Multiple sequence alignment - TraesCS1B01G430800

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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 TraesCS1B01G430800 chr1B 100.000 4133 0 0 1 4133 655105350 655101218 0.000000e+00 7633
1 TraesCS1B01G430800 chr1B 87.939 1053 90 19 2315 3338 655271553 655272597 0.000000e+00 1206
2 TraesCS1B01G430800 chr1D 92.608 3815 157 40 356 4133 471303716 471299990 0.000000e+00 5367
3 TraesCS1B01G430800 chr1D 92.635 353 22 4 2 352 471304324 471303974 4.770000e-139 505
4 TraesCS1B01G430800 chr1D 85.957 470 30 14 2869 3303 471432553 471433021 1.740000e-128 470
5 TraesCS1B01G430800 chr1D 84.424 321 35 9 3456 3767 471297175 471296861 6.710000e-78 302
6 TraesCS1B01G430800 chr1D 82.069 145 13 2 3626 3762 471295361 471295222 1.210000e-20 111
7 TraesCS1B01G430800 chr3D 90.063 2707 206 40 1024 3705 461199574 461202242 0.000000e+00 3450
8 TraesCS1B01G430800 chr3A 90.959 2389 179 23 1024 3407 603790182 603792538 0.000000e+00 3181
9 TraesCS1B01G430800 chr3A 86.159 289 25 7 3427 3705 603792719 603793002 8.690000e-77 298
10 TraesCS1B01G430800 chr3B 90.426 2392 193 20 1024 3410 611676601 611678961 0.000000e+00 3116
11 TraesCS1B01G430800 chr7D 90.340 1884 140 24 1844 3705 29536558 29534695 0.000000e+00 2433
12 TraesCS1B01G430800 chr7D 87.986 591 56 7 1249 1839 29537521 29536946 0.000000e+00 684
13 TraesCS1B01G430800 chr7D 82.310 684 60 24 3115 3772 613450060 613449412 1.690000e-148 536
14 TraesCS1B01G430800 chr1A 82.720 1875 287 23 1271 3133 20815109 20816958 0.000000e+00 1633
15 TraesCS1B01G430800 chr1A 87.612 557 36 5 1157 1713 565571869 565572392 2.110000e-172 616
16 TraesCS1B01G430800 chr1A 88.636 176 20 0 982 1157 565570010 565570185 9.000000e-52 215
17 TraesCS1B01G430800 chr7A 89.857 769 67 7 1249 2012 29781385 29780623 0.000000e+00 977
18 TraesCS1B01G430800 chr7A 82.138 683 56 27 3115 3772 704893838 704893197 3.660000e-145 525
19 TraesCS1B01G430800 chrUn 87.612 557 36 11 1157 1713 1368159 1368682 2.110000e-172 616
20 TraesCS1B01G430800 chrUn 87.832 452 29 2 1262 1713 396328458 396328033 1.330000e-139 507
21 TraesCS1B01G430800 chrUn 88.636 176 20 0 982 1157 349798081 349797906 9.000000e-52 215
22 TraesCS1B01G430800 chrUn 88.824 170 19 0 982 1151 1366301 1366470 4.190000e-50 209
23 TraesCS1B01G430800 chr6D 85.912 362 30 9 3779 4133 461356570 461356917 2.350000e-97 366
24 TraesCS1B01G430800 chr6D 85.449 323 34 8 3457 3771 461358578 461358895 1.430000e-84 324
25 TraesCS1B01G430800 chr6A 85.635 362 34 9 3779 4133 607953800 607954150 8.440000e-97 364
26 TraesCS1B01G430800 chr6B 85.635 362 31 9 3779 4133 702827140 702827487 1.090000e-95 361
27 TraesCS1B01G430800 chr6B 83.851 322 40 10 3457 3771 702829279 702829595 3.120000e-76 296
28 TraesCS1B01G430800 chr7B 97.170 106 3 0 3026 3131 703302126 703302021 3.280000e-41 180
29 TraesCS1B01G430800 chr7B 91.150 113 10 0 2873 2985 703302238 703302126 1.990000e-33 154


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 TraesCS1B01G430800 chr1B 655101218 655105350 4132 True 7633.00 7633 100.0000 1 4133 1 chr1B.!!$R1 4132
1 TraesCS1B01G430800 chr1B 655271553 655272597 1044 False 1206.00 1206 87.9390 2315 3338 1 chr1B.!!$F1 1023
2 TraesCS1B01G430800 chr1D 471295222 471304324 9102 True 1571.25 5367 87.9340 2 4133 4 chr1D.!!$R1 4131
