Multiple sequence alignment - TraesCS4B01G239900

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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 TraesCS4B01G239900 chr4B 100.000 5076 0 0 1 5076 497550385 497555460 0.000000e+00 9374.0
1 TraesCS4B01G239900 chr4A 93.231 2792 103 39 308 3054 59480717 59483467 0.000000e+00 4030.0
2 TraesCS4B01G239900 chr4A 93.779 1061 45 12 3335 4383 59483790 59484841 0.000000e+00 1574.0
3 TraesCS4B01G239900 chr4A 93.842 341 13 2 4744 5076 59484836 59485176 1.630000e-139 507.0
4 TraesCS4B01G239900 chr4A 97.203 143 3 1 3108 3250 59483568 59483709 1.830000e-59 241.0
5 TraesCS4B01G239900 chr4A 91.525 59 5 0 3066 3124 607427344 607427402 1.170000e-11 82.4
6 TraesCS4B01G239900 chr4D 98.557 1663 24 0 1392 3054 402208385 402210047 0.000000e+00 2939.0
7 TraesCS4B01G239900 chr4D 90.169 1424 77 26 1 1399 402205846 402207231 0.000000e+00 1796.0
8 TraesCS4B01G239900 chr4D 95.434 1117 33 8 3250 4353 402210288 402211399 0.000000e+00 1764.0
9 TraesCS4B01G239900 chr4D 88.472 772 28 18 4346 5076 402211558 402212309 0.000000e+00 876.0
10 TraesCS4B01G239900 chr6D 76.761 809 156 24 1399 2191 436225221 436224429 1.690000e-114 424.0
11 TraesCS4B01G239900 chr6D 78.571 196 37 4 3798 3989 436222301 436222107 1.920000e-24 124.0
12 TraesCS4B01G239900 chr6B 76.797 793 160 19 1411 2191 659236414 659235634 1.690000e-114 424.0
13 TraesCS4B01G239900 chr6B 79.024 205 37 5 3793 3993 659233499 659233297 8.860000e-28 135.0
14 TraesCS4B01G239900 chr5A 78.667 225 40 5 3729 3949 413043886 413044106 5.300000e-30 143.0
15 TraesCS4B01G239900 chr6A 79.000 200 37 4 3794 3989 583269448 583269250 1.150000e-26 132.0
16 TraesCS4B01G239900 chr6A 91.228 57 4 1 3177 3233 223554249 223554304 5.450000e-10 76.8
17 TraesCS4B01G239900 chr2D 95.161 62 2 1 3173 3233 529037601 529037540 4.180000e-16 97.1
18 TraesCS4B01G239900 chr2B 93.548 62 3 1 3173 3233 628399750 628399689 1.950000e-14 91.6
19 TraesCS4B01G239900 chr2B 92.982 57 4 0 3066 3122 161932932 161932988 3.260000e-12 84.2
20 TraesCS4B01G239900 chr3B 94.545 55 3 0 3060 3114 164568440 164568386 9.050000e-13 86.1
21 TraesCS4B01G239900 chr3B 96.154 52 1 1 3066 3116 819775602 819775551 3.260000e-12 84.2
22 TraesCS4B01G239900 chr1B 94.643 56 1 1 3067 3122 27074566 27074513 9.050000e-13 86.1
23 TraesCS4B01G239900 chr1B 89.855 69 3 4 3059 3127 641036471 641036535 9.050000e-13 86.1
24 TraesCS4B01G239900 chr1B 94.340 53 2 1 3066 3118 268547760 268547709 4.210000e-11 80.5
25 TraesCS4B01G239900 chr5B 94.545 55 1 2 3059 3113 291498471 291498523 3.260000e-12 84.2
26 TraesCS4B01G239900 chrUn 89.394 66 5 1 3060 3125 324448656 324448719 1.170000e-11 82.4
27 TraesCS4B01G239900 chr7D 94.000 50 2 1 3174 3223 445118555 445118603 1.960000e-09 75.0
28 TraesCS4B01G239900 chr7B 92.157 51 2 2 3174 3224 461473687 461473735 2.540000e-08 71.3
29 TraesCS4B01G239900 chr5D 87.097 62 6 2 3174 3233 453818765 453818826 9.120000e-08 69.4
30 TraesCS4B01G239900 chr7A 90.385 52 3 2 3174 3225 567378791 567378742 3.280000e-07 67.6


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 TraesCS4B01G239900 chr4B 497550385 497555460 5075 False 9374.00 9374 100.00000 1 5076 1 chr4B.!!$F1 5075
