Multiple sequence alignment - TraesCS1D01G176400

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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 TraesCS1D01G176400 chr1D 100.000 5390 0 0 1 5390 250921503 250926892 0.000000e+00 9954.0
1 TraesCS1D01G176400 chr1D 89.691 970 90 7 982 1951 30025634 30026593 0.000000e+00 1229.0
2 TraesCS1D01G176400 chr1D 86.000 1050 123 11 909 1954 8387992 8389021 0.000000e+00 1103.0
3 TraesCS1D01G176400 chr1A 93.530 1731 105 7 3654 5379 321113752 321115480 0.000000e+00 2569.0
4 TraesCS1D01G176400 chr1A 96.038 1565 37 15 652 2198 321110181 321111738 0.000000e+00 2523.0
5 TraesCS1D01G176400 chr1A 85.230 1063 125 15 904 1954 9968454 9969496 0.000000e+00 1064.0
6 TraesCS1D01G176400 chr1A 84.876 1091 86 27 2563 3610 321112696 321113750 0.000000e+00 1027.0
7 TraesCS1D01G176400 chr1A 91.557 379 27 3 287 661 321109778 321110155 8.000000e-143 518.0
8 TraesCS1D01G176400 chr1A 90.580 276 15 6 2197 2464 321111843 321112115 6.640000e-94 355.0
9 TraesCS1D01G176400 chr1A 100.000 31 0 0 2457 2487 321112325 321112355 2.100000e-04 58.4
10 TraesCS1D01G176400 chr1B 93.140 1720 93 18 3688 5390 363477994 363476283 0.000000e+00 2499.0
11 TraesCS1D01G176400 chr1B 95.691 1462 34 7 652 2111 363480954 363479520 0.000000e+00 2324.0
12 TraesCS1D01G176400 chr1B 86.391 992 121 5 964 1954 11406863 11407841 0.000000e+00 1072.0
13 TraesCS1D01G176400 chr1B 91.864 762 37 6 2814 3574 363478816 363478079 0.000000e+00 1040.0
14 TraesCS1D01G176400 chr1B 88.296 675 48 13 4 661 363481640 363480980 0.000000e+00 780.0
15 TraesCS1D01G176400 chr1B 87.281 629 45 15 2150 2772 363479518 363478919 0.000000e+00 686.0
16 TraesCS1D01G176400 chr1B 97.917 48 1 0 2767 2814 363478881 363478834 3.460000e-12 84.2
17 TraesCS1D01G176400 chr3D 88.545 1100 97 17 867 1955 41784538 41783457 0.000000e+00 1306.0
18 TraesCS1D01G176400 chr3B 88.140 1113 105 18 867 1970 66170774 66171868 0.000000e+00 1299.0
19 TraesCS1D01G176400 chr3B 84.485 651 97 3 3719 4367 66172884 66173532 1.640000e-179 640.0
20 TraesCS1D01G176400 chr3A 88.284 1084 104 14 868 1946 53738518 53739583 0.000000e+00 1277.0
21 TraesCS1D01G176400 chr3A 80.758 660 108 8 3708 4367 53740723 53741363 1.040000e-136 497.0
22 TraesCS1D01G176400 chr2A 84.025 651 104 0 3717 4367 723650474 723649824 1.270000e-175 627.0
23 TraesCS1D01G176400 chr7D 75.641 624 147 3 3718 4340 451029034 451029653 6.780000e-79 305.0
24 TraesCS1D01G176400 chr7B 73.858 635 161 5 3718 4351 468773531 468774161 1.160000e-61 248.0
25 TraesCS1D01G176400 chr4D 79.333 150 20 7 234 373 318281883 318281735 1.600000e-15 95.3
26 TraesCS1D01G176400 chr6B 85.484 62 6 3 3895 3954 255192235 255192175 1.620000e-05 62.1
27 TraesCS1D01G176400 chr6A 100.000 29 0 0 3896 3924 205115837 205115865 3.000000e-03 54.7


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 TraesCS1D01G176400 chr1D 250921503 250926892 5389 False 9954.000000 9954 100.000000 1 5390 1 chr1D.!!$F3 5389
1 TraesCS1D01G176400 chr1D 30025634 30026593 959 False 1229.000000 1229 89.691000 982 1951 1 chr1D.!!$F2 969
2 TraesCS1D01G176400 chr1D 8387992 8389021 1029 False 1103.000000 1103 86.000000 909 1954 1 chr1D.!!$F1 1045
3 TraesCS1D01G176400 chr1A 321109778 321115480 5702 False 1175.066667 2569 92.763500 287 5379 6 chr1A.!!$F2 5092
