Multiple sequence alignment - TraesCS5A01G499300

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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 TraesCS5A01G499300 chr5A 100.000 3139 0 0 1 3139 666037985 666041123 0.000000e+00 5797
1 TraesCS5A01G499300 chr5A 83.333 576 72 21 989 1561 665982642 665983196 7.770000e-141 510
2 TraesCS5A01G499300 chr5A 89.770 391 40 0 1744 2134 665978102 665978492 4.670000e-138 501
3 TraesCS5A01G499300 chr5A 88.193 415 47 2 1744 2157 665892411 665892824 7.820000e-136 494
4 TraesCS5A01G499300 chr5A 91.837 343 26 2 1228 1569 665892000 665892341 7.880000e-131 477
5 TraesCS5A01G499300 chr5A 91.317 334 29 0 1228 1561 665970017 665970350 1.030000e-124 457
6 TraesCS5A01G499300 chr5A 93.151 146 10 0 1744 1889 665817134 665817279 6.820000e-52 215
7 TraesCS5A01G499300 chr5A 80.247 162 22 7 2619 2772 665893001 665893160 2.560000e-21 113
8 TraesCS5A01G499300 chr4D 89.516 2747 155 53 2 2693 484886607 484889275 0.000000e+00 3354
9 TraesCS5A01G499300 chr4D 88.454 511 45 7 1641 2139 484840755 484841263 3.460000e-169 604
10 TraesCS5A01G499300 chr4D 86.493 422 52 4 1744 2164 484809276 484809693 2.850000e-125 459
11 TraesCS5A01G499300 chr4D 91.592 333 26 2 1228 1559 484840417 484840748 2.850000e-125 459
12 TraesCS5A01G499300 chr4D 90.671 343 30 2 1228 1569 484808865 484809206 3.690000e-124 455
13 TraesCS5A01G499300 chr4D 87.692 195 24 0 1366 1560 484770825 484771019 8.760000e-56 228
14 TraesCS5A01G499300 chr4D 94.286 140 8 0 1013 1152 484770313 484770452 6.820000e-52 215
15 TraesCS5A01G499300 chr4D 79.290 338 47 18 2443 2771 484805763 484806086 6.820000e-52 215
16 TraesCS5A01G499300 chr4D 93.571 140 9 0 1744 1883 484771252 484771391 3.170000e-50 209
17 TraesCS5A01G499300 chr4D 82.412 199 17 11 2798 2996 484812242 484812422 1.170000e-34 158
18 TraesCS5A01G499300 chr4D 79.817 218 12 13 2824 3041 484889546 484889731 2.540000e-26 130
19 TraesCS5A01G499300 chr4D 81.366 161 21 5 2619 2772 484828584 484828742 4.250000e-24 122
20 TraesCS5A01G499300 chr4B 89.919 2470 116 45 631 3058 618158010 618160388 0.000000e+00 3059
21 TraesCS5A01G499300 chr4B 86.592 537 56 7 1641 2164 618075093 618075626 2.100000e-161 579
22 TraesCS5A01G499300 chr4B 93.114 334 21 2 1228 1560 618074755 618075087 3.640000e-134 488
23 TraesCS5A01G499300 chr4B 85.266 414 43 7 184 589 618131567 618131970 8.100000e-111 411
24 TraesCS5A01G499300 chr4B 77.867 375 54 25 1013 1373 617765316 617765675 4.100000e-49 206
25 TraesCS5A01G499300 chr7D 78.025 314 57 8 339 646 614693345 614693038 1.490000e-43 187


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 TraesCS5A01G499300 chr5A 666037985 666041123 3138 False 5797.000000 5797 100.000000 1 3139 1 chr5A.!!$F5 3138
1 TraesCS5A01G499300 chr5A 665982642 665983196 554 False 510.000000 510 83.333000 989 1561 1 chr5A.!!$F4 572
2 TraesCS5A01G499300 chr5A 665892000 665893160 1160 False 361.333333 494 86.759000 1228 2772 3 chr5A.!!$F6 1544
3 TraesCS5A01G499300 chr4D 484886607 484889731 3124 False 1742.000000 3354 84.666500 2 3041 2 chr4D.!!$F5 3039
4 TraesCS5A01G499300 chr4D 484840417 484841263 846 False 531.500000 604 90.023000 1228 2139 2 chr4D.!!$F4 911
5 TraesCS5A01G499300 chr4D 484805763 484812422 6659 False 321.750000 459 84.716500 1228 2996 4 chr4D.!!$F3 1768