1 TraesCS4B01G239900 chr4A 59480717 59485176 4459 False 1588.00 4030 94.51375 308 5076 4 chr4A.!!$F2 4768
2 TraesCS4B01G239900 chr4D 402205846 402212309 6463 False 1843.75 2939 93.15800 1 5076 4 chr4D.!!$F1 5075
3 TraesCS4B01G239900 chr6D 436222107 436225221 3114 True 274.00 424 77.66600 1399 3989 2 chr6D.!!$R1 2590
4 TraesCS4B01G239900 chr6B 659233297 659236414 3117 True 279.50 424 77.91050 1411 3993 2 chr6B.!!$R1 2582

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
417 433 0.103208 CCACCAGATCGTGTAGAGCC 59.897 60.000 0.89 0.0 35.47 4.70 F
418 434 0.248661 CACCAGATCGTGTAGAGCCG 60.249 60.000 0.00 0.0 35.47 5.52 F
759 802 0.395173 AAGACACACACCCACCCAAC 60.395 55.000 0.00 0.0 0.00 3.77 F
909 979 1.211969 CGTTCTTCCTTCTCGCCGA 59.788 57.895 0.00 0.0 0.00 5.54 F
1491 2722 1.409064 CCGCTCTTCCACTACATGCTA 59.591 52.381 0.00 0.0 0.00 3.49 F
2853 4090 2.037136 CAAGAGCCCCACTGCGAAG 61.037 63.158 0.00 0.0 36.02 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 3439 0.608640 ACGCCTCGTTGATCCTCTTT 59.391 50.000 0.00 0.0 36.35 2.52 R
2520 3757 2.825387 GCGCACTCCATGGCATCA 60.825 61.111 6.96 0.0 0.00 3.07 R
2706 3943 2.273908 GTCAAGCGAGACCACCCTA 58.726 57.895 0.68 0.0 32.36 3.53 R
2853 4090 2.735762 GCTGTTGAGTATCTGGACCGAC 60.736 54.545 0.00 0.0 34.92 4.79 R
3366 4989 1.003233 GCGTCCCTCTTCAGCCTTT 60.003 57.895 0.00 0.0 0.00 3.11 R
4919 7286 0.108945 GCTCAGCATGGCCTTTTGAC 60.109 55.000 3.32 0.0 36.16 3.18 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
32 33 2.607750 ACACAGAGGGCCACCGAT 60.608 61.111 6.18 0.00 43.47 4.18
127 128 4.514585 AGCACCACCGGCCAAACA 62.515 61.111 0.00 0.00 0.00 2.83
132 133 2.427245 CCACCGGCCAAACACCAAA 61.427 57.895 0.00 0.00 0.00 3.28
154 155 4.590487 GGAAATCTCCGTGCACGA 57.410 55.556 39.10 23.33 43.02 4.35
155 156 2.079049 GGAAATCTCCGTGCACGAC 58.921 57.895 39.10 19.05 43.02 4.34
156 157 1.359459 GGAAATCTCCGTGCACGACC 61.359 60.000 39.10 23.16 43.02 4.79
183 184 1.381327 TCCTGTCCCATCCCTCGTC 60.381 63.158 0.00 0.00 0.00 4.20
203 204 4.620184 CGTCTTTCTTGTAGTAAACCCTCG 59.380 45.833 0.00 0.00 0.00 4.63
204 205 4.928020 GTCTTTCTTGTAGTAAACCCTCGG 59.072 45.833 0.00 0.00 0.00 4.63
213 214 0.248289 TAAACCCTCGGCTTTCCTCG 59.752 55.000 0.00 0.00 0.00 4.63
215 216 3.775654 CCCTCGGCTTTCCTCGCT 61.776 66.667 0.00 0.00 0.00 4.93
217 218 2.580867 CTCGGCTTTCCTCGCTCG 60.581 66.667 0.00 0.00 0.00 5.03
225 226 2.234913 TTTCCTCGCTCGCCTTACCC 62.235 60.000 0.00 0.00 0.00 3.69
267 283 2.816777 AAGGCAAGGGAGGAAGAATC 57.183 50.000 0.00 0.00 0.00 2.52
268 284 0.543749 AGGCAAGGGAGGAAGAATCG 59.456 55.000 0.00 0.00 0.00 3.34
273 289 1.501582 AGGGAGGAAGAATCGGGAAG 58.498 55.000 0.00 0.00 0.00 3.46
310 326 2.583441 CCTGTCGCTCCCTTGTCCA 61.583 63.158 0.00 0.00 0.00 4.02
412 428 2.756760 GGTAGTTCCACCAGATCGTGTA 59.243 50.000 0.89 0.00 38.55 2.90
413 429 3.181489 GGTAGTTCCACCAGATCGTGTAG 60.181 52.174 0.89 0.00 38.55 2.74
414 430 2.803956 AGTTCCACCAGATCGTGTAGA 58.196 47.619 0.89 0.00 31.47 2.59
415 431 2.755655 AGTTCCACCAGATCGTGTAGAG 59.244 50.000 0.89 0.00 31.47 2.43
416 432 1.103803 TCCACCAGATCGTGTAGAGC 58.896 55.000 0.89 0.00 35.01 4.09
417 433 0.103208 CCACCAGATCGTGTAGAGCC 59.897 60.000 0.89 0.00 35.47 4.70