4 TraesCS1D01G176400 chr1A 9968454 9969496 1042 False 1064.000000 1064 85.230000 904 1954 1 chr1A.!!$F1 1050
5 TraesCS1D01G176400 chr1B 363476283 363481640 5357 True 1235.533333 2499 92.364833 4 5390 6 chr1B.!!$R1 5386
6 TraesCS1D01G176400 chr1B 11406863 11407841 978 False 1072.000000 1072 86.391000 964 1954 1 chr1B.!!$F1 990
7 TraesCS1D01G176400 chr3D 41783457 41784538 1081 True 1306.000000 1306 88.545000 867 1955 1 chr3D.!!$R1 1088
8 TraesCS1D01G176400 chr3B 66170774 66173532 2758 False 969.500000 1299 86.312500 867 4367 2 chr3B.!!$F1 3500
9 TraesCS1D01G176400 chr3A 53738518 53741363 2845 False 887.000000 1277 84.521000 868 4367 2 chr3A.!!$F1 3499
10 TraesCS1D01G176400 chr2A 723649824 723650474 650 True 627.000000 627 84.025000 3717 4367 1 chr2A.!!$R1 650
11 TraesCS1D01G176400 chr7D 451029034 451029653 619 False 305.000000 305 75.641000 3718 4340 1 chr7D.!!$F1 622
12 TraesCS1D01G176400 chr7B 468773531 468774161 630 False 248.000000 248 73.858000 3718 4351 1 chr7B.!!$F1 633

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
430 440 0.315568 GCGGATCAACGGCTCTAGAT 59.684 55.0 0.00 0.0 40.81 1.98 F
856 921 1.481871 CTACTCCTCCGCCCAAACTA 58.518 55.0 0.00 0.0 0.00 2.24 F
2247 2912 0.519175 CGGCGATCGAGCTGTTTTTG 60.519 55.0 21.57 0.0 42.43 2.44 F
3305 5402 0.175989 TGGTGTTGTAGTGCGTGTCA 59.824 50.0 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1913 3.307108 TCCACCATGTCCGCGTCA 61.307 61.111 4.92 4.31 0.00 4.35 R
2554 4567 0.107993 TCAAGGGAGCAAGCTCGATG 60.108 55.000 15.20 13.17 43.59 3.84 R
4035 6199 0.106519 CCGGATCCTTCCATGCCTTT 60.107 55.000 10.75 0.00 42.74 3.11 R
4441 6605 0.605589 CACCTCTGACCAGACACCTC 59.394 60.000 0.00 0.00 33.22 3.85 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
80 81 7.818930 TGACCTCATGAAAAGCAAAATAATTCC 59.181 33.333 0.00 0.00 0.00 3.01
81 82 7.678837 ACCTCATGAAAAGCAAAATAATTCCA 58.321 30.769 0.00 0.00 0.00 3.53
82 83 7.603784 ACCTCATGAAAAGCAAAATAATTCCAC 59.396 33.333 0.00 0.00 0.00 4.02
83 84 7.603404 CCTCATGAAAAGCAAAATAATTCCACA 59.397 33.333 0.00 0.00 0.00 4.17
84 85 8.309163 TCATGAAAAGCAAAATAATTCCACAC 57.691 30.769 0.00 0.00 0.00 3.82
100 101 6.433847 TTCCACACAAGGAAGAGAAATAGA 57.566 37.500 0.00 0.00 42.56 1.98
101 102 6.042638 TCCACACAAGGAAGAGAAATAGAG 57.957 41.667 0.00 0.00 33.93 2.43
102 103 5.780282 TCCACACAAGGAAGAGAAATAGAGA 59.220 40.000 0.00 0.00 33.93 3.10
103 104 6.270000 TCCACACAAGGAAGAGAAATAGAGAA 59.730 38.462 0.00 0.00 33.93 2.87
104 105 6.936900 CCACACAAGGAAGAGAAATAGAGAAA 59.063 38.462 0.00 0.00 0.00 2.52
105 106 7.095017 CCACACAAGGAAGAGAAATAGAGAAAC 60.095 40.741 0.00 0.00 0.00 2.78
106 107 7.442364 CACACAAGGAAGAGAAATAGAGAAACA 59.558 37.037 0.00 0.00 0.00 2.83
110 111 6.760291 AGGAAGAGAAATAGAGAAACAACGT 58.240 36.000 0.00 0.00 0.00 3.99
140 142 5.885465 AGGATTGAAAGGAAGAACACAGAT 58.115 37.500 0.00 0.00 0.00 2.90
160 162 3.198863 TGACGCGAAAGAGAAGAGTAC 57.801 47.619 15.93 0.00 33.96 2.73
169 171 5.854338 CGAAAGAGAAGAGTACTGAACAGTC 59.146 44.000 10.81 3.99 42.54 3.51
199 201 2.777692 ACAAGTGGACCAAGGAAGAAGA 59.222 45.455 0.00 0.00 0.00 2.87
201 203 3.710209 AGTGGACCAAGGAAGAAGATG 57.290 47.619 0.00 0.00 0.00 2.90
221 223 4.508551 TGATCAGTAACATGGATGGCTT 57.491 40.909 0.00 0.00 0.00 4.35
226 228 3.758023 CAGTAACATGGATGGCTTGAACA 59.242 43.478 0.00 0.00 0.00 3.18
246 248 6.490040 TGAACAGGGTTGAAGAATAAAGAAGG 59.510 38.462 0.00 0.00 0.00 3.46