3 TraesCS1B01G430800 chr3D 461199574 461202242 2668 False 3450.00 3450 90.0630 1024 3705 1 chr3D.!!$F1 2681
4 TraesCS1B01G430800 chr3A 603790182 603793002 2820 False 1739.50 3181 88.5590 1024 3705 2 chr3A.!!$F1 2681
5 TraesCS1B01G430800 chr3B 611676601 611678961 2360 False 3116.00 3116 90.4260 1024 3410 1 chr3B.!!$F1 2386
6 TraesCS1B01G430800 chr7D 29534695 29537521 2826 True 1558.50 2433 89.1630 1249 3705 2 chr7D.!!$R2 2456
7 TraesCS1B01G430800 chr7D 613449412 613450060 648 True 536.00 536 82.3100 3115 3772 1 chr7D.!!$R1 657
8 TraesCS1B01G430800 chr1A 20815109 20816958 1849 False 1633.00 1633 82.7200 1271 3133 1 chr1A.!!$F1 1862
9 TraesCS1B01G430800 chr1A 565570010 565572392 2382 False 415.50 616 88.1240 982 1713 2 chr1A.!!$F2 731
10 TraesCS1B01G430800 chr7A 29780623 29781385 762 True 977.00 977 89.8570 1249 2012 1 chr7A.!!$R1 763
11 TraesCS1B01G430800 chr7A 704893197 704893838 641 True 525.00 525 82.1380 3115 3772 1 chr7A.!!$R2 657
12 TraesCS1B01G430800 chrUn 1366301 1368682 2381 False 412.50 616 88.2180 982 1713 2 chrUn.!!$F1 731
13 TraesCS1B01G430800 chr6D 461356570 461358895 2325 False 345.00 366 85.6805 3457 4133 2 chr6D.!!$F1 676
14 TraesCS1B01G430800 chr6B 702827140 702829595 2455 False 328.50 361 84.7430 3457 4133 2 chr6B.!!$F1 676

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
902 1163 0.598065 GGTTTCACATGTGCACTCCC 59.402 55.000 21.38 11.68 0.00 4.30 F
904 1165 1.537202 GTTTCACATGTGCACTCCCTC 59.463 52.381 21.38 2.10 0.00 4.30 F
1778 3736 2.482664 CCTCCAACGATCCTGATGACAG 60.483 54.545 0.00 0.00 43.12 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 3776 0.738762 CAGCATCCGAGTCACACAGG 60.739 60.000 0.00 0.0 0.00 4.00 R
2079 4426 1.257936 CACACCGTGTTCAAGAAGTCG 59.742 52.381 0.00 0.0 0.00 4.18 R
3737 6300 0.386476 TTGCACTTTGAAGCAGCAGG 59.614 50.000 10.13 0.0 42.39 4.85 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
41 42 5.420725 AGTGCTTTGTGTACATCATAGGA 57.579 39.130 0.00 2.80 33.54 2.94
98 99 6.903419 AGTAGCTTGCAGTTTTTATGAGTTC 58.097 36.000 0.00 0.00 0.00 3.01
206 207 4.507388 AGTTTTGCATGTATTGTGTTGTGC 59.493 37.500 0.00 0.00 0.00 4.57
208 209 1.606189 TGCATGTATTGTGTTGTGCGT 59.394 42.857 0.00 0.00 35.46 5.24
232 233 9.977490 CGTTTTTATTAACCGTTGTTACATTTC 57.023 29.630 0.00 0.00 36.69 2.17
265 266 5.824429 TCTTGCTGATGTCTTTTGTTCTTG 58.176 37.500 0.00 0.00 0.00 3.02
333 335 8.895932 AACAAGCTATAAATTTAAGTCGCAAG 57.104 30.769 1.21 2.94 0.00 4.01
409 665 4.223556 TGTGTCTAAGTTTGGTGTTCCA 57.776 40.909 0.00 0.00 42.66 3.53
433 689 2.549754 GCAACACATGTACACTCAGCTT 59.450 45.455 0.00 0.00 0.00 3.74
443 699 8.040727 ACATGTACACTCAGCTTGTATTTATCA 58.959 33.333 0.00 0.00 32.18 2.15
444 700 7.827819 TGTACACTCAGCTTGTATTTATCAC 57.172 36.000 0.28 0.00 32.18 3.06
506 766 4.061596 GCTCATCTACTCTTACCAATGCC 58.938 47.826 0.00 0.00 0.00 4.40
523 783 5.239525 CCAATGCCTTTAGCCTTCTACATAC 59.760 44.000 0.00 0.00 42.71 2.39
541 801 4.940046 ACATACAGTTCATCTTTGGCTCAG 59.060 41.667 0.00 0.00 0.00 3.35
567 827 9.892130 GCAAAATACCTATAGCTATAAGGATGT 57.108 33.333 24.43 11.95 0.00 3.06
573 833 7.479579 ACCTATAGCTATAAGGATGTCCAAGA 58.520 38.462 24.43 1.11 38.89 3.02
577 837 5.716979 AGCTATAAGGATGTCCAAGACCTA 58.283 41.667 1.30 0.00 38.89 3.08
581 841 4.494091 AAGGATGTCCAAGACCTATGTG 57.506 45.455 1.30 0.00 38.89 3.21
