Multiple sequence alignment - TraesCS3D01G171700

Loading Multiple Alignment...

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 TraesCS3D01G171700 chr3D 100.000 4509 0 0 1 4509 152551448 152555956 0.000000e+00 8327
1 TraesCS3D01G171700 chr3A 94.652 1870 63 12 2023 3886 178135487 178133649 0.000000e+00 2865
2 TraesCS3D01G171700 chr3A 92.595 1283 61 7 725 2000 178136738 178135483 0.000000e+00 1812
3 TraesCS3D01G171700 chr3A 89.242 409 26 3 3885 4293 178133625 178133235 3.130000e-136 496
4 TraesCS3D01G171700 chr3A 92.793 222 15 1 4289 4509 178133159 178132938 2.020000e-83 320
5 TraesCS3D01G171700 chr3B 93.183 1775 79 10 1940 3692 223033868 223035622 0.000000e+00 2569
6 TraesCS3D01G171700 chr3B 92.757 1215 52 11 742 1944 223032598 223033788 0.000000e+00 1724
7 TraesCS3D01G171700 chr3B 96.289 539 19 1 2512 3049 223030205 223029667 0.000000e+00 883
8 TraesCS3D01G171700 chr3B 90.602 415 27 7 3882 4293 223035812 223036217 1.430000e-149 540
9 TraesCS3D01G171700 chr3B 93.694 222 13 1 4289 4509 223036325 223036546 9.350000e-87 331
10 TraesCS3D01G171700 chr3B 95.312 192 8 1 3696 3886 223035600 223035791 2.040000e-78 303
11 TraesCS3D01G171700 chr3B 82.278 158 23 5 3998 4153 640671843 640671997 1.020000e-26 132
12 TraesCS3D01G171700 chr3B 82.166 157 22 6 3999 4153 647176064 647175912 3.660000e-26 130
13 TraesCS3D01G171700 chr3B 90.722 97 7 1 634 730 571261484 571261390 1.320000e-25 128
14 TraesCS3D01G171700 chr5D 98.104 633 8 2 1 631 42870470 42869840 0.000000e+00 1099
15 TraesCS3D01G171700 chr2A 96.238 638 18 1 1 632 29284346 29284983 0.000000e+00 1040
16 TraesCS3D01G171700 chr1B 95.925 638 20 1 1 632 646956291 646955654 0.000000e+00 1029
17 TraesCS3D01G171700 chr6B 95.611 638 22 1 1 632 666083855 666084492 0.000000e+00 1018
18 TraesCS3D01G171700 chr6B 95.691 557 18 1 1 551 666070448 666071004 0.000000e+00 891
19 TraesCS3D01G171700 chr6B 95.691 557 18 1 1 551 666078473 666079029 0.000000e+00 891
20 TraesCS3D01G171700 chr4A 95.721 631 21 1 1 625 594694046 594694676 0.000000e+00 1011
21 TraesCS3D01G171700 chr1A 95.268 634 28 1 1 632 465271994 465271361 0.000000e+00 1003
22 TraesCS3D01G171700 chr1A 95.248 463 20 1 170 630 560822077 560821615 0.000000e+00 732
23 TraesCS3D01G171700 chr4B 86.585 164 19 3 3999 4161 22464611 22464772 1.290000e-40 178
24 TraesCS3D01G171700 chr7A 87.179 156 17 3 3999 4153 579808527 579808374 1.670000e-39 174
25 TraesCS3D01G171700 chr7B 89.431 123 13 0 3441 3563 577563533 577563655 6.040000e-34 156
26 TraesCS3D01G171700 chr7D 88.618 123 14 0 3441 3563 535727908 535728030 2.810000e-32 150
27 TraesCS3D01G171700 chr5A 85.417 144 18 3 4011 4153 556687523 556687382 3.630000e-31 147
28 TraesCS3D01G171700 chr5B 81.250 160 25 5 3996 4153 405561954 405561798 1.700000e-24 124
29 TraesCS3D01G171700 chr1D 84.034 119 14 4 4036 4154 100313959 100313846 4.770000e-20 110


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 TraesCS3D01G171700 chr3D 152551448 152555956 4508 False 8327.00 8327 100.0000 1 4509 1 chr3D.!!$F1 4508
1 TraesCS3D01G171700 chr3A 178132938 178136738 3800 True 1373.25 2865 92.3205 725 4509 4 chr3A.!!$R1 3784
2 TraesCS3D01G171700 chr3B 223032598 223036546 3948 False 1093.40 2569 93.1096 742 4509 5 chr3B.!!$F2 3767
3 TraesCS3D01G171700 chr3B 223029667 223030205 538 True 883.00 883 96.2890 2512 3049 1 chr3B.!!$R1 537
4 TraesCS3D01G171700 chr5D 42869840 42870470 630 True 1099.00 1099 98.1040 1 631 1 chr5D.!!$R1 630
5 TraesCS3D01G171700 chr2A 29284346 29284983 637 False 1040.00 1040 96.2380 1 632 1 chr2A.!!$F1 631
