.000 0.00 0.00 0.00 3.16
6336 8281 2.499289 AGGACGAGCATTCAGTTCTGAT 59.501 45.455 3.28 0.00 0.00 2.90
6458 8419 2.878406 CCGTTTGGAAGTGTCAGTTCAT 59.122 45.455 19.66 0.00 37.49 2.57
6510 8472 2.932194 AGGAGCTCCAGCAAGCCA 60.932 61.111 33.90 0.00 43.56 4.75
6550 8512 2.678324 GTCTGTCAGAGCTGTTACACC 58.322 52.381 1.75 0.00 0.00 4.16
6552 8514 0.317160 TGTCAGAGCTGTTACACCGG 59.683 55.000 0.00 0.00 0.00 5.28
6570 8532 0.326618 GGGAGGGGATCTTGGTGAGA 60.327 60.000 0.00 0.00 39.13 3.27
6615 8577 3.072330 TGAAGGCTGGTGATAGAAACACA 59.928 43.478 0.00 0.00 39.65 3.72
6619 8581 2.875672 GCTGGTGATAGAAACACAGCCA 60.876 50.000 0.00 0.00 39.65 4.75
6622 8584 3.244875 TGGTGATAGAAACACAGCCATGT 60.245 43.478 0.00 0.00 41.57 3.21
6661 8623 8.201464 GGAAAAGAACTTTGTATTGGGAAAGAA 58.799 33.333 0.00 0.00 34.02 2.52
6723 8685 5.011635 GGATGTTTGGTGGGTTTAGAAATGT 59.988 40.000 0.00 0.00 0.00 2.71
6724 8686 5.941555 TGTTTGGTGGGTTTAGAAATGTT 57.058 34.783 0.00 0.00 0.00 2.71
6808 8771 2.134201 TCTCATATGCCAACTACGCG 57.866 50.000 3.53 3.53 0.00 6.01
6814 8777 5.956642 TCATATGCCAACTACGCGATTATA 58.043 37.500 15.93 0.00 0.00 0.98
6864 8827 8.964420 TTCAACATTTCGTCCAATTTTATCTC 57.036 30.769 0.00 0.00 0.00 2.75
6907 8870 8.758633 TCTAACTATTCTCAGCTGTTAAACAC 57.241 34.615 14.67 0.00 0.00 3.32
7234 9197 6.374333 TCTGGAATGTTCTACAAATAACCTGC 59.626 38.462 0.00 0.00 0.00 4.85
7304 9268 6.875972 AGTCCAGTTGGTGTATTAGATCTT 57.124 37.500 0.00 0.00 36.34 2.40
7309 9273 6.108687 CAGTTGGTGTATTAGATCTTGAGCA 58.891 40.000 0.00 0.00 0.00 4.26
7473 9437 4.621460 GGAAAGCCTCGAATTGTTTTTAGC 59.379 41.667 0.00 0.00 0.00 3.09
7625 9589 7.482169 ACAAGAGAAGTATATGTTGAGGACA 57.518 36.000 0.00 0.00 43.71 4.02
7685 9649 9.474313 TTTGTAGGTATGCTTCCATCTAAAAAT 57.526 29.630 0.00 0.00 32.85 1.82
7707 9671 9.777297 AAAATTGTTTGTAGGTATGATGCTTTT 57.223 25.926 0.00 0.00 0.00 2.27
7741 9705 4.582240 GGAAAAGAATATCCCCTTGCAGAG 59.418 45.833 0.00 0.00 0.00 3.35
7745 9709 4.820775 AGAATATCCCCTTGCAGAGACTA 58.179 43.478 0.00 0.00 0.00 2.59
7748 9712 3.922171 ATCCCCTTGCAGAGACTAAAG 57.078 47.619 0.00 0.00 0.00 1.85
7753 9718 2.746362 CCTTGCAGAGACTAAAGGCTTG 59.254 50.000 0.00 0.00 33.28 4.01
7754 9719 3.406764 CTTGCAGAGACTAAAGGCTTGT 58.593 45.455 0.00 0.00 0.00 3.16
7766 9731 9.384764 AGACTAAAGGCTTGTGTATTATCTTTC 57.615 33.333 0.00 0.00 0.00 2.62
7768 9733 6.436843 AAAGGCTTGTGTATTATCTTTCCG 57.563 37.500 0.00 0.00 0.00 4.30