589 849 6.582636 TGTCCAAGACCTATGTGTATTGATC 58.417 40.000 5.64 0.00 39.24 2.92
595 855 3.244215 ACCTATGTGTATTGATCGCCTGG 60.244 47.826 0.00 0.00 0.00 4.45
609 869 3.248024 TCGCCTGGACCATAGGATATTT 58.752 45.455 3.92 0.00 37.52 1.40
614 874 7.181305 TCGCCTGGACCATAGGATATTTAATTA 59.819 37.037 3.92 0.00 37.52 1.40
693 953 5.572896 GCAAAACCATATGAACTGTGCTTAC 59.427 40.000 3.65 0.00 0.00 2.34
727 987 6.761312 TCAGAATCCAGCAATTTTGTCAATT 58.239 32.000 0.00 0.00 0.00 2.32
769 1029 4.365514 TTGGAATCACTGCAAAGGAGTA 57.634 40.909 0.00 0.00 31.54 2.59
771 1031 2.680339 GGAATCACTGCAAAGGAGTAGC 59.320 50.000 0.00 0.00 0.00 3.58
773 1033 4.383118 GGAATCACTGCAAAGGAGTAGCTA 60.383 45.833 0.00 0.00 0.00 3.32
878 1139 2.826128 TCTAACGGCTGAGTCATGAGTT 59.174 45.455 4.13 2.12 0.00 3.01
879 1140 2.086054 AACGGCTGAGTCATGAGTTC 57.914 50.000 4.13 2.38 0.00 3.01
892 1153 4.393062 GTCATGAGTTCGATGGTTTCACAT 59.607 41.667 0.00 0.00 0.00 3.21
893 1154 4.392754 TCATGAGTTCGATGGTTTCACATG 59.607 41.667 0.00 0.00 35.46 3.21
894 1155 3.738982 TGAGTTCGATGGTTTCACATGT 58.261 40.909 0.00 0.00 0.00 3.21
895 1156 3.498018 TGAGTTCGATGGTTTCACATGTG 59.502 43.478 20.18 20.18 0.00 3.21
896 1157 2.226437 AGTTCGATGGTTTCACATGTGC 59.774 45.455 21.38 7.58 0.00 4.57
897 1158 1.889545 TCGATGGTTTCACATGTGCA 58.110 45.000 21.38 13.23 0.00 4.57
898 1159 1.535028 TCGATGGTTTCACATGTGCAC 59.465 47.619 21.38 18.21 0.00 4.57
900 1161 2.413239 CGATGGTTTCACATGTGCACTC 60.413 50.000 21.38 12.41 0.00 3.51
902 1163 0.598065 GGTTTCACATGTGCACTCCC 59.402 55.000 21.38 11.68 0.00 4.30
903 1164 1.609208 GTTTCACATGTGCACTCCCT 58.391 50.000 21.38 0.00 0.00 4.20
904 1165 1.537202 GTTTCACATGTGCACTCCCTC 59.463 52.381 21.38 2.10 0.00 4.30
966 1227 4.530857 CCACATCGCCGTCCTCCC 62.531 72.222 0.00 0.00 0.00 4.30
967 1228 3.770040 CACATCGCCGTCCTCCCA 61.770 66.667 0.00 0.00 0.00 4.37
979 1242 2.641746 CCTCCCACCTCCTCCTCCT 61.642 68.421 0.00 0.00 0.00 3.69
1239 3189 3.365265 GTCACCGCCAAGGCCAAG 61.365 66.667 5.01 0.00 46.52 3.61
1778 3736 2.482664 CCTCCAACGATCCTGATGACAG 60.483 54.545 0.00 0.00 43.12 3.51
1812 3776 2.597520 GAGGTGTACGAGAAGCTCAAC 58.402 52.381 5.52 0.00 40.00 3.18
2079 4426 0.535335 TTGTAGTCTCCCATGACCGC 59.465 55.000 0.00 0.00 37.66 5.68
2094 4441 1.213094 ACCGCGACTTCTTGAACACG 61.213 55.000 8.23 0.00 0.00 4.49
2502 4849 3.584848 ACAGGCCAGACTTCAAGTTATCT 59.415 43.478 5.01 0.00 0.00 1.98
2688 5035 3.536570 TGTTGACTTGTTGACGATGGAA 58.463 40.909 0.00 0.00 0.00 3.53
2853 5201 2.719354 GCCCGTGTTGTGTTCACC 59.281 61.111 0.37 0.00 32.86 4.02
3023 5371 1.089920 GTTTGTGCCGATGAGCAGAT 58.910 50.000 0.00 0.00 45.14 2.90
3024 5372 1.470098 GTTTGTGCCGATGAGCAGATT 59.530 47.619 0.00 0.00 45.14 2.40
3213 5574 9.832445 TTCTTCTGAAATCCCATGTATTACTAC 57.168 33.333 0.00 0.00 0.00 2.73
3381 5765 7.811117 TTGTGCAAAACTATTGTACTAAGGT 57.189 32.000 10.04 0.00 36.26 3.50
3413 5810 5.048713 GTGGTATTACCTCCATATTGCTTGC 60.049 44.000 13.90 0.00 39.58 4.01
3470 6018 8.293699 TGAGCTAATATCGCCAGATTCTAATA 57.706 34.615 0.00 0.00 38.26 0.98
3471 6019 8.918116 TGAGCTAATATCGCCAGATTCTAATAT 58.082 33.333 0.00 0.00 38.26 1.28
3493 6041 9.823647 AATATATGATATGCTTGGTACTACTGC 57.176 33.333 0.00 0.00 0.00 4.40
3534 6087 1.135141 TGTGTTTTCAACCAGCTGTGC 60.135 47.619 13.81 0.00 0.00 4.57
