Multiple sequence alignment - TraesCS4B01G157400

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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 TraesCS4B01G157400 chr4B 100.000 5693 0 0 1 5693 296299182 296293490 0.000000e+00 10514.0
1 TraesCS4B01G157400 chr4B 76.206 601 90 30 3716 4269 34729730 34729136 9.400000e-68 268.0
2 TraesCS4B01G157400 chr4B 72.032 497 108 19 3753 4221 139630915 139630422 1.000000e-22 119.0
3 TraesCS4B01G157400 chr4A 92.374 3252 164 39 4 3223 346058926 346062125 0.000000e+00 4554.0
4 TraesCS4B01G157400 chr4A 90.033 913 54 6 3682 4583 346063084 346063970 0.000000e+00 1147.0
5 TraesCS4B01G157400 chr4A 91.569 510 19 8 4591 5083 346064103 346064605 0.000000e+00 682.0
6 TraesCS4B01G157400 chr4A 95.779 308 8 5 3219 3526 346062254 346062556 5.120000e-135 492.0
7 TraesCS4B01G157400 chr4A 78.707 634 93 23 3673 4266 578216575 578217206 8.950000e-103 385.0
8 TraesCS4B01G157400 chr4A 79.123 570 84 18 3727 4266 579425779 579426343 1.510000e-95 361.0
9 TraesCS4B01G157400 chr4A 79.392 296 39 15 3897 4172 24941407 24941700 7.530000e-44 189.0
10 TraesCS4B01G157400 chr4A 80.282 142 21 4 5538 5674 122255190 122255329 3.630000e-17 100.0
11 TraesCS4B01G157400 chr4D 98.141 2152 32 3 903 3054 204734335 204732192 0.000000e+00 3746.0
12 TraesCS4B01G157400 chr4D 93.004 1558 53 13 3639 5142 204731662 204730107 0.000000e+00 2222.0
13 TraesCS4B01G157400 chr4D 88.262 886 69 17 44 910 204855556 204854687 0.000000e+00 1027.0
14 TraesCS4B01G157400 chr4D 92.632 475 20 9 5220 5683 204724279 204723809 0.000000e+00 669.0
15 TraesCS4B01G157400 chr4D 95.935 246 10 0 3334 3579 204731907 204731662 3.200000e-107 399.0
16 TraesCS4B01G157400 chr4D 79.022 634 92 25 3673 4266 25211276 25211908 4.130000e-106 396.0
17 TraesCS4B01G157400 chr4D 96.651 209 7 0 3053 3261 204732110 204731902 1.170000e-91 348.0
18 TraesCS4B01G157400 chr4D 96.000 50 2 0 315 364 109367411 109367460 1.310000e-11 82.4
19 TraesCS4B01G157400 chr4D 100.000 38 0 0 5141 5178 204724816 204724779 2.850000e-08 71.3
20 TraesCS4B01G157400 chr2B 79.708 616 87 20 3681 4266 87357341 87357948 1.480000e-110 411.0
21 TraesCS4B01G157400 chr2B 86.093 151 9 7 4122 4260 397053632 397053782 9.880000e-33 152.0
22 TraesCS4B01G157400 chr3D 78.806 670 96 28 3630 4269 416142092 416141439 5.310000e-110 409.0
23 TraesCS4B01G157400 chr3D 77.445 634 94 21 3673 4272 348146080 348146698 3.290000e-87 333.0
24 TraesCS4B01G157400 chr3D 79.389 393 47 22 3788 4151 448291100 448291487 4.410000e-61 246.0
25 TraesCS4B01G157400 chr2D 79.158 499 68 24 3812 4281 55160166 55160657 4.280000e-81 313.0
26 TraesCS4B01G157400 chr3A 82.410 307 28 14 3984 4266 272796320 272796624 1.580000e-60 244.0
27 TraesCS4B01G157400 chr6B 77.839 361 54 16 3745 4086 198404579 198404932 3.480000e-47 200.0
28 TraesCS4B01G157400 chr2A 83.598 189 17 9 4086 4260 433394860 433395048 1.270000e-36 165.0
29 TraesCS4B01G157400 chr5D 80.729 192 34 3 3897 4086 396416165 396416355 4.600000e-31 147.0
30 TraesCS4B01G157400 chr5A 86.719 128 17 0 5216 5343 702190758 702190885 5.950000e-30 143.0
31 TraesCS4B01G157400 chr5A 94.286 35 2 0 5552 5586 593099653 593099687 3.000000e-03 54.7
32 TraesCS4B01G157400 chr5B 73.409 440 85 26 329 747 73469876 73469448 9.950000e-28 135.0
33 TraesCS4B01G157400 chr1B 79.720 143 21 6 5538 5674 432461863 432461723 4.700000e-16 97.1
34 TraesCS4B01G157400 chr7D 76.033 121 27 2 5550 5668 38640856 38640976 1.710000e-05 62.1


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 TraesCS4B01G157400 chr4B 296293490 296299182 5692 True 10514.00 10514 100.00000 1 5693 1 chr4B.!!$R3 5692