418 434 0.248661 CACCAGATCGTGTAGAGCCG 60.249 60.000 0.00 0.00 35.47 5.52
419 435 1.360551 CCAGATCGTGTAGAGCCGG 59.639 63.158 0.00 0.00 35.47 6.13
420 436 1.101635 CCAGATCGTGTAGAGCCGGA 61.102 60.000 5.05 0.00 35.47 5.14
435 451 1.079127 CGGAGCAGTCCCGTTTGAT 60.079 57.895 0.00 0.00 40.20 2.57
488 516 9.216117 TCTGATGATGATGATGATATGTTTGTC 57.784 33.333 0.00 0.00 0.00 3.18
535 563 0.534412 CGTCACAGGCTGAGGAAGAT 59.466 55.000 23.66 0.00 36.98 2.40
602 640 2.515901 GCCAGGGGAATACGGCAT 59.484 61.111 0.00 0.00 44.25 4.40
647 686 3.697045 CACCCCTTGTGTCAAAAGTACAA 59.303 43.478 2.04 0.00 40.26 2.41
669 712 3.671740 AAGGCCCTCTTTATCTTTCCC 57.328 47.619 0.00 0.00 29.99 3.97
670 713 2.865199 AGGCCCTCTTTATCTTTCCCT 58.135 47.619 0.00 0.00 0.00 4.20
671 714 2.780592 AGGCCCTCTTTATCTTTCCCTC 59.219 50.000 0.00 0.00 0.00 4.30
672 715 2.158593 GGCCCTCTTTATCTTTCCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
673 716 2.780592 GCCCTCTTTATCTTTCCCTCCT 59.219 50.000 0.00 0.00 0.00 3.69
674 717 3.181449 GCCCTCTTTATCTTTCCCTCCTC 60.181 52.174 0.00 0.00 0.00 3.71
675 718 4.302930 CCCTCTTTATCTTTCCCTCCTCT 58.697 47.826 0.00 0.00 0.00 3.69
676 719 4.346709 CCCTCTTTATCTTTCCCTCCTCTC 59.653 50.000 0.00 0.00 0.00 3.20
677 720 5.215845 CCTCTTTATCTTTCCCTCCTCTCT 58.784 45.833 0.00 0.00 0.00 3.10
757 800 1.225983 CAAGACACACACCCACCCA 59.774 57.895 0.00 0.00 0.00 4.51
759 802 0.395173 AAGACACACACCCACCCAAC 60.395 55.000 0.00 0.00 0.00 3.77
762 805 3.024356 ACACACCCACCCAACCCA 61.024 61.111 0.00 0.00 0.00 4.51
765 808 2.917227 CACCCACCCAACCCAAGC 60.917 66.667 0.00 0.00 0.00 4.01
766 809 4.233558 ACCCACCCAACCCAAGCC 62.234 66.667 0.00 0.00 0.00 4.35
769 812 3.914713 CACCCAACCCAAGCCCCT 61.915 66.667 0.00 0.00 0.00 4.79
818 874 3.583380 TTGCTGAGCCCAGGCCTT 61.583 61.111 0.00 0.00 43.17 4.35
833 889 2.034687 CTTGGCACCTCCCCACAG 59.965 66.667 0.00 0.00 30.65 3.66
834 901 2.449518 TTGGCACCTCCCCACAGA 60.450 61.111 0.00 0.00 30.65 3.41
909 979 1.211969 CGTTCTTCCTTCTCGCCGA 59.788 57.895 0.00 0.00 0.00 5.54
937 1007 2.686816 CGCCGTTCCTCGCCAAATT 61.687 57.895 0.00 0.00 38.35 1.82
960 1030 2.109181 CCCTTCTCGCCGAATCCC 59.891 66.667 0.00 0.00 0.00 3.85
962 1032 2.962253 CTTCTCGCCGAATCCCGC 60.962 66.667 0.00 0.00 36.84 6.13
1027 1097 1.562783 GAGCTCCTACTCCAACCTGT 58.437 55.000 0.87 0.00 0.00 4.00
1305 1375 2.042435 AAGAGCTCCTCCTCCCCG 60.042 66.667 10.93 0.00 32.17 5.73
1491 2722 1.409064 CCGCTCTTCCACTACATGCTA 59.591 52.381 0.00 0.00 0.00 3.49
2064 3301 3.464833 ACATATTCAAGGGGATCAGCCTT 59.535 43.478 0.00 0.00 36.66 4.35
2202 3439 2.609747 GAGGAGACCTATGCCATGGTA 58.390 52.381 14.67 9.89 36.59 3.25
2520 3757 3.665675 GAACATCGAGGCCGTGGCT 62.666 63.158 11.25 0.00 42.48 4.75
2523 3760 3.157252 ATCGAGGCCGTGGCTGAT 61.157 61.111 11.25 9.08 38.98 2.90
2706 3943 3.292159 GGTTTCGGCCTGCGGTTT 61.292 61.111 0.00 0.00 0.00 3.27
2853 4090 2.037136 CAAGAGCCCCACTGCGAAG 61.037 63.158 0.00 0.00 36.02 3.79
3054 4297 4.279169 ACATTCTTGCAAGCTTAGCTCAAA 59.721 37.500 21.99 7.69 38.25 2.69
3056 4299 3.213506 TCTTGCAAGCTTAGCTCAAACA 58.786 40.909 21.99 0.60 38.25 2.83
3057 4300 3.631686 TCTTGCAAGCTTAGCTCAAACAA 59.368 39.130 21.99 8.82 38.25 2.83
3058 4301 4.097741 TCTTGCAAGCTTAGCTCAAACAAA 59.902 37.500 21.99 0.00 38.25 2.83