6 TraesCS3D01G171700 chr1B 646955654 646956291 637 True 1029.00 1029 95.9250 1 632 1 chr1B.!!$R1 631
7 TraesCS3D01G171700 chr6B 666083855 666084492 637 False 1018.00 1018 95.6110 1 632 1 chr6B.!!$F3 631
8 TraesCS3D01G171700 chr6B 666070448 666071004 556 False 891.00 891 95.6910 1 551 1 chr6B.!!$F1 550
9 TraesCS3D01G171700 chr6B 666078473 666079029 556 False 891.00 891 95.6910 1 551 1 chr6B.!!$F2 550
10 TraesCS3D01G171700 chr4A 594694046 594694676 630 False 1011.00 1011 95.7210 1 625 1 chr4A.!!$F1 624
11 TraesCS3D01G171700 chr1A 465271361 465271994 633 True 1003.00 1003 95.2680 1 632 1 chr1A.!!$R1 631

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
843 850 1.202486 TGTTCCTTGTCGCGAGAAACT 60.202 47.619 19.83 0.00 45.01 2.66 F
1363 1374 0.527600 TCGTTGAATGCCGATCGGAG 60.528 55.000 37.64 12.91 37.50 4.63 F
2150 2257 1.298340 CAGGTGCCCGTGGACATAA 59.702 57.895 0.00 0.00 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2118 0.829990 TCATATTCAGCCTCGGTGCA 59.170 50.0 0.11 0.0 0.00 4.57 R
2172 2279 0.932955 ACCATCCCATGCCAATACCA 59.067 50.0 0.00 0.0 0.00 3.25 R
3687 3819 0.034089 GGCAAGGTAGTCCCAAGCAT 60.034 55.0 0.00 0.0 37.09 3.79 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
446 447 7.670140 AGGAAAATAAAGAAAACCCTAGTCCTG 59.330 37.037 0.00 0.00 0.00 3.86
654 661 3.906115 AACCAGGGTTAGGAGGTGA 57.094 52.632 0.90 0.00 36.46 4.02
655 662 2.361085 AACCAGGGTTAGGAGGTGAT 57.639 50.000 0.90 0.00 36.46 3.06
656 663 2.361085 ACCAGGGTTAGGAGGTGATT 57.639 50.000 0.00 0.00 32.04 2.57
657 664 2.197465 ACCAGGGTTAGGAGGTGATTC 58.803 52.381 0.00 0.00 32.04 2.52
658 665 2.196595 CCAGGGTTAGGAGGTGATTCA 58.803 52.381 0.00 0.00 0.00 2.57
659 666 2.092914 CCAGGGTTAGGAGGTGATTCAC 60.093 54.545 8.34 8.34 0.00 3.18
660 667 2.571653 CAGGGTTAGGAGGTGATTCACA 59.428 50.000 18.09 0.00 35.86 3.58
661 668 3.200825 CAGGGTTAGGAGGTGATTCACAT 59.799 47.826 18.09 11.52 35.86 3.21
662 669 4.408921 CAGGGTTAGGAGGTGATTCACATA 59.591 45.833 18.09 3.24 35.86 2.29
663 670 4.656112 AGGGTTAGGAGGTGATTCACATAG 59.344 45.833 18.09 0.00 35.86 2.23
664 671 4.409247 GGGTTAGGAGGTGATTCACATAGT 59.591 45.833 18.09 4.93 35.86 2.12
665 672 5.104485 GGGTTAGGAGGTGATTCACATAGTT 60.104 44.000 18.09 3.61 35.86 2.24
666 673 6.415573 GGTTAGGAGGTGATTCACATAGTTT 58.584 40.000 18.09 1.37 35.86 2.66
667 674 7.365295 GGGTTAGGAGGTGATTCACATAGTTTA 60.365 40.741 18.09 0.52 35.86 2.01
668 675 7.494952 GGTTAGGAGGTGATTCACATAGTTTAC 59.505 40.741 18.09 6.83 35.86 2.01
669 676 6.620877 AGGAGGTGATTCACATAGTTTACA 57.379 37.500 18.09 0.00 35.86 2.41
670 677 7.016153 AGGAGGTGATTCACATAGTTTACAA 57.984 36.000 18.09 0.00 35.86 2.41
671 678 7.458397 AGGAGGTGATTCACATAGTTTACAAA 58.542 34.615 18.09 0.00 35.86 2.83
672 679 7.942341 AGGAGGTGATTCACATAGTTTACAAAA 59.058 33.333 18.09 0.00 35.86 2.44
673 680 8.237267 GGAGGTGATTCACATAGTTTACAAAAG 58.763 37.037 18.09 0.00 35.86 2.27
674 681 8.918202 AGGTGATTCACATAGTTTACAAAAGA 57.082 30.769 18.09 0.00 35.86 2.52
675 682 9.520515 AGGTGATTCACATAGTTTACAAAAGAT 57.479 29.630 18.09 0.00 35.86 2.40
676 683 9.774742 GGTGATTCACATAGTTTACAAAAGATC 57.225 33.333 18.09 0.00 35.86 2.75
679 686 9.994432 GATTCACATAGTTTACAAAAGATCAGG 57.006 33.333 0.00 0.00 0.00 3.86
680 687 7.921786 TCACATAGTTTACAAAAGATCAGGG 57.078 36.000 0.00 0.00 0.00 4.45
681 688 6.884295 TCACATAGTTTACAAAAGATCAGGGG 59.116 38.462 0.00 0.00 0.00 4.79
682 689 6.659242 CACATAGTTTACAAAAGATCAGGGGT 59.341 38.462 0.00 0.00 0.00 4.95
683 690 7.176690 CACATAGTTTACAAAAGATCAGGGGTT 59.823 37.037 0.00 0.00 0.00 4.11