1 TraesCS4B01G157400 chr4B 34729136 34729730 594 True 268.00 268 76.20600 3716 4269 1 chr4B.!!$R1 553
2 TraesCS4B01G157400 chr4A 346058926 346064605 5679 False 1718.75 4554 92.43875 4 5083 4 chr4A.!!$F5 5079
3 TraesCS4B01G157400 chr4A 578216575 578217206 631 False 385.00 385 78.70700 3673 4266 1 chr4A.!!$F3 593
4 TraesCS4B01G157400 chr4A 579425779 579426343 564 False 361.00 361 79.12300 3727 4266 1 chr4A.!!$F4 539
5 TraesCS4B01G157400 chr4D 204730107 204734335 4228 True 1678.75 3746 95.93275 903 5142 4 chr4D.!!$R3 4239
6 TraesCS4B01G157400 chr4D 204854687 204855556 869 True 1027.00 1027 88.26200 44 910 1 chr4D.!!$R1 866
7 TraesCS4B01G157400 chr4D 25211276 25211908 632 False 396.00 396 79.02200 3673 4266 1 chr4D.!!$F1 593
8 TraesCS4B01G157400 chr4D 204723809 204724816 1007 True 370.15 669 96.31600 5141 5683 2 chr4D.!!$R2 542
9 TraesCS4B01G157400 chr2B 87357341 87357948 607 False 411.00 411 79.70800 3681 4266 1 chr2B.!!$F1 585
10 TraesCS4B01G157400 chr3D 416141439 416142092 653 True 409.00 409 78.80600 3630 4269 1 chr3D.!!$R1 639
11 TraesCS4B01G157400 chr3D 348146080 348146698 618 False 333.00 333 77.44500 3673 4272 1 chr3D.!!$F1 599


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
828 876 0.035439 AGTATTTGTGTCCCGCCTGG 60.035 55.000 0.00 0.0 0.00 4.45 F
829 877 0.035820 GTATTTGTGTCCCGCCTGGA 60.036 55.000 0.00 0.0 42.41 3.86 F
871 931 0.608035 TTAAAGTCTGCAAGCGGGGG 60.608 55.000 0.37 0.0 0.00 5.40 F
1638 1700 1.514443 GCAGAGACAGTACGCCGAC 60.514 63.158 0.00 0.0 0.00 4.79 F
3608 4009 0.108992 TGGACGTGTCTGCGGATAAC 60.109 55.000 0.00 0.0 35.98 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1904 0.032515 TGATCGCTGAGACCCCCTTA 60.033 55.0 0.0 0.0 0.00 2.69 R
1869 1931 1.056660 ATAGATGGCCGTACTTGGGG 58.943 55.0 0.0 0.0 0.00 4.96 R
1878 1940 1.224075 CAGACAGCAATAGATGGCCG 58.776 55.0 0.0 0.0 41.11 6.13 R
3627 4028 0.846427 AGAGTTGGATGGCTCCCCAA 60.846 55.0 0.0 0.0 46.14 4.12 R
5355 6699 0.038310 GGCAAGCCCTGTAGTTTCCT 59.962 55.0 0.0 0.0 0.00 3.36 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.644966 TGTTTTCAACTGGGACACTCT 57.355 42.857 0.00 0.00 0.00 3.24
21 22 3.278574 TGTTTTCAACTGGGACACTCTG 58.721 45.455 0.00 0.00 0.00 3.35
22 23 3.279434 GTTTTCAACTGGGACACTCTGT 58.721 45.455 0.00 0.00 0.00 3.41
23 24 2.910688 TTCAACTGGGACACTCTGTC 57.089 50.000 0.00 0.00 46.23 3.51
73 75 0.322816 AACCGCTGGCATCTGAACAT 60.323 50.000 0.00 0.00 0.00 2.71
96 98 4.284550 GGGTTCAGGTGCCAGCCA 62.285 66.667 0.00 0.00 0.00 4.75
155 157 0.681564 ACCGACGAGCTCATCTCCTT 60.682 55.000 15.40 0.00 38.62 3.36
219 221 1.189524 CCGGGACACCTAGTTCACCA 61.190 60.000 0.00 0.00 33.28 4.17
226 228 0.038526 ACCTAGTTCACCAACGAGCG 60.039 55.000 0.00 0.00 37.61 5.03
227 229 0.242825 CCTAGTTCACCAACGAGCGA 59.757 55.000 0.00 0.00 37.61 4.93
238 240 4.103103 CGAGCGAGACCAGCGACA 62.103 66.667 0.00 0.00 40.04 4.35
298 300 0.616111 GAGCTGGTGAAGGAGGAGGA 60.616 60.000 0.00 0.00 0.00 3.71
299 301 0.617249 AGCTGGTGAAGGAGGAGGAG 60.617 60.000 0.00 0.00 0.00 3.69
306 308 0.930726 GAAGGAGGAGGAGGAGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
313 315 0.634465 GAGGAGGAGGAGAAGGAGGT 59.366 60.000 0.00 0.00 0.00 3.85
420 422 1.022735 CAGAGTATAGGTCGCCGTGT 58.977 55.000 0.00 0.00 0.00 4.49
481 483 2.261671 GCACTCGTGGTCGTGGAT 59.738 61.111 0.00 0.00 38.33 3.41
509 511 3.345808 CCGTGCACGTCCAAGTGG 61.346 66.667 34.81 15.31 42.09 4.00
538 540 1.276415 GAGCTGAAGCAACTAGAGCG 58.724 55.000 4.90 0.00 45.16 5.03