7774 9739 6.508088 GCTTGTGTATTATCTTTCCGTTCTCG 60.508 42.308 0.00 0.00 0.00 4.04
7784 9749 2.230940 CCGTTCTCGCAGCATACCG 61.231 63.158 0.00 0.00 35.54 4.02
7788 9753 1.600511 TTCTCGCAGCATACCGGTCA 61.601 55.000 12.40 0.00 0.00 4.02
7812 9777 3.773860 TTGCAATGTATTGGCGGTTAG 57.226 42.857 0.00 0.00 38.21 2.34
7833 9798 2.096218 GCAGAAGTGTGCTTAGGAAACG 60.096 50.000 0.00 0.00 40.54 3.60
7838 9803 3.508762 AGTGTGCTTAGGAAACGTATCG 58.491 45.455 0.00 0.00 0.00 2.92
7843 9808 3.243636 TGCTTAGGAAACGTATCGGATCC 60.244 47.826 0.00 0.00 36.47 3.36
7844 9809 3.243636 GCTTAGGAAACGTATCGGATCCA 60.244 47.826 13.41 0.00 37.89 3.41
7845 9810 4.560919 GCTTAGGAAACGTATCGGATCCAT 60.561 45.833 13.41 7.21 37.89 3.41
7846 9811 3.662247 AGGAAACGTATCGGATCCATC 57.338 47.619 13.41 0.00 37.89 3.51
7847 9812 3.231818 AGGAAACGTATCGGATCCATCT 58.768 45.455 13.41 0.00 37.89 2.90
7888 9853 2.959516 TGCAGTCGTATGTTGAAGGAG 58.040 47.619 0.00 0.00 0.00 3.69
8004 9974 3.859745 AATACGAGCGCATACAATGTG 57.140 42.857 11.47 0.00 43.42 3.21
8166 10139 1.859080 GAGCTAGTTTTATCCGTGGCG 59.141 52.381 0.00 0.00 0.00 5.69
8303 10302 2.577112 CGTACTGCGACTCAGCCG 60.577 66.667 0.00 0.00 46.76 5.52
8381 10380 0.947244 CCACAGTCAAGGCACAGTTC 59.053 55.000 0.00 0.00 0.00 3.01
8390 10389 0.877071 AGGCACAGTTCGAAATGCAG 59.123 50.000 24.26 17.83 39.92 4.41
8591 10606 2.725641 GTTCAACGGGTGCCCAAC 59.274 61.111 8.14 0.54 35.37 3.77
8719 10737 3.486542 GCTAGTTGCTGAACTAATGCTGC 60.487 47.826 0.00 0.00 42.82 5.25
8724 10742 2.290514 TGCTGAACTAATGCTGCTTCCT 60.291 45.455 0.00 0.00 0.00 3.36
8731 10749 1.538687 AATGCTGCTTCCTTGTGGCC 61.539 55.000 0.00 0.00 0.00 5.36
8750 10768 1.632422 CAAACTGATCATTTGCGGGC 58.368 50.000 13.83 0.00 30.77 6.13
8940 10964 1.609320 GGTGAACAAGACCTCTGCTCC 60.609 57.143 0.00 0.00 0.00 4.70
8941 10965 0.687354 TGAACAAGACCTCTGCTCCC 59.313 55.000 0.00 0.00 0.00 4.30
8942 10966 0.980423 GAACAAGACCTCTGCTCCCT 59.020 55.000 0.00 0.00 0.00 4.20
9000 11024 2.081161 GGGAGAGGCATGACCCCAT 61.081 63.158 6.50 0.00 40.58 4.00
9049 11073 1.135689 CACCACGCAATTCAGTAAGCC 60.136 52.381 0.00 0.00 0.00 4.35
9075 11106 0.177836 CCGTCCACCATGCATGTAGA 59.822 55.000 24.58 14.91 0.00 2.59
9076 11107 1.290203 CGTCCACCATGCATGTAGAC 58.710 55.000 24.58 22.99 0.00 2.59
9077 11108 1.405391 CGTCCACCATGCATGTAGACA 60.405 52.381 26.97 9.18 0.00 3.41
9078 11109 2.742856 CGTCCACCATGCATGTAGACAT 60.743 50.000 26.97 7.88 36.96 3.06