3059 4302 4.589216 TGCAAGCTTAGCTCAAACAAAT 57.411 36.364 7.36 0.00 38.25 2.32
3065 4308 7.362662 CAAGCTTAGCTCAAACAAATACTTCA 58.637 34.615 7.36 0.00 38.25 3.02
3067 4310 7.940850 AGCTTAGCTCAAACAAATACTTCAAA 58.059 30.769 0.00 0.00 30.62 2.69
3068 4311 8.078596 AGCTTAGCTCAAACAAATACTTCAAAG 58.921 33.333 0.00 0.00 30.62 2.77
3070 4313 9.736023 CTTAGCTCAAACAAATACTTCAAAGTT 57.264 29.630 0.00 0.00 40.37 2.66
3086 4329 8.837389 ACTTCAAAGTTAGTACAAAGTTGGATC 58.163 33.333 0.00 0.00 35.21 3.36
3089 4332 8.999431 TCAAAGTTAGTACAAAGTTGGATCATC 58.001 33.333 0.00 0.00 0.00 2.92
3090 4333 9.003658 CAAAGTTAGTACAAAGTTGGATCATCT 57.996 33.333 0.00 0.00 0.00 2.90
3097 4340 9.739276 AGTACAAAGTTGGATCATCTATTTTGA 57.261 29.630 12.56 0.00 0.00 2.69
3100 4343 9.696917 ACAAAGTTGGATCATCTATTTTGAAAC 57.303 29.630 12.56 0.00 0.00 2.78
3101 4344 8.853345 CAAAGTTGGATCATCTATTTTGAAACG 58.147 33.333 0.00 0.00 0.00 3.60
3104 4347 6.925610 TGGATCATCTATTTTGAAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
3105 4348 5.822519 TGGATCATCTATTTTGAAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
3107 4350 5.429681 TCATCTATTTTGAAACGGAGGGA 57.570 39.130 0.00 0.00 0.00 4.20
3108 4351 5.428253 TCATCTATTTTGAAACGGAGGGAG 58.572 41.667 0.00 0.00 0.00 4.30
3166 4557 5.125356 TGGTATGTTGCATCATAGGTTCAG 58.875 41.667 16.09 0.00 32.01 3.02
3238 4629 6.317391 AGCCTCCTTTTCGAAGAAAATCATAG 59.683 38.462 8.18 4.66 45.90 2.23
3366 4989 2.950975 TCTGAAATGTGCTGCACTGAAA 59.049 40.909 30.43 13.25 35.11 2.69
3720 5870 1.135859 CCGCTCACAGAATTCTTGTGC 60.136 52.381 22.67 22.13 33.93 4.57
3860 6010 1.421268 TGTTCCAGTTCATCACCAGCT 59.579 47.619 0.00 0.00 0.00 4.24
3997 6150 4.509737 GGGCTGGCGTACGTCTCC 62.510 72.222 21.92 20.16 0.00 3.71
4098 6251 1.099879 GGAGCTGGAATGAAGCGCAT 61.100 55.000 11.47 0.00 45.59 4.73
4249 6409 6.626302 AGTATGAGACTTGCTTTAGAGTGTC 58.374 40.000 0.00 0.00 33.13 3.67
4277 6444 4.634199 CTCCGTTTGAAAACCTGGTAGTA 58.366 43.478 0.00 0.00 35.51 1.82
4293 6460 4.522405 TGGTAGTACTAGTTACCGCAACAA 59.478 41.667 15.80 0.00 41.80 2.83
4327 6494 3.864243 TCTGAATGCCATGGAAAAATGC 58.136 40.909 18.40 1.96 0.00 3.56
4328 6495 3.516300 TCTGAATGCCATGGAAAAATGCT 59.484 39.130 18.40 0.00 0.00 3.79
4329 6496 4.710865 TCTGAATGCCATGGAAAAATGCTA 59.289 37.500 18.40 0.00 0.00 3.49
4335 6502 5.904941 TGCCATGGAAAAATGCTACTAATG 58.095 37.500 18.40 0.00 0.00 1.90
4346 6513 6.668541 AATGCTACTAATGTGTGCTGTTAG 57.331 37.500 0.00 0.00 0.00 2.34
4362 6695 4.674101 GCTGTTAGAACATATTTTGCGCCA 60.674 41.667 4.18 0.00 38.41 5.69
4372 6705 1.500108 TTTTGCGCCAATTCTGCTTG 58.500 45.000 4.18 0.00 0.00 4.01
4373 6706 0.945265 TTTGCGCCAATTCTGCTTGC 60.945 50.000 4.18 0.00 0.00 4.01
4374 6707 2.085042 TTGCGCCAATTCTGCTTGCA 62.085 50.000 4.18 0.00 0.00 4.08
4375 6708 2.090524 GCGCCAATTCTGCTTGCAC 61.091 57.895 0.00 0.00 0.00 4.57
4378 6711 0.033781 GCCAATTCTGCTTGCACCAA 59.966 50.000 0.00 0.00 0.00 3.67
4379 6712 1.540797 GCCAATTCTGCTTGCACCAAA 60.541 47.619 0.00 0.00 0.00 3.28
4381 6714 2.545106 CCAATTCTGCTTGCACCAAAAC 59.455 45.455 0.00 0.00 0.00 2.43
4382 6715 2.531522 ATTCTGCTTGCACCAAAACC 57.468 45.000 0.00 0.00 0.00 3.27
4383 6716 0.102120 TTCTGCTTGCACCAAAACCG 59.898 50.000 0.00 0.00 0.00 4.44