582 590 2.050351 ACGAGCCGACGACAGTTG 60.050 61.111 0.00 0.00 37.03 3.16
615 653 1.134901 CTCTTCGTCGACCTCACCG 59.865 63.158 10.58 0.00 0.00 4.94
616 654 1.296755 CTCTTCGTCGACCTCACCGA 61.297 60.000 10.58 0.00 0.00 4.69
620 658 2.479650 GTCGACCTCACCGACGAG 59.520 66.667 3.51 0.00 45.23 4.18
621 659 2.031516 GTCGACCTCACCGACGAGA 61.032 63.158 3.51 0.00 45.23 4.04
622 660 1.301953 TCGACCTCACCGACGAGAA 60.302 57.895 0.00 0.00 34.79 2.87
623 661 0.886043 TCGACCTCACCGACGAGAAA 60.886 55.000 0.00 0.00 34.79 2.52
624 662 0.454620 CGACCTCACCGACGAGAAAG 60.455 60.000 0.00 0.00 34.79 2.62
625 663 0.879765 GACCTCACCGACGAGAAAGA 59.120 55.000 0.00 0.00 34.79 2.52
626 664 0.882474 ACCTCACCGACGAGAAAGAG 59.118 55.000 0.00 0.00 34.79 2.85
627 665 0.171455 CCTCACCGACGAGAAAGAGG 59.829 60.000 0.00 1.66 36.98 3.69
628 666 1.166129 CTCACCGACGAGAAAGAGGA 58.834 55.000 0.00 0.00 34.79 3.71
629 667 0.879765 TCACCGACGAGAAAGAGGAC 59.120 55.000 0.00 0.00 0.00 3.85
630 668 0.109226 CACCGACGAGAAAGAGGACC 60.109 60.000 0.00 0.00 0.00 4.46
631 669 0.538977 ACCGACGAGAAAGAGGACCA 60.539 55.000 0.00 0.00 0.00 4.02
632 670 0.109226 CCGACGAGAAAGAGGACCAC 60.109 60.000 0.00 0.00 0.00 4.16
633 671 0.109226 CGACGAGAAAGAGGACCACC 60.109 60.000 0.00 0.00 0.00 4.61
653 694 7.565680 ACCACCAGATCTAGGTTTTACTTATG 58.434 38.462 12.50 1.75 37.23 1.90
654 695 7.182206 ACCACCAGATCTAGGTTTTACTTATGT 59.818 37.037 12.50 0.00 37.23 2.29
655 696 8.047310 CCACCAGATCTAGGTTTTACTTATGTT 58.953 37.037 12.50 0.00 37.23 2.71
656 697 9.449719 CACCAGATCTAGGTTTTACTTATGTTT 57.550 33.333 12.50 0.00 37.23 2.83
696 737 8.637281 TTAATATATGAACAGACTTTTCGCGA 57.363 30.769 3.71 3.71 0.00 5.87
697 738 4.842139 ATATGAACAGACTTTTCGCGAC 57.158 40.909 9.15 0.00 0.00 5.19
799 847 7.933577 AGAAAAACATTGATCGCATCTATAGGA 59.066 33.333 0.00 0.00 0.00 2.94
812 860 4.406648 TCTATAGGACGACGGACAAGTA 57.593 45.455 0.00 0.00 0.00 2.24
813 861 4.965814 TCTATAGGACGACGGACAAGTAT 58.034 43.478 0.00 0.00 0.00 2.12
814 862 5.371526 TCTATAGGACGACGGACAAGTATT 58.628 41.667 0.00 0.00 0.00 1.89
815 863 4.996788 ATAGGACGACGGACAAGTATTT 57.003 40.909 0.00 0.00 0.00 1.40
816 864 2.955614 AGGACGACGGACAAGTATTTG 58.044 47.619 0.00 0.00 40.24 2.32
826 874 1.073284 ACAAGTATTTGTGTCCCGCCT 59.927 47.619 2.38 0.00 45.54 5.52
828 876 0.035439 AGTATTTGTGTCCCGCCTGG 60.035 55.000 0.00 0.00 0.00 4.45
829 877 0.035820 GTATTTGTGTCCCGCCTGGA 60.036 55.000 0.00 0.00 42.41 3.86
849 909 2.590092 GGCCCGTTGGAGTAGCAT 59.410 61.111 0.00 0.00 0.00 3.79
869 929 4.601019 CATAATTAAAGTCTGCAAGCGGG 58.399 43.478 0.37 0.00 0.00 6.13
870 930 1.463674 ATTAAAGTCTGCAAGCGGGG 58.536 50.000 0.37 0.00 0.00 5.73
871 931 0.608035 TTAAAGTCTGCAAGCGGGGG 60.608 55.000 0.37 0.00 0.00 5.40
872 932 1.774894 TAAAGTCTGCAAGCGGGGGT 61.775 55.000 0.37 0.00 0.00 4.95
886 946 2.793288 GGGGGTCCGTCTTTTCATTA 57.207 50.000 0.00 0.00 0.00 1.90
891 951 5.407502 GGGGTCCGTCTTTTCATTATTTTG 58.592 41.667 0.00 0.00 0.00 2.44
953 1015 1.841450 CGGCCTCGTAGACAAATCTC 58.159 55.000 0.00 0.00 36.29 2.75
1638 1700 1.514443 GCAGAGACAGTACGCCGAC 60.514 63.158 0.00 0.00 0.00 4.79
1790 1852 3.134127 GGATGCCAAGGCGACCAC 61.134 66.667 17.30 3.75 45.51 4.16
1869 1931 2.869192 GGTCTCAGCGATCAGATTTTCC 59.131 50.000 0.00 0.00 0.00 3.13
1878 1940 3.877508 CGATCAGATTTTCCCCCAAGTAC 59.122 47.826 0.00 0.00 0.00 2.73
2490 2552 3.584733 AAGAAGAAGAGGTTTGCAGGT 57.415 42.857 0.00 0.00 0.00 4.00
2745 2807 9.774742 GACAAGATAAACATATGAAAACACCTC 57.225 33.333 10.38 0.00 0.00 3.85
2807 2869 5.678921 GCACCATTGCTGTTTAAATTGTTC 58.321 37.500 0.00 0.00 46.17 3.18