6 TraesCS5A01G499300 chr4D 484770313 484771391 1078 False 217.333333 228 91.849667 1013 1883 3 chr4D.!!$F2 870
7 TraesCS5A01G499300 chr4B 618158010 618160388 2378 False 3059.000000 3059 89.919000 631 3058 1 chr4B.!!$F3 2427
8 TraesCS5A01G499300 chr4B 618074755 618075626 871 False 533.500000 579 89.853000 1228 2164 2 chr4B.!!$F4 936

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
76 78 0.036732 TCTTTGCTCCTTGCCGATGT 59.963 50.0 0.0 0.0 42.00 3.06 F
80 82 0.613260 TGCTCCTTGCCGATGTAACT 59.387 50.0 0.0 0.0 42.00 2.24 F
1570 3690 0.107848 AAGAGGTAATCCAACGCCGG 60.108 55.0 0.0 0.0 35.89 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1115 1140 0.680280 GGTGAGCGAGGAGGTGTAGA 60.680 60.000 0.00 0.0 0.0 2.59 R
1997 4183 1.217244 GACCCACTTGCCGTCGTAT 59.783 57.895 0.00 0.0 0.0 3.06 R
2466 4798 0.098376 GACTCGCGACGTTATCCACT 59.902 55.000 3.71 0.0 0.0 4.00 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
55 57 1.398390 CGCAGAGCTTGGGATTTGTAC 59.602 52.381 7.01 0.00 42.02 2.90
57 59 2.699954 CAGAGCTTGGGATTTGTACGT 58.300 47.619 0.00 0.00 0.00 3.57
75 77 0.449388 GTCTTTGCTCCTTGCCGATG 59.551 55.000 0.00 0.00 42.00 3.84
76 78 0.036732 TCTTTGCTCCTTGCCGATGT 59.963 50.000 0.00 0.00 42.00 3.06
78 80 2.083774 CTTTGCTCCTTGCCGATGTAA 58.916 47.619 0.00 0.00 42.00 2.41
79 81 1.448985 TTGCTCCTTGCCGATGTAAC 58.551 50.000 0.00 0.00 42.00 2.50
80 82 0.613260 TGCTCCTTGCCGATGTAACT 59.387 50.000 0.00 0.00 42.00 2.24
81 83 1.291132 GCTCCTTGCCGATGTAACTC 58.709 55.000 0.00 0.00 35.15 3.01
82 84 1.134670 GCTCCTTGCCGATGTAACTCT 60.135 52.381 0.00 0.00 35.15 3.24
83 85 2.815478 CTCCTTGCCGATGTAACTCTC 58.185 52.381 0.00 0.00 0.00 3.20
95 97 5.463392 CGATGTAACTCTCTCTCTCTCTCTG 59.537 48.000 0.00 0.00 0.00 3.35
97 99 5.487433 TGTAACTCTCTCTCTCTCTCTGTG 58.513 45.833 0.00 0.00 0.00 3.66
101 103 3.673902 TCTCTCTCTCTCTCTGTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
103 105 3.145286 TCTCTCTCTCTCTGTGTGTGTG 58.855 50.000 0.00 0.00 0.00 3.82
122 124 3.696548 TGTGAATGTTGTTTGTGTGCCTA 59.303 39.130 0.00 0.00 0.00 3.93
123 125 4.340666 TGTGAATGTTGTTTGTGTGCCTAT 59.659 37.500 0.00 0.00 0.00 2.57
125 127 5.752955 GTGAATGTTGTTTGTGTGCCTATTT 59.247 36.000 0.00 0.00 0.00 1.40
138 140 2.094675 GCCTATTTGTCATGCAGTGGT 58.905 47.619 0.00 0.00 0.00 4.16
140 142 2.352651 CCTATTTGTCATGCAGTGGTCG 59.647 50.000 0.00 0.00 0.00 4.79
195 198 9.129209 GGATGCTTCAGTTTGAGTTAATAAAAC 57.871 33.333 1.64 0.00 34.68 2.43
314 317 9.107367 CTTCAATGTCTAAAAGTCAAATTCGAC 57.893 33.333 0.00 0.00 36.08 4.20
325 328 6.391227 AGTCAAATTCGACTGTTCCAAAAT 57.609 33.333 0.00 0.00 44.59 1.82
412 416 8.740123 TCCAAACTTGAAATACACACTTAGAA 57.260 30.769 0.00 0.00 0.00 2.10
468 477 4.825085 ACGGGAAGACAAAAGCTAAAATGA 59.175 37.500 0.00 0.00 0.00 2.57
532 545 6.976925 GGCATATTTCAAGTTTGGATCTGAAG 59.023 38.462 0.00 0.00 0.00 3.02
550 563 3.131400 TGAAGTTTTTAGGGGTTGCACAC 59.869 43.478 0.00 0.00 0.00 3.82
552 565 2.429250 AGTTTTTAGGGGTTGCACACAC 59.571 45.455 0.00 0.00 0.00 3.82
553 566 2.145397 TTTTAGGGGTTGCACACACA 57.855 45.000 0.00 0.00 0.00 3.72
561 574 1.480205 GTTGCACACACATGTCTTGC 58.520 50.000 13.56 13.56 36.72 4.01
572 585 3.058708 CACATGTCTTGCGAACATTCACT 60.059 43.478 0.00 0.00 35.19 3.41