684 691 8.387813 ACATAGTTTACAAAAGATCAGGGGTTA 58.612 33.333 0.00 0.00 0.00 2.85
685 692 9.408648 CATAGTTTACAAAAGATCAGGGGTTAT 57.591 33.333 0.00 0.00 0.00 1.89
686 693 9.990868 ATAGTTTACAAAAGATCAGGGGTTATT 57.009 29.630 0.00 0.00 0.00 1.40
688 695 9.990868 AGTTTACAAAAGATCAGGGGTTATTAT 57.009 29.630 0.00 0.00 0.00 1.28
693 700 9.197306 ACAAAAGATCAGGGGTTATTATTTACC 57.803 33.333 0.00 0.00 0.00 2.85
704 711 7.930217 GGGTTATTATTTACCCGGTTTTAGAC 58.070 38.462 0.00 0.00 44.25 2.59
705 712 7.775093 GGGTTATTATTTACCCGGTTTTAGACT 59.225 37.037 0.00 0.00 44.25 3.24
706 713 9.177608 GGTTATTATTTACCCGGTTTTAGACTT 57.822 33.333 0.00 0.00 0.00 3.01
708 715 9.956640 TTATTATTTACCCGGTTTTAGACTTCA 57.043 29.630 0.00 0.00 0.00 3.02
709 716 7.910441 TTATTTACCCGGTTTTAGACTTCAG 57.090 36.000 0.00 0.00 0.00 3.02
710 717 2.853235 ACCCGGTTTTAGACTTCAGG 57.147 50.000 0.00 0.00 0.00 3.86
711 718 1.350019 ACCCGGTTTTAGACTTCAGGG 59.650 52.381 0.00 0.00 43.03 4.45
712 719 1.339727 CCCGGTTTTAGACTTCAGGGG 60.340 57.143 0.00 0.00 34.19 4.79
713 720 1.339727 CCGGTTTTAGACTTCAGGGGG 60.340 57.143 0.00 0.00 0.00 5.40
714 721 1.350019 CGGTTTTAGACTTCAGGGGGT 59.650 52.381 0.00 0.00 0.00 4.95
715 722 2.568509 CGGTTTTAGACTTCAGGGGGTA 59.431 50.000 0.00 0.00 0.00 3.69
716 723 3.008266 CGGTTTTAGACTTCAGGGGGTAA 59.992 47.826 0.00 0.00 0.00 2.85
717 724 4.505390 CGGTTTTAGACTTCAGGGGGTAAA 60.505 45.833 0.00 0.00 0.00 2.01
718 725 5.577100 GGTTTTAGACTTCAGGGGGTAAAT 58.423 41.667 0.00 0.00 0.00 1.40
719 726 6.014647 GGTTTTAGACTTCAGGGGGTAAATT 58.985 40.000 0.00 0.00 0.00 1.82
720 727 6.071560 GGTTTTAGACTTCAGGGGGTAAATTG 60.072 42.308 0.00 0.00 0.00 2.32
721 728 3.739401 AGACTTCAGGGGGTAAATTGG 57.261 47.619 0.00 0.00 0.00 3.16
722 729 2.100197 GACTTCAGGGGGTAAATTGGC 58.900 52.381 0.00 0.00 0.00 4.52
723 730 1.273041 ACTTCAGGGGGTAAATTGGCC 60.273 52.381 0.00 0.00 0.00 5.36
729 736 2.478033 GGGTAAATTGGCCGGCTCG 61.478 63.158 28.56 0.00 0.00 5.03
780 787 6.488006 AGCTAAGCACGAATTTCATGGATTAT 59.512 34.615 0.00 0.00 0.00 1.28
787 794 4.378770 CGAATTTCATGGATTATGCTCCGG 60.379 45.833 0.00 0.00 38.21 5.14
788 795 3.576078 TTTCATGGATTATGCTCCGGT 57.424 42.857 0.00 0.00 38.21 5.28
789 796 4.698201 TTTCATGGATTATGCTCCGGTA 57.302 40.909 0.00 0.00 38.21 4.02
790 797 4.698201 TTCATGGATTATGCTCCGGTAA 57.302 40.909 0.00 0.00 38.21 2.85
791 798 4.698201 TCATGGATTATGCTCCGGTAAA 57.302 40.909 0.00 0.00 38.21 2.01
792 799 4.641396 TCATGGATTATGCTCCGGTAAAG 58.359 43.478 0.00 0.00 38.21 1.85
793 800 4.346709 TCATGGATTATGCTCCGGTAAAGA 59.653 41.667 0.00 0.00 38.21 2.52
794 801 4.764050 TGGATTATGCTCCGGTAAAGAA 57.236 40.909 0.00 0.00 38.21 2.52
795 802 5.105567 TGGATTATGCTCCGGTAAAGAAA 57.894 39.130 0.00 0.00 38.21 2.52
796 803 5.123227 TGGATTATGCTCCGGTAAAGAAAG 58.877 41.667 0.00 0.00 38.21 2.62
843 850 1.202486 TGTTCCTTGTCGCGAGAAACT 60.202 47.619 19.83 0.00 45.01 2.66
939 946 2.544844 TCTCCTCCTTGACCCGTAAT 57.455 50.000 0.00 0.00 0.00 1.89
1230 1237 2.035961 TCCCGATCCTTGCTTCTAATCG 59.964 50.000 0.00 0.00 39.05 3.34
1241 1248 2.738964 GCTTCTAATCGGCGGTTCTCTT 60.739 50.000 9.49 0.00 0.00 2.85
1269 1280 2.597805 GCGCGGAGGAGGGAGATA 60.598 66.667 8.83 0.00 0.00 1.98
1277 1288 0.868186 AGGAGGGAGATATCGGGGTT 59.132 55.000 0.00 0.00 0.00 4.11
1300 1311 7.013942 GGTTAGGAAGTAGAATTTTGGTGTTGT 59.986 37.037 0.00 0.00 0.00 3.32
1363 1374 0.527600 TCGTTGAATGCCGATCGGAG 60.528 55.000 37.64 12.91 37.50 4.63
1415 1427 2.685106 ATTCCCCTGCGAGATCTCTA 57.315 50.000 20.26 8.54 0.00 2.43
1444 1456 3.900601 TGCAATAGGGGTCACAATTTTGT 59.099 39.130 0.00 0.00 43.36 2.83