2871 2933 9.846248 GATTTAGATTGTGCAGTATGTCTTTTT 57.154 29.630 0.00 0.00 39.31 1.94
2958 3020 5.880887 GCTAGAAGGGTAGTTTAGTTTGCAT 59.119 40.000 0.00 0.00 0.00 3.96
3019 3081 6.324819 CACACAAACTTGATTATGATGTCCC 58.675 40.000 0.00 0.00 0.00 4.46
3174 3319 4.085357 TGTTACTGATTGTGTTGGCTCT 57.915 40.909 0.00 0.00 0.00 4.09
3182 3327 0.682532 TGTGTTGGCTCTTTGGTGCA 60.683 50.000 0.00 0.00 34.07 4.57
3267 3545 1.610522 CCTGGACCACTGCTCTTTTTG 59.389 52.381 0.00 0.00 0.00 2.44
3272 3550 3.003793 GGACCACTGCTCTTTTTGTCTTC 59.996 47.826 0.00 0.00 0.00 2.87
3273 3551 2.952310 ACCACTGCTCTTTTTGTCTTCC 59.048 45.455 0.00 0.00 0.00 3.46
3274 3552 2.951642 CCACTGCTCTTTTTGTCTTCCA 59.048 45.455 0.00 0.00 0.00 3.53
3275 3553 3.571401 CCACTGCTCTTTTTGTCTTCCAT 59.429 43.478 0.00 0.00 0.00 3.41
3276 3554 4.320788 CCACTGCTCTTTTTGTCTTCCATC 60.321 45.833 0.00 0.00 0.00 3.51
3400 3678 2.133553 CATCTTCTACATGCCGCTGAG 58.866 52.381 0.00 0.00 0.00 3.35
3458 3736 6.308766 CCCATTCAAAAGAACTCGCAAATTAG 59.691 38.462 0.00 0.00 0.00 1.73
3573 3974 2.288152 CCATCAAAACGGACACCCAAAG 60.288 50.000 0.00 0.00 0.00 2.77
3593 3994 1.507141 CGTTTGTGGGCAGTCTGGAC 61.507 60.000 1.14 0.00 0.00 4.02
3608 4009 0.108992 TGGACGTGTCTGCGGATAAC 60.109 55.000 0.00 0.00 35.98 1.89
3611 4012 0.885879 ACGTGTCTGCGGATAACAGA 59.114 50.000 0.00 0.00 41.78 3.41
3612 4013 1.476891 ACGTGTCTGCGGATAACAGAT 59.523 47.619 0.00 0.00 45.40 2.90
3613 4014 2.686405 ACGTGTCTGCGGATAACAGATA 59.314 45.455 0.00 0.00 45.40 1.98
3614 4015 3.243101 ACGTGTCTGCGGATAACAGATAG 60.243 47.826 0.00 0.00 45.40 2.08
3615 4016 3.643763 GTGTCTGCGGATAACAGATAGG 58.356 50.000 0.00 0.00 45.40 2.57
3616 4017 2.628178 TGTCTGCGGATAACAGATAGGG 59.372 50.000 0.00 0.00 45.40 3.53
3617 4018 2.028930 GTCTGCGGATAACAGATAGGGG 60.029 54.545 0.00 0.00 45.40 4.79
3618 4019 1.276421 CTGCGGATAACAGATAGGGGG 59.724 57.143 0.00 0.00 37.32 5.40
3619 4020 1.132977 TGCGGATAACAGATAGGGGGA 60.133 52.381 0.00 0.00 0.00 4.81
3620 4021 1.550976 GCGGATAACAGATAGGGGGAG 59.449 57.143 0.00 0.00 0.00 4.30
3621 4022 2.180276 CGGATAACAGATAGGGGGAGG 58.820 57.143 0.00 0.00 0.00 4.30
3622 4023 2.552367 GGATAACAGATAGGGGGAGGG 58.448 57.143 0.00 0.00 0.00 4.30
3623 4024 2.552367 GATAACAGATAGGGGGAGGGG 58.448 57.143 0.00 0.00 0.00 4.79
3624 4025 1.336347 TAACAGATAGGGGGAGGGGT 58.664 55.000 0.00 0.00 0.00 4.95
3625 4026 0.327576 AACAGATAGGGGGAGGGGTG 60.328 60.000 0.00 0.00 0.00 4.61
3626 4027 1.462238 CAGATAGGGGGAGGGGTGG 60.462 68.421 0.00 0.00 0.00 4.61
3627 4028 1.952766 AGATAGGGGGAGGGGTGGT 60.953 63.158 0.00 0.00 0.00 4.16
3628 4029 1.005690 GATAGGGGGAGGGGTGGTT 59.994 63.158 0.00 0.00 0.00 3.67
3629 4030 1.308746 ATAGGGGGAGGGGTGGTTG 60.309 63.158 0.00 0.00 0.00 3.77
3630 4031 2.876033 ATAGGGGGAGGGGTGGTTGG 62.876 65.000 0.00 0.00 0.00 3.77
3634 4035 3.339093 GGAGGGGTGGTTGGGGAG 61.339 72.222 0.00 0.00 0.00 4.30
3651 4052 3.305398 GGAGCCATCCAACTCTATACG 57.695 52.381 0.00 0.00 45.87 3.06
3671 4072 1.080569 CAAATGCCCGCACCTGTTC 60.081 57.895 0.00 0.00 0.00 3.18
4063 4746 0.524414 TGCATGATCACACAAGCTGC 59.476 50.000 0.00 2.51 0.00 5.25
4128 4826 2.481289 AAACAGGCTTAGAGCACTCC 57.519 50.000 2.04 0.00 44.75 3.85
4131 4829 1.699634 ACAGGCTTAGAGCACTCCAAA 59.300 47.619 2.04 0.00 44.75 3.28
4132 4830 2.307098 ACAGGCTTAGAGCACTCCAAAT 59.693 45.455 2.04 0.00 44.75 2.32
4133 4831 2.681848 CAGGCTTAGAGCACTCCAAATG 59.318 50.000 2.04 0.00 44.75 2.32
4134 4832 1.403323 GGCTTAGAGCACTCCAAATGC 59.597 52.381 2.04 0.00 44.75 3.56
4153 4853 2.032620 GCCCTCGACATCCTTTCTAGA 58.967 52.381 0.00 0.00 0.00 2.43
