Multiple sequence alignment - TraesCS7D01G282200

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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 TraesCS7D01G282200 chr7D 100.000 5772 0 0 1 5772 285462352 285468123 0.000000e+00 10659.0
1 TraesCS7D01G282200 chr7D 91.538 130 8 3 2100 2228 454079410 454079283 5.940000e-40 176.0
2 TraesCS7D01G282200 chr7D 73.723 274 56 12 447 717 270700359 270700099 6.160000e-15 93.5
3 TraesCS7D01G282200 chr7B 96.186 2596 60 17 691 3269 276733448 276736021 0.000000e+00 4209.0
4 TraesCS7D01G282200 chr7B 96.866 2138 51 9 3187 5313 276736022 276738154 0.000000e+00 3563.0
5 TraesCS7D01G282200 chr7B 91.171 555 47 2 1 555 276731691 276732243 0.000000e+00 752.0
6 TraesCS7D01G282200 chr7B 91.848 184 12 3 5350 5531 276738148 276738330 2.670000e-63 254.0
7 TraesCS7D01G282200 chr7B 100.000 28 0 0 5592 5619 276738360 276738387 1.000000e-02 52.8
8 TraesCS7D01G282200 chr7A 96.523 1553 39 8 3945 5492 320981174 320979632 0.000000e+00 2555.0
9 TraesCS7D01G282200 chr7A 96.799 1312 26 9 2121 3425 320983454 320982152 0.000000e+00 2176.0
10 TraesCS7D01G282200 chr7A 96.203 790 17 5 893 1669 320984261 320983472 0.000000e+00 1280.0
11 TraesCS7D01G282200 chr7A 99.059 425 3 1 3523 3946 320981760 320981336 0.000000e+00 761.0
12 TraesCS7D01G282200 chr7A 90.244 410 34 5 1 406 320985715 320985308 1.100000e-146 531.0
13 TraesCS7D01G282200 chr7A 91.579 95 5 1 5528 5619 320979629 320979535 1.690000e-25 128.0
14 TraesCS7D01G282200 chr7A 72.464 276 57 11 446 716 634931616 634931355 2.890000e-08 71.3
15 TraesCS7D01G282200 chr3B 83.941 878 103 22 2523 3384 28534805 28535660 0.000000e+00 806.0
16 TraesCS7D01G282200 chr3B 83.941 878 102 23 2523 3384 28445857 28446711 0.000000e+00 804.0
17 TraesCS7D01G282200 chr3B 83.864 880 100 23 2523 3384 28399952 28400807 0.000000e+00 800.0
18 TraesCS7D01G282200 chr3B 83.845 879 103 23 2523 3384 28413337 28414193 0.000000e+00 800.0
19 TraesCS7D01G282200 chr3B 83.827 878 104 22 2523 3384 28523401 28524256 0.000000e+00 800.0
20 TraesCS7D01G282200 chr3B 83.732 879 104 23 2523 3384 28459848 28460704 0.000000e+00 795.0
21 TraesCS7D01G282200 chr3B 82.949 868 102 22 2532 3384 28482889 28483725 0.000000e+00 741.0
22 TraesCS7D01G282200 chr2D 80.515 272 42 7 446 717 27670082 27670342 1.270000e-46 198.0
23 TraesCS7D01G282200 chr4B 93.077 130 7 2 2100 2228 178081266 178081138 7.640000e-44 189.0
24 TraesCS7D01G282200 chr2A 92.969 128 7 2 2102 2228 578387717 578387591 9.880000e-43 185.0
25 TraesCS7D01G282200 chr2A 93.182 44 3 0 5534 5577 511062687 511062644 1.340000e-06 65.8
26 TraesCS7D01G282200 chr5B 79.273 275 43 9 446 717 497377195 497377458 4.600000e-41 180.0
27 TraesCS7D01G282200 chr4D 91.538 130 9 2 2100 2228 10985974 10986102 1.650000e-40 178.0
28 TraesCS7D01G282200 chr3D 90.441 136 9 4 2094 2228 482202484 482202352 5.940000e-40 176.0
29 TraesCS7D01G282200 chr1A 91.406 128 9 2 2102 2228 564757338 564757212 2.140000e-39 174.0
30 TraesCS7D01G282200 chr1A 89.630 135 12 2 2095 2228 71070588 71070721 2.770000e-38 171.0
31 TraesCS7D01G282200 chr1A 90.698 129 10 2 2101 2228 495445888 495446015 2.770000e-38 171.0
32 TraesCS7D01G282200 chr1A 74.545 275 52 16 447 717 147685340 147685600 2.840000e-18 104.0