625 638 5.712152 AACTGACTTTTTAGGCATTGGAG 57.288 39.130 0.00 0.00 0.00 3.86
626 639 3.507622 ACTGACTTTTTAGGCATTGGAGC 59.492 43.478 0.00 0.00 0.00 4.70
627 640 3.495331 TGACTTTTTAGGCATTGGAGCA 58.505 40.909 0.00 0.00 35.83 4.26
629 642 5.260424 TGACTTTTTAGGCATTGGAGCATA 58.740 37.500 0.00 0.00 35.83 3.14
633 646 3.492102 TTAGGCATTGGAGCATAGGAC 57.508 47.619 0.00 0.00 31.92 3.85
701 717 7.232737 AGGGATTAGGTTCCTTTTAACAAAGTG 59.767 37.037 0.00 0.00 38.22 3.16
703 719 7.014905 GGATTAGGTTCCTTTTAACAAAGTGGT 59.985 37.037 0.00 0.00 38.22 4.16
719 735 2.158355 AGTGGTAGTACTCCCTGTGTGT 60.158 50.000 6.02 0.00 0.00 3.72
721 737 2.158430 TGGTAGTACTCCCTGTGTGTCA 60.158 50.000 6.02 0.00 0.00 3.58
1048 1073 4.144727 TCCCGCTCCTCCTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
1193 1218 4.750098 TCAGTTTTCTTCTTCACACCGATC 59.250 41.667 0.00 0.00 0.00 3.69
1253 3187 6.716173 TGATTCTGATGGTTTGATTGTCTTGA 59.284 34.615 0.00 0.00 0.00 3.02
1265 3241 1.817099 GTCTTGATCTGCAGCCGGG 60.817 63.158 9.47 0.00 0.00 5.73
1569 3689 1.006832 CAAGAGGTAATCCAACGCCG 58.993 55.000 0.00 0.00 35.89 6.46
1570 3690 0.107848 AAGAGGTAATCCAACGCCGG 60.108 55.000 0.00 0.00 35.89 6.13
1571 3691 1.219935 GAGGTAATCCAACGCCGGT 59.780 57.895 1.90 0.00 35.89 5.28
1572 3692 0.808847 GAGGTAATCCAACGCCGGTC 60.809 60.000 1.90 0.00 35.89 4.79
1585 3705 1.918800 CCGGTCCCCCTCTCTGTTT 60.919 63.158 0.00 0.00 0.00 2.83
2096 4282 2.580470 GCAGATCACCGACATCGCG 61.580 63.158 0.00 0.00 38.18 5.87
2145 4331 3.363844 GAGAGGAGGTGACTGGCGC 62.364 68.421 0.00 0.00 44.43 6.53
2161 4347 4.742201 GCCGAGGCAAGCAGACGA 62.742 66.667 9.58 0.00 41.49 4.20
2259 4445 0.967380 CTGGAAATTTCGGCTGGGCT 60.967 55.000 11.95 0.00 0.00 5.19
2338 4528 4.263462 TGCTTATCCAACTCTTGTGGACAT 60.263 41.667 0.00 0.00 34.19 3.06
2369 4559 1.006922 TGCAGCTGACGTGTGAGAG 60.007 57.895 20.43 0.00 0.00 3.20
2402 4608 4.332543 CAGTAGCAACCATGAAGCGATAAA 59.667 41.667 0.00 0.00 0.00 1.40
2403 4609 5.008019 CAGTAGCAACCATGAAGCGATAAAT 59.992 40.000 0.00 0.00 0.00 1.40
2405 4611 3.947196 AGCAACCATGAAGCGATAAATGA 59.053 39.130 0.00 0.00 0.00 2.57
2406 4612 4.036027 AGCAACCATGAAGCGATAAATGAG 59.964 41.667 0.00 0.00 0.00 2.90
2407 4613 4.201950 GCAACCATGAAGCGATAAATGAGT 60.202 41.667 0.00 0.00 0.00 3.41
2408 4614 5.007626 GCAACCATGAAGCGATAAATGAGTA 59.992 40.000 0.00 0.00 0.00 2.59
2441 4773 1.194218 CTGAATCCCCGGCCAAAATT 58.806 50.000 2.24 0.00 0.00 1.82
2452 4784 1.737236 GGCCAAAATTCAAAATCCGGC 59.263 47.619 0.00 0.00 37.57 6.13
2466 4798 0.606096 TCCGGCGACTTTTCTCATCA 59.394 50.000 9.30 0.00 0.00 3.07
2481 4813 0.846401 CATCAGTGGATAACGTCGCG 59.154 55.000 0.00 0.00 30.87 5.87
2552 4884 2.735134 GTTTACTCGCCTGACAAACGAT 59.265 45.455 0.00 0.00 34.94 3.73
2593 4925 1.922570 CTCGATCGTCCCGTTTGAAT 58.077 50.000 15.94 0.00 0.00 2.57
2649 4986 0.796113 GACGGACGAAACTAGTCGCC 60.796 60.000 0.00 1.98 45.00 5.54
2674 5011 3.323691 TCTTCCAGGATTCACTGAACGAA 59.676 43.478 0.00 0.00 40.97 3.85
2680 5017 3.576982 AGGATTCACTGAACGAACTGGTA 59.423 43.478 0.00 0.00 0.00 3.25
2694 5031 5.484998 ACGAACTGGTAAGGAAATTAGGGTA 59.515 40.000 0.00 0.00 0.00 3.69
2695 5032 6.013466 ACGAACTGGTAAGGAAATTAGGGTAA 60.013 38.462 0.00 0.00 0.00 2.85
2775 7240 1.511043 CGGTGCGCCATTAACGTTG 60.511 57.895 18.18 0.00 34.09 4.10