4350 5079 3.996921 AGATTCTCATGTCAACCTGCT 57.003 42.857 0.00 0.00 0.00 4.24
4394 5123 9.423061 GTTTTCCTGTAAAATTGCTCATATGTT 57.577 29.630 1.90 0.00 39.22 2.71
4444 5173 7.462109 TTGTTGAGTTCATTACATTTGCAAC 57.538 32.000 0.00 0.00 35.10 4.17
4491 5220 8.455598 TTTGTTCTTAAGTTGTGTTAAAGTGC 57.544 30.769 1.63 0.00 0.00 4.40
4492 5221 6.557110 TGTTCTTAAGTTGTGTTAAAGTGCC 58.443 36.000 1.63 0.00 0.00 5.01
4504 5246 2.674796 AAAGTGCCTATCGTGGAGAC 57.325 50.000 0.00 0.00 0.00 3.36
4585 5327 8.387354 CCGAATAACTATATGCATATTTTCGCA 58.613 33.333 23.71 4.58 43.45 5.10
4659 5526 6.930731 ACAATTTTCTTTACTTGTGGTGTGT 58.069 32.000 0.00 0.00 31.00 3.72
4679 5546 8.349983 GGTGTGTCATTAACTCTTTTGTACAAT 58.650 33.333 9.56 0.00 0.00 2.71
4883 5754 4.713824 TCCAACTACCGTCTAGTTCATG 57.286 45.455 0.81 0.00 35.76 3.07
4884 5755 3.119245 TCCAACTACCGTCTAGTTCATGC 60.119 47.826 0.81 0.00 35.76 4.06
4931 5816 5.486526 TGCACCATTCAGTTTTTCAACTTT 58.513 33.333 0.00 0.00 40.66 2.66
4954 5839 4.974399 ACTTCTAGGACTTTGGTTTCAGG 58.026 43.478 0.00 0.00 0.00 3.86
4959 5844 6.192044 TCTAGGACTTTGGTTTCAGGTTTTT 58.808 36.000 0.00 0.00 0.00 1.94
4960 5845 5.339008 AGGACTTTGGTTTCAGGTTTTTC 57.661 39.130 0.00 0.00 0.00 2.29
4962 5847 5.483937 AGGACTTTGGTTTCAGGTTTTTCTT 59.516 36.000 0.00 0.00 0.00 2.52
4963 5848 6.013725 AGGACTTTGGTTTCAGGTTTTTCTTT 60.014 34.615 0.00 0.00 0.00 2.52
5104 5989 3.802685 ACTATTTGATTCTTCGGCTACGC 59.197 43.478 0.00 0.00 40.69 4.42
5132 6017 0.523519 CTCCCTGCGCTTTCCTTTTC 59.476 55.000 9.73 0.00 0.00 2.29
5178 6063 4.868171 GTCAAACTTCCCAACTTTCCAAAC 59.132 41.667 0.00 0.00 0.00 2.93
5179 6064 4.528596 TCAAACTTCCCAACTTTCCAAACA 59.471 37.500 0.00 0.00 0.00 2.83
5181 6066 3.708451 ACTTCCCAACTTTCCAAACACT 58.292 40.909 0.00 0.00 0.00 3.55
5182 6067 4.093743 ACTTCCCAACTTTCCAAACACTT 58.906 39.130 0.00 0.00 0.00 3.16
5183 6068 4.159693 ACTTCCCAACTTTCCAAACACTTC 59.840 41.667 0.00 0.00 0.00 3.01
5184 6069 3.702792 TCCCAACTTTCCAAACACTTCA 58.297 40.909 0.00 0.00 0.00 3.02
5212 6130 4.022589 ACAGTCTTTGATGCATGACTTTGG 60.023 41.667 13.22 6.84 37.64 3.28
5214 6132 3.057033 GTCTTTGATGCATGACTTTGGCT 60.057 43.478 2.46 0.00 0.00 4.75
5217 6135 6.038603 GTCTTTGATGCATGACTTTGGCTATA 59.961 38.462 2.46 0.00 0.00 1.31
5218 6136 6.774170 TCTTTGATGCATGACTTTGGCTATAT 59.226 34.615 2.46 0.00 0.00 0.86
5257 6600 7.764695 TGAACATGTATAAATGGTGTAGTCG 57.235 36.000 7.81 0.00 31.46 4.18
5366 6710 6.693315 TCTTTTTGACCAAGGAAACTACAG 57.307 37.500 0.00 0.00 42.68 2.74
5386 6731 1.037579 GGCTTGCCCCCTCAACATAC 61.038 60.000 0.00 0.00 0.00 2.39
5460 6805 9.634021 TGGCATATGTACATAAATAAAGTTCCA 57.366 29.630 19.11 8.37 0.00 3.53
5461 6806 9.893305 GGCATATGTACATAAATAAAGTTCCAC 57.107 33.333 19.11 0.00 0.00 4.02
5474 6823 8.474006 AATAAAGTTCCACAAGTGAAACAAAC 57.526 30.769 5.14 1.20 41.43 2.93
5617 6969 6.831868 ACTTGGTTGGTATTGTAGAAGTTTGT 59.168 34.615 0.00 0.00 0.00 2.83
5675 7027 5.010012 AGTTTGACCTGAAACAAGCCTATTG 59.990 40.000 0.00 0.00 38.14 1.90
5679 7031 4.980573 ACCTGAAACAAGCCTATTGTGTA 58.019 39.130 0.00 0.00 32.22 2.90
5680 7032 5.003804 ACCTGAAACAAGCCTATTGTGTAG 58.996 41.667 0.00 0.00 32.22 2.74
5681 7033 5.003804 CCTGAAACAAGCCTATTGTGTAGT 58.996 41.667 0.00 0.00 32.22 2.73
5682 7034 6.170506 CCTGAAACAAGCCTATTGTGTAGTA 58.829 40.000 0.00 0.00 32.22 1.82
5683 7035 6.092259 CCTGAAACAAGCCTATTGTGTAGTAC 59.908 42.308 0.00 0.00 32.22 2.73
5684 7036 6.765403 TGAAACAAGCCTATTGTGTAGTACT 58.235 36.000 0.00 0.00 32.22 2.73
5685 7037 6.872020 TGAAACAAGCCTATTGTGTAGTACTC 59.128 38.462 0.00 0.00 32.22 2.59