33 TraesCS7D01G282200 chr1A 80.769 104 9 1 5475 5578 58951464 58951556 2.890000e-08 71.3
34 TraesCS7D01G282200 chr6D 76.825 315 41 16 5450 5759 457668061 457667774 1.300000e-31 148.0
35 TraesCS7D01G282200 chr6D 100.000 29 0 0 689 717 472139288 472139316 3.000000e-03 54.7
36 TraesCS7D01G282200 chr6A 76.052 309 42 17 5449 5753 604590023 604589743 1.310000e-26 132.0
37 TraesCS7D01G282200 chr1D 79.605 152 11 8 5472 5616 60322947 60323085 2.210000e-14 91.6
38 TraesCS7D01G282200 chr1B 91.837 49 4 0 5485 5533 96463420 96463372 1.040000e-07 69.4
39 TraesCS7D01G282200 chr5D 100.000 28 0 0 689 716 434347675 434347702 1.000000e-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 TraesCS7D01G282200 chr7D 285462352 285468123 5771 False 10659.00 10659 100.000000 1 5772 1 chr7D.!!$F1 5771
1 TraesCS7D01G282200 chr7B 276731691 276738387 6696 False 1766.16 4209 95.214200 1 5619 5 chr7B.!!$F1 5618
2 TraesCS7D01G282200 chr7A 320979535 320985715 6180 True 1238.50 2555 95.067833 1 5619 6 chr7A.!!$R2 5618
3 TraesCS7D01G282200 chr3B 28534805 28535660 855 False 806.00 806 83.941000 2523 3384 1 chr3B.!!$F7 861
4 TraesCS7D01G282200 chr3B 28445857 28446711 854 False 804.00 804 83.941000 2523 3384 1 chr3B.!!$F3 861
5 TraesCS7D01G282200 chr3B 28399952 28400807 855 False 800.00 800 83.864000 2523 3384 1 chr3B.!!$F1 861
6 TraesCS7D01G282200 chr3B 28413337 28414193 856 False 800.00 800 83.845000 2523 3384 1 chr3B.!!$F2 861
7 TraesCS7D01G282200 chr3B 28523401 28524256 855 False 800.00 800 83.827000 2523 3384 1 chr3B.!!$F6 861
8 TraesCS7D01G282200 chr3B 28459848 28460704 856 False 795.00 795 83.732000 2523 3384 1 chr3B.!!$F4 861
9 TraesCS7D01G282200 chr3B 28482889 28483725 836 False 741.00 741 82.949000 2532 3384 1 chr3B.!!$F5 852

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
877 2389 0.671796 TCCGCAAACTCGAACTCTCA 59.328 50.000 0.0 0.0 0.0 3.27 F
1556 3268 0.610174 TTCAGCTCTGCAATCTCCGT 59.390 50.000 0.0 0.0 0.0 4.69 F
2312 4041 2.171003 GGTTAGTTTGCTGCTCCCATT 58.829 47.619 0.0 0.0 0.0 3.16 F
3473 5305 1.229241 TCCCACGACCACCACCATA 60.229 57.895 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 4041 5.871396 TTACAAAATGGCACTAAAACCCA 57.129 34.783 0.0 0.0 0.0 4.51 R
3473 5305 0.614812 GGAGCAAACAATGGGGCAAT 59.385 50.000 0.0 0.0 0.0 3.56 R
4102 6393 2.745281 GTTATGAGCAAGCCGGTTACAA 59.255 45.455 1.9 0.0 0.0 2.41 R
5384 7680 0.244450 CGTACCGACAGTTTAGCCCA 59.756 55.000 0.0 0.0 0.0 5.36 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
89 94 8.894768 AAATCAAAGCTCTGACATAGTATACC 57.105 34.615 0.00 0.00 0.00 2.73
111 116 1.167851 CTCTTTCTTTCCATGCGCCA 58.832 50.000 4.18 0.00 0.00 5.69
116 121 1.213537 CTTTCCATGCGCCAACCAG 59.786 57.895 4.18 0.00 0.00 4.00
134 139 2.228822 CCAGAACCAAAATCAAGGACCG 59.771 50.000 0.00 0.00 0.00 4.79
150 155 1.290955 CCGTCGGGTAAGACAAGCA 59.709 57.895 2.34 0.00 40.98 3.91
159 164 4.638304 GGGTAAGACAAGCAACAACTCTA 58.362 43.478 0.00 0.00 0.00 2.43
208 213 2.339418 CGGGTTCGCAACATAGTTGTA 58.661 47.619 11.09 0.00 34.06 2.41
218 223 5.277490 CGCAACATAGTTGTATAGCATGCTT 60.277 40.000 28.02 15.84 34.06 3.91
254 259 4.079787 TGGATGGATAAGGGAACAAAGGAG 60.080 45.833 0.00 0.00 0.00 3.69
255 260 4.079730 GGATGGATAAGGGAACAAAGGAGT 60.080 45.833 0.00 0.00 0.00 3.85