3538 6091 1.473258 TTTCAACCAGCTGTGCAAGT 58.527 45.000 13.81 0.00 0.00 3.16
3544 6097 1.691976 ACCAGCTGTGCAAGTGTACTA 59.308 47.619 13.81 0.00 0.00 1.82
3552 6105 5.694910 GCTGTGCAAGTGTACTAGTTCTTTA 59.305 40.000 0.00 0.00 0.00 1.85
3579 6132 5.924786 CAGAACATGCTTTGTGTAGAGAAG 58.075 41.667 0.00 0.00 38.99 2.85
3580 6133 4.999950 AGAACATGCTTTGTGTAGAGAAGG 59.000 41.667 0.00 0.00 38.99 3.46
3721 6284 5.746307 AGCATGCTATATGTGTGAAACTG 57.254 39.130 21.21 0.00 38.04 3.16
3737 6300 5.350365 GTGAAACTGTTTTTCTTTTCCCCAC 59.650 40.000 7.28 3.39 0.00 4.61
3743 6306 1.703411 TTTCTTTTCCCCACCTGCTG 58.297 50.000 0.00 0.00 0.00 4.41
3750 6313 1.531365 CCCCACCTGCTGCTTCAAA 60.531 57.895 0.00 0.00 0.00 2.69
3817 6386 1.852626 CCCCAACTCTCCCCTTGGT 60.853 63.158 0.00 0.00 35.99 3.67
3842 6411 3.331478 CTGGAAGCATGAGTTGTCTCT 57.669 47.619 0.00 0.00 40.98 3.10
3843 6412 3.001414 CTGGAAGCATGAGTTGTCTCTG 58.999 50.000 0.00 0.00 40.98 3.35
3853 6422 3.323979 TGAGTTGTCTCTGGGGAAGTAAC 59.676 47.826 0.00 0.00 40.98 2.50
3854 6423 3.579151 GAGTTGTCTCTGGGGAAGTAACT 59.421 47.826 0.00 0.00 37.68 2.24
3869 6438 3.487372 AGTAACTTTTCTGGTTCAGGCC 58.513 45.455 0.00 0.00 31.51 5.19
3870 6439 2.452600 AACTTTTCTGGTTCAGGCCA 57.547 45.000 5.01 0.00 36.97 5.36
3872 6441 0.961753 CTTTTCTGGTTCAGGCCACC 59.038 55.000 5.01 4.25 34.36 4.61
3874 6443 1.440618 TTTCTGGTTCAGGCCACCTA 58.559 50.000 5.01 0.00 35.07 3.08
3876 6445 0.178903 TCTGGTTCAGGCCACCTAGT 60.179 55.000 5.01 0.00 35.07 2.57
3879 6448 1.626825 TGGTTCAGGCCACCTAGTTAC 59.373 52.381 5.01 0.00 35.07 2.50
3894 6463 6.018425 CACCTAGTTACTGCTGCATATCAAAG 60.018 42.308 1.31 0.00 0.00 2.77
3910 6479 3.966979 TCAAAGGGCTTATCTTGCATCA 58.033 40.909 0.00 0.00 0.00 3.07
3912 6481 4.957954 TCAAAGGGCTTATCTTGCATCATT 59.042 37.500 0.00 0.00 0.00 2.57
3913 6482 6.128486 TCAAAGGGCTTATCTTGCATCATTA 58.872 36.000 0.00 0.00 0.00 1.90
3914 6483 6.039717 TCAAAGGGCTTATCTTGCATCATTAC 59.960 38.462 0.00 0.00 0.00 1.89
3915 6484 5.316158 AGGGCTTATCTTGCATCATTACT 57.684 39.130 0.00 0.00 0.00 2.24
3918 6487 5.218139 GGCTTATCTTGCATCATTACTTGC 58.782 41.667 0.00 0.00 39.33 4.01
3919 6488 5.009410 GGCTTATCTTGCATCATTACTTGCT 59.991 40.000 0.00 0.00 39.60 3.91
3920 6489 6.141462 GCTTATCTTGCATCATTACTTGCTC 58.859 40.000 0.00 0.00 39.60 4.26
3922 6491 5.752892 ATCTTGCATCATTACTTGCTCAG 57.247 39.130 0.00 0.00 39.60 3.35
3923 6492 3.376234 TCTTGCATCATTACTTGCTCAGC 59.624 43.478 0.00 0.00 39.60 4.26
3924 6493 2.713877 TGCATCATTACTTGCTCAGCA 58.286 42.857 0.00 0.00 39.60 4.41
3925 6494 2.681344 TGCATCATTACTTGCTCAGCAG 59.319 45.455 0.00 0.00 40.61 4.24
3926 6495 2.941064 GCATCATTACTTGCTCAGCAGA 59.059 45.455 0.00 0.00 40.61 4.26
3927 6496 3.376234 GCATCATTACTTGCTCAGCAGAA 59.624 43.478 0.00 0.00 40.61 3.02
3928 6497 4.496010 GCATCATTACTTGCTCAGCAGAAG 60.496 45.833 0.00 0.00 40.61 2.85
3929 6498 3.005554 TCATTACTTGCTCAGCAGAAGC 58.994 45.455 0.00 0.00 40.61 3.86
3944 6513 3.249559 GCAGAAGCTACAGTATGGAATGC 59.750 47.826 0.00 0.00 38.07 3.56
3970 6539 2.358737 GGGCAAGTCTGGTGGTCG 60.359 66.667 0.00 0.00 0.00 4.79
3975 6544 0.389948 CAAGTCTGGTGGTCGTAGCC 60.390 60.000 0.00 0.00 0.00 3.93
3984 6553 0.606604 TGGTCGTAGCCCAACTCTTC 59.393 55.000 0.00 0.00 0.00 2.87
3985 6554 0.896226 GGTCGTAGCCCAACTCTTCT 59.104 55.000 0.00 0.00 0.00 2.85