5686 7038 5.340439 ACAAGCCTATTGTGTAGTACTCC 57.660 43.478 0.00 0.00 0.00 3.85
5687 7039 4.161754 ACAAGCCTATTGTGTAGTACTCCC 59.838 45.833 0.00 0.00 0.00 4.30
5688 7040 4.267341 AGCCTATTGTGTAGTACTCCCT 57.733 45.455 0.00 0.00 0.00 4.20
5689 7041 4.216708 AGCCTATTGTGTAGTACTCCCTC 58.783 47.826 0.00 0.00 0.00 4.30
5690 7042 3.321396 GCCTATTGTGTAGTACTCCCTCC 59.679 52.174 0.00 0.00 0.00 4.30
5691 7043 3.568853 CCTATTGTGTAGTACTCCCTCCG 59.431 52.174 0.00 0.00 0.00 4.63
5692 7044 2.592102 TTGTGTAGTACTCCCTCCGT 57.408 50.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.161249 GACAGAGTGTCCCAGTTGAAAACA 61.161 45.833 0.00 0.00 44.88 2.83
2 3 3.541632 GACAGAGTGTCCCAGTTGAAAA 58.458 45.455 0.00 0.00 41.37 2.29
16 17 2.118513 ACGGCAGGAGGACAGAGT 59.881 61.111 0.00 0.00 0.00 3.24
17 18 2.575993 CACGGCAGGAGGACAGAG 59.424 66.667 0.00 0.00 0.00 3.35
18 19 2.997315 CCACGGCAGGAGGACAGA 60.997 66.667 0.00 0.00 0.00 3.41
19 20 4.767255 GCCACGGCAGGAGGACAG 62.767 72.222 2.36 0.00 41.49 3.51
24 25 4.162690 GTAGGGCCACGGCAGGAG 62.163 72.222 10.83 0.00 44.11 3.69
42 44 4.778143 GCGGTTCAGCGGGTGGAT 62.778 66.667 7.42 0.00 0.00 3.41
73 75 0.116342 TGGCACCTGAACCCTCTCTA 59.884 55.000 0.00 0.00 0.00 2.43
96 98 0.178970 GCATGATGGGAGGCCAGAAT 60.179 55.000 5.01 0.00 0.00 2.40
155 157 0.952280 GGTCGTAGCGGAGATCATCA 59.048 55.000 0.00 0.00 0.00 3.07
219 221 3.362797 TCGCTGGTCTCGCTCGTT 61.363 61.111 0.00 0.00 0.00 3.85
226 228 1.226717 GATCGGTGTCGCTGGTCTC 60.227 63.158 0.00 0.00 36.13 3.36
227 229 2.885861 GATCGGTGTCGCTGGTCT 59.114 61.111 0.00 0.00 36.13 3.85
298 300 0.257616 CTCGACCTCCTTCTCCTCCT 59.742 60.000 0.00 0.00 0.00 3.69
299 301 0.753848 CCTCGACCTCCTTCTCCTCC 60.754 65.000 0.00 0.00 0.00 4.30
306 308 0.252103 TTGTAGGCCTCGACCTCCTT 60.252 55.000 9.68 0.00 41.50 3.36
459 461 4.742201 CGACCACGAGTGCCCCAG 62.742 72.222 0.00 0.00 42.66 4.45
489 491 2.047274 CTTGGACGTGCACGGGAT 60.047 61.111 39.21 21.97 44.95 3.85
501 503 4.263572 CACGCCCACCCACTTGGA 62.264 66.667 0.00 0.00 39.24 3.53
509 511 4.329545 TTCAGCTCCACGCCCACC 62.330 66.667 0.00 0.00 40.39 4.61
525 527 2.353208 CCTCTTGACGCTCTAGTTGCTT 60.353 50.000 8.36 0.36 0.00 3.91
596 616 1.296755 CGGTGAGGTCGACGAAGAGA 61.297 60.000 9.92 0.00 0.00 3.10
615 653 0.966920 TGGTGGTCCTCTTTCTCGTC 59.033 55.000 0.00 0.00 34.23 4.20
616 654 0.969894 CTGGTGGTCCTCTTTCTCGT 59.030 55.000 0.00 0.00 34.23 4.18
617 655 1.257743 TCTGGTGGTCCTCTTTCTCG 58.742 55.000 0.00 0.00 34.23 4.04
618 656 3.103742 AGATCTGGTGGTCCTCTTTCTC 58.896 50.000 0.00 0.00 34.23 2.87
619 657 3.197927 AGATCTGGTGGTCCTCTTTCT 57.802 47.619 0.00 0.00 34.23 2.52
620 658 3.386402 CCTAGATCTGGTGGTCCTCTTTC 59.614 52.174 5.18 0.00 34.23 2.62
621 659 3.246167 ACCTAGATCTGGTGGTCCTCTTT 60.246 47.826 13.91 0.00 36.30 2.52
622 660 2.316372 ACCTAGATCTGGTGGTCCTCTT 59.684 50.000 13.91 0.00 36.30 2.85
623 661 1.933765 ACCTAGATCTGGTGGTCCTCT 59.066 52.381 13.91 0.00 36.30 3.69
624 662 2.463047 ACCTAGATCTGGTGGTCCTC 57.537 55.000 13.91 0.00 36.30 3.71
625 663 2.950990 AACCTAGATCTGGTGGTCCT 57.049 50.000 15.00 1.64 37.93 3.85
626 664 4.470304 AGTAAAACCTAGATCTGGTGGTCC 59.530 45.833 15.00 6.82 37.93 4.46
627 665 5.678955 AGTAAAACCTAGATCTGGTGGTC 57.321 43.478 15.00 5.57 37.93 4.02
628 666 7.182206 ACATAAGTAAAACCTAGATCTGGTGGT 59.818 37.037 15.00 12.51 37.93 4.16
629 667 7.565680 ACATAAGTAAAACCTAGATCTGGTGG 58.434 38.462 15.00 11.97 37.93 4.61
630 668 9.449719 AAACATAAGTAAAACCTAGATCTGGTG 57.550 33.333 15.00 5.56 37.93 4.17
684 725 8.589335 AATATATACATTGTCGCGAAAAGTCT 57.411 30.769 18.02 10.35 0.00 3.24