258 263 3.197116 GGATAAGGGAACAAAGGAGTCGA 59.803 47.826 0.00 0.00 0.00 4.20
276 281 3.607987 GAGGCGTTCGCGATGACG 61.608 66.667 24.77 24.77 44.71 4.35
305 310 5.350365 CCATTTTACCGAAAGATCTCGTTCA 59.650 40.000 0.00 0.00 37.11 3.18
412 417 2.857618 GCGTTCGGCAATATGTTTTCA 58.142 42.857 0.00 0.00 42.87 2.69
414 419 3.857093 GCGTTCGGCAATATGTTTTCAAT 59.143 39.130 0.00 0.00 42.87 2.57
454 459 2.835764 ACTCGCAAATTGGTACTCCCTA 59.164 45.455 0.00 0.00 0.00 3.53
455 460 3.454812 ACTCGCAAATTGGTACTCCCTAT 59.545 43.478 0.00 0.00 0.00 2.57
475 480 3.564053 TGGTCCTTTTTACTCCACGTT 57.436 42.857 0.00 0.00 0.00 3.99
476 481 4.686191 TGGTCCTTTTTACTCCACGTTA 57.314 40.909 0.00 0.00 0.00 3.18
497 502 8.280497 ACGTTATAGATTTGTGACAAGTCAAAC 58.720 33.333 20.49 18.04 41.85 2.93
727 1808 1.334243 GAGGGAGTACGATGTCTTCCG 59.666 57.143 0.00 0.00 34.69 4.30
827 2337 8.796475 AGGCCGAATCGTAGTTAATATAAGTAA 58.204 33.333 0.82 0.00 0.00 2.24
828 2338 9.410556 GGCCGAATCGTAGTTAATATAAGTAAA 57.589 33.333 0.82 0.00 0.00 2.01
877 2389 0.671796 TCCGCAAACTCGAACTCTCA 59.328 50.000 0.00 0.00 0.00 3.27
882 2394 1.792949 CAAACTCGAACTCTCAACCGG 59.207 52.381 0.00 0.00 0.00 5.28
1069 2768 2.456840 CTCCTCCCCTCAACCCCT 59.543 66.667 0.00 0.00 0.00 4.79
1076 2775 2.306384 CCCTCAACCCCTACCCCAC 61.306 68.421 0.00 0.00 0.00 4.61
1288 3000 1.474498 GGGGTTCGGATCGCTTGTTAT 60.474 52.381 3.57 0.00 0.00 1.89
1526 3238 1.957668 ACCTGTTAACACCGTGTTCC 58.042 50.000 20.06 12.52 40.22 3.62
1556 3268 0.610174 TTCAGCTCTGCAATCTCCGT 59.390 50.000 0.00 0.00 0.00 4.69
1559 3271 2.467826 GCTCTGCAATCTCCGTGGC 61.468 63.158 0.00 0.00 0.00 5.01
1615 3327 9.594038 CACTAATAACATAAATTCGCCATGTAC 57.406 33.333 0.00 0.00 32.70 2.90
1712 3427 4.976116 GTGCCTGTTAAACAGTTTCATCAC 59.024 41.667 0.48 3.81 44.50 3.06
1727 3442 7.119407 CAGTTTCATCACTGAATCTCATTGACT 59.881 37.037 0.00 0.00 46.29 3.41
1837 3560 9.949174 TGTATGACATATCAATGTTTTACATGC 57.051 29.630 0.00 0.00 46.49 4.06
1851 3574 5.720261 TTTACATGCAATTACGATACGCA 57.280 34.783 0.00 0.00 36.95 5.24
2048 3772 9.167311 CAGTACCTTCAATCACTTTTAAGCTAT 57.833 33.333 0.00 0.00 0.00 2.97
2213 3939 4.868171 TCACTCATTTTGCTCCGTATGTAC 59.132 41.667 0.00 0.00 0.00 2.90
2312 4041 2.171003 GGTTAGTTTGCTGCTCCCATT 58.829 47.619 0.00 0.00 0.00 3.16
2473 4202 4.096532 GGCTCAAACTTTGTCCTAATAGGC 59.903 45.833 0.34 0.00 34.61 3.93
3333 5164 4.823442 TCTATGTATACCGTCCATTCACGT 59.177 41.667 0.00 0.00 38.14 4.49
3345 5176 5.957220 CGTCCATTCACGTAAATGTGTATTG 59.043 40.000 10.50 0.00 40.74 1.90
3425 5257 6.515272 AATTTCATCTTTGGTAGCGACATT 57.485 33.333 0.00 0.00 0.00 2.71
3473 5305 1.229241 TCCCACGACCACCACCATA 60.229 57.895 0.00 0.00 0.00 2.74
3516 5352 2.348362 TGCTGTTGCTCGACATTATTCG 59.652 45.455 0.00 0.00 40.48 3.34
3792 5918 7.770801 TTATTGGTATGATATATCGCACTGC 57.229 36.000 8.19 0.00 0.00 4.40
3793 5919 5.405935 TTGGTATGATATATCGCACTGCT 57.594 39.130 8.19 0.00 0.00 4.24
3914 6041 2.777692 TCCTGAACTGGTCCAAGAAGTT 59.222 45.455 0.00 0.00 36.87 2.66
4232 6523 6.591448 TCACACTTGCTATTCTTATGACACAG 59.409 38.462 0.00 0.00 0.00 3.66
4468 6762 7.540400 TCGTATTTTGGTTGATGTGCTTATTTG 59.460 33.333 0.00 0.00 0.00 2.32
4470 6764 9.632807 GTATTTTGGTTGATGTGCTTATTTGTA 57.367 29.630 0.00 0.00 0.00 2.41
4657 6952 2.490903 TCCTTCTCACACTACTAACGCC 59.509 50.000 0.00 0.00 0.00 5.68