9154 11185 1.671379 GGACAAGGCGGTGTCTTCC 60.671 63.158 19.35 5.03 45.98 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.866015 AGGTCGTGAGGGAATGATCA 58.134 50.000 0.00 0.00 0.00 2.92
40 41 3.713288 CTTGTGAAGTTGTAGGTCGTGA 58.287 45.455 0.00 0.00 0.00 4.35
59 60 3.623060 CCTATACGACATGCTTGTTGCTT 59.377 43.478 17.64 9.37 40.41 3.91
60 61 3.198068 CCTATACGACATGCTTGTTGCT 58.802 45.455 17.64 9.53 40.41 3.91
180 181 7.761409 TGTATGTTCCACTAAAATGCATCTTC 58.239 34.615 0.00 0.00 0.00 2.87
193 194 6.899393 ACATGTTTGAATGTATGTTCCACT 57.101 33.333 0.00 0.00 39.01 4.00
203 204 5.889853 AGGAGCATCATACATGTTTGAATGT 59.110 36.000 20.60 9.49 39.78 2.71
205 206 6.379133 ACAAGGAGCATCATACATGTTTGAAT 59.621 34.615 20.60 11.19 36.25 2.57
209 210 5.012239 ACACAAGGAGCATCATACATGTTT 58.988 37.500 2.30 0.00 36.25 2.83
218 219 1.133823 ACAACCACACAAGGAGCATCA 60.134 47.619 0.00 0.00 36.25 3.07
225 226 7.647715 CAGTTAAATAAGAACAACCACACAAGG 59.352 37.037 0.00 0.00 0.00 3.61
284 286 3.377439 CAATGATCACATTCGCCAATGG 58.623 45.455 8.95 0.00 43.76 3.16
321 323 2.369394 CTTTTGATGTGGGGCTAGTCC 58.631 52.381 4.21 4.21 0.00 3.85
332 334 0.609131 CCCCGTCAGCCTTTTGATGT 60.609 55.000 0.00 0.00 33.23 3.06
347 349 0.691078 TCCCCTCTTGAAGATCCCCG 60.691 60.000 0.00 0.00 0.00 5.73
348 350 0.840617 GTCCCCTCTTGAAGATCCCC 59.159 60.000 0.00 0.00 0.00 4.81
355 358 2.221299 CCACCGGTCCCCTCTTGAA 61.221 63.158 2.59 0.00 0.00 2.69
359 362 4.974438 TTGCCACCGGTCCCCTCT 62.974 66.667 2.59 0.00 0.00 3.69
389 392 1.210538 TCTTGAGATGCCATCCAGCT 58.789 50.000 0.00 0.00 44.25 4.24
394 397 3.557228 ACTCCTTCTTGAGATGCCATC 57.443 47.619 0.00 0.00 36.22 3.51
403 406 6.017109 GCACATGTAGAAAAACTCCTTCTTGA 60.017 38.462 0.00 0.00 34.90 3.02
405 408 5.241728 GGCACATGTAGAAAAACTCCTTCTT 59.758 40.000 0.00 0.00 34.90 2.52
493 496 4.819630 GCATCCACCGAATACATAAAAGGA 59.180 41.667 0.00 0.00 0.00 3.36
498 501 7.004555 AGATTAGCATCCACCGAATACATAA 57.995 36.000 0.00 0.00 0.00 1.90
506 509 2.481276 CGTTGAGATTAGCATCCACCGA 60.481 50.000 0.00 0.00 0.00 4.69
530 533 7.537596 TTAACATTGAGTGGGATCAAACATT 57.462 32.000 0.00 0.00 42.21 2.71
538 541 6.015918 TGTTTCCATTAACATTGAGTGGGAT 58.984 36.000 0.00 0.00 33.31 3.85
542 545 7.424803 TGTCTTGTTTCCATTAACATTGAGTG 58.575 34.615 0.00 0.00 37.81 3.51
548 551 7.537596 TGGAATGTCTTGTTTCCATTAACAT 57.462 32.000 0.37 0.00 44.92 2.71
602 605 3.064271 CCGAAGTTGGTCGAAAACAAAGA 59.936 43.478 13.12 0.00 43.86 2.52
606 609 2.027003 ACCGAAGTTGGTCGAAAACA 57.973 45.000 13.12 0.00 43.86 2.83