728 769 5.618236 TGTTGGGATGCATTTCAAATTTCA 58.382 33.333 14.46 7.95 0.00 2.69
771 812 9.941664 CTATAGATGCGATCAATGTTTTTCTTT 57.058 29.630 0.00 0.00 0.00 2.52
772 813 8.562892 CCTATAGATGCGATCAATGTTTTTCTT 58.437 33.333 0.00 0.00 0.00 2.52
785 833 1.738350 CCGTCGTCCTATAGATGCGAT 59.262 52.381 0.00 0.00 34.80 4.58
799 847 3.054878 GACACAAATACTTGTCCGTCGT 58.945 45.455 0.00 0.00 44.15 4.34
812 860 3.166434 TCCAGGCGGGACACAAAT 58.834 55.556 0.91 0.00 42.15 2.32
824 872 4.856801 CCAACGGGCCGATCCAGG 62.857 72.222 35.78 21.00 36.21 4.45
826 874 3.781307 CTCCAACGGGCCGATCCA 61.781 66.667 35.78 12.53 36.21 3.41
828 876 1.067582 CTACTCCAACGGGCCGATC 59.932 63.158 35.78 0.00 0.00 3.69
829 877 3.090219 GCTACTCCAACGGGCCGAT 62.090 63.158 35.78 20.37 0.00 4.18
849 909 3.013921 CCCCGCTTGCAGACTTTAATTA 58.986 45.455 0.00 0.00 0.00 1.40
869 929 6.262193 TCAAAATAATGAAAAGACGGACCC 57.738 37.500 0.00 0.00 0.00 4.46
891 951 5.294552 CGGGAGGAGATTTGTATCTTGTTTC 59.705 44.000 0.00 0.00 41.23 2.78
953 1015 2.047560 GTTTCGTCGGGACAGGGG 60.048 66.667 0.00 0.00 0.00 4.79
1157 1219 4.452733 GACGGGAGGTGGAAGCGG 62.453 72.222 0.00 0.00 40.95 5.52
1158 1220 4.452733 GGACGGGAGGTGGAAGCG 62.453 72.222 0.00 0.00 40.95 4.68
1159 1221 3.003763 AGGACGGGAGGTGGAAGC 61.004 66.667 0.00 0.00 0.00 3.86
1790 1852 1.270094 TGGGAATATAACAGCGCTCGG 60.270 52.381 7.13 0.00 0.00 4.63
1842 1904 0.032515 TGATCGCTGAGACCCCCTTA 60.033 55.000 0.00 0.00 0.00 2.69
1869 1931 1.056660 ATAGATGGCCGTACTTGGGG 58.943 55.000 0.00 0.00 0.00 4.96
1878 1940 1.224075 CAGACAGCAATAGATGGCCG 58.776 55.000 0.00 0.00 41.11 6.13
2490 2552 1.818060 GCATAACCTGCCACAATGTGA 59.182 47.619 15.91 0.00 45.66 3.58
2937 2999 6.516693 GCAAATGCAAACTAAACTACCCTTCT 60.517 38.462 0.00 0.00 41.59 2.85
2958 3020 2.591923 TGTAATGGACCTTGCTGCAAA 58.408 42.857 16.74 1.02 0.00 3.68
2965 3027 8.681486 TGATAATCTGAATGTAATGGACCTTG 57.319 34.615 0.00 0.00 0.00 3.61
2968 3030 8.778358 GTCTTGATAATCTGAATGTAATGGACC 58.222 37.037 0.00 0.00 0.00 4.46
3019 3081 6.259550 AGTTCTAGCCATAAGTTTTTGCAG 57.740 37.500 0.00 0.00 0.00 4.41
3174 3319 2.645297 TGGTAGATAAGGGTGCACCAAA 59.355 45.455 35.78 20.94 43.89 3.28
3182 3327 6.064717 GCATCAAGAAATGGTAGATAAGGGT 58.935 40.000 0.00 0.00 0.00 4.34
3272 3550 5.180271 ACAAAGCCTTGCATTTTATGATGG 58.820 37.500 0.00 0.00 35.84 3.51
3273 3551 6.539324 CAACAAAGCCTTGCATTTTATGATG 58.461 36.000 0.00 0.00 35.84 3.07
3274 3552 5.122711 GCAACAAAGCCTTGCATTTTATGAT 59.877 36.000 0.00 0.00 43.04 2.45
3275 3553 4.451774 GCAACAAAGCCTTGCATTTTATGA 59.548 37.500 0.00 0.00 43.04 2.15
3276 3554 4.714851 GCAACAAAGCCTTGCATTTTATG 58.285 39.130 0.00 0.00 43.04 1.90
3573 3974 2.639286 CAGACTGCCCACAAACGC 59.361 61.111 0.00 0.00 0.00 4.84
3583 3984 2.024319 GCAGACACGTCCAGACTGC 61.024 63.158 11.63 11.63 44.88 4.40
3593 3994 2.209838 ATCTGTTATCCGCAGACACG 57.790 50.000 0.00 0.00 44.52 4.49
3608 4009 1.462238 CCACCCCTCCCCCTATCTG 60.462 68.421 0.00 0.00 0.00 2.90
3611 4012 1.308746 CAACCACCCCTCCCCCTAT 60.309 63.158 0.00 0.00 0.00 2.57
3612 4013 2.126372 CAACCACCCCTCCCCCTA 59.874 66.667 0.00 0.00 0.00 3.53
3617 4018 3.339093 CTCCCCAACCACCCCTCC 61.339 72.222 0.00 0.00 0.00 4.30
3618 4019 4.048470 GCTCCCCAACCACCCCTC 62.048 72.222 0.00 0.00 0.00 4.30
3621 4022 3.662117 GATGGCTCCCCAACCACCC 62.662 68.421 0.00 0.00 46.14 4.61
3622 4023 2.043953 GATGGCTCCCCAACCACC 60.044 66.667 0.00 0.00 46.14 4.61
3627 4028 0.846427 AGAGTTGGATGGCTCCCCAA 60.846 55.000 0.00 0.00 46.14 4.12
3629 4030 1.439543 ATAGAGTTGGATGGCTCCCC 58.560 55.000 1.34 0.00 41.29 4.81