2777 7242 1.579084 GGTGCGCCATTAACGTTGGA 61.579 55.000 12.58 0.00 36.26 3.53
2857 7355 2.758979 TGGCCAGTAGAACTAGTAGTGC 59.241 50.000 0.00 0.97 0.00 4.40
2861 7359 4.142138 GCCAGTAGAACTAGTAGTGCATGT 60.142 45.833 11.05 0.00 0.00 3.21
2862 7360 5.067413 GCCAGTAGAACTAGTAGTGCATGTA 59.933 44.000 11.05 0.00 0.00 2.29
2863 7361 6.239064 GCCAGTAGAACTAGTAGTGCATGTAT 60.239 42.308 11.05 0.00 0.00 2.29
2867 7365 8.557864 AGTAGAACTAGTAGTGCATGTATTACG 58.442 37.037 11.05 1.53 0.00 3.18
2880 7378 5.064707 GCATGTATTACGGGCCAATATGTAG 59.935 44.000 4.39 0.00 0.00 2.74
2881 7379 5.811796 TGTATTACGGGCCAATATGTAGT 57.188 39.130 4.39 0.00 0.00 2.73
2882 7380 6.914654 TGTATTACGGGCCAATATGTAGTA 57.085 37.500 4.39 0.00 0.00 1.82
2883 7381 6.927416 TGTATTACGGGCCAATATGTAGTAG 58.073 40.000 4.39 0.00 0.00 2.57
2884 7382 4.877378 TTACGGGCCAATATGTAGTAGG 57.123 45.455 4.39 0.00 0.00 3.18
2885 7383 2.966915 ACGGGCCAATATGTAGTAGGA 58.033 47.619 4.39 0.00 0.00 2.94
2990 7488 2.812178 GCCGTCGCACCGTGTAAT 60.812 61.111 0.00 0.00 34.03 1.89
3016 7514 2.226200 CCATGCAATCTGTCGAACACAA 59.774 45.455 0.00 0.00 33.31 3.33
3018 7516 2.284190 TGCAATCTGTCGAACACAACA 58.716 42.857 0.00 0.00 33.31 3.33
3020 7518 2.287915 GCAATCTGTCGAACACAACACT 59.712 45.455 0.00 0.00 33.31 3.55
3044 7542 2.095059 GCTCAAAATTCAGGCACACGAT 60.095 45.455 0.00 0.00 0.00 3.73
3058 7556 1.083015 ACGATCAAAACGTGCGTGC 60.083 52.632 0.00 0.00 42.37 5.34
3059 7557 2.131407 CGATCAAAACGTGCGTGCG 61.131 57.895 0.00 0.00 37.94 5.34
3061 7559 1.320382 GATCAAAACGTGCGTGCGTG 61.320 55.000 7.12 0.00 45.00 5.34
3062 7560 2.042520 ATCAAAACGTGCGTGCGTGT 62.043 50.000 7.12 0.00 45.00 4.49
3063 7561 2.022207 AAAACGTGCGTGCGTGTC 59.978 55.556 7.12 0.00 45.00 3.67
3064 7562 3.443261 AAAACGTGCGTGCGTGTCC 62.443 57.895 7.12 0.00 45.00 4.02
3065 7563 4.884257 AACGTGCGTGCGTGTCCT 62.884 61.111 7.12 0.00 45.00 3.85
3066 7564 4.884257 ACGTGCGTGCGTGTCCTT 62.884 61.111 5.68 0.00 43.99 3.36
3067 7565 2.731721 CGTGCGTGCGTGTCCTTA 60.732 61.111 0.00 0.00 0.00 2.69
3068 7566 2.092291 CGTGCGTGCGTGTCCTTAT 61.092 57.895 0.00 0.00 0.00 1.73
3069 7567 0.799152 CGTGCGTGCGTGTCCTTATA 60.799 55.000 0.00 0.00 0.00 0.98
3070 7568 0.643820 GTGCGTGCGTGTCCTTATAC 59.356 55.000 0.00 0.00 0.00 1.47
3071 7569 0.528924 TGCGTGCGTGTCCTTATACT 59.471 50.000 0.00 0.00 0.00 2.12
3072 7570 1.197910 GCGTGCGTGTCCTTATACTC 58.802 55.000 0.00 0.00 0.00 2.59
3073 7571 1.836383 CGTGCGTGTCCTTATACTCC 58.164 55.000 0.00 0.00 0.00 3.85
3074 7572 1.404391 CGTGCGTGTCCTTATACTCCT 59.596 52.381 0.00 0.00 0.00 3.69
3075 7573 2.159282 CGTGCGTGTCCTTATACTCCTT 60.159 50.000 0.00 0.00 0.00 3.36
3076 7574 3.187700 GTGCGTGTCCTTATACTCCTTG 58.812 50.000 0.00 0.00 0.00 3.61
3077 7575 2.829720 TGCGTGTCCTTATACTCCTTGT 59.170 45.455 0.00 0.00 0.00 3.16
3078 7576 4.018490 TGCGTGTCCTTATACTCCTTGTA 58.982 43.478 0.00 0.00 35.37 2.41
3079 7577 4.647853 TGCGTGTCCTTATACTCCTTGTAT 59.352 41.667 0.00 0.00 43.62 2.29
3080 7578 4.982916 GCGTGTCCTTATACTCCTTGTATG 59.017 45.833 0.00 0.00 41.55 2.39
3081 7579 5.451520 GCGTGTCCTTATACTCCTTGTATGT 60.452 44.000 0.00 0.00 41.55 2.29
3082 7580 6.207213 CGTGTCCTTATACTCCTTGTATGTC 58.793 44.000 0.00 0.00 41.55 3.06
3083 7581 6.183360 CGTGTCCTTATACTCCTTGTATGTCA 60.183 42.308 0.00 0.00 41.55 3.58