651 654 2.920645 CGAGTCTGCGGTGGTGTCT 61.921 63.158 0.00 0.00 0.00 3.41
699 702 3.164576 GCGATGTGCGTGCTACAA 58.835 55.556 0.00 0.00 43.41 2.41
716 719 0.038744 AAGGGTGTCAGGCAAGATGG 59.961 55.000 0.00 0.00 0.00 3.51
725 728 2.287788 GCACAACAATGAAGGGTGTCAG 60.288 50.000 0.00 0.00 0.00 3.51
744 747 2.391724 GACGGTGAACTCCCTTGGCA 62.392 60.000 0.00 0.00 0.00 4.92
787 790 0.179134 ATCGGCGAGAAAAGGAGACG 60.179 55.000 17.22 0.00 36.29 4.18
805 821 5.653255 ACATAAATACCTCTTGGCCTCAT 57.347 39.130 3.32 0.00 36.63 2.90
813 829 7.775053 TGAGCCAAAAACATAAATACCTCTT 57.225 32.000 0.00 0.00 0.00 2.85
872 888 6.206395 TCAATGAGCTTTGTTGAAACTTGA 57.794 33.333 6.84 0.00 0.00 3.02
913 929 4.894798 TGCGTTGTGTTGTTTCTTTTTC 57.105 36.364 0.00 0.00 0.00 2.29
971 991 2.122768 CCTAGTGATGGGGAAAGAGCT 58.877 52.381 0.00 0.00 0.00 4.09
983 1003 1.464376 CCGCCGATGGTCCTAGTGAT 61.464 60.000 0.00 0.00 0.00 3.06
984 1004 2.125326 CCGCCGATGGTCCTAGTGA 61.125 63.158 0.00 0.00 0.00 3.41
985 1005 2.417516 CCGCCGATGGTCCTAGTG 59.582 66.667 0.00 0.00 0.00 2.74
986 1006 3.537874 GCCGCCGATGGTCCTAGT 61.538 66.667 0.00 0.00 0.00 2.57
987 1007 4.647615 CGCCGCCGATGGTCCTAG 62.648 72.222 0.00 0.00 36.29 3.02
1349 1374 3.271706 TTACACAGGGACGACGCGG 62.272 63.158 12.47 0.00 0.00 6.46
1411 1490 6.242396 ACAAACTTGGTAATACATGGCACTA 58.758 36.000 0.00 0.00 0.00 2.74
1445 1524 2.844281 GCGTGCGTGACCAAATATAACG 60.844 50.000 0.00 0.00 37.32 3.18
1587 1666 6.946340 TCACCTATCAGAAATGTACACATGT 58.054 36.000 0.00 0.00 36.56 3.21
1622 1701 2.191908 GTGTCCAGTGCCACCACA 59.808 61.111 0.00 0.00 44.53 4.17
1773 1856 5.406780 CCTGCTTCCACGACAGATATAATTC 59.593 44.000 0.00 0.00 33.10 2.17
1806 1889 4.644234 TCCACGTCCATGCATATTTCAAAT 59.356 37.500 0.00 0.00 0.00 2.32
2174 2257 2.875094 ATCTTCTTGACTTGCTGCCT 57.125 45.000 0.00 0.00 0.00 4.75
3015 3103 4.807443 ACATCAGTCATCAGCTATCATCG 58.193 43.478 0.00 0.00 0.00 3.84
3030 3118 7.416664 GCCACCAAATATTCACATAACATCAGT 60.417 37.037 0.00 0.00 0.00 3.41
3031 3119 6.919662 GCCACCAAATATTCACATAACATCAG 59.080 38.462 0.00 0.00 0.00 2.90
3032 3120 6.379417 TGCCACCAAATATTCACATAACATCA 59.621 34.615 0.00 0.00 0.00 3.07
3033 3121 6.804677 TGCCACCAAATATTCACATAACATC 58.195 36.000 0.00 0.00 0.00 3.06
3034 3122 6.788598 TGCCACCAAATATTCACATAACAT 57.211 33.333 0.00 0.00 0.00 2.71
3035 3123 6.571605 CATGCCACCAAATATTCACATAACA 58.428 36.000 0.00 0.00 0.00 2.41