1470 1482 8.443160 TGATGTTTGATCTAATTCTGTTTCGTC 58.557 33.333 0.00 0.00 0.00 4.20
1472 1484 8.378172 TGTTTGATCTAATTCTGTTTCGTCTT 57.622 30.769 0.00 0.00 0.00 3.01
1557 1570 7.436080 GCAATGTTTCTTTCAGTTTCTTGATGA 59.564 33.333 0.00 0.00 0.00 2.92
1558 1571 9.472361 CAATGTTTCTTTCAGTTTCTTGATGAT 57.528 29.630 0.00 0.00 0.00 2.45
1559 1572 9.472361 AATGTTTCTTTCAGTTTCTTGATGATG 57.528 29.630 0.00 0.00 0.00 3.07
1588 1601 2.159268 CCAAATTGGCATGTATCGTGCA 60.159 45.455 14.42 0.00 46.93 4.57
1922 1942 9.200817 ACCATTTGGCAAATATACAGAAGTAAT 57.799 29.630 23.93 0.00 39.32 1.89
1941 2045 7.513371 AGTAATGGATGTAGCAGTCTACTAC 57.487 40.000 3.56 3.56 44.26 2.73
2014 2118 4.620982 GTTGGTTGTTGCAGCTTCTAATT 58.379 39.130 1.17 0.00 0.00 1.40
2055 2159 7.285783 TGACGATCGTAATTTTTCCTAGTTG 57.714 36.000 22.79 0.00 0.00 3.16
2065 2169 7.770801 AATTTTTCCTAGTTGTTTCACTTGC 57.229 32.000 0.00 0.00 0.00 4.01
2085 2192 8.575454 CACTTGCTGTTTATAAGAATTTTACGC 58.425 33.333 0.00 0.00 0.00 4.42
2150 2257 1.298340 CAGGTGCCCGTGGACATAA 59.702 57.895 0.00 0.00 0.00 1.90
2171 2278 1.033746 CATGACCGCCTTCCATGCTT 61.034 55.000 0.00 0.00 32.47 3.91
2172 2279 0.323725 ATGACCGCCTTCCATGCTTT 60.324 50.000 0.00 0.00 0.00 3.51
2187 2294 1.272928 TGCTTTGGTATTGGCATGGGA 60.273 47.619 0.00 0.00 0.00 4.37
2316 2423 6.876257 ACTATGCTGTTGCTTTAGCTATATCC 59.124 38.462 3.10 0.00 42.66 2.59
2355 2462 7.058806 CGACAAATTTCTTGTTCTGAAGATTCG 59.941 37.037 0.00 0.00 31.98 3.34
3076 3190 2.076863 GTGTTTCGGCATACTTCAGCT 58.923 47.619 0.00 0.00 0.00 4.24
3102 3216 9.190858 TGTTGCACAACATATCATTTTAAGTTC 57.809 29.630 12.02 0.00 45.42 3.01
3197 3324 8.481974 TCATCAAAGAATGCATTAAATGTTGG 57.518 30.769 12.97 6.03 0.00 3.77
3300 3432 6.418057 TGCATGATGGTAGTGTCATATACA 57.582 37.500 0.00 0.00 33.52 2.29
3301 3433 6.458210 TGCATGATGGTAGTGTCATATACAG 58.542 40.000 0.00 0.00 39.29 2.74
3302 3434 6.041979 TGCATGATGGTAGTGTCATATACAGT 59.958 38.462 0.00 0.00 44.22 3.55
3303 3435 7.232534 TGCATGATGGTAGTGTCATATACAGTA 59.767 37.037 0.00 0.00 42.03 2.74
3418 3550 7.989741 TGCCACCTTTATTTTTCAAATTCTGAA 59.010 29.630 0.00 0.00 42.48 3.02
3633 3765 3.084039 TCAATGCATGACAAGGAGAACC 58.916 45.455 0.00 0.00 31.50 3.62
3681 3813 3.445008 TCAGATTGAGACTACCTTGCCT 58.555 45.455 0.00 0.00 0.00 4.75
3682 3814 3.840666 TCAGATTGAGACTACCTTGCCTT 59.159 43.478 0.00 0.00 0.00 4.35
3683 3815 3.937706 CAGATTGAGACTACCTTGCCTTG 59.062 47.826 0.00 0.00 0.00 3.61
3684 3816 3.584848 AGATTGAGACTACCTTGCCTTGT 59.415 43.478 0.00 0.00 0.00 3.16
3685 3817 2.839486 TGAGACTACCTTGCCTTGTG 57.161 50.000 0.00 0.00 0.00 3.33
3686 3818 1.270839 TGAGACTACCTTGCCTTGTGC 60.271 52.381 0.00 0.00 41.77 4.57
3695 3827 2.263540 GCCTTGTGCATGCTTGGG 59.736 61.111 20.33 15.71 40.77 4.12
3696 3828 2.277591 GCCTTGTGCATGCTTGGGA 61.278 57.895 20.33 0.00 40.77 4.37
3697 3829 1.588082 CCTTGTGCATGCTTGGGAC 59.412 57.895 20.33 8.76 0.00 4.46
3698 3830 0.896940 CCTTGTGCATGCTTGGGACT 60.897 55.000 20.33 0.00 0.00 3.85
3699 3831 1.614051 CCTTGTGCATGCTTGGGACTA 60.614 52.381 20.33 4.20 0.00 2.59
3700 3832 1.470098 CTTGTGCATGCTTGGGACTAC 59.530 52.381 20.33 6.41 0.00 2.73
3701 3833 0.322456 TGTGCATGCTTGGGACTACC 60.322 55.000 20.33 0.00 40.81 3.18
3702 3834 0.035056 GTGCATGCTTGGGACTACCT 60.035 55.000 20.33 0.00 41.11 3.08
3703 3835 0.698238 TGCATGCTTGGGACTACCTT 59.302 50.000 20.33 0.00 41.11 3.50
3704 3836 1.098050 GCATGCTTGGGACTACCTTG 58.902 55.000 11.37 0.00 41.11 3.61
3705 3837 1.098050 CATGCTTGGGACTACCTTGC 58.902 55.000 0.00 0.00 41.11 4.01