4384 6717 0.749818 TCTGCTTGCACCAAAACCGA 60.750 50.000 0.00 0.00 0.00 4.69
4385 6718 0.318107 CTGCTTGCACCAAAACCGAG 60.318 55.000 0.00 0.00 0.00 4.63
4386 6719 1.661509 GCTTGCACCAAAACCGAGC 60.662 57.895 0.00 0.00 0.00 5.03
4405 6742 4.492645 CGAGCGCGATATCTACTGATTAAC 59.507 45.833 12.10 0.00 40.82 2.01
4434 6771 9.289782 GTGTCAAAGATTATATGGCTTCCTAAT 57.710 33.333 0.00 0.00 0.00 1.73
4435 6772 9.866655 TGTCAAAGATTATATGGCTTCCTAATT 57.133 29.630 0.00 0.00 0.00 1.40
4444 6781 7.756395 ATATGGCTTCCTAATTCATCAAGTG 57.244 36.000 0.00 0.00 0.00 3.16
4445 6782 4.922206 TGGCTTCCTAATTCATCAAGTGT 58.078 39.130 0.00 0.00 0.00 3.55
4446 6783 5.324409 TGGCTTCCTAATTCATCAAGTGTT 58.676 37.500 0.00 0.00 0.00 3.32
4447 6784 5.183713 TGGCTTCCTAATTCATCAAGTGTTG 59.816 40.000 0.00 0.00 0.00 3.33
4448 6785 5.393461 GGCTTCCTAATTCATCAAGTGTTGG 60.393 44.000 0.00 0.00 0.00 3.77
4449 6786 5.415701 GCTTCCTAATTCATCAAGTGTTGGA 59.584 40.000 0.00 0.00 0.00 3.53
4450 6787 6.071952 GCTTCCTAATTCATCAAGTGTTGGAA 60.072 38.462 0.00 0.00 0.00 3.53
4451 6788 7.523709 GCTTCCTAATTCATCAAGTGTTGGAAA 60.524 37.037 0.00 0.00 30.82 3.13
4470 6807 6.980593 TGGAAACCTAATTCATCAAGTGTTG 58.019 36.000 0.00 0.00 0.00 3.33
4479 6816 4.320608 TCATCAAGTGTTGGAAAAAGGC 57.679 40.909 0.00 0.00 0.00 4.35
4547 6884 0.316204 CAAAGCCCAAGTGAAGCCTG 59.684 55.000 0.00 0.00 0.00 4.85
4572 6910 2.033927 GGCAGCTCTAGGCAATTTAAGC 59.966 50.000 6.07 0.00 44.79 3.09
4577 6915 5.586243 CAGCTCTAGGCAATTTAAGCAAGTA 59.414 40.000 6.07 0.00 44.79 2.24
4606 6944 3.622612 CCAAAGAAACCAAAGTTGCCAAG 59.377 43.478 0.00 0.00 35.97 3.61
4608 6946 1.762370 AGAAACCAAAGTTGCCAAGGG 59.238 47.619 0.00 0.00 35.97 3.95
4622 6960 2.800250 CCAAGGGCTCAAAAGATGACT 58.200 47.619 0.00 0.00 33.47 3.41
4638 6976 6.131972 AGATGACTCAAAAGGAAGATGGAA 57.868 37.500 0.00 0.00 0.00 3.53
4728 7095 2.879756 GCTAGGCATGGTCCTGTTCAAA 60.880 50.000 2.35 0.00 37.01 2.69
4765 7132 5.522824 GGAACACCAAACTAGATCGTTATCC 59.477 44.000 0.00 0.00 31.98 2.59
4919 7286 2.203209 GGGCTTCACATAGCGGGG 60.203 66.667 0.00 0.00 42.15 5.73
4976 7351 1.377202 ACCGTATGCAAGTGCCAGG 60.377 57.895 0.00 1.82 41.18 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.750637 GTGGACGGCGGAGAGAGA 60.751 66.667 13.24 0.00 0.00 3.10
57 58 1.685355 AAACAACTGGGGGCAGCAAC 61.685 55.000 0.00 0.00 0.00 4.17
127 128 2.162681 CGGAGATTTCCTTGCTTTGGT 58.837 47.619 0.10 0.00 41.67 3.67
154 155 3.063084 GACAGGAGGCGACGAGGT 61.063 66.667 0.00 0.00 0.00 3.85
155 156 3.827898 GGACAGGAGGCGACGAGG 61.828 72.222 0.00 0.00 0.00 4.63
156 157 3.827898 GGGACAGGAGGCGACGAG 61.828 72.222 0.00 0.00 0.00 4.18
183 184 3.683340 GCCGAGGGTTTACTACAAGAAAG 59.317 47.826 0.00 0.00 0.00 2.62
204 205 1.153628 TAAGGCGAGCGAGGAAAGC 60.154 57.895 0.00 0.00 0.00 3.51
213 214 3.516866 GATCGGGGGTAAGGCGAGC 62.517 68.421 0.00 0.00 0.00 5.03
215 216 3.221389 CGATCGGGGGTAAGGCGA 61.221 66.667 7.38 0.00 0.00 5.54
217 218 4.620937 GCCGATCGGGGGTAAGGC 62.621 72.222 33.98 14.22 37.61 4.35
239 255 1.895798 CTCCCTTGCCTTTCTTTTCCC 59.104 52.381 0.00 0.00 0.00 3.97
298 314 0.038166 TGGTGATTGGACAAGGGAGC 59.962 55.000 0.00 0.00 0.00 4.70
385 401 0.991920 CTGGTGGAACTACCCATGGT 59.008 55.000 11.73 1.30 40.09 3.55