379 389 2.363306 TGCATCTATTTTCCGGCCAT 57.637 45.000 2.24 0.00 0.00 4.40
384 394 4.270808 GCATCTATTTTCCGGCCATTTTTG 59.729 41.667 2.24 0.00 0.00 2.44
402 412 3.810310 TTGGCCGAAACAACTTTTCAT 57.190 38.095 0.00 0.00 0.00 2.57
430 440 0.315568 GCGGATCAACGGCTCTAGAT 59.684 55.000 0.00 0.00 40.81 1.98
603 624 9.074576 TCTCTCCGTGCTCATATAATTAGTAAA 57.925 33.333 0.00 0.00 0.00 2.01
777 833 7.221838 GGAAAGAAACGTTGAAAAATGTGATGA 59.778 33.333 0.00 0.00 0.00 2.92
780 836 7.202526 AGAAACGTTGAAAAATGTGATGATGT 58.797 30.769 0.00 0.00 0.00 3.06
820 876 5.128499 ACATGTCTCAACCTAATCTGGAGAG 59.872 44.000 0.00 0.00 35.47 3.20
821 877 4.935578 TGTCTCAACCTAATCTGGAGAGA 58.064 43.478 0.00 0.00 38.44 3.10
822 878 5.523588 TGTCTCAACCTAATCTGGAGAGAT 58.476 41.667 11.23 0.00 41.00 2.75
823 879 5.596361 TGTCTCAACCTAATCTGGAGAGATC 59.404 44.000 11.23 0.00 38.03 2.75
824 880 5.833131 GTCTCAACCTAATCTGGAGAGATCT 59.167 44.000 0.00 0.00 38.03 2.75
825 881 6.016276 GTCTCAACCTAATCTGGAGAGATCTC 60.016 46.154 15.29 15.29 38.03 2.75
856 921 1.481871 CTACTCCTCCGCCCAAACTA 58.518 55.000 0.00 0.00 0.00 2.24
1815 1913 1.006102 CAAGAGCCCTGACGACGTT 60.006 57.895 0.13 0.00 0.00 3.99
2076 2201 6.525121 AAAAAGGCAAGCGATTTTCTTTAC 57.475 33.333 10.02 0.00 0.00 2.01
2077 2202 3.850122 AGGCAAGCGATTTTCTTTACC 57.150 42.857 0.00 0.00 0.00 2.85
2078 2203 3.421844 AGGCAAGCGATTTTCTTTACCT 58.578 40.909 0.00 0.00 0.00 3.08
2080 2205 3.417185 GCAAGCGATTTTCTTTACCTCG 58.583 45.455 0.00 0.00 0.00 4.63
2081 2206 3.124636 GCAAGCGATTTTCTTTACCTCGA 59.875 43.478 0.00 0.00 0.00 4.04
2082 2207 4.378046 GCAAGCGATTTTCTTTACCTCGAA 60.378 41.667 0.00 0.00 0.00 3.71
2083 2208 5.685841 CAAGCGATTTTCTTTACCTCGAAA 58.314 37.500 0.00 0.00 0.00 3.46
2099 2224 7.559590 ACCTCGAAAGAAATCCTGATTTATG 57.440 36.000 5.16 0.00 40.77 1.90
2189 2476 1.405463 AGTGCAAGCGATATCTGACGA 59.595 47.619 0.34 0.00 0.00 4.20
2190 2477 2.035193 AGTGCAAGCGATATCTGACGAT 59.965 45.455 0.34 0.00 0.00 3.73
2191 2478 2.797156 GTGCAAGCGATATCTGACGATT 59.203 45.455 0.34 0.00 38.60 3.34
2192 2479 3.981416 GTGCAAGCGATATCTGACGATTA 59.019 43.478 0.34 0.00 36.42 1.75
2193 2480 4.623167 GTGCAAGCGATATCTGACGATTAT 59.377 41.667 0.34 0.00 36.42 1.28
2247 2912 0.519175 CGGCGATCGAGCTGTTTTTG 60.519 55.000 21.57 0.00 42.43 2.44
2249 2914 1.201965 GGCGATCGAGCTGTTTTTGAG 60.202 52.381 21.57 0.00 37.29 3.02
2250 2915 1.201965 GCGATCGAGCTGTTTTTGAGG 60.202 52.381 21.57 0.00 0.00 3.86
2544 4557 2.040544 CATGTGTTGGCCCGAGGTC 61.041 63.158 0.00 0.00 0.00 3.85
2554 4567 2.187946 CCGAGGTCAGGGCACATC 59.812 66.667 0.00 0.00 0.00 3.06
2558 4571 0.531532 GAGGTCAGGGCACATCATCG 60.532 60.000 0.00 0.00 0.00 3.84
2597 4611 0.466372 TCGTCCACATTTTGCACCCA 60.466 50.000 0.00 0.00 0.00 4.51
2649 4663 0.516001 GCAGTAGAGACACGTGACGA 59.484 55.000 25.01 6.71 0.00 4.20
2723 4737 1.861971 GTATACACTACGGGCAAGCC 58.138 55.000 1.52 1.52 0.00 4.35
2731 4745 2.813226 TACGGGCAAGCCGCTTTCAT 62.813 55.000 1.86 0.00 41.91 2.57
2763 4778 4.681483 CACCATGACGTAGCATACATACAG 59.319 45.833 0.00 0.00 43.24 2.74
2779 4839 1.999648 ACAGTAGGTACGTTGGACCA 58.000 50.000 8.64 0.00 39.65 4.02
2864 4942 1.667236 TAACAATGCCAGATCCAGCG 58.333 50.000 0.59 0.00 0.00 5.18
2942 5020 1.154197 CTTCGTTCGAGGGGGAAAAC 58.846 55.000 0.00 0.00 0.00 2.43
3081 5172 5.734855 TGTACTTTTCAGTTCTCACTTGC 57.265 39.130 0.00 0.00 34.06 4.01