4928 7223 6.927416 ACTTCATGCAAGCATTTCTAATCAA 58.073 32.000 4.52 0.00 35.17 2.57
5122 7418 7.814107 TGCCTTTTGCTTTCTTTATACTTGATG 59.186 33.333 0.00 0.00 42.00 3.07
5142 7438 2.685897 TGTAAACACTTTGCAGGGTCAC 59.314 45.455 0.00 0.00 34.53 3.67
5230 7526 7.436118 AGTTTTGAGAGCATGCAAATTTTCTA 58.564 30.769 21.98 0.00 34.36 2.10
5279 7575 1.072331 GTTGTTCCTCTCTTGCCCTGA 59.928 52.381 0.00 0.00 0.00 3.86
5283 7579 0.252881 TCCTCTCTTGCCCTGATGGT 60.253 55.000 0.00 0.00 36.04 3.55
5318 7614 6.942976 TCCCGAGAACAGATTATTTTACTGT 58.057 36.000 0.00 0.00 45.02 3.55
5378 7674 9.696572 ATCTACCTCGAGGCATATATAGTTTTA 57.303 33.333 31.56 10.14 39.32 1.52
5517 7817 4.445385 GTGCATCAACAAGGAATCAAACAC 59.555 41.667 0.00 0.00 0.00 3.32
5518 7818 3.989817 GCATCAACAAGGAATCAAACACC 59.010 43.478 0.00 0.00 0.00 4.16
5520 7820 5.048083 GCATCAACAAGGAATCAAACACCTA 60.048 40.000 0.00 0.00 33.34 3.08
5521 7821 6.615088 CATCAACAAGGAATCAAACACCTAG 58.385 40.000 0.00 0.00 33.34 3.02
5523 7823 3.421844 ACAAGGAATCAAACACCTAGCC 58.578 45.455 0.00 0.00 33.34 3.93
5525 7825 4.082125 CAAGGAATCAAACACCTAGCCTT 58.918 43.478 0.00 0.00 35.03 4.35
5526 7826 3.690460 AGGAATCAAACACCTAGCCTTG 58.310 45.455 0.00 0.00 31.78 3.61
5566 7866 2.763448 GCATGGTAAAGGCCCAATAACA 59.237 45.455 0.00 0.00 35.14 2.41
5584 7887 7.696453 CCAATAACAAACTAGGCTAACATTTCG 59.304 37.037 0.00 0.00 0.00 3.46
5622 7925 9.469097 TGGTTTACATACAATATTATATGCCCC 57.531 33.333 12.65 8.45 32.92 5.80
5623 7926 9.695155 GGTTTACATACAATATTATATGCCCCT 57.305 33.333 12.65 0.00 32.92 4.79
5702 8005 3.984508 TTTTTGGTCGCAAATAACCGA 57.015 38.095 0.00 0.00 38.45 4.69
5703 8006 4.506886 TTTTTGGTCGCAAATAACCGAT 57.493 36.364 0.00 0.00 38.45 4.18
5704 8007 3.479505 TTTGGTCGCAAATAACCGATG 57.520 42.857 0.00 0.00 38.45 3.84
5705 8008 2.388310 TGGTCGCAAATAACCGATGA 57.612 45.000 0.00 0.00 38.45 2.92
5706 8009 2.701107 TGGTCGCAAATAACCGATGAA 58.299 42.857 0.00 0.00 38.45 2.57
5707 8010 3.275143 TGGTCGCAAATAACCGATGAAT 58.725 40.909 0.00 0.00 38.45 2.57
5708 8011 3.311322 TGGTCGCAAATAACCGATGAATC 59.689 43.478 0.00 0.00 38.45 2.52
5709 8012 3.311322 GGTCGCAAATAACCGATGAATCA 59.689 43.478 0.00 0.00 35.76 2.57
5710 8013 4.201871 GGTCGCAAATAACCGATGAATCAA 60.202 41.667 0.00 0.00 35.76 2.57
5711 8014 4.728608 GTCGCAAATAACCGATGAATCAAC 59.271 41.667 0.00 0.00 35.76 3.18
5712 8015 3.718864 CGCAAATAACCGATGAATCAACG 59.281 43.478 5.92 5.92 0.00 4.10
5718 8021 2.293677 CCGATGAATCAACGGTCTGA 57.706 50.000 21.50 0.00 43.21 3.27
5719 8022 1.927174 CCGATGAATCAACGGTCTGAC 59.073 52.381 21.50 0.00 43.21 3.51
5720 8023 1.583856 CGATGAATCAACGGTCTGACG 59.416 52.381 4.95 0.16 40.31 4.35
5721 8024 2.731027 CGATGAATCAACGGTCTGACGA 60.731 50.000 4.95 0.00 37.61 4.20
5722 8025 2.347697 TGAATCAACGGTCTGACGAG 57.652 50.000 1.07 1.16 37.61 4.18
5723 8026 1.611977 TGAATCAACGGTCTGACGAGT 59.388 47.619 1.07 1.81 37.61 4.18
5724 8027 2.815503 TGAATCAACGGTCTGACGAGTA 59.184 45.455 1.07 0.00 37.61 2.59
5725 8028 3.253921 TGAATCAACGGTCTGACGAGTAA 59.746 43.478 1.07 0.00 37.61 2.24
5726 8029 3.928727 ATCAACGGTCTGACGAGTAAA 57.071 42.857 1.07 0.00 37.61 2.01
5727 8030 3.713858 TCAACGGTCTGACGAGTAAAA 57.286 42.857 1.07 0.00 37.61 1.52
5728 8031 4.044336 TCAACGGTCTGACGAGTAAAAA 57.956 40.909 1.07 0.00 37.61 1.94