3706 3838 0.034089 ATGCTTGGGACTACCTTGCC 60.034 55.000 0.00 0.00 41.11 4.52
3910 4071 0.391661 TCTCTGCTCAACGCCATTCC 60.392 55.000 0.00 0.00 38.05 3.01
3932 4093 3.370672 CACGCACTTGTACATCTGCATTA 59.629 43.478 19.78 0.00 0.00 1.90
3968 4129 3.768757 TGTTGAAATGTGATTGGGGGATC 59.231 43.478 0.00 0.00 0.00 3.36
3981 4142 1.402787 GGGGATCGATGCCACAAATT 58.597 50.000 33.38 0.00 40.49 1.82
4009 4170 2.134789 TACGGTTCTACTCCCTCCAC 57.865 55.000 0.00 0.00 0.00 4.02
4022 4183 8.453681 TCTACTCCCTCCACTCACATATATAAA 58.546 37.037 0.00 0.00 0.00 1.40
4032 4193 8.786898 CCACTCACATATATAAAATGTTCAGGG 58.213 37.037 2.21 3.35 35.39 4.45
4056 4217 7.298122 GGTATTTCAATATGAACTACATGCGG 58.702 38.462 17.06 0.00 41.45 5.69
4059 4220 5.017294 TCAATATGAACTACATGCGGACA 57.983 39.130 0.00 0.00 39.77 4.02
4086 4247 6.639632 ATGAGTGAACAAGCACACTAAAAT 57.360 33.333 0.00 0.00 45.54 1.82
4161 4323 4.960469 TGAACGGAGGGAGTAACATTCTAT 59.040 41.667 0.00 0.00 0.00 1.98
4230 4394 4.568359 TCAGCGATAAAGAGAACTTGCATC 59.432 41.667 0.00 0.00 36.39 3.91
4231 4395 3.553511 AGCGATAAAGAGAACTTGCATCG 59.446 43.478 15.94 15.94 44.89 3.84
4232 4396 3.854881 CGATAAAGAGAACTTGCATCGC 58.145 45.455 0.00 0.00 40.91 4.58
4233 4397 3.306973 CGATAAAGAGAACTTGCATCGCA 59.693 43.478 0.00 0.00 40.91 5.10
4234 4398 4.025396 CGATAAAGAGAACTTGCATCGCAT 60.025 41.667 0.00 0.00 40.91 4.73
4239 4403 2.005451 AGAACTTGCATCGCATGTCTC 58.995 47.619 7.81 7.95 44.18 3.36
4345 4621 8.471609 TCATACTGACAGTTAATTTGGATACGA 58.528 33.333 14.50 0.00 42.51 3.43
4389 4666 4.686191 AGGAACTGGATAGCTTCATGAG 57.314 45.455 0.00 0.00 37.18 2.90
4401 4679 7.281999 GGATAGCTTCATGAGAGCTTTAAAAGT 59.718 37.037 26.50 11.06 39.79 2.66
4402 4680 6.890979 AGCTTCATGAGAGCTTTAAAAGTT 57.109 33.333 20.08 0.00 35.02 2.66
4409 4687 8.567948 TCATGAGAGCTTTAAAAGTTTACTTGG 58.432 33.333 0.00 0.00 36.12 3.61
4450 4728 4.715792 ACAGGAGACAGAGATCACAATGAT 59.284 41.667 0.00 0.00 40.34 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
446 447 3.826236 TCATCGCTCTAATAGGTACGC 57.174 47.619 0.00 0.00 0.00 4.42
635 642 3.502051 ATCACCTCCTAACCCTGGTTA 57.498 47.619 8.43 8.43 39.31 2.85
636 643 2.361085 ATCACCTCCTAACCCTGGTT 57.639 50.000 6.81 6.81 41.65 3.67
637 644 2.197465 GAATCACCTCCTAACCCTGGT 58.803 52.381 0.00 0.00 0.00 4.00
638 645 2.092914 GTGAATCACCTCCTAACCCTGG 60.093 54.545 1.10 0.00 0.00 4.45
639 646 2.571653 TGTGAATCACCTCCTAACCCTG 59.428 50.000 11.24 0.00 32.73 4.45
640 647 2.915869 TGTGAATCACCTCCTAACCCT 58.084 47.619 11.24 0.00 32.73 4.34
641 648 3.933861 ATGTGAATCACCTCCTAACCC 57.066 47.619 11.24 0.00 32.73 4.11
642 649 5.615925 ACTATGTGAATCACCTCCTAACC 57.384 43.478 11.24 0.00 32.73 2.85
643 650 8.038944 TGTAAACTATGTGAATCACCTCCTAAC 58.961 37.037 11.24 2.45 32.73 2.34
644 651 8.141298 TGTAAACTATGTGAATCACCTCCTAA 57.859 34.615 11.24 0.00 32.73 2.69
645 652 7.727578 TGTAAACTATGTGAATCACCTCCTA 57.272 36.000 11.24 0.00 32.73 2.94
646 653 6.620877 TGTAAACTATGTGAATCACCTCCT 57.379 37.500 11.24 0.00 32.73 3.69
647 654 7.681939 TTTGTAAACTATGTGAATCACCTCC 57.318 36.000 11.24 0.00 32.73 4.30
648 655 8.999431 TCTTTTGTAAACTATGTGAATCACCTC 58.001 33.333 11.24 0.00 32.73 3.85
649 656 8.918202 TCTTTTGTAAACTATGTGAATCACCT 57.082 30.769 11.24 3.50 32.73 4.00
650 657 9.774742 GATCTTTTGTAAACTATGTGAATCACC 57.225 33.333 11.24 0.00 32.73 4.02
653 660 9.994432 CCTGATCTTTTGTAAACTATGTGAATC 57.006 33.333 0.00 0.00 0.00 2.52
654 661 8.960591 CCCTGATCTTTTGTAAACTATGTGAAT 58.039 33.333 0.00 0.00 0.00 2.57
655 662 7.393234 CCCCTGATCTTTTGTAAACTATGTGAA 59.607 37.037 0.00 0.00 0.00 3.18