3085 5176 4.943705 ACTTTTCAGTTCTCACTTGCTTCA 59.056 37.500 0.00 0.00 0.00 3.02
3099 5190 1.514678 GCTTCATTCACGCCCACACA 61.515 55.000 0.00 0.00 0.00 3.72
3100 5191 0.238289 CTTCATTCACGCCCACACAC 59.762 55.000 0.00 0.00 0.00 3.82
3101 5192 0.464554 TTCATTCACGCCCACACACA 60.465 50.000 0.00 0.00 0.00 3.72
3102 5193 1.163420 TCATTCACGCCCACACACAC 61.163 55.000 0.00 0.00 0.00 3.82
3103 5194 1.153066 ATTCACGCCCACACACACA 60.153 52.632 0.00 0.00 0.00 3.72
3104 5195 1.444119 ATTCACGCCCACACACACAC 61.444 55.000 0.00 0.00 0.00 3.82
3105 5196 2.804828 TTCACGCCCACACACACACA 62.805 55.000 0.00 0.00 0.00 3.72
3106 5197 2.822255 ACGCCCACACACACACAC 60.822 61.111 0.00 0.00 0.00 3.82
3231 5324 1.201877 CCGACTTTTTATGGTGCGTCG 60.202 52.381 0.00 0.00 42.54 5.12
3233 5326 2.720590 CGACTTTTTATGGTGCGTCGTG 60.721 50.000 0.00 0.00 39.30 4.35
3274 5367 2.828549 ATAAGCTTTGGCCGGCCG 60.829 61.111 39.00 26.48 39.73 6.13
3305 5402 0.175989 TGGTGTTGTAGTGCGTGTCA 59.824 50.000 0.00 0.00 0.00 3.58
3312 5409 0.317479 GTAGTGCGTGTCACCTTCCT 59.683 55.000 0.00 0.00 46.81 3.36
3322 5419 4.211374 CGTGTCACCTTCCTAAGTGAAAAG 59.789 45.833 0.00 0.00 0.00 2.27
3324 5421 4.141482 TGTCACCTTCCTAAGTGAAAAGCT 60.141 41.667 0.00 0.00 0.00 3.74
3325 5422 4.452795 GTCACCTTCCTAAGTGAAAAGCTC 59.547 45.833 0.00 0.00 0.00 4.09
3326 5423 4.348168 TCACCTTCCTAAGTGAAAAGCTCT 59.652 41.667 0.00 0.00 0.00 4.09
3327 5424 4.693095 CACCTTCCTAAGTGAAAAGCTCTC 59.307 45.833 0.00 0.00 0.00 3.20
3328 5425 4.348168 ACCTTCCTAAGTGAAAAGCTCTCA 59.652 41.667 0.00 0.00 0.00 3.27
3329 5426 5.163195 ACCTTCCTAAGTGAAAAGCTCTCAA 60.163 40.000 0.24 0.00 0.00 3.02
3330 5427 5.180304 CCTTCCTAAGTGAAAAGCTCTCAAC 59.820 44.000 0.24 0.00 0.00 3.18
3331 5428 4.642429 TCCTAAGTGAAAAGCTCTCAACC 58.358 43.478 0.24 0.00 0.00 3.77
3332 5429 4.102524 TCCTAAGTGAAAAGCTCTCAACCA 59.897 41.667 0.24 0.00 0.00 3.67
3333 5430 4.821805 CCTAAGTGAAAAGCTCTCAACCAA 59.178 41.667 0.24 0.00 0.00 3.67
3381 5478 2.081462 CCCTAAGCTTTGTACCAACCG 58.919 52.381 3.20 0.00 0.00 4.44
3383 5480 2.147958 CTAAGCTTTGTACCAACCGCA 58.852 47.619 3.20 0.00 0.00 5.69
3405 5502 4.799419 TCGTTTTCTTTACTTTCACGGG 57.201 40.909 0.00 0.00 0.00 5.28
3439 5540 2.587194 CTCGGCCCTTCTGCGATG 60.587 66.667 0.00 0.00 0.00 3.84
3531 5633 2.910688 ATTGGACACCTATGCTACGG 57.089 50.000 0.00 0.00 0.00 4.02
3539 5644 1.329256 CCTATGCTACGGCCTACTGT 58.671 55.000 0.00 0.00 39.33 3.55
3546 5651 2.734492 GCTACGGCCTACTGTTACTGTG 60.734 54.545 0.00 0.00 36.55 3.66
3563 5668 3.812203 GCGCATGCATGACACCTA 58.188 55.556 30.64 0.00 42.15 3.08
3573 5678 2.874701 GCATGACACCTATTTGCGATCT 59.125 45.455 0.00 0.00 0.00 2.75
3575 5680 2.809446 TGACACCTATTTGCGATCTCG 58.191 47.619 0.00 0.00 43.27 4.04
3579 5684 4.000988 ACACCTATTTGCGATCTCGTTTT 58.999 39.130 1.14 0.00 42.22 2.43
3582 5687 6.982141 ACACCTATTTGCGATCTCGTTTTATA 59.018 34.615 1.14 0.00 42.22 0.98
3592 5697 7.272731 TGCGATCTCGTTTTATATACTGTATGC 59.727 37.037 10.51 1.11 42.22 3.14
3596 5701 7.641760 TCTCGTTTTATATACTGTATGCGTCA 58.358 34.615 10.51 0.00 0.00 4.35
3601 5706 9.406828 GTTTTATATACTGTATGCGTCATCTGA 57.593 33.333 10.51 0.00 0.00 3.27
3602 5707 9.626045 TTTTATATACTGTATGCGTCATCTGAG 57.374 33.333 10.51 0.00 0.00 3.35
3603 5708 8.561738 TTATATACTGTATGCGTCATCTGAGA 57.438 34.615 10.51 0.00 0.00 3.27
3604 5709 3.428746 ACTGTATGCGTCATCTGAGAC 57.571 47.619 0.00 0.00 35.19 3.36