3036 3124 5.463061 GCATGCCACCAAATATTCACATAAC 59.537 40.000 6.36 0.00 0.00 1.89
3052 3140 4.559153 AGTAAATGAAACAAGCATGCCAC 58.441 39.130 15.66 0.34 0.00 5.01
3576 5180 6.238211 GCTTCGATTTCTTGCAGCTTAGATAA 60.238 38.462 0.00 0.00 0.00 1.75
3885 5489 8.640063 TTAATGGGGAAGGAGTAAAAAGTTAC 57.360 34.615 0.00 0.00 40.05 2.50
3933 5537 1.337703 TGTCAATGCTTGCCTGTCAAC 59.662 47.619 0.00 0.00 0.00 3.18
4205 5809 3.019564 ACAGCATAAGTTCAATGGGAGC 58.980 45.455 0.00 0.00 0.00 4.70
4425 6044 4.981806 TTCCAGTTTGTAATGCCTATGC 57.018 40.909 0.00 0.00 38.26 3.14
4688 6361 8.735315 CACATACCACCAATGTTAAGAATACAA 58.265 33.333 0.00 0.00 35.39 2.41
4787 6466 9.986157 TCTAGTTCTCTTACTACCTTTTCCATA 57.014 33.333 0.00 0.00 0.00 2.74
5117 6816 0.322816 AACATTCACCGCTGCCTCAT 60.323 50.000 0.00 0.00 0.00 2.90
5266 6965 8.644318 AGGTTAAATTAGTACACTTCATAGCG 57.356 34.615 0.00 0.00 0.00 4.26
5317 7016 4.202101 ACAAGAATTTTCATGGCGTTGACA 60.202 37.500 0.00 0.00 30.67 3.58
5406 7105 4.201891 GCTTCACTATCCATTGCAAGAGTG 60.202 45.833 4.94 12.46 36.48 3.51
5862 7561 1.985473 ACAGTTCCAGCATCTGCAAA 58.015 45.000 4.79 0.00 45.16 3.68
6032 7731 3.067106 ACACTGCCTTGTATCTGTTTCG 58.933 45.455 0.00 0.00 0.00 3.46
6188 8133 5.550403 TGAAATTAGGGGTGGAAGTTACTCT 59.450 40.000 0.00 0.00 0.00 3.24
6245 8190 4.643387 GGGACCTGCAGCCACGTT 62.643 66.667 8.66 0.00 0.00 3.99
6255 8200 2.224621 CCTAACTGGCATATGGGACCTG 60.225 54.545 4.56 4.24 0.00 4.00
6331 8276 6.138967 TGGACAGATGAGGAGATAAATCAGA 58.861 40.000 0.00 0.00 0.00 3.27
6336 8281 7.732140 AGATGTATGGACAGATGAGGAGATAAA 59.268 37.037 0.00 0.00 39.50 1.40
6431 8376 0.535102 ACACTTCCAAACGGCTCCTG 60.535 55.000 0.00 0.00 0.00 3.86
6433 8378 0.534203 TGACACTTCCAAACGGCTCC 60.534 55.000 0.00 0.00 0.00 4.70
6521 8483 2.031012 CTGACAGACGCCCAAGCA 59.969 61.111 0.00 0.00 39.83 3.91
6524 8486 2.210013 AGCTCTGACAGACGCCCAA 61.210 57.895 17.79 0.00 0.00 4.12
6550 8512 1.689233 TCACCAAGATCCCCTCCCG 60.689 63.158 0.00 0.00 0.00 5.14
6552 8514 1.813102 ATCTCACCAAGATCCCCTCC 58.187 55.000 0.00 0.00 40.99 4.30
6570 8532 0.916358 AGTCAACCCTGGGCTGCTAT 60.916 55.000 14.08 0.00 0.00 2.97
6593 8555 3.072330 TGTGTTTCTATCACCAGCCTTCA 59.928 43.478 0.00 0.00 35.25 3.02
6615 8577 0.995024 ACCTCCTTGCTAACATGGCT 59.005 50.000 0.00 0.00 40.21 4.75
6619 8581 3.806949 TTTCCACCTCCTTGCTAACAT 57.193 42.857 0.00 0.00 0.00 2.71
6622 8584 4.141251 AGTTCTTTTCCACCTCCTTGCTAA 60.141 41.667 0.00 0.00 0.00 3.09