656 663 6.884295 CCCCTGATCTTTTGTAAACTATGTGA 59.116 38.462 0.00 0.00 0.00 3.58
657 664 6.659242 ACCCCTGATCTTTTGTAAACTATGTG 59.341 38.462 0.00 0.00 0.00 3.21
658 665 6.790319 ACCCCTGATCTTTTGTAAACTATGT 58.210 36.000 0.00 0.00 0.00 2.29
659 666 7.703058 AACCCCTGATCTTTTGTAAACTATG 57.297 36.000 0.00 0.00 0.00 2.23
660 667 9.990868 AATAACCCCTGATCTTTTGTAAACTAT 57.009 29.630 0.00 0.00 0.00 2.12
662 669 9.990868 ATAATAACCCCTGATCTTTTGTAAACT 57.009 29.630 0.00 0.00 0.00 2.66
667 674 9.197306 GGTAAATAATAACCCCTGATCTTTTGT 57.803 33.333 0.00 0.00 0.00 2.83
680 687 8.737168 AGTCTAAAACCGGGTAAATAATAACC 57.263 34.615 6.32 0.00 34.85 2.85
682 689 9.956640 TGAAGTCTAAAACCGGGTAAATAATAA 57.043 29.630 6.32 0.00 0.00 1.40
683 690 9.603921 CTGAAGTCTAAAACCGGGTAAATAATA 57.396 33.333 6.32 0.00 0.00 0.98
684 691 7.555195 CCTGAAGTCTAAAACCGGGTAAATAAT 59.445 37.037 6.32 0.00 0.00 1.28
685 692 6.880529 CCTGAAGTCTAAAACCGGGTAAATAA 59.119 38.462 6.32 0.00 0.00 1.40
686 693 6.408869 CCTGAAGTCTAAAACCGGGTAAATA 58.591 40.000 6.32 0.00 0.00 1.40
687 694 5.250982 CCTGAAGTCTAAAACCGGGTAAAT 58.749 41.667 6.32 0.00 0.00 1.40
688 695 4.505390 CCCTGAAGTCTAAAACCGGGTAAA 60.505 45.833 6.32 0.00 0.00 2.01
689 696 3.008266 CCCTGAAGTCTAAAACCGGGTAA 59.992 47.826 6.32 0.00 0.00 2.85
690 697 2.568509 CCCTGAAGTCTAAAACCGGGTA 59.431 50.000 6.32 0.00 0.00 3.69
691 698 1.350019 CCCTGAAGTCTAAAACCGGGT 59.650 52.381 6.32 0.00 0.00 5.28
692 699 1.339727 CCCCTGAAGTCTAAAACCGGG 60.340 57.143 6.32 0.00 0.00 5.73
693 700 1.339727 CCCCCTGAAGTCTAAAACCGG 60.340 57.143 0.00 0.00 0.00 5.28
694 701 1.350019 ACCCCCTGAAGTCTAAAACCG 59.650 52.381 0.00 0.00 0.00 4.44
695 702 4.645863 TTACCCCCTGAAGTCTAAAACC 57.354 45.455 0.00 0.00 0.00 3.27
696 703 6.071560 CCAATTTACCCCCTGAAGTCTAAAAC 60.072 42.308 0.00 0.00 0.00 2.43
697 704 6.014012 CCAATTTACCCCCTGAAGTCTAAAA 58.986 40.000 0.00 0.00 0.00 1.52
698 705 5.576128 CCAATTTACCCCCTGAAGTCTAAA 58.424 41.667 0.00 0.00 0.00 1.85
699 706 4.569015 GCCAATTTACCCCCTGAAGTCTAA 60.569 45.833 0.00 0.00 0.00 2.10
700 707 3.053917 GCCAATTTACCCCCTGAAGTCTA 60.054 47.826 0.00 0.00 0.00 2.59
701 708 2.291605 GCCAATTTACCCCCTGAAGTCT 60.292 50.000 0.00 0.00 0.00 3.24
702 709 2.100197 GCCAATTTACCCCCTGAAGTC 58.900 52.381 0.00 0.00 0.00 3.01
703 710 1.273041 GGCCAATTTACCCCCTGAAGT 60.273 52.381 0.00 0.00 0.00 3.01
704 711 1.485124 GGCCAATTTACCCCCTGAAG 58.515 55.000 0.00 0.00 0.00 3.02
705 712 0.323908 CGGCCAATTTACCCCCTGAA 60.324 55.000 2.24 0.00 0.00 3.02
706 713 1.304952 CGGCCAATTTACCCCCTGA 59.695 57.895 2.24 0.00 0.00 3.86
707 714 1.756561 CCGGCCAATTTACCCCCTG 60.757 63.158 2.24 0.00 0.00 4.45
708 715 2.687266 CCGGCCAATTTACCCCCT 59.313 61.111 2.24 0.00 0.00 4.79
709 716 3.151710 GCCGGCCAATTTACCCCC 61.152 66.667 18.11 0.00 0.00 5.40
710 717 2.043349 AGCCGGCCAATTTACCCC 60.043 61.111 26.15 0.00 0.00 4.95
711 718 2.478033 CGAGCCGGCCAATTTACCC 61.478 63.158 26.15 0.02 0.00 3.69
712 719 3.107447 CGAGCCGGCCAATTTACC 58.893 61.111 26.15 1.15 0.00 2.85
713 720 2.322999 CTGCGAGCCGGCCAATTTAC 62.323 60.000 26.15 6.53 0.00 2.01
714 721 2.045829 TGCGAGCCGGCCAATTTA 60.046 55.556 26.15 1.59 0.00 1.40
715 722 3.443045 CTGCGAGCCGGCCAATTT 61.443 61.111 26.15 2.91 0.00 1.82
723 730 1.490693 ATATTTGACGCTGCGAGCCG 61.491 55.000 30.47 0.00 38.18 5.52
729 736 1.286501 TCGTGGATATTTGACGCTGC 58.713 50.000 0.00 0.00 33.11 5.25
780 787 2.418197 CGATCCTTTCTTTACCGGAGCA 60.418 50.000 9.46 0.00 31.70 4.26
787 794 1.587034 CGCGGTCGATCCTTTCTTTAC 59.413 52.381 0.00 0.00 38.10 2.01
788 795 1.470285 CCGCGGTCGATCCTTTCTTTA 60.470 52.381 19.50 0.00 38.10 1.85