3084 7582 7.203910 GTGTCCTTATACTCCTTGTATGTCAG 58.796 42.308 0.00 0.00 41.55 3.51
3085 7583 6.183360 TGTCCTTATACTCCTTGTATGTCAGC 60.183 42.308 0.00 0.00 41.55 4.26
3086 7584 5.897250 TCCTTATACTCCTTGTATGTCAGCA 59.103 40.000 0.00 0.00 41.55 4.41
3087 7585 5.986135 CCTTATACTCCTTGTATGTCAGCAC 59.014 44.000 0.00 0.00 41.55 4.40
3088 7586 2.770164 ACTCCTTGTATGTCAGCACC 57.230 50.000 0.00 0.00 0.00 5.01
3089 7587 1.279271 ACTCCTTGTATGTCAGCACCC 59.721 52.381 0.00 0.00 0.00 4.61
3090 7588 0.249120 TCCTTGTATGTCAGCACCCG 59.751 55.000 0.00 0.00 0.00 5.28
3091 7589 1.369091 CCTTGTATGTCAGCACCCGC 61.369 60.000 0.00 0.00 38.99 6.13
3092 7590 0.673333 CTTGTATGTCAGCACCCGCA 60.673 55.000 0.00 0.00 42.27 5.69
3093 7591 0.673333 TTGTATGTCAGCACCCGCAG 60.673 55.000 0.00 0.00 42.27 5.18
3105 7603 3.736483 CCGCAGGCTAAATCGCAT 58.264 55.556 0.00 0.00 46.14 4.73
3106 7604 1.280746 CCGCAGGCTAAATCGCATG 59.719 57.895 0.00 0.00 46.14 4.06
3107 7605 1.159713 CCGCAGGCTAAATCGCATGA 61.160 55.000 0.00 0.00 46.14 3.07
3108 7606 0.657312 CGCAGGCTAAATCGCATGAA 59.343 50.000 0.00 0.00 43.79 2.57
3109 7607 1.265095 CGCAGGCTAAATCGCATGAAT 59.735 47.619 0.00 0.00 43.79 2.57
3110 7608 2.658285 GCAGGCTAAATCGCATGAATG 58.342 47.619 0.00 0.00 43.79 2.67
3130 7628 2.496899 CTGGAATAGCTGGTGTGGTT 57.503 50.000 0.00 0.00 0.00 3.67
3131 7629 3.627395 CTGGAATAGCTGGTGTGGTTA 57.373 47.619 0.00 0.00 0.00 2.85
3132 7630 3.950397 CTGGAATAGCTGGTGTGGTTAA 58.050 45.455 0.00 0.00 0.00 2.01
3133 7631 4.526970 CTGGAATAGCTGGTGTGGTTAAT 58.473 43.478 0.00 0.00 0.00 1.40
3134 7632 4.929479 TGGAATAGCTGGTGTGGTTAATT 58.071 39.130 0.00 0.00 0.00 1.40
3135 7633 6.068461 TGGAATAGCTGGTGTGGTTAATTA 57.932 37.500 0.00 0.00 0.00 1.40
3136 7634 6.119536 TGGAATAGCTGGTGTGGTTAATTAG 58.880 40.000 0.00 0.00 0.00 1.73
3137 7635 5.008712 GGAATAGCTGGTGTGGTTAATTAGC 59.991 44.000 0.00 0.00 0.00 3.09
3138 7636 2.723273 AGCTGGTGTGGTTAATTAGCC 58.277 47.619 11.22 11.22 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.785512 AGCTCTGCGAACGCGAGG 62.786 66.667 26.88 16.31 45.51 4.63
28 29 3.105782 CAAGCTCTGCGAACGCGA 61.106 61.111 15.93 12.55 45.51 5.87
29 30 4.139420 CCAAGCTCTGCGAACGCG 62.139 66.667 3.53 3.53 45.51 6.01
30 31 3.793144 CCCAAGCTCTGCGAACGC 61.793 66.667 12.33 12.33 42.35 4.84
31 32 1.021390 AATCCCAAGCTCTGCGAACG 61.021 55.000 0.00 0.00 0.00 3.95
32 33 1.135575 CAAATCCCAAGCTCTGCGAAC 60.136 52.381 0.00 0.00 0.00 3.95
33 34 1.167851 CAAATCCCAAGCTCTGCGAA 58.832 50.000 0.00 0.00 0.00 4.70
36 37 1.398390 CGTACAAATCCCAAGCTCTGC 59.602 52.381 0.00 0.00 0.00 4.26
37 38 2.673368 GACGTACAAATCCCAAGCTCTG 59.327 50.000 0.00 0.00 0.00 3.35
75 77 5.351465 CACACAGAGAGAGAGAGAGAGTTAC 59.649 48.000 0.00 0.00 0.00 2.50
76 78 5.012664 ACACACAGAGAGAGAGAGAGAGTTA 59.987 44.000 0.00 0.00 0.00 2.24
78 80 3.327757 ACACACAGAGAGAGAGAGAGAGT 59.672 47.826 0.00 0.00 0.00 3.24
79 81 3.686241 CACACACAGAGAGAGAGAGAGAG 59.314 52.174 0.00 0.00 0.00 3.20
80 82 3.072330 ACACACACAGAGAGAGAGAGAGA 59.928 47.826 0.00 0.00 0.00 3.10
81 83 3.189080 CACACACACAGAGAGAGAGAGAG 59.811 52.174 0.00 0.00 0.00 3.20
82 84 3.145286 CACACACACAGAGAGAGAGAGA 58.855 50.000 0.00 0.00 0.00 3.10
83 85 3.145286 TCACACACACAGAGAGAGAGAG 58.855 50.000 0.00 0.00 0.00 3.20