3986 6555 1.135053 GGTCGTAGCCCAACTCTTCTC 60.135 57.143 0.00 0.00 0.00 2.87
3987 6556 1.819903 GTCGTAGCCCAACTCTTCTCT 59.180 52.381 0.00 0.00 0.00 3.10
3988 6557 2.231721 GTCGTAGCCCAACTCTTCTCTT 59.768 50.000 0.00 0.00 0.00 2.85
3994 6563 2.685388 GCCCAACTCTTCTCTTTATGGC 59.315 50.000 0.00 0.00 0.00 4.40
3996 6565 3.944015 CCCAACTCTTCTCTTTATGGCAG 59.056 47.826 0.00 0.00 0.00 4.85
4031 6607 9.603298 CATGGAAATGTCATATTTATCAAGTCG 57.397 33.333 0.00 0.00 0.00 4.18
4033 6609 9.389755 TGGAAATGTCATATTTATCAAGTCGAA 57.610 29.630 0.00 0.00 0.00 3.71
4049 6625 7.208080 TCAAGTCGAATATCTAGCCCTTTTAC 58.792 38.462 0.00 0.00 0.00 2.01
4050 6626 6.099159 AGTCGAATATCTAGCCCTTTTACC 57.901 41.667 0.00 0.00 0.00 2.85
4057 6633 5.816955 ATCTAGCCCTTTTACCTCATCTC 57.183 43.478 0.00 0.00 0.00 2.75
4064 6640 1.893315 TTTACCTCATCTCCCCAGGG 58.107 55.000 0.00 0.00 0.00 4.45
4091 6667 4.077822 GCCATGCAAGGAGATAAGCTAAT 58.922 43.478 13.26 0.00 0.00 1.73
4092 6668 4.082895 GCCATGCAAGGAGATAAGCTAATG 60.083 45.833 13.26 0.00 0.00 1.90
4093 6669 4.082895 CCATGCAAGGAGATAAGCTAATGC 60.083 45.833 0.35 0.00 40.05 3.56
4094 6670 3.133691 TGCAAGGAGATAAGCTAATGCG 58.866 45.455 0.00 0.00 45.42 4.73
4095 6671 3.134458 GCAAGGAGATAAGCTAATGCGT 58.866 45.455 0.00 0.00 45.42 5.24
4096 6672 4.202212 TGCAAGGAGATAAGCTAATGCGTA 60.202 41.667 0.00 0.00 45.42 4.42
4097 6673 4.932200 GCAAGGAGATAAGCTAATGCGTAT 59.068 41.667 0.00 0.00 44.29 3.06
4098 6674 5.409826 GCAAGGAGATAAGCTAATGCGTATT 59.590 40.000 3.69 3.69 42.32 1.89
4099 6675 6.619446 GCAAGGAGATAAGCTAATGCGTATTG 60.619 42.308 9.16 0.60 42.32 1.90
4100 6676 4.932200 AGGAGATAAGCTAATGCGTATTGC 59.068 41.667 9.16 10.18 42.32 3.56
4104 6680 0.937304 AGCTAATGCGTATTGCCGTG 59.063 50.000 9.16 0.00 45.60 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 184 4.507388 GCACAACACAATACATGCAAAACT 59.493 37.500 0.00 0.00 33.27 2.66
187 188 2.033927 ACGCACAACACAATACATGCAA 59.966 40.909 0.00 0.00 33.27 4.08
189 190 2.330231 ACGCACAACACAATACATGC 57.670 45.000 0.00 0.00 0.00 4.06
198 199 4.734370 ACGGTTAATAAAAACGCACAACAC 59.266 37.500 0.00 0.00 0.00 3.32
206 207 9.977490 GAAATGTAACAACGGTTAATAAAAACG 57.023 29.630 0.00 0.00 40.95 3.60
232 233 5.366460 AGACATCAGCAAGATCACCAATAG 58.634 41.667 0.00 0.00 33.72 1.73
285 286 7.502226 TGTTCTTGCTCGGGATTTAAATCATAT 59.498 33.333 25.55 0.00 37.15 1.78
300 301 9.214953 CTTAAATTTATAGCTTGTTCTTGCTCG 57.785 33.333 0.00 0.00 40.35 5.03
333 335 6.456795 AATATTTGGAGTCCTTTTGCTAGC 57.543 37.500 11.33 8.10 0.00 3.42
367 623 8.604640 ACACAAATGCACAAAATATTTGATCA 57.395 26.923 12.34 0.00 41.81 2.92
372 628 9.762933 ACTTAGACACAAATGCACAAAATATTT 57.237 25.926 0.00 0.00 0.00 1.40
382 638 4.400884 ACACCAAACTTAGACACAAATGCA 59.599 37.500 0.00 0.00 0.00 3.96
383 639 4.932146 ACACCAAACTTAGACACAAATGC 58.068 39.130 0.00 0.00 0.00 3.56
384 640 5.977129 GGAACACCAAACTTAGACACAAATG 59.023 40.000 0.00 0.00 0.00 2.32
385 641 5.654650 TGGAACACCAAACTTAGACACAAAT 59.345 36.000 0.00 0.00 0.00 2.32
388 644 4.223556 TGGAACACCAAACTTAGACACA 57.776 40.909 0.00 0.00 0.00 3.72
409 665 3.076621 CTGAGTGTACATGTGTTGCCAT 58.923 45.455 9.11 0.00 0.00 4.40
420 676 7.382898 TGTGATAAATACAAGCTGAGTGTACA 58.617 34.615 0.00 0.00 34.41 2.90
423 679 6.467677 ACTGTGATAAATACAAGCTGAGTGT 58.532 36.000 2.51 0.00 0.00 3.55
462 719 4.726416 CACAAACATGACATGACCTAAGC 58.274 43.478 22.19 0.00 0.00 3.09