5729 8032 3.798337 TCAACGGTCTGACGAGTAAAAAC 59.202 43.478 1.07 0.00 37.61 2.43
5730 8033 2.747436 ACGGTCTGACGAGTAAAAACC 58.253 47.619 1.07 0.00 37.61 3.27
5731 8034 2.363359 ACGGTCTGACGAGTAAAAACCT 59.637 45.455 1.07 0.00 37.61 3.50
5732 8035 2.729882 CGGTCTGACGAGTAAAAACCTG 59.270 50.000 1.07 0.00 35.47 4.00
5733 8036 3.551454 CGGTCTGACGAGTAAAAACCTGA 60.551 47.826 1.07 0.00 35.47 3.86
5734 8037 4.374399 GGTCTGACGAGTAAAAACCTGAA 58.626 43.478 1.07 0.00 0.00 3.02
5735 8038 4.812626 GGTCTGACGAGTAAAAACCTGAAA 59.187 41.667 1.07 0.00 0.00 2.69
5736 8039 5.277202 GGTCTGACGAGTAAAAACCTGAAAC 60.277 44.000 1.07 0.00 0.00 2.78
5737 8040 4.505191 TCTGACGAGTAAAAACCTGAAACG 59.495 41.667 0.00 0.00 0.00 3.60
5738 8041 4.431809 TGACGAGTAAAAACCTGAAACGA 58.568 39.130 0.00 0.00 0.00 3.85
5739 8042 4.268405 TGACGAGTAAAAACCTGAAACGAC 59.732 41.667 0.00 0.00 0.00 4.34
5740 8043 4.183101 ACGAGTAAAAACCTGAAACGACA 58.817 39.130 0.00 0.00 0.00 4.35
5741 8044 4.269363 ACGAGTAAAAACCTGAAACGACAG 59.731 41.667 0.00 0.00 37.61 3.51
5742 8045 4.524749 GAGTAAAAACCTGAAACGACAGC 58.475 43.478 0.00 0.00 36.67 4.40
5743 8046 2.863401 AAAAACCTGAAACGACAGCC 57.137 45.000 0.00 0.00 36.67 4.85
5744 8047 1.029681 AAAACCTGAAACGACAGCCC 58.970 50.000 0.00 0.00 36.67 5.19
5745 8048 0.822121 AAACCTGAAACGACAGCCCC 60.822 55.000 0.00 0.00 36.67 5.80
5746 8049 1.990160 AACCTGAAACGACAGCCCCA 61.990 55.000 0.00 0.00 36.67 4.96
5747 8050 1.966451 CCTGAAACGACAGCCCCAC 60.966 63.158 0.00 0.00 36.67 4.61
5748 8051 1.966451 CTGAAACGACAGCCCCACC 60.966 63.158 0.00 0.00 0.00 4.61
5749 8052 2.112297 GAAACGACAGCCCCACCA 59.888 61.111 0.00 0.00 0.00 4.17
5750 8053 1.966451 GAAACGACAGCCCCACCAG 60.966 63.158 0.00 0.00 0.00 4.00
5751 8054 2.676163 GAAACGACAGCCCCACCAGT 62.676 60.000 0.00 0.00 0.00 4.00
5752 8055 2.279037 AAACGACAGCCCCACCAGTT 62.279 55.000 0.00 0.00 0.00 3.16
5753 8056 2.358737 CGACAGCCCCACCAGTTC 60.359 66.667 0.00 0.00 0.00 3.01
5754 8057 2.358737 GACAGCCCCACCAGTTCG 60.359 66.667 0.00 0.00 0.00 3.95
5755 8058 3.901797 GACAGCCCCACCAGTTCGG 62.902 68.421 0.00 0.00 42.50 4.30
5770 8073 4.679654 CCAGTTCGGTTTTTGAAACTATGC 59.320 41.667 3.85 0.00 0.00 3.14
5771 8074 4.679654 CAGTTCGGTTTTTGAAACTATGCC 59.320 41.667 3.85 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 5.710513 TTGATTTAGCAAAGCTCACATGT 57.289 34.783 0.00 0.00 40.44 3.21
89 94 0.097674 CGCATGGAAAGAAAGAGGCG 59.902 55.000 0.00 0.00 37.17 5.52
111 116 3.641436 GGTCCTTGATTTTGGTTCTGGTT 59.359 43.478 0.00 0.00 0.00 3.67
116 121 2.095919 CGACGGTCCTTGATTTTGGTTC 60.096 50.000 1.91 0.00 0.00 3.62
134 139 1.873698 TGTTGCTTGTCTTACCCGAC 58.126 50.000 0.00 0.00 34.52 4.79
144 149 6.708054 GCCTATCATATAGAGTTGTTGCTTGT 59.292 38.462 0.00 0.00 0.00 3.16
150 155 7.618019 TCCTTGCCTATCATATAGAGTTGTT 57.382 36.000 0.00 0.00 0.00 2.83
159 164 7.357471 GGGGATTAATTCCTTGCCTATCATAT 58.643 38.462 12.74 0.00 44.75 1.78
208 213 0.475906 GACCTCCCCAAGCATGCTAT 59.524 55.000 23.00 8.64 0.00 2.97
218 223 2.121832 ATCCACACGACCTCCCCA 59.878 61.111 0.00 0.00 0.00 4.96
254 259 3.736482 ATCGCGAACGCCTCTCGAC 62.736 63.158 15.24 0.00 43.60 4.20
255 260 3.506096 ATCGCGAACGCCTCTCGA 61.506 61.111 15.24 3.11 44.80 4.04
258 263 2.202623 GTCATCGCGAACGCCTCT 60.203 61.111 15.24 0.00 39.84 3.69