3630 4031 2.028930 CGTATAGAGTTGGATGGCTCCC 60.029 54.545 1.34 0.00 41.29 4.30
3631 4032 2.628657 ACGTATAGAGTTGGATGGCTCC 59.371 50.000 0.00 0.00 42.45 4.70
3632 4033 3.318275 TGACGTATAGAGTTGGATGGCTC 59.682 47.826 0.00 0.00 0.00 4.70
3633 4034 3.296854 TGACGTATAGAGTTGGATGGCT 58.703 45.455 0.00 0.00 0.00 4.75
3634 4035 3.728076 TGACGTATAGAGTTGGATGGC 57.272 47.619 0.00 0.00 0.00 4.40
3651 4052 1.805428 AACAGGTGCGGGCATTTGAC 61.805 55.000 12.34 0.00 0.00 3.18
4063 4746 0.673644 GACGTTGTGGGAGGTGATGG 60.674 60.000 0.00 0.00 0.00 3.51
4119 4815 4.751431 GGGCATTTGGAGTGCTCT 57.249 55.556 0.00 0.00 39.95 4.09
4128 4826 1.755179 AAGGATGTCGAGGGCATTTG 58.245 50.000 0.00 0.00 0.00 2.32
4131 4829 1.207791 AGAAAGGATGTCGAGGGCAT 58.792 50.000 0.00 0.00 0.00 4.40
4132 4830 1.757118 CTAGAAAGGATGTCGAGGGCA 59.243 52.381 0.00 0.00 0.00 5.36
4133 4831 2.032620 TCTAGAAAGGATGTCGAGGGC 58.967 52.381 0.00 0.00 0.00 5.19
4134 4832 4.586841 AGAATCTAGAAAGGATGTCGAGGG 59.413 45.833 0.00 0.00 0.00 4.30
4350 5079 9.619316 CAGGAAAACAAATACATTAACGAATCA 57.381 29.630 0.00 0.00 0.00 2.57
4394 5123 7.102993 TCATCAAATTGTCGAGGTAAGATTCA 58.897 34.615 0.00 0.00 0.00 2.57
4490 5219 2.380084 TGTTTGTCTCCACGATAGGC 57.620 50.000 0.00 0.00 43.77 3.93
4491 5220 5.631026 CATTTTGTTTGTCTCCACGATAGG 58.369 41.667 0.00 0.00 43.77 2.57
4492 5221 5.088739 GCATTTTGTTTGTCTCCACGATAG 58.911 41.667 0.00 0.00 46.19 2.08
4504 5246 8.600625 CAATAGATCCTTCATGCATTTTGTTTG 58.399 33.333 0.00 0.00 0.00 2.93
4635 5502 6.930731 ACACACCACAAGTAAAGAAAATTGT 58.069 32.000 0.00 0.00 36.34 2.71
4659 5526 9.462174 CTGCAAATTGTACAAAAGAGTTAATGA 57.538 29.630 13.23 0.00 0.00 2.57
4679 5546 4.285517 TGCCAAATCTTTAATCCCTGCAAA 59.714 37.500 0.00 0.00 0.00 3.68
4931 5816 5.605488 ACCTGAAACCAAAGTCCTAGAAGTA 59.395 40.000 0.00 0.00 0.00 2.24
4954 5839 4.402583 GCACCAGCAAAACAAAGAAAAAC 58.597 39.130 0.00 0.00 41.58 2.43
5104 5989 2.604046 AGCGCAGGGAGTATAACAAG 57.396 50.000 11.47 0.00 0.00 3.16
5132 6017 9.961265 TGACTGAAGACAAACCTATATTATACG 57.039 33.333 0.00 0.00 0.00 3.06
5178 6063 5.333645 GCATCAAAGACTGTACAGTGAAGTG 60.334 44.000 32.51 21.94 42.66 3.16
5179 6064 4.752101 GCATCAAAGACTGTACAGTGAAGT 59.248 41.667 32.51 8.97 42.66 3.01
5181 6066 4.702831 TGCATCAAAGACTGTACAGTGAA 58.297 39.130 32.51 8.59 42.66 3.18
5182 6067 4.335400 TGCATCAAAGACTGTACAGTGA 57.665 40.909 32.51 22.38 42.66 3.41
5183 6068 4.692155 TCATGCATCAAAGACTGTACAGTG 59.308 41.667 32.51 17.92 42.66 3.66
5184 6069 4.692625 GTCATGCATCAAAGACTGTACAGT 59.307 41.667 28.27 28.27 45.84 3.55
5212 6130 9.251792 TGTTCAATTCATGCATTTTGATATAGC 57.748 29.630 14.10 0.00 0.00 2.97
5217 6135 7.915293 ACATGTTCAATTCATGCATTTTGAT 57.085 28.000 14.10 1.79 44.26 2.57
5343 6687 5.592688 CCTGTAGTTTCCTTGGTCAAAAAGA 59.407 40.000 0.00 0.00 0.00 2.52
5344 6688 5.221244 CCCTGTAGTTTCCTTGGTCAAAAAG 60.221 44.000 0.00 0.00 0.00 2.27
5355 6699 0.038310 GGCAAGCCCTGTAGTTTCCT 59.962 55.000 0.00 0.00 0.00 3.36
5435 6780 9.893305 GTGGAACTTTATTTATGTACATATGCC 57.107 33.333 16.16 8.20 0.00 4.40
5453 6798 5.461032 TGTTTGTTTCACTTGTGGAACTT 57.539 34.783 21.20 0.00 38.04 2.66
5455 6800 6.532365 TTTTGTTTGTTTCACTTGTGGAAC 57.468 33.333 15.82 15.82 37.35 3.62
5456 6801 7.736447 ATTTTTGTTTGTTTCACTTGTGGAA 57.264 28.000 0.64 0.00 0.00 3.53
5458 6803 8.472683 TCTATTTTTGTTTGTTTCACTTGTGG 57.527 30.769 0.64 0.00 0.00 4.17
5649 7001 3.769300 AGGCTTGTTTCAGGTCAAACTTT 59.231 39.130 0.00 0.00 37.20 2.66



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

AutoCloner maintained by Alex Coulton.