463 720 4.456911 AGCACAAACATGACATGACCTAAG 59.543 41.667 22.19 8.02 0.00 2.18
506 766 8.200792 AGATGAACTGTATGTAGAAGGCTAAAG 58.799 37.037 0.00 0.00 0.00 1.85
523 783 2.156917 TGCTGAGCCAAAGATGAACTG 58.843 47.619 0.23 0.00 0.00 3.16
541 801 9.892130 ACATCCTTATAGCTATAGGTATTTTGC 57.108 33.333 25.23 0.00 39.24 3.68
567 827 5.739070 GCGATCAATACACATAGGTCTTGGA 60.739 44.000 0.00 0.00 0.00 3.53
569 829 4.449068 GGCGATCAATACACATAGGTCTTG 59.551 45.833 0.00 0.00 0.00 3.02
573 833 3.244215 CCAGGCGATCAATACACATAGGT 60.244 47.826 0.00 0.00 0.00 3.08
577 837 2.485479 GGTCCAGGCGATCAATACACAT 60.485 50.000 0.00 0.00 0.00 3.21
581 841 2.550830 ATGGTCCAGGCGATCAATAC 57.449 50.000 0.00 0.00 34.48 1.89
589 849 3.703001 AAATATCCTATGGTCCAGGCG 57.297 47.619 0.00 0.00 32.82 5.52
614 874 6.650807 TCTTCTTGTGACTCGCTTTTGATAAT 59.349 34.615 0.00 0.00 0.00 1.28
693 953 3.005050 TGCTGGATTCTGAACTTGCTTTG 59.995 43.478 0.00 0.00 0.00 2.77
751 1011 3.604582 AGCTACTCCTTTGCAGTGATTC 58.395 45.455 0.00 0.00 0.00 2.52
759 1019 3.194968 TGGTAGTGTAGCTACTCCTTTGC 59.805 47.826 23.84 8.87 46.99 3.68
765 1025 4.673441 CACATGTGGTAGTGTAGCTACTC 58.327 47.826 23.84 20.05 46.99 2.59
769 1029 1.623311 TGCACATGTGGTAGTGTAGCT 59.377 47.619 26.55 0.00 38.02 3.32
771 1031 3.254060 GAGTGCACATGTGGTAGTGTAG 58.746 50.000 26.55 0.00 38.02 2.74
773 1033 1.270839 GGAGTGCACATGTGGTAGTGT 60.271 52.381 26.55 0.00 38.02 3.55
878 1139 1.535028 GTGCACATGTGAAACCATCGA 59.465 47.619 29.80 0.00 34.36 3.59
879 1140 1.536766 AGTGCACATGTGAAACCATCG 59.463 47.619 29.80 0.00 34.36 3.84
892 1153 1.527433 CGAGACAGAGGGAGTGCACA 61.527 60.000 21.04 0.00 0.00 4.57
893 1154 1.214062 CGAGACAGAGGGAGTGCAC 59.786 63.158 9.40 9.40 0.00 4.57
894 1155 0.539669 TTCGAGACAGAGGGAGTGCA 60.540 55.000 0.00 0.00 0.00 4.57
895 1156 0.109039 GTTCGAGACAGAGGGAGTGC 60.109 60.000 0.00 0.00 0.00 4.40
896 1157 0.528470 GGTTCGAGACAGAGGGAGTG 59.472 60.000 0.00 0.00 0.00 3.51
897 1158 0.612453 GGGTTCGAGACAGAGGGAGT 60.612 60.000 0.00 0.00 0.00 3.85
898 1159 0.323908 AGGGTTCGAGACAGAGGGAG 60.324 60.000 0.00 0.00 0.00 4.30
900 1161 1.324005 GGAGGGTTCGAGACAGAGGG 61.324 65.000 0.00 0.00 0.00 4.30
902 1163 1.203523 CTTGGAGGGTTCGAGACAGAG 59.796 57.143 0.00 0.00 0.00 3.35
903 1164 1.257743 CTTGGAGGGTTCGAGACAGA 58.742 55.000 0.00 0.00 0.00 3.41
904 1165 0.969894 ACTTGGAGGGTTCGAGACAG 59.030 55.000 0.00 0.00 0.00 3.51
966 1227 1.075600 GGAGGAGGAGGAGGAGGTG 60.076 68.421 0.00 0.00 0.00 4.00
967 1228 1.230819 AGGAGGAGGAGGAGGAGGT 60.231 63.158 0.00 0.00 0.00 3.85
1104 1367 3.733960 GACTTGGGTTTCGGCGCC 61.734 66.667 19.07 19.07 0.00 6.53
1151 1414 1.457643 TCGCCCATGTAGGAGGAGG 60.458 63.158 0.00 0.00 41.22 4.30
1152 1415 1.043116 TGTCGCCCATGTAGGAGGAG 61.043 60.000 0.00 0.00 41.22 3.69
1235 3185 3.698820 GCTTGGCCTTGGCCTTGG 61.699 66.667 28.37 18.95 0.00 3.61
1236 3186 3.698820 GGCTTGGCCTTGGCCTTG 61.699 66.667 28.37 21.17 46.69 3.61
1449 3402 1.076533 CCTTGATGTTCCCGTCGACG 61.077 60.000 30.33 30.33 39.44 5.12
1450 3403 0.245539 TCCTTGATGTTCCCGTCGAC 59.754 55.000 5.18 5.18 0.00 4.20
1451 3404 0.245539 GTCCTTGATGTTCCCGTCGA 59.754 55.000 0.00 0.00 0.00 4.20
1452 3405 0.037697 TGTCCTTGATGTTCCCGTCG 60.038 55.000 0.00 0.00 0.00 5.12
1453 3406 2.280628 GATGTCCTTGATGTTCCCGTC 58.719 52.381 0.00 0.00 0.00 4.79