272 277 3.663995 TCGGTAAAATGGAAGTCGTCA 57.336 42.857 0.00 0.00 0.00 4.35
276 281 6.237861 CGAGATCTTTCGGTAAAATGGAAGTC 60.238 42.308 0.00 0.00 36.95 3.01
305 310 2.872245 CAGAGAACACAATCACGTTGGT 59.128 45.455 0.00 0.00 42.28 3.67
338 343 3.266510 TCACCGCTAGATTTTGAGCAT 57.733 42.857 0.00 0.00 38.69 3.79
454 459 3.782656 ACGTGGAGTAAAAAGGACCAT 57.217 42.857 0.00 0.00 33.19 3.55
455 460 3.564053 AACGTGGAGTAAAAAGGACCA 57.436 42.857 0.00 0.00 0.00 4.02
476 481 7.649306 GCAAAGTTTGACTTGTCACAAATCTAT 59.351 33.333 19.82 0.00 38.66 1.98
705 1786 1.334243 GAAGACATCGTACTCCCTCCG 59.666 57.143 0.00 0.00 0.00 4.63
706 1787 1.682323 GGAAGACATCGTACTCCCTCC 59.318 57.143 0.00 0.00 0.00 4.30
707 1788 1.334243 CGGAAGACATCGTACTCCCTC 59.666 57.143 0.00 0.00 0.00 4.30
736 1817 0.251608 AACACGGCTGCCCCTATTTT 60.252 50.000 14.12 0.00 0.00 1.82
827 2337 2.911926 GCAGTTGGAGCCTCCCCTT 61.912 63.158 8.62 0.00 35.03 3.95
828 2338 3.334054 GCAGTTGGAGCCTCCCCT 61.334 66.667 8.62 0.83 35.03 4.79
829 2339 4.785453 CGCAGTTGGAGCCTCCCC 62.785 72.222 8.62 0.00 35.03 4.81
877 2389 0.832135 TCTTCTCTGCTGTCCCGGTT 60.832 55.000 0.00 0.00 0.00 4.44
882 2394 1.135517 GTCTCGTCTTCTCTGCTGTCC 60.136 57.143 0.00 0.00 0.00 4.02
1288 3000 2.690881 CCGACCCTTCCCATCCCA 60.691 66.667 0.00 0.00 0.00 4.37
1362 3074 2.046314 ACCAGGCGATCCAAACCG 60.046 61.111 0.00 0.00 33.74 4.44
1526 3238 0.035458 AGAGCTGAACCAGAAACCCG 59.965 55.000 0.00 0.00 32.44 5.28
1556 3268 1.406898 TGCAAAGACAACAAATCGCCA 59.593 42.857 0.00 0.00 0.00 5.69
1559 3271 6.456447 AATTGATGCAAAGACAACAAATCG 57.544 33.333 0.00 0.00 36.16 3.34
1712 3427 9.258826 CCAGATAGTAAAGTCAATGAGATTCAG 57.741 37.037 0.00 0.00 0.00 3.02
1812 3535 9.949174 TGCATGTAAAACATTGATATGTCATAC 57.051 29.630 0.00 0.00 44.14 2.39
2048 3772 9.688091 TGGGTGTAACTAATTTTGCTGATTATA 57.312 29.630 0.00 0.00 36.74 0.98
2049 3773 8.588290 TGGGTGTAACTAATTTTGCTGATTAT 57.412 30.769 0.00 0.00 36.74 1.28
2065 3789 8.825667 ACAATTACAAAATGAATGGGTGTAAC 57.174 30.769 0.00 0.00 37.46 2.50
2213 3939 8.930846 AGTGATTAATCATTCCAATAAGGGAG 57.069 34.615 20.65 0.00 39.30 4.30
2312 4041 5.871396 TTACAAAATGGCACTAAAACCCA 57.129 34.783 0.00 0.00 0.00 4.51
2341 4070 6.440328 ACATTTACTGGGGTAAAATTCAGCAT 59.560 34.615 5.61 0.00 46.64 3.79
3144 4880 4.462483 AGGCAAGTGTTTGAGAAAAACTGA 59.538 37.500 2.96 0.00 37.98 3.41
3312 5140 6.631971 TTACGTGAATGGACGGTATACATA 57.368 37.500 5.01 0.00 43.84 2.29
3317 5146 4.569162 CACATTTACGTGAATGGACGGTAT 59.431 41.667 29.59 10.25 43.84 2.73
3318 5147 3.927758 CACATTTACGTGAATGGACGGTA 59.072 43.478 29.59 0.00 43.84 4.02
3319 5148 2.739913 CACATTTACGTGAATGGACGGT 59.260 45.455 29.59 11.50 43.84 4.83
3320 5149 2.739913 ACACATTTACGTGAATGGACGG 59.260 45.455 29.59 19.99 43.84 4.79
3321 5150 5.712217 ATACACATTTACGTGAATGGACG 57.288 39.130 29.59 21.29 45.09 4.79
3322 5151 6.128117 ACCAATACACATTTACGTGAATGGAC 60.128 38.462 29.59 0.00 40.50 4.02
3323 5152 5.941058 ACCAATACACATTTACGTGAATGGA 59.059 36.000 29.59 18.16 40.50 3.41
3345 5176 8.076178 GCATCAAAATGGTATGTATCAACTACC 58.924 37.037 0.00 0.00 36.30 3.18
3419 5251 7.245604 GGTAACACAATAAAACCCTAATGTCG 58.754 38.462 0.00 0.00 0.00 4.35
3461 5293 0.755327 GGGGCAATATGGTGGTGGTC 60.755 60.000 0.00 0.00 0.00 4.02