418 434 1.207329 ACTATCAAACGGGACTGCTCC 59.793 52.381 0.00 0.00 35.50 4.70
419 435 2.674796 ACTATCAAACGGGACTGCTC 57.325 50.000 0.00 0.00 0.00 4.26
420 436 4.755266 AATACTATCAAACGGGACTGCT 57.245 40.909 0.00 0.00 0.00 4.24
435 451 6.842437 TGGTAAAATTGCCAGCAAATACTA 57.158 33.333 9.44 8.34 38.05 1.82
535 563 6.294231 CGCAGGAAAGACTTGATAGATAGCTA 60.294 42.308 0.00 0.00 0.00 3.32
556 584 2.351244 TGTAGCTCACTCCCCGCAG 61.351 63.158 0.00 0.00 0.00 5.18
601 639 2.627699 ACCTTTCGTGCAATTTGGTGAT 59.372 40.909 0.00 0.00 0.00 3.06
602 640 2.028130 ACCTTTCGTGCAATTTGGTGA 58.972 42.857 0.00 0.00 0.00 4.02
647 686 4.045974 AGGGAAAGATAAAGAGGGCCTTTT 59.954 41.667 7.89 5.17 42.13 2.27
669 712 3.203040 AGAGAGAGAAAGGGAGAGAGGAG 59.797 52.174 0.00 0.00 0.00 3.69
670 713 3.197983 AGAGAGAGAAAGGGAGAGAGGA 58.802 50.000 0.00 0.00 0.00 3.71
671 714 3.669939 AGAGAGAGAAAGGGAGAGAGG 57.330 52.381 0.00 0.00 0.00 3.69
672 715 5.110814 TGTAGAGAGAGAAAGGGAGAGAG 57.889 47.826 0.00 0.00 0.00 3.20
673 716 5.522315 TTGTAGAGAGAGAAAGGGAGAGA 57.478 43.478 0.00 0.00 0.00 3.10
674 717 6.790232 AATTGTAGAGAGAGAAAGGGAGAG 57.210 41.667 0.00 0.00 0.00 3.20
675 718 7.340743 CACTAATTGTAGAGAGAGAAAGGGAGA 59.659 40.741 0.00 0.00 0.00 3.71
676 719 7.488322 CACTAATTGTAGAGAGAGAAAGGGAG 58.512 42.308 0.00 0.00 0.00 4.30
677 720 6.127310 GCACTAATTGTAGAGAGAGAAAGGGA 60.127 42.308 0.00 0.00 0.00 4.20
768 811 3.077556 CTGACCGACCTGGGGGAG 61.078 72.222 12.37 0.00 44.64 4.30
769 812 4.715130 CCTGACCGACCTGGGGGA 62.715 72.222 12.37 0.00 44.64 4.81
818 874 3.249189 GTCTGTGGGGAGGTGCCA 61.249 66.667 0.00 0.00 38.95 4.92
833 889 0.318762 AGTTGAAGCGGAGAGTGGTC 59.681 55.000 0.00 0.00 0.00 4.02
834 901 0.034059 CAGTTGAAGCGGAGAGTGGT 59.966 55.000 0.00 0.00 0.00 4.16
909 979 3.799755 GAACGGCGCGGCTTCAAT 61.800 61.111 30.60 11.47 0.00 2.57
1305 1375 4.302455 CGATGTAGATGAACTCCATGGAC 58.698 47.826 11.44 1.49 35.17 4.02
1533 2770 2.184579 GAGACGTAGGCCTGCCAC 59.815 66.667 17.99 9.71 38.92 5.01
2202 3439 0.608640 ACGCCTCGTTGATCCTCTTT 59.391 50.000 0.00 0.00 36.35 2.52
2520 3757 2.825387 GCGCACTCCATGGCATCA 60.825 61.111 6.96 0.00 0.00 3.07
2706 3943 2.273908 GTCAAGCGAGACCACCCTA 58.726 57.895 0.68 0.00 32.36 3.53
2853 4090 2.735762 GCTGTTGAGTATCTGGACCGAC 60.736 54.545 0.00 0.00 34.92 4.79
3058 4301 9.841295 TCCAACTTTGTACTAACTTTGAAGTAT 57.159 29.630 0.00 0.00 38.57 2.12
3059 4302 9.841295 ATCCAACTTTGTACTAACTTTGAAGTA 57.159 29.630 0.00 0.00 38.57 2.24
3074 4317 9.696917 GTTTCAAAATAGATGATCCAACTTTGT 57.303 29.630 0.00 0.00 0.00 2.83
3076 4319 8.028938 CCGTTTCAAAATAGATGATCCAACTTT 58.971 33.333 0.00 0.00 0.00 2.66
3077 4320 7.393234 TCCGTTTCAAAATAGATGATCCAACTT 59.607 33.333 0.00 0.00 0.00 2.66
3078 4321 6.884295 TCCGTTTCAAAATAGATGATCCAACT 59.116 34.615 0.00 0.00 0.00 3.16
3079 4322 7.083875 TCCGTTTCAAAATAGATGATCCAAC 57.916 36.000 0.00 0.00 0.00 3.77
3080 4323 6.318648 CCTCCGTTTCAAAATAGATGATCCAA 59.681 38.462 0.00 0.00 0.00 3.53
3081 4324 5.822519 CCTCCGTTTCAAAATAGATGATCCA 59.177 40.000 0.00 0.00 0.00 3.41
3082 4325 5.239525 CCCTCCGTTTCAAAATAGATGATCC 59.760 44.000 0.00 0.00 0.00 3.36
3086 4329 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
3089 4332 5.484715 TGTACTCCCTCCGTTTCAAAATAG 58.515 41.667 0.00 0.00 0.00 1.73