1629 3587 1.909302 AGGACATCGATGTTCTTGGGT 59.091 47.619 30.04 11.26 44.08 4.51
1788 3752 1.226323 CTTCTCGTACACCTCGGCG 60.226 63.158 0.00 0.00 0.00 6.46
1812 3776 0.738762 CAGCATCCGAGTCACACAGG 60.739 60.000 0.00 0.00 0.00 4.00
2079 4426 1.257936 CACACCGTGTTCAAGAAGTCG 59.742 52.381 0.00 0.00 0.00 4.18
2094 4441 6.364165 GCAAATGTATGATATCATTGCACACC 59.636 38.462 25.47 11.60 37.76 4.16
2502 4849 3.573110 TGTCAATGCCAACATCAACATCA 59.427 39.130 0.00 0.00 34.62 3.07
2688 5035 3.375299 GCAGATACTGAACCGCATTTTCT 59.625 43.478 2.81 0.00 32.44 2.52
2765 5112 1.536766 GCAAGCCAAATTTTCCAAGCC 59.463 47.619 0.00 0.00 0.00 4.35
2853 5201 3.842820 AGGATGCGACATTGATATCGAG 58.157 45.455 0.00 0.00 40.86 4.04
3023 5371 3.119319 TCCACAACCCATATCTGGCTAA 58.881 45.455 0.00 0.00 41.64 3.09
3024 5372 2.705658 CTCCACAACCCATATCTGGCTA 59.294 50.000 0.00 0.00 41.64 3.93
3213 5574 5.072040 AGACCAAAACAAACAAACTCTGG 57.928 39.130 0.00 0.00 0.00 3.86
3381 5765 4.898268 TGGAGGTAATACCACCCAAGATA 58.102 43.478 20.65 0.94 46.88 1.98
3455 6003 8.864087 AGCATATCATATATTAGAATCTGGCGA 58.136 33.333 0.00 0.00 0.00 5.54
3470 6018 7.179160 TCAGCAGTAGTACCAAGCATATCATAT 59.821 37.037 11.19 0.00 0.00 1.78
3471 6019 6.493458 TCAGCAGTAGTACCAAGCATATCATA 59.507 38.462 11.19 0.00 0.00 2.15
3476 6024 4.278310 TCTCAGCAGTAGTACCAAGCATA 58.722 43.478 11.19 0.68 0.00 3.14
3493 6041 2.093973 ACCTGTAATGGCTCGTTCTCAG 60.094 50.000 0.00 0.00 0.00 3.35
3534 6087 8.534333 TCTGCAATAAAGAACTAGTACACTTG 57.466 34.615 0.00 0.00 0.00 3.16
3567 6120 9.739276 ACATATTGATTTTCCTTCTCTACACAA 57.261 29.630 0.00 0.00 0.00 3.33
3616 6171 6.528537 AATTCAGCAGCCATAACACATAAA 57.471 33.333 0.00 0.00 0.00 1.40
3671 6226 8.791327 ACAACTCAATTTCCTCAAAACAAAAT 57.209 26.923 0.00 0.00 0.00 1.82
3687 6250 8.347771 CACATATAGCATGCTAAACAACTCAAT 58.652 33.333 30.06 13.73 31.73 2.57
3690 6253 7.011389 TCACACATATAGCATGCTAAACAACTC 59.989 37.037 30.06 0.00 31.73 3.01
3721 6284 2.434336 AGCAGGTGGGGAAAAGAAAAAC 59.566 45.455 0.00 0.00 0.00 2.43
3731 6294 2.005606 TTTGAAGCAGCAGGTGGGGA 62.006 55.000 0.86 0.00 0.00 4.81
3737 6300 0.386476 TTGCACTTTGAAGCAGCAGG 59.614 50.000 10.13 0.00 42.39 4.85
3743 6306 2.159254 TCCACACTTTGCACTTTGAAGC 60.159 45.455 0.00 0.00 0.00 3.86
3750 6313 2.949177 TGGTATCCACACTTTGCACT 57.051 45.000 0.00 0.00 0.00 4.40
3770 6333 4.962122 GCAAGGCGCACACACGTG 62.962 66.667 15.48 15.48 46.56 4.49
3773 6336 2.353839 CAAGCAAGGCGCACACAC 60.354 61.111 10.83 0.00 46.13 3.82
3774 6337 4.268939 GCAAGCAAGGCGCACACA 62.269 61.111 10.83 0.00 46.13 3.72
3775 6338 4.268939 TGCAAGCAAGGCGCACAC 62.269 61.111 10.83 0.00 46.13 3.82
3776 6339 3.968568 CTGCAAGCAAGGCGCACA 61.969 61.111 10.83 0.00 46.13 4.57
3777 6340 4.712425 CCTGCAAGCAAGGCGCAC 62.712 66.667 10.83 0.00 46.13 5.34
3778 6341 3.841137 TACCTGCAAGCAAGGCGCA 62.841 57.895 10.83 0.00 46.13 6.09
3780 6343 0.387239 GTTTACCTGCAAGCAAGGCG 60.387 55.000 9.47 0.00 0.00 5.52
3782 6345 0.603065 GGGTTTACCTGCAAGCAAGG 59.397 55.000 0.00 2.85 35.85 3.61
3783 6346 0.603065 GGGGTTTACCTGCAAGCAAG 59.397 55.000 0.00 0.00 40.03 4.01
3785 6348 0.105964 TTGGGGTTTACCTGCAAGCA 60.106 50.000 0.00 0.00 40.03 3.91
3786 6349 0.317160 GTTGGGGTTTACCTGCAAGC 59.683 55.000 0.00 0.00 40.03 4.01
3817 6386 0.251033 AACTCATGCTTCCAGCTGCA 60.251 50.000 8.66 3.00 42.97 4.41