6661 8623 3.070018 CCTCTTCGTTCATCAAAGCACT 58.930 45.455 0.00 0.00 0.00 4.40
6695 8657 1.703411 AACCCACCAAACATCCACTG 58.297 50.000 0.00 0.00 0.00 3.66
6723 8685 1.557832 CAATCCGACACCTTCCCCTAA 59.442 52.381 0.00 0.00 0.00 2.69
6724 8686 1.200519 CAATCCGACACCTTCCCCTA 58.799 55.000 0.00 0.00 0.00 3.53
6814 8777 5.394115 GCCGGAAAATAATGAGAATTGTGGT 60.394 40.000 5.05 0.00 0.00 4.16
6864 8827 9.852091 ATAGTTAGAACTTAGAACCAAGTAACG 57.148 33.333 0.00 0.00 37.78 3.18
7234 9197 7.385205 ACACTCTTATAAACTGTAACAGCACTG 59.615 37.037 0.00 0.00 34.37 3.66
7304 9268 3.500982 GTGCGCAATTTAAGAATGCTCA 58.499 40.909 14.00 3.67 0.00 4.26
7309 9273 4.881920 ACTTTGGTGCGCAATTTAAGAAT 58.118 34.783 14.00 0.00 0.00 2.40
7387 9351 5.145564 ACCCGTAACTGTATGACTGGATAT 58.854 41.667 5.34 0.00 0.00 1.63
7456 9420 5.121221 ACCAAGCTAAAAACAATTCGAGG 57.879 39.130 0.00 0.00 0.00 4.63
7658 9622 9.474313 TTTTTAGATGGAAGCATACCTACAAAT 57.526 29.630 0.00 0.00 0.00 2.32
7707 9671 9.807921 GGGGATATTCTTTTCCATCTACAAATA 57.192 33.333 0.00 0.00 33.43 1.40
7708 9672 8.514504 AGGGGATATTCTTTTCCATCTACAAAT 58.485 33.333 0.00 0.00 33.43 2.32
7709 9673 7.882755 AGGGGATATTCTTTTCCATCTACAAA 58.117 34.615 0.00 0.00 33.43 2.83
7710 9674 7.465900 AGGGGATATTCTTTTCCATCTACAA 57.534 36.000 0.00 0.00 33.43 2.41
7711 9675 7.290061 CAAGGGGATATTCTTTTCCATCTACA 58.710 38.462 0.00 0.00 33.43 2.74
7741 9705 8.613482 GGAAAGATAATACACAAGCCTTTAGTC 58.387 37.037 0.00 0.00 0.00 2.59
7745 9709 5.944007 ACGGAAAGATAATACACAAGCCTTT 59.056 36.000 0.00 0.00 0.00 3.11
7748 9712 5.585047 AGAACGGAAAGATAATACACAAGCC 59.415 40.000 0.00 0.00 0.00 4.35
7753 9718 4.802039 TGCGAGAACGGAAAGATAATACAC 59.198 41.667 0.00 0.00 36.84 2.90
7754 9719 5.001237 TGCGAGAACGGAAAGATAATACA 57.999 39.130 0.00 0.00 36.84 2.29
7766 9731 2.230940 CGGTATGCTGCGAGAACGG 61.231 63.158 0.00 0.00 40.15 4.44
7768 9733 1.146358 GACCGGTATGCTGCGAGAAC 61.146 60.000 7.34 0.00 0.00 3.01
7774 9739 2.529151 CAATTTTGACCGGTATGCTGC 58.471 47.619 7.34 0.00 0.00 5.25
7784 9749 4.201705 CGCCAATACATTGCAATTTTGACC 60.202 41.667 20.28 13.04 36.48 4.02
7788 9753 3.936564 ACCGCCAATACATTGCAATTTT 58.063 36.364 9.83 2.14 36.48 1.82
7812 9777 2.096218 CGTTTCCTAAGCACACTTCTGC 60.096 50.000 0.00 0.00 37.33 4.26
7825 9790 4.404640 AGATGGATCCGATACGTTTCCTA 58.595 43.478 7.39 0.00 30.72 2.94
7827 9792 3.662247 AGATGGATCCGATACGTTTCC 57.338 47.619 7.39 0.00 0.00 3.13
7854 9819 1.517832 CTGCAAGTAGTCCCTCCCG 59.482 63.158 0.00 0.00 0.00 5.14