789 796 0.739813 CCGCGGTCGATCCTTTCTTT 60.740 55.000 19.50 0.00 38.10 2.52
790 797 1.153628 CCGCGGTCGATCCTTTCTT 60.154 57.895 19.50 0.00 38.10 2.52
791 798 1.392710 ATCCGCGGTCGATCCTTTCT 61.393 55.000 27.15 0.00 38.10 2.52
792 799 0.940047 GATCCGCGGTCGATCCTTTC 60.940 60.000 27.15 5.65 38.10 2.62
793 800 1.067582 GATCCGCGGTCGATCCTTT 59.932 57.895 27.15 0.00 38.10 3.11
794 801 1.672854 TTGATCCGCGGTCGATCCTT 61.673 55.000 27.15 0.61 38.10 3.36
795 802 2.076622 CTTGATCCGCGGTCGATCCT 62.077 60.000 27.15 1.93 38.10 3.24
796 803 1.661821 CTTGATCCGCGGTCGATCC 60.662 63.158 27.15 9.40 38.10 3.36
843 850 5.350365 CGACGGAGAGAAAATATTGGTTTCA 59.650 40.000 0.00 0.00 37.43 2.69
939 946 2.751259 ACTCCGCTCGTATCAACAGTTA 59.249 45.455 0.00 0.00 0.00 2.24
1208 1215 3.492656 CGATTAGAAGCAAGGATCGGGAA 60.493 47.826 0.00 0.00 36.79 3.97
1230 1237 2.269241 CTCCCCAAGAGAACCGCC 59.731 66.667 0.00 0.00 46.50 6.13
1269 1280 5.970501 AAATTCTACTTCCTAACCCCGAT 57.029 39.130 0.00 0.00 0.00 4.18
1277 1288 7.284074 TCACAACACCAAAATTCTACTTCCTA 58.716 34.615 0.00 0.00 0.00 2.94
1363 1374 4.941309 ACCGGTTCCACGCCCAAC 62.941 66.667 0.00 0.00 0.00 3.77
1415 1427 0.475906 GACCCCTATTGCATCCTGCT 59.524 55.000 0.34 0.00 45.31 4.24
1444 1456 8.322906 ACGAAACAGAATTAGATCAAACATCA 57.677 30.769 0.00 0.00 0.00 3.07
1472 1484 4.441356 GGCAATCAGAGTTTTGACACCAAA 60.441 41.667 0.00 0.00 40.24 3.28
1525 1537 3.319122 ACTGAAAGAAACATTGCAGGGTC 59.681 43.478 0.00 0.00 37.43 4.46
1557 1570 4.468510 ACATGCCAATTTGGATCAAGACAT 59.531 37.500 19.76 7.95 40.96 3.06
1558 1571 3.833650 ACATGCCAATTTGGATCAAGACA 59.166 39.130 19.76 5.91 40.96 3.41
1559 1572 4.460948 ACATGCCAATTTGGATCAAGAC 57.539 40.909 19.76 0.00 40.96 3.01
1588 1601 4.287067 ACATCACCTACATCAAACAGGACT 59.713 41.667 0.00 0.00 33.44 3.85
1941 2045 5.528690 TCAAGGACAAAGACAAGAACATGAG 59.471 40.000 0.00 0.00 0.00 2.90
1988 2092 1.384525 AGCTGCAACAACCAACGTAA 58.615 45.000 1.02 0.00 0.00 3.18
2014 2118 0.829990 TCATATTCAGCCTCGGTGCA 59.170 50.000 0.11 0.00 0.00 4.57
2065 2169 6.739100 TGTGCGCGTAAAATTCTTATAAACAG 59.261 34.615 8.43 0.00 0.00 3.16
2085 2192 5.961843 CAGAAATAGCAAGATTAAGTGTGCG 59.038 40.000 0.00 0.00 41.90 5.34
2150 2257 1.315257 GCATGGAAGGCGGTCATGTT 61.315 55.000 14.72 0.00 40.07 2.71
2171 2278 1.290431 ACCATCCCATGCCAATACCAA 59.710 47.619 0.00 0.00 0.00 3.67
2172 2279 0.932955 ACCATCCCATGCCAATACCA 59.067 50.000 0.00 0.00 0.00 3.25
2187 2294 7.765695 AACAATGATCACTTACAGAAACCAT 57.234 32.000 0.00 0.00 0.00 3.55
2316 2423 7.521509 AGAAATTTGTCGTTAGGATTACTCG 57.478 36.000 0.00 0.00 0.00 4.18
2355 2462 3.059120 GCACCAAGAAAGAAACCGAGTAC 60.059 47.826 0.00 0.00 0.00 2.73
2863 2972 6.098838 TCACTAAGTGCTCCTGATACATGATT 59.901 38.462 0.00 0.00 32.98 2.57
2953 3067 9.911788 AATAATCAGATCCAACTTCATTGTACT 57.088 29.630 0.00 0.00 36.47 2.73
3102 3216 3.996150 AGTGTCCAAAAGTTCATGCAG 57.004 42.857 0.00 0.00 0.00 4.41
3418 3550 5.826737 CAGCAAATGGTTCTCATTAGGATCT 59.173 40.000 0.00 0.00 44.68 2.75
3618 3750 3.077359 GGACTTGGTTCTCCTTGTCATG 58.923 50.000 0.00 0.00 37.89 3.07
3633 3765 5.766150 TTTGTGACCATAACAAGGACTTG 57.234 39.130 10.34 10.34 45.58 3.16
3681 3813 1.533625 GTAGTCCCAAGCATGCACAA 58.466 50.000 21.98 0.00 0.00 3.33
3682 3814 0.322456 GGTAGTCCCAAGCATGCACA 60.322 55.000 21.98 0.00 0.00 4.57
3683 3815 0.035056 AGGTAGTCCCAAGCATGCAC 60.035 55.000 21.98 8.85 34.66 4.57
3684 3816 0.698238 AAGGTAGTCCCAAGCATGCA 59.302 50.000 21.98 0.00 34.66 3.96
3685 3817 1.098050 CAAGGTAGTCCCAAGCATGC 58.902 55.000 10.51 10.51 34.66 4.06