3836 6405 4.658901 AGAAAAGTTACTTCCCCAGAGACA 59.341 41.667 0.00 0.00 0.00 3.41
3842 6411 4.079672 TGAACCAGAAAAGTTACTTCCCCA 60.080 41.667 0.00 0.00 0.00 4.96
3843 6412 4.466827 TGAACCAGAAAAGTTACTTCCCC 58.533 43.478 0.00 0.00 0.00 4.81
3853 6422 0.961753 GGTGGCCTGAACCAGAAAAG 59.038 55.000 3.32 0.00 41.46 2.27
3854 6423 0.555769 AGGTGGCCTGAACCAGAAAA 59.444 50.000 12.97 0.00 41.46 2.29
3869 6438 4.948847 TGATATGCAGCAGTAACTAGGTG 58.051 43.478 0.00 0.00 36.39 4.00
3870 6439 5.614324 TTGATATGCAGCAGTAACTAGGT 57.386 39.130 0.00 0.00 0.00 3.08
3872 6441 5.468072 CCCTTTGATATGCAGCAGTAACTAG 59.532 44.000 0.00 0.00 0.00 2.57
3874 6443 4.202441 CCCTTTGATATGCAGCAGTAACT 58.798 43.478 0.00 0.00 0.00 2.24
3876 6445 2.951642 GCCCTTTGATATGCAGCAGTAA 59.048 45.455 0.00 0.00 0.00 2.24
3879 6448 1.688772 AGCCCTTTGATATGCAGCAG 58.311 50.000 0.00 0.00 0.00 4.24
3894 6463 5.766222 CAAGTAATGATGCAAGATAAGCCC 58.234 41.667 0.00 0.00 0.00 5.19
3922 6491 3.249559 GCATTCCATACTGTAGCTTCTGC 59.750 47.826 0.00 0.00 40.05 4.26
3923 6492 3.812053 GGCATTCCATACTGTAGCTTCTG 59.188 47.826 0.00 0.00 0.00 3.02
3924 6493 3.181450 GGGCATTCCATACTGTAGCTTCT 60.181 47.826 0.00 0.00 35.00 2.85
3925 6494 3.142174 GGGCATTCCATACTGTAGCTTC 58.858 50.000 0.00 0.00 35.00 3.86
3926 6495 2.509548 TGGGCATTCCATACTGTAGCTT 59.490 45.455 0.00 0.00 41.46 3.74
3927 6496 2.126882 TGGGCATTCCATACTGTAGCT 58.873 47.619 0.00 0.00 41.46 3.32
3928 6497 2.638480 TGGGCATTCCATACTGTAGC 57.362 50.000 0.00 0.00 41.46 3.58
3963 6532 1.079336 GAGTTGGGCTACGACCACC 60.079 63.158 0.00 0.00 42.46 4.61
3970 6539 5.119694 CCATAAAGAGAAGAGTTGGGCTAC 58.880 45.833 0.00 0.00 0.00 3.58
3975 6544 4.394300 CACTGCCATAAAGAGAAGAGTTGG 59.606 45.833 0.00 0.00 0.00 3.77
3984 6553 2.421424 GCTGGTTCACTGCCATAAAGAG 59.579 50.000 0.00 0.00 38.01 2.85
3985 6554 2.224744 TGCTGGTTCACTGCCATAAAGA 60.225 45.455 0.00 0.00 42.74 2.52
3986 6555 2.161855 TGCTGGTTCACTGCCATAAAG 58.838 47.619 0.00 0.00 42.74 1.85
3987 6556 2.284754 TGCTGGTTCACTGCCATAAA 57.715 45.000 0.00 0.00 42.74 1.40
3988 6557 2.093890 CATGCTGGTTCACTGCCATAA 58.906 47.619 0.00 0.00 42.74 1.90
3994 6563 2.559668 ACATTTCCATGCTGGTTCACTG 59.440 45.455 2.68 0.00 39.03 3.66
3996 6565 2.557924 TGACATTTCCATGCTGGTTCAC 59.442 45.455 2.68 0.00 39.03 3.18
4025 6601 6.424207 GGTAAAAGGGCTAGATATTCGACTTG 59.576 42.308 0.00 0.00 0.00 3.16
4027 6603 5.839606 AGGTAAAAGGGCTAGATATTCGACT 59.160 40.000 0.00 0.00 0.00 4.18
4031 6607 7.912719 AGATGAGGTAAAAGGGCTAGATATTC 58.087 38.462 0.00 0.00 0.00 1.75
4033 6609 6.442244 GGAGATGAGGTAAAAGGGCTAGATAT 59.558 42.308 0.00 0.00 0.00 1.63
4034 6610 5.780793 GGAGATGAGGTAAAAGGGCTAGATA 59.219 44.000 0.00 0.00 0.00 1.98
4049 6625 3.174265 GGCCCTGGGGAGATGAGG 61.174 72.222 16.03 0.00 37.50 3.86
4050 6626 1.773391 ATGGCCCTGGGGAGATGAG 60.773 63.158 16.03 0.00 37.50 2.90
4076 6652 5.409826 GCAATACGCATTAGCTTATCTCCTT 59.590 40.000 0.00 0.00 41.79 3.36
4079 6655 4.201628 CGGCAATACGCATTAGCTTATCTC 60.202 45.833 0.00 0.00 45.17 2.75
4085 6661 0.937304 CACGGCAATACGCATTAGCT 59.063 50.000 0.00 0.00 45.17 3.32
4091 6667 1.301795 TGGAACACGGCAATACGCA 60.302 52.632 0.00 0.00 45.17 5.24
4092 6668 3.568686 TGGAACACGGCAATACGC 58.431 55.556 0.00 0.00 41.28 4.42


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

AutoCloner maintained by Alex Coulton.