3605 5710 3.020274 ACTGTATGCGTCATCTGAGACT 58.980 45.455 0.00 0.00 36.38 3.24
3606 5711 3.181492 ACTGTATGCGTCATCTGAGACTG 60.181 47.826 0.00 0.00 36.38 3.51
3607 5712 2.755103 TGTATGCGTCATCTGAGACTGT 59.245 45.455 0.00 0.00 36.38 3.55
3608 5713 3.945285 TGTATGCGTCATCTGAGACTGTA 59.055 43.478 0.00 0.00 36.38 2.74
3609 5714 4.580580 TGTATGCGTCATCTGAGACTGTAT 59.419 41.667 0.00 0.00 36.38 2.29
3610 5715 3.699779 TGCGTCATCTGAGACTGTATC 57.300 47.619 0.00 0.00 36.38 2.24
3611 5716 3.282885 TGCGTCATCTGAGACTGTATCT 58.717 45.455 3.90 0.00 41.91 1.98
3612 5717 3.696548 TGCGTCATCTGAGACTGTATCTT 59.303 43.478 3.90 0.00 38.00 2.40
3613 5718 4.881850 TGCGTCATCTGAGACTGTATCTTA 59.118 41.667 3.90 0.00 38.00 2.10
3614 5719 5.532779 TGCGTCATCTGAGACTGTATCTTAT 59.467 40.000 3.90 0.00 38.00 1.73
3615 5720 6.710744 TGCGTCATCTGAGACTGTATCTTATA 59.289 38.462 3.90 0.00 38.00 0.98
3616 5721 7.391833 TGCGTCATCTGAGACTGTATCTTATAT 59.608 37.037 3.90 0.00 38.00 0.86
3617 5722 8.884726 GCGTCATCTGAGACTGTATCTTATATA 58.115 37.037 3.90 0.00 38.00 0.86
3677 5782 3.424829 CGCATGTATGACACCTGTTTGTC 60.425 47.826 0.00 0.00 45.34 3.18
3954 6118 2.382882 CTACTCCTCCATGAGACTGCA 58.617 52.381 0.00 0.00 36.22 4.41
4011 6175 1.475751 GGCTCCCGTGTCATGATCAAT 60.476 52.381 0.00 0.00 0.00 2.57
4216 6380 3.921767 CTCGCCGTTGCTCAGCTCA 62.922 63.158 0.00 0.00 34.43 4.26
4448 6612 2.032681 GCACAGGGTGGAGGTGTC 59.967 66.667 0.00 0.00 35.05 3.67
4524 6688 8.014517 TGCATTTTGTTGTTGTTTTTCTTCTTC 58.985 29.630 0.00 0.00 0.00 2.87
4554 6718 5.243507 TGCCTTTTGAATTCTGATACTGCAA 59.756 36.000 7.05 0.00 0.00 4.08
4700 6864 6.071391 GGCCCAGATTCTGTAAATTTTCTTCA 60.071 38.462 12.54 0.00 0.00 3.02
4737 6901 1.386533 AGATCGCAAAGATTGGCCTG 58.613 50.000 3.32 0.00 40.26 4.85
4757 6921 7.001073 GGCCTGTCCTTTTTCTTATCTCATAT 58.999 38.462 0.00 0.00 0.00 1.78
4758 6922 8.157476 GGCCTGTCCTTTTTCTTATCTCATATA 58.843 37.037 0.00 0.00 0.00 0.86
4824 6989 2.351641 CCACGCTTCTGCAATTTGCTTA 60.352 45.455 21.19 7.44 45.31 3.09
4839 7004 2.695359 TGCTTAGGTACTTCAAAGCCG 58.305 47.619 9.31 0.00 42.87 5.52
4840 7005 2.038033 TGCTTAGGTACTTCAAAGCCGT 59.962 45.455 9.31 0.00 42.87 5.68
4842 7007 3.501062 GCTTAGGTACTTCAAAGCCGTTT 59.499 43.478 1.94 0.00 41.75 3.60
4889 7056 6.425577 TCGGATTTTTAGAACAATAACGGG 57.574 37.500 0.00 0.00 0.00 5.28
4939 7106 1.068055 TCCCTAGTGTCGAAAACGCTC 60.068 52.381 0.00 0.00 45.69 5.03
4940 7107 1.336517 CCCTAGTGTCGAAAACGCTCA 60.337 52.381 0.00 0.00 45.69 4.26
4941 7108 2.400399 CCTAGTGTCGAAAACGCTCAA 58.600 47.619 0.00 0.00 45.69 3.02
4947 7119 5.997385 AGTGTCGAAAACGCTCAAATATTT 58.003 33.333 0.00 0.00 45.69 1.40
4956 7128 4.023291 ACGCTCAAATATTTTGGGATGGT 58.977 39.130 16.63 0.00 0.00 3.55
4959 7131 4.405358 GCTCAAATATTTTGGGATGGTGGA 59.595 41.667 4.08 0.00 0.00 4.02
5153 7325 3.119137 TCCACAGTTCGTACAGGATGATG 60.119 47.826 0.00 0.00 39.69 3.07
5183 7355 7.611770 AGTGCGATAATCTAGGCATTAATGTA 58.388 34.615 16.61 1.88 37.77 2.29
5371 7551 5.410924 GGCAGAATTGGTTAAGAAATGACC 58.589 41.667 0.00 0.00 38.18 4.02
5385 7565 3.757745 AATGACCGCGTAAGGAATTTG 57.242 42.857 4.92 0.00 38.28 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.093850 GCAAGTTCATGCCATCATTTTTCC 59.906 41.667 0.00 0.00 40.49 3.13
1 2 4.201647 CGCAAGTTCATGCCATCATTTTTC 60.202 41.667 0.00 0.00 43.47 2.29