7888 9853 7.709947 TCTTCATATGCTGGAATTTGAATGAC 58.290 34.615 0.00 0.00 30.43 3.06
8004 9974 4.137543 AGTTCACAAAACTCACAGGGATC 58.862 43.478 0.00 0.00 0.00 3.36
8108 10081 1.411246 TGAAGTAACTGACTGCGGTGT 59.589 47.619 0.80 0.00 36.31 4.16
8166 10139 0.597637 CCCGTGGATGATCGTAGCAC 60.598 60.000 0.00 0.00 0.00 4.40
8209 10208 7.748241 GCTTTCAATAGAGCAAAGAGTTACAAG 59.252 37.037 0.00 0.00 38.73 3.16
8263 10262 1.831106 TCACGTGAGGATAACCATGCT 59.169 47.619 15.76 0.00 38.94 3.79
8287 10286 1.801913 CACGGCTGAGTCGCAGTAC 60.802 63.158 6.29 0.00 46.62 2.73
8292 10291 3.432051 ATAGGCACGGCTGAGTCGC 62.432 63.158 6.29 0.00 32.11 5.19
8303 10302 1.512926 CGGCTTATGGTGATAGGCAC 58.487 55.000 0.00 0.00 46.98 5.01
8381 10380 0.316442 CACGCCTATGCTGCATTTCG 60.316 55.000 21.56 21.10 34.43 3.46
8390 10389 0.808453 TAAGAACGCCACGCCTATGC 60.808 55.000 0.00 0.00 0.00 3.14
8435 10442 1.222115 GCCGACAGTGTGAGAACCAC 61.222 60.000 0.00 0.00 45.88 4.16
8437 10444 0.320771 ATGCCGACAGTGTGAGAACC 60.321 55.000 0.00 0.00 0.00 3.62
8591 10606 0.609131 ATGGAAACGAGTGGCTTGGG 60.609 55.000 0.00 0.00 0.00 4.12
8592 10607 0.804989 GATGGAAACGAGTGGCTTGG 59.195 55.000 0.00 0.00 0.00 3.61
8593 10608 0.804989 GGATGGAAACGAGTGGCTTG 59.195 55.000 0.00 0.00 0.00 4.01
8594 10609 0.693049 AGGATGGAAACGAGTGGCTT 59.307 50.000 0.00 0.00 0.00 4.35
8595 10610 0.693049 AAGGATGGAAACGAGTGGCT 59.307 50.000 0.00 0.00 0.00 4.75
8719 10737 1.691196 TCAGTTTGGCCACAAGGAAG 58.309 50.000 3.88 0.00 37.97 3.46
8724 10742 3.803021 GCAAATGATCAGTTTGGCCACAA 60.803 43.478 21.58 0.00 37.12 3.33
8731 10749 1.632422 GCCCGCAAATGATCAGTTTG 58.368 50.000 5.50 14.09 39.08 2.93
8750 10768 5.231357 CCTGCATCATCATCAAAATTTCACG 59.769 40.000 0.00 0.00 0.00 4.35
8915 10936 1.202818 AGAGGTCTTGTTCACCTTGCC 60.203 52.381 0.00 0.00 44.87 4.52
8941 10965 4.717629 TTGTCGTCGCAGCCGGAG 62.718 66.667 5.05 0.00 34.56 4.63
8973 10997 2.764547 GCCTCTCCCCGGCTAACT 60.765 66.667 0.00 0.00 44.17 2.24
9000 11024 2.369633 ACCTCGCTCATGATGCCCA 61.370 57.895 0.00 0.00 0.00 5.36
9037 11061 1.287425 GCGCGTAGGCTTACTGAATT 58.713 50.000 8.43 0.00 36.88 2.17
9040 11064 2.493030 GGCGCGTAGGCTTACTGA 59.507 61.111 8.43 0.00 42.90 3.41
9049 11073 4.508128 ATGGTGGACGGCGCGTAG 62.508 66.667 6.90 4.46 41.37 3.51
9075 11106 6.771076 CAATTAATGCACACGTACTACATGT 58.229 36.000 2.69 2.69 0.00 3.21
9154 11185 2.509916 GCCAGCTCCATCTCCAGG 59.490 66.667 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.