3473 5305 0.614812 GGAGCAAACAATGGGGCAAT 59.385 50.000 0.00 0.00 0.00 3.56
3792 5918 7.210873 AGTACTACCAGTCAAAACTCAGAAAG 58.789 38.462 0.00 0.00 31.71 2.62
3793 5919 7.069578 AGAGTACTACCAGTCAAAACTCAGAAA 59.930 37.037 0.00 0.00 34.27 2.52
3982 6272 5.316987 CCATCATAGGTAATTTCCACCCTC 58.683 45.833 3.73 0.00 36.67 4.30
4102 6393 2.745281 GTTATGAGCAAGCCGGTTACAA 59.255 45.455 1.90 0.00 0.00 2.41
4468 6762 4.458989 TGATGCTGAAACCCAAACTCATAC 59.541 41.667 0.00 0.00 0.00 2.39
4470 6764 3.499338 TGATGCTGAAACCCAAACTCAT 58.501 40.909 0.00 0.00 0.00 2.90
4595 6890 3.263170 ACACAAAAAGGAAGCAAAAGGGT 59.737 39.130 0.00 0.00 0.00 4.34
4657 6952 9.778993 AAGTTTATCTGAATGAAATGTGATTCG 57.221 29.630 0.00 0.00 32.19 3.34
4907 7202 6.762702 TCTTGATTAGAAATGCTTGCATGA 57.237 33.333 8.98 0.00 0.00 3.07
4928 7223 9.933240 AAAGGAAAATGATCCATATCTTCTTCT 57.067 29.630 0.00 0.00 42.27 2.85
5122 7418 2.034179 GGTGACCCTGCAAAGTGTTTAC 59.966 50.000 0.00 0.00 0.00 2.01
5142 7438 9.265901 AGAATGACGATGTAAAATTCTAGATGG 57.734 33.333 0.00 0.00 36.17 3.51
5230 7526 6.265196 TGCCAACATGTTCATTTAAGACTTCT 59.735 34.615 8.48 0.00 0.00 2.85
5283 7579 2.257207 GTTCTCGGGATATGGGATGGA 58.743 52.381 0.00 0.00 0.00 3.41
5318 7614 1.133915 ACGTCAGGCCAAAAGAAGGAA 60.134 47.619 5.01 0.00 0.00 3.36
5324 7620 0.387622 CATGCACGTCAGGCCAAAAG 60.388 55.000 5.01 0.00 0.00 2.27
5325 7621 1.106351 ACATGCACGTCAGGCCAAAA 61.106 50.000 5.01 0.00 0.00 2.44
5326 7622 1.528076 ACATGCACGTCAGGCCAAA 60.528 52.632 5.01 0.00 0.00 3.28
5327 7623 2.112928 ACATGCACGTCAGGCCAA 59.887 55.556 5.01 0.00 0.00 4.52
5328 7624 2.669229 CACATGCACGTCAGGCCA 60.669 61.111 5.01 0.00 0.00 5.36
5378 7674 2.621526 CCGACAGTTTAGCCCAGTTTTT 59.378 45.455 0.00 0.00 0.00 1.94
5383 7679 1.734707 CGTACCGACAGTTTAGCCCAG 60.735 57.143 0.00 0.00 0.00 4.45
5384 7680 0.244450 CGTACCGACAGTTTAGCCCA 59.756 55.000 0.00 0.00 0.00 5.36
5507 7807 3.691609 CCTCAAGGCTAGGTGTTTGATTC 59.308 47.826 0.00 0.00 0.00 2.52
5523 7823 0.538057 TGCCTCAAGGTTGCCTCAAG 60.538 55.000 0.00 0.00 37.57 3.02
5525 7825 0.538057 CTTGCCTCAAGGTTGCCTCA 60.538 55.000 0.00 0.00 37.77 3.86
5526 7826 2.261215 CTTGCCTCAAGGTTGCCTC 58.739 57.895 0.00 0.00 37.77 4.70
5545 7845 2.763448 TGTTATTGGGCCTTTACCATGC 59.237 45.455 4.53 0.00 37.93 4.06
5550 7850 5.393787 GCCTAGTTTGTTATTGGGCCTTTAC 60.394 44.000 4.53 0.00 32.86 2.01
5566 7866 7.448748 AAATCACGAAATGTTAGCCTAGTTT 57.551 32.000 0.00 0.00 0.00 2.66
5682 7985 3.984508 TCGGTTATTTGCGACCAAAAA 57.015 38.095 0.00 0.00 43.58 1.94
5683 7986 3.502595 TCATCGGTTATTTGCGACCAAAA 59.497 39.130 0.00 0.00 43.58 2.44
5684 7987 3.075148 TCATCGGTTATTTGCGACCAAA 58.925 40.909 0.00 0.00 44.39 3.28
5685 7988 2.701107 TCATCGGTTATTTGCGACCAA 58.299 42.857 0.00 0.00 35.63 3.67
5686 7989 2.388310 TCATCGGTTATTTGCGACCA 57.612 45.000 0.00 0.00 35.63 4.02
5687 7990 3.311322 TGATTCATCGGTTATTTGCGACC 59.689 43.478 0.00 0.00 0.00 4.79
5688 7991 4.530094 TGATTCATCGGTTATTTGCGAC 57.470 40.909 0.00 0.00 0.00 5.19
5689 7992 4.493382 CGTTGATTCATCGGTTATTTGCGA 60.493 41.667 8.87 0.00 0.00 5.10
5690 7993 3.718864 CGTTGATTCATCGGTTATTTGCG 59.281 43.478 8.87 0.00 0.00 4.85
5691 7994 4.035017 CCGTTGATTCATCGGTTATTTGC 58.965 43.478 22.42 0.00 40.53 3.68
5700 8003 1.583856 CGTCAGACCGTTGATTCATCG 59.416 52.381 9.62 9.62 0.00 3.84