2 3 3.680937 CGCAAGTTCATGCCATCATTTTT 59.319 39.130 0.00 0.00 43.47 1.94
32 33 2.820059 TGAGCAGTTCGTCATGTTCT 57.180 45.000 0.00 0.00 0.00 3.01
42 43 4.005650 TCATGAGGTCAATTGAGCAGTTC 58.994 43.478 32.68 23.44 44.42 3.01
80 81 7.442364 TGTTTCTCTATTTCTCTTCCTTGTGTG 59.558 37.037 0.00 0.00 0.00 3.82
81 82 7.509546 TGTTTCTCTATTTCTCTTCCTTGTGT 58.490 34.615 0.00 0.00 0.00 3.72
82 83 7.969536 TGTTTCTCTATTTCTCTTCCTTGTG 57.030 36.000 0.00 0.00 0.00 3.33
83 84 7.171678 CGTTGTTTCTCTATTTCTCTTCCTTGT 59.828 37.037 0.00 0.00 0.00 3.16
84 85 7.171678 ACGTTGTTTCTCTATTTCTCTTCCTTG 59.828 37.037 0.00 0.00 0.00 3.61
91 92 7.582435 TGATCACGTTGTTTCTCTATTTCTC 57.418 36.000 0.00 0.00 0.00 2.87
98 99 4.703897 TCCTTTGATCACGTTGTTTCTCT 58.296 39.130 0.00 0.00 0.00 3.10
99 100 5.613358 ATCCTTTGATCACGTTGTTTCTC 57.387 39.130 0.00 0.00 0.00 2.87
100 101 5.530915 TCAATCCTTTGATCACGTTGTTTCT 59.469 36.000 0.00 0.00 36.94 2.52
101 102 5.757886 TCAATCCTTTGATCACGTTGTTTC 58.242 37.500 0.00 0.00 36.94 2.78
102 103 5.766150 TCAATCCTTTGATCACGTTGTTT 57.234 34.783 0.00 0.00 36.94 2.83
103 104 5.766150 TTCAATCCTTTGATCACGTTGTT 57.234 34.783 0.00 0.00 41.38 2.83
104 105 5.278463 CCTTTCAATCCTTTGATCACGTTGT 60.278 40.000 0.00 0.00 41.38 3.32
105 106 5.048782 TCCTTTCAATCCTTTGATCACGTTG 60.049 40.000 0.00 0.00 41.38 4.10
106 107 5.070001 TCCTTTCAATCCTTTGATCACGTT 58.930 37.500 0.00 0.00 41.38 3.99
110 111 6.777091 TGTTCTTCCTTTCAATCCTTTGATCA 59.223 34.615 0.00 0.00 41.38 2.92
140 142 2.812591 AGTACTCTTCTCTTTCGCGTCA 59.187 45.455 5.77 0.00 0.00 4.35
169 171 0.537371 GGTCCACTTGTTCCACCCTG 60.537 60.000 0.00 0.00 0.00 4.45
171 173 0.106419 TTGGTCCACTTGTTCCACCC 60.106 55.000 0.00 0.00 0.00 4.61
199 201 4.719026 AGCCATCCATGTTACTGATCAT 57.281 40.909 0.00 0.00 0.00 2.45
201 203 4.454678 TCAAGCCATCCATGTTACTGATC 58.545 43.478 0.00 0.00 0.00 2.92
221 223 6.490040 CCTTCTTTATTCTTCAACCCTGTTCA 59.510 38.462 0.00 0.00 0.00 3.18
226 228 7.950124 TCAATTCCTTCTTTATTCTTCAACCCT 59.050 33.333 0.00 0.00 0.00 4.34
246 248 4.731773 GCATCGTCCCTTCATGTTCAATTC 60.732 45.833 0.00 0.00 0.00 2.17
295 305 6.163476 TCTTGTATGAATACTTCGTGCAACT 58.837 36.000 8.05 0.00 43.28 3.16
328 338 4.115516 CCCTCTCAATACGAGACAACATG 58.884 47.826 0.00 0.00 46.18 3.21
331 341 2.166664 AGCCCTCTCAATACGAGACAAC 59.833 50.000 0.00 0.00 46.18 3.32
351 361 6.237915 GCCGGAAAATAGATGCAAATTTGAAG 60.238 38.462 22.31 0.00 0.00 3.02
379 389 4.315803 TGAAAAGTTGTTTCGGCCAAAAA 58.684 34.783 2.24 0.00 0.00 1.94
384 394 4.857037 GTGATATGAAAAGTTGTTTCGGCC 59.143 41.667 0.00 0.00 0.00 6.13
402 412 1.590525 GTTGATCCGCGCCGTGATA 60.591 57.895 0.00 0.00 0.00 2.15
499 519 6.039382 ACAGGTATGAAAGGTCAAAGTCAAAC 59.961 38.462 0.00 0.00 37.30 2.93
821 877 3.181423 GGAGTAGGTGAGATCAGGGAGAT 60.181 52.174 0.00 0.00 40.48 2.75
822 878 2.175931 GGAGTAGGTGAGATCAGGGAGA 59.824 54.545 0.00 0.00 0.00 3.71
823 879 2.176798 AGGAGTAGGTGAGATCAGGGAG 59.823 54.545 0.00 0.00 0.00 4.30
824 880 2.175931 GAGGAGTAGGTGAGATCAGGGA 59.824 54.545 0.00 0.00 0.00 4.20
825 881 2.593026 GAGGAGTAGGTGAGATCAGGG 58.407 57.143 0.00 0.00 0.00 4.45
826 882 2.593026 GGAGGAGTAGGTGAGATCAGG 58.407 57.143 0.00 0.00 0.00 3.86
827 883 2.226330 CGGAGGAGTAGGTGAGATCAG 58.774 57.143 0.00 0.00 0.00 2.90
828 884 1.751032 GCGGAGGAGTAGGTGAGATCA 60.751 57.143 0.00 0.00 0.00 2.92
829 885 0.955905 GCGGAGGAGTAGGTGAGATC 59.044 60.000 0.00 0.00 0.00 2.75