3686 3818 1.098050 GCAAGGTAGTCCCAAGCATG 58.902 55.000 0.00 0.00 35.86 4.06
3687 3819 0.034089 GGCAAGGTAGTCCCAAGCAT 60.034 55.000 0.00 0.00 37.09 3.79
3688 3820 1.133809 AGGCAAGGTAGTCCCAAGCA 61.134 55.000 0.00 0.00 37.09 3.91
3689 3821 0.038310 AAGGCAAGGTAGTCCCAAGC 59.962 55.000 0.00 0.00 35.27 4.01
3690 3822 1.073923 ACAAGGCAAGGTAGTCCCAAG 59.926 52.381 0.00 0.00 34.66 3.61
3691 3823 1.145571 ACAAGGCAAGGTAGTCCCAA 58.854 50.000 0.00 0.00 34.66 4.12
3692 3824 0.400213 CACAAGGCAAGGTAGTCCCA 59.600 55.000 0.00 0.00 34.66 4.37
3693 3825 0.690762 TCACAAGGCAAGGTAGTCCC 59.309 55.000 0.00 0.00 0.00 4.46
3694 3826 2.561478 TTCACAAGGCAAGGTAGTCC 57.439 50.000 0.00 0.00 0.00 3.85
3695 3827 2.162408 GCATTCACAAGGCAAGGTAGTC 59.838 50.000 0.00 0.00 38.24 2.59
3696 3828 2.162681 GCATTCACAAGGCAAGGTAGT 58.837 47.619 0.00 0.00 38.24 2.73
3697 3829 2.421424 GAGCATTCACAAGGCAAGGTAG 59.579 50.000 0.00 0.00 41.41 3.18
3698 3830 2.224744 TGAGCATTCACAAGGCAAGGTA 60.225 45.455 0.00 0.00 41.41 3.08
3699 3831 1.251251 GAGCATTCACAAGGCAAGGT 58.749 50.000 0.00 0.00 41.41 3.50
3700 3832 1.250328 TGAGCATTCACAAGGCAAGG 58.750 50.000 0.00 0.00 41.41 3.61
3701 3833 3.374220 TTTGAGCATTCACAAGGCAAG 57.626 42.857 0.00 0.00 41.41 4.01
3702 3834 5.229423 GTTATTTGAGCATTCACAAGGCAA 58.771 37.500 0.00 0.00 41.41 4.52
3703 3835 4.321899 GGTTATTTGAGCATTCACAAGGCA 60.322 41.667 0.00 0.00 41.41 4.75
3704 3836 4.082026 AGGTTATTTGAGCATTCACAAGGC 60.082 41.667 0.00 0.00 38.73 4.35
3705 3837 5.649782 AGGTTATTTGAGCATTCACAAGG 57.350 39.130 0.00 0.00 31.71 3.61
3706 3838 6.680810 TCAAGGTTATTTGAGCATTCACAAG 58.319 36.000 0.00 0.00 32.39 3.16
3769 3902 5.828747 TGCTAGTACAGTATAAGAAAGCCG 58.171 41.667 0.00 0.00 0.00 5.52
3864 3999 1.047002 CAATGGTGGTTCCTTTGGCA 58.953 50.000 0.00 0.00 43.40 4.92
3910 4071 1.147473 TGCAGATGTACAAGTGCGTG 58.853 50.000 21.41 6.69 38.84 5.34
3968 4129 4.685169 AGAACTGTAATTTGTGGCATCG 57.315 40.909 0.00 0.00 0.00 3.84
3981 4142 4.702131 GGGAGTAGAACCGTAAGAACTGTA 59.298 45.833 0.00 0.00 43.02 2.74
4022 4183 9.479549 AGTTCATATTGAAATACCCTGAACATT 57.520 29.630 19.93 7.06 39.03 2.71
4056 4217 4.035558 TGTGCTTGTTCACTCATTTCTGTC 59.964 41.667 0.00 0.00 37.81 3.51
4059 4220 4.202441 AGTGTGCTTGTTCACTCATTTCT 58.798 39.130 0.00 0.00 40.28 2.52
4086 4247 6.263754 TCTGAATCAGATGTATATAGGCCCA 58.736 40.000 9.18 0.00 35.39 5.36
4116 4277 8.398665 GTTCACAAATCATAGGATGTTCTAACC 58.601 37.037 0.00 0.00 32.92 2.85
4128 4290 4.122776 CTCCCTCCGTTCACAAATCATAG 58.877 47.826 0.00 0.00 0.00 2.23
4132 4294 2.474410 ACTCCCTCCGTTCACAAATC 57.526 50.000 0.00 0.00 0.00 2.17
4161 4323 8.877864 ATTCAGAACCATAATACAAGGAAACA 57.122 30.769 0.00 0.00 0.00 2.83
4211 4375 3.306973 TGCGATGCAAGTTCTCTTTATCG 59.693 43.478 14.36 14.36 43.34 2.92
4230 4394 2.584418 CCTCTGGCGAGACATGCG 60.584 66.667 0.00 0.00 39.74 4.73
4231 4395 2.894387 GCCTCTGGCGAGACATGC 60.894 66.667 0.00 0.00 39.62 4.06
4252 4416 2.159014 AGGCGTTCTACTGTTGTGTTGA 60.159 45.455 0.00 0.00 0.00 3.18
4338 4614 7.318893 ACCTTTTAGTCAGTTAACTCGTATCC 58.681 38.462 4.77 0.00 0.00 2.59
4345 4621 6.039382 CCTGCAAACCTTTTAGTCAGTTAACT 59.961 38.462 1.12 1.12 0.00 2.24
4389 4666 7.645402 TGTAGCCAAGTAAACTTTTAAAGCTC 58.355 34.615 4.42 0.00 33.11 4.09
4401 4679 4.591498 TCTCCTGTTCTGTAGCCAAGTAAA 59.409 41.667 0.00 0.00 0.00 2.01
4402 4680 4.021368 GTCTCCTGTTCTGTAGCCAAGTAA 60.021 45.833 0.00 0.00 0.00 2.24
4409 4687 3.321497 CTGTTGTCTCCTGTTCTGTAGC 58.679 50.000 0.00 0.00 0.00 3.58
4450 4728 5.466058 TGAAAGAAACGTAGCGAAACCAATA 59.534 36.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.