95 97 4.089780 CACACAAACAACATTCACACACAC 59.910 41.667 0.00 0.00 0.00 3.82
97 99 3.060628 GCACACAAACAACATTCACACAC 59.939 43.478 0.00 0.00 0.00 3.82
101 103 3.163630 AGGCACACAAACAACATTCAC 57.836 42.857 0.00 0.00 0.00 3.18
103 105 5.752955 ACAAATAGGCACACAAACAACATTC 59.247 36.000 0.00 0.00 0.00 2.67
122 124 1.167851 CCGACCACTGCATGACAAAT 58.832 50.000 0.00 0.00 0.00 2.32
123 125 0.888736 CCCGACCACTGCATGACAAA 60.889 55.000 0.00 0.00 0.00 2.83
125 127 2.347114 CCCGACCACTGCATGACA 59.653 61.111 0.00 0.00 0.00 3.58
138 140 1.202710 ACACAATAAGCACACACCCGA 60.203 47.619 0.00 0.00 0.00 5.14
140 142 3.067461 TGAAACACAATAAGCACACACCC 59.933 43.478 0.00 0.00 0.00 4.61
195 198 8.557029 GGACTTGATTCATTTATAAAGGGTACG 58.443 37.037 9.79 0.00 0.00 3.67
211 214 4.082125 ACCAGGAATGTTGGACTTGATTC 58.918 43.478 0.00 0.00 39.08 2.52
314 317 8.661352 AATGTTTTCAGGTTATTTTGGAACAG 57.339 30.769 0.00 0.00 42.39 3.16
425 429 5.872617 CCCGTGACACTATTTCTGTTGAATA 59.127 40.000 3.68 0.00 31.56 1.75
432 436 3.927142 GTCTTCCCGTGACACTATTTCTG 59.073 47.826 3.68 0.00 34.80 3.02
434 438 3.921677 TGTCTTCCCGTGACACTATTTC 58.078 45.455 3.68 0.00 39.23 2.17
468 477 7.220030 AGGAGAAATCATTATGTGAATAGCGT 58.780 34.615 0.00 0.00 40.97 5.07
532 545 2.166664 TGTGTGTGCAACCCCTAAAAAC 59.833 45.455 0.00 0.00 34.36 2.43
536 549 1.133637 ACATGTGTGTGCAACCCCTAA 60.134 47.619 0.00 0.00 37.14 2.69
599 612 8.189119 TCCAATGCCTAAAAAGTCAGTTTTAT 57.811 30.769 0.00 0.00 37.37 1.40
605 618 3.507233 TGCTCCAATGCCTAAAAAGTCAG 59.493 43.478 0.00 0.00 0.00 3.51
607 620 4.725790 ATGCTCCAATGCCTAAAAAGTC 57.274 40.909 0.00 0.00 0.00 3.01
622 635 5.763876 ATATTAAGGTGGTCCTATGCTCC 57.236 43.478 0.00 0.00 44.35 4.70
625 638 7.255836 GGGAAAAATATTAAGGTGGTCCTATGC 60.256 40.741 0.00 0.00 44.35 3.14
626 639 8.004801 AGGGAAAAATATTAAGGTGGTCCTATG 58.995 37.037 0.00 0.00 44.35 2.23
627 640 8.004801 CAGGGAAAAATATTAAGGTGGTCCTAT 58.995 37.037 0.00 0.00 44.35 2.57
633 646 6.889722 TGAGACAGGGAAAAATATTAAGGTGG 59.110 38.462 0.00 0.00 0.00 4.61
701 717 2.522185 TGACACACAGGGAGTACTACC 58.478 52.381 17.30 17.30 0.00 3.18
703 719 5.617528 TTTTTGACACACAGGGAGTACTA 57.382 39.130 0.00 0.00 0.00 1.82
736 752 7.907563 GTCGTTAGTAGTACAGCCTAACTTAAG 59.092 40.741 18.83 0.00 38.78 1.85
738 754 6.316390 GGTCGTTAGTAGTACAGCCTAACTTA 59.684 42.308 18.83 10.04 38.78 2.24
744 760 2.373224 GGGTCGTTAGTAGTACAGCCT 58.627 52.381 2.52 0.00 0.00 4.58
1048 1073 3.847602 CGGGAGGGAGCAGAGCAG 61.848 72.222 0.00 0.00 0.00 4.24
1115 1140 0.680280 GGTGAGCGAGGAGGTGTAGA 60.680 60.000 0.00 0.00 0.00 2.59
1193 1218 6.898442 GCAGTTGCATGAATCGATCGATCG 62.898 50.000 35.91 35.91 45.27 3.69
1209 1234 8.867935 CAGAATCATAGTACTATATGCAGTTGC 58.132 37.037 15.03 0.00 42.50 4.17
1238 3165 4.730657 CTGCAGATCAAGACAATCAAACC 58.269 43.478 8.42 0.00 0.00 3.27
1253 3187 3.790437 CAGGACCCGGCTGCAGAT 61.790 66.667 20.43 0.00 0.00 2.90
1585 3705 4.862018 CGCTGTTGGTGAAAAGAAAGAAAA 59.138 37.500 0.00 0.00 0.00 2.29
1937 4123 4.479993 GCCAGGCTCGTGCTCCAT 62.480 66.667 3.29 0.00 39.59 3.41
1997 4183 1.217244 GACCCACTTGCCGTCGTAT 59.783 57.895 0.00 0.00 0.00 3.06
2006 4192 3.636231 TCGGCCCAGACCCACTTG 61.636 66.667 0.00 0.00 0.00 3.16
2145 4331 2.811317 GTCGTCTGCTTGCCTCGG 60.811 66.667 0.00 0.00 0.00 4.63
2156 4342 0.605589 CTCCTCTTGGCTTGTCGTCT 59.394 55.000 0.00 0.00 0.00 4.18