830 886 0.468400 GGCGGAGGAGTAGGTGAGAT 60.468 60.000 0.00 0.00 0.00 2.75
856 921 2.574824 GGAGGGTGCCGGGTTTATATAT 59.425 50.000 2.18 0.00 0.00 0.86
1815 1913 3.307108 TCCACCATGTCCGCGTCA 61.307 61.111 4.92 4.31 0.00 4.35
1979 2096 8.765219 GCGCATATATGGTAGTAATTGATTAGG 58.235 37.037 14.51 0.00 0.00 2.69
2076 2201 6.543831 ACCATAAATCAGGATTTCTTTCGAGG 59.456 38.462 10.32 6.52 40.99 4.63
2077 2202 7.559590 ACCATAAATCAGGATTTCTTTCGAG 57.440 36.000 10.32 0.00 40.99 4.04
2078 2203 8.265055 ACTACCATAAATCAGGATTTCTTTCGA 58.735 33.333 10.32 0.00 40.99 3.71
2114 2239 3.610911 ACAAACCATTTTCCCGCAAAAA 58.389 36.364 0.00 0.00 37.52 1.94
2247 2912 4.817517 TCTGGACGATAAAAACTGACCTC 58.182 43.478 0.00 0.00 0.00 3.85
2249 2914 4.995487 ACTTCTGGACGATAAAAACTGACC 59.005 41.667 0.00 0.00 0.00 4.02
2250 2915 6.867293 AGTACTTCTGGACGATAAAAACTGAC 59.133 38.462 0.00 0.00 0.00 3.51
2326 3801 6.153067 GCCGTATATATGGAGATATCTGCAC 58.847 44.000 26.91 13.35 46.89 4.57
2515 4528 4.160252 GGGCCAACACATGACAAATAATCT 59.840 41.667 4.39 0.00 0.00 2.40
2526 4539 2.034066 ACCTCGGGCCAACACATG 59.966 61.111 4.39 0.00 0.00 3.21
2527 4540 2.351276 GACCTCGGGCCAACACAT 59.649 61.111 4.39 0.00 0.00 3.21
2544 4557 0.463295 AAGCTCGATGATGTGCCCTG 60.463 55.000 0.00 0.00 0.00 4.45
2548 4561 0.304098 GAGCAAGCTCGATGATGTGC 59.696 55.000 6.28 0.00 33.06 4.57
2554 4567 0.107993 TCAAGGGAGCAAGCTCGATG 60.108 55.000 15.20 13.17 43.59 3.84
2649 4663 2.529632 GGAAGGGGAGAAAAATGTGCT 58.470 47.619 0.00 0.00 0.00 4.40
2731 4745 0.250684 ACGTCATGGTGGTTCATGCA 60.251 50.000 0.00 0.00 42.96 3.96
2763 4778 4.884164 ACTAGTATGGTCCAACGTACCTAC 59.116 45.833 7.47 7.29 37.91 3.18
2779 4839 8.964772 ACGTAAGGAGACAAACATAACTAGTAT 58.035 33.333 0.00 0.00 46.39 2.12
2842 4920 2.555757 GCTGGATCTGGCATTGTTATCC 59.444 50.000 0.00 0.00 37.27 2.59
2847 4925 2.117156 GCGCTGGATCTGGCATTGT 61.117 57.895 0.00 0.00 0.00 2.71
2948 5026 2.100631 GTTCATGGTCGAGGCGTGG 61.101 63.158 0.00 0.00 0.00 4.94
2983 5065 3.001902 TAGTTCCGCCTGCACCGAG 62.002 63.158 3.74 0.00 0.00 4.63
3081 5172 0.238289 GTGTGTGGGCGTGAATGAAG 59.762 55.000 0.00 0.00 0.00 3.02
3085 5176 1.153066 TGTGTGTGTGGGCGTGAAT 60.153 52.632 0.00 0.00 0.00 2.57
3099 5190 1.295357 CGGTGTGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
3100 5191 1.295357 ACGGTGTGTGTGTGTGTGTG 61.295 55.000 0.00 0.00 0.00 3.82
3101 5192 1.004320 ACGGTGTGTGTGTGTGTGT 60.004 52.632 0.00 0.00 0.00 3.72
3102 5193 1.423450 CACGGTGTGTGTGTGTGTG 59.577 57.895 0.00 0.00 43.88 3.82
3103 5194 3.883462 CACGGTGTGTGTGTGTGT 58.117 55.556 0.00 0.00 43.88 3.72
3231 5324 4.523813 CGTGTGACATAAGGTGAAAACAC 58.476 43.478 0.00 0.00 36.51 3.32
3233 5326 3.002862 TGCGTGTGACATAAGGTGAAAAC 59.997 43.478 0.00 0.00 0.00 2.43
3276 5369 2.718747 TACAACACCAAGTCGGCCGG 62.719 60.000 27.83 11.50 39.03 6.13
3277 5370 1.289109 CTACAACACCAAGTCGGCCG 61.289 60.000 22.12 22.12 39.03 6.13
3305 5402 4.348168 TGAGAGCTTTTCACTTAGGAAGGT 59.652 41.667 0.00 0.00 33.04 3.50
3312 5409 4.275936 GCTTGGTTGAGAGCTTTTCACTTA 59.724 41.667 1.72 0.00 36.01 2.24
3322 5419 1.803555 GTTGAGAGCTTGGTTGAGAGC 59.196 52.381 0.00 0.00 39.17 4.09
3324 5421 2.037772 GAGGTTGAGAGCTTGGTTGAGA 59.962 50.000 0.00 0.00 32.79 3.27
3325 5422 2.038295 AGAGGTTGAGAGCTTGGTTGAG 59.962 50.000 0.00 0.00 32.79 3.02
3326 5423 2.050144 AGAGGTTGAGAGCTTGGTTGA 58.950 47.619 0.00 0.00 32.79 3.18