3090 4333 5.486735 TGTACTCCCTCCGTTTCAAAATA 57.513 39.130 0.00 0.00 0.00 1.40
3091 4334 4.360951 TGTACTCCCTCCGTTTCAAAAT 57.639 40.909 0.00 0.00 0.00 1.82
3092 4335 3.842007 TGTACTCCCTCCGTTTCAAAA 57.158 42.857 0.00 0.00 0.00 2.44
3093 4336 3.842007 TTGTACTCCCTCCGTTTCAAA 57.158 42.857 0.00 0.00 0.00 2.69
3094 4337 4.360951 AATTGTACTCCCTCCGTTTCAA 57.639 40.909 0.00 0.00 0.00 2.69
3095 4338 4.360951 AAATTGTACTCCCTCCGTTTCA 57.639 40.909 0.00 0.00 0.00 2.69
3096 4339 5.350640 CACTAAATTGTACTCCCTCCGTTTC 59.649 44.000 0.00 0.00 0.00 2.78
3097 4340 5.243207 CACTAAATTGTACTCCCTCCGTTT 58.757 41.667 0.00 0.00 0.00 3.60
3098 4341 4.323257 CCACTAAATTGTACTCCCTCCGTT 60.323 45.833 0.00 0.00 0.00 4.44
3099 4342 3.197116 CCACTAAATTGTACTCCCTCCGT 59.803 47.826 0.00 0.00 0.00 4.69
3100 4343 3.793559 CCACTAAATTGTACTCCCTCCG 58.206 50.000 0.00 0.00 0.00 4.63
3101 4344 3.054655 TGCCACTAAATTGTACTCCCTCC 60.055 47.826 0.00 0.00 0.00 4.30
3104 4347 3.681593 TGTGCCACTAAATTGTACTCCC 58.318 45.455 0.00 0.00 0.00 4.30
3105 4348 4.700213 ACATGTGCCACTAAATTGTACTCC 59.300 41.667 0.00 0.00 0.00 3.85
3107 4350 6.318648 CCATACATGTGCCACTAAATTGTACT 59.681 38.462 9.11 0.00 0.00 2.73
3108 4351 6.317642 TCCATACATGTGCCACTAAATTGTAC 59.682 38.462 9.11 0.00 0.00 2.90
3166 4557 3.185188 CGATGCACACAGCCATAGAATAC 59.815 47.826 0.00 0.00 44.83 1.89
3285 4722 5.404096 TGCAATGCAACTGATCATGTTAAG 58.596 37.500 5.01 0.00 34.76 1.85
3366 4989 1.003233 GCGTCCCTCTTCAGCCTTT 60.003 57.895 0.00 0.00 0.00 3.11
3720 5870 1.845809 GCTCACGCCCTGTTGTTCAG 61.846 60.000 0.00 0.00 43.27 3.02
3775 5925 2.593978 CACATGCCCCTCTCCTGG 59.406 66.667 0.00 0.00 0.00 4.45
4098 6251 3.855503 CTTCCTGCTGTGCTGCCCA 62.856 63.158 0.00 0.00 0.00 5.36
4110 6268 1.069022 CAACACGACAATGCCTTCCTG 60.069 52.381 0.00 0.00 0.00 3.86
4249 6409 1.333791 GGTTTTCAAACGGAGCTCACG 60.334 52.381 17.19 18.28 39.77 4.35
4277 6444 8.726870 ACATTATTATTGTTGCGGTAACTAGT 57.273 30.769 10.27 0.00 40.05 2.57
4293 6460 7.610692 CCATGGCATTCAGAGAGACATTATTAT 59.389 37.037 0.00 0.00 0.00 1.28
4327 6494 7.834068 ATGTTCTAACAGCACACATTAGTAG 57.166 36.000 1.62 0.00 43.04 2.57
4328 6495 9.884636 AATATGTTCTAACAGCACACATTAGTA 57.115 29.630 1.62 0.00 43.04 1.82
4329 6496 8.792830 AATATGTTCTAACAGCACACATTAGT 57.207 30.769 1.62 0.00 43.04 2.24
4335 6502 5.283717 CGCAAAATATGTTCTAACAGCACAC 59.716 40.000 1.62 0.00 43.04 3.82
4346 6513 4.259930 GCAGAATTGGCGCAAAATATGTTC 60.260 41.667 10.83 4.57 0.00 3.18
4373 6706 1.355796 TATCGCGCTCGGTTTTGGTG 61.356 55.000 5.56 0.00 36.13 4.17
4374 6707 0.461339 ATATCGCGCTCGGTTTTGGT 60.461 50.000 5.56 0.00 36.13 3.67
4375 6708 0.232303 GATATCGCGCTCGGTTTTGG 59.768 55.000 5.56 0.00 36.13 3.28
4378 6711 1.607628 AGTAGATATCGCGCTCGGTTT 59.392 47.619 5.56 0.00 36.13 3.27
4379 6712 1.069159 CAGTAGATATCGCGCTCGGTT 60.069 52.381 5.56 0.00 36.13 4.44
4381 6714 0.796927 TCAGTAGATATCGCGCTCGG 59.203 55.000 5.56 0.00 36.13 4.63
4382 6715 2.815657 ATCAGTAGATATCGCGCTCG 57.184 50.000 5.56 0.00 31.14 5.03
4383 6716 4.794246 GGTTAATCAGTAGATATCGCGCTC 59.206 45.833 5.56 0.00 33.08 5.03
4384 6717 4.217767 TGGTTAATCAGTAGATATCGCGCT 59.782 41.667 5.56 0.00 33.08 5.92
4385 6718 4.482386 TGGTTAATCAGTAGATATCGCGC 58.518 43.478 0.00 0.00 33.08 6.86