2158 4344 0.832135 TCCTCCTCTTGGCTTGTCGT 60.832 55.000 0.00 0.00 0.00 4.34
2159 4345 0.108424 CTCCTCCTCTTGGCTTGTCG 60.108 60.000 0.00 0.00 0.00 4.35
2160 4346 0.392327 GCTCCTCCTCTTGGCTTGTC 60.392 60.000 0.00 0.00 0.00 3.18
2161 4347 0.839853 AGCTCCTCCTCTTGGCTTGT 60.840 55.000 0.00 0.00 0.00 3.16
2259 4445 8.337118 ACTAATCTCTATCCTTCCAATTCCAA 57.663 34.615 0.00 0.00 0.00 3.53
2302 4492 2.288518 GGATAAGCAACGAGGGCTCTAG 60.289 54.545 0.00 0.00 41.66 2.43
2369 4559 6.802608 TCATGGTTGCTACTGTACATACTAC 58.197 40.000 0.00 0.00 0.00 2.73
2402 4608 2.786495 CCACGGCCTCGCTACTCAT 61.786 63.158 0.00 0.00 40.63 2.90
2403 4609 3.449227 CCACGGCCTCGCTACTCA 61.449 66.667 0.00 0.00 40.63 3.41
2434 4649 2.666022 GTCGCCGGATTTTGAATTTTGG 59.334 45.455 5.05 0.00 0.00 3.28
2441 4773 2.482721 GAGAAAAGTCGCCGGATTTTGA 59.517 45.455 5.05 0.00 33.05 2.69
2452 4784 5.004821 CGTTATCCACTGATGAGAAAAGTCG 59.995 44.000 0.00 0.00 32.18 4.18
2466 4798 0.098376 GACTCGCGACGTTATCCACT 59.902 55.000 3.71 0.00 0.00 4.00
2531 4863 2.129607 TCGTTTGTCAGGCGAGTAAAC 58.870 47.619 0.00 0.00 0.00 2.01
2552 4884 0.108898 CGGCGCCCATGAATGAAAAA 60.109 50.000 23.46 0.00 0.00 1.94
2593 4925 4.904590 CCGCCACCAACCAACCCA 62.905 66.667 0.00 0.00 0.00 4.51
2649 4986 1.550524 TCAGTGAATCCTGGAAGACCG 59.449 52.381 0.00 0.00 39.42 4.79
2694 5031 9.467258 CGAATTGTGCTTTCCAATCATTATATT 57.533 29.630 0.00 0.00 31.49 1.28
2695 5032 8.084073 CCGAATTGTGCTTTCCAATCATTATAT 58.916 33.333 0.00 0.00 31.49 0.86
2698 5035 5.417266 TCCGAATTGTGCTTTCCAATCATTA 59.583 36.000 0.00 0.00 31.49 1.90
2699 5036 4.220382 TCCGAATTGTGCTTTCCAATCATT 59.780 37.500 0.00 0.00 31.49 2.57
2700 5037 3.763360 TCCGAATTGTGCTTTCCAATCAT 59.237 39.130 0.00 0.00 31.49 2.45
2701 5038 3.057596 GTCCGAATTGTGCTTTCCAATCA 60.058 43.478 0.00 0.00 31.49 2.57
2702 5039 3.057596 TGTCCGAATTGTGCTTTCCAATC 60.058 43.478 0.00 0.00 31.49 2.67
2705 5042 1.974265 TGTCCGAATTGTGCTTTCCA 58.026 45.000 0.00 0.00 0.00 3.53
2706 5043 2.228822 ACATGTCCGAATTGTGCTTTCC 59.771 45.455 0.00 0.00 0.00 3.13
2707 5044 3.559238 ACATGTCCGAATTGTGCTTTC 57.441 42.857 0.00 0.00 0.00 2.62
2794 7259 1.394917 GAGTAGATGGTTGCAGTTGCG 59.605 52.381 0.00 0.00 45.83 4.85
2857 7355 6.170506 ACTACATATTGGCCCGTAATACATG 58.829 40.000 0.00 0.00 0.00 3.21
2861 7359 6.255287 TCCTACTACATATTGGCCCGTAATA 58.745 40.000 0.00 0.00 0.00 0.98
2862 7360 5.088730 TCCTACTACATATTGGCCCGTAAT 58.911 41.667 0.00 0.00 0.00 1.89
2863 7361 4.482030 TCCTACTACATATTGGCCCGTAA 58.518 43.478 0.00 0.00 0.00 3.18
2867 7365 5.484290 ACATACTCCTACTACATATTGGCCC 59.516 44.000 0.00 0.00 0.00 5.80
2880 7378 1.473434 GCCAGCACCACATACTCCTAC 60.473 57.143 0.00 0.00 0.00 3.18
2881 7379 0.830648 GCCAGCACCACATACTCCTA 59.169 55.000 0.00 0.00 0.00 2.94
2882 7380 1.604378 GCCAGCACCACATACTCCT 59.396 57.895 0.00 0.00 0.00 3.69
2883 7381 1.452108 GGCCAGCACCACATACTCC 60.452 63.158 0.00 0.00 0.00 3.85
2884 7382 1.815421 CGGCCAGCACCACATACTC 60.815 63.158 2.24 0.00 0.00 2.59
2885 7383 2.268920 CGGCCAGCACCACATACT 59.731 61.111 2.24 0.00 0.00 2.12
2990 7488 4.940654 TGTTCGACAGATTGCATGGATAAA 59.059 37.500 0.00 0.00 0.00 1.40
3016 7514 2.035066 GCCTGAATTTTGAGCACAGTGT 59.965 45.455 1.61 0.00 0.00 3.55
3018 7516 2.309613 TGCCTGAATTTTGAGCACAGT 58.690 42.857 0.00 0.00 0.00 3.55