5701 8004 2.854777 CTCGTCAGACCGTTGATTCATC 59.145 50.000 0.00 0.00 0.00 2.92
5702 8005 2.231478 ACTCGTCAGACCGTTGATTCAT 59.769 45.455 0.00 0.00 0.00 2.57
5703 8006 1.611977 ACTCGTCAGACCGTTGATTCA 59.388 47.619 0.00 0.00 0.00 2.57
5704 8007 2.349297 ACTCGTCAGACCGTTGATTC 57.651 50.000 0.00 0.00 0.00 2.52
5705 8008 3.928727 TTACTCGTCAGACCGTTGATT 57.071 42.857 0.00 0.00 0.00 2.57
5706 8009 3.928727 TTTACTCGTCAGACCGTTGAT 57.071 42.857 0.00 0.00 0.00 2.57
5707 8010 3.713858 TTTTACTCGTCAGACCGTTGA 57.286 42.857 0.00 0.00 0.00 3.18
5708 8011 3.060070 GGTTTTTACTCGTCAGACCGTTG 60.060 47.826 0.00 0.00 0.00 4.10
5709 8012 3.126073 GGTTTTTACTCGTCAGACCGTT 58.874 45.455 0.00 0.00 0.00 4.44
5710 8013 2.363359 AGGTTTTTACTCGTCAGACCGT 59.637 45.455 0.00 0.00 0.00 4.83
5711 8014 2.729882 CAGGTTTTTACTCGTCAGACCG 59.270 50.000 0.00 0.00 0.00 4.79
5712 8015 3.986277 TCAGGTTTTTACTCGTCAGACC 58.014 45.455 0.00 0.00 0.00 3.85
5713 8016 5.555818 CGTTTCAGGTTTTTACTCGTCAGAC 60.556 44.000 0.00 0.00 0.00 3.51
5714 8017 4.505191 CGTTTCAGGTTTTTACTCGTCAGA 59.495 41.667 0.00 0.00 0.00 3.27
5715 8018 4.505191 TCGTTTCAGGTTTTTACTCGTCAG 59.495 41.667 0.00 0.00 0.00 3.51
5716 8019 4.268405 GTCGTTTCAGGTTTTTACTCGTCA 59.732 41.667 0.00 0.00 0.00 4.35
5717 8020 4.268405 TGTCGTTTCAGGTTTTTACTCGTC 59.732 41.667 0.00 0.00 0.00 4.20
5718 8021 4.183101 TGTCGTTTCAGGTTTTTACTCGT 58.817 39.130 0.00 0.00 0.00 4.18
5719 8022 4.758561 CTGTCGTTTCAGGTTTTTACTCG 58.241 43.478 0.00 0.00 0.00 4.18
5720 8023 4.524749 GCTGTCGTTTCAGGTTTTTACTC 58.475 43.478 7.01 0.00 36.12 2.59
5721 8024 3.314357 GGCTGTCGTTTCAGGTTTTTACT 59.686 43.478 7.01 0.00 36.12 2.24
5722 8025 3.549423 GGGCTGTCGTTTCAGGTTTTTAC 60.549 47.826 7.01 0.00 36.12 2.01
5723 8026 2.619646 GGGCTGTCGTTTCAGGTTTTTA 59.380 45.455 7.01 0.00 36.12 1.52
5724 8027 1.407618 GGGCTGTCGTTTCAGGTTTTT 59.592 47.619 7.01 0.00 36.12 1.94
5725 8028 1.029681 GGGCTGTCGTTTCAGGTTTT 58.970 50.000 7.01 0.00 36.12 2.43
5726 8029 0.822121 GGGGCTGTCGTTTCAGGTTT 60.822 55.000 7.01 0.00 36.12 3.27
5727 8030 1.228154 GGGGCTGTCGTTTCAGGTT 60.228 57.895 7.01 0.00 36.12 3.50
5728 8031 2.430367 GGGGCTGTCGTTTCAGGT 59.570 61.111 7.01 0.00 36.12 4.00
5729 8032 1.966451 GTGGGGCTGTCGTTTCAGG 60.966 63.158 7.01 0.00 36.12 3.86
5730 8033 1.966451 GGTGGGGCTGTCGTTTCAG 60.966 63.158 0.00 0.00 38.35 3.02
5731 8034 2.112297 GGTGGGGCTGTCGTTTCA 59.888 61.111 0.00 0.00 0.00 2.69
5732 8035 1.966451 CTGGTGGGGCTGTCGTTTC 60.966 63.158 0.00 0.00 0.00 2.78
5733 8036 2.113139 CTGGTGGGGCTGTCGTTT 59.887 61.111 0.00 0.00 0.00 3.60
5734 8037 2.676163 GAACTGGTGGGGCTGTCGTT 62.676 60.000 0.00 0.00 0.00 3.85
5735 8038 3.168528 AACTGGTGGGGCTGTCGT 61.169 61.111 0.00 0.00 0.00 4.34
5736 8039 2.358737 GAACTGGTGGGGCTGTCG 60.359 66.667 0.00 0.00 0.00 4.35
5737 8040 2.358737 CGAACTGGTGGGGCTGTC 60.359 66.667 0.00 0.00 0.00 3.51
5738 8041 3.953775 CCGAACTGGTGGGGCTGT 61.954 66.667 0.00 0.00 0.00 4.40
5747 8050 4.679654 GCATAGTTTCAAAAACCGAACTGG 59.320 41.667 0.00 0.00 46.41 4.00
5748 8051 4.679654 GGCATAGTTTCAAAAACCGAACTG 59.320 41.667 0.00 0.00 34.46 3.16
5749 8052 4.866921 GGCATAGTTTCAAAAACCGAACT 58.133 39.130 0.00 0.00 36.42 3.01


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

AutoCloner maintained by Alex Coulton.