4386 6719 5.569441 CACTGGTTAATCAGTAGATATCGCG 59.431 44.000 20.77 0.00 45.24 5.87
4405 6742 6.016777 GGAAGCCATATAATCTTTGACACTGG 60.017 42.308 0.00 0.00 0.00 4.00
4423 6760 4.922206 ACACTTGATGAATTAGGAAGCCA 58.078 39.130 0.00 0.00 0.00 4.75
4424 6761 5.393461 CCAACACTTGATGAATTAGGAAGCC 60.393 44.000 0.00 0.00 0.00 4.35
4434 6771 7.286546 TGAATTAGGTTTCCAACACTTGATGAA 59.713 33.333 0.00 0.00 0.00 2.57
4435 6772 6.775142 TGAATTAGGTTTCCAACACTTGATGA 59.225 34.615 0.00 0.00 0.00 2.92
4436 6773 6.980593 TGAATTAGGTTTCCAACACTTGATG 58.019 36.000 0.00 0.00 0.00 3.07
4437 6774 7.451255 TGATGAATTAGGTTTCCAACACTTGAT 59.549 33.333 0.00 0.00 0.00 2.57
4438 6775 6.775142 TGATGAATTAGGTTTCCAACACTTGA 59.225 34.615 0.00 0.00 0.00 3.02
4439 6776 6.980593 TGATGAATTAGGTTTCCAACACTTG 58.019 36.000 0.00 0.00 0.00 3.16
4440 6777 7.287696 ACTTGATGAATTAGGTTTCCAACACTT 59.712 33.333 0.00 0.00 0.00 3.16
4441 6778 6.777580 ACTTGATGAATTAGGTTTCCAACACT 59.222 34.615 0.00 0.00 0.00 3.55
4442 6779 6.863126 CACTTGATGAATTAGGTTTCCAACAC 59.137 38.462 0.00 0.00 0.00 3.32
4443 6780 6.549364 ACACTTGATGAATTAGGTTTCCAACA 59.451 34.615 0.00 0.00 0.00 3.33
4444 6781 6.981722 ACACTTGATGAATTAGGTTTCCAAC 58.018 36.000 0.00 0.00 0.00 3.77
4445 6782 7.432869 CAACACTTGATGAATTAGGTTTCCAA 58.567 34.615 0.00 0.00 0.00 3.53
4446 6783 6.015519 CCAACACTTGATGAATTAGGTTTCCA 60.016 38.462 0.00 0.00 0.00 3.53
4447 6784 6.208599 TCCAACACTTGATGAATTAGGTTTCC 59.791 38.462 0.00 0.00 0.00 3.13
4448 6785 7.214467 TCCAACACTTGATGAATTAGGTTTC 57.786 36.000 0.00 0.00 0.00 2.78
4449 6786 7.595819 TTCCAACACTTGATGAATTAGGTTT 57.404 32.000 0.00 0.00 0.00 3.27
4450 6787 7.595819 TTTCCAACACTTGATGAATTAGGTT 57.404 32.000 0.00 0.00 0.00 3.50
4451 6788 7.595819 TTTTCCAACACTTGATGAATTAGGT 57.404 32.000 0.00 0.00 0.00 3.08
4452 6789 7.599998 CCTTTTTCCAACACTTGATGAATTAGG 59.400 37.037 0.00 0.00 0.00 2.69
4453 6790 7.116805 GCCTTTTTCCAACACTTGATGAATTAG 59.883 37.037 0.00 0.00 0.00 1.73
4470 6807 1.080501 GCAAGCTCCGCCTTTTTCC 60.081 57.895 0.00 0.00 0.00 3.13
4479 6816 1.818850 CATGAATTTCGCAAGCTCCG 58.181 50.000 0.00 0.00 37.18 4.63
4485 6822 1.273048 AGCCTTGCATGAATTTCGCAA 59.727 42.857 0.00 10.13 43.02 4.85
4547 6884 0.750911 ATTGCCTAGAGCTGCCTTGC 60.751 55.000 0.00 1.34 44.23 4.01
4572 6910 4.202305 TGGTTTCTTTGGCCCATTTACTTG 60.202 41.667 0.00 0.00 0.00 3.16
4577 6915 3.201930 ACTTTGGTTTCTTTGGCCCATTT 59.798 39.130 0.00 0.00 0.00 2.32
4606 6944 4.321527 CCTTTTGAGTCATCTTTTGAGCCC 60.322 45.833 0.00 0.00 34.17 5.19
4608 6946 5.695851 TCCTTTTGAGTCATCTTTTGAGC 57.304 39.130 0.00 0.00 34.17 4.26
4622 6960 2.039746 TCGGCTTCCATCTTCCTTTTGA 59.960 45.455 0.00 0.00 0.00 2.69
4638 6976 1.261238 CCTCTCCTTGTTCCTCGGCT 61.261 60.000 0.00 0.00 0.00 5.52
4728 7095 3.979911 TGGTGTTCCATTGAGCCATAAT 58.020 40.909 0.00 0.00 39.03 1.28
4765 7132 0.692419 ACCAGGGCATAGAGTGGGAG 60.692 60.000 0.00 0.00 34.07 4.30
4908 7275 1.094785 CCTTTTGACCCCGCTATGTG 58.905 55.000 0.00 0.00 0.00 3.21
4919 7286 0.108945 GCTCAGCATGGCCTTTTGAC 60.109 55.000 3.32 0.00 36.16 3.18
4976 7351 1.003108 GGCTAAGAGCAAGCTTCGAC 58.997 55.000 0.00 0.00 44.75 4.20


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

AutoCloner maintained by Alex Coulton.