3044 7542 2.022069 CACGCACGCACGTTTTGA 59.978 55.556 0.00 0.00 45.75 2.69
3058 7556 6.145338 ACATACAAGGAGTATAAGGACACG 57.855 41.667 0.00 0.00 41.47 4.49
3059 7557 7.108841 TGACATACAAGGAGTATAAGGACAC 57.891 40.000 0.00 0.00 41.47 3.67
3060 7558 6.183360 GCTGACATACAAGGAGTATAAGGACA 60.183 42.308 0.00 0.00 41.47 4.02
3061 7559 6.183360 TGCTGACATACAAGGAGTATAAGGAC 60.183 42.308 0.00 0.00 41.47 3.85
3062 7560 5.897250 TGCTGACATACAAGGAGTATAAGGA 59.103 40.000 0.00 0.00 41.47 3.36
3063 7561 5.986135 GTGCTGACATACAAGGAGTATAAGG 59.014 44.000 0.00 0.00 41.47 2.69
3064 7562 5.986135 GGTGCTGACATACAAGGAGTATAAG 59.014 44.000 0.00 0.00 41.47 1.73
3065 7563 5.163343 GGGTGCTGACATACAAGGAGTATAA 60.163 44.000 0.00 0.00 41.47 0.98
3066 7564 4.344102 GGGTGCTGACATACAAGGAGTATA 59.656 45.833 0.00 0.00 41.47 1.47
3067 7565 3.134804 GGGTGCTGACATACAAGGAGTAT 59.865 47.826 0.00 0.00 44.20 2.12
3068 7566 2.500098 GGGTGCTGACATACAAGGAGTA 59.500 50.000 0.00 0.00 37.06 2.59
3069 7567 1.279271 GGGTGCTGACATACAAGGAGT 59.721 52.381 0.00 0.00 0.00 3.85
3070 7568 1.740380 CGGGTGCTGACATACAAGGAG 60.740 57.143 0.00 0.00 0.00 3.69
3071 7569 0.249120 CGGGTGCTGACATACAAGGA 59.751 55.000 0.00 0.00 0.00 3.36
3072 7570 1.369091 GCGGGTGCTGACATACAAGG 61.369 60.000 0.00 0.00 38.39 3.61
3073 7571 0.673333 TGCGGGTGCTGACATACAAG 60.673 55.000 0.00 0.00 43.34 3.16
3074 7572 0.673333 CTGCGGGTGCTGACATACAA 60.673 55.000 0.00 0.00 42.14 2.41
3075 7573 1.079197 CTGCGGGTGCTGACATACA 60.079 57.895 0.00 0.00 42.14 2.29
3076 7574 1.815421 CCTGCGGGTGCTGACATAC 60.815 63.158 2.29 0.00 42.14 2.39
3077 7575 2.584064 CCTGCGGGTGCTGACATA 59.416 61.111 2.29 0.00 42.14 2.29
3080 7578 3.605749 TTAGCCTGCGGGTGCTGAC 62.606 63.158 14.55 0.00 42.14 3.51
3081 7579 2.196997 ATTTAGCCTGCGGGTGCTGA 62.197 55.000 14.55 0.00 42.14 4.26
3082 7580 1.718757 GATTTAGCCTGCGGGTGCTG 61.719 60.000 14.55 0.00 43.34 4.41
3083 7581 1.452108 GATTTAGCCTGCGGGTGCT 60.452 57.895 14.55 7.52 43.34 4.40
3084 7582 2.823829 CGATTTAGCCTGCGGGTGC 61.824 63.158 14.55 0.00 43.20 5.01
3085 7583 2.823829 GCGATTTAGCCTGCGGGTG 61.824 63.158 14.55 0.00 34.28 4.61
3086 7584 2.513897 GCGATTTAGCCTGCGGGT 60.514 61.111 14.55 8.99 37.19 5.28
3087 7585 1.893808 ATGCGATTTAGCCTGCGGG 60.894 57.895 7.41 7.41 36.02 6.13
3088 7586 1.159713 TCATGCGATTTAGCCTGCGG 61.160 55.000 0.00 0.00 33.67 5.69
3089 7587 0.657312 TTCATGCGATTTAGCCTGCG 59.343 50.000 0.00 0.00 33.67 5.18
3090 7588 2.658285 CATTCATGCGATTTAGCCTGC 58.342 47.619 0.00 0.00 33.67 4.85
3091 7589 2.658285 GCATTCATGCGATTTAGCCTG 58.342 47.619 0.00 0.00 44.67 4.85
3111 7609 2.496899 AACCACACCAGCTATTCCAG 57.503 50.000 0.00 0.00 0.00 3.86
3112 7610 4.584638 ATTAACCACACCAGCTATTCCA 57.415 40.909 0.00 0.00 0.00 3.53
3113 7611 5.008712 GCTAATTAACCACACCAGCTATTCC 59.991 44.000 0.00 0.00 0.00 3.01
3114 7612 5.008712 GGCTAATTAACCACACCAGCTATTC 59.991 44.000 0.00 0.00 0.00 1.75
3115 7613 4.887655 GGCTAATTAACCACACCAGCTATT 59.112 41.667 0.00 0.00 0.00 1.73
3116 7614 4.461198 GGCTAATTAACCACACCAGCTAT 58.539 43.478 0.00 0.00 0.00 2.97
3117 7615 3.881220 GGCTAATTAACCACACCAGCTA 58.119 45.455 0.00 0.00 0.00 3.32
3118 7616 2.723273 GGCTAATTAACCACACCAGCT 58.277 47.619 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.