3327 5424 2.149578 CAGAGGTTGAGAGCTTGGTTG 58.850 52.381 0.00 0.00 32.79 3.77
3328 5425 2.050144 TCAGAGGTTGAGAGCTTGGTT 58.950 47.619 0.00 0.00 32.79 3.67
3329 5426 1.346068 GTCAGAGGTTGAGAGCTTGGT 59.654 52.381 0.00 0.00 36.21 3.67
3330 5427 1.338579 GGTCAGAGGTTGAGAGCTTGG 60.339 57.143 0.00 0.00 36.21 3.61
3331 5428 1.345741 TGGTCAGAGGTTGAGAGCTTG 59.654 52.381 0.00 0.00 36.21 4.01
3332 5429 1.346068 GTGGTCAGAGGTTGAGAGCTT 59.654 52.381 0.00 0.00 36.21 3.74
3333 5430 0.972883 GTGGTCAGAGGTTGAGAGCT 59.027 55.000 0.00 0.00 36.21 4.09
3373 5470 2.172851 AGAAAACGATGCGGTTGGTA 57.827 45.000 0.00 0.00 36.69 3.25
3381 5478 4.611366 CCGTGAAAGTAAAGAAAACGATGC 59.389 41.667 0.00 0.00 0.00 3.91
3383 5480 5.058490 TCCCGTGAAAGTAAAGAAAACGAT 58.942 37.500 0.00 0.00 0.00 3.73
3405 5502 3.134458 CCGAGGCTTAACATGATTCCTC 58.866 50.000 0.00 6.91 37.37 3.71
3439 5540 2.556287 CTTTTCGGCGTGCACTCC 59.444 61.111 16.14 16.14 0.00 3.85
3531 5633 0.669318 TGCGCACAGTAACAGTAGGC 60.669 55.000 5.66 0.00 0.00 3.93
3546 5651 0.664761 AATAGGTGTCATGCATGCGC 59.335 50.000 22.25 20.76 39.24 6.09
3563 5668 8.589335 ACAGTATATAAAACGAGATCGCAAAT 57.411 30.769 1.39 0.00 44.43 2.32
3573 5678 8.294577 AGATGACGCATACAGTATATAAAACGA 58.705 33.333 0.00 0.00 0.00 3.85
3575 5680 9.406828 TCAGATGACGCATACAGTATATAAAAC 57.593 33.333 0.00 0.00 0.00 2.43
3579 5684 7.824779 AGTCTCAGATGACGCATACAGTATATA 59.175 37.037 0.00 0.00 41.47 0.86
3582 5687 4.824537 AGTCTCAGATGACGCATACAGTAT 59.175 41.667 0.00 0.00 41.47 2.12
3651 5756 2.496070 ACAGGTGTCATACATGCGTACT 59.504 45.455 0.00 0.00 44.60 2.73
3936 6100 1.193323 CTGCAGTCTCATGGAGGAGT 58.807 55.000 5.25 0.00 35.20 3.85
3954 6118 2.651361 CCGACAACGCAGTCCTCT 59.349 61.111 2.66 0.00 45.00 3.69
4035 6199 0.106519 CCGGATCCTTCCATGCCTTT 60.107 55.000 10.75 0.00 42.74 3.11
4206 6370 4.007644 CCGTGGGTGAGCTGAGCA 62.008 66.667 7.39 0.00 0.00 4.26
4404 6568 4.096532 CGGTAGATACCATAGATCGCACAT 59.903 45.833 9.61 0.00 46.80 3.21
4441 6605 0.605589 CACCTCTGACCAGACACCTC 59.394 60.000 0.00 0.00 33.22 3.85
4448 6612 1.372683 CACCACCACCTCTGACCAG 59.627 63.158 0.00 0.00 0.00 4.00
4532 6696 7.652909 TGTTTTGCAGTATCAGAATTCAAAAGG 59.347 33.333 8.44 0.00 34.12 3.11
4824 6989 2.876550 GACAAACGGCTTTGAAGTACCT 59.123 45.455 13.77 0.00 39.43 3.08
4839 7004 3.740832 GTGCCCTTAAAATGCAGACAAAC 59.259 43.478 0.00 0.00 35.33 2.93
4840 7005 3.640967 AGTGCCCTTAAAATGCAGACAAA 59.359 39.130 0.00 0.00 35.33 2.83
4842 7007 2.875296 AGTGCCCTTAAAATGCAGACA 58.125 42.857 0.00 0.00 35.33 3.41
4886 7053 1.521580 ATTTTTGTGCAAATGCCCCG 58.478 45.000 2.46 0.00 41.18 5.73
4887 7054 5.879777 AGTATTATTTTTGTGCAAATGCCCC 59.120 36.000 2.46 0.00 41.18 5.80
4889 7056 8.027440 TGAAGTATTATTTTTGTGCAAATGCC 57.973 30.769 2.46 0.00 41.18 4.40
4975 7147 7.875554 TGATAAACATAGTTGAGTAGTTGTGCA 59.124 33.333 0.00 0.00 0.00 4.57
5153 7325 6.787085 ATGCCTAGATTATCGCACTTAAAC 57.213 37.500 0.00 0.00 33.31 2.01
5183 7355 6.017109 GTGACCAAATCATGTACTCACAAGTT 60.017 38.462 0.00 0.00 40.28 2.66
5189 7361 4.632327 TGGTGACCAAATCATGTACTCA 57.368 40.909 0.00 0.00 40.28 3.41
5345 7525 5.123820 TCATTTCTTAACCAATTCTGCCGAG 59.876 40.000 0.00 0.00 0.00 4.63
5371 7551 2.176140 TGGGCAAATTCCTTACGCG 58.824 52.632 3.53 3.53 0.00 6.01


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

AutoCloner maintained by Alex Coulton.